@article {pmid41786735,
year = {2026},
author = {Wen, Y and Gao, M and Wang, Z and Liu, X and Zhang, Y and Lin, G and He, P and Yang, H and Xiao, Y and Lyu, W},
title = {Dietary copper-driven colonic dysbiosis mediates oxidative stress and butyrate deficiency to facilitate the spread of resistome in pigs.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41786735},
issn = {2055-5008},
support = {10417000025CE0615G//State Key Laboratory for Managing Biotic and Chemical Threats to the Safety of Agro-products/ ; 32372907//National Natural Science Foundation of China/ ; LR25C170001//Natural Science Foundation of Zhejiang Province/ ; },
mesh = {Animals ; *Oxidative Stress/drug effects ; Swine ; *Dysbiosis/microbiology/chemically induced ; *Butyrates/metabolism ; *Copper/administration & dosage ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Colon/microbiology/drug effects ; *Bacteria/genetics/classification/drug effects/isolation & purification/metabolism ; Dietary Supplements ; Metagenomics ; Animal Feed/analysis ; Copper Sulfate/administration & dosage ; },
abstract = {Copper-induced transmission of antimicrobial resistance has been well documented in livestock farming environments, but the in vivo mechanisms driving fecal resistome development remain unclear. Here, 120 mg/kg CuSO4 and copper-peptide were supplemented to piglets, and the fecal resistome development was first analyzed by metagenomic sequencing. In this study, dietary CuSO4 drove abundant and diverse ARGs and MRGs. Following CuSO4 deprivation, ARGs and copper resistance exhibited a persistent promotion, whereas most MRGs rapidly declined. The resistance development was characterized by abundant MGEs. This phenomenon expanded the multiple-antibiotic resistance reservoir in fecal community, which was preferentially harbored by pathogens. Furthermore, dietary CuSO4 disturbed colonic homeostasis, characterized by impaired epithelial integrity and reduced butyrate-producing bacteria abundance, which coincided with an oxidative stress environment and increased prevalence of multiple-resistant pathogens, such as Escherichia coli and Enterococcus spp. In vitro validation further supported these associations, showing that butyrate supplementation and hypoxic conditions alleviated Cu[2+]-induced ROS generation and reduced the frequency of ARGs conjugative transfer. Overall, this study suggests that dietary inorganic copper may contribute to microbial disturbances linked to oxidative stress and potentially facilitate antimicrobial resistance transmission among pathogens, highlighting organic copper as a sustainable alternative for mitigating resistance risks in farmed animals.},
}
@article {pmid41981426,
year = {2026},
author = {Muzhabaier, K and Li, Y and Wang, F and Guo, X and Chen, Q and Zhang, X and Cao, L},
title = {[Differential analysis of gut microbiome in patients with periprosthetic joint infection, aseptic failure, and osteoarthritis].},
journal = {Zhongguo xiu fu chong jian wai ke za zhi = Zhongguo xiufu chongjian waike zazhi = Chinese journal of reparative and reconstructive surgery},
volume = {40},
number = {4},
pages = {548-556},
doi = {10.7507/1002-1892.202601002},
pmid = {41981426},
issn = {1002-1892},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Prosthesis-Related Infections/microbiology ; Female ; Middle Aged ; Aged ; *Osteoarthritis/microbiology ; Dysbiosis/microbiology ; Prosthesis Failure ; Arthroplasty, Replacement, Knee/adverse effects ; },
abstract = {OBJECTIVE: To explore the differences in gut microbiota diversity and structural characteristics among patients with periprosthetic joint infection (PJI), aseptic failure (AF), and osteoarthritis (OA), and to analyze the association between gut microbiota dysbiosis and the occurrence of PJI, thereby providing a new theoretical basis for elucidating the pathogenesis and treatment strategies of PJI in clinical practice.<br><br>METHODS: The study enrolled patients with PJI and AF admitted between February 2024 and December 2024, as well as OA patients admitted in February 2024. A total of 52 PJI patients, 19 AF patients, and 29 OA patients who met the selection criteria were included in the analysis. Significant differences were observed among the three groups in terms of gender, age, surgical site, preoperative C-reactive protein levels, and erythrocyte sedimentation rate (P<0.05), while no significant difference was found in American Society of Anesthesiologists (ASA) classification and body mass index (P>0.05). Among the PJI patients, infection staging was as follows: 9 cases in the acute phase, 28 cases in the delayed phase, and 15 cases in the chronic phase; 23 cases were accompanied by sinus tract formation. Fecal samples were collected at different time points: for the PJI group, samples were obtained preoperatively and on postoperative days (7&#xb1;1) and (14&#xb1;1); for the AF group, preoperatively and on postoperative day (7&#xb1;1); and for the OA group, preoperatively only. Metagenomics next-generation sequencing were employed to analyze gut microbiota &#x3b1;-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) and differential bacterial genera (screened using the LEfSe algorithm).<br><br>RESULTS: Analysis of gut microbiota diversity showed that the preoperative &#x3b1;-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) in the PJI group were significantly lower than those in AF group and OA group (P<0.05). Compared with the AF group on postoperative day (7&#xb1;1), the &#x3b1;-diversity indices in the PJI group on postoperative day (7&#xb1;1) were lower, but the difference was not significant (P>0.05); by postoperative day (14&#xb1;1), these indices further decreased, and the difference was significant (P<0.05). In the PJI group, no significant difference was observed in any of the indices across different time points postoperatively (P>0.05). Analysis of gut microbiota structural characteristics revealed that the PJI group exhibited characteristic dysbiosis both before and after operation. Preoperatively, the PJI group was characterized by enrichment of Pseudomonadota (relative abundance 13.19%), Enterobacteriaceae (Escherichia 3.26%, Klebsiella 1.90%), and opportunistic pathogens such as Enterococcus faecium (0.43%), while the relative abundances of Firmicutes (51.83%) and Bifidobacterium (0.24%) decreased. Postoperatively, the &#x3b1;-diversity in the PJI group further declined, with increased relative abundances of Escherichia and Klebsiella, and the relative abundance of Firmicutes decreased to 40.24%. LEfSe analysis of preoperative gut microbiota composition between the PJI group and AF group indicated that the AF group was predominated by Firmicutes, Bifidobacterium, and Roseburia preoperatively, with greater postoperative microbial stability compared to the PJI group.<br><br>CONCLUSION: Patients with PJI exhibited a gut microbiota profile characterized by reduced diversity and enrichment of opportunistic pathogens. Postoperative antibiotic treatment further aggravated this dysbiosis, providing new clinical insights into the role of gut microbiota imbalance in the pathogenesis and progression of PJI.},
}
@article {pmid41981681,
year = {2026},
author = {Brachmann, S and Kiesewetter, KN and Liddicoat, C and Wallace, KJ and Breed, MF and Eisenhauer, N and Barnes, AD},
title = {Urban forest restoration enhances soil microbial functional potential and functional insurance via shifts in β-diversity.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00896-6},
pmid = {41981681},
issn = {2524-6372},
support = {UOWX2101//Ministry of Business, Innovation and Employment/ ; UOWX2101//Ministry of Business, Innovation and Employment/ ; UOWX2101//Ministry of Business, Innovation and Employment/ ; },
abstract = {BACKGROUND: Forest restoration has primarily been evaluated through changes in aboveground communities, while belowground microbial communities-critical drivers of ecosystem functions-remain less understood. Moreover, studies of soil microbes have focused largely on community structure, which does not necessarily reflect the recovery of functional capacity and stability.<br><br>METHODS: To determine how forest restoration affects microbial community structure and function and how microbial diversity relates to ecosystem multifunctional potential and stability, we analysed soil microbial communities from 79 urban forest restoration sites across New Zealand, spanning 0-63&#xa0;years since initial plantings. Shotgun metagenomic sequencing was used to characterize taxonomic composition and functional potential, with diversity quantified using alpha and beta metrics. To evaluate links between diversity and ecosystem function, we assessed ecosystem multifunctional potential (EMF) which describes the ecosystem's capacity to simultaneously provide multiple functions, and we developed a novel functional insurance (FI) index grounded in ecological theory as an indicator of functional stability and resilience. To calculate FI in microbial systems from sequencing data, we quantified functional overlap by estimating over 250 million species-function correlations per sample.<br><br>RESULTS: Contrary to our expectations, only beta diversity, not alpha diversity, was positively associated with EMF and FI, indicating that community composition and dissimilarity rather than species richness underpins microbial functional capacity and stability. EMF and FI were positively correlated, showing that high functional diversity and functional overlap can co-occur in microbial systems. In addition, archaeal turnover increased with closing forest canopies, contributing to higher EMF and FI, while bacterial turnover was only weakly associated with restoration parameters. Notably, restoration time did not play a role in shaping microbial diversity, EMF and FI.<br><br>CONCLUSIONS: Our findings demonstrate that microbial compositional turnover, rather than increases in species richness, are critical for restoring soil ecosystem functions. Incorporating microbial functional metrics like the FI index into restoration frameworks that recognise both above and belowground dynamics could promote resilient and multifunctional urban forests.},
}
@article {pmid41983569,
year = {2026},
author = {Vogel, MA and Machairas, F and Ferchiou, S and Osvatic, J and Alzubaidy, H and Séneca, J and Hausmann, B and Klun, K and Petersen, JM},
title = {Symbiont diversity within Loripes orbiculatus and the case for multiple hosts.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag094},
pmid = {41983569},
issn = {1751-7370},
abstract = {Seagrasses support immense biodiversity and are critical for maintaining coastal ecosystem health. These foundation species benefit from a 'three-way' facultative relationship with one of the common inhabitants of seagrass meadows, lucinid bivalves, which host specific bacterial Ca. Thiodiazotropha symbionts. Relatives of the bivalve symbionts have been detected on seagrass roots raising the possibility that these symbionts may colonize both animals and plants; however, no study has yet compared bivalve- and seagrass-associated symbionts at the same site and time. Our combination of 16S rRNA gene amplicon and metagenome sequencing revealed a greater diversity than was previously observed within both lucinid bivalves and on seagrass roots from the Adriatic Sea and resulted in the closed genome of one prominent symbiont species. We show that two of the Ca. Thiodiazotropha ASVs found on seagrass roots are identical to those found in bivalve hosts at the same site. This suggests that symbiont sharing may occur in the seagrass habitat between these two host species, which has important evolutionary and ecological implications for both hosts and symbionts.},
}
@article {pmid41983840,
year = {2026},
author = {Ibadullayeva, A and Khamzina, A and Smagulov, D and Khamzin, K},
title = {An overview of the livestock microbiome: sheep, horses, cattle, camels, and chickens.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {86},
number = {},
pages = {e299936},
doi = {10.1590/1519-6984.299936},
pmid = {41983840},
issn = {1678-4375},
mesh = {Animals ; Cattle/microbiology ; *Livestock/microbiology ; Camelus/microbiology ; Sheep/microbiology ; *Microbiota/genetics/physiology ; Chickens/microbiology ; Horses/microbiology ; },
abstract = {The animal microbiome plays a crucial role in determining the health, productivity, and welfare of livestock species, including sheep, horses, cattle, camel, and chicken. These animal species were selected due to the high consumption of their products in Kazakhstan. Enhancing their productivity, while maintaining the safety and quality of meat and milk derived from them, represents a pressing research priority. This review article includes current research on the composition, diversity, and purposes of the microbiota found within different organ systems of these species. This study focuses on recent advancements in sequencing technology, including metagenomics, 16S rRNA sequencing, and multiomic methods, to combine data on microbial diversity, composition, and functionality within the gastrointestinal tract and other organs. The key findings show differences in microbial communities associated with breed, age, and diet, the impact of microbiota on methane emissions and feed efficiency in ruminants, and the possibility of using microbiome management techniques (e.g., probiotics, prebiotics, and feed additives) to enhance livestock production. The microbiome influences various species, extending its effects beyond digestion and immunity to reproductive health and behavior. Despite advancements, translating microbiome data into actionable interventions is interfered by variability resulting from genetic, environmental, and management factors. Integrating microbiome research more closely with animal genetics and livestock production methods could lead to innovative approaches for improving the health, efficiency, and welfare of farm animals, ultimately supporting sustainable livestock farming practices.},
}
@article {pmid41984912,
year = {2026},
author = {Fri, J and Njanje, I and Mahopo, TC and Mavhandu-Ramarumo, LG and Bessong, PO and , },
title = {The Gut Bacterial Resistome in the First Two Years of Life: Protocol for a Longitudinal Observational Birth Cohort Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e86058},
doi = {10.2196/86058},
pmid = {41984912},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Infant, Newborn ; Female ; Infant ; Longitudinal Studies ; Prospective Studies ; Birth Cohort ; South Africa ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Observational Studies as Topic ; Rural Population ; Milk, Human/microbiology/chemistry ; Male ; Risk Factors ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global health threat that increases the burden of infectious diseases and disproportionately affects communities of low socioeconomic status. Despite the call for community-level AMR data, prospective studies from rural sub-Saharan African communities to inform appropriate targeted interventions remain scarce. Given the role of enteric bacteria in AMR transmission dynamics, there is a need to understand the timing, risk factors, and ecological drivers of gut resistome acquisition and development during infancy.<br><br>OBJECTIVE: This study aimed to characterize the temporal dynamics of enteric bacterial resistomes during the first 2 years of life and to identify drivers of AMR acquisition and development in a community-based, prospective, observational birth cohort study in a rural South African community.<br><br>METHODS: The study aims to enroll 200 newborns and their mothers within 17 days post partum. Data on key exposures and variables include sociodemographics; perinatal and anthropometrics; feeding practices and dietary exposures; illness, medication, and vaccination history; breast milk metabolomic profiles; household socioeconomic status; maternal psychosocial and behavioral factors; hygiene and sanitation practices; and environmental exposures including hydro-meteorological variables, in-house livestock and pets, and drinking water quality. Biological samples include stools from monthly collections and diarrhea episodes for metagenomic analysis and breast milk for metabolomics. Planned analyses include assessing the infant microbiome and resistome structure (diversity, abundance, and composition) across time points and modeling associations between risk factors and AMR outcomes. Additionally, a cross-sectional community survey on knowledge, attitudes, and practices regarding antimicrobial use is conducted to inform knowledge translation through responsive dialogues, thereby developing ethnographically relevant packages for community-level AMR stewardship.<br><br>RESULTS: Participant identification and enrollment began in August 2023. By October 2025, 167 newborns had been enrolled, with 20 having completed the 24-month follow-up. The characteristics of the enrolled participants are presented in this protocol.<br><br>CONCLUSIONS: This study will offer a unique opportunity to generate longitudinal resistome data from a rural sub-Saharan African setting. The study is expected to contribute knowledge on the microbiome and resistome structure dynamics and trajectories associated with key risk factors of acquisition and development. In addition, co-produced ethnographically tailored educational packages, informed by knowledge, attitudes, and practices and bacterial resistome data, will drive sustainable community-centered AMR awareness interventions.},
}
@article {pmid41985067,
year = {2026},
author = {Sarmah, MP and Zoramthara, K and Manngaihsiam, R and Boro, HH and Baraka, AGA and Saeed, AL and Gurusubramanian, G and Kharat, KR},
title = {Microbiome Simplification During Metamorphosis in Larva and Adults of Armigeres subalbatus (Coquillett, 1898) (Culicidae) Revealed by Shotgun Metagenomics.},
journal = {Archives of insect biochemistry and physiology},
volume = {121},
number = {4},
pages = {e70159},
doi = {10.1002/arch.70159},
pmid = {41985067},
issn = {1520-6327},
support = {EM/Dev/11/SG/01993/2024//Indian Council of Medical Research/ ; DST/INSPIRE Fellowship/[IF240039]//Department of Science &amp; Technology, New Delhi, India (INSPIRE-JRF)/ ; },
mesh = {Animals ; Larva/microbiology/growth &amp; development ; *Microbiota ; Metagenomics ; *Culicidae/microbiology/growth &amp; development ; *Metamorphosis, Biological ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {Armigeres subalbatus is medically significant vector for filarial worms and the Japanese encephalitis virus. Shotgun metagenomic sequencing was employed to investigate the bacterial communities in A. subalbatus mosquitoes. The diversity metrics (Shannon H', Simpson 1-D, Berger-Parker) were calculated for larval and adult stages. De novo assembly and binning were used to recover metagenome-assembled genomes (MAGs) with > 82% completeness and < 4% contamination. Functional profiling assessed gene expression via transcripts per million (TPM) and clusters of orthologous groups (COG) categories. Larval microbiomes showed high alpha diversity (Shannon H' ≈ 1.336 ± 0.163, Simpson 1-D = 0.684 ± 0.046), dominated by Gammaproteobacteria (Aeromonas, Morganella, and Yersinia) and Bacteroidota, with persistent Shewanella and Acinetobacter. Adult microbiomes exhibited low diversity (Shannon H' = 0.637 ± 0.100, Berger-Parker = 0.682 ± 0.026), near-monoculture dominated by Aeromonas hydrophila, alongside low-abundance Stenotrophomonas, Pseudomonas, and Microbacterium. Six high-quality MAGs were recovered: larval (Bacteroidota, Shewanella, and Acinetobacter); adult (Acinetobacter, Stenotrophomonas, and Shewanella), confirming persistence of Shewanella and Acinetobacter, absence of Bacteroidota, and emergence of Stenotrophomonas in adults. Adult microbiomes displayed metabolic hyperactivity, with 1.5-4 times higher transcriptional output across COG categories compared to larvae. Chemotaxis [Methyl-accepting chemotaxis protein (MCP), K03406: ~6000 TPM in adults vs. < 1000 TPM in larvae] and ABC transporters (PF00005: > 10,000 TPM in adults) dominated adults, while larval expression was balanced among housekeeping functions. The microbiome undergoes significant restructuring during mosquito development, shifting from diverse larval communities to metabolically active, low-diversity adult assemblages. Recovered MAGs provide a genomic basis for future studies on mosquito microbiota dynamics and functions.},
}
@article {pmid41985330,
year = {2026},
author = {Kwiendacz, H and Cembrowska-Lech, D and Skonieczna-Żydecka, K and Klimontowicz, K and Podsiadło, K and Wierzbicka-Woś, A and Styburski, D and Kaczmarczyk, M and Gumprecht, J and Łoniewski, I and Nabrdalik, K},
title = {Multi-strain probiotic enhances metformin tolerance by modulating gut microbiome and bile acid pathways: Insight from multi-omics post-hoc analysis (ProGasMet trial).},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {198},
number = {},
pages = {119370},
doi = {10.1016/j.biopha.2026.119370},
pmid = {41985330},
issn = {1950-6007},
abstract = {BACKGROUND: Metformin is the cornerstone therapy for type 2 diabetes, but gastrointestinal intolerance commonly limits dose escalation and long-term adherence. In the ProGasMet trial, multi-strain probiotic supplementation improved metformin tolerability. However, the underlying microbiome-metabolome mechanisms remain unclear.<br><br>METHODS AND ANALYSIS: We performed an exploratory multi-omics analysis using Period 1 of a randomized, double-blind, placebo-controlled trial. Participants with metformin intolerance received a multi-strain probiotic or placebo for 12 weeks. Paired stool samples collected at baseline and end of treatment were available from 34 participants (68 samples). We integrated shotgun metagenomic species profiles, predicted gut metabolic modules, and untargeted faecal LC-MS metabolomics using multi-block sparse PLS (DIABLO), complemented by longitudinal covariate-adjusted feature-level analyses and associations with gastrointestinal symptom burden (QACSMI and a simplified GI score).<br><br>RESULTS: In multi-omics integration at 12 weeks, bile acid-related metabolites were among the strongest contributors to group separation, with hyodeoxycholic acid and related compounds enriched in the probiotic arm. Global biodiversity and community-wide turnover did not differ between groups. Feature-level analyses suggested modest, directionally coherent changes in selected taxa, functional modules, and metabolites. Higher hyodeoxycholic acid concentrations were associated with lower gastrointestinal symptom burden in probiotic-treated participants, a pattern not observed under placebo.<br><br>CONCLUSION: Probiotic supplementation may be associated with coordinated microbiome-metabolome shifts in metformin-intolerant type 2 diabetes, highlighting bile acid remodelling, particularly hyodeoxycholic acid, as a plausible candidate for improved tolerability. These results support prioritising secondary bile acid-microbiome pathways for confirmation in larger trials incorporating targeted bile acid quantification and causal modelling.},
}
@article {pmid41792508,
year = {2026},
author = {Li, M and Li, Y and Li, C and Liu, A and Liu, Y and Li, Y and Xiao, J and Zhang, D and Jin, Y and Wang, G and Pang, X and Jiang, K and Yin, Y},
title = {Dynamic reorganisation of intratumoural bacterial florae during colorectal cancer progression.},
journal = {British journal of cancer},
volume = {134},
number = {9},
pages = {1261-1275},
pmid = {41792508},
issn = {1532-1827},
support = {81874235/82030081//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Colorectal Neoplasms/microbiology/pathology ; Humans ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome ; *Microbiota ; Prevotella/genetics/isolation &amp; purification ; Male ; Female ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) exhibits distinct bacterial community compositions compared to healthy mucosae, which intimately correlate with CRC clinical outcomes. There is a lack of explanation for the inducements of microbiota remodelling.<br><br>METHODS: FISH experiments and 16S rRNA sequencing were conducted to determine the inducements of various bacterial colonisation within tissues. Community cultivation was conducted to estimate the capacity of tumours to remodel bacterial communities. Metagenomic analyses were utilised to determine the remodelled communities of CRC with distant metastasis. Scratch tests and three-dimensional (3D) cultivation were employed to investigate the influence of specific taxa on tumour cell behaviours.<br><br>RESULTS: Colorectal tumours exhibit heterogeneous and individualised preferences in constantly remodelling intratumoural bacterial florae. Various degrees of colorectal gland differentiation within tumours cause heterogeneous intratumoural bacterial colonisation. CRC progression further alters bacterial community composition. Particularly, Prevotella is significantly enriched in the newly established communities colonising the primary foci of metastatic CRC. Furthermore, Prevotella intermedia (P. intermedia) promotes the invasion, migration, and ectopic tumorigenesis of CRC cells.<br><br>CONCLUSIONS: Individual evaluation of the preference of tumours in microbiota may pave the way to the development of CRC therapeutic strategies, and Prevotella is an emerging genus worthy of clinical attention.},
}
@article {pmid41931897,
year = {2026},
author = {Zhang, K and Chang, S and Zhu, Y and Shang, H and Fu, Q and Tu, X and Yu, Y and Feng, Y},
title = {Metagenomic analysis of urban water systems uncovers the interplay between antibiotic resistance genes and microbial communities in response to PFAS contamination.},
journal = {Journal of hazardous materials},
volume = {508},
number = {},
pages = {141890},
doi = {10.1016/j.jhazmat.2026.141890},
pmid = {41931897},
issn = {1873-3336},
mesh = {*Water Pollutants, Chemical/analysis/toxicity ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Wastewater/analysis ; RNA, Ribosomal, 16S/genetics ; *Fluorocarbons/analysis/toxicity ; *Microbiota/drug effects/genetics ; Cities ; Water Microbiology ; Bacteria/genetics/drug effects ; },
abstract = {Urban water systems (UWS) are facing the severe challenge of coexisting emerging contaminants per- and polyfluoroalkyl substances (PFAS) and antibiotic resistance genes (ARGs). Herein, we analyze 15 PFAS at all key nodes within the UWS and the manufacturing plant park (MPP) in industrial clusters. Meanwhile, 16S rRNA and metagenomic approach were employed to annotate microbial community and ARGs, investigating their response to PFAS contamination. Fifteen PFAS were detected in MPP wastewater with total concentrations ranging from 30.28 to 3738.51 (557.68 ± 1072.03) ng/L, with short-chain accounting for 63.5%. Wastewater treatment plant (WWTP) serves as both sink and source of PFAS, with a negative average removal efficiency (mean = -158.6%) ultimately contributing to the prevalence of PFAS in the drinking water treatment plants (DWTPs) and tap water (17.64 -84.72, 36.06 ± 18.52 ng/L). 1141 ARGs subtypes were identified by metagenomic with significant differences in relative abundance between different nodes samples (p = 0.00). Additionally, the co-occurrence network revealed 14 genera may as potential hosts for 25 ARGs subtypes. However, significant differences in microbial diversity and abundance were observed at different nodes samples (R = 0.408, p = 0.00), with PFAS reducing microbial community diversity, particularly in river system (R = 0.723, p = 0.00). Finally, the structural equation modeling (SEM) revealed that PFAS exerted the greatest negative contribution to ARGs profiles (total effect = -1.39) through synergistic effects involving direct negative impacts on microbial diversity (-0.679) and mobile genetic elements (MGEs) (-0.121). This suggests that PFAS may influence the ARGs profiles by synergistically inhibiting gene-level transfer mediated by MGEs within potential host microbial. Additionally, physicochemical parameters (0.42), nutrient levels (-0.29), and ion concentrations (0.06) were also minor drivers of ARGs profiles.},
}
@article {pmid41934858,
year = {2026},
author = {Chen, Z and Zheng, M and He, J and Ye, C and Zheng, W and Liang, Y and Yu, X and Guo, F},
title = {Trait-mediated restructuring of gut microbiota under chlorinated drinking water exposure.},
journal = {Journal of hazardous materials},
volume = {508},
number = {},
pages = {141965},
doi = {10.1016/j.jhazmat.2026.141965},
pmid = {41934858},
issn = {1873-3336},
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; *Drinking Water/chemistry ; Animals ; *Chlorine/toxicity ; Halogenation ; Humans ; Mice ; Bacteria/genetics/drug effects ; *Water Pollutants, Chemical/toxicity ; Male ; },
abstract = {Chlorine residuals in drinking water are environmentally relevant oxidants regulated within distribution systems and ingested during routine consumption. Here, we use longitudinal, within-subject designs in humans (0.5 mg/L chlorine exposure) and a parallel mouse model (10 mg/L) to assess the ecological impact of chlorine residuals on gut microbiota under realistic conditions. Crucially, overall diversity, total bacterial biomass, antibiotic resistance genes, and phage communities remained largely unaffected. However, we report a lineage-independent de-dominance effect, where initially dominant taxa decline following exposure. Genome-resolution analysis reveals that microbes with larger genomes and functional enrichment in energy metabolism and membrane biogenesis are more likely to increase, enabling accurate prediction of microbial responses to chlorination. These patterns can be interpreted within the Competitor-Stress-tolerator-Ruderal life-history framework, in which disturbance of chlorine residuals transiently reduces the advantage of competitive dominant taxa and favors stress-tolerant taxa. Our findings demonstrate that chlorination residuals act as subtle, trait-mediated ecological stressors in the gut microbiome, producing selective yet predictable shifts. These insights frame chlorine residuals as hazardous environmental agents and inform microbiome-aware optimization of water disinfection and residual control.},
}
@article {pmid41972785,
year = {2026},
author = {He, X and Liu, J and Cheng, H and Zhu, X and Lin, H and Li, D-W and Yang, Y and Liu, R and Song, D and Zheng, Y and Lea-Smith, DJ and Pedentchouk, N and Todd, JD and Zhao, M and Zhang, X-H},
title = {Metabolically diverse microorganisms mediating hydrocarbon cycling in the subseafloor sediment of the Challenger Deep.},
journal = {mBio},
volume = {},
number = {},
pages = {e0394325},
doi = {10.1128/mbio.03943-25},
pmid = {41972785},
issn = {2150-7511},
abstract = {Hadal subseafloor sediments host abundant and active microbial biosphere with considerable heterotrophic activity. However, carbon and nutrient cycling processes and mechanisms driven by hadal subsurface microorganisms remain poorly understood. Using culture-dependent and culture-independent methods, we characterized the diversity, metabolism, and vertical dynamics of hydrocarbon-degrading (HYD) bacteria in a subsurface sediment core (MT20-750, ~750 cm below seafloor [cmbsf]) collected from the Challenger Deep (10,816 m below sea level) in the Mariana Trench. The sediment core contained high concentrations of mid- and long-chain n-alkanes (310-8,724 ng/g), although no <C18 n-alkanes at detectable levels were present, in contrast to proximal hadal seawater samples where these compounds were highly abundant. Metagenomic analysis identified diverse genes for aerobic and anaerobic degradation of n-alkanes and aromatic compounds, distributed across a wide range of taxa, dominated by Chloroflexota, Planctomycetes, Proteobacteria, and Actinobacteria, alongside six novel HYD phyla. Metabolic reconstruction of 120 HYD metagenome-assembled genomes (MAGs) suggests distinct hydrocarbon degradation preferences and metabolic strategies among different bacterial groups. Additionally, hadal bacterial isolates from Proteobacteria, Actinobacteria, and Firmicutes were able to degrade n-alkanes (C18-36), with Dietzia maris HXX048 removing ~50% of n-eicosane within 45 days under 5°C and 50 MPa. Predicted substrate binding of C10 and C20 with AhyA and heterologous expression of almA in Chloroflexota genomes supported their degradative capacity under anaerobic and aerobic conditions. The detection of putative hydrocarbon synthesis genes, specifically oleBC and oleC, suggests that hadal heterotrophic microorganisms may synthesize hydrocarbons. These findings provide evidence for microbial hydrocarbon production and thereby support a previously unrecognized sedimentary hydrocarbon cycle.IMPORTANCEOur findings suggest that hydrocarbon degradation may play an important role in organic matter decomposition and carbon cycling in the hadal subseafloor. This degradation capacity is likely distributed through diverse metabolic pathways across a wide range of phylogenetic taxa. The detection of genes likely encoding enzymes involved in aerobic and anaerobic hydrocarbon degradation, as well as the identification of novel hydrocarbon-degrading (HYD) phyla, highlights the complexity and significance of microbial processes in hadal subsurface sediment. The widespread distribution of hydrocarbon degradation capacity in different hadal sediments suggests hydrocarbons as a potential carbon source sustaining microbial life in this extreme environment. Moreover, the presence of genes associated with hydrocarbon synthesis suggests that hadal sediment microbes possess the genetic potential for both degrading and producing hydrocarbons, pointing to a dynamic and multifaceted hydrocarbon cycle within hadal subsurface sediment.},
}
@article {pmid41975182,
year = {2026},
author = {Kleinbölting, N and Fiore, A and Cangioli, L and Visca, A and Huang, L and Hett, J and Costanzo, M and Sevi, F and Tabacchioni, S and Aprea, G and Mengoni, A and Pihlanto, A and Neuhoff, D and Sczyrba, A and Schlüter, A and Bevivino, A},
title = {Impact of microbial consortia and fertilization regimes on the soil microbiome in maize field trials.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47528-0},
pmid = {41975182},
issn = {2045-2322},
support = {818431//Horizon 2020 Framework Programme/ ; },
abstract = {Beneficial microbial consortia provide an eco-friendly alternative to conventional inorganic fertilizers and can serve as a complementary management tool for enhancing soil fertility and crop productivity. This study aimed to assess the impact of microbial consortia application on the indigenous maize rhizosphere microbiome under different fertilization regimes in organically managed fields in Germany. Three experimental microbial consortia (MC_B, MC_C, MC_C_AMF) and one commercial product (Micosat F) were tested in combination with three fertilization levels (unfertilized, 110 kg nitrogen ha[- 1], and 200 kg nitrogen ha[- 1]) in a split plot design. The diversity, composition and functional potential of the maize rhizosphere microbiome were analyzed at different maize growth stages. Fertilization levels exerted a stronger influence than microbial consortia, significantly shaping community composition and functional traits of the indigenous soil microbiome. Increasing fertilization intensity altered the abundance of specific plant growth-promoting (PGP)-determinants, either stimulating or suppressing potential PGP bacteria. In contrast, microbial consortia application did not impact PGP-associated abundance profiles. Overall, the results indicate that multifunctional microbial consortia can act as effective biofertilizers in sustainable maize cultivation without compromising resident microbiome diversity, thereby reducing long-term ecological risks on natural biodiversity.},
}
@article {pmid41975274,
year = {2026},
author = {Nikolaidis, M and Hu, C and Juran, BD and McCauley, BM and Schlicht, EM and Bianchi, JK and Ali, AH and Tragaki, V and Atkinson, EJ and Johnson, S and Mars, RA and Eaton, JE and Carey, EJ and Franke, A and Schramm, C and Kashyap, PC and Go, YM and Tran, V and Teeny, S and Jones, DP and Grant, CW and Athreya, AP and Miller, GW and LaRusso, NF and Gores, GJ and Karlsen, TH and Hov, JR and Amoutzias, GD and Lazaridis, KN},
title = {Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2655793},
doi = {10.1080/19490976.2026.2655793},
pmid = {41975274},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolome ; Female ; Male ; Middle Aged ; Feces/microbiology/chemistry ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Liver Cirrhosis, Biliary/microbiology/metabolism/pathology ; *Cholangitis, Sclerosing/microbiology/metabolism/pathology ; Aged ; },
abstract = {Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are rare, idiopathic, chronic cholestatic liver diseases that respond differently to limited medical therapies and often lead to liver transplantation. We examined the compositional and functional differences in the gut microbiome, mycobiome, and metabolome of these diseases to better understand their impact on pathogenesis and outcomes. Stool sample metagenomes and metabolomes from patients with PSC (n = 245), PBC (n = 280) and matched controls (n = 245 and n = 278, respectively) were analyzed by shotgun sequencing and ultrahigh-resolution mass spectrometry. Comparisons were conducted with covariate-adjusted linear models. The gut microbiomes of patients with PSC and PBC were characterized by reduced diversity and increased abundance of pathobionts and virulence factors, coupled with altered microbial metabolism, including a reduction of short-chain fatty acids and B-vitamins. Untargeted stool metabolomics supported these results. Patients were stratified into groups using their microbial signatures, and each group had distinct patterns of microbiome-related changes. Cox regression analysis revealed that pathogenic microbial species were predictive of hepatic decompensation, whereas beneficial species had a protective effect. Based on previous groundwork and our new results, microbiome-based interventions such as probiotics, short-chain fatty acid supplementation, and phage therapy represent promising therapeutic options for cholestatic liver diseases.},
}
@article {pmid41977149,
year = {2026},
author = {Liszkowska-Walisiak, W and Motyl, I and Płacheta-Kwiatkowska, B and Wlaźlak, M and Ruman, T and Nizioł, J and Wilkowska, A and Maher, A and Berłowska, J},
title = {Apple Pomace Fermented with Non-Saccharomyces Yeast as a Factor Modulating Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
doi = {10.3390/ijms27072960},
pmid = {41977149},
issn = {1422-0067},
mesh = {*Malus/metabolism/chemistry ; *Gastrointestinal Microbiome ; *Fermentation ; Humans ; *Yeasts/metabolism ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/genetics ; },
abstract = {The valorisation of agro-industrial by-products through fermentation offers an opportunity to develop functional ingredients with targeted effects on gut microbiota. This study evaluates the impact of apple pomace fermented at a low temperature (15 °C) by cold-adapted yeast on the structure and metabolic activity of human gut microbiota, simulated using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]). The fermented apple pomace preparation was characterised by high stability under gastrointestinal conditions, supporting its potential applicability as a functional food ingredient. Supplementation with fermented apple pomace induced distinct changes in the composition and activity of gut microbiota compared to the non-fermented substrate, including increased abundance of the genera Akkermansia, Coriobacteriaceae, and Parabacteroides, and reduced abundance of Bifidobacterium, Klebsiella, Serratia, and Raoultella. The fermented preparation was associated with reduced accumulation of metabolites typically linked to proteolytic fermentation and a more stable metabolic profile throughout the supplementation and washout phases. Short-chain fatty acid analysis indicated that fermentation influenced both the quantity and proportional balance of microbial fermentation products, promoting profiles closer to physiological reference ranges. Overall, fermentation of apple pomace at 15 °C enhanced its functional properties and modulated gut microbiota metabolism in a manner consistent with improved ecosystem stability. These findings highlight the potential of fermented fruit by-products as sustainable ingredients for dietary strategies aiming to support gut microbial functionality.},
}
@article {pmid41977414,
year = {2026},
author = {Wang, C and Hou, L and Wang, Y and Gao, G and Geng, Y and Pan, J},
title = {Preliminary Study on the Synergistic Degradation Mechanism of the Microbial Community on the Wood of the Dingtao M2 Tomb.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
doi = {10.3390/ijms27073233},
pmid = {41977414},
issn = {1422-0067},
support = {2024YFF0907700//National Key R&amp;D Program of China/ ; N/A//Fundamental Research Funds for the Central Universities/ ; N/A//Preservation Research Center of the Mausoleum of the Dingtao King/ ; },
mesh = {*Wood/microbiology/metabolism ; *Microbiota ; Lignin/metabolism ; *Penicillium/metabolism/genetics ; Metagenomics/methods ; },
abstract = {According to our investigation carried out in July 2023, the wood of the Western Han Dynasty Dingtao M2 Tomb, stored in the preservation room, exhibited signs of microbial degradation. Our metagenomic analysis first revealed Penicillium as the dominant genus on the end of the wrapped wood. Furthermore, functional annotations demonstrated that the resident microbial community possessed cellulolytic and ligninolytic capabilities. Targeted metabolomic analysis evaluated the degradation capacity of Penicillium charlesii DTP_1, a strain isolated from the wrapped wood. We hypothesize that DTP_1 provides an acidic microenvironment via the production of organic acids; the functional microbial community then decomposes lignin into small metabolites via enzymatic action, and these products are then utilized by the microbial community, including DTP_1. Finally, we verified that liquid cinnamaldehyde and volatile gaseous allicin and carvacrol exhibit better inhibitory efficacy. Nevertheless, further optimization of plant-derived agents and application methods are still required. This study proposes a putative mechanism underlying the degradation of the Dingtao M2 Tomb wood by the microbial community, thereby providing theoretical support for the conservation of wooden cultural heritage and relics.},
}
@article {pmid41979145,
year = {2026},
author = {Alderete, TL and Holzhausen, EA and Liang, D and Jones, RB and Lurmann, F and Goran, MI and Chang, HH and Sarnat, JA},
title = {Early-Life Air Pollution Exposure Is Associated with the Infant Gut Microbiome and Fecal Metabolome in the First Two Years of Life.},
journal = {Research report (Health Effects Institute)},
volume = {},
number = {237},
pages = {1-58},
pmid = {41979145},
issn = {1041-5505},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Feces/chemistry/microbiology ; Female ; *Metabolome/drug effects ; Infant ; Male ; *Air Pollution/adverse effects/analysis ; *Air Pollutants/adverse effects/analysis ; Pregnancy ; Particulate Matter/adverse effects/analysis ; *Environmental Exposure/adverse effects ; California ; Prenatal Exposure Delayed Effects ; Infant, Newborn ; },
abstract = {INTRODUCTION: Obesity is a major public health concern because it increases the risk of numerous diseases, including cardiovascular disease and type 2 diabetes. Ambient and near-roadway air pollution has been associated with childhood obesity risk, independent of diet and physical activity. However, the biological mechanisms underlying these relationships remain unclear. Based on our previous work and existing literature, we hypothesized that exposure to air pollutants alters the developing infant gut microbiome and fecal metabolome, with implications for childhood obesity risk. In this study, we aimed to determine whether prenatal or early-life exposure to ambient air pollution and near-roadway air pollution is associated with the gut microbiome and fecal metabolome during the first 2 years of life.<br><br>METHODS: Our analysis had two components, both of which examined participants from the Southern California Mother's Milk Study, a Latino cohort in which we collected detailed information regarding maternal and child health during the first 24 months of life. Residential-based estimates of exposure to ambient particulate matter (particulate matter &#x2264;2.5 &#xb5;m and &#x2264;10 &#xb5;m in aerodynamic diameter: PM2.5 and PM10, respectively), nitrogen dioxide (NO2), and ozone (O3), as well as near-roadway air pollution (NOx), were modeled using residential address histories. High-throughput metagenomics and metabolomics were performed on stool samples collected at 1, 6, 12, 18, and 24 months of age. Overall, our sample included 207 unique individuals with gut microbiome data and 127 unique individuals with fecal metabolomics data. In the first analysis component, we examined the cross-sectional associations of pre- and postnatal exposure to ambient and near-roadway pollutants with the infant gut microbiome and fecal metabolome at 1, 6, 12, 18, and 24 months of age. In the second analysis component, we examined the longitudinal associations of pre- and postnatal exposure to air pollutants with the trajectory of the developing infant gut microbiome and fecal metabolome.<br><br>RESULTS: Our findings indicate that exposure to air pollutants during prenatal and postnatal periods is associated with significant changes in the developing gut microbiome and its metabolic output, as evidenced by perturbations in the fecal metabolome. These molecular alterations were evident in both cross-sectional and longitudinal analyses. The results suggest that early-life exposure to air pollution can disrupt the developmental trajectory of the gut microbiome, potentially leading to changes with substantial health implications. These findings underscore the importance of mitigating air pollution exposure during critical developmental periods to protect and promote gut health and overall well-being in infants.<br><br>CONCLUSIONS: We identified gut microbes and fecal metabolites associated with early-life exposure to air pollution. Many of these markers of gut bacterial composition and function have been linked to childhood obesity. These findings contribute to our understanding of mechanisms underlying the obesogenic effects of air pollutants in early life. Future work in this cohort will include integrated mixture and multi-omics analyses to explore the joint impact of air pollution exposure on the gut microbiome and fecal metabolome.},
}
@article {pmid41980652,
year = {2026},
author = {Back, JP and Klain, V and Pintro, VO and Lopes, FC and Marques, AL and Kray, J and Beys-da-Silva, WO and Santi, L and Schrank, A and Mayer, FQ and Vainstein, MH},
title = {Viral Diversity of Coastal Restinga Soils From Southern Brazil.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70343},
doi = {10.1111/1758-2229.70343},
pmid = {41980652},
issn = {1758-2229},
support = {441167/2023-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 382064/2025-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 383394/2024-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 314485/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 305705/2025-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303971/2025-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 313620/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303945/2025-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; },
mesh = {Brazil ; *Soil Microbiology ; *Biodiversity ; *Viruses/classification/genetics/isolation &amp; purification ; Phylogeny ; Metagenomics ; Soil/chemistry ; },
abstract = {Coastal ecotones are highly dynamic environments for viral studies due to their extreme abiotic conditions, transitional nature between marine and terrestrial domains and high biodiversity. In Brazil, the Restinga is a coastal ecotone along the shoreline, characterized by nutrient-poor sandy soils, high salinity, strong winds and intense solar radiation, hosting poorly explored microbial communities essential for ecological balance. This exploratory study provides a preliminary characterization of viral diversity across three Restinga localities in southern Brazil (Imbé, Cidreira and Mostardas) using metagenomics. We identified 261 viral families, 2023 genera and 6064 species, with 'Unknown' representing 44%-46% of families and ~9% of genera. Among known taxa, Mimiviridae was most frequent (15%-16%), followed by Phycodnaviridae (9%), Peduoviridae (5%) and Kyanoviridae (4%-5%). Genera such as Tupanvirus and Fadolivirus were abundant (~5%), with Fadolivirus algeromassiliense and Donellivirus gee among the most frequent species. Although alpha diversity and composition did not differ significantly among sites, landscape features influenced viral communities. Viral richness and abundance increased with urban land cover and isolation but decreased with Restinga cover and patch fragmentation.},
}
@article {pmid41519162,
year = {2026},
author = {Olmstead, M and Van Nest, K and Swistek, S and Cohnstaedt, LW and Oppert, B and Shults, P},
title = {Microbial communities in filth flies collected from dairy and poultry farms for supplemental animal feed.},
journal = {Journal of economic entomology},
volume = {119},
number = {2},
pages = {778-789},
doi = {10.1093/jee/toaf283},
pmid = {41519162},
issn = {1938-291X},
support = {NP104- 3020-32000-20-00D//USDA/ ; //The Boehringer Ingelheim Veterinary Scholars Program/ ; //Kansas State University College of Veterinary Medicine Office of Research/ ; //Kansas State University/ ; //USDA/ ; //Veterinary Research Scholars Programs/ ; },
mesh = {Animals ; *Animal Feed/analysis ; *Microbiota ; *Bacteria/isolation &amp; purification/genetics/classification ; Poultry ; *Diptera/microbiology ; Dairying ; },
abstract = {Alternative protein sources are needed due to the rising demand and increasing cost of protein ingredients in livestock diets. Mass collection of wild-caught flies from locations with high insect pressure may be an economical and environmentally sustainable approach to supplement livestock feed, but there may be feed safety issues from microbes found in field-caught insects. Therefore, we evaluated a sequencing-based approach to accurately identify potential pathogens in wild-caught flies captured on 2 different livestock farms. In this study, we combined whole-genome shotgun metagenomic sequencing with total RNA-seq to identify a broad range of microbial taxa present in and on wild-caught flies. We describe several databases tailored to the host insect, host animals, and pathogens associated with livestock and humans. Sequences were identified from potentially pathogenic bacteria including Escherichia coli, Gallibacterium anatis, Helicobacterium pullorum, Morganella morganii, Proteus mirabilis, and Providencia alcalifaciens. In addition, sequences from the pathogenic fungi Aspergillus fumigatus and viruses such as the fly pathogen Musca hytrosavirus were found. Despite the limitations of current database curation, a combination of metagenomics and total RNA-seq approaches to taxa identification can provide insight into a broad spectrum of potential pathogens in insects used as supplemental livestock feed.},
}
@article {pmid41765316,
year = {2026},
author = {Lyu, Y and Ye, Y and Zhang, C and Zhong, W and Zhu, L},
title = {Bisphenol A bis (diphenyl phosphate) disrupts tryptophan metabolism through microbiota dysbiosis to promote intestinal toxicity.},
journal = {Environmental research},
volume = {297},
number = {},
pages = {124140},
doi = {10.1016/j.envres.2026.124140},
pmid = {41765316},
issn = {1096-0953},
mesh = {Animals ; *Tryptophan/metabolism ; Zebrafish ; *Benzhydryl Compounds/toxicity ; *Phenols/toxicity ; *Dysbiosis/chemically induced ; *Gastrointestinal Microbiome/drug effects ; *Intestines/drug effects/pathology/microbiology ; *Flame Retardants/toxicity ; Interleukin-22 ; Bisphenol A Compounds ; },
abstract = {Organophosphorus flame retardants (OPFRs) are associated with intestinal injury. Bisphenol A bis(diphenyl phosphate) (BDP), an emerging OPFR that presents widely in organisms and humans, may induce intestinal toxicity, yet the effect and underlying mechanism remains unclear. In this study, zebrafish were exposed to BDP at 2, 20 and 200 μg/L for 21 days. Distinct histopathological changes in the intestine of zebrafish were observed, and the relative expressions of mucus secretion and tight junction related genes (MUC-2, Occuludin a and ZO-1) were all downregulated. Through the integrated analysis combining metabolomics and metagenomics, the results demonstrated that BDP exposure downregulated the abundances of microbiota Peptostreptococcus, Clostridium, Bombilactobacillus and Sporolactobacillus in zebrafish intestines, to depress tryptophan metabolism and eventually reduce the abundances of tryptophan metabolites. As a result, the expression of AhR, an important receptor activated by tryptophan metabolites, was inhibited to downregulate IL-22 expression, promoting intestinal toxicity. In vivo experiment with indole-3-propionic acid supplement alleviated the pathological changes, which further confirmed that BDP destroyed microbiota-tryptophan metabolism homeostasis to interfere with the AhR-IL-22 axis, eventually promoted pathological toxicity in the intestines. This study highlights vulnerability of intestines to BDP, and provides first insight into the mechanism through which BDP threats intestinal health.},
}
@article {pmid41791469,
year = {2026},
author = {Ma, J and Liu, J and Guo, Z and Zhu, M and Chai, Z and Jiang, F and Li, Z and Liang, Z and Jiang, Z},
title = {Characteristics of the microbial carbon pump in kelp farming areas and the impact of artificial reefs: A metagenomic and ecological perspective.},
journal = {Environmental research},
volume = {297},
number = {},
pages = {124166},
doi = {10.1016/j.envres.2026.124166},
pmid = {41791469},
issn = {1096-0953},
mesh = {*Coral Reefs ; *Kelp ; Metagenomics ; Geologic Sediments/microbiology ; *Carbon/metabolism ; RNA, Ribosomal, 16S ; Carbon Cycle ; Microbiota ; Aquaculture ; },
abstract = {The microbial carbon pump (MCP) can transform labile dissolved organic carbon (LDOC) into recalcitrant dissolved organic carbon (RDOC), yet how sedimentary MCP efficiency is regulated by natural gradients of organic carbon input remains unclear. In this study, we investigated sediments in a kelp farming environment, leveraging the contrast between artificial reef (AR) areas and adjacent non-reef (NR) areas. We combined full-length 16S rRNA sequencing, metagenomics, and fluorescent dissolved organic matter (FDOM) characterization to compare microbial processing under these contrasting depositional regimes. Elevated LDOC inputs in the AR zones were associated with reshaped community metabolic profiles and with enhanced turnover and potential formation of RDOC. High substrate availability was linked to coordinated metabolic functional potential, in which increased genetic potential for upstream catabolism covaried with genomic features indicative of expanded acetyl-CoA supply potential. This putative metabolic overflow was more strongly associated with the mevalonate (MVA) pathway than with the alternative methylerythritol phosphate pathway, consistent with a potential routing toward isoprenoid and terpenoid backbone biosynthesis and the formation of carboxyl-rich alicyclic molecule (CRAM) precursors. Genome-resolved reconstructions further suggested metabolic complementarity among taxa, with predicted cross-feeding interactions that could help sustain carbon processing in MVA-enriched copiotrophs. Overall, humic-like FDOM signals co-vary with organic loading driven by artificial reefs, indicating that these engineering interventions serve as controllable levers, providing a scientific basis for optimizing the carbon sink function of marine ranching through strategic artificial reef deployment.},
}
@article {pmid41905375,
year = {2026},
author = {Wrønding, T and Vomstein, K and Lundgaard, AT and DeLong, K and Mollerup, S and Mortensen, B and Bosma, EF and Hellerung, AM and Engel, EV and Wiil, KD and Heintz, JE and Halkjær, SI and Hugerth, LW and Hartwig, TS and Petersen, AM and Thomsen, AB and Westergaard, D and la Cour Freiesleben, N and Westh, H and van Hylckama Vlieg, JET and Ensign, LM and Nielsen, HS},
title = {Vaginal microbiota transplantation for treatment of vaginal dysbiosis without the use of antibiotics: a double-blind, randomised controlled trial in women with vaginal dysbiosis.},
journal = {The Lancet. Microbe},
volume = {7},
number = {4},
pages = {101294},
doi = {10.1016/j.lanmic.2025.101294},
pmid = {41905375},
issn = {2666-5247},
mesh = {Humans ; Female ; *Dysbiosis/therapy/microbiology ; Adult ; *Vagina/microbiology ; Double-Blind Method ; Young Adult ; Adolescent ; *Microbiota ; Lactobacillus/isolation &amp; purification ; Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; Denmark ; },
abstract = {BACKGROUND: A vaginal microbiota dominated by Lactobacillus species is associated with reduced risk of infection and adverse reproductive outcomes. Effective interventions to restore healthy microbiota remain scarce. In this study, we aimed to assess the efficacy of vaginal microbiota transplants (VMTs) without antibiotic pretreatment in achieving conversion to a Lactobacillus-dominated vaginal microbiome.<br><br>METHODS: This single-centre, double-blind, randomised controlled trial was done at Copenhagen University Hospital (Hvidovre, Denmark) between June 1, 2021, and March 1, 2023. We enrolled women aged 18-40 years with asymptomatic or symptomatic molecular vaginal dysbiosis (<10% total relative abundance of Lactobacillus spp and >20% relative abundance of Gardnerella spp, Fannyhessea vaginae, and Prevotella spp) who were otherwise healthy premenopausal women and not pregnant as recipients; donors were healthy women aged 18-40 years with a Lactobacillus-dominated vaginal microbiota (>80%) and a low (<5%) abundance of Gardnerella spp, F vaginae, and Prevotella spp, and negative screening for sexually transmitted infections. Participants were randomly assigned (3:1) to the intervention or placebo through a computer-generated schedule with block randomisation and stratification by hormonal contraception. Participants and investigators were masked to the group. Up to three administrations of VMT or placebo were given across three menstrual cycles, with follow-up for six cycles. The primary endpoint was resolution of dysbiosis at any timepoint during follow-up, defined as at least 70% relative abundance of Lactobacillus spp and less than 10% combined abundance of Gardnerella spp, F vaginae, and Prevotella spp, as assessed by shotgun metagenomic sequencing of vaginal samples. This analysis was done in the intention-to-treat population, excluding any participants who withdrew consent. An extension study assessed the effect of antiseptic pretreatment before additional VMT in refractory participants. This study was registered with ClinicalTrials.gov (NCT04855006) and is completed.<br><br>FINDINGS: A total of 302 women were screened, of whom 49 were enrolled. 37 women were randomly assigned to the VMT group (mean age 26&#xb7;1 years [SD 3&#xb7;8]) and 12 to the placebo group (27&#xb7;3 years [4&#xb7;8]). The primary outcome showed no significant difference in dysbiosis resolution between active and placebo groups (HR 0&#xb7;65; 95% CI 0&#xb7;20-2&#xb7;16, p=0&#xb7;49). In an extension study of refractory participants, five (50%) of the ten women who received antiseptic pretreatment followed by VMT had a microbiome conversion. Adverse events occurred in 15 (42%) VMT participants and five (42%) placebo participants; none were serious or led to withdrawal. A single pregnancy and one new human papillomavirus infection occurred, both unrelated to treatment.<br><br>INTERPRETATION: VMT without antibiotics did not significantly improve microbiome conversion in this trial. However, findings from the extension study suggest that antiseptic pretreatment might enhance efficacy. Future trials should explore optimised dosing and use donor engraftment as a primary outcome.<br><br>FUNDING: Freya Biosciences.},
}
@article {pmid41910593,
year = {2026},
author = {Bartelli, TF and Baydogan, S and Sahin, I and Hoffman, KL and Petrosino, J and Blackburn, KW and Zhao, J and Wood, A and Ayvaz, T and Surathu, A and Cagigas, MN and Barcenas, EC and Mata, T and Nguyen, VK and Zulbaran-Rojas, A and Li, L and Faraoni, EY and White, JR and Ajami, N and Li, L and Yadav, D and Conwell, DL and Serrano, J and Pandol, SJ and Fogel, EL and Van Den Eden, SK and Vege, SS and Topazian, MD and Park, WG and Hart, PA and Forsmark, C and Bellin, MD and Maitra, A and Bhutani, MS and Kim, M and Van Buren, G and Fisher, WE and McAllister, F and , },
title = {Whole Metagenomic Profiling Identifies a Gut Microbial Signature for Chronic Pancreatitis via Machine Learning.},
journal = {Pancreas},
volume = {55},
number = {5},
pages = {e458-e468},
pmid = {41910593},
issn = {1536-4828},
support = {U01 DK108327/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Pancreatitis, Chronic/microbiology/diagnosis ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Adult ; Feces/microbiology ; Prospective Studies ; Saliva/microbiology ; Aged ; Whole Genome Sequencing ; Dysbiosis/microbiology ; *Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Pancreatitis significantly alters the microbial composition of the oral and intestinal compartments, causing dysbiosis that may contribute to disease mechanisms and potentially serve as a basis for diagnosis or treatment.<br><br>OBJECTIVE: To determine whether the oral or gut microbial signature can classify chronic pancreatitis (CP).<br><br>METHODS: Stool samples (n=707) were collected from participants in the Prospective Evaluation of Chronic Pancreatitis for Epidemiologic and Translational Studies (PROCEED). Samples were distributed among 200 healthy (HC), 310 CP, 49 acute pancreatitis (AP), and 148 recurrent acute pancreatitis (RAP). In addition, saliva samples were collected for a subset of participants (n=156). Whole genome sequencing was performed to assess microbiome composition. Machine learning algorithms were utilized to identify a signature with microbial features predictive of CP.<br><br>RESULTS: Gut alpha diversity was significantly decreased in AP, RAP, and CP compared with HC, with CP exhibiting the lowest diversity. In contrast, oral microbial diversity showed no significant variation across groups. Beta diversity analysis revealed distinct gut microbiome compositions between HC and pancreatitis subtypes, with CP showing the most pronounced differences. Random forest models using gut microbial species demonstrated robust predictive performance for CP using a minimum of 10 species (Area under the curve-AUC: 0.834; accuracy: 0.774). Despite similarities in gut microbiome composition across pancreatitis subtypes, a unique gut microbial signature for CP was identified highlighting the microbiome's potential in CP diagnosis.<br><br>CONCLUSION: Our study reveals a gut microbial signature predictive of CP using machine learning models in a large US multi-institutional cohort.},
}
@article {pmid41932525,
year = {2026},
author = {Liu, Q and Wei, S and Li, Y and Yu, X and Zhang, Z and Li, J},
title = {Synthetic microbial community drive methane oxidation coupled to Cr(VI) reduction via division of labor and extracellular electron transfer.},
journal = {Bioresource technology},
volume = {451},
number = {},
pages = {134546},
doi = {10.1016/j.biortech.2026.134546},
pmid = {41932525},
issn = {1873-2976},
mesh = {*Methane/metabolism ; Oxidation-Reduction ; *Chromium/metabolism ; Electron Transport ; Biodegradation, Environmental ; *Microbial Consortia ; },
abstract = {While methane oxidation coupled to Cr(VI) reduction has been widely investigated, the functional specialization and division of labor within microbial consortia remain insufficiently understood. In this study, a synthetic microbial community (SynCom) was constructed by controlling methane concentration and chromium load. The maximum Cr(VI) removal load of this system reached 20.63 mg/L/d. The metagenomic assembly genome analysis showed that under hypoxic conditions, Methylocystis (6.30%) was the core microorganism driving methane oxidation. It achieved extracellular electron transfer (EET) through multiheme c-type cytochromes and conductive pili, or jointly with dominant genera such as Hyphomicrobium and Thiobacillus, to couple methane oxidation with Cr(VI) reduction. Integrated multi-omics revealed significant enrichment of differentially expressed proteins involved in quorum sensing and methane metabolism, along with elevated expression of ABC transporter substrate-binding protein and porin. The primary metabolites included N-Methyl-L-Proline, L-Histidine, and Hypaphorin, with L-Glutamine serving as a central node connecting the highest number of pathways in the metabolic network. The inhibition experiments confirmed that inhibiting the methane oxidation would directly reduce the efficiency of Cr(VI) reduction. This study revealed the microbial division of labor and the microscopic process of EET driven by aerobic methanotrophs under hypoxic conditions, and expanded its application potential in bioremediation from the perspective of SynCom. It could be a scientific foundation for pollution control technologies of methane-based biotransformation and utilization.},
}
@article {pmid41933601,
year = {2026},
author = {Chen, J and Yan, Y and Xie, K and Gao, M and Ma, Y},
title = {Effect of delivery mode and temperature control of microbial consortium-based compound enzyme on anaerobic digestion of food waste: Decipherment from engineering and energy angles.},
journal = {Bioresource technology},
volume = {451},
number = {},
pages = {134536},
doi = {10.1016/j.biortech.2026.134536},
pmid = {41933601},
issn = {1873-2976},
mesh = {Anaerobiosis ; Methane/biosynthesis ; *Temperature ; *Microbial Consortia/physiology ; *Food ; Hydrolysis ; *Refuse Disposal/methods ; Archaea/metabolism ; Bioreactors/microbiology ; Food Loss and Waste ; },
abstract = {Microbial consortium-based compound enzyme (MCE) has been developed as an alternative to commercial enzyme for food waste (FW) decomposition, yet how to deliver it to anaerobic digestion (AD) system for maximum energy recovery remains unclear. This study systematically compared the simultaneous hydrolysis and AD (Sim mode), as well as separate hydrolysis and AD (Sep mode) at mesophilic and thermophilic temperatures, and dissected their influencing mechanisms on methane production from FW. Results showed that Sep mode and mesophilic temperature were the optimal conditions for methane production, where over 70% of soluble COD and 96% of soluble carbohydrate were consumed within 1 d, and the highest cumulative methane yield reached 507.32 mL/g VS. Dynamics of microbial communities revealed that temperature exerted greater influence on bacterial and archaeal succession than delivery modes, and mesophilic temperature-driven transition from hydrogenotrophic archaea to acetotrophic archaea was a key factor in enhancing methane production. Metagenomic analysis further elucidated that key metabolic functions were temperature-dependent, and Methanothrix was identified as the dominant contributor to these metabolic functions. Moreover, energy balance unveiled that Sep mode respectively increased net energy recovery (ΔEtotal) and energy ratio (Er) by 68.33% and 25.90%, achieving concurrent maximization of quantity and efficiency of energy recovery.},
}
@article {pmid41936935,
year = {2026},
author = {Wang, J and Bi, Y and Fu, Z and Qiao, H and Liu, F},
title = {Harvesting reed (Phragmites australis) for wetland nitrogen removal: Productivity, microbial communities, and underlying mechanisms.},
journal = {Bioresource technology},
volume = {451},
number = {},
pages = {134553},
doi = {10.1016/j.biortech.2026.134553},
pmid = {41936935},
issn = {1873-2976},
mesh = {*Wetlands ; *Nitrogen/isolation &amp; purification/metabolism ; *Poaceae/metabolism/growth &amp; development ; *Microbiota ; Biomass ; Biodegradation, Environmental ; Nitrates ; Water Purification/methods ; },
abstract = {Non-point source nitrogen (N) pollution is a primary driver of aquatic eutrophication. While reed (Phragmites australis) wetlands effectively intercept N, the optimal harvesting strategy for maximizing N removal while maintaining ecosystem function remains unclear. This study investigated the effects of different harvesting frequencies on N removal, plant productivity, and associated microbial mechanisms in wetland microcosms over a three-year period. Four treatments were evaluated: unplanted control (CK), planted with no harvest (T0), annual harvest (T1), and biennial harvest (T2). Results demonstrated that all planted treatments significantly enhanced N removal compared to CK. Although not statistically significant among planted groups, T1 consistently achieved the highest average removal efficiencies for total nitrogen, ammonium-nitrogen, and nitrate-nitrogen. Furthermore, T1 produced the greatest aboveground biomass, facilitating the largest export of N and other nutrients. Metagenomic analysis revealed that reed planting shifted the microbial community, suppressing Cyanobacteria (e.g., Stanieria) and Nitrospirota (e.g., Nitrospira F), while enriching Proteobacteria and Chloroflexota. These compositional changes were coupled with a functional shift that key dissimilatory pathways (denitrification and dissimilatory nitrate reduction) were upregulated, while assimilatory nitrate reduction was suppressed. Additionally, annual harvesting fostered a more complex and stable microbial co-occurrence network. Structural equation modeling indicated that harvesting enhanced N removal primarily through plant-microbe interactions, with increased plant N accumulation promoting microbial N-functional gene abundance, and ultimately driving N removal. Overall, annual harvesting optimally coupled high biomass production with microbial N removal, presenting a sustainable management strategy for wetlands that balances water purification with resource recovery.},
}
@article {pmid41966559,
year = {2026},
author = {Jordán, M and Bustos-Caparros, E and Gago, JF and Zhang, Z and Tian, Z and Singleton, DR and Rossello-Mora, R and Grifoll, M and Vila, J},
title = {Unraveling acridine degradation mechanisms in PAH-contaminated soils using DNA-SIP combined with metagenomics and soil transcriptomics.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142004},
doi = {10.1016/j.jhazmat.2026.142004},
pmid = {41966559},
issn = {1873-3336},
abstract = {Polycyclic aromatic nitrogen heterocycles (PANHs), also known as azaarenes, are common co-contaminants at sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Recent non-target analysis of PAH-contaminated soil samples has revealed an unexpected abundance and diversity of PANHs, with acridine standing out as a predominant compound within this group. Despite its known toxicity and prevalence in contaminated soils, the microbial communities and biochemical mechanisms responsible for acridine degradation remain poorly understood. We conducted DNA-stable isotope probing (DNA-SIP) using newly synthesized uniformly labeled [13]C-acridine to comprehensively assess the bacterial taxa and functional genes involved in acridine biodegradation in a creosote-contaminated soil. Metagenomic analysis of [13]C-enriched DNA from soil incubations identified a member of the genus Sphingobium as the primary acridine degrader. Transcriptomic analysis based on its 16S rRNA gene expression demonstrated a strong correlation with acridine removal from the soil. Shotgun metagenomic sequencing enabled the reconstruction of one metagenome-assembled genome (MAG). Functional annotation of this MAG revealed five gene clusters potentially involved in acridine biodegradation, and their actual contribution was assessed by gene expression analysis in soil incubations. Based on these findings, we reconstructed the metabolic pathway for putative acridine degradation in PAH-contaminated soil.},
}
@article {pmid41967476,
year = {2026},
author = {Wang, H and Di, D and Du, S and Tateno, R and Peñuelas, J and Migliavacca, M and Chen, Q and Guan, J and Song, Y and Shi, W},
title = {Plant functional trait differentiation and microbial life-history strategy shifts drive soil respiration under long-term forest restoration.},
journal = {Tree physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpag042},
pmid = {41967476},
issn = {1758-4469},
abstract = {Soil respiration (Rs) represents a major carbon (C) flux linking plant productivity with microbial decomposition; however, the mechanisms by which contrasting forest restoration pathways regulate Rs and its components remain insufficiently understood. We conducted a six-year field observation (2017-2022) across abandoned farmland (AF), Quercus liaotungensis forest (QF), and Robinia pseudoacacia plantation (RP) on the Loess Plateau, China, integrating measurements of Rs, autotrophic (Ra), heterotrophic (Rh), plant functional traits, soil physicochemical properties, and microbial C metabolic potential. Afforestation significantly increased Rs, with a stronger enhancement observed in QF than in RP. Although Ra did not differ significantly between the two forest types, Rh accounted for approximately 70% of Rs and primarily explained the significant differences in Rs between restoration pathways. Elevated Rh in QF was strongly associated with greater abundances of microbial functional genes involved in the degradation of C substrates. Integrated analyses further revealed that differentiation in plant functional traits between QF (conservative strategy) and RP (acquisitive strategy) indirectly amplified Rh contributions to Rs by reshaping soil substrate availability and coordinating shifts in microbial life-history strategies. Collectively, our findings identify plant functional trait differentiation as a key driver of long-term Rs dynamics, mediated by shifts in microbial life-history strategies.},
}
@article {pmid41969653,
year = {2026},
author = {Dai, Z and Hu, Y and Tai, A and Lu, Y and Hu, S and Pan, J and Xiao, Y and Ma, X and Fu, Q and Zhao, H and Su, Z and Tong, P and Hao, Z and Yao, G and Wang, J},
title = {Characterization of a Klebsiella pneumoniae mutant strain wGF 1-2 with attenuated virulence, altered morphology, and reduced biofilm formation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1761564},
pmid = {41969653},
issn = {2235-2988},
mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/virology/physiology ; *Biofilms/growth &amp; development ; Animals ; Mice ; Virulence ; Klebsiella Infections/microbiology/pathology ; Disease Models, Animal ; Mutation ; Proteomics ; Host-Pathogen Interactions ; Bacteriophages ; Gene Expression Profiling ; Gastrointestinal Microbiome ; Female ; Metagenomics ; },
abstract = {INTRODUCTION: The global rise of antimicrobial resistance has positioned multidrug-resistant Klebsiella pneumoniae as a critical health threat, necessitating alternative therapeutic strategies such as phage therapy. However, the long-term evolutionary consequences of phage-bacteria interactions remain poorly understood. This study characterizes a unique attenuated mutant, wGF 1-2, derived from a hypervirulent K. pneumoniae strain (GF) during phage isolation efforts.<br><br>METHODS: The wGF 1-2 mutant was serendipitously isolated during attempts to obtain lytic phages against the parental GF strain. We performed an integrated multi-omics and phenotypic characterization, including genomic sequencing, proteomic profiling, and transcriptomic analysis. Host-pathogen interactions were assessed using a murine infection model (evaluating survival and tissue colonization), and the impact on the gut microbiota was analyzed via metagenomics.<br><br>RESULTS: Compared to the parental strain, wGF 1-2 exhibited a significant reduction in biofilm formation and distinct morphological alterations. In a murine model, the mutant was avirulent, resulting in 100% survival even at a high challenge dose (10&#x2076; CFU), with minimal tissue colonization. Multi-omics analysis revealed extensive genomic structural variations (81 insertions and 64 deletions). Proteomic shifts included the downregulation of proteins involved in metal ion binding and metabolic pathways. Furthermore, infection with wGF 1-2 led to host inflammatory suppression and a restructuring of the gut microbiota characterized by an increase in beneficial Bacteroidota.<br><br>DISCUSSION: This study provides a comprehensive characterization of an attenuated K. pneumoniae mutant, wGF 1-2. The extensive genomic and phenotypic alterations observed highlight the significant evolutionary potential of bacterial pathogens during phage interactions. These findings underscore the necessity of thorough safety assessments, including evolutionary risk evaluations, for the future development of phage-based therapies.},
}
@article {pmid41972428,
year = {2026},
author = {Wang, YF and Wang, YN and Lin, D and Xu, JY and Qi, FY and Cui, HL and Lu, HJ and Qiao, M and Topp, E and Zhu, D and Rillig, MC and Zhu, YG},
title = {Diversity of Pharmaceuticals Enhances Antibiotic Resistance in the Invertebrate Gut via Biofilm-Mediated Mechanisms.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e18849},
doi = {10.1002/advs.202518849},
pmid = {41972428},
issn = {2198-3844},
support = {42307169//National Natural Science Foundation of China/ ; 42577136//National Natural Science Foundation of China/ ; U25A20803//National Natural Science Foundation of China/ ; 2023J02031//Fujian Provincial Natural Science Foundation of China/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; 2023321//Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; },
abstract = {The environmental accumulation of non-antibiotic pharmaceuticals is an emerging driver of antibiotic resistance. While individual compounds are known to shape the soil resistome, and contaminant diversity also plays a role, the impact of pharmaceutical diversity on the gut resistome of soil invertebrates remains unclear. Here, we combined metagenomics and metaproteomics to examine the collembolan gut and soil resistome across a gradient of pharmaceutical diversity under diurnal warming. Increasing pharmaceutical diversity at a constant total concentration significantly enriched antibiotic resistance genes (ARGs) in the gut microbiome, with no comparable effect in surrounding soils. This enrichment was mainly driven by multidrug resistance associated with efflux activity and biofilm-related processes, accompanied by increases in ARG-carrying taxa such as Gordonia and Ochrobactrum. Notably, Ochrobactrum encoded biofilm-related aryl polyene pathways. In vitro experiments confirmed that biofilm formation promotes resistance through coordinated cellular responses. Metaproteomic data indicated that Ochrobactrum initiates early biofilm formation by recruiting extracellular matrix producers such as Bacillus and Pseudomonas. Diurnal warming modulated these responses, indicating an interaction between chemical diversity and climate stress. These findings identify pharmaceutical diversity as an independent driver of ARG enrichment in host-associated microbiomes and establish chemical complexity as a key factor in assessing the ecological risks of pharmaceutical pollution.},
}
@article {pmid41651131,
year = {2026},
author = {Hantsoo, L and Ford, E and Friedman, ES and Hao, F and Patterson, AD and Bittinger, K and Wu, GD and Zemel, BS and Tanes, C},
title = {The impact of adverse childhood experiences on gut microbiota and markers of inflammation is mediated by obesity and depression.},
journal = {Brain, behavior, and immunity},
volume = {134},
number = {},
pages = {106479},
pmid = {41651131},
issn = {1090-2139},
support = {R03 HD101336/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/physiology ; Pregnancy ; *Depression/microbiology/metabolism ; *Adverse Childhood Experiences ; *Inflammation/metabolism/microbiology ; *Obesity/microbiology/metabolism/psychology ; Adult ; Biomarkers/blood ; Body Mass Index ; Feces/microbiology ; },
abstract = {BACKGROUND: Adverse childhood experiences (ACEs) are associated with poor health outcomes in adulthood including obesity, psychiatric symptoms, and elevated levels of inflammatory markers. Our previous work found ACEs are associated with altered gut microbiota composition. In the present work, we examined ACE associations with gut microbiota and peripheral measures of inflammation in pregnant women with or without obesity, and explored potential modifying factors including diet and depressive symptoms.<br><br>METHODS: Female participants were recruited in the third trimester of pregnancy as part of a larger growth study of African-American infants. Participants were categorized as healthy weight (BMI&#xa0;<&#xa0;25) or obese (BMI&#xa0;&#x2265;&#xa0;30) based on their early pregnancy BMI. They completed the Adverse Childhood Experiences Questionnaire (ACE-Q) and Center for Epidemiologic Studies Depression Scale (CES-D). Stool samples, blood, and dietary data were collected in the third trimester. Shotgun metagenomic sequencing was performed on DNA isolated from stool. Statistical models assessed relationships between gut microbiota and ACE. A false discovery rate (fdr) adjusted p-value q&#xa0;<&#xa0;0.1 was considered statistically significant.<br><br>RESULTS: 107 women completed questionnaires and provided stool in the third trimester. ACEs were positively associated with BMI and depressive symptom severity but not with gut microbiota composition. Depressive symptoms were significantly negatively associated with abundance of gut Bifidobacterium longum (q&#xa0;=&#xa0;0.02) and positively associated with Bacteroides thetaiotaomicron (q&#xa0;=&#xa0;0.02). Path analysis revealed that ACEs predicted pre-pregnancy BMI which predicted elevated inflammatory markers. ACEs also predicted more severe depressive symptoms in pregnancy, which was associated with gut microbiome composition. Finally, ACEs interacted with dietary intake of sugar and whole grains to impact markers of inflammation, the gut microbiome, and enzymes produced by gut microbiota.<br><br>DISCUSSION: ACEs led to two risk pathways in pregnancy: one in which high pre-pregnancy BMI was linked with high levels of serum inflammatory markers during pregnancy, and the other in which greater depressive symptom severity was associated with alterations to the gut microbiome. Further, data suggested ACEs may influence the metabolic potential of the gut microbiome.},
}
@article {pmid41740635,
year = {2026},
author = {Hsu, CY and Almajidi, YQ and Abohassan, M and Gafarov, R and Basunduwah, TS and Hjazi, A and Arora, V and Nayak, PP and Shukla, SK and Jayabalan, K},
title = {Pharmacomicrobiomics in blood cancers: How the gut microbiome and its metabolites shape drug efficacy and toxicity.},
journal = {Critical reviews in oncology/hematology},
volume = {221},
number = {},
pages = {105229},
doi = {10.1016/j.critrevonc.2026.105229},
pmid = {41740635},
issn = {1879-0461},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Hematologic Neoplasms/drug therapy/metabolism/microbiology ; *Antineoplastic Agents/therapeutic use/adverse effects ; Metabolome ; Animals ; },
abstract = {Clinical management of hematologic cancers is frequently complicated by marked, unpredictable inter-patient variation in both therapeutic benefit and adverse effects. Beyond host genetics, accumulating mechanistic and translational data implicate the gut microbiota and its small-molecule metabolome as active modifiers of drug chemistry, host immune tone, and clinical outcomes. In this review we synthesize three recurring, actionable findings: (1) discrete microbial enzymes, most prominently bacterial β-glucuronidases, repeatedly re-activate hepatic drug-glucuronides in the gut and amplify local gastrointestinal toxicity (e.g., irinotecan and mycophenolate), a pathway successfully targeted in preclinical and translational studies. (2) loss of anaerobic short-chain fatty acid production, especially butyrate, is a recurrent, causal mediator of mucosal injury and aggravated graft-versus-host disease after allogeneic hematopoietic cell transplantation. (3) reduced gut microbial diversity and the depletion of key functional taxa predict worse transplant outcomes (including mortality), arguing that baseline ecosystem state is a prognostic biomarker that merits routine consideration in trial design. Building on these syntheses, we propose a compact clinical framework for hematology trials and practice: (A) baseline ecosystem phenotyping (shotgun metagenome + targeted metabolite panel including butyrate and measured bacterial β-glucuronidase activity), (B) risk-stratified interventions (enzyme-targeted inhibitors, defined consortia, or metabolite replacement for high-risk patients), and (C) embedded holo-omic endpoints to confirm on-target biochemical modulation and link molecular change to clinical benefit. Together, these elements move Pharmacomicrobiomics beyond descriptive cataloging toward mechanistic stratification and testable interventions that can reduce unexplained variability in drug response and toxicity for patients with leukemia, lymphoma and myeloma.},
}
@article {pmid41819291,
year = {2026},
author = {Kalimuthu, S and Muthusamy, A},
title = {MobiRes: An integrative pipeline for resistome risk prediction through mobilome profiling.},
journal = {Journal of microbiological methods},
volume = {244},
number = {},
pages = {107448},
doi = {10.1016/j.mimet.2026.107448},
pmid = {41819291},
issn = {1872-8359},
mesh = {Humans ; *Metagenomics/methods ; DNA Transposable Elements/genetics ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; Animals ; *Bacteria/genetics/drug effects ; Interspersed Repetitive Sequences/genetics ; *Drug Resistance, Bacterial/genetics ; Microbiota/genetics ; Machine Learning ; *Computational Biology/methods ; Metagenome ; Bacteriophages/genetics ; Risk Assessment ; Feces/microbiology ; },
abstract = {Antimicrobial resistance (AMR) poses a significant global health challenge, with the environment serving as a crucial reservoir and conduit for resistance determinants. Although antibiotic resistance genes (ARGs) have been extensively studied in environmental contexts, systematic approaches for assessing and prioritizing the risks associated with mobile genetic elements (MGEs), such as plasmids, phages, transposons, and integrative elements (IEs), remain unclear. To address this gap, we present MobiRes, an open-source computational framework designed to predict resistome risk by integrating information from the mobilome and microbiome. The pipeline was evaluated using a wide range of publicly available metagenomic datasets spanning diverse environments, including wastewater, poultry, soil, sediments, and human fecal samples. To validate the framework, statistical analyses and machine learning models were applied to evaluate the role of MGEs in driving ARG dissemination. The pipeline identified transposons as the dominant MGE class while capturing environment-specific variation in plasmid, phage, and IE -associated ARGs. Transposon-associated ARGs showed the most consistent environmental differentiation (ANOVA p = 0.0017; Kruskal-Wallis p = 0.018), whereas plasmid and phage-associated ARGs varied moderately (p = 0.015-0.040) and IE-associated ARGs remained comparatively stable across environments (p > 0.05). The Random Forest (RF) model achieved an AUC of 0.82, and subsequent feature importance and SHapley Additive exPlanations (SHAP) analyses revealed that transposon abundance is the primary factor driving ARG dissemination across diverse environments. By integrating host, mobility, and ecological factors, MobiRes provides a scalable and One Health-oriented framework for comprehensive AMR risk assessment. This pipeline is publicly available at https://github.com/santhiyakc17/MobiRes_Pipeline.},
}
@article {pmid41921761,
year = {2026},
author = {Nee, GW and Agrawal, K and Dalan, R and Kasahara, K and Xiang Darren, LY and Ali, Y and Wong, S},
title = {The oral-gut microbiome axis in diabetes mellitus: a systematic review and emerging clinical perspectives.},
journal = {Diabetes research and clinical practice},
volume = {235},
number = {},
pages = {113232},
doi = {10.1016/j.diabres.2026.113232},
pmid = {41921761},
issn = {1872-8227},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mouth/microbiology ; *Diabetes Mellitus/microbiology/metabolism ; Dysbiosis/microbiology ; },
abstract = {Emerging evidence suggests that diabetes mellitus (DM) is not only a metabolic disorder but also a mucosal disease shaped by microbial interactions across body niches. This review synthesizes current evidence on the oral-gut microbiome axis in DM, focusing on microbial transmission, functional overlap, and clinical relevance. A systematic search of six databases identified studies profiling paired oral and gut microbiomes in individuals with diabetes. Across included studies, consistent findings demonstrate concurrent dysbiosis in both niches. Notably, oral-associated taxa such as Streptococcus, Prevotella, Fusobacterium, and Porphyromonas were detected in the gut, suggesting ectopic colonization and inter-niche microbial transmission. Functional analyses revealed shared disruptions in key metabolic pathways, including short-chain fatty acid production and glycine betaine metabolism, with downstream effects on inflammation and insulin resistance. These microbial alterations correlated with established clinical markers such as HbA1c, fasting glucose, and inflammatory indices. Emerging machine-learning models integrating oral and gut microbiota demonstrated promising diagnostic performance (AUC > 0.83). Collectively, these findings support a potential bidirectional oral-gut axis associated with metabolic dysregulation in DM. Despite limitations including cross-sectional design and heterogeneity, this axis represents a novel target for biomarker development and therapeutic intervention. Future longitudinal and interventional studies are required to determine causal relationships and clinical utility.},
}
@article {pmid41963048,
year = {2026},
author = {Diaz, M and Wilson, N and Ponsero, AJ and Seecharran, T and Som, N and Al-Khanaq, H and Gutiérrez, AV and Gilmour, M},
title = {Microbial community succession and functional potential during processing and storage of cooked ham assessed by shotgun metagenomics.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105075},
doi = {10.1016/j.fm.2026.105075},
pmid = {41963048},
issn = {1095-9998},
mesh = {Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Animals ; Swine ; Food Storage ; *Meat Products/microbiology/analysis ; Cooking ; *Microbiota ; Food Microbiology ; Food Handling ; },
abstract = {Wet-cured ham is a ready-to-eat meat product in which microbial communities contribute to desired product characteristics related to product quality, while also presenting as a spoilage risk. Microorganisms are introduced early during the live brining of raw meat, with the brine representing a long-standing, complex and active culture that influences nitrate generation, preservation, and flavour development. To support quality control and identify early indicators of spoilage, this study investigated taxonomic and functional microbiome changes across production stages, from brining and cooking to cold storage, slicing, and packaging under modified atmosphere. Using metagenomics, we characterised microbial community composition and functional profiles across 67 samples from raw ingredients, intermediate production steps, and final products. Microbial communities differed significantly between stages, despite sharing a related taxonomic structure. Brining markedly reduced diversity, and cooking further decreased richness and evenness. A set of 28 taxa was consistently detected across stages, though their relative abundance varied. Latilactobacillus curvatus was abundant prior to cooking but declined sharply afterwards, while Arthrobacter rhombi, initially rare, became dominant in the cooked product. During chilled storage, microbial succession continued, with some taxa re-emerging after being nearly eliminated by cooking. Functional gene profiling revealed distinct metabolic pathway shifts across stages, particularly involving respiration, amino acid metabolism, and fermentation. These findings provide a detailed baseline of microbial and functional dynamics in the production and storage of wet-cured ham. The results offer a foundation for spoilage risk assessment and contribute to the development of microbiological monitoring strategies to support product safety and shelf-life management.},
}
@article {pmid41964107,
year = {2026},
author = {Zhang, Z and Chen, C and Zhang, M and Zhu, J and Xu, X and Wang, Z and Zhou, L and Wu, C and Zong, M and Yin, T and Cao, Z and Gao, A and Zhang, C and Su, T and Jiang, L and Zhou, W and Zhou, W and Zhou, Y and Wang, J and Ning, G and Jiang, Y and Liu, R and Wang, W},
title = {Gut microbiota signatures in primary aldosteronism and functional identification of an aldosterone-degrading gut bacterium.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2657047},
doi = {10.1080/19490976.2026.2657047},
pmid = {41964107},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Hyperaldosteronism/microbiology/metabolism ; Animals ; *Aldosterone/metabolism/blood ; Male ; Mice ; Feces/microbiology/chemistry ; Middle Aged ; Female ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Ruminococcus/metabolism/genetics ; Blood Pressure ; Aged ; *Eubacteriales/metabolism ; Metagenomics ; Essential Hypertension/microbiology ; },
abstract = {Primary aldosteronism (PA), a major cause of secondary hypertension, is characterized by autonomous aldosterone overproduction. Although the gut microbiota is closely linked to blood pressure regulation, its role in PA remains unclear. We performed metagenomic sequencing on fecal samples from 13 patients with essential hypertension (EH), 57 with unilateral PA (UPA), and 51 with bilateral PA (BPA). Despite comparable overall microbial diversity, gut microbial compositional differences were observed among EH and PA subtypes, particularly at finer taxonomic levels. We next identified 39 microbial species that were positively associated with plasma aldosterone concentration (PAC), and 29 that were negatively associated. In the co-abundance network, Ruminococcus gnavus emerged as one of the top three central nodes and was negatively correlated with PAC. Functionally, R. gnavus efficiently degraded aldosterone and multiple natural steroid hormones in vitro, and aldosterone degradation was accompanied by the generation of 3α,5β-tetrahydroaldosterone. R. gnavus-colonized germ-free mice showed reduced fecal aldosterone levels and downregulated expression of aldosterone downstream genes in the intestine. In an aldosterone infusion model, R. gnavus similarly decreased fecal aldosterone and improved systolic blood pressure (SBP) and serum potassium. Logistic regression further revealed that the presence of R. gnavus was associated with lower odds of having a historical highest SBP ≥ 160 mmHg in patients with PA. Collectively, this study reveals different gut microbial signatures in PA and highlights the aldosterone-metabolizing capacity and blood pressure regulation of R. gnavus. These findings advance our understanding of gut microbiota-steroid hormone interactions in PA and provide a basis for exploring microbiota-based stratification and intervention strategies in steroid hormone-related conditions.},
}
@article {pmid41781966,
year = {2026},
author = {Srivastava, AK and Mishra, P and Kumari, S and Uddin, N and Chen, S and Zhao, Y and Xie, X},
title = {Post translational modifications as biomarkers of soil microbe responses to nano-pesticides.},
journal = {Journal of nanobiotechnology},
volume = {24},
number = {1},
pages = {},
pmid = {41781966},
issn = {1477-3155},
support = {32272514//National Natural Science Foundation of China/ ; },
mesh = {*Soil Microbiology ; *Protein Processing, Post-Translational/drug effects ; Biomarkers/metabolism/analysis ; Microbiota/drug effects ; *Nanoparticles/toxicity/chemistry ; Proteomics ; },
abstract = {Nano-pesticides represent a significant technology advancement in modern agricultural, offering improved target specificity and reduced chemical load. However, their potential to induce subtle, sub-lethal disturbance in soil microbial function remains poorly resolved and is not adequately capture by conventional indicators such as microbial diversity, abundance, or bulk enzymatic activity. The central novelty of this review lies in proposing post-translational modifications (PTMs) as functional, early-warning biomarkers for nano-pesticide induced microbial stress, providing a molecular resolution that bridges exposure and ecological outcome. This review critically examines the current evidence on nano-pesticides-microbiome interaction and PTM-centric framework to interpret microbial responses at the protein regulation level. We highlight phosphorylation, acetylation, and ubiquitination regulate microbial stress responses, modulating detoxification enzymes, efflux pumps, and cellular signalling pathways under nanoparticle-induced stress. Unlike prior reviews that emphasize toxicity endpoints or gene-level responses, this work integrates metaproteomic evidence demonstrating PTM enrichment within stress-responsive functional protein groups across real environmental datasets, underscoring their relevance as conserved biomarkers of adaptive and maladaptive responses. By integrating metagenomics with metaproteomic and metabolomics, this review illustrates how PTM profiling enables mechanistic insight into microbial adaptation, functional impairment, and resilience under nano-pesticide pressure. Furthermore, we introduce a systems-level perspective that combines PTM data with computational modelling and AI-assisted bioinformatics to predict microbiome shifts and ecological risk, an approach not previously synthesized within the context of nano-pesticide assessment. Collectively, this review bridges nanomaterial design, microbial molecular regulation, and environmental risk evaluation, and proposes PTM-based assessment as a new paradigm for developing microbiome-safe, eco-compatible nano-pesticides and advancing molecular environmental monitoring strategies.},
}
@article {pmid41782011,
year = {2026},
author = {Wang, X and Tian, S and Zhang, Y and Yang, L and Hu, D and Wang, Z and Yang, X and Li, S and Wei, J and Zhou, W and Wang, S and Deng, L and Li, F and Hou, S and Li, P and Ru, J},
title = {Bacteria and phage consortia modulate cecal SCFA production and host metabolism to enhance feed efficiency in ducks.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41782011},
issn = {2049-2618},
support = {CARS-42-2//China Agriculture Research System of MOF and MARA/ ; 32341055//National Natural Science Foundation of China/ ; 273124240//Deutsche Forschungsgemeinschaft/ ; 226-2025-00030//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; *Ducks/microbiology/metabolism/virology ; *Cecum/microbiology/metabolism/virology ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism/biosynthesis ; Animal Feed/analysis ; *Bacteria/metabolism/classification/genetics/virology/isolation &amp; purification ; *Bacteriophages/genetics/physiology ; Metagenome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The gut microbiota influences poultry health, nutrition, feed efficiency (FE), and overall productivity. However, the relationship between gut microbes, including bacteria and phages, and FE in ducks remains underexplored. To address this, we integrated cecal 16S amplicon, metagenome, microbiota-derived short-chain fatty acids (SCFAs) profiling, liver transcriptome, and serum metabolome data to illustrate the contribution of the gut microbiome (bacteria and viruses) to duck FE.<br><br>RESULTS: We reconstructed viral genomes and prokaryotic metagenome-assembled genomes (MAGs) and annotated their genes using comprehensive databases. Prokaryotic hosts of viruses were also predicted to understand virus-host dynamics within the gut ecosystem. Our results revealed that high-FE ducks have higher concentration of propionate and butyrate in cecum compared with low-FE ducks. The metagenome sequencing revealed distinct cecal microbiota profiles between two groups, with increased relative abundance of representative SCFA producers, especially Paraprevotella sp905215575 and Bacteroides sp944322345, and enhanced SCFA-biosynthesis pathways in high-FE ducks. Virome genome assembly identified two phages encoding auxiliary metabolic genes (AMGs) involved in pyruvate metabolism, enhancing nutrient availability for host bacteria to produce SCFAs (e.g., temperate phage-encoded pyruvate phosphate dikinase) or exploiting host central metabolic pathways for viral replication (e.g., lytic phage-encoded formate C-acetyltransferase). Furthermore, these representative SCFA-producing bacteria and phage consortia were associated with serum metabolites (including L-histidine and 4-hydroxydecanedioylcarnitine) linked to duck FE.<br><br>CONCLUSION: Collectively, these findings provide novel insights into the gut microbial factors regulating FE in ducks, offering potential strategies to optimize poultry nutrition and productivity. Video Abstract.},
}
@article {pmid41782139,
year = {2026},
author = {Mao, K and Zang, Y and Wang, C and Yang, W and Lu, G and Qiu, Q and Ouyang, K and Zhao, X and Song, X and Liang, H and Xu, L and Qu, M and Li, Y},
title = {Rumen microbiota-associated stress alleviation by creatine pyruvate in newly received cattle: a multi-omics study.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41782139},
issn = {2049-2618},
support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; No. 3230810//the National Natural Science Foundation of China/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; },
mesh = {Animals ; *Rumen/microbiology ; Cattle ; Mice ; Metagenomics ; *Creatine/pharmacology/administration &amp; dosage ; *Stress, Physiological/drug effects ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/drug effects ; Metabolomics ; *Pyruvic Acid/pharmacology/metabolism ; Prevotella/isolation &amp; purification ; Multiomics ; },
abstract = {BACKGROUND: Stress experienced by newly received cattle is a significant challenge in the beef industry, frequently resulting in weakened immune responses and impaired growth. The rumen microbiota is essential to host health, and its imbalance can exacerbate stress. This study investigates the mechanisms by which creatine pyruvate (CrPyr) mitigates stress in newly received cattle through multi-omics approaches, including metagenomics, metabolomics, in vitro and in vivo experiments, and rumen microbiota transplantation (RMT) in mice.<br><br>RESULTS: Our results revealed that CrPyr significantly reduces stress-related hormones (cortisol and adrenocorticotropic hormone) and inflammatory markers (IL-6, IL-1&#x3b2;, and TNF-&#x3b1;), and enhanced antioxidant capacity (SOD: 57.38 versus 46.93&#xa0;U/mL, P&#x2009;<&#x2009;0.05; GSH-Px: 305.87 versus 217.07&#xa0;U/mL, P&#x2009;<&#x2009;0.05; T-AOC: 9.62 versus 7.66&#xa0;U/mL, P&#x2009;<&#x2009;0.05). Metagenomic analysis demonstrated that CrPyr increased Prevotella abundance, a key rumen bacterium involved in volatile fatty acid (VFA) production, and enriches metabolic pathways associated with energy metabolism (ATP synthesis, and pyruvate metabolism) and antioxidant defense (glutathione metabolism, FC&#x2009;=&#x2009;1.08, P&#x2009;<&#x2009;0.05). In vitro and in vivo experiments, as well as RMT studies in mice, further validate these findings, demonstrating that CrPyr promote VFA synthesis and increased ATP production through the electron transport phosphorylation pathway.<br><br>CONCLUSIONS: CrPyr modulates the abundance of ruminal Prevotella in transport-stressed cattle to enhance glutathione and VFA metabolism and to accelerate ATP and nucleotide synthesis, thereby alleviating stress in newly received cattle. This multimodal approach established CrPyr as an effective nutritional intervention that improves rumen function and increases livestock productivity. Video Abstract.},
}
@article {pmid41963036,
year = {2026},
author = {Hou, J and Li, Y and Liu, M and Li, L and Chen, H and An, Y and Xu, H and Yao, Y},
title = {Antibiotic resistance genes (ARGs) in rice: Source attribution and putative mobility patterns.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105055},
doi = {10.1016/j.fm.2026.105055},
pmid = {41963036},
issn = {1095-9998},
mesh = {*Oryza/microbiology/genetics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Phylogeny ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Seeds/microbiology ; Microbiota ; Metagenome ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; },
abstract = {Rice grains can harbor antibiotic resistance genes (ARGs), yet the relative roles of seed-associated and environmental reservoirs remain unclear. We used shotgun metagenomics on rice tissues (grain, seed, leaf, stem, root) and surrounding matrices (bulk/rhizosphere soil, irrigation water, rainwater, PM10). In total, 1019 ARG subtypes were detected; grains contained 395, the largely overlapping with seeds (290) and environmental samples (322). FEAST source tracking revealed contrasting attribution patterns: seed sources explained nearly half of the grain microbiome (average contribution 49.49%) versus 8.45% from environmental sources, whereas environmental sources contributed more strongly to the grain resistome (20.68%). 747 metagenome-assembled genomes (MAGs) were reconstructed, including 275 ARG-carrying MAGs. Phylogenetic screening identified 39 near-identical (≥99%) ARG linkages across samples, operationally classified by host consistency (same vs different predicted hosts) into 11 putative VGT-like and 28 putative HGT-like patterns. For example, blaGOB-50 in grains and seeds shared near-identical sequences within Elizabethkingia anopheles (VGT-like), while APH(9)-Ic in grains (Burkholderia) matched PM10 (Comamonas), consistent with an HGT-like linkage. In selected cases, ARG-MGE co-localization (e.g., umuC, cca) further supported mobility interpretations. Together, these results indicate seedborne signatures in the grain microbiome but comparatively stronger environmental association for the grain resistome, informing efforts to trace ARG reservoirs in rice systems.},
}
@article {pmid40549455,
year = {2025},
author = {Goryanin, I and Sorokin, A and Seitov, M and Emilov, B and Iskakov, M and Goryanin, I and Osmonov, B},
title = {Metagenome and metabolome study on inhaled corticosteroids in asthma patients with side effects.},
journal = {Journal of integrative bioinformatics},
volume = {22},
number = {3},
pages = {},
pmid = {40549455},
issn = {1613-4516},
mesh = {Humans ; *Asthma/drug therapy/metabolism/microbiology ; *Metabolome/drug effects ; *Adrenal Cortex Hormones/adverse effects/administration &amp; dosage ; Male ; Female ; Administration, Inhalation ; Adult ; *Metagenome ; Middle Aged ; *Gastrointestinal Microbiome/drug effects ; Metabolomics ; },
abstract = {This study investigates the gut microbiome and metabolome of asthma patients treated with inhaled corticosteroids (ICS), some of whom experience adverse side effects. We analyzed stool samples from 24 participants, divided into three cohorts: asthma patients with side effects, those without, and healthy controls. Using next-generation sequencing and LC-MS/MS metabolomics, we identified significant differences in bacterial species and metabolites. Multi-Omics Factor Analysis (MOFA) and Global Sensitivity Analysis-Partial Rank Correlation Coefficient (GSA-PRCC) provided insights into key contributors to side effects, such as tryptophan depletion and altered linolenate and glucose-1-phosphate levels. The study proposes dietary or probiotic interventions to mitigate side effects. Despite the limited sample size, these findings provide a basis for personalized asthma management approaches. Further studies are required to confirm initial fundings.},
}
@article {pmid40770112,
year = {2026},
author = {Liu, C and Mansoldo, FRP and Li, H and Vermelho, AB and Zeng, RJ and Li, X and Yao, M},
title = {A workflow for statistical analysis and visualization of microbiome omics data using the R microeco package.},
journal = {Nature protocols},
volume = {21},
number = {4},
pages = {1300-1324},
pmid = {40770112},
issn = {1750-2799},
support = {U22A20608//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42077206//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42477117//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; Workflow ; *Software ; Metabolomics/methods ; *Computational Biology/methods ; Humans ; Machine Learning ; },
abstract = {The increasing complexity of experimental designs and the volume of data in the microbiome field, along with the diversification of omics data types, pose substantial challenges to statistical analysis and visualization. Here we present a step-by-step protocol based on the R microeco package (https://github.com/ChiLiubio/microeco) that details the statistical analysis and visualization of microbiome data. The omics data types shown consist of amplicon sequencing data, metagenomic sequencing data and nontargeted metabolomics data. The analysis of amplicon sequencing data specifically involves data preprocessing and normalization, core taxa, alpha diversity, beta diversity, differential abundance testing and machine learning. We consider various data analysis scenarios in each section to exhibit the comprehensiveness of the protocol. We emphasize that different normalized data produced by various methods are selected for subsequent analysis of each part based on the best analytical practices. Additionally, in the differential abundance test analysis, we adopt parametric community simulation to enable the performance evaluation of various testing approaches. For the analysis of metagenomic data, the focus is on how bioinformatic analysis data are read and preprocessed, which refers to the major usage differences from amplicon sequencing data. For metabolomics data, we mainly demonstrate the differential test, machine learning and association analysis with microbial abundances. To address some complex analyses, this protocol extensively combines different types of methods to build an analysis pipeline. This protocol is more comprehensive and scalable compared with alternative methods. The provided R codes can run in about 6 h on a laptop computer.},
}
@article {pmid41655253,
year = {2026},
author = {Shi, Y and He, S and Li, C and Chan, H and Liu, Z and Yang, B and Li, Q},
title = {Bifidobacterium Breve Yang08 Alleviates Atopic Dermatitis By Enriching Akkermansia Muciniphila and Inhibiting Neutrophil Extracellular Traps Formation In Mice.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {20},
pages = {e18588},
doi = {10.1002/advs.202518588},
pmid = {41655253},
issn = {2198-3844},
support = {32470958//National Natural Science Foundation of China/ ; 82403246//National Natural Science Foundation of China/ ; 82574001//National Natural Science Foundation of China/ ; 2025A04J4030//Guangdong Provincial Science and Technology Plan Project/ ; },
mesh = {Animals ; Mice ; *Bifidobacterium breve ; *Extracellular Traps/metabolism/immunology ; *Dermatitis, Atopic/microbiology/therapy/immunology ; Disease Models, Animal ; Gastrointestinal Microbiome ; Humans ; *Neutrophils/metabolism/immunology ; Dysbiosis ; Probiotics ; Mice, Inbred C57BL ; Akkermansia ; },
abstract = {Atopic dermatitis (AD) is linked to gut microbiota dysbiosis, yet the mechanisms connecting specific commensals to cutaneous immunoregulation remain elusive. We observed reduced Bifidobacterium breve (B. breve) abundance in AD patients. A new B. breve strain was isolated from human stools and nomenclated as Yang08. In MC903-induced AD-like mouse models, Yang08 outperformed a standard strain, ameliorating disease severity, including reduced ear thickening, epidermal hyperplasia, and mast cell infiltration in a manner dependent on viable bacteria and an intact gut microbiota. Antibiotic-mediated microbiota depletion abrogated its efficacy, while fecal microbiota transfer from Yang08-treated mice conferred protection, confirming microbial remodeling as essential. Metagenomics revealed Yang08 specifically enriched Akkermansia muciniphila, which was required for therapeutic effects in germ-free mice. Mechanistically, Yang08 abolished both neutrophil influx and NET deposition in lesions, with ex vivo experiments showing blunted NETosis capacity. Its therapeutic benefits were reversed by neutrophil depletion, NET degradation, or PAD4 inhibition. Overall, Yang08 alleviates AD by enriching A. muciniphila and inhibiting skin NETosis, emerging as a promising prophylactic candidate prevention for AD prevention.},
}
@article {pmid41707923,
year = {2026},
author = {do Nascimento, AC and de Albuquerque, TMR and de Oliveira, DG and de Oliveira, AP and da Costa, PCT and de Sales, LCS and da Silva, JYP and Lins, JDS and E Silva, AL and da Silva, EF and do Nascimento, YM and Tavares, JF and Lima, MDS and Bezerra, TKA and de Oliveira, MEG and El-Bacha, T and Alves, JLB and de Souza, EL},
title = {Integrated metagenomic and metabolomic profiling in an in vitro colonic fermentation study to assess the impacts of conventional, unconventional, and whole edible beet (Beta vulgaris L.) parts on the composition and metabolic responses of the intestinal microbiota of hypertensive individuals.},
journal = {The Journal of nutritional biochemistry},
volume = {153},
number = {},
pages = {110316},
doi = {10.1016/j.jnutbio.2026.110316},
pmid = {41707923},
issn = {1873-4847},
mesh = {*Beta vulgaris/chemistry ; *Gastrointestinal Microbiome ; Humans ; Fermentation ; *Hypertension/microbiology/metabolism ; Metabolomics ; Dietary Fiber/analysis ; Plant Leaves/chemistry ; Antioxidants ; *Colon/microbiology/metabolism ; Metagenomics ; Male ; Middle Aged ; Feces/microbiology ; Plant Roots/chemistry ; Bacteria/genetics/classification ; Nutritive Value ; Metabolome ; },
abstract = {Beet (Beta vulgaris L.) has been widely studied as a functional food, particularly for its bioactive compounds. This study evaluated the physicochemical characteristics, nutritional composition, antioxidant capacity, and the impacts of freeze-dried beet root (FDBR), freeze-dried beet stems and leaves (FDBSL), and freeze-dried whole beet (FDWB) on the composition and metabolic responses of the intestinal microbiota of hypertensive individuals. FDBR, FDBSL, and FDWB had high nutritional value. FDWB had the highest protein content (10.6/100 g), while FDBSL had the highest total dietary fiber content (46.6/100 g). Twenty-eight phenolic compounds were identified, and the antioxidant capacity reached up to 60.6 µmol Trolox/g in FDBR. 16S rRNA amplicon sequencing analysis demonstrated that colonic fermentation of FDBR, FDBSL, and FDWB with fecal inoculum from hypertensive individuals decreased the Firmicutes/Bacteroidetes ratio, decreased or maintained the bacterial diversity, increased the relative abundance of Bifidobacteriaceae, Lactobacillaceae, and Enterobacteriaceae, and decreased Lachnospiraceae, Oscillospiraceae, and Peptostreptococcaceae. Colonic fermentation of FDBR mainly increased the abundance of Bifidobacterium (1.18-7.63%), while FDBSL increased the abundance of Phocaeicola. FDBR, FDBSL, and FDWB decreased the pH values (6.74-5.09) and altered the metabolic profile during colonic fermentation by consuming sugar and producing several metabolites associated with health-promoting properties, while maintaining antioxidant capacity. FDBR, FDBSL, and FDWB may be circular resources with beneficial effects on the composition and metabolic responses of the intestinal microbiota in hypertensive individuals and could be exploited as dietary adjuvant strategies in the management of arterial hypertension.},
}
@article {pmid41864063,
year = {2026},
author = {Jian, X and Yu, P and Zhang, Y and Pan, H and Wu, K and Zhang, H and Zhang, H and Huang, Y and Zhao, Y and Wang, Y and Wang, Y and Zhou, Q and Zhang, X and Zhao, G and Li, B and Guo, J and Xia, K and Tang, B and Li, J},
title = {Large-scale profiling of blood microbial signatures in patients with Parkinson's disease and its association with disease progression: a cross-sectional study.},
journal = {EBioMedicine},
volume = {126},
number = {},
pages = {106224},
pmid = {41864063},
issn = {2352-3964},
mesh = {Humans ; *Parkinson Disease/microbiology/blood/diagnosis ; Disease Progression ; Male ; Female ; Aged ; Biomarkers/blood ; Middle Aged ; Cross-Sectional Studies ; *Microbiota ; Whole Genome Sequencing ; *Bacteria/genetics/classification ; Metagenomics/methods ; },
abstract = {BACKGROUND: Emerging evidence supports the presence of microbial signatures in the blood, yet their clinical relevance remains poorly understood. In this study, we profiled blood microbial signatures in patients with Parkinson's disease (PD) and investigated their associations with disease progression.<br><br>METHODS: We analysed 4018 whole-genome sequencing (WGS) data of blood samples from two independent cohorts. The high-quality non-human reads were extracted for microbial annotation using Kraken 2 and Bracken software with the PlusPF database. To identify PD-associated signatures, we implemented a population-based, cross-cohort filtration process with resequencing validation to minimise noise and putative contaminants.<br><br>FINDINGS: Microbial DNA signals, predominantly bacterial, were extensively detected in the sequencing data and were more abundant in individuals with PD than in controls. Across the two cohorts, 126 bacterial species were identified as key signatures, nearly two-thirds of which are known to colonise human body sites. Among these, 19 species exhibited increased abundance and higher prevalence in PD, and could serve as features to discriminate effectively patients from controls. Furthermore, several microbial signatures were correlated with more severe clinical manifestations, such as motor dysfunction and cognitive impairment.<br><br>INTERPRETATION: Our findings supported blood microbial signatures as promising biomarkers in PD, although their origin and functional relevance remain to be validated. The analytical framework may facilitate future investigations into the potential clinical implications of blood microbial signatures in disease contexts.<br><br>FUNDING: This work was supported by Hunan Innovative Province Construction Project, National Natural Science Foundation of China, and Natural Science Foundation of Hunan Province.},
}
@article {pmid41888912,
year = {2026},
author = {Krull, J and Sidhu, C and Solanki, V and Bligh, M and Rößler, L and Singh, RK and Huang, G and Robb, CS and Teeling, H and Seeberger, PH and Schweder, T and Crawford, CJ and Hehemann, JH},
title = {Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41888912},
issn = {2049-2618},
support = {101029842//MSCA/ ; Project number 570219261//Deutsche Forschungsgemeinschaft/ ; HE 7217/5-1//DFG/ ; 101044738//ERC/ ; },
mesh = {*Mannans/metabolism/chemistry ; *Diatoms/metabolism/chemistry/microbiology ; *Microbiota ; *Seawater/microbiology ; Metagenome ; Oceans and Seas ; Metagenomics/methods ; Sulfates/metabolism ; Bacteria/genetics/metabolism/classification ; Bacteroidetes/metabolism/genetics ; },
abstract = {BACKGROUND: Diatoms, a keystone phylum in Earth's ecosystems, are responsible for substantial oxygen production and the fixation of carbon dioxide in the form of carbohydrates that fuel global food webs. They host diverse prokaryotes, yet how diatoms preferentially recruit those with complementary metabolic traits remains unknown.<br><br>RESULTS: We discovered that diatoms exude a C6-sulfated &#x3b1;-1,3-mannan that serves as a selective carbon source for adapted Polaribacter. Its structure was resolved using NMR spectroscopy, chromatography, chemical synthesis, and enzymatic dissection. Biochemical, physiological, and structural analyses demonstrated, that specialized Bacteroidota employ a four-enzyme pathway to metabolize this glycan. Metagenomic and transcriptomic data revealed that sulfated mannan utilization loci are globally abundant and actively expressed in surface ocean bacterioplankton. Because this mannan provides only carbon, oxygen, sulfur, and hydrogen, bacteria must obtain other essential elements elsewhere, reinforcing metabolic interdependence.<br><br>CONCLUSIONS: Together, these results define a chemically specific interaction between diatoms and specialized bacteria that is mediated by a single sulfated polysaccharide and a dedicated four-enzyme degradation pathway. Presence of this pathway in marine metagenomes and transcriptomes indicates that a sulfated mannan from diatoms exerts selection pressure in the sunlit ocean microbiome. Video Abstract.},
}
@article {pmid41951715,
year = {2026},
author = {Wang, H and Wu, SH and Zhang, K and Chen, KH and Vilgalys, R and Liao, HL},
title = {Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09820-7},
pmid = {41951715},
issn = {2399-3642},
abstract = {Profiling the taxonomic and functional composition of mycobiome using metagenomic and metatranscriptomic sequencing is advancing our understanding of fungal functions in ecosystems. However, the sensitivity and accuracy of mycobiome classification using genome- or core protein-based approaches, is limited by the availability of reference genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel tool to identify taxonomically useful reads from metagenomic or metatranscriptomic data, enabling taxonomic identification of community members based on multiple hypervariable markers. We applied MicroFisher to profile the simulated fungal communities to assess the performance of the developed tool, and found higher performance in fungal prediction and abundance estimation compared to existing tools. In addition, we also used metagenomes from forest soil and metatranscriptomes of root eukaryotic microbes to test our method and found that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. MicroFisher leverages high-resolution hypervariable marker gene databases and weighted integration algorithms to deliver more accurate fungal community classification compared to existing state-of-the-art tools. Additionally, it enables the detection of rare taxa, which is challenging with other available tools. Thus, MicroFisher serves as a novel pipeline for classification of fungal communities from metagenomes and metatranscriptomes.},
}
@article {pmid41956515,
year = {2026},
author = {Rober, AR and Reese, LC and Brown, SP and McMahon, KD and Louca, S and Cieslik, J and Kane, ES and Turetsky, MR and Wyatt, KH},
title = {Hydrologic History Regulates Microbial Biofilm Diversity and Ecosystem Function.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70300},
doi = {10.1111/1462-2920.70300},
pmid = {41956515},
issn = {1462-2920},
support = {MCB-2514370//National Science Foundation/ ; DEB-2141285//National Science Foundation/ ; DEB LTREB-2011286//National Science Foundation/ ; DEB LTREB-2011257//National Science Foundation/ ; DEB-1636476//National Science Foundation/ ; RJVA-PNW-01-JV-11261952-231//Pacific Northwest Research Station/ ; //USDA Forest Service/ ; },
mesh = {*Biofilms/growth &amp; development ; *Ecosystem ; *Biodiversity ; Bacteria/genetics/classification/isolation &amp; purification ; Fungi/genetics/classification/isolation &amp; purification ; Cyanobacteria/genetics/classification ; Hydrology ; Droughts ; Floods ; Metagenomics ; },
abstract = {Aquatic biofilms are an understudied component of northern peatlands and are expected to play a more prominent role in ecosystem processes in areas where aquatic habitat is expanding. The goal of this study was to investigate how hydrologic history influences biofilm diversity and functional genes. This study was conducted in a long-term water table manipulation that simulates drought (lowered water table treatment) and flooding (raised water table treatment) conditions relative to a control treatment (no manipulation). We used a combination of metabarcoding and metagenomic approaches to (1) examine the diversity of eukaryotic algae, cyanobacteria, bacteria and fungi within the biofilm and (2) identify functional genes associated with alternating wet-dry transitional states. Historical flooding, but not drought, led to broad changes in composition and functional genes, especially those associated with carbon metabolism and nitrogen cycling. Differences were related to changes in relative abundance rather than the presence/absence of individual taxa or genes. Hydrologic history influenced community diversity by reducing interspecific competition or by alleviating resource limitation. These findings show that hydrologic history regulates species membership of the community (and thereby associated genes) but differences in water chemistry and interspecific interactions alter the relative abundance of species and their functional potential.},
}
@article {pmid41957864,
year = {2026},
author = {Mawarda, PC and Speksnijder, A and Krijger, D and Berkhout, J and Hoogenboom, A and Duijker, DA and Khoiri, AN and Kraaijeveld, K and Stech, M and Wittink, F},
title = {Functional redundancy and stability support the resilience of the Evernia prunastri holobiont under urbanization.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00886-8},
pmid = {41957864},
issn = {2524-6372},
support = {NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {BACKGROUND: Lichens are now recognized as holobionts comprising a mycobiont, photobiont, and diverse microbiomes, yet the functional roles of these additional microbial partners remain poorly characterized, especially under urbanization. Here, we used the epiphytic lichen Evernia prunastri from urban and natural areas to test the hypothesis that its resilience to urbanization is underpinned by functional stability and redundancy within its multi-kingdom consortium.<br><br>RESULTS: Using an integrated approach of amplicon and shotgun metagenomic sequencing, we found that the bacterial community structure and the functional potential of the mycobiont, bacteria, and fungi remained stable despite urbanization, highlighting stability and resistance to urban environmental stress. Furthermore, by focusing on symbiosis-related functions, we found that each partner shows tendencies toward certain roles, yet we discovered broad functional overlap, suggesting microbial contributions that buffer the symbiosis. Finally, we found that E. prunastri and its microbiome harbors diverse biosynthetic gene clusters with predicted ecological functions relevant for the symbiosis, spanning photoprotection, oxidative stress mitigation, nutrient acquisition, defense, and chemical communication.<br><br>CONCLUSIONS: Our study provides unprecedented genomic evidence that lichen resilience is an emergent property of the integrated holobiont, where functional complementarity and redundancy among diverse symbiotic partners maintain stability under urban environmental conditions.},
}
@article {pmid41957950,
year = {2026},
author = {van der Heijden, M and Clubb, JHA and Erawijantari, PP and Ronkainen, A and Arias, V and Jirovec, E and Kudling, T and Pakola, SA and Ojala, N and Haybout, L and Basnet, S and Grönberg-Vähä-Koskela, S and Karoliina Raatikainen, S and Hemminki, O and Kanerva, A and Quixabeira, DCA and Cervera-Carrascon, V and Manuel Dos Santos, J and Lahti, L and Hemminki, A},
title = {Alistipes and Eggerthella shape the response to oncolytic adenovirus therapy in mice and humans through short-chain fatty acid metabolism.},
journal = {Oncoimmunology},
volume = {15},
number = {1},
pages = {2656514},
doi = {10.1080/2162402X.2026.2656514},
pmid = {41957950},
issn = {2162-402X},
mesh = {*Oncolytic Virotherapy/methods ; Humans ; Animals ; Mice ; *Adenoviridae/genetics ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; *Oncolytic Viruses ; Feces/microbiology ; Female ; *Neoplasms/therapy/microbiology ; Male ; },
abstract = {Accumulating evidence implicates the microbiome as an important determinant of clinical outcomes in cancer therapies; however, the role of the microbiome in oncolytic virus therapy remains largely unexplored. We investigated the gut microbiome of cancer patients following treatment with the oncolytic adenovirus igrelimogene litadenorepvec (Ad5/3-E2F-d24-hTNF-IRES-hIL2; TILT-123). Baseline fecal samples from phase I clinical trials (NCT04695327 and NCT05271318) were analyzed using shotgun metagenomic sequencing and compared to treatment outcomes. A higher relative abundance of Alistipes was observed in patients with treatment benefit, while elevated Eggerthella was observed with reduced benefit. These associations were validated in a preclinical mouse model where administration of Alistipes shahii improved the efficacy of adenovirus therapy. In addition, enrichment analysis in patient samples showed a positive correlation between higher relative abundance of Alistipes and elevated short-chain fatty acids in both feces and serum, which in turn revealed higher circulating neutrophil counts. Finally, in a case study, we observed that adenovirus treatment resulted in increased Alistipes relative abundance and reduced Eggerthella relative abundance, indicating that adenovirus therapy may beneficially modulate the microbiome. Overall, our findings reveal a novel association between Alistipes, Eggerthella, and the therapeutic response to oncolytic adenovirus therapy, highlighting their potential as biomarkers or targets for microbiome-based interventions such as pre-, pro-, or postbiotics.},
}
@article {pmid41958036,
year = {2026},
author = {Shin, H and Jeon, MK and Hur, HG},
title = {A Cautionary Case for Host Assignment Based on Broad Environmental blaOXA Carriers.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70327},
doi = {10.1111/1758-2229.70327},
pmid = {41958036},
issn = {1758-2229},
support = {RS-2023-NR076613//National Research Foundation of Korea/ ; },
mesh = {*beta-Lactamases/genetics ; Metagenomics/methods ; *Bacteria/genetics/drug effects/enzymology/isolation &amp; purification/classification ; Anti-Bacterial Agents/pharmacology ; Wastewater/microbiology ; Metagenome ; *Bacterial Proteins/genetics ; Microbiota ; Drug Resistance, Bacterial/genetics ; },
abstract = {Metagenomic analyses rely heavily on contig assembly and reference databases, which can introduce substantial bias when predicting the hosts of antibiotic resistance genes (ARGs) in complex environmental microbiomes. Reference-based metagenomic pipelines assign ARGs mostly to clinically important pathogens because publicly available genomic repositories are dominated by clinically relevant isolates. Motivated by this limitation, we investigated whether metagenomic inferences accurately reflect the true bacterial hosts of ARGs in a wastewater treatment plant, also integrating culture-based validation. Metagenomic screening suggested that ARGs (blaOXA) were primarily associated with clinical taxa. In contrast, culture-based screening identified a wider host distribution of blaOXA genes. Our results imply that environmental bacteria, rather than clinically important taxa, are also hosts of blaOXA genes. Phenotypic testing showed elevated cephalosporin minimal but no carbapenem resistance, consistent with the nature of carbapenem-hydrolysing class D β-lactamases. Our findings reveal that reliance on reference-based metagenomic host prediction can underestimate the diversity of environmental ARG reservoirs. This integrated approach highlights the need for cautious interpretation of metagenomic host assignments and the importance of coupling metagenomic pipelines with culture-dependent validation when assessing ARG ecology in the natural environments.},
}
@article {pmid41958322,
year = {2026},
author = {Yang, D and Bao, C and Xia, Y and Ling, Y and Zhang, F and Ji, R and Zhong, J and Zhang, T and Tian, H and Xu, X and Sun, B},
title = {Insights Into Variations in the Gut Virome of Tibetan Macaques (Macaca thibetana) Across Wild, Captive, and Semi-Provisioned Environments.},
journal = {American journal of primatology},
volume = {88},
number = {4},
pages = {e70148},
doi = {10.1002/ajp.70148},
pmid = {41958322},
issn = {1098-2345},
support = {32171488//National Natural Science Foundation of China/ ; 32300400//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Macaca/virology/microbiology ; *Virome ; Tibet ; Male ; Animals, Zoo/virology ; Female ; },
abstract = {Viruses are integral components of the mammalian gut ecosystem, playing crucial roles in regulating the gut microbiome and maintaining host health. However, the impact of human activity on the gut virome of mammals remains poorly understood. This study investigated the gut viromes of Tibetan macaques (Macaca thibetana), a primate species endemic to China, under three distinct human-influenced environments (wild, semi-provisioned, and captive) using metagenomic sequencing. Our results revealed that semi-provisioned macaques supported the highest viral diversity, while captive and wild groups exhibited lower diversity, with distinct functional shifts among groups. Furthermore, the co-variation and highly coupled KEGG functional profiles between viral and bacterial communities suggest they function as an integrated synergistic network, where changes in one directly impact the metabolic output of the other. Co-occurrence network analysis further demonstrated that the virus-bacterium interaction network in the captive group was the most fragile, with a structure indicative of a high risk of micro-ecosystem imbalance. Microbial system imbalance is characterized by alterations in both community composition and function, resulting in diminished resilience and stability, which may ultimately compromise host intestinal health. Our results demonstrate that captivity and provisioning drive divergence in the Tibetan macaque gut virome. The fragile, skewed networks in captive individuals highlight a potential cost to microbial health, which may underlie broader health and adaptation risks such as heightened pathogen susceptibility and diminished capacity to cope with environmental perturbations. Thus, monitoring the virome offers a novel early-warning system, informing strategies to enhance welfare and conservation outcomes.},
}
@article {pmid41961886,
year = {2026},
author = {Cosma, BM and Pillay, S and Calderón-Franco, D and Abeel, T},
title = {Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0345919},
doi = {10.1371/journal.pone.0345919},
pmid = {41961886},
issn = {1932-6203},
mesh = {Humans ; *Metagenomics/methods ; Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Inflammatory Bowel Diseases/microbiology ; Neural Networks, Computer ; Multiomics ; },
abstract = {Imbalances in the gut microbiome have been linked to conditions such as inflammatory bowel disease, diabetes, and cancer. While metagenomics and amplicon sequencing are commonly used to study the microbiome, they do not capture all layers of microbial functions. Other meta-omics data can provide more insights, but these are more costly and laborious to procure. The growing availability of paired meta-omics data offers an opportunity to develop machine learning models that can infer connections between metagenomics data and other forms of meta-omics data, enabling the prediction of these other forms of meta-omics data from metagenomics. We evaluated several machine learning models for predicting meta-omics features from various meta-omics inputs. Simpler architectures such as elastic net regression and random forests generated reliable predictions of transcript and metabolite abundances, with correlations of up to 0.77 and 0.74, respectively, but predicting protein profiles was more challenging. We also identified a core set of well-predicted features for each meta-omics output type, and showed that multi-output regression neural networks performed similarly when trained using fewer output features. Lastly, our experiments demonstrated that predicted features can be used for the downstream task of inflammatory bowel disease classification, with performance comparable to that of experimental data.},
}
@article {pmid41963033,
year = {2026},
author = {Tzora, A and Nikolaou, K and Lagkouvardos, I and Voidarou, C and Intze, E and Fotou, K and Skoufos, I},
title = {A novel classification system based on cheese microbial profiles for the assessment of cheese typicity.},
journal = {Food microbiology},
volume = {138},
number = {},
pages = {105049},
doi = {10.1016/j.fm.2026.105049},
pmid = {41963033},
issn = {1095-9998},
mesh = {*Cheese/microbiology/classification/analysis ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Animals ; Milk/microbiology ; Phylogeny ; Greece ; },
abstract = {Cheese typicity reflects the unique characteristics influenced by raw ingredients, traditional tools employed, environmental and production conditions, the cheese-making process and the specific geographical region of origin. In the present study, the typicity of Greek cheeses was studied and compared with cheeses from various countries worldwide, based on microbiota profiles. The dataset included publicly available and 63 newly generated sequences, totaling 322 cheese samples, derived from seven different countries. The analysis incorporated next generation sequencing (NGS) technology, with Illumina sequencing of the 16S rRNA gene hypervariable regions V3-V4, followed by a standardized analytical pipeline process. Through de novo clustering, four main Cheese Microbial Profiles (CMP) - clusters and nine sub-clusters were identified. Core microbiota was identified within sub-clusters. The dominant bacterial genera were Lactobacillus in CMP1, Lactococcus in CMP2 and CMP3, and Streptococcus in CMP4. Distinct cheese types exhibited a statistically significant tendency for specific microbial profiles within clusters. However, no clear signatures of geographic origin were detected, nor were associations found between microbial communities and cheese production parameters such as cheese type, milk source, starter culture addition or milk pasteurization. Additionally, we developed a novel model capable of accurately classifying new cheese samples into clusters and sub-clusters, based on their bacterial ecological community structure. Our findings could support future initiatives, especially when combined with multi-omic approaches, to better identify cheese typicity, verify authenticity, potentially trace geographical origin, and ultimately enhance the quality and safety of cheeses.},
}
@article {pmid41421358,
year = {2026},
author = {Wang, J and Qian, X and Li, Q and Jin, Z and Liu, N and Zhao, J and Chen, W and Wang, S and Tian, P},
title = {Bacteriocin gene-mediated ecological adaptation of Bifidobacterium breve in the adult human gut.},
journal = {Cell genomics},
volume = {6},
number = {4},
pages = {101106},
doi = {10.1016/j.xgen.2025.101106},
pmid = {41421358},
issn = {2666-979X},
mesh = {*Bifidobacterium breve/genetics/physiology/metabolism ; Humans ; *Bacteriocins/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Adult ; Phylogeny ; *Adaptation, Physiological/genetics ; Infant ; Symbiosis ; Gene Transfer, Horizontal ; },
abstract = {The ecological persistence of Bifidobacterium breve across life stages reflects adaptive strategies beyond the classical infant- versus adult-type dichotomy, historically attributed to differential nutrient utilization. Here, comparative genomics revealed no major differences in shared carbohydrate-related genes or accessory genome content between infant- and adult-derived strains. Instead, a distinct type III lanthipeptide bacteriocin cluster, lanKC, was specifically detected in adult-derived isolates. Functional assays combining gene knockout, in vitro co-cultivation, and human intervention demonstrated that lanKC enhances strain-level competitive fitness and promotes community stability. Phylogenetic and metagenomic analyses of 5,475 lanKC homologs and 6,122 infant gut metagenomes further suggested a possible early-life acquisition via intra-genus horizontal gene transfer. These findings uncover a previously unrecognized genetic basis underlying B. breve adaptation to the gut environment and support a multi-factorial model in which metabolic flexibility and interference competition jointly sustain bifidobacterial persistence and host-microbe symbiosis throughout life.},
}
@article {pmid41679417,
year = {2026},
author = {Dash, S and Zhao, D and Schuppe-Koistinen, I and Du, J},
title = {Female reproductive microbiome in fertility care.},
journal = {Fertility and sterility},
volume = {125},
number = {4},
pages = {558-573},
doi = {10.1016/j.fertnstert.2026.02.015},
pmid = {41679417},
issn = {1556-5653},
mesh = {Humans ; Female ; *Microbiota/physiology ; *Infertility, Female/microbiology/therapy/diagnosis/physiopathology ; *Fertility ; *Genitalia, Female/microbiology ; *Reproduction ; },
abstract = {The microbiome has emerged as a critical determinant of female reproductive health and fertility outcomes. Although conventional infertility evaluations, encompassing medical history, ovulation assessment, uterine and tubal evaluation, genetic screening, hormonal profiling, and reproductive tract imaging, provide essential diagnostic information, a substantial proportion of infertility cases remain unexplained, prompting increased attention to microbial factors. This review provides a comprehensive, critical evaluation of the methods for assessing the female reproductive microbiome, spanning traditional culture-based microbiology to contemporary molecular approaches. We systematically discuss the diagnostic performance, clinical utility, and established techniques, including microscopic examination, Nugent scoring, and Amsel criteria, alongside modern molecular methods such as quantitative PCR panels, 16S rRNA gene sequencing, shotgun metagenomics, and other multiomics. Critically, we evaluate the current microbiome testing platforms in clinical validity and utility. We identify significant gaps between research-grade methodologies and clinically actionable diagnostics, including a lack of standardized protocols, inconsistent reporting of absolute bacterial loads vs. relative abundances, and limited validation against reproductive outcomes. We propose evidence-based criteria for selecting appropriate diagnostic approaches on the basis of clinical context and discuss emerging technologies, including multiomics integration for implementing microbiome assessment in fertility care.},
}
@article {pmid41823694,
year = {2026},
author = {Pessi, IS and Eronen-Rasimus, E and Näkki, P and Thomas, DN and Kaartokallio, H},
title = {Bioplastic biodegradability shapes microbial communities in a coastal brackish environment.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag052},
pmid = {41823694},
issn = {1751-7370},
support = {332174//Research Councils of Finland/ ; },
mesh = {*Seawater/microbiology ; Biodegradation, Environmental ; *Bacteria/metabolism/classification/genetics ; Metagenomics ; *Biodegradable Plastics/metabolism ; Cellulose/metabolism/analogs &amp; derivatives ; *Microbiota ; },
abstract = {Microorganisms are metabolically versatile and central to marine ecosystems, yet the potential of marine microbial communities to degrade different bioplastics and the effect of environmental factors are poorly understood. Employing multi-seasonal in situ and in vitro experiments, we assessed the biodegradation of six commonly used bio-based bioplastic materials at a coastal site in the brackish Baltic Sea and characterized the associated microbial communities using metagenomics and metatranscriptomics. Cellulose acetate (CA), polybutylene succinate (PBS), and polyhydroxybutyrate/valerate (PHB) degraded at varying rates across materials, seasons, and experimental settings, with up to 28% weight attrition after 97 weeks in situ (CA) and 56% carbon loss as CO2 after 4 weeks in vitro (PBS). The three biodegraded plastics developed similar microbial communities that differed markedly from those on the other materials (cellulose acetate propionate, polyamide, and polyethylene) and in the water column. The main microbial populations on the biodegraded plastics included aerobic and facultative anaerobic heterotrophs with a broad capacity for carbohydrate metabolism. Populations with the potential for nitrogen fixation and denitrification were more prevalent on the biodegraded plastics, suggesting that bioplastic biodegradation is constrained by and coupled to the marine nitrogen cycle. Based on the metatranscriptomic signal of key genes involved in the initial hydrolysis of CA, PBS, and PHB, we identified diverse microbial populations that can potentially drive the biodegradation of these materials in the Baltic Sea, many of which encoded the potential to degrade multiple bioplastics. We propose the term 'bioplastisphere' to denote the distinctive microbial communities associated with biodegradable plastics.},
}
@article {pmid41880538,
year = {2026},
author = {Consuegra-Asprilla, JM and Cuesta-Astroz, Y and González, &#xc1;},
title = {Characterization of the vaginal microbiome and its metabolic potential in Colombian patients with recurrent vulvovaginal candidiasis.},
journal = {Medical mycology},
volume = {64},
number = {4},
pages = {},
doi = {10.1093/mmy/myag026},
pmid = {41880538},
issn = {1460-2709},
support = {2019-2020//Programmatic Health Sciences Call/ ; //Universidad de Antioquia/ ; },
mesh = {Humans ; Female ; Adult ; *Candidiasis, Vulvovaginal/microbiology/epidemiology ; *Vagina/microbiology ; *Microbiota ; Middle Aged ; Colombia ; Young Adult ; Recurrence ; Lactobacillus/isolation &amp; purification ; Dysbiosis/microbiology ; Metagenomics ; },
abstract = {Recurrent vulvovaginal candidiasis (RVVC) is a multifactorial condition in which vaginal microbiota dysbiosis plays a key role. This study aimed to characterize the vaginal microbiome of patients with RVVC using metagenomic sequencing. Vaginal scraping samples were collected from 34 women aged 20-47 years and classified into three groups: (1) 14 women with RVVC who had experienced 3-7 episodes of VVC in the previous year; (2) 9 women with severe RVVC, defined as ≥8 episodes in the last year; and (3) 11 healthy women as controls. The results revealed an increased relative abundance of bacteria associated with bacterial vaginosis-including Gardnerella vaginalis, G. swidsinskii, and Prevotella bivia-as well as higher levels of Lactobacillus iners in both RVVC groups. In contrast, healthy women showed a greater abundance of L. crispatus and L. gasseri. Diversity analyses indicated lower α-diversity in the healthy group compared to RVVC patients. Metabolic potential profiling showed a differential increase in sequences related to the phosphotransferase system, fructose/mannose metabolism, pentose phosphate pathway, and cysteine/methionine and purine metabolism in RVVC groups relative to controls; no significant differences were observed between RVVC groups, indicating that microbial profiles alone do not correlate with the degree of disease severity. These findings provide relevant insights into the taxonomic and functional characteristics of the vaginal microbiome in women with RVVC and may support the development of targeted therapeutic strategies.},
}
@article {pmid41904571,
year = {2026},
author = {Kolenda, R and Hassan, MM and Arrieta-Gisasola, A and Kamara, A and Ansorge, R and Sidorczuk, K and Acton, L and Thilliez, G and Baker, DJ and Burdukiewicz, M and Stares, MD and Browne, HP and Le Gall, G and Torres, RC and Chavez-Arroyo, A and Garrett, J and Stevens, MP and Lawley, TD and Bäumler, AJ and La Ragione, R and Hildebrand, F and Kingsley, RA},
title = {Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41904571},
issn = {2049-2618},
support = {BB/W003155/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Salmonella typhimurium/drug effects/genetics ; Swine/microbiology ; *Copper/pharmacology ; Feces/microbiology ; Metagenomics/methods ; Salmonella Infections, Animal/microbiology ; Genomic Islands ; Drug Resistance, Bacterial ; },
abstract = {BACKGROUND: Foodborne pathogens, including Salmonella enterica serovar Typhimurium (S. Typhimurium), pose a significant threat to both human health and livestock productivity. The pandemic S. Typhimurium ST34 clone acquired a genomic island (SGI-4) conferring high copper resistance, an adaptation relevant in the context of the widespread use of copper sulphate at therapeutic levels in pig farming. We investigated how high dietary copper influences the piglet gut microbiota and Salmonella-microbiota interactions that may explain the global spread of S. Typhimurium ST34.<br><br>RESULTS: An on-farm study combined with faecal shotgun metagenomics revealed that several potential Salmonella competitor species, including Bifidobacterium, Escherichia, and Lactobacillus, were less abundant in piglets on high-copper diets. Anaerobic and aerobic culturing alongside whole genome sequencing of 131 species and copper sulphate susceptibility testing identified copper resistance gene acquisition in selected microbes, particularly within Escherichia. Niche competition assays demonstrated that copper resistance is critical for inter-species competition under high-copper conditions, with Salmonella's Type VI Secretion System providing a distinct advantage over Escherichia in the copper-modified niche.<br><br>CONCLUSIONS: Our findings suggest that copper supplementation alters the piglet gut environment, impacting competitive dynamics between pathogenic and commensal bacteria, likely to influence the zoonotic transmission of pathogens. Video Abstract.},
}
@article {pmid41921531,
year = {2026},
author = {Li, W and Lv, M and Cheng, M and Han, Y and Yu, H and Huang, Y and Meng, D and Xu, X and Sun, L and Lu, Z and Liu, Q},
title = {Feasibility of low-biomass exhaled breath microbiome sequencing using a PDC-sampler in febrile and healthy individuals.},
journal = {Journal of breath research},
volume = {20},
number = {2},
pages = {},
doi = {10.1088/1752-7163/ae5a51},
pmid = {41921531},
issn = {1752-7163},
mesh = {Humans ; Breath Tests/instrumentation/methods ; *Microbiota/genetics ; Feasibility Studies ; Male ; Adult ; Female ; Exhalation ; *Fever/microbiology ; Middle Aged ; Healthy Volunteers ; Biomass ; },
abstract = {Exhaled breath is a noninvasive and repeatable biological matrix offering new opportunities for respiratory microbiome analysis, yet its extremely low microbial biomass limits current high-throughput applications. Building on our previously developed phase-change drywall cyclone sampler (PDC-sampler), which integrates condensational growth with dry-wall cyclone separation, we established a validated workflow for efficient aerosol collection and multi-Omics sequencing of exhaled breath. Using this platform, exhaled breath from 15 febrile patients and 6 healthy volunteers was analyzed via shotgun metagenomic and 16 S rRNA sequencing to assess microbial composition, diversity, and functional features. The PDC-sampler significantly increased microbial DNA yield, enabling stable detection of bacterial taxa dominated byPseudomonadota, Bacillota, Bacteroidota, andActinomycetota. Functional annotations and diversity metrics revealed distinct microbial and metabolic patterns between individuals, confirming the platform's analytical sensitivity and biological representativeness. This work experimentally validates the feasibility of exhaled breath microbiome sequencing using the PDC-sampler, providing a practical and generalizable framework for noninvasive respiratory microecology studies and future diagnostic applications.},
}
@article {pmid41950191,
year = {2026},
author = {Kador, SM and Shila, JF and Afrin, S and Jannat, J and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Hasan, MS and Sakib, N and Rahman, MS and Islam, OK and Islam, MT},
title = {Microbial diversity, functional genomics and antibiotic resistance in integrated chicken and fish farming systems of Bangladesh.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0344367},
pmid = {41950191},
issn = {1932-6203},
mesh = {Animals ; Bangladesh ; *Chickens/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Aquaculture ; *Drug Resistance, Microbial/genetics ; *Fishes/microbiology ; Genomics ; Anti-Bacterial Agents/pharmacology ; Biodiversity ; Microbial Sensitivity Tests ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The integrated chicken and fish farming system in Bangladesh is widely practiced for its resource efficiency, yet its microbial structure, functional potential, and associated antimicrobial resistance risks remain poorly understood. This study investigated microbial communities, metabolic functions, and antimicrobial resistance profiles across multiple components of integrated farming systems, including chicken gut, chicken droppings, feed, fish intestine, and pond sediment. Microbial profiling was performed using 16S ribosomal ribonucleic acid (rRNA) gene sequencing, functional metagenomic prediction, and culture-based isolation, complemented by antimicrobial susceptibility testing. A total of 2,838 operational taxonomic units were identified, with bacteria constituting the vast majority of detected microorganisms. Microbial community composition was strongly shaped by sample type, reflecting distinct ecological niches within the farming system. Chicken gut samples were dominated by Firmicutes, feed samples by Cyanobacteria, and sediment samples exhibited the highest microbial diversity, including taxa involved in biogeochemical cycling. Functional analysis revealed that pathways related to amino acid and carbohydrate metabolism were most abundant across all samples, while sediment and feed were enriched in pathways associated with xenobiotic degradation, suggesting a role in environmental detoxification. Culture-based methods isolated clinically relevant bacteria, including Escherichia coli and Proteus mirabilis, although metagenomic analysis indicated that these organisms represented only a minor fraction of the overall microbial community. Antimicrobial susceptibility testing demonstrated notable resistance, particularly to tetracyclines and fluoroquinolones. Metagenomic analysis further identified multiple antimicrobial resistance genes, with several showing strong associations with specific bacterial genera. This study provides the first comprehensive characterization of microbial diversity, functional capacity, and antimicrobial resistance within integrated chicken and fish farming systems in Bangladesh, highlighting potential environmental reservoirs of resistance and underscoring the need for improved management strategies to enhance sustainability and reduce public health risks.},
}
@article {pmid41576933,
year = {2026},
author = {Hernandez-Leyva, AJ and Berna, AZ and Bui, MH and Liu, Y and Rosen, AL and Lint, MA and Whiteside, SA and Jaeger, N and McDonough, RT and Joardar, N and Santiago-Borges, J and Tomera, CP and Luo, W and Odom John, AR and Kau, AL},
title = {The gut microbiota shapes the human and murine breath volatilome.},
journal = {Cell metabolism},
volume = {38},
number = {4},
pages = {779-793.e8},
pmid = {41576933},
issn = {1932-7420},
support = {T32 GM007200/GM/NIGMS NIH HHS/United States ; R01 HD109963/HD/NICHD NIH HHS/United States ; R21 AI154370/AI/NIAID NIH HHS/United States ; R33 HD105594/HD/NICHD NIH HHS/United States ; F30 DK127584/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/physiology ; *Volatile Organic Compounds/analysis/metabolism ; Mice ; Breath Tests/methods ; Child ; Male ; Female ; Asthma/microbiology/metabolism ; Mice, Inbred C57BL ; Germ-Free Life ; Gas Chromatography-Mass Spectrometry ; Feces/microbiology ; Exhalation ; },
abstract = {The gut microbiota is crucial to health, yet implementation of microbiota-based therapeutics is limited by the lack of rapid diagnostics. We hypothesize that breath contains gut microbe-derived volatile organic compounds (VOCs) reflecting microbiota composition and metabolism. In healthy children, we found that breath VOC composition (or volatilome), assessed by gas chromatography-mass spectrometry, correlates with gut microbiome composition and function. By capturing exhaled breath from human-stool-colonized and monocolonized gnotobiotic mice, we profiled breath VOCs and discovered that murine breath is also significantly influenced by the gut microbiome. VOCs from cultured gut microbes were identified in vivo in monocolonized gnotobiotic colonized mice. As a proof of principle, we demonstrated that exhaled breath predicts the abundance of a disease-associated bacterium, Eubacterium siraeum, in children with asthma. Altogether, our studies identify microbe-derived VOCs in breath, show that gut bacterial metabolism directly contributes to mammalian breath VOC profiles, and inform the development of non-invasive microbiome diagnostics.},
}
@article {pmid41745125,
year = {2026},
author = {Gori Savellini, G and Alessandri, G and Beligni, G and Badano, D and Fanciulli, PP and Frati, F and Cusi, MG},
title = {Metagenomic sequencing discloses the virome composition of mosquitoes and sandflies from Central-Southern Tuscany, Italy.},
journal = {Microbiology spectrum},
volume = {14},
number = {4},
pages = {e0186725},
pmid = {41745125},
issn = {2165-0497},
support = {PE00000007 CUP B63C22001400007 INF-ACT//Ministero dell'Universit&#xe0; e della Ricerca/ ; Programma Nazionale per la Ricerca (PNR) (D.M. 737)//Ministero dell'Universit&#xe0; e della Ricerca/ ; PRIN2022 PNRR Grant No. P2022WYNAH)//Ministero dell'Universit&#xe0; e della Ricerca/ ; },
mesh = {Animals ; Italy ; *Virome/genetics ; Metagenomics ; *Psychodidae/virology ; *Aedes/virology ; Flavivirus/genetics/isolation &amp; purification/classification ; Phlebovirus/genetics/isolation &amp; purification/classification ; Humans ; Mosquito Vectors/virology ; Seasons ; Culex/virology ; },
abstract = {Mosquitoes and sandfly species are well-known vectors of viral pathogens of public health concern. However, the diversity and ecology of viruses within mosquitoes, including those responsible for clinical and sub-clinical infections in humans, remain poorly understood. In this study, we investigated the presence of phleboviruses and flaviviruses in Aedes albopictus and Culex pipiens mosquitoes, as well as Phlebotominae species, collected from the Siena and Grosseto districts (Tuscany, Italy) during the 2022-2024 summer season. Furthermore, A. albopictus and C. pipiens larvae were reared under laboratory conditions, and adults were collected for further virological analysis. Molecular investigations (reverse-transcription polymerase chain reaction [RT-PCR]) detected phleboviruses and/or flaviviruses in several batches of both field-collected and laboratory-reared flies. Notably, the highest incidence and co-circulation of both viral genera were observed in samples from the 2024 season. Furthermore, metagenomic analysis was performed on only 42 out of 67 RT-PCR-positive pools of mosquitoes and sandflies. This approach aimed to identify wild-type or recombinant viruses and assess the virome of autochthonous arthropods, contributing to knowledge on viral ecology in southern Tuscany and potential threats to humans. The resulting data revealed a wide viral community shared among mosquitoes, spanning over 30 taxonomic virus families, albeit no potential human pathogen virus was identified. Furthermore, our findings confirmed the mosquito specificity of certain endogenous arthropod viruses and provided evidence of their potential transovarial transmission in some cases. The present study provides a comprehensive analysis of the mosquitoes and sandflies virome, contributing to viral surveillance efforts and underscoring the need for enhanced monitoring of arthropod-borne pathogens.IMPORTANCEIn this study, we analyzed the co-circulating phleboviruses and flaviviruses, providing foundational data on the diversity, composition, and transmission of insect-specific and vector-borne viruses in Central-Southern Tuscany, an area increasingly exposed to arbovirus threats due to climate change and globalization. This is the first comprehensive metagenomic study to characterize the virome of Aedes albopictus, Culex pipiens, and Phlebotomine spp. in this region. Furthermore, we identified for the first time Punique virus (PUNV) in Italy, a phlebovirus with potential (though not yet confirmed) human pathogenicity.},
}
@article {pmid41748627,
year = {2026},
author = {Huang, Z and Petersen, JM},
title = {Recovery of metagenome-assembled genomes from Spartina alterniflora root microbiome in Fujian Province, China.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41748627},
issn = {2052-4463},
support = {2025J01967//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; },
mesh = {China ; *Microbiota ; *Plant Roots/microbiology ; *Metagenome ; *Poaceae/microbiology ; *Genome, Bacterial ; Genome, Archaeal ; },
abstract = {The saltmarsh cordgrass Spartina alterniflora proliferates along the coast of China. Like all plants, S. alterniflora hosts a specific microbiome that plays crucial roles in sustaining plant growth and health. Till now, very few studies have investigated the root microbiome of S. alterniflora in China, where it is considered an invasive pest. Here, ~350 Gbp metagenomes of S. alterniflora were generated from 8 sampling sites in South Fujian Province, China. 798 bacterial metagenome-assembled genomes (MAGs) and 7 archaeal MAGs were obtained, which were de-replicated into 205 and 3 representative genomes at a 95% ANI cutoff. The recovered bacterial MAGs mainly belonged to Gammaproteobacteria, Alphaproteobacteria, Bacteroidia and Campylobacterota. Sedimenticolaceae were prevalent at all sampling sites, accounting for 4-30% of the corresponding MAGs. These genomic datasets provide a new resource for investigating S. alterniflora root microbiomes, particularly valuable considering current efforts to eradicate this species in China.},
}
@article {pmid41757890,
year = {2026},
author = {Tarasov, K and Zarubin, M and Yakhnenko, A and Gangapshev, A and Kravchenko, E},
title = {Metagenomic analysis of the biofilm community at the oxic-anoxic interface of a deep-underground saline spring at the Baksan Neutrino Observatory.},
journal = {Microbiology spectrum},
volume = {14},
number = {4},
pages = {e0210325},
pmid = {41757890},
issn = {2165-0497},
support = {24-24-00003//Russian Science Foundation/ ; },
mesh = {*Metagenomics/methods ; *Biofilms/growth &amp; development ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Archaea/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota/genetics ; Metagenome ; Russia ; *Natural Springs/microbiology ; Phylogeny ; },
abstract = {In this work, the first-ever metagenomic study of the microbial community from the deep-underground saline spring located at the Baksan Neutrino Observatory (BNO) (Kabardino-Balkaria, Russia) is presented. Using the metagenomic approach, we obtained 19 metagenome-assembled genomes (MAGs) attributed to the phyla Pseudomonadota (the dominant phyla), Planctomycetota, Myxococcota, Nitrospirota, Gemmatimonadota, Armatimonadota, and Cyanobacteriota. Archaea are generally absent in the metagenome. The microbial community of the Baksan Neutrino Observatory demonstrates a high metabolic diversity, including carbon dioxide-fixing, methane-oxidizing, dinitrogen-fixing, nitrate- and iron-reducing, anammox, nitrifying, and predatory bacteria. Hydrogen, methane, ammonia, and reduced iron compounds, present in the ecosystem, provide energy for primary organic production. The abundance and diversity of bacteria capable of carrying out various stages of the nitrogen cycle suggest that nitrogen compounds are of great significance for microbial community metabolism. On the basis of the Genome Taxonomy Database Toolkit classification of MAGs and comparison to the closest RefSeq genomes, we have identified six new genera, with the proposed names-"Candidatus Jinrbaksania," "Candidatus Neutrinellum," "Candidatus Jinrextremum," "Candidatus Inrsubterrania," "Candidatus Inralta," and "Candidatus Neutrinobacter." Comparative analysis with metagenomes of microbial communities from the deep underground granitic sites and karst caves reveals that the BNO microbial community represents a unique transitional ecosystem on the boundary between the deep anoxic and surface aerobic biosphere.IMPORTANCEThe deep biosphere makes up 12-20% of the Earth's biomass and is poorly studied due to its inaccessibility. To date, only a few metagenomic studies of local deep biospheres have been performed in Russia. The Baksan Neutrino Observatory (BNO) is a deep-underground laboratory, with some abandoned tunnels. One of them hosts a mineral spring saturated with volcanic gases from the peripheral magma chamber of Mount Elbrus. The metagenomic analysis of the biofilm from this mineral spring has revealed the presence of unique microbial community whose composition occupies a transitional position between deep-underground microbial communities and communities of karst caves. We believe that this study of the microbial metagenome of the saline spring of the BNO will make a valuable contribution to understanding the composition and functioning of microbial communities formed at the oxic-anoxic interface.},
}
@article {pmid41759554,
year = {2026},
author = {Dai, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Xu, H and Sun, J},
title = {Insights into antibiotic resistomes from gut metagenome-assembled genomes of the free-range pigs.},
journal = {Microbiology spectrum},
volume = {14},
number = {4},
pages = {e0240725},
pmid = {41759554},
issn = {2165-0497},
support = {24D1J01//CARS | National Swine Industry Technology System/ ; 2024M762004//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; Swine/microbiology ; *Gastrointestinal Microbiome/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; China ; Feces/microbiology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Metagenome/genetics ; Metagenomics ; Genome, Bacterial ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; },
abstract = {The pig gut microbiome serves as a reservoir for antibiotic resistance genes (ARGs), which pose a threat to public health and environmental safety. To investigate the presence of ARGs carried by free-range pigs, which have frequent contact with humans and their environment, we characterized the resistome of the pig gut microbiome through metagenomic sequencing of fecal samples from 120 pigs across four provinces in China (Yunnan, Guizhou, Sichuan, and Jiangsu). By constructing metagenome-assembled genomes (MAGs) and gene catalogs, we explored the microbial community structure and ARG distribution. Our analysis revealed a highly diverse array of ARGs, particularly those conferring resistance to multidrug, glycopeptide, peptide, and tetracycline antibiotics. Bacillota A and Actinomycetota were the dominant phyla across samples. However, notable regional differences in microbiota composition and resistance profiles were observed. These differences were likely influenced by local farming practices and environmental conditions. Guizhou harbored 11 unique ARG types, followed by Sichuan (seven), which showed region-specific resistome signatures. Escherichia coli and other microbial taxa were closely linked with ARG abundance, suggesting potential vectors for horizontal gene transfer. Analysis of mobile genetic elements (MGEs) further supported this, revealing a strong linear correlation between MGE and ARG abundance, with transposase elements particularly associated with multidrug ARGs. These findings highlight the central role of MGEs in ARG dissemination and underscore the need for targeted strategies to curb antibiotic resistance in livestock systems. Regional variation in resistome profiles further emphasizes the influence of local agricultural practices on resistance dynamics.IMPORTANCEThe growing prevalence of antibiotic resistance poses a significant global health threat, making it imperative to trace the origins and transmission routes of ARGs. This study delivers a comprehensive genomic reference for the porcine gut microbiota and clarifies how regional farming practices shape distinct resistome profiles. Integrating these data with analyses of mobile genetic elements and microbial hosts reveals the complex interplay among host, microbiota, and environment, thereby extending current knowledge of the pig gut ecosystem. These findings provide an evidence-based foundation for targeted surveillance and intervention strategies to curb antibiotic resistance in livestock and safeguard public health.},
}
@article {pmid41759557,
year = {2026},
author = {Yang, W and Shi, L and Li, X and Rao, F and Luo, R and Huang, C},
title = {Alterations in the gut virome of children with allergic rhinitis: enrichment of pro-inflammatory bacteriophages and depletion of fungal viruses.},
journal = {Microbiology spectrum},
volume = {14},
number = {4},
pages = {e0327625},
pmid = {41759557},
issn = {2165-0497},
mesh = {Humans ; *Virome ; Child ; *Rhinitis, Allergic/virology/microbiology/immunology ; *Gastrointestinal Microbiome ; Female ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Male ; Feces/virology/microbiology ; Immunoglobulin E/blood ; Metagenomics ; *Fungal Viruses/genetics/isolation &amp; purification ; Child, Preschool ; Bacteria/classification/genetics/isolation &amp; purification ; Viruses/classification/genetics/isolation &amp; purification ; Allergens/immunology ; },
abstract = {This study aimed to characterize the gut virome in children with allergic rhinitis (AR) and explore its interactions with immune markers and allergens. Metagenomic sequencing was performed on fecal samples from 16 AR and 17 healthy control (HC) children. Viral genes (VGs) were identified and taxonomically annotated using BLASTP against the NCBI NR database. Virome diversity, differential abundance, and correlations with IgE were analyzed using LEfSe, random forest, and Spearman correlation. While alpha diversity did not differ, beta diversity revealed subtle compositional trends. Taranisvirus was enriched in AR and positively correlated with total IgE (ρ = 0.4647, P = 0.045). Mitovirus and Duamitovirus were depleted in AR and negatively correlated with allergens. Virus-bacteria co-occurrence network analysis revealed a reconfigured ecological interactome in AR, characterized by pro-phage-centric associations that may disrupt mucosal immune homeostasis. Random forest identified total IgE, milk, and dust mite as top discriminators. This first study of the gut virome in pediatric AR reveals a pro-inflammatory phage enrichment and protective fungal virus depletion, implicating the virome in modulating Th2 immunity. These findings suggest a potential correlation between virome alterations and allergic diseases, which may inform future research on virome-targeted interventions.IMPORTANCEAllergic rhinitis is a prevalent childhood condition with a significant impact on quality of life, yet its pathogenesis is not fully understood. While the bacterial microbiome has been studied, the role of the gut virome remains largely unexplored. Our study provides the first evidence of gut virome dysbiosis in children with allergic rhinitis. We identified specific pro-inflammatory bacteriophages that are enriched and correlated with IgE levels, as well as protective fungal viruses that are depleted. These findings offer new perspectives on allergic disease pathogenesis by suggesting a potential role of the virome in modulating host immunity. This work not only opens a new avenue for understanding the environmental and microbial drivers of allergic diseases but also suggests the potential for novel virome-based diagnostics and therapeutic strategies, such as phage therapy, which could have a broad impact on clinical practice.This study is registered with ClinicalTrials.gov as ChiCTR2400085982.},
}
@article {pmid41773858,
year = {2026},
author = {Vijayakumar Padmavathy, B and Shanmugavel, AK and Shanmugam, S and Narayanan, M},
title = {Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome.},
journal = {Microbiology spectrum},
volume = {14},
number = {4},
pages = {e0222025},
pmid = {41773858},
issn = {2165-0497},
support = {SB24250033CSIITM008892//Women Leading IIT Madras (WLI)/ ; SB21221740CSRBEI008892//Robert-Bosch Center for Data Science and Artificial Intelligence/ ; },
mesh = {Humans ; *COVID-19/microbiology/complications/virology ; *Sputum/microbiology ; *Coinfection/microbiology ; *Microbiota/genetics ; SARS-CoV-2/isolation &amp; purification ; Middle Aged ; Male ; Female ; *Tuberculosis/microbiology/complications ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Whole Genome Sequencing ; Dysbiosis/microbiology ; },
abstract = {UNLABELLED: Tuberculosis (TB) and COVID-19 are both respiratory diseases, and understanding their interaction is important for effective co-infection management. Although some studies have investigated TB and COVID-19 co-infection in terms of immune responses, microbial dysbiosis in such cases remains unexplored. In this study, we understand the interface between TB and COVID-19 by systematically inspecting the microbial composition of sputum samples collected from four groups of individuals: TB only, COVID-19 only, and both TB and COVID-19 (TBCOVID) infected patients, and uninfected group (Controls). Besides metagenomic analysis of the microbiome of these sputum samples, we also performed whole-genome sequencing analysis of a subset of TB-positive samples. Different bioinformatic analyses ensured data quality and revealed significant differences in the microbial composition between Control vs disease groups. To understand the effect of COVID-19 on TB, we compared TBCOVID vs TB samples and observed (i) higher read counts of TB-causing bacteria in the TBCOVID group, and (ii) differential abundance of several taxa, including Capnocytophaga gingivalis. Functional profiling with PICRUSt2 revealed elevated pathways, including the pulmonary surfactant lipid metabolism pathway (with a fold change of 7.46) in the TBCOVID group. Further clustering of these pathways revealed a sub-cluster of individuals with adverse treatment outcomes. Two individuals in this sub-cluster had a respiratory pathogen, Stenotrophomonas maltophilia-knowing such information on key respiratory pathogens in a patient can help personalize the patient's antibiotic regimen. Overall, our study reveals the effect of COVID-19 on the airway microbiome of TB patients and encourages the use of co-microbial/co-pathogen profiling to personalize TB treatment.<br><br>IMPORTANCE: The community of microbes in an individual's airway tract can play a complex role in respiratory diseases like tuberculosis (TB) and COVID-19. Although changes in microbial composition in TB and COVID-19 patients have been studied separately, we present a first-of-its-kind investigation of the airway-tract microbiome of individuals simultaneously infected with TB and COVID-19 pathogens. Our results highlight that co-infection with COVID-19 in TB patients alters the abundance of certain bacterial species and their related pathways. For instance, Capnocytophaga gingivalis is abundant in co-infected patients, but not in TB-only patients. This species and other differentially abundant species we identified in the co-morbid condition, if replicated in independent cohorts, can help explain how COVID-19 could exacerbate the severity of lung infection in TB patients. Our study also stimulates future longitudinal studies using expanded data sets to understand the role of concomitant pathogens and assess whether adjusting the antibiotic regimen accordingly can improve TB treatment outcomes.},
}
@article {pmid41778788,
year = {2026},
author = {Lee, S and Kim, H-L and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Cho, J and Kim, H-N},
title = {Gut microbial community structure, metabolic signature, and resistome in dyslipidemia: implications for cardiovascular disease management.},
journal = {Microbiology spectrum},
volume = {14},
number = {4},
pages = {e0097125},
pmid = {41778788},
issn = {2165-0497},
support = {RS-2023-NR077149//National Research Foundation of Korea/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Dyslipidemias/microbiology/metabolism ; *Cardiovascular Diseases/microbiology ; Male ; Female ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Middle Aged ; Cross-Sectional Studies ; Metagenomics ; Adult ; Lipid Metabolism ; Aged ; Fatty Acids, Volatile/metabolism ; },
abstract = {Dyslipidemia, characterized by abnormal blood lipid levels, constitutes a significant risk factor for cardiovascular disease. Emerging evidence indicates that the gut microbiota influences lipid metabolism, although findings across studies have been inconsistent. In this cross-sectional investigation, we analyzed the composition of gut microbiota, associated metabolic pathways, predicted gut metabolites, and the resistome in 1,384 participants (including 895 individuals with dyslipidemia and 489 controls) through shotgun metagenomic sequencing. Our findings demonstrated that Bacteroides caccae was enriched among dyslipidemia cases, potentially contributing to inflammation and altered lipid metabolism. Conversely, Coprococcus eutactus and Coprococcus catus, recognized producers of short-chain fatty acids (SCFAs) involved in lipid regulation, as well as Blautia obeum, known to be positively affected by SCFAs, were more prevalent in the control group. Additionally, we identified an enrichment of the gene family responsible for dTDP-beta-D-fucofuranose biosynthesis, associated with bacterial pathogenicity, in dyslipidemia cases, with Bacteroides stercoris serving as a major contributor. Dyslipidemia cases also exhibited depletion of glycogen and peptidoglycan biosynthesis pathways, which may compromise energy storage and immune function, alongside decreased levels of pseudouridine, a molecule involved in RNA metabolism. Furthermore, a marginal increase in abundance of antibiotic-resistance genes, tetQ, was observed in dyslipidemia cases, suggesting a potential link between the gut resistome and metabolic dysregulation. These results offer novel insights into the role of gut microbiota in the pathophysiology of dyslipidemia and underscore potential microbiome-targeted interventions for metabolic disease management.IMPORTANCEDyslipidemia, characterized by abnormal blood lipid levels, is a significant risk factor for cardiovascular disease. Emerging evidence suggests that the gut microbiota plays a role in lipid metabolism, although findings across studies have varied. This study analyzed the gut microbiota, metabolic pathways, predicted gut metabolites, and antimicrobial resistance genes in 1,384 participants using shotgun metagenomic sequencing. Individuals with dyslipidemia exhibited an imbalance in gut bacteria, including an increase in Bacteroides caccae, a species associated with inflammation, and a decrease in short-chain fatty acid-producing bacteria such as Coprococcus eutactus and Blautia obeum, which support metabolic health. Furthermore, we identified significant changes in microbial metabolic pathways related to energy storage and immune function, as well as an increased abundance of tetracycline resistance genes (tetQ), suggesting a potential link between dyslipidemia and antimicrobial resistance. Our study provides a comprehensive overview of dyslipidemia-associated gut microbial alterations, highlighting potential mechanistic links and therapeutic targets.},
}
@article {pmid41784373,
year = {2026},
author = {Aizpurua, O and Martin-Bideguren, G and Gaun, N and Alberdi, A},
title = {Grass supplementation to a pellet-based diet fails to enrich gut microbiomes with wild-like functions in captive-bred hares.},
journal = {Microbiology spectrum},
volume = {14},
number = {4},
pages = {e0369125},
pmid = {41784373},
issn = {2165-0497},
support = {CF20-0460//Carlsbergfondet/ ; DNRF143//Danmarks Grundforskningsfond/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Animal Feed/analysis ; *Hares/microbiology ; *Poaceae/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Metagenomics ; Animals, Wild/microbiology ; *Diet ; *Dietary Supplements ; Metagenome ; Feces/microbiology ; },
abstract = {Reintroducing captive-bred animals into the wild often faces limited success, with the underlying causes frequently unclear. One emerging hypothesis is that maladapted gut microbiota may play a significant role in these challenges. To investigate this possibility, we employed genome-resolved metagenomics to analyze the taxonomic and functional differences in the gut microbiota of 45 wild and captive European hares (Lepus europaeus), as well as to assess the impact of fresh grass supplementation to a pellet-based diet aimed at pre-adapting captive hares to wild conditions. Our analyses recovered 860 metagenome-assembled genomes, with 87% of them representing novel species. We found significant taxonomic and functional differences between the gut microbiota of wild and captive hares, notably the absence of Spirochaetota in captive animals and differences in amino acid and sugar degradation capacities. While grass supplementation induced some minor changes in the gut microbiota, it did not lead to statistically significant shifts toward a more wild-like microbial community. The increased capacity for degrading amino acids and specific sugars observed in wild hares suggests that, instead of bulk grass, dietary interventions tailored to their specific dietary preferences might be necessary for pre-adapting hare gut microbiota to wild conditions.IMPORTANCEThis study sheds light on the role of gut microbiota in the success of reintroducing captive-bred animals into the wild. By comparing the collection of 860 near-complete genomes of wild and captive European hares, we identified significant taxonomic and functional differences, including the absence of key microbial groups in captive hares. Grass supplementation to a pellet-based diet yielded limited success in restoring a microbiota similar to that of wild counterparts, highlighting the need for more tailored approaches to mimic natural diets. With 87% of recovered microbial genomes representing novel species, this research also enriches our understanding of microbial diversity in wildlife. These findings emphasize that maladapted gut microbiota may hinder the survival and adaptation of reintroduced animals, suggesting that microbiome-targeted strategies could improve conservation efforts and the success of animal rewilding programs.},
}
@article {pmid41789915,
year = {2026},
author = {Chen, S and Li, Y and Xue, J and Hao, Y and Shaalan, MGA and Ghallab, EHS and Guo, Z and Jin, S and Fang, Y and I M Khater, E and Li, S},
title = {Metagenomic sequencing reveals viral diversity of mosquitoes from Egypt: co-circulation of multiple insect-specific viruses.},
journal = {Microbiology spectrum},
volume = {14},
number = {4},
pages = {e0213525},
pmid = {41789915},
issn = {2165-0497},
support = {2022FY100900//Science &amp; Technology Fundamental Resources Investigation Program/ ; 2022FY100904//Science &amp; Technology Fundamental Resources Investigation Program/ ; 32161143036, 32311540013//National Natural Science Foundation of China-Yunnan Joint Fund/ ; ASRT/NSFC 2022-2024//Academy of Scientific Research and Technology/ ; GWVI-11.1-12//Three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai/ ; },
mesh = {Animals ; Egypt ; Phylogeny ; Metagenomics ; *Mosquito Vectors/virology ; *Insect Viruses/genetics/classification/isolation &amp; purification ; Genome, Viral ; *Culex/virology ; *Culicidae/virology ; Virome/genetics ; Genetic Variation ; *Aedes/virology ; },
abstract = {UNLABELLED: Mosquito-borne virus surveillance is pivotal for investigating mosquito viromes, facilitating understanding of viral evolutionary histories and genetic diversity. Natural viral communities in mosquitoes include not only insect-specific viruses (ISVs) but also viruses infecting symbiotic microorganisms. In this study, a total of 654 mosquito samples-encompassing species from the Aedes and Culex genera-were collected from Egypt and subjected to metagenomic sequencing analysis. Over 130 virus species were identified, grouped into 35 families or equivalent taxonomic ranks. Detected ISVs included Culex flavivirus (CxFV), Kustavi Toti-like virus, Hanko Toti virus 5, Culex phasma-like virus (CPLV), Culex Iflavi-like virus 1, Culex Iflavi-like virus 4, Guadeloupe Culex rhabdovirus (GCRV), and Sarawak virus, confirming concurrent ISV circulation in Egyptian mosquitoes. Phylogenetic analyses of these ISVs revealed their closest evolutionary affinities to viral genome sequences originating from the Middle East, Europe, Oceania, and Asia. Specifically, Egyptian CxFV strains exhibited a closer genetic relationship with the tropical lineage within the Latin American/Caribbean/Africa genotype. Furthermore, our study uncovered 10 putative novel viruses, which are distributed across seven viral families: Amagaviridae, Chrysoviridae, Mitoviridae, Totiviridae, Virgaviridae, Narnaviridae, and Orthomyxoviridae. Collectively, our findings emphasize the necessity for more in-depth investigations into arthropod viromes-encompassing both mosquitoes and ticks-in Egypt, as well as in neighboring African and Middle Eastern countries. Such research is critical for enhancing our understanding of viral diversity and evolutionary biology, elucidating their roles in mosquito-pathogen-host interactions, and exploring their potential as biocontrol agents against vector-borne diseases of public health importance.<br><br>IMPORTANCE: Mosquito-borne viruses are estimated to cause over 100 million human infections annually, making surveillance of these pathogens increasingly crucial amid growing international travel and trade. Egypt, situated in northeastern Africa, serves as a geopolitical and geographical hub connecting Asia, Europe, and Africa-a unique location that complicates the surveillance of mosquito-borne viruses. Arboviruses persist in nature through cyclical transmission between arthropod vectors (e.g., mosquitoes, ticks, and midges) and susceptible vertebrate hosts. Despite this, systematic investigations into mosquito viromes remain relatively scarce in Egypt. The present study aimed to explore the genetic diversity and evolutionary relationships of mosquito-associated viruses in Egypt using metaviromic sequencing. Our findings significantly expand the current knowledge of both known and previously uncharacterized mosquito-associated viruses in the region, while also providing complete genome sequences of several viruses that may infect arthropods or vertebrates, and potentially interfere with the replication of pathogenic arboviruses.},
}
@article {pmid41789923,
year = {2026},
author = {Yao, J and Yang, C and Wang, H and Zhang, C and Meng, J},
title = {Metagenomic analysis of gut bacteria in different developmental instars of Spodoptera litura.},
journal = {Microbiology spectrum},
volume = {14},
number = {4},
pages = {e0208125},
pmid = {41789923},
issn = {2165-0497},
support = {2024XM05//Science and Technolugy Program of Guizhou Tobacco Company/ ; 110202201020(LS-04), 110202201022(LS-06)//Major Project of China National Tobacco Corporation/ ; No. 2022XM12//Zunyi Tobacco Company Program/ ; },
mesh = {Animals ; *Spodoptera/microbiology/growth &amp; development ; *Gastrointestinal Microbiome/genetics ; Larva/microbiology/growth &amp; development ; Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification ; Pupa/microbiology/growth &amp; development ; Phylogeny ; },
abstract = {Spodoptera litura is a globally distributed agricultural pest across Asia and Australia (EPPO database, https://gd.eppo.int/taxon/PRODLI/distribution), whose gut microbiota significantly influences host feeding, digestion, immunity, and development. We used whole metagenomic sequencing to analyze the diversity and functional roles of gut bacteria at different developmental stages (eggs, first to sixth instar larvae, pupae, and adults). Findings revealed that Pseudomonadota predominated at the phylum level, with notable differences across instars: Bacillota was dominant in young larvae, whereas Verrucomicrobiota was added in older larvae, eggs, pupae, and adults. At the genus level, Pseudomonas dominated, Enterococcus was prevalent in larvae, and Piscirickettsia was prevalent in eggs, pupae, and adults. Metagenomic analysis identified numerous carbohydrate-active enzymes (CAZy database) aiding in plant cell wall polysaccharide digestion. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated differential gene expression in metabolism and xenobiotic degradation across instars, with metabolic gene annotation levels declining as development progressed. Detoxification-related enzyme genes were predominantly expressed in early instar larvae and adults, uncovering microbial origins of these enzymes.IMPORTANCEOur study provides evidence that the gut microbiota significantly modulates the physiology of Spodoptera litura, with profound effects on its dietary habits, metabolic processes, and host fitness. Using whole metagenomic sequencing, we analyzed gut bacteria across different life stages. At the phylum level, Pseudomonadota and Bacillota were dominant, while at the genus level, Pseudomonas was the most abundant taxon. Metagenomic analysis identified enzymes aiding in plant cell wall digestion. Kyoto Encyclopedia of Genes and Genomes analysis showed varying gene expression in metabolism and detoxification, with higher expression in early instar larvae and adults. This research enhances understanding of S. litura gut microbiota-host interactions and supports novel pest control strategies targeting gut microbiota.},
}
@article {pmid41841761,
year = {2026},
author = {Ward, B and Bindels, LB and Balligand, J-L and Bearzatto, B and Bommer, G and Cani, PD and De Greef, J and Dewulf, JP and Gatto, L and Haufroid, V and Jodogne, S and Kabamba, B and Pyr Dit Ruys, S and Vertommen, D and Yombi, JC and Belkhir, L and Elens, L},
title = {Association of nasopharyngeal Dolosigranulum pigrum and Corynebacterium species with post-acute sequelae of SARS-CoV-2 in a longitudinal cohort.},
journal = {Microbiology spectrum},
volume = {14},
number = {4},
pages = {e0231325},
pmid = {41841761},
issn = {2165-0497},
support = {2021-I4201010-221801//Fondation Saint Luc/ ; HC01020F//Fonds De La Recherche Scientifique - FNRS/ ; ARC 25/30-151//Fonds Sp&#xe9;ciaux de Recherche/ ; WELBIO-CR-2022A-02P//Walloon excellence in life sciences and biotechnology/ ; EOS 40007505//Fonds De La Recherche Scientifique - FNRS/ ; FRC//Fondation Saint Luc/ ; 2021//Fonds Sp&#xe9;ciaux de Recherche/ ; },
mesh = {Humans ; *COVID-19/microbiology/complications/virology ; *Nasopharynx/microbiology ; *Corynebacterium/isolation &amp; purification/genetics/classification ; Longitudinal Studies ; Female ; Male ; Middle Aged ; Adult ; SARS-CoV-2 ; Microbiota ; Aged ; *Carnobacteriaceae/isolation &amp; purification/genetics/classification ; Metagenomics ; },
abstract = {This longitudinal study investigated the differential composition of the nasopharyngeal microbiome in patients presenting different COVID-19 infectious phenotypes and its evolution during convalescence, with a focus on post-acute sequelae of SARS-CoV-2 (PASC) and its potential microbiome-related mechanisms. Microbiota composition was assessed for a cohort of healthy participants (n = 25), influenza patients (n = 24), and patients with moderate (n = 50) and severe (n = 57) COVID-19. Samples were collected at two time points: during the acute infection phase and at approximately 3-month follow-up. From collected nasopharyngeal swab samples, metagenomics using shotgun sequencing was performed and the microbiota composition was analyzed. Alpha and beta diversity analyses revealed no significant differences in overall community diversity between patient groups across visits. However, differential abundance testing identified specific species, such as Dolosigranulum pigrum and various Corynebacterium species, whose profiles correlated with PASC development. Furthermore, the analysis of microbial co-associations identifies commensal species, including D. pigrum and Corynebacterium species, which are less abundant in patients who develop PASC, consistent with a potential protective role suggested by experimental studies but not proven by our observational data. Antibiotic use was associated with lower levels of key protective taxa, which may increase susceptibility to PASC in case of superinfection. These findings highlight the potential importance of the nasopharyngeal microbiome in acute COVID-19 disease outcomes and suggest that preserving or restoring a balanced respiratory microbiome could mitigate the risk of COVID-19 persistent symptoms and PASC development. Our results may set the stage for future clinical interventions involving probiotics or microbial-derived metabolites to promote respiratory health post-COVID-19.IMPORTANCEThis study highlights the importance of bacteria naturally found in the upper respiratory tract, particularly the nasopharynx (the nasopharyngeal microbiome), in shaping how severely COVID-19 affects patients and whether they experience persistent symptoms, also called long-COVID or post-acute sequelae of SARS-CoV-2 (PASC). By examining microbiome samples from healthy people, influenza patients, and individuals with COVID-19 during acute and convalescent phases, we found that certain commensal bacteria, namely, Dolosigranulum pigrum and Corynebacterium species, were less abundant in individuals who developed long-COVID and more abundant in those who fully recovered. We also observed that antibiotic treatment was associated with lower abundances of these commensal taxa, in turn coinciding with a higher frequency of PASC. These findings suggest that the composition of the nasopharyngeal microbiome is associated with recovery trajectories after COVID-19 and motivate future research into treatments aimed toward the microbiome to improve respiratory health following infection.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05557539.},
}
@article {pmid41856866,
year = {2026},
author = {Jelen, BI and Baker, BJ},
title = {Mapping environmental microbiomes across an entire country.},
journal = {Trends in microbiology},
volume = {34},
number = {4},
pages = {342-344},
doi = {10.1016/j.tim.2026.02.013},
pmid = {41856866},
issn = {1878-4380},
mesh = {*Microbiota ; Ecosystem ; Denmark ; Biodiversity ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Environmental Microbiology ; Nitrification ; },
abstract = {Microbial diversity underpins ecosystem function and resilience, yet large-scale spatial baselines remain rare. Singleton et al. present a Danish atlas of environmental microbiomes, revealing nationwide patterns of diversity. By emphasizing gamma diversity, they show how nitrifying communities differ in scale and composition between natural and disturbed habitats.},
}
@article {pmid41943157,
year = {2026},
author = {Bruna, P and Barra, PJ and García, M and Liachko, I and de la Luz Mora, M and Dutilh, BE and Abanto, M},
title = {Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00887-7},
pmid = {41943157},
issn = {2524-6372},
support = {2023-21230832//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDECYT Regular 1241293//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; 1230084//Agencia Nacional de Investigaci&#xf3;n y Desarrollo (ANID)/ ; FONDECYT Regular 1251164//Agencia Nacional de Investigaci&#xf3;n y Desarrollo (ANID)/ ; Consolidator grant 865694/ERC_/European Research Council/International ; Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Phosphorus (P) is a fundamental macronutrient for plant and microbial growth, but its availability in soils is often constrained by strong interactions with minerals and organic matter. While the role of bacteriophages in P cycling has gained attention, plasmids remain comparatively underexplored despite their central role in horizontal gene transfer. This study aimed to investigate the occurrence, diversity, and ecological relevance of plasmid-borne genes involved in P acquisition across soils with contrasting P availability.<br><br>RESULTS: Using curated plasmid databases and soil metagenomes from diverse biomes, we identified a broad repertoire of plasmid-encoded P-acquisition genes. These genes encompassed regulatory pathways, transport systems, organic P mineralization, and inorganic P solubilization. Regulatory and transporter genes were the most abundant categories, with phoB, phoP, and ugpC among the most frequently detected. When additional analyses were performed using habitat-specific P classifications and continuous P gradients, these associations appeared weak and were not significant after multiple-testing correction. These results suggest that plasmid-encoded P-acquisition genes are broadly distributed across environments rather than tightly constrained by measured soil P levels, while taxonomic assignment revealed that Pseudomonadota were the predominant plasmid hosts, followed by Bacillota and Actinobacteriota, suggesting broad host diversity.<br><br>CONCLUSIONS: This study provides a genomic overview of plasmid-borne genes associated with P acquisition in soils. Our results show that these genes are widespread across plasmids from diverse environments and host taxa, suggesting that the soil mobilome may represent an important reservoir of functions related to microbial P metabolism. While the presence and relative abundance of these genes indicate their potential ecological relevance, functional expression and ecological impact remain to be experimentally validated. These findings expand current knowledge of plasmid contributions to nutrient cycling and highlight the mobilome as a potential target for future studies aiming to better understand microbial strategies for P acquisition in soil ecosystems.},
}
@article {pmid41943678,
year = {2026},
author = {Zhou, G and Chen, L and Ma, L and Liu, J and Feng, B and Zhang, C and Ma, D and Zhang, H and Liang, Y and Zhang, J},
title = {Sodicity Thresholds Alter Biodiversity-Multifunctionality Relationships Through Fungal Dominance and Microbial Trait-Based Strategies.},
journal = {Global change biology},
volume = {32},
number = {4},
pages = {e70843},
doi = {10.1111/gcb.70843},
pmid = {41943678},
issn = {1365-2486},
support = {42277336//National Natural Science Foundation of China/ ; 42425703//National Natural Science Foundation of China/ ; BK20221561//Natural Science Foundation of Jiangsu Province/ ; CX(24)1003//Jiangsu Agricultural Science and Technology Innovation Fund/ ; NMKJXM202401-01//Key Special Projects of the "Science and Technology Revitalizing Inner Mongolia" Action Fund/ ; CARS-03//China Agriculture Research System/ ; CARS-52//China Agriculture Research System/ ; //Chinese Academy of Sciences/ ; },
mesh = {*Soil Microbiology ; *Biodiversity ; China ; *Soil/chemistry ; *Fungi/physiology ; Ecosystem ; *Sodium/analysis ; Salinity ; },
abstract = {Increasing soil sodicity represents a critical threat to global agroecosystem health, but how exchangeable sodium percentage (ESP) modulates relationships between biodiversity and ecosystem multifunctionality (BEF) is unresolved. We surveyed 378 soil samples from 189 paired saline-sodic lands and adjacent farmlands across four major saline-sodic regions of China spanning ~2000 km. Random forest models demonstrated that ESP emerged as the primary abiotic predictor of soil multifunctionality, defining sharp thresholds ~13% for cropped systems and ~44% for natural saline-sodic habitats beyond which BEF relationships undergo fundamental reorganization. These breaks coincide with significant shifts toward fungal dominance within microbial communities. Notably, under hyper-sodic conditions, fungal diversity emerges as essential for sustaining ecosystem functions. Metagenomic and trait-based analyses further characterized three functional dimensions of microbial trait-based strategies-environmental responsiveness, metabolic capacity, and nutrient recycling. We then mechanistically linked microbial life-history strategies to soil multifunctionality. Our results showed that in farmland soils, nutrient recycling was positively associated with multifunctionality, whereas metabolic capacity was negatively correlated with multifunctionality, and in saline-sodic soils metabolic capacity exhibited a positive association with multifunctionality. Collectively, this study establishes ESP as a key regulator of BEF relationships and microbial eco-evolutionary adaptations, providing mechanistic insights for managing saline-sodic soils under escalating climate change.},
}
@article {pmid41947790,
year = {2026},
author = {Sun, W and Li, Y and Su, J and Mao, S and Yang, S and Zhu, Y and Liu, Y and Ma, J and You, W and Zhang, Y and Guo, H and Xing, G and Li, S and Yan, Q and Ma, X},
title = {Multi-kingdom metagenomic characterization of the gut bacteriome, mycobiome, and virome in chronic functional constipation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1744020},
pmid = {41947790},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome ; *Mycobiome ; *Constipation/microbiology/virology ; Metagenomics ; Feces/microbiology/virology ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Middle Aged ; *Fungi/classification/genetics/isolation &amp; purification ; Adult ; Dysbiosis/microbiology ; Viruses/classification/genetics/isolation &amp; purification ; Metagenome ; Chronic Disease ; Aged ; },
abstract = {BACKGROUND: Chronic functional constipation (CFC) is a common gastrointestinal disorder increasingly linked to gut microbiome dysbiosis. However, multi-kingdom metagenomic characterization of bacterial, fungal, and viral communities in CFC remains limited.<br><br>METHODS: Fecal samples from 53 CFC patients and 48 healthy controls were analyzed using whole-metagenome shotgun sequencing. Microbial composition, function, cross-kingdom interactions, and diagnostic potential were evaluated using diversity analyses, KEGG annotation, network analysis, and random forest modeling.<br><br>RESULTS: Compared with healthy controls, CFC patients exhibited marked alterations across multiple microbial kingdoms. The gut bacteriome showed significant community-structure shifts despite comparable &#x3b1;-diversity, characterized by depletion of health-associated Firmicutes (e.g., Faecalibacterium and Roseburia) and enrichment of Proteobacteria (e.g., Klebsiella). The mycobiome displayed selective changes in diversity and composition, with several potentially pathogenic fungal taxa enriched in CFC (e.g., Fusarium sp. c181). In the virome, community composition differed significantly between groups, with higher viral richness in CFC and widespread depletion of diverse bacteriophages in CFC patients. Functional profiling suggested feature-level functional differences without a clear global shift, including reduced carbohydrate transport and utilization pathways and relatively higher abundance of stress-response and metabolic adaptation modules in CFC. Cross-kingdom network analysis demonstrated substantially denser microbial interactions in CFC, dominated by viral associations, with Faecalibacterium prausnitzii and Faecalibacterium_SGB15346 acting as central hubs. Machine-learning models showed strong discriminatory power for CFC classification based on bacterial and viral features, whereas fungal features contributed less.<br><br>CONCLUSIONS: CFC is associated with coordinated multi-kingdom gut microbiome dysbiosis involving bacteria, fungi, and viruses, accompanied by functional shifts and intensified cross-kingdom interactions. Bacterial and viral signatures show strong potential as microbiome-based biomarkers for CFC, highlighting the importance of integrating multi-kingdom analyses to better understand disease-associated gut ecosystem alterations.},
}
@article {pmid41949970,
year = {2025},
author = {Lerhzouli, H and Al Ibrahmi, B and Khal-Layoun, S and Bour, A},
title = {New therapeutic approaches based on modulation of the intestinal microbiota to correct dysbiosis in patients with type 2 diabetes.},
journal = {La Tunisie medicale},
volume = {103},
number = {11},
pages = {1707-1717},
doi = {10.62438/tunismed.v103i11.6101},
pmid = {41949970},
issn = {2724-7031},
mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/microbiology/therapy ; *Dysbiosis/therapy/microbiology/etiology ; *Gastrointestinal Microbiome/drug effects/physiology ; Probiotics/therapeutic use ; Hypoglycemic Agents/therapeutic use ; Insulin Resistance ; },
abstract = {Type 2 diabetes is a chronic disease characterized by insulin resistance and reduced insulin production in pancreatic cells. Conventional treatment of type 2 diabetes relies on hypoglycemic drugs, physical activity and a balanced low-carbohydrate diet, but with technological advances in metagenomics and metabolomics researchers have developed new therapeutic approaches aimed to modulate, the gut microbiota to correct the dysbiosis confirmed in people with type 2 diabetes. This literature review provides an update on therapies aimed to modulate the gut microbiota to correct dysbiosis in type 2 diabetics and summarizes the latest advances in this field.},
}
@article {pmid41320324,
year = {2026},
author = {Liu, C and Gong, J and Luo, Z and Lai, P and Guo, S and Liang, D and Chen, G and Xing, M and Yu, J and Xie, Y and Liu, D and Zeng, W and He, Z and Lan, P},
title = {Gut microbe alleviates stress-related cancer metastasis by oleic acid degradation.},
journal = {Gut},
volume = {75},
number = {5},
pages = {968-983},
doi = {10.1136/gutjnl-2025-335627},
pmid = {41320324},
issn = {1468-3288},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Oleic Acid/metabolism ; Humans ; Mice ; *Colorectal Neoplasms/pathology/microbiology/metabolism ; *Stress, Psychological/complications/microbiology ; Neoplasm Metastasis ; *Dysbiosis/microbiology ; Male ; Female ; },
abstract = {BACKGROUND: Chronic stress is a known risk factor for cancer metastasis. However, the underlying mechanisms, particularly those involving the gut microbiota and their metabolites, remain unclear.<br><br>OBJECTIVE: To investigate whether gut microbiota dysbiosis and metabolic alterations mediate the sustained pro-metastatic effects of chronic stress, even after normalisation of stress hormone levels.<br><br>DESIGN: Multiple metastatic models were performed after stress cessation. Shotgun metagenomics and metabolomics were performed to assess changes in microbiota and metabolites. The effects of Bifidobacterium animalis and oleic acid (OA) on metastasis were evaluated in vivo and in vitro. Moreover, we explored how B. animalis degraded OA. Mechanistically, we discovered the interaction between corticosteroids and gut bacteria through guanine metabolism assays. Human samples were collected from patients with colorectal cancer (CRC) with varying perceived stress scores and metastatic status for validation.<br><br>RESULTS: Mice that underwent chronic stress exhibited increased metastasis even after hormone levels recovered. The gut microenvironment was altered, with a significant reduction in B. animalis and an increase in OA. B. animalis administration reduced OA levels and suppressed metastasis, while OA supplementation had the opposite effect. B. animalis expresses oleate hydratase, an enzyme that degrades OA. Stress hormones inhibited B. animalis by altering guanine metabolism in the intestinal epithelium. In patients, high stress was associated with more OA, lower B. animalis levels and increased metastasis.<br><br>CONCLUSIONS: Chronic stress promotes metastasis by altering microbiota and increasing OA. Targeting B. animalis and OA may help prevent stress-related tumour progression.},
}
@article {pmid41576514,
year = {2026},
author = {Hao, Y and Li, Y and Liu, F and Long, J and Yang, H},
title = {Metagenomic insights into the influence of goose farming on the gut microbiome and antibiotic resistome of workers.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106487},
pmid = {41576514},
issn = {1525-3171},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Geese/microbiology ; Humans ; Metagenomics ; Feces/microbiology ; *Bacteria/genetics/drug effects/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; *Animal Husbandry ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; *Metagenome ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) seriously threatens the health of humans and animals. Antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) were enriched in the goose farms. However, the influence of goose farming exposure on the gut microbiota and ARGs of workers was unclear. In this study, metagenomic analysis was used to characterize gut microbiome structures, annotate bacterial taxa, and quantify the abundances of ARGs and MGEs in geese and human samples. Results showed that goose feces harbored more abundant ARGs and ARB than human feces. Significantly higher abundances of special ARGs (such as vanY, lsaE, AAC3-IId and ampC) were identified in workers compared to villagers. Compositions of gut bacteria were significantly different between workers and villagers, and some certain gut pathogens were abundant in the feces of workers, including Bacillus anthracis, Clostridium perfringens, and Escherichia coli O45:K1:H7. A total of 51 ARGs were pinpointed in the metagenome-assembled genomes (MAGs). Based on ARG-MGE associations and co-occurrence signals in MAGs, the potential for horizontal gene transfer (HGT) was inferred. With this transfer capacity and ubiquitous gut colonization, E. coli carrying 38 ARGs is proposed as a putative AMR indicator for the goose farm. This study demonstrates that goose farming had non-ignorable influences on the gut microbiome and antibiotic resistome of workers. More efforts should be made to control the ARGs and ARB in the goose farm.},
}
@article {pmid41610602,
year = {2026},
author = {Phusathian, B and Pongmanee, K and Theapparat, Y and Saikhwan, N and Trairatapiwan, T and Chaosap, C and Seemacharoensri, A and Tactacan, GB and Wong, LY and Ruangpanit, Y},
title = {Bacterial xylanase supplementation improves nutrient utilization, gut integrity, and microbial metabolism in broilers fed energy-reduced diets.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106515},
pmid = {41610602},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/microbiology/growth &amp; development ; Male ; Diet/veterinary ; Animal Feed/analysis ; *Endo-1,4-beta Xylanases/administration &amp; dosage/metabolism ; *Gastrointestinal Microbiome/drug effects ; Dietary Supplements/analysis ; Animal Nutritional Physiological Phenomena/drug effects ; Random Allocation ; *Digestion/drug effects ; *Nutrients/metabolism ; *Bacterial Proteins/administration &amp; dosage/metabolism ; },
abstract = {This study evaluated the effects of bacterial xylanase supplementation on growth performance, nutrient digestibility, intestinal integrity, and microbial metabolic function in broilers fed energy-reduced diets. A total of 1,050 one-day-old male Ross 308 broiler chicks were randomly assigned to three dietary treatments, each comprising 14 replicates of 25 birds: a positive control (CON; standard corn-soybean meal diet), a negative control with reduced energy (NC; -85 kcal/kg), and an energy-reduced diet supplemented with bacterial xylanase (NCX; 100 g/ton Belfeed Xylanase™). During the starter phase, broilers fed the NC diet exhibited higher feed intake and FCR compared with those fed the CON and NCX diets (P < 0.05), with no significant difference between the CON and NCX diets. Apparent digestibility of dry matter, crude protein, and fat did not differ among dietary treatments (P > 0.05). However, broilers fed the NCX diet showed higher (P < 0.05) digestibility of crude fiber, NDF, and ADF than those fed the CON or NC diets. Apparent metabolizable energy was higher in broilers fed the CON and NCX diets compared with the NC diet. Furthermore, broilers receiving the CON and NCX diets exhibited significantly lower serum fluorescein isothiocyanate-dextran concentrations than those fed the NC diet, indicating improved intestinal barrier integrity. Bacterial xylanase supplementation increased microbial alpha diversity and altered beta diversity clustering, with enrichment of beneficial taxa such as Bifidobacteriaceae and Lactobacillaceae. Functional metagenomic prediction suggested greater representation of carbohydrate metabolism and energy production pathways in the NCX diet, whereas the NC diet was associated with enrichment of stress-related and xenobiotic degradation pathways. Overall, bacterial xylanase supplementation mitigated the adverse effects of dietary energy reduction by improving fiber utilization, maintaining gut integrity, and modulating the cecal microbiota toward a more favorable metabolic profile.},
}
@article {pmid41619482,
year = {2026},
author = {Wang, M and Ye, X and Hsu, CY and Fugate, H and Zhang, X and Adhikari, PA and Fan, P and Elliott, K and Macklin, K and Zhang, L},
title = {Application of culturomics to explore the cultivable microbiota and enable targeted bacterial isolation from the ceca of broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106527},
pmid = {41619482},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/isolation &amp; purification/classification/genetics ; RNA, Ribosomal, 16S/analysis/genetics ; *Bacteriological Techniques/veterinary/methods ; DNA, Bacterial/analysis ; },
abstract = {Metagenomic analyses have significantly advanced our understanding of microbial composition in the poultry gut. However, many microbes identified through metagenomic studies remain uncultured, largely due to the lack of understanding of their cultivation conditions, which hinders efforts to explore their functional roles in gut health and metabolism. In this study, we performed culturomics, a culture-dependent approach that combines diverse culture conditions with high-throughput 16S rRNA gene sequencing, to comprehensively assess the cultivability of chicken cecal microbiota and provide guidance for isolating target species of interest. Microbial profiling was performed using both culture-dependent (CD) and culture-independent (CI) approaches. For CI, genomic DNA (gDNA) was directly extracted from six broiler chicken cecal samples and subjected to full-length 16S rRNA gene sequencing. For CD, the same samples were cultured under 28 conditions, yielding 161 colony mixtures for sequencing. Based on diversity profiles of the colony mixtures, 10 conditions were selected for single-colony isolation and analysis. Results showed that CD and CI approaches identified 350 and 502 bacterial species, respectively, with 160 species detected by both methods. The dominant species recovered by the CD approach,including Escherichia coli, Proteus mirabilis, Limosilactobacillus reuteri, Enterococcus faecalis, and Ligilactobacillus salivarius, were detected at much lower abundances in the CI analysis, highlighting the capacity of culturomics to enrich and recover minority taxa that are often poorly detected by CI apparoach. Cultivation profiling showed that MRS selectively enriched Limosilactobacillus and Ligilactobacillus as well as Lactobacillus, whereas CNAB and MSA enriched Enterococcus and Bacillus, respectively. Community diversity and structure were significantly influenced by culture conditions (P < 0.01), with medium as the primary factor and air condition as a secondary factor. Subsequent single-colony analysis from 10 selected culture conditions identified 150 single-species isolates belonging to 14 distinct bacterial species. This study provides foundational insight into the cultivability of chicken cecal microbiota, facilitating future research to isolate specific strains and characterize their roles in poultry health and nutrition.},
}
@article {pmid41619490,
year = {2026},
author = {Deng, S and Zheng, X and Chu, H and Hong, L and Zhang, J and Yang, H and Gu, L and Pu, L},
title = {Antibiotic-free Wenchang chickens may promote blood levels of B vitamins by modulating the gut microbiota: An integrated analysis of cecal content metagenomics and serum metabolomics.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106506},
pmid = {41619490},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology/blood/genetics/metabolism ; *Gastrointestinal Microbiome ; Cecum/microbiology ; Metagenomics ; Metabolomics ; *Vitamin B Complex/blood ; Animal Feed/analysis ; Diet/veterinary ; Male ; },
abstract = {Through the selective breeding of superior strains, livestock and poultry can achieve enhanced disease resistance and production performance, thereby improving farming efficiency and increasing chicken meat yield. This study analyzed the expression of gut health-related genes, cecal microbiota, and untargeted serum metabolomics in Wenchang chickens from the NS strain (Normal strain) and the AFS strain (Antibiotic-free strain), and explored the relationships between their cecal microbiota and serum metabolites. Our results show that in the ileum, antioxidant-related indicators T-AOC (P < 0.05), T-SOD (P < 0.05), and GSH-PX (P < 0.05) were significantly higher in the AFS strain than in the NS strain, while MDA (P < 0.05) was significantly lower in the AFS strain than in the NS strain. The mRNA expression level of RORγt/FoxP3, which is related to immune regulation, was significantly lower in the AFS strain than in the NS strain (P < 0.05). The differential microorganisms in the cecum primarily included Muribaculum, Cryptobacteroides, Blautia, Enterocloster, Lachnoclostridium, Hydrogenoanaerobacterium, Ruminococcus, Subdoligranulum, Clostridioides, and Evtepia. The main differential metabolites in serum included folinic acid, biotin, lysophosphatidic acid (LPA), 3-hydroxy-3-methylbutanoic acid, 3-hydroxybutyric acid, and others. The differential metabolites are primarily enriched in the following metabolic pathways: gap junction, glycolipid metabolism, and fatty acid biosynthesis. In addition, the Pearson correlation analysis between the gut microbiota and serum metabolites showed that Blautia was positively correlated with folinic acid (P < 0.05) and biotin (P < 0.05); Lachnoclostridium was positively correlated with biotin (P < 0.01); and Ruminococcus was positively correlated with 3-hydroxybutyric acid (P < 0.05). This study mainly elucidates the metabolic characteristics of the antibiotic-free Wenchang chicken strain by analyzing gut microbiota and serum metabolites.},
}
@article {pmid41698575,
year = {2026},
author = {Du, Y and Zhao, S and Hu, Y and Wang, X and Zhang, L and Lin, B and Wang, M and Xu, Q},
title = {Dietary selection of starters drives changes in growth performance, fermentation, hindgut microbiome, and metabolism in preweaning calves.},
journal = {Journal of dairy science},
volume = {109},
number = {4},
pages = {3970-3990},
doi = {10.3168/jds.2025-27473},
pmid = {41698575},
issn = {1525-3198},
mesh = {Animals ; Cattle/growth &amp; development ; *Gastrointestinal Microbiome ; Animal Feed/analysis ; *Diet/veterinary ; Fermentation ; Dietary Fiber ; Animals, Newborn/growth &amp; development ; Animal Nutritional Physiological Phenomena ; Weaning ; Starch ; },
abstract = {Early feeding of starter is an effective strategy for modulating gastrointestinal microbiota in newborn calves. However, the effects of starter nutrient composition on calf gut microbiota vary significantly. Although both fiber and starch are essential for early calf nutrition, each has distinct advantages and disadvantages. This study investigated how high-starch and high-fiber diets influence growth performance, hindgut health, and microbiota in calves. Two groups of calves were fed experimental starters with distinct nutrient compositions: a high-starch (HS, n = 8) diet containing 40.4% starch and 13.3% NDF, and a high-fiber (HF, n = 7) diet containing 18.8% starch and 30.5% NDF (DM basis). The experiment spanned calf ages 14 to 63 d, with weekly BW and body size measurements using calibrated scales and measuring tape. Serum was collected via jugular venipuncture for metabolic marker analysis. At trial end, animals were slaughtered to collect hindgut tissues and contents for immunoblotting, metagenomic sequencing, and metabolite analysis. We identified a fundamental trade-off that HS feeding shaped a Bifidobacterium-dominated enterotype, correlating with superior growth performance. In contrast, HF feeding selected for a Bacteroides-dominated, more mature microbiota and significantly enhanced gut barrier integrity by upregulating key tight junction proteins (ZO-1, claudin-1, and E-cadherin). Multiomics integration revealed that this trade-off was underpinned by different microbial metabolic pathways. The HS hindgut was enriched in enzymes and metabolites for carbohydrate and AA fermentation, driving growth. Conversely, the HF hindgut exhibited enhanced enzymatic capacity for fiber degradation (e.g., starch phosphorylase) and a metabolic profile favoring arginine biosynthesis and acetate production, which supported barrier function. This functional divergence was further evidenced in distinct short-chain fatty acid (SCFA) profiles. The HF group exhibited significantly elevated acetate and a trend for higher total SCFA concentration, whereas the HS group showed increased branched-chain fatty acids (isovalerate) and a trend toward higher butyrate and valerate proportions. Our findings provide a mechanistic model linking dietary carbohydrate source to a fundamental choice between growth optimization and gastrointestinal health in preweaning calves, offering novel insights for targeted nutritional strategies.},
}
@article {pmid41748159,
year = {2026},
author = {Liu, W and Lu, Y and Ng, SC and Chan, FK and Sung, JJ and Yu, J},
title = {Bacterial genomic structural variations in children with autism serve as diagnostic biomarkers.},
journal = {Gut},
volume = {75},
number = {5},
pages = {937-948},
doi = {10.1136/gutjnl-2025-337280},
pmid = {41748159},
issn = {1468-3288},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Animals ; Mice ; Child ; Male ; Feces/microbiology ; Female ; *Dysbiosis/microbiology ; *Autism Spectrum Disorder/microbiology/diagnosis ; Biomarkers ; *Genomic Structural Variation ; Child, Preschool ; Disease Models, Animal ; *Genome, Bacterial ; },
abstract = {BACKGROUND: Gut microbiota dysbiosis is linked to autism spectrum disorder (ASD) in children. However, the role of bacterial genomic structural variations (SVs) in ASD remains largely unexplored.<br><br>OBJECTIVE: We aimed to identify bacterial SVs associated with ASD and explore their mechanistic role and clinical application.<br><br>DESIGN: We collected faecal metagenomes from 452 children (261 ASD, 191 neurotypical) across an in-house and seven public datasets. Using linear mixed-effects modelling, we identified ASD-associated SVs and compositional shifts and validated candidate SVs in humanised gut microbiome mice.<br><br>RESULTS: We identified 100 bacterial SVs significantly associated with ASD (p<0.05). These SVs were enriched in genes involved in critical biological processes, including ion and amino acid metabolism and bacterial growth regulation in ASD. In particular, we found important SVs in Bacteroides uniformis related to thiamine and iron metabolism. Moreover, SVs in Ruminococcus torques were associated with the MazF (endoribonuclease toxin) and MazE (antitoxin) system, a key regulator of pathobiont proliferation. Validation in humanised mouse models confirmed significant correlations between these SV signatures and ASD-like behaviours, such as reduced social interaction and increased repetitive behaviours. Both phylogeographically conserved and regionally restricted SVs showed strong associations with ASD. A diagnostic model combining nine SVs and three bacterial species achieved an area under the receiver operating characteristic curve of 81.1%, outperforming models based solely on variable SVs (79.1%), deletion SVs (75.2%) or bacterial species abundance alone (72.3%).<br><br>CONCLUSION: Our findings suggest the significant role of bacterial genomic SVs in ASD and highlight their potential as diagnostic biomarkers.},
}
@article {pmid41803498,
year = {2026},
author = {Zhou, H and Sun, R and Nie, X and Xia, L and Dong, H and Liu, Y and Hou, S and Dong, W and Zhu, X and Yao, Y and Zhao, GP and Lu, S and Wang, Y and Yang, C},
title = {A clinic-responder-derived defined microbial consortium enhances anti-PD-1 immunotherapy efficacy in mice.},
journal = {Nature microbiology},
volume = {11},
number = {4},
pages = {993-1007},
pmid = {41803498},
issn = {2058-5276},
support = {82241228//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32230060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31925001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073152//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82241227//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82030045//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Humans ; *Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors/immunology ; *Immunotherapy/methods ; Fecal Microbiota Transplantation ; *Carcinoma, Non-Small-Cell Lung/therapy/immunology/microbiology ; Feces/microbiology ; *Lung Neoplasms/therapy/immunology/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; CD8-Positive T-Lymphocytes/immunology ; Female ; *Immune Checkpoint Inhibitors/therapeutic use ; Mice, Inbred C57BL ; Cell Line, Tumor ; Metagenomics ; Disease Models, Animal ; },
abstract = {Targeting the gut microbiota is a promising strategy to enhance the efficiency of cancer immunotherapy; however, success has been limited. Here we combined metagenomic analysis and in silico prediction to identify bacterial species associated with immunotherapy response in patients with non-small-cell lung cancer. We constructed a defined consortium (RCom) of 15 bacterial species, most of which were isolated from responder patient faeces, associated with improved clinical response to anti-programmed cell death protein 1 (PD-1) treatment. Metabolic models and in vitro experiments revealed that RCom is a stable and cooperative community, and in vivo experiments showed that RCom engrafts and produces immunomodulatory metabolites. Oral administration of RCom improved the anti-tumour activity of anti-PD-1 by increasing the intratumoural infiltration and cytotoxic function of CD8[+] T cells in syngeneic tumour models and across mice with heterogeneity in baseline gut microbiota composition. RCom supplementation also limited anti-PD-1 resistance in mice conferred by faecal microbiota transplantation from individual non-responsive patients. These findings suggest that RCom is a potential adjuvant to improve responsiveness to anti-PD-1 therapy in cancer.},
}
@article {pmid41927536,
year = {2026},
author = {Dong, Y and Wang, M and Zhou, X and Wang, P and Yan, K and Wang, S and Zhong, JC and Li, H and Zhao, L and Li, B and Li, J},
title = {Multi-cohort analysis of metagenome for type 2 diabetes identified universal gut microbiota signatures across populations.},
journal = {Nutrition &amp; diabetes},
volume = {16},
number = {1},
pages = {},
pmid = {41927536},
issn = {2044-4052},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; *Metagenome ; Cohort Studies ; Europe ; Feces/microbiology ; Asia ; Dysbiosis/microbiology ; Aged ; Adult ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: Several studies have investigated the association between the gut microbiota and type 2 diabetes mellitus (T2D) in various populations. Nonetheless, noises specific to individual cohorts might distort the microbial dysbiosis characteristics and result in inconsistent findings across studies. Thus, we aimed to identify the universal features of perturbed gut microbiota across diverse populations.<br><br>METHODS: A total of 433 fecal shotgun metagenomic sequences were analyzed to profile and compare the gut microbiome shifts between patients with T2D and healthy controls from cohorts in Europe and Asia.<br><br>RESULTS: Based on cross-cohort integrative analysis, patients with T2D showed significantly higher microbial alpha diversity, and distinctive microbial structures compared to healthy individuals. By excluding bacteria exhibiting divergent directional changes, consistent characteristics with ten T2D-enriched bacteria, such as Clostridium bolteae and Clostridium citroniae and eight T2D-depleted bacteria, including Streptococcus thermophiles and Haemophilus parainfluenzae were revealed across populations. Particularly, these reliable bacterial markers, which were robust against demographic variation, distinguished patients with T2D from healthy controls with high accuracy (AUCs&#x2009;>&#x2009;0.8) in both European and Asian cohorts. Correlation analysis demonstrated that T2D-enriched and T2D-depleted bacteria, respectively, formed their own mutualistic networks that were negatively linked to each other. Moreover, T2D-enriched bacteria were dramatically positively associated with fasting blood glucose and glycated hemoglobin. Functionally, 10 KEGG pathways with consistent directional changes across European, Asian, and combined cohorts were identified. Specifically, the Nucleotide excision repair pathway was markedly downregulated in patients with T2D, while the AGE-RAGE signaling pathway in diabetic complications was consistently enriched in patients with T2D across cohorts.<br><br>CONCLUSIONS: Our results elucidated reproducible profiles of gut commensal bacteria in patients with T2D, which are robust across populations. Identifying the universal gut microbiome signatures of T2D in heterogeneous cohorts offers valuable insights for understanding disease development and is crucial for prevention and diagnosis across diverse populations.},
}
@article {pmid41942205,
year = {2026},
author = {Zhang, F and Wang, X and Wang, J and Fan, X and Kong, Y and Li, X and Zeng, X and Li, H and Liu, W and Zhang, A and Song, D and Gong, H},
title = {Revealing the microbial diversity and functional annotation during postharvest storage of sweet cherry using metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {233},
number = {Pt 1},
pages = {118955},
doi = {10.1016/j.foodres.2026.118955},
pmid = {41942205},
issn = {1873-7145},
mesh = {*Food Storage/methods ; *Prunus avium/microbiology ; *Metagenomics/methods ; *Food Microbiology ; *Microbiota ; Bacteria/classification/genetics ; *Fruit/microbiology ; },
abstract = {This study aimed to investigate the dynamic changes in the quality characteristics, microbial community diversity, functional annotation and metabolic pathways of sweet cherries stored at 25 °C for 0, 1, 3, 5 or 7 days. The results showed that the quality characteristics of sweet cherries gradually deteriorated with increasing storage time, and the abundance of Proteobacteria increased gradually. Mucoromycota appeared on D3 group, which may be one of the main microbial groups causing sweet cherry rot. In addition, 3D principal coordinate analysis showed that the species composition of sweet cherries stored for 1 day and fresh cherries was highly similar. The results of the Bray-Curtis distance analysis indicate a significant trend towards separation in species composition from the third day of storage. Moreover, KEGG annotations of metabolites and enzymes suggest that glycolysis and pyruvate metabolism are important in the storage of sweet cherries. Meanwhile, the pathway diagram shows that the main substances maintaining the pathway are pyruvate kinase and pyruvate dehydrogenase, which are detected in groups D5 and D7 groups. This study examines the changes in microbial communities and functional annotations that occur during the storage of sweet cherries after harvest. This provides a theoretical basis for developing new, efficient antibacterial agents for storing sweet cherries.},
}
@article {pmid41875555,
year = {2026},
author = {Lu, L and Li, M and Kang, G and Wu, P and Wang, N and Tan, Y and Su, G and Ruan, J and Zhang, S},
title = {Fate of per- and polyfluoroalkyl substances (PFAS) and microbial communities in wastewater treatment: Disinfection-driven changes in microbial dynamics and PFAS profiles.},
journal = {Ecotoxicology and environmental safety},
volume = {314},
number = {},
pages = {120059},
doi = {10.1016/j.ecoenv.2026.120059},
pmid = {41875555},
issn = {1090-2414},
mesh = {*Fluorocarbons/analysis ; *Wastewater/microbiology/chemistry ; *Water Pollutants, Chemical/analysis ; Disinfection ; China ; *Waste Disposal, Fluid/methods ; *Microbiota/drug effects ; },
abstract = {Municipal wastewater treatment plants (MWWTPs) are both sinks and sources of per- and polyfluoroalkyl substances (PFAS) due to limited removal efficiency in current treatment systems. However, the role of treatment processes, especially disinfection, in altering PFAS and microbial communities remains underexplored. In this study, we investigated the occurrence of 17 PFAS in two MWWTPs in Northwest China and characterized microbial communities through metagenomic sequencing. Results showed that total PFAS concentrations increased from 56.8 to 60.3 ng/L in MWWTPA and from 5.1 to 19.1 ng/L in MWWTPB, indicating ineffective removal. Perfluoropentanoic acid (PFPeA) and perfluorononanoic acid (PFNA) dominated the influent, accounting for 86.6% and 33.3% in MWWTPA and MWWTPB, respectively. In contrast, perfluorooctanesulfonic acid (PFOS, 46.8-52.4%) and perfluorooctanoic acid (PFOA, 5.1-8.9%) concentrations increased markedly in the effluent, becoming the predominant PFAS. Meanwhile, disinfection also altered microbial diversity and homogenized community structures between the two MWWTPs. Further analysis revealed strong associations (p < 0.01) between elevated PFAS levels and specific microbial taxa, including Actinomycetia and Thermoprotei, alongside increased relative abundance of genes annotated as haloacid dehalogenases, monooxygenases, and cytochrome P450. These associations may reflect potential influences on PFAS precursor dynamics. Overall, these findings highlight the importance of considering both chemical and microbial shifts when evaluating PFAS behavior during wastewater treatment.},
}
@article {pmid41881873,
year = {2026},
author = {Zhao, C and Yao, R and Xiong, M and Liu, X and Yu, J and Jumpponen, A and Romantschuk, M and Ur Rahman, S and Hui, N},
title = {Microbial exposure and antibiotic resistance gene dynamics shift between indoor and outdoor school activities.},
journal = {Ecotoxicology and environmental safety},
volume = {314},
number = {},
pages = {120044},
doi = {10.1016/j.ecoenv.2026.120044},
pmid = {41881873},
issn = {1090-2414},
mesh = {Humans ; Schools ; *Drug Resistance, Microbial/genetics ; China ; *Microbiota ; Hand/microbiology ; Adolescent ; Male ; Female ; Child ; Genes, Bacterial ; Nasal Cavity/microbiology ; *Environmental Exposure ; Bacteria/genetics ; },
abstract = {School curricular and extracurricular activities, including indoor study and sports like basketball, significantly impact adolescent physical and mental health. However, their effects on hand and nasal microbiomes, particularly regarding antibiotic resistance genes (ARGs), are underexplored. Here, we recruited 42 junior middle school students in Shanghai to investigate microbial composition and ARGs, collecting 336 hand and nasal samples after handwashing, indoor study, indoor basketball, and outdoor basketball. Our results showed that playing basketball either indoors or outdoors increased microbial diversity in nasal cavities and on hands, compared to post-handwashing. Notably, nasal microbiomes were predominantly derived from hand microbiomes, regardless of the activity performed. Among ARGs, macB genes were more abundant after outdoor basketball than indoor basketball, with this difference more pronounced in nasal cavities than on hands. Metagenomic sequencing identified Aureimonas phyllosphaerae as the primary macB gene host. Although this bacterium harbors ARGs, it is non-pathogenic and lacks mobile genetic elements, indicating a low potential for horizontal gene transfer or interspecies ARG transmission. Collectively, even though students may be exposed to more ARGs during outdoor activities, the health risks are likely minimal because the observed ARG bacteria are non-pathogenic and the likelihood of interspecies ARG transmission is low.},
}
@article {pmid41910951,
year = {2026},
author = {Dasgupta, S},
title = {Metagenomics in Obstructive Lung Diseases: Insights into Microbial Dysbiosis, Host-Microbe Interactions, and the Gut-Lung Axis.},
journal = {Omics : a journal of integrative biology},
volume = {30},
number = {4},
pages = {191-202},
doi = {10.1177/15578100261419483},
pmid = {41910951},
issn = {1557-8100},
mesh = {Humans ; *Dysbiosis/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Host Microbial Interactions ; Lung/microbiology ; *Lung Diseases, Obstructive/microbiology ; *Pulmonary Disease, Chronic Obstructive/microbiology ; Host-Pathogen Interactions ; },
abstract = {Obstructive lung diseases (OLDs), including asthma and chronic obstructive pulmonary disease (COPD), arise from complex interactions among microbial ecosystems, host immunity, metabolic regulation, and environmental exposures. Metagenomic approaches have substantially advanced understanding of these interactions by enabling comprehensive profiling of respiratory and gut-associated microbiomes and their functional potential. Evidence indicates that asthma is frequently associated with early-life microbial perturbations, reduced community diversity, enrichment of Streptococcus, Moraxella, and allergen-associated fungi, and gut dysbiosis that influences immune maturation and tolerance. In contrast, COPD is characterized by adult-onset dysbiosis with Proteobacteria dominance, depletion of commensal anaerobes such as Prevotella and Veillonella, and functional signatures linked to chronic inflammation, xenobiotic metabolism, and exacerbation risk. Across both diseases, alterations in gut microbial composition and metabolite profiles, including short-chain fatty acids, highlight the gut-lung axis as a key regulatory interface shaping airway immune responses. Despite these advances, critical knowledge gaps remain, including limited longitudinal data, incomplete multi-kingdom analyses, and insufficient mechanistic and translational validation of disease-associated microbiome signatures. This review integrates current metagenomic evidence to delineate disease-specific and shared microbial patterns, examines host-microbe interaction pathways within molecular and clinical contexts, and critically evaluates the implications and limitations of microbiome-based interventions. By framing microbiome research within a systems biology and public health perspective, this article underscores the importance of context-dependent interpretation and identifies priorities for future longitudinal, mechanistic, and translational studies in OLDs.},
}
@article {pmid41934196,
year = {2026},
author = {Alvarez-Sala, A and Jiménez-Hernández, N and Artacho, A and Ruiz-Pérez, S and Pascual, EC and Pons, J and Sorlí, JV and Corella, D and Gosalbes, MJ},
title = {Multi-Omic Insights Into Mediterranean Diet-Associated Microbiota.},
journal = {Molecular nutrition &amp; food research},
volume = {70},
number = {7},
pages = {e70450},
pmid = {41934196},
issn = {1613-4133},
support = {UGP-19-038//FISABIO/ ; UGP-21-205//FISABIO/ ; CIAICO/2022/27//Conselleria de Innovaci&#xf3;n, Universidades, Ciencia y Sociedad Digital/ ; Prometeo2021/021//Conselleria de Innovaci&#xf3;n, Universidades, Ciencia y Sociedad Digital/ ; CB06/03/0035//CIBEROBN/ ; },
mesh = {Humans ; *Diet, Mediterranean ; Male ; Female ; Adult ; Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; Middle Aged ; Olive Oil ; *Gastrointestinal Microbiome ; Feces/microbiology ; Fruit ; Vegetables ; Multiomics ; },
abstract = {This study aimed to evaluate the gut microbiota and mycobiota composition, depending on the Mediterranean diet (MD) adherence, using metataxonomics. Combining metagenomics and metatranscriptomics, we also investigate the gene expression level in the bacterial community. Two groups of healthy subjects greatly differing in adherence were selected. Significant differences in microbiota composition were observed between individuals with high adherence (HAMD; mean 10.5 +/- 0.9 points) and low adherence (LAMD; 5.23 +/- 83 points). Notably, the olive oil, vegetable, and fruit consumption presented an important discriminant power between groups. Saccharomyces, Penicillium, and Candida were the most abundant genera. Mycobiota richness was higher in LAMD than in HAMD. Aspergillus was identified as a biomarker for LAMD, whereas Yarrowia, a potential probiotic, was a biomarker for HAMD. Metatranscriptomics indicated that Bacillota was the most metabolically active phylum in the gut microbiota. The low-abundant genus, Methanobrevibacter, showed high transcriptional activity, contributing to the crucial methanogenesis process. Gene expression analyses further highlighted functional differences. Overall, HAMD microbiota presented increased metabolic activity, protein synthesis, and cellular mobility. Overexpression of flagellin and urease genes may enhance immune response in HAMD. Further metatranscriptomic studies are necessary to deepen our understanding of intestinal microbiota transcriptional programs and their interactions with the diet and human health.},
}
@article {pmid41934511,
year = {2026},
author = {Kumar, KS and Jeyabal, J and Yagoo, A and Vilvest, J and Vaishnika, AM},
title = {Dietary chitosan enhances gut microbial diversity and modulates beneficial and pathogenic communities in Channa striata fingerlings.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {41934511},
issn = {1572-9699},
mesh = {*Chitosan/administration &amp; dosage/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Diet ; Dietary Supplements ; *Fishes/microbiology ; Biodiversity ; Aquaculture ; },
abstract = {Dietary modulation of the gut microbiome is a promising approach for improving fish health and sustainability in aquaculture. Chitosan, a biopolymer derived from Artemia shells, has gained attention as a functional prebiotic feed additive due to its antimicrobial and immunomodulatory properties. The effects of dietary chitosan on gut microbial diversity and community composition were evaluated in Channa striata (murrel) fingerlings. Fish were fed three experimental diets: a basal diet (Exp-1), a black soldier fly larvae (BSFL)-based control diet (in which BSFL meal was used as a primary protein ingredient, with its nutritional composition considered during formulation), and a chitosan-supplemented diet (Exp-2). Gut microbiota were characterized using high-throughput 16S rRNA gene sequencing, and microbial diversity, composition, and interaction networks were analyzed. Alpha diversity analysis demonstrated that the chitosan-based diet significantly enhanced microbial richness (Chao1 = 531.62) and promoted a more balanced gut microbial structure compared to the basal diet, which showed reduced diversity and relative dominance of certain taxa previously reported to include opportunistic species. Chitosan supplementation enriched genera such as Lactobacillus, Bacteroides, and Alloprevotella, along with members of Muribaculaceae, which are commonly associated in the literature with functions such as polysaccharide degradation and short-chain fatty acid production, although functional roles cannot be conclusively assigned at the genus level. In contrast, the basal diet group showed a higher abundance of taxa including Plesiomonas and Clostridium sensu stricto, which have been reported in some contexts to include opportunistic strains. Network analysis further revealed stronger clustering and connectivity among microbial taxa under chitosan supplementation, suggesting improved microbial stability. Overall, dietary chitosan appears to influence gut microbial composition and diversity, suggesting a possible role in influencing gut microbial balance. These findings highlight its possible application as a sustainable feed additive in aquaculture, although further functional validation is required.},
}
@article {pmid41937465,
year = {2026},
author = {Do, TT and Le, VV and Nguyen, LTT and Nguyen, TTK and Vu, NTH and Trinh, HN and Lee, SA and Ngo, CC and Phi, QT},
title = {Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2508050},
doi = {10.4014/jmb.2508.08050},
pmid = {41937465},
issn = {1738-8872},
mesh = {*Petroleum/metabolism ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Salinity ; Soil Microbiology ; Metagenomics/methods ; Biodegradation, Environmental ; Soil Pollutants/metabolism ; Hydrocarbons/metabolism ; *Microbiota ; Phylogeny ; },
abstract = {Soil salinization and crude oil contamination are critical global threats to ecosystems, agriculture, and human health. Bioremediation is widely recognized as a cost-effective and eco-friendly strategy for removing petroleum pollutants from soil. In this study, we investigated salinity-driven bacterial community dynamics collected from crude oil-contaminated soil in Cam Ranh Bay, Khanh Hoa, over a 21-day enrichment cultivation, using shotgun metagenomic and culture-based approaches. The enrichment cultivation was performed in Bushnell-Haas mineral salts (BHMS) medium supplemented with 5% (v/v) crude oil-diesel mixture (5:95) and 1.5% NaCl. Shotgun metagenomic analysis revealed that after 21 days of enrichment, the relative abundance of crude oil-degrading genera increased markedly in the enriched samples compared to the native samples-for example, Pseudomonas rose from 0.44% to 3.51%, Gordonia from 0.03% to 78.68%, and Achromobacter from 0.03% to 3.77%. Functional analysis further identified metabolic pathways, including hydrocarbon degradation, osmoprotection, and heavy metal detoxification. In addition, 36 representative bacterial strains were isolated from the enriched cultures, predominantly belonging to the genera Pseudomonas, Bacillus, Stenotrophomonas, and Achromobacter. All isolates were able to degrade crude oil under salinity stress conditions of up to 4%. Notably, Rhodococcus sp. KH5 and Gordonia sp. KH53 maintained consistently high degradation efficiencies across 0-4% salinity, ranging from 17.67-35.00% and 28.67-36%, respectively. Overall, our findings demonstrate that saline enrichment shifts the bacterial community toward halotolerant hydrocarbon and crude oil degraders.},
}
@article {pmid41940802,
year = {2026},
author = {Yersin, S and Gody, JC and Mazel, F and Djimbele, E and Nigateloum, SN and Gondje, BP and Vondo, SS and Kaleb Jephté Estimé, K and Raub, A and Teo, Y and Djorie, SG and Kapel, N and Sansonetti, PJ and Vonaesch, P and , },
title = {Strain-level translocation and enrichment dynamics of oral bacteria in the lower gastrointestinal tract of stunted children.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2653550},
doi = {10.1080/19490976.2026.2653550},
pmid = {41940802},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Mouth/microbiology ; Female ; *Bacteria/classification/isolation &amp; purification/genetics ; Feces/microbiology ; Child, Preschool ; Saliva/microbiology ; Infant ; Cross-Sectional Studies ; *Bacterial Translocation ; *Growth Disorders/microbiology ; Child ; *Gastrointestinal Tract/microbiology ; Metagenomics ; },
abstract = {Emerging evidence suggests that ectopic colonization of oral bacteria in the lower digestive tract may exacerbate gastrointestinal disorders. Nevertheless, it remains unclear whether bacteria of oral origin are continuously translocating from the oral cavity to the lower gastrointestinal tract or are locally adapted and persist in their respective niches. We investigated strain translocation dynamics in 44 healthy and stunted children from Bangui, Central African Republic. Using cross-sectional shotgun metagenomic sequencing of saliva, gastric, duodenal, and fecal samples, and isolation and whole-genome sequencing of 87 Streptococcus salivarius isolates, we showed the translocation of members of the genera Streptococcus, Veillonella, Rothia, and Haemophilus. Fecal isolates were more closely related to oral isolates from the same individuals than to those from other individuals. Additionally, saliva showed higher S. salivarius nucleotide diversity compared to other compartments, which is consistent with frequent intraindividual translocations from the oral cavity to the lower gastrointestinal tract. Finally, we showed that overrepresentation of oral bacteria in the duodenum of stunted children is related to increased biomass, while in the colon, it is linked to depletion of overall biomass, including in butyrate-producing strains. Our study quantifies dynamics of oral-to-gut translocation and enrichment of oral taxa, providing key insights into microbiota disruption in stunted children.},
}
@article {pmid41942192,
year = {2026},
author = {Xia, Y and Kuda, T and Zhou, Q and He, Q},
title = {Bidirectional modulation of microbial communities by tea polyphenols and gallic acid enhances quality in dry fermented sausages.},
journal = {Food research international (Ottawa, Ont.)},
volume = {233},
number = {Pt 1},
pages = {118924},
doi = {10.1016/j.foodres.2026.118924},
pmid = {41942192},
issn = {1873-7145},
mesh = {*Gallic Acid/pharmacology ; *Meat Products/microbiology/analysis ; *Polyphenols/pharmacology ; Fermentation ; *Tea/chemistry ; *Food Microbiology ; *Microbiota/drug effects ; Antioxidants/pharmacology ; Animals ; *Fermented Foods/microbiology ; Humans ; Food Quality ; Taste ; },
abstract = {Tea polyphenols (TP) and its primary component gallic acid (GA) possess antibacterial and antioxidant properties, serving as natural additives to enhance the safety and quality of fermented meat products. This study investigated the bidirectional regulatory effects of TP and GA on microbial dynamics and quality attributes in dry fermented sausages. TP (1-4 mg/mL) enhanced the growth of Lactiplantibacillus plantarum while inhibiting Staphylococcus aureus and Escherichia coli, promoting lactic acid bacteria (LAB) dominance and reducing spoilage and pathogenic bacteria. Sausages treated with TP showed reduced levels of biogenic amines (291.06 vs. 376.22 mg/kg) and NDMA (0.86 vs. 1.32 μg/kg), improved texture (hardness and springiness), and better color stability, all without affecting sensory acceptability. Metabolomic and metagenomic analyses suggested that GA enriched beneficial Lactococcus garvieae and suppressed spoilage-associated Enterococcus faecalis and Citrobacter freundii. Besides, it promoted the microbial-mediated production of key antioxidant metabolites and flavor enhancers (e.g., purpurogallin, sesamol). These results indicated that TP and GA could serve as multifunctional additives that enhance fermentation efficiency, microbial safety, and sensory quality by precisely regulating microbial communities and their metabolic functions.},
}
@article {pmid41485494,
year = {2026},
author = {Miyachi, H and Shibata, R and Javornik Cregeen, SJ and Surathu, A and Sijaric, M and Espinola, JA and Sullivan, AF and Mansbach, JM and Camargo, CA and Zhu, Z},
title = {Interactions between host genetics and gut microbiome influence susceptibility to childhood asthma and lung function.},
journal = {The Journal of allergy and clinical immunology},
volume = {157},
number = {4},
pages = {868-878},
doi = {10.1016/j.jaci.2025.12.1005},
pmid = {41485494},
issn = {1097-6825},
support = {R01 AI127507/AI/NIAID NIH HHS/United States ; R01 ES036966/ES/NIEHS NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; K01 AI153558/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; },
mesh = {Humans ; *Asthma/genetics/microbiology/physiopathology/epidemiology ; *Gastrointestinal Microbiome ; Female ; Male ; Child ; Cross-Sectional Studies ; *Lung/physiopathology ; Genetic Predisposition to Disease ; Respiratory Function Tests ; },
abstract = {BACKGROUND: The gut microbiome is thought to influence risk of childhood allergic diseases; however, the data on species-level links to childhood asthma and lung function are limited, and the role of host genetics in the gut-lung axis remains unclear.<br><br>METHODS: In a multicenter cross-sectional study of children with a history of bronchiolitis from the 35th Multicenter Airway Research Collaboration, we performed shotgun metagenomic profiling of stool samples obtained at age 6 years and examined associations of the gut microbiome with asthma prevalence and lung function. We also calculated polygenic risk scores (PRSs) of asthma and lung function to investigate the interaction between host genetics and the gut microbiome in relation to these traits.<br><br>RESULTS: In the 300 children included for this study, 3 bacterial species (ie, Bacteroides vulgatus, Eisenbergiella massiliensis, and Butyricimonas virosa) were differentially associated with FEV1 value and 4 bacterial species were differentially associated with ratio of FEV1 value to forced vital capacity (FVC) (eg, Bifidobacterium longum) (false discovery rate [FDR] according to the R package MaAsLin < 0.25). Furthermore, host genetics-gut microbiome interaction analysis showed association of B vulgatus (FDR = 0.037) and Bacteroides uniformis (FDR = 0.037) with FEV1/FVC ratio among children with a high FEV1/FVC ratio PRS. Additionally, Ruminococcus bromii (FDR = 0.067) and Alistipes indistinctus (FDR = 0.13) were suggested to have protective associations with asthma, specifically in children with a high asthma PRS, indicating that host genetics can modulate the effect of the gut microbiome on these respiratory outcomes.<br><br>CONCLUSION: By applying the metagenomic approach to a multicenter cohort of children with a history of bronchiolitis during infancy, this study suggests potential interplay of host genetics with the gut microbiome, as well as their integrated relationship with childhood asthma and lung function.},
}
@article {pmid41582602,
year = {2026},
author = {Hernani, R and Albert, E and Hernani-Morales, C and Zúñiga, S and Benzaquén, A and González-Castillo, L and Colomer, E and Morell, J and Català-Senent, JF and Piñana, JL and Giménez, E and Pérez, A and Hernández-Boluda, JC and Arroyo, I and Rivada, M and Barber, T and Alemany, T and Santacatalina, E and Rentero-Garrido, P and Terol, MJ and Díaz, R and Navarro, D and Solano, C},
title = {Microbiome-Based Modeling of CAR-T Therapy Response in Lymphoma: Insights From Shotgun Metagenomics Sequencing.},
journal = {European journal of haematology},
volume = {116},
number = {5},
pages = {646-662},
doi = {10.1111/ejh.70121},
pmid = {41582602},
issn = {1600-0609},
support = {//Fundaci&#xf3;n FERO and the Fundaci&#xf3;n para la Promoci&#xf3;n de Acciones Solidarias/ ; //European Union through the Operational Program of the European Regional Development Fund/ ; CA23/00007//bioinformatics technician/ ; //2023 Strategic Action in Health/ ; //Instituto de Salud Carlos III/ ; //European Union/ ; },
mesh = {Humans ; *Metagenomics/methods ; Middle Aged ; Male ; Female ; *Immunotherapy, Adoptive/methods/adverse effects ; Aged ; Adult ; Treatment Outcome ; *Gastrointestinal Microbiome ; *Receptors, Chimeric Antigen/genetics ; *Microbiota ; Machine Learning ; Dysbiosis ; Feces/microbiology ; *Lymphoma, B-Cell/therapy/mortality/microbiology ; },
abstract = {The interplay between the commensal microbiota and the mammalian immune system may influence the outcomes of T cell-driven cancer immunotherapies. However, clinical studies supporting microbiota-based interventions in chimeric antigen receptor T-cell (CAR-T) therapy remain scarce. This study included 30 adult patients with B-cell lymphoma treated with axicabtagene ciloleucel (axi-cel) or 4-1BB investigational product. Shotgun metagenomics sequencing (SMS) of fecal samples, collected before lymphodepletion and 1 month post infusion, enabled species-level resolution. We also trained 25 microbiome-based machine-learning (ML) models for response prediction. Neither prior "high-risk" antibiotics exposure nor alpha diversity influenced toxicity, response, or survival. However, dysbiosis was observed between 11 healthy controls and patients, particularly in those treated with axi-cel. SMS identified species associated with clinical outcomes. Increased abundance of Alistipes senegalensis and Alistipes onderdonkii correlated with lower neurotoxicity and improved survival, respectively. Bifidobacterium longum was associated with reduced cytokine release syndrome, whereas Bifidobacterium adolescentis , Bifidobacterium bifidum , and Bifidobacterium breve correlated with poorer survival. ML models demonstrated strong predictive performance, with some identifying non-responders using only six species selected by the Boruta method (Bacteroides xylanisolvens , Bifidobacterium bifidum , Bifidobacterium breve , Eubacteriaceae bacterium Marseille-Q4139, Negativibacillus massiliensis, and Sellimonas intestinalis). These findings deepen current knowledge and support prospective microbiota-based strategies in CAR-T therapy.},
}
@article {pmid41687784,
year = {2026},
author = {Thriene, K and Stanislas, V and Huang, KD and Strowig, T and Michels, KB},
title = {Impact of Yogurt and Rolled Oats Consumption on the Gut Microbiome: A Randomized Crossover Study Displaying Individual Responses and General Resilience.},
journal = {The Journal of nutrition},
volume = {156},
number = {4},
pages = {101408},
doi = {10.1016/j.tjnut.2026.101408},
pmid = {41687784},
issn = {1541-6100},
mesh = {Humans ; *Yogurt ; *Avena ; *Gastrointestinal Microbiome ; Cross-Over Studies ; Male ; Female ; Adult ; Feces/microbiology ; Young Adult ; Probiotics ; Middle Aged ; Diet ; Prebiotics ; },
abstract = {BACKGROUND: Yogurt and rolled oats are commonly linked to gut health through probiotic and prebiotic effects, but these potential benefits remain insufficiently studied, especially in healthy individuals.<br><br>OBJECTIVES: This study primarily aimed to investigate the effects of daily yogurt and rolled oats consumption on gut microbial composition. Secondary outcomes included stool metabolites and blood-based health markers.<br><br>METHODS: In this randomized, open-label, 2-period crossover trial, 119 healthy participants were randomly assigned to 1 of 2 sequences: 250 g of yogurt daily followed by 250 g of yogurt with 50 g of rolled oats, or the reverse with a washout period in between. Stool and blood samples were collected at baseline and post intervention. Metagenomic sequencing and metabolomic analyses were conducted on stool samples, whereas health markers related to metabolic control, inflammation, immune response, oxidative stress, and gut permeability were assessed in the participants' blood.<br><br>RESULTS: Of the 119 randomly divided participants, 110 completed the study (53 yogurt first, 57 yogurt and rolled oat first). Yogurt consumption transiently increased yogurt-associated bacteria, with Streptococcus thermophilus rising from absent to 0.97% [95% confidence interval (CI): 0.71, 1.26] in the yogurt intervention and 0.79% (95% CI: 0.58, 1.03) in the yogurt with oats intervention. In a small Prevotella-predominant subgroup (n = 8), adding rolled oats increased microbial evenness (q < 0.001) and reduced interindividual divergence (q < 0.05), suggesting a temporary slight homogenization. No additional effects on fecal short-chain fatty acids concentrations or human health markers were identified. Functional metagenomic changes were mainly driven by yogurt-derived bacterial enrichment.<br><br>CONCLUSIONS: A healthy gut microbiota is largely stable and resilient to short-term diet changes, yet individual differences highlight the importance of personalized dietary recommendations.<br><br>(German Trial Register): DRKS00023146 (https://drks.de/search/en/trial/DRKS00023146/details).},
}
@article {pmid41929479,
year = {2026},
author = {Pan, Y and Li, B and Liu, L and Wang, Z and Liu, X},
title = {Gut dysbiosis induces the development of asthenozoospermia through butanoate metabolism.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1760881},
pmid = {41929479},
issn = {1664-3224},
mesh = {Male ; *Dysbiosis/complications/microbiology/metabolism ; Animals ; *Gastrointestinal Microbiome ; *Asthenozoospermia/metabolism/etiology/microbiology ; Humans ; Mice ; Case-Control Studies ; Fecal Microbiota Transplantation ; Adult ; Fatty Acids, Volatile/metabolism ; Butyrates/metabolism ; Sperm Motility ; Metabolomics ; Testis/metabolism ; },
abstract = {BACKGROUND: Asthenozoospermia is a leading cause of male infertility with a rising incidence. While gut dysbiosis is implicated in metabolic disease, its role in asthenozoospermia pathogenesis remains unclear.<br><br>MATERIALS AND METHODS: We conducted a case-control study comparing the fecal microbiomes of men with isolated asthenozoospermia (n=60) and healthy controls (n=60) using shotgun metagenomic sequencing. Causality was assessed by fecal microbiota transplantation (FMT) from patients or controls into germ-free male mice. Metabolic perturbations were profiled by untargeted serum metabolomics and targeted short-chain fatty acid (SCFA) quantification in humans, alongside untargeted testicular metabolomics and serum SCFAs in recipient mice.<br><br>RESULTS: Metagenomic analysis (LEfSe) identified species-level differences, with marked depletion of butyrate-producing taxa in asthenozoospermia, most notably the prototypical butyrate producer Faecalibacterium prausnitzii. The relative abundance of F. prausnitzii was significantly positively correlated with sperm motility and progressive motility, linking gut composition to sperm quality in asthenozoospermia. Untargeted serum metabolomics identified 39 differential metabolites; KEGG enrichment prioritized butanoate metabolism. Targeted SCFA profiling confirmed significantly lower serum butyrate in asthenozoospermia versus controls. In germ-free males, FMT with patient-derived microbiota reduced sperm motility and progressive motility and induced histopathological abnormalities, including decreased interstitial Leydig cells, loss and atrophy of select intratubular cells, and an increased proportion of abnormal seminiferous tubules. Following patient FMT, recipient mice exhibited significantly reduced serum butyrate; testicular metabolomics revealed distinct profiles with 140 key differential metabolites, again implicating butanoate metabolism. Mechanistically, reduced F. prausnitzii-derived butyrate might impair Leydig cell steroidogenesis via disrupted PPAR signaling.<br><br>CONCLUSIONS: Asthenozoospermia is associated with gut dysbiosis characterized by loss of butyrate-producing bacteria, systemic and testicular disturbances in butyrate metabolism, and microbiota-mediated transmission of impaired sperm quality. These findings implicate the gut-testis axis in asthenozoospermia pathogenesis and nominate butyrate metabolism as a potential therapeutic target.},
}
@article {pmid41823302,
year = {2026},
author = {Al, KF and Jia, S and Silverman, M and Reid, G and Burton, JP and Parvathy, SN},
title = {Prebiotic modulation of FMT donor microbiota enhances MASLD-relevant taxa and functions in an in vitro gut model.},
journal = {Journal of applied microbiology},
volume = {137},
number = {4},
pages = {},
doi = {10.1093/jambio/lxag074},
pmid = {41823302},
issn = {1365-2672},
support = {//Lawson/ ; //Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Humans ; *Prebiotics/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Inulin/pharmacology ; *Fecal Microbiota Transplantation ; Feces/microbiology ; *Non-alcoholic Fatty Liver Disease/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Oligosaccharides/pharmacology ; Bacteria/genetics/classification/isolation &amp; purification ; Fatty Acids, Volatile/analysis/metabolism ; Male ; Adult ; Middle Aged ; Female ; Glucuronates ; },
abstract = {AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD, formerly non-alcoholic fatty liver disease) is a prevalent and progressive condition closely linked to gut microbiota composition. Fecal microbiota transplantation (FMT) may help restore a health-associated microbiome, but its efficacy is often limited by inconsistent engraftment of beneficial taxa. Prebiotics may selectively support keystone microbes associated with reduced MASLD risk. This study evaluated two prebiotics, inulin and xylooligosaccharides (XOS), for their ability to modulate the microbiota of healthy FMT donors in an in vitro gut model, focusing on enriching beneficial taxa and functions associated with MASLD resilience.<br><br>METHODS AND RESULTS: Stool from eight clinically qualified FMT donors was cultured anaerobically for 24 h with or without prebiotics. Microbiota composition was assessed by 16S rRNA gene sequencing and short-chain fatty acid (SCFA) concentrations were measured using nuclear magnetic resonance. Functional potential was inferred using predictive metagenomic analysis. Prebiotic responses were highly donor-specific, yet both inulin and XOS consistently enriched Bifidobacterium and Bacteroides-genera associated with SCFA production and metabolic health. XOS preferentially enriched Lactobacillus and Parabacteroides, while inulin enhanced Holdemanella and Mediterraneibacter. Functional pathways relevant to MASLD pathophysiology were enriched, including carbohydrate metabolism, vitamin biosynthesis, fatty acid metabolism, and tryptophan degradation. Both prebiotics significantly increased acetate levels, while butyrate showed a donor-dependent increasing trend.<br><br>CONCLUSIONS: These findings suggest that prebiotic supplementation can selectively enrich MASLD-relevant microbial taxa and functions in donor-derived FMT material, supporting their potential as adjuvants to enhance the efficacy and disease-specificity of FMT interventions for MASLD.},
}
@article {pmid41857392,
year = {2026},
author = {Zhai, X and Jin, J and Yu, M and Liu, R and Li, J and Liu, Y and Zhang, XH and Liu, J},
title = {Spatial Heterogeneity of Microbial Communities and Biogeochemical Function in Water Column of Site F Cold Seep, South China Sea.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41857392},
issn = {1432-184X},
support = {202172002//the Fundamental Research Funds for the Central Universities/ ; LSKJ202203206//the Science &amp; Technology Innovation Project of Laoshan Laboratory/ ; ZR2022YQ038, ZR2024JQ006//Shandong Province Natural Science Foundation/ ; },
abstract = {UNLABELLED: Cold seep is a distinctive deep-sea environment mainly formed by methane-rich fluids leaking on the seafloor, gaps remain regarding the influence of seepage on microorganisms inhabiting water column across vertical and horizontal dimensions. Site F cold seep, located at 1,120 m depth on the northern South China Sea (SCS) slope, is one of the most active cold seeps in SCS. We performed 16S rRNA gene and metagenomic sequencing on samples collected by Niskin bottles mounted on Conductivity-Temperature-Depth profiler and Remote Operated Vehicle to analyze the structure and metabolic potentials of microbial communities throughout the water column at Site F. Microbial abundance generally decreased with depth at all sampling spots and was higher at sites adjacent to the seepage compared to those farther away, indicating a potential vertical and horizonal influence of methane seepage on water microbial community. High microbial abundance at deeper depths may attribute to a higher proportion of Gammaproteobacteria, comprised mainly of Alcanivoracaceae, Alteromonadaceae, Marinobacteraceae, methylotrophs represented by Methylophagaceae and Methylococcales (mainly Methylomonadaceae), and sulfur-oxidizing bacteria represented by SUP05 and Ectothiorhodospiraceae. Consistently, the aerobic methane oxidation gene pmoA was more prevalent in the deeper water and was found in four bacterial classes in addition to Gammaproteobacteria. Sulfur-oxidizing genes also exhibited higher abundances at depths and were primarily affiliated with Rhodobacteraceae. These microbes likely play important roles in aerobic oxidation of methane and sulfur, contributing to methane depletion during upward diffusion. By integrating sampling across vertical and horizontal dimensions, we demonstrate that seepage shapes the microbial community and biogeochemical functions in the water column at Site F.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02722-5.},
}
@article {pmid41929449,
year = {2026},
author = {Røsland, A and Amin, H and Lie, SA and Malinovschi, A and Bunæs, DF and Bertelsen, RJ},
title = {Effect of periodontal therapy on the oral microbiome and lung function: an intervention study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1725666},
pmid = {41929449},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; Male ; *Periodontitis/therapy/microbiology ; Female ; Middle Aged ; *Mouth/microbiology ; Longitudinal Studies ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; *Lung/physiology ; Metagenomics ; Aged ; },
abstract = {INTRODUCTION: The oral cavity harbors over 700 bacterial species, and disruption of this balance can lead to periodontitis, which has been linked to systemic conditions including respiratory disease.<br><br>METHODS: In this longitudinal clinical trial, 57 never-smoking adults with stage I-II periodontitis underwent full-mouth periodontal disinfection. Airway resistance and subgingival plaque sampling (analyzed by shotgun metagenomics) was measured at baseline and six weeks after therapy.<br><br>RESULTS: Periodontal treatment significantly improved clinical periodontal parameters, and was associated with reductions in airway resistance. Microbiome analysis showed a shift from periodontitis-associated taxa, including Prevotella, Porphyromonas, and Tannerella, toward health-associated species such as Actinomyces oris, and Rothia dentocariosa. Higher airway resistance was associated with a greater relative abundance of periodontitis-associated bacteria.<br><br>DISCUSSION: Together, findings suggest that periodontal therapy promotes a healthier oral microbiome and is associated with improved lung function in non-smokers with no prior lung disease.},
}
@article {pmid41666926,
year = {2026},
author = {Kim, CY and Podlesny, D and Schiller, J and Khedkar, S and Fullam, A and Orakov, A and Schudoma, C and Robbani, SM and Grekova, A and Kuhn, M and Bork, P},
title = {Planetary microbiome structure and generalist-driven gene flow across disparate habitats.},
journal = {Cell},
volume = {189},
number = {7},
pages = {2073-2091.e21},
doi = {10.1016/j.cell.2025.12.051},
pmid = {41666926},
issn = {1097-4172},
mesh = {*Microbiota/genetics ; Humans ; *Ecosystem ; *Gene Flow/genetics ; Metagenome/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics/classification ; Earth, Planet ; },
abstract = {Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersal, driven by natural processes and human activities, interconnects microbiomes across habitats, yet most comparative studies focus on specific ecosystems. To study planetary microbiome structure, function, and inter-habitat interactions, we systematically integrated 85,604 public metagenomes spanning diverse habitats worldwide. Using species-based unsupervised clustering and parameter modeling, we delineated 40 habitat clusters and quantified their ecological similarity. Our framework identified key drivers shaping microbiome structure, such as ocean temperature and host lifestyle. Regardless of biogeography, microbiomes were structured primarily by host-associated or environmental conditions, also reflected in genomic and functional traits inferred from 2,065,975 genomes. Generalists emerged as vehicles thriving and facilitating gene flow across ecologically disparate habitat types, illustrated by generalist-mediated horizontal transfer of an antibiotic resistance island across human gut and wastewater, further dispersing to environmental habitats, exemplifying human impact on the planetary microbiome.},
}
@article {pmid41672407,
year = {2026},
author = {Furst, AJ and Johnson, KE and Nagel, EM and Yerabandi, N and Kats, AM and Gallagher, TT and Gale, CA and Palmsten, K and Pierce, S and Hoffman, S and Jacobs, K and Fields, DA and Isganaitis, EM and Bode, L and Demerath, EW},
title = {Gestational diabetes, human milk oligosaccharide concentrations, and their links to infant weight gain and the gut microbiome in a United States observational cohort.},
journal = {The American journal of clinical nutrition},
volume = {123},
number = {4},
pages = {101235},
doi = {10.1016/j.ajcnut.2026.101235},
pmid = {41672407},
issn = {1938-3207},
support = {R00 HD113834/HD/NICHD NIH HHS/United States ; R01 HD080444/HD/NICHD NIH HHS/United States ; R01 HD109830/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; *Milk, Human/chemistry ; Female ; *Oligosaccharides/analysis/metabolism ; *Gastrointestinal Microbiome ; Pregnancy ; *Diabetes, Gestational/metabolism ; Infant ; Adult ; United States ; *Weight Gain ; Feces/microbiology ; Infant, Newborn ; Cohort Studies ; Male ; },
abstract = {BACKGROUND: Gestational diabetes mellitus (GDM) increases offspring obesity risk, but whether this occurs via changes in human milk composition, including alterations in human milk oligosaccharides (HMOs), is unknown.<br><br>OBJECTIVES: This study aimed to identify differences in HMO concentrations in mothers with and without GDM and test whether GDM-associated HMOs are associated with infant growth, body composition, and fecal microbiome characteristics over the first 6-mo of life.<br><br>METHODS: Human milk was collected at 1-mo postpartum from 337 females (49 with GDM) who fed their infants breastmilk exclusively. HMOs were quantified by high-performance liquid chromatography and multivariate regression models were used to test differences in HMO concentrations by GDM status (false discovery rate adjustment for multiple testing set at q < 0.05). HMOs associated with GDM were then tested for associations with infant growth, body composition, and 1 and 6-mo infant fecal microbial abundances measured by metagenomic whole-genome sequencing.<br><br>RESULTS: Participants with GDM had &#x223c;1 SD higher milk 6'sialyllactose (6'SL) {[&#x3b2; (95% confidence interval): 0.58 (0.20, 0.96)] and lacto-N-fucopentaose III (LNFP III) III [95% CI: 0.55 (0.16, 0.94)]}
compared with those without GDM and 6'SL concentration was also positively associated with weight and length gain. Although infants of mothers with GDM had lower 1-mo fecal &#x3b1;-diversity and altered abundances of 6 of 56 microbial species detected compared with those without GDM, microbial features were not associated with the concentration of either 6'SL or LNFP III and evidence for mediation of GDM-growth and GDM-microbiome by HMOs was not found.<br><br>CONCLUSIONS: Mothers with a GDM diagnosis had higher milk concentrations of LNFP III and 6'SL, and 6'SL was in turn associated with increased infant growth rate, but neither HMO was associated with differential infant gut microbial abundances. The results suggest that the link between 6'SL and faster infant growth, if causal, occurs via mechanisms independent of the infant gut microbiome. This study was registered at clinicaltrials.gov as NCT03301753.},
}
@article {pmid41747730,
year = {2026},
author = {Matias Rodrigues, JF and Tackmann, J and Malfertheiner, L and Patsch, D and Perez-Molphe-Montoya, E and Näpflin, N and Gaio, D and Rot, G and Danaila, M and Peluso, ME and Dmitrijeva, M and Schmidt, TSB and von Mering, C},
title = {The MicrobeAtlas database: Global trends and insights into Earth's microbial ecosystems.},
journal = {Cell},
volume = {189},
number = {7},
pages = {2092-2107.e17},
doi = {10.1016/j.cell.2026.01.021},
pmid = {41747730},
issn = {1097-4172},
mesh = {*Microbiota ; *Bacteria/genetics/classification ; Earth, Planet ; Ecosystem ; },
abstract = {Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the entire planet-from the deep subsurface to the mountaintops-covering a myriad of hosts, biomes, and conditions. Yet, the diversity of sequencing and processing strategies hampers universal insights. MicrobeAtlas unifies more than two million microbiome samples in a single resource, harmonized to facilitate discoveries across technologies. Communities are hierarchically quantified at adjustable small subunit rRNA marker gene resolution and feature detailed metadata, including rich geographic information. Connections to the genome, phenotype, and ecological resources enable multimodal insights. Microbial lineages can be reliably tracked across environments, including a "long tail" of rare, uncharacterized species. Recurring community structures and geographic preferences become apparent, and global, taxonomy-specific generalism trends emerge. With MicrobeAtlas (www.microbeatlas.org), known and newly described species and communities can readily be placed into their ecological context, taking full advantage of earlier work.},
}
@article {pmid41833574,
year = {2026},
author = {Saibu, S and Obayori, OS and Diagboya, PN and Oso, SO and Shedrack, AE and Agbomeji, RO and Eletu, MO and Ajibike, OR and Ishola, FM and Adimabua, RN and Oyetibo, GO},
title = {Spatial variation in bacterial community structure and pollution response in river sediment.},
journal = {Journal of contaminant hydrology},
volume = {279},
number = {},
pages = {104923},
doi = {10.1016/j.jconhyd.2026.104923},
pmid = {41833574},
issn = {1873-6009},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification ; Polycyclic Aromatic Hydrocarbons/analysis ; RNA, Ribosomal, 16S/genetics ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Microbiota ; },
abstract = {Rivers are unique ecosystems where pollution frequently occurs, altering the biogeochemical characteristics of both water bodies and sediments. However, little is known about the effects of human activities on the lower course of River Ogun. This study assessed the association between anthropogenic activities and sediment bacterial communities at the time of sampling by comparing sediment physicochemical properties and the bacterial community structures of samples. Samples were taken from four distinct sites along the lower course of the river. Bacterial community structure of these sites was investigated using the 16S rRNA gene PacBio sequencing. Total polycyclic aromatic hydrocarbons (PAHs) were lowest at Location B (6.95 mg/kg) and highest at Location A (15.6 mg/kg). The dominant bacterial phyla in the sediments were Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota. A notable abundance of Thauera was observed across all the locations, particularly at Location A, and Psychrobacter known for plastic degradation was detected exclusively at this site. Among all the sites, Location A exhibited the lowest bacterial diversity, as indicated by both species' richness and evenness, where the Thauera selenatis group and Psychrobacter maritimus were dominant. Location B exhibited the highest bacterial diversity, Location C and D displayed intermediate diversity, sharing a 40% similarity index. Environmental variables that significantly explained beta diversity patterns included pH, anthracene and fluoranthene. This study provides insights into bacterial metagenomes of a freshwater inundated with plastics, heavy metals and consortium of persistent organic compounds. The findings highlight the value of integrating metagenomic and physicochemical analyses to identify correlations that help explain the key drivers shaping ecosystem dynamics.},
}
@article {pmid41855987,
year = {2026},
author = {Demaria, F and Suleiman, M and Bargiela, R and Ferrer, M and Hernández, SB and Núñez, AE and Petchey, OL and Corvini, PF and Junier, P},
title = {Micropollutant-driven bacterial adaptation enables resilient pharmaceuticals biodegradation at trace concentrations in biologically treated wastewater.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141801},
doi = {10.1016/j.jhazmat.2026.141801},
pmid = {41855987},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Wastewater/microbiology/chemistry ; Bioreactors/microbiology ; Pharmaceutical Preparations/metabolism ; *Bacteria/metabolism/genetics ; Microbial Consortia ; Waste Disposal, Fluid ; Adaptation, Physiological ; },
abstract = {Pharmaceutical residues are persistent contaminants that resist conventional wastewater treatment and can disrupt ecosystems; however, microorganisms provide a promising biobased solution to transform or mineralize these complex xenobiotics. Whether pollutant-adapted communities maintain their degradative capacity under realistic environmental conditions remains a long-standing debate in environmental biotechnology. Here, microbial consortia enriched in six membrane bioreactors under high pharmaceutical concentration (100 mg/L) retained full biodegradation capacity across a 5000-fold concentration range. After prolonged exposure to six model compounds (atenolol, caffeine, diclofenac, enalapril, ibuprofen, and paracetamol) complete removal occurred for all except diclofenac. Degradation remained efficient even at lower and environmentally relevant concentrations (1 mg/L-20 µg/L) and recovered rapidly upon re-exposure to higher loads (100 mg/L). Metagenomic profiling revealed enrichment of oxygenase-mediated catabolic pathways supporting this resilience. When transferred to a 7 liters bioreactor treating real wastewater, the adapted community removed targeted and untargeted pharmaceuticals, demonstrating robustness, scalability, and strong potential for sustainable micropollutant remediation.},
}
@article {pmid41865575,
year = {2026},
author = {Xie, H and Zhou, J and Shi, Y},
title = {Bioaugmentation of weathered petroleum-contaminated soil with a yeast-based consortium: Degradation performance and mechanism insights.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141830},
doi = {10.1016/j.jhazmat.2026.141830},
pmid = {41865575},
issn = {1873-3336},
mesh = {*Soil Pollutants/metabolism ; Biodegradation, Environmental ; *Petroleum/metabolism ; *Soil Microbiology ; *Saccharomyces cerevisiae/metabolism ; *Hydrocarbons/metabolism ; Microbial Consortia ; Soil/chemistry ; },
abstract = {Bioremediation of total petroleum hydrocarbons (TPHs) in weathered soil is often constrained by the inefficiency of indigenous microbial synergistic networks. The mechanisms governing these network responses remain poorly understood, frequently overlooking the system-level functional dynamics. This 7-week study contrasted biostimulation (NZ) with yeast-based bioaugmentation (NS), linking microbial succession and functional network reconstruction to TPHs degradation. The NS group showed a clear advantage in TPHs removal (83.1%) and, crucially, in degrading the heavy C22-C40 fraction (76.3%). The NZ community, despite possessing degradation genes, was trapped in a "functional lock", lacking a cohesive synergistic network. The TPHs and heavy C22-C40 fraction removal efficiencies of the NZ community are only 75.3% and 39.3%, respectively. In contrast, the introduced Saccharomyces cerevisiae in the NS group acted as a pioneer species. It initiated a system-wide reconstruction by (1) altering the soil microenvironment through intense metabolic stress responses (e.g., upregulation of protein quality control systems and high-affinity MFS transporters) and (2) activating a novel, synergistic indigenous consortium, including Altererythrobacter and Cellulosimicrobium. It is indicated that effective bioaugmentation is not the mere addition of strains but a deliberate ecological network reconstruction. The pioneer species alleviates the functional stagnation of the native community, driving the emergence of a novel, highly effective synergistic degradation system. This provides a key theoretical basis for developing bioremediation technologies centered on ecological network regulation.},
}
@article {pmid41923636,
year = {2026},
author = {Xiong, C and Delgado-Baquerizo, M and Liang, J and Wang, J and Yan, Z and Jensen, SO and Gao, M and Sáez-Sandino, T and Guirado, E and Muñoz-Rojas, M and Román, R and Maestre, FT and Singh, BK},
title = {Soil microbial diversity associates with lower prevalence of human bacterial pathogens across global soils.},
journal = {Cell host &amp; microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.03.011},
pmid = {41923636},
issn = {1934-6069},
abstract = {Soil-inhabiting pathogens threaten human health, but their biogeography and associations with soil biodiversity remain poorly understood. Here, we present global patterns of dominant human bacterial pathogens by integrating 1,602 soil metagenomes from 59 countries across continents. We show that dominant human pathogens are more prevalent (i.e., relative abundance) in wet (tropical and temperate) ecosystems and are particularly abundant in cropland soils. We find a global negative association between soil microbiome diversity and pathogen prevalence. We further reveal a significant and positive correlation between the abundance of dominant human pathogens and both disease virulence and global patterns of mortality associated with infectious diseases. Many dominant pathogens are likely to increase their proportion under global change scenarios. Our work provides a global atlas of dominant soil-inhabiting human pathogens and reveals their biogeography and ecology. These findings can guide the development of effective surveillance and risk management strategies to reduce outbreaks and pandemics.},
}
@article {pmid41925105,
year = {2026},
author = {Zu, S and Yu, X and Song, J and Xiao, Y and Yi, H and Li, H},
title = {The Role of Gut Microbiota and Their Derived Metabolites in Chemotherapy-Induced Nausea and Vomiting in Ovarian Cancer.},
journal = {Cancer medicine},
volume = {15},
number = {4},
pages = {e71752},
pmid = {41925105},
issn = {2045-7634},
support = {2023QH1193//Startup Fund for Scientific Research, Fujian Medical University/ ; YCXH 22-10//Nursing Research Special Fund of Fujian Maternal and Child Health Hospital/ ; },
mesh = {Female ; *Gastrointestinal Microbiome ; Animals ; Humans ; Rats ; Middle Aged ; *Ovarian Neoplasms/drug therapy ; Rats, Sprague-Dawley ; *Vomiting/chemically induced/microbiology/metabolism ; *Nausea/chemically induced/microbiology/metabolism ; Dysbiosis/microbiology ; *Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Cisplatin/adverse effects/administration &amp; dosage ; Metabolomics ; Fecal Microbiota Transplantation ; Aged ; Carboplatin/adverse effects/administration &amp; dosage ; Feces/microbiology ; Paclitaxel/adverse effects/administration &amp; dosage ; Metabolome ; Adult ; },
abstract = {OBJECTIVE: This study aimed to investigate the relationship between gut microbiota and chemotherapy-induced nausea and vomiting (CINV) in patients with ovarian cancer undergoing platinum-based chemotherapy (carboplatin or cisplatin combined with paclitaxel).<br><br>METHODS: Clinical data and fecal samples were collected from patients with ovarian cancer after admission but prior to the initiation of their first chemotherapy cycle. Patients were divided into the CINV (n&#x2009;=&#x2009;25) and non-CINV (n&#x2009;=&#x2009;25) groups on the basis of symptoms occurring after chemotherapy. No additional samples were collected during chemotherapy. Integrated metagenomic sequencing and untargeted metabolomic profiling identified CINV-associated microbial taxa and metabolites. Additionally, fecal microbiota transplantation (FMT) in SD rats validated causal links between gut dysbiosis and CINV pathogenesis.<br><br>RESULTS: Bacteroides caccae, Corynebacteriales, and Corynebacterium were significantly enriched in the CINV group. KEGG enrichment revealed upregulated pathways in CINV, including focal adhesion, lysosome function, and eukaryotic cellular communities. Metabolomic analysis identified 19 significantly increased metabolites in the fecal samples of CINV patients versus 10 in non-CINV controls. KEGG enrichment revealed that the pentose phosphate pathway, glutathione metabolism, and lipoic acid metabolism were significantly implicated in CINV pathogenesis. Multi-omics integration revealed Bacteroides sp. A1C1 strongly correlated with hesperetin, arbutin, orciprenaline, and myristolic acid. In rats, cisplatin-induced CINV models showed higher kaolin consumption versus controls (p&#x2009;<&#x2009;0.05). FMT from non-CINV donors reduced kaolin consumption in cisplatin-treated rats (p&#x2009;<&#x2009;0.05). The expression of 5-HT3R, NK1R, and NK2R in the medulla oblongata and colon was significantly increased in the cisplatin model group (p&#x2009;<&#x2009;0.05) and partially reversed by non-CINV FMT (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: Gut microbiota dysbiosis directly contributes to CINV pathogenesis. Bacteroides sp. A1C1 and its putatively identified metabolites (hesperetin, arbutin, orciprenaline, and myristolic acid) represent potential diagnostic biomarkers for CINV.},
}
@article {pmid41741786,
year = {2026},
author = {Flinn, H and Marshall, A and Holcomb, M and Burke, M and Kara, G and Cruz-Pineda, L and Soriano, S and Treangen, TJ and Villapol, S},
title = {Antibiotic-induced gut microbiome remodeling reduces neuroinflammation in traumatic brain injury.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41741786},
issn = {2399-3642},
support = {R56AG080920//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; EF-2126387//NSF | BIO | Division of Emerging Frontiers (EF)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Brain Injuries, Traumatic/drug therapy/microbiology/complications ; *Anti-Bacterial Agents/pharmacology ; Male ; Mice ; *Neuroinflammatory Diseases/drug therapy/prevention &amp; control/microbiology/etiology ; Mice, Inbred C57BL ; Dysbiosis/drug therapy ; Fatty Acids, Volatile ; },
abstract = {Traumatic brain injury induces neuroinflammation and gut microbiome dysbiosis, yet the effects of short-term antibiotic treatment on these processes remain poorly understood. To address this, male mice received controlled brain injuries followed by a brief course of oral antibiotics. Antibiotic treatment reduced bacterial abundance in feces and altered microbial diversity, with more pronounced shifts after two injuries. Despite this disruption, antibiotic-treated mice exhibited smaller lesion volumes, reduced cell death, attenuated microglial and macrophage activation, lower pro-inflammatory cytokine levels, and decreased astrogliosis and peripheral immune cell infiltration compared with vehicle-treated mice after two injuries. In the gut, increasing injury severity was associated with villus shortening and loss of mucus-producing cells, and antibiotic treatment further modified these injury-related changes. Circulating levels of short-chain fatty acids and associated microbial metabolic functions were reduced by antibiotic exposure. In contrast, germ-free mice showed increased lesion volumes and exacerbated gliosis following brain injury. Long-read metagenomic sequencing identified Parasutterella excrementihominis and Lactobacillus johnsonii as taxa that persisted despite antibiotic treatment. Collectively, these results suggest that antibiotics can reduce brain damage after injury through mechanisms not explained by short-chain fatty acids, while also highlighting potential drawbacks of altering the gut microbiome.},
}
@article {pmid41742321,
year = {2026},
author = {Mazzoni, C and Ochana, BL and Orlanski-Meyer, E and Ya'acov, AB and Focht, G and Harpenas, E and Shmorak, S and Ledder, O and Lev-Tzion, R and Shemer, R and Shteyer, E and Dor, Y and Yassour, M},
title = {Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41742321},
issn = {2049-2618},
mesh = {Humans ; *Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; Child ; Adult ; Female ; Male ; Adolescent ; Metagenomics/methods ; Young Adult ; Middle Aged ; DNA Methylation ; *Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Child, Preschool ; Cohort Studies ; Sequence Analysis, DNA ; Israel ; Netherlands ; Inflammation/microbiology ; },
abstract = {BACKGROUND: Feces represent a complex biological matrix that provides valuable information about intestinal physiology and gut microbial activity. Comprehensive fecal DNA sequencing is mostly utilized as a non-invasive way to profile the gut microbiome, and both clinical practice and research on inflammatory bowel diseases (IBD) would greatly benefit from accurate and non-invasive methods to monitor gut inflammation in IBD patients. In IBD, excessive immune cell recruitment and epithelial cell shedding in the gut increase the amount of human DNA in feces, making fecal DNA profiling a desirable approach to monitor gut inflammation dynamics.<br><br>METHODS: We used a combination of sequencing techniques to comprehensively characterize the fecal DNA diversity in a newly established cohort of pediatric IBD patients and controls (Pediatric cohort, N&#x2009;=&#x2009;134 children, Israel). We performed methylation-based human cell-specific profiling together with shotgun metagenomics to characterize the human and the microbial DNA content in feces, respectively. Moreover, we included a large complementary external cohort including adult IBD patients and controls (Adult cohort, N&#x2009;=&#x2009;689 adults, the Netherlands), not only to compare microbial patterns across the age spectrum, but also to extend our findings from the methylation-based profiling to the more broadly-available quantification of human DNA in metagenomic sequencing.<br><br>RESULTS: We found that neutrophil DNA dominates fecal human DNA content in IBD patients, and our measurements were highly correlated with fecal calprotectin levels. Combining neutrophil and other cell type DNA fractions in one metric was able to distinguish between remissive and active cases of IBD. Human reads percentage by metagenomics was well correlated with disease severity and species richness, which had distinct trends in CD and UC over time. We used a combination of species richness, human DNA percentage, and microbiome composition data to predict IBD and distinguish CD from UC in both adult and pediatric IBD cohorts.<br><br>CONCLUSIONS: The comprehensive characterization of human and microbiome fecal DNA is a useful approach to track immune response level and investigate the interaction that the immune system has with gut microbiome richness and composition over time, enriching opportunities for better disease monitoring and thus better treatment of IBD patients. Video Abstract.},
}
@article {pmid41860568,
year = {2026},
author = {Zhang, Y and Wu, Y and Li, X and Ren, T and Zhang, H and Chen, J},
title = {Klebsiella enrichment is associated with disease severity in ulcerative colitis.},
journal = {Journal of applied microbiology},
volume = {137},
number = {4},
pages = {},
doi = {10.1093/jambio/lxag079},
pmid = {41860568},
issn = {1365-2672},
mesh = {Humans ; *Colitis, Ulcerative/microbiology/pathology ; Female ; Feces/microbiology ; Male ; Adult ; Prospective Studies ; Middle Aged ; Severity of Illness Index ; *Gastrointestinal Microbiome ; *Klebsiella/isolation &amp; purification/genetics ; Intestinal Mucosa/microbiology ; Metabolomics ; Young Adult ; Aged ; },
abstract = {BACKGROUND AND OBJECTIVE: Ulcerative colitis (UC), a chronic inflammatory bowel disease. This study uniquely undertook a parallel, severity-stratified comparison of both fecal and mucosal microbiota and metabolites in UC patients. Our objective was to identify niche-specific (fecal vs. mucosal) and severity-associated microbial and metabolic signatures, clarifying its potential clinical utility.<br><br>METHODS: A prospective cohort study (ChiCTR2300071816) enrolled 83 UC patients (&#x2265;18 years) from the First Affiliated Hospital of Nanjing Medical University and Northern Jiangsu People's Hospital (Jan 2022-Dec 2024) and 30 healthy controls. Clinical data, stool, and rectal mucosal samples were collected. Metagenomic sequencing and metabolomics were performed. Disease severity was stratified by modified Mayo score to analyze microbiota diversity, differential genera, metabolites, and enriched metabolic pathways.<br><br>RESULTS: Fecal microbiota &#x3b1;-diversity was significantly lower in UC vs. controls (Shannon index 4.15&#xa0;vs. 5.44, P&#xa0;=&#xa0;0.005); mucosal diversity showed no difference (P&#xa0;=&#xa0;0.63). Beta diversity did not differ. Severe UC exhibited a non-significant decrease in &#x3b1;-diversity (fecal: 3.99&#xa0;vs. 4.37, P&#xa0;=&#xa0;0.14; mucosal: 3.40&#xa0;vs. 3.72, P&#xa0;=&#xa0;0.92), significantly higher fecal/mucosal Klebsiella abundance, and lower Erysipelatoclostridium and Blautia abundance vs. mild-to-moderate UC. Metabolomics identified 363 fecal differential metabolites (e.g. allopurinol, histidine), enriching tyrosine, and alanine/aspartate/glutamate metabolism pathways. Mucosal analysis revealed 127 differential metabolites (e.g. quinic acid, sphingosine), implicating sphingolipid metabolism and lysine synthesis.<br><br>CONCLUSION: UC demonstrates gut dysbiosis and metabolic disruption correlating with severity. Elevated Klebsiella abundance suggests a pathogenic role in progression. Distinct fecal and mucosal metabolic pathway alterations provide novel insights for disease classification and therapeutic targeting.},
}
@article {pmid41862052,
year = {2026},
author = {Gunasekaran Rajalakshmi, S and K, RB and Viswanathan, P},
title = {Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR.},
journal = {Life sciences},
volume = {393},
number = {},
pages = {124336},
doi = {10.1016/j.lfs.2026.124336},
pmid = {41862052},
issn = {1879-0631},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Dysbiosis/microbiology ; Male ; *Renal Insufficiency, Chronic/microbiology ; Female ; Middle Aged ; *Metagenomics/methods ; *Diabetes Mellitus, Type 2/complications/microbiology ; RNA, Ribosomal, 16S/genetics ; Adult ; Aged ; Feces/microbiology ; Real-Time Polymerase Chain Reaction/methods ; },
abstract = {BACKGROUND: Type 2 diabetes (T2D) is a major contributor to diabetic nephropathy, the leading cause of chronic kidney disease (CKD). This study investigated gut microbial dysbiosis and composition shift among healthy individuals and diabetic patients with or without CKD using a 16S rRNA metagenomic approach, validated by qRT-PCR and clinical data integration to identify the significant key genera associated with disease progression.<br><br>METHODS: Stool samples from 22 individuals were analysed using 16S rRNA amplicon sequencing to assess gut microbiota composition. Differential abundance analysis, LEfSe, and network-based methods were employed to identify key taxa. Significant features were validated by qRT-PCR. Integrated approaches, including Pearson correlation, WGCNA, random forest, and propensity score matching, were used to associate microbial features with clinical markers. Functional enrichment of microbial pathways was predicted using PICRUSt2.<br><br>KEY FINDINGS: A total of 1409 amplicon sequence variants (ASVs) were identified. Bray-Curtis dissimilarity showed significant microbial diversity differences between disease and healthy subjects (p&#xa0;<&#xa0;0.031). Key taxa associated with eGFR and serum creatinine (sCr) included Bacteroidetes uniformis (LFC +9), Ruminococcus (LFC +8.1), and Dialister succinatiphilus (LFC +6.7), linked to disease progression and metabolic regulation. In contrast, protective taxa such as Bifidobacterium adolescentis (LFC -9.5), Faecalibacterium prausnitzii (LFC -6.39), Collinsella, and Megasphaera elsdenii were reduced. Integration of Pearson correlation, WGCNA, propensity score matching, and random forest classification revealed microbial features associated with clinical covariates.<br><br>SIGNIFICANCE: Our findings show the gut microbiome shifts begin in diabetics without CKD conditions but become more pronounced in diabetics with CKD, with a lower ratio of beneficial bacteria, reflecting a gradual microbial imbalance along disease progression.},
}
@article {pmid41922261,
year = {2026},
author = {Adebayo, AA and Babalola, OO},
title = {Rhizosphere Microbiome as an Underexplored Resource for Agroecosystem Sustainability: Insights From the Carrot Root Zone.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70325},
doi = {10.1111/1758-2229.70325},
pmid = {41922261},
issn = {1758-2229},
support = {CRP/ZAF22-93//International Centre for Genetic Engineering and Biotechnology/ ; },
mesh = {*Daucus carota/microbiology/growth &amp; development ; *Rhizosphere ; *Plant Roots/microbiology ; *Microbiota ; *Soil Microbiology ; Agriculture ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; },
abstract = {Rhizosphere microbiome is critical for nutrient turnover, pathogen suppression, and stress modulation, forming the basis of microbial products relevant to agriculture. However, microbial communities associated with carrot root zone remain relatively underexplored, with limited studies focused beyond descriptive surveys. Here, we synthesise existing information on the structural, functional, and ecological dynamics of the carrot rhizomicrobiome, highlighting its emerging yet underdeveloped mechanistic profiling. Existing literature indicates that carrot-associated microbes may play a role in nutrient mobilisation, growth promotion, and antagonism. The early proof-of-concept works demonstrate that the microbes may gain potential applications in biofertilizers, biostimulants, and biocontrol agents. While these functions are strongly influenced by soil properties, genotype, and management, only a few carrot-specific isolates/consortia have been multi-environmentally validated. The limited progress partly reflects the overall underrepresentation of vegetables in microbiome-based studies, compared to other major crops. We explored the key characteristics, economic, and agricultural significance of the carrot rhizosphere, highlighting its richness with beneficial microorganisms. Among the gaps identified are inadequate functional-level and field trial, and insufficient multi-omics integration, which currently limit biotechnological translation. Addressing these gaps through targeted isolation, mechanistic functional and field validation could position carrot rhizosphere microbiome as a valuable yet underexplored resource for enhancing agroecosystem sustainability.},
}
@article {pmid41922337,
year = {2026},
author = {Doni, L and Trinanes, J and Bosi, E and Vezzulli, L and Martinez-Urtaza, J},
title = {Deciphering the Hidden Ecology and Connectivity of Vibrio in the Oceans.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71231-3},
pmid = {41922337},
issn = {2041-1723},
abstract = {Long-range dispersals of marine bacteria in the oceans have remained largely indecipherable, which is particularly relevant for Vibrio, responsible for global epidemics in humans and animals. Here, we combine the analysis of 40 terabases of metagenomic data and satellite-tracked surface drifter data, from across the globe revealing that Vibrio are abundant members of the ocean surface and show a strong association with microplankton, which appears to govern their distribution and connectivity at a global scale. We identify long-distance biological corridors connecting Vibrio communities, including potentially pathogenic Vibrio. These corridors allow movement over thousands of kilometres in a fairly short time, with estimates of less than 1.5 years to cross an ocean basin. These findings have deep implications for the demography and community dynamics of Vibrio species and the epidemiology of associated diseases.},
}
@article {pmid41923466,
year = {2026},
author = {King, Z and Buckley, HL and Lear, G and Seale, B and Lee, KC and Schwendenmann, L and Lacap-Bugler, DC},
title = {Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70324},
doi = {10.1111/1758-2229.70324},
pmid = {41923466},
issn = {1758-2229},
support = {C09X1817//New Zealand's Biological Heritage/ ; //Ministry of Business, Innovation and Employment/ ; },
mesh = {*Phytophthora/genetics/isolation &amp; purification ; *Soil Microbiology ; New Zealand ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Forests ; *Microbiota ; Plant Diseases/microbiology/parasitology ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Nucleic Acid Amplification Techniques ; Phylogeny ; },
abstract = {Soil-borne pathogens can influence microbial communities and ecosystem function, making it important to understand their broader ecological impacts. We investigated interactions between Phytophthora agathidicida (the causal agent of kauri tree dieback) and soil microbial communities, while also comparing detection and community-profiling methods. Soils from 60 kauri trees across three sites in the Waitākere Ranges, New Zealand, were analysed using loop-mediated isothermal amplification (LAMP) for pathogen detection, and 16S rRNA gene/ITS gene amplicon sequencing alongside shotgun metagenomics for community characterisation. LAMP detected P. agathidicida in 39/60 samples, while shotgun sequencing detected Phytophthora-associated DNA at low abundance across all samples. Microbial community structure and functional potential showed weak association with pathogen presence, though differential abundance testing identified several genera enriched in pathogen-detected soils, including taxa previously linked to disease suppression. Amplicon and shotgun profiles indicated broadly comparable patterns at higher taxonomic and functional levels, while differences between approaches emerged primarily at finer taxonomic resolution. Importantly, functional predictions from PICRUSt2 closely matched shotgun-derived profiles at broader scales, indicating its suitability as a cost-effective tool for broad-scale monitoring. These findings suggest limited direct pathogen effects on microbial communities and highlight how integrating molecular approaches provides complementary insights into soil microbiome-pathogen interactions.},
}
@article {pmid41923582,
year = {2026},
author = {Menezes, GA and Sekar, P and Akhter, A and Tayade, KD and Fathima, S and Hussain, ZFZ and Nigam, A},
title = {Gut Microbiota and Dyslipidemia in Type 2 Diabetes: A Pilot Study of 16S rRNA Profiles and Predicted Functional Shifts.},
journal = {Journal of diabetes research},
volume = {2026},
number = {1},
pages = {e9317962},
doi = {10.1155/jdr/9317962},
pmid = {41923582},
issn = {2314-6753},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology/complications/blood ; Pilot Projects ; Middle Aged ; *Dyslipidemias/microbiology/blood ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; Aged ; Adult ; Bacteria/genetics/classification ; },
abstract = {Hyperlipidemia is a major, modifiable driver of global cardiovascular risk. The intestinal microbiota, comprising bacteria, archaea, fungi, and viruses, modulates lipid metabolism through bile acid transformation, energy harvest, and inflammatory signaling. This study profiled the gut microbiota of 15 adults with type 2 diabetes mellitus (T2DM) and explored associations with fasting lipid measures using 16S rRNA gene sequencing (V3-V4 region) on the Illumina MiSeq platform and PICRUSt2 functional prediction. Overall α-diversity was reduced, and community composition was dominated by Firmicutes and Actinobacteria with relative depletion of Bacteroidetes. At lower taxonomic ranks, enrichment of Prevotella copri, Collinsella spp., Ruminococcus spp., and selected Bifidobacterium spp. was observed, alongside depletion of short-chain fatty acid (SCFA)-linked taxa, including Akkermansia muciniphila, Lactobacillus plantarum, and members of the Bacteroides and Parabacteroides lineages. Exploratory within-cohort trends indicated that higher triglycerides (TGs) and lower HDL-C tended to co-occur with increased Collinsella and clostridial signals and reduced SCFA-associated taxa. Predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog functions suggested shifts in lipid, carbohydrate, and secondary bile acid metabolism, consistent with a metabolically activated and proinflammatory intestinal milieu. In this single-arm cohort of adults with T2DM, a low-diversity, Firmicutes/Actinobacteria-weighted microbiome with depletion of SCFA-linked taxa paralleled an atherogenic lipid profile, supporting an association between gut microbial dysbiosis and lipid abnormalities in adults with T2DM. These findings suggest the potential of microbiota-informed adjuncts, including dietary fermentable fiber, targeted probiotics and next-generation biotherapeutics, and bile-acid-modulating strategies as supportive approaches to lipid management in T2DM. This was a pilot, single-arm, exploratory study without a nondiabetic control group, and findings should be interpreted as hypothesis-generating. Nevertheless, the cross-sectional design, small sample size, and 16S-based taxonomic resolution limit causal interpretation. Larger, longitudinal studies integrating shotgun metagenomics and metabolomics are needed to confirm these associations, validate biomarkers, and elucidate mechanistic pathways that could guide precision interventions for diabetic dyslipidemia.},
}
@article {pmid41679750,
year = {2026},
author = {Lamont, RF and Jørgensen, JS},
title = {The Influence of the Vaginal Microbiome on the Prediction and Prevention of Preterm Birth.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {133},
number = {6},
pages = {1129-1146},
doi = {10.1111/1471-0528.70173},
pmid = {41679750},
issn = {1471-0528},
mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Premature Birth/prevention &amp; control/microbiology ; *Microbiota ; *Vaginosis, Bacterial/microbiology/complications/drug therapy ; *Dysbiosis/complications/microbiology ; Probiotics/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: Spontaneous preterm labour that leads to preterm birth is known to be associated with vaginal dysbiosis, particularly bacterial vaginosis, and this may explain why progress has been slow in the last few decades. Bacterial vaginosis was considered enigmatic with unknown aetiology, difficulty in diagnosis, different response to treatment, be that persistence or recurrence, and different phenotypic outcomes.<br><br>METHODOLOGY: A narrative review.<br><br>RESULTS: New information from the Human Microbiome Project using molecular-based, culture-independent technology has added important new knowledge to our understanding of vaginal eubiosis and dysbiosis. While this metagenomics are currently mainly research tools, we hope further studies will better elucidate the full profile of dysbiosis. This will hopefully aid the choice of antibiotic to suit each dysbiotic profile identified rather than for a single organism. By measuring abundance and diversity of the vaginal microbiome, we can develop molecular means of differentiating eubiosis and dysbiosis to predict preterm birth. We can also choose which antibiotic is appropriate for different dysbiotic subtypes, the local subtype of milieu created by that microbiota, the host response, and the phenotypical outcomes of which preterm birth is paramount. In addition, we can develop suitable probiotic species of lactic acid producing bacteria to aid in the prevention of preterm birth.},
}
@article {pmid41770016,
year = {2026},
author = {Silva, JM and Martins, I and Almeida, JR},
title = {HYMET: a hybrid metagenomic pipeline for accurate and efficient taxonomic classification.},
journal = {GigaScience},
volume = {15},
number = {},
pages = {},
doi = {10.1093/gigascience/giag024},
pmid = {41770016},
issn = {2047-217X},
support = {UID/00127/2025//FCT/ ; 101081813//European Commission/ ; },
mesh = {*Metagenomics/methods ; Humans ; Metagenome ; *Software ; Gastrointestinal Microbiome/genetics ; Computational Biology/methods ; },
abstract = {BACKGROUND: Reliable taxonomic classification of metagenomic sequences remains constrained by high mutation rates, fragmented assemblies, and large heterogeneous reference databases. HYMET (Hybrid Metagenomic Tool) was developed to overcome these challenges through a 2-stage hybrid design combining adaptive Mash-based screening with Minimap2 alignment and a coverage-weighted Lowest Common Ancestor classifier. Its sample-adaptive thresholds and on-the-fly reference database construction enable efficient, domain-agnostic classification while maintaining accuracy across divergent genomes.<br><br>RESULTS: Across 7 CAMI assembly datasets in contig mode, HYMET achieved a mean F1 of 83.89%, with genus-level F1 of 76.75% and species-level F1 of 60.18%, while averaging 115.93&#x2009;s runtime and a mean peak memory of 6.24&#x2009;GB. Performance remained stable under mutation rates up to 30% for most domains (F1 $\ge$ 0.8), with viral sequences showing the expected decline (F1 $\approx$ 0.5 at 30%). Read and contig inputs produced nearly identical results when sharing reference caches, and real-world datasets confirmed robustness with the human gut metagenome, which reproduced typical anaerobic profiles, while in the ZymoBIOMICS mock community, HYMET recovered all bacterial members; a further ground-truth evaluation on the ZymoBIOMICS Gut Microbiome Standard (D6331) yielded near-perfect genus-level concordance (Pearson $r = 0.998$, Bray-Curtis $= 0.04$) across bacteria, fungi, and archaea.<br><br>CONCLUSIONS: HYMET achieves a practical balance of accuracy, efficiency, and scalability for metagenomic classification. Its adaptive candidate selection, alignment-anchored taxonomy, and reproducible reference caching collectively enhance performance across domains. HYMET source code is fully available at https://github.com/ieeta-pt/HYMET.},
}
@article {pmid41865821,
year = {2026},
author = {Wang, X and Liang, BJ and Wu, DN and Zhang, XM and Zhao, HP and Lai, CY},
title = {Efficient anaerobic metformin biodegradation driven by a Cross-Feeding Consortium: Novel Pathways, Enzymes, and toxicity dynamics.},
journal = {Bioresource technology},
volume = {450},
number = {},
pages = {134473},
doi = {10.1016/j.biortech.2026.134473},
pmid = {41865821},
issn = {1873-2976},
mesh = {*Metformin/metabolism/toxicity ; Biodegradation, Environmental ; Anaerobiosis ; Bioreactors/microbiology ; *Microbial Consortia ; },
abstract = {Metformin is one of the most widely prescribed antidiabetic drugs worldwide and is now ubiquitously detected in aquatic environments, yet its anaerobic biodegradation remains largely unexplored and mechanistically unresolved. Here, an anaerobic membrane bioreactor (AnMBR) was operated and near-complete metformin removal (∼98%) at influent concentrations up to 5.3 mg/L was achieved, corresponding to a maximum degradation rate of 7.2 mg/L/d, approximately sixfold higher than previously reported anaerobic systems degrading metformin. High-resolution mass spectrometry identified three concurrent anaerobic metformin transformation pathways. Notably, a previously unreported biological -C-N bond cleavage route yielding dimethylguanidine was discovered, expanding the known anaerobic metabolic repertoire of metformin. In silico toxicity prediction revealed a non-monotonic toxicity trajectory during metformin transformation, with transiently elevated toxicity at intermediates (particularly 2,4-AMT) followed by an overall attenuation at the terminal product guanidine. Metagenomic and metatranscriptomic analyses uncovered a cooperative, cross-feeding microbial network dominated by Ignavibacterium album and Denitrolinea symbiosum, and identified HypAB (metformin-to-guanylurea), YafV and AmiA/B/C/E (guanylurea-to-guanidine), and, critically, SpeB as the key enzyme initiating the newly proposed -C-N bond cleavage pathway. Molecular dynamics simulations further suggested stable binding of metformin to SpeB with strong affinity, providing mechanistic support for SpeB-mediated initiation of the novel pathway. Overall, this study establishes the first mechanistic framework for anaerobic metformin biodegradation, reveals an unprecedented -C-N scission pathway, and demonstrates that high-rate, low-carbon pharmaceutical removal can be achieved through intrinsic microbial metabolism, offering new conceptual and practical foundations for energy-efficient treatment of emerging pharmaceutical contaminants.},
}
@article {pmid41875745,
year = {2026},
author = {Zhang, H and Li, B and Ni, R and Ye, L and Bai, G and Zhao, J},
title = {Stable functional consortium assembly via uncoupled SAD/anammox inoculation drives synergistic nitrogen‑sulfur removal in sediment.},
journal = {Water research},
volume = {297},
number = {},
pages = {125768},
doi = {10.1016/j.watres.2026.125768},
pmid = {41875745},
issn = {1879-2448},
mesh = {*Geologic Sediments/chemistry ; *Nitrogen ; *Sulfur/metabolism ; Denitrification ; Oxidation-Reduction ; Ammonia/metabolism ; Microbial Consortia ; Autotrophic Processes ; Nitrates ; },
abstract = {The remediation of black‑odorous sediments remains challenging due to the intricate sediment matrix, the co-occurrence of multiple pollutants, and the difficulty in maintaining stable functional microbial consortia under fluctuating redox conditions. Although calcium nitrate (CN) is a used chemical oxidant, its sole application often results in incomplete nitrogen removal and risks of secondary pollution. While the integration of CN with sulfur-autotrophic denitrification (SAD) and anaerobic ammonia oxidation (anammox) presents a promising alternative, the microbial, especially concerning the assembly and efficacy of different microbial inoculation strategies, are poorly understood. This study systematically compared two distinct bioaugmentation approaches: the pre-coupled addition of a SAD and anammox consortium versus an uncoupled strategy involving separate additions of SAD and anammox consortium, both in combination with CN. Results demonstrated that the CN+S+A (uncoupled) treatment achieved optimal performance, enhancing the removal of NH4[+], NO3[-], and total nitrogen by 42%, 40%, and 35%, respectively, compared to CN alone, while also effective oxidizing acid‑volatile sulfide. Mechanistic analysis revealed that CN first optimized the sediment microenvironment. The uncoupled inoculation uniquely fostered a stable, dual-core microbial consortium dominated by Thiobacillus (3.00%) and Candidatus Brocadia (0.83%), which established a sustainable "sulfur-driven nitrogen removal" cycle. Metagenomic and isotopic tracing confirmed the enrichment of key functional genes and elevated process rates underpinning this synergy. These findings highlight that CN combined with uncoupled bioaugmentation is a novel and effective strategy for rebuilding stable nitrogen-sulfur cycles in black-odorous sediments.},
}
@article {pmid41896653,
year = {2026},
author = {Zhao, Z and Yang, Y and Zhang, L and He, X and Ding, K and Chen, Y and Huo, Y and Li, P and Li, R and Ali, T and Zhao, D and Choe, H and Ma, J and Shang, D and Zhang, L},
title = {Multi-omics and network pharmacology reveal the mechanisms of Scutellaria barbata D.Don and Scleromitrion diffusum (Willd.) R.J.Wang against pancreatic cancer.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41896653},
issn = {2045-2322},
support = {2022-BS-244//Liaoning Provincial Doctoral Research Startup Fund Project/ ; XLYC1907113//Liaoning Revitalization Talents Program/ ; 2022RJ19//Distinguished Young Scholars in Dalian/ ; },
mesh = {Humans ; Animals ; *Scutellaria/chemistry ; *Pancreatic Neoplasms/drug therapy/metabolism/pathology ; Mice ; Network Pharmacology/methods ; Cell Line, Tumor ; Apoptosis/drug effects ; *Plant Extracts/pharmacology ; Xenograft Model Antitumor Assays ; Mice, Nude ; Cell Proliferation/drug effects ; Gastrointestinal Microbiome/drug effects ; Cell Survival/drug effects ; Cell Movement/drug effects ; *Antineoplastic Agents, Phytogenic/pharmacology ; Proteomics ; Metabolomics/methods ; Multiomics ; },
abstract = {Pancreatic cancer (PC) is a common gastrointestinal malignancy whose initiation and progression may be closely linked to the gut microbiota. Previous research indicates that Scutellaria barbata D. Don and Scleromitrion diffusum (Willd.) R.J. Wang (SB-SD) exhibit diverse biological activities, such as anti-inflammatory, antioxidant, and antitumor effects, though their precise regulatory mechanisms are not fully elucidated. Here, we treated PC cells with SB-SD to assess its impact on cell viability, apoptosis, migration, and cell cycle progression, while Western blotting analyzed the expression of HSP90AA1, MAPK3, p53, CDK1, and p21. We also established a pancreatic cancer xenograft model in nude mice to evaluate the in vivo inhibitory effect of SB-SD on tumor growth. Furthermore, we employed metagenomic sequencing, untargeted metabolomics, and quantitative proteomics to comprehensively profile changes in the gut microbiota, serum metabolites, and differentially expressed proteins, with Western blotting subsequently validating BCKDK, GATM and p53 expression. The results show that SB-SD significantly inhibited PC cell proliferation, promoted apoptosis, and induced S/G2 phase cell cycle arrest, potentially via modulation of the HSP90AA1/MAPK3 signaling pathway. Measurements of tumor volume and weight, complemented by histopathological analysis, confirmed that SB-SD effectively suppressed the growth of PANC-1 xenograft tumors. Integrated multi-omics analyses suggest that the antitumor effects of SB-SD may involve the modulation of key gut microbes like Bacteroides caccae and Lactobacillus, the promotion of choline metabolism, and the regulation of BCKDK and GATM. Together, these findings not only corroborate the direct antitumor activity of SB-SD against pancreatic cancer but also offer novel mechanistic insights by constructing a microbiota-metabolite-protein interaction network.},
}
@article {pmid41914171,
year = {2026},
author = {Yildirim, EA and Laptev, GY and Tiurina, DG and Filippova, VA and Ilina, LA and Novikova, NI and Sokolova, KA and Ponomareva, ES and Brazhnik, EA and Zaikin, VA and Klyuchnikova, IA and Bolshakov, VN and Korochkina, EA and Vorobyov, NI and Griffin, DK and Romanov, MN},
title = {Compositional and Functional Metabolic Shifts in the Endometrial Microbiota of Cows (Bos taurus) During the Transition Period: A Metagenomic Next-Generation Sequencing Approach.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {18},
number = {1},
pages = {39439},
doi = {10.31083/FBE39439},
pmid = {41914171},
issn = {1945-0508},
support = {24-16-00131//Russian Science Foundation/ ; },
mesh = {Animals ; Female ; Cattle/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; },
abstract = {BACKGROUND: Significant alterations in feeding, housing, and physiology are observed in dairy cows during the transition period (3 weeks pre- and post-calving), in addition to changes in the composition and abundance of the endometrial microbiota. Thus, this study aimed to evaluate any changes in the composition and predicted metabolic pathways in the cow uterine microbiome during this transition period.<br><br>METHODS: Scrapings were sampled from the endometrial surface of clinically healthy cows (n = 3) in dynamics as follows: in the 10 Days period before, and on Days 3, 5, and 20 after calving. Total DNA was isolated from the samples, and the composition of the microbial community was assessed using targeted next-generation sequencing (NGS) technology. Based on the subsequent NGS data, the dynamics of the predicted metabolic pathways of the microbiota were evaluated.<br><br>RESULTS: Seven superphyla and phyla of microorganisms were found in the endometrial microbiota of cows during the transition period. Among these, the phylum Firmicutes (with a dominant class of Clostridia) and the superphylum Fusobacteriota (represented by a single class of Fusobacteriia) can be considered the dominant bacteria in the endometrium, with representation noted from 25.2 to 68.2% and from 12.3 to 51.1%, respectively. The microbiome composition underwent significant changes (p < 0.05) during the transition period. In particular, the high abundance of the Fusobacteriaceae family (up to 68.2%) in the uterus of clinically healthy cows was unexpected, given the potential association of Fusobacteriaceae with the occurrence of metritis in cows. The numbers of microorganisms in two dominant classes, Fusobacteriia and Clostridia, showed generally opposite changes in their relative abundance during the transition period. The predicted functional potential level for 32 pathways in the endometrium changed (p < 0.05) in cows during the transition period. Indeed, the activity of the predicted pathways, such as pyridoxal 5'-phosphate biosynthesis I and teichoic acid (poly-glycerol) biosynthesis, was lowered on day 3 postpartum (p < 0.05).<br><br>CONCLUSIONS: Microbiota composition and the activity of the predicted metabolic pathways in the cow endometrium underwent significant changes at different critical stages in the transition period. Moreover, even clinically healthy cows exhibited signs of dysbiotic disorders.},
}
@article {pmid41917109,
year = {2026},
author = {Foresto, L and Radaelli, E and Leuzzi, D and Palladino, G and Scicchitano, D and Bejaoui, S and Turroni, S and Rampelli, S and Santolini, C and Pari, A and Marcellini, F and Danovaro, R and Corinaldesi, C and Candela, M},
title = {Metagenomic profiling reveals distinct signatures of pathogens, antibiotic-resistance genes and human viruses in urban river mouths of the north-western Adriatic coast.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45229-2},
pmid = {41917109},
issn = {2045-2322},
}
@article {pmid41918132,
year = {2026},
author = {Gao, L and Fang, BZ and Yang, J and Lian, ZH and Chen, Y and Mohamad, OAA and Xu, QY and Liu, YH and Wu, D and Yuan, Y and Abdugheni, R and Li, MM and Wang, P and Ortúzar, M and Li, XY and Huang, JR and Liu, L and Jiang, HC and Shu, W and Hedlund, BP and Li, WJ and Jiao, JY},
title = {Microbial decomposer diversity and metabolic function during the decomposition of brine shrimp carcasses in a saline lake.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02361-5},
pmid = {41918132},
issn = {2049-2618},
support = {2022B0202110001//Guangdong S&amp;T Program/ ; },
abstract = {BACKGROUND: Decomposition of brine shrimp carcasses has a crucial role in carbon cycling of saline lakes, yet the microbial dynamics remain poorly understood.<br><br>RESULTS: Here we integrated metagenomics, metatranscriptomics, culturomics, metabolomics, and microcosm experiments to investigate microbial community succession and function during brine shrimp (Artemia sp.) carcass decomposition in Barkol Lake, a hypersaline lake in China. A total of 149 metagenome-assembled genomes (MAGs) and 77 pure culture genomes were recovered across 33 phyla, with 72.12% genomes representing species-level novel lineages. Our results reveal diverse bacterial and archaeal taxa, including novel lineages from CG03, T1Sed10-126 and rare archaeal taxa (Asgardarchaeota, Thermoplasmatota, Nanoarchaeota, and Halobacteriota), involved in degradation of biomacromolecules-proteins, carbohydrates, lipids, and nucleic acids-via extracellular hydrolysis, nutrient transport, and intracellular catabolism. These taxa exhibit substrate preferences, rapidly responding to the breakdown of polysaccharides and proteins, followed by lipids and nucleic acids. Hydrolyzed oligomers are further oxidized by various microbes through fermentation, sulfate reduction, and methanogenesis via metabolic handoffs. Additionally, viral auxiliary metabolic genes (AMGs) further enhance microbial host functions, contributing to key ecological processes such as carbon cycling and stress response. A temporally structured microbial decomposer network (MDN) was observed, driving mineralization cascades from fermentation to sulfate reduction and methanogenesis.<br><br>CONCLUSIONS: This study reveals microbial metabolic handoffs and virus-mediated modulation as critical mechanisms for organic matter turnover, expanding the known diversity and function of decomposers in saline ecosystems. Our findings offer new insights into biogeochemical processes in saline lakes and highlight a synergistic microbial decomposer network involving bacteria, archaea, and viruses that collectively drive nutrient cycling during brine shrimp carcass decomposition. Video Abstract.},
}
@article {pmid41918874,
year = {2026},
author = {Su, X and Yang, J and Le, Z and Xiao, J and Zhao, D},
title = {Integrative multi-omics analysis reveals probiotic-induced microbiota shifts in women with gestational diabetes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1782744},
pmid = {41918874},
issn = {2235-2988},
mesh = {Humans ; Female ; *Probiotics/administration &amp; dosage ; *Diabetes, Gestational/microbiology ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; Adult ; Metabolomics/methods ; Metagenomics ; Multiomics ; },
abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) is a common pregnancy disorder. It is associated with impaired glucose tolerance and insulin resistance, increasing the potential risks for both maternal and fetal complications. GDM is associated with an increased risk of type 2 diabetes later in life. Management is a big issue in maternal health. New work has underscored the role of the gut microbiota in metabolism and immune function. This indicates that probiotics might exert their mode of action through modulating the microbiota and controlling metabolism.<br><br>METHODS: This study employs a multi-omics strategy to assess the impact of probiotic administration on gut microbiota composition, metabolomic profiles, and host gene expression in GDM women. Women with GDM received probiotics for 8 weeks. Metagenomic sequencing quantified alterations of gut microbiota composition and LC-MS provided untargeted metabolomics in serum and urine. Gene expression was analyzed by qRT-PCR in reference to other physiological factors such as insulin signaling, inflammation, oxidative stress, and gut barrier. Data integration was performed using Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and network analysis, then pathway enrichment analysis was conducted with KEGG and MetaboAnalyst.<br><br>RESULTS: The supplementation of probiotics resulted in a significant change of gut microbiota (Lactobacillus 7.6-fold; Bifidobacterium 6.4-fold). Escherichia/Shigella was reduced. The amounts of short-chain fatty acids (SCFAs), especially butyrate and acetate, were increased 3.1 fold and 2.5 fold, respectively. In a gene expression assessment, the insulin receptor and AKT increased 2.5- and 1.9-fold higher, respectively, indicating greater insulin sensitivity. Levels of TNF-&#x3b1; and IL-6 decreased; however, genes related to gut barrier function (ZO-1, CLDN1) increased.<br><br>DISCUSSION: The administration of probiotic has a great impact on gut microbiome, metabolic activity, and host gene expression in women with GDM. Our data indicate that probiotics may represent a non-invasive and safe treatment for gestational diabetes through enhancing insulin sensitivity, anti-inflammatory environment, and gut health status. Larger confirmatory studies are needed to corroborate these findings and augment future clinical application of probiotics in GDM patients.},
}
@article {pmid41136135,
year = {2026},
author = {Du, R and Li, X and Xu, Y and Jing, K and Ao, L and Deng, B and Xu, Q and Song, P and Yu, J},
title = {Metagenomics reveals potential antimicrobial peptides in Chinese baijiu fermentation.},
journal = {Food microbiology},
volume = {134},
number = {},
pages = {104918},
doi = {10.1016/j.fm.2025.104918},
pmid = {41136135},
issn = {1095-9998},
mesh = {Metagenomics ; Fermentation ; Food Microbiology ; *Fermented Beverages/microbiology ; *Antimicrobial Peptides/biosynthesis/chemistry/pharmacology ; Cell Line, Tumor ; Phylogeny ; Genome, Bacterial ; Microbiota ; Genome, Archaeal ; Cell Survival/drug effects ; Bacterial Proteins/chemistry/metabolism ; Escherichia coli/drug effects ; Molecular Docking Simulation ; },
abstract = {Antimicrobial peptides (AMPs) from food fermentation microbiota hold promise for food preservation and as potential antimicrobial agents. However, the biosynthetic potential of AMPs in food fermentations remains largely unclear. Here, using Chinese baijiu fermentation as a model, we provided a workflow for AMP mining by combining metagenomics and machine learning. We recovered 389 metagenome-assembled genomes (MAGs) spanning both bacteria and archaea from 18 fermented samples. In total, 414 AMPs, including 290 novel AMPs, were predicted in 59.38 % of these MAGs using a machine learning model. Correlation network analysis showed that AMP-producing microorganisms potentially mediated negative microbial interactions. We selected ten AMPs for experimental validation, and eight AMPs exhibited antimicrobial activity against five human pathogens and two food spoilage microorganisms. One peptide, AMP_22, showed a broad-spectrum activity (all seven test strains) with high potency (MIC = 3.06-200 μg/mL) and cytotoxicity was not observed below 25 μg/mL using HepG2 and A549 cell lines. We further investigated the antimicrobial mechanism of AMP_22 using Escherichia coli as a model. Treatment with AMP_22 caused severe damage to the bacterial cell membrane, inhibited intracellular protein synthesis, and led to a significant accumulation of reactive oxygen species (ROS). Furthermore, molecular docking analysis indicated that AMP_22 can bind to DNA gyrase and dihydrofolate reductase via hydrogen bonding. This study highlights the potential of food-derived AMPs for application as preservatives and antimicrobial agents.},
}
@article {pmid41476057,
year = {2025},
author = {Wu, Y and Wong, O and Chen, S and Wang, Y and Lu, W and Cheung, CP and Ching, JYL and Cheong, PK and Chan, S and Leung, P and Chan, FKL and Su, Q and Ng, SC},
title = {Distinct diet-microbiome associations in autism spectrum disorder.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41476057},
issn = {2041-1723},
mesh = {*Autism Spectrum Disorder/microbiology ; Humans ; Female ; Male ; Child ; *Gastrointestinal Microbiome/genetics/physiology ; *Diet/adverse effects ; Feces/microbiology ; Child, Preschool ; Adolescent ; Food Additives/adverse effects ; Metagenomics ; },
abstract = {Autism spectrum disorder (ASD) is linked to both altered gut microbiota and unhealthy diets; however, the mechanistic connections remain elusive. In this study, we conducted a systematic analysis of fecal microbiome metagenomic data, paired with granular dietary assessments and phenotypic profiles, across a cohort of 818 children (462 with ASD, 356 without ASD; mean age = 8.4 years; 27.3% female). By integrating dietary indices, nutrient intake, and food additive exposures, we uncovered ASD-specific linkages to the microbiome. Poor dietary quality correlated with aggregated core autistic symptoms, gastrointestinal complications, and atypical eating behaviors. Notably, children with ASD exhibited a more pronounced diet-microbiome interaction network compared to neurotypical peers, suggesting heightened microbial sensitivity to nutritional inputs. Furthermore, synthetic emulsifiers-specifically polysorbate-80 and carrageenan-were associated with disrupted microbial connectivity in ASD, a phenomenon attenuated in neurotypical children. Our findings elucidate the mechanistic links between dietary factors-particularly synthetic food additives-and microbiome dysregulation in ASD, urging a re-evaluation of dietary guidelines for ASD populations and laying the groundwork for personalized nutritional strategies.},
}
@article {pmid41711071,
year = {2026},
author = {Boeckel, C and Lisovski, S and Stoof-Leichsenring, KR and Weiß, JF and Liu, S and Harms, L and Herzschuh, U},
title = {DNA virus-host patterns in lake and marine environments over the last glacial cycle.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag025},
pmid = {41711071},
issn = {1751-7370},
support = {//International Science Program for Integrative Research/ ; 772852/ERC_/European Research Council/International ; },
mesh = {*Lakes/virology/microbiology ; *DNA Viruses/genetics/classification/isolation &amp; purification/physiology ; *Geologic Sediments/virology ; Bacteria/virology ; Archaea/virology ; *Seawater/virology/microbiology ; Ecosystem ; DNA, Ancient/analysis ; Siberia ; Antarctic Regions ; Metagenomics ; Virome ; *Host Microbial Interactions ; },
abstract = {Viruses are integral to population dynamics, biogeochemical cycling, and host evolution, making them essential for ecosystem function. We explore long-term virus-host interactions mainly within microbial ecosystems in lake and marine environments across the late Pleistocene and Holocene. Sedimentary ancient DNA (sedaDNA) from five Siberian lakes and three Subarctic/Antarctic marine cores were analysed to infer past DNA virus taxa from metagenomic sequences. Viruses accounted for 357 161 reads (0.089% of total mapped reads), distributed across 2084 unique viral taxa. Virus communities differ between lakes and marine sites, with lakes dominated by Caudoviricetes and marine environments featuring Caudoviricetes and Algavirales. Each time series shows compositional changes from the Pleistocene to the Holocene, supporting sedaDNA as a tool to reconstruct time-resolved ancient viral assemblages. Among the most abundant viruses, we identified 83 virus-host pairs documented in published literature, spanning bacterial, archaeal, and eukaryotic hosts, and assessed their associations based on co-occurrence correlations. Over millennia, virus-host co-variations are particularly stable in marine systems, especially for phytoplankton-infecting viruses. However, in the Bering Sea, we find a lack of virus-host correlation, likely because an Arctic Pelagibacter strain expanded after the Bering Strait opened, potentially due to absent viral infection, although database limitations prevent clear interpretation. Antagonistic patterns also appear between bacteriophages and hosts, possibly linked to shifts between lytic and lysogenic cycles in response to environmental changes. This study demonstrates that sedaDNA time-series can reveal ancient viral community structures and long-term ecological patterns, highlighting the value of ancient viromes in understanding ecosystem-specific responses to environmental change.},
}
@article {pmid41789917,
year = {2026},
author = {Chen, D and Zhang, Z and Wang, S and Li, W and He, Y and Zhang, W and Sun, W and Chen, M and Zou, S and Qian, X},
title = {Differential assembly and functional roles of bacterial communities in coniferous and mixed conifer-broadleaf forest soils.},
journal = {mSphere},
volume = {11},
number = {3},
pages = {e0062725},
doi = {10.1128/msphere.00627-25},
pmid = {41789917},
issn = {2379-5042},
support = {202510389028//Fujian Agriculture and Forestry University/ ; S202510389078//Fujian Agriculture and Forestry University/ ; },
mesh = {*Soil Microbiology ; *Forests ; *Bacteria/classification/genetics ; *Tracheophyta/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; *Microbiota ; Metagenomics ; DNA, Bacterial/genetics ; },
abstract = {Forest soils harbor a diverse array of bacteria that play a crucial role in nutrient cycling. However, the differential effects of coniferous versus mixed conifer-broadleaf forests on the distribution of both abundant and rare bacterial taxa remain poorly understood. In this study, we integrated 16S rRNA gene amplicon sequencing with metagenomic shotgun sequencing to conduct a comparative analysis of soil bacterial communities in a conifer plantation and an adjacent mixed conifer-broadleaf forest, specifically examining their community structure, assembly mechanisms, co-occurrence networks, and functional potential. Both abundant and rare taxa showed significant differences in community composition between the two forest types. Soil pH and organic matter content significantly influenced the total and abundant bacterial communities, while available phosphorus and potassium were key determinants of rare community composition. Co-occurrence network analysis revealed that abundant communities formed highly clustered, simplified networks, contrasting with more fragmented and keystone-rich networks in rare communities. Null model analyses indicated that community assembly was largely driven by stochastic processes, with ecological drift accounting for about 80% of the variation in total and rare communities, and dispersal limitation explaining nearly 72% of the variation in abundant communities. Functional predictions indicated that bacterial communities in mixed forests were enriched in pathways linked to glycosylation, carbohydrate degradation, and nitrogen fixation, while coniferous forests favored pathways related to autophagy, signaling, and stress responses. This study highlights the complementary roles of abundant and rare bacterial taxa in forest soil ecosystems and underscores the importance of preserving mixed forests to sustain microbial functional diversity.IMPORTANCEForest soils host a complex web of common and rare bacteria that quietly regulate nutrient cycles. By comparing pure conifer stands with mixed conifer-broadleaf forests, we found that abundant species underpin essential functions while rarer microbes fill specialized niches. Acidity and nutrients strongly influence which bacteria thrive; mixed stands favored microbes that break down carbohydrates and fix nitrogen, whereas conifer soils supported organisms adapted to stress and nutrient-poor conditions. These findings emphasize the importance of preserving diverse forest ecosystems for soil health, carbon storage, and effective forest management strategies in climate change adaptation.},
}
@article {pmid41912482,
year = {2026},
author = {Shao, Y and Wang, J and Liu, Y and Ni, Y and Liu, Z and Li, Y and Jia, Q and Li, Q and Wang, X and Li, T and Liu, M and Zhang, S and Guo, Y and Guo, X and Wang, D and Liu, Y and Liu, C and Cai, H and Ning, Y and Zhang, J and Xu, G and Le, W},
title = {Distinct metabolomic and proteomic signatures in Parkinson's disease patients with REM sleep behavior disorder.},
journal = {Signal transduction and targeted therapy},
volume = {11},
number = {1},
pages = {},
pmid = {41912482},
issn = {2059-3635},
support = {82271524//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401742//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024RY003//Dalian Science and Technology Bureau/ ; No. 2023-MS-262//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; },
mesh = {Humans ; *Parkinson Disease/genetics/metabolism/complications/microbiology/pathology/blood ; Female ; Male ; *REM Sleep Behavior Disorder/genetics/metabolism/pathology/blood/complications/microbiology ; *Metabolomics ; Middle Aged ; Aged ; *Proteomics ; Gastrointestinal Microbiome/genetics ; },
abstract = {Rapid eye movement sleep behavior disorder (RBD) is the most specific prodromal marker of Parkinson's disease (PD), affecting 40-50% of PD patients. PD with RBD (RBD-PD) represents a clinically aggressive subtype characterized by more severe motor and nonmotor symptoms, prominent autonomic dysfunction, and accelerated disease progression; however, its underlying pathogenesis remains poorly understood. Here, we integrated multiplatform metabolomics and proteomics with precise clinical phenotyping to delineate molecular signatures in plasma across different PD subtypes. Our analyses demonstrated that PD patients exhibit significant metabolic reprogramming, characterized by a shift in energy metabolism from the tricarboxylic acid cycle toward glycolysis, a dysregulated urea cycle, and lipid remodeling, as well as extensive activation of inflammatory and immune responses involving the PI3K-Akt, IL-17, NF-kappaB, MAPK and TNF signaling pathways. Notably, the RBD-PD subgroup exhibited distinctive metabolic disturbances characterized by the accumulation of gut microbiota-derived toxic aromatic amino acid catabolites. Importantly, these alterations were also observed in idiopathic RBD (iRBD) patients, representing the prodromal stage of PD. By integrating metagenomic profiles, we further revealed that gut microbial dysbiosis in RBD-PD and iRBD drives a functional shift away from dietary fiber fermentation and toward enhanced degradation of protein, aromatic amino acids, glycine, and intestinal mucin glycans. This metabolic reprogramming is associated with exacerbated oxidative stress, neuroinflammation, and accelerated pathological progression. These findings provide multiomic evidence that clarifies the molecular heterogeneity in PD and highlights gut microbiota-driven dysfunction as a key contributor to both the iRBD and RBD-PD subtypes.},
}
@article {pmid41913691,
year = {2026},
author = {Erens, J and Heine, C and Lötters, S and Krehenwinkel, H and Crawford, AJ and Rueda-Solano, LA and Plewnia, A},
title = {A Field-Deployable eDNA Metabarcoding Workflow Including De Novo Reference Assembly for Characterising Understudied Biodiversity Hotspots.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70122},
doi = {10.1111/1755-0998.70122},
pmid = {41913691},
issn = {1755-0998},
support = {//Ministerium f&#xfc;r Wirtschaft, Verkehr, Landwirtschaft und Weinbau Rheinland-Pfalz/ ; //Deutsche Gesellschaft f&#xfc;r Herpetologie und Terrarienkunde/ ; //Forschungsfonds of Trier University/ ; //Forschungsinitiative Rheinland-Pfalz through Trier University/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Biodiversity ; *Amphibians/classification/genetics ; *DNA, Environmental/genetics ; Workflow ; *Metagenomics/methods ; },
abstract = {Field-deployable DNA metabarcoding offers a transformative approach to biodiversity research and monitoring, yet its application remains limited due to technical constraints and a lack of reference data in poorly studied ecosystems. Combining isothermal Recombinase Polymerase Amplification (RPA) and Oxford Nanopore sequencing, we introduce a two-step approach that uses non-invasive species barcoding to directly generate reference sequences for use in environmental DNA (eDNA) metabarcoding, and enables real-time, PCR-free and cost-effective molecular assessment of ecological communities in the field. Using an endemic and understudied tropical amphibian assemblage as a model, we demonstrate the functionality of this novel workflow. De novo generation of a reference sequence library from amphibian skin swab samples significantly improved the accuracy and taxonomic resolution of sequence assignments from eDNA samples, particularly on the species level, in turn allowing a characterisation of fine-scale patterns in community composition. Beyond generating new RPA-compatible amphibian metabarcoding primers, our results show that combining field-based eDNA metabarcoding with the offline assembly of a local reference database can directly bridge existing data gaps in molecular biodiversity monitoring, providing a scalable solution to accelerate biodiversity assessments in data-deficient ecosystems. This workflow paves the way for broader deployment of molecular tools in global biodiversity hotspots-particularly in remote and resource-limited tropical regions-to directly contribute critical baseline data, and support conservation efforts in regions where they are most urgently needed.},
}
@article {pmid40186063,
year = {2026},
author = {Saveetha, K and Somala, CS and Anand, T and Balamurugan, D and Vasudevan, V and Saravanan, KM and Senthil, R},
title = {Impact of Soil Microbiomes on Mung Bean Cultivation: Insights from 16S rRNA Metagenomics.},
journal = {Molecular biotechnology},
volume = {68},
number = {3},
pages = {1214-1228},
pmid = {40186063},
issn = {1559-0305},
mesh = {*Soil Microbiology ; *RNA, Ribosomal, 16S/genetics ; *Vigna/growth &amp; development/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; Soil/chemistry ; Biodiversity ; Phylogeny ; },
abstract = {Cyclic nutrient processes, soil health maintenance, and plant development are contingent upon soil microbiomes. The microbial makeup of the soil of Maruthupandiyar College, Thanjavur, is assessed using 16S rRNA gene sequencing. QIIME2, in conjunction with the SILVA database, analyzed the sequencing data to examine microbial diversity and composition. The experimental results revealed a diverse array of bacteria in soil physicochemical properties. The alpha and beta diversity assessment revealed significant microbial community complexity and distribution patterns disparities. The research revealed bacterial groups associated with biological nitrogen fixing, suggesting their potential to enhance mung bean growth. The current study illustrates the significance of microbial interactions in soil for sustaining soil fertility and enhancing crop output. Research findings provide essential insights into improving the sustainability of tropical agriculture through intentional microbial management to create sustainable soil health systems.},
}
@article {pmid41904606,
year = {2026},
author = {Birkeland, S and Rohde Mæhlum, I and Senneset, M and Wik Taxerås, I and Snipen, L and Markov Arnesen, H and Boysen, P and Carlsen, H},
title = {A naturalized gut microbiome interacts with dietary fibers to protect against colonic inflammation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2649435},
doi = {10.1080/19490976.2026.2649435},
pmid = {41904606},
issn = {1949-0984},
mesh = {Animals ; *Dietary Fiber/metabolism/administration &amp; dosage ; *Gastrointestinal Microbiome ; Mice ; *Colitis/prevention &amp; control/microbiology/chemically induced ; Feces/microbiology ; Dextran Sulfate ; Colon/microbiology/pathology ; Mice, Inbred C57BL ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Male ; Disease Models, Animal ; Intestinal Mucosa/metabolism/microbiology ; },
abstract = {"Feralized" mice, housed in farmyard-type environments, show a matured immunophenotype, altered intestinal barrier, and a shifted gut microbiome compared to conventionally housed laboratory mice. Since dietary fibers support gut health in part by microbial fermentation into immunomodulatory short-chain fatty acids, we hypothesized that feralization influences the intestinal barrier by enhancing the fiber-degrading properties of the microbiome. We explored whether susceptibility to low-grade dextran sulfate sodium-induced colitis differed between feralized and clean laboratory mice fed diets high or low in fermentable fibers. Feralized mice were protected against colitis, displaying low disease scores and biomarkers of inflammation in feces, plasma, and liver; and altered colonic mucosal gene expression, compared to clean mice. This protection was strongest with a fiber-rich diet, which, in contrast, worsened colitis in clean mice. Transfer of fecal microbiota from feralized mice to clean recipients conferred colitis protection. Fecal metagenome-assembled genomes revealed that the fiber-rich diet enriched the microbiome with predicted genes encoding fiber-degrading enzymes, while the low-fiber diet promoted mucin-degrading enzyme genes. However, the dominant microbial species contributing to these functions differed between feralized and laboratory mice. Differential abundance of bacterial taxa in feralized and laboratory mice further identified potential microbial modulators of colitis that merit targeted investigation in future studies. Overall, these findings suggest that fibers affect intestinal inflammation in a microbiota-dependent manner, underscoring the complex interplay between diet and microbiota in disease development.},
}
@article {pmid41907005,
year = {2026},
author = {Jeunen, GJ and Mills, S and Bailie, M and Mauvisseau, Q and Lamare, M and Mariani, S and Pearman, W and Zavodna, M and Treece, J and Ferreira, S and Gemmell, NJ},
title = {Recovering Historical eDNA From Museum-Preserved Filter Feeders via Non-Destructive Metabarcoding.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70132},
doi = {10.1111/1755-0998.70132},
pmid = {41907005},
issn = {1755-0998},
support = {MFP-UOO2116//Royal Society of New Zealand Marsden Fast-Start Fund/ ; ANTA1801//Ministry of Business, Innovation, and Employment/ ; //University of Otago Research Grant (UORG)/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Museums ; Animals ; *Metagenomics/methods ; *Specimen Handling/methods ; RNA, Ribosomal, 16S/genetics ; *Preservation, Biological/methods ; Fishes/genetics ; },
abstract = {Recent technical advances have significantly enhanced the value of museum specimens for molecular research, with metagenomic and metabarcoding approaches expanding further the utility of museum collections. However, given the finite number of specimens, there is a critical need to move past destructive DNA extraction approaches and to explore non-destructive techniques. In this proof-of-concept study, we evaluated the feasibility of extracting historical eDNA from the ethanol preservative used to store museum specimens. We compared a variety of extraction methods (centrifugation, evaporation, filtration, and precipitation) using ten replicate samples per treatment for statistical analyses. To assess potential differences in preservative-derived eDNA recovery across different filter-feeding taxonomic groups, we included a bryozoan, a demosponge, and a glass sponge. Comparative analyses with tissue biopsies revealed that 10 mL ethanol filtration performed equal to or, in some instances, outperformed tissue biopsies for all three specimens when examining the historical eDNA of Antarctic fish using a 16S rRNA metabarcoding approach, both for the number of species detected (α-diversity) and community characterisation (β-diversity). This initial study demonstrates the potential of ethanol preservative as a valuable, non-destructive source of historical eDNA from museum-stored filter-feeding specimens. These findings highlight the viability of non-destructive sampling for molecular research on museum collections, preserving specimen integrity while enabling biodiversity assessments. Further refinement of non-destructive eDNA extraction could expand its applicability across taxa, collection types, and preservation methods, ensuring the long-term sustainability of museum-based genomic, metagenomic, and metabarcoding research.},
}
@article {pmid41909847,
year = {2026},
author = {Huang, Y and Cai, Q and Chen, Y and Amutijiang, D and Lu, Y and Huang, W and Li, L},
title = {Phage characterization analysis in respiratory samples from infected patients based on metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1779296},
pmid = {41909847},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing ; Sputum/virology/microbiology ; Bronchoalveolar Lavage Fluid/virology/microbiology ; *Respiratory Tract Infections/virology/microbiology ; Male ; Female ; Middle Aged ; Bacteria/virology/genetics ; Aged ; Computational Biology ; Adult ; Virome ; },
abstract = {BACKGROUND: Respiratory tract infections are common infectious diseases, with microbial dysbiosis closely linked to clinical outcomes in the host. As key regulators of bacteria, phages can influence the structure and stability of microbial communities by infecting host bacteria. Metagenomic next-generation sequencing (mNGS) enables comprehensive analysis of phage community characteristics in clinical samples.<br><br>METHODS: This study included 6,404 clinical samples, comprising 4,837 bronchoalveolar lavage fluids (BALF) and 1,567 sputum samples, for metagenomic next-generation sequencing (mNGS), while collecting patient demographics, sample types, mNGS results, and clinical outcomes. Host-derived sequences were removed post-sequencing and aligned against viral reference databases. Phage community structures across sample types were assessed using alpha and beta diversity metrics. Spearman correlation analysis explored associations between phages and bacteria. Further bioinformatics analysis was performed on 194 samples, including viral sequence assembly and identification using SPAdes, VirSorter2, and PhaMer; CD-HIT clustering and redundancy removal; CheckV quality assessment; PhaTYP lifestyle prediction; Prodigal protein gene annotation; and BLASTP alignment against the CARD database to screen for phage resistance genes.<br><br>RESULTS: The sputum and BALF groups exhibited comparable richness, diversity, and evenness, yet their community structures differed significantly. Intensive Care Unit (ICU) admission status was closely associated with reduced phage community diversity and significant alterations in community structure, and the abundance distribution of several phage families (Peduoviridae, Autoscriptoviridae, Casjensviridae, Demerecviridae) also changed significantly. Additionally, the phage community structure in sputum samples was significantly associated with patient clinical outcomes. Correlation analysis demonstrated that the Aliceevansviridae family in sputum samples had extensive positive associations with various bacteria. After assembly, 69.5% of pOTUs were predicted to be temperate phages, and 28.9% were predicted to be virulent phages; moreover, the vast majority (99.2%) of phage sequences showed low similarity to antibiotic resistance genes.<br><br>CONCLUSION: This study identifies distinct phage community characteristics across respiratory sample types and reveals that ICU patients exhibit reduced phage diversity and markedly altered community structures. Furthermore, the phage composition in upper respiratory tract samples shows a clear relationship with patient prognosis, providing new insights into respiratory infection microecology.},
}
@article {pmid41910214,
year = {2026},
author = {Zhang, F and Xu, W and Zeng, R and Chen, J and Huang, J},
title = {Limosilactobacillus reuteri normalizes gut microbiota dysfunction and social deficits of rat offspring associated with prenatal exposure to stress.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2649440},
doi = {10.1080/19490976.2026.2649440},
pmid = {41910214},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; Pregnancy ; *Limosilactobacillus reuteri/physiology ; Rats ; *Prenatal Exposure Delayed Effects/microbiology ; Male ; Social Behavior ; Oxytocin/metabolism ; Fecal Microbiota Transplantation ; *Stress, Psychological/microbiology ; Rats, Sprague-Dawley ; *Probiotics/administration &amp; dosage ; Paraventricular Hypothalamic Nucleus/metabolism ; Behavior, Animal ; },
abstract = {Prenatal stress (PS) is a potential risk factor for social behavior impairment in offspring. Here, we demonstrate that PS induces gut microbiota alterations that are associated with impaired sociability and social novelty preference in rat offspring. In addition, we found that these behavioral deficits could be partially rescued through either cohousing with normal offspring or fecal microbiota transplantation from control donors. Metagenomic analysis identified Limosilactobacillus reuteri (L. reuteri) as a key species based on the considerable difference in its abundance between the PS and control offspring. Subsequent investigations revealed that supplementing L. reuteri during critical neurodevelopmental windows restored oxytocin levels in the paraventricular nucleus (PVN) and rescued dopamine reward pathway function, thereby ameliorating PS-induced social deficits. Notably, these beneficial effects were completely abolished by either treatment with an oxytocin receptor antagonist or subdiaphragmatic vagotomy. Thus, both oxytocin signaling and vagal afferent pathways play essential roles in the observed benefits of L. reuteri. Our findings indicate that social behavior impairments in offspring exposed to prenatal maternal stress can be explained by a novel mechanism involving the gut microbiota-brain axis: whereby PS-induced depletion of specific commensal bacteria (particularly L. reuteri) disrupts vagus nerve-mediated oxytocinergic modulation of PVN-to-VTA dopaminergic circuits, ultimately leading to social behavior impairments in offspring.},
}
@article {pmid41911519,
year = {2026},
author = {Zhang, H and Cao, Z and Zha, X and Wang, W and Jashenko, R and Hu, H and Ji, R},
title = {Host intestinal microbiota adaptive changes following Paranosema locustae infection and mechanism of chronic pathogenesis.},
journal = {Journal of insect science (Online)},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/jisesa/ieag027},
pmid = {41911519},
issn = {1536-2442},
support = {2023D01D08//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; TSYCLJ0016//Tianshan Talent Training Program/ ; 32260254//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Female ; Male ; *Orthoptera/microbiology ; Bacteria/classification ; },
abstract = {Paranosema locustae infection reduces the abundance and diversity of the intestinal bacteria in locusts, although the microbial adaptive changes and the underlying mechanism of chronic pathogenesis remain unclear. In this study, the intestinal microbial changes in Calliptamus italicus (Linnaeus, 1758) (Orthoptera: Acrididae) were analyzed with metagenomic sequencing after P. locustae infection. Results showed that the diversity of intestinal microbial communities in C. italicus declined after P. locustae infection, while the abundance of infection-specific taxa in C. italicus in the experimental groups was significantly higher than those in the control groups, irrespective of sex (P<0.05). The populations of opportunistic pathogenic bacteria such as Klebsiella aerogenes and Enterococcus faecalis increased significantly (P < 0.05). Meanwhile, the abundances of probiotics such as Pediococcus acidilactici and Enterobacter hormaechei increased significantly (P <0.05), which could inhibit the pathogenicity of P. locustae. The results suggested that the interplay of changes in the species and quantities of probiotics and pathogenic bacteria in the intestine of C. italicus after P. locustae infection was an important factor contributing to the difficulty of P. locustae in quickly breaching the host defense system and to its chronic pathogenicity.},
}
@article {pmid41912361,
year = {2026},
author = {Rathwell, C and Fuchsman, CA and Rocap, G},
title = {Hi-C Links Reveal Viral Activity and Infection Within the Free-Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70274},
doi = {10.1111/1462-2920.70274},
pmid = {41912361},
issn = {1462-2920},
support = {DGE-2140004//National Science Foundation/ ; DEB-1542240//National Science Foundation/ ; OCE-2022911//National Science Foundation/ ; },
mesh = {Pacific Ocean ; *Bacteria/virology/genetics/classification/metabolism ; Phylogeny ; *Chlorophyll/metabolism/analysis ; *Microbiota ; *Seawater/microbiology/virology ; *Bacteriophages/genetics/classification/isolation &amp; purification ; Metagenomics ; },
abstract = {Oxygen-deficient zones (ODZs) influence global nitrogen cycling as key sites for the removal of bioavailable nitrogen through denitrification and anammox. Despite their importance, many microbes and viruses in ODZs remain uncultivated, limiting our understanding of their ecological roles. This study employed Hi-C proximity linkages, combined with long and short read metagenomic sequencing to characterise active viral interactions in the prokaryotic community at a secondary chlorophyll maximum in the Eastern Tropical North Pacific ODZ. Among the identified 861 assembled viral contigs over 10 kb, 75 showed significant links to microbial genomes. Virus-host linkages indicated 19 novel virus-microbe pairs that were likely infectious, and which conventional in silico host prediction methods largely missed. The virus-host relationships involved nine distinct microbial phyla, with previously unrecorded viral infections of Planctomycetes, Chloroflexota, Alphaproteobacteria, Gammaproteobactera, Myxococcota and Verrucomicrobia. Most hosts carried the genomic potential for denitrification. Phylogenetic analysis of the terminase large subunit (terL) genes from linked viruses suggested that many active phages resemble known temperate phages, indicating that lysogeny may be an ecological strategy in ODZs. Our comprehensive metagenomic approach offers new insights into viral-host interactions in this ecosystem, highlighting the importance of including proximity methods in viral ecology studies of uncultivated microbial populations.},
}
@article {pmid41759241,
year = {2026},
author = {Myers, PN and van Beijsterveldt, IALP and Snowden, SG and Eriksen, C and Nielsen, HB and Hughes, IA and Ong, KK and Hokken-Koelega, ACS and Koulman, A and Brix, S},
title = {Breastfed infants receiving formula supplementation show altered lipid and gut microbiota profiles at 3 months of age.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {59},
number = {},
pages = {106602},
doi = {10.1016/j.clnu.2026.106602},
pmid = {41759241},
issn = {1532-1983},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Infant ; *Breast Feeding ; *Infant Formula ; Female ; Lipidomics ; *Lipids/blood ; Male ; Prospective Studies ; Feces/microbiology ; *Infant Nutritional Physiological Phenomena ; Milk, Human ; },
abstract = {BACKGROUND &amp; AIMS: Exclusive breastfeeding offers numerous health benefits. Despite advancements in formula, significant differences compared with breast milk remain. We aimed to assess how milk feeding type and volume at 3 months affect the infant plasma lipidome and gut microbiota.<br><br>METHODS: Infants were classified into exclusive breastfeeding (EBF), mixed feeding (MF), or exclusive formula feeding (EFF) groups based on feeding data collected prospectively across two European cohorts (n = 519). Lipidomics and shotgun metagenomics were applied to plasma and stool samples, respectively.<br><br>RESULTS: Feeding type explained major variation in both lipidomic and microbial profiles. Plasma lipids showed distinct signatures across groups, particularly in sphingomyelins and diacylglycerols. Microbiota diversity and species richness increased with formula exposure. Formula rich in intact whey protein was linked to higher S. thermophilus abundance in the infant gut. Random forest classification of feeding type using either lipidomic or gut microbiota features achieved high discriminatory accuracy (AUROC >0.90) in training and validation datasets.<br><br>CONCLUSION: Early nutrition is a critical determinant of the lipidome and gut microbiome during the breastfeeding phase.},
}
@article {pmid41825203,
year = {2026},
author = {Fu, Q and Dai, H and Wang, J and Zheng, S and Zhou, Y and Liu, H and Xu, F and Cheng, C and Jiang, H and Qian, Y and Zhang, S and Liu, L and Zheng, H and Li, Y and Zhang, L and Chen, Y and Cheng, X and Yang, T},
title = {Multi-omics analysis of dynamic profiles in response to various nutrient loads provides novel insights into obesity.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {59},
number = {},
pages = {106607},
doi = {10.1016/j.clnu.2026.106607},
pmid = {41825203},
issn = {1532-1983},
mesh = {Humans ; *Obesity/metabolism/microbiology/blood ; Male ; Female ; Adult ; Postprandial Period/physiology ; *Nutrients ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Metabolomics/methods ; *Diet ; Proteomics ; Feeding Behavior ; Overweight ; Body Mass Index ; Multiomics ; },
abstract = {BACKGROUND&amp; AIMS: Obesity is a global health issue driven by improper nutrient intake and metabolic dysregulation. The complexity of dietary components and the dynamic nature of postprandial metabolism limit our understanding of how different nutrient loads associated with obesity. This study aims to characterize the dynamic metabolic responses to nutrient intake using multi-omics approaches, assess the influence of dietary habits and gut microbiota, and evaluate the acute obesity-risk signature (AORS) associated with different macronutrients.<br><br>METHODS: We conducted a mixed meal tolerance test (MMTT) in 147 non-diabetic individuals (54 controls, 38 overweight, 55 obese). Blood samples were collected at multiple time points for untargeted metabolomics, lipidomics, proteomics, and hormone assays. Gut microbiota was profiled via metagenomic sequencing. A separate single macronutrient tolerance test (SMNTT) involving glucose, whey protein, butter, and olive oil was performed in 24 healthy volunteers to compare acute metabolic responses and derive an AORS based on postprandial multi-omics data.<br><br>RESULTS: Postprandial multi-omic analytes showed stronger associations with obesity indicators than fasting measures. Distinct temporal changes in metabolites, lipids, and proteins were observed across different BMI groups, with enrichment in pathways such as bile acid biosynthesis, triglyceride metabolism, and complement activation. Dietary habits and gut microbiota significantly influenced postprandial metabolic profiles, with specific metabolites and proteins mediating their effects on obesity. In SMNTT, glucose load exhibited the lowest AORS among isocaloric macronutrients (0.1082 &#xb1; 0.1917 %). Gut microbiota composition further modulated metabolic responses, with olive oil showing divergent AORS between Bacteroides- and Prevotella-dominated enterotypes (p = 0.043).<br><br>CONCLUSION: Postprandial multi-omics provides superior insights into obesity pathophysiology compared to fasting measurements. Our findings reveal that dietary habits and gut microbiota significantly influence postprandial metabolism and obesity risk, and demonstrate that different macronutrients confer distinct AORS values, which are further modified by an individual's gut microbiota composition. This underscores the potential for personalized nutritional strategies based on dynamic metabolic responses and microbial ecology.},
}
@article {pmid41843957,
year = {2026},
author = {Zhu, L and Huang, C and Tian, Y and Zuo, W and Shan, G},
title = {Targeted enhancement of ammonia assimilation and microbial community metabolic synergy in chicken manure aerobic composting mediated by tricarboxylic acid cycle modulators.},
journal = {Waste management (New York, N.Y.)},
volume = {216},
number = {},
pages = {115471},
doi = {10.1016/j.wasman.2026.115471},
pmid = {41843957},
issn = {1879-2456},
mesh = {*Ammonia/metabolism ; Animals ; *Composting/methods ; *Citric Acid Cycle ; *Manure/microbiology/analysis ; Chickens ; Nitrogen/metabolism ; Microbiota ; Citric Acid/metabolism ; },
abstract = {Reducing nitrogen loss during composting is essential. To investigate the effects of directly modulating the tricarboxylic acid (TCA) cycle on microbial ammonia assimilation during composting, this study employed paired stable isotope labeling combined with metagenomic analysis to assess the role of the TCA cycle regulator citric acid (CA) in enhancing ammonia assimilation efficiency and regulating carbon-nitrogen metabolism within the microbial community. CA markedly reduced NH3 emissions (0.5-2265 ppm) and increased organic nitrogen retention (4.2%-17.7%), primarily through improved ammonia assimilation efficiency (0.06-0.22 mg N·kg[-1]·d[-1]) rather than weakened mineralization. Mechanistically, CA upregulated IDH1 (5.4%-18.5%) and increased IDH enzyme activity (0.35-0.66 IU/g), combined with NH3 uptake, balancing oxoglutarate and ammonium supply. Moreover, CA strengthened the glutamine synthetase-glutamate synthase (GS-GOGAT) pathway (3.4%-23.4%) and enzyme activity (0.08-0.74 IU/g), particularly in the initial and thermophilic phases. In addition, CA induced an upregulation (14.8%-28.4%) of genes encoding succinyl-CoA synthetase, providing sufficient energy to support the ammonia assimilation process. Furthermore, CA enhanced microbial diversity and metabolic cooperation while reducing competition, thereby promoting NH3 assimilation and glutamate synthesis. Inorganic and amino acid metabolism emerged as critical cooperative processes within core microbial populations.},
}
@article {pmid41902210,
year = {2026},
author = {Zhang, Y and Ding, X and Tao, X and Tuohuti, N and Wang, X and Maimaiti, A and Su, Z and Ma, X},
title = {Viral Metagenomic Analysis Reveals High Prevalence of Dromedary Camel Bocavirus and Porcine Astrovirus in Bactrian Camel Intestinal Tissue.},
journal = {Viruses},
volume = {18},
number = {3},
pages = {},
pmid = {41902210},
issn = {1999-4915},
support = {2022KY025//Autonomous Region Science and Technology Commissioner Project of Xinjiang Uygur Autonomous Region, China/ ; },
mesh = {Animals ; *Camelus/virology ; *Bocavirus/genetics/isolation &amp; purification/classification ; Phylogeny ; Metagenomics ; *Parvoviridae Infections/veterinary/epidemiology/virology ; *Astroviridae Infections/veterinary/epidemiology/virology ; *Intestines/virology ; China/epidemiology ; Prevalence ; *Mamastrovirus/genetics/isolation &amp; purification/classification ; Swine ; Virome ; },
abstract = {Bactrian camels (Camelus bactrianus) are economically vital livestock in arid regions; however, their intestinal virome is poorly understood. We employed viral metagenomics to analyze intestinal tissue samples from deceased camels at a breeding facility in Urumqi, Xinjiang, China, and uncovered a diverse viral population dominated by dromedary camel bocavirus (DBoV1) and porcine astrovirus (PoAstV5). A molecular epidemiological survey of 261 anal swab samples collected across Xinjiang revealed prevalence rates of 36.40% (95/261) for DBoV1 and 26.44% (69/261) for PoAstV5, indicating their widespread circulation. Phylogenetic analyses of the DBoV1 NS1 and PoAstV5 ORF1a genes showed close relationships with known strains, with no evidence of recombination. This study expands the known viral spectrum of Bactrian camels, marking the first report of PoAstV5 in this species, a finding suggestive of cross-species transmission. These results enhance our understanding of camel viral diversity and provide critical data for managing enteric diseases in camel populations, with potential implications for livestock health and surveillance of zoonotic risks.},
}
@article {pmid41903026,
year = {2026},
author = {Wolthuis, JC and Schultheiss, JPD and Magnúsdóttir, S and Stigter, E and Tang, YF and Jans, J and Oldenburg, B and de Ridder, J and van Mil, S},
title = {Univariate- and machine learning-based plasma metabolite signature differentiates PSC-IBD from IBD and is predicted to be driven by gut microbial changes.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {2},
pages = {},
pmid = {41903026},
issn = {1573-3890},
mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/diagnosis/blood/metabolism/microbiology ; *Cholangitis, Sclerosing/diagnosis/blood/metabolism ; *Metabolomics/methods ; Male ; Female ; Biomarkers/blood ; Adult ; Middle Aged ; Crohn Disease/diagnosis/blood ; Colitis, Ulcerative/diagnosis/blood/metabolism ; Metabolome ; Mass Spectrometry ; },
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is a group of chronic inflammatory conditions of the gastrointestinal tract comprising two major phenotypes, Crohn's disease (CD) and ulcerative colitis (UC). Up to 8% of patients with IBD also develop primary sclerosing cholangitis (PSC), characterised by cholestasis and progressive destruction of the biliary tree, resulting in cirrhosis, end-stage liver disease and cholangiocarcinoma. Clinical outcome can currently not be improved through medication, denoting the importance of diagnosis prior to irreversible damage, which requires biomarkers of (early) disease.<br><br>OBJECTIVES: We employed direct infusion mass spectrometry (DI-MS)-based metabolomics on plasma to build predictive, potentially diagnostic models for PSC-IBC and other phenotypes including IBD subtype, stricture and fistula presence and more. We used this dataset to simultaneously investigate aetiology of these phenotypes.<br><br>METHODS: Samples of 348 IBD patients were included for analysis. The data was analysed using our previously reported tool, MetaboShiny. We built predictive models using Random Forest (RF), and subsequently combined with univariate statistics to rank m/z features connected to PSC-IBD. This ranking was used to perform mummichog enrichment analysis connected to metabolic and metagenomic changes.<br><br>RESULTS: The highest performing predictive model differentiated PSC-IBD from PSC. The metabolic signature was enriched in changes to amino acid and vitamin metabolism, alongside changes to the metagenome suggesting decreases in anti-inflammatory microbial species and increases in pro-inflammatory species.<br><br>CONCLUSION: These results demonstrate the potential of DI-MS-based metabolomics with machine learning to create diagnostic models and generate hypotheses on the metabolomic-metagenomic level. Sharing our dataset of patients will enrich future human IBD metabolomics research possibilities.},
}
@article {pmid41714781,
year = {2026},
author = {Su, JW and Elsheikha, HM and Guo, L and Liu, R and Shang, KM and Yu, HL and Ma, H and Ni, HB and Chen, BN and Zhang, XX and Yang, X},
title = {Metagenomic analysis of antimicrobial resistance, virulence, and mobile genetic elements in the gut microbiota of Caprinae species.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41714781},
issn = {2399-3642},
support = {2022KJ169//Department of Education of Shandong Province (Department of Education, Shandong Province)/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Interspersed Repetitive Sequences ; *Metagenomics ; Virulence/genetics ; *Drug Resistance, Bacterial/genetics ; Virulence Factors/genetics ; *Goats/microbiology ; Anti-Bacterial Agents/pharmacology ; China ; *Bacteria/genetics/pathogenicity/drug effects ; Metagenome ; },
abstract = {The livestock gut microbiota serves as a reservoir for antimicrobial resistance (AMR), yet Caprinae species remain understudied. Here, we present a large-scale metagenomic analysis of 779 gut samples from Caprinae animals, primarily originating from China (95.38%), including Capra hircus (79.85%) and Ovis aries (17.33%). We reconstruct 17,023 metagenome-assembled genomes (MAGs), and identify 2,440 antimicrobial resistance genes (ARGs) and 5,401 virulence factor genes (VFGs). Escherichia coli represents a major host for both. Correlation analyses between ARGs, VFGs, and mobile genetic elements (MGEs) suggest potential co-selection mechanisms. Although MGEs were detected in only 1.45% of MAGs, likely reflecting limitations in identifying MGEs within incomplete assemblies, 19 ARGs are physically co-located with MGEs, indicating mobility potential. Additionally, three ARGs are embedded within viral genomes, implicating bacteriophages in AMR dissemination. Comparative analyses reveal 184 distinct ARGs shared between Caprinae and humans, including 17 clinically critical genes such as tetX and van variants. These findings expand understanding of the Caprinae gut resistome and highlight its potential role in cross-host AMR transmission, and underscore the need for targeted AMR surveillance in this reservoir.},
}
@article {pmid41725015,
year = {2026},
author = {Wang, R and Wang, Z and Liao, W and Wang, T and Su, Y},
title = {Mikania micrantha invasion restructures rhizosphere nitrogen cycling through enzyme activation, microbial recruitment, and allelopathic regulation.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41725015},
issn = {2049-2618},
support = {31872670//National Natural Science Foundation of China/ ; 2021A1515010911//Guangdong Basic and Applied Basic Research Foundation/ ; 202206010107//Science and Technology Projects in Guangzhou/ ; JCYJ20210324141000001//Project of Department of Science and Technology of Shenzhen City, Guangdong, China/ ; },
mesh = {*Rhizosphere ; *Mikania/microbiology/growth &amp; development/metabolism ; *Soil Microbiology ; Nitrogen/metabolism ; *Nitrogen Cycle ; *Introduced Species ; Glutamate-Ammonia Ligase/metabolism/genetics ; Metagenomics ; Soil/chemistry ; Allelopathy ; Nitrogen Fixation ; Metabolomics ; Glutamate Dehydrogenase/metabolism/genetics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification/enzymology ; Nitrate Reductase/genetics/metabolism ; },
abstract = {BACKGROUND: Plant invasions profoundly influence terrestrial ecosystems by reshaping nutrient cycling processes. However, the mechanisms through which invasive plants such as Mikania micrantha modulate soil nitrogen (N) cycling and microbial communities remain insufficiently explored. Moreover, comparative studies with indigenous congener are scarce, limiting insights into whether such effects reflect species-specific strategies or genus-wide traits. This study investigates how M. micrantha modulates nitrogen metabolic pathways and rhizosphere microecology using combined metagenomic and metabolomic analyses.<br><br>RESULTS: Integrated analyses revealed that M. micrantha established a distinctive "high total nitrogen-low mineral nitrogen" profile in the rhizosphere soil. Metagenomic profiling showed consistent enrichment of key ammonium assimilation enzymes, including glutamine synthetase and glutamate dehydrogenase, promoting enhanced incorporation of NH&#x2084;&#x207a; into organic nitrogen pools. In contrast, genes encoding nitrate reductase and nitrate transporters were significantly lower in relative abundance, limiting nitrate assimilation. Mikania micrantha also selectively enriched nitrogen-fixing microbes (notably rhizobia genera) and plant growth-promoting rhizobacteria (PGPR), thereby enhancing biological nitrogen fixation capacity. Metabolomic analysis further identified several allelopathic compounds in invaded soils at higher relative abundance, particularly epicatechin, which exhibited inhibitory effects on nitrifying bacteria. Compared with the congener Mikania cordata, which exerted weaker impacts on soil nitrogen cycling and microbial assembly, M. micrantha deployed a more comprehensive strategy integrating biochemical, microbial, and metabolic regulation.<br><br>CONCLUSIONS: These findings demonstrate that under greenhouse-controlled conditions, M. micrantha reconfigures rhizosphere nitrogen cycling through a multi-dimensional strategy that couples biochemical regulation, microbial recruitment, and metabolite-mediated interference, thereby suggesting a potential mechanism that may contribute to its ecological advantage in natural settings. Video Abstract.},
}
@article {pmid41730992,
year = {2026},
author = {Escalante, C and Reyes, AM and Zhao, C and Balkcom, KS and Jacobson, AL and Strayer-Scherer, A and Martin, KM and Koebernick, J and Huseth, A and Kozieł, E and Small, I and Greene, JK and Otulak-Kozieł, K and Mulvaney, MJ and Price, PP and Briseño, RIA and Bag, S and Conner, K},
title = {Metatranscriptomics analysis reveals the cotton virome in the southern United States.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41730992},
issn = {2045-2322},
mesh = {*Gossypium/virology/genetics ; *Virome/genetics ; *Plant Viruses/genetics/classification ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Phylogeny ; Plant Diseases/virology ; *Transcriptome ; United States ; Metagenomics ; Gene Expression Profiling ; },
abstract = {High-throughput sequencing (HTS) has expanded our perspective on the distribution and diversity of plant viruses. Furthermore, improvements in HTS and decreasing sample costs have enabled the discovery of novel plant viruses in field-collected samples. This study examined the putative virome of cotton samples collected from fields across the southern United States. Leaf samples were collected, and total RNA was extracted. Library preparation was performed from pooled samples within locations before sequencing on an Illumina platform. Sequenced libraries were mapped to the cotton reference genome, and the resulting sequences were de novo assembled. A metatranscriptomics analysis revealed complete genome contigs of cotton leafroll dwarf virus in all tested samples. Additionally, 29 putative families of RNA and DNA plant viruses co-infecting cotton were found. Seven families of RNA viruses were more prevalent across all locations. These families included Botourmiaviridae, Hypoviridae, Mitoviridae, Narnaviridae, Partitiviridae, Solemoviridae, and Totiviridae. The information obtained in this investigation will help develop a broader perspective on cotton virus diversity and whether co-infections of viruses can influence (negatively or positively) plant physiology, product quality, and yield.},
}
@article {pmid41731555,
year = {2026},
author = {Yasuda, S and Palomo, A and Smets, BF and Terada, A},
title = {Potential survival strategies of novel comammox and nitrite-oxidizing Nitrospira synthesizing osmoprotectants in a wastewater microbiome treating high-ammonia brackish landfill leachate.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41731555},
issn = {2049-2618},
mesh = {*Ammonia/metabolism ; *Nitrites/metabolism ; *Wastewater/microbiology ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Oxidation-Reduction ; *Microbiota/genetics ; Metagenome ; Nitrification ; Phylogeny ; Water Pollutants, Chemical/metabolism ; Waste Disposal Facilities ; },
abstract = {BACKGROUND: In the late stages of landfill operation, leachate becomes brackish and contains high concentrations of ammonia with limited organic carbon. At leachate treatment facilities, it is typically subjected to nitrification followed by denitrification, with methanol supplied as an external electron donor. This unique environment may harbor novel microorganisms, including nitrifiers. Although a variety of microorganisms are involved in nitrification, their substrate specificity and salinity tolerance remain insufficiently understood. In this study, a genome-centric metagenome analysis was conducted on the microbiome from a leachate treatment facility at a closed landfill.<br><br>RESULTS: A total of 68 metagenome-assembled genomes (MAGs) were reconstructed, including 64 putative novel species. Among these, two Nitrospira MAGs were recovered: a novel complete ammonia-oxidizing bacterium (comammox), Nitrospira LAS72 (88.72% completeness, 2.10% contamination), and canonical nitrite-oxidizing Nitrospira LAS18 (99.98% completeness, 2.29% contamination). Comparative genomic analysis with 260 publicly available Nitrospira genomes revealed that LAS18 represents a new sub-lineage within lineage VII of the Nitrospira genus. Two ammonia-oxidizing archaea (AOA), Candidatus Nitrosocosmicus LAS21 and Nitrosarchaeum LAS73, were also identified, while canonical ammonia-oxidizing bacteria were not detected. Given the brackish conditions (1.23% salinity) and the methanol-fed operation of the treatment facility, the genomic potential for osmotic stress adaptation and methanol metabolism was investigated. Comammox Nitrospira LAS72 harbors biosynthetic pathways for several compatible solutes (osmoprotectants), including glycine betaine, proline, trehalose, and L-glutamate. Moreover, comammox Nitrospira LAS72 possesses genetic potential for oxidizing formaldehyde, suggesting that it may exploit these methanol-derived intermediates as energy sources. These features indicate that LAS72 may withstand osmotic fluctuations through the production of various osmoprotectants and thrive under the unique conditions of a methanol-fed environment.<br><br>CONCLUSIONS: The discovery of novel comammox Nitrospira and canonical Nitrospira forming a new sub-lineage within lineage VII of the Nitrospira genus in an ammonia-rich brackish environment provides the first genomic evidence for evolutionary adaptation among nitrifiers to saline, methanol-fed environments. These findings enhance our understanding of the ecological and evolutionary dynamics shaping nitrifier communities in complex treatment ecosystems. Video Abstract.},
}
@article {pmid41895971,
year = {2026},
author = {Silva, FA and Cabral, L and de Assis, BBT and Ferreira, DP and Egea, MB and Pimentel, TC and Magnani, M},
title = {Microbiota of foods: a comprehensive review of diversity and potential implications.},
journal = {Food research international (Ottawa, Ont.)},
volume = {232},
number = {},
pages = {118899},
doi = {10.1016/j.foodres.2026.118899},
pmid = {41895971},
issn = {1873-7145},
mesh = {*Food Microbiology ; *Fermented Foods/microbiology ; *Microbiota ; Fermentation ; Metagenomics ; Humans ; Metabolomics ; Bacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; },
abstract = {Microbial communities play a central role in food ecosystems. Fermented foods, in particular, host complex and dynamic microbiomes that are shaped by raw materials, fermentation substrates, processing environments, and regional production practices. This review provides an in-depth analysis of microbial diversity in various spontaneously fermented food products, including beverages, dairy products, and ethnic and other traditional food products. It highlights how microbial composition evolves throughout fermentation and how specific microorganisms contribute to the safety and sensory profiles of the final products. The field has undergone a methodological transformation, moving from classical culture-based methods to advanced omics technologies. Culture-independent approaches such as metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metabolomics enable a more comprehensive characterization of microbial communities, providing insights not only into their taxonomic composition but also into their functional roles. Despite increasing interest in metagenomics and metatranscriptomics, metataxonomic high-throughput sequencing, particularly 16S rRNA and ITS gene analyses, remains the most widely used technique due to its lower cost and accessibility. However, it provides limited resolution at the species level and cannot distinguish between live and dead cells. Microbiome characterization using omics has practical implications for the food industry, including the identification of microbial signatures in artisanal foods and the improvement of understanding fermentation processes. Our manuscript emphasizes a broad comparative overview of microbial diversity across multiple categories of fermented foods and integrates this with a methodological perspective on omics approaches used to characterize these communities. Findings outline the main methodological approaches, sequencing platforms, primer sets, and bioinformatic tools used in studies, as well as the current limitations and future directions in the field. Integrative multi-omics strategies are expected to significantly enhance food safety, quality, traceability, and functionality across diverse food systems.},
}
@article {pmid41896490,
year = {2026},
author = {Zheng, M and Yang, X and Tian, R and Xia, X and Xu, Q and Hui, Y and Chen, S and Liu, Y and Wang, A},
title = {A Segatella Copri-centered Gut Microbiota-mediated Metabolic Dysregulation Associated with Transition from Asymptomatic to Symptomatic Intracranial Atherosclerosis.},
journal = {Translational stroke research},
volume = {17},
number = {2},
pages = {},
pmid = {41896490},
issn = {1868-601X},
support = {82504498//National Natural Science Foundation of China/ ; 82473699//National Natural Science Foundation of China/ ; 2022YFC3600600//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Middle Aged ; *Intracranial Arteriosclerosis/metabolism/microbiology ; Case-Control Studies ; Aged ; Biomarkers/blood ; Metabolomics ; *Ischemic Stroke/metabolism/microbiology ; },
abstract = {The mechanisms underlying the continuum from asymptomatic intracranial atherosclerotic stenosis (aICAS) to symptomatic intracranial large-artery atherosclerotic ischemic stroke (iLAA-IS) remain unclear. We investigated the gut microbiota-metabolite axis in this transition to identify predictive biomarkers and clarify key functional pathways. In a case-control study (63 iLAA-IS cases; 56 aICAS controls), fecal shotgun metagenomics and untargeted plasma metabolomics were profiled. Using machine learning with 10-fold nested cross-validation, we identified five robust biomarkers associated with the transition: Alistipes putredinis (risk-associated) and four protective features (Segatella copri, Gln-Gly, Methionine Sulfoxide, and N6-Acetyl-L-Lysine). Integrated models incorporating these markers significantly improved predictive performance relative to conventional risk factors (e.g., mean AUC of Gln-Gly: 0.9104 vs. 0.7188). Mechanistic analyses revealed a Segatella copri-centered metabolic dysregulation: its depletion coincided with a broad loss of anabolic pathways (BCAA biosynthesis, folate-SAM-methionine metabolism, and tRNA charging), which were positively linked to amino acid-related metabolites. In contrast, the pathways of Alistipes putredinis showed no such coupling. These findings suggest that the aICAS-to-iLAA-IS transition is characterized by chronic metabolic dysregulation, involving a Segatella copri-centered microbiota-metabolite axis. This multi-omic signature offers novel insights into stroke pathogenesis and potential targets for prevention.},
}
@article {pmid41896639,
year = {2026},
author = {Puetz, LC and O Delmont, T and Mitchell, AL and Finn, RD and Zhang, G and Shepeleva, DV and Kharlamova, AV and Kukekova, AV and Trut, LN and Gilbert, MTP},
title = {Gut microbiome community structure correlates with different behavioral phenotypes in the Belyaev Farm-Fox Experiment.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41896639},
issn = {2399-3642},
support = {NIH R35 GM144276//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; RSF-21-44-04405//Russian Science Foundation (RSF)/ ; DNRF143 Center for Evolutionary Hologenomics//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Behavior, Animal ; *Foxes/microbiology/physiology ; Phenotype ; Domestication ; Male ; },
abstract = {Domestication represents one of the largest biological shifts of life on Earth, and for many animal species, behavioral selection is thought to facilitate early stages of the process. The gut microbiome of animals can respond to environmental changes and have diverse and powerful effects on host behavior. As such, we hypothesize that selection for tame behavior during early domestication, may have indirectly selected on certain gut microbiota that contribute to the behavioral plasticity necessary to adapt to the new social environment. Here, we explore the gut microbiome of foxes from the tame and aggressive strains of the "Russian-Farm-Fox-Experiment". Microbiota profiles reveal a significant depletion of bacteria in the tame fox population that have been associated with aggressive and fear-related behaviors in other mammals. Our metagenomic survey allows for the reconstruction of microbial pathways enriched in the gut of tame foxes, such as glutamate degradation, which converge with host genetic and physiological signals, revealing a potential role of functional host-microbiota interactions that could influence behaviors associated with domestication. Overall, by characterizing how compositional and functional potential of the gut microbiota and host behaviors co-vary during early animal domestication, we provide further insight into our mechanistic understanding of this adaptive, eco-evolutionary process.},
}
@article {pmid41898386,
year = {2026},
author = {Tahtouh Zaatar, M and Othman, R and Abushawish, M and Akl, M and Alachkar, MT and Almatboona, G and Alriyami, F and Alshaibani, A and Ashkanani, D and Basharova, M and Imam, M and Khassay, N and Mikhael, MS and Naderi Far, R and Shaqra, S and Verwey, K and Suleimanova, A and Yousafzada, M and Burmagina, Y},
title = {The Women's Microbiome: Molecular Insights, Clinical Gaps, and Future Frontiers in Precision Health with Implications for Gulf Cooperation Council Populations.},
journal = {International journal of molecular sciences},
volume = {27},
number = {6},
pages = {},
doi = {10.3390/ijms27062521},
pmid = {41898386},
issn = {1422-0067},
mesh = {Humans ; Female ; *Microbiota ; *Women's Health ; *Precision Medicine ; Probiotics ; Pregnancy ; Vagina/microbiology ; Gastrointestinal Microbiome ; },
abstract = {The human microbiome has emerged as a central regulator of health and disease; however, women-specific microbiome research has only recently gained focused scientific attention. Accumulating evidence demonstrates that microbial ecosystems across the gut, vagina, skin, breast tissue, and reproductive tract are dynamically shaped by female hormones, life-stage transitions, and environmental exposures. These interactions influence immune regulation, metabolic homeostasis, reproductive outcomes, mental health, and cancer risk, in part through microbiome-mediated endocrine pathways such as the estrobolome. Advances in high-resolution molecular technologies-including metagenomics, metabolomics, spatial and single-cell profiling, and artificial intelligence-driven modeling-have shifted microbiome research from descriptive taxonomy toward functional, mechanistic, and predictive science. These approaches highlight microbial function and metabolite production as stronger determinants of health outcomes than taxonomic composition alone. Nonetheless, major gaps persist, including limited causal evidence, methodological heterogeneity, underrepresentation of non-Western populations, and barriers to clinical translation. Microbiome-targeted interventions, including probiotics, prebiotics, postbiotics, and emerging microbiota-based therapies, have garnered increasing interest in women's health. Select Lactobacillus and Bifidobacterium strains show potential in modulating vaginal and gastrointestinal health, pregnancy outcomes, and immune function; however, clinical effects remain highly strain-specific and context-dependent. Discrepancies between experimental findings, commercial claims, and validated clinical use underscore the need for rigorous, women-centered trials and standardized outcome measures. This narrative review synthesizes current molecular insights into the women's microbiome across endocrine interactions, pregnancy, reproductive and metabolic health, lifestyle influences, and microbiome-based therapeutic strategies. We integrate clinical perspectives to identify diagnostic and translational challenges and propose future directions emphasizing precision microbiome medicine, validated biomarkers, careful evaluation of microbiome-targeted interventions, and inclusive research frameworks, including populations from the Gulf Cooperation Council (GCC). Collectively, this review positions the microbiome as a critical yet underutilized axis in women's health and outlines a roadmap toward personalized, evidence-based care across the female lifespan.},
}
@article {pmid41898595,
year = {2026},
author = {Makiel, K},
title = {Anti-Inflammatory Diets in Metabolic Syndrome and Obesity: Multi-Omics Perspectives on the Interplay Between Gut Microbiota, DNA Methylation, and Adipokine Regulation-A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {6},
pages = {},
doi = {10.3390/ijms27062734},
pmid = {41898595},
issn = {1422-0067},
support = {//University of Physical Education, 31-571 Cracow, Poland/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolic Syndrome/diet therapy/metabolism/genetics/microbiology ; *Obesity/diet therapy/metabolism/genetics/microbiology ; *Adipokines/metabolism/genetics ; *DNA Methylation ; *Diet ; Animals ; Inflammation ; Nutrigenomics ; Multiomics ; },
abstract = {An anti-inflammatory dietary pattern represents a key component of non-pharmacological management in obesity and metabolic syndrome (MetS), as it targets chronic low-grade inflammation, adipose tissue dysfunction, insulin resistance, and disturbances of the gut-metabolic axis. In the present work, we outline a framework for an "omics-based" approach that integrates data on gut microbiota composition and function (metagenomics), adipokine profiles, nutrigenomics, epigenetics, and related transcriptomic and metabolomic layers in order to enable more precise characterization of the metabolic phenotype and to support precision nutrition strategies. The proposed dietary model emphasizes the quality rather than merely the quantity of macronutrients, with particular focus on lipid profile optimization. Specifically, total fat intake is recommended to remain below 30% of total energy through the reduction in saturated fatty acids (SFA), trans fats, and excessive omega-6 fatty acids, alongside increased consumption of omega-3 PUFA (EPA/DHA) and plant-based sources of α-linolenic acid (ALA). Concurrently, greater intake of lean protein sources and low-glycemic-index carbohydrates rich in dietary fibre-particularly fermentable fractions-is recommended. The model also highlights the importance of polyphenols with antioxidant and immunomodulatory properties. To enhance feasibility and long-term adherence, recommendations are structured as flexible food substitutions rather than rigid prescriptions. Further well-designed interventional studies are required to confirm the impact of a multi-omics-based anti-inflammatory diet on both molecular and clinical endpoints.},
}
@article {pmid41898625,
year = {2026},
author = {Chaplin, AV and Podoprigora, IV and Shcherbakova, VA and Zakharzhevskaya, NB and Evseev, PV and Vasilyeva, AA and Koshkin, FA and Kardonsky, DA and Vorobyeva, EA and Kashatnikova, DA and Kazakova, VD and Efimov, BA},
title = {Parabacteroides vesiculifaciens sp. nov., a Novel Immunomodulatory, Vesicle-Producing Gut Commensal Isolated from the Human Gut.},
journal = {International journal of molecular sciences},
volume = {27},
number = {6},
pages = {},
doi = {10.3390/ijms27062763},
pmid = {41898625},
issn = {1422-0067},
support = {24-75-10100//Russian Science Foundation/ ; },
mesh = {Humans ; Phylogeny ; *Gastrointestinal Microbiome ; *Bacteroidetes/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Genome, Bacterial ; Animals ; HT29 Cells ; Extracellular Vesicles/metabolism ; Mice ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The genus Parabacteroides comprises widespread gastrointestinal commensals, known to produce immunomodulatory molecules and extracellular vesicles, yet its full diversity is incompletely cataloged. This study describes strain ASD2025[T], isolated from healthy child feces, using a polyphasic taxonomic approach including phenotypic profiling, chemotaxonomy, and comparative genomics. Cells were non-motile, polymorphic rods that produced extracellular vesicles. Phylogenomic analysis placed ASD2025[T] within the genus Parabacteroides within a species complex consisting of P. acidifaciens, P. hominis, "P. massiliensis", P. merdae, and P. johnsonii, with average nucleotide identities to the type strains of 85.5-89.9%. The large genome (5.16 Mbp, 46.2% GC content) contained integrative conjugative elements harboring antibiotic resistance genes and hankyphage-related prophage. The strain produced succinate as the major metabolic end product, and its major fatty acids were anteiso-C15:0, iso-C17:0 3-OH, and C15:0. Conditioned medium from ASD2025[T] antagonized the interleukin-8 response caused by E. coli lipopolysaccharide in HT29 cells. The majority of related metagenome-assembled genomes originate from mouse microbiomes. Based on these distinct characteristics, strain ASD2025[T] (=VKM B-3926[T] = JCM 37967[T]) represents a novel species of the genus Parabacteroides, for which the name Parabacteroides vesiculifaciens sp. nov. is proposed.},
}
@article {pmid41898646,
year = {2026},
author = {Dang, X and Hanson, BA and Lopez, M and Miller, J and Jimenez, M and Koralnik, IJ},
title = {Predictive Utility of ViroFind Detection of Blood and CSF Virome for Viral Presence in Human Brain Tissue.},
journal = {International journal of molecular sciences},
volume = {27},
number = {6},
pages = {},
doi = {10.3390/ijms27062789},
pmid = {41898646},
issn = {1422-0067},
support = {DA048493/DA/NIDA NIH HHS/United States ; },
mesh = {Humans ; *Brain/virology ; *Virome ; HIV Infections/virology/blood/cerebrospinal fluid ; Male ; Female ; Herpesvirus 4, Human/isolation &amp; purification/genetics ; Adult ; High-Throughput Nucleotide Sequencing ; Middle Aged ; Torque teno virus/genetics/isolation &amp; purification ; Viral Load ; Viruses/genetics/isolation &amp; purification ; },
abstract = {Viral presence in the brain may contribute to chronic neurologic diseases. However, investigating these associations is limited by the difficulty of directly sampling brain tissue in living individuals. Here, we evaluated whether peripheral viral detection using unbiased target-enrichment next-generation sequencing could inform viral presence in the brain across a diverse set of viral taxa. We applied ViroFind to matched brain, blood (peripheral blood mononuclear cells, spleen, and/or lymph node), and cerebrospinal fluid (CSF) to assess the predictive utility of viral detection in blood and CSF for identifying viral presence in brain samples obtained from the National NeuroAIDS Tissue Consortium, including both HIV-infected (HIV[+]) and HIV-uninfected (HIV[-]) individuals without known active viral infection of the brain. Blood negativity was generally more informative for predicting the absence of viruses in the brain than blood positivity for predicting viral presence. CSF viral detection demonstrated limited predictive utility for brain presence across most viral taxa examined. Among blood[+] individuals, viral burden differed significantly between brain[+] and brain[-] cases for Epstein-Barr virus (EBV), parvovirus, and torque teno virus (TTV). Blood viral burden showed moderate ability to distinguish brain[+] from brain[-] cases for EBV and parvovirus, and strong discriminatory ability for TTV, with similar decision thresholds across HIV[+] and HIV[-] individuals.},
}
@article {pmid41898837,
year = {2026},
author = {Li, S and Chiodi, C and Maucieri, C and Della Lucia, MC and Zardinoni, G and Ravi, S and Squartini, A and Concheri, G and Geng, G and Wang, Y and Stevanato, P},
title = {Profiling Soil-Plant-Microbial Communities: DNA and Multi-Omics Techniques.},
journal = {Genes},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/genes17030303},
pmid = {41898837},
issn = {2073-4425},
mesh = {*Soil Microbiology ; Rhizosphere ; Metagenomics/methods ; *Microbiota/genetics ; *Plants/microbiology/genetics ; Genomics/methods ; Metabolomics/methods ; Plant Roots/microbiology/genetics ; Crops, Agricultural/microbiology/genetics ; Multiomics ; },
abstract = {Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches-marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays-and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge-cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship.},
}
@article {pmid41900342,
year = {2026},
author = {Ntzouvaras, A and Koletti, A and Zografaki, ME and Marka, S and Skliros, D and Vasilakis, G and Karavidas, I and Koukouvinis, AK and Efrose, RC and Kalloniati, C and Tzovenis, I and Flemetakis, E},
title = {Isolation and Characterization of Microalgae Isolates from Hydroponic Effluent Water: Metagenomics and Biotechnological Insights.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030582},
pmid = {41900342},
issn = {2076-2607},
support = {PRIMA2019-04//European Union research and innovation Horizon 2020/ ; },
abstract = {Hydroponic systems are gaining prominence in sustainable agriculture, yet their nutrient-rich effluents remain an underexplored source of microbial biodiversity with potential biotechnological interest. In this study, shotgun metagenomic sequencing was employed to profile, with a high taxonomic resolution, the photosynthetic microbial community in hydroponic effluent before and after a natural algal bloom, revealing pronounced shifts in microbial composition. Notably, relative abundance increased sixfold for Chlamydomonas reinhardtii and tenfold for Bigelowiella natans. Four dominant microalgal strains (PR1-PR4) were subsequently isolated and characterized through integrative morphological and molecular taxonomy, with phylogenetic analyses based on four genetic markers (18S rRNA, ITS, rbcL and tufA) confirming that each isolate represents a distinct lineage within Chlorophyceae families, including Chlorella sp., Chlamydomonas sp., and Scenedesmus sp. Growth kinetics under three temperature regimes, typical of Greek environmental conditions from spring to autumn (15 °C, 23 °C, 32 °C), demonstrated broad ecological plasticity and rapid biomass production, highlighting strains with strong adaptive resilience. Biochemical profiling of the isolates revealed significant inter-strain differences in primary and secondary metabolite content, including proteins (up to 43% DW), lipids (up to 31% DW), carbohydrates (up to 44% DW), photosynthetic pigments, phenolics, flavonoids, and antioxidant activity. The observed metabolic diversity of autochthonous microalgal strains from hydroponic environments, combined with their high growth rates, underscores their potential for applications in bioremediation, bioenergy, and the development of value-added products within a circular bioeconomy framework.},
}
@article {pmid41901100,
year = {2026},
author = {Kim, HJ and Park, J and Oh, S and Kim, D and Kim, HJ and Jo, C and Kim, EB and Jang, A},
title = {Effect of Alpha-Lipoic Acid, Betaine, and L-Carnitine Supplementation on Gut Microbiota and Obesity Biomarkers in Mice.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
doi = {10.3390/nu18060925},
pmid = {41901100},
issn = {2072-6643},
support = {2022R1A2C1005235//National Research Foundation of Korea/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Carnitine/pharmacology/administration &amp; dosage ; *Obesity/microbiology/metabolism ; *Betaine/pharmacology/administration &amp; dosage ; Male ; *Thioctic Acid/pharmacology/administration &amp; dosage ; Mice, Inbred C57BL ; *Dietary Supplements ; Diet, High-Fat/adverse effects ; Biomarkers/blood ; Mice ; Disease Models, Animal ; Leptin/blood ; },
abstract = {Background/Objectives: This exploratory study (n = 6 per group) investigated the associations between supplementation with α-lipoic acid (AL), betaine (BT), and L-carnitine (LC) and gut microbiota composition in a high-fat diet (HFD)-induced obesity mouse model. Methods: Four-week-old male C57BL/6J mice were fed a control diet (10% fat), HFD (60% fat), or HFD supplemented with AL, BT, or LC (300 mg/kg BW/day) for nine weeks. Results: All three compounds were associated with shifts in microbial composition compared to the HFD-only group. While AL and BT supplementation moderately modulated specific Firmicutes and Bacteroidetes taxa, LC supplementation was linked to a more pronounced reduction in the Firmicutes/Bacteroidetes ratio and a decreased abundance of genera such as Christensenellaceae, Lachnospiraceae, and Coprococcus 3. These microbial changes were correlated with obesity-related metabolic and adiposity markers, including leptin and lipid parameters. Furthermore, functional profiling via PICRUSt suggested potential alterations in amino acid metabolism; however, these findings represent inferred metabolic potential rather than direct metagenomic measurements. Conclusions: Collectively, these results indicate differential associations between dietary supplementation and gut microbiota composition in HFD-fed mice. Although this study was conducted within an exploratory framework and utilized a modest sample size, the observed microbial shifts consistently paralleled metabolic alterations, supporting biologically plausible associations that warrant further mechanistic investigation.},
}
@article {pmid41901112,
year = {2026},
author = {Solano-Aguilar, G and Lakshman, S and Chen, C and Beshah, E and Molokin, A and Vinyard, B and Dawson, HD and Santin-Duran, M and Bruna, G and Smith, A and Urban, JF},
title = {Fruit and Vegetable Supplemented-Diet Ameliorates Dextran Sodium Sulfate (DSS)-Induced Colitis by Modulating Host Transcriptome and Gut Metagenome Response.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
doi = {10.3390/nu18060937},
pmid = {41901112},
issn = {2072-6643},
support = {Cris 8040-51000-058-00D//United States Department of Agriculture/ ; },
mesh = {Animals ; Dextran Sulfate ; *Fruit ; *Colitis/chemically induced/prevention &amp; control/microbiology/diet therapy ; *Transcriptome ; *Gastrointestinal Microbiome ; *Dietary Supplements ; *Vegetables ; Swine ; *Metagenome ; Disease Models, Animal ; *Diet ; Colon/pathology ; },
abstract = {Background/Objectives: Dietary intake of fruits and vegetables (FVs) has been inversely associated with a lower risk of ulcerative colitis. Using a pig model, we evaluated the effect of FV supplementation on dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet (negative control), grower diet + 4% DSS (positive control), half-FV diet + DSS, or full-FV diet + DSS. FV levels matched half or full daily recommendations from the Dietary Guidelines for Americans (DGA). Clinical signs were monitored; proximal colon contents (PCs) and mucosa (PCM) were analyzed for metagenome, transcriptome and histopathology. Results: Full-FV pigs showed no diarrhea, less fecal occult blood (FOB), crypt hyperplasia, but no changes in gene expression or microbiome diversity (p < 0.05). Half-FV pigs had increased FOB, differentially expressed genes (DEGs) linked to tissue remodeling, crypt/goblet cell hyperplasia and two cases of diarrhea (p < 0.05). DSS controls showed reduced immune-related DEGs, altered microbiome, PCM erosion, FOB, and persistent diarrhea in one pig (p < 0.05). Conclusions: A three-week full-FV diet conferred protection against DSS-induced colitis, with a dose-dependent protection of intestinal tissue and gut metagenome under inflammatory challenge.},
}
@article {pmid41901695,
year = {2026},
author = {Philips, CA and Oommen, TT and Theruvath, AH and Sreemohan, A and Baby, A and Alex, AA and Thomas, S and John, SM and Ahamed, R and Tharakan, A and Augustine, P},
title = {Novel Insights on Clinical Outcomes Using Integrated Shotgun Metagenomic Profiling of the Gut Microbiome, Resistome, and Host Immune-Inflammatory Response in Hospitalized Patients with Decompensated Cirrhosis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/pathogens15030241},
pmid = {41901695},
issn = {2076-0817},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Liver Cirrhosis/microbiology/immunology/mortality ; Male ; *Metagenomics/methods ; Female ; Middle Aged ; Aged ; Hospitalization ; Adult ; India ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Background and Aims: Sepsis drives mortality in cirrhosis, yet the gut antimicrobial resistance (AMR) landscape remains unmapped in high-burden settings like India. This study aimed to integrate shotgun metagenomics with deep immunophenotyping to define the gut-immune-resistome axis and correlate specific microbial and genetic signatures with clinical outcomes in decompensated cirrhosis. Methods: We analysed 78 hospitalized patients with cirrhosis using stool shotgun metagenomics, multiplex cytokine arrays, and flow cytometry. The microbiome and resistome (AMR genes) were mapped and correlated with disease severity, immune function (monocyte HLA-DR, neutrophil CD64), and clinical endpoints including mortality. Results: Disease severity was characterized by a "Gram-negative bloom" (Klebsiella) alongside pathogenic Enterococcus expansion and novel markers: Clostridium sp. C5-48 (severe decompensation) and Sutterella (ascites). A specific, dense resistome predicted adverse outcomes; the quinolone-resistance gene QnrB4 correlated with mortality and immune paralysis, while the carbapenemase OXA-833 gene was linked to gastrointestinal bleeding. Notably, the commensal Ligilactobacillus salivarius was associated with systemic inflammatory cytokines. Conclusions: This study reveals a "pathogenic ecosystem" in Indian decompensated cirrhosis where the resistome is intrinsically linked to host immune failure. The identification of specific prognostic markers (QnrB4, OXA-833) and inflammatory associations with L. salivarius challenges generic probiotic use and underscores the urgent need for precision, resistome-targeted therapies.},
}
@article {pmid41560360,
year = {2026},
author = {Zhang, J and Wang, Z and Li, S and Luo, C and Li, H and Ma, S and Wang, P and Liu, H and Sun, L and Yin, Y and Zhang, W and Wang, Q},
title = {Phocaeicola coprophilus-Derived 6-Methyluracil Attenuates Radiation-Induced Intestinal Fibrosis by Suppressing the IDO1-Kynurenine-AHR Axis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {18},
pages = {e18502},
doi = {10.1002/advs.202518502},
pmid = {41560360},
issn = {2198-3844},
support = {JDYY15202429//Youth Development Fund of the First Hospital of Jilin University/ ; JDYY-DEP-2022006//Doctor of Excellence Program (DEP), The First Hospital of Jilin University/ ; YDZJ202402012CXJD//Department of Science and Technology of Jilin Province/ ; 82330017//National Natural Science Foundation of China/ ; 82270610//National Natural Science Foundation of China/ ; 20240484505//Beijing Nova Program/ ; 2024ZD0530100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; },
mesh = {Animals ; Mice ; *Kynurenine/metabolism ; *Fibrosis/metabolism ; *Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism ; Gastrointestinal Microbiome ; *Receptors, Aryl Hydrocarbon/metabolism ; Humans ; *Uracil/analogs &amp; derivatives/metabolism/pharmacology ; Male ; *Intestines/pathology/radiation effects ; Mice, Inbred C57BL ; Disease Models, Animal ; },
abstract = {Therapeutic options for radiation-induced intestinal fibrosis (RIF) remain limited. This study reveals that intestinal kynurenine (Kyn) is persistently elevated after radiation and correlates with fibrosis severity in both murine models and human rectal cancer samples. Exogenous Kyn exacerbated RIF, whereas inhibition of indoleamine 2,3-dioxygenase 1 (IDO1) attenuated fibrotic progression. Mechanistically, Kyn activates the aryl hydrocarbon receptor (AHR) to promote fibroblast activation and fibrosis. Antibiotic depletion of gut microbiota abrogates radiation-induced IDO1-Kyn upregulation and protects against RIF. Conversely, fecal microbiota transplantation from irradiated mice recapitulates the elevated IDO1-Kyn phenotype. Metagenomic analysis identify radiation-induced depletion of Phocaeicola coprophilus (P. coprophilus), whose abundance inversely correlates with Kyn levels. Supplementation with live P. coprophilus suppresses IDO1-Kyn signaling and ameliorates RIF. Untargeted metabolomics further show that radiation reduces 6-methyluracil, a metabolite derived from P. coprophilus. Exogenous 6-methyluracil replenishment inhibits repression of the IDO1-Kyn axis and mitigates fibrosis. Together, these findings define a microbiota-metabolite-host pathway in which radiation depletes P. coprophilus, leading to loss of 6-methyluracil and derepression of the IDO1-Kyn-AHR axis, thereby driving fibrogenesis. Restoration of either P. coprophilus or its metabolite 6-methyluracil represents a promising therapeutic strategy against RIF.},
}
@article {pmid41618858,
year = {2026},
author = {Yang, T and Gao, Z and Huang, H and Zhang, C and Tang, Y and Qu, Q and Li, H and Ke, J and Chen, Z and Feng, M and Zhou, H and Shu, Y and Yuan, W},
title = {Gut-Metabolome-Proteome Interactions in Age-Related Hearing Loss: Insights from Fecal Microbiota Transplantation and Multi-Omics Analyses.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {18},
pages = {e14269},
doi = {10.1002/advs.202514269},
pmid = {41618858},
issn = {2198-3844},
support = {81873702//National Natural Science Foundation of China/ ; 81470694//National Natural Science Foundation of China/ ; 82225014//National Natural Science Foundation of China/ ; 82171114//National Natural Science Foundation of China/ ; 2024NF008//National Clinical Research Center for Otolaryngologic Diseases/ ; CSTB2023TIAD-KPX0059//Chongqing Technology Innovation and Application Development Special Project/ ; 2022DBXM006//Major Programs of Chongqing Science and Health Union/ ; cstc2022ycjh-bgzxm0126//Chongqing Talent Project/ ; CSTB2022NSCQ-MSX0553//Chongqing Natural Science Foundation/ ; },
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/physiology ; *Fecal Microbiota Transplantation/methods ; *Proteome/metabolism ; *Metabolome/physiology ; Proteomics/methods ; Disease Models, Animal ; *Presbycusis/metabolism/microbiology ; Male ; Metabolomics/methods ; Mice, Inbred C57BL ; Aging/metabolism ; Multiomics ; },
abstract = {Age-related hearing loss (ARHL) is a prevalent sensory disorder lacking disease-modifying interventions. The biological drivers, particularly the contribution of the gut microbiota and gut-inner ear crosstalk, remain poorly defined. Here, we utilize germ-free (GF) mice and fecal microbiota transplantation (FMT) to isolate microbiota-dependent effects on ARHL progression. Through integrated metagenomic, metabolomic, and proteomic profiling, we map molecular signatures of auditory aging and uncover functional gut-inner ear network, prioritizing 5-hydroxytryptophan (5-HTP) as a key intermediate metabolite within this network. Furthermore, in an aging-like House Ear Institute-Organ of Corti 1 (HEI-OC1) model, 5-HTP exhibits protective effects, potentially mediated through the PI3K/Akt-antioxidant signaling axis. Collectively, this study provides a valuable multi-omics resource and highlights microbiota-derived metabolic regulation as a promising avenue for biomarker discovery and therapeutic development in ARHL.},
}
@article {pmid41709267,
year = {2026},
author = {Baquer, F and Grillon, A},
title = {Interaction between tick and host microbiotas: a four-step waltz.},
journal = {Parasites &amp; vectors},
volume = {19},
number = {1},
pages = {},
pmid = {41709267},
issn = {1756-3305},
mesh = {Animals ; *Microbiota ; Humans ; *Tick-Borne Diseases/microbiology/transmission ; *Ticks/microbiology ; Symbiosis ; Skin/microbiology/immunology ; *Host Microbial Interactions ; Host-Pathogen Interactions ; },
abstract = {Tick-borne diseases represent a growing public health concern worldwide, yet the microbial factors that govern pathogen transmission remain incompletely understood. Over the past decade, high-throughput metagenomics and functional studies have revealed that two distinct microbial communities-the vertebrate host's skin microbiota and the tick's own microbiome-act synergistically as key modulators of pathogen acquisition, persistence within the vector, and successful transmission to the vertebrate host. At the feeding site, the skin microbiota orchestrates local cutaneous immunity, influences inflammatory responses, and can either hinder or inadvertently facilitate dermal establishment of tick-borne pathogens such as Borrelia burgdorferi sensu lato (s.l.), Anaplasma phagocytophilum, Rickettsia species, Babesia spp., and tick-borne encephalitis virus. Tick feeding itself induces rapid and sometimes long-lasting dysbiosis of the skin microbial community, creating temporal windows of vulnerability for pathogen invasion. Concurrently, within the tick vector, a core set of endosymbiotic bacteria, including Rickettsia buchneri, Midichloria mitochondrii, Coxiella-like, and Francisella-like endosymbionts, engage in complex mutualistic, competitive, and facilitative interactions. These symbionts regulate vector competence through nutrient provisioning (especially B-vitamins), direct competition for niche space, and immune priming or suppression of the tick's innate immune system. Such interactions ultimately determine the maintenance, abundance, and transmissibility of tick-borne pathogens. By integrating these dual host-vector microbiome perspectives in a comprehensive review, we highlight emerging mechanistic insights into transmission ecology and biologically grounded targets for the prevention and control of tick-borne diseases, including anti-microbiota vaccines and paratransgenic and microbiome-based approaches.},
}
@article {pmid41712385,
year = {2026},
author = {Hong, J and Xue, W and Wang, T},
title = {Universal gene-level bimodality in natural microbial communities.},
journal = {Cell reports},
volume = {45},
number = {3},
pages = {117013},
doi = {10.1016/j.celrep.2026.117013},
pmid = {41712385},
issn = {2211-1247},
mesh = {Humans ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Machine Learning ; },
abstract = {Bimodality-the coexistence of two peaks in trait distributions-is common in natural ecosystems. In microbiomes, bimodality of species abundances is known. However, whether this pattern applies to community functionality remains unclear. Here, we systematically investigate the abundance distributions of individual genes in different microbiomes, from human gut to ocean, revealing widespread gene-level bimodality. The bimodal genes are enriched in niche-specific pathways, suggesting their roles in ecological adaptation of the community. Based on their abundances, we develop a framework for microbiome functional typing, offering a gene-centric alternative to the taxonomy-based paradigm. Applied to the human gut, our approach identifies eleven genes exhibiting robust bimodality across western countries. These genes are associated with diseases such as liver cirrhosis. Machine learning models leveraging these genes are predictive of these diseases, underscoring their potential as clinically relevant biomarkers. Our work provides critical insights for microbiome functional architecture and has implications for microbiome-based diagnostics.},
}
@article {pmid41715166,
year = {2026},
author = {Zhang, J and Xu, L and Ge, X and Zi, X and Chen, S and Liu, C and Wang, K and Zhou, J and Dou, T and Wong, JWC and Lin, Q and Kang, X and Cao, Z},
title = {Cross-kingdom genomic variation in chicken gut microbiomes: insights from China's diverse local breeds.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41715166},
issn = {2049-2618},
support = {2024A1515140076//Guangdong Basic and Applied Basic Research Foundation/ ; 202401AU070079//Yunnan Fundamental Research Projects/ ; 221110133//Dongguan University of Technology Top Talent Professor Start Up Fund/ ; 202301BD070001-136//Key Project of Yunnan Province Agricultural Joint Special Project/ ; 202305AC160040//Yunnan Province Young and Middle-aged Academic and Technical Leader Reserve Talent Project/ ; },
mesh = {Animals ; China ; *Chickens/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; *Genetic Variation ; *Bacteria/genetics/classification/isolation &amp; purification ; Gene Transfer, Horizontal ; Metagenome ; Polymorphism, Single Nucleotide ; Bacteriophages/genetics/classification ; },
abstract = {BACKGROUND: The gut microbiome possesses substantial genetic diversity that supports microbial adaptation, but the genomic variation patterns across its prokaryotic and viral populations remain incompletely characterized.<br><br>RESULTS: Through integrated metagenomic and metatranscriptomic analysis of ten indigenous chicken breeds from China, we recovered 1527 representative prokaryotic MAGs, 37,555 representative DNA viral contigs, and 1867 representative RNA viral contigs (primarily comprising Bacillota/Bacteroidota, Uroviricota, and Lenarviricota/Pisuviricota, respectively). By integrating complementary short-read and long-read metagenomics with metatranscriptomics, we identified structural variants (SVs) and single-nucleotide variants (SNVs) in these cross-kingdom genomes. Positive SV-SNV density correlations occurred consistently across all microbial groups, indicating coordinated mutational processes. DNA viruses exhibited the highest variant prevalence (86.9% SNVs, 47.7% SVs), with temperate phages accumulating significantly more variants than virulent phages. Functionally, prokaryotic variants accumulated in carbohydrate metabolism and amino acid metabolism, while viral variants demonstrated broad metabolic hijacking. Horizontal gene transfer (HGT) was characterized by a strong virus-associated signature (69.40% of 536 events) and marked by an asymmetric pattern, with phage-to-bacteria (P-to-B) flow alone constituting 37.50% of all events. Random forest analysis revealed a strong bidirectional predictive relationship between SV and SNV densities across prokaryotic, DNA viral, and RNA viral populations, suggesting coupled genomic instability. Niche breadth emerged as a major driver of SNVs across kingdoms and was positively correlated with variant density. In prokaryotes, HGT events significantly shaped variant patterns. For viruses, genomic GC content was an important factor and consistently showed a negative correlation with SNV density in both DNA and RNA viruses.<br><br>CONCLUSIONS: These findings demonstrate that coordinated mutational processes and kingdom-specific intrinsic factors drive genomic variation, with viruses serving as key genetic exchange vectors in chicken gut ecosystems. Video Abstract.},
}
@article {pmid41719127,
year = {2026},
author = {Wang, S and Su, LY and Lan, D and Pan, H and Xiong, M and Yao, M and Deng, Y and Fan, Z and Cao, Y and Zhou, H},
title = {Adenosine signaling driven by the gut microbiota underlies chronic alcohol-induced anesthetic resistance.},
journal = {Cell reports},
volume = {45},
number = {3},
pages = {117015},
doi = {10.1016/j.celrep.2026.117015},
pmid = {41719127},
issn = {2211-1247},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Adenosine/metabolism ; *Signal Transduction/drug effects ; Mice ; Humans ; *Ethanol/pharmacology ; Male ; Mice, Inbred C57BL ; *Anesthetics/pharmacology ; Female ; },
abstract = {Chronic alcohol consumption increases anesthetic tolerance, yet the underlying in vivo mechanisms remain unclear. Here, we demonstrate that long-term alcohol exposure reduces anesthetic efficacy in both humans and mice, prolonging induction and shortening maintenance. Fecal microbiota transplantation from alcohol-exposed donors recapitulated this phenotype in naive mice, indicating a causal role of gut microbiome alterations. Metagenomic and metabolomic analyses identified elevated adenosine as a key microbiota-derived metabolite. Adenosine supplementation decreased anesthetic sensitivity, likely via downregulation of gamma-aminobutyric acid (GABA) receptors. Our findings reveal a gut microbiota-adenosine pathway mediating alcohol-induced anesthetic resistance.},
}
@article {pmid41840625,
year = {2026},
author = {Zhang, Y and Zhang, Q and Luo, Y and Li, X and Zhao, R and Xu, Y and Zhang, S and Bai, X and Chen, H and Li, H and Hong, Y and Xie, Z},
title = {Bifidobacterium breve inhibits colorectal cancer via extracellular vesicles containing formate acetyltransferase.},
journal = {Journal of nanobiotechnology},
volume = {24},
number = {1},
pages = {},
pmid = {41840625},
issn = {1477-3155},
support = {82574649//National Natural Science Foundation of China/ ; JCYJ20250604175304006//Shenzhen Municipal Science and Technology Innovation Council/ ; 2023B03J1382//Guangzhou Science and Technology Program/ ; 2022ZD004//Nansha Science and Technology Program/ ; },
mesh = {*Colorectal Neoplasms/therapy/microbiology/pathology ; Animals ; Humans ; Mice ; *Bifidobacterium breve/enzymology/metabolism ; *Extracellular Vesicles/metabolism ; Cell Line, Tumor ; Gastrointestinal Microbiome ; Probiotics/pharmacology ; *Acetyltransferases/metabolism ; Apoptosis/drug effects ; Female ; Feces/microbiology ; Male ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer-related mortality worldwide. The gut microbiota exerts unique therapeutic advantages against CRC, and the probiotic Bifidobacterium breve (B. breve) has been extensively documented to suppress CRC initiation in murine models. Although the role of B. breve in CRC has been established, whether its extracellular vesicles (EVs), as key mediators of bacteria-host crosstalk, exert a functional impact remains undefined. Here, we aim to explore the therapeutic potential of B. breve-derived EVs (B.breEVs) and their active cargo, formate acetyltransferase (pflB), in CRC.<br><br>RESULTS: Integrative analysis of the curated database of human gut metagenomes cohort (GMrepo) database and an MC38 subcutaneous tumor model revealed a significant reduction of B. breve abundance in faecal samples from CRC patients and tumor-bearing mice. Administration of live B. breve or its cell-free supernatant markedly inhibited tumor growth, whereas pasteurized bacteria or GW4869-mediated EVs blockade abolished this effect, indicating that EVs are the critical effector entities. Isolated B.breEVs selectively accumulated within tumor tissue, directly triggered apoptosis of colorectal cancer cells, and elevated the proportion of IFN-&#x3b3;&#x207a; CD8&#x207a; cytotoxic T lymphocytes (CTLs) in tumor while concurrently ameliorating gut microbial structure and function. Mass-spectrometric profiling identified the pflB as an important active protein within B.breEVs. Recombinant pflB selectively inhibited MC38 cell viability in vitro and significantly reduced CRC burden in vivo. RNA sequencing of tumor issue demonstrated that pflB up-regulated granzyme B, perforin1 and CTL/NK-associated transcripts, and activated the intrinsic apoptotic pathway. Immuno-combination studies further revealed that pflB plus anti-PD1 therapy markedly increased the infiltration of CD8&#x207a; CTL and NK cells, and enhanced their cytotoxicity compared to either monotherapy.<br><br>CONCLUSIONS: B. breve secretes pflB-loaded EVs that reshape the intestinal micro-ecology, activate CD8&#x207a; CTL/NK anti-tumor immunity, directly induce mitochondrial apoptosis in malignant cells, and enhance the effects of immune checkpoint blockers to overcome drug resistance, offering a precision "probiotic-EVs-active protein" triadic intervention strategy for CRC.},
}
@article {pmid41860897,
year = {2026},
author = {Olaleye, M and O'Ferrall, AM and Goodman, RN and Kabila, DW and Peters, M and Falq, G and Samuel, J and Doyle, D and Gomez, D and Oloruntuyi, G and Isah, S and Adetunji, AS and Farley, E and Evans, NJ and Sherlock, M and Roberts, AP and Amirtharajah, M and Ainsworth, S},
title = {Shotgun metagenomic analysis of the oral microbiomes of children with noma.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {3},
pages = {e0014118},
doi = {10.1371/journal.pntd.0014118},
pmid = {41860897},
issn = {1935-2735},
mesh = {Humans ; Male ; Female ; Child ; Metagenomics ; *Microbiota/genetics ; *Noma/microbiology ; Child, Preschool ; *Saliva/microbiology ; Metagenome ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Nigeria ; *Bacteria/genetics/classification/isolation &amp; purification ; Dysbiosis/microbiology ; Treponema/genetics/isolation &amp; purification ; Adolescent ; },
abstract = {Noma is a rapidly progressive orofacial gangrene that predominantly affects children living in extreme poverty. Despite its documentation since antiquity and its designation as a World Health Organisation Neglected Tropical Disease in 2023, the microbiological cause of noma remains poorly understood, with no specific organisms confidently identified as definitive aetiological agents. Here, we present the first deep shotgun metagenomic profiling of oral saliva microbiomes from 19 Nigerian children with acute noma. Our analyses of this preliminary study reveal marked microbial dysbiosis in noma microbiomes, with machine learning and multivariate statistical analyses indicating significant enrichment of Treponema, Porphyromonas, and Bacteroides, alongside depletion of Streptococcus and Rothia, as key microbial signatures of noma disease. From the dataset we recovered 40 high-quality Treponema metagenome assembled genomes (MAGs) spanning 19 species, 14 of which were novel. Notably, a novel species designated Treponema sp. A was detected in 15 of the 19 noma participants and was entirely absent from an internationally representative set of healthy saliva metagenomes. Re-analysis of previously published 16S rRNA datasets from children with noma in Niger also revealed Treponema sp. A to be highly prevalent in noma cases but extremely rare in controls. While these findings highlight Treponema, particularly Treponema sp. A, as an organism of interest and a potential contributor to noma pathogenesis, further comprehensive studies will be required to confirm this association and to clarify whether it reflects a causal role and/or is a genuine marker of noma dysbiosis. Additionally, analysis of antimicrobial resistance determinants detected in noma metagenomes revealed concerning levels of resistance to antibiotics commonly used in noma treatment, particularly β-lactams and metronidazole, especially among Prevotella spp. These findings provide the first high-resolution microbial framework for noma and offer a foundation for future research into its pathogenesis and the development of novel diagnostics, therapeutics, and preventive strategies in endemic settings.},
}
@article {pmid41887904,
year = {2026},
author = {Jin, R and Chen, C and Zhang, J and Li, Y and Wu, Y and Wang, F and Chen, Z and Huang, T and Cheng, Q and Yu, X and Jia, P},
title = {Solid waste dumping differentially impacts soil prokaryotic, fungal, and viral communities: Insights from metagenomics.},
journal = {Journal of environmental sciences (China)},
volume = {163},
number = {},
pages = {867-879},
doi = {10.1016/j.jes.2025.10.021},
pmid = {41887904},
issn = {1001-0742},
mesh = {*Soil Microbiology ; Metagenomics ; *Microbiota ; Fungi ; *Solid Waste ; Soil/chemistry ; Soil Pollutants/analysis ; *Refuse Disposal ; Environmental Monitoring ; },
abstract = {Rapid urbanization and industrialization have dramatically increased global solid waste generation, placing immense pressure on waste management systems. In many developing countries, illegal and uncontrolled dumping remains widespread, yet its ecological impacts, particularly on soil microbial communities, are still poorly understood. To address this knowledge gap, we applied high-throughput amplicon sequencing and metagenomic profiling to analyze soil microbiomes across three categories of solid waste dumping. Our results show that solid waste dumping significantly altered both biotic and abiotic components of soil ecosystems. Soil properties shifted abruptly, with elevated pH and increased concentrations of pollutants such as petroleum hydrocarbons and fluorides. Microbial communities were extensively restructured, exhibiting both taxonomic turnover and functional adaptations. Viral communities displayed greater sensitivity to dumping-induced disturbances than prokaryotic or fungal communities. These findings provide new insights into soil microbiome responses to anthropogenic pollution and highlight taxon-specific adaptation strategies. To our knowledge, this is among the first comparative studies integrating prokaryotic, fungal, and viral responses to solid waste dumping using high-throughput molecular approaches. Our findings present a novel perspective that may guide future monitoring efforts and enhance approaches to environmental damage identification and assessment.},
}
@article {pmid41891399,
year = {2026},
author = {Elsheikh, M and Ibrahim, MA and Fares, S and Bhongade, M and Adhem, K and Ramirez-Morales, XI and Kaseb, AO and Petrosino, J and Hassan, MM and Jalal, PK},
title = {Influence of Gut Microbiota on Response to Immune Check Point Inhibitors in MASLD Patients With HCC: Unraveling the Connection.},
journal = {Cancer medicine},
volume = {15},
number = {4},
pages = {e71738},
doi = {10.1002/cam4.71738},
pmid = {41891399},
issn = {2045-7634},
support = {R21CA293626/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Liver Neoplasms/drug therapy/immunology/microbiology/complications ; *Carcinoma, Hepatocellular/drug therapy/immunology/microbiology/complications ; Dysbiosis/microbiology ; Drug Resistance, Neoplasm ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; },
abstract = {Immune checkpoint inhibitors (ICIs) have emerged as a promising treatment for various cancers, including advanced hepatocellular carcinoma (HCC). However, a significant proportion of patients with HCC, particularly those with metabolic dysfunction-associated liver disease (MASLD), exhibit resistance to ICI therapy. Studies have revealed that the presence of specific gut bacteria, such as Akkermansia, Bifidobacterium, and Lachnoclostridium, is associated with improved outcomes with ICI-treated HCC patients. Conversely, the overgrowth of bacteria like Enterobacteriaceae is linked to resistance to therapy. This review investigates the role of gut microbiota in shaping immune checkpoint inhibitor responses in MASLD-related hepatocellular carcinoma, focusing on how dysbiosis may contribute to ICI resistance and exploring microbiome modulation strategies, such as fecal microbiota transplantation and probiotics, aiming to optimize therapeutic outcomes.},
}
@article {pmid41891698,
year = {2026},
author = {Li, Y and Ji, M and Tu, Q},
title = {Patterns and drivers of macro- and micro-diversity of mudflat intertidal archaeomes along the Chinese coasts.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0143425},
doi = {10.1128/msystems.01434-25},
pmid = {41891698},
issn = {2379-5077},
abstract = {Archaea are widespread in Earth's ecosystems, contributing to ecosystem multifunctioning and stability. Compared to bacteria, our understanding of the biodiversity and underlying drivers of archaeal communities in representative ecosystems remains much less tapped. In this study, the macro- and micro-diversity of mudflat intertidal archaeomes were comprehensively analyzed at a large geographic scale, aiming to resolve the ecological drivers determining the variations in archaeal biodiversity. The compositions of mudflat intertidal archaeal taxa highly varied, especially the dominant Thaumarcheota and Euryarchaeota, but maintained relatively stable functional potential across space, demonstrating that functional traits were selected by the ecosystem in priority. While archaeal communities carried important functional traits mediating various biogeochemical cycling processes, horizontal gene transfer played critical roles in endowing functional genes for many archaeal lineages, such as the citric acid cycle in Methanosarcinia and various amino acid metabolism genes in Thermoplasmata. Spatial scaling, including latitudinal diversity gradient and distance-decay patterns (DDR), was clearly observed for archaeal taxonomic groups, but only DDR was weakly observed for functional traits. Intra-population genetic variations were significantly and positively associated with community macro-diversity, demonstrating covariations between nucleotide-level micro- and community-level macro-diversity. The compositions of intertidal archaeomes were mainly structured by homogeneous selection, with different phylogenetic bins being shaped by distinct ecological processes and remarkable variations across different sites. The study contributes to a comprehensive insight into the mechanisms shaping archaeal diversity and ecological characteristics within a fluctuating ecosystem.IMPORTANCEThe dynamic intertidal mudflat ecosystems host intense biogeochemical activities mediated by microbial communities, among which archaea contribute as an essential component but remain much less understood compared to bacteria. To gain better insights into the diversity, functional potential, and ecological drivers of archaeal communities in intertidal mudflats, archaeal phylogenetic signatures and genomic sequences were recovered via amplicon sequencing of 16S rRNA genes and shotgun metagenomes, targeting both macro- and micro-diversity. The results showed that archaeal taxonomic composition highly varied across space, whereas the functional potential remained relatively stable. Horizontal gene transfer served as an important source of archaeal metabolic diversity, obtaining additional genes linked to key biochemical pathways. The dominance of environmental selection further demonstrated the ecological forces governing archaeal communities in highly variable coastal habitats. This study established a large-scale framework for understanding the microbial ecology of intertidal archaeomes in dynamic coastal ecosystems.},
}
@article {pmid41892424,
year = {2026},
author = {Gomes, E and Mesquita, TG and Serra, P and Araújo, D and Almeida, C and Machado, A and Oliveira, R and Castro, J},
title = {Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/antibiotics15030262},
pmid = {41892424},
issn = {2079-6382},
support = {https://doi.org/10.54499/2024.13640.PEX//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; https://doi.org/10.54499/2022.07654.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; APTA4shiga (number 14840)//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; },
abstract = {Antimicrobial resistance (AMR) poses a critical global public health threat, with the food chain serving as a significant transmission route connecting animals, environment, and humans. This review adopts a One Health perspective to analyze the key drivers of AMR dissemination across animal agriculture, aquaculture and food processing. We evaluate detection methodologies, contrasting the regulatory gold standard of culture-based phenotypic testing with rapid molecular advancements, including Whole Genome Sequencing (WGS), metagenomics, and emerging CRISPR-Cas diagnostics. While molecular tools offer unprecedented speed and resolution, challenges such as matrix interference, the viable but non-culturable (VBNC) state, and the genotype-phenotype disconnect remain. Finally, integrated mitigation strategies are also described, ranging from on-farm antimicrobial stewardship and innovative biofilm control to consumer hygiene practices. It is essential to bridge the technical and regulatory gaps in AMR surveillance in order to develop effective interventions and ensure a safer food system.},
}
@article {pmid41894564,
year = {2026},
author = {McCartin, LJ and Vohsen, SA and Wood, AL and Horowitz, J and Orozco-Juarbe, JJ and Pittoors, N and Morrissey, D and Vaga, CF and Hansel, CM and Collins, AG and Quattrini, AM and Herrera, S},
title = {Accounting for Intra- and Intergenomic Sequence Variation in Reference Barcodes Improves eDNA Metabarcoding Biodiversity Assessment.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70130},
doi = {10.1111/1755-0998.70130},
pmid = {41894564},
issn = {1755-0998},
support = {NA18OAR0110289//NOAA Ocean Exploration/ ; NA21OAR0110202//NOAA Ocean Exploration/ ; NA18NOS4780166//National Centers for Coastal Ocean Science/ ; //Smithsonian Institution/ ; //Smithsonian Women's Committee/ ; //Bureau of Ocean Energy Management/ ; 2000013668//National Academies of Sciences, Engineering, and Medicine/ ; //NOAA Fisheries Office of Science and Technology/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Animals ; *DNA, Environmental/genetics ; Puerto Rico ; *Anthozoa/genetics/classification ; *Genetic Variation ; *Metagenomics/methods ; RNA, Ribosomal, 28S/genetics ; },
abstract = {Environmental DNA (eDNA) metabarcoding can rapidly characterise biodiversity, yet its accuracy and effectiveness are limited by incomplete DNA barcode reference databases. We evaluated how comprehensive reference databases that include sequence variation within genomes (intragenomic) and across individuals and species (intergenomic) improve eDNA-based biodiversity assessments. We collected coral tissue and water samples at deep sites offshore Puerto Rico for reference barcoding and eDNA metabarcoding. Genome skimming coral specimens yielded 28S barcodes for 314 of 346 samples (90.8%) and revealed divergent intragenomic 28S lineages in multiple octocoral families. Incorporating local reference barcodes substantially changed ASV taxonomic classifications: 22 ASVs (8.9%) gained genus-level resolution, 19 ASVs (7.7%) were reassigned to different genera, and 14 ASVs (5.7%) lost incorrect genus-level classifications. Thus, incomplete reference databases produce not only unclassified ASVs but also false positive detections and ecologically meaningful misclassifications. When intragenomic 28S lineages were excluded from the reference database, 18 ASVs (7.4%) could not be classified to family or genus, demonstrating that unrecognised intragenomic variation can be mistaken for unsampled taxa. Integrating reference genome skimming and eDNA metabarcoding expanded known coral family richness by 36% at depths shallower than 1000 m and by 181% at depths greater than 1000 m. eDNA also detected two coral families previously unknown off Puerto Rico and nearby islands, underscoring its potential for biodiversity discovery.},
}
@article {pmid41895941,
year = {2026},
author = {Zhang, J and Li, Y and Zhao, X and Wang, Q and Li, J and Xia, Y and Jambal, T and Dorjgotov, D and Zha, M and Chen, Y},
title = {The cheese of Xilingol: A comparative study on microbial diversity and metabolic profiles across typical and meadow steppes.},
journal = {Food research international (Ottawa, Ont.)},
volume = {232},
number = {},
pages = {118860},
doi = {10.1016/j.foodres.2026.118860},
pmid = {41895941},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; Milk/microbiology ; *Food Microbiology ; Animals ; Moraxella/isolation &amp; purification/metabolism ; Lactococcus lactis/isolation &amp; purification/metabolism ; *Microbiota ; *Metabolome ; Amino Acids/analysis ; China ; },
abstract = {Xilingol cheese (hurood), a traditional product of Inner Mongolia, acquires its superior flavor and quality from region-specific microbial communities. Understanding the microorganisms and metabolites of hurood across different grassland ecosystems is crucial. This study collected milk and hurood samples from typical and meadow steppes. A total of 179 species were identified, with Moraxella osloensis being more abundant in milk and Lactococcus lactis dominant in hurood. Additionally, 26 differential metabolites were screened from different grasslands, with 19 metabolites found in higher concentrations in hurood, such as N-lactoyl-phenylalanine and N-Acetyl-L-Histidine. These differential metabolites are mainly involved in lipid, carbohydrate, amino acid, and energy metabolism. Spearman correlation analysis revealed that L. lactis was significantly and positively correlated with differential metabolites such as O-phospho-l-serine and gluconic acid, which may affect hurood quality through carbohydrate and protein metabolism, especially amino acid metabolism. M. osloensis was positively correlated with metabolites such as 2-Methylhippuric acid and γ-Glu-Cys. Samples from typical steppe showed a richer microbial diversity, while samples from meadow steppe exhibited a higher enrichment of beneficial microorganisms and metabolites. Superior milk quality and the environmental conditions for lactic acid bacteria colonization may both promote the formation of superior flavor characteristics and functional components. This observational study offers valuable insights into the microbial and metabolic characteristics of hurood, thereby supporting efforts to improve hurood quality.},
}
@article {pmid39422492,
year = {2024},
author = {Lu, F and Huang, T and Chen, R and Yin, H},
title = {Multi-omics analysis reveals the interplay between pulmonary microbiome and host in immunocompromised patients with sepsis-induced acute lung injury.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0142424},
pmid = {39422492},
issn = {2165-0497},
support = {2024A04J4179//GDSTC | Basic and Applied Basic Research Foundation of Guangdong Province ()/ ; },
mesh = {Humans ; *Sepsis/complications/microbiology/immunology ; *Immunocompromised Host ; *Microbiota/genetics ; Female ; Male ; Middle Aged ; *Lung/microbiology/immunology ; *Acute Lung Injury/microbiology/immunology/etiology ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Adult ; Transcriptome ; Gene Expression Profiling ; Multiomics ; },
abstract = {UNLABELLED: The mechanisms behind the high inflammatory state and immunocompromise in severe sepsis remain unclear. While microbiota's role in immune regulation is known, the impact of pulmonary microbiota on sepsis progression is not fully understood. This study aims to investigate pulmonary microbial characteristics in septic patients and their relationship with host immune-related genes and clinical features. Fifty-four sepsis patients were divided into the immunocompromised host (ICH) group (n = 18) and the control group (n = 36). Bronchoalveolar lavage fluid (BALF) was analyzed using metagenomic next-generation sequencing (mNGS) to assess the pulmonary microbiome, and transcriptomic sequencing evaluated host gene expression. The pulmonary microbiota network in the ICH group showed notable alterations. Symbiotic bacteria like Streptococcus salivarius and Streptococcus oralis were key taxa in the control group. In contrast, opportunistic pathogens such as Campylobacter concisus and Prevotella melaninogenica, typically linked to infections in various body sites, dominated in the ICH group. Transcriptomic analysis revealed differential genes between the two groups. The downregulated differential genes in the ICH group were primarily enriched in pathways related to T-cell activation and the Type I interferon signaling pathway, both crucial for the immune system. Further correlation analysis identified significant associations between certain microbes and host genes, as well as clinical indicators, particularly with species like Campylobacter concisus, Streptococcus salivarius, Streptococcus oralis, and several species of Veillonella. These findings suggest that alterations in the pulmonary microbiome, especially the presence of opportunistic pathogens, may contribute to immune dysregulation in immunocompromised septic patients, warranting further research to explore causal relationships.<br><br>IMPORTANCE: Recent research has substantiated the significant role of microbiota in immune regulation, which could influence high inflammatory state and immunocompromise in patients with severe sepsis, as well as provide new opportunities for acute lung injury induced by sepsis diagnosis and treatment. Our study identified some potential critical microbes (Campylobacter concisus and several species of Veillonella), which were correlated with immune-related genes and might be the novel target to regulate immunotherapy in sepsis.},
}
@article {pmid39472002,
year = {2024},
author = {Yang, B and Zhang, C and Guan, C and Feng, X and Yan, D and Zhang, Z and Qin, Y and Xiong, S and Zhang, W and Cai, X and Hu, L},
title = {Analysis of the composition and function of rhizosphere microbial communities in plants with tobacco bacterial wilt disease and healthy plants.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0055924},
pmid = {39472002},
issn = {2165-0497},
support = {D2021194//Jiangxi Tobacco company/ ; D2019052//Shanghai Tobacco Group Co. Ltd/ ; 2020-079//Shanxi Scholarship Council of China (SSCC)/ ; 201901D111194//Shanxi Province Natural Science Foundation/ ; XD1807//Science Research Start-up Fund for Doctors of Shanxi Medical University/ ; },
mesh = {*Rhizosphere ; *Nicotiana/microbiology ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Soil/chemistry ; *Microbiota ; Nitrogen/analysis ; Ralstonia solanacearum ; Plant Roots/microbiology ; China ; Potassium/analysis ; Phosphorus/analysis ; },
abstract = {To explore the factors influencing the occurrence of bacterial wilt, the differences in the physicochemical properties, microbial community composition and function between rhizosphere soil of tobacco plants with bacterial wilt and healthy plants in the tobacco planting area of Fuzhou City, Jiangxi Province were analyzed and compared. The results showed that the rhizosphere soil of diseased tobacco exhibited significantly reduced levels of exchangeable potassium, water-soluble potassium, nitrate nitrogen, total nitrogen and pH, in comparison to the rhizosphere soil of healthy plants. Conversely, the available phosphorus content of the rhizosphere soil of diseased tobacco was significantly increased. The amount of Ralstonia solanacearum in soil was negatively correlated with pH, nitrate nitrogen and total nitrogen, and positively correlated with exchangeable potassium and water-soluble potassium. A total of 43 genera were significantly different between the two groups of rhizosphere soil, of which 24 genera were enriched in the rhizosphere of healthy plants, including Ideonella, Rhizophagus, Rhizobacter, Altererythrobacter and Ignavibacterium associated with plant disease resistance, Thermodesulfovibrio, Syntrophorhabdus, Syntrophus, Chlorobium, Hydrogenophaga and Limnohabitans associated with soil sulfur metabolism, as well as Ignavibacterium, Ideonella, Derxia and Azohydromonas associated with soil nitrogen cycling. Kyoto Encyclopedia of Genes and Genomes functional analysis of the unigenes obtained by metagenomic sequencing also showed that the differential unigenes were significantly enriched in the sulfur metabolism pathway. In addition, the rhizosphere soil of diseased tobacco plants exhibited a higher abundance of antibiotic-producing actinomycetes and an increased load of antibiotic resistance genes compared to that of healthy plants. In general, lower pH value, less content of nitrate nitrogen and total nitrogen, and more content of exchangeable potassium and water-soluble potassium could contribute to onset of bacterial wilt. Twenty-four genera, including Ideonella and Rhizophagus, may construct a healthy microecological network in the rhizosphere of tobacco plants. All these factors may interact with each other to control the development of bacterial wilt. This complicated interaction network needs to be explored further. IMPORTANCE Previous studies have mainly focused on the differences in microbial species composition between healthy and diseased soils, but the differences in microbial community functions between two types of soil have not been well characterized. In this study, soil samples in diseased and healthy plant rhizospheres were collected for physicochemical property testing and metagenomic sequencing. We focused on analyzing the differences in physicochemical properties and microbial community functions between these soils, as well as the correlation between these factors and pathogen content. The results of this study provide a theoretical basis for further understanding the occurrence of tobacco bacterial wilt in the field.},
}
@article {pmid39475247,
year = {2024},
author = {Xu, Z and Yeoh, YK and Tun, HM and Fei, N and Zhang, J and Morrison, M and Kamm, MA and Yu, J and Chan, FKL and Ng, SC},
title = {Variation in the metagenomic analysis of fecal microbiome composition calls for a standardized operating approach.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0151624},
pmid = {39475247},
issn = {2165-0497},
support = {//InnoHK/ ; },
mesh = {Humans ; *Feces/microbiology ; *Metagenomics/methods/standards ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Male ; Middle Aged ; DNA, Bacterial/genetics/isolation &amp; purification ; Adult ; Specimen Handling/methods/standards ; Reproducibility of Results ; Aged ; Colorectal Neoplasms/microbiology ; Inflammatory Bowel Diseases/microbiology ; Diabetes Mellitus, Type 2/microbiology ; },
abstract = {The reproducibility in microbiome studies is limited due to the lack of one gold-standard operating procedure. The aim of this study was to examine the impact of protocol variations on microbiome composition using metagenomic data sets from a single center. We assessed the variation in a data set consisted of 2,722 subjects, including 9 subcohorts harboring healthy subjects and patients with various disorders, such as inflammatory bowel disease, colorectal cancer, and type 2 diabetes. Two different DNA extraction kits, with or without lyticase, and two sample storage methods were compared. Our results indicated that DNA extraction had the largest impact on gut microbiota diversity among all host factors and sample operating procedures. Healthy subjects matched by age, body mass index, and sample operating methods exhibited reduced, yet significant differences (PERMANOVA, P < 0.05) in gut microbiota composition across studies. The variations contributed by DNA extraction were primarily driven by different recovery efficiency of gram-positive bacteria, e.g., phyla Firmicutes and Actinobacteria. This was further confirmed by a parallel comparison of fecal samples from five healthy subjects and a standard mock community. In addition, the DNA extraction method influenced DNA biomass, quality, and the detection of specific lineage-associated diseases. Sample operating approach and batch effects should be considered for cohorts with large sample size or longitudinal cohorts to ensure that source data were appropriately generated and analyzed. Comparison between samples processed with inconsistent methods should be dealt with caution. This study will promote the establishment of a sample operating standard to enhance our understanding of microbiome and translating in clinical practice.IMPORTANCEThe reproducibility of human gut microbiome studies has been suboptimal across cohorts and study design choices. One possible reason for the disagreement is the introduction of systemic biases due to differences in methodologies. In our study, we utilized microbial metagenomic data sets from 2,722 fecal samples generated from a single research center to examine the extent to which sample storage and DNA extraction influence the quantification of microbial composition and compared this variable with other sources of technical and biological variation. Our research highlights the impact of DNA extraction methods when analyzing microbiome data and suggests that the microbiome profile may be influenced by differences in the extraction efficiency of bacterial species. With metagenomics sequencing being increasingly used in clinical biology, our findings provide insight into the challenges using metagenomics sequencing in clinical diagnostics, where the detection of certain species and its abundance relative to a "healthy reference" is key.},
}
@article {pmid39475249,
year = {2024},
author = {Liang, Y and Huang, Z and Fan, S and Li, C and Huang, L and Huang, C and Hutchins, AP and Fang, C and Zhang, X},
title = {Highlight signatures of vaginal microbiota and metabolome contributed to the occurrence and recurrence of vulvovaginal candidiasis.},
journal = {Microbiology spectrum},
volume = {12},
number = {12},
pages = {e0152124},
pmid = {39475249},
issn = {2165-0497},
support = {JCYJ20190809101409603//Science and Technology Planning Project of Shenzen Municipality (Science and Technology Planning Project of Shenzhen of China)/ ; JCYJ20220530160206014//Science and Technology Planning Project of Shenzen Municipality (Science and Technology Planning Project of Shenzhen of China)/ ; 82201793//National Natural Science Foundation of China (NSFC)/ ; KYQD2022145, KYQD202211//Scientific Research Foundation of PEKING UNIVERSITY SHENZHEN HOSPITAL/ ; YBH2019-260//Shenzhen High-level Hospital Construction/ ; no. SZXK027//Shenzhen Key Medical Discipline Construction/ ; no. SZSM202011016//Sanming Project of Medicine in Shenzhen/ ; },
mesh = {Female ; Humans ; *Candidiasis, Vulvovaginal/microbiology/metabolism ; *Vagina/microbiology ; *Microbiota ; Adult ; *Metabolome ; Recurrence ; Lactobacillus/isolation &amp; purification/genetics/metabolism ; Young Adult ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; },
abstract = {UNLABELLED: Vulvovaginal candidiasis (VVC) is a common vaginal infectious disease caused by Candida. The high recurrence rate of VVC is a great clinical challenge, with recurrent VVC (RVVC) defined as four or more episodes within a year. In this study, we recruited 31 RVVC patients, 28 VVC patients, and 29 healthy women. Vaginal samples were collected for metagenomic and metabolic analysis. RVVC and VVC groups presented similar clinical symptoms, with only a significantly increased incidence of swelling in the VVC group. Vaginal microbiota in VVC/RVVC exhibited a decreased abundance of Lactobacillus and increased bacterial vaginosis-associated bacteria, such as Gardnerella, Prevotella, and Atopobium. Notably, Lactobacillus iners was higher in RVVC, suggesting not all Lactobacillus species are protective. Healthy women showed lower overall microbiota diversity, emphasizing single-species dominance for stability. Glycogen metabolism pathways were enriched in RVVC/VVC, and were correlated with Atopobium vaginae, Prevotella bivia, and Lactobacillus jensenii. Peptidoglycan synthesis pathways, associated with P. bivia, were enriched, with the substrate L-glutamate elevated in RVVC, possibly promoted by L. iners. These findings shed light on potential therapeutic targets for recurrent VVC, contributing to the understanding of the intricate interplay between the metabolism of vaginal microbiome and disease.<br><br>IMPORTANCE: This study enhances our knowledge of the vaginal microbiota dynamics and the role of associated metabolites in individuals with vulvovaginal candidiasis (VVC) and recurrent vulvovaginal candidiasis through shotgun sequencing and multi-omics analysis. The relationship between metabolites and vaginal microbiota and disease state was revealed. The accumulation of L-glutamate generated in glycogen metabolism, which is governed by Lactobacillus iners or bacterial vaginosis-associated bacteria, may contribute to the incidence and recurrence of VVC. Such insights have the potential to impact the treatment and prevention strategies for these common yet distressing conditions, potentially leading to targeted therapies and improved patient outcomes.},
}
@article {pmid41123352,
year = {2025},
author = {Akinsola, OA and Dahunsi, SO and Odekanle, EL},
title = {Metagenomic study of food waste anaerobic digestion.},
journal = {Microbiology spectrum},
volume = {13},
number = {12},
pages = {e0208725},
pmid = {41123352},
issn = {2165-0497},
mesh = {Anaerobiosis ; *Metagenomics ; Methane/metabolism/biosynthesis ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Archaea/metabolism/genetics/classification ; Biofuels ; Fermentation ; Microbiota/genetics ; Food ; Food Loss and Waste ; },
abstract = {This study explores anaerobic digestion of food waste to understand the microbial community dynamics and metabolic pathways that drive the conversion of organic waste into biogas. Sampling was done at multiple time points during those 4 weeks (weekly) to capture microbial succession/changes over time. The microbial profile was evaluated using QIIME2 and BV-BRC, while functional annotation tools (PICRUSt2) were used to identify dominant pathways. The results reveal a temporal shift in microbial communities, with fermentative bacteria, such as Lactobacillus and Clostridia, dominating the early stages of digestion, followed by methanogenic archaea like Methanomicrobia in the later stages. Pathway analysis showed that fermentation, aromatic compound degradation, and methanogenesis were the primary metabolic processes, with methanogenesis becoming more prominent by week 3 (FW3_S162_R1). The study highlights the critical role of microbial community adaptation in maximizing methane production and offers new insights into optimizing anaerobic digestion for more efficient food waste biogas generation. By combining metagenomic and metabolomic approaches, this research provides a comprehensive understanding of the microbial and metabolic factors that shape the anaerobic digestion process, contributing to the development of sustainable waste management practices.IMPORTANCEThis study employs a metagenomic approach to elucidate the intricate microbial communities and metabolic processes involved in the anaerobic digestion of food waste. It highlights microbial interactions that influence biogas production, offering insights for optimizing waste-to-energy conversion. Understanding these dynamics is key to improving digestion efficiency, reducing environmental impacts, and advancing sustainable waste management and circular economy strategies. The findings provide a valuable foundation for future innovations addressing global waste and energy challenges.},
}
@article {pmid41143528,
year = {2025},
author = {Mukherjee, SD and Adler, A and Dang, T and Taylor, EN and Curhan, G and Miller, AW},
title = {Evaluating the use of biobanked urine specimens for human urobiome studies.},
journal = {Microbiology spectrum},
volume = {13},
number = {12},
pages = {e0216424},
pmid = {41143528},
issn = {2165-0497},
support = {R01 DK121689/DK/NIDDK NIH HHS/United States ; //Lerner Research Institute, Cleveland Clinic/ ; },
mesh = {Humans ; *Biological Specimen Banks ; *Microbiota/genetics ; Male ; Female ; *Urine/microbiology ; *Urinary Tract/microbiology ; Metagenomics/methods ; Middle Aged ; Specimen Handling/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Aged ; },
abstract = {Case-control studies focused on the urinary tract microbiome, or urobiome, have consistently reported significant associations with disease. However, clinical urobiome studies have typically been small, averaging ~50 patients per study. While these sample sizes are sufficient to detect large effect sizes, they have not been able to differentiate disease phenotypes within a larger disease complex (e.g., different types of kidney stones), which have unique etiological origins. Biobanked urine specimens can help fill this void. However, since these specimens were not collected specifically for urobiome studies, they must be validated before drawing any strong conclusions. The objective of this study was to evaluate microbiome data derived from metagenomic analysis of biobanked urine specimens against the following criteria: (i) level of contaminants; (ii) retention of high-quality DNA; (iii) overgrowth of a few dominant bacteria; and (iv) preservation of sex-specific taxa. A total of 174 samples were assessed from biobanked or freshly collected specimens (N = 118 patients total), in addition to multiple positive and negative controls. While there were significant differences in diversity (alpha/beta; P < 0.001) based on whether or not samples were biobanked, these differences can largely be explained by study-specific variation. With these criteria, we find that biobanked urine specimens provide similar data to fresh specimens collected using standardized protocols and can be used for clinical urobiome studies.IMPORTANCEThe urinary tract microbiome, or urobiome, is an emerging field of study that has shown promise as an important contributor to urologic health and disease. However, since this field is relatively new, clinical studies to evaluate the urobiome in the context of urologic disease have been relatively small. The use of biobanked urine specimens would allow for much larger studies to be conducted in a relatively short period of time. However, the use of biobanked urine specimens must first be validated. In this study, we sought to evaluate the use of biobanked urine specimens through multiple metrics, compared to previous studies conducted specifically to assess the impact of the urobiome. Results of our study suggest that biobanked urine specimens produce similar data to urine samples collected under rigorously controlled conditions and can be used in casecontrol studies of urologic conditions.},
}
@article {pmid41196055,
year = {2025},
author = {Plaza Oñate, F and Quinquis, B and Thirion, F and Gilles, M and Morabito, C and Valeille, K and Martin, R and Guidet, B and Kern, C and Pécastaings, S},
title = {Assessment of protocols for characterization of the human skin microbiome using shotgun metagenomics and comparative analysis with 16S metabarcoding.},
journal = {Microbiology spectrum},
volume = {13},
number = {12},
pages = {e0173225},
pmid = {41196055},
issn = {2165-0497},
support = {ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; },
mesh = {Humans ; *Skin/microbiology/virology ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *DNA Barcoding, Taxonomic/methods ; Viruses/classification/genetics/isolation &amp; purification ; Fungi/classification/genetics/isolation &amp; purification ; Forehead/microbiology ; Adult ; DNA, Bacterial/genetics ; Male ; Sequence Analysis, DNA ; Female ; Skin Microbiome ; },
abstract = {The skin microbiome includes bacteria, fungi, and viruses, with composition varying significantly across body sites. Although 16S rRNA gene sequencing is common, it excludes non-prokaryotic taxa and offers limited functional data. Shotgun metagenomics provides broader taxonomic and functional insights but is challenging for low-biomass skin samples due to limited microbial DNA and high host contamination. In this study, we characterized the microbiome of the forehead and armpits in healthy individuals using shotgun metagenomics and assessed the strategies to improve sequencing success. We compared collection kits, DNA extraction protocols, and tested multiple displacement amplification (MDA). We found that sampling with D-Squame discs followed by an in-house DNA extraction protocol was the most effective combination to maximize DNA yields. MDA introduced significant compositional biases and is not recommended. Shotgun sequencing, without MDA, produced microbial compositions and diversity indices broadly consistent with 16S rRNA metabarcoding, although it showed discrepancies in the relative abundance of some genera. Consistent with prior studies, the armpit microbiome was dominated by Staphylococcus spp., whereas the forehead microbiome was dominated by Cutibacterium spp. Critically, shotgun sequencing provided additional insights into viral and eukaryotic microorganisms and revealed the functional potential of microbial communities, demonstrating its clear advantages over 16S rRNA metabarcoding for comprehensive skin microbiome research.IMPORTANCEWith growing evidence of the role of microorganisms in maintaining healthy skin, accurately characterizing the skin microbiome remains a significant challenge. In this study, we demonstrate that shotgun sequencing, carried out with adapted wet lab protocols, provides deep insights into the microbiome composition of specific areas, such as the forehead or the armpits. Notably, it enables the characterization of fungi and viruses while offering direct functional insights into microbial communities, providing a clear advantage over 16S ribosomal RNA gene sequencing. Our findings highlight the potential of shotgun metagenomics as a powerful tool for comprehensive skin microbiome analysis. They emphasize the importance of tailored protocols for low-biomass samples, improving the reliability of shotgun sequencing and paving the way for more robust clinical studies focused on the skin microbiome.},
}
@article {pmid41196057,
year = {2025},
author = {Fait Kadlec, T and Ilett, EE and da Cunha-Bang, C and Sengeløv, H and Brieghel, C and Gulay, A and Rafiq, S and Ravn, HB and Zheng, C and Nielsen, RV and Sørensen, SS and Zargari Marandi, R and Niemann, CU},
title = {Explainable machine learning to identify chronic lymphocytic leukemia and medication use based on gut microbiome data.},
journal = {Microbiology spectrum},
volume = {13},
number = {12},
pages = {e0094425},
pmid = {41196057},
issn = {2165-0497},
mesh = {Humans ; *Leukemia, Lymphocytic, Chronic, B-Cell/microbiology/drug therapy/diagnosis ; *Gastrointestinal Microbiome/drug effects ; *Machine Learning ; Male ; Female ; Aged ; Middle Aged ; Denmark ; Aged, 80 and over ; Adult ; Anti-Bacterial Agents/therapeutic use ; Cohort Studies ; Metagenomics ; },
abstract = {Medication, particularly antibiotics, significantly alters gut microbiome composition, often reducing microbial diversity and affecting host health. Given that the gut microbiome may influence cancer progression, we integrated clinical, shotgun metagenomic, and medication data to assess microbiome composition across diseased and healthy cohorts, as well as the impact of medication on microbiome variation. The study cohorts included patients with chronic lymphocytic leukemia (CLL, n = 85), acute myeloid leukemia (AML, n = 61), myeloid dysplastic syndrome (MDS), and other severe hematological malignancies (n = 104); patients scheduled for elective cardiac surgery (n = 89); and kidney donors (n = 9), all collected as part of a consecutive microbiome sampling effort at Copenhagen University Hospital, Denmark; and healthy individuals (N = 59). First, our analyses revealed similarities in both diversity and composition between microbiomes of patients with CLL and patients prior to elective cardiac surgery, whereas patients with AML and MDS exhibited the least diverse and most distinct microbiomes. Second, when we quantified sources of microbiome variation, the combination of medication, disease, age, and sex accounted for 4% of variation between all cohorts and 10.4% of variation between CLL and pre-cardiac surgery patients only; the two cohorts selected for comparison due to their similar microbiomes. Notably, this left 90%-95% of the variation unexplained, emphasizing the need for better identification of the parts of the microbiome variation impacting health and disease. Third, using a machine learning approach, we validated and further refined the CLL-associated microbiome pattern from our previous studies. Overall, our data provide a foundation for further investigation into disease-specific microbial signatures and the potential interactions between medication, underlying disease, and the microbiome, with the ultimate goal to improve our understanding and clinical management of CLL.IMPORTANCEThis study reveals how disease and medication influence the gut microbiome in patients with chronic lymphocytic leukemia (CLL) when compared to other more severe hematological malignancies, a cohort of patients scheduled for elective cardiac surgery representing a severely diseased nonhematological cohort, and a cohort of healthy individuals. We found that patients with CLL and those scheduled for cardiac surgery had the most similar microbiome diversity and composition. Similarities across very different disease contexts suggest that disease status alone has limited impact. Consistently, across all cohorts, medication, disease, age, and sex together explained only less of microbiome variation, leaving 90%-95% unexplained. This underscores the important need for better identification of factors shaping the microbiome. In addition, we validated a previously published, machine learning-based CLL-associated microbiome signature, demonstrating the robustness of our previous findings differentiating the microbiome signature for CLL as compared to healthy individuals. The findings expand knowledge on how disease states and medical treatments shape gut microbiome composition and diversity, potentially leading to new ways of managing CLL and improving patient outcomes through microbiome signatures.},
}
@article {pmid41802510,
year = {2026},
author = {Gou, X and Shen, Y and Liu, F and Wang, Y and Zong, Y and Qu, D and Ren Zeng, C and Nhamdriel, T and Kuang, T and Fan, G},
title = {Swertia chirayita ameliorates MAFLD by improving intestinal microenvironment and hepatic lipogenesis.},
journal = {Journal of ethnopharmacology},
volume = {364},
number = {},
pages = {121471},
doi = {10.1016/j.jep.2026.121471},
pmid = {41802510},
issn = {1872-7573},
mesh = {Animals ; *Lipogenesis/drug effects ; *Liver/drug effects/metabolism/pathology ; Male ; Rats ; *Swertia/chemistry ; *Plant Extracts/pharmacology/therapeutic use ; Rats, Sprague-Dawley ; Diet, High-Fat/adverse effects ; Intestines/drug effects ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Metabolic-associated fatty liver disease (MAFLD) is emerging as a very serious threat to human health. The search for effective remedies for MAFLD from natural herbs is gaining increasing attention. Swertia chirayita (SC) is a famous herb in China, India, and Nepal. It has long been employed within the traditional Tibetan medical system for managing hepatic disorders. Nevertheless, the therapeutic impacts and possible mechanisms of SC in the context of MAFLD are unclear.<br><br>AIM OF THE STUDY: This present investigation was designed to research the pharmacological influence and potential mechanisms of SC in MAFLD rats. We conducted a particular examination of its effects on the intestinal microenvironment and hepatic lipogenesis.<br><br>MATERIALS AND METHODS: The pharmacological effects of SC were evaluated in MAFLD rats established through a 12-week high-fat diet (HFD) feeding. After 8 weeks of SC administration, biochemical assessments were conducted for body fat, liver function, glucose metabolism, lipid parameters, and inflammatory factors. The main chemical constituents of SC and three short-chain fatty acids (SCFAs) in rat feces were quantitatively analyzed by HPLC. Furthermore, targeted metabolomics, transcriptomics, metagenomics, and Western blotting were employed to investigate possible mechanisms by which SC improves MAFLD.<br><br>RESULTS: Treatment with SC significantly ameliorated excessive fat accumulation and insulin resistance in MAFLD rats. It also improved hepatic enzyme activities (AST and ALT), several lipid metrics (TG, TC, and LDL-C), and liver histopathological changes. Moreover, SC attenuated systemic inflammation, as shown by decreased circulating IL-1&#x3b2;, TNF-&#x3b1;, LPS, and IL-6. Metagenomic profiling revealed that SC administration helped reestablish the dysregulation of multiple types of gut microbiota (bacteria, fungi, archaea, and viruses) in MAFLD rats. It improved microbial diversity, community composition, and transkingdom correlations. In addition, SC enhanced gut barrier function by raising the amount of butyric acid, acetic acid, and propionic acid and upregulating the expression of several ZO-1, occludin, and claudin-1. Liver transcriptomic analysis suggested that SC could regulate the metabolism of bile acids (BAs). Importantly, targeted metabolite analysis and western blotting demonstrated that SC improved bile acid dysfunction in MAFLD rats. In particular, SC increased TCDCA, TCA, and DCA, thereby activating the FXR/FGF15 signaling axis. This activation then controlled the production of SHP and SREBP-1c proteins in the hepatic, thereby inhibiting hepatic lipogenesis to improve MAFLD.<br><br>CONCLUSIONS: SC has shown a good therapeutic effect on MAFLD by improving intestinal microenvironment and hepatic lipogenesis. Specifically, it improves the imbalance of multiple types of gut microbiota, restores disrupted transkingdom interactions, promotes creation of beneficial SCFAs and bile acid, protects the intestinal barrier, and inhibits hepatic lipogenesis by regulating the BAs/FXR/FGF15 and SHP/SREBP-1c signaling pathways.},
}
@article {pmid41803907,
year = {2026},
author = {Fernández-de-Bobadilla, MD and Pérez-Cobas, AE and Andremont, A and Martínez, JL and Baquero, F and Lanza, VF and Coque, TM},
title = {The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the "robust-yet-fragile" architecture of human gut microbiomes.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41803907},
issn = {2049-2618},
support = {pFIS F19/00366//Instituto de Salud Carlos III/ ; CB21/13/00084//Instituto de Salud Carlos III/ ; CC23140547//Fundaci&#xf3;n Francisco Soria Melguizo/ ; MISTAR AC21_2/00041//Joint Programming Initiative on Antimicrobial Resistance/ ; "Ayudas de atracci&#xf3;n de talento investigador C&#xe9;sar Nombela" 2023-T1/SAL-GL28953//Comunidad de Madrid/ ; FP7#282004//European Union/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; French Guiana ; Metagenomics/methods ; Feces/microbiology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Metals/pharmacology ; Male ; Female ; Adult ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Metagenome ; *Drug Resistance, Microbial/genetics ; },
abstract = {BACKGROUND: Metagenomics enables detailed profiling of genes encoding antimicrobial resistance. However, most studies focus exclusively on antibiotic resistance genes (ARGs), excluding those associated with non-antibiotic antimicrobials (metals, biocides), and often rely on methods with low-sensitivity and low-specificity. Furthermore, they rarely examine populations exposed to minimal anthropogenic pollution. We analyzed fecal resistomes of 95 Wayampi individuals, an Indigenous community in remote French Guiana, using a targeted metagenomic capture platform covering 8667 genes, including ARGs, metal resistance genes (MRGs) and biocide resistance genes (BRGs) (PMID: 29335005). Resistome profiles were compared with those of Europeans to assess population-level differences.<br><br>RESULTS: ARG richness was similar between groups (259 in Wayampi vs. 264 in Europeans, 159 shared), but MRGs&#x2009;+&#x2009;BRGs gene richness was significantly higher in Wayampi (11,930 vs. 7419). Most genes appeared in a minority of individuals (mean 5% for ARGs, 2% for MRGs&#x2009;+&#x2009;BRGs), but several ARGs for tetracyclines [tet(32), tet(40), tet(O), tet(Q), tet(W), tet(X), tetAB(P)], aminoglycosides (ant6'-I, aph3-III), macrolides (ermB, ermF, mefA), and sulfonamides (sul2) were present in all individuals. Tetracycline resistance genes predominated overall, while beta-lactam resistance genes were more common in Wayampi, and genes conferring resistance to aminoglycosides, amphenicols, and folate inhibitors were more frequent in Europeans. Among MRGs, copper and arsenic resistance genes prevailed in both groups, followed by those for zinc, iron, cobalt, and nickel. Up to 76% of Wayampiis carried acquired MRGs for copper (pcoABCDRS and tcrB), silver (silACFPRS), arsenic (ars), and mercury (mer) detoxification. Shannon diversity indices were similar for ARGs, MRGs, and BRGs, but composition and evenness differed significantly. UMAP and ADONIS analyses distinguished cohorts based on ARG profiles (p&#x2009;<&#x2009;0.001), but not on MRGs or BRGs. Correlation analysis revealed conserved gene-sharing networks and introgression of acquired ARGs and MRGs within both gut microbiomes.<br><br>CONCLUSIONS: The diverse and balanced Wayampi resistome reflects a less perturbed microbiome compared to industrialized populations, and reveals a background of "core" and "shell" acquired ARGs and MRGs, consistent with the "robust-yet-fragile" architecture of scale-free networks. The patchy yet resilient gene distribution suggests varying levels of conserved gene sharing highways among populations, likely shaped by long-term microbial-human evolution, and supports a broader view on acquired antimicrobial resistance. Video Abstract.},
}
@article {pmid41882399,
year = {2026},
author = {Çilkiz, M},
title = {Microbial Biotechnology in Agriculture.},
journal = {Progress in molecular and subcellular biology},
volume = {62},
number = {},
pages = {251-306},
pmid = {41882399},
issn = {0079-6484},
mesh = {*Agriculture/methods ; *Biotechnology/methods ; Soil Microbiology ; Metagenomics/methods ; Crops, Agricultural/growth &amp; development/microbiology ; Metabolomics/methods ; Fertilizers ; },
abstract = {Global food security has become one of the greatest challenges of the twenty-first century due to the rapidly growing world population's food demands and environmental threats such as climate change, soil erosion, and the depletion of freshwater resources. The extensive use of chemical fertilizers and pesticides throughout conventional agriculture has increased productivity significantly, but it has additionally resulted in major ecological and socioeconomic problems, such as soil acidity, groundwater resource pollution, and decreased biodiversity. In this regard, microbial biotechnology is a particularly noteworthy technique that improves agricultural production while promoting environmental sustainability, maintaining ecological balance, and making effective use of resources. This application makes use of microorganisms to enhance soil health and structure, promote plant growth, and minimize both abiotic and biotic stresses. Microbial applications include nitrogen fixation, as well as biofertilizers that reduce the dependency on synthetic materials and biopesticides. Microbial consortia and biostimulants that improve plant physiology by producing phytohormones produce more dependable and durable consequences in the field. Metagenomics and metabolomics are the two types of omic technologies used in these areas of study that provide a thorough description of the variety and roles of microorganisms. Furthermore, the intentional production of microbes targeted at specific organisms has been made practical via synthetic biology and gene editing techniques. In-depth case studies performed in several countries reveal that microbial technologies significantly reduced expenses and improved soil production, advancing the sustainable development goals. Nevertheless, there are several barriers to the widespread use of microbial biotechnology in agriculture. These include unpredictable conditions in the fields, strict regulations, especially related to genetically modified organisms' problems with product quality, and farmers' insufficient understanding. Microbial biotechnology aims to accomplish its full potential as an advancement in technology and as an essential aspect of resource-efficient and environmentally friendly agricultural systems via responsible innovation, adaptable regulations, and worldwide cooperation.},
}
@article {pmid41882401,
year = {2026},
author = {Erözden, AA and Tavşanlı, N and Çalışkan, M and Arıkan, M},
title = {Microbial Omics.},
journal = {Progress in molecular and subcellular biology},
volume = {62},
number = {},
pages = {333-366},
pmid = {41882401},
issn = {0079-6484},
mesh = {*Metabolomics/methods ; *Proteomics/methods ; *Genomics/methods ; Metagenomics/methods ; *Computational Biology/methods ; Transcriptome ; Microbiota ; *Bacteria/genetics/metabolism ; },
abstract = {Omics technologies have revolutionized research across diverse fields, and their increasing use in microbiology has provided new opportunities for understanding microbial life. These methods enable detailed investigation of the molecular biology of individual organisms as well as the complex interactions within microbial communities. In this chapter, we describe key single-organism omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, as well as meta-omics techniques such as metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics. We also discuss integrative multi-omics strategies for studying microbial ecosystems. For each omics method, we outline its main features, experimental and bioinformatic workflows, major applications, and commonly used computational tools, thereby providing a practical guide for researchers aiming to explore microbial structure, function and interactions at multiple molecular levels.},
}
@article {pmid41883376,
year = {2026},
author = {Mao, C and Wang, Y and Li, X and Kong, Q and Al-Farraj, SA and Xu, EG and Grossart, HP and Huang, J and Song, W},
title = {Resistance Gene Dynamics, Biogeochemical Coupling, and Ecological Risks in Sediments of Anthropogenically Impacted Lake Wetlands in China.},
journal = {Environment &amp; health (Washington, D.C.)},
volume = {4},
number = {3},
pages = {420-433},
pmid = {41883376},
issn = {2833-8278},
abstract = {Antibiotic resistance is a growing global threat to both public health and ecosystem stability. While the "One Health" framework emphasizes the need to monitor antibiotic resistance genes (ARGs) across diverse environments worldwide, the risks posed by ARGs in lakes affected by human activities, particularly in lake sediments that serve as natural reservoirs of ARGs, remain poorly understood. Metagenomics enables culture-independent analysis of microbial communities and resistance genes, providing essential insights into ARG dynamics. This study investigates microbial communities, ARGs, metal resistance genes (MRGs), and mobile genetic elements (MGEs) in sediments from Lake Donghu and Lake Weishan in China, two contrasting lake ecosystems subject to urbanization and agricultural activities for over four decades, using high-throughput metagenomic sequencing and assembly. ARGs and MRGs were more strongly influenced by deterministic environmental factors, particularly heavy metals (Cd, Pb, Cu), whereas microbial community structures were predominantly shaped by stochastic processes. Metagenomic binning yielded 293 metagenome-assembled genomes (MAGs), 125 of which were identified as potential ARG hosts, with Proteobacteria and Desulfobacterota being the most common. These hosts frequently cocarried MGEs, virulence factor genes (VFGs), and MRGs and exhibited metabolic pathways linked to carbon, nitrogen, and greenhouse gas (CO2 and N2O) cycling. Dissolved organic carbon (DOC) was determined as a key factor influencing microbial metabolism and promoting resistance gene dissemination. Our findings highlight a tight coupling between ARG dissemination, microbial ecological functions, and biogeochemical processes, underscoring ecosystem-level risks associated with resistance proliferation in human-impacted wetlands of China and elsewhere.},
}
@article {pmid41887859,
year = {2026},
author = {Chen, J and Li, G and Liu, J and Yuan, X and Zhao, G and Yang, X and Huang, S and Zheng, Z},
title = {Comparative assessment of novel nematicide trifluenfuronate and fosthiazate on soil ecosystem: From microbial community structure to KEGG functional pathways.},
journal = {Journal of environmental sciences (China)},
volume = {163},
number = {},
pages = {409-419},
doi = {10.1016/j.jes.2025.05.033},
pmid = {41887859},
issn = {1001-0742},
mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; Soil/chemistry ; *Antinematodal Agents/toxicity ; Ecosystem ; *Microbiota/drug effects ; RNA, Ribosomal, 16S ; Bacteria ; Organophosphorus Compounds ; Thiazolidines ; },
abstract = {In recent years, the increasing demand for environmentally friendly pesticides in agricultural production has driven the development of novel pesticides characterized by high efficiency, low toxicity, and improved environmental compatibility. Simultaneously, greater emphasis is being placed on evaluating their impact on the soil ecosystem to ensure sustainable pesticide use and the stability of agroecosystems. In this study, we employed 16S rRNA gene high-throughput sequencing and metagenomic analysis to compare the effects of the novel nematicide trifluenfuronate and the commonly used nematicide fosthiazate on soil physicochemical properties, bacterial community structure, and metabolic functions in cucumber cultivation soils. Results showed that soil enzyme activity, microbial community structure and diversity exhibited the most significant differences on day 7 following nematicide application but stabilized by day 100. Both nematicide type and concentration were key factors influencing bacterial community structure. Compared to fosthiazate, trifluenfuronate more significantly enhanced soil bacterial community abundance while exerting fewer negative impacts on related enzyme activities and KEGG pathways. In addition, fosthiazate preferentially regulated membrane-associated efflux genes, whereas trifluenfuronate primarily interfered with the transcriptional regulation of target genes to mitigate antibiotic stress. These alterations in microbial community structure and function led to changes in soil nutrient bioavailability. This made the trifluenfuronate treatment group have higher available nitrogen and phosphorus content to supply to cucumber. This research contributes to understanding their ecological effects and paves the way for future sustainable pesticide research.},
}
@article {pmid39612216,
year = {2025},
author = {Wang, T and Luo, Y and Kong, X and Fang, L and Zhu, L and Yu, B and Zheng, P and Huang, Z and Mao, X and Jie, Y and Luo, J and Yan, H and He, J},
title = {Multiomics comparative analysis of feces AMRGs of Duroc pigs and Tibetan and the effect of fecal microbiota transplantation on AMRGs upon antibiotic exposure.},
journal = {Microbiology spectrum},
volume = {13},
number = {5},
pages = {e0198324},
pmid = {39612216},
issn = {2165-0497},
support = {No. U20A2056//MOST | National Natural Science Foundation of China (NSFC)/ ; 2020YFN0147//SPDST | Key Research and Development Program of Sichuan Province ()/ ; SCCXTD-2024-8//The Innovation Team of Sichuan Province/ ; },
mesh = {Animals ; Swine/microbiology ; *Feces/microbiology ; *Fecal Microbiota Transplantation ; *Anti-Bacterial Agents/pharmacology ; Tibet ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Gastrointestinal Microbiome ; Multiomics ; },
abstract = {UNLABELLED: Fecal matter is recognized as both a reservoir and a transmission source for various antimicrobial resistance genes (AMRGs). However, the transcriptional activity of AMRGs in swine feces is not well understood. In addition, the effect of fecal microbiota transplantation (FMT) on the excretion of AMRGs has rarely been reported. Our study explored the diversity, abundance, transcriptional activity, and bacterial hosts of AMRGs in Tibetan and Duroc pig feces using metagenomic and metatranscriptomic sequencing technologies. We discovered a significantly higher genomic abundance of AMRGs in the feces of Duroc pigs compared to Tibetan pigs (P < 0.001), although the transcript levels did not show a significant difference. The results showed that the core composition of AMRGs in pig feces varied considerably, with the most transcriptionally active AMRGs being oqxB, tetQ, Bla1, dfrA1, and amrB. Furthermore, the Firmicutes phylum is the main host of AMRGs. By transplanting fecal flora from Tibetan and Duroc pigs into the intestines of Duroc Landrace Yorkshire (DLY) piglets after acute antibiotic exposure, we found that only Tibetan pig fecal flora significantly reduced AMRGs in the feces of DLY piglets (P < 0.05). The effectiveness of Tibetan pig fecal microorganisms in removing AMRGs from DLY pig feces was mainly influenced by microbial communities, especially the Bacteroidota phylum. These findings offer valuable insights for the prevention and control of AMRG pollution.<br><br>IMPORTANCE: To the best of our knowledge, this study represents the first comprehensive analysis of antimicrobial resistance gene (AMRGs) expression in the fecal microbiota of Tibetan and Duroc pigs, employing an integrated metagenomic and metatranscriptomic approach. Our findings indicate a higher risk of AMRGs transmission in the feces of Duroc pigs compared to Tibetan pigs. Given the escalating antimicrobial resistance crisis, novel therapeutic interventions are imperative to mitigate gut colonization by pathogens and AMRGs. In this regard, we investigated the impact of fecal microbiota from Tibetan and Duroc pig sources on AMRGs excretion in Duroc Landrace Yorkshire (DLY) piglets' feces following acute antibiotic exposure. Remarkably, only fecal microbiota sourced from Tibetan pigs exhibited a reduction in AMRGs excretion in DLY piglets' feces. This underscores the significance of evaluating the presence of AMRGs within donor fecal microbiota for effective AMRGs decolonization strategies.},
}
@article {pmid40084855,
year = {2025},
author = {Brock, ML and Tavares-Reager, JF and Dong, J and Larkin, AA and Lam, T and Pineda, N and Olivares, CI and Mackey, KRM and Martiny, AC},
title = {Bacterial response to the 2021 Orange County, California, oil spill was episodic but subtle relative to natural fluctuations.},
journal = {Microbiology spectrum},
volume = {13},
number = {5},
pages = {e0226724},
pmid = {40084855},
issn = {2165-0497},
support = {T32 AI141346/AI/NIAID NIH HHS/United States ; 10.46936/10.25585/60001365//U.S. Department of Energy/ ; OCE-2135035//National Science Foundation/ ; 101813-Z7554214//National Oceanic and Atmospheric Administration/ ; 80NSSC21K1654/NASA/NASA/United States ; T32AI141346/NH/NIH HHS/United States ; 567367//Simons Foundation/ ; },
mesh = {California ; *Petroleum Pollution/analysis ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Seawater/microbiology/chemistry ; *Water Pollutants, Chemical/analysis/metabolism ; Polycyclic Aromatic Hydrocarbons/analysis/metabolism ; Petroleum ; Metagenome ; Microbiota ; },
abstract = {An oil spill began in October 2021 off the coast of Orange County, California, releasing 24,696 gallons of crude oil into coastal environments. Although oil spills, such as this one, are recurrent accidents along the California coast, no prior studies have been performed to examine the severity of the local bacterial response. A coastal 10-year time series of short-read metagenomes located within the impacted area allowed us to quantify the magnitude and duration of the disturbance relative to natural fluctuations. We found that the largest change in bacterial beta-diversity occurred at the end of October. The change in taxonomic beta-diversity corresponded with an increase in the sulfur-oxidizing clade Candidatus Thioglobus, an increase in the total relative abundance of potential hydrocarbon-degrading bacteria, and an anomalous decline in the picocyanobacteria Synechococcus. Similarly, changes in function were related to anomalous declines in photosynthetic pathways and anomalous increases in sulfur metabolism pathways as well as aromatic degradation pathways. There was a lagged response in taxonomy and function to peaks in total PAHs. One week after peaks in total PAH concentrations, the largest shifts in taxonomy were observed, and 1 week after the taxonomy shifts were observed, unique functional changes were seen. This response pattern was observed twice during our sampling period, corresponding with the combined effect of resuspended PAHs and increased nutrient concentrations due to physical transport events. Thus, the impact of the spill on bacterial communities was temporally extended and demonstrates the need for continued monitoring for longer than 3 months after initial oil exposure.IMPORTANCEOil spills are common occurrences in waterways, releasing contaminants into the aquatic environment that persist for long periods of time. Bacterial communities are rapid responders to environmental disturbances, such as oil spills. Within bacterial communities, some members will be susceptible to the disturbance caused by crude oil components and will decline in abundance, whereas others will be opportunistic and will be able to use crude oil components for their metabolism. In many cases, when an oil spill occurs, it is difficult to assess the oil spill's impact because no samples were collected prior to the accident. Here, we examined the bacterial response to the 2021 Orange County oil spill using a 10-year time series that lies within the impacted area. The results presented here are significant because (i) susceptible and opportunistic taxa to oil spills within the coastal California environment are identified and (ii) the magnitude and duration of the in situ bacterial response is quantified for the first time.},
}
@article {pmid40130858,
year = {2025},
author = {Vaccaro, M and Pilat, AM and Gusmano, L and Pham, MTN and Barich, D and Gibson, A and Epalle, M and Frost, DJ and Volin, E and Slimak, ZC and Menke, CC and Fennessy, MS and Slonczewski, JL},
title = {Pond water microbiome antibiotic resistance genes vary seasonally with environmental pH and tannins.},
journal = {Microbiology spectrum},
volume = {13},
number = {5},
pages = {e0303424},
pmid = {40130858},
issn = {2165-0497},
support = {1923077//National Science Foundation/ ; },
mesh = {*Tannins/analysis ; Hydrogen-Ion Concentration ; *Microbiota/genetics ; *Ponds/microbiology/chemistry ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Seasons ; *Drug Resistance, Microbial/genetics ; Ohio ; Anti-Bacterial Agents/pharmacology ; *Water Microbiology ; Genes, Bacterial ; Metagenome ; Fresh Water/microbiology/chemistry ; },
abstract = {UNLABELLED: Microbial communities of small freshwater bodies interact dynamically with environmental factors in unknown ways. Longitudinal sampling of four ponds in Knox County, Ohio, revealed relationships among antibiotic resistance genes (ARGs) and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration, and metagenomes were analyzed by short-read sequencing. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database. The top 30 ARGs showed increased abundance at the end of the growing season. The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and acid stress response (mtrA). The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannic acids). Acidity amplifies the transmembrane pH difference component of the proton-motive force, thus increasing the cell's energy available for pump function and ARG expression. Association with microbial taxa was tested by the Kraken2/Bracken predictor of taxa profiles. The ARG profiles showed the strongest acid dependence in ponds with a high proportion of Proteobacteria, whereas a pond with high Cyanobacteria showed the lowest ARG counts. Efflux pumps such as SmeABC and transcriptional activation by MtrA incur large energy expenditures whose function may be favored at low external pH, where the cell's proton-motive force is maximal.<br><br>IMPORTANCE: Compared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes (ARGs). Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity of freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes how aquatic ARG prevalence may depend on environmental factors such as pH and tannic acid levels.},
}
@article {pmid40197060,
year = {2025},
author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL},
title = {Spatial ecology of the Neisseriaceae family in the human oral cavity.},
journal = {Microbiology spectrum},
volume = {13},
number = {5},
pages = {e0327524},
pmid = {40197060},
issn = {2165-0497},
support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; R01 DE030136, R01 DE022586, 2R01 DE016937/NH/NIH HHS/United States ; },
mesh = {Humans ; *Mouth/microbiology ; Microbiota ; Dental Plaque/microbiology ; *Neisseria/genetics/classification/isolation &amp; purification ; Metagenomics ; Ecosystem ; Genome, Bacterial ; Gingiva/microbiology ; Phylogeny ; },
abstract = {The human oral microbiome is a diverse ecosystem in which bacterial species have evolved to occupy specific niches within the oral cavity. The Neisseriaceae family, which includes human oral species in the genera Neisseria, Eikenella, Kingella, and Simonsiella, plays a significant role in both commensal and pathogenic relationships. In this study, we investigate the distribution and functional adaptations of Neisseriaceae species across oral habitats, focusing on their site tropisms and ecological roles. We employed a metapangenomic approach in which a curated set of reference genomes representing Neisseriaceae diversity was used for competitive mapping of metagenomic reads. Our analysis revealed distinct habitat preferences among Neisseriaceae species, with Kingella oralis, Neisseria elongata, and Neisseria mucosa primarily found in dental plaque; Neisseria subflava on the tongue dorsum; and Neisseria cinerea in the keratinized gingiva. Functional enrichment analyses identified genes and pathways underpinning habitat-specific adaptations. Plaque specialists showed metabolic versatility, with adaptations in nitrogen metabolism, including nitrate reduction and denitrification, lysine degradation, and galactose metabolism. Tongue dorsum specialists exhibited adaptations including enhanced capabilities for amino acid biosynthesis, short-chain fatty acid and glycerol transport, as well as lipopolysaccharide glycosylation, which may aid in resisting antimicrobial peptides and maintaining membrane integrity. These findings provide insights into the ecological roles and adaptive strategies of Neisseriaceae species within the human oral microbiome and establish a foundation for exploring functional specialization and microbial interactions in these niches.IMPORTANCEUnraveling the distribution and functional adaptations of Neisseriaceae within the human oral microbiome is essential for understanding the roles of these abundant and prevalent commensals in both health and disease. Through a metapangenomic approach, we uncovered distinct habitat preferences of various Neisseriaceae taxa across the oral cavity and identified key genetic traits that may drive their habitat specialization and role in host-microbe interactions. These insights enhance our understanding of the microbial dynamics that shape oral microbial ecology, offering potential pathways for advancing oral health research.},
}
@article {pmid40231684,
year = {2025},
author = {Glenna, S and Birkeland, EE and Orr, RJ and Gilfillan, GD and Dalland, M and Økstad, OA and Voie, &#xd8;A and Rounge, TB},
title = {Skin bacterial community dynamics of hands and forearms before and after military field exercise.},
journal = {Microbiology spectrum},
volume = {13},
number = {5},
pages = {e0295324},
pmid = {40231684},
issn = {2165-0497},
support = {332591//Norges Forskningsr&#xe5;d/ ; //SoftOx Solutions/ ; },
mesh = {Humans ; *Military Personnel ; *Skin/microbiology ; *Microbiota/genetics ; *Forearm/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Hand/microbiology ; Male ; *Exercise ; Adult ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Norway ; },
abstract = {The human skin microbiome is crucial for health and immunity, especially under the extreme conditions military personnel face. Soldiers often encounter unique stressors and hygienic challenges that can alter their skin's microbial composition, particularly in field environments. In this study, we aimed to investigate the impact of military field exercises on the diversity and composition of the skin bacterial microbiota using 16S rRNA sequencing. We conducted a longitudinal study of Norwegian soldiers (n = 19) participating in outdoor training operations during the NATO winter exercise Cold Response 2022. Skin swabs were taken from soldiers' hands and forearms before and after the 10-day military exercise, and following a 3-week post-exercise leave. Our results reveal hand- and forearm-specific shifts in bacterial populations associated with the exercise, likely influenced by environmental exposure, reduced hygiene, and heightened social contact. Alpha diversity increased on forearms while remaining stable on hands, which appeared more resilient to perturbations. Both sites exhibited temporal changes in composition, with soil- and water-associated bacteria enriched post-exercise; most being transient on hands but more sustained on forearms. The soldiers' microbiomes converged during the exercise, then diverged in the post-exercise leave period, and neither skin site returned to baseline composition at follow-up. Our findings highlight the impact of collaborative outdoor activities on microbial communities and suggest that resilience and stability differ between skin sites.IMPORTANCEOptimizing soldier health and resilience is critical for maintaining military readiness and operational effectiveness. The skin, as the body's first line of defense, is subjected to numerous challenges in military environments. Unique environmental and hygiene challenges can disrupt the skin microbiome and increase susceptibility to skin and soft tissue infections. This longitudinal research provides valuable insights into the effects of military service on the bacterial dynamics of the skin microbiome but can also inform hygiene management and disease prevention in comparable situations.},
}
@article {pmid41587946,
year = {2026},
author = {Quraishi, MN and Moakes, CA and Yalchin, M and Blackwell, C and Segal, J and Ives, NJ and Magill, L and Manzoor, SE and Gerasimidis, K and McMullan, C and Mathers, J and Horniblow, R and Loi, S and Kaur, M and Loman, NJ and Sharma, N and Hawkey, P and McCune, V and Quick, J and Nicholls, S and McMurray, C and Nichols, B and Svolos, V and Raguideau, S and Kerbiriou, C and Oo, YH and Beggs, AD and Crees, N and Hansen, R and Hart, AL and Gaya, DR and Quince, C and Iqbal, TH},
title = {Mechanistic insights into fecal microbiota transplantation for the treatment of ulcerative colitis: analysis of the STOP-Colitis trial.},
journal = {Journal of Crohn's &amp; colitis},
volume = {20},
number = {3},
pages = {},
doi = {10.1093/ecco-jcc/jjag006},
pmid = {41587946},
issn = {1876-4479},
support = {13/179/01//National Institute for Health and Care Research/ ; },
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Colitis, Ulcerative/therapy/microbiology/immunology ; Male ; Adult ; Female ; Middle Aged ; Prospective Studies ; Feces/microbiology/chemistry ; Pilot Projects ; Gastrointestinal Microbiome ; Colonoscopy ; Treatment Outcome ; Intubation, Gastrointestinal ; Fatty Acids, Volatile/metabolism ; },
abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) is a promising therapy for ulcerative colitis, but variable responses and unclear mechanisms limit its efficacy. We aimed to compare nasogastric versus colonic FMT delivery and define the microbial and immunological changes associated with clinical response.<br><br>METHODS: In this prospective, open-label, randomized pilot trial (STOP-Colitis), 30 adults with active ulcerative colitis were randomized to receive multidose FMT via nasogastric tube or colonoscopy with subsequent enemas. Key endpoints were clinical outcomes at week 8 and longitudinal multi-omic analyses of stool and biopsies to define changes in microbial composition (16S rRNA and shotgun metagenomics), short-chain fatty acids (SCFAs), mucosal T-cells, and host gene expression.<br><br>RESULTS: Colonic FMT was superior to nasogastric delivery, with a higher clinical response rate at week 8 (75% [9/12] vs 25% [2/8]; risk ratio 2.94, 95% CI 0.84-10.30-per protocol analysis). Response was underpinned by successful microbial engraftment, leading to significantly increased fecal microbial diversity and enrichment of SCFA-producing taxa, including Oscillospiraceae and Christensenellaceae. This correlated with reduced fecal calprotectin. Responders showed a significant increase in mucosal regulatory T cells (P&#x2009;=&#x2009;.01), with a concurrent decrease in Th17 (P&#x2009;=&#x2009;0.03) and CD8+ T cells. This anti-inflammatory shift was confirmed by mucosal transcriptomics, which revealed upregulation of metabolic pathways and downregulation of proinflammatory defense pathways in responders. (Trial registration: ISRCTN74072945).<br><br>CONCLUSION: Colonic FMT is a more effective delivery route than nasogastric administration. Clinical response is driven by the engraftment of immunomodulatory bacteria that restore a healthy host-microbe dialogue, providing rationale for developing targeted microbial therapeutics.},
}
@article {pmid41876513,
year = {2026},
author = {Jovicic, D and Anestis, K and Fiutowski, J and Jørgensen, BB and Kjeldsen, KU and Rotaru, AE},
title = {Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41876513},
issn = {2041-1723},
support = {1026-00159B//Natur og Univers, Det Frie Forskningsr&#xe5;d (Natural Sciences, Danish Council for Independent Research)/ ; 101045149//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Geologic Sediments/microbiology ; *Metagenomics/methods ; Acetates/metabolism ; Oxidation-Reduction ; Electron Transport ; Phylogeny ; *Microbial Consortia/genetics ; Methane/metabolism ; Methanosarcina/metabolism/genetics ; Charcoal ; Cytochromes/metabolism/genetics ; Genome, Bacterial ; },
abstract = {Conductive particles are common in coastal sediments, yet their role in shaping methane-producing communities and pathways remains unclear. We applied genome-resolved metagenomics to a sediment-derived consortium serially transferred for a decade and obligately dependent on granular activated carbon (GAC). We discovered a particle-obligate food web composed of electrogenic syntrophic acetate oxidizers (SAO), an electrotrophic methanogen, and necromass recyclers. The primary SAO electrogen, Candidatus Geosyntrophus acetoxidans, represents a new genus and possesses a complete acetate oxidation pathway and extracellular electron-transfer (EET) machinery, including two porin-cytochrome conduits, 43 additional multiheme cytochromes and conductive pili. A secondary SAO, a Lentimicrobium sp. with a giant PCC-cluster, supplies an alternative EET-linked acetate-oxidation route. Electrons from electrogens transfer via GAC to a Methanosarcina equipped with the heptaheme cytochrome MmcA and flagellin for electron uptake. These results provide a genomic blueprint of this particle-obligate environmental consortium and suggest an overlooked acetate-to-methane electron-transfer route in geoconductor-rich anoxic sediments.},
}
@article {pmid41877461,
year = {2026},
author = {Tagliabue, A and Furfaro, G and Pallavicini, A and Martino, F and Zane, L and Sattin, E and Valle, G and Piraino, S and Turon, X},
title = {Comparative Multi-Marker Environmental DNA Metabarcoding of Marine Metazoan Communities: Water vs. Sediment.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70126},
doi = {10.1111/1755-0998.70126},
pmid = {41877461},
issn = {1755-0998},
support = {MCIU/AEI/10.13039/501100011033//BlueDNA PID2023-146307OB/ ; CCI 2014IT16M2OP005//Programma Operativo Nazionale Ricerca e Innovazione 2014-2020/ ; ECS00000043//Interconnected Nord-Est Innovation Ecosystem/ ; //European Regional Development Fund/ ; 2020J3W3WC//Italian Ministry of Education, Universities and Research/ ; D33C22000960007//National Recovery and Resilience Plan/ ; C93C22002810006//National Recovery and Resilience Plan/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; Animals ; *Geologic Sediments ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Electron Transport Complex IV/genetics ; *Metagenomics/methods ; *Seawater ; },
abstract = {This study investigates the metazoan biodiversity in the Southern Adriatic Sea using environmental DNA (eDNA) metabarcoding. Sediment and adjacent water samples were collected from three sites (one pristine, two impacted by human activities) at three distances from the coast across two seasons. The complex four-factor experimental design (576 samples) addresses key sources of eDNA variability and provides a valuable comparison of markers (COI and 18S) and sample types, which remain rare in the literature. Results showed differences in the number and type of taxa identified, taxonomic resolution, and number of amplicon sequence variants (ASV) per operational taxonomic unit (OTU) across markers. The obtained overall community structure (beta-diversity) was similar for both markers. Sediment samples had higher OTU richness, but lower diversity than water samples. The two sample types provided distinct and only partially overlapping views of biodiversity. Sediment samples were rich in benthic species, whereas water samples featured mostly planktonic and nektonic species. Biodiversity varied by site and season, with sediment samples showing less seasonal variability. The pristine site did not host higher biodiversity than impacted sites, likely because of the latter's habitat heterogeneity. This study confirms the effectiveness of eDNA metabarcoding for biodiversity assessment in coastal ecosystems and provides a foundational dataset for future monitoring. By highlighting the complementary nature of COI and 18S markers and the role of sample type, this research supports integrating eDNA metabarcoding into routine environmental monitoring programs while emphasising the need for further standardisation and improved reference databases.},
}
@article {pmid41878266,
year = {2026},
author = {Huang, J and Yan, X and Su, Q and Tu, H and Yu, Z and Liu, D and Wu, B},
title = {Temporal dynamics of gut microbiota and virome in preterm infants: insights from longitudinal metagenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1598786},
pmid = {41878266},
issn = {2235-2988},
mesh = {Humans ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Infant, Newborn ; *Metagenomics ; *Virome ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Male ; Feces/microbiology/virology ; Enterococcus faecalis ; Gastrointestinal Tract/microbiology ; },
abstract = {INTRODUCTION: Preterm infants exhibit heightened vulnerability to morbidity and mortality due to their underdeveloped immune systems and immature gastrointestinal tract. The gut microbiota plays a pivotal role in neonatal health, yet its establishment is influenced by multiple factors, including prematurity, antibiotic exposure, and feeding modalities. This study aimed to examine the interactions among gut bacteriophages, bacterial communities, and clinical variables in preterm infants to identify potential microbial biomarkers associated with health outcomes.<br><br>METHODS: We employed metagenomic shotgun sequencing and co-occurrence network analysis to characterize the virome and bacterial communities in 12 preterm neonates at 14 and 28 days post-birth. This approach enabled the identification of dynamic microbial colonization patterns and key bacterial species and bacteriophages associated with clinical parameters.<br><br>RESULTS: Staphylococcus epidermidis exhibited a significant decline over time, whereas Enterococcus faecalis and its associated bacteriophages showed progressive enrichment, becoming predominant by day 28. In contrast, the relative abundances of Clostridioides difficile and Klebsiella pneumoniae remained statistically stable between the two time points (14 vs. 28 days).<br><br>DISCUSSION: These findings suggest that microbial changes during the first month of life may reflect a combination of host developmental processes and external influences, such as antibiotic exposure or delivery mode. The observed microbial signatures provide preliminary insights into early gut microbiota and virome development in preterm infants. However, their functional relevance and long-term stability require confirmation in larger, well-powered longitudinal studies with denser temporal sampling. The enrichment of Enterococcus faecalis may indicate its opportunistic colonization potential in the preterm gut and warrants further investigation regarding its role in gut homeostasis and immune system maturation.},
}
@article {pmid41879886,
year = {2026},
author = {Chen, W and Li, X and Zhao, X and Zuo, Z and Wang, D and Zhao, F},
title = {GMW: a hybrid graph-based approach for post-assembly metagenome analysis and decontamination.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41879886},
issn = {1869-1889},
abstract = {Accurate genome assembly from metagenomic sequencing data remains challenging, particularly in mixed infections involving multiple pathogens, due to data complexity and contaminant sequences. Here, we present GMW (Genomic Microbe-Wise), a novel computational tool that improves pathogen genome assembly accuracy and enhances contaminant removal capabilities by simplifying the post-assembly graph. GMW leverages community detection algorithms, sequence similarity analysis, and coverage patterns to resolve strain mixtures and improve assembly accuracy. Using datasets of influenza A virus subtypes, we demonstrate GMW's ability to disentangle mixed infections and reconstruct complete viral genomes with high precision. Additionally, GMW outperforms traditional sequence similarity methods in classifying target contigs from contaminants. This tool also provides interactive visualization modules to streamline the inspection of assembly outputs, including simplified representations of complex assembly graphs. By enhancing assembly quality and contamination filtering, GMW emerges as a versatile solution for applications in clinical diagnostics, microbial ecology, and pathogen surveillance.},
}
@article {pmid41881444,
year = {2026},
author = {Kringeland, GD and Tangedal, S and Julian, D and Paytuví-Gallart, A and Sanseverino, W and Bertelsen, RJ and Husebø, GR and Knudsen, KS and Lehmann, S and Nielsen, R and Eagan, TML},
title = {Antimicrobial resistance genes and antibiotic use in chronic lung disease: a bronchoscopy study of the lower airways microbiome.},
journal = {BMJ open respiratory research},
volume = {13},
number = {1},
pages = {},
doi = {10.1136/bmjresp-2025-003864},
pmid = {41881444},
issn = {2052-4439},
mesh = {Humans ; Male ; Female ; Cross-Sectional Studies ; Bronchoscopy ; Middle Aged ; Aged ; *Anti-Bacterial Agents/therapeutic use ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy ; Case-Control Studies ; *Lung Diseases/microbiology/drug therapy ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Chronic Disease ; },
abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) in the respiratory microbiome are poorly characterised. We compared the presence of ARGs in healthy controls with patients with chronic lung disease in a cross-sectional study, adjusted for time since antibiotic use.<br><br>METHODS: Bronchoalveolar lavage was collected from 100 controls, and 93 patients with chronic obstructive pulmonary disease (COPD), 13 with asthma, 34 with sarcoidosis, 12 with idiopathic pulmonary fibrosis (IPF) and 11 patients with unclassifiable interstitial lung disease (uILD). Participants had not used antibiotics 14 days prior to sampling. Shotgun metagenomic sequencing was performed with Illumina NovaSeq. ARGs were identified using the National Database of Antibiotic-Resistant Organisms. Sample reads were normalised to counts per million.<br><br>RESULTS: In total, 38% of controls had at least one ARG, compared with 51%, 39%, 65% and 83% of patients with COPD, asthma, sarcoidosis and IPF, respectively (p=0.01). ARGs against tetracycline (33%) were the most common ARG class, followed by beta-lactam and macrolide resistance (both 26%). In a logistic regression analysis adjusted for sex, age, body composition, smoking and antibiotic use, the OR (95%&#x2009;CI) for having ARGs in the lower airways was 1.30 (0.70 to 2.41) in COPD, 1.00 (0.29 to 3.52) in asthma, 3.52 (1.40 to 8.83) in sarcoidosis, 6.40 (1.25 to 32.73) in IPF and 3.27 (0.76 to 14.16) in uILD compared with controls. Overall mean (SD) ARG counts per million were 403.8 (537.7) in the 35 subjects who had used antibiotics &#x2264;3 months before bronchoscopy, compared with 197.6 (355.9) in the 228 subjects without (p=0.02).<br><br>CONCLUSION: The presence of ARGs in the lower airways microbiome was significantly higher in patients with sarcoidosis and IPF than in controls. The counts per million for ARGs were significantly associated with recent antibiotic use.},
}
@article {pmid41881804,
year = {2026},
author = {Gutiérrez, J and Vergara-Amado, J and Martorell, C and Navedo, JG and Wille, M and Guajardo-Leiva, S and Castro-Nallar, E and Verdugo, C},
title = {Functional Shifts in the Gut DNA Virome in a Long-Distance Migratory Shorebird During the Pre-Migratory Fattening.},
journal = {Molecular ecology},
volume = {35},
number = {6},
pages = {e70315},
doi = {10.1111/mec.70315},
pmid = {41881804},
issn = {1365-294X},
support = {FONDECYT N&#xb0;1191769//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANILLO ATE220062//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Doctoral scholarship N&#xb0;21201700//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; //The Pathogen Watchtower Program (Biotia Inc. &amp; The Rockefeller Foundation)/ ; //Universidad Austral de Chile/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Charadriiformes/virology/physiology ; *Animal Migration ; *Virome/genetics ; Feces/virology ; Metagenomics ; Metagenome ; },
abstract = {Migration represents one of the most energetically demanding phases in the life cycle of long-distance migratory birds. Pre-migratory fattening is a critical preparatory stage characterized by hyperphagia, rapid fat accumulation, organ remodelling, and immune modulation. Although the gut microbiome has been recognized as a key contributor to these physiological adaptations, the role of the gut virome remains poorly understood. In this study, the diversity, functional potential, and temporal dynamics of the gut DNA virome in a trans-hemispheric migratory shorebird, the Hudsonian godwit (Limosa haemastica), were assessed during pre-migratory fattening. Adult individuals were maintained under controlled aviary conditions for 15 weeks during the preparation for northbound migration, and faecal samples were collected at two distinct physiological time points: at the beginning and the end of pre-migratory fattening. Shotgun metagenomic sequencing revealed 798 high-quality viral operational taxonomic units (vOTUs), the majority of which were bacteriophages (92%). Potential functional annotation identified auxiliary metabolic genes (AMGs) associated with nucleotide metabolism, redox balance, and host adaptation. Although overall gut virome diversity did not differ between stages, significant changes in potential functional profiles of phages were observed, especially during the final stage of fattening when energy demands are at their highest. In addition to bacteriophages, we report two divergent adenoviruses potentially associated with the Siadenovirus and Aviadenovirus genera. These findings suggest that dynamic viral communities may play underrecognized roles in supporting host physiology during energetically costly life stages.},
}
@article {pmid41603333,
year = {2026},
author = {Tiwari, P and Gupta, A and Kaushik, M and Dwivedi, R and Tripathi, M and Dada, R},
title = {Association of yoga with cognitive and gut microbiome changes in Alzheimer's disease: An exploratory case-control study.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {110},
number = {2},
pages = {562-575},
doi = {10.1177/13872877261415612},
pmid = {41603333},
issn = {1875-8908},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Alzheimer Disease/psychology/microbiology/therapy ; Male ; *Yoga/psychology ; Female ; Case-Control Studies ; Aged ; *Cognition/physiology ; Middle Aged ; Depression/psychology/therapy ; Cognitive Dysfunction ; },
abstract = {BackgroundAlzheimer's disease (AD) is marked by cognitive decline, depressive symptoms, and gut microbial dysbiosis. Yoga may support cognitive and emotional health while modulating gut microbiota, but integrative clinical evidence is limited.ObjectiveTo evaluate the effects of a 12-week yoga intervention on cognition, depressive symptoms, and gut microbial diversity, composition, and function in Indian patients with mild AD.MethodsIn this hospital-based case-control study, 16 AD patients and 17 cognitively healthy controls (HCs) were recruited at AIIMS, New Delhi. AD diagnosis followed NIA-AA criteria, supported by Montreal Cognitive Assessment (MoCA) and Patient Health Questionnaire-9 (PHQ-9) assessments. AD participants underwent 60-min supervised yoga sessions daily for 12 weeks. Cognitive performance, depressive symptoms, and stool microbiota were assessed pre- and post-intervention. Metagenomic sequencing enabled taxonomic and functional profiling, with alpha diversity, beta diversity (Bray-Curtis distance), and differential abundance analyses performed using standard bioinformatics tools.ResultsYoga was associated with improved cognition (MoCA: 22.33 ± 2.34 → 25.44 ± 2.01; p = 0.001) and reduced depressive symptoms (PHQ-9: 5.78 ± 3.11 → 2.22 ± 1.71; p = 0.007). Alpha diversity remained stable, while beta diversity shifted post-yoga AD samples toward the HC cluster. Beneficial taxa (Faecalibacterium prausnitzii, Roseburia intestinalis, Bifidobacterium, Akkermansia) increased, whereas pro-inflammatory taxa (Collinsella aerofaciens, Klebsiella spp.) decreased. Functional analysis showed partial recovery of metabolic and short-chain fatty acid pathways.ConclusionsA 12-week yoga intervention was associated with cognitive and mood improvements and partial normalization of gut microbial function in mild AD. Larger randomized trials with lifestyle monitoring and multi-omics integration are warranted to confirm causal mechanisms.},
}
@article {pmid41615149,
year = {2026},
author = {Mora-Martínez, C and Molina-Mendoza, G and Cenit, MC and Medina-Rodríguez, EM and Larroya-García, A and Sanchez-Carro, Y and Gonzalez-Blanco, L and Bobes, J and Lopez-Garcia, P and Zandio-Zorrilla, M and Lahortiga-Ramos, F and Gili, M and Garcia-Toro, M and Barcelo, B and Ibarra, O and Sanz, Y},
title = {Gut microbiome signatures associated with depression and obesity.},
journal = {mSystems},
volume = {11},
number = {3},
pages = {e0126325},
doi = {10.1128/msystems.01263-25},
pmid = {41615149},
issn = {2379-5077},
support = {EarlyCause 848158//Horizon 2020 Framework Programme/ ; Centro de Excelencia Severo Ochoa CEX2021-001189-S/MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n/ ; FPI PRE2018-083895//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Miguel Servet CP22/00031//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology/complications ; Male ; Female ; Case-Control Studies ; *Major Depressive Disorder/microbiology ; Middle Aged ; Adult ; Body Mass Index ; Metagenomics/methods ; Metagenome ; },
abstract = {UNLABELLED: Depression and obesity are highly comorbid and likely involve common risk factors and pathophysiological mechanisms, which could crosslink to gut microbiome dysfunction. Here, we performed a case-control study with a total of 105 subjects, 43 with major depressive disorder (MDD) and 62 non-depressed controls free from psychiatric comorbidities, to identify gut microbiome signatures associated with MDD and dissect its relation to body mass index (BMI) and lifestyle (diet and exercise). We performed shotgun metagenomics, followed by taxonomic and functional annotations. Using different machine learning methods, we were able to classify subjects into depressed and non-depressed controls with a balanced accuracy of 0.90 and into depressed or non-depressed and normal weight or overweight with a balanced accuracy of 0.78 based solely on taxonomic profiles. We identify novel bacterial taxa associated with depression, including reductions in Butyrivibrio hungatei and Anaerocolumna sedimenticola, and also replicate previously reported associations, such as decreased Faecalibacterium prausnitzii in patients with MDD. Functional annotation of metagenomes shows differences in pathways linked to the synthesis of fundamental nutrients, which have been associated with diet, as well as inflammation. Strikingly, we found an increase in tryptophan degradation and a decrease in queuosine synthesis pathways, both of which are directly related to a decrease in monoaminergic neurotransmitter availability. Additionally, our functional analysis shows that most of the functions that are more abundant in controls than in depressed subjects are encoded by F. prausnitzii. These findings reveal distinct microbial and functional signatures associated with depression, including taxa and pathways linked to neurotransmitter metabolism and independent of other covariates. This suggests that gut microbiome profiling could support diagnosis and the development of gut-directed depression treatments.<br><br>IMPORTANCE: This study identifies gut microbiome signatures that are predictive of major depressive disorder (MDD) and explores their links to body mass index (BMI). We uncover bacterial species and metabolic pathways that are associated with MDD, some of them related to neurotransmitter metabolism and inflammation. Among the differences identified, depletion of Faecalibacterium prausnitzii stands out as an important feature in the MDD microbiome, which suggests the possible use of this species to improve depression symptoms. Importantly, we demonstrate shared microbiome features between MDD and BMI, suggesting common underlying mechanisms. This research not only provides a framework for developing microbiome-based diagnostics but also informs future stratified interventions targeting gut microbial functions to improve mental health outcomes.},
}
@article {pmid41636510,
year = {2026},
author = {Anne Hallowell, H and Malogan, J and Suez, J},
title = {Tools and approaches to study the human gut virome: from the bench to bioinformatics.},
journal = {mSystems},
volume = {11},
number = {3},
pages = {e0100225},
doi = {10.1128/msystems.01002-25},
pmid = {41636510},
issn = {2379-5077},
mesh = {Humans ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Computational Biology/methods ; *Viruses/genetics ; Feces/virology ; Bacteriophages/genetics ; Genome, Viral ; Bacteria/virology/genetics ; },
abstract = {The human gastrointestinal tract is home to a diverse community of microorganisms from all domains of life, collectively referred to as the gut microbiome. While gut bacteria have been studied extensively in relation to human host health and physiology, other constituents remain underexplored. This includes the gut virome, the collection of bacteriophages, eukaryotic viruses, and other mobile genetic elements present in the intestine. Like gut bacteria, the gut virome has been causatively linked to human health and disease. However, the gut virome is substantially more difficult to characterize, given its high diversity and complexity, as well as multiple challenges related to in vitro cultivation and in silico detection and annotation. In this mini-review, we describe various methodologies for examining the gut virome using both culture-dependent and culture-independent tools. We highlight in vitro and in vivo approaches to cultivate viruses and characterize viral-bacterial host dynamics, as well as high-throughput screens to interrogate these relationships. We also outline a general workflow for identifying and characterizing uncultivated viral genomes from fecal metagenomes, along with several key considerations throughout the process. More broadly, we aim to highlight the opportunities to synergize and streamline wet- and dry-lab techniques to robustly and comprehensively interrogate the human gut virome.},
}
@article {pmid41734043,
year = {2026},
author = {Thakur, M and Dolker, S and Wangmo, LK and Sharma, LK and Acharya, S and Mohapatra, P},
title = {Illumina-Based Metagenomic Insights into the Gut Microbiome of Amblyomma helvolum (Koch, 1844) Parasitizing Xenochrophis trianguligerus from Great Nicobar Island, India.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {26},
number = {4},
pages = {233-240},
doi = {10.1177/15303667261423035},
pmid = {41734043},
issn = {1557-7759},
mesh = {Animals ; India ; *Gastrointestinal Microbiome ; *Amblyomma/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenomics ; *Snakes/parasitology ; *Tick Infestations/veterinary/parasitology/epidemiology ; },
abstract = {During a faunal survey in Great Nicobar Island, we collected four Amblyomma helvolum ticks infesting the snake Xenochrophis trianguligerus and processed for gut-metagenomic analysis using Illumina paired-end sequencing. A total of 8.7 million high-quality reads were generated, revealing that the gut microbiome was dominated by Bacteria (∼99.9%), primarily represented by Proteobacteria (∼95.7%), followed by minor fractions of Firmicutes, Actinobacteria, and Bacteroidetes. The predominant bacterial families were Alcaligenaceae, Bradyrhizobiaceae, Boseaceae, and Rickettsiaceae, with Achromobacter xylosoxidans emerging as the most abundant species (∼30% of total reads). Species-level analyses revealed a complex microbial community dominated by Achromobacter, Brevibacillus, Stutzerimonas, and Aeromicrobium. Several putative opportunistic pathogens were detected, including Myroides sp., Sphingobacterium sp., Stutzerimonas stutzeri, Cutibacterium acnes, Mycobacterium abscessus, Staphylococcus hominis, Achromobacter xylosoxidans, and Pseudomonas otitidis. This study represents the first metagenomic characterization of A. helvolum from India and provides baseline data on reptile-tick-associated microbial diversity from Great Nicobar Island. The findings underscore the importance of molecular surveillance in remote ecosystems and highlight the potential of reptile ticks as reservoirs of opportunistic and zoonotic bacteria.},
}
@article {pmid41744504,
year = {2026},
author = {Firrman, J and Liu, L and Mahalak, K and Lemons, JMS and Narrowe, A and Friedman, ES and Wu, GD and Van de Weile, T},
title = {An in vitro model of the small intestinal microbiota provides key insights into interindividual variability in structure and function.},
journal = {mSystems},
volume = {11},
number = {3},
pages = {e0137325},
doi = {10.1128/msystems.01373-25},
pmid = {41744504},
issn = {2379-5077},
support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Metabolomics/methods ; Metagenomics/methods ; *Intestine, Small/microbiology ; Bacteria/classification/genetics/metabolism ; Male ; Female ; *Ileum/microbiology ; },
abstract = {UNLABELLED: Although there is clear evidence demonstrating the importance of the small intestinal microbiota (SIM) for nutrient utilization within the upper gastrointestinal tract, research is limited by difficulties accessing this community in vivo. Additionally, the high level of interindividual variability in taxonomic structure, which is well documented for the SIM, raises the question of how such divergent communities fill the same physiological roles. Here, we designed and evaluated an in vitro model of the terminal ileum representative of four unique donors and utilized it to interrogate interindividual variability. Shotgun sequencing confirmed that the in vitro communities were representative of their specific inocula and composed of facultative and obligate anaerobic taxa typical of the SIM, such as Klebsiella, Escherichia, Streptococcus, and Enterococcus. Untargeted metabolomics revealed a high degree of similarity between communities in terms of which metabolites were produced. Combining metagenomics and metabolomics, a core set of genes, features, and metabolites was found shared across all communities despite the high degree of structural variability observed. These results indicated that while the taxonomic structure of the SIM was variable between individuals, there were similarities in functional outcome due to underlying gene representation in the microbiome. Moving forward, this model system may serve as a starting point to further elucidate the role of the SIM in nutrition and health.<br><br>IMPORTANCE: The small intestinal microbiota (SIM) plays a pivotal role in nutrient digestion and absorption and immune function, with researchers continuing to find connections between this community and human health. Expanding on the currently available methods within the field to study this community, here, an in vitro model of the SIM was developed and designed to mimic the terminal ileum. Metagenomic and metabolomic analysis confirmed that this model recapitulated the unique communities of four different donors while maintaining the interindividual variability canonical of the SIM. Despite variation in taxonomic structure, in-depth analysis found that there was a core set of genes shared among the four in vitro communities that correlated with a relatively consistent metabolomic signature. These significant findings provided unique insight into the relationship between structural and functional variability for the SIM and furthered the field's understanding of how such structurally variable communities have such similar physiological outcomes.},
}
@article {pmid41789894,
year = {2026},
author = {Liu, M and Wang, L and Liu, J and Yuan, Q and Zhang, Y and Wu, S and Zhang, Y and Guo, R and Zhang, Y and Lu, T and Yan, Q and Li, S and Xing, G and Dong, B and Zheng, N},
title = {Gut virome and metabolic associations in patients with acute pancreatitis.},
journal = {mSystems},
volume = {11},
number = {3},
pages = {e0140025},
doi = {10.1128/msystems.01400-25},
pmid = {41789894},
issn = {2379-5077},
mesh = {Humans ; *Virome ; *Gastrointestinal Microbiome ; Male ; Female ; *Pancreatitis/virology/metabolism/microbiology ; Middle Aged ; Adult ; Metagenomics ; Case-Control Studies ; Acute Disease ; Aged ; },
abstract = {Acute pancreatitis (AP) is a frequent inflammatory disorder with outcomes ranging from mild disease to severe forms marked by infection and organ failure. Gut microenvironment disruption and barrier dysfunction are increasingly recognized as key drivers of AP progression, yet most microbiome studies have focused on bacteria. The gut virome modulates bacterial ecology and host immune responses and remains poorly characterized in AP. We aimed to comprehensively profile virome alterations in AP and evaluate their associations with disease severity, etiology, and clinical parameters. Metagenomic sequencing data from AP patients and healthy controls (HCs) were analyzed using the viromic tools. Viral diversity, taxonomy, functional composition, and predicted viral-host linkages were profiled. Microbial-viral-metabolite networks were constructed, and classification performance was evaluated using random forest models. AP viromes exhibited significantly reduced Shannon and Simpson diversity and distinct β-diversity separation from HCs. AP-enriched phages predominantly targeted Parabacteroides, Escherichia, and Bacteroides, while HC-enriched phages were linked to SCFA-producing commensals. Functional analysis revealed enrichment of replication- and lysis-related auxiliary metabolic genes (AMGs) in AP-enriched viral operational taxonomic units (vOTUs), whereas HC-associated vOTUs carried stability-related functions. Severity- and etiology-stratified analyses indicated consistent enrichment of Peduoviridae infecting Enterobacteriaceae and higher prevalence of eukaryotic viruses in advanced stages. Network analyses revealed denser microbial-viral-metabolite interactions in AP, correlated with hepatobiliary and lipid metabolic markers. A minimal seven-virus panel achieved an AUC of 97.5% for AP classification. AP is characterized by profound gut virome remodeling reflecting disease severity and etiology, with diagnostic and mechanistic relevance for future therapeutic strategies.IMPORTANCEThis study highlights the gut virome as a previously underappreciated component of acute pancreatitis (AP)-associated dysbiosis and suggests that viral communities may influence disease severity and metabolic disturbances beyond bacterial effects alone. By demonstrating the diagnostic potential of virome-based signatures, our findings support expanding microbiome research in AP to include viral components, with implications for improved disease stratification and future therapeutic development.},
}
@article {pmid41818685,
year = {2026},
author = {Qu, Q and Jia, Y and Wang, S and Hu, K and Liu, C and Hu, X and Mu, L},
title = {Responses of Microbial Communities in River to Atmospheric Deposition.},
journal = {Environmental science &amp; technology},
volume = {60},
number = {11},
pages = {8583-8592},
doi = {10.1021/acs.est.6c01648},
pmid = {41818685},
issn = {1520-5851},
mesh = {*Rivers/microbiology ; Atmosphere ; Bacteria ; Fungi ; Nitrogen ; China ; Microbiota ; Air Pollutants ; },
abstract = {Atmospheric deposition threatens aquatic ecosystems, yet its effects on the microbial diversity, composition, and function in rivers remain unclear. Here, we examined the responses of microbial communities to atmospheric pollutants across 105 Chinese rivers. We found that PM2.5 and PM10 were associated with reduced bacterial and fungal diversity and richness. Structural equation modeling revealed that atmospheric deposition (e.g., PM2.5, SO2, NO2, and organic matter aerosol) was directly and indirectly associated with bacterial and fungal community composition through cascading pathways mediated by dissolved oxygen, pH, Mn, inorganic nitrogen, nitrate nitrogen, ammonium nitrogen, and chlorophyll-a. Compared with fungal communities, bacterial communities exhibited broader environmental thresholds and greater sensitivity to atmospheric pollutants. Ecological network analysis further revealed that deposition preferentially disrupted mutualistic motifs in bacterial networks but intensified competitive interactions in fungal networks. Metagenomic analysis revealed that atmospheric pollution is significantly associated with key microbial functional genes involved in carbon degradation (e.g., glucoamylase, pullulanase, and β-glucosidase), nitrogen assimilation and reduction (e.g., nifD, narB, and nirS), and sulfur reduction (e.g., sat, aprA, and dsrA) in rivers. Our findings underscore the importance of air quality mitigation in terms of protecting river ecosystem health.},
}
@article {pmid41872229,
year = {2026},
author = {Ji, M and Li, Y and Wang, M and Liu, X and Gong, X and Tu, Q},
title = {Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71095-7},
pmid = {41872229},
issn = {2041-1723},
abstract = {Large DNA viruses (LDVs) are unique members of the Earth's virosphere, remarkable for their extra-large genome sizes and broad metabolic potential. However, our knowledge of this viral group remains very limited, particularly in complex dynamic habitats. In this study, 237 metagenome-assembled LDV genomes are comprehensively recovered from intertidal mudflats using multiple sampling and sequencing strategies totaling 5.3 TB data. A phylogenetically distinct subgroup within Imitervirales is identified, showing broad associations with multiple eukaryotic lineages. Certain LDV populations can persist locally and exhibit significant genomic variations potentially driven by dynamic intertides. Ecological patterns are observed at both community and genetic levels, with giant viruses showing steeper community turnover but weaker nucleotide diversity variations than large phages. Moreover, LDVs exhibit similar macroecological patterns to their potential hosts, which substantially shape LDV community assembly. The intertidal LDVs encode diverse functional genes, most of which remain uncharacterized, with a 27.32% improvement for unknown phage genes using a protein language model. Although giant viruses and large phages share comparable functional gene composition, they exhibit distinct preferences for specific metabolic pathways, especially those associated with carbon and nitrogen cycling. This study broadens our understanding of the biodiversity and ecology of LDVs in the understudied intertidal ecosystems.},
}
@article {pmid41875072,
year = {2026},
author = {van der Heyde, M and Curran, M and Floeckner, S and Nevill, P and White, NE and Austin, AD and Guzik, MT},
title = {Validating COI eDNA Metabarcoding Primers for Detection of Subterranean Fauna.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70127},
doi = {10.1111/1755-0998.70127},
pmid = {41875072},
issn = {1755-0998},
support = {LP190100555//Australia Research Council Linkage Project/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA Primers/genetics ; *DNA, Environmental/genetics ; *Electron Transport Complex IV/genetics ; Animals ; Biodiversity ; *Metagenomics/methods ; },
abstract = {Subterranean ecosystems host a diverse range of ancient fauna, but studying these ecosystems is challenging due to significant sampling difficulties. Environmental DNA (eDNA) metabarcoding offers a promising approach for monitoring subterranean biodiversity, yet issues such as primer bias and non-target amplification can complicate its effectiveness. Thus, thorough validation of metabarcoding primers is crucial for accurate and comprehensive assessments of subterranean faunal diversity. This study aimed to address the need for robust primer validation through in silico, in vitro and in situ analyses, shedding light on primer performance across various subterranean taxa. The primary objective was to evaluate the effectiveness of COI metabarcoding primers for assessing subterranean faunal diversity. In silico analyses involved curating COI sequences from the Barcode of Life Database (BOLD) and selecting 14 primer combinations for in vitro testing using mock communities. Results revealed varying primer performance in terms of PCR efficiency and detection limits across different taxa. One primer combination (BF1/jgHCO2198) detected 82% of taxa in the mock community, but only at high DNA concentrations of the target taxa. The highest proportion of subterranean taxa detected in a diluted mock community was 68% using the fwhF2/fwhR2n primer combination. For in situ field validation, this same primer set detected 13 out of 16 subterranean taxa identified in haul net samples, along with an additional four taxa not identified by haul net. These findings highlight the potential of COI metabarcoding and the critical importance of primer selection for eDNA studies aimed at conserving subterranean biodiversity.},
}
@article {pmid41530018,
year = {2026},
author = {FitzGerald, JA and Lester, KL and O' Sullivan, N and Crispie, F and Lawton, EM and Cotter, PD and McNally, P and Cox, DW},
title = {Parallel metagenomic- and culture-based approaches show nasal swabs are a good proxy for broncho-alveolar lavage in children with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {25},
number = {2},
pages = {232-239},
doi = {10.1016/j.jcf.2025.12.011},
pmid = {41530018},
issn = {1873-5010},
mesh = {Humans ; *Cystic Fibrosis/microbiology/diagnosis ; *Bronchoalveolar Lavage/methods ; *Metagenomics/methods ; Child, Preschool ; Male ; Female ; Specimen Handling/methods ; Oropharynx/microbiology ; Microbiota ; Child ; *Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {BACKGROUND: Broncho-Alveolar Lavage (BAL) is the reference standard for airway surveillance in clinical management of cystic fibrosis (CF), but is invasive and requires general anaesthesia in children. Non-invasive alternatives can lack specificity (Oropharyngeal swabs; OPS), or evaluation in paediatric CF (Middle meatus sampling; MMS). We sought to determine if MMS via nasal-swabs performed better than OPS at representing the microbiological attributes of BAL.<br><br>METHODS: In a stable preschool CF cohort attending a single specialist centre, we evaluated the microbiological yield of BAL, MMS, and OPS sampling using both standard clinical culturing, and shotgun metagenomic sequencing (Illumina NextSeq 500).<br><br>RESULTS: Matched BAL, MMS, and OPS from 30 preschool children provided 88 samples. While both culture and metagenomic surveillance performed well at detecting S. pneumoniae in BAL, MMS performed better at detecting S. aureus, M. catarrhalis and Escherichia coli, while OPS performed better at detecting H. Influenzae. Metagenomics revealed a significantly more diverse microbiome in OPS than BAL or MMS. While agreement on pathogen profiles varied widely between metagenomics and culture methods, MMS more accurately represented BAL, particularly for Streptococcus, M. catarrhalis, and Escherichia.<br><br>CONCLUSIONS: MMS and OPS cultures performed well as proxies for BAL in relation to certain pathogens. Metagenomics detected pathogens in many samples that were unobserved in culture, and showed the oropharynx microbiome to be much more diverse. Lung and nares microbiomes were more similar in composition and diversity. Our data suggest that nasal sampling of the middle meatus may be a more accurate surrogate for lower airway samples.},
}
@article {pmid41560354,
year = {2026},
author = {He, N and Wang, H and Yang, Z and Li, H and Liu, B and Chen, K and Wu, Z and Zhao, X and Liang, H and Wang, M and Li, X and Zhong, Y and Zhang, H and Xiao, L and Kristiansen, K and Peng, J and Zou, Y and Li, S},
title = {The Gut Commensal Butyricimonas Virosa Modulates Gut Microbiota-Dependent Thiamine Metabolism and Attenuates Mouse Steatotic Liver Disease.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {17},
pages = {e17596},
doi = {10.1002/advs.202517596},
pmid = {41560354},
issn = {2198-3844},
support = {82470615//National Natural Science Foundation of China/ ; 2024KJJ042//Shandong Provincial Youth Entrepreneurship Program for Colleges and Universities/ ; ZR2022MH217//Shandong Provincial Natural Science Foundation/ ; 2023TD52//Central Public-interest Scientific Institution Basal Research Fund/ ; 2023TD76//Central Public-interest Scientific Institution Basal Research Fund/ ; KCXFZ20240903094006009//Shenzhen Municipal Government of China/ ; JCYJ20241202124801003//Shenzhen Municipal Government of China/ ; No.25-1-5-smjk-13-nsh//Qingdao Municipal Demonstration Project for Science &amp; Technology to Benefit the People/ ; 2025YFA1310200//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Thiamine/metabolism ; Male ; Mice, Inbred C57BL ; *Fatty Liver/metabolism/microbiology ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Liver/metabolism ; Prebiotics/administration &amp; dosage ; *Eubacteriales/metabolism ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a common chronic liver disease. This study investigates the anti-MASLD effects of dietary prebiotic stachyose (STA) on disease progression identifying Butyricimonas virosa as a key bacterium boosted by STA supplementation. Oral gavage of B. virosa to high fat diet (HFD)-fed mice significantly suppresses the progression of MASLD and modulates gut microbiota composition. Integration of metagenomic and metabolomic data demonstrates that B. virosa treatment significantly enhances the production of thiamine monophosphate (TMP), as well as its conversion to thiamine and subsequent accumulation in the liver. The accumulation of hepatic thiamine further leads to elevated thiamine pyrophosphate (TPP) concentrations enhancing the activity of branched-chain α-keto acid dehydrogenase E1 subunit α (BCKDHA) associated with augmented degradation of branched chain amino acids (BCAAs). Administration of B. virosa compensates via production of gut bacterial-derived TMP for hepatic TPP deficiency in mice fed a thiamine-deficient HFD. A population-based analysis reveals an inverse correlation between plasma thiamine levels, abundances of bacterial genes involved in thiamine synthesis and metabolism, and phenotypes associated with MASLD, suggesting that key genes involved in fecal thiamine metabolism, as well as serum thiamine determination, may potentially serve as biomarkers for the diagnosis of MASLD.},
}
@article {pmid41747689,
year = {2026},
author = {Zhang, F and Zhou, T and Feng, Y and Chen, Y and Zhao, Q and Han, Q and Liu, J and Zhang, D and Jiang, H and Zhang, H},
title = {Metagenomic insights into the impacts of Vulcanococcus proliferation on microbial communities in a coastal bay.},
journal = {Marine environmental research},
volume = {217},
number = {},
pages = {107939},
doi = {10.1016/j.marenvres.2026.107939},
pmid = {41747689},
issn = {1879-0291},
mesh = {Metagenomics ; Seawater/microbiology ; Bays/microbiology ; *Metagenome ; *Microbiota ; *Enterococcaceae/genetics/physiology ; },
abstract = {Cyanobacterial blooms pose a major ecological challenge globally, with their outbreaks exerting profound effects on aquatic ecosystems. Vulcanococcus, a recently described cyanobacterial genus previously thought to be restricted to freshwater habitats, was documented in this study proliferation in seawater for the first time. Here, we reconstructed prokaryotic metagenome-assembled genomes (MAGs), including Vulcanococcus and the associated bacteria, enabling the assessment of their metabolic potential and influence of proliferation of Vulcanococcus on marine ecosystems. The proliferation of Vulcanococcus significantly altered the prokaryotic community compositions in the water, leading to a marked decline in the stability of prokaryotic co-occurrence networks. Comparative genomic analysis revealed that Vulcanococcus MAGs clustered within the freshwater Vulcanococcus clade, suggesting a possible freshwater origin. The high-quality Vulcanococcus MAG possess a complete set of urea transporter genes as well as urease genes, highlighting its potential for efficient urea utilization. The genome of Vulcanococcus encodes critical genes involved in vitamin B1 biosynthesis and is capable for de novo vitamin B12 synthesis, implying that proliferation of Vulcanococcus may serve as an important source of B vitamins for phytoplankton. Furthermore, Vulcanococcus exhibited significant correlations with eukaryotic phytoplankton, including diatoms and dinoflagellates, suggesting that Vulcanococcus may enhance B-vitamin availability for phytoplankton. Overall, these findings provide novel insights into the ecological roles and metabolic versatility of Vulcanococcus in marine environments, underscoring its potential impact on microbial community dynamics and nutrient cycling.},
}
@article {pmid41773424,
year = {2026},
author = {Valdés-Varela, L and Goyache, I and Virto, R and Sáinz, N and López-Yoldi, M and Sánchez-Vicente, A and López-Giral, N and Gil, AG and Milagro, FI and Aranaz, P},
title = {Companilactobacillus alimentarius CNTA 209 alleviates diet-induced obesity in mice through adipose tissue browning and gut barrier modulation.},
journal = {Food &amp; function},
volume = {17},
number = {6},
pages = {2851-2870},
doi = {10.1039/d5fo04242a},
pmid = {41773424},
issn = {2042-650X},
mesh = {Animals ; *Obesity/metabolism ; *Probiotics/administration &amp; dosage/pharmacology ; Mice ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Male ; *Adipose Tissue, Brown/metabolism ; Rats ; Rats, Wistar ; *Lactobacillaceae/physiology ; },
abstract = {The use of probiotics with health-promoting effects has emerged as a promising therapeutic strategy for managing obesity and metabolic syndrome. In this study, we characterized the probiotic properties of a novel strain, Companilactobacillus alimentarius CNTA 209, and investigated its potential anti-obesity effects and safety in rodent models. C. alimentarius exhibited sensitivity to all tested antibiotics, resistance to simulated gastric and intestinal conditions in vitro, and functional activities including β-galactosidase activity and short-chain fatty acid (SCFA) production. C. alimentarius supplementation mitigated liver damage induced by a high-fat, high-fructose diet and significantly reduced adiposity in obese C57BL/6 mice by enhancing brown adipose tissue metabolic activity. Metagenomic analysis revealed a beneficial modulation of gut microbiota composition, associated with improved intestinal barrier function. A comprehensive toxicological assessment conducted in Wistar rats confirmed the safety of the strain at a dose of 1 × 10[9] CFU per animal per day for oral administration. This study provides the first documented evidence of anti-obesity and metabolic benefits conferred by a strain of C. alimentarius, positioning CNTA 209 as a novel and safe candidate for the development of probiotic-based interventions targeting obesity and related metabolic disorders.},
}
@article {pmid41793958,
year = {2026},
author = {Li, X and Sun, Z and Lin, L and Deng, T and Xu, M},
title = {Attenuation of sulfamethoxazole and associated antimicrobial resistome by enriched electroactive microbial consortia.},
journal = {Environment international},
volume = {209},
number = {},
pages = {110182},
doi = {10.1016/j.envint.2026.110182},
pmid = {41793958},
issn = {1873-6750},
mesh = {*Sulfamethoxazole/metabolism ; *Microbial Consortia ; Biofilms ; Biodegradation, Environmental ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/metabolism ; },
abstract = {Electroactive biofilms with the capacity of extracellular electron transfer (EET) have shown great promise for mitigating antibiotics and antibiotic resistance genes (ARGs). However, detailed interactions between antibiotics and electroactive microorganisms, along with ARGs dissemination dynamics within the electroactive consortia, remained poorly understood. In this study, stable electroactive microbial consortia were enriched, and their influences on the fates of sulfamethoxazole (SMX) and associated ARGs were systematically investigated. The results showed the enriched consortia could degrade SMX effectively within a wide concentration range through co-metabolism which was stimulated by their electrogenic respiration. Moreover, with accelerated SMX removal, the abundances of associated ARGs including sul1 and sul2 in the consortia decreased significantly due to alleviated SMX-induced selective pressure and probably weakened horizontal gene transfer mediated by mobile genetic elements (e.g., IS91 and tnpA). Degrader isolation and metagenomic analysis identified the core EET-proficient genera (e.g., Geobacter and Alcaligenes) as essential for the accelerated co-metabolism biodegradation of SMX, whereas the proliferation of other bacteria with limited or no EET capacity (e.g., Hydrogenophaga, Burkholderia, Comamonas, Desulfovibrio and Pseudomonas) was closely linked to the ARGs dissemination. This work provides a mechanistic elucidation of how electroactive microbial consortia stimulate antibiotic degradation and attenuate ARGs proliferation, offering strategic insights for risk control of the resistome during wastewater treatment.},
}
@article {pmid41797015,
year = {2026},
author = {Jeon, J and Lee, DH and Kim, JH and Choi, Y and Jin, YK and Hong, JK and Lee, YM},
title = {Methanotrophic community structure and metabolic potential in the sulfate-methane transition zone of the ARAON mounds, Arctic Chukchi Sea.},
journal = {Marine environmental research},
volume = {217},
number = {},
pages = {107959},
doi = {10.1016/j.marenvres.2026.107959},
pmid = {41797015},
issn = {1879-0291},
mesh = {*Methane/metabolism ; Sulfates/metabolism ; Arctic Regions ; *Microbiota ; Archaea/metabolism ; Geologic Sediments/microbiology ; Bacteria/metabolism ; Oxidation-Reduction ; },
abstract = {Anaerobic oxidation of methane (AOM) mediated by archaea is a pivotal process for methane consumption in gas seepage-associated sediments. Despite its importance in regulating methane flux, the ecological roles and metabolic potential of microbial communities involved in AOM remain poorly understood in Arctic regions. In this study, we investigated the microbial community structures and methanotrophic signatures in sediments from gas hydrate-bearing and non-gas hydrate-bearing sites in ARAON Mounds (AMs) and reference sites. Microbial communities in AMs were distinct from those in reference sites, with high relative abundances of Euryarchaeota (45.5 ± 11%), Lokiarcheota (35 ± 6.1%), and Atribacterota (50.1 ± 23.3%). Anaerobic methanotrophic archaea (ANME) showed site- and depth-specific distributions, with ANME-1a, ANME-1b, and ANME-2c predominating the sulfate-methane transition zone (SMTZ) of the gas hydrate-bearing sites, and ANME-1a prevailing at non-gas hydrate-bearing sites. Sulfate-reducing bacteria (SRB) affiliated with Seep-SRB1 co-occurred with ANME-1a and ANME-1b within the AMs. Metagenome-assembled genomes (MAGs) of ANME-1b and ANME-2c recovered from the SMTZ of the gas hydrate-bearing site (AM6) harbored key AOM-related genes, and their putative syntrophic bacterial partner, ETH-SRB1, possessed essential genes for sulfate reduction. Additionally, Lokiarchaeota and Atribacterota MAGs encoded genes involved in protein degradation, fermentation, and hydrogen metabolism, indicating their possible roles in methane cycling. Collectively, these results reveal distinct microbial assemblages and their functional genomic traits, suggesting niche specialization associated with methane oxidation potential at the SMTZ of the gas hydrate-bearing site.},
}
@article {pmid41870053,
year = {2026},
author = {Pasaribu, B and Vincent Mishael Dilens, C and Wahyudin Lewaru, M and Ayuningrum, D and Patria, MP and Juliandri Prihadi, D and Purba, NP and Untung Kurnia Agung, M and Maqbul, I and Sulistiowati, S},
title = {Shotgun metagenomic dataset of seawater bacterial communities from Pari Islands, Indonesia.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0147625},
doi = {10.1128/mra.01476-25},
pmid = {41870053},
issn = {2576-098X},
abstract = {Pari Island is located in Seribu Islands, Indonesia, and is well-known for its marine biodiversity. Shotgun metagenomic sequencing was performed using the DNaseq-G400 platform, and bioinformatics approaches were applied to analyze the sequence data.},
}
@article {pmid41572814,
year = {2026},
author = {Fathima, N and Mascarenhas, R and Umar, D and Rekha, PD and Shetty, S and Amin, V},
title = {Impact of removing fixed orthodontic appliances on oral microbial dysbiosis: A longitudinal study and metagenomic sequencing analysis.},
journal = {Journal of orthodontics},
volume = {53},
number = {1},
pages = {34-44},
doi = {10.1177/14653125251408048},
pmid = {41572814},
issn = {1465-3133},
mesh = {Humans ; Longitudinal Studies ; *Orthodontic Appliances, Fixed/microbiology/adverse effects ; Male ; Female ; Metagenomics ; *Dysbiosis/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Adolescent ; DNA, Bacterial ; *Mouth/microbiology ; Young Adult ; Bacteria/classification ; },
abstract = {OBJECTIVE: To investigate the impact of appliance removal on oral microbial diversity, composition, and abundance using metagenomic sequencing. It aims to identify the core microbiome and assess changes between mid-treatment and 2 weeks after debonding to understand the relationship between orthodontic therapy and oral health better.<br><br>METHODS: This longitudinal cohort study recruited 26 patients undergoing fixed orthodontic treatment between January 2022 and June 2023. Saliva samples were collected at two predefined time points: mid-treatment (T0, defined as before appliance removal) and 2 weeks after debonding (T1). Microbial DNA was extracted and the V1-V3 hypervariable regions of the 16S rRNA gene were sequenced using Illumina NovaSeq. Bioinformatics analysis was performed using QIIME and the SILVA database to evaluate microbial diversity and composition at T0 and T1. Beta diversity metrics and statistical tests, including PERMANOVA and Wilcoxon signed-rank tests, were applied to identify significant differences (P < 0.05). Effect sizes with 95% confidence intervals (CIs) were reported.<br><br>RESULTS: The analysis revealed significant shifts in microbial diversity and composition between T0 and T1. A total of 189 species across 63 genera were identified, with Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria as dominant phyla. Genera such as Fusobacterium periodonticum (&#x2191; 12.4%, 95% CI = 10.1-14.7) and Veillonella parvula (&#x2191; 9.8%, 95% CI = 7.6-11.3) increased after debonding, while Prevotella melaninogenica (&#x2193; 10.2%, 95% CI = 8.1-12.0) and Rothia dentocariosa (&#x2193; 7.9%, 95% CI = 6.3-9.2) decreased. Beta diversity analysis confirmed a statistically significant microbial community shift (P < 0.05).<br><br>CONCLUSION: This study demonstrated significant microbial shifts between mid-treatment and 2 weeks after debonding, including increases in potentially pathogenic genera and alterations in the core microbiome. These findings indicate microbial changes persist for at least 2 weeks after appliance removal. Further research with pre-treatment baselines and extended follow-up is required to better define the long-term trajectory of these changes.},
}
@article {pmid41793822,
year = {2026},
author = {Li, P and Wang, Y and Bao, Z and He, X and Wang, S and Su, X and Nie, W and Xu, F and Zhou, H and Li, H and Xu, B},
title = {Metagenomics-based insights into the microbial community composition and quality characteristics development potentiality in traditional dry-cured ham.},
journal = {International journal of food microbiology},
volume = {453},
number = {},
pages = {111705},
doi = {10.1016/j.ijfoodmicro.2026.111705},
pmid = {41793822},
issn = {1879-3460},
mesh = {Animals ; Metagenomics ; Swine ; *Meat Products/microbiology/analysis ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Volatile Organic Compounds/analysis/metabolism ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; Food Microbiology ; Peptides ; },
abstract = {The objective of this study was to elucidate the formation mechanisms of quality characteristics in traditional dry-cured ham. The microbial community composition in three types of dry-cured ham was analyzed using metagenomics technology. Volatile flavor profiles were characterized via gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS), while peptide profiles were determined using liquid chromatography-mass spectrometry (LC-MS). Based on metagenomic data, biosynthetic pathways of volatile flavor compounds and bioactive peptides in dry-cured hams were reconstructed. Key microorganisms identified include Staphylococcus equorum, Staphylococcus saprophyticus, Aspergillus glaucus, Aspergillus ruber, Debaryomyces hansenii, and Debaryomyces fabryi. Using GC-MS and GC-IMS, 25 volatile compounds were identified in dry-cured ham, with branched-chain compounds exhibiting higher odor activity values (OAVs). LC-MS analysis identified 203 microbial-derived peptide fragments, predominantly possessing angiotensin-converting enzyme (ACE) inhibitory, dipeptidyl peptidase-IV (DPP-IV) inhibitory, and antioxidant activities. Further investigation into the contribution of microbial communities to the characteristic quality attributes revealed that Staphylococcus species promote the formation of 3-methyl-butanal via branched-chain amino acid transaminase (BCAT) and 3-hydroxy-2-butanone via acetolactate synthase (ALS). With regard to functional bioactive peptides, Staphylococcus indirectly contributes to the synthesis of NPPKFD, DLEE, and KRQKYD via glutamyl endopeptidase activity. Additionally, proteins derived from Aspergillus glaucus (actin-related protein 5) and Staphylococcus equorum (chromosome segregation protein) serve as direct precursors for bioactive peptides, yielding potential sequences such as KNSKDPVSI and LEDDI. This study provides evidence indicating the role of microbial communities in shaping the quality characteristics of dry-cured ham.},
}
@article {pmid41825563,
year = {2026},
author = {An, M and Yu, J and Lin, X and Lu, Y and Li, X and He, J and Zhao, G},
title = {Multi-stage synthetic microbial consortia outperform single-stage augmentation by remodeling metabolism and mediating function-stability trade-off in anaerobic digestion.},
journal = {Bioresource technology},
volume = {449},
number = {},
pages = {134417},
doi = {10.1016/j.biortech.2026.134417},
pmid = {41825563},
issn = {1873-2976},
mesh = {Anaerobiosis ; *Microbial Consortia/physiology ; Methane/metabolism/biosynthesis ; Bioreactors/microbiology ; Fatty Acids, Volatile/metabolism ; },
abstract = {Anaerobic digestion (AD) of food waste often suffers from low methane yield and volatile fatty acids (VFAs) accumulation, primarily due to inefficiencies or imbalances within the native microbial community. To address these metabolic and ecological limitations, we constructed two synthetic microbial communities (SynComs) using a function-driven strategy: a methanogen-only consortium (SynCom-J) and a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members (SynCom-YSJ). Both SynComs were introduced into semi-continuous reactors that already harbored a metabolically complete native microbiome, serving as bioaugmentation agents. When fed daily with partially hydrolyzed feedstock containing residual macromolecular organics and short-chain VFAs, SynCom-YSJ consistently outperformed SynCom-J during the entire hydraulic retention time. Compared to the non-bioaugmented control under identical operating conditions, SynCom-YSJ increased methane yield by 22% (vs. 8% for SynCom-J) and nearly eliminated the start-up lag phase, while both consortia reduced propionate accumulation by 1.6-fold. Successful colonization of the SynComs reshaped the AD microenvironment-characterized by elevated acetate, reduced propionate, and a moderate, non-inhibitory increase in total ammonia nitrogen-thereby imposing deterministic selection on the resident community. Metagenomic analysis revealed that SynCom-YSJ triggered broader metabolic reprogramming, upregulating genes involved in hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis. Notably, a trade-off between microbial network stability and process performance emerged: SynCom-J promoted a more robust network, whereas SynCom-YSJ formed a more complex and high-efficiency network that prioritized methane yield. This study demonstrates that coordinated multi-stage bioaugmentation optimizes methanogenesis through targeted metabolic remodeling and provides an ecology-informed design principle for engineering SynComs that balance system performance with stability. These findings highlight the potential of multi-stage bioaugmentation to enhance both functional robustness and system resilience in food waste AD.},
}
@article {pmid41831799,
year = {2026},
author = {Qi, H and Wu, R and Liao, J and Alvarez, PJJ and Yu, P},
title = {Longitudinal multi-omics reveal phase-dependent viral adaptive strategies and functional potential during formation of algal-bacterial granular sludge.},
journal = {Bioresource technology},
volume = {449},
number = {},
pages = {134410},
doi = {10.1016/j.biortech.2026.134410},
pmid = {41831799},
issn = {1873-2976},
mesh = {*Sewage/microbiology/virology ; *Bacteria/genetics/virology ; Symbiosis ; Metagenome ; Microbiota ; Bacteriophages/genetics ; Multiomics ; },
abstract = {Virus-prokaryote interactions within microbial aggregates critically influence microbiome function and stability, yet the interactive dynamics during microbial aggregation remain largely unexplored. Here, longitudinal multi-omics revealed that prokaryotic host community diversity underwent decline and subsequent recovery during algal-bacterial granular sludge (ABGS) formation from activated sludge. Declined host diversity in the collapse phase enriched for lysogenic viruses and facilitated virus-host mutualistic symbiosis, during which the proportion of lysogenic metagenome-assembled genomes (MAGs) peaked at 84% (841,649 TPM), with auxiliary metabolic genes (AMGs) primarily involved in genetic information processing and amino acid metabolism. Moreover, low host diversity increased viral microdiversity by 1.97-fold and selected for virion structure genes that were conducive to viral fitness and replication. As host diversity recovered during the recovery phase, viruses and hosts engaged in an evolutionary arms race, with both host defense systems (DS) (Spearman's Rho = 0.68, P < 0.05) and viral anti-defense systems (ADS) (Spearman's Rho = 0.51, P < 0.05) enriched along with granule maturation. Furthermore, active lysogenic infections were accompanied by the dissemination of AMGs predominantly associated with the metabolism of cofactors, vitamins, terpenoids, and polyketides. Despite their phase-dependent functional profiles, lysogenic phages with AMGs putatively enhanced the structural and functional stability of the microbiome during ABGS formation. Overall, our study unveils a phase-dependent co-evolutionary interplay between viruses and prokaryotic hosts during ABGS formation, providing insights into virus-mediated microbial structural and functional resilience in engineered ecosystems.},
}
@article {pmid41839407,
year = {2026},
author = {Chen, S and Zhao, A and Zhang, W and Liu, Q and Li, D},
title = {Metabolic reprogramming disrupts the resistome-mobilome nexus and enhances bio-sanitization in synthetic microbial community-mediated composting.},
journal = {Bioresource technology},
volume = {449},
number = {},
pages = {134433},
doi = {10.1016/j.biortech.2026.134433},
pmid = {41839407},
issn = {1873-2976},
mesh = {*Composting/methods ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Lignin/metabolism ; Bacteria/metabolism/genetics ; Metabolic Reprogramming ; },
abstract = {The persistence of antibiotic resistance genes (ARGs) and pathogens during manure composting poses critical risks within the One Health framework. However, the ecological and metabolic mechanisms by which microbiome engineering disrupts the dissemination of these biohazards remain poorly understood. This study evaluated a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum) in mitigating these risks. KEGG analysis highlighted a pivotal metabolic reprogramming from a biofilm-dependent defense-survival model to an active motility-metabolism mode, characterized by depleted lipopolysaccharide biosynthesis and enriched flagellar assembly. This metabolic shift implies a fitness cost trade-off that physically restricts horizontal gene transfer (HGT) opportunities. Metagenomic analysis showed SynCom inoculation caused a transient ARG rebound followed by profound attenuation. While thermophilic hosts temporarily enriched specific ARGs, SynCom ultimately achieved a significant reduction in multidrug resistance genes and virulence factors by intensifying thermophilic fermentation. Mantel correlation analysis revealed the SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification were critical environmental drivers, restricting ARGs and alleviating co-selection pressure on metal resistance genes. Network analysis demonstrated SynCom induced a structural collapse of high-risk interactomes (reducing potential host-gene associations by 26.6%), effectively disrupting ARG and mobile genetic element connections by suppressing key recombinases (XerD, IntI1) and eliminating Pseudomonadota hub hosts. Consequently, deep bio-sanitization was achieved by synchronously eliminating high-risk pathogens (e.g., Pseudomonas aeruginosa), phytopathogens, and specific virulence factors. These findings indicate that SynCom provides a robust microbiome engineering strategy to disrupt the genetic dissemination of biohazards and ensure organic fertilizer biosafety.},
}
@article {pmid41863619,
year = {2026},
author = {Jonathan, AR and Balasubramanian, VK and Ho, ST and Chen, YP and Khunnamwong, P and Chou, JY},
title = {Next-generation strategies for PLA degradation: microbial consortia, metagenomics, enzyme engineering and AI-guided approaches.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41863619},
issn = {1432-072X},
support = {MOST 111-2621-B-018-001 to Jui-Yu Chou//Ministry of Science and Technology, Taiwan/ ; },
mesh = {*Metagenomics/methods ; *Microbial Consortia ; Biodegradation, Environmental ; *Polyesters/metabolism ; Artificial Intelligence ; Fungi/metabolism/genetics ; Bacteria/metabolism/genetics ; },
abstract = {Polylactic acid (PLA) is one of the most widely used biodegradable bioplastics; however, its slow degradation under natural conditions limits its environmental sustainability. This review summarizes recent advances in microbial and biotechnological strategies that enhance PLA biodegradation across diverse ecosystems. Emerging approaches include screening insect gut microbiota, isolating fungal species with strong adsorption or enzymatic capacities, and exploring soil, compost, and aquatic microbiomes using metagenomics and environmental DNA (eDNA) tools. Microbial consortia, thermophilic degraders, and co-culture systems are highlighted as effective solutions to overcome the intrinsic crystallinity and hydrolysis-dependent breakdown of PLA. Beyond natural systems, this review emphasizes the increasing role of synthetic biology, directed evolution, and artificial intelligence (AI) in engineering high-performance PLA-degrading enzymes. AI-driven structural prediction and machine-learning platforms offer new possibilities for designing robust depolymerases with improved specificity, thermostability, and catalytic efficiency. Collectively, these multidisciplinary strategies provide a roadmap for accelerating PLA degradation in industrial composting, wastewater treatment, and bioremediation. Future integration of ecological screening with computational enzyme engineering is expected to advance scalable and sustainable PLA waste management.},
}
@article {pmid41673004,
year = {2026},
author = {Niu, M and Fu, L and Yan, Q and He, Z and Li, D and Zhen, Y and Wang, M and Li, C},
title = {35 metagenomic datasets from the northern and southern parts of the Yap trench sediments.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41673004},
issn = {2052-4463},
mesh = {*Metagenome ; Metagenomics ; *Microbiota ; *Geologic Sediments/microbiology ; Bacteria/classification/genetics ; },
abstract = {The hadal trench is the deepest part of the global ocean and harbors highly abundant microbial cells. However, the diversity and function of the majority of microbial communities in this part of the ocean are still unclear. Here, we collected 35 metagenomes from three push cores across different sites in both the northern and southern Yap trench to construct a comprehensive gene and genome dataset. A total of 32 million non-redundant genes were predicted from the whole metagenome datasets, with 63% assigned to known functional groups based on currently available databases. A total of 404 metagenome-assembled genomes (MAGs) with completeness >50% and contamination <10% were retrieved, and their taxonomy was highly diverse across 26 phyla. Alpha- and Gammaproteobacteria, Phycisphaerae, Nitrospiria, and Dehalococcoidia were dominant classes across all samples. The nonredundant gene and MAG datasets are valuable resources for advancing our understanding of the diversity, composition, and functions of microbiota in the sediment of the hadal trench.},
}
@article {pmid41776310,
year = {2026},
author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA},
title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.},
journal = {Nature aging},
volume = {6},
number = {3},
pages = {682-702},
pmid = {41776310},
issn = {2662-8465},
support = {#00034120//Pew Charitable Trusts/ ; T32 AG052374/AG/NIA NIH HHS/United States ; No. 58-1950-7-707//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; T32 AG052374/AG/NIA NIH HHS/United States ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/physiology ; *Ovary/physiology ; *Fecal Microbiota Transplantation ; Mice ; *Aging/physiology ; Mice, Inbred C57BL ; Transcriptome ; *Menopause ; Metagenomics ; Fertility ; },
abstract = {The decline in ovarian function with age affects fertility and is associated with increased risk of age-related diseases, including osteoporosis and dementia. Notably, earlier menopause is linked to shorter lifespan, yet the molecular mechanisms underlying ovarian aging remain poorly understood. Recent evidence suggests the gut microbiota may influence ovarian health. Here we show that ovarian aging is associated with distinct gut microbial profiles in female mice and that the gut microbiome can directly influence ovarian health. Using fecal microbiota transplantation from young or estropausal female mice, we demonstrate that heterochronic microbiota transfer remodels the ovarian transcriptome, reduces inflammation-related gene expression and induces transcriptional features consistent with ovarian rejuvenation. These molecular changes are accompanied by enhanced ovarian health and increased fertility. Integrating metagenomics-based causal mediation analyses with serum untargeted metabolomics, we identify candidate microbial species and metabolites that may contribute to the observed effects. Our findings reveal a direct link between the gut microbiota and ovarian health.},
}
@article {pmid41498484,
year = {2026},
author = {Huang, T and Ge, H and Wu, Z and Zhang, Y and Wang, L and Dang, C and Fu, J},
title = {Resistance of Microbial Community in Activated Sludge to Nano-Ag Stress Through Regulation of N-Acyl Homoserine Lactones-Mediated Quorum Sensing.},
journal = {Biotechnology and bioengineering},
volume = {123},
number = {4},
pages = {995-1010},
doi = {10.1002/bit.70155},
pmid = {41498484},
issn = {1097-0290},
support = {22306068//National Natural Science Foundation of China/ ; 42476142//National Natural Science Foundation of China/ ; //2022 HUST-UTS Key Partnership Research Seed Funding/ ; 2024AFD091//Hubei Provincial Natural Science Foundation of China/ ; },
mesh = {*Quorum Sensing/drug effects ; *Sewage/microbiology ; *Acyl-Butyrolactones/metabolism ; *Silver/toxicity ; Bioreactors/microbiology ; *Microbiota/drug effects ; Bacteria/drug effects/genetics/metabolism ; },
abstract = {Nano-Ag is increasingly detected in WWTP due to its widespread application, posing a significant threat to microbial communities responsible for wastewater treatment efficiency. Prior studies have demonstrated that quorum sensing (QS) can modulate bacterial tolerance to various environmental stressors in sludge systems. However, the feasibility and mechanisms of N-acyl homoserine lactones (AHLs)-mediated QS regulation to improve the resistance of microorganisms in WWTPs to nano-Ag shocks have been unexplored. Hence, we conducted sequencing batch reactor experiments, and as expected, nano-Ag significantly reduced the treatment performance of bioreactors. However, with the addition of AHLs (C6-HSL, C10-HSL, and C14-HSL) in the bioreactors, the microbial resistance in activated sludge to nano-Ag stress had been evidently enhanced, including the restoration of the sludge morphology, settleability, biomass and extracellular polymeric substances (EPS), as well as the treatment performance of bioreactors on removals of ammonium nitrogen (NH4 [+]-N), chemical oxygen demand (COD), and suspended solids. The joint analysis of metagenomics, metatranscriptomics, and metametabolomics indicated the multifunctional bacteria (e.g., Amaricoccus, Hydrogenophaga, and Brevundimonas) played a very important role during the regulation of AHLs-mediated QS, which harbored functional genes associated with nitrogen metabolism, carbon metabolism, silver resistance, and AHLs response. The upregulation on glutathione-dependent metabolisms (e.g., glutathione-oxidized glutathione redox cycle) and biosynthesis of EPS (e.g., poly-N-acetylglucosamine) were beneficial for the enhancement of microbial resistance to nano-Ag. This study provided a potentially feasible strategy and important theoretical basis to enhance the robustness and restore the function of microorganisms in wastewater treatment systems by using AHLs-mediated QS regulation.},
}
@article {pmid41654729,
year = {2026},
author = {Wang, P and Yao, Y and Yan, K and Wang, S and Wang, M and Liu, X and Hu, C and Dong, Y and Li, J},
title = {A validation for sex differences in gut microbiome of essential hypertension based on cohort analysis.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41654729},
issn = {1471-2180},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; Feces/microbiology ; *Essential Hypertension/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Sex Factors ; Cohort Studies ; Metagenomics ; Aged ; Adult ; Fatty Acids, Volatile/metabolism ; China ; Hypertension/microbiology ; Sex Characteristics ; },
abstract = {BACKGROUND: Prior research has demonstrated sex-specific differences in hypertension (HTN). The gut microbiota (GM) and its metabolic functions have emerged as key players in the development of HTN. To explore potential sex-based heterogeneity in gut bacteria among hypertensive patients, we conducted this study with the aim of validating sex differences in the gut flora associated with HTN.<br><br>METHODS: Here, we leveraged a metagenomic dataset comprising 106 fecal samples from a Chinese cohort of individuals with essential HTN to systematically analyze and compare alterations in the gut microbiome between male and female patients, as well as relative to a healthy control group.<br><br>RESULTS: Our study confirmed a statistically significant difference in the &#x3b2;-diversity of GM between hypertensive patients and healthy controls. When the subjects were further stratified by sex, significant differences in the distribution of gut flora were observed exclusively in females, whereas none was noted between groups in males. It was observed that certain genera of GM exhibit negative correlations with blood pressure. Notably, the relative abundance of these bacterial genera, including Lachnospira, Faecalibacterium, and Roseburia, was significantly diminished in female hypertensive patients. These organisms are primarily involved in the biosynthesis of short-chain fatty acids (SCFAs), with a notable emphasis on butyrate production. Ruminococcus gnavus was specifically enriched in hypertensive males, whereas certain bacteria, such as Lactobacillus, were notably depleted. The abnormality of the SCFAs-producing flora in female hypertensive patients may be related to that women are more likely to develop hypertensive organ damage.<br><br>CONCLUSIONS: The findings of our study indicate that GM dysbiosis is more significantly associated with HTN in females. Consequently, sex constitutes a critical factor in evaluating the role of intestinal flora in the pathogenesis of HTN.},
}
@article {pmid41713418,
year = {2026},
author = {Shao, Y and Wang, S and Gichuki, BM and Stares, MD and Rozday, TJ and Kumar, N and Browne, HP and Dawson, NJR and Njunge, JM and Tigoi, C and Ngao, N and Chisti, MJ and Singa, BO and Kariuki, S and Diallo, AH and Saleem, AF and Ali, SA and Mupere, E and Mbale, E and Tickell, KD and Voskuijl, WP and Lancioni, CL and Bandsma, RHJ and Ahmed, T and Walson, JL and Berkley, JA and Lawley, TD},
title = {Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design.},
journal = {Cell},
volume = {189},
number = {6},
pages = {1854-1873.e17},
doi = {10.1016/j.cell.2026.01.007},
pmid = {41713418},
issn = {1097-4172},
mesh = {*Probiotics ; Humans ; Infant ; *Genome, Bacterial/genetics ; *Bifidobacterium longum/genetics/classification ; Phylogeny ; *Bifidobacterium longum subspecies infantis/genetics/classification ; Genomics ; Gastrointestinal Microbiome/genetics ; Infant, Newborn ; Milk, Human/microbiology ; },
abstract = {Bifidobacterium longum and B. infantis are pioneer colonizers of the neonatal gut and are widely used as probiotics to support infant growth, development, and disease resistance. However, commercial strains derived largely from high-income countries (HICs) may be suboptimal for infants in low- and middle-income countries (LMICs). We assembled a global genomic atlas of more than 4,000 genomes from 48 countries, increasing representation from LMICs by 12- to 17-fold. High-resolution phylogenomic and functional analyses support delineating B. longum and B. infantis as distinct species with divergent functions and epidemiological patterns. B. infantis dominates early-life microbiota in LMICs but is rarely detected in HICs. Natural B. infantis strains show extreme biogeographic stratification and predicted adaptations to local plant-glycan-rich diets and breast-milk-derived substrates, including urea and B vitamins. This genomic resource enables genome-guided selection of geographically matched strains to inform more effective probiotics and precision microbiome therapeutics for diverse infant populations.},
}
@article {pmid41785249,
year = {2026},
author = {Pucci, N and Kaan, AM and Ujčič-Voortman, J and Verhoeff, AP and Zaura, E and Mende, DR},
title = {Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.},
journal = {PLoS computational biology},
volume = {22},
number = {3},
pages = {e1013185},
doi = {10.1371/journal.pcbi.1013185},
pmid = {41785249},
issn = {1553-7358},
mesh = {Humans ; *Mouth/microbiology ; Infant ; *Microbiota/genetics ; Female ; Phylogeny ; Metagenome/genetics ; Metagenomics ; Male ; Streptococcus/genetics/classification ; Longitudinal Studies ; Computational Biology ; },
abstract = {Early-life oral microbiome development is a complex community assembly process that influences long-term health outcomes. Nevertheless, microbial functions and interactions driving these ecological processes remain poorly understood. In this study, we analyze oral microbiomes from a longitudinal cohort of 24 mother-infant dyads at 1 and 6 months postpartum using shotgun metagenomics. We identify two previously undescribed Streptococcus and Rothia species to be among the most prevalent, abundant and strongly co-occurring members of the oral microbiome of six-month-old infants. By leveraging metagenome-assembled genomes (MAGs) and genome-scale metabolic models (GEMS) we reveal their genomic and functional characteristics relative to other infant-associated species and predict their metabolic interactions within a network of co-occurring oral taxa. Our findings highlight unique functional features, including genes encoding adhesins and carbohydrate-active enzymes (CAZymes). Metabolic modeling identified potential exchange of key amino acids, particularly ornithine and lysine, between these species, suggesting metabolic cross-feeding interactions that may explain their co-abundance across infant oral microbiomes. Overall, this study provides key insights into the functional adaptations and microbial interactions shaping early colonization in the oral cavity, providing testable hypotheses for future experimental validation.},
}
@article {pmid41857857,
year = {2026},
author = {Ngoumou, GB and Ngandeu Schepanski, S and Blakeslee, SB and Diedering, A and Twal, E and Raue, SL and Schroeder, M and Wicaksono, WA and Stritter, W and Berg, G and Seifert, G},
title = {Effects of fermented versus unfermented red cabbage on symptoms, immune response, inflammatory markers and the gut microbiome in young adults with allergic rhinoconjunctivitis: a randomised controlled trial protocol.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e115290},
doi = {10.1136/bmjopen-2025-115290},
pmid = {41857857},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Adult ; Young Adult ; *Brassica ; Quality of Life ; *Fermented Foods ; Adolescent ; Randomized Controlled Trials as Topic ; *Conjunctivitis, Allergic/immunology/diet therapy ; *Rhinitis, Allergic/immunology/diet therapy ; Female ; Male ; Biomarkers ; },
abstract = {INTRODUCTION: Allergic rhinoconjunctivitis (ARC) is a highly prevalent immune-mediated condition associated with substantial symptom burden, impaired quality of life and increased healthcare use. Emerging evidence highlights the role of the gut microbiome in immune regulation and allergic disease. Fermented foods may contain live microbes (when unpasteurised or uncooked) and bioactive postbiotic metabolites that can modulate immune responses. Despite growing interest in dietary strategies targeting the microbiome, no randomised controlled trial has compared fermented versus unfermented red cabbage for ARC.<br><br>METHODS AND ANALYSES: This single-centre, randomised, controlled trial with a sensory-matched, unfermented cabbage comparator investigates the effects of daily consumption of fermented red cabbage for 8 weeks compared with an unfermented red cabbage control in young adults (18-35 years) with ARC. A total of 158 participants will be randomly assigned (1:1). The primary outcome is change in Total Nose and Eye Symptom Score from baseline to week 8. Secondary outcomes include daily symptoms and medication use captured via mobile ecological momentary assessments, quality of life, psychological well-being, gastrointestinal symptoms, systemic inflammatory markers, total IgE, immune cell profile and metagenomic characterisation of stool samples. A nested qualitative component explores participants' experiences and acceptability of the intervention. Analyses will include mixed-effects models, time-series analyses incorporating daily pollen counts and comprehensive microbiome statistics. Safety outcomes and adverse events will also be assessed.<br><br>ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Charit&#xe9;-Universit&#xe4;tsmedizin Berlin (EA4/043/25) and is conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Results will be disseminated through peer-reviewed publications, conference presentations and a lay summary provided to participants. Anonymised datasets and analysis scripts will be made available in public repositories, and metagenomic sequencing data will be deposited in an international sequence archive to ensure transparency and reproducibility.<br><br>TRIAL REGISTRATION NUMBER: DRKS00036475.},
}
@article {pmid41858251,
year = {2026},
author = {Morissette, O and Côté, G and Couillard, MA and Pouliot, R and Bernatchez, L},
title = {Trait-Based Biomonitoring Using eDNA Metabarcoding to Assess Anthropogenic Disturbances on Freshwater Fish Communities.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70131},
doi = {10.1111/1755-0998.70131},
pmid = {41858251},
issn = {1755-0998},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/classification/genetics ; *DNA, Environmental/genetics ; Quebec ; Ecosystem ; Fresh Water ; Rivers ; *Biological Monitoring/methods ; Biodiversity ; *Environmental Monitoring/methods ; *Metagenomics/methods ; *Biota ; },
abstract = {Various anthropogenic disturbances affect the succession of aquatic habitats along dendritic river networks. Bioindicator taxa, such as fish, can be used to assess the effects of these disturbances on habitat quality. Environmental DNA (eDNA) metabarcoding offers a novel approach to complement traditional sampling and analysis of bioindicator taxa. Here, we apply a trait-based biomonitoring framework, focusing on fish tolerance to pollution, to assess habitat quality and fragmentation within two watersheds in southern Québec (Canada). We sampled 193 sites within the dendritic networks of the Châteauguay and St. François watersheds and estimated fish community tolerance indices on the basis of 12S metabarcoding. We found a significant correlation between the fish community tolerance index and environmental factors such as subwatershed land use, precipitation and elevation. We also found that river fragmentation caused by dams affected fish assemblages and native fish movement but also prevented the spread of the non-native common carp. Finally, we applied random-forest modelling to predict the tolerance of fish communities to disturbances in unsampled areas, providing a broader understanding of habitat quality within catchments. Our research highlights how eDNA metabarcoding for large-scale biomonitoring and river fragmentation studies provides a cost-effective and non-invasive method for assessing fish biodiversity and riverine ecosystem health.},
}
@article {pmid41858257,
year = {2026},
author = {Geerts, MM and Curto, M and Alverson, AJ and Stone, J and Gante, HF},
title = {Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in eDNA Metagenomic Data.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70128},
doi = {10.1111/1755-0998.70128},
pmid = {41858257},
issn = {1755-0998},
support = {STG/21/044//KU Leuven Research Fund/ ; 11Q4724N//Fonds Wetenschappelijk Onderzoek/ ; UIDP/50027/2020//InBIO Program&#xe1;tico FUI 2020-2023/ ; DEB-2331644//Division of Environmental Biology/ ; },
mesh = {*Metagenomics/methods ; *Diatoms/genetics/classification ; Phylogeny ; *Computational Biology/methods ; *DNA, Environmental/genetics ; *Eukaryota/genetics/classification ; Metagenome ; *Biodiversity ; Czech Republic ; Fresh Water/microbiology ; },
abstract = {Genome assembly graphs contain valuable yet frequently overlooked information that can enhance assembly completeness by revealing contig connectivity. Here, we demonstrate how leveraging these information-rich structures enables the discovery of hidden microeukaryotic diversity in environmental DNA shotgun metagenomic datasets. While GetOrganelle has previously been used for organellar genome assembly from isolated tissues, we present its first application to water eDNA metagenomic data, using diatoms as an example. We tested the efficiency of this organellar genome assembly tool on three freshwater eDNA metagenomic datasets with varying diatom abundances, finding that GetOrganelle alone yields fragmented scaffolds due to mixed-species complexity. By implementing manual disentanglement of assembly graphs, we successfully recovered complete organellar genomes from these assemblies. From high-abundance bloom samples, we recovered complete plastomes of Stephanodiscus hantzschii with 99.9% pairwise identity across distant geographical locations (USA and Czech Republic). From a lower abundance non-bloom sample, we reconstructed a potentially novel Cyclotella plastome with only 94.0% identity to its closest available reference, Cyclotella atomus. Our assembly quality assessment confirmed effective manual disentanglement even at low diatom abundances. By integrating sequence similarity, gene order conservation and phylogenetic analysis, we achieved robust species-level resolution and resolved previous taxonomic uncertainties. Our findings demonstrate that mining eDNA metagenomic data with GetOrganelle reveals previously hidden microeukaryotic diversity and provides higher taxonomic resolution than traditional binning methods. This approach proves especially valuable for microeukaryotes, where reference organellar genomes remain underrepresented in existing databases.},
}
@article {pmid40064789,
year = {2026},
author = {Wang, H and Ma, H and Yan, H and Pei, Z and Zhao, J and Zhang, H and Zhang, Z and Lu, W},
title = {Study on the Effect of Bifidobacterium adolescentis CCFM1066 on Exercise Performance, Gut Microbiota, and Its Metabolites in Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {1},
pages = {54-67},
pmid = {40064789},
issn = {1867-1314},
support = {32172212, 32394052//National Natural Science Foundation of China/ ; 2022YFF1100403//National Key Research and Development Program of China/ ; WMCC202403//Cohort and Clinical Research Program of Wuxi Medical Center, Nanjing Medical University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Probiotics/administration &amp; dosage/pharmacology ; *Physical Conditioning, Animal ; *Bifidobacterium adolescentis/physiology ; Male ; },
abstract = {Prolonged high-intensity exercise consumes significant energy, leading to fatigue and decreased performance. This study explores the effects of Bifidobacterium adolescentis CCFM1066 on exercise performance, gut microbiota, and its metabolites in mice. The results of the mouse experiments showed the mice which were intervened by Bifidobacterium adolescentis CCFM1066 have a significant increase in exercise performance, including forceful swimming time, fatigue baton turning time, and forelimb grip strength. Through metagenomic sequencing and differential metabolites, analysis indicated that the intervention of CCFM1066 increased Lachnospiraceae bacterium, Parabacteroides goldsteinii, Bacteroides xylanisolvens, and Bifidobacterium adolescentis and altered the key metabolic pathways including protein digestion and absorption and biosynthesis of amino acids. Supplementation with CCFM1066 modulates the production of short-chain fatty acids (SCFAs) and fatty acid amides (FAAs) by gut microbiota, decreasing levels of lactic acid (LA), blood urea nitrogen (BUN), lactate dehydrogenase (LDH), and creatine kinase (CK) while increasing muscle and hepatic glycogen content, thus reducing central nervous system fatigue and thereby improving exercise endurance and performance. These findings provide new insights into nutritional interventions for sports performance.},
}
@article {pmid40193036,
year = {2026},
author = {Kim, SY and Seol, D and Jeong, M and Kwak, W and Kim, H and Cho, S and Kim, TH},
title = {Assessing the Efficacy of Ligilactobacillus salivarius CLS0420 and Lacticaseibacillus paracasei CLPC0603 on Vaginal Well-Being in Healthy Women: A Pilot, Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {1},
pages = {368-380},
pmid = {40193036},
issn = {1867-1314},
mesh = {Humans ; Female ; *Probiotics/administration &amp; dosage/pharmacology ; Adult ; Double-Blind Method ; *Vagina/microbiology ; Pilot Projects ; Middle Aged ; Young Adult ; *Vaginosis, Bacterial/prevention &amp; control/microbiology ; *Lacticaseibacillus paracasei/physiology ; Gardnerella vaginalis/drug effects ; Microbiota ; Candida albicans/drug effects ; },
abstract = {Despite the growing development of probiotics for preventing bacterial vaginosis (BV), their effectiveness in women without BV has not been thoroughly investigated. This pilot, randomized, double-blind, placebo-controlled study aims to assess the impact of orally administered probiotic strains, exhibiting in vitro antimicrobial activity against Gardnerella vaginalis and Candida albicans, on vaginal well-being in women without preexisting health conditions. Healthy women (n = 30, aged 19-50) were enrolled and randomly assigned using simple randomization to receive either probiotic or placebo capsules. After excluding dropouts, 26 participants (15 in the probiotic group, 11 in the placebo group) completed the study, undergoing a 3-week intervention. Vaginal well-being was assessed before and after the intervention using self-assessed health on a 5-point Likert scale, along with analysis of the vaginal microbiome by targeting the 16S-ITS-23S rRNA operon region with the Nanopore sequencing platform and MIrROR database. Notably, only the probiotic group exhibited a significant improvement in self-assessed overall gut and vaginal health following the intervention (p = 0.009 and p = 0.003, respectively). Nevertheless, no significant changes were observed in the vaginal bacterial community following the intervention and confirming the vaginal colonization of orally ingested probiotic strains through metagenome sequencing proved challenging. In summary, these findings suggest that while oral probiotics may improve perceived vaginal well-being, their role in modulating the vaginal microbiome in healthy women remains inconclusive. Additional research with a larger sample size is necessary to substantiate the endorsement of oral probiotic consumption for preventing BV or maintaining vaginal health in healthy women. This study was retrospectively registered at Clinical Research Information Service (CRIS) (KCT0008957, November 15, 2023).},
}
@article {pmid40423879,
year = {2026},
author = {Zhao, Y and Dai, Z and Lang, Y and Li, R and Zheng, H and Mi, J and He, X and Liu, J and Xiang, R and Mei, X and Liu, Y and Wang, Y and Guo, H and Yang, Q and Ren, K and Yang, T},
title = {Screening of Fecal Bacteroides Strains and Discovery of Bacteroides eggerthii S13-F8 with Protective Effects Against Chemotherapy-Induced Diarrhea.},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {1},
pages = {1003-1019},
pmid = {40423879},
issn = {1867-1314},
support = {2024NSFSC0044//the Natural Science Foundation of Sichuan province/ ; No. 2024kjTzn04//CMC Excellent-talent Program/ ; },
mesh = {Animals ; *Diarrhea/chemically induced/prevention &amp; control/microbiology ; Mice ; Fluorouracil/adverse effects ; *Feces/microbiology ; *Bacteroides/isolation &amp; purification/genetics/classification/physiology ; Humans ; Male ; Gastrointestinal Microbiome ; *Probiotics/administration &amp; dosage ; Female ; },
abstract = {Chemotherapy-induced diarrhea (CID) is a frequent gastrointestinal side effect in cancer patients, particularly associated with the use of 5-fluorouracil (5-FU). This study aimed to isolate multiple Bacteroides strains from the feces of healthy individuals and identify Bacteroides eggerthii (B. eggerthii) S13-F8 as the optimal candidate for alleviating CID. Whole-genome sequencing of B. eggerthii S13-F8 was conducted to uncover its functional characteristics and explore the potential mechanisms underlying its protective effects against CID. The anti-CID efficacy of B. eggerthii S13-F8 was assessed using multiple parameters, including diarrhea severity, food intake, and body weight changes. Comprehensive analyses, including blood tests, intestinal histopathology, colon transcriptomics, and fecal metagenomics, were performed to elucidate its underlying mechanisms. In a 5-FU-induced mouse model, B. eggerthii S13-F8 significantly alleviated weight loss and diarrhea. Histological examination revealed that B. eggerthii S13-F8 preserved the villus height-to-crypt depth (V/C) ratio and protected goblet cells in colonic tissues. Gene expression analysis showed that B. eggerthii S13-F8 upregulated protective markers, such as Aqp8, Slc26a3, and mucin-related genes (TFF3, FCGBP, and Muc2), while downregulating pro-inflammatory mediators, including IL-1α, IL-22, and Cxcl2. Furthermore, B. eggerthii S13-F8 modulated gut microbiota composition by suppressing pathogenic bacteria (Pseudomonas aeruginosa, Salmonella, γ-Proteobacteria, and Shigella) and enriching beneficial taxa, such as Lactobacillus and Akkermansia muciniphila. In conclusion, B. eggerthii S13-F8 demonstrates significant potential in mitigating severe diarrhea caused by 5-FU chemotherapy, providing a strong foundation for its development as a live biotherapeutic for CID treatment.},
}
@article {pmid40824425,
year = {2026},
author = {İstanbullugil, FR and Sanli, K and Ozturk, T and Keskin, BC and Düyşöbayeva, A and Risvanli, A and Acaröz, U and Acaröz, DA and Salykov, R and Sahin, M},
title = {Koumiss Microbiome: Investigation of the Microbial Composition and Functional Potential of a Unique Beverage of Fermented Milk Produced at Kyrgyz Mountains.},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {1},
pages = {18-34},
pmid = {40824425},
issn = {1867-1314},
support = {KTMU-BAP-2023.FB.15//KTMU Scientific Research Projects Unit/ ; },
mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Cultured Milk Products/microbiology ; Kyrgyzstan ; Yeasts/classification/isolation &amp; purification/genetics ; Animals ; Bacteriophages/isolation &amp; purification/classification/genetics ; Archaea/classification/isolation &amp; purification/genetics ; Metagenomics ; },
abstract = {This study aims to investigate the microbial composition of koumiss made via traditional methods in Kyrgyz mountain pastures. We collected koumiss samples produced in plastic (P), wood (T), and leather (D) containers at household settings. These samples were subjected to shotgun metagenomic sequencing. As a result of the metagenome analyses, we identified a diversity of bacteria, yeasts, bacteriophages, and archaea in koumiss produced within different containers. Koumiss' microbial community was predominantly composed of lactic acid bacteria (LAB), particularly Lactobacillus helveticus and Lactococcus lactis. Additional LAB species such as Lactobacillus kefiranofaciens, Lactococcus raffinolactis, Lactiplantibacillus plantarum, and Lactococcus cremoris, as well as non-LAB taxa such as Kluyvera intermedia, Raoultella planticola, and Hafnia alvei were also identified as part of the koumiss microbiota. Nonetheless, the opportunistic pathogen, Enterobacter hormaechei, was among the detected species. The most abundant yeast species was identified as Brettanomyces bruxellensis. Other yeast species involving Monosporozyma unispora, Monosporozyma servazzii, and Yarrowia lipolytica were also detected within the metagenome. Despite the type of container material not significantly affecting the microbial diversity, Bifidobacterium spp. and bacteriophages were identified at higher levels in plastic containers. We detected various antimicrobial resistance genes and gene clusters that produce bioactive compounds within koumiss samples. This study highlights koumiss' rich microbial composition and its potential health impacts. It underscores the importance of effectively utilizing metagenomic and bioinformatics methods for better comprehension of the microbiota of koumiss.},
}
@article {pmid41418935,
year = {2026},
author = {Chen, S and Li, W and Fan, L and Xu, C and Liu, S and Li, H and Liu, P and Zhu, W and Wu, X and Qin, P and Li, J and Ma, X and Wei, Y},
title = {Metatranscriptomics profiling reveals rodent- and shrew-borne viral diversity and evolutionary relationships in Guangzhou, China.},
journal = {Virologica Sinica},
volume = {41},
number = {1},
pages = {35-47},
doi = {10.1016/j.virs.2025.12.009},
pmid = {41418935},
issn = {1995-820X},
mesh = {Animals ; China/epidemiology ; *Shrews/virology ; *Rodentia/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; *Virome ; Rats ; Genetic Variation ; Evolution, Molecular ; Metagenomics ; Gene Expression Profiling ; },
abstract = {Emerging zoonotic infectious diseases, predominantly caused by viruses, pose increasing public health threats globally. Rodents and shrews are natural hosts for a variety of zoonotic viruses. Guangzhou is one of China's most densely populated cities and experiences frequent international and domestic population movements, making it a hotspot for infectious diseases. This study reports the metatranscriptomics virome of 208 rodents and shrews collected between June 2023 and December 2024 from four main urban areas (Tianhe, Baiyun, Liwan, Yuexiu) and five non-main urban areas (Zengcheng, Huadu, Conghua, Panyu, Nansha) in Guangzhou. Individual libraries were constructed from mixed tissue samples (liver, spleen, lung, and kidney) of each animal. Metatranscriptomics sequencing revealed diverse viral communities, identifying 24 viral strains across eight mammalian-associated viral families. Notably, we identified 17 known viruses and seven potentially novel viruses, including Seoul virus (5.2% prevalence in Rattus norvegicus from Panyu), Wenzhou mammarenavirus (13.2% in Rattus norvegicus from Conghua and Huadu), Jeilongvirus (29.4% in Rattus andamanensis from Panyu), and a divergent lineage of arteriviruses that may represent a new genus (maximum positivity rates of 2.9% in Rattus norvegicus and 5.7% in Rattus tanezumi). Phylogenetic analysis elucidated evolutionary relationships within key families such as Hantaviridae, Arenaviridae, Flaviviridae, and Parvoviridae, revealing distinct viral carriage patterns in Guangzhou City that are shaped by host species and geographical location. This is the first macro-level study of rodent and shrew viromes in Guangzhou and provides a scientific basis for strengthening surveillance of mammalian-associated viruses and preventing emerging zoonotic infectious diseases in the region.},
}
@article {pmid41690672,
year = {2026},
author = {Zhang, Y and Bai, Y and Ni, J and Shi, J and Zhang, Y and Bell-Sakyi, L and Wu, X and He, C and Deng, F and Yin, F and Shen, S and Fang, Y},
title = {Evidence of human exposure to tick-borne viruses based on viromes of ticks and presence of specific antibodies among patients in Hainan Island, southern China.},
journal = {Virologica Sinica},
volume = {41},
number = {1},
pages = {70-83},
doi = {10.1016/j.virs.2026.02.008},
pmid = {41690672},
issn = {1995-820X},
mesh = {Animals ; China/epidemiology ; Humans ; *Tick-Borne Diseases/virology/epidemiology ; *Antibodies, Viral/blood ; *Viruses/classification/genetics/isolation &amp; purification/immunology ; *Ticks/virology ; Middle Aged ; *Virome ; Male ; Adult ; Female ; Phylogeny ; Aged ; Young Adult ; Islands ; Metagenomics ; *Virus Diseases/epidemiology/virology ; Adolescent ; },
abstract = {Hainan Island, located in the South China Sea, is known as an area with diseases related to Rickettsia spp. or spirochete infection; however, the potential threat there from infection with tick-borne viruses (TBVs) remains obscure. In the present study, the dominant tick species, including Rhipicephalus sanguineus and Rhipicephalus microplus, were collected in Hainan Island, and tick viromes were investigated by metagenomic sequencing. In total, 27 viral species were identified belonging to the families Orthomyxoviridae, Flaviviridae, Nairoviridae, Phenuiviridae, Totiviridae, Chuviridae, Rhabdoviridae, and Parvoviridae, amongst which one novel virus and 13 new strains were discovered. Subsequently, individual ticks were screened for seven TBVs, Huanggang Rhabd tick virus 1 (HRTV1), Lihan tick virus (LHTV), Mivirus (MIV), Guangdong tick quaranjavirus (GTQV), Wenchang Ephemerovirus (WEPMV), Jingmen tick virus (JMTV), and brown dog tick phlebovirus (BDPTV), resulting in high prevalence rates of 16.97%, 9.59%, 10.33%, 7.38%, 7.01%, 6.27%, and 3.69%, respectively. While co-infection with multiple viruses was more frequent in R. sanguineus, R. microplus ticks generally had higher viral loads. Four febrile patients showed antibody responses to three TBVs, one each to LHTV and JMTV, and two to GTQV; the patient with antibodies to JMTV also showed neutralizing activity against this virus. This study promoted our understanding of the diversity and complexity of the TBV community in Hainan Island. The results provide serological evidence that human exposure to TBVs like JMTV may have occurred in Hainan, raising concern about potential risks from TBVs and the need to perform further surveys of TBVs among ticks, animals and humans.},
}
@article {pmid41699049,
year = {2026},
author = {Wu, LL and Liao, YJ and Peng, WH and Chen, LK and Huang, YC and Chen, CY and Juan, CC},
title = {FK506-binding protein-5 in high-fat diet-induced metabolic dysfunction-associated steatotic liver disease.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41699049},
issn = {2045-2322},
support = {108-2320-B-010-045-MY3, 110-2320-B-002-080-MY3, MOST 111-2314-B-A49-072, NSTC 112-2314-B-A49-028-MY3, NSTC 112-2740-B-A49-002, NSTC 113-2740-B-A49-003, NSTC 113-2321-B-A49-014-, NSTC 114-2321-B-A49-004 -, NSTC 114-2740-B-A49-003//Ministry of Science and Technology, Taiwan/ ; MOST 106-2320-B-010-009-MY3//Ministry of Science and Technology, Taiwan/ ; CI-110-22 and CI-111-24//Yen Tjing Ling Medical Foundation/ ; },
mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Tacrolimus Binding Proteins/metabolism/genetics ; Mice ; Gastrointestinal Microbiome ; Mice, Knockout ; *Fatty Liver/metabolism/etiology ; Male ; Obesity/metabolism ; Mice, Inbred C57BL ; Liver/metabolism/pathology ; *Non-alcoholic Fatty Liver Disease/metabolism/etiology ; Dysbiosis ; Disease Models, Animal ; Inflammation ; },
abstract = {A high-fat diet (HFD) alters the gut microbiota (GM), impairs metabolic efficiency, and increases gut permeability and inflammation. Obesity and insulin resistance are associated with GM dysbiosis. The GM is strongly associated with metabolic disorders and fatty liver disease. The co-chaperone protein FK506-binding protein-5 (FKBP5) regulates several vital cellular processes. Although FKBP5 has been implicated in stress-related disorders, it has not been directly linked to HFD-induced metabolic fatty liver disease. This study aimed to elucidate how FK506 binding protein 5 impairment affects the GM in HFD-induced metabolic dysfunction-associated fatty liver disease and metabolic dysfunction-associated steatotic liver disease (MASLD). Wild-type and FKBP5-knockout (FKKO) mice were fed a normal chow diet or a high-fat diet for 16 weeks. Mouse GM was examined using 16 S rRNA metagenomic analysis. The number of gut-liver immune cells was measured using flow cytometry. HFD-induced hepatic steatosis and inflammation were prevented in FKBP5-deficient mice. FKKO animals showed higher butyric acid levels and GM resistance to diet-induced obesity alterations according to 16 S ribosomal rRNA gene analysis and displayed an HFD-specific gut-liver immunological response that maintained gut barrier failure and mucosal immunity, which are important for GM homeostasis. FKBP5 helps the GM address inadequate immunological responses, including lower gut and liver CD11b[+]Ly6C[+] monocytes and neutrophils, and protects against obesity by improving the GM response to HFD-induced MASLD. FKBP5 protects against HFD-induced MASLD through metabolic coordination between the gut barrier and intrahepatic immunity.},
}
@article {pmid41707175,
year = {2026},
author = {Huang, X and Deng, K and Zhu, G and Huang, W and Gong, G and Liu, H and Yang, T and Gui, Y and Li, W},
title = {Dynamics of soil microbiome throughout the cultivation life cycle of Phallus rubrovolvatus.},
journal = {Canadian journal of microbiology},
volume = {72},
number = {},
pages = {1-14},
doi = {10.1139/cjm-2025-0279},
pmid = {41707175},
issn = {1480-3275},
mesh = {*Soil Microbiology ; *Microbiota ; China ; Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Metagenomics ; Metagenome ; },
abstract = {Phallus rubrovolvatus is a valuable edible fungus extensively cultivated in Guizhou Province, China. However, the changes in the soil microbiome throughout its growth cycle remain poorly understood. In this study, we collected 35 casing soil samples across five growth stages covering the entire 120-day cultivation cycle of Phallus rubrovolvatus and conducted metagenomic sequencing to examine alterations in soil microbial composition, diversity, key biomarkers, and functional potential. Our analyses revealed significant stage-dependent shifts in microbial community structure, with alpha diversity reaching its lowest at the primordium stage (Shannon of 5.12) and network complexity peaking at harvest stage (1.8-fold increase in connectivity). Through LEfSe analysis, we identified 37 stage-specific microbial biomarkers primarily affiliated with Actinomycetota and Acidobacteriota. Notably, Acidobacteriota biomarkers dominated at the primordium stage, while Nitrospirota enrichment characterized the harvest stage. Functional analyses revealed that membrane transport and energy metabolism pathways were enriched during early mycelial colonization, whereas secondary metabolite biosynthesis and signaling pathways became prominent during fruiting body maturation. Correlation analyses identified available nitrogen as the primary soil variable associated with microbial community composition. These findings provide foundational knowledge of microbiome dynamics during Phallus rubrovolvatus cultivation and suggest that microbiome-based management strategies may benefit from stage-specific interventions synchronized with fungal developmental transitions.},
}
@article {pmid41775266,
year = {2026},
author = {Han, Z and Sun, Z and Zhao, Q and Du, L and Zhen, D and Liu, X and Jiang, S and Liu, YY and Zhang, J},
title = {Competition and compromise between exogenous probiotics and native microbiota.},
journal = {Cell systems},
volume = {17},
number = {3},
pages = {101516},
doi = {10.1016/j.cels.2025.101516},
pmid = {41775266},
issn = {2405-4720},
mesh = {*Probiotics/pharmacology ; Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; Feces/microbiology ; Bifidobacterium animalis ; Mice, Inbred C57BL ; Dietary Fiber ; Male ; Bifidobacterium ; },
abstract = {Probiotic interventions are effective strategies to modulate the gut microbiome, but how exogenous probiotics compete with native gut microbiota remains elusive. Here, we use a mouse model and a well-documented probiotic, Bifidobacterium animalis subsp. lactis V9 (BV9), to mechanistically investigate its competitive strategies. We perform metagenomic and whole-genome sequencing of stool samples and isolated BV9, longitudinally collected from 24 mice orally administered with BV9 and different diets. Results show that a high-fiber diet most effectively supports the colonization of BV9, where BV9 selectively competes with Parabacteroides distasonis (P. distasonis), rather than extensively with other gut bacteria. By comparing the genomic structures of BV9 and P. distasonis isolated during the washout period, we infer their co-evolution mechanisms, highlighting their competition and compromise in utilizing inulin-derived glucose. Finally, our in vitro co-culture experiments validate such competitive dynamics. This study fills a critical gap in our understanding of niche competition in colonization.},
}
@article {pmid41852102,
year = {2026},
author = {Qu, X and Liao, Y and Muthuri, CW and Winowiecki, LA and Zi, H and Zhang, Y and Li, X},
title = {Soil Functionality Undermined by Symbiotic Fungal Decline Following Forest Conversion.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70268},
doi = {10.1111/1462-2920.70268},
pmid = {41852102},
issn = {1462-2920},
support = {W2412011//National Natural Science Foundation of China/ ; 32430069//National Natural Science Foundation of China/ ; jxsq2023102214//Double Thousand Plan of Jiangxi Province/ ; },
mesh = {*Soil Microbiology ; *Forests ; *Symbiosis ; *Soil/chemistry ; *Fungi/genetics/classification/physiology ; China ; Phosphorus/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Biodiversity ; Bacteria/genetics/classification ; Ecosystem ; },
abstract = {The conversion of native forests to other terrestrial ecosystems represents a profound form of land-use change, threatening aboveground biodiversity and biomass. However, its impact on soil ecological functions remains uncertain, particularly the regulatory role of soil microbial communities. To address this, we evaluated soil functionality related to carbon, nitrogen and phosphorus cycling by measuring nine enzyme activities in soils from native forests, plantations and croplands in subtropical China. Our results demonstrated a significant decline in soil functionality following the conversion of native forests, with the most pronounced reductions observed in croplands. This decline in soil functionality was strongly associated with a decrease in fungal richness but was independent of bacterial alpha-diversity. Specifically, the reduction in the abundance of symbiotic fungi, including key taxa such as Lactifluus and Tomentella, was identified as a primary driver of the functional impairment. Metagenomic analyses further confirmed that the loss of microbial functional genes was linked to the observed decline in soil functionality. Our findings underscore the critical role of key fungal taxa in maintaining soil processes and highlight the importance of their conservation and restoration to ensure ecosystem functionality in managed landscapes.},
}
@article {pmid41852435,
year = {2025},
author = {Trubl, G and Malard, L and Rahlff, J},
title = {Editorial: Ecology, evolution, and biodiversity of microbiomes and viromes from extreme environments.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1604002},
doi = {10.3389/frmbi.2025.1604002},
pmid = {41852435},
issn = {2813-4338},
}
@article {pmid41852664,
year = {2026},
author = {Shibata, N and Yoshifuji, A and Oyama, E and Komatsu, M and Azegami, T and Hayashi, K and Ishii, Y and Hasegawa, N and Namkoong, H},
title = {Urinary microbiota and bacterial membrane vesicles in chronic kidney disease: contribution to antimicrobial-resistant urinary tract infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1748638},
pmid = {41852664},
issn = {2235-2988},
mesh = {Humans ; Male ; *Urinary Tract Infections/microbiology ; *Renal Insufficiency, Chronic/complications/microbiology ; Middle Aged ; *Microbiota ; *Drug Resistance, Bacterial ; RNA, Ribosomal, 16S/genetics ; Aged ; *Urine/microbiology ; Metagenomics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Adult ; Microscopy, Electron, Transmission ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/chemistry/genetics ; *Extracellular Vesicles/ultrastructure ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Chronic kidney disease (CKD) is associated with an increased risk of severe urinary tract infections (UTIs), particularly those caused by antimicrobial-resistant bacteria. Although urinary microbiota and bacterial membrane vesicles (BMVs) are thought to contribute to UTI pathogenesis, their roles in CKD remain insufficiently understood. In this exploratory study, urine samples were collected from 10 male patients with CKD (eGFR <45 mL/min/1.73 m[2]) and 10 male non-CKD controls (eGFR ≥60 mL/min/1.73 m[2]). Urinary microbiota and BMV fractions were isolated and analyzed to compare microbial composition and antimicrobial resistance gene (ARG) profiles, and to evaluate their potential involvement in UTI development and the emergence of antimicrobial resistance in CKD. Both fractions were subjected to shotgun metagenomic sequencing; metagenomic analysis of BMVs was performed using pooled samples within each group. In addition, BMV fractions were characterized by transmission electron microscopy and 16S rRNA gene PCR. Urinary microbiota α-diversity was significantly lower in patients with CKD than in controls (ACE index, p = 0.04). Vesicle-like structures consistent with BMVs, with diameters of 20-200 nm, were detected in urine samples from both controls and patients with CKD. Principal coordinate analysis demonstrated that BMV fractions clustered within the corresponding urinary microbiota profiles. Furthermore, multiple antimicrobial resistance genes (ARGs), including ftsI and adeF, were identified in both urinary microbiota and BMV fractions. This study provides exploratory evidence of reduced urinary microbiota α-diversity in patients with CKD and the presence of ARGs in both urinary microbiota and BMV fractions from controls and patients with CKD. These findings suggest microbiological factors that may contribute to the high incidence of antimicrobial-resistant UTIs in this population. Future validation in larger cohorts with individual-level BMV profiling will be required to determine whether analyses focusing on urinary microbiota and BMVs can contribute to a better understanding of antimicrobial-resistant UTIs and to improved infection risk assessment in patients with CKD.},
}
@article {pmid41852665,
year = {2026},
author = {Zhang, Y and Wang, H and Yan, R and Wang, K and Man, J and Yang, L},
title = {Research advances on the urinary microbiome in non-infectious urinary tract diseases: from community composition to clinical prospects.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1728182},
pmid = {41852665},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; Dysbiosis/microbiology ; *Urologic Diseases/microbiology/diagnosis ; *Urinary Tract/microbiology ; *Urine/microbiology ; Prostatic Neoplasms/microbiology ; },
abstract = {INTRODUCTION: With the rapid development of 16S rRNA sequencing and metagenomic technologies, the traditional concept of sterile urine has been completely overturned, and a diverse urinary microbiome has been identified even in healthy individuals. Increasing evidence indicates that dysbiosis of the urinary microbiome is closely associated with the onset and progression of various non-infectious urological diseases.<br><br>METHODS: This review systematically summarizes recent advances in the role of the urinary microbiome in non-infectious urological diseases, including bladder cancer, benign prostatic hyperplasia, prostate cancer, nephrolithiasis, interstitial cystitis/bladder pain syndrome, and urinary incontinence, with a focus on microbial dysbiosis, pathogenic mechanisms, and clinical applications.<br><br>RESULTS: Studies have shown that alterations in the composition and diversity of the urinary microbiome are closely related to chronic inflammation, immune dysregulation, metabolic disturbances, and changes in the local microenvironment. These alterations may contribute to disease pathogenesis through mechanisms such as persistent low-grade inflammation, abnormal metabolic activity, and biofilm formation. In recent years, non-invasive detection based on urinary microbial profiles has shown promising potential in the early diagnosis of bladder and prostate cancers, with some machine learning models achieving diagnostic accuracies above 80 percent. Furthermore, the urinary microbiome may influence the efficacy of immunotherapy, offering new insights for personalized precision medicine.<br><br>CONCLUSIONS: This review summarizes the mechanisms, research status, and clinical prospects of the urinary microbiome in non-infectious urological diseases, emphasizing the importance of methodological standardization and highlighting its potential applications in early screening, diagnostic stratification, and microbiome-targeted interventions.},
}
@article {pmid41852689,
year = {2026},
author = {Anandan, S and Ali, A and Selvarajoo, A and Supramaniam, CV},
title = {Trichoderma combined with palm kernel shell biochar promotes root health and rhizosphere biodiversity in young oil palm seedlings infected with Ganoderma boninense.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1742803},
pmid = {41852689},
issn = {2813-4338},
abstract = {Oil palm (Elaeis guineensis) contributes up to 3% of gross domestic product (GDP) in Malaysia. Long-term monoculture production reduced natural biodiversity and increased severe threat by Ganoderma boninense, a causal agent of basal stem rot (BSR) disease. BSR recorded projections of 860,610 hectares of plantations to be devastated by BSR by 2040. While disease management has prioritised good sanitation practices, Trichoderma spp. is a potential solution to combatting G. boninense. In this study, we determined the efficacy of Trichoderma spp. isolate 4A added to palm kernel shell (PKS) biochar (T-mix) to improve oil palm root health. Three-month-old seedlings were observed in control treatments, T1 to T4 and Trichoderma sp. treatments, T5 to 12 with Ganoderma added in T7,8, 11 and 12. Root development parameters such as root architecture, length, diameter, and surface area were observed every two months for six months. Root length of T5 (3.3 m) and T9 (4.4 m) was higher than no-treatment control, T1 (2.5 m) indicating Trichoderma sp. support of root health. T9 (T-mix) has significantly improved root architecture in root scan with denser and multiple root branches as while all other diseased oil palms exhibit stunted roots. The diameter of roots shows similar trend to root length of T9 roots with the highest reading at 5.4 mm. T11 showed the overall improved fungal biodiversity at 6 months post inoculation with potential disease suppressive effects against other common pathogens such as Fusarium sp. This study highlights a new perspective of Trichoderma spp. treatment with biochar to provide protection to growing young oil palm root health, beyond disease control, indicating a beneficial role for early application at seedling stage. For long term application, Trichoderma spp. combined with biochar support healthy fungal dynamics without over-dominating indigenous fungal inhabitants. This is the first study to highlight the role of combined Trichoderma spp. and biochar in influencing the root architecture and rhizosphere dynamics of a perennial oil palm at the seedling stage. Overall, this study presents an exciting opportunity to use a new Trichoderma sp.-biochar solution in the battle against G. boninense.},
}
@article {pmid41853343,
year = {2023},
author = {Ionescu, D and Zoccarato, L and Cabello-Yeves, PJ and Tikochinski, Y},
title = {Extreme fluctuations in ambient salinity select for bacteria with a hybrid "salt-in"/"salt-out" osmoregulation strategy.},
journal = {Frontiers in microbiomes},
volume = {2},
number = {},
pages = {1329925},
pmid = {41853343},
issn = {2813-4338},
abstract = {Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper "salt-in" and more expensive "salt-out" strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies.},
}
@article {pmid41853717,
year = {2026},
author = {Matturro, B and Tucci, M and Firrincieli, A and Niccolini, L and Peña-Álvarez, V and Resitano, M and Trinchillo, M and Peláez, AI and Rossetti, S and Petruccioli, M and Viggi, CC and Aulenta, F},
title = {Multi-guild microbial cooperation sustains long-term anaerobic toluene degradation through sulfur cycling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1773863},
pmid = {41853717},
issn = {1664-302X},
abstract = {Anaerobic degradation of aromatic hydrocarbons such as toluene plays a critical role in the natural and engineered attenuation of contaminated environments. Here, we developed and characterized a microbial consortium enriched under strictly anoxic conditions, capable of sustained toluene degradation through sulfate reduction. By integrating biodegradation kinetics, long-read 16S rRNA profiling, and genome-resolved metagenomics, we elucidated the structure and function of a multi-guild community. The consortium was co-dominated by Desulfoprunum, a sulfate-reducing bacterium (SRB), and Sulfurovum-affiliated sulfur oxidizers (~34% each), with additional members including Stenotrophomonas, Achromobacter, and Stutzerimonas. Such co-dominance appears uncommon, as sulfate-reducing enrichments are often characterized by low diversity and the predominance of a single lineage, such as Desulfobacula or Desulfosarcina in marine systems. Genome-resolved analyses recovered seven metagenome-assembled genomes (MAGs) with distinct but complementary metabolic roles. Desulfoprunum encoded the fumarate-addition pathway (bss/bbs) for anaerobic toluene activation and dissimilatory sulfate reduction (aprAB, dsrAB). In contrast, Sulfurovum and several Gammaproteobacteria encoded sulfide:quinone oxidoreductase (sqr), coupling H2S detoxification to energy conservation, while a Moranbacterales MAG carried a putative sulfhydrogenase (hydAB) potentially catalyzing elemental sulfur (S°) reduction. Additional MAGs encoded assimilatory sulfate reduction (cys), suggesting integration of sulfur into biosynthetic pathways. Together, these features are consistent with the presence of a putative distributed sulfur redox loop, in which biogenic H2S may be recycled via oxidation and reduction reactions mediated by co-occurring taxa. This sulfur loop is hypothesized to contribute to buffering sulfide toxicity and stabilize redox dynamics, thereby potentially supporting long-term toluene degradation under sulfidic conditions. Our findings highlight anaerobic degradation as a community-driven process enabled by sulfur-cycling interactions. By revealing the role of cryptic sulfur cycling in stabilizing hydrocarbon degradation, this work offers a new framework for designing bioremediation strategies in contaminated anoxic environments.},
}
@article {pmid41853994,
year = {2026},
author = {Yang, Q and Aghdam, R and Tran, PQ and Anantharaman, K and Solís-Lemus, C},
title = {Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70245},
doi = {10.1111/1758-2229.70245},
pmid = {41853994},
issn = {1758-2229},
support = {506328//A Community Science Program New Investigator award/ ; //Natural Science and Engineering Research Council of Canada (NSERC)/ ; DBI-2047598//National Science Foundation/ ; DEB-2144367//National Science Foundation/ ; Hatch 1025641//USDA National Institute of Food and Agriculture/ ; //University of Wisconsin-Madison/ ; //Joint Genome Institute/ ; //Office of Science/ ; },
mesh = {*Ecosystem ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota/genetics ; Metagenome ; *Lakes/microbiology ; *Fresh Water/microbiology ; Metagenomics ; Transcriptome ; },
abstract = {Freshwater lakes are dynamic ecosystems, with varying oxygen dynamics that influence microbiome structure, composition, and transcriptomic activity. In many freshwater studies, ecological function and abundance metrics are used to discover keystone species; however, it is well established that abundance does not equal activity. Despite the existence of long-term time series spanning multiple years, no previous study has looked at how microbial community and activity (metatranscriptomics) are influenced by shifting oxygen conditions across depths at the microbial network level. In this study, we leverage metagenome-assembled genomes and transcriptomic activity to identify keystone taxa in the ecosystem. Using the SPIEC-EASI and CARlasso methods, we mapped key microbial associations and used permutation-based analyses to assess the robustness of keystone identification. Our results reveal that a taxon's ecological centrality is context-dependent and that many species identified as keystone by abundance alone do not exhibit corresponding transcriptional activity. Notably, members of Bacteroidota and other lineages emerged as keystone taxa only when both abundance and activity were considered. Our study underscores the importance of combining metagenomic and metatranscriptomic approaches for accurate identification of functionally relevant keystone species in freshwater ecosystems, providing a framework for future microbial ecology studies.},
}
@article {pmid41854683,
year = {2026},
author = {Wang, J and Shi, Y and Jia, Y and Peng, J},
title = {Effect of Diosmetin on Gut Microbiota and Serum Metabolites in Acute Pancreatitis Mice: A Metagenomic and Metabolomic Study.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {6},
pages = {e71679},
doi = {10.1096/fj.202503650RRR},
pmid = {41854683},
issn = {1530-6860},
support = {2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; 82170661//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Flavonoids/pharmacology ; Mice ; *Pancreatitis/drug therapy/metabolism/microbiology/blood/chemically induced ; Male ; Metabolomics/methods ; Metagenomics/methods ; Fecal Microbiota Transplantation ; Mice, Inbred C57BL ; *Metabolome/drug effects ; },
abstract = {Diosmetin is a bioactive flavonoid that exhibits well-documented antioxidant, anti-inflammatory, and anti-tumor properties. However, its potential to attenuate acute pancreatitis (AP) progression through gut microbiota modulation has not yet been elucidated. In this study, mice were pretreated with varying oral doses of diosmetin for 1 week before AP induction via intraperitoneal (i.p.) caerulein injections. The therapeutic efficacy and optimal dosage were determined through histopathological analysis of pancreatic tissue and serological biomarker assessment. Additionally, transcriptomic profiling and western blot were employed to elucidate the underlying signaling pathways. Furthermore, based on integrated metagenomic and metabolomic analyses, a core gut microbiota-metabolite-gene interaction network modulated by diosmetin was constructed. Finally, fecal microbiota transplantation (FMT) experiments validated the critical role of gut microbiota in the effects of diosmetin against AP. The results showed that medium-dose diosmetin treatment significantly attenuated pancreatic histopathological damage and acinar cell apoptosis in AP mice, while suppressing the activation of the MAPK inflammatory signaling pathway. Notably, diosmetin treatment was associated with restored microbial diversity, altered bacterial community structure, and changes in key metabolic pathways, reversing gut microbiota dysbiosis. Specifically, a diosmetin-responsive interaction network was constructed, highlighting associations between core bacterial taxa (Butyricimonas faecalis, Enterocloster bolteae, Roseburia intestinalis), key metabolites (3-indoleacrylic acid, 2-methoxy-4-vinylphenol, nitrite), and MAPK pathway-related genes. Finally, the protective effect of diosmetin was further substantiated by FMT, suggesting a potential role of the gut microbiota in this process. In conclusion, diosmetin ameliorated pancreatic injury in a murine model of caerulein-induced AP by modulating gut microbiota composition and associated metabolic profiles. These findings suggested that diosmetin represented a promising therapeutic option for AP, offering a scientific foundation for its clinical application and the underlying mechanisms involved.},
}
@article {pmid41856620,
year = {2026},
author = {Lan, HY and Yang, XY and Zhang, YH and Lyu, YW and Bao, LL and Yu, YY},
title = {[Study on the characteristics and differences of intestinal microbiota in children with allergic diseases].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {60},
number = {3},
pages = {346-358},
doi = {10.3760/cma.j.cn112150-20251015-00988},
pmid = {41856620},
issn = {0253-9624},
support = {GSWS2024031//Research Project of the Gusu Talent Program of Suzhou City/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Child, Preschool ; *Hypersensitivity/microbiology ; Case-Control Studies ; Infant ; Dermatitis, Atopic/microbiology ; Female ; Food Hypersensitivity/microbiology ; Male ; Feces/microbiology ; Child ; Metagenomics ; },
abstract = {Objective: Based on metagenomic sequencing technology, this study aims to investigate the characteristics and differences of the intestinal microbiota in children with different allergic diseases, providing a theoretical basis for the early prevention and treatment of allergic diseases. Methods: The study adopted a case-control research method. 214 children with allergic diseases (Group A) who visited the Suzhou Hospital Affiliated to Nanjing Medical University from March 2023 to June 2024 were selected. According to age matching, 93 healthy controls (Group H) who participated in physical examinations during the same period were also included. Fecal samples and clinical data of the subjects were collected. The subjects were grouped according to age and type of allergic disease, and the fecal samples of the subjects were analyzed using metagenomic sequencing technology to study the characteristics and differences of the gut microbiota in different groups. The subjects were divided into 0-1 year old group (A1 and H1), 1-3 year old group (A2 and H2), and≥3 year old group (A3). According to the disease type, A1 was divided into food allergy without atopic dermatitis (F1) group and food allergy with atopic dermatitis (F2) group, A2 was divided into atopic dermatitis (AD) group, allergic rhinitis (AR) group and AD with AR group. A3 was divided into AR group, AD with AR group and AR with asthma (AS) group. Results: With age increase, the number of species annotated at the genus level in the microbiota showed a gradually increasing trend. There were significant differences in the diversity and composition of the intestinal microbiota between the allergic disease group and the control group. In the diversity analysis, it was found that there were differences in species richness between group A and group H (chao index, group A: 955.2±226.1, group H: 762.3±260.9, W=5 664, P<0.000 1), and significant differences in β-diversity between group A2 and group H2, and between group A3 and group AD-AR and group AR-AS (R=0.045, P=0.018, R=0.044, P=0.011). At the species level, the allergic disease group was mainly enriched with Bifidobacterium, Enterococcus, Escherichia, Mediterraneibacter and Blautia, while the control group was mainly enriched with Bifidobacterium. By age group analysis, the relative abundance of Mediterraneibacter and Blautia in group A1 (0-1 years old) was significantly higher than that in group H1 (Mediterraneibacter: A1: 5.2±9.4, H1: 0.9±2.1, W=718, P=0.000 8; Blautia: A1: 3.5±6.0, H1: 1.3±3.2, W=701, P= 0.000 5). In group A2 (1-3 years old), the relative abundance of Bacteroides and Faecalibacterium was significantly higher than that in group H2 (Bacteroides: A2: 5.6±8.7, H2: 3.1±5.8, W=456, P=0.020 8; Faecalibacterium: A2: 2.6±2.8, H2: 1.2±1.9, W=395, P=0.002 8). In the clinical subtype analysis, the relative abundance of Blautia and Fusicatenibacter was significantly increased in AR children (Blautia: AD: 8.0±7.9, AD-AR: 13.5±8.3, AR: 20.2±7.8, H=9.300 8, P=0.009 6; Fusicatenibacter: AD: 0.5±0.9, AD-AR: 1.2±1.6, AR: 2.2±2.4, H=7.878 3, P=0.019 5), and the relative abundance of Escherichia was significantly increased in AD children (AD: 3.3±4.3, AD-AR: 1.8±4.5, AR: 0.8±2.0, H=9.476 6, P=0.008 8). In group A3 (≥3 years old), Mediterraneibacter was significantly enriched (A3: 6.3±6.9, H3: 2.9±1.9, W=571, P=0.039 7), and the relative abundance of Anaerostipes was significantly increased in AR children (AD-AR: 2.9±2.9, AR: 5.2±4.9, AR-AS: 3.2±3.5, H=7.269, P=0.026 4). Conclusion: In infancy, the species of intestinal flora gradually increase with age. There are significant differences in the composition of intestinal flora among children with different allergic diseases. Bifidobacterium, as the main dominant species in infancy, has a lower relative abundance in the allergic disease group at different ages than in the healthy control group, suggesting that the lack of Bifidobacterium may be related to the occurrence and development of allergic diseases.},
}
@article {pmid38922826,
year = {2026},
author = {Parthasarathy, G and Malhi, H and Bajaj, JS},
title = {Therapeutic manipulation of the microbiome in liver disease.},
journal = {Hepatology (Baltimore, Md.)},
volume = {83},
number = {4},
pages = {948-969},
pmid = {38922826},
issn = {1527-3350},
support = {R01 DK111378/DK/NIDDK NIH HHS/United States ; U01 AA021788/AA/NIAAA NIH HHS/United States ; },
mesh = {Humans ; *Liver Diseases/therapy/microbiology ; *Gastrointestinal Microbiome/drug effects/physiology ; Probiotics/therapeutic use ; Animals ; Prebiotics ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Myriad associations between the microbiome and various facets of liver physiology and pathology have been described in the literature. Building on descriptive and correlative sequencing studies, metagenomic studies are expanding our collective understanding of the functional and mechanistic role of the microbiome as mediators of the gut-liver axis. Based on these mechanisms, the functional activity of the microbiome represents an attractive, tractable, and precision medicine therapeutic target in several liver diseases. Indeed, several therapeutics have been used in liver disease even before their description as a microbiome-dependent approach. To bring successful microbiome-targeted and microbiome-inspired therapies to the clinic, a comprehensive appreciation of the different approaches to influence, collaborate with, or engineer the gut microbiome to coopt a disease-relevant function of interest in the right patient is key. Herein, we describe the various levels at which the microbiome can be targeted-from prebiotics, probiotics, synbiotics, and antibiotics to microbiome reconstitution and precision microbiome engineering. Assimilating data from preclinical animal models, human studies as well as clinical trials, we describe the potential for and rationale behind studying such therapies across several liver diseases, including metabolic dysfunction-associated steatotic liver disease, alcohol-associated liver disease, cirrhosis, HE as well as liver cancer. Lastly, we discuss lessons learned from previous attempts at developing such therapies, the regulatory framework that needs to be navigated, and the challenges that remain.},
}
@article {pmid41679688,
year = {2026},
author = {Tibi, MF and Argote, YM and Walker, AC and Pandey, S and Puente, C and Ellward, GL and Safwat, A and Rincon-Limas, DE and Czyż, DM},
title = {Modulation of host proteostasis by Prevotella corporis via induction of the heat shock response.},
journal = {Cell stress &amp; chaperones},
volume = {31},
number = {2},
pages = {100150},
pmid = {41679688},
issn = {1466-1268},
support = {R01 AG077534/AG/NIA NIH HHS/United States ; },
mesh = {*Proteostasis ; Animals ; Caenorhabditis elegans/metabolism/microbiology ; *Prevotella/physiology/metabolism ; *Heat-Shock Response ; Gastrointestinal Microbiome ; Humans ; HSP70 Heat-Shock Proteins/metabolism ; },
abstract = {Neurodegenerative protein conformational diseases (PCDs) are progressive, currently incurable disorders driven by toxic protein aggregation that leads to neuronal death. Emerging evidence supports a microbial role in PCDs, including the most prevalent: Alzheimer's and Parkinson's disease. While metagenomic studies consistently associate gut dysbiosis with these disorders, the mechanisms by which microbes influence host proteostasis remain poorly understood. In particular, considerable attention has been given to proteotoxic bacteria, whereas the mechanisms by which commensal microbes confer proteoprotection have received comparatively little attention. We previously employed Caenorhabditis elegans models to characterize the role of over 220 bacterial isolates from the Human Microbiome Project on host proteostasis. Strikingly, members of the Prevotella genus exhibited proteoprotective effects. Most notably, transient exposure to Prevotella corporis uniquely induced Hsp70, a critical molecular chaperone that maintains proteostasis, and significantly reduced aggregation of polyglutamine (polyQ), Aβ42, and α-synuclein. In the present study, we expand on these findings, demonstrating that among 13 Prevotella species tested, P. corporis robustly activates the heat shock response (HSR) and confers conserved aggregate-suppressing activity in Drosophila melanogaster. We further demonstrate that transient exposure to P. corporis results in the activation of protective stress pathways and promotes disaggregation of existing intestinal polyQ aggregates in C. elegans, leading to a general enhancement of global proteostasis. This is supported by significantly improved survival and enhanced thermotolerance. Together, our findings reveal a beneficial niche for P. corporis in activating the HSR to enhance organismal proteostasis and support a microbe-mediated gut-proteostasis axis. This work underscores the therapeutic potential of targeting the gut microbiota for the management of PCDs, highlights the importance of species-level resolution in microbiome studies, and supports the emerging view of the intestine as a proteostasis-modulating organ.},
}
@article {pmid41700856,
year = {2026},
author = {Zhang, R and Poulain, AJ and Pu, Q and Liu, J and Abdelhafiz, MA and Feng, X and Meng, B and Grégoire, DS},
title = {Methane cycling microbes are important predictors of methylmercury accumulation in rice paddies.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {3},
pages = {e0202825},
doi = {10.1128/aem.02028-25},
pmid = {41700856},
issn = {1098-5336},
support = {[2024]013//Guizhou Provincial Major Scientific and Technological Program/ ; RGPIN-2022-04891//Natural Sciences and Engineering Research Council of Canada/ ; 42394092//National Natural Science Foundation of China/ ; },
mesh = {*Methylmercury Compounds/metabolism/analysis ; *Oryza/growth &amp; development/metabolism/microbiology ; *Methane/metabolism ; *Soil Microbiology ; Mercury/metabolism ; *Soil Pollutants/metabolism/analysis ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Rhizosphere ; Microbiota ; },
abstract = {Microbial production of methylmercury from inorganic mercury in rice paddies poses health risks to consumers of this essential dietary staple. Although mercury-methylating communities are well characterized, the microbial guilds contributing to methylmercury accumulation in rice paddies remain unclear. Here, we collected paddy soils across a mercury concentration gradient throughout the rice-growing season to identify microbial and environmental factors influencing methylmercury dynamics. We show that hgcA gene abundance, the key gene required for methylation, was not a significant predictor of methylmercury concentration in paddy soils. We also show that the merB gene abundance correlated with methylmercury in mercury-polluted rhizosphere samples. Methane cycling genes were actively expressed, and their beta-diversity was significantly associated with methylmercury levels. Methanogen abundance correlated with higher methylmercury under elevated total mercury concentrations. Analysis of the methanotroph-associated mbnT gene, implicated in demethylation, revealed an unexpected positive correlation with methylmercury. Multiple regression and machine learning models converged on mercury bioavailability and methanogen/methanotroph abundances as key predictors of methylmercury, with methanogen-associated hgcA gene abundance and methanogen-methanotroph interactions highlighted under flooded, low-redox conditions. These findings suggest that methane-cycling microbes play key roles in methylmercury cycling dynamics and point to management strategies that could simultaneously mitigate mercury pollution and greenhouse gas emissions.IMPORTANCEMethylmercury is a microbially derived neurotoxin that accumulates in the food staple rice (Oryza sativa). Mitigating the health effects of methylmercury exposure requires predicting mercury cycling dynamics in rice paddies. This task is challenging because of the complex interplay of microbial and environmental factors. Our study coupled genomic and geochemical measurements with machine learning models to identify the key biological indicators of methylmercury accumulation. We demonstrated that the abundance of methanogens and methanotrophs is a major microbial predictor of methylmercury variability. This predictive framework, which considers the interactions between these coupled microbial guilds, offers greater power than methods relying only on mercury methylation genes. These findings inform better management and remediation strategies for rice paddies, offering a path to reduce methylmercury exposure and mitigate greenhouse gas emissions.},
}
@article {pmid41705822,
year = {2026},
author = {Guo, Z and Xiao, Y and Zhao, J and Tang, Z and Lin, Y and Yang, K},
title = {MetaRanker: precise profiling of antibiotic resistome risk in metagenomes by integrating abundance and genetic co-occurrence.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {3},
pages = {e0242225},
doi = {10.1128/aem.02422-25},
pmid = {41705822},
issn = {1098-5336},
support = {22176133//National Natural Science Foundation of China/ ; },
mesh = {*Metagenome ; *Anti-Bacterial Agents/pharmacology ; Microbiota ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; *Computational Biology/methods ; },
abstract = {The proliferation of antibiotic resistance genes (ARGs) in environmental microbiomes represents a major and growing threat to public health, creating a critical demand for precise and efficient tools to monitor resistance risk. Current approaches often depend on contig-based quantification or lack comprehensive risk indices, which compromises their accuracy and utility. To address this, we developed MetaRanker (https://github.com/SteamedFish6/MetaRanker), a computational pipeline that assesses resistome risk by integrating the abundance of ARGs, mobile genetic elements (MGEs), and virulence factors (VFs)-calculated directly from sequencing reads-with their genetic co-occurrence on contigs into a unified risk index (RI). This index reflects the potential for horizontal transfer and pathogen emergence. Evaluated using in silico and diverse real-world metagenomes (n = 353), MetaRanker demonstrated superior accuracy and stronger discriminatory power than existing methods. Its optimized compact database (29.6 MB) and alignment strategy reduced runtime by over 50% in comparison to MetaCompare 2.0 under identical hardware configurations (32 CPU cores, 128 GB RAM). Practical applications confirmed that MetaRanker effectively discriminates risk levels across environments (e.g., hospital wastewater versus natural soil) and quantifies risk mitigation through wastewater treatment. As a robust, lightweight, and sequencing-platform-agnostic tool, MetaRanker offers a powerful solution for comprehensive environmental resistome surveillance and evidence-based risk management.IMPORTANCEThe environmental reservoir of antibiotic resistance is a key contributor to the global health crisis of antimicrobial resistance. Effective surveillance and risk assessment of complex microbial communities are essential for prioritizing interventions and safeguarding public health. However, existing methods often provide fragmented or computationally demanding analyses, limiting their practical application for large-scale environmental monitoring. The significance of our work lies in developing MetaRanker, which overcomes these barriers by delivering a fast, accurate, and integrated metric of resistome risk. By simultaneously accounting for the abundance, mobility potential, and pathogenicity linkage of resistance determinants, MetaRanker enables a more realistic threat assessment. This tool empowers researchers and public health officials to track resistance hotspots, evaluate the impact of human activities such as waste disposal, and monitor the effectiveness of mitigation strategies, ultimately supporting data-driven decisions to curb the environmental spread of resistance.},
}
@article {pmid41747700,
year = {2026},
author = {Zhang, H and Du, Y and Guan, E and Xu, X and Zhang, P and Gao, L},
title = {Microbial mechanisms of protein degradation and nicotine removal during aerobic composting of tobacco waste as the sole nitrogen source.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141461},
doi = {10.1016/j.jhazmat.2026.141461},
pmid = {41747700},
issn = {1873-3336},
mesh = {*Composting ; *Nicotiana/metabolism ; *Nicotine/metabolism ; *Nitrogen/metabolism ; Plant Leaves/metabolism ; Biodegradation, Environmental ; Aerobiosis ; Cattle ; Animals ; Microbiota ; Fermentation ; *Plant Proteins/metabolism ; Manure ; Peptide Hydrolases/metabolism ; Bacteria/metabolism ; },
abstract = {The massive accumulation of tobacco waste poses threats to environment safety and human health due to its high nicotine content. While aerobic composting represents an effective strategy for managing waste biomass, its application to fresh discarded tobacco leaves remains unreported. This study pioneered the use of tobacco leaves in aerobic composting and investigated the microbial mechanisms driving substrate transformation. Waste tobacco leaves are rich in protein and can be used as the sole nitrogen source of composting. The microbiota was characterized by a higher abundance of Bacillota and Pseudomonadota, but a lower abundance of Actinomycetota, compared with that during cattle manure composting as a control. The degradation of proteins in tobacco leaves was primarily mediated by proteases (e.g., families S8, S9, M42) secreted by Bacillota. Notably, a greater abundance of S8 family proteases was induced, of which two exhibiting larger substrate cavity volumes. Nicotine content decreased rapidly during initial fermentation, achieving a removal rate exceeding 97 % and meeting European Union safety standards. This degradation was primarily driven by the pyrrolidine pathway via Stutzerimonas stutzeri and Pseudomonas sp. Seed germination and pot experiments demonstrated the superior growth promoting effects of fermented tobacco leaves over cattle manure product. These findings elucidate the microbial mechanisms of tobacco waste fermentation and provide a theoretical basis for screening efficient nicotine-degrading strains and developing value-added fermentation products.},
}
@article {pmid41762461,
year = {2026},
author = {Shen, S and Wang, L and An, X and Liu, H and Shi, M and Tu, Y and Ji, W and He, Z and Li, A},
title = {Basin governance coincides with lower MGE loads yet rewired ARG mobility: a hazard‑oriented, platform‑centric assessment.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141608},
doi = {10.1016/j.jhazmat.2026.141608},
pmid = {41762461},
issn = {1873-3336},
mesh = {*Drug Resistance, Microbial/genetics ; *Rivers/microbiology ; China ; Environmental Monitoring ; *Genes, Bacterial ; Metagenomics ; Microbiota ; },
abstract = {Antibiotic resistance genes (ARGs) serve as critical indicators for evaluating the ecological success of river restoration policies. We investigated the restructuring of the riverine resistome in the Yangtze River following the implementation of the "Ten-Year Fishing Ban" and the Yangtze River Protection Law. Using basin-wide surveys in the Jiangsu reach (2021 vs. 2023), we integrated shotgun metagenomics and RT-qPCR functional validation with a noise-filtering sampling design to assess how the removal of anthropogenic pressures reshaped resistance dissemination. Results show that policy-driven ecological recovery significantly altered microbial assembly mechanisms. While total ARG abundance declined, microbial communities shifted toward a more dispersal-dominated regime, with neutral model fits increasing from 0.817 to 0.913. Crucially, RT-qPCR analysis confirmed that the transcriptional activity of key resistance elements remained significantly elevated relative to a pristine baseline, suggesting persistent functional risks despite lower overall abundance. As localized selective pressures relaxed, the resistome transitioned toward integrated genetic platforms, evidenced by a significant rise in the mosaic index (MGI) from 12.81% to 22.50% (p < 0.05). Structural equation modeling (R2 = 0.766) identified a dominant sequential pathway from environmental co-selectors to mobile genetic elements and subsequently to ARGs, with intensified roles for integrons and insertion sequences (intI1, IS26). These findings demonstrate that policy success requires evaluation through both abundance-based and structural indicators. We propose a platform-centric surveillance framework incorporating the mosaic index as an early-warning tool for environmental agencies.},
}
@article {pmid41762466,
year = {2026},
author = {Ma, Q and López, MJ and Zhang, S and Jin, L and Wei, D and Yang, J and Liu, J and Ruan, Z},
title = {Carbon source-dependent activation of herbicide-mixture degradation in a synthetic microbial community enriched from black soil.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141615},
doi = {10.1016/j.jhazmat.2026.141615},
pmid = {41762466},
issn = {1873-3336},
mesh = {*Herbicides/metabolism ; *Soil Microbiology ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; *Carbon/metabolism ; *Microbial Consortia ; Cyclohexanones/metabolism ; Atrazine/metabolism ; Glucose/metabolism ; RNA, Ribosomal, 16S/genetics ; Sulfonylurea Compounds/metabolism ; Microbiota ; Pyridines ; },
abstract = {The extensive use of herbicides in agriculture has resulted in persistent soil contamination. Although microbial degradation of single herbicides has been extensively investigated, the responses and co-metabolism of microbial consortia to complex herbicide mixtures remain unclear. This study aimed to investigate the influence of a simple carbon source (glucose) on herbicide degradation by a natural microbial consortium (NMC) and identify key degraders for constructing an efficient synthetic microbial community (SynCom). An NMC enriched from herbicide-stressed agricultural black soil in Northeast China was inoculated into mineral salt media containing a mixture of herbicides (atrazine, nicosulfuron and mesotrione) as the sole carbon/nitrogen source, without (MSM) or with glucose supplementation (GSM). Significant herbicide degradation occurred only in the GSM system, with degradation rates of 97.27% for nicosulfuron, 68.00% for mesotrione, and 22.91% for atrazine after 8 days. Integrated 16S rRNA gene sequencing and metagenomic analysis linked the glucose amendment to a specific shift in the microbial community structure and activation of central carbon metabolism (tricarboxylic acid [TCA] and glycolytic), which enhanced cellular energy supply and environmental acidification for co-metabolic degradation of herbicides. In contrast, metabolism in the MSM system was biased toward biosynthesis. Combined random forest (RF) and co-occurrence network analyses identified the Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter as the keystone taxa. Metagenomic screening showed that these taxa were enriched for functional genes associated with herbicide degradation, including atzF (allophanate hydrolase) and gst (glutathione S-transferase). A simplified four-isolate SynCom, constructed based on these functional associations, degraded the herbicide mixtures more efficiently than either the individual isolates or the NMC in the GSM system. These findings elucidate the role of labile carbon in driving the co-metabolism of complex herbicides and provide direct candidate strains and a construction strategy, facilitating practical bioremediation applications.},
}
@article {pmid41775186,
year = {2026},
author = {Geromino, P and LeMoine, CM and Drahun, I and Cassone, BJ},
title = {Co-supplementation of a polyethylene diet for improved fitness of Galleria mellonella larvae.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141617},
doi = {10.1016/j.jhazmat.2026.141617},
pmid = {41775186},
issn = {1873-3336},
mesh = {Animals ; Larva/growth &amp; development/drug effects ; *Moths/growth &amp; development/physiology ; *Polyethylene/metabolism ; Diet ; Gastrointestinal Microbiome ; },
abstract = {A growing number of plastivore insects have been discovered that readily consume and biodegrade various petro plastics, including LDPE. The caterpillar larvae of Galleria mellonella are capable of breaking down the polymers at expedited rates; however, feeding on LDPE as a sole nutrient source is inefficient and detrimentally impacts larval survival, growth, and development. The objective of our study was to improve fitness parameters and feeding activities of LDPE-fed larvae through the addition of various macro- and micronutrients. Each co-supplementation recovered fitness and consumption to some extent in comparison to pure LDPE; however, artificial sources produced outcomes that were well below those of the caterpillar's natural diet, regardless of the combination. Co-supplementation of LDPE, honeycomb, and corn syrup was the most successful, with larval fitness and consumption approximating their natural diet. To provide mechanistic insights into this recovery, qPCR and metagenomics analyses indicated the co-supplementation promoted greater gut bacterial abundance and species richness and evenness. In addition, GC-MS analyses identified notable differences in their fat body metabolic profiles that may contribute to slower developmental rates. We also assessed the capability of the larvae to eliminate food wastes, which showed promise and could represent a potential co-supplement source for LDPE biodegradation.},
}
@article {pmid41792922,
year = {2026},
author = {Mertz, CM and Mancuso, CJ and Robinson, DM and Yeboah, LD and Fogel, ML and Takacs-Vesbach, C and Newsome, SD},
title = {Microbially derived essential amino acids compensate for dietary deficiencies in an ecologically relevant mammalian host.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag044},
pmid = {41792922},
issn = {1751-7370},
support = {1755402//NSF Division of Integrative Organismal Systems/ ; 1755353//NSF Division of Integrative Organismal Systems/ ; 2439853//NSF Graduate Research Fellowship Program/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Amino Acids, Essential/metabolism/biosynthesis ; *Peromyscus/microbiology/metabolism ; Diet ; Muscle, Skeletal/metabolism ; Dietary Proteins/metabolism ; Mice ; Carbon Isotopes/analysis ; *Bacteria/metabolism/classification/genetics ; },
abstract = {Protein is the main structural and functional component of cells, making it crucial for the survival of all living organisms. Yet mammalian herbivores and omnivores often consume diets deficient in the amount of protein required for growth, homeostasis, and reproduction. To compensate, mammals likely rely on their gut microbiota to synthesize essential amino acids (AAESS), particularly during periods of dietary protein limitation. We quantified the contribution of microbially synthesized AAESS to skeletal muscle in captive, wild-derived deer mice (Peromyscus maniculatus) fed diets varying in macromolecular quantity and quality. Using amino acid carbon isotope (δ13C) analysis combined with genetic sequencing, we assessed the origin of AAESS incorporated into host muscle and identified gut microbial taxa with the genetic potential for AAESS biosynthesis. We estimate that up to 25% of host muscle AAESS were microbially derived, with greater microbial contributions in mice fed diets containing low protein or more complex macronutrients. Gut microbial populations with the genetic potential for AAESS biosynthesis were more abundant in mice with larger contributions of microbially-derived AAESS in their tissues. These results demonstrate the crucial and likely pervasive role the gut microbiome plays in host protein metabolism, especially in mammals facing seasonal or persistent dietary protein limitation.},
}
@article {pmid41845564,
year = {2026},
author = {Zhang, Y and Wang, DD},
title = {Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644682},
doi = {10.1080/19490976.2026.2644682},
pmid = {41845564},
issn = {1949-0984},
mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Animals ; *Diet ; Metabolomics ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Proteomics ; Multiomics ; },
abstract = {Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes-including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid-related metabolism-that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and "dark matter" in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function-supporting microbiome-informed precision nutrition-and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.},
}
@article {pmid41846126,
year = {2026},
author = {Wang, X and Zhao, L and Teng, Y and Hu, W and Xu, Y and Ma, J and Song, J and Ren, W and Zhang, J and Zhu, H and Wang, X and Wang, Y and Luo, Y and Kuramae, EE},
title = {Decoding the adaptive strategies of versatile diazotrophs to multi-metal(loid) stress in mercury-mining impacted farmland soils.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141760},
doi = {10.1016/j.jhazmat.2026.141760},
pmid = {41846126},
issn = {1873-3336},
abstract = {Diazotrophs are crucial for Earth's nitrogen cycle via biological nitrogen fixation, while also modulating other elemental cycles and exhibiting bioremediation potential. However, their responses to co-occurring heavy metal(loid) (HM) contaminants in polluted soils remain poorly understood. Using combined nifH (encoding nitrogenase) amplicon and metagenomic sequencing, we characterized the taxonomic structure and metabolic potential of diazotrophic community across multi-HM contamination gradients in mercury-mining impacted farmlands (paddy vs. upland). Results identified selenium (upland soils: 0-3.08 mg kg[-1]) and arsenic (paddy soils: 5.38-17.1 mg kg[-1]) as the primary HMs shaping diazotrophic diversity, whereas mercury (0.067-99.6 mg kg[-1]) showed a significant but weak correlation. Selenium and mercury correlated positively with diversity in upland soils (arsenic negatively), whereas all three HMs correlated negatively in paddy soils. Diazotrophic indicator taxa varied by HM type, yet certain taxa tolerated all three HMs simultaneously-notably Chromatiaceae/Pseudomonadaceae in upland soils and Xanthobacteraceae in paddy soils. Moreover, diazotrophs in upland soils exhibited synergistic associations with functional guilds involved in HM resistance and element cycling (e.g., carbon fixation and hydrogen metabolism), contrasting with the negative correlations in paddy soils. Metagenomic binning indicated that dominant diazotrophs were primarily aerobic heterotrophs with versatile metabolic potentials, including multi-HM resistance (e.g., arsenic/mercury reduction, efflux, and antioxidation) and energy acquisition via trace gas (CO, H2), manganese, and sulfide oxidation. These findings provide novel insights into diazotrophic adaptive strategies under multi-HM stress, advancing our understanding of their ecological and environmental functions.},
}
@article {pmid41849467,
year = {2026},
author = {Ferreira, LDS and Silva, JFBR and Vilhena, MPSP and Alegria, OC and Ramos, RTJ and Sousa, MPA},
title = {Bacterial diversity of lowland soils under cocoa cultivation in Amazon.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {86},
number = {},
pages = {e295836},
doi = {10.1590/1519-6984.295836},
pmid = {41849467},
issn = {1678-4375},
mesh = {*Cacao/growth &amp; development ; *Soil Microbiology ; Brazil ; *Biodiversity ; *Bacteria/classification/genetics ; },
abstract = {This study investigated bacterial diversity in soils from six cacao-producing islands in Mocajuba, Pará, Brazil. Using next generation sequencing shotgun metagenomic DNA, we characterized the microbial composition and ecological structure of floodplain soils cultivated with Theobroma cacao. Taxonomic classification revealed a rich bacterial community encompassing 21 phyla, 54 classes, 121 orders, 240 families, 604 genera, and 2,289 species. The dominant phyla, Actinomycetota and Pseudomonadota, are known for their ecological roles in organic matter decomposition, antibiotic production, nitrogen cycling, and plant growth promotion. Alpha diversity metrics varied among samples, with P3 showing the highest species richness and P5 exhibiting the highest Shannon, Simpson, and evenness indices, suggesting a more balanced community. Beta diversity analysis based on Bray-Curtis dissimilarity under Total Sum Scaling (TSS) normalization revealed ecological gradients ranging from 0.228 to 0.527. Spatial ordination and hierarchical clustering indicated gradual shifts in community composition, supporting the concept of a compositional continuum shaped by environmental gradients. Functionally, Burkholderia lata was dominant in P1, reflecting its role in potassium solubilization, while Streptomyces species-detected in five of the six samples-contribute to biogeochemical cycling and pathogen suppression. Bradyrhizobium and Paraburkholderia, identified in P3, P5, and P6, are associated with nitrogen fixation and plant hormone regulation. These findings reveal the ecological complexity and functional potential of cacao soil microbiomes, providing insights for sustainable management of Amazonian floodplain agroecosystems.},
}
@article {pmid41524860,
year = {2026},
author = {Parab, C and Yadav, KD and Prajapati, V},
title = {Metagenomic Insights into Microbial Community Succession and its Functional Changes during Natural Fermentation of Food Waste.},
journal = {Applied biochemistry and biotechnology},
volume = {198},
number = {3},
pages = {2053-2081},
pmid = {41524860},
issn = {1559-0291},
mesh = {*Fermentation ; *Metagenomics ; *Microbiota ; *Bacteria/genetics/metabolism ; *Food ; Food Loss and Waste ; },
abstract = {Food waste is a global concern, necessitating sustainable management strategies. While fermentation offers a promising approach to valorizing food waste, studies about microbial dynamics and functionality assessment of semi-controlled naturally fermented food waste are still seldom. This study employed whole-genome metagenomic sequencing to investigate the microbial succession and functional pathways during natural fermentation of food waste over 15 days. Physicochemical analysis revealed that pH decreased from 5.20 to 4.32 on day 3 and then neutralized. Protein, lipids, and carbohydrate were in the range of 4.03-4.90%, 9.99-17.78%, and 85.44-77.84%, respectively. Taxonomic profiling revealed clear community restructuring from an initially diverse consortium dominated by Enterobacter, Klebsiella, Pseudomonas, and Acinetobacter (collectively > 45% relative abundance at day 0) to a highly specialized lactic acid bacteria (LAB) community (> 80% by day 15). Lactobacillus helveticus and Limosilactobacillus panis emerged as the late-stage co-dominant species, together accounting for 60-75% of the total reads. Functional annotation based on the PFAM, eggNOG, GO, and EC databases revealed a progressive reduction in gene family richness and metabolic breadth, with early samples being enriched in carbohydrate-active enzymes, membrane transporters, and amino acid metabolism pathways. By contrast, late-stage communities were dominated by LAB-associated fermentative functions, including lactate and acetate production, stress-response modules, and transport systems supporting acid tolerance, driven mainly by Lactobacillus, Weissella, Streptococcus, Gluconobacter, Aeromonas, Saccharomyces, Klebsiella, and Cronobacter. These findings provide insights into the microbial dynamics and functional adaptations during natural fermentation of food waste, contributing to the development of optimized waste valorization strategies.},
}
@article {pmid41762508,
year = {2026},
author = {Zhang, L and Jiang, L and Zhang, Z and Wang, Y and Yao, C and Yu, K and Tao, H and Sun, W and He, X and Gu, J and Qian, X},
title = {Unraveling metal-organic frameworks impact on resistome and virome dynamics in swine manure anaerobic digestion via metagenomic.},
journal = {Journal of environmental management},
volume = {402},
number = {},
pages = {129121},
doi = {10.1016/j.jenvman.2026.129121},
pmid = {41762508},
issn = {1095-8630},
mesh = {*Manure/microbiology ; Animals ; Swine ; Anaerobiosis ; *Metal-Organic Frameworks ; Drug Resistance, Microbial ; *Virome ; },
abstract = {Livestock manure is a major hotspot of antibiotic resistance genes (ARGs). However, the efficacy and mechanisms of anaerobic digestion (AD) in reducing ARGs, along with the ecological roles and risks of viral communities, remain poorly understood. This study demonstrates that AD significantly reduces total ARG abundance and diversity, with addition of metal-organic frameworks (MOFs) further enhancing the reduction of high-risk and clinically critical ARGs. ARG abundance decline was primarily driven by core ARGs, whereas diversity reduction was mainly attributed to the depletion of rare ARGs. ARGs exhibit a broad host distribution, alongside pervasive pathogenic host species. Viral communities display high diversity and novelty, with the Drexlerviridae family as the dominant virome. Viruses exhibit strong host specificity, with Actinobacteria (47.4%) and Atribacterota (12.7%) as primary hosts. Only eight viral contigs carried ANT(6)-Ia and lsa(B), indicating limited viral contribution to ARG horizontal transfer. Viruses enhance host metabolic capabilities by introducing diverse and unique auxiliary metabolic genes (AMGs). The AD process predominantly influences viral diversity, lifestyle, and AMG carriage. Mechanistically, AD reduces ARGs via decreasing co-occurrence frequencies of ARGs and plasmids, coupled with reduced abundances of ARG-hosting. These findings provide new insights for optimizing AD processes to control the diffusion of ARGs.},
}
@article {pmid41841491,
year = {2026},
author = {Vidal, E and Phanthanourak, AL and Gharib, A and Webel, H and Assis, J and Ayala-Ruano, S and Cunha, AF and Santos, A},
title = {ABaCo: addressing heterogeneity challenges in metagenomic data integration with adversarial generative models.},
journal = {Nucleic acids research},
volume = {54},
number = {5},
pages = {},
doi = {10.1093/nar/gkag227},
pmid = {41841491},
issn = {1362-4962},
support = {NNF20CC0035580//Novo Nordisk Foundation/ ; Pasteur Network, Sep/2023//Calmette &amp; Yersin PhD Grant/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Software ; Microbiota/genetics ; Metagenome ; Algorithms ; },
abstract = {The rapid advancement of high-throughput metagenomics has produced extensive and heterogeneous datasets with significant implications for environmental and human health. Integrating these datasets is crucial for understanding the functional roles of microbiomes and the interactions within microbial communities. However, this integration remains challenging due to technical heterogeneity and the inherent complexity of these biological systems. To address these challenges, we introduce ABaCo, a generative model that combines a variational autoencoder with an adversarial discriminator specifically designed to handle the unique characteristics of metagenomic data. Our results demonstrate that ABaCo effectively integrates metagenomic data from multiple studies, corrects technical heterogeneity, outperforms existing methods, and preserves taxonomic-level biological signals. We have developed ABaCo as an open-source, fully documented Python library to facilitate, support and enhance metagenomics research in the scientific community.},
}
@article {pmid41841524,
year = {2026},
author = {Akresi, JE and Do, TVT and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, JM and Yin, Y},
title = {Limousia bacteria encode mucinolysome for mucin utilization in animal gut microbiomes.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2645267},
doi = {10.1080/19490976.2026.2645267},
pmid = {41841524},
issn = {1949-0984},
mesh = {*Mucins/metabolism ; Animals ; *Gastrointestinal Microbiome ; Humans ; Feces/microbiology ; Metagenome ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics ; },
abstract = {Mucins create a physical barrier that protects human and animal tissues from microbial pathogens. Here, we provide evidence that mucin degradation can be mediated by unique mucinolysomes, defined as extracellular cellulosome-like multi-enzyme complexes specializing in mucin degradation. We predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of three anaerobic species of Limousia, including seven MAGs from human gut microbiome samples from six countries. We validated that mucins can support the growth of the Limousia strain ET540 as its sole carbon source, triggering the upregulation of most mucinolysome-related genes in ET540. We modeled the mucinolysome assembly by predicting cohesin‒dockerin interactions among most of the mucinolysome proteins using AlphaFold3. We performed metagenomic read mapping of 2897 fecal samples from various human cohorts and wild/domesticated animals against Limousia MAGs. We found that Limousia has a greater abundance and prevalence in farm animals than in humans. This study characterizes and adds the Limousia bacteria as unique member to the list of human and animal gut mucin glycan-degrading bacteria. Overall, we discovered that this novel gut bacteria genus (Limousia) uses a previously unrecognized molecular mechanism for highly organized mucin glycan degradation, shedding new light on microbe‒host interactions in the gastrointestinal tracts of diverse animal hosts, including humans.},
}
@article {pmid41841712,
year = {2026},
author = {Oganesyan, EG and Zhuk, AS and Venchakova, VV and Dolgo-Saburova, YV and Zhorzh, ON and Zhang, FM and Vasilyeva, NV and Taraskina, AE},
title = {Microbiome associated with recurrent vulvovaginal candidiasis: key characteristics and potential therapeutic targets.},
journal = {Biomeditsinskaia khimiia},
volume = {72},
number = {1},
pages = {62-74},
doi = {10.18097/PBMCR1644},
pmid = {41841712},
issn = {2310-6972},
mesh = {Humans ; Female ; *Candidiasis, Vulvovaginal/microbiology/drug therapy ; *Microbiota ; Adult ; Case-Control Studies ; *Vagina/microbiology ; Recurrence ; Lactobacillus/genetics/isolation &amp; purification ; Prevotella ; },
abstract = {Recurrent vulvovaginal candidiasis (RVVC) is one of the most complex forms of urogenital infection in terms of its clinical burden, impact on quality of life, and difficulty in preventing relapses. The aim of this study was to comprehensively characterize the taxonomic composition and functional potential of the vaginal microbiome associated with RVVC. This case-control study included patients with RVVC and conditionally healthy women. Vaginal samples were analyzed using shotgun metagenomic sequencing, followed by taxonomic and functional annotation of the microbiome using data quality control, taxonomic classification (Kraken2, MetaPhlAn4), and functional annotation (HUMAnN 3.9). At the community structure level, the RVVC microbiome exhibited pronounced interindividual variability and did not represent a uniform microbiota configuration. The taxonomic profile of the microbiome in RVVC was characterized by an increased relative abundance of Lactobacillus iners and anaerobic taxa (Prevotella bivia, Dialister microaerophilus), forming a compact "core" of intergroup differences. Functional analysis revealed a limited but reproducible set of metabolic pathways associated with RVVC; these included pathways of purine metabolism, central carbohydrate metabolism, and biosynthesis of cofactors and cell wall components. RVVC is associated not only with changes in the taxonomic composition of the microbiota but also with a stable reconfiguration of its functional potential. The identified shifts in metabolic pathway patterns reflect a transition of the vaginal microbial community to an alternative functional state, thus highlighting the need to develop new therapeutic strategies alternative to traditional antifungal-based approaches.},
}
@article {pmid41842581,
year = {2026},
author = {Wang, X and Chen, J and Xia, J and Ma, T and Yang, W and Shan, T and He, W and Zhang, G and Xia, Z and Wang, W and Liu, Z and Zheng, Y and Nong, K and Niu, P and Chen, T},
title = {Brain-Targeted RVG-Liposomal Melatonin Ameliorates Manganese Neurotoxicity by Enhancing Neurogenesis and Modulating Systemic Amino Acid Profiles.},
journal = {Journal of pineal research},
volume = {78},
number = {2},
pages = {e70137},
doi = {10.1111/jpi.70137},
pmid = {41842581},
issn = {1600-079X},
support = {82173489//National Natural Science Foundation of China/ ; 7232234//Beijing Natural Science Foundation/ ; },
mesh = {Animals ; *Melatonin/pharmacology/administration &amp; dosage ; Mice ; *Manganese/toxicity ; Liposomes ; *Brain/metabolism/drug effects ; *Neurogenesis/drug effects ; *Glycoproteins/pharmacology ; *Amino Acids/metabolism ; Male ; Mice, Inbred C57BL ; *Neurotoxicity Syndromes/drug therapy/metabolism ; *Neuroprotective Agents/pharmacology ; Gastrointestinal Microbiome/drug effects ; Peptide Fragments ; Viral Proteins ; },
abstract = {Chronic manganese (Mn) exposure induces severe neurotoxicity, characterized by impaired neurogenesis and disrupted metabolic homeostasis. Although melatonin (MT) possesses established neuroprotective properties, its clinical utility is hindered by poor bioavailability and limited brain delivery. Here, we developed a brain-targeted, rabies virus glycoprotein (RVG)-modified liposomal delivery system encapsulating melatonin (MT@RVG-Lip) to enhance therapeutic efficacy. Multi-omics analyses including brain and intestinal transcriptomics, serum metabolomics, and gut metagenomics were conducted to elucidate the underlying mechanisms. MT@RVG-Lip significantly improved motor deficits and enhanced neurogenesis while reducing neuroinflammation in Mn-exposed mice. Compared with regular MT and CaNa2-EDTA, MT@RVG-Lip more effectively alleviated Mn-disrupted gene expression in neurogenesis regions, particularly genes involved in amino acid metabolism. Additionally, MT@RVG-Lip demonstrated a regulatory effect on serum amino acid profiles and intestinal transporter gene expression. Gut microbiota analysis further revealed that MT@RVG-Lip partially reversed Mn-associated dysbiosis and promoted the improvement of key amino acid-related microbiota-mediated metabolic pathways. The RVG-modified liposomal formulation conferred sustained release and improved brain-targeting capability, prolonging MT bioavailability and enhancing therapeutic outcomes. These findings provide a new mechanistic framework for MT-based interventions in neurodegenerative diseases and highlight the therapeutic potential of multifunctional delivery strategies.},
}
@article {pmid41842880,
year = {2026},
author = {González-Mercado, VJ and Jean Lim, S and Kumar Singh, P and Sales-Martinez, S and Fernandez-Cajavilca, M and Marrero, LM and Pedro, E and D'Eramo Melkus, G},
title = {Dietary Quality and Microbiome Profiles among Rectal Cancer Patients: A Cross-Sectional Pilot Study.},
journal = {Puerto Rico health sciences journal},
volume = {45},
number = {1},
pages = {3-10},
pmid = {41842880},
issn = {2373-6011},
mesh = {Humans ; *Rectal Neoplasms/therapy/microbiology ; Male ; Female ; Middle Aged ; Pilot Projects ; *Gastrointestinal Microbiome ; *Diet ; Cross-Sectional Studies ; Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Metagenomics ; Neoadjuvant Therapy ; },
abstract = {OBJECTIVE: Examining whether gut microbial taxa abundances and predicted functional pathways correlate with dietary quality scores at the end of neoadjuvant chemoradiotherapy (nCRT) for rectal cancer (RC); identifying differentially abundant bacterial species from the pantothenate and acetyl-coenzyme A biosynthesis pathways that differ among dietary quality groups in a subset of participants.<br><br>METHODS: RC patients (n = 30) provided stool samples for 16S rRNA gene sequencing. To validate pathway predictions from the 16S rRNA gene data, stool samples from a subset of 17 participants underwent shallow shotgun metagenomics sequencing (SMS). Dietary quality was calculated using the Prime Diet Quality Score (PDQS; 24-hour recall). 16S rRNA gene data were analyzed using QIIME2, and SMS data were analyzed using HUMAnN2.<br><br>RESULTS: At the genus level, Parvimonas, Caproiciproducens, and uncultured Eggerthellaceae abundances positively correlated (Spearman's rho = 0.36 to 0.50) with PDQS scores, whereas abundances of Prevotella, Rothia, Peptostreptococcus, Paeniclostridium, Enterococcus, and Howardella correlated negatively (Spearman's rho = -0.43 to 0.36). Predicted pathways, including those related to B-vitamin biosynthesis and enzyme cofactor biosynthesis (e.g., B5/pantothenate [phosphopantothenate biosynthesis I]), were correlated with higher PDQS scores. Mean abundances of species predicted to encode the vitamin B5-CoA pathway were greater in the high- diet-quality group.<br><br>CONCLUSION: Findings suggest important associations between the taxa abundances of gut bacteria and the abundances of predicted B-vitamin biosynthesis pathways and dietary quality at the end of nCRT. Three bacterial species encoding vitamin B5-CoA biosynthesis pathways were prominent in high-dietaryquality participants.},
}
@article {pmid41843710,
year = {2026},
author = {Qian, C and Jeunen, GJ and Han, W and Chan, TY and Jiang, Y and Fu, W and Seymour, M},
title = {Developing and Evaluating Aquatic Passive Sampling of Environmental DNA for Microbial Community Profiling.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70121},
doi = {10.1111/1755-0998.70121},
pmid = {41843710},
issn = {1755-0998},
support = {MCEF21003//Marine Conservation Enhancement Fund/ ; },
mesh = {*DNA, Environmental/isolation &amp; purification/genetics ; Biodiversity ; *Specimen Handling/methods ; Bacteria/genetics/classification ; *Microbiota ; *Metagenomics/methods ; Phylogeny ; },
abstract = {Environmental DNA (eDNA) metabarcoding has transformed biodiversity monitoring across taxa from bacteria to mammals, yet sample collection remains a major bottleneck. Passive sampling via adsorption and entrapment has emerged as a promising alternative to overcome the limitations of conventional active filtration. However, the performance of passive sampling for microbial biodiversity monitoring remains unknown. Here, we developed passive sampling-based microbial community profiling by testing five submersion times and three common eDNA extraction methods in mesocosms, and comprehensively evaluated it by comparing results with active filtration in estuarine and coastal environments. We found that passive sampling for 24 h with enzymatic extraction yielded significantly more eDNA and higher biodiversity than shorter durations and mechanical extractions. Passive sampling consistently outperformed active filtration at every field site, with average increases of >100% in eDNA yields and >50% in taxonomic and phylogenetic diversities. Additionally, active filtration and passive sampling yielded significantly different prokaryotic and microeukaryotic community compositions, driven primarily by turnover rather than nestedness (on average 4-fold larger), implying that passive sampling is better suited for spatiotemporal detection than active filtration. Passive sampling showed greater sensitivity in identifying key environmental factors (3 vs. 2) and potential environmental bioindicators (40 vs. 20) compared with active filtration. Overall, this study establishes an efficient and practical passive sampling method for microbial biodiversity monitoring and environmental assessment in aquatic environments.},
}
@article {pmid41220286,
year = {2026},
author = {Lee, JY and Yoo, JH and Kim, JE and Bae, JW and Lee, CK},
title = {Translating Gut Microbiota into Diagnostics: A Multidimensional Approach for the Diagnosis of Inflammatory Bowel Disease.},
journal = {Gut and liver},
volume = {20},
number = {2},
pages = {199-212},
doi = {10.5009/gnl250360},
pmid = {41220286},
issn = {2005-1212},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/diagnosis/microbiology ; Biomarkers/analysis ; Metagenomics/methods ; Machine Learning ; Metabolomics/methods ; Proteomics ; Feces/chemistry/microbiology ; },
abstract = {The gut microbiota has emerged as a key factor in the pathophysiology of inflammatory bowel disease (IBD), providing novel opportunities for diagnostic innovation. Traditional biomarkers, such as C-reactive protein and fecal calprotectin, are widely used in clinical practice; however, their ability to reflect disease complexity and microbial dysregulation remains limited. Recent advances in metagenomics and multi-omics integration have enabled high-resolution profiling of microbial communities and their functional capacities and associated metabolites. Differential abundance analysis and machine learning models have been used to identify microbial biomarkers that can distinguish patients with IBD from healthy individuals. Multicohort studies integrating microbiome and metabolomic data have further improved diagnostic accuracy and generalizability. Transcriptomic and proteomic analyses provide complementary insights into host-microbe interactions and disease mechanisms. In this review, we explored the potential of metagenomic biodata as diagnostic markers for IBD, with an emphasis on a multidimensional analytical approach. We highlight the recent developments in sequencing technologies, computational pipelines for microbial feature selection, and machine learning strategies applied to biomarker discovery. The integration of multi-omics data deepens our understanding of host-microbe interactions and facilitates the development of microbiota-informed diagnostic tools. As multidimensional microbial profiling evolves, its clinical utility for the diagnosis and stratification of IBD requires further investigation.},
}
@article {pmid41622335,
year = {2026},
author = {Ota, C and Bamba, M and Sato, S and Tsuchimatsu, T},
title = {Soil microbial composition and abundance influence the growth of Lotus japonicus.},
journal = {Journal of plant research},
volume = {139},
number = {2},
pages = {195-205},
pmid = {41622335},
issn = {1618-0860},
mesh = {*Lotus/microbiology/growth &amp; development ; *Soil Microbiology ; Symbiosis ; *Mesorhizobium/physiology/genetics ; Root Nodules, Plant/microbiology ; *Microbiota ; Rhizobium/physiology ; Nitrogen Fixation ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In mutualistic symbiosis between plants and bacteria, the abundance and composition of symbiotic bacterial groups in the soil microbiota can be important for plant growth. Here, we focused on the nitrogen-fixing mutualism between Lotus japonicus and nodule bacteria to investigate whether and how much the abundance of symbiotic rhizobia in the soil microbiota of natural environments contributes to variations in host plant growth. An inoculation experiment of soil microbiota revealed extensive variations in plant growth phenotypes, even between microhabitats. We found that the local presence of L. japonicus and the relative abundance of Mesorhizobium bacteria showed positive correlations with plant growth supported by both 16S amplicon sequencing and shotgun metagenome analyses. Among bacteria investigated, the abundance of Mesorhizobium was most strongly associated with plant growth phenotypes, supporting its role as the primary symbiotic rhizobia in natural environments. Given the specificity and the selectivity of plants for favorable rhizobia, legume-rhizobia interactions could trigger a positive plant-soil feedback that enriches favorable rhizobia into the soil surrounding legume plant habitats.},
}
@article {pmid41724250,
year = {2026},
author = {Li, Y and Kang, L and Qin, X and Fei, R and Lu, A and Qishuang, H},
title = {Dual mechanism of electrochemical regulation to reduce soil Nitrous Oxide emissions-microbial recruitment and electron transfer pathway optimization.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134255},
doi = {10.1016/j.biortech.2026.134255},
pmid = {41724250},
issn = {1873-2976},
mesh = {*Nitrous Oxide/metabolism ; *Soil/chemistry ; *Soil Microbiology ; Electron Transport ; Oxidation-Reduction ; Fertilizers ; Denitrification ; Nitrogen/metabolism ; Microbiota ; *Electrochemical Techniques/methods ; Urea ; },
abstract = {Greenhouse gas emissions from agricultural nitrogen cycling, primarily Nitrous Oxide (N2O), are intrinsically linked to fertilizer dynamics. Conventional mitigation strategies emphasize synthetic fertilizer reduction, yet suffer from inefficiency and lack of sustainability. This study introduces an electrochemical regulation approach and, through comparative analysis of two fertilizers (ammonium sulfate vs. urea), elucidates dual mechanisms (redox modulation and microbial community engineering). Key findings: (1) 500 mV electrostimulation enriched nitrate-reducing microbiota, reducing N2O by 11.9 ± 5.9% (sulfate) and 14.2 ± 4.4% (urea) via enhanced denitrification; (2) Electrode interventions accelerated N2O-to-N2 conversion (15.8 ± 1.4% and 14.9 ± 8.9%) by optimizing redox fluxes and boosting electroautotrophic Pseudomonas spp. activity; (3) Urea exhibited delayed electroresponsiveness (6-10 h lag) due to slower amide nitrogen hydrolysis kinetics compared to sulfate; (4) Metagenomics confirmed upregulation of nitrogen metabolic genes (norC: 2.9×, nirD: 2.7×, narI: 2.6 ×) and restructured microbial networks. This study elucidates a fundamental electro-microbial mechanism that reconfigures nitrogen-transforming networks, providing a novel paradigm for managing soil biogeochemical cycles.},
}
@article {pmid41793890,
year = {2026},
author = {Dong, M and Zhang, Q and Wang, Y and Wang, S and Feng, G and Qi, H},
title = {Restructuring tilth layers suppresses cotton Verticillium wilt through the niacinamide-mediated enrichment of beneficial Pseudomonas.},
journal = {Microbiological research},
volume = {307},
number = {},
pages = {128491},
doi = {10.1016/j.micres.2026.128491},
pmid = {41793890},
issn = {1618-0623},
mesh = {Rhizosphere ; *Plant Diseases/microbiology/prevention &amp; control ; *Verticillium/drug effects ; Soil Microbiology ; *Gossypium/microbiology ; *Niacinamide/metabolism/pharmacology ; *Pseudomonas/metabolism/drug effects/growth &amp; development ; Metabolomics ; Microbiota ; Plant Roots/microbiology ; Metagenomics ; },
abstract = {Restructuring tilth layers (RTL) is an innovative tillage practice that involves the vertical exchange of topsoil and subsoil while the deeper layer is loosened, and this practice has been verified to significantly reduce the incidence of cotton Verticillium wilt. However, the ecological mechanisms underlying disease suppression remain unclear. In this study, we integrated field experiments, metagenomic sequencing, untargeted metabolomics, and functional validation to elucidate the effects of RTL on the rhizosphere ecosystem from the perspectives of microbe and metabolite interactions. RTL significantly altered the diversity and composition of the rhizosphere microbial communities and increased their network complexity and stability. Linear discriminant analysis effect size (LEfSe) revealed that RTL promoted the enrichment of beneficial taxa such as Pseudomonas, Lysobacter, and Mesorhizobium. Metabolomic profiling revealed that the abundance of niacinamide was 19.11-fold higher (P < 0.05) in the RTL rhizosphere than in the control rhizosphere. Exogenous supplementation and antagonistic assays demonstrated that niacinamide stimulated Pseudomonas enrichment and activation in the rhizosphere. Although niacinamide did not have direct antifungal activity, its coapplication with Pseudomonas reduced the disease index of Verticillium wilt by 81.89%. Overall, RTL suppresses Verticillium wilt through two pathways, by establishing a more stable and complex microbial network and regulating rhizosphere metabolite composition, particularly niacinamide accumulation, which drives the colonization and activation of defense mediated by beneficial microbes, forming an ecological defense mechanism that links metabolite signaling, microbial response, and pathogen suppression.},
}
@article {pmid41834952,
year = {2026},
author = {Tu, Y and Niu, C and Huang, Z},
title = {[Analysis of the Characteristics of the Oral Virome in Metabolic Dysfunction-Associated Fatty Liver Disease].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {1},
pages = {65-72},
pmid = {41834952},
issn = {1672-173X},
mesh = {Humans ; *Virome ; *Saliva/virology ; Male ; Female ; Middle Aged ; Adult ; *Fatty Liver/virology ; *Mouth/virology ; *Dental Plaque/virology ; },
abstract = {OBJECTIVE: To investigate the characteristics of salivary and supragingival plaque viromes in patients with metabolic dysfunction-associated fatty liver disease (MAFLD), and provide new insights for noninvasive oral screening and ecological intervention for MAFLD.<br><br>METHODS: This study included 21 MAFLD patients and 20 healthy controls. Saliva and supragingival plaque samples were collected, and metagenomic sequencing was used to analyze the characteristics of the oral virome.<br><br>RESULTS: The &#x3b1;-diversity and &#x3b2;-diversity of the salivary virome did not differ significantly between MAFLD patients and healthy individuals (P > 0.05). However, compared with healthy individuals, the &#x3b1;-diversity (Shannon index) and &#x3b2;-diversity (Bray-Curtis distance) of the supragingival plaque virome showed significant differences (P = 0.0303, P = 0.001). For species with a relative abundance greater than 0.1%, 14 viral species in saliva and 5 in supragingival plaque differed significantly in relative abundance between the two groups (P < 0.05), with multiple Streptococcus phages enriched in the saliva of MAFLD patients. LEfSe and random forest analyses identified potential biomarkers in saliva and supragingival plaque. Receiver operating characteristic (ROC) curve analysis showed strong diagnostic performance for these biomarkers in both saliva (area under the curve [AUC] = 0.9548, 95% CI: 0.8898-1.0000) and supragingival plaque (AUC = 0.8952, 95% CI: 0.7774-1.0000). Spearman correlation analysis revealed associations between viral species in saliva or supragingival plaque and various disease indicators (P < 0.05). Compared with healthy individuals, MAFLD patients showed higher node counts, significant relationship numbers, and average node degrees in the co-occurrence networks of salivary and supragingival plaque viromes.<br><br>CONCLUSION: Differences in the species composition and structure of the oral virome between MAFLD patients and healthy individuals suggest that oral viral species could serve as potential biomarkers for diagnosing MAFLD.},
}
@article {pmid41835092,
year = {2026},
author = {Pérez, T and Vacelet, J and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the carnivorous sponge, Lycopodina hypogea (Vacelet &amp; Boury-Esnault, 1996) (Poecilosclerida: Cladorhizidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {130},
pmid = {41835092},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Lycopodina hypogea (carnivorous sponge; Porifera; Demospongiae; Poecilosclerida; Cladorhizidae). The genome sequence has a total length of 235.10 megabases. Most of the assembly (98.85%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 31.1 kilobases. Gene annotation of this assembly by Ensembl identified 16 317 protein-coding genes. From the metagenome data we recovered 39 bins, of which 27 were high-quality MAGs, including four fully circularised genomes. The MAGs included archaea and bacteria involved in nitrification and sulfate-reduction as well as known sponge symbionts affiliated with Gammaproteobacteria (Candidatus Spongiihabitans, Porisulfidus) and Acidimicrobiales (Candidatus Poriferisodalaceae), among others.},
}
@article {pmid41836173,
year = {2026},
author = {Fuques, E and Massey, AL and Qureshi, F and Campos-Silva, JV and Ferreira da Silva, DJ and Peres, CA and Levi, T and Vega Thurber, RL},
title = {Large-scale metagenomic surveillance study expands the known diversity of RNA viruses in mosquito populations from the Amazon Basin.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20880},
doi = {10.7717/peerj.20880},
pmid = {41836173},
issn = {2167-8359},
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation &amp; purification ; *Metagenomics ; *Culicidae/virology ; Brazil ; Phylogeny ; Female ; *Mosquito Vectors/virology ; Virome ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; },
abstract = {The Amazon Basin is one of the most biologically diverse regions on Earth, yet its viral diversity remains poorly characterized. Mosquitoes are important vectors and reservoirs of RNA viruses, but little is known about the composition and structure of their viromes in remote areas of the Amazon. In this study, we performed a large-scale metagenomics survey of RNA viruses associated with mosquito populations collected from the Jurua River region in the Western Amazon Basin of Brazil. We analyzed 211 pooled samples of adult female mosquitoes collected across thirty-seven sites, representing one of the most comprehensive mosquito virome studies conducted in this region to date. Utilizing high-throughput sequencing and de novo assembly, we identified over 500 viral sequences from 18 families, including 21 complete or nearly complete genomes. Our analysis revealed 18 putative novel viral species spanning diverse families and strains of nine previously described viruses. Phylogenetic analyses also revealed undocumented diversity within several virus families, including Iflaviridae, Mesoniviridae, Phasmaviridae, Phenuiviridae, Togaviridae, and Totiviridae, encompassing both novel species and previously known viruses detected for the first time in this region. Our findings highlight the immense, yet largely unexplored, diversity of RNA viruses circulating in mosquito populations in this ecologically rich but understudied region and provide critical insights into the evolutionary dynamics of mosquito-associated viruses. By leveraging high-throughput sequencing to uncover novel viral strains, this research demonstrates the value of metagenomic approaches in expanding the known diversity, distribution, and evolutionary relationships of RNA viruses, contributing to a broader understanding of virus-mosquito interactions and genome evolution.},
}
@article {pmid41837347,
year = {2026},
author = {Arnold, MJ and Bergner, LM and Malik, H and Ten Doeschate, M and Davison, NJ and Brownlow, A and Mollentze, N and Babayan, SA and Streicker, DG},
title = {Drivers of Viral Diversity and Sharing in Marine Mammals.},
journal = {Molecular ecology},
volume = {35},
number = {6},
pages = {e70294},
doi = {10.1111/mec.70294},
pmid = {41837347},
issn = {1365-294X},
support = {217221/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 218518/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BB/V003798/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DEB 2011069/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; PLP-2020-362//Leverhulme Trust/ ; NE/X01424X/1//Natural Environment Research Council/ ; INV-003079/GATES/Gates Foundation/United States ; INV-030025/GATES/Gates Foundation/United States ; MC_UU_00034/3/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Viruses/genetics/classification ; Scotland ; *Aquatic Organisms/virology ; *Cetacea/virology ; *Mammals/virology ; },
abstract = {Knowledge of viral infection in marine mammals, a group severely threatened by human activity, is largely limited to the pathology and epidemiology of few endemic viruses. The recent emergence in marine mammals of high-consequence viruses, such as H5N1 avian influenza and rabies, underscores the importance of understanding the ecology of viral transmission in these species. Metatranscriptomic approaches now enable relatively unbiased characterisation of full viral communities that can reveal ecological and evolutionary drivers of infection. We sequenced RNA from 15 marine mammal species (42 pools, 237 tissues, 128 animals) sampled in Scotland through the Scottish Marine Animal Strandings Scheme. Viral sequences were detected in 41 of 42 pools, representing more than 120 distinct viral taxonomic units (vOTUs). Virus host network analysis showed that viral communities were partly structured by host taxonomy, with clear differences between seals and cetaceans. However, vOTUs were frequently shared between species, mirroring reported ecological interactions, including cross-order sharing between seals and cetaceans. Generalised linear models showed no effect of host taxonomy on viral richness. Instead, age was the strongest predictor: juvenile pools contained roughly twice as many viral taxa as adults and more than neonates, indicating that changing population demography may impact viral transmission in marine mammals. These results provide a basis for understanding how anthropogenic stressors may exacerbate viral transmission in marine mammals and demonstrate the increasing practicality of using genomics to understand ecological and evolutionary drivers of virus infection in natural populations.},
}
@article {pmid40588027,
year = {2026},
author = {Zhang, J and Yu, Z and Gao, Y and Li, Y and Hu, X and Gu, H and Tang, C and Liu, J and Liu, J and Zhang, S and Sima, X and Wang, G and Liu, P and Rui, Y and Franks, A and Liu, X and Jin, J},
title = {Warming-induced unstable microbial community metabolically lowers straw-carbon sequestration in paddy soils.},
journal = {Journal of advanced research},
volume = {82},
number = {},
pages = {33-44},
doi = {10.1016/j.jare.2025.06.075},
pmid = {40588027},
issn = {2090-1224},
mesh = {*Soil Microbiology ; *Soil/chemistry ; Oryza ; *Carbon/metabolism ; *Carbon Sequestration/physiology ; *Microbiota/physiology ; Temperature ; Global Warming ; },
abstract = {INTRODUCTION: Growing academic attention has been given to the crucial role of soil microorganisms in the net loss of soil organic carbon (SOC) under climate warming and the effectiveness of straw-C sequestration to replenish the SOC stock. However, the lack of empirical investigations in anaerobic paddy soils hinders accurate estimation of the global soil C-climate feedback and development of countermeasures.<br><br>OBJECTIVES: This study aimed to unravel the impact of warming on the complexity of the microbial community network of the paddy soil in response to warming, and correspondent changes of microbial metabolic functions relevant to the transformation of straw-C in SOC pools.<br><br>METHODS: We added [13]C/[15]N-labeled rice straw into a long-term paddy soil and incubated under three temperature treatments (25, 35 and 45&#xa0;&#xb0;C) for 140&#xa0;days to quantify straw-C sequestration in various SOC fractions, and further deployed metagenomic sequencing and solid-state [13]C NMR analyses to explore relevant biochemical mechanisms.<br><br>RESULTS: Warming (35&#xa0;&#xb0;C and 45&#xa0;&#xb0;C vs. 25&#xa0;&#xb0;C) enhanced SOC decomposition, but straw amendment did not replenish the loss C in mineral-associated C, a major SOC fraction of this soil, especially at 45&#xa0;&#xb0;C. Compared to 25&#xa0;&#xb0;C, temperature increases to 35&#xa0;&#xb0;C and 45&#xa0;&#xb0;C led to decreases in microbial diversity indices by an average of 19&#xa0;% and 43&#xa0;%, respectively. Warming also destabilized the microbial community network with less connectivity and keystone nodes in the paddy soil. Furthermore, warming decreased the abundances of organic C- and N-mineralization genes. Those genes encode enzymes involved in the degradation of both labile and recalcitrant organic compounds, including starch, cellulose, hemicellulose, chitin, pectin and aromatics, as well as in N mineralization, such as glutamate dehydrogenase and glutamate synthase. A subsequent deficiency in the synthesis of those enzymes appeared to suppress the transformation of straw-C and N, thereby reducing their sequestration efficiency in the mineral-associated C fraction in the paddy soil.<br><br>CONCLUSION: The detrimental impact of warming on the microbial metabolic profiles lowered the role of straw amendment in sustaining SOC stability under warming. An improved understanding of the warming-induced loss of microbial community diversity and correspondent weakening metabolic functions for the turnover of exogenous C should be accounted for global mitigation practices in paddy fields under climate warming.},
}
@article {pmid41702980,
year = {2026},
author = {Paoli, JE and Aung, O and Lilak, AA and Maw, MT and Cleary, NG and Watto, E and Hassell, J and Win, YT and Thein, WZ and Evans, TS and Valitutto, M and Goldstein, T and Johnson, CK and Mazet, JA and Fleischer, R and VanTassel, N and Subramaniam, K and Anderson, BD and von Fricken, ME and Mavian, CN and Murray, S},
title = {Detection of Wencheng shrew virus and cardiovirus from small mammals in Myanmar.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41702980},
issn = {2045-2322},
support = {AID-OAA-A-14-00102 , GHN-A-OO-09-0001000//United States Agency for International Development/ ; },
abstract = {UNLABELLED: Myanmar is one of the most biodiverse countries from a species perspective in Southeast Asia, yet there is minimal published data on zoonotic viruses in small mammals. From July 2017 to August 2018, wildlife sampling was conducted at human-animal interfaces at sites in the Yangon Region and Kayin State. To investigate virus diversity of commensal rodents and shrew, rectal swabs were collected from mice (Mus sp., N = 3), rats (Rattus norvegicus, N = 80; Rattus rattus, N = 6), and Southeast Asian shrews (Crocidura fuliginosa, N = 8). RNA was extracted from rectal swabs, made into cDNA, and subjected to metagenomic next-generation sequencing followed by phylogenetic analysis for virus identification and taxonomic placement. The study provides the first detection of Wencheng shrew virus (WESV) in Myanmar and the first report in C. fuliginosa. A novel member of the genus Cardiovirus was also detected in R. norvegicus and clustered with Cardiovirus theileri sequences previously identified in wild rats from China. Further characterization of viruses circulating in small mammals will help inform public health officials of potential zoonotic risks in a region with virus surveillance gaps and ongoing land use change which may be increasing the risk of zoonotic disease emergence.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-38406-w.},
}
@article {pmid41748043,
year = {2026},
author = {Alvaro-Fuss, M and DeClercq, V and Blodgett, JM and Theou, O and Langille, MGI and Beiko, RG},
title = {Effect of bedrest on the human gut and oral microbiome: implications for frailty.},
journal = {Experimental gerontology},
volume = {216},
number = {},
pages = {113079},
doi = {10.1016/j.exger.2026.113079},
pmid = {41748043},
issn = {1873-6815},
mesh = {Humans ; *Gastrointestinal Microbiome ; Aged ; Middle Aged ; Male ; *Bed Rest/adverse effects ; Female ; *Frailty/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Feces/microbiology ; Aging/physiology ; RNA, Ribosomal, 16S/genetics ; Exercise ; },
abstract = {The physiological effects of spaceflight resemble those of ageing and prolonged inactivity, and ground-based microgravity analogs have emerged as promising models for studying frailty. The human microbiome is increasingly recognised for its role in age-associated decline, although precise mechanisms remain unclear. Here, we evaluate the gut and oral microbiomes of twenty-two participants, aged 55-65, who were enrolled in a head-down tilt bedrest (HDBR) study, the first Canadian HDBR study conducted in an older cohort. Participants were randomly assigned to an inactivity or multi-modality exercise intervention group for fourteen days of HDBR, followed by seven days of rehabilitation and additional follow-up appointments. Gut (n = 343) and oral (n = 344) taxonomic profiles were generated using V4-V5 16S rRNA gene sequencing from fecal and salivary samples collected throughout the study. Gut functional profiles were generated using metagenomic (n = 86) data, used for pathway inference, and metabolomic (n = 83) data. Frailty was measured using a 36-item frailty index. Inactivity-associated changes to the gut microbiome during HDBR included decreasing α-diversity, decreasing Akkermansia and Lactobacillus, and increasing Bacteroides. Exercise-associated changes included increasing gut Roseburia. Both gut and oral β-diversity were associated with frailty scores and individual frailty components. We conclude that inactivity-associated changes to the human microbiome are associated with the early stages of frailty development, and that exercise may serve as an effective countermeasure against these effects. These results may inform strategies to preserve the health of both older adults facing prolonged periods of inactivity, as well as astronauts during longer space exploration missions.},
}
@article {pmid41771404,
year = {2026},
author = {Zhang, C and Zheng, L and Zhang, Q and Zhang, Y and Zheng, X},
title = {Synergistic removal of methanethiol and other odorant gases by a metabolically complementary synthetic consortia isolated from food waste.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134313},
doi = {10.1016/j.biortech.2026.134313},
pmid = {41771404},
issn = {1873-2976},
mesh = {*Odorants/analysis ; *Sulfhydryl Compounds/isolation &amp; purification/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; *Gases/isolation &amp; purification/metabolism ; *Food ; Hydrogen Sulfide ; Food Loss and Waste ; },
abstract = {Methanethiol (MeSH), a typical volatile sulfur compound, contributes significantly to environmental malodor and poses ecological risks. In this study, three bacterial strains capable of MeSH removal efficiencies exceeding 40% were isolated from food waste. These strains were taxonomically identified asAgrobacterium cavarae,Mycolicibacterium neoaurum, andPseudomonas qingdaonensis. Metagenomic annotation by Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that all strains possess key enzymes for the methionine and cysteine metabolism pathway, suggesting potential for MeSH degradation. In binary consortia, the combination of A. cavarae R1 and P. qingdaonensis CF (5:1 ratio) exhibited the optimal degradation performance, achieving removal efficiency of 87.2% for MeSH, 98.7% for H2S, and complete NH3 elimination (100%) after a 6-day cultivation. Among ternary consortia, the A. cavarae R1/M. neoaurum CD/ P. qingdaonensis CF combination at 3:2:1 and 3:1:2 ratios demonstrated superior removal efficiency for all three target odorants. Specifically, the 3:2:1 ratio consortium achieved 94.7% MeSH degradation, while the 3:1:2 ratio showd 91.7% NH3 removal efficiency. These results demonstrate the feasibility of using composite microbial agents for odor control in waste management systems.},
}
@article {pmid41780079,
year = {2026},
author = {Zhao, B and Xu, Y and Li, F and Song, S and Liu, Z and Liu, J and Liu, Z and Chen, X and Zhou, M and Zhao, L and Wang, X},
title = {Cyclosporine A ameliorates ulcerative colitis by inhibiting cellular senescence, modulating the JAK2-STAT3/NF-κB signaling pathway, and regulating the gut microbiota-metabolite axis.},
journal = {International immunopharmacology},
volume = {175},
number = {},
pages = {116452},
doi = {10.1016/j.intimp.2026.116452},
pmid = {41780079},
issn = {1878-1705},
mesh = {Animals ; *Colitis, Ulcerative/drug therapy/chemically induced/pathology/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; STAT3 Transcription Factor/metabolism ; *Cyclosporine/therapeutic use/pharmacology ; Signal Transduction/drug effects ; Janus Kinase 2/metabolism ; Cellular Senescence/drug effects ; NF-kappa B/metabolism ; Mice ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; Humans ; Disease Models, Animal ; *Immunosuppressive Agents/pharmacology/therapeutic use ; },
abstract = {Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease characterized by immune dysregulation, compromised intestinal barrier integrity, and disruptions in the microbiota-metabolite axis. Current clinical management of UC remains limited, underscoring the need for novel therapeutic approaches. Cellular senescence is increasingly recognized as a significant contributor to the pathogenesis of this disease. Senescent cells promote inflammatory responses via the sustained release of pro-inflammatory mediators such as IL-6, IL-1β, and TNF-α. Conversely, persistent inflammation drives further cellular senescence, establishing a self-amplifying cycle that exacerbates disease progression. Additionally, gut microbiota dysbiosis (reduced Akkermansia abundance) and metabolic abnormalities (disrupted bile acid metabolism) may further compromise intestinal barrier integrity. Cyclosporine A (CsA), a classical immunosuppressant, has unclear mechanisms in UC, particularly regarding its potential effects on senescence and the microbiota-metabolite axis. In this investigation, using a dextran sulfate sodium (DSS)-induced UC model, we demonstrated that CsA significantly alleviated DSS-induced acute colitis in mice and senescence-associated pathological changes. Multi-omics analyses integrating network pharmacology, transcriptomics, metabolomics, and metagenomics demonstrated that CsA likely exerts its therapeutic effects through inhibition of the JAK2-STAT3/NF-κB signaling pathway. This leads to reduced release of pro-inflammatory cytokines, modulation of intestinal microbiota composition and metabolite profiles, and enhanced intestinal barrier function.These findings elucidate new mechanisms by which CsA improves DSS-induced colitis in mice through anti-senescence effects and microbiota-metabolic regulation, providing potential therapeutic targets for UC.},
}
@article {pmid41831863,
year = {2026},
author = {Patel, SS and Shree, T and Kumar, A},
title = {Microbial consortia interactions and bioremediation of pesticides: A review on designing, mechanism and efficacy.},
journal = {Pesticide biochemistry and physiology},
volume = {219},
number = {},
pages = {106993},
doi = {10.1016/j.pestbp.2026.106993},
pmid = {41831863},
issn = {1095-9939},
mesh = {*Pesticides/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; Soil Microbiology ; *Soil Pollutants/metabolism ; },
abstract = {Ecosystems and human health are at serious risk due to the extensive application of pesticides in the agricultural system for controlling pests and diseases. The use of microbial consortia (MicroCons) has emerged as a promising solution for the remediation of pesticide-contaminated soil, offering a sustainable and eco-friendly alternative to physical and chemical methods; however, a systematic review on this aspect is still lacking. This comprehensive review provides an in-depth analysis of the current knowledge on microbial consortia-based remediation of pesticides in agricultural soil. Efficacy of single-strain vs multiple strains in MicroCons have been discussed to unravel the workload distribution between microbial strains in pesticide degradation. We also discuss the design and optimization of microbial consortia for remediation, highlighting the role of advanced tools and the mechanisms of MicroCons action. Furthermore, emerging trends and future directions in the field, including the potential of synthetic biology, machine learning (ML), and artificial intelligence (AI) are also covered. This review aims to critically expand the mechanistic understanding of how microbe-mediated remediation strategies might reduce pesticide phytotoxicity, enhance crop production in pesticide-stressed soils, and inspire future research and practices in MicroCons-based remediation to achieve the Sustainable Development Goals (SDGs).},
}
@article {pmid41829938,
year = {2026},
author = {Kroplewski, B and Przybyłowicz, KE and Sawicki, T and Przemieniecki, SW},
title = {Supplementation with Animal- and Plant-Derived Proteins Modulates the Structure and Predicted Metabolic Potential of the Gut Microbiota in Elite Football Players.},
journal = {Nutrients},
volume = {18},
number = {5},
pages = {},
doi = {10.3390/nu18050768},
pmid = {41829938},
issn = {2072-6643},
support = {MEiN/2023/DPI/2862//Minister of Science Republic of Poland/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Dietary Supplements ; Male ; Whey Proteins/administration &amp; dosage ; Young Adult ; Adult ; Pea Proteins/administration &amp; dosage ; *Plant Proteins/administration &amp; dosage ; Oryza ; Resistance Training ; *Soccer ; RNA, Ribosomal, 16S/genetics ; Athletes ; *Animal Proteins, Dietary/administration &amp; dosage ; Animals ; },
abstract = {BACKGROUND/OBJECTIVES: The primary outcome of this 8-week randomized, controlled, parallel trial was to assess longitudinal shifts in gut microbiota structure and predicted metabolic potential in 45 elite football players following protein supplementation.<br><br>METHODS: Participants combined resistance training with daily intake (30 g) of whey protein concentrate (WPC), pea protein isolate (PPI), rice protein isolate (RPI), or a plant-protein blend (MIX). For the acquisition of prokaryotic metataxonomic data, the V3-V8 region of the 16S rRNA gene was sequenced using Oxford Nanopore Technology (ONT). Functional potential was inferred through the MACADAM database and STAMP software. Strict dietary monitoring and gravimetric adherence checks were performed to isolate the intervention effect.<br><br>RESULTS: While microbial alpha-diversity indices (Chao1, Shannon, Simpson) remained stable across all groups, significant source-specific shifts in taxonomic structure and predicted metabolic activity were identified. Whey protein concentrate (WPC) was associated with an increase in Bacteroidetes abundance and greater balance within the microbial community structure, whereas pea protein isolate (PPI) and the MIX correlated with reduced fermentative bacteria and elevated taxa potentially involved in cadaverine biosynthesis. Rice protein isolate (RPI) supplementation was associated with a higher predicted representation of taxa involved in succinate-to-butyrate fermentation pathways. These functional markers and differential responses of selected bacterial groups to particular protein types were observed.<br><br>CONCLUSIONS: The data indicate complex interactions between supplement type, exposure duration, and microbiome response, underscoring the necessity for individualized dietary recommendations and supplementation strategies to optimize gut health and training adaptation in professional football players.},
}
@article {pmid41828538,
year = {2026},
author = {Chen, J and Xu, Y and Liu, Z},
title = {Enzymatic Synergy-Driven Biotransformation Generates a Postbiotic-Rich Functional Matrix That Reprograms Gut Microbiota Metabolic Pathways Under Stress Conditions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {5},
pages = {},
doi = {10.3390/ijms27052313},
pmid = {41828538},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome ; Animals ; Biotransformation ; Mice ; *Stress, Physiological ; Fermentation ; *Metabolic Networks and Pathways ; Lactiplantibacillus plantarum/metabolism ; Metabolomics/methods ; Male ; },
abstract = {The physiological efficacy of plant-based matrices is often limited because bioactive compounds are sequestered within complex lignocellulosic architectures, restricting their release and downstream activity. Fermentation-driven enzymatic biotransformation can overcome these structural barriers; however, the mechanisms by which fermentation-derived, non-viable functional ingredients (postbiotics) confer benefits remain incompletely defined. Here, we examined whether a postbiotic-rich, co-fermented plant matrix enhances host resilience under metabolic stress and whether such effects are accompanied by a remodeling of gut microbial functional capacity. A functional plant matrix was produced by solid-state co-fermentation using two Lactobacillus plantarum strains selected for complementary lignocellulolytic profiles. Untargeted metabolomics and deep shotgun metagenomic sequencing were integrated with a hydrocortisone-induced murine metabolic stress model to quantify substrate remodeling, host neuroendocrine/behavioral outcomes, and microbiome functional reprogramming. Co-fermentation markedly remodeled the phytochemical landscape, increasing extractable flavonoids and generating distinct metabolite clusters. In vivo, administration of the postbiotic-rich matrix partially normalized stress-responsive neuroendocrine markers (ACTH, TRH, and testosterone) and improved behavioral outcomes in open-field and forced swim assays. These systemic changes were paralleled by a coordinated shift in microbial functional potential, including the enrichment of carbohydrate-active enzyme (CAZyme) families involved in complex polysaccharide utilization (e.g., AA9, GH129, CE14) and attenuation of phosphotransferase system modules and cytochrome P450-related functions. Enzymatic synergy-driven biotransformation yields a postbiotic-rich functional matrix that is associated with a selective remodeling of gut microbiome metabolic potential under stress and concomitant improvement in host physiological resilience. This study underscores microbial functional remodeling as a critical mechanistic interface linking fermentation-modified substrates to host physiological recovery, providing a molecular framework for the development of targeted postbiotic interventions.},
}
@article {pmid41730403,
year = {2026},
author = {Liu, W and Zhang, Z and Wu, W and Yan, X and Huang, Y and Feng, H and Mou, Q and Wan, J and Yan, M and Tang, H and Liang, J and Zhang, Y and Peng, C and Pan, X},
title = {Ligilactobacillus murinus confers a dual benefit: Counteracting crotonis fructus-induced intestinal toxicity and synergizing with its processed form against ulcerative colitis.},
journal = {Journal of ethnopharmacology},
volume = {363},
number = {},
pages = {121420},
doi = {10.1016/j.jep.2026.121420},
pmid = {41730403},
issn = {1872-7573},
mesh = {Animals ; *Colitis, Ulcerative/chemically induced/microbiology/drug therapy/pathology ; Caenorhabditis elegans ; Gastrointestinal Microbiome/drug effects ; *Croton/chemistry/toxicity ; Mice ; *Probiotics/pharmacology/administration &amp; dosage/therapeutic use ; Male ; Disease Models, Animal ; Dextran Sulfate ; *Lactobacillus ; Mice, Inbred C57BL ; *Plant Extracts/toxicity ; },
abstract = {Ulcerative colitis (UC) poses a major clinical challenge. Classical Chinese medical texts record the use of Crotonis Fructus (CF), the seeds of Croton tiglium L., for treating conditions like "chronic dysentery" presenting symptoms similar to UC. However, the clinical application of both raw and processed CF is limited due to intestinal toxicity.<br><br>AIM OF THE STUDY: This study investigates the role of gut microbiota in mitigating the intestinal toxicity induced by CF and in enhancing the anti-UC efficacy of its processed form.<br><br>METHODS: Metagenomic analysis investigated CF-induced intestinal toxicity. The benefits of probiotics combined with CF or processed CF cream were evaluated in Caenorhabditis elegans (C. elegans) and a dextran sulfate sodium (DSS)-induced mouse model. Their combined effect was further assessed in DSS-exposed C. elegans, with qRT-PCR measuring intestinal barrier integrity.<br><br>RESULTS: Metagenomic analysis revealed that CF-induced intestinal toxicity was associated with gut microbiota dysbiosis characterized by a pronounced reduction in Ligilactobacillus murinus (L. murinus). Supplementation with L. murinus alleviated CF-induced damage in C. elegans. In DSS-induced UC mice, both L. murinus and processed CF cream ameliorated colitis and suppressed TNF-&#x3b1;, IL-6, and IL-1&#x3b2;. When co-administered in DSS-exposed C. elegans, two agents acted synergistically, leading to greater restoration of intestinal barrier integrity and more pronounced upregulation of barrier-function genes.<br><br>CONCLUSION: This study demonstrates that L. murinus plays a dual role: it mitigates CF-induced intestinal toxicity and acts synergistically with processed CF cream to enhance UC treatment, providing a microbiome-based strategy for safer clinical application.},
}
@article {pmid41724049,
year = {2026},
author = {Wang, D and Xin, J and Lai, C and Sun, N and Yang, Y and He, Y and Duan, L and Luo, J and He, Y and Zhang, Y and Zhang, Y and Wang, H and Zeng, D and Bai, Y and Ni, X},
title = {High fluoride exposure disrupts gut microbiota and induces intestinal barrier damage via RhoA/ROCK-mediated cytoskeletal remodeling.},
journal = {Ecotoxicology and environmental safety},
volume = {312},
number = {},
pages = {119898},
doi = {10.1016/j.ecoenv.2026.119898},
pmid = {41724049},
issn = {1090-2414},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; rho-Associated Kinases/metabolism ; Mice ; Cytoskeleton/drug effects ; rhoA GTP-Binding Protein/metabolism ; *Fluorides/toxicity ; Male ; Intestinal Mucosa/drug effects ; Signal Transduction/drug effects ; Intestines/drug effects ; Permeability ; Mice, Inbred C57BL ; },
abstract = {Fluoride pollution-whether of geological or anthropogenic origin-disrupts gut microbiota-host homeostasis and compromises the intestinal barrier. We established an acute high-fluoride mouse model via intragastric NaF, integrating metagenomics, metabolomics, and molecular biological techniques to clarify the underlying mechanism of enhanced intestinal permeability caused by fluoride exposure in vivo. Mechanistically, high fluoride exposure activates the RhoA/ROCK signaling pathway, increases the level of phosphorylated myosin light chain (p-MLC), induces filamentous actin (F-actin) rearrangement, and disrupts the apical junctional complex (AJC)-characterized by downregulated expression or abnormal localization of AJC-related proteins (ZO-1, Claudin-1, β-catenin, Occludin). It also alters the morphology of intestinal epithelial cells, ultimately increasing ileal permeability. At the microbiota level, high fluoride disrupted the ileal microbiota; specifically, at the species level, Bifidobacterium sp. SO1 and Schaalia turicensis were identified as the key species with high specificity and high occupancy under fluoride exposure. Lactobacillus and Akkermansia were abnormally enriched in the intestines of mice exposed to fluoride. Metabolomic analysis revealed that high fluoride exposure enriched multiple pathways including linoleic acid metabolism and sphingolipid metabolism, altering the levels of 11 cytoskeleton-related metabolites. Correlation analysis confirmed that Bifidobacterium sp. SO1 and Schaalia turicensis were strongly correlated with damage phenotypes, pathway molecules, and metabolites, indicating that these two strains are closely associated with cytoskeleton changes and increased intestinal permeability under high fluoride exposure. Collectively, our findings reveal that gut microbiota drive fluoride-induced intestinal barrier dysfunction through the "microbiota-RhoA/ROCK-cytoskeleton" axis, highlighting a novel host-microbe interaction mechanism underlying environmental toxin-mediated gut injury.},
}
@article {pmid41713817,
year = {2026},
author = {Zhao, Q and Cao, Y and Zhang, Z and Yang, Y and Wang, L and Xu, M and Mao, Y and Zhang, X and Zeng, M and Yang, P and Chen, Q and Yan, H and Yang, G},
title = {Xiao-Chaihu-Tang preserves intestinal barrier and ameliorates irinotecan-evoked delayed diarrhea by anchoring endogenous tryptophol to modulate inflammation and oxidation dependent on AhR-UGT1A1-microbiota axis.},
journal = {Journal of ethnopharmacology},
volume = {363},
number = {},
pages = {121380},
doi = {10.1016/j.jep.2026.121380},
pmid = {41713817},
issn = {1872-7573},
mesh = {Animals ; *Irinotecan/toxicity ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Gastrointestinal Microbiome/drug effects ; Male ; *Diarrhea/chemically induced/drug therapy/prevention &amp; control/metabolism ; Receptors, Aryl Hydrocarbon/metabolism ; Rats ; Rats, Sprague-Dawley ; Glucuronosyltransferase/metabolism ; *Indoles/metabolism ; Intestinal Mucosa/drug effects/metabolism ; Inflammation/drug therapy ; Oxidation-Reduction ; Fecal Microbiota Transplantation ; },
abstract = {Xiao-Chaihu-Tang (XCHT), a well-known traditional formula, is commonly used to treat various types of diarrhea. It also exhibits promising efficacy against chemotherapy irinotecan (CPT-11)-induced delayed diarrhea (DD). However, its underlying mechanisms, specifically concerning endogenous metabolites, key pathways, and functional gut bacteria at the species level, remain unclear, severely restricting its clinical application.<br><br>AIM OF THE STUDY: This study aimed to elucidate the biomarkers, pathways, and functional bacteria involved in XCHT's alleviating CPT-11-evoked DD using multi-omics approaches, antagonists, and fecal microbiota transplantation (FMT).<br><br>MATERIALS AND METHODS: First, the ingredients of XCHT and absorbed compounds in rat plasma were identified using liquid chromatography-mass spectrometry (LC-MS). Next, the therapeutic effects of XCHT were assessed by monitoring perianal status, body weight, disease activity index, food and water intake, and histopathological changes in the colon (hematoxylin and eosin, alcian blue-periodic acid-schiff staining). The underlying mechanisms were studied using metabolomics and network pharmacology, which highlighted the role of endogenous biomarkers and associated pathways. Tryptophol was identified as a key correlate, and its efficacy was further validated in rat and Caco-2 models using antagonists of potential targets (AhR and UGT1A1). The levels of inflammatory cytokines, and oxidative stress markers, intestinal barrier proteins, and mucins were detected by enzyme-linked immunosorbent assay (ELISA), Western blotting, and immunofluorescence. Furthermore, functional gut bacteria were identified using metagenomic sequencing and validated using FMT, while gut leakage was detected using fluorescence in situ hybridization (FISH). Finally, the interactions between tryptophol with targets of AhR and UGT1A1 were examined using molecular docking, molecular dynamics, and surface plasmon resonance.<br><br>RESULTS: LC-MS analysis identified 43 phytochemicals in XCHT and 17 compounds absorbed in plasma. XCHT, similar to tryptophol, attenuated DD by improving perianal status, disease activity index, and colon pathology, while increasing body weight, food intake, and water intake. Metabolomics analysis revealed 33 potential endogenous biomarkers, including PGB3, LysoPA, and so on. Integrated with network pharmacology, the results indicated that the therapeutic effect of XCHT involved the regulation of tryptophan metabolism, arachidonic acid metabolism, inflammation, and oxidative stress. Tryptophol, which exhibited a strong correlation with efficacy indices, reduced inflammation and oxidation in vivo/vitro, and enhanced intestinal barrier protein and mucin expression in an AhR-UGT1A1-dependent manner. Furthermore, metagenomic sequencing and FISH demonstrated that both XCHT and tryptophol normalized the abundance of 10 gut bacterial species (for example, Lactobacillaceae bacterium, Massiliimalia timonensis, and Limosilactobacillus reuteri) and inhibited bacterial invasion. Molecular interaction studies confirmed the strong binding between tryptophol with AhR and UGT1A1.<br><br>CONCLUSION: This study demonstrates that XCHT preserves intestinal barrier integrity in rats and alleviates CPT-11-induced DD. This protective effect is mediated by modulating inflammation and oxidative stress via the tryptophol- AhR-UGT1A1-microbiota axis, providing a novel paradigm for mechanistic studies on toxicity reduction in clinical chemotherapy drugs.},
}
@article {pmid41688638,
year = {2026},
author = {Dekkers, KF and Pertiwi, K and Baldanzi, G and Lundmark, P and Hammar, U and Moksnes, MR and Coward, E and Nethander, M and Salih, GA and Miari, M and Nguyen, D and Sayols-Baixeras, S and Eklund, AC and Holm, JB and Nielsen, HB and Volpiano, CG and Méric, G and Thangam, M and Hakaste, L and Tuomi, T and Ahlqvist, E and Smith, CA and Allen, M and Reimann, F and Gribble, FM and Ohlsson, C and Hveem, K and Melander, O and Nilsson, PM and Engström, G and Smith, JG and Michaëlsson, K and Ärnlöv, J and Orho-Melander, M and Fall, T},
title = {Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation.},
journal = {Nature genetics},
volume = {58},
number = {3},
pages = {540-549},
pmid = {41688638},
issn = {1546-1718},
support = {2019-01471//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2020-02191//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2020-01392//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 521-2013-2756//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2019-01236//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2021-02273//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2019-01291//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2019-01015, 2020-00243//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2018-02784, 2018-02837, EXODIAB 2009-1039//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2023-0687//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 20200173//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2022-0344//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2018-0343//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 2020-0711//Hj&#xe4;rt-Lungfonden (Swedish Heart-Lung Foundation)/ ; GNT2013468//Department of Health | National Health and Medical Research Council (NHMRC)/ ; MRC_MC_UU_12012/3//RCUK | Medical Research Council (MRC)/ ; 220271/Z/20/Z//Wellcome Trust (Wellcome)/ ; 190C0055250 and 22OC0078421//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; KAW 2015.0317//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; LU2021-0096//Lars Erik Lundbergs Stiftelse f&#xf6;r Forskning och Utbildning (Lundberg Foundation for Research and Education)/ ; CKFUU-1025348, 987986, 976460, 963488, 936407, 695401, and 797891//Centrum f&#xd6;r Klinisk Forskning Dalarna (Center for Clinical Research Dalarna)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Genome-Wide Association Study ; Male ; Female ; Sweden ; Adult ; Polymorphism, Single Nucleotide ; Metagenomics ; Fatty Acids/metabolism ; Genetic Variation ; Middle Aged ; Galactoside 2-alpha-L-fucosyltransferase ; },
abstract = {Despite the importance of the gut microbiome to health, the role of human genetic variation in shaping its composition remains poorly understood. Here we report genome-wide association analyses of harmonized metagenomic data from 16,017 adults in four Swedish population-based studies, with replication in 12,652 people from the Norwegian HUNT study. We identified variants in the OR51E1-OR51E2 locus, encoding sensors for microbiome-derived fatty acids, associated with microbial richness. We further identified 15 study-wide significant genetic associations (P < 5.4 × 10[-11]) involving eight loci and 14 common bacterial species, of which 11 associations at six loci were replicated. The results confirm previously reported associations at LCT, ABO and FUT2, and provide evidence for new loci MUC12, CORO7-HMOX2, SLC5A11, FOXP1 and FUT3-FUT6, with supporting data from metabolomics and gene expression analyses. Our findings link gut microbial variation genetically to gastrointestinal functions, including enteroendocrine fatty acid sensing, bile composition and mucosal layer composition.},
}
@article {pmid41651883,
year = {2026},
author = {Pantiukh, K and Org, E},
title = {Human gut archaea collection from Estonian population.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41651883},
issn = {2052-4463},
support = {PRG1414//Eesti Teadusagentuur (Estonian Research Council)/ ; 3573//European Molecular Biology Organization (EMBO)/ ; },
mesh = {Estonia ; *Archaea/genetics ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; *Genome, Archaeal ; Metagenomics ; Feces/microbiology ; },
abstract = {While microbiota plays a crucial role in maintaining overall health, archaea, a component of microbiota, remain relatively unexplored. Here, we present a newly assembled set of archaeal metagenome-assembled genomes (MAGs) from 1,878 fecal microbiome samples. These MAGs were reconstructed from metagenomic reads of the Estonian Microbiome Deep (EstMB-deep) cohort, which were reused here specifically for archaeal MAG reconstruction. We identified 273 archaeal MAGs, representing 21 species and 144 strains which we curated into the "EstMB MAGdb Archaea-273" MAGs collection.},
}
@article {pmid41558076,
year = {2026},
author = {Zhao, M and Wu, F and Feng, S and Li, C and Liu, S and Chen, S and Liu, Y and Chen, B and Zhang, G and Han, S},
title = {Ursolic acid modulates gut microbiota and metabolites to enhance Treg/Th17 balance and intestinal health in broilers.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106427},
pmid = {41558076},
issn = {1525-3171},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Chickens/immunology/microbiology/physiology ; *T-Lymphocytes, Regulatory/drug effects/immunology ; *Triterpenes/administration &amp; dosage/metabolism/pharmacology ; Ursolic Acid ; Dietary Supplements/analysis ; Diet/veterinary ; *Intestines/drug effects/physiology/microbiology ; Animal Feed/analysis ; *Th17 Cells/drug effects/immunology ; Random Allocation ; Dose-Response Relationship, Drug ; Male ; },
abstract = {Ursolic acid (UA), a naturally occurring pentacyclic triterpenoid abundant in various plants, possesses potent biological activities. However, its effects and mechanisms on immune competence in broilers remain unclear. In this study, 320 one-day-old Cobb broilers were randomly allocated to four groups (8 replicates of 10 birds each) for a 42-day trial: a control group (CON) and three treatment groups supplemented with 50, 200, or 400 mg/kg UA (UA 50, UA 200, or UA 400). We employed enzyme-linked immunosorbent assay (ELISA), alcian blue-periodic acid schiff (AB-PAS) staining, immunofluorescence (IF), immunohistochemistry (IHC), qRT-PCR, metagenomics, and untargeted metabolomics to analyze the effects of UA on immune factors, inflammatory cytokines, intestinal barrier function, regulatory T (Treg) cell / T helper 17 (Th17) cell balance, as well as intestinal microbial composition and metabolism in broilers. The results indicated that UA significantly increased immune factor levels while reducing pro-inflammatory cytokine concentrations in broilers. Regarding intestinal barrier function, UA supplementation effectively reduced lipopolysaccharide (LPS) and D-lactic acid levels, promoted goblet cell proliferation, and enhanced the expression of tight junction proteins (Claudin-1, ZO-1). Notably, UA also significantly modulated Treg/Th17 balance. Furthermore, UA supplementation modulated the gut microbial composition, which was marked by an increase in the beneficial Lactobacillus johnsonii and a concurrent suppression of the pathobiont Escherichia coli. Furthermore, UA reduced the enrichment of microbial pathways associated with pathogenic Escherichia coli and Salmonella infection. Further analysis indicated that UA modulated propionate and tryptophan metabolism, thereby increasing the concentrations of propionic acid and the tryptophan metabolites (5-Hydroxyindole-3-Acetic Acid (5HIAA) and Indole-3-Acetic Acid (IAA)). In summary, our findings demonstrate that UA enhances broiler immunity and intestinal barrier function. These benefits appear to be mediated by the UA-driven enrichment of Lactobacillus johnsonii, which promotes the production of propionate and tryptophan-derived metabolites (5-HIAA and IAA), thereby rebalancing the Treg/Th17 balance and ultimately reinforcing intestinal integrity. These findings underscore the potential of UA as a natural supplement for sustainable poultry production.},
}
@article {pmid41544440,
year = {2026},
author = {Yang, L and Ru, J and Guo, S and Yang, X and Li, P and Deng, L and Wang, X},
title = {Research note: The chicken gut virome: Spatiotemporal dynamics and divergent responses to antibiotic versus phytogenic supplementation.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106373},
pmid = {41544440},
issn = {1525-3171},
mesh = {Animals ; *Chickens/virology ; *Anti-Bacterial Agents/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; *Bacteriophages/drug effects/physiology/genetics ; Dietary Supplements/analysis ; *Virome/drug effects ; Animal Feed/analysis ; Diet/veterinary ; *Chlortetracycline/pharmacology/administration &amp; dosage ; *Plant Extracts/pharmacology/administration &amp; dosage ; },
abstract = {This study employed metagenomic sequencing data to comprehensively investigate the gut virome, with a focus on the bacteriophage communities (the phageome), across intestinal regions and developmental stages in 360 chickens. We characterized the spatiotemporal dynamics of phage communities and assessed the impact of chlortetracycline (CTC), an antibiotic, and Macleaya cordata extract (MCE), a phytogenic supplement. Our analysis revealed that phage community assembly was highly structured, exhibiting distinct successional patterns across age and between foregut and hindgut segments. A key finding was the identification of a potential antibiotic-phage synergy, mediated by phage-encoded auxiliary metabolic genes (AMGs) involved in bacterial immune evasion, suggesting a novel mechanism for enhanced infectivity under antibiotic pressure. In contrast, phytogenic supplementation promoted gut ecosystem homeostasis by fostering significantly richer and more diverse phage communities. Our results delineate the fundamental ecology of the chicken gut virome and provide mechanistic insights into how different growth promoters exert contrasting effects on viral populations, supporting the use of phytogenics as sustainable alternatives for animal husbandry.},
}
@article {pmid41539238,
year = {2026},
author = {Sitthipunya, A and Uthaipaisanwong, P and Sinwat, N and Kanjanavaikoon, K and Cheevadhanarak, S and Kusonmano, K},
title = {Metagenomic insights into the effects of Clostridium butyricum and Bacillus subtilis probiotics on the gut microbiome and metabolic pathways of industrial broilers in Thailand.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106371},
pmid = {41539238},
issn = {1525-3171},
mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; *Bacillus subtilis/chemistry ; *Chickens/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Clostridium butyricum/chemistry ; Animal Feed/analysis ; Diet/veterinary ; *Metabolic Networks and Pathways/drug effects ; Thailand ; Metagenomics ; Dietary Supplements/analysis ; *Metagenome ; },
abstract = {Probiotic supplementation has become increasingly important in broiler production due to its safety and well-documented health benefits. The gut microbiome of broilers plays a vital role in feed digestion and maintaining intestinal homeostasis, which directly influences the efficacy of probiotics under specific farm conditions. This study aims to investigate the effects of single Bacillus subtilis probiotics and double-strain probiotics of Clostridium butyricum and B. subtilis supplementation on the gut microbiome of broilers in industrial farms. We evaluated sequencing data obtained from broilers supplemented with these probiotics through amplicon sequencing and metagenomic analysis. Our study revealed that probiotics significantly influence the cecal microbiome and its functionality in broilers. The use of double-strain probiotics increased butanoate metabolism, as well as the metabolism of glycine, serine, and threonine. This suggests their contribution from microbial gut species, including Alistipes onderdonkii, Alistipes finegoldii, Bacteroides uniformis, and Phocaeicola dorei. Supporting this finding, network analysis shows more connections between probiotics and commensal cecal microbiota, highlighting a cascade-linked association with butanoate-producing microbiota. Furthermore, single-strain B. subtilis probiotic supplementation uniquely enhanced arginine and proline metabolism, likely due to the presence of species such as Bacteroides sp. zj-18, Bacteroides cellulosilyticus, and Parabacteroides distasonis. Overall, our findings indicate that double-strain probiotics increased richness in the cecal microbial community, reshaped the microbial network, and enriched short-chain fatty acid and amino acid metabolism, contributing to improved gut health and performance in broiler production.},
}
@article {pmid41512665,
year = {2026},
author = {Wu, CE and Wang, SY and Chen, JW and Yang, WY},
title = {Effects of Ligilactobacillus salivarius on the control of pullorum disease and cecal microbiota in red-feathered native chickens.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106384},
pmid = {41512665},
issn = {1525-3171},
mesh = {Animals ; *Chickens ; *Poultry Diseases/microbiology/prevention &amp; control ; Cecum/microbiology ; *Salmonella Infections, Animal/microbiology/prevention &amp; control ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/pharmacology/administration &amp; dosage ; Random Allocation ; Anti-Bacterial Agents/pharmacology ; Amoxicillin/pharmacology ; *Bacillaceae/physiology ; *Lactobacillaceae/physiology ; },
abstract = {Pullorum disease (PD), caused by Salmonella Pullorum (SP), remains a persistent challenge in native chicken production in Asia. Recurrent outbreaks and reliance on antibiotics have raised concerns about antimicrobial resistance. This study established a reproducible clinical PD model in red-feathered native chickens (RFCs) and evaluated Ligilactobacillus salivarius (LS) as a potential alternative to antibiotic. Oral administration of a field SP isolate (SPB6) at 1 × 10[8] CFU per chick for four consecutive days induced typical PD signs and persistent bacterial colonization, whereas a single-dose challenge failed to produce consistent disease. Using this model, 100 SP-free RFCs were randomly assigned to five groups of 20 RFCs each: SP challenge only (A), SP + amoxicillin treatment (B), LS prophylaxis + SP (C), SP + nine-day LS treatment (D), and an unchallenged control group (E). Both amoxicillin and LS treatments reduced SP shedding and tissue colonization; notably, nine-day LS regimen achieved sustained suppression of SP isolation rates and bacterial loads comparable to those observed with amoxicillin on days 7, 10, and 17 after infection. Metagenomic analysis in cecal microbiota revealed that nine-day LS treatment enriched the abundance of short-chain fatty acid-producing species, such as Faecalicatena contorta and Lacrimispora saccharolytica, which are associated with intestinal integrity and immune resilience. In conclusion, LS reduced SP shedding and intestinal colonization, with greater efficacy following prolonged administration. LS also modulated the cecal microbiota in PD-affected RFCs by increasing the relative abundance of beneficial taxa. These findings provide experimental support for the evaluation of LS as a potential alternative to antibiotics for PD control. Further studies that extend the duration of LS administration are warranted and are likely to enhance its protective effects.},
}
@article {pmid41825251,
year = {2026},
author = {Chang, L and Su, X and Hu, W and Fang, Y and Liu, J and Li, J and Huang, L and Shu, W},
title = {Genomic insights into adaptation and microevolution of two novel non-AOA Nitrososphaeria, Acidarchaeum fankouense and Thermosulfuris yongpingense, in acid mine drainage ecosystems.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {3},
pages = {126711},
doi = {10.1016/j.syapm.2026.126711},
pmid = {41825251},
issn = {1618-0984},
abstract = {The class Nitrososphaeria is best known for ammonia-oxidizing archaea (AOA), yet deeply branching non-AOA lineages remain poorly characterized, leaving a critical gap in our understanding of the group's early evolution and ecological diversification. Herein, we recovered 44 non-AOA Nitrososphaeria metagenome-assembled genomes (MAGs) from acid mine drainage (AMD) sediments in diverse metal mines, representing two novel genera within the family Thermosulfuridaceae, Acidarchaeum and Thermosulfuris. A meta-analysis of 251 AMD-associated metagenomes worldwide showed that these potentially thermophilic lineages were detected only in China and were typically rare, with localized blooms (up to ∼7.65%) at a few sites, particularly Fankou lead-zinc mine. Metabolic reconstruction suggested a facultatively anaerobic, mixotrophic lifestyle capable of CO oxidation and sulfur reduction, and extensive acid- and heavy-metal resistance mediated primarily by ether-linked archaeal lipids, ion efflux systems, and enzymatic reduction. Genus-specific traits include dissimilatory sulfate reduction in Thermosulfuris and urea utilization in Acidarchaeum, illuminating distinct ecological niches. Population-genomic analyses reveal low homologous recombination and pervasive purifying selection in these non-AOA populations, together with local relaxation of selection and elevated diversity, the former being correlated with geochemical stressors (notably copper), pointing to long-term, geochemically driven adaptation. Overall, these findings provide insights into the biodiversity, ecophysiology, and evolutionary dynamics of non-AOA Nitrososphaeria.},
}
@article {pmid41821330,
year = {2026},
author = {Yi, XH and Zhu, HX and He, MY and Gao, S and Li, M},
title = {Decoding Links between Gut Microbiota and Metabolic-associated Fatty Liver Disease: Meta-analysis and Mediation Study Uncover Species-specific Taxa and a Novel Bile Acid Mediator.},
journal = {Biomedical and environmental sciences : BES},
volume = {39},
number = {2},
pages = {202-214},
doi = {10.3967/bes2025.162},
pmid = {41821330},
issn = {2214-0190},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Bile Acids and Salts/metabolism ; Mendelian Randomization Analysis ; Species Specificity ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Fatty Liver/microbiology ; Bacteria/classification/genetics ; },
abstract = {OBJECTIVE: Previous Mendelian randomization (MR) studies have suggested an association between the gut microbiome and metabolic-associated fatty liver disease (MAFLD). However, the reliance on 16S rRNA sequencing data has led to inconsistent findings and limited species-level insights. To address this, we conducted a de novo MR analysis using species-level shotgun metagenomic data, combined it with a meta-analysis to consolidate the existing evidence, and explored metabolite-mediated pathways.<br><br>METHODS: Bidirectional MR analyses were performed between 883 gut microbiota taxa (derived from shotgun metagenomic genome-wide association study) and MAFLD. Published MR studies (up to December 1, 2024) were identified using PubMed, Embase, Web of Science, and the Cochrane Library for meta-analysis. Multivariable MR (MVMR) and mediation analyses were applied to assess the mediating effects of 1,400 blood metabolites.<br><br>RESULTS: The de novo MR identified 25 MAFLD-associated microbial taxa. Integration with 7 published studies revealed 34 causal taxa, including 10 at the species level. Among the 1,400 metabolites, 53 showed causal links with MAFLD. MVMR and mediation analyses identified deoxycholate as a mediator of the effect of Bifidobacterium on MAFLD risk (22.06% mediation proportion).<br><br>CONCLUSION: This study elucidated the connections between species-level gut microbiota and MAFLD, highlighting the interplay between microbiota, metabolites, and disease pathogenesis. These findings provide novel insights into the potential therapeutic targets for MAFLD.},
}
@article {pmid41820832,
year = {2026},
author = {Vela-Chauvin, MG and Ramirez-Villacis, DX and Armijos, CE and Narvaez, M and Quelal-Madrid, F and Bustamante, G and Torres-Sobrevilla, C and Debut, A and Corredor, F and Calero-Cáceres, W and Machado, A and Zapata-Mena, S},
title = {Characterization and evaluation of a phage cocktail targeting Salmonella enterica in a Turkey farm.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04849-4},
pmid = {41820832},
issn = {1471-2180},
support = {FSPI grant (Project ID 17827)//French Embassy in Ecuador/ ; Collaboration Grant (Project ID 23185)//Universidad San Francisco de Quito/ ; },
}
@article {pmid41791253,
year = {2026},
author = {Fu, CX and Cai, JJ and Liu, JL and Qiu, GY and Chen, XD and Zhang, JB and Qiao, M and Tong, WB and Guo, B},
title = {Mechanistic investigation of the associations between bacterial community composition and cadmium distribution in Zizania latifolia.},
journal = {Ecotoxicology and environmental safety},
volume = {312},
number = {},
pages = {119972},
doi = {10.1016/j.ecoenv.2026.119972},
pmid = {41791253},
issn = {1090-2414},
mesh = {*Cadmium/metabolism/analysis ; *Soil Pollutants/metabolism/analysis ; Rhizosphere ; *Bacteria/metabolism/classification/genetics ; Plant Roots/microbiology/metabolism ; Soil Microbiology ; *Poaceae/microbiology/metabolism ; Plant Leaves/metabolism/microbiology ; *Microbiota ; },
abstract = {The role of bacteria in external niches regulating cadmium (Cd(II)) in plant tissues remains unclear. We explored Cd(II) profiles and identified bacterial contributors among phyllosphere, rhizoplane, and rhizosphere of four Zizania latifolia varieties through integrated metagenomic and chemical analyses. Zizania latifolia accumulated Cd(II) in leaves (0.06-0.77 mg/kg), roots (0.73-1.57 mg/kg), and rhizosphere (0.43-3.15 mg/kg), respectively. The highest enrichment coefficient (leaf-Cd(II)/soil-Cd(II)) was observed in Genotype 3 (0.6). Among top 10 genus-level bacteria, Enterococcus in phyllosphere, Streptomyces and Dechloromonas in rhizoplane, and Bradyrhizobium, Pseudolabrys, Mycobacterium, and Dechloromonas in rhizosphere were significantly related to Cd(II). Enterococcus adsorbed Cd(II) by extracellular polysaccharides and precipitated Cd(II) sulfide. Rhizoplane and rhizosphere bacteria absorbed Cd(II) by cell-surface functional groups, and fixed Cd(II) through synthesizing polyphosphate and driving Fe (II) oxidation. Additionally, 64.4%-80% of bacteria were shared between rhizoplane and rhizosphere, 5.5%-6.9% between rhizoplane and phyllosphere, and 4.4%-6.1% between rhizosphere and phyllosphere. Metagenomic analysis indicated that Cd(II) disturbed bacterial secretion system and amino acid metabolic pathways. These findings provided comprehensive insights into interrelationships between Cd(II) and bacteria in leaves, roots, and rhizosphere of Zizania latifolia, offering valuable foundations for developing targeted strategies to mitigate Cd(II) accumulation in aquatic vegetables.},
}
@article {pmid41772715,
year = {2026},
author = {Merenstein, C and Litichevskiy, L and Thaiss, C and Collman, RG and Bushman, FD},
title = {Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41772715},
issn = {2049-2618},
support = {F31 HL170550/NH/NIH HHS/United States ; T32 HG000046/NH/NIH HHS/United States ; DP2 AG067492/NH/NIH HHS/United States ; U54 AG089323/NH/NIH HHS/United States ; U19 AI174998/NH/NIH HHS/United States ; F31 HL170550/NH/NIH HHS/United States ; T32 HG000046/NH/NIH HHS/United States ; DP2 AG067492/NH/NIH HHS/United States ; U54 AG089323/NH/NIH HHS/United States ; U19 AI174998/NH/NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Bacteriophages/genetics/classification/isolation &amp; purification/physiology ; *Caloric Restriction ; *Bacteria/virology/genetics/classification ; Longevity ; Genome, Viral ; Metagenome ; Male ; Longitudinal Studies ; Female ; },
abstract = {BACKGROUND: The majority of bacteria in the vertebrate gut harbor integrated bacterial viruses ("bacteriophages" or "phages"; integrated phage are termed "prophages"). To probe phage replication strategies in the mammalian gut microbiome, we investigated phage activity in a large longitudinal study of diversity outbred mice (913 animals) undergoing extreme dietary restriction with detailed phenotypic characterization across lifespan.<br><br>RESULTS: We assembled 54,119 candidate DNA viral genomes from 2997 longitudinal metagenomes, forming 6462 viral operational taxonomic units (vOTUs). Over 85% of vOTUs annotated as novel. Viruses annotated predominantly as prophages in the Caudoviricetes class. We detected no eukaryotic DNA viruses, and none of the strictly lytic Crassvirales order that is abundant in human gut. The most prevalent phages had the widest predicted host ranges. The relative abundance of most phages was highly correlated to that of their inferred host bacteria, suggesting quiescent prophages dominate viral metagenomes, consistent with "piggyback-the-winner" dynamics. After accounting for close phage-bacterial covariation, we did identify a subset of phages changing in relative abundance and prevalence relative to their hosts in response to dietary restriction and aging. In particular, phages with larger genomes become less common in diets with restricted calories, potentially reflecting a higher fitness cost to their host. Generalist phages were enriched for a gene encoding a single-strand DNA binding protein which is reportedly involved in DNA repair and protection from nucleases encoded by host cells. Lytic phages became more common with aging, and we observed a reduction in phage richness with age, both findings previously observed in human cohorts.<br><br>CONCLUSION: These studies enrich our understanding of DNA phage dynamics in gut while emphasizing the predominance of "piggyback-the-winner" strategies.},
}
@article {pmid41713162,
year = {2026},
author = {Liu, X and Cai, H and Zhao, L and Ke, D and Xu, X and Li, J and Yu, J and Shen, Y and Zhu, L and Jin, Y and Zhang, M and Liu, S and Du, J and Zheng, J and Dong, R},
title = {Microplastic-associated gut microbial profile and antibiotic resistance in preschool children: a multicentre cross-sectional study in China.},
journal = {EBioMedicine},
volume = {125},
number = {},
pages = {106177},
pmid = {41713162},
issn = {2352-3964},
mesh = {Humans ; China/epidemiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Cross-Sectional Studies ; Child, Preschool ; Female ; Male ; *Microplastics/adverse effects ; *Drug Resistance, Microbial/genetics ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Bacteria/genetics/drug effects/classification ; },
abstract = {BACKGROUND: Microplastics (MPs) are ubiquitous in ecosystems and present in the human body, causing a worldwide environmental issue. However, the extent of human exposure to MPs remains largely unknown. Although mice exposed to MPs exhibit gut microbiota dysbiosis, the impact of MPs on the human intestinal microbiota remains unclear. Furthermore, MPs can carry and spread antibiotic resistance genes (ARGs). However, their potential influence on ARG abundance is underexplored.<br><br>METHODS: A multicentre cross-sectional study was conducted in Xiamen, Shanghai, and Nanjing in China from October 2022 to March 2023. A total of 335 couples of faecal samples were collected and analysed for MPs using Py-GC/MS and gut microbiota using 16S rRNA and metagenomic sequencing.<br><br>FINDINGS: Eight types of MPs were detected in 335 faecal samples, with a median concentration of 212.1 &#x3bc;g/g dw. MP exposure may be associated with the composition of the host gut microbiota. Microbial function analysis indicated the significant enrichment of 62 pathways primarily related to the metabolic pathways of macronutrients, vitamins, and bioactive substances. Total plastic concentration was significantly related to the relative abundance of species and ARGs, however this could not be attributed to specific plastic polymers after adjusting for covariates.<br><br>INTERPRETATION: This study provides baseline data on the gap in understanding of preschoolers' MP exposure, supporting the hypothesis that MP exposure might disrupt gut bacterial constitution and functions. This raises concerns regarding the potential adverse effects on the human gut when exposed to MPs, particularly drug resistance risks in younger populations.<br><br>FUNDING: Project of Shanghai Municipal Financial Professional foundation (Food Safety Risk Assessment) (grant number: RA-2023-10), National Natural Science Foundation of China (grant number: 2023YFF1104800), and Key Disciplines in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025) (grant number: GWVI-11.1-42).},
}
@article {pmid41691988,
year = {2026},
author = {Pan, Y and Zong, G and Liu, M and Wang, Z and Zhu, H and Wei, Z and Shan, Y and Lu, Y},
title = {Restoring gut microbiota homeostasis to ameliorate colitis via Huangqin decoction.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {153},
number = {},
pages = {157929},
doi = {10.1016/j.phymed.2026.157929},
pmid = {41691988},
issn = {1618-095X},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Drugs, Chinese Herbal/pharmacology ; Mice ; Mice, Inbred C57BL ; Homeostasis/drug effects ; *Colitis, Ulcerative/drug therapy/microbiology ; Disease Models, Animal ; Male ; *Colitis/drug therapy ; Wnt Signaling Pathway/drug effects ; Dextran Sulfate ; Anti-Inflammatory Agents/pharmacology ; Eubacteriales/drug effects ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is an inflammatory gut disorder involving dysregulated host-microbiota interactions. Huangqin decoction (HQD) is an herbal formula with known anti-inflammatory and microbiota-modulating effects, but its protective mechanism in ulcerative colitis remains unclear.<br><br>PURPOSE: To investigate whether HQD ameliorates colitis by rebalancing gut microbiota homeostasis and to elucidate the underlying immunological and regenerative mechanisms involved.<br><br>METHODS: A DSS-induced colitis mouse model was used to evaluate the effects of HQD. Colitis severity and inflammation were evaluated by the clinical disease index, histological analysis, and cytokine levels, and the gut microbiota profiles were analyzed via metagenomic sequencing. We used mechanistic assays to evaluate the effects of specific bacterial strains on intestinal organoids and neutrophil NETosis.<br><br>RESULTS: HQD significantly alleviated colitis symptoms and inflammation. It remodelled the gut microbiota, suppressing Desulfovibrionaceae while enriching Lachnospiraceae. This microbiota shift drove reduced NETosis and activated Wnt/&#x3b2;-catenin signaling to enhance intestinal stem cell (ISC) proliferation, thereby promoting mucosal repair. In organoid cultures, Lachnospiraceae promoted organoid growth, whereas Desulfovibrionaceae caused epithelial damage and, independently, triggered NETosis in immune contexts. Notably, administration of the Lachnospiraceae bacterium ameliorated colitis and increased colonic Wnt/&#x3b2;-catenin signaling, confirming its regenerative role.<br><br>CONCLUSION: HQD ameliorates colitis by rebalancing the gut microbiota, thereby suppressing harmful inflammation and promoting epithelial regeneration. These findings provide mechanistic support for HQD as a microbiota-mediated therapeutic strategy in colitis.},
}
@article {pmid41679496,
year = {2026},
author = {Jing, M and Zhang, X and Li, X and Tan, L and Niu, Z and Ma, Y},
title = {Direct Evidence of Microplastic-Mediated Microbial Migration Across the River-Sea Transition via a Novel Field-Laboratory Coupled Approach.},
journal = {Environmental research},
volume = {296},
number = {},
pages = {123973},
doi = {10.1016/j.envres.2026.123973},
pmid = {41679496},
issn = {1096-0953},
mesh = {*Microplastics/toxicity ; *Rivers/microbiology ; *Seawater/microbiology ; *Water Pollutants, Chemical/toxicity ; *Microbiota/drug effects ; Bacteria ; Environmental Monitoring ; Biofilms ; *Water Microbiology ; },
abstract = {Large amounts of microplastics (MPs) are transported annually from river into the ocean. Biofilm-covered MPs, termed as the "plastisphere", may mediate microbial transfer. Previous studies have mostly focused on the evolution of the plastisphere itself, covering field experiments and its transformation during migration. Direct evidence for their impact on marine communities is still limited. To address this, we combined field and laboratory experiments to directly evaluate the effects of MPs on marine microbial communities along the river-sea shift. MPs were incubated for 0, 28, and 140 days in freshwater. They were then transferred to a laboratory-simulated marine micro-ecosystem constructed with a fresh seawater microbiome to allow the microbial communities to acclimate, and then further incubated in the laboratory for 1, 3, and 7 days. Microbial community dynamics were examined using metagenomic analysis. Long-term incubated plastispheres (140 days) rapidly shifted marine community structure toward plastisphere-like composition as early as Day 1. However, this overall structural change faded by Day 7. Interestingly, the presence of 28-day and 140-day plastispheres led to a consistent increase in microbial species diversity and a higher number of antibiotic resistance genes (ARGs) and virulence factors (VFs), this effect persisted through Day 7. Additionally, salt-tolerant, potentially pathogenic bacteria were also detected, reflecting the as carrier roles of plastispheres. This study provides direct evidence that plastispheres mediate microbial transfer, thereby enhancing diversity and spreading ARGs and VFs, contributing to a better understanding of the potential ecological and environmental risks of microplastics.},
}
@article {pmid41644553,
year = {2026},
author = {Wen, R and Xin, Y and Bao, S and Zhang, X and Wang, Q and Dang, Z and Zhou, Z and Wu, J and Song, D and Fu, L and Li, W and Niu, J and Wen, Y and Zhou, X and Han, M and Zhao, J},
title = {The gut microbiota mediates depression-like behaviors in mice with chronic Echinococcus multilocularis infection.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41644553},
issn = {2055-5008},
support = {NO. 32160181//National Natural Science Foundation of China/ ; 2022AAC02076//Ningxia Natural Science Found Project/ ; 2024BEG02028//Key research and development projects of the Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Echinococcus multilocularis/physiology ; Mice ; *Depression/microbiology/etiology ; *Echinococcosis/microbiology/psychology/parasitology ; Mice, Inbred BALB C ; Disease Models, Animal ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Behavior, Animal ; Metabolomics ; Metagenomics ; },
abstract = {Alveolar echinococcosis (AE), a chronic parasitic disease caused by Echinococcus multilocularis (E. multilocularis), remains poorly characterized with respect to central nervous system (CNS) involvement, and its long-term effects on mental health have not been systematically investigated. In this study, we established a BALB/c mouse model of chronic E. multilocularis infection and applied an integrative framework combining behavioral assessments, histomorphological analyses (hematoxylin-eosin staining, Nissl staining, and transmission electron microscopy), cytometric bead array (CBA), and multi-omics approaches (16S rRNA sequencing, metagenomics, and untargeted metabolomics) to investigate infection-induced neuroimmune-gut microbiota interactions. Chronically infected mice exhibited pronounced depression-like behavioral phenotypes, accompanied by hippocampal neuronal nuclear membrane atrophy and disrupted microglial homeostasis. Both peripheral and central inflammatory profiling revealed elevated levels of pro-inflammatory mediators, particularly IL-6 and MCP-1, suggesting coordinated systemic immune activation and neuroimmune alterations. Notably, fecal microbiota transplantation (FMT) from infected donors was sufficient to induce depression-like behaviors in recipient mice, supporting a contributory role of infection-associated gut microbiota alterations in behavioral abnormalities. Integrated multi-omics analyses further revealed a marked reduction in Lactobacillus abundance in infected mice, which was positively correlated with decreased levels of key metabolites within the tryptophan/5-hydroxytryptamine (5-HT) metabolic pathway. Collectively, these findings suggest that chronic E. multilocularis infection may be associated with depression-like behaviors through gut microbiota dysbiosis and related metabolic perturbations. This study provides initial insights into the potential mechanisms underlying neuropsychiatric complications in AE and proposes a conceptual framework for future investigations into early intervention and microbiota-targeted therapeutic strategies.},
}
@article {pmid41558030,
year = {2026},
author = {Fan, C and Hayase, T and Chang, CC and Glover, IK and Flores, II and McDaniel, LK and Ortega, MR and Sanchez, CA and El-Himri, RK and Brown, AN and Karmouch, JL and Jamal, MA and Ahmed, SS and Halsey, TM and Jin, Y and Tsai, WB and Prasad, R and Enkhbayar, A and Mohammed, A and Schmiester, M and Damania, A and Ajami, NJ and Wargo, JA and Peterson, CB and Rondon, G and Al-Juhaishi, T and Alousi, AM and Molldrem, JJ and Champlin, RE and Shpall, EJ and Martens, E and Arias, CA and Jenq, RR and Hayase, E},
title = {Fecal carbohydrate-degrading bacteria are associated with reduced incidence of lower gastrointestinal GVHD.},
journal = {Blood advances},
volume = {10},
number = {6},
pages = {1979-1991},
doi = {10.1182/bloodadvances.2025016780},
pmid = {41558030},
issn = {2473-9537},
mesh = {Humans ; *Graft vs Host Disease/etiology/epidemiology/microbiology ; Hematopoietic Stem Cell Transplantation/adverse effects ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Female ; Male ; Incidence ; Middle Aged ; *Bacteria/metabolism ; Adult ; *Carbohydrate Metabolism ; Retrospective Studies ; *Gastrointestinal Diseases/etiology/epidemiology/microbiology ; Metagenomics ; },
abstract = {Lower gastrointestinal graft-versus-host disease (LGI-GVHD) carries morbidity and mortality for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), with critical contributions from the intestinal microbiome. In a retrospective cohort of metagenomic sequencing of stool from patients with allo-HSCT (N = 90), we found that a reduction in specific Parabacteroides and Bacteroides species around the time of engraftment contributes to LGI-GVHD risk. Given the known diverse carbohydrate-degrading functionality of these bacteria, we investigated gene abundances for carbohydrate-active enzymes (CAZymes) and found that Parabacteroides merdae, P distasonis, and Bacteroides ovatus abundances were significantly correlated with CAZymes in patients who did not develop LGI-GVHD compared with those who did. The specific gene abundances of xylosidase, which contribute to the degradation of xylose-containing polysaccharides, were significantly associated with a reduced risk of LGI-GVHD. All these findings show the importance of the carbohydrate-degrading functionality of putative beneficial bacteria in mediating risk of LGI-GVHD.},
}
@article {pmid41544986,
year = {2026},
author = {Liu, X and Zhang, J and Niu, Y and Bai, Y and Jia, X and Cai, S and Wang, Y and Zhang, X and Shi, B and Hu, J and Zhang, C and Zhao, Z},
title = {Dynamic changes in rumen fermentation, microbial communities, and metabolite profiles of non-pregnant and gestational Ashidan yaks.},
journal = {Genomics},
volume = {118},
number = {2},
pages = {111205},
doi = {10.1016/j.ygeno.2026.111205},
pmid = {41544986},
issn = {1089-8646},
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Fermentation ; Female ; Cattle/microbiology/metabolism ; *Metabolome ; *Gastrointestinal Microbiome ; Pregnancy ; *Microbiota ; Metagenome ; },
abstract = {Rumen microbiota and their metabolites in ruminants across reproductive stages benefit the animals' growth, health and offspring's development. However, the impact of rumen fermentation profiles, microbial composition, and metabolite dynamics between non-pregnant and gestating Ashidan yaks remains poorly understood. This study analyzed the rumen fermentation, metagenome and metabolome of five 2-3-year-old Ashidan yaks during the non-pregnant period (NP; 11-30 days pre-mating) and the gestational period (GP; 112-148 days post-conception). Research has found that gestation had higher acetic acid and ammonia nitrogen (NH3-N) (P < 0.05), increased Ascomycota, Apicomplexa, Rhodococcus, Acinetobacter, Methanosphaera (P < 0.05); differential metabolites enriched in valine, leucine, isoleucine biosynthesis and histidine metabolism (P < 0.05), with L-threonine and urocanic acid as major ones. Additionally, microorganisms, metabolites and fermentation parameters correlated. The study shows Ashidan yaks adapt to reproductive stages via regulating rumen microbiota and metabolism, providing a basis for feeding management.},
}
@article {pmid41539415,
year = {2026},
author = {Liu, P and He, G and Guo, Z and Tang, Y and Tan, Z and Song, Y and He, T and Lee, SL},
title = {Characteristics of microbial community succession and functional metabolite accumulation during microaerobic fermentation of high-sugar-load fruit and vegetable residues: Potential implications for guiding home production of environmental-friendly bioactive fertilizer.},
journal = {Genomics},
volume = {118},
number = {2},
pages = {111204},
doi = {10.1016/j.ygeno.2026.111204},
pmid = {41539415},
issn = {1089-8646},
mesh = {*Fruit/metabolism/microbiology ; *Fermentation ; *Vegetables/metabolism/microbiology ; *Microbiota ; *Fertilizers ; Lactuca/growth &amp; development ; Germination ; Sugars/metabolism ; },
abstract = {Household fermentation tanks offer simple, low-cost solutions for fruit and vegetable waste utilization, yet staged metabolite formation during sugar-mediated fermentation remains understudied. Using metagenomic and metabolomic approaches, we characterized microbial succession and metabolite dynamics over 28 days. Three phases emerged: substrate activation (1-7d) with Enterobacter/Escherichia dominance producing organic acids; metabolic transition (8-21d) with Lactiplantibacillus proliferation (312.5% increase) accumulating phytohormones 3-hydroxycinnamic acid (2.84-fold) and adenine (1.38-fold); functional stability (21-28d) establishing Lactiplantibacillus-Acetobacter synergy enriching antioxidants and antimicrobial peptides. Multi-omics analysis revealed strong correlations between amino acid metabolism and functional metabolites (r = 0.78, p < 0.01). Fermentation broth (1:500 dilution) enhanced lettuce germination to 92.22% (p < 0.05).Although the potential of household agriculture is demonstrated through staged microbial community development and the formation of bioactive products, functional characteristics still need to be verified in the soil-plant system beyond seed germination assays.},
}
@article {pmid41524878,
year = {2026},
author = {Ohsawa, M and Nishi, H and Hamai, Y and Emi, M and Ibuki, Y and Komatsuzawa, H and Kawaguchi, H and Okada, M},
title = {Relationship Between the Oral Microbiome and Treatment Efficacy in Esophageal Squamous Cell Carcinoma.},
journal = {Annals of surgical oncology},
volume = {33},
number = {4},
pages = {3203-3213},
pmid = {41524878},
issn = {1534-4681},
mesh = {Humans ; *Esophageal Neoplasms/therapy/microbiology/pathology ; Male ; Female ; *Microbiota ; Middle Aged ; *Esophageal Squamous Cell Carcinoma/microbiology/therapy/pathology/mortality ; Prognosis ; Survival Rate ; *Esophagectomy/mortality ; Aged ; Neoadjuvant Therapy/mortality ; Follow-Up Studies ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Bacteria/genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: As the relationship between oral microbiota and treatment efficacy in esophageal cancer remains unexplored, we aimed to clarify it using metagenomic analysis.<br><br>PATIENTS AND METHODS: Of the 140 consecutive patients with esophageal squamous cell carcinoma (ESCC) who underwent esophagectomy with R0 resection at Hiroshima University Hospital between April 2020 and May 2024, 74 who received neoadjuvant therapy were included in this study. 16S rRNA gene from oral tongue coating samples was amplified using polymerase chain reaction and subjected to next-generation sequencing. The oral microbiome data were analyzed using QIIME2 and linear discriminant analysis effect size, and the relationship between the oral microbiota and treatment efficacy and prognosis was assessed.<br><br>RESULTS: Alpha diversity of the oral microbiota was significantly correlated with the pathological response. Univariate and multivariate analyses showed that the alpha diversity of the oral microbiome (high versus low) was a significant predictor of a good pathological response. Patients with high alpha diversity had significantly improved recurrence-free survival and overall survival compared with those with low alpha diversity. Furthermore, eight bacterial groups (Lactobacillales, Peptostreptococcales-Tissierellales, Bifidobacteriaceae, Erysipelotrichaceae, Lactobacillaceae, Anaerovoracaceae, Staphylococcaceae, and Aerococcaceae) were significantly more abundant in individuals who responded well to neoadjuvant therapy and two bacterial groups (Streptococcaceae and Corynebacteriaceae) were significantly more abundant in poor responders.<br><br>CONCLUSIONS: Our results demonstrate a correlation between the oral microbiome and ESCC treatment efficacy, suggesting that it is a significant prognostic factor. Our findings may also help predict the efficacy of esophageal cancer treatment.},
}
@article {pmid41519314,
year = {2026},
author = {Su, J and Jiang, S and Chu, M and Dong, X and Zhang, C and Li, X and He, K},
title = {Time-course with multi-omics reveals hyperlipidemia dysregulates diurnal rhythms in gut-liver axis.},
journal = {Genomics},
volume = {118},
number = {2},
pages = {111198},
doi = {10.1016/j.ygeno.2026.111198},
pmid = {41519314},
issn = {1089-8646},
mesh = {Animals ; *Hyperlipidemias/metabolism/genetics ; *Circadian Rhythm/genetics ; *Liver/metabolism ; Mice ; *Gastrointestinal Microbiome ; Male ; Diet, High-Fat/adverse effects ; Lipid Metabolism/genetics ; Transcriptome ; Mice, Inbred C57BL ; Multiomics ; },
abstract = {BACKGROUND: Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by diurnal rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Diurnal rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems.<br><br>RESULTS: Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes-including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1-that are regulated by the hepatic circadian clock and modulate metabolites via the gut-liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism.<br><br>DISCUSSION: Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the diurnal rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind to hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut-liver axis-a key mechanism in hyperlipidemia pathogenesis.<br><br>CONCLUSIONS: This study identifies critical temporal windows and core microbial taxa involved in microbiota-metabolite-gene crosstalk via the gut-liver axis, offering a theoretical foundation for diurnal rhythm-targeted interventions in metabolic diseases.},
}
@article {pmid41814421,
year = {2026},
author = {Lee, CZ and Worsley, SF and Davies, CS and Komdeur, J and Hildebrand, F and Dugdale, HL and Richardson, DS},
title = {Host immunogenetic variation and gut microbiome functionality in a wild vertebrate population.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41814421},
issn = {2049-2618},
mesh = {*Gastrointestinal Microbiome/genetics/immunology ; Animals ; Metagenomics/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; *Songbirds/microbiology/immunology/genetics ; *Major Histocompatibility Complex/genetics ; Animals, Wild/microbiology/immunology ; Immunogenetics ; },
abstract = {BACKGROUND: The gut microbiome (GM) -important for host health and survival- is partially shaped by host immunogenetics. However, to date, no study has investigated the influence of host Major Histocompatibility Complex (MHC) genes on gut microbiome functionality in a wild population. Here we use a natural population of the Seychelles warbler (Acrocephalus sechellensis) to assess the effects of MHC genes on GM taxonomy and functionality using shotgun metagenomics.<br><br>RESULTS: Our results show that taxonomic GM composition was associated with MHC-II diversity and the presence of one specific MHC-I allele (Ase-ua 7). Specifically, MHC-II diversity was associated with decreased Lactococcus lactis and increased Staphylococcus lloydii abundance, while Ase-ua 7 was linked to reduced Enterococcus casselifavus and Gordonia sp OPL2 but increased Escherichia coli and Vulcaniibacterium thermophilum. These taxonomic changes may reflect differences in MHC-mediated microbial recognition. In contrast, functional GM composition was significantly associated with increasing individual MHC-I diversity but not MHC-II diversity. In particular, increasing MHC-I diversity was associated with an increased prevalence of microbial defence genes but a reduced prevalence of microbial metabolism genes. Analysis also revealed that functional GM networks were more fragmented in high compared to low MHC-I diversity hosts.<br><br>CONCLUSION: These results suggest that MHC variation (particularly at MHC-I) plays an important role in shaping both the taxonomy and function of the GM in wild vertebrates. In the Seychelles warbler, this results in trade-offs whereby there is an increase in microbial defence and a reduction in GM metabolic potential in individuals with higher MHC-I diversity. Thus, this work sheds light on the possible costs and benefits of maintaining a healthy microbiome, which is essential for understanding how the GM and immune system co-evolve. Video Abstract.},
}
@article {pmid41813975,
year = {2026},
author = {Telles-de-Deus, J and Claro, IM and Bertanhe, M and Whittaker, C and Port-Carvalho, M and Rocha, EC and Coletti, TM and da Silva, CAM and Valença, IN and Lima-Camara, TN and Bicudo de Paula, M and Cunha, MS and de Jesus, JG and Dos Santos Andrade, P and Cox, V and de Azevedo, NCCF and Guerra, JM and Summa, JL and Teixeira, APP and Bergo, ES and Pereira, M and Moreira, FRR and Felix, AC and de Paula, AV and de Araujo Eliodoro, RH and da Silva Lima, M and de Oliveira, FM and de Souza, VR and Franco, LAM and Nardi, MS and Sanches, TC and da Silva, ETBC and Coimbra, AAC and Dos Santos, PR and Lima de Gouveia, K and Vilela, FESP and Hill, SC and Oliveira, DAG and Piedade, HM and Guimarães-Luiz, T and Abreu, CMG and Casoni da Rocha, G and Abade, L and de Souza, WM and Lambert, B and Pereira de Souza, R and Pinter, A and Sabino, EC and Mucci, LF and Faria, NR},
title = {Evolution and spillover dynamics of yellow fever at the forest-urban interface in Brazil.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41813975},
issn = {2058-5276},
support = {316633/Z/24/Z//Wellcome Trust (Wellcome)/ ; 226075/Z/22/Z//Wellcome Trust (Wellcome)/ ; 226075/Z/22/Z//Wellcome Trust (Wellcome)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/X020258/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; MR/S0195/1//RCUK | Medical Research Council (MRC)/ ; },
abstract = {Yellow fever virus (YFV) continues to threaten human and wildlife populations in the Americas, yet its transmission at the forest-urban interface remains unclear. Here we integrate ground- and canopy-level mosquito surveillance, systematic monitoring of non-human primate carcasses and viral metagenomics to describe the dynamics of a sylvatic YFV outbreak in a 186-hectare Atlantic Forest fragment embedded within metropolitan São Paulo, Brazil, between 2017 and 2018. Our analyses reveal that transmission was primarily driven by a single genetic cluster introduced during a period of high abundance of the main vector, Haemagogus leucocelaenus mosquitoes. A near-complete hepatitis A virus genome was detected in a YFV-infected howler monkey, suggesting potential co-infections at the human-wildlife interface. Phylogenetic and epidemiological modelling estimated a basic reproduction number, R0, for sylvatic yellow fever of 8.2 (95% CI 5.1-12.2), substantially higher than previous estimates for urban outbreaks. Our findings demonstrate that multisource surveillance could provide actionable early warnings in regions at risk for zoonotic spillover.},
}
@article {pmid41811805,
year = {2026},
author = {Vilkoite, I and Silamiķelis, I and Kloviņš, J and Tolmanis, I and Lejnieks, A and Runce, E and Cēbere, K and Margole, K and Sjomina, O and Silamiķele, L},
title = {Colorectal adenoma presence is associated with decreased menaquinone pathway functions in the gut microbiome of patients undergoing routine colonoscopy.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344050},
pmid = {41811805},
issn = {1932-6203},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/pathology ; *Adenoma/microbiology/metabolism/pathology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Colonoscopy ; Case-Control Studies ; Aged ; *Vitamin K 2/metabolism ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: Colorectal adenomas are key precancerous lesions and a major target for colorectal cancer prevention. While gut microbiome alterations are well described in colorectal cancer, microbial composition and functional capacity at the adenoma stage remain poorly understood. Emerging metagenomic data suggest early adenomas are associated with loss of microbial metabolic functions supporting epithelial and immune homeostasis.<br><br>OBJECTIVES: To investigate the association between gut microbiome composition and functional pathways and the presence of colorectal adenomas in patients undergoing routine colonoscopy.<br><br>MATERIALS AND METHODS: This cross-sectional case-control study included adult patients undergoing routine colonoscopy. Participants were enrolled based on strict inclusion and exclusion criteria to minimize confounding factors such as inflammatory bowel disease, prior colorectal surgery, and recent antibiotic or probiotic use. Fecal samples were collected prior to bowel preparation, and gut microbiome taxonomic composition and functional pathways were analyzed using shotgun metagenomic sequencing.<br><br>RESULTS: A total of 136 participants were included, of whom 56 had colorectal adenomas. Alpha diversity indices did not differ significantly between adenoma-positive and adenoma-negative groups. In contrast, beta diversity analysis revealed significant differences in overall microbial community structure. Descriptive genus-level differences suggested features of dysbiosis in adenoma-positive patients, including higher relative abundance of Bacteroides and Prevotella and lower abundance of Faecalibacterium and Anaerostipes. Differential abundance analysis identified a single species-level feature, UBA7597 sp003448195, enriched in the adenoma group. Functional profiling showed reduced microbial pathways related to menaquinone (vitamin K&#x2082;) biosynthesis, Stickland fermentation, and short-chain fatty acid (propionate) production in patients with adenomas.<br><br>CONCLUSIONS: The presence of colorectal adenomas was associated with reduced microbial metabolic functions linked to vitamin K&#x2082; biosynthesis, amino acid fermentation, and propionate production, alongside compositional shifts toward a less functionally robust gut microbiome. These findings indicate that early colorectal neoplasia is accompanied by functional microbiome alterations that may serve as markers of adenoma-associated dysbiosis and provide insight into early metabolic changes in the colonic microenvironment.},
}
@article {pmid41811526,
year = {2026},
author = {Tammi, R and Maukonen, M and Kaartinen, NE and Koponen, K and Niiranen, T and Méric, G and Albanes, D and Eriksson, JG and Jousilahti, P and Koskinen, S and Pajari, AM and Knight, R and Havulinna, AS and Salomaa, V and Männistö, S},
title = {Interplay between colorectal cancer-related lifestyles and the gut microbiome: an exploratory analysis of metagenomic data.},
journal = {Cancer causes &amp; control : CCC},
volume = {37},
number = {4},
pages = {},
pmid = {41811526},
issn = {1573-7225},
support = {352481//Strategic Research Council/ ; 352483//Strategic Research Council/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology/etiology ; Middle Aged ; *Life Style ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Adult ; Metagenomics/methods ; Risk Factors ; Finland/epidemiology ; Metagenome ; Diet ; },
abstract = {PURPOSE: The gut microbiome may modify the associations between lifestyle factors and colorectal cancer (CRC) risk, but their complex interplay, including the interactions between lifestyle factors, remain underexplored. We examined associations between CRC-related lifestyle patterns and gut microbiome diversity and composition in Finnish adults.<br><br>METHODS: Our data included 1,228 adults aged 25-64&#xa0;years from the National FINRISK/FINDIET 2002 Study. Information on lifestyle and background factors was obtained through self-administered questionnaires. Dietary data were gathered using a 48-h dietary recall. CRC-related lifestyles were modelled using a CRC lifestyle index based on nine major risk factors for CRC. Lower index points reflected higher-risk lifestyles. The gut microbiome profiles were analyzed using shallow shotgun metagenome sequencing. Associations between the index and microbial diversity and composition were assessed using, e.g., linear regression and permutational multivariate ANOVA adjusted for relevant confounders.<br><br>RESULTS: The index explained 0.2% of the variation in microbial composition between participants (p&#x2009;<&#x2009;0.05). Higher-risk lifestyles for CRC were associated with lower microbial diversity (&#x3b2; 0.037, p 0.009). Higher-risk lifestyles were also associated with a higher relative abundance of species representing primarily the family Lachnospiraceae and genera such as Dorea and Mediterraneibacter, and lower relative abundance of species within the genus Bifidobacterium (<&#x2009;0.0001).<br><br>CONCLUSIONS: Participants with higher- and lower-risk lifestyles showed clear differences in their gut microbiome diversity and composition, higher-risk lifestyles being associated with potentially adverse microbial traits. These findings contribute to identifying microbial features that may characterize early stages of CRC development in individuals with high-risk lifestyles.},
}
@article {pmid41810553,
year = {2026},
author = {Boscá-Sánchez, I and Rodríguez-Díaz, J and Yebra, MJ},
title = {Sequence-Based and Functional Analysis for the Discovery of N-Glycan Degrading Glycosidases From the Microbial Metagenome of the Infant Gut.},
journal = {MicrobiologyOpen},
volume = {15},
number = {2},
pages = {e70264},
pmid = {41810553},
issn = {2045-8827},
support = {PID2023-148094OB (C21 and C22)//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {Humans ; *Glycoside Hydrolases/metabolism/genetics ; *Polysaccharides/metabolism ; Infant ; *Gastrointestinal Microbiome ; *Metagenome ; Feces/microbiology ; Substrate Specificity ; Infant, Newborn ; },
abstract = {The role of bacterial glycosyl hydrolases (GHs) in degrading free human milk oligosaccharides is well documented. However, their activity on glycoconjugates is less well known. Here, an in silico analysis of the metagenome of the fecal microbiome of breastfed infants was employed to identify GH2 β-galactosidases, GH20 exo-N-acetylglucosaminidases and GH18 endo-N-acetylglucosaminidases active on N-glycans. A total of nine β-galactosidases were recombinantly expressed and two of them, Gal1b and Gal99, were able to remove galactose from the G2 peptide and asialofetuin. Gal1b, Gal25, Gal37c, Gal99 and Gal296 hydrolyzed lactose and N-acetyllactosamine, indicating specificity for galactose β1,4-linked to glucose or GlcNAc. All of the exo-β-N-acetylglucosaminidases studied here (Exo10a, Exo18, Exo38, Exo39b, Exo360 and Exo399) hydrolyzed the disaccharide N-acetylglucosaminyl-β1,2-mannose, which forms part of the N-glycan structures. Exo10a, Exo38 and Exo360 hydrolyzed N-acetylglucosamine (GlcNAc) from the G2 peptide pretreated with Gal1b. Notably, Exo360 hydrolyzed GlcNAc at both the α1,3 and α1,6 branches of the G2 peptide core mannose simultaneously, whereas Exo10a showed a preference for GlcNAc at one branch. Exo38 and Exo360 also release GlcNAc from asialofetuin once galactose has been removed. The whole structures of N-glycans were liberated from glycoproteins by the action of the endo-N-acetylglucosaminidases Endo38 and Endo358. These enzymes hydrolyze the N,N'-diacetylchitobiose core of N-linked glycans of the high-mannose and non-sialylated complex types, respectively. Overall, these results provide insight into the range of glycosyl hydrolases present in the infant gut microbiota that act on glycoconjugates, which may play a role in the establishment and composition of the newborn microbiota.},
}
@article {pmid41759320,
year = {2026},
author = {Yin, Y and Wu, H and French, CE and Lu, Z},
title = {Triclosan induced restructuring of microbial communities and antibiotic resistance gene dynamics in activated sludge: insights and mitigation strategies.},
journal = {Water research},
volume = {296},
number = {},
pages = {125614},
doi = {10.1016/j.watres.2026.125614},
pmid = {41759320},
issn = {1879-2448},
mesh = {*Triclosan/pharmacology ; *Sewage/microbiology ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; RNA, Ribosomal, 16S/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics ; },
abstract = {The widespread presence of emerging contaminants, such as triclosan (TCS), in environmental systems raises significant concerns regarding their ecological risks, particularly the propagation of antibiotic resistance genes (ARGs). In this study, sequencing batch reactors (SBRs) were exposed to a TCS concentration gradient to simulate the accumulation of TCS in activated sludge and to elucidate its effects on microbial community structure, ARG dissemination, and horizontal gene transfer (HGT). Using a multi-omics approach that integrated 16S rRNA amplicon sequencing, short- and long-read metagenomics, and genome-scale metabolic modeling, we demonstrated that increasing TCS concentrations progressively reduced microbial diversity and stability. At lower TCS concentrations (0-1.0 mg/L), ARG-carrying bacteria were enriched, whereas at higher concentrations (10 mg/L), TCS eliminated ARG-carrying bacteria and selected for strains rich in mobile genetic element (MGE). Notably, HGT led to genome expansion of Acidomonas methanolica (from 3.75 Mb to 7.13 Mb), disrupting the microbial interaction networks within the community. Additionally, the introduction of a triclosan-degrading hydrogel-magnetic biochar-engineered strain composite mitigated the destabilizing effects of TCS stress on the microbial community, enhanced its resilience, and facilitated TCS degradation, thus reducing associated environmental risks. Our findings highlight how gradient TCS exposure reshapes microbial communities, promotes the dominance of MGE-enriched taxa, and has profound implications for the ecological and evolutionary dynamics of microbial communities in aquatic ecosystems. This study provides novel insights into the role of emerging contaminants in the propagation of resistance and microbial adaptation.},
}
@article {pmid41747725,
year = {2026},
author = {Chen, K and Liu, Y and Rong, J and Dai, N and Xu, C and Li, H and Zhong, L and Wang, B and Ji, Z and Xie, S and Xu, Y and Yang, F and Wang, J and Li, D and Gu, Y and Zhou, X and Li, Y and Chen, M and Chen, Y and Li, W and Tang, Z and Cai, J and Xu, J and Xia, S and Zhan, Q and Zhou, Z},
title = {Strain-level genetic heterogeneity and colonization dynamics drive microbiome therapeutic efficacy.},
journal = {Cell host &amp; microbe},
volume = {34},
number = {3},
pages = {393-405.e5},
doi = {10.1016/j.chom.2026.02.002},
pmid = {41747725},
issn = {1934-6069},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Genetic Heterogeneity ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology ; *Lung Neoplasms/therapy/microbiology ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Metagenome ; Female ; Bacteria/classification/genetics ; Male ; Phylogeny ; Treatment Outcome ; },
abstract = {Fecal microbiota transplantation (FMT) has shown immunotherapeutic promise, yet its efficacy in non-small-cell lung cancer (NSCLC) remains unclear. We demonstrate that FMT improves anti-PD-1 efficacy and progression-free survival in a single-arm trial of advanced PD-L1-negative NSCLC. Analyzing over 2,000 metagenomes from diverse disease cohorts and healthy controls via a high-resolution strain-tracking framework, we reveal that phylogenetically distinct strains within identical species exert opposing therapeutic effects, resolving prior inconsistencies. We identify conserved ecological principles where engraftment relies on species-intrinsic metabolic and immune evasion traits. Crucially, successful colonization by specific beneficial strain variants correlates with positive clinical outcomes. Finally, we identify 38 priority species with robust engraftment potential and significant heterogeneity as candidates for precision therapeutics. These findings establish a strain-function-efficacy paradigm, elucidating the mechanistic basis of variable outcomes and guiding next-generation microbiome drug development.},
}
@article {pmid41720032,
year = {2026},
author = {Kong, X and He, Y and Guo, J and Chen, Y and An, D},
title = {Chain-length-associated response patterns of chlorinated paraffins on activated sludge systems driven by microbial community response.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141542},
doi = {10.1016/j.jhazmat.2026.141542},
pmid = {41720032},
issn = {1873-3336},
mesh = {*Sewage/microbiology/chemistry ; *Water Pollutants, Chemical/chemistry/toxicity ; *Microbiota/drug effects ; *Paraffin/chemistry/toxicity ; Bioreactors/microbiology ; Nitrogen/metabolism ; Phosphorus/metabolism ; Bacteria/genetics/drug effects/metabolism ; *Hydrocarbons, Chlorinated/chemistry/toxicity ; },
abstract = {Chlorinated paraffins (CPs) are emerging contaminants detected in wastewater treatment plants, yet their impacts on activated sludge systems remain poorly understood. In this study, parallel sequencing batch reactors were employed to comprehensively evaluate the effects of short-chain (SCCP), medium-chain (MCCP), and long-chain (LCCP) CPs on pollutant removal performance, sludge properties, and microbial ecological responses. Under the tested nominal loading, the C24-LCCP standard led to a clear reduction in nitrogen removal efficiency, whereas MCCP and SCCP maintained stable or even enhanced phosphorus removal performance. CP exposure generally increased oxidative stress and cytotoxicity, while SCCP and MCCP further stimulated extracellular polymeric substances secretion, consistent with an enhanced floc/cell-interface protective phenotype. Metagenomic analysis revealed that SCCP and MCCP enriched genera (Acinetobacter, Dechloromonas, Zoogloea) associated with phosphorus removal and increased the abundance of key nitrogen transformation genes, whereas the C24-LCCP standard exhibited comparatively weaker shifts in functional gene profiles. Metatranscriptomic profiling indicated treatment-associated differences in transcriptional responses under the tested nominal loading, with SCCP showing the largest DEG set (>30,000 genes) in this dataset. Integrated metagenomic and metatranscriptomic analyses revealed a coordinated stress‑response program under SCCP, characterized by activation of efflux pumps, DNA repair, redox regulation, environmental stress responses, and biofilm-associated functions, together with elevated energy metabolism and ABC transporter signals. These molecular and community-level patterns aligned with the observed variations in treatment performance and sludge properties, providing convergent evidence for a chain-length-associated response framework. These findings provide comparative molecular and phenotypic evidence that may inform future risk assessment and hypothesis-driven mitigation studies on CP impacts in biological wastewater treatment systems.},
}
@article {pmid41707391,
year = {2026},
author = {Werid, GM and Hemmatzadeh, F and Batterham, T and Miller, D and Edwards, R and Trott, DJ and Petrovski, K},
title = {Metagenomic and metatranscriptomic analyses reveal microbial dysbiosis and bacteria-virus interactions in the lungs of Australian feedlot cattle with bovine respiratory disease.},
journal = {Veterinary microbiology},
volume = {315},
number = {},
pages = {110926},
doi = {10.1016/j.vetmic.2026.110926},
pmid = {41707391},
issn = {1873-2542},
mesh = {Animals ; Cattle ; *Lung/microbiology/virology ; *Cattle Diseases/microbiology/virology ; Metagenomics ; *Dysbiosis/veterinary/microbiology/virology ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Virome ; Microbiota ; Australia ; *Bovine Respiratory Disease Complex/microbiology/virology ; Bacteriophages/genetics ; },
abstract = {Bovine respiratory disease (BRD) remains the leading cause of feedlot cattle morbidity and mortality. Despite its polymicrobial aetiology, microbial population structure and inter-pathogen dynamics within the lungs of cattle with BRD remain poorly understood. To characterise the lung microbiome and virome of feedlot cattle with (n = 23) and without BRD (n = 9), we applied RNA-sequencing and full-length 16S rRNA gene sequencing to bovine lung tissue samples collected at post-mortem. Host-depleted RNA-seq reads were assembled and profiled, bacterial communities were classified, and diversity, differential abundance, bacteria-virus correlations, co-occurrence networks, and phage-host links analysed. Lung samples from BRD- cattle revealed pathogen-dominated communities with reduced within-sample diversity. Metamycoplasmataceae/Mycoplasmataceae, and Pasteurellaceae accounted for approximately 65.3 % of the bacterial population in samples from cattle with BRD, compared to approximately 11.3 % in lung samples from non-BRD cattle. At the species level, a significantly increased abundance of Pasteurella multocida was observed in BRD cattle. The virome was bacteriophage-dominated in both groups (led by Peduoviridae) but revealed distinct BRD-associated changes. Strong correlation between bacterial genomic abundance and transcriptional activity was observed in cattle with BRD, particularly for Mycoplasmopsis bovis, P. multocida, and Trueperella pyogenes. Network analyses consistently identified M. bovis, P. multocida, and Histophilus somni as highly connected hubs, whereas phages predicted to infect BRD-associated bacteria and Pestivirus bovis were more prevalent and/or abundant in lung samples from BRD cattle. Overall, BRD is characterised by a shift to low-diversity, pathogen-centred bacterial communities within a phage-rich virome that includes enrichment of bacterial pathogen-associated phages. These findings provide a basis for microbiome-informed, multi-pathogen diagnostics and help prioritise surveillance and control strategies that can be included into feedlot BRD management programmes to reduce antimicrobial use, animal losses, and economic impacts.},
}
@article {pmid41697021,
year = {2025},
author = {Han, B and Wen, H and Li, Y and Wang, Y and Lv, X and Kang, M and Huang, W and Lan, Y and Tong, S and Zhang, M and Chen, D and Zhu, C and Jiang, Y and Tang, D},
title = {Gut microbial production of lithocholic acid reprograms pro-resolutive macrophages to enhance vedolizumab responsiveness via the TGR5/FXR-NF-κB axis.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag028},
pmid = {41697021},
issn = {1751-7370},
support = {LHGJ20250299//Henan Provincial Medical Science and Technology Research Joint Venture Project/ ; 2025M772035//China Postdoctoral Science Foundation/ ; 82460108//National Natural Science Foundation of China/ ; 2023GXNSFAA026135//Guangxi Natural Science Foundation/ ; 2025GXNSFDA069030//Key Project of Guangxi Natural Science Foundation/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Lithocholic Acid/metabolism ; Mice ; *Receptors, G-Protein-Coupled/metabolism/genetics ; NF-kappa B/metabolism/genetics ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Macrophages/metabolism/drug effects ; Humans ; Disease Models, Animal ; *Crohn Disease/drug therapy ; Fecal Microbiota Transplantation ; Colitis/drug therapy/chemically induced ; *Gastrointestinal Agents/therapeutic use/pharmacology ; Signal Transduction ; Metabolomics ; },
abstract = {Crohn's disease (CD) is a complex chronic transmural inflammatory bowel disease. Although vedolizumab (VDZ) markedly improves clinical outcomes in CD, treatment non-response remains a significant limitation, constraining its broader utility. Elucidating the mechanisms underlying VDZ responsiveness is thus critically needed. In this research, we employed a humanized mouse model of 2,4,6-trinitrobenzene sulfonic acid-induced colitis to investigate VDZ treatment response in CD. Our findings indicate that VDZ significantly alleviated disease phenotypes in a portion of CD mice. Integrated metagenomic and metabolomic profiling identified baseline gut microbiota-derived secondary bile acids as potential predictors of VDZ efficacy. Subsequent fecal microbiota transplantation from clinical donors into pseudo-germ-free mice confirmed that gut microbial composition critically influences VDZ responsiveness. Targeted metabolomics further pinpointed lithocholic acid (LCA) as a key microbially derived metabolite correlated with therapeutic remission. Single-cell RNA sequencing also revealed that intestinal macrophages serve as pivotal mediators of LCA-driven modulation of treatment outcomes. Furthermore, transcriptomic analyses demonstrated that LCA polarizes macrophages toward an M2-resolutive phenotype via concurrent engagement of the TGR5/FXR and their downstream nuclear factor kappa-B (NF-κB) pathways. Ultimately, using a conditioned medium co-culture system, we established that the regulatory effects of pro-resolutive macrophage niche on treatment response in a manner dependent on the TGR5/FXR-NF-κB axis. Taken together, our study elucidates a microbiota-immune circuit in which gut microbial metabolite LCA augments VDZ responsiveness in CD by reprogramming macrophages toward a pro-resolutive phenotype via the TGR5/FXR-NF-κB signaling network. These insights provide a mechanistic foundation for biomarker development and personalized therapeutic strategies in inflammatory bowel disease.},
}
@article {pmid41666920,
year = {2026},
author = {da Silva, AC and Lapkin, J and Yin, Q and Muller, E and Almeida, A},
title = {Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health.},
journal = {Cell host &amp; microbe},
volume = {34},
number = {3},
pages = {379-392.e5},
doi = {10.1016/j.chom.2026.01.013},
pmid = {41666920},
issn = {1934-6069},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Bacteria/classification/genetics/isolation &amp; purification ; Vitamin B 12/biosynthesis ; Metagenomics ; },
abstract = {The human gut microbiome is important for host health, yet over 60% of gut species remain uncultured and inaccessible to experimental manipulation. Here, we analyze 11,115 human gut metagenomes from 39 countries, 13 noncommunicable diseases, and healthy individuals to understand the clinical relevance of the uncultured microbiome worldwide. We identify 317 species linked to distinct clinical states, noting an overrepresentation of uncultured bacteria in healthy subjects. The genus CAG-170 emerged as the strongest health-associated lineage across multiple diseases and geographies, standing as the most central taxon based on ecological networks of healthy populations. We find that CAG-170 is temporally stable, with its abundance and subspecies diversity negatively correlated with gut imbalance over time. Functional predictions show CAG-170 species have greater vitamin B12 biosynthesis capacity and cross-feeding potential, providing important biological insights into this elusive genus. Our findings shed light on the underexplored role of uncultured gut species in health and disease.},
}
@article {pmid41633028,
year = {2026},
author = {Xue, L and Zhao, W and Wang, C and Ma, Y and Tian, J and Yang, L and Ma, L and Jiang, Q and Chen, Y and Tian, X and Ji, X and Zhang, J and Gu, Y},
title = {Integrating multi-omics to characterize the dynamics of rumen microorganisms and metabolites in Angus cattle at different growth stages.},
journal = {Research in veterinary science},
volume = {203},
number = {},
pages = {106092},
doi = {10.1016/j.rvsc.2026.106092},
pmid = {41633028},
issn = {1532-2661},
mesh = {Animals ; Cattle/growth &amp; development/microbiology/metabolism ; *Rumen/microbiology/metabolism ; Male ; Metabolomics ; *Gastrointestinal Microbiome ; Metagenomics ; *Metabolome ; *Microbiota ; Multiomics ; },
abstract = {The development of the bovine rumen microbiome is crucial for growth, yet the dynamic interactions between the microbiome and metabolome during key growth stages remain poorly understood. This study aims to integrate metagenomics and metabolomics approaches to decipher the stage-specific patterns of rumen microbial community and metabolite changes in castrated Angus cattle at three critical growth stages (6, 12, and 18 months of age), and to elucidate their associations with host growth performance. We collected rumen fluid samples from 24 Angus steers (8 per age group) reared under standardized conditions and performed metagenomic and non-targeted metabolomic analyses. Integrated analysis revealed distinct rumen ecosystem succession patterns: multiple species represented by Prevotella_sp._ne3005 dominated at 6 months, Fibrobacter_succinogenes showed significantly increased abundance at 12 months, and Methanobrevibacter_millerae exhibited the most pronounced enrichment at 18 months. Concurrently, key metabolites 12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol exhibited a significant positive correlation with age. Further Pearson correlation analysis revealed strong correlations between the 18-month-enriched characteristic microorganism Methanobrevibacter_millerae and key metabolites (12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol) as well as higher body weight. This study delineates a dynamic map of synergistic interactions between the rumen microbiome and metabolome, confirming their close association with host growth performance. This work provides a systematic multi-omics framework for understanding rumen development in ruminants and identifies potential targets for optimizing beef cattle production performance through microbial or metabolic interventions.},
}
@article {pmid40757465,
year = {2026},
author = {Andréasson, K and Young, A and Joshi, S and Labus, JS and Low, AHL and Smith, V and McMahan, Z and Proudman, S and Valenzuela, A and Hunter, P and Kim, GH and Bozovic, G and Goldin, J and Aja, E and Jacobs, JP and Volkmann, ER},
title = {International Investigation of the Gut-Lung Axis in Systemic Sclerosis-Interstitial Lung Disease.},
journal = {Arthritis care &amp; research},
volume = {78},
number = {3},
pages = {352-361},
doi = {10.1002/acr.25623},
pmid = {40757465},
issn = {2151-4658},
support = {K23 HL150237/HL/NHLBI NIH HHS/United States ; //Ulla och Roland Gustafssons Donationsfond, Alfred &#xd6;sterlunds Stiftelse and Anna-Greta Crafoords Stiftelse/ ; //Boehringer Ingelheim/ ; //Anonymous Patient Donation/ ; K23 HL150237/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Scleroderma, Systemic/microbiology/complications/diagnosis ; *Lung Diseases, Interstitial/microbiology/diagnostic imaging/etiology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; *Lung/diagnostic imaging/microbiology ; Feces/microbiology ; Dysbiosis ; *Bacteria/genetics/classification ; Adult ; Severity of Illness Index ; },
abstract = {OBJECTIVE: Mounting evidence supports an association between the intestinal microbiota and diverse pulmonary pathologies (ie, gut-lung axis). Although intestinal dysbiosis is a feature of systemic sclerosis (SSc), no prior studies have investigated the relationship between intestinal microbiota and SSc-associated interstitial lung disease (ILD) in a multinational cohort. This study aimed to characterize the intestinal microbiota of SSc-ILD and determine whether specific bacterial species and functional pathways are associated with ILD severity.<br><br>METHODS: Patients with SSc with and without ILD from seven SSc Centers across five continents provided a stool sample. Shotgun metagenomic sequencing was performed using the Illumina NovaSeq 6000 to characterize microbial composition at the species level. Quantitative image analysis of high-resolution computed tomography scans of the chest was used to measure radiologic extent of ILD (QILD). Multivariate sparse partial least squares analyses were employed to identify a species signature of ILD and to determine whether specific species and functional pathways are associated with QILD.<br><br>RESULTS: Among 285 participants (mean disease duration of 9.8 years), 62.5% had ILD. In a multivariate analysis of all participants, patients with ILD had a unique microbial signature compared to those without ILD characterized by increased abundance of candidate pathobiont species. In a subgroup of participants with SSc-ILD (n = 103), specific bacterial species and functional pathways were associated with QILD.<br><br>CONCLUSION: This multicenter study demonstrates that distinct intestinal bacterial species are linked to the presence and radiologic extent of ILD in SSc. These species and/or their metabolic products may influence ILD pathogenesis and represent novel treatment targets.},
}
@article {pmid37329328,
year = {2023},
author = {Lledós, M and Prats-Sánchez, L and Llucià-Carol, L and Cárcel-Márquez, J and Muiño, E and Cullell, N and Gallego-Fabrega, C and Martín-Campos, JM and Aguilera-Simón, A and Guasch-Jiménez, M and Guisado-Alonso, D and Ramos-Pachón, A and Martínez-Domeño, A and Izquierdo, A and Marín, R and Camps-Renom, P and Martí-Fàbregas, J and Fernández-Cadenas, I},
title = {Ischaemic stroke patients present sex differences in gut microbiota.},
journal = {European journal of neurology},
volume = {30},
number = {11},
pages = {3497-3506},
doi = {10.1111/ene.15931},
pmid = {37329328},
issn = {1468-1331},
support = {//Centres de Recerca de Catalunya/ ; //ERA-NET NEURON/ ; //European Regional Development Fund/ ; //Instituto de Salud Carlos III/ ; //NextGeneration EU/ ; //RICORS-ICTUS/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Ischemic Stroke/microbiology/genetics ; Middle Aged ; Aged ; *Sex Characteristics ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; },
abstract = {BACKGROUND: Gut microbiota plays a role in the pathophysiology of ischaemic stroke (IS) through the bidirectional gut-brain axis. Nevertheless, little is known about sex-specific microbiota signatures in IS occurrence.<br><br>METHODS: A total of 89 IS patients and 12 healthy controls were enrolled. We studied the taxonomic differences of the gut microbiota between men and women with IS by shotgun metagenomic sequencing. To evaluate the causal effect of several bacteria on IS risk, we performed a two-sample Mendelian randomisation (MR) with inverse-variance weighting (IVW) using genome-wide association analysis (GWAS) summary statistics from two cohorts of 5959 subjects with genetic and microbiota data and 1,296,908 subjects with genetic and IS data, respectively.<br><br>RESULTS: &#x3b1;-Diversity analysis measured using Observed Species (p&#x2009;=&#x2009;0.017), Chao1 (p&#x2009;=&#x2009;0.009) and Abundance-based Coverage Estimator (p&#x2009;=&#x2009;0.012) indexes revealed that IS men have a higher species richness compared with IS women. Moreover, we found sex-differences in IS patients in relation to the phylum Fusobacteria, class Fusobacteriia, order Fusobacteriales and family Fusobacteriaceae (all Bonferroni-corrected p&#x2009;<&#x2009;0.001). MR confirmed that increased Fusobacteriaceae levels in the gut are causally associated with an increased risk of IS (IVW p&#x2009;=&#x2009;0.02, &#x3b2;&#x2009;=&#x2009;0.32).<br><br>CONCLUSIONS: Our study is the first to indicate that there are gut microbiome differences between men and women with IS, identifying high levels of Fusobacteriaceae in women as a specific risk factor for IS. Incorporating sex stratification analysis is important in the design, analysis and interpretation of studies on stroke and the gut microbiota.},
}
@article {pmid41809656,
year = {2026},
author = {Burakova, I and Smirnova, Y and Morozova, P and Pogorelova, S and Kryukova, O and Kislova, T and Korneeva, O and Syromyatnikov, M},
title = {The effect of short-term consumption of Bifidobacterium bifidum on the gut microbiome of obese individuals.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {251},
number = {},
pages = {10894},
pmid = {41809656},
issn = {1535-3699},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Obesity/microbiology ; *Probiotics/administration &amp; dosage/therapeutic use ; *Bifidobacterium bifidum/physiology ; Male ; Female ; Adult ; Middle Aged ; Dysbiosis/microbiology ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {It is known that gut microbiota dysbiosis can lead to obesity by disrupting energy consumption and metabolism. Probiotic supplements are a potential therapeutic option for improving intestinal homeostasis. The aim of this study was to investigate the effect of a probiotic supplement containing Bifidobacterium bifidum on the intestinal microbiome of people with obesity using high-throughput sequencing on the DNBSEQ-G50 platform. The study demonstrated a positive effect of the supplement on bacterial species such as Bacteroides uniformis, Alistipes putredinis, Alistipes shahii, Dysosmobacter welbionis, and Gemmiger formicilis. Therefore, we suggest the potential use of this bacterial species in the treatment of gut microbiota dysbiosis of obese individuals.},
}
@article {pmid41808525,
year = {2026},
author = {Jiménez, DJ and Rosado, AS},
title = {Discovering PETases: An Interlink Between Engineering Enzymes and Microbiomes.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70272},
doi = {10.1111/1462-2920.70272},
pmid = {41808525},
issn = {1462-2920},
support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {*Microbiota ; *Polyethylene Terephthalates/metabolism ; *Hydrolases/metabolism/genetics ; Metagenomics ; Biocatalysis ; *Bacteria/enzymology/genetics ; },
abstract = {Polyethylene terephthalate (PET), an abundant synthetic polyester, is the only plastic that has been enzymatically recycled at an industrial scale. Over the last decades, research efforts have focused on screening and engineering PET-degrading hydrolases (PETases), aiming to identify variants that can operate efficiently in both environmental and industrial settings. The detection of potential PETases from marine and terrestrial ecosystems has primarily been conducted via metagenomics using homology strategies. However, the use of benchmark PETases as references has limited the searches, narrowing the sequence landscape. Currently, there remains a need to identify efficient thermophilic, halotolerant and pH-robust PETases for the industrial biocatalysis of PET. In line with this, in this article, we discuss recent findings related to the following topics: (i) the identification of suitable ecosystems for mining PETases; (ii) the discovery of PETases via the restructuring of microbiomes; (iii) advancements in metagenomics and artificial intelligence (AI)-based approaches for the detection and ranking of PETases and (iv) the future of PET biocatalysis. Overall, we suggest that disrupting microbiomes with polyester-rich substrates, combined with innovative computational and AI-based strategies, can be an effective pathway for the discovery of PETases that can be used as scaffolds for protein engineering and biotechnological applications.},
}
@article {pmid41738431,
year = {2026},
author = {Khade, K and Dadachanji, R and Bhonde, G and Patil, A and Bhor, VM and Mukherjee, S},
title = {Gut microbiota dysbiosis in Indian women with PCOS may be linked to metabolic and hormonal dysregulation.},
journal = {Future microbiology},
volume = {21},
number = {2},
pages = {153-165},
doi = {10.1080/17460913.2026.2634572},
pmid = {41738431},
issn = {1746-0921},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; *Polycystic Ovary Syndrome/microbiology/metabolism ; *Dysbiosis/microbiology/metabolism ; Adult ; India ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Fatty Acids, Volatile/metabolism/analysis ; Feces/microbiology/chemistry ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Protein Precursors ; Hyperandrogenism/microbiology/metabolism ; Sex Hormone-Binding Globulin/metabolism ; Haptoglobins ; },
abstract = {AIM: Polycystic ovary syndrome (PCOS) is a common gynecological and cardiometabolic disorder in reproductive-aged women. Recently gut microbiota alterations have been identified as key contributors to PCOS pathophysiology, but it remains understudied in Indian population.<br><br>METHODS: 16S rRNA gene amplicon sequencing using Illumina-MiSeq platform was conducted in 57 PCOS and 30 control women. Diversity indices were assessed and significantly altered taxa were identified by differential abundance tests (Wilcoxon-rank-sum test, ANCOMBC2 and LEfSe) in total and hyperandrogenism-based PCOS subgroups. We quantified levels of short-chain fatty acids (SCFAs) and gut barrier integrity marker, zonulin and LPS by HPLC and ELISA respectively.<br><br>RESULTS: Our study showed significantly altered beta diversity between PCOS and control groups, driven by hyperandrogenism. PCOS women demonstrate enrichment of Ligilactobacillus species, not previously reported to our knowledge, along with Collinsella species and markedly reduced SCFA-producing taxa, Oscillospiraceae. Additionally, levels of zonulin and fecal butyric acid, a potent SCFA, were significantly altered in PCOS women. Significantly altered taxa correlated with gonadotropin and SHBG levels and were involved in important metabolic pathways in total and PCOS subgroups.<br><br>CONCLUSION: Our study offers new insights into the mapping of gut microbiota in PCOS women from western India and implicates hyperandrogenism in driving dysbiosis.},
}
@article {pmid41713270,
year = {2026},
author = {Jiao, X and Ji, W and Zhang, X and Zhang, S and Dolfing, J and Yang, K and Xie, B and Zhang, Y and Feng, J and Wu, D},
title = {Microcystins 'steer' antibiotic resistome dynamics by synergetic metabolism and horizontal gene transfer in a megacity's water supply catchment microbiota.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141525},
doi = {10.1016/j.jhazmat.2026.141525},
pmid = {41713270},
issn = {1873-3336},
mesh = {*Gene Transfer, Horizontal ; *Microcystins/metabolism ; *Microbiota ; China ; *Microcystis/genetics/metabolism/growth &amp; development ; *Drug Resistance, Microbial/genetics ; Water Supply ; Water Microbiology ; Drinking Water/microbiology ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; },
abstract = {The proliferation of Microcystis has been linked to the widespread occurrence of antibiotic resistance genes (ARGs). Yet, the underlying mechanisms driven by the proliferation-induced microbial metabolic interactions and elevated microcystins (MCs) levels remain unclear. Here, through a year-long field study conducted in Shanghai's largest drinking water supply catchment, we demonstrated that Microcystis proliferation significantly increased ARG relative abundance (by 0.28 ± 0.05 log10(RPKM+1), corresponding to an approximately 60 % increase in abundance; P < 0.05, n = 63) and markedly reshaped the resistome structure (PERMANOVA, P < 0.01). During the whole Microcystis biomass cycle, the MCs were identified as the most predominant driver of the dynamics of waterborne ARGs (SNPs-RDA > 0.6, P < 0.01). Metagenomic binning and metabolic network reconstruction revealed that MC enhanced metabolic cooperation between ARG hosts and surrounding microorganisms (iNAP, Student's T-test, P < 0.001), suggesting MC-involved and nutrient co-metabolism that facilitated persistence of ARGs and the associated bacteria. Furthermore, plasmid conjugation experiments indicated that MCs significantly elevated plasmid-mediated ARG-transfer efficiency by twofold (Wilcoxon test, P < 0.05), promoting the spread of multidrug-resistant genes such as MexB, which may enable MCs to efflux. To quantify these effects, an MC index (MI) and a physiochemical index (PI) were developed, co-explaining > 80 % of ARG variation and identifying dissemination thresholds (TITAN, MI > 0.490 and PI > -0.032) for dominant resistance types. Our findings highlight MC as a natural promoter of ARG transmission, and the proposed indices offer viable tools for monitoring and mitigating antibiotic resistance in drinking water sources.},
}
@article {pmid41711070,
year = {2025},
author = {Beauvais, M and Schatt, P and Soulié, T and Lambert, S and Montiel, L and Gaudin, M and Chaffron, S and Logares, R and Bouget, FY and Galand, PE},
title = {Functional complementarity between vitamin B1 and B12 metabolisms shapes seasonal marine microbial communities.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag029},
pmid = {41711070},
issn = {1751-7370},
support = {ANR-24-CE02-7681//French Agence Nationale de la Recherche/ ; },
abstract = {Marine microbial communities are fundamental to nutrient and biogeochemical cycling, with intricate networks of metabolic interdependencies influencing their structure and dynamics. Among these, vitamins B1 (thiamin) and B12 (cobalamin) play crucial roles as enzymatic cofactors in central metabolic pathways. Despite their importance, the temporal dynamics of vitamin production, bioavailability, and associated microbial interactions remain poorly understood. Using a 7-year monthly metagenomic time series from the NW Mediterranean Sea (SOLA station), we found that vitamin B1/B12 auxotrophs (need for an exogenous vitamin source) were present throughout the year. Among B1 auxotrophs, those requiring the thiamin precursor pyrimidine were the most prevalent, with peak abundances in summer. Distinct metagenome-assembled genome co-abundance patterns between B1 and B12 producers/auxotrophs across seasons suggested mutualistic relationships. Double B1/B12 vitamin complementarities were more common in summer, and single vitamin complementarity was dominant in winter. As previously shown for vitamin B12, which is limiting during winter, bioassays revealed variable availability of vitamin B1 in winter seawater despite the abundance of its producers, suggesting potential transfer of vitamin B1 among microorganisms. Finally, microcosm experiments showed that B1 and B12 amendments significantly influenced the composition of microbial communities, with temporal variations in their impact. In some cases, B12 and B1 amendments favored both vitamin auxotrophs and producers, highlighting complex interdependencies between B1 and B12 producers and consumers. Our findings highlight the complexity of B vitamin-mediated metabolic interactions that shape microbial community dynamics and underscore the need for long-term, high-resolution studies to better understand vitamin-driven ecological processes in marine systems.},
}
@article {pmid41707423,
year = {2026},
author = {Francés, &#xc1; and López, M and González-Raurich, M and Cobo-Díaz, JF and Prieto, M and Allende, A and Gil, MI and Truchado, P and Alvarez-Ordóñez, A and Oliveira, M},
title = {Characterization of microbial diversity, chemical hazards and antimicrobial resistant bacteria in wash water from a fresh-cut vegetable processing plant.},
journal = {International journal of food microbiology},
volume = {452},
number = {},
pages = {111667},
doi = {10.1016/j.ijfoodmicro.2026.111667},
pmid = {41707423},
issn = {1879-3460},
mesh = {*Bacteria/drug effects/genetics/isolation &amp; purification/classification ; *Vegetables/microbiology ; *Drug Resistance, Bacterial ; *Water Microbiology ; Food Handling ; Anti-Bacterial Agents/pharmacology ; Microbiota ; Pesticides/analysis ; Microbial Sensitivity Tests ; },
abstract = {This study investigated the quality of process wash water (PWW) in an industrial fresh-cut produce facility. Traditional microbiological and physico-chemical parameters, such as aerobic mesophilic counts, coliforms, molds and yeasts, pH, free chlorine, oxidation-reduction potential, and organic matter indicators, were monitored to contextualize water quality dynamics across the workday. Additionally, untargeted analyses were performed to characterize the microbiome and resistome and identify chemical hazards in PWW, highlighting the occurrence of antimicrobial-resistant bacteria and the presence of some pesticides at low levels, including chlorantraniliprole, cyprodinil, fludioxonil, and propyzamide, in a real-world processing environment. Antimicrobial susceptibility tests and whole genome sequencing of twelve coliform isolates revealed multidrug-resistant strains, including Enterobacter mori, Enterobacter ludwigii, and Klebsiella oxytoca, carrying resistance genes such as oqxB, fosA, and blaACT-12, as well as the plasmid-borne blaOXY-2-2. Metagenome analyses revealed a microbial community dominated by the genus Pseudomonas, together with high abundance of Rheinheimera mangrovi and Pantoea agglomerans. Moreover, resistome analysis disclosed that 83% of detected antimicrobial resistance genes were associated with beta-lactam resistance. Additionally, the efficacy of chlorine against one K. oxytoca isolate obtained from PWW using a dynamic system simulating a produce washing operation confirmed that maintaining pH at 6.5 and stable free chlorine levels of 6 mg/L was sufficient for complete inactivation. These findings demonstrate the importance of implementing proper wash water management practices in fresh produce processing, including preventing excessive organic matter accumulation through adequate water replenishment and maintaining chemical parameters within the validated operational range, supported by systematic verification and monitoring.},
}
@article {pmid41687578,
year = {2026},
author = {Zhou, Q and Liang, H and Huang, J and Klümper, U and Fang, P and Yu, Z and Wang, Y and Berendonk, TU and Lin, L and Li, X and Li, B},
title = {Impact of sulfonamides on microbial community and antibiotic resistome profiles in anaerobic digestion of swine wastewater.},
journal = {Journal of hazardous materials},
volume = {505},
number = {},
pages = {141426},
doi = {10.1016/j.jhazmat.2026.141426},
pmid = {41687578},
issn = {1873-3336},
mesh = {Animals ; *Sulfonamides/pharmacology ; Swine ; *Wastewater/microbiology ; Anaerobiosis ; *Microbiota/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Water Pollutants, Chemical ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects ; },
abstract = {Residual antibiotics in swine wastewater promote the proliferation of the antibiotic resistome, posing significant threats to environmental and human health. Although anaerobic digestion (AD) is widely applied for treating swine wastewater, the effects of antibiotics on the microbial community and resistome during AD remain unclear. This study employed amplicon and metagenomic sequencing, combined with long- and short-read hybrid assembly, to comprehensively investigate the impact of sulfonamides on the microbiome and resistome during AD. Enterococcus, a genus capable of utilizing exogenous folate, was identified as the dominant genus under sulfonamide stress. A total of 24 antibiotic resistance gene (ARG) types and 440 subtypes were identified. Sulfonamide stress selectively enriched sulfonamide resistance genes, with no notable co-selective effects on ARGs for other antibiotic classes. Short-term exposure significantly enriched sul2 (3.8-fold) and sul3 (4.0-fold), while long-term exposure enriched sul1 (1.6-fold). Sulfonamides especially promoted the proliferation of sulfonamide resistance genes on both mobilizable and non-mobilizable plasmids. The co-occurrence of multiple categories of mobile genetic elements and ARGs on contigs was inferred to play a critical role in driving ARG dissemination. Whereas a strain belonging to Enterococcus_I emerged as the dominant resistant bacterium in the AD system, a particular multidrug-resistance risk was identified for a strain belonging to the Filifactoraceae family. This work provides a new perspective on the impact of antibiotics on microbial community and antibiotic resistome composition and dynamics during the AD treatment process of swine wastewater.},
}
@article {pmid41687083,
year = {2026},
author = {Olaniyi, K and Moodley, J and Moodley, R and Mackraj, I},
title = {Assessment of human placental microbial signatures in pre-eclampsia using shotgun metagenomics.},
journal = {Canadian journal of physiology and pharmacology},
volume = {104},
number = {},
pages = {1-11},
doi = {10.1139/cjpp-2025-0274},
pmid = {41687083},
issn = {1205-7541},
mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology ; *Placenta/microbiology ; *Metagenomics/methods ; Adult ; *Bacteria/genetics/isolation &amp; purification/classification ; *Microbiota ; },
abstract = {This study evaluated the presence of bacterial species in the placenta of women with pre-eclampsia and compared with that of normotensive women. One hundred and twenty participants, comprising 60 pre-eclamptic (30 early- and late-onset, respectively) and 60 age-matched normotensive women (30 early and late-gestation normotensive, respectively) were recruited. After informed consent was obtained, the placenta were obtained through caesarean section with sterile and standardized clinical procedures. DNA was extracted from each tissue, and the samples were pooled into six libraries and sequenced on Illumina NextSeq500 using a shotgun metagenomic approach. Bioinformatics was used to analyse the reads with the implementation of Kraken2/MetaPhlAn classification methods and complemented by multi-layered contamination assessment strategy that included frequency-based decontam filtering. Most reads were classified as belonging to the phyla Cutibacterium acnes, Staphylococcus epidermidis, and various Bradyrhizobium species. PE samples showed notable Corynebacterium tuberculostearicum and Pseudomonas species, while Bradyrhizobium and Cutibacterium acnes dominated normotensive samples. Further analysis showed no significant difference between bacterial species of pre-eclamptic and normotensive placental samples. The results show very low levels of bacteria in the placental samples. In addition, a little difference was observed between the bacterial compositions of pre-eclamptic and age-matched normotensive placental tissues, but not statistically significant.},
}
@article {pmid41642002,
year = {2026},
author = {Williams, A and Maros, A and France, MT and Ravel, J and Holm, JB},
title = {Not all vaginal microbiomes are equal: functional context shapes immune landscapes.},
journal = {mBio},
volume = {17},
number = {3},
pages = {e0364525},
doi = {10.1128/mbio.03645-25},
pmid = {41642002},
issn = {2150-7511},
support = {UH2AI083264//National Institute of Allergy and Infectious Diseases/ ; K01AI163413//National Institute of Allergy and Infectious Diseases/ ; T32AI162579//National Institute of Allergy and Infectious Diseases/ ; R01NR015495/NR/NINR NIH HHS/United States ; OPP1189217//Bill and Melinda Gates Foundation/ ; },
mesh = {Female ; *Vagina/microbiology/immunology ; Humans ; *Microbiota/immunology/genetics ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; *Gardnerella/genetics/classification/immunology/isolation &amp; purification ; Algorithms ; Metagenome ; Dysbiosis/microbiology ; Host Microbial Interactions/immunology ; },
abstract = {Taxonomic classification alone fails to capture the ecological and functional diversity of vaginal microbiomes, particularly those dominated by Gardnerella species. Using the expanded VIRGO2 gene catalog, we developed the vaginal inference of subspecies and typing algorithm (VISTA), a novel ortholog-based framework that defined metagenomic subspecies and 25 metagenomic community state types (mgCSTs), including six distinct Gardnerella-dominated profiles. The mgCSTs exhibit marked differences in species composition, functional gene content, transcriptional activity, and host immune responses. These findings reveal that Gardnerella predominance does not uniformly equate to dysbiosis and underscore the importance of functional context in shaping host-microbiome interactions. VISTA provides scalable classifiers and an interactive application to support mechanistic studies of vaginal microbiome function and its implications for reproductive health.IMPORTANCEThe vaginal microbiome plays a central role in reproductive and gynecologic health, yet its functional diversity and ecological organization remain poorly understood. Traditional 16S rRNA approaches provide only a partial view of this complexity, overlooking the strain-level variation that often determines microbial behavior and host outcomes. By applying metagenomic sequencing and scalable computational modeling, we developed the vaginal inference of subspecies and typing algorithm, a framework that defines gene-based subspecies and community state types across diverse populations. These classifications reveal new insights into the genomic and ecological foundations of vaginal community structure and offer a standardized resource for comparative and translational microbiome research. This work establishes the foundation for functionally informed diagnostics and precision interventions targeting women's reproductive health.},
}
@article {pmid41633137,
year = {2026},
author = {Zhang, FY and Shu-Kui, D and Wang, LL and Ma, YT and Wu, MZ and Yuan, HM and Yang, JN and Zhang, Y and Zhang, GA and Zhao, J and Liu, C and Guan, DW and Zhao, R},
title = {Metagenomic profiling reveals lung multi-kingdom microbes as forensic markers for aquatic corpses investigation.},
journal = {Forensic science international. Genetics},
volume = {83},
number = {},
pages = {103435},
doi = {10.1016/j.fsigen.2026.103435},
pmid = {41633137},
issn = {1878-0326},
mesh = {*Lung/microbiology ; Animals ; *Drowning/diagnosis/microbiology ; Humans ; *Microbiota ; Metagenomics ; Mice ; Biomarkers ; Postmortem Changes ; Immersion ; Real-Time Polymerase Chain Reaction ; Male ; Bacteria/genetics ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The forensic investigation of corpses recovered from aquatic environments presents a major practical challenge. Recent studies have demonstrated that the bacterial community in the lung serves as a valuable indicator for diagnosing drowning, determining the drowning medium and estimating postmortem submersion interval (PMSI). However, the application and significance of lung multi-kingdom microbiome (archaea, eukaryota, and viruses) remains inadequately characterized. Meanwhile, the insufficient sequencing depth of commonly employed techniques, such as amplicon sequencing, restricts our understanding of microbial communities. In this study, we characterized the postmortem lung microbiome of mice submerged in water for up to 10 days using metagenomic sequencing, and subsequently validated the potential microbial biomarkers in both murine and human forensic specimens via qPCR. Integrated analyses were conducted followed by the confirmation of significant lung bacterial communities for drowning diagnosis, inference of drowning site, and estimation of the PMSI. Our findings revealed that bacteria constituted the predominant component of the lung microbiome in submerged murine carcasses, with eukaryota serving as the secondary dominant taxa. Seventeen bacterial and nine eukaryotic features at the species level were identified as potential biomarkers for drowning diagnosis. By detecting the specific molecular markers for Aeromonas species in both murine and human samples, the positive detection of Aeromonas species, particularly Aeromonas hydrophila, provides solid evidence for drowning diagnosis. Additionally, 14 and 17 bacterial species were identified as biomarkers for the inference of drowning site and estimation of PMSI, respectively. Based on the identified potential biomarkers, robust forensic models were constructed using the random forest (RF) algorithm. The accuracy of the bacterial model for drowning diagnosis was 89.29 %, while the accuracy of the eukaryotic model was 87.5 %. For the inference of the drowning site, the bacterial model achieved an accuracy of 100 %. Furthermore, the estimation of the PMSI yielded a mean absolute error of 0.66 ± 0.097 days. Collectively, our findings revealed that the selected 17 bacterial and 9 eukaryotic features in the lungs, particularly Aeromonas hydrophila, are beneficial for drowning diagnosis. Additionally, the other selected bacterial species contribute to the estimation of the drowning site and PMSI, thereby providing more comprehensive and refined information for accurate forensic investigations of corpses recovered from aquatic environments.},
}
@article {pmid41514203,
year = {2026},
author = {You, S and Zou, Y and Xiao, Y and He, L and Liu, L and Sun, Y and Jia, Y and Ge, G and Du, S},
title = {Animal performance and gut microbiota of cattle as affected by the unfermented or fermented total mixed ration.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41514203},
issn = {1471-2180},
mesh = {Animals ; Cattle/microbiology/growth &amp; development ; *Gastrointestinal Microbiome ; *Animal Feed/analysis ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; RNA, Ribosomal, 16S/genetics ; *Diet/veterinary ; Fermentation ; Metagenomics ; DNA, Bacterial/genetics ; },
abstract = {Diet regulates the gut microbiota, which in turn affects animal performance, but how diet shapes the animal performance and gut microbiota remains largely unknown. To fill this gap, the author conducted a comprehensive study of the influence of total mixed ration (TMR) or fermented TMR (FTMR) on the animal performance and gut microbiome. Sixteen Simmental male cattle were randomly allocated to two treatments (one cattle per pen). The animals were fed with the TMR and FTMR diets respectively. The results showed that the contents of ADF, NDF, cellulose and total cellulose in the FTMR were significantly decreased (p < 0.05), the average daily weight gain of the Simmental male cattle shows an increasing trend (TMR: 0.31 vs. FTMR: 0.62), while no significant (p = 0.2382) difference was found between the two treatments. The metagenomics analysis showed significant (p < 0.05) difference in the α-diversity and β-diversity, and the dominant bacterial genera were Weissella, Lactiplantibacillus, Levilactobacillus and Companilactobacillus. The 16S rRNA sequencing indicated that a significant (p = 0.018) difference in the bacterial communities between the cattle fed with TMR or FTMR diet, while no significant (p < 0.05) differences were detected on the primary genus. It can be found that the FTMR diet increased the average daily gain of cattle by improving the chemical composition and microbial functional profile of the FTMR diet, and affected the growth performance of cattle.},
}
@article {pmid41484024,
year = {2026},
author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and De Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L},
title = {Gut microbiome profiles and associated functional pathways are linked to Mediterranean diet adherence and blood glucose control in adults with type 1 diabetes mellitus.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {36},
number = {4},
pages = {104487},
doi = {10.1016/j.numecd.2025.104487},
pmid = {41484024},
issn = {1590-3729},
mesh = {Humans ; *Diet, Mediterranean ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 1/diagnosis/blood/diet therapy/microbiology ; Male ; Cross-Sectional Studies ; Female ; Adult ; *Glycemic Control ; *Blood Glucose/metabolism/drug effects ; Glycated Hemoglobin/metabolism ; *Bacteria/genetics/growth &amp; development/classification ; Middle Aged ; Biomarkers/blood ; *Diet, Healthy ; Feces/microbiology ; Young Adult ; *Patient Compliance ; Treatment Outcome ; },
abstract = {BACKGROUND AND AIMS: The Mediterranean diet (MD) has been associated with better glycaemic control in children with type 1 diabetes mellitus (T1DM) and favourable microbiome profiles in healthy individuals. However, it remains unclear whether MD adherence is associated with glycaemic control via microbiome. This study examined the relationships among MD adherence, gut microbiome, and glycaemic control in adults with T1DM and assessed the microbiome's ability to predict clinical and dietary outcomes.<br><br>METHODS AND RESULTS: In a cross-sectional study of 253 adults with T1DM, dietary intake was assessed using the EPIC food frequency questionnaire, and MD adherence was measured using the rMED score. Participants were stratified by adherence level (low, medium, high). Glycaemic control was evaluated using HbA1c and CGM metrics. Shotgun metagenomic sequencing of stool samples (n&#xa0;=&#xa0;103) assessed the gut microbiome. Statistical analyses included ANOVA, PERMANOVA, LEfSe, and machine learning modeling. Higher MD adherence was associated with lower HbA1c levels (7.1&#xa0;% vs 7.7&#xa0;%; p&#xa0;<&#xa0;0.001), greater time in range (67.0&#xa0;% vs 59.4&#xa0;%; p-trend&#xa0;=&#xa0;0.03), and higher HDL cholesterol (1.62 vs 1.39&#xa0;mmol/L; p&#xa0;=&#xa0;0.01). High MD adherence was linked to a greater abundance of bacterial species such as Faecalibacterium prausnitzii. Both high MD adherence and lower HbA1c were associated with distinct microbiome functional pathways. Microbiome-based machine learning models predicted dietary patterns and clinical metrics.<br><br>CONCLUSIONS: In adults with T1DM, greater MD adherence is associated with better glycaemic control and a favourable gut microbiome. Specific microbial pathways may underlie these associations. Integrating diet and microbiome data supports personalized care. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.},
}
@article {pmid41453848,
year = {2026},
author = {Li, XL and Li, ZQ},
title = {Gut microbiota of economically important termites: functional convergence, harmfulness and precision control.},
journal = {Pest management science},
volume = {82},
number = {4},
pages = {2808-2824},
doi = {10.1002/ps.70490},
pmid = {41453848},
issn = {1526-4998},
support = {//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Isoptera/microbiology ; *Gastrointestinal Microbiome ; *Insect Control/methods ; },
abstract = {As typical social insects and key decomposers in ecosystems, termites, like other insects, harbor a complex array of microbial communities with diverse functions in their gut. These microorganisms are not only closely related to key survival aspects of termites, including nutritional acquisition, metabolic adaptation and colony resilience, but also play crucial roles in their ecological adaptability. This demonstrates that termite survival strategies are highly dependent on the synergistic interactions within their gut microbiota. Notably, some termites, such as Coptotermes formosanus, exhibit both decomposition ability and damaging capacity. Whether their gut microbiota is closely related to their destructive potential has become one of the core issues of concern to researchers. Moreover, with the rapid development of metagenomics and bioinformatics technologies in recent years, an increasing number of termite gut microbiota functions have been predicted and validated, making it possible to analyze their destructive capacity from a microbial perspective. Therefore, based on a systematic synthesis of the functional commonalities and mechanistic roles of gut microbiota in economically significant termite species, this review further highlights evidence linking microbial functions with termite damaging capacity and discusses microbiota-based strategies for precision control of pest termites. It aims to provide comprehensive references and a solid theoretical foundation for in-depth research and rational utilization of termite gut microbiota, as well as scientifically grounded and targeted management of destructive termite pests. © 2025 Society of Chemical Industry.},
}
@article {pmid37759740,
year = {2023},
author = {Witkowska, AM and Salem, JE},
title = {Pharmacological and Nutritional Modulation of Metabolome and Metagenome in Cardiometabolic Disorders.},
journal = {Biomolecules},
volume = {13},
number = {9},
pages = {},
pmid = {37759740},
issn = {2218-273X},
mesh = {Humans ; *Metabolome/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Cardiovascular Diseases/metabolism/microbiology/drug therapy ; *Metagenome/drug effects ; *Metabolic Diseases/metabolism/microbiology ; Animals ; Diet ; Metabolomics ; },
abstract = {Cardiometabolic disorders are major causes of morbidity and mortality worldwide. A growing body of research indicates that the gut microbiota, whether it interacts favorably or not, plays an important role in host metabolism. Elucidating metabolic pathways may be crucial in preventing and treating cardiometabolic diseases, and omics methods are key to studying the interaction between the fecal microbiota and host metabolism. This review summarizes available studies that combine metabolomic and metagenomic approaches to describe the effects of drugs, diet, nutrients, and specific foods on cardiometabolic health and to identify potential targets for future research.},
}
@article {pmid37748344,
year = {2023},
author = {Yang, Y and Deng, Y and Liu, L and Yin, X and Xu, X and Wang, D and Zhang, T},
title = {Establishing reference material for the quest towards standardization in environmental microbial metagenomic studies.},
journal = {Water research},
volume = {245},
number = {},
pages = {120641},
doi = {10.1016/j.watres.2023.120641},
pmid = {37748344},
issn = {1879-2448},
mesh = {*Metagenomics/standards/methods ; Reference Standards ; Microbiota ; Sewage/microbiology ; *Environmental Microbiology ; Sequence Analysis, DNA ; },
abstract = {Breakthroughs in DNA-based technologies, especially in metagenomic sequencing, have drastically enhanced researchers' ability to explore environmental microbiome and the associated interplays within. However, as new methodologies are being actively developed for improvements in different aspects, metagenomic workflows become diversified and heterogeneous. Through a single-variable control approach, we quantified the microbial profiling variations arising from 6 common technical variables associated with metagenomic workflows for both simple and complex samples. The incurred variations were constantly the lowest in replicates of DNA isolation and DNA sequencing library construction. Different DNA extraction kits often caused the highest variation among all the tested variables. Additionally, sequencing run batch was an important source of variability for targeted platforms. As such, the development of an environmental reference material for complex environmental samples could be beneficial in benchmarking accrued non-biological variability within and between protocols and insuring reliable and reproducible sequencing outputs immediately upstream of bioinformatic analysis. To develop an environment reference material, sequencing of a well-homogenized environmental sample composed of activated sludge was performed using different pre-analytical assays in replications. In parallel, a certified mock community was processed and sequenced. Assays were ranked based on the reconstruction of the theoretical mock community profile. The reproducibility of the best-performing assay and the microbial profile of the reference material were further ascertained. We propose the adoption of our complex environmental reference material, which could reflect the degree of diversity in environmental microbiome studies, to facilitate accurate, reproducible, and comparable environmental metagenomics-based studies.},
}
@article {pmid37713802,
year = {2023},
author = {Vieira, TR and de Oliveira, EFC and Cibulski, SP and Silva, NMV and Borba, MR and Oliveira, CJB and Cardoso, M},
title = {Comparative resistome, mobilome, and microbial composition of retail chicken originated from conventional, organic, and antibiotic-free production systems.},
journal = {Poultry science},
volume = {102},
number = {11},
pages = {103002},
pmid = {37713802},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology ; *Animal Husbandry/methods ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Interspersed Repetitive Sequences ; *Meat/microbiology ; Organic Agriculture ; *Bacteria/drug effects/genetics/isolation &amp; purification ; *Microbiota ; Cross-Sectional Studies ; },
abstract = {The aim of this study was to investigate the microbial composition, and the profiles of antimicrobial resistance genes (ARGs, resistome) and mobile genetic elements (mobilome) of retail chicken carcasses originated from conventional intensive production systems (CO), certified antimicrobial-free intensive production systems (AF), and certified organic production systems with restricted antimicrobial use (OR). DNA samples were collected from 72 chicken carcasses according to a cross-sectional study design. Shot-gun metagenomics was performed by means of Illumina high throughput DNA sequencing followed by downstream bioinformatic analyses. Gammaproteobacteria was the most abundant bacterial class in all groups. Although CO, AF, and OR did not differ in terms of alpha- and beta-microbial diversity, the abundance of some taxa differed significantly across the groups, including spoilage-associated organisms such as Pseudomonas and Acinetobacter. The co-resistome comprised 29 ARGs shared by CO, AF and OR, including genes conferring resistance to beta-lactams (blaACT-8, 10, 13, 29; blaOXA-212;blaOXA-275 and ompA), aminoglycosides (aph(3')-IIIa, VI, VIa and spd), tetracyclines (tet KL (W/N/W and M), lincosamides (inu A,C) and fosfomycin (fosA). ARGs were significantly less abundant (P < 0.05) in chicken carcasses from AF and OR compared with CO. Regarding mobile genetic elements (MGEs), transposases accounted for 97.2% of the mapped genes. A higher abundance (P = 0.037) of MGEs was found in CO compared to OR. There were no significant differences in ARGs or MGEs diversity among groups according to the Simpson´s index. In summary, retail frozen chicken carcasses from AF and OR systems show similar ARGs, MGEs and microbiota profiles compared with CO, even though the abundance of ARGs and MGEs was higher in chicken carcasses from CO, probably due to a higher selective pressure.},
}
@article {pmid37702790,
year = {2023},
author = {Zou, D and Chen, J and Zhang, C and Kao, SJ and Liu, H and Li, M},
title = {Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {22},
pages = {6897-6909},
pmid = {37702790},
issn = {1432-0614},
support = {32225003//National Natural Science Foundation of China/ ; 31970105//National Natural Science Foundation of China/ ; 2022M722175//Postdoctoral Research Foundation of China/ ; JCYJ20200109105010363//Shenzhen Science and Technology Innovation Program/ ; },
mesh = {China ; *Estuaries ; *Archaea/classification/genetics/metabolism/physiology ; *Ammonia/metabolism ; Phylogeny ; Oxidation-Reduction ; Salinity ; Metagenomics ; *Adaptation, Physiological ; *Biodiversity ; Ecosystem ; },
abstract = {Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.},
}
@article {pmid37690533,
year = {2023},
author = {Zhao, X and Zhao, J and Li, D and Yang, H and Chen, C and Qin, M and Wen, Z and He, Z and Xu, L},
title = {Akkermansia muciniphila: A potential target and pending issues for oncotherapy.},
journal = {Pharmacological research},
volume = {196},
number = {},
pages = {106916},
doi = {10.1016/j.phrs.2023.106916},
pmid = {37690533},
issn = {1096-1186},
mesh = {Humans ; Animals ; *Probiotics/therapeutic use ; *Neoplasms/microbiology/therapy/immunology/drug therapy ; *Gastrointestinal Microbiome ; Akkermansia ; },
abstract = {In the wake of the development of metagenomic, metabolomic, and metatranscriptomic approaches, the intricate interactions between the host and various microbes are now being progressively understood. Numerous studies have demonstrated evident changes in gut microbiota during the process of a variety of diseases, such as diabetes, obesity, aging, and cancers. Notably, gut microbiota is viewed as a potential source of novel therapeutics. Currently, Next-generation probiotics (NGPs) are gaining popularity as therapeutic agents that alter the gut microbiota and affect cancer development. Akkermansia muciniphila (A. muciniphila), a representative commensal bacterium, has received substantial attention over the past decade as a promising NGP. The components and metabolites of A. muciniphila can directly or indirectly affect tumorigenesis, in particular through its effects on antitumor immunosurveillance, including the stimulation of pattern recognition receptors (PRRs), which also leads to better outcomes in a variety of situations, including the prevention and curation of cancers. In this article, we systematically summarize the role of A. muciniphila in tumorigenesis (involving gastrointestinal and non-gastrointestinal cancers) and in tumor therapy. In particular, we carefully discuss some critical scientific issues that need to be solved for the future using A. muciniphila as a representative beneficial bacterium in tumor treatment, which might provide bright clues and assistance for the application of drugs targeting A. muciniphila in clinical oncotherapy.},
}
@article {pmid37666200,
year = {2023},
author = {Xu, M and Wang, W and Su, S and Li, W and Hu, X and Zhang, J},
title = {Arecoline alleviated loperamide induced constipation by regulating gut microbes and the expression of colonic genome.},
journal = {Ecotoxicology and environmental safety},
volume = {264},
number = {},
pages = {115423},
doi = {10.1016/j.ecoenv.2023.115423},
pmid = {37666200},
issn = {1090-2414},
mesh = {*Constipation/chemically induced/drug therapy ; Loperamide/toxicity ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Colon/drug effects/metabolism ; Male ; *Arecoline/pharmacology/therapeutic use ; Rats, Sprague-Dawley ; Rats ; Fatty Acids, Volatile/metabolism ; Transcriptome/drug effects ; },
abstract = {This study aimed to investigate the effects of arecoline on constipation by intervening at different times to explore its preventive and therapeutic effects. Symptoms related to constipation, gut microbes, short-chain fatty acid (SCFA) content in the cecum, and gene expression in the colon were measured to examine the effect of arecoline on relieving constipation. The results showed that arecoline intervention alleviated loperamide-induced constipation, as evidenced by significantly shortened intestinal transit time, increased fecal water content, improved small bowel propulsion, and increased defecation frequency. In addition, arecoline significantly reduced the levels of gastrointestinal regulatory peptides such as somatostatin and vasoactive intestinal peptide in the serum, thereby regulating intestinal peristalsis. Histopathological analysis showed that arecoline ameliorated intestinal injury caused by constipation. Gut microbial analysis indicated that arecoline altered the taxonomic composition and levels of its metabolite SCFAs in the gut microbiota. Furthermore, the colonic transcriptome results indicated that genes expression related to intestinal diseases were significantly down-regulated by arecoline intervention. In conclusion, the results of the correlation analysis propose a possible mechanism of arecoline in alleviating constipation by modulating the gut microbes and their metabolites and regulating the gut genome.},
}
@article {pmid37660873,
year = {2023},
author = {Bhardwaj, L and Reddy, B and Dubey, SK},
title = {Deciphering insights into rhizospheric microbial community and soil parameters under the influence of herbicides in zero-tillage tropical rice-agroecosystem.},
journal = {Environmental research},
volume = {237},
number = {Pt 2},
pages = {117033},
doi = {10.1016/j.envres.2023.117033},
pmid = {37660873},
issn = {1096-0953},
mesh = {*Herbicides/toxicity ; *Soil Microbiology ; Oryza/growth &amp; development ; *Rhizosphere ; *Microbiota/drug effects ; Soil/chemistry ; *Soil Pollutants/analysis/toxicity ; Agriculture ; Bacteria/drug effects ; Fungi/drug effects ; Acetanilides ; Aniline Compounds ; },
abstract = {Extensive use of chemicals like herbicides in rice and other fields to manage weeds is expected to have a lasting influence on the soil environment. Considering this rationale, we aimed to decipher the effects of herbicides, Pendimethalin and Pretilachlor, applied at 0.5 and 0.6 kg ha[-1], respectively on the rhizosphere microbial community and soil characteristics in the tropical rice field, managed under zero tillage cultivation. The quantity of herbicide residues declined gradually since application up to 60 days thereafter it reached the non-detectable level. Most of the soil variables viz., microbial biomass, soil enzymes etc., exhibited slight reduction in the treated soils compared to the control. A gradual decline was observed in Mineral-N, MBC, MBN and enzyme activities. Quantitative polymerase chain reaction results showed maximal microbial abundance of bacteria, fungi and archaea at mid-flowering stage of rice crop. The 16 rRNA and ITS region targeted amplicons high throughput sequencing microbial metagenomic approach revealed total of 94, 1353, and 510 species for archaea, bacteria and fungi, respectively. The metabarcoding of core microbiota revealed that the archaea comprised of Nitrososphaera, Nitrosocosmicus, and Methanosarcina. In the bacterial core microbiome, Neobacillus, Nitrospira, Thaurea, and Microvigra were found as the predominant taxa. Fusarium, Clonostachys, Nigrospora, Mortierella, Chaetomium, etc., were found in core fungal microbiome. Overall, the study exhibited that the recommended dose of herbicides found to be detrimental to the microbial dynamics, though a negative relation between residues and soil variables was observed that might alter the microbial diversity. The outcomes offer a comprehensive understanding of how herbicides affect the microbial community in zero tillage rice soil, thus has a critical imputation for eco-friendly and sustainable rice agriculture. Further, the long-term studies will be helpful in elucidating the role of identified microbial groups in sustaining the soil fertility and crop productivity.},
}
@article {pmid37641353,
year = {2023},
author = {Moore, SG and Feehily, C and Doyle, RC and Buckley, F and Lonergan, P and Cotter, PD and Butler, ST},
title = {Associations between the postpartum uterine and vaginal microbiota and the subsequent development of purulent vaginal discharge vary with dairy cow breed and parity.},
journal = {Journal of dairy science},
volume = {106},
number = {11},
pages = {8133-8151},
doi = {10.3168/jds.2022-22720},
pmid = {37641353},
issn = {1525-3198},
mesh = {Animals ; Female ; Cattle ; *Vagina/microbiology ; Postpartum Period ; *Microbiota ; *Uterus/microbiology ; *Vaginal Discharge/veterinary/microbiology ; Parity ; Pregnancy ; *Cattle Diseases/microbiology ; },
abstract = {The objective of this study was to characterize the species composition and functional potential of the vaginal and uterine microbiota at 1 wk postpartum in dairy cows diagnosed with or without purulent vaginal discharge (PVD) at 3 wk postpartum. The hypothesis was that differences in the vaginal and uterine microbiota between cows diagnosed with (PVD+) or without (PVD-) PVD were dependent on parity and breed. Cytobrush samples of the vagina and uterus were collected at 1 wk postpartum from 36 Holstein-Friesian (7 primiparous and 29 multiparous) and 29 Jersey (10 primiparous and 19 multiparous) cows. Microbial DNA was isolated from each sample and processed for shotgun metagenomic sequencing. The odds of multiparous cows being diagnosed as PVD+ was less compared with primiparous cows (OR = 0.21). Neither the α-diversity nor β-diversity of the uterine and vaginal microbiota were associated with PVD but the β-diversity was different between breeds and between parities. In the vagina of primiparous cows, differences in the microbiota of PVD- and PVD+ cows were minor, but the microbiota of multiparous PVD+ cows had greater relative abundance of Fusobacterium necrophorum, Trueperella pyogenes, Porphyromonas levii, and greater functional potential for amino acid and protein synthesis, energy metabolism, and growth compared with PVD- cows. The uterus of primiparous PVD+ cows had lesser relative abundance of Bacteroides heparinolyticus compared with PVD- cows. In the uterine microbiota, differences included greater functional potential for cellulose biosynthesis and fucose catabolism in multiparous PVD+ cows compared with PVD- cows. In the uterine microbiota of primiparous PVD+ cows, the functional potential for gram-negative cell wall synthesis and for negative regulation of tumor necrosis factor signaling was lesser compared with multiparous PVD+ cows. In the vagina of Holstein-Friesian PVD+ cows, the relative abundance of Caviibacter abscessus was greater whereas in the vagina of Jersey PVD+ cows the relative abundance of Catenibacterium mitsuokai, Finegoldia magna, Klebsiella variicola, and Streptococcus anginosus was greater compared with PVD- cows. In the uterine microbiota of Holstein-Friesian cows, the functional potential for spermidine biosynthesis was reduced compared with PVD- cows. In summary, differences in the species composition and functional potential of the vaginal and uterine microbiota between PVD- and PVD+ cows were dependent on parity and breed. The findings suggest that alternative strategies may be required to treat PVD for different parities and breeds of dairy cow.},
}
@article {pmid37638757,
year = {2023},
author = {Chaturvedi, A and Li, X and Dhandapani, V and Marshall, H and Kissane, S and Cuenca-Cambronero, M and Asole, G and Calvet, F and Ruiz-Romero, M and Marangio, P and Guigó, R and Rago, D and Mirbahai, L and Eastwood, N and Colbourne, JK and Zhou, J and Mallon, E and Orsini, L},
title = {The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome.},
journal = {Nucleic acids research},
volume = {51},
number = {18},
pages = {9785-9803},
pmid = {37638757},
issn = {1362-4962},
support = {NE/N016777/1//NERC/ ; 965406//European Union/ ; 101028700//Marie Sk&#x142;odowska-Curie/ ; IC160121//Royal Society International Collaboration Award/ ; },
mesh = {Animals ; *Daphnia/genetics/microbiology ; *DNA Methylation ; *Genome ; *Evolution, Molecular ; Metagenome ; *Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Transcriptome ; Daphnia magna ; },
abstract = {Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.},
}
@article {pmid37558110,
year = {2023},
author = {Tian, F and Wang, Y and Guo, G and Ding, K and Yang, F and Wang, C and Wang, H and Yan, M},
title = {Meta-genome analysis of a newly enriched azo dyes detoxification halo-thermophilic bacterial consortium.},
journal = {Environmental research},
volume = {237},
number = {Pt 1},
pages = {116828},
doi = {10.1016/j.envres.2023.116828},
pmid = {37558110},
issn = {1096-0953},
mesh = {*Azo Compounds/metabolism ; *Coloring Agents/metabolism ; *Microbial Consortia/genetics ; *Genome, Bacterial ; *Water Pollutants, Chemical/metabolism ; *Bacteria/genetics/metabolism ; Wastewater ; Biodegradation, Environmental ; },
abstract = {Treating textile wastewaters were always inhibited by its higher salt concentration and temperature. In this study, a halo-thermophilic bacterial consortium YM was enriched with ability to decolorize acid brilliant scarlet GR (ABS) at 55 °C and 10% salinity. Under optimum conditions of pH (8), temperature (55 °C), and salinity (10%), YM decolorized 97% of ABS under anaerobic conditions. Alteribacillus was identified to be the dominant genus in consortium YM. Consortium YM showed significant decolorization ability under a wide range of salinity (1%-10%), pH (7-9) and temperature (45 °C-60 °C). The degradation pathway of ABS was proposed by the combination of UV-vis spectral analysis, Fourier transform infrared (FTIR), gas chromatography mass spectrometric (GC-MS), and metagenomic analysis. Azoreductase, which was an important enzyme in decolorization process, was identified with great variation in the genome of consortium YM. Meanwhile, the metabolic intermediates after decolorization was identified with low biotoxicity by phytotoxicity tests. This study first identified that Alterbacillus play an important role in azo dye decolorization and degradation process under halo-thermophlic conditions and provided significant knowledge for azo dye decolorization and degradation process.},
}
@article {pmid41806446,
year = {2026},
author = {Lo Giudice, A and Papale, M and Bertolino, M and Reboa, A and Rizzo, C},
title = {Diversity and ecology of the prokaryotic microbiome associated with marine sponges across Antarctica.},
journal = {The Science of the total environment},
volume = {1025},
number = {},
pages = {181655},
doi = {10.1016/j.scitotenv.2026.181655},
pmid = {41806446},
issn = {1879-1026},
abstract = {Antarctic sponges host diverse and functionally relevant microbial communities that play central roles in the structure and resilience of polar benthic ecosystems. This review provides a focused analysis of the prokaryotic microbiomes associated with Antarctic sponges, with an emphasis on three ecologically significant species: Mycale (Oxymycale) acerata, Dendrilla antarctica, and Hymeniacidon torquata. Drawing from recent molecular studies, we examine the composition, predicted functional potential, and environmental responsiveness of these bacterial and archaeal communities. Comparative analyses with surrounding seawater and sediments reveal both overlaps and distinct host-specific microbial signatures, suggesting that sponge-associated microbiomes are shaped by selective pressures at the host and habitat levels. A conserved microbial core appears to coexist with more variable taxa influenced by host physiology and environmental gradients. We also discuss the impact of environmental stressors on microbiome structure and stability. Functional insights from metagenomic data highlight key microbial contributions to nutrient cycling, symbiotic lifestyles, secondary metabolite and vitamin production, quorum sensing, and the biodegradation of aromatic compounds. This review critically assesses current knowledge on Antarctic sponge-associated prokaryotic microbiomes, identifying recurrent taxonomic and functional patterns and evaluating evidence for core microbial functions across species and regions. We hypothesize that, despite taxonomic variability and geographical sampling bias, Antarctic sponge microbiomes share conserved functional traits shaped by host- and environment-driven selective pressures. Although foundational knowledge has expanded, particularly for shallow-water species, significant gaps persist-especially in underexplored habitats and in linking predicted functions to ecological dynamics. We conclude by outlining research priorities, including standardized protocols, broader spatial and temporal sampling, and multi-omics integration to better understand microbiome resilience under climate-driven change.},
}
@article {pmid41805117,
year = {2026},
author = {Chen, S and Li, C and Wang, Z and Teng, Y and Ren, W and Wang, H and Ma, J and Ma, W and Luo, Y and Kuramae, EE},
title = {Specific Metabolites Modulate Core Microbes and Microbial Interactions to Drive Fomesafen Dissipation in the Soybean Rhizosphere.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c15254},
pmid = {41805117},
issn = {1520-5118},
abstract = {Rhizosphere metabolites regulate organic pollutant dissipation through microbiome modulation, yet dynamic interrelationships among metabolite shifts, microbial assembly, and pollutant removal remain unclear. Using multiomics (16S rRNA sequencing, metabolomics, and metagenomics), this study deciphered the temporal dynamics of rhizosphere metabolites and microbiome during the dissipation of fomesafen in soybean pots. Fomesafen dissipation exhibited biphasic kinetics during soybean growth, with an initial rapid phase followed by prolonged stabilization, which was synchronized with time-dependent microbiome perturbations of initial enrichment and subsequent attenuation. Metabolomics revealed fomesafen-induced shifts in rhizosphere metabolites, with 2-naphthalenesulfonic acid (↓20.84%) and 2-hydroxyoctadecanoic acid (↑13.30%) exhibiting opposing effects on microbial assembly, which ultimately affect fomesafen dissipation, as outlined in our conceptual model. Microcosm experiments further demonstrated 2-naphthalenesulfonic acid enhanced while 2-hydroxyoctadecanoic acid inhibited fomesafen dissipation. Our findings highlight the significance of rhizosphere metabolite-mediated interactions between core microbes and potential fomesafen-degraders in governing fomesafen dissipation.},
}
@article {pmid41804664,
year = {2026},
author = {Bai, Y and Xu, Y and Wu, D and Su, Y and Zhan, M and Xie, B},
title = {The Polymer-Plastisphere-Function Nexus Links to Divergent Biodegradation of Microplastics During Composting.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70278},
doi = {10.1111/1462-2920.70278},
pmid = {41804664},
issn = {1462-2920},
support = {22276059//National Natural Science Foundation of China/ ; 2018YFC1901000//National Key Research and Development Program of China/ ; },
mesh = {Biodegradation, Environmental ; *Composting ; *Microplastics/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Polymers/metabolism/chemistry ; *Soil Microbiology ; Microbiota ; Polyesters/metabolism ; *Soil Pollutants/metabolism ; Soil/chemistry ; },
abstract = {Microplastic (MP) biodegradation is critical for mitigating plastic pollution, yet the ecological mechanisms linking polymer properties to plastisphere microbiome assembly and catalytic function remain unclear. Using thermophilic composting as an accelerated model, we reveal a fundamental dichotomy in which biodegradable MPs (BMPs: polylactic acid [PLA] > polybutylene succinate [PBS] > poly (butylene adipate-co-terephthalate) [PBAT]) undergo rapid thermophilic degradation shaped by stronger environmental filtering of diverse degraders, whereas conventional MPs (CMPs: low-density polyethylene [LDPE]) exhibit delayed degradation with greater stochastic influence. Metagenomics uncovered 489 degradative genes predominantly distributed across uncultured taxa, enabling reconstruction of polymer-specific multi-enzyme pathways, supported by isolating 32 potential degraders (31 candidate novel). PLA/PBS degradation primarily relied on thermophilic-phase PLA depolymerase and cutinase, PBAT on late-stage polyesterase and PETase, and LDPE on alkane monooxygenase and laccase. Statistical modelling showed BMP degradation strongly associated with plastisphere-physicochemical interactions (> 90% variance), whereas CMP appeared primarily constrained by material properties (e.g., degrader succession in PLA, enrichment in PBS/PBAT, and high molecular weight in LDPE). Functionally dominant degraders (1.9% of total microbes) were estimated to contribute 52.4%-80.6% of biodegradation efficiency. This work elucidates the core polymer-plastisphere-functional nexus underlying MP biodegradation during composting, providing a predictive framework and microbial resource for targeted remediation.},
}
@article {pmid41803086,
year = {2026},
author = {Faure, E and Pommellec, J and Noel, C and Cormier, A and Delpech, LM and Eren, AM and Fernandez-Guerra, A and Vanni, C and Fourquez, M and Houssais, MN and Guyet, U and Da Silva, C and Gavory, F and Perdereau, A and Labadie, K and Wincker, P and Poulain, J and Hassler, C and Lin, Y and Cassar, N and Maignien, L},
title = {Water mass specific genes dominate the Southern Ocean microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41803086},
issn = {2041-1723},
support = {18-CE02-0024//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {*Microbiota/genetics ; *Seawater/microbiology ; Oceans and Seas ; Metagenome/genetics ; Antarctic Regions ; *Bacteria/genetics/classification ; Sulfonium Compounds/metabolism ; Arctic Regions ; Plankton/genetics ; Phylogeny ; },
abstract = {The Southern Ocean (SO) plays a key role in regulating global biogeochemical cycles and climate, yet microbial genes sustaining its biological activity remain poorly characterized. We introduce a microbial genes collection from 218 metagenomes sampled during the Antarctic Circumnavigation Expedition, the majority of which are missing from functional databases. 38% even lack homologs in current reference marine gene catalogs, defining a singular genetic seascape. We show that SO gene assemblages exhibit a common polar signature with the Arctic Ocean while being structured by water masses at the SO-scale. We analyze genomic markers of diverse SO biomes, focusing on dimethylsulphoniopropionate (DMSP) cleavage by polar-adapted bacteria, organic matter consumption in the blooming Mertz polynya and adaptation to polar conditions in the ubiquitous bacteria Pelagibacter. Our work takes a step towards a comprehensive understanding of SO's plankton ecology and evolution, capturing the current state of the unique microbial diversity in this rapidly changing Ocean.},
}
@article {pmid41673107,
year = {2026},
author = {Shepard, DM and Hahn, S and Chitre, M and Neff, H and Ward, DV and Jadhav, N and Richmond, JM and Ramirez-Ortiz, ZG},
title = {SCARF1 deficiency exacerbates gut inflammation and autoimmune pathology.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41673107},
issn = {2045-2322},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Lupus Erythematosus, Systemic/pathology/immunology/genetics/microbiology ; *Inflammation/pathology/genetics ; Mice, Knockout ; Disease Models, Animal ; Dysbiosis ; Autoimmunity ; Mice, Inbred C57BL ; },
abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease known for its heterogeneity in both manifestation and presentation. Recent evidence has increasingly implicated the gut microbiome within immunomodulation and autoimmunity. This study aims to characterize the intestinal inflammation and microbial profile associated with autoimmune diseases, particularly SLE, and to identify unique biomarkers and shared microbial signatures for potential therapeutic measures. Our lab identified scavenger receptor class F, member 1 (SCARF1, SREC-1) as an efferocytosis receptor essential for the clearance of apoptotic debris, and its deficiency results in the development of lupus-like disease. SCARF1 is crucial in immune homeostasis, and defects in efferocytosis lead to inflammation. However, the role of SCARF1 in gut homeostasis remains to be elucidated. To answer our question, we analyzed and compared the metagenomic datasets generated through whole genome shotgun sequencing between our Scarf1[-/-] lupus-prone mouse model and healthy counterparts. We found that Scarf1[-/-] mice had significantly lengthened intestines, elevated immune cell infiltration, and structural changes in the colon. Microbiome analysis revealed gut dysbiosis, including reduced alpha diversity and increased Firmicute/Bacteroidetes ratio. Notably, beneficial taxa such as Akkermansia muciniphila was absent in Scarf1[-/-] mice. Linear regression analysis identified positive associations between lupus disease severity and increased abundances of Alistipes, Lachnospiraceae, and Clostridium. Function analysis of the gut microbiome in Scarf1[-/-] mice indicated downregulation of multiple pathways related to cell proliferation. These findings highlight the role of SCARF1 involvement in the gut microbiome and immune regulation in the context of inflammation and SLE.},
}
@article {pmid41645054,
year = {2026},
author = {Zhang, XX and Zhang, H and Zhao, JX and Yu, HL and Wang, CR and Shang, KM and Wei, YJ and Qin, Y and Li, JM and Zhao, ZY and Xia, CY and Chen, BN and Elsheikha, HM and Ma, H},
title = {Gut microbiota response to Enterocytozoon bieneusi infection in wild rodents: enhanced vitamin B and K2 biosynthesis pathways.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41645054},
issn = {1471-2164},
support = {Grant No. 32170538//the National Natural Science Foundation of China/ ; 2022YFF0710503//the National Key R&amp;D Program of China/ ; 32500449//the National Natural Science Foundation of China-Youth Science Fund/ ; ZD2022C006//the Natural Science Foundation of Heilongjiang Province/ ; Grant No. 667/2424025//the Horizontal Project of Qingdao Agricultural University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Enterocytozoon/physiology ; *Vitamin K 2 ; *Rodentia/microbiology ; *Microsporidiosis/microbiology/veterinary/metabolism ; Biosynthetic Pathways ; },
abstract = {Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that affects immunocompromised individuals, including those with HIV, and represents a major cause of diarrhea. It can severely impact human health, causing gastrointestinal disease, nutritional deficits, and life-threatening complications. However, the microbial mechanisms by which E. bieneusi affects host nutrition are not well understood. Wild rodents have long been considered valuable models for studying human diseases due to similarities in gut microbiota dynamics and immune responses, making them particularly relevant for investigating parasitic infections. Here, we assembled a comprehensive catalog of 9,929 non-redundant microbial genomes from wild rodent gut metagenomes and evaluated their potential for B vitamins and vitamin K2 biosynthesis using comparative functional genomics. We identified 2,307 genomes encoding complete pathways for de novo biosynthesis of at least one essential vitamin, though no single genome encoded all pathways, indicating a distributed metabolic capacity within the microbial community. Infection with E. bieneusi significantly altered the microbial composition and the potential for vitamin biosynthesis, with a notable expansion of Methanobacteriota and reprogramming of pyridoxine (vitamin B6) biosynthesis pathways. These changes reveal a functional shift in microbial metabolism in response to parasitic pressure. By elucidating the microbial basis of vitamin biosynthesis in wild rodents and the impact of E. bieneusi infection on microbial functions, this study provides new insights into the role of gut microbiota in maintaining host health and supporting nutrient provision under parasitic stress. Moreover, the findings will provide valuable insights into the prevention and control of E. bieneusi infection in a variety of host, including humans.},
}
@article {pmid41448605,
year = {2026},
author = {Goh, CE and Bohn, B and Genkinger, JM and Molinsky, R and Roy, S and Paster, BJ and Chen, CY and Johnson, S and Yuzefpolskaya, M and Colombo, PC and Rosenbaum, M and Knight, R and Desvarieux, M and Papapanou, PN and Jacobs, DR and Demmer, RT},
title = {Dietary Nitrate Intake and 16S rRNA-Inferred Nitrite-Generating Capacity of the Subgingival Microbiome May Influence Glucose Metabolism: Results From the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS).},
journal = {Journal of clinical periodontology},
volume = {53},
number = {4},
pages = {508-519},
doi = {10.1111/jcpe.70084},
pmid = {41448605},
issn = {1600-051X},
support = {R00 DE018739/NH/NIH HHS/United States ; R21 DE022422/NH/NIH HHS/United States ; R01 DK 102932/NH/NIH HHS/United States ; T32HL007779/NH/NIH HHS/United States ; DK-63608//Vagelos College of Physicians and Surgeons, Columbia University/ ; UL1TR001873/TR/NCATS NIH HHS/United States ; R00 DE018739/NH/NIH HHS/United States ; R21 DE022422/NH/NIH HHS/United States ; R01 DK 102932/NH/NIH HHS/United States ; T32HL007779/NH/NIH HHS/United States ; UL1TR001873/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Female ; Cross-Sectional Studies ; Adult ; *RNA, Ribosomal, 16S/genetics ; Male ; *Insulin Resistance ; *Nitrates/administration &amp; dosage/metabolism ; *Gingiva/microbiology ; *Microbiota/genetics ; *Nitrites/metabolism ; *Diet ; Blood Glucose/metabolism ; *Glucose/metabolism ; Biomarkers ; Cardiometabolic Risk Factors ; *Glucose Intolerance/metabolism/microbiology ; },
abstract = {AIMS: To investigate whether the association between the nitrite-generating capacity of the subgingival microbiome and early cardiometabolic risk biomarkers varies by dietary nitrate intake.<br><br>MATERIALS AND METHODS: Cross-sectional data from 668 participants (mean age 31&#x2009;&#xb1;&#x2009;9&#x2009;years, 73% women) were analysed. Dietary nitrate intake was calculated from food frequency questionnaires. Subgingival 16S rRNA sequencing (Illumina, MiSeq) and PICRUSt2 estimated microbial genes. The Microbiome-Induced Nitric Oxide Enrichment Score (MINES) was calculated as a ratio of microbial gene abundances representing enhanced net capacity for NO generation. Adjusted multivariable linear models regressed cardiometabolic risk biomarkers (HbA1c, glucose, insulin, insulin resistance (HOMA-IR), blood pressure) on nitrate intake and MINES together with a MINES &#xd7; nitrate intake interaction term.<br><br>RESULTS: Mean nitrate intake was 190&#x2009;&#xb1;&#x2009;171&#x2009;mg/day. Significant interactions of MINES and nitrate intake were observed for insulin and HOMA-IR (p&#x2009;<&#x2009;0.05). Among participants with a low MINES, higher nitrate intake was associated with lower HOMA-IR (1.2 [1.1-1.4] vs. 1.5 [1.3-1.6]; p&#x2009;=&#x2009;0.002), but levels were similar in those with high MINES (p&#x2009;=&#x2009;0.84).<br><br>CONCLUSIONS: A biomarker of higher microbial NO-generating capacity in subgingival plaque is associated with lower insulin and insulin resistance among individuals with lower dietary nitrate intake. Future trials evaluating the cardiometabolic benefits of nitrate-rich diets should incorporate measures of the entire oral microbiome.},
}
@article {pmid37762509,
year = {2023},
author = {Zabolotneva, AA and Gaponov, AM and Roumiantsev, SA and Vasiliev, IY and Grigoryeva, TV and Kit, OI and Zlatnik, EY and Maksimov, AY and Goncharova, AS and Novikova, IA and Appolonova, SA and Markin, PA and Shestopalov, AV},
title = {Alkylresorcinols as New Modulators of the Metabolic Activity of the Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {24},
number = {18},
pages = {},
pmid = {37762509},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Resorcinols/pharmacology/metabolism ; Humans ; Mice ; Feces/microbiology/chemistry ; Mice, Inbred C57BL ; Male ; Fecal Microbiota Transplantation ; Receptors, LDL/genetics ; Female ; },
abstract = {Alkylresorcinols (ARs) are polyphenolic compounds with a wide spectrum of biological activities and are potentially involved in the regulation of host metabolism. The present study aims to establish whether ARs can be produced by the human gut microbiota and to evaluate alterations in content in stool samples as well as metabolic activity of the gut microbiota of C57BL, db/db, and LDLR (-/-) mice according to diet specifications and olivetol (5-n-pentylresorcinol) supplementation to estimate the regulatory potential of ARs. Gas chromatography with mass spectrometric detection was used to quantitatively analyse AR levels in mouse stool samples; faecal microbiota transplantation (FMT) from human donors to germ-free mice was performed to determine whether the intestinal microbiota could produce AR molecules; metagenome sequencing analysis of the mouse gut microbiota followed by reconstruction of its metabolic activity was performed to investigate olivetol's regulatory potential. A significant increase in the amounts of individual members of AR homologues in stool samples was revealed 14 days after FMT. Supplementation of 5-n-Pentylresorcinol to a regular diet influences the amounts of several ARs in the stool of C57BL/6 and LDLR (-/-) but not db/db mice, and caused a significant change in the predicted metabolic activity of the intestinal microbiota of C57BL/6 and LDLR (-/-) but not db/db mice. For the first time, we have shown that several ARs can be produced by the intestinal microbiota. Taking into account the dependence of AR levels in the gut on olivetol supplementation and microbiota metabolic activity, AR can be assumed to be potential quorum-sensing molecules, which also influence gut microbiota composition and host metabolism.},
}
@article {pmid37648194,
year = {2023},
author = {Kakakhel, MA and Narwal, N and Kataria, N and Johari, SA and Zaheer Ud Din, S and Jiang, Z and Khoo, KS and Xiaotao, S},
title = {Deciphering the dysbiosis caused in the fish microbiota by emerging contaminants and its mitigation strategies-A review.},
journal = {Environmental research},
volume = {237},
number = {Pt 2},
pages = {117002},
doi = {10.1016/j.envres.2023.117002},
pmid = {37648194},
issn = {1096-0953},
mesh = {Animals ; *Dysbiosis/chemically induced/veterinary/microbiology ; *Fishes/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; *Fish Diseases/microbiology/chemically induced ; },
abstract = {The primary barrier to nutrient absorption in fish is the intestinal epithelium, followed by a community of microorganisms known as the gut microbiota, which can be thought of as a hidden organ. The gastrointestinal microbiota of fish plays a key role in the upholding of overall health by maintaining the homeostasis and disease resistance of the host. However, emerging contaminants as the result of anthropogenic activities have significantly led to disruptions and intestinal dysbiosis in fish. Which probably results in fish mortalities and disrupts the balance of an ecosystem. Therefore, we comprehensively seek to compile the effects and consequences of emerging contaminations on fish intestinal microbiota. Additionally, the mitigation strategies including prebiotics, probiotics, plant-based diet, and Biofloc technology are being outlined. Biofloc technology (BFT) can treat toxic materials, i.e., nitrogen components, and convert them into a useful product such as proteins and demonstrated promising elevating technique for the fish intestinal bacterial composition. However, it remains unclear whether the bacterial isolate is primarily responsible for the BFT's removal of nitrate and ammonia and the corresponding removal mechanism. To answer this, real time polymerase chain reaction (RT-PCR) with metagenomics, transcriptomics, and proteomics techniques probably provides a possible solution.},
}
@article {pmid37634690,
year = {2023},
author = {Liu, L and Xin, Y and Guang, SB and Lin, GF and Liu, CX and Zeng, LQ and He, SQ and Zheng, YM and Chen, GY and Zhao, QB},
title = {Planktonic microbial community and biological metabolism in a subtropical drinking water river-reservoir system.},
journal = {Environmental research},
volume = {237},
number = {Pt 2},
pages = {116999},
doi = {10.1016/j.envres.2023.116999},
pmid = {37634690},
issn = {1096-0953},
mesh = {*Rivers/microbiology ; *Drinking Water/microbiology ; *Microbiota ; China ; *Plankton ; Bacteria/metabolism/classification ; *Water Microbiology ; Environmental Monitoring ; },
abstract = {To understand the dynamics of planktonic microbial community and its metabolism processes in subtropical drinking water river-reservoir system with lower man-made pollution loading, this study selected Dongzhen river-reservoir system in Mulan Creek as object to investigate spatial-temporal characteristics of community profile and functional genes involved in biological metabolism, and to analyze the influence of environmental factors. The results indicated that Proteobacteria and Actinobacteria were the most diverse phyla with proportion ranges of 9%-80% in target system, and carbohydrate metabolism (5.76-7.12 × 10[-2]), amino acid metabolism (5.78-7.21 × 10[-2]) and energy metabolism (4.07-5.17 × 10[-2]) were found to be the dominant pathways of biological metabolism. Although there were variations in biological properties both spatially and temporally, seasonal variation had a greater influence on microbial community and biological metabolism, than locational differences. Regarding the role of environmental factors, this study revealed that microbial diversity could be affected by multiple abiotic factors, with total organic carbon, total phosphorus and temperature being more influential (absolute value of standardized regression weights >2.13). Stochastic processes dominated the microbial community assembly (R[2] of neutral community model = 0.645), while niche-based processes differences represented by nutrients, temperature and pH level played secondary roles (R > 0.388, P < 0.01). Notably, the synergistic influences among the environmental factors accounted for the higher percentages of community variation (maximum proportion up to 17.6%). Additionally, pH level, temperature, and concentrations of dissolved oxygen, carbon and nitrogen were found to be the significant factors affecting carbon metabolism pathways (P < 0.05), yet only total organic carbon significantly affected on nitrogen transformation (P < 0.05). In summary, the microbial profile in reservoir is not completely dominated by that in feeding river, and planktonic microbial community and its metabolism in subtropical drinking water river-reservoir system are shaped by multiple abiotic and biotic factors with underlying interactions.},
}
@article {pmid37541958,
year = {2023},
author = {Patil, PK and Nagaraju, VT and Baskaran, V and Avunje, S and Rameshbabu, R and Ghate, SD and Solanki, HG},
title = {Development of microbial enrichments for simultaneous removal of sulfur and nitrogenous metabolites in saline water aquaculture.},
journal = {Journal of applied microbiology},
volume = {134},
number = {8},
pages = {},
doi = {10.1093/jambio/lxad173},
pmid = {37541958},
issn = {1365-2672},
mesh = {*Aquaculture/methods ; *Sulfur/metabolism ; Ammonia/metabolism ; *Saline Waters ; *Nitrogen/metabolism ; Nitrites/metabolism ; *Bacteria/metabolism/genetics ; *Microbial Consortia ; Nitrates/metabolism ; Nitrification ; Sulfides/metabolism ; Animals ; Water Purification/methods ; Salinity ; },
abstract = {AIM: The aim of the study was to develop microbial enrichments from the nitrifying microbial consortia and the environment for simultaneous removal of ammonia, nitrate, and sulfide in aquaculture systems at varied salinities.<br><br>METHODS AND RESULTS: Sulfur and nitrogen metabolites are the major factors affecting the farmed aquatic animal species and deteriorate the receiving environments causing ecological damage. The present study reports the development of microbial enrichments from the nitrifying microbial consortia and the environment. The enrichments used thiosulfate or thiocyanate as an energy source and simultaneously removed sulfur, ammonia, and nitrite in spiked medium (125&#xa0;mg/l ammonia; 145&#xa0;mg/l nitrite). Further, the microbes in the enrichments could grow up to 30&#xa0;g/l salinity. Metagenomic studies revealed limited microbial diversity suggesting the enrichment of highly specialized taxa, and co-occurrence network analysis showed the formation of three micro-niches with multiple interactions at different taxonomic levels.<br><br>CONCLUSIONS: The ability of the enrichments to grow in both organic and inorganic medium and simultaneous removal of sulfide, ammonia, and nitrite under varied salinities suggests their potential application in sulfur, nitrogen, and organic matter-rich aquaculture pond environments and other industrial effluents.},
}
@article {pmid37470119,
year = {2023},
author = {Chen, Q and Ren, R and Sun, Y and Xu, J and Yang, H and Li, X and Xiao, Y and Li, J and Lyu, W},
title = {The combination of metagenome and metabolome to compare the differential effects and mechanisms of fructose and sucrose on the metabolic disorders and gut microbiota in vitro and in vivo.},
journal = {Food &amp; function},
volume = {14},
number = {15},
pages = {7284-7298},
doi = {10.1039/d3fo02246c},
pmid = {37470119},
issn = {2042-650X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Fructose/metabolism/adverse effects ; Mice ; *Sucrose/metabolism/adverse effects ; Male ; *Metabolome/drug effects ; *Metagenome/drug effects ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Mice, Inbred C57BL ; *Metabolic Diseases/metabolism/microbiology ; },
abstract = {Sucrose and fructose are the most commonly used sweeteners in the modern food industry, but there are few comparative studies on the mechanisms by which fructose and sucrose affect host health. The aim of the present study was to explain the different effects of fructose and sucrose on host metabolism from the perspective of gut microbiota. Mice were fed for 16 weeks with normal drinking water (CON), 30% fructose drinking water (CF) and 30% sucrose drinking water (SUC). Compared with fructose treatment, sucrose caused significantly higher weight gain, epididymal fat deposition, hepatic steatosis, and jejunum histological injury. Sucrose increased the abundance of LPS-producing bacteria which was positively correlated with obesity traits, while fructose increased the abundance of Lactobacillus. An in vitro fermentation experiment also showed that fructose increased the abundance of Lactobacillus, while sucrose increased the abundance of Klebsiella and Escherichia. In addition, combined with microbial functional analysis and metabolomics data, fructose led to the enhancement of carbohydrate metabolism and TCA cycle capacity, and increased the production of glutamate. The cross-cooperation network greatly influenced the microbiota (Klebsiella, Lactobacillus), metabolites (glutamate, fructose 1,6-biosphosphate, citric acid), and genes encoding enzymes (pyruvate kinase, 6-phosphofructokinase 1, fructokinase, lactate dehydrogenase, aconitate hydratase, isocitrate dehydrogenase 3), suggesting that they may be the key differential factors in the process of fructose and sucrose catabolism. Therefore, the changes in gut microbiome mediated by fructose and sucrose are important reasons for their differential effects on host health and metabolism.},
}
@article {pmid37385587,
year = {2023},
author = {Taniguchi, M and Okumura, R and Matsuzaki, T and Nakatani, A and Sakaki, K and Okamoto, S and Ishibashi, A and Tani, H and Horikiri, M and Kobayashi, N and Yoshikawa, HY and Motooka, D and Okuzaki, D and Nakamura, S and Kida, T and Kameyama, A and Takeda, K},
title = {Sialylation shapes mucus architecture inhibiting bacterial invasion in the colon.},
journal = {Mucosal immunology},
volume = {16},
number = {5},
pages = {624-641},
doi = {10.1016/j.mucimm.2023.06.004},
pmid = {37385587},
issn = {1935-3456},
mesh = {Animals ; Mice ; *Mucin-2/metabolism ; *Sialyltransferases/genetics/metabolism ; *Colon/microbiology/metabolism/immunology ; *Mucus/metabolism ; *Galactosyltransferases/genetics/metabolism ; Mice, Knockout ; Humans ; *Intestinal Mucosa/metabolism/microbiology ; Gastrointestinal Microbiome ; Mice, Inbred C57BL ; *Inflammatory Bowel Diseases/immunology/metabolism ; Polysaccharides/metabolism ; Disease Models, Animal ; N-Acetylneuraminic Acid/metabolism ; Glycosylation ; },
abstract = {In the intestine, mucin 2 (Muc2) forms a network structure and prevents bacterial invasion. Glycans are indispensable for Muc2 barrier function. Among various glycosylation patterns of Muc2, sialylation inhibits bacteria-dependent Muc2 degradation. However, the mechanisms by which Muc2 creates the network structure and sialylation prevents mucin degradation remain unknown. Here, by focusing on two glycosyltransferases, St6 N-acetylgalactosaminide α-2,6-sialyltransferase 6 (St6galnac6) and β-1,3-galactosyltransferase 5 (B3galt5), mediating the generation of desialylated glycans, we show that sialylation forms the network structure of Muc2 by providing negative charge and hydrophilicity. The colonic mucus of mice lacking St6galnac6 and B3galt5 was less sialylated, thinner, and more permeable to microbiota, resulting in high susceptibility to intestinal inflammation. Mice with a B3galt5 mutation associated with inflammatory bowel disease (IBD) also showed the loss of desialylated glycans of mucus and the high susceptibility to intestinal inflammation, suggesting that the reduced sialylation of Muc2 is associated with the pathogenesis of IBD. In mucins of mice with reduced sialylation, negative charge was reduced, the network structure was disturbed, and many bacteria invaded. Thus, sialylation mediates the negative charging of Muc2 and facilitates the formation of the mucin network structure, thereby inhibiting bacterial invasion in the colon to maintain gut homeostasis.},
}
@article {pmid37382438,
year = {2023},
author = {Goffredi, SK and Panossian, B and Brzechffa, C and Field, N and King, C and Moggioli, G and Rouse, GW and Martín-Durán, JM and Henry, LM},
title = {A dynamic epibiont community associated with the bone-eating polychaete genus Osedax.},
journal = {mBio},
volume = {14},
number = {4},
pages = {e0314022},
pmid = {37382438},
issn = {2150-7511},
support = {IOS-0923775//National Science Foundation (NSF)/ ; NE/M018016/1//UKRI | Natural Environment Research Council (NERC)/ ; 213981/Z/18/Z//Wellcome Trust (WT)/ ; },
mesh = {Animals ; Symbiosis ; *Polychaeta/microbiology ; Phylogeny ; *Microbiota ; Metagenome ; Bone and Bones ; },
abstract = {Osedax, the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, which help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-yr study, we reveal a dynamic, yet persistent, shift of Campylobacterales integrated into the epidermis of Osedax, which change over time as the whale carcass degrades on the sea floor. The Campylobacterales associated with seven species of Osedax, which comprise 67% of the bacterial community on the trunk, appear initially dominated by the genus Arcobacter (at early time points <24 mo), the Sulfurospirillum at intermediate stages (~50 mo), and the Sulfurimonas at later stages (>140 mo) of whale carcass decomposition. Metagenome analysis of the epibiont metabolic capabilities suggests potential for a transition from heterotrophy to autotrophy and differences in their capacity to metabolize oxygen, carbon, nitrogen, and sulfur. Compared to free-living relatives, the Osedax epibiont genomes were enriched in transposable elements, implicating genetic exchange on the host surface, and contained numerous secretions systems with eukaryotic-like protein (ELP) domains, suggesting a long evolutionary history with these enigmatic, yet widely distributed deep-sea worms. IMPORTANCE Symbiotic associations are widespread in nature and we can expect to find them in every type of ecological niche. In the last twenty years, the myriad of functions, interactions and species comprising microbe-host associations has fueled a surge of interest and appreciation for symbiosis. During this 14-year study, we reveal a dynamic population of bacterial epibionts, integrated into the epidermis of 7 species of a deep-sea worm group that feeds exclusively on the remains of marine mammals. The bacterial genomes provide clues of a long evolutionary history with these enigmatic worms. On the host surface, they exchange genes and appear to undergo ecological succession, as the whale carcass habitat degrades over time, similar to what is observed for some free-living communities. These, and other annelid worms are important keystone species for diverse deep-sea environments, yet the role of attached external bacteria in supporting host health has received relatively little attention.},
}
@article {pmid37209219,
year = {2023},
author = {Ma, W and Yu, J and Yang, F and Zhang, X and Zhang, F and Jin, W and Sun, Z and Zhao, Z and Jia, S and Zhong, C and Xue, J},
title = {Metagenomic analysis of the relationship between the microorganisms and the volatiles' development in the wines during spontaneous fermentation from the eastern foothills of the Ningxia Helan mountains in China.},
journal = {Journal of the science of food and agriculture},
volume = {103},
number = {13},
pages = {6429-6439},
doi = {10.1002/jsfa.12718},
pmid = {37209219},
issn = {1097-0010},
support = {2022A02002-2//the Xinjiang Autonomous Region Key Project of Science and Technology/ ; 2019YFD1002500//the National Key Research and Development Project/ ; },
mesh = {Fermentation ; *Wine/microbiology/analysis ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; China ; *Flavoring Agents/metabolism/chemistry ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Taste ; Metagenomics ; *Fungi/metabolism/genetics/classification/isolation &amp; purification ; *Vitis/microbiology/metabolism/chemistry ; Gas Chromatography-Mass Spectrometry ; Microbiota ; Odorants/analysis ; },
abstract = {BACKGROUND: The natural fermentation of multispecies microbial communities is responsible for unique flavors of winery regions of the eastern foothills of the Ningxia Helan Mountains in China. However, the participation of different microorganisms in the metabolic network for the development of important flavor substances is not clearly defined. Microbial population and diversity on different fermentation phases of Ningxia wine were analyzed by metagenomic sequencing approach.<br><br>RESULTS: Gas chromatography-mass spectrometry and ion chromatography were used to identify flavor components, and 13 esters, 13 alcohols, nine aldehydes and seven ketones were detected in volatile substances with odor activity values >&#x2009;1, and eight organic acids were detected as important flavor components in young wine. Thus, 52&#x2009;238 predicted protein-coding genes from 24 genera were identified in the Kyoto Encyclopedia of Genes and Genomes level 2 pathways of global and overview maps, and the genes were primarily involved in amino acid metabolism and carbohydrate metabolism. Major microbial genera (Saccharomyces, Tatumella, Hanseniaspora, Lactobacillus, and Lachancea) were closely related to self-characteristic compound metabolism and further contributed to wine flavor.<br><br>CONCLUSION: This study clarifies the different metabolic roles of microorganisms in flavor formation during Ningxia wine spontaneous fermentation. Saccharomyces, dominant fungi involved in glycolysis and pyruvate metabolism, produces not only ethanol but also two important precursors, pyruvate and acetyl-CoA, which are necessary for the tricarboxylic acid cycle, fatty acid metabolism, amino acid metabolism, and flavor formation. Lactobacillus and Lachancea, dominant bacteria involved in lactic acid metabolism. Tatumella, dominant bacteria involved in amino acid metabolism, fatty acid metabolism, and acetic acid metabolism to produce esters in the Shizuishan City region samples. These findings provide insights into the use of local functional strains to generate unique flavor formation, as well as improved stability and quality, in wine production. &#xa9; 2023 Society of Chemical Industry.},
}
@article {pmid37189250,
year = {2023},
author = {Tong, CCL and Lin, X and Seckar, T and Koptyra, M and Kohanski, MA and Cohen, NA and Kennedy, DW and Adappa, ND and Papagiannopoulos, P and Kuan, EC and Baranov, E and Jalaly, JB and Feldman, MD and Storm, PB and Resnick, AC and Palmer, JN and Wei, Z and Robertson, ES},
title = {A metagenomic analysis of the virome of inverted papilloma and squamous cell carcinoma.},
journal = {International forum of allergy &amp; rhinology},
volume = {13},
number = {11},
pages = {2055-2062},
doi = {10.1002/alr.23182},
pmid = {37189250},
issn = {2042-6984},
mesh = {Humans ; *Papilloma, Inverted/virology/pathology ; *Carcinoma, Squamous Cell/virology ; *Papillomavirus Infections/virology/epidemiology ; Male ; Female ; Middle Aged ; *Virome/genetics ; Metagenomics ; Aged ; Human papillomavirus 16/genetics ; *Paranasal Sinus Neoplasms/virology ; *Papillomaviridae/genetics ; Human papillomavirus 18/genetics ; Adult ; },
abstract = {INTRODUCTION: Inverted papilloma (IP) is a sinonasal tumor with a well-known potential for malignant transformation. The role of human papillomavirus (HPV) in its pathogenesis has been controversial. The purpose of this study was to determine the virome associated with IP, with progression to carcinoma in situ (CIS), and invasive carcinoma.<br><br>METHODS: To determine the HPV-specific types, a metagenomics assay that contains 62,886 probes targeting viral genomes in a microarray format was used. The platform screens DNA and RNA from fixed tissues from eight controls, 16 IP without dysplasia, five IP with CIS, and 13 IP-associated squamous cell carcinoma (IPSCC). Paired with next-generation sequencing, 48 types of HPV with 857 region-specific probes were interrogated against the tumors.<br><br>RESULTS: The prevalence of HPV-16 was 14%, 42%, 70%, and 73% in control tissue, IP without dysplasia, IP with CIS, and IPSCC, respectively. The prevalence of HPV-18 had a similar progressive increase in prevalence, with 14%, 27%, 67%, and 74%, respectively. The assay allowed region-specific analysis, which identified the only oncogenic HPV-18 E6 to be statistically significant when compared with control tissue. The prevalence of HPV-18 E6 was 0% in control tissue, 25% in IP without dysplasia, 60% in IP with CIS, and 77% in IPSCC.<br><br>CONCLUSIONS: There are over 200 HPV types that infect human epithelial cells, of which only a few are known to be high-risk. Our study demonstrated a trend of increasing prevalence of HPV-18 E6 that correlated with histologic severity, which is novel and supports a potential role for HPV in the pathogenesis of IP.},
}
@article {pmid41801404,
year = {2026},
author = {Petouhoff, A and Hicks, R and Husain, M and Hoyd, R and Xu, M and Dravillas, C and Patel, SH and Johns, A and Grogan, M and Li, M and Lopez, G and Miah, A and Liu, Y and Muniak, M and Schmidt, M and Das, A and Lathrop, H and Das, P and Secor, A and Haddad, T and Tinoco, G and Carbone, D and Kendra, K and Otterson, GA and Presley, CJ and Mace, T and Spakowicz, D and Owen, DH},
title = {Impact of proton pump inhibitors on immunotherapy is modulated by prior chemotherapy and linked to gut microbiome-immune cell signatures.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {75},
number = {4},
pages = {},
pmid = {41801404},
issn = {1432-0851},
support = {P30CA016058/NH/NIH HHS/United States ; UL1TR002733/TR/NCATS NIH HHS/United States ; Innovator Award 1046611//American Lung Association/ ; Research Scholar Award RSG-23-1023205//American Cancer Society/ ; },
mesh = {Humans ; *Proton Pump Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Middle Aged ; Aged ; *Immunotherapy/methods ; Retrospective Studies ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Prospective Studies ; *Neoplasms/drug therapy/immunology/mortality ; Melanoma/drug therapy/immunology ; Carcinoma, Non-Small-Cell Lung/drug therapy/immunology ; },
abstract = {Proton pump inhibitors (PPIs) are one of the most widely used medications in the world. They have been associated with an altered microbiome, which is demonstrated to be important for immune checkpoint inhibitor (ICI) response. We sought to determine whether PPI use was associated with shorter overall survival (OS) in patients treated with ICIs, and whether these changes were associated with altered microbiomes and immune cell composition. Our retrospective study of patients with advanced cancer (n = 1078) evaluated the impact of PPI use on OS. We also analyzed stool samples from melanoma patients treated with ICIs (n = 42) and stool and blood samples from patients with non-small cell lung cancer (NSCLC) and renal cell carcinoma treated with ICIs (n = 8). With the data from our prospective study, we assessed microbiome composition from stool samples using metagenomic whole-genome shotgun; immune cell populations from blood samples were determined using CyTOF. Associations between PPI use, clinical outcomes, the microbiome, and immune cell populations were evaluated using survival analyses, diversity metrics, and multivariable models. PPI use was associated with shorter OS in patients with advanced cancers treated with ICIs, with the strongest effects seen in melanoma. PPI use was associated with worse clinical outcomes and microbiome alterations in patients with advanced cancers treated with ICIs, suggesting that its use may influence the efficacy of immunotherapy; prospective studies implicate its effect on the microbiome. These findings underscore the importance of considering the microbiome and concomitant medications when to enhance treatment response and efficacy.},
}
@article {pmid41798955,
year = {2026},
author = {Xiao, Y and Zhang, T and Chen, Q and Zhang, Y and Chen, B and Wang, M and Zhang, Y and Huang, M and Su, Y and Guo, J},
title = {Multi-omics analysis reveals the mechanism of verbenalin in treating gout via modulating purine metabolism, gut microbiota, and inflammatory pathways.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1761558},
pmid = {41798955},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; Male ; *Purines/metabolism ; Disease Models, Animal ; *Gout/drug therapy/metabolism ; Inflammation/drug therapy/metabolism ; Signal Transduction/drug effects ; *Anti-Inflammatory Agents/pharmacology ; Hyperuricemia/drug therapy ; Rats, Sprague-Dawley ; Metabolomics/methods ; Arthritis, Gouty/drug therapy/metabolism ; Multiomics ; },
abstract = {BACKGROUND: Gout is a prevalent metabolic disorder characterized by hyperuricemia and inflammation. Verbenalin, an iridoid glycoside from Verbena officinalis, possesses anti-inflammatory properties; however, its therapeutic potential and underlying mechanisms in gout remain underexplored.<br><br>OBJECTIVE: This study aimed to evaluate the pharmacological effects and elucidate the molecular mechanisms of verbenalin in a rat model of gout.<br><br>METHODS: Hyperuricemia and acute gouty arthritis were induced in rats using potassium oxonate/hypoxanthine and monosodium urate, respectively. Verbenalin was administered orally for 7 days. Therapeutic efficacy was assessed via physical symptom scores (inflammation, gait, swelling), renal/hepatic function indices, and histopathology. Furthermore, a multi-omics strategy integrating transcriptomics, metagenomics, and metabolomics, combined with Western blotting, was employed to investigate the pharmacological mechanisms.<br><br>RESULTS: Verbenalin treatment significantly alleviated joint inflammation and swelling while improving gait scores. It effectively lowered serum uric acid (UA), creatinine, and BUN levels, inhibited hepatic xanthine oxidase (XOD) activity, and promoted urinary UA excretion. Histopathological damage in the joints, kidneys, and liver was markedly mitigated. Mechanistically, verbenalin downregulated the expression of urate transporters (URAT1, GLUT9) and inflammatory mediators (NLRP3, IL-1&#x3b2;) by inhibiting the PI3K-AKT and MAPK signaling pathways. Multi-omics analysis further revealed that verbenalin restored gut microbiota diversity and modulated purine metabolism, correlating with reduced UA levels.<br><br>CONCLUSION: These findings demonstrate that verbenalin may exert anti-gout effects through the potential synergy of modulating purine metabolism, shifting gut microbiota composition, and suppressing PI3K-AKT and MAPK inflammatory signaling pathways. This study provides a preliminary scientific basis for further investigation into verbenalin as a prospective multi-target therapeutic candidate.},
}
@article {pmid41797508,
year = {2026},
author = {Huang, C and Xiao, W and Zhao, J and Zhong, R and Gao, L and Ma, H and Tian, L and Yue, P and Lin, Y and He, Q and Xia, B and Yuan, J and Yang, M and Meng, W},
title = {Gut Microbiome Dysbiosis Promotes Gallstone Formation via Bile Acid Metabolic Disorder: A Multiomics Study.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {6},
pages = {e71656},
doi = {10.1096/fj.202503254RRRRRR},
pmid = {41797508},
issn = {1530-6860},
support = {82204123//MOST | National Natural Science Foundation of China (NSFC)/ ; 82473707//MOST | National Natural Science Foundation of China (NSFC)/ ; LCYSSQ20220823091203008//Funding of Shenzhen Clinical Research Center for Gastroenterlogy (Gastrointestinal Surgery)/ ; 2022YFC2407405//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bile Acids and Salts/metabolism ; *Dysbiosis/microbiology/metabolism/complications ; *Gallstones/microbiology/metabolism/etiology ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; Aged ; Multiomics ; Amidohydrolases ; },
abstract = {Gallstone disease is a common global digestive disorder. This study intends to analyze gut microbiota-gallstone disease interactions, to inform disease mechanism and microbiota-targeted prevention and treatment strategies. Participants were recruited from health check-up populations, outpatients, and inpatients. Basic information and biological samples were collected: fecal samples for metagenomic sequencing, and serum samples for bile acid metabolism detection. A total of 62 gallstone patients and 62 healthy controls were enrolled in this study. Compared with the control group, gallstone patients exhibited increased level of bile salt hydrolase (BSH)-producing bacteria, including the genera Bacteroides, Enterococcus, Bifidobacterium, and the family Lactobacillaceae. Further KEGG analysis revealed that the significantly enriched signaling pathways in the gallstone patients were mainly related to bile acid biosynthesis, lipid and bile acid precursor metabolism. Subsequently, we found that in gallstone patients, the levels of hydrophobic bile acids, (e.g., lithocholic acid, LCA), was increased, while the levels of hydrophilic bile acids taurolithocholic acid (TLCA) were decreased. In the correlation analysis between differential bile acids and differential bacterial species, Bacteroides intestinalis was positively correlated with LCA, while Bacteroides fragilis was negatively correlated with TLCA. These results further confirm the role of BSH-active bacteria in bile acid dysregulation. This study proposes the "intestinal microbiota imbalance-bile acid metabolic disorder-gallbladder stone formation" axis, and confirms that gallstone patients exhibit intestinal dysbiosis, which leads to bile acid dysregulation. Furthermore, the accumulation of hydrophobic bile acids is identified as a key factor in gallbladder stone formation.},
}
@article {pmid41775000,
year = {2026},
author = {Mammeri, M and Obregon, D and Chevillot, A and Abuin-Denis, L and Skičková, &#x160; and Kratou, M and Wu-Chuang, A and Maitre, A and Christine, J and Polack, B and Cabezas-Cruz, A and Adjou, KT},
title = {Yeast probiotic protects gut microbiota diversity and metabolic potential against Cryptosporidiosis-induced disruption in goat kids.},
journal = {Veterinary parasitology},
volume = {343},
number = {},
pages = {110729},
doi = {10.1016/j.vetpar.2026.110729},
pmid = {41775000},
issn = {1873-2550},
mesh = {Animals ; Goats ; *Probiotics/administration &amp; dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Cryptosporidiosis/parasitology/prevention &amp; control ; Male ; *Goat Diseases/parasitology/prevention &amp; control/microbiology ; *Saccharomyces cerevisiae ; Cryptosporidium parvum/physiology ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/veterinary/prevention &amp; control ; },
abstract = {Cryptosporidiosis, caused by Cryptosporidium parvum, is a major cause of enteric disease and gut microbiota disruption in neonatal ruminants. It can lead to impaired growth, increased susceptibility to pathogens, and long-term gut dysfunction. In this study, we investigated whether supplementation with a live yeast probiotic (Saccharomyces cerevisiae Sc47) could help preserve gut microbiota resilience and functional homeostasis during an experimental C. parvum oral infection in goat kids. Thirty male French Alpine goat kids were assigned to three groups: uninfected control (healthy), infected, and infected with yeast supplementation. Longitudinal 16S rRNA gene sequencing, network analysis, and functional metagenomic predictions were used to assess microbial diversity, community composition, co-occurrence patterns, and metabolic potential, with a focus on short-chain fatty acid (SCFA) biosynthesis. Infection induced marked dysbiosis, characterised by a substantial reduction in microbial richness and a widespread loss of SCFA-producing commensals and metabolic functions. In contrast, yeast supplementation significantly reduced oocyst excretion by more than 84% throughout the experiment, attenuated pathogen-induced community shifts, and maintained beneficial genera such as Butyricicoccus and members of the Oscillospiraceae family. Furthermore, network analysis revealed that probiotic treatment preserved microbial association structures and reduced community fragmentation. Consistent with these findings, functional profiling showed the retention of pathways involved in carbohydrate metabolism, amino acid biosynthesis, and SCFA production, suggesting enhanced microbiota resilience. These findings demonstrate that S. cerevisiae supplementation can mitigate infection-associated dysbiosis by controlling pathogenic overgrowth while sustaining commensal bacterial stability and functional capacity. This highlights its potential as a microbiota-targeted strategy to support gut health in neonatal ruminants.},
}
@article {pmid41747516,
year = {2026},
author = {Hu, X and Yu, K and Chai, B and Tang, Q and Gao, X and Wang, J and Yan, Z and Li, Y and Zhang, L and Wang, C and Lei, X and Chen, B and He, L},
title = {Polyethylene microplastics specifically drive the dissemination of ARGs: Mechanisms involving microbial community restructuring and horizontal gene transfer.},
journal = {The Science of the total environment},
volume = {1021},
number = {},
pages = {181587},
doi = {10.1016/j.scitotenv.2026.181587},
pmid = {41747516},
issn = {1879-1026},
mesh = {*Microplastics/toxicity ; *Gene Transfer, Horizontal ; *Water Pollutants, Chemical/toxicity/analysis ; *Polyethylene ; *Drug Resistance, Microbial/genetics ; *Microbiota/drug effects ; Lakes/microbiology ; },
abstract = {As emerging contaminants, the impact of microplastics (MPs) on antibiotic resistance genes (ARGs), virulence factors (VFs), and host microbial communities in lakes remains unclear. To address this, we conducted a 28-day incubation experiment using water from Yiquan Lake, employing metagenomic sequencing to investigate the effects of different types of microplastics-polyethylene (PE), polystyrene (PS), polypropylene (PP), and a mixture (Mix), each at a concentration of 1 item/L-compared to a raw water control (RAW). Results showed significant enrichment of Proteobacteria and Bacteroidetes in PE and Mix groups. Genera such as Agrobacterium and Microbacterium increased in PE and PS groups, serving as major hosts of ARGs and VFs. Network analysis revealed positive correlations between Agrobacterium, Escherichia, and ARGs, suggesting horizontal gene transfer may facilitate the spread of resistance and virulence. Two-factor PS formed highly connected yet competitive networks, whereas Mix constructed modular and stable networks. Single-factor PE enhanced microbial connectivity but reduced ARGs connectivity, while Mix increased the modularity of both microbes and ARGs. PE elevated the abundance of ARGs, VFs, and mobile genetic elements, with multidrug resistance and efflux pumps as dominant mechanisms. Additionally, PE downregulated quorum sensing transporter genes while upregulating regulatory factors, significantly promoting RND efflux systems (AcrAB-TolC) to maintain resistome homeostasis. This study highlights the distinct environmental effects of different MPs, underscoring the need to prioritize PE-related risks in aquatic ecosystems. Improved management of plastic waste in and around lakes is recommended to mitigate MP-mediated ARG dissemination and preserve freshwater ecosystem services.},
}
@article {pmid41740355,
year = {2026},
author = {Lee, J and Hong, S and Choi, J and Song, H and Han, JH and Suh, YD and Yeon, SC and Cho, S},
title = {Whole-genome shotgun metagenomics reveals environmental perturbations in the gut microbiome and resistome of wild raccoon dogs rescued at a wildlife center.},
journal = {The Science of the total environment},
volume = {1021},
number = {},
pages = {181588},
doi = {10.1016/j.scitotenv.2026.181588},
pmid = {41740355},
issn = {1879-1026},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Raccoon Dogs/microbiology ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Raccoon dogs are potential vectors for the transmission of zoonotic pathogens and antimicrobial resistance, with their gut microbiome carrying genetic determinants of virulence and resistance. However, previous studies have primarily relied on traditional culture-based approaches, limiting our understanding of the entire dynamics and genetic potential of the gut microbiome in raccoon dogs. In this study, we employed both culture-dependent approach and whole-genome shotgun sequencing in raccoon dogs undergoing rehabilitation for eight weeks. We integratively assessed how rehabilitation-related environmental shifts influence the gut microbiome and resistome. Rehabilitation induced shifts in gut microbiome composition. Notably, within-group diversity decreased at week eight, indicating increased compositional similarity. Throughout rehabilitation, a total of 18 genera (e.g., Paeniclostridium, Psychrobacter) significantly increased, and 40 genera (e.g., Intestinimonas, Erysipelatoclostridium) decreased in abundance. Rehabilitation also induced shifts in the gut resistome, with reduced within-group diversity at weeks four and eight, indicating increased compositional similarity over time. Overall, 253 antimicrobial resistance genes (ARGs) present at week 0 disappeared, whereas 273 ARGs were acquired during rehabilitation. Additionally, the abundance of 15 ARGs significantly decreased and that of 33 increased, with beta-lactamases being the most common among the latter. Culture-dependent methods revealed a marked increase in bacteria resistant to third-generation cephalosporins, monobactams, and sulfonamides. Changes in microbiome composition during rehabilitation indirectly influenced the resistome and virulome through mobile genetic elements. Our findings suggest that rehabilitation-induced perturbations in the gut microbiome and resistome of raccoon dogs are likely driven by environmental shifts such as diet and habitat. These changes may affect their post-release fitness and raise concerns owing to the potential dissemination of zoonotic pathogens and antimicrobial resistance.},
}
@article {pmid41736367,
year = {2026},
author = {Keum, HL and Sul, WJ and Kim, S and Chung, IY and Koh, A and Kim, HS},
title = {Preliminary characterization of the skin microbiota in basal cell carcinoma: An exploratory pilot study in Korean patients.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {64},
number = {2},
pages = {e2511012},
doi = {10.71150/jm.2511012},
pmid = {41736367},
issn = {1976-3794},
support = {//Incheon St. Mary's Hospital/ ; //Catholic University of Korea/ ; //National Research Foundation of Korea/ ; 2023R1A2C1007759//Ministry of Science and ICT/ ; //Korea Health Industry Development Institute/ ; RS-2023-KH-136575//Ministry of Health and Welfare/ ; RS-2025-02217860//Ministry of Health and Welfare/ ; },
mesh = {Humans ; *Basal Cell Carcinoma/microbiology ; Pilot Projects ; *Skin/microbiology ; *Microbiota/genetics ; *Skin Neoplasms/microbiology ; RNA, Ribosomal, 16S/genetics ; Male ; Middle Aged ; Female ; Republic of Korea ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; DNA, Bacterial/genetics ; Aged, 80 and over ; Skin Microbiome ; },
abstract = {Basal cell carcinoma (BCC) is the most common form of skin cancer, with ultraviolet radiation recognized as the primary environmental driver; however, the potential contribution of alterations in the skin microbiota remains incompletely understood, particularly in Asian populations. This exploratory pilot study describes bacterial community patterns in BCC lesions compared with contralateral clinically normal skin in 20 Korean patients. Lesional and contralateral samples were obtained using paired skin swabs and punch biopsies and analyzed by full-length 16S rRNA gene sequencing, with targeted quantitative PCR (qPCR) of the roxP antioxidant gene of Cutibacterium acnes. Given the low-biomass nature of skin samples and the exploratory design, analyses focused on descriptive trends rather than confirmatory inference. Across available samples, C. acnes was the dominant taxon, with a trend toward lower relative abundance in BCC lesions, particularly in biopsy-derived datasets. Microbial evenness appeared higher in lesions than controls. Predictive functional profiling suggested reduced representation of vitamin B6 metabolism pathways in lesions, while qPCR analysis of swab samples showed a trend toward lower roxP/16S rRNA ratios in BCC-associated microbiota. These findings should be interpreted cautiously in light of methodological constraints, including sample heterogeneity, lidocaine exposure prior to biopsy, absence of sequencing-based negative controls, and reliance on predictive functional inference. Overall, this pilot study highlights potential differences in skin bacterial community structure between BCC lesions and contralateral skin in a Korean cohort. Larger, methodologically optimized studies incorporating metagenomic and functional validation will be required to determine whether these microbiota shifts contribute to, or result from, BCC-associated changes in the cutaneous environment.},
}
@article {pmid41689511,
year = {2026},
author = {Xu, R and Mayer, MJ and Philo, M and Gall, GL and Mulaw, G and Ponsero, A and Narbad, A},
title = {Combining Lactiplantibacillus plantarum and Bifidobacterium adolescentis can improve GABA production in faecal fermentations.},
journal = {Journal of applied microbiology},
volume = {137},
number = {3},
pages = {},
doi = {10.1093/jambio/lxag047},
pmid = {41689511},
issn = {1365-2672},
support = {BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/QU/230001D/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //China Scholarship Council/ ; },
mesh = {Fermentation ; *Feces/microbiology ; *gamma-Aminobutyric Acid/biosynthesis/metabolism ; *Probiotics/metabolism ; *Lactiplantibacillus plantarum/metabolism ; *Bifidobacterium adolescentis/metabolism/growth &amp; development ; Humans ; Coculture Techniques ; Gastrointestinal Microbiome ; Fatty Acids, Volatile/metabolism ; Hydrogen-Ion Concentration ; Lactic Acid/metabolism ; },
abstract = {AIMS: This project aimed to investigate production of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) from potential probiotic strains. We studied production in co-cultures and faecal fermentations and examined the effect of selected strains on the faecal microbiome composition and metabolome in vitro.<br><br>METHODS AND RESULTS: Strains of intestinally derived Bifidobacterium adolescentis and Lactiplantibacillus plantarum from fermented cereals were grown singly, in co-culture and in faecal fermentations designed to simulate colonic conditions. Isolates synthesized varying amounts of GABA in vitro; GABA production could be increased by co-culture, lactic acid, or reduced pH but was decreased in the presence of high buffering. In faecal fermentations, selected strains inoculated singly or in combination persisted over 24 h and increased the GABA concentration without causing major disruptions in the microbiome or metabolome. Bifidobacterium adolescentis supplementation increased short-chain fatty acids acetate and propionate, and L. plantarum was associated with increased succinate levels, while all treatments exhibited a reduction in Escherichia compared to the controls.<br><br>CONCLUSIONS: GABA production from these lactic acid bacteria is strain-specific and the combination of these two species shows potential for future next-generation probiotic development.},
}
@article {pmid41572438,
year = {2026},
author = {Maes, M and Almulla, AF and Vasupanrajit, A and Jirakran, K and Tunvirachaisakul, C and Maes, A and Chanchaem, P and Klomkliew, P and Payungporn, S and Zhang, Y},
title = {Functional shotgun metagenomic insights into gut microbial pathway and enzyme disruptions linking metabolism, affect, cognition, and suicidal ideation in major depressive disorder.},
journal = {Acta neuropsychiatrica},
volume = {38},
number = {},
pages = {e16},
doi = {10.1017/neu.2026.10056},
pmid = {41572438},
issn = {1601-5215},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; *Major Depressive Disorder/microbiology/metabolism/psychology ; Metagenomics ; Male ; Female ; Adult ; *Suicidal Ideation ; Middle Aged ; Dysbiosis/microbiology ; Cognition/physiology ; Affect/physiology ; },
abstract = {BACKGROUND: Major depression (MDD) is linked to neuro-immune, metabolic, and oxidative stress (NIMETOX) pathways. The gut microbiome may contribute to these pathways via leaky gut and immune–metabolic processes.<br><br>AIMS: To identify gut microbial alterations in MDD and to quantify functional pathways and enzyme gene families and integrate these with the clinical phenome and immune&#x2013;metabolic biomarkers of MDD.<br><br>METHODS: Shotgun metagenomics with taxonomic profiling was performed in MDD versus controls using MetaPhlAn v4.0.6, and functional profiling was conducted using HUMAnN v3.9, aligning microbial reads to species-specific pangenomes (Bowtie2 v2.5.4) followed by alignment to the UniRef90 v201901 protein database (DIAMOND v2.1.9).<br><br>RESULTS: Gut microbiome diversity, both species richness and evenness, is quite similar between MDD and controls. The top enriched taxa in the multivariate discriminant profile of MDD reflect gut dysbiosis associated with leaky gut and NIMETOX mechanisms, that is, Ruminococcus gnavus, Veillonella rogosaem, and Anaerobutyricum hallii. The top four protective taxa enriched in controls indicate an anti-inflammatory ecosystem and microbiome resilience, that is, Vescimonas coprocola, Coprococcus, Faecalibacterium prausnitzii, and Faecalibacterium parasitized. Pathway analysis indicates loss of barrier protection, antioxidants, and short-chain fatty acids, and activation of NIMETOX pathways. The differential abundance of gene families suggests that there are metabolic distinctions between both groups, indicating aberrations in purine, sugar, and protein metabolism. The gene and pathway scores explain a larger part of the variance in suicidal ideation, recurrence of illness, neurocognitive impairments, immune functions, and atherogenicity.<br><br>CONCLUSION: The gut microbiome changes might contribute to activated peripheral NIMETOX pathways in MDD.},
}
@article {pmid41197508,
year = {2025},
author = {Wen, M and Deng, C and Lei, J and Yang, X and Li, J and Al-Dhabi, NA and Wen, S and Tang, W and Feng, B and Zhang, P},
title = {Amoxicillin effects on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) in the algal-bacterial biofilm.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140363},
doi = {10.1016/j.jhazmat.2025.140363},
pmid = {41197508},
issn = {1873-3336},
mesh = {*Water Purification ; Biofilms/drug effects ; Bioreactors/microbiology ; *Amoxicillin/pharmacology ; *Bacterial Proteins/biosynthesis ; *Drug Resistance, Bacterial/genetics ; Water Pollutants/isolation &amp; purification ; *Microbial Consortia/drug effects ; Cyanobacteria/drug effects ; *Metagenome/drug effects ; Gene Transfer, Horizontal ; },
abstract = {The algal-bacterial wastewater treatment process is characterized by its efficiency in water quality purification and bioresource recovery. This study investigated the effects of amoxicillin (AMX) on pollutant removal, cyanophycin synthesis, and the proliferation of antibiotic resistance genes (ARGs) within the algal-bacterial biofilm. AMX significantly suppressed ammonia and phosphorus removal by inhibiting nitrogen and phosphorus assimilation in cyanobacteria. A total of 72 metagenomic assembled genomes carrying cyanophycin biosynthetic genes were identified, with Pantanalinema and Planktothrix being the primary cyanophycin-producing species. AMX concentrations of 0.5 and 1 mg/L suppressed both cyanobacterial growth and cyanophycin synthesis, with the inhibitory effect intensifying as AMX concentration increased. AMX also promoted the proliferation of sul1, OXA-101, VEB-3, and qacEdelta1, while decreased the abundance of OXA-36, erm(F), and tet types. Pseudomonadota and Bacteroidota were the primary hosts for ARGs proliferation and dissemination, with bacA and tetX1 actively spreading within the algal-bacterial biofilm. Cyanobacteria played a negligible role in the propagation of ARGs. This study offers new insights into the spread of ARGs and bioresource recovery in algal-bacterial systems, focusing on both gene and strain levels.},
}
@article {pmid41794462,
year = {2026},
author = {Di Gianvito, P and Sáez, V and Dimopoulou, M and Papandreou, C and Francesca, N and Vrhovsek, U and Rantsiou, K and Cocolin, L and Arapitsas, P and Englezos, V},
title = {The role of mycobiome in terroir and during Muscat grapes fermentation unveiled by multi-omic analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118577},
doi = {10.1016/j.foodres.2026.118577},
pmid = {41794462},
issn = {1873-7145},
mesh = {*Fermentation ; *Vitis/microbiology ; *Wine/microbiology/analysis ; *Mycobiome ; Italy ; Metabolomics/methods ; Greece ; Saccharomyces cerevisiae/metabolism ; Metagenomics/methods ; Food Microbiology ; Metabolome ; Kluyveromyces/metabolism ; Multiomics ; },
abstract = {The wine microbiome is a key determinant in shaping wine terroir. To date, a comprehensive understanding of how microbial signatures influence wine metabolic profile remains poorly understood. To address this, in the present study an integrated shotgun metagenomics and untargeted metabolomic approach was employed to investigate the wine metabolome and connect the composition and functions of microbiomes involved in wine fermentation of Muscat grapes harvested in Italy and Greece. Beta diversity highlighted the dissimilarity between Italian and Greek fungal terroirs. A marked reduction in diversity during fermentation underscored the dominance of the inoculated Saccharomyces cerevisiae starter culture. The LEfSe analysis revealed an enrichment of Torulaspora delbrueckii in Greek samples, while Kluyveromyces marxianus and lactis were more abundant in Italian samples. Functional analysis revealed geographic differences in nucleotide, fatty acids and lysine metabolisms. Significant shifts were observed in energy, carbohydrate, and amino acid metabolisms, reflecting terroir-specific microbial activity. The metabolomics data highlighted regional differences in oligosaccharides, glycosylated phenolics, peptide and amino acid turnover, and central redox metabolites, suggesting divergent microbial responses and metabolic trajectories shaped by terroir and fermentation conditions. Obtained results highlight the effectiveness of this multi-omics approach in identifying product-specific fungal communities and wine metabolite signatures, providing new tools that could be used to ensure wine authenticity and quality control.},
}
@article {pmid41609371,
year = {2026},
author = {Panattoni, A and De Boeck, I and Wittouck, S and Deffner, P and Lillie-Jaschniski, K and Stadler, J and Lebeer, S and Theuns, S},
title = {Exploring the functional microbiome of pigs within the porcine respiratory disease complex: viral-bacterial co-infections and virulence factor profiling.},
journal = {Microbiology spectrum},
volume = {14},
number = {3},
pages = {e0191025},
pmid = {41609371},
issn = {2165-0497},
support = {HBC.2023.0154//Agentschap Innoveren en Ondernemen/ ; },
mesh = {Animals ; Swine ; *Virulence Factors/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/pathogenicity ; *Swine Diseases/microbiology/virology ; *Coinfection/microbiology/veterinary/virology ; *Respiratory Tract Infections/veterinary/microbiology/virology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Porcine respiratory and reproductive syndrome virus/isolation &amp; purification/genetics ; Influenza A virus/isolation &amp; purification/genetics ; *Bacterial Infections/veterinary/microbiology ; Respiratory System/microbiology/virology ; Metagenomics ; },
abstract = {Respiratory infections are among the most impacting on pigs' health and economic productivity. Despite this, detailed insights into the microbial community of the lower respiratory tract (LRT) are currently lacking, mainly because of difficulties in the processing of respiratory samples. In this study, we characterized the microbiota of the LRT of finisher pigs aged 3-5 months with respiratory symptoms for both the viral and bacterial components, using a previously validated metagenomic diagnostic assay and a full-length 16S rRNA gene sequencing approach, respectively. Functional characterization was carried out using metagenomic shotgun sequencing, revealing the presence of specific virulence factors (VFs). Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and swine Influenza A Virus (swIAV) were the most prevalent viruses, being detected in 30% and 23% of the tested samples, respectively. Mesomycoplasma hyopneumoniae, Glaesserella parasuis, and Pasteurella multocida were the three most abundant bacterial taxa based on both sequencing approaches, while other detected bacterial taxa consisted mainly of Streptococcus, Clostridium, and Rothia species. Detected virulence factors belonged mainly to Mesomycoplasma and Pasteurella and consisted of adhesion factors such as p102, p97, p146, mhp108, mhp107 and the hemolysin-encoding gene hlyA for Mesomycoplasma, and adhesin-encoding ptfA and endoxtoxin-related gene lpxC for Pasteurella. Our data show how the microbial community of the lower respiratory tract in pigs with respiratory symptoms includes key viral (PRRSV, swIAV) and bacterial pathogens (M. hyopneumoniae, G. parasuis, and P. multocida), along with specific virulence factors likely contributing to disease.IMPORTANCEThe obtained results offer insights into the composition of the swine respiratory tract microflora, opening new perspectives on its correlation with viral infections, functional characteristics, and overall health conditions. Moreover, the present study provides technical advancement on the possibility of extracting and amplifying bacterial DNA from low-biomass respiratory samples, with the resulting possibility of identifying virulence factors and better understanding their contribution to the disease state. These discoveries pave the way for future studies aimed at improving diagnostic accuracy and treatment strategies for respiratory disease in both veterinary and human medicine.},
}
@article {pmid41570402,
year = {2026},
author = {Nitert, MD and Sternes, PR and Altemani, F and Callaway, LK and McIntyre, H and Tyson, GW and Barrett, HL},
title = {Gut microbiota is different before the development of preeclampsia.},
journal = {Pregnancy hypertension},
volume = {43},
number = {},
pages = {101415},
doi = {10.1016/j.preghy.2026.101415},
pmid = {41570402},
issn = {2210-7797},
mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology/physiopathology/diagnosis ; *Gastrointestinal Microbiome ; Adult ; Feces/microbiology ; Blood Pressure ; Case-Control Studies ; },
abstract = {OBJECTIVES: The gut microbiota contributes to the regulation of blood pressure during and outside pregnancy. Preeclampsia (PE) is characterised by the development of hypertension along with renal, liver or other systemic complications. In women with PE, alterations in the gut microbiota composition have been reported.<br><br>STUDY DESIGN: We investigated whether changes in the gut microbiota composition were present before the onset of symptoms in a group of 10 women who developed late-onset PE and 24 women who remained normotensive throughout pregnancy. Faecal samples were obtained at 28&#xa0;weeks' gestation from a subset of participants of the Study of PRobiotics IN Gestational diabetes (SPRING) and sequenced by metagenomic sequencing.<br><br>MAIN OUTCOME MEASURES: Taxonomic and functional characteristics were compared between the groups.<br><br>RESULTS: There were no taxonomic or functional differences in alpha diversity; however, for beta diversity, women who developed PE demonstrated a different taxonomic composition compared to women who remained normotensive. Women who developed PE had lower abundance of numerous taxa and functions. Both systolic and diastolic blood pressure were correlated with the abundances of specific species, though members of the same genus did not show consistency in the direction of correlation.<br><br>CONCLUSION: Despite a limited sample size, this study demonstrates numerous taxonomic and functional alterations in the gut microbiota composition. However, a clear signature to identify women at high risk of developing late-onset PE remains to be uncovered. The species-level data indicate that the regulation of blood pressure by the gut microbiota in pregnancy is complex and needs further investigation.},
}
@article {pmid41312680,
year = {2026},
author = {Koike, Y and Morisaki, H and Motooka, D and Matsumoto, M and Takenaka, M and Murota, H},
title = {Postauricular Skin Mycobiome Profiles in Atopic Dermatitis Treated With Dupilumab or Cyclosporine A: A Descriptive Case Series.},
journal = {The Journal of dermatology},
volume = {53},
number = {3},
pages = {430-436},
doi = {10.1111/1346-8138.70083},
pmid = {41312680},
issn = {1346-8138},
support = {//Leading Medical Research Core Unit, Life Science Innovation, Nagasaki University Graduate School of Biomedical Sciences/ ; 25K11567//Japan Society for the Promotion of Science/ ; JP256f0137009//Japan Agency for Medical Research and Development/ ; },
mesh = {Humans ; *Dermatitis, Atopic/drug therapy/microbiology/immunology ; *Cyclosporine/therapeutic use/pharmacology ; Male ; Female ; Adult ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Skin/microbiology/drug effects/immunology ; Middle Aged ; *Mycobiome/drug effects ; Malassezia/isolation &amp; purification ; Young Adult ; Calcineurin Inhibitors/therapeutic use/pharmacology ; DNA, Fungal/isolation &amp; purification ; Treatment Outcome ; },
abstract = {Atopic dermatitis (AD) essentially exhibits dysbiosis of skin fungal microbiome, mycobiome, characterized by depletion of Malassezia. The effects of recent systemic therapies for AD on skin mycobiome were not understood enough. We examined changes of skin mycobiome before and after systemic treatments with anti-IL-4Rα antibody (dupilumab: DUP) and calcineurin inhibitor (cyclosporine, CyA). Swab samples from postauricular areas in 19 AD patients treated with dupilumab (n = 13) and cyclosporine (n = 6) were collected before and 4-8 weeks after starting each treatment. Fungal DNA was amplified from the samples and sequenced with ITS1 metagenomic analysis, and taxonomic classification was performed. Fungi belonging to total 89 genera were detected. The share of the fungus was most occupied by Malassezia (81.3%), followed by Aspergillus (3.7%), and Trametes (1.1%) before DUP and CyA treatment, and occupied by Malassezia (87.3%), followed by Aspergillus (1.9%), and Candida (1.7%) after treatment. Three AD patients whose ratio of Malassezia in the skin mycobiome was under 50%, showed an exploratory increase of Malassezia after treatments (before 17.3%, after 67%). Analysis of the Malassezia species revealed an increase in M. restricta (before 70.5%, after 79.5%) and a decrease in M. globosa (before 23.9%, after 16.1%). No consistent patterns distinguishing DUP and CyA were observed. Systemic treatment with DUP and CyA was associated with shifts toward higher Malassezia abundance and modulation between M. restricta and M. globosa. These findings are exploratory and require validation in larger controlled studies.},
}
@article {pmid41025937,
year = {2026},
author = {Garvey, SM and Blonquist, TM and Brutscher, LM and Walsh, DM and Kaden, VN and Beckman, DB and Zeng, M and Bruno, RS and Cook, CM and Spears, JL},
title = {Dietary Supplementation with the Probiotic Bacillus velezensis BV379 Decreases Abdominal Bloating Without Perturbing the Commensal Gut Microbiota: A Randomized, Double-Blind, Placebo-Controlled Trial in Healthy Adults.},
journal = {Journal of the American Nutrition Association},
volume = {45},
number = {3},
pages = {250-265},
doi = {10.1080/27697061.2025.2563894},
pmid = {41025937},
issn = {2769-707X},
mesh = {Humans ; *Probiotics/administration &amp; dosage/therapeutic use ; Double-Blind Method ; Female ; *Gastrointestinal Microbiome/drug effects ; Male ; *Bacillus ; Middle Aged ; Adult ; *Dietary Supplements ; Feces/microbiology ; Flatulence ; },
abstract = {OBJECTIVE: Various bacterial Bacillaceae and Bacillus strains have demonstrated health benefits, but less is known about probiotic characteristics of strains of Bacillus velezensis. In this randomized, double-blind, placebo-controlled clinical trial, we investigated the safety and efficacy of B. velezensis BV379 supplementation for 8 weeks (2 × 10[9] colony-forming units (CFU)/day).<br><br>METHODS: During the baseline and final weeks, GI symptoms were recorded daily using the 8-item Gastrointestinal Tolerance Questionnaire (GITQ). The primary outcome was the proportion of participants showing an improvement from baseline to week 8 in the 7-day, 3-item composite score for abdominal distention/bloating, burping, and gas/flatulence. Plasma chemistry, hematology, intestinal permeability, and fecal metagenomes were also investigated.<br><br>RESULTS: Eighty participants (54% female; age: 50.3&#x2009;&#xb1;&#x2009;10.1&#x2009;years) were randomized to BV379 (n&#x2009;=&#x2009;39) or placebo (n&#x2009;=&#x2009;41). At end of study, no significant difference was observed in the percentage of participants with improvement in the 3-item composite GITQ score (BV379: 36.1%; placebo: 28.2%; p&#x2009;=&#x2009;0.46). Analysis of individual GI symptoms showed that more participants experienced improvement in abdominal distention/bloating with BV379 compared to placebo (38.9% vs 17.9%; p&#x2009;=&#x2009;0.044). There were no clinically meaningful changes in plasma chemistry, hematology, or intestinal permeability between groups. Fecal metagenomic analyses showed no overall shifts in microbial composition between groups. In addition to B. velezensis, a few commensal species such as Lacticasei bacillus casei were significantly enriched in the BV379 group.<br><br>CONCLUSION: Despite not significantly improving the composite GITQ score of distention/bloating, burping, and gas/flatulence, BV379 supplementation was a well-tolerated approach to specifically lower abdominal bloating.},
}
@article {pmid40175821,
year = {2026},
author = {Takagi, K and Tamura, Y and Narita, N and Komatsu, S and Yamazaki, S and Matsumura, A and Kubota, K and Matsumiya, T and Sawada, K and Nakaji, S and Mikami, T and Kobayashi, W},
title = {Involvement of Megasphaera in the oral microbiome and dyslipidemia onset: evidence from a community-based study in Japan.},
journal = {Folia microbiologica},
volume = {71},
number = {1},
pages = {143-154},
pmid = {40175821},
issn = {1874-9356},
support = {21K10202//Japan Society for the Promotion of Science/ ; 22K17281//Japan Society for the Promotion of Science/ ; 24K13233//Japan Society for the Promotion of Science/ ; JPMJCE 1302//Japan Science and Technology Agency/ ; JPMJCA&#x3000;2201//Japan Science and Technology Agency/ ; JPMJPE 2210//Japan Science and Technology Agency/ ; },
mesh = {Humans ; *Dyslipidemias/microbiology/epidemiology ; Japan/epidemiology ; Male ; Female ; Middle Aged ; *Mouth/microbiology ; *Microbiota ; Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; },
abstract = {Dyslipidemia is a major risk factor for cardiovascular diseases and is influenced by genetic and environmental factors, including diet. Emerging research suggests a link between the gut microbiome and metabolic disorders. While the connection between the gut microbiota and dyslipidemia is well documented, the specific relationship between oral bacteria and dyslipidemia has not been thoroughly investigated. This study aimed to identify oral bacterial species associated with dyslipidemia in a community-based Japanese population. We conducted a metagenomic analysis on tongue coating samples from 763 participants in the Iwaki Health Promotion Project, which were collected during health checkups in 2017 and 2019. Dyslipidemia was diagnosed using standard lipid level criteria. The oral microbiome was analyzed via 16S rDNA amplicon sequencing. Statistical analyses included multiple regression and β diversity assessments. Our analysis revealed that the abundances of several bacterial genera, including Veillonella, Atopobium, Stomatobaculum, Tanneralla, and Megasphaera, are significantly associated with dyslipidemia. A higher relative abundance of Megasphaera was specifically observed in individuals with dyslipidemia. Moreover, Megasphaera abundance was closely associated with the onset of dyslipidemia (P = 0.038, odds ratio: 1.005, 95% confidence interval: 1.000-1.009), suggesting its role in metabolic regulation. This study revealed a significant association between the abundance of specific oral bacteria and dyslipidemia, suggesting the potential of using the oral microbiota as a biomarker for the early detection and management of dyslipidemia. Future research should explore the mechanisms through which oral bacteria influence lipid metabolism and the potential for microbioma-based therapies.},
}
@article {pmid41794459,
year = {2026},
author = {Cai, J and Huang, A and You, L and Wang, Z and Huang, C and Huang, R and Li, Y and Liang, T and Zhang, F and Wu, Q and Wang, J and Zhu, Z and Ding, Y},
title = {Neomycin-sensitive gut bacteria-derived brassicasterol mediates the anti-obesity effects of Cordyceps militaris polysaccharide.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118574},
doi = {10.1016/j.foodres.2026.118574},
pmid = {41794459},
issn = {1873-7145},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Obesity/prevention &amp; control/drug therapy ; Diet, High-Fat/adverse effects ; Mice ; *Neomycin/pharmacology ; Mice, Inbred C57BL ; *Cordyceps/chemistry ; Male ; *Anti-Obesity Agents/pharmacology ; Anti-Bacterial Agents/pharmacology ; Liver/metabolism ; *Fungal Polysaccharides/pharmacology ; Lipid Metabolism/drug effects ; },
abstract = {Diet-based modulation of the gut microbiota has emerged as a promising strategy to alleviate obesity and its related complications. Our previous study demonstrated that polysaccharide derived from Cordyceps militaris (CMP) exerts anti-obesity effects, yet the specific mechanism linking gut microbiota to its metabolic impact remains unclear. Herein, we utilized murine models with distinct gut microbial profiles created via antibiotic cocktails to investigate these mechanisms. The protective effects of CMP against high-fat diet (HFD)-induced obesity and associated metabolic disturbances were substantially impaired in mice depleted of neomycin-sensitive gut bacteria. Metagenomic analyses further established that CMP required these bacteria to restore gut microbial homeostasis. Notably, we observed that CMP elevated hepatic levels of brassicasterol in a manner dependent on neomycin-sensitive gut bacteria. Brassicasterol treatment alone replicated the anti-obesity effects of CMP, as indicated by reduced body weight gain, improved lipid and glucose metabolism, and decreased inflammation. Through transcriptomic and functional analyses, we identified hepatic Apoa4 as a key downstream effector of brassicasterol. Our results indicated that brassicasterol upregulated Apoa4, facilitating lipid transport and suppressing inflammation both in vitro and in vivo. Collectively, our findings indicate that CMP exerts its anti-obesity effects through a neomycin-sensitive gut bacteria-brassicasterol-Apoa4 pathway. This work expands the mechanistic understanding of CMP and highlights a novel microbiota-metabolite-host regulatory axis for dietary intervention in metabolic disorders.},
}
@article {pmid41791723,
year = {2026},
author = {Raj, A and Pant, A and Kumar, A and Kumar, A and Kalamdhad, AS and Khwairakpam, M},
title = {Systems-Level Insights Into Microbial Naphthalene Biodegradation: An Integrated In Silico and Omics Perspective.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70264},
doi = {10.1111/1462-2920.70264},
pmid = {41791723},
issn = {1462-2920},
support = {IITG/R&amp;D/IPDF/2024-25/20240815P852//Indian Institute of Technology Guwahati/ ; },
mesh = {*Naphthalenes/metabolism ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics ; Systems Biology ; Computer Simulation ; *Environmental Pollutants/metabolism ; Microbial Consortia ; },
abstract = {Naphthalene, a widely detected polycyclic aromatic hydrocarbon (PAH), is among the 16 priority PAHs identified as major environmental hazards due to its persistence, ubiquity, and toxicity to ecosystems and human health. Its occurrence in crude oil, combustion residues, vehicle emissions, and household products highlights the urgent need for sustainable remediation strategies. Microbial-based bioremediation stands out as an eco-friendly and cost-effective approach that harnesses the metabolic versatility of diverse microorganisms, their genes, and enzymes responsible for naphthalene degradation. Recent advances in omics technologies and high-throughput sequencing have expanded our understanding of novel microbial taxa, metabolic pathways, and stress responses under naphthalene exposure. Complementarily, computational modelling, in silico tools, machine learning, and systems biology have enabled the prediction of degradation dynamics and the design of synthetic microbial consortia optimised for field use. Despite these advances, challenges such as environmental fluctuations, co-contaminant effects, and the gap between laboratory and field outcomes remain. Overcoming these requires an integrative framework that connects microbial ecology, omics insights, and computational modelling. This review consolidates current knowledge on microbial degradation of naphthalene, emphasising key taxa, genes, and pathways, and highlights how omics, in silico tools and systems biology can drive sustainable remediation in the Anthropocene.},
}
@article {pmid41790499,
year = {2026},
author = {Liu, G and Bai, P and Ren, M and Li, Q and Li, T},
title = {Vitamin B12-associated interactions between Mesorhizobium sp. TaiHu and Synechococcus sp. PCC 7002 revealed by multi-omics analysis.},
journal = {Microbial genomics},
volume = {12},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001665},
pmid = {41790499},
issn = {2057-5858},
mesh = {*Vitamin B 12/metabolism/biosynthesis/genetics ; *Mesorhizobium/genetics/metabolism ; *Synechococcus/genetics/metabolism/growth &amp; development ; Metagenomics/methods ; *Microbial Interactions ; Microbial Consortia/genetics ; Transcriptome ; Gene Expression Profiling ; Multiomics ; },
abstract = {The marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) is a model organism that lacks the gene cluster required for vitamin B12 biosynthesis, necessitating cooperative interactions with other microbes. In this study, we established a synthetic microbial consortium by co-culturing Syn7002 with a bloom-forming Microcystis community, followed by purification, and subsequently investigated the interactions between Syn7002 and the associated microbial community. Electron microscopy revealed numerous rod-shaped bacteria clustered around Syn7002 cells, indicating close spatial associations between species. Metagenomic analysis showed that the early-stage community consisted mainly of Syn7002, Mesorhizobium sp. TaiHu (MesTH) and Pseudomonas sp. TaiHu (PseTH), although the abundance of PseTH declined after community stabilization. Investigation of vitamin B12 regulation between MesTH and Syn7002 through metatranscriptomic analysis revealed upregulation of nitrogen metabolism-related genes in the microbial community. Transcriptomic data further indicated that vitamin B12 biosynthesis and transport genes were significantly upregulated in MesTH. Combined with vitamin B12-positive control experiments, these results confirm potential vitamin B12 complementarity between the two strains. The results further suggest that MesTH promotes the growth of Syn7002 in the community by providing the small amount of vitamin B12 needed for its growth. These findings provide new insights into vitamin-mediated microbial interactions and reveal additional transcriptional features of the synthetic community.},
}
@article {pmid41785052,
year = {2026},
author = {Roy, P and Roy, D and Bhattacharjee, S and Ghosh, A and Saha, S},
title = {MDPD reveals specific microbial signatures in human pulmonary diseases.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
pmid = {41785052},
issn = {1477-4054},
mesh = {Humans ; *Lung Diseases/microbiology ; *Microbiota ; *Databases, Factual ; Bacteria/classification/genetics ; Machine Learning ; },
abstract = {Pulmonary diseases are becoming a serious threat worldwide, and enormous data from different human microbiomes have been generated to understand these complex diseases. Here, we introduce Microbiome Database of Pulmonary Diseases (MDPD), an open-access, comprehensive systemic catalog of pulmonary diseases by manually curating global studies from 2012 to 2024 (13 years). We have compiled 59 362 runs from 430 BioProjects, encompassing data from 10 body sites related to 19 pulmonary diseases and healthy groups covering 278 distinct sub-groups. MDPD enables users to analyze each BioProject and customize analysis with multiple BioProjects to identify taxonomic profiles and disease group/sub-group specific microbial signatures. The re-analyzed intermediate Biological Observation Matrix files are provided for each BioProject for the accessibility of users for further applications, such as machine learning-based classification. Identified microbes (bacteria, fungi, viruses) in MDPD are annotated with several attributes, providing further insights into their disease-causing potential and specificity to certain diseases and body sites. MDPD is freely available at: https://bicresources.jcbose.ac.in/ssaha4/mdpd/.},
}
@article {pmid41761979,
year = {2026},
author = {Guo, Z and Gao, Z and Zhao, Y and Ni, X and Zhang, W and Li, L and Ren, S and Li, Q and Guo, D and Yue, L and Liu, Y and Lin, L and Fan, S and Hai, X},
title = {Administering Bifidobacterium pseudolongum With Arsenic Trioxide Attenuates Acute Promyelocytic Leukemia in Mice by Restoring Immune Microenvironment and Intestinal Homeostasis.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {2},
pages = {48584},
doi = {10.31083/FBL48584},
pmid = {41761979},
issn = {2768-6698},
support = {82274028//National Natural Science Foundation of China/ ; 2022ZX02C09//Heilongjiang Key R&amp;D Program/ ; //Fundamental Research Funds for the Provincial Universities in Heilongjiang Province (2025)/ ; JJ2025PL0189//Natural Science Foundation of Heilongjiang Province/ ; 2024M10//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 2024M25//Innovation Fund of the First Affiliated Hospital of Harbin Medical University/ ; 230000253533210000086//2025 Central Government Fiscal Subsidy Fund for Medical Care Compliance and Capacity Enhancement (Traditional Chinese Medicine Undertakings and Inheritance and Development Component)/ ; },
mesh = {*Arsenic Trioxide/pharmacology/therapeutic use ; Animals ; Gastrointestinal Microbiome/drug effects ; Mice ; *Leukemia, Promyelocytic, Acute/immunology/drug therapy/microbiology/therapy ; Homeostasis/drug effects ; Humans ; *Bifidobacterium ; RNA, Ribosomal, 16S/genetics ; Male ; Female ; *Tumor Microenvironment/drug effects/immunology ; *Antineoplastic Agents/therapeutic use/pharmacology ; Dysbiosis ; *Intestines/drug effects/microbiology/immunology ; *Probiotics/administration &amp; dosage ; Disease Models, Animal ; },
abstract = {OBJECTIVE: Arsenic trioxide (ATO) is a cornerstone of acute promyelocytic leukemia (APL) therapy but induces severe gut microbiota dysbiosis, limiting its efficacy and safety. This study investigated whether adjunctive Bifidobacterium pseudolongum (BP) could mitigate these adverse effects and enhance therapeutic outcomes.<br><br>METHODS: 16S rRNA gene sequencing data of gut microbiota were obtained from a cohort of 22 APL patients treated with ATO-based regimens (20 of 22 data were obtained and analysis further), accessible under BioProject ID PRJNA935705. To evaluate the within-sample microbial community richness and evenness, alpha and beta diversity indices were calculated. Using a murine APL model, we compared ATO monotherapy with ATO+BP co-treatment. Analyses included fecal metagenomic sequencing, single-cell RNA sequencing (sc-RNA-seq), flow cytometric immune profiling, and assessment of intestinal tight junction proteins (claudin-1, occludin, and ZO-1) via immunofluorescence.<br><br>RESULTS: ATO treatment significantly reduced gut microbial diversity and depleted beneficial taxa. Sc-RNA-seq data showed that ATO could orchestrate the APL immune microenvironment mainly through functional activation of CD8+ T cells and monocytes. BP supplementation restored microbial homeostasis and synergistically enhanced ATO's antileukemic effect, reducing the leukemic burden in peripheral blood by 72% and in bone marrow by 64% compared to ATO alone. Mechanistically, BP preserved intestinal barrier integrity by upregulating tight junction protein expression and modulated anti-tumor immunity, notably increasing bone marrow CD8+ T cells by 2.21-fold.<br><br>CONCLUSIONS: BP is an effective adjunct to ATO therapy, counteracting gut dysbiosis, intestinal damage, and the immune microenvironment while synergistically improving antileukemic efficacy. Targeting the gut-leukemia axis with BP represents a promising strategy for improving the precision and safety of APL treatment.},
}
@article {pmid41747903,
year = {2026},
author = {Li, LX and Yang, TT and Yuan, Y and Han, YL and Zhao, Q and Wang, WH and Sun, Y and Cao, XX and Jiang, XL and Li, T and Wang, X},
title = {Rapid enrichment of ternary carbon-fixing microbial consortia from anaerobic sludge via pressurized pre-autotrophic strategy for scalable microbial electrosynthesis.},
journal = {Bioresource technology},
volume = {447},
number = {},
pages = {134276},
doi = {10.1016/j.biortech.2026.134276},
pmid = {41747903},
issn = {1873-2976},
mesh = {*Sewage/microbiology ; *Microbial Consortia/physiology ; Anaerobiosis ; Acetates/metabolism ; *Autotrophic Processes ; *Carbon Cycle ; *Bioelectric Energy Sources/microbiology ; Pressure ; Electrodes ; Carbon/metabolism ; Carbon Dioxide/metabolism ; },
abstract = {As a promising platform for microbially catalyzed carbon capture, microbial electrosynthesis (MES) is constrained by inoculation strategies that limit carbon fixation efficiency and scalability. Mixed-culture inocula outperform pure cultures in functional redundancy and ecological resilience in large systems, but slow acclimation and erratic community composition yield inconsistent performance. Here, this study presents a pressurized pre-autotrophic (PA) strategy that rapidly enriches carbon-fixing microorganisms (CFMs) from anaerobic sludge, in comparison with direct autotrophic (DA) and electrode reversal (ER) strategies. PA increased CFM abundance to 51%, 3.5-fold higher than in DA-MES and ER-MES (both 15%). Acetate production in PA-MES reached 14.47 g·m[-2]·d[-1]. In addition to enhanced acetate productivity, PA-MES exhibited superior electrochemical performance, achieving the highest Faradaic efficiency for acetate and energy efficiency among the tested systems, together with the lowest energy consumption per unit acetate. Metagenomic analysis revealed a PA-defined core community with coordinated activation of the Wood-Ljungdahl, rTCA, and methanogenic pathways, providing redundant routes for stable CO2 fixation. By transforming mixed-culture inocula into a functionally cohesive carbon-fixing community, the PA strategy enables rapid startup and sustained carbon fixation, offering a practical framework for scalable MES.},
}
@article {pmid41707528,
year = {2026},
author = {Wang, Y and Ding, C and Zheng, Z and Liu, W and Shi, Y},
title = {The spatial distribution of heavy metal contamination, microbial communities, and resistance genes in agricultural soil near a manganese mine in China.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119865},
doi = {10.1016/j.ecoenv.2026.119865},
pmid = {41707528},
issn = {1090-2414},
mesh = {China ; *Soil Microbiology ; *Metals, Heavy/analysis ; *Soil Pollutants/analysis ; Mining ; *Environmental Monitoring ; Manganese/analysis ; Agriculture ; Soil/chemistry ; Bacteria/genetics/classification ; *Microbiota ; Genes, Bacterial ; },
abstract = {The large-scale manganese mining causes severe heavy metal contamination, posing a significant potential risk to human health. Songtao County is one of the most important manganese mining areas in China, where the disorderly mining and extensive production has inevitably caused serious pollution. However, it's still unclear how Mn production activities affect agricultural soils located relatively far from the mining sites. Therefore, we investigated the horizontal and vertical distribution of heavy metal contamination, microbial communities, and resistance genes in the agricultural soils located at Songtao County. Metagenomic sequencing revealed that Proteobacteria, Acidobacteria, Rokubacteria, Chloroflexi, and Actinobacteria were the most abundant phyla. The diversity and composition of the bacterial communities varied significantly between different sampling sites and depths. Redundancy and Spearman correlation analysis indicated that total nitrogen, total organic carbon, total K, and Mn were the primary environmental factors determining the distribution of bacterial communities. The bacterial communities in Wuluo were influenced by Hg, Zn, Cu, Ni, and As, whereas in Mushu, it was primarily affected by Mn levels. A large account of heavy metal resistance genes, manganese resistance genes, and antibiotics resistance genes were identified. The relative abundances and correlation analysis of these resistance genes exhibited observed correlations based on the potential co-selection mechanisms, suggesting that Mn and heavy metals, as well as antibiotics, might shape the microbiome and resistome in this agricultural soil. These findings provide an insight for the surveillance, maintenance, and remediation of the agricultural soil and offer theoretical evidence for improving the agricultural soil environment.},
}
@article {pmid41699270,
year = {2026},
author = {Bashiardes, S and Heinemann, M and Adlung, L and Valdés-Mas, R and Mahdi, JA and Nobs, SP and Tuganbaev, T and Yamada, T and Horn, M and Mor, U and Cohen, Y and Israel, S and Korem, M and Oster, Y and Olshtain-Pops, K and Orenbuch-Harroch, E and Arslan, MD and Molina, S and Zur, M and Eliyahu-Miller, S and Bukimer, A and Federici, S and Dori-Bachash, M and Amar, N and Elbirt, D and Cohen-Poradosu, R and Turner, D and Hershcovici, T and Vainer, E and Stettner, N and Harmelin, A and Gebremeskel, H and Kebede, Y and Schmidt, S and Zmora, N and Dhamodaran, A and Puschhof, J and Bentwich, Z and Shapiro, H and Amit, I and Elinav, H and Elinav, E},
title = {Human immunodeficiency virus-associated gut microbiome impacts systemic immunodeficiency and susceptibility to opportunistic gut infection.},
journal = {Nature microbiology},
volume = {11},
number = {3},
pages = {690-703},
pmid = {41699270},
issn = {2058-5276},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; Dysbiosis/microbiology/immunology ; Mice ; Fecal Microbiota Transplantation ; Feces/microbiology ; Female ; Ethiopia ; Male ; *HIV Infections/immunology/microbiology/complications ; Israel ; *Opportunistic Infections/immunology/microbiology ; Cryptosporidiosis/immunology/microbiology ; Adult ; CD4-Positive T-Lymphocytes/immunology ; Metagenomics ; Middle Aged ; Disease Susceptibility ; Cryptosporidium parvum ; Intestinal Mucosa/immunology ; },
abstract = {The gut microbiome of people living with human immunodeficiency virus (PLWH) has been characterized, but its role in influencing host immunity and associated clinical features are unclear. Here we used shotgun metagenomics to characterize the faecal microbiome of two geographically distinct cohorts of PLWH and healthy controls in Israel and Ethiopia. We uncovered disease-specific, geographically divergent microbial patterns including a shift from Bacteroides to Prevotella species in an Israeli cohort and multiple Enterobacteriaceae species including Escherichia coli and Klebsiella quasivariicola in an Ethiopian cohort. We identified correlations between human immunodeficiency virus-related dysbiosis and the extent of systemic immunodeficiency, as proxied by peripheral CD4[+] T cell counts. Faecal microbiome transplantation from PLWH with high peripheral CD4[+] T cell counts induced colonic epithelium-associated CD4[+] T cells in germ-free or antibiotic-treated recipient mice. Impaired epithelium-associated lymphocyte induction in recipients of faecal microbiome transplantation from severely immunodeficient PLWH donors was associated with altered protection from Cryptosporidium parvum infection. Collectively, our results suggest a link between systemic immunodeficiency and associated intestinal dysbiosis in PLWH, resulting in impaired gut mucosal immunity.},
}
@article {pmid41679088,
year = {2026},
author = {Leducq, JB and St-Amand, LP and Ross, D and Kembel, SW},
title = {A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on hyphomicrobiales dark matter.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {2},
pages = {126697},
doi = {10.1016/j.syapm.2026.126697},
pmid = {41679088},
issn = {1618-0984},
mesh = {*Phylogeny ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Plant Leaves/microbiology ; Microbiota/genetics ; Biodiversity ; DNA, Bacterial/genetics ; *Alphaproteobacteria/classification/genetics ; Lichens/microbiology ; Bacteria/classification/genetics ; Sequence Analysis, DNA ; },
abstract = {The phyllosphere, or above-ground part of plants, hosts diverse bacterial communities that play critical ecological roles and provide beneficial functions for the plant. The Hyphomicrobiales (Alphaproteobacteria) are a highly diverse and ecologically important clade known to be key members of the plant microbiome, in particular in association with plant roots, but their diversity remains largely uncharacterized in the phyllosphere. Using a meta-analysis combining metabarcoding, metagenomics and phylogenomics, we explored the diversity of leaf-associated Hyphomicrobiales. We confirmed Methylobacterium was ubiquitous in the phyllosphere and revealed the dominance of two under-characterized Hyphomicrobiales taxa: Lichenihabitantaceae, a lichen-associated family previously identified as "1174-901-12" in taxonomic databases, and RH-AL1, an undescribed lineage of bacteria related to Beijerinckiaceae. Despite their abundance in the phyllosphere, Lichenihabitantaceae and RH_AL1 could not be properly identified by 16S rRNA gene barcoding, due in part to limitations of short read sequencing leading to a lack of recognition of certain Hyphomicrobiales genera, and to incongruencies in the assignment of genera to families among existing taxonomic databases. A significant proportion of Lichenihabitantaceae were detected in association with lichens and in environments with harsh conditions like exposed surfaces, air and snow. Overall, our study stresses the need to agree on a common systematic framework to properly classify and identify key leaf-associated Hyphomicrobiales taxa, and to move toward metagenomics and culturomics to increase their representation in reference databases, to provide a better understanding of the evolutionary and functional mechanisms underpinning bacteria adaptations to living on plants.},
}
@article {pmid41668418,
year = {2026},
author = {Moguel, B and Carrillo Olivas, L and Guerrero-Osornio, MG and Herrera Paredes, S},
title = {Recent Microbial Evolutionary Insights From Metagenomics.},
journal = {Genome biology and evolution},
volume = {18},
number = {3},
pages = {},
pmid = {41668418},
issn = {1759-6653},
support = {2022-000002-01NACF-03333//DGAPA-PAPIIT/ ; 2023-000002-01NACF-03323//SECIHTI/ ; IN212524//SECIHTI/ ; //DGAPA-PAPIIT/ ; },
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Evolution, Molecular ; Humans ; *Biological Evolution ; Phylogeny ; },
abstract = {Microorganisms have profoundly shaped Earth's biological and geological history, from the origins of oxygenic photosynthesis to present-day global biogeochemical cycles. Metagenomics-through its ability to recover genomic information directly from environmental samples-has revolutionized our understanding of microbial evolution by uncovering unbeknownst lineages, revealing functional adaptations, and reshaping our view of the Tree of Life. By bypassing the need for cultivation, shotgun metagenomics and metabarcoding approaches have enabled researchers to investigate microbial diversity, ecology, and evolutionary processes across aquatic, terrestrial, extreme, and host-associated environments. This review highlights recent advances in evolutionary biology driven by metagenomics, including studies on deep evolutionary branching events, microbial adaptation to extreme environments, the evolution of host-associated microbiomes, and the emergence and spread of pathogens and antimicrobial resistance. The integration of ancient DNA has expanded our ability to reconstruct past ecosystems and disease dynamics, offering insights into long-term microbial evolution. In parallel, studies of microbial domestication and urban settings reveal how human practices have shaped microbial genomes over millennia. Despite significant progress, key challenges remain-including improving bioinformatic tools for degraded ancient DNA, resolving deep phylogenetic relationships, identifying adaptive variants, and linking genomic shifts to ecosystem-level processes. The future of microbial evolutionary research will depend on combining longitudinal metagenomic data, experimental evolution, functional assays, and predictive modeling to better understand microbial responses to climate change and anthropogenic pressures. Together, these approaches will deepen our understanding of microbial evolution and its consequences for life on Earth-past, present, and future.},
}
@article {pmid41655417,
year = {2026},
author = {Chen, Z and Tang, X and Su, Y and Liu, T and Klümper, U and Ju, F and Liu, M and Han, P},
title = {Impact of human activities on groundwater biogeochemical cycles and microbial communities: Insights from metagenomic analysis.},
journal = {Water research},
volume = {294},
number = {},
pages = {125493},
doi = {10.1016/j.watres.2026.125493},
pmid = {41655417},
issn = {1879-2448},
mesh = {*Groundwater/microbiology/chemistry ; Metagenomics ; Humans ; Human Activities ; Microbiota ; China ; Nitrogen ; Bacteria/genetics ; },
abstract = {Anthropogenic nitrogen pollution poses a systemic threat to microbial interaction networks and biogeochemical cycling in groundwater ecosystems, yet the underlying mechanisms remain poorly understood. Employing an endpoint gradient comparison, we conducted metagenomic analyses of urban groundwater under severe nitrogen stress (Shanghai, China; with NH4[+] and NO3[-] concentrations ∼28× and ∼10× background levels, respectively) versus a near-pristine mountain aquifer (Calistoga, USA). This revealed a multi-level collapse and adaptive restructuring of microbial communities under nitrogen stress. Pollution triggered a fundamental restructuring of bacterial communities, with system type (urban vs. mountain) explaining 74 % of the compositional variation, accompanied by a significant reduction in bacterial alpha-diversity (Shannon index decreased by 34 %) and a taxonomic shift from Actinomycetota-dominated mutualistic networks in the mountain system to Pseudomonadota-dominated communities (> 0.86 relative abundance) in urban groundwater. Functionally, urban systems exhibited multi-pathway suppression of energy-intensive processes, including nitrification (e.g., hao, nxrB genes), methanogenesis, and inorganic sulfur oxidation, aligning with the theory of "pollution-induced metabolic decoupling." To survive, the microbial community pivoted to low-energy strategies, significantly enriching genes for organic sulfur metabolism (e.g., dddT, tsdB), which may exacerbate nitrogen retention by inhibiting denitrifiers via metabolites like H2S. Co-occurrence network topology analysis indicated a catastrophic loss of complexity in urban groundwater, with a ∼90 % reduction in connectivity and a collapse in modularity (from 19.94 to 3.33), alongside an abnormally high proportion of positive correlations (94.4 %), signaling a major loss of ecosystem stability and functional redundancy. Random Forest and redundancy analyses jointly identified ammonium (NH4[+]) as the core environmental driver of this cascading failure, explaining 86 % of the variance in functional gene profiles and likely disrupting the nitrification pathway through specific suppression of the rate-limiting hao gene (which explained 76 % of the variance in nitrification rates). Based on these insights, we propose a dual-track restoration framework that couples external NH4[+] source control with internal microbial network rewiring (e.g., restoring keystone taxa, regulating sulfur feedback loops) to break the nitrogen-sulfur inhibition cycle and restore ecological function. Our findings underscore the critical importance of integrating microbial network resilience into strategies for managing and rehabilitating contaminated groundwater ecosystems.},
}
@article {pmid41644796,
year = {2026},
author = {Krukowski, H and Valkenburg, S and Vich Vila, A and Maciel, LF and Vázquez-Castellanos, JF and Gryp, T and Joossens, M and Van Biesen, W and Verbeke, F and Derrien, M and Huys, GRB and Glorieux, G and Raes, J},
title = {Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function.},
journal = {Nature microbiology},
volume = {11},
number = {3},
pages = {664-677},
pmid = {41644796},
issn = {2058-5276},
support = {860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101149152//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
mesh = {*Renal Insufficiency, Chronic/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; Humans ; Glomerular Filtration Rate ; Male ; Female ; Feces/microbiology ; Middle Aged ; Dysbiosis/microbiology ; *Kidney/physiopathology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Aged ; Cresols/metabolism ; Biomarkers ; Disease Progression ; Adult ; },
abstract = {Despite recent progress, microbial associations reported in chronic kidney disease (CKD) remain inconsistent. Here we combined quantitative faecal metagenomics (n = 130) and cross-study biomarker comparisons (ntotal = 4,420) to study microbiome associations with estimated glomerular filtration rate (eGFR; kidney function) and 4-year CKD progression. Intestinal transit time (ITT) and medications significantly explained microbiome variation, surpassing eGFR-related effects. Lower eGFR was associated with increased p-cresol and indole biosynthetic potential and reduced plant-to-animal CAZyme ratios. This was consistent with community-wide saccharolytic-to-proteolytic microbiome transitions linked to dietary guidelines and slowed-down ITT. Peritoneal dialysis patients showed distinct microbiome dysbiosis accompanied by increased intestinal inflammation. Only Escherichia coli, an unnamed Alistipes species and Bifidobacterium adolescentis were covariate-independent markers for eGFR, but neither these nor previous microbial markers convincingly replicated across 11 studies. No predictors for CKD progression were found. Nevertheless, our study adds insight into plausible ITT and nutrition-related effects, highlighting their potential in CKD interventions.},
}
@article {pmid41620544,
year = {2026},
author = {Kirsche, L and Leary, P and Blaser, MJ and Scharl, M and Negussie, A and Müller, A},
title = {Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41620544},
issn = {2399-3642},
support = {310030_192490//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {Humans ; Ethiopia/epidemiology ; *Gastrointestinal Microbiome ; Child, Preschool ; Female ; Male ; Feces/microbiology ; *Urban Population ; *Diet, Western/adverse effects ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; *Life Style ; *Bacteria/classification/genetics ; },
abstract = {Gut microbiota composition has been extensively studied in European and North American pediatric cohorts, as well as in rural African children. Much less attention has been paid to urban African children, whose families have transitioned to a "Western" lifestyle characterized by smaller family sizes, access to perinatal care including C-section delivery, non-traditional food sources and widespread availability of antibiotics. We analyzed fecal samples from ~200 Ethiopian children aged 2-5 years from Adama, Ethiopia, using 16S rRNA gene sequencing and shotgun metagenomics. We found that well-studied factors such as delivery mode, breastfeeding and family size have only minor effects on α-diversity, whereas household crowding (single vs. multiple rooms) and consumption of the traditional fermented cereal Eragrostis tef predict higher α-diversity. Stunted growth and absence of Helicobacter pylori infection were additional factors associated with increased fecal microbial diversity. Metagenomic profiling revealed that rural African signature genera such as Segatella and Prevotella were largely absent; instead, urban Ethiopian children displayed a high Firmicutes/Bacteroidota ratio and enrichment of metabolic pathways linked to a westernized diet, resembling European rather than rural Ethiopian children. These results indicate that an urban westernized lifestyle alters gut microbiota composition, which may be partially offset by a traditional fermented diet.},
}
@article {pmid41617724,
year = {2026},
author = {Dong, Z and Sun, MS and He, YD and Zhou, L and Xiang, W and Li, X and Huang, P and Zeng, JG},
title = {Fungal photobiont and microbiome genome composition in the Cladonia uncialis tripartite symbiosis.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41617724},
issn = {2052-4463},
mesh = {*Symbiosis ; *Lichens/microbiology ; *Ascomycota/genetics ; *Microbiota ; *Genome, Fungal ; Metagenome ; },
abstract = {As symbiotic complexes formed through the association of bacteria or algae with fungi, lichens exhibit exceptional adaptability to extreme environments and function as pioneer species in rocky habitat ecological succession. The absence of high quality chromosome-level genome has constrained investigations into lichen adaptive evolution, while functional contributions of symbiotic bacterial communities remain inadequately explored. This study presents the chromosome-level genome assembly of the mycobiont Cladonia uncialis, comprising 28 chromosomes with a total size of 43.49 Mb, generated through integrated PacBio HiFi and Hi-C methodologies. We characterized the symbiotic microbiota using integrated short and long-read sequencing and constructed 31 metagenome-assembled genomes. The community was dominated by Ascomycota (41.16%), Proteobacteria (17.61%), and Bacteroidota (14.20%). Long-read sequencing significantly enhanced detection sensitivity for low-abundance taxa. This study provides essential genomic resources and comprehensive profiles of the symbiotic microbiota, enabling mechanistic exploration of adaptive evolution within lichen symbiotic systems under extreme environmental conditions.},
}
@article {pmid41616686,
year = {2026},
author = {Sattari Khavas, D and Schwartz, SK and Bird, P and Truong, A and Silberg, JJ},
title = {Microbial spies and bloggers: programming cells to convert environmental information into discernible signals.},
journal = {Current opinion in biotechnology},
volume = {98},
number = {},
pages = {103436},
doi = {10.1016/j.copbio.2026.103436},
pmid = {41616686},
issn = {1879-0429},
mesh = {*Biosensing Techniques/methods ; *Microbiota ; Synthetic Biology ; },
abstract = {Microbes regulate their dynamic behaviors using the chemical and physical characteristics of their environment. The ability of microbes to continuously convert this physicochemical information into biochemical information and to use organic matter in the environment as a power source makes these organisms attractive as chassis for building sensors. However, most biosensors have severe limitations when considering applications in hard-to-image settings like soils, sediments, and wastewater. Emerging technologies at the interface of biomolecular design, microbiome engineering, and synthetic biology offer new tools to program cells and communities as biosensors for these settings. In this review, we describe innovations in biosensor outputs that are enabling new applications in complex environments, including reporters that are read out using electrochemical, gas chromatography, hyperspectral imaging, and next-generation sequencing methods. We also discuss computational advances that are accelerating the diversification of sensing components by mining metagenomics data for new transcriptional regulators and by designing allosteric protein switches that directly regulate reporter outputs using analytes. We highlight emerging opportunities for programming undomesticated microbes in communities to function as distributed sensors in the environment. Finally, we discuss the need for responsible biosensor development and to modernize regulatory frameworks to support evidence-based assessment of environmental biosensors.},
}
@article {pmid41605932,
year = {2026},
author = {Raethong, N and Patumcharoenpol, P and Vongsangnak, W},
title = {Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {41605932},
issn = {2055-5008},
support = {N42A660907//National Research Council of Thailand/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Thailand ; *Prebiotics/administration &amp; dosage ; Adult ; *Diet ; Fatty Acids, Volatile/metabolism ; Male ; Female ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics ; Models, Biological ; Young Adult ; Middle Aged ; Systems Biology ; Southeast Asian People ; },
abstract = {The impact of diet on gut microbial metabolism is essential for advancing microbiome-based health interventions. This study introduces a novel systems biology pipeline that integrates genome-scale metabolic models (GSMMs) with Thai dietary intake data to simulate gut microbiome metabolism and assess prebiotic responses. Utilizing metagenomic data from healthy Thai adults and an average Thai diet derived from national surveys, community-scale metabolic models (CSMMs) were developed and simulated under both typical dietary and prebiotic-supplemented condition. Flux variability analysis was employed to assess metabolic capacities, short-chain fatty acids (SCFAs) production in relation to microbial taxonomy. The results promisingly revealed inter-individual variability in SCFA profiles, with Bacteroides and Phocaeicola notably linked to isobutyrate production and Bifidobacterium emerged as a key responder to prebiotic supplementation. This integrative framework offers biological insights into diet-gut microbiome interactions and provides a foundation for the development of precision nutrition strategies tailored to the Thai population.},
}
@article {pmid41579975,
year = {2026},
author = {Ferrero, G and Mastrocola, R and Tarallo, S and Pardini, B and Scheijen, J and van de Waarenburg, M and Gallo, G and Chatziioannou, AC and Robinot, N and Keski-Rahkonen, P and Piccinno, G and Segata, N and Aglago, EK and Hughes, DJ and Jenab, M and Schalkwijk, CG and Naccarati, A},
title = {Integrative analyses of dicarbonyls and advanced glycation end-products with multiomic profiles across tissue, plasma and stool samples reveal methylglyoxal accumulation in colon cancer.},
journal = {Free radical biology &amp; medicine},
volume = {246},
number = {},
pages = {518-530},
doi = {10.1016/j.freeradbiomed.2026.01.034},
pmid = {41579975},
issn = {1873-4596},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Humans ; *Pyruvaldehyde/metabolism/blood ; *Glycation End Products, Advanced/metabolism/blood ; *Colonic Neoplasms/metabolism/pathology/genetics/blood/microbiology ; Male ; Female ; Feces/chemistry/microbiology ; Middle Aged ; Glyoxal/metabolism ; Aged ; Lactoylglutathione Lyase/genetics/metabolism ; Gastrointestinal Microbiome ; Deoxyglucose/analogs &amp; derivatives/metabolism ; Metabolomics ; Receptor for Advanced Glycation End Products/genetics/metabolism ; },
abstract = {Advanced Glycation Endproducts (AGEs) arise from the reaction of proteins with highly reactive dicarbonyl compounds such as methylglyoxal (MGO), glyoxal (GO) and 3-deoxyglucosone (3-DG), which have been implicated in inflammation and carcinogenesis. How dicarbonyls and AGEs are distributed across tumor tissue and surrogate specimens, and how they relate to systemic metabolism, AGE-related pathways, and alterations in gut microbiota in colon cancer, remains poorly understood. An integrative multi-specimen analysis of MGO, GO, 3-DG and major AGEs was performed using targeted tandem mass spectrometry in matched tumor tissue, adjacent normal mucosa, plasma, and stool from 26 sporadic colon cancer patients. These measurements were combined with tumor RNA-sequencing, untargeted plasma metabolomics, and stool shotgun metagenomics generated from the same individuals. A marked accumulation of MGO was observed in tumor tissue when compared with adjacent mucosa, accompanied by higher levels of the MGO-derived AGE Nδ-[5-hydro-5-methyl-4-imidazolon-2-yl]-ornithine (MG-H1). Tissue MG-H1 concentrations significantly correlated with corresponding plasma levels. Elevated tumor MGO levels were associated with up-regulation of GLO1 (encoding for the detoxifying enzyme glyoxalase-1), DDOST (coding for the AGE-clearance receptor AGE-R1), and the glycolytic flux marker triose phosphate isomerase (TPI), alongside down-regulation of the AGE-scavenger receptor CD36. These findings suggest a candidate remodeling of dicarbonyl-handling pathways. The MGO/GO ratio in tumors was positively associated with the relative abundances of Fusobacterium nucleatum and Parvimonas micra, two bacterial species related to colorectal carcinogenesis, and with metagenomic signatures of oral-derived taxa colonizing the gut. This pilot integrative analysis highlighted novel coherent associations among tissue, circulating, and stool levels of MGO-derived AGEs, the expression of AGE-related metabolic pathways, and microbial signatures in colon cancer. If confirmed in larger studies, these candidate molecular and microbial interactions may provide novel insights into the dicarbonyl stress involvement in tumor biology.},
}
@article {pmid41570514,
year = {2026},
author = {Yan, S and Ahmad, HA and Xie, Y and Liu, S and Wu, J and Cui, J and Yang, B and Su, L and Ding, T and Liu, T},
title = {Metagenomic insights into the trophic gradient influence on nitrogen cycling microbiomes in plateau lakes.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119288},
doi = {10.1016/j.marpolbul.2026.119288},
pmid = {41570514},
issn = {1879-3363},
mesh = {*Lakes/microbiology ; *Microbiota ; *Nitrogen Cycle ; Metagenomics ; *Metagenome ; Nitrogen/metabolism ; Denitrification ; Bacteria ; Ecosystem ; },
abstract = {The increasing prevalence of nitrogen (Nr) pollution in lake ecosystems is a growing global concern. Understanding the dynamics of Nr-cycling microbial communities in these environments is crucial for assessing how ecosystem processes and functions respond to trophic gradients. This study investigates the microbial Nr-metabolism in plateau lakes with varying trophic states across a broad geographical range. A detailed metagenomic study revealed that increasing trophic status index (TSI) reduced the α-diversity of Nr-cycling microbial communities, while TSI and altitude jointly shaped the β-diversity patterns. The Nr-cycling microorganisms predominantly belonged to the phylum Proteobacteria, with the most abundant functional genes associated with organic Nr degradation and synthesis, dissimilatory/assimilatory nitrate reduction to ammonium (DNRA and ANRA), and denitrification processes (DNiF). Key Nr functional genes exhibited differential enrichment across lakes, indicating changes in Nr-metabolism strategies along the trophic gradient. A total of 126 metagenome-assembled genomes (MAGs) contributed to Nr-cycling, with the majority assigned to Proteobacteria (36) and Planctomycetes (25). Among these, MAG110 was enriched in eutrophic lakes and possessed near-complete DNiF and ANRA pathways, while MAG115, predominant in oligotrophic lakes, relied solely on ANRA. This functional divergence reflects trophic-specific ecological adaptations, that denitrification is favored in nutrient-rich, low-oxygen conditions and Nr- retention is prioritized under Nr-limited environments. Moreover, enzymes like nitronate monooxygenase (encoded by both genomes) and nitroalkane oxidase highlight a novel metabolic interaction between Nr-transformations and organic C1 compound oxidation in freshwater ecosystems. Overall, this study highlights the complex relationship among trophic status, microbial diversity, and Nr-metabolism in lake ecosystems.},
}
@article {pmid41565819,
year = {2026},
author = {Ricci, L and Heidrich, V and Punčochář, M and Armanini, F and Ciciani, M and Nabinejad, A and Fazaeli, F and Piperni, E and Servais, C and Pinto, F and Valles-Colomer, M and Asnicar, F and Segata, N},
title = {Baby-to-baby strain transmission shapes the developing gut microbiome.},
journal = {Nature},
volume = {651},
number = {8104},
pages = {191-200},
pmid = {41565819},
issn = {1476-4687},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics/physiology ; Infant ; Female ; Feces/microbiology ; Male ; Infant, Newborn ; Longitudinal Studies ; Anti-Bacterial Agents/pharmacology ; Siblings ; Adult ; Bacteria/classification/genetics/isolation &amp; purification/drug effects ; Metagenomics ; },
abstract = {The early infant microbiome is largely primed by microbial transmission from the mother between birth and the first few weeks of life[1-3], but how interpersonal transmission further shapes the developing microbiome in the first year remains unexplored. Here we report a metagenomic survey to model microbiome transmission in the nursery setting among babies attending the first year, their educators and their families (n = 134 individuals). We performed dense longitudinal microbiome sampling (n = 1,013 faecal samples) during the first year of nursery and tracked microbial strain transmission within and between nursery groups across 3 different facilities. We detected extensive baby-to-baby microbiome transmission within nursery groups even after only 1 month of nursery attendance, with nursery-acquired strains accounting for a proportion of the infant gut microbiome comparable to that from family by the end of the first term. Baby-to-baby transmission continued to grow over the nursery year, in an increasingly intricate transmission network with single strains spreading in some classes, and with multiple baby-acquisition and species-transmissibility patterns. Having siblings was associated with higher microbiome diversity and reduced strain acquisition from nursery peers, while antibiotic treatment was the condition that most accounted for the increased influx of strains. This study shows that microbiome transmission between babies is extensive during the first year of nursery, and points to social interactions in infancy as crucial drivers of infant microbiome development.},
}
@article {pmid41558447,
year = {2026},
author = {Han, Y and Wang, A and Zhang, Z and Liu, L and Chen, Q and Fan, W and Tan, E and Tang, K},
title = {Multi-omics reveal the prevalence of Thaumarchaeota and their biogeochemical roles in coastal low oxygen zones.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119293},
doi = {10.1016/j.marpolbul.2026.119293},
pmid = {41558447},
issn = {1879-3363},
mesh = {*Archaea ; *Oxygen/analysis ; China ; Seawater/microbiology/chemistry ; Nitrogen/metabolism ; Eutrophication ; Microbiota ; Bacteria ; Proteomics ; Multiomics ; },
abstract = {The intensification of coastal hypoxia under anthropogenic eutrophication and climate change necessitates understanding microbial adaptive mechanisms. However, the composition of microbial communities and their biogeochemical roles in response to oxygen gradients remain poorly understood. Here, we employed ‌integrated multi-omics‌ approaches to analyze microbial communities and their biogeochemical functions across oxic to low oxygen gradients off the Yangtze River Estuary in East China Sea. Results revealed that surface oxic waters hosted phytoplankton (Synechococcus) and opportunistic bacteria (Flavobacteriia, Pelagibacterales), while bottom layers enriched chemolithoautotrophs (Thaumarchaeota, Nitrospina) and facultative anaerobes (Planctomycetes, Marine Group II), with sediment resuspension further amplified particle-attached taxa. Meanwhile, a remarkable shift in microbial nitrogen metabolism was observed between oxic and low oxygen waters, with dissolved nitrogen assimilation dominated in oxic waters. Despite genomic potential for complete nitrogen reduction in low oxygen waters, our metaproteomics revealed only a significant expression of nitrate reductases. This decoupling between genomic potential and proteomic expression implies that ambient oxygen levels remain above thresholds for full pathway activation, showcasing microbial metabolic plasticity. Both metagenomic and metaproteomic have confirmed that Thaumarchaeota, particularly the genus Nitrosopumilus, emerged as keystone taxa, contributing to nitrification and dark carbon fixation, thereby coupling nitrogen‑carbon biogeochemical cycling in coastal hypoxic zones. These findings highlight redox-driven microbial niche differentiation and metabolic adaptation, providing predictive insights into biogeochemical feedbacks under expanding coastal deoxygenation.},
}
@article {pmid41387308,
year = {2026},
author = {Zhao, Z and Li, Q and Bai, X and Zhai, E and Dai, W and Qian, Y and Zhang, T and Huang, Z and Huang, Z and Meng, F and Chen, J and Zuo, T and Cai, S and Zhao, R},
title = {Gut Bacterium Lysinibacillus Sphaericus Exacerbates Aspirin-induced Intestinal Injury by Production of Carboxylesterase EstB.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {12},
pages = {e17747},
pmid = {41387308},
issn = {2198-3844},
support = {82100626//National Natural Science Foundation of China/ ; 82173239//National Natural Science Foundation of China/ ; 32470958//National Natural Science Foundation of China/ ; 82403246//National Natural Science Foundation of China/ ; 823B2010//National Natural Science Foundation of China/ ; 202206010014//Special Project of Guangzhou Science and Technology Innovation Development/ ; },
mesh = {*Aspirin/adverse effects/toxicity/metabolism ; Animals ; *Gastrointestinal Microbiome/physiology/drug effects ; Mice ; Male ; Intestines/drug effects ; Disease Models, Animal ; Mice, Inbred C57BL ; *Carboxylesterase/metabolism ; *Carboxylic Ester Hydrolases/metabolism ; *Intestinal Diseases/chemically induced/microbiology ; },
abstract = {Aspirin provides long-term health benefits but can cause gastrointestinal toxicity, and the role of gut microbiota in aspirin metabolism and enterotoxicity remains unclear. In this study, the contribution and mechanisms of microbiota-aspirin interactions in intestinal injury are investigated. In a mouse model, aspirin-induced enteropathy is found to be more severe in microbiota-replete than in microbiota-depleted mice, implicating a detrimental role of gut microbiota. Co-cultivation experiments revealed that gut microbes facilitated the biotransformation of aspirin into salicylic acid, a metabolite more harmful than aspirin itself in disrupting epithelial cell integrity and renewal, both in vitro and in vivo. Through metagenomic screening, selective bacterial interrogation, and functional validation, Lysinibacillus sphaericus is identified as the culprit bacterium, and its secreted carboxylesterase EstB as the key enzyme catalyzing aspirin hydrolysis to salicylic acid. Importantly, inhibition of microbial EstB with the dietary compound flavanomarein abrogated aspirin biotransformation and prevented intestinal injury. Together, these findings reveal L. sphaericus and EstB as central drivers of aspirin enterotoxicity, highlight the functional importance of gut microbiota in drug metabolism, and suggest microbiota- and metabolite-guided precision prevention strategies.},
}
@article {pmid41350118,
year = {2026},
author = {Fukase, S and Kouketsu, A and Tamahara, T and Saito, T and Ito, A and Higashi, Y and Kajita, T and Kurobane, T and Miyakoshi, M and Iikubo, M and Shimizu, R and Takahashi, T and Yamauchi, K and Sugiura, T},
title = {Differences in the Oral Microbiome Between Patients With and Without Oral Squamous Cell Carcinoma.},
journal = {Journal of oral pathology &amp; medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology},
volume = {55},
number = {3},
pages = {368-380},
pmid = {41350118},
issn = {1600-0714},
mesh = {Humans ; *Carcinoma, Squamous Cell/microbiology/pathology ; Male ; *Microbiota/genetics ; *Mouth Neoplasms/microbiology/pathology ; Female ; Middle Aged ; Aged ; Saliva/microbiology ; Case-Control Studies ; Adult ; *Mouth/microbiology ; DNA, Bacterial ; },
abstract = {BACKGROUND: Although studies have demonstrated a relationship between pathogenic microorganisms and oral cancer, no study has demonstrated a relationship between changes in bacterial flora and oral squamous cell carcinoma (OSCC). Therefore, we investigated the association between oral microbiota and oral squamous cell carcinoma using metagenomic analysis.<br><br>METHODS: Saliva samples from 64 patients with OSCC and 50 healthy controls who visited the Department of Oral Surgery, Tohoku University Hospital, were collected, and bacterial genomic DNA was extracted using polymerase chain reaction amplification. Single-end sequencing was performed using the Illumina MiSeq platform, and sequence data were analyzed using the Quantitative Insights Into Microbial Ecology 2 platform. The Steel-Dwass test was used for between-group comparisons, and Analysis of Compositions of Microbiomes with Bias Correction was used to detect significant differences in microbiome composition.<br><br>RESULTS: Significant differences were observed in alpha-diversity indices of bacterial flora (richness, Faith- phylogenetic diversity, Shannon index) in the OSCC group compared to those in the control group. Among the OSCC group, patients with larger tumor diameters and lymph node metastases (T3/T4, N1 or greater) formed independent clusters in the beta diversity analysis of the bacterial flora. Bacteria of the Actinomycetia phylum, such as Actinomyces and Rothia, were significantly reduced in patients with higher stage and pathological grade. Conversely, bacteria of the phylum Spirochaetia and Proteobacteria, particularly those of the genus Treponema, were significantly elevated in advanced cancer cases.<br><br>CONCLUSIONS: Our results suggest that changes in the oral microbiota may play a role in OSCC development and progression.},
}
@article {pmid41078118,
year = {2026},
author = {Wang, Y and Yang, J and Hou, H and Song, L and Cheng, X and Liu, YX},
title = {Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.},
journal = {Plant biotechnology journal},
volume = {24},
number = {3},
pages = {1189-1203},
pmid = {41078118},
issn = {1467-7652},
support = {32470055//National Natural Science Foundation of China/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-BRC-CB-2025-01//Basic Research Center for Crop Biosafety Sciences/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; },
mesh = {*Microbiota/genetics ; *Plants/microbiology/genetics ; *Metagenomics/methods ; *DNA, Plant/genetics/isolation &amp; purification ; CRISPR-Cas Systems ; },
abstract = {Plants provide ecological habitats for diverse microorganisms, making accurate metagenomic sequencing essential for understanding the complex interactions that support plant growth, development and disease resistance. However, host DNA contamination poses a major challenge in plant microbiome studies, obscuring microbial genetic signatures and complicating the accurate analysis of microbial genomes. This review provides a comprehensive overview of current host DNA depletion strategies, including physical separation (e.g., filtration, gradient centrifugation), selective lysis and enzymatic treatments targeting plant cell walls. Advanced techniques such as targeted sequence capture with magnetic beads, methylation-based enrichment and nanopore selective sequencing offer additional options for host DNA removal. Despite these advances, current methods still face challenges in efficiency, specificity and applicability, emphasising the need for tailored strategies and the exploration of novel approaches for microbial enrichment. Innovations like CRISPR-Cas9 and chromatin immunoprecipitation-based host DNA depletion methods are proposed to provide novel directions for addressing current limitations. The development and refinement of host depletion techniques tailored to plant systems are crucial for enabling high-resolution, cost-effective metagenomic studies. These efforts promise to deepen our understanding of microbial diversity and functionality, ultimately accelerating microbiome-based innovations in crop improvement, sustainable agriculture and ecosystem resilience.},
}
@article {pmid41078079,
year = {2026},
author = {Shibata, R and Li, Y and Yaskolka Meir, A and Cregeen, SJ and Ross, MC and Espinola, JA and Sullivan, AF and Liang, L and Hasegawa, K and Camargo, CA and Zhu, Z},
title = {Nasopharyngeal Microbiome-Epigenome-Wide Association Analysis in Infants With Severe Bronchiolitis.},
journal = {Allergy},
volume = {81},
number = {3},
pages = {764-780},
pmid = {41078079},
issn = {1398-9995},
support = {//the Harvard University William F. Milton Fund/ ; R01 AI127507/AI/NIAID NIH HHS/United States ; R01 ES036966/ES/NIEHS NIH HHS/United States ; R01 AI148338/AI/NIAID NIH HHS/United States ; R01 AI137091/AI/NIAID NIH HHS/United States ; //American Lung Association Innovation Award/ ; K01 AI153558/AI/NIAID NIH HHS/United States ; UG3 OD023253/OD/NIH HHS/United States ; //Massachusetts General Hospital/ ; R01 AI134940/AI/NIAID NIH HHS/United States ; U01 AI087881/AI/NIAID NIH HHS/United States ; //Environmental influences on Child Health Outcomes (ECHO) Program Opportunities and Innovation Fund (OIF)/ ; R01 AI114552/AI/NIAID NIH HHS/United States ; UH3 OD023253/OD/NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {Humans ; *Bronchiolitis/microbiology/genetics/etiology ; Infant ; *Microbiota ; *Nasopharynx/microbiology ; Female ; Male ; DNA Methylation ; *Epigenome ; Prospective Studies ; Genome-Wide Association Study ; Severity of Illness Index ; Asthma ; Infant, Newborn ; },
abstract = {BACKGROUND: Bronchiolitis exposes infants to both acute burdens (e.g., hospitalization in cases of severe bronchiolitis) and increased risks for chronic respiratory sequelae (e.g., asthma). In severe bronchiolitis, recent evidence suggests distinct pathobiological roles of microbiota (e.g., viruses, bacteria) and host responses influenced by genetic and epigenetic factors. However, the relationship of airway microbiota with host DNA methylation (DNAm) in infants with severe bronchiolitis remains unknown.<br><br>METHODS: In a multi-center prospective cohort of 504 multi-ethnic infants with severe bronchiolitis (age <&#x2009;1&#x2009;year), using nasopharyngeal microbiome (exposure) and blood DNAm (outcome, Infinium MethylationEPIC BeadChip, Illumina) data within 24&#x2009;h of the hospitalization, we conducted microbiome-epigenome-wide association studies (mbEWAS). We examined microbiota-associated differentially methylated CpGs (mbDMCs, false discovery rate [FDR]&#x2009;<&#x2009;0.05), regions (mbDMRs, FDR <&#x2009;0.05), and DNAm age acceleration. We also determined the associations of DNAm age acceleration with asthma development by age 6&#x2009;years. Furthermore, we focused on asthma-related pathogenic bacteria-Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae-for functional analyses by examining serum mbDMR-related proteins (Proseek Multiplex, Olink) and their enriched pathways (FDR <&#x2009;0.10).<br><br>RESULTS: Across 23 common taxa-observed at least in 25% of the infants, we identified 1 mbDMC (S. pneumoniae, cg16594639, chr20: 39528675) and 96 mbDMRs (e.g., S. pneumoniae, chr5:27038497-27038802, CDH9; chr6:48068669-48068940, PTCHD4). A higher H. influenzae abundance was associated with DNAm age deceleration, and the deceleration was associated with a higher risk of developing asthma. In 29 mbDMRs of the asthma-related pathogenic bacteria, we identified 156 mbDMR-related proteins (e.g., MMP9, XCL1). These proteins were enriched in immune response-related pathways (e.g., regulation of ERBB signaling and eosinophil chemotaxis and migration pathways).<br><br>CONCLUSIONS: In this multi-center prospective cohort study of severe bronchiolitis, our mbEWAS suggested the microbiota-host associations that regulate immune responses.},
}
@article {pmid41015495,
year = {2026},
author = {Castells-Nobau, A and Fumagalli, A and Del Castillo-Izquierdo, &#xc1; and Rosell-Díaz, M and de la Vega-Correa, L and Samulėnaitė, S and Motger-Albertí, A and Arnoriaga-Rodríguez, M and Garre-Olmo, J and Puig, J and Ramos, R and Burokas, A and Coll, C and Zapata-Tona, C and Perez-Brocal, V and Ramio, L and Moya, A and Swann, J and Martín-García, E and Maldonado, R and Fernández-Real, JM and Mayneris-Perxachs, J},
title = {Gut microbial modulation of 3-hydroxyanthranilic acid and dopaminergic signalling influences attention in obesity.},
journal = {Gut},
volume = {75},
number = {4},
pages = {705-724},
doi = {10.1136/gutjnl-2025-336391},
pmid = {41015495},
issn = {1468-3288},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Obesity/metabolism/microbiology/psychology ; Mice ; *3-Hydroxyanthranilic Acid/metabolism ; Tryptophan/metabolism/blood ; Humans ; Male ; Fecal Microbiota Transplantation ; Drosophila melanogaster ; Female ; *Dopamine/metabolism ; Metagenomics ; Mice, Inbred C57BL ; Signal Transduction ; ortho-Aminobenzoates/metabolism ; Metabolomics ; },
abstract = {BACKGROUND: Obesity-related alterations in the gut microbiota have been linked to cognitive decline, yet their relationship with attention remains poorly understood.<br><br>OBJECTIVE: To evaluate the possible relationships among gut metagenomics, plasma metabolomics and attention.<br><br>DESIGN: We conducted faecal shotgun metagenomics and targeted plasma tryptophan metabolomics across three independent cohorts (n=156, n=124, n=804) with functional validations in preclinical models, including three faecal microbiota transplantation (FMT) experiments in mice and Drosophila melanogaster.<br><br>RESULTS: Obesity was consistently associated with reduced attention. Metagenomics analyses identified Proteobacteria species and microbial functions related to tryptophan biosynthesis from anthranilic acid (AA) as negatively associated with attention in obesity. Plasma tryptophan metabolic profiling and machine learning revealed that 3-hydroxyanthranilic acid (3-HAA) was positively associated with attention, particularly in obesity, while AA showed a negative association. Bariatric surgery improved attention and enriched microbial species linked to attention. In mice, diet-induced obesity (DIO) and microbiota depletion reduced 3-HAA and 5-hydroxy-indole acetic acid (5-HIAA) concentrations in the prefrontal cortex (PFC), which were restored by FMT. Global metabolic profiling (>600 metabolites) of PFC from the FMT group identified 3-HAA and the tryptophan and tyrosine pathways among the most significant in mice receiving microbiota from high-attention donors. A second FMT experiment also revealed a consistent enrichment of the tryptophan and tyrosine metabolism at the transcriptional level in the PFC, with Haao (3-hydroxyantrhanilic acid dioxygenase) and Aox4 (aldehyde oxidase 4), key in 3-HAA and 5-HIAA degradation, among the significantly regulated genes. In a third FMT study, attentional traits were transmitted from humans to mice alongside modulation of serotonergic and dopaminergic pathways. In Drosophila, mono-colonisation with Enterobacter cloacae and DIO induced attention deficit-like behaviours, which were mitigated by 3-HAA supplementation.<br><br>CONCLUSIONS: We have identified the microbiota and 3-HAA as potential therapeutic targets to improve attention, especially in obesity.},
}
@article {pmid40696533,
year = {2025},
author = {Liu, W and Wang, J and Xue, Y and Li, J and Huang, Y and Zhu, S and Wang, L and Wang, G and Chen, W and Zhao, J},
title = {The impact of Bifidobacterium longum CCFM1112 on chronic constipation: a randomised, double-blind, placebo-controlled study.},
journal = {Beneficial microbes},
volume = {17},
number = {2},
pages = {109-125},
doi = {10.1163/18762891-bja00085},
pmid = {40696533},
issn = {1876-2891},
mesh = {Humans ; *Constipation/therapy/microbiology ; *Probiotics/administration &amp; dosage/therapeutic use ; Double-Blind Method ; Male ; Female ; *Bifidobacterium longum/physiology ; Middle Aged ; Adult ; Gastrointestinal Microbiome ; Quality of Life ; Feces/microbiology/chemistry ; Chronic Disease/therapy ; Treatment Outcome ; },
abstract = {A mounting body of evidence suggests that probiotics may mitigate constipation through their favourable modulation of gut microbiota and its metabolic byproducts. The precise mechanisms underlying this effect remain to be fully elucidated. This randomised, double-blind, placebo-controlled study investigates the clinical efficacy of Bifidobacterium longum (B. longum) CCFM1112 in treating chronic constipation. Fifty-six volunteers diagnosed with chronic constipation according to the Rome IV criteria were randomly assigned to either the B. longum CCFM1112 group or a placebo group for a 4-week intervention. Key outcomes measured included weekly spontaneous bowel movements (SBM), stool consistency (Bristol Stool Form Scale [BSFS]), Patient Assessment of Constipation-Symptoms (PAC-SYM) questionnaire, and Quality of Life (PAC-QOL) questionnaire. In addition, gut microbiota was detected using metagenomic sequencing, and non targeted metabolomics was used to detect fecal and serum metabolites. Results demonstrated that B. longum CCFM1112 significantly reduced PAC-QOL scores and improved BSFS in patients with chronic constipation. Correlation analyses revealed that B. longum CCFM1112 significantly increased the abundance of the genera Blautia, Anaerobutyricum, and Streptococcus. Furthermore, the abundance of species, including Blautia massiliensis, Blautia sp. SC05B48, Anaerobutyricum hallii, and Streptococcus salivarius, was also significantly elevated. Furthermore, it elevated fecal levels of linoleic acid, gamma-aminobutyric acid (GABA), and arachidonic acid, while increasing L-glutamic acid and decreasing adenosine in serum. Our research findings provide evidence that the intake of B. longum CCFM1112 can alleviate constipation.},
}
@article {pmid41790792,
year = {2026},
author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Rahman, R and Hassan, J and Islam, T and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT},
title = {Shotgun metagenomic profiling reveals Bacillus-dominated bacterial communities in urban rooftop and surface garden soils of Bangladesh.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344114},
doi = {10.1371/journal.pone.0344114},
pmid = {41790792},
issn = {1932-6203},
mesh = {*Soil Microbiology ; Bangladesh ; *Bacillus/genetics/classification/isolation &amp; purification ; *Metagenomics/methods ; *Microbiota/genetics ; Gardens ; Soil/chemistry ; Biodiversity ; },
abstract = {Urban rooftop and surface garden systems play a critical role in food security in densely populated regions, yet their soil microbiomes remain understudied. To date, no baseline data exists on rooftop and surface garden soil microbiomes in Bangladesh. Understanding these communities is vital for enhancing soil health, nutrient cycling, and resilience for sustainable, climate-adapted urban agriculture. This study therefore investigated the bacterial diversity and community structure of rooftop and surface garden soils across Dhaka and Gazipur, Bangladesh. The goal was to uncover location- and garden-type-specific patterns that influence soil functionality. Using shotgun metagenomics of 27 garden soil samples (seven Dhaka rooftop [DRG], six Dhaka surface [DSG], eight Gazipur rooftop [GRG], and six Gazipur surface [GSG]), we identified 755 bacterial species dominated by Firmicutes (65-83%) and Proteobacteria (3-25%). While alpha diversity was consistent across sites (p > 0.05), beta diversity revealed distinct community structuring (p = 0.017), with surface gardens harboring greater bacterial richness (DSG:717, GSG:750 species) and elevated Bacteroidota (DSG:11.5%, GSG:2.7%) compared to rooftop soils. Strikingly, Bacillus species dominated all soils (>53% relative abundance) but exhibited location-specific distributions. DRG soils were notably enriched with B. paralicheniformis (28.3%) and B. licheniformis (25.2%). In contrast, DSG was characterized by B. cereus sensu lato (16.0%), Brevibacillus agri (12.1%), and Flavobacterium thermophilum (11.4%). GRG soils were dominated by B. cereus sensu lato (42.4%) and B. agri (11.5%). GSG soils showed diverse Bacillus species, including B. stratosphericus (14.6%), B. licheniformis (12.7%), B. safensis (9.7%), and B. altitudinis (8.8%). Of 41 detected Bacillus species, more than 58.0% were shared across gardens, yet their abundances varied with microhabitat. Moreover, KEGG profiling revealed marked functional divergence among urban garden soils. Carbohydrate metabolism dominated all sites (9.30-11.07%). DRG was uniquely enriched in photosynthesis (8.40%) and methane metabolism (8.62%), whereas DSG, GRG, and GSG showed higher oxidative phosphorylation (3.75-4.08%), two-component systems (3.24-3.73%), and biosynthetic pathways. This study unveils the ecological dominance of Bacillus species in urban agricultural soils, with location-driven compositional and functional shift. These findings are pivotal for optimizing sustainable urban agriculture in rapidly developing regions, where soil bacteriomes can be harnessed to improve crop resilience and food security.},
}
@article {pmid41778780,
year = {2026},
author = {Mambuque, E and Del Amo-de Palacios, A and Huete, SG and Marsh, CC and Theron, G and García-Basteiro, AL and Serrano-Villar, S},
title = {Beyond bacilli: integrating the microbiome into the TB research agenda.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638004},
pmid = {41778780},
issn = {1949-0984},
mesh = {Humans ; *Tuberculosis/microbiology/diagnosis/therapy ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Animals ; Antitubercular Agents/therapeutic use ; Metabolomics ; Lung/microbiology ; },
abstract = {Tuberculosis (TB) remains a leading infectious killer, with growing evidence that the human microbiome-particularly in the gut and lungs-shapes susceptibility, progression, and treatment outcomes. Over the past decade, studies have reported that TB-associated dysbiosis, which is more common in the gut than in the lung, is often marked by the loss of short-chain fatty acid-producing taxa and the expansion of opportunistic microbes. However, findings are frequently confounded by diet, antibiotic exposure, comorbidities, geography, and methodological variability. Most research has relied on compositional profiling, offering limited insight into functional mechanisms. This narrative review synthesizes recent evidence, emphasizing the need to integrate multiomics approaches-metagenomics, metatranscriptomics, and metabolomics-and experimental validation to uncover causal links between microbiome alterations and TB pathogenesis or therapy response. We discuss potential clinical applications, including microbiome-based diagnostics (such as stool-based microbial or metabolite signatures for TB risk stratification), prognostic indicators (such as gut microbiome recovery predicting immune normalization during therapy), and adjunctive interventions (including microbiome-derived products to reduce drug-induced liver injury or fecal microbiota transplantation, which has been shown to be safe in people with HIV on stable ART) to mitigate drug toxicity or enhance immune recovery. Key priorities include methodological standardization, confounder control, mechanistic studies, and the inclusion of high-burden settings. By moving beyond descriptive surveys toward functional, translational research, integrating insights from different microbiome methods into TB prevention, diagnosis, and treatment could redefine the clinical research agenda and open new avenues for precision medicine in this global disease.},
}
@article {pmid41778161,
year = {2026},
author = {Wang, D and Han, J and Wang, X and Wang, J and You, C and Wu, Z},
title = {Lacticaseibacillus rhamnosus B6 alleviates metabolic dysfunction-associated fatty liver disease by suppressing intestinal LPS synthesis and regulating lipid metabolism.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1755982},
pmid = {41778161},
issn = {1664-2392},
mesh = {Animals ; *Lacticaseibacillus rhamnosus/physiology ; *Probiotics/pharmacology ; Mice ; *Lipid Metabolism/drug effects ; Male ; *Gastrointestinal Microbiome ; *Lipopolysaccharides/biosynthesis/metabolism ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Metabolic Diseases/metabolism ; },
abstract = {INTRODUCTION: Metabolic dysfunction-associated fatty liver disease (MAFLD) has become a global epidemic with an unclear etiology and no effective therapeutic options. Disruption of the gut-liver axis driven by intestinal dysbiosis is closely implicated in MAFLD pathogenesis, making gut microbiota-targeted probiotic interventions promising preventive strategies.<br><br>METHODS: Lacticaseibacillus rhamnosus B6, a probiotic strain isolated from homemade Bulgarian fermented milk, synthesizes immunomodulatory macromolecules and regulates the intestinal flora. In the present study, we comprehensively investigated the colonization ability and MAFLD-alleviating effects of L. rhamnosus B6 in a high-fat diet (HFD)-induced murine MAFLD model using an integrated approach encompassing metagenomics, untargeted metabolomics, serum biochemical assays, and liver histopathological analysis.<br><br>RESULTS: Supplementation with L. rhamnosus B6 markedly decreased the relative abundance of Cupriavidus, Desulfovibrionaceae, and Enterobacteriacea, and inhibited the predicted lipopolysaccharide (LPS) synthesis pathway, thereby suppressing the inflammatory response. Furthermore, L. rhamnosus B6 intervention elevated unsaturated fatty acid levels by modulating lipid metabolic pathways, specifically mitochondrial &#x3b2;-oxidation of long-chain saturated fatty acids, &#x3b1;-linolenic acid, linoleic acid, and sphingolipid metabolism, while downregulating predicted myo-inositol degradation pathways, collectively contributing to MAFLD alleviation. In vitro, the metabolites of L. rhamnosus B6 exerted potent inhibitory activity against LPS-producing bacteria (e.g., Escherichia coli and Salmonella enterica).<br><br>DISCUSSION: These findings demonstrate that L. rhamnosus B6 is a promising probiotic for MAFLD alleviation via dual mechanisms of attenuating inflammation and regulating lipid metabolism. This study provides compelling evidence for the specific protective effects of L. rhamnosus B6 against MAFLD and offers a novel probiotic-based therapeutic strategy for MAFLD.},
}
@article {pmid41770401,
year = {2026},
author = {Han, T and Yang, T and Liu, Y and He, Z and Hao, Y and Cao, W and Ren, J and Wang, G and Gong, C and Hou, J},
title = {Dietary supplementation with allicin enhances growth performance and antioxidant capacity, and reduces gut pathogens and antibiotic resistance genes in Trachidermus fasciatus.},
journal = {Fish physiology and biochemistry},
volume = {52},
number = {2},
pages = {},
pmid = {41770401},
issn = {1573-5168},
support = {2025JNZ-C01//the earmarked fund of Hebei Agricultural S&amp;T Achievements Transformation/ ; 21326307D//the Key R&amp;D Program of Hebei Province, China and the National Marine Genetic Resource Center/ ; },
mesh = {Animals ; *Sulfinic Acids/pharmacology/administration &amp; dosage ; Disulfides ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; Animal Feed/analysis ; *Drug Resistance, Microbial/genetics ; Diet/veterinary ; *Fishes/growth &amp; development/microbiology ; },
abstract = {Allicin, a bioactive sulfur compound from garlic known for its antimicrobial and immunomodulatory properties, was evaluated in this study for its effects on growth, antioxidant activity, gut microbiota, and antibiotic resistance genes (ARGs) in Trachidermus fasciatus. Fish were administered allicin at concentrations of 100 mg/kg, 200 mg/kg, and 300 mg/kg. The 200 mg/kg allicin group had significantly higher WGR, LGR, and SGR than the control group. Hepatic SOD and LZM activities were also higher in the 200 mg/kg group. Metagenomics showed that allicin altered the gut microbiota composition, decreased the diversity, and altered the community structure. Allicin-treated fish had significantly reduced levels of potentially damaging bacteria, including Pseudomonas and Vibrio species. The ARGs showed that genes associated with multidrug resistance, including specific subtypes, were markedly reduced in the 200 mg/kg allicin-treated fish. The control group had a markedly decreased number of genes resistant to β-lactam antibiotics. Allicin reduced the number of genes resistant to rpoB2 and mdtC, suggesting the potential for antibiotic resistance. Network analysis of co-occurrence patterns showed that genes resistant to multiple drugs, tetracyclines, and peptides were prevalent, with most possible potential host taxa belonging to Ascomycota and Firmicutes. These results indicate the importance of allicin for fish health as a sustainable alternative to antibiotic resistance and provide a viable alternative to antibiotic resistance for fish farming.},
}
@article {pmid41769343,
year = {2026},
author = {Yan, X and Zhang, X and Wang, L and Song, W and Qi, T and Wang, Z and Tang, Y and Sun, J and Xu, S and Yang, J and Shao, Y and Chen, Y and Wang, J and Chen, J and Zhang, R and Liu, L and Shen, Y},
title = {Gut microbiota alterations and microbial translocation in HIV/SARS-CoV-2 co-infected patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1688580},
pmid = {41769343},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/complications ; *HIV Infections/microbiology/complications ; Male ; Female ; *Bacterial Translocation ; *Coinfection/microbiology/virology ; Middle Aged ; Adult ; Lipopolysaccharide Receptors/blood ; Lipopolysaccharides/blood ; Feces/microbiology ; SARS-CoV-2 ; Cohort Studies ; Severity of Illness Index ; Haptoglobins ; Protein Precursors/blood ; },
abstract = {OBJECTIVE: To characterize gut microbiome alterations and microbial translocation in human immunodeficiency virus (HIV)/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infected patients and identify microbial signatures associated with COVID-19 severity.<br><br>METHODS: In this cohort study, blood and fecal samples from 38 HIV/AIDS patients (20 SARS-CoV-2 co-infected [PC group]; 18 SARS-CoV-2-negative [NC group]) were analyzed. The PC group was stratified by COVID-19 severity: mild-to-moderate (PC1, n=13), severe-to-critical (PC2, n=3), and mixed infections (PC3, n=4). Serum lipopolysaccharide (LPS), soluble CD14 (sCD14), and zonulin levels were measured to assess microbial translocation and gut barrier integrity. Fecal metagenomic profiling was performed via whole-genome shotgun sequencing (Illumina NovaSeq/HiSeq).<br><br>RESULTS: Co-infected patients exhibited significantly elevated plasma LPS (78.09 vs 48.72 pg/mL, p=0.032) and sCD14 (2667 vs 1927 ng/mL, p=0.0015) compared to controls. Although no differences in &#x3b1;-diversity or overall taxonomic abundance were observed between the PC and NC groups, 329 PC-unique and 216 NC-unique microbial species were identified. Nine genera demonstrated diagnostic potential for co-infection [Area Under the Curve (AUC), >0.7] with Akkermansia showing the highest predictive value (AUC = 0.811). Critically, Blautia abundance was significantly reduced in severe-to-critical cases (PC2) versus mild-moderate cases (PC1, p=0.043) and controls (NC, p=0.006). Besides, our function prediction for gut microbiota suggested that SARS-CoV-2 may exacerbate lipid metabolic dysregulation in HIV-infected individuals.<br><br>CONCLUSIONS: HIV/SARS-CoV-2 co-infection is characterized by heightened microbial translocation and species-specific microbiota alterations rather than global dysbiosis. Blautia depletion may correlate with COVID-19 severity.},
}
@article {pmid41762228,
year = {2026},
author = {Liu, T and Ding, H and Lv, Z and Yan, C and Feng, S and Lu, D and Hang, F and Meng, X},
title = {Lactobacillus Taiwanensis Inhibits Gallstone Formation by Regulating Ileal Metabolism.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41762228},
issn = {1432-0991},
support = {82270598//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Lactobacillus/physiology ; *Ileum/metabolism/microbiology ; Mice ; *Gallstones/microbiology/prevention &amp; control/metabolism ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; Male ; *Probiotics/administration &amp; dosage ; Disease Models, Animal ; Colon/microbiology ; },
abstract = {In recent years, gut microbiota has been recognized to participate in gallstone formation via the gut-liver axis, yet the specific changes and roles of ileal microbiota remain unclear. This study aims to investigate the effects of microbial communities in different digestive tract segments on the formation of gallstones and the underlying mechanisms. Six-week-old C57BL/6J mice were randomly divided into a lithogenic diet group and a normal diet group. Ileal and colonic contents were collected separately for metagenomic sequencing.The Lactobacillus taiwanensis gavage model was constructed to compare its effects on gallstone formation and ileal metabolism. An intraperitoneal injection model of Lipoxin A4 (LXA4) was established to investigate the mechanisms by which Lactobacillus taiwanensis and LXA4 inhibit gallstone through Western blot analysis and ELISA methods. We found that there were significant differences in the intestinal microbiota between the group with gallstone formation and the control group in the small intestine and colon. Species-level analysis indicated that the lithogenic diet reduced the abundance of Lactobacillus taiwanensis in the small intestine. When Lactobacillus taiwanensis was administered intragastrically to mice, the incidence of gallstones decreased. Through metabolomics analysis and experimental verification, we demonstrated that Lactobacillus taiwanensis could down-regulate the expression of NETs in the liver and bile by increasing the level of LXA4, thereby reducing gallstone. The ileal and colonic microbiota exert site-specific effects in gallstone formation. Lactobacillus taiwanensis may inhibit gallstone formation by regulating ileal metabolism, may contribute to prevention and treatment of gallstones.},
}
@article {pmid41758194,
year = {2026},
author = {Chen, J and Wang, Y and Xu, L and Li, X and Zhao, L},
title = {Exploring the gut microbiome and metabolomic interactions of antimetabolite drugs to optimize therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2638009},
pmid = {41758194},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Antimetabolites/pharmacology/therapeutic use/pharmacokinetics ; Dysbiosis/chemically induced/microbiology ; Bacteria/metabolism/drug effects/genetics/classification ; Animals ; Metabolomics ; Neoplasms/drug therapy ; },
abstract = {Antimetabolite drugs are cornerstones in treating various cancers and autoimmune diseases; however, their clinical utility is often hampered by systemic toxicity caused by drug-induced gut microbiota dysbiosis. Predicting patient responses remains a significant challenge. Several studies have highlighted the influence of gut microbiota on antimetabolite treatment outcomes, revealing complex bidirectional interactions between the drugs and microbial communities. This review synthesizes the effects of common antimetabolites (including 5-fluorouracil, methotrexate, gemcitabine, capecitabine, 6-mercaptopurine, and thioguanine) on gut microbial communities and outlines a framework (pharmacokinetics, endogenous metabolite production, immune modulation, and apoptotic pathway modulation) for assessing chemotherapy-microbiota interactions. Additionally, potential microbial biomarkers for predicting treatment responses and strategies for manipulating the gut microbiota to enhance therapeutic efficacy are discussed. Therefore, advances in methodologies such as metagenomics and real-time microbial monitoring will be essential for unraveling these interactions and promoting the precise application of antimetabolite drugs.},
}
@article {pmid41754473,
year = {2026},
author = {Vilela, C and Mendoza, L and Vilela, R and Moreira Jardilino, FD and Brilhante Bhering, CL and Moreno, A},
title = {Microbial Diversity and Composition Uncovered on Obturator Prosthesis Biofilms: Exploratory Findings from a Pilot Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754473},
issn = {2076-0817},
mesh = {*Biofilms/growth &amp; development ; Humans ; Pilot Projects ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *Microbiota ; *Biodiversity ; Archaea/genetics/isolation &amp; purification/classification ; Fungi/genetics/classification/isolation &amp; purification ; Male ; Viruses/classification/genetics/isolation &amp; purification ; Female ; Middle Aged ; },
abstract = {Microbial communities on obturator prosthesis biofilms have yet to be investigated. This pilot study explores eukaryotes, prokaryotes, and viruses present on obturator prosthesis biofilms using metagenomics. The prostheses of the selected patients (n = 3) were collected and their biofilms were physically removed. The total genomic DNA was extracted, followed by metagenomic analysis. The microbial diversity in each of the investigated biofilms was exceptionally abundant. Between 2616 to 3024 species were detected in the three biofilms. The highest percentage included prokaryotes and unclassified species, followed by low percentages of fungi, viruses, and archaea. Unusual pathogens rarely reported in oral biofilms, such as Mycobacterium and other species, were also found at very low percentages. Unigenes for functional pathways related to metabolism, cellular processes, human disease, and other microbial unigenes were abundant. In addition, unigenes for several antibiotic-resistance mechanisms were also detected. This study reveals, for the first time, that biofilm formation on obturator prostheses comprises a variety of dynamic microbial communities, suggesting a putative role in health and disease in patients following maxillofacial surgery.},
}
@article {pmid41754400,
year = {2026},
author = {Wang, X and Duan, R and Ming, A and Zhang, Y and Liu, T and Wang, X and Diao, M},
title = {Age-Dependent Dynamics of the Biliary Microbiome in Children with Choledochal Cysts: Functional Remodeling Underlying Taxonomic Conservation.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
pmid = {41754400},
issn = {2076-0817},
mesh = {Humans ; Child, Preschool ; *Choledochal Cyst/microbiology ; Infant ; Male ; Female ; Child ; Age Factors ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *Biliary Tract/microbiology ; },
abstract = {Choledochal cyst (CC), a congenital biliary anomaly, is associated with recurrent infections, chronic inflammation, and an increased risk of malignancy. Although emerging evidence implicates the biliary microbiome in disease pathophysiology, its developmental dynamics in pediatric CC remain unclear. Using deep metagenomic sequencing and comprehensive functional annotation, this study characterized age-dependent changes in the biliary microbiome of 201 pediatric CC patients stratified into infancy (<1 year), early childhood (1-5 years), and later childhood (5-12 years). We found that while the taxonomic composition and alpha diversity of the microbiota remained conserved across age groups, profound functional remodeling occurred with host development. A core set of microbial species(Bacteroidota, Actinomycetota, Bacillota, and Pseudomonadota) and functional pathways was shared across all ages; however, early childhood (1-5 years) exhibited the greatest number of unique functional genes, metabolic pathways, and carbohydrate-active enzymes, identifying this period as a critical window for microbial metabolic adaptation. Age-specific patterns were also evident in clinically relevant traits: infants (<1 year) harbored the most unique antibiotic resistance and virulence factor genes, whereas the resistome and virulome became more streamlined in older children. These findings establish a paradigm of "taxonomic conservation coupled with functional remodeling" in the CC microbiome and highlight age as a key determinant of microbial community function. This study offers novel insights into the microbial dynamics underlying CC progression and suggests potential age-specific targets for future therapeutic strategies.},
}
@article {pmid41754175,
year = {2026},
author = {Wang, Z and Wei, J and Huang, Z and Liu, X and Li, S and Fang, Z and Hu, L and Li, R and Tao, L and Li, C and Chen, H},
title = {Metagenomics and Machine Learning Identify TMA-Producing Serratia Induced by High-Fat/Choline Diet: A Novel Obesity Target for TMA.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
pmid = {41754175},
issn = {2072-6643},
support = {2023ZYD0129//Sichuan Province Central Leading Local Science and Technology Development Special Project/ ; 2024YFD2101003//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Methylamines/metabolism/blood ; *Diet, High-Fat/adverse effects ; Male ; Mice, Inbred C57BL ; *Choline/administration &amp; dosage/metabolism ; *Gastrointestinal Microbiome ; *Obesity/microbiology/metabolism/etiology ; Mice ; *Metagenomics ; *Machine Learning ; Liver/metabolism/pathology ; Feces/microbiology ; },
abstract = {BACKGROUND: High-fat diet-induced metabolic disorders are associated with trimethylamine (TMA)/trimethylamine N-oxide (TMAO), whose production is linked to gut microbial choline metabolism. However, changes in specific gut microbiota under a high-fat diet and the relationship between these changes and choline in TMA/TMAO production remain unclear.<br><br>METHODS: A total of 48 7-week-old male C57BL/6J mice were subjected to one-week acclimatization feeding, and then randomly divided into four groups (12 mice per group) to establish a 2 &#xd7; 2 factorial design animal experiment: the control group (CON, basal diet), the choline-supplemented control group (CON + C, basal diet supplemented with 1% choline), the high-fat diet group (HF, high-fat diet), and the high-fat plus choline group (HF + C, high-fat diet supplemented with 1% choline). The experiment lasted for 9 weeks, during which dynamic monitoring of TMAO levels in mice was performed in the first 4 weeks. At the ninth week, the mice were sacrificed and samples were collected for subsequent assays, including the concentrations of TMA and TMAO in serum, colonic contents and feces; the pathological morphology of liver tissue, adipocyte staining characteristics and serum biochemical parameters; and the expression levels of key genes and proteins in liver, small intestine and colon tissues. Meanwhile, metagenomic analysis was conducted on colonic contents, combined with machine learning to predict the correlation between gut microbiota and TMA. In addition, gene cloning, multiple sequence alignment, molecular simulation and in vitro culture experiments were carried out to verify the TMA-producing function of the target strain.<br><br>RESULTS: This study elucidated that high-fat diet and high choline exert a significant interaction in TMA/TMAO production through a 2 &#xd7; 2 animal experiment; meanwhile, the significantly increased TMA/TMAO levels co-induced by the two factors further exacerbate metabolic disorders. Notably, through combined metagenomics and machine learning, we identified Serratia marcescens as the primary TMA-producing microorganism under high-fat/choline diet induction. In vitro cultures simulating the intestinal environment revealed that the TMA conversion ability of Serratia marcescens is time-dependent, reaching 60 &#xb1; 2.49% after 24 h of anaerobic culture with choline chloride. Multiple sequence alignment and molecular simulation further demonstrated that the CutC enzyme of Serratia marcescens has a conserved amino acid sequence and high affinity for choline.<br><br>CONCLUSIONS: We uncovered a two-factor synergistic effect of a high-fat/choline diet on TMA/TMAO, and for the first time identified the genus Serratia as a TMA-producing bacterium. These findings provide a new potential target for intervening in metabolic disorders mediated by high-fat diet-induced TMAO elevation.},
}
@article {pmid41754080,
year = {2026},
author = {Qin, P and Berzina, L and Geiker, NRW and Sandby, K and Krarup, T and Kristiansen, K and Magkos, F},
title = {Associations Between Gut Microbiome Enterotypes and Body Weight Change During Whole Milk Consumption.},
journal = {Nutrients},
volume = {18},
number = {4},
pages = {},
pmid = {41754080},
issn = {2072-6643},
support = {NA//Arla Food for Health/ ; NA//Danish Milk Levy Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; *Milk ; Animals ; Feces/microbiology/chemistry ; Adult ; Bacteroides ; *Body Weight ; Obesity/microbiology/diet therapy ; Middle Aged ; Streptococcus thermophilus ; },
abstract = {Background: Evidence is accumulating that gut bacterial communities modulate the outcome of dietary interventions. Objective: To assess how gut microbial enterotypes correlate with obesity-related outcomes during one month of whole milk consumption. Methods: This post hoc analysis used data from a previously published trial, which included a lead-in phase during which men with abdominal adiposity replaced habitual dairy product consumption with 400 g/day of whole milk for one month. We compared body weight, urinary metabolites, fecal metabolites, and gut microbiome composition and function based on shotgun metagenomic sequencing at the beginning and at the end of the lead-in phase between individuals with the two most prevalent enterotypes, the Bacteroides1 (B1) enterotype (n = 24) and the Ruminococcaceae (R) enterotype (n = 38). Results: Individuals with the B1 enterotype, but not those with the R enterotype, exhibited decreases in body weight and the relative abundance of Streptococcus thermophilus. Multiple linear regression analysis identified enterotype as a strong predictor of body weight change (p = 0.0034). In addition, urinary taurine level change was positively associated with body weight change in B1 individuals, not in R individuals. Conclusions: Our findings reveal an enterotype-specific response to an identical dietary modification, underscoring the value of integrating enterotype information into nutrition-intervention design and personalized nutrition strategies.},
}
@article {pmid41752220,
year = {2026},
author = {Kareem, HA and Khan, MF},
title = {Current Research Advances and Future Prospects on Microbial Consortia for Sustainable PFAS Remediation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
pmid = {41752220},
issn = {1422-0067},
support = {82930-NP//University College Dublin Internal Fund/ ; },
mesh = {Biodegradation, Environmental ; *Microbial Consortia ; *Soil Pollutants/metabolism ; *Fluorocarbons/metabolism ; Soil Microbiology ; *Environmental Restoration and Remediation/methods ; },
abstract = {Soil contamination by per- and polyfluoroalkyl substances (PFAS) represents a pressing environmental and public health concern due to the exceptional persistence of carbon-fluorine bonds, which prevent natural attenuation and limit the effectiveness of conventional remediation. Agricultural and industrial soils serve as long-term sinks for PFAS, continuously releasing these pollutants into groundwater and facilitating their transfer through the food chain. Conventional chemical and physical remediation methods are often costly, energy-intensive, and yield incomplete removal, underscoring the need for sustainable and biologically driven alternatives. Microbial consortia have emerged as a promising solution due to their metabolic complementarities, cross-feeding interactions, and ecological resilience, which together enable PFAS transformation and partial defluorination under complex soil and subsurface conditions. Key enzymes such as oxygenases, reductive dehalogenases, and hydrolases are often operating within co-metabolic networks, which play central roles in these processes. Advances in metagenomics, CRISPR-based functional screening, and metabolic modelling are rapidly uncovering novel PFAS-degrading microbes and pathways. Integration of machine learning with multi-omics and environmental datasets further enables the prediction of degradation mechanisms, identification of keystone degraders, and rational design of synthetic consortia. Emerging sustainable strategies, including biochar- and nutrient-amended soil microcosms, plant-microbe partnerships for coupled soil-groundwater phytoremediation, and bioelectrochemical systems that offer new avenues for enhancing PFAS biodegradation in situ. This review synthesises recent research progress and provides critical perspectives on the mechanistic, ecological, and engineering dimensions of PFAS bioremediation, proposing an integrated conceptual framework linking microbial consortia dynamics, enzymatic pathways, and environmental engineering interventions to guide scalable field applications and sustainable management of PFAS-contaminated soil-groundwater ecosystems.},
}
@article {pmid41752202,
year = {2026},
author = {Jung, S},
title = {Microbiome-Genome Crosstalk in Colorectal Cancer: Colibactin Signatures and Fusobacterium nucleatum in Epidemiology, Driver Selection, and Translation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {4},
pages = {},
pmid = {41752202},
issn = {1422-0067},
support = {RS-2022-NR069378//National Research Foundation of Korea/ ; RS-2025-18732993//National Research Foundation of Korea/ ; },
mesh = {*Colorectal Neoplasms/epidemiology/genetics/microbiology ; Humans ; *Fusobacterium nucleatum/genetics ; *Polyketides/metabolism ; *Peptides/metabolism ; *Gastrointestinal Microbiome ; Mutation ; *Bacteriocins/metabolism/genetics ; *Microbiota ; },
abstract = {Colibactin, a genotoxin produced by pks[+]E. coli, imprints highly specific mutational signatures SBS88 and ID18 in colorectal cancer (CRC) and even in normal colonic crypts. Population-scale analyses show these signatures are enriched in early-onset CRC, vary geographically, and are imprinted early during tumor evolution, where probabilistic attribution indicates that colibactin contributes to a measurable fraction of APC driver mutations in colibactin-positive cancers. Beyond colibactin, Fusobacterium nucleatum exerts clade-specific effects on tumor ecology and therapy response, with data supporting both chemoresistance and sensitization to anti-PD-1 in microsatellite stable (MSS) CRC. This article covers mechanistic, genomic, and molecular epidemiology evidence, outlines analytic standards for signature detection (whole-genome sequencing (WGS)/whole-exome sequencing (WES), single-sample fitting, and limits at low mutation counts), and charts translational paths spanning noninvasive screening (stool metagenomics + mutational signatures in tissue/circulating tumor DNA (ctDNA)), risk stratification, and microbial-targeted interventions (antibiotics, phages, ClbP inhibitors). Framing microbiome-genome crosstalk as a tractable axis enables testable clinical hypotheses for precision oncology.},
}
@article {pmid41746975,
year = {2026},
author = {Wang, G and Liu, L and Zhang, H and Mao, P and Lu, S and Zhang, X and Li, X and Song, C},
title = {Effects of tacrolimus treatment on the gut microbiota and metabolites in liver transplant recipients.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0343817},
pmid = {41746975},
issn = {1932-6203},
mesh = {Humans ; *Tacrolimus/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Liver Transplantation/adverse effects ; Male ; Female ; Middle Aged ; *Immunosuppressive Agents/therapeutic use/pharmacology ; Adult ; Feces/microbiology ; Aged ; Dysbiosis ; Transplant Recipients ; Tandem Mass Spectrometry ; Metabolome/drug effects ; },
abstract = {BACKGROUND: Liver transplantation (LT) is an effective treatment for patients with end-stage liver disease. In recent years, more and more evidence has supported the association between gut microbiota dysbiosis and the pathogenesis and progression of liver diseases.<br><br>METHODS: The study included 36 patients who received tacrolimus treatment after liver transplantation. Patients were stratified into subgroups according to three key variables: tacrolimus treatment duration, whole-blood tacrolimus concentration, and tacrolimus concentration-to-dose (C/D) ratio. Fecal samples and whole-blood specimens were collected from all participants. The Illumina HiSeq X platform was used to detect the gut metagenome, analyzing the composition and characteristics of the gut microbiota. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) technology was employed to detect metabolites of the gut microbiota, revealing their metabolic profiles.<br><br>RESULTS: As the duration of tacrolimus use increased, the diversity of the gut microbiota also increased, and the abundance of Escherichia coli_D and Bacteroides stercoris rose. Additionally, the abundance of Brunovirus and Uetakevirus tended to decrease. The abundance of gene functions related to chemical carcinogenesis and bacterial invasion of epithelial cells significantly decreased. In the gut microbiota metabolites, 16 substances like Astragaloside A and Acetyl-L-carnitine significantly increased, while 108 substances like Capsaicin and TLK significantly decreased. Within a certain range, as the concentration of tacrolimus in whole blood increased, the diversity of the gut microbiota increased. The abundance of Phocaeicola and Klebsiella increased, and the abundance of Peduovirus among viruses also rose. However, excessively high concentrations may lead to a decrease in the diversity of the gut microbiota and a decrease in the abundance of Phocaeicola. With respect to the C/D ratio, increased ratios were linked to significantly higher levels of 57 fecal metabolites (e.g., PC 34:2, 5-Methyl-2'-deoxycytidine), whereas 13 metabolites (e.g., FAHFA 2:0/16:0) showed substantial declines.<br><br>CONCLUSIONS: Tacrolimus treatment is associated with distinct alterations in gut microbiota and metabolites among LT recipients. These findings provide a preliminary framework for future investigations aimed at optimizing immunosuppressive regimens, although their clinical translational potential requires validation in larger-scale, prospective cohort studies.},
}
@article {pmid41729067,
year = {2026},
author = {Liu, Y and Zhang, T and Liu, J and Dong, X},
title = {Lactiplantibacillus plantarum Fermentation Enhances the Bioactivity of Polymeric Proanthocyanidins: Gut Microbiota Regulation via Caffeic Acid Production.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {8},
pages = {6824-6839},
doi = {10.1021/acs.jafc.5c14510},
pmid = {41729067},
issn = {1520-5118},
mesh = {*Proanthocyanidins/metabolism/chemistry ; *Caffeic Acids/metabolism ; Fermentation ; *Gastrointestinal Microbiome ; *Lactiplantibacillus plantarum/metabolism/isolation &amp; purification/genetics ; Probiotics/metabolism ; Humans ; *Polymers/metabolism/chemistry ; Feces/microbiology ; *Lactobacillaceae/metabolism/genetics/isolation &amp; purification ; Animals ; },
abstract = {Polymeric proanthocyanidins (PPC) typically exhibit low bioavailability. While probiotic metabolism can enhance polyphenol bioactivity, the interaction between Lactiplantibacillus plantarum and PPC remains underexplored. In this study, L. plantarum SFFI23, a strain exhibiting excellent capacity to metabolize PPC, was selectively isolated. During in vitro digestion and fecal fermentation, SFFI23 reduced the degree of polymerization of PPC and enhanced overall antioxidant capacity. Metagenomic analysis revealed that SFFI23-PPC metabolism resulted in Firmicutes enrichment, accompanied by opportunistic pathogen reduction and an upregulation of health-associated pathways such as quorum sensing. Metabolomics analysis showed significant enrichment in 17 metabolic pathways. Multiomics analyses revealed that caffeic acid, derived from SFFI23-PPC metabolism, contributes to improved gut health by regulating gut microbiota and promoting metabolic reprogramming. This study outlines a triadic mechanism: "biotransformation by L. plantarum-metabolic activation of PPC-gut microbiota regulation", highlighting the potential of SFFI23 as an adjunct for enhancing PPC bioactivity.},
}
@article {pmid41719987,
year = {2026},
author = {Dang, X and Xu, S},
title = {Exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate is associated with aberrant barbering behavior in diabetic mice.},
journal = {Ecotoxicology and environmental safety},
volume = {311},
number = {},
pages = {119906},
doi = {10.1016/j.ecoenv.2026.119906},
pmid = {41719987},
issn = {1090-2414},
mesh = {Animals ; Male ; Mice ; Hippocampus/drug effects ; *Behavior, Animal/drug effects ; Molecular Docking Simulation ; Diabetes Mellitus, Experimental ; *Alkanesulfonic Acids/toxicity ; Salmonella enterica ; Gastrointestinal Microbiome/drug effects ; *Environmental Pollutants/toxicity ; Molecular Dynamics Simulation ; Colon/microbiology ; Fluorobenzenes ; },
abstract = {This study originated from an incidental behavioral observation. We found that exposure to environmentally relevant concentration of sodium p-perfluorous nonenoxybenzene sulfonate (OBS; 3 μg/L), as reported in a previous field measurement study, was associated with aberrant barbering behavior in diabetic mice. To investigate the underlying mechanisms, sixteen 8-week-old male db/db mice were administered OBS at 3 μg/L for 91 days. Biochemical assays of endothelial- and barrier-related markers, hippocampal OBS quantification, stereotaxic hippocampal OBS administration, and metagenomic sequencing of the colonic contents and hippocampal tissues were performed. Based on the metagenomic results, computational biology analyses, including molecular docking, molecular dynamics simulations, and protein functional annotation, were conducted to assess potential OBS-bacterial protein interactions. The results showed that exposure to environmentally relevant concentration of OBS was associated with aberrant barbering behavior in the experimental mice (100 % prevalence). Circulating markers of endothelial activation and basal lamina injury were significantly elevated. Metagenomic analysis revealed that the abundance of Salmonella enterica subsp. diarizonae was significantly increased in both the colonic contents and hippocampal tissues, with hippocampal abundance positively correlated with colonic abundance. Molecular docking and molecular dynamics simulations indicated that OBS binds effectively to two bacterial proteins. Functional annotation suggested that these proteins are associated with central metabolic and biosynthetic processes relevant to bacterial proliferation. Together, these findings suggest that exposure to environmentally relevant concentration of OBS is associated with aberrant barbering behavior in diabetic mice and may be associated with increased colonic S. enterica subsp. diarizonae abundance and its presence in the hippocampus.},
}
@article {pmid41715225,
year = {2026},
author = {Ding, L and Yang, S and Wu, F and Pilling, D and Zhang, J and Pool, K and Nishvanthi, M and Babington, S and Maloney, SK and Chen, L and Shi, J and Wang, Y and Blache, D and Wang, M},
title = {Association between the gut microbiome and plasma metabolites linked to vocalization-based temperament in Merino sheep.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41715225},
issn = {2049-2618},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Sheep/microbiology/physiology/blood ; *Temperament/physiology ; *Vocalization, Animal/physiology ; Rumen/microbiology ; *Metabolome ; Female ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; gamma-Aminobutyric Acid/metabolism ; },
abstract = {BACKGROUND: Temperament, as a determinant of behavioural and emotional responses, has a substantial adaptive value in different environments. This study aims to investigate the association between the gut microbiota and temperament plasticity, and clarify the potential metabolic mechanism that underpins that association by running a multi-omics study in sheep.<br><br>METHODS: The TrackSheep research cohort was generated using 200 healthy juvenile Merino ewes, and the rumen microbiota, plasma metabolome, and temperament phenotype was measured.<br><br>RESULTS: Rumen metagenomic analysis identified 25 microbial species and 16 MetaCyc pathways that explained 37.5% and 11.1%, respectively, of the variation in temperament as estimated using the vocal reactivity to stress. Among these, the &#x3b3;-aminobutyric acid (GABA) shunt and allantoin degradation pathways showed the strongest associations with vocal behaviour. Multi-omic integration linked these microbial pathways to plasma metabolites that are involved in neurotransmission, antioxidant defense, and energy metabolism, including acetyl-L-carnitine (ALCAR) and urocortisone, which partially mediated the effects of microbial pathways on vocalisations. Notably, functional genomic and mediation analyses indicated that the abundance of Cryptobacteroides sp902761655 was associated with the activity of GABA shunt pathway, where GABA co-occurred with succinate production, in turn correlating with reduced inhibitory effects of ALCAR on stress-susceptible temperament. Although plasma metabolite shifts observed immediately after behavioural tests reflected stress exposure, their associations with rumen microbiota highlight microbiome-metabolite interplay that could underly behavioural variation.<br><br>CONCLUSIONS: Our study provides the first large-scale multi-omics evidence linking the rumen microbiome to a dimension of emotional reactivity in livestock, while underscoring the need for longitudinal and experimental validation to establish causal mechanisms. Video Abstract.},
}
@article {pmid41691814,
year = {2026},
author = {Guo, H and Liu, Q and Han, H and Xu, W and Shi, W and Zhao, M and Xiao, X and Liu, J and Li, T},
title = {Unveiling the adaptive evolution of halotolerant aceticlastic methanogenesis: Multi-scale responses and energy partition.},
journal = {Water research},
volume = {294},
number = {},
pages = {125552},
doi = {10.1016/j.watres.2026.125552},
pmid = {41691814},
issn = {1879-2448},
mesh = {Methane/metabolism ; Wastewater ; Microbiota ; Acetates/metabolism ; },
abstract = {The high concentration of salt ions in saline organic wastewater poses significant challenges for wastewater treatment technologies, particularly impacting the stability of anaerobic digesters. Aceticlastic methanogenesis is a crucial pathway for converting acetate into methane through methanoarchaea whose metabolism is adversely impacted by salt stress. To address this, long-term adaptive laboratory evolution (ALE) was conducted to cultivate halotolerant aceticlastic methanoarchaea, incorporating metagenomics, metatranscriptomic sequencing, metabolomics, and metabolic modeling to delineate genetic and metabolic responses. The evolved microbiome achieved a substantial increase in methanogenic activity at 5 % sodium chloride, reaching 82.25 % theoretical conversion of acetate to methane, significantly outperforming the original microbiome. This ALE process overcame the natural scarcity of aceticlastic methanogens in hypersaline environments. Key adaptation mechanisms were confirmed at the transcriptional level, primarily involving the upregulation of genes for inorganic ion transport, compatible solute uptake, and de novo biosynthesis. Horizontal gene transfer also contributed significantly through the transfer of osmoregulation genes, particularly those for compatible solute transport, suggesting an energy-efficient adaptation strategy of accumulating rather than synthesizing solutes. Metabolic flux analysis revealed that adjustments in energy distribution under salt stress are driven by the energetic cost of synthesizing compatible solutes, which highlights the importance of solute transporters for energy conservation. This study elucidates the complex interplay between metabolic reprogramming and gene transfer in enhancing microbial resilience under salt stress, thereby deepening our understanding of microbial adaptations in extreme environments and advancing biotechnological approaches for saline wastewater treatment.},
}
@article {pmid41669888,
year = {2026},
author = {Yeo, LF and Palmu, J and Havulinna, AS and Pärnänen, K and Salomaa, V and Lahti, L and Knight, R and Niiranen, T},
title = {Prospective association between the gut microbiome and incident hypertension: a 20-year cohort study.},
journal = {Journal of hypertension},
volume = {44},
number = {4},
pages = {673-681},
pmid = {41669888},
issn = {1473-5598},
mesh = {Humans ; *Hypertension/epidemiology/microbiology ; Middle Aged ; Female ; Male ; *Gastrointestinal Microbiome ; Adult ; Aged ; Prospective Studies ; Finland/epidemiology ; Incidence ; Risk Factors ; Cohort Studies ; },
abstract = {INTRODUCTION: Hypertension remains the leading modifiable risk factor attributable to 10.8 million premature deaths. Hence the study of hypertension and gut microbiome as a therapeutic target is very important. Yet the links between the gut microbiome and long-term incidence of hypertension are unknown.<br><br>AIM: This study assessed the association between gut microbiome and incident hypertension.<br><br>METHOD: The study sample consisted of 3311 nonhypertensive individuals (60.7% women) aged 25-74 &#x200a;years who were drawn from the general population in Finland. In the baseline examination performed in the year 2002, the participants underwent a health examination and provided a stool sample. The gut microbiome was assessed using shallow shotgun metagenomic sequencing. Microbiome analyses were performed with Cox proportional hazards model.<br><br>RESULTS: In total, 675 participants developed hypertension over a follow-up period of nearly 20&#x200a;years. In multivariable-adjusted models, overall gut microbiome composition was not related to risk of future hypertension. Eight genera, including Agathobaculum, Blautia_A_141780, Blautia_A_141781, Mediterraneibacter_A_155590, Enterocloster , Bariatricus , CAG-317-146760 , and CAG-628 were significantly associated with incident hypertension in the age-adjusted and sex-adjusted models, but none remained significant in the multivariable-adjusted models. No functional pathways were associated with hypertension risk.<br><br>CONCLUSION: Our results do not provide strong evidence for an association between the gut microbiome and risk of future hypertension, especially after adjusting for covariates that are known to influence the gut microbiome.},
}
@article {pmid41653958,
year = {2026},
author = {Gamez, I and Fouladi, F and Gonzalez, A and Ward, J and Wang, Z and Beane Freeman, LE and Motsinger-Reif, A and Peddada, SD and Knight, R and Lee, M and London, SJ},
title = {Household environmental characteristics influence the house dust metagenome.},
journal = {Environmental research},
volume = {295},
number = {},
pages = {123889},
doi = {10.1016/j.envres.2026.123889},
pmid = {41653958},
issn = {1096-0953},
mesh = {*Dust/analysis ; *Metagenome ; Humans ; *Microbiota ; *Family Characteristics ; Housing ; *Air Pollution, Indoor/analysis ; *Environmental Exposure ; },
abstract = {Environmental exposures can shape microbial community compositions inside homes. Metagenomic sequencing methods can further elucidate the role of household exposures like indoor moisture and the surrounding landscape. To identify household environmental exposures associated with the house dust metagenome. Microbial communities in vacuumed dust from 771 homes in the Agricultural Lung Health Study were characterized using whole metagenome shotgun sequencing (5821 taxa across 45 phyla). Household characteristics (i.e. presence of leaks, de-humidifier, humidifier use) were assessed by questionnaires or field technicians. We evaluated associations between exposures and both overall microbial diversity and differentially abundant taxa (ANCOM-BC2). Additionally, we explored microbial networks based on Spearman correlations (SECOM). Microbial diversity was higher in homes with mold/mildew (p-value<0.05), leaks, humidifier use, or occupants removing shoes before entering (p-value<0.1). Examining individual species, <10 taxa were significantly differentially abundant (p-value<0.05 after Holm-Bonferroni correction) in relation to both mold/mildew and leaks. Greater than 10 species were significantly differentially abundant in relation to removing shoes and humidifier use. Additionally, the genera Clostridium, Prevotella, and Cryptobacteroides were positively associated with removing shoes. In this farming population, the house dust microbiome differed by moisture-related exposures, and removing shoes before entering the home. Many novel associations were identified between individual taxa and these exposures. Our findings further knowledge of the impact of environmental conditions inside the home on the indoor microbiome.},
}
@article {pmid41636495,
year = {2026},
author = {Kopp, OS and Morandi, SC and Kreuzer, M and Uldry, A-C and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC},
title = {Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease.},
journal = {Microbiology spectrum},
volume = {14},
number = {3},
pages = {e0226425},
pmid = {41636495},
issn = {2165-0497},
support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique F&#xe9;d&#xe9;rale de Lausanne), Lausanne, Switzerland/ ; },
mesh = {Humans ; Female ; *Tears/chemistry/metabolism ; Male ; *Dry Eye Syndromes/microbiology/etiology ; *Proteome/analysis ; *Microbiota ; Adult ; *Contact Lenses/adverse effects ; Bacteria/classification/genetics/isolation &amp; purification ; Young Adult ; Middle Aged ; Eye Proteins ; },
abstract = {Although contact lens wear is widespread and known to affect the ocular surface, its impact on the ocular surface microbiome (OSM) remains poorly understood, with existing studies reporting conflicting findings. Additionally, the relationship between contact lens wear, tear proteome, and dry eye disease (DED) is unclear. In this study, we aimed to characterize the OSM (via whole-metagenome shotgun sequencing) and the tear proteome of 25 contact lens wearers and 23 age- and sex-matched controls. The dominant phyla were Actinobacteria, Proteobacteria, and Firmicutes, with Cutibacterium acnes being the most abundant species. No significant differences in microbial composition, diversity, or tear proteome were observed between contact lens wearers and controls. DED parameters (tear breakup time, Schirmer's test, tear osmolarity, and Ocular Surface Disease Index [OSDI]) also showed no significant differences, although contact lens wearers reported a trend toward higher subjective symptoms (OSDI). Sex-stratified analysis revealed a marginal difference in microbial beta diversity between male contact lens wearers and male controls, along with increased tear production in male contact lens wearers. Female contact lens wearers reported a higher OSDI compared to female controls. These findings suggest that contact lens wear does not significantly alter the OSM or tear proteome in healthy individuals, although sex-specific responses may warrant further investigation.IMPORTANCEContact lenses are worn by millions of people, yet the scientific literature contains conflicting reports about their impact on the microbial communities that are naturally present on the eye surface. This study addresses these knowledge gaps by examining both the eye microbiome and tear proteins using advanced sequencing and linking them to dry eye symptoms. Understanding the relationship between contact lens wear, natural eye bacteria, and tear composition is essential for resolving contradictory findings in the field. Additionally, identifying potential sex-specific differences in how individuals respond to contact lens wear could lead to more personalized approaches to contact lens management.},
}
@article {pmid41634815,
year = {2026},
author = {Hao, X and Wang, X and Wang, X and Wang, C and Li, C and Lu, Y and Cheng, Q and Chen, Z and Zhu, L and Li, C and Shen, X},
title = {Synthetic community derived from the root core microbes of a desert shrub Caragana korshinskii enhances wheat drought tolerance.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41634815},
issn = {2049-2618},
mesh = {*Triticum/growth &amp; development/microbiology/physiology ; *Droughts ; *Caragana/microbiology ; *Plant Roots/microbiology ; Biofilms/growth &amp; development ; *Microbiota ; Desert Climate ; Quorum Sensing ; Metagenomics/methods ; Bacteria/classification/genetics/isolation &amp; purification ; Drought Resistance ; },
abstract = {BACKGROUND: Drought, intensified by climate change, poses a mounting threat to global food security by severely constraining crop productivity. While microbial inoculants offer promise for drought tolerance, their poor adaptability remains insufficient for extremely water-deficient environments. Desert plants host unique drought-adapted microbiomes that remain largely unexplored for agricultural applications.<br><br>RESULTS: Here, we investigated the microbial community of the desert shrub Caragana korshinskii and identified a core set of drought-responsive strains. A synthetic microbial community (SynCom) derived from these strains significantly improved wheat growth under drought stress. Metagenomic analyses revealed that microbial functions related to biofilm formation, quorum sensing, and carbon metabolism were enriched, with Pseudomonas identified as a key functional taxon. Guided by inter-strain interactions in biofilm assembly, we streamlined the consortium into a five-member synthetic community, where quorum-sensing signals promoted community-wide biofilm formation. Community biofilm production improved strain colonization and conferred greater drought tolerance compared to monocultures. In plants, mechanistic investigations indicated that the simplified SynCom inoculation universally upregulated MAPK and jasmonic acid signaling pathways. Furthermore, carbohydrate metabolic pathways such as starch and sucrose metabolism were specifically activated, suggesting a multi-level mechanism underlying SynCom-mediated drought tolerance.<br><br>CONCLUSIONS: These findings demonstrate that SynCom constructed on the endophytic flora of desert plants can significantly enhance crop drought tolerance. Our work highlights the pivotal role of community biofilm synthesis in facilitating root colonization and activating a multidimensional drought tolerance network in plants. This study not only gives an ecological perspective on desert microbiome adaptations but also offers a strategic framework for developing effective microbial inoculants for arid-region agriculture. Video Abstract.},
}
@article {pmid41619209,
year = {2026},
author = {Tang, R and Wang, J and Wang, X and Zeng, M and Gao, W and Yang, K and Xu, L and Li, Y and Zhou, C and Yue, B and Fan, Z and Song, Z},
title = {Large-scale metagenomic analysis reveals host genetics shapes microbiomes in wild freshwater fish gut and skin.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116930},
doi = {10.1016/j.celrep.2026.116930},
pmid = {41619209},
issn = {2211-1247},
mesh = {Animals ; *Skin/microbiology ; *Metagenomics/methods ; Fresh Water ; *Fishes/microbiology/genetics ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Microbiota/genetics ; },
abstract = {Wild freshwater fish microbiomes remain underexplored despite their ecological and economic importance. Through metagenomic sequencing of 903 gut/skin samples from 121 species in southwest China, we constructed the Wild Freshwater Fish Microbiome Catalog, comprising 705 metagenome-assembled genomes and 3,271 viral operational taxonomic units. Host phylogeny dominates microbial community variation, explaining 48.2% (skin) and 22.28% (gut) of the variation. Significant phylosymbiosis occurs in wild freshwater fish, particularly Cyprinidae, with a stronger skin than gut signal. Deterministic selection underpins phylosymbiosis via host-specific ecological filtering. Lifestyle factors (diet, living water layer) and geographical location also impact microbial communities. Notably, wild freshwater fish microbiota harbor a complete set of vitamin B12de novo biosynthesis genes, with Cetobacterium as a keystone genus with probiotic potential. Our work expands gut and skin microbial genome resources, reveals host-microbe coevolution in freshwater fishes, and provides probiotic resources for aquaculture.},
}
@article {pmid41617733,
year = {2026},
author = {Thangaraj, S and Sun, J},
title = {Depth Resolved Metagenomic Dataset from Surface and Deep Chlorophyll Maximum Layers in the Western Pacific Ocean.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {41617733},
issn = {2052-4463},
mesh = {Pacific Ocean ; *Metagenomics ; *Metagenome ; *Chlorophyll/analysis ; *Seawater/microbiology ; *Microbiota ; },
abstract = {Stratified microbial communities are central to ocean biogeochemical cycles, yet their vertical structure and functional potential remain under characterized in oligotrophic regions. We present a metagenomic dataset from surface ocean and the deep chlorophyll maximum (DCM) layers of the stratified Western Pacific Ocean, sampled at four stations spanning approximately 800 kilometres. Each of the eight samples generated over 22.9 Gb of high-quality Illumina HiSeq 2500 paired end reads (Q20 > 95%, Q30 > 90%). De novo assemblies yielded 1.3-1.9 million contigs per sample, with total assembly sizes of 948 Mb to 1.33 Gb and N50 values of 632-749 bp. Gene prediction identified ~5.26 million non-redundant genes across all samples, reflecting substantial microbial diversity and depth-specific variation. Assembly statistics, taxonomic profiles, and functional annotations of genes are included for technical validation of the dataset, demonstrating data completeness and analytical depth. This dataset offers annotated sequence data and environmental metadata suitable for benchmarking, method development, and comparative studies of marine metagenomes.},
}
@article {pmid41617710,
year = {2026},
author = {Shrestha, B and Romero, MF and Villada, JC and , and Blaby-Haas, CE and Schulz, F},
title = {Global metagenomics reveals plastid diversity and unexplored algal lineages.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41617710},
issn = {2041-1723},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
mesh = {*Plastids/genetics/classification ; *Metagenomics/methods ; Phylogeny ; Symbiosis/genetics ; Cyanobacteria/genetics/classification ; Biodiversity ; Genetic Variation ; Haptophyta/genetics/classification ; Cryptophyta/genetics/classification ; Genome, Plastid ; Alveolata/genetics ; Photosynthesis/genetics ; Evolution, Molecular ; },
abstract = {Photosynthetic organelles in eukaryotes originated through primary endosymbiosis with a cyanobacterium, an event that profoundly shaped the evolutionary landscape of the eukaryotic tree of life. Primary plastids in Archaeplastida, especially in cultivable plants and algae, contribute most to known plastid diversity. Secondary and higher-order endosymbiosis, involving eukaryotic hosts and algal endosymbionts, further spread photosynthesis among protists within the CASH lineages (Cryptophyta, Alveolata, Stramenopila, and Haptophyta). Despite various hypotheses explaining secondary plastid evolution and distribution, empirical support remains limited. Here, we employ cultivation-independent global metagenomics to expand plastid diversity and investigate plastid origins. We capture 1,027 plastid sequences, including 300 novel sequences belonging to previously unsequenced plastids and representing yet-to-be described microeukaryotes. This includes a new lineage that offers insights into plastid evolution in haptophytes and cryptophytes. Our results confirm that Archaeplastida plastids originate from an early branching cyanobacterial lineage closely related to Gloeomargaritales and identify the closest extant relative of Paulinella plastids. Additionally, our findings suggest two independent origins of secondary red-algal plastids, contributing to plastid diversity in CASH lineages and challenging the prevailing model of single secondary plastid origin. Our study highlights the importance of metagenomic data in uncovering biological diversity and advancing understanding of plastid relationships across photosynthetic eukaryotes.},
}
@article {pmid41587576,
year = {2026},
author = {Mburu, D and Kumar, S and Wang, Y and Namagerdi, AA and Bai, K and Ali, B and Minalla, A and Gonzales, KO and Abdelhalim, KA},
title = {The oxalobiome: unraveling the role of gut microbiota in oxalate metabolism and its implications for kidney health and disease management.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {584},
number = {},
pages = {120852},
doi = {10.1016/j.cca.2026.120852},
pmid = {41587576},
issn = {1873-3492},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Oxalates/metabolism ; *Kidney/metabolism ; Hyperoxaluria/metabolism ; Disease Management ; },
abstract = {The oxalobiome, comprising microbial communities involved in oxalate metabolism, plays a critical role in maintaining oxalate homeostasis and preventing associated health issues, particularly calcium oxalate nephrolithiasis. Key organisms, notably Oxalobacter formigenes, are essential for degrading oxalate, yet their abundance is influenced by factors such as diet, genetics, and antibiotic use. Recent advances in research have elucidated the complex interactions between the gut microbiome and oxalate metabolism, highlighting the potential for therapeutic interventions. Innovative strategies, including RNA interference therapies (e.g., lumasiran, nedosiran), engineered probiotics, and gene-editing technologies, show promise in managing conditions like primary hyperoxaluria. However, challenges remain, including limitations in oxalate measurement techniques and variability in microbial populations. Multi-omics approaches and metagenomic analyses have enhanced our understanding of the oxalobiome, revealing novel microbial taxa and metabolic pathways involved in oxalate degradation. Despite the potential of emerging therapies, clinical translation is still in its infancy, necessitating further research to establish efficacy and safety. Future studies should focus on mechanistic insights, standardized methodologies, and targeted microbiome-based therapies to optimize management strategies for hyperoxaluria and related systemic diseases. A comprehensive understanding of the oxalobiome is essential for developing precision medicine approaches that effectively address oxalate dysregulation and improve patient outcomes.},
}
@article {pmid41540332,
year = {2026},
author = {Wang, Y and Wu, C and Zhu, Q and Fan, C and Zhu, Y and Chen, Y and Wei, X and Feng, L},
title = {Comparative metagenomic characterization of gut microbiota and antibiotic resistome in multi-facility SPF mice.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41540332},
issn = {1471-2180},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics/drug effects ; Mice ; *Metagenomics/methods ; Mice, Inbred C57BL ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; Mice, Inbred BALB C ; Specific Pathogen-Free Organisms ; Cecum/microbiology ; Metagenome ; *Drug Resistance, Microbial/genetics ; },
abstract = {Specific pathogen-free (SPF) mice are pivotal preclinical models linking basic microbiology to clinical translation, yet comprehensive high-resolution profiling of their gut microbiome, especially antibiotic resistance genes (ARGs), remains limited. To address this gap, metagenomic sequencing was conducted on cecal contents from C57BL/6 and BALB/c SPF mice from five Shanghai laboratory animal facilities, generating 141 Gbp high-quality sequencing data. From 1,761,909 predicted genes, 1,048,575 non-redundant genes were identified for analysis. Taxonomic annotation identified Bacillota (73.0%), Bacteroidota (16.6%), and Actinomycetota (2.9%) as dominant phyla. At the genus level, microbial communities varied markedly across facilities, with Muribaculaceae prevailing in SHA/SHD and Blautia or Enterococcus enriched in SHB/SHE. Beta diversity analysis showed communities clustered by facility, indicating breeding environment had a stronger impact on gut microbiota diversity than host strain. KEGG, COG, and GO functional annotation revealed broad metabolic and molecular diversity. Antibiotic resistome profiling identified 11 ARG categories, predominantly associated with glycopeptides (18.1%) and tetracycline (11.3%) resistance. The most enriched ARG carriers were Pseudomonadota (acrD, emrB, mdtB etc.), Bacillota (tet(44), tet(M), tet(O) etc.), Bacteroidota (tet(Q), mel, tet(X) etc.), and Actinomycetota (rpoB, ileS). Furthermore, ARGs resistance mechanisms varied between facilities with distinct beta-diversity clustering: SHB and SHE mice mainly employed antibiotic target alteration against glycopeptides, whereas SHA, SHD, and SHC-C57BL/6 primarily utilized antibiotic target protection against tetracyclines. This study presents a high-resolution comparison of gut microbiota and ARGs in SPF mice from multiple facilities, highlighting facility-dependent microbial and resistome variation and providing valuable references for preclinical microbiological standardization and risk assessment.},
}
@article {pmid41527291,
year = {2026},
author = {Chen, W and Guo, R and Zhang, W and Yan, Q and Wang, X and Chen, R and Hu, X and Liang, J and Xing, G and Xu, D and Ma, X and Chen, Q and Sha, S and Tao, E and Cheng, L and Fan, S and Liu, H and Lu, T and Yu, H and Su, J and Xu, J and Qin, Y and Liu, J and Zhong, X and Hu, X and Hu, X and Zheng, W and Hu, Z and Kang, J and Yang, J},
title = {Alterations of the gut virome in patients with Parkinson's disease.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {81},
number = {3},
pages = {},
doi = {10.1093/gerona/glag001},
pmid = {41527291},
issn = {1758-535X},
support = {82370563//National Natural Science Foundation of China/ ; 2024JJ7423//Natural Science Foundation of Hunan Province/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; },
mesh = {Humans ; *Parkinson Disease/virology/microbiology ; *Gastrointestinal Microbiome ; *Virome ; Male ; Female ; Aged ; Case-Control Studies ; Middle Aged ; Metagenomics ; },
abstract = {Gut microbiota plays a pivotal role in Parkinson's disease (PD) pathogenesis. However, the role of enteric viruses remains underexplored. Here, we reanalyzed publicly available metagenomic datasets from two independent cohorts, including 79 PD patients and 79 controls, to characterize gut virome profiles and explore the potential role of enteric viruses in PD pathogenesis and early diagnosis. Our findings indicate increased richness and diversity of the gut virome in PD, with 640 vOTUs differing in abundance between groups. Notably, Siphoviridae and Myoviridae were more abundant in PD patients. A variety of viruses enriched in PD or healthy subjects (HS) preferentially infect bacterial hosts that produce short-chain fatty acids. Furthermore, specific viral functional orthologs, such as thymidylate synthase (K00560) and integrases (K14059), displayed notable differences in prevalence between PD-enriched and HS-enriched vOTUs. Finally, we constructed a random forest model using the top 22 most significant vOTUs, which achieved an AUC of 0.822, demonstrating strong performance in distinguishing PD patients from healthy controls. This is the first study to characterize the gut virome profile in PD, laying a robust foundation for future investigations into the underlying mechanisms and early diagnosis strategies for PD as well as other neurodegenerative disorders.},
}
@article {pmid41468749,
year = {2026},
author = {Liu, X and Ma, T and Khan, I and Chen, L and Zhang, H},
title = {Age-dependent variations in aerosol-borne particulates and microbial communities in multi-tier broiler housing systems: A metagenomics environmental health risk assessment.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106308},
pmid = {41468749},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology/physiology ; *Particulate Matter/analysis ; *Housing, Animal ; Metagenomics ; *Microbiota ; Risk Assessment ; *Air Microbiology ; Aerosols/analysis ; *Air Pollutants/analysis ; Bacteria/isolation &amp; purification/classification ; Age Factors ; Animal Husbandry ; },
abstract = {By investigating the temporal dynamics of airborne microbial communities associated with particulate matter in multi‑tier broiler housing, this study offers a systematic reference for understanding how environmental microbiota shift with broiler age. Fine particulate matter (PM2.5) and total suspended particulate (TSP) were collected from the housing environment at three growth stages: D10 (10-day-old), D24 (24-day-old), and D38 (38-day-old). The concentration and LPS content of the collected TSP and PM2.5 samples from each stage were measured, followed by metagenomic sequencing. Results revealed that the concentrations of TSP and PM2.5 peaked at D24 (P < 0.05), showing a trend of first increasing and then decreasing, and the change trend of mortality in the early stage was similar. Metagenomic results identified that Faecalibacterium, Pseudomonas, and Acinetobacter were the dominant genera at D24, whereas Enterococcus and Macrococcus were the dominant genera at D10 and D38, respectively. Correlation analysis further indicated that TSP was positively associated with mortality and g_Pseudomonas, while PM2.5 was positively associated with g_Faecalibacterium. Significant enrichment was observed in metabolic pathways such as glycosyltransferase 35 and glycoside hydrolase 23, macB, LOS(CVF494), and other antibiotic resistance and virulence genes in TSP and PM2.5 (P < 0.05). Collectively, these findings elucidate the stage‑specific dynamics of environmental microbiota in broiler housing and underscore particulate matter as a potential driver of both microbial shifts and health outcomes, thereby providing evidence to inform interventions aimed at improving environmental and flock health.},
}
@article {pmid41413233,
year = {2026},
author = {Ikagawa, Y and Okamoto, S and Taniguchi, K and Mizoguchi, R and Hashimoto, A and Imamura, R and Arakawa, H and Ogura, K and Yanagihara, M and Tsujiguchi, H and Hara, A and Nakamura, H and Hosomichi, K and Karashima, S},
title = {Gut microbiota-derived polyamine pathways associated with mean blood pressure.},
journal = {Hypertension research : official journal of the Japanese Society of Hypertension},
volume = {49},
number = {3},
pages = {958-968},
pmid = {41413233},
issn = {1348-4214},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Male ; *Blood Pressure/physiology ; *Polyamines/metabolism ; Female ; *Hypertension/microbiology/metabolism/physiopathology ; Aged ; Adult ; Feces/microbiology ; },
abstract = {Hypertension is a common lifestyle-related disease and is influenced by various factors, including excessive salt intake. Recently, the gut microbiota (GM) has gained attention for its potential involvement in blood pressure regulation; however, polyamine metabolism involvement remains poorly understood. Sixty participants aged ≥40 years from Shika Town, Japan, were stratified into four groups (n = 15 each) based on mean blood pressure and urinary sodium chloride (u-NaCl) excretion. The clinical parameters were evaluated, and fecal samples were analyzed using shotgun metagenomic sequencing to assess the microbial composition and abundance of genes related to arginine-polyamine metabolism. Three major findings were observed: (1) Significant differences in the α-diversity of GM were observed between salt-sensitive and non-salt-sensitive hypertensive groups; (2) The abundance of spermidine synthase (EC 2.5.1.16), a key enzyme in polyamine metabolism with known antihypertensive effects, was significantly higher in normotensive individuals, independent of u-NaCl excretion; and (3) Bacterial species harboring polyamine metabolic enzyme genes, including EC 2.5.1.16, differed significantly between groups, suggesting group-specific microbial metabolic traits. These findings suggest that GM-mediated polyamine metabolism may contribute to the regulation of salt-sensitive blood pressure. While variations in spermidine-producing bacteria and the involvement of EC 2.5.1.16 were observed, these factors alone do not fully account for the intergroup differences related to salt intake. Thus, polyamine metabolism likely plays a part in salt sensitivity, but additional microbial and host factors are also involved. Further studies are needed to validate these findings and to explore microbiota-targeted strategies for the prevention and treatment of hypertension.},
}
@article {pmid41401693,
year = {2026},
author = {Chen, J and Li, J and Lin, Z and Zhang, Y and Lin, L and Guo, S and Huang, S and Li, X and Ma, J},
title = {Research note: Virome of Alectoris chukars by metagenomic analysis in Guangdong, southern China.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106246},
pmid = {41401693},
issn = {1525-3171},
mesh = {China/epidemiology ; Animals ; *Virome ; Metagenomics ; *Galliformes/virology ; *Metagenome ; },
abstract = {Alectoris Chukar (Chukar) has been introduced to numerous countries for stocking farms or release for hunting purposes. China imported commercial chuckars in the 1980s, and Guangdong Province was the first province in mainland China to feed on this species on stock farms; however, few reports have described the species and amount of virus circulating in it. In this study, meta-transcriptome analysis was conducted to reveal the virome in 34 unexplained dead chukars in Guangdong, southern China, which identified 2 novel viruses and 1 known virus, including the Alectoris chukar Avian leukosis-like virus (ACALLV) in the family Retroviridae, the GD-Alectoris chukar orthobunya virus (GD-ACOBV) in the family Peribunyaviridae, and an infectious bronchitis virus strain GD-Alectoris chukar strain (IBV-GDAC). These findings are the first to reveal the virome of chukars in Guangdong Province, providing more information to identify the virus circulating in chukars.},
}
@article {pmid41364878,
year = {2026},
author = {Yoon, SE and Kang, W and Cho, J and Cho, HJ and Chalita, M and Oh, HS and Hyun, DW and Han, S and Kim, H and Sung, H and Lee, JY and Park, B and Ryu, KJ and Kim, HY and Cho, D and Kim, WS and Kim, SJ},
title = {Microbiome and metabolite biomarkers of CAR T-cell therapy outcomes in relapsed/refractory diffuse large B-cell lymphoma.},
journal = {Blood advances},
volume = {10},
number = {5},
pages = {1634-1645},
pmid = {41364878},
issn = {2473-9537},
mesh = {Humans ; *Lymphoma, Large B-Cell, Diffuse/therapy/microbiology/metabolism/mortality ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Immunotherapy, Adoptive/adverse effects/methods ; Aged ; Biomarkers ; Treatment Outcome ; Adult ; Recurrence ; },
abstract = {CD19 chimeric antigen receptor (CAR) T-cell therapy has revolutionized treatment for relapsed/refractory diffuse large B-cell lymphoma (R/R-DLBCL), but challenges such as posttreatment failure and immune-related adverse events (AEs) persist. This study explores the gut microbiome as a predictive biomarker for CAR T-cell therapy outcomes and toxicity. Stool and serum samples from patients with R/R-DLBCL were analyzed at apheresis (47 samples) and 1 month after infusion (32 samples) using whole-genome sequencing metagenomics. When compared with healthy controls and newly-diagnosed DLBCL, R/R-DLBCL showed significant gut dysbiosis, characterized by increased Proteobacteria and Enterobacteriaceae. Responders had higher levels of Bacteroides fragilis, whereas nonresponders exhibited higher levels of Faecalibacterium prausnitzii. Functional metagenomic analysis suggested enrichment of inosine biosynthesis pathways in responders, and elevated serum inosine demonstrated an exploratory association with improved progression-free survival. Distinct microbial taxa and serum fatty acid profiles were also linked to CAR T-cell-related AEs, with higher acetate and butyrate levels in patients without AEs and increased isovalerate in those with AEs. These findings indicate that gut microbiome features-particularly Bacteroides fragilis and inosine metabolism-may serve as candidate biomarkers for CAR T-cell therapy outcomes and toxicity. However, given the exploratory nature of these analyses and the limited cohort size, results should be interpreted cautiously. Larger, prospective studies will be required to validate these observations and to assess the potential of microbiome-based strategies to optimize CAR T-cell therapy in R/R-DLBCL.},
}
@article {pmid41093027,
year = {2026},
author = {Li, KY and Zhou, JL and Tian, ZH and Gao, F},
title = {N-acyl-homoserine lactone regulation of nutrient removal, microbial community assembly, and process efficacy in dialysis membrane-algal-bacterial photobioreactors.},
journal = {Bioresource technology},
volume = {440},
number = {},
pages = {133502},
doi = {10.1016/j.biortech.2025.133502},
pmid = {41093027},
issn = {1873-2976},
mesh = {Serine/analogs &amp; derivatives/analogs &amp; derivatives ; Quorum Sensing ; Microbial Consortia ; Microbiota ; *Photobioreactors/microbiology ; Microalgae/physiology ; Nitrogen/analysis/metabolism ; Phosphorus/analysis/metabolism ; Biomass ; Membranes, Artificial ; 4-Butyrolactone/analogs &amp; derivatives/metabolism ; Bacteria/metabolism ; Metagenomics ; Chlorella/physiology ; Water Purification/methods ; },
abstract = {Quorum sensing is a central mechanism by which signal bacteria sense and integrate signaling molecules to coordinate gene expression and physiological activities at the community level. To investigate how exogenous signal molecules regulate the maintenance of algal-bacterial symbiosis, this study constructed a dialysis membrane-coupled algal-bacterial photobioreactor and separately amended it with N-butyryl-l-homoserine lactone (C4-HSL), N-hexanoyl-l-homoserine lactone (C6-HSL), and N-(3-oxodecanoyl)-l-homoserine lactone (3-oxo-C10-HSL), systematically investigated their effects on nutrient removal, microbial community composition, and functional characteristics within the system. Compared with the control, all three N-acyl-homoserine lactones (AHLs) enhanced total nitrogen and total phosphorus removal and stimulated biomass (sludge) growth, while redirecting microalgal carbon allocation toward lipid accumulation; notably, the C6-HSL treatment achieved the highest nitrogen (80.39 %) and phosphorus (53.01 %) removal efficiencies. Metagenomic analyses revealed that exogenous AHLs exerted selective effects on the microbial assemblage, enriching dominant signal-responsive bacteria whose relative abundance was positively correlated with nitrogen and phosphorus removal performance. Furthermore, genes associated with nitrogen metabolism, the tricarboxylic acid cycle, and glycolysis were more abundant in the 3-oxo-C10-HSL and C6-HSL groups, indicating that strengthened metabolic coupling likely underpins the observed biomass increase and enhanced nutrient removal. Collectively, these findings demonstrate that AHL-mediated signaling is a key driver shaping algal-bacterial interactions, community assembly, and functional expression.},
}
@article {pmid40814761,
year = {2026},
author = {Qin, P and Kragsnaes, MS and Holm, DK and Horn, HC and Nilsson, AC and Kjeldsen, J and Kristiansen, K and Ellingsen, T},
title = {Clinical Significance of Gut Microbiota Community Types for Long-Term Response to Fecal Microbiota Transplantation in Patients With Psoriatic Arthritis.},
journal = {Arthritis &amp; rheumatology (Hoboken, N.J.)},
volume = {78},
number = {2},
pages = {320-331},
pmid = {40814761},
issn = {2326-5205},
support = {Sundhedsdonationer 2022-0026//Sygeforsikringen "danmark"/ ; //Fabrikant Vilhelm Pedersen's Mindelegat (on recommendation by the Novo Nordisk Foundation)/ ; //Medicine Fund of the Danish Regions (Regionernes Medicin- og behandlingspulje)/ ; //University of Southern Denmark Research Fund/ ; //the Danish Rheumatism Association/ ; //the Danish Psoriasis Research Foundation/ ; //Research Fund of Odense University Hospital/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Male ; Female ; Middle Aged ; *Arthritis, Psoriatic/therapy/microbiology ; Bacteroides ; Adult ; Prevotella ; Treatment Outcome ; Feces/microbiology ; Clinical Relevance ; },
abstract = {OBJECTIVE: Fecal microbiota transplantation (FMT) holds promises as a beneficial supplement to methotrexate in patients with psoriatic arthritis (PsA). We therefore investigated how gut bacterial signatures in patients and donor strain engraftment were associated with long-term response to FMT.<br><br>METHODS: This exploratory study is based on the FLORA trial cohort, encompassing 31 patients with moderate-to-high PsA disease activity and four FMT donors. Of the 15 patients receiving one single-donor FMT, 13 were included in the per-protocol (PP) population. Stool samples were collected before and after FMT (week 4, 12, and 26). We performed shotgun metagenomics to characterize gut microbiota features.<br><br>RESULTS: At baseline, 17 patients (55%) had a gut microbiota community type dominated by the Bacteroides genus (B-type), whereas 14 (45%) had a Prevotella-driven community type (P-type). The B- and P-type patients did not differ in disease activity or demographics, but the B-type had a significantly higher species diversity compared to the P-type (P = 0.005). In the PP population, five of seven B-type patients versus none of six P-type patients (P = 0.021) achieved a long-term clinical beneficial response at week 26. Bacterial strain richness increased significantly from baseline to week 4 and week 26 in B-type (P = 0.016), but not in P-type, patients. Eighteen engrafted strains persisted only in B-type recipients by week 26, including a Bacteroides clarus strain, which demonstrated a negative effect size regarding arthritis pain and the patients' global assessment of disease.<br><br>CONCLUSION: Recipients with a Bacteroides-dominated community structure were more likely to achieve long-term beneficial response following one FMT.},
}
@article {pmid40554061,
year = {2026},
author = {Yang, W and Zou, P and He, S and Cui, H and Yang, Z and An, H and Chen, Q and Huang, W and Guo, H and Liu, J and Ling, X and Cao, J and Ao, L},
title = {Perfluorooctane sulfonic acid impairs spermatogenesis via the liver-gut microbiota-testis axis: a central role of chenodeoxycholic acid metabolism.},
journal = {Journal of advanced research},
volume = {81},
number = {},
pages = {897-914},
pmid = {40554061},
issn = {2090-1224},
mesh = {Male ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Testis/drug effects/metabolism ; Mice ; *Chenodeoxycholic Acid/metabolism ; *Alkanesulfonic Acids/toxicity ; *Spermatogenesis/drug effects ; *Fluorocarbons/toxicity ; *Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Fecal Microbiota Transplantation ; Metabolome/drug effects ; },
abstract = {INTRODUCTION: Perfluorooctane sulfonic acid (PFOS) as a global contaminant is ubiquitously presented in the environmental media and human body. The association between PFOS exposure and reduced male fertility has been recently discovered. However, the relevant mechanism remains unexplored.<br><br>OBJECTIVES: Our study aimed to investigate the effect and mechanism of PFOS exposure on male reproductive function.<br><br>METHODS: In a murine PFOS exposure model, single-nucleus transcriptome sequencing was performed to delineate the transcriptomic landscape of mouse testes at the single-cell resolution. We examined the serum metabolomic profile and conducted in-depth analysis of hepatic transcriptome datasets to explore the metabolic connections between liver and testis under PFOS exposure. Through integrating chenodeoxycholic acid intervention, fecal microbiota transplantation (FMT), metagenomic sequencing, testicular metabolome, Ligilactobacillus murinus (L. murinus) metabolome, and administration of L. murinus, we confirmed the role of the liver-gut microbiota-testis axis and screened the critical gut microbiota involved in PFOS-mediated spermatogenic disorders.<br><br>RESULTS: The results showed that PFOS exposure led to spermatogenic arrest and abnormal spermatogenic microenvironment in the mouse testis. The PFOS-repressed hepatic chenodeoxycholic acid (CDCA) synthesis contributed to the reduced serum/testicular levels of essential fatty acid (linoleic acid) and lipid-soluble vitamins (retinol, vitamin D3), which was responsible for the spermatogenic arrest. Beyond this, PFOS-mediated impaired CDCA production decreased the abundance of gut L. murinus, which affected spermatogenesis through the potential involvement of aspartic acid metabolism. For the first time to our knowledge, we comprehensively assessed the effects of PFOS exposure on the spermatogenic process and elucidated the unrecognized role of liver-gut microbiota-testis axis in PFOS-induced abnormal spermatogenesis.<br><br>CONCLUSIONS: The unveiled organ crosstalks provide new insights into the metabolism-disrupting properties, hepatotoxicity, and reproductive toxicity of PFOS, which may facilitate the development of molecule-, metabolite-, and microbe-based strategies for PFOS-induced metabolic diseases and reproductive disorders.},
}
@article {pmid41783570,
year = {2026},
author = {Lin, H and Zhu, XY and Xue, CX and Yao, P and Fu, L and Yang, Z and Zhang, XH and Moreau, JW},
title = {Metagenomics reveals diverse community of putative mercury methylators across different biogeochemical niches in Sansha Yongle blue hole.},
journal = {Marine life science &amp; technology},
volume = {8},
number = {1},
pages = {206-220},
doi = {10.1007/s42995-025-00332-7},
pmid = {41783570},
issn = {2662-1746},
abstract = {UNLABELLED: Methylmercury (MeHg) is a potent neurotoxin and bioaccumulates in food webs. Microbial transformation of inorganic mercury (Hg) produces most of the MeHg in the marine environment. The gene pair hgcAB encodes for Hg methylation, a process predominantly attributed to anaerobic bacteria. However, recent studies indicate the formation of methylmercury in low-oxygen zones within marine water columns, although the mechanisms remain poorly understood. "Blue holes" are marine sinkholes containing redox gradients stratified with depth and high microbial diversity across a range of biogeochemical cycles. Here, we present the first metagenomic analysis focused on the potential for Hg methylation in a blue hole ecosystem. Yongle Blue Hole (YBH), currently the world's deepest known blue hole, was selected as a representative site to investigate the genetic potential for Hg methylation and to explore the functional capabilities of putative Hg-methylators within this unique environment. Metagenomic analysis showed that the anoxic sulfidic deep water was likely to be a hotspot for Hg methylation, driven by abundant and diverse Deltaproteobacteria. In the suboxic intermediate layer, Nitrospina and Myxococcota dominated the Hg-methylating community. Furthermore, Hg methylators were found to have different lifestyles (free-living or particle-associated) and to occupy distinct ecological niches within the YBH. In addition, the contribution of sinking particles to Hg methylation, especially in the deep anoxic water column, was highlighted. Our study unveils the biodiversity and survival strategies of Hg methylators across distinct environments. The findings suggest that blue holes could serve as model stratified ecosystems for studying Hg methylation processes across different habitats.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00332-7.},
}
@article {pmid41115830,
year = {2025},
author = {Yang, F and Xu, W and Zhu, L and Tian, X and Duan, Y and Xu, Y and Huang, Q and Zhao, F},
title = {Multiple Roles of Extracellular Vesicles in Promoting Microbial-Driven Manganese Reduction.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {43},
pages = {23275-23288},
doi = {10.1021/acs.est.5c05310},
pmid = {41115830},
issn = {1520-5851},
mesh = {*Extracellular Vesicles/metabolism ; *Manganese/metabolism ; Electron Transport ; Soil Microbiology ; Metagenomics ; *Shewanella/metabolism ; Biofilms ; Microbiota ; },
abstract = {Microbial-driven manganese (Mn) reduction influences the geochemical cycling of Mn and the environmental fate of various organic and inorganic substances. Extracellular vesicles (EVs) are known to impact microbial metabolic activities, but their specific role in Mn reduction remains arcane. Here, we explored the potential involvement of environmental EVs in this process through metagenomic analysis and validated their function using representative functional strains. There are 8.05 and 12.89% of EVs originating from electroactive microorganisms in soil and wastewater, respectively. The addition of EVs increases the birnessite reduction rate of Shewanella oneidensis MR-1 from 2.31 μmol/(L·h) to 20.86 μmol/(L·h). Microbial physiological assays and in situ electrochemical analyses revealed that EVs enhanced cellular metabolism, promoted biofilm formation, and facilitated extracellular electron transfer (EET). The presence of diverse redox enzymes and metabolites in EVs contributed to more efficient substrate utilization and energy conservation, which promoted biomass accumulation and increased substrate consumption by 45.33%. The inner and outer membrane c-type cytochromes, along with flavins contained in the EVs, are essential for promoting microbial EET. These findings highlight the multifaceted role of EVs in microbial-driven Mn reduction, which might also participate in other element cycles in the same way.},
}
@article {pmid41775849,
year = {2026},
author = {Plewnia, A and Hildwein, T and Quezada Riera, AB and Terán-Valdez, A and Crawford, AJ and Heine, C and Franco-Mena, D and Székely, D and Armijos-Ojeda, D and Siavichay, FR and Arpi, JD and Salazar, J and Erens, J and Páez-Vacas, MI and Székely, P and Böning, P and Stassen, R and Carvajal-Endara, S and Lötters, S and Guayasamin, JM},
title = {Environmental DNA metabarcoding facilitates integrative conservation assessments and species rediscoveries in tropical biodiversity hotspots.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41937-x},
pmid = {41775849},
issn = {2045-2322},
}
@article {pmid41774204,
year = {2026},
author = {Gulumbe, BH and Alum, EU and Abdulrahim, A and Abubakar, TM and Bagwai, MA and Ali, M},
title = {The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41774204},
issn = {1432-0991},
abstract = {Antimicrobial resistance (AMR) poses an escalating global health challenge with important environmental dimensions. While the environment is well known as a reservoir and conduit for antibiotic resistance genes (ARGs), the regulatory role of environmental microbiomes in modulating ARG dissemination remains inadequately studied. This review synthesizes current knowledge on how environmental microbiomes influence the spread of AMR by acting as buffers, amplifiers, or gatekeepers of ARG flow in natural and human-impacted ecosystems. We synthesize findings from metagenomic analyses, ecological experiments, and theoretical frameworks to evaluate how microbial diversity, community composition, and ecological interactions shape the persistence and horizontal transfer of ARGs in the environment. Evidence suggests that diverse and resilient microbial communities can inhibit ARG persistence and limit gene transfer, whereas environmental disturbances and biodiversity loss may facilitate ARG propagation. These dynamics highlight the importance of microbial ecosystem structure in shaping AMR trajectories. Understanding the ecological role of environmental microbiomes in AMR dissemination offers new perspectives for antimicrobial stewardship within the One Health framework. Integrating this knowledge into practical interventions, such as engineered microbial consortia and bioremediation can help manage environmental sources of resistance and strengthen global efforts against AMR.},
}
@article {pmid41766731,
year = {2026},
author = {Peddle, SD and Cando-Dumancela, C and Costin, S and Davies, T and Doane, MP and Edwards, RA and Hodgson, RJ and Krauss, SL and Liddicoat, C and Breed, MF},
title = {Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73172},
pmid = {41766731},
issn = {2045-7758},
abstract = {Soil microbiomes are fundamental ecosystem components that are increasingly used to monitor the efficacy of restoration efforts. However, given high levels of functional redundancy among soil microbial taxa and the subsequent lack of definitive taxa-function links, taxonomic assessments (e.g., via metabarcoding) alone are limited for inferring ecological recovery. Here, we used shotgun metagenomics on soils from six post-agricultural restoration sites in southwest Western Australia to test whether soil microbial functional potential recovers following restoration plantings. We compared taxonomic and functional gene diversity and composition across degraded, passively regenerated, revegetated, and remnant land conditions. Effective number of functions (alpha diversity) did not differ across land conditions. However, functional composition (beta diversity) differed between remnant and revegetated conditions and associated with altered soil abiotic properties, especially elevated phosphorus. Remnant soils supported a greater diversity of phosphorus metabolism functions despite lower available phosphorus, indicating a microbial adaptation to nutrient limitation in phosphorus deficient soils. Rather than indicating a lack of functional recovery, these results suggest a functional response to persistent agricultural legacies that may reflect a shift toward an alternative state. Restoration interventions that aim to target the soil microbiome (e.g., soil inoculations) or directly address abiotic legacies (e.g., phosphorus mining plants) may therefore be required to facilitate recovery of the soil microbial functions and the wider ecosystem.},
}
@article {pmid41747902,
year = {2026},
author = {Corso, D and Melita, M and Massaccesi, N and Quero, GM and Basili, M and Di Cesare, A and Sabatino, R and Sbaffi, T and Fazi, S and Rakaj, A and Luna, GM and Amalfitano, S},
title = {Constructed wetlands for aquaculture wastewater treatment: Insights on the structural and functional shifts of the aquatic microbial community.},
journal = {Bioresource technology},
volume = {448},
number = {},
pages = {134278},
doi = {10.1016/j.biortech.2026.134278},
pmid = {41747902},
issn = {1873-2976},
abstract = {Aquaculture practices generate nutrient-rich effluents with associated microbiological hazards, such as pathogens and antimicrobial resistance genes (ARGs). Despite their growing popularity as nature-based solutions, little is known about how constructed wetlands (CWs) affect the dynamics of microbial communities at the field scale. By combining flow cytometry, 16S rRNA gene sequencing, shotgun metagenomics, and metabolic potential assays, we investigated the structural and functional responses of the aquatic microbial community following the recurrent exposure to CW-treated effluents from an intensive marine fish farm (Orbetello lagoon, Italy). While the CW promoted abundant, metabolically active, and functionally redundant microbial communities, the phylogenetic composition diverged primarily between water and sediments. Microbial profiles in CW outlet waters converged towards those of the lagoon baselines, suggesting gradual ecological recovery. The CW attenuated the occurrence of potential pathogens, such as members of the genera Francisella and Campylobacter, and acted as a buffer system in ARG dissemination, with sediments serving as reservoirs of microbial and genetic signatures. Functional profiles, dominated by chemoheterotrophy, denitrification, and sulfur respiration, remained stable across environments, reflecting microbial resilience. Our results highlight CWs as effective, field-proven solutions to mitigate aquaculture wastewater impacts while preserving core ecosystem services.},
}
@article {pmid41736978,
year = {2026},
author = {Ling, Y and Yang, DX and Xia, YN and Bao, CP and Zhang, F and Xu, XJ and Sun, BH},
title = {Effects of Age, Sex, and Social Network on Antibiotic Resistance Genes in the Gut Microbiome of Tibetan Macaques (Macaca thibetana).},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e73137},
pmid = {41736978},
issn = {2045-7758},
abstract = {The transmission and dissemination of antibiotic resistance genes (ARGs) have increasingly drawn global attention. However, our knowledge of the antibiotic resistance gene pool in wild primates' gut microbiomes and its influencing factors remains limited. In this study, we focus on a social group of Tibetan macaques (Macaca thibetana) in Huangshan, utilizing behavioral and metagenomic data to investigate the effects of host sex, age, and social network on the ARG profiles of the gut microbiome. Our results demonstrate a high diversity of ARGs in the gut microbiota of Tibetan macaques, with multidrug, glycopeptide, and peptide resistance genes being the most prevalent. Although host age, sex, and social networks did not significantly affect the overall diversity of ARGs, these factors were significantly correlated with the relative abundance of several highly abundant ARG types, including gryB, rpoB, macB, novA, efrA, patB, Staphylococcus aureus mupA conferring mupirocin resistance, RanA, and cdeA. Further analysis revealed extensive interactions between gut bacteria and ARGs, with age emerging as a potentially key factor in this covariation process. These findings provide new insights into the formation and transmission mechanisms of antibiotic resistance in the gut microbiome of wildlife, particularly in social primates.},
}
@article {pmid41736795,
year = {2026},
author = {Pan, H and Wu, L and Sheng, S},
title = {Metagenomic profiling of the gut microbiome to predict orthopedic healing responses in postmenopausal women.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1771312},
pmid = {41736795},
issn = {2235-2988},
mesh = {Humans ; Female ; *Postmenopause ; *Gastrointestinal Microbiome/genetics ; Aged ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Metagenomics/methods ; Bacteria/classification/genetics/isolation &amp; purification ; *Wound Healing ; },
abstract = {INTRODUCTION: Recovery following orthopedic procedures in postmenopausal women is often prolonged and more complex due to age-related physiological changes, including reduced bone mineral density, altered hormonal profiles, impaired immune regulation, and delayed tissue regeneration. Conventional recovery assessment methods such as radiographic imaging, range-of-motion evaluation, and functional mobility tests provide valuable clinical information but offer limited insight into the underlying biological processes that influence healing. Emerging evidence indicates that the gut microbiome plays a critical role in regulating inflammation, immune homeostasis, and tissue repair, highlighting its potential as a predictive biomarker for post-surgical recovery outcomes. This study investigated the association between gut microbiome dynamics and recovery following orthopedic surgery in postmenopausal women.<br><br>METHODS: Stool samples were collected from preoperative (baseline) and 6 weeks postoperative time points. Microbial profiling was performed using 16S rRNA gene sequencing on the Illumina MiSeq platform, and data processing and taxonomic analysis were conducted using QIIME2. Microbial diversity was evaluated through alpha diversity metrics to assess community richness and beta diversity to characterize compositional differences over time. Clinical recovery was assessed using radiographic imaging, the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), and the Timed Up and Go (TUG) functional mobility test. To evaluate the predictive potential of the gut microbiome, a random forest machine learning model was trained using microbial abundance data and correlated with clinical recovery outcomes.<br><br>RESULTS: The results revealed significant temporal shifts in gut microbial composition during the recovery period. Bacterial diversity varied across time points, with Firmicutes and Bacteroidetes identified as the dominant phyla. Increased abundance of these taxa was strongly associated with improved functional outcomes and faster recovery. In contrast, elevated levels of Proteobacteria and Escherichia were linked to delayed healing and poorer clinical performance. The predictive model achieved an accuracy of 85%, demonstrating the robustness of gut microbiome signatures as indicators of postoperative recovery.<br><br>DISCUSSION: Overall, this study highlights the significant influence of gut microbiome composition on orthopedic recovery in postmenopausal women. Identification of microbial biomarkers associated with favorable healing outcomes provides a foundation for developing microbiome-guided, personalized therapeutic strategies to enhance postoperative recovery and improve long-term musculoskeletal health.},
}
@article {pmid41736790,
year = {2026},
author = {Yu, S and Niu, H and Zhang, Y and Yu, L and Zhang, Q and Liu, X and Sang, Y and Wang, R and Zhang, M},
title = {Characterization of gut microbiota in patients with diabetic kidney disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1713005},
pmid = {41736790},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Diabetic Nephropathies/microbiology ; Feces/microbiology ; Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: Diabetic kidney disease (DKD) is a major complication of diabetes mellitus (DM). Although dysbiosis of the gut microbiota in DKD has been reported, the specific microbial species associated with disease progression from DM to DKD remain insufficiently defined.<br><br>METHODS: We conducted shotgun metagenomic sequencing on fecal samples from 55 healthy participants, 47 patients with DM, and 38 patients with DKD. Gut microbiota diversity, composition, and functional pathways were compared across groups; correlations with glycemic and renal indices were evaluated.<br><br>RESULTS: Overall alpha-diversity showed no significantly difference between DKD and healthy controls; however, the simpson's index was higher in DKD than in DM (p < 0.05). There was a difference in beta-diversity between DKD and the healthy control (p = 0.002), but no significant difference was observed between the DKD and DM group. Bacteria significantly enriched in DM/DKD include Mediterraneibacter, Enterocloster, Shigella, Limosilactobacillus, and Thomasclavelia, which showed positive correlations with glycemic indicators (HbA1c, fasting blood glucose) and renal indicators (BUN, UACR). In contrast, health-enriched bacteria, Phocaeicola, Faecalibacterium, Lachnospira, Agathobacter, Odoribacter, and Paraprevotella were negatively correlated with these parameters. Functional analysis revealed that compared to the DM group, the DKD group enriched pathways related to aromatic amino acid biosynthesis (phenylalanine, tyrosine, tryptophan), biofilm formation, and lipopolysaccharide biosynthesis. Gut microbial shifts along the DM-DKD correlates with adverse glycemic and renal phenotypes, as well as functional characteristics associated with inflammation and barrier injury. These findings suggest that microbially driven metabolic and structural pathways represent potential targets for mitigating the progression of DKD.<br><br>CONCLUSION: This study elucidates the distinct characteristics of the gut microbiota in DKD patients and highlights potential microbial markers involved in the progression from DM to DKD.},
}
@article {pmid41736479,
year = {2026},
author = {Kong, S and Ning, Z and Chen, Z and Zhang, M},
title = {Broad-Spectrum Co-Metabolic Substrates Enhance the Bioremediation of 1,2,3-Trichloropropane in Groundwater by a Non-Dehalogenimonas Consortium.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {3},
pages = {e70318},
doi = {10.1002/wer.70318},
pmid = {41736479},
issn = {1554-7531},
support = {252S7601D//Hebei Province Science and Technology Support Program/ ; 242S4201Z//Hebei Province Science and Technology Support Program/ ; },
mesh = {*Groundwater/chemistry/microbiology ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Propane/analogs &amp; derivatives/metabolism ; *Microbial Consortia ; },
abstract = {1,2,3-Trichloropropane (TCP), a highly mobile chemical byproduct, has severely exacerbated groundwater environment deterioration. Due to the lack of effective natural attenuation pathways, TCP typically exhibits a fate of persistent retention within aquifers. To address this challenge, instead of relying on limited specific strains, this study focused on exploring broad-spectrum co-metabolic substrates to enhance the degradation efficiency of a non-Dehalogenimonas synergistic consortium optimized through long-term directed domestication. Results indicated that the average degradation rate of the domesticated consortium increased to 19.06 μmol L[-1] d[-1], achieving complete removal within 3.5 days, thereby effectively altering the environmental persistence of TCP. Microbial community and metagenomic analyses revealed that this transformation process was driven by a synergistic alliance comprising Fusibacter, Desulfovibrio, Nitratidesulfovibrio, and Parabacteroides, realized through a coupled metabolic module of "hydrogen production, cofactor synthesis, and reductive dechlorination". Crucially, the consortium demonstrated exceptional broad-spectrum adaptability to various co-metabolic substrates, where sodium acetate and lactate significantly enhanced the degradation efficiency. This study confirms that utilizing suitable co-metabolic substrates can effectively activate the non-Dehalogenimonas consortium to regulate the migration and fate of pollutants in complex groundwater environments, offering an efficient bioremediation strategy to arrest groundwater contamination.},
}
@article {pmid41736423,
year = {2026},
author = {Dongqi, LI and Tongxing, W and Zixuan, W and Yihui, Y and Jie, LI and Jiaojiao, GU and Cuiru, LI and Aili, W and Lingling, S and Yongjie, M and Zeyu, Z and Yunlong, H and Huailin, G},
title = {Improving glucose tolerance in obese rats: the role of Jinlida granules () in gut microbiota modulation.},
journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan},
volume = {46},
number = {1},
pages = {62-72},
pmid = {41736423},
issn = {2589-451X},
support = {2017YFC700500//National Key Research and Development Program 'Modernization Research of Traditional Chinese Medicine': Cardiovascular Event Chain (Metabolic Syndrome, Atherosclerosis, Myocardial Infarction, Arrhythmia, Heart Failure)/ ; 223777155D//Key R&amp;D Program of Hebei: Traditional Chinese Medicine Innovation Project: Clinical Research on the Treatment of Diabetes Foot with Collateral Drugs and the Mechanism of Its Influence on Collateral Vessel Reconstruction/ ; 2023179//Scientific Research Project of Hebei Provincial Administration of Traditional Chinese Medicine: Clinical Study on Jinlida Granules in Treating Intestinal Dysfunction of diabetes and Its Effect on Short Chain Fatty Acids/ ; 2018200//Scientific Research Project of Hebei Provincial Administration of Traditional Chinese Medicine: Clinical Study on Tongluo Therapy for Diabetes Foot and Its Influence on Microcirculation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; Rats ; *Obesity/drug therapy/microbiology/metabolism/genetics ; Male ; *Drugs, Chinese Herbal/administration &amp; dosage ; Humans ; Glucose Tolerance Test ; Diet, High-Fat/adverse effects ; Zonula Occludens-1 Protein/metabolism/genetics ; Claudin-1/metabolism/genetics ; Blood Glucose/metabolism ; },
abstract = {OBJECTIVE: To investigate the effects of Jinlida granules (, JLD) on body weight, glucose tolerance, intestinal inflammation and barrier function in high-fat diet (HFD)-induced obese rats and explore the regulation of the gut microbiota as a potential treatment mechanism.<br><br>METHODS: Sprague-Dawley rats were divided into control, HFD, low-dose JLD (L-JLD), high-dose JLD (H-JLD), and sitagliptin groups. The rats, with the exception of those in the control group, were fed a HFD to establish an obesity model while simultaneously receiving 0.5% carboxymethyl cellulose, L-JLD, H-JLD or sitagliptin for 25 weeks. We assessed body weight, conducted oral glucose tolerance tests, and analysed faecal samples using metagenomic sequencing. Haematoxylin-eosin (HE), Masson and immunohistochemical (IHC) staining were employed to evaluate histological changes in the colon tissue. Immunofluorescence (IF) staining was used to measure the expression levels of Zonula occludens-1 (ZO-1) and Claudin-1 in colon tissue. The colon tissue was also subjected to transcriptomic evaluation.<br><br>RESULTS: JLD treatment significantly reduced body weight and enhanced glucose tolerance in obese rats. It alleviated colonic tissue damage, decreased collagen deposition, inhibited macrophage infiltration, and increased the expression of the tight junction proteins ZO-1 and Claudin-1. Metagenomic analysis revealed JLD-induced shifts in the gut microbiota composition (increasing the abundance of Turicibacter, Faecalibaculum, Coriobacteriaceae and Lactobacillus reuteri), enriching beneficial bacteria and metabolic pathways (increasing the biosynthesis of various secondary metabolites, ascorbate and aldarate metabolism, oxidative phosphorylation, C5-branched dibasic acid metabolism and beta-alanine metabolism). Transcriptomic analysis revealed downregulation of inflammatory and immune pathways (inhibition of the tumour necrosis factor signalling pathway, advanced glycation end products-receptor for advanced glycation end products signalling pathway, toll-like receptor signalling pathway, and interleukin-17 signalling pathway), suggesting a comprehensive modulatory effect of JLD on intestinal health and metabolic function.<br><br>CONCLUSIONS: JLD granules effectively improve glucose tolerance and ameliorate obesity-related intestinal dysfunctions in HFD-induced obese rats. These benefits are likely mediated through the modulation of the gut microbiota, the suppression of intestinal inflammation, the enhancement of barrier function, and the attenuation of proinflammatory pathways. Our findings offer novel insights into the therapeutic potential of JLD, emphasizing its role in integrating gut microbiota management into the treatment of metabolic disorders.},
}
@article {pmid41734489,
year = {2026},
author = {Sabatino, R and Gini, C and Borgomaneiro, G and Sbaffi, T and Corno, G and Sun, K and Zhang, XH and Di Cesare, A},
title = {Sinking particles as repository of antimicrobial resistome diversity in the Sansha Yongle Blue Hole.},
journal = {The Science of the total environment},
volume = {1021},
number = {},
pages = {181585},
doi = {10.1016/j.scitotenv.2026.181585},
pmid = {41734489},
issn = {1879-1026},
abstract = {The aquatic environment plays a central role in the selection and spread of antimicrobial resistance genes (ARGs). Using metagenomic approaches, several studies have provided a comprehensive view of the antimicrobial resistome across different aquatic ecosystems. However, unique aquatic systems, such as oceanic blue holes, remain largely unexplored. Free-living and particle-associated samples from the Sansha Yongle Blue Hole (South China Sea) were analyzed by shotgun metagenomics to characterize the antimicrobial resistome and the potential mobility of detected ARGs. The diversity of the antimicrobial resistome significantly decreased with increasing water depth. This trend was driven by the free-living bacterial community, whereas it remained stable in particle-associated communities. Additionally, the latter showed a higher frequency of co-occurring ARGs and mobile genetic elements on the same contigs, with a frequent plasmid localization of these genes. Overall, particle-associated bacteria proved essential for sustaining antimicrobial resistome diversity. Furthermore, these findings suggest that horizontal transfer of ARG may be more frequent within particle-associated communities along the water column of the blue holes, potentially contributing to the persistence of resistances in deep marine waters.},
}
@article {pmid41731616,
year = {2026},
author = {Fan, S and Lu, J and Cui, H and Ding, W and Li, S and Sun, J and Li, YX and Zhang, W},
title = {Unlocking the unexplored AMPSphere in marine rare species.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02326-0},
pmid = {41731616},
issn = {2049-2618},
abstract = {BACKGROUND: Antimicrobial peptides (AMPs) have advantages over traditional antibiotics in fighting against drug-resistant bacterial infections. Natural microbial communities are considered as the priority targets for next-generation AMP bioprospecting initiatives. While progress has been made in characterizing AMPs from the dominant microbial taxa in natural ecosystems, current research largely overlooks the biosynthetic potential of rare species. Given their distinct evolutionary pressures, rare species likely produce AMPs with novel structures and unconventional mechanisms of action.<br><br>RESULTS: In this study, enrichment cultivation of a marine biofilm was conducted in 138 carbon source- and oxygen level-based conditions, followed by metagenomic sequencing using both Illumina and Nanopore platforms. Analysis of 435 high-quality genomes derived from the metagenomes suggests that these bacterial strains are significantly underrepresented (<&#x2009;0.01%) in global marine biofilm communities. Through multi-model prediction, we identified 3,054,472 candidate AMPs from the genomes, including 1048 high-confidence ones, thereby significantly expanding the previously known AMPSphere. Furthermore, AMPs derived from the rare bacterial species exhibit unique sequence characteristics, structural diversity, remarkable stability under diverse pH conditions and pepsin exposure, and strong therapeutic potential in animal models, reflecting their specialized adaptive and defensive strategies developed within ecological systems.<br><br>CONCLUSIONS: The features of the underexplored AMPs from low-abundance bacteria in marine biofilms provide valuable resources and theoretical foundations for the development of highly effective antimicrobial agents. Video Abstract.},
}
@article {pmid41729207,
year = {2026},
author = {Gouda, MNR and Subramanian, S},
title = {Functional Genomics and Enzymatic Diversity of Gut Bacteria in Apis mellifera: A Multi-Approach Study from India.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41729207},
issn = {1432-0991},
mesh = {Bees/microbiology ; Animals ; India ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/enzymology/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Phylogeny ; Genomics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {The gut microbiota of the western honey bee Apis mellifera plays a vital role in host nutrition, digestion, immunity, and overall colony health. Although the functional and enzymatic capabilities of bee-associated microbes are increasingly recognized, studies integrating culture-dependent screening with metagenomic functional profiling remain scarce. This study characterizes the gut bacterial communities of forager and hive bees from the Indian subcontinent using cultivation, 16S rRNA gene sequencing, enzyme assays, and metagenomic analysis. A total of 165 isolates were obtained, yielding 85 unique strains deposited in GenBank. Metagenomic assembly generated 7.78 million non-redundant genes, including 11,050 KEGG-annotated and 2.43 million CAZy-annotated genes. Forager bees showed pronounced enrichment of carbohydrate-processing pathways such as glycolysis/gluconeogenesis (22.9%), galactose metabolism (4.42%), starch and sucrose metabolism, and ABC transporters (9.80%), consistent with their nectar- and pollen-rich diet. Culture-based biochemical assays revealed substantial enzymatic diversity among isolates belonging to Bacillus, Enterobacter, Serratia, Cedecea, Clostridium, Lysinibacillus, and Aneurinibacillus. High invertase activities were recorded in Xanthomonas sp. HAmf44 (2.509 U/mg), Clostridium argentinense HAmf20 (2.470 U/mg), Lysinibacillus fusiformis HAmh15 (2.509 U/mg), and Bacillus paralicheniformis HAmh05 (2.333 U/mg). Strong lipolytic activities were observed in Cedecea davisae HAmf19 (6.062 U/mg), Pseudomonas aeruginosa HAmh21 (5.927 U/mg), and Enterobacter cloacae HAmf26 (3.349 U/mg). Significant variation among isolates (p = 0.001) underscored the functional diversity of the gut microbiota. Integrating KEGG orthologs with species abundance revealed that dominant taxa-including Gilliamella, Snodgrassella, Lactobacillus, and Bifidobacterium-drive key metabolic pathways. Overall, this study provides the first combined enzymatic and metagenomic assessment of A. mellifera gut microbiota from India and identifies high-performing strains with probiotic potential to enhance honey bee nutrition and colony productivity.},
}
@article {pmid41724868,
year = {2026},
author = {Aciole Barbosa, D and de Maria, YNLF and Menegidio, FB and de Oliveira, RC and Jabes, DL and Nunes, LR},
title = {Dysbiosis of the enteric DNA virome correlates with the development of cachexia in a murine Lewis lung carcinoma (LLC) model.},
journal = {Archives of virology},
volume = {171},
number = {3},
pages = {},
pmid = {41724868},
issn = {1432-8798},
mesh = {Animals ; *Cachexia/virology/etiology/microbiology ; *Dysbiosis/virology ; *Virome ; Mice ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Disease Models, Animal ; *Carcinoma, Lewis Lung/complications/virology ; *DNA Viruses/genetics/classification/isolation &amp; purification ; Male ; },
abstract = {Cachexia, a multifaceted wasting syndrome, profoundly impacts quality of life and survival rates in cancer patients. Gut inflammation is identified as a key player among the contributing factors for its development. Consequently, numerous studies have sought to characterize changes in gut microbiota of cachectic individuals, given the well-established roles of the gut microbiota in controlling and/or triggering both local and systemic inflammation in their hosts. Most of these investigations have applied mouse models of tumor-induced cachexia to show correlations between alterations in bacterial and fungal abundance in the digestive tract and the onset of cancer cachexia (CC). However, the role of viral dysbiosis in CC development remains unexplored. The present study aims to address this gap by characterizing the gut virome during the progression of murine cancer cachexia. Although our approach was limited to DNA viruses, our findings reveal that cachectic animals with Lewis lung carcinoma exhibited a subtle yet statistically significant modulation in composition (R[2] = 0.17622; p = 0.05). A linear discriminant analysis effect size (LEfSe) analysis revealed that the dysbiosis observed in the gut virome of CC animals was mostly characterized by a significant enrichment in giant viruses of the family Phycodnaviridae (LDA score, 4.2582; p-value, 0.004; pwrapp, 0.9984) and significantly decreased populations of bacteriophages of the families Microviridae (LDA score, 4.3458; p-value, 0.0127; pwrapp, 0.9065) and Inoviridae (LDA score, 3.3028; p-value, 0.0017; pwrapp, 0.9992). This cachexia-associated viral dysbiosis shares similarities with virome alterations documented in other conditions linked to gut inflammation, including, ulcerative colitis, Crohn's disease, and Clostridioides difficile infection. These new insights suggest the potential contributions of viral communities to the pathophysiology of CC and other inflammation-driven diseases.},
}
@article {pmid41722974,
year = {2026},
author = {Ji, M and Gong, J and Liu, Z and Liu, X and Wang, X and Ao, C and Tan, J},
title = {Multi-omics investigation of microbial community dynamics and metabolic regulation in mulberry wine fermentation under temperature and acid stress.},
journal = {Food microbiology},
volume = {137},
number = {},
pages = {105022},
doi = {10.1016/j.fm.2025.105022},
pmid = {41722974},
issn = {1095-9998},
mesh = {Fermentation ; *Wine/microbiology/analysis ; *Morus/microbiology/metabolism ; Saccharomyces cerevisiae/metabolism/genetics ; *Microbiota ; Temperature ; Hydrogen-Ion Concentration ; Ethanol/metabolism ; Metabolomics ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenomics ; *Acids/metabolism ; Lactobacillus/metabolism/genetics ; Stress, Physiological ; Multiomics ; },
abstract = {This study employed an integrated approach of metagenomics and metabolomics to investigate microbial community dynamics during mulberry wine fermentation under varying temperatures (17-29 °C) and pH levels (3.0-4.5). Twenty treatment combinations, spanning 27 days, captured the temporal dynamics of microbial communities and metabolic activity. Environmental stress significantly shaped community assembly, with Saccharomyces cerevisiae acting as the dominant fermentation organism and Lactobacillus spp. associated with organic acids. Core population analysis revealed specialized functions in ethanol production, acid resistance, and flavor biosynthesis. An optimal fermentation efficiency of 82 % and an ethanol content of 9.1 % vol. were achieved with the response surface method, resulting in optimal fermentation conditions of 23 ± 1 °C with a pH of 3.5 ± 0.1. Multi-omics correlation network analysis revealed coordinated associations among gene expression, enzymatic activities, and metabolite profiles, including coordinated expression patterns of flavor compound biosynthesis pathways. This research provides evidence-based optimization strategies for industrial mulberry wine production, enhancing understanding of stress-responsive microbial adaptation mechanisms.},
}
@article {pmid41722379,
year = {2026},
author = {Steinberger, Y and Doniger, T and Marchi, E and Eshel, G and Bocchi, S and Zapperi, S and La Porta, CAM},
title = {Fungal community structure and network connectivity as indicators of soil health under long-term land use.},
journal = {The Science of the total environment},
volume = {1020},
number = {},
pages = {181545},
doi = {10.1016/j.scitotenv.2026.181545},
pmid = {41722379},
issn = {1879-1026},
abstract = {Agriculture practices induce profound changes in soil biological properties and soil functioning. However, we still lack an understanding of how soil fungal biodiversity responds to various practices. Metagenomic tools were used to investigate soil fungal communities and inferred ecological functions based on functional guild classification in response to the effect of climate region and land management. This study assessed how seasonal timing and long-term land management affect soil fungal communities, with the aim of exploring their potential as candidate indicators of soil biological status. We collected soil samples across two regions of Israel (Mediterranean north and semi-arid south), three land-use types-orchard (OR), field crops (FC), and non-cultivated control (CO)-and two seasons-autumn and spring. Abiotic parameters varied significantly by season, region, and depth, underscoring the importance of considering sampling time in soil assessment. Fungal community composition showed marked differences between land uses, suggesting sensitivity to long-term management. CO and OR soils consistently exhibited higher fungal diversity and network connectivity, while FC soils had lower richness and unique taxa. A stable core community of 10 genera was found across treatments. Functional guilds were dominated by saprotrophs, though specific taxa and guild contributions varied by management type and season. Overall, our results emphasize the importance of sampling timing and land-use history in shaping fungal communities and support the potential of fungal-based indicators for assessing soil status across agricultural systems.},
}
@article {pmid41721873,
year = {2026},
author = {Sankar, SA and Girijan, SK and Shambhugowda, YB and Busala, SKK and Narayanane, S},
title = {Decoding the biotic networks and functional potential of seamount sediments in the Arabian sea.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41721873},
issn = {1573-4978},
mesh = {*Geologic Sediments/microbiology ; Metagenomics/methods ; Biodiversity ; Nitrogen/metabolism ; Seawater/microbiology ; Oceans and Seas ; Metagenome/genetics ; Fungi/genetics ; Microbiota/genetics ; Bacteria/genetics ; Phylogeny ; },
abstract = {BACKGROUND: The Arabian Sea is ecologically and environmentally significant due to its high biotic diversity and its potential role as a reservoir of emerging resistance determinants. However, molecular-level insights into the taxonomic composition, functional potential, and resistome of sediment associated communities from deep-sea seamount sediments remain limited.<br><br>METHODS AND RESULTS: A metagenomic approach was employed to investigate the biotic composition, metabolic potential, resistome profiles, and physicochemical characteristics of two seamount sediment samples (SM1 and SM7) collected from the Arabian Sea. Distinct environmental conditions were observed, with SM1 enriched in inorganic nitrogen, whereas SM7 exhibited higher organic carbon content and pigment concentrations, indicating differences in substrate availability. These variations were consistent with differences in the community structure, with SM1 harbouring a less diverse assemblage dominated by Actinomycetota and fungi, while SM7 supported a broader community comprising Actinomycetota, diverse fungi, protists, metazoans, and a richer viral component. Functional annotation revealed enrichment of nitrogen metabolism pathways in SM1, whereas SM7 showed increased representation of carbohydrate metabolism and a higher proportion of novel gene content. Both sediment samples encoded antibiotic and heavy metal resistance genes; however, SM7 exhibited greater abundance and diversity of putative resistance-associated genes, including resistance to mupirocin, triclosan, and sulfonamides, along with broader metal resistance and stress response genes.<br><br>CONCLUSIONS: The results based on two samples demonstrate pronounced sample specific variation in community structure, metabolic potential, and resistome profiles across Arabian Sea seamount sediments. These findings highlight Arabian Sea deep-sea sediments as important molecular reservoirs of microbial diversity and adaptive potential shaped by local environmental conditions.},
}
@article {pmid41718551,
year = {2026},
author = {Gröger, L and Rishik, S and Ludwig, N and Beganovic, A and Koch, M and Rheinheimer, S and Hart, M and König, P and Trampert, T and Paul, P and Boese, A and Lehr, CM and Becker, SL and Fuhrmann, G and Keller, A and Meese, E},
title = {Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2630482},
pmid = {41718551},
issn = {1949-0984},
mesh = {Humans ; *Extracellular Vesicles/metabolism/genetics ; MicroRNAs/metabolism/genetics ; Caco-2 Cells ; *RNA, Bacterial/metabolism/genetics ; *Epithelial Cells/microbiology/metabolism ; *Gastrointestinal Microbiome ; },
abstract = {While extracellular vesicles (EVs) are established mediators of intra-species signaling, their contribution to cross-kingdom communication remains incompletely understood. Here, we investigate the EV-mediated interactions between human colon epithelial cells and both Gram-positive and Gram-negative gut bacteria. We show that bacterial EVs (BEVs) derived from Lacticaseibacillus casei, Enterococcus faecalis, and Proteus mirabilis induce distinct transcriptomic changes in Caco-2 cells depending on the bacterial species, with up to ~6,000 differentially expressed genes, including CCL20, CXCL8, or CXCL10. Transfection of BEV-derived RNA independently induces a subset of similar effects, indicating that the EV-mediated communication is partially driven by the RNA cargo. Conversely, we demonstrate that bacteria interact with Caco-2-derived EVs and miR-192-5p, which is highly abundant (~36.4-fold higher) in EVs isolated from conditioned medium compared with EVs from unconditioned medium, with modest effects on bacterial growth. Furthermore, we show that lipid-based packaging of miR-192-5p modulates its association with the bacteria. Our findings support a conceptual model in which EVs and their RNA cargo contribute to species-dependent host-microbe interactions. This study introduces a framework for understanding EVs as cross-kingdom regulators and underscores the importance of tailored, context-specific analyses for understanding the scope of EV-mediated interactions in microbiome-host homeostasis and disease.},
}
@article {pmid41715233,
year = {2026},
author = {Choi, Y and Zhou, M and Oba, M and Romero-Pérez, A and Beauchemin, KA and Duval, S and Kindermann, M and Guan, LL},
title = {Comparative analysis of rumen metagenomes with dietary supplementation of 3-nitrooxypropanol revealed divergent modes of action in hydrogen metabolism and reductant pathways between beef and dairy cattle.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {72},
pmid = {41715233},
issn = {2049-2618},
support = {Award ID 22-000373//Foundation for Food &amp; Agriculture Research Greener Cattle Initiative/ ; Award ID 22-000373//Foundation for Food &amp; Agriculture Research Greener Cattle Initiative/ ; Award ID 22-000373//Foundation for Food &amp; Agriculture Research Greener Cattle Initiative/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; FDE.18.21C//Beef Cattle Research Council Cluster/ ; ALLRP 588541-23//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and NSERC Alliance program/ ; ALLRP 588541-23//Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery and NSERC Alliance program/ ; },
mesh = {Metagenome ; *Rumen/enzymology/microbiology ; Animals ; *Cattle/microbiology ; Dietary Supplements ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Fatty Acids, Volatile/biosynthesis ; *Methane/biosynthesis ; Hydrogen/metabolism ; Metabolic Networks and Pathways/drug effects ; },
abstract = {BACKGROUND: The compound 3-nitrooxypropanol (3-NOP), an inhibitor of methyl-coenzyme M reductase (MCR), reduces enteric methane production in both beef and dairy cattle. Although the proposed mechanisms of 3-NOP involve on inhibiting the activity of MCR in vivo, it is unknown how this process could affect rumen microbiome as a whole and if it differs between beef and dairy cattle. This study conducted a comparative analysis of the rumen microbiome and its functional shifts in four different cattle studies (two beef and two dairy cattle studies) that evaluated 3-NOP supplementation using metataxonomics and metagenomics.<br><br>RESULTS: Comparative analysis of 281 rumen metataxonomic datasets (143 beef and 138 dairy cattle) revealed that dietary supplementation with 3-NOP affected rumen bacteria and methanogens. Further, comparative analysis of 54 metagenomic datasets (24 beef and 30 dairy cattle) revealed that 3-NOP inhibited mcrA, decreased the abundances of Methanobrevibacter gottschalkii and the protozoal species Isotricha prostoma, while increased the abundances of Methanobrevibacter ruminantium and Methanosphaera sp., Prevotella sp. was a significant bacterial taxon in both beef and dairy cattle, contributing to various pathways such as propionate and butyrate production. Its increased abundance after 3-NOP supplementation may also be linked to the decrease in Isotricha prostoma. Hydrogenotrophic methanogenesis decreased after 3-NOP supplementation with the abundance of genes involved in methylenetetrahydromethanopterin dehydrogenase decreased in beef cattle, while that of 4Fe-4S ferredoxin gene decreased in dairy cattle. The abundance of protozoal Polyplastron multivesiculatum increased after long-term 3-NOP supplementation in beef cattle, potentially due to changes in hydrogen (H2) partial pressure. During 3-NOP-mediated methanogenesis reduction, abundance of genes encoding methanogenic hydrogenase and H2 producing hydrogenase were decreased, while those encoding H2 sensory hydrogenase increased. Acyl-CoA dehydrogenase gene involved in propionate and butyrate production pathways increased in both beef and dairy cattle, while nitrite reductase increased specifically in beef cattle, indicating a rise in alternative H2 sinks. Video Abstract CONCLUSION: Our findings revealed broad effects of 3-NOP on rumen microbiome and functions in vivo, with varied effects in beef and dairy cattle, which provide mechanistic insights into the supplementation of 3-NOP in both beef and dairy cattle, supporting its more sustainable and effective use in the future.},
}
@article {pmid41714786,
year = {2026},
author = {Paládi, P and Benmazouz, I and Tóth, M and Kövér, L and Lengyel, S},
title = {Spatial and temporal dynamics in the use of urban habitats by Hooded Crows.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40561-z},
pmid = {41714786},
issn = {2045-2322},
}
@article {pmid41712566,
year = {2026},
author = {Bedoya-Urrego, K and Peñuela-Martínez, AE and Alzate, JF},
title = {Uncovering the hidden yeast diversity in fermented coffee: Insights from a shotgun metagenomic approach.},
journal = {PloS one},
volume = {21},
number = {2},
pages = {e0332370},
pmid = {41712566},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; Fermentation ; *Coffee/microbiology ; Phylogeny ; *Yeasts/genetics/classification ; Metagenome ; Biodiversity ; Genome, Fungal ; },
abstract = {Yeasts play a pivotal role in coffee fermentation, shaping microbial succession and contributing to the development of final flavor profiles. Despite their importance, yeast taxonomy in this context remains poorly resolved. Traditional classification methods often result in misidentifications due to the limited resolution of classical microbiological techniques and the rapidly evolving taxonomic framework driven by advances in phylogenomic. Moreover, the diversity of budding yeasts in coffee fermentations remains underexplored using high-resolution approaches such as metagenomics. To address this gap, we applied a shotgun metagenomic strategy and reconstructed metagenome-assembled genomes (MAGs) from multiple coffee fermentation samples and, using a robust phylogenomic framework based on 832 conserved single-copy genes. We confidently classified 22 yeast MAGs within the subphylum Saccharomycotina. These included well-known taxa such as Pichia kluyveri, Hanseniaspora spp., Torulaspora delbrueckii, and members of the Kurtzmaniella clade. Most MAGs were placed in strongly supported monophyletic groups (ultrafast bootstrap = 100), with short intra-clade branch lengths indicative of intraspecific variation. Pichia kluyveri emerged as the most abundant and widespread species, detected in all analyzed metagenomes, followed by Hanseniaspora spp. Our results underscore the power of high-resolution phylogenomic for classifying yeast MAGs and highlight the ecological importance of Pichia, Hanseniaspora, Torulaspora, and Kurtzmaniella in spontaneous coffee fermentations.},
}
@article {pmid41708187,
year = {2026},
author = {Fang, M and He, J and Zhou, S and Hong, P and Ke, L and Wu, H and Shu, Y},
title = {Pleurotus ostreatus polysaccharides improve microcystin-LR-induced intestinal damage in tadpoles by regulating the interaction between microbiota and intestine.},
journal = {Harmful algae},
volume = {153},
number = {},
pages = {103056},
doi = {10.1016/j.hal.2026.103056},
pmid = {41708187},
issn = {1878-1470},
mesh = {Animals ; *Intestines/drug effects/microbiology ; *Microcystins/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Pleurotus/chemistry ; *Polysaccharides/pharmacology ; Larva/drug effects/microbiology ; *Ranidae ; Marine Toxins ; Oxidative Stress/drug effects ; },
abstract = {Exposure to microcystins (MCs) can cause severe intestinal damage. This study aimed to assess the efficacy of Pleurotus ostreatus polysaccharide in alleviating intestinal damage induced by microcystin-leucine-arginine (MC-LR) in tadpoles. Over a 30-day period, tadpoles (Pelophylax nigromaculatus) received daily exposures to MC-LR and were provided with diets either supplemented with or devoid of P. ostreatus polysaccharide. Results revealed that feeding P. ostreatus polysaccharide conferred protection against MC-LR-induced intestinal damage by mitigating barrier damage, lowering intestinal permeability, and reducing the tissue burden of MC-LR. The LPS/TLR4 pathway response was attenuated, reducing inflammation, and oxidative stress-mediated apoptosis response was also diminished. Gram-negative bacteria (e.g., Bacteroides) in the intestine show a positive correlation with LPS content and the transcription of key genes in the LPS/TLR4 pathway. Metagenomic and metabolite analysis of intestinal contents revealed increased abundance of the alanine-glyoxylate aminotransferase gene (agxt)-the key enzyme converting glyoxylic acid to glycine-and elevated glycine content in the MC-LR-exposed group fed polysaccharide. Results from the corresponding fecal microbiota transplantation experiment aligned with the trends observed in the exposure experiment. Therefore, polysaccharide alleviates MC-LR-induced intestinal damage by enhancing intestinal microbiota-mediated glycine synthesis, supplying raw materials for intestinal GSH production, reducing oxidative stress levels, and simultaneously dampening the LPS/TLR4 pathway response. Moreover, feeding polysaccharides might also regulate the intestine's defense against pathogens after MC-LR exposure by enhancing lysozyme activity. There is no evidence of intestinal damage in the P. ostreatus exopolysaccharide group. This study highlights for the first time the role of P. ostreatus polysaccharides in mitigating MC-LR-induced intestinal tissue damage, potentially offering novel insights for their application in aquaculture.},
}
@article {pmid41704501,
year = {2026},
author = {Yoshioka, Y and Ando, C and Yamashita, H and Kawamitsu, M and Kawachi, M and Tsunematsu, Y and Shoguchi, E},
title = {A dataset for forty complete bacterial genome sequences in cultures of the toxic dinoflagellate Ostreopsis cf. ovata.},
journal = {Data in brief},
volume = {65},
number = {},
pages = {112499},
pmid = {41704501},
issn = {2352-3409},
abstract = {Increasing occurrences of toxic dinoflagellate blooms are a growing concern under climate change. The benthic dinoflagellate Ostreopsis blooms through mechanisms that remain poorly understood and is assumed to produce palytoxin-like compounds such as ovatoxins. Recent studies have highlighted the diversity of bacterial communities associated with Ostreopsis and suggested a possible role for these bacteria in toxin biosynthesis. However, genome information on potential bacterial toxin producers remains limited. Here, we report a dataset of bacterial metagenome-assembled genomes (MAGs) obtained from the culture of the toxic dinoflagellate Ostreopsis cf. ovata strain (NIES-3351). HiFi long reads from PacBio Revio system were assembled with hifiasm-meta. We identified forty complete bacterial MAGs, each with an estimated completeness of 93-100%. These MAGs span a wide range of genome sizes (1.5 Mb to 6.7 Mb) and GC contents (36% to 67%). The dataset is available at DDBJ/ENA/GenBank under accession number PRJDB37958.},
}
@article {pmid41703832,
year = {2026},
author = {Yao, X and Chen, X and Niu, J and Li, J and Li, W and Zhu, H and Li, X and Sun, B},
title = {Storage time drives divergent microbial functions and flavor metabolism in high-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118363},
doi = {10.1016/j.foodres.2026.118363},
pmid = {41703832},
issn = {1873-7145},
mesh = {*Food Storage/methods ; *Taste ; *Hot Temperature ; *Alcoholic Beverages/microbiology/analysis ; *Microbiota ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Metagenomics ; Metabolomics ; Time Factors ; Bacteria/metabolism/classification ; *Flavoring Agents/metabolism ; },
abstract = {Baijiu is a traditional Chinese distilled liquor, whose unique flavor highly relies on the synergistic metabolism of diverse microbial communities during the brewing process. The high-temperature Daqu (HTD) used in sauce-flavor Baijiu plays a crucial role in flavor synthesis due to its enrichment of heat-resistant functional microbiota. However, traditional techniques have limited understanding of microbial community succession and functional dynamics during Daqu storage, hindering precise quality and flavor regulation. This study systematically investigated the dynamic evolution of physicochemical indexes, microbial community structure, metabolic functions, and flavor compounds in HTD during different storage periods (1st, 3rd, and 6th months) through integrated metagenomics and GC-MS metabolomics. Results showed continuous decreases in moisture, starch, and pH during storage, while aminopeptide nitrogen and acidity peaked at the 3rd month. Esters reached their highest levels at the 1st month (YQ), alcohols peaked at the 3rd month (EQ), and aldehydes dominated at the 6th month (SQ). LEfSe analysis identified Kroppenstedtia eburnea and Paecilomyces variotii as biomarkers for YQ, Saccharopolyspora rectivirgula and Aspergillus chevalieri for EQ, and Rasamsonia emersonii for SQ. Metagenomic analysis revealed differential carbohydrate and amino acid metabolism pathways: YQ showed highest enzyme abundance for phenethyl alcohol metabolism, EQ exhibited peak enzymes for pyrazine synthesis and ethanol metabolism, while SQ demonstrated superior glucoamylase activity. In addition, maximum tetramethylpyrazine at the 3rd month and highest microbial diversity in later storage (6th month).},
}
@article {pmid41703795,
year = {2026},
author = {Pais, ACS and Ribeiro, TB and Coscueta, ER and Salsinha, AS and Pintado, MM and Silvestre, AJD and Santos, SAO},
title = {Phenolic compounds' impact on gut microbiota: Insights from in vitro batch fecal fermentation for composition modulation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {228},
number = {},
pages = {118167},
doi = {10.1016/j.foodres.2025.118167},
pmid = {41703795},
issn = {1873-7145},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Feces/microbiology ; *Fermentation ; Fatty Acids, Volatile/metabolism/analysis ; *Phenols/pharmacology/metabolism ; Prebiotics ; Flavanones/pharmacology/metabolism ; Ellagic Acid/pharmacology/metabolism ; Bacteria/drug effects/genetics/metabolism ; Male ; Adult ; Female ; },
abstract = {The relationship between phenolic compounds and gut microbiota (has been widely studied to explore the health benefits of these bioactive dietary compounds. Phenolic compounds are metabolized by gut microbiota, while also modulating its composition. However, the individual effects of these compounds on human gut microbiota remain underexplored. To address this, three phenolic compouds-ellagic acid, naringenin, and phloroglucinol-underwent in vitro batch fermentation with fecal samples from healthy donors. Samples were analyzed through 16S metagenomics sequencing, and short-chain fatty acids (SCFAs) were measured using gas chromatography. Results showed that ellagic acid and phloroglucinol had prebiotic properties, producing SCFAs like acetic, propanoic, and butyric acids and promoting the growth of beneficial bacteria such as Lactobacillus and Bifidobacterium. In contrast, naringenin was linked to the growth of pathogenic genera like Escherichia and Salmonella. This study provides valuable insights into how specific phenolic compounds influence gut microbiota composition, contributing to potential pharmaceutical or nutraceutical developments.},
}
@article {pmid41702408,
year = {2026},
author = {Hernández-Vázquez, A and Garcia-Arellano, H and González-Cervantes, RM and López-Pérez, M and Soto, LMH and Meza, JAC and Aguirre-Garrido, JF},
title = {Study of Microbial Communities in the Soda Lake of Isabel Island: Identification of Polyhydroxybutyrate (PHB) Degrading Enzymes.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70279},
pmid = {41702408},
issn = {1758-2229},
mesh = {*Lakes/microbiology ; Phylogeny ; *Bacteria/genetics/classification/enzymology/isolation &amp; purification/metabolism ; *Hydroxybutyrates/metabolism ; Mexico ; Metagenome ; Bacterial Proteins/genetics/metabolism ; *Polyesters/metabolism ; *Microbiota ; Geologic Sediments/microbiology ; *Carboxylic Ester Hydrolases/genetics/metabolism ; Polyhydroxybutyrates ; },
abstract = {Crater Lake (Isabel Island, Mexico) is a meromictic, stratified, haloalkaline system. To identify and characterise PHB depolymerases across the vertical physicochemical gradients of the lake, we analysed seven metagenomes from the water column (0-23 m), one sediment metagenome, and the genomes of two organisms (HB105m and VN105m) isolated from 5 m. Taxonomic profiles revealed vertical stratification: Actinobacteriota and Cyanobacteriota dominated surface waters, while Pseudomonadota, Bacillota, and Bacteroidota prevailed in deeper layers and sediments. Alpha-diversity indices peaked at 5 and 20 m and declined at 23 m. We identified 16 putative PHB depolymerases spanning a broader phylogenetic range than previously documented for haloalkaline ecosystems. These included homologues affiliated with Vreelandella, Thiomicrorhabdus, Chloroflexota, Candidatus Cloacimonadota, and Desulfobacterales. The structural variation observed in lipase-box motifs and signal peptides suggests functional differentiation linked to redox and oxygen gradients across depths. Phylogenetic analysis of predicted and reference enzymes showed depth-specific clustering, with extracellular depolymerases predominant in oxic layers and intracellular forms more common in microoxic-anoxic zones. Overall, our results expand the known diversity of PHB-degrading lineages in extreme environments and highlight several candidate enzymes with potential biotechnological relevance for future experimental characterisation.},
}
@article {pmid41700136,
year = {2026},
author = {Hubot, N and Giering, SLC and Orel, N and Klun, K and Herndl, GJ and Hohaus, F and Lucas, CH and Tinta, T},
title = {Jellyfish mucus-derived organic matter as a source of labile nutrients for the ambient microbial community.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20784},
pmid = {41700136},
issn = {2167-8359},
mesh = {*Scyphozoa/chemistry/metabolism ; Animals ; *Microbiota ; *Mucus/chemistry/metabolism ; Seawater/microbiology/chemistry ; Nitrogen/metabolism/analysis ; *Nutrients/metabolism ; Ecosystem ; Amino Acids/metabolism ; },
abstract = {Jellyfish are increasingly recognized as a significant contributor to marine organic matter (OM) on a global scale, with implications for ecosystem dynamics. While the role of jellyfish detritus in microbial nutrient cycling has been explored, the contribution of OM released by live jellyfish-primarily as mucus (hereinafter referred to as mucus-associated OM, or MAOM)-remains understudied. This study investigates the release of organic and inorganic nutrients through MAOM from live jellyfish and their effects on ambient microbial communities in the northern Adriatic Sea using a series of leaching and short-term microcosm experiments. Our results show that per gram of MAOM dry weight from the jellyfish Aurelia spp, approximatively 2 µmol of phosphate, 4 µmol of dissolved inorganic nitrogen, 18 µmol dissolved organic nitrogen, 134 µmol of dissolved organic carbon and 15 µmol of dissolved free amino acids can be released in the ambient seawater in 24 h. Almost half of the OM is released as dissolved OM (DOM), of which a substantial part is low molecular weight (<1 kDa) molecules. During the first 20 h, the DOM fraction of MAOM was rapidly consumed by the ambient microbial community without a corresponding increase in biomass, likely due to nitrogen limitation. In the subsequent 22 h, microbial growth accelerated to 0.19 ± 0.03 h[-1] until phosphate became limiting, leading to a sharp decline in microbial production. Our metagenomics analysis revealed that the MAOM-degrading microbial community, dominated by Gammaproteobacteria opportunistic copiotrophs, exhibited increased functional capacity for nutrient assimilation and OM degradation, particularly in the transport and metabolism of amino acids (particularly glycine and taurine) and phosphorus. These traits mirror those found in detritus-degrading microbial communities, suggesting that jellyfish blooms promote the emergence of specialized microbial consortia with shared metabolic capabilities. Taken together, our findings highlight that live jellyfish, through the release of OM, play an active and previously underappreciated role in shaping ambient microbial community dynamics and nutrient fluxes in marine systems affected by jellyfish blooms.},
}
@article {pmid41697419,
year = {2026},
author = {Ni, W and Huang, H and Wang, X and Yu, A and Ren, J and Li, H},
title = {Metagenomic Analysis Reveals Alterations in the Gut Microbiome of Preterm Infants with Extrauterine Growth Restriction.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {177},
pmid = {41697419},
issn = {1432-0991},
support = {No. 82101811//National Natural Science Foundation of China/ ; No. RCJC20231211085923029//Shenzhen Science and Technology Program/ ; No. SZSM202311027//Sanming Project of Medicine in Shenzhen/ ; Guangdong High-level Hospital Construction Fund//Guangdong High-level Hospital Construction Fund/ ; Clinical key specialty construction project of Guangdong Province//Clinical key specialty construction project of Guangdong Province/ ; No. 20232011//Project of Guangdong Provincial Administration of Traditional Chinese Medicine/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature/growth &amp; development ; Infant, Newborn ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification ; Female ; Feces/microbiology ; Male ; },
abstract = {Extrauterine growth restriction (EUGR) is a pervasive clinical issue in preterm infants, affecting neonatal development and their long-term health. This study aimed to characterize the gut microbiome and its derived genes in preterm neonates with EUGR using metagenomic sequencing. Sixty-two preterm infants hospitalized in the neonatal intensive care unit at Guangdong Women and Children Hospital were enrolled in this study. Participants were divided into two groups: the EUGR group (n = 34) and the normal growth group (AGA, n = 28). Fecal samples were collected at one month postnatally. Total bacterial DNA was extracted and sequenced using the Illumina HiSeq X Ten system. Significant differences in the gut microbial community between the EUGR and AGA groups were observed, as evidenced by the Bray-Curtis dissimilarity index. The EUGR group exhibited a notable increase in Klebsiella pneumoniae and Enterococcus faecalis, along with a significant decrease in Streptococcus raffinosi, Rothia mucilaginosa, Parabacteroides merdae and Eggerthella lenta compared to the AGA group. Functional annotation of metagenomic genes identified 415 genes with significantly different relative abundances between the groups. A classification model incorporating five discriminatory genes achieved effective separation of EUGR from AGA infants. Additionally, the EUGR group exhibited a higher relative abundance of antibiotic resistance genes. This study elucidates the alterations in the gut microbiome and its derived genes in preterm neonates with EUGR. These findings provide new insights into the potential microbial signatures associated with impaired growth, although further mechanistic studies are needed to clarify causal relationships.},
}
@article {pmid41696869,
year = {2026},
author = {Ju, Y and Lin, S and Hu, S and Jin, X and Xiao, L and Zhang, T and Zhang, Y and Zhang, L and Ma, X and Zhu, F and Guo, R},
title = {GutMIND: A multi-cohort machine learning framework for integrative characteristics of the microbiota-gut-brain axis in neuropsychiatric disorders.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2630563},
pmid = {41696869},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Machine Learning ; *Mental Disorders/microbiology ; *Brain ; Cohort Studies ; Bacteria/classification/genetics/isolation &amp; purification ; Male ; Metagenomics ; Female ; *Brain-Gut Axis ; Biomarkers ; },
abstract = {Emerging evidence underscores bidirectional communication along the microbiota-gut-brain axis in neuropsychiatric disorders. However, the field lacks dedicated metagenomic resources with standardized phenotyping for these conditions. Existing single-cohort studies face inherent limitations due to restricted sample sizes, confounding heterogeneity, and methodological fragmentation, compromising reproducibility and mechanistic insights. To overcome these challenges, we constructed the Gut Microbiome in Multinational Integrated Neuropsychiatric Disorders (GutMIND) database, a comprehensive resource integrating shotgun metagenomic data with harmonized metadata. Adhering to a standardized preprocessing protocol and rigorous quality control workflow, this dataset represents the largest gut-brain microbiome repository to date, encompassing 31 studies across 12 countries (n = 3,492) spanning 14 neuropsychiatric conditions. Utilizing this dataset, we characterized microbial community heterogeneity, which was significantly elevated in patients compared to healthy controls. Subsequently, we developed a computational framework, MetaClassifier, enabling the diagnosis of neuropsychiatric disorders and the identification of microbial biomarkers. Employing a comprehensive two-stage validation strategy, we first assessed the model utilizing taxonomic abundance profiles via nested cross-validation in the high-quality discovery cohort (n = 2,734), achieving a mean AUROC of 0.69 (range: 0.55-0.78) across 8 disorders. Its robustness was further confirmed in an independent platform-extended validation cohort (n = 400), yielding a mean AUROC of 0.71 (range: 0.60-0.76). We also developed the Microbial Gut-Brain Axis Health Index (MGBA-HI), which effectively distinguished neuropsychiatric status in both the high-quality cohort and the platform-extended cohort. Furthermore, integrative analysis of health-abundant species, index-derived biomarkers, and ecological prevalence, we identified 9 core neuropsychiatric-protective microbiota. These species predominantly exhibited metabolic capacities linked to glutamate synthesis and acetate production. Building upon this, the GutMIND framework ensures robust cross-cohort comparability while minimizing technical heterogeneity, thereby enhancing inferential rigor in gut microbiome-neuropsychiatry research. Notably, the MetaClassifier, MGBA-HI, and core microbiota hold translational potential for developing microbiome-based prognostic tools and personalized therapeutic strategies in neuropsychiatric disorders. The source code and usage instructions for MetaClassifier are accessible at https://github.com/juyanmei/MetaClassifier.},
}
@article {pmid41696361,
year = {2026},
author = {Yin, L and Xu, L and Shan, YN and He, Z and Li, Y and Chen, W},
title = {Microbiota-driven therapeutic efficacy of Hyperoside in ulcerative colitis and associated anxiety.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1734356},
pmid = {41696361},
issn = {2235-2988},
mesh = {Animals ; *Colitis, Ulcerative/drug therapy/microbiology/complications ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Anxiety/drug therapy ; Disease Models, Animal ; *Quercetin/analogs &amp; derivatives/pharmacology/therapeutic use ; Male ; Cytokines/metabolism ; Colon/pathology/drug effects ; Mice, Inbred C57BL ; Molecular Docking Simulation ; Signal Transduction/drug effects ; Metabolomics ; Brain-Derived Neurotrophic Factor/metabolism ; Anti-Inflammatory Agents/pharmacology ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is subtype of inflammatory bowel disease that is frequently comorbid with anxiety disorders. However, effective dual-targeting therapies are still lacking. Hyperoside (HYP), a natural flavonoid, exhibits anti-inflammatory and neuroprotective properties, yet its potential therapeutic effects on UC and associated anxiety, as well as the underlying mechanisms, remain largely unexplored.<br><br>METHODS: A murine model of DSS-induced colitis was established and treated with HYP. Disease activity was assessed through body weight, colon length, and histopathology. Anxiety-like behaviors were evaluated using open field and elevated plus maze tests. Neuroinflammation was examined through immunohistochemistry of BDNF expression and microglial activation. Gut microbiota composition was profiled by metagenomic sequencing, and metabolomic profiling was conducted using the Q300 Kit. Network pharmacology and molecular docking were employed to predict signaling pathways, which were further validated by Western blotting. Additionally, antibiotic depletion experiments were conducted to determine microbiota dependency.<br><br>RESULTS: HYP administration significantly ameliorated DSS-induced colitis, as evidenced by attenuated weight loss, restored colon length, and improved histopathology. It suppressed pro-inflammatory cytokines (TNF-&#x3b1;, IL-6, IL-1&#x3b2;) and restored intestinal barrier integrity by upregulating Mucin-2 and ZO-1. Furthermore, HYP also alleviated anxiety-like behaviors and mitigated neuroinflammation by increasing BDNF levels and suppressing microglial activation. HYP treatment also restored gut microbial homeostasis, enriching beneficial bacteria such as Enterobacter ludwigii while reducing the abundance of Enterobacter hormaechei, Escherichia coli, and Acinetobacter baumannii. Metabolomic analysis revealed that HYP significantly promoted arginine biosynthesis. Network pharmacology and molecular docking identified the MAPK, PI3K-Akt, and NF-&#x3ba;B pathways as potential targets, with HYP showing strong binding affinity to MAPK3, AKT1, and NF&#x3ba;B1. Importantly, the therapeutic effects of HYP were abolished in microbiota-depleted mice.<br><br>CONCLUSION: Our findings demonstrate that HYP effectively alleviates DSS-induced colitis and comorbid anxiety-like behaviors. Its efficacy is dependent on the gut microbiota and is associated with the restoration of microbial homeostasis, enhancement of arginine metabolism, and modulation of the MAPK/PI3K-Akt/NF-&#x3ba;B signaling pathways. HYP represents a promising microbiota-targeting therapeutic candidate for UC and its neuropsychiatric comorbidities.},
}
@article {pmid41694529,
year = {2026},
author = {Vivarelli, S and De Francesco, C and Paba, E and Giambò, F and Fenga, C},
title = {The resistome bridge between livestock and workers: novel frameworks for early detection and monitoring of antimicrobial resistance.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1746385},
pmid = {41694529},
issn = {2296-2565},
mesh = {Animals ; *Livestock/microbiology ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Occupational Exposure ; One Health ; },
abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, driven by the extensive use of antibiotics in both human medicine and livestock production. In the context of the One Health framework, this review investigates the role of the gut microbiome and resistome, which represents the collection of antimicrobial resistance genes (ARGs), within livestock and among occupationally exposed workers. Intensive farming practices often involve routine, subtherapeutic antibiotic use, fostering antibiotic-resistant bacteria (ARB) in the gastrointestinal tract of animals. These ARB and ARGs are excreted into the environment, contributing to resistance spread through mobile genetic elements. From a Planetary Health perspective, this environmental dissemination reflects how human-driven livestock practices can perturb ecosystems, creating global health risks that link animal, human, and environmental well-being. Human exposure, particularly among farm workers and veterinarians, raises significant concerns about zoonotic transmission of pathogens and, potentially, ARB. Novel advances in metagenomic and metatranscriptomic technologies enhanced our understanding of gut microbial communities and their resistomes, revealing overlaps in ARG profiles between animals and livestock workers. These technologies also support the development of novel microbiome-targeted strategies, including prebiotics, probiotics, food supplementation and workplace-improvement strategies, aimed at reducing antimicrobial use and restoring healthy microbiome balance. The review also highlights the importance of integrated surveillance and cross-sectoral collaboration to monitor and control AMR transmission. Understanding the ecological dynamics of the gut resistome in livestock systems is essential for designing effective interventions that safeguard both animal and human health.},
}
@article {pmid41693971,
year = {2026},
author = {Xu, T and Hou, WX and Yang, ST and Shao, YP and Wang, J and Han, TT and Li, JN},
title = {Danggui-Baishao herb pair protects against dextran sulfate sodium-induced colitis by modulating the Wnt/β-catenin pathway.},
journal = {World journal of gastroenterology},
volume = {32},
number = {5},
pages = {113024},
pmid = {41693971},
issn = {2219-2840},
mesh = {Animals ; Dextran Sulfate/toxicity ; *Wnt Signaling Pathway/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry ; Disease Models, Animal ; Mice ; Humans ; Molecular Docking Simulation ; *Colitis/chemically induced/drug therapy/pathology/prevention &amp; control ; Colon/pathology/drug effects ; Male ; beta Catenin/metabolism ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Intestinal Mucosa/drug effects/pathology ; Glucosides/pharmacology ; Metabolomics ; Pyrimidinones ; Bridged Bicyclo Compounds, Heterocyclic ; },
abstract = {BACKGROUND: The Danggui-Baishao herb pair is the foundation of a traditional Chinese medicine formula known as Shaoyao decoction, which is widely used in the treatment of colitis.<br><br>AIM: To uncover the mechanisms underlying the anti-colitis effects of the Danggui-Baishao herb pair.<br><br>METHODS: The chemical composition of the herb pair was characterized by high performance liquid chromatography-quadrupole/time of flight mass spectrometry analysis. A mouse model of colitis was induced by administering 2.5% dextran sulfate sodium. The therapeutic effects of the herb pair were evaluated based on body weight changes, colon length, histopathological, intestinal inflammation, and barrier function. To investigate the underlying mechanisms, RNA sequencing, metabolomics, 16S rRNA sequencing, metagenomics, and the &#x3b2;-catenin inhibitor ICG-001 were utilized. Furthermore, molecular docking and dextran sulfate sodium-treated HCT 116 cells were conducted to explore the protective mechanisms of benzoylpaeoniflorin.<br><br>RESULTS: The herb pair improved body weight, colon length, intestinal inflammation, and barrier function. Additionally, the herb pair upregulated the expression of intestinal stem cells marker leucine-rich repeat-containing G-protein coupled receptor 5 and proliferation-related proteins. RNA sequencing analysis showed that the herb pair activated the Wnt/&#x3b2;-catenin signaling pathway. Metabolomic analysis revealed changes in bile acids composition. Through 16S rRNA and metagenomic sequencing, it was observed that the herb pair modulated the gut microbiota, with an enrichment of probiotics and a depletion of pathogenic bacteria. Following intraperitoneal injection of antagonist ICG-001, the therapeutic efficacy was diminished. Molecular docking showed that benzoylpaeoniflorin can bind to &#x3b2;-catenin. Furthermore, benzoylpaeoniflorin can activated the Wnt/&#x3b2;-catenin signaling pathway and the therapeutic efficacy was also diminished by the ICG-001 in vitro.<br><br>CONCLUSION: The herb pair effectively reduces colonic inflammation and maintains the integrity of the intestinal barrier. Moreover, the anti-colitis efficacy of the herb pair is closely associated with activation of the Wnt/&#x3b2;-catenin pathway.},
}
@article {pmid41693862,
year = {2025},
author = {Zhang, H and Zhang, L and Yang, B and Gao, C and Liu, H and Zhang, Y and Chen, X},
title = {Metagenomic and metatranscriptomic profiling of bronchoalveolar lavage fluid identifies microbial and host biomarkers of drug-resistant tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1726935},
pmid = {41693862},
issn = {2235-2988},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Tuberculosis, Multidrug-Resistant/microbiology/diagnosis/immunology ; Mycobacterium tuberculosis/genetics ; Male ; Female ; Gene Expression Profiling ; Biomarkers/analysis ; Metagenomics ; Prospective Studies ; Middle Aged ; Adult ; Microbiota ; Transcriptome ; Bacteriophages/genetics ; Lung/microbiology ; },
abstract = {BACKGROUND: Drug-resistant tuberculosis (DR-TB) undermines global TB control, yet how resistant Mycobacterium tuberculosis strains interact with the lung microbiome, phage communities, and local host immunity remains poorly defined.<br><br>METHODS: In a prospective cohort of 130 pulmonary TB patients (49 DR-TB, 81 drug-susceptible TB [DS-TB] patients), bronchoalveolar lavage fluid (BALF) was subjected to paired metagenomic and transcriptomic profiling. Microbial and bacteriophage community structures were assessed by diversity metrics and differential abundance testing, whereas host responses were characterized by gene expression, pathway enrichment, and immune cell deconvolution. A Random Forest model was trained to evaluate the diagnostic potential of host transcriptional signatures.<br><br>RESULTS: DR-TB airways presented distinct microbial beta diversity, with enrichment of Streptococcus spp. and streptococcal-targeting phages (e.g., Javan variants, phi-Ssu5SJ28rum). Transcriptomic analysis revealed 494 differentially expressed genes, which were associated with increased oxidative phosphorylation, suppressed ion channel and transporter activity, and enrichment of extracellular matrix remodeling pathways. Immune profiling demonstrated a significant reduction in &#x3b3;&#x3b4; T cells in DR-TB patients (P = 0.0059). An 8-gene host-derived signature (ARHGEF5, PTGES3L, GAL3ST1, RANBP17, ACTA2_AS1, CBY3, MAMSTR, and LOC102031319) discriminated DR-TB from DS-TB with high accuracy (AUC = 0.837).<br><br>CONCLUSION: This dual-omics study defines the airway niche of DR-TB as a convergence of microbial dysbiosis, phage imbalance, and host immune-metabolic dysfunction. By uncovering DR-TB-specific microbial and transcriptional signatures, and deriving a predictive host-based classifier, our findings provide mechanistic insights and highlight novel opportunities for microbiome- and host-directed interventions in drug-resistant tuberculosis.},
}
@article {pmid41693402,
year = {2026},
author = {Parveen, S and Shafi, Z and Shahid, M and Iqbal, MZ and Naznine, F and Ansari, MI},
title = {Omics-Driven Insights Into Soil Microbial Diversity and Phytopathogen Interactions for Sustainable Agriculture and Food Security.},
journal = {Journal of basic microbiology},
volume = {66},
number = {2},
pages = {e70155},
doi = {10.1002/jobm.70155},
pmid = {41693402},
issn = {1521-4028},
support = {//The authors are thankful for the support received from the Department of Science and Technology-Funds for Improvement of Science and Technology Infrastructure (DST-FIST), with grant acknowledgment and sanction number (SR/FST/LS-1/2017/13(C)). The authors express their deep gratitude to Integral University, Lucknow-226026, India, for their generous support of this work and for providing the manuscript communication number (IU/R&amp;D/2025-MCN0003515)./ ; //Department of Science and Technology-Funds/ ; },
mesh = {*Soil Microbiology ; *Food Security ; *Agriculture/methods ; Biodiversity ; Metabolomics/methods ; Crops, Agricultural/microbiology/growth &amp; development ; Proteomics ; Metagenomics ; Microbiota ; Plant Diseases/microbiology ; Bacteria/genetics/metabolism ; Ecosystem ; },
abstract = {Soil microbial diversity plays a pivotal role in sustainable agriculture by regulating nutrient cycling, organic matter turnover, and natural suppression of phytopathogens, thereby supporting crop productivity and ecosystem resilience. However, intensive agricultural practices and environmental stressors have led to a decline in soil biodiversity, compromising soil functionality and food security. Recent advances in omics technologies-including metagenomics, transcriptomics, proteomics, and metabolomics offer powerful tools to unravel the complexity, of soil microbial communities and their interactions with plants and pathogens. These integrated approaches provide high-resolution insights into microbial structure, functional dynamics, metabolic pathways, and the mechanisms underpinning plant-microbe-pathogen interactions. Furthermore, omics-driven understanding supports the development of sustainable strategies such as organic farming, conservation practices, and microbial bioinoculants, which restore microbial diversity, enhance nutrient use efficiency, reduce chemical inputs, and mitigate disease pressure. By linking soil health to crop nutritional quality and broader food system sustainability, this review highlights the potential of omics-guided approaches to optimize soil microbial ecosystems for resilient agriculture and global food security.},
}
@article {pmid41691253,
year = {2026},
author = {Daryani, NE and Jazayeri, SM and Izadi, N and Ahmadi, H and Baghi, HB and Shirmohammadi, M and Sabbaghian, M and Shekarchi, AA and Marvi, SS and Azadi, A and Poortahmasebi, V},
title = {Characterizing the gut virome in ulcerative colitis and crohn's disease: signatures of disease severity.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {46},
pmid = {41691253},
issn = {1743-422X},
support = {979157//National Institute for Medical Research Development/ ; },
mesh = {Humans ; *Virome ; *Crohn Disease/virology/pathology ; Cross-Sectional Studies ; Male ; *Colitis, Ulcerative/virology/pathology ; Adult ; Female ; Severity of Illness Index ; Middle Aged ; Feces/virology ; *Viruses/classification/genetics/isolation &amp; purification ; Iran ; Metagenomics ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; Young Adult ; Bacteriophages/genetics/classification ; Computational Biology ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is a chronic disorder marked by intestinal inflammation and immune dysregulation. While bacterial dysbiosis has been widely investigated, the gut virome remains less explored. Altered viral communities, particularly bacteriophages, may destabilize microbial balance and amplify host inflammation.<br><br>METHODS: To characterize virome alterations, we conducted a cross-sectional observational study in Tabriz, Iran, involving fifty participants divided into five groups: mild UC, severe UC, mild CD, severe CD, and healthy controls. Stool samples were processed for viral nucleic acid extraction and analyzed using metagenomic next-generation sequencing. Bioinformatics pipelines included diversity assessment, taxonomic profiling, functional annotation, and discriminant analysis (LEfSe). Predictive modeling was performed with random forest classifiers.<br><br>RESULTS: Virome richness and diversity were reduced in severe UC and CD compared with controls, whereas mild cases showed values closer to healthy individuals. Taxonomic profiling revealed depletion of crAss-like phages and microviridae in IBD, along with enrichment of Caudovirales families such as siphoviridae and myoviridae. Among eukaryotic viruses, anelloviridae were prominent in severe IBD, and herpesviridae were enriched specifically in severe UC. Functional annotation highlighted enrichment of structural and lytic phage proteins in severe groups, whereas lysogeny-associated domains were more abundant in healthy controls. Random forest models based on viral features achieved appropriate accuracy, with an AUC of 0.89 for distinguishing IBD from controls and 0.83 for classifying mild versus severe disease.<br><br>CONCLUSION: Thus, IBD is associated with reduced virome diversity, loss of core protective phages, and selective enrichment of bacteriophages and eukaryotic viruses. These findings suggest that virome features may have potential as biomarkers for non-invasive diagnosis and severity stratification in IBD, requiring validation in larger and longitudinal cohorts.},
}
@article {pmid41690221,
year = {2026},
author = {Jiang, Y and Shu, W and Wan, J and Yan, J and Liu, Q and Jiang, Y},
title = {Impacts of co-exposure to nanoplastics and ofloxacin on marine planktonic microbial communities and DMSP dynamics.},
journal = {Marine environmental research},
volume = {216},
number = {},
pages = {107908},
doi = {10.1016/j.marenvres.2026.107908},
pmid = {41690221},
issn = {1879-0291},
mesh = {*Water Pollutants, Chemical/toxicity ; *Plankton/drug effects ; *Ofloxacin/toxicity ; *Sulfonium Compounds/metabolism ; Seawater/microbiology/chemistry ; *Microbiota/drug effects ; Anti-Bacterial Agents/toxicity ; *Microplastics/toxicity ; },
abstract = {Dimethylsulfoniopropionate (DMSP) is a key organic sulfur compound in marine food webs and the main precursor of the climate-active gas dimethyl sulfide (DMS), yet its water-column cycling under the joint influence of emerging pollutants remains poorly constrained. A 19-day microcosm experiment was conducted to examine the long-term effects of single and combined exposure to nanoplastics (NPs) and the antibiotic ofloxacin on planktonic microbial communities and DMSP cycling in coastal seawater. Combined exposure induced much stronger inhibitory effects than either single pollutant, markedly weakening the late-phase biomass recovery observed under the antibiotic-only treatment. DMSP dynamics exhibited a biphasic disruption pattern: an initial transient accumulation was followed by persistently low concentrations later in the experiment, coinciding with pronounced declines in microeukaryotic and total biomass. Combined metagenomic and flow cytometric analyses revealed a "functional decoupling" scenario, in which the surviving community displayed elevated relative abundances of DMSP biosynthesis- and degradation-related genes, while the sharp reduction in microeukaryotic biomass and overall community size constrained the maintenance and renewal of the water-column DMSP pool. Co-occurrence network analysis further showed that co-exposure simplified the microbial network from a more distributed, complex structure to a highly centralized one, with fewer nodes and keystone taxa and decreased robustness indices along the pollution gradient. Together, these findings indicate that the co-occurrence of nanoplastics and antibiotics can disturb DMSP-related functions by eroding community structural stability and functional redundancy, providing experimental evidence for the vulnerability of coastal DMSP cycling to mixed-pollutant stress.},
}
@article {pmid41688119,
year = {2026},
author = {Akpulu, CP and Maikudi Sada, H and Ahmed, H and Idris, HB and Yakubu, R and Aminu, A and Iregbu, K and Oduwo, J and Owinoh, E and Lankapalli, AK and De Nies, L and Achi, CR and Thomson, K and Stracy, M and Walsh, TR and Sands, K},
title = {Cohort profile: Infant Gut Bacterial Study in Nigeria (INBUGS-NG).},
journal = {BMJ open},
volume = {16},
number = {2},
pages = {e111007},
pmid = {41688119},
issn = {2044-6055},
mesh = {Humans ; Nigeria ; *Gastrointestinal Microbiome ; Female ; Infant ; *Anti-Bacterial Agents/therapeutic use ; Prospective Studies ; Male ; Infant, Newborn ; Longitudinal Studies ; Feces/microbiology ; Adult ; Breast Feeding/statistics &amp; numerical data ; Milk, Human/microbiology ; Delivery, Obstetric ; Pregnancy ; },
abstract = {PURPOSE: The Infant Gut Bacterial Study in Nigeria (INBUGS-NG) investigates how delivery mode, antibiotic exposure, feeding practices and environmental factors shape gut microbiome development and acquisition of antibiotic resistance genes (ARGs) during the first year of life in northern Nigeria.<br><br>PARTICIPANTS: Between February and July 2024, 90 mother-infant dyads were enrolled at a tertiary hospital in Kano city, Nigeria. This was a prospective longitudinal cohort with follow-ups at 10 scheduled time points: days 0, 1, 3, 5, 7, 14, 28, 90, 180 and 365. We also intensified stool sampling after infant antibiotic administration, enabling dense early-life sampling. To date, the cohort has contributed 480 infant stool samples, 232 maternal rectal swabs, 254 breast milk samples and 806 environmental samples (total 1772). In parallel, socio-demographic, clinical and cultural data were collected using Research Electronic Data Capture (REDCap) and household visit diaries.<br><br>FINDINGS TO DATE: Baseline data show that 84/90 mothers (93.3%) received postpartum antibiotics, and 26/90 infants (28.9%) received antibiotics within the first 3 months of life. Only 8% of infants were exclusively breastfed, with early water supplementation common. Caesarean deliveries accounted for 25% of births, and the mean gestational age was 38.5 weeks. Across the cohort, high retention was achieved, and the study has generated a unique long-read metagenomic resource from an African infant population, with analyses ongoing.<br><br>FUTURE PLANS: Shotgun long-read metagenomic sequencing (Oxford Nanopore) will enable strain-level and plasmid-level profiling of microbial communities and ARGs. Planned analyses include associations between early-life exposures and resistome dynamics, as well as cross-cohort comparisons with a parallel study in Pakistan. Follow-up will continue through 12 months.},
}
@article {pmid41687847,
year = {2026},
author = {Wang, N and Kang, Z and Wang, X and Zhang, Y and Li, X and Sun, Y and Xi, J and Shen, L},
title = {Sewage-sludge-derived biostimulant enables fertilizer reduction while maintaining rice yield through microbiome-mediated nutrient cycling.},
journal = {Environmental research},
volume = {296},
number = {},
pages = {124020},
doi = {10.1016/j.envres.2026.124020},
pmid = {41687847},
issn = {1096-0953},
abstract = {Modern agriculture relies heavily on chemical fertilizers to sustain high yields, yet excessive inputs contribute to soil acidification, water eutrophication, greenhouse gas emissions, and biodiversity loss. Sewage-sludge-derived biostimulants (SS-BS) may help reduce fertilizer dependency while sustaining crop performance through plant-soil-microbiome interactions. Here, we evaluated SS-BS in a paddy rice field trial conducted during a single growing season (2024) under conventional management. Three fertilization regimes were compared: low-fertilizer control (CK), conventional fertilization (FP), and reduced mineral fertilization supplemented with SS-BS (BS). Across the 2024 season, rice yield and key yield components in BS were comparable to, or approached, those in FP with reduced mineral fertilizer input. Shotgun metagenomic profiling indicated that BS was associated with shifts in microbial functional pathways related to nitrogen, phosphorus, and potassium cycling, and with changes in the relative abundance of taxa linked to nutrient transformation processes. Partial least squares path modeling (PLS-PM) further suggested that microbial functional attributes were associated with the relationships among fertilization regime, soil properties, and yield outcomes. Collectively, these results from a single-season field experiment indicate that SS-BS has the potential to support fertilizer-reduction strategies in rice systems and motivate multi-season validation of its agronomic performance and microbiome-associated effects.},
}
@article {pmid41686173,
year = {2026},
author = {Yang, Z and Zhang, F and Li, H and Liu, B and Liu, P and Wu, Z and Li, Y and Miao, J and Li, X and Liang, H and Zhong, Y and Xiao, L and Zou, Y and He, N and Li, S},
title = {Gut Commensal Phocaeicola vulgatus AF107-22 Alleviates Obesity-Induced Metabolic Syndrome via Promoting Gut Microbiota-Derived Spermidine Synthesis.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {7},
pages = {6218-6229},
doi = {10.1021/acs.jafc.5c14443},
pmid = {41686173},
issn = {1520-5118},
mesh = {*Spermidine/biosynthesis/metabolism ; *Gastrointestinal Microbiome ; Animals ; *Obesity/complications/microbiology/metabolism ; *Metabolic Syndrome/microbiology/metabolism/etiology/therapy ; Mice ; Male ; Humans ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; *Probiotics/administration &amp; dosage ; },
abstract = {Obesity-induced metabolic syndrome (MetS) is a prevalent metabolic disorder, and therapeutic strategies targeting the gut microbiota hold considerable promise. Phocaeicola vulgatus (P. vulgatus) is a gut commensal bacterium that plays an important role in modulating the composition and metabolism of gut microbiota. This study demonstrated that the abundance of P. vulgatus is significantly negatively correlated to obesity-induced MetS and complications in human metagenomic data. Oral gavage of P. vulgatus significantly ameliorated high-fat-diet (HFD)-induced MetS symptoms in mice, reducing body weight, systemic inflammation, and hepatic steatosis. Furthermore, multiomics analyses indicated that P. vulgatus treatment significantly enhanced the production of gut microbiota-derived spermidine and spermine. Subsequently, population-based analysis confirmed a strong negative correlation between plasma spermidine levels and MetS progression, supporting that such parameters may serve as potential biomarkers for MetS. This study reveals a potential mechanism, bridging commensal probiotic and spermidine metabolism, with implications for treating obesity-induced MetS.},
}
@article {pmid41684896,
year = {2025},
author = {Das, R and Malard, L and Pearce, DA and Convey, P and Rahlff, J},
title = {Diversity of DNA viruses in the atmosphere of sub-Antarctic South Georgia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1726848},
pmid = {41684896},
issn = {1664-302X},
abstract = {Studying airborne viruses in remote environments like the sub-Antarctic island of South Georgia offers key insights into viral ecology, diversity, and their role in shaping ecosystems through microbial and nutrient interactions. We analyzed airborne viral community composition at two sites in South Georgia. Sampling took place using multiple methodologies, with the data produced subjected to viral metagenomics. The Coriolis μ device (wet collection) was the most effective, yielding 30 viral scaffolds. Two-thirds of the scaffolds were only obtained from the coastal location, indicating that location influences airborne viral diversity. Protein-based clustering of 39 viral operational taxonomic units (vOTUs) revealed similarities of 15 with known marine viruses, suggesting oceanic influence on the airborne viral community. Protein homologs related to UV damage protection and photosynthesis from two airborne vOTUs were widely distributed across major oceans, suggesting their potential role in supporting the resilience of marine microorganisms under changing climate conditions. Some vOTUs had protein similarities to viruses infecting extremophiles, indicating viral adaptations to harsh environments. This study provides a baseline for understanding the complexity and sustainability of airborne viral communities in remote ecosystems. It underscores the need for continued monitoring to assess how these communities respond to shifting atmospheric and ecological conditions.},
}
@article {pmid41684743,
year = {2025},
author = {Díaz-Velis, L and Salvador-Sagüez, F and Roach, F and Mancilla, E and Campos, MA and Ruiz-Gil, T and López-Moral, M and Garrido, G and Lázaro-Martínez, JL},
title = {Metagenomic and ribosomal transcript profiles of diabetic foot osteomyelitis in Hispanic patients: underestimated bacteria in biofilm persistence.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1729196},
pmid = {41684743},
issn = {2235-2988},
mesh = {Humans ; *Diabetic Foot/microbiology/complications ; *Osteomyelitis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Biofilms/growth &amp; development ; Male ; Middle Aged ; Female ; Hispanic or Latino ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Chile ; Microbiota/genetics ; Metagenomics ; DNA, Bacterial/genetics ; Adult ; Bone and Bones/microbiology ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics ; White ; },
abstract = {BACKGROUND: Diabetic foot osteomyelitis (DFO) is a serious complication of diabetes and a leading cause of lower-limb amputations. Conventional culture-based diagnostics often underestimate the microbial diversity of infected bone tissue. This study represents the first characterization of both total and ribosomally active bone microbiota in Hispanic patients with DFO using high-throughput 16S rRNA gene sequencing. The work aims to contribute to the inclusion of underrepresented populations in microbiome research and informing molecular-based antimicrobial strategies.<br><br>METHODS: Bone specimens (n = 13) were collected from seven Chilean patients with histologically confirmed DFO. Samples were analyzed using conventional aerobic culture and 16S rRNA gene sequencing from both genomic DNA (gDNA) and complementary DNA (cDNA) to characterize the total bacterial community and the ribosomally active fraction. In three patients, samples were stratified by bone depth (superficial/top, middle and bottom). Microbial diversity and relative abundance were assessed across patients and bone layers.<br><br>RESULTS: Acute osteomyelitis was the predominant histopathological pattern. Culture yielded 19 bacterial isolates, 95% of which were Gram-negative bacilli. Sequencing identified 3,412 operational taxonomic units (OTUs), with Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as dominant phyla. Enterobacteriaceae and Enterococcaceae were the most ribosomally active families. Microbial community composition varied substantially among patients and across bone depths. Staphylococcus aureus was infrequent (5% of culture isolates; ~1% of sequence reads), whereas low-abundance but ribosomally active taxa, such as Corynebacteriaceae, were consistently detected across all layers.<br><br>DISCUSSION: This combined metagenomic and ribosomal transcript analysis reveals a polymicrobial, patient-specific bone microbiota in Chilean patients with DFO, highlighting potentially active bacteria frequently overlooked by standard diagnostic methods. These findings underscore the value of integrating molecular approaches into clinical workflows to improve pathogen detection and support more personalized antimicrobial strategies, while also helping to address gaps in microbiome research among underrepresented populations.},
}
@article {pmid41684459,
year = {2026},
author = {Sgarabotto, E and Zadra, N and Tyrell, JA and Rossi, C and Hewson, I and Searle, JB and Hauffe, HC},
title = {Virome analysis reveals ORF7 sequences of type 2 porcine respiratory and reproductive syndrome virus (PRRSV) for the first time in a rodent host (Microtus pennsylvanicus).},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101345},
pmid = {41684459},
issn = {2352-7714},
abstract = {The lung virome of meadow vole (Microtus pennsylvanicus) from six neighbouring locations in New York State, USA was investigated using metagenomics to determine the circulation of potentially zoonotic viruses in a common wild rodent. This study provides the first evidence of the occurrence of Type 2 Porcine Respiratory and Reproductive Syndrome Virus (PRRSV2) in a rodent, or indeed in any species apart from wild and domestic pigs (Sus scrofa). PRRSV has the highest economic impact on the pig husbandry industry of any pathogen, but up to now, farm-to-farm transmission of this virus has been assumed to be associated with movement of and contact with infected pigs and fomites. Our results showing the natural occurrence of this virus in potential transmission hosts other than wild or domestic pigs challenge this scenario. Phylogenetic analysis of assembled partial genomes from four of our pooled samples and all other nucleocapsid protein (ORF7) sequences available in Genbank showed that the sequences recovered from meadow voles unambiguously clustered within the PRRSV2 clade together with sequences derived from wild and domestic pigs. Historical research suggests that spillover from voles to domestic pigs may be the most parsimonious explanation for these results; however, we cannot rule out the reverse: that the source of PRRSV2 in these wild voles derives from pigs. From a One Health perspective, our results reinforce the importance of characterizing wildlife viromes to survey possible sources of zoonotic pathogens, which is vital for making evidence-based decisions regarding potential threats to the health of humans, livestock and wild fauna.},
}
@article {pmid41683346,
year = {2026},
author = {Fathima, S and Kilgore, PE and Sarkar, T and Sharma, N and Nguyen, HH},
title = {Muno-IgY Supplementation Improves Respiratory Health, Immune Response, and Exercise-Induced Physiological Stress in Healthy Adults: A Randomized Controlled Pilot Study.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683346},
issn = {2072-6643},
mesh = {Humans ; Pilot Projects ; Male ; Adult ; Female ; *Dietary Supplements ; Double-Blind Method ; *Exercise/physiology ; *Respiratory Tract Infections/prevention &amp; control/immunology/epidemiology ; Gastrointestinal Microbiome/drug effects ; *Stress, Physiological/drug effects ; *Immunoglobulins/administration &amp; dosage/pharmacology ; Biomarkers/blood ; Young Adult ; Middle Aged ; },
abstract = {BACKGROUND/OBJECTIVES: Upper respiratory tract infections (URTIs) and exercise-induced immune perturbations are common in adults and may adversely affect quality of life, productivity, and physical performance. Immunoglobulin Y (IgY), a food-derived antibody with broad antimicrobial activity, has demonstrated immunomodulatory potential in preclinical and limited clinical studies. This study evaluated the effects of a multi-pathogen-specific IgY supplement (Muno-IgY) on respiratory health, immune and inflammatory markers, exercise-induced physiological stress, and gut microbiome composition in healthy adults.<br><br>METHODS: In this 12-week, double-blind, placebo-controlled trial, 28 healthy adults with a history of URTI were randomly allocated to receive Muno-IgY or placebo and URTI incidence, duration, and severity were recorded daily. Serum immune and inflammatory biomarkers were assessed longitudinally and in response to a standardized exercise challenge. Gut microbiome composition was analyzed using shotgun metagenomic sequencing at baseline and week 12. Safety and tolerability were assessed throughout the study.<br><br>RESULTS: URTI incidence was lower in the Muno-IgY group compared with placebo (14.3% vs. 35.7%), with shorter average duration and fewer missed workdays, though differences were not statistically significant (p > 0.05). Following an acute exercise challenge, Muno-IgY supplementation resulted in a significant increase in serum IgA at 24 h post-exercise (p = 0.022) and a significantly greater reduction in lactate dehydrogenase at 1 h post-exercise compared with placebo (p < 0.0001). Exploratory gut microbiome analyses suggested favorable directional shifts, though these changes were not statistically tested.<br><br>CONCLUSIONS: In this exploratory pilot study, Muno-IgY supplementation was safe and associated with significant improvements in selected markers of exercise-induced immune response and muscle damage. Numerical trends in URTI incidence and gut microbiome composition were observed but were not statistically significant. These findings are hypothesis-generating and support further evaluation of Muno-IgY in larger, adequately powered clinical trials.},
}
@article {pmid41683205,
year = {2026},
author = {Yu, W and Tang, K and An, R and Ma, S and Tan, H and Chen, M},
title = {Study on Association Between Gut Microbiota, Serum Metabolism and Gestational Diabetes Mellitus Based on Metagenomic and Metabolomics Analysis.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683205},
issn = {2072-6643},
mesh = {Humans ; Female ; *Diabetes, Gestational/microbiology/blood/metabolism ; Pregnancy ; *Gastrointestinal Microbiome/physiology ; Case-Control Studies ; Adult ; *Metabolomics/methods ; *Metagenomics ; Feces/microbiology ; Pregnancy Trimester, First ; },
abstract = {Background/Objectives: This study aimed to explore the association between maternal gut microbiota and metabolic profiles in the first trimester and the subsequent risk of gestational diabetes mellitus (GDM), as well as to characterize association patterns linking gut microbiota, serum metabolites, and metabolic traits. Methods: A nested case-control study was conducted among women with GDM (n = 47) and those without GDM (n = 94). Metagenomic sequencing was applied to analyze fecal microbiota, and liquid chromatography-mass spectrometry (LC-MS) was used for non-targeted plasma metabolomics. Differential microbiota and metabolites between groups were identified, and correlation analyses were conducted to assess their associations with clinical indicators. Results: Women who later developed GDM showed lower alpha diversity and higher beta diversity. Eleven differential species were identified, with Collinsella aerofaciens and Clostridium bartlettii enriched in GDM, while nine species such as Alistipes putredinis and Bacteroidales bacterium ph8 were enriched in controls. Sixty-four plasma metabolites differed between groups, including increased glycerol-3-phosphate, aromatic amino acids, and glycerophosphocholine, and decreased cysteine, tryptophan, niacinamide, and stearic acid. Correlation analyses revealed significant relationships between Alistipes putredinis, Eubacterium eligens, and Bacteroidales bacterium ph8 with metabolic and clinical indicators (e.g., TG, TC, LDL). Conclusions: In this nested case-control study, women who later developed GDM exhibited reduced gut microbial diversity and altered metabolic profiles during the first trimester of pregnancy. Several microbial taxa and microbiota-metabolite associations were observed in relation to subsequent GDM status, highlighting early-pregnancy microbial and metabolic features that may be relevant to GDM-related metabolic changes.},
}
@article {pmid41680567,
year = {2026},
author = {Chen, L and Hong, C and Xie, Y},
title = {Bridging the gap between microbiome function and clinical benefit in sarcopenia.},
journal = {Aging clinical and experimental research},
volume = {38},
number = {1},
pages = {76},
pmid = {41680567},
issn = {1720-8319},
mesh = {Humans ; *Sarcopenia/microbiology/therapy/physiopathology ; *Gastrointestinal Microbiome/physiology ; Probiotics/therapeutic use ; Aged ; Muscle Strength ; },
abstract = {We read the recent systematic review and meta-analysis on nutrition-based, gut microbiota-targeted interventions for sarcopenia in older adults with great interest. While the evidence suggests that probiotics and fiber-enriched diets may improve surrogate outcomes such as muscle strength and gait speed, we highlight two priorities to strengthen future mechanistic and clinical translation. First, microbiome measurements in existing trials are often limited to genus-level taxonomic shifts, which can be biologically misleading because a single genus may include members with divergent immunomodulatory properties. Even species-level profiling may be insufficient, as strains within the same species can differ markedly in genetic content and metabolic capacity. Moreover, taxonomic composition does not necessarily reflect functional output due to functional redundancy across microbial communities. We therefore recommend transitioning to whole-genome shotgun metagenomics to enable strain-level resolution and functional profiling, allowing investigators to quantify pathways and metabolites relevant to muscle preservation, including short-chain fatty acids and vitamin biosynthesis. Second, we argue that improvements in sarcopenia-defining parameters should be linked to patient-centered clinical benefit. Future randomized controlled trials should be adequately powered to assess hard endpoints, including falls, fractures, hospitalization rates, and functional independence, alongside muscle mass and performance measures, to establish whether microbiota modulation delivers meaningful reductions in healthcare burden.},
}
@article {pmid41679837,
year = {2026},
author = {Sacco, O and Johansen, EL and Tian, Y and Holck, J and Kirkensgaard, JJK and Blennow, A and De Lise, F and Shaikh-Ibrahim, A and Moracci, M and Curci, N and Svensson, B and Cobucci-Ponzano, B and Wang, Y},
title = {Biochemical characterisation of the 4-α-glucanotransferase from the hyperthermophilic archaeon Pyrobaculum arsenaticum and its formation of high-amylose resistant starch.},
journal = {Carbohydrate polymers},
volume = {378},
number = {},
pages = {124919},
doi = {10.1016/j.carbpol.2026.124919},
pmid = {41679837},
issn = {1879-1344},
mesh = {*Glycogen Debranching Enzyme System/metabolism/chemistry ; *Amylose/chemistry/metabolism ; *Pyrobaculum/enzymology ; *Starch/chemistry ; Hot Temperature ; Hydrolysis ; Hydrogen-Ion Concentration ; },
abstract = {High-amylose starch (HAS) is gaining attention in biotechnology for its thermal stability, structural resilience and health benefits. Its dense crystalline structure hinders hydrolysis by human gut enzymes, making it a promising source of type 2 resistant starch for hydro-thermal and enzymatic upgrading. 4-α-Glucanotransferases (4αGTs) of glycoside hydrolase family 77 catalyse disproportionation of α-1,4-glucan chains in HAS, enhancing functionality and nutritional properties. Here, a 4αGT, ParGT from the hyperthermophilic archaeon Pyrobaculum arsenaticum, identified in a metagenomic dataset from Pisciarelli hot spring (85 °C, pH 5.5; Naples, Italy), showed highest activity at 100 °C and pH 5.5, and specific activity of maltotriose disproportionation at 75 °C of 1170 U/mg. ParGT effectively modified HAS granules under controlled heating (annealing) at 75 °C, altering crystallinity, surface order and chain length. Comparative analysis of native, heat-treated and ParGT-modified HAS granules from wheat, potato, maize, and barley revealed distinct effects of botanical source, enzymatic modification, and heating. Notably, ParGT increased the resistant starch (RS) contents in wheat and potato HASs subjected to in vitro digestion. Interfacial kinetics correlated the increased resistance to decreased density of glucoamylase attack sites. Overall, ParGT showed strong potential in enzyme- and hydro-thermal modifications developing starch-based ingredients for health and food applications.},
}
@article {pmid41679819,
year = {2026},
author = {Ding, Y and Li, X and Hao, Y and Ding, P and Chen, N and Luo, L and Wan, C and Wu, M},
title = {Structural elucidation and effects on gut microbiota of soluble galactans from edible Boletus.},
journal = {Carbohydrate polymers},
volume = {378},
number = {},
pages = {124886},
doi = {10.1016/j.carbpol.2026.124886},
pmid = {41679819},
issn = {1879-1344},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Galactans/chemistry/pharmacology/isolation &amp; purification ; Fermentation ; *Agaricales/chemistry ; Molecular Docking Simulation ; Fatty Acids, Volatile/metabolism ; Prebiotics ; },
abstract = {Edible Boletus mushrooms hold considerable development potential due to their exceptional nutritional and biological profiles. This study characterized two novel galactans, NBP and BRP, extracted from Neoboletus brunneissimus and Butyriboletus roseoflavus, respectively. Structural analysis revealed that both NBP and BRP possess a backbone composed of α-1,6-linked galactopyranosyl residues substituted at O-2, with structural diversity arising from variations in the side-chain substituents. Although both polysaccharides exhibit low viscosities, BRP forms a shear-stable elastic gel network, contrasting with the predominantly linear structure of NBP. In vitro fermentation demonstrated that both galactans markedly promoted the proliferation of beneficial probiotics, optimized gut microbiota composition, and enriched butyrate-producing bacteria including Faecalibacterium prausnitzii. Furthermore, they stimulated the production of lactic acid and short-chain fatty acids (SCFAs), leading to a reduction in fermentation pH and thereby modulating microbial ecology and host energy metabolism. Metagenomic annotation revealed that galactan degradation was driven by glycoside hydrolases (GHs) from Bacteroidaceae, and molecular docking analyses indicated that these GHs exhibit distinct binding preferences for specific structural regions of the polysaccharides. These results explain the basis for the microbiota-dependent improvement of gut health by Boletus galactans, providing a theoretical foundation for their development as precision prebiotics.},
}
@article {pmid41678593,
year = {2026},
author = {Chen, HC and Tang, TWH and Pasaribu, SNN and Wu, DC and Rey, FE and Hsieh, PCH},
title = {Gut-Heart Axis in Myocardial Repair: Mechanisms, Cross-Organ Networks, and Therapeutic Opportunities.},
journal = {Circulation research},
volume = {138},
number = {4},
pages = {e326978},
pmid = {41678593},
issn = {1524-4571},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Myocardium/metabolism/pathology ; *Regeneration ; *Heart/physiology ; },
abstract = {Cardiovascular diseases remain the leading global cause of morbidity and mortality, placing an escalating burden on health care systems and economies. While the gut microbiota is well recognized in atherosclerosis and cardiometabolic disorders, its influence on myocardial injury, repair, and regeneration is only beginning to emerge. Growing evidence reveals that gut microbes and their metabolites regulate myocardial health through intricate cross-organ networks, including the gut-brain-heart, gut-liver-heart, and gut-lung-heart axes. These findings suggest that the heart plays a key role in systemic host-microbe communication. Advances in metagenomics, metabolomics, and single-cell transcriptomics are now defining the molecular and cellular pathways by which microbial metabolites modulate immune tone, endothelial integrity, metabolic resilience, and cardiomyocyte survival. Studies in gnotobiotic models have established causal links between specific microbial taxa and myocardial outcomes while illuminating their roles in fibrosis resolution, angiogenesis, and regeneration. In this review, we synthesize current knowledge on the bidirectional gut-heart dialogue, emphasizing immunometabolic signaling, cross-organ integration, and regenerative mechanisms. We propose that coupling high-resolution multiomics with mechanistic modeling in controlled microbial systems will be pivotal for next-generation, microbiota-informed diagnostics, and therapeutics. We explore the emerging role of the gut-myocardium axis as both a driver of disease and as a promising modifiable therapeutic target and highlight a new frontier in precision cardiovascular medicine, with the potential to transform strategies for prevention, repair, and tissue regeneration.},
}
@article {pmid41677732,
year = {2026},
author = {Dos Santos, LCRM and de Almeida, JDR and de Sousa, NSO and Fernandes, FDS and Ennes, JFV and Frickmann, H and de Souza, JVB and de Souza, &#xc9;S},
title = {Amazonian Fungal Diversity and the Potential of Basidiomycetes as Sources of Novel Antimicrobials.},
journal = {Biology},
volume = {15},
number = {3},
pages = {},
pmid = {41677732},
issn = {2079-7737},
support = {EDITAL N. 020/2024 - PRODUTIVIDADE EM CT&amp;I//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Amazonas/ ; CNPq/MCTI Universal Call No. 10/2023//National Council for Scientific and Technological Development/ ; },
abstract = {The Amazon Forest harbors one of the largest fungal diversities on the planet, occupying a wide variety of ecological niches comprising terra firme (non-flooded forest), várzea (white-water floodplains), and igapó (black-water floodplains). In this review article, we examine Amazonian fungal diversity based on three complementary approaches-culture-based surveys, in situ inventories of macrofungi, and environmental DNA/metagenomic analyses-discussing advances, limitations, and contributions to regional mycological knowledge. Subsequently, we present a critical synthesis of the potential of Amazonian basidiomycetes regarding the production of metabolites with antimicrobial activity, highlighting the main genera reported in the literature, the chemical classes involved (e.g., terpenes, steroids, quinones, and bioactive peptides), and the metabolic pathways responsible for their biosynthesis. The integration between biodiversity and bioprospecting underscores the importance of Amazonian fungi both for understanding ecological processes and for the development of new solutions to the antimicrobial resistance challenge. This work seeks to fill current gaps in the academic literature and to contribute to future strategies for the conservation and sustainable use of regional mycobiota.},
}
@article {pmid41674272,
year = {2026},
author = {Macey, MC and Mahnert, A and Stephens, BP and Kucukkilic-Stephens, E and Olsson-Francis, K},
title = {An ensemble binning approach to identify functional diversity in cleanroom environments.},
journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
volume = {384},
number = {2314},
pages = {},
doi = {10.1098/rsta.2024.0438},
pmid = {41674272},
issn = {1471-2962},
support = {//UK Space Agency/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Metagenome ; *Environment, Controlled ; Spacecraft ; },
abstract = {Cleanroom environments, crucial for spacecraft assembly, are subject to stringent sterilization protocols to minimize microbial contamination. However, tolerant microbes can persist and pose a potential risk for planetary protection. This study employs an ensemble binning approach, integrating multiple metagenome binning programs, to analyse published metagenomic datasets generated from NASA cleanrooms to investigate functional diversity within cleanrooms. Twenty-six medium and high-quality, non-redundant metagenome-assembled genomes (MAGs) spanning six bacterial phyla were generated. Functional analysis of these MAGs identified potential metabolic pathways for the degradation of commonly used cleaning agents, suggesting that these compounds could serve as carbon sources. Furthermore, genomic analyses identified diverse physiological tolerances, with many MAGs possessing polyextremophilic traits, including resistance to high salinity, temperature and alkalinity. Growth rate index (GRiD) analysis also suggested some MAGs were actively replicating within the cleanroom environments. This study demonstrates the power of ensemble binning in revealing the functional diversity and adaptive strategies of cleanroom microbiomes and provides critical insights for refining planetary protection protocols. This article is part of the theme issue 'Planetary Protection for sustainable space exploration'.},
}
@article {pmid41674065,
year = {2026},
author = {Jo, S and Seo, H and Lee, KA and Kim, S and Rahim, MA and Barman, TI and Kim, HS and Song, HY},
title = {Skin Microbiome Profiling in Patients with Primary Sjögren Disease Compared to Healthy Individuals.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2510010},
pmid = {41674065},
issn = {1738-8872},
mesh = {Humans ; *Sjogren's Syndrome/microbiology ; *Skin/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Female ; Middle Aged ; Male ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; DNA, Bacterial/genetics ; Aged ; Biodiversity ; Case-Control Studies ; Sequence Analysis, DNA ; Skin Microbiome ; },
abstract = {Primary Sjögren disease (SjD) is a systemic autoimmune disease characterized by inflammation of exocrine glands, most commonly leading to dry mouth and dry eyes. Although the etiology of SjD remains unclear, emerging evidence suggests that the microbiome modulates immune homeostasis. This study aimed to compare the skin microbiomes of SjD patients with those of healthy controls (HCs) using 16S rRNA gene sequencing. Taxonomic composition, alpha and beta diversity, and predicted functional profiles were evaluated. We observed a significant depletion of Cutibacterium and a marked reduction in microbial diversity in SjD patients. Beta diversity analyses revealed distinct clustering among groups. Functional prediction suggested the downregulation of metabolic pathways associated with microbial homeostasis. Our findings propose that alterations in the skin microbiota may contribute to SjD pathogenesis and serve as potential biomarkers or therapeutic targets.},
}
@article {pmid41673713,
year = {2026},
author = {Touchette, D and Michoud, G and Boutroux, M and Gonzalez Mateu, M and Baier, F and Altshuler, I and Peter, H and Battin, TJ},
title = {Experimental insights in taxon-specific functional responses to droughts in glacier-fed stream biofilms.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {65},
pmid = {41673713},
issn = {2049-2618},
support = {197325/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Biofilms/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Droughts ; *Microbiota ; *Rivers/microbiology ; Metagenomics/methods ; Metagenome ; Switzerland ; Diatoms/genetics ; Viruses/classification/genetics/isolation &amp; purification ; Cyanobacteria/genetics/classification ; },
abstract = {BACKGROUND: Glacier-fed streams are predicted to face increasingly frequent and intense droughts. However, the impacts of drought events on benthic biofilm, including bacteria, eukaryotes, and viruses, the dominating life form in glacier-fed streams, remain poorly understood.<br><br>RESULTS: Using streamside flume mesocosms in the Swiss Alps, we grew glacier-fed stream biofilms over 103&#xa0;days and exposed them to three droughts. Using a multi-omics approach (metagenomics, metatranscriptomics, and metaproteomics), we assessed the effects of a series of droughts on the taxonomy and metabolic activity of bacterial, eukaryotic, and viral metagenome-assembled genomes (MAGs). We found that the first drought (6&#xa0;h) caused only minor changes, including mild upregulation of heterotrophic metabolism and signs of stress in diatoms. In contrast, the second drought (24&#xa0;h) significantly altered both the composition and functionality of the microbiome, shifting phototrophic dominance from diatoms to Cyanobacteriota, while maintaining overall phototropic biomass and further upregulating the heterotrophic metabolism. Interestingly, a third 24&#xa0;h drought had no detectable transcriptomic effect between pre- and post-drought conditions, suggesting a certain level of adaptive responses to droughts, but with the low diatom abundance being maintained.<br><br>CONCLUSIONS: These findings indicate that glacier-fed biofilm microorganisms initially resisted short-term drought, but a second longer drought caused important shifts in their community structure, activity, and function. Climate-induced increases in drought frequency or duration may therefore have a lasting impact on microbial ecosystem functioning in glacier-fed streams. Video Abstract.},
}
@article {pmid41672513,
year = {2026},
author = {Nishijima, S and Hattori, M and Nagata, N},
title = {The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.},
journal = {Proceedings of the Japan Academy. Series B, Physical and biological sciences},
volume = {102},
number = {2},
pages = {82-103},
doi = {10.2183/pjab.102.006},
pmid = {41672513},
issn = {1349-2896},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Japan ; *Health ; *Disease ; East Asian People ; },
abstract = {Metagenomics has become a powerful approach for deciphering the structure and function of the human gut microbiome, a complex microbial ecosystem in the gut. The human gut microbiome plays a crucial role in health and disease through multifaceted interactions with various factors, including age, diet, lifestyle, and medications. This review summarizes key advances in gut microbiome research over the past two decades and presents several topics from a recent large-scale, data-driven study, specifically a cohort-based initiative, the Japanese 4D microbiome project. These include a population-level characterization of the Japanese gut microbiome in a global context through comparison with 31,695 gut metagenomes from 37 countries, as well as an extensive analysis of the effects of medications. This review provides new insights into the ecology and uniqueness of the Japanese gut microbiome and highlights the importance of large-scale, well-phenotyped cohorts in advancing microbiome science.},
}
@article {pmid41671864,
year = {2026},
author = {Cui, W and Cui, Y and Hao, Y and Li, Y and Wang, Y and Liu, F and Long, J and Jin, Y and Chen, S and Duan, G and Yang, H},
title = {The effect of pet dog exposure on gut antibiotic resistome and microbiome of their owners.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141429},
doi = {10.1016/j.jhazmat.2026.141429},
pmid = {41671864},
issn = {1873-3336},
mesh = {Dogs ; Animals ; Humans ; *Gastrointestinal Microbiome/genetics ; *Pets/microbiology ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Adult ; Male ; Female ; Acinetobacter baumannii/genetics/drug effects ; Enterococcus faecium/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Pet dogs provide well-documented physical and mental health benefits to humans through close interactions. However, the potential role of pet dogs as reservoirs of antibiotic resistance genes (ARGs) and the impact on shaping the gut microbiomes of their owners remains poorly characterized. The growing dual challenges of global antimicrobial resistance and widespread pet ownership underscore the importance of understanding human-animal resistome interactions crucial for One Health solutions. Consequently, this study conducted a metagenomic analysis of pet dogs, dog owners, and non-dog owners to investigate the effects of dogs on the microbiota composition, ARGs profiles, and mobile genetic elements (MGEs) of the human gut. The results indicated that pet dogs exhibited significantly higher gut abundance of both ARGs and ESKAPE pathogens (Enterococcus faecium and Acinetobacter baumannii) compared to humans. Moreover, the abundance of aminoglycoside resistance genes aac(6')-Im and aac(6')-Ie-aph(2'')-Ia, tetracycline resistance genes tetO and tet40 were was significantly higher in dog owners than in non-dog owners. Enterobacteriaceae were identified as shared core ARG hosts in both dog and human guts. Collectively, our results indicate that cohabitation with pet dogs is associated with a shared gut resistome, reflecting correlated patterns of ARGs and resistant microbes. These findings emphasize the necessity of monitoring antibiotic resistance in companion animals, while maintaining the benefits of human-dog relationships.},
}
@article {pmid41671795,
year = {2026},
author = {Ji, J and Wang, Q and Hu, F and Yang, H and Li, Y and Wu, G and Dong, Y and Du, J and Li, H and Shen, B and Wang, B},
title = {Advantages of partial denitrification-anaerobic ammonium oxidation system under sulfamethoxazole stress: Adaptive mechanisms and synergistic metabolism.},
journal = {Bioresource technology},
volume = {446},
number = {},
pages = {134181},
doi = {10.1016/j.biortech.2026.134181},
pmid = {41671795},
issn = {1873-2976},
mesh = {*Denitrification/drug effects ; *Sulfamethoxazole/pharmacology ; *Ammonium Compounds/metabolism ; Oxidation-Reduction/drug effects ; Anaerobiosis/drug effects ; Nitrogen/metabolism ; Bioreactors/microbiology ; Microbiota ; },
abstract = {The widespread use of antibiotics has led to their persistence in aquatic environments, posing serious challenges to biological treatment systems. This study systematically compared the performance and adaptive mechanisms of partial denitrification (PD)/anaerobic ammonium oxidation (anammox) and single anammox systems under long-term sulfamethoxazole (SMX) stress over 193 days. At an influent SMX concentration of 3 mg/L, the PD/anammox system retained 75% of its initial total inorganic nitrogen (TIN) removal efficiency, significantly higher than that of the single anammox system (49%). The PD/anammox achieved an SMX degradation efficiency of 80%, substantially exceeding that of the single system (39%). Metagenomic analyses revealed higher abundances of key nitrogen metabolism genes (hzs, hdh, narG/H/I, napA/B, nirK/S) and SMX degradation genes (sadA, sadC, tmoABCDEF, dmpB/D) in the PD/anammox system. The enhanced performance was closely associated with the enrichment of the denitrifying microbiome (e.g., Thauera, Zoogloea, unclassified_f_Rhodocyclaceae), which provided a stable nitrite supply and carried SMX degradation genes. Both systems relied on extracellular polymeric substances (EPS) as a protective barrier under low SMX stress (1 mg/L). Under higher SMX concentrations (>1 mg/L), the PD/anammox system exhibited dynamic enrichment of sulfonamide resistance genes (sul1). These results demonstrated the superiority of the PD/anammox system over the single anammox system. The combined effects of a diverse microbiome, multi-level stress-response mechanisms involving EPS and antibiotic resistance genes, and efficient functional gene expression make PD/anammox a robust and promising technology for the treatment of antibiotic-containing wastewater.},
}
@article {pmid41670415,
year = {2026},
author = {Hasegawa, T and Iwai, S and Ikeda, HO and Miyaoka, D and Sato, N and Fujimoto, K and Wei, X and Kusaka, M and Miyata, M and Numa, S and Otsuka, Y and Imoto, S and Uematsu, S and Tsujikawa, A},
title = {Increased Gut Microbiota Diversity in Patients With Retinitis Pigmentosa and Implications for Disease Phenotypes and Progression.},
journal = {Investigative ophthalmology &amp; visual science},
volume = {67},
number = {2},
pages = {27},
pmid = {41670415},
issn = {1552-5783},
mesh = {*Gastrointestinal Microbiome/genetics/physiology ; Animals ; Humans ; *Retinitis Pigmentosa/microbiology/physiopathology ; Mice ; Female ; Male ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Disease Models, Animal ; Phenotype ; Adult ; Feces/microbiology ; Electroretinography ; Anti-Bacterial Agents/pharmacology ; Tomography, Optical Coherence ; Aged ; Mice, Inbred C57BL ; *Bacteria/genetics/isolation &amp; purification ; },
abstract = {PURPOSE: Inflammation is often present in retinitis pigmentosa (RP) and is reported to affect visual outcome. Gut microbiota plays a crucial role in inflammatory diseases. This study aimed to elucidate the relationship between the gut microbiota and RP.<br><br>METHODS: The 16S rRNA gene sequencing analysis was performed on stool samples collected from 103 patients with RP and 64 healthy individuals. The &#x3b1; and &#x3b2; diversities of gut microbiota, along with relative abundances, were compared between patients and healthy individuals, as well as between patients with or without cystoid macular edema (CME). The RP model rd10 mice were treated with or without antibiotics starting at 7 days of age. Retinal structure and function were evaluated.<br><br>RESULTS: Gut microbiota diversity was higher in patients with RP than in healthy individuals (P < 0.001). Moreover, patients with CME had greater diversity than did those without CME and showed a higher abundance of Romboutsia and Ruminococcus (P < 0.05). Antibiotics-treated rd10 mice showed suppressed apoptosis, attenuated decrease of photoreceptors, and a significantly lower incidence of retinal detachment. Retinal function was significantly preserved in mice treated with antibiotics. In antibiotics-treated mice, the expression of Il-1&#x3b2;, Nlrp3, Caspase-1, pNFkb, pJNK, and pCREB1 was downregulated, suggesting suppression of the NLRP3 inflammasome.<br><br>CONCLUSIONS: Patients with RP exhibited distinct gut microbiota characteristics compared to that of healthy individuals. Treatment with antibiotics attenuated disease progression in the RP model mouse. Modifying the gut microbiota may be a potential therapeutic strategy for modifying disease progression in RP in future investigations.},
}
@article {pmid41669550,
year = {2026},
author = {Bunyoo, C and Phonmakham, J and Morikawa, M and Thamchaipenet, A},
title = {Species-level profiling of Landoltia punctata (duckweed) microbiome under nutrient stress using full-length 16S rRNA sequencing.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20648},
pmid = {41669550},
issn = {2167-8359},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Araceae/microbiology ; *Bacteria/genetics/classification ; *Nutrients ; *Stress, Physiological ; Phylogeny ; Biodegradation, Environmental ; },
abstract = {Duckweed is a rapidly-growing aquatic plant utilized as food/feed and for wastewater remediation. It coexists with complex microbial communities that play crucial roles in its growth and capability for phytoremediation. In a previous study, microbiomes associated with four duckweed species (Spirodela polyrhiza, Landoltia punctata, Lemna aequinoctialis, and Wolffia globosa) grown under natural and nutrient-deficient conditions, were investigated using V3V4 16S rRNA sequencing. However, species-level classification was not achieved due to the partial 16S rRNA sequences obtained, restricting the selection of potential microbial species for further application. In this study, L. punctata samples from the previous work were investigated further by employing full-length 16S rRNA sequencing. A total of 31 predominant microbial species were identified. Under stress, the proportion of Proteobacteria increased significantly, along with potentially beneficial bacteria such as Roseateles depolymerans, Pelomonas saccharophila, Acidovorax temperans, Ensifer adhaerens and Rhizobium straminoryzae. Functional metagenomic predictions suggest that associated microbes adapt to stressors and may confer benefits to duckweed, including pathways related to host adhesion, biofilm formation, microbial growth modulation, and co-factors and vitamin biosynthesis. Furthermore, the study demonstrates both the advantages and limitations of full-length 16S rRNA amplicon sequencing. The findings provide more insight into L. punctata microbiomes at species-level, facilitating establishment of stable, beneficial microbial communities for duckweed applications. Ongoing investigations aim to isolate key microbial species from L. punctata and validate their roles through co-cultivation, along with establishing potential synthetic microbial communities based on the metagenomic findings.},
}
@article {pmid41668733,
year = {2025},
author = {Sui, Q and Yu, J and Cui, S},
title = {An oral microbiome model for predicting atherosclerotic cardiovascular disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1707599},
pmid = {41668733},
issn = {2235-2988},
mesh = {Humans ; Middle Aged ; Male ; Female ; Aged ; Retrospective Studies ; *Atherosclerosis/microbiology/diagnosis ; *Microbiota ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; ROC Curve ; Risk Factors ; Bacteria/classification/genetics/isolation &amp; purification ; *Cardiovascular Diseases/microbiology/diagnosis ; Metagenomics ; },
abstract = {OBJECTIVE: This study aimed to construct a predictive model for the early onset of atherosclerotic cardiovascular disease (ASCVD) by integrating oral microbiome data with traditional clinical risk factors.<br><br>METHODS: A retrospective study was conducted involving participants aged 50-70 years without pre-existing ASCVD. The patients were divided into a training set and a validation set at a ratio of 7:3 by the complete randomization method. The characteristics of the oral microbiome were characterized by 16S rRNA/metagenomic sequencing. In the training set, univariate analysis and multivariate Logistic regression analysis were applied to screen predictive variables, and Random Forest (RF), Gradient Boosting (GB), and K-nearest Neighbor (KNN) were constructed. The receiver operating characteristic (ROC) curve was validated. The model performance was evaluated by net reclassification improvement (NRI) and integrated discrimination improvement (IDI).<br><br>RESULTS: A total of 331 patients were enrolled and randomly divided into a training set (n=231) and a validation set (n=100). 40 out of 331 participants experienced major adverse cardiovascular events (MACE). Multivariate Logistic regression analysis confirmed that age, relative abundance of Fusobacterium nucleatum, Prevotella, Porphyromonas, Leptotrichia, Streptococcus and Actinomyces were significantly associated with ASCVD event risk (all P < 0.05). Three machine learning models (RF, GB, and KNN) were constructed, with the RF model achieving the highest predictive performance. The AUC values of the RF, GB, and KNN models in the training set were 0.888 (95% CI: 0.818-0.958), 0.823 (95% CI: 0.745-0.901), and 0.812 (95% CI: 0.727-0.898) respectively, and in the validation set were 0.845 (95% CI: 0.740-0.951), 0.746 (95% CI: 0.621-0.871), and 0.767 (95% CI: 0.647-0.887) respectively. Additionally, the integrated model showed significant improvements in net reclassification improvement (NRI = 0.315, P < 0.05) and integrated discrimination improvement (IDI = 0.227, P < 0.05) compared to traditional clinical models.<br><br>CONCLUSION: The integration of the oral microbiome and clinical data can improve the accuracy of the ASCVD risk prediction model, providing a novel biomarker strategy for primary cardiovascular prevention.},
}
@article {pmid41668731,
year = {2025},
author = {Gao, H and Li, J and Liu, L and Gu, Z and Yu, H and Xing, D and Zhao, T and Li, C},
title = {Multi-omics profiling reveals associations between gut microbiota and olfactory gene expression in mosquitoes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1745848},
pmid = {41668731},
issn = {2235-2988},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Culex/microbiology/genetics/physiology ; Metagenomics ; *Smell/genetics ; Gene Expression Profiling ; Arthropod Antennae/metabolism ; Transcriptome ; Computational Biology ; Multiomics ; },
abstract = {INTRODUCTION: The interplay between gut microbiota and host physiological processes has been extensively studied in vertebrates, where it plays a crucial role in regulating appetite, emotion, immunity, and other physiological functions. However, whether a similar regulatory mechanism exists in insects remains unclear, especially regarding the long-distance regulation of olfactory function. This study focused on three Culex subspecies (Culex quinquefasciatus, Culex pipiens pallens, and Culex pipiens molestus) that are closely related but exhibit significant differences in olfaction-dependent ecological habits. By integrating antennal transcriptomic and gut metagenomic data, we systematically analyzed the expression characteristics of olfactory-related genes, the structure of gut microbial communities, and their intrinsic associations.<br><br>METHODS: We integrated antennal transcriptomic and gut metagenomic sequencing to analyze olfactory-related gene expression, gut microbial community structure, and their intrinsic associations in male and female individuals of the three Culex subspecies. Bioinformatics analyses included differential gene screening, functional enrichment, microbial taxonomic annotation, and Spearman correlation analysis.<br><br>RESULT: The results showed that a large number of sex-specific and species-specific differentially expressed genes (DEGs) were identified in the antennae of the three Culex subspecies. Among these, 345 DEGs were shared sex-specific genes across species, which were significantly enriched in pathways such as odor binding, signal transduction, and xenobiotic metabolism. At the phylum level, the&#xa0;gut microbial composition was dominated by Proteobacteria, Bacteroidetes, and Firmicutes, showing a conserved structure; at the genus level, 11 dominant&#xa0;genera (including Wolbachia, Elizabethkingia, and Asaia) exhibited distinct species-specific distribution patterns. Diversity analysis revealed that&#xa0;the gut&#xa0;microbial richness of male individuals was significantly higher than that of&#xa0;females, and the &#x3b2;-diversity showed an obvious "sex clustering" pattern.Correlation analysis further indicated that 152 DEGs were significantly correlated with 107 microbial genera. Among them, olfactory-related genes were closely associated with several core genera (e.g., Wolbachia, Asaia, Serratia). Gut microbes may remotely regulate the expression and function of&#xa0;olfactory genes in antennae through metabolites or signaling molecules, thereby influencing mosquito behaviors such as host localization, mating, and oviposition.<br><br>DISCUSSION: This study reveal the intrinsic association between gut microbes and olfactory function in Culex mosquitoes, providing a new perspective for understanding the "microbe-host" cross-organ regulatory mechanism and laying a theoretical foundation for the development of novel mosquito vector control strategies based on microbial or olfactory interference.},
}
@article {pmid41667397,
year = {2026},
author = {Le Bastard, Q and Gschwind, R and Lao, J and Vibet, MA and Batard, E and Corvec, S and Montassier, E and Ruppé, E},
title = {Pre-existing β-lactamase gene diversity is associated with lower risk of ESBL-producing Enterobacterales colonization in patients exposed to ceftriaxone.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2627692},
pmid = {41667397},
issn = {1949-0984},
mesh = {Humans ; *Ceftriaxone/therapeutic use/pharmacology ; *beta-Lactamases/genetics/metabolism ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Male ; Female ; Middle Aged ; Prospective Studies ; *Gastrointestinal Microbiome/drug effects ; *Enterobacteriaceae Infections/microbiology/drug therapy ; Aged ; *Enterobacteriaceae/genetics/drug effects/enzymology/isolation &amp; purification ; Genetic Variation ; Adult ; Rectum/microbiology ; },
abstract = {Exposure to broad-spectrum antibiotics, particularly to third-generation cephalosporins (3GC), increases the risk of colonization by extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E). While clinical risk factors for ESBL-E acquisition are well established, the role of the gut microbiome and resistome remains unclear. We conducted a prospective study of patients with suspected bacterial infections receiving ceftriaxone to identify microbiome and resistome features associated with ESBL-E acquisition. Rectal samples collected before antibiotic administration, during treatment, and 30 d after initiation were analyzed by shotgun metagenomic sequencing. Among 80 patients, 12 (15%) acquired ESBL-E colonization by day 30. Ceftriaxone exposure induced a profound and sustained reduction in microbial richness and diversity across all patients. However, no specific taxonomic signature predicted subsequent ESBL-E colonization. In contrast, patients who did not acquire ESBL-E displayed a significantly richer and more diverse repertoire of β-lactamase-encoding genes at baseline, which was independently associated with protection against colonization. Moreover, patients exposed to multiple antibiotics experienced greater and more sustained microbiome disruption compared with those receiving ceftriaxone alone. These findings provide the first real-world evidence that pre-existing β-lactamasome diversity may confer ecological protection against antibiotic-driven colonization by ESBL-E in infected patients, highlighting the importance of functional resistome diversity over taxonomic composition in colonization resistance.},
}
@article {pmid41666847,
year = {2026},
author = {Matijašević, D and Kljajević, N and Malešević, M and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K},
title = {Heating-season dynamics of the airborne microbiome, resistome and mobilome in Belgrade, Serbia.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110114},
doi = {10.1016/j.envint.2026.110114},
pmid = {41666847},
issn = {1873-6750},
mesh = {Serbia ; *Microbiota ; Seasons ; *Air Microbiology ; Environmental Monitoring ; Air Pollution/statistics &amp; numerical data ; *Drug Resistance, Microbial/genetics ; *Air Pollutants/analysis ; },
abstract = {Antimicrobial resistance (AMR) and air pollution are critical global health challenges, but their interplay remains poorly understood, particularly in Europe. Serbia, characterized by extensive antibiotic use, high prevalence of multidrug-resistant isolates and severe air pollution, provides a relevant model to study airborne AMR dissemination. During the heating season, air samples were collected at eight locations in Belgrade, representing industrial, traffic loaded and background environments. Shotgun metagenomics, co-occurrence networks and NMDS ordinations were applied to investigate the relationships between atmospheric pollutants, antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and mobile genetic elements (MGEs). Autumn microbiomes were dominated by Lactococcus spp., whereas winter lacked such dominance. ARGs associated with antibiotic inactivation accounted for > 50% in autumn and > 75% in winter, with β-lactam resistance (blaTEM) predominating in both seasons. Winter resistomes also showed more consistent patterns of BRGs and MRGs, with multibiocide/acid and multimetal resistance prevailing. Integron analysis revealed predominance of class 1 integrons (intI1) commonly associated with Escherichia coli. Plasmid-related contigs were most similar to sequences reported in Acinetobacter baumannii and E. coli, while plasmid signatures related to Lactococcus lactis were also detected in autumn. Crucially, the network analysis revealed a seasonal restructuring of the airborne resistome. Autumn networks displayed fragmented structure, showing antagonism between Lactococcus and Escherichia, whereas winter networks coalesced into a densely interconnected superhub that could facilitate horizontal gene transfer and co-selection of resistance determinants. These findings suggest that prolonged air pollution and seasonality jointly shape airborne resistomes, reinforcing the need for integrated environmental and AMR surveillance in highly polluted urban areas.},
}
@article {pmid41666834,
year = {2026},
author = {S, H and A, P},
title = {Insights into microbial carbon sequestration mechanisms in the Eastern Arabian Sea using metagenomic analysis.},
journal = {Marine environmental research},
volume = {216},
number = {},
pages = {107903},
doi = {10.1016/j.marenvres.2026.107903},
pmid = {41666834},
issn = {1879-0291},
mesh = {*Carbon Sequestration ; *Seawater/microbiology ; Seasons ; Metagenomics ; *Microbiota ; Bacteria ; *Environmental Monitoring ; Cyanobacteria ; *Water Microbiology ; },
abstract = {This investigation elucidated how depth- and season-dependent environmental gradients shape microbial community composition, metabolic potential, and carbon sequestration pathways in the Eastern Arabian Sea (EAS). The study encompassed six stations (L1-L6) spanning coastal to offshore regimes, three depth zones (surface, 200 m, and 1000 m), and three monsoonal phases: Spring Inter-Monsoon (SIM), Summer Monsoon (SM), and Winter Monsoon (WM). A total of 10,500 taxa were identified across all samples. Alpha-diversity indices showed peak diversity during the SM and SIM periods. Across all depths, Pseudomonadota (53.2 ± 16.2%) remained the dominant phylum, underscoring its broad ecological adaptability. Cyanobacteria (31.3 ± 19%) were abundant in surface waters during SIM and WM, but declined sharply with depth (<2%), where Actinomycetota dominated (25 ± 16%), highlighting strong vertical niche portioning. Distinct seasonal restructuring was evident, particularly during the SM, when upwelling-driven nutrient enrichment resulted in a marked decline in Cyanobacteria and a concomitant increase in copiotrophic taxa such as Rhodobacterales, Flavobacteriales, Pseudomonadales, and Oceanospirillales, indicative of intensified heterotrophic processing of organic matter. In contrast, oligotrophic taxa (Pelagibacterales, Prochlorococcus, Synechococcus) prevailed during SIM and WM, suggesting nutrient-limited and microbially driven carbon cycling. Remarkably, even deep-water communities (200-1000 m) exhibited significant seasonal restructuring (p < 0.05), with Alteromonadales and Oceanospirillales enriched during SM and Sphingomonadales and Rhodobacterales dominating during WM, indicating active coupling between surface productivity and deep microbial assemblages. Functional analyses revealed pronounced depth-dependent stratification of metabolic potential (p < 0.05) reflecting shifts from growth-oriented processes in surface waters to adaptive and recycling strategies at depth. Collectively, these findings reveal robust monsoon-driven and depth-stratified microbial dynamics in the EAS and provide novel evidence inferred based on microbial community structure and functional potential that both the Biological Carbon Pump and the Microbial Carbon Pump operate concurrently across this climatically sensitive and highly productive region.},
}
@article {pmid41666549,
year = {2026},
author = {Kang, X and Zhao, Z and Zhu, X and Ju, F},
title = {Uncovering plasticizer-degrading potential in landfill microbiomes with curated PzDE-HMM database and multi-scale validation from isolates to synthetic consortia.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141398},
doi = {10.1016/j.jhazmat.2026.141398},
pmid = {41666549},
issn = {1873-3336},
mesh = {*Plasticizers/metabolism ; *Microbiota ; Biodegradation, Environmental ; Waste Disposal Facilities ; *Bacteria/genetics/metabolism ; Phthalic Acids/metabolism ; },
abstract = {Plasticizers are widely used additives that leach from plastic products and accumulate in landfills, yet the microbial functions supporting their degradation remain poorly resolved. Here, we combined curated functional annotation, substrate-driven enrichment, and isolate-level validation to dissect plasticizer degradation in landfill microbiomes. A plasticizer-degrading enzyme (PzDE) hidden Markov model database (PzDE-HMM) was assembled from 49 experimentally validated enzyme families. It was applied to metagenomes from five landfill niches, identifying 2219 candidate plasticizer-degrading genes, which is 3.6- and 19-fold more than those identified by KofamScan- and BLASTp-based annotation methods, respectively. Enrichment with three legacy phthalates (DEHP, DIDP, DBP) and three non-phthalate plasticizers (DOTP, DOA, ATBC) drove pronounced shifts in landfill microbial communities and functional gene repertoires, revealing coexisting broad-spectrum and substrate-specific degraders. Culture-based isolation from enriched media yielded 51 strains, and three representative isolates showed concordance between PzDE-HMM-predicted gene repertoires, substrate breadth, and degradation ability. Synthetic consortia assembled from these strains exhibited complementary degradation capacities and achieved higher removal of several plasticizers than the best single strains, illustrating how complementary gene sets can be combined to enhance multi-substrate degradation. Together, PzDE-HMM annotation workflow and this multilevel prediction-enrichment-isolate-consortium framework uncover the plasticizer-degrading and bioremediation potential of landfill microbiomes and provide a reusable resource and workflow for future plasticizer-focused microbiome studies.},
}
@article {pmid41665263,
year = {2026},
author = {Hutchinson, TF and Holland, SR and Clarke, DA and Ricci, F and Jirapanjawat, T and Leung, PM and Lappan, R and Liu, WPA and Bay, SK and Bliss, A and McGeoch, MA and Chown, SL and Greening, C},
title = {Resilient Antarctic soil bacteria consume trace gases across wide temperature ranges.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag020},
pmid = {41665263},
issn = {1751-7370},
abstract = {Polar desert soils host diverse microbial communities despite limited nutrients and frequent temperature and light fluctuations. Adapting to these extremes, most bacteria possess high-affinity hydrogenases and carbon monoxide dehydrogenases, enabling them to use atmospheric trace gases such as hydrogen (H2) and carbon monoxide (CO) to generate energy and fix carbon (aerotrophy). Despite the foundational importance of this process in polar desert ecosystems, little is known about the thermal sensitivity of trace gas oxidation or how this process will respond to climate warming. Here, we show through in situ and ex situ incubations that H2 consumption is an exceptionally thermally resilient process that can occur from -20 to +75°C, at rates comparable to temperate ecosystems (peaking at 8.56 nmol H2 h-1 g dry soil-1 at 25°C). Temperature ranges of CO (-20 to 42°C) and methane (CH4; -20 to 30°C) oxidation are also wider than expected, though thermal sensitivity patterns conform with general theory. Metagenomic analyses, including generation of 554 medium- to high-quality metagenome-assembled genomes, support these data, revealing that aerotrophs are widespread, diverse, and abundant, and suggesting most Antarctic bacteria function below their temperature optima for these processes. Modelling of seasonal temperatures across ice-free Antarctica under current and future emissions scenarios indicates that H2 and CO oxidation can occur year-round, increasing by up to 35% or 44%, respectively, by 2100. Our results indicate constitutive aerotrophic activity contributing to Antarctic ecosystem functioning and biodiversity across spatial and temporal scales, with further studies required to understand how it interacts with photosynthesis in a changing climate.},
}
@article {pmid41664936,
year = {2026},
author = {Shaikh-Ibrahim, A and De Lise, F and Curci, N and Gargano, M and Sacco, O and Di Fenza, M and Moracci, M and Cobucci-Ponzano, B},
title = {A Hyperthermostable Archaeal GH78 Rhamnosidase Efficiently Hydrolyzes Flavonoid Glycosides for Juice Debittering.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {6},
pages = {5562-5574},
pmid = {41664936},
issn = {1520-5118},
mesh = {*Glycoside Hydrolases/chemistry/genetics/metabolism ; *Flavonoids/chemistry/metabolism ; *Glycosides/chemistry/metabolism ; Enzyme Stability ; *Fruit and Vegetable Juices/analysis ; Hydrolysis ; *Archaeal Proteins/chemistry/genetics/metabolism ; *Archaea/enzymology/genetics/chemistry ; Hot Temperature ; Hydrogen-Ion Concentration ; Substrate Specificity ; Hot Springs/microbiology ; },
abstract = {α-L-Rhamnosidases are a class of glycosyl hydrolases (GHs) that catalyze the hydrolysis of terminal α-L-rhamnose residues from diverse glycoconjugates. While extensively characterized in bacterial and fungal sources, no archaeal α-L-rhamnosidases have been characterized to date. Herein, we report the identification and characterization of the first thermostable archaeal α-L-rhamnosidase (ArRha), derived from the metagenomic data set of Pisciarelli solfatara hot spring. ArRha, classified in glycoside hydrolase family GH78, efficiently hydrolyzes α-1,2 and α-1,6 rhamnosyl linkages in flavonoid glycosides with notable biological activities. The novel enzyme showed remarkable temperature stability, wide-range pH activity, organic solvent tolerance, and no metal dependence. Combined with a thermostable β-glucosidase, ArRha converts naringin to prunin and naringenin in sweet and blood orange juices, achieving >95% conversion within 2 h at 65 °C. This represents the first report of a hyperthermostable archaeal GH78 α-L-rhamnosidase with promising applications in industrial enzymatic juice debittering and sustainable flavonoid biotransformation.},
}
@article {pmid41664657,
year = {2026},
author = {Chuckran, PF and Blazewicz, SJ and Ceja-Navarro, JA and Pett-Ridge, J and Schwartz, E and Dijkstra, P},
title = {The relationship between gene traits and transcription in soil microbial communities varies by environmental stimulus.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20641},
pmid = {41664657},
issn = {2167-8359},
mesh = {*Soil Microbiology ; *Transcription, Genetic ; *Microbiota/genetics ; Glucose/metabolism ; Codon Usage ; Carbon/metabolism ; },
abstract = {Codon and nucleotide frequencies are known to relate to the rate of gene transcription, yet how these traits shape transcriptional profiles of soil microbial communities remains unclear. Here we test the prediction that functional genes with high codon optimization and energetically lower cost nucleotides (i.e., nucleotides requiring less adenosine triphosphate (ATP) for synthesis) have higher transcriptional expression in a soil microbial community. In laboratory incubations, we subjected an agricultural soil to two separate short-term environmental changes: labile carbon (glucose) addition or a sudden 30-min increase in temperature from 20 °C to 60 °C. Using the total genomic codon frequencies to predict preferred codon usage for each taxon, we then estimated codon optimization for each transcript. On the community level, we found a higher average level of codon optimization after the addition of glucose. Synonymous nucleotide composition in the transcript pool also shifted towards energetically cheaper nucleotides, favoring uracil (U) over adenine (A) and cytosine (C) over guanine (G). Similarly, we found that encoded amino acid usage shifted towards energetically cheaper amino acids in response to labile carbon. In contrast, in communities responding to heat shock, there were no significant differences in the averaged gene traits of expressed transcripts. We used metagenome-assembled-genomes to further examine the ability of gene traits to predict transcriptional responses within and between taxa. We found that traits of individual genes could not reliably predict the level of transcription of a gene within or between taxa-highlighting the limits of this approach. However, we did find that when traits were averaged across several related genes, codon optimization was able to predict levels of transcription in metabolic pathways associated with growth and nutrient uptake in response to glucose. Similar relationships were not observed in response to heat, or for functions associated with stress-such as genes associated with sporulation or heat shock. These results demonstrate that gene traits, such as codon usage, nucleotide selection, and amino acid selection, relate to the transcriptional expression of genes in soil microbial communities and suggests that these relationships may be dependent on both gene function and the specific type of environmental stimuli.},
}
@article {pmid41660616,
year = {2025},
author = {Liu, H and Liang, L and Wang, C and Luo, R and Luo, Q and Huang, C},
title = {Gut mycobiota dysbiosis and an emergent state of "co-dysbiosis" are associated with IgE sensitization in children with comorbid allergic rhinitis and constipation.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1745580},
pmid = {41660616},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; Child ; *Rhinitis, Allergic/immunology/microbiology/epidemiology ; *Immunoglobulin E/immunology/blood ; *Gastrointestinal Microbiome/immunology ; Female ; Male ; Child, Preschool ; *Constipation/immunology/microbiology/epidemiology ; Case-Control Studies ; *Fungi/immunology ; Comorbidity ; Pilot Projects ; *Mycobiome/immunology ; Metagenomics ; },
abstract = {BACKGROUND: The comorbidity of allergic rhinitis (AR) and functional constipation (FC), termed ARFC, implies shared gut-immune pathways. Although bacterial dysbiosis has been implicated, the role of the gut mycobiota (fungal community) in this specific comorbidity remains unexplored.<br><br>METHODS: This pilot case-control study characterized the gut mycobiota in 19 ARFC and 17 healthy control (HC) children aged 3-6 years using metagenomic sequencing. Fungal community structure, taxonomic composition, and correlations with IgE levels were analyzed. Cross-kingdom bacterial-fungal interaction networks were constructed, and functional potential was predicted.<br><br>RESULTS: Alpha diversity was comparable, whereas beta diversity revealed significant structural shifts in the ARFC gut mycobiota. Key immunomodulatory fungi, including Cenococcum, Dentiscutata, Ambispora, and Saccharomyces, were markedly depleted in ARFC. These taxa served as top discriminators in random forest models and exhibited significant inverse correlations with total and allergen-specific IgE levels. Cross-kingdom network analysis identified dramatic ecological restructuring: the HC network was characterized by prevalent competitive interactions, whereas the ARFC network shifted exclusively to positive correlations, a state termed "co-dysbiosis." No significant differences were observed in predicted KEGG functional pathways.<br><br>CONCLUSION: This study provides the first evidence that gut mycobiota dysbiosis-marked by depletion of immunoregulatory fungi and an ecological shift toward cooperative interkingdom interactions ("co-dysbiosis")-is associated with IgE sensitization in ARFC children. These findings position the gut mycobiota as a novel element of the gut-nose axis in allergic disease, warranting further investigation.},
}
@article {pmid41660426,
year = {2026},
author = {Wang, S and Yang, Y and Lei, L and Wan, R and Su, Z and Liu, Y and Tang, H and Hu, G and Li, C and Li, C and Meng, J and Yang, K},
title = {SSTDhunter: a curated gene database for investigating androgen producing potential in microbiota species.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1754671},
pmid = {41660426},
issn = {2235-2988},
mesh = {*Androgens/biosynthesis/metabolism ; *Databases, Genetic ; Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Transketolase/genetics/metabolism ; *Clostridium/genetics/enzymology/metabolism ; *Microbiota ; Prostatic Neoplasms ; },
abstract = {Androgens are critical for the growth of prostate cells, as well as prostate tumor cells. For prostate cancer patients under Androgen Deprivation Therapy (ADT) such as castration treatment, investigating the potential for androgen production by gut microbes is crucial. In microbe species, the side chain cleavage activity of steroid-17, 20-desmolase (SSTD) is responsible for 11-oxy-androgens production by biotransformation from cortisol, as well as from other endogenous steroids and pharmaceutical glucocorticoids. The side-chain cleavage product of prednisone could significantly promote the proliferation of prostate cancer cells. The SSTD is a complex formed by N-terminal and C-terminal transketolases encoded by desA and desB genes, whose activity has been well-characterized in Clostridium scindens ATCC 35704. While a void still existed in evaluating the androgen producing potential by gut microbiota owing to relatively low abundance of SSTD-carrying species and the lack of professional gene database. Meanwhile, mining SSTD encoding genes in explosion sequencing data has become computationally expensive and time-consuming using comprehensive database. Here, a professional database consisted of SSTD-coding genes, named SSTDhunter, was constructed using a large-scale genomic analysis along with homologous genes as background. These SSTD-coding genes were reconstruction through comprehensive characteristics consisted of operon structures, sequence identities, phylogenetic topologies and comparative analysis. To reduce false positives, protein sequences of homologous genes tktA, which encode component of sugar transketolase, were also included in SSTDhunter database as background noise. SSTDhunter is for rapid investigation of SSTD-coding genes in massive metagenomic data, which is freely available at http://www.orgene.net/SSTDhunter/.},
}
@article {pmid41651389,
year = {2026},
author = {Shi, B and Zhang, L and Jia, X and Tao, Y and Wang, M},
title = {Profiles of gut microbiome in Litopenaeus vannamei artificially infected with Vibrio parahaemolyticus causing translucent post-larva disease.},
journal = {Developmental and comparative immunology},
volume = {176},
number = {},
pages = {105565},
doi = {10.1016/j.dci.2026.105565},
pmid = {41651389},
issn = {1879-0089},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Vibrio parahaemolyticus/physiology ; *Penaeidae/microbiology/immunology ; *Vibrio Infections/immunology/microbiology ; Virulence ; Host-Pathogen Interactions ; },
abstract = {As the primary defense against pathogen invasion, the dynamic equilibrium of the shrimp gut microbiome is recognized as a critical factor influencing pathogen colonization. In recent years, translucent post-larva disease (TPD) outbreaks during the early stages of shrimp farming have become a serious threat to the sustainable development of the shrimp industry. Compared with other vibriosis, TPD caused by certain Vibrio strains possessing drug resistance and high-virulence genes exhibits greater virulence in shrimp tissues, with mortality rates reaching up to 90%. However, no studies have yet explored the association between this pathogen and the gut microbiome. This study employed metagenomic sequencing technology to analyze differences in the axial distribution of the gut microbiome in shrimp at varying degrees of TPD infection. Histopathological sections revealed that multiple tissue lesions induced by TPD infection in shrimp were primarily concentrated in the midgut. Alpha diversity analysis indicated that the alpha diversity index of the shrimp gut microbiome showed an upward trend as pathogen load increased. Beta diversity analysis revealed the intestinal segment with the most significant microbial community changes during pathogen colonization. Within this region, the abundance of probiotics decreased, while that of pathogenic bacteria increased. Functional prediction results indicate that under TPD stress, the gut microbiome activates a multi-layered, synergistic defense adaptation program through nutritional metabolism shifts, biofilm reinforcement, and toxin efflux. This study elucidates the pathogenic mechanism of TPD from the perspective of pathogen-gut microbiome interactions, suggesting that controlling pathogen load and restoring targeted probiotics may serve as effective strategies for preventing and controlling TPD.},
}
@article {pmid41651079,
year = {2026},
author = {Xin, Y and Ma, H and Li, X and Sun, R and Fang, L and Pan, L},
title = {Multi-omics reveal the key role of gut microbiota metabolism in adenine-induced chronic kidney disease.},
journal = {Toxicology and applied pharmacology},
volume = {509},
number = {},
pages = {117754},
doi = {10.1016/j.taap.2026.117754},
pmid = {41651079},
issn = {1096-0333},
mesh = {*Gastrointestinal Microbiome/drug effects/physiology ; Animals ; *Adenine/toxicity ; *Renal Insufficiency, Chronic/chemically induced/metabolism/microbiology ; *Metabolomics/methods ; Male ; Mice ; Mice, Inbred C57BL ; Disease Models, Animal ; Kidney/metabolism ; Metagenomics ; Bile Acids and Salts/metabolism ; Multiomics ; },
abstract = {The gut microbiota plays a crucial role in the progression of chronic kidney disease (CKD). The adenine-induced CKD mouse model is widely employed in preclinical research, yet the effects of adenine on the composition and metabolic function of the gut microbiota remain to be elucidated. This study aimed to test the hypothesis that adenine-induced alterations in the structure and function of the gut microbiota are significantly associated with the onset and progression of CKD. To this end, a mouse CKD model was established by alternating feeding with 0.15% and 0.20% adenine for 7 weeks. Multi-omics analysis (untargeted metabolomics, metagenomics, and spatial metabolomics) was performed to compare the adenine-induced CKD group with a standard diet-fed normal control group. Integrated analysis of plasma metabolomics and intestinal content metabolomics identified 94 differentially co-regulated metabolites: among these, indolelactic acid was significantly upregulated, while indole-3-propionic acid was significantly downregulated. The bile acid metabolic pathway also underwent marked perturbations: taurochenodeoxycholic acid and tauro-β-muricholic acid (two taurine-conjugated bile acids) were significantly elevated, whereas nordeoxycholic acid and norcholic acid were notably reduced. Integrated metabolomics-metagenomics analysis further demonstrated that Lactobacillus exhibited a significant positive correlation with a subset of upregulated metabolites (including indolelactic acid), while Taurinivorans muris showed a strong negative correlation with the taurine-conjugated bile acids. Additionally, renal spatial metabolomics revealed that phospholipid metabolic disorders in the adenine-induced CKD group directly contributed to the aggravation of renal inflammatory responses. Collectively, these findings reveal a gut microbiota-metabolite-kidney axis perturbed by adenine, providing novel insights into the pathogenesis of CKD and potential targets for metabolic intervention.},
}
@article {pmid41650276,
year = {2026},
author = {Chen, L and Camargo, AP and Qin, Y and Koonin, EV and Wang, H and Zou, Y and Duan, Y and Li, H},
title = {Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism.},
journal = {Science advances},
volume = {12},
number = {6},
pages = {eaeb6265},
pmid = {41650276},
issn = {2375-2548},
mesh = {*Gastrointestinal Microbiome ; *Bacteriophages/genetics/physiology ; Animals ; Humans ; Metagenome ; Phylogeny ; Genome, Viral ; Bacteroides/virology ; },
abstract = {Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (jumbo gut) phages with genomes of 360 to 402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38 to 57% identity, suggesting horizontal acquisition from other phages. Over 1500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.},
}
@article {pmid41649278,
year = {2026},
author = {Selleri, E and Tarracchini, C and Petraro, S and Mancabelli, L and Milani, C and Turroni, F and Shao, Y and Browne, HP and Lawley, TD and van Sinderen, D and Ventura, M and Lugli, GA},
title = {Assessment of genome evolution in Bifidobacterium adolescentis indicates genetic adaptation to the human gut.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0117325},
doi = {10.1128/msystems.01173-25},
pmid = {41649278},
issn = {2379-5077},
abstract = {UNLABELLED: Bifidobacterium adolescentis is one of the most frequently encountered bifidobacterial species present in the adult human gut microbiota, with a prevalence of approximately 60%. Despite its high prevalence, B. adolescentis has not been extensively studied and characterized, and our understanding of its physiological traits, genetic diversity, and potential interactions with other members of the human gut microbiota or with its host is therefore fragmentary. In the current study, a data set comprising 1,682 B. adolescentis genomes was compiled by combining publicly available data and metagenome assemblies from 131 projects to uncover the unique genetic characteristics of this species. A pangenome analysis of B. adolescentis identified 203 clusters of orthologous genes absent from the other five human-associated Bifidobacterium species, six of which were in silico predicted to encode functions unique to this taxon. Furthermore, 2,597 genes were predicted to have been acquired by horizontal gene transfer, including genes encoding extracellular structures involved in interaction with the host and other microorganisms, and phage defense mechanisms against bacteriophages. Detailed phylogenetic analysis revealed seven clusters within the B. adolescentis species, each partially associated with the origin of strain isolation, suggesting phylogenetic differentiation shaped by geographical strain origin. Moreover, a large-scale metagenomic analysis of over 10,000 human gut metagenomes from healthy adults revealed that B. adolescentis co-occurs with 36 putative beneficial commensals and butyrate-producing taxa, highlighting its role as a key bifidobacterial species involved in microbial networking within the adult human gut microbiota.<br><br>IMPORTANCE: To comprehensively explore the biodiversity within a microbial species, the reconstruction of a substantial number of genomes is essential. In this study, we successfully uncovered the genetic diversity of Bifidobacterium adolescentis by retrieving a large number of genomes from human gut metagenomic samples. The complete overview of the B. adolescentis pangenome enabled us to investigate the genetic features that distinguish this gut commensal from other bifidobacterial species residing in the human intestinal microbiota.},
}
@article {pmid41645099,
year = {2026},
author = {Qiu, Y and Mo, F and Chen, Y and Lai, Y and Zhang, K and Huang, Z},
title = {Intersite differences in gut microbiome are associated with habitat quality in a limestone forest-dwelling langur.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04800-7},
pmid = {41645099},
issn = {1471-2180},
support = {2023GXNSFBA026045//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; no.32170488//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Studying the compositional structure and function of the gut microbiome is essential for evaluating adaptability of wildlife to their environment. Given the high plasticity of the gut microbiome in primates, studying conspecific populations under different habitat quality can provide valuable insights for the conservation and management. To investigate intersite differences in composition and function of the gut microbiome of endangered François' langurs (Trachypithecus francoisi), we employed 16S rRNA and metagenomic sequencing.<br><br>RESULTS: The results showed that higher gut microbiota diversity of Fran&#xe7;ois' langurs was associated with higher habitat quality, possibly driven by the dietary diversity. In contrast, Fran&#xe7;ois' langurs inhabiting lower-quality habitats had a higher relative abundance of Bacillota and more enriched functional genes related to amino acid metabolism and metabolic pathways than those in higher-quality habitats, which support enhanced fiber degradation to meet energy demands. Additionally, the proportion of tetracycline-related ARGs (tetA(58)) was more abundant in lower-quality habitats, likely due to villagers applying livestock and poultry manure.<br><br>CONCLUSION: Our study concludes that intersite differences in gut microbiome are associated with habitat quality in the Fran&#xe7;ois' langurs, underscoring its role in habitat adaptation and necessity for physiological indicators to elucidate the mechanisms by which wildlife responds to human disturbance and ecological variability. In addition, we recommend prioritizing the restoration of native vegetation diversity in the langurs' habitats, which leverages their gut microbiota's adaptive potential to provide a suitable fundamental environment for the langurs' long-term survival.},
}
@article {pmid41644585,
year = {2026},
author = {Zhou, Y and Liu, K and Gong, P and Wu, J and Ren, Z and Jin, E},
title = {Integrated metagenomic and 16S rRNA analysis reveals temporal associations between resistance genes and microbial communities during dairy manure composting.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41644585},
issn = {2045-2322},
mesh = {*Manure/microbiology ; *Composting/methods ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Animals ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Dairying ; Metagenome ; *Drug Resistance, Bacterial/genetics ; Soil Microbiology ; Cattle ; Genes, Bacterial ; },
abstract = {Dairy manure composting is widely applied to stabilize organic waste and reduce environmental pollution, yet the behavior of resistance determinants during this process remains insufficiently resolved. In this study, shotgun metagenomic sequencing was used to characterize temporal changes in antibiotic resistance genes (ARGs), metal resistance genes (MRGs), biocide resistance genes (BRGs), mobile genetic elements (MGEs), and microbial community composition during dairy manure composting. Rather than inferring direct mechanistic causation, our analyses focused on identifying statistically supported trends, associations, and co-occurrence patterns across composting stages. We observed a rapid decline in the relative abundance of ARGs compared with MRGs and BRGs during the thermophilic phase, coinciding with increasing temperature, while specific genes such as sul2 persisted throughout the process. Shifts in microbial community composition, particularly changes in the relative dominance of Actinobacteria and Proteobacteria, were significantly associated with variations in resistome profiles. Correlation and network analyses further revealed strong associations among ARGs, MRGs, BRGs, and MGEs, suggesting potential co-selection and horizontal gene transfer linkages without implying direct causal mechanisms. In addition, several opportunistic bacterial genera showed positive associations with aminoglycoside- and macrolide-lincosamide-streptogramin-type ARGs, indicating possible dissemination risks following compost application. Overall, this study provides an integrated, association-based overview of resistome and microbial community dynamics during dairy manure composting and highlights the importance of considering multiple resistance determinants when evaluating composting as a manure management strategy.},
}
@article {pmid41644290,
year = {2026},
author = {Yang, F and Xiang, B and Xia, D and Wu, Y and Chang, X and Sun, P and Zhang, M and Zhang, Y},
title = {Lipidomic and Metagenomic Profiling of Chinese Female Emerging Adults With Oily Scalp.},
journal = {Journal of cosmetic dermatology},
volume = {25},
number = {2},
pages = {e70714},
pmid = {41644290},
issn = {1473-2165},
support = {//Proya Cosmetics Co. Ltd/ ; },
mesh = {Humans ; Female ; *Sebum/metabolism ; *Lipidomics/methods ; *Scalp/microbiology/metabolism ; Young Adult ; Adult ; *Dermatitis, Seborrheic/microbiology ; Metagenomics ; Microbiota ; *Scalp Dermatoses/microbiology ; China ; Dandruff/microbiology ; Lipids/analysis ; Paper ; East Asian People ; },
abstract = {BACKGROUND: Excessive sebum secretion leads to oily scalps, which can disturb microbial homeostasis and cause various scalp issues, such as sensitive scalp, dandruff, and seborrheic dermatitis.<br><br>AIMS: This study aimed to investigate the characteristics of scalp lipids and microbiota in a group of females with excessive sebum secretion using omics technology, and to identify important relationships between feature lipids and dominant functional microbes on oily scalp.<br><br>METHODS: Through comparison of three lipidomic sampling methods, we first selected absorbent paper (AP) as a cost-effective and practical method for untargeted lipidomic profiling. Using this method, we then collected scalp surface lipids from 85 Chinese female emerging adults with varying degrees of excessive sebum and performed internal standard quantified lipidomic profiling using UPLC-QE Plus-MS equipped with LipidSearch software version 5.1. Simultaneously, we collected and analyzed scalp microorganisms using PE150 pair-end metagenomic sequencing on the Illumina NovaSeq platform followed by taxonomic and functional annotation with bioinformatic tools and databases. Afterwards, multivariate statistical analysis and bioinformatics were used to identify feature lipids related to high sebum levels, discern the roles of dominant microbes involved in lipid metabolism, and explore potential correlations between feature lipids and dominant functional microbes of oily scalp.<br><br>RESULTS: After comparison of three lipidomic sampling materials, absorbent paper (AP) was selected to collect scalp surface lipids from 85 volunteers. A total of 13 lipid classes were annotated and the most abundant in ESI (+) mode was triacylglycerol (TG, 99.18%) whereas in ESI (-) mode were fatty acid (FA, 56.94%) and O-acyl-(gamma-hydroxy) FA (OAHFA, 34.15%). We identified 27 TGs and 3 FAs as the major lipid molecules contributing to high sebum levels. Seventy percent of these TGs were unsaturated (33% monounsaturated, 26% diunsaturated, 11% triunsaturated), and 30% were saturated. Meanwhile, we found that although the dominant microorganisms, Cutibacterium, Lawsonella, Malassezia, and Staphylococcus were all involved in lipid metabolism on the scalp, only some of them were related to the degree of sebum level and also displayed species-specific preferences for lipids. Among them, Lawsonella clevelandensis and Malassezia globosa were weakly negatively associated with both unsaturated and saturated TGs, while Malassezia restricta and Cutibacterium granulosum were only weakly negatively correlated with saturated TGs, and Cutibacterium namnetense was weakly positively correlated with FA (26:0).<br><br>CONCLUSIONS: This study describes relevant lipid molecules contributing to higher sebum production, and reveals that L. clevelandensis, M. restricta, M. globosa, C. namnetense, and C. granulosum on the scalp are closely correlated with these lipids, showing species-specific preference. These findings provide new insights into the interaction between key surface lipids and dominant functional microorganisms on oily scalps.},
}
@article {pmid41644119,
year = {2026},
author = {Hung, JY and Cooke, I and Sato, Y and Miller, DJ and Bourne, DG},
title = {Microbial Metabolism and Disease Virulence Changes Across Day and Night in Coral Black Band Disease Lesions.},
journal = {Environmental microbiology},
volume = {28},
number = {2},
pages = {e70219},
pmid = {41644119},
issn = {1462-2920},
support = {//Earthwatch Institute/ ; //James Cook University/ ; //Mitsubishi Corporation/ ; //JCU CTBMB grant/ ; //JCU OIRS Morris Family Trust grant/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; Virulence ; *Bacteria/metabolism/genetics/pathogenicity ; *Cyanobacteria/metabolism/genetics ; Photosynthesis ; Metagenome ; Microbiota ; Light ; },
abstract = {Coral black band disease (BBD) is characterised as a cyanobacteria-dominated microbial mat that rapidly kills underlying coral tissue. Solar radiation promotes lesion progression by fuelling the cyanobacterial photosynthesis, while sulphate-reducing bacteria and sulphide-oxidising bacteria are implicated in sulphide dynamics within the mat. How the metabolism of the key microbial communities in the mat varies under light and dark conditions and impacts lesion virulence is poorly characterised, however. To compare microbial gene expression under different light regimes, we recovered 28 near-complete BBD-derived metagenome-assembled genomes (MAGs) using Oxford Nanopore Technologies long-read sequencing and profiled Illumina metatranscriptomic reads from BBD lesions collected at day and night by mapping to these MAGs. Genes from the cyanobacterium Roseofilum reptotaenium dominated the differentially expressed genes, with photosynthesis highly represented during the daytime. Relative expression of sulphur and nitrogen metabolism, cofactor biosynthesis, chemotaxis and motility increased among the non-cyanobacterial members at night. Enhanced sulphur reduction by Campylobacteriales and Desulfovibrionaceae at night likely supports a sulphide-rich and low oxygen micro-environment in the lesion, while increased chemotaxis and motility by Campylobacteriales and other heterotrophic bacteria drive lesion progression towards healthy coral tissue. This study provides insights into how diurnal light dynamics drive microbial metabolic pathways changes, thereby promoting BBD virulence.},
}
@article {pmid41640872,
year = {2026},
author = {Chen, YX and Sun, NQ and Mo, SJ},
title = {Rhapontin activating nuclear factor erythroid 2-related factor 2 to ameliorate Parkinson's disease-associated gastrointestinal dysfunction.},
journal = {World journal of gastroenterology},
volume = {32},
number = {4},
pages = {114468},
pmid = {41640872},
issn = {2219-2840},
mesh = {*NF-E2-Related Factor 2/metabolism ; Gastrointestinal Microbiome/drug effects ; Animals ; Humans ; *Parkinson Disease/complications ; *Gastrointestinal Diseases/etiology/therapy/microbiology ; Mice ; Disease Models, Animal ; Kelch-Like ECH-Associated Protein 1/metabolism ; Signal Transduction/drug effects ; Fecal Microbiota Transplantation ; Brain-Gut Axis/drug effects ; 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine ; },
abstract = {This commentary provides a critical evaluation of the study by Wang et al, which focuses on rhapontin activating colonic nuclear factor erythroid 2-related factor 2 (NRF2) to explore its therapeutic potential for Parkinson's disease (PD)-associated gastrointestinal dysfunction. The commentary acknowledges the academic value of the study: It has not only validated intestinal NRF2 as a therapeutic target for PD but also provided experimental support for the "enteric pathology hypothesis". However, several key gaps remain unresolved in the study. At the gut microbiota level, the exploration of the causal relationship of the microbiota is insufficient, with no validation conducted via methods such as fecal microbiota transplantation; additionally, it fails to systematically integrate the gut-brain axis with PD and does not assess the impact of rhapontin on the composition or function of the gut microbiota. At the pathway mechanism level, it lacks an analysis of the crosstalk between NRF2 and other rhapontin-targeted pathways, including nuclear factor kappa-B, mitogen-activated protein kinase, adenosine monophosphate-activated protein kinase, and sirtuin 1. At the experimental method level, the behavioral testing methods for PD mouse models and the limitations of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse models need attention. Additionally, certain flaws exist in some experimental result figures. Furthermore, this commentary puts forward improvement suggestions for the study. Future research should prioritize multi-omics analysis, encompassing combined metabolomics and metagenomics detection, while conducting mechanistic validation of NRF2-interacting molecules (KEAP1 and p62). In addition, it is necessary to improve refined behavioral tests, focusing on incorporating cognitive function and anxiety-related assessment items.},
}
@article {pmid41640388,
year = {2026},
author = {Li, S and Li, W and Zhang, X and Zhou, H and Zhan, J},
title = {Harnessing Population Genomics, Gut Microbiota, and Environmental DNA Surveillance for the Conservation of Chinese Spotted Seals in a Changing World.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e72952},
pmid = {41640388},
issn = {2045-7758},
abstract = {The triple planetary crisis-encompassing climate change, biodiversity loss, and pollution-poses escalating threats to Earth's systems, particularly impacting marine mammals. The spotted seal (Phoca largha Pallas 1811), currently recognized as the only pinniped species known to breed in China, holds the status of a National Grade I protected species in China. To elucidate the genetic diversity of Chinese spotted seal populations and provide scientific foundations for their conservation and management, this review systematically summarized the fundamental biological characteristics and documented migration routes of spotted seal populations in China, with particular emphasis on reviewing molecular-level research advancements regarding population genetic structure. Early studies primarily employed molecular markers such as microsatellite DNA and mitochondrial DNA (mtDNA), revealing relatively low genetic diversity levels within Chinese spotted seal populations. In recent years, rapid developments in omics technologies have enabled comprehensive investigations into both genomic compositions, as well as gut microbial community diversity and functional profiles of this species. Furthermore, this review critically examined current research limitations and challenges while proposing the potential advantages and developmental trends of environmental DNA (eDNA) technology in future population studies. These technological and strategic advancements are anticipated to significantly enhance survey efficiency and conservation effectiveness for Chinese spotted seal populations.},
}
@article {pmid41639568,
year = {2026},
author = {Zeng, Y and Qi, H and Guo, W and Tan, X and Huang, B and Hu, R and Ouyang, X},
title = {Multi-omics insights into Shenling Baizhu Powder's amelioration of murine asthma through gut microbiota and Glutamine-GLS1 pathway.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41639568},
issn = {2045-2322},
support = {2023BSQD002//Doctoral Scientific Initiate Project of Shunde Women and Children's Hospital of Guangdong Medical University (Maternity &amp; Child Healthcare Hospital of Shunde Foshan)/ ; 20241090//The Project of Administration of Traditional Chinese Medicine of Guangdong Province/ ; 2023A04J0550//Guangzhou Municipal Science and Technology Project/ ; 20250403//Medical Research Project of Foshan Municipal Health Bureau/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Asthma/drug therapy/metabolism/pathology/microbiology ; Mice ; *Glutamine/metabolism ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Metabolomics ; Disease Models, Animal ; Mice, Inbred BALB C ; Th17 Cells/immunology/drug effects ; Powders ; Cytokines/metabolism ; Female ; Lung/pathology/drug effects ; Ovalbumin ; Th2 Cells/immunology/drug effects ; Multiomics ; },
abstract = {Shenling Baizhu Powder (SLBZP) is a prominent formulation widely used in the treatment of pulmonary diseases. However, studies examining the mechanisms of SLBZP for treating asthma are limited. This study aimed to clarify the efficacy and possible mechanisms of SLBZP in the context of asthma from the perspective of gut microbiota-metabolism-immune crosstalk. Key parameters including airway hyperresponsiveness, lung pathological features and the expression of inflammatory mediators from Th2 and Th17 cells were employed to validate the anti-inflammatory properties of SLBZP. The anti-asthma mechanism of SLBZP was investigated using metagenomic sequencing, metabolomics, flow cytometry, RT-qPCR, immunohistochemistry (IHC) and immunofluorescence (IF). SLBZP demonstrated significant capacity to mitigate histopathological alterations associated with ovalbumin-induced asthma and suppress the secretion of inflammatory mediators (IL-4, IL-5, IL-13 and IL-17A) in BALF. Metagenomic results demonstrated that the protective effects of SLBZP were primarily associated with Ligilactobacillus, Eubacterium and Clostridium. Additionally, metabolomics results identified that three vital metabolic pathways were substantially regulated by SLBZP in asthmatic mice, especially D-glutamine and -glutamate metabolism. Furthermore, IHC and IF results showed that SLBZP significantly inhibited the expression of GLS1 and GOT1, which inhibited the conversion of L-glutamine to α-ketoglutarate and regulated the imbalance of Th1/Th2 and Treg/Th17. RT-qPCR results showed that SLBZP promoted the expressions of T-bet, IFN-γ, IL-10 and Foxp3 mRNA, and inhibited the expression of GATA3, IL-4, IL-5, IL-13, IL-17A and RORγt mRNA. The findings from flow cytometry provided additional evidence. Thus, this modulated the imbalance of Th1/Th2 and Treg/Th17 and exerted the immunomodulatory properties of SLBZP. SLBZP exerted protective effects against OVA-induced asthma and modified the structure and functional characteristics of the gut microbiota, and serum metabolite profiles in asthmatic mice. The anti-asthma mechanism of SLBZP may be associated with the modulation of the gut microbiota and Glutamine-GLS1 pathway.},
}
@article {pmid41638014,
year = {2026},
author = {Song, Y and Song, X and Liu, X and Jiang, L and Chai, L},
title = {Metagenomics and targeted metabolomics uncover concomitant gut microbiota dysbiosis and bile acid metabolism alteration in norfloxacin-exposed Bufo gargarizans tadpoles.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {292},
number = {},
pages = {107742},
doi = {10.1016/j.aquatox.2026.107742},
pmid = {41638014},
issn = {1879-1514},
mesh = {Animals ; Larva/drug effects/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; Metagenomics ; *Norfloxacin/toxicity ; *Bile Acids and Salts/metabolism ; *Anti-Bacterial Agents/toxicity ; Metabolomics ; *Dysbiosis/chemically induced/veterinary ; *Bufonidae/microbiology ; },
abstract = {Norfloxacin (NOR) is a fluoroquinolone antibiotic widely detected in aquatic environments, yet little is known about its toxic effects on amphibians. Bile acids (BAs) are crucial metabolites derived from gut microbiota-host co-metabolism and play vital roles in maintaining host health. BA composition is regulated by the gut microbiota through specific enzymes: bile salt hydrolases (BSHs) deconjugate primary BAs; bile acid-inducible enzymes (BAIs) and hydroxysteroid dehydrogenases (HSDHs) then convert them into secondary BAs. This study investigated the effects of NOR on Bufo gargarizans tadpoles using a combination of intestinal-targeted BA metabolomics, metagenomics, and histopathological analysis. Tadpoles were exposed to 10 and 100 μg/L NOR from Gs26 to Gs36, with 4 independent biological replicates per group. Our results showed that NOR exposure significantly increased the relative abundance of gut microbiota encoding BAIs, HSDHs, and/or BSHs, which was accompanied by a decrease in the ratios of primary/secondary BAs and conjugated/deconjugated BAs. Meanwhile, NOR treatment elevated antibiotic resistance gene abundance and induced intestinal histopathological alterations in tadpoles, characterized by reduced epithelial cell height and hypertrophy of smooth muscle cells (SMCs). In summary, environmentally relevant concentrations (10 and 100 μg/L) of NOR affected the intestinal microbiota, thereby disrupting BAs biotrasformation, ultimately potentially compromising intestinal health in tadpoles. This highlighted the potential ecological risks posed by NOR pollution in aquatic ecosystems.},
}
@article {pmid41635749,
year = {2025},
author = {de Oliveira Guimarães, L and de Almeida, AR and Ramos, EDSF and Telles-de-Deus, J and Helfstein, VC and Morais, VDS and Dos Santos, JM and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, &#xc9;},
title = {Evolutionary features of new picorna-like viruses in Culex (Melanoconion) mosquitoes.},
journal = {Current research in parasitology &amp; vector-borne diseases},
volume = {8},
number = {},
pages = {100333},
pmid = {41635749},
issn = {2667-114X},
abstract = {In this study, we investigated unclassified picorna-like viruses in Culex (Melanoconion) mosquitoes from São Paulo, Brazil, an area of high mosquito biodiversity and arbovirus activity. Two mosquito pools were processed using next-generation sequencing (NGS), and datasets were analyzed via de novo assembly to reconstruct viral genomes and assess evolutionary relationships. We identified two highly similar viral genomes, named Culex (Melanoconion) picorna-like virus, CmV_B38 and CmV_B39, exhibiting 99.93% nucleotide identity, both of which encode a three-domain replication block characteristic of viruses within the order Picornavirales. Phylogenetic reconstruction based on the RNA-dependent RNA polymerase (RdRp) gene revealed that these viruses form a distinct, previously undescribed clade, most closely related to Yongsan picorna-like virus 4 and several other unclassified viruses that have been reported predominantly in Asian regions. These findings may indicate possible geographical connectivity or convergence in viral evolution across distinct ecosystems. Notably, the results highlight the underexplored diversity of insect-specific viruses, particularly those associated with mosquito vectors. Furthermore, the data are consistent with the hypothesis that ecological factors and host specificity could influence the evolutionary dynamics of these viral lineages. The study not only enhances our understanding of the mosquito-associated virome but also emphasizes the critical need for ongoing viral surveillance, especially in biodiverse regions. Such efforts are essential for elucidating the evolutionary dynamics of RNA viruses and for anticipating the emergence of novel viral pathogens that may pose future risks to public health or agriculture.},
}
@article {pmid41634308,
year = {2026},
author = {Campos-Madueno, EI and Aldeia, C and Endimiani, A},
title = {Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {7016},
pmid = {41634308},
issn = {2045-2322},
support = {192514//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Humans ; Africa ; Feces/microbiology ; Nanopores ; Switzerland ; Anti-Bacterial Agents/pharmacology ; Metagenome ; *Bacteria/genetics/classification/drug effects ; Nanopore Sequencing ; Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The gut microbiota and resistome may change upon exposure to environments with high prevalence of multidrug-resistant pathogens, potentially impacting health and contributing to the spread of antimicrobial resistance genes (ARGs). In this context, expatriates may acquire endemic microbial communities and ARGs while living abroad. In this work, we investigated the microbiota and resistome of Swiss expatriates living in African countries using Nanopore shotgun metagenomics (SMS).Stool samples from expatriates residing in African and European countries (n = 33 and n = 39, respectively) were sequenced using Nanopore V14 chemistry. Taxonomic and resistome profiling was performed with Kraken2 and ResFinder, respectively. Diversity metrics (e.g., Shannon, Simpson) assessed microbial composition. ARG and bacteria associations were determined using GTDB-Tk on metagenome-assembled genomes (MAGs). Plasmid-borne ARGs were characterized with PlasmidFinder.Our results indicated that microbiota composition did not differ between expatriates in African and European countries. However, resistome analysis revealed a higher prevalence of tetracycline (tet) and folate pathway antagonist (dfr, sul) ARGs in those residing in Africa, suggesting adaptation to the local microbial environment or antibiotic policy. Unique plasmid families were also identified in Gram-negative (IncF) and -positive (repUS43) bacteria across African and European cohorts, indicating the potential for ARG dissemination via mobile genetic elements. Overall, Nanopore-based SMS may provide an alternative approach to monitor microbiota and resistome dynamics, and thus assisting early epidemiological surveys.},
}
@article {pmid41632094,
year = {2026},
author = {Gómez-Martínez, D and Ngou, JS and Ugolini, V and Lai, FY and Nilsson, RH and Kristiansson, E and Corcoll, N},
title = {Antibiotic resistance gradient along a large Scandinavian river influenced by wastewater treatment plants.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {3},
pages = {},
pmid = {41632094},
issn = {1574-6941},
support = {AF2022-0079//Adlerbertska forkningsstifelsen/ ; 2019-01161//Formas/ ; },
mesh = {*Rivers/microbiology ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology/analysis ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Geologic Sediments/microbiology ; Sweden ; Genes, Bacterial ; Water Purification ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Sewage/microbiology ; },
abstract = {Recent studies have identified the environment as a key reservoir from which antibiotic resistance genes (ARGs) can be acquired and transmitted to pathogens. However, our knowledge about the presence of ARGs in high-flow river sediments is still limited. We analyzed the resistome of sediment bacterial communities along the Swedish river Göta Älv and investigated the potential dissemination of ARGs and antimicrobials from effluents of wastewater treatment plants (WWTPs). While we detected nine different antimicrobials in the effluent water from the WWTPs through HPLC-MS, their presence was not observed in the river surface water. Analysis by qPCR revealed that the genes sul1 and ermB were the most dominant ARGs among sediment, sludge, and effluent samples. Shotgun metagenomics revealed unique differences between the sludge resistomes of the WWTPs. Moreover, our findings show that ARGs increase downstream of the Göta Älv and their diversity differs from that of the upstream sites. Efflux pump resistance-related genes were most abundant in sediment samples, and beta-lactams and tetracyclines were the most common antibiotic classes targeted by ARGs. Our study emphasizes the importance of urban river sediments as a reservoir of ARGs, as tracking ARGs in WWTPs and their receiving environments improves our understanding of their spread and characteristics.},
}
@article {pmid41629580,
year = {2026},
author = {Khurajog, B and Saenkankam, I and Apiwatsiri, P and Supimon, N and Kamwa, R and Niyomtham, W and Yindee, J and Phupolphan, C and Hampson, DJ and Prapasarakul, N},
title = {Effectiveness of probiotic supplementation on growth performance, gut microbiota, and Salmonella reduction in broiler chicks challenged with Salmonella Typhimurium.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6983},
pmid = {41629580},
issn = {2045-2322},
support = {FOOD66310012//the 2022-Fundamental Fund, Thailand Science Research and Innovation (TSRI), Chulalongkorn University/ ; },
mesh = {Animals ; *Probiotics/administration &amp; dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Chickens/microbiology/growth &amp; development ; *Salmonella typhimurium ; *Salmonella Infections, Animal/microbiology/prevention &amp; control ; *Poultry Diseases/microbiology/prevention &amp; control ; Dietary Supplements ; Animal Feed ; Ligilactobacillus salivarius ; },
abstract = {Salmonella infection poses a major threat to poultry production, affecting both animal health and food safety. With rising concerns over antimicrobial resistance, probiotics have gained attention as effective non-antibiotic interventions to control enteric pathogens while supporting gut health. This study evaluated the efficacy of a locally isolated probiotic blend comprising Ligilactobacillus salivarius BF12, and Pediococcus acidilactici strains BF9 and BYF20 (ProCU) in comparison with a commercial Clostridium butyricum-based probiotic (TOP GUT) in broiler chicks challenged with Salmonella Typhimurium (ST). A total of 196 chicks were assigned to seven groups receiving different treatments with or without Salmonella challenge. Parameters assessed included growth performance, intestinal histomorphometry, cecal Salmonella load, and microbiota composition and function. Before challenge, ProCU increased fecal lactic acid bacteria (LAB) and enriched amino acid and carbohydrate metabolism pathways. Post-challenge, TOP GUT significantly reduced Salmonella load and maintained growth, while ProCU showed a limited effect on pathogen reduction. Both probiotics improved intestinal morphology, increased Lactobacillus and Akkermansia abundance, and upregulated oxidative stress defense genes. Notably, TOP GUT also enriched Parabacteroides and other Bacteroidetes members and prolonged microbial metabolic activity. These findings emphasize strain-specific probiotic effects and suggest that continuous supplementation, particularly with spore-forming strains, may enhance gut health and reduce the Salmonella burden in poultry.},
}
@article {pmid41627741,
year = {2026},
author = {Castañeda, S and Ramírez, JD and Poveda, C},
title = {Microbiome Profiling in Chagas Disease: Sample Collection, Sequencing, and Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3013},
number = {},
pages = {265-297},
pmid = {41627741},
issn = {1940-6029},
mesh = {*Chagas Disease/microbiology/parasitology ; Animals ; Mice ; Trypanosoma cruzi ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; },
abstract = {Chagas disease, caused by Trypanosoma cruzi, leads to chronic cardiac and gastrointestinal complications. Emerging evidence shows the gut microbiome plays a key role in modulating disease severity, with shifts in microbial composition influencing immune responses and metabolic pathways. Here, we describe a workflow for microbiome analysis in T. cruzi-infected mice. Methods included sample collection from feces and gastrointestinal tissues, DNA extraction, sequencing, and quality control. Then, we outline bioinformatic analyses covering taxonomic profiling, diversity assessment, and microbial network construction. Finally, protocols for functional prediction tools are also included to explore microbial capabilities and the identification of signatures associated with disease progression.},
}
@article {pmid41627460,
year = {2026},
author = {Do, TH and Dao, TK and Pham, TTN and Nguyen, MH and Nguyen, TQ and To, LA and Nguyen, TVH and Phung, TBT},
title = {Understanding the bacteriome, phageome and phage-associated bacteriome in healthy Vietnamese children under two years of age.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {167},
pmid = {41627460},
issn = {1432-072X},
support = {DTDLCN.63/22//Ministry of Science and Technology/ ; },
mesh = {Humans ; Infant ; Vietnam ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Bacteria/classification/genetics/isolation &amp; purification/virology ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Child, Preschool ; Male ; Female ; Metagenome ; Diarrhea/microbiology ; Southeast Asian People ; },
abstract = {The establishment of the intestinal microbiota during early life plays an important role in physical and mental development and in shaping disease susceptibility in adult. However, knowledge of the gut microbiota in healthy Vietnamese children remains limited. In this study, real-time PCR was used to detect 24 diarrheal pathogens in stool samples, revealing that 41% of healthy infants aged 6-24 months living in Hanoi, Hung Yen were asymptomatic carriers of Escherichia coli (29.1%), Clostridioides difficile (10.3%) and Sapovirus. Pooled metagenomes of gut bacteria (HMG1, HMG2) and viruses (HV1, HV2) from two groups of pathogen-negative infants aged 6-11 months (n = 17) and 12-24 months (n = 13) were subsequently sequenced. As expected, from the classified reads, HMGs comprised of 99.99% bacterial reads, while HVs comprised of bacteria (78.5% in HV1, 42.3% in HV2), phages (8.3% in HV1, 41.0% in HV2) and viruses. The gut microbiota was formed by core bacteria: Actinobacteria (82.6-84.5%), Firmicutes, Proteobacteria and Bacteroidetes, with abundance of Bifidobacterium (> 80%), phages: Podoviridae (65.5-70.2%), Siphoviridae, Myoviridae with dominant crAssphage. The HMGs and HVs shared core bacterial composition but differed in relative abundance. The gut microbiota of older children was characterized by an increase of probiotic bacteria, Escherichia phage, Lactococcus phage and decrease of bacterial pathogens and phages targeting Lactobacillus, Klebsiella, Acinetobacter. Bacterial genes in the gut phage fraction may reflect bacterial community in recent past. Overall, this study provides a scientific basis for understanding the gut microbiome in relation to health and diseases in children particularly within the Vietnamese population.},
}
@article {pmid41627458,
year = {2026},
author = {Jiang, F and Gu, H and Song, P and Zhang, J and Cai, Z and Liang, C and Gao, H and Zhang, R and Zhang, T},
title = {Post-defecation exposure alters gut microbiota of forest musk deer with implications for conservation metagenomics.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {53},
pmid = {41627458},
issn = {1432-0614},
support = {32200408//National Natural Science Foundation of China/ ; 2023-ZJ-952Q//Natural Science Foundation of Qinghai Province/ ; 2023M743743//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Deer/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Forests ; DNA, Bacterial/genetics ; Endangered Species ; Conservation of Natural Resources ; Time Factors ; Sequence Analysis, DNA ; },
abstract = {In endangered species conservation, fecal samples are a vital non-invasive tool for gut microbiota analysis. Yet, the influence of external exposure time on microbial composition and function remains unclear, constraining data accuracy and reliability. To address this, we investigated the time-gradient effect in the globally endangered forest musk deer (Moschus berezovskii). Using non-invasive sampling under standardized captive conditions, fecal samples were collected at six storage times: (0, 1, 2, 4, 6, 8 days). Gut microbiota composition, diversity, enterotypes, and functional differences were assessed through 16S rRNA gene sequencing on the Illumina MiSeq platform. In total, 147,013 valid ASVs (amplicon sequence variants) were obtained showing significant shifts in microbial composition with storage time. Dominant phyla included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Increasing storage time led to declining α-diversity, reduced community stability, and more unique genera. PCoA (principal coordinates analysis) and NMDS (non-metric multidimensional scaling) indicated progressive separation of experimental groups from control groups, with Anosim and Adonis confirming progressive separation with storage time. Structurally, Firmicutes decreased while Proteobacteria, specifically the Acinetobacter genus, increased with storage time. Community assembly shifted from deterministic to stochastic processes, reflecting stronger environmental disturbance effects. These results demonstrate that the gut microbiota composition, diversity, and ecological functions in forest musk deer feces are highly sensitive to storage time. Thus, preservation duration must be strictly controlled as a critical variable in microbiome studies. This work establishes methodological standards for non-invasive fecal metagenomics in endangered species, providing theoretical insights and practical guidance for improving scientific rigor in conservation-related microbiome research. KEY POINTS: Fecal microbiota diversity and stability decline significantly with longer storage. Firmicutes decrease while Proteobacteria, especially Acinetobacter, increase over time. Storage duration strongly impacts microbiome data, requiring strict sampling control.},
}
@article {pmid41628276,
year = {2026},
author = {Habib, I and Hernandez-Valencia, JC and Martinu, J and Novakova, E},
title = {Viral metagenome characterization reveals species-specific virome profiles in Triatominae populations from the southern United States.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {2},
pages = {e0013576},
pmid = {41628276},
issn = {1935-2735},
mesh = {Animals ; *Virome ; *Metagenome ; *Triatominae/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; Species Specificity ; Texas ; Female ; Arizona ; Insect Vectors/virology ; New Mexico ; },
abstract = {Kissing bugs (Triatominae) are hematophagous insects and the principal vectors of Trypanosoma cruzi, the causative agent of Chagas disease. While their bacterial microbiomes have received considerable attention, the diversity of viruses associated with these insects remains poorly understood. To address this gap, we investigated the metavirome of five Triatominae species from the southern United States (Triatoma rubida, T. sanguisuga, T. gerstaeckeri, T. indictiva, and Hospesneotomae protracta), sampled in Texas, New Mexico, and Arizona. We sequenced 23 samples, including abdomen, gut and reproductive tissues from 13 field-collected individuals and assembled 41 viral operational taxonomic units (vOTUs), 40 of which are novel and together constitute 13 viral families, including Chuviridae, Arenaviridae, Orthomyxoviridae, Partitiviridae, Solemoviridae, Circoviridae, Rhabdoviridae, Microviridae, Xinmoviridae, Astroviridae, Narnaviridae, Tombusviridae, and the order Elliovirales. The vOTUs composition and abundance analysis examined variables including species, sex, tissue type, blood meal, and T. cruzi infection status, showing that metavirome diversity varied significantly among Triatominae species. Our findings demonstrate a species-specific metavirome and the presence of virus taxa linked to insects, plants, and vertebrates, highlighting the complex ecological interactions between viruses and triatomines. This study uncovers a diverse and largely novel set of metaviromes within North American Triatominae, providing a foundation for future research on virus-vector interactions.},
}
@article {pmid41625985,
year = {2026},
author = {Taboada, S and Riesgo, A and Busch, K and Erpenbeck, D and Hentschel, U and Galià, C and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {15},
pmid = {41625985},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Phakellia ventilabrum (Porifera; Demospongiae; Bubarida; Bubaridae). The genome sequence has a total length of 211.92 megabases. Most of the assembly (99.97%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.36 kilobases in length. Gene annotation of this assembly by Ensembl identified 21 622 protein-coding genes. Thirty-three binned genomes were generated from the metagenome assembly, of which eight were classified as high-quality metagenome assembled genomes (MAGs) and of which four of the MAGs are fully circular. The MAGs were taxonomically assigned to Pseudomonadota (i.e. Candidatus Poriferihabitaceae), Nitrospirota, Nitrospinota, and the archaeal Nitrosopumilus clade.},
}
@article {pmid41624426,
year = {2026},
author = {Santi, I and Pavloudi, C and Abagnale, M and Azua, I and Baña, Z and Bastianini, M and Belser, C and Berg, K and Bilbao, J and Bird, K and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Cunliffe, M and Daguin, C and Deneudt, K and Díaz de Cerio, O and Exter, K and Fauvelot, C and Fontana, Y and Frada, MJ and Galand, PE and Gallia, R and Garczarek, L and González Fernández, J and Guillou, L and Heynderickx, H and Koplovitz, G and Labrune, C and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhães, C and Margiotta, F and Moal, H and Moussy, A and Not, F and Percopo, I and Paredes Rosendo, E and Péru, E and Poulain, J and Praebel, K and Rigaut-Jalabert, F and Romac, S and Rzeznik-Orignac, J and Sarno, D and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Tramontano, F and Trano, AC and Wincker, P and Pade, N},
title = {Next release of the European Marine Omics Biodiversity Observation Network (EMO BON) shotgun metagenomic data from water and sediment samples (Release 2).},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e178484},
pmid = {41624426},
issn = {1314-2828},
abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is a long-term genomic observatory run by the European Research Infrastructure European Marine Biological Resource Centre (EMBRC). It was established in 2021 to support the challenges of biodiversity observation and unsystematic management of biodiversity data in the European seas. EMO BON introduced and coordinated the systematic and harmonised observation of biodiversity amongst more than fourteen marine stations in the European coastline. Here, we report the next release (Release 2) of shotgun metagenomic data from seawater and sediment microbial communities.},
}
@article {pmid41621514,
year = {2026},
author = {Ren, X and Zhang, W and Liu, M and Ge, J and Yang, H and Chi, G},
title = {Colon-targeted probiotic delivery system based on oxidized konjac glucomannan/thiolated chitosan/bacterial cellulose: Enhanced survival, mucoadhesion, and gut microbiota modulation.},
journal = {International journal of biological macromolecules},
volume = {346},
number = {},
pages = {150646},
doi = {10.1016/j.ijbiomac.2026.150646},
pmid = {41621514},
issn = {1879-0003},
mesh = {*Probiotics/administration &amp; dosage/pharmacology/chemistry ; *Chitosan/chemistry ; *Mannans/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Colon/microbiology/drug effects/metabolism ; Animals ; Microspheres ; *Cellulose/chemistry ; Intestinal Mucosa/metabolism ; *Drug Delivery Systems ; Oxidation-Reduction ; Humans ; Sulfhydryl Compounds/chemistry ; },
abstract = {Probiotics play a critical role in maintaining human health homeostasis, yet their oral delivery faces challenges due to poor gastrointestinal survival, uncontrolled release, and inefficient targeted colonization. To address these limitations, we developed colon-targeted mucoadhesive (sCS-BC)/OKGM-SA microspheres using a W1/O/W2 double emulsion technique combined with ionic crosslinking, employing oxidized konjac glucomannan (OKGM), thiolated chitosan (sCS), and bacterial cellulose (BC). In vitro digestion assays revealed that the microspheres effectively shielded probiotics under simulated gastric and bile salt, while enabling pH- and enzyme-responsive release in the intestinal, achieving a viable probiotic count of 1.5 × 10[8] CFU/mL. Rheological characterization and in vivo gastrointestinal transit studies demonstrated that the microspheres enhanced colonic colonization through interactions with the intestinal mucus layer. Histological analysis further indicated that the microspheres stimulated colonic goblet cell proliferation and mucus layer formation. Metagenomic and metabolomic profiling confirmed that oral administration of the probiotic-loaded microspheres markedly enriched gut microbial diversity and helped preserve intestinal barrier integrity, showing potential in modulating gut immune function. The (sCS-BC)/OKGM-SA system integrates upper gastrointestinal protection, colon-targeted delivery, mucus adhesion, and probiotic proliferation, offering a novel strategy for targeted probiotic delivery. This work establishes a foundational framework for designing next-generation colon-targeted probiotic carriers and underscores their therapeutic promise in modulating intestinal ecosystems.},
}
@article {pmid41621269,
year = {2026},
author = {Li, J and Dong, W and Kong, A and Wang, G and Yang, J and Zhou, Y and Song, K and Kong, L and Tong, L},
title = {Floating macrophyte growth and decomposition greatly affects the exogenous antimony mobility and microbial community functions in water-sediment system.},
journal = {Water research},
volume = {293},
number = {},
pages = {125448},
doi = {10.1016/j.watres.2026.125448},
pmid = {41621269},
issn = {1879-2448},
mesh = {*Antimony/metabolism ; *Geologic Sediments/microbiology/chemistry ; Water Pollutants, Chemical ; *Amaranthaceae/growth &amp; development/metabolism ; Microbiota ; Biodegradation, Environmental ; },
abstract = {Anthropogenic antimony (Sb) contamination in aquatic systems poses persistent ecological risks, yet the role of floating macrophyte life-cycle processes in regulating Sb migration and speciation remains poorly understood. In this study, a mesocosm experiment was conducted to investigate how the growth and decomposition of Alternanthera philoxeroides (AP) influence Sb mobility and transformation following exogenous Sb(V) input. Results show that Sb was ultimately sequestered in sediments, which acted as a dynamic regulator rather than a passive sink, controlling Sb retention and long-term reactivity. Rapid surface adsorption was followed by progressive downward migration driven by redox-sensitive remobilization and re-adsorption onto deeper mineral phases, with Sb predominantly associated with amorphous and poorly crystalline Fe/Al (hydr)oxides (67.3-84.1%). Growth of AP accelerated Sb removal from the water column mainly through indirect, DOM-mediated sequestration rather than direct plant uptake, while simultaneously enhancing the vertical redistribution of bioavailable Sb within sediments. In contrast, AP removal followed by decomposition caused pronounced physical and biogeochemical disturbances. These disturbances induced transient reducing conditions, organic matter release, and a marked increase in pH (up to 9.14), collectively promoting Sb remobilization and Sb(III) release into the overlying water. As a result, Sb(III) concentrations were up to 67-fold higher than those in the unvegetated control. Exogenous Sb strongly reshaped sediment microbial communities, selectively enriching metal-tolerant taxa such as Actinomycetota (genus Streptomyces) and favoring functional traits related to Sb detoxification and elemental cycling. Metagenomic evidence indicates that Sb resistance, coupled with coordinated C, N, P, and S cycling functions, enables the indigenous microbiome to actively regulate Sb speciation and mobility, particularly under organic matter inputs derived from macrophyte growth and decomposition. These findings demonstrate that floating macrophytes exert process-level control over Sb cycling, with life-cycle-mediated biogeochemical feedbacks governing its mobility, speciation, and persistence in water-sediment systems.},
}
@article {pmid41620752,
year = {2026},
author = {Sharma, A and Küsel, K and Wegner, CE and Pérez-Carrascal, OM and Taubert, M},
title = {Two worlds beneath: Distinct microbial strategies of the rock-attached and planktonic subsurface biosphere.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41620752},
issn = {2049-2618},
support = {218627073//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Th&#xfc;ringer Ministerium f&#xfc;r Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; },
mesh = {*Groundwater/microbiology ; *Plankton/classification/genetics ; *Microbiota/genetics ; Biofilms/growth &amp; development ; Metagenomics/methods ; Oxidation-Reduction ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Ecosystem ; Metagenome ; Proteobacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Microorganisms in groundwater ecosystems exist either as planktonic cells or as attached communities on aquifer rock surfaces. Attached cells outnumber planktonic ones by at least three orders of magnitude, suggesting a critical role in aquifer ecosystem function. However, particularly in consolidated carbonate aquifers, where research has predominantly focused on planktonic microbes, the metabolic potential and ecological roles of attached communities remain poorly understood.<br><br>RESULTS: To investigate the differences between attached and planktonic communities, we sampled the attached microbiome from passive samplers filled with crushed carbonate rock exposed to oxic and anoxic groundwater in the Hainich Critical Zone Exploratory and compared it to a previously published, extensive dataset of planktonic communities from the same aquifer ecosystem. Microbial lifestyle (attached vs. planktonic) explained more variance in community composition than redox conditions, prompting us to further investigate its role in shaping functional and activity profiles. Metagenomic analysis revealed a striking taxonomic and functional segregation: the 605 metagenome-assembled genomes (MAGs) from attached communities were dominated by Proteobacteria (358 MAGs) and were enriched in genes for biofilm formation, chemolithoautotrophy, and redox cycling (e.g., iron and sulfur metabolism). In contrast, the 891 MAGs from planktonic communities were dominated by Cand. Patescibacteria (464 MAGs) and Nitrospirota (60 MAGs) and showed lower functional versatility. Only a few genera were shared, and even closely related MAGs (>&#x2009;90% average nucleotide identity) differed in assembly size and metabolic traits, demonstrating lifestyle-specific functional adaptation. Analysis of active replication indicated that the active fraction of the attached community was primarily represented by the most abundant MAGs. Planktonic communities featured a higher fraction of active MAGs compared to attached communities, but overall with lower relative abundances.<br><br>CONCLUSIONS: The high abundance, metabolic specialization, and carbon fixation potential of attached microbes suggest that they are key drivers of subsurface biogeochemical processes. Carbonate aquifers may act as much larger inorganic carbon sinks than previously estimated based on CO2 fixation rates of the planktonic communities alone. Our findings underscore the need to incorporate attached microbial communities into models of subsurface ecosystem function. Video Abstract.},
}
@article {pmid41620643,
year = {2026},
author = {Ratcliff, JS and Kumari, M and Varga-Weisz, P and O'Gorman, R},
title = {Socioeconomic position and the gut microbiota: a narrative synthesis of the association and recommendations.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2623356},
pmid = {41620643},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Socioeconomic Factors ; Bacteria/classification/genetics/isolation &amp; purification ; *Social Class ; },
abstract = {Evidence suggests that socioeconomic position (SEP) may shape the gut microbiota (GM), representing a mechanism through which social and environmental factors may drive health inequalities, yet no systematic review has examined this association. In this narrative systematic review, we searched PubMed, Web of Science, and Scopus up to 30 November 2024 for observational studies examining associations between measures of SEP and GM diversity, composition, or function in participants of any age, ethnicity, or location. We identified 1,479 unique studies, of which 26 met the inclusion criteria for this review. Associations were observed between SEP indicators and GM features, including alpha (α) and beta (β) diversity, taxonomic composition, and functional pathways. Notably, socioeconomic patterns in α-diversity differed by context, with greater diversity observed in advantaged groups in high-income countries (HICs) but in disadvantaged groups in low- and middle-income countries (LMICs). Differences in β-diversity suggest that advantaged and disadvantaged groups have distinct GM profiles. Furthermore, considerable heterogeneity was evident across studies, particularly in sampling, sequencing, and analytical methods. Overall, socioeconomic-related differences in the GM are evident globally, highlighting the microbiota as a potential target for interventions aimed at reducing health disparities. Further research employing larger and more diverse cohorts, longitudinal designs, metagenomic sequencing approaches, and comprehensive measurement and adjustment of key covariates is needed to deepen understanding of this relationship.},
}
@article {pmid41619556,
year = {2026},
author = {Xiao, Y and Ke, C and Wang, D and Chen, N and Chen, G and Qu, L and Liu, Y},
title = {Atractyloside-A ameliorates spleen deficiency diarrhea in mice via modulating Lactobacillus johnsonii-butyric acid-GPR43 axis and NF-κB -NLRP3 signaling pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {152},
number = {},
pages = {157875},
doi = {10.1016/j.phymed.2026.157875},
pmid = {41619556},
issn = {1618-095X},
mesh = {Animals ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Signal Transduction/drug effects ; NF-kappa B/metabolism ; *Diarrhea/drug therapy ; Mice ; Receptors, G-Protein-Coupled/metabolism ; Gastrointestinal Microbiome/drug effects ; Male ; *Sesquiterpenes/pharmacology ; Fatty Acids, Volatile/metabolism ; Disease Models, Animal ; Lactobacillus/drug effects ; Mice, Inbred C57BL ; *Lactones/pharmacology ; *Saponins/pharmacology ; Spleen/drug effects ; },
abstract = {BACKGROUND: Spleen deficiency diarrhea (SDD) is regarded as a common gastrointestinal dysfunction in Traditional Chinese Medicine (TCM), which may lead to intestinal barrier damage and trigger intestinal inflammation. Previous studies have shown that Atractylenolide-A (AA) can effectively treat SDD by regulating intestinal flora. However, it remains uncertain whether AA can increase the levels of short-chain fatty acids (SCFAs) by restoring intestinal microbiota, thereby activating specific signaling pathways to regulate target protein and subsequently alleviate issues related to intestinal barrier function and inflammation.<br><br>PURPOSE: This study focused on examining the function of the signaling pathway involving microbiota, SCFAs, and G protein-coupled receptors (GPRs) in the anti-SDD effects of AA.<br><br>METHODS: The effects of AA on the Senna (SE) - induced SDD mouse model were assessed through various methods, including diarrhea scoring, H&amp;E staining, qRT-PCR, and ELISA analysis. Subsequently, targeted metabolomics was employed to pinpoint essential metabolites that influence the intestinal microenvironment, while western blotting was utilized to measure the expression of GPRs and the NLRP3 inflammasome. Additionally, experiments involving dietary supplementation with SCFAs and AAV-shGPR43 were performed to determine whether the pharmacological effects of AA operate through SCFAs and rely on GPR43. Key bacterial species that play a role in AA's modulation of SCFAs' pharmacological effects were identified through metagenomic sequencing and single-strain experiments.<br><br>RESULTS: The findings of this research revealed that AA is capable of significantly reducing the intestinal inflammatory response, reversing damage to mucin synthesis, and alleviating the pathological symptoms linked to SDD. Furthermore, the use of Lactobacillus johnsonii, sodium butyrate (NaB), and SCFAs individually can lead to notable enhancements in various phenotypes related to SDD. In terms of mechanism, AA achieves its anti-SDD effects by elevating the levels of Lactobacillus johnsonii, facilitating the concentration of butyric acid, boosting GPR43 expression, and modulating the TLR4/NF-&#x3ba;B signaling pathway, which in turn inhibits the assembly of the NLRP3 inflammasome. Nonetheless, following the injection of AAV-shGPR43, the advantageous effects of both AA and NaB were negated, underscoring the significance of this target.<br><br>CONCLUSIONS: Gut microbiota-SCFAs-GPRs axis and NF-&#x3ba;B-NLRP3 pathway involve in the alleviation of diarrhea and inflammation in SDD mice intervened with AA, AA promotes the production of butyrate by influencing Lactobacillus johnsonii, stimulates GPR43, and suppresses the formation of the NLRP3 inflammasome via the regulation of the TLR4/NF-&#x3ba;B signaling pathway, which subsequently improves SDD in mice.},
}
@article {pmid41619464,
year = {2026},
author = {Umunnawuike, C and Abutu, D and Nwaichi, PI and Nyah, F and Agi, A},
title = {Thermophilic biohydrogen production from reservoir residual hydrocarbons using palm oil mill effluent-derived microbial consortia.},
journal = {The Science of the total environment},
volume = {1016},
number = {},
pages = {181482},
doi = {10.1016/j.scitotenv.2026.181482},
pmid = {41619464},
issn = {1879-1026},
mesh = {*Palm Oil ; *Hydrogen/metabolism ; *Microbial Consortia ; *Petroleum/metabolism ; Biodegradation, Environmental ; Bioreactors ; Oil and Gas Fields ; Hydrocarbons/metabolism ; Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/metabolism ; },
abstract = {Residual crude oil remaining in depleted reservoirs represents a largely untapped carbon source for biological hydrogen generation. Previous studies have relied on indigenous bacteria present in oil reservoirs but reported low hydrogen yields, as not all reservoir microorganisms are hydrogen-producing. Therefore, in this study, external mixed culture bacterial consortia obtained from palm oil mill effluent (POME) were used to degrade crude oil for hydrogen production. Morphological changes in microbial communities were assessed using field emission scanning electron microscopy. Metagenomic profiling was conducted to identify the dominant microbial taxa capable of producing biohydrogen. Thereafter, a high-temperature and high-pressure (800 °C/30 MPa) stainless-steel bioreactor containing crude oil was inoculated with mixed culture consortia to simulate an oilfield reservoir for hydrogen production. Box-Behnken design was applied to systematically examine the effects of exposure time (6-90 h), crude oil volume (10-40 mL), and temperature (35-70 °C) on continuous hydrogen production. Statistical analysis of variance was used to evaluate model parameters. Heat pretreatment selectively enriched hydrogenogenic spore-formers (Clostridium and Bacillus), resulting in a ~ 4-fold increase (97.40 ± 0.02 mL/L) in hydrogen yield compared to 25.68 ± 0.04 mL/L POME for untreated sludge. In the presence of crude oil, the optimum hydrogen production was 152.50 ± 0.01 mL/L at 50 °C, compared to 125.45 ± 0.03 mL/L and 29.95 ± 0.01 mL/L crude oil at 35 °C and 70 °C, respectively. Predicted hydrogen production, with R[2] value of 97.4% close to unity, indicates that the model was highly consistent with the experimental results, with high precision and reliability. Thermodynamic analysis shows negative Gibbs free energy changes of -122 to -236 kJ/mol, demonstrating that hydrocarbon-to‑hydrogen conversion was energetically favorable and feasible across all tested temperatures. Overall, the experimental, statistical, and thermodynamic analyses establish the technical and energetic feasibility of microbial enhanced hydrogen recovery in depleted oil reservoirs.},
}
@article {pmid41619244,
year = {2025},
author = {Zahanuddin, A and Rahim, FF and Lau, YL and Mokhtar, AS},
title = {Genetic diversity, microbiome composition and socio-sanitary predictors of head lice (Pediculus humanus capitis) among disadvantaged children in Klang Valley, Malaysia.},
journal = {Tropical biomedicine},
volume = {42},
number = {4},
pages = {435-445},
doi = {10.47665/tb.42.4.010},
pmid = {41619244},
issn = {2521-9855},
mesh = {Humans ; Malaysia/epidemiology ; *Pediculus/genetics/classification ; Animals ; *Microbiota ; Male ; *Lice Infestations/epidemiology/parasitology ; Female ; Child ; Child, Preschool ; *Genetic Variation ; RNA, Ribosomal, 16S/genetics ; Vulnerable Populations ; Infant ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Pediculosis capitis remains a neglected public health issue in Malaysia, particularly among disadvantaged children. While the genetic diversity of head lice is well studied, their associated microbiome and links to socio-sanitary conditions remain unclear. This study examined 266 children from ten children's establishments in Klang Valley and Greater Kuala Lumpur, of whom 89 (33.46%) were positive for pediculosis capitis. Cytochrome c oxidase subunit I (COI) barcoding identified two clades: A (36%) and C (64%). 16S rRNA metagenomic profiling of pooled samples revealed higher microbial diversity in Clade C compared to Clade A, with opportunistic bacteria, including Propionibacterium acnes, Streptococcus spp., Bacteroides fragilis, and Staphylococcus aureus being detected. Logistic regression identified age, head lice awareness, and eating with hands as significant predictors of infection. These findings demonstrate that head lice not only cluster genetically but also may harbour clade-dependent microbiomes, with potential health implications. The integration of genetic diversity, microbial variation, and socio-sanitary data highlights the multifactorial risks of pediculosis capitis in vulnerable populations, underscoring the importance of combined ectoparasite control and hygiene interventions.},
}
@article {pmid41618437,
year = {2026},
author = {Chong-Nguyen, C and Fuentes Artiles, R and Pilgrim, T and Yilmaz, B and Döring, Y},
title = {The gut-heart axis in coronary artery disease: a scoping and narrative review of sex-based microbial and metabolic disparities.},
journal = {Biology of sex differences},
volume = {17},
number = {1},
pages = {24},
pmid = {41618437},
issn = {2042-6410},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Coronary Artery Disease/microbiology/metabolism ; *Sex Characteristics ; Female ; Male ; },
abstract = {BACKGROUND: The gut microbiota significantly influences cardiovascular health by regulating host metabolism and generating bioactive compounds like trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), both linked to coronary artery disease (CAD). Emerging research indicates sex-based differences in microbial composition and metabolite production, yet their impact on CAD pathophysiology remains unclear. This scoping review summarizes current findings on sex-specific microbial and metabolic differences in individuals with CAD.<br><br>METHODS: A systematic search of PubMed and EMBASE was conducted through March 2025 for peer-reviewed studies comparing gut microbiota or metabolite profiles between male and female patients with CAD. Eligible studies used 16S rRNA sequencing, shotgun metagenomics, or metabolite profiling to analyze microbial communities and atherosclerosis-associated metabolites. Mechanistic links from genetics, epigenetics, and hormone-microbiota interactions were integrated to provide a more comprehensive understanding of how gut microbiota may contribute to sex differences in CAD.<br><br>RESULTS: Eleven studies met the inclusion criteria for this review. Men with CAD exhibited increased relative abundances of taxa such as Prevotella, Clostridia_UCG_014, UCG_010, and other pro-inflammatory genera, whereas women microbiota was comparatively enriched in Barnesiella, Bifidobacteriales, and other potentially beneficial taxa. Parallel differences emerged in microbial metabolite profiles: men demonstrated elevated plasma levels of TMAO and IS, both associated with heightened cardiovascular risk and disease burden. Conversely, women with CAD had higher circulating levels of secondary bile acids and lower TMAO concentrations.<br><br>CONCLUSION: Preliminary studies suggest sex-related differences in gut microbiota composition and metabolite profiles in CAD patients. Integrating mechanistic links from microbial metabolism, genetics, epigenetics, and hormones supports a potential role of the microbiota in sex-dependent disease pathways. Current evidence is limited and mostly observational; well-designed studies are needed to clarify mechanisms, clinical relevance of sex-specific microbiome signatures and specifically assess whether these sex-specific microbial and metabolic differences influence CAD progression and outcomes.},
}
@article {pmid41618383,
year = {2026},
author = {Pérez-Pérez, L and Arguello, H and Cobo-Díaz, JF and Galisteo, C and Puente, H and Gómez-Martínez, S and Carvajal, A},
title = {From predisposition to recovery: field evidence of interactions between the gut microbiota and Brachyspira hyodysenteriae infection.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {25},
pmid = {41618383},
issn = {1297-9716},
support = {PRE2020-093762//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; EDU-1868-2022//Junta de Castilla y Le&#xf3;n/ ; },
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; *Swine Diseases/microbiology ; *Gram-Negative Bacterial Infections/veterinary/microbiology ; *Brachyspira hyodysenteriae/physiology ; Feces/microbiology ; Disease Susceptibility/veterinary/microbiology ; },
abstract = {Restrictions on antibiotics use have increased interest in the gut microbiota relationship to host health, particularly in enteric infections. The present field study, performed on two farms with endemic swine dysentery (SD) infection, characterises the faecal microbiota in 102 faecal samples from 13 diseased and 13 non-diseased pigs by shotgun metagenomic sequencing. The samples were collected during four samplings, which allowed us to monitor the animals before, during and after the clinical disease to investigate the role of the gut microbiota in disease outcome, assess the impact of infection on microbial composition and evaluate the microbiota evolution following recovery. Samples collected before disease demonstrated that SD susceptible pigs had lower microbial diversity, with significantly lower abundance of Treponema rectale, Prevotella spp. or Ruminiclostridium E compared with SD resistant pigs, which remained healthy. Marked alterations in microbial species composition and their functional profiles were evident during clinical disease. Brachyspira hyodysenteriae, Dysosmobacter sp. BX15, Acetivibrio ethanolgignens and Mucispirillum sp. 910586745 were significantly increased in abundance, which was associated with an increase of functions such as Bacteroides capsular polysaccharide transcription antitermination proteins or pterin carbinolamine dehydratase. No changes in the microbiota were observed after the disease when compared with non-diseased pigs, thus evidencing a restoration of the microbiota composition after therapeutic treatment and recovery. The study demonstrates that the microbiota may play a relevant role in SD disease outcome and evidences the changes that occur during clinical disease do not persist over time after pig therapeutic treatment.},
}
@article {pmid41617723,
year = {2026},
author = {Pratama, AA and Pérez-Carrascal, O and Sullivan, MB and Küsel, K},
title = {Diversity and ecological roles of hidden viral players in groundwater microbiomes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68914-2},
pmid = {41617723},
issn = {2041-1723},
support = {EXC 2051, Project-ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DE-SC0023307//U.S. Department of Energy (DOE)/ ; },
abstract = {Groundwater ecosystems harbor diverse microbial communities adapted to energy-limited, light-deprived conditions, yet the role of viruses in these environments remains poorly understood. Here, we analyzed 1.24 terabases of metagenomic and metatranscriptomic data from seven wells in the Hainich Critical Zone Exploratory (CZE) to characterize groundwater viromes. We identified 257,252 viral operational taxonomic units (vOTUs) (≥ 5 kb), with 99% novel at order, family and genus levels against global ocean, freshwater and/or other publicly available datasets. In silico host predictions suggest that vOTUs primarily targeted Proteobacteria, Candidate Phyla Radiation (CPR) bacteria, and DPANN archaea, which reflects abundant and active groundwater microbial members. Patterns of virus-host abundance ratios, CRISPR-spacers, and prophage screening suggest the potential for multi-layer interactions involving CPR/DPANN lineages, their hosts, and viruses. Additionally, we identified 289 KEGG metabolic modules, 31.1% of which were targeted by 3378 vOTUs encoded auxiliary metabolic genes (AMGs) linked to carbon, nitrogen, and sulfur cycling. These findings provide a baseline for exploring how viruses influence microbial community dynamics, metabolic reprogramming and nutrient cycling in groundwater.},
}
@article {pmid41616776,
year = {2026},
author = {Liu, C and Sun, S and Ren, X and Geisen, S and Wang, S and Jiang, G and Xu, Y and Shen, Q and Jousset, A and Wei, Z and Xiong, W},
title = {Predation by soil protists shifts bacterial metabolism from competitive to cooperative interactions.},
journal = {Cell host &amp; microbe},
volume = {34},
number = {2},
pages = {201-211.e6},
doi = {10.1016/j.chom.2026.01.006},
pmid = {41616776},
issn = {1934-6069},
mesh = {*Soil Microbiology ; *Bacteria/metabolism/genetics/classification ; Rhizosphere ; *Microbial Interactions ; *Soil/parasitology ; Microbiota ; *Eukaryota/physiology ; Metagenomics ; },
abstract = {Many soil protists are bacterivores, yet how protist predation reshapes bacterial metabolic interactions and functions remains poorly understood. Here, we combine global soil samples with microbial metabolic simulations, along with soil microcosm-pot validations, to investigate the influence of protists on bacterial metabolic interactions. Across 3,785 metabolic simulations spanning 757 soils, increased protists predicted higher bacterial metabolic interaction potential and cross-feeding but lower metabolic resource overlap and competition. These patterns were confirmed using an independent rhizosphere dataset and metagenomic analysis. Protist predation selected bacterial communities containing GC-rich genomes, acid-carbon-preferring taxa, and enhanced metabolite exchange. Additionally, exposing a synthetic community (SynCom) to protist predation elevated the expression of bacterial genes associated with plant growth-promoting functions. Consistently, microcosm- and pot-based experiments showed that protist addition increased bacterial cross-feeding over time and improved plant performance. Together, we establish a scalable framework to evaluate protist-driven bacterial cooperation and function to guide rational rhizosphere microbiome engineering.},
}
@article {pmid41616716,
year = {2026},
author = {Breyer, GM and Torres, MC and Rebelatto, R and Wuaden, CR and Pastore, J and Lazzarotti, M and Nicoloso, RDS and Dorn, M and Kich, JD and Siqueira, FM},
title = {From farm to environment: the microbiome and the silent spread of antimicrobial resistance genes in soil despite manure management in swine farms.},
journal = {Journal of environmental management},
volume = {400},
number = {},
pages = {128747},
doi = {10.1016/j.jenvman.2026.128747},
pmid = {41616716},
issn = {1095-8630},
mesh = {*Manure/microbiology ; Animals ; Swine ; *Microbiota ; *Soil Microbiology ; Farms ; Soil ; Fertilizers ; Bacteria ; },
abstract = {The swine industry generates large amounts of organic waste containing antimicrobial residues, requiring efficient manure management to reduce environmental risks. Covered lagoon biodigesters (CLBs) and waste stabilization ponds (WSPs) are commonly used digestion systems, with digestates subsequently applied as organic fertilizers. Although these systems successfully reduce pathogenic bacteria, their effectiveness in removing antimicrobial resistance genes (ARGs) remains unclear. In this study, we compared microbiome and resistome profiles from CLB- (n = 23) and WSP-farms (n = 20) using shotgun metagenomic sequencing of raw and digested manure, as well as fertilized and non-fertilized soils. Our findings indicate that digestate application slightly shifted soil microbial communities and significantly increased bacterial diversity, suggesting the introduction of diverse manure-derived bacteria. Reads from taxonomic markers associated with clinically important pathogens, including Enterobacterales, streptococci (groups A and B), Enterococcus faecium, Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, and Salmonella enterica were still detected in digestates and fertilized soils, regardless of the digestion system. Moreover, DNA sequences associated with ARGs against critical antimicrobials, such as carbapenems, cephalosporins, and glycopeptides persisted. Notably, WSPs exhibited greater accumulation of some ARGs, including OXA-347 and vanG. Overall, although CLBs exerted a lower impact on soil microbial communities and resistomes compared to WSPs, neither system effectively eliminated ARGs. These findings highlight the potential for environmental dissemination of ARGs through manure fertilization and underscore the urgent transition toward more sustainable production practices, including eliminating non-therapeutic antimicrobial use in the swine industry, as well as the need for improved digestion technologies and continuous monitoring under the One Health framework.},
}
@article {pmid41616624,
year = {2026},
author = {Sun, Y and Zhang, M and Teng, Y and Yin, Y and Ran, J and Su, H and Li, H and Huang, X and Long, Z and Sun, X and Pan, H and Wang, X and Li, M},
title = {Human activities and horizontal gene transfer shape the resistome landscapes of non-human primates.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141276},
doi = {10.1016/j.jhazmat.2026.141276},
pmid = {41616624},
issn = {1873-3336},
mesh = {Animals ; *Gene Transfer, Horizontal ; *Primates/microbiology ; Humans ; *Human Activities ; China ; *Drug Resistance, Microbial/genetics ; Soil Microbiology ; *Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Antibiotic resistance represents a growing threat to human, animal, and ecosystem health, yet its dynamics in wildlife remain poorly understood. We conducted a systematic analysis of the gut resistomes in non-human primates (NHPs) and environmental soils in Guizhou Province, China, a biodiversity hotspot. Metagenomic analyses reveal that human activities and horizontal gene transfer (HGT) influence primate resistome landscapes and enhance their dissemination potential. A total of 1927 antibiotic resistance ontologies (AROs) distributed across 1477 species-level genome bins (SGBs), providing a comprehensive genomic catalog of the NHPs resistome. Bacterial genera such as Pseudomonas, Stenotrophomonas, and Comamonas drive ARG mobilization, with a core subset of ARGs that reliably predict overall resistance burdens. Notably, widely distributed primate species, with large habitat ranges and frequent interspecies interactions exhibit the most potential for ARG dissemination. Ecological modeling identifies current and future hotspot regions requiring prioritized monitoring amid ongoing human disturbance and climate change. These findings provide a molecular-indicator-based framework for environmental antibiotic resistance (AR) monitoring and conservation strategies for endangered species. Despite limitations in temporal and spatial coverage, our study highlights the need to integrate wildlife, particularly NHPs, as sentinel species into "One Health" AR surveillance and policy. This approach will strengthen our understanding of ARG transmission dynamics and their long-term impacts on host adaptation, ecosystem stability, and public health.},
}
@article {pmid41615027,
year = {2025},
author = {Jiménez, DJ and Marasco, R and Schultz, J and Díaz Rodríguez, CA and Nogales, J and Rodriguez-R, LM and Overmann, J and Rosado, AS},
title = {Discovery and cultivation of prokaryotic taxa in the age of metagenomics and artificial intelligence.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wrag012},
pmid = {41615027},
issn = {1751-7370},
support = {MCIN/AEI/10.13039/501100011033//Spanish Ministry of Science and Innovation/ ; 101081782 (deCYPher)//European Union/ ; 101036768 (PROMISEANG)//European Union/ ; PID2022-139247OB-I00 (Rob3D)//European Union/ ; BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {*Metagenomics/methods ; *Artificial Intelligence ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; Microbiota ; *Archaea/genetics/classification/isolation &amp; purification/growth &amp; development ; },
abstract = {Despite advances in sequencing, microbial genomics, and cultivation techniques, the vast majority of prokaryotic species remain uncultured, which is a persistent bottleneck in microbiology and microbial ecology. This perspective outlines a conceptual framework to improve the transition from genome-resolved metagenomics to the targeted isolation of yet-uncultured prokaryotic taxa. The proposed framework integrates the induced reshaping of microbiomes, genome-based inferences of physiological and phenotypic traits, culture media design, and targeted culturomics, enabling hypothesis-driven cultivation. In addition, this manuscript addresses the critical limitations in the field, including the sequence-to-function gap, and emphasizes the synergistic potential of experimental microbiology, microbial ecology, metagenomics, and artificial intelligence-based predictions to enhance rational and actionable roadmaps for discovering and cultivating novel prokaryotic lineages.},
}
@article {pmid41612472,
year = {2026},
author = {Wang, Y and Shen, Y and Shen, J and Bi, J and Xu, J and Wei, T and Wang, R and Wu, X and Li, F and Bai, J and Jie, Z and Hou, D and Song, Y},
title = {Airway microbiome dysbiosis in severe pneumonia: metagenomic evidence of pathogen expansion and commensal depletion.},
journal = {European journal of medical research},
volume = {31},
number = {1},
pages = {},
pmid = {41612472},
issn = {2047-783X},
support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-18//Shanghai Three-year Action Plan to Strengthen the Construction of Public Health System/ ; 82130001//National Natural Science Foundation of China/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; GZNL2024A02003//R&amp;D Program of Guangzhou National Laboratory/ ; W2020-013//The Construction of Multi-Disciplinary Treatment System for Severe Pneumonia/ ; 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Male ; Female ; Middle Aged ; *Microbiota/genetics ; Prospective Studies ; Aged ; Metagenomics ; *Pneumonia/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {BACKGROUND: The pulmonary microbiome is increasingly recognized as a key determinant of pneumonia severity, yet its clinical implications remain incompletely understood. Disruption of microbial ecology, or dysbiosis, may impair host immune responses and exacerbate disease progression. This study aimed to characterize microbiome alterations associated with severe pneumonia and their correlation with host inflammatory and coagulative parameters.<br><br>METHODS: In this multicenter, prospective observational cohort study conducted across nine hospitals in Shanghai (2021-2025), bronchoalveolar lavage fluid (BALF) samples from 306 patients with clinically diagnosed pulmonary infections were analyzed using metagenomic next-generation sequencing (mNGS). Patients were stratified into severe (n&#x2009;=&#x2009;196) and non-severe (n&#x2009;=&#x2009;110) groups using WHO-derived severe pneumonia criteria at the time of bronchoalveolar lavage (BAL). Microbial taxonomic profiles, diversity indices, co-occurrence networks, and correlations with clinical markers were comprehensively assessed using standard bioinformatic and statistical approaches.<br><br>RESULTS: Severe pneumonia was associated with marked microbial dysbiosis, including reorganization of co-occurrence network topology with centrality shifting away from commensals toward opportunistic taxa in severe disease, characterized by reduced &#x3b1;-diversity, altered &#x3b2;-diversity, and enrichment of opportunistic Gram-negative pathogens including Acinetobacter and Klebsiella. In contrast, commensals such as Rothia and Prevotella were depleted. Co-occurrence network analysis revealed fragmentation of microbial interactions in severe cases, with centrality shifting from commensals to opportunists like Corynebacterium striatum. Shannon diversity negatively correlated with SOFA scores, and specific taxa positively associated with systemic inflammation (CRP, PCT) and coagulation abnormalities. Nearly all samples demonstrated polymicrobial infection, with distinct microbial patterns observed across monomicrobial and polymicrobial subgroups.<br><br>CONCLUSION: Our multicenter observational analysis suggests that severe pneumonia is associated with marked ecological disruption of the lower-airway microbiome, characterized by commensal loss, opportunist expansion, and fragmented interspecies networks, and with concurrent inflammatory and coagulative abnormalities. These hypothesis-generating findings warrant external validation in independent, multi-region cohorts and longitudinal sampling to test directionality and causality before informing clinical decision-making.},
}
@article {pmid41611865,
year = {2026},
author = {Ulloa, MA and Serrano, AV and Camelo, LC and Guyot, R and Vela, D and Muñoz, AR},
title = {Bacterial genome reconstruction and community profiling in Neotropical Drosophila.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6601},
pmid = {41611865},
issn = {2045-2322},
mesh = {Animals ; *Drosophila/microbiology/genetics ; *Genome, Bacterial ; Phylogeny ; *Microbiota/genetics ; Metagenomics/methods ; Ecuador ; *Bacteria/genetics/classification ; },
abstract = {Drosophila species serve as key models for microbiota research due to their relatively simple microbial communities. However, microbial diversity and dynamics in Neotropical Andean Drosophila remain underexplored. Here we applied shotgun metagenomics to characterize the microbiota of 24 Neotropical Drosophila species from Ecuador, reconstructing 64 high-quality bacterial genomes predominantly from Acetobacteraceae and Enterobacterales. Microbial communities were consistently dominated by yeasts, lactic acid bacteria, acetic acid bacteria, and Wolbachia. Comparative analyses revealed no strong correlation between host phylogeny and microbial community composition, suggesting environmental factors and microbial interactions shape these communities. Notably, shifts in relative abundances indicate dynamic ecological succession and metabolic cooperation among microbes. These findings expand genomic resources for Drosophila-associated bacteria and highlight the complex ecological processes influencing host-microbiota relationships in natural populations.},
}
@article {pmid41611767,
year = {2026},
author = {Jain, AG and Agwan, D and Kumar, A and Pancha, I and Rathod, J and Mohapatra, B},
title = {Mixing regimes shape microbial community composition, nutrient regimes, and plant growth attributes in Jeevamrit: metagenomics and culturomics-based insights.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6603},
pmid = {41611767},
issn = {2045-2322},
support = {GSBTM/JD(R&amp;D)/661/2022-23/00173054//GSBTM/ ; },
mesh = {*Metagenomics/methods ; *Soil Microbiology ; *Microbiota ; *Plant Development ; Soil/chemistry ; *Bacteria/genetics/classification ; *Nutrients/metabolism ; Nitrogen/metabolism ; },
abstract = {Jeevamrit, a microbial inoculant widely used in zero-budget natural farming (ZBNF) that relies on local farm-based resources to enhance overall biological health of soil, is reported for inconsistent crop yield enhancements. This is mainly due to variability in its preparation methods, e.g., mixing intensity, incubation regimes, and quality of ingredients used. Hence, the current study aimed to decipher the effect of mixing intensity (extent of oxygenation) on microbial community composition, nutrient transformation, and plant growth attributes of Jeevamrit, using a combined metagenomics-culturomics approach. Frequent mixing (Constant/Intermediate) enhanced nutrient solubilization (Fe, Zn, Cu, Mn) with higher total N and dissolved organic carbon, while less mixing (Anoxic/No-mix) led to accumulation of soluble Fe and NH4[+]-N with higher microbial diversity. Mixing-driven differential enrichment of taxa were noted, i.e., constant mixing (CM) dominated by Acinetobacter (~ 40%), Comamonas, Pseudomonas, and Lysinibacillus, linked to oxidative C/N cycling and metal dissolution. Whereas, anoxic (AO) favored Clostridium sensu stricto, Lactobacillales, Enterococcus, and Enterobacterales (> 60%), correlating to fermentative metabolism-driven reductive elemental cycling. Co-occurrence network analysis identified Acinetobacter, Pseudomonas, Comamonas, Trichococcus, and Stenotrophomonas as hubs, indicating keystone functions in structuring metabolic interactions. The metagenome-recovered MAGs belonged to Acinetobacter sp., Clostridium saccharobutylicum, Trichococcus flocculiformis, and Enterococcus gallinarum with potential to participate in multiple nutrient cycling. Cultivable members of Shigella, Rhodococcus, and Bacillus spp. showed high IAA production (135-145 µg mL[-][1]), NH3 release (~ 0.12 µg mL[-][1]), and K and P solubilization (~ 55.2 µg mL[-][1]). We hypothesize that oxygenation drives the Jeevamrit's microbial guild assembly, where mixing intensity modulates oxido-reductive metabolism and nutrient mobilization efficiency, indicating the requirement for standardization of formulation aligned to soil-specific conditions.},
}
@article {pmid41611051,
year = {2026},
author = {Shi, J and Sun, C and Su, Y and Wu, Y and Zhan, M and Ji, C and Wang, R and Lv, B},
title = {Ecosystem-specific composition and drivers of plastisphere resistome in freshwater and marine environments.},
journal = {Environmental research},
volume = {294},
number = {},
pages = {123858},
doi = {10.1016/j.envres.2026.123858},
pmid = {41611051},
issn = {1096-0953},
mesh = {Fresh Water/microbiology ; *Seawater/microbiology ; *Microbiota ; *Ecosystem ; *Water Pollutants, Chemical ; *Microplastics ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; },
abstract = {Microplastics in aquatic environments facilitate the formation of specific plastisphere microbiomes and serve as potential hotspots for antibiotic resistance genes (ARGs) propagation. However, the systematic comparisons of ARG profiles on microplastics from different aquatic ecosystems remain limited, particularly the prevalent ARGs and their bacterial hosts. This study performed a comparative meta-analysis of existing metagenomic datasets to investigate the resistome between freshwater and seawater microplastics (FMP and SMP) and their driving factors. Our results revealed that the ARG profiles on both FMP and SMP were significantly distinct from their surrounding waterbody. Moreover, FMP exhibited a higher diversity and abundance of ARGs rather than SMP. Ten core ARGs were shared on FMP and SMP, while 23 core ARGs were exclusively detected on FMP. The bacterial community on microplastics exhibited an ecosystem-specific composition, and was identified as the primary determinant shaping the ARG profiles. Notably, more complex bacteria-ARG co-occurrence pattern was identified on FMP, involving a broader spectrum of core genera and potential pathogenic hosts (e.g., Mycobacterium, Streptomyces). Furthermore, a significant and specific correlation between mobile genetic elements and ARGs was identified on FMP but not SMP, suggesting a markedly elevated horizontal gene transfer potential, with mechanistic support from the concurrent enrichment of oxidative stress and SOS response genes on FMP. These findings provide a comprehensive characterization of ARGs on aquatic microplastics, and especially highlight the role of FMP in the ARG dissemination.},
}
@article {pmid41609355,
year = {2026},
author = {Li, Y and Li, Q and Quan, K and Xie, Y and Yang, N and Ma, T and Zheng, L and Zhou, W and Li, Y and Jin, H and Sun, Z and Chen, Y and Kwok, L-Y and Lu, N and Zhu, W and Liu, W and Zhang, H},
title = {Adjunctive probiotic therapy sustains symptom relief in gastroesophageal reflux disease through gut microbiome-metabolome remodeling.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0156825},
pmid = {41609355},
issn = {2379-5077},
support = {No.2022LJRC0003//the Inner Mongolia Autonomous Region Science and Technology Leading Talent Team Project/ ; No. U22A20540//National Natural Science Foundation of China/ ; No. 2022YFD2100700//National Key Research and Development Program of China/ ; CARS-36//the Earmarked Fund for China Agriculture Research System/ ; BX20250337//the China National Postdoctoral Program for Innovative Talents/ ; },
mesh = {Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Middle Aged ; *Gastroesophageal Reflux/microbiology/drug therapy/metabolism/therapy ; Double-Blind Method ; Adult ; *Metabolome/drug effects ; Treatment Outcome ; Rabeprazole/therapeutic use ; Proton Pump Inhibitors/therapeutic use ; Aged ; },
abstract = {Proton pump inhibitors (PPIs) are standard therapy for gastroesophageal reflux disease (GERD), but long-term use causes dysbiosis, gastrointestinal side effects, and symptom relapse after discontinuation. Probiotics may offer adjunctive benefits by modulating the gut ecosystem. The study aimed to evaluate the efficacy of a multi-strain probiotic (Lihuo) with rabeprazole in GERD and its impact on gut microbiota and metabolome. A randomized, double-blind, placebo-controlled trial was conducted in 120 GERD patients assigned to receive rabeprazole with either Lihuo (n = 64) or placebo (n = 56) for 8 weeks, followed by 4 weeks of probiotic or placebo alone. The primary outcome was change in the Reflux Disease Questionnaire (RDQ) score. Secondary outcomes included Gastrointestinal Symptom Rating Scale, endoscopic healing, and multi-omics profiling (shotgun metagenomics, phageome, and untargeted/targeted metabolomics). Compared with the placebo group, the probiotic group exhibited a pronounced 36.51% reduction in RDQ scores after 12 weeks of intervention (P = 0.017), alongside a higher numerical endoscopic healing rate (36.84% vs 12.50%; P = 0.365). Metagenomics revealed enrichment of Bifidobacterium animalis, Lactiplantibacillus plantarum, and Clostridium sp900540255, with reductions in Bacteroides uniformis and Clostridium Q fessum. Metabolomics showed increased γ-aminobutyric acid, succinate, citrulline, and short-chain fatty acids levels, with interesting microbe-metabolite correlations such as Bifidobacterium animalis-γ-aminobutyric acid and Bacteroides fragilis-succinate (r ≥ 0.30, P < 0.01). Our findings support that adjunctive probiotic therapy sustains post-PPI symptom relief, associated with targeted modulation of gut microbiota and bioactive metabolites.IMPORTANCELong-term proton pump inhibitor use in gastroesophageal reflux disease (GERD) may disrupt gut microbiota and cause symptom relapse after discontinuation. We found that adjunctive probiotic therapy sustained reflux reduction post-proton pump inhibitor. Probiotic use enriched beneficial taxa (Bifidobacterium and Lactiplantibacillus plantarum) and increased γ-aminobutyric acid, succinate, citrulline, and short-chain fatty acids. Strong correlations linked microbial shifts to metabolic and clinical improvements. This study demonstrates that adjunctive probiotic therapy enhances symptom control and supports microbial-metabolic homeostasis in GERD.CLINICAL TRIALSThis study is registered with the Chinese Clinial Trial Registry as ChiCTR2000038409.},
}
@article {pmid41609167,
year = {2026},
author = {Koo, WLY and Thng, KX and Tiew, PY and Chotirmall, SH},
title = {The Airway Microbiome in Chronic Obstructive Pulmonary Disease (COPD): A Guide for Clinicians.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {87},
number = {1},
pages = {50163},
doi = {10.31083/BJHM50163},
pmid = {41609167},
issn = {1750-8460},
support = {MOH-001636//National Research Foundation Singapore/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000710//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001275-00//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000955//Singapore Ministry of Health's National Medical Research Council/ ; RT1/22//Singapore Ministry of Education/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/therapy ; *Microbiota ; Dysbiosis/microbiology ; *Lung/microbiology ; Disease Progression ; },
abstract = {Chronic obstructive pulmonary disease (COPD) is a progressive and debilitating respiratory condition marked by chronic symptoms and frequent exacerbations, contributing to significant morbidity and mortality. The advent of molecular microbiology and next-generation sequencing (NGS) has expanded our understanding of the lung microbiome, and integration of microbiome datasets with other omics reveals important microbial-metabolic-immuno-inflammatory interactions that influence COPD pathogenesis. Recent studies have highlighted dysbiosis of the airway microbiome, with shifts in bacterial, viral, and fungal communities playing a crucial role in disease progression, exacerbations and clinical outcomes. Moreover, microbiome changes are observed in COPD associated overlap syndromes, complicating diagnosis and treatment. This review synthesizes current microbiome research in COPD, focusing on its clinical relevance, including its potential as a diagnostic and prognostic tool. We additionally discuss the challenges of integrating microbiome data into clinical practice, emphasizing the need for personalized, precision medicine approaches to optimize COPD management and improve patient outcomes.},
}
@article {pmid41606855,
year = {2025},
author = {Yang, J and He, Y and Huang, J and Li, M and Wu, X and Pei, X and Yang, X},
title = {Decoding resistome profiles and horizontal transfer of antibiotic resistance genes across the pork production chain under One Health sectors.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 1},
pages = {117259},
doi = {10.1016/j.foodres.2025.117259},
pmid = {41606855},
issn = {1873-7145},
mesh = {*Gene Transfer, Horizontal ; Animals ; Swine ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *One Health ; *Drug Resistance, Bacterial/genetics ; *Pork Meat/microbiology ; Food Microbiology ; Abattoirs ; Metagenome ; Microbiota/genetics ; Metagenomics ; Bacteria/genetics ; },
abstract = {The emergence of antimicrobial resistance has become a global threat to public health. Intensive antibiotic use in swine farming has accelerated the proliferation of antibiotic resistance genes (ARGs) in animal-derived foods, making the production chain a potential ARG transmission route to humans. However, shared resistome profiles and horizontal gene transfer (HGT) mechanisms along this chain remain unclear. Here, we systematically investigated the resistome profile, ARGs' host, and potential HGT of ARGs across interconnected swine farm, slaughterhouse, and retail market by metagenomic assembly and binning. From 42 metagenomes, 1354 ARG subtypes were identified, with 303 shared across all interfaces. Both microbiome and mobile genetic elements (MGEs) contributed to the variation in ARG profiles. Pseudomonadota were the dominant drivers that shape the resistome through plasmid-mediated HGT. Among the 133 reconstructed ARG-carrying genomes (ACGs), 38 of them carried multiple ARGs, indicating the potential mobility of ARGs. Notably, 3 ACGs taxonomically assigned to Pseudomonas_E alcaligenes, Serratia_J grimesii, and Escherichia coli carrying 9, 13, and 41 ARGs, respectively. Furthermore, MetaCHIP analysis uncovered 445 potential HGT events, and ARGs including CpxR, macB, fusA, and vanR were annotated as potentially transferred subtypes. This study decodes the resistome profiles and tracks horizontal ARG transfer at the community level across the entire pork supply chain - from swine farms to retail outlets. To our knowledge, few studies have explored ARG transmission subtypes and directional flows among humans, pigs, and environmental compartments in the pork production chain using metagenomic approaches. These findings highlight the important role of the pork production chain as a critical transmission vector for ARGs under One Health framework.},
}
@article {pmid41606854,
year = {2025},
author = {Okoye, CO and Abhadiomhen, SE and Ezenwanne, BC and Chen, X and Jiang, H and Wu, Y and Jiang, J},
title = {Machine learning-based predictive modeling of foodborne pathogens and antimicrobial resistance in food microbiomes using omics techniques: A systematic review.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 1},
pages = {117255},
doi = {10.1016/j.foodres.2025.117255},
pmid = {41606854},
issn = {1873-7145},
mesh = {*Machine Learning ; *Food Microbiology ; *Foodborne Diseases/microbiology ; *Microbiota ; *Drug Resistance, Bacterial/genetics ; Animals ; Genomics/methods ; Metagenomics ; Salmonella/pathogenicity/genetics ; Food Safety ; Humans ; },
abstract = {The globalization of food systems has heightened the risk of foodborne pathogens such as Salmonella, Listeria monocytogenes, and Campylobacter, exacerbated by rising antimicrobial resistance (AMR). Traditional pathogen identification and AMR risk surveillance methods are often labor-intensive and low-throughput, while single-omics approaches fail to capture microbial complexity. Moreover, reliance on individual machine learning (ML) models limits predictive robustness, posing challenges to food safety and public health. This systematic review evaluates ML-based predictive modeling integrated with omics techniques (genomics, metagenomics, and transcriptomics) for foodborne pathogen and AMR risk surveillance. Following PRISMA guidelines, 1245 articles from PubMed, Scopus, and other databases (2015-2025) were screened, selecting 13 relevant studies. These studies applied ML algorithms, including Random Forest (RF), Extreme Gradient Boosting (XGBoost), and Support Vector Machines (SVM), to enhance predictive accuracy. The selected studies demonstrated predictive accuracies up to 99 % and AUROC scores above 0.90. Key discoveries include genetic markers for Salmonella virulence, Listeria attribution to fruits and dairy, and 145 mobile antimicrobial resistance genes (ARGs) in poultry. Despite these advancements, limitations such as small sample sizes, inconsistent metadata, overfitting, and computational scalability hinder real-world implementation. This review underscores the potential of ML-driven omics frameworks to revolutionize foodborne pathogen and AMR risk monitoring, paving the way for smarter, more resilient food safety systems. However, methodological inconsistencies necessitate standardized protocols, larger datasets, and explainable AI (XAI) to improve reliability and applicability in global food safety monitoring.},
}
@article {pmid41606218,
year = {2026},
author = {Abdelhameed, A and Hussein, RH and Hatem, ZA and Bağcı, C and Ziemert, N},
title = {From niche to niche: investigating microbial communities and their specialised metabolite gene clusters in human microbiomes.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {2},
pages = {65},
pmid = {41606218},
issn = {1573-0972},
mesh = {Humans ; *Multigene Family ; *Microbiota/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics ; Biosynthetic Pathways/genetics ; Metagenome ; },
abstract = {Diverse microbial communities within the human microbiome perform vital functions which influence both health and disease in hosts. Specialized metabolites produced by microbes via biosynthetic gene clusters (BGCs) drive ecological interactions and offer possibilities for therapeutic application. The biosynthetic capabilities of microorganisms present in human microbiomes are still mostly unexplored despite metagenomics advancements. The study examines the variety of microbial communities and BGC locations through metagenomic data from 1,191 samples across eight human microbiomes taken from the IMG/M database. Kraken2 executed taxonomic classification while antiSMASH v6.1.1 identified BGCs. The study used BiG-SCAPE to build a sequence similarity network while Bracken and Pavian tools analyzed microbial diversity. A total of 25,681 BGCs were identified, of which 97.5%, showed no significant match to existing clusters in MIBIG database, indicating substantial potential for novel biosynthetic discoveries . Showing no match to existing clusters in the MIBiG database which shows huge potential for new biosynthetic discoveries. New strains were discovered that produce unique RiPPs, NRPs, and siderophores primarily within the microbiomes of the large intestine, oral cavity, and skin. The large intestine showed maximum microbial and biosynthetic diversity compared to other areas while the biliary tract and nasal cavity displayed minimal diversity. New BGCs associated with antibiotic, cytotoxic, and immune-modulating functions present potential therapeutic uses. The investigation uncovers essential information about how microbial communities develop specific functions within various body regions. Uncharacterized BGC discoveries present new opportunities for drug development and treatments that target microbiomes.},
}
@article {pmid41604303,
year = {2026},
author = {Guo, Z and Cheng, H and Shi, H and Liu, D and Zhai, X and Li, X and Zhang, X and Liu, L and Zhang, XH and Zhang, Y},
title = {Potential for microbial methanethiol-dependent dimethylsulfide production in different marine sediments.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116891},
doi = {10.1016/j.celrep.2025.116891},
pmid = {41604303},
issn = {2211-1247},
abstract = {Dimethyl sulfide (DMS) plays a pivotal role in sulfur cycling and climate regulation. This study investigates microbial DMS production via the methylation of hydrogen sulfide (H2S) and methanethiol (MeSH) in nearshore, pelagic deep-sea, and cold-seep sediments using culture-dependent and -independent methods. DMS production is detected in all sediments with exogenous MeSH addition. High mdd abundance is found in pelagic deep-sea sediments (24.55%-26.73%) from the Kuroshio-Oyashio Extension region, as well as in the nearshore sediments (25.78%). Metagenomic analyses reveal previously unrecognized Mdd-encoding taxa, such as Polyangia, and eight Bacteroidota and Bacillota isolates may possess unknown Mdd enzymes. Importantly, a widespread alternative pathway that converts H2S to MeSH is identified, representing a significant source of MeSH. These findings reveal a prevalent and diverse microbial pathway for DMS production in marine sediments, underscoring the need for further investigation to discover Mdd[+] microbial contributors.},
}
@article {pmid41602774,
year = {2025},
author = {Zhang, M and Zhu, Y and Sun, Z and Wang, B and Chen, J and Zhou, F and Zeng, J and Li, M and Zou, D and Jiang, Z},
title = {Correction: Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1766907},
doi = {10.3389/fmicb.2025.1766907},
pmid = {41602774},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1671267.].},
}
@article {pmid41602101,
year = {2025},
author = {Deng, Q and Liu, Y and Zhang, J and Zhang, H and Zhang, Y and Wang, M and Jia, M and Ding, D and Fang, Y and Wang, Y and Gu, H and Wang, H},
title = {Clinical validation and utility of targeted nanopore sequencing for rapid pathogen diagnosis and precision therapy in lung cancer patients with pulmonary infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1730098},
pmid = {41602101},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/complications/microbiology ; *Nanopore Sequencing/methods ; Male ; Female ; Middle Aged ; Aged ; Sputum/microbiology ; *Precision Medicine/methods ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; Metagenomics/methods ; Microbiota ; Bacteria/genetics/isolation &amp; purification/classification ; Sensitivity and Specificity ; Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Pulmonary infections are common in patients with lung cancer (LC), complicating diagnosis and treatment. This study explored the diagnostic performance and clinical utility of targeted nanopore sequencing (TNPseq) for detecting pathogens in LC-related pulmonary infections.<br><br>METHODS: A total of 143 patients with LC or benign pulmonary diseases complicated by pulmonary infections were included and stratified into diagnostic and therapeutic cohorts. Sputum samples underwent conventional culture, metagenomic next-generation sequencing (mNGS), and TNPseq analyses. Microbiota profiles were compared across disease groups and correlated with tumor therapy responses. In the therapeutic cohort, clinical outcomes were assessed between empirical therapy and TNPseq-guided therapy.<br><br>RESULTS: TNPseq identified a significantly higher proportion of clinically relevant pathogens compared to mNGS (48.76% vs. 16.80%, p < 0.001) and demonstrated superior sensitivity (81.25% vs. 68.75%), with a 40.7% reduction in turnaround time (16 hours vs. 27 hours). Both sequencing methods revealed an enrichment of Lactobacillus species in non-initial diagnosis lung cancer (NDLC) patients (p < 0.01). Patients exhibiting partial response or stable disease (PR/SD) showed increased abundance of Neisseria, Veillonella, and Prevotella species (p < 0.05). Clinical remission was achieved in all patients; however, 68.4% of those initially receiving empirical therapy subsequently required a switch to TNPseq-guided treatment due to its ineffectiveness. Compared to this empirical-to-TNPseq group, the median treatment duration was significantly shorter under direct TNPseq guidance (total: 6 days vs. 13 days, p < 0.01; LC subgroup: 5 days vs. 15.5 days, p < 0.05), thereby reducing unnecessary antibiotic exposure.<br><br>CONCLUSIONS: By enabling rapid pathogen detection and profiling of the pulmonary microbiome, TNPseq facilitates targeted therapy and reduces antibiotic overuse in LC patients. These findings highlight the potential of TNPseq as a promising, rapid, and non-invasive diagnostic candidate for first-line use, offering a comprehensive view of both infection and host-microbe interactions in immunocompromised patients.},
}
@article {pmid41601218,
year = {2025},
author = {Li, CT},
title = {[Applications and challenges of forensic microbiomics].},
journal = {Fa yi xue za zhi},
volume = {41},
number = {5},
pages = {441-442},
doi = {10.12116/j.issn.1004-5619.2025.551105},
pmid = {41601218},
issn = {1004-5619},
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Forensic Medicine/methods ; *Gastrointestinal Microbiome ; China ; Genomics ; Human Genome Project ; *Forensic Sciences ; Metagenome ; },
}
@article {pmid41599943,
year = {2026},
author = {Rocha, HR and Ribeiro, P and Rodrigues, PM and Gomes, AM and Pintado, M and Coelho, MC},
title = {Bioinformatic Insights into the Carotenoids' Role in Gut Microbiota Dynamics.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
pmid = {41599943},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Carotenoids/pharmacology/chemistry ; *Computational Biology ; Humans ; Fermentation ; Lycopene/pharmacology ; Lutein/pharmacology ; Bacteria/drug effects/genetics/classification ; beta Carotene/pharmacology ; },
abstract = {Background/Objectives: Carotenoids are bioactive pigments with well-established antioxidant and immunomodulatory properties, yet their impact on gut microbiota remains poorly understood from a chemical standpoint. This study explores how carotenoid structure and gastrointestinal stability shape microbial responses combining in vitro fermentation with bioinformatic analyses. Methods: Individual carotenoids (beta (β)-carotene, lutein, lycopene) and combined carotenoids, as well as algal-derived extracts were subjected to 48 h in vitro fermentation, and microbial composition and activity were assessed through sequencing and computational analysis. Results: β-carotene and lycopene promoted acid-tolerant taxa such as Escherichia-Shigella, whereas lutein, due to its higher polarity, supported more transient fluctuations. Mixtures and algal carotenoids exhibited synergistic effects, sustaining beneficial genera including Bifidobacterium and Bacteroides and promoting structured ecological trajectories. Conclusions: These findings provide a chemistry-driven perspective on how carotenoids act as modulators of microbial ecosystems, with direct implications for the formulation of carotenoid-enriched functional foods and dietary interventions.},
}
@article {pmid41599039,
year = {2026},
author = {Wang, Z and Chen, G and Yang, M and Wang, S and Fang, J and Shi, C and Gu, Y and Ning, Z},
title = {Host-Filtered Blood Nucleic Acids for Pathogen Detection: Shared Background, Sparse Signal, and Methodological Limits.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
pmid = {41599039},
issn = {2076-0817},
support = {2024-PWXZ-04//New Quality Clinical Specialty Program of High-end Medical Disciplinary Construction in Shanghai Pudong New Area/ ; 2024ZDXK0019//Shanghai Municipal Health Commission, Key Discipline of Shanghai Health System, Cardiology/ ; PW2025D-01//The Scientific Research Program of Shanghai Pudong New Area Health Commission (the Joint Research and Development Program)/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Tuberculosis/microbiology/diagnosis/blood ; Microbiota/genetics ; *Cell-Free Nucleic Acids/blood/genetics ; *Coronary Artery Disease/microbiology/diagnosis/blood ; Mycobacterium tuberculosis/genetics/isolation &amp; purification ; Male ; Female ; Cohort Studies ; },
abstract = {Plasma cell-free RNA (cfRNA) metagenomics is increasingly explored for blood-based pathogen detection, but the structure of the shared background "blood microbiome", the reproducibility of reported signals, and the practical limits of this approach remain unclear. We performed a critical re-analysis and benchmarking ("stress test") of host-filtered blood RNA sequencing data from two cohorts: a bacteriologically confirmed tuberculosis (TB) cohort (n = 51) previously used only to derive host cfRNA signatures, and a coronary artery disease (CAD) cohort (n = 16) previously reported to show a CAD-shifted "blood microbiome" enriched for periodontal taxa. Both datasets were processed with a unified pipeline combining stringent human read removal and taxonomic profiling using the latest versions of specialized tools Kraken2 and MetaPhlAn4. Across both cohorts, only a minority of non-host reads were classifiable; under strict host filtering, classified non-host reads comprised 7.3% (5.0-12.0%) in CAD and 21.8% (5.4-31.5%) in TB, still representing only a small fraction of total cfRNA. Classified non-host communities were dominated by recurrent, low-abundance taxa from skin, oral, and environmental lineages, forming a largely shared, low-complexity background in both TB and CAD. Background-derived bacterial signatures showed only modest separation between disease and control groups, with wide intra-group variability. Mycobacterium tuberculosis-assigned reads were detectable in many TB-positive samples but accounted for ≤0.001% of total cfRNA and occurred at similar orders of magnitude in a subset of TB-negative samples, precluding robust discrimination. Phylogeny-aware visualization confirmed that visually "enriched" taxa in TB-positive plasma arose mainly from background-associated clades rather than a distinct pathogen-specific cluster. Collectively, these findings provide a quantitative benchmark of the background-dominated regime and practical limits of plasma cfRNA metagenomics for pathogen detection, highlighting that practical performance is constrained more by a shared, low-complexity background and sparse pathogen-derived fragments than by large disease-specific shifts, underscoring the need for transparent host filtering, explicit background modeling, and integration with targeted or orthogonal assays.},
}
@article {pmid41597665,
year = {2026},
author = {Khachatryan, A and Vardanyan, A and Zhang, R and Zhang, Y and Shi, X and Willscher, S and Nguyen, NHA and Vardanyan, N},
title = {Metagenome Insights into Armenian Acid Mine Drainage: A Novel Thermoacidophilic Iron-Oxidizing Bacterium with Perspectives for Copper Bioleaching.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
pmid = {41597665},
issn = {2076-2607},
support = {22rl-031//Higher Education Science Committee of Armenia/ ; 23-YSIP-012//Higher Education Science Committee of Armenia/ ; },
abstract = {The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities' structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously "Proteobacteria") (68-72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes.},
}
@article {pmid41597231,
year = {2026},
author = {Feng, Y and Geng, Y and Liu, S and Huang, X and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y},
title = {Overwinter Syndrome in Grass Carp (Ctenopharyngodon idellus) Links Enteric Viral Proliferation to Mucosal Disruption via Multiomics Investigation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
pmid = {41597231},
issn = {2073-4409},
support = {2024YFD2401102//National Key R&amp;D ProgramNational Key R&amp;D Program/ ; 2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; },
mesh = {Animals ; *Carps/virology/microbiology ; *Fish Diseases/virology/microbiology/genetics ; *Intestinal Mucosa/virology/pathology/microbiology ; Gastrointestinal Microbiome ; Metagenomics ; Transcriptome ; Multiomics ; },
abstract = {Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the 'low-temperature-pathogen' model and shifts focus to mucosal barrier dysfunction and host-microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host-microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.},
}
@article {pmid41597216,
year = {2026},
author = {Mamun, MAA and Rakib, A and Mandal, M and Li, W and Miller, DD and Chen, H and Nagarkatti, M and Nagarkatti, P and Singh, UP},
title = {VERU-111 Promotes an Anti-Tumor Response Through Restoration of Gut Microbial Homeostasis and Associated Metabolic Dysregulation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
pmid = {41597216},
issn = {2073-4409},
support = {AI140405//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; *Homeostasis/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; Azoxymethane ; Dextran Sulfate ; *Antineoplastic Agents/pharmacology ; Male ; Humans ; },
abstract = {The rising global burden of colorectal cancer (CRC) has now positioned it as the third most common cancer worldwide. Chemotherapy regimens are known to disrupt the composition of the gut microbiota and lead to long-term health consequences for cancer patients. However, the alteration of gut microbiota by specific chemotherapeutic agents has been insufficiently explored until now. The purpose of this study was to assess changes in the gut microbiota following treatment with VERU-111 as a chemotherapy agent for the treatment of CRC. We thus performed a metagenomic study using 16S rRNA gene amplicon sequencing of fecal samples from different experimental groups in the azoxymethane (AOM) and dextran sodium sulfate (DSS)-induced murine model of CRC. To predict the functional potential of microbial communities, we used the resulting 16S rRNA gene sequencing data to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We found that the administration of VERU-111 led to a restructured microbial community that was characterized by increased alpha and beta diversity. Compared to the mice treated with DSS alone, VERU-111 treatment significantly increased the relative abundance of several bacterial species, including Verrucomicrobiota species, Muribaculum intestinale, Alistipes finegoldii, Turicibacter, and the well-known gut-protective bacterial species Akkermansia muciniphila. The relative abundance of Ruminococcus, which is negatively correlated with immune checkpoint blockade therapy, was diminished following VERU-111 administration. Overall, this metagenomic study suggests that the microbial shift after administration of VERU-111 is associated with suppression of several metabolic and cancer-related pathways that might, at least in part, facilitate the suppression of CRC. These favorable shifts in gut microbiota suggest a novel therapeutic dimension of using VERU-111 to treat CRC and emphasize the need for further mechanistic exploration.},
}
@article {pmid41596659,
year = {2026},
author = {Sánchez-Recillas, E and Almanza-Aguilera, E and Bars-Cortina, D and Zamora-Ros, R and Godínez-Santillán, RI and Sánchez-Tusié, AA and Vergara-Castañeda, HA},
title = {Effect of Garambullo (Myrtillocactus geometrizans) Consumption on the Intestinal Microbiota Profile in an Early-Phase Rat Model of Colon Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
pmid = {41596659},
issn = {1422-0067},
support = {1560335//Secretar&#xed;a de Ciencia, Humanidades, Tecnolog&#xed;a e Innovaci&#xf3;n/ ; FME202404//Autonomous University of Queretaro - FONFIVE/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colonic Neoplasms/microbiology/chemically induced/pathology/drug therapy ; Male ; Rats ; Rats, Sprague-Dawley ; Disease Models, Animal ; Azoxymethane ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Dextran Sulfate ; *Plant Extracts/pharmacology ; Bacteria/genetics/classification ; },
abstract = {Bioactive compounds in food contribute to reducing the risk of developing colon cancer by modulating the gut microbiota. We have recently demonstrated that garambullo (Myrtillocactus geometrizans), an endemic fruit of Mexico rich in bioactive compounds, attenuates aberrant crypt foci in an animal model. However, its potential to modulate the gut microbiota is unknown. The main objective of this study was to evaluate whether its consumption modulates colon carcinogenesis by altering the microbiota in an in vivo model induced by azoxymethane and dextran sulfate sodium (AOM/DSS). Fecal samples were collected from twelve male Sprague-Dawley rats and analyzed for microbiota composition after 0, 8, and 16 weeks of treatment with saline (control), AOM/DSS, garambullo (G), or residue of garambullo (RG) with AOM/DSS (G+AOM/DSS and RG+AOM/DSS, respectively). Characterization of the microbiome was based on the conserved region of the 16S rRNA V3-V4 gene, and analyzed by the ZymoBIOMICS' Targeted Metagenomics Sequencing (Zymo Research) service. In an animal model induced with AOM/DSS for 8 weeks, consumption of G and its residue increased the bacterial genera Shuttleworthiia, Subdoligranulum, Lactobacillus, Faecalibacterium, and Alloprevotella (p < 0.05). Consumption of G and its residue allowed the proliferation of bacteria that produce short-chain fatty acids and are associated with protective mechanisms of the colon.},
}
@article {pmid41596486,
year = {2026},
author = {Sá, L and Machado, E and Ginani, V and Timbó, R and Romiti, R and Kurizky, P and Gomes, C},
title = {Species-Level Comparative Metagenomic Analysis of the Bacterial Abundance of the Gut Microbiome in Psoriasis, Hidradenitis Suppurativa, and Pemphigus Foliaceous Patients Using Shotgun Next-Generation Sequencing.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
pmid = {41596486},
issn = {1422-0067},
support = {00193-00000279/2023-70//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Distrito Federal (FAP-DF)/ ; 445040/2023-8//National Council for Scientific and Technological Development/ ; 21/2023//Departamento de Ci&#xea;ncia e Tecnologia, da Secretaria de Ci&#xea;ncia, Tecnologia, Inova&#xe7;&#xe3;o e Com-plexo da Sa&#xfa;de, do Minist&#xe9;rio da Sa&#xfa;de (Decit/SECTICS/MS)/ ; },
mesh = {Humans ; *Psoriasis/microbiology ; *Pemphigus/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Middle Aged ; Adult ; *Hidradenitis Suppurativa/microbiology ; Feces/microbiology ; *Bacteria/genetics/classification ; Aged ; },
abstract = {Recent studies have revealed a specific relationship between gut bacteria and inflammatory skin profiles. We aimed to perform a species-level comparative metagenomic analysis of the gut microbiome in patients with psoriasis, hidradenitis suppurativa (HS), and pemphigus foliaceus (PF). We included omnivorous nonsmokers and nondrinkers with psoriasis (n = 24), HS (n = 10), and PF (n = 11), as well as healthy controls (n = 10). We collected faecal samples from all patients for classic parasitological analysis. Gut microbiome analysis was conducted using shotgun next-generation sequencing. We used the Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2 bioinformatics tools to evaluate concordance and differential abundance between patients. Thirteen patients (23.64%) were diagnosed with active intestinal parasitosis. The presence of intestinal parasitosis was significantly related to immunosuppression (p = 0.009). The most abundant microorganism species found in the faeces of the patients evaluated was Escherichia coli. Psoriasis patients presented a greater abundance of bacteria from the Veillonellaceae family, whereas PF patients presented a greater abundance of Firmicutes bacteria. Patients with PF showed increased E. coli virulence and antibiotic resistance functional markers. Immunosuppression significantly influenced the presence of intestinal parasitosis as well as increased the virulence of functional markers in patients with PF receiving systemic corticosteroid therapy.},
}
@article {pmid41595535,
year = {2026},
author = {Ma, Y and Wang, L and Hu, H and Shieh, AR and Li, E and He, D and He, L and Liu, Z and Paing, TM and Chen, X and Cao, Y},
title = {Composition and Function of Gut Microbiome: From Basic Omics to Precision Medicine.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
pmid = {41595535},
issn = {2073-4425},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; Animals ; Genomics/methods ; Probiotics ; },
abstract = {The gut microbiome is defined as the collective assembly of microbial communities inhabiting the gut, along with their genes and metabolic products. The gut microbiome systematically regulates host metabolism, immunity, and neuroendocrine homeostasis via interspecies interaction networks and inter-organ axes. Given the importance of the gut microbiome to the host, this review integrates the composition, function, and genetic basis of the gut microbiome with host genomics to provide a systematic overview of recent advances in microbiome-host interactions. This encompasses a complete technological pipeline spanning from in vitro to in vivo models to translational medicine. This technological pipeline spans from single-bacterium CRISPR editing, organoid-microbiome co-culture, and sterile/humanized animal models to multi-omics integrated algorithms, machine learning causal inference, and individualized probiotic design. It aims to transform microbiome associations into precision intervention strategies that can be targeted and predicted for clinical application through interdisciplinary research, thereby providing the cornerstone of a new generation of precision treatment strategies for cancer, metabolic, and neurodegenerative diseases.},
}
@article {pmid41595438,
year = {2025},
author = {Vougiouklaki, D and Letsiou, S and Ladias, K and Tsakni, A and Mavrokefalidou, I and Siateli, Z and Halvatsiotis, P and Houhoula, D},
title = {Lactobacillus-Dominated Cervical Microbiota Revealed by Long-Read 16S rRNA Sequencing: A Greek Pilot Study.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
pmid = {41595438},
issn = {2073-4425},
mesh = {Female ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Pilot Projects ; *Cervix Uteri/microbiology ; Greece ; *Lactobacillus/genetics/isolation &amp; purification/classification ; Adult ; Middle Aged ; Vagina/microbiology ; },
abstract = {Background/Objectives: The vaginal microbiota constitutes a highly dynamic microbial ecosystem shaped by the distinct mucosal, hormonal, and immunological environment of the female genital tract. Accumulating evidence suggests that shifts in cervical microbial composition and function may influence host-microbe interactions and contribute to gynecological disease risk. Within this framework, the present study aimed to perform an in-depth genomic characterization of the cervical microbiota in a well-defined cohort of Greek women. The primary objective was to explore the functional microbial landscape by identifying dominant bacterial taxa, taxon-specific signatures, and potential microbial pathways implicated in cervical epithelial homeostasis, immune modulation, and disease susceptibility. Methods: Microbial genomic DNA was isolated from 60 cervical samples using the Magcore Bacterial Automated Kit and analyzed through full-length 16S rRNA gene sequencing using the Nanopore MinION™ platform, allowing high-resolution taxonomic assignment and enhanced functional inference. In parallel, cervical samples were screened for 14 HPV genotypes using a real-time PCR-based assay. Results: The cervical microbial communities were dominated by Lactobacillus iners, Lactobacillus crispatus, and Aerococcus christensenii, collectively representing over 75% of total microbial abundance and suggesting a functionally protective microbiota profile. A diverse set of low-abundance taxa-including Stenotrophomonas maltophilia, Stenotrophomonas pavanii, Acinetobacter septicus, Rhizobium spp. (Rhizobium rhizogenes, Rhizobium tropici, Rhizobium jaguaris), Prevotella amnii, Prevotella disiens, Brevibacterium casei, Fannyhessea vaginae, and Gemelliphila asaccharolytica-was also detected, potentially reflecting niche-specific metabolic functions or environmental microbial inputs. No HPV genotypes were detected in any of the cervical samples. Conclusions: This genomic profiling study underscores the functional dominance of Lactobacillus spp. within the cervical microbiota and highlights the contribution of low-abundance taxa that may participate in metabolic cross-feeding, immune signaling, or epithelial barrier modulation. Future large-scale, multi-omics studies integrating metagenomics and host transcriptomic data are warranted to validate microbial functional signatures as biomarkers or therapeutic targets for cervical health optimization.},
}
@article {pmid41595429,
year = {2025},
author = {Wu, H and Li, J and Long, J and Liao, H and Zhan, K and Chen, H and Lei, F},
title = {Enhancing Ecological Functions in Chinese Yellow Earth: Metagenomic Evidence of Microbial and Nitrogen Cycle Reassembly by Organic Amendments.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
pmid = {41595429},
issn = {2073-4425},
support = {Grants 2022YFD1901500 and 2022YFD1901505//the National Key R&amp;D Program of China/ ; Grant U2420626//the National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil Microbiology ; Soil/chemistry ; *Nitrogen Cycle/genetics ; Metagenomics/methods ; Nitrogen/metabolism ; China ; Zea mays/growth &amp; development ; Fertilizers ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics/classification ; Charcoal ; },
abstract = {BACKGROUND: Chinese Yellow Earth is a key subtropical agricultural resource in southwestern China; however, its productivity is limited by acidity and poor nutrient retention. This study examined how reduced nitrogen plus organic amendments affect its soil microbial structure and maize yield.<br><br>METHODS: A field experiment with four treatments evaluated reduced nitrogen fertilization amended with rice husk plus rapeseed cake (RS) or RS with biochar (BC). Soil properties (pH, nitrogen, organic matter) and maize yield were analyzed. Metagenomic analysis (NR database) characterized microbial communities, and correlation analysis with Mantel tests identified key relationships.<br><br>RESULTS: Combined organic amendments under reduced N significantly increased soil pH, nitrogen components, and organic matter, increasing maize yield by 4.41-8.97%. Metagenomics revealed enriched beneficial genera including Sphingomonas and Bradyrhizobium. Yield positively correlated with nitrate nitrogen and a beneficial microbial cluster containing Lysobacter and Reyranella, whereas Steroidobacter negatively correlated with key fertility indicators. Mantel tests revealed nitrate nitrogen as the primary correlate of functional gene community succession.<br><br>CONCLUSIONS: This study reveals that reduced nitrogen with organic amendments promotes soil improvement and microbial modulation, demonstrating potential as a sustainable practice to maintain crop productivity in Chinese Yellow Earth. The observed trend toward yield improvement underscores its promise and warrants further validation through additional trials. Overall, the findings highlight the beneficial effects of these amendments on soil health and their role in supporting sustainable subtropical agriculture under reduced nitrogen input.},
}
@article {pmid41594879,
year = {2026},
author = {Han, H and Yang, Y and Zhu, X and Wangdwei, M and Yang, L},
title = {Age-Specific Composition and Predicted Function of Gut Microbiota in Plateau Pikas (Ochotona curzoniae).},
journal = {Biology},
volume = {15},
number = {2},
pages = {},
pmid = {41594879},
issn = {2079-7737},
support = {202401ZR0101//Natural Science Foundation of the Xizang Autonomous Region/ ; 2021-GSP-B015//High-level Personnel Training Program of Xizang University/ ; },
abstract = {Gut microbes play a crucial role in regulating physiological processes such as host energy metabolism, nutrient absorption, and environmental adaptation. The predicted functions of gut microbes can be influenced by many factors, both extrinsic and intrinsic to the hosts. The plateau pika is a key species in the alpine ecosystem of the Qinghai-Tibet Plateau. Previous research on the plateau pika primarily examined how extrinsic factors affected its gut microbiota. However, studies on intrinsic factors are scarce. Here, we used live-trapping to capture plateau pikas and collect cecum contents. Using metagenomic sequencing of cecum content samples, we characterized and compared the gut microbial composition and predicted function of plateau pika in adult (n = 9) and juvenile (n = 9) populations. The results indicated that Bacillota and Bacteroidete were the major bacterial phyla. The core gut microbial genera were the same, but the relative abundance of Oscillospira in juveniles was significantly lower than that in adults. The changes in the proportion of cellulose-degradation-related bacterial communities in juveniles suggest that they tend to choose low-fiber diets. In this study, we found no significant differences in the gut microbial composition and diversity, KEGG level 1 metabolic pathways, or CAZy class level between adult and juvenile plateau pikas. In total, the composition and predicted functions of cecal microorganisms in juvenile and adult male plateau pikas were not different. Regarding KEGG level 2 metabolic pathways, the juvenile group had a higher relative abundance of metabolic pathways for cofactors and vitamins, terpenoids, and polyketides, whereas the adult group had a higher relative abundance of energy metabolism. However, the resulting differences remain unclear. Therefore, future research should validate the above findings on a broader spatio-temporal scale and conduct cross-species comparisons to construct a microbial ecological framework for the health management of plateau wild animals.},
}
@article {pmid41594560,
year = {2025},
author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB},
title = {Gut Microbial Composition and Short-Chain Fatty Acid Metabolism in Cognitively Unimpaired Adults Stratified by Amyloid-β Status.},
journal = {Biomolecules},
volume = {16},
number = {1},
pages = {},
pmid = {41594560},
issn = {2218-273X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; Female ; Male ; *Amyloid beta-Peptides/metabolism ; Aged ; Feces/microbiology/chemistry ; Middle Aged ; Alzheimer Disease/metabolism ; Cognition ; },
abstract = {Short-chain fatty acids (SCFAs) produced by gut microbial fermentation influence host metabolism and neuroinflammatory processes implicated in Alzheimer's disease (AD). However, the relationship between fecal SCFAs, microbial taxa, and cerebral amyloid-β (Aβ) burden in cognitively unimpaired individuals remains unclear. Fecal SCFAs were quantified using GC-MS, and microbial species were profiled by shotgun metagenomics in 87 participants. Associations between SCFAs, demographics, APOE ε4 status, and Aβ burden were tested using nonparametric statistics and multivariable regression. Microbial-SCFA links were evaluated using Spearman correlations and multivariate ordinations, with mediation analysis exploring potential indirect pathways. Acetate was the predominant SCFA and demonstrated the most robust microbial associations. Higher acetate concentrations were positively associated with Bacteroides ovatus and Faecalibacterium prausnitzii, whereas lower acetate levels were linked to species such as Bifidobacterium animalis and Lachnoclostridium scindens. Stratified analyses indicated that individuals with elevated Aβ burden exhibited more pronounced species-SCFA relationships, including a notable association between Bacteroides thetaiotaomicron and butyrate. Multivariate ordination further identified a significant overall coupling between SCFA profiles and microbial community structure. Mediation analysis suggested that an Oscillospiraceae species may represent a potential intermediary linking valerate concentrations with Aβ status. SCFA concentrations were not strongly influenced by demographic or genetic factors, but specific species demonstrated robust associations with acetate levels. Distinct SCFA-microbial interaction patterns in Aβ High individuals suggest subtle early gut microbial alterations linked to amyloid burden. These findings highlight the potential role of SCFA-related microbial pathways in preclinical AD.},
}
@article {pmid41593747,
year = {2026},
author = {Lin, L and Zheng, X and Tao, Y and Zhu, W and Guan, LL and Mao, S},
title = {Genome-resolved metagenomics uncovers diversity and functional landscapes of the gastrointestinal epithelium-associated microbiome in cattle.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {44},
pmid = {41593747},
issn = {1474-760X},
support = {U2202203//NSFC-Regional Innovation and Development Joint Fund/ ; 3236114378//NSFC-International (Regional) Cooperation Research and Exchange Programme/ ; },
mesh = {Animals ; Cattle/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Rumen/microbiology ; Metagenome ; },
abstract = {BACKGROUND: The ruminant gastrointestinal epithelium harbors a diverse and functionally critical remains poorly characterized microbial community due to persistent host-derived DNA contamination in metagenomic studies.<br><br>RESULTS: We develop Dilute-MetaSeq (dilution-based metagenomic sequencing), a novel, metagenomic workflow integrating gradient dilution with multiple displacement amplification. Dilute-MetaSeq reduces host DNA interference by 52.4-fold and achieves&#x2009;>&#x2009;90% microbial sequencing efficiency to assess gastrointestinal epithelium-associated microbiome. This enables the construction of the microbial genome atlas of gastrointestinal epithelium (MGA-GE). This comprehensive resource, comprising 1,907 nonredundant prokaryotic and 5,603 viral genomes, reveals extraordinary microbial diversity and novelty, with 41.4% of prokaryotic and 99.9% of viral genomes representing taxonomically unclassified lineages. Spatial profiling identifies the rumen and reticulum as a biodiversity hotspot dominated by epithelium-adapted Butyrivibrio and methylotrophic Methanomassiliicoccales, while functional annotation uncovers 1,200 biosynthetic gene clusters (primarily RiPPs and NRPSs) and 1,212 viral auxiliary metabolic genes linked to host metabolism modulation. Pangenome analysis of 987 strains, including a novel Butyrivibrio clade with reduced genome sizes, elevated GC content, and butyrate synthesis from amino acid-derived substrates (e.g., glutarate, lysine), highlights metabolic adaptations to the nutrient-scarce epithelial niche compared to digesta-associated microbes.<br><br>CONCLUSIONS: Collectively, the MGA-GE provides transformative insights into host-microbe-virus interactions and establishes a foundation for developing microbiome-based intervention strategies to enhance ruminant health, agricultural productivity, and bioactive discovery.},
}
@article {pmid41593440,
year = {2026},
author = {Lv, J and Liu, R and Sun, Z and Zhang, J and Zhang, Y and Zhao, X and Liu, J and Zhou, X and Zhang, M and Liu, Q and Gao, F},
title = {Gut Microbiota as Neuroimmune Modulators in Myasthenia Gravis: Mechanistic Insights from the Gut-Brain Axis to Therapeutic Innovations.},
journal = {The American journal of Chinese medicine},
volume = {54},
number = {1},
pages = {65-85},
doi = {10.1142/S0192415X26500023},
pmid = {41593440},
issn = {1793-6853},
mesh = {*Gastrointestinal Microbiome/immunology/physiology ; Humans ; *Myasthenia Gravis/immunology/therapy/microbiology ; *Neuroimmunomodulation ; Dysbiosis/immunology ; Probiotics ; *Brain/immunology ; Fecal Microbiota Transplantation ; Animals ; *Brain-Gut Axis/immunology ; },
abstract = {Myasthenia gravis (MG) is a chronic autoimmune disorder characterized by an immune-mediated attack on neuromuscular junction acetylcholine receptors (AChRs), and its pathogenesis is closely linked to immune dysregulation. Emerging evidence has highlighted the pivotal role of the gut microbiota in the pathophysiology of MG through immunomodulation, microbial metabolite signaling, and gut-brain axis interactions. This review combines 16S rRNA sequencing, metagenomic, and metabolomic data to reveal distinct gut microbial signatures in patients with MG. These signatures include reduced α-diversity, depletion of beneficial taxa like Bacteroides and Bifidobacterium, enrichment of pathobionts such as Escherichia and Enterococcus, and diminished levels of the short-chain fatty acids (SCFA), which were inversely correlated with disease severity. Experimental models have demonstrated that fecal microbiota transplantation (FMT) and probiotic supplementation with strains like Bifidobacterium ameliorate symptoms by restoring Th17/Treg equilibrium, suppressing the expression of pro-inflammatory cytokines including IL-6 and TNF-α, and enhancing intestinal barrier integrity. Mechanistically, gut dysbiosis exacerbates autoimmunity via NF-αB pathway activation, disrupts tryptophan metabolism and impairs gut-brain signaling. While existing studies have established microbiota-MG associations, further causal validation, personalized therapeutic strategies, and multi-omics integration remain critical priorities. Microbiota-targeted interventions, including precision FMT and metabolite delivery, hold translational potential, but their validation via large-scale randomized controlled trials and interdisciplinary approaches like AI-driven microbiota profiling is essential if they are to advance precision medicine for MG management.},
}
@article {pmid41593438,
year = {2026},
author = {Wang, X and Tian, D and Han, B and Zhao, K and Hao, W and Du, K and Li, X and Duan, Z},
title = {Exploring the impact of rumen microbiome on ovine flavor-related compounds and comparing flavor profiles between Tibetan sheep and Small-tail Han sheep.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41593438},
issn = {1471-2180},
support = {2024YFF0728800//National Key Research and Development Program of China/ ; 2024-ZJ-949//the Natural Science Foundation of Qinghai Province/ ; XDA26040305//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
mesh = {Animals ; *Rumen/microbiology ; Sheep/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Gastrointestinal Microbiome ; Fatty Acids, Volatile/analysis/metabolism ; Metagenomics ; Tibet ; *Flavoring Agents/metabolism/analysis ; Taste ; Tandem Mass Spectrometry ; },
abstract = {The characteristic 'mutton flavor', primarily attributed to branched-chain fatty acids (BCFAs), is influenced by various factors including rumen microbes. This study aims to elucidate the disparities in meat flavor compounds and their underlying regulatory mechanisms mediated by rumen microbes between two important sheep breeds on the Qinghai-Tibetan Plateau. We used LC-MS/MS to analyze BCFAs and rumen short-chain fatty acids (SCFAs), along with metagenomic sequencing to characterize the rumen microbiome. Compared to Tibetan sheep, Small Tail Han sheep exhibited significantly higher concentrations of BCFAs, including 4-ethyloctanoic acid (EOA) and 4-methyloctanoic acid (MOA), as well as SCFAs such as pentanoate, glutarate, and propionate. In contrast, acetate levels were inversely correlated with these fatty acids. Metagenomics revealed a predominance of Bacteroidota (formerly Bacteroidetes) and Bacillota (formerly Firmicutes) in sheep. Furthermore, random forest and LEfSe analyses identified seven bacterial biomarkers, including Lactobacillus, Ligilactobacillus, Blautia, Anaerovibrio, Selenomonas, Phocaeicola, Sodaliphilus. Functional analysis indicated differences in carbohydrate degradation capabilities of two breeds. Likewise, strong positive correlations of propionate with MOA, and glutarate with EOA were observed, respectively. The findings are expected to provide critical insights into the potential for modulating meat flavor through nutritional strategies targeting rumen microbes.},
}
@article {pmid41593363,
year = {2026},
author = {Sorensen, PO and Karaoz, U and Beller, HR and Bill, M and Bouskill, NJ and Banfied, JF and Chu, RK and Hoyt, DW and Eder, E and Eloe-Fadrosh, E and Sharrar, A and Tfaily, MM and Toyoda, J and Tolic, N and Wang, S and Wong, AR and Williams, KH and Zhong, Y and Brodie, EL},
title = {Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt.},
journal = {Nature microbiology},
volume = {11},
number = {2},
pages = {359-374},
pmid = {41593363},
issn = {2058-5276},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DBI-1315705//National Science Foundation (NSF)/ ; },
mesh = {*Bacteria/metabolism ; Biomass ; Bradyrhizobium/metabolism ; Climate Change ; Metagenome ; Microbiota ; Nitrogen/metabolism ; *Nitrogen Compounds/metabolism ; *Nitrogen Cycle ; *Seasons ; *Snow ; *Soil Microbiology ; Ecosystem ; Multiomics ; },
abstract = {Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.},
}
@article {pmid41592403,
year = {2026},
author = {Zhang, B and Wang, M and Zheng, J and Yu, C and Wei, C and Ren, J and Sun, S and Wang, G and Wang, J and Lu, Y and Lin, L and Zhang, C},
title = {Strain-specific impacts of Pichia kudriavzevii on metabolite profiles and microbial community dynamics in Chinese Baijiu fermentation: Integrated metabolomics and metagenomics analysis.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111660},
doi = {10.1016/j.ijfoodmicro.2026.111660},
pmid = {41592403},
issn = {1879-3460},
mesh = {Fermentation ; Metagenomics ; Metabolomics ; *Pichia/metabolism/genetics/classification ; China ; *Microbiota ; *Wine/microbiology/analysis ; Species Specificity ; },
abstract = {Pichia kudriavzevii is a dominant yeast species in Chinese baijiu fermentation, yet its intraspecific diversity remains underexplored. This study used metabolomics and metagenomics analysis to investigate the impact of four distinct P. kudriavzevii strains (PK12, PK25, PK97, and PK360) on the metabolite profiles and microbial community structure in a controlled baijiu solid-state fermentation. Metabolomics analysis identified 49 key volatile compounds and 2792 non-volatile metabolites. Strain PK97 exhibited exceptional capacity for butanoic acid metabolism, inducing a 55.27-fold increase in butanoic acid and a 30.54-fold enhancement in ethyl butanoate production. Strain PK25 specialized in acetoin biosynthesis, while PK360 maximized 2-phenylethanol production. Metagenomic analysis uncovered that strains PK12, PK25, and PK360 promoted Lactobacillus acetotolerans population, increasing its relative abundance to 67.39%, 58.57%, and 71.79%, respectively. In contrast, strain PK97 orchestrated a dramatic ecological shift, elevating Enterobacter mori abundance from 0.56% to 17.60%, transforming the community from Lactobacillus-dominated to Enterobacteriaceae-enriched. Integration of metabolomic and metagenomic data revealed that strain PK97's promotion of Enterobacter mori correlated with significant upregulation of key enzymes including α-amylase (EC 3.2.1.1), enoyl-CoA hydratase (EC 4.2.1.17), and succinyl-CoA synthetase (EC 6.2.1.5), creating a metabolic environment favoring enhanced starch hydrolysis, altered TCA cycle flux, and butanoic acid accumulation. Strain PK25 specifically upregulated acetyl-CoA hydrolase (EC 3.1.2.1), facilitating acetic acid and acetoin formation. Strain PK360 enhanced glucose pyrophosphorylase (EC 2.7.7.9) and asparagine synthetase (EC 6.3.1.1) activities, accelerating galactose metabolism and amino acid transformations. These findings illustrate the impact of P. kudriavzevii intraspecific diversity on reshaping microbial ecology and flavor chemistry in Chinese baijiu, offering novel insights for targeted fermentation control and quality enhancement strategies in baijiu production.},
}
@article {pmid41592401,
year = {2026},
author = {Sandes, S and Figueiredo, N and Pires, S and Assis, D and Pedroso, S and Paiva, MJ and Neumann, E and Alvarenga, VO and Contreras-Castillo, CJ and Sant'Ana, AS},
title = {Lactic acid spraying on split carcasses reshapes microbial succession and reduces the occurrence of blown pack spoilage in vacuum-packaged beef stored at different temperatures over extended shelf life.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111659},
doi = {10.1016/j.ijfoodmicro.2026.111659},
pmid = {41592401},
issn = {1879-3460},
mesh = {Animals ; Food Packaging/methods ; Cattle ; Vacuum ; *Bacteria/drug effects/genetics/isolation &amp; purification/classification/growth &amp; development ; *Lactic Acid/pharmacology ; Temperature ; Food Storage ; Food Microbiology ; *Food Preservation/methods ; *Red Meat/microbiology ; Hydrogen-Ion Concentration ; Volatile Organic Compounds/analysis ; Microbiota/drug effects ; },
abstract = {Beef is a highly perishable product due to its high moisture content, neutral pH, and rich nutrient profile, which favor microbial growth and spoilage. While vacuum packaging extends shelf life by limiting aerobic bacteria, it may promote the proliferation of anaerobic and facultative anaerobic spoilage organisms, leading to blown pack spoilage. This study investigated the effects of lactic acid spraying on split carcasses categorized by two pH levels (high or ideal) on microbial succession and volatile organic compound (VOC) production in vacuum-packaged sirloins, stored at 0 °C, 4 °C, and 7 °C for up to 120 days. Using culture-based methods, 16S rRNA gene sequencing, and VOC profiling, it has been found that lactic acid treatment significantly reduced initial bacterial loads, especially in high-pH split carcasses (P < 0,05), and modulated microbial communities over time. Treated samples exhibited a lower incidence of blown pack spoilage (BPS) under specific storage time-temperature conditions. Nevertheless, bacterial changes under specific time-temperature storage conditions were characterized by a microbiota dominated by Lactococcus, Lactobacillus, Leuconostoc, Enterococcus, Carnobacterium, Hafnia-Obesumbacterium, and Serratia, regardless type of treatment. Overall microbial diversity was not significantly affected; however, the composition of dominant bacterial genera and VOC profiles differed between treated and non-treated groups, suggesting that specific bacterial taxa and compounds may serve as indicators of spoilage progression in vacuum-packed meat under defined storage conditions.},
}
@article {pmid41591867,
year = {2026},
author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C},
title = {Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70215},
doi = {10.1002/mbo3.70215},
pmid = {41591867},
issn = {2045-8827},
support = {//European Union, NextGeneration EU, PNRR-M4C2- I1.1, PRIN 2022 - Project Code 20229LEB99 - CUP Code D53D23014150006/ ; T5-AN-11//Piano di Sviluppo e Coesione of the Italian Ministry of Health 2014-2020/ ; },
mesh = {*Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; *Databases, Genetic ; Microbiota/genetics ; Environmental Pollutants/metabolism ; Metagenome ; Metagenomics ; },
abstract = {Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.},
}
@article {pmid41591576,
year = {2026},
author = {Robayo, MIG and Armijo, JHC and Rosa, LH and Passarini, MRZ},
title = {Metagenomic analysis of the fungal community present in unimpacted and oil-impacted soil, South Shetland Islands, maritime Antarctica.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {2},
pages = {62},
pmid = {41591576},
issn = {1573-0972},
support = {440218/2023-3//CNPq PROANTAR/ ; PRPPG N&#xba; 118/2024//Institutional Program to Support Research Groups/ ; CNPq 18/2024//National Council for Scientific and Technological Development/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Fungi/genetics/classification/isolation &amp; purification ; *Metagenomics/methods ; *Mycobiome/genetics ; Soil/chemistry ; Islands ; Phylogeny ; Biodiversity ; Nitrogen/analysis ; },
abstract = {We assessed the fungal diversity and functional profile of two soils collected in contrasting environments: one unimpacted soil, Hennequin Point, King George Island, and the other impacted by whale oil, Whalers Bay, Deception Island, Maritime Antarctica, using metagenomic approaches. Taxonomic assignment revealed a predominance of Ascomycota in both soils. A total of 20 and 23 fungal genera were identified at King George and Deception islands, respectively. The rare genera Thermothielavioides, Pyricularia, Fulvia, and Coccidioides were detected in the Antarctic environment. The highest fungal diversity was observed in the soil of Deception Island. Canonical analysis of King George Island soil displayed higher values of total organic carbon, sulfur, and lead, which may have favored the presence of the genera Puccinia, Lachancea, and Akanthomyces. The soil of Deception Island presented correlations with higher levels of nitrogen, chromium, and iron, with a predominance of genera such as Aspergillus, Trichoderma, and Malassezia. Functional analysis revealed distinct adaptive strategies among the soils. Domains related to translation, gene regulation, and metabolic efficiency were observed for fungi in Hennequin Point soil, King George Island, suggesting resource optimization in a cold, moss-covered environment. In Deception Island soil, fungal redox metabolism, iron acquisition, and the degradation of nitrogen compounds were highlighted, reflecting adaptation to an anthropogenic soil rich in metal oxides. Both soils exhibited functional fungal networks involved in hydrolytic enzymatic pathways that may act in the decomposition of organic compounds. New sequencing must be performed due to the insufficient depth of the data. Our results indicated that the soil from Hennequin Point and Whalers Bay exhibited distinct fungal communities, which can be influenced by environmental and ecological factors such as moss, oil, and heavy metals encountered in pristine and oil-impacted soils resulting from anthropogenic activities over the years.},
}
@article {pmid41590723,
year = {2026},
author = {Atak, E and Tavčar Verdev, P and Petek, M and Coll, A and Bosch, D and Dolinar, M and Komarysta, V and Glavaš, N and Rotter, A},
title = {Identification and Cultivation of Biotechnologically Relevant Microalgal and Cyanobacterial Species Isolated from Sečovlje Salt Pans, Slovenia.},
journal = {Marine drugs},
volume = {24},
number = {1},
pages = {},
pmid = {41590723},
issn = {1660-3397},
support = {L4-4564//The Slovenian Research and Innovation Agency/ ; Euro-MED 0200514//Interreg Euro-MED Program/ ; },
mesh = {*Cyanobacteria/isolation &amp; purification/genetics/metabolism ; *Microalgae/isolation &amp; purification/genetics ; Salinity ; Slovenia ; Metagenomics/methods ; Biodiversity ; Biotechnology/methods ; Ecosystem ; },
abstract = {Studies of complex natural environments often focus on either biodiversity or on isolating organisms with specific properties. In this study, we sought to widen this perspective and achieve both. In particular, hypersaline ecosystems, such as the Sečovlje salt pans (Slovenia), are particularly promising sources of novel bioactive compounds, as their microorganisms have evolved adaptations to desiccation and high light intensity stress. We applied shotgun metagenomics to assess microbial biodiversity under low- and high-salinity conditions, complemented by isolation and cultivation of photosynthetic microorganisms. Metagenomic analyses revealed major shifts in community composition with increasing salinity: halophilic Archaea became dominant, while bacterial abundance decreased. Eukaryotic assemblages also changed, with greater representation of salt-tolerant genera such as Dunaliella sp. Numerous additional microorganisms with biotechnological potential were identified. Samples from both petola and brine led to the isolation and cultivation of Dunaliella sp., Tetradesmus obliquus, Tetraselmis sp. and cyanobacteria Phormidium sp./Sodalinema stali, Leptolyngbya sp., and Capilliphycus guerandensis. The newly established cultures are the first collection from this hypersaline environment and provide a foundation for future biodiscovery, production optimization, and sustainable bioprocess development. The methods developed in this study constitute a Toolbox Solution that can be easily replicated in other habitats.},
}
@article {pmid41589896,
year = {2026},
author = {Conrad, RE and Tsementzi, D and Meziti, A and Hatt, JK and Montoya, J and Konstantinidis, KT},
title = {Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {2},
pages = {e0258925},
pmid = {41589896},
issn = {1098-5336},
support = {ECOGIG Consortium//Gulf of Mexico Research Initiative/ ; 1831582//National Science Foundation/ ; 2129823//National Science Foundation/ ; },
mesh = {Gulf of America ; *Metagenome ; *Fresh Water/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Seawater/microbiology ; *Microbiota ; Metagenomics ; },
abstract = {Genomic and metagenomic explorations of the oceans have identified well-structured microbial assemblages showing endemic genomic adaptations with increasing depth. However, deep water column surveys have been limited, especially of the Gulf of Mexico (GoM) basin, despite its importance for human activities. To fill this gap, we report on 19 deeply sequenced (~5 Gbp/sample) shotgun metagenomes collected along a vertical gradient, from the surface to about 2,000 m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station. However, a community-level pangenome style gene content analysis revealed ~54% of predicted gene sequences to be station-specific within our GoM samples. Of the 154 medium-to-high-quality MAGs recovered, 145 represent novel species compared with the NCBI genomes and Tara Oceans MAGs databases. Two of these MAGs were relatively abundant at both surface and deep samples, revealing remarkable versatility across the water column. A few MAGs of freshwater origin (~6% of total detected) were relatively abundant at 600 m deep and 270 miles from the coast at one station, revealing that the effects of freshwater input in the GoM can sometimes be far-reaching and long-lasting. Notably, 1,447/16,068 of the total COGs detected were positively (Pearson's r ≥ 0.5) or negatively (Pearson's r ≤ -0.5) correlated with depth, including beta-lactamases, dehydrogenases, and CoA-associated oxidoreductases. Taken together, our results reveal substantial novel genome and gene diversity across the GoM's water column, and testable hypotheses for some of the diversity patterns observed.IMPORTANCETo what extent microbial communities are similar between different ocean basins at similar depths, and what the impact of freshwater input by major rivers may be on these communities, remain poorly understood issues with potentially important implications for modeling and managing marine biodiversity. In this study, we performed metagenomic sequencing and recovered 154 medium-to-high-quality metagenome-assembled genomes (MAGs) from three stations in the Gulf of Mexico (GoM) and from various depths up to about 2,000 m. Comparison to MAGs recovered from other ocean basins highlighted the unique diversity harbored by the GoM, which could be driven by more substantial input from the Mississippi River and by human activities, including offshore oil drilling. The data and results provided by this study should be useful for future comparative analysis of marine biodiversity and contribute to its more complete characterization.},
}
@article {pmid41588163,
year = {2026},
author = {Young, V and Dohai, B and Halder, H and Fernandez-Macgregor, J and van Heusden, NS and Hitch, TCA and Weller, B and Hyden, P and Saha, D and Pieren, DKJ and Rittchen, S and Lambourne, L and Maseko, SB and Lin, CW and Tun, YM and Bibus, J and Pletschacher, L and Boujeant, M and Choteau, SA and Bergogne, L and Perrin, J and Ober, F and Schwehn, P and Rothballer, ST and Altmann, M and Altmann, S and Strobel, A and Rothballer, M and Tofaute, M and Kotlarz, D and Heinig, M and Clavel, T and Calderwood, MA and Vidal, M and Twizere, JC and Vincentelli, R and Krappmann, D and Boes, M and Falter, C and Rattei, T and Brun, C and Zanzoni, A and Falter-Braun, P},
title = {Effector-host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation.},
journal = {Nature microbiology},
volume = {11},
number = {2},
pages = {442-460},
pmid = {41588163},
issn = {2058-5276},
support = {01EA1803//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; 101003633//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 210592381//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 403224013//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 11819559//&#xd6;sterreichische Forschungsf&#xf6;rderungsgesellschaft (Austrian Research Promotion Agency)/ ; ANR-16-CONV-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-HDIM-000//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Type III Secretion Systems/genetics/metabolism/immunology ; Bacterial Proteins/metabolism/genetics ; NF-kappa B/metabolism ; *Host-Pathogen Interactions/immunology ; Metagenomics ; *Host Microbial Interactions/immunology ; Cytokines/metabolism ; Protein Interaction Maps ; },
abstract = {Pseudomonadota (formerly Proteobacteria) are prevalent in the commensal human gut microbiota, but also include many pathogens that rely on secretion systems to support pathogenicity by injecting proteins into host cells. Here we show that 80% of Pseudomonadota from healthy gut microbiomes also have intact type III secretion systems (T3SS). Candidate effectors predicted by machine learning display sequence and structural features that are distinct from those of pathogen effectors. Towards a systems-level functional understanding, we experimentally constructed a protein-protein meta-interactome map between human proteins and commensal effectors. Network analyses uncovered that effector-targeted neighbourhoods are enriched for genetic variation linked to microbiome-associated conditions, including autoimmune and metabolic diseases. Metagenomic analysis revealed effector enrichment in Crohn's disease but depletion in ulcerative colitis. Functionally, commensal effectors can translocate into human cells and modulate NF-κB signalling and cytokine secretion in vitro. Our findings indicate that T3SS contribute to microorganism-host cohabitation and that effector-host protein interactions may represent an underappreciated route by which commensal gut microbiota influences health.},
}
@article {pmid41588069,
year = {2026},
author = {Muñoz-Hisado, V and Bartolomé, M and Osácar, MC and Giménez, R and Cazenave, G and Garcia-Lopez, E and Moreno, A and Cid, C},
title = {Microbial communities and biomineralization potential within mountain permafrost of the Devaux ice cave in the Central Pyrenees.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6232},
pmid = {41588069},
issn = {2045-2322},
support = {HORIZON-MSCA-2022-PF-01 (01107943)//European Union/ ; PTA2022-021737-I//the Spanish Ministry of Science and Innovation/State Agency of Research MCIN/ ; },
mesh = {*Permafrost/microbiology ; *Caves/microbiology ; *Biomineralization ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/metabolism ; Phylogeny ; *Microbiota ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Ice caves constitute one of the last cryospheric environments studied in the meridional regions. They are undergoing a pronounced ice reduction, and are an important example of ecosystems that have not yet been thoroughly explored from a microbiological point of view. The Devaux cave, in the Central Pyrenees, still hosts perennial ice. To test whether this ice contained microbial communities, prokaryotic and eukaryotic microorganisms were searched by sequencing their 16S and 18S rRNA genes. From the taxonomic information, the potential functional pathways of these communities were predicted using bioinformatic techniques. In addition, the genome of the microorganisms housed in the perennial ice samples was investigated, and through metagenomic studies their metabolic capacity was elucidated. The cryogenic mineralization of the Devaux cave leads to the production of various Ca and Mg carbonates: calcite, aragonite, vaterite, Mg-rich calcite, and nesquehonite, whose formation may have been favored by the microorganisms in the cave. Among the genes encoding enzymes that enable reactions involved in biomineralization, those belonging to the nitrate and sulfate reduction dissimilatory pathways as well as ureases, ammonia lyases, and carbonic anhydrases were identified. This research takes a further step in the investigation of biomineralization, using the Devaux cave as a model.},
}
@article {pmid41586525,
year = {2026},
author = {Díaz-González, F and Rojas-Villalobos, C and Issotta, F and Reyes-Impellizzeri, S and Hedrich, S and Johnson, DB and Temporetti, P and Quatrini, R},
title = {Trait-based meta-analysis of microbial guilds in the iron redox cycle.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0148825},
pmid = {41586525},
issn = {2379-5077},
support = {ANID/BASAL FB210008//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANID/FONDECYT 1221035//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANID/FONDECYT 3230527//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANID/BECAS 21241467//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANID/Becas 21241350//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Beca 10202955//Vicerrectoria de Investigacion y Doctorados Universidad San Sebastian/ ; },
mesh = {Oxidation-Reduction ; *Iron/metabolism ; *Bacteria/metabolism/classification/genetics ; Phylogeny ; Microbiota ; },
abstract = {UNLABELLED: Microbial iron (Fe) redox cycling underpins key biogeochemical processes, yet the functional diversity, ecological roles, and trait architectures of iron-transforming microbes remain poorly synthesized across global environments. Here, we present a systematic review and trait-based meta-analysis of 387 microbial taxa spanning 314 studies and 76 years of research, integrating phenotypic, genomic, and environmental data to define ecologically coherent microbial iron redox cycle guilds. Rather than relying on taxonomy, our framework delineates first-order functional guilds-Fe(III) reducers, Fe(II) oxidizers, and dual-capacity Fe oxidizers/reducers-and resolves second-order guilds based on trait syndromes, such as acidophily, redox flexibility, or metabolic breadth. Trait profiling revealed that iron-cycling capacities frequently transcend phylogenetic boundaries, with multiple guilds converging in chemically stratified hotspots like hot springs, hydrothermal vents, and acid mine drainages. Dual-capacity Fe oxidizers/reducers (e.g., Acidithiobacillus ferrooxidans and Metallosphaera sedula) emerged as overlooked mediators of "cryptic" iron cycling, possessing genomic repertoires capable of toggling between oxidative and reductive modes in response to redox oscillations. Hierarchical clustering and kernel density analyses of ecophysiological traits highlighted niche partitioning along key environmental filters, including pH, iron availability, salinity, and temperature. Collectively, this work introduces the Guild Exploitation Pattern as a conceptual lens for understanding iron microbiome assembly, providing a data-driven foundation for predicting microbial contributions to iron cycling under changing environmental conditions.<br><br>IMPORTANCE: Iron redox reactions shape nutrient turnover, contaminant mobility, and primary productivity, yet the microbes driving these processes are often studied in isolation. By integrating decades of data into a trait-based guild framework, we reveal the ecophysiological diversity and niche differentiation of microbial iron redox cycling taxa across environments. Our synthesis exposes major gaps, such as limited trait data for >80% of dual-capacity Fe oxidizing/reducing species and highlights the need for functional trait surveys to complement metagenomics and cultivation efforts. The guild framework presented here advances predictive microbial ecology by linking metabolic traits with environmental gradients, offering a robust foundation for incorporating iron cycling into ecosystem models and biogeochemical forecasts.},
}
@article {pmid41586524,
year = {2026},
author = {Bloemen, B and Delvoye, M and Hoffman, S and Marchal, K and Vanneste, K and Fraiture, M-A and Roosens, NHC and De Keersmaecker, SCJ},
title = {Recovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0128225},
pmid = {41586524},
issn = {2379-5077},
mesh = {*Gastrointestinal Microbiome/genetics ; DNA Methylation ; *Interspersed Repetitive Sequences/genetics ; Humans ; Plasmids/genetics ; *Bacillus/genetics ; Bacteriophages/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Bioreactors/microbiology ; },
abstract = {UNLABELLED: Mobile genetic elements (MGEs) are major drivers of horizontal gene transfer, including the spread of antimicrobial resistance (AMR) genes. However, determining the microbial host of an MGE in complex microbiomes remains challenging. Here, we spike a niche-aspecific Bacillus velezensis strain carrying a plasmid and linear phage-plasmid into a batch bioreactor simulating the human gut, and use it as a spike-in control to assess the performance of Hi-C sequencing and Oxford Nanopore Technologies (ONT)-enabled DNA methylation detection to identify MGE-host pairs. To improve recovery of low-abundance genomes, we used a novel ONT adaptive sampling (AS) strategy that depletes de novo assembled, sample-specific high-abundance contigs, rather than relying on reference genomes. This approach led to an approximately twofold enrichment of low-abundance replicons, including the spike-in strain. Methylation-based host assignment failed for the B. velezensis MGEs, likely due to the absence of DNA methylation. In contrast, Hi-C successfully linked the phage-plasmid to its host, but not the plasmid, likely due to non-intact cells, and only after removing artefactual signals through bioinformatic processing. For a native Escherichia coli strain, Hi-C and methylation data linked it to two plasmids. Selective isolation and whole-genome sequencing of both the native E. coli and spike-in B. velezensis then confirmed the metagenomic observations. Our results highlight that Hi-C and methylation data can provide powerful insights into MGE-host associations, but their interpretation requires careful computational analysis and biological validation. Moreover, our AS strategy offers a cost-efficient method to boost coverage of low-abundance genomes, improving metagenomic investigation of MGEs in complex microbiomes.<br><br>IMPORTANCE: Mobile genetic elements are important contributors to horizontal gene transfer, including of antimicrobial resistance genes. Understanding which microbes carry these mobile elements is vital to assess the spread of resistance. Here, we use a nanopore adaptive sampling approach to increase detection of low-abundance bacteria and mobile elements and use DNA methylation detection and Hi-C sequencing to determine mobile element hosts. By introducing a known bacterium and isolating a native strain, we could evaluate the performance of these methods, indicating that although powerful, they require careful experimental design, interpretation, and validation. However, when combined, these approaches enable a comprehensive investigation of mobile elements and gene transfer dynamics in complex environments.},
}
@article {pmid41586370,
year = {2025},
author = {Zeng, B and Peng, X and Xiao, P and Nie, K and Zhang, G and Xia, L},
title = {Salt sensitivity potentiates high-salt diet-induced intestinal barrier disruption and gut microbiome dysbiosis in rats.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1718782},
pmid = {41586370},
issn = {1664-302X},
abstract = {INTRODUCTION: The high-salt diet is a prevalent eating habit associated with health risks. This study investigated the impact of high salt on intestinal barrier disruption and gut microbiome dysbiosis using Wistar and Dahl salt-sensitive rat models.<br><br>METHODS: Rats were fed a normal diet or a high-salt diet for eight weeks. Body weight and plasma inflammatory cytokines were monitored in the study. Colon tissue damage was assessed via histopathological examination, and metagenomic sequencing was utilized to analyze alterations in microbial composition, functional pathways, and biodiversity.<br><br>RESULTS: The results indicated that high salt significantly elevated pro-inflammatory cytokine levels and induced structural damage in the colon. Metagenomic analysis revealed that high salt concentrations resulted in approximately a 15% difference in microbial species composition. And led to a decrease in Alpha diversity, along with an increase in the Firmicutes/Bacteroidetes ratio. Taxon-specific alterations included reduced abundance of Lactobacillus and Clostridium, and increased abundance of Enterobacter and Bifidobacterium. Correlation analyses further revealed a positive correlation between Bifidobacterium abundance and tumor necrosis factor-&#x3b1; level in Dahl salt-sensitive rats.<br><br>DISCUSSION: This study illuminates the gut microbiota's role in salt-sensitivity and provides a foundational basis for developing microbiota-targeted interventions for at-risk individuals.},
}
@article {pmid41586308,
year = {2025},
author = {Wang, X and Ye, L and Liu, Y and Li, H and Shi, H and Zheng, L},
title = {Metagenomic analysis reveals severity-dependent microbial succession and correlation with host inflammatory response in oral and maxillofacial space infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1695928},
pmid = {41586308},
issn = {2235-2988},
mesh = {Humans ; Cross-Sectional Studies ; *Metagenomics ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Microbiota/genetics ; Aged ; Severity of Illness Index ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; *Inflammation/microbiology ; *Abscess/microbiology ; },
abstract = {BACKGROUND: Oral and maxillofacial space infections (OMSI) vary widely in clinical severity, yet the relationships between microbial community patterns in the abscess niche and host inflammatory responses remain incompletely characterized.<br><br>METHODS: We conducted a retrospective, cross-sectional, severity-stratified study of 197 patients diagnosed with OMSI between January 2020 and November 2023. Patients were stratified into mild (n=90), moderate (n=41), and severe (n=66) groups based on established clinical criteria. We performed mNGS on abscess pus samples to characterize the microbial community composition and assessed associations between these features and systemic inflammatory markers.<br><br>RESULTS: Although &#x3b1;-diversity did not differ significantly among severity groups, &#x3b2;-diversity analysis revealed distinct microbial communities. Pairwise analyses indicated a threshold-like community shift, characterized by a significant divergence between mild and severe infections, while the moderate group exhibited an intermediate composition that overlapped with both. Severe infections were characterized by an enrichment of Prevotella. Furthermore, analysis of predominant taxa (>30% abundance) revealed considerable microbial heterogeneity, challenging a simple monoinfection model. Notably, a machine learning-identified microbial profile comprising Streptococcus, Corynebacterium, and Pseudomonas was significantly correlated with elevated systemic inflammatory markers.<br><br>CONCLUSION: This study characterizes associations between abscess-site microbial communities and host inflammatory profiles across OMSI severity strata. Given the cross-sectional design and the lack of an external validation cohort, the present findings should be interpreted as exploratory and non-causal. Future multicenter prospective studies including independent validation cohorts are warranted to test reproducibility and to evaluate whether any candidate features possess generalizable predictive value.},
}
@article {pmid41582618,
year = {2026},
author = {Wu, X and Lim, KJ and Ma, Y and Gu, J and Jiang, Y and Zhu, L and Chen, Y and Sun, J},
title = {The Effects of Soy Protein-Rich Meals on Muscle Health of Older Adults Are Linked to Gut Microbiome Modifications.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {1},
pages = {e70212},
pmid = {41582618},
issn = {2190-6009},
mesh = {Humans ; Male ; Female ; Aged ; *Gastrointestinal Microbiome/drug effects ; *Soybean Proteins/administration &amp; dosage/pharmacology ; Aged, 80 and over ; *Muscle, Skeletal/physiology ; *Meals ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; *Sarcopenia/diet therapy ; },
abstract = {BACKGROUND: Sarcopenia is characterized by accelerated muscle mass and function loss in older adults. The role of nutritional interventions in sarcopenia is uncertain. This study investigates whether a soy protein-rich diet can enhance muscle health in older adults via gut microbiota changes.<br><br>METHODS: A 12-week randomized controlled trial was conducted with 84 older adults from a long-term care facility. Participants in the intervention group consumed three daily meals containing 10&#x2009;g of soy protein (totalling 30&#x2009;g/day), while the control group maintained their usual diets. Faecal samples from 53 participants were collected at Weeks 0, 6 and 12. We assessed changes in muscle function, gut microbiota composition and faecal short-chain fatty acids (SCFA).<br><br>RESULTS: The intervention group showed preserved calf circumference, while the control group experienced a decrease (W12-W0: Intervention, 0.56&#x2009;&#xb1;&#x2009;0.22&#x2009;cm; Control, -0.91&#x2009;&#xb1;&#x2009;0.26&#x2009;cm, p(interaction)&#x2009;<&#x2009;0.001). Metagenomic analysis revealed significant alterations in gut microbiota among intervention participants who showed improvement in muscle performance parameters. The intervention increased SCFA-producing bacteria (Roseburia faecis, Intervention: 0.42&#x2009;&#xb1;&#x2009;0.21%, Control: -0.06&#x2009;&#xb1;&#x2009;0.16, p(interaction)&#x2009;<&#x2009;0.05; Agathobaculum butyriciproducens, Intervention: 0.02&#x2009;&#xb1;&#x2009;0.007%, p(time)&#x2009;<&#x2009;0.01, Control: -0.04&#x2009;&#xb1;&#x2009;0.01) and decreased species associated with poorer muscle outcomes (Alistipes putredinis, Intervention: -0.88&#x2009;&#xb1;&#x2009;0.40%, Control: 0.62&#x2009;&#xb1;&#x2009;0.63, p(interaction)&#x2009;<&#x2009;0.05; Eubacterium_sp_CAG_38, Intervention: -0.64&#x2009;&#xb1;&#x2009;0.28%, Control: 0.10&#x2009;&#xb1;&#x2009;0.22, p(interaction)&#x2009;<&#x2009;0.05). Functional pathway analysis showed enrichment of anaerobic amino acid degradation pathways and vitamin biosynthesis, with depletion of inflammatory pathways, particularly lipopolysaccharide biosynthesis. Microbiome phenotype prediction revealed a decrease in aerobic bacteria abundance in the intervention group (W12-W0, Intervention: -0.004&#x2009;&#xb1;&#x2009;0.002; Control: 0.001&#x2009;&#xb1;&#x2009;0.001, p(interaction)&#x2009;<&#x2009;0.05). Interaction (group&#x2009;&#xd7;&#x2009;time) for SCFA was not statistically significant; within-group increases at Week 6 were observed in only the intervention group (butyric acid, Intervention: 0.74&#x2009;&#xb1;&#x2009;0.34&#x2009;mg/g, p(time)&#x2009;<&#x2009;0.05, Control: 0.12&#x2009;&#xb1;&#x2009;0.43&#x2009;mg/g; isobutyric acid, Intervention: 0.14&#x2009;&#xb1;&#x2009;0.08&#x2009;mg/g, p(time)&#x2009;<&#x2009;0.05, Control: 0.08&#x2009;&#xb1;&#x2009;0.10&#x2009;mg/g; isovaleric acid, Intervention: 0.27&#x2009;&#xb1;&#x2009;0.14&#x2009;mg/g, p(time)&#x2009;<&#x2009;0.05; Control: 0.16&#x2009;&#xb1;&#x2009;0.20&#x2009;mg/g), with partial reversal by Week 12. These changes, positively correlated with improved muscle function parameters, suggest intervention benefits on gut health and muscle function.<br><br>CONCLUSION: A soy protein-rich intervention improved muscle health in older adults through beneficial gut microbiota. These findings support the gut-muscle axis hypothesis and suggest dietary soy protein may alleviate sarcopenia by promoting a healthier gut microbiome.},
}
@article {pmid41582543,
year = {2026},
author = {Tang, ZH and Lin, ZN and Li, JX and Liu, FC and Cao, J and Chen, SF and Huang, KY and Li, HF and Hu, DS and Huang, JF and Gu, DF and Lu, XF},
title = {Plasma Metabolites Mediate the Associations of Gut Microbial Diversity with Ambulatory Blood Pressure and Its Variability.},
journal = {Biomedical and environmental sciences : BES},
volume = {39},
number = {1},
pages = {26-35},
doi = {10.3967/bes2025.089},
pmid = {41582543},
issn = {2214-0190},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Blood Pressure ; *Hypertension/microbiology ; Prospective Studies ; Aged ; Blood Pressure Monitoring, Ambulatory ; China ; Adult ; },
abstract = {OBJECTIVE: Evidence suggests that depleted gut microbial α-diversity is associated with hypertension; however, whether metabolic markers affect this relationship remains unknown. We aimed to determine the potential metabolites mediating the associations of α-diversity with blood pressure (BP) and BP variability (BPV).<br><br>METHODS: Metagenomics and plasma targeted metabolomics were conducted on 523 Chinese participants from the MetaSalt study. The 24-hour, daytime, and nighttime BP and BPV were calculated based on ambulatory BP measurements. Linear mixed models were used to characterize the relationships between &#x3b1;-diversity (Shannon and Chao1 index) and BP indices. Mediation analyses were performed to assess the contribution of metabolites to the observed associations. The influence of key metabolites on hypertension was further evaluated in a prospective cohort of 2,169 participants.<br><br>RESULTS: Gut microbial richness (Chao1) was negatively associated with 24-hour systolic BP, daytime systolic BP, daytime diastolic BP, 24-hour systolic BPV, and nighttime systolic BPV (P < 0.05). Moreover, 26 metabolites were strongly associated with richness (Bonferroni P < 0.05). Among them, four key metabolites (imidazole propionate, 2-hydroxy-3-methylbutyric acid, homovanillic acid, and hydrocinnamic acid) mediated the associations between richness and BP indices (proportions of mediating effects: 14.1%-67.4%). These key metabolites were also associated with hypertension in the prospective cohort. For example, each 1-standard deviation unit increase in hydrocinnamic acid significantly reduced the risk of prevalent (OR [95% CI] = 0.90 [0.82, 0.99]; P = 0.03) and incident hypertension (HR [95% CI] = 0.83 [0.71, 0.96]; P = 0.01).<br><br>CONCLUSION: Our results suggest that gut microbial richness correlates with lower BP and BPV, and that certain metabolites mediate these associations. These findings provide novel insights into the pathogenesis and prevention of hypertension.},
}
@article {pmid41582242,
year = {2026},
author = {Chethan, D and Kavya, BS and Arati, and Chandana, R and Gowtham, HP and Ashika, S and Chanchala, S and Nagaraju, N and Reddy, CNL and Kunjeti, SG and Ningaraju, TM},
title = {Endophyte profiling of tomato leaf curl virus (ToLCV) resistant and susceptible tomato genotypes: Insights into microbial diversity and growth promotion.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {5348},
pmid = {41582242},
issn = {2045-2322},
mesh = {*Solanum lycopersicum/virology/genetics/microbiology/growth &amp; development ; *Endophytes/genetics/isolation &amp; purification/classification ; *Begomovirus/pathogenicity ; *Plant Diseases/virology/genetics/microbiology ; *Disease Resistance/genetics ; Genotype ; Biodiversity ; Bacteria/isolation &amp; purification/genetics/classification ; },
abstract = {Tomato (Solanum lycopersicum L.) is one of the most widely cultivated vegetable crops globally. Still, its productivity is significantly constrained by tomato leaf curl virus (ToLCV), a devastating begomovirus transmitted by whiteflies. This study examined the diversity and plant growth-promoting potential of culturable endophytes associated with tomato cultivars differing in resistance to tomato leaf curl virus (ToLCV). A total of 59 fungal and bacterial endophytes were isolated. Resistant cultivars (Nandi, Sankranthi, and Vybhav) harboured more diverse and compositionally distinct communities than the susceptible cultivar Arka Vikas, as indicated by Shannon, Simpson, and Chao-1 indices and multivariate analyses. Several isolates, particularly from the genera Xylaria, Fusarium, Arcopilus, Epicoccum, Bacillus, Pseudomonas, Stutzerimonas, and Paenibacillus, displayed strong nutrient-solubilizing traits in vitro, highlighting their potential as plant growth-promoting candidates. Eleven promising isolates were further evaluated on the susceptible cultivar Arka Vikas. At 30 days after sowing, Epicoccum nigrum and Bacillus subtilis significantly increased seedling height, biomass, and leaf number relative to the control. Overall, the study reveals that resistant cultivars are associated with greater culturable endophyte diversity and identifies several isolates with strong potential for promoting plant growth. Future research should assess the antiviral potential of these endophytes under ToLCV challenge and employ metagenomic studies to elucidate their functional roles in enhancing plant health.},
}
@article {pmid41581932,
year = {2026},
author = {Selvaraj, C and Desai, D and Santos-Villalobos, SL and Jayaprakashvel, M and Muthezhilan, R and Singh, SK},
title = {Marine-derived antimicrobial peptides (AMPs): Blue biotechnological assets for sustainable healthcare and circular bioeconomy.},
journal = {Advances in protein chemistry and structural biology},
volume = {149},
number = {},
pages = {171-201},
doi = {10.1016/bs.apcsb.2025.08.002},
pmid = {41581932},
issn = {1876-1631},
mesh = {*Biotechnology/economics ; *Antimicrobial Peptides/chemistry/pharmacology ; *Aquatic Organisms/chemistry ; Humans ; Animals ; Delivery of Health Care/economics ; *Anti-Bacterial Agents/pharmacology/chemistry ; },
abstract = {The global antimicrobial resistance (AMR) crisis drives the demand for novel therapeutics, positioning marine-derived antimicrobial peptides (AMPs) as sustainable alternatives with unique structural and functional advantages. These cationic, amphipathic molecules, from the source of diverse marine organisms, such as invertebrates, extremophiles, and cyanobacteria, exhibit broad-spectrum activity against drug-resistant pathogens through mechanisms like membrane disruption and immunomodulation. Their low resistance propensity and multifunctional bioactivity (eg., antioxidant, antimicrobial, anticancer) underscore therapeutic potential beyond the conventional antibiotics. Advances in genomic and metagenomic tools, machine learning, and synthetic biology are revolutionizing AMP discovery, enabling targeted mining of marine biodiversity and peptide optimization for enhanced stability and specificity. Biotechnological innovations support scalable production through heterologous expression and marine biomass valorization, which aligns with the principles of the circular economy. Marine-sourced AMPs demonstrate transformative applications across various healthcare, aquaculture, food safety, and environmental remediation, that majorly reduce the dependence on synthetic chemicals. Their integration into blue bioeconomy frameworks is promoting sustainable bio-prospects, marine ecosystem conservation, and progress towards the United Nations Sustainable Development Goals. This review narrates the collective research and also addresses the critical challenges, including production scalability and regulatory frameworks, to outline a clear pathway for the marine sourced AMP commercialization. By bridging the antimicrobial innovation with circular biotechnology, marine-sourced AMPs are exemplifying the ocean's role as a reservoir of sustainable solutions for global health and bioeconomic resilience.},
}
@article {pmid41581489,
year = {2026},
author = {Liu, Z and Zhao, F and Li, Q and Shang, Q and Fang, D and Li, X and Li, H and He, Q and Zhang, D and Cheng, J and Zhu, Y and Li, Z and Silva, AS and Chen, J},
title = {Multi-omics chemical and biochemical profiling reveals ellagic acid enhances insulin sensitivity via gut microbiota-tryptophan-indole signaling mechanism.},
journal = {Food chemistry},
volume = {505},
number = {},
pages = {147984},
doi = {10.1016/j.foodchem.2026.147984},
pmid = {41581489},
issn = {1873-7072},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Insulin Resistance ; *Indoles/metabolism ; *Tryptophan/metabolism ; Mice ; *Ellagic Acid/metabolism/pharmacology ; Male ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Humans ; Multiomics ; },
abstract = {Ellagic acid (EA) is a dietary polyphenol with limited systemic bioavailability, resulting in substantial intestinal exposure. However, the biochemical mechanisms by which EA modulates gut microbiota and metabolism remain unclear. Here, EA improved glucose tolerance and enhanced insulin sensitivity, with histology confirming reduced lipid accumulation and restored tissue architecture in liver, skeletal muscle, brown adipose tissue, and mesenteric fat. Consistently, metagenomic analysis showed that EA enriched Akkermansia muciniphila, Muribaculum intestinale, and Duncaniella dubosii, while reducing Lachnoclostridium phocaeense. These microbial shifts were accompanied by elevated levels of tryptophan-derived metabolites-indole-3-propionic acid, indole, and indole-3-acrylic acid-known to enhance insulin sensitivity. Lipidomics revealed EA decreased triacylglycerols and ceramides, along with restored phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine levels. Transcriptomics revealed EA suppressed hepatic lipogenesis, inhibited MAPK signaling in skeletal muscle, activated thermogenic and oxidative phosphorylation in adipose tissues. Our findings highlight EA, a food-derived polyphenol, might alleviate insulin resistance through a gut microbiota-indole metabolite-multi-tissue axis.},
}
@article {pmid41581442,
year = {2026},
author = {Chen, Y and Huang, S and Zhang, S and Wang, H and Song, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Wang, X and Zhang, W},
title = {Viral metagenomics reveals the RNA viral composition of herbivorous wildlife on the Qinghai-Tibet Plateau.},
journal = {Virology},
volume = {617},
number = {},
pages = {110814},
doi = {10.1016/j.virol.2026.110814},
pmid = {41581442},
issn = {1096-0341},
mesh = {Animals ; *Metagenomics ; *Animals, Wild/virology ; Phylogeny ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Feces/virology ; Tibet ; *Virome ; Genome, Viral ; Genetic Variation ; Mammals/virology ; RNA, Viral/genetics ; },
abstract = {RNA viruses, a widely distributed group of pathogens in nature, possess exceptionally high genetic diversity and rapid evolutionary potential. High-altitude ecosystems, represented by the Qinghai-Tibet Plateau, with their unique environmental conditions, may harbor distinct viral communities. However, there remains a lack of systematic understanding regarding the composition and distribution of RNA viruses in wildlife under such extreme environments. In this study, a total of 741 fecal samples were collected from three regions on the Qinghai-Tibet Plateau, and viral metagenomics technology was used to reveal the composition and diversity of RNA viruses in the fecal samples of six species of herbivorous wild animals on the plateau. We identified a substantial abundance of RNA viruses, classified into 18 distinct viral families. Furthermore, the structure of the viral communities varied among different host species. Through assembly, 28 viral sequences belonging to the families Astroviridae, Picornaviridae, Picobirnaviridae, Tobaniviridae, and Caliciviridae were identified. Phylogenetic analysis revealed that the newly identified viral strains share close relationships with viruses found in humans, marmots, and other mammals. The results indicate that wildlife in this region are reservoirs of unidentified RNA viruses, some of which may pose potential threats to public health and the animal husbandry. These findings provide crucial scientific evidence and data support for future virus surveillance, ecological risk assessment, and the prevention and control of emerging infectious diseases at their source.},
}
@article {pmid41581292,
year = {2026},
author = {Diehl, C and Breyer, GM and Torres, MC and Wuaden, CR and Rebelatto, R and Pastore, J and da Silveira Nicoloso, R and Dorn, M and Kich, JD and Siqueira, FM},
title = {Shaping soil fungal communities: How swine waste treatment systems and geography drive fungal community shifts.},
journal = {The Science of the total environment},
volume = {1015},
number = {},
pages = {181376},
doi = {10.1016/j.scitotenv.2026.181376},
pmid = {41581292},
issn = {1879-1026},
mesh = {Animals ; *Soil Microbiology ; Swine ; *Fungi/classification ; Brazil ; Fertilizers ; *Mycobiome ; Soil/chemistry ; Manure ; },
abstract = {The use of swine waste as an organic fertilizer is an important practice in sustainable agriculture. This study aims to evaluate the effects of two common swine waste treatment systems, Covered Lagoon Biodigesters (CLB) and Waste Stabilization Ponds (WSP), on fungal community structure in soil. Soil and waste samples were collected from swine farms across five Brazilian states, representing different geographical regions with distinct climate, soil types, and vegetation. A metagenomic approach was employed to analyze the fungal communities present in the samples. Our results revealed that fertilization with swine waste did not significantly affect the overall diversity of fungal communities, although distinct shifts in community composition were observed between fertilized and non-fertilized soils. Notably, reads assigned to Sugiyamaella lignohabitans were detected only in samples from waste stabilization ponds, suggesting that this environment may favor fungal taxa associated with lignocellulose degradation. Furthermore, the fungal genera Fusarium and Rhizophagus exhibited contrasting responses to fertilization, with Fusarium being more abundant in fertilized soils and Rhizophagus decreasing in abundance. Geographic variation in fungal community composition was also observed, correlating with the physicochemical properties of the soil. These findings indicate that, in our dataset, the waste treatment systems had little influence on the fungal diversity of waste samples, whereas soil fertilization with swine waste was associated with marked shifts in fungal community composition, particularly in terms of taxonomic structure.},
}
@article {pmid41581112,
year = {2026},
author = {Lett, JM and Scussel, S and Chéhida, SB and Hoareau, M and Filloux, D and Fernandez, E and Roumagnac, P and Parvedy, E and Quirin, E and Clain, C and Minatchy, J and Roux, E and Teycheney, PY and Lefeuvre, P},
title = {Metagenomic screening of the virome of symptomatic tomato plants from La Réunion Island uncovers a complex of viruses including a newly identified whitefly-transmitted polerovirus.},
journal = {Archives of virology},
volume = {171},
number = {2},
pages = {62},
pmid = {41581112},
issn = {1432-8798},
mesh = {*Plant Diseases/virology ; *Solanum lycopersicum/virology ; *Hemiptera/virology ; Animals ; Phylogeny ; *Virome/genetics ; Reunion ; Metagenomics ; *Luteoviridae/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; },
abstract = {Using unbiased high-throughput sequencing for metagenomic screening of viruses in diseased tomato plants, we identified a viral complex that includes viruses previously reported in tomato crops on La Réunion Island as well as a novel polerovirus, tentatively named "tomato necrotic yellowing virus" (ToNYV, proposed species, "Polerovirus ToNYV"). Molecular characterization and phylogenetic analysis revealed that ToNYV is closely related to two recently described poleroviruses from Africa and the Middle East, one of which is transmitted by the whitefly Bemisia tabaci, a trait uncommon among poleroviruses. Our transmission experiments demonstrated that ToNYV is also transmitted by B. tabaci and is prevalent across major tomato-growing regions of La Réunion. These findings highlight the value of metagenomic virome analysis in diseased plants for identifying novel viruses potentially involved in emerging plant diseases, either individually or as components of viral complexes.},
}
@article {pmid41578762,
year = {2025},
author = {Shen, F and Xu, C and Wang, C},
title = {Gut Microbiome Diagnostic Biomarkers for Colorectal Cancer.},
journal = {The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology},
volume = {37},
number = {1},
pages = {62-74},
pmid = {41578762},
issn = {2148-5607},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Feces/microbiology ; Female ; Middle Aged ; *Biomarkers, Tumor/analysis ; Aged ; *Adenoma/microbiology/diagnosis ; Case-Control Studies ; Disease Progression ; Early Detection of Cancer/methods ; Fusobacterium nucleatum/isolation &amp; purification ; Adult ; },
abstract = {BACKGROUND/AIMS: Gold standard diagnostic methods, such as invasive procedures and serum biomarkers, have limited sensitivity and specificity for the detection of colorectal cancer (CRC). Thus, the development of more accurate and noninvasive detection approaches is imperative. Emerging research elucidating the intricate role of the gut microbiota in CRC pathogenesis underscores the need for precision screening tailored to high-risk cohorts to improve early detection and intervention strategies and comprehensively address this challenging clinical problem.<br><br>MATERIALS AND METHODS: Fecal metagenomic sequencing datasets were employed to identify potential bacterial biomarkers for CRC diagnosis and selected relevant microbial taxa for subsequent validation. A total of 180 participants were enrolled: 65 healthy controls (HC), 65 colorectal adenoma patients, and 50 CRC patients, and fecal samples were analyzed using fluorescence quantitative polymerase chain reaction to confirm biomarker relative abundance, culminating in the establishment of an evolutionary model for CRC progression; furthermore, a treatment efficacy and prognostication model supported by comprehensive statistical methodologies was established.<br><br>RESULTS: This study analyzed fecal microbial biomarkers associated with CRC progression and identified differentially abundant bacterial species across HCs, adenoma, and CRC patient groups. Notably, Fusobacterium nucleatum (Fn) and Peptostreptococcus anaerobius (P. anaerobius) showed significant correlations with CRC stage and metastasis, highlighting their potential as diagnostic biomarkers. Among individual microbes, P. anaerobius exhibited the highest diagnostic value when combined with Fn.<br><br>CONCLUSION: The results underscore the potential application of fecal microbial markers, particularly Fn and P. anaerobius, for diagnosing CRC and monitoring its progression. &#xa0; Cite this article as: Shen F, Xu C, Wang C. Gut microbiome diagnostic biomarkers for colorectal cancer. Turk J Gastroenterol. 2026;37(1):62-74.},
}
@article {pmid41578124,
year = {2026},
author = {Candeliere, F and Sola, L and Busi, E and Pedroni, S and Raimondi, S and Amaretti, A and Greco, S and Dominici, M and Rossi, M},
title = {Altered abundance in cancer patients gut of diadenylate cyclase-encoding bacteria.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6070},
pmid = {41578124},
issn = {2045-2322},
support = {Progetto identificato con codice PE00000019, Titolo "HEAL ITALIA" - Spoke 5 - CUP E93C22001860006//PIANO NAZIONALE DI RIPRESA E RESILIENZA(PNRR) - MISSIONE 4 COMPONENTE 2/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/enzymology/genetics ; *Neoplasms/microbiology ; *Phosphorus-Oxygen Lyases/metabolism/genetics ; Female ; Male ; },
abstract = {c-di-AMP is a bacterial second messenger recognized by host immune sensors such as the STING pathway, linking gut microbiota activity to tumor immunity. This interaction holds significant therapeutic potential particularly for oncologic patients, given the increasingly recognized relationship between gut microbiota and tumor immunity. Recent evidence shows that microbial c-di-AMP can enhance anti-tumor responses and improve the efficacy of PD-1/PD-L1 blockade and radiotherapy. This study identified gut microbial species capable of synthesizing c-di-AMP by mining the Unified Human Gastrointestinal Protein catalogue for diadenylate cyclases (DACs), generating a database of 4,228 DACs across 3,901 species out of 4,744 presents in the Unified Human Gastrointestinal Genome catalogue. Analysis of metagenomic data from 190 healthy subjects and 569 cancer patients (melanoma, NSCLC, renal carcinoma) revealed a significantly higher abundance of DAC-encoding species in healthy microbiota, with no differences between responders and non-responders to immunotherapy. These findings indicate that c-di-AMP-producing bacteria are depleted in cancer-associated microbiota, supporting further studies on their role in modulating anti-tumor immunity.},
}
@article {pmid41577947,
year = {2026},
author = {Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Henry, AR and Davis, RL and Laboune, F and Longtine, ER and Godbole, S and Horigan, S and Ruhs, EC and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Heraud, JM and Dussart, P and Douek, DC and Brook, CE},
title = {Co-speciation and host-switching drives diversity of picornaviruses and sapoviruses in Malagasy fruit bats.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6583},
pmid = {41577947},
issn = {2045-2322},
support = {P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; OPP1211841//Bill and Melinda Gates Foundation/ ; D18AC00031//Defense Sciences Office, DARPA/ ; P200A210054/NH/NIH HHS/United States ; 1R01AI129822-01/NH/NIH HHS/United States ; 5DP2AI171120-S1/NH/NIH HHS/United States ; },
abstract = {UNLABELLED: Bats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. Picornavirales are an order of enteric viruses that cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of Picornavirales worldwide. Picornaviridae and Caliciviridae (families within Picornavirales) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Prior work in Madagascar has described numerous bat viruses, some with zoonotic potential, that demonstrate both high identity to and extreme divergence from viruses found in sister bat species in Africa. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats (Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis), we identify and describe 13 full-length and 38 partial-length genomic sequences within the Picornaviridae and Caliciviridae families (36 picornavirus and 15 Sapovirus sequences). We find evidence that host-switching between Madagascar and mainland African bat picornaviruses and sapoviruses, followed by host-parasite co-speciation, likely shaped the diversification pattens of these novel sequences, with little evidence for cross-species transmission among Malagasy bat species in close contact.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34969-2.},
}
@article {pmid41576942,
year = {2026},
author = {Masi, D and Watanabe, M and Clément, K},
title = {Gut microbiome and obesity care: Bridging dietary, surgical, and pharmacological interventions.},
journal = {Cell reports. Medicine},
volume = {7},
number = {2},
pages = {102573},
pmid = {41576942},
issn = {2666-3791},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/therapy/diet therapy ; Animals ; *Diet ; Mice ; },
abstract = {In the mid-2000s, mouse studies suggested that the gut microbiome might influence energy harvest, fat storage, appetite, insulin sensitivity, and inflammation. Since then, our understanding of the gut microbiome's role in obesity has advanced significantly. Mechanistic studies identified microbial metabolites, such as short-chain fatty acids, bile acids, branched-chain amino acids, tryptophan catabolites, and imidazole propionate, as key modulators of metabolism, inflammation, and gut-brain communication. Metagenomic and multi-omics technologies now provide deeper insights into the intricate interactions between microbes, metabolites, and host factors, reshaping obesity research and reinforcing the need for phenotype stratification by recognizing microbiome-driven metabolic profiles. Integrating gut microbiome data into clinical strategies may enable targeted interventions for specific obesity subtypes, advancing prevention and personalized care. However, as new anti-obesity medications emerge, it is imperative to determine how microbiome-based therapies can complement them, considering efficacy, cost, and patient-specific variability.},
}
@article {pmid41576939,
year = {2026},
author = {Nalapareddy, K and Haslam, DB and Kissmann, AK and Alenghat, T and Stahl, S and Rosenau, F and Zheng, Y and Geiger, H},
title = {Microbiota from young mice restore the function of aged ISCs.},
journal = {Stem cell reports},
volume = {21},
number = {2},
pages = {102788},
pmid = {41576939},
issn = {2213-6711},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Aging ; *Stem Cells/metabolism/cytology ; Wnt Signaling Pathway ; *Intestinal Mucosa/microbiology/metabolism/cytology ; Mice, Inbred C57BL ; Basic Helix-Loop-Helix Proteins/metabolism/genetics ; Regeneration ; *Microbiota ; Akkermansia ; },
abstract = {Homeostasis in the intestinal epithelium depends on intestinal stem cells (ISCs). A reduction in the function of ISCs, caused by a decline of canonical Wnt signaling in ISCs, contributes to a reduced regenerative potential of the aged intestine. The composition of the intestinal microbiota changes upon aging. We report here that aging-associated changes in the composition of the microbiota result in reduced canonical Wnt signaling through Ascl2 in ISCs, which causes a decline in the regenerative potential of aged ISCs in vivo. We demonstrate, using microbiota transfer experiments, that interestingly, elevated levels of Akkermansia muciniphila in the intestine cause a reduction of Ascl2-mediated canonical Wnt signaling in ISCs and thus reduced regeneration of the aged epithelium. The composition of the intestinal microbiota thus plays a critical role in regulating the function of ISCs. Our data imply potential therapeutic approaches via modulation of the composition of microbiota for aging-associated changes in the function of ISCs.},
}
@article {pmid41575223,
year = {2026},
author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W},
title = {Hidden reservoir of highly adaptable multi-host plasmids that propagate antibiotic genes in healthy human populations.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {41575223},
issn = {1751-7370},
support = {//The National Key Research and Development Program of China/ ; Project32098//National Science and Technology Major Project/ ; },
mesh = {Humans ; *Plasmids/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Metagenome ; *Bacteria/genetics/drug effects/classification ; Healthy Volunteers ; Genome, Bacterial ; Gene Transfer, Horizontal ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; },
abstract = {Plasmids are key vectors for disseminating antibiotic resistance genes, yet their diversity and dynamics in the healthy human gut microbiome remain largely unexplored. Using fecal metagenomes from two cohorts (n = 498 samples), we constructed a comprehensive atlas of the healthy human gut plasmidome. We observed a polarization: while 97.4% of 19 151 plasmid clusters exhibited low prevalence (<5%), we identified 17 plasmid clusters that were detected in >30% of individuals. Among these, the plasmid pGut1 emerged as a paradigm of a stealth vector. Prevalent globally (>50% in independent cohorts), pGut1 possesses a minimal 4-kb conserved backbone ensuring stability and a hypervariable region acting as a "plug-and-play" module. We documented 40 distinct cargo inserts, including multiple antibiotic resistance genes such as cfr(C), erm(B), and aphA, across individuals, within individuals over time, and even within single fecal samples- validated by single-cell and long-read Nanopore sequencing. Screening of 2.3 million bacterial genomes revealed pGut1 in 93 strains across 49 genera and 2 phyla, including pathogenic Clostridioides difficile and three distinct Salmonella enterica strains. This pattern suggests potential repeated cross-species transmission events, equipping diverse pathogens with new antibiotic resistance genes. Our study exposes a hidden reservoir of highly adaptable, multi-host plasmids like pGut1 silently propagating antibiotic resistance genes in healthy populations. These plasmids, pre-adapted for cross-boundary dissemination, may pose a threat by fueling the emergence of multidrug-resistant pathogens.},
}
@article {pmid41574290,
year = {2025},
author = {Chen, J and Gong, G and Su, X and Song, X and Zhang, J and Wu, P and Wang, H and Shan, T and Zhang, W},
title = {Viral metagenomic analysis of fecal samples from Bos grunniens on the Qinghai-Tibet Plateau reveals novel picornaviruses and diverse CRESS-DNA viruses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1719300},
pmid = {41574290},
issn = {2235-2988},
mesh = {*Feces/virology ; Animals ; Phylogeny ; *Metagenomics ; *DNA Viruses/genetics/classification/isolation &amp; purification ; Tibet ; Cattle/virology ; *Virome ; *Picornaviridae/genetics/classification/isolation &amp; purification ; Genome, Viral ; China ; },
abstract = {INTRODUCTION: The Qinghai-Tibet Plateau (QTP), one of the most extreme environments on Earth, provides a unique natural setting for exploring viral diversity and evolution under conditions of high altitude, hypoxia, and intense ultraviolet radiation. The yak (Bos grunniens), a key endemic ruminant species of the QTP, plays an essential ecological and economic role, yet its fecal virome remains poorly characterized.<br><br>METHODS: In this study, we analyzed 43 yak fecal samples collected from Yushu, Qinghai Province, and constructed nine metagenomic libraries to investigate the composition, diversity, and phylogenetic characteristics of the yak fecal virome.<br><br>RESULTS: Metagenomic sequencing generated approximately 463 million raw reads, of which 2.87 million were classified as viral. The viral reads in the sequenced libraries were primarily composed of single-stranded DNA viruses (92.46%), particularly members of Smacoviridae, Circoviridae, and Genomoviridae, whereas RNA viruses such as Picornaviridae accounted for a minor fraction (0.71%). Phylogenetic analyses revealed that several circular single-stranded DNA (CRESS-DNA) virus and picornavirus genomes share high similarity with known ruminant-associated viruses, while forming independent evolutionary clades, suggesting potential cross-species transmission among plateau animals. The large-scale divergence within Smacoviridae further reflects extensive lineage expansion under the plateau's extreme environmental pressures.<br><br>DISCUSSION: Compared with our previous yak virome study, this work provides independent and complementary insights into the genomic and evolutionary characteristics of key viral taxa. Overall, our findings expand the genomic landscape of the yak fecal virome and highlight the Qinghai-Tibet Plateau as an important reservoir for exploring viral diversity, evolution, and host-environment interactions in extreme ecosystems.},
}
@article {pmid41572827,
year = {2025},
author = {Xu, B and Liu, P and Yan, N and Wang, T and Liu, L and Cheng, Y},
title = {Multi-omics insights into gut microbial dysbiosis and metabolic alterations in immune checkpoint inhibitor-induced thrombocytopenia.},
journal = {Immunotherapy},
volume = {17},
number = {17-18},
pages = {1231-1239},
doi = {10.1080/1750743X.2026.2618937},
pmid = {41572827},
issn = {1750-7448},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Dysbiosis/metabolism ; *Immune Checkpoint Inhibitors/adverse effects ; Proteomics/methods ; Male ; Female ; Metabolomics/methods ; *Thrombocytopenia/chemically induced/metabolism/etiology ; Middle Aged ; Aged ; *Neoplasms/drug therapy/immunology ; Multiomics ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors-induced thrombocytopenia (ICIs-TCP) is a rare immune-related adverse events (irAEs). The physiological changes underlying ICIs-TCP remain incompletely elucidated.<br><br>METHODS: We performed multi-omics analysis (gut microbiome, plasma metabolomics/proteomics) comparing microbial/metabolic alterations in cancer patients with (n&#x2009;=&#x2009;8) and without ICIs-TCP (n&#x2009;=&#x2009;8). Fecal metagenomic shotgun sequencing was performed to assess microbial composition and function, while plasma metabolomics and proteomics analyses identified systemic metabolic and protein expression changes associated with ICIs-TCP.<br><br>RESULTS: Patients with ICIs-TCP exhibited distinct gut microbiota profiles, with an increased abundance of Segatella, Prevotella, and Clostridium, alongside a depletion of Bacteroides and Roseburia. Functional analysis revealed significant downregulation of metabolic pathways, including arginine biosynthesis, alanine, aspartate, and glutamate metabolism. Plasma metabolomics identified reduced arginine levels and disruptions in key amino acid and energy metabolism pathways, suggesting systemic arginine depletion. Proteomic analysis further demonstrated down-regulation of folate hydrolase 1 (FOLH1), a key enzyme in glutamate metabolism, implicating metabolic dysregulation in TCP pathogenesis.<br><br>CONCLUSION: The depletion of arginine and associated metabolic disruptions are associated with ICIs-TCP and may represent a potential therapeutic target for mitigating TCP risk in patients receiving ICIs.},
}
@article {pmid41572308,
year = {2026},
author = {Natalia, Z and Aleksandra, S and Egor, S and Ksenia, K},
title = {Bacteriophages in gut metagenomes: from analysis to application.},
journal = {Virology journal},
volume = {23},
number = {1},
pages = {40},
pmid = {41572308},
issn = {1743-422X},
support = {23-75-10125//Russian Science Foundation/ ; },
mesh = {*Bacteriophages/genetics/classification/isolation &amp; purification/physiology ; Humans ; *Gastrointestinal Microbiome ; *Metagenome ; Metagenomics/methods ; Computational Biology/methods ; Genome, Viral ; *Virome ; },
abstract = {Bacteriophages constitute a major component of the human gut virome, playing very important roles in shaping of the structure and function of the gut microbiota. Moreover, bacteriophages interact with the human immune system, thereby influencing various disease processes. Recent advancements in metagenomic sequencing and computational analysis have substantially expanded our understanding of gut phage diversity and the scale of the so-called 'viral dark matter'. In this review, we summarize current bioinformatic approaches for identifying and annotating bacteriophage sequences in metagenomic data, discuss key challenges in taxonomic classification and host prediction of phages, as well as the limitations associated with the assembly and analysis of viral metagenome-assembled genomes (vMAGs). We also analyze the therapeutic potential of bacteriophages, including their application in cancer immunotherapy, inflammatory diseases, and liver diseases, and their promise as diagnostic and prognostic biomarkers.},
}
@article {pmid41570777,
year = {2026},
author = {Wang, Z and Lu, J and Wang, X and An, W and Zhao, Y and Han, B and Tao, H and Liu, J and Guo, J and Wang, J},
title = {Long-term pet ownership promotes resistome similarity between cats and their owners.},
journal = {Environment international},
volume = {208},
number = {},
pages = {110074},
doi = {10.1016/j.envint.2026.110074},
pmid = {41570777},
issn = {1873-6750},
mesh = {Animals ; Cats ; *Pets/microbiology ; *Ownership ; Humans ; *Gastrointestinal Microbiome ; *Drug Resistance, Microbial/genetics ; Feces/microbiology ; },
abstract = {Pet ownership offers physical and mental health benefits, but the risks of antibiotic resistance genes (ARGs) transmission between pets and humans remain underexplored. In this study, we used metagenomics analysis of fecal samples to compare resistome profiles among four groups: owned cats and their owners, and caged cats and non-cat owners. Our findings show significant similarities in gut microbial composition, ARGs, and mobile genetic elements (MGEs) between owned cats and their owners, identifying 73 shared core ARGs and 80 shared MGEs. In contrast, caged cats and non-cat owners shared only 30 ARGs and 73 MGEs. Long-term contact was positively correlated with a higher number of shared ARGs (from 20 + to 60 +) and MGEs (from 10 + to 40 +), as well as increased resistome risk (2.47- to 4.92-fold) between pet cats and owners. The gut microbiota played a key role in shaping the ARGs and MGEs profiles, with Escherichia coli and Klebsiella pneumoniae identified as primary carriers, each genome harboring 20 to 62 ARGs and 6 to 29 MGEs. ARGs transfer events were more frequent between pet cats and their owners than in other groups. These findings underscore a potential risk of shared antimicrobial resistance between companion animals and humans within the studied population in China.},
}
@article {pmid41570646,
year = {2026},
author = {Sidikjan, N and Li, Y and Chen, Y and Guo, XP and Liu, M and Huang, Y},
title = {Multimedia profiling of metal resistance genes in the Yangtze Estuary: Biofilm dominance and community-driven regulatory pathways.},
journal = {Ecotoxicology and environmental safety},
volume = {310},
number = {},
pages = {119769},
doi = {10.1016/j.ecoenv.2026.119769},
pmid = {41570646},
issn = {1090-2414},
mesh = {*Biofilms/drug effects ; *Estuaries ; *Metals, Heavy/toxicity/analysis ; *Water Pollutants, Chemical/analysis/toxicity ; China ; Environmental Monitoring ; Genes, Bacterial ; Geologic Sediments/microbiology ; Drug Resistance, Microbial/genetics ; Microbiota ; },
abstract = {Biofilms are critical microbial assemblages that function as sinks and potential reservoirs of metal resistance genes (MRGs) in contaminated aquatic systems. In this study, metagenomic sequencing and environmental profiling were employed to characterize MRGs distribution, heavy metal contamination, and microbial community structure across water, sediment, and biofilm samples in the Yangtze Estuary. Biofilms exhibited significantly higher concentrations of heavy metals and MRGs than other matrices, particularly for key genes such as corS (Cu-resistance), nrsS (Ni-resistance), and pbrA (Pb-resistance). Ecological risk assessment identified cadmium as the primary risk contributor, especially in biofilms. Partial redundancy analysis revealed that microbial community composition was the dominant factor shaping MRGs distribution, rather than metal concentrations alone. Network and canonical correspondence analyses further demonstrated strong co-occurrence patterns between MRGs and antibiotic resistance genes (ARGs), regulated by eutrophication (TN, Chl-a) and heavy metals (Pb, Cd, Cu). Notably, Pb-resistance genes in biofilm communities were significantly enriched and closely associated with Cyanobacteria and Proteobacteria, reflecting a multi-stage co-occurrence pattern potentially involving pbrT, pbrA, cadD, and czcD. These findings highlight the ecological significance of biofilms in MRGs enrichment, dissemination, and risk propagation in estuarine ecosystems under combined pollution stress.},
}
@article {pmid41570486,
year = {2026},
author = {Lahariya, R and Anand, G and Kumari, B and Priyadarshi, K},
title = {Postbiotics and the gut-brain axis: A mechanistic review on modulating neuroinflammation and cognitive aging.},
journal = {Journal of neuroimmunology},
volume = {413},
number = {},
pages = {578870},
doi = {10.1016/j.jneuroim.2026.578870},
pmid = {41570486},
issn = {1872-8421},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/drug effects ; Animals ; *Neuroinflammatory Diseases/metabolism ; *Probiotics/administration &amp; dosage ; *Cognitive Aging/physiology ; *Brain-Gut Axis/physiology/drug effects ; *Brain/metabolism ; *Dysbiosis/metabolism ; *Aging ; },
abstract = {Aging triggers gut microbiota dysbiosis that disrupts the gut-brain axis (GBA), promoting neuroinflammation and neurodegeneration. Elderly exhibit reduced microbial diversity, depleted beneficial bacteria, and expanded pathobionts, elevating neurotoxic metabolites-lipopolysaccharides (LPS), trimethylamine-N-oxide, kynurenine derivatives, and secondary bile acids. These drive "inflammaging," blood-brain barrier breakdown, microglial activation, mitochondrial impairment, and proteinopathies in Alzheimer's and Parkinson's disease. Conversely, neuroprotective metabolites from commensals-short-chain fatty acids, indole-3-propionic acid, and urolithins-preserve gut integrity, suppress inflammation, upregulate BDNF for synaptic plasticity, and enhance mitophagy. Postbiotics, stable probiotic-derived bioactives (butyrate, polyphenol metabolites, and lactate derivatives), surpass live probiotics in safety and precision. They modulate GBA via histone deacetylase inhibition, GPR41/43 signaling, NF-κB blockade, and microglial M2 shift, blocking LPS translocation and bolstering neuronal resilience. Preclinical rodent studies demonstrate robust neuroprotection, but human translation reveals challenges: inter-individual microbiota variability (diet/genetics/comorbidities), inconsistent metabolite absorption/brain penetration between species, methodological limitations (16S rRNA vs. functional metagenomics), postbiotic standardization barriers, and sparse Phase I/II trials showing biomarker benefits without cognitive endpoints. This review synthesizes gut dysbiosis-metabolite-brain aging mechanisms, positioning postbiotics as precision therapeutics. Multi-omics stratified controlled trials are essential to validate long-term efficacy for delaying neurodegeneration and extending cognitive health.},
}
@article {pmid41569365,
year = {2026},
author = {Duarte, M and Mansilha, C and Melo, A and Sobral, D and Ferreira, R and Gomes, JP and Rebelo, H and Veber, A and Puskar, L and Schade, U and Jordao, L},
title = {Detection of polycyclic aromatic hydrocarbons, microplastic presence and characterization of microbial communities in the soil of touristic zones at Alqueva's edges (Alentejo, Portugal).},
journal = {Environmental science and pollution research international},
volume = {33},
number = {4},
pages = {1447-1458},
pmid = {41569365},
issn = {1614-7499},
mesh = {*Polycyclic Aromatic Hydrocarbons/analysis ; Portugal ; *Soil Microbiology ; *Microplastics/analysis ; Soil/chemistry ; *Soil Pollutants/analysis ; Environmental Monitoring ; Microbiota ; Bacteria ; },
abstract = {Environmental pollution is a growing concern. Here, we assessed the occurrence of two groups of persistent organic pollutants (POPs-polycyclic aromatic hydrocarbons (PAHs) and microplastics (MPs)) and bacterial populations in the topsoil of three tourist spots located at the Alqueva's edges during 1 year, once per season. Soil chemical analysis revealed low content of total organic carbon, pH close to neutrality, and nitrogen and phosphorus levels consistent with acquisition of these nutrients only by atmospheric deposition. PAH's concentrations were in the range of ng/kg, being significantly below the "reference values" for contaminated soils. Nevertheless, potentially carcinogenic PAHs, detected at all locations, raise ecotoxicological concerns. Polyamide, polyester, polystyrene, and styrene acrylonitrile resin MPs were found. Six bacterial phyla constitute the core microbiome in the three locations and include genera of bacteria reported as plastic degraders, such as Bacillus, Exiguobacterium, Paenibacillus, and Pseudomonas. The presence of POPs, even at low levels, in the soil at the edges of a water reservoir should be monitored. The identification of bacteria reported as plastic degraders in the soil, and previously in the water, is promising, and their ability to spontaneously ensure the detoxification of the ecosystem should be further investigated.},
}
@article {pmid41569097,
year = {2026},
author = {Ayala-Montaño, S and Afolayan, AO and Kociurzynski, R and Loeber, U and Reuter, S},
title = {Mitigation and detection of putative microbial contaminant reads from long-read metagenomic datasets.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41569097},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; Humans ; Computational Biology/methods ; *DNA Contamination ; *Metagenome ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Infant, Newborn ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; },
abstract = {Metagenomic sequencing of clinical samples has significantly enhanced our understanding of microbial communities. However, microbial contamination and host-derived DNA remain a major obstacle to accurate data interpretation. Here, we present a methodology called 'Stop-Check-Go' for detecting and mitigating contaminants in metagenomic datasets obtained from neonatal patient samples (nasal and rectal swabs). This method incorporates laboratory and bioinformatics work combining a prevalence method, coverage estimation and microbiological reports. We compared the 'Stop-Check-Go' decontamination system with other published decontamination tools and commonly found poor performance in decontaminating microbiologically negative patients (false positives). We emphasize that host DNA decreased by an average of 76% per sample using a lysis method and was further reduced during post-sequencing analysis. Microbial species were classified as putative contaminants and assigned to 'Stop' in nearly 60% of the dataset. The 'Stop-Check-Go' system was developed to address the specific need of decontaminating low-biomass samples, where existing tools primarily designed for short-read metagenomic data showed limited performance.},
}
@article {pmid41568738,
year = {2026},
author = {Warren, A and Wynia, Z and Corr, PG and Devin, MF and Celikkol, Z and Gordon, L and Farah, M and Karam, M and Villarreal, D and Jackson, SA and Frame, LA},
title = {The microbiota-gut-brain axis in mild cognitive impairment and Alzheimer's disease: a scoping review of human studies.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {1},
pages = {e71023},
pmid = {41568738},
issn = {1552-5279},
support = {//TMCity/ ; },
mesh = {Humans ; *Cognitive Dysfunction/microbiology ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Probiotics/therapeutic use ; *Brain ; },
abstract = {Alzheimer's disease (AD) is projected to become the highest-burden neurological disorder globally. Mounting evidence implicates the gut microbiome in AD pathogenesis. This scoping review of gut microbiomes in mild cognitive impairment (MCI) and AD included dietary and probiotic interventions. We included original research and systematic reviews/meta-analyses. Animal and non-English studies were excluded. We searched PubMed, Scopus, and Cochrane Library through February 2023. Using Arksey and O'Malley's framework and the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA)-Extension for Scoping Reviews (ScR) checklist, we screened 4751 articles, with 58 meeting predefined inclusion criteria. Our results demonstrated that gut dysbiosis was frequently reported in MCI and AD, including increased Pseudomonadota and Actinomycetota in AD and reduced diversity in some cases. Probiotic and dietary interventions showed promise in modulating cognition and microbiota, inconsistently. Emerging evidence links dysbiosis to cognitive decline; however, methodological heterogeneity and limited follow-up impede causal inference. Research should prioritize standardized protocols, functional microbiome analysis, and longitudinal human studies to clarify therapeutic potential. HIGHLIGHTS: Gut dysbiosis is a common feature of MCI and AD, with phylum-level microbial shifts frequently observed. Pseudomonadota and Actinomycetota are enriched in AD across multiple human studies. Beneficial genera like Faecalibacterium and Roseburia are consistently reduced in MCI and AD in a small number of studies. Probiotic and dietary interventions are promising to modulate the microbiota-cognition axis. More longitudinal human studies are needed to assess causal microbiome relationships.},
}
@article {pmid41568034,
year = {2025},
author = {Yu, F and Song, J and Qi, L and Liu, J and Yang, Y and Li, W and Li, L and Ma, ZS},
title = {Gene and function diversity-area relationships in the inflammatory bowel disease fecal and mucosal microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1660973},
pmid = {41568034},
issn = {1664-302X},
abstract = {The diversity-area relationship (DAR), an extension of the classic species-area relationship (SAR), provides a powerful framework for understanding how biodiversity scales across space. In this study, we applied DAR and its metagenomic counterpart (m-DAR) to investigate the spatial scaling of metagenomic genes (MGs) and metagenomic functional gene clusters (MFGCs) of seven functional databases in the gut microbiomes of individuals with inflammatory bowel disease (IBD) and healthy cohorts. Using shotgun sequencing data from 42 mucosal and 22 fecal samples from both healthy and IBD cohorts, we modeled how this MGs and MFGCs accrues with area (samples), estimating diversity scaling parameters (z), pair-wise diversity overlap (PDO), and maximal accrual diversity (MAD), which reflects the total potential diversity. We found that mucosal communities exhibited greater dissimilarity (less pair-wise diversity overlap) between individuals than fecal cowmmunities at the levels of gene richness and evenness (q = 1, 2), whereas fecal communities showed a stronger influence from dominant, abundant genes (q = 2, 3). Furthermore, healthy gut microbiomes showed greater similarity than those of IBD at the level of gene richness (q = 0), but showed greater dissimilarity at the level of abundant genes and dominant genes. Healthy gut microbiomes generally demonstrated a higher potential total diversity compared to those from IBD patients. Notably, fecal samples captured a broader range of microbial diversity than mucosal samples. Additionally, mucosal communities showed greater dissimilarity than fecal communities in almost all the MFGCs of the seven databases except ARDB, which showed the same trend as MGs. We also identified that specific functional clusters related to antibiotic resistance, such as genes for chloramphenicol and vancomycin resistance, displayed distinct scaling behaviors, suggesting their potential role in IBD pathogenesis. These findings demonstrate that the gut microbiome in IBD is not merely less diverse but is fundamentally restructured in its spatial architecture. The application of DAR provides a novel, quantitative insight to diagnose and understand this dysbiosis, moving beyond simple diversity metrics to capture the spatial diversity scaling of microbial genes and functions.},
}
@article {pmid41566339,
year = {2026},
author = {Fernández-Trapote, E and Cobo-Díaz, JF and Oliveira, M and Puente, A and Berdejo, D and Puente, H and Cordero-García, R and López, M and Prieto, M and Argüello, H and Alvarez-Ordóñez, A},
title = {Microbiome and resistome successions in pig carcasses and fresh pork meat throughout slaughtering, processing and shelf-life.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {67},
pmid = {41566339},
issn = {2049-2618},
support = {FPU21/03421//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades, Spain/ ; PRE2021-098910//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades, Spain/ ; CNS2022-136066//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades, Spain/ ; No 818368//European Commission under the European Union&#xb4;s Horizon 2020/ ; PID2020-118813GB-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
mesh = {Animals ; *Microbiota/genetics ; Swine/microbiology ; Abattoirs ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; *Pork Meat/microbiology ; Metagenome ; Food Microbiology ; *Drug Resistance, Bacterial/genetics ; *Red Meat/microbiology ; *Meat/microbiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {BACKGROUND: Slaughterhouses and meat cutting plants represent potential hotspots for the spread and transfer of spoilage and pathogenic, including antimicrobial resistant, bacteria to meat and meat products. Here, we characterise the progression of the microbiome and resistome of two pork cuts (loin and sirloin) at different stages of processing, from the slaughter line to the end of shelf-life. To this end, we analysed samples from facility surfaces, carcasses, and meat cuts using whole metagenome sequencing.<br><br>RESULTS: The taxonomic and antimicrobial resistance gene (ARG) profiles of carcasses and meat cuts were significantly influenced by the point of sampling and the processing room. The facility surfaces were found to be the main source of some abundant genera, such as Anoxybacillus, Acinetobacter, Pseudomonas, and Brochothrix, in carcasses and meat cuts. A total of 1,291 metagenome-assembled genomes were reconstructed, corresponding to the most prevalent species identified in the taxonomic analysis at the read level. A reduction in bacterial and ARGs richness and diversity was observed for carcasses and meat cuts along the production chain, which suggests that processing procedures are effective in reducing bacterial and ARGs loads. Nonetheless, an increase in the ARGs load was observed at two sampling points: the carcass after evisceration and the sirloin at the end of its shelf-life (in this case linked to the increase of a single gene, tet(L)). The ARGs most frequently detected were those associated with resistance to tetracyclines, aminoglycosides, and lincosamides. Acinetobacter (in processing environments and carcass/meat samples) and Staphylococcus (in carcasses and meat) were identified as the main genera associated with the ARGs found.<br><br>CONCLUSIONS: Overall, our results provide the most detailed metagenomics-based perspective on the microbial successions of pig carcasses and fresh meat cuts during slaughtering, processing, and commercialisation. The observations made suggest that selection pressures imposed by processing steps and contact with facility surfaces contribute to shaping the microbiome and resistome of the two pork products throughout their production line and shelf-life. Video Abstract.},
}
@article {pmid41565669,
year = {2026},
author = {Schneeberger, PHH and Dommann, J and Rahman, N and Hürlimann, E and Sayasone, S and Ali, S and Coulibaly, JT and Keiser, J},
title = {Profound taxonomic and functional gut microbiota alterations associated with trichuriasis: cross-country and country-specific patterns.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {45},
pmid = {41565669},
issn = {2055-5008},
support = {101019223/ERC_/European Research Council/International ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Trichuriasis/microbiology/parasitology/epidemiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Trichuris ; Tanzania/epidemiology ; Animals ; Laos/epidemiology ; Metagenomics/methods ; Fatty Acids, Volatile/metabolism ; Female ; Feces/microbiology ; Male ; Adult ; Mucins/metabolism ; },
abstract = {The human gut microbiota is vital for immune function, metabolism, and resistance to pathogens. Soil-transmitted helminths like Trichuris trichiura can disrupt this microbial community, but the extent and functional significance of these disruptions across diverse regions remain unclear. We investigated the impact of T. trichiura infection on gut microbiota composition and function in three endemic regions-Côte d'Ivoire, Laos, and Tanzania-using standardized, high-resolution metagenomic profiling. Our findings reveal consistent depletion of key short-chain fatty acid (SCFA) producers, including Blautia sp. MSJ 9 and Holdemanella biformis, and enrichment of mucin-degrading genera such as Ruminococcus and Bacteroides. These changes coincided with increased microbial utilization of host-derived carbohydrates and destabilization of microbial networks, notably with the emergence of Segatella copri in infected individuals. Although taxa-level responses varied by region, similar trends in SCFA depletion and mucin degradation were observed across sites, pointing to a potentially shared metabolic response to infection. These alterations suggest compromised gut barrier function and immune modulation, potentially promoting parasite persistence. Our results underscore the potential of microbiome-based strategies, such as targeted probiotics or dietary interventions, to support helminth control by restoring microbial balance and improving host resilience.},
}
@article {pmid41565402,
year = {2026},
author = {Zhou, Y and Wang, H and Guo, L and Liu, X and Wang, X and Liu, Y and Shang, M and Zheng, B and Li, K and Liu, L and Li, J and Ding, G},
title = {Human umbilical cord MSC-derived exosomes attenuate radiation-induced pulmonary fibrosis via remodeling the gut-lung axis in mice.},
journal = {Life sciences in space research},
volume = {48},
number = {},
pages = {204-215},
doi = {10.1016/j.lssr.2025.11.011},
pmid = {41565402},
issn = {2214-5532},
mesh = {*Exosomes/metabolism ; Humans ; Animals ; Mice ; *Mesenchymal Stem Cells/cytology/metabolism ; *Pulmonary Fibrosis/etiology/therapy ; *Umbilical Cord/cytology ; Gastrointestinal Microbiome ; *Lung/radiation effects/metabolism/pathology ; Male ; Mice, Inbred C57BL ; },
abstract = {OBJECTIVE: To investigate whether human umbilical cord mesenchymal stem cell-derived exosomes (hUC-MSC-Exos) attenuate radiation-induced pulmonary fibrosis (RIPF) through modulation of the gut-lung axis.<br><br>METHODS: The therapeutic efficacy of hUC-MSC-Exos was evaluated in a mouse model of RIPF through histopathology and western blot analysis of fibrosis markers (&#x3b1;-SMA, Vimentin, and E-cadherin). Gut barrier integrity (ZO-1, Occludin) and intestinal inflammation (IL-6, IL-1&#x3b2;) were examined using immunohistochemistry, RT-qPCR, and ELISA. Gut microbial composition and metabolic profiles were characterized via metagenomics and untargeted metabolomics, followed by integrated bioinformatics analyses to identify key pathways and metabolites.<br><br>RESULTS: hUC-MSC-Exos significantly reduced pulmonary collagen deposition and restored fibrosis markers expression, concomitant with enhanced gut barrier function and attenuated intestinal inflammation. Multi-omics analysis revealed restoration of gut microbiota homeostasis and metabolic reprogramming, with the alanine, aspartate, and glutamate pathway being notably co-regulated. L-Glutamic acid was the most significantly altered metabolite and correlated significantly positively with the severity of pulmonary fibrosis and gut dysfunction. Gut microbiota associated with L-Glutamic acid (e.g., Duncaniella, Ruminococcus) were also significantly restructured.<br><br>CONCLUSIONS: hUC-MSC-Exos attenuate RIPF through a comprehensive remodeling of the gut-lung axis, in which L-Glutamic acid and its associated microbiota serve as potential mediators. These findings highlight the gut-lung axis as a promising therapeutic target for RIPF.},
}
@article {pmid41564978,
year = {2026},
author = {Yuan, C and Jin, P and He, Z and Guo, J and Xiong, M and Sun, J and Wang, L and Wang, Z and Han, N and Feng, W and Hou, Y and Qi, H and Jia, Z},
title = {Maxing Shigan decoction serves as a key component of Lianhua Qingwen in alleviating lung and gut injury by restoring gut microbiota homeostasis and inhibiting inflammation via TLR4/NF-κB and JAK2/STAT3 dual regulation.},
journal = {Microbial pathogenesis},
volume = {212},
number = {},
pages = {108285},
doi = {10.1016/j.micpath.2026.108285},
pmid = {41564978},
issn = {1096-1208},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Toll-Like Receptor 4/metabolism ; *Drugs, Chinese Herbal/pharmacology ; NF-kappa B/metabolism ; STAT3 Transcription Factor/metabolism ; Mice ; *Acute Lung Injury/drug therapy ; Janus Kinase 2/metabolism ; Inflammation/drug therapy ; Lung/drug effects/pathology ; Male ; Lipopolysaccharides ; Colitis, Ulcerative/drug therapy/chemically induced ; Homeostasis/drug effects ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Disease Models, Animal ; Cytokines/metabolism ; },
abstract = {Lianhua Qingwen (LHQW), a clinically validated herbal medicine containing Maxing Shigan Decoction (MXSGT) and others, shows broad efficacy in various respiratory disease. However, its regulatory role on the gut-lung axis, particularly the contribution of its MXSGT components, remains unexplored. This study employed a formula-disassembled approach to decipher this mechanism. Three preparations, including the complete LHQW prescription, LHQW excluding MXSGT components (LHQW-MXSGT), and MXSGT along, were administered to LPS-induced acute lung injury and DSS-induced ulcerative colitis to evaluate their therapeutic effects via the gut-lung axis. Pathological changes, mucosal barrier integrity, inflammatory cell infiltration and pro-inflammatory cytokine levels were evaluated by H&amp;E staining, histochemical staining, immunofluorescence, ELISA, RT-qPCR and Western blot. Metagenomic analysis (16S rDNA sequencing) was conducted to examine their regulatory role of gut microbiota. Network pharmacology analysis and cellular validation was employed to explore their underlying mechanisms. Our analyses demonstrated that LHQW and MXSGT, but not LHQW-MXSGT, significantly attenuated lung/intestinal pathology damage, reduced pro-inflammatory cytokines (TNF-α, IL-1β, IL-6), and restored gut barrier proteins (ZO-1, Occludin, MUC2). LHQW/MXSGT suppressed pathogenic bacteria (Escherichia coli, Salmonella, Klebsiella pneumoniae) while enriching Akkermansia muciniphila, correlating with decreased systemic LPS. Network pharmacology and subsequent validation identified dual inhibition of TLR4/NF-κB and JAK2/STAT3 pathways as key mechanism of MXSGT. In conclusion, MXSGT serves a pivotal pharmacologically active component of LHQW for its gut-lung axis regulation, acting through gut microbiota homeostasis restoration, intestinal barrier integrity maintenance, and anti-inflammatory signaling pathways, providing compelling scientific evidence supporting LHQW's potential therapeutic application in managing diseases characterized by comorbid gut and lung inflammation.},
}
@article {pmid41564488,
year = {2026},
author = {Huang, Z and Shen, J and Wang, J and Wang, C and Liu, H and Tian, C and Feng, J and Wang, X},
title = {Seasonal dynamics of sedimentary dissolved organic matter in plateau lakes: Driving effects on microbial community and functional genes in elements cycling.},
journal = {Journal of environmental management},
volume = {399},
number = {},
pages = {128688},
doi = {10.1016/j.jenvman.2026.128688},
pmid = {41564488},
issn = {1095-8630},
mesh = {*Lakes/chemistry ; Seasons ; *Geologic Sediments/chemistry ; Microbiota ; Carbon ; },
abstract = {Plateau lakes, as sensitive zones to global climate change and critical hubs for land-water carbon exchange, remain understudied in terms of the seasonal dynamics of their sedimentary dissolved organic matter (DOM) and its interactions with microbial ecological function. This study employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic techniques to unravel the seasonal variations of DOM and their regulatory roles in microbial community and elements cycling. During the dry season, low water temperature (WT), dissolved oxygen (DO), and high electrical conductivity (EC) promoted accumulation of lignin-like and carboxyl-rich aliphatic molecules (CRAMs), with Fuxian Lake exhibiting the strongest sequestration. The subsequent wet period raised microbial biomass carbon (MBC) and easily oxidizable organic carbon (EOC), lowered average mass-to-charge ratios and increased both nominal hydrogen-to-carbon ratios (H/C) and the molecular lability index (MLB%). Labile sugars and peptides enhanced microbial α-diversity, whereas refractory compounds selected for specialist taxa and intensified community differentiation. Random forest identified sugars, peptides, O3S + O5S, biological index (BIX), and WT as core drivers of element cycling genes expression. Functional gene modules diverged along trophic status. The oligotrophic deep lake underwent seasonal turnover, whereas the eutrophic shallow lake preserved stable supermodules integrating multiple metabolic pathways to buffer perturbations. Anthropogenic disturbances elevated sulfur/nitrogen-containing heteroatomic compounds and threatened sediment carbon sinks and element cycling balance. This study advances the understanding of DOM-driven biogeochemical cycles and provides a scientific framework for managing multi-element interactions in climatically sensitive plateau lakes.},
}
@article {pmid41562342,
year = {2026},
author = {Winkler, M and Seel, W and Kornblum, C and Simon, MC and Reimann, J},
title = {The MicroIBioM study: the gut microbiome in inclusion body myositis.},
journal = {Clinical and experimental rheumatology},
volume = {44},
number = {2},
pages = {186-193},
doi = {10.55563/clinexprheumatol/1b8sv1},
pmid = {41562342},
issn = {0392-856X},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Aged ; Middle Aged ; *Myositis, Inclusion Body/microbiology/diagnosis ; Feces/microbiology ; Case-Control Studies ; *Bacteria/genetics/classification ; Severity of Illness Index ; RNA, Ribosomal, 16S/genetics ; Ribotyping ; Aged, 80 and over ; },
abstract = {OBJECTIVES: Inclusion body myositis (IBM) is a disorder with features of both inflammation and degeneration yet without effective treatment. Influences of the gut microbiome on degenerative as well as inflammatory disorders and immune treatments are known. We sought to investigate whether the gut microbiome might influence the development or recalcitrance of IBM.<br><br>METHODS: We appealed to IBM patients and their unaffected spouses/cohabitants for stool samples and data on clinical symptoms, gathering questionnaire data (modified Gastrointestinal Symptom Rating Scale (mGSRS), IBM Functional Rating Scale (IBMFRS) and Bristol Stool Scale) and stool samples for 16S rRNA V3V4 metagenomic analysis from 21 IBM and 20 control probands. Bioinformatic analyses used QIIME2 and MicrobiomeAnalyst software packages. LEfSe and Random Forest analysis aimed to identify group specific biomarkers. PICRUSt was used to perform pathway analysis.<br><br>RESULTS: No overall differences of alpha and beta diversity were found between IBM and control group. No impact of immune treatments was found, but a reduction in alpha diversity was identified comparing older (&#x2265; 72 years) IBM and control probands. Increased abundances of some genera, in particular Bacteroides, were detected in the IBM group. Bacteroides, Clostridium CAG 352, and Eggerthella were identified as IBM biomarkers at genus level. Gastrointestinal symptoms (mGSRS) correlated with disease severity (IBMFRS).<br><br>CONCLUSIONS: General differences of gut microbiome seem unlikely to play a role in the genesis of IBM. Whether the late occurring or the more specific differences detected are part of the disease course needs to be addressed by investigations of further biosamples.},
}
@article {pmid41562094,
year = {2025},
author = {Tang, K and Zhang, Y and Meneses, C and Rogerio, LA and Willen, L and Iniguez, E and Kamhawi, S and Valenzuela, JG and Oliveira, F and Cecilio, P},
title = {Phlebotomus duboscqi gut microbiota dynamics in the context of Leishmania infection.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1717935},
pmid = {41562094},
issn = {1664-3224},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Phlebotomus/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; *Leishmaniasis/parasitology ; *Insect Vectors/microbiology/parasitology ; Bacteria/genetics/classification ; },
abstract = {INTRODUCTION: The manipulation of the gut microbiota of disease vectors has emerged as a new approach to use in the integrated control of vector-borne diseases. For this purpose, a deep knowledge of their gut microbial communities is essential. To our knowledge, to date, no study has documented the gut microbiome dynamics of Phlebotomus duboscqi sand flies over the entire time-period required for the maturation of a Leishmania infection. Here, we address this limitation.<br><br>METHODS: P. duboscqi midguts were dissected both before and at different days after L. major infection and subjected to genomic DNA extraction followed by amplification of the V3-V4 hypervariable regions of the 16S rRNA, sequencing, and metagenomics analysis.<br><br>RESULTS: We observed a decrease in the number of Amplicon Sequence Variants (ASVs) early after infection, at D2, and late after infection, at D12. More so Sphingomonas, Ochrobactrum, and Serratia emerged as the most prevalent genera in relative terms, before, early after, and late after infection, respectively. These results translated into a separation between the 3 groups in the context of a beta diversity analysis, with statistical relevance. Importantly, we were able to establish Corynebacterium spp. and Enterococcus spp. as potential markers of non-infected and infected sand flies, respectively, as well as Streptococcus spp., Sphingomonas spp., Ralstonia spp., and Abiotrophia spp. as potential specific markers of late infections (ANCOM-BC analysis).<br><br>DISCUSSION: Overall, we show that the composition of the gut microbiota of P. duboscqi sand flies changes significantly over the course of an infection with L. major parasites.},
}
@article {pmid41561096,
year = {2025},
author = {Wan, L and Huang, C and Kong, W and Li, M and Lu, C},
title = {The analysis of gut microbiota characteristics in children with global developmental delay.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1606453},
pmid = {41561096},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Female ; Feces/microbiology ; Male ; *Developmental Disabilities/microbiology ; Child, Preschool ; *Bacteria/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Child ; DNA, Bacterial/genetics ; Infant ; Biodiversity ; China ; },
abstract = {OBJECTIVE: To explore the composition and functional changes of gut microbiota in children with Global Developmental Delay(GDD),and to explore the role of gut microbiota in the pathogenesis of GDD using high-throughput sequencing.<br><br>METHODS: A prospective study was conducted to select 26 children diagnosed with GDD at Longgang District Maternal and Child HealthCare Hospital of Shenzhen City from January 2024 to December 2024 as the disease group(GDD), and 59 healthy children of the same age were selected as the healthy group(HC).General information of the children was collected through a questionnaire survey, and fecal samples from all participants were collected. Total DNA was extracted and amplified, and high-throughput sequencing of the 16S rRNA gene was performed for biological analysis of the sequencing results.<br><br>RESULTS: The alpha diversity analysis revealed a significant reduction in microbial diversity in the GDD group (Chao1 index, P = 0.007), while the beta diversity showed significant segregation between groups (R&#xb2; = 0.067, P = 0.001);At the phylum level, the relative abundance of Actinobacteria was significantly increased (P < 0.01), while the abundance of Bacteroidetes was significantly decreased (P < 0.05) in the GDD group;At the genus level, the abundance of Bifidobacterium, Fusicatenibacter, and Erysipelatoclostridium were significantly increased in the GDD group (all P < 0.001), while the abundance of Faecalibacterium, Phascolarctobacterium, and Alistipes were significantly reduced (all P < 0.001);Functional prediction based on 16S rRNA data suggested potential differences in microbial metabolic pathways, including mRNA surveillance, proteasome, and atrazine degradation, in the GDD group. These findings hypothesize a functional shift in the gut microbiome associated with GDD, which requires validation by direct metagenomic or metabolomic methods.<br><br>CONCLUSION: Children with GDD have significant differences in gut microbiota composition and diversity compared to HC,and the abundance and abnormal metabolic pathway may be closely related to the neuroinflammatory process, suggesting that intestinal microecological regulation may become a new intervention target for GDD.},
}
@article {pmid41561086,
year = {2025},
author = {Zhang, MY and Chen, SY and Lin, YH and Yuan, XX},
title = {Gut microbiota modulation in gastrointestinal disorders: current evidence and therapeutic perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1740322},
pmid = {41561086},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Gastrointestinal Diseases/therapy/microbiology ; Probiotics/therapeutic use ; Animals ; Fecal Microbiota Transplantation ; Gastrointestinal Tract/microbiology ; Phage Therapy ; Dysbiosis/therapy ; },
abstract = {Gut microbiome medicine is a promising field in functional medicine, offering personalized treatment strategies for gastrointestinal disorders. Advanced metagenomic and metabolomic technologies have revealed the gut microbiome's systemic influence, extending to distant organs like the brain and lungs. While small molecules and genes facilitate these effects, the gut microbiota's greatest abundance and activity are concentrated in the gastrointestinal tract, particularly in the distal regions. The balance of microbial communities in the small and large intestines is crucial for gastrointestinal health. However, the dominance of pathogenic bacteria can disrupt this balance, leading to tissue damage and contributing to gastrointestinal disorders. Emerging interventions, such as probiotics, fecal microbiota transplantation, and dietary enrichment with short-chain fatty acids, show potential in restoring microbial balance, enhancing immune function, and potentially protecting against carcinogenesis. Current evidence from clinical trials and animal models supports the therapeutic role of gut microbiome modulation in reversing gastrointestinal disorders. However, variability in study outcomes highlights the need for further research to standardize these approaches for clinical practice. This review underscores the gut microbiome's pivotal role in gastrointestinal health and the therapeutic promise of functional medicine in addressing these disorders. This review also explores emerging interventions, such as phage therapy and engineered microbes, and provides comparative analyses of microbiota signatures and therapeutic approaches across different gastrointestinal disorders.},
}
@article {pmid41558481,
year = {2026},
author = {Keller, V and Calchera, A and Otte, J and Tuovinen Nogerius, V and Schmitt, I},
title = {Ubiquitous occurrence of the black fungus Melanina gundecimermaniae in the lichen Umbilicaria pustulata.},
journal = {Current biology : CB},
volume = {36},
number = {3},
pages = {748-759.e5},
doi = {10.1016/j.cub.2025.12.046},
pmid = {41558481},
issn = {1879-0445},
mesh = {*Lichens/microbiology/physiology ; *Symbiosis ; *Ascomycota/physiology/genetics ; Metagenome ; Europe ; North America ; Genome, Fungal ; },
abstract = {Lichen symbioses frequently include additional fungal associates beyond the canonical mycobiont (fungus) and photobiont (alga/cyanobacterium). Despite the prevalence and diversity of these lichen cohabitants, their geographic distribution and role within the lichen consortium remain poorly understood. Combining genomics, metagenomics, and advanced microscopy, we identified the black fungus Melanina gundecimermaniae as a constant cohabitant in the lichen Umbilicaria pustulata. We analyzed metagenomes from 149 individuals across 15 populations, spanning the Europe-wide range of U. pustulata. Additionally, we screened pooled metagenomes of U. pustulata and Umbilicaria phaea along five elevation gradients (Europe and North America). Genome mapping, using a near-complete reference genome of M. gundecimermaniae, revealed that the black fungus was present in 100% of the screened lichen metagenomes, with 0.85%-3.78% of reads mapping against the reference. Among all lichen-associated fungi, it was one of the most common. These findings indicate that the black fungus is widely distributed and associated with different lichen species, underscoring its potential ecological significance. Using fluorescence in situ hybridization coupled with confocal laser scanning microscopy, we confirmed the presence of M. gundecimermaniae within various structures of U. pustulata, including vegetative symbiotic propagules involved in dispersal. Elucidating its widespread occurrence across continents, consistent presence in U. pustulata, and ability to be dispersed together with the lichens' canonical partners, our findings suggest a potential interaction of M. gundecimermaniae that extends beyond incidental colonization. Our study contributes to the growing body of evidence that organismal complexity within lichens is a prevalent and largely unexplored dimension of the lichen symbiosis.},
}
@article {pmid41557465,
year = {2026},
author = {Ivanov, A and Popov, V and Morozov, M and Olekhnovich, E and Ulyantsev, V},
title = {MetaFX: feature extraction from whole-genome metagenomic sequencing data.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {2},
pages = {},
pmid = {41557465},
issn = {1367-4811},
support = {23-75-10125//Russian Science Foundation/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Software ; *Whole Genome Sequencing/methods ; Gastrointestinal Microbiome/genetics ; *Metagenome ; Machine Learning ; Inflammatory Bowel Diseases/microbiology ; Databases, Genetic ; },
abstract = {MOTIVATION: Microbial communities consist of thousands of microorganisms and viruses and have a tight connection with an environment, such as gut microbiota modulation of host body metabolism. However, the direct relationship between the presence of certain microorganism and the host state often remains unknown. Toolkits using reference-based approaches are limited to microbes present in databases. Reference-free methods often require enormous resources for metagenomic assembly or results in many poorly interpretable features based on k-mers.<br><br>RESULTS: Here we present MetaFX-an open-source library for feature extraction from whole-genome metagenomic sequencing data and classification of groups of samples. Using a large volume of metagenomic samples deposited in databases, MetaFX compares samples grouped by metadata criteria (e.g. disease, treatment, etc.) and constructs genomic features distinct for certain types of communities. Features constructed based on statistical k-mer analysis and de Bruijn graphs partition. Those features are used in machine learning models for classification of novel samples. Extracted features can be visualized on de Bruijn graphs and annotated for providing biological insights. We demonstrate the utility of MetaFX by building classification models for 590 human gut samples with inflammatory bowel disease. Our results outperform the previous research disease prediction accuracy up to 17%, and improves classification results compared to taxonomic analysis by 9&#xb1;10% on average.<br><br>MetaFX is a feature extraction toolkit applicable for metagenomic datasets analysis and samples classification. The source code, test data, and relevant information for MetaFX are freely accessible at https://github.com/ctlab/metafx under the MIT License. Alternatively, MetaFX can be obtained via http://doi.org/10.5281/zenodo.16949369.},
}
@article {pmid41556662,
year = {2026},
author = {Zhang, N and Atoni, E and Nyaruaba, R and Kibaba, P and Shadrack, K and Wang, F and Agwanda, B and Zheng, Z and Dai, J and Yuan, Z and Xia, H},
title = {Host and geography shape microbial communities in Kenyan mosquitoes: insights from metatranscriptomics.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0142725},
pmid = {41556662},
issn = {2379-5077},
support = {2022YFC2302700, 2023YFC2305900//National Key Research and Development Program of China/ ; },
mesh = {Animals ; Kenya ; *Microbiota/genetics ; *Aedes/microbiology/virology ; *Culex/microbiology/virology ; *Transcriptome ; Phylogeny ; Bacteria/genetics/classification/isolation &amp; purification ; Geography ; Virome ; Mosquito Vectors/microbiology/virology ; },
abstract = {Mosquitoes harbor diverse microbial communities that influence their potential to transmit pathogens. However, the ecological drivers shaping these microbiomes, particularly in under-sampled regions like Africa, remain poorly resolved. We conducted a large-scale metatranscriptomic survey of 3,940 Aedes and Culex mosquitoes from diverse ecological zones across Kenya. Our analyses revealed that viruses dominated the overall transcriptome, while bacteria exhibited the greatest taxonomic richness. Geographic location emerged as the primary driver of microbial community structure, whereas host genus identity shaped virome diversity at local or city-level scales. Culex mosquitoes harbored higher viral richness, particularly in coastal regions, while Aedes supported more diverse bacterial assemblages. Microbial co-occurrence networks exhibited distinct topologies across hosts: Culex networks featured cross-domain interactions and viral keystone taxa, whereas Aedes networks were more cohesive and robust, centered on bacterial hubs. We identified 102 distinct viruses from 24 families, including 31 putative novel RNA viruses. Segment-resolved phylogenies revealed cryptic clades within Bunyavirales, Picornavirales, and other lineages. Collectively, our findings highlight the scale-dependent influences of geography and host identity on mosquito microbiomes in East Africa and demonstrate the utility of metatranscriptomics in uncovering hidden microbial diversity and ecological interactions. These insights provide a foundation for ecologically informed arthropod vector surveillance and microbiome-based intervention strategies.IMPORTANCEMosquitoes are more than just flying syringes; they are complex ecosystems hosting a variety of microbes. Understanding what shapes this microbial world inside mosquitoes is key to developing new control strategies. Our study of nearly 4,000 mosquitoes from Kenya reveals that where a mosquito lives matters most for its overall microbial makeup, but its genus dictates which viruses it carries. We discovered that different mosquito types have distinct microbial social networks: one type has a fragile network centered on viruses, while the other has a resilient network built around bacteria. This means that strategies to disrupt disease transmission by targeting mosquito microbes may need to be tailored to a specific mosquito genus. Our work provides a map of these microbial ecosystems, highlighting potential new viruses and offering insights for future public health surveillance and interventions.},
}
@article {pmid41556507,
year = {2026},
author = {Cheng, S and Tang, X and Huang, X and Li, Y and Huang, S and He, D and Moreno-Jiménez, E and Xu, J and Rillig, MC and Dai, Z and Delgado-Baquerizo, M},
title = {Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies.},
journal = {Global change biology},
volume = {32},
number = {1},
pages = {e70704},
doi = {10.1111/gcb.70704},
pmid = {41556507},
issn = {1365-2486},
support = {41721001//National Natural Science Foundation of China/ ; 2019YFC1803704//National Key Research and Development Program of China/ ; +226-2024-00029//The Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; Metagenomics ; *Metagenome ; *Stress, Physiological ; Biodiversity ; *Climate Change ; Ecosystem ; Bacteria/genetics/classification ; },
abstract = {Soil microorganisms constitute the largest portion of Earth's biodiversity. However, soil microorganisms are also highly sensitive to on-going global change, and the influence of an increasing number of stressors on common, rare, and unknown taxa across large environmental gradients remains virtually unknown. Here, we combined a large-scale spatial field survey across multiple different ecosystems and found that the diversity and abundance of soil rare taxa were significantly reduced under high environmental stressor number (i.e., a high number of stressors passing a 75% stressor threshold). Strikingly, the abundance of unknown soil taxa and unknown genes increased with increasing environmental stress number. We further identified the metagenome-assembled genomes (MAGs) that were considered as relatively common taxa using metagenomics. Compared to 9% of negative responders, 32% of common MAGs were resistant or positively responsive to multiple stress, displaying a reduced potential for cellular processes and an enhanced potential for environmental, genetic, and metabolic processes. Our study suggests that as stress increases, we would have less rare, but more unknown microorganisms and unique genomes of resistant common taxa, suggesting major changes in the soil microbiome in a world subjected to multiple global change stressors.},
}
@article {pmid41555453,
year = {2026},
author = {Orr, RJS and Brynildsrud, O and Bøifot, KO and Gohli, J and Skogan, G and Kelly, FJ and Hernandez, MT and Udekwu, K and Lee, PKH and Mason, CE and Dybwad, M},
title = {Spatial and temporal patterns of public transit aerobiomes.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {64},
pmid = {41555453},
issn = {2049-2618},
mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; Humans ; *Air Microbiology ; Metagenomics/methods ; *Microbiota/genetics ; Cities ; Seasons ; Biodiversity ; Spatio-Temporal Analysis ; },
abstract = {BACKGROUND: Aerobiome diversity is extensive; however, species-level community structure remains poorly resolved. Likewise, microbiomes of public transit systems are of public interest due to their importance for health, though few studies have focused on these ecosystems whilst utilising shotgun metagenomics. Aerosol studies have focused predominantly on individual cities, with limited between-city comparisons suggesting specific community structures. Longitudinal studies show aerobiome diversity as dynamic, fluctuating during seasonal and daily cycles, though interannual cycles remains to be considered. Further, a bacterial bias has limited fungal aerobiome studies, with few considering both fractions collectively. As such, the objective of this study was to examine spatial and temporal patterns in the species diversity of public transit aerobiomes, with an emphasis on bacteria and fungi.<br><br>RESULTS: Air samples taken over a 3-year period (2017-2019) from six global cities were subjected to shotgun metagenomic sequencing. Improved classification databases, notably for fungi, applying stringent parameters for trimming, exogenous contamination removal and classification yielded high species-level resolution. Microbial diversity varied substantially among cities, while human and environmental factors, recorded in parallel, were of secondary significance. Bacteria dominated the public transit aerobiome with increased presence in cities with higher population densities. All aerobiomes had complex compositions, consisting of hundreds to thousands of species. Interannual variation had limited significance on the public transit aerobiome diversity and community structure.<br><br>CONCLUSIONS: Cities were the most important factor contributing to diversity and community structure, demonstrating specific bacterial and fungal signatures. Further, possible correlation between geographical distance and genetic signatures of aerobiomes is suggested. Bacteria are the most abundant constituent of public transit aerobiomes, though no single species is globally dominant, conversely indicating a large inter-city variation in community structure. The presence of a ubiquitous global species core is rejected, though an aerobiome sub-core is confirmed. For the first time, local public transit aerobiome cores are presented for each city and related to ecological niches. Further, the importance of a robust bioinformatics analysis pipeline to identify and remove exogenous contaminants for studying low-biomass samples is highlighted. Lastly, a core and sub-core definition of contaminant aerobiome species with taxon tables, to facilitate future environmental studies, is presented. Video Abstract.},
}
@article {pmid41554846,
year = {2026},
author = {Sumithra, TG and Sharma, SRK and Gayathri, S and Gop, AP and Shravana, KS and Jagannivasan, A and Nair, AV and Sudarsan, KS and Santhosh, B and Ebeneezar, S and Gopalakrishnan, A},
title = {Egg disinfection improves larval survival and shapes the microbial community in snubnose pompano (Trachinotus blochii).},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {5761},
pmid = {41554846},
issn = {2045-2322},
support = {BT/AAQ/3/SP28267/2018//Department of Biotechnology, Government of India/ ; },
mesh = {Animals ; Larva/microbiology/drug effects/growth &amp; development ; *Disinfection/methods ; *Microbiota/drug effects ; *Ovum/microbiology/drug effects ; RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology/growth &amp; development ; Disinfectants/pharmacology ; Bacteria/genetics/classification/drug effects ; },
abstract = {Early microbial colonization is crucial for immunity and survival in aquatic animals. This study evaluated the impact of egg disinfection on microbial colonization and larval performance in Trachinotus blochii, a high-value mariculture fish. Optimal egg disinfection protocols were initially identified as 20 ppm iodophor for 10 min, 400 ppm H2O2 for 10 min, and 40 ppm glutaraldehyde for 5 min to improve hatchability. Sequential analyses included 16S rRNA amplicon sequencing of larval microbiota at 10-days post hatching (DPH) and assessment of survival and antioxidant status till 25 DPH. Disinfection significantly enhanced hatchability (up to 90.88 ± 2% with 40 ppm glutaraldehyde), larval survival (up to 34.80 ± 1.1% in glutaraldehyde and 31.18 ± 1.5% in H2O2), and catalase activity. Notably, egg disinfection reshaped the larval microbiota, enriching microbial diversity measures and beneficial bacterial taxa, such as Hyphomonadaceae, Halieaceae, Nannocystaceae, and Alteromonadaceae. Improved survival correlated with enhanced taxonomic and functional metagenomic diversity, lower Proteobacteria: Bacteroidota ratio and higher combined proportions of Fusobacteriota, Firmicutes, and Bacteroidota relative to Proteobacteria. The findings suggest that egg disinfection acts as a microbiota programming strategy to promote larval health, offering a practical approach to enhance sustainability in T. blochii aquaculture.},
}
@article {pmid41552949,
year = {2026},
author = {Dani, M and Beszteri, S and Castellanos, AB and Schimani, K and Skibbe, O and Zimmermann, J and Soares, AR and Griesdorn, L and Probst, AJ and Kahlert, M and Beszteri, B},
title = {Species delimitation within the Achnanthidium minutissimum complex (Bacillariophyta), based on morphological, molecular, and ecophysiological approaches.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70124},
pmid = {41552949},
issn = {1529-8817},
support = {CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; ZI 1628/2-1//Deutsche Forschungsgemeinschaft/ ; Dnr. 18/171//Swedish EPA, Swedish Agency for Marine and Water Management/ ; },
abstract = {The benthic diatom species Achnanthidium minutissimum belongs to a species complex with a challenging taxonomy. Achnanthidium minutissimum has been reported to be a widespread and abundant species occurring in a broad range of freshwater habitats. However, differentiating and delimiting it from other Achnanthidium species is challenging due to the small size and great similarity of the different species, often with overlaps in morphological features. Therefore, reports of the occurrence of these taxa probably come with a large uncertainty due to potential misidentification. To gain a better understanding of the boundaries between species within the A. minutissimum species complex, we applied an integrative taxonomic approach and investigated the congruence between morphological, molecular, and ecophysiological variability among 13 monoclonal strains isolated from Germany, Sweden, and Spitsbergen. In addition to the characterization of valve morphology, we assessed their growth under different temperatures and salt concentrations and compared sequences of the rbcL marker gene as well as of a broad set of homologous loci sampled by genome skimming. Molecular and ecophysiological variability was mostly congruent with scanning electron microscopy-based morphological identification; the main exception was that two pairs of strains identified as A. cf. microcephalum and A. jackii could be distinguished neither in their ecophysiological profiles nor in their DNA sequences. Extending this integrated taxonomic approach to more strains will be beneficial for a better understanding of the morphological, molecular, and niche differentiation among different Achnanthidium species. The added value of the combined morphological-molecular-ecophysiological approach is an improved delineation of morphological features applicable for species differentiation and a better understanding of ecological differentiation.},
}
@article {pmid41552936,
year = {2026},
author = {Lu, Y and Chang, L and Liu, S and Wang, M and Zhao, Y},
title = {Rutin alleviates dietary advanced glycation end products (AGEs)-induced insulin resistance in mice by modulation of gut microbiota.},
journal = {Food &amp; function},
volume = {17},
number = {3},
pages = {1451-1464},
doi = {10.1039/d5fo04604a},
pmid = {41552936},
issn = {2042-650X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Rutin/pharmacology/administration &amp; dosage ; Male ; *Insulin Resistance ; *Glycation End Products, Advanced/adverse effects/metabolism ; Mice ; Mice, Inbred C57BL ; Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Dietary Advanced Glycation End Products ; },
abstract = {Dietary advanced glycation end products (AGEs), formed during thermal food processing, are associated with metabolic disorders. This study investigated the efficacy of rutin in alleviating AGEs-induced insulin resistance (IR) in a mouse model. Male C57BL/6 mice were fed a high-AGEs diet for 12 weeks to induce IR, followed by 8 weeks of rutin intervention (100 mg per kg body weight per day). Rutin supplementation markedly ameliorated IR, as indicated by reduced hyperglycemia and dyslipidemia, a reduced homeostasis model assessment of insulin resistance (HOMA-IR) index, an elevated insulin sensitivity (HOMA-IS) index, and upregulation of insulin receptor substrates IRS-1 and IRS-2. Metagenomic analysis demonstrated that rutin intervention restored gut microbial richness and diversity and induced structural shifts in the microbiota composition. Specifically, rutin enriched beneficial genera, including Akkermansia, Bifidobacterium, Faecalibacterium, Lactobacillus, and Coriobacteriales, while reducing populations of IR-associated taxa such as Erysipelotrichaceae, Coprobacillus, Enterococcus, Adlercreutzia, and Allobaculum. Concurrently, rutin increased fecal concentrations of short-chain fatty acids (SCFAs), notably acetic acid and propionic acid. Spearman's correlation analysis confirmed negative associations between rutin-modulated microbiota and IR indicators. These results demonstrate that rutin mitigates AGEs-induced IR by reshaping the gut microbiome and promoting beneficial microbial metabolites.},
}
@article {pmid41552860,
year = {2026},
author = {Wang, F and Xiong, W and Huang, X and Li, S and Zhan, A},
title = {Residual eDNA in eRNA Extracts Skews eRNA-Based Biodiversity Assessment: Call for Optimised DNase Treatment.},
journal = {Molecular ecology resources},
volume = {26},
number = {2},
pages = {e70102},
pmid = {41552860},
issn = {1755-0998},
support = {2025ZD1207600//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2025ZD1200800//Jing-Jin-Ji Regional Integrated Environmental Improvement - National Science and Technology Major Project/ ; 2024ZY0128//Guiding Funds of Central Government for Supporting the Development of Local Science and Technology/ ; 32471608//National Natural Science Foundation of China/ ; },
mesh = {*DNA, Environmental/isolation &amp; purification/genetics ; *Biodiversity ; *Deoxyribonucleases/metabolism ; *DNA Barcoding, Taxonomic/methods ; Animals ; *Fishes/classification/genetics ; Rivers/chemistry ; *Metagenomics/methods ; },
abstract = {Environmental RNA (eRNA) metabarcoding has rapidly emerged as a powerful tool for assessing contemporary biodiversity patterns across diverse ecosystems. However, the potential for false positive detections caused by co-extracted environmental DNA (eDNA) remains unquantified. Distinguishing true signals from false positives caused by residual eDNA is a technical challenge in eRNA-based metabarcoding. To address this issue, we employed a freshwater river receiving treated effluent from a wastewater treatment plant as a model system. In such settings, eDNA in the treated effluent can lead to the detection of non-local species (e.g., marine taxa). Treated effluent typically contains minimal or no eRNA, making it well-suited for evaluating the influence of eDNA carryover. By comparing DNase-treated and untreated eRNA samples, we assessed the impact of residual eDNA on fish species richness and community composition. Our results showed that omitting DNase treatment significantly inflated taxonomic richness, with untreated samples detecting a conservative estimate of over 25% more taxa per site. Fold-change analysis revealed that residual eDNA inflated taxon abundances in both high- and low-abundance taxa, with some showing over 10-fold increases. Community composition analyses revealed clear clustering between treated and untreated samples, highlighting substantial shifts driven by residual eDNA. These findings demonstrate that co-extracted eDNA can severely distort eRNA-based biodiversity estimates, leading to false positives and misrepresented contemporary community profiles. We recommend further evaluation of DNase treatment parameters, including enzyme concentration, incubation time and treatment times, and the adoption of optimised protocols to standardise and improve the accuracy of eRNA-based biodiversity monitoring.},
}
@article {pmid41551931,
year = {2026},
author = {Mak, L and Tierney, B and Wei, W and Ronkowski, C and Toscan, RB and Turhan, B and Toomey, M and Andrade-Martínez, JS and Fu, C and Lucaci, AG and Solano, AHB and Setubal, JC and Henriksen, JR and Zimmerman, S and Kopbayeva, M and Noyvert, A and Iwan, Z and Kar, S and Nakazawa, N and Meleshko, D and Horyslavets, D and Kantsypa, V and Frolova, A and Kahles, A and Danko, D and Elhaik, E and Labaj, P and Mangul, S and , and Mason, CE and Hajirasouliha, I},
title = {CAMP: a modular metagenomics analysis system for integrated multistep data exploration.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {1},
pages = {lqaf172},
pmid = {41551931},
issn = {2631-9268},
support = {R01 AI151059/AI/NIAID NIH HHS/United States ; R35 GM138152/GM/NIGMS NIH HHS/United States ; T32 GM083937/GM/NIGMS NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; *Software ; Workflow ; *Computational Biology/methods ; Microbiota ; },
abstract = {Computational analysis of large-scale metagenomics sequencing datasets provides valuable isolate-level taxonomic and functional insights from complex microbial communities. However, the ever-expanding ecosystem of metagenomics-specific methods and file formats makes designing scalable workflows and seamlessly exploring output data increasingly challenging. Although one-click bioinformatics pipelines can help organize these tools into workflows, they face compatibility and maintainability challenges that can prevent replication. To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed the Core Analysis Modular Pipeline (CAMP), a module-based metagenomics analysis system written in Snakemake, with a standardized module and directory architecture. Each module can run independently or in sequence to produce target data formats (e.g. short-read preprocessing alone or followed by de novo assembly), and provides output summary statistics reports and Jupyter notebook-based visualizations. We applied CAMP to a set of 10 metagenomics samples, demonstrating how a modular analysis system with built-in data visualization facilitates rich seamless communication between outputs from different analytical purposes. The CAMP ecosystem (module template and analysis modules) can be found at https://github.com/Meta-CAMP.},
}
@article {pmid41549294,
year = {2026},
author = {Noronha, JM and Hudson, SB and Sharma, G and Ghadi, SC},
title = {Metagenomic Insights into Viral Diversity from an Underexplored Khazan Creek and a Tropical Freshwater Lake.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {139},
pmid = {41549294},
issn = {1432-0991},
mesh = {*Lakes/virology ; *Metagenomics ; *Viruses/genetics/classification/isolation &amp; purification ; *Virome ; Genome, Viral ; India ; Phylogeny ; Ecosystem ; Biodiversity ; Fresh Water/virology ; Bacteriophages/genetics/classification/isolation &amp; purification ; },
abstract = {The virus communities of inland aquatic ecosystems have typically received less attention from the research perspective than those of marine ecosystems. In this study, we compared the viromes of an estuarine creek (Santana Creek) belonging to the khazan ecosystem and an agriculturally relevant freshwater lake (Verna Lake), both located in Goa, India. Taxonomically, the viral realm Duplodnaviria predominated in both the lake and creek communities, Varidnaviria had a minor presence in both, and Monodnaviria was exclusively present in the lake community. Sequences identified in the creek virome bore a greater resemblance to those of marine ecosystems than those in the lake virome. Functional annotation confirmed the taxonomic findings, indicating most proteins were involved in the infective and replicative functions of bacteriophages. Predicted complete viral genomes included those of Synechococcus and Proteus phages in the creek dataset, and of Gokushovirinae phages in the lake dataset. Viral communities of the khazan ecosystem and similar ecosystems worldwide are understudied, and hence the present virome analysis offers a valuable reference for further studies on these ecosystems.},
}
@article {pmid41548675,
year = {2026},
author = {Li, D and Wang, Y and Qiang, H and Liu, Z and He, Z and Liu, W and Yue, X and Zhou, A},
title = {Tailoring microbial communities for medium chain fatty acid production from waste activated sludge: Comparative performance of endogenous vs. exogenous consortia.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {134038},
doi = {10.1016/j.biortech.2026.134038},
pmid = {41548675},
issn = {1873-2976},
mesh = {*Sewage/microbiology ; *Fatty Acids/biosynthesis ; *Microbial Consortia/physiology ; *Microbiota ; Bioreactors/microbiology ; Bacteria/metabolism ; },
abstract = {Optimizing medium chain fatty acid (MCFA) production from waste activated sludge (WAS) requires tailoring microbial communities, yet it remains unclear whether combining substrate sterilization with exogenous caproate-synthesizing bacteria (CSB) can enhance chain elongation. Here, we compared the MCFA production achieved using this strategy with that driven by the endogenous microbiomes in both the solid residue and the supernatant. Among all experimental groups, this strategy achieved the highest MCFA production in the supernatants (3935 ± 21 mg COD/L). This strategy increased CSB abundance in both the solid residue and the supernatant relative to the abundance in the endogenous microbiome systems. Notably, in supernatant systems, this strategy not only enriched acidogens but also led to the highest soluble protein utilization rate, maximal CO2 release/uptake, and an increased gene abundance related to pyruvate generation. Life cycle assessment confirmed economic and environmental benefits. This work provides new insights into optimizing MCFA recovery from WAS.},
}
@article {pmid41548304,
year = {2026},
author = {Mao, C and Zhao, A and Chen, Z and Ge, F and Tang, T and Qiao, Z and Wu, Z and Zhang, Y and Liu, G and Wang, H and Li, Q and Li, T},
title = {Spatiotemporal transmission mechanisms of resistance genes in the Chishui River: Perspectives from environmental drivers and microbial interactions.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141134},
doi = {10.1016/j.jhazmat.2026.141134},
pmid = {41548304},
issn = {1873-3336},
mesh = {*Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; *Microbial Interactions ; Bacteria/genetics ; Genes, Bacterial ; Microbiota ; China ; Water Microbiology ; *Drug Resistance, Bacterial/genetics ; },
abstract = {The accelerating spread of antimicrobial resistance in natural ecosystems, driven principally by the dissemination of antibiotic resistance genes (ARGs), represents an escalating challenge for both environmental integrity and public health security. Aquatic systems contaminated with ARGs alongside associated virulence factors (VFs) and metal resistance elements (MRGs) have emerged as critical reservoirs of resistance propagation. This study employed metagenomic approaches to analyze microbial communities and functional diversity in the Chishui River, which spans three distinct regions under significant anthropogenic influence. The results revealed that microbial communities exhibit distinct spatiotemporal variations predominantly governed by temperature, DO, TP, and TN. In addition, variations in land use types across different regions also directly shaped microbial diversity patterns, subsequently exerting direct and indirect effects on mobile genetic elements (MGEs), ARGs, and VFs, ultimately leading to the enrichment and dissemination of high-risk resistance genes. Both microbial communities and ARGs exhibited short-distance migration patterns. Notably, a synergistic covariation pattern was observed between antibiotic resistance genes (ARGs) and dissimilatory nitrate reduction to ammonium (DNRA) functional genes, indicating a potential ecological linkage between these two genetic traits. A total of 138 metagenome-assembled genomes have been identified as potential vectors for ARG dissemination. We further revealed a novel synergistic link between ARG abundance and the DNRA process, and the class Gammaproteobacteria was identified as the primary vector of resistance dissemination, functioning as dominant co-hosts for ARGs, MRGs, VFs, and DNRA genes in the Chishui River. These findings offer new insights into river ecosystems, underscoring the importance of monitoring the fate of ARGs to enhance our understanding of how river ecosystems respond to human activities.},
}
@article {pmid41547908,
year = {2026},
author = {Kim, YC and Won, SY and Jeong, BH},
title = {Identification of an altered gut microbiome and the protective effect of microbiome changer in prion diseases.},
journal = {Veterinary research},
volume = {57},
number = {1},
pages = {31},
pmid = {41547908},
issn = {1297-9716},
support = {2022R1C1C2004792//National Research Foundation of Korea/ ; RS-2023-00273199//National Research Foundation of Korea/ ; 2017R1A6A1A03015876//National Research Foundation of Korea/ ; B0080529001944//Gyeongbuk RISE CENTER/ ; 2021R1A6C101C369//Korea Basic Science Institute/ ; },
mesh = {Animals ; *Prion Diseases/microbiology/prevention &amp; control/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Catechin/analogs &amp; derivatives/pharmacology ; Mice ; Mice, Inbred C57BL ; Biomarkers ; Male ; },
abstract = {Prion diseases are fatal and contagious brain disorders caused by a pathogenic prion protein (PrP[Sc]) derived from the benign prion protein (PrP[C]). To date, there are no therapeutic substances to completely block prion diseases. Thus, the development of a therapeutic substance is necessary, and the identification of a novel biomarker of prion disease is the first essential step to develop new drugs. In the present study, we carried out a metagenomic analysis to identify microbiome biomarkers for prion disease using next-generation sequencing and bioinformatics tools in intraperitoneally prion-infected mice. In addition, we evaluated the protective effects of epigallocatechin-3-gallate (EGCG), a potent microbiome changer, in prion-infected mice by western blotting and survival analysis. We found a total of 14 differentially abundant taxa between prion-infected and control mice. In addition, we found that prion diseases caused altered microbiome networks and upregulation of DNA repair-related pathways. Furthermore, we observed the protective effect of the microbiome changer EGCG against prion disease in prion-infected mice. Given previous reports of microbiome alterations in prion diseases, we further validated these associations and demonstrated the protective effects of a microbiome-modulating compound.},
}
@article {pmid41547860,
year = {2026},
author = {Castillo-Fernandez, J and Gilroy, R and Jones, RB and Honaker, RW and Whittle, MJ and Watson, P and Amos, GCA},
title = {Waltham catalogue for the canine gut microbiome: a complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {25},
pmid = {41547860},
issn = {2049-2618},
mesh = {Animals ; Dogs/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Feces/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The canine microbiome is a vastly understudied area relative to the importance of dogs in society, particularly given the potential importance of the microbiome in veterinary medicine. This has led to a large knowledge gap in the basic taxonomy and functions of the canine gut microbiome and an overreliance on human databases for canine-specific research. Using a broad sample set, long read sequencing, short read sequencing, and metagenomic assembly approaches, we have produced the most comprehensive microbiome resource in all companion animal research.<br><br>RESULTS: Here, we describe the recovery of 240 core species that account for&#x2009;>&#x2009;80% of the canine gut microbiome when tested on an independent validation dataset. We uncovered&#x2009;>&#x2009;900 new canine-specific strains, 89 novel species, and 10 novel genera, providing a dramatic increase in previous knowledge of the canine microbiome and allowing for mapping rates of up to 95%, a 70% increase on historic mapping rates of&#x2009;~&#x2009;25% using publicly available resources. Through detailed annotation of function, we demonstrate the potential importance of the novel species and genera to health and nutrition and provide evidence of new canine-adapted strains of existing genera and species previously unknown to inhabit canines that provide important metabolic function to the canine host. We discovered the canine microbiome has an expansive ability to metabolize carbohydrates, providing insight into how canines process diverse carbohydrates given their known limited host genomic potential. We uncovered a range of species with abilities to produce butyrate, propionate, and vitamins, highlighting the importance of the canine microbiome to host nutrition. We describe two novel Peptacetobacter species that could regulate host bile acid metabolism, an important finding in the context of chronic GI disease in pets. We demonstrated all new species and genera had no known virulence, suggesting they are commensal and, finally, provided a baseline for antimicrobial resistance in the microbiota species of healthy pets.<br><br>CONCLUSIONS: This work gives entirely new perspectives on the functional capabilities of the canine gut microbiome, suggesting the canine microbiome is distinct, presumably having evolved to its host, diet, and environment over several millennia. Video Abstract.},
}
@article {pmid41547150,
year = {2026},
author = {Liu, J and Huang, X and Wang, Y and Wang, Y and Luo, R and Lu, X and Cao, K and Xing, J and Tu, Y and Zheng, W},
title = {Metagenomics insights into the effects of lactic acid bacteria inoculation on the microbial communities and antibiotic resistance genes in mare milk.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111622},
doi = {10.1016/j.ijfoodmicro.2026.111622},
pmid = {41547150},
issn = {1879-3460},
mesh = {Animals ; Horses ; *Milk/microbiology ; Metagenomics ; *Lactobacillales/genetics/physiology ; Fermentation ; *Microbiota ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Female ; Food Microbiology ; },
abstract = {Antibiotic resistance genes (ARGs) are emerging contaminants threatening public health, yet their transmission risk via mare milk products remains understudied. Using metagenomics, we analyzed lactic acid bacteria (LAB)-inoculated fermented, naturally fermented, raw, and pasteurized mare milk to investigate the effect of LAB inoculation on the distribution and transmission pathways of ARGs in mare milk. The results showed that naturally fermented, raw, and pasteurized mare milk had the highest number of pathogens, relative abundance of ARGs, and relative abundance of mobile genetic elements (MGEs), while LAB inoculation significantly reduced these (p < 0.05). Bacillota was the dominant microbial group in different samples. Compared to naturally fermented and raw mare milk, LAB-inoculated fermentation significantly altered microbial community structure (p < 0.05). This not only reduced or eliminated certain harmful bacteria but also decreased the abundance of total ARGs and multiple ARG subtypes by reducing host bacteria and MGEs. Microbes and MGEs jointly drove ARG transmission, with microbes being key. Transposon, Bacteroidota, and Pseudomonadota are the major MGEs and microbial taxa for ARG transmission. LAB inoculation can effectively inhibit the spread of 11 ARG types, including β-lactam and multidrug resistance, by weakening the co-occurrence network among microbes, ARGs, and MGEs. This study enhances understanding of resistance genes in diverse equine dairy products, elucidates the impact of LAB fermentation on ARG distribution and transmission pathways in mare milk, and provides valuable data references and theoretical guidance for safer equine dairy processing.},
}
@article {pmid41545429,
year = {2026},
author = {Maharaj, SD and Nkuna, R and Matambo, TS},
title = {Shotgun metagenomic and physicochemical profiling of municipal wastewater treatment plants using activated sludge and trickling filters.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {5486},
pmid = {41545429},
issn = {2045-2322},
mesh = {*Sewage/microbiology/chemistry ; *Wastewater/microbiology/chemistry ; *Metagenomics/methods ; Bacteria/genetics/classification ; *Metagenome ; South Africa ; *Water Purification/methods ; *Waste Disposal, Fluid/methods ; High-Throughput Nucleotide Sequencing ; Biological Oxygen Demand Analysis ; Filtration ; Microbiota ; },
abstract = {In this study, which aimed to evaluate wastewater treatment and provide data to support improved wastewater treatment plant (WWTP) design, operation and ongoing monitoring strategies, mixed liquor, return activated sludge, primary effluent and secondary effluents of two WWTPs (n = 15) and five of the industries they service (n = 15) in Emfuleni municipality, Gauteng Province, South Africa, were characterised following a 5-month monitoring study. Following physical and chemical analysis, the parameters, including the Chemical Oxygen Demand (COD), were higher than local limits (75 mg/L) for both WWTPs and extremely high for the abattoir industry (13400 mg/L). In particular, high ammonia levels were recorded in both WWTPs. Following Illumina high-throughput sequencing and analysis using the Whole Metagenome Sequencing Assembly-based (WGSA2) pipeline on the Nephele platform, Bacteria was the dominant domain in the WWTPs. The dominant phyla were Proteobacteria (87.7%), followed by Firmicutes (8.25%), Actinobacteria (2.71%) and Bacteroidetes (0.68%). Aeromonas (39.86%) was the most dominant genus, with Acinetobacter (9.29%), Pseudomonas (6.78%), Bacillus (5.99%), and Thauera following (4.78%). Total Suspended Solids (TSS), pH, Total Dissolved Solids (TDS), and DO have influenced the diversity and distribution of the microbiome. Krona charts elucidated the xenobiotics degradation and metabolism distribution potential of the microbiome of each sampled site. This study reiterates the need for constant monitoring of WWTPs due to the high pollution parameters recorded from the WWTP effluent. The metagenomic data generated in this study provides insight into the diversity and functionality of the microbiome present in WWTPs of different process configurations which can inform existing WWTP configurations and future designs.},
}
@article {pmid41544592,
year = {2026},
author = {Zheng, Z and Lyu, H and Li, Z and Tang, J and He, J},
title = {Unraveling water depth dependent microplastic aging driven by functional microbial community interaction in a real urban river.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141133},
doi = {10.1016/j.jhazmat.2026.141133},
pmid = {41544592},
issn = {1873-3336},
mesh = {*Microplastics/metabolism/analysis/chemistry ; *Rivers/microbiology/chemistry ; Biofilms ; *Water Pollutants, Chemical/metabolism/analysis ; Bacteria/genetics/metabolism ; Polyvinyl Chloride/chemistry ; *Microbiota ; Polyesters/chemistry ; Biodegradation, Environmental ; Water Microbiology ; Cities ; },
abstract = {Microplastic (MPs) biofilms are dynamic microhabitats that regulate substance transformation processes. However, the influence of natural urban water depth gradients on the biofilm functions and subsequent aging of MPs remains poorly understood. Herein, we characterized the aging process of MPs in different depths of a real urban river, and the biofilm driven aging mechanism was illustrated. Surface characterization of the MPs showed an increase in oxygen-containing functional groups (CO, C-O) and O/C in polylactic acid (PLA) during aging, which indicated oxidation and hydrolysis reactions, especially at 2.0 m deep water depth. In polyvinyl chloride (PVC) MPs, carbonyl index (CI) was 2 times higher at 2.0 m as compared to 0.1 m water depth and lower chlorine content was found, indicating higher oxidative degradation and dechlorination processes in deeper water. Moreover, biofilms may regulate the synergism between oxygenase and hydrolases in PLA biofilms and oxygenase and dehalogenase in PVC biofilms. Microorganisms with both denitrification and MPs degradation functions, such as Acidovorax, Comamonas, Dechloromonas, were enriched in MPs biofilm. In addition, a positive correlation was found between MPs degradation genes (TGL2, katG, ncd2) and denitrification genes (napA, nirS, norB) in PLA biofilms at deeper water depth, suggesting a potential effect of denitrification functions on MPs aging (45 d incubation). This research challenges the conventional thoughts of higher MPs aging in shallow water, emphasizing the significant role of moderate depth gradients water in regulating the ecological function of microplastic biofilm, which is essential for evaluating the fate of MPs in real urban rivers.},
}
@article {pmid41543328,
year = {2026},
author = {Ji, Q and Wang, Y and Huo, L and Qiao, C and Li, F and Yang, F and Pan, L},
title = {Therapeutic Mechanisms of Lactiplantibacillus plantarum NXU0014 Against Chronic Alcohol-Induced Liver Injury Mediated by Gut-Liver Axis Modulation.},
journal = {Molecular nutrition &amp; food research},
volume = {70},
number = {1},
pages = {e70375},
doi = {10.1002/mnfr.70375},
pmid = {41543328},
issn = {1613-4133},
support = {2023BCF01028//Key R &amp; D Program of Ningxia Hui Autonomous Region/ ; 2023BCF01029//Key R &amp; D Program of Ningxia Hui Autonomous Region/ ; 2024AAC05047//Ningxia Hui Autonomous Region Excellent Young Scientists Fund/ ; NYG2024042//Higher Education Scientific Research Grant, Department of Education of Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; Male ; *Lactiplantibacillus plantarum/physiology ; *Probiotics/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects/physiology ; Mice, Inbred C57BL ; *Liver Diseases, Alcoholic/therapy/microbiology ; Liver/metabolism ; Mice ; Dysbiosis ; NF-E2-Related Factor 2/metabolism/genetics ; Oxidative Stress ; Bile Acids and Salts/metabolism ; Disease Models, Animal ; },
abstract = {This study investigated the protective effects of Lactobacillus plantarum NXU0014 against chronic alcoholic liver injury (CALI) and its underlying mechanisms in a mouse model. Forty-eight male C57BL/6J mice were divided into four groups: blank control, model, silymarin, and L. plantarum NXU0014. The CALI model was induced by administering 56% Hongxing Erguotou liquor. Multi-omics analyses revealed that alcohol intake induced gut microbiota dysbiosis, characterized by an increased Firmicutes/Bacteroidetes ratio and decreased abundance of probiotics (e.g., Lactobacillus and Bifidobacterium). These changes were associated with hepatic pro-inflammatory upregulation, downregulation of antioxidant genes (Nrf2, HO-1), and impaired intestinal barrier function (ZO-1). Metabolomic disturbances featured elevated fecal bile acids, reduced amino acids, and enriched pathways for ABC transporters and bile secretion. Intervention with NXU0014 restored probiotic levels (including Bifidobacterium pseudodanubicum and Lactobacillus reuteri), alleviated hepatic inflammation and oxidative stress by activating the Nrf2/HO-1 pathway, and repaired the intestinal barrier. Integrated microbiome-metabolome analysis revealed a negative correlation between Lactobacillus and toxic bile acids, and a positive correlation between Bifidobacterium and anti-inflammatory metabolites. These findings demonstrate that NXU0014 mitigates liver injury by modulating gut-liver axis metabolic interactions, highlighting its potential as a novel probiotic-based therapy for alcoholic liver disease.},
}
@article {pmid41543249,
year = {2026},
author = {Beals, DG and Carper, DL and Hochanadel, LH and Jawdy, SS and Klingeman, DM and Piatkowski, BT and Weston, DJ and Doktycz, MJ and Pelletier, DA},
title = {Genomic signatures in Variovorax enabling colonization of the Populus endosphere.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0160525},
pmid = {41543249},
issn = {2379-5077},
mesh = {*Populus/microbiology ; Plant Roots/microbiology ; Rhizosphere ; *Comamonadaceae/genetics/classification ; *Genome, Bacterial ; Metagenomics ; Soil Microbiology ; Microbiota/genetics ; Genomics ; },
abstract = {Microbial colonization of plant roots involves strong selective pressures that shape the structure and function of root-associated communities. In particular, the endosphere represents a highly selective environment requiring host entry and in planta persistence. However, strain-specific microbial traits that enable endosphere colonization remain poorly understood. Here, we use a defined, genome-resolved community of 28 Variovorax strains isolated from the roots of Populus deltoides and Populus trichocarpa (poplar trees) to determine which strains partition between rhizosphere and endosphere compartments and to identify the genomic traits associated with endosphere specialization. By combining strain-resolved metagenomic profiling, comparative genomics, and functional assays, we demonstrate that dominant endosphere colonizers are enriched in genes related to nutrient metabolism, redox balance, transcriptional regulation, and a conserved L-fucose utilization pathway experimentally shown to enhance root colonization. Not all strains succeed through the same strategy. Community-wide functional profiling revealed a distinct and reduced set of traits in the endosphere, including orthogroups associated with low-abundance strains that were overlooked in strain-level analyses. These findings reveal that multiple ecological strategies, such as metabolic competition, regulatory adaptation, and niche specialization, can support endosphere colonization. Our results advance the understanding of how bacterial colonization traits are distributed and deployed within a plant microbiome and suggest that host filtering selects for distinct, and sometimes complementary, microbial strategies. This work supports a shift toward mechanistic, genome-resolved models of microbiome assembly and offers a framework for linking microbial function to host colonization success.IMPORTANCEPlants often depend on diverse microbial partners to support their growth, resilience, and adaptation to changing environments. Among these microbes, some bacteria inhabit the rhizosphere (the narrow zone around roots where microbes interact with the plant) while others are able to enter and persist within root tissues. The traits that distinguish these two lifestyles remain poorly understood. In this study, we examined a group of related Variovorax strains from poplar tree root microbiomes to ask why some rhizosphere-associated strains also become successful endosphere colonizers. We found that strains appear to succeed through different strategies: some may benefit from rapid growth on plant-derived carbon sources, while others may rely on stress tolerance or fine-tuned regulation. These results suggest that there is no single path from the rhizosphere into the root interior, but rather multiple strategies shaped by the host environment. Understanding this diversity can inform efforts to design resilient plant-microbe communities.},
}
@article {pmid41540059,
year = {2026},
author = {St John, E and Reysenbach, AL},
title = {Global deep-sea hydrothermal deposit metagenomes and metagenome-assembled genomes over time and space.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {283},
pmid = {41540059},
issn = {2052-4463},
support = {DEB-2409507//National Science Foundation/ ; },
mesh = {*Metagenome ; *Hydrothermal Vents/microbiology ; *Archaea/genetics ; Bacteria/genetics/classification ; Microbiota ; *Genome, Archaeal ; },
abstract = {Actively venting high temperature deep-sea hydrothermal vent deposits along tectonic spreading centers and in backarc basins harbor a rich diversity of thermophilic Bacteria and Archaea, many of which have no representatives in cultivation nor any genomic representation in databases. Here, in order to produce a global-scale time series metagenomic resource for studying the microbial functional and genomic diversity in these high temperature ecosystems, we obtained 70 metagenomes from collections across spatial and temporal gradients from 21 different vent fields spanning 16 years (1993-2009). The dataset (Deep-Sea Hydrothermal Vent dataset (DSV70)) includes 3.56 Tbp of raw DNA sequence reads, that have been assembled to produce 7,422 medium- to high-quality (based on CheckM2) metagenome-assembled genomes (MAGs) of Bacteria (6,063 MAGs) and Archaea (1,359 MAGs). Collectively, this DSV70 dataset and the published 40 metagenomes from more recent deep-sea collections (2004 to 2018), represent a valuable resource for exploring the functional and phylogenomic diversity of the deep-sea hydrothermal microbiomes, and provide many reference genomes for studies in the taxonomy and systematics of poorly studied microbial lineages. Further, with the interest in mining the mineral resources at deep-sea vents, the DSV70 provides a genomic legacy for monitoring impacts on the microbial communities in these systems.},
}
@article {pmid41539854,
year = {2026},
author = {Choi, S and Kwon, H and Kim, WK and Ko, G},
title = {Attenuation of Clostridioides difficile Infection by Clostridium hylemonae.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2510017},
pmid = {41539854},
issn = {1738-8872},
mesh = {*Clostridium Infections/microbiology/therapy/prevention &amp; control ; Animals ; *Clostridium/physiology/genetics ; Gastrointestinal Microbiome ; Mice ; *Clostridioides difficile ; Disease Models, Animal ; Feces/microbiology ; Metagenomics ; },
abstract = {Clostridioides difficile infection (CDI) is a bacterial infection of the colon that can cause diarrhea and colitis. The use of antimicrobials disrupts the intestinal microbiota, weakening colonization resistance and creating an environment in which C. difficile can establish infection. It is, therefore, necessary to identify specific bacteria that are helpful for the recovery of the intestinal microbiota in individuals with CDI. Previous studies have identified several strains that showed a negative correlation with C. difficile. Among these strains, C. hylemonae DSM 15053, which possesses the bai operon similar to Clostridium scindens, was selected. To test this hypothesis, we utilized a CDI mouse model and evaluated the inhibitory effect of C. hylemonae DSM 15053. Furthermore, to gain insights into the underlying mechanisms, we performed gut microbiota analysis. Contrary to our expectations, C. hylemonae DSM 15053 did not significantly produce SBAs. Interestingly, however, microbial diversity and richness were significantly higher in the C. hylemonae DSM 15053-treated group compared with the PBS control group. In addition, we observed a higher abundance of the genera Phocaeicola, Akkermansia, and Parabacteroides in the C. hylemonae DSM 15053 group. Moreover, metagenomic and metabolomic analyses revealed that C. hylemonae DSM 15053 mitigates CDI through a mechanism distinct from that of C. scindens KCTC 5591, which primarily functions as a regulator of bile acid metabolism.},
}
@article {pmid41539810,
year = {2026},
author = {Liu, Y and Guo, Y and Mu, H and Aaqil, M and Zhang, F and Zheng, J and Sheng, J and Tian, Y and Zhao, C},
title = {Microbial succession-potential influence mechanism on flavor modulation in spontaneously fermented Moringa oleifera leaves: An integrative multi-omics approach.},
journal = {Food research international (Ottawa, Ont.)},
volume = {226},
number = {},
pages = {118184},
doi = {10.1016/j.foodres.2025.118184},
pmid = {41539810},
issn = {1873-7145},
mesh = {*Fermentation ; *Moringa oleifera/microbiology/chemistry ; *Taste ; *Plant Leaves/microbiology/chemistry ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis ; Odorants/analysis ; Amino Acids/analysis ; *Food Microbiology ; Flavoring Agents ; *Fermented Foods/microbiology ; Bacteria/metabolism/classification/genetics ; Microbiota ; Metagenomics ; Multiomics ; },
abstract = {In this study, the relationship between flavor composition and microbial succession in Moringa oleifera pickles (MOPs) at different stages of spontaneous fermentation was systematically investigated. The results demonstrated a significant increase in the content of organic acids and amino acids during fermentation including malonic acid, citric acid, valine (Val), and asparagine (Asn). These compounds not only enhanced the overall flavor profile but also provided favorable nutritional conditions that supported microbial succession. Furthermore, an integrated aroma network was established through the combined application of gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS). GC-MS identified key aroma-active compounds such as ethyl caproate (fruity note), 3-hexenal (green, grassy note), and 2-phenylethanol (floral, rosy note). Complementarily, GC-IMS confirmed that esters, alcohols, and terpenes were the major contributors to fruit-like, mushroom-like, and fresh herbal aromas, indicating their critical role as flavor-modulating compounds throughout fermentation. Metagenomic analysis revealed Corynebacterium, Escherichia, Pseudomonas, Xanthomonas, and Pantoea as the dominant microbial genera involved in fermentation. These microbes primarily participated in amino acid, carbohydrate, and nucleotide metabolism and exhibited a close association with the formation of key flavor compounds. The strong influence of microbial succession on flavor evolution is likely driven by the observed correlations between microbial taxa and volatile organic compounds (VOCs). These correlations may stem from a series of complex ecological and metabolic interactions, including substrate competition, niche adaptation, and upstream-downstream dependencies within microbial metabolic networks. This study provides a theoretical foundation for the quality control of MOPs and the mitigation of potential pathogenic microorganisms, thereby supporting its application in enhancing product quality and consumer sensory satisfaction in the pickle industry.},
}
@article {pmid41539526,
year = {2026},
author = {Uddin, G and Song, J and Lu, Z and Chaofie, Z and Sajjad, W and Li, P and Fan, Q},
title = {Microbial taxonomic and functional responses to heavy metal gradients in mining-impacted stream sediments.},
journal = {Environmental research},
volume = {293},
number = {},
pages = {123778},
doi = {10.1016/j.envres.2026.123778},
pmid = {41539526},
issn = {1096-0953},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Metals, Heavy/analysis/toxicity ; *Mining ; Archaea/drug effects/classification ; *Water Pollutants, Chemical/analysis/toxicity ; Bacteria/drug effects/classification ; *Rivers/microbiology/chemistry ; China ; Fungi/drug effects/classification ; *Microbiota/drug effects ; Environmental Monitoring ; },
abstract = {Legacy heavy metal pollution from historical mining restructures sediment microbial composition and function directly impacting contaminant fate and ecosystem health. The Dongdagou stream (Baiyin, China) possesses a pronounced geochemical gradient caused by long-term discharge of potentially toxic metals including Cd, Cu, Pb, and Zn. We employed this natural gradient to characterize microbial taxonomic and functional responses to metal stress. Sediment samples from four zones along the contamination gradient were analyzed for geochemistry, metal concentrations, and microbial composition (bacteria, archaea, and fungi) via high-throughput amplicon sequencing, with functional potential inferred using PICRUSt2. We found that microbial community structure and function were primarily shaped by metal concentration, with db-RDA explaining 18.1 %, 12.4 %, and 12.9 % of the variance for bacteria, archaea, and fungi, respectively. Cadmium was identified as the strongest individual predictor for both bacterial (r[2] = 0.50, p = 0.001) and fungal (r[2] = 0.38, p = 0.001) communities. Bacterial diversity increased significantly downstream as contamination declined, with Shannon diversity increasing from 5.17 in the Source Zone to 6.28 in the Distal Zone (Tukey's multiple comparison test, p < 0.05). Upstream sediments were dominated by metal-tolerant taxa such as Sulfurifustis (17.4 %) and Acidithiobacillus (5.0 %), while downstream taxa shifted to heterotrophic genera like Gallionella (4.8 %) with diverse metabolic capabilities. Despite cadmium being a key predictor, archaeal and fungal communities demonstrated greater compositional stability than bacteria, as shown by their lower beta-dispersion (ANOSIM R = 0.3152 and 0.5762, respectively, compared to 0.7222 for bacteria), indicating potential functional redundancy. Metagenomic predictions revealed a significant enrichment of genes for metal detoxification, anaerobic respiration, and oxidative stress response in polluted zones. These findings establish that microbial communities are both sensitive bioindicators and key mediators of contaminant dynamics, providing a framework for using microbial signatures to assess sediment health and monitor remediation efficacy.},
}
@article {pmid41539094,
year = {2026},
author = {Wang, L and Xiong, Z and Chen, J and Liu, J and Liu, M and Yan, X and Fang, Z},
title = {Synergistic gut microbiome-host lipid axis underlies the antihypertensive effect of Qianyang Yuyin formula.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {151},
number = {},
pages = {157804},
doi = {10.1016/j.phymed.2026.157804},
pmid = {41539094},
issn = {1618-095X},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Rats, Inbred SHR ; *Drugs, Chinese Herbal/pharmacology ; Male ; Rats ; *Antihypertensive Agents/pharmacology ; *Lipid Metabolism/drug effects ; Blood Pressure/drug effects ; Dysbiosis/drug therapy ; Fecal Microbiota Transplantation ; Hypertension/drug therapy ; *Prehypertension/drug therapy ; Disease Models, Animal ; },
abstract = {BACKGROUND: Prehypertension (Pre-HTN) is highly prevalent and substantially increases the risk of developing hypertension and cardiovascular disease. Gut microbiota (GM) dysbiosis and altered lipid metabolism are increasingly recognized as critical regulators of blood pressure (BP). Traditional Chinese Medicine (TCM) formulas, such as Qianyang Yuyin Granules (QYYY), offer multi-target interventions, yet their preventive mechanisms in Pre-HTN remain unclear.<br><br>PURPOSE: This study aimed to investigate the antihypertensive effects of QYYY and elucidate its underlying mechanisms in a prehypertensive rat model.<br><br>METHODS: Prehypertensive spontaneously hypertensive rats (SHRs) were treated with QYYY for four weeks. Multi-omics analyses, including metagenomics, plasma metabolomics, and transcriptomics, were conducted. Causal involvement of GM was tested using antibiotic-induced pseudo-germ-free SHRs with fecal microbiota transplantation (FMT) from QYYY-treated donors, administered alone or in combination with QYYY. Gut barrier integrity, systemic inflammation, and vascular function were evaluated by histology, immunofluorescence, transmission electron microscopy, and ELISA.<br><br>RESULTS: QYYY significantly lowered SBP and DBP, reversed GM dysbiosis, normalized the Firmicutes/Bacteroidetes ratio, and modulated differential bacteria including Frisingicoccus and Blautia. These microbial shifts correlated with restoration of lysophosphatidylethanolamines (LPEs), inversely associated with BP, revealing a GM-lipid-BP axis. FMT alone was insufficient, whereas the combination of FMT+QYYY produced the strongest antihypertensive effect, restoring intestinal barrier integrity, enhancing ZO-1 expression, and normalizing Ang-II and NO levels. Transcriptomic analyses suggested PPAR and ROS signaling pathways as potential mechanisms mediating the antihypertensive effect of QYYY.<br><br>CONCLUSION: QYYY prevents BP elevation in Pre-HTN via synergistic microbiota-dependent and independent mechanisms, offering a comprehensive strategy for early hypertension prevention.},
}
@article {pmid41538522,
year = {2026},
author = {Hoyos-López, R and Echeverri-De la Hoz, D and Martínez-Bravo, C and Gastelbondo-Pastrana, B and Alemán-Santos, M and Garay, E and López, Y and Contreras, H and Galeano, K and Arrieta, G and Mattar, S},
title = {Viral metagenomics in mosquitoes as potential vectors of arboviruses in the Colombian Caribbean: characterisation of a "core" regional RNA virome.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {120},
number = {},
pages = {e250131},
pmid = {41538522},
issn = {1678-8060},
mesh = {Animals ; *Mosquito Vectors/virology/classification ; *Arboviruses/genetics/isolation &amp; purification ; Colombia ; *Culicidae/virology/classification ; *Virome/genetics ; *RNA, Viral/genetics ; Metagenomics ; Seasons ; Caribbean Region ; *RNA Viruses/genetics/classification ; Arbovirus Infections/transmission ; },
abstract = {BACKGROUND: Mosquitoes are critical vectors in tropical regions where arboviruses like dengue and Zika are prevalent. This study focuses on characterising the RNA virome of mosquitoes in the Colombian Caribbean, emphasising the core regional virome and its role in the dynamics of arboviruses.<br><br>OBJECTIVES: The objective was to identify and analyse the core RNA virome of mosquitoes across different genera and seasons in the Colombian Caribbean to understand its composition and potential influence on arbovirus transmission dynamics.<br><br>METHODS: In 2023, 4,074 mosquitoes from the genera Mansonia, Coquillettidia, and Anopheles were collected across C&#xf3;rdoba, Sucre, Bol&#xed;var, and Magdalena during rainy and dry seasons. Specimens were pooled in groups of 50, subjected to RNA extraction, and sequenced on the MGI-G50&#x2122; platform. Bioinformatic analyses utilised the DIAMOND-MEGANizer pipeline and R packages (phyloseq, vegan, ggplot2) to identify viral communities.<br><br>FINDINGS: The analysis identified 22 viral families and 24 unclassified RNA viruses. The core regional virome, consistently present across species and seasons, was dominated by insect-specific viruses (ISVs) such as Aedes aegypti to virus 1 and 2, Astopletus, and Cumbaru, alongside Picornaviridae (30% of reads), Rhabdoviridae (20%), Orthomyxoviridae, and Bunyavirales. Mansonia titillans (38 species) and Coquillettidia nigricans (21 species) exhibited the highest viral richness. No significant arboviruses were detected, highlighting ISV dominance. Virome composition varied seasonally, with greater diversity in the rainy season due to increased breeding site availability and temperature.<br><br>MAIN CONCLUSIONS: The stability of the core virome suggests it modulates vector competence, potentially reducing arbovirus transmission. These findings advocate the use of metagenomics for enhanced vector surveillance and biological control strategies in neotropical ecosystems.},
}
@article {pmid41537582,
year = {2026},
author = {Robertson, S and Mosca, A and Ashraf, S and Corral, A and Alegria Terrazas, R and Arnton, C and Thorpe, P and Morris, J and Hedley, PE and Babbi, G and Savojardo, C and Martelli, PL and Møller, FD and Nielsen, HN and Leekitcharoenphon, P and Aarestrup, FM and Halder, R and Laczny, CC and Wilmes, P and Pietrantonio, L and Di Cillo, P and Catara, V and Abbott, J and Bulgarelli, D},
title = {Acinetobacter enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants.},
journal = {mSphere},
volume = {11},
number = {2},
pages = {e0084225},
pmid = {41537582},
issn = {2379-5042},
support = {818290//Horizon 2020 Framework Programme/ ; 2734186/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Solanum lycopersicum/microbiology/growth &amp; development ; *Acinetobacter/genetics/classification/isolation &amp; purification ; Soil Microbiology ; *Microbiota ; Rhizosphere ; Metagenomics ; Plant Roots/microbiology ; Metagenome ; },
abstract = {Tomato is a staple crop and an excellent model to study host-microbiota interactions in the plant food chain. In this study, we describe a "lab-in-the-field" approach to investigate the microbiota of field-grown tomato plants. High-throughput amplicon sequencing revealed a three-microhabitat partition, phyllosphere, rhizosphere, and root interior, differentiating host-associated communities from the environmental microbiota. An individual bacterium, classified as Acinetobacter sp., emerged as a dominant member of the microbiota at the plant-soil continuum. To gain insights into the functional significance of this enrichment, we subjected rhizosphere specimens to shotgun metagenomics. Similar to the amplicon sequencing survey, a "microhabitat effect," defined by a set of rhizosphere-enriched functions, was identified. Mobilization of mineral nutrients, as well as adaptation to salinity and polymicrobial communities, including antimicrobial resistance genes (ARGs), emerged as a functional requirement sustaining metagenomic diversification. A metagenome-assembled genome representative of Acinetobacter calcoaceticus was retrieved, and metagenomic reads associated with this species identified a functional specialization for plant-growth promotion traits, such as phosphate solubilization, siderophore production, and reactive oxygen species detoxification, which were similarly represented in a tomato genotype-independent fashion. Our results revealed that the enrichment of a beneficial bacterium capable of alleviating plant abiotic stresses appears decoupled from ARGs facilitating microbiota persistence at the root-soil interface.IMPORTANCETomatoes are at center stage in global food security due to their high nutritional value, widespread cultivation, and versatility. Tomatoes provide essential vitamins and minerals, contribute to diverse diets, and support farmer livelihoods, making them a cornerstone of sustainable food systems. Beyond direct dietary benefits, the intricate relationship between tomatoes, their associated microbiota, and antimicrobial resistance gene (ARG) is increasingly recognized. Tomato plants host diverse microbial communities in association with their organs, which influence plant health and productivity. Crop management impacts the composition and function of these communities, contributing to the prevalence of ARGs in the soil and on the plants themselves. These genes can potentially transfer to human pathogens, posing a food safety and public health risk. Understanding these complex interactions is critical for developing sustainable agricultural practices capable of mitigating the impact of climatic modifications and the global threat of antimicrobial resistance.},
}
@article {pmid41537457,
year = {2026},
author = {Chari, NR and DeAngelis, KM and Aguilar, AA and Chan, ALH and Burgin, GA and Frey, SD and Taylor, BN},
title = {Warming mitigates root exudate-induced priming effects via changes to microbial biomass, community structure, and gene abundance.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {41537457},
issn = {1751-7370},
support = {DEB-1456610//Long-Term Research in Environmental Biology/ ; DEB-1832110//U.S. National Science Foundation (NSF) Long-Term Ecological Research Program/ ; },
mesh = {*Plant Roots/metabolism/microbiology ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; *Biomass ; Soil/chemistry ; Carbon/metabolism ; *Bacteria/genetics/classification ; *Plant Exudates/metabolism ; Climate Change ; Metagenomics ; DNA, Bacterial/genetics/chemistry ; Forests ; *Microbiota ; DNA, Ribosomal/chemistry/genetics ; },
abstract = {Root exudation, the export of soluble carbon compounds from living plant roots into soil, is an important pathway for soil carbon formation, but high rates of exudation can also induce rapid soil organic matter decomposition - a phenomenon known as the priming effect. Long-term soil warming associated with climate change could alter exudation rates and impact soil microbes by changing soil carbon chemistry. We hypothesized that warming-induced changes to exudation rate combined with direct effects of long-term warming on soil microbial communities would regulate the microbial priming effect. We tested this hypothesis with an artificial root exudate experiment using intact soil cores from a long-term soil warming experiment in a temperate forest. We found that chronic soil warming did not alter soil carbon formation from exudates, but did reduce the exudate-induced priming effect; exudation caused greater soil carbon loss in unwarmed than warmed soils. We used DNA stable isotope probing with 16S ribosomal RNA gene and shotgun metagenomic sequencing to determine whether long-term warming affected which microbes consume 13carbon-labeled artificial exudates. We found significant differences in bacterial community composition and relative gene abundances of 13carbon-enriched compared to natural abundance DNA. Both soil bacterial community composition and specific enzyme-coding gene families were strongly correlated with soil carbon priming in unwarmed treatments, but these effects were absent in warmed treatments. Our results suggest that the root exudate-induced priming effect is mediated by microbial biomass, community structure, and gene abundance, and that chronic warming reduces the priming effect by altering these microbial variables.},
}
@article {pmid41536238,
year = {2026},
author = {Corona-Cervantes, K and Urrutia-Baca, VH and Gámez-Valdez, JS and Jiménez-López, B and Rodríguez-Gutierrez, NA and Chávez-Caraza, K and Espiricueta-Candelaria, F and Villalobos, UAS and Ramos-Parra, PA and Uribe, JAG and Brunck, M and Chuck-Hernández, C and Licona-Cassani, C},
title = {Maternal obesity alters human milk oligosaccharides content and correlates with early acquisition of late colonizers in the neonatal gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2607043},
pmid = {41536238},
issn = {1949-0984},
mesh = {Humans ; *Milk, Human/chemistry ; Female ; *Oligosaccharides/analysis/metabolism ; *Gastrointestinal Microbiome ; Infant, Newborn ; Feces/microbiology ; Longitudinal Studies ; Adult ; Pregnancy ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Pregnancy in Obesity/microbiology/metabolism ; Infant ; Male ; Body Mass Index ; Mexico ; },
abstract = {Metabolic and immune development in neonates are shaped by the succession of the gut microbiome. Maternal obesity can perturb this process by altering interactions of human milk bioactive elements, including oligosaccharides (HMOs), microbial populations, and metabolites. We conducted a longitudinal study of Mexican mother-infant dyads to examine maternal BMI-associated variations in HMOs and infant fecal microbiota. Breastmilk samples from 97 mothers were collected at 48 h, one month, and three months postpartum. We used targeted and untargeted metabolomics to profile breastmilk samples, while shotgun metagenomics was used to analyze infant fecal microbiome composition in a subset of samples. Mothers with obesity showed decreased concentration of key HMOs shortly after birth, correlating with an altered succession of their infant's gut microbiota. This included reduced early colonizers (Enterobacteriaceae) and increased abundance of intermediate and late colonizers (Bifidobacterium and members of the Lachnospiraceae family), over subsequent months. These taxa negatively correlated with HMOs such as 6'SL, LNnT, and LNT. Additionally, functional profiling revealed alterations in metabolic pathways related to polyamine biosynthesis, suggesting changes in microbial metabolism linked to maternal BMI. Despite the cohort's size, our study offers unique insights into the relationship between maternal obesity, HMO composition, and early infant microbial colonization in Latin-American mothers. This exploratory research serves as proof of concept, underscoring the need for larger-scale studies to validate these findings and better understand their implications for infant health. More importantly, our results highlight the interplay between maternal BMI and human milk bioactives, underscoring the importance of correlating microbial succession with maternal metabolic health to better understand early immune development in neonates.},
}
@article {pmid41535719,
year = {2026},
author = {Almonte, AA and Thomas, S and Iebba, V and Kroemer, G and Derosa, L and Zitvogel, L},
title = {Gut dysbiosis in oncology: a risk factor for immunoresistance.},
journal = {Cell research},
volume = {36},
number = {2},
pages = {103-120},
pmid = {41535719},
issn = {1748-7838},
support = {INCA_16698//CNIB (INCA)/ ; 955575//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/immunology/microbiology/complications ; Risk Factors ; Immune Checkpoint Inhibitors/therapeutic use ; Animals ; },
abstract = {The gut microbiome is recognized as a determinant of response to immune checkpoint inhibitor (ICI) therapies in cancer. However, the clinical translation of microbiome science has been hampered by inconsistent definitions of dysbiosis, inadequate biomarker frameworks, and limited mechanistic understanding. In this review, we synthesize the current state of knowledge on how gut microbial composition and function influence ICI efficacy, highlighting both correlative and causal evidence. We discuss computational approaches based on α-diversity or taxonomic abundance and argue for more functionally and clinically informative models, such as the topological score (TOPOSCORE) and other dysbiosis indices derived from machine learning. Using retrospective analyses of metagenomic datasets from thousands of patients and healthy controls, we examine microbial patterns that distinguish responders from non-responders. We also explore how dysbiosis perturbs immunoregulatory pathways, including bile acid metabolism, gut permeability, and mucosal immunomodulation. Finally, we assess emerging therapeutic strategies aimed at correcting microbiome dysfunction - including dietary modification, bacterial consortia, and fecal microbiota transplantation - and describe how they are being deployed in multiple clinical trials. We conclude with a brief discussion of the ONCOBIOME initiative, which works with international partners to incorporate microbiome science into oncology workflows. By refining our understanding of gut-immune interactions and translating it into action, microbiome-informed oncology may unlock new therapeutic potential for patients previously resistant to immunotherapy.},
}
@article {pmid41535683,
year = {2026},
author = {Chen, S and Yuan, Y and Wang, Y and Peng, Y and Tun, HM and Jiang, Z and Miao, Y and Lee, S and Yin, X and Shen, X and DeLeon, O and Chang, EB and Chan, FKL and Sun, Y and Ng, SC and Su, Q},
title = {Identification of antimicrobial peptides from ancient gut microbiomes.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {1788},
pmid = {41535683},
issn = {2041-1723},
support = {2025 Youth Science and Technology Talent Development Program//China Association for Science and Technology (China Association for Science &amp; Technology)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Antimicrobial Peptides/pharmacology/isolation &amp; purification/chemistry ; Feces/microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Metagenomics/methods ; Mice ; Bacteria/drug effects ; },
abstract = {Fecal coprolites preserve ancient microbiomes and are a potential source of extinct but highly efficacious antimicrobial peptides (AMPs). Here, we develop AMPLiT (AMP Lightweight Identification Tool), an efficient tool deployable to portable hardware for AMP screening in metagenomic datasets. AMPLiT demonstrates AUPRC performances of 0.9486 ± 0.0003 and reasonable overall training time of 3200 ± 53 s. By computationally utilizing AMPLiT, we analyze seven ancient human coprolite metagenomes, identifying 160 AMP candidates. Of 40 representative peptides synthesized, 36 (90%) peptides demonstrate measurable antimicrobial activity at 100 μM or less in vitro. Strikingly, approximately two-thirds of these peptides are sourced from Segatella copri, a dominant ancient gut commensal that is conspicuously underrepresented in modern populations, particularly those with Westernized lifestyles. Representative S. copri-derived AMPs exhibit disruptions against membranes of pathogenic bacteria, coupled with low cytotoxicity and hemolytic risk. In vivo, lead peptides demonstrate potent antibacterial and wound-healing efficacy comparable to traditional antibiotics, especially in combating gram-positive pathogens. Our findings highlight the ancient gut microbiomes as sources of novel AMPs, offering valuable insights into the historical role of S. copri in human health and its decline in contemporary populations.},
}
@article {pmid41535300,
year = {2026},
author = {Wong, OWH and Xu, Z and Chan, SSM and Mo, FYM and Shea, CKS and Su, Q and Wan, MYT and Cheung, CP and Ching, JYL and Tang, W and Tun, HM and Chan, FKL and Ng, SC},
title = {A novel synbiotic (SCM06) for anxiety and sensory hyperresponsiveness in children with autism spectrum disorder: an open-label pilot study.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {36},
pmid = {41535300},
issn = {2055-5008},
support = {NCI202346//New Cornerstone Science Foundation/ ; },
mesh = {Humans ; Pilot Projects ; Male ; *Autism Spectrum Disorder/microbiology/therapy/complications ; Female ; Child ; *Synbiotics/administration &amp; dosage ; *Anxiety/therapy/microbiology ; Gastrointestinal Microbiome ; Feces/microbiology ; Metagenomics ; Treatment Outcome ; Bacteria/classification/genetics/isolation &amp; purification ; Metabolomics ; },
abstract = {Anxiety and sensory hyperresponsiveness are common in children with autism spectrum disorder (ASD), but effective treatments are lacking. Targeting the microbiota-gut-brain axis is a promising strategy. This open-label pilot study evaluated SCM06, a novel synbiotic designed to target anxiety and sensory hyperresponsiveness, in 30 children with ASD (mean age 8.2 years, 22 males). We assessed symptom improvement, compliance, and safety, and collected stool samples for metagenomics and metabolomic analysis over 12 weeks. SCM06 was safe and well-tolerated, and significant improvements were observed in anxiety, sensory hyperresponsiveness, and abdominal pain. Following SCM06 treatment, increase in Bifidobacterium pseudocatenulatum was associated with improved functional abdominal pain (p = 0.0011, p_adj = 0.054), while the abundances of valeric acid and butyric acid increased (p_adj = 0.004 and p_adj = 0.072). Key microbial species, Coprococcus comes and Veillonella dispar, were candidate mediators of symptom improvements. Further randomised controlled trials are warranted to confirm its clinical efficacy.},
}
@article {pmid41534355,
year = {2026},
author = {He, S and Wang, Z and Zhong, Z and Shi, C and Li, D and Yin, F},
title = {Soil salinization alters biogeochemical cycles in agricultural ecosystems by reducing carbon-cycling microorganisms.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119706},
doi = {10.1016/j.ecoenv.2026.119706},
pmid = {41534355},
issn = {1090-2414},
mesh = {*Soil Microbiology ; *Salinity ; *Soil/chemistry ; *Carbon Cycle ; Ecosystem ; Agriculture ; Bacteria/genetics/metabolism ; Microbiota ; Metagenomics ; },
abstract = {Salinity stress can decline crop yield in agricultural systems. Beyond the environmental conditions that drive agricultural plant growth, the diverse roles of microbes represent a critical, often overlooked factor in shaping crop health and productivity. Salinization exerts a profound effect on soil microbial communities, with consequences for biogeochemical cycles. However, the salinity adaptation mechanisms of microorganisms participating in biogeochemical cycles remain incompletely understood, which hold considerable promise for microbial solutions in saline agriculture. In this study, metagenomics-based technology was employed to analyze agricultural soils within a region-scale irrigation area characterized by varying degrees of salinization. According to the results of generalized linear models, bell-shaped trends were observed for the diversity and abundance of biogeochemical cycling genes along the soil salinity gradient, all of which peaked at a salinity of approximately 7.5 ‰. Further comparisons indicated reduced total abundance of all biogeochemical cycling genes in high salinity soils (>7.5 ‰) compared to those in low salinity soils (<7.5 ‰). Furthermore, correlation analysis indicated the coupling of different biogeochemical cycling genes, which were observed to be possessed by similar functional microorganisms, with a predominance of Gammaproteobacteria and Alphaproteobacteria. The presence of elevated salt levels resulted in a decline in the abundance of various microorganisms that play roles in biogeochemical cycling, including members of the Alphaproteobacteria, Actinomycetia, Limnocylindira, and Gemmatimonadetes phyla. Concurrently, there was an enrichment of a limited number of salt-tolerant bacteria, predominantly classified under the Bacteroidia and Bacilli taxonomic groups. The coupling of different biogeochemical cycling genes in some metagenome-assembled genomes (MAGs) was confirmed through metagenomics binning. Three MAGs (strains of Methylophaga, Salinimicrobium, and Sediminibacterium, respectively) with diverse biogeochemical cycling functions were recognized as potential plant-growth-promoting bacteria under salinity stress. These findings contribute to the existing body of knowledge on the salinity adaptability of soil microbial communities and offer guidance for the management of saline agriculture.},
}
@article {pmid41532487,
year = {2026},
author = {Goh, KM and Nurhazli, NAA and Tan, JH and Liew, KJ and Chan, KG and Pointing, SB and Sani, RK},
title = {Thermophiles in the genomic Era (2015-2025): a review on biodiversity, metagenome-assembled genomes, and future directions.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/1040841X.2026.2614431},
pmid = {41532487},
issn = {1549-7828},
abstract = {Thermophile research has been transformed over the past decade by advances in genome sequencing. Once centered on culture collections and physiological studies of terrestrial hot springs and deep-sea hydrothermal vents, the field now employs amplicon sequencing, shotgun metagenomics, and long-read platforms to reveal the diversity, ecology, and genomic potential of thermophiles. Metagenome-assembled genomes (MAGs), metatranscriptomes, and metaproteomes have become crucial for linking taxonomy with function, uncovering previously hidden microbial dark matter in heated ecosystems. Bioinformatics, increasingly integrated with machine learning, has expanded insights into microbial biology, biomolecules, and ecological interactions. These advances highlight the broader environmental significance of thermophiles, spanning fundamental roles in ecosystem processes to practical applications. In 2015, we published Thermophiles in the Genomic Era: Biodiversity, Science, and Application to capture early next-generation sequencing milestones. A decade later, with tremendous progress achieved, this review revisits the field by synthesizing recent advances across viruses, planktonic thermophiles, and biofilm communities, emphasizing the power of genome-resolved approaches. We also highlight overlooked areas, opportunities for ecological integration and predictive modeling, and the importance of translating discoveries into biotechnological innovation. Our aim is to provide young researchers with a roadmap of emerging questions and strategies likely to shape the next decade of thermophile research.},
}
@article {pmid41531093,
year = {2026},
author = {Liu, SE and Dong, ZF and Zhang, AH and Min, W},
title = {[Effect of Biodegradable Mulching Film on Soil Microbial Community in Cotton Field was Revealed Based on Metagenomics].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {1},
pages = {650-662},
doi = {10.13227/j.hjkx.202411219},
pmid = {41531093},
issn = {0250-3301},
mesh = {*Soil Microbiology ; *Gossypium/growth &amp; development ; Metagenomics ; Soil/chemistry ; Biodegradation, Environmental ; *Agriculture/methods ; Microbiota ; },
abstract = {Biodegradable mulching films （BMPs） have been widely used as an alternative to conventional plastic mulching films （CMPs）. However， the long-term effects of BMPs on soil microbial community structure remain unclear. Therefore， in this study， we set up two treatments， CMPs and BMPs， and conducted a field experiment with 26 a of CMPs and 11 a of BMPs coverage. Using metagenomics technology， the effects of BMPs on soil microbial community structure in cotton fields in arid areas were investigated. The results showed that compared with those under the CMPs treatment， the BMPs treatment significantly reduced soil water content （SWC）， bulk density （BD）， and available phosphorus （AP） by 25.00%， 12.50%， and 12.09%， respectively， but significantly increased soil porosity （SP） by 10.07%. The BMPs treatment （124） significantly reduced the number of unique species compared with that in the CMPs treatment （182）. At the phylum level， the BMPs treatment significantly increased the relative abundance of Proteobacteria and significantly decreased the relative abundance of Actinobacteria. At the genus level， the BMPs treatment significantly increased the relative abundances of Nocardioides， Solirubrobacter， and Nitrospira and significantly decreased the relative abundance of Sphingomonas. Meanwhile， the proportion of positive correlations and the average degree between microbial communities in the BMPs treatment were increased significantly by 16.32% and 8.71% compared with those in the CMPs treatment， respectively， reducing the modularization degree of the microbial community by 1.89% and promoting the symbiotic relationship and stability of the microbial community. The BMPs treatment significantly increased the relative abundance of genes such as xylA， narG/nxrA， and nasA and significantly decreased the relative abundance of genes such as accA， frdA， nirB， nrtA， gcd， and phoR， promoting carbon degradation， denitrification， and assimilative nitrate reduction processes and inhibiting dissimilatory nitrate reduction and inorganic phosphorus solubilization processes. Soil SWC and AP were the key environmental factors affecting microbial community composition. Biodegradable mulching film increased the complexity and stability of soil microbial communities compared with traditional mulching film， and soil SWC and AP were the key environmental factors affecting the composition of microbial communities.},
}
@article {pmid41530917,
year = {2026},
author = {Lee, HG and Song, JY and Yoon, J and Chung, Y and Kwon, SK and Kim, JF},
title = {metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611544},
pmid = {41530917},
issn = {1949-0984},
mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Big Data ; *Software ; Colorectal Neoplasms/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Computational Biology/methods ; Gastrointestinal Microbiome ; Reproducibility of Results ; },
abstract = {Metagenomic approaches offer unprecedented opportunities to characterize microbial community structure and function, yet several challenges remain unresolved. Inconsistent genome quality impairs reliability of metagenome-assembled genomes, lack of unified taxonomic criteria limits cross-study comparability, and multi-step workflows involving numerous programs and parameters hinder reproducibility and accessibility. We benchmarked existing programs and parameters using simulated metagenomic data to identify optimal configurations. metaFun is an open-source, end-to-end pipeline that integrates quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomic analysis, pangenome annotation, network analysis, and strain-level microdiversity analysis into a unified framework. Interactive modules support standardized data interpretation and exploratory visualization. The pipeline is implemented with Nextflow and containerized with Apptainer, ensuring environment reproducibility and scalability. Comprehensive documentation is available at https://metafun-doc.readthedocs.io/en/main. The pipeline was validated using a colorectal cancer cohort dataset. By addressing key methodological gaps, metaFun facilitates accessible and reproducible metagenomic analysis for the broader research community.},
}
@article {pmid41530170,
year = {2026},
author = {Maeke, MD and Hassenrück, C and Aguilar-Muñoz, P and Aravena, C and Burmeister, C and Crispi, O and Diallo, POD and Fernández, C and Gouriou, M and Jamont, A and Laymand, E and Marie, B and Molina, V and Ortega-Retuerta, E and Rabouille, S and Sajeeb, MI and Sierks, M and Stevens, M and Turon, R and Valdés-Castro, V and Beier, S},
title = {Metabarcoding and metagenomic data across aquatic environmental gradients along the coasts of France and Chile.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {29},
pmid = {41530170},
issn = {2052-4463},
support = {Laboratoire international associ&#xe9; program//Centre National de la Recherche Scientifique (National Center for Scientific Research)/ ; 1211977//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico (National Fund for Scientific and Technological Development)/ ; BE 5937/2-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Chile ; France ; Metagenomics ; Ecosystem ; *DNA Barcoding, Taxonomic ; *Metagenome ; Seawater/microbiology ; Salinity ; Microbiota ; },
abstract = {Coastal marine environments, such as lagoons, fjords or estuaries, experience pronounced environmental variability, with fluctuations in salinity, temperature and nutrient levels shaping microbial community structure and function. These gradients result in diverse habitats, which may harbour taxonomic and genetic novelty with biogeochemical and biotechnological relevance. To explore microbial diversity and functional potential across these dynamic ecosystems, we sampled 26 sites along the coasts of France and Chile, including lagoons, estuaries, fjords, harbours, as well as coastal and offshore marine sites. Surface waters were collected from all sites, with deeper layers included at three sites. Monthly sampling at six sites in France enabled the assessment of seasonal dynamics. In total, 116 samples were processed for both metabarcoding and metagenomic sequencing yielding over 53,000 amplicon sequence variants (ASVs) and 1,372 metagenome-assembled genomes (MAGs). This dataset further includes a comprehensive gene catalogue and environmental variables such as salinity, temperature, nutrient concentrations, productivity, as well as oxygen consumption metrics collected across the different ecosystems.},
}
@article {pmid41530166,
year = {2026},
author = {Zhang, Q and Chen, B and Zhang, Z and Yu, Y and Jin, M and Lu, T and Zhang, Z and Pang, Q and Xu, N and Sun, J and Chen, J and Wang, J and Zhu, D and Qian, H and Penuelas, J and Zhu, YG},
title = {Cobamide-producing microbes as a model for understanding general nutritional interdependencies in soil food webs.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {1533},
pmid = {41530166},
issn = {2041-1723},
support = {2022C02029//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Food Chain ; *Soil Microbiology ; *Soil/chemistry ; *Bacteria/metabolism/genetics/classification ; Microbiota ; Animals ; Phylogeny ; Metagenomics ; },
abstract = {Nutrient crossfeeding critically governs microbiome-host interactions and ecosystem stability. Cobamides, synthesized only by prokaryotes, offer a powerful and tractable model for studying nutrient-mediated interdependencies in soil food webs; however, their ecological role in sustaining soil health remains unclear. Here, we construct the Soil Cobamide Producer database (SCP v.1.0) by integrating over 48,000 metagenomic and genomic datasets from 1,123 sampling sites. This database catalogs phylogenetically diverse prokaryotes (19 phyla, 302 genera) with cobamide biosynthetic potential. Using this resource, we identify host-specific colonization patterns of cobamide-producing microbes in fauna. These microbes also carry diverse functional traits that may contribute to trophic cascades and microbial community stability. In an Enchytraeid model, these colonizers support host development, modulate gene expression, and promote gut stability through transkingdom interactions, with cobamide biosynthesis serving as one representative trait among multiple microbial functions. At macroecological scales, cobamide-producing microbes occur across relatively high trophic levels, reflecting a broader principle of nutrient transfer that may also apply to other essential metabolites. This framework provides a general basis for studying nutritional microbes in soil food webs and advances One Health research.},
}
@article {pmid41529631,
year = {2026},
author = {Wang, Y and Qian, Y and Shi, C and Bi, J and Dong, P and Zou, Y and Yang, Y and Tao, Y and Li, H},
title = {Seasonal dynamics and stability of gut antibiotic resistance genes in plateau pika (Ochotona curzoniae) and plateau zokor (Eospalax baileyi).},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141112},
doi = {10.1016/j.jhazmat.2026.141112},
pmid = {41529631},
issn = {1873-3336},
mesh = {Seasons ; Animals ; *Lagomorpha/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Bacteria/genetics ; },
abstract = {The extreme ecosystems of the Tibetan Plateau harbor an alarming reservoir of antibiotic resistance genes (ARGs) within wildlife gut microbiomes-an emerging contaminant with significant implications for One Health. However, seasonal dynamics and pathogenic risks of these ARGs remain poorly understood. Through a 2.5-year study comparing the subterranean plateau zokor (Eospalax baileyi) and the surface-dwelling plateau pika (Ochotona curzoniae), we demonstrate how species-specific ecological strategies shape distinct ARG transmission patterns. Our results demonstrated striking eco-evolutionary trade-offs: surface pikas showed 1.3 times higher ARG diversity with strong seasonal variation, influenced by temperature-modulated bacterial community turnover and mobile genetic elements (MGEs). Conversely, subterranean zokors maintained stable, were enriched with high-risk ARGs dominated by mepA and tetO, reflecting their isolated niche. Both species consistently carried pathogenic-ARG complexes (Clostridium-bacA, Staphylococcus-Ermb) across seasons, genders, and ages, indicating established resistance reservoirs in plateau food webs. Metagenomic binning revealed co-transfer potential between ARGs and MGEs. This pioneering longitudinal study exposes a dual pattern: seasonal changes cause temporary turnover of ARGs, which harbor lower resistance risk in surface-dwelling animals, while subterranean hosts retain stable, higher-risk resistance. These findings establish critical baselines for monitoring antimicrobial resistance in vulnerable ecosystems and underscore the need for integrated One Health strategies.},
}
@article {pmid41529347,
year = {2026},
author = {Singh, S and Bajaj, A and Manickam, N},
title = {Microbiome of soil waste dumpsite and adjacent river habitat harbors dynamic plastic degrading bacterial diversity and abundant functional enzymes.},
journal = {The Science of the total environment},
volume = {1014},
number = {},
pages = {181331},
doi = {10.1016/j.scitotenv.2025.181331},
pmid = {41529347},
issn = {1879-1026},
mesh = {*Microbiota ; Biodegradation, Environmental ; Rivers/microbiology ; *Soil Microbiology ; Bacteria/classification ; *Plastics/metabolism ; India ; *Soil Pollutants/metabolism/analysis ; Waste Disposal Facilities ; Water Pollutants, Chemical/analysis ; Biodiversity ; },
abstract = {Landfill leachates and adjacent riverine ecosystems are usually the reservoirs of plastic-derived contaminants and other xenobiotics. Yet these sites are still less explored for their degradation potential. This study employed a whole metagenome analysis to characterize microbial communities and functional genes from the Ghaila municipal dumpsite and the Gomti river, Lucknow, India. Physicochemical analyses revealed neutral to slightly alkaline pH and elevated BOD and COD in downstream river sites, indicating high organic and plastic-associated pollutant loads. Taxonomic profiling identified 57 phyla, dominated by Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, with occurrence of key genera such as Pseudomonas, Acinetobacter, Flavobacterium, and Sphingomonas in abundance. Functional annotation of the metagenomic sequences detected 31 enzymes targeting 24 polymeric substances, including PETase, MHETase, urethanases, laccases, and nylon hydrolases in both dumpsite leachate and sludge (p < 0.05) samples. Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were widely distributed, particularly in leachate and sludge, underscoring their role as resistance reservoirs. These findings demonstrate that municipal dumpsite ecosystems are hotspots for plastic and xenobiotic degradation, highlighting their potential as genetic resources for bioremediation and advancing understanding of contaminant-driven microbial adaptation at landfill-river interfaces. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The complete metagenome sequence has been deposited at NCBI GenBank having accession no: SAMN42678420 to SAMN42678429 (BioProject).},
}
@article {pmid41528122,
year = {2026},
author = {McMurray-Jones, A and Spann, K and Yarlagadda, PKDV and Fernando, J and Roberts, LW},
title = {Environmental surveillance of bacteria in a new intensive care unit using plate sweeps.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41528122},
issn = {2057-5858},
mesh = {*Intensive Care Units ; *Bacteria/genetics/isolation &amp; purification/classification/drug effects ; Humans ; Queensland ; *Environmental Monitoring/methods ; Drug Resistance, Bacterial/genetics ; Microbiota/genetics ; Metagenomics/methods ; Cross Infection/microbiology ; },
abstract = {The hospital environment plays a critical role in the transmission of infectious diseases. Surveillance methods often rely on selective enrichment or deep metagenomic sequencing, which both have significant drawbacks in terms of community resolution and cost. Plate sweeps provide a practical moderate approach to cultivate a wide range of bacteria, capturing more diversity than a single colony pick without high sequencing costs. Here, we use this approach to characterize a newly built hospital intensive care unit (ICU) in Queensland, Australia. Between November 2023 and February 2024, we sampled 78 sites within an 8-bed private hospital ICU pre- and post-patient introduction to the environment. Samples were enriched on non-selective media before DNA was extracted from whole plate sweeps and sequenced using Illumina. We assessed species, antimicrobial resistance (AMR) genes, virulence genes and transmission across all samples and between the pre- and post-patient samples using Kraken2, AbritAMR and Tracs. While the rate of positive microbial growth within the ICU environment did not change significantly pre- and post-patient introduction, the post-patient microbiome consisted of largely different bacterial species; of 22 genera identified, only 3 genera were represented at both timepoints. Post-patient samples were enriched in AMR genes, including resistance to fosfomycin, quinolones and beta-lactams. Common genera identified post-patient were Pseudomonas, Delftia and Stenotrophomonas, often associated with areas of plumbing. Cluster analysis identified 17 possible transmission links from a single timepoint, highlighting several areas in the ICU (e.g. communal bathrooms) as key areas for transmission. We demonstrate the utility of plate sweeps as a means of economical non-selective environmental surveillance and highlight their ability to identify hotspots of transmission within a hospital ward that could be targeted by infection control prior to an outbreak of a more serious pathogen.},
}
@article {pmid41527012,
year = {2026},
author = {Weber, C and Wind, D and Petzsch, P and Supprian, T and Dilthey, A and Christl, J and Finzer, P},
title = {Dysbiotic shift in the oral microbiota of patients with Alzheimer's disease compared to their healthy life partners-a combinatorial approach and a paired study design.},
journal = {Alzheimer's research &amp; therapy},
volume = {18},
number = {1},
pages = {23},
pmid = {41527012},
issn = {1758-9193},
mesh = {Humans ; *Alzheimer Disease/microbiology ; Male ; Female ; Aged ; *Microbiota ; *Dysbiosis/microbiology ; *Mouth/microbiology ; Aged, 80 and over ; Middle Aged ; Saliva/microbiology ; },
abstract = {BACKGROUND: The oral microbiota has been associated with Alzheimer's disease (AD). However, earlier studies provided conflicting results using varying sampling methods, sequencing techniques, and statistics, as well as independent subjects.<br><br>METHODS: To robustly identify disease-associated microbial features, we recruited patients and their healthy life partners from the same households sharing a more similar microbiota compared to independent individuals increasing statistical power via paired design and combined three different sequencing methods - including metagenomics-and several bioinformatic pipelines. We recruited 26 AD-patients and their life partners. Salivary and supragingival samples were collected and a clinical examination of the mouth was performed.<br><br>RESULTS: Both groups showed comparable oral health. By focusing primarily on recurrently identified species across the different datasets we were able to identify a Core dysbiosis. This Core dysbiosis surprisingly spares the most central of oral diseases pathogens, namely Porphyromonas gingivalis. However, it includes numerous other species commonly associated with oral pathologies such as Prevotella nigrescens, Streptococcus anginosus, Dialister invisus, Anaeroglobus geminatus, Olsenella uli and Mogibacterium timidum. In contrast, more host-compatible species such as Prevotella melaninogenica or Streptococcus parasanguinis are identified in controls.<br><br>CONCLUSIONS: This is the first study using a combined sequencing approach and a paired study design to identify robust features of the oral microbiota of AD-patients. Although promising, the results should nevertheless be interpreted with caution, as the cross-sectional study design limits the possibilities of interpretation, and larger, longitudinal data are necessary for causal conclusions. However, this combined approach on multiple processing levels to identify intra-partnership differences still offers the possibility to better identify disease-associated microbial features potentially involved in AD-pathogenesis.<br><br>TRIAL REGISTRATION: This study was prospectively registered at the German Clinical Trials Register (DRKS00023456) at the 30th of November 2020.},
}
@article {pmid41526362,
year = {2026},
author = {Ascandari, A and Aminu, S and Benhida, R and Daoud, R},
title = {Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {40},
pmid = {41526362},
issn = {2055-5008},
mesh = {*Colorectal Neoplasms/microbiology ; Humans ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Virulence Factors/genetics ; *Bacteria/genetics/drug effects/classification/pathogenicity/isolation &amp; purification ; Cohort Studies ; Metagenome ; },
abstract = {The gut microbiome is increasingly implicated in colorectal cancer (CRC), yet the functional signatures associated with disease progression remain poorly resolved across populations. We performed an assembly-based metagenomic analysis of more than 500 samples from three geographically distinct cohorts to characterize resistome and virulome patterns associated with CRC. Using a cross-validated modeling framework based on Partial Least Squares (PLS) regression, we identified two reproducible latent functional gradients that structured variation in antimicrobial-resistance and virulence-factor profiles. One gradient was enriched for adhesion, efflux, and biofilm-associated functions, while the second reflected immunomodulatory and barrier-related pathways. These components were statistically robust, directionally stable across cohorts, and consistent with functional themes frequently reported in CRC microbiome studies. To summarize variation along these gradients, we derived an exploratory Dual-Axis Index (DAI) based on the two stable PLS components. Although its discriminative performance was moderate, the DAI provided an interpretable low-dimensional representation of how resistome-virulome patterns differed across healthy, adenoma, and carcinoma states. These results suggest that functional gene profiles in CRC are organized along reproducible statistical axes, and highlight functional modules, such as adhesion-, iron-associated, and immune-interaction pathways that may complement taxonomic or metabolic biomarkers in future multimodal approaches. Our work provides a reproducible, assembly-based framework for examining the functional organization of CRC-associated microbiomes across diverse populations.},
}
@article {pmid41525322,
year = {2026},
author = {Karagiannis, TT and Chen, Y and Bald, S and Tai, A and Reed, ER and Milman, S and Andersen, SL and Perls, TT and Segrè, D and Sebastiani, P and Short, MI},
title = {Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013883},
pmid = {41525322},
issn = {1553-7358},
support = {S10 OD032203/OD/NIH HHS/United States ; },
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Aging/genetics/physiology ; *Longevity/genetics/physiology ; Aged ; Male ; Computational Biology ; Female ; Aged, 80 and over ; Feces/microbiology ; Metagenome/genetics ; Middle Aged ; },
abstract = {There are various well-validated taxonomic classifiers for profiling shotgun metagenomics data, with two popular methods, MetaPhlAn (marker-gene-based) and Kraken (k-mer-based), at the forefront of many studies. Despite differences between classification approaches and calls for the development of consensus methods, most analyses of shotgun metagenomics data for microbiome studies use a single taxonomic classifier. In this study, we compare inferences from two broadly used classifiers, MetaPhlAn4 and Kraken2, applied to stool metagenomic samples from participants in the Integrative Longevity Omics study to measure associations of taxonomic diversity and relative abundance with age, replicating analyses in an independent cohort. We also introduce consensus and meta-analytic approaches to compare and integrate results from multiple classifiers. While many results are consistent across the two classifiers, we find classifier-specific inferences that would be lost when using one classifier alone. Both classifiers captured similar age-associated changes in diversity across cohorts, with variability in species alpha diversity driven by differences by classifier. When using a correlated meta-analysis approach (AdjMaxP) across classifiers, differential abundance analysis captures more age-associated taxa, including 17 taxa robustly age-associated across cohorts. This study emphasizes the value of employing multiple classifiers and recommends novel approaches that facilitate the integration of results from multiple methodologies.},
}
@article {pmid41525137,
year = {2026},
author = {Jackson, SA and Hrab, P and Zdouc, MM and Clarke, DJ and Dobson, ADW},
title = {New insights into the microbiome of the deep-sea sponge Inflatella pellicula and the secondary metabolic potential of metagenome-assembled genomes and the wider microbiome.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41525137},
issn = {2057-5858},
mesh = {*Porifera/microbiology ; Animals ; *Metagenome ; *Microbiota/genetics ; Secondary Metabolism/genetics ; Phylogeny ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Multigene Family ; Genome, Bacterial ; Sequence Analysis, DNA ; },
abstract = {Marine sponges are found in all of the world's oceans, from the surface waters to the deepest abyssal zones. The marine sponge holobiont is a rich source of microbial and chemical diversity. Up to 63 bacterial phyla have been observed to be associated with sponges, and thousands of unique natural products have been extracted from sponges or their microbial symbionts. However, sponges from the deep sea and their associated microbial communities are relatively understudied, largely due to sampling-associated difficulties. Secondary metabolism biosynthetic gene clusters are phylogenetically distinct and hold the potential to produce novel chemistry with potential pharmacological or industrial utility. In order to gain further insights into the microbiome of the deep-sea sponge Inflatella pellicula, the metagenome of this sponge, sampled from a depth of 2,900 m, was sequenced. A large fraction of the sequence reads appeared to be 'biological dark matter' and could not be taxonomically classified. Further, unlike similar studies from different marine ecosystems, relatively few metagenome-assembled genomes (MAGs) could be assembled, and relatively few secondary metabolism biosynthetic gene clusters were identified. The identified clusters were, however, very dissimilar to known characterized clusters, but some shared similarities with clusters annotated in MAGs assembled from sponge metagenomes from disparate geographic locations. Therefore, renewed efforts to cultivate the hosts of these gene clusters may yield valuable small-molecule natural products.},
}
@article {pmid41524921,
year = {2026},
author = {Nayab, GE and Ur Rahman, R and Hanan, F and Khan, I and Fahim, M},
title = {Metagenomic Exploration of the Bacteriome Reveals Natural Wolbachia Infections in Yellow Fever Mosquito Aedes aegypti and Asian Tiger Mosquito Aedes albopictus.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {133},
pmid = {41524921},
issn = {1432-0991},
mesh = {Animals ; *Aedes/microbiology/classification ; *Wolbachia/genetics/classification/isolation &amp; purification ; Phylogeny ; Pakistan ; Metagenomics ; *Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; Female ; *Microbiota ; *Metagenome ; Electron Transport Complex IV/genetics ; DNA, Bacterial/genetics ; },
abstract = {Dengue and associated complications are spreading to non-endemic regions of Pakistan. Vector control, the foremost and widely adopted strategy for managing dengue has been implemented through various measures in Pakistan. Biological control through the use of Wolbachia, a bacterium naturally present in various insect genera, including Aedes, has demonstrated promising results globally. In this study we collected Aedes species and investigated its microbiomes with a particular focus on identifying the endosymbiont Wolbachia. Mosquitoes were collected via Gravitraps in the Peshawar region of Pakhtunkhwa province in the northwest of Pakistan. The identity of the mosquitoes was initially confirmed through morphological characters followed by molecular identification using species-specific Cytochrome oxidase I (COI) primers. The DNA from female Ae. aegypti and Ae. albopictus was further subjected to 16 S rRNA sequencing. The hypervariable regions V3/V4 of 16 S rRNA were used for sequencing using the paired-end Illumina MiSeq platform. The phylogenetic analysis of the COI gene in our samples demonstrated similarity to Aedes species previously documented in Pakistan. In comparative analysis of the microbiomes, Ae. albopictus was found to harbor 921 bacterial species, while Ae. aegypti only had 239 species. The metagenomic analysis revealed single-strain Wolbachia pipientis infection in Ae. aegypti, while Ae. albopictus harbored a double-strain infection involving a supergroup A strain (referred to as Wolbachia pipientis in 16 S EzBioCloud database) and a supergroup B strain (referred to as Wolbachia bourtzisii in16S EzBioCloud database).},
}
@article {pmid41524715,
year = {2026},
author = {Pasqualini, J and Maritan, A and Rinaldo, A and Facchin, S and Savarino, EV and Altieri, A and Suweis, S},
title = {Linking complex microbial interactions and dysbiosis through a disordered Lotka-Volterra model.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {41524715},
issn = {2050-084X},
support = {ANR-23-CE30-0012-01//Agence Nationale de la Recherche/ ; CUP 2022WPHMXK//National Recovery and Resilience Plan/ ; PNC0000002-DARE//DigitalLifelong Prevention/ ; },
mesh = {*Dysbiosis/microbiology ; *Microbial Interactions ; Humans ; *Microbiota ; Metagenomics ; Models, Biological ; },
abstract = {The rapid advancement of environmental sequencing technologies, such as metagenomics, has significantly enhanced our ability to study microbial communities. The eubiotic composition of these communities is crucial for maintaining ecological functions and host health. Species diversity is only one facet of a healthy community's organization; together with abundance distributions and interaction structures, it shapes reproducible macroecological states, that is, joint statistical fingerprints that summarize whole-community behavior. Despite recent developments, a theoretical framework connecting empirical data with ecosystem modeling is still in its infancy, particularly in the context of disordered systems. Here, we present a novel framework that couples statistical physics tools for disordered systems with metagenomic data, explicitly linking diversity, interactions, and stability to define and compare these macroecological states. By employing the generalized Lotka-Volterra model with random interactions, we reveal two different emergent patterns of species interaction networks and species abundance distributions for healthy and diseased microbiomes. On the one hand, healthy microbiomes have similar community structures across individuals, characterized by strong species interactions and abundance diversity consistent with neutral stochastic fluctuations. On the other hand, diseased microbiomes show greater variability driven by deterministic factors, thus resulting in less ecologically stable and more divergent communities. Our findings suggest the potential of disordered system theory to characterize microbiomes and to capture the role of ecological interactions on stability and functioning.},
}
@article {pmid41523161,
year = {2025},
author = {Sanchez, G and Simakov, O and Nyholm, S and Nishiguchi, M and McFall-Ngai, M and Lami, R and Heath-Heckman, E and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the bigfin reef squid, Sepioteuthis lessoniana d'Orbigny, 1826 and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {351},
pmid = {41523161},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from a specimen of Sepioteuthis lessoniana (bigfin reef squid; Mollusca; Cephalopoda; Myopsida; Loliginidae). The genome sequence has a total length of 5,056.23 megabases. Most of the assembly (86.4%) is scaffolded into 44 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 28,970 protein-coding genes.},
}
@article {pmid41522496,
year = {2026},
author = {Gedam, PA and Khandagale, K and Barvkar, VT and Bhandari, S and Patil, S and Wayal, S and Bhangare, I and Bhagat, KP and Landage, K and Kale, R and Bhoite, V and More, S and Mahajan, V and Gawande, S},
title = {Microbial allies: shaping growth, physiology, and rhizosphere dynamics of onion (Allium cepa L.).},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20566},
pmid = {41522496},
issn = {2167-8359},
mesh = {*Rhizosphere ; *Onions/microbiology/growth &amp; development/physiology ; *Soil Microbiology ; Fertilizers ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; },
abstract = {The present study investigates the dual impact of microbial biofertilizers on the phenotypic performance and rhizosphere microbiome composition in an onion crop. A pot experiment was conducted with seven treatments of microbial inoculants, such as Azotobacter, Azospirillum, Piriformospora indica, phosphate solubilizing bacteria (PSB), and control treatments with and without chemical fertilizers. The growth, physiological, and biochemical traits of onion were assessed alongside rhizospheric soil microbiome profiling using 16S rRNA metagenomic sequencing. Significant enhancement in plant height, leaf number, leaf area, chlorophyll content, photosynthetic rate, and antioxidant enzyme activity with low leaf temperature was observed in plants inoculated with Azotobacter and Azospirillum. Notably, the Azotobacter treatment yielded a significant enhancement in the bulb phenol content. Rhizosphere metagenomic analysis revealed 17 dominant phyla, with Actinobacteria (25.3%), Proteobacteria (22.2%), Firmicutes (12.8%), and Chloroflexi (11.02%) comprising over 70% of the total microbiome. Alpha and beta diversity metrics indicated that microbial inoculation, especially with Azospirillum and PSB, enriched the soil microbial community structure. Distinct clustering and correlations with specific microbial taxa such as Candidatus Nitrososphaera and Pseudomonas were observed in response to individual biofertilizer treatments. This study highlights the potential of biofertilizers not only in enhancing onion growth and development but also in modulating beneficial rhizosphere microbial communities. Integrating biofertilizers into onion production systems could reduce the dependency on chemical fertilizers and promote sustainable crop management.},
}
@article {pmid41518802,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG},
title = {Multi-omics assessment of synthetic microbiome-mediated remediation of cyclotetramethylene tetranitroamine (HMX) contaminated water.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141026},
doi = {10.1016/j.jhazmat.2026.141026},
pmid = {41518802},
issn = {1873-3336},
mesh = {*Water Pollutants, Chemical/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Nitrosamines/metabolism ; Bacteria/metabolism/genetics ; Multiomics ; Triazines ; },
abstract = {Cyclotetramethylene tetranitroamine (HMX) is a typical high-energy nitramine pollutant with an environmental persistence and toxic effects that pose serious ecological risks. In this study, a synthetic microbiome with complementary functions is built that enables the integration of multigroup technology to conduct a systematic analysis of the mechanism of remediation of HMX-contaminated water bodies. Four core bacterial strains (Bacillus altitudinis, B. cereus, B. subtilis, and Pseudomonas stutzeri) were directionally domesticated and screened from HMX-contaminated water. Through functional verification, they were confirmed to express key enzymes NfsA, YdhA, FdhA, and NirS, respectively, to form a complete HMX deep degradation-level connection path. The synthetic microbiome achieved 100 % removal of HMX and its intermediates within 60 days, and isotope tracing (δ[15]N enrichment +2.7 ‰) confirmed its complete mineralization ability. Multiomic analysis showed that the restoration process is accompanied by a systematic reshaping of the water microecology and chemical environment, so that the microbial community structure is optimized and the synthetic microbiome is successfully colonized and becomes the core node. Meanwhile, the energy metabolic network (glycolysis, TCA cycle, oxidative phosphorylation) is significantly enhanced; metagenomic data also revealed reduced viral abundance. Ionomics revealed that key nutrient elements, such as P and S, are efficiently assimilated and utilized. These findings identify an efficient HMX bioremediation strategy that utilizes the multiple dimensions of "community structure-metabolic function-environmental effects" through a multigroup integration framework. More importantly, this study provides a theoretical basis and practical paradigm for the rational design of functional microbial communities.},
}
@article {pmid41518158,
year = {2026},
author = {Barberá, A and Ortolá, R and Sotos-Prieto, M and Rodríguez-Artalejo, F and Moya, A and Ruiz-Ruiz, S},
title = {The Role of the Gut Microbiome in the Complex Network of Frailty Syndrome and Associated Comorbidities in Aging.},
journal = {Aging cell},
volume = {25},
number = {2},
pages = {e70365},
pmid = {41518158},
issn = {1474-9726},
support = {PID2019-105969GB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PMPTA22/00107//Carlos III Health Institute (ISCIII)/ ; PMPTA22/00037//Carlos III Health Institute (ISCIII)/ ; PMPTA23/00001//Carlos III Health Institute (ISCIII)/ ; INVEST/2022/309//Next Generation-EU/ ; 22/1111//ISCIII/ ; //The Secretary of R&#x2009;+&#x2009;D&#x2009;+&#x2009;I/ ; //ERDF/ESF/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Frailty/microbiology ; Male ; Female ; Aged ; *Aging ; Comorbidity ; Aged, 80 and over ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; },
abstract = {The gut microbiota changes throughout life, potentially influencing health and triggering physiological disorders. Frailty syndrome (FS) is an age-related condition that reduces quality of life and increases hospitalization and mortality risks, making early detection and prevention essential in older populations. This study analyzed 16S rRNA gene and metagenomics sequencing of fecal samples from 203 older adults (FS: n = 64, non-FS (NFS): n = 139) to assess the role of gut microbiota in FS and related comorbidities, such as sarcopenia and impaired lower extremity function (ILEF) or anthropometric variables. Consistent taxonomic patterns were observed: Eggerthella, Parabacteroides, and Erysipelatoclostridium were significantly abundant in FS, while Christensenellaceae R-7 group, Erysipelotrichaceae UCG-003, and Hungatella were enriched in NFS. Christensenellaceae R-7 group was also associated with better mobility. Metagenomics analysis identified 680 KEGG functions differing between groups, categorized into 28 metabolic pathways. FS individuals had overrepresented biotin metabolism, antimicrobial resistance, and energy production, but underrepresented ribosomal and protein synthesis and sporulation pathways. Resistome analysis found the tetM/tetO (K18220) gene most abundant, alongside tetracycline, β-lactam, and macrolide resistance, primarily mediated by antibiotic efflux and transporters. These findings highlight distinct microbial and functional signatures associated with FS, underscoring the complex interplay between the gut microbiota and host physiology in aging. Adjusting for covariates, age and diabetes acted as confounding factors in FS for both 16S gene and metagenomics sequencing. This study offers new insights into fundamental questions in the biology of aging and opens avenues for microbiota-targeted strategies to improve the quality of life in older adults.},
}
@article {pmid41516169,
year = {2025},
author = {Uvarova, YE and Khlebodarova, TM and Vasilieva, AR and Shipova, AA and Babenko, VN and Zadorozhny, AV and Slynko, NM and Bogacheva, NV and Bukatich, EY and Shlyakhtun, VN and Korzhuk, AV and Pavlova, EY and Chesnokov, DO and Peltek, SE},
title = {Genetic Characterisation of Closely Related Lactococcus lactis Strains Used in Dairy Starter Cultures.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516169},
issn = {1422-0067},
support = {075-15-2025-516//Ministry of Science and Higher Education of the Russian Federation (the Federal Scientific-technical program for genetic technologies development for 2019-2030)/ ; FWNR- 2022-0022//Ministry of Science and Higher Education project "Study of metabolic control networks in living systems under environmental interaction, including in genetically modified organisms."/ ; },
mesh = {*Lactococcus lactis/genetics/classification/isolation &amp; purification/metabolism ; *Cheese/microbiology ; Food Microbiology ; Phylogeny ; Genome, Bacterial ; Fermentation ; Microbiota/genetics ; },
abstract = {The complex microbiota of cheese starters plays a key role in determining the structure and flavour of the final product, primarily through their acid-forming capacity, protease activity, and exopolysaccharide synthesis. However, the specific microbial communities underlying the unique qualities of artisanal cheeses remain poorly understood. This study presents the microbiological and molecular genetic characterisation of the microbiome isolated from an artisanal cheese starter in Kosh-Agach, Altai, Russia. Metagenomic analysis of this starter revealed the presence of three bacterial genomes corresponding to those of Lactococcus lactis. Pure cultures from this starter were obtained by sequential subculture, and seventeen colonies displaying distinct characteristics on differential media were selected. Genome sequencing was performed for each colony. Bioinformatic analysis based on the rpoB gene grouped the isolates into three clusters, each corresponding to a distinct strain of Lactococcus lactis subsp. diacetilactis. This classification was further confirmed by microbiological and microscopic analyses. A notable finding was that none of the strains produced the characteristic aroma compounds of L. l. subsp. diacetilactis, namely, diacetyl and CO2. The functional properties and metabolic characteristics of this starter consortium are discussed.},
}
@article {pmid41516078,
year = {2025},
author = {Lupusoru, R and Moleriu, LC and Mare, R and Sporea, I and Popescu, A and Sirli, R and Goldis, A and Nica, C and Moga, TV and Miutescu, B and Ratiu, I and Belei, O and Olariu, L and Dumitrascu, V and Dragomir, RD},
title = {AI-Guided Multi-Omic Microbiome Modulation Improves Clinical and Inflammatory Outcomes in Refractory IBD: A Real-World Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516078},
issn = {1422-0067},
support = {without a Grant Number.//"Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Adult ; Female ; Male ; *Inflammatory Bowel Diseases/microbiology/therapy ; Middle Aged ; Biomarkers/blood ; *Artificial Intelligence ; Feces/microbiology ; Inflammation/microbiology ; Metagenomics/methods ; Treatment Outcome ; Young Adult ; Multiomics ; },
abstract = {Inflammatory bowel disease (IBD) remains difficult to manage in patients who fail multiple therapeutic lines, and growing evidence suggests that alterations in the gut microbiome contribute to persistent symptoms and inflammatory activity. This study evaluated a three-month, AI-guided, multi-omic personalized microbiome modulation program in adults with treatment-refractory IBD. Baseline stool metagenomic sequencing, blood biomarkers, micronutrient panels, and clinical data were integrated through an artificial intelligence platform to generate individualized plans combining dietary adjustments, targeted synbiotics, selective antimicrobials, and micronutrient correction. Clinical outcomes, inflammatory markers, and microbial signatures were reassessed after three months. Across 358 participants, stool frequency decreased substantially, urgency and rectal bleeding resolved in most patients, and over 70% reported a "much improved" overall condition. Inflammatory biomarkers showed marked normalization, with reductions in hs-CRP and fecal calprotectin observed in over 85% of cases. Micronutrient deficiencies, particularly iron and zinc, also improved, and beneficial microbial taxa such as Faecalibacterium prausnitzii, Bifidobacterium longum, and Akkermansia muciniphila increased significantly. These findings suggest that personalized, multi-omic microbiome modulation may support clinically meaningful improvements by targeting microbial, metabolic, and immune imbalances rather than symptoms alone. While encouraging, these results require confirmation in randomized controlled studies.},
}
@article {pmid41515236,
year = {2025},
author = {Zhang, Z and Wang, S and Sun, G and Pan, D},
title = {Intermittent Fasting and Probiotics for Gut Microbiota Modulation in Type 2 Diabetes Mellitus: A Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515236},
issn = {2072-6643},
support = {82204030//National Natural Science Foundation of China/ ; 2025M770748//China Postdoctoral Science Foundation/ ; 2024T170134//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; Humans ; Blood Glucose/metabolism ; *Diabetes Mellitus, Type 2/microbiology/therapy ; Dysbiosis ; *Fasting ; *Gastrointestinal Microbiome/physiology ; Intermittent Fasting ; *Probiotics/therapeutic use/administration &amp; dosage ; },
abstract = {Background: Type 2 diabetes mellitus (T2DM) is a global epidemic in which gut microbiota dysbiosis contributes to impaired glucose homeostasis and chronic inflammation. Intermittent fasting (IF) and probiotic supplementation have independently demonstrated glycemic benefits in T2DM, largely through microbiota remodeling. This narrative review synthesizes evidence up to October 2025 to clarify the microbiota-dependent mechanisms of IF and probiotics, and to evaluate the biological plausibility and preliminary clinical data for their combined application in T2DM management. Methods: We conducted a comprehensive literature review of preclinical and clinical studies (PubMed, Embase, Web of Science, and Cochrane Library) examining IF regimens (primarily time-restricted feeding and 5:2 protocols) and multi-strain probiotics containing Lactobacillus and Bifidobacterium species in T2DM or relevant models. Mechanistic pathways, microbial compositional shifts, and metabolic outcomes were qualitatively synthesized, with emphasis on overlapping signaling (short-chain fatty acids, bile acids, GLP-1, and barrier function). Results: IF consistently increases Akkermansia muciniphila and, variably, Faecalibacterium prausnitzii abundance, restores microbial circadian rhythmicity, and enhances SCFA and secondary bile acid production. Multi-strain probiotics modestly reduce HbA1c (-0.3% to -0.6%) and fasting glucose, outperforming single-strain preparations. Both interventions converge on reduced endotoxaemia and improved intestinal integrity. Preclinical models indicate potential synergy, whereas the only direct human trial to date showed neutral results. Conclusions: IF and probiotics engage overlapping microbiota-mediated pathways, supporting their combined use as an adjunctive strategy in T2DM. Adequately powered randomized trials incorporating deep metagenomics, metabolomics, and hard clinical endpoints are now required to confirm additive or synergistic efficacy.},
}
@article {pmid41515159,
year = {2025},
author = {Robert, M and Saha, S and Dizman, N and Rohlfs, M and Sirmans, E and Simon, J and Amaria, RN and Glitza Oliva, IC and Tawbi, HA and Davies, MA and Ikeguchi, A and Basen-Engquist, K and Schadler, K and Roth, ME and Song, W and Zhang, X and Ajami, NJ and Cohen, L and Wargo, JA and Peterson, CB and McQuade, JL and Daniel, CR},
title = {Investigating Chronic Toxicity, Diet, Patient-Reported Outcomes and the Microbiome in Immunotherapy-Treated Metastatic Melanoma Survivors: A New Frontier.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515159},
issn = {2072-6643},
support = {na/MRA/Melanoma Research Alliance/United States ; na//Andrew Sabin Family Fellowship/ ; na//MD Anderson Melanoma Moon Shot/ ; 1P30CA016672/NH/NIH HHS/United States ; 1R01CA291965/NH/NIH HHS/United States ; 1P50CA221703/NH/NIH HHS/United States ; 1R01HL158796/NH/NIH HHS/United States ; },
mesh = {Humans ; *Melanoma/therapy/drug therapy/psychology ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; *Patient Reported Outcome Measures ; *Cancer Survivors/psychology ; *Diet ; Aged ; Adult ; *Immunotherapy/adverse effects ; Quality of Life ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; Depression ; Anxiety ; Prospective Studies ; Exercise ; },
abstract = {Background/Objectives: Immune checkpoint blockade (ICB) therapies have significantly improved outcomes in metastatic melanoma. However, immune-related adverse events (irAEs) and persistent chronic toxicities (CTs) among this emerging survivor population likely influence different facets of quality of life. This study characterized CT, patient-reported outcomes (PROs), diet, physical activity and gut microbiome features in a cohort of long-term survivors with a history of ICB-treated metastatic melanoma. Methods: Forty-eight patients with a history of metastatic melanoma who initiated ICB treatment at least 3 years earlier and were not currently on treatment were prospectively enrolled from a melanoma survivorship clinic. Participants completed screening questionnaires for depression, anxiety, diet and physical activity. The gut microbiome was characterized via metagenomic sequencing in a subsample (n = 39). Patients' clinicopathological characteristics and experience of irAEs (during treatment) and CT (persisting >6 months after completion of therapy) were extracted retrospectively from the medical record. Results: In the overall cohort, 60% were experiencing CT, while 16% and 20% reported clinically relevant levels of depression and anxiety symptoms, respectively. We observed significant differences in overall gut microbiome composition between survivors with and without CT (p = 0.02). Consumption of fruit and vegetables was inversely associated with anxiety (ρ = 0.3, p = 0.038). Added sugar consumption was correlated with the severity of experienced symptoms (ρ = 0.4, p = 0.003), with pronounced associations across the spectrum of symptoms, including pain, fatigue and shortness of breath (p < 0.05). Conclusions: These results suggest that CT is experienced by a substantial proportion of ICB-treated metastatic melanoma survivors. Patients experiencing CT also showed distinct microbiome features. However, additional research in prospective settings is needed to confirm these hypotheses.},
}
@article {pmid41514452,
year = {2026},
author = {Weiss, A and Elena, AX and Klümper, U and Dumack, K},
title = {Viral and eukaryotic drivers of prokaryotic and antibiotic resistance gene diversity in wastewater microbiomes.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {24},
pmid = {41514452},
issn = {2049-2618},
support = {544004729//Deutsche Forschungsgemeinschaft/ ; 01DO2200//Bundesministerium f&#xfc;r Forschung, Technologie &amp; Raumfahrt/ ; },
mesh = {*Wastewater/microbiology/virology ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Drug Resistance, Microbial/genetics ; *Viruses/genetics/classification/isolation &amp; purification ; Metagenomics/methods ; *Eukaryota/genetics/classification ; Metagenome ; Genetic Variation ; },
abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) are proliferating in wastewater microbiomes, yet the biotic forces shaping their diversity remain poorly understood. Here, we integrate 14 months of metagenomic and metatranscriptomic data from a wastewater treatment plant to reveal that viruses and microeukaryotes, long-overlooked trophic actors, may play an important role in shaping bacterial and ARG diversity.<br><br>RESULTS: We show that viral and microeukaryotic communities exhibit strong seasonal dynamics that cascade through the microbial food web, significantly structuring prokaryotic communities and subsequently ARG profiles. Crucially, we find that viral and microeukaryotic diversity are positively associated with bacterial diversity, which in turn shapes ARG diversity, underscoring the regulatory potential of ecological interactions.<br><br>CONCLUSIONS: Our findings challenge the abiotic-centric paradigm and establish the central role of multi-trophic interactions in shaping ARG dynamics in wastewater ecosystems. Video Abstract.},
}
@article {pmid41514445,
year = {2026},
author = {Li, M and Zhu, S and Sun, H and Huo, Y and Cao, Q and Deng, Z and Li, K and He, Y and Lu, X and Gao, J and Xu, C},
title = {Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {61},
pmid = {41514445},
issn = {2049-2618},
support = {32402957//National Natural Science Foundation of China/ ; 32125038//National Natural Science Foundation of China/ ; BX20240417//China National Postdoctoral Program for Innovative Talents/ ; 2024M753563//China Postdoctoral Science Foundation funded project/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Lactation/physiology ; Female ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Stress, Physiological ; Milk/metabolism ; Oxidative Stress ; Metabolomics ; Archaea/classification/genetics/isolation &amp; purification ; Methane/metabolism ; },
abstract = {BACKGROUND: Early lactation (EL) in high-yield dairy cows represents a critical lactation phase marked by significant metabolic stress, which often provokes health disorders and production losses. The rumen microbiome is instrumental in regulating host health and metabolism. However, its contribution to metabolic stress experienced by EL cows has been largely unexplored.<br><br>RESULTS: Metabolic stress was prominently observed during EL in the form of elevated oxidative stress (OS), inflammation, and lipolysis. This stress gradually decreased with the progression of lactation from day in milk (DIM) 21 to 90. To identify the underlying mechanisms, this study analyzed EL cows (DIM 32) and peak lactation (PL, DIM 72) using an integrative approach including rumen metagenomics, rumen metabolomics, host metabolomics, and their interactions. Metagenomic analysis revealed a higher abundance of methanogenic archaea (Methanobrevibacter and Methanosphaera) in EL cows, driving increased methane production and subsequent energy loss. This energy waste likely worsened the negative energy balance and caused excessive lipolysis in EL cows. In contrast, the rumen microbiota of PL cows was enriched with Prevotella species and anti-inflammatory bacterial genera (Bacteroides, Parabacteroides, and Alistipes), which are associated with the alleviation of host metabolic stress. Functional analysis of the rumen microbiota uncovered increased tryptophan biosynthesis in EL cows, driving kynurenine production. Conversely, PL cows exhibited a greater abundance of enzymes involved in tryptophan metabolism, thus facilitating the production of indole-3-acetic acid (IAA). Metabolomics analysis also identified the tryptophan metabolism pathway as a shared link between the rumen and serum. Specifically, the kynurenine pathway, associated with OS and inflammation, was upregulated in EL cows, while the indole pathway, particularly the production of IAA, was markedly elevated in PL cows, which attenuated OS and inflammation.<br><br>CONCLUSIONS: The study results indicate that the rumen microbiota is pivotal in mitigating metabolic stress in EL cows by modulating tryptophan metabolism. Specifically, the transition from EL to PL was characterized by an enhanced tryptophan-indole pathway and a suppressed tryptophan-kynurenine pathway. The results offer meaningful insights into the microbial mechanisms underlying metabolic stress and identify potential strategies for improving cow health and productivity during lactation. Video Abstract.},
}
@article {pmid41514433,
year = {2026},
author = {Yang, J and Feng, Y and Guo, T and Guo, S and Yang, M and Zhou, D and Lin, P and Wang, A and Jin, Y},
title = {The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {60},
pmid = {41514433},
issn = {2049-2618},
support = {2023YFD1801100//National Key R&amp;D Program of China/ ; 2022GD-TSLD-46//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2018BBF33001//The Key R&amp;D Program of Ningxia Hui Autonomous Region/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Gastrointestinal Microbiome ; Female ; Milk/chemistry/metabolism ; *Rectum/microbiology ; Metagenomics ; Lactation ; Metabolomics ; Bacteria/classification/genetics/isolation &amp; purification ; Dairying ; Longevity ; },
abstract = {BACKGROUND: In high-producing dairy systems, the average productive lifespan of cows is around 2.5-4 years. Persistent productivity and longevity are key determinants of dairy cow production performance and herd profitability. Although gastrointestinal microbiota influences dairy cow productivity, the mechanisms by which host-microbiome interactions support sustained productivity in long-lived dairy cows remain unclear. Therefore, this study integrated the metagenomics and metabolomics of the rumen and rectum, along with serum and milk metabolomics, to elucidate the potential impact of the rumen and rectum microbiota on the productivity of long-lived dairy cows.<br><br>RESULTS: Serum alanine aminotransferase (ALT), alkaline phosphatase (ALP), total cholesterol (TC), and high-density and low-density lipoprotein cholesterol (HDL-C and LDL-C) levels in long-lived dairy cows were positively correlated with milk yield (MY) and elevated in long-lived high-yielding (LH) dairy cows, whereas insulin (INS) and glucagon (GCG) were negatively correlated with MY and higher in long-lived low-yielding (LL) dairy cows. Rumen propionate level was elevated in LH group and positively correlated with MY. The rumen microbiome, in LH cows upregulated pathways involved in amino acid, cofactor, and vitamin metabolism. LH cows' rumen and rectum microbial networks had cohesion and vulnerability levels similar to those of LL cows and exhibited dependence on key nodes. The rumen and rectum MY-associated purine metabolites, guanosine and D-ribose-1-phosphate, mediated 65.56% and 67.55% of the significant positive effects of Acidaminococcaceae bacterium and Parabacteroides sp. on MY, respectively. Furthermore, the specific lipid metabolism-associated rumen microbiota module enhanced serum eicosapentaenoic acid (EPA) levels by modulating rumen &#x3b1;-linolenic acid metabolism, thereby promoting the synthesis of Pe(20:5/0:0) in milk, which positively contributed to MY.<br><br>CONCLUSIONS: This study revealed the potential contributions of the rumen and rectum microbiota to the productivity of long-lived dairy cows via purine metabolites, as well as the potential role of the rumen microbial network module in influencing productivity through &#x3b1;-linolenic acid metabolism, providing new insights for nutritional management strategies aimed at improving the persistent production capacity of dairy cows. Video Abstract.},
}
@article {pmid41514032,
year = {2026},
author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S},
title = {Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {39},
pmid = {41514032},
issn = {1432-184X},
support = {PAIDI-DOCTOR 21_00571//Junta de Andaluc&#xed;a/ ; FPU21/04133//Ministerio de Universidades/ ; FPU22/02078//Ministerio de Universidades/ ; PID2021-124750NB-I00//Ministerio de Ciencia e Innovaci&#xf3;n/ ; },
mesh = {*Plant Leaves/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; *Salt-Tolerant Plants/microbiology ; Soil Microbiology ; Plant Roots/microbiology ; Metagenome ; },
abstract = {Hydro- and xerohalophytes withstand stress thanks to the resistance traits they have, complemented with the functions of their associated microbiota. Besides, given a higher exposition of the phyllosphere to environmental conditions compared to roots, their endospheric bacteria should be more resistant to stress. In this study, we analysed the composition and functional traits of the bacterial leaf endosphere of six xero- and hydrohalophytes species in two seasons. We sequenced their endospheric metagenomes by shotgun and annotated genes related with Plant-Growth-Promoting (PGP) properties. We showed that the composition, structure and functions of the bacterial endosphere are mainly influenced by host plant species, followed by functional type. Moreover, plant species and functional type promoted a different relative abundance of, respectively, 62 and 6 PGP properties. This study shows that not only the composition but also the functionality of the bacterial leaf endosphere of halophytes is more influenced by host species than functional type. Moreover, the leaf endosphere of the different plant species and functional type could be an important source of bacteria with diverse PGP properties.},
}
@article {pmid41512763,
year = {2026},
author = {Liu, X and Li, J and Ma, C},
title = {Sublethal aflatoxin B1 exposure triggers multidimensional damage in honeybee (Apis mellifera) midgut: Integrative evidence from histomorphology, transcriptomics, and metagenomics.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141076},
doi = {10.1016/j.jhazmat.2026.141076},
pmid = {41512763},
issn = {1873-3336},
mesh = {Animals ; *Aflatoxin B1/toxicity ; Bees/drug effects/microbiology/genetics ; Metagenomics ; Transcriptome/drug effects ; Gene Expression Profiling ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Aflatoxin B1 (AFB1), a highly carcinogenic mycotoxin produced by Aspergillus fungi, has been increasingly identified as a global contaminant in bee pollen. Chronic exposure of honeybees (Apis mellifera) to AFB1-contaminated pollen poses substantial threats to colony health, yet its toxicological impacts remain poorly characterized despite the critical ecological role of these pollinators. In this study, we employed a multidimensional approach to investigate the toxicological effects of sublethal AFB1 exposure on honeybee midgut by integrated morphological, transcriptomic, and metagenomic analyses. Histopathological examination revealed severe midgut epithelium damage, including nuclear disintegration and enhanced apoptosis. Transcriptomic profiling coupled with enzyme activity assays unveiled significant dysregulation in immune response and oxidative stress-related pathways. Furthermore, metagenomic sequencing indicated substantial midgut microbiota alterations, characterized by a pronounced reduction in microbial diversity and beneficial microbe levels. These findings elucidate sublethal AFB1-induced honeybee health deterioration at cellular, molecular, and microbial levels, advancing our understanding of mycotoxin impacts on pollinators.},
}
@article {pmid41512751,
year = {2026},
author = {Zhao, Z and Wei, Y and Pan, X and Zhang, G and Luo, M and Wang, Y and Yi, G and Lei, Y and Sun, G and Li, R},
title = {Fishing boats as underestimated vectors for the transmission of high-risk genetic elements in nearshore ecosystems.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {140812},
doi = {10.1016/j.jhazmat.2025.140812},
pmid = {41512751},
issn = {1873-3336},
mesh = {*Biofilms ; *Ecosystem ; Gene Transfer, Horizontal ; *Ships ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Virulence Factors/genetics ; Water Microbiology ; },
abstract = {Aquatic biofilms on anthropogenic surfaces have been increasingly recognized as key vectors for the cross-boundary transmission of microorganisms and genetic determinants between distinct ecosystems. Current research remains disproportionately centered on ballast water and large vessels, overlooking small fishing boats. This is despite the fact that these boats are common vectors moving between mariculture and nearshore zones, with hull biofilms that can form potential reservoirs for pathogenic and resistant bacteria. Here, we employ a range of genomics approaches to systematically evaluate how hull material (wood, iron, and foam) influences biofilm composition, function, and risk. The biofilm communities exhibit a high abundance of pioneer microorganisms, strong ecological competitiveness, and low metabolic overlap with native assemblages. Further analysis of antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) in biofilms, assembling 379 ARG-VF-MGE-carrying contigs into 50 metagenomic bins, highlighting a substantial potential for horizontal gene transfer (HGT) and pathogen dissemination mediated by fishing boats. Finally, considering their enhanced biofilm colonization potential and the abundance of high-risk genetic elements, iron-hulled boats are likely to serve as significant vectors for the dispersal of resistant and virulent microorganisms into sensitive coastal environments, thereby posing elevated ecological and health risks. Our findings underscore the critical role of hull material in shaping biofilm community assembly and function and identify fishing boats as a key vector for the dispersal of high-risk genetic elements in nearshore environments.},
}
@article {pmid41511111,
year = {2026},
author = {Chen, X and Chen, C and Lan, X and Zhang, X and Li, T and Zhang, P and Cheng, G and Zhou, W and Wang, Z and Xie, Y and Zeng, S and Zhou, W and Wang, M},
title = {Machine learning and causal inference applied to the gut metagenome-metabolome axis reveals a link between neonatal jaundice and autism spectrum disorder.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0140525},
pmid = {41511111},
issn = {2379-5077},
support = {82571963//National Natural Science Foundation of China/ ; 2025A1515012162, 2024A1515010590//Natural Science Foundation of Guangdong Province/ ; JCYJ20250604145739052 and JCYJ20240813144117023//Shenzhen Science and Technology Program/ ; Y2024001//Resear Initaion Fund of Longgang District Maternity &amp; Child Healthcare Hospital of Shenzhen City/ ; Postdoctoral fellow stationed in Shenzhen second batch in 2022//Shenzhen Municipal Human Resources and Social Security Bureau/ ; },
mesh = {Humans ; *Autism Spectrum Disorder/metabolism/etiology/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; *Machine Learning ; Female ; Infant, Newborn ; *Jaundice, Neonatal/complications/metabolism ; *Metabolome ; Feces/microbiology ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Bile Acids and Salts/metabolism ; Infant ; Child, Preschool ; },
abstract = {UNLABELLED: Neonatal jaundice (NJ) might increase the risk of autism spectrum disorder (ASD) in children. This study examined whether alterations in the gut microbiota could explain the link between NJ and ASD. We analyzed three cohorts: NJ cohort 1 comprised 68 neonates with NJ and 68 healthy controls (HCs); NJ cohort 2 included 56 infants with NJ and 14 HCs; and the ASD cohort consisted of 43 children with ASD and 31 typically developing children. Fecal samples were collected aseptically. We performed 16S rRNA sequencing (NJ cohort 1), liquid chromatography with tandem mass spectrometry metabolomics (NJ cohort 1 and ASD cohort), and shotgun metagenomics (NJ cohort 2 and ASD cohort). We characterized the gut DNA virome, quantified bile acid metabolism genes, and integrated multi-omics data using causal mediation and machine learning causal inference. Both NJ and ASD were associated with increased diversity of bile acid metabolism genes, suggesting biomarker potential. The gut DNA virome was also identified as a potential biomarker. Causal mediation analysis showed that the gut DNA virome influences bile acid metabolism genes in both conditions. Using machine learning-based causal modeling, we further found that gut human betaherpesviruses and human mastadenoviruses contribute to NJ and ASD, respectively, mediated by gut bile acid-metabolizing bacteria. These findings suggest that perturbations in the virome and bile acid-metabolizing bacteria may explain the link between NJ and ASD. Our results indicate that NJ and ASD are associated with bile acid metabolism alterations, which are also influenced by the gut DNA virome. Dysbiosis of the gut DNA virome and bile acid-metabolizing bacteria may mechanistically link NJ and ASD.<br><br>IMPORTANCE: Human epidemiological studies have established an association between perinatal pathogenic infections and autism spectrum disorder (ASD), and the gut microbiota plays an extremely important role in this relationship. Neonatal jaundice (NJ) may increase the risk of ASD in children. However, it remains unclear whether alterations in the gut microbiota affect the association between NJ and ASD. Both NJ and ASD are linked to altered gut bile acid metabolism and significantly elevated gene diversity among bile acid metabolism enzymes, and these relationships are influenced by the gut virome. Gut human betaherpesviruses and human mastadenoviruses influence the development of NJ and ASD, respectively, by influencing the abundance of gut bile acid-metabolizing microbes. Alterations of the gut virome and bile acid-metabolizing bacteria appear to explain the link between NJ and ASD. There is a lack of effective treatment options for ASD. We found that both NJ and ASD are linked to altered bile acid metabolism. Gaining a comprehensive understanding of the role of the bile acid-gut microbiota axis in the pathogenesis of NJ and ASD, as well as regulating this axis, may be crucial for developing novel preventive and therapeutic strategies for ASD.},
}
@article {pmid41511078,
year = {2026},
author = {Bowerman, KL and Soo, RM and Chaumeil, PA and Blyton, MDJ and Sørensen, M and Gunbilig, D and Malig, M and Islam, M and Zaugg, J and Wood, DLA and Liachko, I and Auch, B and Morrison, M and Krause, L and Lindberg Møller, B and Neilson, EHJ and Hugenholtz, P},
title = {A molecular inventory of the faecal microbiomes of 23 marsupial species.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41511078},
issn = {2057-5858},
support = {INV-044643/GATES/Gates Foundation/United States ; },
mesh = {*Feces/microbiology/virology ; Animals ; *Marsupialia/microbiology/virology/classification ; Phylogeny ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Viruses/genetics/classification ; },
abstract = {Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where, despite their iconic status, direct sequencing-based analyses remain limited. Here, we present a metagenomic and metabolomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80 %) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalypt folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages was observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals, likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes.},
}
@article {pmid41510663,
year = {2026},
author = {Gong, K and Wang, N and Chen, Y and Yu, J and Kuang, C and Xiong, X and Wan, R and Xing, F and Suzuki, M and Peng, L and Chun, C and Zuo, Y},
title = {Enhancing Iron Nutrition in Citrus: Synergistic Roles of Proline-2'-deoxymugineic Acid in Root Physiology and Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {2},
pages = {1998-2011},
doi = {10.1021/acs.jafc.5c09250},
pmid = {41510663},
issn = {1520-5118},
mesh = {*Citrus/metabolism/microbiology/growth &amp; development/physiology/genetics ; *Plant Roots/metabolism/microbiology/physiology/growth &amp; development ; Microbiota/drug effects ; *Iron/metabolism/analysis ; Rhizosphere ; Bacteria/genetics/isolation &amp; purification/classification/metabolism ; *Azetidinecarboxylic Acid/analogs &amp; derivatives/metabolism/pharmacology ; Soil Microbiology ; *Proline/analogs &amp; derivatives/metabolism/pharmacology ; Fertilizers/analysis ; },
abstract = {Iron (Fe) deficiency severely impairs plant growth and development in calcareous soils. Proline-2'-deoxymugineic acid (PDMA), a phytosiderophore analog that enhances Fe availability, alleviates Fe deficiency in field and vegetable crops but remains untested in perennial woody crops. Herein, we conducted pot and field trials on citrus, integrating physiological assays, RNA sequencing, 16S rRNA profiling, and metagenomics to evaluate PDMA/PDMA-Fe(III) effects on Fe nutrition, yield, root gene expression, and rhizosphere microbial dynamics. Results showed that PDMA/PDMA-Fe(III) significantly improved citrus Fe nutrition-outperforming traditional EDTA-Fe(III)- by increasing rhizosphere Fe availability, thereby increasing yield and downregulating Fe uptake- and stress response-related genes,with PDMA-Fe(III) had stronger suppression. PDMA-Fe(III) minimally disrupted the rhizosphere microbiome, while PDMA recruited plant growth-promoting rhizobacteria (e.g., Pseudomonas, Nitrospira); both treatments enriched microbial carbon fixation pathways. Collectively, PDMA/PDMA-Fe(III) represent eco-efficient Fe fertilizers for citrus orchards, providing sustainable remediation of Fe deficiency in calcareous soils.},
}
@article {pmid41508741,
year = {2026},
author = {Zhao, Y and Feng, M and Chi, H and Liu, K and Wen, R and Zhang, W and Liu, P},
title = {Diversity, Function and Activity of DNA Viruses in the Qiangyong Proglacial Lake Sediment, the Tibetan Plateau.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70262},
pmid = {41508741},
issn = {1758-2229},
support = {24YFFA006//Key Research and Development Program of Gansu Province/ ; XZ202301ZY0008G//Key Research and Development Plan of Tibet Autonomous Region/ ; 42222105//National Natural Science Foundation of China for Excellent Young Scientists Fund Program/ ; 42171144//National Natural Science Foundation of China General Program/ ; 42201056//Young Scientists Fund of the National Natural Science Foundation of China/ ; //Global Ocean Negative Carbon Emissions (ONCE) Program/ ; },
mesh = {*Lakes/virology ; *DNA Viruses/genetics/classification/isolation &amp; purification ; *Geologic Sediments/virology ; Tibet ; Metagenomics ; Phylogeny ; *Biodiversity ; Metagenome ; },
abstract = {Viruses are the most abundant biological entities on Earth and play crucial roles in regulating ecosystem processes and biogeochemical cycling. Proglacial lakes-key components of cryosphere aquatic systems-host diverse microbial communities despite extreme environmental conditions. However, the composition and ecological roles of DNA viral communities in proglacial lake sediments remain poorly understood. In this study, we applied metagenomic and metatranscriptomic approaches to investigate the diversity, function, activity and host interactions of DNA viruses in sediments from Qiangyong proglacial lake on the Tibetan Plateau. We recovered 4039 viral operational taxonomic units (vOTUs), with 76.6% unclassified at the family level, highlighting a vast reservoir of uncharacterized viral lineages. Host prediction linked 1.8% of vOTUs to key microbial taxa involved in carbon, nitrogen and sulphur cycling. We identified a broad array of virus-encoded auxiliary metabolic genes (AMGs) involved in host resource utilization and metabolic transformation. Moreover, 63 AMGs not previously reported in the literature were discovered, significantly expanding the known viral functional gene repertoire. These findings offer new insights into the diversity and ecological potential of sediment-associated DNA viruses in proglacial lakes, and emphasize their possible roles in shaping microbial communities and influencing biogeochemical processes in cold-region ecosystems.},
}
@article {pmid41508656,
year = {2026},
author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL},
title = {Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian Breakthrough Cancer Study.},
journal = {Cancer research communications},
volume = {6},
number = {1},
pages = {70-76},
pmid = {41508656},
issn = {2767-9764},
support = {//Cancer Council Victoria/ ; //Gandel Foundation/ ; //Perpetual (Perpetual Ltd)/ ; //State Trustees Australia Foundation (STAF)/ ; //Winifred and John Webster Charitable Trust Fund/ ; //Pf - Alan (AGL)/ ; //Shaw Family Foundation (SFF)/ ; //Broomhead Family Foundation/ ; },
mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Prospective Studies ; Male ; Female ; *Specimen Handling/methods ; Middle Aged ; Australia ; Aged ; Occult Blood ; Adult ; *Neoplasms/microbiology ; Surveys and Questionnaires ; Metagenomics/methods ; },
abstract = {UNLABELLED: Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home fecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomized into four groups defined by fecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted-in, and of those, 88% returned a sample. Of those asked to provide a fecal sample via fecal occult blood test (FOBT) card and complete a short "day-of-sample" questionnaire, 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole-genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home fecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.<br><br>SIGNIFICANCE: The expansion of this successful pilot to the larger Australian Breakthrough Cancer Study will facilitate future metagenomic and other host- and microbiome-related analyses in this large prospective cohort and potentially as part of an extended international pooling project.},
}
@article {pmid41507798,
year = {2026},
author = {Zhao, J and Cai, W and Zhang, X and Fang, H and Zhuge, J and Zhang, L and Wang, J and Sun, L and Hua, Z and Fu, J},
title = {Exploring lung microbiota and clinical application of BALF-mNGS in patients with pulmonary mycobacterial diseases: a multicenter retrospective study.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {130},
pmid = {41507798},
issn = {1471-2180},
support = {2020ZZ002,2021ZZ003//Project of Zhejiang Administration of Traditional Chinese Medicine/ ; LZ22H150001//Natural Science Foundation of Zhejiang Province/ ; 82072161//National Natural Science Foundation of China/ ; 2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; },
mesh = {Humans ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Lung/microbiology ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; Nontuberculous Mycobacteria/genetics/isolation &amp; purification ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Adult ; },
abstract = {BACKGROUND: Pulmonary mycobacterial diseases (PMDs) remain a leading cause of infectious disease-related mortality worldwide, with the majority of cases attributed to the Mycobacterium tuberculosis complex (MTBC). However, non-tuberculous mycobacteria (NTM) can also cause PMDs, and the incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has been increasing in recent years.<br><br>OBJECTIVES: This study aimed to explore the lung microbiota and assess the clinical application of bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) in patients with PMDs caused by MTBC or NTM.<br><br>METHODS: This multicenter, retrospective study included patients with suspected PMDs between July 2021 to June 2025. mNGS and conventional diagnostic methods (CDTs), including GeneXpert, BALF culture, acid-fast bacillus (AFB) staining, and T-SPOT, were performed. Based on the microbiological diagnosis, patients were classified into TB and NTM-PD groups. We further analyzed the clinical impact of different MTBC/NTM abundance levels. The relative abundance of MTBC/NTM was represented by reads ten per million (RTPM). Patient clinical characteristics, length of hospital stay (LOHS), laboratory results, and treatment effectiveness were collected from the electronic medical record system.<br><br>RESULTS: Compared with the TB group, patients with NTM-PD exhibited a higher prevalence of immunosuppression (34.96% vs. 53.85%, P = 0.013), particularly prolonged corticosteroid or immunosuppressant therapy (8.94% vs. 21.54%, P = 0.016). In the TB group, higher MTBC abundance was associated with increased positivity of CDTs and alterations in pulmonary microbiota, including enrichment of Candida albicans and other opportunistic pathogens. In the NTM-PD group, although CDTs positivity did not significantly differ between high- and low-abundance subgroups (21.21% vs. 20.00%, P = 0.906), higher NTM abundance was linked to distinct microbial community patterns and a markedly higher ineffective treatment rate (66.67% vs. 39.39%, P = 0.043). Notably, in both TB and NTM-PD groups, elevated MTBC or NTM abundance was associated with longer hospital stays and lower treatment effectiveness, indicating that pathogen abundance is significantly associated with clinical outcomes in pulmonary mycobacterial diseases.<br><br>CONCLUSION: BALF-mNGS not only provides superior pathogen detection in patients with PMDs but also shows that lower MTBC/NTM abundance is associated with better clinical prognosis, including shorter hospital stay and better treatment effectiveness, highlighting its potential role as a prognostic indicator.},
}
@article {pmid41507780,
year = {2026},
author = {Gaonkar, PP and Santana-Pereira, ALR and Golden, R and Lambert, A and Higgins, C and Adhikari, Y and Bailey, M and Macklin, K and Huber, L},
title = {Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {126},
pmid = {41507780},
issn = {1471-2180},
support = {G00017930//United States Department of Agriculture (USDA)/ ; Intramural funding//Alabama Agricultural Experiment Station/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Microbiota/drug effects/genetics ; *Bacteria/drug effects/genetics/classification/isolation &amp; purification ; Animal Husbandry/methods ; *Anti-Bacterial Agents/pharmacology ; Farms ; *Drug Resistance, Bacterial ; Soil Microbiology ; Poultry Diseases/microbiology ; *Anti-Infective Agents/pharmacology ; },
abstract = {BACKGROUND: Antimicrobial use (AMU) in poultry production is central to curb the Antimicrobial Resistance (AMR) crisis. Institutional and market pressure led many commercial poultry operations to practice distinct levels of AMU restriction. On-farm data remains one of the main bottlenecks in understanding the impacts of AMU restriction at the farm level and across production systems. However, AMR dynamics in company-wide production chains remain largely unexplored, precluding improvement of AMU policies and stewardship.<br><br>STUDY AIM: Here, we shotgun sequenced soil and litter samples from 26 poultry farms and carcass rinses from a processing plant to reconstruct the microbiome and resistome of two vertically integrated commercial poultry operations to explore their dynamics under AMU restriction.<br><br>RESULTS: Shotgun sequencing revealed that litter microbiome and resistome changed significantly by production stage and company, reflecting management practices and possible effects of historical AMU. Meanwhile, broiler farms had increased detection of potential pathogens and AMR diversity. We found no evidence of farm-to-fork transmission. Effective biosecurity protocols largely maintained the separation between the internal and external environments of the poultry houses, except on two farms where breaches might have led to external spread of pathogens and AMR.<br><br>CONCLUSION: Our study highlights that AMR in commercial poultry system reflects the combined effect of production-stage, company practices, and environmental boundaries. Future studies should integrate quantitative AMR data and culture-based techniques with metagenomic findings to strengthen tracking and surveillance of AMR in poultry farm environments.},
}
@article {pmid41507585,
year = {2026},
author = {Hsu, CL and Shukla, S and Freund, L and Chou, AC and Yang, Y and Bruellman, R and Raya Tonetti, F and Cabré, N and Mayo, S and Lim, HG and Magallan, V and Cordell, BJ and Lang, S and Demir, M and Stärkel, P and Llorente, C and Palsson, BO and Mandyam, C and Boland, BS and Hohmann, E and Schnabl, B},
title = {Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.},
journal = {Nature microbiology},
volume = {11},
number = {2},
pages = {415-428},
pmid = {41507585},
issn = {2058-5276},
support = {BX004594//Biomedical Laboratory Research and Development, VA Office of Research and Development (VA Biomedical Laboratory Research and Development)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; K99 AA031328/AA/NIAAA NIH HHS/United States ; R01 AA029106, R21 AA030654, P30 AR073761//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; K99 AA031328/AA/NIAAA NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Feces/microbiology/chemistry ; *Ethanol/metabolism ; Male ; Female ; Middle Aged ; Adult ; Cohort Studies ; Metagenomics ; Fecal Microbiota Transplantation ; Escherichia coli/metabolism/genetics ; Fermentation ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Proteobacteria/metabolism/genetics/isolation &amp; purification ; Anti-Bacterial Agents/therapeutic use ; *Alcoholic Intoxication/microbiology ; Klebsiella pneumoniae/metabolism/genetics ; Metabolomics ; Metabolic Networks and Pathways/genetics ; },
abstract = {Auto-brewery syndrome (ABS) is a rarely diagnosed disorder of alcohol intoxication due to gut microbial ethanol production. Despite case reports and a small cohort study, the microbiological profiles of patients remain poorly understood. Here we conducted an observational study of 22 patients with ABS and 21 unaffected household partners. Faecal samples from individuals with ABS during a flare produced more ethanol in vitro, which could be reduced by antibiotic treatment. Gut microbiome analysis using metagenomics revealed an enrichment of Proteobacteria, including Escherichia coli and Klebsiella pneumoniae. Genes in metabolic pathways associated with ethanol production were enriched, including the mixed-acid fermentation pathway, heterolactic fermentation pathway and ethanolamine utilization pathway. Faecal metabolomics revealed increased acetate levels associated with ABS, which correlated with blood alcohol concentrations. Finally, one patient was treated with faecal microbiota transplantation, with positive correlations between gut microbiota composition and function, and symptoms. These findings can inform future clinical interventions for ABS.},
}
@article {pmid41506577,
year = {2026},
author = {Sagar, K and Priti, K and Chandra, H},
title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.},
journal = {Journal of microbiological methods},
volume = {241},
number = {},
pages = {107390},
doi = {10.1016/j.mimet.2026.107390},
pmid = {41506577},
issn = {1872-8359},
mesh = {*Artificial Intelligence ; *Metagenome/genetics ; *Metagenomics/methods ; Microbiota/genetics ; Computational Biology/methods ; Machine Learning ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.},
}
@article {pmid41506424,
year = {2026},
author = {Shi, R and Han, T and Zhang, H and Huang, H and Xiong, L and Liu, Y and Qi, Z},
title = {Response of sediment microbial community composition and function to mangrove restoration from an aquaculture pond in Southern China.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123718},
doi = {10.1016/j.envres.2026.123718},
pmid = {41506424},
issn = {1096-0953},
mesh = {*Geologic Sediments/microbiology ; China ; Aquaculture ; *Wetlands ; *Microbiota ; Ponds/microbiology ; Bacteria/classification ; *Environmental Restoration and Remediation ; },
abstract = {Mangrove ecosystems, as highly sensitive and productive habitats, host diverse microbial communities essential to biogeochemical cycling. In recent years, large-scale mangrove restoration in former aquaculture ponds has expanded rapidly in China. This represents a typical land-use shift that likely reshapes microbial communities. However, despite its increasing implementation, the accompanying changes in microbial composition and function remain insufficiently understood. Therefore, we compared sediment microbial community composition, diversity, and functional potential between mangrove-planted and reference areas. By absolute-quantification sequencing and metagenomics, we aimed to assess how mangrove restoration regulates the microbial dynamics and their metabolic potentials for carbon, sulfur, and nitrogen cycling after two years of restoration. Mangrove restoration induced a marked phylum shift from Chloroflexota to Pseudomonadota and significantly increased microbial β-diversity (p < 0.05), reflecting enhanced phylogenetic niche differentiation. Specialist species in restored sediments were predominantly Pseudomonadota (e.g., Gammaproteobacteria), contrasting with the Chloroflexota- and Actinobacteriota-dominated reference sites. Functional analysis revealed significant up-regulation of genes involved in polysaccharide metabolism (celB/chbC, sacB, treC, fruB; p < 0.05), assimilatory sulfate reduction, sulfur oxidation (soxZ; p < 0.05), nitrogen fixation (nifH; p < 0.05), and assimilatory nitrate reduction. Furthermore, most high-abundance metagenome-assembled genomes (MAGs) from mangrove sediments encoded sulfate reduction genes. Notably, microbial carbon cycling potential correlated with particulate organic nitrogen, while nitrate concentration linked to nitrogen and sulfur cycling genes, highlighting cross-element synergies. These findings demonstrated that two years of mangrove restoration alters sediment microbiomes and their biogeochemical functions potential, thereby may influence carbon sequestration and nutrient cycling in coastal ecosystems.},
}
@article {pmid41505640,
year = {2026},
author = {Du, S and He, L and Sun, L and Shi, X and Xiao, Y and Jia, Y and Ge, G},
title = {Strategy Development for Improving Ensiling Performance of Ceratoides arborescens (Krascheninnikovia arborescens (Losinsk.) Czerep.) Silage Based on Integrated Omics.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {2},
pages = {2438-2451},
pmid = {41505640},
issn = {1520-5118},
mesh = {*Silage/analysis/microbiology ; Fermentation ; Animals ; Rumen/metabolism/microbiology ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Lactiplantibacillus plantarum/metabolism ; Animal Feed/analysis ; Digestion ; Gastrointestinal Microbiome ; },
abstract = {This study investigated the effects of Lactiplantibacillus plantarum (L. plantarum) on the constituent characteristics, in vitro ruminal fermentation properties, bacterial community structure, metagenome profiles, and metabolite compositions of Ceratoides arborescens silage. Fourier transform infrared spectroscopy analysis demonstrated that L. plantarum inoculation significantly altered the chemical composition, fermentation quality, and in vitro digestibility of the silage. The fermentation process was predominantly driven by Lentilactobacillus and Lactiplantibacillus. Metagenomic profiling and metabolic analyses revealed functional shifts and metabolic alterations, with significant differences observed in the absolute abundance of the carbohydrate-active enzymes. In conclusion, L. plantarum fermentation improved the nutritional value and fermentation properties of Ceratoides arborescens silage by modulating the bacterial community structure, functional gene expression, and metabolic activity. These findings provide mechanistic insights into the beneficial effects of L. plantarum during silage fermentation and offer potential strategies for enhancing the silage quality and ruminal fermentation efficiency.},
}
@article {pmid41505541,
year = {2026},
author = {Leung, PM and Jeffrey, LC and Bay, SK and Gomez-Alvarez, P and Hall, M and Johnston, SG and Dittmann, J and Deschaseaux, E and Hopkins, B and Haskell, J and Jirapanjawat, T and Hutchinson, TF and Coleman, NV and Dong, X and Maher, DT and Greening, C},
title = {Bark microbiota modulate climate-active gas fluxes in Australian forests.},
journal = {Science (New York, N.Y.)},
volume = {391},
number = {6781},
pages = {eadu2182},
doi = {10.1126/science.adu2182},
pmid = {41505541},
issn = {1095-9203},
mesh = {*Methane/metabolism ; *Plant Bark/microbiology ; Australia ; *Microbiota ; *Forests ; *Hydrogen/metabolism ; Carbon Monoxide/metabolism ; Metagenomics ; *Trees/microbiology ; *Bacteria/metabolism/genetics/classification ; Anaerobiosis ; },
abstract = {Recent studies suggest that microbes inhabit tree bark, yet little is known about their identities, functions, and environmental roles. Here we reveal, through gene-centric and genome-resolved metagenomics, that the bark of eight common Australian tree species hosts abundant and specialized microbial communities. The predominant bacteria are hydrogen-cycling facultative anaerobes adapted to dynamic redox and substrate conditions. Furthermore, bark-associated methanotrophs are abundant and can coexist with hydrogenotrophic methanogens. Microcosm experiments showed that bark microorganisms aerobically consume methane, hydrogen, and carbon monoxide at in planta concentrations and produce these gases under anoxia. Combined with in situ field measurements, we show that tree-dwelling microbiota metabolize multiple climate-active gases at marked rates within tree stems, highlighting a potentially substantial role in global atmospheric cycles.},
}
@article {pmid41504449,
year = {2026},
author = {Xu, J and Ma, J and Lin, H and Yan, S and Niu, H},
title = {Metagenomic and metabolomic analyses of rumen fiber digestion in Mongolian cattle fed fresh grass versus hay.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0305125},
pmid = {41504449},
issn = {2165-0497},
support = {32460813//National Natural Science Foundation of China/ ; 2022MS03074, 2025MS03005, 2023YFDZ0079, 2023YFDZ0068, 2025YFDZ0123//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; NJYT22054//Education Department of Inner Mongolia Autonomous Region/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle/microbiology ; *Animal Feed/analysis ; *Poaceae/metabolism ; Fermentation ; Metagenomics ; *Dietary Fiber/metabolism ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Gastrointestinal Microbiome ; Female ; Metabolomics ; Mongolia ; Digestion ; Fungi/classification/genetics/metabolism/isolation &amp; purification ; Metagenome ; },
abstract = {Mongolian cattle exhibit exceptional roughage tolerance due to their rumen microbiome's robust fiber-degrading capacity, enabling efficient utilization of low-quality forage under the Mongolian Plateau's seasonal fluctuations. This study compared rumen microbial composition, CAZyme profiles, fermentation parameters, and metabolic pathways in cattle fed fresh grass (FG) versus hay to elucidate microbe-metabolite interactions underlying fiber digestion. Thirty non-pregnant female Mongolian cattle (460 ± 35 kg, 3-4 years old) were randomly divided into two groups (n = 15/group): one grazed on FG, the other housed and fed autumn-harvested hay (HG). Six animals per group were subsampled for rumen fluid collection and multi-omics analyses (n = 6/group, total n = 12). Compared with the FG group, the HG group showed an increased molar proportion of acetate and a higher acetate-to-propionate ratio, along with reduced molar proportions of propionate and butyrate in rumen fermentation parameters. Metagenomic analysis revealed a higher abundance of Bacteroidalesbacteria and anaerobic fungi (including Neocallimastix sp.JGI-2020a and Piromyces sp.E2) in the HG group. Functional annotation further indicated enriched carbohydrate metabolism pathways in the HG group, along with a greater diversity of CAZymes, particularly those involved in hemicellulose and pectin degradation. Metabolomics identified 13 differentially abundant carbohydrate metabolites, with gluconolactone upregulated in the HG group. Additionally, carbohydrate metabolism pathways identified in the metabolome corroborated the reliability of the metagenomic functional annotations. Correlation network analysis revealed positive associations of Bacteroidaceaebacteria, Neocallimastix sp.JGI-2020a, and Piromyces sp.E2 with acetate, hemicellulose-degrading GHs, and carbohydrate metabolic pathways. In conclusion, hay feeding enhanced ruminal fiber degradation in Mongolian cattle through increased Bacteroidales and anaerobic fungi, diversified CAZymes (especially hemicellulases/pectinases), and upregulated carbohydrate metabolism, reflecting microbial adaptation to low-quality forage.IMPORTANCEMongolian cattle's superior roughage tolerance depends on a specialized rumen microbiome that degrades fibrous substrates via diverse CAZymes. However, microbe-metabolite interactions driving fiber digestion in this breed remain poorly understood. This study revealed an increased abundance of bacteria and fungi involved in rumen fiber degradation, which may be responsible for secreting enzymes associated with hemicellulose and pectin breakdown. Furthermore, the upregulation of key metabolites, including gluconolactone, indirectly promotes acetate production through pathways such as glycolysis and the pentose phosphate pathway. These findings reveal microbial adaptations enhancing low-quality forage utilization, offering new strategies for improving ruminant efficiency in seasonal or resource-limited grazing systems.},
}
@article {pmid41504158,
year = {2025},
author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F},
title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {6},
pages = {42590},
doi = {10.31083/IJVNR42590},
pmid = {41504158},
issn = {0300-9831},
support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Hyperuricemia/microbiology ; Male ; Female ; *Overweight/microbiology ; Middle Aged ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).<br><br>METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.<br><br>RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced &#x3b1;-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.<br><br>CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.},
}
@article {pmid41503791,
year = {2026},
author = {Jin, J and Yao, G and Zhang, X and Zhang, T and Ye, H and Zhou, X and Yu, Y and Zhao, Y and Qin, Z and Chen, H and Bi, Y and Wang, X and Ren, X and Zhang, Y and Wang, Z and Zhang, Q},
title = {Gut virome dysbiosis contributes to premature ovarian insufficiency by modulating gut bacteriome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611645},
pmid = {41503791},
issn = {1949-0984},
mesh = {Female ; Animals ; *Dysbiosis/microbiology/virology ; *Primary Ovarian Insufficiency/microbiology/virology/therapy ; *Gastrointestinal Microbiome ; Rats ; Humans ; Adult ; *Virome ; Fecal Microbiota Transplantation ; *Bacteria/genetics/classification/isolation &amp; purification/virology ; Young Adult ; Feces/virology ; Ovary ; Rats, Sprague-Dawley ; },
abstract = {BACKGROUND: Premature ovarian insufficiency (POI) significantly impairs female fertility and poses substantial health risks; however, its pathogenesis is incompletely understood, and effective therapeutic interventions are limited. Although gut bacteriome has been closely associated with ovarian dysfunction, the role and therapeutic potential of gut viruses, which far outnumber bacteria, remain largely unexplored.<br><br>RESULTS: Therefore, we recruited 60 healthy reproductive-aged women and recently diagnosed POI patients and investigated these concerns using various techniques, including whole-genome shotgun sequencing of virus-like particle (VLP) and fecal virome transplantation (FVT) in CTX-induced POI rats. We found considerable interindividual variability in the gut virome. The virome of POI patients exhibited significant dysbiosis, characterized by a marked reduction in virulent phage, significant changes in predominant phages, and a notable increase in horizontal gene transfer of resistance genes and virulence factors. Furthermore, gut VLPs from the healthy reproductive-aged women significantly improved the condition of POI rats. Conversely, gut VLPs from POI patients markedly impaired the ovarian function and reproductive capacity of healthy rats. The above regulatory effect is primarily due to modulations of gut bacteriome, specifically the estrobolome, and intestinal barrier integrity, which subsequently affect hypothalamic-pituitary-ovarian axis hormone levels and regulate ovarian oxidative stress and inflammation, thereby influencing ovarian function.<br><br>CONCLUSIONS: Our findings demonstrate the critical roles of the gut virome in regulating ovarian function and provide new insights into the pathogenesis of POI. This study also underscores the therapeutic potential of the gut virome in improving ovarian dysfunction and female infertility including POI.},
}
@article {pmid41502197,
year = {2025},
author = {Hasan, I},
title = {Short-Chain Fatty Acids in the Gut-Brain-Liver Axis: Implications for Hepatic Encephalopathy.},
journal = {Acta medica Indonesiana},
volume = {57},
number = {4},
pages = {433-435},
pmid = {41502197},
issn = {2338-2732},
mesh = {Humans ; *Hepatic Encephalopathy/metabolism/etiology/epidemiology/microbiology ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; *Liver Cirrhosis/complications ; Indonesia/epidemiology ; *Liver/metabolism ; *Brain/metabolism ; Cross-Sectional Studies ; Feces/chemistry ; },
abstract = {Hepatic encephalopathy (HE) is one of the serious complications of liver cirrhosis, characterized by a broad spectrum of neuropsychiatric symptoms, ranging from subtle cognitive impairment to coma, due to brain dysfunction associated with acute or chronic liver failure and/or portosystemic shunting. Globally, the prevalence of hepatic encephalopathy (HE) is reported to range from 20% to 80% in patients with liver cirrhosis, depending on whether the assessment includes minimal (MHE) or overt (OHE) forms. In Indonesia, determining the true prevalence of HE is challenging due to diagnostic difficulties, with estimates ranging from 30% to 84%. At Cipto Mangunkusumo General Hospital, the prevalence of HE in 2009 was 63.2%. In recent years, evidence has highlighted the role of the gut microbiota in the pathogenesis of hepatic encephalopathy (HE), a concept now widely referred to as the "gut-liver-brain axis." Short-chain fatty acids (SCFAs) are gut microbial-derived metabolites that provide numerous health benefits. SCFA has been demonstrated to impact gut barrier function, immunomodulation, and glucose homeostasis. In this issue, Ferdianto et al. conducted a cross-sectional observational study comparing the amount and composition of fecal SCFA in cirrhotic patients with and without HE. The study revealed no significant difference in SFA levels between HE and non-HE groups; however, the HE groups demonstrated higher levels of total SCFA, acetate, and butyrate compared to the non-HE groups. While this study contributes valuable early evidence from an Indonesian cohort, several important limitations should be acknowledged. First, the diagnostic approach for covert or minimal HE requires clarification. The authors did not explicitly state the neuropsychological tools and specific criteria used. Clear definitions are essential, as minimal and covert HE is susceptible to the choice of diagnostic method and can substantially influence group classification. Second, although SCFAs represent key microbial metabolites, the study did not explore the underlying microbiome composition. Without bacterial taxonomy or species-level data, it remains difficult to determine whether differences in SCFA levels truly reflect gut dysbiosis or altered microbial diversity. SCFA concentrations may be influenced by multiple factors, and therefore, inclusion of metagenomic or sequencing data would strengthen the mechanistic interpretation and allow linking specific bacterial taxa with cognitive impairment. Future studies that include larger and more heterogeneous cohorts, alongside integrated analyses of microbiome composition and validated neurocognitive testing, will be crucial to validate the role of SCFAs in HE development.},
}
@article {pmid41502165,
year = {2026},
author = {Keller, LM and Colman, DR and Stefánsson, A and Boyd, ES},
title = {Cross-Feeding of Carbon and Nitrogen Between Aquificales and Thermus in Hot Springs.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70225},
pmid = {41502165},
issn = {1462-2920},
support = {80NSSC19M0150/NASA/NASA/United States ; MSU D19//W. M. Keck Foundation/ ; },
mesh = {*Hot Springs/microbiology ; *Thermus/metabolism/growth &amp; development/genetics ; *Nitrogen/metabolism ; *Carbon/metabolism ; Iceland ; Nitrogen Fixation ; Carbon Dioxide/metabolism ; Metagenomics ; },
abstract = {Acquisition and cycling of carbon and nitrogen among members of hot spring communities are not well understood. Metagenomic analyses of 105 communities inhabiting high temperature hot springs across Yellowstone and Iceland showed a co-distribution pattern of putatively autotrophic and/or diazotrophic (nitrogen-fixing) Aquificales and Thermus populations. Targeted enrichment of autotrophic and diazotrophic populations in an Icelandic hot spring produced a co-culture of Pampinifervens (Aquificales) that encoded carbon dioxide and nitrogen fixation pathways and Thermus (Thermales). Growth experiments revealed Pampinifervens could support the fixed carbon and nitrogen demands of Thermus, enabling growth. Interestingly, growth of Thermus was enhanced in co-cultures when Pampinifervens was forced to fix both carbon and nitrogen versus just carbon (ammonia-amended cultures). Further experimentation with Thermus, when grown in isolation, showed it preferred amino acids over ammonia as a nitrogen source. These findings demonstrate the importance of metabolic interactions among populations that can dictate the co-distribution of taxa in hot springs, drive community assembly, and maintain biodiversity. Further, these results highlight the fundamental role of Aquificales in the functioning of hot spring ecosystems, particularly those limited in organic carbon and fixed nitrogen like those in Iceland and to a lesser extent Yellowstone.},
}
@article {pmid41502126,
year = {2026},
author = {Gutierrez, F and Vargas, S and Machado-Perez, F and Wilson, J and García-Maldonado, JQ and Beman, JM},
title = {Microbial Community Metagenomics in the Eastern Tropical North Pacific Oxygen Minimum Zone Reveals Functional Differences Along Biogeochemical Gradients.},
journal = {Environmental microbiology},
volume = {28},
number = {1},
pages = {e70226},
doi = {10.1111/1462-2920.70226},
pmid = {41502126},
issn = {1462-2920},
support = {OCE-1555375//National Science Foundation/ ; //University of California Alianza MX/ ; },
mesh = {*Oxygen/metabolism/analysis ; *Seawater/microbiology/chemistry ; *Metagenomics ; Pacific Ocean ; *Microbiota/genetics ; *Metagenome ; Photosynthesis/genetics ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Chlorophyll/metabolism ; Nitrites/metabolism ; },
abstract = {Oxygen Minimum Zones (OMZs) are pivotal ocean regions defined by low dissolved oxygen concentrations [DO]. However, biogeochemical variations within OMZs-both laterally and with depth-may select for fundamentally different microbial metabolisms important for ocean biogeochemistry. We used metagenome sequencing to investigate potential differences by specifically targeting biogeochemically-important features-including the primary and secondary nitrite maxima (PNM and SNM), the secondary chlorophyll maximum (SCM), and the upper edge of the OMZ (defined by 20 μM [DO]). Read-based analysis identified variations in 5389 functional genes but high similarity among SCM and SNM metagenomes at multiple stations. 690 genes showed significant differences between different features and included key functional genes involved in photosynthesis elevated in the PNM, while carbon fixation, anaerobic nitrogen cycling, and organic sulphur cycling genes increased in the SCM and SNM. Metagenome assembled genomes from a distinct upper OMZ edge sample included multiple Flavobacteriaceae and Rhodobacteraceae, with annotated functions contributing to metabolism of carbohydrates and amino acids, as well as aerobic anoxygenic photosynthesis (in Rhodobacteraceae). Our results identify functional genes and metabolic pathways that are enriched in unique SCM and SNM features, while also demonstrating sharp shifts in functional capacity in the overlying upper water column, within the ocean's largest OMZ.},
}
@article {pmid41501865,
year = {2026},
author = {Sun, J and Meng, Y and Chen, Z and Zhao, T and Yang, C and Chen, S and Wang, J and Tian, L and Song, F and Duan, Y and Cai, W and Zhang, X and Li, H},
title = {Gut microbiome convergence and functional adaptation underlie the evolution of predation in stink bugs (Heteroptera: Pentatomidae).},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {56},
pmid = {41501865},
issn = {2049-2618},
support = {31730086//National Natural Science Foundation of China/ ; 110202101046[LS-06]//Pests and Diseases Green Prevention and Control Major Special Project/ ; xinkywdzc-2025001-91//Project of Fund for Stable Support to Agricultural Sci-Tech Renovation/ ; },
mesh = {Animals ; *Heteroptera/microbiology/physiology ; *Gastrointestinal Microbiome ; *Predatory Behavior ; Biological Evolution ; Bacteria/classification/genetics/isolation &amp; purification ; Phylogeny ; Symbiosis ; Adaptation, Physiological ; Feeding Behavior ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: True bugs (Heteroptera) have undergone repeated evolutionary shifts between phytophagous and carnivorous feeding strategies. Although gut microbiomes are recognized for aiding dietary adaptation, their function in mediating these transitions is still unclear, specifically, how microbial communities change during dietary evolution and influence the diversification of feeding traits.<br><br>RESULTS: Here, we selected a stink bug lineage of the subfamily Asopinae (Pentatomidae), representative of an independent feeding trait transition from phytophagy to carnivory. Their gut microbiomes were analyzed and compared to those of closely related phytophagous species within the Pentatomidae family, as well as predatory assassin bugs from the Reduviidae family, which represent the ancestral heteropteran feeding trait of predation. It was found that Asopinae lack the gammaproteobacterial&#xa0;symbionts and midgut crypts that are conserved in their phytophagous counterparts. Instead, their gut microbiomes converged on a community dominated by Enterococcus (Firmicutes) and select Proteobacteria (Serratia, Yokenella, Proteus), mirroring the microbiome of assassin bugs. This core community persisted despite prey variation, likely maintained through pentatomid ancestral eggshell-piercing behavior, enabling vertical transmission. Metagenomic analysis linked the Asopinae microbiome to functions potentially associated with predation adaptation, including the digestion of chitinous substrates likely sourced from prey's internal body. Through bacterial isolation, genomics, and functional assays, we demonstrated that Serratia mediates chitin degradation, which along with a potential coordination in diet digestion, may also have been involved in an antifungal effect. Meanwhile, an Enterococcus strain exhibits inhibition to multiple pathogens such that may provide protections to the host, potentially via a class III lanthipeptide.<br><br>CONCLUSIONS: Our findings reveal a coordinated restructuring of the gut microbiome during dietary shifts. The convergence of Asopinae and Reduviidae microbiomes underscores how microbial communities may have facilitated the ecological adaptation, likely by enabling hosts to exploit new dietary niches and providing defense against bacterial and fungal pathogens. Video Abstract.},
}
@article {pmid41501250,
year = {2026},
author = {Liu, C and Xing, Y and Su, J and Liu, Y and Dou, Y and Wang, Z and Sha, S and Yan, Q and Xu, M and Zhao, L and Tian, Y and Xing, G and Li, S and Kang, J and Kong, X},
title = {Multi-kingdom gut microbiota characterization in Chinese patients with idiopathic inflammatory myopathies.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {3801},
pmid = {41501250},
issn = {2045-2322},
support = {XJ2023001102//The Cultivating Scientific Research Project of the Second Hospital of Dalian Medical University/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; JCH22023017//Dalian Medical University Interdisciplinary Research Cooperation Project Team Funding/ ; 82370563//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; *Myositis/microbiology ; Middle Aged ; Adult ; China ; Feces/microbiology ; Metagenomics/methods ; Dysbiosis/microbiology ; Bacteria/genetics/classification ; Virome ; Machine Learning ; Case-Control Studies ; Metagenome ; Asian People ; Aged ; East Asian People ; },
abstract = {Idiopathic inflammatory myopathies (IIMs) are systemic autoimmune disorders with unknown etiology. Despite the established link between gut microbes and immunity, the roles of gut bacteriome, mycobiome, and virome in IIM are unexplored. We performed shotgun metagenomic sequencing on fecal samples from 34 IIM patients and 37 healthy controls to profile gut microbiota. Taxonomic, functional, network, and machine-learning analyses revealed microbial dysbiosis and its potential for discriminating IIM. All three microbial kingdoms were significantly altered in IIM. Several inflammation-associated bacterial taxa (e.g., Rothia mucilaginosa, Streptococcus parasanguinis, Trueperella pyogenes) and opportunistic fungi (e.g., Aspergillus spp.) were enriched in IIM, while SCFA-producing bacteria and fungi were depleted. Virome analysis revealed substantial shifts, with higher abundance of Siphoviridae in IIM. Altered viral functional gene profiles suggesting enhanced phage-mediated genome integration, recombination, and bacterial stress adaptation. Multi-kingdom network analysis showed extensive rewiring in IIM, characterized by increased network connectivity and a shift toward fungi-centered ecological hubs, contrasting with bacteria/virus-dominated networks in controls. In machine-learning models, the virome demonstrated the strongest discriminatory power, and viral signatures dominated the combined multi-kingdom classifier (AUC = 0.997). This first comprehensive multi-kingdom gut microbiota analysis in IIM provides a foundation for developing diagnostic and therapeutic strategies.},
}
@article {pmid41500299,
year = {2026},
author = {Zhang, W and Gu, L and Yan, W and Zhao, D and Liu, J},
title = {Acetochlor and sulfamethoxazole co-selection alter soil microbial nitrogen metabolism and resistome in agroecosystem.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123688},
doi = {10.1016/j.envres.2026.123688},
pmid = {41500299},
issn = {1096-0953},
mesh = {*Sulfamethoxazole/toxicity ; *Soil Microbiology ; *Nitrogen/metabolism ; *Toluidines/toxicity ; *Microbiota/drug effects ; *Herbicides/toxicity ; *Soil Pollutants/toxicity ; Anti-Bacterial Agents ; Ecosystem ; Bacteria/drug effects ; },
abstract = {Agricultural soils increasingly face co-contamination by herbicides and antibiotics, yet the ecological impacts of such multipollutant exposure remain poorly understood. This study employed a soil-plant microcosm combined with metagenomic sequencing to investigate the co-selective effects of acetochlor (ACE) and sulfamethoxazole (SMX) on soil microbiomes and antibiotic resistance genes (ARGs). The results showed that SMX functioned as the dominant ecological filter, significantly reducing microbial diversity and restructuring community composition via suppressing Pseudomonadota while enriching Acidobacteriota. Co-exposure further decreased diversity and shifted nitrogen metabolic pathways: SMX inhibited denitrification and nitrogen fixation, whereas co-combination synergistically enhanced the potential of nitrous oxide emission. Critically, herbicide-antibiotic co-exposure drove the emergence of clinically relevant ARGs (e.g., CMY-80, MCR-2.5) and enhanced their dissemination by increasing network complexity among host microorganisms. Moreover, ACE acted as an 'antibiotic adjuvant', accelerating resistance evolution through stress-induced physiological responses and mobility activation. ACE dose-dependent responses revealed the dual ecological role of agrochemicals: signaling molecules at low concentrations (2.5 mg/kg) and stressors at elevated levels (5.0 mg/kg). Genomic analysis further showed a higher chromosomal than plasmid-borne ARG abundance, reflecting a dynamic equilibrium between persistent and mobile resistance under fluctuating environmental pressures. These findings underscore the necessity of incorporating multipollutant scenarios into risk assessment, as single-contaminant evaluations underestimate the ecological and public health risks in agricultural ecosystems.},
}
@article {pmid41499937,
year = {2026},
author = {Wu, X and Zhang, T and Feng, J and Park, S},
title = {Herba Patriniae with probiotics targets Escherichia fergusonii and the 5-hydroxytryptophan-trimethylamine N-oxide axis in Parkinson's disease.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157758},
doi = {10.1016/j.phymed.2025.157758},
pmid = {41499937},
issn = {1618-095X},
mesh = {Humans ; *Parkinson Disease/drug therapy/microbiology/metabolism ; Gastrointestinal Microbiome/drug effects ; *Probiotics/pharmacology ; Caco-2 Cells ; Animals ; *Methylamines/metabolism ; Rats ; *5-Hydroxytryptophan/metabolism ; PC12 Cells ; Male ; *Plant Extracts/pharmacology ; Female ; Faecalibacterium prausnitzii ; Aged ; },
abstract = {BACKGROUND: Parkinson's disease (PD) exhibits a distinct gut microbiota and microbial metabolites, with specific enterotypes potentially influencing disease susceptibility. Current research lacks systematic comparisons of different enterotypes in PD susceptibility and targeted intervention efficacy. This study identifies their gut microbiota-metabolite biomarkers and validates a "probiotic plus herbal medicine" intervention in vitro to explore enterotype-stratified precision strategies for PD prevention and treatment.<br><br>PURPOSE: This study aimed to identify a high-risk enterotype for PD and its associated microbial and metabolic signatures using public metagenomic data. Furthermore, we evaluated the therapeutic efficacy of a combination therapy, comprising Patrinia scabiosaefolia Fisch (Herba Patriniae; HP) extract and the probiotics, Faecalibacterium prausnitzii and Lactiplantibacillus plantarum (F.l-HP), in a PD-relevant in vitro model.<br><br>METHODS: Public metagenomic data from PD patients and healthy controls (HC) were analyzed to characterize enterotypes. An in vitro gut-brain axis (GBA) model was established by co-culturing PC12 neuronal cells and Caco-2 intestinal epithelial cells to validate the pathogenic role of Escherichia fergusonii. The effects of the F.l-HP combination therapy were then assessed on bacterial growth, key metabolites (5-hydroxytryptophan (5-HTP), trimethylamine N-oxide (TMAO), butyrate), neuroinflammation, oxidative stress, mitochondrial function, and gut barrier integrity, with a focus on the underlying p-Akt and p-AMPK&#x3b1; signaling pathways.<br><br>RESULTS: The Bacteroidaceae enterotype (ET-B) was identified as a high-risk enterotype for PD, characterized by an enrichment of E. fergusonii. This bacterium was associated with the consumption of neuroprotective 5-HTP and the production of pro-inflammatory TMAO. The F.l-HP combination therapy significantly suppressed the growth of E. fergusonii while promoting the proliferation of beneficial probiotics. This intervention restored metabolic balance by reducing 5-HTP consumption and TMAO production and increasing butyrate levels. Consequently, F.l-HP treatment alleviated neuroinflammation and oxidative stress in neuronal cells, restoring mitochondrial function via the p-Akt pathway. In intestinal cells, it enhanced gut barrier integrity by upregulating zonula occludens-1 expression and activating p-AMPK&#x3b1; signaling.<br><br>CONCLUSION: E. fergusonii may participate in a 5-HTP-TMAO metabolic axis potentially linked to PD risk. F.l-HP intervention suppressed E. fergusonii activity, reduced 5-HTP consumption and TMAO production, modulated Akt and AMPK&#x3b1; signaling pathway, and alleviated neuroinflammation while enhancing intestinal barrier integrity.},
}
@article {pmid41499920,
year = {2026},
author = {Vázquez-Bolea, N and Mora-Martínez, C and Cuervo, M and Martinez, JA and Gil-Campos, M and Leis, R and Babio, N and Moreno, LA and Corella, D and Moreira Echeverria, A and Aguilera, CM and Castro-Collado, C and Picáns-Leis, R and Hernández-Cacho, A and Miguel-Berges, ML and Martin-Climent, P and Jurado-Castro, JM and Vázquez-Cobela, R and Plaza-Diaz, J and Rueda-De Torre, I and Pastor-Villaescusa, B and de la Torre-Aguilar, MJ and Salas-Salvadó, J and Sanz, Y and Navas-Carretero, S},
title = {Gut microbiota composition and derived enterotypes are associated with ponderal status in preschool children. Childhood obesity risk assessment longitudinal study (CORALS) cohort.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {57},
number = {},
pages = {106558},
doi = {10.1016/j.clnu.2025.106558},
pmid = {41499920},
issn = {1532-1983},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Child ; Child, Preschool ; Female ; Male ; *Pediatric Obesity/microbiology ; Longitudinal Studies ; Cross-Sectional Studies ; Feces/microbiology ; Body Mass Index ; Risk Assessment ; *Thinness/microbiology ; Overweight/microbiology ; Cohort Studies ; Bacteria/classification ; },
abstract = {BACKGROUND AND AIMS: Childhood obesity is a growing public health concern increasingly linked to gut microbiota. We analysed associations between microbiota composition, functionality, and weight status in 1134 children aged 3-6 years from the CORALS cohort.<br><br>METHODS: The baseline cross-sectional study stratified participants by weight status (underweight, normal weight, overweight, obesity) and performed shotgun metagenomic sequencing of stool samples. Analyses in R assessed alpha/beta diversity, taxonomic composition, enterotypes, and microbial pathways.<br><br>RESULTS: Alpha diversity decreased with increasing BMI, particularly in obesity (Shannon adj.P = 0.00301; Simpson adj.P = 0.00158). Beta diversity revealed distinct microbial structures across groups (p = 0.001). Four enterotypes were identified: obesity was associated with Enterotype 3 (Segatella-dominated, p = 0.023), while Enterotype 1 (Alistipes, Akkermansia, Coprococcus) was enriched in underweight/normal weight. Species linked to obesity included higher Phocaeicola dorei (adj.P = 0.003) and Segatella hominis (adj.P = 0.001), and lower Longicatena caecimuris (adj.P = 0.03) and Blautia parvula (adj.P = 0.003). Functional analyses showed downregulation of vitamin and nucleotide biosynthesis pathways and reduced carbohydrate metabolism in overweight/obesity.<br><br>CONCLUSIONS: Gut microbiota composition and functionality are strongly associated with weight status in early childhood, suggesting microbial biomarkers and metabolic pathways relevant to understand early obesity development.<br><br>CLINICALTRIALS: gov ID NCT06317883.},
}
@article {pmid41499829,
year = {2026},
author = {Huang, Z and Liu, H and Wang, C and Wang, J and Tian, C and Feng, J and Shen, J and Wang, X},
title = {Regulation of carbon cycling in plateau lakes by trophic states and seasonal variations: A focus on dissolved organic matter and microbial interactions.},
journal = {Water research},
volume = {292},
number = {},
pages = {125312},
doi = {10.1016/j.watres.2025.125312},
pmid = {41499829},
issn = {1879-2448},
mesh = {*Lakes/chemistry/microbiology ; Seasons ; *Carbon Cycle ; Eutrophication ; Carbon ; Microbial Interactions ; Microbiota ; },
abstract = {Plateau lakes are highly sensitive to climate change and anthropogenic disturbances. The intensification of seasonal variations caused by global warming has complicated the biogeochemical interactions between dissolved organic matter (DOM) and microbial communities. However, how DOM's chemical composition regulates microbial community dynamics and carbon cycling under varying trophic states and seasonal conditions remains unclear. Here, we employed Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomic sequencing to investigate the seasonal and trophic controls on DOM composition, microbial communities, and carbon cycling in plateau lakes. The results showed that in the dry season, DOM in the eutrophic lake exhibited pronounced aromaticity, with carboxyl-rich alicyclic molecules (CRAMs) constituting 42.80 % of the molecular pool. Conversely, during the wet season, sulfur- and nitrogen-containing compounds like CHOS and CHONS significantly increased, particularly in the eutrophic lake. The oligotrophic lake displayed the highest molecular lability, characterized by hydrogen-to-carbon (H/C) ratios of 1.24 and molecular lability indices (MLB%) of 34.76 %. Eutrophication altered microbial interaction networks, enhancing interspecies interactions and metabolic specialization. This metabolic shift drove preferential utilization of labile sugars in dry seasons and facilitated the degradation of recalcitrant carbon substrates in wet seasons, thereby optimizing carbon source partitioning. Notably, mesotrophic and oligotrophic lakes fostered resource cooperation by reducing network modularity and shaping carbon cycling through the coordinated action of multiple microbial groups. This study elucidates that carbon cycling in plateau lakes is governed by synergistic effects of trophic states and seasonal dynamics, with DOM serving as a critical mediator in microbial-driven carbon cycling dynamics.},
}
@article {pmid41499817,
year = {2026},
author = {Liu, Y and Zhong, L and Zhou, C and Zhang, Y and Zhang, K and Gan, Y and Wang, J and Lin, S and Xie, G and Zhong, W and Ye, X and Linghu, D and Chen, Q and Peng, W and Cao, C and Li, Z},
title = {Di-n-pentyl phthalate exposure alters intestinal structure and gut microbiota composition and characteristics in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119669},
doi = {10.1016/j.ecoenv.2025.119669},
pmid = {41499817},
issn = {1090-2414},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Phthalic Acids/toxicity ; Mice, Inbred C57BL ; Mice ; Male ; *Plasticizers/toxicity ; Dysbiosis/chemically induced ; *Intestines/drug effects ; Cytokines/metabolism ; },
abstract = {BACKGROUND: Di-n-pentyl phthalate (DnPP), a ubiquitous plasticizer structurally analogous to the gut toxicant di-(2-ethylhexyl) phthalate (DEHP), poses environmental persistence and human exposure risks, yet its gastrointestinal toxicity remains poorly characterized. We hypothesized DnPP disrupts intestinal homeostasis via gut microbiota dysbiosis, mirroring mechanisms of other phthalates.<br><br>METHODS: C57BL/6 mice (n&#x202f;=&#x202f;10 per group) were orally gavaged with DnPP (1-100&#x202f;mg/kg/d) for 21 days. Intestinal tissues and microbiota were analyzed using histomorphometry and metagenomic sequencing with functional annotation (GO/KEGG/CARD databases). Taxonomic and functional shifts were identified via Metastats and LEfSe (FDR < 0.05).<br><br>RESULTS: DnPP exposure induced dose-dependent villus degeneration (100&#x202f;mg/kg/d, P&#x202f;<&#x202f;0.05) and colon shortening (P&#x202f;<&#x202f;0.01), accompanied by upregulated pro-inflammatory cytokines (IL-6, TNF-&#x3b1;) and downregulated tight junction proteins (ZO-1, occludin) in small intestinal and colonic tissues. Metagenomic analysis revealed tissue-specific dysbiosis: colonic samples showed Bacteroidota enrichment and Firmicutes depletion, while the small intestine exhibited increased Bacteroidota and Bifidobacterium. Functional analyses demonstrated reduced glycan/lipid metabolism pathways (P&#x202f;<&#x202f;0.001) and elevated antibiotic resistance genes (CARD, P&#x202f;<&#x202f;0.05).<br><br>CONCLUSION: DnPP disrupts mouse intestinal structure, triggers inflammation, reduces probiotic abundance, upregulates antibiotic resistance genes, and impairs gut microbiota metabolic capacities, highlighting non-negligible health risks for intestinal and systemic metabolism, as well as potential risks of metabolic and infectious diseases. These findings provide critical evidence for phthalate ester health hazard mechanistic studies.},
}
@article {pmid41499519,
year = {2026},
author = {Ocampo Morales, BN and Hernández Montes, A and Estrada, K and Valadez Moctezuma, E},
title = {Physicochemical and microbiome changes in queso Crema de Chiapas during ripening.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0323038},
pmid = {41499519},
issn = {1932-6203},
mesh = {*Microbiota ; *Cheese/microbiology/analysis ; Bacteria/genetics/classification/isolation &amp; purification ; Food Microbiology ; },
abstract = {The dynamic changes in the physicochemical, microbiological, and metagenomic profiles of Crema de Chiapas cheese were evaluated across three ripening stages (2, 29, and 58 days). Although the main physicochemical properties -including fat content- remained remarkably stable, salt and protein levels showed noticeable variation throughout ripening. Protein content had the strongest influence on sample differentiation across ripening stages in unsupervised multivariate models, enabling the clustering of microbial diversity according to maturation time. A clear shift in microbial diversity was detected, marked by a reduction in bacterial genera and a concurrent decline in fungal and yeast populations as ripening advanced. The predominant bacterial genera throughout ripening were Streptococcus, Lactobacillus, and Lactococcus. While Streptococcus and Lactobacillus increased over time, Lactococcus exhibited the opposite trend. Metagenomic analysis revealed a decrease in Candida etchellsii and a concomitant increase in Candida tropicalis as ripening progressed. Quantitative PCR (qPCR) confirmed the presence of C. etchellsii at T1 (Ct = 7.22) and C. tropicalis at T3 (Ct = 9.84). The presence of three additional bacterial genera-Chryseobacterium, Aeromonas, and Enterobacter-identified by next-generation sequencing (NGS), was also assessed by qPCR. Chryseobacterium was detected at T2 (Ct = 3.26), whereas Aeromonas and Enterobacter were absent across all stages. Collectively, these findings suggest that potentially pathogenic microorganisms were not present at biologically relevant levels.},
}
@article {pmid41499358,
year = {2026},
author = {Cao, A and Lin, Y and Guan, S and Chen, Y and Zhai, W and Zhou, Y and Feng, S and Guan, Y and Zhang, Y and Huang, M and Wang, X and Long, H},
title = {Baseline multi-omics signatures could predict therapeutic response to neoadjuvant anti-PD-1 immunochemotherapy in non-small-cell lung cancer.},
journal = {Clinical and translational medicine},
volume = {16},
number = {1},
pages = {e70579},
pmid = {41499358},
issn = {2001-1326},
support = {82474002//National Natural Science Foundation of China/ ; 82020108031//National Natural Science Foundation of China/ ; 82404752//National Natural Science Foundation of China/ ; 81973398//National Natural Science Foundation of China/ ; WKZX2023CX020006//Development Center for Medical Science &amp; Technology National Health Commission of the People's Republic of China/ ; 2025A1515012521//Natural Science Foundation of Guangdong Province/ ; 2020B1212060034//Guangdong Provincial Key Laboratory of Construction Foundation/ ; 2017B030314030//Guangdong Provincial Key Laboratory of Construction Foundation/ ; 2017YFC0909300//National Key Research and Development Program/ ; B16047//The 111 project/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy ; Female ; Male ; *Neoadjuvant Therapy/methods ; Middle Aged ; Aged ; *Lung Neoplasms/drug therapy ; Gastrointestinal Microbiome/drug effects ; Metabolomics/methods ; Multiomics ; },
abstract = {BACKGROUND: Neoadjuvant anti-programmed cell death 1 (PD-1) immunochemotherapy has shown promising efficiency in the treatment of early-stage non-small-cell lung cancer (NSCLC), but it has not consistently yielded durable responses. Biomarkers for the prediction of efficacy are warranted.<br><br>METHODS: We performed shotgun metagenomic and plasma/faecal metabolomic studies in 44 NSCLC patients who underwent neoadjuvant tislelizumab plus platinum-based doublet chemotherapy. Samples were collected at baseline and before surgical resection, and the major pathologic response (MPR) was evaluated.<br><br>RESULTS: MPR patients showed a significantly higher gut-microbial alpha diversity, an enrichment of Ruminococcaceae, Lachnospiraceae and Clostridiales species, and an increased plasma level of tryptophan metabolites at baseline. On the contrary, non-MPR patients were characterized by enrichment of Prevotella species in faecal samples and higher plasma levels of linoleic acid metabolites. A high predictive accuracy was achieved using a small panel of differential microbial (Clostridium sp. M62/1 and Eisenbergiella tayi) or metabolomic features (linoleic acid, oxindole-3-acetic acid and quinolinic acid) with AUCs&#xa0;>&#xa0;.85.<br><br>CONCLUSIONS: The baseline characteristics of the gut microbiota and plasma metabolites could provide early predictions of the response to neoadjuvant anti-PD-1 immunochemotherapy.<br><br>TRIAL REGISTRATION: NCT05244837.<br><br>KEY POINTS: Baseline metagenomic and metabolomic signatures were significantly associated with the major pathologic response of neoadjuvant anti-PD-1 immunochemotherapy. Integrated microbial model (consists of Clostridium sp. M62/1 and Eisenbergiella tayi) and metabolomic model (consists of linoleic acid, oxindole-3-acetic acid and quinolinic acid) could provide early predictions of the response.},
}
@article {pmid41496864,
year = {2025},
author = {Shi, H and Zhang, X and Liu, L and Thompson, F and Li, X and Sun, H and Mi, H and Zhang, XH and Zhang, Y},
title = {Vertically stratified carbon fixation and coupling processes in deep-sea sediment.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf242},
pmid = {41496864},
issn = {2730-6151},
abstract = {Deep-sea sediments represent a vast yet underexplored reservoir of microbial carbon fixation, playing a critical role in global carbon cycling. However, the vertical distribution of carbon-fixing microorganisms, metabolic pathways, and the underlying energy sources and environmental drivers remain poorly understood. In this study, we investigated microbial carbon fixation and associated energy metabolism in South China Sea (SCS) sediment across 0-690 cm depth. Our findings revealed that dissolved inorganic carbon (DIC) and ammonium (NH4[+]) concentrations were key environmental drivers of carbon fixation and linked redox processes. Carbon fixation gene diversity increased with sediment depth, while the network complexity of functional genes and taxa involved in these processes declined. A distinct vertical succession of dominant microbial carbon-fixation pathways and their associated energy metabolisms was observed along the sediment depth: the Calvin-Benson-Bassham (CBB) and reductive glycine (rGLY) pathways dominated surface sediments, driven by nitrite oxidation, whereas the Wood-Ljungdahl (WL) pathway prevailed in deeper anoxic layers, supported by hydrogen and carbon monoxide oxidation. Taxonomically, Gammaproteobacteria and Methylomirabilia were abundant carbon-fixing groups in surface sediments, while Desulfobacterota, Chloroflexota, and Aerophobota became predominant at depth. Most carbon-fixing metagenome-assembled genomes (MAGs) exhibited mixotrophic lifestyles, and representative carbon fixation MAGs from Methylomirabilota, Dehalococcoidia (Chloroflexota) and Aerophobetes exhibited different metabolic features compared to their counterparts from other environments. These findings underscore the carbon fixation potential of deep-sea subsurface microbial communities and advance the understanding of carbon fluxes in deep biosphere.},
}
@article {pmid41496502,
year = {2026},
author = {Majzoub, ME and Santiago, FS and Raich, SS and Sirigeri, P and Simovic, I and Tedla, N and Kaakoush, NO},
title = {Immunoglobulin A protease from Sutterella wadsworthensis modifies outcome of infection with Campylobacter jejuni and is associated with microbiome diversity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611543},
pmid = {41496502},
issn = {1949-0984},
mesh = {Humans ; *Immunoglobulin A/metabolism ; Animals ; Phylogeny ; *Campylobacter jejuni/physiology ; *Campylobacter Infections/microbiology/immunology ; *Gastrointestinal Microbiome ; Mice ; *Eubacteriales/enzymology/genetics/classification ; Neutrophils/immunology/microbiology ; *Bacterial Proteins/genetics/metabolism ; China ; Phagocytosis ; Epithelial Cells/microbiology ; Serine Endopeptidases ; },
abstract = {Sutterella wadsworthensis is an enigmatic member of the microbiota, previously reported to be present in healthy humans yet also associated with certain gut diseases and their therapeutic outcomes. Here, we report on S. wadsworthensis classified to S. wadsworthensis_A that encodes an immunoglobulin A (IgA) protease that digests human IgA1 and IgA2 but not mouse IgA. The activity of this IgA protease could influence the trajectory of Campylobacter jejuni infection in human epithelial cells and phagocytosis in primary neutrophils. Comparative genomics and screening of metagenomic samples revealed that the protease shared sequence identity with an IgA protease from a bacterium that colonized other mammals and that S. wadsworthensis harboring IgA protease can be detected in individuals globally. Individuals positive for S. wadsworthensis IgA protease in China and Fiji (detection at >90% similarity) were found to have a different microbiome when compared to individuals where the protease was not detected. Phylogenetic analysis of pathogen IgA proteases along with IgA proteases from members of the microbiota suggested that there may be a unique subset of microbiota-derived IgA proteases. Our results highlight the importance of taxonomic resolution in microbiome studies and identify a subgroup of S. wadsworthensis that may be of potential clinical relevance.},
}
@article {pmid41496335,
year = {2026},
author = {Li, G and Zhao, Z and Machitani, M and Ishikawa, R and Ishikawa, K and Yokota, N and Haba, R and Nakamura, K and Sun, Z and Kurahara, LH and Hirano, K},
title = {Elucidation of mechanisms underlying the therapeutic effects of cordycepin on pulmonary hypertension, with a focus on cell senescence and gut microbiota.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {194},
number = {},
pages = {118923},
doi = {10.1016/j.biopha.2025.118923},
pmid = {41496335},
issn = {1950-6007},
mesh = {Animals ; *Deoxyadenosines/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Cellular Senescence/drug effects ; Mice ; Rats ; *Hypertension, Pulmonary/drug therapy/microbiology/pathology/metabolism ; Male ; Humans ; Mice, Inbred C57BL ; Myocytes, Smooth Muscle/drug effects/metabolism/pathology ; Pulmonary Artery/drug effects/pathology/metabolism ; Rats, Sprague-Dawley ; Macrophages/drug effects/metabolism ; Disease Models, Animal ; Vascular Remodeling/drug effects ; },
abstract = {INTRODUCTION: Pulmonary hypertension (PH) is a progressive cardiopulmonary disorder characterized by excessive pulmonary vascular remodeling and aberrant proliferation of pulmonary artery smooth muscle cells (PASMCs). Emerging evidence suggests that gut microbiota dysbiosis contributes to PH development. Cordycepin, a natural adenosine analogue derived from Cordyceps militaris, has demonstrated antiproliferative and microbiota-modulating properties; however, its mechanism of action in PH remains unclear.<br><br>OBJECTIVE: Elucidate the mechanisms underlying the therapeutic effects of cordycepin on PH, focusing on cellular senescence and gut microbiota.<br><br>METHODS: The effects of cordycepin on PH pathology were investigated by transcriptome analysis of PASMCs from patients, and metagenomic analysis of rodent PH models. Cellular senescence was analyzed in lung tissue from p16[Ink4a]-Cre[ERT2] reporter mice and in rat bone marrow-derived macrophages (BMDMs).<br><br>RESULTS: RNA sequencing analysis revealed activation of p53 signaling by cordycepin in PASMCs. Cordycepin suppressed CDK1 expression and TERT phosphorylation at threonine 249. It ameliorated vascular and cardiac remodeling in PH rat and mouse models. Cordycepin induced M1-like macrophage senescence in p16 [Ink4a] reporter mice lungs and rat BMDMs. Cordycepin significantly reshaped the gut microbiota, increasing beneficial genera (e.g. Alistipes and Acetatifactor) and reducing proinflammatory taxa (e.g., Ruminococcus), with modulating key metabolic pathways, including short-chain fatty acid, tryptophan, and vitamin K2 metabolism.<br><br>CONCLUSION: Cordycepin exerts multi-target therapeutic effects in PH by inhibiting PASMC proliferation via the p53-CDK1/pTERT axis, modulating gut microbiota-linked immunometabolism and induces proinflammatory macrophage senescence. These findings support cordycepin as a promising candidate for PH therapies targeting the vascular, immune, and gut-lung axes.},
}
@article {pmid41496069,
year = {2026},
author = {Zhao, Y and Wang, H and Lu, Y and Lou, D},
title = {Evolving landscapes in childhood asthma-gut microbiota research: A bibliometric analysis from 2000 to 2024.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46594},
pmid = {41496069},
issn = {1536-5964},
support = {ZHGF2024-1//The Key Construction Discipline of Immunology and Pathogen biology in Zhuhai Campus of Zunyi Medical University/ ; NO. QKHRC-CXTD&#xe3;&#x20ac;"2025&#xe3;&#x20ac;&#x2022;046//The Program for High level Innovative Talents in the Guizhou Province/ ; },
mesh = {Humans ; *Asthma/microbiology/immunology ; *Bibliometrics ; *Gastrointestinal Microbiome ; Child ; Dysbiosis ; *Biomedical Research/trends ; },
abstract = {BACKGROUND: Pediatric asthma, a chronic inflammatory airway disorder, is increasingly recognized for its association with gut microbiota dysbiosis, mediated through immune dysregulation and systemic inflammation. Recent advancements in multi-omics technologies and the "gut-lung axis" hypothesis have propelled this field into a research frontier. This bibliometric study delineates global research trends, collaborative networks, and emerging directions in pediatric asthma-gut microbiota research.<br><br>METHODS: Publications from the Web of Science Core Collection (2000-2024) were systematically retrieved using keywords related to asthma, children, and gut microbiota. Data from 635 articles (392 original studies, 243 reviews) were analyzed via CiteSpace and VOSviewer to map country/institutional contributions, author networks, citation metrics, and keyword clusters. Non-English publications, patents, and conference abstracts were excluded.<br><br>RESULTS: Global output demonstrated exponential growth, with 62% of articles published between 2018 to 2022. The United States led in productivity (180 articles, 28.35%) and citations (10,851), while Canada achieved the highest citation impact (121.12 citations/article). Key contributors included Prof Stuart E. Turvey (19 articles, 2463 citations) and Prof B. Brett Finlay (140.07 citations/article). The University of British Columbia dominated institutional contributions (28 articles, 149.11 citations/article). The Journal of Allergy and Clinical Immunology emerged as the top journal (33 articles, 126.48 citations/article). Seminal works highlighted early-life gut dysbiosis (e.g., reduced Lachnospira and Faecalibacterium) and cesarean delivery's role in asthma risk. Keyword clustering revealed 6 themes: disease phenotypes (asthma-allergy comorbidity), microbiota dynamics (dysbiosis, short-chain fatty acids [SCFAs]), immune mechanisms (T helper 17 cells/Treg imbalance, gut-lung axis), developmental exposures (antibiotics, breastfeeding), methodologies (metagenomics), and therapeutic strategies.<br><br>CONCLUSION: This study underscores a paradigm shift from descriptive microbial profiling to mechanistic exploration of microbiota-derived metabolites (e.g., SCFAs) and early-life interventions. Future priorities include elucidating causal pathways via longitudinal cohorts, developing microbiota-targeted therapies, and leveraging multi-omics integration. Despite limitations in database scope, this analysis highlights accelerating translation from basic research to clinical applications through global collaboration. Researchers should prioritize interdisciplinary studies to unravel the "microbiome-immune-development" triad and optimize personalized asthma management.},
}
@article {pmid41495863,
year = {2026},
author = {Ali, H and Rafiq, M and Manzoor, M and Gillani, SW and Degen, A and Iqbal, A and Wang, W and Rafiq, MK and Shang, Z},
title = {Seasonal shifts in vegetation, soil properties, and microbial communities in Western Himalayan forests.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {22},
pmid = {41495863},
issn = {2524-6372},
support = {31961143012//Natural Science Foundation of China/ ; ANSO-SBA-2023-02//Science-based Advisory Program of The Alliance of National and International Science Organizations for the Belt and Road Regions/ ; },
abstract = {BACKGROUND: The western Himalayan forest ecosystem faces escalating pressures from climate change and anthropogenic activities, demanding improved conservation strategies. Effective management requires understanding the seasonal fluctuations in vegetation, soil properties and microbial communities, but they remain poorly characterized across high altitude forests. We assessed these variables in 10 forest sites during the winter of 2023 and summer of 2024, analysing vegetation diversity, soil parameters, and microbial metagenomics.<br><br>RESULTS: We found pronounced seasonal shifts in plant and microbial diversities, and in soil properties. Plant species richness, and Shannon and Simpson diversity indices were higher (p&#x2009;<&#x2009;0.001) in summer than in winter while the community maturity index was higher (p&#x2009;<&#x2009;0.02) in winter than in summer. Soil properties exhibited clear seasonal patterns: pH, available phosphorus (AP), microbial biomass carbon (MBC) and cation exchange capacity (CEC) were higher (p&#x2009;<&#x2009;0.05) in summer, whereas soil moisture (SM) and soil organic carbon (SOC) were higher (p&#x2009;<&#x2009;0.05) in winter. Microbial alpha diversity indices (Shannon, Chao, and Sobs) were elevated (p&#x2009;<&#x2009;0.05) in summer, while the Simpson index was elevated in winter, indicating a shift in community dominance. Beta diversity analyses revealed a significant seasonal shift in overall metabolic potential (KEGG orthologs; ANOSIM R&#x2009;=&#x2009;0.222, p&#x2009;=&#x2009;0.016), but not in general protein functions (COG), carbohydrate-active enzymes (CAZy), or taxonomic composition (RefSeq). Therefore, despite taxonomic turnover, core metabolic functions were maintained, indicating strong functional redundancy. Structural equation models (SEM) confirmed distinct seasonal dynamics, revealing stronger plant-soil-microbe interactions and a greater proportion of variance explained by the model in summer (R[2]=0.64-0.72 for key paths) than in winter (R[2]=0.52-0.63).<br><br>CONCLUSIONS: The findings demonstrate that the western Himalayan ecosystem undergoes a fundamental seasonal reorganization. Summer is characterized by increased biodiversity, distinct soil conditions, and more dynamic microbial-ecosystem interactions, while winter exhibits greater community maturity and functional stability. The resilience of core ecosystem processes is underpinned by microbial functional redundancy, which ensures metabolic continuity despite taxonomic shifts. We recommend that forest management strategies account for these seasonal dynamics and focus on preserving the conditions that support this critical functional redundancy.},
}
@article {pmid41495321,
year = {2026},
author = {Sato, Y and Sato, Y and Deki, O and Tsuji, K and Tsurui-Sato, K},
title = {Estimated predator composition using environmental DNA analyses and color patterns of male guppies in introduced rivers.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {4066},
pmid = {41495321},
issn = {2045-2322},
support = {17K19298//Japan Society for the Promotion of Science/ ; 26249024//Japan Society for the Promotion of Science/ ; 19K12419//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Poecilia/genetics/physiology ; Male ; *Predatory Behavior ; Rivers ; *DNA, Environmental/analysis/genetics ; *Introduced Species ; Japan ; *Pigmentation ; Ecosystem ; DNA Barcoding, Taxonomic ; Color ; },
abstract = {Understanding the mechanisms underlying the successful invasion of the guppy, Poecilia reticulata, a globally invasive species, is important in the field of invasion biology. The body color pattern of male guppies is known to influence predation risk; however, the relationship between body color pattern and local predator guilds has been addressed in only a few studies. To investigate this relationship, we analyzed 32 water samples and 305 male guppies from eight introduced populations on the main island of Okinawa, Japan. The environmental DNA metabarcoding analysis of teleosts from the waters identified six potential guppy predator families, Anguillidae, Eleotridae, Gobiidae, Cichlidae, Mugilidae, and Cyprinidae; however, there was no detection of Characiformes, which are one of the major predators of guppies in their original habitat. Using imaging analysis of color spot areas of male guppies, we found that 16 of 18 potential predator × color combinations exhibited a statistically significant association between body color and the presence of predator families. For example, a negative association between orange spots and Anguillidae, and a positive association between blue-green spots and Cichlidae. These results suggest that the guppy in Okinawa was ecologically released from a major predator in its native habitat and adapted to the new environment through color pattern changes.},
}
@article {pmid41495312,
year = {2026},
author = {Kiran, R and Sharma, M and Subramanian, S and Patil, SA},
title = {Halophilic Anaerobic Cultures Enriched with CO2:H2 from Different Saline Environments Reveal Unknown Autotrophic Bacterial Diversity and Modular Carbon Fixation Pathways.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {40},
pmid = {41495312},
issn = {1432-184X},
mesh = {*Carbon Dioxide/metabolism ; *Geologic Sediments/microbiology ; *Carbon Cycle ; *Hydrogen/metabolism ; Formates/metabolism ; Autotrophic Processes ; Seawater/microbiology ; Acetic Acid/metabolism ; Lakes/microbiology ; Biodiversity ; Phylogeny ; *Bacteria, Anaerobic/metabolism/genetics/classification/isolation &amp; purification ; *Bacteria/metabolism/classification/genetics ; Metagenome ; Metagenomics ; },
abstract = {The subsurface sediments of saline-aquatic systems host diverse microbes, with unclear ecological roles and challenging lab cultivability. Chemolithotrophic anaerobes involved in CO2-fixation are one of the poorly studied groups. This study focused on understanding these bacteria from subsurface sediments of four representative saline environments, two marine (i.e., Coastal Arabian and Bay of Bengal seas) and two lake (Sambhar and Lonar) systems through enrichment and metagenomics. Enrichment cultures with bicarbonate/CO2 and hydrogen as the carbon and energy sources, respectively, showed CO2 fixation, producing acetic and formic acids as the major organic products. Enriched culture with Sambhar Lake sediment produced more formic acid (391 ± 8 mg/L) than acetic acid (92 ± 20 mg/L); however, other enriched cultures produced considerably higher acetic acid (up to 966 ± 24 mg/L) than formic acid (up to 367 ± 30 mg/L). The organics production was accompanied by unique thread-like (up to 500 μm long) aggregates, harbouring chains of rod and oval-shaped microbes in all cultures. Metagenome sequencing revealed dominance of Vibrio spp. (relative sequence abundance of 91% to 97%) across all cultures, while canonical CO2-fixing taxa were nearly absent (< 0.01%). KEGG analysis revealed partial genes for various CO2 fixation pathways, including Wood-Ljungdahl, reverse-TCA, dicarboxylate-hydroxybutyrate, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate, and the reductive-glycine pathway. The presence of a near-complete serine variant of the reductive glycine pathway, which has been demonstrated in engineered systems, suggests that this pathway may play an operational role in natural systems. The consistent production of organic acids and incomplete pathway representation suggests modular CO2 fixation within the Vibrio-dominated enriched mixed cultures.},
}
@article {pmid41494287,
year = {2026},
author = {Feng, N and Fu, C and You, J and Wang, D and Feng, X and Su, Y},
title = {Controlled release of coated antioxidants inhibits Citrobacter rodentium colonization in the colon of rats by reducing gut redox potential.},
journal = {Redox biology},
volume = {89},
number = {},
pages = {104005},
pmid = {41494287},
issn = {2213-2317},
mesh = {Animals ; *Citrobacter rodentium/drug effects/pathogenicity ; Oxidation-Reduction/drug effects ; Rats ; *Antioxidants/pharmacology/administration &amp; dosage/chemistry ; *Colon/microbiology/drug effects/metabolism ; Delayed-Action Preparations/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Enterobacteriaceae Infections/microbiology/drug therapy/metabolism ; Male ; Coumaric Acids/pharmacology/administration &amp; dosage ; },
abstract = {Intestinal redox potential serves as a critical parameter reflecting the dynamic characteristics of the gut microenvironment. To precisely modulate the intestinal redox potential and evaluate its inhibition of pathogenic colonization, this study built a controlled release system and further investigated its role in gut health under a lower redox potential. The results demonstrated that the controlled release formulation significantly reduced fecal redox potential more effectively than uncoated antioxidants. By optimizing the hydrodynamic size and zeta potential of ethoxyquin (EQ) and ferulic acid (FA), the coated FA formulation maintained high efficiency in reducing redox potential and reversed body weight loss induced by pathogenic infection. Both coated EQ (EQC) and FA (FAC) selectively enriched beneficial genera, such as Lactobacillus and Limosilactobacillus, while suppressing opportunistic pathogens like Klebsiella. Notably, coated FA demonstrated enhanced efficacy in alleviating Citrobacter rodentium (C. rodentium)-induced weight loss and reducing pathogens burden compared to uncoated FA. Mechanistically, coated FA promoted the enrichment of Lactobacillus reuteri (L. reuteri), suppressed the proliferation of Enterobacteriaceae, and enhanced intestinal Muc2 gene expression. Functional metagenomic analysis revealed that FAC significantly downregulated ABC transporter activity in Enterobacteriaceae, thereby impairing biofilm formation and synergizing with mucus secretion to inhibit pathogen colonization. Further in vitro co-culture trials confirmed that under a lower redox system, L. reuteri had a stronger inhibitory effect on C. rodentium as well as the expression of their virulence genes ((tir, ler). Collectively, these findings suggest that precise modulation of colonic redox potential through controlled release strategies represents a promising approach to enhance host defense against enteric pathogens via microbiota reprogramming.},
}
@article {pmid41494246,
year = {2026},
author = {Ding, J and Guo, T and Xia, H and Huang, K and Li, M and Li, F},
title = {Earthworm mediated microbial quorum sensing accelerates organic matter transformation during vermicomposting of dewatered sludge.},
journal = {Waste management (New York, N.Y.)},
volume = {212},
number = {},
pages = {115332},
doi = {10.1016/j.wasman.2026.115332},
pmid = {41494246},
issn = {1879-2456},
mesh = {*Oligochaeta/physiology ; *Quorum Sensing ; Animals ; *Composting/methods ; *Sewage/microbiology ; Biodegradation, Environmental ; Humic Substances ; Microbiota ; Bacteria/metabolism ; Acyl-Butyrolactones/metabolism ; },
abstract = {Vermicomposting (VC) relies on the synergistic interaction between earthworms and microorganisms to drive the degradation of organic matter (OM). Quorum sensing (QS), which governs earthworm-microorganism interactions, may influence dissolved organic matter (DOM) transformation during VC. However, the presence of QS and the functional roles of signaling molecules during VC remain unclear. This study investigated earthworm mediated microbial QS in driving microbial community succession and accelerating DOM transformation during VC, by contrasting the process without earthworms. The results showed that VC exhibited a distinct decomposition pathway, achieving significantly faster DOM degradation and mineralization (P < 0.01), compared to the control. Additionally, earthworms markedly facilitated the transformation of protein-like compounds into humic-like substances over a shorter period. Their presence also modified acyl-homoserine lactone (AHL) synthesis patterns and suppressed AHLs hydrolysis, resulting in a 96.14 % increase (P < 0.01) in short-chain AHLs. Metagenomic analysis revealed that earthworm in VC significantly altered the bacterial diversity (P < 0.05), enriching modularity coefficient and deterministic processes by 18.75 % and 87.03 %, respectively. Finally, AHL-responsive microorganisms significantly influencing physicochemical and DOM transformation during the VC. This study suggests that earthworms enhance AHL-type QS regulation in microbial communities, improving their metabolic functions and accelerating DOM transformation.},
}
@article {pmid41493379,
year = {2026},
author = {Forry, SP and Servetas, SL and Kralj, JG and Hunter, ME and Dootz, JN and Jackson, SA},
title = {A mathematical framework to correct for compositionality in microbiome data sets.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {1},
pages = {e0112625},
pmid = {41493379},
issn = {1098-5336},
mesh = {Humans ; *Metagenomics/methods ; *Microbiota ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; },
abstract = {The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease. However, the inherent compositionality of MGS data, where the relative abundance of each taxon depends on the abundance of all other taxa, complicates the measurement of individual taxa and the interpretation of microbiome data. Here, we describe an experimental design that incorporates exogenous internal standards in routine MGS analyses to correct for compositional distortions. A mathematical framework was developed for using the observed internal standard relative abundance to calculate "Scaled Abundances" for native taxa that were (i) independent of sample composition and (ii) directly proportional to actual biological abundances. Through analysis of mock community and human gut microbiome samples, we demonstrate that Scaled Abundances outperformed traditional relative abundance measurements in both precision and accuracy and enabled reliable, quantitative comparisons of individual microbiome taxa across varied sample compositions and across a wide range of taxon abundances. By providing a pathway to accurate taxon quantification, this approach holds significant potential for advancing microbiome research, particularly in clinical and environmental health applications where precise microbial profiling is critical.IMPORTANCEMetagenomic sequencing (MGS) analysis has become central to modern characterizations of microbiome samples. However, the inherent compositionality of these analyses, where the relative abundance of each taxon depends on the abundance of all other taxa, often complicates interpretations of results. We present here an experimental design and corresponding mathematical framework that uses internal standards with routine MGS methods to correct for compositional distortions. We validate this approach for both amplicon and shotgun MGS analysis of mock communities and human gut microbiome (fecal) samples. By using internal standards to remove compositionality, we demonstrate significantly improved measurement accuracy and precision for quantification of taxon abundances. This approach is broadly applicable across a wide range of microbiome research applications.},
}
@article {pmid41492410,
year = {2025},
author = {Wallau, GDL and Barbier, E and Machado, LC and da Silva, AF and Dias, YJM and Dezordi, FZ and Tomazatos, A and Horváth, B and Lins, RD and Bernard, E and Cadar, D},
title = {Ambecovirus, a novel Betacoronavirus subgenus circulating in neotropical bats, sheds new light on bat-borne coronaviruses evolution.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf094},
pmid = {41492410},
issn = {2057-1577},
abstract = {Understanding the viral diversity harboured by wildlife is essential for effective mapping and prevention of future zoonotic outbreaks. Bats, in particular, are recognized as natural reservoirs for several high-impact zoonotic viral pathogens, including coronaviruses responsible for Severe Acute Respiratory Syndrome (SARS), the rabies virus, diverse paramyxoviruses, Marburg, Ebola, Nipah, and Hendra viruses. However, a large extent of bat viruses remains unexplored, especially in highly biodiverse regions of the Neotropics such as Brazilian ecosystems. We used a meta-transcriptomic approach to characterize new virus genomes found in blood, oral, and anal samples collected from cave- and noncave bats from Northeast Brazil, Caatinga, and Atlantic Forest biomes. From a total of 19 coronavirus-positive bats, we have assembled two complete genomes of a new Betacoronavirus subgenus, named Ambecovirus (American betacoronavirus). The subgenus herein described is phylogenetically placed between the Sarbeco-/Hibeco-/Nobecovirus and the Merbeco-/Embecovirus clades, being basal to the former. While the conserved S2 region of the spike protein retained hallmark domains, including HR1 and HR2, the S1/S2 cleavage site and the furin cleavage site, the S1 region consistently displayed only the N-terminal domain. The receptor-binding domain from the C-terminal domai (CTD) region could not be identified due to high dissimilarity relative to known congeners. The detection of Ambercovirus in sympatric Pteronotus gymnonotus and Carollia perspicillata bats suggests potential interspecies transmission. Longitudinal sampling confirmed persistent Ambecovirus infection in P. gymnonotus over multiple years and virus dispersion at a minimum distance of 270 km between caves. The present study confirms that viral diversity in neotropical hosts remains largely unknown, not just in Brazil but likely in the other countries of the region, supporting the need for a systematic approach to virome exploration and analysis followed by in vitro experimentation to assess zoonotic potential.},
}
@article {pmid41492364,
year = {2025},
author = {Solly, EF and Jaeger, ACH and Barthel, M and Six, J and Mueller, RC and Hartmann, M},
title = {Soil water limitation intensity alters nitrogen cycling at the plant-soil interface in Scots pine mesocosms.},
journal = {Plant and soil},
volume = {516},
number = {1},
pages = {705-723},
pmid = {41492364},
issn = {0032-079X},
abstract = {BACKGROUND AND AIM: More intense episodes of drought are expected to affect terrestrial nitrogen (N) cycling by altering N transformation rates, the functioning of soil microorganisms, and plant N uptake. However, there is limited empirical evidence of how progressive water loss affects N cycling at the plant-soil interface.<br><br>METHODS: We adopted [15]N tracing techniques and metagenomic analyzes of microbial genes involved in N cycling to assess how different levels of soil water availability influenced the fate of N derived from decomposing litter in mesocosms with Scots pine saplings.<br><br>RESULTS: With increasing water limitation, the release of N from decomposing litter into the soil declined rapidly. However, moderate levels of water limitation barely affected the microbial metagenome associated with N cycling and the uptake of N by the saplings. Comparatively, severe levels of water limitation impaired plant N uptake, and increased the prevalence of microbial N-cycling genes potentially involved in mechanisms that protect against water stress. Genes associated with the uptake and release of N during mineralization and nitrification declined under low soil water contents.<br><br>CONCLUSIONS: When soil water becomes largely unavailable, the cycling of N at the plant-soil interface is slowed down, and microbial and plant tolerance mechanisms may prevail over N uptake and microbial decomposition.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-07758-z.},
}
@article {pmid41491699,
year = {2026},
author = {Wang, R and Zhang, W and He, Z and Zhou, Y and Chen, C and Song, K and Shang, Q and Wu, Y and Gu, P and Shu, D and Zhao, L},
title = {Core microbiota recruited by healthy grapevines enhance resistance against root rot disease.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {13},
pmid = {41491699},
issn = {1474-760X},
support = {2023BCF01026//Key Research and Development Program of Ningxia/ ; 2025NC-YBXM-068//Key Research and Development Projects of Shaanxi Province/ ; 32372501//National Natural Science Foundation of China/ ; },
mesh = {*Vitis/microbiology/genetics ; *Disease Resistance/genetics ; *Microbiota ; *Plant Diseases/microbiology/genetics ; *Plant Roots/microbiology ; Rhizosphere ; Soil Microbiology ; Fusarium/pathogenicity ; Metagenomics ; Bacteria/genetics ; },
abstract = {BACKGROUND: Root rot disease caused by fungal pathogens of wine grapevines poses a serious threat to their growth and results in a substantial economic impact on grape industry. The rhizosphere microbiome recruited to plants is critical for mitigating soil-borne pathogens. However, how beneficial microbes influence disease resistance remains unclear.<br><br>RESULTS: We investigate the composition and gene functions of microorganisms in wine grapevines with root rot disease and healthy controls by amplicon and metagenomic sequencing. We use culturomics and in vivo experiments to verify the pathogen and beneficial strains to improve plant health. We find that root rot disease in grapevines significantly affects rhizosphere microbiome diversity and composition. The microbial interkingdom network indicates that the disease destabilizes the bacteria-fungi co-occurrence network. We find that plants recruit the potentially beneficial bacteria Pseudomonas, Bacillus and Streptomyces in healthy rhizosphere soil. By culturomics, we confirm that Fusarium solani is the main pathogen causing root rot disease. We further observe that these three key beneficial bacteria from the co-occurrence networks enhance the resistance of grapevines to pathogens. Furthermore, metagenomic analysis reveals that beneficial bacterial strains suppress pathogens by enriching potential functional genes in pathways involved in disease resistance.<br><br>CONCLUSIONS: Our findings highlight the critical role of disease resistance pathways of potentially beneficial microorganisms in fighting disease and supporting plant health, offering new insight for the exploration of beneficial microbial resources and providing a basis for the development of biological control of grape root rot disease.},
}
@article {pmid41491581,
year = {2026},
author = {Chen, T and Yu, S and Li, K and Huang, K and Shi, W and Chen, H and Hong, Q and Zhang, Y and Wang, J and Yu, Z and Wang, J},
title = {Rumen microbiota inoculation indicates collaborative mechanisms enhancing propionate supply to alleviate weaning stress in lambs.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {54},
pmid = {41491581},
issn = {2049-2618},
support = {2023YFD1300901//the Ministry of Science and Technology of the People's Republic of China/ ; D21C170001//the Natural Science Foundation of Zhejiang Province/ ; 31622056//the National Natural Science Foundation of China/ ; 226-2025-00026//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Propionates/metabolism ; Weaning ; Fermentation ; Sheep/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Stress, Physiological ; Animal Feed ; Liver/metabolism ; Metagenomics ; Gluconeogenesis ; },
abstract = {BACKGROUND: The transition from milk to solid feed during weaning often imposes metabolic stress on young ruminants due to energy deficits. Previous studies suggest that ruminal microbiota transplantation from adults to juveniles can alleviate weaning stress, but the underlying mechanisms remain poorly defined.<br><br>RESULTS: In this study, 48 Hu lambs were randomly assigned to two groups (n&#x2009;=&#x2009;24 each): an inoculated group (Inoc) that received lyophilized ruminal microbiota and a control group (Ctrl) that received no inoculation. We evaluated rumen fermentation characteristics, blood metabolites, hepatic glycogen levels, expression of hepatic gluconeogenic genes, and shifts in the rumen microbiome at three key time points-the end of weaning, 1 and 2 weeks post-weaning. Oral inoculation significantly elevated rumen propionate concentration, upregulated the gene expression of hepatic pyruvate carboxylase (EC 6.4.1.1) and glucose-6-phosphatase (EC 3.1.3.9), and increased hepatic glucose production. Microbiome analysis revealed increased colonization by lactic acid-producing bacteria (e.g., Olsenella and Sharpea) and propionate producers, such as Megasphaera elsdenii, alongside enriched families associated with propionate production, including Prevotellaceae, Succinivibrionaceae, and Erysipelotrichaceae. Genome-resolved metagenomics further demonstrated an increased abundance of metagenome-assembled genomes (MAGs) carrying polysaccharide utilization loci (PULs) and genes involved in lactate-to-propionate conversion. Notably, the inoculation promoted co-occurrence of functionally complementary MAGs-such as s_Megasphaera elsdenii (MAG98), s_Bilifractor sp902797025 (MAG125), s_Prevotella sp002391185 (MAG342), and s_Prevotella sp900540375 (MAG298)-that carry a wide repertoire of genes involved in polysaccharide degradation and lactate-to-propionate fermentation. In vitro co-culture experiments with Megasphaera elsdenii and Bilifractor porci confirmed their synergistic role in promoting propionate production.<br><br>CONCLUSIONS: This study demonstrates that oral inoculation of pre-weaned lambs with starter feed-adapted adult rumen microbiota facilitates the establishment of a microbial consortium capable of enhanced lactate and propionate production, thereby enhancing hepatic gluconeogenesis and energy homeostasis, which ultimately mitigates weaning stress. This approach may offer a promising strategy to facilitate dietary transition and enhance metabolic resilience in young ruminants during weaning by modulating rumen microbial composition toward a propionate-producing community. Video Abstract.},
}
@article {pmid41491053,
year = {2026},
author = {Manirakiza, B and Zhang, S and Addo, FG and Ifon, BE and James, N and Kiribou, R and Nadine, NIA and Nyandwi, V and Sebaziga, JN and Mukasekuru, R and de Dieu Uwizelimana, J},
title = {Untapped Microbial Diversity, Assemblages, and Interactions in Rwandan Geothermal Spring Mats, Africa.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {123},
pmid = {41491053},
issn = {1432-0991},
support = {E51879084//National Natural Science Foundation of China/ ; E51579075//National Natural Science Foundation of China/ ; },
mesh = {*Hot Springs/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Rwanda ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; RNA, Ribosomal, 18S/genetics ; *Eukaryota/classification/genetics/isolation &amp; purification ; Phylogeny ; },
abstract = {Research on prokaryotes living in geothermal ecosystems have broadened our understanding of their compositions and response to extreme environmental stresses, especially for plankton bacterial communities in hot spring water. However, the comprehensive exploration of microbial diversity, assemblages, and interactions in geothermal spring mats in Africa, particularly in Rwanda, remain underexplored. This study explored the bacterial and eukaryotic communities' biodiversity, assemblages, and interactions within microbial mats from the Bugarama hot pool (BHP; 40-47 °C) and Gisenyi hot springs (GHS; 58-71.4 °C) in Rwanda, using high-throughput sequencing of the 16S rRNA gene and 18S rRNA gene, complemented by null and neutral community models and physicochemical analytical methods. Interestingly, the bacterial Shannon, Evenness, and Simpson indices were significantly different (P < 0.05) among geothermal spring mats. In BHP and GHS, the abundances of Chloroflexota, Proteobacteria, Firmicutes, and Acidobacteriota were significantly higher in BHP (P < 0.05) than in GHS, whereas Cyanobacteria, Bacteroidota, Planctomycetota, Verrucomicrobiota, and Spirochaetota were significantly more abundant in GHS (P < 0.01). Conversely, Chloroplastida, Mucoromycota, Arthropoda, and Cryptomycota were significantly more prevalent in BHP (P < 0.05), while the SAR supergroup, Ascomycota, Nematoda, and Amoebozoa dominated in GHS (P < 0.05). Through null and neutral modeling, stochastic processes exerted greater influence on bacterial and eukaryotic community assembly in fine-scale variations within geothermal spring mats. Despite this stochastic predominance, abiotic environmental factors (deterministic processes) such as temperature, pH, salinity (EC and TDS), and nitrate cannot be entirely ruled out. Moreover, Co-occurrence network analysis (|r|> 0.7, P < 0.05) revealed more complex and stable microbial interactions at higher temperatures (GHS). These findings highlight the rich underexplored microbial diversity and interactions in Rwandan geothermal spring mats through metagenomic analysis, shedding light on ecological processes and dynamics in extreme environments. Despite being ignored in metagenomic studies, eukaryotic communities highlight novel temperature-tolerant taxa: Echinamoeba and Tubulinea in phylum Amoebozoa, Monhysterida in phylum Nematoda, and Novel_Clade_Gran-5 in phylum Cercozoa, which are both pathogens and fierce predators thriving in geothermal habitats.},
}
@article {pmid41490675,
year = {2026},
author = {Li, Y and Cao, L and Li, W and Yan, Y and Zuo, W and Xi, B and Huang, C},
title = {Unveiling nitrogen and sulfur cycling mechanisms of odor reduction in kitchen waste composting driven by exogenous bacterial consortia.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {133923},
doi = {10.1016/j.biortech.2026.133923},
pmid = {41490675},
issn = {1873-2976},
mesh = {*Odorants/prevention &amp; control/analysis ; *Composting/methods ; *Nitrogen/metabolism ; *Sulfur/metabolism ; *Microbial Consortia ; *Bacteria/metabolism ; Hydrogen Sulfide ; Ammonia ; },
abstract = {Odor emissions, primarily ammonia (NH3) and hydrogen sulfide (H2S) restrict the application of kitchen waste (KW) composting. Microbial inoculation is a promising strategy, yet mechanisms underlying odor mitigation remain unclear. KW composting with and without an immobilized bacterial consortium (IBC) was compared by monitoring physicochemical conditions, odor emissions, and microbial and functional profiles. IBC extended the thermophilic phase, improved composting efficiency, and reduced cumulative H2S (-44 %) and NH3 (-18 %). IBC reshaped bacterial, fungal and archaeal communities and strengthened microbial network connectivity. Metagenomic analysis showed IBC enriched nitrogen-fixation genes and suppressed ammonification, nitrification, denitrification, and nitrate reduction. IBC also enhanced thiosulfate and sulfite oxidation while inhibited reductive pathways linked to H2S formation. Partial least squares path model confirmed odor mitigation resulting from coordinated shifts in environmental conditions, microbial structure, and metabolic pathways. Overall, microbial inoculation effectively reduces odor emissions and enhances composting performance by redirecting nitrogen and sulfur transformations.},
}
@article {pmid41489025,
year = {2026},
author = {Pace, R and Monti, MM and Cuomo, S and Affinito, A and Ruocco, M},
title = {Machine Learning Approaches to Assess Soil Microbiome Dynamics and Bio-Sustainability.},
journal = {Physiologia plantarum},
volume = {178},
number = {1},
pages = {e70719},
pmid = {41489025},
issn = {1399-3054},
mesh = {*Soil Microbiology ; *Machine Learning ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Fungi/genetics ; Soil/chemistry ; Agriculture ; Principal Component Analysis ; },
abstract = {Understanding soil microbiota dynamics is essential for enhancing bio-sustainability in agriculture, yet the complexity of microbial communities hampers the prediction of their functional roles. Artificial intelligence (AI) and machine learning (ML) offer powerful tools to analyse high-dimensional microbiome data generated by high-throughput sequencing. Here, we apply unsupervised AI-based algorithms to uncover microbial patterns that are not immediately recognisable but are crucial for characterising the biological status of agricultural soils. Soil samples were collected from a site in Northern Italy managed under four strategies: conventional farming without organic matter (C), with organic matter (C + O), with beneficial microorganisms but without organic matter (M), and with both beneficial microorganisms and organic matter (M + O). Metagenomic amplicon sequencing of the 16S ribosomal RNA (rRNA) gene and the internal transcribed spacer (ITS) region was used to profile bacterial and fungal communities. Principal component analysis (PCA), k-means clustering, and t-distributed stochastic neighbour embedding (t-SNE) revealed coherent temporal trajectories in both datasets, with sampling time and crop presence emerging as dominant drivers of community assembly and only subtle compositional shifts attributable to treatments. Fungal communities exhibited higher plasticity and a stronger response to management than bacterial communities, which converged towards a stable oligotrophic core. Our findings highlight the complementary roles of fungal and bacterial guilds and show that unsupervised ML-based workflows provide an effective framework to disentangle temporal and treatment effects in complex microbiome datasets. This exploratory study lays the groundwork for future predictive models aimed at identifying microbial indicators of soil biological status and supporting bio-sustainable agronomic decisions.},
}
@article {pmid41485666,
year = {2026},
author = {He, H and Han, L and Ni, W and Yu, J and Liu, K and Li, W and Li, C and Hu, S and Li, C and Li, X},
title = {The horse gut microbiota genome represents a vast novel reservoir of CAZymes.},
journal = {International journal of biological macromolecules},
volume = {339},
number = {Pt 2},
pages = {150042},
doi = {10.1016/j.ijbiomac.2025.150042},
pmid = {41485666},
issn = {1879-0003},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Horses/microbiology ; Phylogeny ; *Glycoside Hydrolases/genetics/metabolism ; *Genome, Bacterial ; Metagenome ; Glycosyltransferases/genetics/metabolism ; Substrate Specificity ; },
abstract = {Herbivores represent crucial subjects for mining highly efficient carbohydrate-active enzymes (CAZymes) from gut microbiomes. Here, we analyzed 12,763 metagenome-assembled genomes (MAGs) from the horse gut, revealing that its microbial community as a rich reservoir of CAZymes diversity, with 5,204,848 glycoside hydrolases (GHs) and 4,596,191 glycosyl transferases (GTs) identified. Our findings demonstrate that Bacteroidota (5,479,287 CAZymes) and Bacillota_A (2,987,684 CAZymes) serve as the primary functional phyla for plant polysaccharide degradation. A total of 17,250 polysaccharide utilization loci (PULs) discovered in Bacteroides species. Through comparative genomic screening, a total of 12,976 hypothetical genes were predicted in PULs. These genes represent a putative novel reservoir of CAZymes. We selected and identified a putative CAZyme, which encodes 452 amino acids and is designated H113. Our research has confirmed that H113 is a metal enzyme (Zn[2+] significantly enhancing its catalytic efficiency) capable of degrading α-1,4 glycosidic bonds in maltotriose and also exhibiting activity toward mannan, demonstrating optimal activity at pH 4.8 and 35 °C (specific activity: maltotriose: 82.2 U/mg, mannan: 2.3 U/mg). Phylogenetic analysis revealed H113 belongs to a conserved enzyme family with 1866 identified homologues. This study not only provides a reference for efficient discovery of novel CAZymes but also offers valuable resources for developing novel biocatalysts.},
}
@article {pmid41485293,
year = {2026},
author = {Meng, Y and Hou, Y and Zhang, R and Guo, Z and Zhang, Z and Li, J and Yan, Y and Chang, Y and Li, D and Chang, L and Li, M and Gao, H},
title = {Jinlida ameliorates diabetic kidney disease via gut microbiota-dependent production of pyridoxamine targeting renal AGEs/RAGE and TGF-β pathways.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157744},
doi = {10.1016/j.phymed.2025.157744},
pmid = {41485293},
issn = {1618-095X},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Pyridoxamine/metabolism/pharmacology ; *Diabetic Nephropathies/drug therapy/metabolism ; Mice ; Male ; Transforming Growth Factor beta/metabolism ; Glycation End Products, Advanced/metabolism ; Mice, Inbred C57BL ; *Drugs, Chinese Herbal/pharmacology ; Fecal Microbiota Transplantation ; Receptor for Advanced Glycation End Products/metabolism ; Kidney/drug effects/metabolism ; Signal Transduction/drug effects ; Vitamin B 6/metabolism ; },
abstract = {BACKGROUND: Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease and end-stage renal disease (ESRD), necessitating novel therapies beyond conventional approaches. Emerging evidence indicates that gut microbiota dysbiosis promotes DKD progression through metabolite-mediated renal injury. Jinlida (JLD) is a clinically validated traditional Chinese medicine with antidiabetic activity, but its microbiota-mediated renoprotective mechanism remains unclear.<br><br>PURPOSE: This study investigates whether JLD alleviates DKD by modulating gut microbiota and vitamin B6 metabolism, and elucidates the renoprotective mechanism of its key metabolite, pyridoxamine (PM).<br><br>METHODS: To assess JLD's microbiota-dependent effects, we employed antibiotic-induced pseudo-germ-free mice and fecal microbiota transplantation (FMT). Metagenomics and untargeted metabolomics delineated gut microbiota and metabolite compositional changes. Renal PM levels were quantified by LC-MS/MS. The renoprotective effects and mechanisms of direct PM supplementation against DKD were further evaluated in vivo and in vitro.<br><br>RESULTS: JLD's therapeutic effects on proteinuria and glomerulosclerosis were shown to partially depend on microbiota homeostasis. Metabolomic analysis demonstrated that JLD significantly upregulated the vitamin B6 metabolic pathway and increased levels of related metabolites, including PM and pyridoxine (PN). Metagenomic analyses indicated that JLD remodeled the gut microbiota composition and enriched pathways related to cofactor biosynthesis, and markedly increased the relative abundance of key enzyme genes involved in the de novo (DXP-dependent) vitamin B6 biosynthesis pathway - namely pdxJ, pdxB, dxs and dxr. Genes related to vitamin B6 activation and conversion (pdxH, aldH) showed no significant changes, suggesting that JLD may promote PM accumulation by enhancing the microbiota's capacity for vitamin B6 biosynthesis rather than its subsequent activation/conversion. Source-tracking pinpointed Paramuribaculum intestinale as the core functional species. In vitro culture experiments showed that JLD markedly promoted the growth of this strain and elevated PM production, and that the strain's conditioned culture medium effectively inhibited formation of advanced glycation end-products (AGEs). Notably, direct supplementation with PM recapitulated the renoprotective effects of JLD in vivo. Mechanistically, PM inhibited the AGEs-RAGE-NF-&#x3ba;B-AP-1 axis and TGF-&#x3b2; receptor signaling, thereby suppressing NF-&#x3ba;B-driven inflammation and Smad2-mediated fibrosis.<br><br>CONCLUSION: JLD remodels the gut microbiota and enhances its de novo vitamin B6 biosynthetic capacity, leading to accumulation of PM. Gut-derived PM enters the circulation and functions as an effector molecule targeting the kidney; through PM's direct carbonyl-trapping activity it scavenges AGEs and suppresses the AGEs-RAGE axis as well as downstream inflammatory and profibrotic signaling, thereby exerting renoprotective effects. This study reveals PM as a microbially derived metabolite with therapeutic potential in DKD and offers a new metabolism-directed strategy for DKD treatment.},
}
@article {pmid41485252,
year = {2026},
author = {Xu, Y and Zhao, B and Li, F and Song, S and Liu, J and Liu, Z and Wang, Y and Ji, J and Liu, Z and Zhou, W and Wang, X and Zhou, M},
title = {Tucidinostat ameliorates DSS-induced ulcerative colitis by inhibiting cellular senescence, modulating the p53 signaling pathway and cell cycle, and restoring the gut microbiota-metabolite Axis.},
journal = {International immunopharmacology},
volume = {171},
number = {},
pages = {116155},
doi = {10.1016/j.intimp.2025.116155},
pmid = {41485252},
issn = {1878-1705},
mesh = {Animals ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism/pathology/microbiology ; *Gastrointestinal Microbiome/drug effects ; Cellular Senescence/drug effects ; Mice, Inbred C57BL ; *Tumor Suppressor Protein p53/metabolism ; Signal Transduction/drug effects ; Mice ; Dextran Sulfate ; Male ; Disease Models, Animal ; Cell Cycle/drug effects ; Humans ; Colon/drug effects/pathology ; },
abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease with a complex etiology, and its pathological process is closely associated with cellular senescence. Based on an anti-senescence drug screening system, this study identified Tucidinostat (TUC) as an agent with anti-senescence properties and investigated its therapeutic potential and mechanisms of action in a DSS-induced ulcerative colitis model. Using an in vitro model of colonic epithelial cells and an in vivo C57BL/6 mouse model, both induced by DSS treatment, we systematically evaluated changes in body weight, colon length, histopathological scores, levels of inflammatory cytokines, and senescence-associated markers. Our results demonstrated that TUC significantly inhibited cellular senescence and effectively alleviated colitis-related symptoms. Transcriptomic analysis and Western blotting further revealed that TUC exerts its effects by modulating the p53 signaling pathway and cell cycle progression. Furthermore, integrated metagenomic and untargeted metabolomic analyses revealed that TUC reshapes the gut microbiota-metabolite axis by promoting the proliferation of beneficial bacteria (e.g., s__Eubacterium plexicaudatum and s__Ligilactobacillus murinus) and increasing the levels of beneficial metabolites, such as alpha-muricholic acid and kynurenic acid. In summary, this study provides the first evidence that Tucidinostat can ameliorate ulcerative colitis by targeting cellular senescence, regulating the p53/cell cycle signaling network, and restoring gut microbiota-metabolite homeostasis, offering a novel potential therapeutic strategy for this disease.},
}
@article {pmid41484966,
year = {2026},
author = {Fu, R and Liang, XJ and Yang, WM and Li, R and Shi, YR and Guo, L and Yu, H and Chen, YH and Wang, HN},
title = {Gut microbial signatures in schizophrenia: exploring archaea, fungi, and bacteria.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {113},
pmid = {41484966},
issn = {1471-244X},
support = {LHJJ24YF06//Interdisciplinary Integration Project of Xijing hospital/ ; 82201679//National Natural Science Foundation of China/ ; 82330043//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Adult ; *Schizophrenia/microbiology ; *Archaea/genetics/isolation &amp; purification ; *Bacteria/genetics/isolation &amp; purification/classification ; *Fungi/genetics/isolation &amp; purification ; *Dysbiosis/microbiology ; Feces/microbiology ; Middle Aged ; Case-Control Studies ; },
abstract = {BACKGROUND: Gut microbial, mainly bacterial dysbiosis, has been demonstrated in patients with schizophrenia (SCH). However, the signatures and differences of minority gut microbiota in SCH, such as archaea and fungi, have been poorly addressed.<br><br>METHODS: We obtained stool samples from 61 SCH patients and 69 healthy controls (HC), and analyzed the compositional and functional alterations of gut archaea, fungi, and bacteria using metagenomic shotgun sequencing (MSS). Additionally, we developed potential biomarkers to distinguish SCH from HC.<br><br>RESULTS: SCH patients showed significantly lower archaeal &#x3b1;-diversity compared with that of HC. Whereas there were significant differences between SCH and HC in &#x3b2;-diversity at the species level of archaea, fungi and bacteria. Meanwhile, the functional differences between the two groups were concentrated in glucose, lipid and amino acid metabolic pathways. Furthermore, we established potential diagnostic archaeal (9 species, AUC&#x2009;=&#x2009;0.73), fungal (8 species, AUC&#x2009;=&#x2009;0.69), and bacterial (22 species, AUC&#x2009;=&#x2009;0.74) microbiomes for differentiating SCH patients from HC.<br><br>CONCLUSIONS: This study describes a more comprehensive understanding of abnormal gut microbiome in SCH and might provide candidate targets for the development of a microbe-based diagnosis for SCH.<br><br>TRIAL REGISTRATION: Chinese Clinical Trial Registry: ChiCTR2000032118, registration date: 2020/04/20.},
}
@article {pmid41482808,
year = {2026},
author = {Ip, YCA and Allan, EA and Hirsch, SL and Kelly, RP},
title = {Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade-Offs in Resource-Limited Settings.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70091},
pmid = {41482808},
issn = {1755-0998},
support = {GR042390//OceanKind/ ; GR016745//David and Lucile Packard Foundation/ ; },
mesh = {*Workflow ; Animals ; *DNA, Environmental/isolation &amp; purification/genetics ; *Fishes/genetics/classification ; *Metagenomics/methods/economics ; Time Factors ; Sensitivity and Specificity ; Computational Biology/methods ; Biodiversity ; Resource-Limited Settings ; },
abstract = {Environmental DNA (eDNA) analysis enables biodiversity monitoring by detecting organisms from trace genetic material, but high reagent costs, cold-chain logistics and computational demands limit its broader use, particularly in resource-limited settings. To address these challenges and improve accessibility, we directly compared multiple workflow components, including four DNA extraction methods, two primer sets, three Nanopore basecalling models, and two demultiplexing pipelines. Across 48 workflow combinations tested in an aquarium with 15 fish species, we mapped trade-offs between cost, sensitivity, and processing speed to assess where time and resource savings are possible without compromising detection. Workflows using the Qiagen Blood and Tissue (BT) extraction kit and amplification using the MiFish-U primer set provided the highest sensitivity, detecting ≥ 12 of 15 species by ~3-5 h and reaching the 15-OTU plateau at ~8-10 h with Oxford Nanopore's high accuracy (HAC) basecalling model. Chelex, an alternative lower-cost extraction method, showed partial recovery only (≤ 9 OTUs by 61 h) even with extended sequencing, and did not recover all 15 OTUs. DirectPCR and QuickExtract offered field-friendly extraction alternatives that achieved comparable recovery in ~10-12 h, though their cost-effectiveness varied. While the MarVer1 primer was designed to broaden vertebrate detection, it recovered the same fish species as MiFish-U, though with fewer total reads. Real-time sequencing trials (0-61 h) revealed that high-efficiency workflows (BT + HAC) reached detection plateaus rapidly, indicating sequencing time can be reduced without sacrificing accuracy. The OBITools4 bioinformatics pipeline enabled automated demultiplexing but discarded more reads than an alternative, ONTbarcoder2.3, which retained low-abundance taxa at the cost of manual curation. Rather than identifying a single 'best' workflow, this study provides a transparent decision framework for prioritising cost, speed, and sensitivity in eDNA applications, supporting scalable, cost-effective eDNA monitoring in resource-limited settings.},
}
@article {pmid41482538,
year = {2026},
author = {Trigodet, F and Sachdeva, R and Banfield, JF and Eren, AM},
title = {Troubleshooting common errors in assemblies of long-read metagenomes.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41482538},
issn = {1546-1696},
abstract = {Assessing the accuracy of long-read assemblies, especially from complex environmental metagenomes that include underrepresented organisms, is challenging. Here we benchmark four state-of-the-art long-read assembly software programs, HiCanu, hifiasm-meta, metaFlye and metaMDBG, on 21 PacBio HiFi metagenomes spanning mock communities, gut microbiomes and ocean samples. By quantifying read clipping events, in which long reads are systematically split during mapping to maximize the agreement with assembled contigs, we identify where assemblies diverge from their source reads. Our analyses reveal that long-read metagenome assemblies can include >40 errors per 100 million base pairs of assembled contigs, including multi-domain chimeras, prematurely circularized sequences, haplotyping errors, excessive repeats and phantom sequences. We provide an open-source tool and a reproducible workflow for rigorous evaluation of assembly errors, charting a path toward more reliable genome recovery from long-read metagenomes.},
}
@article {pmid41482085,
year = {2026},
author = {Yang, B and Xia, Q and Ji, X and Su, K and Yu, T and Xiao, Z and Shi, C and Luo, Z and Wang, X and Xu, W and Gao, Y and Hua, H and Shan, J},
title = {Ganjie Decoction protects against respiratory syncytial virus infection by activating PI3K/AKT-apoptosis axis and regulating gut microbiota metabolism.},
journal = {Journal of ethnopharmacology},
volume = {360},
number = {},
pages = {121142},
doi = {10.1016/j.jep.2025.121142},
pmid = {41482085},
issn = {1872-7573},
mesh = {Animals ; *Respiratory Syncytial Virus Infections/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Proto-Oncogene Proteins c-akt/metabolism ; Mice ; Phosphatidylinositol 3-Kinases/metabolism ; Mice, Inbred BALB C ; Apoptosis/drug effects ; Signal Transduction/drug effects ; Humans ; *Antiviral Agents/pharmacology ; Lung/drug effects/pathology/virology ; Molecular Docking Simulation ; Female ; Male ; },
abstract = {Ganjie Decoction (GJD), a traditional Chinese medicine (TCM) formula commonly used for respiratory diseases, has shown therapeutic potential against RSV pneumonia. However, its pharmacological mechanisms against respiratory syncytial virus (RSV) pneumonia are not fully understood.<br><br>AIM OF STUDY: This study aimd to characterize the active components of GJD and systematically investigate its therapeutic effects and underlying mechanisms in RSV-induced pneumonia.<br><br>MATERIALS AND METHODS: To evaluate the therapeutic efficacy of GJD in RSV-infected mice, we monitored body weight, performed qPCR, and conducted histopathological examination of lung tissues. The chemical constituents of GJD were characterized using UPLC-MS. Key bioactive compounds and their potential targets were predicted using network pharmacology and molecular docking. The underlying mechanisms were further elucidated using immunohistochemistry and western blotting. The interactions between GJD and the gut microbiota were explored using antibiotic depletion, fecal microbiota transplantation (FMT), metagenomic sequencing, and in vitro co-culture assays. Untargeted metabolomics was employed to assess GJD-induced metabolic alterations. Finally, the role of the key metabolite 4-hydroxyphenylacetic acid (4-HPA) was investigated in vivo and in vitro through qPCR, immunohistochemistry, ELISA, Western blot, cell viability assays and immunofluorescence.<br><br>RESULTS: GJD significantly mitigated weight loss, attenuated pulmonary viral load, and suppressed inflammation in RSV-infected mice. Network pharmacology and molecular docking revealed that specific compounds in GJD target the PI3K/AKT signaling pathway. This finding was validated by western blotting and immunohistochemistry, which demonstrated that GJD suppresses PI3K/AKT pathway activation, thereby attenuating apoptosis and ameliorating RSV-induced pneumonia. Notably, these protective effects were markedly attenuated in mice with depleted gut microbiota, while therapeutic effects of GJD against RSV pneumonia were transferable via gut microbiota transplantation. GJD restored RSV-induced dysbiosis of the gut microbiota, with Lactobacillus reuteri emerging as one of the most enriched microbes following treatment. Metabolomics analysis identified 4-HPA as a microbiota-dependent metabolite significantly upregulated by GJD. Remarkably, administration of 4-HPA reproduced GJD's therapeutic effects in RSV-infected mice and activated the KEAP1/NRF2 antioxidant pathway, suggesting that 4-HPA functions as a key mediator of GJD's anti-RSV activity.<br><br>CONCLUSIONS: These findings suggest that GJD alleviates RSV pneumonia through a synergistic mechanism that modulates the PI3K/AKT-apoptosis pathway, restores gut microbial balance, and normalizes metabolic disturbances. This study systematically elucidates the mechanistic basis underlying the therapeutic effects of GJD against RSV pneumonia.},
}
@article {pmid41481471,
year = {2026},
author = {Regan, MD and Chiang, E and Grahn, M and Tonelli, M and Assadi-Porter, FM and Suen, G and Carey, HV},
title = {Host-microbiome mutualism drives urea carbon salvage and acetogenesis during hibernation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {1},
pages = {e2518978123},
pmid = {41481471},
issn = {1091-6490},
support = {IOS-1558044//NSF (NSF)/ ; P41GM136463//HHS | NIH (NIH)/ ; DGE-1747503//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; RGPIN-2021-03109//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; 21HLSRM06//Canadian Space Agency (CSA)/ ; },
mesh = {Animals ; *Hibernation/physiology ; *Urea/metabolism ; *Sciuridae/microbiology/physiology/metabolism ; *Carbon/metabolism ; *Acetates/metabolism ; *Gastrointestinal Microbiome/physiology ; *Symbiosis/physiology ; Acetic Acid/metabolism ; Fatty Acids, Volatile/metabolism ; *Host Microbial Interactions/physiology ; },
abstract = {Hibernation is a seasonal survival strategy employed by certain mammals that, through torpor use, reduces overall energy expenditure and permits long-term fasting. Although fasting solves the challenge of winter food scarcity, it also removes dietary carbon, a critical biomolecular building block. Here, we demonstrate a process of urea carbon salvage (UCS) in hibernating 13-lined ground squirrels, whereby urea carbon is reclaimed through gut microbial ureolysis and used in reductive acetogenesis to produce acetate, a short-chain fatty acid (SCFA) of major value to the host and its gut microbiota. We find that urea carbon incorporation into acetate is more efficient during hibernation than the summer active season and that while both host and gut microbes oxidize acetate for energy supply throughout the year, the host's ability to absorb and oxidize acetate is highest during hibernation. Metagenomic analysis of the gut microbiome indicates that genes involved in the degradation of gut mucins, an abundant endogenous nutrient, are retained during hibernation. The hydrogen disposal associated with reductive acetogenesis from urea carbon helps facilitate this mucin degradation by providing a luminal environment that sustains fermentation, thereby generating SCFAs and other metabolites usable by both the host and its gut microbes. Our findings introduce UCS as a mechanism that enables hibernating squirrels and their gut microbes to exploit two key endogenous nutrient sources-urea and mucins-in the resource-limited hibernation season.},
}
@article {pmid41481285,
year = {2026},
author = {Zhu, J and Huang, Z and Lin, Y and Zhu, J and Min, R and Wan, Z and Chen, Y and Zhu, J and Xing, L and Li, S and Olovo, CV and Wang, X and Li, G and Zhang, P},
title = {The potential immunological mechanisms of gut microbiota dysbiosis caused by antibiotics exacerbate the lethality of influenza viruses.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2609451},
pmid = {41481285},
issn = {1949-0984},
mesh = {Animals ; *Dysbiosis/immunology/chemically induced/microbiology ; *Gastrointestinal Microbiome/drug effects/immunology ; *Anti-Bacterial Agents/adverse effects ; Mice ; *Orthomyxoviridae Infections/immunology/drug therapy/mortality/virology/microbiology ; Antiviral Agents/therapeutic use/pharmacology ; *Influenza A virus/drug effects/pathogenicity/immunology ; Lung/immunology/virology/pathology/drug effects ; Humans ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Antibiotics are not recommended to treat influenza A virus (IAV). However, antibiotic misuse for IAV persists worldwide. How to scientifically use antibiotics for IAV-infected patients remains a considerable challenge.<br><br>RESULTS: Here, we investigated the impact of antibiotics on viral pathogenicity, pulmonary-intestinal antiviral immunity, and antiviral drug efficacy. Our findings indicated that antibiotic intervention exacerbated IAV-caused mortality and lung injury in mice, manifested as increased mortality rates, shortened survival time, aggravated pulmonary injury, and excessive inflammatory responses. Furthermore, antibiotic pretreatment significantly diminished the efficacy of antivirals. Metagenomic sequencing revealed that antibiotics reduced the diversity and abundance of beneficial gut microbiota, including Lactobacillus and Bifidobacterium, while promoting the proliferation of pathogenic bacteria such as Klebsiella pneumoniae and Escherichia coli. Mechanistically, antibiotic intervention exacerbated IAV-caused excessive inflammatory responses by the blockage of pulmonary-intestinal antiviral immune pathways, which were caused by the upregulation of PKR, RIG-I, ISG15, and TRIM25 levels while downregulating IPS-1 mRNA levels. However, it is noteworthy that the combination of antibiotics and antiviral drugs effectively offset the adverse effects of antibiotic pretreatment on influenza mortality by upregulating IPS-1 levels and partially restoring pulmonary-intestinal immune homeostasis.<br><br>CONCLUSIONS: Pulmonary-intestinal immune homeostasis imbalance caused by antibiotic misuse can not only markedly exacerbate the lethality of IAV, but also significantly attenuate the efficacy of antiviral drugs. A mechanistic study confirmed that gut microbes dysbiosis caused by antibiotic pretreatment exacerbates the homeostasis imbalance of host antiviral immunity by blocking the RIG/MDA5/IPS-1 antiviral signaling pathway. However, combination therapy with antibiotics and antivirals effectively reversed the fatal outcome exacerbated by antibiotic pretreatment. Collectively, our findings not only provide a scientific explanation from the perspective of antiviral immunity as to why antibiotics should not be arbitrarily used to treat viral infections but also lay the scientific foundation for the rational clinical use of antivirals and antibiotics for treating influenza.},
}
@article {pmid41480317,
year = {2025},
author = {Zakharzhevskaya, NB and Erdes, SI and Belousova, EA and Samolygo, IS and Manina, MA and Kondrashova, PV and Lomakina, EY and Kardonsky, DA and Vorobyeva, EA and Shagaleeva, OY and Silantyev, AA and Kazakova, VD and Kashatnikova, DA and Kalachnuk, TN and Kolesnikova, IV and Chaplin, AV and Markelova, MI and Grigoryeva, TV and Olekhnovich, EI and Veselovsky, VA and Morozov, MD and Zoruk, PY and Boldyreva, DI and Vanyushkina, AA and Efimov, BA},
title = {Combined metabolomic and metagenomic analysis reveals inflammatory bowel disease diversity in pediatric and adult patients.},
journal = {World journal of gastroenterology},
volume = {31},
number = {48},
pages = {112653},
pmid = {41480317},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metabolomics/methods ; *Colitis, Ulcerative/microbiology/diagnosis/metabolism ; *Crohn Disease/microbiology/diagnosis/metabolism ; Feces/microbiology ; Child ; Middle Aged ; Male ; Female ; *Metagenomics/methods ; Adolescent ; Child, Preschool ; Aged ; Biomarkers/metabolism/analysis ; Age Factors ; Adult ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; },
abstract = {BACKGROUND: The gut microbiota displays pronounced compositional differences between pediatric and adult populations, both under normal conditions and during the development of inflammatory bowel disease (IBD). These structural variations are accompanied by substantial changes in microbial metabolic activity.<br><br>AIM: To identify novel early diagnostic biomarkers of IBD, we performed an integrated multi-omics analysis that included assessing microbial community structure and profiling microbial metabolic activity in pediatric and adult cohorts with ulcerative colitis (UC) and Crohn's disease (CD).<br><br>METHODS: The study cohort consisted of two distinct age groups with confirmed IBD diagnoses: Adult patients (aged 45 to 70) and pediatric patients (aged 5 to 15), each diagnosed with either CD or UC. 16S rRNA gene sequencing was performed using the MinION&#x2122; Mk1B platform, with data acquisition carried out via MinKNOW software version 22.12.7 (Oxford Nanopore Technologies). Stool samples were analyzed using a Shimadzu QP2010 Ultra GC/MS system equipped with a Shimadzu HS-20 headspace extractor.<br><br>RESULTS: Comparative analysis revealed significant age-related differences in the abundance of Bacteroidota, with pediatric IBD patients showing a lower prevalence compared to adults. Microbial profiling identified Streptococcus salivarius and Escherichia coli as potential biomarkers for assessing IBD risk in children. Furthermore, metagenomic analysis uncovered five microbial signatures with diagnostic potential for CD: Ralstonia insidiosa, Stenotrophomonas maltophilia, Erysipelatoclostridium ramosum, Blautia spp., and Coprococcus comes. Using comprehensive metabolomic profiling, we developed and validated novel risk prediction algorithms for pediatric IBD. The CD risk stratification model identifies high-risk patients based on two key biomarkers: An elevated IBD risk coefficient score and reduced levels of 1H-indole-3-methyl. The UC risk prediction model incorporates three metabolic biomarkers indicative of increased disease risk: An elevated risk coefficient score, increased acetate levels, decreased pentanoic acid, and altered excretion of p-cresol (4-methylphenol).<br><br>CONCLUSION: Functional metabolomics holds transformative potential for IBD diagnostics across all age groups, with especially significant implications for pediatric patients. The distinct metabolic and metagenetic profiles observed in the pediatric cohort may represent primary alterations in IBD, providing valuable insights for exploring novel mechanisms underlying disease pathogenesis.},
}
@article {pmid41480270,
year = {2025},
author = {Bustos-Caparros, E and Viver, T and Gago, JF and Venter, SN and Bosch, R and Konstantinidis, KT and Rodriguez-R, LM and Rossello-Mora, R},
title = {Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf228},
pmid = {41480270},
issn = {2730-6151},
abstract = {An unbiased and accurate estimation of intraspecies diversity, i.e. the extent of genetic diversity within species (or microdiversity), is crucial for clinical and environmental microbiome studies. Although it is well appreciated that sequencing depth (or coverage depth) below 10X can provide biased estimates of microdiversity, typically underestimating diversity due to the random sampling of alleles, there is a widely accepted convention that microdiversity estimates tend to be relatively stable at sequencing depth exceeding 10X. Therefore, discarding species with <10X or rarefying to 10-20X sequencing depth are generally used to compare microdiversity among taxa and samples. Our findings showed that these biases may persist even at depth levels above 50-200X for all popular sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. The biases mostly, but not always, represent an underestimation of diversity and were attributable to the incomplete recovery of Single Nucleotide Variants (SNVs) at lower sequencing depth levels. To address this issue, we recommend using rarefaction-based approaches to standardize data at least 50X, and ideally at 200X sequencing depth, which reduces differences between observed and expected microdiversity values to <0.5%. Furthermore, the Average Nucleotide Identity of reads (ANIr) metric is significantly less sensitive to sequencing depth variability than nucleotide diversity (π), making it a robust alternative for estimating microdiversity at sequencing depth close or exceeding 10X, without a need to rarefying data. Therefore, the sequencing depth thresholds proposed herein provide a more standardized framework for direct comparisons of microdiversity across samples and studies.},
}
@article {pmid41480265,
year = {2025},
author = {Ren, G and Gubry-Rangin, C and Wang, W and Liu, R and Liu, J and Liu, J and Zhang, XH and Liu, J},
title = {Purifying selection and low recombination facilitated sequential colonization of benthic and pelagic coastal ocean by ammonia-oxidizing archaea.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf234},
pmid = {41480265},
issn = {2730-6151},
abstract = {The evolutionary adaptation of archaea to ecologically diverse habitats remains poorly understood. Ammonia-oxidizing archaea (AOA) exhibit significant diversification across various environmental conditions; however, their ecological dynamics, diversification, and associated evolutionary processes are still largely unexplored in coastal environments, which contain extensive ecosystem heterogeneity. Combining newly assembled metagenomic data from Chinese marginal seas (2059 km coverage) with global datasets (spanning over 16 000 km), these knowledge gaps were explored across a continental-scale latitudinal gradient. It revealed that coastal AOA genomic diversity is latitude-dependent, with predicted optimum growth temperatures and substrate metabolic pathways explaining the geographical distribution. The two dominant genus-level clades exhibited significantly distinct benthic-pelagic niches, associated with specific genes involved in nutrient uptake and stress resistance. Phylogenomic reconstructions suggest that AOA initially colonized the coastal ocean sediments around 718 million years ago (Mya), and subsequent purifying selection and low recombination facilitated the AOA niche expansion into marine coastal environments. By revealing the evolutionary trajectories of Nitrososphaeria and their differential colonization patterns, our findings offer a novel perspective on the mechanisms of AOA diversification in the coastal ocean. This work advances our understanding of microbial diversification and niche differentiation of AOA in coastal ecosystems as well as the evolutionary forces shaping their global biogeography.},
}
@article {pmid41480263,
year = {2025},
author = {Ma, M and Wang, M and Liang, Y and Guo, Y and Zhang, H and Cao, L and Fu, L and Hu, G and Li, C and Mock, T and Li, C},
title = {Microbial communities and metabolic functions vary with spatial heterogeneity in cold-seep carbonates.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf232},
pmid = {41480263},
issn = {2730-6151},
abstract = {Cold-seep carbonates, formed through interactions among methane, fluid chemistry, and microbial chemosynthesis, represent biodiversity hotspots in the deep sea. Spatial heterogeneity within these carbonates arises from variations in methane flux, yet the microbial contributions to this heterogeneity remain underexplored. Here we combined remotely operated vehicle-based in situ measurements, X-ray imaging, metagenomics, qPCR, and [13]C-CH4 stable-isotope labeling to investigate microbial communities across carbonate habitats in the South China Sea. We found that methane flux linked to carbonate structural properties, shapes microbial metabolic interactions, notably anaerobic methane oxidation coupled with aragonite and FeS precipitation. These processes may contribute to self-sealing carbonate features, potentially reducing methane permeability and influencing geochemical gradients and geomorphology. Our findings reveal that microbiomes and their feedbacks play a significant role in shaping habitat-scale spatial heterogeneity of cold-seep carbonates, improving our understanding of methane cycling and carbonate ecosystem dynamics.},
}
@article {pmid41478678,
year = {2026},
author = {Wang, Y and He, L and Hu, X and Guan, Y and Chen, X and Du, J and Chen, J and Ma, C and Ye, L},
title = {Metagenomic and culture-based genomics reveal virulence and resistance risks in Manila clam microbiomes.},
journal = {Food microbiology},
volume = {136},
number = {},
pages = {105001},
doi = {10.1016/j.fm.2025.105001},
pmid = {41478678},
issn = {1095-9998},
mesh = {Animals ; *Bivalvia/microbiology ; Metagenomics ; *Bacteria/genetics/isolation &amp; purification/pathogenicity/drug effects/classification ; *Microbiota ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence ; Genomics ; *Drug Resistance, Bacterial ; Vibrio/genetics/pathogenicity/isolation &amp; purification/drug effects ; Shellfish/microbiology ; Phylogeny ; },
abstract = {Bivalves are important aquaculture products whose safety is shaped by their microbiomes. Here, we present the first comprehensive characterization of Manila clam (Ruditapes philippinarum) microbiomes using both shotgun metagenomics (6 clams) and culture-based genomics (169 isolates, 40 draft genomes), integrating community, functional, and antimicrobial resistance profiling. Communities were dominated by Proteobacteria (99.3-99.9 %), with Pseudoalteromonas and Vibrio collectively accounting for 74.9-99.7 % and showing strong inverse correlations, defining Pseudoalteromonas-dominated, Vibrio-dominated, and mixed states. Species richness ranged from 22 to 180 per sample. Recognized human pathogens occurred at low abundance (<0.3 %), including Vibrio parahaemolyticus, Vibrio alginolyticus, and Photobacterium damselae, while opportunistic vibrios expanded in some clams (e.g., Vibrio cyclitrophicus 57.9 %). We reconstructed 34 high-quality MAGs, seven resolved to species (Pseudoalteromonas tetraodonis, V. cyclitrophicus, Shewanella aquimarina), alongside unclassified lineages. Metagenomes encoded 14 virulence-factor categories with 2281 subtypes, and isolate genomes added 93 further subtypes, including high-virulence loci in Escherichia coli and type III secretion genes in V. parahaemolyticus. Resistomes spanned 18 antibiotic classes with 511 subtypes; isolates contributed 22 additional antibiotic resistance genes(ARGs), including extended-spectrum β-lactamases (blaCTX-M-102) and blaNDM-1. Four carbapenemase-producing isolates (three Shewanella algae, one V. parahaemolyticus) carried blaNDM-1 on IncC plasmids, with the V. parahaemolyticus plasmid transferable to E. coli. Two P. tetraodonis MAGs encoded RiPP-like and terpene biosynthetic clusters plus phage-defense systems, consistent with Vibrio suppression. These findings demonstrate that clam microbiomes fluctuate between protective (Pseudoalteromonas) and pathogenic (Vibrio-Shewanella) states, providing a first integrated framework for assessing microbial risk, antimicrobial resistance, and food safety interventions in bivalve aquaculture.},
}
@article {pmid41478124,
year = {2026},
author = {Xing, W and Gai, X and Cheng, X and Fang, Z and Chen, G},
title = {Rhizosphere microbiome drives Betula luminifera adaptation to antimony mining sites through functional traits and transcriptional reprogramming.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140972},
doi = {10.1016/j.jhazmat.2025.140972},
pmid = {41478124},
issn = {1873-3336},
mesh = {*Rhizosphere ; Mining ; *Antimony/toxicity ; *Microbiota ; *Soil Pollutants/toxicity ; Adaptation, Physiological ; Soil Microbiology ; Plant Roots/microbiology/growth &amp; development ; },
abstract = {Rhizosphere microbiome are pivotal for plant adaptation to extreme environments. However, the regulatory mechanisms underlying their control of the ecological adaptation of native woody plants in mining areas remain unclear. Here, we integrated metagenomic and transcriptomic analyses to elucidate how the rhizosphere microbiome facilitates Betula luminifera adaptation to antimony (Sb) mining sites. Under sterile conditions, B. luminifera from mining sites prioritized shoot growth, whereas control-origin seedlings favored root development. Microbial inoculation mitigated this growth dichotomy, balancing above- and belowground biomass allocation. Notably, B. luminifera from control sites upregulated antioxidant biosynthesis genes (α- and β-tocopherol pathways), while B. luminifera from mining sites enhanced lignin synthesis under Sb stress. After inoculation with rhizosphere microbiome from the mining-site, genes related to Sb/As resistance (ACR3, arsB/C) and soil nutrient cycle (narG, phnM) were significantly enriched in the rhizosphere of B. luminifera, which were contributed by Proteobacteria and Actinobacteria. Transcriptional profiling revealed that microbial inoculation triggered systemic upregulation of phytohormone-related genes (auxin, cytokinin, abscisic acid), enhancing stress resilience and growth. These findings unveil a synergistic plant-microbe adaptation mechanism in Sb polluted soils in mining sites, highlighting microbial-mediated trait trade-offs and transcriptional plasticity as drivers of ecological success in extreme environments.},
}
@article {pmid41478064,
year = {2026},
author = {Zhang, H and Zhang, S and Li, X and Wang, W and Kuang, H},
title = {Bupleurum polysaccharide improves CUMS-induced depressive behavior in rats by regulating the "microbiota-gut-brain Axis": a mechanism study based on metabolomics and metagenomics.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1270},
number = {},
pages = {124905},
doi = {10.1016/j.jchromb.2025.124905},
pmid = {41478064},
issn = {1873-376X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Depression/metabolism/drug therapy/microbiology ; Male ; *Polysaccharides/pharmacology/chemistry ; Metabolomics/methods ; Metagenomics/methods ; Rats, Sprague-Dawley ; *Bupleurum/chemistry ; *Antidepressive Agents/pharmacology/chemistry ; Brain/drug effects/metabolism ; *Stress, Psychological/metabolism ; Metabolome/drug effects ; Disease Models, Animal ; Behavior, Animal/drug effects ; },
abstract = {This study aimed to comprehensively investigate the antidepressant mechanisms of Bupleurum polysaccharide (BP) through the microbiota-gut-brain axis, employing an integrated multi-omics approach. Using a chronic unpredictable mild stress (CUMS) rat model of depression, we evaluated BP's effects on depressive-like behaviors and analyzed its regulatory mechanisms on metabolites and gut microbiota through combined metabolomics and metagenomics. Structural characterization revealed that Bupleurum polysaccharide SPAP-1 is an acidic homogeneous polysaccharide with a molecular weight of approximately 100 kDa, primarily composed of glucose, mannose, rhamnose, and other monosaccharides. Pharmacodynamic assessments demonstrated that BP significantly ameliorated CUMS-induced depressive behaviors, including weight loss, reduced food intake, anhedonia, and behavioral despair (P < 0.05). Metabolomic analysis identified 19 differential metabolites, with BP reversing 11 of them, primarily involved in phenylalanine and tryptophan metabolism pathways. Western blot analysis confirmed BP's regulatory effects on key enzymes Got1 and Lta4h. Metagenomic results showed that BP remarkably reshaped gut microbiota structure, restored microbial diversity, optimized the Firmicutes/Bacteroidetes ratio, enriched beneficial genera (Agathobacter, Phocaeicola), and inhibited pathogenic genera (Ruminococcus). Crucially, integrated multi-omics analysis revealed significant microbiota-metabolite correlations, demonstrating that BP-promoted beneficial bacteria positively correlated with neurotransmitter precursors, while BP-inhibited pathogenic bacteria associated with pro-inflammatory mediators. Mediation analysis further established the "microbiota → metabolite → behavior" causal chain, with Ruminococcus → LTB4 → despair behavior accounting for 42.3 % of the mediation effect. In conclusion, Bupleurum polysaccharide ameliorates depressive-like behaviors through multi-target regulation of the metabolite-microbiota interaction network, highlighting its potential as an antidepressant agent or functional food and providing a novel research paradigm for understanding the multi-target characteristics of traditional Chinese medicine polysaccharides.},
}
@article {pmid41474788,
year = {2025},
author = {Wong, KX and Chen, ST and Ong, JJ and Gan, WY and Abdul Murad, NA and Chong, CW and Ramzi, NH},
title = {Exploring gut microbiome and nutritional status among children with Autism Spectrum Disorder (MY-ASD Microbiome): A study protocol.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0338801},
pmid = {41474788},
issn = {1932-6203},
mesh = {Child ; Child, Preschool ; Female ; Humans ; Male ; *Autism Spectrum Disorder/microbiology ; Case-Control Studies ; Feces/microbiology ; *Gastrointestinal Microbiome ; Malaysia ; *Nutritional Status ; Saliva/microbiology ; Observational Studies as Topic ; },
abstract = {BACKGROUND: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterised by persistent deficits in social communication and the presence of restricted, repetitive behaviours or interests. Previous literature has identified a link between the gut and ASD; however, the underlying mechanisms remain unclear. Gut microbiota dysbiosis has been extensively reported in cohort studies of ASD, and specific microbial metabolites or by-products may serve as potential biomarkers for ASD. Additionally, children with ASD often exhibit food refusal, have a limited food repertoire and display a tendency to consume the same foods frequently; thus, these behaviours increase their risk of malnutrition (over-nutrition or under-nutrition) compared to typically developing (TD) healthy children. This study primarily aims to identify oral and gut microbiota among children with ASD and TD healthy children. The secondary aim is to determine the associations between oral and gut microbiota with nutritional status among children with ASD. The findings will enhance understanding of the aetiology of ASD and inform early intervention strategies to mitigate disease severity and early identification of malnutrition in genetically at-risk children.<br><br>METHODS AND ANALYSIS: This observational, age-matched, case-control study is conducted in Malaysia among 40 male children with ASD and age-matched with 40 TD healthy controls aged 4-10 years. The dependent variables include the microbiota profile, identified through metagenomic sequencing analysis of saliva and faecal samples, and autism severity, assessed through validated questionnaires. Independent variables include nutritional status, determined through Subjective Global Nutrition Assessment (SGNA), anthropometry and dietary measurements, gastrointestinal symptoms, eating behaviour, behavioural profile, and sleep quality. Data collection is expected to be completed by June 2026. The study nature may limit causality establishment. Analyses will use chi-square/ANOVA for group comparisons, SparCC for microbiota correlations, and mixed-effects logistic regression to model associations.<br><br>CONCLUSION: This study advances understanding of ASD-related microbiota, guiding personalised nutrition and precision healthcare in Malaysia.},
}
@article {pmid41474524,
year = {2025},
author = {Luo, S and Li, Z and Peng, Y and Xie, X and Zeng, Y and Dai, L and Zhang, X},
title = {Comparative metagenomics reveals the differential gut microbiota involved in bile acid metabolism in patients with crohn's disease.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {42},
number = {1},
pages = {21},
pmid = {41474524},
issn = {1573-0972},
support = {32101368//National Natural Science Foundation of China/ ; 2022YFE0119600//National Key Research and Development Program of China/ ; 2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; },
mesh = {Humans ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/genetics ; *Crohn Disease/microbiology/metabolism ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Male ; Female ; Adult ; Feces/microbiology ; Middle Aged ; },
abstract = {Gut microbiota plays a critical role in bile acid (BA) metabolism within healthy populations, yet the differential species involved in BA metabolism in patients with Crohn's disease (CD) remains poorly characterized. To address this knowledge gap, we conducted a comparative metagenomics for nine CD patients and nine healthy controls. Integrated metagenomic species profiling and functional annotation, accompanied with species-function network analysis, reduced abundance in metabolism-associated genes and lower species-function correlation were predicted, suggesting a possible imbalance of microbial communities in CD group. Focused on functional genes involved in BA metabolism and their associated bacterial taxa, our results revealed that Anaerostipes hadrus-like (P = 0.001317), Roseburia intestinalis-like (P = 0.03542), and Coprococcus catus-like (P = 0.0005787), the microbial species related to bile salt hydrolase-coding gene, showed significantly lower abundance in CD patients. Conversely, Ruminococcus gnavus-like, related to 3α-hydroxysteroid dehydrogenase (3α-HSDH)- and 3β-HSDH-coding genes, demonstrated relatively higher abundance (P = 0.0257). Escherichia coli-like, the species for 7α-HSDH-coding genes, also exhibited higher abundance in CD group (P = 0.01044). Further network correlation analysis indicated that there was a potential association between these differential species with other co-occurring gut microbiota. Collectively, the findings identify and characterize the differential gut microbiota involved in BA metabolism in CD patients, which may provide the possible target microorganisms for future therapeutic interventions.},
}
@article {pmid41473771,
year = {2025},
author = {Mao, X and Hu, X and Fang, J},
title = {Gut microbiota-metabolite interactions in drug-induced liver injury: mechanisms, biomarkers, and therapeutic perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1737234},
pmid = {41473771},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Chemical and Drug Induced Liver Injury/microbiology/metabolism/therapy ; Biomarkers/metabolism ; Dysbiosis ; Animals ; Liver/metabolism ; },
abstract = {Drug-induced liver injury (DILI) remains a major obstacle in clinical pharmacotherapy and a leading cause of acute liver failure and drug withdrawal worldwide. Conventional mechanistic models centered on hepatic xenobiotic metabolism, oxidative stress, and immune injury cannot fully account for the substantial interindividual variability and the unpredictable nature of idiosyncratic DILI. Increasing evidence shows that the gut microbiota and its metabolites critically shape hepatic susceptibility through modulation of drug metabolism, inflammatory signaling, and intestinal barrier integrity. This review summarizes current understanding of the gut-liver axis in DILI pathogenesis, with a focus on microbial enzymes such as β-glucuronidase that reactivate detoxified drug conjugates, microbial dysbiosis that disrupts bile acid homeostasis, and depletion of short chain fatty acids and indole derivatives that normally support epithelial defenses and immunologic tolerance. Drug-specific microbial patterns are discussed, including acetaminophen, amoxicillin-clavulanate, anti-tuberculosis regimens, and immune checkpoint inhibitors. We introduce the concept of metabotype-dependent hepatotoxicity, which emphasizes that individual microbial metabolic profiles influence DILI risk. Advances in metagenomics, metabolomics, and integrative multi-omics enable the identification of microbial biomarkers and functional pathways associated with DILI susceptibility. Emerging therapeutic strategies include restoration of microbial homeostasis, selective inhibition of microbial enzymes, and supplementation of hepatoprotective metabolites. Finally, we outline key challenges and future directions toward translating microbiome-based insights into clinical prediction and precision prevention of DILI. Importantly, this review integrates microbial metabolic functions with precision hepatology concepts, highlighting how metabotype-driven variability can be leveraged for individualized DILI risk assessment.},
}
@article {pmid41472301,
year = {2025},
author = {Yagi, K and Ethridge, AD and Asai, N and Malinczak, CA and Arzola Martinez, L and Rasky, AJ and Morris, SB and Falkowski, NR and Fonseca, W and Huffnagle, GB and Lukacs, NW},
title = {Changes in Microbiome Correspond with Diminished Lung Pathophysiology Following Early-Life Respiratory Syncytial Virus Infection or Antibiotic Treatment: Microbiome Following RSV Infection.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
pmid = {41472301},
issn = {1999-4915},
mesh = {*Respiratory Syncytial Virus Infections/microbiology/physiopathology/drug therapy/virology ; Animals ; *Lung/physiopathology/microbiology/virology/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice ; Mice, Inbred BALB C ; Dysbiosis ; *Microbiota/drug effects ; Gastrointestinal Microbiome/drug effects ; Animals, Newborn ; Disease Models, Animal ; Ampicillin/pharmacology ; Respiratory Syncytial Viruses ; Humans ; Female ; },
abstract = {Early-life respiratory syncytial virus (EL-RSV) infection has been implicated in long-term pulmonary disease in children. In these studies, neonatal BALB/c mice were infected at day 7 of life, leading to >35% losses in critical lung function, airway mucus metaplasia, and transcriptional hallmarks of mucus hypersecretion four weeks after RSV infection. While EL-RSV minimally reshaped the resident lung microbiota, it led to significant gut dysbiosis, including a long-term reduction of Proteobacteria that can be a source of protective metabolites related to barrier and immune function. Subsequent studies assessing whether a common infant antibiotic (ampicillin) could mitigate EL-RSV-induced lung alterations revealed further severe gut microbiome alterations and, on its own, later in life, recapitulated the full spectrum of RSV-associated alterations in lung function. Metagenomic inference showed that both RSV and ampicillin administered during early life reduced biosynthetic pathways for microbiome-derived metabolites, which are known to reinforce tight junctions, regulate inflammation, and preserve extracellular matrix elasticity. The shared loss of these metabolic programs provides a mechanistic bridge linking distinct early-life exposures to the microbiome changes and airway mechanical deficits later in life. Collectively, the data suggest that RSV and/or antibiotic-triggered gut dysbiosis is the primary insult that likely promotes improper lung maturation/repair through a metabolite-mediated mechanism and may suggest metabolite restoration as a strategy to promote proper developmental lung function.},
}
@article {pmid41472294,
year = {2025},
author = {Mandal, E and Noirungsee, N and Disayathanoowat, T and Kil, EJ},
title = {TSWV Infection Differentially Reshapes the Symbiotic Microbiome of Two Frankliniella Thrips Species.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
pmid = {41472294},
issn = {1999-4915},
support = {0//Gyeongkuk National University/ ; },
mesh = {*Thysanoptera/microbiology/virology ; Animals ; *Symbiosis ; *Microbiota ; *Tospovirus/physiology ; Serratia/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Insect Vectors/virology/microbiology ; Metagenomics ; Plant Diseases/virology ; Wolbachia/genetics ; },
abstract = {Vectoring tomato spotted wilt virus (TSWV) by two well-known thrips species, Frankliniella occidentalis Pergande and F. intonsa Trybom (Thysanoptera: Thripidae), is facilitated in different ways. Symbiotic bacteria positively influence thrips fitness, but the interaction between these bacteria and tospovirus inside the thrips' body remains unknown. Metagenomic profiling of symbionts in nonviruliferous and viruliferous Frankliniella thrips was performed to elucidate the interactions between symbiotic bacteria and the virus. A total of 97 operational taxonomic units (OTUs) were identified by profiling the microbes, where Proteobacteria was the most abundant phylum, with a high richness in Serratia spp. F. occidentalis showed lower variation in bacterial diversity between nonviruliferous and viruliferous treatments than F. intonsa. RT-qPCR validation for Serratia and Escherichia revealed opposite abundance patterns between the two thrips species. In contrast, Enterobacteriaceae and Pantoea showed similar patterns with higher abundance in nonviruliferous conditions. Wolbachia was detected exclusively in F. intonsa, with a higher bacterial titer in the viruliferous sample. Our findings suggest that TSWV association may influence the abundance of different bacterial symbionts within the thrips' body, potentially via induction of antimicrobial peptides in response to viral invasion, and to our knowledge this is the first report addressing this tripartite interaction. These findings improve our understanding of how virus-symbiont association contributes to thrips vector competence.},
}
@article {pmid41472203,
year = {2025},
author = {Lapshina, VK and Guskova, NI and Stetsenko, IF and Luong, MT and Tran, TV and Matsvay, AD and Shipulin, GA and Yudin, SM and Skvortsova, VI},
title = {Characterizing the Bat Virome of Vietnam: A Systematic Review of Viral Diversity and Zoonotic Potential.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
pmid = {41472203},
issn = {1999-4915},
support = {388-00084-24-00//Federal Medical Biological Agency/ ; },
mesh = {Animals ; Humans ; Biodiversity ; *Chiroptera/virology ; Disease Reservoirs/virology ; Genetic Variation ; Vietnam/epidemiology ; *Viral Zoonoses/epidemiology/virology ; *Virome ; *Viruses/genetics/classification/isolation &amp; purification ; },
abstract = {Bats have been identified as reservoir hosts for an exceptional diversity of viruses, including multiple taxa of high zoonotic concern. Over a hundred bat species inhabit Vietnam, which, combined with significant biodiversity, carry high risk of zoonotic spillover due to dense human-animal interfaces, extensive wildlife trade, and proximity to recent outbreak epicenters. This review systematically synthesizes data on the bat virome in Vietnam and neighboring Southeast Asian countries, assessing viral diversity, host species involvement, and zoonotic potential. By prioritizing virus groups with established zoonotic capacity and pandemic potential, the systematic search identified studies reporting viruses from 32 families across 13 bat families. Based on the WHO 2024 risk classification, seven of these viral families were categorized as high-risk, three as medium-risk, and twelve as low-risk. The comparatively higher viral diversity reported in neighboring countries suggests that the current study likely represents an underestimation of the true virome present in Vietnamese bat populations. We emphasize the urgent need for expanded virological studies integrating metagenomic sequencing, serological surveys, and ecological modeling to improve early detection of emerging threats, as the comparatively higher viral diversity reported in neighboring countries suggests existing research likely represents an underestimation of the true virome present in Vietnamese bat populations. Strengthening regional collaboration is critical for establishing proactive pandemic prevention strategies in this high-risk zoonotic hotspot.},
}
@article {pmid41471876,
year = {2025},
author = {Wang, Y and Gong, L and Gao, Z and Dong, D and Li, X},
title = {Comparative Analysis of Sponge-Associated, Seawater, and Sediment Microbial Communities from Site F Cold Seep in the South China Sea.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471876},
issn = {2076-2607},
support = {42176114//National Natural Science Foundation of China/ ; ZR2023MD100//the Shandong Provincial Natural Science Foundation/ ; CAS-TAX-24-30//Biological Resources Programme, Chinese Academy of Sciences/ ; },
abstract = {Microbial communities at Site F cold seep, ubiquitous in both the environment and the associated fauna, demonstrate clear habitat-specific partitioning. Metagenomic sequencing and binning demonstrated a striking partitioning of microbial taxa at the cold seep: whereas the sponge-associated microbiome was distinctly enriched with specialized sulfur- and methane-oxidizing bacteria that were rare in the environment, it simultaneously exhibited a significantly reduced archaeal content, lower α-diversity, and a simpler overall community structure compared to the sediment and seawater communities. Distinct evolutionary lineages and varying abundances were observed among the microbiomes from seawater, sediment, and sponges. Furthermore, their Metagenome-Assembled Genomes (MAGs) exhibited significant differences in genomic features, including genome size and GC content. The sponge-associated microbiome exhibits lower diversity but maintains a high abundance of key functional genes, particularly those involved in sulfur cycling (e.g., apr, dsr, metZ), indicating enhanced metabolic efficiency in energy conservation and nutrient acquisition. This study reveals that the seawater, sediment, and sponge-associated microbiomes exhibit genome simplification and functional specialization in the cold seep environment, with varying lifestyles driving structural optimization and functional remodeling of the symbiotic microbiomes.},
}
@article {pmid41469026,
year = {2026},
author = {Yao, L and Solania, A and Luissint, AC and Balana, AT and Zhang, H and Sangaraju, D and Lai, Z and Kuo, J and Storek, KM and Wolan, DW},
title = {The Secreted Metabolite Isopentenyladenine from Faecalibacterium prausnitzii Is Anti-inflammatory with Barrier-Protective Properties.},
journal = {ACS infectious diseases},
volume = {12},
number = {1},
pages = {224-236},
doi = {10.1021/acsinfecdis.5c00771},
pmid = {41469026},
issn = {2373-8227},
mesh = {Animals ; *Faecalibacterium prausnitzii/metabolism ; Mice ; *Anti-Inflammatory Agents/pharmacology/metabolism ; *Colitis/chemically induced/prevention &amp; control/drug therapy/microbiology ; Mice, Inbred C57BL ; Disease Models, Animal ; Gastrointestinal Microbiome ; Humans ; Inflammatory Bowel Diseases ; Administration, Oral ; Female ; },
abstract = {Colonic microbiome dysbiosis is correlated with inflammatory bowel disease (IBD), and depletion of the commensal bacterium Faecalibacterium prausnitzii (F. prausnitzii) is routinely observed in the metagenomic analyses of IBD patient microbiome samples. F. prausnitzii is likely beneficial to hosts, as oral administration of F. prausnitzii strain A2-165 has anti-inflammatory properties in murine models of colitis. Previous studies attribute the anti-inflammatory effects of F. prausnitzii A2-165 to production of the short-chain fatty acid butyrate, as well as a secreted protein known as microbial anti-inflammatory molecule (MAM). Here, we verified that oral dosing of strain A2-165 protects against DSS-induced murine colitis and further showed that the aqueous-soluble secreted fraction of overnight cultures from a collection of F. prausnitzii strains inhibits inflammatory signatures, including the activation of the host's NF-κB pathway, production of IL-8, and differentiation of naïve T cells into the TH17 lineage. Our findings against a panel of in vitro assays suggested that the anti-inflammatory responses were attributable to secreted small-molecule or peptide metabolites, as both heat-inactivated and proteinase K-treated F. prausnitzii culture supernatants retained activity. Untargeted and targeted mass spectrometry metabolomics analyses on the soluble anti-inflammatory secretome yielded several unique F. prausnitzii metabolites, including isopentenyladenine. We demonstrated that isopentenyladenine independently modulates host cellular signaling and immune responses and suggest that this newly identified metabolite with human immunomodulatory properties may be useful toward the discovery of IBD-focused therapeutics.},
}
@article {pmid41468674,
year = {2026},
author = {Feng, W and Ma, R and Guo, Y and Zhang, B and Lan, J and Liu, J and Chen, S},
title = {Rhizosphere metagenomics and metabolomes provide new insights into the relationship between rhizosphere microecology and early bolting of Angelica dahurica.},
journal = {Microbiological research},
volume = {305},
number = {},
pages = {128435},
doi = {10.1016/j.micres.2025.128435},
pmid = {41468674},
issn = {1618-0623},
mesh = {*Rhizosphere ; *Angelica/microbiology/growth &amp; development/metabolism ; *Metagenomics/methods ; Soil Microbiology ; Plant Roots/microbiology/chemistry ; *Metabolome ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Microbiota ; Soil/chemistry ; Coumarins/analysis/metabolism ; Quorum Sensing ; Metabolomics ; Acyl-Butyrolactones/metabolism ; },
abstract = {Angelica dahurica is a medicinal and edible plant with a wide range of pharmaceutical and food applications. However, the early bolting, which leads to reduced yield and loss of bioactive constituents, has become a major obstacle to the industrial development of A. dahurica. Rhizosphere microecology affects plant growth and secondary metabolite accumulation, but the association of rhizosphere microecology with the early bolting of A. dahurica is not fully understood. This study integrated metagenomic and metabolomic analyses to systematically characterize the differences in rhizosphere microecology of non-bolting and early bolting A. dahurica plants. Results revealed significant disparities in soil physicochemical properties, root exudate profiles, and microbial community composition between two groups, all of which exhibited correlations with the coumarin compounds content, the primary pharmacologically active constituents of A. dahurica. Integrated analysis suggested that root-derived acyl-homoserine lactone (AHL) quorum-sensing signals, as the primary chemical signals of the prevalent Gram-negative bacteria, may participate in regulating the microbial community structure and soil properties, thereby influencing the bolting and flowering process. This study proposes a potential complex regulatory network of "rhizosphere microbiome - quorum-sensing signals - soil nitrogen cycle - bolting and flowering" linking the rhizosphere microecology to early bolting in A. dahurica, thereby addressing a key knowledge gap in this area. The findings offer a scientific foundation and innovative strategy for the simultaneous prevention of early bolting and quality improvement in A. dahurica through soil microecological management, which is of significant importance for promoting the sustainable commercial development of the A. dahurica industry.},
}
@article {pmid41468660,
year = {2026},
author = {Yu, X and Huang, S and Tang, J and Peng, C and Wen, Q and Chen, S and Lei, L and Yang, C and Liu, Y and Xiang, W and Zhang, Q and Lin, H and Zhang, M},
title = {Multi-omics reveals efficient thiamethoxam biodegradation but altered flavor profile by native microbiota during Pixian broad bean paste fermentation.},
journal = {International journal of food microbiology},
volume = {449},
number = {},
pages = {111600},
doi = {10.1016/j.ijfoodmicro.2025.111600},
pmid = {41468660},
issn = {1879-3460},
mesh = {Fermentation ; *Thiamethoxam/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Neonicotinoids/metabolism ; *Insecticides/metabolism ; *Vigna/microbiology/chemistry/metabolism ; Guanidines/metabolism ; Taste ; Metagenomics ; Multiomics ; Thiazoles ; },
abstract = {Thiamethoxam (TH), a systemic neonicotinoid insecticide, poses food safety risks due to its persistence and uptake in crops. Microbial degradation during fermentation offers a promising decontamination strategy, but the underlying mechanisms and impact on food quality remain unclear. This study investigated TH and its toxic metabolite clothianidin biodegradation in Pixian broad bean paste (PBP) fermentation, assessed the impact of residue dissipation on product quality, and revealed microbial responses and metabolic adaptations under pesticide stress. Results demonstrated that TH and clothianidin were nearly completely degraded in the PBP fermentation system within 16 days, with a half-life of 3.25 days. Metagenomic analysis revealed that TH stress enriched pollutant-degrading microbes (e.g., Aspergillaceae, Desulfobacterota) and upregulated xenobiotic degradation genes (e.g., drug metabolism). However, volatile flavor compounds analysis indicated that TH treatment altered the flavor profile by reducing esters and phenols while increasing ketones and acids. Integrated metabolomics demonstrated that TH may disrupt organic acid metabolism during early fermentation, suppressing downstream flavonoid transformation and amino acid biosynthesis, ultimately compromising nutritional quality and flavor attributes. Multi-omics integration revealed that TH stress reshaped microbial community structure and enabled dual regulation of pesticide degradation and fermentation pathways through coordinated gene expression, ultimately altering PBP fermentation quality. Therefore, these findings demonstrate that the native microbial community in PBP efficiently degrades neonicotinoid pesticides, providing a novel strategy for the bioremediation of fermented foods and serving as an emerging reservoir of potential safe degrading bacteria, while highlighting the necessity for optimized microbial interventions to minimize adverse effects on product quality.},
}
@article {pmid41467811,
year = {2026},
author = {Ha, LH and On, YY and Pohan, C and Lee, J and How, SHC and Teo, Y-Y and Seedorf, H and Gounot, J-S and Nagarajan, N},
title = {High-throughput single-cell isolation of Bifidobacterium strains from the human gut microbiome.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0303325},
pmid = {41467811},
issn = {2165-0497},
support = {NRFI09-0015//National Research Foundation Singapore/ ; CIRG22jul-0023//National Medical Research Council/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Bifidobacterium/isolation &amp; purification/genetics/classification ; Feces/microbiology ; *Single-Cell Analysis/methods ; Whole Genome Sequencing ; Genome, Bacterial ; Phylogeny ; },
abstract = {UNLABELLED: Bifidobacterium represents a diverse genus of commensal gut bacteria with key roles in human health, from metabolizing indigestible fibers to protecting against pathogens. While metagenomic studies have highlighted significant strain diversity for Bifidobacterium species within individuals, their systematic isolation and phenotypic characterization can be hampered by the significant effort and biases inherent in traditional culturomics. Here, we explored the utility of a high-throughput single-cell dispensing system (B.SIGHT)-based workflow for accelerating the process of isolating diverse Bifidobacterium strains from fecal samples. Systematic assessment of this workflow revealed a high single-cell dispensing frequency (>88%) and the ability to preserve species diversity when a pool of Bifidobacterium strains was dispensed. Culturing-related factors including the use of an effective selection medium, such as the Bifidus Selective Medium supplemented with mupirocin, and the length of pre-dispensing incubation were found to be critical in determining isolation success. Leveraging this workflow, we obtained a total of 622 viable isolates from five Singaporean fecal samples, of which >98% were found to be from Bifidobacterium species. Whole-genome sequencing of 96 isolates identified six different Bifidobacterium species with both inter- and intra-subject strain and lineage diversity, and the majority (>66%) were novel relative to large public genomic databases. Our findings highlight the ability of this high-throughput culturomics workflow to accelerate the recovery of diverse and novel Bifidobacterium strains, enabling further interrogation of their functional characteristics and advancing our understanding of important bacterial species in the gut microbiome.<br><br>IMPORTANCE: The field of high-throughput microbial culturomics is still in its early stages. Enhancing our ability to isolate and phenotypically test bacterial strains from complex communities is crucial for advancing microbiome research and healthcare development. Given the time and cost inefficiencies of traditional culturing methods, a more efficient, high-throughput approach to obtain isolates is needed. In the present study, we assessed a single-cell dispensing platform and developed a workflow to isolate diverse Bifidobacterium strains from fecal samples. We demonstrated here the capability of this novel technology to efficiently obtain hundreds of isolates of a targeted group, covering both species and strain diversities. This generalizable and scalable method can potentially allow for the high-throughput recovery of microbes from other taxonomic groups, providing a fundamental step in improving the culturomics framework to complement metagenomic approaches and enable isolate-level functional studies of important microbes.},
}
@article {pmid41467786,
year = {2026},
author = {McParland, EL and Wittmers, F and Bolaños, LM and Carlson, CA and Curry, R and Giovannoni, SJ and Michelsen, M and Parsons, RJ and Kido Soule, MC and Swarr, GJ and Temperton, B and Vergin, K and Worden, AZ and Longnecker, K and Kujawinski, EB},
title = {Seasonal patterns of DOM molecules are linked to microbial functions in the oligotrophic ocean.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0154025},
pmid = {41467786},
issn = {2379-5077},
support = {//Woods Hole Oceanographic Institution/ ; //Simons Foundation/ ; },
mesh = {*Seasons ; *Seawater/microbiology/chemistry ; *Microbiota ; Oceans and Seas ; *Organic Chemicals/analysis/metabolism ; Bacteria/metabolism/genetics/classification ; },
abstract = {Hundreds of thousands of individual microbe-molecule interactions regulate the flux, transformation, and fate of carbon stored in the climatically important reservoir of marine dissolved organic matter (DOM). While marine microbial communities have been characterized at high resolution for over a decade, observations of the molecules cycled by the microbial-chemical network at similar resolution are limited. In addition, bulk characterizations of DOM can mask the complex network of interactions comprised of rich chemical diversities. Here, we present a three-year, depth-resolved, molecular time-series of DOM and prokaryoplankton at the Bermuda Atlantic Time-series Study (BATS) site. Both time-series exhibited seasonality that was compositionally distinct and primarily endemic to one sampling depth. We also putatively identified four exometabolites (gonyol, glucose-6-sulfate, succinate, and trehalose) that exhibit seasonal accumulation. We hypothesize these patterns result from environmental conditions that alter community composition on a seasonal timescale and thus shift the relative proportions of microbial functions that produce and consume the substrates. Critically, we observed the interannual composition of seasonal DOM molecules to be more stable than the taxonomy of the microbial community. This points to an important role of functional redundancy in regulating DOM composition. We tested this observation by querying metagenomes for pathways that utilize metabolic by-products putatively identified in the DOM time-series. We find that core microbial metabolisms, either those required by all or by a subset of marine microbes, are important predictors of DOM composition. The molecular-level characterization of DOM herein highlights the potential imprint of microbial activity on seasonal DOM composition.IMPORTANCEMarine dissolved organic matter (DOM) is a major carbon reservoir that acts as a critical control on the Earth's climate. DOM dynamics are largely regulated by a complex web of chemical-microbial interactions, but the mechanisms underpinning these processes are not well understood. In a three-year time-series, we found that the identity of the microbes is more likely to change between years than the composition of the DOM molecules. The taxonomic variability suggests that metabolisms shared across taxa, encoded by genes that conduct core microbial functions, are responsible for the more stable composition of DOM. While more than three decades of marine prokaryoplankton time-series are available, a similar reference for DOM molecules was missing. This time-series provides an improved understanding of the different responses of DOM molecules and microbes to seasonal environmental changes.},
}
@article {pmid41467315,
year = {2025},
author = {Sun, Y and Li, P and Wang, X and Jiang, D and Shao, Y},
title = {Gut dysbiosis in early severe burns contributes to acute lung injury by impairing neutrophil chemotaxis.},
journal = {Journal of leukocyte biology},
volume = {118},
number = {1},
pages = {},
doi = {10.1093/jleuko/qiaf169},
pmid = {41467315},
issn = {1938-3673},
support = {82302800//National Natural Science Foundation of China/ ; 2024M751108//China Postdoctoral Science Foundation/ ; SDCX-ZG-202400032//Postdoctoral Innovation Program in Shandong Province/ ; },
mesh = {Animals ; *Dysbiosis/complications/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Acute Lung Injury/etiology/pathology/microbiology/immunology ; *Neutrophils/immunology/pathology ; Humans ; Mice ; *Burns/complications/microbiology/pathology/immunology ; *Chemotaxis, Leukocyte ; Male ; Female ; Mice, Inbred C57BL ; Butyrates/pharmacology ; Disease Models, Animal ; Neutrophil Infiltration ; Chemotaxis ; },
abstract = {Severe burns complicated by acute lung injury are critical causes of respiratory failure and multiple organ dysfunction syndrome. Neutrophils extensively infiltrate lung tissues early postburn to mediate pulmonary damage, but the underlying mechanisms remain unclear. We analyzed gut microbiota of severe burn patients via metagenomics and metabolomics, assessed neutrophil chemotaxis using a self-developed in vitro agarose model, and validated Faecalibacterium prausnitzii and butyrate's effects on restoring neutrophil chemotaxis in gut microbiota-depleted mice via oral gavage (plus in vivo validation with small animal imaging). Bronchoalveolar lavage fluid biomarkers and pulmonary function tests evaluated pulmonary injury from impaired neutrophil chemotaxis. Early postburn, F. prausnitzii and its metabolite butyrate were significantly depleted in patients, concurrent with impaired neutrophil chemotaxis-restored by butyrate supplementation. In murine burn models, F. prausnitzii or butyrate rescued neutrophil chemotaxis, reduced pulmonary neutrophil infiltration, and attenuated lung injury. Mechanistically, butyrate restored neutrophil function in a severe burn patient plasma-stimulated model by downregulating P2X1 receptor expression and suppressing myosin light chain phosphorylation. Our findings indicate postburn gut microbiota dysbiosis and metabolite alterations disrupt neutrophil chemotaxis, causing excessive pulmonary neutrophil infiltration/activation. This highlights gut microbiota-derived metabolites as potential therapeutics for mitigating neutrophil-driven lung injury early postsevere burns.},
}
@article {pmid41466385,
year = {2025},
author = {Zhao, L and Li, M and Wang, Y and Chen, L},
title = {Combined effects of sound and temperature on the composition and function of bacterial and fungal communities in loess.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {803},
pmid = {41466385},
issn = {1471-2180},
support = {31920250052; 22YF7FA172; Z2101707; 31560120//the Fundamental Research Funds for the Central Universities; the Key Research and Development Program of Gansu Province; Talent Introduction Program of Northwest Minzu University; National Natural Science Foundation of China/ ; },
mesh = {*Fungi/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Temperature ; *Soil Microbiology ; China ; *Sound ; Biodiversity ; *Mycobiome ; Metagenomics ; Phylogeny ; Soil/chemistry ; *Microbiota ; },
abstract = {In Northwest China, the dominant soil type is loess, which is highly susceptible to various environmental factors. Of these, limited research has focused on the impacts of sound disturbance and temperature fluctuations on the microbial communities in loess. An orthogonal experiment was conducted by varying sound intensity (70 dB, 90 dB, 110 dB), sound duration (2 h, 4 h, 6 h), and temperature (- 5 °C, 15 °C, 35 °C). Metagenomic sequencing was then applied to investigate the effects of sound and temperature on the composition and function of bacterial and fungal communities in loess. Our results show that under the combined effects of sound and temperature, the dominant phyla and genera of bacteria and fungi have different responses and preferences to temperature and sound decibels. Alpha diversity analysis revealed that the Shannon index of the bacterial community differed significantly under the 90 dB treatment at - 5 °C and under the 110 dB treatment at 15 °C (P < 0.05). For the fungal community, both the Simpson and Shannon indices showed significant differences under the 70 dB treatment at - 5 °C and under the 110 dB treatment at 15 °C (P < 0.05). Notably, the richness of rare fungal taxa and overall species richness in the loess fungal community were significantly enhanced at 90 dB compared with the control and other treatment groups, while these indices were significantly reduced at 110 dB. In the loess microbial treatment groups subjected to the combined effects of sound and temperature, the gene abundance of CAZy family genes was lowest under high decibel (110 dB) sound stimulation. Among the six enzyme-encoding gene categories within the CAZy family, the highest number of annotated species was observed in Group A (2 h, 70 dB, - 5 °C), whereas the lowest was recorded in Group C (6 h, 110 dB, - 5 °C). Among the metabolic pathway functional genes annotated in the KEGG database, the abundance of metabolic genes in Group C (6 h, 110 dB, - 5 °C) was significantly lower than that in other treatment groups.},
}
@article {pmid41466331,
year = {2025},
author = {Li, J and Zhang, X and Zhao, X and Gong, G and Li, J and Dalai, B and Mo, Z and Xu, X and Jia, X and Li, Y and Lai, J and Wang, P and Sun, L and Liu, Y and Luo, X},
title = {Characterising gut microbiome dysbiosis in diarrhoea calves from multiple farms in Inner Mongolia using 16S and metagenomics.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {259},
pmid = {41466331},
issn = {2049-2618},
support = {2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; },
mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/genetics ; *Diarrhea/microbiology/veterinary/epidemiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; China/epidemiology ; *Dysbiosis/microbiology/veterinary ; *Cattle Diseases/microbiology/epidemiology ; Feces/microbiology ; Escherichia coli/genetics/isolation &amp; purification/pathogenicity ; *Bacteria/classification/genetics/isolation &amp; purification ; Farms ; },
abstract = {BACKGROUND: The pathogenesis of neonatal calf diarrhoea (NCD), a critical disease that contributes to neonatal mortality in calves, remains nebulous.<br><br>RESULTS: Inner Mongolia, a key region for cattle farming in China, was selected as a study area to provide a comprehensive overview of the epidemiology and treatment of calf diarrhoea. No significant correlation was found between the incidence of diarrhoea and sampling points or medications. The severity of diarrhoea cases was stratified into five levels based on faecal characteristics. To elucidate the pathogenesis of NCD, 16S rRNA gene and metagenomic sequencing analyses were performed across severity levels. Microbial diversity analyses revealed distinct variations in microbial communities at different severity levels. Employing binning and LEfSe methodologies, two potential bacterial pathogens were identified: Escherichia coli (bin.216), leveraging non-canonical virulence mechanisms; and Streptococcus ruminantium (bin.338), an uncharacterised diarrhoeagenic bacterium. Furthermore, the viral agent Escherichia phage VpaE1_ev108 was significantly associated with disease progression. Gene function enrichment analysis revealed a broad spectrum of antibiotic resistance genes even in farms without direct antibiotic treatment, underscoring the pervasive prevalence of drug resistance.<br><br>CONCLUSIONS: The findings of this study revealed significant gut microbial dysbiosis in calves with severe diarrhoea, through which two putative NCD-associated pathogens were identified: E. coli (bin.216) and S. ruminantium (bin.338). Marked enrichment of Bacteroides spp. and Methanobrevibacter_A sp. 900313645 was observed in healthy cohorts, suggesting their potential protective roles. Therapeutic strategies employing phage-mediated pathogen targeting combined with probiotic transplantation have demonstrated dual benefits, potentially reducing antimicrobial dependency and preserving microbial homeostasis through ecological network reconstruction. Video Abstract.},
}
@article {pmid41466105,
year = {2025},
author = {Zhang, H and Shen, C and Lei, W and Wang, J and Liu, J and Qiu, Z},
title = {Pilot Clinical Trial of Fecal Microbiota Transplantation for Constipation in Parkinson's Disease.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2509029},
pmid = {41466105},
issn = {1738-8872},
mesh = {Humans ; *Constipation/therapy/etiology/microbiology ; *Fecal Microbiota Transplantation/methods ; *Parkinson Disease/complications/therapy/microbiology ; Aged ; Pilot Projects ; Middle Aged ; Male ; Gastrointestinal Microbiome ; Female ; Prospective Studies ; Feces/microbiology ; Treatment Outcome ; Dysbiosis/therapy ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {The purpose of this study was to evaluate the safety and efficacy of fecal microbiota transplantation in patients with constipation due to parkinson's disease. Gut dysbiosis has long been associated with parkinson's and recent studies have shown that FMT can restore the normal flora of the gut. Therefore, this clinical trial aimed to test the therapeutic efficacy of FMT in 5 patients aged 55 to 71 diagnosed with PD who presented with constipation. The study was conducted as an open label, prospective trial and consisted of FMT performed every 3 days via nasojejunal tube placement followed by 8 weeks of patient follow-up to evaluate response to drug therapy and to assess neurological function using UPDRS-III OFF scores, and improvement in constipation assessed with Wexner scores. Samples taken before and after FMT were collected for shotgun metagenomic sequencing to analyze the composition of the microbial communities present in patients. Untargeted non-targeted metabolomic studies were performed to investigate the impact of FMT on metabolome changes due to FMT. The results indicate an improvement in constipation and neurological functioning following FMT, and significant alteration of the gut microbiota. Significant increases in Bifidobacteria bifidus, Alistipes shahi, Anaerotruncus coli, and uncharacterized Flavonifractor were found post-treatment compared to the baseline. Many of the other strains present prior to treatment, including Acinetobacter sp. and Proteobacteria sp., had significantly decreased after the FMT. The metabolomic studies found shifts in metabolic pathways involved with unsaturated fatty acid synthesis and amino acid metabolism due to FMT. FMT may be an effective treatment option for constipation and neurological symptoms associated with PD.},
}
@article {pmid41465859,
year = {2025},
author = {Angelova, B and Boteva, S and Traykov, I and Tsvetkov, M and Kenarova, A},
title = {Bacterial Community Composition and Structure in the Littoral of Rila Mountains Glacial Lakes.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {41465859},
issn = {2075-1729},
support = {KP-06-M71/2//The Bulgarian National Science Fund/ ; },
abstract = {High-mountain lakes are biodiversity hotspots sensitive to increasing regional and global climate warming. However, their microbial communities remain insufficiently characterized due to their remoteness and limited accessibility. This study aimed to determine how seasonal environmental parameters shape the composition, structure and diversity of littoral bacterial communities in three glacial lakes in Rila Mountains (Bulgaria). Water samples were collected during ice-free periods in 2023 and 2024, and bacterial taxonomic composition was analysed by Next-generation sequencing. A total of 1158 bacterial OTUs were identified encompassing 18 phyla and 165 families. Actinomycetota, Pseudomonadota, and Bacteroidota were dominant at the phylum level, and Sporichthyaceae, Comamonadaceae, Chitinophagaceae and Mycobacteriaceae were most abundant among the families. Community richness and diversity peaked in June, immediately after ice melting, particularly in the highest-altitude lake (Sulzata Lake), and declined during the warm season (August), when the relative abundances of Sporichthyaceae and Mycobacteriaceae (Actinomycetota) increased. Seasonal restructuring occurred across phyla and families even in a single taxon, with water temperature and organic carbon availability identified as the main environmental drivers. The findings have improved our understanding of temperature-driven bacterial responses. They have also highlighted the vulnerability of cold-adapted taxa to regional climate warming which may contribute to more effective biodiversity conservation strategies for these unique ecosystems.},
}
@article {pmid41465567,
year = {2025},
author = {Zhao, H and Wang, H and Zhao, X and Song, Y and Liang, D and Ma, Y and Xu, Z},
title = {Bifidobacterium adolescentis Strengthens Gut Barrier in Post-Voyage Functional Constipation.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465567},
issn = {1422-0067},
support = {2024QN019//University-level research project of the Naval Medical University/ ; },
mesh = {*Constipation/microbiology/therapy/etiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Bifidobacterium adolescentis/physiology ; *Probiotics ; Mice, Inbred C57BL ; Feces/microbiology ; Male ; Humans ; Gastrointestinal Motility ; },
abstract = {Prolonged periods of sailing may contribute to the development of functional constipation, which can significantly impair an individual's work efficiency. Currently, the efficacy of Bifidobacteria in treating functional constipation is gaining recognition. However, since the therapeutic effects of Bifidobacteria are strain-specific, further research is required on strains isolated from pre-voyage fecal samples. This study examines the role of gut microbiota in post-stroke constipation, aiming to identify specific microbial biomarkers for the development of targeted therapeutic strategies. B. adolescentis was identified through metagenomic analysis and subsequently isolated for validation. In the experimental group (EG), C57BL/6J mice received fecal suspension treatment following a 12-day navigation period, which was subsequently followed by a 12-day oral administration of B. adolescentis. After treatment, EG significantly improved fecal volume, intestinal motility, and goblet cells; reversed microbial ecological imbalance; reduced pathogens (E. coli and Klebsiella) by restoring arginine/bile acid metabolism, decreasing Tauro-ursodeoxycholic acid (TUDCA) content, 5-Hydroxytryptamine 4 Receptor (5-HT4R)/Slc8a1 signaling, and Ca[2+] signaling pathway; and restoring beneficial species (B. adolescentis, Pseudomonas aeruginosa). This study provides new insights into probiotics in improving human intestinal health.},
}
@article {pmid41465246,
year = {2025},
author = {Sokolova, EA and Smirnova, NV and Fedorets, VA and Khlistun, IV and Mishukova, OV and Tromenschleger, IN and Savenkov, OA and Saprikin, OI and Rogaev, EI and Buyanova, MD and Filippova, IM and Mayorova, TM and Glukhova, MA and Ivanovna, MM and Manakhov, AD and Voronina, EN},
title = {Microbial Consortium Application Under Temperature Stress: Effects on the Rhizosphere Microbiome and Plant Growth.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465246},
issn = {1422-0067},
support = {075-15-2025-473//Ministry of Science and Higher Education of the Russian Federation (the Federal Scientific-technical programme for genetic technologies development for 2019-2030)/ ; },
mesh = {*Rhizosphere ; Soil Microbiology ; *Microbiota ; *Microbial Consortia ; *Stress, Physiological ; *Plant Development ; Crops, Agricultural/growth &amp; development/microbiology ; Temperature ; Bacteria/genetics ; Triticum/growth &amp; development/microbiology ; Fagopyrum/growth &amp; development/microbiology ; },
abstract = {The aim of the present study was to investigate the effect of a synthetic microbial consortium (SMC) containing five functionally different bacterial strains (Rahnella aquatilis, Rothia endophytica, Stenotrophomonas indicatrix, Burkholderia contaminans, Lelliotia amnigena) on the growth and development of three agricultural crops (wheat, buckwheat, and rapeseed) on two soil types (chernozem and gray forest soil) under field conditions. The experiment was conducted from June to September 2024 under extreme field conditions, with temperatures reaching 43.8 °C. This study evaluates SMC efficacy under severe abiotic stress, reflecting increasingly common climate extremes. Metagenomic data analysis showed that the introduced strains did not establish stable populations in the soil, possibly due to heat-induced bacterial mortality, though other factors including competition with indigenous microflora and lack of protective formulations may have also contributed. No statistically significant effects on plant morphometric parameters were observed. The extreme temperature and water stress conditions appear to have been the dominant limiting factors, overriding any potential benefits from microbial inoculation, as evidenced by the lack of response to mineral fertilizer application as well. Crop-specific effects were revealed: when cultivating rapeseed on chernozem, a significant increase in available phosphorus content was noted (from 278 ± 45 to 638 ± 92 mg/kg with SMC application, p < 0.001).},
}
@article {pmid41463847,
year = {2025},
author = {Moreira, G and Rodrigues, S and Gomes-Gonçalves, S and Silva, G and Amorim, I and Silva, E and Carmezim, S and Soeiro, V and Mesquita, JR},
title = {Highly Virulent Newcastle Disease Virus in Eurasian Collared Doves in the North of Portugal.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {24},
pages = {},
pmid = {41463847},
issn = {2076-2615},
abstract = {Newcastle disease (ND), caused by avian orthoavulavirus 1 (AOAV-1), poses a global threat to poultry and wild birds. In early 2025, an outbreak of pigeon paramyxovirus type 1 (PPMV-1, genotype VI AOAV-1) was detected in a wildlife rehabilitation centre in northern Portugal, affecting Streptopelia decaocto, Streptopelia risoria, and Columba livia. Birds showed acute neurological signs and died rapidly. Necropsy revealed brain and pulmonary congestion, splenomegaly, and cloacal lesions, while histopathology demonstrated hepatocellular necrosis, hemorrhage, and eosinophilic intracytoplasmic inclusions in hepatocytes and renal tubular cells. Matrix (M) gene PCR using standard primers was negative, but metagenomic sequencing identified genotype VI as being closely related to strains from Iran and Cyprus. Partial fusion (F) gene analysis revealed the velogenic RRQKRF motif. These findings confirm the circulation of highly virulent PPMV-1 in Portugal, highlight that standard, recommended primers may fail to detect some genetically diverse strains, and emphasize the role of Columbidae as reservoirs with potential transmission to domestic poultry.},
}
@article {pmid41461922,
year = {2026},
author = {Jin, S and Cenier, A and Wetzel, D and Arefaine, B and Moreno-Gonzalez, M and Stamouli, M and Mohamad, M and Lupatsii, M and Ríos, E and Lee, S and Zamalloa, A and Chokshi, S and Mardinoglu, A and Shoaie, S and Beraza, N and Patel, VC and Schirmer, M},
title = {Microbial collagenase activity is linked to oral-gut translocation in advanced chronic liver disease.},
journal = {Nature microbiology},
volume = {11},
number = {1},
pages = {211-227},
pmid = {41461922},
issn = {2058-5276},
support = {426120468//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; BBS/E/F/000PR13632//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/CCG1860/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 268211/1134579//Foundation for Liver Research/ ; },
mesh = {Humans ; Feces/microbiology ; *Collagenases/metabolism/genetics ; *Gastrointestinal Microbiome ; Mice ; Animals ; Saliva/microbiology ; Male ; Female ; Veillonella/genetics/enzymology/isolation &amp; purification ; Middle Aged ; Streptococcus/genetics/enzymology/isolation &amp; purification ; Metagenome ; *Bacterial Translocation ; *Bacteria/enzymology/genetics/classification/isolation &amp; purification ; Adult ; Disease Models, Animal ; *Mouth/microbiology ; Aged ; Liver Cirrhosis/microbiology ; *Liver Diseases/microbiology ; },
abstract = {Microbiome perturbations are associated with advanced chronic liver disease (ACLD), but how microorganisms contribute to disease mechanisms is unclear. Here we analysed metagenomes of paired saliva and faecal samples from an ACLD cohort of 86 individuals, plus 2 control groups of 52 healthy individuals and 14 patients with sepsis. We identified highly similar oral and gut bacterial strains, including Veillonella and Streptococcus spp., which increased in absolute abundance in the gut of patients with ACLD compared with controls. These microbial translocators uniquely share a prtC gene encoding a collagenase-like proteinase, and its faecal abundance was a robust ACLD biomarker (area under precision-recall curve = 0.91). A mouse model of hepatic fibrosis inoculated with Veillonella and Streptococcus prtC-encoding patient isolates showed exacerbation of gut barrier impairment and hepatic fibrosis. Furthermore, faecal collagenase activity was increased in patients with ACLD and experimentally confirmed for the prtC gene of translocating Veillonella parvula. These findings establish mechanistic links between oral-gut translocation and ACLD pathobiology.},
}
@article {pmid41461486,
year = {2026},
author = {Kang, S and Lee, JY and Cho, KS},
title = {Bacterial and fungal metagenomes associated with atmospheric particulates in Republic of Korea: Comparison of PM2.5 and TSP larger than PM2.5.},
journal = {Journal of environmental sciences (China)},
volume = {161},
number = {},
pages = {400-410},
doi = {10.1016/j.jes.2025.08.021},
pmid = {41461486},
issn = {1001-0742},
mesh = {*Particulate Matter/analysis ; Republic of Korea ; Bacteria/genetics ; *Air Pollutants/analysis ; *Environmental Monitoring ; Particle Size ; *Fungi/genetics ; *Metagenome ; *Air Microbiology ; Microbiota ; Air Pollution/statistics &amp; numerical data ; },
abstract = {Particulate matter (PM) significantly contributes to air pollution, potentially causing health issues, with PM-associated microorganisms implicated in some cases. While studies have explored microbial concentration and structure in PM based on particle size, comprehensive analysis of microbial functional traits and environmental influences is limited. This study evaluated microbial concentrations and diversity in PM with a diameter of 2.5 µm or lower (PM2.5) and total suspended particles (TSP) greater than PM2.5 (PM>2.5) samples relative to air temperature and other factors. DNA extracted from PM2.5 and PM>2.5 filters was sequenced to characterize bacterial and fungal community structures and functional genes. Results showed that microbial concentrations and diversity were greater in PM>2.5, with similar dominant species across PM sizes. Higher air temperatures correlated with increased microbial concentrations and diversity in PM>2.5, attributed to enhanced microbial growth. An Asian dust event from the Mongolian desert disrupted the PM microbiome. Despite consistent species dominance, gene function analysis revealed abundant drug resistance pathways in bacterial communities of both particle types, while pathotroph prevalence was higher in PM2.5 fungal communities. These findings indicate that PM2.5 microbial community analysis suffices for understanding PM ecosystems, offering valuable insights for air quality management and microbial pollution control, especially concerning potential pathogens.},
}
@article {pmid41461466,
year = {2026},
author = {Cui, M and Chen, S and Zhang, Z and Yu, Y and Xu, Y and Liu, L and Gao, H and Chen, X and Liu, Z and Zhang, X and Yuan, W and Chen, S and Li, D and Chen, L and Xing, X and Xiao, Y and Chen, W and Liu, Y and Wang, Q},
title = {Nanoplastics and triclosan co-exposure aggravates DSS-induced colitis in mice by interfering with Akkermansia muciniphila and tryptophan metabolism.},
journal = {Journal of environmental sciences (China)},
volume = {161},
number = {},
pages = {189-200},
doi = {10.1016/j.jes.2025.06.029},
pmid = {41461466},
issn = {1001-0742},
mesh = {Animals ; Mice ; *Colitis/chemically induced ; *Tryptophan/metabolism ; *Triclosan/toxicity ; Dextran Sulfate/toxicity ; *Microplastics/toxicity ; Akkermansia ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; *Environmental Pollutants/toxicity ; },
abstract = {The global incidence of inflammatory bowel disease (IBD) has been escalating. Recent studies have identified co-exposure to polystyrene nanoplastics (PSNP) and triclosan (TCS), two prevalent environmental pollutants, as emerging risk factors for IBD. However, the molecular mechanisms contributing to its deteriorative effect remain elusive. To explore the mechanisms, we conducted an integrative analysis of metagenomic and metabolomic data in a mouse model of colitis induced by dextran sulfate sodium (DSS) following co-exposure to PSNP and TCS. Results demonstrated that co-exposure to PSNP and TCS significantly exacerbated DSS-induced colitis, as evidenced by elevated disease activity indices and pro-inflammatory cytokine levels. Mechanistically, this aggravation correlated with a marked reduction in Akkermansia muciniphila abundance, which was further associated with the disruption of tryptophan metabolism. Specifically, the disruption of this metabolic pathway led to decreased production of two key tryptophan-derived metabolites: indole acetic acid (IAA) and indole acetamide (IAM). In-vitro experiments confirmed that co-exposure to PSNP and TCS inhibited the growth of A. muciniphila rather than affecting the integrity of intestinal epithelial cells. Additionally, IAA and IAM reduced inflammatory cytokine secretion in THP-1 cells. These findings suggest that the reduction in A. muciniphila abundance might decrease the production of IAA and IAM by disrupting tryptophan metabolism. This disruption ultimately contributes to the inflammatory response induced by co-exposure to PSNP and TCS. Our study offers a novel insight into microbiota-host interactions and potential therapeutic targets for intestinal disease.},
}
@article {pmid41460777,
year = {2025},
author = {Geraerts, M and Gombeer, S and Nebesse, C and Akaibe, D and Akaibe, D and Baelo, P and Chaber, AL and Gaubert, P and Gembu, GC and Joffrin, L and Laudisoit, A and Laurent, N and Leirs, H and Mande, C and Mariën, J and Ngoy, S and Těšíková, J and Vanderheyden, A and van Vredendaal, R and Verheyen, E and Gryseels, S},
title = {A wide diversity of viruses detected in African mammals involved in the wild meat supply chain.},
journal = {PLoS pathogens},
volume = {21},
number = {12},
pages = {e1013643},
pmid = {41460777},
issn = {1553-7374},
mesh = {Animals ; *Meat/virology ; *Mammals/virology ; *Animals, Wild/virology ; Democratic Republic of the Congo ; *Viruses/genetics/isolation &amp; purification/classification ; Zoonoses/virology ; Humans ; Phylogeny ; Belgium ; Genetic Variation ; },
abstract = {The processes involved in acquiring, trading, preparing, and consuming wild meat pose significant risks for the emergence of zoonotic infectious diseases. Several major viral outbreaks have been directly linked to the wild meat supply chain, yet our knowledge of the virome of many mammals involved in this chain remains limited and disproportionately focused on certain mammalian taxa and pathogens. Here, we present the findings of a metagenomic viral screening of 101 mammalian specimens belonging to 28 wild African species and one domesticated species, all traded for their meat. The study focuses on tissue and swab samples collected in various regions in the Democratic Republic of the Congo and in Brussels, Belgium. A total of sixteen virus strains were detected, belonging to the families Arteriviridae, Retroviridae and Sedoreoviridae (primates), Picobirnaviridae (primates and rodents), Picornaviridae (rodents), Hepadnaviridae (hyrax), Orthoherpesviridae (artiodactylid and carnivore) and Spinareoviridae (carnivore). Several strains were detected in mammalian hosts for the first time, expanding their host range and genetic diversity. Of note is the presence of viruses genetically related to recognised zoonotic pathogens, i.e., human picobirnavirus (Orthopicobirnavirus hominis) (primates and rodents), simian foamy viruses (Simiispumavirus) (primates), and rotavirus A (Rotavirus alphagastroenteritidis) (primates). The presence of these viruses in primates is concerning as non-human primates are phylogenetically closely related to humans, which can facilitate interspecies viral transmission. These findings underscore the high diversity of mammalian viruses and the potential risk of human infection through cross-species transmission during close interactions with wildlife in the wild meat supply chain.},
}
@article {pmid41460655,
year = {2026},
author = {Oso, TA and Ahmed, MM and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Othman, ZK and Lucero-Prisno, DE},
title = {Exploring the gut-brain-microbiome axis in Alzheimer's disease: Integrating metagenomics, metabolomics, and artificial intelligence for next-generation biomarker discovery.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {109},
number = {4},
pages = {1542-1557},
doi = {10.1177/13872877251407700},
pmid = {41460655},
issn = {1875-8908},
mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; *Metabolomics/methods ; *Artificial Intelligence ; Biomarkers/metabolism ; *Metagenomics/methods ; *Brain/metabolism ; Dysbiosis/metabolism ; },
abstract = {Alzheimer's disease (AD), a progressive neurodegenerative disorder, is increasingly understood as a multifactorial condition influenced by systemic and environmental factors beyond the central nervous system. A growing body of evidence shows that the gut-brain-microbiome axis (GBMA), a complex bidirectional communication network, is involved in neural, endocrine, immune, and metabolic pathways in AD pathogenesis. This narrative review synthesizes emerging insights into the role of gut microbiota dysbiosis in promoting neuroinflammation, amyloid-β aggregation, blood-brain barrier disruption, and cognitive decline. We explored recent advancements in metagenomics and metabolomics for profiling microbial communities and their functional metabolites linked to AD. Alterations in microbe-derived compounds, such as short-chain fatty acids and tryptophan metabolites, influence neurodevelopment, glial activation, and mitochondrial dysfunction. Multi-omics integration, enhanced by artificial intelligence (AI), enables precise biomarker discovery, patient stratification, and the development of personalized therapeutic strategies. Translational opportunities include microbiome-based diagnostics, probiotic therapy, and stratified interventions. However, clinical translation faces challenges such as methodological heterogeneity, inter-individual microbiome variation, data governance issues, and algorithmic bias. We emphasize the need for diverse reference panels, longitudinal multimodal cohorts, and shared AI-ready datasets to enhance the reproducibility and global equity of research. Strategic investment in integrative, ethically governed, and interdisciplinary approaches is essential to unlock the full therapeutic and diagnostic potential of GBMA in AD.},
}
@article {pmid41459746,
year = {2025},
author = {Duncan, A and Koon, W and Sidorczuk, K and Quince, C and Frioux, C and Hildebrand, F},
title = {Detecting signatures underlying the composition of biological data.},
journal = {Nucleic acids research},
volume = {53},
number = {22},
pages = {},
pmid = {41459746},
issn = {1362-4962},
support = {BB/Z516168/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //UK Research and Innovation/ ; //Earlham Institute Strategic Programme/ ; BBX011070/1//Grant Cellular Genomics/ ; BBS/E/ER/230001C//workpackage/ ; BBS/E/ER/230002A//workpackage/ ; BBS/E/F/000PR13631//workpackage/ ; ISP BBX011089/1//Decoding Biodiversity/ ; ISP BB/X011054/1//Quadram Institute Bioscience/ ; erc-stg-948219/ERC_/European Research Council/International ; ANR-22-PEAE-001//French National Research Agency/ ; //Earlham Institute and Quadram Institute Bioscience/ ; },
mesh = {Humans ; *Software ; Metagenome ; Rhizosphere ; Microbiota/genetics ; *Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Carcinoma, Non-Small-Cell Lung/genetics/pathology/microbiology ; Lung Neoplasms/genetics/pathology ; },
abstract = {Biological compositional data is inherently multidimensional and therefore difficult to visualize and interpret. To allow for the automatic decomposition of large compositional data and to capture gradients in co-occurring features, called signatures, we developed a new software package 'cvaNMF'. Our benchmarks on synthetic data show the effectiveness of cross-validation and our novel signature-similarity method to identify a suitable decomposition using non-negative matrix factorization (NMF). This software provides a complete set of tools to identify and visualize biologically informative signatures which we demonstrate in a wide range of microbial and cellular datasets: 'Enterosignatures' detected in gut metagenomes differentiated human hosts with diverse diseases; five 'terrasignatures' from rhizosphere metagenomes differentiated root- or soil-associated microbiomes, while being refined enough to infer geographic distances between plants. Large-scale data from >13 000 metagenomes representing 25 biomes were decomposed into environmental and host-associated microbiomes based on five newly discovered signatures. Finally, analysis of the cell composition of non-small cell lung cancer samples allowed separation of cancerous and inflamed tissues based on four cell-type signatures.},
}
@article {pmid41459742,
year = {2026},
author = {Kwon, Y and Choi, J and Kim, SH and Kim, PJ and Lee, SM and Cha, JK and Park, H and Kang, JW and Jo, S and Kwak, YS and Kim, D and Kim, WJ and Lee, JH and Ryu, CM},
title = {Rice gs3 allele and low-nitrogen conditions enrich rhizosphere microbiota that mitigate methane emissions and promote beneficial crop traits.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {41459742},
issn = {1751-7370},
support = {RS-2022-RD010405//Cooperative Research Program for Agriculture Science and Technology Development/ ; //Rural Development Administration/ ; //National Research Foundation/ ; NRF-2021M3A9I5021439//Ministry of Science and ICT/ ; RS-2023-00219213//Ministry of Science and ICT/ ; KRIBB//Korea Research Institute of Bioscience and Biotechnology/ ; //Initiative Program, South Korea/ ; },
mesh = {*Oryza/genetics/microbiology/metabolism ; *Rhizosphere ; *Methane/metabolism ; *Nitrogen/metabolism ; *Microbiota ; Soil Microbiology ; Alleles ; *Crops, Agricultural/genetics ; Metagenomics ; Metagenome ; Plant Roots/microbiology ; Nitrogen Fixation ; Bacteria/genetics/metabolism/classification ; },
abstract = {Methane emissions from rice paddies represent a critical environmental concern in agriculture. Although genetic strategies for mitigating emissions have gained attention, the specific microbial and molecular mechanisms remain underexplored. Here, we investigated how the gs3 loss-of-function allele in the near-isogenic rice line Milyang360 modulates rhizosphere and endosphere microbial communities under distinct nitrogen regimes. Field experiments revealed that Milyang360 consistently reduced methane emissions compared with its parental line Saeilmi particularly under low-nitrogen conditions. Integrated plant transcriptomic and rhizosphere metagenomic analyses, including the reconstruction of Metagenome-Assembled Genomes, demonstrated that the gs3 allele upregulated genes related to root hair elongation and promoting microbial nitrogen fixation. This physiological change limited substrate availability for methanogens and facilitated the colonization by beneficial microorganisms. Consequently, we observed a functional shift in the microbiome, characterized by the enrichment of methanotrophs and nitrogen-fixing bacteria. This microbial restructuring was most prominent under low-nitrogen conditions, indicating a strong genotype by environment interaction. Our findings highlight the gs3 allele's dual role in reducing methane emissions and improving nitrogen use efficiency by recruiting a beneficial microbiome. Our study provides a clear mechanistic link between a plant gene and rhizosphere ecology, offering a promising genetic target for developing sustainable, low emission rice cultivars.},
}
@article {pmid41459106,
year = {2025},
author = {Wróbel, M and Gawryś, R and Tereba, A and Frąk, M and Sikora, K and Sokołowski, K and Boczoń, A},
title = {Dependence of Bacterial OTUs on Selected Features of Beaver Ponds.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72790},
pmid = {41459106},
issn = {2045-7758},
abstract = {Ponds created by beavers represent unique aquatic ecosystems that influence hydrological, chemical and biological conditions, including the microbiology of the water. The activity of these animals promotes biodiversity and water purification processes, but can also lead to the accumulation of pollutants. Water retention in beaver ponds promotes the development of bacteria and other microorganisms that play an important role in biogeochemical cycles. Long-term water stagnation can lead to anaerobic conditions and the formation of toxic compounds, which in turn can limit the diversity of benthic organisms. Beavers play a key role in shaping these habitats, and microbiological studies of their reservoirs provide a better understanding of their impact on aquatic ecosystems, self-purification processes and potential biological threats. Metagenomic analysis revealed the presence of 365 bacterial species in water and sediment samples, belonging to 174 genera and 83 families. 83 operational taxonomic units (OTUs) were identified, 62 of which were present in both water and sediments. Although the overall OTU composition was similar in both environments, greater variability was observed in the sediments. The statistical differences in OTU distribution between water and sediments were confirmed using the Wilcoxon test.},
}
@article {pmid41457319,
year = {2026},
author = {Smith, DDN and Subasinghe, RM and Kehoe, C and Grégoire, DS},
title = {Multi-omics provides functional insights and underscores practical challenges in assessing the composition and performance of a nitrifying microbial consortium.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {1},
pages = {e0198425},
pmid = {41457319},
issn = {1098-5336},
support = {GRDI-AMR2 One Health,STAGE//Environment and Climate Change Canada/ ; 2022-04891//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Microbial Consortia ; Ammonia/metabolism ; *Nitrification ; Wastewater/microbiology ; *Bacteria/metabolism/genetics/classification ; Multiomics ; },
abstract = {UNLABELLED: Microbial consortia show promise for bioremediation of environmental pollution, but performance optimization and risk assessment remain challenging due to unculturable species and limitations of traditional biochemical and sequencing tools. This study demonstrates how a multi-omics approach can provide deeper insight into the performance and risks of using a model aerobic ammonia-oxidizing consortium under conditions representative of wastewater treatment. Long-read DNA sequencing recovered several high-quality genomes, revealing dominance by an unclassified Nitrosospira species with expected ammonia oxidation capabilities. Lower-abundance taxa with nitrogen cycling potential were also detected, though species-level identification was limited by poor taxonomic database representation. Multi-omics and nitrogen analyses showed shifts in community composition and nitrogen cycling activity when the consortium was grown along a redox gradient typical of wastewater. All cultures accumulated ammonia over 4 weeks, with only aerobic cultures reducing ammonia levels thereafter. The dominant Nitrosospira population declined in abundance and activity in aerobic cultures while shifting toward nitrogen reduction under anoxic conditions. This metabolic shift would not have been detected using amplicon sequencing alone. Multi-omics also supported risk assessment through detection of waterborne pathogens from the Legionella genus and other lineages harboring virulence genes resembling those from known pathogens. This study highlights the value of multi-omics for optimizing microbial consortia and assessing biosafety risks but also underscores challenges related to effective data analyses and the feasibility of risk assessment under realistic conditions. Addressing these challenges will be essential to support the broader adoption of multi-omics strategies by stakeholders working with microbial consortia across diverse environmental applications.<br><br>IMPORTANCE: Microbial consortia are increasingly used to advance a sustainable bioeconomy. Optimizing consortia for environmental applications and ensuring regulatory compliance remains challenging, largely due to reliance on culturing microbes with unknown physiology. In this study, we apply cutting-edge sequencing to a consortium designed for ammonia removal from wastewater. Long-read DNA sequencing enabled complete genome recovery and revealed that populations integral to nitrogen cycling are poorly represented in taxonomic databases. By integrating multi-omics with biochemical assays, we uncovered how environmental conditions drive off-target nitrogen reactions and the potential risks of exposure to pathogens carrying virulence genes. Our findings underscore how whole-community approaches provide insights that are not obtainable with traditional amplicon sequencing and biochemical analysis methods. However, our study also provides recommendations on how hurdles related to data integration and environmental representation must be addressed to support stakeholders adopting such approaches in the context of commercializing microbial consortia.},
}
@article {pmid41457274,
year = {2025},
author = {Catry, A and Abrouk, D and Fierling, N and Mendoza, AIS and Rey, M and Vesga, P and Heiman, CM and Garrido-Sanz, D and Bouffaud, ML and Buscot, F and Giongo, A and Smalla, K and Comte, G and Keel, C and Muller, D and Moënne-Loccoz, Y},
title = {Biogeography influences plant-microbe interactions and natural soil suppressiveness to black root rot disease of tobacco.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {16},
pmid = {41457274},
issn = {1474-760X},
support = {BiodivERsA3 ERA-Net SuppressSOIL//Biodiversa+/ ; grant SuppressSOIL no. ANR19-EBI3-0007//Agence Nationale de la Recherche/ ; grant SuppressSOIL no. 31BD30_186540//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; grant no. 51NF40_180575//NCCR Microbiomes/ ; BU 941/30-1//Deutsche Forschungsgemeinschaft/ ; project DiControl 031A560A-F//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
mesh = {*Nicotiana/microbiology ; *Soil Microbiology ; Rhizosphere ; *Plant Diseases/microbiology ; Plant Roots/microbiology ; Soil/chemistry ; Microbiota ; },
abstract = {BACKGROUND: In disease-suppressive soils, the rhizosphere microbiota protects plants from root disease(s). However, the soil microbiome follows distinct spatial patterns, and the biogeographic factors shaping plant-microbe interactions and soil suppressiveness remain poorly understood. Here, we use Swiss and Savoie soils suppressive or conducive to Thielaviopsis basicola-mediated black root rot of tobacco, to test the hypothesis that plant-microbe interactions and suppressiveness are influenced by both the geological origin and geographic positioning of soils. Soils are compared based on tobacco health, soil physicochemistry and organic matter profiles, taxonomic and functional microbial diversity, and plant physiological responses.<br><br>RESULTS: Soil physicochemistry and metabolomic profiling of soil organic matter show differences based on suppressiveness status, soil geology and geography. The taxonomic (metabarcoding of prokaryotes and fungi) and functional (metagenomics) diversity of the tobacco rhizosphere reveals that the microbiota is influenced by geography and geology which, in turn, affects suppressiveness. Additionally, shoot metabolomics shows that tobacco responses are impacted by soil geography and geology, particularly in Savoie soils regarding two nicotinic derivatives.<br><br>CONCLUSIONS: Overall, suppressiveness is influenced by both the geological origin and geographic positioning of the soils, with distinct patterns in the two regions. In Swiss soils, suppressiveness is primarily associated with major differences in rhizosphere microbiota composition and functions between suppressive and conducive soils. In contrast, in Savoie soils, suppressiveness is linked to distinct plant physiological responses (pointing to induced systemic resistance) rather than strong microbial shifts. This study highlights the importance of considering the biogeographic features shaping disease-suppressive soils and their microbiota-plant interactions.},
}
@article {pmid41457176,
year = {2025},
author = {Paul, D and Talukdar, D and Kapuganti, RS and Gupta, V and Narendrakumar, L and Jana, P and Kumar, P and Singh, J and Kumari, S and Basak, C and Kamboj, K and Bakshi, S and Lal, S and Tanwar, S and Kumar, R and Babele, P and Bajpai, M and Kumar, Y and Mutreja, A and Mandal, S and Wadhwa, N and Banerjee, SK and Das, B},
title = {Antibiotic contamination and antimicrobial resistance dynamics in the urban sewage microbiome in India.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {1274},
pmid = {41457176},
issn = {2041-1723},
support = {RAD/22017/19/2022-KGD-DBT//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; GCI-13012/2/2025-GCl//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; },
mesh = {*Sewage/microbiology ; India ; *Anti-Bacterial Agents/pharmacology/analysis ; *Microbiota/genetics/drug effects ; *Bacteria/genetics/drug effects/isolation &amp; purification/classification ; Drug Resistance, Multiple, Bacterial/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Humans ; Interspersed Repetitive Sequences/genetics ; Cities ; Microbial Sensitivity Tests ; },
abstract = {The emergence and spread of antimicrobial resistance (AMR) in clinically important bacterial pathogens has severely compromised the effectiveness of commonly used antibiotics in healthcare. Acquisition and transmission of AMR genes (ARGs) are often facilitated by sublethal concentrations of antibiotics in microbially dense environments. In this study, we use sewage samples (n = 381) collected from six Indian states between June and December 2023 to assess the concentration of eleven antibiotics, microbial diversity, and ARG richness. We find antibiotics from seven drug classes and detect over 2000 bacterial amplicon sequence variants (ASVs). Metagenomic (n = 220) and isolated genome sequences (n = 305) of aerobic and anaerobic bacterial species identify 82 ARGs associated with 80 mobile genetic elements (MGEs). These MGEs are predominantly present in multidrug-resistant (MDR) bacterial pathogens. Comparative core genome analysis of MDR bacterial isolates (n = 7166) shows strong genetic similarity between sewage-derived strains and clinical pathogens. Our results highlight sewage as a significant reservoir for ARGs, where genetic exchanges occur and facilitate the evolution and spread of AMR pathogens in both community and healthcare settings. Additionally, the dipstick-based assay developed for ARGs detection can be used for sewage surveillance in low-resource settings for better understanding of resistance prevalence.},
}
@article {pmid41457077,
year = {2025},
author = {Peng, L and Chen, JW and Chen, YZ and Di, XP and Lin, LD and Li, BY and Zhang, C and Wang, W and Gao, XS and Ma, YC and Shen, SH and Li, HR and Xu, XF and Zeng, X and Shen, H and Sun, Q and Jin, T and Luo, DY},
title = {Multi-omics analysis identifies a microbiota-bile acid-TLR signaling axis driving bladder injury in interstitial cystitis.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {1299},
pmid = {41457077},
issn = {2041-1723},
support = {82422015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82270720//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82400904//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82500827//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024M752250//China Postdoctoral Science Foundation/ ; 2025T180613//China Postdoctoral Science Foundation/ ; },
mesh = {*Cystitis, Interstitial/microbiology/metabolism/pathology ; Animals ; *Toll-Like Receptor 3/metabolism/genetics ; *Urinary Bladder/pathology/metabolism/microbiology/injuries ; Signal Transduction ; Humans ; Mice ; *Bile Acids and Salts/metabolism ; Female ; Urothelium/metabolism/pathology ; Metabolomics/methods ; *Microbiota ; Single-Cell Analysis ; Mice, Inbred C57BL ; Male ; Multiomics ; },
abstract = {Hunner-type interstitial cystitis/bladder pain syndrome (HIC) is a debilitating condition defined by bladder pain and urinary urgency, yet its upstream drivers remain poorly understood. To identify upstream mechanisms that exacerbate urothelial injury, here we apply an integrative multi-omics framework combining metagenomic sequencing, targeted metabolomics of urine and serum, and single-cell RNA sequencing. This approach reveals a microbial signature enriched in Enterococcus avium and a marked alteration in bile acid metabolism, including increased taurochenodeoxycholic acid (TCDCA). Single-cell analysis indicates that these changes converge on Toll-like receptor 3 (TLR3) activation in urothelial cells. Further validations show that a microbiota-bile acid-TLR3 axis disrupts epithelial barrier integrity and triggers inflammatory responses in experimental models. Transplantation and metabolite administration confirm the causal role of E. avium and TCDCA, while TLR3 inhibition ameliorates injury. These findings uncover an upstream pathway linking gut-derived metabolites to bladder pathology and suggest opportunities for biomarker development and targeted therapies for HIC.},
}
@article {pmid41456824,
year = {2026},
author = {Quan, H and Ouyang, J and Fu, X and Lin, D and Wu, Q and Li, D and Li, Y and Yang, F and Wu, S and Li, C and Mao, W},
title = {Elucidating the therapeutic mechanism of Orthosiphon aristatus in hyperuricemic nephropathy: An integrated microbiome-metabolomics approach.},
journal = {Journal of ethnopharmacology},
volume = {359},
number = {},
pages = {121115},
doi = {10.1016/j.jep.2025.121115},
pmid = {41456824},
issn = {1872-7573},
mesh = {Animals ; *Hyperuricemia/drug therapy/complications ; Male ; Rats ; *Plant Extracts/pharmacology/therapeutic use/isolation &amp; purification ; *Kidney Diseases/drug therapy/pathology ; Metabolomics ; Rats, Sprague-Dawley ; Uric Acid/blood ; *Gastrointestinal Microbiome/drug effects ; *Orthosiphon/chemistry ; Kidney/drug effects/pathology/metabolism ; Disease Models, Animal ; },
abstract = {Hyperuricemic nephropathy (HN) remains challenging to treat due to the limitations, including variable efficacy and side effects, of conventional drugs. Orthosiphon aristatus (O. aristatus), used for over 2000 years in Dai medicine to treat kidney disorders by "clearing heat and promoting diuresis," shows strong potential for HN management. However, its mechanisms of action against HN remain unclear.<br><br>AIM OF THE STUDY: This study aimed to elucidate the nephroprotective effects and underlying mechanisms of O. aristatus against HN using an integrated strategy focusing on the gut-kidney axis.<br><br>METHODS: A rat model of HN was established by combined oral administration of potassium oxonate (750&#xa0;mg/kg) and uric acid (300&#xa0;mg/kg) daily for 7 weeks. Model rats were treated with a low- or high-dose aqueous extract of O. aristatus (3.125 or 6.25&#xa0;g/kg/day), using allopurinol (5&#xa0;mg/kg/day) as a positive control. Renal function was assessed by measuring serum levels of uric acid, creatinine, and urea nitrogen. Renal pathological injury and fibrosis were evaluated through histopathological examination (H&amp;E and Masson's trichrome staining), immunohistochemistry (&#x3b1;-SMA, vimentin), and transmission electron microscopy. To elucidate the underlying mechanisms, an integrated multi-omics approach was employed: gut microbiota composition was profiled by metagenomic sequencing, and metabolic alterations in cecal content and kidney tissue were characterized using UPLC-MS-based metabolomics. Furthermore, the protein expression of key targets involved in intestinal barrier function (Occludin, Claudin-1) and the IDO1/AhR signaling pathway was validated by Western blot analysis.<br><br>RESULTS: O. aristatus treatment significantly ameliorated renal dysfunction and pathological injury, as demonstrated by marked reductions in serum uric acid (sUA), creatinine (Scr), and blood urea nitrogen (BUN) levels (all p&#xa0;<&#xa0;0.001), alongside attenuated tubular injury and fibrosis. Concurrently, it restored gut microbiota diversity (e.g., increased Shannon index, p&#xa0;<&#xa0;0.05) and composition, characterized by an enrichment of beneficial Prevotella and a reduction in Bacteroides. Integrated metabolomics analysis further linked these effects to the rectification of tryptophan metabolism, manifested by decreased renal kynurenine levels (p&#xa0;<&#xa0;0.01) and enhanced intestinal barrier integrity (e.g., elevated Occludin and Claudin-1, p&#xa0;<&#xa0;0.05). Collectively, our results delineate that the renoprotective effect of O. aristatus is mediated through the suppression of the renal IDO1/kynurenine/AhR pro-fibrotic signaling axis, unveiling a novel gut microbiota-metabolite-kidney interaction mechanism.<br><br>CONCLUSION: This study elucidates that the renoprotective effect of O. aristatus against HN is mediated through modulation of the gut-kidney axis, by restoring microbial ecology, reprogramming host tryptophan metabolism, and subsequently inhibiting the IDO1/kynurenine/AhR pro-fibrotic pathway.},
}
@article {pmid41456557,
year = {2026},
author = {Li, Y and Chen, Y and Du, Z and Guo, Y and Zhang, W and Xu, X and Liu, Z and Duan, H and Duan, X and Zhang, A and Zhou, A and Li, X and Makinia, J},
title = {Oriented butyrate production through a novel bacteria-yeast microbiome: batch verification, key electron donor identification, and long-term validation.},
journal = {Bioresource technology},
volume = {443},
number = {},
pages = {133892},
doi = {10.1016/j.biortech.2025.133892},
pmid = {41456557},
issn = {1873-2976},
mesh = {*Saccharomyces cerevisiae/metabolism ; *Butyrates/metabolism ; Ethanol/metabolism ; *Microbiota ; Fermentation ; *Electrons ; *Bacteria/metabolism ; RNA, Ribosomal, 16S/genetics ; Clostridium/metabolism ; },
abstract = {Recovering butyrate from organic waste enables its high-value conversion, aligning with the principles of a circular economy. Traditional butyrate fermentation emphasizes carbohydrates and protein degradation, with limited focus on chain elongation (CE). This study, for the first time, systematically evaluated the effects of different Saccharomyces cerevisiae (SC) concentrations (1, 2, 4, 6, and 8 g/L) on ethanol production (a key electron donor) and subsequent CE for butyrate synthesis, identifying 2 g/L as the optimal SC dosage. At this concentration, butyrate production reached 15.41 ± 2.84 g COD/L, which was 2.72 times higher than that of the blank. Metabolic pathway analysis revealed that yeast not only enhanced substrate degradation (＞90 %) but also facilitated the in situ generation and utilization of ethanol. 16S rRNA indicated 54.10 % relative abundance of butyrate-producing bacteria (Clostridium). Long-term tests found that adding SC reversed the halt in production from prolonged distiller yeast inoculum, stabilising output at 15 g COD/L. Metagenomic analysis revealed that SC inoculation primarily enriched Clostridium luticellarii and Clostridium tyrobutyricum. In addition to raising reverse β-oxidation gene abundance, this treatment also enhanced lactate utilization genes, thereby strengthening acetyl-CoA to butyrate conversion. Through further experiments involving different electron donor ratios and long-term operation, this study highlights the critical role of yeast-bacteria synergy in enhancing butyrate synthesis, providing a theoretical foundation and technical strategy for food waste valorization in line with circular economy principles.},
}
@article {pmid41455576,
year = {2026},
author = {Kitagawa, H and Kajihara, T and Yahara, K and Kitamura, N and Shigemoto, N and Doi, H and Shimbara, K and Yoshimura, K and Nakashima, I and Uegami, S and Watadani, Y and Kawada-Matsuo, M and Komatsuzawa, H and Ohge, H and Sugai, M},
title = {Impact of antimicrobial prophylaxis in colorectal cancer surgery on the gut and oral microbiome and resistome: A prospective observational cohort study.},
journal = {Journal of global antimicrobial resistance},
volume = {46},
number = {},
pages = {227-234},
doi = {10.1016/j.jgar.2025.12.014},
pmid = {41455576},
issn = {2213-7173},
mesh = {Humans ; Prospective Studies ; Male ; Female ; *Colorectal Neoplasms/surgery/microbiology ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; Feces/microbiology ; Aged ; *Antibiotic Prophylaxis ; *Anti-Bacterial Agents/therapeutic use ; *Mouth/microbiology ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Microbiota/drug effects ; Metagenomics ; Drug Resistance, Bacterial ; },
abstract = {BACKGROUND: The use of antibiotics may facilitate the colonisation of antimicrobial-resistant organisms and genes within the host microbiome. However, studies on the effects of antibiotics on microbiomes and resistomes in clinical settings are limited.<br><br>AIM: The aim of this study was to determine the effects of antibiotic prophylaxis during colorectal cancer surgery on the oral and gut microbiomes and resistomes of patients.<br><br>METHODS: We conducted a single-centre prospective observational cohort study on patients who underwent colorectal cancer surgery with antibiotic prophylaxis. DNA was extracted from oral and stool samples 1 day prior to the procedure and on postoperative days 1, 7, and 28. Subsequently, metagenomic sequencing was performed.<br><br>FINDINGS: Among the eight patients with colorectal cancer, &#x3b1;-diversity in the oral and stool samples significantly decreased from baseline to each of the three post-administration time points. The abundance of anaerobic genera significantly decreased from baseline to Day 7. In the stool samples, Enterococcus, Limosilactobacillus, and Lacticaseibacillus abundances were markedly increased. Total antibiotic resistance gene (ARG) abundance significantly increased from the baseline to Day 7 in both oral and stool samples. The impact of the increase observed on Day 7 decreased but still persisted until Day 28 for diversity and total abundance of ARGs.<br><br>CONCLUSIONS: Oral and gut microbiomes and resistomes exhibited marked alterations that gradually reversed over time. Changes in the microbiome were associated with the spectrum of antibiotics used.},
}
@article {pmid41455545,
year = {2026},
author = {Zhang, JS and Zhang, Y and Huang, S and Chu, CH and Jakubovics, NS and Yu, OY},
title = {High-resolution microbial changes in root caries revealed by Type IIB Restriction-site associated DNA for microbiome.},
journal = {Journal of dentistry},
volume = {165},
number = {},
pages = {106319},
doi = {10.1016/j.jdent.2025.106319},
pmid = {41455545},
issn = {1879-176X},
mesh = {Humans ; *Root Caries/microbiology ; *Microbiota/genetics ; Male ; Female ; Aged ; Biofilms ; Dental Plaque/microbiology ; Middle Aged ; *DNA, Bacterial/genetics/analysis ; *Tooth Root/microbiology ; Case-Control Studies ; },
abstract = {OBJECTIVES: This study aimed to characterize the species-level microbial and functional alterations in the dental biofilms associated with root caries leveraging the high-resolution sequencing.<br><br>METHODS: Twenty-five older adults with active root caries (Patients) and 31 older adults without untreated caries (Healthy controls) were enrolled. Site-specific supragingival plaque was collected from spatially-matched carious (CC) and caries-free (CH) root surfaces from patients, and from caries-free root surfaces of healthy controls (HH). Plaque samples were analysed using Type IIB Restriction-site Associated DNA for Microbiome (2bRAD-M). Microbial diversity, species-level relative abundance, and predicted functional pathways were compared across groups using nonparametric tests.<br><br>RESULTS: No significant differences in overall microbial diversity were observed between groups. The microbial divergence between paired carious (CC) and caries-free (CH) root microbiota from patients was significantly greater than that between paired caries-free (HH) root microbiota in healthy controls. Several species showed increased abundance in CC microbiota compared to CH microbiota, with Propionibacterium acidifaciens, Prevotella multisaccharivorax, Mitsuokella sp000469545, and Parascardovia denticolens exhibiting the highest level of abundance difference. Predicted metagenomic analysis indicated that nine KEGG pathways, primarily involved in alternative carbohydrate metabolism, were positively associated with root caries status.<br><br>CONCLUSION: Within-subject comparison revealed a significant difference in microbiota between carious and caries-free root surfaces. These differences were characterized by shifts in specific species and their associated metabolic potentials, rather than by broad changes in community diversity.<br><br>CLINICAL SIGNIFICANCE: This study underscores the importance of tooth-level resolution in investigating the microbial etiology of root caries and revealed the species-level changes in carious root microbiota.},
}
@article {pmid41455311,
year = {2026},
author = {Kolathingal-Thodika, N and Elayadeth-Meethal, M and Dunshea, FR and Eckard, R and Flavel, M and Chauhan, SS},
title = {Harnessing methane proxies to understand and mitigate enteric emissions from ruminant production systems.},
journal = {The Science of the total environment},
volume = {1012},
number = {},
pages = {181258},
doi = {10.1016/j.scitotenv.2025.181258},
pmid = {41455311},
issn = {1879-1026},
mesh = {*Methane/analysis/metabolism ; Animals ; *Ruminants/metabolism ; *Environmental Monitoring/methods ; *Animal Husbandry ; Rumen/microbiology ; Gastrointestinal Microbiome ; *Air Pollutants/analysis ; },
abstract = {Methane emissions from livestock, particularly ruminants, significantly contribute to global warming, necessitating the development of accurate methane monitoring systems. Direct methane measurement is technically complex, time-consuming, labour-intensive, and costly. Recent advances in methane inhibitors, such as 3-nitrooxy propanol and halogenated analogues, plant secondary compounds, including polyphenols and essential oils, to reduce methane emissions have necessitated the discovery of processes underlying rumen methane synthesis and inhibition. The identification of methane proxies, such as behavioural and input proxies (dry matter intake, neutral detergent fibre), microbial community proxies (rumen metagenome profiles), metabolic pathway proxies (fatty acids), molecular and genetic proxies (microbial genes), and downstream and non-invasive proxies (milk fatty acids and faecal lipidomes), is leading to more viable solutions. New developments in 'omic' techniques, including lipidomics, metagenomics and metatranscriptomics, have enabled the detection of proxies at the molecular level utilising rumen liquor, milk, blood, urine, and faeces. In addition to traditional methane proxies, rumen microbiota profiles, and specific genes involved in rumen methanogenesis (such as mcr and mrt, which encode methyl coenzyme reductase 1 and 2), these markers can be used to identify methane-producing pathways. Protozoa-associated methanogens (PAMs), propionate-producing bacteria, and methane-oxidising methanotrophs (Methylocystis sp.) are emerging as new proxies. Methane proxies provide scalable, affordable, and mechanistically insightful alternatives to conventional direct measuring techniques, which improve the understanding of rumen function and the biological causes of methane releases, enabling large-scale methane monitoring and will enable designing effective methane mitigation strategies in livestock production systems.},
}
@article {pmid41455002,
year = {2025},
author = {Karim, F and Lin, Q and Xie, H and Nargis, S and Xiao, H and Yang, S and Xiong, Y and Xie, M and Ni, Q and Yao, Y and Xu, H},
title = {Seasonal dynamics of gut microbiota in rhesus macaques (Macaca mulatta) from western Sichuan Plateau and their adaptability to high altitude climate change.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {99},
pmid = {41455002},
issn = {1432-0991},
support = {31870355//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Macaca mulatta/microbiology ; *Gastrointestinal Microbiome ; Seasons ; Altitude ; Feces/microbiology ; *Climate Change ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; China ; },
abstract = {Seasonal fluctuations in diet and climate shape animal gut microbiota, especially those living in extreme climatic conditions. Yet their role in facilitating primate adaptation to high-altitude remains unclear. This study investigates the seasonal dynamics in gut microbiome of wild rhesus macaques (Macaca mulatta) from high altitude (over 3,000 m) in Yajiang couke. We collected 117 fecal samples across four seasons and analyzed using 16S rRNA high-throughput sequencing combined with predictive functional metagenomics. We observed clear seasonal shifts in gut microbial diversity and composition. High α-diversity in autumn and winter reflected increased dietary diversity during these periods. Firmicutes predominated in summer, while Bacteroidota increased during winter. LEfSe analysis revealed seasonal specific taxa: UCG-005, Christensenellaceae R-7, and Prevotella_9 were dominated in winter but declined in summer and spring, whereas Blautia peaked during summer and decreased toward winter. Redundancy analysis showed that temperature, humidity, and precipitation were positively associated with Blautia and Sarcina, but negatively with Monoglobus and Helicobacter, underscoring the strong influence of climatic variables on gut community structure. Functional predictions revealed seasonal differences in gut microbiota related to energy metabolism (spring), glycan biosynthesis (summer), membrane transport (autumn), and environmental adaptation (winter) indicating microbial contributions to host adaptation under fluctuating climatic conditions. These findings demonstrate that gut microbiome of high-altitude macaques is highly responsive to changes in seasonal diet and climate. By integrating microbiome dynamics with climatic drivers, our study provides new insights into host-microbe-environment interactions and advances our understanding of primate adaptation under extreme climatic conditions.},
}
@article {pmid41454222,
year = {2025},
author = {Li, J and Sun, Z and Chai, S and Li, H and Wang, Y and Tian, J},
title = {AR-CDT NET: a deep deformable convolutional network for gut microbiome-based disease classification.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {23},
pmid = {41454222},
issn = {1471-2105},
support = {No.GZY-ZJ-SY-2303//Zhejiang Province Traditional Chinese Medicine Key Laboratory Project/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Deep Learning ; Metagenomics/methods ; Computational Biology/methods ; },
abstract = {Advances in metagenomic sequencing have increasingly implicated gut microbiome dysbiosis in numerous complex diseases, yet its application for precise differential diagnosis remains a major challenge. Existing computational approaches often show limited predictive performance and insufficient robustness when applied to large-scale, imbalanced microbiome datasets, and they typically lack mechanisms to effectively capture microbial community-level or functional guild interactions. To address these limitations, we developed AR-CDT Net, a novel deep learning framework that integrates a Multi-Scale Deformable Convolution (MS-DConv) module with a Channel-wise Dynamic Tanh (CD-Tanh) activation function to achieve more accurate and robust classification of host disease states. Evaluated on a large-scale cohort comprising over 8000 samples spanning eight disease phenotypes, AR-CDT Net demonstrated highly competitive within-cohort performance, outperforming nine representative models across the majority of classification tasks. Importantly, in a stringent cross-dataset generalization test, the model was trained on the highly imbalanced primary multi-disease cohort and validated on relatively balanced independent external cohorts. It achieved a statistically significant AUC of 0.7921 on the highly heterogeneous external T2D cohort, confirming that AR-CDT captures transferable biological signals rather than dataset-specific artifacts. Furthermore, by combining dimensionality reduction with SHAP-based interpretation of our One-vs-Rest (OvR) classifiers, AR-CDT disentangles disease-specific pathogenic signatures from the shared dysbiotic background among clinically distinct yet microbially similar diseases.},
}
@article {pmid41453903,
year = {2025},
author = {Lin, Z and Li, S and Liu, M and Li, J and Liu, F and Cao, J and Chen, S and Huang, K and Wang, Y and Li, H and Wang, Y and Yang, B and Xing, D and Wang, Q and Ji, X and Bai, X and Hu, D and Zhang, M and Guo, D and Huang, J and Geng, B and Gu, D and Lu, X},
title = {Gut microbiota-derived metabolite isovalerylcarnitine modulates salt sensitivity of blood pressure and incident hypertension: a multicenter dietary salt intervention trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {808},
pmid = {41453903},
issn = {2041-1723},
support = {91857118//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82030102//National Natural Science Foundation of China (National Science Foundation of China)/ ; 12126602//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Female ; Humans ; Male ; Middle Aged ; Rats ; *Blood Pressure/drug effects/physiology ; *Carnitine/analogs &amp; derivatives/metabolism/blood ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology/drug effects ; *Hypertension/metabolism/microbiology ; Metabolome ; *Sodium Chloride, Dietary/adverse effects ; },
abstract = {This study aims to investigate the roles of gut microbiota and plasma metabolites in salt sensitivity (SS) of blood pressure (SSBP) and hypertension. A 23-day, multicenter, dietary salt intervention trial (the MetaSalt study) recruited 528 participants who underwent a baseline observation, low-salt, and high-salt interventions. SSBP was assessed and used as the primary outcome, and fecal shotgun metagenome and plasma targeted metabolome were measured. We found that high salt significantly altered 85 gut-microbial species (p < 9.42 × 10[-5]) and 70 metabolites (p < 2.26 × 10[-4]). Among them, the changes in 22 species and 8 metabolites were associated with SSBP (p < 0.05), and a gut microbiota-acylcarnitine network implicated in SSBP was identified, with a gut microbiota-derived metabolite, isovalerylcarnitine, as the core metabolite. Isovalerylcarnitine was also inversely associated with SSBP in the GenSalt study (p = 0.0102). Importantly, increased isovalerylcarnitine attenuated SS hypertension and improved endothelial function in rats, and was associated with reduced risk (ranging from 13% to 19%) of BP progression and incident hypertension in a prospective cohort (n = 3907, median follow-up = 5.5 years). This study demonstrated that the gut-acylcarnitine axis may play roles in the development of SS hypertension. Trial number: ChiCTR1900025171.},
}
@article {pmid41452254,
year = {2026},
author = {Pan, LH and Hu, WF and Fu, ZY and Yu, XC and Li, ZQ and Guo, MF and Wu, JW and Zhu, H},
title = {Yacon (Smallanthus sonchifolius) Root Increases Bowel Movement Frequency in Healthy Adults via Modulating Gut Microbiota and Intestinal Metabolites: A Pilot Study.},
journal = {Molecular nutrition &amp; food research},
volume = {70},
number = {1},
pages = {e70358},
doi = {10.1002/mnfr.70358},
pmid = {41452254},
issn = {1613-4133},
support = {TZKY2024RC01//Scientific Research Starting Foundation for High-level Talents of Taizhou School of Clinical Medicine, Nanjing Medical University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Pilot Projects ; Adult ; *Plant Roots/chemistry ; Male ; Female ; Middle Aged ; Young Adult ; *Intestines/microbiology/drug effects ; *Plant Extracts/pharmacology ; *Defecation/drug effects ; },
abstract = {Yacon root (YR) is a functional food that can increase bowel movement frequency, but with an unclear mechanism. In this study, a UPLC-Orbitrap-MS/MS system was employed to characterize the chemical composition of YR. Subsequently, a 10-day pilot intervention trial involving 11 healthy adults was conducted to evaluate the effects of YR on bowel movement frequency. Concurrently, the involved mechanisms were explored through metagenomic and metabolomic approaches. A total of 82 chemical components were identified in YR. Clinical trials indicated that continuous intake of YR significantly increased bowel movement frequency without noticeable adverse effects. Metagenomic analysis revealed that YR substantially increased the abundance of beneficial bacteria such as Bifidobacterium and inhibited the generation of potential pathogens, including Escherichia-Shigella, thereby promoting a more balanced and healthier gut microbiota structure. Metabolomic analysis indicated that YR significantly upregulated metabolites, including cholic acid, taurine, and amino acids, which mainly focus on the biosynthesis of primary bile acid and the metabolism of taurine and hypotaurine. In summary, YR can safely and effectively increase bowel movement frequency in healthy individuals. The mechanism may involve synergistic regulation of gut microbiota and metabolites, which offered new insights to support YR as a natural functional food for laxative effects.},
}
@article {pmid41451983,
year = {2026},
author = {Fan, Y and Ju, T and Bhardwaj, T and Korver, DR and Willing, BP},
title = {Chicken cecal microbial functional gene content and resistome differ by age and barn disinfection practice.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0373725},
pmid = {41451983},
issn = {2165-0497},
support = {RGPIN-2019-06336//Natural Sciences and Engineering Research Council of Canada/ ; //Agriculture Funding Consortium/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Disinfection/methods ; *Gastrointestinal Microbiome/genetics/drug effects ; Disinfectants/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Age Factors ; Housing, Animal ; Metagenomics ; },
abstract = {Chemical disinfectants and water-wash methods are widely employed in sanitizing broiler chicken barns. Studies showed that disinfectants affect environmental microbial composition and antibiotic resistance genes (ARGs). However, little is known regarding how barn disinfection treatments impact the chicken gut resistome and microbial functional gene content. The current study compared the effects of disinfection and water-wash method on the gut microbiome and resistome of commercial broilers using a crossover experimental design after two production cycles at seven barns. Shotgun metagenomic sequencing performed on cecal contents collected at days 7 and 30 also allowed the evaluation of age-associated characteristics of the microbiome. The age of the chickens had the largest effects on the resistome, with younger birds having higher relative abundance of total ARGs (P < 0.05) and differences in resistance mechanism; however, functional gene content and resistome differences were also identified by barn sanitation practice. At day 7, chickens in chemically disinfected barns had decreased gene content related to amino acid synthesis compared to the water-wash group. Additionally, genes related to stringent response were enriched in chickens raised under chemically disinfected conditions (FDR-P < 0.05), suggesting the selection for stress resistance. Lower abundance of genetic pathways encoding amino acid biosynthesis associated with cecal Helicobacter pullorum was observed in the disinfection group at day 30 compared to the water-wash group, with the same pattern in short-chain fatty acid biosynthesis (FDR-P < 0.05). Overall, while the use of disinfectants in barn sanitation slightly affected the relative abundance of some ARGs in the gut, age had a dominant effect on the microbial gene function and resistome.IMPORTANCEThis is the first study to evaluate the effect of sanitation practices on microbial functional gene content and resistome of chickens in a commercial setting. It is also amongst the biggest metagenomics studies on the gut microbiome of broiler chickens. It provides new insights into the changes in resistance profiles with age that agree with other studies examining maturation of the microbiome in other species. Finally, the current study provides valuable insights for informing industry sanitation practices and future studies on broiler gut microbiome and resistome.},
}
@article {pmid41450573,
year = {2025},
author = {Zhang, G and Zeng, L and Chen, B and Dai, H and Tang, K and Huang, R and Xiang, X and Yang, J and Yang, J and Song, X and Ma, Y and Lin, R and Huang, Y},
title = {Biliary microbiota in disease-free, obstructive and post-drainage biliary tracts.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1674341},
pmid = {41450573},
issn = {2235-2988},
mesh = {Humans ; *Bile/microbiology ; *Biliary Tract/microbiology ; Drainage/adverse effects ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Microbiota ; Female ; Male ; Middle Aged ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: Despite years of research, knowledge about the microbial populations of human physiological bile has remained limited. Bile sampling techniques, such as Endoscopic Retrograde Cholangiopancreatography (ERCP), percutaneous biliary drainage, and intra-operative sampling, are invasive procedures typically performed only in the presence or suspicion of biliary tract disease. Furthermore, the increased incidence of bacterial infections following biliary drainage poses a significant clinical concern; however, the relationship between biliary drainage and biliary flora remains poorly understood. In this study, we present a distinct taxonomic composition of bacterial communities identified in bile samples from disease-free individuals, as well as from obstructive and post-drainage biliary tracts.<br><br>METHODS: A metagenomic sequence analysis of bile samples from patients with MBO who underwent percutaneous biliary drainage (PTBD) at our center from 1st May 2021 to 1st March 2022, which were divided into 2 groups, as the MBO group (n = 29) and BD group (n = 27). Eight liver donors were included as a control group.<br><br>RESULTS: Abundant bacterial populations were detected in the bile of liver donors, revealing a highly similar microbial composition in both disease-free and malignant obstructive biliary trees. Notably, biliary drainage was found to alter the composition of bile microbiota, resulting in decreased microbial diversity and an association with an increase in antibiotic resistance genes.<br><br>DISCUSSION: These findings provide fundamental knowledge on the composition of the human bile microbiota and present new evidence to support that biliary drainage induces a shift in bile microbiota, rendering it more aggressive and resistant to antibiotics.},
}
@article {pmid41448339,
year = {2026},
author = {Ghosh, S and Ganguly, A and Dong, TS and Lagishetty, V and Jacobs, JP and Devaskar, SU},
title = {Intestinal microbiome in response to air pollutant exposure in pregestational and gestational murine females and their male and female offspring.},
journal = {Reproductive toxicology (Elmsford, N.Y.)},
volume = {140},
number = {},
pages = {109150},
doi = {10.1016/j.reprotox.2025.109150},
pmid = {41448339},
issn = {1873-1708},
mesh = {Female ; Animals ; Male ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; *Prenatal Exposure Delayed Effects/microbiology ; *Air Pollutants/toxicity ; Mice, Inbred C57BL ; Mice ; Maternal Exposure ; Bacteria/genetics/drug effects/classification ; },
abstract = {We investigated the impact of chronic air pollutant (AP) exposure upon intestinal microbial diversity, composition, and metagenomic inferred functional pathways in murine pregestational and late gestational adult females, and male and female postnatal offspring (P21), compared to age- and sex- matched controls (CON). Intestinal microbiome analysis was undertaken with certain phenotypic characteristics in adult non-pregnant and pregnant females and the male and female offspring. In response to AP, pooled male and female offspring displayed no difference in E19 fetal and P1 postnatal body weights. At P21, females exposed in-utero to AP were heavier with increased fat and muscle mass at one month versus CON. Males were no different at P21 and 1 month revealing decreased fat mass and hyperglycemia. In pregestational/gestational females, AP did not change microbial α- or β-diversity from the respective CON. Gestational females showed AP induced changes in taxonomic composition such as reduced Bacteroides and increased Firmicutes, Verrucomicrobia, and Akkermansia, among others. In response to intra-uterine AP exposure, the offspring intestinal microbiome revealed more compelling differences in α- and β- diversity than adult females. While certain microbial changes were common in both sexes, sex-specific differences also emerged with reduced α-diversity, decreased Bacteroides and increased Akkermansia in males only. The metagenomic inferred pathways revealed perturbations in multiple pathways. We conclude that the offspring exposed in-utero to AP revealed sex-specific changes in microbial diversity, composition and function, displaying certain similarities with distinct differences from mothers. These early life changes were associated with the subsequent emergence of pre-diabetes and adiposity.},
}
@article {pmid41448087,
year = {2026},
author = {Yi, J and Li, Z and Han, X and Li, J and Liu, H and Zhu, L and Wang, M},
title = {Metformin drives the antibiotic resistome in activated sludge by reshaping microbial communities and promoting horizontal gene transfer.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140887},
doi = {10.1016/j.jhazmat.2025.140887},
pmid = {41448087},
issn = {1873-3336},
mesh = {*Sewage/microbiology ; *Gene Transfer, Horizontal/drug effects ; *Metformin/pharmacology ; *Microbiota/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics/drug effects ; },
abstract = {Aerobic granular sludge (AGS) serves as a major reservoir and dissemination hotspot for human bacterial pathogens (HBPs) and antibiotic resistance genes (ARGs). Metformin (MET) as an emerging contaminant, which exacerbates antibiotic resistance and poses a problem for the stable operation of the activated sludge process in wastewater treatment plants. However, the specific mechanisms underlying the effects of MET stress on microbial communities and ARGs propagation in activated sludge remain poorly understood. In this study, we employed metagenomic analysis to investigate the effects of MET exposure, under a composite antibiotic background, on microbial community dynamics and resistome profiles in AGS systems and interpreted these effects from the perspectives of energy metabolism and community competition. Our findings demonstrate that MET exposure significantly enriched HBPs and multidrug resistance-related ARGs. Co-occurrence network analysis further identified that, among all sludge samples, 27 high-risk HBPs were strongly correlated with ARGs, virulence factor genes, and mobile genetic elements. Additionally, MET was also found to enhance ATP production in specific HBPs, conferring a competitive edge that facilitates ARG accumulation. Furthermore, the natural transformation and conjugation experiments further demonstrated the key role of MET in promoting horizontal gene transfer. In summary, this study underscores the role of MET in exacerbating the ecological risk of antibiotic resistance in AGS systems by concurrently enriching pathogenic bacteria and facilitating the horizontal transfer of ARGs, thereby highlighting the potential environmental impacts of MET as a pervasive contaminant on the propagation of resistance within wastewater treatment ecosystems.},
}
@article {pmid41447958,
year = {2026},
author = {Lee, Y and Liu, Q and Sun, Y and Maszczyk, P and Wang, M and Yang, Z and Lee, JS},
title = {Hypoxia and the microbiome: Significance and application for ecotoxicological studies.},
journal = {Marine pollution bulletin},
volume = {224},
number = {},
pages = {119171},
doi = {10.1016/j.marpolbul.2025.119171},
pmid = {41447958},
issn = {1879-3363},
mesh = {*Ecotoxicology ; *Microbiota ; *Oxygen ; },
abstract = {Hypoxia, or low oxygen availability, is a growing environmental concern that significantly impacts microbial communities. Recent studies highlight the effects of hypoxia on microbial composition and function, favoring anaerobic taxa involved in nitrogen, sulfur, and carbon cycling. These shifts influence ecotoxicological processes by modulating pollutant degradation, metal bioavailability, and greenhouse gas emissions. For instance, oxygen depletion enhances the activity of anaerobic dechlorinators but may reduce heavy metal detoxification. Advances in metagenomics and multi-omics have offered new perspectives on microbial adaptation under hypoxic stress, revealing key metabolic pathways linked to pollutant transformation. However, knowledge gaps remain in our understanding of the long-term ecological consequences of hypoxia-induced microbiome shifts. This review synthesizes recent findings on hypoxia-microbiome interactions, focusing on both environmental (e.g., sediment and water column) and host-associated (e.g., gut) microbiomes, and emphasizes their application in ecotoxicology. In addition, we discuss how hypoxia-induced microbial shifts in hypoxic environments and highlight potential applications of microbiome-based approaches for environmental risk assessment. Future research integrating experimental and modeling approaches is crucial to better predict the ecological impacts of hypoxia-driven microbial changes in contaminated environments.},
}
@article {pmid41446276,
year = {2025},
author = {Chen, S and Jiang, Y and Lv, D and Zheng, Y and Zhang, R and Dai, H and Wang, Z and Li, S and Qi, R and Xu, H and Yu, Y and Xu, C and Lu, X and Xu, Y and Jin, S and Wu, X},
title = {Identification of subtypes and construction of a predictive model for novel subtypes in severe community-acquired pneumonia based on clinical metagenomics: a multicenter, retrospective cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1676502},
pmid = {41446276},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; *Community-Acquired Infections/microbiology/mortality/classification/diagnosis ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; China/epidemiology ; *Pneumonia/microbiology/classification/mortality ; Adult ; Microbiota/genetics ; Prognosis ; ROC Curve ; Bronchoalveolar Lavage Fluid/microbiology ; Intensive Care Units ; High-Throughput Nucleotide Sequencing ; Nomograms ; Community-Acquired Pneumonia ; },
abstract = {OBJECTIVE: It is well recognized that high heterogeneity represents a key driver of the elevated mortality in severe community-acquired pneumonia (sCAP). Precise subtype classification is therefore critical for both treatment strategy formulation and prognostic evaluation in this patient population. This study aimed to develop a predictive model for novel clinical subtypes of sCAP, leveraging microbiome profiles identified via metagenomic next-generation sequencing (mNGS).<br><br>METHODS: This retrospective multicenter cohort study enrolled adult patients with sCAP who underwent clinical mNGS testing of bronchoalveolar lavage fluid in intensive care units (ICUs) across 17 medical centers in China. Based on mNGS-identified microbiome characteristics, unsupervised machine learning (UML) was employed for clustering analysis of sCAP patients. LASSO regression and random forest (RF) algorithms were applied to screen and identify predictors of novel sCAP subtypes. A predictive model for the new clinical subtypes was constructed according to the screening results, with a nomogram generated. The discriminative ability, calibration, and clinical utility of the model were evaluated using ROC curves, calibration curves, and decision curve analysis, respectively.<br><br>RESULTS: A total of 1,051 sCAP patients were included in the final analysis. The 28-day all-cause mortality rate was 45% (473/1,051). UML clustering identified two distinct sCAP subtypes: the 28-day mortality rate was 42.19% (343/813) in subtype 1 and 54.62% (130/238) in subtype 2. Incorporating clinical and microbial features, a predictive model for the novel sCAP subtypes was developed using the following predictors: immunosuppression (OR = 37,411.46, P < 0.001), connective tissue disease (CTD) (OR = 12,144.60, P = 0.004), hematological malignancy (HM) (OR = 107,768.13, P < 0.001), chronic kidney disease (CKD) (OR = 49.71, P < 0.001), cytomegalovirus (CMV) (OR = 0.00, P < 0.001), Epstein-Barr virus (EBV) (OR = 131.97, P < 0.001), Pneumocystis (OR = 47,949.56, P < 0.001), and Klebsiella (OR = 0.02, P = 0.003). The model demonstrated excellent discriminative ability with an area under the ROC curve (AUC) of 0.992. Calibration curves showed good agreement between predicted and observed outcomes. Decision curve analysis confirmed high clinical utility for predicting novel sCAP subtypes.<br><br>CONCLUSION: This study identified novel clinical subtypes of sCAP based on mNGS-derived microbiome characteristics. This approach exhibits superior performance in identifying high-risk sCAP patients, facilitating precise subtyping.},
}
@article {pmid41444596,
year = {2025},
author = {Tang, R and Shi, M and Ji, X and Zhang, Y and Fan, L and Huang, F and Li, X},
title = {Integrative oral and gut microbiome profiling highlights microbial correlates of complications in type 1 diabetes: a cross-sectional analysis.},
journal = {Cardiovascular diabetology},
volume = {24},
number = {1},
pages = {461},
pmid = {41444596},
issn = {1475-2840},
support = {2024XQLH049//Graduate Innovation Project of Central South University/ ; grant 2023ZD0508200 and 2023ZD0508205//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; grant 82470871//National Natural Science Foundation of China/ ; grant R2023001//Hunan Provincial Health High-Level Talent Scientific Research Project/ ; LYF2022039//Sinocare Diabetes Foundation/ ; },
mesh = {Humans ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 1/diagnosis/microbiology/blood/complications ; Male ; Female ; Adult ; Dysbiosis ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Mouth/microbiology ; Case-Control Studies ; Middle Aged ; *Diabetic Angiopathies/microbiology/diagnosis ; Young Adult ; Risk Factors ; Feces/microbiology ; Biomarkers/blood ; Host-Pathogen Interactions ; Risk Assessment ; Metagenomics ; Blood Glucose/metabolism ; },
abstract = {BACKGROUND/OBJECTIVE: Chronic vascular complications are the primary threat in long-standing type 1 diabetes (T1D) patients. We examined the associations between oral-gut microbiome dysbiosis and these complications, offering novel insights into therapeutic strategies and underlying mechanisms.<br><br>METHODS: This cross-sectional study enrolled 75 T1D participants (disease duration&#x2009;&#x2265;&#x2009;10&#xa0;years) and 43 healthy controls who underwent comprehensive clinical assessment, including blood glucose, lipid profile, and complication-related examinations. Fecal and oral rinse samples were collected for shotgun metagenomic sequencing. T1D participants were stratified by the presence of microvascular (retinopathy, nephropathy, or neuropathy) or macrovascular complications separately. Microbial differences across groups were assessed.<br><br>RESULTS: Significant differences in oral and gut microbiota compositions were observed between T1D participants with and without complications (both microvascular and macrovascular). A core set of 26 gut and 8 oral microbial species was specifically associated with vascular complications. Butyrate-producing gut bacteria (Blautia wexlerae, Anaerobutyricum hallii, Roseburia inulinivorans, A. soehngenii) and specific oral Neisseria species were enriched in T1D without complications individuals, suggesting protective effects against complications. Mediation analysis indicated associations consistent with partial mediation between certain microbial species and the relationships of glycemic control or insulin resistance (HbA1c, glucose risk index, estimated glucose disposal rate) with complication risk. Moreover, potential oral-gut microbiome interconnections were implicated in complication development. Finally, classification models integrating both oral and gut microbial features significantly outperformed models based on either site alone in distinguishing T1D patients with complications.<br><br>CONCLUSIONS: Distinct oral and gut microbiome features are associated with chronic vascular complications in T1D. These findings highlight the potential of microbiome-targeted strategies for understanding and preventing T1D-related complications.},
}
@article {pmid41443199,
year = {2026},
author = {Lucas, TN and Biehain, U and Gautam, A and Gemeinhardt, K and Lass, T and Konzalla, S and Ley, RE and Angenent, LT and Huson, DH},
title = {MMonitor for real-time monitoring of microbial communities using long reads.},
journal = {Cell reports methods},
volume = {6},
number = {1},
pages = {101266},
pmid = {41443199},
issn = {2667-2375},
mesh = {Humans ; *Metagenomics/methods ; *Software ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Computational Biology/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Whole Genome Sequencing ; },
abstract = {Real-time monitoring of microbial communities offers valuable insights into microbial dynamics across diverse environments. However, many existing metagenome analysis tools require advanced computational expertise and are not designed for monitoring. We present MMonitor, an open-source software platform for real-time analysis and visualization of metagenomic Oxford Nanopore Technologies (ONT) sequencing data. MMonitor includes two components: a desktop application for running bioinformatics pipelines through a graphical user interface (GUI) or command-line interface (CLI) and a web-based dashboard for interactive result inspection. The dashboard provides taxonomic composition over time, quality scores, diversity indices, and taxonomy-metadata correlations. Integrated pipelines enable automated de novo assembly and reconstruction of metagenome-assembled genomes (MAGs). To validate MMonitor, we tracked human gut microbial populations in three bioreactors using 16S rRNA gene sequencing and applied it to whole-genome sequencing (WGS) data to generate high-quality annotated MAGs. We compare MMonitor with other real-time metagenomic tools, outlining their strengths and limitations.},
}
@article {pmid41440692,
year = {2025},
author = {Lv, X and Wang, H and Wang, W},
title = {Agaricus sinodeliciosus and Coprinus comatus Improve Soil Fertility and Microbial Community Structure.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {12},
pages = {},
pmid = {41440692},
issn = {2309-608X},
support = {41761107//National Natural Science Foundation of China/ ; 2025-ZJ-969T//The Natural Science Foundation of Qinghai Province/ ; W2412148//International (Regional) Cooperation and Exchange (ICE) Projects of the National Natural Science Foundation of China (NSFC)/ ; D23029//111 Project/ ; },
abstract = {Agaricus sinodeliciosus (A. sinodeliciosus) and Coprinus comatus (C. comatus) are precious macrofungi found in Qinghai Province, China. As decomposers, they play a crucial role in the terrestrial ecosystem. The article takes A. sinodeliciosus and C. comatus growing in the saline-alkali land of the Qaidam Basin in Qinghai Province as the research objects, and deeply analyzes the influence of the two macrofungi on soil. The results show that, compared with the control soil, the total carbon (TC) content in the soil of A. sinodeliciosus and C. comatus increased by 27.48% and 113.24%, the total nitrogen (TN) content increased by 95.16% and 108.06%, the hydrolyzable nitrogen (HN) increased by 87.36% and 97.90%, and the available potassium (AK) increased by 182.72% and 596.09%, respectively. In addition, C. comatus significantly increased the available phosphorus (AP) by 163.14%. This proves that both macrofungi can enhance soil fertility, and C. comatus has a stronger fertilization effect. In terms of soil microorganisms, A. sinodeliciosus significantly influenced the distribution of soil bacteria and fungi, increasing the abundance of Streptomyces and reducing alpha diversity. C. comatus had a greater impact on bacteria, significantly increasing the relative abundance of Pseudomonas in the soil, but had no significant effect on fungi. Additionally, there was a close relationship between soil microbial abundance and physicochemical properties. pH, AP, TC, and AK were the main factors influencing bacteria, while total salt was the main factor affecting fungi. These findings reveal that A. sinodeliciosus and C. comatus influence the soil microenvironment by regulating soil physicochemical properties and microbial communities.},
}
@article {pmid41439481,
year = {2026},
author = {Zou, Y and Li, N and Li, X and Kuang, M and Xu, X and Guan, L and Li, X and Zheng, P and Li, L and Wan, J and Lu, N and Liu, J and He, C and Zhu, Y},
title = {Gut microbiota dysbiosis exacerbates acute pancreatitis via Escherichia coli-driven neutrophil heterogeneity and NETosis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2606480},
pmid = {41439481},
issn = {1949-0984},
mesh = {Animals ; *Dysbiosis/microbiology/immunology/complications ; *Gastrointestinal Microbiome ; Mice ; Humans ; *Neutrophils/immunology ; *Extracellular Traps/immunology/metabolism ; *Escherichia coli/physiology ; *Pancreatitis/microbiology/immunology/pathology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Fecal Microbiota Transplantation ; Female ; Specific Pathogen-Free Organisms ; },
abstract = {Gut microbiota dysbiosis contributes to acute pancreatitis (AP) severity, but the specific microbes and mechanisms remain unclear. In this study, we employed both germ-free (GF) and specific-pathogen-free (SPF) murine models of AP to investigate the role of the intestinal microbiota. Our findings demonstrate that GF mice exhibited markedly attenuated pancreatic injury, inflammatory cell infiltration, and neutrophil extracellular traps (NETs) formation. Through fecal microbiota transplantation (FMT) from AP patients, differential antibiotic modulation, and single-bacterial colonization experiments, we identified Gram-negative bacteria, particularly Escherichia coli (E. coli), as critical microbial drivers of disease exacerbation. Single-cell RNA sequencing revealed that microbiota dysbiosis profoundly reprogrammed both local pancreatic and systemic immune landscapes. Specifically, dysbiosis promoted emergency granulopoiesis in the bone marrow, enhanced neutrophil mobilization and activation, and facilitated the expansion of pro-inflammatory neutrophil subpopulations (Neutrophils_2 and Neutrophils_3). These subsets exhibited upregulated signaling through NETosis-associated pathways, including TLR, NF-κB, and IL-17 axes. Conversely, in GF conditions, we observed a predominance of an anti-inflammatory neutrophil subset (Neutrophils_4), characterized by the expression of tissue repair-associated genes such as Reg1 and Reg2. Shotgun metagenomic profiling of fecal samples from patients with AP revealed an enrichment of E. coli during the acute phase, positively correlating with circulating cell-free DNA, a marker of NETosis. Together, these insights suggest that gut microbiota dysbiosis, notably increased E. coli abundance, may aggravate AP by reshaping immunity and promoting aberrant NETs formation, supporting microbiota or NETs targeted therapies.},
}
@article {pmid41437386,
year = {2025},
author = {Aminu, S and Ascandari, A and Mokhtar, MM and Allali, AE and Benhida, R and Daoud, R},
title = {Genome-resolved surveillance and predictive ecological risk modeling of urban microbiomes.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {45},
pmid = {41437386},
issn = {2049-2618},
mesh = {*Microbiota/genetics ; Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenome ; Sewage/microbiology ; Cities ; Metagenomics/methods ; Machine Learning ; Genome, Bacterial ; },
abstract = {BACKGROUND: Human-built environment microbiomes mediate pathogen persistence and antimicrobial resistance (AMR) circulation, yet their ecological organization and resilience remain poorly quantified. Hospitals, sewage systems, ambulances, and public transport form interconnected microbial networks where contamination potential and compositional stability define biosurveillance risk. Understanding these dynamics requires genome-resolved frameworks capable of linking community composition to ecological behavior.<br><br>METHODS: We analyzed 767 publicly available Illumina metagenomes from four urban environments using the GRUMB workflow. Quality-filtered reads were assembled into 10,834 metagenome-assembled genomes (MAGs) and dereplicated into 1542 species-level representatives. Functional annotation with CARD and VFDB identified ARG- and VF-carrying species, producing a genome-resolved abundance matrix used for ecological and predictive modeling. Alpha and beta diversity, indicator taxa, and prevalence were assessed in R, while machine learning (Random Forest, scikit-learn) achieved a nested cross-validation balanced accuracy of 0.97&#x2009;&#xb1;&#x2009;0.01. Synthetic donor-recipient simulations (&#x3b1;&#x2009;=&#x2009;0-1) implemented in Python modeled compositional blending, entropy-based uncertainty, and Minimal Detectable Contamination (MDC) thresholds.<br><br>RESULTS: Microbial communities exhibited strong environment-specific structure (PERMANOVA R[2]&#x2009;=&#x2009;0.12, p&#x2009;<&#x2009;0.001). Hospital sewage contained the highest richness and compositional heterogeneity, whereas ambulances and hospital environments showed low-diversity, surface-filtered microbiomes. Machine learning identified consistent ecological predictors (Pseudomonas_E fragi, Sphingomonas sp000797515, Acinetobacter variabilis, Roseomonas mucosa) that delineated environmental identity. Synthetic blending revealed a directional source-sink hierarchy with hospital sewage acting as the primary donor (MDC&#x2009;=&#x2009;0.2-0.3), while hospital environments displayed the greatest compositional resilience (MDC&#x2009;&#x2265;&#x2009;0.8). Entropy-based uncertainty analysis identified tipping zones (&#x3b1;&#x2009;=&#x2009;0.3-0.5), and dominance mapping highlighted hospital environments as stabilizing ecological nodes. WHO-priority pathogens (Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli) occupied central positions in the network, bridging environmental and clinical compartments.<br><br>CONCLUSIONS: This genome-resolved and simulation-driven framework reveals a directional microbial continuum across urban infrastructures governed by dominance, resilience, and clinical connectivity. Hospital sewage functions as a microbial donor, while hospital environments act as ecological stabilizers anchoring built-environment microbiomes. These findings advance biosurveillance from descriptive profiling to predictive ecological modeling, offering quantitative metrics for risk-informed infrastructure design. Video Abstract.},
}
@article {pmid41437205,
year = {2026},
author = {Dinesh, D and Morgan, XC and Kim, H and Scott, TM and Garelnabi, M and Lee, JS and Mangano, KM and Nguyen, LH and Huttenhower, C and Tucker, KL and Palacios, N},
title = {Gut Microbial Variations Associated With Proton Pump Inhibitor Use in the Boston Puerto Rican Health Study.},
journal = {Pharmacology research &amp; perspectives},
volume = {14},
number = {1},
pages = {e70205},
pmid = {41437205},
issn = {2052-1707},
support = {RF1AG075922/AG/NIA NIH HHS/United States ; P01 AG023394/NH/NIH HHS/United States ; R01 NS09772/NH/NIH HHS/United States ; RF1 AG075922/AG/NIA NIH HHS/United States ; P50 HL105185/NH/NIH HHS/United States ; R01 AG055948/NH/NIH HHS/United States ; //University of Massachusetts/ ; R01 AG055948/AG/NIA NIH HHS/United States ; P50 HL105185/HL/NHLBI NIH HHS/United States ; P01 AG023394/AG/NIA NIH HHS/United States ; },
mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Boston ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Hispanic or Latino ; Prospective Studies ; *Proton Pump Inhibitors/adverse effects/pharmacology ; Puerto Rico/ethnology ; },
abstract = {Proton pump inhibitors (PPI), used to treat gastrointestinal disorders, are associated with alterations in the gut microbiome. However, this is understudied in Puerto Ricans who have unique lifestyle characteristics. Puerto Ricans, including participants of the Boston-Puerto Rican Health Study (BPRHS), report high PPI use. Therefore, we examined gut microbial variations associated with PPI use in the BPRHS. BPRHS is a prospective cohort. 309 BPRHS participants self-reported PPI use and self-collected, metagenomically profiled, stool samples. PPI use was classified as any use in the past 30 days. Cross-sectional associations between gut microbial taxa, functional pathways, and PPI use were examined using omnibus analyses, multivariate linear modeling in MaAsLin2, and random forest classifier in feature-wise analyses. We further compared our results with the non-Hispanic Health Professionals Follow-Up Study (HPFS) to validate key findings and examine ethnicity-related differences. Among 309 participants (mean age 68.8 years; female 74.6%), 112 (36%) self-reported PPI use. After adjusting for relevant covariates, we observed an enrichment of Streptococcus parasanguinis (β = 3.16, FDR p = 0.01), S. anginosus (β = 2.89, FDR p < 0.01), S. salivarius (β = 2.56, FDR p = 0.01), S. gordonii (β = 1.98, FDR p = 0.15), and Rothia mucilaginosa (β = 1.54, FDR p = 0.06), among PPI users compared to non-users. Streptococci, Lactobacilli, and Enterococci predominantly contributed to the functional pathways associated with PPI use. The observed enrichment of oral-typical taxa, such as Streptococci, among PPI users in the BPRHS suggests the potential of PPIs to alter gut microbial composition. More studies are needed to understand the impact of PPI use on the gut microbiome in different ethnicities. Trial Registration: Parent study (BPRHS) NCT01231958.},
}
@article {pmid41436448,
year = {2025},
author = {Manghi, P and Antonello, G and Schiffer, L and Golzato, D and Wokaty, A and Beghini, F and Mirzayi, C and Long, K and Gravel-Pucillo, K and Piccinno, G and Gamboa-Tuz, SD and Bonetti, A and D'Amato, G and Azhar, R and Eckenrode, K and Zohra, F and Giunchiglia, V and Keller, M and Pedrotti, A and Likhotkin, I and Elsafoury, S and Geistlinger, L and Blanco-Miguez, A and Thomas, AM and Zolfo, M and Ramos, M and Valles-Colomer, M and Tamburini, S and Asnicar, F and Jones, HE and Huttenhower, C and Carey, V and Davis, S and Pasolli, E and Oh, S and Segata, N and Waldron, L},
title = {Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {196},
pmid = {41436448},
issn = {2041-1723},
support = {R01 CA230551/CA/NCI NIH HHS/United States ; 5R01CA230551//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; },
mesh = {Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; *Mouth/microbiology ; },
abstract = {Large public datasets of the human microbiome now exist but combining them for large-scale analysis is difficult due to a lack of standardization. We developed curatedMetagenomicData (cMD) 3, a uniformly processed collection of over 22,000 human microbiome samples with manually curated metadata from 94 studies and 42 countries. This large and diverse resource allows for meta-analysis of the links between microbes and human health. Through meta-analysis, we identified hundreds of microbial species and thousands of microbial functions significantly associated with a person's sex, age, body mass index, and disease status, and catalog these as references. We developed an "oral enrichment score" (OES) based on the relative abundance of bacteria typically found in the oral cavity and not in the gut. Higher OES in the gut is a consistent feature in individuals with disease, suggesting that the relative abundance of oral bacteria in the gut is a simple and quantifiable signal of altered microbiome health. These analyses identify modest but widely shared patterns in human microbiomes, serving as a reproducible and readily updatable reference.},
}
@article {pmid41435895,
year = {2026},
author = {Zhang, PP and Cui, MY and Yang, SY and Han, B and Yu, W and Wei, TT and Zeng, KW and Tu, PF},
title = {Astragalus membranaceus improves blood glucose and renal function in diabetic kidney disease mice via gut microbial metabolite axis.},
journal = {Fitoterapia},
volume = {189},
number = {},
pages = {107048},
doi = {10.1016/j.fitote.2025.107048},
pmid = {41435895},
issn = {1873-6971},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Astragalus propinquus/chemistry ; Mice ; *Diabetic Nephropathies/drug therapy ; Male ; *Plant Extracts/pharmacology ; *Kidney/drug effects ; *Blood Glucose/drug effects ; Mice, Inbred C57BL ; Diabetes Mellitus, Experimental/drug therapy ; },
abstract = {Recent studies have demonstrated the therapeutic potential of Astragalus membranaceus in diabetic kidney disease (DKD); however, the underlying mechanisms remain incompletely elucidated. In this study, we established a streptozotocin-induced DKD mouse model to evaluate the effects of A. membranaceus extract (AME) on glycemic control, renal function, gut microbiota composition, and metabolic profiles. Biochemical analyzes revealed that A. membranaceus significantly attenuated hyperglycemia and improved renal function, as indicated by reduced serum creatinine and blood urea nitrogen levels. Metagenomic sequencing demonstrated that A. membranaceus reversed microbial dysbiosis by suppressing pathogenic bacteria (e.g., Aerococcus urinaeequi) and enriching beneficial probiotics (e.g., Thomasclavelia cocleata). Furthermore, LC/MS-based metabolomics identified key metabolic pathways, including glycerophospholipid metabolism and bile acid synthesis, as potential mediators of the therapeutic effects. These findings underscore the crucial role of the gut-renal axis in DKD pathogenesis and provide a mechanistic basis for the clinical application of A. membranaceus.},
}
@article {pmid41432724,
year = {2026},
author = {Zhang, Z and Ye, B and He, J and Xiang, L and Li, S and Zhao, J and Chen, W and Zhang, Q and Zhao, W and Yang, J and Li, Y and Ju, J and Liu, Y and Xia, M},
title = {Microbial metabolites associated with healthy lifestyles in relation to metabolic syndrome and vascular health: a cross-sectional study.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0143325},
pmid = {41432724},
issn = {2379-5077},
mesh = {Humans ; *Metabolic Syndrome/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Cross-Sectional Studies ; Middle Aged ; Adult ; *Healthy Lifestyle/physiology ; Feces/microbiology ; Bacteria/metabolism/classification/genetics ; Metabolome ; Aged ; },
abstract = {UNLABELLED: Lifestyle behaviors influence the risk of metabolic syndrome (MetS) and affect vascular health. However, the interactions between gut microbiota and lifestyle behaviors in relation to MetS, as well as the specific microbial taxa and metabolites involved, remain unclear. Here, we aimed to investigate the associations among healthy lifestyle behaviors, gut microbiota, and MetS and to explore the potential mediating roles of microbially derived metabolites in these associations. A total of 1,342 participants with complete assessments of the Healthy Lifestyle Score (HLS), MetS, and vascular health were enrolled. Fecal samples were collected and subjected to metagenomic sequencing. Host genetic data were obtained using a high-density genotyping array, and plasma metabolites were quantified by liquid chromatography-mass spectrometry. Using generalized linear models, we found that increased abundances of Alistipes putredinis, Odoribacter splanchnicus, and Roseburia hominis were associated with higher HLS and a reduced risk of MetS. Eleven microbial metabolic pathways were independently correlated with both HLS and MetS. Furthermore, increased plasma levels of cinnamoylglycine and betaine, driven by enhanced microbial capacity for homolactic fermentation, were identified as potential microbial effectors associated with MetS and vascular health. These findings indicate that the association between HLS and MetS may involve modulation of the gut microbiota and their metabolites and highlight the potential to enhance the beneficial effects of healthy behaviors on MetS and vascular health through microbiota-modifying interventions.<br><br>IMPORTANCE: Metabolic syndrome raises the risk of heart disease and diabetes, yet practical levers to prevent it remain limited. We show that everyday healthy habits align with a gut microbial "signature" linked to better vascular health and lower metabolic risk. Using metagenomics, metabolomics, and genetic causal analyses, we identify specific bacteria (Alistipes putredinis, Odoribacter splanchnicus, and Roseburia hominis) and microbially produced molecules-especially cinnamoylglycine and betaine from enhanced homolactic fermentation-that may mediate these benefits. These findings connect lifestyle, the gut microbiome, and blood metabolites in a single framework, suggesting actionable biomarkers to monitor risk and potential microbiota-targeted strategies (diet and pre/probiotics) to improve cardiometabolic health. By highlighting concrete microbial pathways and metabolites, our work advances the path toward precision prevention and low-cost interventions for metabolic syndrome and vascular disease.},
}
@article {pmid41432437,
year = {2026},
author = {Bowerman, KL and Lu, Y and McRae, H and Volmer, JG and Zaugg, J and Pope, PB and Hugenholtz, P and Greening, C and Morrison, M and Soo, RM and Evans, PN},
title = {Metagenomic analysis of fecal microbiomes reveals genetic potential for diverse hydrogen management strategies in marsupials.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0160825},
pmid = {41432437},
issn = {2379-5077},
support = {DP210103991//Department of Education and Training | Australian Research Council (ARC)/ ; DP150104202//Department of Education and Training | Australian Research Council (ARC)/ ; FT210100812//Department of Education and Training | Australian Research Council (ARC)/ ; //Australian Government (Federal Government)/ ; B.STU.1909//Meat and Livestock Australia/ ; //University of Queensland/ ; },
mesh = {Animals ; *Hydrogen/metabolism ; *Marsupialia/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Methane/metabolism ; *Metagenomics/methods ; *Metagenome ; Bacteria/genetics/metabolism/classification ; },
abstract = {Methane is an end product of plant biomass digestion by gut microbiota, though the amount produced and/or released varies between hosts. On a per-unit-of-feed basis, macropodid marsupials (e.g., kangaroos) have been reported to emit less methane than ruminant livestock, despite a similar diet, although measurements exist for only a subset of macropodid species. Competition for hydrogen within the gut microbiome, particularly through alternative hydrogen sinks to methanogenesis, influences methane production; therefore, characterizing hydrogen management strategies within a host system can provide insights into methane emission profiles. In this study, we analyzed 33 fecal microbiomes of 14 marsupial species (predominantly captive animals) to provide the first systematic characterization of methanogen types and hydrogen-cycling genetic capacity across marsupial gut microbiomes. We recovered 1,394 metagenome-assembled genomes and identified host-associated bacterial signatures that varied significantly between marsupial species. Comparative analysis with fecal microbiomes from high- and low-methane-emitting mammals revealed that marsupials display heterogeneous hydrogen management strategies: some harbor elevated methanogenesis genes (mcrA, methanogen-specific hydrogenases), while others show enrichment of bacterial hydrogen-uptake hydrogenases and alternative electron acceptor pathways (nitrate/nitrite reduction, sulfite reduction). This predicted functional variation occurs both between and within marsupial families and gut types, suggesting that hydrogen management capacity may differ within taxonomic and anatomical classifications. These results demonstrate that marsupial gut microbiomes cannot be treated as a functionally homogenous group regarding methane emissions and highlight the need for species-specific measurements to accurately assess their methanogenic potential and inform ecological models of greenhouse gas production.IMPORTANCEHerbivorous marsupials such as kangaroos and wallabies have been reported to produce significantly lower methane emissions than ruminant livestock despite eating a similar diet, yet the microbial mechanisms underlying this difference remain poorly understood. Here, we conduct a comparative study of fecal microbiomes of 14 marsupial species to provide the first investigation of hydrogen-cycling genetic capacity across these animals. Through comparative analysis with fecal microbiomes of high- and low-methane-producing animals, we identify enrichment of bacterial genes for alternative hydrogen uptake and disposal pathways in some marsupials, supporting competition for hydrogen playing a role in the level of methane production. These data also indicate variation in hydrogen management between marsupials, including within species, suggesting methane emission capacity may vary at the level of the individual.},
}
@article {pmid41432253,
year = {2026},
author = {Ricci, F and Hutchinson, T and Leung, PM and Nguyen-Dinh, T and Zeng, J and Jirapanjawat, T and Eate, V and Wong, WW and Cook, PLM and Greening, C},
title = {Chemosynthesis enables microbial communities to flourish in a marine cave ecosystem.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf286},
pmid = {41432253},
issn = {1751-7370},
support = {ECPF24-4273843556//Early Career Postdoctoral Fellowship/ ; //Faculty of Medicine, Nursing and Health Science at Monash University/ ; DE250101210//ARC DECRA Fellowships/ ; FT240100502//ARC Future Fellowship/ ; SR200100005//ARC SRIEAS/ ; //Securing Antarctica's Environmental Future/ ; },
mesh = {*Caves/microbiology ; *Bacteria/metabolism/genetics/classification ; *Geologic Sediments/microbiology ; *Archaea/metabolism/genetics/classification ; *Ecosystem ; Metagenome ; *Microbiota ; Photosynthesis ; Eukaryota/genetics/metabolism/classification ; Seawater/microbiology ; },
abstract = {Chemosynthesis, an ancient metabolism that uses chemical compounds for energy and biomass generation, occurs across the ocean. Although chemosynthesis typically plays a subsidiary role to photosynthesis in the euphotic ocean, it is unclear whether it plays a more important role in aphotic habitats within this zone. Here, we compared the composition, function, and activity of microorganisms colonising the sediment of a marine cave at mesophotic depth, across a transect from the entrance to the interior. Microbes thrived throughout this ecosystem, with interior communities having higher diversity than those at the entrance. Analysis of 132 species-level bacterial, archaeal, and eukaryotic metagenome-assembled genomes revealed niche partitioning of habitat generalists distributed along the cave, alongside specialists enriched across the entrance and interior environments. Photosynthetic microbes and photosystem genes declined in the inner cave, concomitant with enrichment of chemosynthetic lineages capable of using inorganic compounds such as ammonium, sulfide, carbon monoxide, and hydrogen. Biogeochemical assays confirmed that the cave communities consume these compounds and fix carbon dioxide through chemosynthesis, with inner communities mediating higher cellular rates. Together, these findings suggest that the persistent darkness and low hydrodynamic disruption in marine cave sediments create conditions for metabolically diverse communities to thrive, sustained by recycling of inorganic compounds, as well as endogenous and lateral organic matter inputs. Thus, chemosynthesis can sustain rich microbial ecosystems even within the traditionally photosynthetically dominated euphotic zone.},
}
@article {pmid41432159,
year = {2026},
author = {Lau, KJX and Ma, A and Chen, B and Thankaraj Salammal, MS and Ramachandran, S and Naqvi, NI},
title = {Controlled irrigation suppresses methane emissions by reshaping the rhizosphere microbiomes in rice.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0297025},
pmid = {41432159},
issn = {2165-0497},
support = {Intramural//Temasek Life Sciences Laboratory/ ; //Philanthropy Asia Alliance/ ; //Bill and Melinda Gates Foundation (GF)/ ; },
mesh = {*Oryza/microbiology/growth &amp; development/metabolism ; *Methane/metabolism ; *Rhizosphere ; *Agricultural Irrigation/methods ; *Microbiota ; Soil Microbiology ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Archaea/metabolism/genetics/classification ; Plant Roots/microbiology ; Metagenomics ; Floods ; },
abstract = {The rhizosphere microbiomes of rice plants under conventional flood irrigation consist of highly complex consortia of microorganisms and, in particular, methanogens purportedly associated with methane emissions therein. Controlled irrigation has been proposed as a cultivation method of choice over continuous flooding to reduce water and fertilizer usage in an aerobic environment. However, a systematic understanding of the assembly and function of microbiota in the rhizosphere under drip and flood irrigation remains unclear. Using empirical analyses, we report a significant reduction in methane emissions in controlled irrigation compared to the flooded environment. Genotypic or varietal differences did not influence such methane emissions under conventional flooded cultivation of rice. Using metagenomic sequencing and computational analyses, we provide a deeper understanding of how drip irrigation or continuous flooding affects the root-associated microbiomes in rice. Rhizosphere soil from two different rice varieties, Huanghuazhan and Temasek rice, grown under drip or flood conditions in a greenhouse, was collected over 2 months post-transplantation for metagenomic analysis. Our results reveal that drip irrigation favors microbes involved in the nitrifying-denitrifying processes, while continuous flooding enriches for methanotrophs and methanogenic archaea. Syntrophic microbiomes associated with methanogenesis were significantly reduced in drip irrigation. Several keystone taxa were evident in the co-occurrence network model related to methanogenic, methanotrophic, nitrifying, sulfur-oxidizing and sulfur-reducing activities. Lastly, oxygen availability and redox potential were identified as key drivers that reshape rhizosphere microbiota and the associated metabolic functional differences observed between the two irrigation regimes, leading up to the microbial mitigation of climate impact.IMPORTANCEUnlike previous studies in alternate wet-dry irrigation systems, this study characterized the rice microbiomes in a controlled drip irrigation setting where water levels were maintained at low levels and soil remained unflooded throughout the entire season in a greenhouse. A reduction of more than 90% in methane emissions was observed with drip irrigation compared to flood irrigation. A significant correlation was found between levels of methane emitted and mcrA gene copies detected, with a Pearson correlation coefficient R of 0.77 and P-value of 2.3e - 10. Methanogens are highly abundant in continuously flooded rice soil and are significantly reduced in drip-irrigated soil. Metagenomic profiling indicates that the shifts in microbial diversity under drip irrigation favor nitrifying microorganisms and are likely influenced by increased oxygen availability due to higher soil redox potential.},
}
@article {pmid41432144,
year = {2026},
author = {Liu, J and Ni, H-B and Yu, M-Y and Qin, S-Y and Elsheikha, HM and Peng, P and Guo, L and Xie, L-H and Liang, H-R and Lei, C-C and Xu, Y and Tang, Y and Yu, H-L and Qin, Y and Liu, J and Sun, H-C and Zhang, X-X and Qiu, B},
title = {Comprehensive profiling of antibiotic resistance, virulence genes, and mobile genetic elements in the gut microbiome of Tibetan antelopes.},
journal = {mSystems},
volume = {11},
number = {2},
pages = {e0144325},
pmid = {41432144},
issn = {2379-5077},
support = {2023YFF1305403//National Key Research and Development Program of China/ ; 2022KJ169//Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; No. 667/2425025//Horizontal Project of Qingdao Agricultural University/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; *Antelopes/microbiology ; Animals ; Tibet ; *Virulence Factors/genetics ; *Interspersed Repetitive Sequences/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Metagenome ; *Bacteria/genetics/pathogenicity/drug effects ; Genes, Bacterial ; },
abstract = {UNLABELLED: Tibetan antelopes, native to high-altitude plateau regions, play an important role in the local ecosystem. Their gut harbors antimicrobial-resistant microbes, including potential pathogens. To explore this, we analyzed 33,925 metagenome-assembled genomes (MAGs), including 7,318 from 68 Tibetan antelopes sequenced in our laboratory. We first profiled the composition of antibiotic resistance genes (ARGs) and then examined their associations with virulence factor genes (VFGs). In total, 2,968 ARGs were identified, conferring resistance to 23 antibiotic classes, with elfamycin resistance being most prevalent. Two ARGs were located on phage-derived sequences, though their phage taxonomy could not be resolved. ARGs were significantly correlated with VFGs, particularly genes linked to adherence and effector delivery systems. Given potential dissemination risks, we further assessed associations between ARGs and mobile genetic elements (MGEs), finding that insertion elements accounted for the largest number of ARG-MGE links. Comparative analysis with other plateau animals and humans revealed seven ARGs uniquely present in Tibetan antelopes. In summary, this study provides the first comprehensive overview of ARG composition in Tibetan antelope gut microbiomes, establishing a baseline for future hypothesis-driven studies and antimicrobial resistance surveillance in wildlife.<br><br>IMPORTANCE: Investigating the drug resistance of Tibetan antelope (Pantholops hodgsonii) gut microbiota serves as a critical biological indicator for assessing the impact of human activities (particularly antibiotic contamination) on the fragile ecosystem of the Qinghai-Tibet Plateau. This study untangles the invasion of antibiotic resistance genes (ARGs) into remote conservation areas, suggesting that Tibetan antelopes may act as potential vectors for ARG dissemination across plateau environments. Such findings not only highlight threats to wildlife health but also provide an ecological warning regarding the pervasive environmental risks posed by the global antimicrobial resistance crisis in natural ecosystems.},
}
@article {pmid41431864,
year = {2026},
author = {Dowrick, JM and Roy, NC and Carco, C and James, SC and Heenan, PE and Frampton, CMA and Fraser, K and Young, W and Cooney, J and Trower, T and Keenan, JI and McNabb, WC and Mullaney, JA and Bayer, SB and Talley, NJ and Gearry, RB and Angeli-Gordon, TR},
title = {Integrated multi-omic and symptom clustering reveals lower-gastrointestinal disorders of gut-brain interaction heterogeneity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2604871},
pmid = {41431864},
issn = {1949-0984},
mesh = {Humans ; Cluster Analysis ; *Gastrointestinal Diseases/physiopathology/microbiology/classification ; Male ; Female ; *Brain/physiopathology ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; *Gastrointestinal Tract/physiopathology ; Multiomics ; },
abstract = {Rome IV disorders of gut-brain interaction (DGBI) subtypes are known to be unstable and demonstrate high rates of non-treatment response, likely indicating patient heterogeneity. Cluster analysis, a type of unsupervised machine learning, can identify homogeneous sub-populations. Independent cluster analyses of symptom and biological data have highlighted its value in predicting patient outcomes. Integrated clustering of symptom and biological data may provide a unique multimodal perspective that better captures the complexity of DGBI. Here, integrated symptom and multi-omic cluster analysis was performed on a cohort of healthy controls and patients with lower-gastrointestinal tract DGBI. Cluster stability was assessed by considering how frequently pairs of participants appeared in the same cluster between different bootstrapped datasets. Functional enrichment analysis was performed on the biological signatures of stable DGBI-predominant clusters, implicating disrupted ammonia handling and metabolism as possible pathophysiologies present in a subset of patients with DGBI. Integrated clustering revealed subtypes that were not apparent using a singular modality, suggesting a symptom-only classification is prone to capturing heterogeneous sub-populations.},
}
@article {pmid41431647,
year = {2025},
author = {Lu, X and Dai, H and Gu, X and Xie, J and Zhong, X and Dong, X and Su, B and Su, J and Wang, L and Sun, T and Geng, L},
title = {The clinical significance of gut microbiota of chronic obstructive pulmonary disease with functional abdominal bloating and distension.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20526},
pmid = {41431647},
issn = {2167-8359},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/complications/physiopathology ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; Case-Control Studies ; Biomarkers ; *Gastrointestinal Diseases/microbiology ; Clinical Relevance ; },
abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a disease with high morbidity and mortality. Functional abdominal bloating/distension (FABD), a functional gastrointestinal disorder characterized by recurrent sensations of abdominal fullness and/or visible abdominal distension without identifiable organic causes. FABD mainly impairs gastrointestinal functions-particularly intestinal transit and gas handling-rather than pulmonary function. This study characterized fecal microbiota in COPD patients with FABD to identify precision medicine biomarkers.<br><br>METHODS: Fecal samples from 20 COPD &amp; FABD, 20 COPD, and 10 healthy controls (HC) were analyzed via metagenomic analysis. Gut microbiota diversity/composition were compared, and immune parameters (serum IgG, CD4+/CD8+ T cells) were assessed.<br><br>RESULTS: COPD/COPD &amp; FABD patients showed significantly higher fecal microbiota &#x3b1;-diversity (COPD vs. HC: Chao1, P = 0.12; ACE, P = 0.14; Shannon, P = 0.0016; Simpson, P = 0.0013; COPD &amp; FABD vs. HC: Chao1, P = 0.031; ACE, P = 0.031; Shannon, P = 0.00032; Simpson, P = 0.0005) vs. HC. &#x3b2;-Diversity analyses (PCA/PCoA) revealed distinct clustering between patients and HC (PCA, P = 0.014; PCoA, P = 0.013), but no separation between COPD and COPD &amp; FABD (P > 0.05). Linear discriminant analysis (LEfSe) identified 50 discriminative biomarkers: 41 enriched in HC (Bacteroides uniformis), five in COPD &amp; FABD (Bacilli, Enterococcus faecium), and four in COPD (Streptococcus parasanguinis). Notably, Enterococcus faecium was highly abundant in patients (22.04-26.92%) but absent in HC, suggesting a potential association with the COPD-FABD condition. Random forest models showed moderate diagnostic accuracy for all microbes (AUC = 0.632) and strong performance for fungal biomarkers (Clostridium fessum, Clostridioides difficile; AUC = 0.856).<br><br>CONCLUSION: Gut microbiota signatures, particularly Enterococcus faecium and fungal taxa, may serve as non-invasive biomarkers for COPD progression and FABD diagnosis, warranting clinical validation.},
}
@article {pmid41431641,
year = {2025},
author = {Nguyen, BN and Nguyen, LTN and Trinh, DTM and Nguyen, HT and Tran, TTT},
title = {Preliminary insights into the gut microbiota of patients with rheumatoid arthritis in Vietnam.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20521},
pmid = {41431641},
issn = {2167-8359},
mesh = {Humans ; *Arthritis, Rheumatoid/microbiology ; Vietnam ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Pilot Projects ; Adult ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; },
abstract = {In Vietnam, rheumatoid arthritis accounts for more than 20% of all joint diseases, with a growing number of young patients. The disease progresses rapidly, but its exact cause remains not fully understood. Environmental and lifestyle factors, such as smoking, pollution, obesity, gut microbiota, and infections, play a role in rheumatoid arthritis development. The presence of Gram-positive bacteria in the gut might promote the release of toxic metabolites into the bloodstream, which in turn triggers joint inflammation. Therefore, this pilot study aimed to compare the gut microbiota in 22 patients with newly diagnosed rheumatoid arthritis and 20 healthy individuals recruited at the Bach Mai Hospital, Hanoi, Vietnam. To this end, we analyzed fecal samples from all participants by 16S rRNA metagenomic sequencing. The sequencing data analysis did not reveal any significant differences in alpha diversity between patients and healthy controls. Conversely, unweighted and weighted UniFrac distances (beta diversity metrics) allowed distinct clustering between groups. The abundance of the Lactococcus, Solobacterium, Faecalibaculum, and Corynebacterium genera was increased, and that of Bacteroides was decreased in patients with rheumatoid arthritis compared with healthy controls. Moreover, patients exhibited distinct gut microbiota profiles in function of their disease activity scores (DAS28-CRP, DAS-ESR), rheumatoid factor, and anti-citrullinated protein antibody concentrations. Overall, our study contributes to bridging this knowledge gap and provides a foundation for the study of gut microbial signatures of autoimmune disease in Vietnamese patients. It also highlights the potential role of gut microbes in rheumatoid arthritis diagnosis and management in Vietnam.},
}
@article {pmid41431440,
year = {2026},
author = {Wang, W and Huang, H and Zhao, K and Lv, J and Liu, X and Xie, S and Feng, J},
title = {The Differing Responses of Chlorophyta and Bacillariophyta to Available Resources Result in Diverse Community Patterns in Lakes Situated to the East of the Hu Line During the Autumn.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {1},
pages = {e70248},
doi = {10.1002/wer.70248},
pmid = {41431440},
issn = {1554-7531},
support = {32270220//National Natural Science Foundation of China/ ; U22A20445//National Natural Science Foundation of China/ ; 2020KJ029//Excellent Achievement Cultivation Project of Higher education in Shanxi/ ; 2024-007//Research Project Supported by Shanxi Scholarship Council of China/ ; 202203021211313//Sanjin Talent Innovation Teams in Natural Sciences and Engineering Technology/ ; },
mesh = {*Lakes ; *Diatoms/genetics/physiology ; *Chlorophyta/genetics/physiology ; Seasons ; Biodiversity ; Ecosystem ; },
abstract = {Phytoplankton communities are of vital importance to the functioning of freshwater ecosystems, but the role of the metabolic capacity of the community in regulating community dynamics under natural conditions has yet to be sufficiently considered. This study investigated 26 lakes situated along the eastern section of the Hu Line, combining field surveys with metagenome-assembled analyses to ascertain the factors responsible for the divergence in Chlorophyta and Bacillariophyta communities. The results demonstrated that the diversity of Chlorophyta was markedly higher than that of Bacillariophyta whereas the abundance was significantly lower. These discrepancies in community attributes were predominantly attributable to variations in the response of the two algal groups to nutrients. The abundance and diversity of diatom metabolic genes were significantly higher than those of green algae. The greater diversity and extent of metabolic genes in Bacillariophyta confer enhanced metabolic capacity and, consequently, greater adaptive capacity. Such differences in metabolic gene composition may be attributed to the disparate evolutionary pathways that these organisms have followed.},
}
@article {pmid41430427,
year = {2025},
author = {De Santis, A and Bevilacqua, A and Corbo, MR and Speranza, B and Francavilla, M and Gatta, G and Carucci, F and Sinigaglia, M},
title = {A statistical approach to model soil microbiota versus heavy metals: a case study on soil samples from Foggia, Southern Italy.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {2586},
pmid = {41430427},
issn = {2045-2322},
mesh = {Italy ; *Metals, Heavy/analysis ; *Soil Microbiology ; *Microbiota ; *Soil Pollutants/analysis ; *Soil/chemistry ; Environmental Monitoring/methods ; Metagenomics ; Models, Statistical ; },
abstract = {Heavy-metal (HM) contamination undermines soil functions and food safety, while risk appraisals often rely on chemical indices that can be unstable in the presence of extremes and only indirectly reflect biological integrity. We present an integrative framework that couples standardized contamination metrics with soil microbiome profiling to deliver stable, interpretable classifications and actionable bioindicators. Twelve peri-urban soils from Southern Italy were analysed for potentially toxic elements, including Arsenic (As), Cadmium (Cd), Chromium (Cr), Copper (Cu), Nickel (Ni), Lead (Pb), and Zinc (Zn) and profiled by shotgun metagenomics. We introduce a Standardized Ecological Risk index (SPERI) that preserves the ranking conveyed by conventional composites yet reduces outlier leverage. SPERI strongly agreed with Improved Potential Ecological Risk Index (IPERI) while stabilizing variance (R[2] = 0.896) and improved between-site comparability. Along the contamination gradient, community structure shifted consistently: families such as Pseudomonadaceae, Xanthomonadaceae and Rhodospirillaceae increased with risk, whereas Geodermatophilaceae and Nocardiaceae declined. Simple decision-tree models trained on family-level relative abundances reliably separated SPERI classes and repeatedly selected Zn- and Cd-enriched sites as primary split drivers, aligning microbial signals with chemical risk. By combining open, reproducible analytics with jointly chemical- and microbiome-informed endpoints, this workflow improves the interpretability and transferability of ecological risk assessment and supports targeted remediation and monitoring in contaminated agro-ecosystems.},
}
@article {pmid41430301,
year = {2025},
author = {Wikki, I and Palmu, J and Kauko, A and Havulinna, A and Jousilahti, P and Lahti, L and Knight, R and Salomaa, V and Niiranen, T},
title = {Prospective association between the gut microbiota and incident pneumonia: a cohort study of 6419 individuals.},
journal = {Respiratory research},
volume = {26},
number = {1},
pages = {354},
pmid = {41430301},
issn = {1465-993X},
support = {330887//Research Council of Finland/ ; 321351, 354447//Research Council of Finland/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Prospective Studies ; Middle Aged ; Incidence ; *Pneumonia/epidemiology/microbiology/diagnosis ; Aged ; Cohort Studies ; Adult ; Follow-Up Studies ; Risk Factors ; Feces/microbiology ; },
abstract = {BACKGROUND: Previous animal studies have identified the protective capacity of the gut microbiota against respiratory infections. Nevertheless, the prospective association between human gut microbiota and pneumonia risk remains unknown.<br><br>OBJECTIVES: To evaluate the links between gut microbiota and incident pneumonia in a representative population sample.<br><br>METHODS: We performed shotgun metagenome sequencing on stool samples from 6419 FINRISK 2002 participants. Participants were followed up for incident pneumonia using nationwide health register data. We employed multivariable-adjusted Cox regression models and permutational multivariate analysis of variance (PERMANOVA) to assess the association of gut microbiome alpha diversity, compositional variation (beta diversity), and taxonomic composition with pneumonia risk.<br><br>RESULTS: Altogether, 685 patients (10.7%) developed pneumonia during a mean follow-up of 17.8 years. Alpha diversity was not associated with incident pneumonia (hazard ratio [HR] 1.00; 95% confidence interval [CI] 0.93&#x2009;-&#x2009;1.08), whereas community composition was (PERMANOVA R[2]&#x2009;=&#x2009;0.03%; P&#x2009;=&#x2009;0.02). We observed an inverse association between the relative abundance of butyrate-producing bacteria and incident pneumonia (HR per 1-SD increase 0.91; 95% CI 0.85-0.98). The relative abundance of Bacteroides_F pectinophilus, Eubacterium_G ventriosum, Agathobaculum butyriciproducens, Butyribacter intestini, Eubacterium_I ramulus, CAG-1427 sp000435675, and CAG-603 sp900066105 were inversely associated with pneumonia risk. The relative abundance of Clostridium_AQ innocuum was positively correlated with pneumonia risk.<br><br>CONCLUSIONS: The gut microbiota composition, and especially the relative abundance of butyrate-producing bacteria, was associated with lower pneumonia risk in the population. These findings warrant further studies to investigate whether microbiome modulation to increase short chain fatty acid production through diet, prebiotics, or probiotics could reduce pneumonia risk.},
}
@article {pmid41429819,
year = {2025},
author = {Chen, Q and Xu, J and Yang, J and Qin, X and Fan, J and Ke, H and Yang, Z and Zheng, W and Li, X and Huang, L and Ning, W},
title = {Gut microbiota analysis in children with autism spectrum disorder and their family members.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44282},
pmid = {41429819},
issn = {2045-2322},
support = {Grant No.3502Z20214001//Project of Xiamen Cell Therapy Research Center, Xiamen, Fujian, China/ ; 2022YFC2704300//National Key Research and Development Program of China/ ; 32400532//National Natural Science Foundation of China/ ; 2024GGB18//Fujian Provincial Health Technology Project/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/microbiology ; Child ; Male ; Female ; Child, Preschool ; Dysbiosis/microbiology ; Feces/microbiology ; Siblings ; Bifidobacterium/isolation &amp; purification/genetics ; Clostridium/isolation &amp; purification/genetics ; Bacteroides/isolation &amp; purification/genetics ; Metagenomics/methods ; Family ; },
abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by deficits in social communication and interaction, alongside restricted, and repetitive behaviors. Emerging evidence suggests that gut microbiota alterations may contribute to ASD pathogenesis via the gut-brain axis. However, many previous studies have not adequately controlled for confounding genetic and environmental variables. In this study, we examined the gut microbiota profiles of 19 children with ASD, 8 siblings with non-ASD, and 36 parents from 17 families, providing a unique design that minimized biases related to shared genetic and familial environments. Metagenomic sequencing revealed significant differences in gut microbiota diversity and composition between groups. Specifically, children with ASD had lower abundances of Bifidobacterium and higher abundances of both Bacteroides and Clostridium species compared to their siblings, with notable dysbiosis correlated to ASD-specific symptoms. These findings highlight the potential role of microbiota alterations in ASD pathogenesis and suggest familial microbiota traits influenced by both genetic and environmental factors. Further exploration of gut microbial therapies could offer promising avenues for ASD intervention.},
}
@article {pmid41429225,
year = {2026},
author = {Chen, J and Cao, H and Xu, Y and Chang, Y and Qin, X and Zhang, Z and Yang, W},
title = {Is light-to-moderate alcohol drinking associated with the onset of metabolic dysfunction-associated steatotic liver disease in a Chinese cohort?.},
journal = {The American journal of clinical nutrition},
volume = {123},
number = {2},
pages = {101144},
doi = {10.1016/j.ajcnut.2025.101144},
pmid = {41429225},
issn = {1938-3207},
mesh = {Humans ; Male ; *Alcohol Drinking/adverse effects ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Adult ; China/epidemiology ; *Fatty Liver/etiology/epidemiology ; Cohort Studies ; Risk Factors ; Asian People ; Aged ; *Metabolic Diseases/etiology ; East Asian People ; },
abstract = {BACKGROUND: The association between light-to-moderate alcohol drinking (≤14 g/d for females; ≤28 g/d for males) and the risk of steatotic liver disease (SLD), including its metabolic dysfunction-associated subtype (MASLD), remains unclear, as does the role of related gut microbiota.<br><br>OBJECTIVES: We investigated the association between light-to-moderate alcohol drinking and incident SLD/MASLD, identified gut microbial species associated with such drinking, and evaluated their associations with disease risk.<br><br>METHODS: Among 1297 adults from a Chinese community-based cohort, alcohol intake was assessed by a validated questionnaire, and SLD was diagnosed by vibration-controlled transient elastography. In a subset with fecal samples at follow-up (n = 665), gut microbiota was profiled using shotgun metagenomic sequencing. We used the mean alcohol intake from baseline and follow-up to represent long-term drinking habits. Species differentially associated with alcohol intake were identified using zero-inflated Gaussian models with false discovery rate (FDR) correction. Cox and logistic regression were used to estimate hazard ratio (HR) and odds ratio (OR) with 95% confidence interval (CI), respectively.<br><br>RESULTS: During follow-up (2020-2025), 513 incident SLD cases were identified. Light-to-moderate drinkers showed higher risks of SLD (HR = 1.27, 95% CI: 1.03, 1.58) and MASLD (HR = 1.27, 95% CI: 1.01, 1.59) compared with abstainers. For the same comparison, liquor consumption was positively associated with SLD (HR = 1.29, 95% CI: 1.01, 1.65). We identified 89 microbial species associated with alcohol intake and constructed a microbial score, which was positively associated with SLD (ORT3 vs T1 = 1.54, 95% CI: 1.03, 2.31, Ptrend = 0.05) and MASLD (ORT3 vs T1 = 1.50, 95% CI: 1.00, 2.26, Ptrend = 0.05). Among these species, Stenotrophomonas maltophilia AQ, Olsenella E timonensis, and Firm 11 sp., which were less abundant in drinkers, showed inverse associations with both conditions after FDR correction.<br><br>CONCLUSIONS: Light-to-moderate alcohol consumption was associated with increased risks of SLD and MASLD. A gut microbial score based on alcohol-associated species also predicted higher disease risk.},
}
@article {pmid41429195,
year = {2026},
author = {Ji, J and Guo, J and Huang, Y and Chen, K and Xu, Y and Liang, W and Lin, Z and Xiong, C and Han, X and Liu, J and Hei, Z and Chen, S and Yao, W and Chen, C},
title = {Electroconvulsive therapy modulates brain plasticity in male depression: Links to gut microbial metabolites and diet-derived regulation of Wnt/BDNF signaling.},
journal = {The Journal of nutritional biochemistry},
volume = {150},
number = {},
pages = {110240},
doi = {10.1016/j.jnutbio.2025.110240},
pmid = {41429195},
issn = {1873-4847},
mesh = {Animals ; Male ; *Gastrointestinal Microbiome/physiology ; *Brain-Derived Neurotrophic Factor/metabolism ; *Neuronal Plasticity ; Mice ; *Electroconvulsive Therapy ; *Depression/therapy/metabolism ; *Wnt Signaling Pathway ; Mice, Inbred C57BL ; Fatty Acids, Volatile/metabolism ; Diet ; Probiotics ; Brain/metabolism ; },
abstract = {Electroconvulsive therapy (ECT) stands as the most effective intervention for treatment-resistant depression; however, its interaction with dietary regulation of the gut-brain axis has not been thoroughly explored. This study aimed to elucidate the mechanistic link between ECT, gut microbiota remodeling, short-chain fatty acid (SCFA) production, and neural plasticity. In this study, mice were subjected to chronic restraint stress (6 h/d for 28 consecutive days) to establish a depression-like model. Utilizing a translational approach that incorporated behavioral assessments, multimodal neuroimaging techniques such as PET-CT and laser speckle contrast imaging, along with multiomics analyses including metagenomics, metabolomics, and transcriptomics in rodent models, we demonstrated that ECT induced significant gut microbiota remodeling, characterized by an enrichment of SCFA-producing genera like Lactobacillus and Bifidobacterium. This remodeling was associated with restored intestinal barrier integrity and elevated plasma SCFA levels. Mechanistically, these microbial metabolites activated hippocampal Wnt/β-catenin signaling pathways, enhancing synaptic plasticity restoration, while concurrent probiotic supplementation further amplified brain-derived neurotrophic factor (BDNF) expression via SCFA-dependent epigenetic mechanisms. Neuroimaging corroborated the normalization of cerebral glucose metabolism and hemodynamic function post-ECT. In conclusion, our findings unveil a novel gut-brain communication pathway by which ECT exerts its antidepressant effects, positioning SCFAs as vital mediators connecting microbial metabolic alterations to neural plasticity. This research not only redefines the role of nutritional biochemistry in neuromodulation but also suggests the potential of microbial metabolite monitoring to tailor antidepressant therapies for enhanced efficacy.},
}
@article {pmid41428602,
year = {2025},
author = {Zhang, Y and Chen, W and Wang, B and Rehman, KU and van Huis, A and Henawy, AR and Cai, M and Zheng, L and Ren, Z and Huang, F and Zhang, J},
title = {Enhancing Salmonella Inhibition in Black Soldier Fly Larvae (Hermetia illucens L.) Conversion by Bioaugmentation With Gut Microbiota.},
journal = {Microbial biotechnology},
volume = {18},
number = {12},
pages = {e70242},
pmid = {41428602},
issn = {1751-7915},
support = {31770136//National Natural Science Foundation of China/ ; 2662022SKYJ006//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY003//Fundamental Research Funds for the Central Universities/ ; 2022hszd013//Major Project of Hubei Hongshan Laboratory/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; },
mesh = {Animals ; Larva/microbiology ; *Gastrointestinal Microbiome ; *Salmonella/growth &amp; development ; Manure/microbiology ; *Diptera/microbiology ; Chickens ; Bacillus ; Metagenomics ; *Antibiosis ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Black soldier fly larvae (BSFL) can efficiently convert organic waste into biomass and reduce pathogenic bacteria in organic waste. The microbial composition of the substrate and the gut of BSFL is a pivotal factor in determining the efficacy of BSFL in pathogen elimination. However, there are insufficient data on the gut microbiology of BSFL in relation to pathogen inhibition. To address this gap, we investigated the dynamics of Salmonella during the conversion of chicken manure by BSFL and examined the role of intestinal bacterial communities and core bacteria in reducing Salmonella levels. The results indicate that BSFL treatment can reduce the amount of Salmonella in chicken manure, with the gut microbiome of the BSFL playing a crucial role in this reduction. Combining metagenomic analysis with culturomics methods, we isolated 158 strains from the larval gut, in which seven gut bacteria belonging to the genus Bacillus can promote BSFL to reduce Salmonella. In reinoculation and validation experiments, the combination of BSFL and Bacillus velezensis A2 enhanced the elimination of Salmonella from chicken manure and larvae. This study provides insight into how BSFL can reduce pathogenic bacteria in chicken manure and suggests that pairing BSFL with functional microorganisms can improve the biosafety of organic waste conversion by BSFL.},
}
@article {pmid41428487,
year = {2026},
author = {Deng, C and Hu, J and Chen, Q and Zhou, S and Ni, J},
title = {Expanded global groundwater microbial diversity reveals bioprospecting potential.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116760},
doi = {10.1016/j.celrep.2025.116760},
pmid = {41428487},
issn = {2211-1247},
mesh = {*Groundwater/microbiology ; Phylogeny ; *Bacteria/genetics/classification ; *Microbiota/genetics ; *Bioprospecting ; Archaea/genetics/classification ; Genome, Bacterial/genetics ; Genome, Archaeal/genetics ; Biodiversity ; Metagenomics ; Metagenome ; },
abstract = {Although the terrestrial subsurface harbors a substantial fraction of Earth's microbial biomass, the genomic diversity of groundwater microbiomes and their potential for bioprospecting remain poorly characterized. Here, we recovered 44,320 bacterial and archaeal genomes from in-house and publicly available metagenomic datasets, establishing a large-scale groundwater microbiota catalog (GWMC) spanning 167 phyla, including four candidate phyla and over 12,000 previously uncharacterized species. This unprecedented phylogenetic diversity was accompanied by a bimodal genome size distribution (0.3-12.8 Mbp), revealing divergent strategies of genomic allocation. By mining extensive genomic resources, we found that small genomes prioritized molecular defense and redox regulation, whereas large genomes frequently harbored greater biosynthetic potential. Notably, we establish the largest selenoprotein catalog to date and highlight groundwater as an overlooked hotspot of microbial selenium metabolism. Overall, this work advances our understanding of microbial diversity in aquifers and uncovers underexplored genomic resources with potential for biotechnology and biomedicine.},
}
@article {pmid41428281,
year = {2025},
author = {Yu, J and Cheng, L and Zhan, H and Huang, Y and Wang, S and Li, H and Liu, Y and Xu, Y and Guo, Y and Li, Y},
title = {Potential Mechanisms and Hypotheses for Pathogenic Microorganisms Triggering Kawasaki Disease.},
journal = {Clinical reviews in allergy &amp; immunology},
volume = {68},
number = {1},
pages = {110},
pmid = {41428281},
issn = {1559-0267},
support = {2024YFA1307604//National Key Research and Development Program of China/ ; 8247082356//Natural Science Foundation of China/ ; },
mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/etiology/immunology/epidemiology/microbiology ; Gastrointestinal Microbiome/immunology ; Animals ; Host-Pathogen Interactions/immunology ; Dysbiosis ; Disease Susceptibility ; *Virus Diseases/immunology/complications ; Superantigens/immunology ; Immunoglobulin A/immunology/metabolism ; Cytokines/metabolism ; },
abstract = {Kawasaki disease (KD) is an acute, self-limiting systemic vasculitis of early childhood and remains the leading cause of acquired heart disease in developed nations. Despite decades of investigation, its etiology and immunopathogenesis are still not fully understood. This review integrates nearly six decades of histopathological, epidemiological, and immunological research to examine infection-driven mechanisms underlying KD. Current evidence indicates that KD may result from a convergence of microbial and host factors: viral infections can trigger mucosal IgA-mediated immune activation; superantigens may induce T-cell receptor (TCR) Vβ-skewed cytokine release; conventional antigens appear to elicit oligoclonal adaptive immune responses consistent with infection-associated vasculitis; and gut microbiota dysbiosis may amplify systemic inflammation through disruption of intestinal barrier integrity and short-chain fatty acid metabolism. Rather than a single-pathogen infection, KD likely reflects infection-triggered immune dysregulation in genetically susceptible children. By contrasting these mechanistic hypotheses, this review highlights the need for longitudinal, multi-omics studies integrating metagenomic, transcriptomic, and serologic analyses to delineate causal microbial signatures, identify diagnostic biomarkers, and guide precision immunomodulatory strategies for this complex pediatric vasculitis.},
}
@article {pmid41427714,
year = {2026},
author = {Bell, AG and Cable, J and Temperton, B and Tyler, CR},
title = {Assessment of the effectiveness of host depletion techniques for profiling fish skin microbiomes and metagenomic analysis.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0183825},
pmid = {41427714},
issn = {2165-0497},
support = {[NE/R011524/1] (2401467)//Natural Environment Research Council/ ; },
mesh = {Animals ; *Skin/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Fishes/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; DNA, Bacterial/genetics/isolation &amp; purification ; Mucous Membrane/microbiology ; },
abstract = {UNLABELLED: Microbiomes on fish mucosal surfaces play crucial roles in nutrient absorption, immune priming, and defense, and disruptions in these microbial communities can lead to adverse health outcomes, including disease. Studying fish microbiomes relies on sequencing microbiota within mucosal-rich samples; however, nucleic acid extraction from these samples is composed predominantly of host DNA, making subsequent bioinformatic processes difficult. Host depletion techniques address this issue by either selectively degrading host DNA before sequencing or retaining bacterial DNA post-extraction. However, their application to fish mucosal samples has been largely unexplored. Here, we assessed the efficacy of various host depletion techniques on fish skin mucosal swabs via either selectively removing CpG-methylated (predominantly eukaryotic) DNA or selectively lysing eukaryotic cells before DNA extraction. Surprisingly, none of the existing methods we assessed effectively reduced host DNA to be practically useful. Furthermore, some methods introduced a bias toward certain bacterial taxa, including the Bacilli class and the Proteobacteria phylum. Our findings illustrate that the currently available host depletion techniques are largely ineffective for reducing host DNA in fish mucosal samples. This poses a major limitation for developing an understanding of the functional composition of fish mucosal microbiomes, as enriching microbiota (and excluding host DNA) is fundamental for cost-effective metagenomic studies and facilitating more accurate analyses of the microbiota metabolome and proteome.<br><br>IMPORTANCE: Microbial communities on fish mucosal surfaces are vital for immune function and disease resistance. However, sequencing these communities is hindered by the dominance of host DNA in mucosal samples, which can exceed 99% of total nucleic acids. While host depletion techniques are routinely used in human and mammalian systems to enrich microbial DNA, their efficacy on fish samples remains uncharacterized. In this study, we assessed multiple commercial and published host depletion methods on fish skin microbiomes. None significantly reduced host DNA to levels suitable for high-quality metagenomic sequencing, and some introduced taxonomic bias. We suggest methodological reasons, including differences in fish cell structure and mucus composition compared to mammalian systems, that may explain these shortcomings. Based on our findings, we propose protocol modifications and highlight key areas for improvement. This work identifies critical limitations and offers a foundation for developing optimized host depletion strategies tailored to fish mucosal microbiome research.},
}
@article {pmid41426650,
year = {2025},
author = {Wang, C and Wei, H and Duan, R and Jin, S and Wen, J and Li, H and Cheng, A and Gao, C and Xue, H and Hou, Y},
title = {Habitat Diversity Sustains Ecosystem Functioning in Plateau Arid-Region Wetlands.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72747},
pmid = {41426650},
issn = {2045-7758},
abstract = {Plateau arid-region wetlands constitute critical ecosystems for regional ecological security, yet exhibit heightened vulnerability under multiple stressors. Current understanding of the mechanisms sustaining the functions of these systems, particularly the pivotal role of habitat diversity, remains limited. Targeting the Jinzihai Wetland (Qaidam Basin, Qinghai-Tibet Plateau), we integrated metagenomic and geochemical profiling to characterize three representative habitats: sandy meadows, peat bogs, and lake sediments. Our analyses revealed that pronounced cross-habitat physicochemical gradients drive community structure differentiation predominantly through species replacement, establishing habitat diversity as a fundamental driver of wetland biodiversity. Concurrently, community differentiation drives spatial divergence in functional gene composition, manifesting distinct functional dominance: sandy meadows govern assimilation and saline-alkaline stress response; peat bogs orchestrate nutrient enrichment and transformation; lake sediments mediate element release and burial. These functionally complementary habitats collectively catalyze biogeochemical cycling. We demonstrate that within plateau arid-region wetlands, habitat diversity stabilizes ecosystem functioning by sustaining both biodiversity and functional diversity of biogeochemical processes. Consequently, prioritizing habitat diversity conservation is imperative for safeguarding the long-term stability of these vulnerable ecosystems within management frameworks.},
}
@article {pmid41423811,
year = {2026},
author = {Gordon, ES and Goc, J and Grier, A and Thomas, C and , and Lentine, J and Sockolow, RE and Sonnenberg, GF},
title = {Altered Gut Microbiota in Pediatric Quiescent Crohn's Disease Patients with Iron Deficiency Anemia.},
journal = {Inflammatory bowel diseases},
volume = {32},
number = {2},
pages = {303-313},
pmid = {41423811},
issn = {1536-4844},
support = {//Weill Cornell Medicine Department of Pediatrics/ ; R01AI143842/NH/NIH HHS/United States ; R01AI123368/NH/NIH HHS/United States ; R01AI145989/NH/NIH HHS/United States ; U01AI095608/NH/NIH HHS/United States ; R01AI162936/NH/NIH HHS/United States ; R01CA274534/NH/NIH HHS/United States ; R37AI174468/NH/NIH HHS/United States ; //Pathogenesis of Infectious Disease/ ; //Burroughs Welcome Fund/ ; //Meyer Cancer Center Collaborative Research Initiative/ ; //Dalton Family Foundation/ ; //Rosanne H. Silbermann Foundation/ ; //Weill Cornell Medicine Division of Pediatric Gastroenterology and Nutrition/ ; },
mesh = {Humans ; *Crohn Disease/microbiology/complications ; *Gastrointestinal Microbiome ; Male ; Female ; Child ; *Anemia, Iron-Deficiency/microbiology/etiology ; Cross-Sectional Studies ; Adolescent ; Case-Control Studies ; Feces/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Iron deficiency anemia (IDA) is the most common extra-intestinal complication in inflammatory bowel disease (IBD). The persistence of iron deficiency in patients living with quiescent IBD remains poorly understood. Given the extensive body of research linking IBD pathogenesis to microbiome disruptions, it is hypothesized that alterations in the microbiota or immune responses may drive the persistence of IDA in quiescent Crohn's disease. This study aimed to determine whether changes in the gut microbiota or immune phenotypes contribute to IDA, while uncovering potential mechanisms driving IDA in quiescent disease.<br><br>METHODS: This cross-sectional, descriptive, and analytical study utilized 141 samples from pediatric Crohn's disease patients with and without iron deficiency as well as healthy controls for initial 16S microbiome analysis and a smaller subset for Shotgun Metagenomics and immunologic analyses. Fecal and peripheral blood samples were obtained from the Jill Roberts Institute Live Cell Bank.<br><br>RESULTS: While no major differences were observed in the overall gut microbiome composition between pediatric patients with quiescent Crohn's disease, with or without IDA, notable shifts in specific microbial strains were identified. Specifically, levels of Anaerobutyricum soehngenii and Alistipes shahii were significantly altered. Metagenomic analysis revealed an enrichment of pathways related to short-chain fatty acid metabolism and ascorbate degradation, indicative of functional change in these microbes.<br><br>CONCLUSIONS: This is the first comprehensive microbiome analysis of quiescent pediatric Crohn's disease with concomitant IDA. The findings indicate modest but significant microbial strain-level differences and associated functional pathways, potentially implicating microbiota-mediated mechanisms in the persistence of IDA.},
}
@article {pmid41423629,
year = {2025},
author = {Cunningham-Oakes, E and Price, V and Mphasa, M and Mallewa, J and Darby, AC and Feasey, NA and Lewis, JM},
title = {Quantifying the bystander effect of antimicrobial use on the gut microbiome and resistome in Malawian adults.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {954},
pmid = {41423629},
issn = {2041-1723},
support = {CL-2019-07-001//DH | National Institute for Health Research (NIHR)/ ; NIHR200632//DH | National Institute for Health Research (NIHR)/ ; 206545/Z/17/Z//Wellcome Trust (Wellcome)/ ; /WT_/Wellcome Trust/United Kingdom ; 109105z/15/a//Wellcome Trust (Wellcome)/ ; },
mesh = {Humans ; Malawi ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Adult ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics/drug effects ; Female ; Male ; Bayes Theorem ; Antimicrobial Stewardship ; Bacteria/drug effects/genetics/classification ; Sepsis/drug therapy/microbiology ; Metagenomics ; Young Adult ; },
abstract = {Antibiotic treatment for sepsis has an unintended yet crucial consequence: it exerts a bystander effect on the microbiome, changing its bacterial composition and resistome. Antimicrobial stewardship aims, in part, to minimise this effect to prevent development of subsequent drug-resistant infection, but data evaluating and quantifying these changes are largely lacking, especially in low-income settings which are disproportionately affected by antimicrobial resistance. Such data are critical to creating evidence-based stewardship protocols. Here, we address this data gap in Blantyre, Malawi. We use longitudinal sampling of human stool and metagenomic deep sequencing to describe microbiome composition and resistome pre-, during- and post-antimicrobial exposure. We develop Bayesian regression models to link these changes to individual antimicrobial agents. We find that ceftriaxone, in particular, exerts strong off-target effects, both increasing abundance of Enterobacterales, and the prevalence of macrolide and aminoglycoside resistance genes. Simulation from the fitted models allows exploration of different stewardship strategies and can inform practice in Malawi and elsewhere.},
}
@article {pmid41422269,
year = {2025},
author = {Wang, Y and Xu, J and Liang, G and Liang, S and Hou, M and Sun, L and Wang, J and Chen, H and Zhao, Y and Chen, W and Wang, E and Huang, J and Jiao, X and Zhang, Y},
title = {Gut microbiome profiling of a migratory Anser serrirostris population reveals two groups with distinct pathogen and ARG contents.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {22},
pmid = {41422269},
issn = {2055-5008},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/pathogenicity/drug effects ; Metagenomics ; Virulence Factors/genetics ; Animal Migration ; Phylogeny ; *Drug Resistance, Bacterial/genetics ; DNA, Bacterial/genetics ; Metagenome ; Sequence Analysis, DNA ; },
abstract = {Migratory birds are key vectors of pathogens and antibiotic-resistance genes (ARGs), yet intrapopulation variation and its microbiome-mediated basis remain poorly understood. Here, we characterized the gut microbiome of 70 individuals from a migratory Anser serrirostris population using full-length 16S rDNA sequencing, followed by metagenomic analysis of 25 representative samples. Both approaches consistently identified two distinct groups (E1 and E2). Network analysis revealed impaired microbial interactions in E1 compared to E2. E1 exhibited higher abundances of opportunistic pathogens (e.g., Pseudomonas, Erwinia) and enriched functions related to pathogenicity and ARGs, predominantly driven by these taxa. Conversely, E2 showed function enrichment in short-chain fatty acid biosynthesis and plant metabolite degradation, mediated mainly by Bradyrhizobium and Ligilactobacillus. Genome-centric analysis identified several pathogenic genomes (e.g., Salmonella, Vibrio parahaemolyticus) harboring critical virulence factors and ARGs predominantly in E1. These results provide valuable insights into microbiome-driven variation in pathogen/ARG loads within migratory bird populations.},
}
@article {pmid41422081,
year = {2025},
author = {Arnaud-Haond, S and Trouche, B and Liautard-Haag, C and Alain, K and Aubé, J and Bonhomme, F and Brandt, MI and Caillarec-Joly, A and Cambon, MA and Cornette, F and Cueff-Gauchard, V and Durand, P and de Vargas, C and Felix, C and Fuchs, S and , and Günther, B and Henry, N and Hourdez, S and Jollivet, D and Le Port, AS and Lesongeur, F and Maignien, L and Comtet-Marre, S and Matabos, M and Omnes, E and Peyret, P and Pradillon, F and Sarrazin, J and Schauberger, C and Tran Lu Y, A and Ulloa, O and Vaz, S and Zeppili, D and Viard, F and Gavory, F and Gaz, S and Guy, J and Jacoby, E and Oliveira, PH and Samson, G and Aury, JM and Wincker, P and Pesant, S and Poulain, J and Belser, C},
title = {Omics exploration of deep-sea biodiversity: data from the "Pourquoi Pas les Abysses?" and eDNAbyss projects.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1982},
pmid = {41422081},
issn = {2052-4463},
support = {ANR-10-INBS-09//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-16-IDEX-0006//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-CE02-0003//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-22-POCE-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; 678760//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 669947//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ANR-10-INBS-09//Commissariat &#xe0; l&apos;&#xc9;nergie Atomique et aux &#xc9;nergies Alternatives (French Alternative Energies and Atomic Energy Commission)/ ; },
mesh = {*Biodiversity ; Metagenomics ; Oceans and Seas ; DNA, Environmental ; DNA Barcoding, Taxonomic ; },
abstract = {The deep-sea floor encompasses more than half of the surface of our planet, yet the extent and distribution of deep-sea biodiversity and its contribution to large biogeochemical cycles remain poorly understood. This knowledge gap stems from several factors, including sampling issues, the magnitude of the work required for morphological inventories, and the difficulty of integrating results from disparate local studies. The application of meta-omics to environmental DNA now makes it possible to assemble interoperable datasets at different spatial scales to move towards a global assessment of deep-sea biodiversity. We present a large-scale dataset on deep-sea biodiversity, with data and metadata openly accessible at ENA and Zenodo. The resource was generated using standardized protocols developed according to FAIR principles, covering fieldwork through bioinformatic analysis, within "Pourquoi Pas les Abysses?" and eDNAbyss projects. Together with information ensuring reproducibility, this dataset -combining metagenomics, metabarcoding across the Tree of Life and capture-by-hybridization- contributes to the international concerted effort to achieve a holistic view of the biodiversity in the largest biome on Earth.},
}
@article {pmid41421776,
year = {2026},
author = {Gao, L and Chen, Y and Li, S and Yang, Z and Guo, W and Lu, Y and Zhu, G and Gaballah, ES},
title = {Low atmospheric pressure of plateau environments shapes microbial communities, nitrogen conversion, and carbon metabolism in biological nitrogen removal systems.},
journal = {Environmental research},
volume = {291},
number = {},
pages = {123595},
doi = {10.1016/j.envres.2025.123595},
pmid = {41421776},
issn = {1096-0953},
mesh = {*Nitrogen/metabolism ; *Carbon/metabolism ; Denitrification ; Bioreactors/microbiology ; *Atmospheric Pressure ; *Microbiota ; *Waste Disposal, Fluid/methods ; Nitrification ; Altitude ; Bacteria/metabolism ; },
abstract = {Wastewater treatment plants in high-altitude regions often exhibit unstable nitrogen removal under low atmospheric pressure, but the coupled impacts on oxygen transfer, microbial metabolism, and community adaptation remain poorly resolved. In this study, long-term bioreactor operation under different atmospheric pressures was performed to elucidate how low pressure reshapes biological nitrogen removal systems through changes in oxygen transfer, microbial metabolism, and community structure. Low pressure reduced oxygen solubility and gas-liquid/liquid-solid transfer, which suppressed nitrification and caused nitrite accumulation, while simultaneous nitrification-denitrification partly sustained total nitrogen removal. Multi-scale analyses integrating batch tests, enzyme activities, and metagenomics showed a consistent shift from oxidative to more electron-efficient pathways, with strengthened denitrification and expanded carbon metabolism that enhanced the use of carboxylic acids and amino acids and secured carbon and electron supply. The microbial community reorganized toward denitrifying polyphosphate-accumulating organisms (DPAOs), denitrifying glycogen-accumulating organisms (DGAOs), and conventional denitrifiers, with stronger functional associations despite a simpler network structure. These findings explain performance deterioration under plateau atmospheric conditions and indicate feasible control points to sustain nitrogen removal in high-altitude wastewater treatment systems.},
}
@article {pmid41421350,
year = {2026},
author = {Chen, W and Wang, X and Zhu, R and Gao, W and Tao, L and Yang, R and Wei, Q and Zhang, Y and Gong, Y and Zhong, H and Huang, L and Zhu, X and Yang, Y and Zhang, L and Wan, L and Yang, G and Li, Y and Jiao, N and Wang, J and Qin, H and Zhu, L},
title = {Integrative multi-omics reveals microbial genomic variants driving altered host-microbe interactions in autism spectrum disorder.},
journal = {Cell reports. Medicine},
volume = {7},
number = {1},
pages = {102516},
pmid = {41421350},
issn = {2666-3791},
mesh = {*Autism Spectrum Disorder/microbiology/genetics/metabolism ; Humans ; *Gastrointestinal Microbiome/genetics ; Child ; *Host Microbial Interactions/genetics ; Metagenomics/methods ; Male ; Female ; Genomics/methods ; Polymorphism, Single Nucleotide/genetics ; Dysbiosis/microbiology ; Metabolomics/methods ; Genetic Variation ; Multiomics ; },
abstract = {Emerging evidence links the gut microbiome to autism spectrum disorder (ASD), yet the role of microbial genomic variation remains underexplored. We generated a large-scale metagenomic and metabolomic dataset from over 1,100 children, integrating public datasets, to characterize ASD-associated microbial changes. We identified 35 species, 213 genes, 28 pathways, and 99 metabolites, alongside 1,369 single-nucleotide variants, 233 insertions/deletions, and 195 structural variants with differential abundance. Profiling of microbial genomic variation revealed 33 species and 196 enzymes lacking abundance differences, yet exhibiting significant sequence variation. Integrated analysis of microbial variants and metabolites uncovered 357 neurological associations, with mediation analysis showing that several metabolites link microbial variants to the ASD phenotype. Importantly, diagnostic models incorporating microbial variant and/or metabolite features achieved superior performance and generalizability. Our findings highlight microbial genomic variation as a critical, previously overlooked dimension of ASD-associated dysbiosis, offering valuable insights for diagnosis and mechanistic studies.},
}
@article {pmid41420859,
year = {2026},
author = {Beghini, F and Brito, IL and Gerstein, M and Christakis, NA},
title = {Characterization of gut microbiomes in rural Honduras reveals uncharacterized species and associations with human genetic variation.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116724},
doi = {10.1016/j.celrep.2025.116724},
pmid = {41420859},
issn = {2211-1247},
mesh = {Humans ; Honduras ; *Gastrointestinal Microbiome/genetics ; *Genetic Variation ; Rural Population ; Male ; Female ; COVID-19/virology/microbiology ; Adult ; Metagenomics ; Middle Aged ; SARS-CoV-2 ; Metagenome ; },
abstract = {The gut microbiome is integral to human health, yet research data to date have emphasized industrialized populations. Here, we performed large-scale shotgun metagenomic sequencing on 1,893 individuals from rural Honduras, providing the most comprehensive microbiome dataset from Central America. We identify a distinct microbial composition enriched in Prevotella species. Longitudinal analysis in 301 individuals reveals microbiome instability, with shifts in taxonomic diversity and metabolic potential, including changes associated with severe acute respiratory syndrome coronavirus 2 infection. Additionally, we characterize the gut virome and eukaryotic microbiome, identifying uncharacterized viral taxa and a high prevalence of Blastocystis species in individuals with greater microbial diversity. Finally, by integrating host genomic data, we uncover significant host-microbiome associations, highlighting the influence of human genetic variation on microbial composition. These findings expand our understanding of microbiome diversity in non-industrialized populations, underscoring the need for global microbiome research.},
}
@article {pmid41420661,
year = {2025},
author = {Ngangbam, AK and Nongmaithem, BD and Haojam, RS and Khundrakpam, L and Singh, LL and Meetei, KB},
title = {First functional and taxonomic insights into the microbiome of edible snail, Cipangopaludina lecythis via shotgun metagenomics.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {1},
pages = {18},
pmid = {41420661},
issn = {1572-9699},
mesh = {*Snails/microbiology ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The freshwater snail Cipangopaludina lecythis holds both ecological and medicinal importance, yet its microbiome remains unexplored. This study presents the first shotgun metagenomic profiling of edible tissues of C. lecythis. Illumina HiSeq sequencing generated over 42 million high-quality reads, revealing 38 bacterial phyla dominated by Pseudomonadota (32%), followed by Bacillota and Actinomycetota. At the genus level, Pseudomonas, Klebsiella, Acinetobacter, Bacillus, Clostridium, Staphylococcus, and Streptomyces were prevalent. Functionally important genera such as Aeromonas, Vibrio, and Pseudoalteromonas which are known for their probiotic and immunomodulatory properties were also detected. The dominant species included Pseudomonas sp. REST10, Escherichia coli, Klebsiella pneumoniae, and Streptomyces sp. T12, many of which were associated with fermentation and host microbe interactions. Interestingly, the microbial profiles differed from those in marine snails, indicating environment-specific microbiome signatures. Functional annotation revealed key enzymes including 17 beta-hydroxysteroid dehydrogenase type 3 (HSD17B3) and malonyl-CoA:ACP transacylase, involved in fatty acid metabolism and energy regulation. Enzymes such as glutathione S-transferase and arylacetamide deacetylase were also detected, along with chitinase and chitin synthases, suggesting host microbe interactions in chitin metabolism. High alpha diversity showed a rich and functional microbiome. Overall, this study highlights the metabolic potential and ecological relevance of the C. lecythis microbiome, supporting its application in biotechnology and nutraceutical industry.},
}
@article {pmid41419973,
year = {2025},
author = {Rojas, MA and Serrano, G and Torres, J and Ortega, J and Gálvez, G and Vilches, E and Parra, V and Reyes-Jara, A and Maracaja-Coutinho, V and Pizarro, L and Latorre, M and Di Genova, A},
title = {Genome-resolved metagenomics and evolutionary analysis reveal conserved metabolic adaptations in extremophile communities from a copper mining tailing.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {153},
pmid = {41419973},
issn = {2524-6372},
support = {ACT210004//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; },
abstract = {BACKGROUND: Microbial communities in mining environments exhibit unique metabolic adaptations to extreme conditions, such as high metal concentrations and low pH. Their relatively low species complexity makes them an attractive model for fine-scale evolutionary analysis; nonetheless, genome-resolved metagenomic data from these environments are still scarce. Here, we employed genome-resolved metagenomics to analyze a high-quality Illumina-sequenced sample from the Cauquenes copper tailing in central Chile, one of the world's largest and oldest copper waste deposits. We aimed to uncover the taxonomic composition, metabolic potential, and evolutionary pressures shaping this extremophile community.<br><br>RESULTS: We reconstructed 44 medium- and high-quality metagenome-assembled genomes (MAGs), predominantly from the phyla Actinomycetota, Pseudomonadota, and Acidobacteriota. Taxonomic analysis revealed limited species-level classification, with only five MAGs assigned to known species, highlighting the challenges of characterizing extreme environments. Functional profiling identified enhanced metabolic capabilities in sulfur and copper pathways, critical for survival in mining ecosystems. Using evolutionary analysis on mining MAGs using dN/dS ratios, we uncoverd strong negative selection on genes involved in sulfur, copper, and iron metabolism, indicative of a conservative evolutionary state. In contrast, genes under positive selection were linked to motility, biofilm formation, and stress resistance, suggesting adaptive mechanisms for resource acquisition and survival.<br><br>CONCLUSIONS: Our study provides a metagenome-wide evolutionary analysis of mining MAGs, demonstrating that microbial communities in copper tailings are highly specialized, with conserved metabolic pathways under strong purifying selection. At the same time, the recovery of previously unclassified species of extremophiles expands the known biodiversity of mining ecosystems. These findings emphasise the challenges of leveraging these communities for biotechnological applications, such as biomining, due to their evolutionary constraints.},
}
@article {pmid41419779,
year = {2025},
author = {Liu, Y and Chen, S and Li, H and Mahtab, N and Sun, Y and Li, Y and Song, J and Sun, D and Liang, M and Chen, J and Sun, J and Gong, B and Jing, J and Bu, R},
title = {Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {125},
pmid = {41419779},
issn = {2052-4463},
support = {2024GXNSFBA010371//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; 2025GXNSFHA069226//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; 2025GXNSFHA069232//Natural Science Foundation of Guangxi Province (Guangxi Natural Science Foundation)/ ; },
mesh = {China ; *Geologic Sediments/microbiology ; Wetlands ; Archaea/genetics ; *Genome, Bacterial ; *Genome, Microbial ; *Genome, Archaeal ; Bacteria/genetics/classification ; Metagenome ; Microbiota ; },
abstract = {Mangrove sediments, being organic-rich and anoxic, host diverse and functionally important microorganisms that play crucial roles in global biogeochemical cycling. In order to characterize this diversity at the genome-resolved level, we collected 38 sediment samples encompassing both surface (0-5 cm) and core (up to 90 cm) depths from six representative mangrove sites across Guangxi Province, China. Using a standardized pipeline for assembly, binning, and dereplication, we reconstructed 2,965 non-redundant metagenome-assembled genomes (MAGs), comprising 2,383 bacterial and 582 archaeal genomes spanning 78 microbial phyla. This dataset captures the high microbial diversity and functional potential within mangrove sediments under variable environmental conditions. It provides a valuable genomic resource for investigating the structure, metabolism, and ecological roles of sediment microbial communities in intertidal, nutrient-rich ecosystems, supporting future studies on microbial adaptation and biogeochemical cycling in global blue carbon environments.},
}
@article {pmid41419527,
year = {2025},
author = {Takeda, Y and Kato-Kogoe, N and Sakaguchi, S and Ieda, S and Tasaka, Y and Mizobata, N and Omori, M and Hamada, W and Nakamura, S and Nakano, T and Ueno, T and Matsumura, T},
title = {Characteristics of salivary IgA responses to oral microbiota in patients with oral lichen planus.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44167},
pmid = {41419527},
issn = {2045-2322},
mesh = {Humans ; *Lichen Planus, Oral/microbiology/immunology ; *Saliva/immunology/microbiology ; Female ; Male ; Middle Aged ; *Microbiota/immunology ; RNA, Ribosomal, 16S/genetics ; Adult ; *Immunoglobulin A, Secretory/immunology ; Aged ; *Immunoglobulin A/immunology ; Bacteria/genetics/classification ; Metagenomics ; Case-Control Studies ; },
abstract = {Oral lichen planus (OLP) is a chronic inflammatory disease of the oral mucosa with a risk of malignant transformation. Oral bacteria are associated with OLP development and progression; however, the immune response, especially the salivary immunoglobulin A (IgA) response to these bacteria remains poorly understood. Therefore, this study aimed to characterize the salivary microbiota in patients with OLP and evaluate the corresponding salivary IgA response. Stimulated saliva samples were collected from 21 patients with OLP and 56 control participants, and 16S rRNA metagenomic analysis was performed to characterize the composition of the microbiota. In addition, IgA-enriched and non-enriched fractions from the saliva samples were separated via magnetic-activated cell sorting, followed by 16S rRNA metagenomic analysis. To evaluate differences in IgA responses to each bacterium between the two groups, we calculated the IgA index. The diversity and bacterial composition of the salivary microbiota differed considerably between the OLP and control groups. Several bacterial genera, including Leptotrichia, Fusobacterium, and Streptococcus, showed markedly lower IgA index in the OLP group than the control group. In conclusion, patients with OLP exhibited a distinctive salivary IgA response to salivary microbiota, suggesting a potential association between OLP and this altered response.},
}
@article {pmid41418855,
year = {2026},
author = {Laue, HE and Kook, D and Khatchikian, C and Coto, SD and Jackson, BP and Palys, TJ and Peacock, JL and Karagas, MR and O'Toole, GA and Hoen, AG and Madan, JC},
title = {Early-life arsenic exposure modulates the developing microbiome in a rural cohort.},
journal = {Environmental research},
volume = {291},
number = {},
pages = {123588},
doi = {10.1016/j.envres.2025.123588},
pmid = {41418855},
issn = {1096-0953},
mesh = {Humans ; *Arsenic/urine/toxicity ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Infant ; Rural Population ; *Environmental Exposure ; Cross-Sectional Studies ; Feces/microbiology/chemistry ; Cohort Studies ; Longitudinal Studies ; *Environmental Pollutants/urine ; },
abstract = {BACKGROUND: Studies reported associations between arsenic and the infant gut microbiome measured contemporaneously. We tested the hypothesis that early-life arsenic associates with longitudinal microbiome differences and examined sex-specific effects.<br><br>METHODS: Participants provided urine and fecal samples at six weeks (6W; n&#xa0;=&#xa0;219) or twelve months (12M; n&#xa0;=&#xa0;219), a subset of whom provided samples at both (n&#xa0;=&#xa0;167). Total arsenic (tAs), inorganic arsenic, monomethylarsinic acid, and dimethylarsinic acid (DMA) were quantified in 6W and 12M urine with high-performance liquid chromatography with inductively-coupled plasma mass spectrometry. We estimated gut microbiome composition at 6W and 12M with metagenomic sequencing. Using generalized linear and mixed-effect models, we evaluated cross-sectional and longitudinal associations of arsenic concentrations with bacterial diversity and species/gene pathway relative abundance.<br><br>RESULTS: DMA and tAs at 6W were associated with bacterial species at 6W but similar associations were not observed at 12M. At 6W, associations between arsenic and metabolic pathways tended to be sex-specific. In longitudinal analyses, tAs associated with higher Shannon diversity [&#x3b2;&#xa0;=&#xa0;0.07 per doubling (95&#xa0;%CI: 0.05, 0.09)], with a diminishing trend in this association with sampling age [&#x3b2;&#xa0;=&#xa0;-0.04 per doubling (95&#xa0;%CI: 0.07, -0.004)]. We observed a similar longitudinal pattern between at least one arsenic measure and ten bacterial species, with stronger associations among males than females.<br><br>CONCLUSIONS: We observed longitudinal and cross-sectional associations of arsenic and the gut microbiome in the first year of life. Early-life arsenic concentrations were more strongly associated with disruptions in the infant gut microbiome than later infancy, highlighting the importance of early-life exposures in microbiome dysbiosis.},
}
@article {pmid41416507,
year = {2025},
author = {Wang, Y and Wan, Y and Wang, H and Yan, J and Sun, J and Yang, J and Zhang, F and Cao, H and Li, D},
title = {Oral Supplementation of Indole-3-acetic Acid Alleviates High-Fat-Induced Obesity by Activating the Gpha2-Mediated Thyroid-Stimulating Hormone Pathway.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {52},
pages = {33126-33140},
doi = {10.1021/acs.jafc.5c14556},
pmid = {41416507},
issn = {1520-5118},
mesh = {Animals ; *Indoleacetic Acids/administration &amp; dosage/metabolism ; Diet, High-Fat/adverse effects ; Mice ; *Obesity/metabolism/drug therapy/genetics ; Mice, Inbred C57BL ; Male ; Dietary Supplements/analysis ; Humans ; Gastrointestinal Microbiome ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; PPAR gamma/metabolism/genetics ; Peroxisome Proliferator-Activated Receptor Gamma Coactivator 1-alpha/metabolism/genetics ; Liver/metabolism/drug effects ; },
abstract = {Obesity is a major global public health challenge. Indole-3-acetic acid (IAA), a gut microbiota-derived tryptophan metabolite, exhibits antiobesogenic potential. In this study, we found that in high-fat-diet-induced obese mice, oral IAA supplementation dose dependently attenuated body weight gain, adiposity, hepatic steatosis, and dyslipidemia while improving insulin sensitivity. Notably, intraperitoneal administration of IAA (50 mg/kg/day) paradoxically exacerbated weight gain. Metagenomic sequencing showed that oral IAA selectively enriched beneficial genera (Ileibacterium, Anaerotignum, and Clostridium) and significantly increased short-chain fatty acid (SCFA) production, particularly acetate and butyrate. In vitro experiments in Saccharomyces cerevisiae further confirmed that IAA directly suppresses de novo fatty acid biosynthesis and triacylglycerol assembly. Mechanistically, IAA upregulated hepatic Gpha2 expression, thereby activating the TSH-THR-PGC-1α-PPARγ signaling cascade and concomitantly repressing key lipogenic genes (Fasn, Acaca, and Srebp-1c). Collectively, these findings position IAA as a promising microbiota-derived metabolite with substantial preventive and therapeutic potential for obesity and related metabolic disorders.},
}
@article {pmid41416110,
year = {2025},
author = {Jun, L and Wan, X and Zhang, D and Zheng, Y and Chen, X and Mi, L and Xiao, B},
title = {Mixed vaginal infection status in women infected with Trichomonas vaginalis: comparison of microscopy method and metagenomic sequencing analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1638464},
pmid = {41416110},
issn = {2235-2988},
mesh = {Female ; Humans ; *Trichomonas vaginalis/genetics/isolation &amp; purification ; *Metagenomics/methods ; Adult ; *Vagina/microbiology/parasitology/pathology ; *Trichomonas Vaginitis/diagnosis/microbiology ; *Microscopy/methods ; Microbiota/genetics ; *Coinfection/microbiology/diagnosis/parasitology ; Young Adult ; Middle Aged ; Lactobacillus/isolation &amp; purification/genetics ; },
abstract = {Trichomonas vaginalis (TV) infection is a common non-viral sexually transmitted infection, often combined with mixed vaginal infections. These mixed infections worsen inflammation, disrupt vaginal microbiota, and affect treatment. Currently, TV and its mixed infections are mainly diagnosed by wet mount microscopy, which has low sensitivity and cannot identify complex microbes well. This study compared microscopy with metagenomic sequencing to explore vaginal microbiota changes and improve diagnosis of TV-related mixed infections. We enrolled 30 participants: 20 TV-infected patients (diagnosed by wet mount microscopy) and 10 healthy controls (with Lactobacillus as dominant vaginal microbiota). Then tested by Gram staining, microscopy, and metagenomic sequencing. We analyzed microbial composition and identified different abundant taxa. We also measured clinical indices (Lactobacillus grade, vaginal pH, Nugent score for BV, Donders score for AV) to assess vaginal microecology. Among 20 TV patients, microscopy and clinical criteria found a 65% mixed infection rate (13/20), including TV+AV (5 cases), TV+BV+AV (7 cases), and TV+VVC (1 case). Metagenomic sequencing showed TV patients had higher alpha diversity (Shannon index: p=0.0276) and different beta diversity (ANOSIM, r=0.21, p=0.000167) than controls. At the genus level, TV patients had more anaerobic taxa (Fannyhessea, Atopobium, Peptostreptococcus, FDR<0.05) and less Lactobacillus (FDR<0.05) than controls. All TV patients were CST IV (low Lactobacillus, high mixed bacteria), including 12 cases of CST IV-C and 7 cases of CST IV-B. Microscopy and sequencing had low diagnostic consistency in diagnosing mixed infections, especially for mixed vaginitis. TV infection causes significant vaginal microecological imbalance (less Lactobacillus, more anaerobes, high mixed infection rate). Metagenomic sequencing is better than microscopy at identifying complex microbes and low-abundance pathogens, making it more accurate for diagnosing TV-related mixed infections. These results suggest molecular diagnostic methods should be used as complementary tools for precise analysis improve TV and its mixed infection diagnosis and treatment.},
}
@article {pmid41415804,
year = {2025},
author = {Zhang, M and Zhu, Y and Sun, Z and Wang, B and Chen, J and Zhou, F and Zeng, J and Li, M and Zou, D and Jiang, Z},
title = {Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1671267},
pmid = {41415804},
issn = {1664-302X},
abstract = {Coastal hypoxia, intensified by global warming and eutrophication, profoundly affects marine nitrogen cycling. However, its impact on diazotrophic communities in large river estuaries remains poorly understood. During an unprecedented hypoxia event (minimum dissolved oxygen at 2.70 μmol L[-1]) in August 2016 in the Changjiang Estuary, we sampled across a dissolved oxygen (DO) gradient spanning hypoxic and non-hypoxic waters. Using nifH gene amplicon sequencing, metagenomic binning, and multivariate statistical analyses, we found that higher diazotrophic biodiversity was observed in hypoxia zone, with non-cyanobacterial diazotrophs dominating the communities. The phylum Thermodesulfobacteriota (with relative abundance of 58.93% totally) exhibited significant hypoxia-specific enrichment. LEfSe analysis identified Thermodesulfobacteriota as potential hypoxia biomarkers, while network analysis revealed their keystone role, representing 68.6% of highly connected nodes. Environmental drivers, including low DO concentrations (7.50-61.88 μmol L[-1] in hypoxic vs. 66.56-255.63 μmol L[-1] in non-hypoxic zones), elevated salinity (30.67-34.50), increased dissolved reactive phosphorus (0.39-1.26 μmol L[-1]), and nitrate depletion (0.30-22.50 μmol L[-1]), collectively created favorable conditions for the development of the observed diazotrophic community under hypoxia. Metagenomic analysis revealed a hypoxia-driven increase in nifH gene abundance, with nifH-carrying metagenome-assembled genomes affiliated with Thermodesulfobacteriota showing approximately a 4.7-fold higher relative abundance in hypoxic zone compared to non-hypoxic zone. Reconstruction of metabolic pathways from metagenome-assembled genomes (MAGs) further suggested their potential involvement in both nitrogen fixation and carbon-sulfur cycling. Amplicon and metagenomic datasets consistently demonstrated Thermodesulfobacteriota's predominant in hypoxia. These findings redefine estuarine nitrogen flux models by highlighting hypoxia-driven taxonomic and functional shifts in diazotrophic communities, and provide a foundation for assessing the potential microbial resilience and ecosystem risks in expanding coastal hypoxic zones. Our study underscores the genomic potential of Thermodesulfobacteriota as key players in the nitrogen cycle under hypoxia, a hypothesis that warrants future validation through direct activity measurements.},
}
@article {pmid41413663,
year = {2026},
author = {McAdams, Z and Gustafson, K and Ericsson, A},
title = {Biological and technical variability in mouse microbiota analysis and implications for sample size determination.},
journal = {Lab animal},
volume = {55},
number = {1},
pages = {29-34},
pmid = {41413663},
issn = {1548-4475},
support = {U42 OD010918/OD/NIH HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; },
mesh = {Animals ; Mice/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Sample Size ; Mice, Inbred C57BL ; Male ; },
abstract = {The gut microbiota (GM) affects host development, behavior and disease susceptibility. Biomedical research investigating GM-mediated influences on host phenotypes often involves collecting fecal samples from laboratory mice. Many environmental factors can affect the composition of the GM in mice. While efforts are made to minimize this variation, biological and technical variability exists and may influence outcomes. Here we employed a hierarchical fecal sampling strategy (that is, sequenced multiple libraries generated from multiple pellets collected from multiple mice) to quantify the effect size of biological and technical variation and to provide practical guidance for the development of microbiome studies involving laboratory mice. We found that while biological and technical sources of variation contribute significant variability to alpha- and beta-diversity outcomes, their effect size is 3-30-times lower than that of the experimental variable in the context of an experimental group with high intergroup variability. After quantifying the variability of alpha-diversity metrics at the technical and biological levels, we simulated whether sequencing multiple fecal samples from mice improves effect size in a two-group experimental design. Our simulation determined that collecting five fecal samples per mouse increased effect size, reducing the minimum number of animals per group required by 5% while dramatically increasing sequencing costs. Our data suggest that the effect size of biological and technical factors may contribute appreciable variability to an experimental paradigm with relatively low mean differences. In addition, repeated sampling improves statistical power; however, its application is probably impractical given the increased sequencing costs.},
}
@article {pmid41412647,
year = {2026},
author = {Chen, T and Mo, S and Shen, M and Du, W and Yu, Q and Chen, Y and Xie, J},
title = {Therapeutic potential of Ficus pumila L. in chronic obstructive pulmonary disease through modulation of the gut microbiota-SCFA-lung signaling pathway.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117952},
doi = {10.1016/j.foodres.2025.117952},
pmid = {41412647},
issn = {1873-7145},
mesh = {*Pulmonary Disease, Chronic Obstructive/drug therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Ficus/chemistry ; *Signal Transduction/drug effects ; *Lung/metabolism/drug effects ; Mice ; *Fatty Acids, Volatile/metabolism ; *Plant Extracts/pharmacology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Polysaccharides/pharmacology ; },
abstract = {Ficus pumila L. has been reported to alleviate pulmonary inflammation, its impact on chronic obstructive pulmonary disease (COPD) pathobiology-specifically via modulation of the gut-lung signaling pathway-has yet to be mechanistically defined. This study investigated how Ficus pumila L. polysaccharides (FP-P) and aqueous extracts (FP-E) remodel the gut microbiome-SCFA network and restore microbial metabolic function in a cigarette smoke-induced COPD mouse model. Microbiota composition was profiled by high-resolution 16S rRNA amplicon sequence variant (ASV) analysis, with concomitant quantification of caecal SCFA using targeted gas chromatography-mass spectrometry (GC-MS) and inference of metagenome function by PICRUSt2. Results demonstrated that FP-P and FP-E alleviated pulmonary pathology, reduced inflammatory cytokine secretion, and significantly restored gut microbiota α-diversity in COPD mice. At the family level, FP-P selectively expanded SCFA-producing Clostridiaceae, and Staphylococcaceae, whereas it contracted pro-inflammatory Helicobacteraceae and Campylobacteraceae. Caecal total SCFA concentration increased by 41.90 %, driven primarily by elevations in butyrate (+23.41 %) and propionate (+45.45 %), without significant changes in acetate. PICRUSt2-inferred metagenomes showed up-regulation of butanoate biosynthesis (PWY-5677), metabolism of cofactors and amino acid (P162-PWY and NAD-BIOSYNTHESIS-II), and carbohydrate degradation (P341-PWY), all of which underpin SCFA production. These functional shifts were accompanied by increased abundance of microbial genes encoding ribosomal proteins and ATP-binding cassette transporters, indicating barrier reinforcement. Collectively, FP-P and FP-E mitigate CS-induced COPD pathology through a gut microbiota-SCFA-lung signaling signaling pathway, highlighting the gut-to-lung communication within the broader gut-lung axis. These findings establish a mechanistic link between microbial metabolism and pulmonary inflammation while acknowledging that the reverse lung-to-gut feedback remains to be elucidated. Future studies will investigate this bidirectional crosstalk and the receptor-mediated signaling of SCFAs in lung tissue.},
}
@article {pmid41412637,
year = {2026},
author = {Ferrocino, I and Biolcati, F and Giordano, M and Bertolino, M and Zeppa, G and Cocolin, L},
title = {Dairy environment and seasons affect the microbiome of a traditional artisanal cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117927},
doi = {10.1016/j.foodres.2025.117927},
pmid = {41412637},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; *Seasons ; *Microbiota ; Animals ; *Food Microbiology ; Italy ; Fungi/classification/genetics/isolation &amp; purification ; *Dairying/methods ; Bacteria/classification/genetics ; Milk/microbiology ; Food Handling/methods ; Cattle ; Metagenomics ; },
abstract = {Cheese microbiome is a complex community shaped by raw ingredients and by the production environment that significantly influences final product characteristics. While environmental microbiome can establish stable resident populations, their composition remains susceptible to seasonal shifts, hygienic practices and other external factors. In this study we investigate the interplay of these factors on the bacterial and fungal communities throughout the production of a full-fat semi cooked semi-hard cow's milk cheese produced in the Piedmont region, North-West of Italy, named Maccagno. Amplicon based sequencing was used to characterize bacterial and fungal diversity across environmental surfaces (contact and non-contact) and during the manufacturing and ripening of Maccagno cheeses over three seasons (autumn, winter and summer). Metabolomic profiling and texture analysis of the ripened cheeses allowed for direct correlation with microbial community shifts. The facility environment maintained a remarkably stable core microbiota, including Staphylococcus, Streptococcus thermophilus, Lactococcus lactis, Debaryomyces, Penicillium and Cladosporium. Among the monitored processing plant sampling sites, the metal stirring tool, milk inlet pipe and the ripening room ventilation system emerged as critical points for microbial transfer and persistence. During ripening, core microbial taxa including Lc. lactis, S. thermophilus and Debaryomyces were observed. Shotgun metagenomics was then performed on final cheeses and genome reconstruction highlighted that Lc. lactis genomes showed impressive seasonal genomic adaptability, particularly in autumn, where it contributed to favorable texture and flavor through proteolytic activity and production of aroma-associated metabolites like acetoin and linear ketons. Conversely, summer production exhibiting the highest prevalence of spoilage-associated microbes such as Acinetobacter and Enterobacteriaceae, mainly of facility origin that led to off-flavor profiles inconsistent with the typical Maccagno sensory identity. The fungal communities, mainly composed by Debaryomyces and Penicillium, also varied seasonally, influenced significantly by the ventilation system in the ripening room. Maccagno cheese quality is a direct reflection of these complex microbial dynamics. Seasonal variations in raw milk microbiome and microbial populations established in specific environmental niches significantly affected the final product's sensory and textural attributes. To this end, understanding seasonal influences and the role of resident environmental populations is crucial for optimizing production protocols, mitigating spoilage risks, and ensuring the consistent quality of traditional cheeses.},
}
@article {pmid41412053,
year = {2026},
author = {Xu, Y and Han, Y and Dong, X and Feng, Y and Wu, F and Xing, F and He, J and Rogers, MJ and Luan, X and Liu, R and He, J and Dang, H and Zhang, D},
title = {Temperature shapes the biogeography of rdhA and reductive dehalogenators in sediment across northwestern Pacific marginal seas.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140847},
doi = {10.1016/j.jhazmat.2025.140847},
pmid = {41412053},
issn = {1873-3336},
mesh = {*Geologic Sediments/microbiology ; Pacific Ocean ; *Temperature ; Halogenation ; Phylogeny ; *Bacteria/genetics/metabolism ; Microbiota ; },
abstract = {Dehalogenating microorganisms are crucial in organohalide detoxification in marine sediments. However, the large-scale biogeography and potential environmental adaptability of reductive dehalogenators (RDGs) in marginal sea sediments remain poorly understood. Here, dehalogenating cultures enriched from different marginal sea sediments across northwestern Pacific showed varied dehalogenation patterns, suggesting diverse reductive dehalogenase genes (rdhA). Genome-resolved metagenomic analysis of in situ marginal sea sediments revealed the presence of rdhA-like genes belonging to six distinct categories, with two novel clades more abundant in hypothermal deep-sea sediments (p<0.05). The results of canonical correspondence analysis and distance decay relationship revealed that temperature outweighed geographical contiguity in determining rdhA biogeography and phylogenetic diversity in sediments. A total of 64 putative RDGs were identified across 13 phyla. Low ratios of non-synonymous and synonymous polymorphisms and nucleotide diversity at gene and genome levels indicated the conservation of dehalogenation metabolism in sediment microbiome. RDGs at higher abundance (p<0.05) in mesothermal (≥17.40 ℃) sediments may rely more on sulfate reduction, whereas those with higher abundance (p<0.05) in hypothermal (≤5.5 ℃) sediments (hyp-RDGs) may rely on nitrate utilization. Additionally, hyp-RDGs were prone to external cobalamin acquisition, possibly as an efficient energy-saving strategy. These findings provide insights into the ecological roles of RDGs in marine sediments.},
}
@article {pmid41411799,
year = {2026},
author = {Chen, M and Meng, S and Guan, R and Dong, Q and Dong, X and Shen, X and Fang, L and Zhao, F},
title = {Lead exposure changes carbohydrate and amino acid metabolism corresponding to a disturbed microbiota-gut-brain axis in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119554},
doi = {10.1016/j.ecoenv.2025.119554},
pmid = {41411799},
issn = {1090-2414},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Amino Acids/metabolism ; Mice ; *Lead/toxicity ; *Brain/drug effects/metabolism ; *Carbohydrate Metabolism/drug effects ; Male ; Feces/chemistry/microbiology ; *Brain-Gut Axis/drug effects ; },
abstract = {Chronic lead exposure can cause irreversible neurological damage. The brain-gut axis's involvement in lead-induced neurotoxicity, a key factor in cognitive deficits, requires further exploration. To deepen our understanding of how lead exposure influences the brain-gut connection, we carried out the behavioral and morphological analysis, as well as metabolome and metagenome analysis associated with the gut-brain axis. The study results suggested that Pb exposure resulted in inflammation in both the brain and gut, along with decreased cognitive ability. The metagenomic data indicated that Pb exposure impacted microbial diversity and composition, with a marked increase in genes linked to carbohydrate and amino acid metabolism. Compared to control mice, the metabolic profiles of brain, feces and serum samples from Pb-exposed mice were differed, with higher levels of amino acids in serum and soluble sugars in feces, but lower levels of amino acids in brain. Key enriched microbial (eg: Tenericutes, Thermotogae, Alistipes_putredinis) was significantly negatively correlated with brain amino acid (eg: proline, asparagine, tryptophan) but positively correlated with serum amino acids (eg: valine, leucine, tyrosine). This research uncovers new perspectives on how lead exposure alters metabolites in the brain-gut axis, regulated by gut microbiota, highlighting the need for additional research on lead's health risks.},
}
@article {pmid41410816,
year = {2025},
author = {He, JH and Wang, H and Qiu, E and Qi, Q and Wang, Z},
title = {Gut Microbiota and Atherosclerosis: Integrative Multi-Omics and Mechanistic Insights.},
journal = {Current atherosclerosis reports},
volume = {28},
number = {1},
pages = {1},
pmid = {41410816},
issn = {1534-6242},
support = {K01 HL169019/HL/NHLBI NIH HHS/United States ; R01 HL170904/HL/NHLBI NIH HHS/United States ; R01HL170904/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Atherosclerosis/microbiology/metabolism ; Metabolomics/methods ; Metagenomics ; Dysbiosis ; Proteomics ; Multiomics ; },
abstract = {PURPOSE OF REVIEW: This review synthesizes and discusses evidence from metagenomics, metabolomics, and proteomics on gut microbiome alterations in atherosclerotic cardiovascular disease (ACVD), with carotid atherosclerosis (CAS) serving as an example.<br><br>RECENT FINDINGS: Evidence on gut microbial &#x3b1;-diversity and &#x3b2;-diversity was mixed and differs by disease status. Pro-inflammatory/pathogenic gut bacterial taxa (e.g., Escherichia coli, Klebsiella spp., Streptococcus spp., and Ruminococcus gnavus) were often enriched in patients with ACVD or CAS, whereas short-chain fatty acid (SCFA) producers (e.g., Faecalibacterium prausnitzii, Roseburia spp., Bacteroides spp., and Eubacterium eligens) were depleted. Targeted and untargeted metabolomics implicated multiple microbial-derived metabolites in relation to ACVD and CAS, including trimethylamine N-oxide, short-chain fatty acids, bile acids, lipopolysaccharides, phenylacetylglutamine, indole-3-propionate and imidazole propionate. Gut dysbiosis contributes to ACVD or CAS possibly via metabolite-mediated effects on endothelial function, inflammation, and lipid metabolism. Future research prioritizing longitudinal and interventional studies integrating microbial metagenomics with host multi-omics are needed to elucidate causal pathways and identify clinically actionable targets.},
}
@article {pmid41410786,
year = {2025},
author = {Senel, E and Ramos-Barbero, MD and Santos, F and Villamor, J and Mutlu, MB and Antón, J},
title = {Viral diversity of brine and precipitated halite of Tuz Lake, an inland hypersaline lake in Turkey.},
journal = {Archives of virology},
volume = {171},
number = {1},
pages = {28},
pmid = {41410786},
issn = {1432-8798},
support = {208F135//the Anadolu University Research Foundation No. 1208F135. ES. was an MSc student of the Erasmus program./ ; },
mesh = {*Lakes/virology/chemistry ; Salinity ; Turkey ; Salts/chemistry ; *Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; *Biodiversity ; Metagenomics ; Genome, Viral ; },
abstract = {The diversity of viral communities in inland hypersaline environments remains largely unexplored. Here, we characterized viral assemblages of the thalassohaline inland hypersaline Tuz Lake (Turkey). To identify viral groups and viral sequences present in multiple samples, brine and precipitated salt samples were analysed using microscopy and metagenomics. Viral assemblages showed an abundance and morphology similar to what is commonly found in hypersaline systems. Despite these similarities, the vast majority of sequences remained unknown with regard to taxonomy and function and could not be characterized, highlighting their novelty. A remarkably high fraction of the viral sequences identified were present in both brine and salt samples, indicating viral stability during salt precipitation and dissolution in the lake, suggesting that Tuz Lake might be of considerable astrobiological interest. Alongside this high level of similarity, read recruitments revealed the presence of some sample-specific viral sequences in the salt sample. Tuz Lake viral assemblages displayed a distinct composition when compared to previously described viral metagenomes and haloviral genomes from hypersaline environments, with the highest similarity to the viral assemblages of the crystallizer ponds in the Bras del Port saltern (Spain).},
}
@article {pmid41409546,
year = {2025},
author = {Zhao, L and Peng, S and Ge, M and Xing, B and Zhao, X and Yang, T and Yu, S and Zhang, C and Liu, J and Miao, Z and Ma, H},
title = {Gut-to-tumor translocation of multidrug-resistant Klebsiella pneumoniae shapes the microbiome and chemoresistance in pancreatic cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1694479},
pmid = {41409546},
issn = {2235-2988},
mesh = {Humans ; *Pancreatic Neoplasms/microbiology/drug therapy/pathology ; *Klebsiella pneumoniae/drug effects/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Drug Resistance, Multiple, Bacterial ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Klebsiella Infections/microbiology ; },
abstract = {BACKGROUND: Despite advances and successes in precision oncology, pancreatic cancer (PC) remains a tumor with extremely low survival rates, and many of these cases experienced postoperative recurrence and metastasis. Alterations in the gut microbiota have been linked to the survival rates of PC patients. Nevertheless, the complexity of gut microbiota composition poses significant challenges in identifying definitive clinical biomarkers for PC.<br><br>METHODS: Fecal samples were collected from PC patients, half of whom had metastasis, and their matched healthy controls (HCs). A metagenomic analysis was employed to further investigate the functional features of gut microbiota with both PC and metastatic PC. The clinical correlations, microbial metabolic pathways and antibiotic resistome were further assessed. In a follow-up validation, intraoperative tumor tissue and pancreatic fluid were sampled from PC patients and underwent comprehensive microbiological analysis, including bacterial culture, mass spectrometry-based identification, and third-generation whole-genome sequencing of Klebsiella pneumoniae isolates.<br><br>RESULTS: We observed a significant alteration of the gut microbiota in PC patients, highlighted by an overall increase in microbial diversity compared to healthy controls (p <&#xa0;0.05). Comparative abundance analysis identified 59 differentially abundant microbial species in non-metastatic pancreatic cancer (NMPC) (56 increased, 3 decreased) and 21 in metastatic pancreatic cancer (MPC) (19 increased, 2 decreased), alongside 18 significantly altered microbial metabolic pathways (FDR-adjusted p&#xa0;<&#xa0;0.05). Notably, Klebsiella pneumoniae, Klebsiella oxytoca, and Akkermansia muciniphila were identified as prominent antibiotic resistance gene (ARG) carriers in the gut microbiota of PC patients, with 653 ARG subtypes detected across fecal samples, 38-47% of which were shared among groups. Strong co-occurrence patterns between ARGs (e.g., acrB, mdtC, cpxA, emr, pmrF) and the above species were observed predominantly in MPC samples (p&#xa0;<&#xa0;0.05). Whole-genome sequencing of 14 isolates obtained from tumor tissue and pancreatic fluid revealed consistent ARG profiles and virulence genes, corroborating the metagenomic findings and supporting the hypothesis of gut-to-tumor translocation and potential intratumoral colonization.<br><br>CONCLUSION: This study provides a comprehensive microbiome-based insight into PC and its metastatic subtypes. By integrating microbiome analysis with microbial culture, this study provides direct evidence of gut-derived multidrug-resistant (MDR) K. pneumoniae colonization in PC tissues.},
}
@article {pmid41409544,
year = {2025},
author = {Liu, J and Qin, SY and Lei, CC and Ma, H and Xie, LH and Liu, Y and Li, JH and Ni, HB and Yu, MY and Liang, HR and Shi, WH and Qin, Y and Jiang, J and Yan, WL and Chen, BN and Li, ZY and Sun, HT},
title = {Blastocystis infection in Tibetan antelopes (Pantholops hodgsonii) alters gut microbiota composition and function.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1719025},
pmid = {41409544},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome ; *Antelopes/microbiology/parasitology ; Animals ; *Blastocystis ; *Blastocystis Infections/veterinary/parasitology/microbiology ; Tibet ; Metagenome ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Feces/microbiology/parasitology ; },
abstract = {INTRODUCTION: The gut microbiota plays an important role in host environmental adaptation, including defense against pathogens. Parasite infections can disrupt gut microbial communities and thus influence host adaptability. However, most current knowledge of Blastocystis-microbiota interactions comes from humans or domestic animals, and data from wild mammals, especially those inhabiting extreme environments, remain scarce.<br><br>METHODS: In this study, we analyzed 68 gut metagenomes from Tibetan antelopes (Pantholops hodgsonii) and screened for infections by four intestinal parasites - Blastocystis, Cryptosporidium, Giardia, and Encephalitozoon bieneusi.<br><br>RESULTS: Among them, 26 individuals were solely infected with Blastocystis subtype ST31. Compositional analysis revealed 25 differential families, with 12 enriched in infected and 13 in healthy individuals. LEfSe further identified 38 species-level biomarkers (LDA > 2, p < 0.05), indicating a significant shift in gut microbial diversity following Blastocystis ST31 infection. Notably, the relative abundance of Arthrobacter sp. 08Y14, associated with environmental resilience, was markedly reduced in infected individuals. Functional profiling showed a decrease in metabolic diversity, with 18 CAZy families detected in the healthy group but only 2 in the infected group. KEGG analysis showed that the average relative abundance of K07497 was higher in the infected group (5.16) than in the healthy group (1.03).<br><br>DISCUSSION: These findings suggest that Blastocystis ST31 infection reshapes the gut microbiota and may impair the high-altitude adaptability of Tibetan antelopes by reducing plateau-adaptive microbes and functional capacity. This study provides the first evidence of Blastocystis-induced gut microbiota changes in Tibetan antelopes and broadens our understanding of parasite-microbiota interactions across hosts.},
}
@article {pmid41408356,
year = {2026},
author = {Yao, QC and Zhang, DY and Du, YP and Chen, C and Lv, YT and Li, D and Xing, YX and Xu, XY and Lin, QQ and Tan, WF and Bai, FH},
title = {Gut microbiome-metabolome dysregulation in systemic sclerosis: a multi-omics study.},
journal = {Rheumatology (Oxford, England)},
volume = {65},
number = {1},
pages = {},
doi = {10.1093/rheumatology/keaf668},
pmid = {41408356},
issn = {1462-0332},
support = {202330//National Clinical Key Speciality Capacity Building/ ; 2021818//Hainan Province Clinical Medical Center/ ; YSPTZX202313//The Innovation Platform for Academicians of Hainan Province/ ; WSJK2024MS150//Joint Project on Health Science and Technology Innovation in Hainan Province/ ; Qhyb2022-133//Hainan Provincial Postgraduate Innovation Research/ ; hnjg2024-67//Hainan Province Education Reform/ ; },
mesh = {Humans ; *Scleroderma, Systemic/microbiology/metabolism ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; *Metabolome/physiology ; Feces/microbiology ; Metabolomics ; Adult ; Aged ; Case-Control Studies ; Metagenomics ; Tandem Mass Spectrometry ; Multiomics ; },
abstract = {OBJECTIVES: The interplay between the gut microbiome (GM), plasma metabolites and systemic sclerosis (SSc) has not been systematically studied. We hypothesized that disruption at the GM-metabolome interface contributes to the pathogenesis of SSc. This study aims to investigate the faecal microbiome composition and plasma metabolite profiles in SSc patients.<br><br>METHODS: To evaluate the interactions, deep shotgun metagenomic sequencing was conducted on faecal samples from 15 SSc patients and 33 healthy controls. Simultaneously, untargeted liquid chromatography-tandem mass spectrometry metabolomic profiling was performed on plasma samples from 14 SSc patients and 30 controls.<br><br>RESULTS: The analysis revealed significant alterations in 11 microbial species and 266 MS2-identified metabolites in SSc patients vs controls. In SSc, elevated levels of Escherichia coli, Lactobacillus mucosae and Parabacteroides distasonis were noticed. Conversely, Phocaeicola plebeius, Blautia hansenii and Agathobaculum butyriciproducens were enriched in the control group. Functional predictions indicated a depletion of amino acid biosynthesis pathways, including L-isoleucine and L-methionine, in SSc patients. The metabolomic analysis demonstrated a significant reduction in lipid-like molecules and amino acid levels in SSc patients. Dysregulated pathways, such as alanine, aspartate and glutamate metabolism, arginine and proline metabolism, and glycine, serine and threonine metabolism, were associated with the development of SSc. Striking microbiota-metabolite correlations (168 significant associations) were identified, with disease-enriched species showing specific metabolic linkages.<br><br>CONCLUSIONS: This study offers a comprehensive characterization of the disrupted GM-metabolite interface in SSc patients, providing new perspectives on SSc pathogenesis and potential therapeutic targets.},
}
@article {pmid41408188,
year = {2025},
author = {Halimi, H and Hesami, Z and Asri, N and Khorsand, B and Rostami-Nejad, M and Houri, H},
title = {Exploring the biliary microbiome in hepatopancreatobiliary disorders: a comprehensive systematic review of microbial signatures and diagnostic potential.},
journal = {BMC gastroenterology},
volume = {26},
number = {1},
pages = {55},
pmid = {41408188},
issn = {1471-230X},
support = {NO. IR.SBMU.RIGLD.REC.1404.036//Shahid Beheshti University of Medical Sciences/ ; },
mesh = {Humans ; Cholangitis, Sclerosing/microbiology/diagnosis ; *Microbiota ; Bile Duct Neoplasms/microbiology/diagnosis ; *Biliary Tract/microbiology ; *Pancreatic Neoplasms/microbiology/diagnosis ; Cholangiocarcinoma/microbiology/diagnosis ; Gallstones/microbiology/diagnosis ; *Pancreatic Diseases/microbiology/diagnosis ; *Biliary Tract Diseases/microbiology/diagnosis ; },
abstract = {BACKGROUND: Hepatopancreatobiliary (HPB) diseases, encompassing hepatobiliary and pancreatic disorders, pose substantial global health challenges due to their high morbidity and mortality rates. Recent research highlights the crucial role of the biliary microbiome in the development of these diseases.<br><br>METHODS: This study provides a comprehensive systematic review of the biliary microbiome's characteristics across various HPB disorders, including cholangiocarcinoma (CCA), pancreatic cancer (PC), primary sclerosing cholangitis (PSC), and gallstone disease (GSD). Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we screened articles from multiple databases, focusing on original research utilizing 16&#xa0;S rRNA gene sequencing or metagenomics.<br><br>RESULTS: Our review included 24 studies that met stringent inclusion criteria. The results indicate distinct alterations in bacterial diversity and composition associated with different HPB conditions, highlighting potential pathogenic mechanisms and candidate taxa as potential microbial indicators. In lithiasis conditions, elevated levels of Pyramidobacter and Citrobacter were associated with recurrent and giant common bile duct (CBD) stones. Proteobacteria were prevalent in PSC and CCA, potentially contributing to these diseases by promoting chronic inflammation. Sphingomonas was associated with both CCA and PSC, with potential implications for lymph node metastasis in PC.<br><br>CONCLUSIONS: These findings suggest the potential of the biliary microbiome as a diagnostic tool, offering insights into the pathophysiology and possible therapeutic targets for HPB diseases. However, given the heterogeneity in methodologies and the limited number of studies including healthy controls, these observations remain preliminary; further prospective validation is required before clinical translation.},
}
@article {pmid41408023,
year = {2026},
author = {Wang, H and Zhang, M and Hua, B and He, J and Yang, Y and Wu, W and Zhang, Y and Wei, F and Cai, Y and Wang, Q},
title = {Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens.},
journal = {Clinical rheumatology},
volume = {45},
number = {2},
pages = {857-873},
pmid = {41408023},
issn = {1434-9949},
support = {C2301008&#xff0c;C2404002//Shenzhen Medical Research Fund/ ; 2023B1515230002//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A1515010294//Guangdong Basic and Applied Basic Research Foundation/ ; 0102018-2019-YBXM-1499-01-0414//Treatment and Prevention Integration Project of Shenzhen Municipal Health Commission/ ; SZSM202311030//Sanming Project of Medicine in Shenzhen/ ; No. NSFC 82302037//The National Natural Science Foundation of China/ ; KYQD2024355//Shenzhen High-level Hospital Construction Fund and Peking University Shenzhen Hospital Scientific Research Fund/ ; },
mesh = {Humans ; *Lupus Erythematosus, Systemic/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Clostridium/genetics ; Female ; Adult ; Male ; Middle Aged ; Metagenomics ; Metabolomics ; Case-Control Studies ; Metabolome ; Dysbiosis/microbiology ; Eubacteriales ; },
abstract = {OBJECTIVES: Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unclear pathogenesis. Emerging evidence indicates that the gut microbiome may play a critical role in immune regulation. This study aimed to investigate gut microbiome and metabolome alterations in SLE patients, with a focus on the pro-inflammatory bacterium Clostridium scindens (C. scindens), and explore its potential contribution to disease pathogenesis.<br><br>METHOD: We performed metagenomic sequencing to analyze gut microbial composition in SLE patients and healthy controls, alongside untargeted metabolomic profiling of peripheral blood to assess systemic metabolic changes. We examined species diversity, taxonomic differences at both phylum and species levels, and metabolic alterations. Statistical analyses identified significant associations and potential diagnostic markers.<br><br>RESULTS: SLE patients did not show a consistent reduction in species diversity, but exhibited significant microbial compositional differences compared to healthy controls. These patterns suggest potential diagnostic utility. Metabolomic analysis revealed systemic metabolic disturbances linked to gut dysbiosis. Ruminococcus gnavus was associated with altered amino acid, lactose, and sphingolipid metabolism, potentially affecting host immunity. Notably, C. scindens appeared to contribute to immune dysregulation via bile acid metabolism.<br><br>CONCLUSIONS: This study reveals distinct microbial and metabolic profiles in SLE, identifying C. scindens as a potential driver of immune imbalance. The findings suggest that targeting the gut microbiome could offer novel strategies for diagnosis and therapeutic intervention in SLE. Key Points &#x2022;&#xa0;Gut microbial composition is significantly altered in SLE patients compared to healthy controls. &#x2022;&#xa0;Metabolomic profiling reveals systemic disturbances linked to gut dysbiosis. &#x2022;&#xa0;Clostridium scindens is associated with bile acid metabolism and immune dysregulation in SLE. &#x2022;&#xa0;The gut microbiome may serve as a potential target for diagnosis and treatment in SLE.},
}
@article {pmid41407286,
year = {2025},
author = {Herbst, R and Ibrahim, A and Hübner, A and Knüpfer, U and Regestein, L and Wiedemann, C and Hellmich, UA and Warinner, C and Stallforth, P},
title = {Actifensin Evolution in the Human Oral Cavity over the Past 100,000 Years.},
journal = {Journal of the American Chemical Society},
volume = {147},
number = {52},
pages = {48060-48071},
pmid = {41407286},
issn = {1520-5126},
mesh = {Humans ; *Mouth/microbiology ; Animals ; *Bacteriocins/genetics/chemistry/metabolism ; *Evolution, Molecular ; Phylogeny ; Microbiota ; Actinomyces/chemistry/metabolism ; *Antimicrobial Peptides/genetics/chemistry ; Biofilms ; },
abstract = {Bacterially produced antimicrobial peptides (AMPs), or bacteriocins, play key roles in shaping microbial communities via interspecies competition. Unlike the more temporally dynamic gut microbiome, the oral microbiome exhibits long-term stability and is preserved into deep time in dental calculus, enabling evolutionary analysis across time. Here, we combine metagenomics, structural modeling, and experimental validation to investigate AMP diversity in ancient and modern dental biofilms from humans, Neanderthals, and nonhuman primates spanning 100,000 years. Using our newly developed platform, AMPcombi, we uncover evolutionary trajectories of bacteriocins and elucidate their ecological functions. Among these, we identify a conserved family of Actinomyces-derived defensin-like peptides, termed actifensins, present across all time periods. Phylogenetic, structural, and functional analyses revealed shared ancestry and adaptive diversification between ancient (paleo-) and modern actifensins, with evidence of positive selection and maintained antimicrobial activity. Our findings position the oral microbiome as a valuable reservoir for natural product discovery. In the face of rising antimicrobial resistance, evolutionary insights into AMP function open a door to next-generation therapeutics. AMPcombi streamlines this process, linking ancient biomolecules with biotechnology.},
}
@article {pmid41406735,
year = {2026},
author = {López-Dávalos, PC and Requena, T and Pozo-Bayón, M&#xc1; and Muñoz-González, C},
title = {In vivo metabolism of fruity carboxylic esters in the human oral cavity is partly driven by microbial enzymes.},
journal = {Food chemistry},
volume = {501},
number = {},
pages = {147554},
doi = {10.1016/j.foodchem.2025.147554},
pmid = {41406735},
issn = {1873-7072},
mesh = {Humans ; *Mouth/microbiology/metabolism/chemistry/enzymology ; *Esters/metabolism/chemistry ; Male ; Adult ; Female ; *Saliva/microbiology/enzymology/chemistry/metabolism ; *Bacteria/enzymology/genetics/isolation &amp; purification/classification/metabolism ; Young Adult ; Microbiota ; *Bacterial Proteins/metabolism/genetics ; Gas Chromatography-Mass Spectrometry ; Middle Aged ; *Carboxylic Acids/metabolism/chemistry ; },
abstract = {Food flavor perception is shaped by biochemical events during oral processing, with oral metabolism remaining poorly understood. This study investigated the oral fate of fruity carboxylic esters and its relationship with salivary and microbiological parameters. Participants (n = 101) rinsed their mouths with either water (control) or an ester-containing solution for 30 s. Esters and their corresponding acids were analyzed by gas chromatography-mass spectrometry before and after rinsing. Results showed a significant decrease in ester and a marked increase in acid levels, indicating rapid metabolic conversion. Ester recovery was associated with the physicochemical properties of the compounds, participants' body mass index, and salivary esterase activity (SEAC). SEAC also correlated with oral microbiota composition and the abundance of microbial genes encoding carboxylic ester hydrolases, as assessed by shotgun metagenomics. These findings provide the first evidence of rapid ester metabolism in the human mouth and its relationship with the salivary microbiome.},
}
@article {pmid41406442,
year = {2026},
author = {Li, Y and Li, H and Lv, C and Hu, X and Zhang, B},
title = {Bacterial changes and quality deterioration of freshwater shellfish Hyriopsis cumingii meat under different temperature storage.},
journal = {Canadian journal of microbiology},
volume = {72},
number = {},
pages = {1-9},
doi = {10.1139/cjm-2025-0056},
pmid = {41406442},
issn = {1480-3275},
mesh = {Animals ; Temperature ; *Bacteria/genetics/classification/isolation &amp; purification ; *Shellfish/microbiology ; RNA, Ribosomal, 16S/genetics ; *Food Storage ; China ; Fresh Water/microbiology ; Food Microbiology ; Microbiota ; },
abstract = {Hyriopsis cumingii is an important economic freshwater shellfish in China and there is a need to understand changes in the microbial community structure resulting in multidimensional quality degradation when the fish is stored at different temperatures. This study integrated 16S rRNA full-length sequencing with multidimensional quality indicators to investigate the temperature-regulated bacterial community shifts and quality deterioration mechanisms in stored H. cumingii meat. The results showed that bacterial richness (Chao1 index) decreased progressively with both refrigerated (4 °C) and room-temperature (25 °C) storage. Community composition underwent significant restructuring, with Bacteroidota decreasing at 25 °C while Bacillota increased compared to 4 °C storage. Additionally, the refrigerated group showed enrichment of Delftia turuhatensis and Chryseobacterium indologenes compared to the room-temperature storage group. Temperature significantly restructured bacterial communities, with notably higher pathogenic bacteria under refrigeration and spoilage bacteria dominance at room temperature. Metagenomic functional profiling revealed temperature-driven metabolic pathway divergence, indicating distinct spoilage mechanism. Predictable quality changes in H. cumingii correlated with temperature-imposed microbial composition.},
}
@article {pmid41405224,
year = {2026},
author = {Kok, CR and Morrison, MD and Thissen, JB and Mabery, S and Carson, ML and Kimbrel, JA and Bennett, JW and Tribble, DR and Millar, EV and Mende, K and Be, NA},
title = {Microbiome dynamics in the congregate environment of U.S. Army Infantry training.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0047425},
pmid = {41405224},
issn = {2165-0497},
support = {Y1-Al-5072//National Institute of Allergy and Infectious Diseases/ ; HU0001190002//U.S. Department of Defense/ ; 20-FS-029//Laboratory Directed Research and Development/ ; },
mesh = {Humans ; *Military Personnel ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; United States ; Metagenomics ; Fungi/classification/genetics/isolation &amp; purification ; Male ; Female ; Adult ; },
abstract = {Within military training and operational environments, individuals from diverse backgrounds share common spaces, follow structured routines and diets, and engage in physically demanding tasks. While there has been interest in leveraging microbiome features to predict and improve military health and performance, the longitudinal convergence of microbiomes in such constrained environments has not been established. To assess the degree of microbiome convergence, we performed shotgun metagenomic sequencing on swab samples from a military trainee cohort. Samples were taken across four different body sites, three timepoints, and two spatially distinct platoons. We observed evidence of convergence in one platoon, whereby similarity in microbiome composition increased over time, with numerous differentially abundant species. We found no indication of strain transfer between individuals, suggesting that convergence was influenced by external environmental factors, diet, and lifestyle. Microbial shifts observed in the convergence process included a decrease in fungal species, such as Malassezia restricta in nasal cavities, and a decrease in Prevotella species at inguinal regions across time. Shifts in multiple Corynebacterium species were also observed with varying magnitudes depending on the body site. Overall, we provide preliminary evidence of convergence of host microbial communities in military-associated environments that were distinguishable using shotgun metagenomic sequencing approaches. The data presented here on microbiome convergence, dynamics, and stability may inform risk-based mitigation in congregate military settings facilitating development of targeted microbial, dietary, or other interventions to optimize health and performance of military populations.IMPORTANCEMicrobiome convergence in deployed environments could impact the health and readiness of the warfighter, with potential implications for susceptibility to biothreats. This study describes a shotgun metagenomic approach used to study the microbiomes of swab samples collected at different body sites in a military trainee cohort. The results presented here provide a foundation for developing future microbiome-based interventions and protocols to enhance operational readiness.},
}
@article {pmid41404904,
year = {2026},
author = {Jensen, EEB and Jespersen, ML and Svendsen, CA and Sonda, T and Otani, S and Aarestrup, FM},
title = {Tanzanian goat gut microbiomes adapt to roadside pollutants and environmental stressors.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0203625},
pmid = {41404904},
issn = {2165-0497},
support = {101103059//European and Developing Countries Clinical Trials Partnership/ ; },
mesh = {Animals ; *Goats/microbiology ; *Gastrointestinal Microbiome/drug effects/genetics ; Tanzania ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification/metabolism ; *Vehicle Emissions/toxicity ; *Environmental Pollutants/toxicity/metabolism ; Metagenome ; Environmental Pollution/adverse effects ; Biodegradation, Environmental ; Metagenomics ; },
abstract = {The impact of environmental pollution reaching and affecting the gut microbiome is rising. Pollution from vehicle emissions can release compounds harmful to both animal and environmental health, and their effect on the host microbiome is yet to be determined, particularly in understudied locations. Here, we have investigated the potential effect of environmental pollution on the gut microbiome of Tanzanian goats grazing near a heavily trafficked road compared to goats living in a more rural setting. We identified 1,468 metagenome-assembled genomes (MAGs), of which 768 were unidentified species, and created a genomic database to which 52% of the bacterial community could be assigned. We find significant differences in the composition of the bacterial communities and resistomes between rural and road-exposed goats, but not a major difference in antimicrobial resistance (AMR) abundance. Genes involved in pollutant biodegradation were significantly more abundant in the microbiome of goats grazing along the road. This includes genes involved in degradation of naphthalene and toluene (both present in motor vehicle exhaust), as well as the detoxification enzyme, glutathione S-transferase. These findings suggest living near a heavily trafficked road selects for xenobiotic degrading functions within the goat gut microbiome, which might aid the host in detoxification of these compounds.IMPORTANCETo the best of our knowledge, this is the first study on the potential effect of environmental pollution on the gut microbiome of Tanzanian goats. Using shotgun metagenomics, we compare the gut microbiome of goats living near a heavily-trafficked road in Kigoma, Tanzania, with the gut microbiome of goats living in a rural area. We find that genes involved in pollutant biodegradation were significantly more abundant in the gut microbiome of the road-exposed goats, which potentially aids pollutant detoxification in the host. The effect of environmental pollution on the gut microbiome remains poorly understood; however, with this study, we link a potential effect of environmental pollution to changes in the gut microbiome of Tanzanian goats.},
}
@article {pmid41404370,
year = {2025},
author = {Liu, M and Wu, M and Tang, Y and Lin, Z and Ye, C and Huang, X and Zhou, L and Lin, Q and Zheng, D and Lu, Y},
title = {Correlation between oral microbial characteristics and overall bone density of Postmenopausal women based on macrogenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663645},
pmid = {41404370},
issn = {2235-2988},
mesh = {Humans ; Female ; *Bone Density ; Middle Aged ; Saliva/microbiology ; *Osteoporosis, Postmenopausal/microbiology ; *Postmenopause ; *Microbiota ; Dental Plaque/microbiology ; *Mouth/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification ; Absorptiometry, Photon ; },
abstract = {BACKGROUND: Postmenopausal osteoporosis (PMO), a prevalent bone disease triggered by estrogen deficiency - induced bone mass reduction and deterioration of bone tissue microarchitecture, escalates the risk of fragility fractures. Recent research has highlighted the pivotal role of oral and gut microbiota in PMO development, giving rise to the "oral - gut - bone axis" concept.<br><br>METHODS: A total of 21 postmenopausal women, aged 50 - 60, were recruited for the study. Based on bone mineral density (BMD) measurements from dual - energy X - ray absorptiometry (DXA), participants were divided into osteopenia, osteoporosis, and healthy groups. Saliva and dental plaque samples were collected for metagenomic sequencing to analyze microbial diversity and community composition, with differences identified via LEfSe analysis. KEGG pathway analysis was used to reveal variations in microbial functions. Based on these analyses, predictive models for bone density status were constructed using LASSO regression and random forest algorithms.<br><br>RESULTS: Significant differences in salivary microbial community structures were found between the osteoporosis and healthy groups (P = 0.041). LEfSe analysis revealed higher abundance of Aggregatibacter, Haemophilus haemolyticus, Haemophilus sputorum, Pasteurellaceae, Neisseria elongata, Aggregatibacter segnis, and Aggregatibacter aphrophilus in the osteopenia group, and higher abundance of Streptococcus pneumoniae and Haemophilus paraphrohaemolyticus in the osteoporosis group compared to the healthy group. The random forest models for osteopenia vs. healthy and osteoporosis vs. healthy yielded AUC values of 0.82 and 0.74, respectively, suggesting potential predictive capability, though further validation in larger cohorts is needed to confirm their generalizability. Functional analysis using LEfSe identified differential KEGG pathways, including glycan biosynthesis and metabolism in cancer, choline metabolism in cancer, and the cGMP-PKG signaling pathway.<br><br>CONCLUSION: This exploratory study utilized metagenomic sequencing to analyze the relationship between oral microbiota and PMO while controlling for key confounders. We identified significant compositional and functional alterations in the oral microbiome associated with bone mineral density status, including specific bacterial species showing marked intergroup differences. A model based on differential microbial features exhibited preliminary discriminative capacity, and functional analysis suggested involvement of inflammatory and metabolic pathways. These findings provide initial evidence linking oral microbiota to PMO.},
}
@article {pmid41403401,
year = {2025},
author = {Lin, H and Zhu, X and Zhu, J and Chen, N and Bao, W and Peng, Z},
title = {High-Throughput Sequencings Revealed That Gut Microbiota Dysbiosis is Implicated in Gouty Arthritis of Red-Crowned Crane (Grus japonensis).},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {2422900},
pmid = {41403401},
issn = {1865-1682},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Arthritis, Gouty/veterinary/microbiology ; *Dysbiosis/veterinary/microbiology/complications ; High-Throughput Nucleotide Sequencing/veterinary ; *Bird Diseases/microbiology ; Feces/microbiology ; China/epidemiology ; RNA, Ribosomal, 16S ; },
abstract = {The red-crowned crane (Grus japonensis) is one of the rarest cranes with a global population of less than 4000 individuals. The population of red-crowned crane could be influenced by health threats, including metabolic and infectious diseases. In the Wildlife Rescue Center of Suining County of Jiangsu Province, gouty arthritis (GA) was observed in all four red-crowned cranes since March 2024. A pooled fecal supernatant was first submitted to metagenomics sequencing for screening disease-associated pathogens. Enterobacteria phage phiEcoM-GJ1 was detected as the predominant virus while Escherichia coli and Aeromonas hydrophila were the dominated bacteria in the mixed fecal sample from red-crowned cranes. The 16S rRNA gene sequencing was further performed on both the mixed fecal sample and four individual samples, which showed that Escherichia-Shigella, Lactobacillus, and Enterococcus were the most abundant gut flora in both mixed and individual fecal samples. Furthermore, bacteria isolation and identification with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) confirmed that Escherichia coli was predominant (19/29 colonies, 65.52%) in the feces. Therefore, anti-uricacid and antibacteria treatments using plantain herb, doxycycline, Vitamin AD3 and multivitamin B were adopted, leading to a full behavioral recovery within 1 month. Overall, this case-based observational study provides first clue on the gut-joint axis in red-crowned cranes, supporting that gut microbiota dysbiosis is closely associated with GA in red-crowned cranes.},
}
@article {pmid41401858,
year = {2026},
author = {Memon, FU and Xu, J and Xie, X and Shu, C and Li, Y and Li, K and Xiao, Y and Tian, L},
title = {Strain-specific gut microbiota modulation is linked to resistance to BmNPV infection in silkworms.},
journal = {Journal of invertebrate pathology},
volume = {215},
number = {},
pages = {108518},
doi = {10.1016/j.jip.2025.108518},
pmid = {41401858},
issn = {1096-0805},
mesh = {Animals ; *Bombyx/microbiology/virology/immunology ; *Gastrointestinal Microbiome ; *Nucleopolyhedroviruses/physiology ; *Disease Resistance ; Species Specificity ; },
abstract = {Bombyx mori nucleopolyhedrovirus (BmNPV) is a major pathogen threatening sericulture, yet the role of gut microbiota in strain-specific resistance remains poorly understood. This study compared three silkworm strains with high (Xinjiu, XJ), intermediate (An3, A3), and low (Zhenchixian, ZCX) resistance to BmNPV. Protein assays showed that the resistant XJ strain exhibited the lowest viral EGFP and VP39 expression and highest survival, whereas the susceptible ZCX strain displayed the opposite trend. Shotgun metagenomics revealed strain-specific microbial responses to infection. XJ and A3 maintained significantly higher alpha diversity and more dynamic beta diversity clustering than ZCX, with infection inducing increased microbial gene abundance and emergence of unique taxa in XJ. Taxonomic profiling showed XJ enriched in Firmicutes and beneficial fungal taxa such as Mucoromycota, Ascomycota, Basidiomycota, and Zoopagomycota, alongside reductions in Actinobacteria and Proteobacteria following infection. At finer resolution, resistant strains were enriched in beneficial bacterial classes (Bacilli, Alphaproteobacteria, Opitutae) and fungal classes (Agaricomycetes, Saccharomycetes), with cooperative co-occurrence networks linking these taxa and antagonizing pathogens. In contrast, ZCX was dominated by Gammaproteobacteria, Actinomycetia, and Hydrogenophilalia, consistent with dysbiosis and susceptibility. Functional analysis demonstrated pronounced metabolic reprogramming in resistant strains, especially XJ, with coordinated activation of carbohydrate, amino acid, nucleotide, and lipid metabolism, forming tightly integrated functional networks. Together, these findings reveal that silkworm resistance to BmNPV is associated with microbiome diversity, restructuring toward beneficial taxa, and synergistic metabolic pathways, offering new insights for probiotic-based antiviral strategies.},
}
@article {pmid41398941,
year = {2025},
author = {Song, Y and Hou, S and Xiang, Y and Zou, D and Gu, S and Pu, X and Liu, Q and Chu, M},
title = {Dietary energy levels modulate rumen metabolites and function in sheep by regulating the rumen microbiome.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {40},
pmid = {41398941},
issn = {1471-2180},
support = {XQSWYZQZ-JBKY-4//Project of State Key Laboratory of Animal Biotech Breeding of China/ ; CAAS-ZDRW202502 and ASTIP-IAS13//Agricultural Science and Technology Innovation Program of China/ ; CARS-38-02//Earmarked Fund for China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; Sheep/microbiology/metabolism ; *Animal Feed/analysis ; *Diet/veterinary ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Fermentation ; Metabolome ; Metabolomics ; Metagenomics ; },
abstract = {In intensive ruminant production, high-energy diets are commonly used to enhance animal productivity, as dietary formulation significantly influences rumen fermentation and microbial communities. This study investigated the effects of varying dietary energy levels on the rumen microbial community structure, function, and metabolic profiles in Small-tailed Han (STH) sheep. Thirty 6-month-old sheep were randomly assigned to three groups: high-energy (HE), conventional-energy (CE), and low-energy (LE). All groups were fed iso-nitrogenous diets formulated to provide high-, conventional-, and low-energy levels of 10.8, 9.5, and 8.2 MJ/kg of digestible energy (DE), respectively. Rumen content was collected post-slaughter and analyzed via metagenomic sequencing to assess microbial composition and function, alongside non-targeted metabolomics to characterize the rumen fluid metabolome. Results revealed that Bacteroidota and Bacillota were the dominant phyla. High-energy feeding significantly reduced the relative abundance of Bacteroidota while increasing that of Bacillota, leading to a markedly higher Bacillota-to-Bacteroidota ratio. Functional analysis indicated significant enrichment of carbohydrate metabolism pathways in the HE group, whereas the LE group exhibited enrichment in fundamental cellular processes such as ABC transporters and ribosome, indicating a "survival mode". Metabolomic analysis demonstrated that dietary energy levels substantially reshaped the rumen metabolomic profile. Metabolites in the HE group were enriched in pathways including steroid hormone biosynthesis and the prolactin signaling pathway, while the LE group showed enrichment in histidine metabolism and the TCA cycle. Several aromatic amino acid metabolic pathways were commonly enriched across comparisons. These findings indicate that while the composition of the dominant phyla (Bacteroidota and Bacillota) was conserved across diets with different digestible energy levels, this dietary variation altered community diversity, structure, functional potential, and profoundly reshaped the rumen metabolic environment. This study provides scientific evidence regarding the impact of dietary energy on rumen fermentation and production performance in fattening sheep.},
}
@article {pmid41398701,
year = {2025},
author = {Wang, M and Zhang, C and Zhao, L and Yin, Q and Cui, Z and Chen, X and Ren, J and Wang, Y and Xu, M and Cao, Y and Wu, S and Yao, J},
title = {Unraveling the interaction between the phageome and bacteriome in the rumen and its role in influencing metabolome dynamics in dairy cows at different lactation stages.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {257},
pmid = {41398701},
issn = {2049-2618},
support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 32272829//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Rumen/microbiology/virology/metabolism ; *Lactation ; Cattle ; Female ; *Bacteriophages/classification/genetics/isolation &amp; purification/physiology ; *Metabolome ; *Bacteria/classification/virology/genetics/metabolism/isolation &amp; purification ; Milk/metabolism ; Longitudinal Studies ; *Gastrointestinal Microbiome ; Metagenomics ; },
abstract = {BACKGROUND: Although the roles of rumen microbiome in milk yield and milk protein synthesis have been widely recognized, knowledge on how ruminal microbiome dynamic changes affect these two traits during the whole lactation is lacking. Phages have been shown to affect the microbiota, but little is known about the shift patterns of ruminal phages and if they may modulate rumen microbiome during lactation. Herein, a longitudinal study was performed to identify the potential roles of ruminal phageome and bacteriome interactions, and metabolic function shift in affecting milk yield and protein content using metagenomic and metabolomic profiling of rumen microbiome from the peak, early, and later mid-lactation stages.<br><br>RESULTS: A total of 780 ruminal bacterial phages were identified, which exhibited two primary shifting patterns: (1) decreasing then increasing; (2) decreasing then stabilizing through the lactation. Bacteriome also showed first increasing then stabilizing or continuously declining besides exhibiting two similar shifting patterns to those of phages. By associating the differentially abundant phages with their host bacteria, we observed that significantly increased Lactococcus phage BM13, Corynebacterium phage P1201, and Campylobacter phage CJIE4-5 in peak lactation, along with Lactobacillus phage Lv-1 in early and later mid-lactation, were positively correlated with the relative abundance of their hosts. However, significantly increased Bacillus phage BCU4 and the Enterococcus phage phiNASRA1 in early mid-lactation were negatively related to their host abundance. In terms of bacteria, Ruminococcus flavefaciens and Faecalibacterium sp. CAG 74 had the highest abundance in peak lactation, whereas most Prevotella species were more abundant in early and later mid-lactation. Notably, ruminal carbohydrate and amino acid metabolism functions were enhanced in early mid-lactation. Further structural equation model and network analysis revealed that abundant Bacillus phage BCU4 and Enterococcus phage phiNASRA1 in early mid-lactation were associated with increased relative abundance of Prevotella species, possibly due to a reduction in Bacillus cereus and Enterococcus faecalis. Additionally, these Prevotella species exhibited positive relationships with rumen metabolites, such as L-phenylalanine, phenylacetylglycine, N-acetyl-D-phenylalanine, and propionate content, which contributed to the improved milk protein yield.<br><br>CONCLUSIONS: This study revealed the bacteriome and phageome interactions at different lactation stages, and the key phages and bacteria regulating the rumen function and metabolism thus contributing to the milk traits of cows. The potential regulatory roles of phages in affecting the rumen bacteriome suggest that they can be powerful targets for future interventions to improve rumen functions. Video Abstract.},
}
@article {pmid41398277,
year = {2025},
author = {Xiao, Y and Liu, H and Wang, P and Zhang, Y and Wang, F and Jing, H},
title = {Microbial population structure along the water columns and sediments in the Diamantina and Kermadec trenches.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {16},
pmid = {41398277},
issn = {1741-7007},
support = {424MS115//the Hainan Provincial Natural Science Foundation of China/ ; 424QN341//the Hainan Provincial Natural Science Foundation of China/ ; 2022YFC2805400//the National Key R&amp;D Program of China/ ; 2022YFC2805505//the National Key R&amp;D Program of China/ ; KJRC2023C37//the Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; },
mesh = {*Geologic Sediments/microbiology ; *Microbiota ; *Seawater/microbiology ; *Bacteria/classification/genetics ; Metagenome ; *Water Microbiology ; },
abstract = {BACKGROUND: Microbes are widespread from the marine surface to the hadal zones and play a significant role in global biogeochemical cycling. Physicochemical properties of hadal zone shift with depth, in turn influencing the distribution profiles, biogeochemical functions, and adaptative mechanisms of microbial communities in hadal trenches. However, the ecological functions and evolutions of microbial communities along the surface water down to the sediments in the Diamantina and Kermadec trenches have been rarely studied.<br><br>RESULTS: Here, we provided a detailed metagenomic analysis of samples along the water columns (0-6553&#xa0;m) and sediments (3060-9232&#xa0;m) in the Diamantina and Kermadec trenches. The euphotic waters had a significantly higher &#x251;-diversity than the deep-sea waters and sediments (p&#x2009;<&#x2009;0.05, ANOSIM). Clear inter/intra-trench discrepancies of microbial communities along water layers appeared, with remarkable vertical connectivity exhibited in the Diamantina Trench (97.5%) than the Kermadec Trench (88.8%). Positive correlations among Proteobacteria, Bacteroidota, Actinobacteria, and Thaumarchaeota in seawaters and between Proteobacteria and Chloroflexi in sediments were revealed from the co-occurrence network. Niche-specific microbial groups showed distinct dominant metabolic pathways in carbon fixation, nitrogen, and sulfur cycles. Furthermore, we reconstructed 119 metagenome-assembled genomes (MAGs) of Rhodobacterales, and their notably low ratios of non-synonymous substitutions to synonymous substitutions (pN/pS, 0.23) and high carbon atoms per residue side chain (C-ARSC, 2.86) in deep-sea sediments suggested a pronounced selection critical for their survival.<br><br>CONCLUSIONS: We found a clear connectivity of microbial communities in vertical profile, and discrepancy existed between the Diamantina and Kermadec trenches; Rhodobacterales' evolutionary adaptation related to genomic features (pN/pS and SNVs/kbp) in the deep-sea trench environments. These findings provided new insights into the community succession and potential adaption mechanism along the water columns to sediments in deep trenches.},
}
@article {pmid41398180,
year = {2025},
author = {Song, X and Fu, Y and Xu, H and Wang, H and Chen, J and Huang, S and Chen, Y and Xu, J and Li, W and Zhang, J and Wu, P and Shen, Q and Yang, S and Wang, X and Liu, Y and Ji, L and Li, Y and Yang, H and Tang, J and Zhou, C and Zhang, W},
title = {Maternal health status is associated with paired maternal and cord blood virome and mother-to-infant transmission.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {14},
pmid = {41398180},
issn = {2055-5008},
support = {JSYGY-1-2023-03(03)//Jiangsu Provincial Hospital Association/ ; SH2023058//Social Development Projects in Zhenjiang/ ; 2023YFD1801300//National Key Research and Development Programs of China/ ; 82341106//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Fetal Blood/virology ; Female ; *Virome ; *Infectious Disease Transmission, Vertical ; Pregnancy ; Phylogeny ; Infant, Newborn ; *Viruses/classification/genetics/isolation &amp; purification ; *Maternal Health ; Metagenomics ; Adult ; Genome, Viral ; Health Status ; },
abstract = {The viromes of maternal peripheral blood (MPB) and umbilical cord blood (UCB) provide crucial insights into mother-to-infant transmission and the associations of maternal health with early-life viral colonization. Using viral metagenomic sequencing of 433 MPB and 426 UCB samples, we assembled 57 near-complete genomes from four core viral families (Anelloviridae, Circoviridae, Parvoviridae, Flaviviridae). MPB viromes were primarily composed of bacteriophages and Anelloviridae, while UCB exhibited relatively increased abundances of Parvoviridae and Human Endogenous Retroviruses. Maternal disease correlated with reduced α-diversity in MPB but elevated richness in UCB. β-Diversity varied significantly with both health status and sample type. Differential abundance analysis identified health-specific signatures, including enriched Parvoviridae in diseased UCB. Phylogenetic evidence indicated possible vertical transmission and high genetic diversity among identified viruses. This study systematically characterizes the maternal-fetal blood virome and reveals associations between maternal health status and viral community structure, providing a basis for understanding early-life viral exposure and informing future preventive strategies.},
}
@article {pmid41396495,
year = {2025},
author = {Sari, DWK and Khamid, NL and Ikhrami, MA and Hardaningsih, I and Satriyo, TB and Suparmin, A},
title = {A Metagenomic Analysis of Gut Microbiome and Growth Performance of Giant Gourami (Osphronemus goramy) Fed with Raw Plant-Based Diet.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {6},
pages = {168},
pmid = {41396495},
issn = {1436-2236},
support = {2938/UN1/PN/PT.01.10/2022//Universitas Gadjah Mada/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Animal Feed/analysis ; Plant Leaves/chemistry ; Aquaculture ; Diet/veterinary ; *Perciformes/growth &amp; development/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Bacteria/classification/genetics ; Diet, Plant-Based ; },
abstract = {The increasing demand for global protein and awareness of environmental issues challenge sustainable aquaculture growth. The freshwater fish giant gourami (Osphronemus goramy) has the potential to be farmed sustainably. The gut microbiome approach is key to sustainable aquaculture by supporting fish health and feed utilization. This study evaluated the effect of taro leaves supplementation on giant gourami growth and gut microbiome composition. Four groups of fish (initial weight 378 ± 26.14 g) were fed commercial feed with 0%, 25%, 50%, and 75% taro leaves substitution for 16 weeks. Growth parameters such as absolute weight gain (AWG), specific growth rate (SGR), protein efficiency ratio (PER), survival rate (SR), and condition factor (CF) were measured, and gut microbiota was analyzed using 16 S rRNA gene sequencing via Oxford Nanopore Technology. The 50% taro leaves group showed significantly higher AWG (78.87 ± 11.96 g, p < 0.05) and PER (1.92 ± 0.37, p < 0.05) compared to the 100% commercial feed (53 ± 5.6 g and 0.54 ± 0.18, respectively). The condition factor of fish in all feeding experiments (1.40-1.55) demonstrated optimal growth conditions. The gut microbiome was dominated by Clostridium, with taro leaves substitution increasing Cellulosilyticum, Fusobacterium, and Ilyobacter, which are linked to cellulose breakdown and SCFA production. These findings suggest that giant gourami do not require solely commercial feed and are promising for sustainable aquaculture practice.},
}
@article {pmid41396065,
year = {2026},
author = {Herrera, G and Zouiouich, S and Diaz-Mayoral, N and Purandare, V and Trabert, B and Wan, Y and Liu, J and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Li, S and Shi, J and Abnet, CC and Vogtmann, E},
title = {Comparison of oral collection methods for 16S rRNA gene and shotgun metagenomic sequencing.},
journal = {Microbiology spectrum},
volume = {14},
number = {2},
pages = {e0180625},
pmid = {41396065},
issn = {2165-0497},
mesh = {Humans ; *Saliva/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Specimen Handling/methods ; *Metagenomics/methods ; *Microbiota/genetics ; Mouthwashes ; Adult ; *Mouth/microbiology ; Male ; Female ; *Bacteria/genetics/classification/isolation &amp; purification ; DNA, Bacterial/genetics ; Young Adult ; Glycerol ; Middle Aged ; },
abstract = {UNLABELLED: To understand how sample collection affects oral microbiome studies, we evaluated the comparability of unpreserved saliva, saliva in glycerol, and mouthwash samples, their room temperature stability, and intraindividual stability over 6 months. Saliva and mouthwash samples were collected from 20 healthy participants 6 months apart. Saliva was divided, with half preserved in glycerol. Some aliquots were frozen immediately, while others were stored at room temperature for a week. DNA was extracted using the PowerSoil Pro and 16S rRNA gene, and shotgun metagenomic sequencing was conducted. Intraclass correlation coefficients (ICCs) from taxonomic and functional tables were compared to assess variability. We estimated sample size requirements based on the intraindividual stability over 6 months. Saliva in glycerol appeared more similar to unpreserved saliva than mouthwash, with higher median ICCs at genus (0.88 vs 0.60), species (0.92 vs 0.64), and gene levels (0.84 vs 0.36; all P < 0.01). Room temperature storage affected saliva in glycerol more than mouthwash (median genus-level ICC = 0.65). No significant differences were observed at the gene level. Intraindividual stability over 6 months was moderate. To detect an odds ratio of 1.5 with one sample per individual, estimated sample sizes ranged from 665 (common species) to 219,547 (rare species). Oral microbiome stability varies by collection method; mouthwash provides greater room temperature stability and may be preferable when immediate freezing is not feasible. For epidemiological studies, consistent use of a single collection method and inclusion of longitudinal sampling can improve reproducibility and power to detect associations with health outcomes.<br><br>IMPORTANCE: The oral microbiome plays a key role in health and disease, yet methodological inconsistencies in sample collection and processing can introduce variability and limit comparability across studies. This study investigates the impact of different oral sample collection methods on microbiome profiling and their stability over time. We demonstrate that sample type significantly influences taxonomic and functional microbiome profiles, with mouthwash showing greater stability during delayed processing and saliva in glycerol more closely resembling fresh saliva. Importantly, intraindividual microbial communities were only moderately stable over 6 months, emphasizing the need for consistent sampling protocols and consideration of temporal variation. These findings have direct implications for microbiome study design, highlighting that methodological choices can affect reproducibility, statistical power, and biological interpretation. Our results support the use of mouthwash as a practical alternative when freezing is delayed and underscore the value of longitudinal sampling for detecting biologically meaningful changes.},
}
@article {pmid41396034,
year = {2026},
author = {Xu, F and Yang, B and Cui, S and Yang, Z and Dai, N and Stanton, C and Ross, RP and Zhao, J and Lai, J and Chen, W and Wang, Y},
title = {Influence of gestational diabetes mellitus on the breast milk microbiota and oligosaccharides and their effects on the infant gut microbiota.},
journal = {Food &amp; function},
volume = {17},
number = {1},
pages = {513-530},
doi = {10.1039/d5fo04527d},
pmid = {41396034},
issn = {2042-650X},
mesh = {Humans ; *Milk, Human/microbiology/chemistry/metabolism ; Female ; *Oligosaccharides/metabolism/analysis ; *Gastrointestinal Microbiome ; Pregnancy ; *Diabetes, Gestational/metabolism/microbiology ; Infant, Newborn ; Adult ; Feces/microbiology ; Infant ; Bacteria/classification/isolation &amp; purification/genetics ; Tandem Mass Spectrometry ; Male ; },
abstract = {While the interplay between gestational diabetes mellitus (GDM) and the maternal-infant microbial axis is increasingly recognized, the specific pathways of influence remain unclear. This study comprehensively investigated the impact of GDM on the breast milk microbiota, human milk oligosaccharides (HMOs), and the subsequent development of the infant gut microbiota. We analyzed breast milk and paired infant fecal samples collected from healthy and GDM-affected mothers at two time points (0-7 and 42 days postpartum). The microbiota of both sample types was profiled by metagenomic sequencing, and HMOs in breast milk were quantified via liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our findings revealed that GDM had a strong influence on the infant gut microbiota via reducing HMO concentrations than via direct alterations to the breast milk microbiota. These GDM-associated HMO alterations induced stage-specific shifts in the offspring's gut microbiota. Notably, the correlation between specific HMOs and gut bacteria reversed from the colostrum stage to the mature milk stage. This suggests that HMOs influence microbial colonization not only through direct utilization but also, and perhaps more importantly, via indirect ecological mechanisms such as cross-feeding. Collectively, our results identify maternal HMOs as a critical link between maternal metabolism and infant gut health, highlighting their potential as a promising nutritional target to improve long-term metabolic outcomes in GDM-exposed infants.},
}
@article {pmid41395968,
year = {2026},
author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S},
title = {Effects of aquaculture practices on Vibrio population dynamics and oyster microbiome.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {1},
pages = {e0198525},
pmid = {41395968},
issn = {1098-5336},
support = {4421050//USDA-Evans-Allen/ ; 2021-38821-34583//USDA-CBG/ ; },
mesh = {Animals ; *Microbiota ; *Aquaculture/methods ; *Ostreidae/microbiology ; *Vibrio parahaemolyticus/genetics/isolation &amp; purification ; *Vibrio vulnificus/genetics/isolation &amp; purification ; *Vibrio ; Population Dynamics ; Metagenomics ; },
abstract = {Oyster aquaculture is essential for ensuring a sustainable food source. Despite stringent controls, cases of oyster-related illnesses linked to pathogenic Vibrio parahaemolyticus (Vp) and Vibrio vulnificus (Vv) persist. This study investigated the impact of aquaculture practices on the oyster microbiome and pathogen levels, focusing on two common systems: on-bottom and floating cages. From June to November 2019, monthly samples were collected from the Chesapeake Bay, including oysters and water from each aquaculture system. Oyster samples included both fresh and temperature-abused oysters. The study utilized the most probable number and real-time PCR (MPN-qPCR) method to quantify total and pathogenic Vp and Vv in water and oyster samples. DNA was extracted from oyster homogenates and filtered water samples for shotgun metagenomic sequencing. The results revealed significant impacts of aquaculture practices on the diversity of the oyster microbiome, particularly affecting the distribution of phages, antibiotic resistance, and virulence factor genes. Shotgun metagenomic sequencing consistently showed higher genetic representation of Vibrio in floating cages for both fresh and temperature-abused oyster samples. MPN-qPCR results differed between practices, showing higher Vibrio levels in bottom cages for fresh oysters and higher levels in floating cages under temperature abuse. These discrepancies are likely explained by the stable conditions in bottom cages, the effects of temperature abuse, and the growth bias inherent to the MPN method. These results underscore the need for a holistic, time-sensitive approach, taking into account microbial states and the dynamic aspects of the oyster environment to understand the complex relationship between aquaculture practices and the oyster microbiome.IMPORTANCEThis study holds great importance for food safety, antibiotic resistance surveillance, aquaculture management, and environmental health. Unraveling the population dynamics of microbial communities in oysters and their responses to different aquaculture practices enhances our ability to ensure safer seafood, monitor antibiotic resistance, optimize aquaculture methods, and mitigate potential public health challenges. Moreover, it demonstrates the applicability of advanced metagenomic tools for future research. Furthermore, this research addresses critical aspects of food safety, food security, public health, and sustainable aquaculture practices, making it highly relevant in today's context.},
}
@article {pmid41395946,
year = {2026},
author = {Jansen, D and Bens, L and Wagemans, J and Green, SI and Hillary, T and Vanhoutvin, T and Van Laethem, A and Vermeire, S and Sabino, J and Lavigne, R and Matthijnssens, J},
title = {Hidradenitis suppurativa patients exhibit a distinctive and highly individualized skin virome.},
journal = {mSystems},
volume = {11},
number = {1},
pages = {e0129025},
pmid = {41395946},
issn = {2379-5077},
support = {1S78021N//Fonds Wetenschappelijk Onderzoek/ ; IDN/20/024//Internal funds KU Leuven/ ; },
mesh = {Humans ; *Virome/genetics ; *Skin/virology/microbiology ; Male ; Female ; Adult ; *Hidradenitis Suppurativa/virology/microbiology ; Middle Aged ; Microbiota ; Bacteriophages/genetics ; Metagenomics ; },
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disease characterized by recurring skin lesions. Despite ongoing research, the exact cause underlying initiation and progression of disease remains unknown. While prior research has linked the skin microbiota to HS pathology, the role of viruses has remained unexplored. To investigate the skin virome, metagenomic sequencing of viral particles was performed on 144 skin samples from 57 individuals (39 HS patients and 18 controls). It was found that the virome is not only linked to BMI, but also to the presence and severity of HS, marking a diverging viral profile in the progression of disease. Despite no differences in alpha-diversity, HS patients exhibited a significantly higher beta-diversity compared to healthy controls, indicating a more personalized virome with reduced viral sharing among patients. We identified distinct groups of commonly shared phages, referred to as the core phageome, associated with either healthy controls or patients. Healthy controls displayed a higher abundance of two core Caudoviricetes phages predicted to infect Corynebacterium and Staphylococcus, comprising normal skin commensals. In contrast, HS patients carried previously uncharacterized phages that were more prevalent in advanced stages of the disease, which likely infect Peptoniphilus and Finegoldia, known HS-associated pathogens. Interestingly, genes involved in superinfection exclusion and antibiotic resistance could be found in phage genomes of healthy controls and HS patients, respectively. In conclusion, we report the existence of distinct core phages that may have clinical relevance in HS pathology by influencing skin bacteria through mechanisms such as superinfection exclusion and antibiotic resistance.IMPORTANCEAn increasing body of research showed that the microbiome has an important role in complex human disease. In line with this, here, we analyzed a longitudinal HS cohort and found a relationship between the skin virome and HS pathology. This relationship was defined by distinct groups of phages associated with either healthy controls or HS patients, yet, in both instances, capable of enhancing bacterial fitness. In healthy individuals, these phages were widely shared, fostering symbiosis by ensuring stability of the commensal skin microbiota. Conversely, in HS patients, these phages revealed a more individualistic nature and could contribute to dysbiosis by providing antibiotic resistance genes to bacterial pathogens. Overall, these findings point to a potential clinical significance of the virome in understanding and addressing HS pathology.},
}
@article {pmid41395693,
year = {2026},
author = {Stone, J and Tripyla, A and Scalise, MC and Balmer, ML and Bally, L and Meinel, DM},
title = {Taxonomic and functional shifts in the microbiome of severely obese, prediabetic patients: Ketogenic diet versus energy-matched standard diet.},
journal = {Diabetes, obesity &amp; metabolism},
volume = {28},
number = {3},
pages = {1826-1835},
pmid = {41395693},
issn = {1463-1326},
support = {PCEFP3_194618/1//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; PCEGP3_186978//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; //Stiftung FHNW/ ; //Nestl&#xe9; Health Science/ ; //Pierre Mercier Foundation/ ; },
mesh = {Humans ; *Diet, Ketogenic ; *Gastrointestinal Microbiome/physiology ; *Prediabetic State/microbiology/diet therapy/complications ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; Diabetes Mellitus, Type 2/microbiology/diet therapy ; *Obesity, Morbid/microbiology/diet therapy/complications ; *Obesity/microbiology/diet therapy ; Caloric Restriction ; },
abstract = {AIMS: Obesity and type 2 diabetes mellitus (T2DM) are among the leading global health challenges of the 21st century. While caloric restriction remains the cornerstone of weight loss interventions, ketogenic diets (KD), characterised by low carbohydrate and high fat intake, have been shown to improve metabolic health partly by modulating the gut microbiome. This study investigated the effects of a short-term KD on gut microbiome composition and function in severely obese, prediabetic patients, compared to an energy-matched standard diet (SD).<br><br>METHODS: In a randomised trial, patients with BMI >35&#x2009;kg/m[2] and prediabetes underwent either a 2-week KD or isocaloric SD, both inducing a 30% energy deficit. Faecal samples collected before and after the intervention, alongside samples from healthy controls, were analysed by whole-genome metagenomic sequencing.<br><br>RESULTS: At baseline, prediabetic patients exhibited greater interindividual variability and lower alpha diversity than healthy controls. KD resulted in a significant reduction of alpha diversity, largely driven by a selective loss of Lachnospiraceae, with a concomitant increase in Bacteroidaceae. Functional profiling revealed that KD, but not SD, altered genes coding for enzymes involved in energy metabolism, amino acid synthesis, nucleic acid activity, RNA modification, and vitamin biosynthesis. Additionally, serum acetate levels increased significantly following KD.<br><br>CONCLUSIONS: These findings underscore that KD, independent of caloric intake, acutely remodels the gut microbiome's taxonomic and functional landscape, highlighting the microbiome as a potential mediator of KD's metabolic effects.},
}
@article {pmid41394107,
year = {2025},
author = {Yang, Y and Jia, XF and Cui, GH and Huang, QY and Lin, MM and Shi, ZM and Ye, H and Zhang, XZ},
title = {Jinghuaweikang capsule alleviates Helicobacter pylori-infected gastric mucosal inflammation and drug resistance by regulating intestinal microbiota and MAPK pathway.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1628594},
pmid = {41394107},
issn = {2235-2988},
mesh = {Animals ; *Helicobacter Infections/drug therapy/microbiology/pathology ; *Helicobacter pylori/drug effects ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/administration &amp; dosage/pharmacology ; Disease Models, Animal ; *Gastric Mucosa/pathology/drug effects/microbiology ; *MAP Kinase Signaling System/drug effects ; *Drug Resistance, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; Male ; Inflammation/drug therapy ; *Gastritis/drug therapy/microbiology ; Capsules ; },
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection represents a prevalent global health burden. Current eradication strategies are complicated by increasing antibiotic resistance and detrimental alterations to the gut microbiome. Jinghuaweikang capsule (JWC), a traditional Chinese medicine, has demonstrated efficacy against H. pylori, yet its mechanisms involving microbiota-inflammation interactions remain incompletely elucidated.<br><br>AIM: This study aimed to investigate the effects of the JWC on gastric mucosal&#xa0;inflammation and the expression of drug-resistance genes in H.&#xa0;pylori-infected mice.<br><br>METHODS: Sixty Kunming mice were randomly allocated into six groups, including normal control group (Control), model group (Model), Western medicine triple group (AC), low-dose JWC group (JWCL), medium-dose JWC group (JWCM), and high-dose JWC group (JWCH). A mouse model of H. pylori infection was established by intragastric administration of an H. pylori SS1 solution for two weeks. The efficacy of this model was evaluated using rapid urease test (RUT) and Warthin-Starry (WS) silver stain. Subsequently, the experimental cohort of mice underwent pharmacological intervention. Hematoxylin and eosin (HE) staining, enzyme-linked immunosorbent assay (ELISA), and quantitative real-time polymerase chain reaction (qRT-PCR) were used to assess the impact of JWC on inflammation within the gastric mucosa of mice infected with H. pylori. Metagenomic sequencing technology was used to identify alterations in the intestinal microbiota and antibiotic resistance genes in the murine models. Western blotting was used to assess the expression levels of proteins involved in the mitogen-activated protein kinase (MAPK) signaling pathway.<br><br>RESULTS: JWC mitigated gastric mucosal inflammation induced by H. pylori infection and reduced the concentrations of interleukin- (IL-) 6, IL-1&#x3b2;, and tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) while inhibiting gene expression level. Metagenomic sequencing revealed that triple therapy in Western medicine markedly diminished the diversity of the intestinal microbiota while elevating the abundance of antibiotic-resistance genes, including macB, arlR, evgS, tetA(58), and mtrA. The diversity and richness of the intestinal microbiota in the JWC group were comparable to those in the control group, with an increase in the abundance of beneficial bacteria such as Muribaculaceae_bacterium. Furthermore, the expression levels of the antibiotic resistance genes macB, tetA(58), bcrA, oleC, and arlS were downregulated. Moreover, the activation of MAPK signaling pathway components phospho-ERK and phospho-p38 was inhibited.<br><br>CONCLUSION: JWC preserves microbial diversity and promotes a beneficial compositional shift, mitigates the risk of antibiotic resistance, modulates the MAPK signaling pathway, and alleviates gastric mucosal inflammation in mice infected with H. pylori.},
}
@article {pmid41392764,
year = {2026},
author = {Wu, Q and Gao, G and Kwok, LY and Qiao, J and Wei, Z and He, Q and Sun, Z},
title = {Bifidobacterium animalis subsp. lactis Bbm-19 ameliorates insomnia by remodeling the gut microbiota and restoring γ-aminobutyric acid and serotonin signaling.},
journal = {Food &amp; function},
volume = {17},
number = {1},
pages = {475-493},
doi = {10.1039/d5fo04374c},
pmid = {41392764},
issn = {2042-650X},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Serotonin/metabolism ; Mice ; *gamma-Aminobutyric Acid/metabolism ; *Sleep Initiation and Maintenance Disorders/metabolism/microbiology/chemically induced ; Male ; *Probiotics ; *Bifidobacterium animalis/physiology ; Humans ; Signal Transduction ; Mice, Inbred C57BL ; Disease Models, Animal ; },
abstract = {Insomnia is associated with dysregulation of the gut-brain axis, yet microbiome-targeted interventions remain underexplored. In this study, we investigated the effects of Bifidobacterium animalis subsp. lactis Bbm-19 (Bbm-19), a strain isolated from human breast milk, in a 4-chloro-DL-phenylalanine-induced mouse model of insomnia. Using integrated behavioral, neurochemical, immunological, and multi-omics approaches, this study demonstrates that insomnia is characterized by shortened sleep duration, prolonged sleep latency, anxiety-like behaviors, and reduced levels of serotonin and gamma-aminobutyric acid in the gut, serum, and brain. Administration of Bbm-19 significantly improved sleep parameters, reduced anxiety-like behaviors, and increased survival. Metagenomic and metabolomic analyses revealed that Bbm-19 restored gut microbiota balance, enriched beneficial taxa, including Muribaculaceae bacterium and Stercoribacter sp., and reprogrammed microbial metabolic modules, particularly those involved in amino acid metabolism (including alanine, aspartate, glutamate, arginine, proline, and tryptophan pathways). Targeted metabolomics confirmed increased levels of gamma-aminobutyric acid and serotonin in fecal and brain tissues, along with normalization of inflammatory cytokine profiles. Spearman correlation analysis linked Bbm-19-enriched taxa to improved neurotransmitter levels and sleep outcomes. Notably, Bbm-19 outperformed lorazepam in modulating gut-specific metabolic functions and synergistically enhanced its effects when co-administered. These findings demonstrate that Bbm-19 ameliorates insomnia through coordinated regulation of the gut microbiota, host metabolism, and neuroimmune signaling, highlighting its potential as a targeted psychobiotic intervention for sleep disorders.},
}
@article {pmid41392335,
year = {2025},
author = {Zheng, X and Luo, X and Zhang, Y and Zou, Z and Yang, J and Liu, H and Lu, Z and Cao, F and Wang, X and Ge, X and Li, X and Wang, J},
title = {Inflammation in Diabetic Kidney Disease Is Linked to Gut Dysbiosis and Metabolite Imbalance.},
journal = {Journal of diabetes},
volume = {17},
number = {12},
pages = {e70175},
pmid = {41392335},
issn = {1753-0407},
support = {XHZDZK019//Mianyang Central Hospital/ ; 2020FH09//Mianyang Central Hospital/ ; 2022HYX005//Mianyang Central Hospital/ ; 2023YFS0470//Science and Technology Department of Sichuan Province/ ; 2023ZYDF073//Mianyang Science and Technology Bureau/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism/immunology ; *Diabetic Nephropathies/microbiology/metabolism/immunology ; Male ; Middle Aged ; Female ; *Inflammation/metabolism/microbiology ; Cytokines/blood ; Case-Control Studies ; Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Diabetic kidney disease (DKD) is characterized by a sustained pro-inflammatory response of the immune system, which leads to renal failure progression and related complications. Emerging evidence suggests that gut microbiota dysregulation may be a pathogenic mediator in DKD, while mechanisms remain unclear. This study aimed to identify differences in the gut microbiota of the DKD group and healthy controls (HC).<br><br>METHODS: Gut microbiota composition was determined using shotgun metagenomic sequencing on fecal samples; serum cytokines were measured via ELISA, immune phenotypes were detected using flow cytometry.<br><br>RESULTS: Significant differences in gut microbiota diversity and richness were observed between patients with DKD and HC, with higher abundances of Enterobacteriaceae, Serratia, and Shigella in the DKD group than in the HC group. Additionally, CD3+ (especially CD4+) T cells were significantly higher in the renal tissue of the DKD group than the HC group. Flow cytometry identified significantly higher circulating levels of NKT cells and CD8+ T cells and lymphocyte ratio in HC than in DKD. CD4+ cells, CD4+ TCM cells, CD8+ TCM cells, and the CD4+/CD8+ cell ratio were significantly higher in the DKD group than in the HC group, as were levels of pro-inflammatory mediators, including IL-6, TNF-&#x3b1;, and sCD14, and expression of the gut barrier dysfunction marker ZO-1.<br><br>CONCLUSIONS: Gut barrier dysfunction and gut microbiota imbalance may mediate the pro-inflammatory immune phenotype observed in patients with DKD and thereby contribute to DKD progression. These findings underscore the important role of the microbiota-immune axis in the development of DKD.},
}
@article {pmid41392116,
year = {2025},
author = {Li, C and Jiang, P and Fan, C and Chen, J and Liang, S and Chen, S and Mi, H},
title = {Characteristics of gut microbiota and metabolites in rats with ketamine-induced cystitis.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1801},
pmid = {41392116},
issn = {2045-2322},
support = {81860142//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Ketamine/adverse effects ; *Cystitis/chemically induced/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; Rats ; Metabolomics/methods ; Male ; Rats, Sprague-Dawley ; Urinary Bladder/metabolism ; *Metabolome ; Disease Models, Animal ; Bacteria/genetics/classification ; },
abstract = {Ketamine-induced cystitis (KC) manifests as lower urinary tract symptoms stemming from prolonged ketamine abuse, yet its precise pathogenesis remains unclear. It is widely recognized that gut microbiota dysregulation can trigger metabolic aberrations in many diseases. This study aimed to address the dearth of knowledge regarding the functional characteristics of gut microbiota and their metabolites in KC, and to explore the underlying mechanisms of KC from the perspective of the gut-bladder axis. Metagenomic and untargeted metabolomic analyses were employed to elucidate critical features of gut microbiota and metabolism in KC rats. Metagenomic sequencing revealed significant gut microbiota dysregulation, characterized by discrepancies in 46 bacterial taxa at the species level, including Bifidobacterium pseudolongum, Erysipelotrichaceae bacterium OPF54, Firmicutes bacterium CAG: 424, and Phocaeicola sartorii. Untargeted metabolomics identified 13 dysregulated metabolites, encompassing Stachydrine, Quinoline, Sedanolide, and others. Correlation analyses among differential gut microbiota, metabolites, and bladder inflammatory factors in KC rats suggested a potential interconnectivity between these factors. Furthermore, the anti-inflammatory property of Stachydrine was experimentally validated using an in vitro model. These findings collectively indicate that KC rats exhibit alterations in gut microbiota composition and metabolites profiles, establishing a preliminary association among gut microbiota, metabolites, and KC pathogenesis. Finally, validation of the anti-inflammatory effects of Stachydrine provides insight into a potential pathogenic pathway involving gut-bladder axis crosstalk, in which dysregulation of gut microbiota and metabolites contributes to the development of KC.},
}
@article {pmid41391639,
year = {2026},
author = {Yuan, F and Wang, L and Nguyen, SM and Shu, XO and Shrubsole, MJ and Wen, W and Cai, Q and Yu, D and Zheng, W},
title = {Plant-based diets, gut microbiota, blood metabolome, and risk of colorectal, liver, and pancreatic cancers: results from a large prospective cohort study of predominantly low-income Americans.},
journal = {The American journal of clinical nutrition},
volume = {123},
number = {2},
pages = {101135},
pmid = {41391639},
issn = {1938-3207},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; Middle Aged ; *Pancreatic Neoplasms/epidemiology/blood ; *Diet, Vegetarian ; Prospective Studies ; *Colorectal Neoplasms/epidemiology/blood ; *Liver Neoplasms/epidemiology/blood ; *Metabolome ; Aged ; Adult ; Risk Factors ; Cohort Studies ; Diet, Plant-Based ; },
abstract = {BACKGROUND: Plant-based diets have been advertised for environmental and health benefits. Their effects on cancer risk, gut microbial, and blood metabolomic profiles remain unclear.<br><br>OBJECTIVES: We investigated plant-based diets in relation to cancer incidence as well as gut microbial composition and blood metabolites in the Southern Community Cohort Study.<br><br>METHODS: Included in the analysis were 71,533 participants. Habitual dietary intake assessed at baseline (2002-2009) was used to derive the overall plant-based diet index (PDI), healthy plant-based diet index (hPDI), and unhealthy plant-based diet index (uPDI). Incident cancer cases were ascertained via linkage to state cancer registries and the National Death Index. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated from Cox proportional hazards models after adjusting for potential confounders. We examined associations of the 3 indices with gut microbiota and blood metabolites using fecal metagenomic and blood metabolomic data from 2 subsets of 417 and 1581 participants, respectively.<br><br>RESULTS: During a median follow-up time of 11.6 y, 783, 316, and 295 incident colorectal, liver, and pancreatic cancer cases were identified. High hPDI was related to a lower liver cancer risk (HR: 0.67, 95% CI: 0.45, 0.99 comparing extreme quartiles, P-trend = 0.03). No apparent association was observed for colorectal cancer (CRC) in the whole cohort. However, among 49,132 CRC screening-na&#xef;ve participants at baseline, PDI was inversely associated (HR: 0.74, 95% CI: 0.58, 0.96, P-trend = 0.01), whereas uPDI was positively associated (HR: 1.39, 95% CI: 1.06, 1.82, P-trend = 0.02) with CRC risk. No index was associated with pancreatic cancer. These diet indices were associated with microbial taxa and blood metabolites that have been implicated in the tumorigenesis of the colorectum and liver.<br><br>CONCLUSIONS: A diet high in healthy plant foods and low in animal foods was inversely associated with liver cancer risk and with CRC risk among screening-na&#xef;ve participants. These associations may be partly mediated through gut microbiota and systemic metabolism.},
}
@article {pmid41391314,
year = {2026},
author = {Yuan, X and Gao, N and Ma, J and Qian, W and Yang, L and Zhu, L and Feng, J},
title = {Warming alters temporal patterns of microbial-mediated nitrogen cycling under microplastics stress in intertidal sediment ecosystems.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140802},
doi = {10.1016/j.jhazmat.2025.140802},
pmid = {41391314},
issn = {1873-3336},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Nitrogen Cycle ; *Microplastics/toxicity ; Ecosystem ; *Water Pollutants, Chemical/toxicity ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Bacteria/genetics/metabolism ; Nitrogen/metabolism ; Polyethylene ; },
abstract = {Intertidal sediments-hotspots of coastal nitrogen cycling-are preferential sinks for microplastics (MPs) influenced by terrestrial and marine inputs. How warming alters sedimentary microbial nitrogen-cycling functions under MPs stress remains unclear. We incubated sediment microcosms with polyethylene (PE) MPs (0, 0.3, 2.0 % w/w) at 25℃ and 30℃ for 31 days. Microbial community dynamics were tracked by 16S rRNA and metagenomics. While α-diversity was largely unaffected, PE-MPs (especially at 2.0 %) markedly altered microbial community composition from day 16 onward at both temperatures, especially at 2.0 %. At 25℃, the 2.0 % PE-MPs increased microbial interactions and network complexity, with interactions shifting from competition toward cooperation over time. Warming further intensified early competitive interactions in 2.0 % PE-MPs group, driving compositional shifts. Functionally, PE-MPs at 2.0 % modulated the expression of dissimilatory nitrate reduction (DNRA) reductases (nrfA and nrfH), attenuating the increase in sediment NH4[+] over time. Concurrently, upregulation of assimilatory nitrate pathway genes lowered NO3[-]. Expression of nitrification and DNRA genes was generally enhanced at 2.0 % MPs, accompanied by downregulation of glnA (NH4[+] assimilation) and nasB (assimilatory nitrate reduction). Thereby, warming at 30℃ reshaped MPs-driven community dynamics and nitrogen-cycling pathways, slowing the time-dependent declines of NH4[+] and NO3[-] relative to 25℃ and reducing the risk of nitrogen loss from intertidal sediments. These findings highlight the need to incorporate temperature and temporal dynamics into ecological risk assessments of MPs under global climate change.},
}
@article {pmid41391220,
year = {2026},
author = {Xu, QY and Habib, T and Gao, L and Wu, D and Li, XY and Khieu, TN and Chen, YH and Zhang, Y and Liu, YH and She, TT and Fang, BZ and Li, WJ},
title = {Wenzhouxiangella psychrophila sp. nov., Wenzhouxiangella indolica sp. nov., and Halotectona sediminis gen. nov., sp.nov., three novel taxa with ability of IAA production from saline lake sediment.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126683},
doi = {10.1016/j.syapm.2025.126683},
pmid = {41391220},
issn = {1618-0984},
mesh = {*Phylogeny ; *Lakes/microbiology ; *Indoleacetic Acids/metabolism ; RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; China ; Sodium Chloride/metabolism ; },
abstract = {Indoleacetic acid synthesis (IAA), a crucial plant hormone, can be produced by many microorganisms through different metabolic pathways. While much research has focused on rhizosphere microorganisms, studies on IAA production functional strains in extreme environments are limited. In this study, two IAA-producing strains of the genus Wenzhouxiangella are isolated from saline lake sediment of Xinjiang, designated strains EGI_FJ10305[T] and EGI_FJ10409[T], which show low 16S rRNA gene sequence identities to other validly published Wenzhouxiangella species (< 98.65 %). A series of phylogenetic analysis concludes that two isolated strains represent two novel species within the genus Wenzhouxiangella. Two halotolerant strains are grown at 0-10.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10305[T]) and 0-8.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10409[T]), respectively. Result of functional test confirms that both isolated strains possess the capability to synthesize indole-3-acetic acid (IAA) with substrate tryptophan. Genomic analysis suggests that this capability likely operates through the tryptamine pathway (TAM) and has been inherited from their ancestors rather than acquired through horizontal gene transfer. The proposed names of strains EGI_FJ10305[T] and EGI_FJ10409[T] are Wenzhouxiangella psychrophile sp. nov. and Wenzhouxiangella indolica sp. nov., respectively. Concurrently, metagenomic analysis of the same samples yielded three high-quality MAGs. Phylogenetic analysis subsequently indicated that these three MAGs potentially represent a new genus within the family Wenzhouxiangellaceae, for which we propose the name Halotectona sediminis gen. Nov. sp. nov., in accordance with the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode).},
}
@article {pmid41390780,
year = {2025},
author = {Bommana, S and Olagoke, O and Hu, YJ and Wang, R and Kama, M and Dehdashti, M and Kodimerla, R and Read, TD and Dean, D},
title = {Azithromycin alters the microbiome composition, function and resistome in women with Chlamydia trachomatis infections.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {235},
pmid = {41390780},
issn = {2055-5008},
support = {R01 AI151075/AI/NIAID NIH HHS/United States ; },
mesh = {*Azithromycin/pharmacology/therapeutic use ; Female ; Humans ; *Chlamydia trachomatis/drug effects/genetics ; *Chlamydia Infections/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota/drug effects ; *Drug Resistance, Bacterial ; Vagina/microbiology ; Metagenomics ; Adult ; Gardnerella vaginalis/drug effects/genetics/isolation &amp; purification ; Cervix Uteri/microbiology ; Rectum/microbiology ; Biofilms/drug effects/growth &amp; development ; Lactobacillus/drug effects/genetics ; },
abstract = {Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes infected with Chlamydia trachomatis (Ct) remain poorly understood. Some data exist on vaginal microbiomes, but none exist for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples collected longitudinally from women who cleared their infection post-treatment (n = 10), had persistent infection (n = 11), or remained uninfected (n = 18) to evaluate azithromycin-induced changes in microbial composition, function, and the resistome over time. Our results show shifts in composition and function post-treatment that support persistent Ct, nonsynonymous Ct L22 amino acid substitutions that may be linked to azithromycin resistance, and significant endocervical increases in azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis strains with moderate/high biofilm formation potential. These findings highlight the unintended ecological consequences of azithromycin treatment, including likely resistance gene propagation, emphasizing the need for novel treatment and microbiome-preserving strategies.},
}
@article {pmid41390665,
year = {2025},
author = {Cotto, I and Albán, V and Durán-Viseras, A and Jesser, KJ and Zhou, NA and Hemlock, C and Ballard, AM and Fagnant-Sperati, CS and Lee, GO and Hatt, JK and Royer, CJ and Eisenberg, JNS and Trueba, G and Konstantinidis, KT and Levy, K and Fuhrmeister, ER and , },
title = {Environmental exposures associated with the gut microbiome and resistome of pregnant women and children in Northwest Ecuador.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {15},
pmid = {41390665},
issn = {2041-1723},
support = {2127509//American Society for Engineering Education (ASEE)/ ; P30 ES007033/ES/NIEHS NIH HHS/United States ; R01 AI137679/AI/NIAID NIH HHS/United States ; R01 AI162867/AI/NIAID NIH HHS/United States ; R01AI162867//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; },
mesh = {Humans ; Female ; Ecuador ; *Gastrointestinal Microbiome/genetics/drug effects ; Pregnancy ; Child ; Adult ; Child, Preschool ; Infant ; *Environmental Exposure/adverse effects ; Klebsiella pneumoniae/genetics/isolation &amp; purification/drug effects ; Escherichia coli/genetics/isolation &amp; purification/drug effects ; *Drug Resistance, Bacterial/genetics ; Animals ; Anti-Bacterial Agents/pharmacology ; Young Adult ; Male ; Hygiene ; Adolescent ; Sanitation ; Feces/microbiology ; Bacteria/genetics/classification/drug effects ; },
abstract = {Inadequate water, sanitation, and hygiene (WASH) infrastructure may increase exposure to antimicrobial resistance (AMR). In addition, close human-animal interactions and unregulated antibiotic use in livestock facilitate the spread of resistant bacteria. We use metagenomic sequence data and multivariate models to assess how animal exposure and WASH conditions affect the gut resistome and microbiome in 53 pregnant women and 84 children in Ecuador. Here we show improving WASH infrastructure and managing animal exposure may be important in reducing AMR but could also reduce taxonomic diversity in the gut. Escherichia coli, Klebsiella pneumoniae, and clinically relevant antimicrobial resistance genes (ARGs) are detected across all age groups, but the highest abundance is found in children compared to mothers. In mothers, higher animal exposure trends towards a higher number of unique ARGs compared to low animal exposure and is significantly associated with greater taxonomic diversity. In addition, mothers with sewer systems or septic tanks and piped drinking water have fewer unique ARGs compared to those without, and mothers with longer duration of drinking water access have lower total ARG abundance. In contrast, few associations are observed in children, likely due to the dynamic nature of the gut microbiome during early childhood.},
}
@article {pmid41390498,
year = {2025},
author = {Freel, KC and Tucker, SJ and Freel, EB and Stingl, U and Giovannoni, SJ and Eren, AM and Rappé, MS},
title = {New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {328},
pmid = {41390498},
issn = {2041-1723},
mesh = {*Genome, Bacterial/genetics ; *Seawater/microbiology ; Phylogeny ; *Metagenome/genetics ; Pacific Ocean ; *Alphaproteobacteria/genetics/classification/isolation &amp; purification ; },
abstract = {The bacterial order Pelagibacterales (SAR11) is widely distributed across the global surface ocean, where its activities are integral to the marine carbon cycle. High-quality genomes from isolates that can be propagated and phenotyped are needed to unify perspectives on the ecology and evolution of this complex group. Here, we increase the number of complete SAR11 isolate genomes threefold by describing 81 new SAR11 strains from coastal and offshore surface seawater of the tropical Pacific Ocean. Our analyses of the genomes and their spatiotemporal distributions support the existence of 29 monophyletic, discrete Pelagibacterales ecotypes that we define as genera. The spatiotemporal distributions of genomes within genera were correlated at fine scales with variation in ecologically-relevant gene content, supporting generic assignments and providing indications of speciation. We provide a hierarchical system of classification for SAR11 populations that is meaningfully correlated with evolution and ecology, providing a valid and utilitarian systematic nomenclature for this clade.},
}
@article {pmid41390384,
year = {2025},
author = {Shetty, P and Bhat, R and Padavu, S and Rai, P and B, KK and Shetty, S},
title = {Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {118},
pmid = {41390384},
issn = {1472-6831},
support = {N(DU)/RD/NUFR 1Grant/ABSMIDS/2021-22/01-1//NITTE University/ ; },
mesh = {Humans ; *Pulpitis/microbiology ; Adult ; *Metagenomics ; Adolescent ; Young Adult ; *High-Throughput Nucleotide Sequencing ; Male ; *Microbiota/genetics ; Chronic Disease ; Female ; *Dental Pulp/microbiology ; },
abstract = {BACKGROUND: Contemporary molecular analytical methodologies have yielded insufficient characterization of the microbial etiology underlying chronic irreversible pulpitis; a pathological condition characterized by irreversible inflammatory alterations of the dental pulp complex necessitating endodontic intervention. This investigation employed shotgun metagenomic sequencing to comprehensively elucidate the microbiome present in affected pulpal tissues, thereby augmenting our understanding of pulpal pathogenesis.<br><br>METHODS: The investigation incorporated six subjects (age range 18-35 years) presenting with clinically diagnosed chronic irreversible pulpitis according to the American Association of Endodontists diagnostic criteria. Pulpal tissue specimens were procured under rubber dam isolation utilizing stringent aseptic protocols following coronal access preparation. Genomic DNA extraction was performed via QIAamp DNA Mini Kit methodology followed by high-throughput sequencing on the Illumina Hiseq platform. Subsequent bioinformatic analysis implemented the WGSA2 pipeline for taxonomic classification, generating approximately 79.906&#xa0;million paired-end reads per specimen.<br><br>RESULTS: Metagenomic analysis of the pulpal microbiome revealed taxonomic predominance of Bacteroidetes (45.095%), Firmicutes (17.424%), Proteobacteria (12.731%), and Actinobacteria (9.071%) at the phylum level. Notably, the investigation identified previously undocumented phyla in pulpal infections, including Euryarchaeota, Thermoproteobacteria, Uroviricota,and Apicomplexa. Propionibacterium acidifaciens emerged as the most consistently detected and ecologically significant species, whereas the conventionally recognized odontopathogen Streptococcus mutans exhibited negligible presence. Shannon diversity indices and taxonomic richness parameters demonstrated substantial inter-subject variability, with species abundance ranging from 574 to 5,468 distinct taxonomic units per pulp sample.<br><br>CONCLUSION: This investigation elucidated unprecedented microbial diversity within chronic irreversible pulpitis, fundamentally challenging established understanding of endodontic pathogenesis and clinical therapeutic approaches. The substantial inter-subject taxonomic heterogeneity observed herein suggests that contemporary standardized therapeutic regimens may be insufficiently targeted to address the complex polymicrobial ecosystem characteristic of pulpal pathosis. The identification of archaeal and viral constituents provides mechanistic insight into persistent endodontic infections despite technically adequate treatment modalities. These findings establish a comprehensive basis for evidence-based precision endodontics, facilitating the development of patient-specific antimicrobial strategies and novel therapeutic interventions targeting previously unrecognized microbial components. The comprehensive characterization of pulpal microbiome diversity represents a significant advancement toward molecularly informed clinical decision-making, with profound implications for treatment outcome optimization and the mitigation of therapeutic failures in contemporary endodontic practice.},
}
@article {pmid41389890,
year = {2026},
author = {Xu, D and Zhang, W and Tao, XR and Gao, K and Zhao, MN and Wang, JW},
title = {Shenqi funeng xingnao prescription regulated the TNF/NOD‒like receptor signaling pathway and brain-gut axis dysfunction caused by exercise-induced fatigue.},
journal = {Journal of ethnopharmacology},
volume = {358},
number = {},
pages = {121035},
doi = {10.1016/j.jep.2025.121035},
pmid = {41389890},
issn = {1872-7573},
mesh = {Animals ; *Fatigue/drug therapy/metabolism/etiology ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Signal Transduction/drug effects ; Male ; Mice ; Physical Conditioning, Animal ; Gastrointestinal Microbiome/drug effects ; Hippocampus/drug effects/metabolism/pathology ; Mice, Inbred C57BL ; Brain/drug effects/metabolism ; *Brain-Gut Axis/drug effects ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {BACKGROUND: Central fatigue is a phenomenon in which changes in the function of the central nervous system lead to decreased athletic ability and increased fatigue symptoms. Shenqi Funeng Xingnao Prescription (SQFNXNP) is a traditional Chinese medicine prescription applied to alleviate exercise-induced fatigue; however, the molecular mechanism underlying its effects on central fatigue remain elusive.<br><br>PURPOSE: This study explored the therapeutic effects and potential molecular mechanisms of SQFNXNP on central fatigue.<br><br>METHODS: A chronic fatigue model was constructed to evaluate the therapeutic effects of SQFNXNP at alleviating central fatigue, including pathological changes in the hippocampus and intestine, as well as abnormal levels of neurotransmitters and inflammation. Transcriptomic analysis revealed core gene targets, which were further validated using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Furthermore, metagenomics was applied to explore changes in gut microbial composition and associated signaling pathways. Further validation of key proteins was conducted using western blotting (WB). Correlation analysis was further applied to identify differentially abundant metabolites related to the core targets. Compounds with prototype structures in the brain tissue after SQFNXNP administration were identified by ultra-high performance liquid chromatography-mass spectrometry analysis. A virtual screening procedure was used to screen for potential ingredients of SQFNXNP that could alleviate central fatigue.<br><br>RESULTS: SQFNXNP alleviated exercise-induced histopathological damage and mitochondrial injury in the hippocampi of mice, decreased cell apoptosis and necrosis, increased cell proliferation, and restored abnormal levels of monoamine neurotransmitters. Moreover, SQFNXNP treatment decreased inflammatory levels in the body, alleviated histopathological damage to the intestine, reduced cell apoptosis in the intestine, increased the expression of key intestinal barrier proteins, restored the goblet cell density and mucus layer integrity in the intestine, and regulated the imbalance in the gut microbiota and central fatigue-related signaling pathways. RT-qPCR and WB further revealed that SQFNXNP regulated the TNF and NOD-like receptor (NLR) signaling pathways by targeting MMP9, PTGS2 (COX-2), MAPK14, BCL2, TLR4, TNF-&#x3b1;, IL1B, P-AKT1, NIKBIA, and IL6 proteins. The virtual screening procedure revealed that the potential components of SQFNXNP for alleviating central fatigue were oleanolic acid and ginsenoside re.<br><br>CONCLUSION: SQFNXNP regulated the TNF/NLR signaling pathway and brain-gut axis dysfunction caused by exercise-induced fatigue, thus providing a traditional Chinese medicine strategy for treating central fatigue in the clinic.},
}
@article {pmid41389850,
year = {2026},
author = {Petrov, VA and Schade, S and Laczny, CC and Hällqvist, J and May, P and Jäger, C and Aho, VTE and Hickl, O and Halder, R and Lang, E and Caussin, J and Lebrun, LA and Schulz, J and Unger, MM and Mills, K and Mollenhauer, B and Wilmes, P},
title = {Resistant starch improves Parkinson's disease symptoms through restructuring of the gut microbiome and modulating inflammation.},
journal = {Brain, behavior, and immunity},
volume = {132},
number = {},
pages = {106217},
doi = {10.1016/j.bbi.2025.106217},
pmid = {41389850},
issn = {1090-2139},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/drug effects ; *Parkinson Disease/diet therapy/microbiology/metabolism ; Male ; Female ; Aged ; Middle Aged ; Inflammation/metabolism/diet therapy ; *Resistant Starch/administration &amp; dosage ; *Starch ; Quality of Life ; Dietary Fiber ; Fatty Acids, Volatile/metabolism ; },
abstract = {Alterations in the gut microbiome and a "leaky" gut are associated with Parkinson's disease (PD), which implies the prospect of rebalancing via dietary intervention. Here, we investigate the impact of a diet rich in resistant starch on the gut microbiome through a multi-omics approach. We conducted a randomized, controlled trial with short-term and long-term phases involving 74 PD patients of three groups: conventional diet, supplementation with resistant starch, and high-fibre diet. Our findings reveal associations between dietary patterns and changes in the gut microbiome's taxonomic composition, functional potential, metabolic activity, and host inflammatory proteome response. Resistant starch supplementation led to an increase in Faecalibacterium species and short-chain fatty acids alongside a reduction in opportunistic pathogens. Long-term supplementation also increased blood APOA4 and HSPA5 and reduced symptoms of PD. Our study highlights the potential of dietary interventions to modulate the gut microbiome and improve the quality of life for PD patients.},
}
@article {pmid41389554,
year = {2026},
author = {Yang, T and Zhan, Y and Sha, J and Zhao, J and Wang, C and Peng, T and Zhang, L},
title = {Integrative multi-omics elucidates the impact of microalgae on growth, quality, phytohormones, and rhizosphere microbiome of Angelica sinensis.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128418},
doi = {10.1016/j.micres.2025.128418},
pmid = {41389554},
issn = {1618-0623},
mesh = {*Rhizosphere ; *Angelica sinensis/microbiology/growth &amp; development/metabolism ; *Plant Growth Regulators/metabolism ; *Microbiota ; *Microalgae/metabolism/physiology ; Nitrogen/metabolism ; Soil Microbiology ; Coumaric Acids/metabolism ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Biomass ; Soil/chemistry ; Metagenomics ; Metabolomics ; Carbon/metabolism ; Chlorella vulgaris/metabolism ; Multiomics ; },
abstract = {Microalgae have recently been recognized as sustainable biofertilizers that improve soil fertility while enhancing crop performance. However, their roles in regulating medicinal plant growth and quality, as well as the underlying ecological mechanisms, remain poorly understood. In this study, we systematically assessed the effects of three representative microalgae-Anabaena cylindrica (AC), Phormidium tenue (PT), and Chlorella vulgaris (CV)-on the growth, quality, hormonal regulation, soil nutrient dynamics, and rhizosphere microbiome of Angelica sinensis. Field inoculation trials demonstrated that all three microalgae significantly promoted biomass accumulation and increased antioxidant capacity. AC and CV further enhanced the accumulation of ferulic acid and flavonoids, which are two key quality determinants. Microalgal inoculation significantly altered rhizosphere soil properties by increasing total organic carbon and alkali-hydrolyzable nitrogen, with AC uniquely elevating available phosphorus and iron. Metagenomic analysis revealed that AC and PT stimulated nitrification while suppressing denitrification, thereby reducing nitrogen loss and stabilizing the soil nitrogen pools. Distinct microbial taxa, including Rhodanobacter, Streptomyces, and Pseudomonas, were identified as the major contributors to carbon and nitrogen cycling. Hormone metabolomics showed that microalgal inoculation reprogrammed A. sinensis phytohormone profiles in a species-specific manner. Partial least squares path modeling suggested that AC and CV promote ferulic acid biosynthesis through distinct mechanisms, with AC associated with reduced investment in C-mineralization processes and CV associated with lower salicylic acid levels, whereas PT enhances biomass accumulation mainly by stimulating N-cycle processes. Collectively, this study provides integrated evidence linking microalgae-mediated nutrient cycling, rhizosphere microbiome shifts and hormonal regulation to enhanced quality formation in A. sinensis.},
}
@article {pmid41389146,
year = {2026},
author = {Vorobeva, M and iAkushev, A and Chen, CC and Orihara, M and Akbar, N and Colley, P and Sehanobish, E and Chung, CHY and Scott, A and O'Brien, E and Chang, CB and Kita, H and Voyich, J and Knoop, K and Jerschow, E},
title = {Impact of Sinus Surgery on Bacteriome Composition in Patients With Chronic Rhinosinusitis With Nasal Polyps.},
journal = {International forum of allergy &amp; rhinology},
volume = {16},
number = {1},
pages = {114-118},
doi = {10.1002/alr.70082},
pmid = {41389146},
issn = {2042-6984},
support = {R21AI171306 to E.J./TR/NCATS NIH HHS/United States ; CTSA 5KL2TR001071/TR/NCATS NIH HHS/United States ; /NH/NIH HHS/United States ; R21AI171306 to E.J./TR/NCATS NIH HHS/United States ; CTSA 5KL2TR001071/TR/NCATS NIH HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {Humans ; *Nasal Polyps/surgery/microbiology ; *Sinusitis/surgery/microbiology ; *Rhinitis/surgery/microbiology ; Chronic Disease ; *Paranasal Sinuses/surgery/microbiology ; Female ; Male ; Middle Aged ; Endoscopy ; Adult ; Staphylococcus aureus/isolation &amp; purification ; *Microbiota ; Aged ; Staphylococcal Infections/microbiology ; Rhinosinusitis ; },
abstract = {Staphylococcus aureus showed a significant increase in relative abundance in CRSwNP patients following endoscopic sinus surgery compared to pre-surgery samples. Other Staphylococcus species were found to correlate positively with S. aureus in patients with nasal polyps; among those, S. caprae correlated strongly while being the most represented in samples. Patients with recurrent nasal polyp growth exhibited a substantially greater postoperative increase in the relative abundance of S. aureus.},
}
@article {pmid41389008,
year = {2026},
author = {Pryor, JC and Hoedt, EC and Soh, WS and Fowler, S and Caban, S and Minahan, K and Sherwin, S and Nieva, C and McCarthy, H and Horvat, J and Hedley, KE and Duncanson, K and Burns, GL and Talley, NJ and Keely, S},
title = {Antibiotics alter duodenal immune populations upon gluten exposure in mice: implications for non-coeliac gluten sensitivity.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {330},
number = {2},
pages = {G137-G153},
doi = {10.1152/ajpgi.00159.2025},
pmid = {41389008},
issn = {1522-1547},
support = {2004860//DHAC | National Health and Medical Research Council (NHMRC)/ ; 2035319//DHAC | National Health and Medical Research Council (NHMRC)/ ; 1170893//DHAC | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {Animals ; *Glutens/immunology ; *Anti-Bacterial Agents/pharmacology ; *Duodenum/immunology/drug effects/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred BALB C ; Intestinal Mucosa/immunology/drug effects/microbiology ; Eosinophils/immunology/drug effects ; Male ; Feces/microbiology ; },
abstract = {A growing proportion of the non-celiac population experiences adverse symptoms to gluten. The pathogenesis of non-celiac gluten sensitivity (NCGS) is unclear, but elevated duodenal eosinophils and altered mucosa-associated microbiota (MAM) populations have been reported. Given the microbiome's role in gluten digestion and its susceptibility to antibiotics, we hypothesized that altering the microbiome with antibiotics would modify immune responses to gluten in mice. BALB/C mice consuming gluten-free chow received amoxicillin/clavulanate (5 mg/kg) or PBS-vehicle daily for 5 days. Mice were then treated with a 3-mg wheat-gluten suspension, or vehicle, on days 4 and 5 before euthanasia on day 7. Duodenal immune cells were analyzed by histology and flow cytometry, whereas the duodenal MAM and fecal microbiome were characterized via 16S rRNA and shotgun metagenomic sequencing, respectively. Antibiotic treatment followed by gluten reintroduction significantly reduced Staphylococcus in the duodenal MAM, enriched Bacteroides in feces, and resulted in altered microbial carbohydrate and lipid metabolism, compared with vehicle controls. Treatment with antibiotics and gluten also increased duodenal eosinophils, which positively correlated with the genus Blautia. Flow cytometry revealed that sequential antibiotic and gluten treatment resulted in a greater proportion of active eosinophils and epithelial γδ T-cells, compared with vehicle control mice. This study demonstrated that modulating the microbiome with antibiotics was sufficient to alter the immune response to gluten in mice, suggesting that the microbiome may determine the capacity for gluten to induce immune responses. These findings contribute valuable insights into possible microbial mechanisms underlying NCGS, such as altered gluten metabolism or production of immunomodulatory metabolites.NEW &amp; NOTEWORTHY A mouse model examined how microbial modulation affects immune responses to gluten. Antibiotic treatment followed by gluten reintroduction reduced duodenal Staphylococcus and altered microbial carbohydrate and lipid metabolism pathways in the fecal microbiome. Antibiotics and gluten treatment resulted in increased abundance and activation of duodenal eosinophils and elevated γδ T-cells in the duodenal epithelium. These findings highlight the role the microbiome plays in gluten-induced immune responses, providing insights into mechanisms behind non-celiac gluten sensitivity.},
}
@article {pmid41388903,
year = {2026},
author = {Wutkowska, M and Nweze, JA and Tláskal, V and Nweze, JE and Daebeler, A},
title = {Uncovering hidden phylo- and ecogenomic diversity of the widespread methanotrophic genus Methylobacter.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {2},
pages = {},
pmid = {41388903},
issn = {1574-6941},
support = {21-17322&#xa0;M//Czech Science Foundation/ ; },
mesh = {*Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Methane/metabolism ; Genome, Bacterial ; *Methylococcaceae/genetics/classification ; Geologic Sediments/microbiology ; Biodiversity ; Metagenome ; Ecosystem ; },
abstract = {The globally distributed genus Methylobacter plays a crucial role in mitigating methane emissions from diverse ecosystems, including freshwater and marine habitats, wetlands, soils, sediments, groundwater, and landfills. Despite their frequent presence and abundance in these systems, we still know little about the genomic adaptations that they exhibit. Here, we used a collection of 97 genomes and metagenome-assembled genomes to ecogenomically characterize the genus. Our analyses suggest that the genus Methylobacter may contain more species than previously thought, with >30 putative species clusters. Some species clusters shared >98.65% sequence identity of the full-length 16S rRNA gene, demonstrating the need for genome-resolved species delineation. The ecogenomic differences between Methylobacter spp. include various combinations of methane monooxygenases, multigene loci for alternative dissimilatory metabolisms related to hydrogen, sulfur cycling, and denitrification, as well as other lifestyle-associated functions. Additionally, we describe and tentatively name the two new Methylobacter species, which we recently cultured from sediment of a temperate eutrophic fishpond, as Methylobacter methanoversatilis, sp. nov. and Methylobacter spei, sp. nov. Overall, our study highlights previously unrecognized species diversity within the genus Methylobacter, their diverse metabolic potential, versatility, as well as the presence of distinct genomic adaptations for thriving in various environments.},
}
@article {pmid41388659,
year = {2025},
author = {Wallbank, JA and Kingsbury, JM and Pantos, O and Weaver, L and Smith, DA and Barbier, M and Theobald, B and Gambarini, V and Lear, G},
title = {Plastic Type and Condition Have Minimal Impact on Associated Marine Biofilm Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {12},
pages = {e70214},
pmid = {41388659},
issn = {1462-2920},
support = {C03X1802//Ministry of Business, Innovation and Employment/ ; },
mesh = {*Biofilms/drug effects/growth &amp; development ; *Seawater/microbiology ; *Plastics ; Fungi/genetics/classification/drug effects/isolation &amp; purification ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; RNA, Ribosomal, 16S/genetics ; *Microbiota/drug effects ; },
abstract = {The ecological impacts of plastics and their additives on marine microbiota remain unclear. We applied prokaryotic 16S rRNA gene and fungal ITS2 region amplicon sequencing, alongside shotgun metagenomic sequencing, to identify compositional and functional changes in microbial communities on marine plastic. Five common plastics, both non-aged and artificially aged, were submerged in Auckland Harbour, Aotearoa-New Zealand. Biofilms on linear low-density polyethylene (LLDPE), nylon-6 (PA), polyethylene terephthalate (PET), polylactic acid (PLA), oxo-biodegradable LLDPE (OXO) and glass were sampled over 12 months. The taxonomy and functional potential of biofilm communities differed from surrounding seawater communities and varied with biofilm age. Younger biofilms were more diverse, with Proteobacteria, unknown fungi and unclassified Metazoa dominating prokaryotic, fungal and eukaryotic communities, respectively. Taxa related to previously reported plastic-degraders were found in very low abundance across all substrates. Plastic type and UV-ageing did not significantly shape biofilm communities over a year. Although some genes differed in relative abundance due to UV-ageing, overall functional profiles remained consistent across plastics. Genes conferring reported plastic-degrading traits were present regardless of plastic type, UV-ageing and biofilm age. Nevertheless, nylon hydrolases were notably associated with PA, suggesting marine plastic impacts may be restricted to taxa or functions involved in its degradation.},
}
@article {pmid41388485,
year = {2026},
author = {Khan, MAS and Bishir, M and Huang, W and Chidambaram, SB and Chang, SL},
title = {Early upregulation of alpha-7 nicotinic acetylcholine receptor in limbic system correlates with gut dysbiosis in mice exposed to binge ethanol.},
journal = {Alcohol, clinical &amp; experimental research},
volume = {50},
number = {1},
pages = {e70210},
doi = {10.1111/acer.70210},
pmid = {41388485},
issn = {2993-7175},
support = {AA029925/AA/NIAAA NIH HHS/United States ; AA029925/AA/NIAAA NIH HHS/United States ; },
mesh = {Animals ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; *Ethanol/administration &amp; dosage ; *Up-Regulation/drug effects ; *Dysbiosis/metabolism/chemically induced ; *alpha7 Nicotinic Acetylcholine Receptor/metabolism/genetics/biosynthesis ; *Binge Drinking/metabolism ; *Limbic System/metabolism/drug effects ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Alcohol use disorder (AUD) causes neuroinflammation and disrupts the gut microbiome through bidirectional communication between the brain and gut. However, it remains unclear whether the brain or gut responds first to alcohol exposure. We hypothesized that brain regions respond to alcohol first, preceding changes in the gut microbiome.<br><br>METHODS: B6 mice were given ethanol (EtOH; 5&#x2009;g/kg/day, 42%v/v, i.g.) at various time points. Fecal samples were collected prior to the first EtOH injection (Day 0), at 24&#x2009;h following the first, second, and third injections (Day 1, Day 2, and Day 3, respectively), and at 96&#x2009;h after the third injection (Day 6). Brain regions, central amygdala (CeA), hypothalamus (Hyp), and nucleus accumbens (NAc) were isolated at 2 min, 12&#x2009;h, 24&#x2009;h, and 192&#x2009;h following the first and third doses of binge EtOH, respectively. mRNA or protein expression levels of TNF-&#x3b1;, IL-1&#x3b2;, P2Y12, ITG&#x3b2;2, and &#x3b1;7nAChR were analyzed by qRT-PCR and western blot, respectively. Fecal microbial composition and abundance were assessed using 16S rRNA metagenomic sequencing.<br><br>RESULTS: Data revealed increased TNF-&#x3b1; expression in the Amg, Hyp, and NAc and increased IL-1&#x3b2; expression in the Amg and NAc, 12&#x2009;h after the first EtOH injection. &#x3b1;7nAChR expression in the CeA, Hyp, and NAc was also upregulated at 24&#x2009;h after the third EtOH dose, compared to the control group. &#x3b1;7nAChR expression in the Hyp was observed at 2&#x2009;min after the first EtOH dose. CHRNA7 mRNA levels were upregulated 24&#x2009;h after the third EtOH dose. ITG&#x3b2;2 showed an increasing trend in the Amg at 12&#x2009;h after the first dose, followed by a significant reduction at 24&#x2009;h, and 192&#x2009;h after the third dose. 16S rRNA sequencing revealed a significant difference in &#x3b2;-diversity on Day 6. The relative abundance of the Prevotellaceae family was higher in EtOH-treated mice compared to controls at Day 3 and Day 6.<br><br>CONCLUSION: This study showed that brain inflammation, indicated by &#x3b1;7nAChR upregulation, occurred before EtOH-induced gut dysbiosis, supporting an anterograde sequence of events.},
}
@article {pmid41388438,
year = {2025},
author = {Chiriac, MC and Layoun, P and Fernandes, C and Szőke-Nagy, T and Kasalicky, V and Okazaki, Y and Woodhouse, JN and Grossart, HP and Piwosz, K and Znachor, P and Sonntag, B and Callieri, C and Orlić, S and Sommaruga, R and Lepère, C and Biderre-Petit, C and Tammert, H and Herlemann, DPR and Ślusarczyk, M and Bednarska, A and Banciu, HL and Zalewski, M and Woźniczka, A and Ghai, R and Salcher, MM and Haber, M},
title = {Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {27},
pmid = {41388438},
issn = {2049-2618},
support = {24-12912M//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 22-03662S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 22-33245S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 20-12496X//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 21-21990S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 017/2022/P//Grant Agency of the University of South Bohemia/ ; JPMJFR2273//JST FOREST/ ; 25K18161//Japan Society for the Promotion of Science/ ; GR1540/37-1//Leibniz-Institut f&#xfc;r Gew&#xe4;sser&#xf6;kologie und Binnenfischerei/ ; KK.01.1.1.01.0003//European Regional Development Fund - the Operational Programme Competitiveness/ ; HRZZ IP-2020-02-9021//Croatian Science Foundation/ ; 760010/30.12.2022//Ministerul Cercet&#x103;rii &#x15f;i Inov&#x103;rii/ ; },
mesh = {*Lakes/microbiology ; Phylogeny ; Genome, Bacterial ; RNA, Ribosomal, 16S/genetics ; Metagenome ; },
abstract = {BACKGROUND: The order Nanopelagicales is the most abundant bacterioplankton lineage in freshwater lakes and exhibits typical streamlined genomic characteristics such as small cell volumes (<0.1 μm[3]), reduced genome sizes (<1.5 Mbp), and low GC content. These characteristics reflect adaptations to a free-living life strategy in oligotrophic environments. While many Nanopelagicales metagenome-assembled genomes and single-amplified genomes are available in public databases, strain-level microdiversity within this lineage remains poorly understood. This is mainly attributed to the incomplete nature of these genomes and the difficulty in isolating and maintaining pure cultures, with only 20 genome-sequenced cultures available to date.<br><br>RESULTS: Here, we report the isolation and genome analysis of 72 new Nanopelagicales strains, including members of Planktophila and a novel, previously uncultured genus, Aquilimus. High interspecific diversity and microdiversity were observed in the&#xa0;genus Planktophila, which likely facilitates the coexistence of closely related species within the same habitats by allowing fine-scale niche partitioning. The unusually high diversity of transporters for small organic compounds, along with carbohydrate-active enzymes, suggests that Planktophila members can degrade plant and algal polymers and import the resulting products to support growth. A notable finding is the repeated, independent loss of the oxidative phase of the pentose phosphate pathway in abundant Nanopelagicales species, which may represent an energy-saving adaptation in oligotrophic waters. Two species (Planktophila vernalis and Nanopelagicus abundans) seem to be equally abundant on a global scale, with water pH likely being the most significant factor influencing the predominance of one group over the other in different water bodies. Additionally, P. vernalis may tolerate periods of anoxia due to genomic encoding of respiratory nitrate reductase and nitrate/nitrite antiporters.<br><br>CONCLUSIONS: In conclusion, this work increased to a great degree the cultivated diversity of the abundant Nanopelagicales order. Analysis of over 1700 metagenomes showed that only a few cultivated species are globally dominant, and time-series analyses revealed consistent spring and autumn peaks. Key metabolic adaptations, such as loss of the oxidative phase of the pentose phosphate pathway and a high microdiversity of genes involved in cell surface biosynthesis and modifications, are likely to help these species survive periods of starvation and avoid predation. These findings highlight the ecological importance of Nanopelagicales and suggest that microdiversity underpins their adaptability. This work lays a foundation for studying their physiology, ecology, and strain-specific functional variation. Video Abstract.},
}
@article {pmid41388019,
year = {2025},
author = {Chac, D and Heller, FJ and Banna, HA and Kaisar, MH and Markiewicz, SM and Pruitt, EL and Chowdhury, F and Bhuiyan, TR and Akter, A and Khan, AI and Dumayas, MG and Rice, A and Karmakar, PC and Dash, P and LaRocque, RC and Ryan, ET and Xu, L and Minot, SS and Harris, JB and Qadri, F and Weil, AA},
title = {Gut bacteria-derived sphingolipids alter innate immune responses to oral cholera vaccine antigens.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {638},
pmid = {41388019},
issn = {2041-1723},
support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; T32HD007233//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI099243/AI/NIAID NIH HHS/United States ; T32 HD007233/HD/NICHD NIH HHS/United States ; R01 AI136979/AI/NIAID NIH HHS/United States ; K08 AI123494/AI/NIAID NIH HHS/United States ; R01 AI106878/AI/NIAID NIH HHS/United States ; D43 TW005572/TW/FIC NIH HHS/United States ; R01 106878//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI AI136979//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI103055/AI/NIAID NIH HHS/United States ; K43 TW010362/TW/FIC NIH HHS/United States ; },
mesh = {Humans ; *Cholera Vaccines/immunology/administration &amp; dosage ; *Immunity, Innate/immunology ; *Gastrointestinal Microbiome/immunology/genetics ; *Sphingolipids/metabolism/immunology ; Vibrio cholerae/immunology ; *Cholera/prevention &amp; control/immunology/microbiology ; Administration, Oral ; Feces/microbiology ; Macrophages/immunology ; Bacteroides/metabolism/immunology ; Female ; Male ; Adult ; },
abstract = {The degree of protection conferred after receiving an oral cholera vaccine (OCV) varies based on age, prior exposure to Vibrio cholerae, and unknown factors. Recent evidence suggests that the microbiota may mediate some of the unexplained differences in oral vaccine responses. Here, we use metagenomic sequencing of the fecal microbiota at the time of vaccination and relate microbial features to immune responses after OCV using a reference-independent gene-level method. We find that the presence of sphingolipid-producing bacteria is associated with the development of protective immune responses after OCV. We test these associations by stimulating human macrophages with Bacteroides xylanisolvens metabolites and find that sphingolipid-containing extracts increase innate immune responses to OCV antigens. Our findings demonstrate a new analytic method for translating metagenomic sequencing data into strain-specific results associated with a biological outcome, and in validating this tool, we identify that microbe-derived sphingolipids impact immune responses to OCV antigens.},
}
@article {pmid41387926,
year = {2025},
author = {Ma, X and Wang, B and Xu, M and Zhang, Y and Liu, N and Teng, L and Li, Z and Yang, H and Xie, X and Zhang, B and Wang, Z and Wang, Y and Liu, J and Bao, J and Luo, H},
title = {Multiomics insights into rumen microbiome and function in grazing lambs: implications for nutrient absorption and grassland sustainability.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {30},
pmid = {41387926},
issn = {2049-2618},
support = {32192463//The Major Program of National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; Grassland ; *Gastrointestinal Microbiome ; Sheep/microbiology ; Animal Feed/analysis ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Metagenomics/methods ; Poaceae ; *Nutrients/metabolism ; Fermentation ; Multiomics ; },
abstract = {BACKGROUND: The center of sustainable development of grassland husbandry is the balance between forage intake and growth characteristics of animals, and one of the keys to restricting the conversion efficiency of forage intake is the digestibility of forage produced by rumen microorganisms. Thus, the interaction between grass intake and rumen microbial fermentation is a key driver of both ruminant productivity and grassland ecosystem health. However, interactions between grass species, supplementary feeding, rumen microbiome, and rumen epithelium function, remain poorly understood.<br><br>RESULTS: We employed metagenomic and metatranscriptomic analyses, coupled with single-cell RNA sequencing (scRNA-seq) of rumen wall and serum metabolomics, to investigate how the rumen microbiome regulates grass intake and host metabolism. In a two-factor (grazing intensity and concentrate supplementation) experiment with 72 lambs, supplementary feeding under moderate grazing increased dry matter intake but decreased grass consumption of Artemisia tanacetifolia. These shifts correlated with contrasting trends between metagenomic and metatranscriptomic profiles of Lachnospiraceae. scRNA-seq revealed an increased abundance of basal cells (BCs), terminally differentiated keratinocytes (TDKs), and differentiated keratinocytes (DKs) in the supplemented group, with solute carrier genes (e.g., SLC16A1) involved in short chain fatty acids (SCFAs) transport enriched in basal cells. We also identified interactions between the rumen microbiome and host epithelial cells, influencing gene expression and localization, which in turn mediated the animal serum nutrient metabolism, particularly in B vitamin, bile acids, and amino acids.<br><br>CONCLUSIONS: Our study identified key microbiome and epithelial cell subtypes involved in grass digestion and SCFAs metabolism in the rumen. This novel link between ruminal microbial function, epithelial cell cluster-based genes, and host metabolism provides critical insights into mechanisms underlying the interaction between grass intake and supplementary feeding for optimizing ruminant management strategies in sustainable grazing systems. Video Abstract.},
}
@article {pmid41387706,
year = {2025},
author = {Bonnet, N and Capeding, MR and Siegwald, L and Garcia-Garcera, M and Desgeorges, T and Tytgat, HLP and Krattinger, LF and Lebumfacil, J and Phee, LC and Moll, JM and Gudjonsson, A and Rodriguez-Garcia, P and Baruchet, M and Feige, JN and Jankovic, I and Chen, Y and Egli, D and Horcajada, MN},
title = {A young child formula with Limosilactobacillus reuteri and GOS modulates gut microbiome and enhances bone and muscle development: a randomized trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {237},
pmid = {41387706},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Limosilactobacillus reuteri/physiology ; Female ; Male ; Child, Preschool ; Feces/microbiology/chemistry ; Double-Blind Method ; *Infant Formula/chemistry ; *Oligosaccharides/administration &amp; dosage/pharmacology ; *Bone Development/drug effects ; Muscle Strength/drug effects ; Vitamin D/blood ; Probiotics/administration &amp; dosage ; Synbiotics/administration &amp; dosage ; },
abstract = {In this randomized, double-blind controlled trial, 182 Filipino children aged 2-3 years received either an experimental young child formula (EYCF) containing a combination of Limosilactobacillus reuteri DSM 17938 and galacto-oligosaccharides (GOS; n = 91) or a minimally fortified milk (CM; n = 91) for 6 months. Primary outcome was tibia speed of sound and secondary outcomes were muscle strength, blood vitamin D levels, bone turnover markers, gut microbiota, fecal calcium fatty acid soaps and gastro-intestinal tolerance. Compared to CM, those in the EYCF group showed increased tibia speed of sound after 3 and 6 months. The intervention remodeled the stool microbiome composition, assessed by shotgun metagenomics, with enrichment of L. reuteri and higher bifidobacteria presence in the EYCF group. Increased L. reuteri abundance after 6 months of EYCF consumption associates with higher bone quality and muscle strength. Stool metabolomics show 45 metabolites modulated by EYCF consumption and associated to microbiome compositional changes, leading to enrichment of tryptophane and indole metabolism. In summary, consumption of EYCF containing a L. reuteri + GOS synbiotic improves musculoskeletal development in toddlers via modulation of microbiota composition and function. These results provide insights on gut-musculoskeletal crosstalk during early life. Clinicaltrial.gov NCT04799028.},
}
@article {pmid41387397,
year = {2025},
author = {Hallgren, J and Dharamshi, JE and Rodríguez-Gijón, A and Nuy, J and Garcia, SL and Jonas, K},
title = {Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11003},
pmid = {41387397},
issn = {2041-1723},
support = {2020-03545//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2024-04942//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 2022-06250//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; ALTF 740-2022//European Molecular Biology Organization (EMBO)/ ; },
mesh = {Phylogeny ; *Caulobacter crescentus/genetics/classification ; *Phototrophic Processes/genetics ; Biological Evolution ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Model bacteria are fundamental for research, but knowledge about their ecology and evolution is often limited. Here, we establish an evolutionary and ecological context for the model organism Caulobacter crescentus-an alphaproteobacterium intensively studied for its dimorphic lifecycle. By analyzing the phylogenetic relatedness and genetic potential of hundreds of Caulobacterales species, we reveal substantial diversity regarding their environmental distribution, morphology, cell development, and metabolism. Our work provides insights into the evolutionary history of morphological features such as the cell curvature determinant crescentin and uncovers a striking case of convergent loss of traits for cellular dimorphism among close relatives of C. crescentus. Moreover, we find that genes for phototrophy are widespread across Caulobacterales and that the new genus Acaudatibacter, described here, includes the first reported Caulobacterales lineage with photoautotrophic potential. Our study advances our understanding of an environmentally widespread bacterial order and sheds light on the evolution of fundamental prokaryotic features.},
}
@article {pmid41387121,
year = {2026},
author = {Ji, Y and Liu, X and Zhao, S and Zhou, S and Yang, Y and Zhang, P and Shi, Y and Qin, W and Zhu, G and Zhu, Y and Gao, Y and Jiang, J and Wang, B},
title = {Unveiling Global Diversity of Patescibacteriota and Functional Interactions with Host Microbes.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {11},
pages = {e09416},
pmid = {41387121},
issn = {2198-3844},
support = {U22A20590//National Natural Science Foundation of China/ ; 42277304//National Natural Science Foundation of China/ ; 42477318//National Natural Science Foundation of China/ ; 42407399//National Natural Science Foundation of China/ ; 2025YFE0103900//National Key R&amp;D Program of China/ ; BK20241558//Natural Science Foundation of Jiangsu Province/ ; BX20240168//China National Postdoctoral Program for Innovative Talents/ ; 2024ZB624//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; },
mesh = {Phylogeny ; *Host Microbial Interactions/genetics/physiology ; *Bacteria/genetics/classification ; Metagenome/genetics ; Ecosystem ; Biodiversity ; Metagenomics/methods ; },
abstract = {Patescibacteriota, also known as Candidate Phyla Radiation (CPR), is a diverse clade of ultra-small bacteria with an epibiotic lifestyle. Despite their ubiquity across diverse ecosystems and ecological importance in microbial networks, the global distribution of Patescibacteriota and functional interactions with their host organisms remain largely unknown. Here, by leveraging comprehensive Patescibacteriota genomic resources and global multi-habitat metagenomic datasets, it is demonstrated that ribosomal protein S3 (rpS3) as a reliable phylogenetic marker, enabling accurate recovery of Patescibacteriota diversity from short-read metagenomes. Using this framework, extensive taxonomic diversity and pronounced community heterogeneity are uncovered across eight ecosystems. Through network analysis and genome-wide functional screening, habitat-specific co-occurrence patterns are also revealed between Patescibacteriota and host-associated bacteria, especially potential functional synergies mediated by metabolic pathway cascades. Notably, Patescibacteriota-encoded NirK may assist sulfate-reducing bacteria in resisting nitrite stress, while NorB can mitigate nitric oxide toxicity for complete ammonia-oxidizing bacteria. Taken together, this study highlights the underappreciated diversity of Patescibacteriota and elucidates its important role in supporting host metabolism through complementary biochemical functions, offering new insights into its ecological significance and evolutionary adaptations in the global ecosystem.},
}
@article {pmid41386031,
year = {2026},
author = {Shu, M and Xue, H and Yang, Y and Zhang, X and Li, S and Bian, T and Yuan, K and Xu, C},
title = {Microbial-enzyme co-fermentation of low-grade tobacco: Metagenomics and metabolomic insights into flavor formation.},
journal = {Enzyme and microbial technology},
volume = {194},
number = {},
pages = {110803},
doi = {10.1016/j.enzmictec.2025.110803},
pmid = {41386031},
issn = {1879-0909},
mesh = {Fermentation ; *Nicotiana/microbiology/metabolism/chemistry ; Plant Leaves/microbiology/metabolism/chemistry ; Metagenomics ; Volatile Organic Compounds/analysis/metabolism ; Metabolomics ; Gas Chromatography-Mass Spectrometry ; Odorants/analysis ; Flavoring Agents/metabolism ; Taste ; Microbiota ; Bacteria/metabolism/genetics/classification ; },
abstract = {Microbial-enzyme co-fermentation effectively enhances the quality of low-grade tobacco leaves quality, but the underlying mechanisms of flavor formation remain unclear. This study investigated the dynamics and relationships of microbial communities and volatile aroma metabolites during low-grade tobacco leaves fermentation through metagenomics and headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS). Results showed that during microbial-enzyme co-fermentation, the tobacco leaves fermented for four days (D4) exhibited the highest levels of total sugars and reducing sugars, the peak total content of aroma metabolites, and the best sensory quality. Pseudomonadota, Bacillota, and Ascomycota were dominant microorganisms during fermentation. During the initial stage (D1-D4), Saccharomyces was the dominant genus, which was subsequently displaced by Pantoea at D5. This microbial succession coincided with a decline in sensory quality, indicating its crucial role in shaping flavor evolution during co-fermentation. During microbial-enzyme co-fermentation process, a total of 46 volatile metabolites were detected in low-grade tobacco leaves. Among them, seven esters with high variable important in projection values and strong microbial correlations were identified as characteristic aroma metabolites, including ethyl phenylacetate, benzyl acetate, phenylethyl acetate, ethyl myristate, ethyl palmitate, ethyl oleate, and methyl linolenate. Gene function annotation revealed carbohydrate metabolism was the most abundant, followed by amino acid metabolism. Spearman correlation analysis elucidated the formation mechanism of characteristic ester metabolites. Specifically, short-chain esters correlated with glycerolipid and amino acid metabolism, while long-chain esters linked to glycolysis and fatty-acid biosynthetic pathways.},
}
@article {pmid41385957,
year = {2026},
author = {Zhang, C and Wang, X and Wang, L and Li, P and Bao, Y and Zhang, Z and Jiang, Z and Feng, C and Chen, L},
title = {Multi-omics reveals gut microbiota-mediated environmental adaptation in Mallards and domesticated Shaoxing ducks.},
journal = {Poultry science},
volume = {105},
number = {1},
pages = {106177},
pmid = {41385957},
issn = {1525-3171},
mesh = {Animals ; *Ducks/microbiology/physiology ; *Gastrointestinal Microbiome ; Domestication ; *Adaptation, Physiological ; Cecum/microbiology ; Ileum/microbiology ; *Metabolome ; Metabolomics ; Multiomics ; },
abstract = {Gut microbiota remodeling is a critical component of the domestication syndrome. However, the structural and functional consequences of domestication on gut microbiomes in ducks remain poorly understood. Understanding how domestication and associated ecological transitions influence gut microbial communities can shed light on host adaptation mechanisms. We performed integrated metagenomic and metabolomic analyses of the ileal and cecal microbiota from Mallards and Shaoxing ducks-two ecotypes of Anas platyrhynchos representing wild and domesticated lineages-to investigate microbial community structure, functional capacity, and host-microbe metabolic interactions. Principal coordinates analysis (PCoA) revealed distinct microbial stratification between intestinal compartments (ileum vs. cecum), with domestication-associated divergence observed primarily in the cecum. Metabolomic profiles were relatively stable across both segments and populations. Mallards harbored a more diverse and metabolically versatile gut microbiota, with significant enrichment in pathways related to carbohydrate, amino acid, and vitamin metabolism. The genus Gemmiger emerged as a key functional contributor, supporting branched-chain amino acid biosynthesis, coenzyme activation, and carbohydrate utilization, thus reflecting enhanced metabolic adaptability. In Shaoxing ducks, the gut microbiome was enriched in the glucagon signaling pathway and glucose-regulatory metabolites such as l-carnitine, myo-inositol, and quinate. Butyricicoccus sp017886875 was identified as a candidate taxon associated with glucose homeostasis. Additionally, immune-related pathways, including the NOD-like receptor signaling and antigen processing and presentation, were significantly enriched and linked to Anaerobiospirillum and Parabasalia, respectively. Co-enrichment of anti-inflammatory metabolites suggests the presence of a host-microbiota feedback mechanism that mitigates inflammation while maintaining immune readiness. These findings reveal that gut microbiota contribute to population-specific environmental adaptation in ducks, with distinct microbiome and functional traits associated with domestication history. The study highlights microbiota-mediated host adaptation as a key feature of domestication-related ecological transitions.},
}
@article {pmid41385764,
year = {2025},
author = {Yang, H and Yu, Y and Cui, R and Zhang, Q and Chen, B and Zhang, Z and Xu, N and Sun, L and Lu, T and Qian, H},
title = {Environmental and Microbial Drivers of Global Rhizosphere Resistome Assembly.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {51},
pages = {32568-32576},
doi = {10.1021/acs.jafc.5c11060},
pmid = {41385764},
issn = {1520-5118},
mesh = {Soil Microbiology ; Rhizosphere ; *Bacteria/genetics/isolation &amp; purification/drug effects/classification/metabolism ; Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Vegetables/microbiology ; Microbiota ; },
abstract = {Soil serves as a critical reservoir for antibiotic resistance genes (ARGs); however, the ecological mechanisms driving ARG assembly at the plant-soil interface remain poorly understood. In this study, we analyzed 383 metagenomic samples and identified 4803 predicted ARGs, which were classified into two distinct clusters. The ARG-abundant cluster exhibited higher rhizospheric ARG abundance and diversity but posed a relatively lower health risk compared to the ARG-scarce cluster. Warm and nutrient-rich soils promote diverse resistomes shaped by complex microbial interactions, whereas humid environments promote more homogeneously predicted ARG compositions. Environmental variables such as the temperature and nitrogen were found to indirectly influence resistome composition by modulating microbial diversity. Notably, relatively high proportions of high-risk predicted ARGs were detected in grains and raw-eat vegetables, highlighting a potential threat to public health. Our findings underscore the importance of incorporating both environmental and microbial perspectives into agricultural practices to mitigate ARG dissemination in soil.},
}
@article {pmid41385173,
year = {2025},
author = {Othman, AA and Mohamed Zain, NI and Eshak, Z and Adman, MA and Abd Latif, Z and Aboshanab, KM and Ahmad, A},
title = {Diversity of necrophagous flies and microbiome profiling of Phumosia promittens as a rainforest health indicator.},
journal = {AMB Express},
volume = {16},
number = {1},
pages = {1},
pmid = {41385173},
issn = {2191-0855},
abstract = {Necrophagous flies play a critical role in decomposition and serve as bioindicators of environmental health and pollution. Malaysia's tropical rainforest ecosystems may host many necrophagous fly species, including unique blowflies and their associated bacteria. However, in many forest reserve areas, the diversity of these flies remains poorly studied. This study examines the diversity of necrophagous flies and their associated surface bacteria community, with a particular focus on Phumosia promittens (Walker in J Proc Linn Soc Lond Zool 4:90-96, 1859) in the Bangi Forest Reserve, Universiti Kebangsaan Malaysia. Sampling was conducted across three plots using baited traps, and collected flies were morphologically identified and processed under sterile conditions. Surface bacteria from P. promittens were isolated and analysed through metagenomic analysis targeting the 16S rRNA (V3-V4) amplicon sequencing gene to characterise their microbial communities comprehensively. Among 2,528 individuals collected, Chrysomya megacephala (Fabricius) was the most dominant species overall, while P. promittens was the most abundant among native forest species, suggesting their ecological adaptability and potential as a bioindicator of healthy rainforest. Shannon-Wiener and Simpson's diversity of flies in the study location were 0.67 ± 0.11 and 0.29 ± 0.06, respectively. Meanwhile, the Shannon-Wiener and Simpson's diversity of bacteria from P. promittens were 5.64 ± 0.70 and 0.96 ± 0.02, respectively. Bacterial microbiome analysis revealed the presence of core genera, including Wohlfahrtiimonas, Dysgonomonas, Vagococcus, and Ignatzschineria, which are implicated in both ecological symbiosis and public health concerns. These bacteria may contribute to nutrient cycling, such as heavy metals and antibiotics. Notably, several of these genera are emerging zoonotic pathogens with antimicrobial resistance, highlighting the dual role of necrophagous flies as ecosystem contributors and disease vectors. The findings underscore the importance of monitoring native fly species and their microbiota to assess the integrity of forest ecosystems and potential public health risks.},
}
@article {pmid41384994,
year = {2025},
author = {Zhang, J and Liu, J and Bayani, A},
title = {Phage therapy and the microbiome in hematologic malignancies: opportunities, mechanisms, and early evidence.},
journal = {Journal of cancer research and clinical oncology},
volume = {152},
number = {1},
pages = {8},
pmid = {41384994},
issn = {1432-1335},
mesh = {Humans ; *Hematologic Neoplasms/therapy/microbiology/immunology ; *Phage Therapy/methods ; Animals ; *Bacteriophages ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Hematologic malignancies remain among the most difficult cancers to treat, challenged by profound heterogeneity, treatment-induced immune dysfunction, and the frequent emergence of drug resistance. Beyond tumor-intrinsic mechanisms, dysbiosis of the gut microbiome is increasingly recognized as a critical determinant of therapeutic outcomes, shaping hematopoiesis, immune responses, and drug metabolism. Bacteriophage (phage) therapy has re-emerged as a precision tool capable of selectively eradicating pathogenic taxa while preserving commensal short-chain fatty acid-producing communities. Preclinical and early human studies demonstrate that phages can recalibrate microbial ecosystems, disrupt antibiotic-tolerant biofilms, and enrich metabolites such as butyrate that support mucosal integrity and immune balance. Mechanistically, phage DNA enriched with CpG motifs engages Toll-like receptor 9, activating dendritic cells and enhancing cytotoxic T lymphocyte responses, suggesting dual benefits in infection control and anti-tumor immunity. Emerging applications extend further, with engineered phages serving as vectors for CRISPR-Cas gene editing, targeted cytokine delivery, and nanocarrier platforms for leukemia therapy. Despite translational promise, major hurdles persist, including immunogenicity, horizontal gene transfer, resistance evolution, and regulatory uncertainty. Addressing these challenges through GMP-compliant manufacturing, metagenomics-guided personalization, and AI-optimized cocktail design could establish phage therapy as a microbiome-informed adjunct to overcome drug resistance in blood cancers. However, direct clinical evidence of phage therapy efficacy in hematologic malignancies remains limited, and current data are largely derived from preclinical and compassionate-use contexts.},
}
@article {pmid41384736,
year = {2026},
author = {Madrid-Restrepo, MA and León-Inga, AM and Peñuela-Martínez, AE and Cala, MP and Reyes, A},
title = {Metagenomic, metabolomic, and sensorial characteristics of fermented Coffea arabica L. var. Castillo beans inoculated with microbial starter cultures.},
journal = {mSystems},
volume = {11},
number = {1},
pages = {e0136425},
pmid = {41384736},
issn = {2379-5077},
mesh = {Fermentation ; *Coffea/microbiology/metabolism/chemistry ; Metabolomics/methods ; Humans ; Metagenomics/methods ; Taste ; Metabolome ; Microbiota ; Coffee/microbiology ; },
abstract = {UNLABELLED: Coffee is one of the most important and widely consumed drinks around the world, and fermentation plays a pivotal role in shaping its quality. This research explores the impact of co-fermentation with "starter cultures" on the sensory and metabolic profiles, as well as on the dynamics of microbial communities involved in coffee processing. Freshly harvested Arabica coffee beans were subjected to two wet-fermentation processes, one inoculated with a microbial starter culture and the other undergoing spontaneous fermentation. Quantitative descriptive analysis revealed that the inoculated coffee outperformed the spontaneous fermentation in all sensory attributes, boasting higher sweetness, reduced acidity and bitterness, and the presence of consumer-preferred notes. Untargeted metabolomic analysis identified over a hundred differential metabolites distinguishing both fermentation processes in green and roasted beans. Inoculated coffee displayed elevated levels of compounds such as sucrose, mannitol, methyl phenylacetate, and organic acids like malic, citric, and quinic acid, compounds likely associated with improved sensory perception. The inoculated process was characterized by shifts in the abundance of lactic acid bacteria and Kazachstania yeasts, groups linked to desirable metabolites such as lactic, acetic, isobutyric, and hexanoic acids. Our results strongly suggest that the use of starter cultures can enhance coffee beverage quality, as reflected by standardized cupping, metabolic profiles, and microbial community dynamics. Future studies should focus on disentangling microbial contributions and metabolite pathways to inform the design of commercially viable starter cultures for coffee fermentation.<br><br>IMPORTANCE: Our study demonstrates that inoculating coffee fermentation alters the sensory qualities of coffee and reshapes the dynamics of bacterial and fungal communities during this process. We identified distinct changes in microbial diversity and metabolite composition associated with inoculation, which correlated with improved sensory attributes. In addition, we detected aminophenol and phenol at higher levels in spontaneously fermented coffees, compounds that are likely responsible for phenolic defects. To our knowledge, this is the first report directly linking these compounds to defective flavor notes in coffee. Together, these findings show that inoculation not only enhances desirable flavor profiles but may also serve as a strategy to reduce the risk of cup defects by modulating the fermentation microbiota. Our work advances the understanding of community-level microbial processes in coffee fermentation and opens opportunities for developing techniques to produce coffee with unique, high-quality, and reproducible sensory characteristics.},
}
@article {pmid41382244,
year = {2025},
author = {Bae, IH and Kim, H and Kim, SM and Lee, YH},
title = {Multi-meta-omics reveal unique symbiotic synchronization between ectomycorrhizal fungus and soil microbiome in Tricholoma matsutake habitat.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {23},
pmid = {41382244},
issn = {2049-2618},
support = {RS-2022-NR072199//National Research Foundation of Korea/ ; RS-2025-00512558//National Research Foundation of Korea/ ; },
mesh = {*Mycorrhizae/physiology/genetics ; *Symbiosis ; *Soil Microbiology ; *Microbiota ; *Tricholoma/physiology ; Soil/chemistry ; Nitrogen/metabolism ; Plant Roots/microbiology ; Ecosystem ; Bacteria/classification/genetics/metabolism ; },
abstract = {BACKGROUND: Ectomycorrhizal (ECM) fungi establish symbiotic relationships with plant roots, enhancing nutrient uptake, improving plant health, and boosting ecosystem resilience. Although previous studies reported molecular interactions among plant-ECM fungi-surrounding microbes near plant roots, microbiome-wide metabolic shifts and associations with the fungi remain unclear.<br><br>RESULTS: Using Tricholoma matsutake as a model, we initially found that T. matsutake induced remarkable microbial community turnover linked to altered soil moisture, nitrogen, and phosphorus levels. Parallel with the compositional alteration, microbiome-wide metabolic capacities, including glutamate metabolism, oligopeptide transport, and siderophore activity, were enriched in the T. matsutake-colonizing soil compared to the soils where the fungus was not colonized. From metatranscriptome data, we found that T. matsutake induced functional remodeling in nitrogen metabolism. Notably, the fungus and soil microbiome were metabolically synchronized with the upregulation of nitrate reduction, glutamate biosynthesis, tryptophan biosynthesis, and indole-3-acetic acid (IAA) biosynthesis. Metabarcoding and metatranscriptome-guided microbial associations revealed potential T. matsutake helper bacteria consisting of Conexibacter and Paraburkholderia. Phage community analyses further showed that the colonization of the ECM fungus influenced phage distributions along with the increase in temperate phage populations. The differential expression of auxiliary metabolic genes also demonstrated that phages could influence bacterial fitness in response to T. matsutake colonization.<br><br>CONCLUSION: Our multi-meta-omics-based approaches revealed unique environmental changes by T. matsutake compared to other mycorrhizal systems, as well as metabolic synchronization between the ECM fungus and surrounding microbiomes. These findings will expand our understanding of ECM symbiotic frameworks by highlighting integrated microbial and viral metabolic dynamics. Video Abstract.},
}
@article {pmid41382192,
year = {2025},
author = {Xue, R and Li, Z and Qin, W and Wang, Y and Zhao, K and Liu, L and Bai, Y},
title = {Prolonged grazing reduces the diversity and weakens virus-host links of metagenome-assembled viral community in acidic karst soil.},
journal = {BMC biology},
volume = {24},
number = {1},
pages = {15},
pmid = {41382192},
issn = {1741-7007},
support = {41907025//National Natural Science Foundation of China/ ; 32160337//National Natural Science Foundation of China/ ; 2025ZNSFSC0202//Natural Science Foundation of Sichuan Province/ ; },
mesh = {*Soil Microbiology ; *Metagenome ; *Soil/chemistry ; Biodiversity ; *Virome ; *Herbivory ; Bacteria/genetics ; Microbiota ; },
abstract = {BACKGROUND: Soil viruses are fundamental yet often overlooked components of terrestrial ecosystems, where they profoundly influence microbial diversity, community assembly, and biogeochemical cycling through predator-prey dynamics and the carriage of auxiliary metabolic genes (AMGs). However, the impact of human-driven land use change on viral communities and their functional potential remains poorly understood.<br><br>RESULTS: In this study, we analyzed viral diversity, virus-host linkage, and functional profiles of AMGs across different land management regimes in acidic karst soil after reclamation. The results showed that both bacterial and viral communities significantly differ across the four land management regimes, which are unused land, grazing pastureland, abandoned pastureland, and fertilized grazing pastureland. Grazing led to a lower viral diversity, a decrease in lysogenic viral abundance, and fewer virus-host linkages. The diversity and function of AMGs were also significantly affected by land management regimes, with grazing leading to a reduction in both AMGs diversity and relative abundance. Furthermore, both the bacterial community and soil physiochemical properties were essential factors that shaped viral diversity and lifestyle.<br><br>CONCLUSIONS: Overall, our findings indicate that inappropriate land use (long-term grazing) disrupts the virus-host balance, thereby altering the functional profiles of the soil viral community.},
}
@article {pmid41381751,
year = {2025},
author = {Tabe, C and Motooka, D and Fujita, T and Makiguchi, T and Taima, K and Tanaka, H and Itoga, M and Ishioka, Y and Akita, T and Ishidoya, M and Chubachi, K and Fukushima, T and Tanaka, Y and Odagiri, H and Kameyama, Y and Kobori, Y and Tasaka, S and Fujii, H},
title = {The gut microbiota as a potential biomarker in patients with EGFR-mutant lung cancer.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1672},
pmid = {41381751},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; ErbB Receptors/genetics/antagonists &amp; inhibitors ; Female ; Male ; *Lung Neoplasms/drug therapy/genetics/microbiology ; Middle Aged ; Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/genetics/microbiology ; *Mutation ; Protein Kinase Inhibitors/therapeutic use/adverse effects ; RNA, Ribosomal, 16S/genetics ; Diarrhea/microbiology/chemically induced ; Biomarkers, Tumor/genetics ; Feces/microbiology ; },
abstract = {Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are highly effective against EGFR-mutant non-small cell lung cancer (NSCLC); however, identifying biomarkers that predict prognosis and adverse events is necessary. Although the gut microbiota is considered to be a biomarker for NSCLC without mutations, no studies have examined its potential as a biomarker for EGFR-mutant NSCLC. Here, we investigated the association between gut microbiota composition and diarrhea, a common side effect caused by EGFR-TKIs. In addition, we examined the association between the efficacy of EGFR-TKIs and the gut microbiota. A total of 21 NSCLC patients with EGFR mutations were enrolled. Fecal samples were collected prior to EGFR-TKI treatment and 16S rRNA metagenome sequencing was performed to evaluate the microbiota profile. In addition, α-diversity, β-diversity, and Linear discriminant analysis Effect Size (LEfSe) analyses were performed. The α-diversity of the gut microbiota was higher in patients with grade 0-1 diarrhea than in those with grade 2-3 diarrhea (Shannon, p = 0.0367). In terms of β-diversity, there was a significant difference in the best overall response between patients with a partial response (PR) to EGFR-TKIs and those with stable disease (SD)/progressive disease (PD) (weighted p = 0.041). Analysis of microbial composition revealed an increased abundance of Ruminococcus in the PR group. In patients taking EGFR-TKIs, a higher α-diversity may be associated with less severe diarrhea. In addition, a high abundance of Ruminococcus may be a potential biomarker for predicting favorable efficacy of EGFR-TKIs.},
}
@article {pmid41381437,
year = {2025},
author = {Hao, C and Dungait, JAJ and Shang, W and Hou, R and Gong, H and Yang, Y and Lambers, H and Yu, P and Delgado-Baquerizo, M and Xu, X and Kumar, A and Deng, Y and Peng, X and Cui, Z and Kuzyakov, Y and Zhou, J and Zhang, F and Tian, J},
title = {Conservation agriculture raises crop nitrogen acquisition by amplifying plant-microbe synergy under climate warming.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11067},
pmid = {41381437},
issn = {2041-1723},
mesh = {*Nitrogen/metabolism ; *Triticum/metabolism/microbiology/growth &amp; development ; Soil Microbiology ; *Crops, Agricultural/metabolism/microbiology ; Plant Roots/metabolism/microbiology ; *Agriculture/methods ; Climate Change ; Soil/chemistry ; Nitrification ; Nitrates/metabolism ; *Conservation of Natural Resources ; Metabolomics ; Microbiota ; Metagenomics ; Bacteria/metabolism/genetics ; },
abstract = {Sustainable crop production in a warming climate requires land management strategies that support plant-soil-microbe interactions to optimize nitrogen (N) availability. Here, we investigate the interacting effects of 10 years' experimental warming and management (conservation vs. conventional agriculture) on wheat N acquisition using in situ [15]N-labeling, root metabolomics and microbial metagenomics. We find that warming amplifies the positive effects on wheat nitrate uptake by 25% in conservation agriculture compared to conventional agriculture, while alleviating microbial competition for N. Additionally, warming increases soil gross N mineralization and nitrification rates by 191% and 159%, but decreases microbial immobilization by 24% in conservation agriculture. Concurrently, microbial genes for mineralization and nitrification are enriched, while those for N immobilization and nitrate reduction are reduced under conservation agriculture with warming. These shifts are driven by alterations in root primary and secondary metabolites, which reshape N-cycling microbial functional niches and optimize multiple microbial N processes beyond mere organic N mining. This reconfiguration increases carbon-nitrogen exchange efficiency, enabling wheat to outcompete soil microorganisms for N. Collectively, our findings suggest that conservation agriculture enhances plant N acquisition by strengthening plant-soil-microbe interactions under climate change, providing a sustainable strategy for future food security.},
}
@article {pmid41381092,
year = {2025},
author = {Lane, KR and Jones, SE and Osborne, TH and Geller-McGrath, D and Nwaobi, BC and Chen, L and Thomas, BC and Hudson-Edwards, KA and Banfield, JF and Santini, JM},
title = {Bioleaching Microbial Community Metabolism and Composition Driven by Copper Sulphide Mineral Type.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70261},
pmid = {41381092},
issn = {1758-2229},
support = {NE/L002485/1//Natural Environment Research Council/ ; BB/N012674/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //Hellenic Coppers Mines Ltd/ ; },
mesh = {*Copper/metabolism/chemistry ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Archaea/metabolism/genetics/classification/isolation &amp; purification ; *Sulfides/metabolism/chemistry ; *Microbial Consortia ; Metagenomics ; *Minerals/metabolism/chemistry ; *Microbiota ; Plasmids/genetics ; },
abstract = {Copper bioleaching is a green technology for the recovery of copper from chalcopyrite (CuFeS2) and chalcocite (Cu2S) ores. Much remains to be learned about how mineral type and surface chemistry influence microbial community composition. Here, we established a microbial consortium from a copper bioleaching column in Cyprus on chalcopyrite and then sub-cultured it to chalcocite to investigate how the community composition shifts due to changes in mineral structure and the absence of mineral-derived Fe. The solution chemistry was determined and microbial communities characterised by genome-resolved metagenomics after 4 and 8 weeks of cultivation. Acidithiobacillus species and strains, a Rhodospirilales, Leptospirillum ferrodiazotrophum and Thermoplasmatales archaea dominated all enrichments, and trends in abundance patterns were observed with mineralogy and surface-attached versus planktonic conditions. Many bacteria had associated plasmids, some of which encoded metal resistance pathways, sulphur metabolic capacities and CRISPR-Cas loci. CRISPR spacers on an Acidithiobacillus plasmid targeted plasmid-borne conjugal transfer genes found in the same genus, likely belonging to another plasmid, evidence of intra-plasmid competition. We conclude that the structure and composition of metal sulphide minerals select for distinct consortia and associated mobile elements, some of which have the potential to impact microbial activity during sulphide ore dissolution.},
}
@article {pmid41381025,
year = {2026},
author = {Zabaleta, WDB and Gomez, JDR and Santofimio Villa, LF and Angarita, NB and Alzate, JF and Garzón, YEG and Cantillo-Barraza, O and Triana-Chavez, O and Vargas, PAO and Urrea, DA},
title = {Metatranscriptomic insights into feeding preferences, bacterial diversity, and insect-specific viruses genomics in Aedes aegypti populations from Ibagué, Colombia.},
journal = {Acta tropica},
volume = {273},
number = {},
pages = {107941},
doi = {10.1016/j.actatropica.2025.107941},
pmid = {41381025},
issn = {1873-6254},
mesh = {Animals ; *Aedes/virology/microbiology/physiology ; Colombia ; Female ; *Mosquito Vectors/virology/microbiology ; *Feeding Behavior ; *Bacteria/classification/genetics/isolation &amp; purification ; *Insect Viruses/genetics/classification/isolation &amp; purification ; Microbiota ; Metagenomics ; Genome, Viral ; },
abstract = {Aedes aegypti is not only the primary vector of medically important arboviruses worldwide, but also a host of a wide range of arthropod-specific viruses (ISVs), whose genomic and biological diversity remains largely unknown across most regions of Colombia. Investigating its associated microbiota including viruses and bacteria is essential, as these interactions can influence vector competence. Metatranscriptomic analysis of this vector provides quantitative insights into the presence of such microorganisms and their potential links to blood meal sources. In this study, we analyzed 320 blood-fed female A. aegypti mosquitoes collected from urban areas of Ibagué, Colombia, using RNA-Seq to identify eukaryotic, prokaryotic, and viral sequences, with particular emphasis on insect-specific viruses (ISVs). This approach allowed us to assess the diversity and relative abundance of microorganisms across four mosquito populations, infer potential feeding sources, identify and recover complete viral genomes, and detect parasite families. Despite inherent limitations related to taxonomic classification based on databases, our findings contribute to a better understanding of the ecological and epidemiological characteristics of A. aegypti populations circulating in Ibagué, Colombia, and their vector-pathogen-host interactions.},
}
@article {pmid41380668,
year = {2025},
author = {Sumner, JT and Huttelmaier, S and Pickens, CI and Moghadam, AA and Abdala-Valencia, H and Shen, J and , and Hauser, AR and Seed, PC and Wunderink, RG and Hartmann, EM},
title = {Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {12},
pages = {2148-2166.e8},
doi = {10.1016/j.chom.2025.11.011},
pmid = {41380668},
issn = {1934-6069},
mesh = {Humans ; *Microbiota/genetics ; *Lung/microbiology ; Disease Progression ; RNA, Ribosomal, 16S/genetics ; *Pneumonia/microbiology/pathology ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; Bacterial Load ; Middle Aged ; Aged ; },
abstract = {The precise microbial determinants driving clinical outcomes in severe pneumonia are unknown. Competing ecological forces produce dynamic microbiota states in health and disease, and a more thorough understanding of these states has the potential to improve pneumonia therapy. Here, we leverage a large collection of bronchoscopic samples from patients with suspected pneumonia to determine lung microbial ecosystem dynamics throughout the course of pneumonia. We combine 16S rRNA gene, metagenomic, and metatranscriptomic sequencing with bacterial-load quantification to reveal clinically relevant drivers of pneumonia progression. Microbiota states are predictive of pneumonia subtypes and exhibit differential stability and pneumonia therapy response. Disruptive forces, such as aspiration, are associated with cohesive changes in gene expression and microbial community structure. In summary, we show that host and microbiota landscapes change in unison with clinical phenotypes and that microbiota state dynamics reflect pneumonia progression. We suggest that distinct pathways of lung microbial community succession mediate pneumonia progression.},
}
@article {pmid41380611,
year = {2026},
author = {Xie, C and Li, Y and Wulijia, B and Dong, X and Wang, L and Song, Y and Liao, X},
title = {Centennial Pb-Zn mining pollution: Spatial distance impacts on agricultural soil microbiota stress response.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119550},
doi = {10.1016/j.ecoenv.2025.119550},
pmid = {41380611},
issn = {1090-2414},
mesh = {*Mining ; *Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; China ; *Lead/analysis/toxicity ; *Microbiota/drug effects ; *Zinc/analysis/toxicity ; Environmental Monitoring ; *Metals, Heavy/analysis/toxicity ; Bacteria/genetics/drug effects/classification ; Agriculture ; Soil/chemistry ; Cadmium/analysis/toxicity ; Stress, Physiological ; },
abstract = {Mining activities pose significant threats to agricultural ecosystems through heavy metals (HMs) contamination, particularly in acidic red soils. Since there was limited research on the response mechanisms of agricultural microorganisms at different distances within typical mining areas to HMs stress, This study investigated HMs pollution patterns, microbial community dynamics, and functional gene responses in farmland surrounding a century-old Pb-Zn mine in Shuikoushan, Hengyang City, China. Soil samples were collected from three zones: Short-Distance (SD, 0-10 km), Medium-Distance (MD, 10-15 km), and Long-Distance (LD, 15-25 km) from the mine. Results revealed a pronounced distance-dependent decline in composite HMs pollution, with Cd (R[2]=0.61) and As (R[2]=0.51) showing the strongest correlations to proximity. SD zone exhibited severe contamination, with Cd (8.25 ± 5.74 mg kg[-1]) and As (58.58 ± 49.63 mg kg[-1]) concentrations exceeding regulatory limits by 27.5 and 1.95 fold, respectively. Bacterial diversity demonstrated significant spatial stratification, with Shannon indices increasing from SD to LD zones (6.8→7.2), while β-diversity decreased, indicating reduced ecological heterogeneity at lower pollution levels. High HMs stress in SD zone favored anaerobic taxa like Thermomarinilinea and acid-tolerant phyla like Acidobacteriota, whereas aerobic taxa like Gaiella dominated less-polluted areas. Metagenomic analysis revealed upregulation of HMs resistance genes (czcABCD, cadCD, arsABCJR) in SD zone. Correlation network analysis highlighted intensified positive interactions among bacterial genus under HMs stress, suggesting cooperative survival strategies. These findings elucidate the dual pressure of HMs toxicity and soil acidification on microbial ecosystems, providing critical insights for ecological risk assessment and bioremediation strategies in mining-impacted agricultural lands. The study underscores the need for distance-based pollution control measures and highlights microbial genetic adaptation as a potential tool for rehabilitating heavy metal-contaminated red soils.},
}
@article {pmid41380282,
year = {2026},
author = {Xu, X and Wang, J and Deng, C and Yu, X and Nie, R and Wang, S and Huang, W},
title = {Metagenomic insights into rhizosphere microbiome dynamics of Oenanthe javanica in ecological floating beds under different hydrodynamic regimes.},
journal = {Journal of contaminant hydrology},
volume = {277},
number = {},
pages = {104795},
doi = {10.1016/j.jconhyd.2025.104795},
pmid = {41380282},
issn = {1873-6009},
mesh = {*Rhizosphere ; *Microbiota ; Metagenomics ; Hydrodynamics ; *Caryophyllaceae/microbiology ; Bacteria/genetics ; Phosphorus/metabolism ; Nitrogen/metabolism ; },
abstract = {Ecological floating beds (EFBs) are a cost-effective and sustainable technology that utilizes macrophyte to remove nutrients from aquatic ecosystems, where rhizosphere bacterial degradation and assimilation play a key role in nutrient removal. However, the current knowledge about how hydrodynamic regimes impact the rhizosphere bacterial community on EFB systems remains limited. Here, we investigated the effects of different hydrodynamic regimes (i.e., stagnant water, pulsed water, and flowing water conditions) on the rhizosphere bacterial community structure and function of Oenanthe javanica in an experimental EFB system based on metagenomic sequencing. We observed that bacterial community compositions on the roots of O. javanica were significantly differed across the three hydrodynamic regimes, with the highest bacterial biodiversity captured from the flowing water condition. Moreover, a total of 65 nitrogen functional genes (NFGs) were identified in the rhizosphere bacterial community, with nitrate reduction pathways dominating the nitrogen cycling processes. In contrast, totally 139 phosphorus functional genes (PFGs) were detected, primarily involved in purine metabolism, which drove the phosphorus cycling dynamics. We found the distinct nitrogen and phosphorus metabolic strategies of rhizosphere bacterial communities in response to hydrodynamic regime changes. Specifically, the relative abundances of NFGs like nasB, narl, and ansB were significantly increased under the pulsed water condition, whereas gdh_K00262 were relative abundant under the flowing condition. Moreover, pulsed water condition promoted the relative abundances of PFGs such asas phnC, phoD, and pgtP in rhizosphere bacterial communities, in contrast to the stagnant condition, which favored genes like ugpC, purK, phoH, and purA. Our study offers technical support for regulating plant degradation of pollutants to improve EFB's performance in engineering applications.},
}
@article {pmid41379797,
year = {2025},
author = {Vásquez, JN and Doncel, P and Camacho, J and Ruiz, E and Recio, V and Tarragó, D},
title = {Targeted virome deep sequencing reveals frequent herpesvirus detection in intestinal biopsies of inflammatory bowel disease patients.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337322},
pmid = {41379797},
issn = {1932-6203},
mesh = {Humans ; *Virome/genetics ; Female ; Male ; *Inflammatory Bowel Diseases/virology/pathology ; Biopsy ; High-Throughput Nucleotide Sequencing ; Adult ; Middle Aged ; *Herpesviridae/genetics/isolation &amp; purification ; Retrospective Studies ; Aged ; Intestinal Mucosa/virology/pathology ; *Intestines/virology/pathology ; Colitis, Ulcerative/virology ; Metagenomics ; Young Adult ; },
abstract = {BACKGROUND: The intestinal virome is increasingly recognized for its impact on intestinal health and disease. Inflammatory bowel disease (IBD) has been linked to microbial dysbiosis, yet most studies rely on fecal samples. Here, we characterized the mucosa-associated virome directly from intestinal biopsies, providing a more localized view of viral activity at the site of pathology.<br><br>METHODS: We conducted a retrospective metagenomic study of 56 residual intestinal biopsy samples from IBD patients including ulcerative colitis (n&#x2009;=&#x2009;37; 66.1%), IBD-Unclassified (n&#x2009;=&#x2009;9; 16.1%), ulcerative proctitis (n&#x2009;=&#x2009;7; 12.5%), and Crohn's disease (n&#x2009;=&#x2009;3; 5.4%), applying high-throughput sequencing after viral nucleic acid enrichment using a probe-based capture approach. Metagenomic data were processed using the Chan Zuckerberg ID (CZ ID) platform.<br><br>RESULTS: Viruses were detected in 58.9% (33/56) of the biopsies, primarily members of the Herpesviridae family. EBV was the most frequently detected virus (33.9%), followed by HHV-7 (21.4%), and both CMV and HHV-6 (12.5% each), after decomposing coinfections. Other viruses such as Norovirus and human papillomavirus (HPV) were detected at lower frequencies. Coinfections were also identified. No statistically significant associations were found between viral presence and IBD (ulcerative colitis, Crohn's disease, ulcerative proctitis, and IBD-Unclassified).<br><br>CONCLUSIONS: Herpesviruses are rarely detected in healthy intestinal viromes and are generally considered absent, whereas their frequent presence in IBD biopsies suggests possible pathological relevance. Our findings highlight the value of metagenomic sequencing in characterizing the intestinal virome to assess the diagnostic or prognostic value of viral biomarkers in IBD.},
}
@article {pmid41379255,
year = {2025},
author = {Špiljak, B and Ozretić, P and Brailo, V and Škrinjar, I and Lončar Brzak, B and Andabak Rogulj, A and Butić, I and Tambić Andrašević, A and Vidović Juras, D},
title = {Microbial dysbiosis and host-microbe interactions in proliferative verrucous leukoplakia: insights into carcinogenic potential.},
journal = {Archives of microbiology},
volume = {208},
number = {1},
pages = {65},
pmid = {41379255},
issn = {1432-072X},
mesh = {Humans ; *Dysbiosis/microbiology ; *Leukoplakia, Oral/microbiology/pathology ; Microbiota ; *Host Microbial Interactions ; Carcinogenesis ; Mouth Neoplasms/microbiology/pathology ; },
abstract = {Proliferative verrucous leukoplakia (PVL) is a rare and aggressive oral potentially malignant disorder (OPMD) characterized by multifocal keratotic plaques, progressive expansion, high recurrence, and a strong risk of malignant transformation. Although its etiology remains unclear, recent evidence emphasizes the role of the oral microbiome as a key factor in disease progression. Alterations in microbial diversity and ecological balance create a shift toward dysbiosis, supporting a chronic inflammatory microenvironment that favors epithelial transformation. Specific taxa, including Fusobacterium and Porphyromonas, have been implicated in biofilm formation, immune evasion, and modulation of epithelial signaling pathways. These interactions highlight the potential of microbial communities to drive oncogenic processes through host-microbe crosstalk. Advanced methodological approaches such as metagenomics, functional microbiome profiling, and multi-omics integration provide novel opportunities to unravel the mechanisms of dysbiosis in PVL. Beyond pathogenesis, microbiome research opens perspectives for the identification of predictive biomarkers, targeted prevention, and microbiome-based therapeutics. This review synthesizes current insights into the microbial basis of PVL and outlines future directions aimed at improving understanding of host-microbe interactions and their role in oral carcinogenesis. Relevant literature was identified through PubMed and Web of Science searches (1985-2025) using terms related to PVL, oral leukoplakia, OPMD, oral microbiome, and oral squamous cell carcinoma. In conclusion, current evidence suggests that while microbial dysbiosis is not an isolated driver, it likely synergizes with genetic, epigenetic, and immunological factors in PVL progression, offering opportunities for biomarker discovery and novel therapeutic strategies. This study also provides a potential direction for the early diagnosis of PVL and the development of microecologically targeted interventions.},
}
@article {pmid41379245,
year = {2025},
author = {Namadara, S and Pragadeesh, ARU and Uthandi, S and Rangasamy, A and Malaichamy, K and Venkatesan, M and Narayanan, MB and Murugaiyan, S},
title = {Comparative metagenomic analysis of bacterial communities associated with two mealybug species, Phenacoccus saccharifolii and Dysmicoccus carens infesting sugarcane in Tamil Nadu, India.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {12},
pages = {504},
pmid = {41379245},
issn = {1573-0972},
support = {DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; DABC/CPN001/ Kothari sugars-AGM,DNRM,CBE/2024//kothari sugars/ ; },
mesh = {*Saccharum/parasitology ; Animals ; India ; *Bacteria/classification/genetics/isolation &amp; purification ; *Hemiptera/microbiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {This study presents a comparative metagenomic analysis of the gut bacterial communities of two sugarcane-infesting mealybug species, Phenacoccus saccharifolii (WR) and Dysmicoccus carens (RR), from Tamil Nadu, India. Using Oxford Nanopore sequencing of the 16s rRNA gene spanning the hypervariable regions V1 - V9 and predictive metagenomics, differences in microbial diversity, taxonomy, and functional potential were assessed to explore the ecological adaptations of the gut microbiota in mealybugs. The D. carens gut microbiome showed higher species richness than P. saccharifolii (WR) (125 vs. 45 species, p < 0.05) but lower community evenness (0.43 vs. 0.61, p < 0.05), resulting in similar overall Shannon diversity (2.08 vs. 2.30) despite markedly different community structures, which may be influenced by their different feeding niches, including the sugarcane crown region, leaf sheath tissues, and basal stem and root portions. Both mealybug species exhibited contrasting bacterial community structures. D. carens (RR) harbored high abundances of endosymbionts (43.8%), Gilliamella (22.3%), Enterobacter (18.3%), and Candidatus Tremblaya (9.3%), representing a symbiont-dominated microbiome typical of many hemipteran insects. P. saccharifolii (WR) displayed a distinct profile with Serratia as the dominant genus (43.2%), followed by Enterobacter (20.1%), Klebsiella (14.6%), and substantially reduced endosymbiont abundances (14.8%). Beta diversity analysis revealed distinct community clustering of species, highlighting the variation driven by feeding habitat and host genotype. Functional profiling indicated largely conserved metabolic capabilities dominated by amino acid and carbohydrate metabolism, which was a key to compensate the nutrient-poor phloem sap diet. The core microbiome identified several genera that form complex ecological networks, emphasizing their importance in community stability. These findings provide insights into the role of symbiotic bacteria in mealybug adaptation to different ecological niches within the sugarcane agroecosystem. Understanding these host-microbiome interactions may facilitate the development of targeted, microbiome-based biocontrol strategies for sustainable mealybug management in sugarcane cultivation.},
}
@article {pmid41379027,
year = {2025},
author = {Esvap, E and Ulgen, KO},
title = {Community Modeling Reveals Disrupted Gut Microbial Secretion in Autism Associated With Redox and Neurometabolic Alterations.},
journal = {Biotechnology journal},
volume = {20},
number = {12},
pages = {e70164},
doi = {10.1002/biot.70164},
pmid = {41379027},
issn = {1860-7314},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Oxidation-Reduction ; Child ; Male ; Feces/microbiology ; *Autism Spectrum Disorder/microbiology/metabolism ; Female ; Child, Preschool ; Metagenomics ; Metabolomics ; Bacteria/metabolism/classification/genetics ; *Autistic Disorder/microbiology/metabolism ; },
abstract = {Emerging evidence suggests that disruptions in the gut microbiome may influence autism spectrum disorder (ASD) through altered microbial metabolism and gut-brain communication. However, the specific metabolic impacts of these microbial changes remain unclear. Community-scale metabolic modeling was applied to shotgun metagenomics data from children with ASD and neurotypical controls to predict secretion of host-impacting metabolites. Modeled ASD-associated communities exhibited altered predicted secretion of metabolites related to redox balance and neurotransmission, including increased 2-ketobutyrate and GABA and reduced riboflavin and inositol, with microbiota transfer therapy (MTT) shifting these profiles toward NT. Empirical fecal metabolomics data showed generally consistent directional trends with model predictions. Reductions in autism severity scores following MTT were associated with increased predicted secretion potentials for inositol and arginine. Taxonomic analysis revealed a depletion of beneficial and an enrichment of pro-inflammatory species, such as Escherichia and Flavonifractor, in ASD. Associations between microbial taxa (e.g., Bacteroides, Bifidobacterium) and neuroactive metabolites highlight microbial modulation as a promising therapeutic strategy in ASD. These results emphasize microbial metabolism as a contributor to ASD traits and a target for therapeutic intervention.},
}
@article {pmid41378778,
year = {2025},
author = {Zhou, Y and Ren, X and Li, B and Tang, H and Guo, Y and Yang, L and Han, J and Zhou, B},
title = {Bis(2-ethylhexyl)-2,3,4,5-tetrabromophthalate Triggers IBD-like Pathology through the Gut Microbiota-Arachidonic Acid Axis: Protective Role of Akkermansia muciniphila.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {50},
pages = {27156-27172},
doi = {10.1021/acs.est.5c12302},
pmid = {41378778},
issn = {1520-5851},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; *Inflammatory Bowel Diseases/chemically induced ; Arachidonic Acid/metabolism ; Akkermansia ; Phthalic Acids ; },
abstract = {Environmental pollutants are increasingly recognized as modulators of gut microbiota and metabolic pathways, contributing to the rising global incidence of inflammatory bowel disease (IBD). The novel brominated flame retardant bis(2-ethylhexyl)-2,3,4,5-tetrabromophthalate (TBPH) is increasingly detected in ecosystems and human tissues, yet its impact on intestinal health remains unclear. Here, we combined shotgun metagenomics, untargeted metabolomics, and targeted biochemical assays in a murine model to reveal how TBPH drives IBD-like pathology. TBPH exposure resulted in shortened colons, disrupted epithelial barriers, and elevated systemic pro-inflammatory cytokines, accompanied by gut microbiota dysbiosis marked by depletion of Akkermansia muciniphila (AKK). Decreased abundance of AKK correlated with arachidonic acid (AA) accumulation and hyperactivation of the phospholipase A2 (PLA2)-cyclooxygenase 2 (COX2)-prostaglandin E2 (PGE2) inflammatory cascade, leading to NF-κB activation and mucosal injury. Supplementation with viable AKK restored AA homeostasis, suppressed inflammatory signaling, and preserved the barrier integrity. These results demonstrate a microbiota-dependent mechanism linking TBPH exposure to AA-driven intestinal inflammation and identify AKK as a critical protective species, which highlights the gut microbiota-AA metabolic axis as a potential mechanism for pollutant-induced intestinal disorders.},
}
@article {pmid41373884,
year = {2025},
author = {Ahlström, MG and Bjerre, RD and Hu, Y and Seifert, M and Boulund, F and Skov, L and Johansen, JD and Engstrand, L},
title = {Resilience of the Skin Microbiome in Atopic Dermatitis During Short-Term Topical Treatment.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
pmid = {41373884},
issn = {1422-0067},
support = {LF-ST-21-500002//LEO Foundation/ ; },
mesh = {Humans ; *Dermatitis, Atopic/microbiology/drug therapy ; *Microbiota/drug effects ; *Skin/microbiology/drug effects ; Adult ; Female ; Male ; Middle Aged ; Administration, Topical ; Young Adult ; Dysbiosis/microbiology ; Skin Microbiome ; },
abstract = {Atopic dermatitis (AD) is associated with microbial dysbiosis and impaired skin barrier function. Topical therapies, such as moisturisers and antimicrobial fragrance compounds, may modulate the skin microbiome and support disease management. The objective was to evaluate how a moisturiser and a fragrance compound (farnesol) influence skin microbiome composition in individuals with AD and healthy controls. In a randomised, controlled, operator-blinded study, 15 AD patients and 15 healthy controls applied a moisturiser, farnesol, moisturiser + farnesol, or no treatment to defined skin areas over 7 days. Microbiome composition, alpha/beta diversity, and core taxa were analysed using shotgun metagenomics. At baseline, AD patients exhibited distinct microbial profiles, including elevated Staphylococcus aureus and Micrococcus luteus. Neither moisturiser nor farnesol significantly altered richness, beta diversity, or core taxa in either AD patients or controls. However, moisturiser use in healthy individuals modestly increased Shannon diversity, reflecting improved microbial evenness. Despite clear microbiome differences between AD and healthy skin, short-term topical treatment did not markedly shift microbial composition. The observed stability underscores the resilience of the skin microbiome and suggests that longer interventions or more targeted formulations may be necessary to influence microbial dysbiosis in AD.},
}
@article {pmid41373768,
year = {2025},
author = {Sobolev, A and Sibiryakina, D and Chevokina, E and Slonova, D and Yurikova, D and Kozlova, S and Trofimova, A and Zubarev, V and Kiselev, A and Konovalova, O and Sutormin, D and Isaev, A},
title = {Benchmarking Cost-Effective DNA Extraction Kits for Diverse Metagenomic Samples.},
journal = {International journal of molecular sciences},
volume = {26},
number = {23},
pages = {},
pmid = {41373768},
issn = {1422-0067},
support = {075-10-2021-114//Ministry of Science and Higher Education/ ; 22-14-00004//Russian Science Foundation/ ; },
mesh = {*Metagenomics/methods/economics ; Animals ; RNA, Ribosomal, 16S/genetics ; Cost-Benefit Analysis ; Feces/microbiology ; Benchmarking ; *Metagenome ; *DNA, Bacterial/isolation &amp; purification/genetics ; Reproducibility of Results ; Geologic Sediments/microbiology ; *DNA/isolation &amp; purification ; Gastrointestinal Microbiome/genetics ; },
abstract = {Extraction of high-quality microbial DNA remains a critical bottleneck in metagenomic research. Environmental samples often produce fragmented DNA and are prone to contaminations that interfere with downstream sequencing, while widely used commercial kits can be prohibitively expensive. Therefore, systematic evaluation of cost-effective alternatives is essential to support large-scale metagenomic studies. In this work, we benchmarked eight commercial DNA extraction kits from Magen, SkyGen, and Sileks against Qiagen reference kits. Four representative sample types were analyzed: freshwater, seafloor sediments, Pacific oyster (Magallana gigas) gut microbiome, and mammalian feces. DNA yield, integrity, purity, PCR inhibitor content, and eukaryotic DNA admixture were assessed. Microbial community composition, alpha diversity, reproducibility, and contamination ("kitome" and "splashome") were further evaluated using 16S rRNA amplicon sequencing. We revealed that several alternative kits performed comparably or better than the Qiagen reference standard. Magen Soil and Magen Bacterial provided high yields and reproducibility, though the latter produced more fragmented DNA. SkyGen Stool excelled with host-associated samples, while Sileks Soil and Metagenomic kits preserved higher diversity in sediments. Magen Microbiome consistently underperformed. This study identifies multiple cost-effective DNA extraction strategies and provides practical guidance for selecting balanced DNA purification methods for different sample types.},
}
@article {pmid41372802,
year = {2025},
author = {Almas, S and Carpenter, RE and Tamrakar, VK and Singh, A and Sharma, A and Sharma, R},
title = {Precision metagenomics reveals microbial landscape in acute upper respiratory infections: a comprehensive dataset.},
journal = {BMC research notes},
volume = {19},
number = {1},
pages = {18},
pmid = {41372802},
issn = {1756-0500},
mesh = {Humans ; *Respiratory Tract Infections/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Acute Disease ; Male ; Female ; Middle Aged ; Adult ; },
abstract = {OBJECTIVES: The comprehension of the microbial composition in upper respiratory tract infections is pivotal for the progression of diagnostic and treatment methodologies. This article presents a dataset derived from Precision Metagenomic next-generation sequencing using hybridization capture-based targeted sequencing. Nasopharyngeal samples from 24 patients with acute URIs were analyzed using the Illumina[®]/IDbyDNA Respiratory Pathogen ID/AMR panel. The dataset contains a wealth of information on the composition of the microbiota, including the relative abundance of known pathogens and their potential clinical significance.<br><br>DATA DESCRIPTION: This dataset serves as a valuable asset for future research in respiratory medicine, infectious disease epidemiology, antimicrobial resistance detection, and therapeutic interventions. Its potential for reuse and integration with other omics datasets enhances its significance. The comprehensive nature of the data facilitates research into relationships between the respiratory microbiota and host factors, including clinical outcomes, immune responses, or genetic predispositions. Moreover, the article underscores the interdisciplinary potential by advocating for the integration of this dataset with other relevant datasets such as transcriptomics or metabolomics, enabling a deeper understanding of the intricate interactions in acute upper respiratory infections. The presented dataset contributes to the expanding knowledge in precision metagenomics and holds the promise to propel research and clinical practices in the field of respiratory diseases.},
}
@article {pmid41372750,
year = {2025},
author = {Zhou, Y and Chang, L and Sun, H and Li, W and Ao, T and Lin, J},
title = {Metagenomic insights into microbial communities and antibiotic resistance in treated wastewater for urban irrigation.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {26},
pmid = {41372750},
issn = {1471-2180},
mesh = {*Wastewater/microbiology/chemistry ; *Metagenomics/methods ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Agricultural Irrigation ; Metals, Heavy/analysis ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Cities ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Water Microbiology ; },
abstract = {BACKGROUND: The increasing reuse of treated wastewater for urban irrigation globally has raised ecological and public health concerns associated with microbial contaminations, antibiotic resistance genes (ARGs), and pathogen dissemination.<br><br>METHODS: Using a metagenomic approach, we analyzed microbial communities, ARGs, and pathogen profiles in three types of treated wastewater (W1, W2, W3) used for urban irrigation. Physicochemical properties, including nutrients and heavy metals, were also assessed to identify potential drivers of microbial and resistance patterns.<br><br>RESULTS: Significant variations in water quality and microbial community were observed across wastewater treatments. W2 showed the highest nutrient and organic pollution levels, while W3 exhibited elevated heavy metals such as zinc (83.37&#xa0;&#xb5;g/L), chromium (1.89&#xa0;&#xb5;g/L), and nickel (4.93&#xa0;&#xb5;g/L). Treated wastewater harbored significantly higher microbial diversity than tap water (P&#x2009;<&#x2009;0.05), with W3 showing the most unique amplicon sequence variants (ASVs; 1 945, 7.31%). ARGs analysis revealed treatment-specific profiles: W1 was enriched in mupirocin and tetracycline resistance, W2 was dominated with beta-lactams and sulfonamides (P&#x2009;<&#x2009;0.05), and W3 was enriched in fosfomycin and diaminopyrimidine resistance. Multidrug resistance genes dominated across all samples. PCoA revealed distinct microbial and ARGs structures across treatments (P&#x2009;<&#x2009;0.05). Pathogens such as Salmonella enterica and Pseudomonas aeruginosa were abundant in treated wastewater, with Escherichia coli and Staphylococcus aureus identified as key pathogen hubs in ARG-pathogen co-occurrence networks. Nutrients (total nitrogen, phosphorus) and heavy metals (Fe and Pb) were key drivers of microbial community composition, ARGs abundance and pathogen prevalence.<br><br>CONCLUSIONS: This study underscores the ecological risks of using treated wastewater in urban environment, particularly due to the persistence of ARGs and pathogenic bacteria. Targeted removal of nutrients and heavy metals during wastewater treatment could help reduce microbial and resistance-related contamination, improving the safety of treated wastewater reuse.},
}
@article {pmid41372637,
year = {2026},
author = {Kosmopoulos, JC and Pallier, W and Malik, AA and Anantharaman, K},
title = {Ecosystem health shapes viral ecology in peatland soils.},
journal = {Nature microbiology},
volume = {11},
number = {1},
pages = {142-154},
pmid = {41372637},
issn = {2058-5276},
support = {DBI2047598//National Science Foundation (NSF)/ ; 2137424//National Science Foundation (NSF)/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Ecosystem ; *Viruses/genetics/classification/isolation &amp; purification ; United Kingdom ; Metagenome ; Microbiota ; Carbon ; Phylogeny ; },
abstract = {Peatlands hold up to one-third of Earth's soil carbon but are increasingly turning from being carbon sinks to becoming carbon sources due to human impacts. Restoration efforts aim to reverse this trend, but viral influences on peatland recovery remain unclear, despite viruses being potent regulators of microbiomes and ecosystem function. Here we sequenced soil metagenomes to study viral communities across seven UK peatlands, each encompassing areas representing three peatland ecosystem health statuses: natural, damaged and restored. We found that viral diversity and community structure were shaped by both geography and ecosystem health. Viruses were geographically widespread, yet exhibited ecosystem health-specific endemism and functional adaptation, highlighting their sensitivity to restoration. Virus-host dynamics ranged from stable 'piggyback-the-winner' relationships to decoupled dynamics in those infecting keystone aerobes, sulfate reducers, carbohydrate degraders and fermenters. These findings position viruses as dynamic drivers of peatland ecosystem recovery and could unlock pathways to bolster carbon retention and accelerate climate mitigation.},
}
@article {pmid41372407,
year = {2026},
author = {Asnicar, F and Manghi, P and Fackelmann, G and Baldanzi, G and Bakker, E and Ricci, L and Piccinno, G and Piperni, E and Mladenovic, K and Amati, F and Arrè, A and Ganesh, S and Giordano, F and Davies, R and Wolf, J and Bermingham, KM and Berry, SE and Spector, TD and Segata, N},
title = {Gut micro-organisms associated with health, nutrition and dietary interventions.},
journal = {Nature},
volume = {650},
number = {8101},
pages = {450-458},
pmid = {41372407},
issn = {1476-4687},
support = {/WT_/Wellcome Trust/United Kingdom ; U01 CA230551/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; *Diet ; Male ; Female ; United Kingdom ; Body Mass Index ; Risk Factors ; United States ; *Health ; Middle Aged ; *Nutritional Status ; Adult ; Metagenomics ; },
abstract = {The incidence of cardiometabolic diseases is increasing globally, and both poor diet and the human gut microbiome have been implicated[1]. However, the field lacks large-scale, comprehensive studies exploring these links in diverse populations[2]. Here, in over 34,000 US and UK participants with metagenomic, diet, anthropometric and host health data, we identified known and yet-to-be-cultured gut microbiome species associated significantly with different diets and risk factors. We developed a ranking of species most favourably and unfavourably associated with human health markers, called the 'ZOE Microbiome Health Ranking 2025'. This system showed strong and reproducible associations between the ranking of microbial species and both body mass index and host disease conditions on more than 7,800 additional public samples. In an additional 746 people from two dietary interventional clinical trials, favourably ranked species increased in abundance and prevalence, and unfavourably ranked species reduced over time. In conclusion, these analyses provide strong support for the association of both diet and microbiome with health markers, and the summary system can be used to inform the basis for future causal and mechanistic studies. It should be emphasized, however, that causal inference is not possible without prospective cohort studies and interventional clinical trials.},
}
@article {pmid41371144,
year = {2026},
author = {Zhao, K and Yang, L and Zhang, Y and Fang, H and Huang, Y and Hou, J and Wang, X and Liu, W and Luo, Y},
title = {Enrichment of a microbial consortium for 1,1,2-trichloroethane remediation: Insights into dechlorinators and community interactions.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140716},
doi = {10.1016/j.jhazmat.2025.140716},
pmid = {41371144},
issn = {1873-3336},
mesh = {*Microbial Consortia ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Trichloroethanes/metabolism ; Chloroflexi/metabolism/genetics ; Halogenation ; Bacteria/metabolism/genetics ; },
abstract = {Chlorinated aliphatic hydrocarbons (CAHs), such as 1,1,2-trichloroethane (1,1,2-TCA), are persistent groundwater pollutants with high toxicity and carcinogenicity. Anaerobic reductive dechlorination by organohalide-respiring bacteria (OHRB) offers a promising remediation strategy. In this study, a stable microbial consortium, designated ZJGTCA, was enriched and shown to dechlorinate 1,1,2-TCA to ethene, achieving a complete dechlorination rate of 51.22 μM·day[-1] and a dihaloelimination rate of 2150 μM·day[-1] . Microbial succession analyses identified Trichlorobacter and Dehalococcoides as key dechlorinators, with qPCR quantifying their abundances as 2.82 × 10 [10] and 8.92 × 10 [11] copies·L[-1] , respectively. Network and metagenomic analyses revealed that Trichlorobacter and Citrobacter contribute critically to cofactor biosynthesis, including biotin, thiamine, and cobalamin pathways. Metagenome-assembled genome (MAG) analysis further established a microbial interaction model in which Trichlorobacter performs dihaloelimination, Dehalococcoides completes hydrogenolysis, and both Trichlorobacter and Citrobacter act as cofactor producers. Fermentative bacteria such as Sphaerochaeta metabolize lactate, propionate, and long-chain fatty acids into acetate and H2, supporting dechlorinators. These complementary functions highlight the ecological interactions sustaining efficient 1,1,2-TCA reductive dechlorination. The ZJGTCA consortium represents a promising bioaugmentation agent for CAHs-contaminated groundwater, offering insights into enhancing pollutant degradation and maintaining microbial community stability.},
}
@article {pmid41371128,
year = {2026},
author = {Zeng, BH and Li, P and Zhang, HR and Xia, BH and Liu, B and Kong, LM and Liu, L and Li, ZH},
title = {The gut as a reservoir of drug-resistant pathogens: Mechanisms of ENR-driven horizontal gene transfer in aquaculture.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140758},
doi = {10.1016/j.jhazmat.2025.140758},
pmid = {41371128},
issn = {1873-3336},
mesh = {*Gene Transfer, Horizontal/drug effects ; Aquaculture ; *Gastrointestinal Microbiome/drug effects ; *Enrofloxacin/pharmacology ; Animals ; *Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; *Drug Resistance, Bacterial/genetics ; Fatty Acids, Volatile/metabolism ; Bacteriophages/genetics ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; },
abstract = {Enrofloxacin (ENR), commonly used in aquaculture, plays a role in the development and dissemination of antibiotic resistance genes (ARGs). While most research on ARGs has focused on the environment, the gut, the host's largest microbial habitat, remains underexplored. Accordingly, this research investigates the gut microbiome, aiming to assess the potential mobility of ARGs after ENR exposure. Additionally, ENR exposure alters short-chain fatty acid (SCFAs) levels. Subsequent conjugation transfer experiments demonstrated that ENR exposure modifies SCFA levels, and this alteration facilitates the spread of ARGs. Both plasmid- and phage-mediated ARGs transmission were observed. ENR exerted selective pressure on the gut microbiota, significantly promoting plasmid-mediated conjugation as a key driver of ARGs dissemination. Simultaneously, environmental stress triggered the release of progeny phages carrying ARGs, further facilitating their spread. Conjugation experiments confirmed that ENR and SCFAs interact with bacterial outer membrane proteins, inducing the production of ROS. As a result of ROS production, membrane integrity is disrupted and membrane permeability is increased, ultimately causing an increase in the frequency of conjugative transfer and facilitating the horizontal delivery of ARGs. Therefore, ENR not only directly influences the transmission of ARGs but also indirectly promotes their transmission by altering SCFA levels. The study findings underscore the risks posed by excessive use of ENR in aquaculture to public health, providing scientific evidence to prevent food safety hazards from market entry of aquatic products carrying drug-resistant pathogens.},
}
@article {pmid41370957,
year = {2026},
author = {Tian, H and Liu, J and Zhang, Y and Yang, T and Hao, G},
title = {Decoding the microplastic Micro-interface: a complex Web of gene transfer and pathogenic threats in wastewater.},
journal = {Environment international},
volume = {207},
number = {},
pages = {109971},
doi = {10.1016/j.envint.2025.109971},
pmid = {41370957},
issn = {1873-6750},
mesh = {*Wastewater/microbiology ; *Gene Transfer, Horizontal ; *Microplastics/analysis ; *Microbiota ; Virulence Factors/genetics ; Waste Disposal, Fluid ; Drug Resistance, Microbial/genetics ; },
abstract = {The microplastic micro-interface (MPMI) in the municipal wastewater treatment system (MWTS) provides a new ecological niche for the microbiome (MGs) and potential pathogens (PPHs), facilitating both vertical and horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). However, the distribution patterns and gene transfer events of PPHs, ARGs, and VFGs in MPMI remain unknown. This study examined three representative MPMIs (PET-MPMI, PE-MPMI, and PP-MPMI) colonized in the transverse gradient of MWTS using metagenomics. MGs, PPHs, ARGs, VFGs, and MGEs varied significantly across transverse gradients and horizontal interfaces. In MPMI, MGs/PPHs exhibited better connectivity and robustness (closeness centrality 19.51/21.45 and betweenness centricity 19.66/14.07), ARG hosts (mostly Escherichia coli and Salmonella enterica) demonstrated greater contig diversity and richness (6.44-7.36%), and adhesive VFGs provided superior competitive advantages. Additionally, MPMI shows a more complex and persistent coexistence pattern of MGs, ARGs, and VFGs (54.30-57.25%), increasing pathogenicity risk. MPMI accelerates the HGT of ARGs mediated by MGEs at the horizontal interface and transverse gradients through PPHs, with MGs, PPHs, MGEs, and VFGs directly influencing the alterations in ARGs within MPMI. This study developed a conceptual framework to understand MPMI gene co-occurrence and transfer across transverse gradients and interfaces, as well as the health risks of MPMI from ARG and VFG metastasis mediated by PPHs.},
}
@article {pmid41370178,
year = {2025},
author = {Peto, L and Fawcett, N and Kamfose, MM and Scarborough, C and Peniket, A and Danby, R and Peto, TEA and Crook, DW and Llewelyn, MJ and Walker, AS},
title = {The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {41370178},
issn = {2050-084X},
support = {NIHR200915//National Institute for Health and Care Research/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Adult ; Cross-Sectional Studies ; Middle Aged ; Aged ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Feces/microbiology ; Metagenomics ; United Kingdom ; *Bacteria/drug effects/classification/genetics ; Young Adult ; },
abstract = {Better metrics to compare the impact of different antimicrobials on the gut microbiome would aid efforts to control antimicrobial resistance (AMR). The Antibiotic Resistance in the Microbiome - Oxford (ARMORD) study recruited inpatients, outpatients, and healthy volunteers in Oxfordshire, UK, who provided stool samples for metagenomic sequencing. Data on previous antimicrobial use and potential confounders were recorded. Exposures to each antimicrobial were considered as factors in a multivariable linear regression, also adjusted for demographics, with separate analyses for those contributing samples cross-sectionally or longitudinally. Outcomes were Shannon diversity and relative abundance of specific bacterial taxa (Enterobacteriaceae, Enterococcus, and major anaerobic groups) and antimicrobial resistance genes (targeting beta-lactams, tetracyclines, aminoglycosides, macrolides, and glycopeptides). 225 adults were included in the cross-sectional analysis, and a subset of 79 patients undergoing haematopoietic cell transplant provided serial samples for longitudinal analysis. Results were largely consistent between the two sampling frames. Recent use of piperacillin-tazobactam, meropenem, intravenous co-amoxiclav, and clindamycin was associated with large reductions in microbiome diversity and reduced abundance of anaerobes. Exposure to piperacillin-tazobactam and meropenem was associated with a decreased abundance of Enterobacteriaceae and an increased abundance of Enterococcus and major AMR genes, but there was no evidence that these antibiotics had a greater impact on microbiome diversity than iv co-amoxiclav or oral clindamycin. In contrast, co-trimoxazole, doxycycline, antifungals, and antivirals had less impact on microbiome diversity and selection of AMR genes. Simultaneous estimation of the impact of over 20 antimicrobials on the gut microbiome and AMR gene abundance highlighted important differences between individual drugs. Some drugs in the WHO Access group (co-amoxiclav, clindamycin) had similar magnitude impact on microbiome diversity to those in the Watch group (meropenem, piperacillin-tazobactam) with potential implications for acquisition of resistant organisms. Metagenomic sequencing can be used to compare the impact of different antimicrobial agents and treatment strategies on the commensal flora.},
}
@article {pmid41369685,
year = {2025},
author = {Mohammadi, R and Morovati, H and Safari, F},
title = {The human mycobiome: a critical yet understudied component of health and disease.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {12},
pages = {},
pmid = {41369685},
issn = {1465-2080},
mesh = {Humans ; *Mycobiome ; *Fungi/genetics/classification/isolation &amp; purification/physiology ; COVID-19/microbiology/complications ; Dysbiosis/microbiology ; SARS-CoV-2 ; Metagenomics ; Neoplasms/microbiology ; },
abstract = {The human body hosts a complex and dynamic microbial community that is crucial for maintaining health. While bacteria dominate this system, fungal communities, collectively called the mycobiome, are increasingly recognized as vital contributors. However, fungi remain understudied due to challenges in culturing many species, limiting our understanding of their roles, interactions and effects on human biology. Advances in next-generation sequencing have transformed mycobiome research, revealing fungal diversity and its impact on health and disease. This review examines the mycobiome's composition and function across major body sites, including the gut, mouth, lungs, reproductive tract and skin. It also explores connections between fungal imbalances (dysbiosis) and diseases such as neurological disorders, cancer and post-COVID-19 complications. Despite progress, challenges persist, including the need for better culture-independent diagnostic tools and standardized research methods. Combining culturomics and metagenomics could help overcome these limitations and identify new treatment targets. By summarizing current knowledge and highlighting research gaps, this review aims to guide future studies on the mycobiome's role in human health.},
}
@article {pmid41369293,
year = {2025},
author = {Liu, R and Wei, H and Xu, Z and Liu, Y and He, J and Wang, Z and Wang, L and Luo, M and Fang, J and Baltar, F and Xu, Y and Liang, Q and Huang, L},
title = {Extensive halogenated organic compound reservoirs and active microbial dehalogenation in Mariana Trench sediments.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {41369293},
issn = {1751-7370},
support = {//ocean negative carbon emissions program (ONCE)/ ; //Shanghai Frontiers Research Fund of the Hadal Biosphere, the deep ocean microbiome and ecosystem program (DOME)/ ; 42276149//National Natural Science Foundation of China/ ; 92251303//National Natural Science Foundation of China/ ; },
mesh = {*Geologic Sediments/microbiology/chemistry ; *Bacteria/metabolism/genetics/classification ; Microbiota ; *Hydrocarbons, Halogenated/analysis/metabolism ; Halogenation ; Carbon/analysis/metabolism ; *Organic Chemicals/metabolism/analysis ; Biodegradation, Environmental ; Metagenomics ; },
abstract = {The hadal trenches, the deepest regions of the ocean, serve as the final sinks for marine particles and "tunnels" for material exchange between the ocean and Earth's interior. Despite their extreme conditions, the trench sediments contain high content of organic carbon and active microbial carbon turnover, are hotspots for deep-sea organic carbon degradation and unique microbial processes. However, little is known about the organic carbon components and microbial metabolisms driving their degradation in trench sediments. This study provides the first comprehensive quantification of total halogenated organic compounds (organohalides) in Mariana Trench sediments. The measured bulk organic halogen concentrations exceeded all previously reported individual compounds by orders of magnitude, with a mean stoichiometric ratio of 1:49 (halogen:carbon) in the sedimentary organic carbon pool. These findings suggest the trench sediments may represent a significant reservoir for organohalides. Metagenomic analysis of global ocean data shows significant enrichment of the genes for organohalides biodegradation (dehalogenation) in trench microbiomes than those in other marine environments. Putative dehalogenating microorganisms in trench sediments encompassed 16 phyla and 52 orders, capable of metabolizing 18 structurally diverse organohalide compounds, revealing an unexpectedly broad phylogenetic distribution of organohalides metabolism and versatile substrate specificity among trench microbial communities. High pressure microcosm experiments demonstrated rapid degradation of typical organohalide compounds and transcription of genes related to organohalides metabolisms, confirming an active organohalides degradation by trench microorganisms. These findings underscore the role of organohalides metabolism in organic carbon remineralization in hadal trenches, advancing our understanding of deep-sea carbon cycling and microbial survival.},
}
@article {pmid41369187,
year = {2025},
author = {Calderón-Osorno, M and Rojas-Jimenez, K},
title = {Depth-driven decline in viral diversity unveils potential novel viruses in global deep-sea ecosystems.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {12},
pages = {},
pmid = {41369187},
issn = {1465-2080},
mesh = {*Seawater/virology ; *Viruses/genetics/classification/isolation &amp; purification ; *Biodiversity ; Ecosystem ; Metagenomics ; Phylogeny ; Microbiota ; Oceans and Seas ; Metagenome ; },
abstract = {Deep-sea ecosystems remain poorly understood due to exploration challenges. Despite the advancements metagenomics have brought to the understanding of the ocean microbiome, the diversity of marine viruses, particularly in the deep sea, is still not well characterized. In this study, we analysed the impact of depth on the composition and diversity of marine viruses in deep-sea waters at a global scale. Raw reads from deep-sea shotgun DNA sequences were retrieved from the Tara and Malaspina expeditions, encompassing depths from 270 to 4,005 m. A total of 80 samples containing viral reads were identified and analysed through a comprehensive bioinformatics pipeline, including quality assessment, taxonomic classification and metabolic annotation. The analysis reveals that microbial viral diversity significantly decreases with depth, with shallower waters exhibiting higher species richness. We determined that a substantial proportion of deep-sea viral sequences remains unclassified - up to 31.9% at depths of 270-1,000 m and 9.6% at 2,400-4,005 m. Additionally, a higher abundance of auxiliary metabolic genes was observed at shallower depths, indicating potential roles in host metabolism and adaptation. Our findings reveal the deep ocean as a vast, largely unexplored source of microbial viral diversity. This research emphasizes how depth influences viral diversity and community makeup in deep-sea environments, underscoring the need for further exploration to fully grasp their complexity and ecological roles.},
}
@article {pmid41368641,
year = {2025},
author = {He, J and Jia, J and Qu, W and Zhang, S and Fan, K and Lin, R and Zhao, W and Niu, Y and Huang, Y and Jia, L},
title = {Bacteroides ovatus-derived N-methylserotonin inhibit colorectal cancer via the HTR1D-mediated cAMP-PKA-NF-κB signaling axis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1696701},
pmid = {41368641},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/metabolism/pathology/drug therapy/microbiology ; Animals ; NF-kappa B/metabolism ; Mice ; Signal Transduction/drug effects ; Cyclic AMP/metabolism ; Gastrointestinal Microbiome ; Male ; *Serotonin/analogs &amp; derivatives/pharmacology/metabolism ; Female ; *Bacteroides/metabolism ; Cyclic AMP-Dependent Protein Kinases/metabolism ; Middle Aged ; Cell Line, Tumor ; Aged ; Disease Models, Animal ; },
abstract = {OBJECTIVE: To analyze differences in gut microbiota composition, metabolites, and metabolic pathways between healthy individuals and colorectal cancer (CRC) patients, and to investigate the inhibitory effects of N-methylserotonin (NMS) produced by Bacteroides ovatus (B.o) from orange fiber on CRC progression and its underlying mechanisms.<br><br>METHODS: (1) Fecal samples from CRC patients (n=26) and healthy controls (n=20) were collected for metagenomic sequencing and untargeted metabolomics analysis; (2) The ability of B.o to produce NMS from orange fiber was validated in vitro; (3) A CRC mouse model was established using azoxymethane (AOM)/dextran sulfate sodium (DSS) induction, followed by evaluation of body weight, rectal bleeding, colorectal length, tumor number, and intestinal barrier function; (4) Network pharmacology, molecular docking, and western blot analysis were combined to verify the mechanism of action; (5) 16S rRNA sequencing was performed to analyze gut microbiota changes.<br><br>RESULTS: (1) CRC patients showed significantly increased metabolic pathways including glycolysis, methane metabolism, beneficial amino acid degradation, and linoleic acid degradation, along with significantly decreased B.o abundance and NMS levels, which were positively correlated; (2) NMS significantly inhibited CRC cell proliferation, migration, and invasion, while promoting apoptosis; (3) Combined treatment with B.o and orange fiber or NMS alone reduced tumorigenesis and improved intestinal barrier function; (4) Mechanistic studies revealed that these effects could be mediated through downregulation of 5-hydroxytryptamine receptor 1D (HTR1D) expression and inhibition of the cAMP/PKA/I&#x3ba;B&#x3b1;/NF-&#x3ba;B pathway; (5) The treatments optimized gut microbiota structure and metabolite composition.<br><br>CONCLUSION: B.o and its metabolite NMS possibly inhibit CRC progression by modulating the HTR1D-mediated cAMP/PKA/NF-&#x3ba;B signaling pathway, while improving gut microbiota structure, providing a novel therapeutic target for CRC prevention and treatment.},
}
@article {pmid41366428,
year = {2025},
author = {Xiong, Z and Dodson, BP and Rogers, MB and Sneiderman, CT and Janesko-Feldman, K and Vagni, V and Manole, M and Li, X and Rajasundaram, D and Clark, RSB and Raphael, I and Morowitz, MJ and Mariño, E and Kochanek, PM and Jha, RM and Kohanbash, G and Simon, DW},
title = {Microbial production of short-chain fatty acids attenuates long-term neurologic impairment after traumatic brain injury.},
journal = {Journal of neuroinflammation},
volume = {22},
number = {1},
pages = {285},
pmid = {41366428},
issn = {1742-2094},
support = {R01 NS127372/NS/NINDS NIH HHS/United States ; R21 NS131689/NS/NINDS NIH HHS/United States ; S10 OD028483/OD/NIH HHS/United States ; R01NS 127372/NH/NIH HHS/United States ; },
mesh = {Animals ; *Brain Injuries, Traumatic/metabolism/complications ; Mice ; Mice, Inbred C57BL ; *Fatty Acids, Volatile/metabolism/biosynthesis ; *Gastrointestinal Microbiome/physiology ; Male ; },
abstract = {BACKGROUND: Traumatic brain injury (TBI) triggers persistent gut microbiome dysbiosis characterized by depletion of short-chain fatty acid (SCFA)-producing bacteria. However, the link between SCFA depletion and long-term neurologic impairment (LTNI) after TBI remains unclear. Previously, we and others noted the involvement of metabolite-sensing receptors and SCFA ligands in mouse models of neurodegenerative diseases, including Alzheimer's. Here, we further investigated SCFA-mediated neuroprotection in LTNI at both microbiome and single-cell resolution using the controlled cortical impact (CCI) model of TBI with a high-yielding SCFA diet to examine their mechanistic role in pathogenesis.<br><br>METHODS: C57BL6/J mice were randomized to CCI (6&#xa0;m/s, 2&#xa0;mm) or sham surgery. Following surgery, mice were randomized to a study diet based on a balanced modification of the AIN93-G diet containing either 15% high amylose maize starch (HAMS) control diet or acetylated and butyrylated HAMS (HAMSAB) for 6 months to model increased SCFA production by bacterial fermentation in the gut. Morris water maze test and nesting assessment were performed at 1, 3, and 6 months after injury. The longitudinal gut microbiome changes were investigated by 16&#xa0;S rRNA amplicon and metagenomic sequencing of fecal pellets at baseline, 1 month, and 6 months post-injury. At 6 months, pericontusional tissue was collected for single-cell RNA-sequencing following the 10X Genomics protocol or histologic analysis.<br><br>RESULTS: Compared to the HAMS control diet, HAMSAB diet remodeled the CCI murine gut microbiome at an early phase, increased various SCFA-producing taxa, and attenuated neurologic deficits up to 6 months after CCI. In mice fed HAMSAB diet, single-cell transcriptomics and pathway analysis identified the promotion of neurogenesis, including increased doublecortin-positive immature neurons. In myeloid cells, HAMSAB induced an anti-inflammatory phenotype, inhibiting pro-inflammatory signaling interaction such as midkine signaling, and promoted differentiation to disease-associated microglia (DAM). Simultaneously, SCFAs reduced neurodegenerative pathway activity in neurons and glial cells and reduced phosphorylated tau deposition in pericontusional cortex.<br><br>CONCLUSIONS: Diet-facilitated microbial production of acetate and butyrate attenuates behavioral deficits of LTNI after TBI and produces enduring benefits at the single-cell level on the neuro-inflammatory and neuro-progenitor responses. This therapeutic approach could have a broader potential to prevent neurodegenerative disease.},
}
@article {pmid41366061,
year = {2026},
author = {Deng, JW and Zhou, YL and Zhang, YX and Zhou, CB and Fang, JY},
title = {The relationship between gut microbiota, lifestyle habits, and early-onset colorectal cancer: shedding light on early prediction.},
journal = {British journal of cancer},
volume = {134},
number = {3},
pages = {469-476},
pmid = {41366061},
issn = {1532-1827},
support = {82203224, 81830081//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/epidemiology/diagnosis/etiology ; *Life Style ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Diet ; Adult ; Aged ; Cohort Studies ; Age of Onset ; },
abstract = {BACKGROUND: The development of early-onset colorectal cancer (EO-CRC) is linked to environmental exposures and gut microbiota alterations. We aimed to discover the connection and develop prediction strategies.<br><br>METHODS: In the observational study, we performed 16S rRNA sequencing and metagenomic sequencing on 76 samples from discovery cohort and validation cohort, and qPCR analysis of selected microbiota, along with lifestyle and dietary assessment on 298 samples from validation cohort. Mediation analysis was employed to investigate the mediating role of gut microbiota. Logistic regression analysis evaluated the optimal prediction model for EO-CRC, with the area under the receiver operating characteristic curves (AUC) assessing diagnostic value.<br><br>RESULTS: Dysbiosis of the EO-CRC gut microbiota was characterised by evaluated abundance of F. nucleatum, P. micra, Pks[+] E. coli, and F. Plautii. Mediation analysis showed that Pks[+] E. coli mediated the relationship between fried food, processed meat and coffee to EO-CRC, while F. nucleatum mediated the adverse effects of snacks. A combination of three bacterial markers along with lifestyle and diet demonstrated strong diagnostic potential (AUC&#x2009;=&#x2009;0.95, 95% CI&#x2009;=&#x2009;0.92-0.98).<br><br>CONCLUSIONS: Our data suggested that the EO-CRC-enriched bacteria may mediate the effects of lifestyle and dietary factors on disease development. A predictive model combining diet, lifestyle, and gut bacteria demonstrated promising early predictive capabilities.},
}
@article {pmid41365917,
year = {2025},
author = {Duarte, VDS and Franklin, FV and Krysmann, A and Porcellato, D},
title = {Longitudinal study of the udder microbiome using genome-centric metagenomics uncovers pathogen-driven adaptation and succession.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {227},
pmid = {41365917},
issn = {2055-5008},
support = {314733//Norges Forskningsr&#xe5;d/ ; 314733//Norges Forskningsr&#xe5;d/ ; 314733//Norges Forskningsr&#xe5;d/ ; 314733//Norges Forskningsr&#xe5;d/ ; },
mesh = {Animals ; Female ; *Mammary Glands, Animal/microbiology ; Cattle ; *Mastitis, Bovine/microbiology ; Longitudinal Studies ; *Metagenomics/methods ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification/pathogenicity ; Lactation ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; },
abstract = {Bovine mastitis remains a major disease affecting dairy herds globally due to its complex and multi-etiological nature. To address gaps in microbial and immunological understanding, this longitudinal study examined the udder microbiome across lactation in 24 Norwegian Red cows. Somatic cell count (SCC) and microbiota composition varied by lactation stage, with low SCC (< 100,000 cells/mL) more frequent in early (80%) and middle (78.9%) than late lactation (53%) and dry-off (53.1%). Microbial diversity was shaped by SCC, lactation stage, and individual variability. Temporal profiling identified persistent infections involving Staphylococcus aureus and Staphylococcus chromogenes, while samples with low SCC were enriched in beneficial genera including Corynebacterium, Bradyrhizobium, and Lactococcus. Shotgun metagenomics revealed pathogen-specific metabolic traits, and genome-centric analysis recovered 142 MAGs characterized via sequence typing, virulence, and resistance profiling. These findings offer valuable insights into microbial adaptation and succession, informing strategies to better manage and prevent mastitis.},
}
@article {pmid41365804,
year = {2025},
author = {Thompson, AR and Adams, BJ and Hogg, ID and Yooseph, S},
title = {Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70249},
pmid = {41365804},
issn = {1758-2229},
support = {ANT 2133685//National Science Foundation/ ; OPP-2224760//National Science Foundation/ ; DBI-2400009//National Science Foundation/ ; OAC-2408259//National Science Foundation/ ; OPP-1043681//National Science Foundation/ ; OPP-1559691//National Science Foundation/ ; OPP-2129685//National Science Foundation/ ; //Antarctica New Zealand (Event K024)/ ; //New Zealand Antarctic Research Institute (Event K024)/ ; //Monte L. Bean Life Science Museum, the Department of Biology, Brigham Young University/ ; //Kravis Department of Integrated Sciences, Claremont McKenna College/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenome ; *Anti-Bacterial Agents/biosynthesis ; Ecosystem ; Soil/chemistry ; *Gases/metabolism ; },
abstract = {The McMurdo Dry Valleys (MDVs) of Antarctica are a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analysed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality metagenome-assembled genomes (MAGs) (≥ 50% completeness and contamination < 10%) and 201 high-quality MAGs (≥ 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: (1) community composition shifts along environmental gradients correlated with soil moisture, elevation and distance to the coast; (2) many MDV bacteria are capable of performing trace gas metabolism; (3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and (4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.},
}
@article {pmid41365368,
year = {2026},
author = {Cheng, T and Zhou, P and Zhang, M and Huang, T and Wu, B and Zhuang, J and Wang, B and Xu, X},
title = {Synergistic division of labor in a bacterial consortium for enhanced phenanthrene mineralization under cadmium stress: mechanisms of degradation-detoxification coordination.},
journal = {Bioresource technology},
volume = {442},
number = {},
pages = {133782},
doi = {10.1016/j.biortech.2025.133782},
pmid = {41365368},
issn = {1873-2976},
mesh = {*Phenanthrenes/metabolism ; *Cadmium/toxicity ; Biodegradation, Environmental/drug effects ; *Microbial Consortia/drug effects ; Arthrobacter/metabolism ; Klebsiella/metabolism ; Minerals/metabolism ; },
abstract = {The remediation of co-contamination by polycyclic aromatic hydrocarbons (PAHs) and heavy metals poses a significant challenge. Although microbial consortia present a promising approach, their synergistic mechanisms under stress conditions are not fully understood. To address this gap, we constructed a functionally specialized bacterial consortium (KZ) by assembling Klebsiella sp. CW-D3T and Arthrobacter sp. SZ-3, which synergistically enhanced phenanthrene (PHE) degradation and mineralization under cadmium stress (25 mg/L Cd[2+]), outperforming monocultures by 1.2-1.9-fold. Through biomass-normalized enzyme activity assays, we uncovered a structured division of labor: SZ-3 exhibited superior upstream catalytic activity (50 % higher 2H1N conversion), while CW-D3T dominated downstream mineralization (>80 % contribution). Mechanistic investigations via metagenomics revealed that CW-D3T utilized high-expression efflux pumps (ZntA/zinT) and antioxidant genes (yhcN) to mitigate cadmium toxicity, whereas SZ-3 employed the frnE-mediated oxidative stress response and limited Cd[2+] uptake via mntH. This study elucidates a synergistic mechanism for concurrent PAH degradation and heavy metal detoxification, offering a novel bioresource for remediating co-contaminated environments.},
}
@article {pmid41365051,
year = {2026},
author = {Wang, H and Congzhu, and Wang, J and Lin, X and Guo, Y and Kiani, FA and Zhou, X and Ding, Y},
title = {Clostridium perfringens can promote the formation of fatty liver in cows.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110826},
doi = {10.1016/j.vetmic.2025.110826},
pmid = {41365051},
issn = {1873-2542},
mesh = {Animals ; Cattle ; *Clostridium perfringens/pathogenicity/physiology ; *Fatty Liver/microbiology/veterinary ; *Cattle Diseases/microbiology ; Female ; *Clostridium Infections/veterinary/microbiology ; Cytokines/metabolism/genetics ; Gastrointestinal Microbiome ; Mice ; Liver/microbiology/pathology ; Dysbiosis/microbiology/veterinary ; Ileum/microbiology ; },
abstract = {During the periparturient period, reduced feed intake often causes negative energy balance in dairy cows, leading to fat mobilization, hepatic lipid accumulation, and fatty liver disease (FLD), ultimately compromising health and milk production. This study investigated the association between FLD and gut microbiota dysbiosis, with a particular focus on the role of Clostridium perfringens within the gut-liver axis. Metagenomic sequencing of ileal contents revealed a marked decrease in microbial diversity in cows with FLD, along with increased abundances of potential pathogens such as C. perfringens, Enterobacter cloacae, and Vibrio alginolyticus. Functional annotation indicated elevated expression of virulence factors (e.g., Hsp60, flagella, mu-toxin), antibiotic resistance genes (e.g., otrA, lsaC), and pathways related to lipopolysaccharide (LPS) biosynthesis and mitogen-activated protein kinase (MAPK) signaling pathways, suggesting enhanced pro-inflammatory potential. qPCR analysis of ileal tissue demonstrated reduced expression of tight junction proteins (zona occludens 1 (ZO-1), Claudin-1, and Occludin) and increased levels of pro-inflammatory cytokines (Interleukin-1 beta (IL-1β), Interleukin-6 (IL-6), Tumour necrosis factor-alpha (TNF-α)), alongside a decrease in the anti-inflammatory cytokine interleukin-10 (IL-10), indicating compromised intestinal barrier function and local inflammation. Given the significant enrichment of C. perfringens in the ileum of FLD cows, we hypothesized its involvement in disease pathogenesis. To test this, C. perfringens was isolated and orally administered to antibiotic-pretreated mice fed a high-fat diet. These mice developed exacerbated hepatic steatosis, metabolic disturbances, and heightened inflammatory responses. Moreover, Western blot analysis revealed reduced expression of intestinal tight junction proteins (ZO-1, Claudin-1, Occludin), indicating increased intestinal permeability. Quantitative PCR confirmed upregulation of pro-inflammatory cytokines (IL-1β, IL-6, TNF-α) and downregulation of IL-10 in both intestinal and hepatic tissues. These findings indicate that C. perfringens may promote FLD by impairing gut barrier integrity and enhancing inflammatory responses. In conclusion, our findings suggest that C. perfringens may contribute to the development of FLD in dairy cows by impairing intestinal barrier integrity and promoting systemic inflammation.},
}
@article {pmid41363534,
year = {2026},
author = {Ren, M and Liu, Y and Wang, Y and Tu, Y and Guo, Y and Sun, X and Niu, G and Wang, Y},
title = {Virome diversity and molecular characterization of two emerging RNA viruses in mosquito populations from Yantai, China.},
journal = {mSphere},
volume = {11},
number = {1},
pages = {e0053925},
pmid = {41363534},
issn = {2379-5042},
mesh = {Animals ; China ; *Virome/genetics ; Phylogeny ; *RNA Viruses/genetics/classification/isolation &amp; purification ; *Culicidae/virology ; Metagenomics ; *Mosquito Vectors/virology ; High-Throughput Nucleotide Sequencing ; *Genetic Variation ; Culex/virology ; },
abstract = {Mosquito-borne viruses represent a major global public health threat, with transmission dynamics governed by climatic, ecological, and anthropogenic factors. Yantai City, Shandong Province, situated in a warm-temperate monsoon climate zone, shares geographical and ecological characteristics with regions where mosquito-borne viruses are endemic, creating potential for virus introduction. We used metagenomics to systematically analyze viral communities in mosquitoes from the Yantai region. We collected 8,111 mosquitoes representing four genera and six species, with Culex being predominant (89.8%). High-throughput sequencing revealed 11 viral species spanning 9 families, including Peribunyaviridae and Picornaviridae. Notably, Serbia mononega-like virus 1 and Biggievirus Mos11 represent the first reports from China, with quantitative reverse transcription PCR revealing minimum infection rates of 0.34% and 0.68%, respectively. Phylogenetic analysis revealed close relationships to known viral strains, with several isolates potentially representing novel genera or species. Analysis revealed that Culex quinquefasciatus harbored the greatest viral diversity (five species), with significantly higher viral diversity in agricultural versus urban areas (P < 0.001). Several viruses demonstrated cross-species transmission potential, including Zhee mosquito virus, Zhejiang mosquito virus 3, and Culex tritaeniorhynchus rhabdovirus, all detected across multiple mosquito species. While most viruses appear mosquito-specific, several show close phylogenetic relationships to known pathogens, potentially posing public health risks warranting surveillance. This study addresses knowledge gaps regarding mosquito-borne viruses in the Bohai Rim region and provides a scientific foundation for regional viral surveillance and early warning systems.IMPORTANCEMosquito-borne viruses are a significant global health threat, with the potential to cause widespread disease outbreaks. This study investigated the viral diversity within mosquito populations in Yantai, China, and characterized the molecular features of two emerging RNA viruses. These findings highlight the remarkable viral diversity harbored by Culex mosquitoes and reveal higher viral diversity in agricultural areas compared to urban settings. Several identified viruses exhibit cross-species transmission potential and close phylogenetic relationships to known pathogens, suggesting that they may pose public health risks. Understanding these interactions is essential for predicting how environmental changes may affect virus transmission and the resilience of surveillance and control strategies.},
}
@article {pmid41361579,
year = {2025},
author = {Anunobi, OO and Abiola, RB and Ogah, CF},
title = {In silico pathogenomics of draft metagenome-assembled genome of gut Enterobacter cloacae from a gastroenteritis patient exhibiting potential determinants of multi-drug resistance and virulence.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {1},
pages = {6},
pmid = {41361579},
issn = {1572-9699},
mesh = {*Enterobacter cloacae/genetics/pathogenicity/drug effects/isolation &amp; purification ; Humans ; *Gastroenteritis/microbiology ; *Genome, Bacterial ; *Drug Resistance, Multiple, Bacterial/genetics ; Virulence/genetics ; Enterobacteriaceae Infections/microbiology ; *Metagenome ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Computer Simulation ; Computational Biology ; Gastrointestinal Microbiome ; Phylogeny ; },
abstract = {Antimicrobial resistance (AMR) is considered one of the top 10 threats to global public health and development. Opportunistic bacteria such as Enterobacter cloacae have been reported to acquire resistance determinants, making them pathogenic reservoirs and a threat to health and most are on the path of becoming superbugs. These bacteria are commonly isolated along with pathogens from the stool and urine of patients diagnosed with typhoid fever, paratyphoid fever, gastroenteritis, urinary tract infection, and bloodstream infection or sepsis. The E. cloacae strain EC78 studied here is a metagenomic-assembled genome that was binned from sequenced data of a mixed bacterial culture taken from a patient diagnosed with gastroenteritis. The isolate was sequenced with Illumina Novaseq 6000 platform and analysed with various bioinformatics tools. EC78 origin strain contained antibiotics resistance genes, insertion sequences, phages, and virulence factors. Notable virulence genes responsible for immune modulation, efflux of drugs, invasion and nutritional virulence previously reported in Klebsiella pneumoniae., Escherichia coli, Shigella sp., and Salmonella sp. etc., were identified in EC78. Genetic characteristics that could contribute to pathogenicity, virulence, and antibiotic resistance, not commonly associated with E. cloacae, were identified in gut-domiciled EC78, suggesting the evolution of counter-therapy in the bacteria, probably driven by its quest for survival in an otherwise competitive biome.},
}
@article {pmid41360901,
year = {2025},
author = {Lima, J and McNeilly, TN and Auffret, MD and Steele, P and Frew, D and Martínez-Álvaro, M and Dewhurst, RJ and Watson, M and Roehe, R},
title = {Rumen microbiome profiles of dairy cattle are affected by the presence of, and vaccination against, the abomasal parasitic nematode Ostertagia ostertagi.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1067},
pmid = {41360901},
issn = {2045-2322},
support = {10045515//Innovate UK/ ; BB/N016742/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N01720X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Cattle ; *Ostertagia/immunology ; *Rumen/microbiology/parasitology ; *Ostertagiasis/veterinary/prevention &amp; control/parasitology/immunology ; *Vaccination/veterinary ; *Cattle Diseases/parasitology/prevention &amp; control/microbiology/immunology ; Abomasum/parasitology ; *Microbiota ; *Gastrointestinal Microbiome ; Feces/parasitology ; },
abstract = {Ostertagia ostertagi is a highly prevalent nematode that affects grazing cattle and impacts performance and welfare by reducing appetite and hindering weight gain. Despite its economic significance, the influence of the abomasal parasite O. ostertagi on the rumen microbiome remains unexplored. We examined the effects of subclinical O. ostertagi infection and vaccination on the rumen microbiome at taxonomic and functional levels. In an experimental trial, calves treated with vaccine or adjuvant-only were orally challenged with O. ostertagi larvae daily for 25 days; 4 groups of animals (UNF: unvaccinated, unchallenged; VAC: vaccinated, challenged; CHE: unvaccinated, challenged, high cumulative faecal egg counts (cFEC), and CLE: unvaccinated, challenged, low cFEC) were selected for whole shotgun metagenomic sequencing. Using a rigorous permutation test based on partial least squares discriminant analyses, we identified 36 (91), 38 (31), 21 (57), 41 (64) and 29 (57) microbial genera (genes) that distinguished VAC, CHE and CLE from UNF, CHE from CLE, and CHE from VAC, respectively. The subclinical infection reshaped the rumen microbiome; enrichment of opportunistic pathogens such as Listeria, and depletion of Filifactor in infected animals were identified as potential biomarkers for host immune response, whereas Actinomyces and Microspora were potential biomarkers of resistance to infection. Microbial biochemical pathways like acetogenesis (e.g., Elusimicrobium, nrfA), pectin and hemicellulose degradation (e.g., Sphaerochaeta), and phosphorus and sulphur metabolism (e.g., Candidatus Accumulibacter and Desulfatibacillum) were also affected by parasitism. Both infection and vaccination altered methanogens, methanotrophs and the methane metabolism pathway, highlighted by distinct gene clustering patterns between infected and uninfected animals. Clustering patterns of infected and vaccinated animals exhibited some similarities, which may reflect immune system modulation of the ruminal microbiome as a result of an abomasal infection. This study unveils critical changes in the rumen microbiome due to the infection by and vaccination against the abomasal parasite O. ostertagi. Our results highlight the importance of monitoring microbial dynamics in the development of effective anthelmintic treatments and vaccines.},
}
@article {pmid41360540,
year = {2026},
author = {Zhang, M and Jiang, Z and Li, J and Marie-Colette, AK and Liu, Q and Hao, N and Wang, J},
title = {Analyzing the contribution of functional microorganism to volatile flavor compounds in Semillon wine and predicting their metabolic roles during natural fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {223},
number = {Pt 2},
pages = {117842},
doi = {10.1016/j.foodres.2025.117842},
pmid = {41360540},
issn = {1873-7145},
mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Volatile Organic Compounds/analysis/metabolism ; *Vitis/microbiology ; Gas Chromatography-Mass Spectrometry ; Taste ; Odorants/analysis ; China ; Microbiota ; Food Microbiology ; *Flavoring Agents/analysis ; *Bacteria/metabolism/classification ; Solid Phase Microextraction ; Hanseniaspora/metabolism ; },
abstract = {Indigenous microorganism plays a pivotal role in natural wine fermenting and its distinctive qualities shaping. However, the contributions of functional microbial taxa to wine flavor formation remain underexplored. This study focuses on the natural fermentation systems of Semillon grapes from Wuwei and Zhangye Gansu sub-regions within the Hexi Corridor of China. We characterized the dynamics of microbial community succession during fermentation using a combination of metagenomic sequence and culture-dependent analysis. Concurrently, volatile compounds were quantified using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry. The mechanistic of functional microorganisms in wine flavor formation were unveiled by constructing KEGG metabolic network. The results revealed distinct microbial succession patterns between the two regions. In Zhangye, Hanseniaspora dominated the early fermentation stage, succeeded by Saccharomyces, Fructobacillus, and Brachyspira in middle and late stages. Conversely, in Wuwei, Pichia prevailed initially, with Brachyspira becoming stably enriched. Volatile esters and higher alcohols were identified as the major flavor components, contributing aroma notes of flowers, fresh greens, and stone fruits to the Semillon wine. Correlation analysis indicated positive associations between most key volatile aroma compounds and Saccharomyces, Brachyspira, Hanseniaspora, and Acetobacter. Metagenomic functional prediction highlighted carbohydrate and amino acid metabolic as the predominant pathways, with key processes involving glycolysis, fatty acid biosynthesis, and esterification. Core microbial taxa (Saccharomyces, Hanseniaspora, Starmerella, etc.) regulated flavor compound synthesis through a synergistic metabolic network. This study elucidates the succession of functional microorganisms and the development of flavor profiles during the natural fermentation of Semillon in the Hexi Corridor providing a reference for the development and application of functional microorganisms.},
}
@article {pmid41358839,
year = {2026},
author = {Li, Y and Fu, X and Sun, F and Dong, M and Wang, Y and Wang, Y and Liu, Q},
title = {Metabolomic and metagenomic insights into WFBG-mediated regulation of gut microbiota and metabolism in broilers.},
journal = {Applied and environmental microbiology},
volume = {92},
number = {1},
pages = {e0189025},
pmid = {41358839},
issn = {1098-5336},
mesh = {Animals ; *Chickens/microbiology/metabolism/growth &amp; development ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics/analysis ; *Animal Feed/analysis ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Metabolomics ; Metagenomics ; Fermentation ; },
abstract = {UNLABELLED: The steady state of gut microbiota is a key factor in regulating the growth of broilers. The regulatory role of wet-fermented brewer's grain (WFBG) in broiler gut development and microbiota is still elusive. In this study, non-targeted metabolomics and 16S rRNA sequencing analysis were used to investigate the effects of WFBG supplementation on serum metabolites and gut microbiota in 42-day-old broilers. Serum metabolomic analysis identified 546 differentially expressed metabolites (DEMs), with GO and KEGG enrichment analyses showing that specific DEMs were enriched in intestinal development-related pathways, including phenylalanine, tyrosine, tryptophan biosynthesis, and alpha-linolenic acid metabolism. 16S rRNA sequencing analysis showed significant intergroup differences in the relative abundances of Ligilactobacillus, Olsenella, Erysipelatoclostridium, and Blautia at the genus level in broiler gut microbiota between the control and WFBG groups. Integrative analysis of 16S rRNA sequencing and non-targeted metabolomics demonstrated that bacterial genera, including Streptococcus and Proteus, were positively correlated with N6,N6-dimethyllysine and quercetin but negatively associated with 18 DEMs, such as 4-methylbenzenesulfonic acid and deoxycholic acid derivatives. Furthermore, we identified potential biomarkers associated with intestinal development induced by 20% WFBG supplementation. Our findings suggest that the maximum recommended inclusion level of WFBG in broiler feed should not exceed 20%. This study provides novel insights into the molecular mechanisms underlying fiber utilization and intestinal maturation in broilers.<br><br>IMPORTANCE: This study investigated the regulatory mechanism of wet-fermented brewer's grain (WFBG) on gut development and microbiota in commercial broilers. Through integrated 16S rRNA sequencing and non-targeted metabolomic analysis, the study not only identified differential gut microbiota, serum metabolites, as well as their correlations, but also discovered potential biomarkers associated with intestinal development induced by 20% WFBG and clarified the maximum recommended inclusion level of WFBG (&#x2264;20%). This not only filled the gap in the molecular mechanism underlying WFBG-mediated regulation of fiber utilization and intestinal maturation in broilers but also provided a theoretical basis and practical guidance for the resource utilization of agricultural by-products, precision feeding of broilers, and intestinal health monitoring.},
}
@article {pmid41358671,
year = {2025},
author = {Ngwese, MM and Adegbite, BR and Zinsou, JF and Fitzstevens, JL and Schmidt, VT and Moure, PAN and Maloum, MN and Tyakht, AV and Huus, KE and Youngblut, ND and Kremsner, PG and Adegnika, AA and Ley, RE},
title = {Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587966},
pmid = {41358671},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/parasitology/microbiology ; Animals ; Gabon/epidemiology ; Female ; Male ; Child ; *Helminthiasis/parasitology/epidemiology/microbiology ; Metagenomics ; *Helminths/isolation &amp; purification/classification/genetics ; Child, Preschool ; Rural Population ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Ascaris lumbricoides/isolation &amp; purification ; Strongyloides stercoralis/isolation &amp; purification ; Necator americanus/isolation &amp; purification ; Trichuris/isolation &amp; purification ; Biodiversity ; },
abstract = {Soil-transmitted helminths (STH) are common in (sub)tropical regions and primarily affect impoverished populations. These parasites reside in the gut, where they interact with both the microbiota and host immunity. Clinical STH detection is laborious and often not performed within the context of gut microbiome studies. Here, we present a proof-of-concept study assessing whether fecal metagenome data could be used to assess STH infection, and to relate STH infection to microbiome features. We leveraged 310 gut metagenomes obtained from mother-child pairs in two different locations in Gabon: one rural and one semi-urban, and assessed the presence of four STH species (Ascaris lumbricoides, Strongyloides stercoralis, Trichuris trichiura, and Necator americanus) using qPCR. Sequence data were used to characterize the microbiomes and to detect these parasites. Metagenomic read mapping and genome coverage metrics closely matched qPCR detection patterns. Within-location analyses revealed that parasite species richness was associated with microbiome diversity and taxonomic composition, with the strongest associations observed in children from the rural site. Applying this approach to published data from five additional African cohorts identified context-specific parasite-microbiome associations, as well as a modest but reproducible association between microbiome alpha diversity and parasite infection. These findings highlight the potential of shotgun metagenomics for concurrent parasite detection and microbiome profiling across diverse geographic and demographic contexts.},
}
@article {pmid41355553,
year = {2025},
author = {Kim, MJ and Park, JH and Eom, YB},
title = {The Transmissibility of the Human Skin Virome: Potential Forensic Implications.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70197},
pmid = {41355553},
issn = {2045-8827},
support = {//Soonchunhyang University (SCH-20130328), Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; //Ministry of Science and ICT, South Korea, RS-2023-NR076438 (NRF-2023R1A2C1003486)/ ; },
mesh = {Humans ; *Virome ; *Skin/virology ; Adult ; *Viruses/classification/genetics/isolation &amp; purification ; Male ; Female ; Young Adult ; Republic of Korea ; Metagenome ; },
abstract = {The objective of this study was to evaluate the temporal stability and object-to-skin transferability of the skin virome in a Korean population. Skin virus metagenomes were collected from the anatomical locations (forehead, left hand, and right hand) of eight healthy adults and monitored over 3 months at intervals of 6 weeks. To assess the potential transfer of virome between skin and objects, subjects were instructed to contact four types of objects (cell phones, door handles, fabric, and plastic). Virome samples were then collected from the surfaces of these objects. Viruses were identified using databases and viral annotation bioinformatics tools. Fifteen viral families were consistently found to be stable and well-transmissible across anatomical locations and four types of objects. Furthermore, the presence/absence profiles of 54 viral species belonging to these 15 viral families exhibited significant individual specificity on both the skin (p < 0.01) and the objects handled by each subject (p < 0.05). We confirmed that these 54 viral markers remain stable over time within individuals and are transferable to contacted surfaces. Additionally, we explored the potential of using the virome as an individual identification marker, which may suggest new approaches for forensic applications.},
}
@article {pmid41355481,
year = {2025},
author = {Becerra, D and Rodríguez-Caballero, G and Marhuenda-Egea, FC and Olaya-Abril, A and Moreno-Vivián, C and Sáez, LP and Luque-Almagro, VM and Roldán, MD},
title = {Microbial Diversity of the Surface of Polypropylene and Low Density Polyethylene-Based Materials (Plastisphere) From an Area Subjected to Intensive Agriculture.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70121},
pmid = {41355481},
issn = {2045-8827},
support = {//This study was supported by Ministerio de Ciencia e Innovaci&#xf3;n, Spain (grant PID2021-124174OB-I00)./ ; },
mesh = {*Polypropylenes/metabolism ; *Polyethylene/metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Agriculture ; *Biodiversity ; Biodegradation, Environmental ; Phylogeny ; },
abstract = {Accumulation of synthetic plastics in the biosphere has led to global pollution, provoking serious consequences for the environment and human health. Uncontrolled agricultural plastic landfills have the risk of becoming a source of agrochemicals and microplastics. Biotechnological approaches to solve plastic pollution include the removal of these polymers through biological degradation, which is a friendly environmental method. The microbial communities colonizing plastic debris (plastisphere) are considered as a potential source of plastic-degrading microorganisms. In this study, a bacterial biodiversity analysis, based on 16S rRNA gene-targeted metagenomic sequencing, was achieved in the plastisphere of low-density polyethylene (LDPE) and polypropylene (PP) polymers from an agricultural landfill. The α-diversity analysis did not show significant differences between LDPE and PP plastispheres and the plastic-free bulk soil, while LDPE and PP bacterial communities clustered close, but separately from the bulk soil in a β-diversity analysis. Although the taxonomic composition of both plastispheres was different, they shared a significantly higher proportion of Cyanobacteria and Deinococcota than the bulk soil. Additional analyses showed different indicator families, genera and species that can be associated with plastispheres. A predictive functional analysis suggests that degradation of plastic additives in both plastispheres is probably occurring. In addition, the existence of degradation processes for specific herbicides in each plastisphere is highlighted, and the possible exposure of LDPE to both physical and biological degradation processes is also described. These results will contribute to characterize the soil plastisphere exposed to different environmental conditions, and to understand the specific biological niches where plastic-degrading microorganisms could survive.},
}
@article {pmid41354993,
year = {2025},
author = {Zhang, W and Zhang, M and Xie, J and Huang, H and Schmitz-Esser, S and Li, W and Liu, H and Li, D},
title = {Dynamics of the gut microbiome and resistome in response to prophylactic antibiotic treatment in post-surgical giant pandas.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43425},
pmid = {41354993},
issn = {2045-2322},
support = {2023NSFSC0011//Natural Science Foundation of Sichuan Province/ ; QD2023A46//Mianyang Teachers' College/ ; 2022 CPB-B09//the grants from the independent project of Chengdu Research Base of Giant Panda Breeding/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; *Ursidae/microbiology ; *Anti-Bacterial Agents/pharmacology/administration &amp; dosage/therapeutic use ; *Antibiotic Prophylaxis ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Cefotaxime/pharmacology/administration &amp; dosage ; Feces/microbiology ; Metagenome ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics/drug effects/classification ; },
abstract = {For giant pandas, the ecological impact of prophylactic postoperative antibiotics on their gut microbial communities and resistome is not well characterized. Here, we assessed the impact of intravenous cefotaxime administration by analyzing longitudinal fecal samples from five giant pandas via 16 S rRNA sequencing (n = 304 samples) and shotgun metagenomics (n = 22 samples). 16 S-based analysis revealed that antibiotic exposure significantly altered bacterial community structure, resulting in a pronounced increase in the abundance of Pseudomonadota (from 50% ± 24% to 60% ± 38%; P < 0.001) and a reduction in Shannon diversity (from 2.8 ± 0.4 to 2.4 ± 1.3; P < 0.05). In contrast, metagenomic analysis indicated that cefotaxime exposure did not significantly increase the overall diversity of antimicrobial resistance genes (ARGs) or virulence factor genes (VFGs). However, we observed a marked expansion in the diversity of the CTX-M β-lactamase family (blaCTX-M), which persisted into the recovery phase. We also recovered 10 metagenome-assembled genomes (MAGs) harboring both ARGs and VFGs, identifying them as potential antibiotic-resistant pathogens (ARPs). Their abundance, however, remained unchanged throughout treatment. These findings provide new insights into the effects of short-term antibiotic exposure in giant pandas, highlighting its transient effect on microbial community structure and a limited effect on resistome diversity.},
}
@article {pmid41354765,
year = {2025},
author = {Su, H and Han, P and Yan, H and Wu, C and Zeng, S and Zhang, P and Wang, Z and Dong, J and Liang, M and Jing, H and Zhang, D and Yang, C and Xie, N and Liu, X and Weng, S and Dong, G and He, J},
title = {Age-dependent patterns of the gut microbiome, antibiotic resistome, and pathogenicity in captive koalas (Phascolarctos cinereus).},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {40},
pmid = {41354765},
issn = {2399-3642},
mesh = {Animals ; *Phascolarctidae/microbiology/virology ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Klebsiella pneumoniae/pathogenicity ; Age Factors ; *Drug Resistance, Microbial/genetics ; Male ; *Bacteria/genetics/pathogenicity/drug effects ; Female ; },
abstract = {Gut microbiome has a profound influence on koalas' health. Yet, the relationships among the gut bacteriome, virome, antibiotic resistome, and pathogenicity throughout different stages in koala's life remain elusive. Here, we presented a metagenome-resolved survey of gut microbiome utilizing 75 fecal samples from three groups of captive koalas. The diversity of bacteriome and virome were age-dependent, predominating in adult koalas. Lytic viruses increased with age as lysogenic viruses and bacterial hosts declined, and virus-to-microbe ratios rose, revealing concomitant age-related shifts in microbial communities, though causality remains unresolved. Antibiotic resistance genes (ARGs) were more prevalent in young koalas, unlike in humans, where they accumulate with age. Two ARG-carrying pathogens, Klebsiella pneumoniae and Escherichia coli, were identified and cultured, with K. pneumoniae and E. coli predominating in young koalas. One age-dependent lytic virus infecting K. pneumoniae only detected in young koalas, and two lysogenic viruses infecting E. coli identified the in young and adult koalas. Analyses showed a positive correlation between mobile genetic elements (MGEs) and virulence factors (VFs), which facilitated the widespread dissemination of VFs and impacted health. Collectively, this study advances the understanding of gut microbiome in health, providing solutions to the treatment and management of captive koalas.},
}
@article {pmid41354674,
year = {2025},
author = {Yang, S and Deng, W and Yang, T and Liu, C and Li, C and Li, G and Wei, R and Li, D and Huang, Y and Zhao, K and Zou, L},
title = {Enriched Streptococcus alactolyticus in non-cub giant panda gut contributes to the regulation of tryptophan and its neuromodulatory derivatives.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {13},
pmid = {41354674},
issn = {2055-5008},
support = {031-2222996053//the Scientific Research Foundation from Sichuan Agricultural University/ ; The Giant Panda Microbiome Research and Biobank Establishment//the International Cooperation Funding Project for Giant Pandas/ ; },
mesh = {*Tryptophan/metabolism/biosynthesis ; Animals ; *Gastrointestinal Microbiome ; *Ursidae/microbiology ; Mice ; *Streptococcus/genetics/metabolism/isolation &amp; purification/classification ; Feces/microbiology/chemistry ; Metagenomics ; Whole Genome Sequencing ; Humans ; Male ; },
abstract = {Despite feeding on a high-lignocellulose bamboo diet, the giant panda (Ailuropoda melanoleuca) retains a typical gut microbiome of Carnivora. We conducted shotgun metagenomic sequencing and functional validation of the giant panda's gut microbiome to elucidate its physiological roles and explore its functional adaptation to the species' specialized diet. Our results revealed that Streptococcus alactolyticus significantly increased in the guts of subadult, adult, and elderly individuals versus that in cubs. The gut microbiome of these non-cub giant pandas was significantly enriched in pathways and modules associated with tryptophan biosynthesis. Whole-genome sequencing and in vitro fermentation of S. alactolyticus demonstrated its ability to biosynthesize tryptophan. Gavage of S. alactolyticus in mice led to the enrichment of aromatic amino acid metabolism pathways in gut microbiome, accompanied by significantly elevated levels of 5-hydroxyindole acetic acid and kynurenine in fecal and/or serum samples (p < 0.05). Transcriptome sequencing of colons from mice revealed that most significant upregulated Gene Ontology (GO) terms mainly were related to spindle checkpoint signaling and chromosome segregation, while most significant downregulated GO terms mainly involved synaptic functional regulation. These findings suggest that S. alactolyticus enriched in the non-cub giant panda gut can regulate tryptophan, influencing host gut physiology via tryptophan metabolites.},
}
@article {pmid41354462,
year = {2026},
author = {Wang, X and Liu, Y and Sun, Z and Li, J and Lu, Z and Huang, J and Hu, S and Cao, P and Cao, X and Li, S and Ruan, J and Liu, J and Xie, J and Sun, H and Chen, T and Li, S and Zhu, Z and Wen, Z and Tuan, RS and Hunter, DJ and Li, ZA and Shi, D and Ding, C},
title = {Multi-Omics Reveal the Dysregulated Gut-Joint Axis in Knee Synovitis: Data from Two Osteoarthritis Studies in China.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {13},
number = {7},
pages = {e12020},
pmid = {41354462},
issn = {2198-3844},
support = {2023YFE0209700//National Key Research and Development Program of China/ ; GZC20231059//Postdoctoral Fellowship Program of CPSF/ ; 2024M761326//China Postdoctoral Science Foundation/ ; 2023A1515110748//Guangdong Basic and Applied Basic Research Foundation/ ; 2024A1515011794//Guangdong Basic and Applied Basic Research Foundation/ ; 82373653//National Science Foundation of China/ ; 82572825//National Science Foundation of China/ ; 2024A04J5169//Science and Technology Projects in Guangzhou/ ; A2401031//Shenzhen Medical Research Funds/ ; 1194737//Arthritis Australia and an NHMRC Investigator Grant Leadership 2/ ; 82325035//National Natural Science Foundation of China for Distinguished Young Scholars/ ; 82530083//Key Project of the National Science Foundation of China/ ; },
mesh = {Humans ; China ; *Synovitis/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Female ; *Osteoarthritis, Knee/metabolism/microbiology ; Middle Aged ; Proteomics/methods ; *Knee Joint/metabolism/pathology ; Aged ; Metabolomics/methods ; Dysbiosis/metabolism ; Synovial Fluid/metabolism ; Multiomics ; },
abstract = {Gut microbiota dysbiosis and associated host immuno-metabolic disorders may play a role in knee synovitis. Herein, integrated multi-omics analyses of stool and blood samples from subjects from Pearl River Osteoarthritis Cohort (PROC, N = 207) are conducted to explore the potential gut-joint axis. Specifically, gut metagenomics, serum metabolomics and plasma proteomics are carried out. Knee synovitis is identified by magnetic resonance imaging. A total of 87 synovitis cases are identified in PROC, which are characterized by increased Firmicutes/Bacteroidetes (F/B) ratio. Alterations in microbial functions of both leucine and geraniol degradation are closely associated with increased serum 3-hydroxyisovaleric acid and decreased geranic acid. These perturbations are significantly correlated with F/B ratio and down-regulated plasma TWEAK. Building upon these, the potential synovial targets are explored using a synovial single-cell dataset and the Nanjing Osteoarthritis Cohort (NOC, N = 22). Synovial fluid proteomics, histological analysis, and in vitro experiments with human fibroblast-like synoviocytes (FLS) are conducted for NOC subjects with different synovitis grades. An upregulated TWEAK receptor is found in higher grade of synovitis. In vitro, higher TWEAK induced down-regulated TWEAK receptor in FLS. The study for the first time revealed the gut-joint axis in knee synovitis, providing new insight into potential targets for synovitis treatment.},
}
@article {pmid41354223,
year = {2026},
author = {Adhikary, P and Maddheshiya, A and Takkar, B and Das, T and Mukherjee, S},
title = {Differential gut microbiome profiles in diabetic retinopathy: A comparative study across continental populations.},
journal = {Diabetes research and clinical practice},
volume = {231},
number = {},
pages = {113043},
doi = {10.1016/j.diabres.2025.113043},
pmid = {41354223},
issn = {1872-8227},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetic Retinopathy/microbiology ; *Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Diabetes Mellitus, Type 2/microbiology/complications ; },
abstract = {Gut dysbiosis damages gut barrier, stimulates inflammation, endotoxemia, and breakdown of blood-retina barrier, promoting diabetic retinopathy (DR). Most microbiome studies on DR relied on 16S rRNA gene sequencing, documenting altered microbial richness, diversity, and shifts in dominant phyla and genera, though these findings remain inconsistent across populations. The only shotgun metagenomic study to date identified species Eubacterium hallii, Firmicutes bacterium and Alistipes finegoldii enriched in DR, with altered metabolic pathways. The β-diversity showed distinct inter-individual variations in diseased individuals compared to healthy controls (HC). The objective of this narrative review is to highlight the key microbial biomarkers, metabolic pathways, and putative microbiota-gut-retina axis integrating both 16S rRNA and shotgun data to compare microbial alterations across HC, T2DM, and DR. The review concludes with a comprehensive understanding of dysbiotic gut taxa associated with DM and DR in different populations showing wide variability in results mostly due to small sample size, geography, antidiabetic medications, lack of demographic and clinical data and limited taxonomic classification by 16S sequencing. This emphasizes the need of a large scale, multi-ethnic shotgun metagenomic sequencing study with systematically collected medical data and dietary information to understand the contributions of gut microbiome in the progression of DR.},
}
@article {pmid41353361,
year = {2025},
author = {France, MT and Chaudry, I and Rutt, L and Quain, M and Shirtliff, B and McComb, E and Maros, A and Alizadeh, M and Hussain, FA and Elovitz, MA and Relman, DA and Rahman, A and Brotman, RM and Price, JT and Kassaro, MP and Holm, JB and Ma, B and Ravel, J},
title = {VIRGO2: an enhanced gene catalog of the vaginal microbiome provides insights into its functional and ecology complexity.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {449},
pmid = {41353361},
issn = {2041-1723},
support = {UH2 AI083264/AI/NIAID NIH HHS/United States ; R01 NR015495/NR/NINR NIH HHS/United States ; OPP1189217//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; T32 AI162579/AI/NIAID NIH HHS/United States ; INV048982//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; U19 AI084044/AI/NIAID NIH HHS/United States ; INV048956//Bill and Melinda Gates Foundation (Bill &amp; Melinda Gates Foundation)/ ; R01 NR014784/NR/NINR NIH HHS/United States ; UH2AI083264//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01 AI116799/AI/NIAID NIH HHS/United States ; T32AI162579//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Female ; *Vagina/microbiology/virology ; *Microbiota/genetics ; Humans ; *Bacteria/genetics/classification ; Metagenome/genetics ; Metagenomics/methods ; Mycobiome/genetics ; Genome, Bacterial ; },
abstract = {Despite the importance of the cervicovaginal microbiome, the mechanisms that govern its composition and drive its impact on host physiology remain poorly understood. With the aim to expand our understanding of the function and ecology of the vaginal microbiome, we present VIRGO2, an enhanced non-redundant gene catalog comprising over 1.7 million well-annotated genes from body-site specific microbes and viruses. Analyses using VIRGO2 reveal insights such as including the identification of previously uncharacterized vaginal bacteria, features of the vaginal mycobiome and phageome, and differential expression of bacterial carbohydrate catabolic genes. Constructed from over 2500 metagenomes and 4000 bacterial genomes, VIRGO2 broadens geographic representation and microbial diversity compared to its predecessor. This updated catalog enables more precise profiling of taxonomic and functional composition from metagenomic and metatranscriptomic datasets. VIRGO2 is a critical resource for integrative analyses of vaginal microbial communities and their interactions with host tissues, thereby enhancing our mechanistic understanding of vaginal health and disease.},
}
@article {pmid41353034,
year = {2026},
author = {McCone, N and Hosokawa, M},
title = {Recovering genomes from uncultured fungi with single-cell genomics.},
journal = {Journal of bioscience and bioengineering},
volume = {141},
number = {3},
pages = {143-151},
doi = {10.1016/j.jbiosc.2025.11.004},
pmid = {41353034},
issn = {1347-4421},
mesh = {*Single-Cell Analysis/methods ; *Genome, Fungal ; *Fungi/genetics/classification ; *Genomics/methods ; Metagenomics/methods ; Spores, Fungal/genetics ; },
abstract = {Single-cell genomics (SCG) complements culture-independent metagenomics for accessing fungal genomes, particularly from lineages that remain uncultured. We contrast metagenomics, which excels when profiling community composition and metabolic potential but often underrepresents low-abundance fungi, with SCG, which first isolates individual cells or nuclei to generate single-amplified genomes (SAGs) and can recover rare or microdiverse taxa. We then organize existing fungal SCG applications into three subgroups: spore-level sequencing from host-enriched or environmental material; single-nucleus genomics for multinucleate fungi; and single-spore sequencing of haploid progeny for diploid linkage and chromosome phasing. Across studies, pooling and co-assembly of cognate cells improves completeness; key hurdles persist in wall lysis, whole-genome amplification bias, and contamination control. Practical advances include shallow sequencing for QC triage, nuclei pooling with normalized co-assembly, and hybrid long- and short-read assembly. SCG adds unique value where strain resolution and genotypic context matter, including host-to-mobile-element linkage, recovery of large biosynthetic gene clusters, and karyotype validation against telomere-to-telomere references. Used alongside metagenomics, SCG enables a strain-resolved view of fungal biodiversity and function, with incremental improvements across the SCG pipeline promising routine access to genomes from early-diverging and other environmentally embedded fungi.},
}
@article {pmid41352476,
year = {2026},
author = {Su, J and Zhao, K and Zhou, X and Pan, Z and Xia, C},
title = {Early-life exposure to linezolid caused gut microbiota dysbiosis can be inherited from parents to offspring.},
journal = {Chemico-biological interactions},
volume = {424},
number = {},
pages = {111863},
doi = {10.1016/j.cbi.2025.111863},
pmid = {41352476},
issn = {1872-7786},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Linezolid/adverse effects/pharmacology ; Male ; *Dysbiosis/chemically induced/microbiology ; Female ; Mice ; *Anti-Bacterial Agents/adverse effects ; },
abstract = {BACKGROUND AND OBJECTIVES: Linezolid is a broad-spectrum antibiotic against Gram-positive bacterial infections. Widespread use of linezolid has brought about significant adverse effects and potential reproductive toxicity, but there is not yet any study regarding to the transgenerational impact.<br><br>METHODS: Gut microbiota and metabolites from the 12-weeks old male mice who were treated with one-week linezolid at 4 weeks of age, as well as those from their offsprings, were analyzed by metagenomics and metabolomics, respectively. Reproductivity of the male parents were monitored, including fertility, litter size, survival and weight gain of offsprings.<br><br>RESULTS: Offsprings survival from the linezolid-treated male parents was obviously decreased, although fertilities, litter size, or weight gain was not affected. The linezolid-induced gut microbiota perturbation in male parents was manifested as lower alpha diversity, distinguishing beta diversity, and the dramatically altered profiles of function genes and metabolites. Especially, linezolid exposure reversed the relationship between Dysosmobacter and butyrogenic species, and that between Dysosmobacter and inflammation-associated species. Interestingly, gut microbiota dysbiosis also existed in both female and male offsprings from the treated male parents. Moreover, it was found that the differential metabolites enriched in ABC transporter pathway were found male parents and offsprings, while those enriched in sphingolipid signaling pathway were only found in offsprings of both sexes.<br><br>CONCLUSIONS: The early-life short-term exposure to linezolid make long-term gut microbiota dysregulation, which was even inherited from parents to offsprings. These findings raised critical concern about the ecological consequences of early-life antibiotic exposure and clinical safety evaluations.},
}
@article {pmid41352011,
year = {2026},
author = {Yang, K and Zhang, L and Zhao, K and Liu, W and Tiehm, A and Zhang, X},
title = {Metabolism regulates spatial distribution patterns of different microbial taxonomic groups in chlorinated aliphatic hydrocarbons contaminated soil.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140640},
doi = {10.1016/j.jhazmat.2025.140640},
pmid = {41352011},
issn = {1873-3336},
mesh = {*Soil Pollutants/metabolism ; Biodegradation, Environmental ; *Soil Microbiology ; *Hydrocarbons, Chlorinated/metabolism ; *Bacteria/metabolism/genetics ; *Archaea/metabolism/genetics ; Microbiota ; },
abstract = {A mechanistic understanding of the distribution and role of subsurface microbial communities is crucial for sustainable environmental management. Bioremediation of chlorinated solvents relies on the bioactivity of organohalide-respiring bacteria and their interaction with syntrophic members. However, the spatial distribution pattern and its influencing factors of these members remain poorly understood. In this study, Distance-decay relationship (DDR) models and Sloan's neutral community models (NCM) were employed to quantify spatial turnover rates and stochastic processes of different taxa in chlorinated aliphatic hydrocarbon-contaminated soil. Incorporating metagenomic analysis and machine learning, this study highlights the contribution of genomic information and reveals how genetic potential for functional mechanisms may relate to distinct spatial distribution patterns. Findings indicate that metabolic potential, rather than environmental preference, primarily governs the heterogeneous distribution of different taxa. Archaeal syntrophic members, Bathyarchaeia, was identified as a potential reliable target for improving bioremediation efficiency. Correlation between parameters of different models suggests that dispersal ability plays an important role in the variation of spatial turnover rate. This was further supported by LASSO regression models in which genomic features relevant to biofilm formation, dormancy, and DNA repair pathways were identified as key predictors of spatial turnover. These findings not only offer actionable insights for enhancing bioremediation strategies at chlorinated solvent-contaminated sites but also demonstrate the potential of incorporating genomic features to understand microbial biogeography.},
}
@article {pmid41351981,
year = {2026},
author = {Li, A and Ju, Z and Zhang, X and Wang, M and Xing, J and Liu, G and Qin, X},
title = {Fangji Huangqi Tang alleviated chronic kidney disease by regulating intestinal bacteria to inhibit the AHR/ROS pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157610},
doi = {10.1016/j.phymed.2025.157610},
pmid = {41351981},
issn = {1618-095X},
mesh = {Animals ; *Drugs, Chinese Herbal/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Renal Insufficiency, Chronic/drug therapy/microbiology/metabolism ; *Receptors, Aryl Hydrocarbon/metabolism ; Male ; Mice ; *Reactive Oxygen Species/metabolism ; Rats ; Rats, Sprague-Dawley ; Disease Models, Animal ; Mice, Inbred C57BL ; Signal Transduction/drug effects ; },
abstract = {BACKGROUND: Fangji Huangqi Tang (FHT) is a traditional Chinese herbal formula that is clinically effective and safe for chronic kidney disease (CKD). However, the mechanism of action of FHT remains unclear.<br><br>PURPOSE: In this study, we investigated the mechanism of the targeted regulation of intestinal flora by Fangji Huangqi Tang to delay CKD.<br><br>METHOD: A CKD model was established in rats and mice by tail vein injection of doxorubicin, and the rats and mice were administered FHT orally. Metagenomic sequencing analysis was employed to screen and identify FHT-regulated key gut bacteria in CKD model rats and mice. In vitro bacterial co-cultures of these taxa were analyzed for metabolite discovery. Oral supplementation of key bacteria in CKD mice was evaluated the therapeutic effects and validated the metabolic changes observed in vitro. Cellular Aryl Hydrocarbon Receptor (AHR) overexpression was conducted to clarify the mechanistic of the metabolite derived from microbiota.<br><br>RESULTS: FHT significantly enriched Corynebacterium stationis (C. stationis) in both CKD rat and mice models. In vitro, C. stationis metabolized tryptophan into Indole-3-Carbinol (I3C) while reducing indole levels. Oral administration of C. stationis in CKD mice attenuated renal dysfunction and elevated systemic I3C. Additionally, it downregulated AHR expression and diminished the expression of ROS-related inflammatory factors, thereby ameliorating CKD. Crucially, AHR overexpression reversed I3C's cytoprotective effects in MPC5 injury models.<br><br>CONCLUSIONS: This study reveals that FHT targets the enrichment of the gut bacterium C. stationis, driving tryptophan metabolism toward I3C conversion. This process suppresses AHR expression, reduces ROS levels and inflammatory injury, and ultimately retards the progression of CKD.},
}
@article {pmid41351708,
year = {2025},
author = {Campbell, KL and Armitage, AR and Labonté, JM},
title = {Microbial Communities Display Key Functional Differences between Reference and Restored Salt Marshes.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {21},
pmid = {41351708},
issn = {1432-184X},
mesh = {*Wetlands ; *Microbiota ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Geologic Sediments/microbiology/virology ; Nitrogen/metabolism ; Poaceae/microbiology ; Carbon/metabolism ; Viruses/classification/genetics/isolation &amp; purification ; Metagenome ; Sulfur/metabolism ; Ecosystem ; },
abstract = {Salt marshes, despite their ecological importance (i.e., carbon sequestration) and rapid decline due to climate change and sea-level rise. Salt marsh ecosystems provide essential services such as removal of pollutants, carbon sequestration, and protection of coastal lands from storm surges. These services are strongly influenced by plant productivity, which is closely linked to microbial processes such as biogeochemical cycling of carbon, nitrogen, and sulfur. To retain carbon sequestration and other ecological functions, substantial efforts are currently directed towards coastal marsh restoration. Restoration efforts often lack comprehensive assessments of ecosystem functioning. Here, in an effort to assess ecosystem functions, we compared the microbial and viral community composition, as well as the genetic potential between reference and 10-year-old restored marshes in Galveston Bay, TX, USA. Duplicate bulk surface sediment in stands of Spartina alterniflora were sampled for metagenomic analysis. Metagenome assembled genomes analysis showed that while the microbial community composition was largely similar among sites, the overall metabolic potential was dissimilar. Restored sites displayed a higher abundance of carbon and nitrogen cycling functions compared to reference sites, which mainly consisted of sulfur cycling. Although the restored sites developed sediment microbial communities that approached reference microbial composition, the differences in the metabolic functions suggest that even after 10 years, the restored sites were still in a transitional stage of development. The differences between the reference and restored sites were even more differentiated in the viral community's predicted host composition. Additionally, viruses potentially play a variety of roles within the sediment community, including population control and biogeochemical cycles participation through auxiliary metabolic genes. These results highlight the prolonged timeline of functional development in restored salt marshes and highlight the need to develop approaches to boost the development of soil microbial communities in newly created habitats.},
}
@article {pmid41351142,
year = {2025},
author = {Sharko, F and Busova, V and Boulygina, E and Burakova, A and Pankova, S and Nedoluzhko, A},
title = {Ancient DNA sheds light on the historical distribution of the rare and ephemeral plant Coleanthus subtilis in Southern Siberia.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {92},
pmid = {41351142},
issn = {1471-2164},
mesh = {Siberia ; *DNA, Ancient/analysis ; *DNA, Plant/genetics ; Archaeology ; Humans ; Phylogeny ; },
abstract = {BACKGROUND: Ancient DNA is a valuable source of information about the distant past of our planet. Reconstructing the past ecosystems is essential for understanding many aspects of life in the steppes of southern Siberia and Central Asia, where numerous human societies representing different archaeological cultures have lived. The remains of their activities, revealed by archaeological excavations, provide a wide range of sources for the cultural and natural/biological history of the region. One of the most enigmatic Iron Age archaeological cultures in southern Siberia is the Tashtyk culture, which dates back to the 1st - 7th centuries AD. The people of this culture inhabited the Minusinsk Basin and practiced different burial rites, including cremation. Thanks to the exceptional preservation of organic remains in individual Tashtyk burials we know of quite an unusual phenomenon: the placement of cremains into the human-like mannequins made from animal skin and filled with herbaceous plants. This study analyses ancient DNA extracted from the grass stuffing of a mannequin found in 2023 at the Oglakhty cemetery, which dates back to 250-300 AD. Our aim is to identify the plant species that were used to stuff the mannequin approximately 1,700 years ago, and to compare their diversity with that of modern-day plant species. This is particularly significant given that the Oglakhty region is part of the Khakassky State Nature Reserve, which was added to the UNESCO Tentative List in 2016 due to its biodiversity and concentration of archaeological sites.<br><br>RESULTS: We sequenced the ancient DNA of a dried historical grass mixture in order to reconstruct the nearly complete chloroplast genomes of several apparent Poaceae species. Our analysis showed that, 1,700 years ago, the diversity of plant species in the Oglakhty area was similar to the modern meadow flora of the Minusinsk Basin. These included typical steppe and forest-steppe zone plant genera of Siberia, such as Holcus, Phleum, Poa, and Stipa. Interestingly, alongside the species commonly found in modern southern Siberian steppes and meadows, we discovered the rare, ephemeral, and protected moss grass, Coleanthus subtilis (Tratt.) Seidel ex Roem. et Schult. whose current distribution range spans highly fragmented areas of northern Eurasia and North America but not the Minusinsk Basin.<br><br>CONCLUSION: The herbaceous plant C. subtilis, whose DNA fragments were obtained through the metagenomic profiling of the human-like mannequin's stuffing at the Oglakhty cemetery, provides new insights into the cultural and natural history of Siberia. Firstly, we identified several grass taxa in the mannequin's stuffing. Most of them are characteristic for the steppe zone; the only exception is C. subtilis, which usually inhabits riverbanks. Therefore, we assume that, despite being primarily stuffed with the steppe plants, the Oglakhty mannequin was crafted on a riverbank, where C. subtilis might have got inside likely by chance. It is important to note that the stuffing process apparently took place after the vegetation season of C. subtilis in second half of summer and the beginning of autumn. Secondly, our research suggests that a population of C. subtilis, which is currently absent from the documented flora of southern Siberia, previously grew in the Minusinsk Basin wetlands. Our study highlights the need for field expeditions aimed to identify endemic populations of C. subtilis in the Yenisei River valley.},
}
@article {pmid41351056,
year = {2025},
author = {Stach, TL and Starke, J and Bouderka, F and Bornemann, TLV and Soares, AR and Wilkins, MJ and Goldman, AE and Stegen, JC and Borton, MA and Probst, AJ},
title = {Conserved environmental adaptations of stream microbiomes in the hyporheic zone across North America.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {253},
pmid = {41351056},
issn = {2049-2618},
support = {426547801//Deutsche Forschungsgemeinschaft/ ; DE-AC05-76RL01830//U.S. Department of Energy/ ; },
mesh = {*Microbiota/genetics ; *Geologic Sediments/microbiology ; *Rivers/microbiology ; North America ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Ecosystem ; Metagenome ; Sulfur/metabolism ; Nitrogen/metabolism ; Nitrogen Cycle ; Adaptation, Physiological ; Metagenomics/methods ; },
abstract = {BACKGROUND: Stream hyporheic zones represent a unique ecosystem at the interface of stream water and surrounding sediments, characterized by high heterogeneity and accelerated biogeochemical activity. These zones-represented by the top sediment layer in this study-are increasingly impacted by anthropogenic stressors and environmental changes at a global scale, directly altering their microbiomes. Despite their importance, the current body of literature lacks a systematic understanding of active nitrogen and sulfur cycling across stream sediment and surface water microbiomes, particularly across geographic locations and in response to environmental factors.<br><br>RESULTS: Based on previously published and unpublished datasets, 363 stream metagenomes were combined to build a comprehensive MAG and gene database from stream sediments and surface water including a full-factorial mesocosm experiment which had been deployed to unravel microbial stress response. Metatranscriptomic data from 23 hyporheic sediment samples collected across North America revealed that microbial activity in sediments was distinct from the activity in surface water, contrasting similarly encoded metabolic potential across the two compartments. The expressed energy metabolism of the hyporheic zone was characterized by increased cycling of sulfur and nitrogen compounds, governed by Nitrospirota and Desulfobacterota lineages. While core metabolic functions like energy conservation were conserved across sediments, temperature and stream order change resulted in differential expression of stress response genes previously observed in mesocosm studies.<br><br>CONCLUSIONS: The hyporheic zone is a microbial hotspot in stream ecosystems, surpassing the activity of overlaying riverine surface waters. Metabolic activity in the form of sulfur and nitrogen cycling in hyporheic sediments is governed by multiple taxa interacting through metabolic handoffs. Despite the spatial heterogeneity of streams, the hyporheic sediment microbiome encodes and expresses conserved stress responses to anthropogenic stressors, e.g., temperature, in streams of separate continents. The high number of uncharacterized differentially expressed genes as a response to tested stressors is a call-to-action to deepen the study of stream systems. Video Abstract.},
}
@article {pmid41350579,
year = {2025},
author = {Tarracchini, C and Longhi, G and Gennaioli, E and Muscò, A and Rizzo, SM and Viappiani, A and Vitale, SG and Mancabelli, L and Lugli, GA and Angioni, S and Turroni, F and van Sinderen, D and Milani, C and Ventura, M},
title = {Compiling an early life human gut microbiome atlas and identification of key microbial drivers.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {4},
pmid = {41350579},
issn = {2055-5008},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Infant ; *Bacteria/classification/genetics/isolation &amp; purification ; Infant, Newborn ; Metagenomics/methods ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {During the first year after birth, the infant gut microbiome undergoes a rapid and profound compositional and functional transformation, impelled by an intricate network of intrinsic and extrinsic factors. This process results in increased taxonomic and functional diversification, alongside greater interindividual variability. To better understand this early-life ecosystem, this study assessed the interindividual variability of the infant gut microbiome using a comprehensive infant gut microbiome database of 5288 fecal metagenomic data from healthy, full-term infants across various geographical locations. Our study identified six reference microbial communities, termed Early-Life Community State Types (ELi-CSTs), which not only capture specific compositional profiles and heterogeneity of the infant gut microbiome, but also record the extensive transformation experienced by this developing microbial community during the first year of human life. Indicative Species analysis and Random Forest modeling assisted the precise identification of unique, key taxonomic signatures that are critical to the structure of each ELi-CST, highlighting microbial taxa with pivotal roles in shaping the infant gut microbiota. To complement these findings, we established a bacterial biobank through dedicated cultivation efforts of the infant microbiota, comprising 182 genome-sequenced isolates corresponding to key taxa involved in early life gut microbiota assembly. This biobank provided the basis for co-cultivation experiments combined with transcriptome analyses, thereby enabling in vitro investigations into microbial cross-talk among key modulators, and yielding novel insights into the molecular interactions and cooperative dynamics behind early microbiome development.},
}
@article {pmid41350543,
year = {2025},
author = {Nickodem, CA and Tran, PQ and Neeno-Eckwall, E and Congdon, AG and Sanford, GR and Silva, EM and Hite, JL},
title = {Soil management strategies drive divergent impacts on pathogens and environmental resistomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43215},
pmid = {41350543},
issn = {2045-2322},
support = {AD00001395//U.S. Department of Agriculture/ ; 58-5090-2-035//U.S. Department of Agriculture/ ; AD00001395//U.S. Department of Agriculture/ ; },
mesh = {*Soil Microbiology ; Manure/microbiology ; Fertilizers ; *Soil/chemistry ; Animals ; Agriculture/methods ; Poultry ; Microbiota ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Humans ; Gene Transfer, Horizontal ; },
abstract = {Antimicrobial resistance (AMR) is a growing global health threat, and the genes that confer drug resistance are increasingly recognized as widespread environmental contaminants. Livestock manure, widely used as a non-synthetic fertilizer, is a potential source of AMR contamination in the environment. Manure fertilizers are well-documented reservoirs of AMR genes (ARGs) and drug-resistant pathogens. However, the role of soil management practices in shaping the persistence and spread of these genes after manure application remains poorly understood. We conducted a large-scale field experiment to evaluate how soil management practices influence the resistome (the genomic content involved in resistance to antimicrobial agents) and the overall microbiome of agricultural soils. Specifically, we ask: Does the use of composted poultry manure in organic soil management practices increase the risk of transmitting ARGs and drug-resistant pathogens? We integrated metagenomic sequencing with risk score analyses to assess the abundance, diversity, and mobility of resistance genes. Contrary to expectations, our results indicate that non-organic practices, despite not applying poultry manure, posed greater risks for transmitting AMR genes and human pathogens - due to significantly higher co-occurrence of ARGs with mobile genetic elements (MGEs), which facilitate horizontal gene transfer. In contrast, organic practices, that applied composted poultry manure, increased overall ARG and metal resistance gene (MRG) abundance, but the genes were less diverse and less mobile. These findings show that focusing solely on ARG and MRG abundance can misrepresent AMR risks and underscore the importance of evaluating gene mobility and management context when assessing AMR hazards. Our study highlights how soil management can be strategically leveraged to mitigate AMR transmission, offering actionable insights for sustainable agriculture, environmental stewardship, and public health protection.},
}
@article {pmid41350329,
year = {2025},
author = {Sato, Y and Kumagai, H and Hirooka, H and Yoshida, T},
title = {Differences in prokaryotic and viral community between rumen and feces.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43232},
pmid = {41350329},
issn = {2045-2322},
mesh = {*Feces/microbiology/virology ; Animals ; *Rumen/microbiology/virology ; Metagenomics/methods ; *Viruses/genetics/classification ; Metagenome ; Bacteria/genetics ; Virome ; *Prokaryotic Cells/virology ; Genome, Viral ; Gastrointestinal Microbiome ; },
abstract = {Ruminants harbor diverse microbial communities, including prokaryotes and viruses, across their digestive tract. Rumen viruses contribute to carbohydrate metabolism; however, their persistence and host interactions in the lower gastrointestinal tract remain unclear. In this study, we investigated the prokaryotic and viral communities in the rumen and feces of the same wethers using whole-metagenomic and virus-like particle metagenomic sequencing. For prokaryotic community analysis, we reconstructed over 300 metagenome-assembled genomes, most of which were novel. These revealed strong site specificity, with distinct prokaryotic community compositions between the rumen and feces. Virome analysis recovered more than 6,000 viral genomes, including many novel viruses. Unlike prokaryotes, several viruses were found to be shared between the rumen and feces. Auxiliary metabolic genes encoding glycoside hydrolases were identified in several rumen-associated viral genomes, whereas fecal-associated viral genomes did not harbor such genes. Host-virus interaction analysis predicted that viruses predominantly infect dominant bacterial taxa and methanogens within each gastrointestinal site, although some viruses may interact with hosts across different sites. These findings highlight the strong site specificity of the prokaryotic communities and the comparatively broader distribution of viruses within the ruminant gastrointestinal tract. These insights advance understanding of virus-prokaryote-host interactions with implications for animal productivity.},
}
@article {pmid41349311,
year = {2026},
author = {Manfreda, C and Ghidini, S and Fuschi, A and Remondini, D and Guarneri, F and Alborali, GL and Fernández-Trapote, E and Cobo-Dìaz, JF and Alvarez-Ordóñez, A and Ianieri, A},
title = {In-depth characterization of microbiome and resistome of carcasses and processing environments in a swine slaughterhouse.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110820},
doi = {10.1016/j.vetmic.2025.110820},
pmid = {41349311},
issn = {1873-2542},
mesh = {Animals ; *Abattoirs ; Swine/microbiology ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/drug effects/genetics/classification/isolation &amp; purification ; Anti-Bacterial Agents/pharmacology ; *Meat/microbiology ; Food Microbiology ; },
abstract = {Antimicrobial resistance represents a critical global health challenge. Within the swine production chain, all stages have been identified as potential reservoirs for antimicrobial resistance genes. In the present study whole metagenomic sequencing technology was applied in a swine slaughterhouse and pig carcasses to investigate microbial communities and their associated antimicrobial resistance genes. Actinomycetota and Pseudomonadota were the dominant phyla across all samples, while Bacillota, Bacteroidota, and Campylobacteriota were more prevalent in the dirty zone and carcass samples than in the clean zone. Key antimicrobial-resistant bacteria included genera such as Acinetobacter, Aeromonas, and Streptococcus, with Acinetobacter spp., Streptococcus suis, and Aliarcobacter cryaerophilus identified as high-priority species for food safety due to their persistence and antimicrobial resistance genes associations. Several genera showed strong correlations with resistance to macrolides, lincosamides, and beta-lactams. Moreover, the plasmid-borne and lateral gene transfer events were associated with dirty zone and carcass samples in comparison to clean zone samples, suggesting the potential dissemination of antimicrobial resistance genes, especially for macrolides and sulphonamides resistance genes. Tetracycline, beta-lactam, and aminoglycoside resistance genes were the most abundant antimicrobial resistance genes across all samples, consistent with a pig slaughterhouse environment. This study highlights distinct microbiome profiles across environmental zones of a pig slaughterhouse, reflecting the adaptation of bacterial taxa to specific processing conditions. The findings have significant implications for food business operators who have to apply appropriate hygienic measures to reduce the dissemination of bacterial food-borne pathogens and to mitigate the risk of antimicrobial resistance transfer along the food chain.},
}
@article {pmid41348832,
year = {2025},
author = {Cervantes-Echeverría, M and Jimenez-Rico, MA and Manzo, R and Hernández-Reyna, A and Cornejo-Granados, F and Bikel, S and González, V and Hurtado Ramírez, JM and Sánchez-López, F and Salazar-León, J and Pedraza-Alva, G and Perez-Martinez, L and Ochoa-Leyva, A},
title = {Human-derived fecal virome transplantation (FVT) reshapes the murine gut microbiota and virome, enhancing glucose regulation.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0337760},
pmid = {41348832},
issn = {1932-6203},
mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Fecal Microbiota Transplantation/methods ; *Virome ; Male ; Diet, High-Fat/adverse effects ; Obesity/therapy/microbiology ; *Feces/virology ; Mice, Inbred C57BL ; *Glucose/metabolism ; Metabolic Syndrome/therapy/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; },
abstract = {The gut microbiome, comprising bacteria, viruses, archaea, fungi, and protists, plays a crucial role in regulating host metabolism and health. This study explored the effects of fecal virome transplantation (FVT) from healthy human donors on metabolic syndrome (MetS) in a diet-induced obesity (DIO) mouse model, without diet change. Mice received a single oral dose of human-derived virus-like particles (VLPs) and continued on a high-fat diet (HFD) for 17 weeks. Despite persistent dietary stress, FVT significantly improved glucose tolerance. Longitudinal profiling by virome shotgun metagenomics and bacterial 16S rRNA sequencing revealed marked, durable shifts in both viral and bacterial community composition. Notable bacterial changes included a decrease in Akkermansia muciniphila and Peptococcaceae and increases in Allobaculum and Coprococcus; A. muciniphila positively correlated with glucose levels and negatively correlated with body weight. Together, these results suggests that human-derived virome can durably reshape gut microbial ecology and improve glucose metabolism in mice with obesity, even without dietary modification, offering a novel avenue for developing phage-based therapies. This proof-of-concept study provides foundational observations for using human-derived VLPs for FVT in standard laboratory mouse models, and provides a foundation for elucidating bacteria-phage interactions and their role in host metabolic health.},
}
@article {pmid41348596,
year = {2025},
author = {Hernández-Velázquez, R and Ziemski, M and Bokulich, NA},
title = {ViromeXplore: integrative workflows for complete and reproducible virome characterization.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
pmid = {41348596},
issn = {1477-4054},
support = {22.00210//Swiss State Secretariat for Education, Research and Innovation/ ; //European Union nor European Research Executive Agency/ ; },
mesh = {*Virome ; *Workflow ; *Metagenomics/methods ; *Software ; High-Throughput Nucleotide Sequencing ; *Computational Biology/methods ; *Viruses/genetics/classification ; Metagenome ; Microbiota ; Genome, Viral ; Reproducibility of Results ; },
abstract = {Viruses play a crucial role in shaping microbial communities and global biogeochemical cycles, yet their vast genetic diversity remains underexplored. Next-generation sequencing technologies allow untargeted profiling of metagenomes from viral communities (viromes). However, existing workflows often lack modularity, flexibility, and seamless integration with other microbiome analysis platforms. Here, we introduce "ViromeXplore," a set of modular Nextflow workflows designed for efficient virome analysis. ViromeXplore incorporates state-of-the-art tools for contamination estimation, viral sequence identification, taxonomic assignment, functional annotation, and host prediction while optimizing computational resources. The workflows are containerized using Docker and Singularity, ensuring reproducibility and ease of deployment. Additionally, ViromeXplore offers optional integration with QIIME 2 and MOSHPIT, facilitating provenance tracking and interoperability with microbiome bioinformatics pipelines. By providing a scalable, user-friendly, and computationally efficient framework, ViromeXplore enhances viral metagenomic analysis and contributes to a deeper understanding of viral ecology. ViromeXplore is freely available at https://github.com/rhernandvel/ViromeXplore.},
}
@article {pmid41348453,
year = {2025},
author = {Li, C and Ge, H and Huang, W and Zilda, DS and Radjasa, OK and Zhao, L and Cong, B and Liu, S and Zhang, Z},
title = {Vertically stratified microbial diversity and keystone species driving element cycling in the Magellan seamount sediments.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001493},
pmid = {41348453},
issn = {2057-5858},
mesh = {*Geologic Sediments/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Archaea/genetics/classification ; Phylogeny ; Biodiversity ; Microbiota ; },
abstract = {Deep-sea polymetallic nodules, rich in cobalt, nickel and titanium, are valuable for electronics, aerospace and energy industries. However, the vertical distribution and ecological functions of prokaryotic communities in sediments beneath nodules from the Magellan seamounts, a unique microbial habitat characterized by ultra-slow sedimentation rates (0.4-4 mm ky[-1]) and heterogeneous metal gradients, remain poorly characterized. In our research, 16S rRNA gene amplicon sequencing and metagenomic analyses of sediment cores (0-20 cm) from the western Pacific polymetallic nodule province revealed statistically significant decreases in prokaryotic diversity (Shannon index: 9.446 to 2.288; P<0.001). Proteobacteria, Crenarchaeota, Chloroflexi and Bacteroidota were the dominant taxa. The microbial co-occurrence network in the surface layer had a longer mean path length (2.11 vs 1 in the bottom layer) and a larger network diameter (11 vs 1), indicating a loose community structure and greater resistance to disturbance, while the bottom microbial network had a higher density (0.037 vs 0.01) and clustering coefficient (0.32 vs 1), suggesting tight microbial interactions. The concentrations of MnO (6.96-9.41 µg g[-1]) and P2O5 (2.55-3.89 µg g[-1]) gradually decreased with increasing depth. The concentrations of Co and Pb were relatively high in the surface sediments (0-8 cm) but decreased significantly below 8 cm. In contrast, the concentrations of Fe2O3 and As increased with depth. The environmental factors depth, MnO, Fe2O3 and heavy metals (Cr, Zn and Cu) were found to be the main drivers of the microbial community structure. We assembled 122 metagenome-assembled genomes from the metagenomic data. Gene abundance analysis revealed that sox genes (soxB/C/D/X/Y/Z) and assimilatory sulphate reduction genes (cysC and cysH) were highly abundant in the surface sediment, whereas the abundance of dissimilatory sulphate reduction genes (dsrA and dsrB) was enhanced in the bottom layer, reflecting a hierarchical adaptive strategy for sulphur metabolism. Our study expands current knowledge on the vertical variations of microbial diversity and microbially driven biogeochemical cycling in deep-sea settings underneath polymetallic nodules. Characterizing the microbial community underneath those nodules may provide insights into microbial resilience in extreme oligotrophic environments and valuable insights for future deep-sea mining activities.},
}
@article {pmid41348443,
year = {2025},
author = {Luu, LDW and Bryant, C and Brown, J and Turner, M and Pham, TH and Mazraani, R and Burke, C and Jury, B and Shrestha, M and Fleming, K and Bateson, D and Russell, D and Bassett, F and Ong, E and Hocking, JS and Sweeney, S and Huston, WM},
title = {Cervicovaginal microbiome composition and absolute quantity are associated with pelvic inflammatory disease.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
pmid = {41348443},
issn = {2057-5858},
mesh = {Humans ; Female ; *Pelvic Inflammatory Disease/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Case-Control Studies ; *Vagina/microbiology ; Adult ; *Cervix Uteri/microbiology ; Vaginosis, Bacterial/microbiology ; Gardnerella vaginalis/genetics ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification ; Young Adult ; },
abstract = {Pelvic inflammatory disease (PID), which involves infection and inflammation of the female reproductive tract, can lead to sequelae including chronic pelvic pain, ectopic pregnancy and tubal factor infertility. A causative pathogen is not identified in many PID cases (idiopathic PID) and does not develop in all women with a sexually transmitted infection or bacterial vaginosis. Therefore, there is a need to better understand the pathogenesis of PID. A case-control study was conducted to explore microbiome, antibiotic resistance and immune gene expression in PID. Microbial profiling using both 16S rRNA gene amplicon and metagenomic approaches revealed that bacterial vaginosis-associated bacteria such as Gardnerella vaginalis, Fannyhessea vaginae, Ureaplasma parvum and members of the Prevotella spp. were significantly enriched in PID cases, while healthy controls were associated with Lactobacillus (L.) crispatus. Quantitative analysis with species-specific quantitative real-time PCR (qPCR) indicated that a high copy number of L. crispatus (measured using calibrated copy estimates by qPCR) was strongly associated with cervical samples from women in the control group, whereas PID cases with this organism had low copies when measured using qPCR. Antibiotic resistance to tetracyclines was more frequently predicted in metagenome-assembled genomes from PID cases, and corresponding isolates cultured from cases were less susceptible to doxycycline (L. iners). Overall, this study supports that PID is associated with cervicovaginal dysbiosis and an absence or low quantity of L. crispatus.},
}
@article {pmid41347789,
year = {2025},
author = {Malina, N and Tollerson, R and Monami, SJ and Rivera, E and Lee, M-K and Bilenker, LD and Ojeda, AS},
title = {Microbial community diversity and geochemistry inform bioremediation of molybdenum-contaminated groundwater.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {12},
pages = {e0098825},
pmid = {41347789},
issn = {1098-5336},
support = {S10 OD034282/OD/NIH HHS/United States ; 1-106223-01-01//Electric Power Research Institute/ ; },
mesh = {*Molybdenum/metabolism ; *Groundwater/microbiology/chemistry ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Microbiota ; },
abstract = {In situ remediation of groundwater at coal combustion product (CCP) sites can be challenging for elements such as molybdenum (Mo), which do not respond well to commonly used treatment. This research was initiated to improve the understanding of geochemistry and microbial diversity associated with a Mo plume at a CCP site toward the development of an in situ treatment scheme. Diffusive microbial samplers were designed and deployed at the study site for 9 weeks. Afterward, geochemical and community analyses were used as the basis to understand how microbial communities respond to elevated Mo concentrations within a plume. Our results show that the Mo and other constituents within the plume do not reduce the diversity of the community, in contrast to trends observed at other industrial sites with metals and metalloids in groundwater. Interestingly, bacteria of the order Burkholderiales were higher in abundance in wells where Mo >0.3 mg/L, and several sulfate-reducing bacteria were less abundant but not absent. Molybdenum sequestration experiments were also performed with sulfate-reducing bacteria enriched from groundwater samples collected at the site. The results show that Desulfomicrobium escambiense played a major role in Mo sequestration and activated a detoxification mechanism. This process involved the sequential activation of periplasmic heavy metal sensors, followed by the activation of atpE ATP synthase, which may function as an exporter of Mo to form Mo-S species in the periplasm of the cell. The results provide important considerations for bioremediation potential in groundwater settings impacted by Mo, especially those who seek to stimulate sulfate-reducing bacteria for Mo sequestration in biogenic sulfide solids.IMPORTANCEBioremediation of contaminated sites has become popular for chlorinated hydrocarbons, but it has not been widely applied to inorganic constituents outside of arsenic. Here, we show the potential for the development of geochemistry-informed bioremediation technologies of Mo-contaminated groundwater by leveraging Mo-tolerant communities despite the suppression of sulfate reduction by Mo.},
}
@article {pmid41346331,
year = {2025},
author = {Preenanka, R and Sivam, V and Sasikala, R and Koombankallil, R and Raveendran, K and Jacob, J and Devadas, AL and Ravikumar, NK and Anbalakan, M and Chigilipalli, H and Thangaraj, RS and Basha, AK and Joseph, TC and Badireddy, MR and Vaiyapuri, M},
title = {Muscle Microbiome Analysis of Indian Mackerel (Rastrelliger kanagurta) Delineated Classical and Novel Spoilage Bacteria.},
journal = {Journal of food science},
volume = {90},
number = {12},
pages = {e70751},
doi = {10.1111/1750-3841.70751},
pmid = {41346331},
issn = {1750-3841},
support = {BT/PR46349/AAQ/3/1063/2022//&#x2003;Department of Biotechnology/ ; //&#x2003;Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {Animals ; *Perciformes/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; *Seafood/microbiology ; Food Packaging/methods ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; *Muscles/microbiology ; Vacuum ; Metagenomics ; Food Storage ; },
abstract = {Metagenomics allows a comprehensive insight into the spoilage-associated muscle microbiome shifts in the air-packed and vacuum-packed Indian mackerel. This study explored the microbial composition and diversity of spoilage flora in air-packed (T1M, T2M, and T3M) and vacuum-packed (T4M, T5M, and T6M) Indian mackerel (Rastrelliger kanagurta) stored at 0 ± 2°C (iced), 5 ± 2°C (chilled), and 30 ± 2°C (abused) temperatures through metagenomics, targeting the V1-V9 region of 16s rRNA. Total Volatile Base Nitrogen and Thiobarbituric Acid were analyzed to confirm the spoilage threshold limit, and accordingly, the fish muscle tissue on the spoilage day was selected for microbiome analysis. Metagenomic analysis revealed distinct variation in the relative abundance and spoilage microbiome between the air-packed and vacuum-packed Indian mackerel stored at iced, chilled, and abused temperatures. The predominant bacterial species responsible for spoilage were Cetobacterium ceti, Clostridium polyendosporum, and Gilliamella apicola in vacuum-packed mackerel, whereas Shewanella arctica, S. aquimarina, S. baltica, Staphylococcus xylosus, and Burkholderia cepacia played a major role in the spoilage of air-packed samples. The observed bacterial population dynamics across different temperatures and packaging significantly influenced the microbiome diversity in Indian mackerel. Summing up, this study emphasizes the unique and diverse microbes contributing to spoilage and provides a valuable guide for the flora that need to be controlled for extending the shelf life of Indian mackerel.},
}
@article {pmid41346299,
year = {2026},
author = {Zhang, C and Zhao, Z and Zhou, F and Shi, C and Zhai, X and Sha, Z and Chu, Q and Liu, H and Liu, S and Pan, Z and Wang, X and Pan, X and Fang, M and Rillig, MC and Wang, Z},
title = {Conventional and Biodegradable Microplastics Both Impair Soil Phosphorus Cycling and Availability via Microbial Suppression.},
journal = {Environmental science &amp; technology},
volume = {60},
number = {1},
pages = {1229-1240},
doi = {10.1021/acs.est.5c11806},
pmid = {41346299},
issn = {1520-5851},
mesh = {*Phosphorus ; *Soil/chemistry ; *Microplastics ; Soil Microbiology ; Soil Pollutants ; Biodegradation, Environmental ; Polyesters ; },
abstract = {Microplastics (MPs) are emerging soil pollutants that can disrupt essential biogeochemical processes, yet their effects on phosphorus (P) cycling remain underexplored. Here, we conducted a 150-day incubation experiment using agricultural soil amended with either polyethylene (PE, conventional) or polylactic acid (PLA, biodegradable) MPs to investigate their impact on microbially mediated P cycling. MPs altered soil P cycling and decreased available phosphorus (AP) by ∼15% after 90 days. Fourier transform infrared spectroscopy revealed weakened AP-associated functional groups (P-O-P, P-O, and P═O), most pronounced under PLA treatment. These shifts were accompanied by reduced abundances of key P-cycling taxa (Bacillus, Paenibacillus, and Sphingomonas) and downregulation of phosphatase gene abundance (phoA/D/X: -65.4% in PE, -59.8% in PLA). Correspondingly, the activities of acid, neutral, and alkaline phosphatases were all suppressed, with alkaline phosphatase in PE-treated soil reduced by 34.1%. Together, these results demonstrate that MPs disturb biotic transformation pathways, leading to subsequent alterations in the chemical speciation of soil P and decreased AP content. Notably, significant disruption was observed for both conventional and biodegradable types. Our findings challenge the prevailing assumption of environmental benignity for biodegradable plastics and underscore the urgent need for mechanistic assessments of their byproducts. Such disruption may hinder microbial P mobilization and decrease fertilizer use efficiency, ultimately threatening soil health and agricultural sustainability.},
}
@article {pmid41345980,
year = {2025},
author = {Jiang, Y and Che, L and Li, SC},
title = {Deciphering the personalized functional redundancy hierarchy in the gut microbiome.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {17},
pmid = {41345980},
issn = {2049-2618},
support = {JCYJ20220818101201004//Shenzhen Science and Technology Innovation Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Non-alcoholic Fatty Liver Disease/microbiology ; Metabolic Networks and Pathways ; Cohort Studies ; },
abstract = {BACKGROUND: Functional redundancy (FR) in the human gut microbiome is crucial for maintaining stability and resilience, exhibiting a hierarchical structure. However, the precise configuration and functional implications of this hierarchy remain elusive and limited by single-metric measurements. We aimed to develop a method that comprehensively characterizes the hierarchical organization of functional redundancy in personalized microbiomes.<br><br>RESULTS: We represented functional redundancy as a network and developed a structural entropy (SE)-based approach to elucidate FR hierarchy, revealing functional redundancy clusters (FRCs)-groups of species capable of independently executing specific metabolic pathways. Through controlled simulations and cross-cohort analyses spanning 4912 gut metagenomes across 28 disease cohorts, we established that our approach offers higher resolution, more comprehensive measurement, and greater robustness in detecting disease-associated functional patterns than traditional FR methods. In healthy individuals, we observed FR network polycentric structure, which shifted to monocentric structure in non-alcoholic steatohepatitis patients. Vitamin biosynthesis FRCs correlated with microbiota transplantation efficiency, while FRCs specialized in short-chain fatty acid production predicted immunotherapy response and patient survival. Permutation tests validated the causal relationship between SE differences and disease phenotypes, while perturbation experiments revealed that FR keystone species exert disproportionate influence on the system's resilience.<br><br>CONCLUSIONS: Our SE-based approach to functional redundancy analysis provides superior sensitivity compared to conventional metrics by integrating multiple hierarchical levels of functional organization. This methodology establishes a novel perspective for understanding microbiome stability through personalized FR networks, positioning FRCs as promising diagnostic markers and therapeutic targets for microbiome-associated diseases. Video Abstract.},
}
@article {pmid41345979,
year = {2025},
author = {Sakanaka, A and Furuno, M and Ishikawa, A and Katakami, N and Inoue, M and Mayumi, S and Kurita, D and Nishizawa, H and Omori, K and Taya, N and Isomura, ET and Kudoh, M and Takeuchi, H and Amano, A and Shimomura, I and Fukusaki, E and Kuboniwa, M},
title = {Diabetes alters the supragingival microbiome through plasma-to-saliva migration of glucose and fructose.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {48},
pmid = {41345979},
issn = {2049-2618},
support = {22H03300, 22H00487, 22K10311, 21K18281//Japan Society for the Promotion of Science/ ; JP16gm0710005//Japan Agency for Medical Research and Development/ ; },
mesh = {Humans ; *Saliva/metabolism/chemistry/microbiology ; Female ; Male ; Dental Caries/microbiology ; *Microbiota ; *Diabetes Mellitus, Type 2/microbiology/metabolism/blood/complications ; *Glucose/metabolism ; Middle Aged ; *Fructose/metabolism/blood ; Adult ; Biofilms/growth &amp; development ; Metabolomics/methods ; Aged ; *Gingiva/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; },
abstract = {BACKGROUND: Dental caries, a dysbiotic biofilm disease driven by polymicrobial acidogenesis, often coexists with type 2 diabetes (T2D). Previous studies suggest covarying relationships between circulating and salivary metabolites in patients with T2D. However, the role of hyperglycemia-induced saccharide migration from plasma to saliva in caries pathogenesis remains unclear. Here, we developed a novel method for untargeted metabolomics profiling of trace saliva from sublingual and submandibular glands, comparing this profile with those of plasma and whole saliva in participants with T2D (n = 31) and those with normoglycemia (n = 30). This comparison aimed to determine how circulating saccharide migration into the oral cavity and its subsequent microbial consumption are linked to dental caries. Additionally, shotgun metagenomic sequencing was combined with this analysis to investigate the cariogenic impact of circulating saccharide migration on the composition and function of supragingival biofilm using MetaPhlAn4 and HUMAnN3 pipelines.<br><br>RESULTS: The metabolomics profiles of glandular saliva showed intermediate dissimilarity between plasma and whole saliva, reflecting cardiometabolic traits more sensitively than whole saliva. Glucose and fructose showed a decreasing positive correlation with glycemic parameters in the order of plasma, glandular saliva, and whole saliva, suggesting systemic-to-oral migration and subsequent microbial consumption. Saccharide migration was more pronounced in participants with dental caries and plaque accumulation, coinciding with shifts in supragingival microbiota, including depletion of Streptococcus sanguinis, Corynebacterium durum, and Rothia aeria, and enrichment of Streptococcus mutans, Veillonella parvula, and Actinomyces sp. oral taxon 448. Glycolytic potential increased at the community level. Improved glycemic control reduced fructose migration and mitigated dysbiosis, decreasing fructose phosphotransferase abundance and shifting the S. mutans-S. sanguinis balance. Experimental validation demonstrated that fructose promotes S. mutans dominance over S. sanguinis in dual-species biofilms.<br><br>CONCLUSIONS: This study establishes saccharide migration as a metabolic driver of supragingival dysbiosis in T2D. The findings highlight the role of both glucose and fructose in caries pathogenesis and suggest that glycemic control could serve as an effective strategy as part of caries control. Video Abstract.},
}
@article {pmid41345831,
year = {2025},
author = {Bu, Y and Sun, F and Liu, L and He, X and Wang, H and Chen, Z and He, T and Xu, S and Zhao, X and Meng, X},
title = {Comparative study on the rumen microbial communities and functions between Wagyu and Holstein calves.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {20},
pmid = {41345831},
issn = {1471-2164},
support = {CX23YQ31//Heilongjiang Agricultural Science and Technology Innovation Leapfrog Project/ ; CARS-37//Supported by China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; *Rumen/microbiology ; Cattle ; Metagenomics ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Understanding the rumen microbiota's development in calves is essential for optimizing breed-specific feeding strategies. This study aimed to comparatively investigate the dynamic changes in the rumen microbial community structure and function in Wagyu and Holstein calves.<br><br>METHODS: Five 3-month-old Wagyu calves and five age-matched Holstein calves were selected. All animals received the same diet consisting of concentrate and hay, with free access to feed and water. Rumen fluid samples were collected monthly from 3 to 6 months of age. Metagenomic sequencing was performed to assess microbial composition (phylum and genus levels), alpha diversity (Shannon, Simpson, ACE, and Chao1 indices), and functional pathway (KEGG-based).<br><br>RESULTS: The cumulative relative abundance of dominant taxa at both phylum and genus levels declined with age in both breeds, more markedly in Wagyu calves than in Holsteins. From 3 to 6 months of age, the top five phyla combined dropped by 3.25% in Wagyu and 0.87% in Holstein calves, whereas the top ten genera combined decreased by 1.63% and 0.63%, respectively. Alpha diversity in Wagyu calves increased significantly with age. At 5 and 6 months, the Shannon, ACE, and Chao1 indices were significantly higher than those at 3 months (P&#x2009;<&#x2009;0.05). Moreover, from 4 to 6 months, Wagyu calves consistently exhibited significantly higher diversity indices than Holsteins (P&#x2009;<&#x2009;0.05). At 6 months, Wagyu calves showed a significant reduction in metabolism-related microbial genes and an increase in genes related to cellular processes and genetic information processing compared to earlier ages and Holstein calves (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: These findings suggest potential breed-specific differences in the succession and functional maturation of rumen microbiota. Holstein calves developed earlier and more stable metabolic functions, while Wagyu calves underwent a more dynamic microbial selection process.<br><br>CLINICAL TRIAL NUMBER: Not applicable.},
}
@article {pmid41345737,
year = {2025},
author = {Li, F and Yan, M and Su, D and Peng, J and Wang, X and Hao, J and Ma, T and Lin, Y and Shi, H},
title = {Integrated meta-omics reveals AFB1 dose-dependent remodeling of the rumen microbiome-virome-metabolome axis driving metabolic impairment in goats.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {18},
pmid = {41345737},
issn = {2049-2618},
support = {grant no. 31902187//National Natural Science Foundation of China/ ; SCCXTD-2024-14//Innovation Team Development Funds for Sichuan Meat Goat and Sheep/ ; },
mesh = {Animals ; *Rumen/microbiology/virology/metabolism/drug effects ; *Goats/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Aflatoxin B1/toxicity/administration &amp; dosage ; Animal Feed/analysis ; *Metabolome/drug effects ; Bacteria/classification/genetics/drug effects/isolation &amp; purification/metabolism ; Fermentation ; Metagenomics/methods ; Fatty Acids, Volatile/metabolism ; },
abstract = {BACKGROUND: Aflatoxin B1 (AFB1), a highly carcinogenic and hepatotoxic mycotoxin frequently contaminating animal feed, presents serious health risks to both humans and livestock. Although AFB1's hepatotoxicity and other organ damage are extensively characterized, how this mycotoxin influences ruminal microbiota dynamics and functional activities in ruminants remains underexplored. Although some studies suggest that AFB1 reduces nutrient digestibility and performance in ruminants, the underlying mechanisms are unclear. To aid in developing effective mitigation strategies for aflatoxicosis in ruminants, this study randomly divided Saanen goats into three groups. The CON group received the standard ration without additives, whereas LD and HD groups were provided identical basal diets fortified with 50 or 500 μg/kg AFB1. Throughout the study, alterations in ruminal fermentation parameters, microbiome, and metabolome profiles were analyzed.<br><br>RESULTS: With increasing AFB1 levels, ruminal pH, the concentration of total volatile fatty acids (VFA), acetate, and propionate decreased quadratically, while butyrate decreased linearly. Metagenomic profiling indicated suppressed populations of Pelagibacter and Flavobacterium following AFB1 exposure, contrasting with promoted growth of Cryptobacteroides. Additionally, seven carbohydrate-active enzymes (CAZymes), specifically GT92, GT20, CE7, GT32, GT35, GT57, and GT50, were found to be more prevalent in the rumen of the CON group. Statistically higher viral loads characterized the HD group when benchmarked against CON group. Metabolomics analysis identified 1197 differential metabolites among the CON, LD, and HD groups, including cytochalasin Ppho and chrysophanol, both known for their teratogenic properties and their ability to induce cell death.<br><br>CONCLUSIONS: This study indicates that dietary AFB1 exposure can alter the ruminal microbial and metabolomic profiles, induce prophage activation, and impact carbohydrate degradation and microbial protein turnover. These alterations may contribute to reductions in ruminal pH and volatile fatty acid concentrations, thereby impairing feed digestibility and animal performance. The findings provide valuable insights into AFB1's effects on rumen health, and further investigations of these metabolic pathways may help develop precision interventions to mitigate AFB1-induced rumen dysfunction and productivity losses. Video Abstract.},
}
@article {pmid41345261,
year = {2026},
author = {Ma, J and Kim, N and Cha, JH and Kim, W and Kim, CY and Lee, YH and Kim, HS and Han, YD and Yong, D and Han, E and Yang, S and Beck, S and Lee, I},
title = {A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.},
journal = {Nature microbiology},
volume = {11},
number = {1},
pages = {317-334},
pmid = {41345261},
issn = {2058-5276},
support = {2022M3A9F3016364//National Research Foundation of Korea (NRF)/ ; 2022R1A2C1092062//National Research Foundation of Korea (NRF)/ ; },
mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; *Archaea/classification/genetics ; *Bacteria/classification/genetics/metabolism ; Colorectal Neoplasms/microbiology ; Crohn Disease/microbiology ; Datasets as Topic ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Molecular Sequence Annotation ; Phylogeny ; Reference Values ; Genes, Bacterial ; },
abstract = {Understanding the human gut microbiome requires comprehensive genomic catalogues, yet many lack geographic diversity and contain medium-quality metagenome-assembled genomes (MAGs) missing up to 50% of genomic regions, potentially distorting functional insights. Here we describe an enhanced Human Reference Gut Microbiome (HRGM2) resource, a catalogue of near-complete MAGs (≥90% completeness, ≤5% contamination) and isolate genomes. HRGM2 comprises 155,211 non-redundant near-complete genomes from 4,824 prokaryotic species across 41 countries, representing a 66% increase in genome count and a 50% boost in species diversity compared to the Unified Human Gastrointestinal Genome catalogue. It enabled improved DNA-based species profiling, resolution of strain heterogeneity and survey of the human gut resistome. The exclusive use of these genomes improved metabolic capacity assessment, enabling high-confidence, automated genome-scale metabolic models of the entire microbiota and revealing disease-associated microbial metabolic interactions. This resource will facilitate reliable functional insights into gut microbiomes.},
}
@article {pmid41345123,
year = {2025},
author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM},
title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1913},
pmid = {41345123},
issn = {2052-4463},
support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; },
mesh = {Ecosystem ; *Metagenome ; Microbiota ; Pacific Ocean ; *RNA, Transfer/genetics ; *Seawater/microbiology ; *Transcriptome ; Datasets as Topic ; },
abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.},
}
@article {pmid41345120,
year = {2025},
author = {Abad-Recio, IL and Rubel, V and Filker, S and Garate, L and Stoeck, T and Logares, R and Lanzén, A},
title = {The Basque Coast Estuarine Sediment Gene Catalogue.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1909},
pmid = {41345120},
issn = {2052-4463},
support = {Fi 2089/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STO 414/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Archaea/genetics ; Bacteria/genetics ; Biodiversity ; Ecosystem ; *Estuaries ; Eukaryota/genetics ; *Geologic Sediments/microbiology ; Metagenomics ; Viruses/genetics ; Datasets as Topic ; },
abstract = {Estuaries are critical transition zones that link marine, riverine, and terrestrial ecosystems, including habitats like intertidal mudflats and tidal marshes. These ecosystems are biodiversity hotspots providing essential ecological functions such as nutrient cycling and pollutant removal. Despite their importance, there is a significant knowledge gap regarding the ecological functioning of these habitats and how they are impacted by anthropogenic pressures. From intertidal estuarine benthos along the Basque Coast 92 microbial metagenomic assemblies were retrieved that allowed us to reconstruct 390 medium plus 81 high quality MAGs, along with 108 million putative genes from bacteria, archaea, eukaryotes, and viruses. This unique dataset will enhance our understanding of ecosystem functioning, biodiversity, and be useful to reveal biogeochemical processes and the role of unculturable biomass.},
}
@article {pmid41345102,
year = {2025},
author = {Pope, R and Visconti, A and Zhang, X and Louca, P and Baleanu, AF and Lin, Y and Asnicar, F and Bermingham, K and Wong, KE and Michelotti, GA and Wolf, J and Segata, N and Berry, SE and Spector, TD and Leeming, ER and Gibson, R and Menni, C and Falchi, M},
title = {Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10051},
pmid = {41345102},
issn = {2041-1723},
support = {/WT_/Wellcome Trust/United Kingdom ; 27/2023//Chronic Disease Research Foundation (CDRF)/ ; },
mesh = {Humans ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet ; Male ; Female ; Metabolome ; Middle Aged ; Metabolomics/methods ; Aged ; Metagenomics ; Adult ; Machine Learning ; },
abstract = {The interplay between diet and gut microbiome composition is complex. Faecal metabolites, the end products of human and microbial metabolism, provide insights into these interactions. Here, we integrate faecal metabolomics, metagenomics, and habitual dietary data from 1810 individuals from the TwinsUK and 837 from the ZOE PREDICT1 cohorts. Using machine learning models, we find that faecal metabolites accurately predict reported intakes of 20 food groups (area under the curve (AUC) > 0.80 for meat, nuts and seeds, wholegrains, tea and coffee, and alcohol) and adherence to seven dietary patterns (AUC from 0.71 for the Plant-based Diet Index to 0.83 for the Dietary Approaches to Stop Hypertension score). Notably, the faecal metabolome is a stronger predictor of atherosclerotic cardiovascular disease risk (AUC = 0.86) than the Dietary Approaches to Stop Hypertension score (AUC = 0.66). We identify 414 associations between 19 food groups and 211 metabolites, that significantly correlate with microbial α-diversity and 217 species. Our findings reveal that faecal metabolites capture mediations between diet and the gut microbiome, advancing our understanding of diet-related disease risk and informing metabolite-based interventions.},
}
@article {pmid41344778,
year = {2026},
author = {Li, Z and Zhao, C and Mao, Z and Zhao, L and Penttinen, P and Zhang, S},
title = {Metagenomics insights into bacterial community, viral diversity and community-scale functions in fermented red pepper.},
journal = {Food microbiology},
volume = {135},
number = {},
pages = {104986},
doi = {10.1016/j.fm.2025.104986},
pmid = {41344778},
issn = {1095-9998},
mesh = {Fermentation ; *Capsicum/microbiology/virology ; Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism/virology ; *Fermented Foods/microbiology/virology ; Gene Transfer, Horizontal ; *Viruses/genetics/classification/isolation &amp; purification ; Bacteriophages/genetics/classification/isolation &amp; purification ; *Microbiota ; Food Microbiology ; },
abstract = {Fermented red peppers (FRPs) provide distinct flavor and possible health benefits, but understanding of their microbial functions, viral diversity, pathogenicity, and horizontal gene transfer (HGT) patterns remains limited. Integrated multi-method analysis revealed FRP's bacterial community was dominated by Bacillus (21.52 %), Lactobacillus sensu lato (14.27 %), and Pantoea (13.60 %). Bacillus drove core fermentation with an over 40 % contribution to carbon degradation and iron reduction. The virome was dominated by Caudoviricetes phages, yet 25.5 % of the functions of viral genes remained unknown. Critically, multidrug resistance genes were the most abundant ARGs, and beneficial bacteria served as major reservoirs for ARGs, co-occurring with potential opportunistic pathogens. Despite inhibitory conditions, these last dominated key metabolic nodes hydrogen generation and acetate oxidation. Counterintuitively, ARG profiles correlated with bacterial composition but not with mobile genetic elements or detected HGT events, challenging HGT as the primary ARG driver. These findings necessitate dual strategies: leveraging key microbes for fermentation efficiency while implementing stringent monitoring to mitigate pathogen and ARG related risks.},
}
@article {pmid41344333,
year = {2026},
author = {Cao, Y and Bowker, MA and Feng, Y and Delgado-Baquerizo, M and Xiao, B},
title = {The Great Wall of China harbors a diverse and protective biocrust microbiome.},
journal = {Current biology : CB},
volume = {36},
number = {1},
pages = {16-27.e4},
doi = {10.1016/j.cub.2025.10.087},
pmid = {41344333},
issn = {1879-0445},
mesh = {China ; *Microbiota ; Humans ; *Soil Microbiology ; Bacteria/classification/genetics ; *Fungi/classification/isolation &amp; purification ; },
abstract = {The Great Wall of China, one of the most emblematic human heritage sites ever built, is largely covered by a living skin that has a potentially distinct microbiome compared with bare wall surfaces. However, the structure and function of this microbiome remain virtually unknown, which hampers any effort to understand the impacts of this microbiome on the long-term conservation of the Great Wall. Here, we investigated the microbiome of the Great Wall at six sampling sites along a 600-km section, which stretches across arid and semiarid climates and is covered by a mosaic of biological soil crusts (biocrusts) and exposed wall surfaces. We hypothesized that these biocrusts could establish a unique microhabitat and support a microbiome with a community structure and function potentially distinct from those on bare walls, thereby modulating the biodeterioration processes affecting the Great Wall. Our findings revealed that biocrust-covered sections exhibited a 12%-62% increase in abundance, diversity, and co-occurrence network complexity for bacterial and fungal communities compared with bare walls. Further metagenomic analyses indicated that the biocrust cover enhanced the abundance of overall functional genes and stress-resistance pathways within the microbiome by 4%-15%, while decreasing the metabolic pathways linked to heritage biodeterioration. Aridity was an additional determinant of the microbiome. Our work serves as a critical step toward understanding the microbiome of the Great Wall, which contributes to conserving this unparalleled human monument for future generations.},
}
@article {pmid41342600,
year = {2025},
author = {Bauchinger, F and Berry, D},
title = {Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {1},
pages = {},
pmid = {41342600},
issn = {1574-6941},
support = {10.55776/COE7//Austrian Science Fund/ ; },
mesh = {Humans ; *Polysaccharides/metabolism ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/metabolism/classification ; *Intestinal Mucosa/metabolism/microbiology ; *Metagenome ; *Transcriptome ; Metagenomics ; Mucins/metabolism ; },
abstract = {The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin, it is still unclear which species transcribe the respective genes. Here, we systematically analysed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized cooccurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although ~60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.},
}
@article {pmid41340567,
year = {2025},
author = {Ouradova, A and Ferrero, G and Bratova, M and Daskova, N and Bohdanecka, A and Dohnalova, K and Heczkova, M and Chalupsky, K and Kralova, M and Kuzma, M and Modos, I and Tichanek, F and Najmanova, L and Pardini, B and Pelantová, H and Tarallo, S and Videnska, P and Gojda, J and Naccarati, A and Cahova, M},
title = {A vegan diet signature from a multi-omics study on different European populations is related to favorable metabolic outcomes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593050},
pmid = {41340567},
issn = {1949-0984},
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Cross-Sectional Studies ; Czech Republic ; *Diet, Vegan ; *Gastrointestinal Microbiome ; Italy ; *Metabolome ; Metagenome ; Multiomics ; Vegans ; },
abstract = {Vegan and omnivorous diets differ markedly in composition, but their effects on the gut microbiome, metabolome, and lipidome across populations remain insufficiently characterized. While both diet and country of origin influence these molecular layers, the relative contribution of diet versus country-specific factors has not yet been systematically evaluated within a multi-omics framework.In this cross-sectional, bicentric, observational study, we profiled healthy vegans (n = 100) and omnivores (n = 73) from the Czech Republic and Italy using integrated microbiome, metabolome, and lipidome analyses. Findings were subsequently validated in an independent cohort (n = 142).Significant differences across all omics layers were observed for both country and diet. The predictive models confirmed diet-associated separation, with validation cohort AUCs of 0.99 (lipidome), 0.89 (metabolome), and 0.87 (microbiome). Functional metagenome analysis revealed enrichment of amino acid biosynthesis, inositol degradation, and the pentose phosphate pathway in vegans, while omnivores presented greater potential for amino acid fermentation, fatty acid biosynthesis, and propanoate metabolism. Linear models identified a robust, country-independent "vegan signature" consisting of 27 lipid metabolites, five non-lipid metabolites, and 11 bacterial species. Several lipid features associated with an omnivorous diet were inversely related to the duration of vegan diet adherence. Some of the vegan-associated metabolites and bacteria have been previously linked to favorable cardiometabolic profiles, although causality remains to be established.These findings demonstrate that vegan diets are associated with reproducible, country-independent molecular and microbial signatures. Our results highlight diet-driven shifts in host-microbiota interactions and provide a framework for understanding how dietary patterns relate to host-microbiota interactions.},
}
@article {pmid41340249,
year = {2025},
author = {Gluvić, Z and Zafirović, S and Sudar-Milovanović, E and Stanimirović, J and Soskić, S and Jevremović, D and Isenović, ER},
title = {Molecular insights into the gut-thyroid axis: microbiota-driven biomarkers and diagnostic applications.},
journal = {Expert review of molecular diagnostics},
volume = {25},
number = {12},
pages = {915-928},
doi = {10.1080/14737159.2025.2599225},
pmid = {41340249},
issn = {1744-8352},
mesh = {Humans ; *Biomarkers/metabolism ; *Gastrointestinal Microbiome ; *Thyroid Gland/metabolism ; *Thyroid Diseases/diagnosis/metabolism/microbiology/etiology ; Metabolomics/methods ; Metagenomics/methods ; },
abstract = {INTRODUCTION: New research has shown an intriguing link between the gut bacteria and the thyroid. A gut-thyroid relationship affects energy production, immunological function, and inflammation. As a result, disrupted gut flora harmony is associated with an increased/altered risk of thyroid dysfunction, autoimmune disorders, and metabolic imbalance. In addition to current diagnostic technology, understanding the gut flora-thyroid relationship could assist in the detection of thyroid-related conditions and modify patient treatment.<br><br>AREAS COVERED: This review explores state-of-the-art molecular techniques, e.g. metagenomics profiling and metabolomics, to uncover clinically relevant microbiota-driven biomarkers related to thyroid disorders.<br><br>EXPERT OPINION: Revealing potential microbiota-driven biomarker candidates is pivotal in enhancing our understanding of the mechanisms of thyroid disorders more precisely and identifying diagnostic and prognostic markers with clinical potential. Precisely, the individualization in the approach to patients with thyroid disorder, inevitably considering the harmonization of the gut microbiota-thyroid hormone relationship, is the basis of rational pharmacotherapy.},
}
@article {pmid41340151,
year = {2025},
author = {Kropp, DR and Glover, ME and Samanta, R and Unroe, KA and Clinton, SM and Hodes, GE},
title = {Perinatal citalopram exposure alters the gut composition and microbial metabolic profiles of Sprague-Dawley rat dams and female offspring but not male offspring.},
journal = {Biology of sex differences},
volume = {17},
number = {1},
pages = {2},
pmid = {41340151},
issn = {2042-6410},
support = {R01 MH105447/MH/NIMH NIH HHS/United States ; R01MH105447-01/NH/NIH HHS/United States ; },
mesh = {Animals ; *Citalopram/pharmacology ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; Pregnancy ; *Selective Serotonin Reuptake Inhibitors/pharmacology ; *Prenatal Exposure Delayed Effects/microbiology ; Rats ; Sex Characteristics ; *Metabolome/drug effects ; Animals, Newborn ; },
abstract = {BACKGROUND: Selective serotonin reuptake inhibitors are widely prescribed during pregnancy. Their main route of administration is through the gut. However, their impact on the maternal and offspring gut microbiome and microbial metabolic pathways remains poorly understood. This study used metagenomic shotgun sequencing to examine the effects of perinatal citalopram exposure in rat dams and their offspring on gut composition and downstream metabolic pathways.<br><br>METHODS: We treated pregnant and nursing rat dams with either citalopram or vehicle (water). Their feces were collected, DNA from these samples was extracted and then sequenced using shotgun metagenomic sequencing. The BioBakery suite of microbiome analysis tools was utilized in tandem with RStudio to analyze the gut composition and microbial metabolic pathways of the rat dams and their offspring.<br><br>RESULTS: Pregnant and nursing dams treated with citalopram exhibited marked shifts in microbial community structure, including phylum-level alterations in Proteobacteria and Defferibacteria. Citalopram treated dams displayed significantly altered beta diversity. Species level alterations due to treatment were composed of five significantly altered microbes, two of which belong to the Proteobacteria phylum. These changes were highly diverse and were not congruent with microbe-level alterations observed in offspring. Alpha diversity of microbial metabolic pathways was compared using the Gini-Simpson index, which was significantly increased in dams suggesting greater metabolic functional diversity with age. Female offspring perinatally exposed to citalopram showed significant changes in gut beta diversity, with seven significant alterations at the microbe level. These microbial shifts were accompanied by twenty-one significantly altered microbial metabolic pathways. In contrast, male offspring showed no significant differences in microbial composition or beta diversity and only minor metabolic changes.<br><br>CONCLUSIONS: These findings demonstrate that maternal citalopram exposure during pregnancy and lactation has lasting, sex-specific impacts on the offspring's gut microbiome and microbial metabolic pathways. The pronounced alterations in female, but not male offspring, suggest that host sex may be a critical determinant in the developmental response to citalopram exposure. This work underscores the value of metagenomic approaches in uncovering complex host-microbiome interactions and highlights the need to consider offspring sex in evaluating the safety and long-term effects of antidepressant use during pregnancy.},
}
@article {pmid41340071,
year = {2025},
author = {Peng, J and Liu, X and Wang, J and Meng, N and Cai, R and Peng, Y and Han, Y and Liao, J and Li, C and Rubin-Blum, M and Ma, Q and Dong, X},
title = {Diverse quorum sensing systems regulate microbial communication and biogeochemical processes in deep-sea cold seeps.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {16},
pmid = {41340071},
issn = {2049-2618},
support = {1359/23//Israel Science Foundation/ ; 32170121//National Natural Science Foundation of China/ ; 92351304//National Natural Science Foundation of China/ ; 2023J06042//Natural Science Foundation of Fujian Province/ ; 3502Z202373076//Natural Science Foundation Project of Xiamen City/ ; 2022025//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; },
mesh = {*Quorum Sensing/genetics ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Archaea/genetics/classification/metabolism ; Metagenome ; *Seawater/microbiology ; Phylogeny ; *Microbiota/genetics ; Ecosystem ; Geologic Sediments/microbiology ; },
abstract = {BACKGROUND: Quorum sensing is a fundamental chemical communication mechanism that enables microorganisms to coordinate behavior and adapt to environmental conditions. However, its contribution in deep-sea cold seep ecosystems, where diverse microbial communities and frequent communication occur, remains poorly understood. In this study, we aimed to elucidate the occurrence and potential ecological roles of quorum sensing in cold seeps.<br><br>RESULTS: We analyzed 170 metagenomes and 33 metatranscriptomes from 17 global cold seep sites, identifying 299,355 quorum sensing genes from the cold seep non-redundant gene catalog. These genes represent 34 types across six quorum sensing systems, with distribution patterns influenced by sediment depth and seep type. A total of 32,500 quorum sensing genes were identified in 3576 metagenome-assembled genomes from 12 archaeal and 108 bacterial phyla, revealing a complex network of intraspecies and interspecies communication. Microbial groups involved in key metabolic processes, such as sulfate-reducing bacteria, anaerobic methanotrophic archaea, diazotrophs, and organohalide reducers, were extensively regulated by quorum sensing, influencing biogeochemical cycles in cold seeps. Phylogenetic analysis and protein domain identification highlighted the involvement of key quorum sensing-related proteins (e.g., PDE, RpfC/G, CahR, and LuxR) in modulating microbial behaviors, such as motility and chemotaxis. Heterologous expression further confirmed the activity of representative LuxI-R pairs, and metabolomic profiling suggested the presence of putative quorum sensing inhibitors in cold seep sediments.<br><br>CONCLUSIONS: Overall, these findings highlight the complexity and significance of quorum sensing in microbial interactions, ecological adaptation, and biogeochemical cycling within cold seep ecosystems, advancing our understanding of microbial communication in the deep biosphere. Video Abstract.},
}
@article {pmid41340070,
year = {2025},
author = {Jeilu, O and Sumner, JT and Moghadam, AA and Thompson, KN and Huttenhower, C and Catlett, C and Hartmann, EM},
title = {Metagenomic profiling of airborne microbial communities from aircraft filters and face masks.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {249},
pmid = {41340070},
issn = {2049-2618},
mesh = {*Air Microbiology ; *Metagenomics/methods ; Humans ; *Bacteria/genetics/classification/isolation &amp; purification ; *Aircraft ; *Masks/microbiology ; *Microbiota/genetics ; *Air Filters/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Airborne microbial communities, although often challenging to study due to low biomass, play crucial roles in public health and pathogen transmission. Through shotgun metagenomics, this study utilizes non-invasive air sampling of face masks and aircraft cabin filters to investigate microbial diversity in environments with frequent human interactions, including hospitals and airplanes. A comprehensive sampling and analysis workflow was developed, incorporating environmental and enrichment protocols to enhance microbial DNA recovery and diversity profiling.<br><br>RESULTS: Despite limitations in biomass, optimized extraction methods allowed for the successful identification of 407 species, with dominant taxa including Cutibacterium acnes, Staphylococcus epidermidis, Sphingomonas hankookensis, and Methylobacterium radiotolerans. Enrichment processing resulted in greater metagenome-assembled genome (MAG) recovery and higher antimicrobial resistance gene (ARG) identification.<br><br>CONCLUSIONS: The findings highlight the presence of ARGs in high-occupancy public spaces, suggesting the importance of monitoring and the potential for mitigating airborne transmission risks in such environments. This study demonstrates the utility of combining environmental and enrichment sampling to capture comprehensive microbial and ARG profiles in confined spaces, providing a framework for enhanced pathogen monitoring in public health contexts. Video Abstract.},
}
@article {pmid41339801,
year = {2025},
author = {Yang, T and Wang, Y and Zhang, Y and Liu, C and Zeng, Y and Shi, P and Zhou, J and Li, Y and Wei, H},
title = {Haemophilus influenzae dominance in fungal ball microbiome revealed through multi-niche metagenomic sequencing.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {15},
pmid = {41339801},
issn = {1471-2180},
support = {7222026//Natural Science Foundation of Beijing Municipality/ ; },
mesh = {Humans ; Male ; Female ; Metagenomics/methods ; Adult ; *Microbiota/genetics ; Middle Aged ; *Haemophilus influenzae/genetics/isolation &amp; purification/classification ; Fungi/genetics/classification/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; *Mycoses/microbiology ; Aspergillus flavus/genetics/isolation &amp; purification ; },
abstract = {OBJECTIVE: This study employed metagenomic sequencing to characterize the sinonasal microbiome in patients with unilateral maxillary sinus fungal ball (MSFB), with specific emphasis on bacterial-fungal interactions and functional pathways implicated in fungal ball pathogenesis.<br><br>METHODS: The study enrolled 30 MSFB patients and 30 healthy controls. Nasal secretion samples were obtained from three anatomical sites in MSFB cases: fungal ball cavity (FC), affected middle nasal meatus (AM), and contralateral unaffected middle nasal meatus (UM). And in the control group, samples were obtained from the healthy middle nasal meatus (HM). Metagenomic sequencing of microbial DNA was performed using the Illumina Novaseq platform. Taxonomic and functional analyses were conducted using Kraken2, Bracken, and HUMAnN2.<br><br>RESULTS: Bacteria dominated the microbiome in the FC group (98.53%), with Haemophilus influenzae identified as a key biomarker (LDA score&#x2009;>&#x2009;5). A negative correlation between H. influenzae and Aspergillus flavus was observed in the FC group (r&#x2009;=&#x2009;-0.46, P&#x2009;=&#x2009;0.013). Functional pathways enriched in the FC group included amino acid biosynthesis (map00290), lipopolysaccharide biosynthesis (map00540), and fatty acid biosynthesis (map00061), supporting H. influenzae survival and immune modulation. FC microbiota showed reduced diversity and distinct composition compared to other groups (PERMANOVA, P&#x2009;<&#x2009;0.001). No significant differences were found in the composition of the microbiota between the bilateral middle nasal meatus groups of MSFB.<br><br>CONCLUSION: This study highlights H. influenzae as a critical bacterial biomarker in MSFB. The inverse relationship between H. influenzae and A. flavus may suggest competitive or immune-mediated interactions. These findings advance understanding of non-invasive fungal sinusitis. Future validation in larger fungal ball cohorts or invasive fungal sinusitis is warranted.},
}
@article {pmid41339745,
year = {2026},
author = {Zhang, L and Marfil-Sánchez, A and Kuo, TH and Seelbinder, B and van Dam, L and Depetris-Chauvin, A and Jahn, LJ and Sommer, MOA and Zimmermann, M and Ni, Y and Panagiotou, G},
title = {Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes.},
journal = {Nature microbiology},
volume = {11},
number = {1},
pages = {94-110},
pmid = {41339745},
issn = {2058-5276},
support = {Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; Excellent Young Scientists Fund (project ID 24HAA01325)//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Mice ; *Phytochemicals/metabolism ; *Diet ; Biotransformation ; *Bacteria/metabolism/genetics/classification/enzymology ; Plants, Edible/metabolism/chemistry ; Metagenomics ; },
abstract = {Food, especially plant-based diet, has complex chemical diversity. However, large-scale phytonutrient-metabolizing activities of gut bacteria are largely unknown. Here we integrated and systematically analysed multiple databases containing information on enzymatic reactions and food health benefits, and 3,068 global public human microbiomes. Transformation of 775 phytonutrients from edible plants was associated with enzymes encoded by diverse gut microbes. In vitro assays validated the biotransformation activity of gut species, for example, Eubacterium ramulus. The biotransformation of phytonutrients demonstrated high interpersonal and geographical variability. Machine learning models based on 2,486 public case-control microbiomes, using the abundances of enzymes associated with modification of phytonutrients present in health-associated foods, discriminated the health status of individuals in multiple disease contexts, suggesting altered biotransformation potential in disease. We validated the association of microbiome-encoded enzymes with the anti-inflammatory activity of common edible plants by combining metagenomics and metatranscriptomics analysis in specific-pathogen-free and germ-free mice. These findings have implications for designing precise, personalized diets to guide an individual towards a healthy state.},
}
@article {pmid41339710,
year = {2025},
author = {Pacheco-Valenciana, A and Tausch, A and Veseli, I and Dharamshi, JE and Bergland, F and Delgado, LF and Rodríguez-Gijón, A and Andersson, AF and Garcia, SL},
title = {Microbial model communities exhibit widespread metabolic interdependencies.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1752},
pmid = {41339710},
issn = {2399-3642},
support = {grant 2022-03077//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; grant 2018-05973//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; grant 2022-06725//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; grant 2022-03077//Science for Life Laboratory (SciLifeLab)/ ; },
mesh = {*Bacteria/metabolism/genetics/classification ; *Metagenome ; *Microbiota ; Genome, Bacterial ; Seawater/microbiology ; Phylogeny ; },
abstract = {Microorganisms thrive in complex communities shaped by intricate interactions, yet the extent and ecological implications of biosynthetic dependencies in natural communities remain underexplored. Here, we used a dilution approach to cultivate 204 microbial model communities from the Baltic Sea and recovered 527 metagenome-assembled genomes (MAGs) that dereplicated into 72 species-clusters (>95% average nucleotide identity, ANI). Of these species, at least 70% represent previously uncultivated lineages. Combined with 1073 MAGs from Baltic Sea metagenomes, we generated a genomic catalog of 701 species-clusters. Our results show that cultures with more than three species included microorganisms with smaller genome sizes, lower biosynthetic potential for amino acids and B vitamins, and higher prevalence and abundance in the environment. Moreover, the taxa found together in the same model communities had complementary biosynthetic gene repertoires. Our results demonstrate that cultivating bacteria in dilution model communities facilitates access to previously uncultivated but abundant species that likely depend on metabolic partners for survival. Together, our findings highlight the value of community-based cultivation for unraveling ecological strategies. Finally, we confirm that metabolic interdependencies and genome streamlining are widespread features of successful environmental microorganisms.},
}
@article {pmid41339548,
year = {2026},
author = {Singleton, CM and Jensen, TBN and Delogu, F and Knudsen, KS and Sørensen, EA and Jørgensen, VR and Karst, SM and Yang, Y and Sereika, M and Petriglieri, F and Knutsson, S and Dall, SM and Kirkegaard, RH and Kristensen, JM and Overgaard, CK and Woodcroft, BJ and Speth, DR and Aroney, STN and , and Wagner, M and Dueholm, MKD and Nielsen, PH and Albertsen, M},
title = {The Microflora Danica atlas of Danish environmental microbiomes.},
journal = {Nature},
volume = {649},
number = {8098},
pages = {971-981},
pmid = {41339548},
issn = {1476-4687},
mesh = {Denmark ; *Microbiota/genetics ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Humans ; Ecosystem ; Biodiversity ; *Environmental Microbiology ; Agriculture ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; },
abstract = {Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans[1], in the human gut[2] and on Earth[3], with compilations encompassing thousands of public datasets[4,5]. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for N2O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.},
}
@article {pmid41339392,
year = {2025},
author = {Muratore, E and Conti, G and Fabbrini, M and Zama, D and Decembrino, N and Muggeo, P and Mura, R and Perruccio, K and Leardini, D and Barone, M and Zecca, M and Cesaro, S and Brigidi, P and Turroni, S and Masetti, R},
title = {Distinct functional and compositional properties in the gut microbiome of children with acute lymphoblastic leukaemia identified by shotgun metagenomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43082},
pmid = {41339392},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Child ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology ; Male ; Female ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Adolescent ; Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {Acute lymphoblastic leukaemia (ALL) represents the most common childhood malignancy, and emerging evidence underscores the impact of the gut microbiome (GM) on its pathogenesis. In this study, we used shotgun metagenomics to investigate the GM of 30 ALL patients at diagnosis-19 with B-ALL and 11 with T-ALL-and compared them to 176 healthy controls (HCs). When considered as a single ALL group versus HCs, clear compositional differences emerged: ALL patients exhibited higher relative abundances of Enterococcus faecium, oral commensals such as Rothia dentocariosa, and multiple opportunistic species, whereas HCs were enriched in short-chain fatty acid producers like Anaerostipes hadrus and Intestinibacter bartlettii. Functionally, the ALL GM relied more on protein and amino acid catabolism, while HCs possessed enhanced pathways for carbohydrate and folate metabolism. These findings broadly align with 16S rRNA-based analyses from previous publications, though some discrepancies highlight differences in technique-driven resolution. In contrast, comparing the two major molecular phenotypes-B-ALL and T-ALL-revealed only minimal taxonomic and functional differences, primarily confined to BAs metabolism pathways. Overall, our results indicate that children with ALL at the time of diagnosis already display a dysbiotic signature, bolstering the notion that a disturbance in GM development during childhood may be linked to the multistep pathogenesis model of ALL.},
}
@article {pmid41339319,
year = {2025},
author = {Harrison, LC and Allnutt, TR and Hanieh, S and Roth-Schulze, AJ and Ngui, KM and Stone, NL and Bandala-Sanchez, E and Backshell, L and Gurruwiwi, G and Gondarra, V and Couper, JJ and Craig, ME and Davis, EA and Huynh, T and Soldatos, G and Wentworth, JM and Vuillermin, P and Penno, MAS and Biggs, BA and , },
title = {Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9904},
pmid = {41339319},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Australia ; Female ; Male ; Bacteria/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Infant, Newborn ; Indigenous Peoples ; Metagenome ; },
abstract = {Studies of traditional Indigenous compared to 'Western' gut microbiomes are underrepresented, and lacking in young children, limiting knowledge of early-life microbiomes in different cultural contexts. Here we analyze the gut metagenomes of 50 Indigenous Australian infants (median age <one year) living remotely with variable access to Western foods, compared to age- and sex-matched non-Indigenous infants living in urban Australia. Indigenous infants had greater alpha diversity and significant differences in bacterial beta diversity, with 114 species and 38 genera differing in abundance. Indigenous infants almost exclusively had higher carriage of Megaspaera, Streptococcus, Caecibacter, Parolsenella and Prevotella species, and markedly higher numbers of gut viruses and fungi. Bifidobacteria ssp. were dominant in Indigenous infants. Despite encroaching Westernisation, the gut microbiome of Indigenous infants retains key features of traditional societies worldwide, attesting to the dominant influence of remote environment and traditional lifestyle in maintaining microbiome diversity.},
}
@article {pmid41338426,
year = {2026},
author = {Yan, L and Su, Y and Xie, X and Peng, K and Zhang, P and Deng, Y and Gan, Y and Li, Q and Zhang, Y},
title = {Decoding microbial-mediated sulfur transformation pathways in mangrove wetland: Metagenomic and hydrogeochemical insights.},
journal = {Environmental research},
volume = {290},
number = {},
pages = {123472},
doi = {10.1016/j.envres.2025.123472},
pmid = {41338426},
issn = {1096-0953},
mesh = {*Wetlands ; *Sulfur/metabolism ; China ; Metagenomics ; *Microbiota ; Geologic Sediments/microbiology ; Bacteria/metabolism/genetics ; Metagenome ; },
abstract = {Sulfur (S) cycling is essential to the ecological function of mangrove wetlands, but how microbial processes and gene-level patterns respond to environmental gradients remains poorly understood. Here, we integrated high-resolution hydrogeochemical profiling with metagenomic sequencing to characterize depth-resolved microbial communities and S-cycling genes in the mangrove wetlands of Dongzhai Harbor, Hainan, China. The results revealed pronounced differences in microbial community composition between zones, with Escherichia dominating mangrove sediments (4.22-20.07 %) and Salmonella prevailing in mudflat sediments (23.87-60.98 %). The abundance of S-cycling genes (e.g., tusA, soeA, aprA, dsrAB, sat) declined markedly with depth. Spatial variation in biogeochemical conditions shaped functional gene distributions: oxidative genes (aprA, soeA) were more abundant in mudflat profiles, whereas sat dominated reductive pathways in mangrove sediments. Environmental gradients structured microbial communities, with salinity, pH, total nitrogen (TN), and total organic carbon (TOC) showing negative correlations, and total sulfur (TS), total phosphorus (TP), SO4[2-] acting as positive drivers. Co-occurrence network analysis indicated tighter microbial associations in surface layers compared to deeper strata. The thiosulfate oxidation pathway was confined to the 5-10 cm interval in mudflat sediments and appeared at both 5-10 cm and 15-20 cm in mangrove sediments, while direct sulfite oxidation occurred in both zones. Moreover, methanogenesis, nitrification, and denitrification were more prominent in mudflat sediments, whereas methane oxidation prevailed in mangrove profiles. These findings advance our understanding of how microbial functional stratification and S metabolic pathways respond to environmental gradients, with implications for biogeochemical coupling in coastal wetland ecosystems.},
}
@article {pmid41338123,
year = {2026},
author = {Huang, S and Yang, P and Wang, X and Zhang, K and Li, L and Yao, S and Qian, L and Liu, C and Guo, J and Shi, L and Liu, F and Xie, W and Guo, Y},
title = {Integrated metagenome and metabolome analysis reveals a disease signature of gut microbiota and the key gut microbiota-associated metabolite proline in schizophrenia.},
journal = {Journal of psychiatric research},
volume = {193},
number = {},
pages = {223-235},
doi = {10.1016/j.jpsychires.2025.11.029},
pmid = {41338123},
issn = {1879-1379},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; *Schizophrenia/microbiology/metabolism ; Male ; Female ; Adult ; *Proline/metabolism ; *Metabolome/physiology ; *Metagenome ; Middle Aged ; },
abstract = {Schizophrenia (SCZ) is a multifaceted psychiatric condition with a complex set of etiological factors. Recent studies have revealed that gut microbiota play a significant role in the neurobiology associated with SCZ. Utilizing metagenomic sequencing and analysis techniques, we obtained composition and functional information of the gut microbiota from 68 SCZ patients and 61 healthy control (HC) subjects. We identified 72 inter-group differential species, 49 differential metabolic pathways, and 1987 differential functional genes. A. odontolyticus and F. prausnitzii were the core species enriched in the SCZ group and the HC group, respectively. Arginine and proline metabolism were the most significant differential metabolic pathways, with K00286 being the differential functional gene catalyzing the synthesis of L-proline in this pathway. Notably, a strong disease classification model was developed based on the gut microbiota data, achieving an outstanding AUC of 0.94, outperforming earlier models, the model achieved AUC values of 0.745 and 0.845 in two separate external datasets, respectively. Furthermore, insights into mechanisms were investigated by analyzing the relationships between microbial species and their associated metabolic pathways. Future research is essential to clarify causal connections, detail specific molecular pathways-particularly those involving functional proteins such as K00286-and to explore the communication processes between the gut microbiota and the brain. Our results underscore the potential for microbiota-based biomarkers and therapeutic targets in SCZ, emphasizing the essential role of gut microbiota in this intricate disorder.},
}
@article {pmid41338072,
year = {2025},
author = {Jose, S and Lohith Kumar, DH and Malla, MA and Featherston, J and Bux, F and Kumari, S},
title = {Insights into microbial community, nitrogen‑phosphorus metabolism from metagenomic and metabolomic analysis of microalgal-cyanobacterial consortium-based bioinoculants.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181092},
doi = {10.1016/j.scitotenv.2025.181092},
pmid = {41338072},
issn = {1879-1026},
mesh = {*Phosphorus/metabolism ; *Nitrogen/metabolism ; *Microalgae/physiology ; *Soil Microbiology ; Fertilizers ; *Cyanobacteria/physiology ; *Microbiota ; Metagenomics ; *Microbial Consortia ; Metabolomics ; Agriculture ; },
abstract = {The intensification of agriculture through chemical fertilizers has led to severe environmental consequences. This study provides a comprehensive investigation on chemical fertilizer, vermiculite and on microalgal-cyanobacterial consortia (bioinoculants) influencing soil microbial community. Chemical fertilizer application significantly altered the microbial community, suppressing the dominant phylum Proteobacteria to 48.3 % abundance from 60.9 % in the control soil. The bioinoculant treatments maintained a high Proteobacteria abundance (58.9 %-59.7 %) and fostered a growth-oriented, anabolic strategy. The 50:50 mix treatment uniquely promoted the fungal phylum Basidiomycota to 18.2 % abundance and showed the highest investment in the Glycolysis/Gluconeogenesis pathway (23.0 %). Chemical fertilizer treatment upregulated genes for rapid nitrogen assimilation (glnA, Log2FC = 0.60) and phosphorus starvation response (phoB, Log2FC = 0.65; pstS, Log2FC = 0.83). The enhanced energy production and conversion (11.83 %), amino acid transport and metabolism (11.20 %), and fatty acid biosynthesis (45.3 %) was observed in bioinoculant treatment. Unlike chemical fertilizer treatment, bioinoculant treatment led to the accumulation of the osmoprotectant trehalose and structural membrane lipids, while the 50:50 mix was uniquely characterized by a higher abundance of xylose. These findings demonstrate that the microalgal-cyanobacterial consortium can enhance nutrient recycling, and potentially boost soil health by reshaping the soil microbiome and metabolic functions, offering a promising strategy for sustainable agriculture.},
}
@article {pmid41335477,
year = {2025},
author = {Riskumäki, M and Ruuskanen, MO and Mäenpää, K and Ruokolainen, L and Mäkelä, MJ and Jousilahti, P and Vartiainen, E and Ottman, N and Laatikainen, T and Haahtela, T and Alenius, H and Fyhrquist, N and Sinkko, H},
title = {Shotgun metagenomics reveals distinct skin microbial species in allergen-sensitized individuals.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001527},
pmid = {41335477},
issn = {2057-5858},
mesh = {Humans ; *Metagenomics/methods ; *Allergens/immunology ; *Skin/microbiology/virology ; Finland ; Adolescent ; *Microbiota/genetics ; Male ; Russia ; Female ; *Hypersensitivity/microbiology/immunology ; Malassezia/genetics/isolation &amp; purification ; Immunoglobulin E/immunology ; Bacteria/genetics/classification ; Child ; },
abstract = {The Karelian region, which spans the border between Finland and Russia, presents distinct environmental exposures and lifestyles on either side of the governmental border. In the more urbanized Finnish Karelia, allergic diseases are markedly more prevalent than in the more rural Russian Karelia. Prior studies, based on amplicon sequencing, have demonstrated major differences in skin microbiotas between the two populations. However, compositional differences in microbiota between sensitized and non-sensitized (NS) individuals have not been characterized. Here, in a selected population of 112 allergen-sensitized and NS adolescents, we used shotgun metagenomics to characterize the prokaryotic, eukaryotic and viral species in the skin potentially involved in allergic sensitization via distinct environmental exposures. In the more urban Finnish Karelia, the microbiome species composition was associated with IgE-mediated allergen sensitization status, while in the more rural Russian Karelia, the composition was associated with exposure to furry pets. Finnish participants showing high IgE-mediated sensitization to common allergens (allergen-specific IgE >7.5 kU/L) had less Cutibacterium acnes and Malassezia in their skin and displayed weaker interconnectedness of the microbial co-occurrence network compared with NS participants. Moreover, Malassezia restricta strain-level differences were related to allergen sensitization in both Finnish and Russian participants. In summary, we found distinct skin microbiomes between allergen-sensitized and NS participants and tracked the bacterial and fungal species associated with the degree of allergic sensitization in the more urbanized part of the Karelian region. These findings provide new insights into the factors that shape the human skin microbiome and influence allergic diseases.},
}
@article {pmid41334589,
year = {2025},
author = {Li, J and Xu, Y and Wang, M and Lin, J and Sun, J and Ma, J and Zhang, H},
title = {Dual-source DPP4 drives intestinal fibrosis in Crohn's disease: synergistic therapeutic targeting of host and microbiota pathways.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593119},
pmid = {41334589},
issn = {1949-0984},
mesh = {Animals ; Humans ; *Dipeptidyl Peptidase 4/metabolism/genetics ; *Crohn Disease/pathology/drug therapy/microbiology/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Male ; Myofibroblasts/metabolism ; Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; *Intestines/pathology ; Sitagliptin Phosphate/pharmacology ; Mice, Inbred C57BL ; Female ; Dextran Sulfate ; },
abstract = {Crohn's disease (CD), a chronic inflammatory bowel disorder, often progresses to intestinal fibrosis and stricture, yet no effective anti-fibrotic treatments exist. This study reveals dipeptidyl peptidase 4 (DPP4) as a pivotal driver of fibrosis through bioinformatics analysis, clinical samples, and experimental models. Elevated DPP4 expression was observed in stenotic intestinal tissues of CD patients and dextran sodium sulfate (DSS)-induced fibrotic mice. Mechanistically, both membrane-bound DPP4 and soluble DPP4 (sDPP4) activated human intestinal myofibroblasts (HIMFs) via the PI3K-AKT pathway, stimulating migration, proliferation, and extracellular matrix deposition. Importantly, metagenomic sequencing revealed enrichment of microbial Dpp4 genes in fecal samples from CD patients with stenosis, and in vivo colonization with engineered E. coli overexpressing microbial DPP4 exacerbated fibrotic remodeling, confirming microbiota-derived DPP4 (mDPP4) as a pathogenic driver. Furthermore, pharmacological inhibition of host DPP4 (sitagliptin) or selective blockade of mDPP4 (Dau-d4) attenuated fibrosis in murine models, with combined therapy showing enhanced efficacy. These findings underscore the roles of DPP4, originating from both host and microbiota, and existing in membrane-bound and soluble forms, in promoting CD-associated intestinal fibrosis. This study identifies DPP4 as a novel therapeutic target, proposing dual-source inhibition as a promising strategy to prevent stricture formation in CD patients, thereby addressing a critical unmet clinical need.},
}
@article {pmid41333806,
year = {2025},
author = {Al Bataineh, MT and Dash, NR and Mysara, M and Saeed, O and Alkhayyal, N and Talaat, IM and Bendardaf, R and Saber-Ayad, M},
title = {Metagenomic analysis of gut microbiota in colorectal adenocarcinoma in the MENA region.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1634631},
pmid = {41333806},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Male ; Female ; Middle Aged ; *Adenocarcinoma/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Aged ; DNA, Bacterial/genetics/chemistry ; Middle East ; Feces/microbiology ; Phylogeny ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {BACKGROUND: Growing evidence suggests that gut microbiota plays a role in the development of colorectal cancer (CRC), and a few bacterial strains have been linked to carcinogenesis. Contrary to the Western population, the relationship between pro-cancer microorganisms and CRC among Middle Eastern individuals remains largely unexplored. Ninety-eight samples from Middle Eastern individuals with and without CRC were subjected to microbial profiling based on the 16S rRNA gene.<br><br>RESULTS: The CRC group exhibited a more complex gut microbiota with clusters that were significantly distinct from those of the control group. The taxonomic orders Caulobacterales, Rhizobiales, Sphingomonadales, and Burkholderiales, along with the genera Recibecterium and Sphingobium, were overrepresented in the CRC samples based on differential abundance testing between the CRC and control groups. Utilizing 16S-based functional prediction, we identified a significant enrichment of pathways vital for pentose and glucuronate interconversions, metabolism of terpenoids and polyketides, spliceosome, and dTMP kinase pathways within the CRC group. Moreover, we observed a link between Herbaspirillum huttiense and the pathways regulating the actin cytoskeleton; this intriguing connection may provide insights into the molecular mechanisms underlying cytoskeletal rearrangement and carcinogenesis triggered by H. huttiense.<br><br>CONCLUSIONS: The findings of this study support the connection between gut microbiota and the development of CRC and highlight region-specific microbial signatures that may serve as non-invasive diagnostic biomarkers or predictive tools for early screening in Middle Eastern populations, where CRC is increasingly diagnosed at advanced stages. These insights could inform the development of microbiome-based screening panels and personalized prevention strategies adapted to the MENA region's unique genetic, dietary, and environmental profiles.},
}
@article {pmid41332430,
year = {2025},
author = {Li, L and Zhou, N and Wang, Z and Wang, T and Wang, Y and Qiao, F and Du, ZY and Zhang, ML},
title = {Intestinal microbiota contributes to the heterogeneity of fat deposition by promoting mitochondrial fatty acid β-oxidation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593076},
pmid = {41332430},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Fatty Acids/metabolism ; Carnitine/biosynthesis/metabolism ; Oxidation-Reduction ; *Mitochondria/metabolism ; Zebrafish ; Lipid Metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Male ; Humans ; Feces/microbiology ; },
abstract = {The gut microbiota plays a crucial role in lipid metabolism in both humans and animals. However, the specific contributions of gut microbiota and their associated metabolites to fat deposition, as well as the underlying mechanisms, remain largely unexplored. In this study, we demonstrated that the intestinal microbiota mediated the heterogeneity of mesenteric fat index (MFI), as evidenced by fecal microbiota transplantation (FMT) experiments. Notably, analysis of the 16S rRNA gene amplicon sequencing of 44 samples revealed a significantly higher abundance of Cetobacterium somerae in the Low MFI group, with a positive correlation to reduced MFI. Serum metabolomics analysis confirmed that L-Carnitine emerged as the most differentially abundant metabolite in the Low MFI group and exhibited a strong positive correlation with C. somerae abundance. Metagenomic analysis showed that microbial genes related to L-Carnitine biosynthesis were significantly enriched in the Low MFI group. Further, C. somerae was isolated and cultured, and its subsequent monocolonization in germ-free zebrafish and tilapia demonstrated its lipid-lowering effects by enhancing mitochondrial fatty acid β-oxidation. Whole genome sequencing demonstrated C. somerae could encode the [EC:1.2.1.3] gene, which promotes the production of 4-trimethylammoniobutanoate, a precursor of L-Carnitine, thereby enhancing L-Carnitine biosynthesis by the host and gut microbiota, leading to the reduced fat deposition in Nile tilapia. In conclusion, C. somerae, a core gut microbe with high abundance in aquatic teleost intestines, plays an important role in host lipid metabolism. This study advances our understanding of how core gut microbes shape host phenotypes and provides novel insights into manipulating core gut colonizers to reduce fat deposition.},
}
@article {pmid41330454,
year = {2026},
author = {Zhao, D and Zou, B and Do, QL and Wu, SK and Shen, Y and Yang, Y and Kang, JX and Su, KP and Wang, B},
title = {Circadian rhythms and gut microbiota Dysbiosis: emerging gut-brain axis pathways in insomnia pathophysiology and Therapeutics.},
journal = {Brain, behavior, and immunity},
volume = {132},
number = {},
pages = {106203},
doi = {10.1016/j.bbi.2025.106203},
pmid = {41330454},
issn = {1090-2139},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; *Sleep Initiation and Maintenance Disorders/physiopathology/microbiology/therapy ; *Dysbiosis/physiopathology/microbiology ; Animals ; Brain/physiopathology ; Probiotics/therapeutic use ; Sleep/physiology ; *Brain-Gut Axis/physiology ; },
abstract = {Insomnia, a widespread sleep disorder, significantly impacts mental and physical health. Emerging research highlights the crucial role of gut microbiota (GM) in modulating circadian rhythms (CR), which regulate sleep-wake cycles. This review explores the interplay between GM dysbiosis, CR disruptions, and insomnia, synthesizing findings from human and animal studies. GM dysbiosis is linked to reduced microbial diversity and altered abundance of key taxa, such as short-chain fatty acid-producing bacteria, which influence clock gene expression and hormonal rhythms. CR disruption exacerbates GM imbalances, forming a feedback loop that impairs sleep regulation through both central and peripheral pathways. We also examine the therapeutic potential of probiotics in restoring GM balance and synchronizing CR. Clinical trials suggest that specific probiotic strains improve sleep quality by modulating microbial metabolites and their downstream effects on the circadian system. However, inconsistencies in outcomes underscore the need for precision interventions. The review concludes by identifying gaps in the current literature, emphasizing the necessity of integrative approaches combining metagenomics and personalized medicine to optimize GM-targeted therapies. These insights pave the way for novel, safer, and more effective strategies to manage insomnia by addressing its biological underpinnings.},
}
@article {pmid41330199,
year = {2026},
author = {Li, S and Wang, XR and Han, JR and Lian, WH and Ali, M and Liu, YH and Liu, J and Huang, J and He, HH and Govindan, R and Abdalla Abdelshafy Mohamad, O and Fang, BZ and Dong, L and Li, WJ},
title = {Genome-centric culture-enriched metagenomics reveals temperature-driven reassembly and functional stratification in culturable desert soil bacteria.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128411},
doi = {10.1016/j.micres.2025.128411},
pmid = {41330199},
issn = {1618-0623},
mesh = {*Soil Microbiology ; *Metagenomics/methods ; Desert Climate ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; Temperature ; Rhizosphere ; Metagenome ; Microbiota/genetics ; Genome, Bacterial ; Soil/chemistry ; Phylogeny ; Ecosystem ; },
abstract = {Desert ecosystems cover nearly one-third of Earth's land surface and face rising temperatures and climatic variability. Soil microbiomes underpin biogeochemical cycling and ecosystem resilience in these arid landscapes, yet the genome-resolved temperature responses of their culturable fraction remain poorly understood. Here, we employed genome-centric culture-enriched metagenomics (CE-MGS) to rhizosphere and bulk desert soils from the Gurbantunggut Desert incubated at 15°C, 30°C, and 45°C. From 90 culture-enriched metagenomes, we reconstructed 1184 cultivated metagenome-assembled genomes (cMAGs), including 218 putative novel genomospecies across 73 bacterial genera, substantially expanding the genomic representation of desert bacteria. Temperature influenced both community composition and interactions, with Actinomycetota, Pseudomonadota, and Bacillota dominating at 15°C, 30°C, and 45°C, respectively. Co-occurrence networks showed that lower temperatures and rhizosphere soils supported more interconnected consortia of culturable bacteria and that key hub taxa shifted across thermal regimes, reflecting temperature-driven reorganization of interactions within the culturable microbial community. Functional profiling revealed that temperature selected for specialized taxa, with elevated temperatures favoring redox-efficient pathways and more energy-efficient resource use. While representing only the culturable fraction of desert soil microbiomes, CE-MGS enables genome reconstruction of experimentally tractable microbes, linking identity, function, and thermal adaptation. These results provide a genome-resolved view of temperature responses, extend understanding of desert microbial adaptation beyond previous culture-independent studies, and establish CE-MGS as a practical approach to access ecologically relevant microbes for conservation and biotechnological applications under a warming climate.},
}
@article {pmid41330099,
year = {2025},
author = {Barman, P and Paul, A and Sinha, S and Saha, T and Mondal, N and Dutta, S and Chatterjee, S and Ghosh, W and Chakraborty, R},
title = {Microbial-viral synergy in Eisenia fetida gut supports earthworm survival, detoxification, and functional resilience.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181101},
doi = {10.1016/j.scitotenv.2025.181101},
pmid = {41330099},
issn = {1879-1026},
mesh = {Animals ; *Oligochaeta/physiology/virology/microbiology ; *Gastrointestinal Microbiome ; Soil Pollutants/metabolism ; Inactivation, Metabolic ; RNA, Ribosomal, 16S ; Biodegradation, Environmental ; Bacteria ; Metagenome ; },
abstract = {The ecological success of Eisenia fetida within decomposer food webs is closely linked to the functional diversity of its gut microbiome. This study integrates 16S rRNA gene profiling, whole-metagenome sequencing, and virome analysis to elucidate how microbial and viral communities within the earthworm gut contribute to nutrient biosynthesis, xenobiotic degradation, and environmental adaptation. Earthworms reared on compost feed enriched with Quisqualis indica plant matter showed selective enrichment of bacterial genera such as Ohtaekwangia, Nocardioides, and Steroidobacter, which are associated with hydrocarbon degradation and aromatic compound detoxification. Functional annotation of the gut metagenome revealed complete biosynthetic pathways for riboflavin, lysine, and methionine, and degradation routes for 3-nitropropionic acid (3-NPA) and aromatic pollutants. The gut virome, dominated by Siphoviridae and Myoviridae, carried auxiliary metabolic genes (AMGs) related to redox and xenobiotic metabolism, highlighting viral contributions to microbial adaptability. Reconstruction of metagenome-assembled genomes (MAGs), including a high-quality Flavobacterium MAG encoding both riboflavin biosynthesis and denitrification genes, underscored metabolic specialization within the gut. Collectively, these findings demonstrate that bacterial-viral metabolic synergy underpins E. fetida survival and ecological resilience, suggesting new microbiome-informed strategies for biowaste valorization and soil health restoration through vermicomposting.},
}
@article {pmid41328758,
year = {2026},
author = {Plewnia, A and Hoenig, BD and Lötters, S and Heine, C and Erens, J and Böning, P and Bending, GD and Krehenwinkel, H and Williams, MA},
title = {The Emergence of a CRISPR-Cas Revolution in Ecology: Applications, Challenges, and an Ecologist's Overview of the Toolbox.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70086},
pmid = {41328758},
issn = {1755-0998},
support = {//University of Warwick/ ; NE/S010270/1//Natural Environment Research Council/ ; },
mesh = {*CRISPR-Cas Systems ; *Ecology/methods ; *Gene Editing/methods ; },
abstract = {CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated nucleases) systems allow researchers to detect, capture, and even alter parts of an organism's genome. However, while the use of CRISPR-Cas has revolutionised many fields in the life sciences, its full potential remains underutilised in ecology and biodiversity research. Here we outline the emerging applications of CRISPR-Cas in ecological contexts, focusing on three main areas: nucleic acid detection, CRISPR-enhanced sequencing, and genome editing. CRISPR-based nucleic acid detection of environmental DNA samples is already reshaping species monitoring, providing highly sensitive and non-invasive tools for both scientists and the public alike, with reduced costs and minimal experience required. Further, CRISPR-enhanced sequencing, including Cas-mediated target enrichment, enables efficient recovery of ecologically relevant loci and supports diverse applications such as amplification-free metagenomics. Finally, while genome editing on wild species remains largely theoretical in ecology, these tools are already being used in controlled settings to study adaptation and resilience in the face of ongoing global stressors. Together, the applications of CRISPR-Cas are paving the way for more affordable, accessible, and impactful applications for species conservation, and promise to improve our ability to tackle the ongoing global biodiversity crisis.},
}
@article {pmid41328492,
year = {2025},
author = {Knoll, RL and Podlesny, D and Fortmann, I and Göpel, W and Zemlin, M and Lynch, S and Bork, P and Gehring, S and Härtel, C},
title = {Staphylococcus aureus colonization and bloodstream infection in very preterm infants.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2592423},
pmid = {41328492},
issn = {1949-0984},
mesh = {Humans ; *Staphylococcal Infections/epidemiology/microbiology ; Infant, Newborn ; Feces/microbiology ; *Staphylococcus aureus/isolation &amp; purification/genetics/growth &amp; development/classification ; Female ; Male ; Infant, Premature ; *Bacteremia/microbiology/epidemiology ; Gastrointestinal Microbiome ; Germany/epidemiology ; Infant ; Cohort Studies ; Infant, Very Low Birth Weight ; Metagenomics ; Incidence ; Gestational Age ; },
abstract = {BACKGROUND: Staphylococcus (S.) aureus remains a frequent pathogen for neonatal late-onset bloodstream infections (BSIs). The impact of colonization screening on BSI incidence is less understood.<br><br>METHODS: We assessed the epidemiology of late-onset S. aureus BSI in two independent multicenter cohorts of preterm infants born at&#x2009;<&#x2009;33 weeks' gestation, the German Neonatal Network (GNN, very low birth weight infants) and PRIMAL (infants with a gestational age 28-32 weeks). In the PRIMAL cohort, we determined S. aureus colonization in fecal samples by culture and shotgun metagenomic sequencing (metaG) during the first year of life. In addition, we integrated publicly available metaG data from preterm infant cohorts born at 23-34 weeks' gestation.<br><br>RESULTS: Late-onset S. aureus BSI was noted in 1.5% (336/21491) in preterm infants in the GNN cohort and 0.5% (3/638) in the PRIMAL cohort, respectively. At day 30 of life, 7.6% (42/553) of fecal samples were positive for S. aureus, while available metaG data of corresponding samples revealed S. aureus positivity in 36.6% (159/434). Every 10-fold increase in S. aureus relative abundance (metaG) was associated with a 2.9-fold higher odds of S. aureus detection in blood culture. We also confirmed S. aureus detection in 22% (393/1782) of samples across several published cohorts of preterm infants by metaG, while 95 samples carried at least one Staphylococcus-specific virulence gene (SVG).<br><br>CONCLUSION: Our study demonstrates that metagenomic quantification of pathobionts such as S. aureus in intestinal samples provides a stronger predictor of colonization than culture. Future prevention strategies should focus on promoting S. aureus colonization resistance through microbiome-informed approaches.},
}
@article {pmid41328416,
year = {2025},
author = {Ueira-Vieira, C and Santos, ACC and Araújo, TN and Augusto, SC and de Avila, NB and Bonetti, AM and Dos Santos, AR},
title = {A Deep Metagenomic Snapshot as a Proof-of-Concept for Resource Generation: Simultaneous Assembly of Host, Food, and Microbiome Genomes From Stingless Bee Larval Food.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72546},
pmid = {41328416},
issn = {2045-7758},
abstract = {Characterizing the complex web of ecological interactions is a central challenge in molecular ecology. Shotgun metagenomics of environmental samples offers a powerful, high-resolution approach, yet its potential for simultaneously generating multiple genomic resources from different trophic levels remains underexplored. This study serves as a proof-of-concept, using deep sequencing of a single, complex sample-the larval food of the stingless bee Tetragonisca angustula-to demonstrate the method's capacity to recover genomic information across varying template abundances. We successfully assembled three genomes of different completeness levels: a near-complete bacterial genome (Acetilactobacillus jinshanensis, 2,097,977 bp with 0.002% ambiguous bases), a draft mitochondrial genome (T. angustula, 15,498-15,549 bp), and a fragmented chloroplast genome (Lactuca sativa, 130,532 bp with 23.47% ambiguous bases). The assembly quality gradient, observed from complete to fragmented, directly reflects the relative abundance of each DNA template in the environmental sample, demonstrating the method's sensitivity and ecological informativeness. Beyond these genomic resources, the data provided a comprehensive biodiversity profile, revealing DNA from seven major taxonomic groups, including 209 bacterial genera, 123 plant families, and 55 insect taxa. Additionally, genomic comparisons using Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (dDDH) analyses suggest that the dominant bacterial strain represents a putative novel species within the genus Acetilactobacillus. This approach simultaneously provided insights into host genetics, food sources, and microbial communities, illustrating the potential of single metagenomic datasets to generate multiple valuable genomic resources for molecular ecology research.},
}
@article {pmid41328248,
year = {2025},
author = {Rossi, E and Pato, U and Ayu, DF and Melia, S and Sukma, A and Rahmayuni, R and Salman, AN},
title = {Bacterial biodiversity and metagenomic study of dadih, traditional fermented buffalo milk from Kampar district, Riau, Indonesia.},
journal = {Journal of advanced veterinary and animal research},
volume = {12},
number = {3},
pages = {717-727},
pmid = {41328248},
issn = {2311-7710},
abstract = {OBJECTIVE: This study aimed to investigate the metagenomic and microbial diversity of dadih in Kampar District, Riau, Indonesia.<br><br>MATERIALS AND METHODS: The dadih samples were collected from dadih producers in three villages, namely Limau Manis (LM), Rumbio (RB), and Muaro Jalai (MJ). DNA samples were extracted and sequenced through Oxford Nanopore Technology (ONT), operated by MinKNOW software version 23.04.5. Library preparations were conducted using kits from ONT.<br><br>RESULTS: The next-generation sequencing analysis on three dadih from Kampar identified two bacterial phyla, Bacillota and Pseudomonadota. Furthermore, there was a slight variation in dadih's microbiota composition between LM, RB, and MJ. The Bacillota phylum dominated the dadih microbiota in LM and RB villages, with a relative abundance of 60%-80%. The dadih from MJ was dominated by the phylum Pseudomonadota, which reached 55%. The dominant species found in all three dadih was Lactococcus lactis, with an abundance of 53.80, 80.80, and 40.31% for dadih LM, RB, and MJ, respectively.<br><br>CONCLUSION: Dadih MJ had the highest Simpson's value (~0.8), showing a relatively even abundance of species in the sample. Furthermore, dadih LM had a high Simpson's value (~0.75), indicating similar conditions to dadih MJ. Dadih RB had the lowest Simpson's value (~0.4), confirming that the microbiota in the sample tends to be dominated by certain species with a less even distribution.},
}
@article {pmid41328030,
year = {2025},
author = {Hickman, B and Korpela, K},
title = {Impact of data compositionality on the detection of microbiota responses.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2590841},
pmid = {41328030},
issn = {1949-0984},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota ; Humans ; Computer Simulation ; *Gastrointestinal Microbiome ; Computational Biology/methods ; *Metagenomics/methods ; },
abstract = {Next-generation sequencing (NGS) data usage is widespread, but its compositional nature poses challenges. We evaluated four normalization methods (relative abundance, CLR, TMM, DESeq2) for identifying true signals in compositional microbiota data using simulations. Two experiments were conducted: one with only increases in specific taxa, and a 1:1 increase/decrease in specific taxa. Simulated sequencing produced compositional data, which were normalized using the four methods. The study compared absolute abundance data and the normalized compositional data using variance explained and false discovery rates. All normalization methods showed decreased variance explained and increased false positives and negatives compared to absolute abundance data. CLR, TMM, and DESeq2 did not improve over relative abundance data and sometimes worsened false discovery rates. The study highlights that false positives and negatives are common in compositional NGS datasets, and current normalization methods do not consistently address these issues. Compositionality artefacts should be considered when interpreting NGS results and obtaining absolute abundances of features/taxa is recommended to distinguish biological signals from artefacts.},
}
@article {pmid41328016,
year = {2025},
author = {Fresno, C and Oropeza-Valdez, JJ and Alvarado-Luis, PI and Peña-González, P and Tovar, AR and Torres, N and Diener, C and Gibbons, S and Resendis-Antonio, O},
title = {MICOMWeb: a website for microbial community metabolic modeling of the human gut.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587968},
pmid = {41328016},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Internet ; *Gastrointestinal Tract/microbiology/metabolism ; Models, Biological ; Software ; Computer Simulation ; Computational Biology/methods ; },
abstract = {MICOMWeb is a user-friendly website for modeling microbial community metabolism in the human gut. This website tackles three constraints when generating in silico metagenome-scale metabolic models: i) the prior Python user knowledge for metabolic modeling using flux balance analysis with the MICOM Python package, ii) predefined and user-defined diets to generate ad hoc metabolic models, and iii) the high-throughput computational infrastructure required to obtain the simulated growth and metabolic exchange fluxes, using real abundance from metagenomic shotgun or 16S amplicon sequencing; we present MICOMWeb's features to easily run in silico experiments as a functional hypothesis generator for experimental validation on three previously published databases. MICOMWeb has a constant run-time independent of the number of samples provided and database complexity. In practical terms, this behavior is upper-bounded by the sample with the greatest microbiota diversity, i.e., the sample with the largest metabolic reconstruction model size. The evidence suggests that the bigger the database, the better the MICOMWeb performs compared to MICOM in terms of consumed RAM (from 3.52 up to 7.13 folds) and total execution time (from 10.87 up to 205.05 folds).},
}
@article {pmid41327428,
year = {2025},
author = {Zorea, A and Moraïs, S and Pellow, D and Gershoni-Yahalom, O and Probst, M and Nadler, S and Shamir, R and Rosental, B and Elia, N and Mizrahi, I},
title = {ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {11},
pmid = {41327428},
issn = {2049-2618},
support = {ISF 1947/19//Israel Science Foundation/ ; 2476/2-1//German-Israeli Project Cooperation (DIP)/ ; ERC 866530//the European Research Council/ ; },
mesh = {*Plasmids/genetics ; *In Situ Hybridization, Fluorescence/methods ; *Single-Cell Analysis/methods ; *Bacteria/genetics/isolation &amp; purification/classification ; *Microbiota/genetics ; Gene Transfer, Horizontal ; Humans ; },
abstract = {BACKGROUND: Plasmids are influential drivers of bacterial evolution, facilitating horizontal gene transfer and shaping microbial communities. Current knowledge on plasmid persistence and mobilization in natural environments is derived from community-level studies, neglecting the single-cell level, where these dynamic processes unfold. Pinpointing specific plasmids within their natural environments is essential to unravel the dynamics between plasmids and their bacterial hosts.<br><br>RESULTS: Here, we overcame the technical hurdle of natural plasmid detectability in single cells by developing SPEci-FISH (Short Probe EffiCIent Fluorescence In Situ Hybridization), a novel molecular method designed to detect and visualize plasmids, regardless of their copy&#xa0;number, directly within bacterial cells, enabling their precise identification at the single-cell level. To complement this method, we created ProFiT (PRObe FInding Tool), a program facilitating the design of sequence-based probes for targeting individual plasmids or plasmid families.<br><br>CONCLUSIONS: We have successfully applied these methods, combined with high-resolution microscopy, to investigate the dispersal and localization of natural plasmids within a clinical isolate, revealing various plasmid spatial patterns within the same bacterial population. Importantly, bridging the technological gap in linking plasmids to hosts in native complex microbial environments, we demonstrated that our method, when combined with fluorescence-activated cell sorting (FACS), can track plasmid-host dynamics in a human fecal sample. This approach identified multiple potential bacterial hosts for a conjugative plasmid that we assembled from this fecal sample's metagenome. Our integrated approach offers a significant advancement toward understanding plasmid ecology in complex microbiomes. Video Abstract.},
}
@article {pmid41327409,
year = {2025},
author = {Jin, J and Wang, X and Zhang, X and Mei, J and Zheng, W and Guo, L and Sun, H and Zhang, L and Liu, C and Ye, W and Guo, L},
title = {Grapevine phyllosphere pan-metagenomics reveals pan-microbiome structure, diversity, and functional roles in downy mildew resistance.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {10},
pmid = {41327409},
issn = {2049-2618},
support = {ZR2024QC241//Shandong Provincial Natural Science Foundation Youth Project/ ; 2024CXPT031//Key R&amp;D Program of Shandong Province/ ; ZR2023JQ010//Natural Science Foundation for Distinguished Young Scholars of Shandong Province/ ; },
mesh = {*Vitis/microbiology ; *Plant Diseases/microbiology ; *Disease Resistance/genetics ; *Microbiota/genetics ; *Metagenomics/methods ; Plant Leaves/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; },
abstract = {BACKGROUND: Grapevines are among the most economically important fruit crops, and the microbiome profoundly influences their health, yield, and quality. However, mechanistic insights into microbiome-orchestrated grapevine biology remain limited.<br><br>RESULTS: Here, we conduct large-scale pan-metagenomic and pan-metatranscriptomic analyses of the phyllosphere microbiome from 107 grapevine accessions spanning 34 Vitis species. We show that the grapevine core microbiome is dominated by phyla Bacillota and Pseudomonadota. Leveraging PacBio sequencing, we assembled 19 high-quality metagenome-assembled genomes (MAGs) from the grapevine pan-microbiome, representing the first MAG reconstruction in plant-associated microbial communities using PacBio reads. These MAGs encode genes associated with antibiotic resistance, secondary metabolism, and carbohydrate-active enzymes (CAZymes), which could potentially influence grapevine biology. During downy mildew (DM) infection, DM-resistant grapevines exhibit significantly higher microbial network complexity than susceptible counterparts. Among the key taxa contributing to this complexity, Bacillota emerged as the dominant phylum, displaying strong abundance correlations with phylum Euglenozoa and Cyanobacteriota, and an isolated Bacillota species from the grapevine leaves, Bacillus cereus, demonstrated potent biocontrol activity against DM infection. Pan-metatranscriptomic analysis further revealed significant upregulation of eukaryotic microbial genes involved in primary and secondary metabolism.<br><br>CONCLUSIONS: This pan-metagenomic study offers unprecedented insights into the complex structure, diversity, and functional roles of the grapevine phyllosphere microbiome and presents valuable genomic and microbial resources for microbiome research and engineering to enhance viticulture productivity and quality. Video Abstract.},
}
@article {pmid41327304,
year = {2025},
author = {Zhang, X and Li, Y and Xiong, Z and Zheng, N and Wang, J and Zhao, S},
title = {Biochanin A improves nitrogen utilization efficiency by regulating ruminal microbial community in dairy goats.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {13},
pmid = {41327304},
issn = {2049-2618},
support = {32402768//National Natural Science Foundation of China/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; CARS-36//Earmarked Fund for CARS/ ; 2022YFD1301000//National Key R&amp;D Program of China/ ; CAAS-ZDRW202304//Agricultural Science and Technology Innovation Program/ ; },
mesh = {Animals ; *Genistein/pharmacology/administration &amp; dosage ; *Nitrogen/metabolism ; *Rumen/microbiology/metabolism ; *Goats/microbiology ; *Gastrointestinal Microbiome/drug effects ; Animal Feed/analysis ; Female ; Dietary Supplements ; Milk/chemistry ; Feces/microbiology ; Metabolomics ; Bacteria/classification/metabolism/genetics ; },
abstract = {BACKGROUND: Rumen microbial nitrogen metabolism is crucial for animal health, productivity, and environmental sustainability in ruminants. Natural products like biochanin A are garnering interest as potential feed additives due to their beneficial effects and safety profiles. Here, we collected total mixed diet, plasma, milk, urine, and feces samples of dairy goats to evaluate the impact of biochanin A on nitrogen metabolism and elucidated regulatory mechanisms of nitrogen metabolism using multi-omics approaches by analyzing plasma metabolites and ruminal microbial communities.<br><br>RESULTS: Supplementation with biochanin A significantly enhanced nitrogen utilization efficiency of dairy goats. Plasma metabolomics revealed that biochanin A altered pathways related to amino acid biosynthesis/metabolism and glycolysis/gluconeogenesis. In the rumen, biochanin A enriched microbial strains from the families Selenomonadaceae and Aminobacteriaceae. Up-regulated proteins predominantly associated with glycolysis were identified by metaproteomics. Integrated metagenomic and metaproteomic analyses demonstrated that biochanin A positively influenced carbohydrate metabolism, amino acid metabolism, and energy metabolism pathways.<br><br>CONCLUSION: Biochanin A enhances nitrogen metabolism by regulating rumen microbial community function, supporting its potential as a natural feed additive to improve nitrogen utilization of ruminants. Video Abstract.},
}
@article {pmid41326129,
year = {2026},
author = {Wu, M and Lu, P and Feng, Y and He, S and Han, G and Hu, S},
title = {Construction and functional characterization of a synthetic consortium for synergistic degradation of dimethachlon.},
journal = {Pesticide biochemistry and physiology},
volume = {216},
number = {Pt 1},
pages = {106807},
doi = {10.1016/j.pestbp.2025.106807},
pmid = {41326129},
issn = {1095-9939},
mesh = {Biodegradation, Environmental ; *Microbial Consortia ; Aniline Compounds/metabolism ; Animals ; Pseudomonas/metabolism/genetics ; *Soil Pollutants/metabolism/toxicity ; Zebrafish ; *Fungicides, Industrial/metabolism/toxicity ; Soil Microbiology ; },
abstract = {The residual dicarboximide fungicide dimethachlon and its primary metabolite 3,5-dichloroaniline entail significant health and ecological risks. Microbial degradation effectively mitigates associated environmental risks. The microbial degradation of organic contaminants is a complex process, typically facilitated by microbial consortia rather than individual species. However, research on the biodegradation of dimethachlon by synergistic microbial consortia is limited. In this study, an enriched bacterial consortium designated as JHJ-2 capable of degrading dimethachlon was obtained. A synthetic consortium was constructed, comprising Bosea sp. S6, which transforms dimethachlon to 3,5-dichloroaniline, and Pseudomonas sp. KH-1, which degrades 3,5-dichloroaniline; both strains were isolated from the enriched consortium JHJ-2 and synergistically degrade dimethachlon. Toxicity assays using the zebrafish showed that dimethachlon is converted into non-toxic products by the synthetic consortium (strains S6 and KH-1). Bioaugmentation with the synthetic consortium led to the complete removal of dimethachlon and its highly toxic metabolite 3,5-dichloroaniline from contaminated soil. In addition, 16 bins were successfully recovered by metagenomic binning, including bin 12 (Bosea sp.) and bin 15 (Pseudomonas sp.), and several potential degradation enzymes were hypothesized in the genomes of bins 12 and 15. Overall, the developed synthetic consortium exhibits significant potential for the enhanced bioremediation and detoxification of dimethachlon-contaminated sites.},
}
@article {pmid41324463,
year = {2025},
author = {Furman, O and Sorek, G and Moraïs, S and Levin, L and Tovar-Herrera, OE and Winkler, S and Mizrahi, I},
title = {Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {41324463},
issn = {1751-7370},
support = {101000213//Horizon2020/ ; ERC 866530/ERC_/European Research Council/International ; ISF 979/25//Israel Science Foundation/ ; },
mesh = {Animals ; *Rumen/microbiology/growth &amp; development ; Cattle ; Metagenomics ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; },
abstract = {The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes, including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.},
}
@article {pmid41324436,
year = {2025},
author = {Gu, H and Liu, Z and Liu, S and Hu, X and Yu, Z and Li, Y and Li, L and Sui, Y and Jin, J and Liu, X and Jia, Z and Sun, L and Adams, JM and van der Heijden, MGA and Liu, J and Wang, G},
title = {Land conversion to cropland homogenizes variation in soil biota, gene assemblages, and ecological strategies on local and regional scales.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {41324436},
issn = {1751-7370},
mesh = {*Soil Microbiology ; China ; *Bacteria/genetics/classification ; Archaea/genetics/classification ; *Agriculture ; Fungi/genetics/classification ; Soil/chemistry ; *Biota ; Metagenome ; Biodiversity ; Ecosystem ; },
abstract = {It is widely considered that conversion of natural landscapes to agriculture results in biotic homogenization. A recent study comparing soil biota of 27 paired natural steppe soil (NS) and agricultural soil (AS) sites across 900 km in north-eastern China found that conversion to agriculture had increased spatial gradients in soil functional genes. Using the same shotgun metagenome samples, and bacterial amplicon data, we instead analyzed total observed variation at the between-site and within-site level. We found that from the perspective of community taxonomic composition, archaeal and fungal community variation was decreased in AS compared to NS at both within- and between-site scales. In contrast, the bacterial and metazoal community was homogenized only at the local scale. Total functional KEGG gene assemblage was homogenized in AS at both the local and regional scale, whereas "Y-A-S" strategies in bacteria were homogenized at the local scale but not the between-site scale. Overall, these results show a clear homogenizing effect of agriculture with respect to multiple aspects of soil taxonomic and functional diversity, though varying by scale. Certain abiotic soil properties showed homogenization in AS at within-site and between-site scales may explain this homogenization, and uniformity of plant cover in croplands likely contribute to the effect. These findings confirm and extend global-scale studies showing homogenization of soil biota in agricultural environments, revealing that effects extend to functional genes and the broad taxonomic spectrum of life-with potential loss of soil ecosystem resilience to environmental change resulting from agriculture.},
}
@article {pmid41322254,
year = {2025},
author = {Al, MA and Wang, Y and Huang, J and Yu, Y and Juneau, P and He, Z and Yan, Q},
title = {Anammox and denitrifying bacteria and their nitrogen removal potential in lake sediments mediated by environmental changes.},
journal = {Marine life science &amp; technology},
volume = {7},
number = {4},
pages = {670-681},
pmid = {41322254},
issn = {2662-1746},
abstract = {UNLABELLED: Anammox and denitrification are key processes for nitrogen removal in lake sediments. However, how environmental changes mediate the community structure and functional genes of nitrogen removal bacteria in lakes remain unclear. Using metagenome and amplicon sequencing, we investigated the anammox and denitrifying bacteria and their nitrogen removing potentials in lakes experiencing significant spatiotemporal and environmental variations. The community structure of anammox and denitrifying bacteria exhibited stronger lake-wide spatial variations than that of seasonality, while only the denitrification-related functional genes showed substantial variations in both lakes. Anammox genes (e.g., hzsA/B/C and hdh) showed no significant spatial variations. However, the abundances of anammox and denitrifying genes were significantly higher in winter than in summer. The mesotrophic Lake Weishan demonstrated a greater capacity for complete denitrification in winter, while the eutrophic Lake Donghu exhibited a higher potential of anammox in summer. Differences in functional gene abundances between lakes were more pronounced than variations in phylogenetic diversity, indicating clear functional adaptations to local environments. The coupled nitrogen removal potentials also reflected ecological interactions among anammox and denitrifying genes. Importantly, anammox and denitrifying bacterial communities and their functional genes were primarily driven by dissolved organic carbon, total phosphorous and zinc (Zn). The dissimilarities of anammox and denitrifying bacterial communities increased with geographic distance, indicating a clear distance-decay effect. This study highlights the anammox and denitrifying bacteria and their nitrogen removal potentials in lake sediments that are mediated by both spatial and seasonal environmental changes.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00310-z.},
}
@article {pmid41321415,
year = {2025},
author = {Horstmann, L and Lipus, D and Bartholomäus, A and Oses, R and Kitte, A and Friedl, T and Wagner, D},
title = {Microbial ecology of subsurface granitic bedrock: a humid-arid site comparison in Chile.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf199},
pmid = {41321415},
issn = {2730-6151},
abstract = {Subsurface microorganisms face extreme challenges such as anoxic, xeric, and oligotrophic conditions. In igneous systems, nutrient limitation is critical, as biomass input relies on surface-derived fluids via tectonic fractures. Despite growing interest in subsurface habitats, little is known about ecosystems beneath arid landscapes, where surface water input is limited by the low annual precipitation. This study compares granitic subsurface environments beneath arid and humid surface ecosystems, highlighting the link between surface climate and subsurface biodiversity. DNA was extracted from granitic subsurface rocks recovered from two endmember sites along a north-south climate gradient in Chile's Coastal Cordillera. Microbial communities inhabiting down to 55 m deep subsurface rocks were characterized using 16S rRNA amplicon and shotgun metagenomic sequencing. We identified an abundant and potentially active subsurface community below both climates dominated by heterotrophic bacteria, including Pseudarthrobacter, Janthinobacterium, and Pseudomonas. However, rare taxa affiliated with common chemolithoautrophs, e.g. Thiobacillus, Sulfuriferula, and Sulfuricurvum, were only observed in the arid subsurface, indicating increased oligotrophic conditions and reliance on inorganic electron donors in the deeper subsurface of the desert. Functional analysis revealed sulphur, hydrogen, and carbon monoxide as potential inorganic electron donors. These findings expand the current understanding of microbial life in the subsurface of granite rocks showing the influence of surface climate on nutrient conditions in the deeper subsurface, providing new insights into the extent and functional capacity of terrestrial subsurface habitats and their role in global biogeochemical processes.},
}
@article {pmid41319542,
year = {2026},
author = {Chen, X and Tie, Y and Zhu, M and Wu, Z and Xu, W and Zhang, Z and Ju, F and Zhang, W},
title = {Unraveling microbial synergy in blended Daqu: A multi-omics approach to decoding the unique flavor profile of Jiuliangxiang baijiu.},
journal = {Food chemistry},
volume = {499},
number = {},
pages = {147314},
doi = {10.1016/j.foodchem.2025.147314},
pmid = {41319542},
issn = {1873-7072},
mesh = {*Flavoring Agents/metabolism/chemistry ; *Bacteria/genetics/metabolism/isolation &amp; purification/classification ; Gas Chromatography-Mass Spectrometry ; Taste ; *Alcoholic Beverages/analysis/microbiology ; Volatile Organic Compounds/chemistry/metabolism ; *Wine/analysis/microbiology ; Microbial Consortia ; Metabolomics ; Multiomics ; },
abstract = {This study deciphers the microbial-ecological basis of Jiuliangxiang Baijiu's (JLX) unique flavor through blended Daqu multi-omics. GC-MS comparative analysis of five market-representative Baijiu types identified 25 aroma-active compounds (OAV ≥ 1) in JLX, with ethyl palmitate (OAV = 2) established as a potential characteristic marker. Subsequent investigation of its blended Daqu revealed how microbial consortia govern flavor formation. Physicochemical and microbial analyses demonstrated that Daqu blending elevated enzymatic capacities, including saccharification (+227.5 % vs single Daqu), esterification (+27.4 %), and liquefaction (+15.4 %), while enhancing microbial diversity. Metabolomic profiling identified glycerophospholipid Gpgro (14:0/16:0) as the ethyl palmitate precursor. Metagenomic tracking revealed that the core ester-producing taxa-primarily Bacillus licheniformis (from high-temperature Daqu) and Kroppenstedtia eburnea (from bacterial Daqu)-harbor complementary genetic potential for both esterase and acyltransferase pathways. The results provide a microbial-ecological framework for rational Daqu blending, offering actionable strategies to engineer microbial consortia for flavor-directed liquor innovation.},
}
@article {pmid41319383,
year = {2026},
author = {Deng, H and Yang, J and Li, R and Li, K and Lu, H and Lin, B and Xu, X and Liao, J and Ye, C and Deng, J and Wu, B and Sun, L},
title = {ASSR-mediated sludge yield reduction couples deterministic enrichment of Nitrospira with metabolic resource partitioning.},
journal = {Water research},
volume = {290},
number = {},
pages = {125031},
doi = {10.1016/j.watres.2025.125031},
pmid = {41319383},
issn = {1879-2448},
mesh = {*Sewage/microbiology ; *Bioreactors/microbiology ; Waste Disposal, Fluid ; Anaerobiosis ; Microbiota ; Wastewater ; },
abstract = {The anaerobic side-stream reactor (ASSR) process offers a microbiome-driven strategy for sustainable wastewater treatment, yet the ecological mechanisms governing its sludge yield reduction efficiency remain unresolved. Here, we demonstrate that a pilot-scale anaerobic-anoxic-oxic (AAO) system with integrated anaerobic side-stream reactor (ASSR) (designated AAO-ASSR/SR) reduced sludge production by 43.6 % compared to a conventional AAO system (designated AAO/CK), while maintaining effluent quality. Through integrated multi-omics and ecological modeling, we revealed the core microbiome-driven mechanism for ASSR-mediated sludge yield reduction. This mechanism is characterized by three key features: (1) enhanced microbial stability via cooperative networks, (2) deterministic assembly selecting slow-growing keystone taxa (e.g., Nitrospira, 18.6 % abundance in SR), and (3) metabolic resource partitioning from biomass synthesis to amino acid cross-feeding. Functional metagenomics revealed that Nitrospira (phylum Nitrospirota, comprising >99 % Nitrospira) and Novosphingobium (phylum Proteobacteria) mediated increased amino acid metabolism and reduced ATP biosynthesis in SR, contrasting with Bacteroidota-dominated biomass synthesis in CK through enhanced protein, nucleotide metabolism and ATP biosynthesis. By coupling deterministic microbial assembly with functional repartitioning, this work contributes to establish a design principle for targeted microbiome engineering in low-sludge systems, advancing sustainable wastewater management through ecological optimization of microbial resource allocation.},
}
@article {pmid41318814,
year = {2026},
author = {Li, J and Liu, L and Tao, M and Han, Z and Ma, M and Jiang, L and Liu, C and Liu, D and Zhang, P and Zhang, M and Xue, R and Gong, J and Zhang, X and Shen, L and Qi, C},
title = {Impact of concomitant medications on efficacy of CLDN18.2-specific CAR-T cell therapy in advanced gastric cancer.},
journal = {British journal of cancer},
volume = {134},
number = {3},
pages = {439-446},
pmid = {41318814},
issn = {1532-1827},
mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Adrenal Cortex Hormones/administration &amp; dosage/therapeutic use ; Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; Antibodies, Monoclonal, Humanized/administration &amp; dosage/therapeutic use ; *Claudins/immunology ; Gastrointestinal Microbiome/drug effects ; Granulocyte Colony-Stimulating Factor/administration &amp; dosage/therapeutic use ; *Immunotherapy, Adoptive/methods ; Retrospective Studies ; *Stomach Neoplasms/therapy/immunology/pathology/drug therapy ; Treatment Outcome ; },
abstract = {BACKGROUND: Claudin18.2 (CLDN18.2)-specific CAR-T cell therapy has demonstrated promise in advanced gastric cancer (GC). However, the impact of concomitant medications on the efficacy outcomes remains unclear.<br><br>METHODS: We retrospectively analyzed advanced GC patients receiving CLDN18.2-specific CAR-T cell therapy from a phase I trial. Concomitant medications were defined as any drugs administered within 30 days before and after CAR-T cell infusion, including corticosteroids, antibiotics, tocilizumab, granulocyte colony-stimulating factor (G-CSF), thrombopoietin (TPO), and erythropoietin. Metagenomic sequencing was employed to elucidate the differences in gut microbiome signatures between responders and non-responders.<br><br>RESULTS: Of 72 patients included in the study, 6 (8.3%) received corticosteroids, 49 (68.1%) received tocilizumab, and 22 (30.6%) received antibiotics, 15 (20.8%) received G-CSF, 5 (6.9%) received thrombopoietin, and no patient received erythropoietin. The median progression-free survival (PFS) (2.6 vs. 5.8 months; P&#x2009;<&#x2009;0.001) and overall survival (OS) (3.9 vs. 9.5 months; P&#x2009;<&#x2009;0.001) were significantly shorter for patients who received antibiotics for infection compared to those who did not. No significant differences were observed in objective response rate (ORR), PFS, and OS between patients who received corticosteroids, tocilizumab, antibiotics for prophylaxis, G-CSF, or TPO and those who did not. A higher abundance of Fusobacterium nucleatum, Lactobacillus mucosae, Prevotella pallens, and Streptococcus pseudopneumoniae in gut microbiome was associated with a superior treatment response.<br><br>CONCLUSIONS: The study indicates that the use of antibiotics for infection reduces the efficacy outcomes of CLDN18.2-specific CAR-T cell therapy for advanced GC, while other concomitant medications do not affect the outcomes. Further research is needed to clarify the optimal administration of these medications and the underlying mechanisms of the gut microbiome in impacting CAR-T treatment response.<br><br>TRIAL REGISTRATION: NCT03874897.},
}
@article {pmid41317994,
year = {2026},
author = {Merrill, LC and Martínez, RL and Palacios, N and Dawson-Hughes, B and Noel, SE and Wang, Y and Tucker, KL and Mangano, KM},
title = {Gut microbes related to the Dietary Approaches to Stop Hypertension score are associated with bone quantity but not with bone quality in a cross-sectional study of older Puerto Rican adults.},
journal = {The American journal of clinical nutrition},
volume = {123},
number = {2},
pages = {101129},
pmid = {41317994},
issn = {1938-3207},
support = {R01 AG055948/AG/NIA NIH HHS/United States ; R01 AR072741/AR/NIAMS NIH HHS/United States ; RF1 AG075922/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; Female ; Male ; Cross-Sectional Studies ; *Bone Density ; Aged ; *Gastrointestinal Microbiome/physiology ; *Dietary Approaches To Stop Hypertension ; Middle Aged ; Puerto Rico/ethnology ; Diet ; *Bone and Bones/physiology ; Absorptiometry, Photon ; Osteoporosis ; },
abstract = {BACKGROUND: Bone mineral density (BMD) explains fractures incompletely; studies relating lifestyle to bone quality are lacking.<br><br>OBJECTIVES: This study aims to examine associations of diet quality with bone measures [bone material strength index (BMSi), trabecular bone score (TBS), BMD], evaluate moderation by inflammation, identify gut microbiome features linked to diet quality, and quantify diet-microbiome-bone relationships.<br><br>METHODS: This cross-sectional study included participants from the Boston Puerto Rican Osteoporosis Study. Diet was assessed with a culturally tailored food frequency questionnairew, and diet quality with the Dietary Approaches to Stop Hypertension (DASH) score. BMSi was measured using microindentation; BMD by dual-energy X-ray absorptiometry (DXA); TBS derived from DXA. Inflammation was assessed with a biomarker score (BMS) and tested as a moderator of diet-bone associations via interaction terms in linear regression. Gut microbiome composition (shotgun metagenomics) was analyzed with microbiome multivariate association with linear models regression to assess diet associations. A machine learning algorithm determined dietary, microbial, and bone-related predictors of bone health; sample sizes varied by outcome: BMSi (n = 86); TBS (n = 204); BMD femoral neck (n = 220), total hip (n = 221), lumbar spine (n = 207).<br><br>RESULTS: DASH score was not associated with BMSi [&#x3b2; = -0.10; 95% confidence interval (CI): -0.46, 0.27; P = 0.60], TBS (&#x3b2; = 0.002; 95% CI: -0.002, 0.005, P = 0.36), BMD at the femoral neck (&#x3b2; = 0.002; 95% CI: -0.002, 0.005; P = 0.30), or lumbar spine (&#x3b2; = 0.002; 95% CI: -0.003, 0.006, P = 0.52) but was at total hip (&#x3b2; = 0.004; 95% CI: 0.003, 0.008; P = 0.03). The association was not moderated by inflammation (&#x3b2; = -0.0001, P = 0.89). Lachnospira eligens was 1 of 4 taxa positively associated with DASH score and BMD. No microbial pathways were associated with the DASH score.<br><br>CONCLUSIONS: DASH score was associated with hip BMD, but not with BMSi or TBS. Select diet-related gut microbes and an inflammation score were associated with BMD. Future studies should examine dietary inflammation in relation to bone quality.},
}
@article {pmid41316726,
year = {2026},
author = {Nishijima, S and Fullam, A and Schmidt, TSB and Kuhn, M and Bork, P},
title = {VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D902-D911},
pmid = {41316726},
issn = {1362-4962},
support = {12/RC/2273-P2//Uehara Memorial Foundation/ ; //EMBL/ ; },
mesh = {*Genome, Viral ; *Virome/genetics ; *Metagenome ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Open Reading Frames ; Microbiota/genetics ; Humans ; Software ; Molecular Sequence Annotation ; },
abstract = {Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a comprehensive resource comprising over 1.7 million high- and medium-quality viral genomes recovered from >100 000 publicly available metagenomes derived from samples that cover diverse ecosystems, including host-associated, aquatic, terrestrial, and anthropogenic environments. Using a unified and scalable pipeline, we systematically assembled viral genomes and provided detailed information on genome completeness, taxonomic classification, predicted lifestyle, and host assignment based on CRISPR spacer matches. VIRE contains >89 million predicted viral open reading frames, as well as detailed functional annotations derived from multiple databases. Importantly, VIRE is seamlessly integrated with related microbiome resources such as SPIRE (https://spire.embl.de) and Metalog (https://metalog.embl.de), enabling users to jointly explore viral genomes, metagenome-assembled genomes, and associated environmental or clinical metadata. Accessible at https://vire.embl.de, VIRE provides an open-access, scalable platform for investigating viral diversity, evolution, and ecology on a planetary scale.},
}
@article {pmid41316344,
year = {2025},
author = {Ren, Y and Liang, J and Xie, J and Hu, W and Lai, M and Li, X and Zhang, J and Zheng, Y and Wu, Q and Zhou, H and Yin, J},
title = {Sodium oligomannate modulates the gut-brain axis to alleviate post-stroke cognitive impairment by restoring butyrate metabolism.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {6},
pmid = {41316344},
issn = {2049-2618},
support = {82171317//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Female ; Male ; Mice ; Bacteria/metabolism ; *Brain-Gut Axis/drug effects ; *Butyrates/metabolism ; Cell Line ; *Cognitive Dysfunction/drug therapy/microbiology ; Gastrointestinal Microbiome ; Glucuronates/metabolism ; *Infarction, Middle Cerebral Artery/complications/microbiology ; *Mannose/analogs &amp; derivatives/pharmacology/therapeutic use ; Mice, Inbred C57BL ; Neurogenesis/drug effects ; *Oligosaccharides/pharmacology/therapeutic use ; Disease Models, Animal ; },
abstract = {BACKGROUND: Post-stroke cognitive impairment (PSCI) affects up to half of stroke survivors, severely impacting their quality of life. Despite its prevalence, the pathogenesis of PSCI remains poorly understood, and no specific pharmacological treatments are currently available.<br><br>RESULTS: In PSCI patients, fecal butyrate levels were significantly reduced and correlated with cognitive scores. A machine learning model incorporating butyrate levels, butyrate-producing bacteria, and clinical factors (education, smoking, body mass index [BMI], hemoglobin) demonstrates strong predictive performance (area under the curve [AUC]: 0.793 internal, 0.795 external validation). In a transient middle cerebral artery occlusion (tMCAO) mouse model, both sexes displayed sustained gut microbiota dysbiosis featuring decreased butyrate-producing bacteria and fecal butyrate concentrations, concomitant with hippocampal neuronal loss and microglial activation.&#xa0;Sodium oligomannate (GV-971) treatment ameliorated cognitive impairment in a sex-independent manner and restored butyrate-producing gut bacteria. Metagenomic analysis revealed that GV-971 enhanced butyrate production by promoting D-glucuronate degradation and upregulating butyrate synthesis pathway abundance. The elevated butyrate promoted acetylation of histone H3 at lysines 9 and 14 (Ac-H3K9/K14) in colonic and hippocampal neurons, stimulating neurogenesis, while concurrently reducing gut-derived lipopolysaccharide (LPS) and microglial inflammation. Antibiotic treatment and fecal microbiota transplantation established the essential role of butyrate-producing microbiota in mediating GV-971's effects.&#xa0;In vitro, butyrate supplementation significantly inhibited HDAC3 enzymatic activity in HT22 cells and alleviated LPS-induced inflammatory responses in BV2 microglia.<br><br>CONCLUSIONS: Intestinal butyrate levels are significantly associated with PSCI. GV-971 mitigates post-stroke cognitive decline by modulating the gut microbiota to increase butyrate production, highlighting its potential as a therapeutic agent for PSCI.},
}
@article {pmid41315665,
year = {2025},
author = {Goraj, W and Kagan, K and Kuźniar, A and Banach, A and Jurczyk, S and Podlewski, J and Wolińska, A},
title = {Spatial and functional differentiation of microbial biofilms in a traditional cheese ripening environment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {45638},
pmid = {41315665},
issn = {2045-2322},
mesh = {*Biofilms/growth &amp; development ; *Cheese/microbiology ; *Bacteria/genetics/classification ; *Fungi/genetics/classification ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Microbiota ; Biodiversity ; Poland ; },
abstract = {Biofilms in historic buildings represent stable microbial ecosystems shaped by long-term environmental filtering. We investigated bacterial and fungal communities forming biofilms on walls and ceilings in a 19th-century cheese ripening cellar in Poland, characterized by low temperature, high humidity, and minimal light - conditions resembling natural subterranean habitats. Using high-throughput 16 S rRNA and ITS sequencing, we revealed distinct taxonomic and predicted functional profiles associated with surface type (wall vs. ceiling) and material (brick vs. stone). The wall biofilms exhibited greater taxonomic and functional diversity, with enrichment in heterotrophic, fermentative, and polymer-degrading taxa and pathways, whereas ceiling biofilms showed predicted enrichment in aerobic, stress-tolerant, and potentially methanogenic lineages. The co-occurrence network analysis revealed more complex and tightly connected associations in wall biofilms, dominated by Actinobacteriota (21-97%) and Ascomycota (60-97%), suggesting stable ecological organization despite the limited sample size. Environmental factors, such as pH, redox potential, and electrolytical conductivity, explained a substantial proportion of the variance in the microbial diversity and predicted functional traits. Overall, this study highlights traditional ripening cellars as semi-natural built ecosystems that sustain specialized, spatially structured microbiomes. The results provide new insights into microbial adaptation, functional potential, and ecological resilience in heritage food environments.},
}
@article {pmid41315430,
year = {2025},
author = {Lynch, KF and Triplett, EW and Hyöty, H and Ahrens, AP and Laiho, JE and Petrosino, JF and Lloyd, RE and Agardh, D},
title = {Microbial associations and viruses on the risk of celiac disease (MAVRiC): a longitudinal post-hoc case-cohort study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42704},
pmid = {41315430},
issn = {2045-2322},
support = {R01 DK124581/DK/NIDDK NIH HHS/United States ; R01 DK124581-01/NH/NIH HHS/United States ; 2022-00537//Swedish research Council, Sweden/ ; },
mesh = {Humans ; *Celiac Disease/virology/epidemiology/microbiology/immunology/etiology ; Female ; Male ; Longitudinal Studies ; Child, Preschool ; *Gastrointestinal Microbiome ; Autoantibodies/immunology ; Risk Factors ; Transglutaminases/immunology ; Child ; Autoimmunity ; Cohort Studies ; Glutens ; },
abstract = {Celiac disease etiopathogenesis requires genetic predisposition and exposure to gluten, yet these factors alone are not sufficient. Larger longitudinal studies are needed to determine the role of time-varying infections and gut microorganisms. The aim was to design a celiac disease case-cohort longitudinal study using The Environmental Determinants of Diabetes in the Young (TEDDY) study. By age 3-years, persistent tissue transglutaminase autoantibodies (tTGA), i.e., celiac disease autoimmunity (CDA), was confirmed in 704 of the 6132 genetically at-risk TEDDY children. Celiac disease onset (CD-onset) was defined as the age CDA developed when followed by a biopsy-proven diagnosis. A competing risk analysis on CD-onset and CDA children with no diagnosis (CDA-only) revealed female-sex, HLA and non-HLA genes and higher gluten-consumption correlate with an increased risk of both outcomes. However, reports of virus-related respiratory infections from August to October correlate consistently with an increased risk of CD-onset and not CDA-only. A sub-cohort of 561 children (9% sampling fraction) has been randomly selected to represent the TEDDY cohort. All incident CD-onset cases (N = 306) were included. The case-cohort will be utilized to analyze virus antibodies and bacteriome from longitudinal plasma and stool samples (the Microbial Associations and Viruses on the Risk of Celiac disease study, MAVRiC).},
}
@article {pmid41315331,
year = {2025},
author = {Jiang, Y and Liu, J and Zhang, Y and Zhou, L and Kao, E and Hou, S and Niu, Q and Liu, Y and Xu, ZZ and Ding, T and Su, YX and Liu, Y and Zhang, G and Wang, X and Teng, F and Huang, S},
title = {High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {223},
pmid = {41315331},
issn = {2055-5008},
support = {10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; 10212276//Health and Medical Research Fund/ ; ZR2024MH23//Natural Science Foundation of Shandong Province/ ; tsqn201909126//Taishan Scholar Award For Young Expert/ ; },
mesh = {Humans ; *Microbiota/genetics ; Saliva/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Mouth Neoplasms/microbiology ; Dental Caries/microbiology ; *Host Microbial Interactions ; *Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Child ; Child, Preschool ; },
abstract = {Characterizing human microbiota in host-dominated samples is crucial for understanding host-microbe interactions, yet is challenged by the high host DNA context (HoC). Current depletion strategies are limited by DNA loss and require immediate processing. In this paper, we introduce 2bRAD-M, a reduced metagenomic sequencing method that enables efficient host-microbe analysis without prior host depletion. Validated on mock samples with >90% human DNA, 2bRAD-M achieved over 93% in AUPR and L2 similarity. In both saliva and oral cancer samples, 2bRAD-M closely matched WMS profiles; in the former, it captured diurnal and host-specific patterns with only 5-10% of the sequencing effort. In an early childhood caries (ECC) study, 2bRAD-M identified key bacterial indicators and distinguished ECC from healthy subjects (AUC = 0.92). By providing high-resolution microbial profiles without host depletion, 2bRAD-M offers a practical and efficient solution for HoC-challenged microbiome research.},
}
@article {pmid41315266,
year = {2025},
author = {He, X and Gu, L and Wang, D and Baer, M and Schaaf, G and Apostolakis, A and Meijide, A and Chen, X and Hochholdinger, F and Yu, P},
title = {Rhizosheath inhabiting Massilia are linked to heterosis in roots of maize.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10777},
pmid = {41315266},
issn = {2041-1723},
support = {444755415//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Zea mays/microbiology/genetics/growth &amp; development/metabolism ; *Hybrid Vigor/genetics ; *Plant Roots/microbiology/genetics ; Soil Microbiology ; Biomass ; Microbiota/genetics ; Flavonoids/metabolism ; Metabolomics ; Rhizosphere ; },
abstract = {Heterosis, or hybrid vigor, describes the superior performance of F1 hybrids compared to parental inbreds. While soil microbiomes are proposed to influence heterosis, it remains unclear how heterotic plants shape their microbiomes and how interactions relate to stress responses. Here, we investigate the role of rhizosheath formation-the soil tightly adhering to roots-in maize heterosis under nitrogen deprivation. Across sterilization, inoculation, and transplantation experiments, hybrids develop larger rhizosheaths than inbreds, and rhizosheath size associates with biomass heterosis. Rhizosheath-enriched genus Massilia correlates with lateral root density, rhizosheath size, and growth. Untargeted metabolomics and flavone-deficient mutants reveal links between Massilia and flavonoid pathways, while growth promotion by Massilia can also occur independently of host flavones. Metagenomic analysis shows that larger rhizosheaths recruit microbial functions related to nutrient cycling and stress adaptation. These findings identify rhizosheath formation as an integrative trait associated with heterosis and a promising target for breeding resilient crops.},
}
@article {pmid41315190,
year = {2025},
author = {Worp, N and Nieuwenhuijse, DF and Izquierdo-Lara, RW and Schapendonk, CME and Brinch, C and Jensen, EEB and Munk, P and Hendriksen, RS and , and Aarestrup, F and Oude Munnink, BB and Koopmans, MPG and de Graaf, M},
title = {Unveiling the global urban virome through wastewater metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10707},
pmid = {41315190},
issn = {2041-1723},
support = {874735//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Societal Challenges | H2020 Health (H2020 Societal Challenges - Health, Demographic Change and Well-being)/ ; },
mesh = {*Wastewater/virology ; *Metagenomics/methods ; *Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation &amp; purification ; Cities ; Animals ; Metagenome ; },
abstract = {Understanding global viral dynamics is critical for public health. Traditional surveillance focuses on individual pathogens and symptomatic cases, which may miss asymptomatic infections or newly emerging viruses, delaying detection and response. Wastewater-based epidemiology has been used to track pathogens through targeted molecular assays, but its reliance on predefined targets limits detection of the full viral spectrum. Here, we analyse longitudinal wastewater samples from 62 cities across six continents (2017-2019) using metagenomics and capture-based sequencing with probes targeting viruses associated with gastrointestinal disease. We detect over 2500 viral species spanning 122 families, many with human, animal, or plant health relevance. The bacteriophage family Microviridae and plant virus family Virgaviridae dominate the metagenomic dataset, while Astroviridae and Picornaviridae prevail in the capture-based sequence dataset. Virus distributions are broadly similar across continents at the family and genus levels, yet distinct city-level fingerprints reveal geographical and temporal variation, enabling spatiotemporal surveillance of viruses such as astroviruses and enteroviruses. Global wastewater-based epidemiology enables early detection of emerging viruses, including Echovirus 30 in Europe and Tomato brown rugose fruit virus. These findings highlight the potential of wastewater sequencing for the early detection of emerging viruses and population-wide virome monitoring across diverse hosts.},
}
@article {pmid41314069,
year = {2025},
author = {Kumari, SP and Hooda, S and Diwan, P and Gupta, RK},
title = {Seasonal variations and functional insights into the urban air microbiome across public transit environments at railway stations in Delhi, India.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181062},
doi = {10.1016/j.scitotenv.2025.181062},
pmid = {41314069},
issn = {1879-1026},
mesh = {India ; Seasons ; *Microbiota ; *Railroads ; *Air Microbiology ; *Environmental Monitoring ; Cities ; Bacteria/classification ; },
abstract = {Airborne microbial communities play an underappreciated yet critical role in shaping urban environmental health, particularly in densely crowded public transit systems. This study aimed to explore the taxonomic and functional landscape of airborne bacteria, highlighting the seasonal disparities across summer and autumn seasons, in the public transit air (railway stations) of Delhi, a populated megacity characterized by extreme pollution levels and one of the world's busiest railway networks. Metagenomic analyses revealed distinct seasonal signatures in microbial community composition and diversity. Alpha diversity was higher during autumn, though not statistically significant, while beta diversity differed significantly between seasons. LEfSe analysis identified season-specific indicator taxa, including Moraxella, Barrientosiimonas, Methylobacterium, for autumn and Stutzerimonas, Caulobacter, Pseudomonas for summer, representing a mix of opportunistic pathogens and environmentally significant taxa. Correlation networks highlighted distinct seasonal clustering patterns. Resistome and virulome profiling revealed the presence of different resistance gene classes and virulence factor categories in abundance. Correlation networks uncovered significant associations between specific genes and bacterial genera, suggesting ecological partitioning in gene carriage. Temperature and air quality index explained a part of the variance observed in the taxonomic and functional dynamics. Metagenome-assembled genomes captured seasonally distinct taxa, and biosynthetic gene cluster screening identified 317 gene clusters, including terpene, RiPP-like, and hserlactone clusters. The findings underscore the ecological complexity and public health relevance of airborne bacteria and raise concerns about their potential role in microbial transmission and long-term respiratory health risks. These insights are crucial for public health surveillance, urban air quality management, and guiding future investigations into the microbial safety of urban environments.},
}
@article {pmid41313993,
year = {2025},
author = {Zheng, Y and Crowther, TW and Qin, Y and Lei, J and Xu, M and Xu, Y and Chu, H and Wu, Q and Shi, Y},
title = {Liquor fermentation industry reshapes soil microbiomes and drives CO2 emissions via microbial dispersal.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128135},
doi = {10.1016/j.jenvman.2025.128135},
pmid = {41313993},
issn = {1095-8630},
mesh = {*Soil Microbiology ; *Carbon Dioxide ; Fermentation ; *Microbiota ; Soil/chemistry ; },
abstract = {The rapid expansion of industrial fermentation has raised concerns about its environmental impacts, particularly regarding microbial dispersal from production facilities into adjacent terrestrial ecosystems; however, the ecological and functional consequences of microbial introductions originating from fermentation facilities remain poorly elucidated. We studied eight Chinese liquor fermentation facilities spanning 26°-47°N and 83°-124°E, covering the major geographical range of the industry. Using large-scale soil metagenomics, in situ CO2 flux measurements, and microcosm experiments, we demonstrate that industrial fermentation significantly alters local soil microbial communities and enhances carbon decomposition potential. The results showed that soil carbon decomposition genes increased 13.6 % around fermentation facilities. Biologically, the fermentation process at the facilities introduced microorganisms into soil, such as Actinobacteria, whose abundance increased by 2.8 %. These microorganisms directly increased the abundance of carbon decomposition genes in the soil, while Actinobacteria also enhance soil carbon decomposition capacity by reducing microbial α diversity. Abiotically, the soil total carbon increased by 3-89 % around facilities, thereby enriching carbon decomposition genes. These soil microbial activities changed by fermentation facilities lead to an increase in soil CO2 emissions. Our study provides the first evidence that industrial fermentation facilities inadvertently modify soil microbial community and function. These findings establish a critical link between fermented food production systems and terrestrial carbon emissions, with important implications for sustainable fermentation practices and climate-smart industrial planning.},
}
@article {pmid41313018,
year = {2025},
author = {Wang, K and Wang, H and Zhao, Z and Shen, X and Zhao, J and Zhang, H},
title = {Bifidobacterium animalis subsp. lactis Probio-M8 enhances chondroitin efficacy for knee osteoarthritis in postmenopausal women via the gut-joint axis.},
journal = {mSystems},
volume = {10},
number = {12},
pages = {e0086225},
pmid = {41313018},
issn = {2379-5077},
support = {2022YFD2100700//National Key Research and Development Program of China/ ; U22A20540//National Natural Science Foundation of China/ ; BR221203//Fundamental Research Funds of Inner Mongolia Agricultural University/ ; },
mesh = {Humans ; Female ; *Osteoarthritis, Knee/drug therapy/microbiology/therapy ; *Probiotics/therapeutic use/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; *Postmenopause ; Middle Aged ; *Bifidobacterium animalis ; Aged ; *Chondroitin Sulfates/therapeutic use ; Treatment Outcome ; *Chondroitin/therapeutic use ; },
abstract = {UNLABELLED: Knee osteoarthritis (KOA) is a chronic joint disease marked by cartilage degradation and inflammation. Probiotics exhibit anti-inflammatory properties and may influence the gut-joint axis. Thus, a 4-month human trial was conducted to assess the adjunctive effects of Bifidobacterium animalis subsp. lactis Probio-M8 on KOA in postmenopausal women. Sixty-five KOA patients were randomly allocated to the probiotic group (n = 37; Probio-M8 and chondroitin sulfate) or placebo group (n = 28; placebo and chondroitin sulfate). Following a 3-month intervention, participants from both groups entered a 1-month observation without probiotic supplementation. Our findings revealed that Probio-M8 co-administration significantly reduced Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores at months 1, 3, and 4 compared to the placebo group (P < 0.001). The probiotic group showed a significant decrease in serum IFN-γ and increases in IL-4 and IL-10 (P < 0.05). Fecal metagenome analysis showed significant changes in the gut microbiota of the probiotic group, with increases in potentially beneficial species, including Agathobaculum butyriciproducens, Bacteroides stercoris, B. animalis, Roseburia hominis, and Ruminococcus bromii, while Dorea formicigenerans decreased (P < 0.05). Changes in B. animalis were strongly associated with WOMAC scores. The gut metabolic potential analysis showed elevated levels of N-oleoylethanolamine and decreased levels of cholesterol and hypoxanthine in probiotic receivers (P < 0.05). Metabolite analysis revealed post-interventional alternations in fecal prostaglandin E2, stearic acid, cholic acid, chenodeoxycholic acid, xanthine, testosterone, and serum bile acids (P < 0.05). Collectively, Probio-M8 enhances the effectiveness of chondroitin sulfate in KOA management through modulating the gut-joint axis, potentially via regulating multiple inflammatory pathways.<br><br>IMPORTANCE: The pathogenesis of knee osteoarthritis (KOA) and its phenotypic expression have been associated with the human gut microbiota. Our study demonstrated that the co-administration of Probio-M8 with chondroitin sulfate significantly alleviates KOA symptoms. This probiotic intervention enhances therapeutic efficacy through modulation of the gut microbiota and associated metabolic pathways, reducing inflammation and improving clinical outcomes. Our results underscore the potential of probiotic-driven therapies as an adjunctive treatment strategy and underscore the importance of the gut-joint axis in KOA management.},
}
@article {pmid41312645,
year = {2026},
author = {Fiamenghi, MB and Camargo, AP and Chasapi, IN and Baltoumas, FA and Roux, S and Egorov, AA and Aplakidou, E and Ndela, EO and Vasquez, YM and Chen, IA and Palaniappan, K and Reddy, TBK and Mukherjee, S and Ivanova, NN and Schulz, F and Woyke, T and Eloe-Fadrosh, EA and Pavlopoulos, GA and Kyrpides, NC},
title = {Meta-virus resource (MetaVR): expanding the frontiers of viral diversity with 24 million uncultivated virus genomes.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D801-D812},
pmid = {41312645},
issn = {1362-4962},
support = {FWP 70880//BER's Genomic Sciences Program/ ; 1U01DE034196-01/GF/NIH HHS/United States ; //Royal Physiographic Society of Lund/ ; 45379//Natural Sciences, Medicine and Technology/ ; //Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//US DOE/ ; U01 DE034196/DE/NIDCR NIH HHS/United States ; },
mesh = {*Genome, Viral ; *Viruses/genetics/classification ; *Databases, Genetic ; Metagenomics/methods ; Phylogeny ; Biodiversity ; Genetic Variation ; Metagenome ; Software ; },
abstract = {Viruses are ubiquitous in all environments and impact host metabolism, evolution, and ecology, although our knowledge of their biodiversity is still extremely limited. Viral diversity from genomic and metagenomic datasets has led to an explosion of uncultivated virus genomes (UViGs) and the development of specialized databases to catalog this viral diversity, though many lack comprehensive integration. Here, we introduce meta-virus resource (MetaVR), the successor of the IMG/VR database, designed to overcome previous limitations such as large-scale querying and programmatic access. Drawing on the increase of publicly available genomes and metagenomes, MetaVR significantly expands viral diversity, now comprising 24,435,662 UViGs, a 57.6% increase from its predecessor, organized into over 12 million viral operational taxonomic units. Key enhancements include the integration of curated eukaryotic host information, the integration of protein clusters and predicted structures for comparative studies, and an API for programmatic data access. Furthermore, MetaVR features an updated taxonomic framework based on ICTV release 39, assignment to Baltimore classes, and enhanced host assignment through novel computational tools like iPHoP. These advancements position MetaVR as a unique resource for exploring viral diversity, evolution, and host interactions across diverse environments. MetaVR can be freely accessed at https://www.meta-virome.org/.},
}
@article {pmid41312302,
year = {2025},
author = {Steindler, L and Maldonado, M and Pita, L and Riesgo, A and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the stone sponge Petrosia ficiformis (Poiret, 1789) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {450},
pmid = {41312302},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Petrosia ficiformis (stone sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence is 191.3 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.89 kilobases in length. Gene annotation of the host organism assembly identified 18,339 protein coding genes. The metagenome of the specimen was also assembled, and 112 binned bacterial genomes were identified, including 57 high-quality MAGs. Besides MAGs characteristic of HMA sponge symbionts (i.e., Chloroflexota, Acidobacteriota), the P. ficiformis specific symbiont Candidatus Synechococcus feldmanni (formerly Aphanocapsa feldmanni (Cyanobacteriota) was recovered, as well as notably MAGs of several candidate phyla (Candidatus Latescibacteria, Poribacteria, Tectomicrobia, Dadabacteria, Kapabacteria and Binatia).},
}
@article {pmid41312195,
year = {2025},
author = {Chen, J and Gong, G and Huang, S and Chen, Y and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ji, L and Zhang, W},
title = {Gut Virome of Tibetan Pigs Reveals the Diversity, Composition, and Distribution of Potential Novel Viruses/Variants.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {5191656},
pmid = {41312195},
issn = {1865-1682},
mesh = {Animals ; Swine ; Tibet/epidemiology ; *Virome ; Phylogeny ; *Swine Diseases/virology/epidemiology ; Feces/virology ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Genetic Variation ; *Gastrointestinal Microbiome ; },
abstract = {As a local breed adapted to the extreme environment of the Tibetan Plateau, Tibetan pigs have not yet been systematically characterized in terms of their gut viral communities. In this study, we applied viral metagenomics to sequence fecal samples from 191 Tibetan pigs (including both healthy and diarrheal individuals) across four farms in Nyingchi, Tibet, aiming to reveal the diversity, composition, and distribution of gut viral communities in Tibetan pigs living at high altitudes. A total of nearly 120 million high-quality viral sequence reads were obtained, which were annotated into 16 viral families. The viral community was predominantly dominated by Microviridae, but its composition varied across different farms and health statuses. Phylogenetic analysis identified numerous virus sequences associated with pigs, including RNA viruses (such as Astroviridae (n = 7), Caliciviridae (n = 6), Picornaviridae (n = 15), etc.) and DNA viruses (such as Circoviridae (n = 3), Genomoviridae (n = 4), Smacoviridae (n = 41), Parvoviridae (n = 11), etc.). Notably, the study found multiple viral sequences exhibiting genetic differences from known strains, suggesting the potential presence of novel viruses or variants. For instance, a papain-like protease (PLP) insertion sequence, identified to have high sequence identity with Torovirus (ToV), was found in six Enterovirus G (EV-G) strains, indicating a cross-family genetic recombination event. This study systematically outlines the viral metagenomic profile of gut viral communities in Tibetan pigs at high altitudes, revealing their unique viral diversity and complex community structure. The results suggest that the gut viral community of Tibetan pigs consists of host-associated viruses, bacteriophages, and potentially viruses originating from the environment or diet, with its composition influenced by farming conditions and host health status. These findings provide an important data foundation for understanding the interactions between viruses, hosts, and the environment in unique ecological settings and offer new insights into the health management and virology research of Tibetan pigs.},
}
@article {pmid41310806,
year = {2025},
author = {Utkina, I and Fan, Y and Willing, BP and Parkinson, J},
title = {Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {248},
pmid = {41310806},
issn = {2049-2618},
support = {RGPIN-2019-06852//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Cecum/microbiology ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Metagenome ; *Bacteroides/metabolism/genetics/classification ; *Bacteria/classification/metabolism/genetics ; Fatty Acids, Volatile/metabolism ; Escherichia coli/metabolism/genetics ; },
abstract = {BACKGROUND: Members of the Bacteroidales, particularly Bacteroides species, with their ability to degrade dietary fibers and liberate otherwise unavailable substrates, exert a substantial influence on the microbiome of the lower intestine. However, our understanding of how this influence translates to the metabolic interactions that support community structure remains limited. In this study, we apply constraint-based modeling to investigate metabolic interactions in chicken cecal communities categorized by the presence or absence of Bacteroides.<br><br>RESULTS: From metagenomic datasets previously generated from 33 chicken ceca, we constructed 237 metagenome-assembled genomes. Metabolic modeling of communities built from these genomes generated profiles of short-chain fatty acids largely consistent with experimental assays and confirmed the role of B. fragilis as a metabolic hub, central to the production of metabolites consumed by other taxa. In its absence, communities undergo significant functional reconfiguration, with metabolic roles typically fulfilled by B. fragilis assumed by multiple taxa. Beyond B. fragilis, we found Escherichia coli and Lactobacillus crispatus also mediate influential metabolic roles, which vary in the presence or absence of B. fragilis. Notably, the microbiome's compensatory adaptations in the absence of B. fragilis produced metabolic alterations resembling those previously associated with inflammatory bowel disease in humans, including energy deficiency, increased lactate production, and altered amino acid metabolism.<br><br>CONCLUSIONS: This work demonstrates the potential of using the chicken cecal microbiome as a model system for investigating the complex metabolic interactions and key contributions that drive community dynamics in the gut. Our model-based predictions offer insights into how keystone taxa like B. fragilis may shape the metabolic landscape and functional organization of microbial communities. The observed metabolic adaptations in the absence of B. fragilis share metabolic similarities with profiles seen in dysbiotic states in humans and underscore the translational relevance of these insights for understanding gut health across different host systems. Video Abstract.},
}
@article {pmid41310797,
year = {2025},
author = {Du, H and Lin, B and Zhu, Y and Hao, X and Tang, M and Wu, W and Wang, D and Yang, Y and Liang, Y and Tang, W and Xu, H and Li, J and Gao, F and Du, X},
title = {Exploring the mechanisms of protective effect of high-energy X-ray FLASH radiotherapy on intestine through multi omics analysis.},
journal = {Radiation oncology (London, England)},
volume = {20},
number = {1},
pages = {179},
pmid = {41310797},
issn = {1748-717X},
support = {2025ZNSFSC0555//Sichuan Science and Technology Program/ ; U2330122//Projects of National Natural Science Foundation/ ; 2023ZYDF073//Minyang Science and Technology Program/ ; miancaijian2022-186//Mianyang Municipal Finance Bureau/ ; },
mesh = {Animals ; Mice ; Female ; Mice, Inbred C57BL ; *Colonic Neoplasms/radiotherapy/pathology ; *Intestines/radiation effects ; X-Rays ; Metabolomics/methods ; Gastrointestinal Microbiome/radiation effects ; Multiomics ; },
abstract = {BACKGROUND: The aim of this study is to investigate the potential mechanisms underlying the protective effects of high-energy X-ray FLASH radiotherapy (FLASH-RT) on intestine through multi-omics analysis.<br><br>METHODS: This study utilized syngeneic colon carcinoma mouse models of CT26 and MC38 to evaluate the therapeutic efficacy of FLASH-RT versus conventional dose rate radiotherapy (CONV-RT) by monitoring survival, tumor size, and body weight. Furthermore, healthy C57BL/6 female mice received whole-abdominal irradiation with either FLASH-RT, CONV-RT, or sham irradiation to compare differences in normal tissue protection. 72&#xa0;h post-irradiation, intestinal contents from mice were collected for metagenomic analysis, and intestinal tissue was harvested for non-targeted metabolic and single-cell sequencing analyses.<br><br>RESULTS: In CT26 and MC38 models, both CONV-RT and FLASH-RT have demonstrated similar anti-tumor efficacy. Compared with CONV-RT, whole-abdominal FLASH-RT significantly alleviated acute intestinal injury in mice, as evidenced by better preservation of crypt numbers and villus architecture in the FLASH group. Metagenomic analysis revealed that the relative abundance of the gut-protective bacterium Ligilactobacillus ruminis was significantly higher in the FLASH group than in the CONVgroup. Non-targeted metabolomic profiling identified 34 differential metabolites, of which 29 were upregulated and 5 were downregulated in the FLASH group. Notably, the abundance of 2-hydroxyglutarate, a metabolite associated with the butyrate metabolism pathway, was significantly elevated in the FLASH group compared with the CONV group (p&#x2009;<&#x2009;0.05). Single-cell sequencing data revealed notable differences in cell distribution and proportions between the groups, with a higher proportion of fibroblasts, proliferative cells, macrophages, and CD4&#x2009;+&#x2009;T cells in the FLASH group compared to the CONV and control groups. Immunofluorescence analysis revealed a significantly greater number of Lgr5&#x207a; intestinal stem cells in the FLASH group compared to the CONV group. Conversely, immunohistochemical analysis demonstrated stronger p50/p65 staining intensity in the CONV group relative to the FLASH group.<br><br>CONCLUSIONS: This study confirms that FLASH-RT, compared to CONV-RT, maintains equivalent antitumor efficacy while mitigating damage to normal intestinal tissues. Moreover, it preliminarily reveals that the protective mechanism of FLASH-RT is multifaceted, involving remodeling of the microbiota-metabolite axis, attenuation of inflammatory responses, and enhanced preservation of stem cells.},
}
@article {pmid41310780,
year = {2025},
author = {Liu, Y and Brinkhoff, T and Simon, M},
title = {Ecogenomics and functional biogeography of the Roseobacter group in the global oceans based on 653 MAGs and SAGs.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {247},
pmid = {41310780},
issn = {2049-2618},
support = {TRR51//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Oceans and Seas ; *Roseobacter/classification/genetics ; Seawater/microbiology ; Biodiversity ; *Phylogeography ; Genome, Bacterial ; },
abstract = {BACKGROUND: The Roseobacter group is a major component of prokaryotic communities in the global oceans. Information on this group is based predominantly on isolates and their genomic features and on the 16S rRNA gene. Assessments of prokaryotic communities in the pelagic of the global oceans indicated an unveiled diversity of this group but studies of the diversity and global biogeography of the entire group are still missing. Hence, we aimed at a comprehensive assessment of the Roseobacter group in the global oceans on the basis of MAGs and SAGs.<br><br>RESULTS: The obtained 610 MAGs and 43 SAGs of high quality were subjected to in-depth analyses of their phylogeny, genomic and functional features. The recruitment locations range from the tropics to polar regions, include all major ocean basins. The phylogenetic analysis delineated the known RCA cluster and five pelagic clusters, two of which were completely novel: TCR (Temperate and Cold Roseobacter), AAPR (Arctic-Atlantic-Pacific Roseobacter, novel), AAR (Arctic-Atlantic Roseobacter, novel), COR (Central Oceanic Roseobacter), LUX (Cand. Luxescamonaceae) cluster. These clusters account for&#x2009;~&#x2009;70% of all Roseobacter MAGs and SAGs in the epipelagic. The TCR, AAPR, AAR, and LUX clusters are among the most deeply branching lineages of the Roseobacter group. These clusters and several sublineages of the RCA and COR clusters exhibit distinct features of genome streamlining, i.e. genome sizes of&#x2009;<&#x2009;2.9 Mbp and G&#x2009;+&#x2009;C contents of&#x2009;<&#x2009;40%. The clusters exhibit differences in their functional features and also compared to other lineages of the Roseobacter group. Proteorhodopsin is encoded in most species of the AAPR, AAR, TCR, and RCA clusters and in a few species of the COR cluster, whereas in most species of the latter, the LUX cluster and in a few species of the RCA cluster aerobic anoxygenic photosynthesis is encoded. Biogeographic assessments showed that the AAPR, AAR, TCR and RCA clusters constitute the Roseobacter group in the temperate to polar regions to great extent whereas the COR and LUX clusters in the tropics and subtropics.<br><br>CONCLUSIONS: Our comprehensive analyses shed new light on the diversification, genomic features, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. Video Abstract.},
}
@article {pmid41310455,
year = {2025},
author = {Feng, Y and Yang, F and Klopatek, SC and Oltjen, JW and Yang, X},
title = {The fecal resistome of beef cattle from conventional grain-fed and grass-fed systems in the Western United States.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {3},
pmid = {41310455},
issn = {1471-2180},
support = {20-1078-000-SG//Antimicrobial Use and Stewardship (AUS) Branch of the California Department of Food and Agriculture/ ; },
mesh = {Animals ; Cattle/microbiology ; *Feces/microbiology ; *Animal Feed/analysis ; *Bacteria/genetics/drug effects/isolation &amp; purification/classification ; *Poaceae ; *Edible Grain ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; United States ; Gastrointestinal Microbiome ; Metagenomics ; },
abstract = {Bacteria in the gastrointestinal tract of cattle may develop antimicrobial resistance (AMR) due to the use of antibiotics in live animals and can be excreted in feces, posing a risk of contamination. However, it remains unclear whether different beef production systems influence the levels of AMR in cattle feces. The objective of this study was to characterize and compare the fecal resistome of cattle raised in grass and grain-feeding systems in the Western United States. Fecal samples were collected from individual cattle at 14 months of age and two days before their respective harvest date. Groups included: (1) Conventional grain-fed (CON, n = 10), (2) Grass-fed for 20 months (20GF, n = 10), (3) Grass-fed and then grain-finished for 45 days (GR45, n = 10), (4) Grass-fed for 25 months (25GF, n = 10). According to metagenomic analysis, grass-feeding systems, particularly the one with extended grass-feeding, are associated with a less diverse resistome. The 25GF group had smaller (P < 0.05) Chao1 value than the other groups at the harvest time. Antimicrobial resistance genes (ARGs) richness and evenness were higher in CON and GR45 than in 20GF and 25GF (P < 0.05). Additionally, the resistome of GR45 and CON differed from 25GF (P = 0.018). In grass-feeding systems where antibiotics were not administered, animals' feces exhibited greater (P < 0.05) diversity in transferable biocide and metal resistant genes (BMRGs) compared with the grass-fed but grain-finished system. Greater ARG diversity in grain-finished feeding systems may enhance the spread of antimicrobial-resistant bacteria (ARB) during production, posing additional risks to food safety. Similarly, higher BMRG diversity observed in grass-fed systems may promote ARB spreading through co-selection mechanisms, which could also contribute to potential food safety concerns.},
}
@article {pmid41310063,
year = {2025},
author = {Plomp, N and Gacesa, R and Slager, J and Samsom, JN and Faber, KN and Jonkers, IH and Withoff, S and Wijmenga, C and Weersma, RK and Harmsen, HJM},
title = {Synergy between culturomics and metagenomics of health status-associated gut bacteria originating from non-IBD and IBD populations.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {45469},
pmid = {41310063},
issn = {2045-2322},
support = {LSHM18057-SGF//Samenwerkende Gezondheidsfondsen/ ; NWO Gravitation project 024.003.001//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 016.136.308//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; MLDS D16-14//Maag Lever Darm Stichting/ ; 101095470//HORIZON EUROPE Framework Programme/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Inflammatory Bowel Diseases/microbiology ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; Feces/microbiology ; Female ; Male ; Adult ; Middle Aged ; Health Status ; },
abstract = {The bacteria in the human intestinal tract are important for health and associate with diseases, such as inflammatory bowel disease (IBD). Although metagenomic studies can identify certain bacteria or even specific strains and associate their presence or specific phenotypes with health or diseases, actual isolates for experimental validation of metagenomic associations are often lacking. Therefore, this study sets out to culture health- and IBD-associated bacteria from 32 fecal samples from 2 cohorts, for which extensive metadata is available. The cultivation of those samples resulted in 4,347 isolates, of which 1,362 isolates were obtained from IBD patients. Irrespective of health or IBD, Actinomycetota, Bacillota and Bacteroidota were the most represented phyla and members of 5 other phyla were less frequently isolated (Campylobacterota, Fusobacteriota, Pseudomonadota, Thermodesulfobacteriota and Verrucomicrobiota). Comparison of the genus richness between the culturomics approach and available metagenomic sequencing data of the corresponding participants revealed that both methods largely capture the same genera. Although not all genera could be identified in both methods, our results show that combining both methods has a synergetic effect, providing a higher identification rate. Furthermore, genetic analysis of 2 isolates of Bifidobacterium adolescentis strains shows that these isolates closely resembled the metagenome-assembled genome that was identified within the same participant. This showcases that it is possible to isolate specific strains that are important in the experimental validation of specific associations within a species. The culture collection that is presented in this study contains bacterial isolates that are strongly associated with health or IBD. Our results show that we are able to generate a valuable culture collection that opens a promising avenue for functional validation experiments of associations that are identified with metagenomic data.},
}
@article {pmid41309890,
year = {2025},
author = {Kuzmichenko, P and Fedorov, D and Galeeva, J and Postoeva, A and Krieger, E and Kudryavtsev, A and Pavlenko, A and Vvedensky, A and Starikova, E and Govorun, V and Ilina, E},
title = {Comparing alignment and de-novo approaches for gut microbiota metagenomic data analysis reveals differences in taxonomic resolution and novel functional insights.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {42423},
pmid = {41309890},
issn = {2045-2322},
support = {/WT_/Wellcome Trust/United Kingdom ; 075-15-2025-530//Ministry of Science and Higher Education of the Russian Federation/ ; 100217/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Metagenomics/methods ; Feces/microbiology ; Metagenome ; Male ; *Bacteria/genetics/classification ; Female ; Adult ; },
abstract = {Microbiome annotation based on metagenomic data is primarily conducted using two global approaches: alignment-based approach (AL) and de novo approach (DN). This study aimed to evaluate the limitations of each approach, explore correlations between their results, and assess the equivalence of findings derived from different methodologies when analyzing the same dataset. Shotgun metagenomic sequencing data from 346 fecal samples, collected longitudinally within individuals in Arkhangelsk, Northwestern Russia, were analyzed. Each of the 173 participants provided two samples, one during 2015-2017 and another in 2022. The alterations in the microbiota associated with BMI served as a critical variable for facilitating the comparisons between the AL and DN. Exploratory analyses, including PERMANOVA, alpha diversity and beta diversity, revealed no significant differences between the two approaches. However, differential abundance analysis based on the AL yielded more statistically significant results, with the DN producing only a subset of these findings. An analysis of the metagenome-assembled genomes (MAGs) of bacteria that were differentially abundant revealed that one group of MAGs of Alistipes onderdonkii encodes the enzyme 2,5-diketo-D-gluconate reductase A. Using AL and DN together offers complementary functional insights, as the methods produce partially overlapping results. The novel enzyme finding suggests a potential role in metabolic pathways and underscores the value of integrative metagenomic analysis.},
}
@article {pmid41309379,
year = {2025},
author = {Kim, H and Jeon, HJ and Jeong, HM and Bang, WY and Lee, HB and Lee, KS and Moon, JS and Kwon, H and Lee, J and Yang, J and Jung, YH},
title = {Modulation of the Gut Microbiome and Metabolomes by Fermentation Using a Probiotic Complex in a Dysbiosis-Associated Fecal Model.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506014},
pmid = {41309379},
issn = {1738-8872},
mesh = {*Probiotics/pharmacology ; *Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Humans ; Fermentation ; *Feces/microbiology ; *Metabolome ; Inflammatory Bowel Diseases/microbiology ; Bifidobacterium/metabolism ; Lactobacillus/metabolism ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Streptococcus/metabolism ; },
abstract = {Inflammatory bowel disease (IBD), affecting up to 0.5% of the global population, is frequently associated with gut microbiota dysbiosis and metabolic imbalances, which contribute to chronic constipation and abdominal discomfort. This study investigated the modulatory effects of an eight-strain probiotic complex comprising Lactobacillus, Bifidobacterium, and Streptococcus species on the gut microbiome and metabolome using an in vitro fecal fermentation model derived from a single IBD patient with dysbiosis. Metagenomic analysis demonstrated that increased abundance of beneficial bacteria, such as Lacticaseibacillus rhamnosus, while suppressing opportunistic pathogens, such as Escherichia coli and Enterococcus faecium. Metabolomic profiling further revealed significant alterations in metabolite levels that may help alleviate gut dysbiosis-related symptoms. These included increases in 3-hydroxybutyric acid, ascorbic acid, cadaverine, L-hydroxyproline, and N-acetylornithine and decreases in lysine and 3-aminoalanine. Given the single-donor design and the use of technical replicates, findings are presented as preliminary and descriptive rather than confirmatory. Collectively, these findings support the potential of probiotic fermentation to modulate microbial composition and metabolic output in a dysbiosis-associated context.},
}
@article {pmid41308447,
year = {2025},
author = {Yang, Z and Chen, B and Zhang, Q and Hu, X and Sun, L and Lu, T and Zhu, L and Ma, Y and Zhong, H and Ni, Y and Qian, H},
title = {Potential of traditional Chinese medicine as an antibiotic alternative for mitigating antibiotic resistance: A case study of Tetrastigma hemsleyanum.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140613},
doi = {10.1016/j.jhazmat.2025.140613},
pmid = {41308447},
issn = {1873-3336},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology ; Mice ; *Drug Resistance, Microbial/drug effects/genetics ; Medicine, Chinese Traditional ; *Drugs, Chinese Herbal/pharmacology ; *Anti-Inflammatory Agents/pharmacology ; Lipopolysaccharides ; Male ; },
abstract = {The overuse of antibiotics in livestock production has accelerated the spread of antibiotic resistance genes (ARGs), posing a serious global public health threat. Identification of safe and effective alternatives to antibiotics has therefore become a research priority. Tetrastigma hemsleyanum (TH), a traditional Chinese medicine, modulates the intestinal microbiota; however, the mechanisms underlying its antibiotic-like effects are not fully understood. In this study, we investigated the anti-inflammatory effects of TH in a lipopolysaccharide-induced mouse model of intestinal inflammation. Metagenomic sequencing was used to evaluate its effects on intestinal microbiota composition and ARG abundance. TH effectively alleviated intestinal inflammation, significantly increased the abundance of beneficial microbes such as Lactobacillus, and suppressed the proliferation of major ARG-carrying pathogens, including Proteus and Shigella. Functional analysis revealed that TH treatment markedly enhanced the Wnt and TGF-β signaling pathways, which are associated with intestinal barrier repair and immune response regulation, respectively. Furthermore, TH supplementation restored ARG diversity, reduced the abundance of high-risk ARGs, and suppressed the spread of multidrug resistance genes, underscoring its potential for mitigating antibiotic resistance risks. These findings highlight the potential of TH as an alternative antibiotic and may be used as a feed additive to reduce antibiotic usage while enhancing animal health.},
}
@article {pmid41307726,
year = {2025},
author = {Ferreira, CM and de Affonseca, DB and Barbosa, FAS and Campos, AB and Menezes, R and Brait, L and Viana, PAB and Trindade-Silva, AE and Loiola, M and Azevedo, AR and Coutinho, FH and Assis, APA and Bruce, T and Ramos, PIP and Ara, A and Brouns, R and Andrade, RFS and Guimarães, PR and Meirelles, PM},
title = {Rare Phyla, Such as CPR and DPANN, Shape Ecosystem-Level Microbial Community Structure Dissimilarities.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {135},
pmid = {41307726},
issn = {1432-184X},
support = {88887-468244-2019-00//Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; 114693/2022-6//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; RYC2022-037094-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; Serra-1709-17818//Instituto Serrapilheira/ ; },
mesh = {*Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Microbiota ; *Ecosystem ; Metagenome ; Biodiversity ; Phylogeny ; Soil Microbiology ; },
abstract = {Rare microbial lineages, such as members of the candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, are increasingly recognized as key components of microbial communities in natural systems. Yet, their global distribution, biogeographic patterns, and broader role in shaping microbial community structure across diverse ecosystems remain poorly characterized. Here, we analyzed 2860 metagenomes spanning nine ecosystems using a curated reference database and a bias-aware taxonomic filtering approach to quantify the richness, relative abundance, and structural influence of low-abundance microbial taxa on community structure across a wide range of ecosystems. Our findings reveal that rare taxa, primarily CPR and DPANN, disproportionately shape microbial community dissimilarities across global ecosystems. We observed that the richness of these two groups, that drives community structure variation, increases with latitude, peaking in temperate regions, thereby contrasting classical latitudinal diversity patterns and suggesting unique biogeographic drivers. CPR and DPANN were predominantly enriched in free-living environments, particularly groundwater and soil, then in host-associated habitats, consistent with niche specialization shaped by environmental filtering and dispersal constraints. These findings challenge abundance-centric assumptions in microbial ecology and highlight the need to integrate low-abundance taxa into macroecological frameworks. Fully resolving their ecological functions, however, will require targeted experimental and multi-omics investigations.},
}
@article {pmid41307322,
year = {2025},
author = {Baima, G and Dabdoub, S and Thumbigere-Math, V and Ribaldone, DG and Caviglia, GP and Tenori, L and Fantato, L and Vignoli, A and Romandini, M and Ferrocino, I and Aimetti, M},
title = {Multi-Omics Signatures of Periodontitis and Periodontal Therapy on the Oral and Gut Microbiome.},
journal = {Journal of periodontal research},
volume = {60},
number = {12},
pages = {1237-1253},
pmid = {41307322},
issn = {1600-0765},
support = {CUP B83C22004800006//Next Generation EU/ ; DM 1557 11.10.2022//Next Generation EU/ ; Prot. P2022YEX5R//Next Generation EU Program and the Italian Ministry of University and Research/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Saliva/microbiology ; *Periodontitis/microbiology/therapy/metabolism ; Male ; Feces/microbiology ; Female ; Metabolomics ; Adult ; Middle Aged ; *Mouth/microbiology ; Multiomics ; },
abstract = {AIM: To characterize the impact of periodontitis and of Steps I-II of periodontal therapy on microbiome composition, function, and metabolic output across the oral and gut environments.<br><br>METHODS: A multi-omics analysis was performed on saliva and stool samples collected from 50 systemically healthy individuals with and without Stage III-IV periodontitis. For participants with periodontitis, samples were analyzed both at baseline and 3&#x2009;months after Steps I-II of periodontal therapy. High-throughput whole metagenome sequencing was used to profile microbial taxa and functional genes, NMR-based metabolomics profiled host-microbial metabolites. Single-omic differential abundance analysis between healthy samples and periodontitis samples was performed with MaAsLin2, while analysis between pre- and post-treatment was conducted with timeOmics. Variable selection and subsequent supervised multivariate analysis to determine group-separating markers utilized multi-level sparse Partial Least Squares Discriminant Analysis (sPLS-DA) through mixOmics. KEGG pathway enrichment was analyzed using clusterProfiler, whereas multi-omic data integration was performed with multi-block Partial Least Squares regression analysis.<br><br>RESULTS: Periodontitis was associated with significant compositional and functional changes in both saliva and stool, with increased abundance of pathobionts and loss of health-associated taxa in both niches. A subset of species was shared across oral and gut habitats, with detectable differences across clinical groups. As functional potential, periodontitis enriched microbial pro-inflammatory pathways (lipopolysaccharide biosynthesis, bacterial motility) and depleted beneficial short-chain fatty acid (SCFA)- and vitamin-producing functions. Metabolomic profiles revealed reduced SCFAs and amino acids in periodontitis, with elevated pro-inflammatory metabolites (succinate, trimethylamine) in both saliva and stool. Following therapy, microbial communities and their metabolic output partially reverted toward health-associated profiles, particularly in saliva. Stool samples showed subtler but consistent shifts, including a decrease in some typically oral species and decreased succinate and methylamine and restoration of amino acid and SCFA-related metabolites.<br><br>CONCLUSIONS: Periodontitis is associated with coordinated microbial and metabolic signatures across the oral and gut environments. Non-surgical periodontal therapy promotes partial ecological restoration in both niches, supporting the view of oral health as a modifiable target for influencing systemic microbial homeostasis.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov identification number: NCT04826926.},
}
@article {pmid41306589,
year = {2025},
author = {Yu, HL and Liu, R and Wang, HT and Hou, QY and Qin, Y and Yang, X and Gao, ZQ and Yang, LH and Zhao, Q and Ma, H},
title = {Metagenomic analysis of gut microbiota composition and function in wild mice (Rattus flavipectus) infected with Enterocytozoon bieneusi.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1708266},
pmid = {41306589},
issn = {2235-2988},
mesh = {Animals ; *Enterocytozoon ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Microsporidiosis/microbiology/veterinary ; Feces/microbiology ; Mice ; China ; Animals, Wild/microbiology ; Virome ; Bacteria/classification/genetics/isolation &amp; purification ; *Murinae/microbiology ; },
abstract = {BACKGROUND: Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that infects a variety of hosts, including wild mice, potentially influencing their gut microbiota. This study aims to explore how E. bieneusi infection influences the gut microbiota composition and function in wild mice.<br><br>METHODS: Fecal samples were collected from 20 wild mice (Rattus flavipectus) in September 2023 in Yunnan Province, China. The PCR results showed that 10 were infected with E. bieneusi and 10 were uninfected, with no samples testing positive for Cryptosporidium spp., Blastocystis, Giardia, Cyclospora or Balantioides coli. DNA was extracted and subjected to metagenomic sequencing using Illumina HiSeq. Gut microbiota composition was assessed using MetaPhlAn4 for species-level annotation. The contigs were used to construct a gene catalog and perform functional annotation. Additionally, viral sequences were identified by analyzing the contigs with software, such as CheckV and Vibrant.<br><br>RESULTS: The gut microbiota diversity showed no significant difference between mice infected with E. bieneusi and the control group, with the dominant phyla being Firmicutes and Bacteroidetes. Virome analysis identified 18,192 high-quality viral sequences, with the E. bieneusi group exhibiting higher viral species diversity. Furthermore, significant differences were observed in 178 viral operational taxonomic units (vOTUs) between the two groups, with 161 vOTUs enriched in the E. bieneusi group. Functional analysis demonstrated significant enrichment of several metabolic pathways in the gut microbiota of wild mice infected with E. bieneusi, particularly in the metabolism of terpenoids and polyketides, digestive system, biosynthesis of other secondary metabolites and metabolism of cofactors and vitamins. Notably, unique virus-bacteria correlations were observed in the E. bieneusi group.<br><br>CONCLUSIONS: E. bieneusi infection significantly alters the gut virome in wild mice, affecting microbial composition and interactions. The infection appears to drive adaptive changes in microbial functions, especially in metabolic processes, suggesting a host response to infection-related stress.},
}
@article {pmid41305578,
year = {2025},
author = {Rehner, J and Gund, M and Becker, SL and Hannig, M and Rupf, S and Schattenberg, JM and Keller, A and The Imagine Consortium, and Molano, LG and Keller, V},
title = {Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
pmid = {41305578},
issn = {2072-6643},
support = {469073465//DFG/ ; },
mesh = {Humans ; *Saliva/microbiology ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Mouth/microbiology ; Male ; Female ; Biomarkers/analysis ; Middle Aged ; Adult ; Dental Plaque/microbiology ; *Bacteria/isolation &amp; purification/classification/genetics ; Metagenome ; },
abstract = {Background: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. Methods: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen types (dental plaque (n = 143; 65 non-obese, 78 obese), saliva (n = 166; 75 non-obese, 91 obese), and stool (n = 109; 57 non-obese, 52 obese)) to compare site-specific microbial shifts between obese (BMI > 30 kg/m[2]) and non-obese individuals. Differential abundance was assessed with ANCOM-BC; effect sizes were summarized as Cohen's d. Results: Across all samples, we detected 240 bacterial species in plaque, 229 in saliva, and 231 in stool, with 46 species present across all three sites. Absolute effect sizes were significantly larger in plaque (mean |d| = 0.26) and saliva (0.25) than in stool (0.21; p = 9 × 10[-3]). Several taxa showed an opposite directionality between oral and gut sites, including Streptococcus salivarius and Bifidobacterium longum, indicating site-specific associations. Notably, Actinomyces sp. and Streptococcus sp. exhibited promising effect sizes as diagnostic markers. Conclusions: The oral and gut microbiomes capture complementary obesity-related signals, with stronger shifts observed in oral sites. We suggest that integrating oral and gut profiling could enhance diagnostic and therapeutic strategies in obesity.},
}
@article {pmid41305529,
year = {2025},
author = {Dong, Y and Fan, S and Zhu, L and Sharshov, K and Wang, W},
title = {Viromic Insights into Gut RNA Virus Diversity Among Three Corvid Species.},
journal = {Viruses},
volume = {17},
number = {11},
pages = {},
pmid = {41305529},
issn = {1999-4915},
support = {grant No. 2022-HZ-812//the program of science and technology international cooperation project of Qinghai province/ ; grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; },
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; Metagenomics ; *Crows/virology ; *Gastrointestinal Microbiome ; *Virome ; *Birds/virology ; Genome, Viral ; Tibet ; Genetic Variation ; },
abstract = {As viromics advances, the diversity and ecological significance of RNA viruses in global ecosystems are gaining growing recognition. Nevertheless, studies on RNA viruses in wildlife, especially non-model avian species, are still relatively scarce. This study employed viral metagenomics to systematically characterize the gut RNA viromes of three widely distributed corvid species on the Qinghai-Tibet Plateau: the Red-billed chough (Pyrrhocorax pyrrhocorax), Daurian jackdaw (Coloeus dauuricus), and Rook (Corvus frugilegus). These three corvid species are closely associated with human-inhabited areas on the Qinghai-Tibet Plateau and display distinctive scavenging behaviors that may lower their exposure to environmental pathogens while concurrently elevating their risk of viral infection, rendering them key targets for viral surveillance and research into zoonotic disease transmission. The analysis annotated viral communities into 4 phyla and 8 classes, with Pisuviricota and Kitrinoviricota emerging as the predominant phyla in all samples. Alpha diversity analysis indicated no significant differences among groups, while beta diversity showed significant compositional differences. KEGG annotation revealed that enriched functional pathways were mainly concentrated in "Global and overview maps", "Drug resistance: antimicrobial", and "Biosynthesis of other secondary metabolites". Furthermore, 4 antibiotic resistance genes and 13 putative virulence factor genes were identified. Phylogenetic analysis further indicated that several identified viruses have the potential for cross-species transmission, underscoring the pivotal role of wild birds in viral ecosystems and disease spread. This study uncovered multi-faceted features of the gut RNA viromes in the three crow species, spanning structural, functional, and evolutionary dimensions. These results offer novel perspectives on the viromes of wild corvids and their potential contributions to viral emergence and dissemination in the Qinghai-Tibet Plateau ecosystem.},
}
@article {pmid41305373,
year = {2025},
author = {Pham, TTN and Dao, TK and Nguyen, TVH and Phung, TBT and Nguyen, HD and Nguyen, TQ and Le, TTH and Do, TH},
title = {Diversity and Functional Predictions of Gut Microbiota in Vietnamese Children Aged 6-24 Months with Persistent Diarrhea of Unknown Etiology.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
pmid = {41305373},
issn = {2076-0817},
support = {&#x110;T&#x110;LCN.63/22//Ministry of Science and Technology/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; *Diarrhea/microbiology ; Male ; Female ; Feces/microbiology ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; *Bacteria/classification/genetics/isolation &amp; purification ; Vietnam ; Biodiversity ; DNA, Bacterial/genetics ; Metagenomics/methods ; Southeast Asian People ; },
abstract = {Persistent diarrhea remains a significant cause of morbidity in young children, yet the role of gut microbiota has not been fully clarified. This prospective study evaluated the diversity and predicted functions of the gut microbiota in 30 children aged 6-24 months with persistent diarrhea of unknown etiology (patient group, PG) and 30 healthy controls (healthy group, HG). Nearly full-length 16S rRNA genes from fecal bacterial metagenomic DNA were sequenced and taxonomically annotated. Subsequently, all downstream analyses, including diversity assessment, differential abundance and functional prediction analyses, and data visualization, were performed using R software (version 4.5.0, 2025). The PG showed lower Shannon and higher Simpson indices than the HG (p < 0.05), reflecting reduced microbial diversity. At the phylum level, Firmicutes predominated in the PG, whereas Actinobacteriota, Bacteroidota, and Verrucomicrobiota were more abundant in the HG (|log2FC| > 1 and FDR < 0.05). At the genus and species levels, the PG exhibited a marked depletion of essential commensals such as Bifidobacterium longum, Faecalibacterium, Lactobacillus, and Eubacterium, alongside an enrichment of opportunistic taxa including Klebsiella, Enterococcus lactis, and Streptococcus spp. (FDR < 0.05). Functional predictions using PICRUSt2 indicated an enrichment of carbohydrate metabolism and reductions in amino acid metabolism, B-vitamin pathways, and the biosynthesis of endogenous antibiotics (FDR < 0.05). These findings suggest that the PG harbors a dysbiotic gut microbiota characterized by reduced diversity, depletion of key commensal taxa, expansion of opportunistic bacteria, and potentially adverse shifts in metabolic functions.},
}
@article {pmid41304309,
year = {2025},
author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN},
title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
pmid = {41304309},
issn = {2076-2607},
support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; },
abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.},
}
@article {pmid41299763,
year = {2025},
author = {Manrique-de-la-Cuba, MF and López-Rodríguez, M and Abades, S and Trefault, N},
title = {Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {243},
pmid = {41299763},
issn = {2049-2618},
support = {Fondecyt 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; DG_02-22//Instituto Antartico Chileno/ ; },
mesh = {*Gene Transfer, Horizontal ; Animals ; Antarctic Regions ; *Microbiota/genetics ; *Porifera/microbiology/physiology ; Cold Temperature ; *Bacteria/genetics/classification/isolation &amp; purification ; Symbiosis ; *Adaptation, Physiological/genetics ; Seawater/microbiology ; Phylogeny ; Acclimatization ; },
abstract = {BACKGROUND: Marine sponges exhibit wide distribution in tropical, temperate, and polar environments. They host diverse microbiomes important to their survival and ecological roles. Antarctic sponges, thriving in extreme cold environments, harbor unique microbial communities. However, functional differences distinguishing Antarctic sponge microbiomes have been poorly investigated. In this study, we investigated how the functional composition of the microbiomes of Antarctic sponges differs from that of their counterparts in other environments, with a particular focus on functions related to cold adaptation. We also assessed the role of horizontal gene transfer (HGT) in driving these functional adaptations.<br><br>RESULTS: Antarctic sponge microbiomes displayed a unique functional signature characterized by significantly higher proportions of genes related to cold adaptation, such as cold shock proteins, chaperones, heat shock proteins, and osmoprotectants, compared to their tropical and temperate counterparts, and antioxidants compared to the surrounding seawater. HGT was prevalent in Antarctic sponge symbionts, particularly in the dominant Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia, contributing equally to metabolic functions and cold adaptation, with an important fraction of the latter exhibiting long-distance horizontal gene transfer (HGT). Conjugation, primarily mediated by integrative and conjugative elements (ICE), is a proposed crucial mechanism driving horizontal gene transfer (HGT) in Antarctic sponge symbionts. The cold shock protein C (CspC), linked to cold adaptation, was restricted to Proteobacteria and identified as a potential horizontally acquired gene exclusive to sponge symbionts compared to free-living bacteria in the Antarctic marine ecosystem.<br><br>CONCLUSIONS: Antarctic sponge microbiomes exhibit higher proportions of functional adaptations for cold environments facilitated by horizontal gene transfer (HGT). These findings highlight the evolutionary importance of HGT mechanisms in shaping microbial symbioses in extreme environments. Further exploration of HGT dynamics and the role of specific symbionts in cold adaptation could reveal novel insights into microbial evolution and host-symbiont interactions in polar ecosystems. Video Abstract.},
}
@article {pmid41299634,
year = {2025},
author = {Meawad, M and Singh, D and Deng, A and Sonthalia, R and Cai, E and Dumeaux, V},
title = {Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {241},
pmid = {41299634},
issn = {2049-2618},
support = {Vector Scholarship in Artificial Intelligence//Vector Institute/ ; Globalink Summer Internship Award//MITACS/ ; 391682//Natural Sciences and Engineering Research Council of Canada/ ; 43481//Canadian Foundation for Innovation J. Evans Leaders Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics/methods ; Adult ; Metagenome ; Female ; Male ; },
abstract = {BACKGROUND: Understanding the functional diversity of the gut microbiome is critical for elucidating its roles in human health and disease. While traditional approaches focus on taxonomic composition, functional configurations of the microbiome remain understudied. This study introduces a deep-learning framework combined with archetypal analysis to identify and characterize functional archetypes in the adult human gut microbiome. This approach aims to provide insights into interindividual variability, function-driven microbiome stability, and the potential confounding role of functional diversity in disease-associated microbial signatures.<br><br>RESULTS: Analyzing 9838 whole-genome metagenomic samples from healthy adults across 29 countries, we identified three distinct functional archetypes that define the boundaries of the gut microbiome's functional space. Each archetype is characterized by unique metabolic potentials: Archetype 1 is enriched in sugar metabolism, branched-chain amino acid biosynthesis, and cell wall synthesis; Archetype 2 is dominated by fatty acid metabolism and TCA cycle pathways; and Archetype 3 is defined by amino acid and nitrogen metabolism. While most gut microbiome communities are a blend of these archetypes, some align closely with a single archetype, potentially reflecting adaptation to host factors such as distinct dietary patterns. Proximity to these archetypes correlates with microbiome stability, with Archetype 2 representing the most resilient state, likely due to its metabolic flexibility and diversity. Functional archetypes emerged as a potential confounder in disease-associated microbial signatures, including in type-2 diabetes, colorectal cancer, and inflammatory bowel disease (IBD). In IBD, archetype-specific shifts were observed: Archetype 1-dominant samples exhibited increased carbohydrate metabolism, while Archetype 3-dominant samples showed enrichment in inflammatory pathways. These findings highlight the potential for archetype-specific functional changes to inform microbiome-targeted interventions.<br><br>CONCLUSIONS: The identified functional archetypes provide a robust framework for addressing interindividual variability and potential confounding in gut microbiome-based disease studies. By incorporating archetypes as potential confounders or stratification factors, researchers can reduce variability, uncover novel pathways, and improve the precision of microbiome-targeted interventions. The deep-learning framework can be applied to other host-associated microbial ecosystems, providing new insights into microbial functional dynamics and their implications for the host's health.},
}
@article {pmid41299624,
year = {2025},
author = {Zhang, XA and Zhang, MQ and Liu, YW and Lin, L and Zhang, JT and George, T and Jalloh, MB and Sevalie, S and Kargbo, KB and Jiang, BG and Mi, ZQ and Wang, SC and Si, GQ and Zhang, L and Fang, LQ and Chen, WW and Dong, G and Huang, WJ and Liu, W},
title = {Virome characterization of wild small mammals provides new insight into zoonotic pathogens in West Africa.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {242},
pmid = {41299624},
issn = {2049-2618},
support = {81825019//National Science Fund for Distinguished Young Scholars/ ; },
mesh = {Animals ; *Virome/genetics ; *Zoonoses/virology/transmission ; Metagenomics/methods ; Chiroptera/virology ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; Africa, Western ; Humans ; Shrews/virology ; Genome, Viral ; *Animals, Wild/virology ; Disease Reservoirs/virology ; *Mammals/virology ; Rodentia/virology ; *Viral Zoonoses/virology/transmission ; },
abstract = {BACKGROUND: A significant number of infectious diseases affecting humans have been associated with zoonotic viruses. Wild small mammals, such as bats, rodents, and shrews, serve as natural reservoirs for a multitude of zoonotic viruses, particularly in Africa, where zoonosis is prevalent. Nevertheless, our knowledge of the virome composition within these hosts remains limited, impeding a more profound understanding of spillover events into human populations.<br><br>RESULTS: We employed a viral metagenomics approach to characterize the virome in 846 wild small mammals sampled from Sierra Leone. Based on the complete RNA-dependent RNA polymerase genome, a total of 39 RNA viruses infecting mammals were identified, comprising 13 known viruses and 26 novel viruses. Notably, the Paramyxoviridae family exhibited the highest diversity of viral species across all three orders of wild mammal. The animal species Hipposideros jonesi and Lophuromys chrysopus were found to harbor the highest viral richness. Among these viral species, 15 were identified as cross-species transmitted viruses shared among different animal species, 3 were classified as zoonotic (Encephalomyocarditis virus, Rocahepevirus sp., and Lassa virus), while 3 others posed a potential risk for spillover (melian virus, Rodent hepacivirus, Hunnivirus A). Cross-species transmission analysis revealed that rodents played central roles in virus sharing, while cross-order viral transmission was less likely to occur in bats. Among 26 newly identified viruses, four viruses (Bat ledantevirus 2, Rattus rattus jeilongvirus, Miniopterus inflatus ribovirus, and Rat mamastrovirus) were predicted to have high zoonotic potential. Among them, Bat ledantevirus 2 exhibited the highest zoonotic potential and phylogenetic relatedness to the known human-infecting virus (Le Dantec virus). Further seroepidemiological analysis in patients, using single-round infectious virus particles as antigens, revealed the presence of neutralizing antibodies against Bat ledantevirus 2, a novel virus belonging to the Rhabdoviridae family.<br><br>CONCLUSIONS: These findings highlight the critical need for enhanced surveillance at the human-animal interface in order to identify viruses with cross-species transmission potential prior to their spillover into human population. Video Abstract.},
}
@article {pmid41299512,
year = {2025},
author = {Kansou, E and Aubry, A and Brochot, E and Priam, A and Cabry-Goubet, R and Bosquet, D and Demey, B},
title = {Human papillomavirus seminal carriage alters virome diversity and male fertility: a case-control study.},
journal = {Reproductive biology and endocrinology : RB&amp;E},
volume = {23},
number = {1},
pages = {154},
pmid = {41299512},
issn = {1477-7827},
mesh = {Humans ; Male ; Case-Control Studies ; *Virome/genetics ; Adult ; *Semen/virology ; Retrospective Studies ; *Papillomavirus Infections/virology/complications ; *Infertility, Male/virology ; *Papillomaviridae/genetics/isolation &amp; purification ; *Fertility/physiology ; Spermatozoa/virology ; Human Papillomavirus Viruses ; },
abstract = {BACKGROUND: A link between idiopathic male infertility and viral infections exhibiting seminal carriage has emerged recently. In this respect, human papillomavirus (HPV) appears to be the most prevalent sexually transmitted agent worldwide. The viruses present in the genital environment comprise the genital virome. HPV infection reportedly disrupts homeostasis of the virome in women but this topic has not previously been studied in men.<br><br>METHODS: This was a retrospective study of males attending the fertility clinic at Amiens University Medical Center (Amiens, France). Men with a multiple-type HPV infection in the sperm (n&#x2009;=&#x2009;15) were considered to be cases, and men with no detectable HPV in the sperm were considered to be controls (n&#x2009;=&#x2009;13). The molecular virome in cases and controls was described via metagenomic next-generation sequencing. The cases and controls were compared with regard to genomic, clinical and sperm-related characteristics.<br><br>RESULTS: The seminal virome analysis revealed the predominance of Papillomaviridae in cases (63.4%). Other virus families found in both groups (albeit with lower proportions of reads in cases than in controls) were Herpesviridae (6.9% vs. 40.5%, respectively), Polyomaviridae (11.3% vs. 17.8%, respectively), and other viral sequences (18.4% vs. 40%, respectively). There was no difference in viral diversity between the two groups (p&#x2009;=&#x2009;0.0692). Viral diversity was correlated with the semen sample volume, progressive sperm motility, total motility, and sperm vitality in cases but not in controls. Univariate and multivariate comparative analyses did not reveal significant differences in sperm parameters between cases and controls.<br><br>CONCLUSIONS: The male seminal virome mainly comprises viruses from the Papillomaviridae, Herpesviridae and Polyomaviridae families. The correlation between viral diversity and sperm parameters in HPV-positive patients suggests that HPV-specific interactions within the seminal virome are responsible for variations in sperm parameters. Hence, alterations in the seminal virome (due mostly to HPV infection) might impact sperm parameters and thus male fertility.},
}
@article {pmid41299176,
year = {2026},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Long-read metagenomics reveals phage dynamics in the human gut microbiome.},
journal = {Nature},
volume = {649},
number = {8098},
pages = {982-990},
pmid = {41299176},
issn = {1476-4687},
support = {R01 AI148623/AI/NIAID NIH HHS/United States ; U54 AG089334/AG/NIA NIH HHS/United States ; T32 GM007276/GM/NIGMS NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; S10 RR026780/RR/NCRR NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Bacteriophages/genetics/physiology/classification/isolation &amp; purification ; Prophages/genetics/physiology/isolation &amp; purification ; Feces/microbiology/virology ; *Bacteria/virology/genetics/classification ; Virus Integration ; Gene Transfer, Horizontal ; Male ; Female ; },
abstract = {Gut bacteriophages profoundly impact microbial ecology and health[1-3]; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations[4]. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain[5]. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.},
}
@article {pmid41298564,
year = {2025},
author = {Qu, T and Koch, L and Mukherjee, R and Tu, Y and Seidel, AL and Püttmann, LD and Winkel, A and Yang, I and Grischke, J and Liu, D and Wolkers, WF and Kittler, S and Chichkov, B and Stiesch, M and Szafrański, SP},
title = {Laser-assisted microbial culturomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10614},
pmid = {41298564},
issn = {2041-1723},
support = {German Cluster of Excellence Ex62/2 Rebirth//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR 298 SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2155 - project number 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Laser-Tissue-Perfude, 101054009//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {Biofilms/growth &amp; development ; Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification/classification/growth &amp; development ; *Lasers ; Dental Plaque/microbiology ; Bioprinting/methods ; Metagenomics/methods ; },
abstract = {Even though metagenomics have revolutionized the characterization of the human microbiome, detailed mechanistic studies are impracticable, as there is a dearth of robust culture collections. We now describe the development and use of a laser-assisted culturomics platform, incorporating the elements of a bioprinter, the culture conditions, the methods to characterize the microorganisms and a biobank. With laser-assisted bioprinting, the microorganisms can be rapidly and precisely transferred from clinical biofilms to highly organized arrays of microbial colonies, which are suitable for co-culturing and molecular analyses. The presented technique has propagated 99 of 100 microbial species and recovered 79% of abundant species from dental plaque in accordance with full 16S rRNA gene profiling of 691,199 sequences. Microscopy, spectroscopy and enzyme assays have been used to guide isolations. Processing of oral biofilms from four individuals has yielded 249 representative isolates, from 14 classes and 124 species in total. Functional profiling with bioprinting has indicated commensals which could potentially contribute to disease development. Isolates from peri-implantitis cover 85.4% of the transcriptionally active clinical biofilms at genus level. Taken together, this work provides the basis for generating on-demand culture collections and biofilms for research and clinical use.},
}
@article {pmid41298409,
year = {2025},
author = {Thorpe, AC and Busi, SB and Warren, J and Hunt, LH and Walsh, K and Read, DS},
title = {National-scale biogeography and function of river and stream bacterial biofilm communities.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10571},
pmid = {41298409},
issn = {2041-1723},
support = {SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015777/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015777/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; BB/X011089/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {*Biofilms/growth &amp; development ; *Rivers/microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; England ; Ecosystem ; Biodiversity ; Metagenomics ; Metagenome ; Microbiota/genetics ; Phylogeny ; },
abstract = {Biofilm-dwelling microorganisms coat the surfaces of stones in rivers and streams, forming diverse communities that are fundamental to biogeochemical processes and ecosystem functioning. Flowing water (lotic) ecosystems face mounting pressures from changes in land use, chemical pollution, and climate change. Despite their ecological importance, the taxonomic and functional diversity of river biofilms and their responses to environmental change are poorly understood at large spatial scales. We conducted a national-scale assessment of bacterial diversity and function using metagenomic sequencing from rivers and streams across England. We recovered 1,014 metagenome-assembled genomes (MAGs) from 450 biofilms collected across England's extensive river network. Substantial taxonomic novelty was identified, with ~20% of the MAGs representing novel genera. Here we show that biofilm communities, dominated by generalist bacteria, exhibit remarkable functional diversity and metabolic versatility, and likely play a significant role in nutrient cycling with the potential for contaminant transformation. Measured environmental drivers collectively explained an average of 71% of variation in the relative abundance of bacterial MAGs, with geology and land cover contributing most strongly. These findings highlight the importance of river biofilms and establish a foundation for future research on the roles of biofilms in ecosystem health and resilience to environmental change.},
}
@article {pmid41298355,
year = {2025},
author = {Holcik, L and von Haeseler, A and Pflug, FG},
title = {Genomic GC bias correction improves species abundance estimation from metagenomic data.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10523},
pmid = {41298355},
issn = {2041-1723},
mesh = {*Metagenomics/methods ; Humans ; Algorithms ; *Gastrointestinal Microbiome/genetics ; Base Composition/genetics ; Colorectal Neoplasms/microbiology ; *Metagenome ; Bacteria/genetics/classification ; Microbiota/genetics ; },
abstract = {Metagenomic sequencing measures the species composition of microbial communities and has revealed the crucial role of microbiomes in the etiology of a range of diseases such as colorectal cancer. Quantitative comparisons of microbial communities are, however, affected by GC-content-dependent biases. Here, we present GuaCAMOLE, a computational method to detect and remove GC bias from metagenomic sequencing data. The algorithm relies on comparisons between individual species in a single sample to estimate the sequencing efficiency at levels of GC content, and outputs unbiased species abundances. GuaCAMOLE thus works regardless of the specific amount or direction of GC-bias present in the data and does not rely on calibration experiments or multiple samples. Applying our algorithm to 3435 gut microbiomes of colorectal cancer patients from 33 individual studies reveals that the type and severity of GC bias vary considerably between studies. In many studies, we observe a clear bias against GC-poor species in the abundances reported by existing methods. GuaCAMOLE successfully removes this bias and corrects the abundance of clinically relevant GC-poor species such as F. nucleatum (28% GC) by up to a factor of two. GuaCAMOLE thus contributes to a better quantitative understanding of microbial communities by improving the accuracy and comparability of species abundances across experimental setups.},
}
@article {pmid41298327,
year = {2025},
author = {Wang, BW and Liu, YF and Chen, LG and Wang, B and Qian, ZH and Yang, F and Cai, JC and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ},
title = {Microbial Community Composition and Function in Jiangsu Oil Reservoir Cores, China.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70229},
pmid = {41298327},
issn = {1758-2229},
support = {52074129//National Natural Science Foundation of China/ ; 42061134011//National Natural Science Foundation of China/ ; 42173076//National Natural Science Foundation of China/ ; 42473082//National Natural Science Foundation of China/ ; 21ZR1417400//Natural Science Foundation of Shanghai Municipality/ ; JKJ01231714//Fundamental Research Funds for the Central Universities/ ; //Research Program of the State Key Laboratory of Bioreactor Engineering/ ; },
mesh = {China ; *Oil and Gas Fields/microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Petroleum/microbiology ; Hydrocarbons/metabolism/analysis ; *Microbiota ; Phylogeny ; Metagenomics ; },
abstract = {Shale oil reservoirs are typically characterised by elevated temperatures, confined spaces and oligotrophic conditions. Understanding the role of microorganisms in shale oil reservoirs is essential for elucidating biogeochemical cycles and the origins of life. However, the composition and metabolic functions of microbial communities in shale oil reservoirs remain elusive. In this study, shale core samples were collected from the HY1-1 and HY7 wells in the Jiangsu Oilfield. A combination of X-ray fluorescence, powder X-ray diffraction and scanning electron microscope analyses revealed that the samples contained various transition metals, abundant clay minerals and numerous pores with diameters greater than 1 μm. Fractionation of extracted crude oil fractions revealed that HY1-1 and HY7 contained 60% and 74% saturated hydrocarbons, primarily comprising C11-C35 n-alkanes. Various hydrocarbon-degrading microorganisms, including Marinobacter, Alcanivorax, Alkanindiges and Nocardioides were present in HY1-1 or HY7 samples. Metagenomic analysis showed the presence of genes associated with aerobic hydrocarbon degradation, denitrification and DNRA in the HY7 sample, suggesting that microorganisms may utilise crude oil for growth and participate in the subsurface carbon and nitrogen cycle. This study elucidates the microbial community structure and functional gene profiles in shale core samples, providing critical insights for harnessing in situ microorganisms in shale oil reservoir development.},
}
@article {pmid41298102,
year = {2026},
author = {Ammer-Herrmenau, C and Meier, R and Antweiler, KL and Asendorf, T and Cameron, S and Capurso, G and Damm, M and Dang, L and Frost, F and Hamm, J and Hoffmeister, A and Kocheva, Y and Meinhardt, C and Nawacki, L and Nunes, V and Panyko, A and Ruiz-Rebollo, ML and Flórez-Pardo, C and Phillip, V and Pukitis, A and Vaselane, D and Rinja, E and Sandru, V and Schaefer, A and Scholz, R and Seelig, J and Sirtl, S and Ellenrieder, V and Neesse, A},
title = {Gut microbiota predict development of postdischarge diabetes mellitus in acute pancreatitis.},
journal = {Gut},
volume = {75},
number = {2},
pages = {316-325},
pmid = {41298102},
issn = {1468-3288},
mesh = {Humans ; *Pancreatitis/complications/microbiology/mortality ; Male ; *Gastrointestinal Microbiome ; Female ; Middle Aged ; *Diabetes Mellitus/microbiology/etiology ; Prospective Studies ; Follow-Up Studies ; Aged ; Adult ; Acute Disease ; Disease Progression ; },
abstract = {BACKGROUND: Postdischarge morbidity and mortality is high in acute pancreatitis (AP) and pathophysiological mechanisms remain poorly understood.<br><br>OBJECTIVES: We aim to investigate the composition of gut microbiota and clinical long-term outcomes of prospectively enrolled patients with AP to predict postdischarge complications.<br><br>DESIGN: In this long-term follow-up study, we analysed clinical and microbiome data of 277 patients from the prospective multicentre Pancreatitis-Microbiome As Predictor of Severity trial. The primary endpoint was the association of the microbial composition with postdischarge mortality, recurrent AP (RAP), progression to chronic pancreatitis, pancreatic exocrine insufficiency, diabetes mellitus (DM) and pancreatic ductal adenocarcinoma.<br><br>RESULTS: Buccal (n=238) and rectal (n=249) swabs were analysed by 16S rRNA and metagenomics sequencing using Oxford Nanopore Technologies. Median follow-up was 2.8 years. Distance-based redundancy analysis with canonical analysis of principal coordinates showed significant differences for &#x3b2;-diversity (Bray-Curtis) for postdischarge mortality (p=0.04), RAP (p=0.02) and DM (p=0.03). A ridge regression model including 11 differentially abundant species predicted postdischarge DM with an area under the receiving operating characteristic of 94.8% and 86.2% in the matched and entire cohort, respectively. Using this classifier, a positive predictive value of 66.6%, a negative predictive value of 96% and an accuracy of 95% was achieved.<br><br>CONCLUSION: Our data indicate that the admission microbiome of patients with AP correlates with postdischarge complications independent from multiple risk factors such as AP severity, smoking or alcohol. Microbiota at admission show excellent capacity to predict postdischarge DM and may thus open new stratification tools for a tailored risk assessment in the future.<br><br>TRIAL REGISTRATION NUMBER: NCT04777812.},
}
@article {pmid41297753,
year = {2026},
author = {Zhong, Z and Ye, W and Li, B and Al-Dhabi, NA and Zhao, J and Li, S and Sun, Y and Zhang, H and Tang, W and Chen, S},
title = {Phosphate-iron modified Enteromorpha Prolifera hydrochar enhances dry anaerobic digestion of food waste: Synergistic mechanisms of electron transfer network, microbial consortia remodeling, and metagenomic insights.},
journal = {Environmental research},
volume = {289},
number = {},
pages = {123385},
doi = {10.1016/j.envres.2025.123385},
pmid = {41297753},
issn = {1096-0953},
mesh = {Anaerobiosis ; Iron/chemistry ; *Microbial Consortia ; Phosphates/chemistry ; *Ulva ; *Refuse Disposal/methods ; Electron Transport ; Metagenomics ; Solid Waste ; Food Loss and Waste ; Edible Seaweeds ; },
abstract = {The dual pressures of marine ecological disasters and urban solid waste treatment pose severe challenges to sustainable development. However, current research mostly focuses on single waste treatment, lacking coordinated governance strategies. This study innovatively proposes a "marine-urban" solid waste collaborative treatment strategy, converting Enteromorpha Prolifera into phosphate - iron composite modified hydrothermal carbon (P-MEPHC) via hydrothermal carbonization technology, and systematically analyzes its enhancement mechanisms in dry anaerobic digestion of food waste. Characterization results indicate that P-MEPHC possesses high electrical conductivity (488 S/m), a hierarchical mesoporous structure (BET specific surface area of 15.15 m[2]/g, average pore size of 10.57 nm), and abundant Fe-P-O active sites. Engineering verification showed that the addition of 52 mg/g VSS (volatile suspended solids) P-MEPHC increased the cumulative methane production to 99.25 mL/g VS (volatile solids), representing a 50.6 % improvement over the control group. Concurrently, the peak value of soluble chemical oxygen demand (SCOD) was elevated to 111.53 g/L, while the inhibition intensity of ammonia nitrogen was reduced by 32 %. Metagenomics indicated that it achieves process enhancement through dual regulatory mechanisms: at the community structure level, it enriches syntrophic acid-producing bacteria Sporanaerobacter (+7.9 %) and hydrogenotrophic methanogens Methanoculleus (+17.7 %); at the metabolic function level, it significantly upregulates the expression of core methanogenic metabolic genes such as acetyl-CoA synthase (ACSS1_2, +255 %), thereby activating the direct interspecies electron transfer pathway. This research provides a technically feasible paradigm with both environmental and economic benefits for the coordinated resource utilization of near - shore algal bloom biomass and organic solid waste, and promotes the closed - loop integration of blue carbon sinks and urban metabolic systems.},
}
@article {pmid41297516,
year = {2026},
author = {Xu, L and Zhang, J and Xiao, Y and Jin, P and Zhang, J},
title = {High-fat diet promotes colorectal tumorigenesis through gut microbiota-mediated metabolic reprogramming and M2 macrophage polarization.},
journal = {Biochemical and biophysical research communications},
volume = {794},
number = {},
pages = {153014},
doi = {10.1016/j.bbrc.2025.153014},
pmid = {41297516},
issn = {1090-2104},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Diet, High-Fat/adverse effects ; *Macrophages/pathology/metabolism/immunology ; *Colorectal Neoplasms/pathology/metabolism/microbiology/etiology ; Mice ; Mice, Inbred C57BL ; *Carcinogenesis/pathology/metabolism ; Male ; Metabolic Reprogramming ; },
abstract = {BACKGROUND: High-fat diet (HFD) drives colorectal cancer (CRC) progression through gut microbiota dysbiosis and M2 macrophage polarization, yet the microbiota-immunity crosstalk remains mechanistically unresolved.<br><br>METHODS: APC[min/+] (CRC model, n&#xa0;=&#xa0;8) and wild-type controls (n&#xa0;=&#xa0;7) received 12-weeks HFD. We employed integrated metagenomic sequencing (Illumina NovaSeq) and immunohistochemistry (targeting CD206+ M2 macrophages) to investigate the linkages between the gut microbiota and the host.<br><br>RESULTS: CRC mice exhibited colonic adenocarcinoma with increased M2 macrophages. Gut microbiota in CRC mice showed enrichment of pro-inflammatory taxa (e.g., Bacteroides massiliensis, Vampirovibrion) and upregulated pathways (carbohydrate metabolism, mucin degradation). Strikingly, the relative abundances of Bacteroides massiliensis and Vampirovibrion showed significant positive correlations with CD206+ M2 macrophage infiltration levels.<br><br>CONCLUSION: HFD induces microbiota-directed metabolic reprogramming and M2 polarization, synergistically accelerating CRC. Notably, targeting key pro-inflammatory taxa (e.g., B. massiliensis) or glycan hydrolysis pathways (e.g. GH95 enzyme) may provide mechanism-guided anti-CRC strategies.},
}
@article {pmid41297400,
year = {2025},
author = {Chen, S and Liu, Q and Li, D},
title = {Engineering the composting microbiome with a synthetic microbial community to accelerate lignocellulose degradation and humus synthesis.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128088},
doi = {10.1016/j.jenvman.2025.128088},
pmid = {41297400},
issn = {1095-8630},
mesh = {*Lignin/metabolism ; *Composting ; *Microbiota ; Manure ; Cattle ; Animals ; Bacteria ; },
abstract = {Bioaugmentation with synthetic microbial communities (SynComs) presents a promising engineering strategy to overcome the bottleneck of lignocellulose recalcitrance in organic waste valorization. However, the mechanisms by which SynComs modulate indigenous microbial networks and steer metabolic fluxes remain elusive. Here, we deconstruct these mechanisms by investigating the impact of a rationally designed five-member bacterial-fungal SynCom on the co-composting of cattle manure and mulberry branches. Through an integrated multi-omics approach, we reveal that SynCom inoculation acts as a potent ecological engineer, accelerating the process by significantly elevating pile temperatures and shortening the maturation period by accelerating entry into the maturation phase by approximately 7 days. Compared with the control, the SynCom treatment enhanced the overall degradation rates of lignin, cellulose, and hemicellulose by 19.3 %, 7.9 %, and 12.0 %, respectively, and boosted humus content by 34.4 %. Metagenomics revealed that the SynCom profoundly restructured the native microbiome, enriching for key functional genera such as Thermobifida and Actinomadura. This engineered community possessed an enhanced genetic toolkit, with a significantly increased abundance of crucial carbohydrate-active enzymes (CAZymes), including cellulases (GH5, GH12), hemicellulases (CE1, CE3), and lignin-modifying auxiliary activity enzymes (AA1, AA6). Untargeted metabolomics further identified a distinct metabolic footprint in the SynCom treatment, characterized by the enrichment of key humification precursors like protocatechuic acid and sinapic acid. Integrated Procrustes and correlation analyses confirmed a tight coupling between the engineered microbiome, its functional gene repertoire and metabolic output. This study deciphers the multi-layered mechanism by which a designed SynCom enhances biowaste valorization and provides a mechanistic blueprint for engineering microbial consortia for advanced biotechnology applications in sustainable agriculture.},
}
@article {pmid41297255,
year = {2025},
author = {Lindstedt, K and Osińska, A and Bargheet, A and Sørum, H and Wick, RR and Holt, KE and Pettersen, VK and Sundsfjord, A and Wasteson, Y},
title = {Microbiota and resistome dynamics in untreated and treated wastewater: A ten-month study leveraging RNA-probe capture and subspecies-level metagenomics.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140566},
doi = {10.1016/j.jhazmat.2025.140566},
pmid = {41297255},
issn = {1873-3336},
mesh = {*Wastewater/microbiology ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; *Microbiota ; Humans ; Norway ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; },
abstract = {Wastewater is regarded as a hotspot for the acquisition and dissemination of antimicrobial resistance genes (ARGs) in bacteria, and wastewater treatment plants are key sites for studying and monitoring these phenomena. This study employed metagenomic approaches, with and without targeted ARG enrichment, to investigate the composition and dynamics of the microbiota, resistome, and mobilome in untreated (UWW) and treated (TWW) wastewater from a full-scale treatment plant serving municipal and hospital wastewater in Oslo, Norway. Over a ten-month period, we observed that wastewater treatment led to a significant reduction in the relative abundance of human gut-associated bacterial species and total load of coliform bacteria, alongside an increase in environmental bacterial taxa. This shift correlated with a significant reduction in the relative abundance and richness of ARGs and mobile genetic elements. Despite this, the effect of treatment on the relative abundance of key AMR-associated pathogens was highly inconsistent. Further subspecies analysis revealed several Escherichia coli and Klebsiella pneumoniae lineages persisted in UWW and TWW over multiple months, suggesting stable colonization and survival despite treatment processes. Targeted RNA probe-hybridisation enrichment detected clinically important ARGs in both UWW and TWW samples, including genes encoding extended-spectrum β-lactamases, carbapenemases, glycopeptide resistance, and colistin resistance. Most of these were undetectable by shotgun metagenomics alone, demonstrating the strength of this technique in high-sensitivity ARG surveillance. These findings highlight the value of combined metagenomic methods in wastewater AMR surveillance, the potential for monitoring high-risk bacterial lineages, and high-sensitivity detection of clinically important ARGs, in a low AMR prevalence setting.},
}
@article {pmid41297254,
year = {2025},
author = {Hatwar, N and Qureshi, A},
title = {Biodegradation of PVC by novel bacterial consortia isolated from municipal solid waste dumpsite.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140589},
doi = {10.1016/j.jhazmat.2025.140589},
pmid = {41297254},
issn = {1873-3336},
mesh = {*Polyvinyl Chloride/metabolism ; Biodegradation, Environmental ; Waste Disposal Facilities ; *Bacteria/metabolism/genetics/isolation &amp; purification ; *Microbial Consortia ; Solid Waste ; Soil Microbiology ; Refuse Disposal ; },
abstract = {In view of environmental issues related to Polyvinyl chloride (PVC), attempts have been made in the present study, to enrich and isolate novel bacteria from landfill dumpsites, capable of degrading PVC with reduced emissions. A potential bacterial consortium (NH_AQ) was designed, which comprised of Lysinibacillus spp., Bacillus spp., Staphylococcus spp., Exiguobacterium spp., and Arthrobacter spp. Metagenomic analysis of landfill soils indicated predominance of these bacterial species, which ensured that the culturable bacteria could be isolated from landfill sites for PVC degradation. This study was carried out at three temperatures (ambient, 37°C and 50°C). The percentage weight reduction of PVC films was 31.45 % ± 2 at 37°C. SEM-EDX showed external erosion and changes in chemical element composition, due to growth of bacteria as biofilms on PVC films at 37 °C. FTIR study confirmed oxidation and dechlorination happening during PVC utilization. TGA analysis indicated PVC thermal shifts in presence of consortia and ion chromatography too showed a significant reduction in chlorine content. Overall findings demonstrated that the designed NH_AQ consortium could degrade PVC effectively, offering a promising and sustainable approach to mitigate PVC pollution through microbial action in future.},
}
@article {pmid41297027,
year = {2026},
author = {Palanisamy, H and Vidyalakshmi, S},
title = {Deciphering the interrelation of gut microbiota and BMI in atherosclerosis: a metagenomic approach.},
journal = {Canadian journal of microbiology},
volume = {72},
number = {},
pages = {1-12},
doi = {10.1139/cjm-2025-0075},
pmid = {41297027},
issn = {1480-3275},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Atherosclerosis/microbiology ; *Body Mass Index ; Metagenomics ; Obesity/microbiology/complications ; Male ; Female ; Middle Aged ; Aged ; Metagenome ; Bacteria/classification/genetics/isolation &amp; purification ; Dysbiosis/microbiology ; Overweight/microbiology ; },
abstract = {Atherosclerotic cardiovascular disease (ASCVD) is a global health concern, leading to higher rates of morbidity and mortality. Gut microbial dysbiosis significantly contributes to obesity related ASCVD. However, the interrelation of gut microbiome in driving obesity or overweight mediated ASCVD has not been sufficiently investigated. To unravel this complex interplay, we have compared the gut microbial shotgun metagenome data of ASCVD subjects across normal BMI (Body Mass Index) and overweight/obese (OW/OB) BMI categories. We identified a distinct gut microbial composition and function in normal and OW/OB ASCVD subjects. Using gut microbial abundance, a machine learning model was built to predict ASCVD in the normal and OW/OB samples. The gut microbiome-based signature for ASCVD discrimination was achieved with an AUC of 0.87 and 0.83 for distinguishing control and ASCVD in normal and OW/OB BMI groups, respectively. In addition, we have also identified that Pseudoflavonifractor capillosus could act as a prognostic organism in identifying OW/OB associated ASCVD. Therefore, an appropriate diet could modify the ASCVD contributing gut microbiome, hence minimizing the risk of ASCVD in OW/OB individuals.},
}
@article {pmid41294355,
year = {2025},
author = {O'Connor, JB and Fouquier, J and Neff, CP and Sterrett, JD and Marden, T and Fiorillo, S and Siebert, JC and Schneider, J and Nusbacher, N and Noe, AT and Fennimore, B and Higgins, J and Campbell, TB and Palmer, BE and Lozupone, C},
title = {Agrarian diet improves metabolic health in HIV-positive men with Prevotella-rich microbiomes: results from a randomized trial.},
journal = {mSystems},
volume = {10},
number = {12},
pages = {e0118525},
pmid = {41294355},
issn = {2379-5077},
support = {T15 LM009451/NH/NIH HHS/United States ; T15 LM009451/LM/NLM NIH HHS/United States ; R01DK108366,R01DK131581/NH/NIH HHS/United States ; R01 DK131581/DK/NIDDK NIH HHS/United States ; UM1 TR004399/TR/NCATS NIH HHS/United States ; R01 DK108366/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; Male ; *Prevotella/isolation &amp; purification ; *HIV Infections/microbiology/metabolism ; Middle Aged ; Adult ; *Gastrointestinal Microbiome ; Feces/microbiology ; Homosexuality, Male ; },
abstract = {UNLABELLED: This study aimed to assess the impact of a high-fiber/low-fat agrarian diet (AD) on inflammation and metabolic outcomes in HIV-positive men who have sex with men (MSM). Since the gut microbiomes of MSM resemble those of individuals in agrarian cultures, including being Prevotella-rich and Bacteroides-poor, we hypothesized that they would have particularly strong health benefits from consumption of a diet matched to their microbiome type. Sixty-six participants, including 36 HIV-positive MSM [HIV(+)MSM], 21 HIV-negative MSM, and 9 HIV-negative men who have sex with women, were randomized to either an AD or a high-fat/low-fiber western diet (WD) for 4 weeks. Plasma, fecal, and colonic biopsy samples were obtained. Metabolic and inflammatory markers were measured in plasma. 16S ribosomal RNA sequencing was performed on fecal and biopsy samples, and shotgun metagenomic sequencing was performed on fecal samples. The AD reduced plasma low-density lipoprotein cholesterol (LDL-C) in HIV(+)MSM, with median reductions of 0.4138 mmoL/L at 2 weeks and 0.2845 mmol/L at 4 weeks. Greater LDL-C reductions were predicted by Prevotella-rich/Bacteroides-poor microbiomes with increased starch utilization potential, emphasizing the importance of personalized microbiome-dietary matching. The AD also reduced T cell exhaustion and pro-inflammatory intermediate monocytes and altered host transcription in the colonic mucosa.<br><br>IMPORTANCE: Our findings suggest tailoring diet interventions to baseline microbiome types can promote metabolic health in Prevotella-rich/Bacteroides-poor MSM, a significant portion of people living with HIV at risk for metabolic syndrome.This study was registered at NCT02610374.},
}
@article {pmid41291881,
year = {2025},
author = {Binod, M and Chang, L and Hung, MW and Dong, TS and Kilpatrick, LA and Tomasevic, A and Choy, M and Shin, A and Mayer, EA and Church, A},
title = {Multi-omics analysis reveal clinical-gut-brain interactions in female ibs patients with adverse childhood experiences.},
journal = {Biology of sex differences},
volume = {16},
number = {1},
pages = {101},
pmid = {41291881},
issn = {2042-6410},
support = {R01 MD015904/GF/NIH HHS/United States ; T32 DK007180/DK/NIDDK NIH HHS/United States ; R01 MD015904/MD/NIMHD NIH HHS/United States ; U54 DK123755/GF/NIH HHS/United States ; U54 DK123755/DK/NIDDK NIH HHS/United States ; T32DK007180/GF/NIH HHS/United States ; },
mesh = {Humans ; Female ; *Irritable Bowel Syndrome/physiopathology/microbiology/psychology/diagnostic imaging ; *Adverse Childhood Experiences ; *Gastrointestinal Microbiome ; Adult ; *Brain/diagnostic imaging/physiopathology ; Middle Aged ; *Brain-Gut Axis ; Magnetic Resonance Imaging ; Young Adult ; Multiomics ; },
abstract = {BACKGROUND: The brain-gut system, which involves bidirectional communication between the central nervous system and the gut, plays a central role in stress responses. Its dysregulation is implicated in irritable bowel syndrome (IBS), a stress-sensitive, female-predominant disorder characterized by abdominal pain and altered bowel habits. Adverse childhood experiences (ACE) increase the risk and severity of IBS, likely by amplifying stress responsiveness and gut-brain dysfunction in females. However, the mechanisms involved are unknown.<br><br>AIM: This study aimed to identify a multi-omic signature linking ACE exposure to IBS females via clinical, neuroimaging, and gut microbiome features as compared to healthy control (HC) females.<br><br>METHODS: Data was analyzed from participants with Rome positive IBS and HCs. Four subgroups were created based on IBS diagnosis and ACE score with high ACE defined as &#x2265;2 and low as ACE 0-1. Validated questionnaires assessed clinical variables. Biological markers included multimodal brain MRI, and gut microbial function using metagenomics. eXtreme gradient boosting (XGBoost) identified key differentiating features between the groups. Connectograms visualized relationships across mutli-omics data within each group.<br><br>RESULTS: Among 188 female participants, the four groups included IBS with high ACE (n=37), IBS with low ACE (n=55), HCs with high ACE (n=19), and HCs with low ACE (n=77). Key findings include: 1. High ACE participants with IBS versus their HC counterparts showed increased depression and anxiety symptoms, GI-symptom related anxiety, perceived stress, somatic symptom severity, and poorer physical and mental health scores. 2. High ACE participants with IBS had negative associations between key bacteria such as Akkermansia (a beneficial bacteria) and somatic symptom severity, and between Bifidobacterium and ACE parental divorce/separation and alterations in the salience and central autonomic networks. 3. The ensemble model accurately distinguished IBS patients with high ACE (AUC of 0.87), demonstrating strong predictive performance with an overall model accuracy of 78%.<br><br>CONCLUSIONS: Our findings highlight the unique microbiota and brain networks contributing to a complex interplay of chronic stress as measured by early life adversity, the brain-gut-microbiome system, and IBS pathophysiology which can inform therapeutic targets aimed at mitigating the long-term impacts of early life stress in female IBS patients.},
}
@article {pmid41291216,
year = {2025},
author = {Jurado, J and Garcia-Vega, A and Vasquez, Y and Villegas-Plazas, M and Roldan, F},
title = {Field-Scale AMD Remediation: Microbial Community Dynamics and Functional Insights in Biochemical Passive Reactors.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {8},
pmid = {41291216},
issn = {1432-184X},
mesh = {Biodegradation, Environmental ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Bioreactors/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Sulfates/metabolism ; Coal Mining ; Water Pollutants, Chemical/metabolism ; },
abstract = {Acid mine drainage (AMD) generated during coal mining activities is characterized by low pH, high concentrations of dissolved metals and metalloids, and elevated sulfate levels, all of which significantly impact surrounding ecosystems. Scaling up biochemical passive reactor (BPR) systems represents a promising approach for the in situ bioremediation of AMD. While numerous laboratory-scale studies have described the taxonomic and functional composition of microbial communities in BPRs, typically dominated by (ligno)cellulolytic organisms and sulfate-reducing bacteria (SRB), it remains unclear whether this composition is maintained at the field-pilot scale under environmental conditions. To address this gap, 16S rRNA gene metabarcoding and shotgun metagenomics analyses were performed to characterize the taxonomic and functional diversity of microbial communities in the BPRs within a multi-unit field-pilot system. The results revealed that bioremediation effectiveness was driven by syntrophic interactions among hydrolytic, fermentative, and sulfate-reducing bacteria, aligning with laboratory-scale observations. While community composition shifts altered specific taxa, core operational dynamics remained preserved.},
}
@article {pmid41291200,
year = {2025},
author = {Zha, Y and Fan, L and Shen, T and Zhang, Y and Ren, H},
title = {Triptolide ameliorates LPS-induced acute lung injury in Balb/c mice through gut-lung axis-mediated regulation of bile acid metabolism and gut microbiota.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {45351},
pmid = {41291200},
issn = {2045-2322},
support = {PW2022A-21//the Scientific Research Program of Shanghai Pudong New Area Health Commission/ ; },
mesh = {Animals ; *Diterpenes/pharmacology/therapeutic use ; *Acute Lung Injury/drug therapy/chemically induced/metabolism/pathology ; *Phenanthrenes/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Epoxy Compounds/pharmacology/therapeutic use ; *Bile Acids and Salts/metabolism ; Mice ; Lipopolysaccharides/toxicity ; *Lung/metabolism/drug effects/pathology ; Mice, Inbred BALB C ; Male ; Disease Models, Animal ; Metabolomics ; Cytokines/metabolism ; },
abstract = {Acute lung injury (ALI) associated with pulmonary edema is a severe clinical condition characterized by acute inflammation, disrupted lung barrier function, and high mortality. Current therapeutic strategies remain limited, highlighting the need for exploring novel agents and their underlying mechanisms. Triptolide (TP), an active component derived from Tripterygium wilfordii, has shown anti-inflammatory and tissue-protective properties[1,2], but its specific role in alleviating ALI and the involvement of the lung-gut axis in metabolic regulation remain poorly understood. This study aims to investigate the therapeutic effects of TP on LPS-induced ALI, focusing on its impact on pulmonary edema and inflammatory injury. By analyzing the lung-gut axis using multi-omics approaches, we seek to clarify the metabolic network regulatory mechanisms through which TP exerts its effects. LPS-induced ALI model was established in Balb/c mice, with TP administered as the therapeutic intervention. Histopathological examination of lung tissues and detection of pro-inflammatory cytokines were performed to assess lung injury. Untargeted metabolomics via LC-MS/MS was used to identify differential metabolites in lung tissues and serum, while metagenomic sequencing analyzed changes in gut microbiota composition. Integrated multi-omics analysis was applied to explore associations between gut microbiota alterations, serum metabolites, and pulmonary bile acid levels. TP administration significantly reduced histopathological damage in lung tissues of ALI mice and decreased pro-inflammatory cytokine levels. Metabolomics profiling revealed distinct changes in key metabolites, including bile acids, amino acid derivatives, and energy metabolism intermediates, in both lung tissues and serum after TP treatment. Metagenomic analysis showed that TP restructured gut microbiota composition, with functional enrichment in glycolysis and thiamine metabolism pathways. Integrated analysis confirmed strong correlations between dynamic microbiota changes, serum metabolite profiles, and pulmonary bile acid levels, indicating a regulatory role of the lung-gut axis. This study demonstrates that TP alleviates pulmonary edema and inflammatory injury in ALI by modulating gut microbial ecology and function, which drives bile acid metabolic reprogramming and regulates metabolite interactions within the lung-gut axis. These findings provide novel insights into TP's therapeutic mechanism and support its potential application in ALI treatment.},
}
@article {pmid41291018,
year = {2025},
author = {Angwong, C and Pientong, C and Ekalaksananan, T and Burassakarn, A and Tongchai, P and Overgaard, HJ and Aromseree, S},
title = {Systematic review and meta-analysis of virome profiles and quantification of Torque teno virus load in blood of acute febrile illness patients.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {45340},
pmid = {41291018},
issn = {2045-2322},
support = {IN66039//Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand/ ; },
mesh = {Humans ; *Torque teno virus/genetics/isolation &amp; purification ; *Viral Load ; *DNA Virus Infections/virology/epidemiology/blood ; *Fever/virology/blood ; *Virome ; Anelloviridae/genetics ; Thailand/epidemiology ; },
abstract = {Acute febrile illness (AFI) is a sudden fever which can be caused by various viruses such as dengue, Zika, and chikungunya viruses. This study aimed to identify viruses present in AFI patients via metagenomic next-generation sequencing (mNGS) through meta-analysis, and to compare the prevalence and viral load of the common viruses between AFI patients and healthy blood donors in northeastern Thailand. Our meta-analysis revealed that human anelloviruses-including torque teno virus (TTV), torque teno mini virus (TTMV), and torque teno midi virus (TTMDV)-were the most prevalent viruses detected. We confirmed their presence in peripheral blood mononuclear cells from 203 AFI patients and 100 healthy blood donors using real-time PCR. TTV was the most identified anellovirus, detected in 84% of healthy donors and 61.08% of AFI patients. The mean TTV load was significantly lower in AFI patients compared to healthy donors. In AFI patients, TTV load increased in those with higher total white blood cell and neutrophil counts but decreased in those with higher lymphocyte counts. Our findings demonstrate high prevalence of anelloviruses, particularly TTV, in both AFI patients and healthy donors, and highlight the potential value of the TTV load in blood as an immune status biomarker in AFI patients.},
}
@article {pmid41290854,
year = {2025},
author = {Chauhan, A and Chukwujindu, C and Pathak, A and Jaswal, R},
title = {A survey of bacterial and fungal community structure and functions in two long-term metalliferous soil habitats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41955},
pmid = {41290854},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification ; *Fungi/genetics/classification ; *Soil Pollutants/analysis ; Mercury/analysis ; Ecosystem ; *Microbiota ; Soil/chemistry ; Metagenomics ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Mercury contamination at legacy nuclear sites such as the Savannah River Site and Oak Ridge Reservation poses persistent ecological risks, yet its impact on soil microbiomes remains incompletely understood. This study integrates qPCR, 16S/ITS amplicon sequencing, and shotgun metagenomics to assess bacterial and fungal community structure, diversity, and functional potential across gradients of total mercury, methylmercury, and bioavailable mercury. Bacterial α-diversity declined with increasing Hg levels, while fungal diversity remained stable and highest in low-contamination soils. Dominant bacterial phyla included Pseudomonadota, Bacteroidota, Bacillota, Acidobacteriota, and Actinomycetota; fungal communities were primarily Ascomycota and Basidiomycota. Canonical correspondence analysis revealed distinct taxon-Hg speciation linkages, and functional gene profiling showed enrichment of stress-response genes, membrane transporters, and phosphate metabolism pathways in contaminated soils. Notably, bioavailable Hg did not correlate directly with total Hg, underscoring the importance of speciation in microbial exposure. These findings highlight the adaptive plasticity of native microbiomes and identify microbial taxa and pathways relevant to bioremediation and can guide ecosystem restoration activities in Hg-impacted soil habitats.},
}
@article {pmid41290836,
year = {2025},
author = {Brito, LFC and Althouse, GC and Pitta, DW and Indugu, N and Sarmiento, MP and Balamurugan, NS},
title = {Temporal dynamics of the resistome in gilts raised in an organic operation in which semen used for artificial insemination is the primary source of antimicrobial exposure.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {41935},
pmid = {41290836},
issn = {2045-2322},
mesh = {Animals ; *Insemination, Artificial/veterinary/methods ; *Semen/microbiology ; Swine ; Female ; Male ; Feces/microbiology ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Metagenomics ; },
abstract = {Natural bacterial contaminants in boar semen make it necessary to use preservative-level antibiotics in semen extenders to ensure long-term sperm viability and artificial insemination (AI) success. While concerns exist about the role of semen extender antibiotics in antimicrobial resistance (AMR), empirical evidence is lacking. This study examined microbiome and resistome dynamics in fecal samples of gilts from an organic farming operation, where AI is the primary source of antimicrobial exposure. Metagenomics was used to analyze microbial communities and antibiotic resistance genes (ARGs) across quarantine, breeding pen introduction, and post-AI production phases. The fecal microbiome was dominated by Bacillota and Bacteroidota. Microbial shifts were likely due to environmental and dietary adaptation, with no major changes observed post-AI. Among 168 identified ARGs, 89% were linked to drug resistance, primarily targeting tetracyclines, aminoglycosides, and macrolides, lincosamides and streptogramins (MLS). The abundance of most ARGs decreased between arrival at the operation and 10 days after introduction into the breeding pen, with no major resistome changes post-AI. Neither exposure to previously inseminated females nor antibiotics in semen extenders increased fecal ARGs. This study found no evidence that rational antibiotic use in swine semen extender contributes to increased antimicrobial resistance in the swine fecal microbiome.},
}
@article {pmid41290716,
year = {2025},
author = {Caesar, L and Barksdale, C and Valiati, VH and Newton, I},
title = {Spatial segregation and cross-kingdom interactions drive stingless bee hive microbiome assembly.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11620},
pmid = {41290716},
issn = {2041-1723},
support = {2022049//National Science Foundation (NSF)/ ; 2005306//National Science Foundation (NSF)/ ; },
mesh = {Bees/microbiology/physiology ; Animals ; *Microbiota/genetics/physiology ; Symbiosis ; Pollination ; Bacteria/genetics/classification/isolation &amp; purification ; Metagenomics ; Hydrogen-Ion Concentration ; Fungi/genetics/classification ; },
abstract = {Studying host-associated microbiome assembly is key to understanding microbial and host evolution and health. While honey bee microbiome have been a central model for such investigations among pollinators, they overlook the diversity of eusocial dynamics and multi-kingdom interactions. Stingless bees-a diverse group of highly eusocial insects that includes managed species, varies in colony biology, and harbors a symbiotic yeast essential for larval development in at least one species-offer a valuable complementary system to study microbiome assembly under an eco-evolutionary context. Using amplicon sequencing, metagenomics, and microbial experiments, we investigate the drivers of microbiome assembly in stingless bee colonies. We reveal a spatially structured, site-adapted microbiome, where high microbial influx hive components are segregated from the brood, which harbors a stable, multi-kingdom community. We show that the brood microbiome is not only physically protected but also maintained through selective bacterial-fungal interactions and abiotic conditions shaped by bees and their symbionts, such as temperature and pH. Our findings uncover multi-layered mechanisms shaping eusocial superorganism microbiomes, from host biology to cross-kingdom interactions, while providing critical insights into microbiome maintenance of important pollinators.},
}
@article {pmid41290652,
year = {2025},
author = {Lin, ZL and Gao, SM and Peng, SX and Tang, LY and Luo, ZH and Lao, XW and Zhang, SY and Shu, WS and Meng, F and Huang, LN},
title = {Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10492},
pmid = {41290652},
issn = {2041-1723},
mesh = {*Geologic Sediments/virology/microbiology ; Genome, Viral/genetics ; China ; Virome/genetics ; Metagenomics ; Mining ; Metagenome ; Phylogeny ; Ecosystem ; Acids ; *Host Microbial Interactions ; },
abstract = {The CPR and DPANN superphyla are globally distributed in anoxic habitats including extreme environments. However, the biogeography and potential ecological functions of their viruses remain unexplored. Here, we recover diverse CPR/DPANN metagenomic viral genomes from 90 acid mine drainage (AMD) sediments sampled across southeast China. Our data reveal deterministic processes as the primary driver of virome assembly shaping the distinct distribution patterns of CPR and DPANN viruses. While lifestyle prediction shows higher lytic virus diversity associated with DPANN, both CPR/DPANN viruses likely use the Piggyback-the-winner (PtW) strategy to co-exist with hosts in AMD sediments, with CPR viromes exhibiting increased lysis in low host-density regimes under intensive acidity/salinity conditions. A subsequent metatranscriptomic analysis uncovers diverse functional genes encoded by CPR and DPANN viruses actively expressed in situ, potentially supplementing host metabolisms yet diverging in replication, transcription, and translation-related functions. Furthermore, partial correlation network analysis suggests that putative symbiotic hosts of the CPR/DPANN may confer protection against viral infection through enhanced antiviral defense. Our results highlight the complex interplays between viruses, DPANN and CPR organisms, and their symbiotic hosts.},
}
@article {pmid41289388,
year = {2025},
author = {Wang, Y and Chang, HW and Cheng, J and Webber, DM and Lynn, HM and Hibberd, MC and Kao, C and Mostafa, I and Ahmed, T and Barratt, MJ and Gordon, JI},
title = {Using gnotobiotic mice to decipher effects of gut microbiome repair in undernourished children on tuft and goblet cell function.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {48},
pages = {e2523178122},
pmid = {41289388},
issn = {1091-6490},
support = {K01DK134840/GF/NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; K01 DK134840/DK/NIDDK NIH HHS/United States ; INV016367//Bill and Melinda Gates Foundation (GF)/ ; DK30292//HHS | NIH (NIH)/ ; INV-016367/GATES/Gates Foundation/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; *Goblet Cells/metabolism/physiology ; *Germ-Free Life ; Female ; Humans ; *Malnutrition/microbiology ; Child ; },
abstract = {Studies have implicated perturbations in the postnatal development of the gut microbiome as a contributing factor to childhood undernutrition. Compared to a standard ready-to-use supplementary food, a microbiome-directed complementary food (MDCF-2) designed to repair these perturbations produced superior improvements in ponderal and linear growth in clinical trials of Bangladeshi children with moderate acute malnutrition. Here, "reverse translation" experiments are performed where intact fecal microbiomes collected from trial participants before and at the end of treatment are introduced into female gnotobiotic mice just after delivery of their pups. Pups received diets designed to resemble those consumed by children in the trials to recreate "unrepaired" and "repaired" gut ecosystems. Analyses of the abundances of bacterial strains (metagenome-assembled genomes), their expressed genes, and metabolic products, combined with assessments of ponderal growth and intestinal epithelial lineage transcriptomes (single-nucleus RNA-Seq with follow-up immunocytochemistry) disclosed effects of MDCF-2 associated microbiome repair that cannot be determined, in part because "no treatment" control arms cannot be ethically incorporated into these trials. Specifically, microbiome repair in these mice produced significant increases in ponderal growth, changes in microbial gene expression consistent with a less virulent gut ecosystem and alterations in expression of i) components of cell junctions in the enterocytic and goblet cell lineages, ii) pathways for synthesis and secretion of eicosanoid immune effectors in chemosensory tuft cells, and iii) goblet cell pathways involved in glycosylation and secretion of mucin. Experiments of the type described can help formulate and test hypotheses about how microbiome repair affects host biology.},
}
@article {pmid41289310,
year = {2025},
author = {Zhao, JX and Zheng, WB and Xie, SC and Ma, H and Chen, XT and Gao, YQ and Tang, LY and Yang, MT and Nan, FL and Jiang, J and Elsheikha, HM and Zhang, XX},
title = {Toxoplasma gondii disrupts intestinal microbiota and host metabolism in a rat model.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {11},
pages = {e0013768},
pmid = {41289310},
issn = {1935-2735},
mesh = {Animals ; *Gastrointestinal Microbiome ; Rats, Sprague-Dawley ; Rats ; *Toxoplasma/physiology ; Disease Models, Animal ; Male ; Metabolomics ; *Toxoplasmosis/metabolism/parasitology/microbiology ; *Toxoplasmosis, Animal/metabolism/microbiology/parasitology ; },
abstract = {Toxoplasma gondii infection disrupts the gut microbiota and host systemic metabolism, which plays a key role in the pathophysiology of toxoplasmosis. To investigate these interactions, we conducted metagenomic sequencing and untargeted serum metabolomics on 18 Sprague-Dawley rats across control, acute, and chronic stages of infection. De novo assembly of 148 Gb of high-quality reads produced a comprehensive non-redundant microbial gene catalog comprising over 5.7 million genes. Infection led to a marked reduction in microbial diversity and significant shifts in community structure. Chronic infection, in particular, was characterized by the enrichment of Lactobacillus johnsonii, Lactobacillus intestinalis, and Limosilactobacillus reuteri, alongside a marked depletion of Akkermansia muciniphila and Rothia nasimurium. These compositional changes coincided with reduced abundance of carbohydrate-active enzymes, suggesting impaired microbial metabolic capacity. Pathway analysis revealed distinct, stage- and gut-region-specific metabolic disruptions, including suppressed amino acid and energy metabolism, and enhanced glycan and carbohydrate pathways during chronic infection. Untargeted LC-MS/MS profiling uncovered 883 differentially abundant serum metabolites, enriched in pathways related to amino acid metabolism, bile acid transformation, and aromatic compound processing. Importantly, L. johnsonii and L. reuteri were positively correlated with metabolites implicated in immune modulation and oxidative stress response, whereas A. muciniphila showed negative associations. These findings demonstrate that T. gondii infection orchestrates a coordinated host-microbiota-metabolome network, advancing our understanding of disease mechanisms and pointing to novel microbial and metabolic targets for therapy.},
}
@article {pmid41288100,
year = {2026},
author = {van Dam, F and Westmeijer, G and Rezaei Somee, M and Ketzer, M and Kietäväinen, R and Ono, S and Bertilsson, S and McIntosh, JC and Dopson, M and Drake, H},
title = {Active methylotrophic methanogenesis by a microbial consortium enriched from a terrestrial meteorite impact crater.},
journal = {mBio},
volume = {17},
number = {1},
pages = {e0301725},
pmid = {41288100},
issn = {2150-7511},
mesh = {*Methane/metabolism/biosynthesis ; *Meteoroids ; Sweden ; *Microbial Consortia ; Bacteria/metabolism/classification/genetics ; Metagenomics ; Phylogeny ; Archaea/metabolism/genetics ; },
abstract = {Microbial methane generation (methanogenesis) is an important metabolic process in the terrestrial deep biosphere and is an analog to early Earth as it is proposed to be one of the most ancient metabolisms on Earth. Signs of methanogenesis in meteorite impact craters are of particular interest in this respect as these settings are proposed hot spots for deep microbial colonization of the upper crust. Yet, reports of active deep rock-hosted methanogenesis are scarce, particularly for methylotrophic methanogenesis, while reports from terrestrial meteorite impact craters are completely lacking. Here, we used indigenous communities in cultures enriched from 400-m deep fluids to confirm and characterize active methane production from several carbon donors, including indigenous oil, in a terrestrial impact crater at Siljan, Sweden. Metagenomic and metatranscriptomic data of the methane-producing cultures revealed a consortium dominated by Acetobacterium sp. KB-1 and Candidatus Methanogranum gryphiswaldense, mediating methanogenesis solely via the methyl-reduction pathway, and resulting in a δ[13]Cmethanol-methane isotope enrichment of up to 98.6‰. These results provide insights into methylotrophic methanogenesis in deep subsurface environments in general, and in particular in fractured meteorite impact structures.IMPORTANCEThis study revealed that microbes enriched from groundwater in a 380-m deep borehole within the Siljan meteorite impact crater in Sweden were capable of producing methane, a key greenhouse gas. This is especially significant because it is the first proof of active methanogens in an impact crater and showing a specific pathway of methane production-methylotrophic methanogenesis-is present in the deep terrestrial subsurface, an environment that is typically hard to study. These findings shed light on life in extreme conditions on Earth and show that meteorite craters can be biological hotspots, rich with ancient life processes.},
}
@article {pmid41286929,
year = {2025},
author = {Liu, J and Wang, M and Xu, C and Jia, L and Lai, S and Zhang, ZC and Zhang, J and Chen, WH and Yang, YT and Zhao, XM},
title = {HGMT: a database of human gut microbiota for tumors and immunotherapy response.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {401},
pmid = {41286929},
issn = {1474-760X},
support = {2024YFA0918500//National Key Research and Development Program of China/ ; 2023YFF1204800//National Key Research and Development Program of China/ ; 24JS2810100//Shanghai Science and Technology Commission Program/ ; 23JS1410100//Shanghai Science and Technology Commission Program/ ; 24KXZNA11//Shanghai Municipal Education Commission/ ; T2225015//National Natural Science Foundation of China/ ; ZDYF2024SHFZ058//Key Science and Technology Project of Hainan Province/ ; GZNL2024A01003//Major Project of Guangzhou National Laboratory/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Immunotherapy ; *Neoplasms/therapy/microbiology ; Metagenomics ; },
abstract = {HGMT is a database designed to analyze, explore, and visualize gut microbiomes from diverse tumor types. We process metagenomic datasets from 18,630 stool samples across 37 tumor types, including 2,207 samples from immunotherapy-treated patients across 12 tumor types. HGMT provides an interactive portal for querying taxonomic and functional profiles, visualizing cross-dataset differential abundance taxa in tumors, and identifying their pan-tumor associations. Our analysis reveals the capability of gut microbiota in diagnosing gastrointestinal tumors and predicting immunotherapy response for non-small cell lung carcinoma. HGMT represents a valuable resource for investigating the roles of gut microbiota in tumors and immunotherapy response.},
}
@article {pmid41286799,
year = {2025},
author = {Lawrence, K and Fibert, P and Toribio-Mateas, M and Gregory, AM and Hobbs, J and Quadt, F and Wright, S and Cotter, PD and Patel, S and Myrissa, K},
title = {Effects of kefir on symptoms, sleep, and gut microbiota in children with ADHD: a randomised controlled trial.},
journal = {BMC psychiatry},
volume = {25},
number = {1},
pages = {1117},
pmid = {41286799},
issn = {1471-244X},
mesh = {Humans ; Child ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; Double-Blind Method ; Adolescent ; *Kefir ; *Sleep ; Attention ; Severity of Illness Index ; },
abstract = {BACKGROUND: Evidence indicates the gut microbiome may be altered in ADHD, suggesting that targeting gut bacteria could alleviate symptoms. This study examined the effects of kefir supplementation on ADHD symptoms, sleep, attention, and gut microbiome composition in children diagnosed with ADHD.<br><br>METHODS: A six-week, randomised, double-blind, placebo-controlled trial was conducted in UK children aged 8-13&#x2009;years with ADHD. Participants were assigned either to a daily kefir or placebo drink group. The primary outcome was ADHD symptom severity measured by the Strengths and Weaknesses of ADHD Symptoms and Normal Behaviour (SWAN) scale. Secondary outcomes included gut microbiota composition (analysed using shotgun metagenomic sequencing), gastrointestinal symptoms, sleep (actigraphy, parent/self-report), attention and impulsivity.<br><br>RESULTS: Fifty-three participants (mean age&#x2009;=&#x2009;10.2&#x2009;years, SD&#x2009;=&#x2009;1.7) completed the study. Kefir had no significant overall effect on parent or teacher-rated ADHD symptom severity. A non-significant interaction was observed between baseline symptom severity and group for teacher-rated SWAN scores, with children in the kefir group who had the highest baseline ADHD symptoms showing lower scores at week six (M&#x2009;=&#x2009;2.03, SE&#x2009;=&#x2009;0.33 vs. 2.86, SE&#x2009;=&#x2009;0.34), p&#x2009;=&#x2009;0.088. Actigraphy revealed the kefir group spent fewer minutes awake during the down period at week six (M&#x2009;=&#x2009;70.10, SE&#x2009;=&#x2009;0.09) than the placebo group (M&#x2009;=&#x2009;89.72, SE&#x2009;=&#x2009;0.07), p&#x2009;=&#x2009;0.04. However, the kefir group self-reported more sleep problems post-intervention (M&#x2009;=&#x2009;39.81, SE&#x2009;=&#x2009;0.75 vs. 37.40, SE&#x2009;=&#x2009;0.65), p&#x2009;=&#x2009;0.02. For Go/NoGo RT variance, a non-significant interaction (p&#x2009;=&#x2009;0.052) between baseline and post intervention scores was found. No other significant group differences were observed. Kefir supplementation did not significantly affect gut microbiota alpha or beta diversity. However, relative abundance of several species including bifidobacterium adolescentis, B. infantis, and B. longum and Alistipes sp021204515 and A. timonensi increased significantly in the kefir group.<br><br>CONCLUSIONS: Kefir supplementation may support modest improvements in sleep quality, in children with ADHD. These findings contribute to our understanding of the potential role of nutrition in ADHD management and may inform clinical guidance for practitioners working with neurodivergent individuals.<br><br>ETHICS: Ethical approval for the study was granted by St Mary's University Ethics Committee.<br><br>TRIAL REGISTRATION: The trial protocol has been prospectively registered with ClinicalTrials.gov: NCT05155696. Registered on 13 December 2021.},
}
@article {pmid41285810,
year = {2025},
author = {Neugent, ML and Hulyalkar, NV and Ghosh, D and Saenz, CN and Zimmern, PE and Shulaev, V and De Nisco, NJ},
title = {Urinary biochemical ecology reveals microbiome-metabolite interactions and metabolic markers of recurrent urinary tract infection.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {216},
pmid = {41285810},
issn = {2055-5008},
support = {F32 DK128975/DK/NIDDK NIH HHS/United States ; R01 DK131267/DK/NIDDK NIH HHS/United States ; F32DK128975/NH/NIH HHS/United States ; R01DK131267/NH/NIH HHS/United States ; },
mesh = {Humans ; *Urinary Tract Infections/microbiology/urine/diagnosis ; Female ; *Microbiota ; Biomarkers/urine ; Recurrence ; Metabolomics ; *Urinary Tract/microbiology ; Metagenomics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Urine/microbiology/chemistry ; Adult ; Middle Aged ; Deoxycholic Acid/urine ; },
abstract = {Recurrent urinary tract infections (rUTIs) are a major clinical challenge, and their increasing prevalence underscores the need to define host-microbiome interactions underlying susceptibility. How the urinary microbiota engages with the biochemical environment of the urogenital tract is yet to be fully defined. Here, we leverage paired metagenomic and quantitative metabolomic data to establish a microbe-metabolite association network of the female urinary microbiome and define metabolic signatures of rUTI. We observe unique metabolic networks of uropathogens and uroprotective species, highlighting potential metabolite-driven ecological shifts influencing rUTI susceptibility. We find distinct metabolites associated with urinary microbiome diversity and identify a lipid signature of active rUTI that accurately distinguishes our cases from controls. Finally, we identify deoxycholic acid as a prognostic indicator for UTI recurrence. Together, these findings provide insight into microbiome-metabolite interactions within the female urinary tract and highlight potential biomarkers for the development of new diagnostic tools to improve patient outcomes.},
}
@article {pmid41285752,
year = {2025},
author = {Schulz, F and Yan, Y and Weiner, AKM and Ahsan, R and Katz, LA and Woyke, T},
title = {Single-cell genomics reveals complex microbial and viral associations in ciliates and testate amoebae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10336},
pmid = {41285752},
issn = {2041-1723},
support = {R15 HG010409/HG/NHGRI NIH HHS/United States ; },
mesh = {Single-Cell Analysis/methods ; Symbiosis/genetics ; *Amoeba/virology/microbiology/genetics ; *Microbiota/genetics ; Metagenomics/methods ; *Ciliophora/virology/microbiology/genetics ; Bacteria/genetics/classification ; Genomics/methods ; Giant Viruses/genetics ; Phylogeny ; Viruses/genetics/classification ; },
abstract = {Protists play important roles in nutrient cycling across ecosystems, yet the composition and function of their associated microbiomes remain poorly studied. Here, we use cultivation-independent single-cell isolation and genome-resolved metagenomics to investigate the microbiomes and viromes of more than 100 uncultivated ciliates and amoebae from diverse environments. Our findings reveal unique microbiome structures and complex associations with bacterial symbionts and viruses, with stark differences between ciliates and amoebae. We recover 117 microbial genomes affiliated with known eukaryotic endosymbionts, including Holosporales, Rickettsiales, Legionellales, Chlamydiae, and Babelota, and 258 genomes linked to host-associated Patescibacteriota. Many show genome reduction and genes related to toxin-antitoxin systems and nucleotide parasitism, indicating adaptation to intracellular lifestyles. We also identify more than 80 giant viruses from diverse lineages, some actively expressing genes in single-cell transcriptomes, along with other viruses predicted to infect eukaryotes or symbiotic bacteria. The frequent co-occurrence of giant viruses and microbial symbionts, especially in amoebae, suggests multipartite interactions. Together, our study highlights protists as hubs of microbial and viral associations and provides a broad view of the diversity, activity, and ecological importance of their hidden partners.},
}
@article {pmid41285454,
year = {2026},
author = {Safika, S and Nisa', C and Supratikno, and Cahyadi, DD},
title = {Gut microbiota profiling of Javan pangolin (Manis javanica).},
journal = {The Journal of veterinary medical science},
volume = {88},
number = {1},
pages = {191-195},
doi = {10.1292/jvms.25-0036},
pmid = {41285454},
issn = {1347-7439},
mesh = {Animals ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Pangolins/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Female ; },
abstract = {Chitin digestion in pangolins and other anteaters is thought to be aided by commensal bacteria in the digestive tract, in addition to their chitinase. This study characterized the gut microbiota of captive Javan pangolins using amplicon sequencing. Fecal samples were collected from two individuals and were sampled twice over one week. The dominant bacterial phyla identified were Firmicutes (Bacillota), Bacteroidetes (Bacteroidota), Proteobacteria (Pseudomonadota), and Actinobacteria (Actinomycetota). The most prevalent genera included Clostridium, Bacteroides, Lactobacillus, Bifidobacterium, Streptococcus, and Sporosarcina. Alpha and beta diversity were relatively low between paired samples, but the short sampling interval limits conclusions about microbial stability. These findings provide insights into the Javan pangolin's gut microbiota and support future research on microbial contributions to their digestion, health, and conservation.},
}
@article {pmid41285255,
year = {2026},
author = {Wang, S and Ma, G and Qi, C and Cheng, S and Lai, H and Zhou, L and Wu, G and Chen, Z and Mao, X and Jing, T and He, Y and Zhou, H},
title = {Trimethylamine-N-oxide disrupts spermatogenesis by inducing mitochondrial oxidative stress injury through Hippo signaling.},
journal = {Free radical biology &amp; medicine},
volume = {243},
number = {},
pages = {452-465},
doi = {10.1016/j.freeradbiomed.2025.11.052},
pmid = {41285255},
issn = {1873-4596},
mesh = {Male ; Animals ; *Mitochondria/metabolism/drug effects/pathology ; *Oxidative Stress/drug effects ; Humans ; Mice ; *Methylamines/metabolism/blood ; *Spermatogenesis/drug effects ; Hippo Signaling Pathway ; Signal Transduction/drug effects ; Testis/metabolism/drug effects/pathology ; Leydig Cells/metabolism/drug effects ; *Protein Serine-Threonine Kinases/metabolism/genetics ; Adult ; Spermatozoa/drug effects/metabolism/pathology ; Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; },
abstract = {BACKGROUND: The gut-testis axis is increasingly recognized as a regulator of male reproductive health; however, the key microbial contributors, metabolites, and underlying mechanisms remain unclear.<br><br>METHODS: We performed fecal metagenomic sequencing in 107 participants to identify microbial taxa associated with abnormal semen parameters. Serum trimethylamine-N-oxide (TMAO) levels were measured and correlated with semen quality. In mouse models, including fecal microbiota transplantation, dietary choline supplementation, mono-colonization, and direct TMAO administration, we assessed sperm morphology, testicular androgen synthesis, and testicular histology. Testicular transcriptomics, in vitro Leydig cell assays, and mitochondrial function analyses were conducted to investigate the effects of TMAO on Hippo signaling, oxidative phosphorylation, mitochondrial membrane damage, and steroidogenesis.<br><br>RESULTS: Choline-to-trimethylamine converting bacteria, including Phocaeicola massiliensis, Veillonella spp., and Klebsiella pneumoniae, were enriched in men with abnormal semen parameters. Circulating TMAO levels were inversely associated with semen volume, total sperm count, and motile sperm count. In mouse models, elevated TMAO induced testicular dysfunction characterized by impaired sperm morphology, reduced testicular androgen synthesis, and histological abnormalities. Consistently, gene set enrichment analysis (GSEA) of testicular transcriptomes revealed significant suppression of mitochondrial translation, membrane integrity, oxidative phosphorylation, and adenosine triphosphate (ATP) metabolism. TMAO also suppressed steroidogenesis by reducing the expression of steroidogenic acute regulatory protein (StAR). Mechanistic studies in TM3 Leydig cells further demonstrated that TMAO, by promoting Yap phosphorylation, disrupted mitochondrial structure and morphology, decreased mitochondrial membrane potential, increased mitochondrial reactive oxygen species (ROS) levels, impaired ATP synthesis, and promoted mitochondrial fragmentation with upregulation of the mitochondrial fission molecule (Fis1).<br><br>CONCLUSIONS: Our findings demonstrate that TMAO activates Hippo signaling to induce mitochondrial dysfunction and suppress testosterone synthesis, thereby impairing spermatogenesis. These results highlight TMAO biosynthesis and its downstream signaling as potential therapeutic targets for improving male fertility.},
}
@article {pmid41283667,
year = {2025},
author = {Zhang, J and Meng, F and Sun, Y and Xu, W and Wu, S and Su, X},
title = {Phylo-Spec: a phylogeny-fusion deep learning model advances microbiome status identification.},
journal = {mSystems},
volume = {10},
number = {12},
pages = {e0145325},
pmid = {41283667},
issn = {2379-5077},
support = {2021YFF0704500//National Key Research and Development Program of China/ ; 32070086//National Natural Science Foundation of China/ ; //Taishan Scholar Project of Shandong Province/ ; //Shandong Talents Team Cultivation Plan of University Preponderant Discipline/ ; },
mesh = {*Deep Learning ; *Phylogeny ; Humans ; *Microbiota/genetics ; Algorithms ; },
abstract = {The human microbiome is crucial for health regulation and disease progression, presenting a valuable opportunity for health state classification. Traditional microbiome-based classification relies on pre-trained machine learning (ML) or deep learning (DL) models, which typically focus on microbial distribution patterns, neglecting the underlying relationships between microbes. As a result, model performance can be significantly affected by data sparsity, misclassified features, or incomplete microbial profiles. To overcome these challenges, we introduce Phylo-Spec, a phylogeny-driven deep learning algorithm that integrates multi-aspect microbial information for improved status recognition. Phylo-Spec fuses convolutional features of microbes within a phylogenetic hierarchy via a bottom-up iteration and significantly alleviates the challenges due to sparse data and inaccurate profiling. Additionally, the model dynamically assigns unclassified species to virtual nodes on the phylogenetic tree based on higher-level taxonomy, minimizing interferences from unclassified species. Phylo-Spec also captures the feature importance via an information gain-based mechanism through the phylogenetic structure propagation, enhancing the interpretability of classification decisions. Phylo-Spec demonstrated superior efficacy in microbiome status classification across two in silico synthetic data sets that simulate the aforementioned cases, outperforming existing ML and DL methods. Validation with real-world metagenomic and amplicon data further confirmed the model's performance in multiple status classification, establishing a powerful framework for microbiome-based health state identification and microbe-disease association. The source code is available at https://github.com/qdu-bioinfo/Phylo-Spec.IMPORTANCEThe human microbiome profoundly influences health and disease, but current computational tools often overlook the evolutionary relationships among microbes, leading to incomplete or inaccurate interpretations of complex microbial data. Phylo-Spec provides a new way to understand the microbiome by combining microbial abundance, taxonomy, and phylogeny within a unified deep learning framework. This model not only improves the accuracy of health status classification but also highlights key microbial contributors linked to disease. By capturing both microbial diversity and evolutionary context, Phylo-Spec bridges the gap between bioinformatics and biological insight, offering a powerful and interpretable approach for advancing microbiome-based diagnostics and precision medicine.},
}
@article {pmid41282988,
year = {2025},
author = {Jia, S and Gu, W and Jiang, L and Zhang, Y and Fu, X and Yin, J and Zhou, Y},
title = {Effect of rainfall on metagenomics in a sewage environment in Hongta District, Yuxi city, Yunnan Province.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20199},
pmid = {41282988},
issn = {2167-8359},
mesh = {*Sewage/microbiology/virology ; China ; *Metagenomics ; *Rain ; Bacteria/genetics/classification/isolation &amp; purification ; *Microbiota ; Archaea/genetics/isolation &amp; purification ; },
abstract = {BACKGROUND: Hongta District of Yuxi city is located in the central region of Yunnan Province, Southwest China. Previous studies have shown a high prevalence of enteric infectious diseases in the area, which may be related to sewage discharge. However, there has been no systematic analysis of the microbiome in sewage in this area. In this study, we investigated environmental sewage in Hongta District, Yuxi city, Yunnan Province.<br><br>METHODS: Surveillance was conducted in Hongta District, Yuxi city, for a period of one year. At both its urban and rural sites, sewage samples were collected for metagenomic sequencing.<br><br>RESULTS: The results revealed that in the sewage samples, bacteria accounted for 98.31% of the total microbiome, followed by Archaea (1.05%), Viruses (0.30%) and Eukaryota (0.34%). At the phylum level, Proteobacteria was the taxon with the highest relative abundance, accounting for 57.57% of all samples, followed by Firmicutes (17.17%), Bacteroidetes (12.23%), Actinobacteria (7.10%), and Synergistetes (1.45%). At the genus level, the taxa with the highest relative abundances of all the microbiomes were Acidovorax (6.63%), Pseudomonas (4.98%), Acinetobacter (4.23%), Comamonas (3.85%), and Aliarcobacter (2.78%). The diversity of the samples grouped by site and rainfall formed their own clusters, but only the compositions of different taxa grouped by rainfall significantly differed (P&#xa0;=&#xa0;0.038 at the family, P&#xa0;=&#xa0;0.019 at the genus and P&#xa0;=&#xa0;0.005 at the species level). In general, the abundance of several taxa at the family, genus and species levels in the dry season group was higher (P&#xa0;<&#xa0;0.05) than that in the rainy season group according to the Kruskal-Wallis test. The relative abundance s of most virulence genes were higher at urban sites than at rural sites, while those in the rainy season was higher than those in the dry season. The distribution of antibiotic resistance genes (ARGs) in urban and rural sewage was significantly different (P&#xa0;=&#xa0;0.018). The relative abundance of multidrug resistance genes in urban sewage was higher than that in rural sewage, and the relative abundance of most resistance genes in the dry season group was higher than that in the rainy season group.<br><br>CONCLUSIONS: In general, the abundance and distribution features of the sewage microbial communities in the Hongta District of Yuxi city were affected by site and rainfall factors, with significant regional and temporal specificity. Strengthening the surveillance of environmental sewage and improving discharge methods are highly important for ensuring public health security.},
}
@article {pmid41282978,
year = {2025},
author = {Han, X and Liu, H and Bai, X and Li, D and Wang, T and Zhong, H and Yao, Y and Sun, J},
title = {Insights into antibiotic resistomes from metagenome-assembled genomes and gene catalogs of soil microbiota across environments.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20348},
pmid = {41282978},
issn = {2167-8359},
mesh = {*Soil Microbiology ; *Metagenome ; China ; *Microbiota/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects ; Metagenomics ; },
abstract = {Antibiotic resistance poses a significant global health threat, and soil is recognized as a critical reservoir for antibiotic resistance genes (ARGs). To investigate soil microorganisms in the areas where both humans and common domestic animals (such as pigs and chickens) are present and active. In this study, we employed metagenomic sequencing to investigate the soil resistome across four Chinese provinces-Yunnan, Guizhou, Sichuan, and Jiangsu. From 111 soil samples, we generated metagenome-assembled genomes (MAGs) and gene catalogs to analyze microbial community composition, ARG distribution, and mobile genetic elements (MGEs). Our results revealed notable regional differences in microbial communities and ARG profiles. Pseudomonadota and Actinomycetota were the dominant phyla across samples, and ARG abundance was significantly higher in Sichuan, Yunnan, and Jiangsu compared to Guizhou. We also identified microbial taxa likely serving as ARG vectors, suggesting potential for horizontal gene transfer. Functional annotation indicated that metabolic functions, particularly carbohydrate and amino acid metabolism, were predominant, which may be associated with the composition of organic matter in the soil environment. Multidrug resistance genes are widespread in soil microbial communities and may spread through food chains or soil-water-plant systems, posing potential ecological and public health risks. MGEs showed significant regional variation and play a key role in the horizontal spread of ARGs. Together, these findings provide new insights into the soil antibiotic resistome and offer a foundation for developing targeted strategies to manage environmental antibiotic resistance.},
}
@article {pmid41278541,
year = {2025},
author = {Khannous-Lleiffe, O and Fuentes-Palacios, D and Májer, D and Gabaldón, T},
title = {MeTAline: enabling reproducible and scalable metagenomic analyses.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf158},
pmid = {41278541},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Software ; Metagenome ; Microbiota/genetics ; Reproducibility of Results ; Computational Biology/methods ; },
abstract = {The taxonomic and functional characterization of microbial communities inhabiting a given niche can elucidate associations between the microbiota and relevant variables, including health and disease. As compared to metabarcoding, shotgun metagenomic sequencing, which analyzes all DNA present in a sample, offers superior taxonomic resolution and additionally enables the inference of functional capabilities encoded within the microbial community of interest. However, this approach requires the use of diverse computational tools and substantial computational resources. Here, we present MeTAline, a bioinformatics pipeline for the analysis of shotgun metagenomics data. Implemented in Snakemake, MeTAline provides an efficient and reproducible workflow encompassing read trimming and filtering, host read removal, taxonomic classification via both k-mer and gene marker-based methodologies, and extensive functional annotation. Containerization in Docker and Singularity ensures ease of installation, portability, and reproducibility. Finally, the pipeline's architecture supports high parallelization, rendering it suitable for both local and high-performance computing environments. MeTAline is freely available at https://github.com/Gabaldonlab/meTAline under an open-source GNU GPL v3.0 license.},
}
@article {pmid41278154,
year = {2025},
author = {Zheng, L and Duan, SL and Wang, K},
title = {Research progress concerning the involvement of the intestinal microbiota in the occurrence and development of inflammatory bowel disease.},
journal = {World journal of gastroenterology},
volume = {31},
number = {42},
pages = {113170},
pmid = {41278154},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/genetics ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Intestinal Mucosa/microbiology/immunology/pathology ; *Crohn Disease/microbiology/therapy/immunology ; *Colitis, Ulcerative/microbiology/therapy/immunology ; Genetic Predisposition to Disease ; Dysbiosis/microbiology/immunology/therapy ; *Inflammatory Bowel Diseases/microbiology/therapy ; Metagenomics ; Animals ; Metabolomics ; Immunity, Mucosal ; },
abstract = {Inflammatory bowel disease (IBD), a chronic disorder characterized by intestinal inflammation and mucosal damage, includes mainly Crohn's disease and ulcerative colitis. However, the cause of its onset remains unclear. The pathogenesis of IBD is closely related to host genetic susceptibility, disorders of the intestinal flora, damage to the intestinal mucosal barrier, and abnormal intestinal mucosal immunity. On the basis of the progress in research on the structure of the intestinal microbiota involved in IBD, the influence of genetics on the intestinal barrier and intestinal microbiota; the metagenomics, metatranscriptomics, and metabolomics of the intestinal microbiota involved in IBD; and treatments such as probiotics and fecal microbiota transplantation are important for the future treatment of IBD and the development of drugs for effective treatment.},
}
@article {pmid41277537,
year = {2026},
author = {Liu, C and Wang, X and Zhang, Z and Wang, W and Wang, T and Zhao, Y and Wang, M and Chen, WH},
title = {GMrepo v3: a curated human gut microbiome database with expanded disease coverage and enhanced cross-dataset biomarker analysis.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D734-D742},
pmid = {41277537},
issn = {1362-4962},
support = {2024YFA0918500//National Key Research and Development Program of China/ ; 5001170159//Hubei Province/ ; 202505AF350080//Yunnan Expert Workstation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Biomarkers/analysis ; RNA, Ribosomal, 16S/genetics ; *Databases, Genetic ; Metagenome/genetics ; Metagenomics/methods ; Disease/genetics ; Phenotype ; Software ; },
abstract = {GMrepo (Gut Microbiome Data Repository) is a curated and consistently annotated database of human gut metagenomes, designed to improve data reusability and enable cross-project and cross-disease comparisons. In this latest release, GMrepo v3 has been expanded to 890 projects and 118 965 runs/samples, including 87 048 16S rRNA and 31 917 metagenomic datasets. The number of annotated diseases has increased from 133 to 302, allowing more comprehensive disease-related microbiome analyses. We systematically identified microbial markers between phenotype pairs (e.g. healthy versus diseased) at the project level and compared them across datasets to detect reproducible signatures. As of this release, GMrepo v3 includes 1299 marker taxa (726 species and 573 genera) associated with 167 phenotype pairs, derived from 275 carefully curated projects. To assess marker stability, we developed the Marker Consistency Index (MCI), which summarizes the prevalence and directional consistency of markers across studies. Among 400 markers showing altered abundances in ≥10 projects, 143 were consistently enriched in healthy controls (MCI > 75%), while 85 were enriched in diseases (MCI < 25%). A marker-centric interface enables users to explore marker behavior across diseases. The GMrepo v3 database is freely accessible at https://gmrepo.humangut.info.},
}
@article {pmid41275679,
year = {2026},
author = {Matu, A and Valverde, A and Cason, E and Gomez-Arias, A and Maleke, M and Castillo, J},
title = {Microbial consortia in mine water bioremediation: principles, design and practical applications.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124956},
doi = {10.1016/j.watres.2025.124956},
pmid = {41275679},
issn = {1879-2448},
mesh = {*Biodegradation, Environmental ; *Mining ; *Microbial Consortia ; Bioreactors ; },
abstract = {The impact of mining activities on water sources is a global concern, especially in water-scarce countries such as Southern Africa, Mediterranean region, western Asia, and South America. Bioremediation emerges as a feasible and attractive alternative to address this environmental issue. However, while biological sulfate reduction and the emerging use of using microbially induced carbonate precipitation (MICP) for remediating polluted mine water have gained attention, strategies for designing effective microbial consortia have seen little advancement. The performance of microbial consortia in these treatments can be quite variable. Most improvement strategies have focused mainly on bioreactor design and selecting suitable carbon sources, addressing technical aspects while neglecting the central players in this process: the microbes themselves. Enhancing consortium effectiveness requires revisiting foundational concepts such as monoculture, co-culture, division of labor, and bottom-up versus top-down approaches. While these concepts offer significant theoretical potential to improve consortium performance, they have seldom been applied in practice for mine water bioremediation. In this literature review, we revisit these principles and explore the integration of novel tools such as metagenomics and bioinformatics. These approaches can deepen our understanding of indigenous microbial diversity, uncover dynamic interactions among microbial species, and identify keystone species as potential candidates for bioremediation. By leveraging their genomic potential, it becomes possible to design consortia that are more efficient and better suited to support the recovery of contaminated water sources.},
}
@article {pmid41275070,
year = {2025},
author = {Gao, H and Wang, Y and Zhao, Y and Jiao, X and Guo, Z and Zheng, L and Li, Y and Su, Y and Wang, Z and Bai, J and Yao, J and Bushman, FD and Luo, S and Song, X and Liang, G},
title = {Human gut prophage landscape identifies a prophage-mediated fucosylation mechanism alleviating colitis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11541},
pmid = {41275070},
issn = {2041-1723},
support = {32200036//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82341116//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92474105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32270945//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Prophages/genetics/physiology ; Animals ; Humans ; *Colitis/chemically induced/microbiology/virology ; Fucosyltransferases/genetics/metabolism ; Mice ; *Trisaccharides/metabolism/biosynthesis ; Female ; *Gastrointestinal Microbiome ; Male ; Galactoside 2-alpha-L-fucosyltransferase ; Mice, Inbred C57BL ; Lysogeny ; Metagenome ; Dextran Sulfate ; Adult ; Middle Aged ; },
abstract = {Functions of the human gut virome are little understood, particularly for the hyperabundant prophages integrated in prokaryotic genomes. Here we identified 254,273 prophage sequences in 47.7% of 289,232 human gut metagenomic genomes, significantly expanding the known taxonomic and functional diversity of prophages in the human gut microbiome. Analysis of 8503 gut metagenomic samples showed the ratios of lysogens (cells harboring prophages) to non-lysogens varied widely associated with age, health condition, and geography, with the latter linked to industrialization. Notably, the alterations of the prophage-encoded genes exhibited disease-specific patterns. For inflammatory bowel diseases, the prophage-encoded futC gene, encoding α-1,2-fucosyltransferase, was less prevalent in affected patients. This enzyme was experimentally validated to direct 2-fucosyllactose (2'-FL) biosynthesis in vitro. Here we show that 2'-FL could diminish colitis in mice induced by treatment with dextran sodium sulfate. Mechanistically, 2'-FL promoted maintenance of mucosal barrier integrity, leading to intestinal IgA secretion and intraepithelial CD4[+]CD8αα[+] T cell development mediated by the gut microbiome. Together, our findings thus link lysogeny to human age, geography, and disease, and demonstrate an immunomodulatory mechanism of prophage-encoded genes in alleviating colitis.},
}
@article {pmid41274878,
year = {2025},
author = {Ferretti, P and Allert, M and Johnson, KE and Rossi, M and Heisel, T and Gonia, S and Knights, D and Fields, DA and Albert, FW and Demerath, EW and Gale, CA and Blekhman, R},
title = {Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother's milk.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11536},
pmid = {41274878},
issn = {2041-1723},
support = {R01 HD080444/HD/NICHD NIH HHS/United States ; R01 HD109830/HD/NICHD NIH HHS/United States ; R01HD080444//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; K99 HD113834/HD/NICHD NIH HHS/United States ; R21 HD099473/HD/NICHD NIH HHS/United States ; F32HD105364//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; F32 HD105364/HD/NICHD NIH HHS/United States ; R01HD109830//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R21HD099473//U.S. Department of Health &amp; Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; },
mesh = {Humans ; *Milk, Human/microbiology ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Adult ; Feces/microbiology ; Infant, Newborn ; Bifidobacterium/genetics/isolation &amp; purification ; Male ; Metagenomics ; Breast Feeding ; },
abstract = {The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as sole nutrition for the infant, little is known about how variation in the milk microbiome shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiomes using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. Microbial taxonomic overlap between milk and the infant gut was driven by Bifidobacterium longum, and infant microbiomes dominated by B. longum showed greater temporal stability than those dominated by other species. We identified numerous instances of strain sharing between milk and the infant gut, involving both commensal (e.g. B. longum) and pathobiont species (e.g. K. pneumoniae). Shared strains also included typically oral species such as S. salivarius and V. parvula, suggesting possible transmission from the infant's oral cavity to the mother's milk. At one month, the infant gut microbiome was enriched in biosynthetic pathways, suggesting that early colonisers might be more metabolically independent than those present at six months. Lastly, we observed significant overlap in antimicrobial resistance gene carriage within mother-infant pairs. Together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.},
}
@article {pmid41274873,
year = {2025},
author = {Peng, H and Andreu-Sanchez, S and Ruiz-Moreno, AJ and Fernández-Pato, A and Wu, J and Gacesa, R and Zhernakova, A and Wang, D and Fu, J},
title = {Longitudinal gut microbiota tracking reveals the dynamics of horizontal gene transfer.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {11543},
pmid = {41274873},
issn = {2041-1723},
mesh = {*Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Humans ; Feces/microbiology ; Metagenome/genetics ; *Bacteria/genetics/classification ; Longitudinal Studies ; Metagenomics/methods ; Male ; Female ; Adult ; },
abstract = {Horizontal gene transfer (HGT) is a major driver of bacterial evolution, but its role in shaping the human gut microbiome over time remains poorly understood. Here, we present a longitudinal metagenomic analysis of 676 fecal samples from 338 individuals in the Lifelines-DEEP study collected ~4 years apart, using a newly developed workflow to detect recent HGT events from metagenome-assembled genomes. We identified 5,644 high-confidence HGT events occurring within the past ~10,000 years across 116 gut bacterial species. We find that species pairs with an HGT relationship were significantly more likely to maintain stable co-abundance relationships over the 4-year period, suggesting that gene exchange contributes to community stability. Notably, HGT and strain replacement act together to disseminate mobile genes in the population. Furthermore, our observation that an individual's mobile gene pool remains highly personalized and stable over time indicates that host lifestyles drive specific gene transfer. For example, proton pump inhibitor usage is linked to increased transfer of multidrug transporter genes. Our findings demonstrate, at the individual gut microbiome level, that HGT is both an integral and stabilizing force in the human gut ecosystem and an important mechanism for disseminating adaptive functions, underscoring HGT potential for tracking host lifestyle.},
}
@article {pmid41273973,
year = {2025},
author = {Peng, L and Yang, F and Zhang, J and Shang, J and Xu, W and Sheng, S and Li, Q and Zou, Y and Yue, Z},
title = {Ecological drivers and functional roles of phage communities in the Yangtze River's freshwater ecosystems.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140564},
doi = {10.1016/j.jhazmat.2025.140564},
pmid = {41273973},
issn = {1873-3336},
mesh = {*Rivers/virology ; China ; *Bacteriophages/genetics/physiology ; *Ecosystem ; Fresh Water/virology ; Virome ; Geologic Sediments ; },
abstract = {The Yangtze River, China's largest and most significant freshwater system, is facing increasing pollution pressures due to rapid urbanization. While bacterial-mediated antibiotic resistance has been extensively studied, the functional roles and ecological risks of phage communities remain poorly understood. Here, we conducted a comprehensive virome analysis across four habitats (free-living setting, particle-associated setting, sediment, and bank soil) using 204 samples from the Yangtze River. We identified 18,865 viral operational taxonomic units (vOTUs) and observed significant correlations between viral communities and metagenome-assembled genomes (MAGs) across all habitats. Notably, the virus-to-host ratio (VHR) decreased significantly with increased elevation. Functional annotation revealed 1367 viruses contigs carrying genes associated with six functional categories, each showing distinct habitat-specific patterns. Carbohydrate-degrading enzymes (CAZy) were abundant in free-living setting water. Among phage-borne ARGs, vancomycin resistance was predominated, especially in sediment and bulk soil, while mercury resistance were most prevalent in sediments. Chitinase genes constituted the most abundant group among phage-encoded genes for plastic degradation. We identified 84 high-confidence virus-host pairs, predominantly infecting Proteobacteria. Random forest modeling identified elevation as the dominant driver of viral community abundance across habitats. Higher elevations were correlated with increased pH and reduced NH4[+]-N concentrations, suggesting nutrient limitation may weaken virus-host interactions. This study provides the first systematic assessment of viral diversity and functional potential in the Yangtze River, offering novel insights into phage ecology in freshwater.},
}
@article {pmid41271709,
year = {2025},
author = {Bay, SK and Ni, G and Lappan, R and Leung, PM and Wong, WW and Ry Holland, SI and Athukorala, N and Knudsen, KS and Fan, Z and Kerou, M and Jain, S and Schmidt, O and Eate, V and Clarke, DA and Jirapanjawat, T and Tveit, A and Featonby, T and White, S and White, N and McGeoch, MA and Singleton, CM and Cook, PLM and Chown, SL and Greening, C},
title = {Microbial aerotrophy enables continuous primary production in diverse cave ecosystems.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10295},
pmid = {41271709},
issn = {2041-1723},
mesh = {*Caves/microbiology ; *Ecosystem ; Carbon Dioxide/metabolism ; Metagenome ; Geologic Sediments/microbiology ; Microbiota/genetics ; Hydrogen/metabolism ; Metagenomics ; *Bacteria/genetics/metabolism/classification ; Biodiversity ; Carbon Monoxide/metabolism ; Biofilms ; Gammaproteobacteria/genetics/metabolism ; },
abstract = {Aerated caves receive minimal light energy, yet host diverse microbial communities and the strategies allowing them to meet energy and carbon needs remain unclear. We determined the processes and mediators of primary production in aerated limestone and basalt caves through paired metagenomic and biogeochemical profiling. Four caves were sampled, including sediments and biofilms, yielding 94 metagenomes. Based on 1458 metagenome-assembled genomes, over half of microbial cells encode enzymes to use atmospheric trace gases as energy and carbon sources. The most abundant microbes are chemosynthetic primary producers, notably the gammaproteobacterial methanotrophic order Ca. Methylocavales and two uncultivated actinobacterial genera predicted to grow on atmospheric hydrogen, carbon dioxide, and carbon monoxide. Biogeochemical and isotopic measurements confirmed that these gases are rapidly consumed at rates likely sustaining a substantial fraction of the community and potentially driving primary production. Conventional chemolithoautotrophs, using ammonium and sulfide, are also enriched and active. Altogether, these results indicate that caves are unique in microbial biodiversity and the biogeochemical processes sustaining them. Consumption of atmospheric trace gases likely has a dual role in caves, providing energy for microbial survival and potentially supporting chemosynthetic growth, thereby introducing organic carbon. This process, defined as 'aerotrophy', operates alongside organic and inorganic inputs.},
}
@article {pmid41270896,
year = {2026},
author = {Diakité, MT and Sun, S and Somboro, AM and Diakité, B and Koné, A and Kassogué, Y and Fofana, D and Balam, S and Traoré, CB and Maiga, A and Kamaté, B and Ba, D and Diarra, M and Boré, S and Maiga, AI and Dai, Q and Nannini, DR and Holl, J and Murphy, R and Hou, L and Fodor, A and Maiga, M},
title = {Characterization of the gut microbiota in patients with stage III colorectal cancer: A case-control study.},
journal = {Gene},
volume = {978},
number = {},
pages = {149913},
pmid = {41270896},
issn = {1879-0038},
support = {D43 CA260658/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/pathology ; Case-Control Studies ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Pilot Projects ; Neoplasm Staging ; Adult ; Bacteria/genetics/classification ; },
abstract = {AIM: To conduct a case-control study (pilot study) in Africa (Mali) in comparing the gut microbiota of patients with stage III colorectal cancer (CRC) using next-generation sequencing.<br><br>METHODS: Shotgun sequencing was performed to characterize participants' fecal microbiota using Illumina's HiSeq platform. This case-control study involved newly diagnosed CRC patients (n&#xa0;=&#xa0;23) prior to any treatment initiation, and unrelated healthy controls (n&#xa0;=&#xa0;24) to elucidate their microbial diversity and relative abundance.<br><br>RESULTS: The findings revealed that the gut microbiota in CRC and in healthy were significantly distinctive according to the PERMANOVA test (R[2]&#xa0;=&#xa0;0.132, P = 0.001), and the alpha-diversity was significantly lower in CRC. Beta-diversity, based on principal coordinate analysis, showed a distinct taxonomy between the CRC and the healthy. Levels of Pseudomonadota, Escherichia, Citrobacter freundii, Klebsiella sp. LTGPAF-6F, Escherichia albertii, Escherichia coli, Caudovirales, Apicomplexa, and Verrucomicrobiota populations were significantly elevated in CRC. The major metabolic pathways with higher relative abundance levels found in CRC compared to healthy were related to HEMESYN2-PWY: heme biosynthesis II (anaerobic), PWY-5154:L-arginine biosynthesis III (via N-acetyl-L-citrulline), FUC-RHAMCAT-PWY: superpathway of fucose and rhamnose degradation, ECASYN-PWY: enterobacterial common antigen biosynthesis, ENTBACSYN-PWY: enterobactin biosynthesis, and AEROBACTINSYN-PWY: aerobactin biosynthesis.<br><br>CONCLUSION: Distinct gut microbiome profiles between healthy and CRC were observed. In particular, the findings showed a significant reduction in microbial diversity in stage III CRC. This study provides initial metagenomic data on Malian patients with CRC. It will be used to create a larger cohort to better understand the relationship between CRC and the gut microbiota in the Malian CRC population.},
}
@article {pmid41270835,
year = {2025},
author = {Gao, W and Yao, Y and Sun, Y and Pu, W and Xu, L},
title = {Metatranscriptomic characterization of the canine fecal virome from pooled samples in Gansu, China.},
journal = {Virus research},
volume = {362},
number = {},
pages = {199666},
pmid = {41270835},
issn = {1872-7492},
mesh = {Animals ; Dogs ; *Feces/virology ; China ; *Virome ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Dog Diseases/virology ; Phylogeny ; Pooled Testing ; },
abstract = {As popular companion animals, dogs present a potential risk for zoonotic viral transmission through close contact with humans. To characterize the fecal virome of dogs in Pingliang City, Gansu Province, China, we performed metatranscriptomic sequencing on 30 fecal samples pooled into three libraries, representing three distinct living environments. A total of 112,900,200 clean reads were obtained, revealing 16 viral genera spanning 15 families and highlighting a diverse viral community comprising animal viruses, bacteriophages, and plant viruses. Notably, we identified five known pathogenic viruses: canine astrovirus (3708 reads), canine dicipivirus (6578 reads), canine norovirus (16 reads), canine vesivirus (74 reads), and canine rotavirus (128 reads). Their presence suggests possible exposure events at the human-animal interface, although the infectivity and transmission risk require further experimental validation. These findings significantly expand our understanding of the canine virome and underscore the importance of "One Health" surveillance in companion animals. However, the actual zoonotic potential of the detected viruses, remains to be elucidated through further targeted investigation.},
}
@article {pmid41270667,
year = {2025},
author = {Kodamatani, H and Yamamoto, M and Takaki, Y and Hamasuna, S and Ichitani, K and Kanzaki, R and Tomiyasu, T},
title = {Three-year dynamics of methylmercury production in Hg[2+]-spiked paddy soils: Mercury speciation, microbial communities, and rice contamination.},
journal = {Chemosphere},
volume = {393},
number = {},
pages = {144767},
doi = {10.1016/j.chemosphere.2025.144767},
pmid = {41270667},
issn = {1879-1298},
mesh = {*Methylmercury Compounds/analysis ; *Oryza/chemistry ; *Mercury/analysis ; *Soil Pollutants/analysis ; *Soil Microbiology ; Soil/chemistry ; Microbiota ; Environmental Monitoring ; },
abstract = {We investigated three-year changes in soil mercury (Hg) pools, methylmercury (MeHg) production, rice contamination, and microbial communities after a single Hg[2+] addition to two soils (Soil I and Soil II). In Soil I, total Hg (T-Hg) concentration of brown rice grain was 0.150 ± 0.023 mg/kg (n = 143) in 2015 and increased to 0.233 ± 0.080 (n = 135) and 0.240 ± 0.118 mg/kg (n = 225) in 2016 and 2017. In Soil II, T-Hg declined from 0.530 ± 0.101 (n = 130) in 2015 to 0.124 ± 0.059 (n = 213) and 0.168 ± 0.059 mg/kg (n = 200) in 2016 and 2017. Variations in T-Hg concentrations in rice grains cultivated in the two soils showed a relationship with soil MeHg concentrations within the same soil, but not between different soils. Sequential extraction, which partitioned soil Hg into seven fractions, indicated that Soil II contained a higher proportion of water-extractable Hg. This finding suggests that the mobility of Hg may have influenced the level of Hg contamination in rice grains. The proportion of Hg sulfide peaked approximately one month after the addition of Hg[2+] in both soils, then decreased over time. In contrast, the fractions of organic-bound and elemental Hg tended to increase over time. In soil II, where DNA extraction was successful, microbial communities showed no clear differences at the phylum level between the Hg-added and non-added samples, but distinct shifts were observed at lower taxonomic levels. Metagenomics showed that the MeHg/T-Hg ratio correlated positively with hgcAB gene abundance (r = 0.85, P < 0.05), while merA/merB showed no clear relationship.},
}
@article {pmid41270588,
year = {2025},
author = {Pramanick, A and Saikh, SR and Mushtaque, MA and Karri, D and Gandhi, N and Das, SK},
title = {Long-range transported bacteria perturbing airborne bacterial diversity and pathogenicity over Eastern Himalayas, India.},
journal = {The Science of the total environment},
volume = {1008},
number = {},
pages = {180981},
doi = {10.1016/j.scitotenv.2025.180981},
pmid = {41270588},
issn = {1879-1026},
mesh = {India ; *Air Microbiology ; *Bacteria/pathogenicity/classification ; *Environmental Monitoring ; *Air Pollutants/analysis ; Biodiversity ; *Microbiota ; Himalayas ; },
abstract = {Long-range transported bacteria have a significant impact on hill-top airborne bacterial diversity and pathogenicity. Present study investigates airborne bacterial community structure over a hill-top region of the Eastern Himalayas, based on two years (2022--23) of investigations on culture-independent metagenomic analysis. Winter-time hill-top microbial loading is found to be a minimum of about 21,401.5 ± 2791.0 × 10[5] m[-3], representing background Himalayan airborne bacterial concentration, and a maximum of 6.7 ± 1.2 × 10[5] m[-3] on dusty summer days. 80 % of the total Himalayan bacterial population is due to long-range transport via horizontal and vertical movement of atmosphere, causing about 60 % perturbation in Himalayan bacterial diversity. Space-borne observations with 3-days back-trajectories analysis reveal a thick dust layer between 2 and 3 km over Eastern Himalayas, coming from the Thar Desert. Long-range transported dust-attached bacteria cause a 40 % enhancement in unique bacterial loading, while 6 % unique genera are noticed in upwelling of foothill pollution, and 8 % unique bacterial genera are found in downwelling from free troposphere to the hill-top atmosphere. Desert dust-attached long-range transported bacteria contain one-third skin-infecting pathogens, while upwelling pollutants carry mainly respiratory-infecting bacteria (45 %), and downwelling transport is dominated by gastrointestinal tract-infecting bacteria (50 %). Interestingly, local Himalayan bacteria (20 %) are consistently loaded with pathogens, predominantly causing respiratory (36 %) and skin (31 %) infections throughout the study period. Present results highlight the profound impact of atmospheric transport processes on regional bacterial diversity and public health in hill-top region, highlighting Himalayan atmosphere as a dynamic and global conveyor of life, including pathogens across long distances.},
}
@article {pmid41269405,
year = {2025},
author = {Liu, S and Chen, Q and Gu, Y and Lei, H and Li, B and Qin, Q},
title = {Microorganisms, Microbial Metabolites and Precision Nutrition: Targeting the Gut-Skin Axis for Immune Microenvironment Remodeling in Atopic Dermatitis.},
journal = {Clinical reviews in allergy &amp; immunology},
volume = {68},
number = {1},
pages = {102},
pmid = {41269405},
issn = {1559-0267},
support = {CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; CG24016//Project of Industrialization of Major Achievements in Heilongjiang Province: "Development and Industrialization Demonstration of Key Technologies for Processing Functional Probiotics"/ ; },
mesh = {Humans ; *Dermatitis, Atopic/immunology/metabolism/microbiology/therapy/etiology ; *Skin/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; Precision Medicine ; Animals ; Dysbiosis ; Disease Susceptibility ; Probiotics ; Cellular Microenvironment/immunology ; },
abstract = {Atopic dermatitis (AD), characterized by skin barrier dysfunction and microbiota dysbiosis, is closely linked to immune microenvironment imbalance. Growing evidence highlights the crucial role of microorganisms and their metabolites in immune regulation. Understanding their molecular mechanisms in AD, combined with precision nutrition-driven personalized network analysis, will accelerate innovative intervention strategies. This review summarizes these regulatory mechanisms and current research progress, outlining applications, challenges, and limitations for key targets, such as the TSLP-ILC2-IL-13 axis, IL-31-TRP channels, and SCFA-GPR43 signaling. The precision nutrition-driven approach will leverage multi-omics data, including metagenomics, metabolomics, and host transcriptomics, with integration techniques such as network analysis and machine learning to explore the spatio-temporal regulation of the immune microenvironment. Beyond immunomodulation, dietary factors significantly impact AD progression. We propose "precision nutrition" strategies to mitigate AD risk and burden, including microbiota-targeted dietary patterns, personalized probiotics, and delivery systems for "precise skin nutrition." Synergizing traditional interventions with localized innovations and interdisciplinary tools is expected to enable precise, spatio-temporal immune regulation. This enhances understanding of microorganism-metabolite, precision nutrition, and immune microenvironment connections, advancing AD intervention and treatment.},
}
@article {pmid41268133,
year = {2025},
author = {Li, J and Popovich, PG and Kigerl, KA and McTigue, DM and Schwab, J and Barnes, S and Yarar-Fisher, C},
title = {Multiomic Analysis of the Gut Microbiome and Serum Metabolome in Response to a Low-Carbohydrate, High-Protein Diet in Individuals With Spinal Cord Injury.},
journal = {Topics in spinal cord injury rehabilitation},
volume = {31},
number = {4},
pages = {111-129},
pmid = {41268133},
issn = {1945-5763},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Spinal Cord Injuries/diet therapy/microbiology/blood/metabolism ; Male ; Female ; *Metabolome ; Adult ; Middle Aged ; *Diet, High-Protein Low-Carbohydrate ; *Diet, High-Protein ; },
abstract = {BACKGROUND: Dietary interventions play a significant role in preventing and managing cardiometabolic diseases partly through their impact on the gut microbiome and circulating metabolites.<br><br>OBJECTIVES: To assess the impact of an 8-week low-carbohydrate, high-protein (LC/HP) diet on gut microbiome composition, function, and serum metabolome in individuals with spinal cord injury (SCI).<br><br>METHODS: Twenty-four adults with chronic SCI were randomized into an LC/HP diet or a control group for 8 weeks. Stool and fasting serum samples were collected at baseline and week 8. The gut microbiome composition and metabolic potential were determined using metagenomic sequencing, while serum metabolome was assessed through untargeted liquid chromatography-tandem mass spectrometry. Statistical analyses focused on diet and time interaction effects, using R (version 4.1.0).<br><br>RESULTS: A trend for increased alpha diversity (Gini-Simpson, P = .09) in the diet group indicated a more evenly distributed microbial community. Compared to the control group, several microbiome species (e.g., Fusicatenibacter saccharivorans, Eubacterium siraeum) that are implicated with better intestinal health and reduced inflammation increased, while other species (e.g., Hungatella hathewayi, Clostridium symbiosum) that are associated with colorectal cancer risk decreased in the diet group. Microbial metabolic pathways related to amino acid and purine nucleotides were altered. Increased tryptophan betaine and decreased 8-hydroxy-deoxyguanosine were observed in the serum in the diet group (P interaction < .05), indicating compliance and reduced oxidative stress, respectively.<br><br>CONCLUSION: Adopting an LC/HP diet resulted in favorable gut microbiome and metabolome adaptations that may reduce the risk for cardiometabolic disease and colorectal cancer in individuals with SCI.},
}
@article {pmid41267624,
year = {2025},
author = {Li, H and Fu, J and Fan, X and He, Z and Wang, Y and Yang, S and Wu, J and Wu, L and Zhou, J},
title = {Eutrophication Reshapes Microbial Communities and Life-History Strategies in the Riverine Ecosystems.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70234},
pmid = {41267624},
issn = {1758-2229},
support = {32100081//Youth Program of National Natural Science Foundation of China/ ; 2024QT03//Central Public-Interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 91428207//Key Program of National Natural Science Foundation of China/ ; //National Key Basic Research Program of China (2012CB417300)/ ; },
mesh = {*Eutrophication ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Metagenomics ; Phylogeny ; },
abstract = {Rivers are increasingly affected by human activities, leading to widespread eutrophication. However, the responses of riverine microbiomes to eutrophication remain poorly understood. In this study, we compared microbiomes between eutrophic urban rivers (UR) and relatively undisturbed natural rivers (NR) to elucidate how eutrophication influences community structures, assembly processes, functions and life-history strategies. Amplicon and metagenomic sequencing revealed that eutrophication substantially enhanced microbial abundance and diversity in riverine ecosystems, with UR harbouring a higher proportion of fast-growing, nitrogen-transforming and antibiotic-resistant taxa. Neutral and null model analyses further revealed that, while stochastic processes predominantly shaped communities in NR, deterministic environmental selection exerted stronger control under eutrophic conditions in UR. Correspondingly, microbial communities in UR exhibited higher 16S rRNA gene copy numbers (median 4.69 vs. 4.28), stronger codon usage bias (0.0209 vs. 0.0204), greater predicted growth rates (0.2664 vs. 0.1567 h[-1]), larger genomes (5.91 vs. 5.19 Mb), higher guanine-cytosine content (57.68% vs. 56.41%) and enriched transposase genes (4.37% vs. 2.98%), collectively indicating a community-wide shift from K-selected to r-selected life-history strategies under eutrophication. Overall, this work elucidates how human activities reshape riverine microbial communities and life-history strategies, providing a basis for predicting the ecological outcomes of nutrient over-enrichment in fluvial environments.},
}
@article {pmid41267035,
year = {2025},
author = {Li, X and Tian, C and Zhuang, D and Shi, X and Tian, L and Bai, L and Gao, H and Zhou, H and Zhao, F and Dai, M and Zhu, L and Yu, J and Wu, Q and Liu, X and Zhang, T and Sang, J and Li, T and Luo, Y and Tang, Z and Sahu, SK and Xu, X and Wang, J and Liu, H and Xiao, L and Kristiansen, K and Zhang, Z},
title = {A unified catalog of 14,062 microbial species reference genomes provides new insight into the gut microbiota in high-altitude mammals.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {236},
pmid = {41267035},
issn = {2049-2618},
support = {no. 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; no. U2002206//the Chinese National Natural Science Foundation/ ; no. 202001BB050001//the Major Science and Technology Project in Yunnan Province of China/ ; no. KC-22221159//Yunnan University graduate Research innovation project/ ; No. XZ202401YD0012//Tibet Autonomous Region Science and Technology Program Project/ ; No. 202407AA110009//the Central Guidance on Local Science and Technology Development Fund of Yunnan Province/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Mammals/microbiology ; Phylogeny ; *Bacteria/classification/genetics/isolation &amp; purification ; *Genome, Bacterial ; Altitude ; Tibet ; Symbiosis ; },
abstract = {BACKGROUND: The gut microbiota is essential for host health and survival. The understanding of the diversity, stability, and functional traits of mammalian gut microbiota, as well as the evolutionary patterns of the host-gut microbiota holobiont in non-human mammals remains limited. Here, we conducted a comprehensive analysis of the gut microbiota in non-human mammals.<br><br>RESULT: We used 1,412 samples from large herbivores living in the Qinghai-Tibetan Plateau (QTP), recovered 14,062 high-confidence species-level genome bins (SGBs), of which more than 88% represent potentially novel species. We found that recurring lineage-specific bacterial gain-loss events along the host phylogeny might drive the shaping of the gut microbiota in these QTP mammals. Functional characteristics of host-specific SGBs showed host-specific functional enrichment, but few cases of convergence in at least two hosts. Our analyses further revealed that both co-phylogeny and host-swap events are frequent between mammalian hosts and their individual gut symbionts at QTP ecosystem. The genome-wide evolutionary analyses of 60 genera, comprising 376 core microbial species occurring within at least two animal hosts, discovered that co-phylogeny or host-swap signals might be impacted by phylogenetic inertia, but not by selective constraints.<br><br>CONCLUSIONS: Our results showed that animals living in harsh environments are promising sources for the discovery of novel biological functions of gut residing microbes. The results of this study provide insight into the diversity and functionality of the gut microbiota in large herbivores living at QTP as well as the diverse evolutionary patterns of host-gut microbiota interaction over evolutionary times. Video Abstract.},
}
@article {pmid41266796,
year = {2025},
author = {Weng, Y and Guccione, C and McDonald, D and Oles, R and Devkota, S and Kopylova, E and Sepich-Poore, GD and Salido, RA and Din, MO and Song, SJ and Curtius, K and Chu, H and Bartko, A and Hasty, J and Knight, R},
title = {Calculating fast differential genome coverages among metagenomic sources using micov.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1624},
pmid = {41266796},
issn = {2399-3642},
support = {R24 AI118629/AI/NIAID NIH HHS/United States ; R01 CA241728/CA/NCI NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 CA270235/CA/NCI NIH HHS/United States ; T32 GM007198/GM/NIGMS NIH HHS/United States ; P30 CA023100/CA/NCI NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; *Genome, Bacterial ; *Metagenome ; *Microbiota/genetics ; Humans ; },
abstract = {Breadth of coverage, the proportion of a reference genome covered by at least one sequencing read, is critical for interpreting metagenomic data, informing analyses from genome assembly to taxonomic profiling. However, existing tools typically summarize coverage breadth at the whole-genome or aggregate-sample level, missing informative variation along genomes and between sample groups. Here we introduce MIcrobiome COVerage (micov), a tool that computes and compares per-sample breadth of coverage across many genomes and samples. micov offers two key advances: (1) rapid cumulative coverage breadth calculations specific to each sample type, and (2) detection of differential coverage breadth along genomes. Applying micov to three metagenomic datasets, we show that it identifies a genomic region in Prevotella copri that explains variation in community composition independent of host country of origin, uncovers dietary association with a partially annotated region in an uncharacterized Lachnospiraceae genome, enabling hypothesis generation for genes of unknown function, and improves sensitivity in low-biomass settings by detecting a single genomic copy of enteropathogenic Escherichia coli (EPEC) in wastewater and distinguishing Mediterraneibacter gnavus across specimen types.},
}
@article {pmid41266356,
year = {2025},
author = {Deng, Y and Zhao, H and Zhang, L and Yang, S and Zou, D and Ma, M and Hou, C},
title = {Symbiotic Enterococcus faecalis potentiates viral pathogenesis via fructose-1,6-bisphosphate-mediated insect gut epithelial damage.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {215},
pmid = {41266356},
issn = {2055-5008},
support = {32300418//National Natural Science Foundation of China/ ; 32300418//National Natural Science Foundation of China/ ; 2024RC1069//The Science and Technology of Innovation Program of Hunan Province/ ; CAAS-BRC-CB-2025-01//Agricultural Science and Technology Innovation Program/ ; GLKY-2022-16//Guangxi Forestry Science and Technology Promotion and Demonstration Project/ ; },
mesh = {Animals ; *Enterococcus faecalis/physiology/genetics ; Bees/virology/microbiology ; *Symbiosis ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Larva/virology/microbiology ; Apoptosis ; },
abstract = {Chinese sacbrood virus (CSBV) is highly lethal to Asian honey bee (Apis cerana) larvae. While gut symbionts are known to regulate viral infection, their role in CSBV pathogenesis remains poorly understood. Through 16S rRNA gene sequence analysis of the field-collected honey bees, we found that the larvae had a substantially higher relative abundance of Enterococcus than pupae or adults. Metagenome sequencing analysis of field-collected larvae demonstrated that CSBV infection significantly induced more than 45-fold enhancement in the abundance of Enterococcus faecalis, an opportunistic pathogen implicated in the development of purulent cystic lesions. In microbiota-free (MF) bees, colonization with E. faecalis markedly suppressed phospholipid metabolism and elevated levels of 4-guanidinobutyric acid and fructose-1,6-bisphosphate (FBP). These metabolic changes were associated with cytotoxicity and apoptosis, which worsened goblet cell damage and thereby facilitated CSBV infection, as indicated by metabolomics and pathological section analysis. Crucially, exogenous FBP administration directly enhanced cytotoxicity and apoptosis of gut in CSBV-infected MF bees, mirroring the CSBV susceptibility was mediated by E. faecalis. Our study unveiled a symbiotic bacteria's involvement in promoting RNA virus infection through metabolic reprogramming and epithelial barrier dysfunction, providing new insights into host-microbe-virus interactions in pollinators.},
}
@article {pmid41266326,
year = {2025},
author = {Stanislawski, MA and Litkowski, E and Arehart, CH and Luo, K and Gilmore, N and Lange, LA and Lange, EM and Barnes, K and Avery, CL and Meyer, KA and Holguin, F and North, KE and Burk, RD and Kaplan, RC},
title = {Relationships among host genetics, gut microbiota, and asthma in US Hispanic/Latino adults.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10223},
pmid = {41266326},
issn = {2041-1723},
support = {R01 DK120870/DK/NIDDK NIH HHS/United States ; N01 HC065236/HL/NHLBI NIH HHS/United States ; K01HL157658//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01 HL105756/HL/NHLBI NIH HHS/United States ; R61 HL157069/HL/NHLBI NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; N01 HC065237/HL/NHLBI NIH HHS/United States ; R01HL136266//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HHSN268200625235C//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R33 HL157069/HL/NHLBI NIH HHS/United States ; N01 HC065233/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; N01 HC065235/HL/NHLBI NIH HHS/United States ; R01 DK119268/DK/NIDDK NIH HHS/United States ; R01HL157069//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01AI152504//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 1OT3HL14715//U.S. Department of Health &amp; Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; OT3 HL147154/HL/NHLBI NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; N01 HC065234/HL/NHLBI NIH HHS/United States ; R01 AI152504/AI/NIAID NIH HHS/United States ; R01 DK134672/DK/NIDDK NIH HHS/United States ; R01 AG085320/AG/NIA NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; K01 HL157658/HL/NHLBI NIH HHS/United States ; R01 HL136266/HL/NHLBI NIH HHS/United States ; R01MD011389//U.S. Department of Health &amp; Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; },
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Asthma/genetics/microbiology/epidemiology/ethnology ; Body Mass Index ; Cross-Sectional Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Hispanic or Latino/genetics ; Obesity/microbiology/genetics/complications ; Risk Factors ; United States/epidemiology ; },
abstract = {Asthma is a heterogeneous condition that is often comorbid with obesity and influenced by diverse risk factors. Elucidating the association of gut microbial characteristics with asthma could improve our understanding of the pathophysiology. Here, we investigate relationships of host genetics and stool microbiota characteristics with asthma among US Hispanic/Latino adults, while considering the influence of obesity status, using host whole genome sequencing and stool shotgun metagenomic microbiota data from participants of the Hispanic Community Health Study/Study of Latinos. We evaluate cross-sectional associations of microbiota characteristics with asthma and analyse whether they are modified by obesity status (body mass index≥30 kg/m[2]). We assess differences in alpha diversity, beta diversity, and taxonomic abundance with asthma, independent of obesity, and interactions between asthma and obesity using covariate-adjusted regression-based methods. We generate an asthma polygenic risk score (PRS) and compare the classification accuracy of genetic and microbial factors for asthma status. We report that asthma is associated with differences in overall taxonomic composition (beta diversity; p = 0.001), which is not dependent on obesity status (p = 0.31). Asthma is not associated with alpha diversity metrics (p > 0.17), though obesity is associated with lower alpha diversity (p < 0.01). We identify multiple taxa that are associated with asthma, including decreased abundance of Lactobacillus and Enterococcus species, and some taxonomic associations vary by obesity status. Compared to models including baseline risk factors and an asthma PRS, microbial information improves classification accuracy of asthma (p = 0.04). Our results support that there are microbiota characteristics associated with asthma in Hispanic/Latino adults independent of obesity.},
}
@article {pmid41264852,
year = {2025},
author = {Kosmopoulos, JC and Anantharaman, K},
title = {Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.},
journal = {Biochemistry},
volume = {64},
number = {24},
pages = {4609-4627},
pmid = {41264852},
issn = {1520-4995},
support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Viruses/genetics/metabolism ; *Viral Proteins/genetics/metabolism ; Microbiota ; *Biotechnology/methods ; Metagenomics/methods ; Ecosystem ; Ecology ; },
abstract = {Viruses are the most abundant biological entities on Earth and play central roles in shaping microbiomes and influencing ecosystem functions. Yet, most viral genes remain uncharacterized, comprising what is commonly referred to as "viral dark matter." Metagenomic studies across diverse environments consistently show that 40-90% of viral genes lack known homologues or annotated functions. This persistent knowledge gap limits our ability to interpret viral sequence data, understand virus-host interactions, and assess the ecological or applied significance of viral genes. Among the most intriguing components of viral dark matter are auxiliary viral genes (AVGs), including auxiliary metabolic genes (AMGs), regulatory genes (AReGs), and host-physiology-modifying genes (APGs), which may alter host function during infection and contribute to microbial metabolism, stress tolerance, or resistance. In this Review, we explore recent advances in the discovery and functional characterization of viral dark matter. We highlight representative examples of novel viral proteins across diverse ecosystems, including human microbiomes, soil, oceans, and extreme environments, and discuss what is known and still unknown about their roles. We then examine the bioinformatic and experimental challenges that hinder functional characterization and present emerging strategies to overcome these barriers. Finally, we highlight both the fundamental and applied benefits that multidisciplinary efforts to characterize viral proteins can bring. By integrating computational predictions with experimental validation and fostering collaboration across disciplines, we emphasize that illuminating viral dark matter is both feasible and essential for advancing microbial ecology and unlocking new tools for biotechnology.},
}
@article {pmid41264233,
year = {2026},
author = {Yun, Y and Duan, C and He, X and Tang, R and Lan, Y and Lu, M and Liu, T and Fan, X and Fan, Z and Ran, J},
title = {Gut microbiome plasticity explains the altitudinal distribution pattern and adaptability in a small mammal species (Apodemus draco).},
journal = {Microbiology spectrum},
volume = {14},
number = {1},
pages = {e0238825},
pmid = {41264233},
issn = {2165-0497},
support = {00204055A1156//Biological Resources Baseline Survey in Chengdu Area of Giant Panda National Park Program/ ; 3240030216//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Altitude ; China ; *Murinae/microbiology/physiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Adaptation, Physiological ; Metagenomics ; Ecosystem ; },
abstract = {Altitudinal distribution patterns of species, a central focus of ecology, predominantly focus on environmental factors and only rarely on the host's intrinsic adaptive capacity. Particularly, the role of gut microbiota has not yet been studied. Here, we used the wild South China Field Mouse (Apodemus draco), a widely distributed small mammal species, as the study subject to investigate the altitudinal distribution pattern of the species and assess how gut microbiota contributes to the formation of this pattern. A total of 219 wild samples were captured in the middle section of the Qionglai Mountains, China, and 121 adult individuals were selected for metagenomic sequencing (e.g., gut microbial diversity, network topology, composition, and functional profiles). Vegetation cover of each sampling quadrat was assessed using Normalized Difference Vegetation Index. Our results indicate that A. draco exhibited a hump-shaped altitudinal distribution, but the peak abundance of A. draco corresponds to lower vegetation cover of habitats. Gut microbial diversity, complexity, robustness, energy harvesting ability, and carbohydrate utilization capacity all peaked at the mid-altitude zone, matching the host's spatial distribution pattern. Furthermore, the gut microbiome in high-altitude A. draco populations facilitates host acclimatization in extreme high-altitude niches by enhancing energy harvesting, hypoxia tolerance, and pathogen resistance.IMPORTANCEWe propose for the first time that the gut microbiome serves as a pivotal factor in structuring the altitudinal distribution pattern of species and further reveal a gut microbiota-mediated adaptive strategy underlying mammalian high-altitude adaptation. These results demonstrate that the gut microbiome fundamentally facilitates host adaptation to ecological niches. The study provides a novel insight into the factors of species' spatial distribution from a gut microbiota perspective.},
}
@article {pmid41263098,
year = {2026},
author = {Yan, Y and Patel, RSKR and Shanmugam, NRS and Akresi, J and Yin, Y},
title = {dbCAN-HGM: CAZyme gene clusters in gut microbiomes of diverse human populations.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D555-D563},
pmid = {41263098},
issn = {1362-4962},
support = {R03OD039979/NH/NIH HHS/United States ; R01 GM140370/GM/NIGMS NIH HHS/United States ; R01GM140370/NH/NIH HHS/United States ; R03 OD039979/OD/NIH HHS/United States ; 58-8042-3-076//United States Department of Agriculture/ ; //Nebraska Tobacco Settlement Biomedical Research Enhancement Funds/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Multigene Family ; Metagenome ; *Databases, Genetic ; Polysaccharides/metabolism ; Metagenomics/methods ; *Glycoside Hydrolases/genetics/metabolism ; *Bacteria/genetics/enzymology/classification ; Genome, Bacterial ; },
abstract = {CAZymes (Carbohydrate Active EnZymes) play key metabolic functions in human gut microbiomes (HGM). Genes of glycan degrading CAZymes often form physically linked CAZyme Gene Clusters (CGCs) in gut bacterial genomes. Here we developed dbCAN-HGM (https://pro.unl.edu/dbCAN_HGM), a comprehensive data repository for human gut bacterial CGCs and CAZymes. dbCAN-HGM has the following unique features: (i) 121 883 CGCs are identified in 6031 high-quality species-level representative metagenome assembled genomes (MAGs), from a wide range of human populations, especially the under-studied African population; (ii) Each CGC page includes metagenomic read mapping results from different diets (vegan, vegetarian, omnivore, flexitarian) and disease statuses (ulcerative colitis [UC and Crohns disease), with interactive coverage plot and Jbrowse alignment tracks; (iii) CGCs are clustered with 1358 polysaccharide utilization loci into CGC families (CGC-Fs) to infer glycan substrates; (iv) Metadata and visualization are available for CGC-Fs by substrate, taxonomy, host geographic distribution, and top abundant CAZyme families; (v) CGCs are fully annotated with CAZymes, transporters, signal transduction proteins, transcriptional factors, sulfatases, peptidases, Pfam families, and protein 3D structure comparison results for unannotated proteins; and (vi) User-friendly and highly interactive web interface is provided for easy browsing and downloading of HGM genomes, CGCs, CGC-Fs by glycan substrates and continents.},
}
@article {pmid41262425,
year = {2025},
author = {Morelle-Hungría, E},
title = {Molecular genetics as evidence of environmental harm in ecocriminological analysis.},
journal = {Open research Europe},
volume = {5},
number = {},
pages = {244},
pmid = {41262425},
issn = {2732-5121},
abstract = {This research focuses on the potential of molecular genetics as a tool that can complement the assessment and evaluation of environmental damage from the perspective of green criminology or ecocriminology. This would have an impact on the effectiveness and efficiency of the mechanisms established for assessing the damage caused to ecosystems. We are facing a planetary crisis with the risk of ecosystem collapse, so it is proposed to overcome the limitations that we can identify in traditional criminal law by adopting an ecocentric approach reinforced with innovative mechanisms provided by science. This requires, among other things, recognising the intrinsic value of nature and committing to ecological justice. Molecular genetics methods, such as environmental DNA, metagenomics and population genetics, allow us to visualise the biological and ecological transformations induced by pollutants, even when these are invisible to the naked eye. These techniques provide objective and quantifiable data on biodiversity loss, changes in community composition and even possible genotoxic effects. Therefore, these molecular tests can complement preventive and restorative measures in environmental crimes. By fostering dialogue between science, law, and ethics, this study advocates for an integrated paradigm of environmental damage analysis in which molecular genetics enhances our ability to detect, understand, and legally address ecological damage. The convergence of green criminology, molecular genetics, and ecological justice reorients institutional responses toward restoring ecosystem integrity and defending the rights of nature.},
}
@article {pmid41261745,
year = {2026},
author = {Liu, B and Zhu, L and Zhou, S and Li, A and Xu, P and Han, Y and Shu, Y and Chen, L and Yang, J and Wu, Z},
title = {ZOVER 2.0: a virome-based platform for zoonotic and vector-borne viruses.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D925-D931},
pmid = {41261745},
issn = {1362-4962},
support = {2022FY100905//Science &amp; Technology Fundamental Resources Investigation Program/ ; 2021-I2M-1-038//CAMS Innovation Fund for Medical Sciences/ ; 2024-I2M-ZD-007//CAMS Innovation Fund for Medical Sciences/ ; 32370176//National Natural Science Foundation of China/ ; 2023-PT310-04//Chinese Academy of Medical Sciences/ ; GZNL2024A01019//Major Project of Guangzhou National Laboratory/ ; },
mesh = {*Virome/genetics ; Animals ; *Metagenomics/methods ; *Viruses/genetics/classification ; High-Throughput Nucleotide Sequencing ; Chiroptera/virology ; *Software ; Ticks/virology ; Zoonoses/virology ; Humans ; Culicidae/virology ; Animals, Wild/virology ; Rodentia/virology ; Metagenome ; Genome, Viral ; },
abstract = {Emerging zoonotic and vector-borne viruses pose a continuous threat to global public health, highlighting the need for effective virome surveillance that targets key wildlife reservoirs and vectors. Addressing this challenge requires a systematic understanding of both viral and host diversity, especially across broad spatiotemporal scales. Building on the previous genome-centric release, the upgraded ZOVER 2.0 (https://www.mgc.ac.cn/ZOVER/) expands its scope by incorporating 5883 curated metagenomic next-generation sequencing libraries from 72 independent projects, spanning 12 years and covering 362 distinct wildlife species of bats, rodents, mosquitoes, and ticks. To ensure consistent and sensitive virome profiling across heterogeneous datasets, ZOVER 2.0 employs a standardized analysis pipeline based on reads for taxonomic annotation and viral abundance estimation. After normalization, sequencing reads were collectively assigned to 110 recognized viral families, substantially expanding the known virome diversity within these four wildlife groups. Furthermore, a series of interactive modules enables users to visualize virome composition and perform comparative analyses across different host taxa, geographic regions, and temporal scales. By integrating current genomic and metagenomic knowledge, ZOVER 2.0 provides a robust platform for virus discovery, ecological interpretation, and surveillance of potential interspecies transmission, thereby contributing to One Health-oriented monitoring of emerging infectious diseases.},
}
@article {pmid41261182,
year = {2025},
author = {Prusty, G and Prasad, BR and Polaki, S and Mereddy, S},
title = {Integrative multi-omics characterization of the gut microbiome in Pila globosa: functional insights into nutrient cycling and detoxification potential.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {12},
pages = {464},
pmid = {41261182},
issn = {1573-0972},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Metagenomics/methods ; Proteomics/methods ; *Snails/microbiology ; Phylogeny ; Metagenome ; Multiomics ; },
abstract = {Pila globosa, a freshwater snail endemic to Indian aquatic ecosystems, plays a pivotal role in nutrient cycling and organic matter turnover. In this study, we present the first integrative multi-omics characterization of its gut microbiome using shotgun metagenomics, metaproteomics, and genome-resolved analyses. The gut microbiota was taxonomically diverse yet compositionally stable, dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, with core genera including Pseudomonas, Clostridium, Bacillus, and Streptomyces. Alpha diversity metrics (Shannon = 4.22 ± 0.15; Simpson = 0.90 ± 0.01) and low Bray-Curtis dissimilarity (0.12-0.15) indicated a conserved core microbiome across replicates. Functional profiling through HUMAnN2 and metaproteomic validation revealed enrichment of pathways related to carbohydrate metabolism, short-chain fatty acid (SCFA) synthesis, amino-acid biosynthesis, and oxidative phosphorylation, reflecting the community's contribution to host nutrition and metabolic balance. Genes and proteins associated with xenobiotic degradation (benzoate, toluene metabolism) and oxidative stress response (superoxide dismutase, catalase, glutathione S-transferase) were abundant, suggesting microbial support for redox regulation and detoxification. Twelve high-quality metagenome-assembled genomes (MAGs) reconstructed from dominant taxa encoded traits for secondary metabolite production, metal resistance, and stress tolerance, underscoring their ecological versatility. Together, these results establish a foundational reference for understanding the functional potential of the P. globosa gut microbiome and its possible role in nutrient transformation and pollutant processing in freshwater systems. The study provides baseline data for future comparative and ecotoxicological investigations of gastropod holobionts.},
}
@article {pmid41260397,
year = {2026},
author = {Abbasi, E},
title = {Metagenomic surveillance of emerging viruses in mosquito populations from high-risk regions of Iran.},
journal = {Journal of virological methods},
volume = {340},
number = {},
pages = {115301},
doi = {10.1016/j.jviromet.2025.115301},
pmid = {41260397},
issn = {1879-0984},
mesh = {Animals ; Iran/epidemiology ; *Culicidae/virology ; *Metagenomics ; Phylogeny ; *Arboviruses/genetics/classification/isolation &amp; purification ; *Mosquito Vectors/virology ; *Virome ; High-Throughput Nucleotide Sequencing ; Epidemiological Monitoring ; Computational Biology ; RNA, Viral/genetics ; },
abstract = {BACKGROUND: Mosquito-borne arboviruses pose a growing threat to public health, particularly in ecologically vulnerable and climatically dynamic regions. This study aimed to investigate the diversity of emerging arboviruses in mosquito populations from high-risk provinces in southern and southeastern Iran using a metagenomic surveillance approach.<br><br>METHODS: Adult mosquitoes were collected from 36 sites across Hormozgan, Sistan and Baluchestan, and Khuzestan provinces. Specimens were pooled by species and location, followed by RNA extraction and high-throughput sequencing. Bioinformatics analysis was performed to identify viral taxa and assess phylogenetic relationships.<br><br>RESULTS: A total of 4275 mosquitoes representing six species were analyzed. Virome analysis revealed 43 viral taxa, including medically important arboviruses such as dengue virus serotype 2 (DENV-2), chikungunya virus (CHIKV), and West Nile virus (WNV). Multiple novel viral sequences were also detected, including putative members of Phenuiviridae and Orthomyxoviridae. Viral diversity was highest in Hormozgan province and positively correlated with ambient temperature.<br><br>CONCLUSION: This study provides the first comprehensive metagenomic insight into mosquito viromes in Iran, revealing both endemic and potentially novel arboviruses. These findings underscore the need for integrated genomic surveillance and regional vector-borne disease preparedness.},
}
@article {pmid41260114,
year = {2025},
author = {Ahmad, W and Ray, R and Khan, AL},
title = {Can silicate types regulate plant defense and rhizospheric microbiome diversity differently during heat stress conditions?.},
journal = {The Science of the total environment},
volume = {1007},
number = {},
pages = {180812},
doi = {10.1016/j.scitotenv.2025.180812},
pmid = {41260114},
issn = {1879-1026},
mesh = {*Rhizosphere ; *Microbiota/drug effects ; *Silicates ; *Heat-Shock Response ; *Soil Microbiology ; *Glycine max/physiology/microbiology ; Hot Temperature ; },
abstract = {Silicates (Si) improve plant growth; however, how different types of silicate sources influence plant growth and rhizosphere microbiome remains underexplored. We compare two Si types (pure and bioavailable silicic acid (Si) and mineral magnesium silicate (MgSi)) applied to the soybean (Glycine max L.) rhizosphere to determine whether two silicate types (Si-types) differently impact plant growth, defense responses, and microbiome diversity and function during heat stress. Under heat stress, Si-type treatments improved biomass (86 % with Si and 82 % with MgSi), reduced H2O2 (26 % phyllosphere; 33 % rhizosphere), and enhanced β-glucosidase activity (2.6-fold rhizosphere) compared to heat-only treatment and increased Proteobacteria relative abundance from ∼65 % (heat-only) to ∼74 % in Si-type-treated rhizospheric soil. Si-types showed downregulation of heat shock transcription factors, suggesting regulatory defense effects during heat stress. Metagenome-assembled genomes (MAGs) analysis revealed significant bacterial shifts across the Si-treatments, with Proteobacteria and Bacteroidetes being the dominant phyla in the rhizospheric soil. Under heat stress, the core microbiome comprised 14 rhizosphere genera (including Pelomonas, Achromobacter, Paracoccus, Nocardioides), whereas Pelomonas was the sole core root genus, and Pelomonas puraquae core species in both compartments. MAGs analysis revealed Si-based shifts in microbial metabolic pathways and enrichment of auxin biosynthesis in Si-treated roots during heat stress. Because MgSi supplies both Mg and Si, effects observed with MgSi are interpreted as combined Si + Mg effects. In conclusion, both Si-types caused shifts in microbiome diversity and function, and impacted plant growth and defense responses under heat stress, providing a foundation for improving thermotolerance in plants.},
}
@article {pmid41260011,
year = {2026},
author = {Wang, J and Zhao, S and Shi, X and Sun, B and Tian, Z and Zhang, H and Zhao, Y and Cui, Z and Zhang, J},
title = {Dynamic succession patterns, nitrogen cycling potential, and multi-scale assembly mechanisms of cross-habitat bacterial communities in lakes driven by seasonal frozen conditions.},
journal = {Marine pollution bulletin},
volume = {223},
number = {},
pages = {119004},
doi = {10.1016/j.marpolbul.2025.119004},
pmid = {41260011},
issn = {1879-3363},
mesh = {*Lakes/microbiology ; *Nitrogen Cycle ; *Freezing ; *Bacteria/classification ; Seasons ; Ecosystem ; *Microbiota ; Ice Cover ; Geologic Sediments/microbiology ; Nitrogen ; },
abstract = {Microorganisms are key bioindicators of aquatic environment, yet their dynamics under seasonal ice cover-affecting 50 % of global lakes-remain poorly understood. This study comprehensively employed metagenomics and bioinformatics to analyze the diversity characteristics, species composition, nitrogen cycling potential, and community assembly mechanisms of bacterial communities during frozen and non-frozen periods. Results showed that bacterial species richness and diversity in water were significantly higher during the frozen period compared to the non-frozen period, with both metrics consistently higher in water than in sediment. In winter, ice formation significantly reshaped the bacterial community structure in water, while exerting no notable disturbance on the sediment bacterial community composition. Freezing exerts contrasting regulatory effects on the primary nitrogen cycling functions of bacterial communities in the water column versus the sediments. In the water column, the potential of ammonia assimilation is significantly suppressed during freezing, whereas mineralization and assimilatory nitrate reduction to ammonium persist. In contrast, within the sediments, ice cover generally enhances the activity of major nitrogen transformation pathways, including ammonia assimilation, mineralization, and nitrification. Notably, sediment nitrogen fixation potential is nearly four times higher in non-frozen periods compared to frozen periods. Stochastic processes dominate bacterial community assembly, while the freezing process shifts the dominant role from drift to dispersal limitation. However, in deterministic processes, heterogeneous selection serves as a key regulatory factor. The study revealed the adaptive strategies of bacterial communities to freezing in shallow lakes of cold-arid regions, providing a theoretical basis for ecological risk prediction in frozen lakes and ecological management of shallow lakes in cold-arid regions.},
}
@article {pmid41259660,
year = {2025},
author = {Wahl, NA and Koutsovoulos, G and Bettisworth, B and Stamatakis, A},
title = {raxtax: a k-mer-based non-Bayesian taxonomic classifier.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {12},
pages = {},
pmid = {41259660},
issn = {1367-4811},
support = {101087081//European Union/ ; },
mesh = {*Software ; *DNA Barcoding, Taxonomic/methods ; Algorithms ; Databases, Genetic ; Metagenomics/methods ; },
abstract = {MOTIVATION: Taxonomic classification in biodiversity studies is the process of assigning the anonymous sequences of a marker gene (barcode) or whole genomes (metagenomics) to a specific lineage using a reference database that contains named sequences in a known taxonomy. This classification is important for assessing the diversity of biological systems. Taxonomic classification faces two main challenges: first, accuracy is critical as errors can propagate to downstream analysis results; and second, the classification time requirements can limit study size and study design, in particular when considering the constantly growing reference databases. To address these two challenges, we introduce raxtax, an efficient, novel taxonomic classification tool for barcodes that uses common k-mers between all pairs of query and reference sequences. We also introduce two novel uncertainty scores which take into account the fundamental biases of reference databases.<br><br>RESULTS: We validate raxtax on three widely-used empirical reference databases and show that it is 2.7-100 times faster than competing state-of-the-art tools on the largest database while being equally accurate. In particular, raxtax exhibits increasing speedups with growing query and reference sequence numbers compared to existing tools (for 100&#x2009;000 and 1&#x2009;000&#x2009;000 query and reference sequences overall, it is 1.3 and 2.9 times faster, respectively), and therefore alleviates the taxonomic classification scalability challenge.<br><br>raxtax is available at https://github.com/noahares/raxtax under a CC-NC-BY-SA license. The scripts and summary metrics used in our analyses are available at https://github.com/noahares/raxtax_paper_scripts. The source code, sequence data, and summarized results of the analyses are available at https://doi.org/10.5281/zenodo.15057027.},
}
@article {pmid41259558,
year = {2025},
author = {Issilbayeva, A and Jarmukhanov, Z and Kozhakhmetov, S and Bakytgul, Y and Chulenbayeva, L and Muniz-Terrera, G and Furukawa, M and Nikawa, H and Supiyev, A and Kushugulova, A and Zhumadilova, A},
title = {Oral microbiome patterns of dental caries in Kazakhstani adolescents.},
journal = {Journal of applied oral science : revista FOB},
volume = {33},
number = {},
pages = {e20250476},
pmid = {41259558},
issn = {1678-7765},
mesh = {Humans ; *Dental Caries/microbiology ; Adolescent ; Male ; *Microbiota/genetics ; Female ; Child ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; DMF Index ; Reference Values ; },
abstract = {OBJECTIVE: The oral microbiome is one of the most complex microbial ecosystems in the host. This study aimed to investigate and characterize the oral microbiome composition in Kazakhstani adolescents associated with dental caries.<br><br>METHODOLOGY: The study included 312 adolescents, with 241 individuals presenting with caries and 71 caries-free, aged 12-15 years. Dental caries assessment was performed using DMFT (Decayed, missed, filled teeth) index. Oral samples were collected, and 16S rRNA (16S ribosomal ribonucleic acid) gene sequencing targeting the V3-V4 hypervariable regions on an Illumina MiSeq platform was performed to profile the microbial communities. Functional metagenomic predictions were generated using PICRUSt2 v2.5.0, using the KEGG database for bacterial pathway abundance estimation. Data analysis was conducted using Python 3.9.16 and R 4.2.2.<br><br>RESULTS: The alpha diversity was insignificant, while beta diversity analysis demonstrated clear distinctions by Bray-Curtis (F=2.5, p=0.003) and weighted UniFrac distances (F=4.4, p=0.002). The Neisseria and Prevotella genera, and Gammaproteobacteria class showed significant associations with dental caries (MaAsLin2 p&#x2264;0.05, LDA&#x2265;2), stronger predictive power (AUC=0.65, F1=0.83), and higher predicted functional activity through glutathione metabolism, RNA degradation, and unsaturated fatty acid metabolism pathways.<br><br>CONCLUSIONS: This study identified specific oral microbiome patterns associated with dental caries in Kazakhstani adolescents, revealing interactions between key bacterial taxa and metabolic pathways.},
}
@article {pmid41258716,
year = {2025},
author = {Marsh, CC and Nel Van Zyl, K and Babalola, OO and Böhmer, R and Cowan, DA and Moganedi, KLM and Moroenyane, I and Naidoo, J and Nieves Delgado, A and Posma, JM and Segal, LN and Setati, ME},
title = {From description to implementation: key takeaways from the 3rd African Microbiome Symposium.},
journal = {mSphere},
volume = {10},
number = {12},
pages = {e0068325},
pmid = {41258716},
issn = {2379-5042},
support = {K43 TW012302/TW/FIC NIH HHS/United States ; K43TW012302/NH/NIH HHS/United States ; KIC240402211772//National Research Foundation/ ; },
mesh = {Humans ; Africa ; Biomedical Research ; Congresses as Topic ; *Microbiota ; South Africa ; Translational Research, Biomedical ; },
abstract = {The 3rd African Microbiome Symposium was held in Cape Town, South Africa, from 20 to 22 November 2024. The symposium featured a diverse range of local and international microbiome research and provided a platform for 79 researchers, students, and industry members to engage in discussions on the microbiome within an African context and focusing on translational research. This meeting review shares highlights, findings, and recommendations derived from the event. Insights from two panel discussions revealed key barriers to microbiome research in Africa, including limited funding, infrastructure gaps, and a shortage of trained local scientists. Recommendations centered on increased investment, institutional training, adherence to ethical guidelines, and the fostering of equitable global partnerships.},
}
@article {pmid41258552,
year = {2025},
author = {Singh, G and Tyagi, I and Tyagi, K and Kumar, V and Donthu, RK},
title = {Multi-marker metagenomic assessment of eukaryotic communities in Najafgarh Drain reveals public health and ecological risks.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {12},
pages = {1354},
pmid = {41258552},
issn = {1573-2959},
support = {core funding//Zoological Survey of India/ ; },
mesh = {*Environmental Monitoring/methods ; Public Health ; *Eukaryota/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Metagenomics ; *Metagenome ; Biodiversity ; },
abstract = {A multi-marker sequencing approach was applied to characterize the eukaryotic microbial community of the Najafgarh Drain. It will provide the first comprehensive view of eukaryotic diversity in this system, highlighting both its ecological significance and pathogenic potential. We combined 18S rRNA, internal transcribed spacer (ITS), and whole-metagenome shotgun (WMS) sequencing; 18S rRNA captured broad protist diversity but offered limited fungal resolution, which was complemented by ITS, while WMS provided higher, often species level resolution across kingdoms. To improve WMS classification, a dual-database strategy was employed, sequences were first classified using a eukaryote-filtered NCBI clustered nr database, unclassified sequences were subsequently analyzed with a combined database comprising of SILVA, MIDORI2, PlantITS, and COInr. This approach consistently increased the number of identified genera and species compared with using a single database. Using the multi-marker and dual database approach, multiple phyla were detected, including Chlorophyta (55.72%), Ciliophora (21.46%), Ascomycota (6.44%), Mucoromycota (1.35%), and Nematoda (0.80%). Beneficial taxa such as Chlorella, members of Ciliophora, and Penicillium, known for organic-matter degradation, nutrient cycling, and heavy-metal remediation, were observed. Additionally, human pathogens such as Pneumocystis jirovecii, Rhizopus arrhizus and Trichuris trichiura along with plant pathogenic fungi such as Fusarium, Sporisorium, and Rhizopus were also observed. These findings underscore the need to incorporate eukaryotic pathogen surveillance into water quality monitoring and environmental policy frameworks. Such measures would contribute to more resilient water management practices and support broader public health protection goals.},
}
@article {pmid41258495,
year = {2025},
author = {Gutiérrez-Sarmiento, W and Fosado-Mendoza, M and Lozano-Flores, C and Varela-Echavarría, A},
title = {The Body Wall Microbiome of the Terrestrial Slug Deroceras laeve Reveals Potential Endosymbionts and Shares Core Organisms with Other Mollusks.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {136},
pmid = {41258495},
issn = {1432-184X},
support = {CBF2023-2024-834//SECIHTI/ ; IN211322//DGAPA-UNAM PAPIIT/ ; },
mesh = {Animals ; *Microbiota ; *Symbiosis ; *Gastropoda/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Archaea/classification/genetics/isolation &amp; purification ; *Fungi/classification/genetics/isolation &amp; purification ; Bacteriophages/isolation &amp; purification/genetics/classification ; Phylogeny ; },
abstract = {The marsh slug Deroceras laeve is an invasive mollusk found in gardens, field crops, and wetlands. It lacks a protective shell, suggesting that microbial communities are associated with its adaptability to the environment. Here, we used a whole shotgun metagenomic approach to analyse the complex microbiome of D. laeve and compared it to that of other mollusks. This demonstrated the presence in D. laeve of bacteriophages such as Erwinia phage, Certrevirus, and Machinavirus, which target plant pathogen bacteria. In the Archaea domain the halophilics Halovivax and Halobaculum predominated, but also present were the methanogens Methanobacterium, Methanobrevibacter, Methanocaldococcus, Methanococcus, and Methanosarcina, involved in phosphate solubilization and methanogenesis during decomposition of organic matter. The Bacteria domain was dominated by γ-Pseudomonadota such as Buttiauxella, Citrobacter, Enterobacter, Klebsiella, Kluyvera, Leclercia, and Pseudomonas which are producers of enzymes that degrade biomass and complex carbohydrates. Regarding the fungal community, filamentous or yeast ascomycetes predominated such as Debaryomyces, Puccina, and Pyricularia known as plant pathogens or associated with decaying organic matter. Consistent with these findings, functional analysis revealed enrichment in genes involved in fermentation and carbohydrate metabolism. Remarkably, regardless of species, ecosystem, and tissue type, we found that the core microbiome of the mollusks in this study is mainly structured by the Phyla Uroviricota, Euryarchaeaota, Pseudomonadota, and Ascomycota, with diversity at the genus level. This suggests ancient symbiotic interactions of these mollusks with specific types of microbes which may have been critical for adaptability to their environment.},
}
@article {pmid41258100,
year = {2025},
author = {Wang, C and Zheng, R and Sun, C},
title = {Deep-sea viral diversity and their role in host metabolism of complex organic matter.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10134},
pmid = {41258100},
issn = {2041-1723},
mesh = {*Seawater/virology/microbiology ; *Viruses/genetics/classification/metabolism ; Virome/genetics ; Metagenomics ; Geologic Sediments/virology/microbiology ; *Host Microbial Interactions ; Genome, Viral ; Oceans and Seas ; Ecosystem ; RNA Viruses/genetics/classification ; Microbiota ; Biodiversity ; Carbon Cycle ; Transcriptome ; },
abstract = {Viruses exert a pervasive influence on biogeochemical cycles in deep-sea ecosystems. Cold seeps and seamounts, globally distributed across the oceans and harboring diverse microbial communities, remain largely unexplored regarding their viral inhabitants and functions. By integrating metagenomic, DNA viromic, RNA viromic, and metatranscriptomic data, coupled with characterization of purified viral communities, we uncover the diversity of DNA and RNA viral communities and virus-host interactions, which vary significantly across distinct deep-sea sediment sites. These sites represent a declining cold seep, a site distant from the declining cold seep (sediment site), a nascent cold seep site, and a seamount. The viral community in the nascent cold seep displays unique characteristics, with an increased proportion of RNA viruses and temperate viruses. Viral genomic and metatranscriptomic analyses reveal viral functional genes are actively expressed, potentially enhancing host metabolism of complex organic matter. Here, our findings underscore the diversity, ecological roles, and host interactions of viral communities in different cold seeps and seamounts, suggesting the importance of viruses in deep-sea carbon cycling and microbial community structure.},
}
@article {pmid41255529,
year = {2025},
author = {Horiachok, M and Potapova, K and Ivanykovych, T and Yerokhovych, V and Ilkiv, Y and Sokolova, L},
title = {Integrating gut microbiota into multidisciplinary perspectives on diabetic neuropathy.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1710868},
pmid = {41255529},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetic Neuropathies/microbiology/therapy/metabolism ; *Dysbiosis/microbiology ; Animals ; Probiotics/therapeutic use ; },
abstract = {Diabetic neuropathy (DN) is one of the most common and debilitating complications of diabetes mellitus, yet its precise pathogenesis remains incomplete. Emerging evidence highlights the gut microbiome as a key factor linking metabolic dysfunction, immune activation, and neuronal damage. Even minor dysbiosis may interfere with microbial metabolite balance and disrupt intestinal integrity, leading to local and, consequently, systemic inflammation, which in turn drives altered pain response via the gut-brain-immune axis. Recent clinical and preclinical data show that reduced short-chain fatty acid availability, altered bile acid and tryptophan metabolism, let alone expansion of pro-inflammatory species collaboratively contribute to DN onset and progression. Moreover, advances in metagenomics and metabolomics reveal reproducible microbiome-derived biomarkers that could predict neuropathy risk and pain phenotypes independent of glycemic control, supporting the microbiome as both a mechanistic driver and a measurable potential diagnostic tool. In the context of management, microbiota-affected interventions, such as probiotics, synbiotics, omega-3 supplementation, and fecal microbiota transplantation, show early promise in alleviating symptoms and improving nerve function. This mini-review synthesizes current evidence on the microbiome's role in DN, emphasizing its dual potential as a biomarker for early diagnosis and a therapeutic target for precision microbiome-based interventions.},
}
@article {pmid41255157,
year = {2026},
author = {Chen, J and Wu, C and Yang, R and Chen, Z and Yang, X and Xu, Y and Cheng, X and Sui, H and Zhang, S and Zhu, X and Wu, M and Huang, Y and Chen, X and Liu, H and Yang, J and Tan, X and Chen, F and Cheng, C and Shao, D and Han, X and Shi, B and Yang, C and Leong, KW and Huang, H},
title = {LPS-Binding Hydrogel for TLR4-Mediated Microbiota-Immune Modulation.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {38},
number = {9},
pages = {e14484},
doi = {10.1002/adma.202514484},
pmid = {41255157},
issn = {1521-4095},
support = {82301148//National Natural Science Foundation of China/ ; 82470955//National Natural Science Foundation of China/ ; 2024T170605//China Postdoctoral Science Foundation/ ; RD-02-202511//Research and Develop Program, West China Hospital of Stomatology Sichuan University/ ; 2025ZNSFSC0758//Sichuan Province Science and Technology Support Program/ ; RCDWJS2024-7//West China School of Stomatology, Sichuan University/ ; 24QNMP060//Health Commission of Sichuan Province/ ; TB2022005//Sichuan Provincial Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Lipopolysaccharides/chemistry/metabolism ; *Hydrogels/chemistry/pharmacology ; Mice ; *Toll-Like Receptor 4/metabolism ; Polymyxin B/chemistry/pharmacology ; *Microbiota/drug effects ; Humans ; Mice, Inbred C57BL ; Wound Healing/drug effects ; Polyethyleneimine/chemistry ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Lipopolysaccharide (LPS), a conserved component of Gram-negative bacteria, is a potent immune activator that disrupts tissue repair when released during microbial dysbiosis. LPS-scavenging strategies are often limited by the poor accessibility of lipid A, the bioactive core of LPS, which is shielded by variable oligosaccharide structures and embedded in bacterial membranes. To address this, a synergistic LPS-binding hydrogel (OCMC-PMBP) is developed, combining polymyxin B (PMB) for lipid A-targeted bacterial lysis and polyethyleneimine (PEI) for electrostatic LPS capture. This system is applied to oronasal-perforating wounds, a complex and infection-prone condition associated with cleft palate repair. Clinical microbiome analysis and murine models reveal that LPS-TLR4 signaling contributes to immune dysregulation and impaired healing. OCMC-PMBP treatment reduces LPS levels, restores microbiota balance, suppresses inflammation, and accelerates epithelial regeneration and collagen remodeling. Integrated 16S rRNA sequencing, metagenomics, and single-cell transcriptomics show that the hydrogel reprograms immune cell phenotypes and modulates macrophage interactions with neutrophils, epithelial cells, and fibroblasts across healing phases. This study introduces a biomaterials design combining antimicrobial and immunomodulatory functions to resolve dysbiosis-induced inflammation and enhance regenerative healing in complex mucosal wounds.},
}
@article {pmid41254331,
year = {2025},
author = {Bersch-Ferreira, &#xc2;C and Fonseca, DC and Tramujas, L and Schiavon, CA and Nakagawa Santos, RH and V Machado, RH and Biasi Cavalcanti, A and Marcadenti, A},
title = {Gut Microbiota Composition and Arterial Hypertension Improvement Post-Roux-en-Y Gastric Bypass: GATEWAY Trial Sub-Analysis After 5 Years.},
journal = {Obesity surgery},
volume = {35},
number = {12},
pages = {5346-5356},
pmid = {41254331},
issn = {1708-0428},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Gastric Bypass ; *Hypertension/microbiology/surgery/complications/physiopathology ; Female ; Male ; Adult ; Cross-Sectional Studies ; Middle Aged ; *Obesity, Morbid/surgery/microbiology/complications ; Feces/microbiology ; Treatment Outcome ; Remission Induction ; },
abstract = {INTRODUCTION: The aim of this study was to explore the relationship between gut microbiota composition and hypertension remission in individuals with obesity and hypertension who underwent Roux-en-Y gastric bypass (RYGB) surgery five years prior.<br><br>METHODS: This is a sub-analysis of the GATEWAY trial using cross-sectional data from participants five years post-surgery. Three groups were included: patients who underwent RYGB and achieved hypertension remission (Group 1, n&#x2009;=&#x2009;12), patients who underwent RYGB but did not achieve remission (Group 2, n&#x2009;=&#x2009;12), and a control group of individuals with obesity and hypertension who did not undergo surgery (Group 3, n&#x2009;=&#x2009;15). Gut microbiota composition was evaluated using metagenomic sequencing of fecal samples, with taxonomic classification at the phylum, class, and order levels.<br><br>RESULTS: No statistically significant differences were found in overall microbiota composition between the groups. However, microbial richness was higher in both surgical groups compared to the control group, suggesting a potential link between bariatric surgery and increased gut microbial diversity.<br><br>CONCLUSION: While gut microbiota composition did not significantly differ between individuals with and without hypertension remission, the observed increase in microbial richness among those undergoing bariatric surgery underscores the complex interplay between obesity treatment, gut microbiota, and blood pressure regulation. Further research is needed to elucidate these long-term relationships.},
}
@article {pmid41253025,
year = {2025},
author = {Tian, R and Chen, N and Liu, Z and Yan, YG and Wang, YW and Zhao, P and Bo Zhao, C and Zhang, L and Zhang, Q and Tang, YP},
title = {Lactobacillus johnsonii alleviates rhubarb-induced diarrhoea by regulating the gut microbiota and TLR4/NF-κB signalling pathway.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {149},
number = {},
pages = {157550},
doi = {10.1016/j.phymed.2025.157550},
pmid = {41253025},
issn = {1618-095X},
mesh = {*Rheum/chemistry/adverse effects ; *Gastrointestinal Microbiome/drug effects ; *Toll-Like Receptor 4/metabolism ; *Diarrhea/chemically induced/therapy/microbiology ; Animals ; NF-kappa B/metabolism ; Signal Transduction/drug effects ; Male ; *Lactobacillus ; Wine ; Mice ; },
abstract = {BACKGROUND: Rhubarb (RH) is a commonly used traditional Chinese medicine (TCM) for treating digestive system diseases. However, long-term or excessive use of RH can cause gastrointestinal adverse reactions, such as diarrhoea. RH steaming with wine (PRH) can affect gut microbiota (GM) and alleviate diarrhoea caused by rhubarb. Nevertheless, the causal relationship between differential strains and wine steaming in alleviating RH-induced diarrhoea remains unclear.<br><br>PURPOSE: This study aimed to further elucidate the mechanism of wine steaming in alleviating the RH-induced diarrhoea through establishing a causal relationship.<br><br>METHODS: The components of RH and PRH were detected using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) technology. Differential strains were screened using metagenomic sequencing technology. To evaluate the alleviating effect of Lactobacillus johnsonii (L. john) on RH-induced diarrhoea, the faecal water rate, intestinal propulsion rate, intestinal transit time, and six-hour defecation volume were measured. Histopathological observations of the duodenum, jejunum, and ileum were conducted using the hematoxylin-eosin (HE) staining method. Meanwhile, the levels of inflammatory factors and immunoglobulins (IgG and IgA) in the ileum were detected by enzyme-linked immunosorbent assay (ELISA). The counts of CD4[+], CD8[+], and T regulatory cells (Treg) in peripheral blood were measured using flow cytometry. The protein expression of toll-like receptor 4 (TLR4), nuclear factor kappa-B (NF-&#x3ba;B), zonula occludens-1 (ZO-1), and occludin in the ileum tissue was detected using immunohistochemistry and Western blotting. Faecal samples were analysed using 16S rRNA sequencing technology, and the levels of short-chain fatty acids (SCFAs) were detected using gas chromatography-mass spectrometry (GC-MS). Endogenous metabolites were analysed using UPLC-MS.<br><br>RESULTS: Thirty-seven chemical ingredients in RH and PRH were identified, mainly containing anthraquinones, phenolic acids, and flavonoids. The relative peak areas of anthraquinone components decreased in PRH. Screened from RH and PRH, the differential strain L. john alleviated diarrhoea induced by RH, decreased faecal water rate and intestinal propulsion rate, and improved the degree of pathological damage in the small intestine. L. john can downregulate the levels of inflammatory factors (IL-6, TNF-&#x3b1;, IL-17, and IFN-&#x3b3;), inhibit the expression of TLR4/NF-&#x3ba;B, upregulate the expression of ZO-1 and Occludin, increase the contents of IgG and IgA, CD4[+]/CD8[+] ratio, and Treg cell percentage. The supplementation of L. john can regulate the composition of GM, with decreased Streptococcus and increased norank_f_Muribaculaceae, and elevate the levels of SCFAs, including acetic acid, propionic acid, and butyric acid mediated by GM. Metabolic analysis showed that L. john alleviated the disorder in the glycerophospholipid metabolic pathway.<br><br>CONCLUSION: L. john can alleviate diarrhoea and intestinal pathological damage caused by RH by improving GM dysbiosis and SCFAs level abnormalities, restoring cellular immune function and intestinal barrier function, and regulating abnormal expression of TLR4/NF-&#x3ba;B and release of inflammatory factors. The findings have revealed the causal relationship between GM and the alleviation of RH-induced diarrhoea by steaming with wine and contributed to the understanding of the mechanism of wine steaming in alleviating the RH-induced diarrhoea.},
}
@article {pmid41252568,
year = {2025},
author = {Severino, A and Marchitto, SA and Bisegna, P and Porcari, S and Rondinella, D and Schepis, T and Barbaro, F and Pecere, S and Maida, M and Spada, C and Gasbarrini, A and Cammarota, G and Facciorusso, A and Ianiro, G},
title = {Measuring gut microbiome as a colorectal cancer screening tool: potential and challenges.},
journal = {Expert review of gastroenterology &amp; hepatology},
volume = {19},
number = {12},
pages = {1285-1298},
doi = {10.1080/17474124.2025.2592078},
pmid = {41252568},
issn = {1747-4132},
mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; *Gastrointestinal Microbiome ; *Early Detection of Cancer/methods ; Biomarkers, Tumor ; Predictive Value of Tests ; Feces/microbiology ; Occult Blood ; },
abstract = {INTRODUCTION: Colorectal cancer (CRC) represents a global public health challenge, ranking as the third most prevalent cancer globally. Population-based screening programs for average-risk populations have proven effective in reducing incidence and mortality of CRC through early detection of cancer. The fecal immunochemical test (FIT), the standard diagnostic method in many nations, still falls short in diagnostic effectiveness, resulting in undetected adenomas and, more significantly, unnecessary colonoscopies.<br><br>AREAS COVERED: One of the primary research focuses in the field of CRC is the discovery of new, noninvasive biomarkers. Recent studies, including metagenomic meta-analyses, have discovered common microbial signatures able to reproducibly discriminate between patients with CRC and healthy controls. Based on this evidence, international guidelines have recently recommended the use of microbiome-based biomarkers for CRC screening in clinical settings, although such studies have yet to be conducted.<br><br>EXPERT OPINION: This field of research needs considerable multidisciplinary efforts, including large and geographically different meta-cohorts, and the application of state-of-the-art computational approaches, to identify reproducible signatures able to predict early lesions. Such diagnostic tool would revolutionize CRC screening. More widely, it would provide a mind-set shift in the clinical and scientific community promoting the exploitation of diagnostic and therapeutic microbiome tools in clinical practice.},
}
@article {pmid41252442,
year = {2026},
author = {Zentgraf, J and Schmitz, JE and Rahmann, S},
title = {Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {1},
pages = {},
pmid = {41252442},
issn = {1367-4811},
mesh = {Humans ; *Software ; *Metagenomics/methods ; *Microbiota/genetics ; *DNA Contamination ; Sequence Analysis, DNA/methods ; Algorithms ; *Metagenome ; },
abstract = {MOTIVATION: The first step when working with DNA data of human-derived microbiomes is to remove human contamination for two reasons. First, many countries have strict privacy and data protection guidelines for human sequence data, so microbiome data containing partly human data cannot be easily further processed or published. Second, human contamination may cause problems in downstream analysis, such as metagenomic binning or genome assembly. For large-scale metagenomics projects, fast and accurate removal of human contamination is therefore critical.<br><br>RESULTS: We introduce Cleanifier, a fast and memory frugal alignment-free tool for detecting and removing human contamination based on gapped k-mers, or spaced seeds. Cleanifier uses a pangenome index of known human gapped k-mers, and the creation and use of alternative references is also possible. Reads are classified and filtered according to their gapped k-mer content. Cleanifier supports two filtering modes: one that queries all gapped k-mers and one that queries only a sample of them. A comparison of Cleanifier with other state-of-the-art tools shows that the sampling mode makes Cleanifier the fastest method with comparable accuracy. When using a probabilistic Cuckoo filter to store the complete k-mer set, Cleanifier has similar memory requirements to methods that use a sampled minimizer index. At the same time, Cleanifier is more flexible, because it can use different sampling methods on the same index.<br><br>Cleanifier is available via gitlab (https://gitlab.com/rahmannlab/cleanifier), PyPi (https://pypi.org/project/cleanifier/), and Bioconda (https://anaconda.org/bioconda/cleanifier). The pre-computed human pangenome index is available at Zenodo (https://doi.org/10.5281/zenodo.15639519).},
}
@article {pmid41252249,
year = {2025},
author = {Febinia, CA and Luqman, H and Kusuma, P and Priliani, L and Lewis, J and Wihandani, DM and Pinatih, GN and Sudoyo, H and Almeida, A and Malik, SG and Jacobs, GS},
title = {From sporulation to village differentiation: The shaping of the social microbiome over rural-to-urban lifestyle transition in Indonesia.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116573},
doi = {10.1016/j.celrep.2025.116573},
pmid = {41252249},
issn = {2211-1247},
mesh = {Humans ; Indonesia ; *Rural Population ; *Life Style ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics/classification ; *Urban Population ; Metagenome ; *Microbiota ; Male ; Female ; },
abstract = {Despite established roles in human health and profound global diversity, microbiome datasets remain biased toward Western urban cohorts, with especial under-representation of Southeast Asia. Here, we present a gut microbiome dataset from 116 Indonesians spanning transitional hunter-gatherer, rural agricultural, and urban lifestyles. We identify 1,304 species and 3,258 subspecies by assembling 11,070 metagenome-assembled genomes, revealing substantial species- (15%) and subspecies- (50%) level novelty. Novel taxa are rare, often village specific, and depleted for sporulation genes, revealing a link between bacterial physiology, transmission, prevalence, and discovery. We identify rural-to-urban clines across multiple levels of biological organization, from species abundance to microbiome composition and diversity. Furthermore, between-community, but not within-community, diet variation is strongly predictive of microbiome composition, suggesting that microbiome divergence is driven by community-level differences. Our work highlights the interplay of host lifestyle, population structure, and bacterial physiology in shaping microbiome diversity and biogeography, at the key scale of human communities.},
}
@article {pmid41250628,
year = {2026},
author = {Yathindra, MR and Badugu, R and Singh, SK and Paluri, S and Poudala, H and Swathi, NL},
title = {The role of the urinary microbiome in diabetes-associated UTIs: current understanding and future directions.},
journal = {Journal of basic and clinical physiology and pharmacology},
volume = {37},
number = {1},
pages = {9-24},
pmid = {41250628},
issn = {2191-0286},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/complications ; *Microbiota/physiology ; Probiotics/therapeutic use/administration &amp; dosage ; *Urinary Tract Infections/microbiology ; Dysbiosis/microbiology ; Prebiotics/administration &amp; dosage ; Animals ; *Urinary Tract/microbiology ; Female ; },
abstract = {This review explores the interplay between type 2 diabetes mellitus (T2DM) and urinary microbiome dysbiosis, focusing on its role in urinary tract infections (UTIs). Once considered sterile, the urinary tract hosts a diverse microbiota that supports mucosal immunity and pathogen resistance. In T2DM, chronic hyperglycemia and glycosuria disrupt microbial balance, impair immune responses, and increase UTI susceptibility. Glycosuria promotes pathogenic colonization, biofilm formation, and microbial shifts, with studies reporting a threefold rise in Escherichia coli and a 56 % reduction in Lactobacillus spp. in diabetic women with recurrent UTIs. Diabetic urine shows reduced diversity, higher abundance of Klebsiella, Pseudomonas, and Enterococcus, and elevated IL-8. Microbiota-targeted interventions, including probiotics (Lactobacillus crispatus, Lactobacillus rhamnosus GR-1), prebiotics (astaxanthin), and phytotherapeutics (cranberry), demonstrate potential via lactic acid, hydrogen peroxide production, competitive exclusion, and NF-κB modulation. A 12-month RCT showed significant UTI recurrence reduction with probiotics. Advances in 16 S rRNA sequencing and metagenomics reveal microbial signatures associated with diabetic UTIs, though methodological heterogeneity limits comparability. A review of 1,200 publications (2000-2024) highlights the need for longitudinal studies and precision microbiota therapeutics to translate findings into clinical practice.},
}
@article {pmid41250240,
year = {2025},
author = {Gwak, HJ and Rho, M},
title = {DeepCOI: a large language model-driven framework for fast and accurate taxonomic assignment in animal metabarcoding.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {393},
pmid = {41250240},
issn = {1474-760X},
support = {RS-2020-II201373//the Korea government (MSIT)/ ; 20220517//Ministry of Oceans and Fisheries, Korea/ ; 2023R1A6C101A009//Korea Basic Science Institute/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; Electron Transport Complex IV/genetics ; *Software ; Biodiversity ; Large Language Models ; },
abstract = {Metabarcoding remains challenging due to incomplete taxonomic annotations and computationally intensive processes. We present DeepCOI, a large language model-based classifier pre-trained on seven million cytochrome c oxidase I gene sequences. DeepCOI enables fast and accurate taxonomic assignment across eight major phyla, achieving an AU-ROC of 0.958 and AU-PR of 0.897-outperforming existing methods while significantly reducing inference time. Additionally, DeepCOI demonstrates interpretability by identifying taxonomically informative sequence positions. By integrating large-scale datasets and self-supervised learning, DeepCOI enhances both the accuracy and efficiency of metabarcoding processes, providing a scalable solution for biodiversity assessment and environmental monitoring.},
}
@article {pmid41249313,
year = {2025},
author = {Kok, PJR and Wisse, BB and Kapuściak, M and Lampo, M},
title = {Amphibian supercooling capacity is not limited to sub-zero thermal environments.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40311},
pmid = {41249313},
issn = {2045-2322},
support = {2020/39/D/NZ8/02399//Narodowe Centrum Nauki/ ; },
mesh = {Animals ; Freezing ; *Amphibians/physiology ; Skin/microbiology ; Cold Temperature ; Acclimatization ; Microbiota ; },
abstract = {Freeze-tolerant amphibians initiate controlled freezing using ice nucleators and survive internal ice formation by accumulating cryoprotectants. In contrast, freeze-avoidant (supercooling) species rely on the inhibition of ice nucleators to prevent freezing altogether. All confirmed supercooling species are native to the Northern Hemisphere and regularly endure negative temperatures. The occurrence, ecological role, and underlying mechanisms of supercooling in amphibians remain poorly understood. Here, we demonstrate for the first time that amphibian supercooling capacity may be present even if not expressed (i.e., latent) and not limited to freezing thermal environments. Exploratory metagenomic data allow us to evaluate whether skin-associated bacteria could contribute to freeze avoidance. In addition, using field experiments, we assess cold and dehydration tolerance limits in two syntopic amphibian species from a high tepui summit (Roraima-tepui in Venezuela) and explore the potential role of cryoprotective dehydration in facilitating supercooling. Despite being syntopic, these species showed striking differences in thermal and dehydration tolerance. Physiological freeze avoidance in tropical montane amphibians is shown to be associated with low critical thermal minima, high dehydration tolerance and possibly antifreeze-producing skin microbiota, although the latter needs further investigation. These traits may determine species persistence under shifting climatic regimes, particularly in thermally variable montane systems.},
}
@article {pmid41249223,
year = {2025},
author = {Li, CM and Cheng, TH and Chen, YJ and Liang, YR and Huang, CL},
title = {Crab shell meal promotes root-knot nematode control through shifts in soil microbial communities and enhanced nitrification.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {40115},
pmid = {41249223},
issn = {2045-2322},
support = {108AS-8.5.2-PI-P2//Ministry of Agriculture, Taiwan/ ; Higher Education Sprout Project//Ministry of Education, Taiwan/ ; },
mesh = {Animals ; *Soil Microbiology ; *Cucumis sativus/parasitology/growth &amp; development ; *Microbiota/drug effects ; *Nitrification/drug effects ; Plant Roots/parasitology ; *Tylenchoidea ; Soil/chemistry ; *Plant Diseases/parasitology/prevention &amp; control ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Brachyura/chemistry ; },
abstract = {With growing environmental awareness, eco-friendly agricultural practices are gaining increased attention. Among these, crab shell meal (CSM) is recognized for its potential to suppress root-knot nematodes (Meloidogyne spp.), largely through the enrichment of chitinolytic bacteria, particularly members of the phylum Actinobacteriota. However, the broader effects of CSM on the soil microbiome remain poorly understood. This study employed 16S amplicon metagenomics to investigate the impact of CSM application on the soil bacterial community associated with root-knot nematode-infected cucumber (Cucumis sativus L.) in a pot experiment. Plant growth parameters and soil chemical properties were also assessed. CSM application at concentrations ranging from 0% to 4% significantly altered the soil microbiome, increasing in the relative abundances of Firmicutes and Actinobacteriota in a dose-dependent manner. These microbial shifts were associated with enhanced cucumber growth and reduced nematode infection severity. Functional predictions indicated that CSM-enriched microbial communities exhibited higher potential for chitin hydrolysis and nitrification, processes that likely contributed to nematode suppression and plant growth promotion. By contrast, the introduction of Streptomyces as a biocontrol agent was less effective, as this strain struggled to establish within the potting system. Overall, the application of CSM successfully enhanced the abundance of chitinolytic bacteria and soil nitrification, providing a dual benefit of nematode control and improved plant growth.},
}
@article {pmid41249177,
year = {2025},
author = {Zhang, D and Hu, Q and Zhou, Y and Yu, H and Cong, W and Cheng, M and Wang, J and Liu, X and Zou, K and Long, S and Zhao, C and Jiang, J and Zhang, Y},
title = {Multi-omic profiling reveals distinct gut microbial and metabolic landscapes in golden snub-nosed monkeys under contrasting conservation strategies.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {209},
pmid = {41249177},
issn = {2055-5008},
support = {2020BCA081//Key Research and Development Project of Hubei Province/ ; 2013BAD03B02//National Key Technology R&amp;D Program of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology/chemistry ; Metagenomics/methods ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Conservation of Natural Resources/methods ; Metabolomics/methods ; Metabolome ; *Colobinae/microbiology ; Endangered Species ; Multiomics ; },
abstract = {Gut microbiota are crucial for the fitness of endangered wildlife, yet how different conservation strategies affect these microbial ecosystems and their metabolic activities remains insufficiently understood. This study employed integrated metagenomic and metabolomic analyses to compare the gut microbial communities and fecal metabolomes of endangered golden snub-nosed monkeys (Rhinopithecus roxellana) under three distinct conservation scenarios: natural wild, food provisioning, and captivity. We established a comprehensive species-specific gut microbial gene catalog and observed significant microbial and metabolic divergence associated with each conservation strategy. Monkeys in managed settings (captive and provisioned) exhibited larger gut microbial gene catalogs than wild individuals. While alpha diversity was highest in the provisioned group, both captive and provisioned groups showed notably altered microbial community structures and co-occurrence networks compared to the wild baseline. Captivity was linked to the most pronounced shifts, including a microbiome assembly more strongly governed by deterministic processes, reduced network stability, and an enrichment of habitat specialists, alongside an increased abundance of antibiotic resistance genes (ARGs) and virulence factors (VFs), and distinct alterations in microbiota-metabolite co-variation patterns, particularly concerning amino acid metabolism. These findings highlight that food provisioning, when managed to emulate natural conditions, is associated with a less disruptive microbial and metabolic profile than intensive captivity, offering crucial insights for developing microbiome-informed conservation practices to enhance the health and long-term viability of this endangered primate.},
}
@article {pmid41247052,
year = {2026},
author = {Huang, X and Zeng, J and Yang, F and Liu, Y and Chen, J and Wang, H and Li, S and Li, C and Zhang, S},
title = {Microbial succession in human tissues postmortem: insights from 2bRAD-M sequencing.},
journal = {Microbiology spectrum},
volume = {14},
number = {1},
pages = {e0266624},
pmid = {41247052},
issn = {2165-0497},
mesh = {Humans ; *Postmortem Changes ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Liver/microbiology ; Spleen/microbiology ; Lung/microbiology ; Cadaver ; Male ; Kidney/microbiology ; Metagenomics/methods ; Female ; },
abstract = {Microbial communities play a crucial role in decomposition, yet their patterns in human tissues remain underexplored. Most previous research has often focused on animal models such as mice and swine, with limited studies on human samples, primarily targeting specific environments like the gut and skin. Consequently, gaps persist in understanding postmortem microbial dynamics within internal human organs. The 2bRAD-M sequencing technology offers a powerful approach for human thanatomicrobiome research, overcoming key limitations of 16S rRNA and metagenomic sequencing methods. In this study, we used 2bRAD-M to profile microbial succession across seven human tissues-heart, liver, spleen, lung, kidney, calf muscle, and gut-at various postmortem intervals (PMIs). Significant variations in microbial community composition were observed across organs and decomposition stages, with Proteobacteria dominating early and Firmicutes later. A comparison of frozen and unfrozen cadavers (PMI 1-7 days) revealed divergent microbial shifts in the liver and spleen, while other tissues exhibited limited variation. These findings highlight complex, organ-specific microbial trajectories and suggest that microbial signatures could serve as biomarkers for PMI estimation. This research deepens our understanding of the microbial succession within internal human organs postmortem and contributes to elucidating the identity and role of microorganisms in human decomposition.IMPORTANCEHumans host a diverse array of microbial communities that play a crucial role in the decomposition process after death. Understanding these postmortem microbial dynamics is essential, as they offer valuable insights into the progression of decomposition with significant implications for forensic science. The role of microorganisms in corpse decomposition has gained increasing attention in both forensic and ecological research, but studies in this area remain in their early stages, requiring further in-depth exploration. This work pioneers the use of 2bRAD-M sequencing to investigate microbial changes across various human organs over increasing postmortem intervals. By enhancing knowledge of postmortem microbiota dynamics, the study contributes to refining and improving the accuracy of forensic methodologies.},
}
@article {pmid41243980,
year = {2026},
author = {Aguilar, C and Fontove-Herrera, F and Pashkov, A and García-Estrada, DA and Contreras-Peruyero, H and Guerrero-Flores, S and Ramírez-Sánchez, O and Sélem-Mojica, N},
title = {MicroAgroBiome: a toolkit for exploring specialized metabolism and ecological interactions in rhizosphere microbiomes of cultivated crops.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D1743-D1752},
pmid = {41243980},
issn = {1362-4962},
support = {320237//Secretar&#xed;a de Ciencia, Innovaci&#xf3;n, Tecnolog&#xed;a e Innovaci&#xf3;n (SECIHTI)/ ; //Secretar&#xed;a de Ciencia, Innovaci&#xf3;n, Tecnolog&#xed;a e Innovaci&#xf3;n (SECIHTI) Postdoctoral Fellowship 2025/ ; IN114323//Universidad Nacional Aut&#xf3;noma de M&#xe9;xico/ ; },
mesh = {*Rhizosphere ; *Crops, Agricultural/microbiology ; *Microbiota/genetics ; Soil Microbiology ; *Metagenomics/methods ; Metagenome ; Software ; },
abstract = {The microbiome is crucial to agroecosystems, as it influences plant nutrition, resilience, and overall health. Recent advances in metagenomics have expanded our understanding of plant-microbe interactions, yet curated, high-resolution data capturing the global diversity of crop-associated microbiomes remain scarce. To fill this gap, we developed MicroAgroBiome, a publicly accessible platform that offers standardized taxonomic and functional data, mainly from the rhizosphere microbiomes of agriculturally important crops. The platform integrates 554 metagenomes from 28 crops and soil sample health, advancing microbiome-informed agricultural strategies. It also underscores Latin America's growing leadership in agricultural microbiome research. MicroAgroBiome is available at https://agrobiom.matmor.unam.mx.},
}
@article {pmid41243436,
year = {2025},
author = {Cen, Q and Cui, Y and Jin, J and Feng, J and Xin, Y and Zhang, Z and Li, J and Wang, J and Zhang, A},
title = {Unraveling multiple sclerosis: a hidden interaction between intestinal microbiota and host lipid metabolism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2576657},
pmid = {41243436},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Multiple Sclerosis/metabolism/microbiology/therapy ; *Lipid Metabolism ; Animals ; },
abstract = {Dysregulation of the structure of the gut microbiota is closely linked to the risk of onset and progression of multiple sclerosis. The intricate interaction between the gut microbiota and lipid metabolism likely serves as a crucial pathway mediating this relationship: the gut microbiota directly or indirectly modifies lipid metabolism (including cholesterol, sphingolipids, phospholipids, and fatty acids) by controlling the production of specific metabolites (such as short-chain fatty acids, tryptophan metabolites, bile acids, trimethylamine-N-oxide, and lipopolysaccharides), thereby impacting core pathological processes in multiple sclerosis. Therefore, elucidating the specific roles and mechanisms of the gut microbiota in modulating lipid metabolism in multiple sclerosis will accelerate the development of precision therapeutic strategies. In this review, we conduct an in-depth exploration of the interaction between the gut microbiota and lipid metabolism in the context of multiple sclerosis and provide a comprehensive summary of existing strategies targeting the gut microbiota and lipid metabolism for treating multiple sclerosis (including microbiota-based therapies, pharmacotherapy, and lifestyle modifications). Finally, we outline the present challenges in this field and offer an in-depth prospect for future directions.},
}
@article {pmid41242205,
year = {2026},
author = {Li, X and Gao, X and Yu, S and Du, F and Liu, J and Kan, X and Liu, X and Yao, D},
title = {Rhizosphere microbiota diversity and salt stress-alleviating functional genes in coastal wild salt-tolerant plants.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128397},
doi = {10.1016/j.micres.2025.128397},
pmid = {41242205},
issn = {1618-0623},
mesh = {*Rhizosphere ; Soil Microbiology ; *Salt-Tolerant Plants/microbiology/genetics ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Salt Stress/genetics ; *Microbiota/genetics ; Soil/chemistry ; Salt Tolerance/genetics ; Metagenomics ; Fungi/genetics/classification/isolation &amp; purification ; Plant Roots/microbiology ; Salinity ; Poaceae/microbiology ; Biodiversity ; High-Throughput Nucleotide Sequencing ; },
abstract = {Saline-alkali land significantly threatens global food security and ecological safety, and root-associated microorganisms help plants survive salt-alkali stress. However, the ecological functions and factors that influence the rhizosphere microbiomes of salt-tolerant plants remain poorly understood. In this study, we used high-throughput sequencing and metagenomics to reveal the microbial communities and functional traits of bulk and rhizosphere soil from salt-tolerant species (Suaeda glauca, Phragmites australis, and Spartina alterniflora) growing in saline soil. Bacterial and fungal taxa were significantly enriched in the rhizosphere soil compared to the non-rhizosphere soil. Metagenomic analyses revealed that metabolic pathways, including glycolysis and ABC transporters, were highly enriched in the rhizosphere. Functional profiling indicated that salt stress-related pathways were more abundant in the core genera Pseudomonas and Woeseia. The abundance of functional genes related to plant growth-promoting traits, including phosphate solubilization and salt adaptation pathways, was higher in the rhizosphere soil than in the non-rhizosphere soil, which was mainly driven by soil salinity, total nitrogen content, and total carbon content. Additionally, P. aeruginosa obtained from the rhizosphere of S. alterniflora exhibited high phosphorus solubilization efficiency (908.38 μg/mL), nitrogen fixation activity (2.84 μg/mL) and salt tolerance (≦ 5 % NaCl). These findings demonstrate that salt-tolerant plants shape microbial activities by controlling the rhizosphere microenvironment, mitigating salt stress, providing a scientific and practical foundation for the development of targeted microbial inoculants for saline-alkali land reclamation.},
}
@article {pmid41241073,
year = {2026},
author = {Du, JY and Qin, FL and Yang, RN and Chen, YL and Tan, GF and Li, WJ and Yang, L and Cai, J and Shen, DL and Zhu, HR and Yuan, ML and Zhang, W},
title = {Metagenomic analysis of the gut microbiota in major depressive disorder with different antidepressant efficacy: A prospective cohort study.},
journal = {Journal of affective disorders},
volume = {394},
number = {Pt B},
pages = {120709},
doi = {10.1016/j.jad.2025.120709},
pmid = {41241073},
issn = {1573-2517},
mesh = {Humans ; Male ; *Major Depressive Disorder/drug therapy/microbiology ; *Gastrointestinal Microbiome/genetics/drug effects ; Female ; Adult ; Prospective Studies ; Middle Aged ; *Selective Serotonin Reuptake Inhibitors/therapeutic use ; Metagenomics ; *Antidepressive Agents/therapeutic use ; Feces/microbiology ; *Serotonin and Noradrenaline Reuptake Inhibitors/therapeutic use ; Treatment Outcome ; },
abstract = {BACKGROUND: Major depressive disorder (MDD) is globally prevalent, with Selective Serotonin Reuptake Inhibitors (SSRIs) and Serotonin-Norepinephrine Reuptake Inhibitors (SNRIs) as first-line treatment. However, 30 %-40 % of patients have inadequate response, and early identification is difficult. Gut microbiota contributes to MDD pathogenesis through the gut-brain axis, but baseline differences between responders and non-responders to SSRIs or SNRIs remain unclear.<br><br>METHODS: 82 MDD individuals were initially screened. However, due to issues with the drug administration and fecal sample availability, a total of 43 people were eventually included. Based on 3-month Hamilton Depression Rating Scale (HAMD-17) changes, 29 patients were responders (39.12&#xa0;&#xb1;&#xa0;15.79&#xa0;years, 8 males), while 14 were non-responders (40.14&#xa0;&#xb1;&#xa0;17.28&#xa0;years, 5 males). Baseline assessments encompassed Depression Anxiety scales, demographics, and fecal metagenomic analysis (taxonomic/functional annotation, and differential analysis of microbial species and pathways).<br><br>RESULTS: Baseline demographic characteristics, lifestyle factors, and anxiety/depression scores were comparable. Non-responders had higher relative abundances of Bacteroidaceae and Bacteroide; LEfSe showed responders enriched Hungatella, Ligilactobacillus_ruminis, and non-responders enriched Anaerostipes, Bacteroides_faecis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis identified 246 differentially expressed KEGG Orthologies and 13 pathways, with the steroid biosynthesis pathway (map00100) being enriched in non-responders and the D-amino acid metabolism pathway (map00470) enriched in responders. The study has limitations: small sample size and it lacks direct mechanism validation.<br><br>CONCLUSIONS: The composition and functional pathways of gut microbiota exhibit significant differences between responders and non-responders to SSRIs or SNRIs among MDD patients, providing clues for the development of new treatment strategies.},
}
@article {pmid41240707,
year = {2025},
author = {Fonseca, A and Kenney, S and Boney, J and Ganda, E},
title = {Mycobiome temporal and functional dynamics in broilers: Ecological perspective on bacterial-fungal correlations and the effect of feed additives.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {106092},
pmid = {41240707},
issn = {1525-3171},
mesh = {Animals ; *Chickens/microbiology ; Animal Feed/analysis ; *Mycobiome/drug effects ; Diet/veterinary ; *Fungi/physiology/classification/drug effects ; *Gastrointestinal Microbiome/drug effects ; Bacteria/classification/drug effects ; Random Allocation ; Probiotics/administration &amp; dosage ; Feces/microbiology ; Dietary Supplements/analysis ; Oils, Volatile/administration &amp; dosage/metabolism ; Anti-Bacterial Agents/administration &amp; dosage ; Male ; Bacitracin ; Salicylates ; },
abstract = {The gut mycobiome (the fungal component of the microbiome) of chickens, though less abundant than bacterial populations, plays a vital role in gut ecology, yet remains underexplored. This study investigated the temporal, dietary, and ecological factors shaping the broiler chicken excreta-associated fungal communities and their correlation with bacterial microbiota. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 days in 32 randomly allocated cages. Treatments consisted of four experimental diets: a Basal Diet, a Basal Diet with an Antibiotic (bacitracin methylene disalicylate), an Essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Shotgun metagenomic sequencing was performed on excreta samples collected at days 1, 10, and 21 to evaluate fungal diversity, composition, cross-kingdom correlation and functional profiling. The fungal community was dominated by Ascomycota and Basidiomycota across all treatments and time points. While alpha diversity metrics did not differ significantly between treatments (P > 0.05), fungal richness and evenness increased significantly over time (P < 0.05), indicating age-driven ecological succession. Beta diversity analysis revealed distinct age-related clustering patterns, with early dominance by Candida albicans and later shifts toward genera such as Fusarium and Malassezia. Feed additives exerted limited influence on fungal composition or diversity metrics, although clustering patterns suggested subtle treatment-specific effects over time. Cross-kingdom correlation analysis identified co-occurring temporal dynamics between the two microbial communities. Candida was positively correlated with Streptococcus and Escherichia/Shigella but negatively associated with beneficial genera like Bifidobacterium and Faecalibacterium. Additionally, microbial functional characteristics were observed in each treatment exhibiting metabolic features. Overall, this study demonstrates that excreta fungal succession in the broiler gut is primarily driven by host age and highlights the temporal plasticity of concurrent changes in fungal and bacteria communities. The findings underscore the importance of multi-kingdom ecological approaches to better understand gut health in poultry production.},
}
@article {pmid41239457,
year = {2025},
author = {Kaczmarczyk, M and Kędzierska-Kapuza, K and Skonieczna-Żydecka, K and Surówka, A and Drożdżal, S and Lechowicz, K and Buszman, M and Szkudlarek, U and Cembrowska-Lech, D and Podsiadło, K and Samborowska, E and Łoniewski, I and Ciechanowski, K},
title = {Modulating effects of microbiota on synbiotic intervention outcomes for microbiota-derived trimethylamine, trimethylamine N-oxide and indoxyl sulfate in healthy young medical students: insights from a 12-week randomized clinical trial.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1287},
pmid = {41239457},
issn = {1479-5876},
mesh = {Humans ; *Methylamines/blood ; *Synbiotics ; *Indican/blood ; Female ; Male ; Young Adult ; *Students, Medical ; *Microbiota ; Adult ; Gastrointestinal Microbiome ; *Healthy Volunteers ; },
abstract = {BACKGROUND: Microbiota-derived metabolites, trimethylamine-N-oxide (TMAO) and indoxyl sulfate (IS), have been implicated in cardiovascular, renal, and metabolic diseases. Synbiotic interventions are a promising strategy to modulate these metabolites, but their efficacy may vary depending on host-microbial characteristics. This study investigated whether a multi-strain synbiotic could reduce serum concentrations of trimethylamine (TMA), TMAO, and IS in healthy young adults, and whether baseline characteristics of the gut microbiota influence individual responses to the intervention.<br><br>METHODS: In a 12-week, double-blind, randomized, placebo-controlled trial, 38 healthy young medical students received either a synbiotic or placebo. Serum levels of TMA, TMAO, and IS were measured at baseline, 6 weeks, and week 12, two hours after consuming two eggs. Gut microbiota composition and function were assessed using 16&#xa0;S rRNA gene sequencing and predicted through metagenomic profiling (PICRUSt2). Weighted Gene Co-expression Network Analysis (WGCNA) was applied to identify groups of co-occurring bacterial taxa (ASVs) and functional orthologous groups - KEGG Orthologs (KOs).<br><br>RESULTS: The synbiotic intervention did not produce significant changes in TMA, TMAO, or IS levels across the entire study population. There were no significant changes in alpha diversity or microbiota composition during the intervention. However, baseline microbiota-related factors influenced individual responses to synbiotic therapy. Two taxonomic WGCNA modules, containing Lachnospiraceae and Ruminococcaceae, were associated with greater reductions in IS levels in participants receiving synbiotics. Also, a module containing Lachnospirales and Oscillospirales showed a potential modulatory effect on TMA levels. A KO module enriched in genes involved in bacterial secretion systems, sulfur metabolism, and methanogenesis pathways - including K14083 (mttB) and K14084 (mttC), both implicated in the conversion of TMA to methane - was significantly associated with reductions in TMA.<br><br>CONCLUSIONS: In this randomized, placebo-controlled trial in healthy young adults, the synbiotic did not produce a significant arm-wide effect on post-challenge serum TMA, TMAO, or indoxyl sulfate over 12 weeks. Exploratory moderation analyses suggest that baseline gut-microbiota features, taxonomic and functional, may modulate individual responses, particularly for IS and TMA, supporting a precision-nutrition framework. The translational significance of this study stems from the observation that primary prevention, which is particularly important in metabolic diseases, should be individualised based on the function of the microbiota.},
}
@article {pmid41239201,
year = {2025},
author = {Akanmu, AM and Lawal, IB and Ibrahim, SL and Marle-Köster, EV and Hassen, A},
title = {Metagenomic data from the rumen of South African Mutton Merino sheep supplemented with crude or encapsulated Acacia tannin extracts.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {86},
pmid = {41239201},
issn = {2730-6844},
support = {SRUG2204254606//National Research Foundation/ ; },
mesh = {Animals ; *Rumen/microbiology ; *Tannins/pharmacology/administration &amp; dosage ; *Acacia/chemistry ; Sheep/microbiology ; *Metagenomics ; Gastrointestinal Microbiome ; *Plant Extracts/pharmacology ; Animal Feed ; Dietary Supplements ; },
abstract = {OBJECTIVES: This dataset was generated as part of a study investigating the impact of crude and encapsulated Acacia mearnsii tannin extracts on the rumen microbiota of South African Mutton Merino sheep. The aim was to provide high-quality metagenomic data to support methane mitigation strategies through dietary interventions targeting rumen microbial communities.<br><br>DATA DESCRIPTION: Rumen fluid was collected from 24 rams (six per treatment) fed a total mixed ration (TMR) supplemented with either distilled water (control), monensin (positive control), crude tannin, or microencapsulated tannin. However, one sample did not yield sufficient sequencing depth, resulting in 23 usable datasets. DNA was extracted and subjected to shotgun metagenomic sequencing on the Illumina NovaSeq 6000 platform. The dataset comprises paired-end reads deposited in the NCBI SRA under accession SRP480487. Taxonomic profiling reveals dominant phyla such as Bacteroidetes and Firmicutes, and the presence of archaeal genera such as Methanobrevibacter. This dataset provides insights into the structural and functional composition of the rumen microbiome and may be useful for comparative studies and biotechnology applications.},
}
@article {pmid41239026,
year = {2025},
author = {Cao, D and Huang, W and Pang, M and Li, J and Huang, H and Ma, H and Li, D and Qin, Y and Peng, X and Fan, H},
title = {Investigation of the Alterations in the Gut Microbiota and Intestinal Mucosa in Mice Infected with Echinococcus multilocularis.},
journal = {Acta parasitologica},
volume = {70},
number = {6},
pages = {211},
pmid = {41239026},
issn = {1896-1851},
support = {No. 2020-ZJ-Y01//Key Laboratory Project of the Science and Technology Department of Qinghai Province/ ; Qinghai[2023]-125//The National Clinical Key Specialty Construction Project of Hepatobiliary Surgery (Hydatidosis) at Qinghai University Affiliated Hospital/ ; Qinghai Research Key Laboratory for Echinococcosis//The 2022 Science and Technology Plan Project of Qinghai Department of Science and Technology/ ; },
mesh = {Animals ; *Echinococcus multilocularis/physiology ; *Gastrointestinal Microbiome ; Mice ; *Intestinal Mucosa/pathology/microbiology/parasitology ; RNA, Ribosomal, 16S/genetics ; *Echinococcosis/parasitology/pathology ; Disease Models, Animal ; Feces/microbiology/parasitology ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {PURPOSE: Alveolar echinococcosis (AE), a zoonotic parasitic disease caused by the larval metacestode of Echinococcus multilocularis (E. multilocularis), primarily affects the liver and can invide other organs. Given its extremely poor prognsis, witha 10-year mortality rate exceeding 90% in untreated cases, this study aimed to investigate the characteristics and compositional alterations of the intestinal microbiota in AE-infected hosts and evaluate associated intestinal mucosal damage.<br><br>METHODS: We established a mouse model of AE for analysis. Fecal samples were collected from 12 AE-infected mice and 12 age-matched healthy controls at 3 and 6 months post-infection. Gut microbiota composition was assessed by 16S rRNA gene sequencing. Intestinal tissues were subjected to histopathological exnamination using hematoxylin-eosin staining (H&amp;E staining), Alcian blue-glucogen staining (AB-PAS staining), and Lendrum's fluorescent peach red staining, to evaluate mucosal structural integrity and quantify the Paneth and goblet cells.<br><br>RESULTS: The analysis revealed significant alterations in intestinal microbiota diversity and composition in AE-infected mice compared with controls, with changes becoming more pronounced as the infection progressed. Minimal disruption in microbial ecology was observed at 3&#xa0;months, whereas substantial reductions in alpha diversity and distinct shifts in beta diversity emerged after 6&#xa0;months of chronic infection. Phylum-level analysis showed an early increase in Verrucomicrobiota, Bacteroidota, and Campylobacterota at 3&#xa0;months, followed by a marked enrichment of Verrucomicrobiota and Actinobacteriota at 6&#xa0;months when compared with controls. At the genus level, AE infection led to a rapid depletion of Ligilactobacillus and Lactobacillus between 3 and 6&#xa0;months, while Akkermansia abundance significantly increased. Histopathological examination of intestinal tissue further demonstrated severe mucosal damage, including villous atrophy, reduced crypt depth, a pronounced decrease in Paneth cell density (P&#x2009;<&#x2009;0.01), and reduced goblet cell counts (P&#x2009;<&#x2009;0.05), collectively indicating compromised intestinal barrier integrity.<br><br>CONCLUSION: AE infection induces progressive gut microbiota dysbiosis and compromises intestinal barrier integrity. The specific microbial shifts, particularly the depletion of Ligilactobacillus and enrichment of Akkermansia, represent promising diagnostic biomarkers and potential targets for probiotic supplementation or microbial modulation. To further clarify their roles, future research should incorporate multi-omics strategies, including metagenomics and metabolomics, within larger cohorts to better characterize microbiota-host metabolic interactions and to validate stage-specific microbial biomarkers in AE.},
}
@article {pmid41238915,
year = {2025},
author = {Morad, G and Damania, AV and Melendez, B and Singh, BB and Veguilla, FJ and Soto, RA and Hoballah, YM and Sahasrabhojane, PV and Wong, MC and Ahmed, MM and Rico, RN and Lewis, KN and Wani, K and Shamsutdinova, DD and Lazcano Segura, RN and Ingram, DR and Goethe, EA and Day, A and Flores, II and McDaniel, LK and Chelvanambi, M and Johnson, SB and Dimitriou, F and Gupta, P and Oberai, S and Zal, MA and Doss, P and Jamal, MA and Hayase, E and Wathoo, C and Norberg, LM and Jenkins, SL and Nass, S and Gumin, J and Long, L and Yang, J and Bradley, GR and Bekal, MP and Dono, AG and Pichardo-Rojas, PS and Andrewes, SW and Ballester, LY and Losh, JS and Liang, J and Huo, L and Nielsen, DC and Parker Kerrigan, BC and Brastianos, PK and Fowlkes, NW and Chang, CC and Jenq, RR and Gomez-Manzano, C and Huse, JT and Davies, MA and Lazar, AJ and Bhat, KP and Tandon, N and Esquenazi, Y and Peterson, CB and Puduvalli, VK and Lang, FF and Johnston, CD and Bullman, S and Ajami, NJ and Ferguson, SD and Wargo, JA},
title = {Microbial signals in primary and metastatic brain tumors.},
journal = {Nature medicine},
volume = {31},
number = {11},
pages = {3675-3688},
pmid = {41238915},
issn = {1546-170X},
support = {F32 CA260769/CA/NCI NIH HHS/United States ; P30 CA016672/CA/NCI NIH HHS/United States ; R01 CA256006/CA/NCI NIH HHS/United States ; R01 CA227156/CA/NCI NIH HHS/United States ; 1R01 CA227156-01//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; S10 OD021685/OD/NIH HHS/United States ; P50 CA221703/CA/NCI NIH HHS/United States ; R21 NS130323/NS/NINDS NIH HHS/United States ; P50 CA127001/CA/NCI NIH HHS/United States ; R21 CA283514/CA/NCI NIH HHS/United States ; S10 RR029552/RR/NCRR NIH HHS/United States ; },
mesh = {Humans ; *Brain Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; Tumor Microenvironment ; Female ; *Glioma/microbiology/pathology ; Male ; Prospective Studies ; Middle Aged ; *Microbiota/genetics ; In Situ Hybridization, Fluorescence ; Aged ; Adult ; Bacteria/genetics ; },
abstract = {Gliomas and brain metastases are associated with poor prognosis, necessitating a deeper understanding of brain tumor biology and the development of effective therapeutic strategies. Although our group and others have demonstrated microbial presence in various tumors, recent controversies regarding cancer-type-specific intratumoral microbiota emphasize the importance of rigorous, orthogonal validation. This prospective, multi-institutional study included a total of 243 samples from 221 patients, comprising 168 glioma and brain metastases samples and 75 non-cancerous or tumor-adjacent tissues. Using stringent fluorescence in situ hybridization, immunohistochemistry and high-resolution spatial imaging, we detected intracellular bacterial 16S rRNA and lipopolysaccharides in both glioma and brain metastases samples, localized to tumor, immune and stromal cells. Custom 16S and metagenomic sequencing workflows identified taxa associated with intratumoral bacterial signals in the tumor microenvironment; however, standard culture methods did not yield readily cultivable microbiota. Spatial analyses revealed significant correlations between bacterial 16S signals and antimicrobial and immunometabolic signatures at regional, neighborhood and cellular levels. Furthermore, intratumoral 16S bacterial signals showed sequence overlap with matched oral and gut microbiota, suggesting a possible connection with distant communities. Together, these findings introduce microbial elements as a component of the brain tumor microenvironment and lay the foundation for future mechanistic and translational studies.},
}
@article {pmid41238729,
year = {2025},
author = {Lee, KY and Shin, SH and Park, G and Kang, SH and Kang, HJ and Kim, J and Lee, JJ and Son, GH and Hong, JY},
title = {Shotgun metagenomics of the vaginal microbiome in cervical shortening and preterm birth risk.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39988},
pmid = {41238729},
issn = {2045-2322},
support = {HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; HI21C1624//Korea Health Industry Development Institute (KHIDI)/ ; RS-2023-00252948//Korea government (the Ministry of Science and ICT, the Ministry of Trade, Industry and Energy, the Ministry of Health &amp; Welfare, the Ministry of Food and Drug Safety)/ ; },
mesh = {*Premature Birth/epidemiology/microbiology/physiopathology/prevention &amp; control ; *Vagina/microbiology ; *Cervix Uteri/microbiology/physiopathology ; Humans ; Female ; Microbiota/genetics ; *Metagenomics ; Cervical Length Measurement ; Risk Factors ; East Asian People/statistics &amp; numerical data ; Risk Assessment/methods ; Prospective Studies ; DNA, Bacterial/genetics/isolation &amp; purification ; Pregnancy ; Adult ; },
abstract = {Preterm birth (PTB), a leading cause of neonatal morbidity and mortality, is frequently associated with premature cervical remodeling and vaginal microbiome dysbiosis. Cervical shortening in mid-pregnancy is a well-established risk factor for spontaneous PTB (sPTB), yet the microbial signatures underlying this condition remain underexplored, especially in Asian populations. In this study, we conducted shotgun metagenomic analysis of vaginal samples from 35 East Asian pregnant women with a short cervix and 12 with normal cervical length. Species-level taxonomic profiling and functional pathway analysis revealed reduced Lactobacillus dominance, increased microbial diversity, and enrichment of non-optimal CST IV species, such as Fannyhessea vaginae, Bifidobacterium breve, and Mycobacterium canetti in the short cervix group. Functional profiling showed group differences in pathways related to folate biosynthesis, carbohydrate metabolism, and epithelial barrier regulation. Among women with a short cervix, those who delivered preterm had vaginal microbiomes enriched in opportunistic pathogens, including Peptoniphilus equinus, Treponema spp., and Staphylococcus hominis. Conversely, B. breve, Lactobacillus gasseri, and Lactobacillus paragasseri were associated with full-term delivery. Functions related to glycosylation, structural stability, and degradation of cervical mucin were enriched in the sPTB group. Network analysis identified distinct microbial interactions between Lactobacillus-dominated clusters and CST IV-associated taxa, providing ecological insights that may reflect competitive dynamics and potential influences on cervicovaginal barrier integrity. These findings enhance our understanding of the taxonomic and functional profiles of the vaginal microbiome linked to cervical shortening and sPTB, contributing to improved risk stratification and management strategies for PTB, particularly in women with cervical shortening.},
}
@article {pmid41237940,
year = {2026},
author = {Borroni, D and Lo Monaco, F and Ferraro, S and Mazzotta, C and Settino, M and Gabrielli, F and Papa, FT and Alfonsi, C and Di Pietro, F and Rizzuto, V and Stroffolini, G and Bonzano, C and Laganovska, G and Vanags, J and Rechichi, M and Rocha-de-Lossada, C and Ballesteros-Sánchez, A and Zeppieri, M and Gagliano, C},
title = {Ocular surface microbiota in primary open angle glaucoma.},
journal = {Experimental eye research},
volume = {262},
number = {},
pages = {110734},
doi = {10.1016/j.exer.2025.110734},
pmid = {41237940},
issn = {1096-0007},
mesh = {Humans ; *Glaucoma, Open-Angle/microbiology/drug therapy ; Cross-Sectional Studies ; Male ; Female ; *Microbiota ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Aged ; *Bacteria/genetics/isolation &amp; purification ; Intraocular Pressure/physiology ; DNA, Bacterial/genetics ; *Conjunctiva/microbiology ; *Dysbiosis/microbiology ; },
abstract = {Primary open-angle glaucoma (POAG) is a leading cause of irreversible blindness, yet the contribution of the ocular-surface (OS) microbiota remains poorly defined. We conducted a cross-sectional study including 27 POAG patients on chronic hypotensive therapy and 119 healthy Italian controls, profiled by 16S rRNA amplicon sequencing (Ion GeneStudio S5) and analyzed with QIIME2/phyloseq. POAG samples showed higher α-diversity (Shannon 4.23 vs 2.77; Observed richness 407 vs 154; Wilcoxon q < 1 × 10[-9]) and a distinct β-diversity profile (PERMANOVA p = 0.001; R[2] = 0.104). Compositional shifts included depletion of Firmicutes with loss of Staphylococcus in controls' place, and enrichment of Proteobacteria (e.g., Pseudomonas) together with unclassified Enterobacterales and a larger unclassified fraction. Differential-abundance testing identified numerous significant taxa separating groups, consistent with a more diverse yet less defined microbiota in POAG. These findings indicate an ocular-surface dysbiosis associated with POAG in a treatment-exposed cohort, supporting the relevance of host-microbe interactions and motivating longitudinal, treatment-naïve and functional studies before causal or translational inferences.},
}
@article {pmid41237630,
year = {2025},
author = {Hemmat-Jou, MH and Li, F and Wang, D and Gao, R and Xiao-Xia, Z and Chen, Y and Fang, L},
title = {Metagenomic analysis reveals global landscape of viruses in biogeochemical cycles and microbial resistance in paddy soils and wetlands.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140469},
doi = {10.1016/j.jhazmat.2025.140469},
pmid = {41237630},
issn = {1873-3336},
mesh = {*Wetlands ; *Soil Microbiology ; Metagenomics ; *Drug Resistance, Microbial/genetics ; *Viruses/genetics ; Metagenome ; Microbiota ; },
abstract = {Paddy soils and wetlands form a critical soil-water interface that supports global crop production and biogeochemical cycling. Understanding the role of viruses in these ecosystems is vital for predicting ecosystem resilience. Considering the significance of viruses in microbial community structure and environmental pollution, we analyzed 163 metagenomes from 18 countries in Asia, Europe, America, and Australia. We characterized the global distribution and potential ecological functions of viruses through viral auxiliary metabolic genes (vAMGs), antibiotic resistance genes (vARGs), and metal(loid) resistance genes (vMRGs). We found viruses with globally consistent compositions and host profiles, characterized by high richness and a dominance of lysogenic families. We identified 497 vAMGs associated with carbon, phosphorus, nitrogen, and sulfur cycling, and detected 279 vARGs (conferring resistance to 10 antibiotic) and 141 vMRGs (against 7 metal(loids)). These genes exhibited strong co-localization and co-selection patterns, and their transduction can promote the emergence of multi-resistant microbes, reshaping microbial communities. Therefore, viruses are key mobile vectors for the environmental spread of these genes. By quantifying these pathways, we provide a crucial advancement for ecological risk identification and assessment. This meta-analysis provides a comprehensive overview of virus-mediated biogeochemical processes and resistance gene propagation. We demonstrate that viruses can disseminate antibiotic and metal(loid) resistance, a pollution-driven process that poses potential health risks. Furthermore, by regulating key metabolic pathways, viruses can influence greenhouse gas fluxes. Our findings underscore the necessity of integrating viruses into climate models, pollution mitigation strategies, and One Health policies to assess ecological risks and to protect ecosystem and public health.},
}
@article {pmid41237622,
year = {2025},
author = {Liu, B and Wang, S and Ren, J and Zhang, Z and Ma, J and Li, T and Zhou, Q and Sun, J},
title = {Impacts of non-spherical polyethylene nanoplastics on microbial communities and antibiotic resistance genes in the rhizosphere of pea (Pisum sativum L.): An integrated metagenomic and metabolomic analysis.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140425},
doi = {10.1016/j.jhazmat.2025.140425},
pmid = {41237622},
issn = {1873-3336},
mesh = {*Pisum sativum/microbiology/growth &amp; development/drug effects/metabolism ; *Rhizosphere ; Metagenomics ; *Drug Resistance, Microbial/genetics ; Metabolomics ; *Polyethylene/toxicity ; Soil Microbiology ; *Microbiota/drug effects ; *Microplastics/toxicity ; *Soil Pollutants/toxicity ; Genes, Bacterial ; Bacteria/genetics/drug effects ; },
abstract = {The ecological effects of nanoplastics (NPs) has become a growing concern; however, the influence of non-spherical NPs-which better represent real-world morphologies-remains poorly understood. This study investigated the impact of non-spherical polyethylene (PE) NPs on the growth of pea (Pisum sativum L.) and its rhizosphere microenvironment across different concentration levels (0, 20, and 200 mg/kg) using integrated metagenomics and metabolomics. Results showed that high-dose (200 mg/kg) exposure significantly inhibited plant growth. Although soil physicochemical properties remained unchanged, the rhizosphere microbial communities experienced significant restructuring, characterized by a marked enrichment of Pseudomonas and a reduction in beneficial Rhizobium populations. Metagenomic analysis revealed a concurrent increase in the abundance and diversity of antibiotic resistance genes (ARGs) under non-spherical PE-NP stress. This was accompanied by a shift in bacterial host composition, with a trend toward a higher prevalence of potentially pathogenic taxa such as Pseudomonas aeruginosa. Metabolomics analysis further revealed that non-spherical PE-NPs altered the rhizosphere metabolite profile, thereby significantly driving the succession of ARG hosts. Our integrated analysis enhances the understanding of how non-spherical PE-NPs disrupt microbial communities and elevate the risks of ARGs in rhizosphere soil, highlighting the significance of incorporating environmentally relevant NPs into environmental risk assessments.},
}
@article {pmid41236809,
year = {2025},
author = {Shuvo, MSH and Kim, S and Jo, S and Rahim, MA and Barman, I and Hossain, MS and Jeong, Y and Jeong, H and Kim, S and Seo, H and Song, HY},
title = {Characterization of Gut Microbiota of Honey Bees in Korea.},
journal = {Polish journal of microbiology},
volume = {74},
number = {4},
pages = {428-445},
pmid = {41236809},
issn = {2544-4646},
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; Republic of Korea ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Phylogeny ; },
abstract = {Korea's unique climate and agricultural environment suggest that the gut microbiome of honey bees may possess distinctive compositions influenced by regional factors. With the decline in honey bee populations and rising health challenges, understanding the role of gut microbiomes is essential for enhancing honey bee health and their resilience to environmental stressors. To explore caste-specific gut microbiota and identify microbial signatures associated with honey bee health, this study examined the gut microbial composition of worker bees, queen bees, and drones of Apis mellifera using 16S rRNA gene amplicon sequencing. Analysis of beta diversity and species richness demonstrated significant differences between worker bees and both drones and queens, with no significant differences identified between drones and queens. Notably, Lactobacillus dominated all groups, comprising 98.6% of the drones, 95.4% of the queens, and 68.3% of the workers. Additionally, Bombella was prominent in queens (4%), whereas Gilliamella (23%) and Frischella (4.7%) were notably enriched in workers. Drones and queens exhibited similar gut microbiome profiles, while workers displayed distinctly different compositions. These findings underscore the variation in gut microbiota composition and potential functional roles across honey bee castes. Such microbial distinctions may reflect caste-specific roles and physiological demands within the colony. Future research should investigate the physiological roles of gut microbiota and their contributions to environmental resilience, paving the way for microbiome-based strategies to promote honey bee health. This study lays a crucial scientific foundation for conserving the honey bee ecosystem and promoting sustainable agriculture.},
}
@article {pmid41236788,
year = {2025},
author = {Artale, S and Filiali, F and Beretta, E and Arosio, F and Cazzaniga, F and Tersalvi, C and Sofia, M and Tagliabue, P and Pozzi, P and Colombo, A and Carbone, C and Pietrogiovanna, L and Verga, M and Nova, P and Calori, R and Renso, R and Rota, S and Aglione, S and Manfrida, I and Facendola, G and Trojani, A and Dazzani, MC and Basciani, S and Valsecchi, MG and Capitoli, G and Cocola, C and Consolandi, C},
title = {The Effects of a Modified Mediterranean Diet on Gut Microbiota and Chemotherapy Side Effects in Patients With Metastatic Colorectal Cancer Undergoing First-Line Chemotherapy With or Without Either Antiepidermal Growth Factor Receptor or Antivascular Endothelial Growth Factor Agent: Protocol for a Randomized Pilot Study in Italy.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e72950},
pmid = {41236788},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/drug therapy/pathology ; *Diet, Mediterranean ; Pilot Projects ; Italy ; Female ; Male ; Prospective Studies ; ErbB Receptors/antagonists &amp; inhibitors ; *Antineoplastic Agents/adverse effects/therapeutic use ; Middle Aged ; Aged ; Randomized Controlled Trials as Topic ; Adult ; },
abstract = {BACKGROUND: The gut microbiota is attracting increasing interest as a factor possibly impacting colorectal cancer risk, therapy toxicity, and, as a consequence, patient's quality of life. It has been observed that microbial imbalance in the gut and in cancer tissue is facilitated by a Western type of diet, rich in meat, sugars, and refined grains, while a Mediterranean diet, rich in low saturated fat and fibers, promotes gut eubiosis, and results in reduced risk of developing colorectal cancer. Specifically, a high fiber content diet has been associated with a reduced incidence of therapy related adverse events in patients with malignant melanoma.<br><br>OBJECTIVE: This study aimed to analyze and compare the gut microbiota of patients with metastatic colorectal cancer undergoing first-line chemotherapy with or without a biological agent (antiepidermal growth factor receptor or antivascular endothelial growth factor), and receiving either a free standard Western diet, or a modified Mediterranean diet, and the impact of microbiota on chemotherapy toxicity.<br><br>METHODS: This is a pilot nondrug, interventional prospective, randomized, controlled, single-center (Italian), open-label trial. Patients (n=40) living in Italy, and with a local style of life, will be randomized 1:1 to either a modified Mediterranean diet or a free Western-type diet. Blood and fecal samples will be collected at baseline and control visits, for metagenomic and metabolomic analysis. The primary endpoint is the Firmicutes:Bacteroidetes ratio after completion of the third cycle of first-line chemotherapy (time T1). Secondary endpoints are (1) the percentage of patients experiencing gastrointestinal side effects at T1, (2) the percentage of patients experiencing grade 3/4 gastrointestinal side effects at T1, and (3) changes in the Firmicutes:Bacteroidetes ratio, overall microbiome composition, and metabolome at T1, and after the sixth chemotherapy cycle (T2) versus baseline.<br><br>RESULTS: This pilot trial received ethics approval on July 24, 2024. By July 2025, a total of 17 participants have been recruited. The study will conclude with the visit at T2 for the last enrolled patient. Results are expected to be published in October 2028.<br><br>CONCLUSIONS: This study has the potential to provide critical insights into the role of diet in modifying the gut microbiota, diminishing chemotherapy-related side effects, and possibly enhancing the therapeutic efficacy in metastatic colorectal cancer by improving tolerability. In addition, data may pave the way for future research in immunotherapy, potentially influencing both clinical practice and public health strategies.<br><br>TRIAL REGISTRATION: Clinicaltrial.gov NCT06794931; https://clinicaltrials.gov/search?term=NCT06794931.<br><br>DERR1-10.2196/72950.},
}
@article {pmid41236031,
year = {2025},
author = {Kim, JR and Byun, JS and Jung, JK and Hong, SH and Lee, HJ},
title = {Altered oral microbiome diversity in patients with oral candidiasis.},
journal = {Archives of oral biology},
volume = {180},
number = {},
pages = {106430},
doi = {10.1016/j.archoralbio.2025.106430},
pmid = {41236031},
issn = {1879-1506},
mesh = {Humans ; *Candidiasis, Oral/microbiology/drug therapy ; *Microbiota/drug effects ; Male ; Saliva/microbiology ; Female ; *Fluconazole/therapeutic use/pharmacology ; Middle Aged ; *Antifungal Agents/therapeutic use/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Mouth/microbiology ; Aged ; Adult ; Streptococcus salivarius/drug effects ; Real-Time Polymerase Chain Reaction ; },
abstract = {OBJECTIVE: Oral candidiasis is a common opportunistic infection caused by Candida albicans, particularly in individuals with local or systemic risk factors. This study aimed to investigate how antifungal therapy affects the composition of the oral bacterial microbiome.<br><br>DESIGN: Unstimulated saliva samples were collected from ten patients diagnosed with acute pseudomembranous oral candidiasis before and after fluconazole treatment. Microbiome profiles were assessed using 16S rRNA gene sequencing. Quantitative PCR was performed to validate changes in specific bacterial species.<br><br>RESULTS: Alpha diversity did not change significantly, whereas beta-diversity analyses indicated modest compositional shifts. Antifungal therapy was associated with an increase in Streptococcus salivarius, a commensal linked to mucosal health. The signal was confirmed by species-specific qPCR in paired samples.<br><br>CONCLUSIONS: Fluconazole treatment for oral candidiasis induces modest shifts in the oral bacterial community, particularly increasing the abundance of S. salivarius. These changes may reflect partial recovery of microbial homeostasis, supporting the role of microbiome monitoring and probiotic approaches in post-treatment care.},
}
@article {pmid41235136,
year = {2025},
author = {Wu, Y and Pan, S and Yin, C and Kong, Y and Huo, W and Wang, Q and Wu, J and Li, L and Wei, J and Lu, C and Han, L and Lu, Y},
title = {PSORI-CM02 Restores Epidermal Differentiation in Psoriasis via the Gut Microbiota-Sphingolipid Axis.},
journal = {Drug design, development and therapy},
volume = {19},
number = {},
pages = {9993-10010},
pmid = {41235136},
issn = {1177-8881},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Psoriasis/drug therapy/metabolism/pathology ; Mice ; Humans ; *Cell Differentiation/drug effects ; *Sphingolipids/metabolism ; *Epidermis/drug effects/pathology/metabolism ; Keratinocytes/drug effects/metabolism ; },
abstract = {BACKGROUND: Psoriasis is linked to gut dysbiosis and disturbed sphingolipid metabolism. PSORI-CM02 improves epidermal differentiation, yet its impact on the microbiota-sphingolipid axis remains unknown.<br><br>METHODS: Transcriptomics of patient keratinocytes, Carmofur inhibition in IMQ mice, and multi-omics (metabolomics, metagenomics) of skin, lymph nodes and gut were combined. SPF, PGF and GF mice underwent FMT to test microbiota dependency.<br><br>RESULTS: Psoriatic lesions showed sphingolipid pathway enrichment. Carmofur enhanced differentiation. PSORI-CM02 lowered PASI, spleen index, and tissue levels of ceramide, S1P, C1P and sphingomyelin while restoring Flg, Krt10 and Krt14. It reduced Turicibacter, Bacteroides, Bifidobacterium and Acetobacter. PSORI-CM02-derived microbiota reproduced therapeutic effects in all FMT settings.<br><br>CONCLUSION: PSORI-CM02 reshapes gut microbiota, normalizes sphingolipid metabolism and improves epidermal differentiation to treat psoriasis.},
}
@article {pmid41233937,
year = {2025},
author = {Zhang, P and Roque, B and Romero, P and Shapiro, N and Eloe-Fadrosh, E and Kebreab, E and Diamond, S and Hess, M},
title = {Red seaweed supplementation suppresses methanogenesis in the rumen, revealing potentially advantageous traits among hydrogenotrophic bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {231},
pmid = {41233937},
issn = {2049-2618},
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Methane/metabolism/biosynthesis ; Cattle ; *Seaweed ; *Dietary Supplements ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Fermentation ; Metagenome ; Metagenomics ; Hydrogen/metabolism ; },
abstract = {BACKGROUND: Macroalgae belonging to the genus Asparagopsis have shown to reduce methane (CH4) production during rumen fermentation, while increasing feed efficiency when added to the feed of cattle. However, little is known about how the rumen microbiome responds to Asparagopsis supplementation, and how changes in the microbiome may contribute to changes in rumen function and host phenotype. Here, we generated and analyzed metagenomic and metatranscriptomic data from the rumen microbiome from cows receiving (treatment) and not receiving (control) an Asparagopsis armata supplemented diet.<br><br>RESULTS: Using a combination of metatranscriptome and metagenome analysis, we found that reduction of CH4 emission from animals receiving A. armata was coupled to a significant reduction in the transcription of methanogenesis pathways. Additionally, a significant decrease in the transcription of genes for carbon catabolism and a reorganization of carbon catabolic gene expression occurred at the species level within the rumen microbiome of animals that received red seaweed with their diet. Increased H2 production, a consequence of methanogenesis suppression, was coupled to a significant increase in the transcription of hydrogenases that mediate hydrogenotrophic metabolism in the treatment group. Metatranscriptome analysis identified a single metagenome assembled genome (MAG) of a Duodenibacillus sp., a hitherto uncultured hydrogenotrophic bacterial species, as the dominant driver of this transcriptional change.<br><br>CONCLUSIONS: Comparative genomic analysis between the Duodenibacillus sp. and other hydrogenotrophic rumen organisms revealed metabolic traits that may provide Duodenibacillus sp. with a competitive advantage in H2 scavenging. Our findings provide an initial understanding of how the rumen microbiome responds to a promising CH4 reducing feed additive and serve as a model for alternative stable rumen microbiome states that produce less methane and increase animal productivity. Ultimately, insights from the work presented here might enable the development of advanced microbiome-based strategies to reduce enteric methane production.},
}
@article {pmid41233936,
year = {2025},
author = {Modolon, F and N Garritano, A and J Hill, L and Duarte, G and Bendia, A and de Moura, R and Pellizari, V and Thomas, T and Peixoto, RS},
title = {Putative promiscuous symbionts in deep-sea corals and crinoids may contribute to nitrogen cycling.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {234},
pmid = {41233936},
issn = {2049-2618},
support = {141954/2019-1//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; ANP 21005-4//Shell, Brazil/ ; BAS/1/1095-01-01 and FCC/1/1976-40-01//KAUST/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; *Symbiosis ; *Nitrogen Cycle ; Metagenomics/methods ; Microbiota ; Brazil ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; },
abstract = {BACKGROUND: Crinoids (feather stars) are frequently found in association with corals, yet the physiological and microbial interactions between these organisms remain poorly understood. Both corals and crinoids host symbiotic microorganisms, but the functional roles of these symbionts, particularly in deep-sea environments, are largely unexplored. This study characterizes the microbiomes of the deep-sea corals Desmophyllum pertusum and Solenosmilia variabilis and their associated crinoid Koehlermetra sp. (Thalassometridae) from the Campos Basin, Brazil, to investigate potential cross-host microbial interactions and their ecological implications. We used multiple approaches for this investigation, including amplicon sequencing surveys, genome-resolved metagenomics, and fluorescence in situ hybridization.<br><br>RESULTS: We found that the same endosymbiotic members of the families Endozoicomonadaceae and Nitrosopumilaceae inhabit both corals and the crinoids, suggesting promiscuity in host-symbiont relationships. Metagenomic analysis revealed a novel and dominant Endozoicomonas species (E. promiscua sp. nov.), whose genome encodes pathways for dissimilatory nitrate reduction to ammonia (DNRA). This metabolic capability could provide a substrate for ammonia-oxidizing archaea (Nitrosopumilaceae), indicating a potential cross-host nitrogen-cycling network. Shared microbial taxa between corals and crinoids further support the hypothesis of symbiont promiscuity, where metabolic redundancy may facilitate colonization across species.<br><br>CONCLUSIONS: Our findings suggest that nitrogen cycling plays a key role in structuring microbial symbioses in deep-sea coral-crinoid holobionts. The promiscuous distribution of symbionts across hosts implies that metabolic interactions, such as DNRA-driven ammonia provisioning, could underpin resilience in nutrient-limited environments. This study highlights the importance of microbial versatility in deep-sea ecosystems and provides new insights into how cross-host symbiosis may contribute to biogeochemical cycling in the ocean. Video Abstract.},
}
@article {pmid41233919,
year = {2025},
author = {Vohsen, SA and Gruber-Vodicka, HR and Osman, EO and Saxton, MA and Joye, SB and Dubilier, N and Fisher, CR and Baums, IB},
title = {Deep-sea corals near cold seeps associate with sulfur-oxidizing chemoautotrophs in the family Ca. Thioglobaceae.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {232},
pmid = {41233919},
issn = {2049-2618},
support = {ECOGIG//Gulf of Mexico Research Initiative/ ; },
mesh = {Animals ; *Anthozoa/microbiology ; *Sulfur/metabolism ; Symbiosis ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Chemoautotrophic Growth ; Metagenomics/methods ; Seawater/microbiology ; },
abstract = {BACKGROUND: Corals are known for their symbiotic relationships, yet there is limited evidence of chemoautotrophic associations. This is despite some corals occurring near cold seeps where chemosymbiotic fauna abound including mussels that host sulfur-oxidizing chemoautotrophs from the SUP05 cluster (family Ca. Thioglobaceae). We investigated whether corals near cold seeps associate with related bacteria and report here that these associations are widespread.<br><br>RESULTS: We screened corals, water, and sediment for Thioglobaceae using 16S metabarcoding and found ASVs associated with corals at high relative abundance (10 - 91%). These ASVs were specific to coral hosts, absent in water samples, and rare or absent in sediment samples. Using metagenomics and transcriptomics, we assembled the genome of one phylotype associated with Paramuricea sp. B3 (ASV 4) which contained the genetic potential to oxidize sulfur and fix carbon, and confirmed that these pathways were transcriptionally active. Furthermore, its relative abundance was negatively correlated with the stable isotopic composition of its host coral's tissue suggesting some contribution of chemoautotrophy to the coral holobiont.<br><br>CONCLUSIONS: We propose that some lineages of Thioglobaceae may facultatively supplement the diet of their host corals through chemoautotrophy at seeps or may provide essential amino acids or vitamins. This is the first documented association between chemoautotrophic symbionts and corals at seeps and suggests that the footprint of chemosynthetic environments is wider than currently understood.},
}
@article {pmid41233799,
year = {2025},
author = {Orschanski, D and Rubén Dandeu, LN and Rivero, MN and Labovsky, V and Fernández, EA},
title = {Dermatological implications of alignment-based de-hosting and bioinformatics pipelines on shotgun microbiome analysis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1276},
pmid = {41233799},
issn = {1479-5876},
mesh = {*Microbiota/genetics ; Humans ; *Computational Biology/methods ; *Skin/microbiology ; Metagenomics ; *Dermatology/methods ; },
abstract = {BACKGROUND: The skin microbiome is a critical component of dermatological health, with its dysbiosis implicated in conditions ranging from atopic dermatitis to cancer. Shotgun metagenomics offers an unparalleled resolution for comprehensive taxonomic and functional profiling, yet its application in dermatology is hampered by the high proportion of host DNA and the lack of consensus on best-practice bioinformatic pipelines. While Illumina's proprietary DRAGEN platform is widely used, its closed-source nature and cost limitations necessitate the validation of robust, open-source alternatives to democratize access and enable customization.<br><br>METHODS: This study evaluates the performance of Kraken-based open-source pipeline as a viable alternative to the DRAGEN platform as well as the effect of currently available alignment-based de-hosting methods-Bowtie2, BWA, and Rsubread-to remove human DNA, assuring the use of highly-curated human reference genome thus avoiding the limitations of potentially incomplete or contaminated k-mer-based databases. By using shotgun metagenomic data from 83 healthy individuals we systematically compared the impact of these de-hosting procedures prior to Kraken2/DRAGEN taxonomic classification and functional profiling using HUMAnN 3.0 to assess the influence of methodological choices on skin microbial community composition and metabolic pathway abundance interpretation.<br><br>RESULTS: Our analysis revealed marked discrepancies arising from the choice of de-hosting tool and taxonomic classifier, leading to substantial variability in microbial and functional profiles that could compromise clinical interpretation. Among the pipelines tested, Bowtie2 de-hosting combined with Kraken2 taxonomic classification and HUMAN functional profiling efficiently recovered well-established sex- and age-related bacterial associations in healthy skin that were missed by all other methods, including DRAGEN. This superior performance, together with its customizable features, underscores the value of this workflow for robust and clinically relevant dermatological metagenomic studies.<br><br>CONCLUSIONS: Our findings underscore the decisive impact of bioinformatic pipeline selection on skin microbiome analysis and offer actionable guidance for reproducible and clinically meaningful research. We present a customizable workflow that enhances reproducibility and transparency while improving the translational value of metagenomic data. This approach strengthens the reliability of microbiome studies and supports the development of precision diagnostics and personalized therapeutic strategies in dermatology.},
}
@article {pmid41233350,
year = {2025},
author = {Kim, YJ and Kim, KE and Kim, HJ and Park, JS and Kim, MJ and Kim, SM and Lee, T and Jung, SW},
title = {Dynamics of the DNA Viral Community in Korean Coastal Waters.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1782},
pmid = {41233350},
issn = {2052-4463},
support = {RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science &amp; Technology promotion)/ ; },
mesh = {Republic of Korea ; *Seawater/virology ; *DNA Viruses/genetics/classification ; DNA, Viral ; *Virome ; Metagenomics ; Bacteriophages/genetics ; },
abstract = {Recent advances in metaviromics have revealed vast viral diversity across aquatic environments, yet coastal marine viromes remain underexplored compared to their open-ocean counterparts. In this study, we analyzed 49 surface water samples from 16 coastal sites around Korea, generating 265 gigabases of metagenomic sequence data. Following quality control, 754 DNA viral contigs of ≥10 kb (medium quality or higher) were recovered, with bacteriophages comprising 95% and nucleocytoplasmic large DNA viruses (NCLDVs) 5% of the total. Among these, Puniceispirillum phage HMO-2011 and Micromonas pusilla virus 12 T exhibited the highest relative abundance within their respective groups. In addition, we provided the dataset of environmental parameters such as water temperature, salinity, etc., as well as viral taxonomic profiling of contig-level metadata. This dataset provides a resource for the investigation of coastal DNA viral communities and supports comparative studies across marine environments.},
}
@article {pmid41233306,
year = {2025},
author = {Wu, F and Wang, Y and Mai, Z and Xu, Z and Li, S and Li, Y and Yin, R and Li, J and Yu, Z and Wu, Y and Tian, X and Feng, X and Huo, X and Wang, C and Ma, X},
title = {Human intestinal fungus Clavispora lusitaniae attenuates colitis through Pyruvate decarboxylase-derived Indole-3-ethanol.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9980},
pmid = {41233306},
issn = {2041-1723},
support = {82225048//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82204594//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82474340//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024-MS-147 and 2025-YQ-13//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; },
mesh = {Animals ; *Colitis/chemically induced/microbiology ; Mice ; Humans ; *Indoles/metabolism/pharmacology ; Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Mice, Inbred C57BL ; *Hypocreales/metabolism/genetics ; Inflammatory Bowel Diseases/microbiology ; Male ; Female ; Feces/microbiology ; Disease Models, Animal ; Colon/microbiology/pathology ; Probiotics ; },
abstract = {Gut mycobiome dysbiosis has been implicated in inflammatory bowel disease (IBD). However, it remains unknown whether specific fungal species identified by sequencing directly contribute to IBD pathogenesis. Here, based on analysis of three fecal metagenome datasets of IBD cohorts and a previously established cultivated gut fungi catalog, we identify an IBD-depleted intestinal fungus Clavispora lusitaniae strain P4013B. We show P4013B attenuates DSS-induced colitis in wild-type, antibiotics-treated, and germ-free mice through activation of aryl hydrocarbon receptor (AHR). Using an activity-guided isolation strategy, we identify the P4013B metabolite indole-3-ethanol (IEt) as the AHR agonist mediating the anti-colitis activity. We further validate the role of IEt via engineering strains that overexpress pyruvate decarboxylases producing high yields of IEt. Tea polysaccharide enhanced the anti-colitis activity of P4013B by promoting its proliferation and colonization in the colon. Together, these results suggest that C. lusitaniae P4013B may be explored as a potential probiotic for the treatment and prevention of IBD.},
}
@article {pmid41232906,
year = {2026},
author = {Kumar, S and Matra, S and Rajput, V and Ghode, H and Rathore, D and Kumar, S and Kamble, S and Dastager, S and Bajaj, A and Qureshi, A and Kapley, A and Dharne, M},
title = {Deciphering the antimicrobial resistomes and microbiome landscape of open drain wastewater using metagenomics in a progressive Indian state.},
journal = {Environmental research},
volume = {288},
number = {Pt 2},
pages = {123287},
doi = {10.1016/j.envres.2025.123287},
pmid = {41232906},
issn = {1096-0953},
mesh = {*Wastewater/microbiology ; India ; Metagenomics ; *Microbiota ; *Drug Resistance, Bacterial ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is a growing environmental and public health concern, with wastewater systems are acting as a critical reservoirs for resistant microorganisms and genes. Open drains in densely populated and industrialized regions can accelerate AMR dissemination into the environment. Despite Maharashtra's high urban density and industrial activity, comprehensive metagenomic surveillance of its wastewater resistome is lacking. This study applied high-throughput nanopore sequencing to 138 wastewater samples collected from 23 open-drain sites across three regions of Maharashtra (Western, Mumbai, and Central). Bioinformatic pipelines were used to characterize microbial communities, resistance genes, mobile genetic elements (MGEs), and resistome risk scores. Microbial composition varied significantly across regions, with Mumbai and Central regions explaining up to 13 % of variance at the family level. Thirty indicator taxa were identified through LEfSe analysis. Resistome profiling revealed 28 drug classes and 808 ARGs, dominated by multidrug (40.49 %), macrolide-lincosamide-streptogramin (15.84 %), beta-lactam (7.95 %), and tetracycline (6.52 %). WHO-priority pathogens such as Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa harbored high-abundance ARGs including sul1, mdr(ABC), and acrB. Resistome risk scores were highest in Mumbai, indicating elevated ecological and human health risks. These findings underscore wastewater as a hotspot for AMR persistence and spread. Integrating wastewater-based surveillance within a One Health framework enables systematic tracking of resistance trends, comprehensive assessment of environmental risks, and evidence-driven regional interventions. This integrated approach supports the development of targeted mitigation strategies to curb the spread of antibiotic-resistant contaminants across ecosystems.},
}
@article {pmid41232227,
year = {2026},
author = {Sharma, V and Goel, S and Bisht, K and Kaura, T and Verma, S and Mewara, A and Grover, GS and Biswal, M},
title = {Unveiling the Presence of Coxiella-like bacteria in Rhipicephalus microplus Ticks from Punjab, North India: A 16S rRNA metagenomic study.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110783},
doi = {10.1016/j.vetmic.2025.110783},
pmid = {41232227},
issn = {1873-2542},
mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; India ; Metagenomics ; *Rhipicephalus/microbiology ; *Coxiella/genetics/isolation &amp; purification ; *Bacteria/genetics/isolation &amp; purification/classification ; Phylogeny ; Microbiota ; DNA, Bacterial/genetics ; },
abstract = {In this study, using 16S rRNA gene-based metagenomics, we aimed to determine the presence of infectious bacteria in the ticks collected from Punjab state in north India. Tick samples were collected from the domesticated animals from the Patiala, Ropar, and Mohali districts of Punjab, India from February 2022- April 2022. DNA was extracted, and the library was prepared by targeting the V3-V4 hypervariable region of the 16S rRNA gene. The sequencing was conducted in Illumina using the 300 bp paired-end chemistry. Eight tick samples were analyzed from the Patiala, Ropar and Mohali districts of Punjab, India, revealing a diverse range of bacterial species within the tick microbiome. Seven out of eight samples were found to harbour Coxiella-like bacteria (46-181,607 reads; closely related to C. burnetii based on 16S rRNA [V3-V4] sequence similarity), indicating their abundance in the tick population. Furthermore, the analysis uncovered the presence of other pathogenic bacterial genera, including Staphylococcus, Streptococcus, Corynebacterium, Enterococcus, Pseudomonas, Bordetella, and Micrococcus in the tick microbiome, highlighting the abundance and diversity of infectious organisms within ticks. 16S rRNA gene-based metagenomics enables valuable insights into infectious agents in disease-transmitting vectors. Coxiella-like bacteria were found to be predominant bacterial species in the tick microbiomes in this study. The public health significance of this finding in animals and humans needs to be explored in this region. However, as 16S rRNA sequencing offers limited resolution for distinguishing closely related taxa, further confirmation using additional loci or whole-genome sequencing is warranted.},
}
@article {pmid41231980,
year = {2025},
author = {Gelsinger, DR and Ronda, C and Ma, J and Kar, OB and Edwards, M and Huang, Y and Mavros, CF and Sun, Y and Perdue, T and Vo, PL and Ivanov, II and Sternberg, SH and Wang, HH},
title = {Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6774},
pages = {eadx7604},
doi = {10.1126/science.adx7604},
pmid = {41231980},
issn = {1095-9203},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Gene Editing/methods ; *Bacteroides/genetics/growth &amp; development ; Humans ; Metagenomics/methods ; *CRISPR-Cas Systems ; Symbiosis ; Mice, Inbred C57BL ; Metagenome ; Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce Metagenomic Editing (MetaEdit) as a platform technology for microbiome engineering that uses optimized CRISPR-associated transposases delivered by a broadly conjugative vector to directly modify diverse native commensal bacteria from mice and humans with new pathways at single-nucleotide genomic resolution. Using MetaEdit, we achieved in vivo genetic capture of native murine Bacteroides by integrating a metabolic payload that enables tunable growth control in the mammalian gut with dietary inulin. We further show in vivo editing of segmented filamentous bacteria, an immunomodulatory small-intestinal microbial species recalcitrant to cultivation. Collectively, this work provides a paradigm to precisely manipulate individual bacteria in native communities across gigabases of their metagenomic repertoire.},
}
@article {pmid41231970,
year = {2025},
author = {Coelho, C and Taborda, A and Lorena, C and Frazão, T and Veríssimo, A and Borges, PT and Brissos, V and Tiago, I and Martins, LO},
title = {Shotgun metagenomic mining reveals a new FAD-dependent D-lactate dehydrogenase in an isopod gut microbiome.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {12},
pages = {e0148025},
pmid = {41231970},
issn = {1098-5336},
support = {2020.07928//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.00194.CEECIND//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.02027.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 2022.13872//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; IF/01061/2014/CP1223/CT000//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; LA/P/0087/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; SFRH/BD/148270/2019//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; UIDB/04612/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Lactate Dehydrogenases/genetics/metabolism/chemistry ; Metagenomics ; *Flavin-Adenine Dinucleotide/metabolism ; Metagenome ; Molecular Docking Simulation ; Crystallography, X-Ray ; Catalytic Domain ; Lactic Acid/metabolism ; },
abstract = {UNLABELLED: Shotgun metagenomic sequencing has emerged as a powerful tool for exploring microbial diversity and uncovering genes encoding novel biocatalysts from complex environments. Here, we report the discovery and characterization of a new FAD-dependent D-lactate dehydrogenase (PdG-D-LDH) from the gut microbiome of the isopod Porcellio dilatatus. The enzyme was identified through in silico screening using BLAST and AlphaFold3 and functionally characterized as a homodimeric, thermoactive, and thermostable protein, demonstrating the robustness required for biotechnological applications. PdG-D-LDH exhibits a strong catalytic preference toward D-lactate and preferentially reduces quinones over cytochrome c or molecular oxygen. X-ray crystallography revealed a VAO/PCMH-like fold with a solvent-accessible active site that harbors both a FAD cofactor and an Fe(II) ion. Molecular docking studies provided insights into the structural determinants of its stereoselective substrate recognition. Under mild conditions, the enzyme catalyzed the oxidation of D-lactate to pyruvate with a 90% yield after 24 h of reaction, using molecular oxygen as the electron acceptor.<br><br>IMPORTANCE: This study illustrates how metagenomics, structural biology, and computational tools can jointly drive the discovery of new enzymes with valuable biotechnological applications aligned with circular economic principles. The newly identified D-lactate dehydrogenase, PdG-D-LDH, exhibits thermostability, stereoselectivity, and high catalytic efficiency, providing new insights into the structure-function relationships of lactate-metabolizing enzymes.},
}
@article {pmid41231285,
year = {2025},
author = {Padur Sankaranarayanan, A and Dhanapal, S and Valliyappan, M and Shyu, DJH and Parthasarathy, TN},
title = {Intestinal microbiome diversity and disparity between wild and captive endangered Asian elephants (Elephas maximus indicus) in southern India.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {191},
pmid = {41231285},
issn = {1572-9699},
support = {31950410559//National Natural Science Foundation [NSFC] of China/ ; },
mesh = {Animals ; *Elephants/microbiology ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; *Animals, Wild/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Endangered Species ; Biodiversity ; Phylogeny ; Animals, Zoo/microbiology ; Male ; DNA, Bacterial/genetics/chemistry ; Feces/microbiology ; Female ; },
abstract = {The gut microbiome affects the physical and mental wellbeing of an animal. Several factors, including diet, host physiology, age, sex, lifestyle, and environmental factors, influence the dynamic gut microbiome. We studied the gut microbiome composition of the endangered Asian elephants (Elephas maximus) kept under prolonged captive conditions (15.8 ± 3.9 years) and their wild counterparts, as both were exposed to two different environmental pressures. A total of 648,581 high-quality sequences were obtained, comprising 208 microbial families from 22 phyla and 97 orders, as determined by high-throughput 16S rRNA gene sequencing. Among them, 90% of the microbes belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. Our analysis revealed a distinct variation in the gut microbiome between captive and wild elephants. The captive elephants had a higher abundance of the microbial phyla Kiritimatiellaeota, Tenericutes, Euryarchaeota, and Verrucomicrobia, which suggests that captivity alters the gut microbiome. These findings reveal distinct patterns of gut microbiome diversity between captive and wild elephants, underscoring the role of diet and environmental conditions in shaping the elephant gut microbiome.},
}
@article {pmid41231233,
year = {2025},
author = {Absolon, DE and Jackson, VLN and Monier, A and Smith, AG and Helliwell, KE},
title = {Metagenomics of the MAST-3 stramenopile, Incisomonas, and its associated microbiome reveals unexpected metabolic attributes and extensive nutrient dependencies.},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
pmid = {41231233},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Stramenopiles/genetics/metabolism/classification ; Bacteria/genetics/metabolism/classification ; Phylogeny ; },
abstract = {Protists are polyphyletic single-celled eukaryotes that underpin global ecosystem functioning, particularly in the oceans. Most remain uncultured, limiting the investigation of their physiology and cell biology. MArine STramenopiles (MASTs) are heterotrophic protists that, although related to well-characterized photosynthetic diatoms and parasitic oomycetes, are poorly studied. The Nanomonadea (MAST-3) species Incisomonas marina has been maintained in co-culture with a bacterial consortium, offering opportunities to investigate the metabolic attributes and nutritional dependencies of the community. Employing a metagenomics approach, the 68 Mbp haploid genome of I. marina was retrieved to an estimated completeness of 93%, representing the most complete MAST genome so far. We also characterized the diversity of, and assembled genomes for, 23 co-cultured bacteria. Auxotrophy of I. marina for B vitamins (B1, B2, B6, B7 and B12), but not vitamins C, B3, B5 and B9, was predicted. Several bacteria also lacked complete B-vitamin biosynthesis pathways, suggesting that vitamins and/or their precursors are exchanged in the consortium. Moreover, I. marina lacked the ability to synthesize half the protein amino acids, although genes encoding the complete urea cycle were identified, like diatoms; this may play a role in recycling organic nitrogen compounds. Unexpectedly, we also identified the gene DSYB for dimethylsulphoniopropionate biosynthesis. Biosynthesis of this important stress protectant and bacterial chemoattractant is typically found in photosynthetic eukaryotes and has not been identified before in heterotrophic stramenopiles. Together, our study reveals the metabolic attributes of a hitherto understudied organism, advancing knowledge of the evolution and adaptations of the stramenopiles and informing future culturing efforts.},
}
@article {pmid41229166,
year = {2025},
author = {Houttu, N and Mokkala, K and Lindgren, H and Lotankar, M and Benchraka, C and Pärnänen, K and Saros, L and Muhli, E and Vahlberg, T and Lahti, L and Laitinen, K},
title = {The Relationship Between Gut Microbiota During Pregnancy and the Level of Postpartum Adiposity.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70128},
pmid = {41229166},
issn = {2045-8827},
support = {//This clinical trial was supported by the State Research Funding for university-level health research in the Turku University Hospital Expert Responsibility Area, Research Council of Finland (#258606), the Diabetes Research Foundation, the Juho Vainio Foundation, the Finnish Cultural Foundation, P&#xe4;ivikki and Sakari Sohlberg Foundation, Sigrid Juselius Foundation, and the Finnish Foundation for Cardiovascular Research. Funding to the University of Turku for the metagenomics analyses was provided by Janssen Research and Development, LLC. Himmi Lindgren was partially supported by the Finnish Doctoral Program Network in Artificial Intelligence (AI-DOC)./ ; },
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; *Adiposity ; *Postpartum Period ; Adult ; Body Mass Index ; *Obesity/microbiology ; Metagenomics ; Young Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Overweight/microbiology ; Waist-Hip Ratio ; },
abstract = {Gut microbiota is linked with health, including obesity, in the general population. It is unknown whether adiposity at postpartum is influenced by gut microbiota already during pregnancy. We investigated the association between the gut microbiota's composition and predicted function by metagenomics during pregnancy and the women's adiposity (body mass index [BMI], waist-to-hip ratio [WHR], body fat%) assessed at 1-, 2-, and 5-6-years' postpartum in 257 women with overweight or obesity based on prepregnancy BMI values. Body fat% at 1-year, but not at 2- or 5-6-years' postpartum, was associated inversely with α-diversity during pregnancy. Bacterial species GGB3034 SGB4030 (family Erysipelotrichaceae) was higher in women with normal weight than those in women with obesity at 1-year postpartum (q = 0.02), other species being borderline statistically significant (q < 0.25). High WHR and body fat% at 1-year postpartum were associated with two species (q < 0.25). Considering predicted functions of bacteria, an association was detected for BMI, WHR, and body fat%, e.g., body fat% and glycogen biosynthesis I (q < 0.25). Gut microbiota during pregnancy predicted the BMI and body fat% at 1-year postpartum (ROC > 0.50, p < 0.02). Postpartum adiposity was associated with several species and α-diversity. Gut microbiota during pregnancy may be involved in the persistence of obesity and its comorbidities after pregnancy.},
}
@article {pmid41228422,
year = {2025},
author = {Diotaiuti, P and Misiti, F and Marotta, G and Falese, L and Calabrò, GE and Mancone, S},
title = {The Gut Microbiome and Its Impact on Mood and Decision-Making: A Mechanistic and Therapeutic Review.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
pmid = {41228422},
issn = {2072-6643},
support = {MUR Decree n. 105123.06.2022 PNRR Missione 4 Componente 2 Investimento 1.5-CUP H33C22000420001//Project ECS0000024 "Ecosistema dell'innovazione-Rome Technopole" financed by EU NextGeneration EU plan/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Affect/physiology ; *Decision Making/physiology ; Animals ; Cognition ; Probiotics ; Dysbiosis/microbiology ; Fecal Microbiota Transplantation ; Prebiotics/administration &amp; dosage ; },
abstract = {Background/Objectives: The gut microbiome is increasingly recognized as a key modulator of central nervous system function through the gut-brain axis. Dysbiosis has been associated with neuropsychiatric disorders such as depression, anxiety, impulsivity, cognitive decline, and addiction. This review aims to synthesize mechanistic insights and therapeutic perspectives on how gut microbiota influence mood regulation, decision-making, and cognitive processes. Methods: A comprehensive narrative review was conducted using peer-reviewed articles retrieved from PubMed, Scopus, and Web of Science up to August 2025. Studies were included if they explored microbiota-related effects on behavior, mood, cognition, or decision-making using human or animal models. Emphasis was placed on molecular mechanisms, microbiome-targeted therapies, and multi-omics approaches. Results: Evidence indicates that gut microbiota modulate neurochemical pathways involving serotonin, dopamine, GABA, and glutamate, as well as immune and endocrine axes. Microbial imbalance contributes to low-grade systemic inflammation, impaired neuroplasticity, and altered stress responses, all of which are linked to mood and cognitive disturbances. Specific microbial taxa, dietary patterns, and interventions such as probiotics, prebiotics, psychobiotics, and fecal microbiota transplantation (FMT) have shown promise in modulating these outcomes. The review highlights methodological advances including germ-free models, metagenomic profiling, and neuroimaging studies that clarify causal pathways. Conclusions: Gut microbiota play a foundational role in shaping emotional and cognitive functions through complex neuroimmune and neuroendocrine mechanisms. Microbiome-based interventions represent a promising frontier in neuropsychiatric care, although further translational research is needed to define optimal therapeutic strategies and address individual variability.},
}
@article {pmid41228409,
year = {2025},
author = {Xu, C and Cui, H and Fang, Q and Tu, P and Cui, X},
title = {Steamed Panax notoginseng Saponins Ameliorate Cyclophosphamide-Induced Anemia by Attenuating Gut-Liver Injury and Activating the cAMP/PI3K/AKT Signaling Pathway.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
pmid = {41228409},
issn = {2072-6643},
support = {202202AG050021//the Yunnan Major Scientific and Technological Projects/ ; },
mesh = {Animals ; *Saponins/pharmacology ; *Panax notoginseng/chemistry ; *Cyclophosphamide/adverse effects ; Signal Transduction/drug effects ; *Anemia/chemically induced/drug therapy ; Proto-Oncogene Proteins c-akt/metabolism ; Mice ; Cyclic AMP/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Gastrointestinal Microbiome/drug effects ; Male ; Liver/drug effects/metabolism ; Colon/metabolism/drug effects ; },
abstract = {Background: Steamed Panax notoginseng saponins (SPNSs) can alleviate cyclophosphamide-induced anemia. However, the hepatointestinal effects of SPNSs and their role in ameliorating cyclophosphamide-induced anemia remain unexplored. Objective: To elucidate the hepatointestinal effects of SPNSs and their role in ameliorating cyclophosphamide-induced anemia. Methods: Blood samples were collected and analyzed on days 7 and 14. Liver tissues and small intestinal villi structures were observed via HE staining. Liver and colon content metabolites were detected by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Liver proteins were analyzed by using an Orbitrap Astral mass spectrometer. Colon content microbiota composition was assessed via metagenomics. Signaling pathway protein expression was analyzed via Western blotting (WB). Results: SPNSs significantly increased the red blood cell (RBC) count and hemoglobin (HGB) level by day 14 and alleviated hepatointestinal damage. Hepatic metabolomics revealed: the most abundant metabolites were fatty acids and stachyose on day 7 and amino acid and arachidonic acid derivatives on day 14. KEGG analysis implicated cAMP signaling. Proteomics revealed upregulated immune-related proteins and enhanced PI3K pathway activity (WB-validated). Colon content metabolomics showed increased daidzein, 3-(2,5-dimethoxyphenyl) propanoic acid, γ-CEHC, and adenosine in SPNS groups on day 14. Metagenomics indicated differential abundances of Heminiphilus faecis, Phocaeicola sartorii, and s-bacterium_J10.2018 on day 14. Multiomics integration demonstrated significant correlations between hepatic metabolites, hematopoietic proteins, colon content metabolites, and probiotic bacteria. Conclusions: SPNS alleviates cyclophosphamide-induced hepato-intestinal injury in anemic mice by modulating the gut microbiota and enhancing hepato-intestinal immune defense. Additionally, SPNSs ameliorate anemia in cyclophosphamide-treated mice by activating the cAMP/PI3K/AKT pathway, promoting hepatocyte proliferation, and increasing hematopoietic protein expression.},
}
@article {pmid41226831,
year = {2025},
author = {Stoyancheva, G and Mihaylova, N and Gerginova, M and Krumova, E},
title = {Endometrial Microbiome and Reproductive Receptivity: Diverse Perspectives.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
pmid = {41226831},
issn = {1422-0067},
support = {&#x41a;&#x41f;-06-&#x41d;83/6//Scientific Research Fund at the Ministry of Education and Science, Bulgaria/ ; },
mesh = {Humans ; Female ; *Endometrium/microbiology ; *Microbiota ; *Embryo Implantation ; Dysbiosis/microbiology ; *Reproduction ; },
abstract = {The human endometrium, previously considered a sterile environment, is now recognized as a low-biomass but biologically active microbial niche critical to reproductive health. Advances in sequencing technologies, particularly shotgun metagenomics, have provided unprecedented insights into the taxonomic and functional complexity of the endometrial microbiome. While 16S rRNA sequencing has delineated the distinction between Lactobacillus-dominant and non-dominant microbial communities, shotgun metagenomics has revealed additional diversity at the species and strain level, uncovering microbial signatures that remain undetected by amplicon-based approaches. Current evidence supports the association of Lactobacillus dominance with endometrial homeostasis and favorable reproductive outcomes. Dysbiosis, characterized by increased microbial diversity and enrichment of anaerobic taxa such as Gardnerella, Atopobium, Prevotella, and Streptococcus, is linked to chronic endometritis, implantation failure, and adverse IVF results. Beyond compositional differences, the endometrial microbiome interacts with the host through immunological, metabolic, and epigenetic mechanisms. These interactions modulate cytokine signaling, epithelial barrier integrity, and receptivity-associated gene expression, ultimately influencing embryo implantation. However, discrepancies between published studies reflect the lack of standardized protocols for sampling, DNA extraction, and bioinformatic analysis, as well as the inherent challenges of studying low-biomass environments. Factors such as geography, ethnicity, hormonal status, and antibiotic exposure further contribute to interindividual variability. Culturomics approaches complement sequencing by enabling the isolation of viable bacterial strains, offering perspectives for microbiome-based biotherapeutics. Emerging 3D endometrial models provide additional tools to dissect microbiome-host interactions under controlled conditions. Taken together, the growing body of data highlights the potential of endometrial microbiome profiling as a biomarker for reproductive success and as a target for personalized interventions. Future research should focus on integrating multi-omics approaches and functional analyses to establish causal relationships and translate findings into clinical practice. This review gives a new insight into current knowledge on the uterine microbiome and its impact on implantation success, analyzed through the lenses of microbiology, immunology, and oxidative stress.},
}
@article {pmid41226812,
year = {2025},
author = {Kondo, T and Kondo, S and Nakayama-Imaohji, H and Tada, A and Tabassum, N and Munyeshyaka, E and Koyano, K and Nakamura, S and Kusaka, T and Kuwahara, T},
title = {Comparative Analysis of Mucosa-Associated and Luminal Gut Microbiota in Pediatric Ulcerative Colitis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
pmid = {41226812},
issn = {1422-0067},
support = {24K14726//JSPS KAKENHI/ ; 23K28020//JSPS KAKENHI/ ; },
mesh = {Humans ; *Colitis, Ulcerative/microbiology/pathology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; *Intestinal Mucosa/microbiology/pathology ; Adolescent ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Dysbiosis/microbiology ; },
abstract = {Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn's disease, are chronic disorders relating to gut microbiota dysbiosis. Despite severe pancolitis being more prevalent in pediatric UC than in adults, alterations in the colon mucosa-associated microbiota (MAM) and their association with disease severity remain to be elucidated. The present study aimed to compare the gut microbiota in colon lavage fluids (CLFs) and fecal samples from 19 pediatric UC and 19 non-IBD patients. The community structure of MAM inferred by 16S metagenomic analysis was similar throughout the colon regardless of disease type. Bacterial compositions between MAM and feces were significantly different in non-IBD, while no difference was observed in pediatric UC, indicating a compromised mucous layer that could not sufficiently separate the MAM and luminal microbiota in UC. In pediatric UC, homogenous distribution of MAM was gradually disordered with increases in disease activity or mucosal inflammation, and bacterial groups of upper digestive tract or environmental origin were more abundant in MAM. Monitoring key bacterial markers in MAM, which include Lactobacillus and Enterococcus or Faecalibacterium and Blautia as increased or reduced members in pediatric UC, respectively, might be useful for evaluation of patient prognosis.},
}
@article {pmid41226502,
year = {2025},
author = {Kuo, TH and Wu, PH and Liu, PY and Chuang, YS and Tai, CJ and Kuo, MC and Chiu, YW and Lin, YT},
title = {Identification of Gut Microbiome Signatures Associated with Serotonin Pathway in Tryptophan Metabolism of Patients Undergoing Hemodialysis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
pmid = {41226502},
issn = {1422-0067},
support = {MOST 111-2314-B-037-032-MY3//Ministry of Science and Technology, Taiwan/ ; MOST 111-2314-B-037 -083 -MY3//Ministry of Science and Technology, Taiwan/ ; KMUH-DK(C)113003//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH-DK(B)110003-4//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2M08//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R21//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R76//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1M60//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1R73//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH110-0M73//Kaohsiung Medical University Hospital, Taiwan/ ; NHRIKMU-111-I003-2//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-113-I005//Kaohsiung Medical University, Taiwan/ ; NYCUKMU-112-I006//Kaohsiung Medical University, Taiwan/ ; KT112P012//Kaohsiung Medical University, Taiwan/ ; KT113P006//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-114-I001//Kaohsiung Medical University, Taiwan/ ; S11209//Kaohsiung Medical University, Taiwan/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Tryptophan/metabolism ; *Serotonin/metabolism ; Male ; Female ; Middle Aged ; *Renal Dialysis ; Aged ; Melatonin/metabolism ; Metagenomics/methods ; Adult ; },
abstract = {Serotonin, a tryptophan metabolite, exerts a significant influence on both brain and gut functionality. While previous research has elucidated the intricate dynamics of the gut-brain axis, the interplay between serotonin pathway metabolites and gut microbiota in individuals undergoing hemodialysis remains largely unexplored. Therefore, this study aimed to investigate gut microbiota composition corresponding to serotonin pathway metabolite levels among patients with hemodialysis. A total of 85 patients undergoing hemodialysis were selected. Their gut microbiota was analyzed using shotgun metagenomic sequencing profiling. The serotonin pathway metabolites, including 5-hydroxytryptophan (5-HTP), serotonin, 5-methoxytryptophan (5-MTP), 5-methoxytryptamine, melatonin, and 6-hydroxymelatonin, were analyzed with the liquid chromatograph-tandem mass spectrometer. The robust linear discriminant analysis Effect Size (LEfSe) was employed to reveal the gut microbiota signature according to levels of serotonin pathway metabolites. A significant β-diversity difference in 5-Methoxytryptamine (p = 0.037) was found, while no variance in α-diversity was detected. Using LefSe analysis, we identified an enriched Tannerellaceae family in the high-hydroxytryptophan (5-HTP) group, the Odoribacteraceae family in the high-serotonin group, the Eubacteriales order in the high-5-methoxytryptophan (5-MTP) group, the Prevotella copri species in the high-5-Methoxytryptamine group, and the Clostridium genus in the high-melatonin group. In contrast, an enriched Clostridiaceae family in the low-5-HTP group, the Clostridiaceae family in the low-serotonin group, and the Bacteroides ovatus species in the low-5-MTP group were found. Distinct gut microbiota signatures linked to serotonin pathway metabolites were identified in patients undergoing hemodialysis. These findings provide insights for future gut-brain axis research and may guide methods to modulate gut microbiota to influence serotonin metabolites.},
}
@article {pmid41225454,
year = {2025},
author = {Ohmichi-Tomiwa, M and Kato-Kogoe, N and Kudo, A and Fujita, D and Sakaguchi, S and Tsuda, K and Omori, M and Hayashi, E and Nakamura, S and Nakano, T and Ohmichi, M and Tamaki, J and Ueno, T},
title = {Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants.},
journal = {BMC pregnancy and childbirth},
volume = {25},
number = {1},
pages = {1198},
pmid = {41225454},
issn = {1471-2393},
mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *Microbiota ; *Mouth/microbiology ; Adult ; Prospective Studies ; Infant ; Infant, Newborn ; *Pregnancy Complications/microbiology ; Case-Control Studies ; Postpartum Period ; },
abstract = {BACKGROUND: Hypothyroidism is a metabolic disorder associated with potentially adverse maternal and neonatal outcomes. Emerging evidence suggests a link between thyroid function and the microbiota; however, little is known about the oral microbiota of pregnant women with hypothyroidism and its potential impact on that of their offspring. This study aimed to characterize the oral microbiota of pregnant women with hypothyroidism and their children as part of the Oral Microbiome Prospective Unicenter Cohort Study (OMPU-CS).<br><br>METHODS: Pregnant women with hypothyroidism (Hypothyroid group, n&#x2009;=&#x2009;31) and those with normal thyroid function (Control group, n&#x2009;=&#x2009;30) were selected from participants in the ongoing OMPU-CS. Oral samples were collected from the women during pregnancy and at one month postpartum, and from their one-month-old infants. Microbiota composition was analyzed using 16&#xa0;S rRNA metagenomic sequencing.<br><br>RESULTS: Compared with pregnant women in the Control group, those in the Hypothyroid group exhibited significantly reduced richness and evenness of the oral microbiota (observed operational taxonomic units, p&#x2009;=&#x2009;0.034; Shannon index, p&#x2009;=&#x2009;0.034). The overall structure of the oral microbiota differed significantly between groups at all phases-in pregnant women, postpartum women, and their infants (unweighted UniFrac distances, p&#x2009;=&#x2009;0.002, p&#x2009;=&#x2009;0.049, and p&#x2009;=&#x2009;0.019, respectively). Linear discriminant analysis effect size (LEfSe) identified several differentially abundant taxa, including a consistently reduced abundance of members of the Rhizobiaceae family in the Hypothyroid group across all three phases compared with that in the Control group.<br><br>CONCLUSIONS: The oral microbiota of pregnant women with hypothyroidism and their one-month-old infants exhibited disease-specific characteristics. These findings suggest that maternal hypothyroidism may influence the oral microbiota of offspring, underscoring the importance of monitoring oral microbiota in mothers with hypothyroidism and their children.},
}
@article {pmid41225248,
year = {2025},
author = {Bignami, G and Monzón-Atienza, L and Leuzzi, D and Scicchitano, D and Candela, M and Gómez-Mercader, A and Jlidi, M and Gustinelli, A and Tedesco, P and Fioravanti, ML and Castro, PL and Acosta, F},
title = {"Effects of Bacillus Velezensis D-18 on Health Status of European Seabass (Dicentrarchus labrax) Experimentally Challenged with Vibrio harveyi".},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41225248},
issn = {1867-1314},
support = {28740//Horizon 2020/ ; },
abstract = {In recent years, the use of probiotics as a possible alternative to antibiotics has generated a growing interest in the global aquaculture field. In this study, the probiotic Bacillus velezensis D-18 was evaluated for its potential protective effect against the marine pathogen Vibrio harveyi. The probiotic was administered through the diet of European seabass (Dicentrarchus labrax) for 30 days, followed by an in vivo challenge with V. harveyi to assess whether the D-18 strain could enhance host resistance to infection. Biofilm formation in tanks was also investigated to analyze its composition and if there are antagonistic interactions between the two bacterial species. From a histological perspective, significant changes were observed in intestinal morphological parameters after infection, the area and base of the villi appeared to increase in the probiotic-fed groups as did the number of goblet cells and in the serum antibacterial activity which was increased in the infected group that received the probiotic compared to baseline levels. The intestinal microbiome was also analyzed to monitor the composition and determine whether different diets before and after infection induced any changes. Although no significant differences were found in the metagenomics of the tank biofilm and the gut microbiome, mortality rates showed that the probiotic provided effective protection against the pathogen. These findings support the potential of B. velezensis D-18 as a viable alternative to antibiotics, particularly when included in the diet prior to disease onset.},
}
@article {pmid41225104,
year = {2026},
author = {Kars, G and Alkebsi, BLA and Keleş, S and Altan, H and Özer, H and Holyavkin, C and Karaselek, MA},
title = {Recent Insights on Dental Caries Microbiota in Pediatric Patients with Inborn Errors of Immunity.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {291-313},
pmid = {41225104},
issn = {0065-2598},
mesh = {Humans ; *Dental Caries/microbiology/immunology ; *Microbiota/immunology ; Child ; Dysbiosis/immunology/microbiology ; *Mouth/microbiology/immunology ; },
abstract = {Inborn errors of immunity (IEIs) are genetic disorders that impair immune defense and regulation, increasing susceptibility to infections, including those in the oral cavity. The oral microbiota plays a vital role in maintaining oral health, and in pediatric patients with IEIs, disruptions in this balance can lead to dental caries and other oral diseases. This chapter provides a comprehensive analysis of the relationship between immune deficiencies and oral microbiota dysbiosis, focusing on dental caries in children with IEIs. Omics technologies, particularly metagenomics, have enhanced understanding of the microbial diversity and metabolic activities within the oral microbiota of the patients. Key findings reveal that compromised immune responses in children with IEIs disrupt the balance of oral bacteria, making them more prone to dental caries. The chapter highlights the importance of an interdisciplinary approach, integrating microbiology, immunology, dentistry, and bioinformatics, to uncover the complex interactions between the oral microbiome and the immune system. The insights gained from this research will contribute to the development of personalized therapeutic strategies, improving the dental and overall health of pediatric patients with IEIs.},
}
@article {pmid41225090,
year = {2026},
author = {Ziaei, H and Rezaei, N},
title = {Introduction to Oral Immunity.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {3-21},
pmid = {41225090},
issn = {0065-2598},
mesh = {Humans ; *Mouth/immunology/microbiology ; Microbiota/immunology ; Animals ; *Immunity, Innate ; *Immunity, Mucosal ; *Mouth Mucosa/immunology/microbiology ; Adaptive Immunity ; },
abstract = {The oral immune system functions as a primary line of defense, composed of oral epithelial barriers, salivary antimicrobial factors, and various innate and adaptive immune components to prevent pathogen entry. Resident immune cells in oral tissues help maintain tolerance to commensal microorganisms while simultaneously responding to harmful external stimuli and contributing to systemic immune regulation. This chapter provides a comprehensive overview of the immunological components and their functions in the oral cavity, emphasizing the dual role of maintaining tolerance to commensal microbes and dietary antigens while initiating protective responses against pathogens. Any disruptions in this balance, such as oral dysbiosis or immune dysregulation, can lead to the development of local inflammatory conditions; it may also contribute to systemic immune disturbances and related pathologies. Immune mechanisms also regulate craniofacial development and postnatal bone remodeling and regeneration, mainly through cytokine-mediated signaling pathways and interactions between stem cells and immune cells. Several local and systemic immunological pathways are often dysregulated in oral inflammatory conditions, which makes them important therapeutic targets. Therapeutic strategies targeting these pathways include immune checkpoint inhibitors, microbiome-directed interventions, stem cell-based therapies, and salivary diagnostics for real-time and noninvasive immune profiling. These offer promising approaches for restoring oral and systemic immune balance. Finally, this chapter has reviewed recent technological advances, such as single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, metagenomics, and multi-omics integration, in the context of oral immunity. These novel techniques are transforming oral immunology, since they enable high-resolution characterization of cellular, microbial, and molecular interactions, and support the transition toward establishing more precise diagnosis and treatment plans. These findings suggest that oral immunity plays a critical role in linking local mucosal defense and systemic immune responses. Therefore, understanding oral immune mechanisms in health and inflammatory conditions is important for revealing disease pathogenesis and guiding targeted interventions.},
}
@article {pmid41224755,
year = {2025},
author = {Gupta, S and Almeida, A},
title = {Integration of metagenome-assembled genomes with clinical isolates expands the genomic landscape of gut-associated Klebsiella pneumoniae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9959},
pmid = {41224755},
issn = {2041-1723},
support = {MR/W016184/1//RCUK | Medical Research Council (MRC)/ ; },
mesh = {*Klebsiella pneumoniae/genetics/isolation &amp; purification/classification/pathogenicity ; Humans ; *Genome, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Klebsiella Infections/microbiology ; *Metagenome/genetics ; Metagenomics/methods ; Virulence Factors/genetics ; Genetic Variation ; },
abstract = {Klebsiella pneumoniae is an opportunistic pathogen causing diseases ranging from gastrointestinal disorders to severe liver abscesses. While clinical isolates of K. pneumoniae have been extensively studied, less is known about asymptomatic variants colonizing the human gut across diverse populations. Developments in genome-resolved metagenomics have offered unprecedented access to metagenome-assembled genomes (MAGs), expanding the known bacterial diversity within the gut microbiome. Here we analysed 656 human gut-derived K. pneumoniae genomes (317 MAGs, 339 isolates) from 29 countries to investigate the population structure and genomic landscape of gut-associated lineages. Over 60% of MAGs were found to belong to new sequence types, highlighting a large uncharacterized diversity of K. pneumoniae missing among sequenced clinical isolates. In particular, integrating MAGs nearly doubled gut-associated K. pneumoniae phylogenetic diversity, and uncovered 86 MAGs with >0.5% genomic distance compared to 20,792 Klebsiella isolate genomes from various sources. Pan-genome analyses identified 214 genes exclusively detected among MAGs, with 107 predicted to encode putative virulence factors. Notably, combining MAGs and isolates revealed genomic signatures linked to health and disease and more accurately classified disease and carriage states compared to isolates alone. These findings showcase the value of metagenomics to understand pathogen evolution and diversity with implications for public health surveillance strategies.},
}
@article {pmid41224035,
year = {2026},
author = {Wu, X and Wang, C and Wang, D and Yu, Z and Meng, F},
title = {Microbiota ecology upon moderate concentrations of total ammoniacal nitrogen enhances methane production of anaerobic membrane bioreactor.},
journal = {Bioresource technology},
volume = {441},
number = {},
pages = {133630},
doi = {10.1016/j.biortech.2025.133630},
pmid = {41224035},
issn = {1873-2976},
mesh = {*Bioreactors/microbiology ; *Methane/biosynthesis ; Anaerobiosis ; *Nitrogen/pharmacology ; *Microbiota/drug effects/genetics ; *Ammonia/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Membranes, Artificial ; Sewage/microbiology ; Biofuels ; },
abstract = {In this study, the ecological responses of microbial community of anaerobic membrane bioreactor (AnMBR) upon exposure to moderate concentration total ammoniacal nitrogen (TAN) were studied to unveil the underlying mechanisms of reactor performance variation. The 16S rRNA gene and community assembly analysis indicated that the moderate ammonia concentration imposed limited selection pressure on the methanogenic community. Instead, the community assembly was governed by the random birth, death, and reproduction of community members. Network analysis further suggested that the moderate concentration of TAN established strong cooperative linkage between hydrogenotrophic methanogens (HM) and syntrophic acetate oxidizing bacteria (SAOB) in AnMBR. Metagenome sequencing analysis provided convergent evidence that there were enriched genes responsible for the SAOB-HM pathway as well as direct interspecific electron transfer. Moreover, the morphology of anaerobic granular sludge (AnGS) suggested that the decreased particle size enhanced substrate mass transfer efficiency among community members and the methanogens in inner layer of AnGS received more protection from its neighbors in moderate TAN phases. Consequently, the biogas production, methane yield and specific methanogenic activity (SMA) of granular sludge in moderate TAN phases were significantly increased compared to the low TAN phase. Together, this study has expanded our understanding of facilitation of moderate concentration TAN-containing wastewater treatment on AnMBR process.},
}
@article {pmid41223471,
year = {2025},
author = {Zhang, Y and Gao, M and Zhang, X and Tang, A and Wang, S and Wang, X},
title = {How microalgae-bacteria consortia adapt sulfamethoxazole pressure: Insights from physiological and genetic responses.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140406},
doi = {10.1016/j.jhazmat.2025.140406},
pmid = {41223471},
issn = {1873-3336},
mesh = {*Sulfamethoxazole/pharmacology/toxicity ; *Microalgae/drug effects/genetics/physiology/metabolism ; *Water Pollutants, Chemical/toxicity ; Adaptation, Physiological ; *Bacteria/drug effects/genetics/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Microbial Consortia/drug effects ; Reactive Oxygen Species/metabolism ; Photosynthesis/drug effects ; },
abstract = {Microalgae-bacteria consortia (MBC) are regarded as an energy-saving alternative for wastewater treatment process, while their reliability is challenged under long-term antibiotic pressure. Unfortunately, the underlying physiological and genetic mechanisms enabling adaptation to such prolonged antibiotic pressure remain largely unknown. This study systematically investigates the adaptive responses of MBC systems to sulfamethoxazole (SMX) pressure during two exposure stages (100 and 200 μg/L). While the system remained stable at 100 μg/L SMX (stage I), its performance declined at 200 μg/L (stage II), with COD and ammonium removal decreasing by 7.5 % and 8.8 %, respectively. This was accompanied by adverse physiological responses, including a 36.3 ± 3.2 % decrease in photosynthetic oxygen production, a 96.2 ± 9.7 % increase in ROS levels, and a 49.0 ± 5.3 % reduction in EPS content. Remarkably, both pollutant removal and physiological state were fully restored following a 100-day recovery period. This resilience may be attributed to the enrichment of microbial communities such as Chlorophyta and Bacillariophyta, whose presence strongly correlated with reduced antibiotic resistance gene (ARG) dissemination. Genetic analysis further indicated that suppressed ATP synthase and electron transfer within the oxidative phosphorylation pathway may represent important adaptive costs. Fortunately, the response regulators within the two-component system functioned as central mediators, coordinating both extracellular EPS secretion and intracellular antioxidant activity. Overall, this study advances current understandings of adaptive mechanism and offers insights for facilitating stable operation under long-term antibiotic pressure.},
}
@article {pmid41222645,
year = {2025},
author = {Rana, S and Das, KK and Singh, SK and Bhattacharyya, D},
title = {Deciphering Fungal Communities in Three Species of Phlogacanthus Nees (Acanthaceae) Using Amplicon-Metagenomic Analysis.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {16},
pmid = {41222645},
issn = {1432-0991},
mesh = {*Acanthaceae/microbiology ; *Fungi/classification/genetics/isolation &amp; purification ; *Mycobiome ; Phylogeny ; DNA, Fungal/genetics ; High-Throughput Nucleotide Sequencing ; Biodiversity ; },
abstract = {Fungal communities play vital roles in plant health, nutrient cycling, and ecological balance. Species of Phlogacanthus Nees, valued for their medicinal and ecological importance, harbor diverse fungal microbiomes that may influence growth, resilience, and metabolite production. This study investigated fungal communities associated with three Phlogacanthus species-P. tubiflorus Nees (SKS-1), P. thyrsiformis (Roxb. ex Hardw.) Mabb. (SKS-2), and P. curviflorus (Wall.) Nees (SKS-3)-using high-throughput amplicon-metagenomic sequencing of the ITS2 region on the Illumina MiSeq platform. A total of 153 operational taxonomic units (OTUs) were identified, with SKS-2 showing the highest richness (129 OTUs), followed by SKS-1 (112) and SKS-3 (95). Seventy OTUs were shared across all species, while 10, 22, and 8 were unique to SKS-1, SKS-2, and SKS-3, respectively. Alpha diversity indices (Chao1, ACE, Shannon, Simpson, Inverse Simpson, Fisher's alpha) confirmed SKS-2 as the most species-rich fungal habitat. A high proportion of unclassified taxa in SKS-2, along with dominance of Pleosporales, suggests the presence of novel fungi with ecological and biotechnological significance. Beta diversity analysis using Bray-Curtis dissimilarity and Principal Coordinate Analysis revealed significant differences among the fungal communities of the three species. Overall, SKS-2 emerged as the most diverse habitat, while SKS-3 supported a unique but less diverse assemblage. This is the first report profiling fungal microbiomes of Phlogacanthus species. The results highlight their potential as reservoirs of endophytes with applications in plant growth promotion, stress tolerance, biocontrol, enzyme production, and bioactive metabolite discovery, offering leads for sustainable agriculture and biotechnology.},
}
@article {pmid41222145,
year = {2025},
author = {Koo, H and Heber, K and Tian, S and Connolly, ST and Hao, F and Zhao, J and Swencki-Underwood, B and Patterson, AD and Townsend, GE and Bisanz, JE},
title = {A synthetic gut microbiota provides an understanding of the maintenance and functional impact of phage.},
journal = {mBio},
volume = {16},
number = {12},
pages = {e0234125},
pmid = {41222145},
issn = {2150-7511},
support = {R01 GM147178/GM/NIGMS NIH HHS/United States ; T32 GM156692/GM/NIGMS NIH HHS/United States ; R35 GM151045/GM/NIGMS NIH HHS/United States ; R00 AI147165/AI/NIAID NIH HHS/United States ; T32 DK120509/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Bacteriophages/physiology/isolation &amp; purification/genetics ; *Bacteroides/virology/genetics ; Germ-Free Life ; },
abstract = {UNLABELLED: Phages are under intense study as therapeutics and mediators of microbial community behavior; however, tractable models are needed to study phages in the context of the mammalian gut. To address this gap, we isolated phages against members of a synthetic gut microbial community (sFMT), identifying the Bacteroides uniformis JEB00023 (DSM 6597) phage HKP09. While resistance to HKP09 was observable within hours of infection in monoculture, high titers of HKP09 were maintained in vitro and in gnotobiotic mouse models over extended periods. Sequencing of resistant B. uniformis lines revealed phase variation upstream of a capsular polysaccharide locus driving the generation of resistant and sensitive subpopulations, thus demonstrating a mechanism allowing stable coexistence of both virus and bacterial host. Communities infected in vitro and in vivo with HKP09 showed transiently reduced loads of B. uniformis DSM 6597. Its impact in the gut was distinct from communities constructed without its host B. uniformis strain (sFMT∆JEB00023). Rather than a compensatory increase in closely related Bacteroides strains, the most significant impacts were observed on distantly related strains, demonstrating that phage perturbations more broadly impact community structure in ways not easily predicted by phylogeny or simple strain exclusion. Metabolomic analyses of the feces of HKP09-infected sFMT-colonized gnotobiotic animals demonstrated altered abundances of amino acids and microbial fermentation products compared to uninfected mice and those colonized with sFMT∆JEB00023. Taken together, these data provide a controlled model for studying phages in the context of the mammalian gut, providing mechanistic insights into phage-host dynamics and their consequences on the function of microbial communities.<br><br>IMPORTANCE: Phages are key members of the gut microbiome, but the understanding of their biological significance for host health lags behind their bacterial hosts. In this study, we demonstrate the use of a phage-infection model using defined, synthetic microbial communities that colonize the intestinal tract of mice. We uncovered that spontaneous inversions in the genome of Bacteroides uniformis perpetually generate subpopulations, which are either sensitive or resistant to phage infection, allowing for the coexistence of predator and prey in this species. Phage infection demonstrated broad impacts on community structure and metabolism in animals, which are not easily predicted by the exclusion of the viral host. This research demonstrates a tractable approach through which the impacts of phage on both the microbiome and mammalian host can be deciphered.},
}
@article {pmid41222144,
year = {2025},
author = {Ericsson, AC and McAdams, ZL and Dorfmeyer, RA and Hart, ML and O'Neill-Blair, A and Amos-Landgraf, J and Franklin, CL},
title = {Dominant effects of the immediate environment on the gut microbiome of mice used in biomedical research.},
journal = {mSystems},
volume = {10},
number = {12},
pages = {e0111225},
pmid = {41222144},
issn = {2379-5077},
support = {U42 OD010918/OD/NIH HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; },
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Biomedical Research ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Environment ; },
abstract = {Studies using genetically engineered mouse (GEM) models are often performed over extended periods. The microbiomes of GEM colonies are expected to retain some of the microbial features present in the founder mice used to generate each GEM model and to acquire new features through dietary and environmental sources. The rate at which these processes occur over time likely varies between institutions. To assess the relative effect size of environment on the microbiome of GEMs used in biomedical research, we performed 16S rRNA metabarcoding of fecal samples from 275 distinct GEM lines (n = 351) maintained by 139 different laboratories at 84 different research institutions in 34 U.S. states or districts and seven other countries, and compared intra-strain, inter-strain, inter-lab, and inter-institution similarities. Reference data from mice harboring supplier-origin (SO) microbiomes (n = 1,171) were used to determine the relative contribution and nature of microbes from known and unknown sources. Paradoxically, the data indicate that the immediate laboratory-level environment is the dominant factor shaping the microbiome of GEM models, but that the microbiome of GEMs develops similarities in beta-diversity, regardless of other factors. Related to this, we detected an unexpectedly high prevalence and abundance of Helicobacter spp. in GEM microbiomes, the abundance of which correlated significantly with the abundance of multiple resident taxa colonizing the mucosa. These findings suggest a higher prevalence of Helicobacter spp. in laboratory mice than previously appreciated, and the possibility of positive and negative interactions with other taxa is found to affect GEM model phenotypes.IMPORTANCEThere are concerns regarding the reproducibility and predictive value of mouse models of human disease. Notwithstanding those legitimate concerns, genetically engineered mouse (GEM) models provide an invaluable platform to investigate gene function or effects of environmental factors in a biological system. The microbiome of GEM models significantly influences model phenotypes and thus represents a possible source of poor reproducibility. While the microbiome is often incorporated in research investigating disease mechanisms using GEMs, limited information is available regarding the similarity of the microbiome of GEM models within and between research labs at the same institution, or across institutions. Moreover, while the microbiome of founder mice from different suppliers is known to differ, the degree to which features present in supplier-origin microbiomes are retained in GEM colonies throughout experimentation is unclear. These data demonstrate the robust effect of lab-level environment and the need for sample collection concurrent with phenotyping.},
}
@article {pmid41218604,
year = {2025},
author = {Lyu, L and Fan, Y and Bryrup, T and Clos-Garcia, M and Brix, S and Eiken, M and Stankevic, E and Lund, AB and Knop, FK and Jørgensen, NR and Vestergaard, H and Hansen, T and Hansen, T and Nielsen, T and Pedersen, O},
title = {Glucocorticoid-induced changes of the gut microbiota and metabolic markers in healthy young men: Outcome of a randomized controlled trial.},
journal = {Cell reports. Medicine},
volume = {6},
number = {11},
pages = {102426},
pmid = {41218604},
issn = {2666-3791},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Glucocorticoids/pharmacology/administration &amp; dosage ; Adult ; Biomarkers/metabolism ; Young Adult ; Prednisolone/pharmacology/administration &amp; dosage ; Healthy Volunteers ; Insulin Resistance ; Methylprednisolone/pharmacology/analogs &amp; derivatives/administration &amp; dosage ; Feces/microbiology ; },
abstract = {Glucocorticoids induce insulin resistance and suppress immunity, but their impact on gut microbiota, which may modulate metabolism and immunity remains under explored. In this 7-day trial, we assess glucocorticoid-induced changes in gut microbiota and metabolic markers in 56 healthy men, randomly assigned to three interventions: oral prednisolone (PO group), intramuscular methylprednisolone acetate (IM group), or saline (CTL group). Shotgun metagenomics reveal that PO glucocorticoid causes shifts in bacterial abundance, increasing Blautia and Collinsella, while decreasing Dysosmobacter welbionis and Anaerotignum faecicola, linked with insulin resistance and immunosuppression markers. Additionally, PO treatment alters microbial pathways and enzymes related to glycolysis and lipid metabolism, with changes in predicted metabolites such as hypoxanthine and phenylacetate. IM treatment results in minimal microbiota changes. These findings underscore the route-dependent effects of glucocorticoids on gut microbiota and their potential impact on host metabolism and immunity. The trial was approved by the Danish Medicine Agency (EudraCT protocol number: 2016-001850-16).},
}
@article {pmid41218435,
year = {2026},
author = {Ren, J and Wang, J and Dong, Y and Xiao, L and Wang, L and Ji, J and Liu, Y},
title = {Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124889},
doi = {10.1016/j.watres.2025.124889},
pmid = {41218435},
issn = {1879-2448},
mesh = {RNA, Ribosomal, 16S/genetics ; Geologic Sediments/microbiology/chemistry ; *Microbiota ; Metagenomics ; Ecosystem ; Nitrates ; Bacteria/genetics ; },
abstract = {Environmental microbial communities are crucial in regulating ecosystem functions and are increasingly affected by human-induced geochemical perturbations. While microbial communities are known to shift under such perturbations, the explicit link between these shifts and corresponding biogeochemical processes remains unclear. Here, we conducted time-series sediment incubation experiments under elevated nitrate conditions, combining 16S rRNA gene sequencing, qPCR, and metagenomics to track microbial taxonomic and functional dynamics. We further developed a gene-centric, process-based biogeochemical model to quantitatively connect microbial community structure to geochemical reaction kinetics. Our results revealed that functional metagenomics provided a broader view of functional diversity than qPCR and enabled detailed analysis of gene co-occurrence. Through modeling, we uncover a quantitative coupling between functional gene abundance and reaction rates under geochemical perturbations. However, this relationship can be obscured by redox-driven abiotic processes affected by perturbations and the nonlinear nature of enzyme-mediated reactions, making it difficult to resolve using standard statistical approaches. Together, these findings improve our understanding of the linkage between microbial function and biogeochemical processes, and underscore the value of gene-centric, process-based models for predicting ecosystem behavior under geochemical stress.},
}
@article {pmid41218045,
year = {2025},
author = {Kitsanayanyong, L and Chongprachavat, N and Rairat, T and Keetanon, A and Wimanhaemin, P and Chuchird, N},
title = {Exploring the gut microbiota of Pacific white shrimp (Litopenaeus vannamei) suffering pale shrimp disease.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0336700},
pmid = {41218045},
issn = {1932-6203},
mesh = {Animals ; *Penaeidae/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Photobacterium/genetics/isolation &amp; purification ; Phylogeny ; Thailand ; Vibrio/genetics/isolation &amp; purification ; },
abstract = {Pale shrimp disease is an emerging threat in Thailand, characterized by pale body coloration in Pacific white shrimp (Litopenaeus vannamei). Although the etiology had been identified as Photobacterium damselae subsp. damselae, the disease effects on gut microbiome remain poorly understood. This study investigated changes in the gut microbiota of Pacific white shrimp suffering from pale shrimp disease (diseased group) compared to disease-free shrimp (healthy group) collected from Surat Thani Province, Thailand. DNA extracted from the intestinal samples was subjected to 16S rRNA metagenomic sequencing, followed by taxonomic identification, diversity analyses, and functional prediction of the metabolic pathways. Despite a limited number of biological replicates, the occurrence of pale shrimp disease was able to reveal alterations in intestinal microbial composition, diversities, and functional features compared to the healthy shrimp. In most cases, the intestinal microbiota of the diseased shrimp were dominated by only 2 genera of bacteria, i.e., Photobacterium (54.63-70.53%) and Vibrio (24.94-26.12%), which together accounted for 79.58-95.47% of the total bacterial community. α-diversity, as indicated by the observed features, Shannon, and Simpson indices, was significantly decreased, and dominance was significantly increased in the diseased shrimp compared to healthy shrimp. Likewise, β-diversity was significantly different between groups; PCoA of un-weighted and weighted UniFrac clearly distinguished intestinal microbiota of the shrimp into 2 clusters, and ANOSIM of these data revealed statistical differences between groups, suggesting different microbiota communities between healthy and diseased shrimp. Moreover, diseased shrimp had significantly higher predicted functional features associated with bacterial virulence factors and antibacterial resistance. These exploratory findings suggest an association among pale shrimp disease, gut microbiota dysbiosis, and the proliferation of opportunistic taxa, particularly Photobacterium.},
}
@article {pmid41217690,
year = {2025},
author = {Nguyen, HN and Kim, OTP and Tran, TT},
title = {Metagenomic analysis of microbial communities and associated resistance genes, virulence genes, and mobile genetic elements in natural honey from Mu Cang Chai, Vietnam.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {11},
pages = {445},
pmid = {41217690},
issn = {1573-0972},
support = {B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; },
mesh = {*Honey/microbiology ; Vietnam ; *Bacteria/genetics/classification/isolation &amp; purification/pathogenicity/drug effects ; *Virulence Factors/genetics ; *Metagenomics/methods ; *Interspersed Repetitive Sequences/genetics ; *Drug Resistance, Bacterial/genetics ; Bees/microbiology ; Animals ; Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; Genes, Bacterial ; Virulence/genetics ; },
abstract = {Natural honey is preferred over honey from farmed bees in Vietnam, often commanding higher prices; therefore, it needs proper guidance. Environmental DNA from natural honey can be used to monitor its safety and authenticate its quality, as it contains DNA traces from various organisms. In this study, shotgun metagenomic sequencing was employed to identify risk factors in three natural honey samples from Mu Cang Chai, one of the central honey-producing regions in Northwest Vietnam. Our data revealed that more than 95% of the identified DNA belonged to bacteria in all three samples. Some opportunistic pathogenic bacteria, such as Klebsiella pneumoniae, Burkholderia contaminans, and Ralstonia picketti, were found dominant in the examined samples. Moreover, the bacteria in these honey samples carried numerous antibiotic resistance genes (ARGs), as well as virulence genes (VGs). The resistome profiles revealed the detection of 491 ARG sequences across three honey samples, belonging to 43 gene families that encode various resistance proteins. The most frequently encountered drug classes associated with these ARGs were cephalosporins, fluoroquinolones, and tetracyclines. On the other hand, the virulome profiles showed a rich composition of VGs: a total of 94 unique VGs linked to 25 virulence factors. They included nutritional factors, secretion systems, biofilm formation, exotoxins, and immunomodulation; the nutritional factors were the most prevalent function of these VGs. Mobilome profiles showed that only a small fraction of ARGs (0.6%) and VGs (15%) were located on mobile genetic elements (MGEs) such as plasmids and proviruses, suggesting most were chromosomally encoded; however, the presence of MGEs carrying these determinants (ARGs and VGs) still indicates a latent potential for horizontal gene transfer. Although these results are based on a case study of only three samples of natural honey collected in Mu Cang Chai, they highlight the need for a broader examination and the importance of monitoring the risk of pathogenicity in unprocessed foods, such as natural honey.},
}
@article {pmid41212311,
year = {2025},
author = {Slobodkin, AI and Rusanov, II and Slobodkina, GB and Chernyh, NA and Stroeva, AR and Merkel, AY},
title = {A culture-independent study of the structure, functions and methane oxidation activity of microbial communities of geothermal springs in Dagestan.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {3},
pages = {42},
pmid = {41212311},
issn = {1433-4909},
mesh = {*Hot Springs/microbiology ; *Methane/metabolism ; *Microbiota ; Oxidation-Reduction ; Russia ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Microbial communities inhabiting geothermal springs in the Republic of Dagestan, Russia, have not been studied by culture-independent methods. We have investigated the taxonomic composition, metabolic potential and rates of methane oxidation of microbial communities in two geothermal springs with methane emission (Artuzen and Miatli) located in Dagestan. Methane oxidation rates measured by the radiotracer technique varied from 3.7 to 96.5 nmol CH4 cm[- 3] day[- 1]. 16S rRNA gene amplicon sequencing indicates that in the Artuzen hot springs (54 °C), with a salinity of 2.5%, the primary production of organic matter is performed by mesophilic cyanobacteria, while in the freshwater Miatli hot springs (58 °C) primary producers are thermophilic cyanobacterium Thermosynechococcus and photosynthetic members of Chloroflexi. Analysis of metabolic capabilities of the metagenome assembled genomes in one of Artuzen samples shows that anaerobic bacteria belonging to Anaerolineae and Marinisomatota are the key decomposers of complex organic substances. The main terminal electron-accepting process in the sediment is acetoclastic methanogenesis carried out by the genus Methanocrinis. The presence of "Candidatus Methanospirareceae" (ANME-1) suggests the involvement of anaerobic archaea in methane oxidation. Thus, our study extends the current knowledge of the phylogenetic and metabolic diversity and activity of the prokaryotes inhabiting terrestrial hydrothermal environments.},
}
@article {pmid41211947,
year = {2025},
author = {Calvez, E and Quétel, I and Saint-Alban, L and Gutiérrez-Bugallo, G and Dollin, C and Ramdini, C and Vega-Rúa, A},
title = {Contrasted impacts of commercial diets and rearing water on Aedes aegypti fitness and microbiota.},
journal = {mSphere},
volume = {10},
number = {12},
pages = {e0054325},
pmid = {41211947},
issn = {2379-5042},
support = {"Une Sant&#xe9;" 2021-2024//Programme Op&#xe9;rationnel FEDER-Guadeloupe-Conseil Regional/ ; Calmette &amp; Yersin postdoctoral fellowship//Institut Pasteur/ ; },
mesh = {Animals ; *Aedes/microbiology/growth &amp; development/physiology ; Female ; *Microbiota ; Mosquito Vectors/growth &amp; development/microbiology ; *Animal Feed/analysis ; Larva/growth &amp; development/microbiology ; *Diet ; *Water ; Metagenomics ; },
abstract = {Mosquito rearing optimization in laboratory conditions is crucial for both vector research and control. Although the addition of nutrients is important for Aedes aegypti development from immature stages to adult mosquitoes, little is known about the nutrient composition of commercial diets used for mosquito rearing and their influence on Ae. aegypti life traits. Here, we evaluated the influence of four commercial diets commonly used to rear Ae. aegypti in the laboratory on its fitness, lifespan, and microbiota. We also compared the effect of these diets on this mosquito when combined with two different rearing waters (laboratory versus field-collected waters). Our investigations demonstrated that higher levels of protein and lipid in commercial diets promote better Ae. aegypti development, lifespan, and size in both water. Metagenomic analysis revealed specific modulations of adult microbiota composition according to both diet and rearing water. Chryseobacterium dominated the microbiota of female mosquitoes reared in laboratory water, except for yeast condition, where a more diverse microbiota was observed. When reared in larval site water, the microbiota diversity was overall higher despite diet addition, except for fish food, which promoted Sphingobacterium dominance. Given the pivotal influence of diet addition during the larval stage on Ae. aegypti microbiota and life traits, rearing conditions should be carefully chosen according to the goals of the research (i.e., vectorial capacity estimations) or vector control intervention.IMPORTANCEAedes aegypti is the main vector of arbovirus, such as dengue, yellow fever, and chikungunya viruses. Vector research and control are primarily carried out in laboratories, with larval stage rearing conducted using commercial diet. If many nutrients are essential for Ae. aegypti development, gaining insight into the influence of these diets and their nutrient levels is important to promote optimized rearing worldwide. In this study, our results indicated a significant impact of commercial diet on Ae. aegypti development, lifespan, size, and microbiota related to contrasted protein, lipid, and carbohydrate levels in these diets. This study will help people working with Ae. aegypti raise awareness in staff working with Ae. aegypti to select optimized diets for their specific purpose.},
}
@article {pmid41211940,
year = {2025},
author = {Roberts, WR and Parks, M and Ashner, M and Ashworth, MP and Denne, N and Ruck, EC and Spiliotopoulos, E and Wang, A and Amin, SA and Schaack, S and Wickett, NJ and Alverson, AJ},
title = {Reference genome for the benthic marine diatom Psammoneis japonica: Bacterial associations and repeat-driven genome size evolution in diatoms.},
journal = {Journal of phycology},
volume = {61},
number = {6},
pages = {1556-1565},
pmid = {41211940},
issn = {1529-8817},
support = {1150213//Division of Molecular and Cellular Biosciences/ ; 1353131//Division of Environmental Biology/ ; 1353152//Division of Environmental Biology/ ; 2331644//Division of Environmental Biology/ ; 2336342//Division of Environmental Biology/ ; },
mesh = {*Diatoms/genetics/microbiology ; *Genome Size ; *Genome, Bacterial ; *Metagenome ; *Evolution, Molecular ; Genome ; Bacteria/genetics ; },
abstract = {We sequenced the genome, transcriptome, and bacterial metagenome of Psammoneis japonica, a benthic, chain-forming, and araphid marine diatom. This combination of traits fills several gaps in genome sequencing coverage across diatoms. The nuclear genome (QPGO00000000) is an estimated 91.4 Mb in length, with 11,047 genes that comprise 18% of the total genome. Repetitive elements account for 33% of the genome, and other noncoding sequences comprise the remaining 49% of the genome. A global analysis of diatom genomes showed that repetitive elements are the principal driver of genome size variation in diatoms. Four complete genomes of Planctomycetota, ɑ-proteobacteria, and Bacteroidota were also recovered, and each had only moderate similarity to previously sequenced bacterial genomes. This finding supports the idea that bacterial species richness in the phycosphere is under-described and far exceeds the number of diatom host species, which themselves number in the tens to hundreds of thousands of species.},
}
@article {pmid41207298,
year = {2026},
author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J},
title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D763-D775},
pmid = {41207298},
issn = {1362-4962},
support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Metagenome ; *Databases, Genetic ; Molecular Sequence Annotation ; Bacteria/genetics/classification ; Software ; Internet ; },
abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.},
}
@article {pmid41206954,
year = {2025},
author = {Mao, Y and Jiang, Z and Wang, T and Hu, Y and Zhan, X},
title = {TCVS: tree-guided compositional variable selection analysis of microbiome data.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {11},
pages = {},
pmid = {41206954},
issn = {1367-4811},
support = {12371287//National Natural Science Foundation of China/ ; 2022YFA1305400//National Key R&amp;D Program of China/ ; },
mesh = {Humans ; *Microbiota ; *Software ; *Gastrointestinal Microbiome ; Algorithms ; *Computational Biology/methods ; *Metagenomics/methods ; Phylogeny ; },
abstract = {MOTIVATION: Studies of microbial communities, represented by the relative abundances of taxa at various taxonomic levels, have underscored the significance of microbiota in numerous aspects of human health and disease. A pivotal challenge in microbiome research lies in pinpointing microbial taxa associated with disease outcomes, which could play crucial roles in prevention, detection, and treatment of various health conditions. Alongside these relative abundance data, taxonomic information sometimes offers a unique lens to explore the impact of shared evolutionary histories on patterns of microbial abundance.<br><br>RESULTS: In pursuit of this goal, we utilize the tree structure to more flexibly identify taxa associated with disease outcomes. To enhance the accuracy of our selection process, we introduce auxiliary knockoff copies of microbiome features designated as noise. This approach allows for the assessment of false positives in the selection process and aids in refining it towards more precise outcomes. Extensive numerical simulations demonstrate that our methodology outperforms several existing methods in terms of selection accuracy. Furthermore, we demonstrate the practicality of our approach by applying it to a widely used gut microbiome dataset, identifying microbial taxa linked to body mass index.<br><br>TCVS R code is available at https://github.com/Yicong1225/TCVS.},
}
@article {pmid41206740,
year = {2025},
author = {Lage, OM and Godinho, O and García-Domínguez, R and Øvreås, L and Devos, DP},
title = {A century of research on the Planctomycetota bacterial phylum, previously known as Planctomycetes.},
journal = {FEMS microbiology reviews},
volume = {49},
number = {},
pages = {},
pmid = {41206740},
issn = {1574-6976},
support = {//European Regional Development Fund/ ; 22008657//Le Conseil r&#xe9;gional des Hauts de France/ ; //Universit&#xe9; de Lille/ ; 325409//Norwegian Research Council/ ; },
mesh = {*Bacteria/genetics/classification/metabolism ; *Planctomycetales/genetics/classification/physiology ; Genome, Bacterial ; History, 20th Century ; History, 21st Century ; },
abstract = {One hundred years after planctomycetes were discovered and 50 years since the first isolate was successfully cultured, this bacterial phylum remains enigmatic in many ways. In the last few decades, a significant effort to characterize new isolates has resulted in >150 described species, allowing a more comprehensive analysis of their features. However, metagenomic studies reveal that a diverse group of planctomycetes has yet to be cultured and characterized, and that many biological surprises are yet to be revealed. This is the case for the recently discovered phagotrophic Candidatus Uabimicrobium, which challenges our understanding of the distinction between prokaryotes and eukaryotes. The unique biology of planctomycete cells, such as their ability to divide without the FtsZ protein, their complex structure and characteristic morphology, their relatively large genomes containing many genes with unknown function, and their variable metabolic capabilities, imposes significant barriers for researchers. Although ubiquitous, the precise ecological roles of planctomycetes in various environments are still not fully understood. However, their distinctive metabolism opens the door to a large number of potential biotechnological applications, which are beginning to be unveiled. In this article, we first review the historical milestones in planctomycetes research and describe the pioneers of the field. We then describe the controversies and their resolutions, we highlight the past discoveries and current interrogations related to planctomycetes, and discuss the ongoing challenges that hinder a comprehensive understanding of their biology. We end up with directions for exploring the biology and ecological roles of these fascinating organisms.},
}
@article {pmid41206461,
year = {2025},
author = {Kifushi, M and Nishikawa, Y and Hosokawa, M and Anai, T and Takeyama, H},
title = {Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {32},
number = {6},
pages = {},
pmid = {41206461},
issn = {1756-1663},
support = {//Government of/ ; JPJ009237//Japan/ ; //Bio-oriented Technology Research Advancement Institution/ ; },
mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Rhizosphere ; *Microbiota ; Plant Roots/microbiology ; *Bacteria/genetics/classification ; Metagenome ; *Genomics/methods ; Single-Cell Analysis/methods ; Genome, Bacterial ; },
abstract = {Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogues in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.},
}
@article {pmid41205408,
year = {2026},
author = {Bao, C and Ma, Y and Li, M and Li, Y and Zhang, C and Liu, X and Fan, R and Cui, W and Fan, X and Zheng, F and Duan, F and Liu, J},
title = {Assessment of glymphatic dysfunction in ulcerative colitis using DKI-ALPS: An innovative imaging biomarker.},
journal = {Journal of neuroradiology = Journal de neuroradiologie},
volume = {53},
number = {1},
pages = {101402},
doi = {10.1016/j.neurad.2025.101402},
pmid = {41205408},
issn = {0150-9861},
mesh = {Humans ; *Colitis, Ulcerative/diagnostic imaging/physiopathology/microbiology/complications ; Male ; Female ; Adult ; Middle Aged ; *Glymphatic System/diagnostic imaging/physiopathology ; Biomarkers ; Gastrointestinal Microbiome ; *Diffusion Magnetic Resonance Imaging/methods ; Case-Control Studies ; *Diffusion Tensor Imaging/methods ; },
abstract = {PURPOSE: Ulcerative colitis (UC) is associated with higher anxiety, depression, and cognitive disorders linked to brain glymphatic dysfunction. In this study, we used along-the-perivascular-space (ALPS) index (based on DTI and DKI) to determine if UC relates to glymphatic dysfunction and explore how microbiota dysbiosis and inflammation affect brain glymphatic function.<br><br>MATERIALS AND METHODS: In this study, 63 patients with UC and 68 healthy controls underwent 3-Tesla MRI scans to evaluate DTI-ALPS and DKI-ALPS index. The protocol included diffusion-weighted imaging (DWI) and diffusion kurtosis imaging (DKI) sequences to calculate the ALPS index, which quantifies glymphatic system function. All participants completed cognitive (MMSE) and depression (SAS/SDS) assessments (SAS/SDS). Patients with UC also underwent assessment for inflammation and gut microbiota (based on metagenomic analysis). Data analysis was performed using correlation analysis and linear regression.<br><br>RESULTS: Patients with UC showed lower DTI-ALPS index (1.25) and DKI-ALPS index (1.40) compared to controls (1.40 vs. 1.69; P < 0.001). In multi-adjusted linear regression models, UC was associated with lower DTI-ALPS index and DKI-ALPS index (&#x3b2; =-0.142 vs.-0.284), with DKI-ALPS showing higher sensitivity. The results remained significant even after stratification by age and sex. The Mayo score correlated negatively with DTI and DKI-ALPS index. The ALPS index correlates with gut microbiota, particularly those involved in butyrate and short-chain fatty acid (SCFA) production. DTI-ALPS index was significantly correlated with ESR (&#x3b2; =-0.003), CRP (&#x3b2; =-0.035), SII (&#x3b2; =-0.062), INFLA (&#x3b2; =-0.010), and SIRI (&#x3b2; =-0.058). We also observed significant correlations between DKI ALPS index and ESR (&#x3b2; =-0.006), CRP (&#x3b2; =-0.051), SII (&#x3b2; =-0.130), INFLA (&#x3b2; =-0.017), SIRI (&#x3b2; =-0.095), IL-6 (&#x3b2; =-0.081) and NLR (&#x3b2; =-0.108).<br><br>CONCLUSIONS: UC is associated with brain glymphatic dysfunction, correlating with inflammation level. DKI-ALPS serves as a more sensitive method than DTI-ALPS, offering a new approach for managing ulcerative colitis through glymphatic dysfunction.},
}
@article {pmid41205292,
year = {2026},
author = {Smallbone, JA and Gregson, BH and McGenity, TJ and Holland, RD and Whitby, C and Cameron, TC and Chamberlain, J and Clift, LG and Hynes, C and McKew, BA},
title = {Effects of the 2023 Poole Harbour oil spill on sediment bacterial communities and ecosystem functioning.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 3},
pages = {118904},
doi = {10.1016/j.marpolbul.2025.118904},
pmid = {41205292},
issn = {1879-3363},
mesh = {*Petroleum Pollution ; *Geologic Sediments/microbiology/chemistry ; *Bacteria ; Biodegradation, Environmental ; *Water Pollutants, Chemical/analysis ; *Ecosystem ; Petroleum ; Environmental Monitoring ; Hydrocarbons/analysis ; Polycyclic Aromatic Hydrocarbons/analysis ; *Microbiota ; },
abstract = {In March 2023, approximately 27 t of fluid from an oil and gas reservoir (containing approximately 85 % water and 15 % crude oil spilt from a fractured pipeline beneath Ower Bay creek, entering Poole Harbour (Dorset, UK). This event provided a unique opportunity to investigate the impacts of hydrocarbon contamination on microbial communities in-situ in a temperate coastal, shallow, fine sediment environment. Our aims were to quantify hydrocarbon concentrations (via gas chromatography mass spectrometry (GC-MS)) and effects on microbial community structure and functional potential (via metagenomic sequencing) to understand the capacity for microbial biodegradation across the impacted region. Hydrocarbon contamination was localised to the Spill Site (approximately an area of 1500 m[2]) at the head of the creek, with minimal impact at the Mid Point (164 m from the Spill Site) and End Point (387 m from the Spill Site) and with no indication of contamination at Brownsea Island located in the heart of the harbour. By October 2023, n-alkane and 4-5 ring PAH concentrations had declined to background levels, highlighting the combined effects of the remediation response and natural hydrocarbon biodegradation at the Spill Site. Clear changes in bacterial community structure were observed in the seven months following the spill, with notable hydrocarbon-degrading bacteria i.e. Anaerolinea, Thiobacillus and Dechloromonas favouring the Spill Site, suggesting a significant increase in anaerobic biodegradation occurred as a result of significant increase in assA (anaerobic alkylsuccinate synthase), abcA (anaerobic benzene carboxylase) and ahyA (anaerobic alkane hydroxylase) genes. Overall, 24 alkane and aromatic hydrocarbon degradation genes, from both aerobic and anaerobic degradation pathways, were identified from contigs throughout the study site, being present within 48 out of 221 Metagenome-Assembled Genomes (MAGs), highlighting the sites capacity for hydrocarbon biodegradation under both aerobic and anaerobic conditions.},
}
@article {pmid41204634,
year = {2025},
author = {Yuan, L and Li, Y and Wang, Z and Xie, X and Wu, Q},
title = {Gut Microbiota-Mediated Antihypertensive Effects of Probiotic Fermented Milk: A Multi-Omics Study.},
journal = {Journal of food science},
volume = {90},
number = {11},
pages = {e70654},
doi = {10.1111/1750-3841.70654},
pmid = {41204634},
issn = {1750-3841},
support = {21977020//National Natural Science Foundation of China/ ; 2022B1111070006//the Key-Area Research and Development Program of Guangdong Province/ ; 2020GDASYL-20200102003//GDAS' Project of Science and Technology Development/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Rats, Inbred SHR ; *Antihypertensive Agents/pharmacology ; Rats ; *Hypertension/diet therapy ; Male ; Blood Pressure/drug effects ; *Cultured Milk Products/microbiology ; Fermentation ; Lactiplantibacillus plantarum/metabolism ; Renin-Angiotensin System/drug effects ; Metabolomics ; Multiomics ; },
abstract = {The precise molecular mechanisms through which gut microbiota mediate the antihypertensive effects of probiotic fermented milk (PFM) remain largely unexplored. This study aimed to elucidate these mechanisms by employing a multi-omics approach, combined with metagenomic deep sequencing technology, non-targeted metabolomics technology, and antibody chip protein detection technology to elucidate the potential mechanisms behind the antihypertensive effects of milk fermented by Lactiplantibacillus plantarum SR37-3 (PFM-SR37-3) in spontaneously hypertensive rats (SHR). Our findings demonstrate that PFM-SR37-3 intervention significantly reduces blood pressure in SHR and is associated with partial inactivation of the renin-angiotensin system (RAS). Notably, long-term administration of PFM-SR37-3 inhibited the progressive rise in systolic blood pressure (SBP), with final measurements of 187.17 ± 3.61 mmHg in the model group versus 172.21 ± 11.81 mmHg in the PFM-SR37-3-treated group after 4 weeks (p < 0.01). PFM-SR37-3 modulates key host metabolic pathways (especially arachidonic acid metabolism) by reshaping the gut microbiota (such as enrichment of Lactobacillaceae), with concomitant reductions in the levels of proinflammatory cytokines (such as ICAM-1 and Fractalkine). This "gut-immune" pathway is an important complement to its partial inhibition of the RAS. Collectively, these data highlight strong associations between PFM-induced gut microbial shifts and antihypertensive effects, providing a multi-faceted view of the potential mechanisms and underscoring the therapeutic potential of PFM in managing hypertension.},
}
@article {pmid41203618,
year = {2025},
author = {Moriel, N and Jones, L and Harpenas, E and Rakow, N and Shmorak, S and Eventov Friedman, S and Ofek Shlomai, N and Yassour, M},
title = {Development of the preterm infant gut and gastric residuals microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9848},
pmid = {41203618},
issn = {2041-1723},
mesh = {Humans ; *Infant, Premature ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Intensive Care Units, Neonatal ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; *Stomach/microbiology ; Gestational Age ; Enteral Nutrition ; },
abstract = {Prematurity, defined as birth before 37 weeks of gestation, is the leading cause of mortality in children under five, affecting ~11% of live births worldwide (≈15 million annually). Despite advances in neonatal care, preterm infants remain at high risk of complications. In neonatal intensive care units, gastric residuals (GRs) are routinely monitored to guide enteral feeding, yet their microbial composition remains poorly understood. We performed metagenomic sequencing of 199 stool and 69 GR samples from 39 preterm infants during hospitalization to characterize stomach and gut microbiomes. To our knowledge, this is the first metagenomic sequencing of the GR in premature infants. We identified 11 GR microbial clusters, commonly dominated by Staphylococcus, Streptococcus, and Klebsiella, with microbial diversity correlating with aspiration frequency. Colonization was dynamic: early GR samples were enriched with Staphylococcus epidermidis and Bradyrhizobium, while later samples featured Escherichia coli, Staphylococcus hominis, and Streptococcus thermophilus. Stool samples formed eight microbial clusters, frequently enriched with Enterobacteriaceae. S. epidermidis was linked to higher gestational age and lower richness, whereas Bifidobacterium breve, a beneficial commensal, appeared later. Comparative analysis showed overlap between gut and gastric microbiota, with GR samples more dynamic and less subject-specific. Strain-level analysis revealed both individual-specific and widely shared taxa, including a pathogenic Klebsiella aerogenes strain associated with bacteremia, detectable a week before clinical isolation. These findings provide new insights into microbial colonization dynamics of preterm infants.},
}
@article {pmid41202544,
year = {2025},
author = {Zhang, H and Sun, H and Pan, X and Wu, D and Liang, H and Tang, J and Fang, H and Wu, X},
title = {Sediment archives urban-rural divergence in antibiotic resistance gene contamination within a freshwater lake.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140322},
doi = {10.1016/j.jhazmat.2025.140322},
pmid = {41202544},
issn = {1873-3336},
mesh = {*Lakes/microbiology ; *Drug Resistance, Microbial/genetics ; China ; *Geologic Sediments/microbiology ; Environmental Monitoring ; *Genes, Bacterial ; Cities ; },
abstract = {Freshwater lakes are critical ecosystems for sustaining biodiversity and human well-being, yet increasing anthropogenic activities threaten their ecological safety through pollution such as antibiotic resistance genes (ARGs). Previous studies on ARG pollution in aquatic systems have largely overlooked the distinct impacts of urban versus rural landscapes, limiting targeted mitigation strategies. Here, we investigate the urban-rural heterogeneity of ARG pollution in Chaohu lake, a major urban-rural junction lake in China, using shotgun metagenomic sequencing and Bayesian source-tracking approaches. Our findings reveal significant spatiotemporal variations in ARG abundance, with urban-adjacent regions (western lake) exhibiting 1.22- to 1.25-fold higher ARG levels than rural-adjacent areas (eastern lake) in water and sediments, respectively. Notably, a significant distance-decay relationship of ARG profiles was observed in sediments, highlighting that sediments act as a stable environmental archive recording the urban-rural divergence. Agricultural activities were identified as the dominant source lake-wide, contributing over 60 % of the total ARG load, thereby surpassing urban sewage inputs. Meanwhile, the abundance of mobile genetic elements (MGEs), particularly transposases, was significantly higher in the western lake, indicating a greater potential for horizontal gene transfer. The presence of multidrug-resistant, ARG-carrying pathogens, such as Stenotrophomonas maltophilia and Pseudomonas putida, was significantly enriched in these areas, correlating with higher ecological and health risks as quantified by the antibiotic resistome risk index. These results underscore the urgent need for landscape-specific management strategies to curb ARG dissemination, prioritizing agricultural non-point source control in urban-rural transitional zones to safeguard freshwater ecosystems and human health.},
}
@article {pmid41201920,
year = {2025},
author = {Soni, S and Mittal, P and Lo, JH and Yang, Y and Smbatyan, G and Lee, K and Wan, J and Kumagai, H and Yen, K and Mehta, HH and Miller, B and Torres-Gonzalez, L and Battaglin, F and Shah, UH and Bartolini, M and Zhang, W and Craig, DW and Millstein, J and Cohen, P and Lenz, HJ},
title = {Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.},
journal = {Neoplasia (New York, N.Y.)},
volume = {70},
number = {},
pages = {101245},
pmid = {41201920},
issn = {1476-5586},
support = {P30 CA014089/CA/NCI NIH HHS/United States ; R01 AG069698/AG/NIA NIH HHS/United States ; },
mesh = {*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Tumor Microenvironment/genetics ; Humans ; *Diet ; *Gene Expression Regulation, Neoplastic ; Disease Models, Animal ; Age Factors ; Male ; *Aging ; },
abstract = {Colorectal Cancer (CRC) is the third most prevalent malignancy, leading to significant morbidity and mortality globally. Epidemiological studies suggest that chronological age and diet are among the major contributing factors correlated with the incidence of CRC. Our study aimed to provide insights into the association between age, diet, and gut microbiome in CRC using molecular techniques including RNA sequencing, cytokine analysis, and metagenomic analysis. We used syngeneic MC38 mice model divided into two age groups (old and young) and three diet groups (standard chow, calorie-restricted and high-fat). The major findings of this study are that age and diet impact intratumoral gene signaling (nuclear and mitochondrial), and hub genes we identified are associated with prognosis in CRC. Fecal microbiome analysis showed that old microbiomes have higher alpha diversity compared to young mice. Our results demonstrate that interactions between host (age) and external (diet) factors regulate tumor growth mediated by cytokines, mitochondrial derived proteins, and the gut microbiome. Collectively, our findings advance current understanding of the mechanisms by which aging, diet and gut microbiota impact CRC onset and progression though further investigation is warranted.},
}
@article {pmid41201839,
year = {2025},
author = {da Silva Fong, D and Abrantes, J and Moura, T and Serra-Pereira, B and Xavier, R and Veríssimo, A and Varsani, A and Neves, F},
title = {Identification and characterization of a novel papillomavirus in thornback skate (Raja clavata).},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
pmid = {41201839},
issn = {2057-5858},
mesh = {Animals ; Phylogeny ; Genome, Viral ; *Skates, Fish/virology ; *Papillomaviridae/genetics/isolation &amp; purification/classification ; *Papillomavirus Infections/virology/veterinary ; Sequence Analysis, DNA ; DNA, Viral/genetics ; },
abstract = {Papillomaviruses are non-enveloped, double-stranded DNA viruses capable of infecting a wide range of vertebrates, from chondrichthyans to mammals. In this study, we report for the first time the identification and complete genome of a papillomavirus in the thornback skate (Raja clavata), named Raja clavata papillomavirus 1 (RclaPV1). The genomic sequence was determined using a metagenomic approach and subsequently confirmed by PCR. The RclaPV1 genome is 5,539 bp in length and displays the typical organization of papillomaviruses, encoding 4 core proteins on a single DNA strand: two early genes (E1 and E2) and two late genes (L1 and L2). Maximum likelihood phylogenetic analyses of the L1 and E1 genes indicate that RclaPV1 belongs to the Secondpapillomavirinae subfamily, clustering with fish and amphibian papillomaviruses and showing closer evolutionary relationships to amphibians than to fish.},
}
@article {pmid41201733,
year = {2026},
author = {Saleh, RM and Hassan, OM},
title = {The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.},
journal = {Infection},
volume = {54},
number = {1},
pages = {111-126},
pmid = {41201733},
issn = {1439-0973},
mesh = {*Biofilms/growth &amp; development ; Humans ; *Coinfection/microbiology/diagnosis ; *Microbiota ; *Precision Medicine/methods ; },
abstract = {Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their shared functional capacities, and the interactions that connect them. We analyze how community-level processes promote persistence, cause diagnostic failure, and drive therapeutic resistance, with emphasis on multispecies biofilms, quorum sensing, horizontal gene transfer, metabolic cooperation, and immune modulation. We also highlight advances in multi-omics and computational integration that now permit high-resolution infectome profiling and reveal taxa and interspecies networks that are not captured by routine culture. Clinical examples such as periodontitis, bacterial vaginosis, chronic rhinosinusitis, device-associated infections, and recurrent urinary tract infections show the translational value of this shift. On the therapeutic side, we discuss infectome-informed options including antivirulence agents, biofilm-disrupting enzymes, bacteriophages and lysins, community-wide susceptibility-guided regimens, and microbiome-restoration strategies. Finally, we identify the main requirements for the field: standardized sampling and analytic workflows, reproducible infectome signatures linked to clinical outcomes, and trial designs able to capture ecological dynamics and meet regulatory expectations for community-targeted interventions. Adopting an infectome perspective can enable precision infectiology and reshape the management of chronic and recurrent infections.},
}
@article {pmid41201223,
year = {2025},
author = {Zha, Y and Xiang, M and Zuo, Y and Liu, D and Wang, Q},
title = {High-dose Dietary Fibre Supplementation Enhances the Gut Microbiome, Health, and Athletic Performance of College Basketball Players.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {5},
pages = {37069},
doi = {10.31083/IJVNR37069},
pmid = {41201223},
issn = {0300-9831},
support = {2019YFF0301702//National Key R&amp;D Program of China/ ; XJ2022000601//Doctoral Research Fund/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Basketball/physiology ; *Athletic Performance/physiology ; Young Adult ; *Dietary Fiber/administration &amp; dosage ; Adolescent ; *Dietary Supplements ; Adult ; Body Composition ; Athletes ; Universities ; },
abstract = {BACKGROUND: Prolonged or intense exercise can disrupt gastrointestinal (GI) function and gut microbiota, impairing athletic performance. Dietary fibre supplementation may enhance gut microbiota diversity, improve body composition, and promote recovery in athletes. This study aimed to explore the effects of dietary fibre supplementation at two doses for 8 weeks on these aspects in college basketball players.<br><br>METHODS: Twenty male college basketball players (aged 17-25 years) were randomly assigned to a high-dose group (HDG; 10 participants; 6.84 g/day dietary fibre) or a low-dose group (LDG; 10 participants; 3.24 g/day dietary fibre). The participants consumed fibre-enriched meals daily while maintaining their regular training schedules. The outcome measures included gut microbiota diversity (metagenomic sequencing), body composition, fatigue recovery markers, glucose and lipid metabolism, and athletic performance. Statistical analyses included paired and independent t tests for within- and between-group comparisons and Spearman's correlation analysis to assess the relationships between gut microbiota and biochemical markers.<br><br>RESULTS: One participant in the high-dose group withdrew, and nineteen ultimately completed the study. Both groups showed significant within-group improvements (p < 0.05) in body weight (HDG: -2.77 &#xb1; 0.76 kg; LDG: -2.40 &#xb1; 0.67 kg), body fat percentage (HDG: -1.87 &#xb1; 0.69; LDG: -1.49 &#xb1; 0.45), cortisol (HDG: -6.79 &#xb1; 4.26 &#x3bc;g/dL; LDG: -4.5 &#xb1; 4.84 &#x3bc;g/dL), maximum power (HDG: 27.16 &#xb1; 9.77 W; LDG: 14.50 &#xb1; 9.43 W), maximal oxygen uptake (HDG: 8.78 &#xb1; 0.97; LDG: 6.90 &#xb1; 1.37), and half-court triangle run times (HDG: -0.48 &#xb1; 0.36 s; LDG: -0.25 &#xb1; 0.20 s). Meanwhile, fasting blood glucose significantly decreased (0.91 &#xb1; 0.55 mmol/L; p = 0.001), and the gut microbiome changes were more stable in the HDG, whereas the LDG presented greater shifts in microbial diversity. No significant between-group differences were observed.<br><br>CONCLUSIONS: Dietary fibre supplementation improved the gut microbiome composition, body composition, fatigue recovery, and athletic performance of college basketball players, regardless of dosage. Further studies are needed to evaluate higher doses and specific fibre types.},
}
@article {pmid41199348,
year = {2025},
author = {Ghozlane, A and Thirion, F and Plaza Oñate, F and Gauthier, F and Le Chatelier, E and Annamalé, A and Almeida, M and Ehrlich, SD and Pons, N},
title = {Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {227},
pmid = {41199348},
issn = {2049-2618},
support = {ANR-11-DPBS-0001//Metagenopolis/ ; },
mesh = {*Metagenomics/methods ; Animals ; Mice ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Software ; Computational Biology/methods ; },
abstract = {BACKGROUND: The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we present Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights from metagenomic samples.<br><br>RESULTS: Meteor2 currently supports 10 ecosystems, gathering 63,494,365 microbial genes clustered into 11,653 metagenomic species pangenomes (MSPs). These genes are extensively annotated for KEGG orthology, carbohydrate-active enzymes (CAZymes) and antibiotic-resistant genes (ARGs). In benchmark tests, Meteor2 demonstrated strong performance in TFSP, particularly excelling in detecting low-abundance species. When applied to shallow-sequenced datasets, Meteor2 improved species detection sensitivity by at least 45% for both human and mouse gut microbiota simulations compared to MetaPhlAn4 or sylph. For functional profiling, Meteor2 improved abundance estimation accuracy by at least 35% compared to HUMAnN3 (based on Bray-Curtis dissimilarity). Additionally, Meteor2 tracked more strain pairs than StrainPhlAn, capturing an additional 9.8% on the human dataset and 19.4% on the mouse dataset. Furthermore, in its fast configuration, Meteor2 emerges as one of the fastest available tools for profiling, requiring only 2.3&#xa0;min for taxonomic analysis and 10&#xa0;min for strain-level analysis against the human microbial gene catalogue when processing 10&#xa0;M paired reads - operating within a modest 5&#xa0;GB RAM footprint. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, demonstrating its ability to deliver an extensive and actionable metagenomic analysis. The unified database design also simplifies the integration of TFSP outputs, making it straightforward for researchers to interpret and compare results.<br><br>CONCLUSIONS: These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.},
}
@article {pmid41198823,
year = {2025},
author = {Navarro Marcos, C and Gutiérrez-Rivas, M and Goiri, I and García-Rodríguez, A and González-Recio, &#xd3;},
title = {The association of the rumen virome with methane emissions in dairy cattle.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1534},
pmid = {41198823},
issn = {2399-3642},
mesh = {Animals ; Cattle ; *Methane/metabolism/biosynthesis ; *Rumen/virology/microbiology/metabolism ; *Virome ; Female ; Viruses/genetics/classification ; Metagenome ; Bacteria/metabolism ; Metagenomics ; },
abstract = {Enteric methane production in ruminants is a major environmental concern, yet its association with the ruminal virome remains largely unexplored. Here, we conduct a bioinformatic analysis on previously published ruminal metagenomes from 448 Holstein cows to investigate the virome and its association with methane production. We identify 8933 viral operational taxonomic units (vOTUs), including bacteriophages, archaeophages, megaviruses, and virophages. Differences between high- and low-emitting cows are observed. Low emitters show greater abundance (mean log-FC = 0.72, Padj ≤ 0.049) of some vOTUs infecting bacteria like Prevotella, whereas greater abundance (mean log-FC = 0.70, Padj ≤ 0.047) of archaeophages and megaviruses infecting Methanobrevibacter, ciliates, and fungi, all microorganisms linked to methane production, are observed in high emitters. Associations between viruses and microorganisms might suggest viruses influence methane emissions by modulating key microbial populations. Although mechanisms remain unclear, rumen viruses could serve as biomarkers for selecting low-emission animals or developing microbial interventions.},
}
@article {pmid41197631,
year = {2026},
author = {Klag, K and Ott, D and Tippetts, TS and Nicolson, RJ and Tatum, SM and Bauer, KM and Stephen-Victor, E and Weis, AM and Bell, R and Weagley, J and Maschek, JA and Vu, DL and Heaver, S and Ley, R and O'Connell, R and Holland, WL and Summers, SA and Stephens, WZ and Round, JL},
title = {Dietary fat disrupts a commensal-host lipid network that promotes metabolic health.},
journal = {Cell metabolism},
volume = {38},
number = {1},
pages = {157-173.e9},
pmid = {41197631},
issn = {1932-7420},
support = {F30 DK127846/DK/NIDDK NIH HHS/United States ; U01 AT012990/AT/NCCIH NIH HHS/United States ; R01 AI181021/AI/NIAID NIH HHS/United States ; R01 DK124317/DK/NIDDK NIH HHS/United States ; R01 DK124336/DK/NIDDK NIH HHS/United States ; F32 CA243501/CA/NCI NIH HHS/United States ; R01 AT011423/AT/NCCIH NIH HHS/United States ; P30 CA042014/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Humans ; Mice ; Diet, High-Fat/adverse effects ; Obesity/metabolism/microbiology ; *Dietary Fats/metabolism ; *Lipid Metabolism ; Mice, Inbred C57BL ; Male ; Ceramides/metabolism ; Gastrointestinal Microbiome ; Lipids ; },
abstract = {The microbiota influences metabolic health; however, few specific microbial molecules and mechanisms have been identified. We isolated a Turicibacter strain from a community of spore-forming bacteria that promotes leanness in mice. Human metagenomic analysis demonstrates reduced Turicibacter abundance in individuals with obesity. Similarly, a high-fat diet reduces Turicibacter colonization, preventing its weight-suppressive effects, which can be overcome with continuous Turicibacter supplementation. Ceramides accumulate during a high-fat diet and promote weight gain. Transcriptomics and lipidomics reveal that the spore-forming community and Turicibacter suppress host ceramides. Turicibacter produces unique lipids, which are reduced during a high-fat diet. These lipids can be transferred to host epithelial cells, reduce ceramide production, and decrease fat uptake. Treatment of animals with purified Turicibacter lipids prevents obesity, demonstrating that bacterial lipids can promote host metabolic health. These data identify a lipid metabolic circuit between bacteria and host that is disrupted by diet and can be targeted therapeutically.},
}
@article {pmid41197619,
year = {2025},
author = {Forbes, M and Ng, DYK and Boggan, RM and Frick-Kretschmer, A and Durham, J and Lorenz, O and Dave, B and Lassalle, F and Scott, C and Wagner, J and Lignes, A and Noaves, F and Jackson, DK and Howe, K and Harrison, EM},
title = {Benchmarking of human read removal strategies for viral and microbial metagenomics.},
journal = {Cell reports methods},
volume = {5},
number = {11},
pages = {101218},
pmid = {41197619},
issn = {2667-2375},
mesh = {Humans ; *Metagenomics/methods ; *Benchmarking/methods ; Microbiota/genetics ; Genome, Human/genetics ; *Viruses/genetics ; Polymorphism, Single Nucleotide/genetics ; Metagenome ; },
abstract = {Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological analysis, and privacy protection. Various in silico methods exist, but their effectiveness depends on the parameters and reference genomes used. Here, we assess different methods, including the impact of the updated telomere-to-telomere (T2T)-CHM13 human genome versus GRCh38. Using a synthetic dataset of viral and human reads, we evaluated performance metrics for multiple approaches. We found that the usage of high-sensitivity configuration of Bowtie2 with the T2T-CHM13 reference assembly significantly improves human read removal with minimal loss of specificity, albeit at higher computational cost compared to other methods investigated. Applying this approach to a publicly available microbiome dataset, we effectively removed sex-determining SNPs with little impact on microbial assembly. Our results suggest that our high-sensitivity Bowtie2 approach with the T2T-CHM13 is the best method tested to minimize identifiability risks from residual human reads.},
}
@article {pmid41197616,
year = {2025},
author = {Gao, P and Yuan, H and Mei, Z and Yin, X and Zeng, Y and Liu, Z and Yang, X and Xue, J and Liu, Z and Jiang, Y and Ye, W and Lu, M and Suo, C and Chen, X},
title = {The comprehensive oral microbiome landscape unveils its interplay with poor oral health in esophageal squamous cell carcinoma risk.},
journal = {Cell reports. Medicine},
volume = {6},
number = {11},
pages = {102431},
pmid = {41197616},
issn = {2666-3791},
mesh = {Humans ; *Microbiota/genetics ; *Oral Health ; *Esophageal Squamous Cell Carcinoma/microbiology ; *Esophageal Neoplasms/microbiology ; Male ; Female ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Risk Factors ; *Mouth/microbiology ; Aged ; Saliva/microbiology ; Bacteria/genetics/classification ; },
abstract = {Growing evidence links poor oral health to an increased esophageal squamous cell carcinoma (ESCC) risk, with the oral microbiome recognized as a key contributor. However, human-based evidence remains limited. Here, we analyze salivary shotgun metagenomic data from 390 ESCC case-control pairs and 16S rRNA sequencing data from 206 incident esophageal cancer (EC) case-control pairs. We identify 50 bacterial species altered in ESCC (e.g., enriched Porphyromonas catoniae and depleted Campylobacter rectus) and disruptions in 54 biochemical pathways (e.g., inosine 5'-phosphate degradation). These features potentially mediate the association between poor oral health and ESCC. Notably, this association is stronger among individuals with lower Streptococcus mitis levels, implicating pathways related to thiamine salvage and energy metabolism. Consistent findings in the validation dataset further support the interplay between the oral microbiome and oral health in EC risk. Our results highlight the promise of precision-targeted microbial interventions to improve oral health for ESCC prevention and management.},
}
@article {pmid41197330,
year = {2025},
author = {Ke, T and Jiang, T and Li, H and Dong, X and Khoo, HE},
title = {Probiotic-fermented milk alleviates hypertension in preeclampsia rats and is associated with increases in branched fatty acid esters of hydroxy fatty acids.},
journal = {Nutrition research (New York, N.Y.)},
volume = {144},
number = {},
pages = {1-15},
doi = {10.1016/j.nutres.2025.10.004},
pmid = {41197330},
issn = {1879-0739},
mesh = {Animals ; Female ; *Probiotics/pharmacology/therapeutic use ; Pregnancy ; *Hypertension ; *Pre-Eclampsia ; Rats ; *Fatty Acids/blood/metabolism ; *Cultured Milk Products ; Gastrointestinal Microbiome ; Blood Pressure/drug effects ; Rats, Sprague-Dawley ; Fermentation ; Esters ; *Milk ; Disease Models, Animal ; Antihypertensive Agents ; },
abstract = {Branched fatty acid esters of hydroxy fatty acids (FAHFAs), a newly-discovered class of endogenous lipids closely associated with obesity, cardiovascular disease, and aging, are potential drug candidates or targets for the prevention and treatment of related conditions. The antihypertensive potential of probiotic-fermented milk has been recognized, but its relevance to preeclampsia (PE) is unclear. It was hypothesized that probiotic-fermented milk could reduce blood pressure in PE rats and influence the contents of FAHFAs, with FAHFAs potentially playing a critical role in this process. To test this hypothesis, the PE rat model was constructed using L-NAME (125 mg/kg), and probiotic-fermented milk (20 mg/kg) was administered for a total of 21 d. Metagenomic sequencing and LC-MS/MS based metabolomics were used. Probiotic-fermented milk substantially attenuated hypertension in PE rats, with an efficacy comparable to that of labetalol (4 mg/kg). Probiotic-fermented milk significantly increased the contents of specific FAHFAs (e.g., 18:0/20:2, 16:0/18:2) in the gut and serum (P < .05) and FAHFAs was negatively correlated with blood pressure (P < .05). Probiotic-fermented milk regulated the composition of gut microbiota (increasing Lactiplantibacillus and Staphylococcus and decreasing Methanobrevibacter and Limosilactobacillus), and down-regulated purine, glyoxylate/dicarboxylate, and amino metabolism, and the one-carbon pool produced by folate. These metabolic shifts were strongly correlated with the gut microbiota and FAHFAs. These results indicate that probiotic-fermented milk alleviates hypertension in PE rats, potentially mediated by FAHFAs. This study provides foundational evidence for the antihypertensive mechanism of probiotic-fermented milk in preeclampsia and supports the development of novel strategies for its prevention and treatment.},
}
@article {pmid41196658,
year = {2026},
author = {Verna, G and De Santis, S and Islam, BN and Sommella, EM and Licastro, D and Zhang, L and De Almeida Celio, F and Miller, EN and Merciai, F and Caponigro, V and Xin, W and Campiglia, P and Pizarro, TT and Chieppa, M and Cominelli, F},
title = {A missense mutation in Muc2 promotes gut microbiome and metabolome-dependent colitis-associated tumorigenesis.},
journal = {The Journal of clinical investigation},
volume = {136},
number = {1},
pages = {},
pmid = {41196658},
issn = {1558-8238},
support = {R37 DK042191/DK/NIDDK NIH HHS/United States ; R56 DK042191/DK/NIDDK NIH HHS/United States ; R01 DK042191/DK/NIDDK NIH HHS/United States ; R56 DK055812/DK/NIDDK NIH HHS/United States ; R01 DK055812/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Mutation, Missense ; Mice ; *Mucin-2/genetics/metabolism ; *Gastrointestinal Microbiome ; *Metabolome ; *Colitis-Associated Neoplasms/genetics/microbiology/metabolism/pathology ; *Colitis, Ulcerative/genetics/microbiology/metabolism/pathology ; *Colitis/genetics/microbiology/metabolism/pathology ; *Carcinogenesis/genetics/metabolism ; Fecal Microbiota Transplantation ; Humans ; Disease Models, Animal ; Female ; },
abstract = {Colitis-associated cancer (CAC) arises from a complex interplay between host and environmental factors. In this report, we investigated the role of the gut microbiome using Winnie mice, an ulcerative colitis-like (UC-like) model with a missense mutation in the Muc2 gene. Upon rederivation from a conventional (CONV) to a specific pathogen-free (SPF) facility, Winnie mice developed severe colitis and, notably, spontaneous CAC that progressively worsened over time. In contrast, CONV Winnie mice showed only mild colitis but no tumorigenesis. By comparison, when re-derived into germ-free (GF) conditions, SPF Winnie mice were protected from colitis and colon tumors, indicating an essential role for the gut microbiome in the development of CAC in these mice. Using shotgun metagenomics, metabolomics, and lipidomics, we identified a distinct proinflammatory microbial and metabolic signature that potentially drives the transition from colitis to CAC. Using either SPF Winnie or WT (Bl/6) donors, fecal microbiota transplantation (FMT) into GF Winnie recipients demonstrated that, while colitis developed regardless of the donor, only FM from SPF Winnie donors resulted in CAC in recipient mice. Our studies present a relevant model of CAC, providing strong evidence that the microbiome plays a key role in its pathogenesis, thus challenging the concept of colon cancer as a strictly nontransmissible disease.},
}
@article {pmid41196050,
year = {2025},
author = {Lee, S and Raza, S and Lee, E-J and Chang, Y and Ryu, S and Kim, H-L and Kang, S-H and Kim, H-N},
title = {Metagenome-assembled genomes reveal microbial signatures and metabolic pathways linked to coronary artery disease.},
journal = {mSystems},
volume = {10},
number = {12},
pages = {e0095425},
pmid = {41196050},
issn = {2379-5077},
support = {RS-2023-NR077149//National Research Foundation of Korea/ ; },
mesh = {Humans ; *Coronary Artery Disease/microbiology/metabolism ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; Female ; Male ; Middle Aged ; *Metabolic Networks and Pathways/genetics ; Aged ; *Bacteria/genetics/classification/metabolism ; Feces/microbiology ; Case-Control Studies ; Metagenomics/methods ; },
abstract = {Gut microbiota has emerged as a critical factor influencing cardiovascular disease (CVD) risk, particularly coronary artery disease (CAD) development. Using fecal metagenomic shotgun sequencing, we investigated gut microbiota signatures associated with CAD and provided strain-resolved insights through metagenome-assembled genome (MAG) reconstruction. We analyzed 14 patients with CAD and 28 propensity score-matched healthy controls. Differential abundance analysis identified 15 CAD-associated bacterial species. Members of the Lachnospiraceae family, previously associated with trimethylamine-N-oxide production, were significantly enriched in patients with CAD. Conversely, short-chain fatty acid-producing bacteria Slackia isoflavoniconvertens and Faecalibacterium prausnitzii were depleted, suggesting a potential contribution to gut-mediated inflammation and metabolic dysregulation. Metabolic pathway analysis revealed significant urea cycle and L-citrulline biosynthesis enrichment in CAD cases, with Alistipes and Coprococcus as key contributors. Among predicted metabolites, inosine, which is implicated in coronary artery relaxation, was elevated in patients with CAD, whereas C18:0e MAG and α-muricholate were depleted. A random forest model achieved a mean AUC of 0.89 for CAD classification, with improved performance when integrating microbial taxa and metabolites. CAD-derived MAGs showed metabolic signatures linked to inflammatory dysbiosis and cardiovascular dysfunction, such as enriched N2 fixation and sulfite reduction. Strain-resolved comparative genomic analysis of MAGs revealed distinctive functional characteristics between CAD-derived and control-derived strains of Akkermansia muciniphila and Megamonas fumiformis. F. prausnitzii MAG from the control group carried non-trimethylamine-producing gene, mtxB, suggesting its potential protective role in CAD pathophysiology. These findings provide insights into gut microbial alterations in CAD and highlight potential targets for microbiome-based therapeutic interventions to reduce CVD risk.IMPORTANCEGut microbiota plays a pivotal role in cardiovascular disease; however, its specific contribution to coronary artery disease (CAD) remains underexplored. This study identified distinct microbial signatures associated with CAD, including the enrichment of pro-inflammatory bacterial taxa and depletion of short-chain fatty acid-producing bacteria, which may contribute to systemic inflammation and metabolic dysregulation. Perturbations in key pathways, such as the urea cycle and glycolysis, suggest metabolic links between the gut microbiota and CAD. Additionally, the metagenome-assembled genome-based analysis revealed strain-resolved functional heterogeneity that shapes host-microbe interactions and may contribute to CAD pathophysiology. These findings provide novel insights into gut dysbiosis in CAD and highlight the potential of microbiome-targeted therapeutic strategies in precision medicine.},
}
@article {pmid41195309,
year = {2025},
author = {Xu, Z and Li, X and Yuan, X and Sun, C and Zhang, M and Chen, R and Wei, H and Chen, L and Du, H and Li, G and Yang, Y and Chen, X and Cui, L and Fang, X and Wu, J and Li, Q and Luo, F},
title = {HLA-C⁣ [∗] 0304 Associates With Beneficial Gut Microbiota and Later Onset of Type 1 Diabetes in Pediatric Cohorts.},
journal = {Pediatric diabetes},
volume = {2025},
number = {},
pages = {3013063},
pmid = {41195309},
issn = {1399-5448},
mesh = {Humans ; *Diabetes Mellitus, Type 1/genetics/microbiology/epidemiology/immunology ; *Gastrointestinal Microbiome/genetics ; Child ; Male ; Female ; Cross-Sectional Studies ; Adolescent ; Child, Preschool ; Age of Onset ; Cohort Studies ; Infant ; },
abstract = {OBJECTIVE: To investigate whether human leukocyte antigens (HLAs) influence gut microbiota composition and contributes to delayed type 1 diabetes mellitus (T1DM) onset in children.<br><br>METHODS: This multicenter cross-sectional study included 106 newly diagnosed pediatric T1DM patients (age <18 years) and 69 healthy controls from nine Chinese cities. Gut microbiota was profiled via whole-metagenome shotgun sequencing, and HLA alleles were genotyped by PCR sequence-based typing. Participants were stratified by HLA-risk scores. Statistical analyses included &#x3b1;/&#x3b2;-diversity metrics, linear discriminant analysis effect size analysis (LEfSe), and Spearman correlation adjusted for confounders.<br><br>RESULTS: Principal coordinates analysis (PCoA) exposed discernible disparities in gut microbiota structures within the high-HLA-risk T1DM cohort relative to both high- and low-HLA-risk control groups (R [2]&#x2009;=&#x2009;0.0562, p=0.003 and R [2]&#x2009;=&#x2009;0.0343, p=0.003). HLA-C [&#x2217;] 0304 carriers exhibited delayed T1DM onset compared to noncarriers (adjusted R [2]&#x2009;=&#x2009;0.225, p=0.017). High-HLA-risk T1DM patients showed distinct microbiota divergence from controls (R [2]&#x2009;=&#x2009;0.0562, p=0.003), driven by reduced Lachnospiraceae and Blautia (butyrate producers) in noncarriers. Conversely, HLA-C [&#x2217;] 0304-positive T1DM patients had enriched Blautia (p=0.005) and Lachnospiraceae (p=0.039), alongside lower opportunistic pathogens (Citrobacter; p < 0.05). High-HLA-risk patients also displayed lower fasting C-peptide levels than low-risk counterparts (0.19&#x2009;&#xb1;&#x2009;0.14 vs. 0.26&#x2009;&#xb1;&#x2009;0.19&#x2009;&#xb5;g/mL, p=0.029).<br><br>CONCLUSIONS: Our study demonstrates that specific HLA class I subtypes (e.g., C [&#x2217;] 0304) may modulate T1DM onset through selective enrichment of beneficial gut microbiota. Elucidating the mechanisms by which HLA variants regulate mucosal immunity and coordinate HLA-microbiota-immune interactions holds significant potential for developing targeted interventions against T1DM pathogenesis.},
}
@article {pmid41194562,
year = {2025},
author = {Martínez-Mercado, MA and Latisnere-Barragán, H and Ramírez-Arenas, PJ and Vázquez-Juárez, R and García-Maldonado, JQ and López-Cortés, A},
title = {Genome-Resolved Approach of Guerrero Negro Hypersaline Microbial Mats Reveals the Metabolic Potential of Key Players in a Stratified Community.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70199},
pmid = {41194562},
issn = {1462-2920},
support = {CF-2019-848287//Consejo Nacional de Humanidades Ciencia y Tecnolog&#xed;a/ ; },
mesh = {*Archaea/genetics/metabolism/classification/isolation &amp; purification ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Genome, Bacterial ; Metagenome ; *Microbiota ; Sulfur/metabolism ; *Geologic Sediments/microbiology ; Salinity ; Genome, Archaeal ; Carbon/metabolism ; Nitrogen/metabolism ; Phylogeny ; },
abstract = {Hypersaline microbial mats at Guerrero Negro harbor a stratified, highly diverse community with diel metabolic changes. While oxygenic photosynthesis and sulfate reduction are the dominant bacterial metabolic processes, methylotrophic methanogenesis is the main archaeal pathway. Although these metabolic processes have been biochemically characterized, the identity and encoded metabolism of the microorganisms have been inferred only from gene-marker data. Here, a genome-resolved approach in both environmental, as well as experimental dark condition samples (control, H2/CO2, TMA, and H2/CO2-TMA) was used to stimulate less-known anaerobic strategies, determine the metabolic potential of the main microbial players, and analyze the community. Representative metagenome-assembled genomes (170 MAGs) were obtained, encompassing 25 bacterial and 4 archaeal phyla. The metabolic analyses of three basic elements (carbon, sulfur, nitrogen) encoded in the MAGs suggested that in environmental samples, phototrophic taxa were the main source of the organic matter that fueled most of the community. Different sulfur species acting as electron acceptors led to the metabolism of partially degraded organic matter in the lower layers of the mat. These results link and clarify the biochemical processes and microbial players, adding a novel genomic component for the ecological understanding of the microbial mats of Guerrero Negro.},
}
@article {pmid41194219,
year = {2025},
author = {Liu, Y and Yu, M and Chen, X and Ran, L and Zhang, XH},
title = {Diversity, metabolic potential and global distribution of the anaerobic fermentative bacteria Phylum Candidatus Cloacimonadota.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {136},
pmid = {41194219},
issn = {2524-6372},
support = {32370118//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2022QNLM030004-3, LSKJ202203201 and LSKJ202203206//Scientific and Technological Innovation Project of Laoshan Laboratory/ ; },
abstract = {BACKGROUND: The phylum Candidatus Cloacimonadota (formerly known as Cloacimonetes, WWE 1) is a group of strictly anaerobic organisms that frequently associated with engineering and wastewater systems. At present, it cannot be cultured using traditional cultivation methods, and the taxonomic position within this phylum remains unclear, with only one class, Candidatus Cloacimonadia. Furthermore, the diversity and metabolic characteristics of Candidatus Cloacimonadota members in marine environments have yet to be explored. Therefore, the taxonomy and metabolism of the phylum Candidatus Cloacimonadota require further investigation.<br><br>RESULTS: In this study, six high-quality metagenome-assembled genomes (MAGs) of Candidatus Cloacimonadota were acquired from the anoxic zone of the Yongle Blue Hole (YBH), potentially representing new taxa. Additionally, 483 Candidatus Cloacimonadota genomes from global databases were downloaded, and all genomes were analyzed and compared. Candidatus Cloacimonadota is widely distributed across diverse environments worldwide, and its class, Candidatus Cloacimonadia, can be divided into two clades, Clade A and Clade B, the latter of which contains six YBH-derived MAGs. The Clade A and Clade B showed distinct genomic features, metabolic strategies and evolutionary histories, which are associated with their environments. For instance, they employ different anaerobic respiratory pathways: Clade B utilizes heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhADG) complex (NiFe/MvhADG-HdrABC), while Clade A utilizes Hnd/FeFe Group A3 hydrogenase complex for hydrogen utilization. Furthermore, YBH-derived MAGs have unique metabolic genes, such as those encoding chitinase and &#x3b1;-galactosidase, and the chitinase activity in MAG213-F140 from YBH was confirmed by heterologous expression. Divergence time analysis revealed that YBH-derived MAGs diverged around 3.36 million years ago.<br><br>CONCLUSION: This study enhances the understanding of the diversity, metabolic potential, and global distribution of Candidatus Cloacimonadota. We found this phylum could be divided into Clades A and B, revealing significant differences in genetic traits and metabolic capabilities between the two clades, and focusing on their ecological roles in marine environments. Moreover, this research holds substantial value for the development and utilization of marine resources, as well as for advancing the understanding of biogeochemical cycles, further highlighting the crucial role of microorganisms in these key ecological processes.},
}
@article {pmid41193697,
year = {2026},
author = {Chica Cardenas, LA and Leonard, MM and Baldridge, MT and Handley, SA},
title = {Gut virome dynamics: from commensal to critical player in health and disease.},
journal = {Nature reviews. Gastroenterology &amp; hepatology},
volume = {23},
number = {2},
pages = {126-144},
pmid = {41193697},
issn = {1759-5053},
mesh = {Humans ; *Virome/physiology ; *Gastrointestinal Microbiome/physiology ; Bacteriophages ; },
abstract = {The gut virome is a complex ecosystem characterized by the interplay of diverse viral entities, predominantly bacteriophages and eukaryotic viruses. The gut virome has a critical role in human health by shaping microbial community profiles, modulating host immunity and influencing metabolic processes. Different viral metagenomics approaches have revealed the remarkable diversity of the gut virome, showing individual-specific patterns that evolve over time and adapt dynamically to environmental factors. Perturbations in this community are increasingly associated with chronic immune and inflammatory conditions, metabolic disorders and neurological conditions, highlighting its potential as a diagnostic biomarker and therapeutic target. The early-life gut virome is particularly influential in establishing lifelong health trajectories through its interactions with diet, immune pathways and others, thereby contributing to inflammatory and metabolic regulation. This Review synthesizes current knowledge of gut virome composition, dynamics and functional relevance, critically evaluating evidence distinguishing causal from correlative roles in disease pathogenesis. The interactions of the virome with other microbiome components and host immunity are examined, and emerging translational applications, including phage therapy and biomarker development, are discussed. Integrating these insights while acknowledging methodological challenges provides a comprehensive framework for understanding the complex roles of the gut virome in health and disease.},
}
@article {pmid41193635,
year = {2025},
author = {Weinheimer, AR and Brown, JM and Thompson, B and Leonaviciene, G and Kiseliovas, V and Jocys, S and Munson-McGee, J and Gavelis, G and Mascena, C and Mazutis, L and Poulton, NJ and Zilionis, R and Stepanauskas, R},
title = {Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes.},
journal = {Nature microbiology},
volume = {10},
number = {12},
pages = {3245-3257},
pmid = {41193635},
issn = {2058-5276},
support = {991222//Simons Foundation/ ; },
mesh = {*Seawater/virology ; *Genome, Viral ; *Genomics/methods ; Metagenomics/methods ; *Viruses/genetics/classification/isolation &amp; purification ; Microbiota/genetics ; Metagenome ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Sequence Analysis, DNA ; },
abstract = {Viruses and other extracellular genetic elements play essential roles in marine communities. However, methods to capture their full diversity remain limited by the constraints of bulk sequencing assemblers or pre-sorting throughput. Here we introduce environmental micro-compartment genomics (EMCG), which vastly improves the throughput and efficiency of single-particle genomic sequencing obtained from nanolitre volumes by compartmentalizing particles of a sample into picolitre-sized, semi-permeable capsules for in-capsule DNA amplification and barcoding. From 300 nanolitres of seawater, EMCG obtained genomic sequences of 2,037 particles. The microbiome composition agreed with other methods, and the virus-like assembly lengths indicated that most were near complete. Many viral assemblies belonged to the Naomiviridae, lacked metagenomic representation and aligned to outlier contigs of abundant, putative host lineages, suggesting their use of non-canonical DNA and overlooked ecological importance. This approach provides opportunities for high-throughput, quantitative and cost-effective genome analyses of individual cells and extracellular particles across complex microbiomes.},
}
@article {pmid41192488,
year = {2026},
author = {Chen, W and Yang, Y and Chang, S and Zhang, K and Xu, T and Li, J and Liang, X and Xu, Y and Nghiem, LD and Johir, MAH and Wei, Y},
title = {Microbial necromass analogues reshape composting humification pathways.},
journal = {Bioresource technology},
volume = {441},
number = {},
pages = {133583},
doi = {10.1016/j.biortech.2025.133583},
pmid = {41192488},
issn = {1873-2976},
mesh = {*Composting/methods ; *Humic Substances/analysis ; Chitin ; *Soil Microbiology ; Animals ; Manure/microbiology ; Soil/chemistry ; Bacteria/metabolism ; Benzopyrans ; Swine ; Biomass ; Metagenomics ; },
abstract = {Microbial necromass is increasingly recognized as a key driver of soil carbon stabilization, yet its mechanistic role in compost humification remains elusive. Here, by integrating metagenomics, quantitative necromass tracing, and partial least squares structural equation modeling (PLS-SEM), the regulatory effects of two microbial necromass analogues-N-acetyl-d-glucosamine (GlcNAc) and chitin-on pig manure composting were systematically investigated. Both analogues significantly altered the physicochemical properties, microbial community composition, and necromass dynamics during composting. Chitin addition markedly enhanced early microbial biomass and bacterial diversity but inhibited humic acid (HA) formation, while promoting fulvic acid (FA) accumulation and resulting in humic substances (HS) with lower molecular complexity. In contrast, GlcNAc selectively stimulated bacterial proliferation during the maturation phase, reduced both bacterial and fungal diversity, and led to increased FA content, accompanied by reduced HS molecular complexity. Metagenomic and PLS-SEM analyses revealed that both analogues fundamentally reprogrammed humification metabolic pathways: chitin suppressed genes involved in complex precursor metabolism, whereas GlcNAc narrowed the functional repertoire and shifted humification toward simpler pathways. These analogue-driven microbial metabolic shifts decoupled necromass accumulation from stable HA formation and favored the accumulation of simpler humic fractions. This study provides the first mechanistic evidence that targeted regulation of necromass transformation can precisely optimize humification efficiency and molecular characteristics, laying a theoretical foundation for improved organic waste utilization and process control in composting.},
}
@article {pmid41192424,
year = {2025},
author = {Li, P and Sun, J and Geng, Y and Jiang, Y and Li, YZ and Zhang, Z},
title = {Assessment of enzyme diversity in the fermented food microbiome.},
journal = {Cell systems},
volume = {16},
number = {11},
pages = {101430},
doi = {10.1016/j.cels.2025.101430},
pmid = {41192424},
issn = {2405-4720},
mesh = {*Fermented Foods/microbiology ; *Microbiota/genetics ; Fermentation ; Food Microbiology/methods ; Metagenome/genetics ; Machine Learning ; *Enzymes/genetics/metabolism ; },
abstract = {Microbial bioactivity is essential for the flavor, appearance, quality, and safety of fermented foods. However, the diversity and distribution of enzymatic resources in fermentation remain poorly understood. This study explored 10,202 metagenome-assembled genomes from global fermented foods using machine learning, identifying over 5 million enzyme sequences grouped into 98,693 homologous clusters, representing over 3,000 enzyme types. Functional analysis revealed that 84.4% of these clusters were unannotated in current databases, with high novelty in terpenoid and polyketide metabolism enzymes. Peptide hydrolases exhibited broad environmental adaptability based on predicted optimal temperatures and pH, and niche breadth calculations indicated 31.3% of enzyme clusters displayed food-type specificity. Additionally, we developed a machine learning model to classify fermented food sources by enzyme clusters, highlighting key enzymes differentiating habitats. Our findings emphasize the untapped potential of fermented food environments for enzyme resource exploration, offering valuable insights into microbial functions for future food research. A record of this paper's transparent peer review process is included in the supplemental information.},
}
@article {pmid41192191,
year = {2026},
author = {Zhou, G and Wang, YS and Zhang, GF and Zhang, SY and Wen, X and Cui, ZB and Shi, QS and Xie, XB},
title = {Gut microbiota composition and antibiotic resistance ontology landscape in Micropterus salmoides: Insights from metagenomic and metabolomic analyses.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {57},
number = {},
pages = {101666},
doi = {10.1016/j.cbd.2025.101666},
pmid = {41192191},
issn = {1878-0407},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Metabolomics ; *Metagenomics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/classification/metabolism ; Anti-Bacterial Agents/pharmacology ; *Fishes/microbiology/metabolism ; Metagenome ; },
abstract = {Micropterus salmoides, a pivotal aquaculture species in China, faces critical challenges including high disease susceptibility and insufficient characterization of gut microbiota-associated antibiotic resistance ontology (ARO). This study integrated metagenomic and metabolomic approaches to systematically characterize the compositional dynamics, diversity patterns, and spatiotemporal distribution of gut microbiota and AROs in M. salmoides across four developmental stages, while clarifying their interactions with metabolic pathways. Metagenomic profiling identified Proteobacteria, Firmicutes, and Fusobacteria as the dominant bacterial phyla, with Acinetobacter baumannii and Alcanivorax profundi exhibiting stage-specific abundance patterns. A total of 150 distinct ARO subtypes were identified, among which tetracycline- and glycopeptide-resistance genes (e.g., tetA and vanR) showing high abundance, with their resistance primarily mediated by efflux-driven mechanisms. Untargeted metabolomics uncovered 4459 metabolites, with robust correlations observed between core microbial genera (e.g., Flavobacterium and Herbaspirillum) and lipid/amino acid metabolic pathways. Co-occurrence network analysis further demonstrated significant interconnections between ARO subtypes and lineages of Proteobacteria/Firmicutes. Our multi-omics framework provides comprehensive insights into the gut microbiota-ARO-metabolism nexus in M. salmoides, thereby establishing a correlative framework for developing precision interventions to control the dissemination of antimicrobial resistance and improve disease management in sustainable aquaculture systems.},
}
@article {pmid41192179,
year = {2025},
author = {Wu, GG and Jin, JA and Han, NN and Guo, WL and Fan, NS and Jin, RC},
title = {Multiomic insights into the regulatory mechanism of anammox consortia: Interspecies cooperation, degradation and self-adaptation to plasticizer stress.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140319},
doi = {10.1016/j.jhazmat.2025.140319},
pmid = {41192179},
issn = {1873-3336},
mesh = {*Diethylhexyl Phthalate/toxicity/metabolism ; Biodegradation, Environmental ; *Plasticizers/toxicity/metabolism ; *Microbial Consortia ; Oxidation-Reduction ; *Water Pollutants, Chemical/metabolism/toxicity ; Anaerobiosis ; Bacteria/metabolism/genetics ; *Ammonium Compounds/metabolism ; },
abstract = {Phthalates are prevalent in wastewater treatment systems and pose a potential threat to microbial communities. In this study, it was found that the nitrogen removal efficiency of anaerobic ammonium oxidation (anammox) process remained at 92.5 ± 2.4 % after the long-term exposure to di-(2-ethylhexyl) phthalate (DEHP). Although the relative abundance of Candidatus Kuenenia decreased by 5.5 %, that of other denitrifying functional bacteria increased to maintain the system stability. The adaptation of anammox consortia to DEHP mainly depended on microbial cooperation and molecular regulation. Combined with metagenomic and metatranscriptomic analyses, Bacillus subtilis functioned as the DEHP-degrading species and exhibited a collaborative relationship with other degrading microorganisms. The expression levels of carbon metabolism, two-component system and quorum sensing related genes were significantly (p < 0.05) upregulated by 0.4-6.6 folds. The structural equation model further proved that biodegradation was the main contributor to mitigating DEHP inhibition. Notably, Ca. Kuenenia and transposons were the host of most antibiotic resistance genes (ARGs) and the main mobile genes elements, respectively. DEHP also triggered oxidative stress and resistance dissemination in anammox consortia. These findings provide molecular insights into the microbial regulatory mechanism in responding to plasticizer stress and drive the expansion of anammox process application.},
}
@article {pmid41192168,
year = {2025},
author = {Skalny, AV and Korobeinikova, TV and Morozova, G and Menshikova, IV and Gritsenko, VA and Zhang, F and Mak, DV and Guo, X and Sotnikova, TI and Aschner, M and Tinkov, AA},
title = {Serum trace element and mineral levels and fecal microbiota in relation to cartilage damage in rheumatoid arthritis patients.},
journal = {Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)},
volume = {92},
number = {},
pages = {127787},
doi = {10.1016/j.jtemb.2025.127787},
pmid = {41192168},
issn = {1878-3252},
mesh = {Humans ; *Arthritis, Rheumatoid/blood/microbiology/pathology ; Male ; Female ; Middle Aged ; *Feces/microbiology ; *Trace Elements/blood ; *Minerals/blood ; *Cartilage/pathology ; *Gastrointestinal Microbiome ; Adult ; Aged ; },
abstract = {UNLABELLED: The objective of the present study was to evaluate serum trace element and mineral levels as well as taxonomic characteristics of gut microbiota and their association with cartilage damage in patients with rheumatoid arthritis (RA).<br><br>MATERIALS AND METHODS: Serum trace element and mineral levels in 41 healthy controls and 41 RA patients were assessed using inductively-coupled plasma mass-spectrometry. Taxonomic characteristics of fecal microbiota were assessed using 16S metagenomic sequencing. RA patients were characterized by increased cartilage oligomeric matrix protein (COMP) and complement component 3 (C3) levels, indicative of cartilage damage and inflammation.<br><br>RESULTS: Serum Ca, Fe, Se, and Zn levels in RA patients were lower, whereas circulating Cr, Cu, and Mo concentrations exceeded the respective control values. 16S metagenomic sequencing of fecal samples revealed lower relative abundance of Firmicutes and Actinomycetota with a reduction in Firmicutes-to-Bacteroidetes ratio in RA patients. At the class level, the relative abundance of Bacilli, Coriobacteria, and Clostridia in RA patients was lower, whereas that of Bacteroidia and Negativicutes was higher compared to the control group. Tight negative association between serum Zn levels and the abundance of Bacteroidetes and Bacteroidia was observed, whereas correlation between Zn and Firmicutes-to-Bacteroidetes ratio was positive. Multiple linear regression analysis demonstrated that serum COMP level was inversely associated with serum Fe and Se levels, as well as relative abundance of Bacilli and Clostridia, being positively associated with serum Ca and C3 levels.<br><br>CONCLUSION: These novel findings demonstrate a multilateral relationship between trace element metabolism, gut microbiota, and cartilage damage in RA.},
}
@article {pmid41192043,
year = {2026},
author = {Kumar, A and Xu, C and Dakal, TC},
title = {Microbiome based precision medicine through integrated multiomics and machine learning.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128384},
doi = {10.1016/j.micres.2025.128384},
pmid = {41192043},
issn = {1618-0623},
mesh = {Humans ; *Machine Learning ; *Precision Medicine/methods ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Metabolomics/methods ; Proteomics/methods ; Dysbiosis/microbiology ; Inflammatory Bowel Diseases/microbiology ; Multiomics ; },
abstract = {Gut microbiome (GME) is a dynamic ecosystem composed of diverse microorganisms with extensive functional potential that influence host physiology, endocrinology, and neurology. This review explores how multiomics (m[OMICS]) and machine learning (ML) enhance understanding of the GME and its implications for human disease and therapy. Integrating metagenomics, metatranscriptomics, metaproteomics, and metabolomics with ML enables the linkage of microbial composition and function to clinical outcomes. Combined m[OMICS] approaches elucidate species and strain dynamics, metabolic pathways, and metabolite production within the gut environment. Techniques such as shotgun metagenomics, metagenome-assembled genomes, and pathway mapping reveal associations between dysbiosis and diseases including inflammatory bowel disease, colorectal cancer, cardiometabolic, and neurological disorders. Mechanistic insights highlight short-chain fatty acids in immune regulation, bile acid transformations in metabolic signaling, and trimethylamine N-oxide in cardiovascular risk. ML models trained on heterogeneous datasets identify disease-related microbial modules, improve patient stratification, and predict therapeutic responses, such as differentiating IBD subtypes and detecting cancer-linked microbial signatures. Network analyses uncover gut microbial interaction patterns influencing host physiology. Emerging integrative tools like MOFA+ , DIABLO, and MintTea strengthen cross-modal analysis and biomarker discovery. Standardized workflows addressing quality control, assembly, binning, annotation, and visualization ensure reproducibility. Together, m[OMICS] and ML establish a robust framework for translating GME ecology into clinically relevant biomarkers and precision interventions. To enhance reliability, GME studies should adopt uniform sampling protocols, correct compositional biases, employ interpretable models, and validate findings across multi-site cohorts to advance microbiome-based diagnostics and therapeutics in precision medicine.},
}
@article {pmid41189709,
year = {2025},
author = {Chen, Y and Zhang, R and Wen, J and Zhao, J and Zhang, J},
title = {Metagenomic analysis of blood microbiota alterations: insights into HIV progression and immune restoration.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1619059},
pmid = {41189709},
issn = {2235-2988},
mesh = {Humans ; *HIV Infections/immunology/drug therapy/microbiology/blood/virology ; Metagenomics ; Male ; Female ; Adult ; *Microbiota ; Middle Aged ; Disease Progression ; Viral Load ; *Bacteria/classification/genetics/isolation &amp; purification ; *Immune Reconstitution ; *Blood/microbiology ; CD4-CD8 Ratio ; },
abstract = {INTRODUCTION: Emerging evidence suggests that the blood microbiome may influence the progression of HIV infection and immune restoration. This study aims to comprehensively characterize blood microbiota alterations associated with HIV infection and antiretroviral therapy (ART), and to evaluate their potential as microbial indicators for assessing infection status and immune restoration.<br><br>METHODS: We recruited 91 participants, including 31 treatment-na&#xef;ve HIV-infected individuals, 30 ART-treated individuals with undetectable viral loads, and 30 healthy controls. Blood samples were collected for metagenomic sequencing and immunological profiling.<br><br>RESULTS: HIV infection profoundly disrupted blood microbiota diversity and composition, with a marked reduction in &#x3b1;-diversity and enrichment of opportunistic pathogens such as Pseudomonas aeruginosa, Acinetobacter baumannii and Stenotrophomonas maltophilia, alongside depletion of beneficial taxa like Bifidobacterium longum. ART partially restored microbial diversity but did not fully reestablish a healthy microbiota. Correlation analysis revealed that Acinetobacter pittii, Xanthomonas campestris and Diaphorobacter nitroreducens were significantly associated with viral load, suggesting their potential role in HIV progression. Additionally, after ART, Acinetobacter junii and Pseudomonas putida were significantly correlated with the CD4/CD8 ratio, indicating their potential role in immune restoration.<br><br>DISCUSSION: These findings provide new insights into the interactions between blood microbiota and HIV progression. The identified blood microbiota may serve as potential indicators for evaluating HIV infection status and treatment efficacy, offering a basis for microbial-based diagnostic and therapeutic strategies.},
}
@article {pmid41189540,
year = {2026},
author = {Inoue, J and Hirai, J and Ikeba, K and Yu, Z and Ahmed, SI and Lin, Z and Lin, Y and Wong, MK and Shinzato, C and Itoh, S and Ito, SI and Saito, H and Hyodo, S},
title = {eDNAmap: A Metabarcoding Web Tool for Comparing Marine Biodiversity, With Special Reference to Teleost Fish.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70066},
pmid = {41189540},
issn = {1755-0998},
support = {21H04922//Japan Society for the Promotion of Science/ ; //The University of Tokyo - FSI Project &#x201b;Ocean DNA'/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/genetics/classification ; *Biodiversity ; Internet ; *DNA, Environmental/genetics ; *Computational Biology/methods ; *Aquatic Organisms/classification/genetics ; *Metagenomics/methods ; *Software ; },
abstract = {Marine environmental DNA (eDNA) metabarcoding data are beginning to accumulate, even for remote and poorly studied areas, such as marine environments. These data enable us to identify distributions of target organisms and then to compare biological compositions between different marine areas. However, there is no platform to effectively utilise and accumulate these data. In this study, we developed eDNAmap, a web-based platform designed to analyse and store marine eDNA metabarcoding data. By uploading species or sequence composition data with location information, eDNAmap users can automatically (1) plot sampling locations on a map, (2) generate a heatmap to evaluate potential batch effects arising from methodological differences and (3) perform nonmetric multidimensional scaling and cluster analyses using similarity indices. Furthermore, users can specify scientific names to display species distributions and upload species lists to assess species compositions of the target sea area. As an example, fish sequence composition data obtained from 55 stations around the Watase line-believed to exist along a geographic canyon known as the Tokara Gap-were used to verify its existence using eDNAmap. The platform includes a database primarily consisting of teleost fish data from the Northwestern Pacific, which users can analyse similarly to their own uploads. Although originally designed for fish, eDNAmap is flexible enough to handle data from other marine organisms. Analysing multiple taxa enables the detection of concordant biogeographic patterns across different groups, which can strengthen ecological interpretations and lay the groundwork for identifying environmental drivers shaping community structures. eDNAmap is available at https://github.com/jun-inoue/eDNAmap.},
}
@article {pmid41189414,
year = {2025},
author = {Zheng, Z and Zhao, L and Liu, Y and Wang, W and Zheng, K and Chen, X and Zhang, S and Sun, Y and Ma, Z and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M and Gao, C and Sun, L and Liang, Y},
title = {Identification and Genomic Analysis of a New Viral Species With Low Similarity to Existing Viruses.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70201},
doi = {10.1111/1462-2920.70201},
pmid = {41189414},
issn = {1462-2920},
support = {LSKJ202203201//Laoshan Laboratory/ ; 42120104006//National Natural Science Foundation of China/ ; 42176111//National Natural Science Foundation of China/ ; 42306111//National Natural Science Foundation of China/ ; //Ocean Negative Carbon Emissions/ ; 2025M770867//China Postdoctoral Science Foundation/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 201812002//Fundamental Research Funds for the Central Universities/ ; 202072001//Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Genome, Viral ; Metagenomics ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Phylogeny ; *Pseudoalteromonas/virology ; Genomics ; *Viruses/genetics/classification/isolation &amp; purification ; },
abstract = {Viruses are among the most abundant and diverse biological entities on Earth. Over the past decades, metagenomic sequencing has revealed thousands of viral genomes. However, viral isolation methods remain indispensable for discovering viruses that are missed by metagenomic sequencing due to limitations like low abundance (1, 2). Here, a novel phage, vB_PshM_Y4, which infects Pseudoalteromonas shioyasakiensis, an economically important, opportunistic marine pathogen was isolated. A comparison of vB_PshM_Y4 with over 15 million viral genomes, including both cultivated and uncultivated viruses in the NCBI and IMG/VR v4 datasets, found no closely related genome. This study provides evidence that traditional isolation methods can detect viruses that cannot be identified through metagenomic sequencing. In addition, a comparison of virus isolates deposited in the NCBI database with uncultured viruses in the IMG/VR viral database shows that approximately only half of the isolates can be detected using metagenomic approaches. Notably, viruses that are not able to be detected by metagenomic sequencing often exhibit low abundance and possess unique genomes. These results suggest that traditional viral isolation methods remain important for obtaining rare, low-abundance viruses and underscore the significance of traditional experimental methods in the era of metagenomes.},
}
@article {pmid41188680,
year = {2025},
author = {Falk, NW and Smith, H and Papudeshi, B and Martin, B and Qian, G and Gerson, AR and Prasad, A and Harmer, SL and Dinsdale, EA},
title = {Metagenomics reveals water, biofilm, and sediment microbial communities exhibit distinct responses and functions in neutral and metalliferous drainage (NMD).},
journal = {Environmental geochemistry and health},
volume = {47},
number = {12},
pages = {547},
pmid = {41188680},
issn = {1573-2983},
support = {CRC TiME project 3.10 and Teck Resources Limited//CRCTiME/ ; },
mesh = {*Geologic Sediments/microbiology ; *Biofilms ; Mining ; *Microbiota ; Metagenomics ; *Water Microbiology ; Western Australia ; Water Pollutants, Chemical/analysis ; Zinc/analysis ; Metagenome ; Bacteria/genetics/classification ; },
abstract = {Neutral and metalliferous drainage (NMD) poses an environmental risk for both operating and legacy mine sites. Near-neutral pH distinguishes NMD from more acidic conditions of acid and metalliferous drainage (AMD), however NMD contains elevated levels of metals that necessitate strict management. Microbial communities are key indicators of ecological conditions and play important roles in NMD biogeochemical cycling, often exhibiting distinct dynamics compared to AMD. Shotgun sequencing and metagenome assembled genomes (MAGs) were used to characterize microbial diversity and functional potential across water, biofilm, and sediment microbiomes along a flow path at a historical lead-zinc mine in Western Australia. Zn levels peaked upstream and declined downstream, corresponding to shifts in microbial diversity. In water microbiomes, a Polynucleobacter MAG became dominant where Zn concentrations dropped below known toxicity thresholds. The genomic traits of Polynucleobacter, including a streamlined genome, Zn- (LpxC) and heat-responsive membrane genes, and enriched lipid metabolism pathways, enabled survival under metal and nutrient stress. Photosynthetic biofilms, dominated by cyanobacteria such as Synechococcaceae and Leptolyngbyaceae, played a central role in ecosystem function. These biofilms contained genes for photosynthesis, metal transport, and motility, and likely contributed organic carbon and sulfur intermediates that supported heterotrophs like Polynucleobacter and Sediminibacterium. Coordinated microbial sulfur metabolism across habitats was evident, with sulfur oxidation occurring in water and biofilms and sulfate reduction localized to sediment, evidenced with ZnS mineral phases associated with increased DsrMKJOP gene abundance. These findings are vital for mine closure and land reclamation, offering knowledge on key microbial adaption and syntrophy in NMD systems.},
}
@article {pmid41188618,
year = {2025},
author = {Saini, K and Kumar, SS and Kumar, V and Bajar, S},
title = {Enhanced biodegradation of ibuprofen using bacterial consortia isolated from landfill leachate.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {12},
pages = {1295},
pmid = {41188618},
issn = {1573-2959},
support = {SR/PURSE/2022/126(G)//Department of Science and Technology (DST), New Delhi, India, under the PURSE grant/ ; },
mesh = {*Ibuprofen/metabolism/analysis ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism/analysis ; *Microbial Consortia ; *Bacteria/metabolism ; *Anti-Inflammatory Agents, Non-Steroidal/metabolism/analysis ; RNA, Ribosomal, 16S ; },
abstract = {The widespread use of non-steroidal anti-inflammatory drugs (NSAIDs), like ibuprofen, has led to a persistent occurrence across various environmental matrices, raising concern regarding potential human health and ecological impacts. The potentially detrimental risks of ibuprofen exposure highlight the need for exploring effective and cost-efficient remediation techniques. The microbial degradation of ibuprofen represents a significant technological and economical approach. The present study investigates the biodegradation of ibuprofen using two distinct microbial consortia (MC I and MC II) isolated from landfill leachate using Postgate media and acclimated with ibuprofen. Batch mode experiments were conducted to assess the removal of 500 mg/L ibuprofen in the presence and absence of a carbon source (glucose and acetate). MC I and MC II achieved complete removal of ibuprofen within 78 h and 60 h, respectively, under substrate-free conditions. When supplemented with glucose, the removal time was reduced to 54 h for MC I and 36 h for MC II, whereas acetate addition resulted in removal extended to 60 h and 48 h, respectively. The metagenomics analysis (16S rRNA sequencing) of microbial consortia revealed Firmicutes (Bacillota), Actinobacteria (Actinomycetota), Proteobacteria, Bacteroidetes, and Thermotogae as the dominant phyla and GC-MS analysis confirmed the presence of significant metabolites (endpoint of the bioassay) in the biodegradation of ibuprofen, i.e., 2-hydroxy ibuprofen, 1,4-hydroquinone, and 2-hydroxy-1,4-quinol. The findings of the study highlight the potential of microbial consortia for efficient ibuprofen biodegradation and provide insights into their metabolic pathway.},
}
@article {pmid41188334,
year = {2025},
author = {Kang, R and Yu, Z and Kim, H and Seo, J and Kim, M and Park, T},
title = {Manually weighted taxonomy classifiers improve species-specific rumen microbiome analysis compared to unweighted or average weighted taxonomy classifiers.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38587},
pmid = {41188334},
issn = {2045-2322},
mesh = {*Rumen/microbiology ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Species Specificity ; Metagenomics/methods ; *Bacteria/classification/genetics ; },
abstract = {Previous research has demonstrated that applying taxonomic weights to shotgun metagenomic data can improve species identification in 16S rRNA gene-based microbiome analysis. However, such an approach does not allow for accurate analysis of samples collected from less studied habitats, such as rumen. In the present study, we developed a method to incorporate taxonomic weights based on relative abundance of species identified from shotgun sequencing and amplicon sequencing data derived from rumen. Using this weighting method, we evaluated latest versions of five prominent databases-SILVA, Greengenes2 (GG2), RDP, NCBI RefSeq, and GTDB-against the BLAST 16S rRNA database, assessing classification counts, fully classified ratios (proportion of ASVs classified to a known genus and species), and error rates. Our results indicated that providing taxonomic weights partially increased classification counts and fully classified ratios, although the extent of improvement varied across databases. A reduction in error rates was also observed compared to the unweighted taxonomy classifier (P < 0.05). While GG2 and SILVA struggled with accurate classification at the species level owing to their inherent database characteristics, GTDB consistently improved all metrics using the manually weighted taxonomy classifier, achieving up to an 8% error rate reduction at the species level. NCBI RefSeq and RDP also exhibited remarkable improvement in the classification counts and fully classified ratios, along with error rate reductions by up to 47% at the species level. These findings demonstrate that amplicon sequencing datasets can enhance rumen microbiome analyses through effective weighting methods. While SILVA is commonly used in metataxonomic analyses of the rumen microbiome, we recommend NCBI RefSeq for species-level classification due to its superior accuracy and minimal ambiguous classification (e.g., "uncultured" or "sp.") in future metataxonomic studies.},
}
@article {pmid41188324,
year = {2025},
author = {Kwak, MS and Cha, JM and Kim, CW and Won, KY and Hwang, CI},
title = {Integrative multi-omics deciphers the potential mechanism and microbial biomarkers for lymph node metastasis in colorectal cancer.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38611},
pmid = {41188324},
issn = {2045-2322},
support = {R37 CA249007/CA/NCI NIH HHS/United States ; R37CA249007/CA/NCI NIH HHS/United States ; NRF- 2022R1A2C100309913//National Research Foundation of Korea/ ; 2022//Medical Science Research Institute grant, Kyung Hee University Hospital at Gangdong/ ; },
mesh = {Humans ; *Colorectal Neoplasms/genetics/pathology/microbiology ; *Lymphatic Metastasis/genetics ; DNA Methylation ; Male ; Female ; *Biomarkers, Tumor/genetics ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Transcriptome ; Gene Expression Regulation, Neoplastic ; Gene Expression Profiling ; Multiomics ; },
abstract = {Understanding and accurate diagnosis of lymph node metastasis (LNM) for patients with colorectal cancer (CRC) is essential to determine treatment and follow-up strategies. Therefore, in this study, we aimed to elucidate the biological process and identify the potential biomarker for LNM in CRC.A total of 30 patients who received a histologically confirmed diagnosis of CRC with Stage I to III and a curative surgery between November 2020 and July 2021 at Kyung Hee university hospital at Gangdong were included. We performed multi-omics approach integrating the data on somatic mutation, transcriptomic expression, DNA methylation, and microbiome with tumor and adjacent matched normal tissues of each patient. In total, 12 significant DEGs between the patients with and without LNM were identified, consisting of significantly upregulated S100A8 gene, a proinflammatory gene. The GSEA revealed that gene sets involving "MULTI CANCER INVASIVENESS" in terms related to epithelial-mesenchymal transition was significantly upregulated in the patients with LNM. Integrated functional analysis of DNA methylation with transcriptome profile shows that significantly hypomethylated promoters of the genes are enriched for LNM. The phylum Proteobacteria, unassigned (p_PU) presented significantly higher proportions in cancer tissues from the adjacent normal tissues. Notably, when compared to the patients without LNM, the gut microbiota of those with LNM appears to exhibit a significantly lower abundance of the p_PU, indicating its potential as promising biomarker for LNM in CRC. We explained the mechanism of tumor spreading using multi-omics analysis and identified the relevant metagenomic biomarker to predict the LNM in CRC by the recognition of host-microbial interaction, thereby can make the cancer surveillance of the patients more individualized and convincing.},
}
@article {pmid41188219,
year = {2025},
author = {Ndiaye, M and Bonilla-Rosso, G and Mazel, F and Engel, P},
title = {Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9738},
pmid = {41188219},
issn = {2041-1723},
mesh = {Animals ; *Bacteriophages/genetics/classification/physiology ; *Gastrointestinal Microbiome/genetics ; Bees/microbiology/virology ; *Bacteria/genetics/classification/virology ; Biodiversity ; Metagenomics ; Metagenome ; },
abstract = {Bacteriophages (phages) play a crucial role in shaping bacterial communities. Documenting the relationship between phage and bacterial diversity in natural systems is fundamental to understand eco-evolutionary dynamics that shape community composition, such as host specificity, emergence of phage resistance and phage-driven microbial diversification. However, our current understanding of this relationship is still limited, particularly in animal-associated microbiomes. Here, we analyze paired bacterial and viral metagenomics data from the gut microbiota of 49 individual honeybees and reconstruct the phage-bacteria interaction network by leveraging CRISPR spacer matches and genome homology. The resulting interaction network displays a highly modular structure with nested phage-bacteria interactions within each module. Viral and bacterial alpha and beta diversity are correlated, particularly at the bacterial strain level and when considering the interaction network. Overall, our results suggest that the most relevant approach to study phage-bacteria diversity patterns should rely on strain-level resolution and the explicit use of the interaction network. This may explain why previous studies have obtained mixed results when testing for phage-bacteria diversity correlations. Finally, we call for further studies building up on these correlation patterns to probe the underlying mechanisms by considering both bottom-up and top-down regulatory mechanisms in microbiome assembly.},
}
@article {pmid41187758,
year = {2025},
author = {Yilmaz, B and Baertschi, I and Meier, KHU and Le Gac, C and Jordi, SBU and Black, C and Li, J and Lindholm, AK and , and König, B and Sauer, U and Stelling, J and Macpherson, AJ},
title = {A global survey of taxa-metabolic associations across mouse microbiome communities.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {11},
pages = {1960-1976.e10},
doi = {10.1016/j.chom.2025.10.010},
pmid = {41187758},
issn = {1934-6069},
mesh = {Animals ; Mice/microbiology ; *Microbiota/physiology ; Metabolomics ; *Bacteria/classification/metabolism/genetics ; Host Microbial Interactions ; Symbiosis ; },
abstract = {Host-microbiota mutualism is rooted in the exchange of dietary and metabolic molecules. Microbial diversity broadens the metabolite pool, with each taxon contributing distinct compounds in varying proportions. In the human microbiome, high variability in consortial composition is largely compensated by similar metabolic functions across different taxa. However, the extent of compensation in lower diversity mouse models, and whether vivaria are metabolically equivalent, is unknown. We provide a searchable resource of microbiome composition variability across 51 murine vivaria and 12 wild mouse colonies worldwide, with vivarium-specific variants mapped according to predicted 3D structures for each microbial species. Our matched metabolomics data show that realized metabolic potential has relatively low variability, providing functional evidence for metabolic compensation. Additionally, variability is related to taxonomic composition rather than vivarium, revealing taxa-metabolite associations that are potentially relevant to phenotypic differences between vivaria. Collectively, this resource offers tools to strengthen microbiome studies and collaborative science.},
}
@article {pmid41187070,
year = {2025},
author = {De Vivo, G and Pelletier, E and Feuda, R and D'Aniello, S},
title = {An Ocean of Opsins.},
journal = {Genome biology and evolution},
volume = {17},
number = {11},
pages = {},
pmid = {41187070},
issn = {1759-6653},
support = {//Stazione Zoologica Anton Dohrn/ ; UF160226//Royal Society University Research Fellowship/ ; URF/R/221011//Royal Society University Research Fellowship/ ; RGF\R1\181012//Royal Society/ ; RGP009/2023//Human Frontier Science Program/ ; },
mesh = {*Opsins/genetics ; Animals ; Phylogeny ; *Evolution, Molecular ; Oceans and Seas ; Vertebrates/genetics ; },
abstract = {In this study, we explored the diversity and evolution of opsins using meta-omic data from the Tara Oceans and Tara Polar Circle expeditions, one of the largest marine datasets available. By using sequence similarity methods and phylogenetic analyses, we identified opsins across the different metazoan groups. Our results indicate that most of the opsin sequences belong to arthropods and vertebrates. We also detected sequences from all known opsin subfamilies, including r-opsin, c-opsin, xenopsin, and Group-4 opsins. Despite the broad taxonomic scope, no new opsin families were discovered; however, we provide valuable taxonomic insights into known opsin subfamilies and reinforce existing phylogenetic hypotheses. Additionally, we present novel opsin sequences from less-studied taxa, such as chaetognaths, rotifers, acoelomates, and tunicates, and which may serve as a valuable resource for future research into opsin function and diversity.},
}
@article {pmid41186403,
year = {2025},
author = {Lugli, GA and Argentini, C and Tarracchini, C and Longhi, G and Mancabelli, L and Bianchi, MG and Taurino, G and Amaretti, A and Candeliere, F and Bussolati, O and Milani, C and Turroni, F and Ventura, M},
title = {Host interactions of Lactococcus lactis and Streptococcus thermophilus support their adaptation to the human gut microbiota.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {12},
pages = {e0154725},
pmid = {41186403},
issn = {1098-5336},
support = {20229LEB99//Ministero della Ricerca e dell'Universit&#xe0;/ ; GR-2018-12365988//Italian Ministry of Health/ ; },
mesh = {*Streptococcus thermophilus/physiology/genetics/metabolism ; *Lactococcus lactis/physiology/genetics/metabolism ; Humans ; *Gastrointestinal Microbiome ; *Adaptation, Physiological ; *Host Microbial Interactions ; Adult ; Gastrointestinal Tract/microbiology ; },
abstract = {UNLABELLED: Within the human gut microbiota, lactic acid bacteria (LAB) play a crucial role in host health by producing lactic acid, which has been shown to shape microbial interactions and support intestinal homeostasis. However, despite their importance, there are limited insights regarding how LAB species interact with the host and other gut commensals. In this study, the investigation of the human gut microbiota of 10,000 healthy adults allowed the identification of Lactococcus lactis and Streptococcus thermophilus as commonly detected food bacteria. Further in silico analyses led to the identification of reference strains of the L. lactis and S. thermophilus species within the human gut, represented by PRL2024 and PRL2025 strains, respectively, which can represent nomadic bacteria. In vitro experiments revealed that both strains are ecologically adapted to survive and interact within the human gastrointestinal tract, while also highlighting their metabolic capacity to utilize a broad range of carbon sources. Specifically, the lactose metabolism was investigated, revealing that S. thermophilus PRL2025, despite high lactic acid output, incompletely metabolizes galactose, whereas L. lactis PRL2024 ensures full galactose utilization with lower acid production.<br><br>IMPORTANCE: The identification and functional characterization of Lactococcus lactis PRL2024 and Streptococcus thermophilus PRL2025 as human-adapted reference strains provide a valuable foundation for further in vivo experimentation. Given their ecological resilience, metabolic versatility, and interaction potential with beneficial gut microbes, these strains represent promising candidates as microbiota-targeted functional foods.},
}
@article {pmid41186205,
year = {2025},
author = {Li, Z and Zhang, X and Peng, L and Fang, Y and Liu, H and Zhou, Y and Wang, J and Lu, W},
title = {Response of Bovine Uterine Microbiota to Staphylococcus aureus Infection.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {94},
number = {5},
pages = {e70178},
doi = {10.1111/aji.70178},
pmid = {41186205},
issn = {1600-0897},
support = {U20A2053//National Natural Science Foundation of China/ ; 2024BBF01007//Key R&amp;D Program of Ningxia Hui Autonomous Region/ ; CARS-37//China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; Female ; Cattle ; *Staphylococcus aureus/physiology ; *Staphylococcal Infections/microbiology/immunology/veterinary ; *Microbiota ; *Uterus/microbiology/immunology ; *Endometritis/microbiology/immunology/veterinary ; *Cattle Diseases/microbiology/immunology ; },
abstract = {BACKGROUND: Endometritis is a highly prevalent reproductive disorder in cows, causing serious adverse effects on reproductive performance, which brings huge economic losses to the livestock industry. Staphylococcus aureus is detected in a high proportion of endometritis pathogens (alone or in combinations of infections). Uterine microbial composition plays an important role in endometritis.<br><br>OBJECT AND METHOD: In order to determine the role of S. aureus in endometritis, we established an endometritis model using this bacterium and utilized metagenomics to detect the structure and function of the bovine uterine microbiota.<br><br>RESULTS: We found that S. aureus infection significantly increased the relative abundance of bacteria such as Escherichia coli, Trueperella pyogenes, and Streptococcus spp., while reducing the relative abundance of Akkermansia and Prevotella bacteria. The functions of microorganisms in the uterus are mainly manifested in metabolic levels, including carbohydrate metabolism, amino acid metabolism, energy metabolism, and lipid metabolism processes. The number of genes continues to increase with the duration of S. aureus infection, which disrupts the balance that maintains the bovine uterine flora.<br><br>CONCLUSION: This study provides a descriptive analysis of changes in the uterine microbiota of cows infected with S. aureus, which contributes to a new understanding of uncultured or unidentified pathogenic bacteria.},
}
@article {pmid41185359,
year = {2025},
author = {Cao, R and Zhou, Q and Ma, Y and Yan, X and Li, A and Du, H and Xu, Y},
title = {Multimodal integration: Mechanisms of temperature dynamics and quality formation critical period in Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117622},
doi = {10.1016/j.foodres.2025.117622},
pmid = {41185359},
issn = {1873-7145},
mesh = {*Fermentation ; Machine Learning ; Metagenomics ; *Temperature ; Microbiota ; Hot Temperature ; Quality Control ; *Food Microbiology ; },
abstract = {The quality of medium-high temperature Daqu, the core starter for strong-aroma Baijiu, is regulated by the synergistic mechanisms of temperature, physicochemical properties, and microbial activity. In this study, we aimed to integrate dynamic monitoring of indicators, metagenomic analysis, and machine learning modeling to establish a multimodal approach. The systematic analysis of the differential contributions of spatiotemporal factors to Daqu fermentation temperature highlighted the dynamic changes in physicochemical and microbial processes during Daqu fermentation, as well as the critical period for quality control. The influence of temporal factors on Daqu temperature was significantly higher than that of spatial heterogeneity. Additionally, the temperature difference generated by the interaction of dual pathways between environmental changes and microbial metabolic heat production could regulate the Daqu fermentation through a heat-flow positive feedback mechanism. By combining temperatural and physicochemical data, machine learning models identified and validated the early fermentation stage (S2-S3) as the critical period for Daqu quality formation. Consequently, the quality control of Daqu can be effectively predicted and guided through monitoring the temperature in the early stage of fermentation. Metagenomic analysis revealed the two-phase characteristics of medium-high temperature Daqu fermentation: the core microbiota construction was completed in the S1-S3 stages, and the microbiota function then entered a stable period in the S4-S6 stages. This explains the dynamic change regularity of Daqu quality critical period formative from a microscopic perspective.},
}
@article {pmid41185305,
year = {2025},
author = {Ying, H and Yang, J and Yu, L and Wei, J and Sheng, Q and Yuan, Y and Yue, T},
title = {Metagenomics and GC-IMSanalyses reveal microbial community differences and flavor characteristics among three types of Feng flavor Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 4},
pages = {117551},
doi = {10.1016/j.foodres.2025.117551},
pmid = {41185305},
issn = {1873-7145},
mesh = {*Metagenomics/methods ; *Taste ; Fermentation ; *Microbiota ; Fungi/classification/genetics/metabolism ; *Alcoholic Beverages/microbiology/analysis ; China ; Bacteria/classification/genetics/metabolism ; *Food Microbiology ; Gas Chromatography-Mass Spectrometry ; Flavoring Agents ; },
abstract = {Feng flavor Baijiu is one of the four famous Baijiu in China, and its quality and flavor are closely related to the microbial flora. Daqu is a saccharifying agent and starter for the production of Feng flavor Baijiu. Different styles of Daqu (Hong-Xin Daqu, Huai-Rang Daqu, Qing-Cha Daqu) reflect different microbial community structures and functions. Understanding the relationship between the microbial characteristics of Daqu and flavor is challenging yet vital for improving Baijiu fermentation. This study used metagenomics combined with GC-IMS to systematically analyze the microbial characteristics and flavor features of three different styles of Feng flavor Daqu. The bacteria mainly include Bacillus, Lactococcus, Lactobacillus and Leuconostoc. Fungi mainly include Aspergillus, Rhizopus, Saccharomyces, Paecilomyces and Rasamsonia. Actinobacteria mainly included Saccharopolyspora and Streptomyces. The community structure and function of microorganisms in different styles of Daqu exhibited strong functional complementarity. The results indicated that the content of esters and alkenes in Qing-Cha Daqu was higher, mainly related to carbon metabolism and amino acid metabolism, and generated aromatic compounds through esterification reactions. While there were more aldehydes, ketones, and esters in Huai-Rang Daqu, mainly participating in enzymatic reactions and biosynthesis of cofactors, generating precursor substances for various aroma compounds. Moreover, the content of ethyl acetate and alkenes in Hong-Xin Daqu was higher, mainly participating in the glycolysis and tricarboxylic acid cycle, generating various alcohols and organic acids. This study revealed the complementary roles of the three styles of Daqu in Feng flavor Baijiu fermentation, providing valuable insights for product enhancement.},
}
@article {pmid41185061,
year = {2025},
author = {Mekuria, Z and Deblais, L and Ojeda, A and Mummed, B and Singh, N and Gebreyes, W and Havelaar, AH and Rajashekara, G and , },
title = {Host clustering of Campylobacter species and enteric pathogens in a longitudinal cohort of infants, family members and livestock in rural Eastern Ethiopia.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {225},
pmid = {41185061},
issn = {2049-2618},
support = {UL1 TR001427/TR/NCATS NIH HHS/United States ; OPP11755487//Bill and Melinda Gates Foundation/ ; },
mesh = {Animals ; Humans ; *Campylobacter/classification/genetics/isolation &amp; purification ; Infant ; *Campylobacter Infections/microbiology/epidemiology/veterinary ; Ethiopia/epidemiology ; *Livestock/microbiology ; Rural Population ; Longitudinal Studies ; Female ; Male ; Chickens/microbiology ; Feces/microbiology ; Metagenomics/methods ; Gastrointestinal Microbiome ; Adult ; Cluster Analysis ; Family ; Child, Preschool ; },
abstract = {BACKGROUND: Livestock are recognized as major reservoirs for Campylobacter species and other enteric pathogens, posing infection risks to humans. High prevalence of Campylobacter during early childhood has been linked to environmental enteric dysfunction and stunting, particularly in low-resource settings.<br><br>METHODS: A total of 280 samples from Campylobacter positive households with complete metadata were analyzed by shotgun metagenomic sequencing followed by bioinformatic analysis via the CZ-ID metagenomic pipeline (Illumina mNGS Pipeline v7.1). Further statistical analyses in JMP PRO 16 explored the microbiome, emphasizing Campylobacter and other enteric pathogens. Two-way hierarchical clustering and split k-mer analysis examined host structuring, patterns of co-infections and genetic relationships. Principal component analysis was used to characterize microbiome composition across the seven sample types.<br><br>RESULTS: The study identified that microbiome composition was strongly host-driven, with more than 3844 genera detected, and two principal components explaining 62% of the total variation. Twenty-one dominant (based on relative abundance) Campylobacter species showed distinct clustering patterns for humans, ruminants, and broad hosts. The broad-host cluster included the most prevalent species, C. jejuni, C. concisus, and C. coli, present across sample types&#xa0;and a sub-cluster within C. jejuni involving humans, chickens, and ruminants. Campylobacter species from chickens showed strong positive correlations with mothers (r&#x2009;=&#x2009;0.76), siblings (r&#x2009;=&#x2009;0.61) and infants (r&#x2009;=&#x2009;0.54), while co-occurrence analysis found a higher likelihood (Pr&#x2009;>&#x2009;0.5) of pairs such as C. jejuni with C. coli, C. concisus, and C. showae. Analysis of the top 50 most abundant microbial taxa showed a distinct cluster uniquely present in human stool and absent in all livestock. The study also found frequent co-occurrence of C. jejuni with other enteric pathogens such as Salmonella, and Shigella, particularly in human and chicken. Additionally, instances of Candidatus Campylobacter infans (C. infans) were identified co-occurring with Salmonella and Shigella species in stool samples from infants, mothers, and siblings.<br><br>CONCLUSIONS: A comprehensive analysis of Campylobacter diversity in humans and livestock in a low-resource setting revealed that infants can be exposed to multiple Campylobacter species early in life. C. jejuni is the dominant species with a propensity for co-occurrence with other notable enteric bacterial pathogens, including Salmonella, and Shigella, especially among infants. Video Abstract.},
}
@article {pmid41183495,
year = {2025},
author = {Hu, CY and Dai, CY and Anh, PNT and Tsai, HY and Chen, YC},
title = {Tetragenococcus halophilus A003 altered microbiota and repressed the accumulation of biogenic amines in the fermentation of fish sauce.},
journal = {Letters in applied microbiology},
volume = {78},
number = {11},
pages = {},
doi = {10.1093/lambio/ovaf128},
pmid = {41183495},
issn = {1472-765X},
support = {112-2313-B-020-017-MY3//National Science and Technology Council of Taiwan/ ; NPUST-KMU-111-P009//National Pingtung University of Science and Technology/ ; },
mesh = {*Biogenic Amines/metabolism/analysis ; Fermentation ; *Enterococcaceae/metabolism/isolation &amp; purification/genetics/classification ; *Fish Products/microbiology/analysis ; *Microbiota ; Animals ; *Fermented Foods/microbiology ; Food Microbiology ; Fishes ; Cadaverine/analysis/metabolism ; },
abstract = {Fish sauce, a seasoning commonly utilized in East Asian cuisine, is produced from fish combined with a substantial quantity of salt. However, biogenic amines (BAs) accumulation poses safety concerns in fermented fish sauce during fermentation. This study characterized Tetragenococcus halophilus A003, isolated from fish sauce, which exhibited the weakest decarboxylase gene activation and lowest BA production among the tested strains. Starter inoculation with A003 yielded minimal chemical alteration compared to natural fermentation. Cadaverine levels were substantially lower (19.1 ± 1.49 mg/l) than those in sauce fermented without a starter or with T. halophilus BCRC12250. Histamine and tyramine were undetectable in isolate A003-inoculated samples. Metagenomic analysis revealed an enrichment of low BA-producing taxa, notably Tetragenococcus and Staphylococcus, comprising 97.91% of the community. These findings suggest T. halophilus A003 confers a selective advantage for low BA microbiota during fish sauce fermentation.},
}
@article {pmid41183487,
year = {2025},
author = {Xu, Q and He, N and Tian, Y and Wu, Z and Wang, H and Liu, B and Yang, Z and Zhang, H and Luo, Q and Zhong, Y and Xiao, L and Li, S and Zou, Y},
title = {Lactobacillus gasseri TF08-1 ameliorates high-fat diet induced nonalcoholic fatty liver disease and regulates gut microbiota in mice.},
journal = {Journal of applied microbiology},
volume = {136},
number = {12},
pages = {},
doi = {10.1093/jambio/lxaf271},
pmid = {41183487},
issn = {1365-2672},
support = {32100009//National Natural Science Foundation of China/ ; KCXFZ20240903094006009//Shenzhen Municipal Government of China/ ; JCYJ20241202124801003//Shenzhen Municipal Government of China/ ; },
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/therapy/microbiology/etiology ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Mice ; *Probiotics/administration &amp; dosage ; *Lactobacillus gasseri/genetics/physiology ; Male ; Lipid Metabolism/genetics ; Mice, Inbred C57BL ; Liver/metabolism ; Triglycerides/blood ; Genome, Bacterial ; },
abstract = {AIMS: This study aimed to investigate the therapeutic potential of Lactobacillus gasseri TF08-1, a gut bacterium isolated from healthy adolescents, in alleviating high-fat diet (HFD)-induced nonalcoholic fatty liver disease (NAFLD). This followed our discovery of lipid metabolism-related genes in its complete genome.<br><br>METHODS AND RESULTS: The high-precision complete genome map of L. gasseri TF08-1 was constructed for the first time, revealing enriched lipid metabolism pathways, including bile salt hydrolase activity and short-chain fatty acid (SCFA) production. After supplementing L. gasseri TF08-1 for 8 weeks in mice fed with a high-fat diet, the serum triglyceride (TG) level decreased by 41.95%, the hepatic total cholesterol (TC) level decreased by 35.09%, and the TNF-&#x3b1; level decreased by 42.91%. Meanwhile, the NAS score decreased by 3.66 points. The treatment significantly reduced hepatic lipid accumulation, lowered proinflammatory cytokines, and improved steatosis scores. Metagenomic analyses showed L. gasseri TF08-1 restored gut microbiota balance, significantly increasing the abundance of beneficial bacteria such as Faecalibacterium prausnitzii and Phocaeicola vulgatus, while also enriching fatty acid degradation pathways.<br><br>CONCLUSIONS: Lactobacillu gasseri TF08-1 demonstrates probiotic efficacy against NAFLD through dual mechanisms: direct metabolic modulation and gut microbiota restoration. The lipid metabolism capacity encoded by its genome likely contributes to therapeutic effects.},
}
@article {pmid41183305,
year = {2025},
author = {Yang, R and Ma, J and Abebe, H and Tu, Y},
title = {Divergent Responses of Soil Microbiome Structure and Function to Salinity and Depth Gradients.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {45},
pages = {28711-28723},
doi = {10.1021/acs.jafc.5c08498},
pmid = {41183305},
issn = {1520-5118},
mesh = {*Soil Microbiology ; *Soil/chemistry ; Salinity ; *Microbiota ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacterial Proteins/genetics/metabolism ; Sodium Chloride/analysis/metabolism ; Sodium/analysis/metabolism ; },
abstract = {Soil salinization profoundly threatens agricultural ecosystems by disrupting soil microbial communities and functions, yet the interplay of salinity and depth on microbiome structure and function is unclear. In the present experiment, soils from two depths (0-20 and 20-40 cm) across a low (LS), medium (MS), and high (HS) salinity gradient were collected. The results indicated that the soil electrical conductivity, available sodium, and available potassium were significantly elevated in HS soil. 16S rRNA gene sequencing identified three key microorganisms associated with soil salinity, including Sphingomonas, Bradyrhizobium, and Chloracidobacterium. Metagenomic analysis indicated that the abundances of carbon and nitrogen cycle genes such as amyA, xylA, nifH, nirK, narG and amoA were significantly upregulated in LS soils. In conclusion, the experiment systematically elucidated the intricate restructuring of soil microbiome responses across distinct salinity gradients and depths, providing new theoretical support for the remediation of soil salinization.},
}
@article {pmid41183096,
year = {2025},
author = {Lv, JX and Pei, YY and Yang, C and Liu, X and Ju, MJ and Holmes, EC and Chen, YM and Zhu, TY and Zhang, YZ},
title = {Extensive diversity of unusual microorganisms associated with severe pneumonia in kidney transplant recipients.},
journal = {PLoS pathogens},
volume = {21},
number = {11},
pages = {e1013667},
pmid = {41183096},
issn = {1553-7374},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; Male ; Female ; Middle Aged ; Adult ; Transplant Recipients ; Bronchoalveolar Lavage Fluid/microbiology/virology ; *Pneumonia/microbiology/virology/immunology ; Immunocompromised Host ; Aged ; Bacteria/isolation &amp; purification/genetics ; Microbiota ; Coinfection/microbiology ; Lung/microbiology/virology ; },
abstract = {Although pneumonia is a common lung disease with a high morbidity and mortality, aside from well-known pathogens little is known about why, which and how many microorganisms are associated with the disease, particularly in immunocompromised individuals. We enrolled 32 kidney transplant cases with severe pneumonia admitted to Shanghai Zhongshan Hospital between 2019 and 2025, and performed both metagenomic and metatranscriptomic sequencing on the bronchoalveolar lavage fluid (BALF) and blood samples from each case. Comprehensive analyses of immune cells and cytokines, as well as BALF and blood metatranscriptomes, revealed that both adaptive and innate immunity inside and outside of their lungs were severely suppressed. Notably, a high diversity of unusual microorganisms were present in BALF samples, including bacteria and DNA viruses that are rare or absent in healthy individuals, as well as RNA viruses and fungi. Of these, 17 bacteria, 46 DNA viruses, eight RNA viruses and two fungi, which were at high abundance, were considered to be responsible for the lung infections. Remarkably, the majority of these patients experienced co-infections of multiple bacteria, DNA and RNA viruses and fungi, reaching 32 virus species in one individual. In sum, these data indicate that the prosperity or overgrowth of accidental, opportunistic and rare microorganisms within the lungs of these kidney transplant patients substantially altered their lung microbiota, with multiple co-infections further exacerbating the severity of pneumonia.},
}
@article {pmid41182689,
year = {2025},
author = {de Kroon, RR and van Wesemael, AJ and van Kaam, AH and Savelkoul, PHM and Boon, M and Budding, AE and Niemarkt, HJ and de Meij, TGJ},
title = {A Novel Untargeted Molecular Detection Technique for Rapid Fecal Microbiota Profiling in Very Preterm Infants: Optimization, Genus-Level Comparison, and Application.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {21},
pages = {e71207},
pmid = {41182689},
issn = {1530-6860},
mesh = {Humans ; *Feces/microbiology ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Intensive Care Units, Neonatal ; *Bacteria/genetics/classification ; },
abstract = {Gut microbiota profiling shows potential for improving care in the neonatal intensive care unit (NICU). However, common techniques, including 16S rRNA gene and metagenomic sequencing, have limited bedside applicability. The IS-pro microbiota assay provides species-level abundances within 5 h. We aimed to optimize the taxa annotation for preterm infants (phase 1), compare its findings to 16S sequencing on the genus level (phase 2), and apply the assay in a preterm cohort (phase 3). 1445 fecal samples from 479 preterm infants (24-30 weeks gestation) across 10 NICUs were analyzed with IS-pro. For phase 1 (optimization), IS-pro amplicons of 32 fecal samples were additionally analyzed with nanopore sequencing to expand the IS-pro matching database. For phase 2 (comparison), 41 samples were compared to 16S sequencing. In phase 3 (application), the optimized IS-pro assay was applied to the total cohort. Following phase 1, a mean relative abundance of 82.5% was successfully annotated. In phase 2, IS-pro showed high concordance with 16S sequencing, with a strong positive correlation between the two techniques (Pearson's correlation coefficient: 0.77, SD 0.24). In phase 3, IS-pro analysis of the full cohort revealed Staphylococcus, Klebsiella, Enterococcus, Escherichia-Shigella, and Streptococcus as the predominant genera in the first 4 weeks of life. Our findings demonstrate that the IS-pro microbiota assay effectively detects and quantifies key bacterial taxa in fecal samples of preterm infants, with outcomes highly concordant with 16S sequencing. Unlike traditional techniques, IS-pro is a rapid tool, illustrating its potential for clinical practice. Future studies should explore its applications in the NICU.},
}
@article {pmid41182235,
year = {2025},
author = {Bisschop, K and Goel, N and Coone, M and Vanoverberghe, I and Greffe, A and Asselman, J and Decaestecker, E},
title = {Host-microbiota matching and epigenetic modulation drive Daphnia magna responses to cyanobacterial stress.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {41182235},
issn = {1751-7370},
support = {12T5622N//FWO/ ; G092619N//FWO/ ; },
mesh = {*Daphnia/microbiology/genetics/physiology ; Animals ; *Epigenesis, Genetic ; *Cyanobacteria/physiology ; DNA Methylation ; *Host Microbial Interactions ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Stress, Physiological ; Daphnia magna ; },
abstract = {Microbial communities are crucial in host adaptation to stressors, particularly in dynamic ecosystems. In aquatic environments, Daphnia magna is ideal for studying host-microbiome interactions due to its ecological importance and sensitivity. Adaptation to toxins, such as those produced by cyanobacteria, may involve both host and microbial gene repertoires. Yet, the influence of microbiota composition and function on host performance remains poorly understood. Because epigenetic mechanisms such as DNA methylation regulate gene expression and mediate adaptive responses, we also investigated whether these associations are reflected in DNA methylation levels. To address this, we conducted a fully factorial transplant experiment using microbiota-depleted Daphnia colonised with microbiota from the same or different genotype, previously exposed to toxic or nontoxic diets, or left uncolonised. We assessed life-history traits, microbial composition (16S rRNA genes), functional profiles (whole-genome-resequencing), and DNA methylation (colorimetric quantification). Daphnia fed nontoxic diets grew larger and reproduced more. Increased methylation occurred when microbiota donors differed from the host genotype and was strongest under toxic diet. Dysbiosis and reduced performance were noted in individuals colonised with toxic-diet microbiota from another genotype, where Limnohabitans spp. was reduced or absent. Signs of hormesis emerged when Daphnia received microbiota from their own genotype reared on nontoxic diets. DNA methylation of both host and microbiota was associated with functional pathways, including increased mitochondrial fatty acid biosynthesis. These findings highlight the importance of host-microbiota matching and microbial environmental history in shaping host performance and epigenetic responses, emphasizing the need to consider host-microbe-environment interactions in evolutionary and ecological studies.},
}
@article {pmid41181328,
year = {2025},
author = {Jo, JW and Kim, SK and Byun, JY and Hong, SM and Kim, BS},
title = {The association between the adenoid microbiome and chronic otitis media with effusion in children differs according to age.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1660939},
pmid = {41181328},
issn = {2235-2988},
mesh = {Humans ; *Otitis Media with Effusion/microbiology ; Child ; *Adenoids/microbiology ; Male ; Female ; Child, Preschool ; Age Factors ; Chronic Disease ; *Microbiota ; Feces/microbiology ; Streptococcus pneumoniae/isolation &amp; purification ; Haemophilus influenzae/isolation &amp; purification ; Gastrointestinal Microbiome ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Infant ; },
abstract = {INTRODUCTION: Chronic otitis media with effusion (COME) can adversely affect childhood development, and while the adenoid has been considered a reservoir for bacterial pathogens contributing to the pathogenesis of COME, the role of the adenoid microbiome in COME remains unclear. This study analyzed both the adenoid and gut microbiome in children with and without COME to identify their potential roles in the disease's pathogenesis.<br><br>METHODS: Adenoid samples were collected during surgery for adenoid microbiome analysis, while fecal samples were collected for gut microbiome analysis. Microbiome was analyzed using whole metagenome sequencing and subsequent bioinformatic analysis.<br><br>RESULTS: A significant association between the adenoid microbiome and COME was detected, while no such association observed for the gut microbiome. The adenoid microbiome varied by age in the control group, but this age-dependent variation was perturbed in the COME group. Notably, in children aged 6-12 years, the adenoid microbiome was significantly associated with COME based on the type of middle ear fluid, where Streptococcus pneumoniae and Haemophilus influenzae were prominent indicators in the mucoid form of COME. The proliferation of these species in mucoid COME group was correlated with indicators for the serous COME group. The altered microbiome in COME patients may influence immune responses through the synthesis of spermidine and acetate, contributing to disease development.<br><br>DISCUSSION: This study highlights the age-dependent contribution of the adenoid microbiome-particularly in children aged 6 to 12 years-to the pathogenesis of COME.},
}
@article {pmid41181319,
year = {2025},
author = {Wang, Z and Song, L and Li, D and Jin, Y},
title = {From commensalism to pathogenesis: the hidden role of the respiratory virome.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1693796},
pmid = {41181319},
issn = {2235-2988},
mesh = {Humans ; *Virome ; *Microbiota ; *Symbiosis ; *Respiratory System/virology/microbiology ; Bacteriophages ; *Viruses/classification/genetics ; Animals ; Metagenomics ; Host-Pathogen Interactions ; Respiratory Tract Infections/virology ; },
abstract = {The respiratory virome, encompassing both eukaryotic viruses and bacteriophages, is an essential but often overlooked component of the airway microbiome. Recent advances in metagenomics have revealed that a diverse viral community exists even in healthy individuals, contributing to immune regulation and microbial balance. However, the field faces several challenges: the baseline composition of the respiratory virome remains incompletely defined, its immunomodulatory functions are not fully understood, and its contributions to respiratory diseases are only beginning to be elucidated. This mini-review summarizes current knowledge of the respiratory virome under physiological conditions, highlights emerging insights into how resident viruses and phages shape host immunity, and discusses alterations observed in asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and pneumonia. By integrating evidence across these conditions, we emphasize the significance of the virome in both health and disease. A deeper understanding of its dynamics may yield novel diagnostic markers and therapeutic strategies, underscoring the importance of future longitudinal and mechanistic studies in this rapidly evolving field.},
}
@article {pmid41177609,
year = {2026},
author = {Lu, N and Du, Z and Feng, G and Xin, X and Che, M and Jia, R and Chu, W},
title = {Metagenomic investigations of microbial community response and antibiotic resistance genes in river sediments polluted by perfluoroalkyl acids.},
journal = {Journal of environmental sciences (China)},
volume = {160},
number = {},
pages = {300-307},
doi = {10.1016/j.jes.2025.04.024},
pmid = {41177609},
issn = {1001-0742},
mesh = {*Fluorocarbons/analysis/toxicity ; *Water Pollutants, Chemical/analysis/toxicity ; *Geologic Sediments/microbiology/chemistry ; Rivers/microbiology/chemistry ; *Drug Resistance, Microbial/genetics ; China ; *Environmental Monitoring ; Metagenomics ; *Microbiota/drug effects ; Caprylates/toxicity ; },
abstract = {Liquid-solid phase transfer promotes the interaction of perfluoroalkyl acids (PFAAs) with the microbial system of river sediments, which may affect the environmental behavior of antibiotic resistance genes (ARGs) contained in benthic environments. Sediments collected from the receiving water of the largest fluoropolymer production facility in China were analyzed to investigate the impact of PFAAs on microbial communities and ARG profiles. The main contributors to the PFAAs were perfluorooctanoic acid and perfluorobutanoic acid, whose proportions (86.9 %-93.4 %) in the downstream surface sediments affected by industrial effluents were significantly higher than in the corresponding upstream samples (53.3 %). A reduction in microbial diversity and richness was observed in the presence of high concentrations of PFAAs at the downstream sites. 144 ARG subtypes, including three high-risk subtypes (bacA, aac (6')-I and aadA), were identified in sediment samples. The discharge of fluorochemical effluents also results in a reduction of ARG diversity at subtype level. PFAAs exert a pronounced influence on the profile of ARGs in sediment. PFAAs and water quality parameters (e.g. pH and total phosphorus) were key drivers of the microbial community composition in the sediment. The regulation of microbial communities by PFAAs may represent an important pathway by which these compounds affect ARG profiles.},
}
@article {pmid41177025,
year = {2025},
author = {Singh, DP and Bijalwan, V and Poonam, J and Lal, R and Palkhade, R and Viramgami, A and Vidhani, H and Kumar, A and Bishnoi, M and Das, S},
title = {Bisphenol-A at an environmentally plausible dose caused gut microbiota-led impaired cognitive performances in adult mice.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140254},
doi = {10.1016/j.jhazmat.2025.140254},
pmid = {41177025},
issn = {1873-3336},
mesh = {Animals ; *Benzhydryl Compounds/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Phenols/toxicity ; Mice ; Male ; *Cognition/drug effects ; Brain/drug effects/metabolism ; Maze Learning/drug effects ; *Cognitive Dysfunction/chemically induced ; Behavior, Animal/drug effects ; Dysbiosis ; Bisphenol A Compounds ; },
abstract = {Omnipresent Bisphenol-A (BPA) exposure is linked to neurobehavioral deficits and gut dysbiosis. However, studies assessed its impact on cognitive performance at environmentally unrealistic doses. Nevertheless, the exact mechanism underlying the neurobehavioral phenotype, linking the role of gut microbiota is poorly understood. Here, we evaluated the effects of environmentally plausible dose of BPA-exposure on cognitive task performances with the functional analysis of gut metagenome to elucidate the role of microflora-gut-brain axis in behavioural regulation. Swiss albino mice were exposed to BPA for 5 weeks assessed for working and spatial navigation task performances. qRT-PCR based gene expression, histological investigation, gut permeability, molecular and biochemical markers of neuro-inflammation, leaky gut, oxido-nitrosative stress and 16 s rRNA gene based metagenomics with functional analysis were performed. BPA exposure altered the cognitive task performances (mean difference for transfer latency in elevated plus maze 20.84 ± 5.64 sec in and -13.12 ± 3.53 in Morris' water maze), changed serotonin levels (-70.95 ± 21.43) and acetylcholinesterase activity (0.0032 ± 0.0008), enhanced ileal permeability (12.36 ± 3.56) and systemic and tissue level inflammation (increased brain LPS, TNF-a, IL-1b, IL-6 and circulating TNF-a and IL-1b), coupled with reduced SCFAs levels (acetate; 32.48 ± 8.48, and butyrate; 28.16 ± 9.86). Faecal microbial transplant cohort replicated similar behavioural, biochemical and molecular patterns, suggesting the role of gut-microbiota in the phenotype determination. Functional pathways prediction suggested altered serotonin, dopamine, SCFAs metabolism and LPS biosynthesis. BPA at a much lower but environmentally relevant dose altered the cognitive performances, which has potential linkage to gut-microbiota mediated pathways.},
}
@article {pmid41176044,
year = {2025},
author = {Sodré, IC and Prist, PR and Mancini, MCS and Bettoni-Rodríguez, G and de Andreazzi, CS and Tambosi, LR and Dos Santos, AFA and D'arc, M and Bueno, MG},
title = {Forest cover influences the fecal virome of Oligoryzomys nigripes in Atlantic Forest remnants, Brazil.},
journal = {Acta tropica},
volume = {272},
number = {},
pages = {107894},
doi = {10.1016/j.actatropica.2025.107894},
pmid = {41176044},
issn = {1873-6254},
mesh = {Animals ; Brazil ; *Feces/virology ; *Forests ; *Virome ; *Viruses/classification/genetics/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; *Sigmodontinae/virology ; Zoonoses/virology ; },
abstract = {Landscape changes driven by human activities can alter host-pathogen interactions, favoring generalist mammal species that act as reservoirs for zoonotic pathogens, potentially leading to spillover events and outbreaks. Here, we investigated how forest cover influences viral diversity in Oligoryzomys nigripes, a generalist rodent known to harbor zoonotic viruses in the Brazilian Atlantic Forest. We employed high-throughput sequencing to explore the fecal virome of 20 specimens collected across three landscapes with varying forest cover (20 %, 40 %, and 60 %) within Atlantic Forest fragments in São Paulo state. We identified 48 viral families, predominantly bacteriophages and vertebrate-associated viruses. Some, found for the first time in this host, exhibited zoonotic potential, including Papillomaviridae, Herpesviridae, Polyomaviridae, Adenoviridae, Alloherpesviridae, Arenaviridae, Paramyxoviridae, Peribunyaviridae, and Picornaviridae. Alpha and beta diversity indices were used to assess the viral community structure. Although alpha diversity indices did not show a statistically significant difference among landscapes, a significant compositional difference in viral community was detected through beta diversity index (Jaccard dissimilarity), indicating that forest cover may shape the composition of viral families present. The presence of a core virome shared across all landscapes, including families with pathogenic potential, reinforces O. nigripes role as a natural reservoir. While forest cover influences viral community structure, it doesn't necessarily reflect greater ecological complexity within fragments, indicating that other landscape-related factors must also be considered. This pioneering study characterizes the fecal virome of O. nigripes, revealing how forest cover may shape viral communities in wild rodents and underscoring their potential for zoonotic virus surveillance.},
}
@article {pmid41175763,
year = {2025},
author = {Lv, Z and Liu, Z and Li, D and Cai, M and Liu, J and Zhang, XH and Shi, X},
title = {Anthropogenic PAHs reshape sedimentary microbiomes and ecotoxicological risks in polar regions: A pan-Arctic/Antarctic metagenomic study.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140321},
doi = {10.1016/j.jhazmat.2025.140321},
pmid = {41175763},
issn = {1873-3336},
mesh = {*Polycyclic Aromatic Hydrocarbons/analysis/toxicity ; *Microbiota/drug effects ; *Geologic Sediments/microbiology/chemistry ; Metagenomics ; Antarctic Regions ; Arctic Regions ; Bacteria/genetics ; Environmental Monitoring ; *Water Pollutants, Chemical/analysis/toxicity ; Ecotoxicology ; Biodegradation, Environmental ; },
abstract = {The analysis of the composition and functional gene responses of sedimentary microbial communities to polycyclic aromatic hydrocarbons (PAHs) is essential for evaluating the pollution status of PAHs in polar regions. PAH concentrations and microbiome characteristics are quantified using advanced instrumental detection combined with metagenomic analysis. Overall, PAHs exhibit relatively high levels of contamination in polar regions, whereas variations in the abundance of functional genes indicate potential degradation propensities among different sedimentary microbial communities. The PAHs in the study area are primarily attributed to fossil fuel combustion, with local anthropogenic emissions considered the main drivers of contaminant accumulation. Sedimentary bacterial communities and their functions are significantly influenced by PAH contamination. Correlation analysis identifies 4H-Naphthalene, Naphthalene, 1-Indanone, Anthracene, Benzo[c]phenanthrene and 1,4-Naphthoquinone as the most critical compounds affecting microbial communities. The co-occurrence of PAH degradation genes with nitrogen- and sulfur-cycling genes in several MAGs suggests that PAH biodegradation may be enhanced through the utilization of nitrate and sulfate as electron acceptors. Within a pan-Arctic and Antarctic framework, the responses of sedimentary microbiomes to PAH contamination are examined, providing novel insights into the comprehensive evaluation of PAH pollution levels and associated ecological risks in polar regions.},
}
@article {pmid41175752,
year = {2025},
author = {Ding, W and Chen, B and Song, M and Liu, M and Lv, B and Qiu, D and Zhu, Y and Zhang, Z and Zhang, M and Zhang, R and Lu, T and Qian, H},
title = {Different effects of heterocyclic compounds on the diversity and functions of soil microbiota.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140318},
doi = {10.1016/j.jhazmat.2025.140318},
pmid = {41175752},
issn = {1873-3336},
mesh = {*Soil Microbiology ; *Microbiota/drug effects ; *Heterocyclic Compounds/toxicity ; *Soil Pollutants/toxicity ; Drug Resistance, Microbial/genetics ; Bacteria/drug effects/genetics ; Virulence Factors/genetics ; },
abstract = {Heterocyclic compounds are extensively used in pharmaceuticals and agrochemicals, yet their persistence and bioavailability in soil may disrupt microbial functions and ecosystem health. To address these impacts, we performed a metagenomic sequencing to assess the impact of three such compounds--cefapirin, pyrimethanil, and quinclorac on soil microbial communities at 15 and 30 d exposure. Our results revealed distinct compound-specific and time-dependent effects. Cefapirin initially induced minimal changes at 15 days but significantly reduced eukaryotic diversity and functional potential by 30 days, while also enriching virulence factors. Pyrimethanil strongly perturbed the community at 15 days, suppressing metabolic pathways and elevating the abundance of antibiotic resistance genes (ARGs) and virulence factors, along with consistently enriching mobile genetic elements (MGEs) associated with these genes-though some effects diminished by 30 days. Quinclorac exerted comparatively milder inducing subtle shifts in virulence factor profiles and exerting limited influence on antibiotic resistance gene abundance. Spearman correlation analysis linked compound-induced shifts in dominant microbial phyla (notably Pseudomonadota and Actinomycetota) to the dynamics of ARGs and virulence factors. These results underscore that the ecological risks of heterocyclic compounds depend critically on both compound properties and exposure duration. Our findings provide valuable insights for guiding risk assessment and sustainable practices to mitigate the ecological risks of agrochemicals.},
}
@article {pmid41175696,
year = {2026},
author = {Li, N and Zhang, Y and Qu, Z and Xu, J and Ming, A and Sun, H and Huang, L},
title = {Rhizosphere resilience: Exploring microbial diversity and metabolic responses in long-term eucalyptus plantations.},
journal = {Microbiological research},
volume = {303},
number = {},
pages = {128381},
doi = {10.1016/j.micres.2025.128381},
pmid = {41175696},
issn = {1618-0623},
mesh = {*Eucalyptus/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Biodiversity ; Soil/chemistry ; Phosphorus/metabolism ; Metabolomics ; Microbiota ; Metagenomics ; Nitrogen/metabolism ; Nitrogen Fixation ; },
abstract = {The large-scale cultivation of eucalyptus has led to significant ecological challenges, such as declines in soil microbial diversity and soil degradation. To address these issues, management practices incorporating nitrogen-fixing species and adjusted rotation periods have been proposed. However, their impacts on rhizosphere soil microorganisms and metabolites remain insufficiently understood. This study employed metagenomic and untargeted metabolomics techniques to investigate the response of rhizosphere microorganisms and metabolites in eucalyptus plantations under different management regimes: monoculture plantation, plantation mixed with a nitrogen-fixing tree species, monoculture second-generation plantation, and second-generation mixed plantation. The results revealed that mixed plantation increased microbial diversity compared to continuous cropping. In contrast, second-generation monoculture led to a loss of unique microbial species and reduced microbial community stability compared to the first-generation monoculture. In nutrient-poor pure second-generation plantations, the bacterium Gemmatimonadetes (relative abundance: PF: 0.13 %, PS: 0.39 %, MF: 0.14 %, MS: 0.21 %)-which plays a key role in soil phosphorus cycle-was enriched. Although continuous cropping improved the organic phosphorus mineralization function, it decreased the abundance of genes related to carbon (rbcL and ppc) and phosphorus cycle (phoP and ppk2). The metabolite fluocinolone is negatively correlated with carbon, nitrogen and phosphorus cycle gene components in our dataset, while echinocystic acid and bezitramide are positively correlated. These findings highlight that mixed plantations enhance the ecological niche of eucalyptus rhizosphere by altering the interaction between rhizosphere microbial composition, function, and host plant metabolism.},
}
@article {pmid41175632,
year = {2026},
author = {Patel, AB and Jain, KR and Gupta, V and Lal, R and Madamwar, D},
title = {Structural and functional responses of microbial communities in coastal sediments towards anthropogenic pollution caused by ship breaking activities.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107665},
doi = {10.1016/j.marenvres.2025.107665},
pmid = {41175632},
issn = {1879-0291},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Microbiota ; *Ships ; *Water Pollutants, Chemical/analysis ; *Environmental Monitoring ; Bacteria/classification ; India ; Metals, Heavy/analysis ; Metagenome ; Biodiversity ; },
abstract = {Coastal ecosystems, like many others on the planet, face chronic threats from anthropogenic activities. The Alang-Sosiya Ship Breaking Yard (ASSBY) located near Bhavnagar in Gujarat, India, represents one such ecosystem impacted by decades of ship-breaking activities. This study aimed to assess the differences in microbial community composition between polluted coastal samples and pristine samples through high-throughput sequencing. Additionally, microbial co-occurrence networks and genes related to antibiotic and heavy metal resistance were predicted using metagenome mining. The analysis confirmed elevated heavy metal concentrations, particularly iron, in polluted samples. In non-polluted sites, alpha diversity indices showed a high microbial diversity compared to polluted sites. The bacterial communities from Deltaproteobacteria at non-polluted sites noticeably shifted to Gammaproteobacteria at polluted sites. Unclassified reads constituted a significant portion of the bacterial diversity. LEfSe (Linear discriminant analysis Effect Size) analysis identified potential bacterial biomarkers, including Pseudomonas, Halomonas and Rhodovulum, which were differentially abundant at polluted sites and may play roles in the biodegradation of xenobiotic compounds. Moreover, Co-occurrence network analysis validated these bacterial biomarkers from polluted sites and revealed their habitat-specific nature. Polluted metagenomes were enriched with genes related to aromatic compound degradation and stress responses, particularly genes for heavy metal and antibiotic resistance. These findings suggest that chronic pollution from ship-breaking activities has led to a shift in microbial communities, leading to an increased presence of resistance mechanisms in the polluted coastal environment to adapt to prolonged heavy pollution.},
}
@article {pmid41175161,
year = {2025},
author = {Demin, KA and Kulikova, DB and Kulikov, MP and Mazanko, MS and Prazdnova, EV},
title = {Gellan gum-based media recover more diverse microbial communities from soil material.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {338},
pmid = {41175161},
issn = {1432-072X},
support = {Strategic Academic Leadership Program "Priority 2030"//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Polysaccharides, Bacterial/chemistry ; *Soil Microbiology ; *Culture Media/chemistry ; *Bacteria/isolation &amp; purification/classification/genetics/growth &amp; development ; *Microbiota ; },
abstract = {Soil microbial communities contain a huge proportion of microorganisms that cannot be cultured using standard microbiological media and are accessible only through molecular methods. These uncultivable microbes may include producers of biologically active compounds valuable for medicine, biotechnology, and agriculture. Development of approaches for cultivation of such groups is of paramount importance. Here we successfully replicate and confirm the accumulated observations on the fact that replacing agar with gellan gum as gelling agent and using nutrient-poor media leads to the more frequent recovery and enrichment of rare and hard-to-culture microbial phyla representatives. We also show that altering the gas mixture in the incubation chamber may promotes the isolation of specific microbial groups. Replacing agar with gellan gum is suggested as a strategy to recover new microbial species.},
}
@article {pmid41174950,
year = {2025},
author = {Vega-Abellaneda, S and Román, E and Soler, Z and Ortiz, M&#xc0; and Rossi, G and Biagini, L and Sánchez, E and Pons-Tarin, M and Laghi, L and Mengucci, C and Kaur, N and Poca, M and Cuyàs, B and Serrano-Gomez, G and Alvarado, E and Manichanh, C and Soriano, G},
title = {A Metagenomics Approach to Frailty in Patients With Cirrhosis Undergoing a Multifactorial Intervention.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {45},
number = {12},
pages = {e70418},
pmid = {41174950},
issn = {1478-3231},
support = {PI19/00275//Instituto de Salud Carlos III/ ; PR-455/2020//Col.legi Oficial d'Infermeres i Infermers de Barcelona/ ; //MENDES SA/ ; //Infisport/ ; },
mesh = {Humans ; *Liver Cirrhosis/complications/therapy/microbiology ; *Frailty/therapy/microbiology ; Male ; Metagenomics ; *Gastrointestinal Microbiome ; Female ; *Probiotics/therapeutic use ; Middle Aged ; Aged ; Feces/microbiology ; Amino Acids, Branched-Chain/therapeutic use ; },
abstract = {The relationship between frailty and gut microbiota has not been previously addressed in patients with cirrhosis. We studied by metagenomic shotgun sequencing the faecal microbiota composition associated with frailty in 29 patients with cirrhosis from a previous study (Román, Hepatol Commun 2024). Frail and prefrail patients were randomised to a multifactorial intervention (home exercise, branched-chain amino acids and a multistrain probiotic) or control for 12 months. We observed a positive correlation between the abundance of Rothia dentocariosa and the Liver frailty index (LFI), and between Bacteroides faecis and gait speed. After the multifactorial intervention, LFI improved and the main changes in the microbiota composition were a decrease in the abundance of Akkermansia muciniphila, and an increase in Streptococcus thermophilus, Lactobacillus acidophilus and several species of Bifidobacterium. We conclude that frailty in patients with cirrhosis was associated with a distinct microbiome signature. After a long-term multifactorial intervention, frailty improved in parallel with changes in microbiome composition. Trial Registration: ClinicalTrials.gov identifier: NCT04243148.},
}
@article {pmid41174518,
year = {2025},
author = {Das, R and Thatal, B and Thakur, N and Kumar, R and Tamang, B},
title = {Metagenomic report of element-microbe synergy and xenobiotic detoxification in the sacred waters of Khecheopalri lake, Eastern Himalaya.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {704},
pmid = {41174518},
issn = {1471-2180},
mesh = {*Lakes/microbiology/chemistry ; *Metagenomics/methods ; India ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Xenobiotics/metabolism ; Microbiota ; Metagenome ; Inactivation, Metabolic ; },
abstract = {BACKGROUND: Khecheopalri Lake, a sacred freshwater body and recently recognized Ramsar Wetland site in Sikkim, India, holds both ecological and cultural significance. The ecological health of this lake is influenced by elemental inputs and environmental parameters, yet its microbial and functional diversity remain poorly characterized. In this study, we employed a multi-omics approach combining shotgun metagenomics, inductively coupled plasma mass spectrometry (ICP-MS), and culture-dependent analyses to provide an integrated understanding of the lake's microbial ecosystem. Shotgun metagenomics revealed taxonomic diversity and functional gene profiles, ICP-MS quantified elemental composition and its potential role in shaping microbial communities, while culture-dependent methods complemented metagenomic insights by isolating representative taxa. Together, these approaches highlight the interactions between microbes and elemental dynamics, offering new perspectives on the ecological functioning of this Himalayan wetland and its potential vulnerability to environmental change.<br><br>RESULTS: ICP-MS analysis revealed phosphorus (P) as the most abundant element, followed by iron (Fe), sodium (Na), magnesium (Mg), and potassium (K). Elevated BOD and COD levels in sample KES4 indicated organic pollution and coincided with the dominance of Microcystis aeruginosa, a cyanobacterium indicative of eutrophication. Shotgun metagenomic sequencing generated approximately 213 million reads, with bacteria constituting 98.85% of the community. Dominant phyla included Pseudomonadota and Cyanobacteria. Culturable isolates confirmed the presence of genera such as Limnohabitans, Microcystis, and Mycolicibacterium. Functional gene profiling showed that metabolism was the most enriched category (71.64%), with several genes (e.g., xylB, pchF, clcD) associated with xenobiotic degradation pathways.<br><br>CONCLUSION: This first comprehensive metagenomic assessment of Khecheopalri Lake reveals diverse microbial populations involved in nutrient cycling and pollutant detoxification. The presence of genes linked to aromatic hydrocarbon degradation highlights the ecological potential of native microbes in mitigating environmental stress.},
}
@article {pmid41174459,
year = {2025},
author = {Tian, Z and Koak, NH and Kinanti, B and Eun, JB and Kim, YM and Zhao, C},
title = {Integration of metagenomics and targeted metabolomics reveals the flavor metabolism network of the microbial community in traditional watermelon soybean paste.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 2},
pages = {117386},
doi = {10.1016/j.foodres.2025.117386},
pmid = {41174459},
issn = {1873-7145},
mesh = {*Metabolomics/methods ; *Citrullus/microbiology ; *Metagenomics/methods ; *Glycine max/microbiology ; *Taste ; Fermentation ; *Microbiota ; Food Microbiology ; Flavoring Agents/metabolism ; Bacteria/metabolism/classification/genetics ; },
abstract = {Watermelon soybean paste (WSP) is an important traditional Chinese condiment known for its unique flavor and nutritional value. However, the correlation between microbial communities and metabolites, especially flavor-related metabolites, as well as the underlying fermentation mechanisms, remains poorly understood. The microbial synthesis pathways of flavor-related metabolites and the composition of microbial communities in traditional watermelon soybean paste during fermentation were investigated through integrated metagenomic and targeted metabolomic analyses. The results demonstrated that Glu, Asp, Pro, Tyr, Ser, Leu, Phe, Val, and 73 metabolites were characterized as the key differential metabolites. An increase in the number of differential metabolites was observed as fermentation progressed. Aspergillus, Klebsiella, Enterococcus, and Weissella were identified as the dominant genus species in WSP samples. Functional composition analysis using both the eggNOG and KEGG databases revealed that valine, leucine, and isoleucine biosynthesis, starch and sucrose metabolism, glycolysis/gluconeogenesis, and pyruvate metabolism were identified as the predominant metabolic pathways. In contrast, GT4 and CBM were identified as the predominant enzyme families. Additionally, correlation analysis and key metabolic pathway investigation revealed that lactic acid bacteria (e.g., Weissella, Lactococcus, Lactobacillus) and Aspergillus were associated with the synthesis of flavor compounds (e.g., vanillin) and nutrient enrichment through amino acid metabolism and isoflavone biosynthesis pathways. This study offers a scientific basis for optimizing starter cultures and improving the flavor quality, contributing to improved quality control of WSP production.},
}
@article {pmid41174397,
year = {2025},
author = {Zhang, L and Li, D and Zhou, L and Zhu, L and Zhang, R and Hong, Q and Liu, S and Li, C},
title = {Characterization of flavor profile and microbial community dynamics in naturally fermented sour watermelon.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 2},
pages = {117319},
doi = {10.1016/j.foodres.2025.117319},
pmid = {41174397},
issn = {1873-7145},
mesh = {*Citrullus/microbiology/chemistry ; *Fermentation ; *Taste ; *Fermented Foods/microbiology/analysis ; Volatile Organic Compounds/analysis ; *Microbiota ; Acetic Acid/analysis ; Odorants/analysis ; Cresols/analysis ; *Food Microbiology ; Flavoring Agents/analysis ; Bacteria/classification/metabolism/genetics ; Gas Chromatography-Mass Spectrometry ; China ; },
abstract = {Sour watermelon (DFSW) is a distinctive fermented food that originated in Hainan, China, known for its unique and pungent flavor. Despite its cultural significance, the microbial dynamics and flavor formation mechanisms of DFSW remain poorly understood. This study employed multi-omics approaches, including HS-SPME-GC-MS and metagenomic sequencing, to analyze the physicochemical properties, volatile flavor compounds, and microbial community structure during DFSW fermentation. Results revealed that p-cresol, acetic acid, ethanol, hexaldehyde, and ethyl acetate were the dominant flavor compounds, endowing DFSW floral, fruity and spicy flavors, with p-cresol being the primary cause of pungent odors. The microbial community was primarily composed of Limosilactobacillus, Lactiplantibacillus, and Lactobacillus, which together made up over 83 % of the total abundance and were closely linked to flavor production. The correlation coefficient values (R) for Lactiplantibacillus and Lactobacillus with p-cresol, lactic acid, and acetic acid were consistently greater than 0.6. Metabolic pathway analysis highlighted the role of microbial carbohydrate and amino acid metabolism in flavor development. The synthesis of p-cresol was mainly related to the metabolism of tyrosine and L-phenylalanine, while the synthesis and metabolism of lactic acid and acetic acid were mainly related to the dominant bacterial genera in the fermentation system. These findings provide valuable insights for the biotechnological optimization of DFSW production, supporting the development of a consistent flavor profile and improved product stability.},
}
@article {pmid41173910,
year = {2025},
author = {Bednarski, OJ and Lehman, SB and Mzinza, D and Kazinga, C and Namazzi, R and Opoka, RO and Ren, J and Tran, TM and Taylor, TE and Seydel, KB and John, CC and Conroy, AL and Schmidt, NW},
title = {Gut bacterial dysbiosis in pediatric severe malaria associates with post-discharge mortality.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9658},
pmid = {41173910},
issn = {2041-1723},
support = {R01 NS055349/NS/NINDS NIH HHS/United States ; T32 GM148382/GM/NIGMS NIH HHS/United States ; D43 TW010928/TW/FIC NIH HHS/United States ; T32GM148382//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; D43TW010928//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; R01 AI148525/AI/NIAID NIH HHS/United States ; R01NS055349//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; TL1 TR002531/TR/NCATS NIH HHS/United States ; },
mesh = {*Dysbiosis/microbiology/mortality/complications ; Humans ; *Gastrointestinal Microbiome/genetics ; Child, Preschool ; *Malaria/mortality/microbiology/complications ; Female ; Male ; Infant ; Feces/microbiology ; Child ; Escherichia coli/isolation &amp; purification/genetics ; Metagenome ; Enterobacteriaceae/isolation &amp; purification/genetics ; Patient Discharge ; },
abstract = {Gut microbiota have been implicated in severe malaria in murine models, but their contribution to the pathogenesis of severe malaria in children is unknown. Here we show through analysis of gut bacteria in stool samples from two separate African studies enrolling children with severe malaria, and children from local communities, that children with severe malaria have gut bacteria dysbiosis. Among children with severe malaria, there is increased abundance of Enterobacteriaceae that associates with multiple clinical complications of severe malaria. Moreover, increased abundance of Escherichia coli was a predictor of post-discharge mortality. Metagenome analysis identify elevated metabolic pathways and genes supporting the utilization of host-derived molecules in children with severe malaria that have the potential to promote the survival and growth of Enterobacteriaceae. Treatments that target Enterobacteriaceae may have the potential to reduce post-discharge mortality in children with severe malaria.},
}
@article {pmid41173905,
year = {2025},
author = {Adhikary, R and Alkhatib, AEA and Hazra, S},
title = {Resistome profiling and bacterial community structure of semi-urban gutter ecosystems of India.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {38127},
pmid = {41173905},
issn = {2045-2322},
mesh = {India ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; *Drug Resistance, Bacterial/genetics ; beta-Lactamases/genetics/metabolism ; Gastrointestinal Microbiome ; Metagenomics/methods ; Humans ; Microbiota ; Metagenome ; },
abstract = {Environmental factors contribute to antimicrobial resistance, a global health threat. Contaminated gutter water in urban areas spreads resistant bacteria, disrupting ecosystems and promoting biofilm formation, causing widespread concern. This study aimed to evaluate antibiotic-resistant bacterial populations across six gutter ecosystems in Roorkee, Uttarakhand, India during summer against different classes of antibiotics, identify presence of beta-lactamase, and explores total bacterial communities, and predicting metabolic pathways through 16S rRNA based metagenomic approach of V3 region. The highest resistant bacterial population was found in HL_NS-6, and HL_NS-2, with highly resistance to Penicillin (ampicillin and oxacillin), Cephalosporin (Cephalothin), aminoglycoside (Kanamycin), fluoroquinolone (ciprofloxacin), and Antifolate (Trimethoprim) class antibiotics. Beta-lactamase activity was detected in all samples except HL_NS-5, indicated by nitrocefin hydrolysis. The microbial community in the six samples were composed with the major families enterobacteriaceae (15.4%) and pseudomonadaceae (8.29%), covering 23.7% of the total population. The highest taxa were found in HL_NS-2 and HL_NS-4, while the largest genera were Pseudomonas (8.3%), Escherichia (8.2%), Hydrogenophaga (6.85%), and Candidatus Moranella (5.4%). There were 21.25% common bacterial genera were present as core microbiome and rest were signified the population diversity among the six-gutter microbiome. The coexistence of common metabolic pathways (citric acid cycle, carbon, nitrogen metabolism etc.), and streptomycin, glycosphingolipid, lipopolysaccharide, cyanoamino acid metabolism pathways might be induced the development of antibiotic resistance in gutter microbiome. This study suggests the presence of antibiotic-resistant bacteria with antibiotic resistant metabolic pathways, and beta-lactamase genes in urban gutter water, which could be harmful to both human health and environmental ecosystems.},
}
@article {pmid41173568,
year = {2025},
author = {Díaz Perdigones, CM and Hinojosa Nogueira, D and Rodríguez Muñoz, A and Subiri Verdugo, A and Vilches-Pérez, A and Mela, V and Tinahones, FJ and Moreno Indias, I},
title = {Taxonomic and functional characteristics of the gut microbiota in obesity: A systematic review.},
journal = {Endocrinologia, diabetes y nutricion},
volume = {72},
number = {9},
pages = {501624},
doi = {10.1016/j.endien.2025.501624},
pmid = {41173568},
issn = {2530-0180},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Bacteria/classification ; },
abstract = {Obesity is a growing public health problem. In recent decades, scientific evidence has linked gut microbiota to obesity. This systematic review summarizes current knowledge on the composition and functional differences in gut microbiota between individuals with obesity and those with normal weight. Following PRISMA 2020 recommendations, studies published in adult populations between January 2014 and May 2024 were reviewed. PubMed, Web of Science, and Scopus databases were searched for observational studies that had used advanced sequencing methods, such as 16S rRNA and shotgun metagenomics, to assess gut microbiota. The quality of these studies was also analyzed using the Newcastle-Ottawa scale. Our review of 16 studies shows a reduction in microbial diversity in individuals with obesity. In addition, a higher relative abundance of the phylum Firmicutes, the families Enterobacteriaceae, Gemellaceae, Prevotellaceae, Streptococcaceae and Veillonellaceae, as well as the genera Blautia, Butyricimonas, Collinsella, Megamonas, and Streptococcus, while beneficial bacteria such as the families Porphyromonadaceae and Rikenellaceae, and the genera Bifidobacterium spp. and Faecalibacterium prausnitzii, were depleted. Functional analysis showed a tendency to an increase in metabolic pathways associated with carbohydrate and lipid metabolism, with reduced pathways related to short-chain fatty acid production. Obesity is associated with altered gut microbiota composition and function. However, the variability across studies regarding population characteristics, dietary pattern, and sequencing techniques limits the comparability of findings. Future research should prioritize standardized methodologies and confounding factors to elucidate the role of the gut microbiome in obesity.},
}
@article {pmid41172852,
year = {2025},
author = {Chen, T and Li, S and Xiao, J and Peng, R and Sha, M and Wang, J and Ma, J and Wang, W and Ma, M and Li, S and Cao, Z and Liu, S},
title = {Carbohydrate-metabolizing gastrointestinal bacteria mediate resistome divergence in high feed efficiency Holstein dairy calves.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140283},
doi = {10.1016/j.jhazmat.2025.140283},
pmid = {41172852},
issn = {1873-3336},
mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome ; Female ; *Animal Feed ; Rumen/microbiology ; Feces/microbiology ; *Carbohydrate Metabolism ; *Bacteria/metabolism/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Improvements in feed efficiency often involve alterations in nutrient metabolism mediated by gastrointestinal microorganisms. These microorganisms serve as carriers of antibiotic resistance genes (ARGs); therefore, metabolic changes may influence the dissemination of ARGs. In this study, we investigated the variations in gastrointestinal ARGs between female Holstein calves exhibiting low residual feed intake (LRFI) with high feed efficiencies and those exhibiting high residual feed intake (HRFI) with low feed efficiencies. Metagenomics was conducted to analyze the underlying factors driving these differences. The LRFI calves exhibited 16.6 % higher ruminal ARG abundance but had reduced fecal ARG diversity. The abundance of Erysipelotrichaceae enrichment in LRFI rumen drove resistance functions and elevated carbohydrate-active enzymes (CAZymes) expression. Correlation analysis linked LRFI rumen enriched bacteria Erysipelotrichaceae and Coprobacillaceae to CAZymes, which were positively associated with multidrug, fluoroquinolone, and MLS resistance functions. Weighted Gene Co-Expression Network Analysis confirmed these resistance functions were dominant in LRFI calves. CAZymes improved substrate utilization, enhanced bacterial efflux resistance, promoted bacterial proliferation, and upregulated resistance genes. Rumen microbes and their resistomes systemically alter microbiota and ARG profiles in the feces. The contributions of fecal microbial abundance and diversity, mobile genetic elements (MGEs), and starch to the differences in ARGs were 14.92 %, 11.18 %, 8.90 %, and 10.25 %, respectively. In summary, LRFI calves require more CAZymes to reshape gut microbiota and ARG carrier populations, which lead to shifts in gastrointestinal ARG abundance/diversity shifts.},
}
@article {pmid41172529,
year = {2025},
author = {Lima, JD and Rivadavea, WR and Calgaro, LC and Alberton, O and Costa, MSSM and Lima, JC and Monteiro, PHR and Kuhn, EV and Silva, GJ},
title = {Biological dynamics of no-tillage soils in the western region of Paraná.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {85},
number = {},
pages = {e298630},
doi = {10.1590/1519-6984.298630},
pmid = {41172529},
issn = {1678-4375},
mesh = {*Soil Microbiology ; *Soil/chemistry ; Brazil ; Nitrogen/analysis ; *Agriculture/methods ; Biomass ; Biodiversity ; Fungi/classification ; Carbon/analysis ; },
abstract = {This study investigates soil dynamics on farms in the western region of Paraná, Brazil, highlighting the importance of biological parameters in agriculture. In particular, focusing on the interaction of management practices with soil biodiversity and biological functions, the aim is to understand and promote sustainable and efficient agricultural practices. To do this, we collected soil samples from 15 farms close to Toledo, Paraná, Brazil. These samples were then analyzed to determine biological and physicochemical parameters using techniques such as carbon and nitrogen microbial biomass, metabolic coefficient, basal respiration, bacterial and fungal biomass, and length of the hyphae. The most contrasting soils were evaluated for physicochemical composition and metagenomic analyses. The results showed significant differences in biological parameters between 2020 and 2021, including fungal biomass, hyphae length, and soil basal respiration. Statistical analyzes revealed strong relationships between biological variables, notably the correlation between fungal hyphae and total nitrogen. Climate changes and management practices appear to influence the microbial composition and biological functions of the soil over the years. Soil P9 stood out with superior biological activity and richer microbial diversity, contrasting with soil P13. These differences reflect the influence of management and climatic conditions on soil composition and biological functions. The microbial comparison of the soils emphasized the need for continuous and careful agricultural management, highlighting the importance of biodiversity and ecological functionality of the soil for agricultural sustainability. So, the study underscores the relevance of considering soil biological parameters, in addition to physicochemical aspects, to optimize soil health and productivity.},
}
@article {pmid41171541,
year = {2025},
author = {Joseph, JS and Selvamani, SB and Thiruvengadam, V and Ramasamy, GG and Subramanian, S and Menon, G and Sivakumar, G and Manjunath, C},
title = {Gut microbiota profiling of Apis cerana indica across biodiversity hotspots in the Western Ghats, India.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {35},
pmid = {41171541},
issn = {1573-4978},
mesh = {Bees/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; },
abstract = {BACKGROUND: The gut microbiome of honey bees plays a crucial role in regulating key physiological traits and metabolic processes, including digestion, detoxification, nutrient assimilation, development and immunity. However, information on the gut bacterial diversity of Apis cerana indica bee populations in India remains limited. This study aims to address this critical knowledge gap in Western Ghats, India with outcomes that may provide valuable insights for improving beekeeping practices in the region.<br><br>METHODS AND RESULTS: To fill this gap, we investigated and characterized the gut bacteriome of A. cerana indica collected from two ecologically distinct regions within the Western Ghats. We employed a combination of next-generation sequencing (NGS) using the Oxford Nanopore platform and traditional culture-based methods targeting the 16S rRNA gene to analyze the microbial communities. Our results revealed that the gut bacterial communities of foraging A. cerana indica bees from both locations displayed unique and overlapping microbiome profiles. A total of 225 bacterial species across 30 bacterial orders were identified via 16S rRNA amplicon sequencing, with 92 species shared between the two sites. Prominent symbiotic bacterial groups included Gammaproteobacteria, Betaproteobacteria, Flavobacteria, Actinobacteria, Firmicutes, Proteobacteria, and Actinomycetota. Notably, core bee-associated symbionts exhibited a negative correlation with pathogenic bacterial taxa.<br><br>CONCLUSION: These findings offer valuable insights into the ecological and functional roles of the gut microbiome in A. cerana indica, a native honeybee species of the Western Ghats. The presence of shared bacterial species across regions suggests their potential significance in formulating conservation strategies for indigenous bee populations.},
}
@article {pmid41171126,
year = {2026},
author = {She, J and Qian, PY and Wu, L},
title = {DOO: integrated multi-omics resources for deep ocean organisms.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D1031-D1045},
pmid = {41171126},
issn = {1362-4962},
support = {2021HJ01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; HJRC2022001//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; SMSEGL24SC01//Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; CCRS25SC01//Otto Poon Center for Climate Resilience and Sustainability/ ; 26104824//Early Career Scheme/ ; JCYJ20220530151207016//Technology Innovation Committee of Shenzhen/ ; 26104824//Technology Innovation Committee of Shenzhen/ ; },
mesh = {Oceans and Seas ; *Genomics/methods ; Transcriptome ; *Databases, Genetic ; *Aquatic Organisms/genetics/classification ; Phylogeny ; Animals ; Metagenome ; Molecular Sequence Annotation ; Multiomics ; },
abstract = {The deep ocean is one of Earth's most vast and least explored frontiers, characterized by extreme conditions such as high pressure, limited light, and nutrient scarcity. These environments pose unparalleled challenges to life, making them invaluable for studying genetic and molecular adaptations to extreme conditions. Emerging omics resources have recently provided significant insights into the advanced understanding of deep ocean ecosystems and evolution. However, a centralized resource for deep ocean multi-omics data remains lacking. To bridge this gap, the Deep Ocean Omics (DOO, https://DeepOceanOmics.org) database, a multi-omics atlas for deep ocean organisms, is presented. DOO integrates diverse omics resources from 68 species across seven phyla and 16 classes, encompassing 72 genomes, 950 bulk transcriptomes, 15 single-cell transcriptomes, and 1112 metagenomes, alongside functional support toolkits for functional and comparative analysis. DOO provides a systematic view of genomic information, including genome assembly, phylogeny, gene annotation, BUSCO genes, transcription factors/ubiquitin family, gene clusters, symbiont and mitochondrial genomes, and fossil records. Moreover, DOO offers co-expression networks with expression views across different tissues, and developmental stages and micro- and macrosynteny analyses to elucidate the pan-evolutionary features of genome structure. As the first comprehensive multi-omics resource dedicated to deep ocean organisms, DOO serves as a pivotal platform for uncovering multi-omics underpinnings of deep ocean organisms and offering insights into the understanding of deep ocean biodiversity, evolution, and genetic adaptation under extreme conditions.},
}
@article {pmid41171125,
year = {2026},
author = {Kuhn, M and Schmidt, TSB and Ferretti, P and Głazek, A and Robbani, SM and Akanni, W and Fullam, A and Schudoma, C and Cetin, E and Hassan, M and Noack, K and Schwarz, A and Thielemann, R and Thomas, L and von Stetten, M and Alves, R and Iyappan, A and Kartal, E and Kel, I and Keller, MI and Maistrenko, O and Mankowski, A and Nishijima, S and Podlesny, D and Schiller, J and Schulz, S and Van Rossum, T and Bork, P},
title = {Metalog: curated and harmonised contextual data for global metagenomics samples.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D826-D834},
pmid = {41171125},
issn = {1362-4962},
support = {668031//Horizon 2020/ ; 101059915//European Union's Horizon Europe research and innovation programme/ ; NNF15OC0016692//MicrobLiver/ ; //Novo Nordisk Foundation/ ; //Deutsche Forschungsgemeinschaft/ ; 460129525//German Research Foundation/ ; //Ministry of Science/ ; //MWK/ ; //German Federal Ministry of Research, Technology and Space/ ; //European Molecular Biology Laboratory/ ; ERC-AdG-669830/ERC_/European Research Council/International ; },
mesh = {*Metagenomics/methods ; Animals ; Humans ; *Databases, Genetic ; Metadata ; Metagenome ; Data Curation ; Gastrointestinal Microbiome/genetics ; },
abstract = {Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data is deposited in public databases, the associated contextual data is often not complete and needs to be retrieved from primary publications. This lack of access to sample-level metadata like clinical data or in situ observations impedes cross-study comparisons and meta-analyses. We therefore created the Metalog database, a repository of manually curated metadata for metagenomics samples across the globe. It contains 80 423 samples from humans (including 66 527 of the gut microbiome), 10 744 animal samples, 5547 ocean water samples, and 23 455 samples from other environmental habitats such as soil, sediment, or fresh water. Samples have been consistently annotated for a set of habitat-specific core features, such as demographics, disease status, and medication for humans; host species and captivity status for animals; and filter sizes and salinity for marine samples. Additionally, all original metadata is provided in tabular form, simplifying focused studies e.g. into nutrient concentrations. Pre-computed taxonomic profiles facilitate rapid data exploration, while links to the SPIRE database enable genome-based analyses. The database is freely available for browsing and download at https://metalog.embl.de/.},
}
@article {pmid41171124,
year = {2026},
author = {Lv, J and Ma, S and Ma, C and Liu, F and Duan, X and Huang, X and Geng, Q and Liu, F and Li, G and Li, Y and Wang, J and Li, C and Zheng, H and Zhang, Y and Sun, Z and Wang, J and Fan, G and Huang, S and Zhang, L and Bao, Z and Wang, S},
title = {Ocean-M: an integrated global-scale multi-omics database for marine microbial diversity, function and ecological interactions.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D813-D825},
pmid = {41171124},
issn = {1362-4962},
support = {2024YFC2816000//National Key Research and Development Program of China/ ; LSKJ202202804//Marine S&amp;T Fund of Shandong Province for Laoshan Laboratory/ ; 2025B1111180001//Guangdong Provincial Key Areas R&amp;D Program Project/ ; SOLZSKY2025013//Hainan Province Science and Technology Special Fund/ ; 32573498//Natural Science Foundation of China/ ; 32222085//Natural Science Foundation of China/ ; QDLYY-2024011//Blue Seed Industry Science and Technology Innovation Project/ ; GZB20250215//Postdoctoral Fellowship Program of CPSF/ ; },
mesh = {Metagenome ; *Databases, Genetic ; *Microbiota/genetics ; Metagenomics/methods ; *Aquatic Organisms/genetics/classification ; Oceans and Seas ; *Seawater/microbiology ; Biodiversity ; Ecosystem ; Bacteria/genetics/classification ; Molecular Sequence Annotation ; Software ; Multiomics ; },
abstract = {Multi-omics analyses have significantly advanced the understanding of complex marine microbial communities and their interactions. Despite notable progress from recent large-scale ocean meta-analysis efforts, the effective integration and accessibility of these diverse datasets remain challenging. To address this, we introduce Ocean-M (http://om.qnlm.ac), a comprehensive and publicly accessible platform for marine microbial multi-omics data integration, analysis, and visualization. Ocean-M provides a systematic view of 54 083 high-quality metagenome-assembled genomes, including genome assembly statistics, genome clustering, gene annotation, and interactive tools for global-scale taxonomic profiling. The platform also incorporates microbial community networks, host-microbiome interactions, and environmental DNA datasets to support an integrated ecological framework for studying microbial interactions and ecosystem functions. Additionally, Ocean-M enables large-scale mining of ecologically and biotechnologically important genes, with curated catalogs of 151 798 biosynthetic gene clusters, 52 699 antibiotic resistance genes, and millions of carbohydrate-active enzymes and plastic-active enzymes. By combining multi-omics data with environmental metadata, Ocean-M serves as a valuable resource for advancing marine microbial ecology, global biogeography, and functional gene discovery.},
}
@article {pmid41168956,
year = {2026},
author = {Ruiz, E and Lamy, T and Mouillot, D and Durand, JD},
title = {Benchmarking the Taxonomic Resolution of Fish eDNA Metabarcodes Against COI Barcodes.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70069},
pmid = {41168956},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Fishes/genetics/classification ; *Electron Transport Complex IV/genetics ; Benchmarking ; *Metagenomics/methods ; *DNA, Environmental/genetics ; Cluster Analysis ; Biodiversity ; Computational Biology/methods ; },
abstract = {Even though environmental DNA metabarcoding is revolutionizing biomonitoring, many critical steps remain unstandardized, leading to arbitrary choices, particularly regarding the selection of metabarcode, clustering method and similarity threshold, among others. Additionally, these studies were hindered by biases resulting from the presence of mislabeled sequences in international databases such as GenBank and the lack of explicit definitions for taxonomic resolution. To address these issues, we developed a robust framework to compare the performance of 22 metabarcodes derived from the same mitogenomes (all available for Actinopterygians in NCBI) against a standardized taxonomic baseline based on COI Barcode Index Numbers (BINs). This framework allows for the separate quantification of over-splitting (splitting the same taxon/BIN) and over-merging (merging different taxon/BIN). Comparison of OTUs obtained with multiple de novo clustering methods to BINs confirmed the metabarcode ranking based on error sums. Although each metabarcode exhibited varying sensitivities to over-merging or over-splitting errors, the clustering threshold emerged as the most important factor influencing biodiversity estimates whatever the clustering method. This led us to propose optimal thresholds for each metabarcode to delineate taxonomic levels (metabarcode gaps). Additionally, we found that taxonomic resolution varied significantly among genes, orders and community diversity, but independently of metabarcode length. Overall, the choice of metabarcode and clustering threshold should aim to minimize over-merging or over-splitting while ensuring accurate lower taxonomic delineations. A set of documented R functions makes this evaluation of taxonomic resolution easily applicable to any other taxonomic group for which a representative set of full genes or mitogenomes is available.},
}
@article {pmid41168883,
year = {2025},
author = {Gabashvili, E and Küsel, K and Pratama, AA and Wang, H and Taubert, M},
title = {Growth of candidate phyla radiation bacteria in groundwater incubations reveals widespread adaptations to oxic conditions.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {224},
pmid = {41168883},
issn = {2049-2618},
support = {390713860//Deutsche Forschungsgemeinschaft/ ; B 715-09075//Th&#xfc;ringer Ministerium f&#xfc;r Wirtschaft, Wissenschaft und Digitale Gesellschaft/ ; 2016 FGI 0024 "BIODIV"//Th&#xfc;ringer Ministerium f&#xfc;r Wirtschaft, Wissenschaft und Digitale Gesellschaft,Germany/ ; },
mesh = {*Groundwater/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/growth &amp; development/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota/genetics ; Phylogeny ; DNA, Bacterial/genetics ; Adaptation, Physiological ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The candidate phyla radiation (CPR) comprises a widespread but poorly understood group of bacteria with limited cultured representatives, largely due to their metabolic dependencies on microbial hosts. In laboratory incubations, CPR often decline sharply in relative abundance, even when samples originate from natural environments where they dominate, such as groundwater, where they can represent over 50% of the microbiome. Suitable enrichment conditions and host interactions remain poorly defined.<br><br>RESULTS: Here, we analyzed 16S rRNA gene amplicon data from 397 groundwater incubation samples across 31 treatments, including 22 under oxic conditions, to identify factors that promote CPR survival and growth. Despite an initial decline, CPR abundances recovered over longer incubation times, reaching up to 11-30% of the microbial community. In total, we detected 1410 CPR amplicon sequence variants (ASVs), spanning six major CPR classes commonly found in groundwater. Enrichment success was treatment-specific: Cand. Saccharimonadia dominated in incubations with polysaccharides (up to 31.4%), while Cand. Parcubacteria were enriched (>&#x2009;23%) in treatments stimulating methylotrophs and autotrophs. ASV-specific growth rates based on quantitative PCR showed that some CPR doubled within 1-2&#xa0;days, comparable to faster-growing non-CPR groundwater bacteria, while most CPR had doubling times around 15&#xa0;days. Strikingly, although the relative abundance of many CPR ASVs showed positive correlation with anoxic conditions, overall CPR reached higher absolute abundances under oxic conditions than under anoxic conditions. Metabolic network analysis based on metagenome-assembled genomes revealed that up to 62% of annotated genes were associated with functions linked to oxic conditions. In fact, 25 CPR genomes encoded enzymes that directly utilize oxygen, challenging the long-standing view of CPR as strictly anaerobic, fermentative organisms.<br><br>CONCLUSIONS: Our findings demonstrate that diverse CPR lineages not only survive but actively grow in groundwater incubations, even under oxic conditions. The discovery of genes for oxygen-dependent reactions and substantial CPR enrichment in oxic treatments reveals unexpected metabolic flexibility, helping to explain their persistence and ecological success across a wide range of environments.},
}
@article {pmid41168882,
year = {2025},
author = {Bowers, RM and Bennett, S and Riley, R and Villada, JC and Da Silva, IR and Woyke, T and Frank, AC},
title = {Host species and geographic location shape microbial diversity and functional potential in the conifer needle microbiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {222},
pmid = {41168882},
issn = {2049-2618},
support = {10.46936/10.25585/60000936//U.S. Department of Energy/ ; DEB-1442348//Directorate for Biological Sciences/ ; },
mesh = {*Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics/methods ; *Tracheophyta/microbiology ; Metagenome ; Phylogeny ; *Plant Leaves/microbiology ; Pinus/microbiology ; },
abstract = {BACKGROUND: The aerial surface of plants, known as the phyllosphere, hosts a complex and dynamic microbiome that plays essential roles in plant health and environmental processes. While research has focused on root-associated microbiomes, the phyllosphere remains comparatively understudied, especially in forest ecosystems. Despite the global ecological dominance and importance of conifers, no previous study has applied shotgun metagenomics to their phyllosphere microbiomes.<br><br>RESULTS: This study uses metagenomic sequencing to explore the microbial phyllosphere communities of subalpine Western conifer needle surfaces from 67 trees at six sites spanning the Rocky Mountains, including 31 limber pine, 18 Douglas fir, and 18 Engelmann spruce. Sites span&#x2009;~&#x2009;1,075&#xa0;km and nearly 10&#xb0; latitude, from Glacier National Park to Rocky Mountain Biological Laboratory, capturing broad environmental variation. Metagenomes were generated for each of the 67 samples, for which we produced individual assemblies, along with three large coassemblies specific to each conifer host. From these datasets, we reconstructed 447 metagenome-assembled genomes (MAGs), 417 of which are non-redundant at the species level. Beyond increasing the total number of extracted MAGs from 153 to 294, the three coassemblies yielded three large MAGs, representing partial sequences of host genomes. Phylogenomics of all microbial MAGs revealed communities predominantly composed of bacteria (n&#x2009;=&#x2009;327) and fungi (n&#x2009;=&#x2009;117). We show that both microbial community composition and metabolic potential differ significantly across host tree species and geographic sites, with site exerting a stronger influence than host.<br><br>CONCLUSIONS: This dataset offers new insights into the microbial communities inhabiting the conifer needle surface, laying the foundation for future research on needle microbiomes across temporal and spatial scales. Variation in functional capabilities, such as volatile organic compound (VOC) degradation and polysaccharide metabolism, closely tracks shifts in taxonomic composition, indicating that host-specific chemistry, local environmental factors, and regional microbial source pools jointly shape ecological roles. Moreover, the observed patterns of mobile genetic elements and horizontal gene transfer suggest that gene exchange predominantly occurs within microbial lineages, with occasional broader transfers dispersing key functional genes (e.g., those involved in polysaccharide metabolism), which may facilitate microbiome adaptation.},
}
@article {pmid41168702,
year = {2025},
author = {Lakamp, A and Adams, S and Kuehn, L and Snelling, W and Wells, J and Hales, K and Neville, B and Fernando, S and Spangler, ML},
title = {Prediction accuracy for feed intake and body weight gain using host genomic and rumen metagenomic data in beef cattle.},
journal = {Genetics, selection, evolution : GSE},
volume = {57},
number = {1},
pages = {64},
pmid = {41168702},
issn = {1297-9686},
support = {2022-33522-38219//National Institute of Food and Agriculture/ ; 2023-68015-40015//National Institute of Food and Agriculture/ ; 2024-33522-43699//National Institute of Food and Agriculture/ ; 2018-67015-27496//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; Cattle/genetics/physiology ; *Rumen/microbiology ; *Metagenome ; *Weight Gain/genetics ; *Eating/genetics ; Metagenomics/methods ; Animal Feed ; Phenotype ; Genomics/methods ; Diet/veterinary ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Host genomic and rumen metagenome data can predict feed efficiency traits, supporting management decisions and increasing profitability. This study estimated the proportion of variation of average daily dry matter intake and average daily gain explained by the rumen metagenome in beef cattle, evaluated prediction accuracy using genomic data, metagenomic data, or their combination, and explored methods for modelling the rumen metagenome to improve phenotypic prediction accuracy. Data from 717 animals on four diets (two concentrate-based and two forage-based) were analyzed. Animal genotypes consisted of 749,922 imputed sequence variants, while metagenomic data comprised 16,583 open reading frames from ruminal microbiota. The metagenome was modelled using six (co)variance matrices, based on combinations of two creation methods and three modifications. Nineteen mixed linear models were used per trait: one with genomic effects only, six with metagenomic effects, six combining genomic and metagenomic effects, and six adding interaction effects. Two cross-validation schemes were applied to evaluate prediction accuracy: fourfold cross-validation balanced for diet type with 5 replicates and leave-one-diet-out cross-validation, where three diets served as training and the fourth as testing. Prediction accuracy was measured as the correlation between an animal's summed random effects and its adjusted phenotype.<br><br>RESULTS: Although minimal, differences existed in parameter estimates and validation accuracy depending on how the metagenome effect was modelled. Median phenotype prediction accuracy ranged from -0.01 to 0.28. No specific set of model characteristics consistently lead to the highest accuracies. Models which combined genome and metagenome data outperformed those using either data source alone. Models where the rumen metagenome (co)variances matrix was scaled within each diet composition generally led to lower prediction accuracies in this study.<br><br>CONCLUSIONS: The rumen metagenome can explain a significant proportion of variation in beef cattle feed efficiency traits. Those traits can also be predicted using either host genome or rumen metagenome, though using both sources of information proved more accurate. Multiple methods of forming the metagenome (co)variance matrix can lead to similar prediction accuracies.},
}
@article {pmid41168432,
year = {2025},
author = {Ginnan, NA and Custódio, V and Gopaulchan, D and Ford, N and Salas-González, I and Jones, DH and Wells, DM and Moreno, &#xc2; and Castrillo, G and Wagner, MR},
title = {Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants.},
journal = {Nature microbiology},
volume = {10},
number = {11},
pages = {2823-2844},
pmid = {41168432},
issn = {2058-5276},
support = {P30 GM122731/GM/NIGMS NIH HHS/United States ; IOS-2016351//National Science Foundation (NSF)/ ; U54 HD090216/HD/NICHD NIH HHS/United States ; S10 OD021743/OD/NIH HHS/United States ; BB/V011294/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; UL1 TR002366/TR/NCATS NIH HHS/United States ; P30 GM145499/GM/NIGMS NIH HHS/United States ; },
mesh = {*Droughts ; *Soil Microbiology ; *Microbiota/genetics ; Zea mays/physiology/genetics/microbiology ; Soil/chemistry ; *Rain ; Kansas ; Plant Roots/microbiology/genetics ; Stress, Physiological ; Metagenome ; Adaptation, Physiological ; Water/metabolism ; *Plants/microbiology/genetics ; Bacteria/classification/genetics ; },
abstract = {Drought alters the soil microbiota by selecting for functional traits that preserve fitness in dry conditions. Legacy effects or ecological memory refers to how past stress exposure influences microbiota responses to future environmental challenges. How precipitation legacy effects impact soil microorganisms and plants is unclear, especially in the context of subsequent drought. Here we characterized the metagenomes of six prairie soils spanning a precipitation gradient in Kansas, United States. A microbial precipitation legacy, which persisted over a 5-month-long experimental drought, mitigated the negative physiological effects of acute drought for a native wild grass species, but not for the domesticated crop species maize. RNA sequencing of roots revealed that soil microbiota with a low precipitation legacy altered expression of plant genes that mediate transpiration and intrinsic water-use efficiency during drought. Our results show how historical exposure to water stress alters soil microbiota, with consequences for future drought responses of some plant species.},
}
@article {pmid41168431,
year = {2025},
author = {Jabbar, KS and Priya, S and Xu, J and Das Adhikari, U and Pishchany, G and Mohamed, ATM and Johansen, J and Thurimella, K and McCabe, C and Vlamakis, H and Okello, S and Delorey, TM and Lankowski, A and Mosepele, M and Siedner, MJ and Plichta, DR and Kwon, DS and Xavier, RJ},
title = {Human immunodeficiency virus and antiretroviral therapies exert distinct influences across diverse gut microbiomes.},
journal = {Nature microbiology},
volume = {10},
number = {11},
pages = {2720-2735},
pmid = {41168431},
issn = {2058-5276},
support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HL141053/HL/NHLBI NIH HHS/United States ; K24 HL166024/HL/NHLBI NIH HHS/United States ; DK120485//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 HL141053/HL/NHLBI NIH HHS/United States ; K24 HL166024/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *HIV Infections/drug therapy/microbiology ; Uganda ; Alkynes ; Metagenomics ; Benzoxazines/therapeutic use/adverse effects ; Male ; Female ; Feces/microbiology ; Cyclopropanes ; Adult ; Botswana ; *Anti-Retroviral Agents/therapeutic use ; Middle Aged ; United States ; Reverse Transcriptase Inhibitors/therapeutic use ; *Anti-HIV Agents/therapeutic use ; Bacteria/classification/genetics/drug effects/isolation &amp; purification ; },
abstract = {Human immunodeficiency virus (HIV) infection alters gut microbiota composition and function, but the impact of geography and antiretroviral therapy remains unclear. Here we determined gut microbiome alterations linked to HIV infection and antiretroviral treatment in 327 individuals with HIV and 260 control participants in cohorts from Uganda, Botswana and the USA via faecal metagenomics. We found that while HIV-associated taxonomic differences were mostly site specific, changes in microbial functional pathways were broadly consistent across the cohorts and exacerbated in individuals with acquired immunodeficiency syndrome. Microbiome perturbations associated with antiretroviral medications were also geography dependent. In Botswana and Uganda, use of the non-nucleoside reverse transcriptase inhibitor efavirenz was linked to depletion of Prevotella, disruption of interspecies metabolic networks, exacerbation of systemic inflammation and atherosclerosis. Efavirenz-associated Prevotella depletion may occur through cross-inhibition of prokaryotic reverse transcriptases involved in antiphage defences, as shown by computational and in vitro experiments. These observations could inform future geography-specific and microbiome-guided therapy.},
}
@article {pmid41168291,
year = {2025},
author = {Arjmand, E and Moghadam, A and Afsharifar, A and Faghihi, MM and Izadpanah, K and Taghavi, SM},
title = {Metagenome analysis of Citrus sinensis rhizosphere infected with Candidatus liberibacter asiaticus reveals distinct structure in bacterial communities.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37987},
pmid = {41168291},
issn = {2045-2322},
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Metagenome ; *Microbiota/genetics ; *Citrus sinensis/microbiology ; *Rhizobiaceae ; Plant Roots/microbiology ; Soil Microbiology ; *Bacteria/genetics/classification ; Phylogeny ; *Liberibacter ; High-Throughput Nucleotide Sequencing ; },
abstract = {The rhizosphere microbiome plays crucial roles in different root-associated biological functions, especially regulating plant defense systems. Huanglongbing (HLB) disease, caused by Candidatus Liberibacter species, is a disaster threat to the global citrus industry. This study investigates changes in rhizosphere bacterial communities of Citrus sinensis trees infected by Candidatus Liberibacter asiaticus (CLas). We performed the high-throughput sequencing of the rhizosphere-associated bacterial metagenome and identified taxonomic profiles. Alpha diversity based on Shannon and Chao1 indices, and beta diversity based on Bray-Curtis dissimilarity and the UniFrac indices, revealed significant differences in the composition and structure of the rhizosphere microbiome between CLas-infected and CLas-free trees. We achieved significant relative abundance at the phylum and family, and genus levels. The abundance of Pseudomonas, Chryseobacterium, and an unknown genus belonging to Aurantimonadaceae was significantly suppressed in infected trees, while Planococcus and an unknown genus belonging to Caulobacteraceae were significantly enriched. These results confirm that CLas have dramatically altered the structure and composition of the rhizosphere microbiome. These changes discovered some valuable biomarkers related to this disease. These clues might be applied in microbial engineering of the rhizosphere to control HLB.},
}
@article {pmid41167188,
year = {2025},
author = {Cha, JH and Kim, N and Ma, J and Lee, S and Koh, G and Yang, S and Beck, S and Byeon, I and Lee, B and Lee, I},
title = {A high-quality genomic catalog of the human oral microbiome broadens its phylogeny and clinical insights.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {11},
pages = {1977-1994.e8},
doi = {10.1016/j.chom.2025.10.001},
pmid = {41167188},
issn = {1934-6069},
mesh = {Humans ; *Mouth/microbiology ; *Phylogeny ; *Microbiota/genetics ; Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Genome, Bacterial ; Periodontitis/microbiology ; Metagenome ; Genomics ; Gastrointestinal Microbiome/genetics ; },
abstract = {The oral microbiome is increasingly linked to human health. To further examine this microbial community, we present the human reference oral microbiome (HROM), with 72,641 high-quality genomes from 3,426 species, including 2,019 previously unidentified species, improving metagenomic sequence read classification over existing catalogs. Notably, HROM unveils 1,137 previously uncharacterized candidate phyla radiation (CPR) species, establishing Patescibacteria as the most prevalent phylum in the oral microbiota and distinct from environmental Patescibacteria. Additionally, an oral CPR subclade is associated with periodontitis, complementing Porphyromonas gingivalis in predicting disease. Finally, comparing HROM with reference genomes of the gut microbiome reveals taxonomic and functional divergence between these microbiomes. HROM contains 42 ectopic oral species, and their relative abundance in gut microbiota is predictive of intestinal, cardiovascular, and liver diseases. Thus, HROM offers an expanded view of the oral microbiome and highlights the clinical importance of further examining the links between oral microbes and systemic disorders.},
}
@article {pmid41166306,
year = {2025},
author = {Zhang, ZF and Huang, JE and Phurbu, D and Qu, ZS and Liu, F and Cai, L},
title = {A deep metagenomic atlas of Qinghai-Xizang Plateau lakes reveals their microbial diversity and salinity adaptation mechanisms.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116483},
doi = {10.1016/j.celrep.2025.116483},
pmid = {41166306},
issn = {2211-1247},
mesh = {*Lakes/microbiology ; *Salinity ; *Metagenomics/methods ; *Adaptation, Physiological/genetics ; *Metagenome/genetics ; Salt Tolerance/genetics ; China ; Biodiversity ; Geologic Sediments/microbiology ; Bacteria/genetics/classification ; },
abstract = {The Qinghai-Xizang Plateau (QXP), harboring the planet's highest density of plateau lakes, offers an exceptional biogeographic environment for studying extremophilic microbial communities and their adaptation to salinity. Through deep metagenomic sequencing, we construct the Qinghai-Xizang Lake Sediment Genome (QXLSG) catalog, a high-resolution genomic catalog comprising 5,866 metagenome-assembled genomes (MAGs), 58.16 million non-redundant protein encoding genes, and 19,008 biosynthetic gene clusters. Notably, 80.78% of the 2,742 species-level MAGs represent undescribed taxa, significantly expanding the known microbial diversity. Salinity emerges as the primary environmental factor influencing microbial community. Functional annotation highlights that the "salt-out" strategy, particularly the uptake of glycine betaine, is the main mechanism for salinity tolerance. This strategy is prevalent in both hypersaline lake communities and the dominant microbial phyla. Overall, this study provides a crucial genetic resource for future bioprospecting and deepens our understanding of the fundamental mechanisms of microbial adaptation to extreme saline environments.},
}
@article {pmid41166145,
year = {2026},
author = {Ding, W and Zhang, H and Wen, J and Xiong, G and Cheng, M and Liu, J and Zhao, Y and Miao, Q and Deng, H and Xu, Z and Mi, L and Tan, Z and Su, L and Long, Y and Ning, K},
title = {A Multiomics Analysis Reveals a Gut Microbiome: LPC Metabolic Axis Driving Postoperative Inflammation in Cardiopulmonary Bypass Patients.},
journal = {Shock (Augusta, Ga.)},
volume = {65},
number = {2},
pages = {188-200},
doi = {10.1097/SHK.0000000000002722},
pmid = {41166145},
issn = {1540-0514},
support = {2023YFA1800900//the National Key R&amp;D Program of China/ ; 2018YFC0910502//the National Key R&amp;D Program of China/ ; 32071465//the National Natural Science Foundation of China/ ; 31871334//the National Natural Science Foundation of China/ ; 31671374//the National Natural Science Foundation of China/ ; 2022-PUMCH-B-115//National High-Level Hospital Clinical Research Founding/ ; 2022-PUMCH-D-005//National High-Level Hospital Clinical Research Founding/ ; 2023&#xe2;&#x20ac;I2M&#xe2;&#x20ac;2&#xe2;&#x20ac;002//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; *Cardiopulmonary Bypass/adverse effects ; Middle Aged ; Aged ; *Inflammation/metabolism/etiology ; *Postoperative Complications/metabolism/microbiology ; *Lysophosphatidylcholines/metabolism ; Metabolomics ; Metabolome ; Multiomics ; },
abstract = {BACKGROUND: Patients undergoing cardiac surgery with cardiopulmonary bypass (CSCPB) are at substantial postoperative risk, which may be influenced by alterations in gut microbiota and metabolites. The roles of these biological changes in postoperative outcomes remain inadequately explored.<br><br>METHODS: We collected 54 preoperative samples and 33 postoperative samples from 60 CSCPB patients. Metagenomic and metabolomic sequencing were performed to identify the gut microbiota and serum and fecal metabolites. We examined the dynamic pattern of these microbiota and metabolites, as well as their associations with the postoperative risks. Additionally, we developed a predictive model for postoperative risk based on preoperative microbiome and metabolome data.<br><br>RESULTS: We revealed significant alterations of gut microbiota (P = 0.012), serum metabolites (P = 3.50 e-10), and fecal metabolites (P = 0.0081) in patients following CSCPB, among which lysophosphatidylcholines (LPCs) exhibited notable changes. Particularly, we identified a potential regulatory function of the microbiota on LPC metabolism, which further influences the postoperative risk. The predictive model for intensive care unit stay duration achieved a mean absolute error of 1.27 days and an R&#xb2; of 0.63, suggesting its utility in assessing postoperative risk. Also, our study provides a valuable resource (catalogue GM3C) for further investigation into potential medical targets in CSCPB patients, comprising more than 2,000 metagenome-assembled genomes and 3 million unigenes.<br><br>CONCLUSIONS: Our study reveals that the gut microbiome and LPC-centered metabolism form a functional network influencing postoperative risk in CSCPB patients. These findings underscore the role of gut-derived signals in modulating noninfectious inflammatory responses and host imbalance, offering a multiomics framework for decoding systemic complications beyond classical sepsis paradigms.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov (NCT04032938). Registered 25 July 2019, https://clinicaltrials.gov/study/NCT04032938#study-record-dates .},
}
@article {pmid41165913,
year = {2025},
author = {de Farias, BO and Dos Santos Lopes, E and Pereira, BC and Pimenta, RL and Parente, CET and Seldin, L and Saggioro, EM},
title = {Poultry slaughterhouse wastewater as a driver of bacterial community shifts and the spread of antibiotic resistance genes in aquatic ecosystems.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {11},
pages = {1268},
pmid = {41165913},
issn = {1573-2959},
mesh = {*Wastewater/microbiology ; Animals ; *Abattoirs ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Poultry ; Genes, Bacterial ; Waste Disposal, Fluid ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Anti-Bacterial Agents ; *Water Microbiology ; Microbiota ; },
abstract = {Poultry slaughterhouse wastewater (PSW) is a source of environmental pollutants, harboring pathogens and antibiotic resistance genes (ARGs). This study aimed to assess the effects of conventional biological treatment of PSW on the bacterial community and its efficiency in removing ARGs, as well as to evaluate the impact of its discharge on the receiving river. Samples were collected from raw sewage, treated effluent, and upstream and downstream river sites. Total metagenomic DNA was extracted for real-time PCR quantification of 16S rRNA, yccT gene (Escherichia coli), and ARGs, which were selected based on their ability to confer resistance to clinically relevant antibiotics and their prevalence in poultry-associated environments, including resistance to tetracyclines (tetM), beta-lactams (blaTEM), sulfonamides (sul1), and quinolones (qnrS). Amplicon sequencing of 16S rRNA V3-V4 region was used to assess bacterial community structure. Treated effluent significantly altered the downstream microbiome, reducing bacterial richness by up to 72.3% and diversity by 25.4%. Effluent-associated phyla such as Pseudomonadota (37%), Bacillota (28%), and Bacteroidota (26%) became dominant in the downstream river samples. Enterobacterales increased after treatment, and E. coli increased by 2.93 logs downstream. All ARGs increased after treatment and remained elevated downstream, with qnrS and sul1 rising by 3.77 and 3.87 logs, respectively. These findings highlight PSW treatment plants as a potential point of selection and dissemination of antimicrobial resistance (AMR)-related bacteria and genes. Inefficient treatment contributes to shifts in river bacterial communities and the spread of AMR.},
}
@article {pmid41164885,
year = {2025},
author = {Hosseinkhani, F and Chevalier, C and Marizzoni, M and Park, R and Bos, S and Dunjko, AK and van Duijn, CM and Harms, AC and Frisoni, GB and Hankemeier, T},
title = {Plasma and feces multiomics unveil cognition-associated perturbations of chronic inflammatory pathways of the gut-microbiota-brain axis.},
journal = {Alzheimer's &amp; dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {10},
pages = {e70844},
pmid = {41164885},
issn = {1552-5279},
support = {184.034.019//Dutch Research Council (NWO)/ ; 175.2019.032//Dutch Research Council (NWO)/ ; //Private Foundation of Geneva University Hospitals: A.P.R.A.-Association Suisse pour la Recherche sur la Maladie d'Alzheimer, Gen&#xe8;ve/ ; //Fondation Segr&#xe9;, Gen&#xe8;ve/ ; //Race Against Dementia Foundation, London, UK/ ; //Fondation Child Care, Gen&#xe8;ve/ ; //Fondation Edmond J. Safra, Gen&#xe8;ve/ ; //Fondation Minkoff, Gen&#xe8;ve/ ; //Fondazione Agusta, Lugano/ ; //McCall Macbain Foundation, Canada/ ; //Nicole et Ren&#xe9; Keller, Gen&#xe8;ve/ ; //Fondation AETAS, Gen&#xe8;ve/ ; //Clinical Research Center, University Hospital and Faculty of Medicine/ ; //Italian Ministry of Health (Ricerca Corrente)/ ; //H&#xf4;pitaux Universitaires de Gen&#xe8;ve/ ; 175.2019.032//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology/chemistry ; Male ; Female ; *Dysbiosis/metabolism ; *Cognitive Dysfunction/metabolism/microbiology ; Aged ; *Inflammation/metabolism ; *Brain/metabolism ; Cytokines/blood ; Multiomics ; },
abstract = {INTRODUCTION: Gut-microbiota dysbiosis has been linked to cognitive decline. Given its role in metabolism, immunity, and environmental interactions, broader molecular signaling alterations are likely.<br><br>METHODS: We analyzed gut microbiota composition, plasma and fecal metabolites, and inflammatory cytokines across cognitive stages, from healthy controls to dementia.<br><br>RESULTS: Alpha diversity declined with increasing cognitive impairment severity. Short-chain fatty acid-producing Firmicutes and Bacteroidota decreased from 76% and 17% in controls to 59% and 11% in dementia, respectively. Proteobacteria (e.g., Escherichia-Shigella) rose from&#xa0;<&#xa0;2% to 4%, and Verrucomicrobiota from 3% to 11%. Despite overall Firmicutes decline, Ruminococcus gnavus, a mucus-degrading species, increased in dementia. These shifts correlated with elevated plasma cytokines, suggesting a link between gut dysbiosis and systemic inflammation. Bacteria-associated metabolites, including bile acids, trimethylamine N-oxide, oxylipins, sugars, and fatty acids were significantly altered. Changes were seen as early as subjective cognitive decline.<br><br>DISCUSSION: Larger studies are needed to validate these findings and explore microbiome-based interventions.<br><br>HIGHLIGHTS: Examined gut microbiota, inflammation, and metabolic changes in cognitive impairment stages Early metabolic changes in feces detected before plasma alterations Observed shifts in gut microbiota and inflammation associated with cognitive decline Suggests potential for early biomarkers based on gut metabolites Calls for larger, longitudinal studies to validate findings.},
}
@article {pmid41164876,
year = {2025},
author = {Chen, H and Lu, Z and Xiao, C and Wang, X and Xi, Y and Yan, Y and Zheng, JS and Chen, YM and Deng, K},
title = {Association Between Alternative Complement Pathway and Carotid Plaque and the Underlying Gut Microbial and Inflammatory Biomarkers: A Cohort Study.},
journal = {Arteriosclerosis, thrombosis, and vascular biology},
volume = {45},
number = {12},
pages = {e594-e607},
doi = {10.1161/ATVBAHA.125.322968},
pmid = {41164876},
issn = {1524-4636},
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome ; Middle Aged ; *Plaque, Atherosclerotic ; *Carotid Artery Diseases/immunology/microbiology/diagnostic imaging/blood/genetics/epidemiology ; Biomarkers/blood ; Prospective Studies ; Aged ; China/epidemiology ; *Complement Pathway, Alternative/genetics ; *Inflammation Mediators/blood ; Mendelian Randomization Analysis ; Risk Factors ; Longitudinal Studies ; Complement C3 ; *Inflammation/blood ; },
abstract = {BACKGROUND: The alternative pathway (AP) plays a crucial role in triggering complement activation and promoting chronic inflammation. This study aims to investigate the longitudinal association between AP and atherosclerosis, and explore the potential role of gut microbiota and inflammatory factors in their association.<br><br>METHOD: This study was based on a 9-year prospective cohort of 3382 participants from Guangzhou, China (mean age&#xb1;SD, 57.75&#xb1;5.85 years; 68.8% female), with data on serum APACPs (AP-associated complement proteins) and carotid plaque (measured by ultrasound) repeatedly measured up to 3&#xd7;. Baseline inflammatory markers were evaluated in 923 participants, and gut shotgun metagenome data were obtained from 1567 participants. Mendelian randomization analysis was performed using genome-wide significant genetic variants as instrumental variables to suggest potential causal associations.<br><br>RESULTS: Both longitudinal and prospective analyses consistently demonstrated positive associations between carotid plaque and 3 complement components: C3 (complement C3; odds ratios [95% Cl] for the highest versus lowest quartiles, 1.36 [1.07-1.74] in longitudinal analysis and 1.29 [1.06-1.56] in prospective analysis), CFB (complement factor B; 1.36 [1.07-1.72] in longitudinal analysis and 1.39 [1.15-1.69] in prospective analysis), and CFH (complement factor H; 1.39 [1.10-1.76] in longitudinal analysis and 1.31 [1.07-1.61] in prospective analysis). Mendelian randomization analysis suggested a potential causal association between CFB and carotid plaque. Inflammatory factors (CRP [C-reactive protein] and IL-6 [interleukin-6]) and microbial species (Ruminococcus bromii, Roseburia hominis, Rothia mucilaginosa, Collinsella stercoris, Olsenella scatoligenes, and Bacteroides massiliensis) were significantly associated with both APACPs and carotid plaque (P<0.05). For example, butyrate-producing bacterium R bromii was inversely associated with CFB and carotid plaque (odds ratios [95% CI], 0.83 [0.79-0.88]) and may mediate the CFB-carotid plaque association (proportion mediated, 13.5%; P=0.005). Microbial risk score (weighted sum of selected microbial species; proportion mediated, 42.6%; P<0.001) and total immune factors (the sum of all inflammatory factors; proportion mediated, 19.0%; P=0.002) mediated the association between Total-APACPs (sum of standardized carotid plaque-related APACPs [C3, CFB, and CFH]) and carotid plaque.<br><br>CONCLUSIONS: Our study showed a negative association between the AP and carotid plaque in a longitudinal cohort. Gut microbiota and inflammatory biomarkers may provide mechanistic insights into the association between the AP and atherosclerosis. Our findings pave the way for the development of new therapeutic targets for atherosclerosis.},
}
@article {pmid41163852,
year = {2025},
author = {Yuan, M and Wang, Q and Lu, Y and Xu, P and Pan, C and Zhang, W and Lu, H},
title = {Comparison of gut viral communities between autism spectrum disorder and healthy children.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1660970},
pmid = {41163852},
issn = {2235-2988},
mesh = {Humans ; *Autism Spectrum Disorder/virology ; Feces/virology ; *Gastrointestinal Microbiome ; Child ; Phylogeny ; *Viruses/classification/genetics/isolation &amp; purification ; Male ; *Virome ; Female ; Metagenomics ; Child, Preschool ; Case-Control Studies ; },
abstract = {INTRODUCTION: Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder, which brings a great burden to the family and society. Gut microbiota is considered to be an important factor in ASD that easily affects function and development of the immune, metabolic, and nervous systems. However, most available studies have mainly focused on the altered gut bacteria, our knowledge of gut viruses in ASD children remains limited.<br><br>METHODS: In this study, we collected fecal samples from ASD children and healthy controls, then analyzed and compared the differences of the gut viral communities between the two groups by viral metagenomic techniques.<br><br>RESULTS: The alpha diversity of the ASD virome was lower than that of the healthy virome, and the beta diversity had a significant difference between ASD and healthy children. Podoviridae accounted for the highest proportion of viruses in ASD patients, while Alphaflexiviridae was dominant in healthy controls. There was a statistical difference in the abundance of Microviridae between the two groups. Additionally, human astrovirus, picobirnavirus, and norovirus were detected by phylogenetic analysis.<br><br>DISCUSSION: This study revealed that alpha diversity was reduced in children with ASD, and different compositions in gut viral communities were observed between ASD patients and healthy controls. Changes in viral diversity and composition deepen our understanding of the differences in the gut viral communities between ASD and healthy children, and also provides a perspective for further exploration of viruses related to ASD children.},
}
@article {pmid41163226,
year = {2025},
author = {Huang, S and Chen, Y and Lu, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Zhang, W},
title = {Virome of canine lymph nodes: identification of viruses with zoonotic potential.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {350},
pmid = {41163226},
issn = {1743-422X},
support = {Nos. 2023YFD1801300 and 2022YFC2603801//National Key Research and Development Programs of China/ ; no. 82341106//National Natural Science Foundation of China/ ; },
mesh = {Dogs ; Animals ; *Lymph Nodes/virology ; Phylogeny ; *Virome ; *Zoonoses/virology ; Genome, Viral ; China ; Humans ; *Viruses/genetics/classification/isolation &amp; purification ; *Dog Diseases/virology ; Metagenomics ; *Viral Zoonoses/virology/transmission ; },
abstract = {BACKGROUND: Zoonotic infectious diseases have significantly impacted global public health, as exemplified by the COVID-19 pandemic that triggered an unprecedented worldwide crisis with millions of infections. Among animals closely associated with humans, canines occupy a prominent position due to their extensive integration into human daily life. Consequently, investigating the virome of canines in close contact with humans holds significant scientific and public health implications.<br><br>RESULTS: This study selected lymph node tissues from 24 dogs in close contact with humans from Shanghai and Henan, specifically collecting submandibular lymph nodes and carefully removing surrounding fat and connective tissues. Through comprehensive metagenomic analysis, we assembled 17 complete viral genomes spanning 6 viral families, including Adenoviridae (n&#x2009;=&#x2009;1), Paramyxoviridae (n&#x2009;=&#x2009;1), Polyomaviridae (n&#x2009;=&#x2009;1), Parvoviridae (n&#x2009;=&#x2009;7), Circoviridae (n&#x2009;=&#x2009;6), and Genomoviridae (n&#x2009;=&#x2009;1). Phylogenetic analysis of these dominant viruses elucidated the evolutionary relationships between the assembled viral sequences in this study and known reference viruses. Notably, we discovered a novel virus belonging to the Genomoviridae family.<br><br>CONCLUSION: This research not only elucidates the remarkable diversity of the virome within canine lymph node tissues but also employs phylogenetic analysis to delineate the evolutionary relationships between these viruses and previously documented strains. Notably, this study represents the first identification of parvoviruses and circoviruses in canine lymph nodes that exhibit high sequence homology with human viral strains, suggesting that these canine-derived and human-associated viruses may have diverged from a common ancestor.},
}
@article {pmid41163171,
year = {2025},
author = {Qiu, X and Zhang, M and Zhang, L and Chen, H and Gao, M and Li, W and Yu, Z and Hou, Z},
title = {Peculiarities of vaginal microbiota in perimenopausal and postmenopausal women with type 2 diabetes mellitus.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {24},
number = {1},
pages = {59},
pmid = {41163171},
issn = {1476-0711},
support = {H2020206490//Natural Science Foundation of Hebei Province,China/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; 2024YFC2510600//Key R&amp;D Program of the China Ministry of Science and Technology/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Diabetes Mellitus, Type 2/microbiology ; Middle Aged ; *Postmenopause ; *Microbiota ; *Perimenopause ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: The changes in the vaginal microbiota and potential dysbiosis adjustment strategies in diabetic patients remain inconclusive. This study was designed to investigate the impact of Type 2 diabetes mellitus (T2DM) on the ecological dynamics of the vaginal microbiota in perimenopausal and postmenopausal women, with a focus on microbial community structure and functional homeostasis.<br><br>METHODS: Vaginal secretion samples from 22 T2DM patients (DM group) and 23 healthy controls (CT group) under perimenopausal and postmenopausal conditions were analyzed via metagenomic sequencing. Alpha diversity (Observe, ACE, Shannon-Weaver, Gini-Simpson indices) and beta diversity (PCoA, NMDS) were assessed. Taxonomic profiling, LEfSe analysis, and co-occurrence network construction were performed to identify differential species and microbial interactions. Neutral community modeling evaluated stochastic vs. deterministic assembly processes.<br><br>RESULTS: No significant differences were observed in age (62.22&#x2009;&#xb1;&#x2009;5.74 vs. 58.23&#x2009;&#xb1;&#x2009;7.55, p&#x2009;=&#x2009;0.052) or perimenopausal/ postmenopausal status (3/19 vs. 5/18, p&#x2009;=&#x2009;0.748) between the DM and CT groups. The DM group exhibited significantly higher alpha diversity (p&#x2009;<&#x2009;0.05) and distinct beta diversity clustering (p&#x2009;<&#x2009;0.05), marked by reduced Lactobacillus relative abundance (28.7% in CT vs. 6.3% in DM) and increased abundance of opportunistic pathogenic genera (Klebsiella, Gardnerella, Staphylococcus). LEfSe identified Firmicutes as CT biomarkers, while the relative abundance of Bacteroidetes and Prevotella increased in DM group. Both fasting blood glucose and HbA1c levels significantly influenced the relative abundance of vaginal Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus iners, showing a significant negative correlation. Co-occurrence networks revealed greater complexity and more integrated in the DM group (more triangles, lower modularity, higher node degrees, higher clustering coefficients, p&#x2009;<&#x2009;0.0001). Neutral modeling indicated stochastic assembly (R&#xb2; >0.5), with Lactobacillus species and opportunistic pathogens deviating from neutral predictions in DM.<br><br>CONCLUSION: Under perimenopausal and postmenopausal conditions, T2DM disrupts vaginal microbiota homeostasis by diminishing protective Lactobacillus populations and promoting pathogen proliferation.},
}
@article {pmid41163130,
year = {2025},
author = {Cole, J and Raguideau, S and Abbaszadeh-Dahaji, P and Hilton, S and Muscatt, G and Mushinski, RM and Nilsson, RH and Ryan, MH and Quince, C and Bending, GD},
title = {Comparative genomic analysis of a metagenome-assembled genome reveals distinctive symbiotic traits in a Mucoromycotina fine root endophyte arbuscular mycorrhizal fungus.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {967},
pmid = {41163130},
issn = {1471-2164},
support = {BB/T00746X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP180103157//Australian Research Council/ ; DP180103157//Australian Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; NE/S010270/1//Natural Environment Research Council/ ; },
mesh = {*Mycorrhizae/genetics/physiology ; *Symbiosis/genetics ; *Plant Roots/microbiology ; Phylogeny ; *Endophytes/genetics ; *Genomics ; *Metagenome ; *Genome, Fungal ; Glomeromycota/genetics ; },
abstract = {BACKGROUND: Recent evidence shows that arbuscular mycorrhizal (AM) symbiosis, as defined by the presence of arbuscules, is established by two distinct fungal groups, with the distinctive 'fine root endophyte' morphotype formed by fungi from the subphylum Mucoromycotina rather than the sub-phylum Glomeromycotina. While FRE forming fungi are globally distributed, there is currently no understanding of the genomic basis for their symbiosis or how this symbiosis compares to that of other mycorrhizal symbionts.<br><br>RESULTS: We used culture-independent metagenome sequencing to assemble and characterise the metagenome-assembled genome (MAG) of a putative arbuscule forming fine root endophyte, which we show belonged to the family Planticonsortiaceae within the order Densosporales. The MAG shares key traits with Glomeromycotina fungi, which indicate obligate biotrophy, including the absence of fatty acid and thiamine biosynthesis pathways, limited enzymatic abilities to degrade plant cell walls, and a high abundance of calcium transporters. In contrast to Glomeromycotina fungi, it exhibits a higher capacity for degradation of microbial cell walls, a complete cellulose degradation pathway, low abundances of copper, nitrate and ammonium transporters, and a complete pathway for vitamin B6 biosynthesis.<br><br>CONCLUSION: These differences, particularly those typically associated with saprotrophic functions, highlight the potential for contrasting interactions between Mucoromycotina and Glomeromycotina fungi with their host plant and the environment. In turn, this could support niche differentiation in resource acquisition and complementary ecological functions.},
}
@article {pmid41162595,
year = {2025},
author = {Wang, C and Yang, S and Liu, Q and Liu, H and Wang, H and Ma, S and Li, J and Cui, L},
title = {Metagenomic next-generation sequencing reveals respiratory flora distribution in COVID-19.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37813},
pmid = {41162595},
issn = {2045-2322},
support = {61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; 61771022, 62071011//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *COVID-19/microbiology/virology/diagnosis ; Middle Aged ; Male ; Female ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Aged ; SARS-CoV-2/isolation &amp; purification ; Adult ; *Respiratory Tract Infections/microbiology ; *Microbiota/genetics ; },
abstract = {This retrospective study compared metagenomic next-generation sequencing (mNGS) and traditional culture for pathogen detection in 43 patients with lower respiratory tract infections (LRTI), including 34 COVID-19 cases (14 critical, 20 non-critical) and 9 non-COVID controls. mNGS demonstrated superior sensitivity (95.35% vs. 81.08%) and broader pathogen coverage, identifying 36.36% of bacteria and 74.07% of fungi detected by cultures. Concordance between methods was observed in 63% of cases. Severe COVID-19 patients exhibited reduced respiratory microbiota abundance, potentially linked to viral dominance or therapeutic interventions. Clinical outcomes correlated positively with inflammatory markers (procalcitonin/PCT, N-terminal pro-B-type natriuretic peptide/N-proBNP, neutrophils, lactate dehydrogenase/LDH, neutrophil-to-lymphocyte ratio/NLR) and negatively with lymphocytes, highlighting systemic inflammation's role in disease progression. While mNGS offers rapid, high-sensitivity pathogen profiling, limitations include small sample sizes, unresolved specificity concerns and unmeasured confounders. The study underscores mNGS as a promising tool for LRTI diagnosis in COVID-19, though larger prospective cohorts and standardized outcome metrics are needed to validate clinical utility, optimize interpretation, and address cost-effectiveness compared to conventional methods.},
}
@article {pmid41162178,
year = {2025},
author = {Zhang, Q and Zhang, Y and Zhu, J and Gao, Y and Zeng, W and Qi, H},
title = {Microbiome Profiling of Pretreated Human Breast Milk Using Shotgun Metagenomic Sequencing.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506012},
pmid = {41162178},
issn = {1738-8872},
mesh = {*Milk, Human/microbiology ; Humans ; Female ; *Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Metagenome ; Sequence Analysis, DNA ; Archaea/genetics/classification/isolation &amp; purification ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {This study explored the metagenomic sequencing methodology for analyzing the breast milk microbiome and elucidated its composition. Twenty-two breast milk samples were collected from 11 healthy lactating women. By optimizing microbial cell wall disruption parameters and developing a nucleic acid extraction method, microbial DNA/RNA libraries were constructed and subjected to metagenomic next-generation sequencing (mNGS), microbial standards spiked into breast milk at serial dilutions served to validate the method's reliability. The sequencing data underwent rigorous quality control and classification using the Kraken2 software and a self-generated database. The breast milk microbiome was found to comprise 21 phyla, 234 genera, and 487 species, with Firmicutes and Proteobacteria being the dominant phyla. At the genus level, Staphylococcus and Streptococcus were the most abundant, while at the species level, Staphylococcus aureus, Streptococcus bradystis, and Staphylococcus epidermidis were the most prevalent. The microbial profiles of the left and right breast milk samples were consistent at the phylum, genus, and species levels. Besides common bacteria, diverse viral, eukaryotic, and archaeal sequences were also detected. Functional profiling revealed that the "lactose and galactose degradation I" pathway accumulated the highest read count, whereas the L-valine biosynthesis pathway was detected most frequently. This study provides a comprehensive understanding of the healthy breast milk microbiome, highlighting the presence of specific flora colonization and the distinct yet correlated microbial environments in bilateral breast milk, laying the groundwork for future research into the interactions between breast milk microbiota and maternal and infant health outcomes.},
}
@article {pmid41162143,
year = {2025},
author = {Hutchings, P and Rowe, CE and Byrne, M and Przeslawski, R},
title = {Taxonomy is a foundation of marine science, and it is in trouble.},
journal = {Advances in marine biology},
volume = {101},
number = {},
pages = {197-212},
doi = {10.1016/bs.amb.2025.08.003},
pmid = {41162143},
issn = {2162-5875},
mesh = {*Classification/methods ; Animals ; Conservation of Natural Resources ; *Aquatic Organisms/classification ; Biodiversity ; *Marine Biology/education ; Australia ; },
abstract = {This volume of Advances highlights not only the importance of marine benthic diversity in several regions of the world but also the impediments to describing this fauna. Taxonomy is the science of classifying organisms and is the bedrock of marine biodiversity research and conservation, yet it faces significant decline in Australia. Thus, it is critical that the scientific community understand why taxonomy is so important. This paper underscores the foundational role of taxonomy in marine ecology, using case studies that highlight its critical relevance to species management, conservation policy, and international trade regulation. Despite extensive research and funding, unresolved taxonomies continue to affect our management of ecologically and economically important taxa, including crown-of-thorns seastar (Acanthaster spp.), exploited sea cucumbers (Holothuroidea), and invasive Cassiopea jellyfish. These ambiguities hamper accurate species identification, hinder effective conservation strategies, and complicate regulatory listings under frameworks such as CITES and the IUCN Red List. Key challenges include dwindling taxonomic expertise, reduced funding, lack of university training, and limited career pathways, all of which contribute to Australia's inability to adequately explore and manage its vast marine jurisdiction. The paper advocates for immediate systemic reforms through a series of 11 recommendations related to revitalizing taxonomic education, fostering museum-university partnerships, supporting early career researchers, and investing in infrastructure to enable species discovery. Taxonomic rigor is also essential to validate modern tools like eDNA, metagenomics, and image-based analysis. Without it, efforts to safeguard biodiversity and to foster a sustainable blue economy risk failure.},
}
@article {pmid41161821,
year = {2025},
author = {Zhou, Z and Lin, JR and Li, J and Huang, X and Yuan, L and Huang, J and Xie, W and Lu, J and Huang, W and He, S and Yu, D and Zhang, H and Ge, X and Li, M and Mao, Y and Yang, F and Cui, ZK and Su, X and Zhan, Y and Liu, L},
title = {Metagenomic next-generation sequencing unraveled the characteristic of lung microbiota in patients with checkpoint inhibitor pneumonitis: results from a prospective cohort study.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {10},
pages = {},
pmid = {41161821},
issn = {2051-1426},
mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Immune Checkpoint Inhibitors/adverse effects/pharmacology ; *Lung/microbiology ; *Metagenomics/methods ; *Microbiota ; *Pneumonia/chemically induced/microbiology/diagnosis ; Prospective Studies ; },
abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) is among the most lethal immune-related adverse events in patients with cancer receiving immunotherapy. This study aims to characterize the lung microbiome in patients with CIP and evaluate its diagnostic potential.<br><br>METHODS: In a prospective clinical trial (NCT06192303), bronchoalveolar lavage fluid samples (BALF) were obtained from 38 patients presenting clinical symptoms and radiographic evidence of pneumonitis following immunotherapy. The cohort included 14 cases of pure-type CIP (PT-CIP), 14 cases of mixed-type CIP, and 10 cases of pulmonary infection (PI). Metagenomic next-generation sequencing (mNGS) of BALF was employed to delineate the lung microbiota profiles. Using linear discriminant analysis effect size, we discerned characteristic microbiota among the three groups and further explored the associations of signature microbiota with host immune-inflammatory markers. Functional enrichment analysis revealed potential metabolic reprogramming and differences in biological functions between patients with CIP and PI. Finally, leveraging four machine-learning models, we ascertained the clinical value of BALF microbiota profiles in diagnosing CIP.<br><br>RESULTS: The composition of lung microbiota differed significantly between patients with CIP and PI. Microbial taxa, such as Porphyromonas, Candida, Peptostreptococcus, Treponema, and Talaromyces, exhibited distinct abundance patterns across the three groups. Correlation analysis revealed a significant positive relationship between Candida abundance and host immune-inflammatory markers, such as neutrophil-lymphocyte ratio, platelet-lymphocyte ratio, monocyte-lymphocyte ratio, and systemic immune inflammation index. In contrast, Porphyromonas demonstrated a significant negative correlation. Compared with the patients with PT-CIP, the lung microbiota of patients with PI exhibited a more diverse biological and metabolic profile. Additionally, machine learning models based on BALF microbiota profiles could accurately diagnose CIP, with the decision tree model showing the best diagnostic performance (area under the curve: 0.88).<br><br>CONCLUSIONS: Our study represents the unique characterization of the lung microbiota profiles across distinct CIP subtypes and establishes a diagnostic model for CIP based on the decision tree. These findings emphasize the value of BALF mNGS in improving the diagnosis of CIP.},
}
@article {pmid41161274,
year = {2025},
author = {Cai, X and Yuan, X and Singh, AK and Chen, C and Zhu, X and Liu, W},
title = {Tradeoffs between microbial life-history strategies drive soil carbon cycling during revegetation in karst ecosystems: A metagenomic perspective.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127802},
doi = {10.1016/j.jenvman.2025.127802},
pmid = {41161274},
issn = {1095-8630},
mesh = {*Soil/chemistry ; *Soil Microbiology ; *Carbon Cycle ; Carbon ; Ecosystem ; Metagenomics ; Nitrogen ; Microbiota ; },
abstract = {Revegetation strongly influences the dynamics of soil organic carbon (SOC) and microbial communities. While microbial communities are known to drive carbon (C) cycling, the specific traits responsible for C stabilization and mineralization during the revegetation of degraded karst ecosystems are not well understood. This study used a combination of metagenomic and instrumental methods to investigate variations in soil physicochemical properties, organic C fractions, C-cycle microbial community traits (diversity, life strategies, and co-occurrence patterns), and C-cycling (fixation and degradation) genes across four karst ecosystems representing a revegetation chronosequence encompassing cropland, grassland, shrubland, and primary forest. Our findings demonstrated that revegetation increased total SOC and recalcitrant OC (ROC) contents, while it decreased dissolved inorganic nitrogen (DIN) and reduced the ratio of labile OC (LOC) to SOC. This indicates enhanced C pool stabilization and storage, alongside reduced soil nutrient availability. These shifts favored the development of C-cycle microbial communities with low diversity and high proportions of K-strategists, which efficiently utilize recalcitrant C under oligotrophic conditions. Consequently, the increased dominance of K-strategists redirected microbial resource acquisition, manifested in a 29 % decrease in C-fixation gene abundances (rTCA, WL, and DC/4-HB pathways) and a 27 % decrease in genes degrading labile C compounds (starch, hemicellulose, cellulose, and chitin). Conversely, genes involved in degrading recalcitrant C compounds (pectin and lignin) increased by 19 %. Furthermore, the elevated proportion of K-strategists enhanced the complexity and stability of microbial taxonomic and functional networks, potentially strengthening community resilience and nutrient cycling efficiency. These results reveal a causal link between shifts in the soil C pool and nutrient availability during revegetation and the subsequent reshaping of C-cycling microbial communities. Such restructured communities, in turn, drive the expression of genes associated with C stabilization and mineralization, thereby impacting the soil C pool. This study provides mechanistic insights into microbial-mediated biochemical processes governing soil C decomposition and stabilization in karst ecosystems, offering critical guidance for ecological restoration in these degraded and fragile regions.},
}
@article {pmid41160250,
year = {2025},
author = {Li, Y and Zhu, M and Wang, W and Xu, Q and Cui, J and Liu, L and Liu, Y and Yang, H and Liu, Y},
title = {Comparable tongue coating microbiota profiles from a simplified single-swab versus different sampling approaches: A pilot study.},
journal = {Clinical oral investigations},
volume = {29},
number = {11},
pages = {543},
pmid = {41160250},
issn = {1436-3771},
support = {GZC20233129//the Postdoctoral Fellowship Program of CPSF/ ; 82374290//National Natural Science Foundation of China/ ; Yue Liu//Young Qihuang Scholar of the "Tens of Millions" Talent Project of China/ ; },
mesh = {Humans ; Pilot Projects ; *Tongue/microbiology ; *Microbiota ; Adult ; Male ; Female ; *Specimen Handling/methods ; Reproducibility of Results ; Biofilms ; },
abstract = {OBJECTIVE: The tongue coating microbiota has emerged as a potential biomarker for systemic diseases. However, the absence of a practical and widely applicable sampling protocol hinders cross-study comparability and limits clinical application. This pilot study aimed to evaluate the reliability of different sampling methods.<br><br>MATERIALS AND METHODS: Tongue coating samples were collected from healthy adults using four different methods, including single and multiple scrapes with sterile swabs or scraper. Metagenomic sequencing was performed to assess microbial diversity, taxonomic composition, and predicted functional profiles. DNA extraction quality, alpha- and beta-diversity metrics, taxonomic abundance at the genus and species levels, and KEGG-based functional predictions were analyzed. Spatial and structural features of the tongue biofilm were considered to interpret microbial sampling consistency.<br><br>RESULTS: The single-scrape method yielded comparable microbial profiles to multi-scrape methods, with no significant differences in alpha-diversity or beta-diversity. Taxonomic compositions at both genus and species levels were consistent across groups, with dominant taxa including Streptococcus, Prevotella, and Rothia. Functional prediction via KEGG annotation revealed minimal variation among groups, with only a few metabolic pathways showing statistically significant differences. These findings highlight the spatial stability and representative sampling potential of the tongue coating microbiota.<br><br>CONCLUSIONS: A single scrape using a sterile flocked swab provides a practical, reproducible, and cost-effective approach for tongue coating microbiota sampling. These pilot findings suggest that this simplified method yields representative microbiome data in healthy adults, although validation in larger and more diverse cohorts is required before clinical application.<br><br>CLINICAL RELEVANCE: This study demonstrates that a single-scrape sampling method yields tongue coating microbiota profiles comparable to conventional multi-scrape protocols. The findings support its potential for standardizing sampling in future large-scale studies.<br><br>TRIAL REGISTRATION: ITMCTR2024000616.},
}
@article {pmid41160143,
year = {2025},
author = {Begum, M and Barsha, KF and Rahman, MM and Sarkar, MMH and Chowdhury, SF and Bhowmik, S and Shormi, AS and Bari, SM},
title = {Gut microbiome profiling of antibiotic-treated Mystus cavasius using culture-based and shotgun metagenomic approaches.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {183},
pmid = {41160143},
issn = {1572-9699},
mesh = {*Anti-Bacterial Agents/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics/methods ; *Bacteria/classification/genetics/drug effects/isolation &amp; purification ; Phylogeny ; Aquaculture ; *Catfishes/microbiology ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; },
abstract = {Antibiotic use in aquaculture prevents disease and promotes growth but can disrupt the gut microbiome and drive resistance. The study profiled the gut microbiome of antibiotic-treated Mystus cavasius using both culture-based and shotgun metagenomic approach. Culture-dependent analysis revealed a significant 2-threefold reduction in total viable bacterial count in treated fish. Phylogenetic analysis of 12 cultured isolates revealed treatment-driven enrichment of Bacillus, Enterobacter and Aeromonas. Antibiotic susceptibility testing further revealed increased resistance profiles among isolates from treated fish. Metagenomic profiling identified over 1400 bacterial species and revealed clear taxonomic shifts. Control groups were enriched with beneficial genera such as Lactiplantibacillus and Arthrospira, while treated fish were dominated by opportunistic or resistant taxa including Plesiomonas, Staphylococcus, and Acinetobacter. These shifts were further reflected at the phylum level, with a decline in Proteobacteria and Bacteroidetes, accompanied by an increase in Firmicutes and the enrichment of antibiotic-tolerant lineages. Treated samples exhibited more uniform alpha diversity indices, suggesting a restructuring of the microbial community hierarchy following oxytetracycline exposure, whereas beta diversity analysis showed a moderate separation between control and treated groups. These findings provide critical insights into the ecological and health risks of antibiotic use in aquaculture and underscore the importance of developing sustainable alternatives for disease management in fish farming.},
}
@article {pmid41159664,
year = {2025},
author = {Schwab, C and Lang, H and Stegmüller, S and Hosek, J and Marietou, A and Huertas-Díaz, L and Li, Q and Krings, APS and Zander, A and Kræmer Sundekilde, U and Richling, E},
title = {Microbial Transformation of Dietary Glycerol Contributes to Intestinal Acrolein Formation and Urinary Excretion.},
journal = {Molecular nutrition &amp; food research},
volume = {69},
number = {24},
pages = {e70289},
pmid = {41159664},
issn = {1613-4133},
support = {RI 1176/12-1//Deutsche Forschungsgemeinschaft DFG/ ; RI 1176/13-1//Deutsche Forschungsgemeinschaft DFG/ ; },
mesh = {*Acrolein/metabolism/urine ; Humans ; *Glycerol/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology/chemistry ; Male ; Adult ; Female ; Biomarkers/urine ; Diet ; Acetylcysteine/urine/analogs &amp; derivatives ; *Intestines/microbiology ; Middle Aged ; Young Adult ; },
abstract = {The aldehyde acrolein has been associated with diabetes, cardiovascular, respiratory, and neurodegenerative diseases, and gut microbiota possesses the potential for acrolein release via the key enzyme glycerol/diol dehydratase (PduCDE). This study aimed at estimating the contribution of gut microbiota to endogenous acrolein production. To minimize confounding sources, we investigated the intestinal acrolein-producing potential of 20 volunteers housed under defined conditions. Glycerol was present in every meal and was detected in feces, suggesting availability to intestinal microbiota. Based on fecal metagenomics and pduC analysis, all volunteers showed potential for intestinal glycerol transformation to acrolein; the genus Anaerobutyricum was the major contributor across donors and time. Levels of urine biomarkers N-acetyl-S-(3-hydroxypropyl)-L-cysteine (3-HPMA) and N-acetyl-S-(carboxyethyl)-L-cysteine (CEMA) were higher after the consumption of meals with high glycerol levels, suggesting immediate microbial transformation to acrolein. Only a small proportion of acrolein metabolites was recovered in urine, possibly due to high compound reactivity. Donors could be separated into 3-HPMA or CEMA phenotypes based on the predominance of urine biomarkers, and phenotypes related to overall fecal microbiota and fermentation metabolite profiles. Our data show that oral fat/glycerol intake together with intestinal microbiota activity might temporarily increase endogenous acrolein formation and that urinary biomarkers link to the intestinal microbiome.},
}
@article {pmid41159034,
year = {2025},
author = {Peipert, D and Montgomery, TL and Toppen, LC and Lee, MFJ and Scarborough, MJ and Krementsov, DN},
title = {Colonization by Akkermansia muciniphila modulates central nervous system autoimmunity in an ecological context-dependent manner.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1655428},
pmid = {41159034},
issn = {1664-3224},
mesh = {Animals ; *Encephalomyelitis, Autoimmune, Experimental/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity ; Mice ; Mice, Inbred C57BL ; *Central Nervous System/immunology/microbiology ; *Multiple Sclerosis/immunology/microbiology ; Female ; Akkermansia ; *Verrucomicrobia/immunology ; Disease Models, Animal ; },
abstract = {INTRODUCTION: Multiple sclerosis is autoimmune disease of the central nervous system (CNS) in which myelin-reactive immune attack drives demyelination and subsequent disability. Various studies have documented elevated abundance of the commensal gut bacterium Akkermansia muciniphila (A. muciniphila) in people with multiple sclerosis compared to healthy control subjects, suggesting that its elevated abundance may be a risk factor for the development of CNS autoimmunity. However, A. muciniphila is considered beneficial in various other pathological contexts, and recent studies suggest that A. muciniphila may be paradoxically associated with reduced disability and progression in multiple sclerosis. Moreover, experimental modulation of A. muciniphila levels in experimental autoimmune encephalomyelitis (EAE), an autoimmune model of multiple sclerosis, has generated conflicting results, suggesting that the effects of this microbe on CNS autoimmunity could be context-dependent.<br><br>METHODS: To address this possibility, we generated two distinct microbiome models in C57BL/6J mice, each stably colonized by A. muciniphila or A. muciniphila-free, providing divergent ecological contexts in which A. muciniphila may exert a differential impact. We used EAE, flow cytometry, full-length 16S DNA sequencing, and mass spectrometry to assess the impact of A. muciniphila colonization on neurological outcomes, immune responses, gut microbiome composition, and short-chain fatty acid (SCFA) production, respectively. Dietary intervention was used to assess the functional consequences of differences in gut microbiota metabolic capacity.<br><br>RESULTS: We found that A. muciniphila colonization increased EAE severity only in a specific microbiome context, in conjunction with increased Th17 responses and CNS-infiltrating immune cells. Profiling of gut microbiome composition revealed that A. muciniphila colonization drove a reduction of Clostridia, key producers of SCFAs, specifically in the microbiome model in which A. muciniphila exacerbates EAE. Inferred metagenomic analyses suggested reduced SCFA production in the presence of A. muciniphila, which was confirmed by mass spectrometry. Consistently, provision of high dietary fiber as a substrate for SCFA production suppressed EAE only in the context of the Clostridia-rich microbiome sensitive to A. muciniphila colonization.<br><br>DISCUSSION: Taken together, our data suggest that the effect of A. muciniphila on CNS autoimmunity is highly dependent on the overall composition of the gut microbiome and suggest that this microbe may contribute to decreased gut SCFA metabolism in multiple sclerosis.},
}
@article {pmid41157632,
year = {2025},
author = {Apanasevich, M and Dubovitskiy, N and Derko, A and Khozyainova, A and Tarasov, A and Kokhanenko, A and Artemov, G and Denisov, E and Shestopalov, A and Sharshov, K},
title = {Genomic Characterization of a Novel Yezo Virus Revealed in Ixodes pavlovskyi Tick Virome in Western Siberia.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
pmid = {41157632},
issn = {1999-4915},
support = {23-64-00005//Russian Science Foundation/ ; 225020408196-1//State-funded budget project/ ; },
mesh = {*Ixodes/virology ; Animals ; Phylogeny ; *Genome, Viral ; Siberia ; *Virome/genetics ; Encephalitis Viruses, Tick-Borne/genetics/isolation &amp; purification/classification ; Metagenomics ; Genomics ; Humans ; Encephalitis, Tick-Borne/virology ; },
abstract = {Ixodid ticks are blood-sucking ectoparasites of vertebrates. They constitute an integral part of natural foci and are responsible for the worldwide transmission of infections to humans, which can result in severe symptoms. For instance, the Tomsk region, where three abundant tick species (Dermacentor reticulatus, Ixodes pavlovskyi, I. persulcatus) occur, is an endemic area for tick-borne encephalitis virus (TBEV). An increasing number of novel infectious agents carried by ticks have been identified using metagenomic sequencing. A notable example is the Yezo virus (Orthonairovirus yezoense, YEZV), which was discovered in patients with fever after tick bites in Japan and China between 2014 and 2025. For the first time, we have performed metagenomic sequencing of the virome of ticks collected in the Tomsk region. In a sample obtained from a pool of I. pavlovskyi ticks, all three segments of the YEZV genome were detected. The phylogenetic analysis showed that the newly identified isolate formed a sister group to previously described virus isolates, indicating the presence of a new genetic variant. This study presents the first report of YEZV detection in I. pavlovskyi ticks in the Tomsk region, thereby expanding the geographical range and number of vector species for YEZV and highlighting the importance of monitoring viral agents circulating among ticks in Western Siberia.},
}
@article {pmid41157620,
year = {2025},
author = {Weary, TE and Zhou, LH and MacDonald, L and Ibañez Iv, D and Jaramillo, C and Dunn, CD and Wright, TF and Hanley, KA and Goldberg, TL and Orr, TJ},
title = {Novel Bat Adenovirus Closely Related to Canine Adenoviruses Identified via Fecal Virome Surveillance of Bats in New Mexico, USA, 2020-2021.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
pmid = {41157620},
issn = {1999-4915},
support = {RAPID Grant 2031816//U.S. National Science Foundation/ ; },
mesh = {Animals ; *Chiroptera/virology ; *Feces/virology ; *Adenoviridae/genetics/classification/isolation &amp; purification ; *Virome ; New Mexico/epidemiology ; Phylogeny ; Dogs ; COVID-19/epidemiology/virology ; Adenoviridae Infections/veterinary/virology/epidemiology ; Metagenomics ; SARS-CoV-2 ; Humans ; },
abstract = {Bats host a wide range of viruses, including several high-profile pathogens of humans and other animals. The COVID-19 pandemic raised the level of concern regarding the risk of spillover of bat-borne viruses to humans and, conversely, human-borne viruses to bats. From August 2020 to July 2021, we conducted viral surveillance on 254 bats from 10 species across urban, periurban, and rural environments in New Mexico, USA. We used a pan-coronavirus RT-PCR to assay rectal swabs and performed metagenomic sequencing on a representative subset of 14 rectal swabs and colon samples. No coronaviruses were detected by either RT-PCR or metagenomic sequencing. However, four novel viruses were identified: an adenovirus (proposed name lacepfus virus, LCPV), an adeno-associated virus (AAV), an astrovirus (AstV), and a genomovirus (GV). LCPV, detected in a big brown bat (Eptesicus fuscus), is more closely related to canine adenoviruses than to other bat adenoviruses, suggesting historical transmission between bats and dogs. All virus-positive bats were either juvenile or adult individuals captured in urban environments; none exhibited obvious clinical signs of disease. Our findings suggest limited or no circulation of enzootic coronaviruses or SARS-CoV-2 in southwestern U.S. bat populations during the study period. The discovery of a genetically distinct adenovirus related to canine adenoviruses highlights the potential for cross-species viral transmission and underscores the value of continued virome surveillance in animals living with and near humans.},
}
@article {pmid41157605,
year = {2025},
author = {Zisi, Z and Ruiz Movilla, I and Basler, N and Close, L and Ghijselings, L and Van der Hoeven, R and Papadaki, MI and Rabbinowitsch, E and Van Reeth, F and Swinnen, J and Vogel, E and Vos, C and Hanssen, I and Matthijnssens, J},
title = {Metagenomics Study of the Commercial Tomato Virome Focused on Virus Species of Epidemiological Interest.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
pmid = {41157605},
issn = {1999-4915},
support = {Baekeland Mandate number HBC.2020.2306//Flanders Innovation and Entrepreneurship/ ; },
mesh = {*Solanum lycopersicum/virology ; *Virome/genetics ; *Metagenomics ; Phylogeny ; *Plant Diseases/virology ; Genome, Viral ; *Plant Viruses/genetics/classification/isolation &amp; purification ; Genotype ; Genetic Variation ; },
abstract = {Plant viruses have detrimental effects on commercial tomato cultivation leading to severe economic consequences. Viral metagenomics studies provide the opportunity to examine in depth the virome composition of a sample set without any pre-existing knowledge of the viral species that are present. In the present study, 101 plant samples were collected from commercial greenhouses in 13 countries in Europe, Africa, Asia, and North America between 2017 and 2024. All samples were processed with the VLP enrichment protocol NetoVIR and the obtained data were analyzed with the ViPER pipeline. Forty-three eukaryotic viral species were identified, with a median identification of 2 species per sample. The most prevalent viral species were pepino mosaic virus (PepMV), tomato brown rugose fruit virus (ToBRFV), and southern tomato virus (STV). The obtained genome sequences were used to study the diversity and phylogeny of these viruses. The three genotypes identified for PepMV showed low diversity within each genotype (96.2-99.0% nucleotide identity). Low isolate diversity was also found for ToBRFV and STV. No significant association could be found between STV identification and the presence of symptoms, questioning the pathogenic potential of STV. Three other pathogenic viral species of particular interest due to their effects on tomato cultivation or recent emergence, namely tomato torrado virus (ToTV), tomato fruit blotch virus (ToFBV), and cucumber mosaic virus (CMV), were part of the virome with low prevalence. Our study provided a comprehensive overview of the analyzed samples' virome, as well as the possibility to inspect the genetic diversity of the identified viral genomes and to look into their potential role in symptom development.},
}
@article {pmid41157584,
year = {2025},
author = {Haisi, A and Nogueira, MF and Possebon, FS and Junior, JPA and Marinho-Prado, JS},
title = {Viral Community and Novel Viral Genomes Associated with the Sugarcane Weevil, Sphenophorus levis (Coleoptera: Curculionidae) in Brazil.},
journal = {Viruses},
volume = {17},
number = {10},
pages = {},
pmid = {41157584},
issn = {1999-4915},
support = {202271250010//Parliamentary Amendment from the S&#xe3;o Paulo State Delegation/ ; 405786/2022-0//National Council for Scientific and Technological Development/ ; 23/2551-0002221-4//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado do Rio Grande do Sul - INCT-One Fapergs/ ; },
mesh = {Animals ; *Weevils/virology ; Brazil ; *Genome, Viral ; Saccharum/parasitology ; *Virome ; Metagenomics ; Phylogeny ; },
abstract = {Sphenophorus levis, commonly known as the sugarcane weevil, is one of the most important pests affecting Brazilian sugarcane crops. It has spread to all sugarcane-producing regions of Brazil, mainly through contaminated stalks. Effective control of this pest is difficult due to the protection conferred by the host plant during the larval stage. As a result, despite current control measures, S. levis populations continue to grow, and reports of new infestations remain frequent. Biotechnological control measures, such as the use of viruses, stands as a promising tool for pest control in agriculture. The aim of this study was to explore the RNA virome associated with S. levis using a viral metagenomic approach. Through the Read Annotation Tool (RAT) pipeline, we characterized, for the first time, the gut-associated viral community in adult weevils, identifying several novel viral genomes. Sphenophorus levis-associated virus (SLAV) had 12,414 nucleotides (nt); Sphenophorus levis tombus-like virus (SLTV) had 4085 nt; and the four genomic segments of Sphenophorus levis reo-like virus (SLRV) ranged from 2021 to 4386 nt. These genomes were assembled from 65,759 reads (SLAV), 114,441 reads (SLTV), and 270,384 reads (SLRV). Among the detected viral families, Partitiviridae was the most abundant. The identification of possible viral pathogens lays the foundation for future research into their potential use as biological control agents against S. levis.},
}
@article {pmid41156832,
year = {2025},
author = {Tokamani, M and Liakopoulos, P and Tegopoulos, K and Zigkou, AM and Triantaphyllidis, G and Kamidis, N and Grigoriou, ME and Sandaltzopoulos, R and Kolovos, P},
title = {Spatiotemporal Dynamics of Microbial and Fish Communities in the Thracian Sea Revealed by eDNA Metabarcoding.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
pmid = {41156832},
issn = {2076-2607},
support = {1671/22-03-2023//Green Fund/ ; },
abstract = {The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing across various stations in the vicinity of the Thracian Sea, in consecutive months (through spring and summer). Seawater samples were collected from the surface and thermocline layers, and environmental parameters were recorded to examine their influence on biodiversity patterns. Microbial communities exhibited strong seasonal and depth-related structuring. Alpha diversity was highest in spring and declined during summer, while beta diversity analyses revealed clear clustering by month and depth. Dominant taxa included Alphaproteobacteria (SAR11), Cyanobacteria (Synechococcus, Prochlorococcus), with distinct core microbiomes. Fish communities, identified via CytB metabarcoding, displayed marked temporal turnover but limited spatial segregation. While alpha diversity metrics did not differ significantly, beta diversity analyses showed seasonal shifts with dominant taxa such as Raja spp., Engraulis spp., and Diplodus sargus. Multivariate and co-structure analyses (Mantel, Procrustes) revealed moderate but significant concordance between microbial and fish communities and support the existence of similar biodiversity responses to environmental parameters across temporal and spatial variability. Co-occurrence networks further present depth-specific associations, with surface communities being more cooperative and phototrophic, while thermocline networks showed modularity and potential ecological specialization. This study highlights the value of integrated eDNA-based monitoring in revealing seasonal biodiversity dynamics and ecological interactions in coastal marine ecosystems, supporting future spatial planning and conservation strategies in the Thracian Sea.},
}
@article {pmid41156619,
year = {2025},
author = {Sultankulova, KT and Kozhabergenov, NS and Shynybekova, GO and Almezhanova, MD and Zhaksylyk, SB and Abayeva, MR and Chervyakova, OV and Argimbayeva, TO and Orynbayev, MB},
title = {Metagenomic Profile of Bacterial Communities of Hyalomma scupense and Hyalomma asiaticum Ticks in Kazakhstan.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
pmid = {41156619},
issn = {2076-0817},
mesh = {Animals ; Kazakhstan ; *Metagenomics/methods ; *Ixodidae/microbiology ; Male ; Female ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Cattle ; *Microbiota ; *Metagenome ; DNA, Bacterial/genetics ; },
abstract = {Ticks are important vectors of pathogens affecting humans and animals, posing a serious threat to health. For the first time, we studied the metagenomic profile of the microbial composition of Hyalomma scupense and Hyalomma asiaticum ticks in Kazakhstan. A total of 94 adult H. asiaticum and H. scupense ticks collected from randomly selected cattle in Kazakhstan in 2023 were analyzed. 16S rRNA gene sequencing was performed using the Ion Torrent NGS platform. Taxonomic classification was carried out in the BV-BRC platform with the Kraken2 database. Metagenomic analysis revealed 26 bacterial genera, including both pathogenic and symbiotic taxa. In H. scupense, the dominant groups were Francisella (89.0%), Staphylococcus (76.0%) and Candidatus Midichloria (61.0%), while in H. asiaticum, they were Francisella (99.0% and 95.0%) and Helcococcus (65.0%). In male H. scupense, the proportion of Francisella reached 89%, whereas in females, it varied from 2% to 28%. In H. asiaticum, Helcococcus accounted for 65% in males compared to 11% in females. This is the first report on the metagenomic profile of the microbiota of H. scupense and H. asiaticum in Kazakhstan. The detection of pathogens indicates a risk of their transmission to humans and animals and highlights the need to develop new tick control strategies.},
}
@article {pmid41156596,
year = {2025},
author = {Dao, TK and Pham, TTN and Nguyen, HD and Dam, QT and Phung, TBT and Nguyen, TVH and Nguyen, TQ and Hoang, KC and Do, TH},
title = {Metagenomic Analysis of the Gastrointestinal Phageome and Incorporated Dysbiosis in Children with Persistent Diarrhea of Unknown Etiology in Vietnam.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
pmid = {41156596},
issn = {2076-0817},
support = {&#x110;T&#x110;LCN.63/22//Ministry of Science and Technology, Vietnam/ ; },
mesh = {Humans ; *Diarrhea/microbiology/virology ; *Dysbiosis/microbiology/virology ; Metagenomics/methods ; Infant ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *Gastrointestinal Microbiome ; Male ; Female ; Vietnam ; Child, Preschool ; *Metagenome ; Bacteria/classification/genetics/virology ; *Virome ; Feces/microbiology/virology ; },
abstract = {Persistent diarrhea of unknown etiology in children under 2 years of age is a common problem and poses a major challenge for the health sector. However, knowledge of the composition and dysbiosis of the intestinal phageome, phage-associated bacteriome in the persistent diarrhea remains limited. In this study, a process for phage enrichment and metagenomic extraction was developed and applied to recover gut phage metagenomes from 30 healthy children and 30 children with persistent diarrhea for high-throughput sequencing. Taxonomic annotation using Kraken2 revealed that, besides Norwalk virus, Primate bocaparvovirus 1 and Human-associated gemykibivirus 2, phage communities in the diarrhea group showed reduced diversity and contained sample-dependent phages targeting Salmonella enterica, Enterobacter, Shigella flexneri, Clostridioides difficile, Pseudomonas aeruginosa, Streptococcus miti, uropathogenic Escherichia coli and functioned balancing bacterial communities. Bacterial fraction in the metagenomic datasets reflected clear patterns of dysbiosis, including a severe deficiency of beneficial bacteria, an increase in Firmicutes, a marked decline in Actinobacteria, Bacteroidetes, Proteobacteria and sample-dependent enrichment of Enterococcus, Escherichia and Acinetobacter in diarrhea cases. This study, for the first time, investigated the dynamics of gut phageome, phage-associated bacteriome in children with persistent diarrhea of unknown causes in Vietnam, providing new insight for complementary treatment.},
}
@article {pmid41156563,
year = {2025},
author = {Modrego, J and Pantoja-Arévalo, L and Gómez-Garre, D and Gesteiro, E and González-Gross, M},
title = {Dairy-Gut Microbiome Interactions: Implications for Immunity, Adverse Reactions to Food, Physical Performance and Cardiometabolic Health-A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {20},
pages = {},
pmid = {41156563},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; *Dairy Products/adverse effects ; Animals ; Milk ; Probiotics ; *Immunity ; Cardiometabolic Risk Factors ; },
abstract = {Background/Objective: Milk and fermented dairy products are widely consumed functional foods and beverages, offering not only essential nutrients but also bioactive compounds with potential to modulate host immunity, metabolism, and the gut microbiome. This narrative review aims to synthesize current knowledge on the relationship between dairy consumption, gut microbiome, immune modulation, adverse reactions to food, physical performance and cardiometabolic health. Methods: An extensive literature analysis was conducted to explore how milk and fermented dairy products modulate the gut microbiome and influence the immune and cardiometabolic health. This study synthesis focused on key dairy bioactive compounds, such as probiotics, miRNAs, milk-derived peptides and exosomes and on evaluating their proposed mechanisms of action in inflammation and metabolic regulation, and their possible influence on physical performance through gut-microbiome interactions. Additionally, advances in metagenomic and metabolomic technologies were reviewed for their potential to uncover host-microbiota interactions relevant to precision nutrition strategies. Results: Fermented dairy products have shown potential in promoting beneficial bacteria growth such as Lactobacillus and Bifidobacterium, short-chain fatty acid synthesis and reduction in proinflammatory biomarkers. Specific dairy-derived peptides and exosomal components may further support gut barrier integrity, immune regulation and improve physical performance and reduce cardiometabolic risk factors. Additionally, emerging evidence links individual gut microbiota profiles to specific metabolic responses, including tolerance to lactose and bovine milk proteins. Conclusions: Integrating microbiome science with traditional nutritional paradigms enhances our understanding of how dairy influences immune and cardiometabolic health. Overall, current evidence suggests that investigating dairy-microbiome interactions, alongside lifestyle factors such as physical activity, may inform future personalized nutrition strategies aimed at supporting metabolic and immune health.},
}
@article {pmid41155136,
year = {2025},
author = {Bitter, M and Weigel, M and Mengel, JP and Ott, B and Windhorst, AC and Tello, K and Imirzalioglu, C and Hain, T},
title = {Assessment of Microbiome-Based Pathogen Detection Using Illumina Short-Read and Nanopore Long-Read Sequencing in 144 Patients Undergoing Bronchoalveolar Lavage in a University Hospital in Germany.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
pmid = {41155136},
issn = {1422-0067},
support = {TRR 84/3 Innate Immunity of the Lung, B08//Deutsche Forschungsgemeinschaft/ ; 519/03/06.001-(0002) LOEWE-Diffusible Signals B03//Hessian Ministry of Science and Research, Arts and Culture (HMWK)/ ; MB2021 JLU TRAINEE//Faculty of Medicine at Justus Liebig University Giessen/ ; },
mesh = {Humans ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Germany ; *Bacteria/genetics/isolation &amp; purification/classification ; Hospitals, University ; Bronchoalveolar Lavage ; Nanopore Sequencing/methods ; Adult ; *Respiratory Tract Infections/microbiology/diagnosis ; Aged, 80 and over ; },
abstract = {Lower respiratory tract infections (LRTIs) represent a significant global health concern, and the accurate identification of pathogens is crucial for patient care. Culture-based methods are the gold standard, but their detection abilities are limited. Next-generation sequencing (NGS) offers a promising method for comprehensive microbial detection, providing valuable information for clinical practice. In this study, 144 bronchoalveolar lavage fluid samples were collected, culture-based diagnostics were performed, and bacterial microbiome profiles were generated by short-read sequencing of the V4 region of the 16S rRNA gene using Illumina technologies and long-read sequencing with Oxford Nanopore Technologies (ONT) to determine the full-length 16S rRNA gene. The most common genera detected by NGS included Streptococcus, Staphylococcus, Veillonella, Prevotella, Rothia, Enterococcus, and Haemophilus. Short-read sequencing detected cultured bacteria at the genus level in ~85% of cases, while long-read sequencing demonstrated agreement with cultured species in ~62% of cases. In three cases, long-read sequencing identified the uncommon potential lung pathogen Tropheryma whipplei not detected with traditional culturing techniques. The NGS results showed a partial overlap with culture as the current diagnostic gold standard in LRTI. Additionally, NGS detected a broader spectrum of bacteria, revealed fastidious potential pathogens, and offered deeper insights into the complex microbial ecosystem of the lungs.},
}
@article {pmid41152727,
year = {2025},
author = {Chen, L and Wang, C and Zhang, H and Wu, Y and Li, F and Shi, H and Ren, Z and Chen, Y and Huang, J and Zhao, D and Pan, J and Lu, H and Zheng, S},
title = {Characterization of microbiota dysbiosis in papillary thyroid carcinoma and benign thyroid nodules: low abundance of intestinal butyrate-producing bacteria.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {691},
pmid = {41152727},
issn = {1471-2180},
support = {2022YFC3602000//National Key Research and Development Program of China/ ; 81874038//the National Natural Science Foundation of China/ ; JNL-2022001A//the Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; *Gastrointestinal Microbiome ; *Thyroid Cancer, Papillary/microbiology ; *Butyrates/metabolism ; Middle Aged ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Feces/microbiology ; *Thyroid Nodule/microbiology ; Adult ; *Thyroid Neoplasms/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: The thyroid-gut axis refers to the intricate relationships among the gut, intestinal microbiota, and thyroid gland, and it is speculated to play an important role in the development of thyroid diseases. The aim of this study was to identify the differentiated bacteria in the intestinal microbiota associated with papillary thyroid carcinoma (PTC) and benign thyroid nodules (BTNs) to offer potential avenues for further exploration and therapeutic interventions.<br><br>METHODS: Faecal microbiotas of 197 subjects (73 from subjects with BTNs, 62 from subjects with PTC, and 62 from sex- and age-matched controls) were characterized by sequencing the V3-V4 region of 16&#xa0;S rDNA using the Illumina NovaSeq 6000 platform. Microbiomics and machine learning-assisted approaches were used to identify the PTC-/BTN-associated intestinal microbial indicators.<br><br>RESULTS: Compared with the abundance of coabundant groups (CAGs) in the PTC, BTN, and control groups, the abundance of two Genus-CAGs consisting of butyrate producers, such as Blautia, Lachnoclostridium, Lachnospiraceae_unclassified, Eisenbergiella, Flavonifractor and Hungatella, was lower in the PTC group than in the control group. In particular, both ANCOM-BC2 and Wilcoxon rank-sum test results consistently demonstrated significant enrichment of the butyrate-producing genera Oscillibacter, Coprobacter, and Colidextribacter in both BTN patients and healthy controls. The majority of discriminatory amplicon sequence variants (ASVs) that could discriminate PTCs from controls, as well as from BTNs, were from Prevotella, Streptococcus, Bacteroides, and butyrate-producing groups, such as the Oscillibacter, Lachnospiraceae, and Christensenellaceae (R7) groups. ASV indicators from Prevotella and Streptococcus were most abundant in the PTC group, and those from Bacteroides and the butyrate-producing/-promoting group were least abundant in the PTC group. Additionally, the ASVs that could discriminate the BTN group from the control group, as well as PTC group included other butyrate-producing groups, the Clostridium_sensu_stricto group, and the Eubacterium_siraeum group.<br><br>CONCLUSIONS: This study demonstrates that dysbiosis linked to thyroid nodules is marked by a substantial decline in intestinal butyrate-producing and butyrate-promoting taxa. Future work to confirm these results should include shotgun metagenomic sequencing paired with quantitative analyses of gene abundance and expression to fully ascertain the functional implications.},
}
@article {pmid41152726,
year = {2025},
author = {Zou, Y and Zou, Q and Wang, Y and Han, C},
title = {Metagenomics reveals seasonal changes of intestinal microbes in Eospalax rothschildi.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {693},
pmid = {41152726},
issn = {1471-2180},
support = {62402344//Youth Found of the National Natural Science Foundation of China/ ; 62373080//National Natural Science Foundation of China/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; *Seasons ; *Metagenomics/methods ; Animals ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; China ; Feces/microbiology ; },
abstract = {BACKGROUND: Seasonal behavioral divergence in zokors, driven primarily by their reproductive cycle, results in distinct ecological strategies between breeding and non-breeding periods. To elucidate how intestinal microbes adapt to these behavioral shifts, we used metagenomics to characterize the seasonal variations in the intestinal microbes of Eospalax rothschildi, a subterranean zokor endemic to China.<br><br>RESULTS: Metagenomics revealed that summer samples showed an increased proportion of carbohydrate-degrading bacteria. Moreover, a significant difference in taxonomic composition was observed between the samples collected in the two seasons. Functional analysis based on the KEGG and CAZy databases revealed stronger carbohydrate degradation capacities in summer samples, notably through enhanced galactose metabolism capabilities. The enhanced galactose metabolism capabilities observed in summer were predominantly driven by increased abundance of &#x3b1;-galactosidase and &#x3b2;-galactosidase genes from enriched microbial populations, particularly Bacteroides, unclassified_f_Lachnospiraceae, Roseburia, and Faecalibacterium. Furthermore, iCAMP analysis revealed that deterministic and stochastic processes jointly governed intestinal microbial assembly in E. rothschildi during summer, as elevated nutritional demands potentially intensified host selection in the breeding season. Conversely, stochastic dominance in autumn may align with relaxed host selection.<br><br>CONCLUSIONS: Collectively, these results demonstrated that season played a crucial role in modulating the composition, function, and assembly process of the intestinal microbes of E. rothschildi.},
}
@article {pmid41152332,
year = {2025},
author = {Ciuchcinski, K and Bluszcz, A and Dziewit, L},
title = {Taxonomy, function and plasmids of microbial soil communities of Polish salt graduation towers.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1702},
pmid = {41152332},
issn = {2052-4463},
support = {BOB-IDUB-622-105/2024//Uniwersytet Warszawski (University of Warsaw)/ ; },
mesh = {*Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Poland ; Salinity ; *Plasmids ; *Microbiota ; Metagenomics ; },
abstract = {Salt graduation towers create hypersaline environments that host specialized microbial communities, offering unique opportunities to study their adaptations to salinity. In this study, we present a comprehensive catalogue of data recovered from soil samples collected across three salt graduation towers in Poland (Ciechocinek, Konstancin-Jeziorna and Busko-Zdrój). Our investigation includes total metagenomic and 16S rRNA amplicon sequencing of nine collected soil samples, as well as metaplasmidome sequencing from most saline samples at each location. We established both solid and liquid enrichment cultures for these high-salinity samples, followed by hybrid long- and short-read sequencing. We also used multiple state-of-the-art tools to fully describe and characterize the recovered sequences. Overall, this comprehensive dataset integrates metagenomic, enrichment culture, 16S rRNA amplicon, and (meta)plasmidome sequencing data with corresponding physicochemical soil parameters, providing a valuable resource for comparative analyses, method development, and studies of microbial diversity and adaptation across saline environments.},
}
@article {pmid41152000,
year = {2025},
author = {Saguti, F and Wang, H and Churqui, MP and Tunovic, T and Holmer, L and Pettersson, &#xc4; and Schleich, C and Pott, BM and Bergstedt, O and Nyström, K and Norder, H},
title = {Variations of the Virome in Raw and Treated Water: A One-Year Follow-Up at Six Different Drinking Water Treatment Plants.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70222},
pmid = {41152000},
issn = {1758-2229},
support = {2020-02710//Svenska Forskningsr&#xe5;det Formas/ ; 20-102//Svenskt Vatten/ ; },
mesh = {*Drinking Water/virology ; *Virome ; *Water Purification/methods ; *Viruses/genetics/classification/isolation &amp; purification ; Sweden ; Metagenomics ; *Water Microbiology ; Genome, Viral ; Bacteriophages/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing ; },
abstract = {Little is known about virome changes in raw and drinking water over time, and differences between raw water sources and treatment technologies. This study used metagenomics to assess viruses prevalent in raw and drinking water samples over 1 year from six Swedish drinking water treatment plants (DWTPs) with varying treatment barriers and with different raw water sources. Sequences homologous to known viruses in the raw water samples were detected by amplification and next-generation sequencing and classified into 152 different virus species belonging to 76 virus families/orders. The majority were small bacteriophages. Other viral genomes were homologous to viruses infecting plants, invertebrates, vertebrates, mammals and giant viruses infecting amoeba or algae. Several virus species were simultaneously found in both raw and drinking water, indicating passage through the purification barriers, although reduced by 1-3 log10 after treatment. Most viruses detected in water samples after ultrafiltration were small viruses, and other barriers appeared more effective at removing smaller viruses. To avoid detecting viruses possibly replicating within DWTPs, viruses were separated according to the possibility that the host could be found in the water sources or not. These results underscore the importance of monitoring both raw and drinking water for small viruses, especially when viral contamination of the source water is at risk, to ensure drinking water quality.},
}
@article {pmid41151807,
year = {2025},
author = {Bontemps, Z and Abrouk, D and Moënne-Loccoz, Y and Hugoni, M},
title = {Functional Characterisation of Microbial Communities Related to Black Stain Formation in Lascaux Cave.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70112},
pmid = {41151807},
issn = {1758-2229},
support = {//DRAC Nouvelle Aquitaine (Bordeaux, France)/ ; },
mesh = {*Caves/microbiology ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota/genetics ; *Fungi/genetics/metabolism/classification/isolation &amp; purification ; Metagenomics ; Melanins/biosynthesis/genetics ; Carotenoids/metabolism ; Phylogeny ; },
abstract = {Anthropization of Palaeolithic caves may cause cave microbiota dysbiosis and promote the development of microbial stains on cave walls. In certain cases, chemical biocides have been used to mitigate rock alterations, but this may exacerbate microbiota unbalance. Here, we tested this model by metagenomics, using black stains that threaten art conservation in Lascaux Cave. Thus, we evidenced a wide range of microbial taxa differing between black stains and neighbouring unmarked surfaces. Genes for synthesis of melanin and carotenoid pigments were more prevalent in black stains and were identified in reconstructed genomes for fungi (as expected) and bacteria. The presence of genes for degradation of aromatic compounds supports the hypothesis that recycling of chemical biocides favoured melanin-producing microorganisms. These findings extend previous predictions by revealing a wider range of microorganisms, potential biotransformations favouring pigment synthesis, as well as microbial interactions influencing microbial dynamics during cave wall alterations.},
}
@article {pmid41151484,
year = {2025},
author = {Wang, Y and Zhang, Q and Luo, Q and Li, H and Li, F and Huang, D and Wu, B and Huang, D and Zhao, X and Zhang, J and Wu, D and Hao, H and Huang, R and Lai, J},
title = {Melatonin ameliorates bronchopulmonary dysplasia by modulating the NF-κB pathway via the gut microbiota-short-chain fatty acid axis.},
journal = {International immunopharmacology},
volume = {167},
number = {},
pages = {115730},
doi = {10.1016/j.intimp.2025.115730},
pmid = {41151484},
issn = {1878-1705},
mesh = {*Melatonin/pharmacology/therapeutic use ; *NF-kappa B/metabolism ; Animals ; *Gastrointestinal Microbiome/drug effects ; Humans ; *Bronchopulmonary Dysplasia/drug therapy/chemically induced/metabolism/pathology ; *Fatty Acids, Volatile/metabolism ; Mice ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Disease Models, Animal ; Bleomycin ; Cell Line ; Lung/pathology/drug effects/metabolism ; Male ; },
abstract = {OBJECTIVE: To elucidate the mechanism by which melatonin ameliorates bronchopulmonary dysplasia (BPD) via modulation of gut microbiota and its metabolite, short-chain fatty acids (SCFAs).<br><br>METHODS: A bleomycin-induced BPD mouse model was developed. Post-melatonin intervention, a comprehensive multi-omics approach, including metagenomics, 16S rRNA sequencing, untargeted metabolomics, and RNA transcriptomics, was employed alongside butyrate supplementation experiments to assess changes in alveolar architecture, oxidative stress, inflammatory cytokine levels, and the NF-&#x3ba;B signaling pathway. In vitro experiments utilizing human bronchial epithelial cells (BEAS-2B) and analyses of publicly available single-cell RNA sequencing data from infant lung tissues were conducted to further substantiate the underlying mechanisms.<br><br>RESULTS: The administration of melatonin led to a significant increase in the abundance of Ligilactobacillus murinus within the gut microbiota and enhanced the production of SCFAs. Notably, butyrate metabolites were found to be enriched in both serum and lung tissues, which was associated with the suppression of NF-&#x3ba;B pathway activation. Intervention with butyrate mirrored the therapeutic effects observed with melatonin, resulting in the alleviation of alveolar simplification, a reduction in oxidative damage and inflammatory cytokines, and the inhibition of both NF-&#x3ba;B pathway activation and pyroptosis in lung tissues. Additionally, in vitro experiments demonstrated that both melatonin and butyric acid directly inhibited NF-&#x3ba;B activation and pyroptosis in BEAS-2B cells injured by bleomycin. Analysis of single-cell data from human infant lungs revealed differential enrichment of genes related to NF-&#x3ba;B and pyroptosis in the bronchial and alveolar epithelial cells of patients with BPD, thereby underscoring the clinical significance of these pathways.<br><br>CONCLUSION: Melatonin ameliorates BPD by modulating the gut microbiota-SCFA metabolic axis, which in turn suppresses NF-&#x3ba;B pathway activation and pyroptosis in lung tissues via systemic circulation. This finding suggests a novel therapeutic strategy for the treatment of BPD.},
}
@article {pmid41150726,
year = {2025},
author = {Ma, M and Li, Q and Wu, F and Zhu, B and Lu, H and Zhang, D and Łukasik, P and Hu, Y},
title = {Symbiotic solutions for colony nutrition: Conserved nitrogen recycling within the bacterial pouch of Tetraponera ants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {44},
pages = {e2514882122},
pmid = {41150726},
issn = {1091-6490},
support = {32370448//MOST | National Natural Science Foundation of China (NSFC)/ ; 2243200009//MOE | Fundamental Research Funds for the Central Universities (Fundamental Research Fund for the Central Universities)/ ; },
mesh = {*Ants/microbiology/physiology/metabolism ; Animals ; *Symbiosis/physiology ; *Nitrogen/metabolism ; Microbiota/physiology ; Larva/microbiology/growth &amp; development ; Amino Acids/metabolism ; *Bacteria/metabolism/genetics ; Urea/metabolism ; },
abstract = {While microbial symbioses are fundamental to the nutrition of many animal groups, current paradigms focus on symbiont functions at the host individual level. It remains unclear whether microbial symbioses can sustain colony-level fitness in social insects, whose ecological success depends on nutrient coordination across castes. Here, we investigate the specialized bacterial pouch, a symbiont-containing organ present exclusively in adult workers of Tetraponera nigra-group ants, revealing its crucial role in colony-wide nutrient provisioning. Using a combination of microscopy, amplicon and metagenomic sequencing, and [15]N-urea feeding experiments on four species in the group, we show that its adult-specific pouch-associated microbiota, primarily Tokpelaia, recycle nitrogen from urea and convert it into amino acids which are provisioned to adult workers and developing larvae. Disruption of this nitrogen-recycling symbiosis severely impairs larval growth and overall colony fitness. Our results show how caste-restricted microbial organs can centralize metabolic functions at the colony level, challenging individual-centric paradigms of host-microbe mutualism and providing insights into the pivotal role of microbial symbionts in superorganismal adaptation to nutritional constraints.},
}
@article {pmid41148396,
year = {2025},
author = {Xie, X and Ren, W and Zhou, W and Wang, Y and Zhu, H and Wu, Y and Lu, Q},
title = {Genetic prediction of the effect of gut microbiota on retinal vein occlusion via blood metabolites.},
journal = {International ophthalmology},
volume = {45},
number = {1},
pages = {447},
pmid = {41148396},
issn = {1573-2630},
support = {2024KY376//Medical Science and Technology Program of Zhejiang Province/ ; 2022L003//Ningbo Clinical Research Center for Ophthalmology/ ; 2016-370 S05//Ningbo Clinical Research Center for Ophthalmology and the Project of NINGBO Leading Medical &amp; Health Disipline/ ; 2021Z054//Technology Innovation 2025 Major Project of Ningbo/ ; 2024Z233//Ningbo"Innovation Yongjiang 2035" Key Technology Breakthrough program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Retinal Vein Occlusion/genetics/blood/microbiology ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Male ; Female ; *Polymorphism, Single Nucleotide ; Biomarkers/blood ; },
abstract = {PURPOSE: Given the unclear causal relationship between gut microbiota (GM) and retinal vein occlusion (RVO) and the potential mediating role of blood metabolites, this study aims to investigate this causal link and the mediating effects of blood metabolites.<br><br>METHODS: Our Mendelian randomization (MR) study used data from genome-wide association studies pooled data, including 473 microbiota taxa (n&#x2009;=&#x2009;5959), 233 blood metabolites (n&#x2009;=&#x2009;136,016), and RVO cases and controls from the FinnGen consortium (cases, n&#x2009;=&#x2009;775; controls, n&#x2009;=&#x2009;308,633). We used bidirectional two-sample MR, multivariate MR, and mediation analysis to assess the causal association between GM and RVO.<br><br>RESULTS: By analyzing gut microbial metagenomic data with adjustment for confounding factors, we identified 1 taxon with significant causal association and 14 taxa with potential causal links to RVO, where Halomonadaceae remained after Bonferroni correction. Parallel analysis of blood metabolites revealed 18 causal associations (2 significant, 16 potential), with apolipoprotein A-I and creatinine retaining significance post-correction. Three GM taxa affected RVO through three blood metabolites. Caloranaerobacteraceae, Rhodococcus, and Citrobacter A affected RVO through Total cholesterol in HDL2, Apolipoprotein A-I, and phenylalanine, respectively. Apolipoprotein A-1 possessed the greatest mediated effect (5.6%) between Rhodococcus and RVO.<br><br>CONCLUSION: These findings provide new insights into the pathogenesis of RVO and may contribute to the development of new strategies for preventing the onset of RVO.},
}
@article {pmid41148242,
year = {2025},
author = {Kumar, R and Nagraik, R and Lakhanpal, S and Abomughaid, MM and Jha, NK and Gupta, R},
title = {Artificial intelligence in gut microbiome research: Toward predictive diagnostics for neurodegenerative disorders.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {72},
number = {4},
pages = {296-312},
doi = {10.1556/030.2025.02725},
pmid = {41148242},
issn = {1588-2640},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Neurodegenerative Diseases/diagnosis/microbiology ; *Artificial Intelligence ; Machine Learning ; Dysbiosis ; },
abstract = {The human gut microbiota plays a pivotal role in maintaining host immunity, regulating metabolism, and sustaining neurophysiological homeostasis. Increasing evidence implicates gut dysbiosis in the onset and progression of neurodegenerative disorders (NDDs), including Alzheimer's and Parkinson's disease, primarily through the gut-brain axis. Recent advances in high-throughput sequencing and multi-omics technologies, such as metagenomics, metabolomics, and metaproteomics have generated vast datasets, yet their clinical translation remains hindered by data heterogeneity, analytical complexity, and the absence of standardized workflows. Disjointed findings across studies underscore the urgent need for reproducible pipelines and integrative computational strategies. This review presents a comprehensive framework that leverages artificial intelligence (AI) and machine learning (ML) for systematic microbiome investigation in NDDs. We highlight how multi-omics integration with AI improves the resolution of host-microbiome interactions, while standardized preprocessing workflows ensure reproducibility and comparability across datasets. The role of explainable AI is emphasized in enhancing interpretability, improving biomarker discovery, and fostering trust in predictive models. We further examine the emerging field of pharmacomicrobiomics, where ML-driven approaches support the development of precision therapies tailored to microbiome-drug interactions in neurodegeneration. Sophisticated models, including random forests (RF), neural networks, and transfer learning, are critically assessed for predictive diagnostics, therapeutic target identification, and cross-cohort generalizability. Finally, the review proposes a roadmap to address current barriers, particularly challenges of heterogeneity and reproducibility, and advocates for validated pipelines and interdisciplinary collaboration. Collectively, AI-driven multi-omics strategies hold transformative potential for advancing microbiome-based precision medicine in NDDs.},
}
@article {pmid41147939,
year = {2025},
author = {Zhang, T and Xing, M and Zhang, H and Song, X and Song, Z and Yuan, C and Zhang, J and Ai, L and Zhang, Z and Xie, F},
title = {Docynia delavayi (Franch.) Schneid polyphenols alleviate dextran sulfate sodium-induced colitis by regulating the gut microbiota.},
journal = {Food &amp; function},
volume = {16},
number = {22},
pages = {8846-8861},
doi = {10.1039/d5fo03604f},
pmid = {41147939},
issn = {2042-650X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Dextran Sulfate/adverse effects ; *Colitis/chemically induced/drug therapy/microbiology ; *Polyphenols/pharmacology/administration &amp; dosage/chemistry ; Mice ; Male ; Anti-Inflammatory Agents/pharmacology ; Mice, Inbred C57BL ; *Plant Extracts/pharmacology/chemistry/administration &amp; dosage ; Disease Models, Animal ; Cytokines/metabolism ; Humans ; },
abstract = {Docynia delavayi (Franch.) Schneid is rich in polyphenols; however, its functions remain unclear. In this study, we identified and characterized the key constituents of D. delavayi fruit polyphenols (DDP), validated their anti-inflammatory effects, and provided insights into their underlying mechanisms of action. UPLC-MS/MS was used to quantify the major phenolic compounds in DDP, including glycitin, procyanidin B2, vitexin, myricitrin, astilbin, chlorogenic acid, phlorizin, (-)-epicatechin, naringenin-7-O-glucoside, taxifolin-7-O-rhamnoside, rhoifolin, methylnissolin-3-O-glucoside, and scutellarein. In the dextran sulfate sodium-induced colitis mouse model, DDP significantly improved colon length and the disease activity index. It also reduced the expression of inflammatory cytokines, including interleukin (IL)-1β, IL-6, and tumor necrosis factor-α. Metagenomic analysis revealed that DDP increased gut microbiota diversity, particularly enriching species capable of producing short-chain fatty acids (SCFAs), such as Lawsonibacter and Ruminiclostridium. Metabolomic data further demonstrated the upregulation of SCFA-associated pathways, such as glycolysis and pyruvate metabolism, with elevated colonic acetate, propionate, and butyrate levels corroborating these findings. Multi-omics analysis linked SCFAs to reduced inflammation. Collectively, these findings suggest that SCFAs play a pivotal role in the anti-inflammatory effects of DDP by modulating the gut microbiota to enhance SCFA biosynthesis. These findings demonstrate that SCFAs serve as critical mediators of the anti-inflammatory properties of DDP, highlighting their considerable potential as natural therapeutic agents for intestinal inflammation.},
}
@article {pmid41147782,
year = {2026},
author = {Zhang, L and Yang, G and Zhang, C and Ji, B and Wu, D},
title = {Symbiotic nitrogen fixation and recycling in xylophagous insects: insights from gut microbiota of Apriona swainsoni larvae.},
journal = {Pest management science},
volume = {82},
number = {2},
pages = {1789-1804},
doi = {10.1002/ps.70323},
pmid = {41147782},
issn = {1526-4998},
support = {81503115//National Natural Science Foundation of China/ ; JNFX2025192//Domestic Visiting Program for Young Key Teachers of Anhui Province/ ; BK2012816//Natural Science Foundation of Jiangsu Province/ ; 201409/WT_/Wellcome Trust/United Kingdom ; CX (16)1005//Jiangsu Agricultural Science and Technology Independent Innovation Project/ ; 2023AH050727//Natural Science Foundation (Key project) of the University in Anhui Province/ ; 2024AH050921//Natural Science Foundation (Key project) of the University in Anhui Province/ ; HZR2436//Hefei Municipal Natural Science Foundation/ ; 2024A755//Anhui Postdoctoral Scientific Research Program Foundation/ ; 201409/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Symbiosis ; *Nitrogen Fixation ; Larva/microbiology/growth &amp; development/physiology/metabolism ; *Coleoptera/microbiology/growth &amp; development/physiology/metabolism ; Nitrogen/metabolism ; Klebsiella oxytoca/physiology/metabolism ; },
abstract = {BACKGROUND: Xylophagous insects, as nitrogen-limited organisms, face severe nutritional constraints due to the inherently low nitrogen content of lignocellulosic substrates-insufficient for growth. To alleviate this limitation, they rely on gut microbiota-mediated symbiotic nitrogen fixation and nitrogenous waste recycling. Apriona swainsoni, a model wood-boring cerambycid, exemplifies this adaptation: under extreme nitrogen scarcity in its xylem diet. While gut symbionts are hypothesized to overcome nitrogen limitation, the underlying mechanisms remain unclear.<br><br>RESULTS: First, metagenomic sequencing and functional gene analysis revealed enrichment of nitrogenase and urease genes in the posterior hindgut (PHG). Metaproteomics detected the nitrogenase gene nifU but no urease proteins, identifying nitrogen fixation as the primary nitrogen limitation mitigation strategy in A. swainsoni larvae. Subsequently, in vivo/in vitro [15]N isotope tracing showed peak [15]N in the PHG (105.02% higher than the natural environment) and&#x2009;~&#x2009;25-fold greater [15]N incorporation in cultured Klebsiella oxytoca versus controls. Targeted amino acid profiling further demonstrated [15]N enrichment in both essential and non-essential amino acids, with a spatial gradient (intestinal tissues > extra-intestinal tissues > frass)-indicating efficient microbial conversion of nitrogen into host-utilizable amino acids. Importantly, we identified that intestinal microbiota primarily mediate ammonia-to-amino acid conversion via the glutamine synthetase-glutamate synthase (GS/GOGAT) pathway in the PHG. This is the first reported GS/GOGAT-mediated nitrogen fixation pathway in cerambycids.<br><br>CONCLUSIONS: Our comprehensive analysis of gut microbial nitrogen metabolism might elucidate a set of mechanisms by which some xylophagous insects may overcome nutritional constraints in nitrogen-deficient niches, via evolutionarily optimized host-microbe metabolic interactions. &#xa9; 2025 Society of Chemical Industry.},
}
@article {pmid41147731,
year = {2025},
author = {Jones, JA and Moczek, AP and Newton, ILG},
title = {The dung beetle microbiome complements host metabolism and nutrition.},
journal = {mSystems},
volume = {10},
number = {11},
pages = {e0117225},
pmid = {41147731},
issn = {2379-5077},
support = {2243725//National Science Foundation/ ; 1901680//National Science Foundation/ ; 2141416//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; },
mesh = {Animals ; *Coleoptera/microbiology/metabolism ; *Microbiota ; Amino Acids/metabolism/biosynthesis ; Bacteria/genetics/metabolism/classification ; },
abstract = {Many multicellular organisms rely on communities of microbial organisms to properly benefit from their diets, for instance, by assisting in the breakdown of complex polysaccharides, the synthesis of essential resources, detoxification, or even preventing putrefaction. Dung beetles commonly rely on herbivore dung as their main source of nutrition, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. The work presented here investigates the potential role of the host-associated microbial community in allowing these insects to thrive on their nutrient-poor diet. Specifically, we investigated whether the microbiota of the bull-headed dung beetle, Onthophagus taurus, may be capable of synthesizing amino acids and breaking down complex plant polysaccharides. To do so, we functionally annotated genes within metagenomically assembled genomes (MAGs) obtained via shotgun-metagenomic sequencing. The annotation of these MAGs revealed that bacteria found in association with O. taurus possess the metabolic potential necessary to bridge the gap between host metabolic needs and the limitations imposed by their diet. Specifically, O. taurus microbiota contain amino acid biosynthesis pathways and genes encoding cellulases and xylanases, both of which are absent in the beetle genome. Further, multiple functionally relevant bacterial taxa identified here have also been observed in other studies across diverse dung beetle species, possibly suggesting a conserved pool of dung beetle symbionts and metabolic functions.IMPORTANCEHost-symbiont interactions allow animals to take advantage of incomplete and/or challenging diets and niches. The work presented here aims to identify the physiological and metabolic means by which host-associated microbial species shape the ecology of one of the most speciose genera in the animal kingdom: dung beetles in the genus Onthophagus. Both larva and adult stages of most Onthophagus rely on herbivore dung, a diet rich in recalcitrant, hard-to-digest plant polysaccharides yet poor in essential amino acids, which animals typically cannot synthesize on their own. To utilize such a challenging diet, Onthophagus vertically transmits a maternally derived microbial community which supports normative development in immature individuals and maintenance and reproduction in adults. Taken together, Onthophagus' extraordinary diversity, complex ecology, and varied relationship with their microbial associates make them an ideal system to investigate mechanisms and diversification of host-diet-microbiome interactions.},
}
@article {pmid41145643,
year = {2025},
author = {Karpęcka-Gałka, E and Zielińska, K and Frączek, B and Łabaj, PP and Kościółek, T and Humińska-Lisowska, K},
title = {High-altitude mountaineering induces adaptive gut microbiome shifts associated with dietary intake and performance markers.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37529},
pmid = {41145643},
issn = {2045-2322},
support = {39/PB/RID/2022//Ministerstwo Edukacji i Nauki/ ; 2020/38/E/NZ2/00598//Narodowe Centrum Nauki/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; *Altitude ; Adult ; *Mountaineering/physiology ; Biomarkers/blood ; *Diet ; Young Adult ; },
abstract = {This study examined how high-altitude exposure and expedition-specific dietary changes influence gut microbiome composition, functional pathways, and their relationships with performance and health markers in alpinists. Seventeen male mountaineers (age 30.29 ± 5.8 years) participating in multi-week expeditions (> 3,000 MASL) were assessed before and after their climbs. Assessments included dietary intake analysis, blood and urine biomarkers, aerobic and anaerobic performance tests, and metagenomic sequencing of the gut microbiome. Bioinformatic and statistical analyses evaluated changes in microbiome composition and function and their correlations with physiological and dietary parameters. High-altitude exposure was associated with significant shifts in gut microbial composition and functional capacity. While the total number of bacterial species and functions remained stable, the glucose degradation pathway increased post-expedition. Participants with greater microbiome shifts showed improved performance and had richer baseline microbiomes. Pre-expedition, certain microbial functions were associated with vitamin B6 and C intake, while post-expedition correlations involved specific macronutrients and micronutrients. Additionally, some microbiome changes correlated with blood markers, indicating links to nutrient metabolism and electrolyte balance. The gut microbiome of alpinists adapts to extreme environmental stress and dietary changes, influencing metabolic, immune, and performance-related processes. Optimizing dietary strategies to support a beneficial microbiome profile may enhance resilience and performance in challenging high-altitude environments.},
}
@article {pmid41145216,
year = {2025},
author = {Peel, N and Martin, S and Heavens, D and Yu, DW and Clark, MD and Leggett, RM},
title = {Real-time analysis and visualization of nanopore metagenomic samples with MARTi.},
journal = {Genome research},
volume = {35},
number = {11},
pages = {2488-2500},
pmid = {41145216},
issn = {1549-5469},
mesh = {*Metagenomics/methods ; *Software ; *Nanopore Sequencing/methods ; *Nanopores ; Metagenome ; Humans ; Computational Biology/methods ; },
abstract = {The emergence of nanopore sequencing technology has the potential to transform metagenomics by offering low-cost, portable, and long-read sequencing capabilities. Furthermore, these platforms enable real-time data generation, which could significantly reduce the time from sample collection to result, a crucial factor for point-of-care diagnostics and biosurveillance. However, the full potential of real-time metagenomics remains largely unfulfilled due to a lack of accessible, open-source bioinformatic tools. We present Metagenomic Analysis in Real-Time (MARTi), an innovative open-source software designed for the real-time analysis, visualization, and exploration of metagenomic data. MARTi supports various classification methods, including BLAST, Centrifuge, and Kraken2, letting users customize parameters and utilize their own databases for taxonomic classification and antimicrobial resistance analysis. With a user-friendly, browser-based graphical interface, MARTi provides dynamic, real-time updates on community composition and AMR gene identification. MARTi's architecture and operational flexibility make it suitable for diverse research applications, ranging from in-field analysis to large-scale metagenomic studies. Using both simulated and real-world data, we demonstrate MARTi's performance in read classification, taxon detection, and relative abundance estimation. By bridging the gap between sequencing and actionable insights, MARTi marks a significant advance in the accessibility and functionality of real-time metagenomic analysis.},
}
@article {pmid41143690,
year = {2026},
author = {Kim, KJ and Garcia, MM and Romero, AS and Jin, Y and Chi, J and Campen, MJ and Gu, H and Richardson, JR and Castillo, EF and Cui, JY},
title = {In vivo exposure of mixed microplastic particles in mice and its impacts on the murine gut microbiome and metabolome.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {209},
number = {1},
pages = {},
pmid = {41143690},
issn = {1096-0929},
support = {R01 ES032037/ES/NIEHS NIH HHS/United States ; T32ES007032//UW Environmental Pathology/Toxicology Training/ ; //Environmental Health and Microbiome Research Center (EHMBRACE)/ ; //Sheldon Murphy Endowment/ ; 5P30ES007033-27//UW EDGE Center/ ; 1U01AG088557/GF/NIH HHS/United States ; 1R01AG070776/GF/NIH HHS/United States ; //Dianne Isakson Distinguished Professorship/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; Mice, Inbred C57BL ; *Microplastics/toxicity ; *Metabolome/drug effects ; Feces/microbiology ; Mice ; Metabolomics ; },
abstract = {Microplastics (MPs) are emerging environmental contaminants due to increasing global plastic production and waste. MPs, defined as plastic particles less than 5 mm in diameter, are formed through the degradation of larger plastics via sunlight, weathering, and microbes. These plastic compounds are widely detected in water, soil, and food, as well as human stool and blood. The gut microbiome, often referred to as our second genome, is important in human health and is the primary point of contact for orally ingested MPs. To investigate the impact of ingested MPs on the gut microbiome and the metabolome, 8-week-old male and female C57BL/6 mice were orally gavaged with mixed plastic (5 µm) exposure consisting of polystyrene, polyethylene, and the biodegradable/biocompatible plastic, poly(lactic-co-glycolic acid), twice a week for 4 weeks at 0, 2, or 4 mg/week (n = 8/group). Fecal pellets were collected for bacterial DNA extraction and metagenomic shotgun sequencing, and serum was subjected to targeted and untargeted metabolomics. A total of 1,162 bacterial species and 1,437 metabolites were evaluated for downstream analysis. MPs' exposure resulted in significant sex-specific and dose-dependent changes to the gut microbiome composition, along with substantial regulation of predicted metabolic pathways. Untargeted metabolomics in serum showed that a low MPs dose displayed a more prominent effect on key metabolic pathways, such as amino acid metabolism, sugar metabolism, and inflammation. Additionally, short-chain fatty acid (SCFA)-targeted metabolomics showed significant changes in neuroprotective SCFA levels in both sexes. Our study demonstrates that MPs dysregulate the gut microbiome and serum metabolome, highlighting potential human disease risks.},
}
@article {pmid41142817,
year = {2025},
author = {Lee, JY and Mahurkar-Joshi, S and Young, A and Labus, JS and He, B and Aja, E and Jacobs, JP and Volkmann, ER},
title = {Ultra-processed food intake is associated with increased gastrointestinal tract symptoms and alterations in gut microbiota in patients with systemic sclerosis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1610360},
pmid = {41142817},
issn = {1664-3224},
mesh = {Humans ; *Scleroderma, Systemic/microbiology/complications ; Female ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Adult ; Aged ; *Gastrointestinal Diseases/etiology/microbiology ; *Dysbiosis ; Feces/microbiology ; Food Handling ; Food, Processed ; },
abstract = {BACKGROUND: Alterations in the gastrointestinal (GI) microbiome (i.e., dysbiosis) are a feature of systemic sclerosis (SSc). Diet is a known modifier of the GI microbiome, and ultra-processed food (UPF) consumption has been associated with adverse changes in GI microbial composition. This study aimed to determine whether UPF consumption affects the GI microbiota and GI symptoms in patients with SSc.<br><br>METHODS: Adult SSc patients provided stool samples and completed both the Diet History Questionnaire II (DHQ-2) and the UCLA Scleroderma Clinical Trial Consortium Gastrointestinal Tract Instrument (GIT 2.0). Shotgun metagenomics were performed using the Illumina NovaSeq 6000 with a target depth of 10 million 150x2 sequences per sample. UPF items (N=54) on the DHQ-2 were identified using the NOVA scale of food classification, and UPF intake was calculated as gram-per-week consumption according to patient reported frequency. General linear models were created to identify differentially abundant species based on UPF consumption and to evaluate the relationship between UPF consumption and GI symptoms as measured by the GIT 2.0. These models adjusted for body mass index (BMI), current proton pump inhibitor (PPI) use, current probiotic use, current or prior immunomodulatory therapy, and presence of small intestinal bacterial overgrowth (SIBO).<br><br>RESULTS: Of the 65 total SSc patients included, 84.6% were female. The mean age was 53.83 &#xb1; 13.19 years, and the mean BMI was 25.25 &#xb1; 4.75. The median UPF consumption was 2395.82 g/week. Increased UPF consumption was significantly associated with increased GI symptoms in our multivariate model (&#x3b2;=0.34; p<0.01). Among 257 species analyzed, 5 bacterial species were significantly associated with UPF consumption in the multivariate models, including Limosilactobacillus fermentum (&#x3b2;=0.32; p<0.01) and Faecalicatena fissicatena (&#x3b2;= -0.36; p-value<0.01), while the abundance of 6 bacterial species was significantly associated with GI symptom severity after adjusting for the aforementioned covariates.<br><br>CONCLUSIONS: SSc patients reporting a higher UPF consumption demonstrated alterations in GI microbial composition as well as increased GI symptoms, even after adjusting for factors known to affect the microbiota of patients with SSc. Future studies are needed to determine whether interventions aimed at lowering UPF consumption may improve GI outcomes for patients with SSc.},
}
@article {pmid41139486,
year = {2025},
author = {Tran, T and Duong, DV and Le, TD and Bui, XT},
title = {Metagenomic Characterization of Biofilm and Suspended Microbial Communities in a Hybrid Algal Turf Scrubber-Based Wastewater Treatment System.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {10},
pages = {e70072},
doi = {10.1111/apm.70072},
pmid = {41139486},
issn = {1600-0463},
mesh = {*Biofilms/growth &amp; development ; *Wastewater/microbiology ; Metagenomics ; *Water Purification/methods ; Aquaculture ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Drug Resistance, Microbial/genetics ; Animals ; Nitrogen/metabolism ; Metagenome ; },
abstract = {This study investigates a hybrid wastewater treatment system combining a biofilm-based Algal Turf Scrubber (ATS) with a membrane-coupled High Rate Algal Pond (ATS-MHRAP) for shrimp aquaculture effluents. Shotgun metagenomic sequencing was used to compare microbial composition, functional pathways, and antibiotic resistance genes (ARGs) across attached biofilm (ATS1) and suspended biomass (ATS2, HRAP1) under three nutrient loading stages. Biofilm samples (ATS1) exhibited higher microbial richness and evenness, with Shannon index values up to 9.25, compared to 6.93 in suspended cultures. Functional pathways enriched in ATS1 included nitrogen cycling, amino acid metabolism, and terpenoid biosynthesis, with elevated expression of amoA, nirK, and nirS genes under moderate loading. These traits coincided with higher removal efficiency of COD (up to 88.6%), phosphate (82.1%), and total nitrogen (73.4%). ARGs were more diverse in ATS1, with up to 11 resistance classes detected, including β-lactam and sulfonamide genes co-occurring with intI1, indicating possible horizontal gene transfer. The ATS-MHRAP system offers a robust and biologically enriched platform for nature-based aquaculture wastewater treatment. Our findings reveal microbial and functional differentiation between attached and suspended communities, with implications for optimizing dissolved oxygen, nutrient ratios, and retention time.},
}
@article {pmid41138869,
year = {2025},
author = {Bamigbade, GB and Subhash, A and Jarusheh, H and Liu, SQ and Palmisano, G and Ayyash, M},
title = {Selenium nanoparticles stabilized by date pulp polysaccharides: Bioactivities, gut microbiota modulation and short chain fatty acids production.},
journal = {International journal of biological macromolecules},
volume = {332},
number = {Pt 2},
pages = {148387},
doi = {10.1016/j.ijbiomac.2025.148387},
pmid = {41138869},
issn = {1879-0003},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Polysaccharides/chemistry/pharmacology ; Humans ; *Fatty Acids, Volatile/biosynthesis ; *Selenium/chemistry/pharmacology ; *Nanoparticles/chemistry ; Antioxidants/pharmacology/chemistry ; Caco-2 Cells ; Prebiotics ; },
abstract = {Natural polysaccharides confer various physiological functions, including prebiotic qualities, modulation of gut microbiota, and regulation of gut health. This study investigated the green synthesis and characterization of bioactive selenium nanoparticles synthesized from complexation of date pulp residues polysaccharides and sodium selenite (UP-SeNPs). UP-SeNPs were evaluated for in vitro bioactivities, digestion, prebiotic properties, and gut microbiota modulation. Structural analysis indicated UP-SeNPs were crystalline, spherical, evenly distributed (size 91.1 ± 2.34 nm, polydispersity index 0.071, zeta potential -25.24 mV). Compared to controls, UP-SeNPs showed significant dose-dependent radical scavenging activities: 66.8 ± 10.49 % (DPPH), 82.8 ± 1.92 % (ABTS), 495.2 ± 8.94 μg/mL (FRAP), and 981.8 ± 9.09 μg/mL (TAC) at 100 mg/L. Inhibition rates of 82.54 %, 52.97 %, and 39.84 % against α-amylase, α-glucosidase, and ACE, respectively, were noted at 100 mg/L. UP-SeNPs (50 mg/L) showed antiproliferative activities of 34.72 % against Caco-2 and 15.16 % against MCF-7. At 100 mg/L, UP-SeNPs exhibited antibacterial properties against four foodborne pathogens. UP-SeNPs supported the proliferation of standard probiotic strains, evidenced by the high Vmax, reduced lag, and extended exponential phases. Metagenomic analysis indicated that Bifidobacterium adolescentis and other species were abundant. In contrast, metabolomic analysis confirmed pathways for the synthesis of short-chain fatty acids (SCFAs), lipids, carbohydrates, amino acids, and vitamins. These findings may offer a basis for the nanobiotechnological and nanomedical applications of UP-SeNPs.},
}
@article {pmid41138860,
year = {2025},
author = {Mishra, S and Vadakkethil, AA and Iquebal, MA and Jaiswal, S and Kumar, D and Singh, BP and Ajlouni, S and Ranadheera, CS and Chakkaravarthi, S},
title = {Deciphering microbial diversity and predicting metabolic functionalities in fermented pigmented rice water using culture-independent characterization.},
journal = {Journal of microbiological methods},
volume = {239},
number = {},
pages = {107295},
doi = {10.1016/j.mimet.2025.107295},
pmid = {41138860},
issn = {1872-8359},
mesh = {*Oryza/microbiology/chemistry ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Fungi/classification/genetics/metabolism/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Food Microbiology ; Biodiversity ; *Fermented Foods/microbiology ; Phylogeny ; },
abstract = {Fermented rice water is gaining importance lately due to its traditional food culture and potential beneficial effects. Flavored fermented rice water (FFRW) produced from pigmented rice varieties, viz., black, brown, and red, is shown to have rich nutritional and functional profiles. However, the microbiota in this spontaneously fermented beverage is scantly known. Hence, this study aimed to explore the total bacterial and fungal diversity using 16S rRNA and Internal Transcribed Spacer (ITS) sequencing, respectively, along with the phytochemicals and their metabolites produced/utilized during storage. The bacterial diversity showed significant differences (p < 0.05) in black FFRW while depicting stability for brown- and red-FFRW on the 0th day and 30th day of refrigerated storage. Lactic acid bacteria (LAB) like Weissella were abundantly recorded; similarly, fungal diversity showed dominance of various yeasts. Predictive functional/metabolic pathways suggested 23 pathways of which the predominant were metabolism amino acids like branched-chain amino acids (BCAAs) viz., leucine, valine, and isoleucine, aromatic amino acids such as tryptophan, and metabolites of glycan biosynthesis, polyphenols, lipids, cofactors and vitamins. KEGG pathways revealed a shift in microbial metabolism from amino acid degradation pathways dominating on day 0 to carbohydrate and fatty acid metabolism by day 30. Enzymes like lactate dehydrogenase showed increased abundance by the 30th day, particularly in red and black-FFRW. The untargeted profiling showed that brown FFRW had more polyphenol-related compounds, followed by black and red FFRW. Decrements in the compounds were detected on the 30th day of storage compared to the 0th day. The findings provide insights into the microbial diversity, metabolic potential, and phytochemical composition of FFRW, supporting its potential as a functional beverage.},
}
@article {pmid41138814,
year = {2025},
author = {Matsumoto, A and Yoshimura, Y and Wakabayashi, H and Nagano, F and Shimazu, S and Kido, Y and Shiraishi, A and Hamada, T and Yoneda, K and Maeda, K},
title = {Polypharmacy is associated with altered gut microbiota diversity in older post-stroke inpatients.},
journal = {Clinical nutrition ESPEN},
volume = {70},
number = {},
pages = {427-433},
doi = {10.1016/j.clnesp.2025.10.015},
pmid = {41138814},
issn = {2405-4577},
mesh = {Humans ; *Polypharmacy ; Male ; Aged ; *Gastrointestinal Microbiome/drug effects ; Female ; Cross-Sectional Studies ; *Stroke/microbiology/drug therapy ; Aged, 80 and over ; Inpatients ; Feces/microbiology ; Phylogeny ; Stroke Rehabilitation ; },
abstract = {RATIONALE: Gut microbiota diversity plays a crucial role in various health outcomes, including metabolic regulation and nutritional status. Polypharmacy, common among older adults, has been linked to adverse clinical outcomes, yet its impact on gut microbiota diversity remains poorly understood. This study aimed to investigate the association between polypharmacy and gut microbiota diversity in older post-stroke patients.<br><br>METHODS: This cross-sectional study included post-stroke inpatients aged 65 years or older undergoing rehabilitation. Polypharmacy was defined as the prescription of five or more drugs. Metagenomic analysis of DNA from patient fecal samples was conducted, calculating three alpha diversity indices: the Shannon Diversity Index, Operational Taxonomic Unit (OTU) richness, and Faith's Phylogenetic Diversity (PD). Multiple linear regression analysis was used to determine whether polypharmacy was independently associated with the gut microbiota diversity upon admission, adjusting for potential confounders.<br><br>RESULTS: A total of 156 patients (mean age 78.4 years; 55.8 % male) were analyzed. The median number of medications taken on admission was 6 (4-8), and 69.9 % of patients had polypharmacy. Polypharmacy was independently associated with decreased Shannon Diversity Index (&#x3b2; = -0.202, p = 0.019). No statistically significant association was found with Observed OTUs (&#x3b2; = -0.159, p = 0.067) and Faith's PD (&#x3b2; = -0.38, p = 0.111).<br><br>CONCLUSIONS: Polypharmacy is associated with qualitative alterations in the gut microbiota of older post-stroke patients, with a potential negative trend in quantitative alterations and phylogenetic classification. The findings underscore the need to consider the impact of polypharmacy on the gut microbiome in stroke management.},
}
@article {pmid41138387,
year = {2025},
author = {Ochoa-Bernal, TG and Huber, DH and Espinosa-Solares, T},
title = {The progressive shift in anaerobic digestion communities under extreme propionate levels led to a redundant microbiome capable of producing methane.},
journal = {Journal of environmental management},
volume = {395},
number = {},
pages = {127698},
doi = {10.1016/j.jenvman.2025.127698},
pmid = {41138387},
issn = {1095-8630},
mesh = {*Methane/metabolism ; *Propionates/metabolism ; *Microbiota ; Animals ; Anaerobiosis ; Chickens ; Bacteria/metabolism ; },
abstract = {Propionate accumulation exerts a significant inhibitory effect on anaerobic digestion, which may result in the cessation of methane production. It has been reported that propionate can be degraded solely by a limited group of syntrophic propionate-oxidizing bacteria belonging to the following genera: Syntrophobacter, Smithella, and Pelotomaculum. Chicken litter is a substrate rich in protein and nitrogen, which makes it more susceptible by total ammonia nitrogen toxicity. This study aimed to elucidate the alterations and responses of microbial communities to extreme concentrations of propionate in co-digestion with chicken litter, thereby providing an extensive overview of community composition and functional potential through shotgun metagenomics sequencing. An enrichment process was conducted over 1220 days in co-digestion with chicken litter, utilizing a 10 L digester operating in semi-continuous mode and progressively increasing sodium propionate concentrations to create a selection pressure. The feed had 12 propionate concentration levels, varying from 0 to 24 g L[-1]; chicken litter was kept at 3 %. At the end of the enrichment process, it was surprisingly observed that the well known syntrophic bacteria were not present; instead, bacteria from the Proteiniphilum, Petrimonas, Vibrio, Corynebacterium, Coprobacter, Brachymacterium, Cloacimonas, and Treponema genera were found. Propionate degradation was mainly attributed to Corynebacterium stationis and Corynebacterium casei, through the ackA and pta enzymes. The putative lactate pathway was also detected by the pct enzyme. Methanogenic archaea increased relative abundance, particularly the genera Methanoculleus, Methanospirillum, Methanococcus, and Methanocella, synthesizing methane in several pathways, mainly hydrogenotrophic in the range from 0.189 to 0.320 mL CH4 kgvsadded[-1]. The enrichment using extreme propionate concentrations in co-digestion with chicken litter resulted in a microbial consortium that stabilized propionate degradation and methane production, which can be attributed to an adaptive functional redundancy.},
}
@article {pmid41138328,
year = {2025},
author = {Bai, X and Bi, J and Li, A and Deng, X and Zhao, Z and Hu, H and Pan, H},
title = {Walnut cake meal improves amino acids, fatty acid composition and flavor of egg yolk via the microbiota-yolk metabolites crosstalk in Jingfen-1 laying hens.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105981},
pmid = {41138328},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/microbiology/metabolism ; Female ; Animal Feed/analysis ; *Egg Yolk/chemistry ; *Amino Acids/analysis/metabolism ; Diet/veterinary ; *Fatty Acids/analysis/metabolism ; *Juglans/chemistry ; Random Allocation ; *Gastrointestinal Microbiome/drug effects ; Animal Nutritional Physiological Phenomena/drug effects ; Taste ; },
abstract = {Egg production is important for both human nutrition and its economic contribution. However, regions with a shortage of soybean meal (SM) may not meet the nutritional needs of the laying hen industry. Walnut cake meal (WM), a by-product of walnut processing, can be reused in laying hen production. In this study, we evaluated the feasibility of using WM to reduce the demand for SM in the laying hen industry. A total of 144 47-week laying hens (with similar performance) were randomly assigned to two groups (12 hens in each replicate and six replicates for each group). One group was fed a maize-SM diet (SM group), and the other was fad a maize-WM diet (WM group). The diets of both groups had similar crude protein and ME contents. After replacing SM with WM, the laying rate, egg weight, and feed efficiency did not significantly change (P > 0.05). WM increased (P < 0.05) the polyunsaturated fatty acids content, particularly linoleic acid, as well as umami and essential amino acids, in the eggs. WM diet also enhanced the flavor of eggs by enriching multiple volatile organic compounds that smell of sweet and herb-like foods. In addition, probiotic bacteria such as Cyanobacteriota and Prevotella, were enriched in the cecal microbiota of laying hens fed WM. Moreover, targeted metabolomics revealed the enrichment of butyric acid, 4-methylvaleric acid, isoleucine, and valine in the cecal digesta of laying hens fed with WM. Metagenomic sequencing revealed genes in the cecal microbiota associated with the synthesis of these enriched metabolites. Increased isoleucine and 4-methylvaleric acid in the digestive system contributed to the enrichment of fatty acids and amino acids in the yolks, whereas elevated flavor substances in the yolk could be associated with more amino acids in the intestine of laying hens. In conclusion, WM can reduce the need for soybean meal, improve cecal metabolism and egg quality, and ultimately achieve sustainable agriculture.},
}
@article {pmid41138185,
year = {2025},
author = {Waschina, S and Pagel, J and Seeger, K and Pasderski, E and Rühlemann, M and Froitzheim, S and Künzel, S and Sommer, F and Franzenburg, S and Fortmann, I and Sugihara, F and Faust, K and Marissen, J and Demmert, M and Baines, JF and Göpel, W and Herting, E and Kaleta, C and Rupp, J and Härtel, C},
title = {Bacterial metabolite patterns of infants receiving multi-strain probiotics and risk of late-onset sepsis.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116431},
doi = {10.1016/j.celrep.2025.116431},
pmid = {41138185},
issn = {2211-1247},
mesh = {Humans ; *Probiotics/therapeutic use ; *Sepsis/microbiology/prevention &amp; control ; Infant, Newborn ; Female ; Male ; Gastrointestinal Microbiome ; Infant, Very Low Birth Weight ; Infant ; Metabolome ; Risk Factors ; *Bacteria/metabolism ; },
abstract = {The effect of multi-strain probiotics containing Bifidobacterium longum (B. longum) on late-onset sepsis (LOS) risk in very-low-birth-weight infants (VLBWIs; birth weight < 1,500 g) remains uncertain. In a single-center study, we analyzed intestinal metagenome and metabolome data in VLBWIs during the period of highest vulnerability of LOS. Using a unit's policy change to routinely administer B. longum subspecies infantis plus Lactobacillus acidophilus as natural experiment, we compared 97 infants (including 38 LOS cases) after change with 78 infants (including 32 LOS cases) before. Probiotic supplementation was associated with more beneficial bacteria and reduced abundance of nosocomial pathobionts, such as Klebsiella spp. Infants in the probiotic group had significantly lower concentrations of B. longum fermentation products prior to sepsis diagnosis than matched non-LOS cases (acetate: padj = 0.0049; lactate: padj = 0.048). Modulation of the gut metabolic milieu is an interesting target for LOS prevention.},
}
@article {pmid41138182,
year = {2025},
author = {Gao, SM and Lan, LY and Yang, L and Chen, T and Fan, PF},
title = {Health-associated key gut microbiota drives the variation in community metabolic interactions in non-human primates.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116477},
doi = {10.1016/j.celrep.2025.116477},
pmid = {41138182},
issn = {2211-1247},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology/genetics ; *Primates/microbiology ; Feces/microbiology ; *Microbial Interactions ; Metagenome ; Bacteria/genetics/metabolism/classification ; },
abstract = {Gut microbiota often undergo metabolic cross-feeding and resource competition. However, our understanding of global variations in these interactions and their implications for host health remain elusive. By analyzing a microbial genome catalog from 841 fecal metagenomes across 53 primate species worldwide, we identified key microbiota assigned to two taxa, i.e., Bacillota_A and Pseudomonadota, which well predicted the trade-off of community-level interaction types between metabolic competition and cooperation. Specifically, Bacillota_A species were inherently competitive and amino acid auxotrophic and typically found in anaerobic habitats. In contrast, members of Pseudomonadota were inherently cooperative, siderophore producers, and more abundant in aerobic conditions. Random forest models successfully distinguished unhealthy gut samples from healthy samples through the key competitive and cooperative microbiota, suggesting potential links between community metabolic interactions and host health. Together, this study enhances our mechanistic understanding of microbial interaction dynamism within complex gut ecosystems, offering new targets for understanding host health.},
}
@article {pmid41138002,
year = {2025},
author = {Yarahmadi, A and Emrahoglu, S and Afkhami, H and Mehdipour, A and Aghaali, M},
title = {Integrative insights into the oral microbiome's role in systemic diseases: novel therapeutic strategies and future directions.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {178},
pmid = {41138002},
issn = {1572-9699},
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Periodontal Diseases/microbiology/therapy ; Dental Caries/microbiology/therapy ; Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The oral microbiome, which is known as the diverse and abundant microbial community within the human oral cavity, is an integral part of the human body. The investigation of its composition and functions in both wellness and illness has received notable attention from researchers in recent times. The presence of oral bacteria directly impacts the disease condition of dental caries and periodontal diseases. The oral microbiota interacts dynamically with the host to influence immune regulation and metabolic processes. Advances in sequencing technologies, including whole-metagenome shotgun sequencing, the examination of 16S ribosomal RNA, and meta-transcriptomes, we now possess the capability to comprehensively explore the diversity and functionalities of oral microorganisms, encompassing those that are not amenable to cultivation. As research advances, there is a growing body of evidence suggesting the notable contribution of the oral microbiome to various health conditions, extending beyond ailments solely associated with the oral cavity. This review advances current understanding by presenting a systemic, integrative perspective on the oral microbiome's role in chronic diseases, offering novel hypotheses and therapeutic directions beyond those explored in prior literature.},
}
@article {pmid41137523,
year = {2025},
author = {Tegegne, HA and Savidge, TC},
title = {Gut microbiome metagenomics in clinical practice: bridging the gap between research and precision medicine.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2569739},
pmid = {41137523},
issn = {1949-0984},
support = {P01 AI152999/AI/NIAID NIH HHS/United States ; T32 AI141349/AI/NIAID NIH HHS/United States ; R01 NR013497/NR/NINR NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01 DK130517/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; },
abstract = {Gut microbiome metagenomics is emerging as a cornerstone of precision medicine, offering exceptional opportunities for improved diagnostics, risk stratification, and therapeutic development. Advances in high-throughput sequencing have uncovered robust microbial signatures linked to infectious, inflammatory, metabolic, and neoplastic diseases. Clinical applications now include pathogen detection, antimicrobial resistance profiling, microbiota-based therapies, and enterotype-guided patient stratification. However, translation into routine care is hindered by significant barriers including methodological variability, limited functional annotation, lack of bioinformatics standardization, and underrepresentation of global populations. This review synthesizes current translational strategies, emphasizing the need for hypothesis-driven designs, multi-omic integration, longitudinal and multi-center cohorts, and mechanistic validation. We also examine critical ethical, regulatory, and equity considerations shaping the clinical landscape. Realizing the full potential of microbiome-informed care will require globally harmonized standards, cross-sector collaboration, and inclusive frameworks that ensure scientific rigor and equitable benefit.},
}
@article {pmid41137517,
year = {2025},
author = {Bayne, J and Charavaryamath, C and Hu, Y and Yousefi, F and Murphy, M and Law, A and Michael, A and Muyyarikkandy, MS and Nibbering, B and Smits, WK and Kuijper, E and Opriessnig, T and Sauer, M and Scaria, J and Sponseller, B and Ramirez, A and Mooyottu, S},
title = {The swine IsoLoop model of the gut host-microbiota interface enables intra-animal treatment comparisons to advance 3R principles.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2568706},
pmid = {41137517},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Swine ; Ileum/microbiology/surgery ; *Host Microbial Interactions ; Humans ; Feces/microbiology ; Clostridioides difficile/physiology ; Fecal Microbiota Transplantation ; Bacteria/classification/genetics/isolation &amp; purification ; Models, Animal ; Disease Models, Animal ; },
abstract = {Understanding gut-host microbiota interactions requires models that replicate human physiology while providing region-specific resolution, translational precision, and minimal animal use. To this end, we developed the IsoLoop model, a swine gut loop platform enabling intra-animal, multi-treatment comparisons. Microbiota-depleted ileal loops were surgically created in pigs, maintaining neurovascular integrity while isolating them from the anastomosed digestive tract. In Experiment 1, loops were inoculated with human fecal microbiota (HFM) or HFM combined with Peptacetobacter hiranonis. In Experiment 2, they were inoculated with Clostridioides difficile. Host-microbiota interactions were compared with respective controls in each experiment. The IsoLoop model reduced animal use by 75% compared to conventional whole-animal designs. Following antibiotic-induced depletion, loops re-established microbial diversity by day 5, despite reduced richness and loss of taxa, including Lactobacillus. HFM transplantation in microbiota-depleted loops induced robust transcriptomic recovery, enriched Akkermansia and Bifidobacterium, and restored specific metabolic pathways, although taxonomic and metabolic restoration remained incomplete and divergent. P. hiranonis promoted normal ileum-like metagenomic functional convergence, activated epithelial repair pathways, and increased specific secondary bile acids. C. difficile challenge recapitulated early infection pathology in IsoLoops. The IsoLoop model offers an ethical and precise platform for investigating host-microbiota crosstalk, localized enteric pathologies, and therapeutic interventions.},
}
@article {pmid41137451,
year = {2025},
author = {Liu, Y and Wu, X and Wegner, CE and Ma, K and Xu, G and Cui, Z and Zhang, F and Liesack, W and Peng, J},
title = {Temperature Increase in Paddy Soils Remodels the Relationship Between the Anaerobic Food Web and the Q10 of CH4 Production.},
journal = {Molecular ecology},
volume = {34},
number = {22},
pages = {e70156},
doi = {10.1111/mec.70156},
pmid = {41137451},
issn = {1365-294X},
support = {2021YFD1900100//National Key Research and Development Program of China/ ; 42277307 and 41977038//National Natural Science Foundation of China/ ; },
mesh = {*Methane/biosynthesis ; *Soil Microbiology ; *Soil/chemistry ; Temperature ; *Food Chain ; Microbiota/genetics ; Oryza ; Metagenomics ; Anaerobiosis ; Climate Change ; },
abstract = {Rice paddies are a major source of anthropogenic CH4 emissions globally, with the temperature sensitivity (Q10) of CH4 production playing a key role in forecasting emissions under future climate scenarios. However, the mechanistic links among Q10, the soil microbiome and mean annual temperature (MAT) in paddy soils remain poorly understood. To address this gap, we employed quantitative PCR, amplicon sequencing, genome-resolved metagenomics and metatranscriptomics to investigate CH4 production dynamics and the response of the methanogenic food web to warming in low MAT (LMAT, 4°C-9°C) and high MAT (HMAT, 14°C-16°C) soils. Our results indicate that CH4 production exhibits a higher Q10 in LMAT soils, while warming exerts a more pronounced impact on the methanogenic food web in HMAT soils. Notably, we identified negative correlations between the Q10 and the metagenomic abundance of genes encoding glycoside hydrolases, carbohydrate-binding modules, polysaccharide lyases-related carbohydrate-active enzymes (CAZymes), hydrogenotrophic methanogenesis, and the average genome size (AGS) of the microbiome. Conversely, genes encoding auxiliary activity CAZymes and those associated with acetate metabolism and fermentation were positively correlated with Q10. Genes linked to acetoclastic and hydrogenotrophic methanogenesis exhibited lower responsiveness to warming in LMAT soils compared to HMAT soils. Additionally, warming led to a significant reduction in both gene and transcript abundances associated with methylotrophic methanogenesis across both MAT regimes. These findings provide novel insights into the temperature-dependent restructuring of methanogenic pathways and resource utilisation strategies in paddy soils, with important implications for predicting CH4 emissions under climate change.},
}
@article {pmid41137068,
year = {2025},
author = {Asin, ICA and Egana, JMC and Paul, RE and Bautista, MAM},
title = {Virome sequencing and analysis of Aedes aegypti and Aedes albopictus from ecologically different sites in the Philippines.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {426},
pmid = {41137068},
issn = {1756-3305},
mesh = {Animals ; *Aedes/virology ; Philippines ; *Virome/genetics ; *Mosquito Vectors/virology ; Metagenomics ; Phylogeny ; *Insect Viruses/genetics/classification/isolation &amp; purification ; },
abstract = {BACKGROUND: Aedes aegypti and Aedes albopictus are important vectors of arthropod-borne viruses (arboviruses) such as dengue, chikungunya, and Zika. Changes in land use have long been considered a factor in the emergence of infectious diseases; thus, it is imperative to look at how the diversity of viruses is also affected by land use.<br><br>METHODS: Viral metagenomics was used to determine the virome compositions of 260 Ae. aegypti and 75 Ae. albopictus collected from the three study sites in Los Ba&#xf1;os, Laguna, Philippines, that differ in topography and land use transformations.<br><br>RESULTS: The virome of Ae. aegypti and Ae. albopictus revealed virus sequences belonging to 12 different taxon groups, dominated by insect-specific viruses (ISVs) such as Phasi Charoen-like phasivirus (PCLV), Humaita Tubiacanga virus (HTV), and Wenzhou sobemo-like virus 4 (WSLV4). Both species were found to share the majority of identified viruses. Moreover, a relatively higher number of viral families were observed in sites that had undergone transformation from agriculture to bare and built-up areas, compared with a forest site.<br><br>CONCLUSIONS: The findings of this study underscore the vast diversity of Ae. aegypti and Ae. albopictus viruses from the selected sites in the Philippines generated by viromics. Results also impact the understanding that land use may contribute to virus diversity. The prevalence of ISVs and nondetection of arboviruses in the virome composition of Ae. aegypti and Ae. albopictus were notable, suggesting further examination of the roles of ISVs in arbovirus transmission.},
}
@article {pmid41136898,
year = {2025},
author = {Junier, T and Palmieri, F and Ubags, ND and Trompette, A and Koutsokera, A and Junier, P and Pagni, M and Neuenschwander, S},
title = {Prevalence of oxalotrophy in the human microbiome.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {954},
pmid = {41136898},
issn = {1471-2164},
support = {40B2-0_194701//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; GRS-064/18//Gebert R&#xfc;f Stiftung/ ; },
mesh = {Humans ; *Oxalates/metabolism ; *Microbiota/genetics ; Metagenome ; Gene Transfer, Horizontal ; *Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Incomplete degradation of oxalate, a compound commonly found in the diet, can lead to disease in humans, particularly affecting the kidneys. The concentration of oxalate in the body depends on several factors, one of which is intestinal absorption-an aspect influenced by oxalotrophy among enteric bacteria. Despite its potential significance, oxalotrophy in the human microbiome remains poorly understood.<br><br>RESULTS: In this study, we conducted a systematic search for the co-occurrence of three key oxalotrophy genes-frc, oxc, and oxlT. We developed and validated specific conservation models for each gene and applied them to genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. Our analysis revealed that oxalotrophy, defined as the capacity to use oxalate as an energy source, is a rare metabolic trait predominantly confined to the gut. We also found evidence that this capacity can be acquired via horizontal gene transfer.<br><br>CONCLUSIONS: While oxalotrophy is relatively uncommon, the broader capacity for oxalate degradation is more widespread. Notably, the genes frc and oxc are frequently found in close proximity within genomes, suggesting a selective advantage for organisms possessing this capability. Incomplete degradation of oxalate, a compound commonly found in the diet, can cause disease in humans, particularly affecting the kidney. Its concentration in the body depends on several factors, one of which is intestinal absorption, which is itself affected by oxalotrophy among enteric bacteria. Oxalotrophy in the human microbiome is poorly known. In this study, we perform a systematic search for the simultaneous presence of the three oxalotrophy genes, namely frc, oxc and oxlT. Thanks to the construction and validation of specific conservation models for all three genes, we were able to search for oxalotrophy in genomes and metagenomes associated with the human digestive tract, oral cavity, and lungs. We report that oxalotrophy-the capacity to use oxalate as an energy source-is a rare metabolic trait, mostly confined to the gut, and also find evidence that it can be acquired by horizontal gene transfer. By contrast, the capacity for oxalate degradation is more widespread, and two genes responsible for it (frc and oxc) are almost always close together in the genome, suggesting selection pressure.},
}
@article {pmid41136439,
year = {2025},
author = {Xue, W and Liu, Z and Zhang, Y and Raza, W and Li, Y and Jiang, L and Tao, Y and Qian, J and Alexandre, J and Zhao, FJ and Xu, Y and Sedlazeck, F and Shen, Q and Jiang, G and Wei, Z},
title = {LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9353},
pmid = {41136439},
issn = {2041-1723},
mesh = {*Metagenome/genetics ; *Metagenomics/methods ; *Microbiota/genetics ; Humans ; Cluster Analysis ; Gastrointestinal Microbiome/genetics ; *Software ; Algorithms ; },
abstract = {Long-read sequencing has transformed metagenomics and improved the quality of metagenome-assembled genomes (MAGs). However, current binning methods struggle with identifying unknown species and managing imbalanced species distributions. Here, we present LorBin, an unsupervised binner specially designed to reconstruct MAGs in natural microbiomes. LorBin deploys a two-stage multiscale adaptive DBSCAN and BIRCH clustering with evaluation decision models using single-copy genes to maximize MAG recovery. LorBin outperforms six competing binners in both simulated and real microbiomes, including oral, gut, and marine samples. LorBin generated 15-189% more high-quality MAGs with high serendipity and identified 2.4-17 times more novel taxa than state-of-the-art binning methods. Together, LorBin is a promising long-read metagenomic binner for accessing species-rich samples containing unknown taxa and is efficient at retrieving more complete genomes from imbalanced natural microbiomes.},
}
@article {pmid41135729,
year = {2025},
author = {Li, M and Wang, H and Chu, H and Wang, Y and Lu, J},
title = {Deciphering microbial dynamics in coastal ecosystems under polycyclic aromatic hydrocarbon stress: Community assembly, interaction networks, and metabolic adaptations.},
journal = {Environmental research},
volume = {287},
number = {},
pages = {123179},
doi = {10.1016/j.envres.2025.123179},
pmid = {41135729},
issn = {1096-0953},
mesh = {*Polycyclic Aromatic Hydrocarbons/toxicity/analysis ; *Water Pollutants, Chemical/toxicity/analysis ; *Microbiota/drug effects ; Geologic Sediments/microbiology/chemistry ; Estuaries ; Ecosystem ; Environmental Monitoring ; Rivers/microbiology/chemistry ; China ; },
abstract = {The significant toxicity and carcinogenicity of polycyclic aromatic hydrocarbons (PAHs) have raised increasing concern about their contamination, particularly in coastal regions with intensive human activities and urbanization. However, limited information exists on microbial response mechanisms across varying levels of PAHs contamination. In this study, sediment samples at 18 locations along the Yantai inland river and estuary were collected in October 2024 to examine the partitioning and spatial dispersal of PAHs, while microbial community assembly, interaction networks, and metabolic adaptations were analysed using metagenomics. Results showed that the average ∑PAHs concentration in the estuary (27.95 ± 2.91 ng/g) was significantly lower than that in the river (77.54 ± 43.39 ng/g), with a correspondingly higher ecological risk in the river. High-molecular-weight (HMW) PAHs dominated in both estuary and river sediments due to their high hydrophobicity and stability. Microbial community analysis revealed increased microbial diversity and a higher abundance of PAHs-degrading microbes (e.g., Ruegeria, known for degrading low-molecular-weight PAHs) under higher PAHs contamination. Co-occurrence network and topological analyses demonstrated dual regulatory effects of PAHs stress on microbial interactions, where elevated PAHs contamination intensified interspecies connectivity while simultaneously inducing destabilizing negative covariance patterns that weakened microbial network integrity. Additionally, neutral community model analysis indicated that stochastic processes dominated community assembly, with higher proportions of stochasticity observed in rivers under high PAHs stress. Notably, elevated PAHs concentrations significantly impaired energy metabolism and nitrogen metabolic pathways (p < 0.05), suggesting altered nitrogen biogeochemistry under PAHs contamination. This study advances the understanding of microbial population responses to different PAHs contamination levels in coastal regions.},
}
@article {pmid41135463,
year = {2025},
author = {Zhang, A and Pan, P and Zhou, NY and Li, T},
title = {Synergistic mineralization of the UV filter benzophenone-3 by a cross-feeding consortium from wastewater treatment plants: Insights into novel pathway and bioremediation strategy.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140176},
doi = {10.1016/j.jhazmat.2025.140176},
pmid = {41135463},
issn = {1873-3336},
mesh = {*Benzophenones/metabolism ; Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; *Wastewater/microbiology ; *Sunscreening Agents/metabolism ; *Microbial Consortia ; Bacteria/metabolism/genetics ; },
abstract = {Benzophenone-3 (BP-3), used as an organic UV filter in diverse consumer products including cosmetics, has been frequently detected in wastewater treatment plants (WWTPs) and aquatic environments. BP-3 and its transformation products are regarded as emerging micropollutants due to their low biodegradability. Here, we investigate the synergistic degradation of BP-3 by a bacterial consortium seeded from aerobic sludge WWTPs. BP-3 is found to be initially degraded through a novel pathway involving a C-C bond cleavage step, producing intermediates 3-methoxyphenol (3MOP) and benzoate, two naturally occurring compounds which can be readily degraded in the environment. Metagenome-guided pure culture isolation and pathway analysis reveal that bacterial strains from genera Pigmentiphaga and Brucella synergistically contribute to the BP-3 mineralization. Specifically, the Pigmentiphaga strain degrades BP-3 into benzoate and 3MOP, with the former being utilized by itself and the latter utilized by the Brucella strain. A reconstructed consortium, consisting of two isolated strains from Pigmentiphaga and Brucella, exhibits similar degradation performance to that of the natural consortium, indicating their crucial roles in environmental BP-3 degradation. These findings provide new insights into BP-3 biodegradation at the microbial community level, offering potential strategies for wastewater treatment applications by manipulating synthetic microbial consortia.},
}
@article {pmid41131658,
year = {2025},
author = {Li, Z and Luo, W and Xie, H and Mo, C and Qin, B and Zhao, Y and Chen, X and Zhang, S and Zhao, Y and Wang, M and Yang, Y and Cai, J and Wang, B and Liu, X and Shi, Y},
title = {Reovirus infection results in rice rhizosphere microbial community reassembly through metabolite-mediated recruitment and exclusion.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {214},
pmid = {41131658},
issn = {2049-2618},
mesh = {*Oryza/virology/microbiology ; *Rhizosphere ; *Reoviridae/physiology/pathogenicity ; Soil Microbiology ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota ; Metagenomics/methods ; *Plant Diseases/virology/microbiology ; Metabolomics/methods ; },
abstract = {BACKGROUND: Microbial assembly plays a critical role in ecosystem function and biodiversity. While numerous studies have explored the effect of abiotic factors on the belowground community assembly, much less is known about the role of biotic interactions, particularly viral infections, in shaping microbial communities. Southern rice black-streaked dwarf virus (SRBSDV), a member of the Fijivirus genus in the Reoviridae family, has caused severe yield losses in rice due to its rapid transmission. However, its specific effects on rhizosphere microbiota and the dynamics of microbial community changes have not been fully elucidated.<br><br>RESULTS: By leveraging metabolomics with amplicon and metagenomics, this study provided a comprehensive understanding of the effect of SRBSDV infection on the rhizosphere microbial community and their functions. The results revealed that SRBSDV invasion led to significant changes in rhizosphere metabolites and microbial assembly processes. Specifically, the estimated overdispersion of cations sharply decreased following viral infection, while anion levels decreased markedly during early infection and then increased rapidly after 15&#xa0;days. Key taxa, such as methanotrophs (e.g., Methylomicrobium), nitrifiers (e.g., Nitrospira), and iron-cycling bacteria (e.g., Sideroxydans), not only increased in abundance but also showed strong involvement in the microbial assembly processes. These key microbes were closely linked to specific metabolites and organized into two distinct network modules. Both modules predominantly recruited beneficial microbes, but one module also actively excluded potentially harmful taxa (e.g., Salmonella), which could disrupt community stability. Further experiments with exogenous metabolites confirmed the vital role of quercetin in attracting beneficial microbes while repelling harmful ones.<br><br>CONCLUSION: The findings indicate that arboviruses can strongly influence the belowground rhizosphere microbial assembly processes by modulating metabolite profiles to selectively recruit or exclude key microbial species. These taxa, in turn, play fundamental roles in rhizosphere functions. These insights lay the groundwork for strategies to enhance rice immunity against viral infections by managing the rhizosphere microbial community. Video Abstract.},
}
@article {pmid41131656,
year = {2025},
author = {Chen, X and Xu, J and Zhang, L and Xie, B and Ren, J and He, J and Liu, T and Liu, Q and Dong, Y and He, X and Yao, J and Wu, S},
title = {Altered ruminal microbiome tryptophan metabolism and their derived 3-indoleacetic acid inhibit ruminal inflammation in subacute ruminal acidosis goats.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {215},
pmid = {41131656},
issn = {2049-2618},
support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; },
mesh = {Animals ; Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; Animal Feed/analysis ; *Tryptophan/metabolism ; *Indoleacetic Acids/metabolism ; *Gastrointestinal Microbiome ; *Inflammation ; *Goat Diseases/microbiology/metabolism ; Diet ; Female ; Metagenomics ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Fermentation ; Metagenome ; },
abstract = {BACKGROUND: Subacute ruminal acidosis (SARA) is a digestive disorder that often severely jeopardizes the health and lactation performance of ruminants fed a high-energy diet. Different dairy ruminants exhibit varying degrees of inflammation accompanied by variations in the rumen microbiota when SARA occurs. Our understanding of the occurrence of SARA and varying degrees of rumen epithelial inflammation is lacking. Hence, we performed rumen metagenomic, metagenome-assembled genome and metabolomic analyses, with transcriptome and single-nucleus RNA sequence analyses, to explore the microbial mechanism of SARA occurrence and different degrees of inflammation.<br><br>RESULTS: A total of 36 goats fed two diets with gradually increasing levels of rumen-degradable starch (RDS) were included in this study, and SARA goats fed 70% concentrate diets supplemented with whole corn (HGW-SARA) and SARA goats fed 70% concentrate diets supplemented with crushed corn (HGC-SARA) were identified. Moreover, 11 goats fed a control basal diet, named LGW-CON, were also included. Compared with those in the LGW-CON group, the rumen fermentation capacity was enhanced, accompanied by ruminal epithelial and systemic inflammation, in goats from HGW-SARA and HGC-SARA. Between them, HGC-SARA goats presented less inflammation. Notably, the ruminal inflammation-related pathways were increased only in the HGW-SARA group but not in the HGC-SARA group. Metagenomic analysis revealed that the &#x3b2; diversity of SARA goats was significantly different from that of LGW-CON goats. Ruminococcus significantly increased in both SARA groups, whereas Prevotella and Bacteroidales significantly decreased, which was accompanied by a decrease in cellulose and hemicellulose enzymes and an increase in lysozymes and lipopolysaccharide synthesis enzymes. Multi-omics analysis of the ruminal contents and tissues suggested that epithelial inflammation was caused by disturbed ruminal microbiome-induced Th17 cell differentiation and IL-17 signalling pathway activation. Comparative analyses between the HGW-SARA and HGC-SARA groups highlighted the importance of Selenomonas and Bifidobacterium, as well as bacterial tryptophan metabolism, in the production of 3-indoleacetic acid, which mitigated ruminal epithelial inflammation by modulating Th17 cells and inhibiting IL-17 signalling. Ruminal microbiota transplantation from HGW-SARA goats to healthy dairy goats and mice revealed the role of microbes in epithelial inflammation. Additionally, 3-indoleacetic acid supplementation reduced rumen inflammation and the IL-17 concentration in the serum, improved VFAs absorption, and enhanced milk production.<br><br>CONCLUSIONS: This study unveiled that after SARA was induced by high-concentrate feeding, the rumen homeostasis was disrupted, and rumen fiber degradation capacity of dairy goats decreased, but the LPS synthesis capacity increased, and inflammation of the rumen epithelium was observed. However, the ruminal microbial species from the Bifidobacterium and Selenomonas genera and bacterial 3-indole acetic acid are pivotal in mitigating ruminal epithelial inflammation during SARA in dairy goats. This could potentially be attributed to the modulation of ruminal Th17 cell proportions and the inhibition of IL-17 signalling pathways. Video Abstract.},
}
@article {pmid41131583,
year = {2025},
author = {Lou, Y and Lv, Y and Wang, X and Luo, Y and Lou, J and Yu, Y and Gu, W and Yu, J and Fang, Y and Zhao, H and Peng, K and Chen, J and Ni, Y},
title = {Ruminococcus torques ameliorates the inflammation bowel disease and gut barrier dysfunction by modulating gut microbiota and bile acid metabolism.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1162},
pmid = {41131583},
issn = {1479-5876},
support = {No. CCCF-QF-2022B04-4//the China Crohn's &amp; Colitis Foundation/ ; 2024KY1171//Medical Science and Technology Project of Zhejiang Province/ ; 82170583//National Natural Science Foundation of China/ ; U23A20167//National Natural Science Foundation of China/ ; 82400595//National Natural Science Foundation of China/ ; 2025C02085//the Key R&amp;D Program of Zhejiang/ ; 2021YFC2701900//the National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Animals ; Male ; *Bile Acids and Salts/metabolism ; *Inflammatory Bowel Diseases/microbiology ; *Ruminococcus/physiology ; *Intestinal Mucosa/pathology/microbiology ; Child ; Colitis/pathology/microbiology ; Mice ; Female ; Mice, Inbred C57BL ; Crohn Disease/microbiology ; Adolescent ; },
abstract = {BACKGROUND: Recent advances in microbiome-targeted therapies have uncovered immunomodulatory bacterial taxa with strain-specific therapeutic potential; however, the microbial signatures driving exclusive enteral nutrition (EEN) efficacy, particularly protective microbiota, and their mechanistic links to therapeutic outcomes remain uncharacterized in pediatric inflammatory bowel disease (IBD). Elucidating these microbial determinants and their functional pathways is critical for advancing targeted probiotic strategies in children.<br><br>METHODS: A cohort of treatment-na&#xef;ve pediatric Crohn's disease (CD) patients and age-matched healthy controls (HC) were enrolled. Fecal samples were collected from both HC and CD patients during active phase and remission following EEN therapy. Metagenomic sequencing, qPCR validation, and targeted bile acid (BA) analysis were conducted to identify candidate protective strains and potential impacts on BA homeostasis. Mechanistic investigations were conducted using dextran sulfate sodium (DSS)- and trinitrobenzene sulfonic acid (TNBS)-induced colitis model in male mice.<br><br>RESULTS: The relative abundance of Ruminococcus torques (R. torques) demonstrated significant depletion in active CD cases (p&#x2009;=&#x2009;0.02) compared to HC, which was restored after EEN treatment at remission status (p&#x2009;<&#x2009;0.001). Its level was negatively correlated with the disease severity index (PCDAI r=-0.64; CDEIS r=-0.70) and positively correlated with the secondary to primary BA ratio (r&#x2009;=&#x2009;0.27). In murine models, R. torques supplementation attenuated colitis severity through enhancing epithelial integrity (claudin-3, 3.3-fold; occludin, 7.5-fold), suppressing pro-inflammatory mediators (TNF-&#x3b1;, -44%; IL-6, -71%), regulating BA metabolism (secondary/unconjugated BAs, 29%) and autophagy pathway (LC3-II/LC3-I ratio, -1.8-fold).<br><br>CONCLUSIONS: Our findings demonstrated R. torques as a novel microbial therapeutic candidate for IBD management. The anti-colitis mechanisms involve the modulation of BA metabolic homeostasis, epithelial barrier reinforcement, and inflammation resolution.},
}
@article {pmid41131465,
year = {2025},
author = {Hamdene, I and Bez, C and Bertani, I and López-Menchero, JR and Yahyaoui, A and Venturi, V and Sadfi-Zouaoui, N},
title = {Endophytic bacterial communities associated with halophytic plants in kebili and Gabes regions of Southern Tunisia.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {683},
pmid = {41131465},
issn = {1471-2180},
mesh = {Tunisia ; *Salt-Tolerant Plants/microbiology ; *Endophytes/classification/isolation &amp; purification/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Soil Microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Plant Roots/microbiology ; DNA, Bacterial/genetics ; Soil/chemistry ; *Microbiota ; Salinity ; Biodiversity ; Sequence Analysis, DNA ; Amaranthaceae/microbiology ; },
abstract = {In the arid regions of southern Tunisia, soil and irrigation water salinity represent major challenges to agricultural sustainability. Despite the increasing interest in plant-associated microbes, the role of endophytic bacteria in conferring salt tolerance remains largely unexplored in this context. To address this gap, twenty-two halophytic plants and their associated soils were sampled from five distinct sites across the Kebili and Gabes governorates. Significant differences in soil physicochemical properties were observed between sampling sites. The soils are generally poorly developed, non-fertile (with very low organic matter and high CaCO3 levels), and highly saline, leading to limited cultivation potential. Molecular identification of plants revealed nine different families and 14 genera, with the Amaranthaceae family being the most prominent, including Atriplex spp. (2), Bassia spp. (2), Suaeda spp. (4), and Halocnemum spp. (1). Bacterial community studies were conducted of both culturable and non-culturable endophyte communities inhabiting the green and root compartments of different halotolerant plants. Endophytic microbiome compositions differed between above-ground and below-ground tissues within the same plant family. A higher prevalence of three phyla Proteobacteria (67.80%), Firmicutes (14.06%), and Actinobacteria (6.57%) was detected across all samples. At the genus level, Acinetobacter, Halomonas, Kushneria, Pseudomonas, Psychrobacter, Stenotrophomonas, and Streptomyces formed the common core microbiome. Functional predictions of endophytic bacteria in halophytes highlighted multiple KEGG functional pathways, indicating recruitment of beneficial bacterial taxa to adapt to extreme hypersaline conditions, including plant growth-promoting, biocontrol, and halophilic bacteria.},
}
@article {pmid41131367,
year = {2025},
author = {Welsh, C and Cabotaje, PR and Marcelino, VR and Watts, TD and Kountz, DJ and Jespersen, M and Gould, JA and Doan, NQ and Lingford, JP and Koralegedara, T and Solari, J and D'Adamo, GL and Huang, P and Bong, N and Gulliver, EL and Young, RB and Land, H and Walter, K and Cann, I and Pereira, GV and Martens, EC and Wolf, PG and Ridlon, JM and Gaskins, HR and Giles, EM and Lyras, D and Lappan, R and Berggren, G and Forster, SC and Greening, C},
title = {A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people.},
journal = {Nature microbiology},
volume = {10},
number = {11},
pages = {2686-2701},
pmid = {41131367},
issn = {2058-5276},
support = {FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE220100965//Department of Education and Training | Australian Research Council (ARC)/ ; FL210100258//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; NNF21OC0066716//Novo Nordisk/ ; "STEM" 48574-1//Energimyndigheten (Swedish Energy Agency)/ ; },
mesh = {*Hydrogenase/metabolism/genetics ; Humans ; Hydrogen/metabolism ; *Gastrointestinal Microbiome ; Fermentation ; *Bacteria/genetics/enzymology/classification/growth &amp; development/metabolism/isolation &amp; purification ; Metagenomics ; Feces/microbiology ; Bacteroidetes/growth &amp; development/metabolism/genetics ; Bacillota/growth &amp; development/genetics/metabolism/enzymology ; Crohn Disease/microbiology ; *Gastrointestinal Tract/microbiology ; Iron-Sulfur Proteins/metabolism/genetics ; Healthy Volunteers ; },
abstract = {Disruption of hydrogen (H2) cycling in the gut is linked to gastrointestinal disorders, infections and cancers. However, the mechanisms and microorganisms controlling H2 production in the gut remain unresolved. Here we show that gut H2 production is primarily driven by the microbial group B [FeFe]-hydrogenase. Metagenomics and metatranscriptomics of stool and tissue biopsy samples show that hydrogenase-encoding genes are widely present and transcribed in gut bacteria. Assessment of 19 taxonomically diverse gut isolates revealed that the group B [FeFe]-hydrogenases produce large amounts of H2 gas and support fermentative growth of Bacteroidetes and Firmicutes. Further biochemical and spectroscopic characterization of purified enzymes show that they are catalytically active, bind a di-iron active site and reoxidize ferredoxin derived from the pyruvate:ferredoxin oxidoreductase reaction. Group B hydrogenase-encoding genes are significantly depleted in favour of other fermentative hydrogenases in patients with Crohn's disease. Finally, metabolically flexible respiratory bacteria may be the dominant hydrogenotrophs in the gut, rather than acetogens, methanogens and sulfate reducers. These results uncover the enzymes and microorganisms controlling H2 cycling in the healthy human gut.},
}
@article {pmid41131078,
year = {2025},
author = {Chen, R and Guo, X and Wu, M and Zheng, T and Chen, S and He, B},
title = {Bacillus velezensis ES2-4 modulates root exudation and microbiome remodeling to enhance soybean resistance against gray mold.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {37098},
pmid = {41131078},
issn = {2045-2322},
support = {32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; 32100240//National Natural Science Foundation of China/ ; },
mesh = {*Bacillus/physiology ; *Glycine max/microbiology/metabolism/immunology ; *Plant Roots/microbiology/metabolism ; *Botrytis/pathogenicity ; *Microbiota ; *Plant Diseases/microbiology/prevention &amp; control ; Rhizosphere ; *Disease Resistance ; Soil Microbiology ; },
abstract = {Gray mold, caused by Botrytis cinerea, represents a significant threat to soybean productivity, while conventional chemical control strategies raise concerns regarding long-term sustainability. Plant-associated beneficial microbes, such as Bacillus velezensis, have been proposed as environmentally sustainable alternatives; however, their specific roles in modulating root-microbe interactions remain insufficiently characterized. This study investigated the mechanisms by which B. velezensis ES2-4 enhances soybean resistance by modulating root exudate composition and restructuring rhizosphere microbial communities. Metabolomic and metagenomic analyses indicated that ES2-4 inoculation led to the upregulation of antifungal metabolites (e.g., oxalic acid, eicosane) in root exudates, which facilitated the recruitment of beneficial bacteria while inhibiting B. cinerea proliferation. Pathogen infection was associated with disruptions in rhizosphere microbial diversity; however, ES2-4 application restored bacterial richness, particularly within the Alphaproteobacteria and Streptomyces lineages, while reducing the relative abundance of fungal pathogens. Co-occurrence network analysis further demonstrated that ES2-4 inoculation promoted microbial interactions associated with stress-responsive pathways, including two-component signaling systems and fatty acid metabolism, while downregulating pathogen-associated metabolic functions. These findings elucidate a dual mechanism through which ES2-4 enhances plant immunity via metabolite-mediated microbiome modulation, highlighting its potential as a sustainable biocontrol agent against soybean gray mold.},
}
@article {pmid41130610,
year = {2025},
author = {Karim, DM and Papp, M and Fehérvári, P and Turan, C and Hegyi, P and Molnar, Z and Madách, K},
title = {No difference in microbial diversity between bronchoalveolar lavage and tracheal sampling: a systematic review and meta-analysis.},
journal = {BMJ open respiratory research},
volume = {12},
number = {1},
pages = {},
pmid = {41130610},
issn = {2052-4439},
mesh = {Humans ; *Trachea/microbiology ; *Microbiota ; *Bronchoalveolar Lavage Fluid/microbiology ; *Bronchoalveolar Lavage/methods ; *Specimen Handling/methods ; },
abstract = {INTRODUCTION: The respiratory microbiome has a vital role in maintaining respiratory health and preventing pathogen colonisation, but traditional diagnostic methods fail to capture a complete picture of it. Metagenomic sequencing has improved our understanding of microbial ecosystems in both acute and chronic pathologies. However, its results have not been systematically compared between different respiratory sampling techniques, as has been done with traditional methods. Our study aims to compare the microbial diversity in bronchoalveolar lavage (BAL) and tracheal samples using microbiome sequencing.<br><br>METHODS: A systematic search was conducted in Medline, Embase and CENTRAL databases to identify studies where lower respiratory tract microbiome specimens were collected simultaneously using BAL and tracheal sampling and diversity was analysed postsequencing. Risk of bias was assessed with our specifically tailored tool. A random-effects model was used for data synthesis, analysing pooled Shannon, Chao1 and Simpson indices.<br><br>RESULTS: We screened 1050 potentially relevant publications, 10 of which were included. No significant difference was found in microbial alpha diversity between BAL and tracheal samples. The subgroup analysis of tracheal sample types, including sputum and endotracheal aspirate, revealed no significant differences compared with BAL.<br><br>CONCLUSIONS: Tracheal sampling methods offer a viable and less invasive alternative to BAL for characterising microbiome alpha diversity in clinical or research settings where segmental sampling is not required. However, further high-quality comparative studies are needed to confirm these findings.<br><br>PROSPERO REGISTRATION NUMBER: CRD42023436934.},
}
@article {pmid41130504,
year = {2026},
author = {Song, Y and Zhang, J and Shen, X and Yang, L and Jia, Y and Song, F and Huang, Y and Han, B and Zhang, N and Ma, G},
title = {Study on the association between microplastic exposure and gut microbiota based on metagenomics: A pilot study on 66 young college students in China.},
journal = {Environmental research},
volume = {288},
number = {Pt 1},
pages = {122995},
doi = {10.1016/j.envres.2025.122995},
pmid = {41130504},
issn = {1096-0953},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Microplastics/analysis ; Pilot Projects ; Metagenomics ; Female ; Male ; Young Adult ; China ; Feces/chemistry/microbiology ; *Environmental Exposure ; Students ; *Environmental Pollutants/analysis ; Adolescent ; Bacteria ; Adult ; },
abstract = {OBJECTIVE: This study aimed to evaluate the types and mass concentrations of microplastics found in the stools of young college students. The underlying connections between microplastic exposure and gut microbiota were revealed.<br><br>METHODS: The study involved 66 participants, from whom stool samples were collected. Pyrolysis gas chromatography/mass spectrometry (Py-GCMS) was used to identify the types and mass concentrations of microplastics. Metagenomic sequencing was performed on the gut microbiota using high-throughput sequencing and metagenomic analysis techniques. Participants were divided into low group (LG) and high group (HG) based on the median mass concentration of microplastics in their stools. The differences in microbial diversity and species with significant differences between the two groups were analyzed. Spearman's correlation analysis was conducted to assess the associations between microbial characteristics and gene functions.<br><br>RESULTS: The detection rate of microplastics in the stool samples was 98.5&#xa0;%, with a median mass concentration of 54.7&#xa0;&#x3bc;g/g. Significant differences were observed in gut microbiota between the two groups in terms of alpha and beta diversities. The relative abundance of Segatella copri was higher in the LG, while the relative abundance of Escherichia coli was higher in the HG. Compared with the LG, the gut microbiota in the HG exhibited an increase in the relative abundance of harmful bacteria, such as Dialister invisus, Clostridium fessum, and Evtepia gabavorous. The ADONIS analysis revealed that PS microplastics had a significant impact on the structure of the gut microbiota. However, no significant differences were observed among the metabolic pathways annotated in the Kyoto Encyclopedia of Genes and Genomes database between the two groups at either level I or II.<br><br>CONCLUSION: Participants with higher mass concentrations of microplastics in their stools exhibited an increase in the abundance of harmful intestinal bacteria. PS microplastics had the most profound impact on the gut microbiota structure.},
}
@article {pmid41130083,
year = {2026},
author = {Tripathy, B and Singh, S and Behera, ID and Mishra, S and Das, AP},
title = {Metagenomic profiling of diversified marine microbiome across microplastic-contaminated niches of Bay of Bengal, India.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 3},
pages = {118872},
doi = {10.1016/j.marpolbul.2025.118872},
pmid = {41130083},
issn = {1879-3363},
mesh = {India ; *Microbiota/genetics ; *Microplastics/analysis ; Bays/microbiology ; Metagenomics ; *Water Pollutants, Chemical/analysis ; Geologic Sediments/microbiology ; Environmental Monitoring ; Seawater/microbiology ; Bacteria/classification/genetics ; *Metagenome ; },
abstract = {Diverse microorganisms in the marine sediment share a significant section of the global marine ecosystem and play a dominant role in marine biogeochemistry. The present study is the first to report an evaluation of shotgun metagenomic sequencing of microplastic-contaminated marine water and sediment samples from the coastal shores of the Bay of Bengal, India, across a stretch of 25 km, which houses a plethora of ubiquitous and uncultured microbial biodiversity coexisting with multitudinous human interventions. Illumina Nova sequencing 6000 suggested the presence of 88,539 scaffolds of data containing 132,568 identified genes of marine microorganisms. Taxonomic identification with the assistance of curated global databases ensued in the presence of Proteobacteria (53.12 %), Bacteroidetes (7.13 %), Actinobacteria (5.87 %), and miscellaneous (33.86 %) in abundance. Azonexus hydrophillus, Mycobacteroides abscessus, and Acidaminobacter hydrogenoformans were identified in profusion from the sequenced samples of the study area. The adaptation, sustenance, and survivability in the presence of plastic pollutants confirm the presence of microplastic-degrading enzymes in the microorganisms. The functional annotations revealed 54.32 % and 58.34 % similarities in genes with KEGG and COG databases, revealing the heavy presence of inorganic and amino acid transport channels. Further metabolic profiling of the identified novel microorganisms will assist in engineering the enhancement of microbial enzymes, such as cutinases, lipases, and esterases, leading to microplastic degradation activity. The present research work signifies the analysis and documentation of native microbiota of the marine shores of the Bay of Bengal and their interactive potentialities with microplastic-contaminated anthropogenic environments.},
}
@article {pmid41130000,
year = {2025},
author = {Jin, G and Wang, M and Wang, X and Yuan, S and Peng, A and Chen, Z},
title = {Effects of sub-inhibitory antibiotic exposure on elemental cycling genes in an aquatic microbial community.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140201},
doi = {10.1016/j.jhazmat.2025.140201},
pmid = {41130000},
issn = {1873-3336},
mesh = {*Anti-Bacterial Agents/pharmacology/toxicity ; *Water Pollutants, Chemical/toxicity ; *Microbiota/drug effects/genetics ; Trimethoprim/pharmacology ; Nitrogen/metabolism ; Lincomycin/pharmacology ; Carbon/metabolism ; *Genes, Bacterial ; Sulfur/metabolism ; Drug Resistance, Microbial/genetics ; *Water Microbiology ; *Bacteria/genetics/drug effects/metabolism ; },
abstract = {Understanding how low concentrations of antibiotics influence biogeochemical cycling mediated by aquatic microbes is essential for assessing the ecological risks of antibiotic pollution. Here we examined the responses of carbon, nitrogen, and sulfur cycling genes in an aquatic microbial community to trimethoprim, lincomycin, and their combined exposure across seven sub-inhibitory concentrations spanning three orders of magnitude. We found that while the diversity of elemental cycling genes remained largely unchanged, the abundance of associated metabolic pathways declined significantly under high antibiotic levels,particularly after seven days of exposure to 10 mg/L lincomycin or ≥ 1 mg/L trimethoprim-lincomycin combinations. Some elemental cycling genes increased in abundance under elevated antibiotic exposure, accompanied by concentration-dependent enrichment of antibiotic resistance genes (ARGs). Metagenomic assembly further revealed that enriched ARGs and cycling genes co-localized on the same contigs. In addition, antibiotic exposure reshaped the topological structure of molecular ecological networks among cycling genes, indicating altered microbial interactions and ecological processes. Together, these findings show that antibiotics not only enrich resistance determinants but also modulate the abundance of carbon, nitrogen, and sulfur cycling genes, underscoring the complex impacts of anthropogenic antibiotic pollution on microbially mediated biogeochemical cycles.},
}
@article {pmid41128819,
year = {2025},
author = {Zhao, Y and Chen, J and Zhu, S and Xu, Y and Zhu, J and Yang, J and Zhou, W and Yang, Y and Lin, M and Chen, Q and Xia, M and Chen, Y and Liu, Y},
title = {Olsenella scatoligenes-derived skatole promotes smooth muscle cell proliferation and migration to aggravate atherosclerosis.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {41128819},
issn = {1751-7370},
support = {2025QNPY01//Fundamental Research Funds for the Central Universities/ ; 2024A04J6477//Guangzhou Science and Technology Project/ ; 82273611//National Natural Science Foundation of China/ ; 21HAA01094//Distinguished Young Scholars of the National Natural Science Foundation of China/ ; 82330105//Key Program of National Natural Science Foundation of China/ ; },
mesh = {*Cell Proliferation ; Humans ; *Cell Movement ; *Atherosclerosis/microbiology/pathology ; *Myocytes, Smooth Muscle/physiology ; Male ; Animals ; Calcium-Binding Proteins/metabolism/genetics ; Microfilament Proteins/metabolism/genetics ; Calponins ; Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/metabolism/genetics ; Female ; Muscle, Smooth, Vascular ; *Actinobacteria/metabolism ; Mice ; Middle Aged ; Coronary Artery Disease/microbiology ; },
abstract = {Coronary artery disease (CAD) remains the leading cause of mortality and morbidity globally. The gut microbiota has been implicated in the development of CAD through unclear mechanisms. Here, we demonstrate that the abundance and interspecies interactions of Olsenella scatoligenes are 4.7- and 1.6-fold higher in patients with CAD, respectively, and positively associated with disease severity. Furthermore, integrative metagenomic and metabolomic analyses identify skatole as the key microbial effector mediating the pro-atherogenic effect of O. scatoligenes. Consistently, supplementation with O. scatoligenes or skatole results in 1.26- and 1.23-fold increases in aortic plaque area, respectively, by promoting vascular smooth muscle cell proliferation and migration to the intima. Mechanistically, O. scatoligenes-derived skatole facilitates nuclear translocation of the aryl hydrocarbon receptor and enhances its binding to the promoter region of calponin 1. Silencing either aryl hydrocarbon receptor or calponin 1 attenuates ~40% of the vascular smooth muscle cell proliferation and migration induced by skatole. Collectively, our study identifies increased skatole production as the principal microbial effector linking O. scatoligenes to aggravated atherosclerosis through activation of the aryl hydrocarbon receptor-calponin 1 axis and underscores the therapeutic potential of targeting skatole production for the management of CAD.},
}
@article {pmid41128541,
year = {2025},
author = {Liu, C and He, Y and Zhang, H and Zhang, D and Ai, C and Tang, X and Yang, Q and Yu, Z and Tan, S and Friman, V-P and Liao, H and Zhou, S},
title = {Metabolic activity and survival strategies of thermophilic microbiomes during hyperthermophilic composting.},
journal = {mSystems},
volume = {10},
number = {11},
pages = {e0095625},
pmid = {41128541},
issn = {2379-5077},
support = {2023YFD1702200//National Key Research and Development Program of China/ ; 42277357//National Natural Science Foundation of China/ ; 2022RC3057//Science and technology innovation Program of Hunan Province/ ; YLS-2025-ZY02039//Yuelushan Laboratory Breeding Program/ ; },
mesh = {*Composting/methods ; *Microbiota ; *Bacteria/metabolism/genetics/classification ; Hot Temperature ; Soil Microbiology ; Metagenome ; Metagenomics ; Transcriptome ; },
abstract = {UNLABELLED: Hyperthermophilic composting (HTC) is a promising strategy for the treatment of organic solid waste, leveraging extreme thermophilic conditions (up to 90°C) driven by specialized microbial communities. While microbial community composition and succession have been previously described during HTC, the metabolic activity and adaptation of thermophilic microbiomes remain largely unexplored. In this study, we conducted time-series metagenomic and metatranscriptomic analyses on samples from a full-scale HTC system to characterize the composition, functional potential, and metabolic activity of thermophilic bacteria. A total of 227 non-redundant metagenome-assembled genomes (MAGs) were recovered, including 45 thermophilic MAGs (optimal growth temperatures > 45°C). Metatranscriptomic profiling revealed that thermophilic taxa-such as Thermus thermophilus, Planifilum fulgidum, and Thermaerobacter spp.-were highly transcriptionally active and played vital roles in heat generation through the upregulation of energy production and carbohydrate metabolism pathways. Additionally, these thermophiles exhibited survival and adaptation strategies involving physiological changes (e.g., spore formation, enhanced motility, and genome streamlining) and the induction of thermal resistance mechanisms (e.g., DNA repair systems, heat-shock proteins, and synthesis of compatible solutes). Overall, this study provides novel insights into the diverse survival strategies of thermophilic microbiomes in HTC and suggests potential avenues for optimizing thermophilic biotreatment processes for solid waste management.<br><br>IMPORTANCE: Despite increasing interest in hyperthermophilic composting as a sustainable waste treatment strategy, the mechanisms by which microbial communities both tolerate and drive extreme thermal conditions remain unclear. This study fills a critical knowledge gap by identifying a small group of highly active thermophilic bacteria that dominate during peak composting temperatures and orchestrate endogenous heat production. Using genome-resolved multi-omics, we demonstrate that these thermophiles couple high metabolic output with specialized survival strategies-such as genome streamlining, thermotolerance systems, and adaptive motility systems. These findings advance our understanding of microbial function under extreme conditions and provide a framework for optimizing thermophilic microbiome performance in engineered ecosystems.},
}
@article {pmid41128412,
year = {2025},
author = {Peng, L and Song, H and Shi, H and Wu, L and Ma, Y and Fan, X and Wu, M and Duan, L and Li, Z and Yuan, H},
title = {Oral Multi-Enzymatic Manganese-Carbon Dots Alleviate Sepsis-Associated Lung Injury via the Gut-Lung Axis.},
journal = {ACS nano},
volume = {19},
number = {43},
pages = {37758-37782},
pmid = {41128412},
issn = {1936-086X},
mesh = {Animals ; *Manganese/chemistry/administration &amp; dosage/pharmacology ; *Sepsis/complications/drug therapy/metabolism ; Mice ; *Carbon/chemistry/administration &amp; dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Lung Injury/drug therapy/etiology/metabolism/pathology ; Administration, Oral ; Male ; *Quantum Dots/chemistry/administration &amp; dosage ; Lung/drug effects/metabolism ; },
abstract = {Sepsis-induced pulmonary injury represents a life-threatening global health challenge due to poorly defined pathological mechanisms. The gut-lung axis has been proven to be widely involved in sepsis-induced lung injury, yet effective interventions targeting gut microbiota homeostasis remain unknown. Single-cell sequencing revealed increased alveolar apoptosis and impaired macrophage efferocytosis during sepsis pathogenesis. Thus, we designed oral manganese-doped carbon dots (Mn-CDs) to alleviate septic lung injury by remodeling gut microbiota homeostasis and targeting the gut-lung axis. Biochemical characterization demonstrated Mn-CDs possess multienzyme mimetic activities (SOD-, CAT-, POD-, GPx-like) and potent ROS scavenging capacity. In murine sepsis models, Mn-CDs significantly improved systemic indices and were associated with macrophage anti-inflammatory states with enhanced efferocytosis, as evidenced by transcriptomic profiling. Integrated metagenomic/metabolomic analyses identified Mn-CDs-mediated enrichment of g_Clostridium and g_Bacteroides, concomitant with elevated indole-3-propionic acid (IPA) production. Subsequent in vitro studies demonstrate that IPA likely binds primarily to the aryl hydrocarbon receptor (AHR), promoting both efferocytosis and anti-inflammatory polarization in macrophages, thereby mitigating septic lung injury. Notably, the fecal microbiota transplantation (FMT) from Mn-CDs-treated mice not only alleviated systemic symptoms but also effectively promoted efferocytic polarization of pulmonary macrophages in septic mice. Depletion of the gut microbiota resulted in a significant loss of the protective efficacy of Mn-CDs in a murine model of septic lung injury. Collectively, the gut-lung axis mediated by microbiota-derived IPA and macrophage efferocytosis contributes to the remediation of septic lung injury, highlighting the potential of Mn-CDs in microbiome-directed critical care.},
}
@article {pmid41125958,
year = {2025},
author = {Fan, Y and Ni, M and Aggarwala, V and Mead, EA and Ksiezarek, M and Cao, L and Kamm, MA and Borody, TJ and Paramsothy, S and Kaakoush, NO and Grinspan, A and Faith, JJ and Fang, G},
title = {Long-read metagenomics for strain tracking after faecal microbiota transplant.},
journal = {Nature microbiology},
volume = {10},
number = {12},
pages = {3258-3271},
pmid = {41125958},
issn = {2058-5276},
support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; R35 GM139655/GM/NIGMS NIH HHS/United States ; },
mesh = {*Fecal Microbiota Transplantation ; *Metagenomics/methods ; Humans ; Clostridium Infections/therapy/microbiology ; Feces/microbiology ; Clostridioides difficile/genetics/classification/isolation &amp; purification ; Inflammatory Bowel Diseases/therapy/microbiology ; Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Accurate tracking of bacterial strains that stably engraft in faecal microbiota transplant (FMT) recipients is critical for understanding the determinants of strain engraftment, evaluating correlations with clinical outcomes and guiding the development of therapeutic consortia. While short-read sequencing has advanced FMT research, it faces challenges in strain-level de novo metagenomic assembly. Here we describe LongTrack, a method that uses long-read metagenomic assemblies for FMT strain tracking. LongTrack shows higher precision and specificity than short-read approaches, especially when multiple strains co-exist in the same sample. We uncovered 648 engrafted strains across six FMT cases involving patients with recurrent Clostridioides difficile infection and inflammatory bowel disease. Furthermore, long reads enabled assessment of the genomic and epigenomic stability of engrafted strains at the 5-year follow-up timepoint, revealing structural variations that may be associated with strain adaptation in a new host environment. Our findings support the use of long-read metagenomics to track microbial strains and their adaptations.},
}
@article {pmid41124778,
year = {2025},
author = {Ohlsson, C and Li, L and Horkeby, K and Lawenius, L and Colldén, H and Sjögren, K and Baldanzi, G and Engström, G and Ärnlöv, J and Orho-Melander, M and Fall, T and Grahnemo, L},
title = {The circulating dihydrotestosterone/testosterone ratio is increased by gut microbial 5α-reductase activity in females.},
journal = {EBioMedicine},
volume = {121},
number = {},
pages = {105978},
pmid = {41124778},
issn = {2352-3964},
mesh = {Humans ; Female ; *Dihydrotestosterone/blood ; Male ; Middle Aged ; *Testosterone/blood ; *Gastrointestinal Microbiome ; Aged ; *3-Oxo-5-alpha-Steroid 4-Dehydrogenase/metabolism/genetics ; Cross-Sectional Studies ; Animals ; },
abstract = {BACKGROUND: Dihydrotestosterone (DHT), the most potent ligand to the androgen receptor, is synthesised from testosterone (T) by 5α-reductase type 1 and 2. While type 1 is expressed in several non-reproductive tissues in both sexes, men also express high levels of the high-affinity type 2 isoform in reproductive tissues; yet women have a higher circulating DHT to T (DHT/T) ratio than men. We hypothesised that the high DHT/T ratio in women is caused by high gut microbiota (GM) 5α-reductase activity or altered β-glucuronidase-induced androgen reabsorption from the gut.<br><br>METHODS: We used a large cross-sectional subsample of the Swedish CArdioPulmonary bioImage Study (2897 women and 4338 men, 50-65 years of age) with GM composition and functionality determined by metagenome sequencing and circulating androgens determined by liquid chromatography-tandem mass spectrometry.<br><br>FINDINGS: We confirmed that women had higher (+194%) circulating DHT/T ratio than men. The relative abundance of microbial genes for 5&#x3b1;-reductase type 1 (P = 3 &#xd7; 10[-4]), but not &#x3b2;-glucuronidase, was positively associated with the DHT/T ratio in women. In women, the GM relative abundances of Odoribacter splanchnicus and Parabacteroides distasonis were positively associated with the relative abundance of microbial genes for 5&#x3b1;-reductase type 1 (P < 2 &#xd7; 10[-149]) and the circulating DHT/T ratio (O. splanchnicus P = 3 &#xd7; 10[-6]; P. distasonis P = 5 &#xd7; 10[-5]). In mechanistic studies, we observed very high DHT/T ratio in intestinal content of female conventionally-raised but not germ-free mice. In female mice, the DHT/T ratio was 86.9% higher in serum from the portal vein than in inferior vena cava (P = 0.007).<br><br>INTERPRETATION: These findings demonstrate that the circulating DHT/T ratio is increased by GM 5&#x3b1;-reductase activity in females. We propose that the GM acts as an endocrine organ influencing the androgenic status in females.<br><br>FUNDING: See Acknowledgements.},
}
@article {pmid41122951,
year = {2026},
author = {Vilonen, L and Thompson, A and Adams, B and Ayres, E and Franco, ALC and Wall, DH},
title = {Characterising Soil Eukaryotic Diversity From NEON Metagenomics Datasets.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70062},
pmid = {41122951},
issn = {1755-0998},
support = {//U.S. National Science Foundation/ ; },
mesh = {*Metagenomics/methods ; *Eukaryota/classification/genetics ; *Biodiversity ; *Soil/parasitology/chemistry ; RNA, Ribosomal, 18S/genetics ; *Soil Microbiology ; Metagenome ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {Belowground eukaryotic diversity serves a vital role in soil ecosystem functioning, yet the composition, structure, and macroecology of these communities are significantly under-characterized. The National Ecological Observatory Network (NEON) provides publicly available datasets from long-term surveillance of numerous taxa and ecosystem properties. However, this dataset is not routinely evaluated for its eukaryotic component, likely because analyzing metagenomes for eukaryotic sequences is hampered by low relative sequence abundance, large genomes, poorer eukaryote representation in public reference databases, and is not yet mainstream. We mined the NEON soil metagenome datasets for 18S rRNA sequences using a custom-built pipeline and produced a preliminary assessment of biodiversity trends in North American soil eukaryotes. We extracted ~800 18S rRNA reads per sample (~22,000 reads per site) from 1455 samples from 495 plots across 45 NEON sites in 11 biomes, which corresponded to 5183 genera in 35 phyla. To our knowledge, this represents the first large-scale soil eukaryote analysis of NEON data. We asked whether taxonomic richness paralleled patterns previously established ecological trends and found that eukaryotic richness was negatively correlated with pH, managed sites lowered eukaryotic richness by 47%, most biomes had a distinct eukaryotic community, and fire decreased eukaryotic richness. These findings parallel generally accepted ecological trends and support the notion that NEON soil metagenome datasets can and should be used to explore spatiotemporal patterns in soil eukaryote diversity, its association with ecosystem functioning, and its response to environmental changes in North America.},
}
@article {pmid41122237,
year = {2025},
author = {Terra Machado, D and Bernardes Brustolini, OJ and Dos Santos Corrêa, E and Ribeiro Vasconcelos, AT},
title = {Prediction of sporulating Firmicutes from uncultured gut microbiota using SpoMAG, an ensemble learning tool.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20232},
pmid = {41122237},
issn = {2167-8359},
mesh = {*Gastrointestinal Microbiome/genetics ; *Machine Learning ; *Spores, Bacterial/genetics ; Animals ; Humans ; *Bacillota/genetics/physiology ; Cattle ; Feces/microbiology ; Metagenome ; Swine ; Phylogeny ; Ensemble Learning ; },
abstract = {Sporulation represents a key adaptive strategy among Firmicutes, facilitating bacterial persistence under environmental stress while mediating host colonization, transmission dynamics, and microbiome stability. Despite the recognized ecological and biomedical significance of spore-forming Bacilli and Clostridia, most taxa remain uncultivated, limiting phenotypic characterization of their sporulation capacity. To bridge this knowledge gap, we developed SpoMAG, an ensemble machine learning framework that predicts sporulation potential of metagenome-assembled genomes (MAGs) through supervised classification models trained on the presence/absence of 160 sporulation-associated genes. This R-based tool integrates Random Forest and support vector machine algorithms, achieving probabilistic predictions with high performance (AUC = 92.2%, F1-score = 88.2%). Application to fecal metagenomes from humans, cattle, poultry, and swine identified 63 putatively spore-forming MAGs exhibiting distinct host- and order-specific patterns. Bacilli MAGs from Bacillales and Paenibacillales orders showed high sporulation probabilities and gene richness, while Clostridia MAGs exhibited more heterogeneous profiles. Predictions included undercharacterized families in the spore-forming perspective, such as Acetivibrionaceae, Christensenellaceae, and UBA1381, expanding the known phylogenetic breadth of sporulation capacity. Nine genes were consistently present across all predicted spore-formers (namely pth, yaaT, spoIIAB, spoIIIAE, spoIIIAD, ctpB, ftsW, spoVD, and lgt), suggesting conserved genetic elements across uncultivated Firmicutes for future research. Average nucleotide identity (ANI) analysis revealed seven cases of species-level sharing (ANI value > 95%) among hosts, including a putative novel Acetivibrionaceae species, suggesting possible cross-host transmission facilitated by sporulation. In all 63 genomes predicted to sporulate, we identified nine genes across sporulation steps. In addition, SHapley Additive exPlanations (SHAP) analysis indicated 16 consensus genes consistently contributing to predictions (namely lytH, cotP, spoIIIAG, spoIIR, spoVAD, gerC, yabP, yqfD, gerD, spoVAA, gpr, ytaF, gdh, ypeB, spoVID, and ymfJ), bringing biologically meaningful features across sporulation stages. By combining gene annotation with interpretable machine learning, SpoMAG provides a reproducible and accessible framework to infer sporulation potential in uncultured microbial taxa. This tool enhances targeted investigations into microbial survival strategies and supports research in microbiome ecology, probiotic discovery, food safety, and public health surveillance. SpoMAG is freely available as an R package and expands current capabilities for functional inference in metagenomic datasets.},
}
@article {pmid41121668,
year = {2025},
author = {Enagbonma, BJ and Modise, DM and Babalola, OO},
title = {Effects of Legume‒Cereal Rotation on Sorghum Rhizosphere Microbial Community Structure and Nitrogen-Cycling Functions.},
journal = {MicrobiologyOpen},
volume = {14},
number = {5},
pages = {e70085},
pmid = {41121668},
issn = {2045-8827},
support = {//This study was supported by the ICGEB Research Project (CRP/ZAF22-03) awarded to O.O.B./ ; },
mesh = {*Sorghum/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Fabaceae/growth &amp; development/microbiology ; Nitrogen/metabolism ; *Nitrogen Cycle ; Soil/chemistry ; Zea mays/microbiology/growth &amp; development ; *Edible Grain/growth &amp; development/microbiology ; Agriculture/methods ; },
abstract = {Legumes form mutualistic interactions with specific soil microbiomes that fix atmospheric nitrogen and improve soil fertility. However, legume-based rotations influence on soil microorganisms and their correlations with soil physicochemical parameters during subsequent crop development are not yet clear. We examined the shifts in microbial community structure and nitrogen genes via shotgun sequencing across cowpea-sorghum, soybean-sorghum, maize-sorghum rotations, and sorghum without precrops. Precropping in rotation significantly affected N-NO3, clay, and silt, and caused a shift in the rhizosphere microbiome. Actinomycetota was the most predominant bacteria across all the cropping systems, followed by Pseudomonadota, whose composition differed across the cropping systems. Legume in rotation increased the relative abundance of Streptomyces and reduced the relative abundances of Pyxidicoccus, Microbacterium, and Microvirga. Nocardioides and Solirubrobacter predominated in the soil after the maize crops. Shannon index, non-metric multidimensional scaling, and permutational multivariate analysis of variance revealed that crop rotation caused significant differences in both the alpha and beta diversity of the microbial community and the nitrogen-cycling functional genes. The relative abundances of amoC, narH, gltB, glnA, ureC, napA, and napA significantly increased in legume monocrops in rotation. The relative abundances of glnA, gltB, narZ, and narH increased in the soil after maize cropping, whereas sorghum without precrops significantly increased the relative abundances of glnA, narZ, and ureC. Several soil physicochemical parameters drive microbial communities. *S, Na, N-NH4, N-NH3, and P were the most significant environmental variables regulating microbiome and nitrogen-cycling genes by crop rotation. This study supports sustainable agricultural practices and promotes sorghum development through rhizosphere microbiome optimization.},
}
@article {pmid41121093,
year = {2025},
author = {Jia, Y and He, M and Wang, F and Zhan, Y and Deng, Q and Shen, J and Wang, X and Ran, Q and Huang, W and Ling, Y and Wen, S},
title = {Indole-3-lactic acid protects the gut vascular barrier following intestinal ischemia injury through AhR/Nrf2/STAT3 mediated claudin 2 downregulation.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {447},
pmid = {41121093},
issn = {1478-811X},
support = {82302457//National Natural Science Foundation of China/ ; 82372187//National Natural Science Foundation of China/ ; 82272223//National Natural Science Foundation of China/ ; 23qnpy134//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Animals ; *Receptors, Aryl Hydrocarbon/metabolism ; *NF-E2-Related Factor 2/metabolism ; Mice ; *Reperfusion Injury/metabolism/pathology/drug therapy ; *Down-Regulation/drug effects ; *STAT3 Transcription Factor/metabolism ; *Indoles/pharmacology ; *Intestinal Mucosa/metabolism/drug effects/pathology ; Male ; Mice, Inbred C57BL ; Gastrointestinal Microbiome/drug effects ; *Basic Helix-Loop-Helix Proteins/metabolism ; Tryptophan ; *Intestines/pathology/blood supply/drug effects ; *Protective Agents/pharmacology ; Signal Transduction/drug effects ; },
abstract = {BACKGROUND &amp; AIMS: Dysfunction of the intestinal epithelial barrier (IEB) and gut vascular barrier (GVB) contributes to the development of intestinal ischemia/reperfusion (IR) injury. Tryptophan (TRP), an essential amino acid, plays a crucial role in maintaining intestinal homeostasis, yet its regulatory effects on the GVB following IR remain unexplored. We aimed to better define the role of TRP in intestinal IR in vivo and in vitro.<br><br>METHODS: Mice underwent intestinal ischemia/reperfusion (IR) and were fed control, TRP-recommended (TRP-r), or TRP-sufficient (TRP-s) diets. Fecal metagenomic sequencing analyzed microbial composition, and targeted metabolomics quantified tryptophan and its metabolites in intestinal and serum samples. ILA's effects on barrier integrity were assessed via tight junction protein expression and FITC-dextran permeability assays. RNA sequencing of intestinal endothelial cells elucidated mechanisms by which ILA modulated GVB function. The STAT3-claudin 2 relationship was validated in vitro by ChIP-qPCR.<br><br>RESULTS: TRP supplementation significantly reshaped the gut microbiota, mitigated tissue damage and enhanced the integrity of both the IEB and GVB. Indole-3-lactic acid (ILA), a key tryptophan metabolite, was identified as an important factor in preserving GVB function. Mechanistically, our results show that the aryl hydrocarbon receptor (AhR)/Nrf2/signal transducer and activator of transcription 3 (STAT3) pathway is essential for ILA-mediated improvement of GVB integrity and downregulation of the pore-forming protein claudin 2.<br><br>CONCLUSIONS: Our findings highlight the dual role of ILA in reinforcing both IEB and GVB functions and shed light on the molecular mechanisms underlying ILA's GVB-protective effects. This study implicates that ILA or other AhR-activating metabolites may serve as promising pharmacological agents for alleviating IR-induced intestinal damage.},
}
@article {pmid41120531,
year = {2025},
author = {Brito, B and DeMaere, M and Lean, I and Hazelton, M and O'Rourke, BA and Holmes, EC and House, JK and Rowe, S and Myers, GSA and Roy Chowdhury, P},
title = {Leveraging metatranscriptomics for the characterisation of bovine blood viromes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36670},
pmid = {41120531},
issn = {2045-2322},
mesh = {Animals ; Cattle ; *Virome/genetics ; *Transcriptome ; *Cattle Diseases/virology/blood/genetics ; Kenya ; *Viruses/genetics/classification ; Gene Expression Profiling ; },
abstract = {Understanding the diversity of the bovine virome is essential for assessing their potential impact on cattle health and transmission risks. Viruses present in the blood comprise both those that establish persistent infections in blood cells and those present during transient viremia. Farm management practices, such as the reuse of syringes for treatments, vaccinations, and supplements, may inadvertently contribute to the spread of blood-borne pathogens, emphasizing the need for improved biosecurity measures. Herein, we used a metatranscriptomic approach to analyse 20 bovine blood transcriptomes from dairy cows in New South Wales, Australia, along with 577 publicly available blood transcriptomes from studies in Australia and Kenya. Our analysis identified several viruses that are known to infect blood cells, transmitted either by direct contact or by vectors, including bovine viral diarrhea virus, bovine gammaherpesvirus 6, hepacivirus, foamy virus, ephemeroviruses and a new species of a coltivirus. Our findings highlight the complexity of the bovine blood virome and underscore the importance of sustained surveillance to identify emerging pathogens and assess their potential role in cattle health. This study provides a framework for integrating transcriptomic data into disease monitoring efforts, ultimately contributing to improved cattle management and biosecurity practices.},
}
@article {pmid41118772,
year = {2025},
author = {Jacoby, C and Scorza, K and Ecker, L and Nol Bernardino, P and Little, AS and McMillin, M and Ramaswamy, R and Sundararajan, A and Sidebottom, AM and Lin, H and Dufault-Thompson, K and Hall, B and Jiang, X and Light, SH},
title = {Gut bacteria metabolize natural and synthetic steroid hormones via the reductive OsrABC pathway.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {11},
pages = {1873-1885.e7},
doi = {10.1016/j.chom.2025.09.014},
pmid = {41118772},
issn = {1934-6069},
mesh = {Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; *Steroids/metabolism ; *Clostridium/metabolism/genetics/enzymology/isolation &amp; purification ; Crohn Disease/microbiology/drug therapy ; Germ-Free Life ; Hydrocortisone/metabolism ; Prednisolone/metabolism ; Metabolic Networks and Pathways ; *Oxidoreductases/metabolism/genetics ; *Gastrointestinal Tract/microbiology ; Glucocorticoids/metabolism ; Oxidation-Reduction ; },
abstract = {Steroid hormone metabolism by the gut microbiome affects host physiology, however, the underlying microbial pathways remain incompletely understood. Here, we isolate a gut bacterial species, which we designate Clostridium steroidoreducens, that reduces cortisol and related steroid hormones to 3β,5β-tetrahydrosteroid products. Through transcriptomics and enzymatic discovery, we establish the C. steroidoreducens OsrABC steroid hormone pathway. OsrA is a 3-oxo-Δ[1]-steroid hormone reductase that targets synthetic glucocorticoids, including prednisolone-a frontline Crohn's disease therapy. OsrB is a 3-oxo-Δ[4]-steroid reductase that converts steroid hormones to 5β-dihydrosteroid intermediates, which OsrC subsequently reduces to 3β,5β-tetrahydro products. Homologs of osrA and osrB predict steroid-reducing activity across gut bacteria and are enriched in metagenomes of Crohn's disease patients. Consistent with a role in modulating drug efficacy, C. steroidoreducens colonization decreases prednisolone bioavailability in gnotobiotic mice. These findings thus define a previously unrecognized pathway for microbial steroid hormone inactivation and establish a mechanistic basis for bacterial interference with anti-inflammatory therapies.},
}
@article {pmid41118252,
year = {2025},
author = {Qi, X and Li, Y and Zhu, Y and Shen, R and Xie, Z},
title = {Rebuilding the gut ecosystem: Emerging strategies targeting the microbiota in antibiotic-associated diarrhea.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {72},
number = {4},
pages = {287-295},
doi = {10.1556/030.2025.02690},
pmid = {41118252},
issn = {1588-2640},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Diarrhea/chemically induced/therapy/microbiology ; *Anti-Bacterial Agents/adverse effects ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Dysbiosis/chemically induced/therapy ; Animals ; },
abstract = {Antibiotic-associated diarrhea (AAD) is a prevalent iatrogenic complication of antibiotic therapy, primarily triggered by dysbiosis and loss of intestinal homeostasis. The traditional interventions, such as empirical probiotic use, have shown a modest and a heterogeneous efficacy. This review integrates the current mechanistic understanding of AAD through the lens of the microbiota-mucosal-immune axis and provides a comprehensive overview of emerging therapeutic strategies. By integrating evidence from metagenomics, metabolomics, and immunology, we highlight next-generation approaches, including rationally engineered probiotics, standardized fecal microbiota transplantation (FMT), and synthetic-biology-derived interventions. Recent progress in multi-omics technologies and machine learning has enabled patient-stratified modulation of the gut microbiota, moving beyond empirical supplementation toward precision ecological reprogramming. These advanced therapies demonstrate superior outcomes in restoring microbial diversity, strengthening epithelial barrier function, and re-establishing immunological homeostasis. Ultimately, the management of AAD requires a systems-biology strategy that leverages real-time microbiome analytics for targeted, accurate, and sustainable restoration of gut health.},
}
@article {pmid41117817,
year = {2025},
author = {Gogoi, R and Bora, SS and Gogoi, B and Naorem, RS and Barooah, M},
title = {Insights into the microbial diversity and functionalities of potential hydrocarbon-degrading bioremediation agents in oil spill sludge of Assam, India.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {325},
pmid = {41117817},
issn = {1432-072X},
mesh = {India ; Biodegradation, Environmental ; *Hydrocarbons/metabolism ; *Petroleum Pollution/analysis ; *Sewage/microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Surface-Active Agents/metabolism ; RNA, Ribosomal, 16S/genetics ; Petroleum/metabolism ; Phylogeny ; Biodiversity ; },
abstract = {Oil spill contamination poses a significant threat to environmental and ecological health, particularly in crude oil-rich regions such as Assam, a north-eastern state of India. This study explores the microbial diversity and functional potential of hydrocarbon-degrading bacteria in crude oil-contaminated sludge. Sludge samples were collected from three contaminated sites in Assam and analyzed for microbial diversity by culture dependent and independent (using 16 S rRNA amplicon sequencing) approaches. Metagenomic analysis revealed a diverse microbial community, with Proteobacteria and Planctomycetes dominating the metagenomes. Seven bacterial isolates, including Diaphorobacter nitroreducens, Lysinibacillus capsici, and Pseudomonas otitidis, were isolated and identified as potential hydrocarbon degraders. The isolates were screened and evaluated for biosurfactant production, hydrocarbon adhesion, and key enzymatic activities involved in degradation. These isolates exhibited significant biosurfactant-producing abilities, with Diaphorobacter nitroreducens MBRG1 showing the highest emulsification index (79%) and strong adherence to hydrocarbons. The enzymatic activities of alkane hydroxylase and alcohol dehydrogenase confirmed the metabolic capabilities of the isolates in hydrocarbon degradation. Optimal growth conditions for biosurfactant production were determined to be pH 7, 30 °C, 2% sucrose as the carbon source, and 3% yeast extract as the nitrogen source. The study highlights the potential of these indigenous bacterial isolates in bioremediation strategies to mitigate oil contamination. Future studies should focus on large-scale bioreactor studies, field trials, and strain improvement of these bacteria to enhance their degradation efficiency and adaptability to varied environmental conditions.},
}
@article {pmid41115930,
year = {2025},
author = {Fitzjerrells, RL and Meza, LA and Yadav, M and Olalde, H and Hoang, J and Paullus, M and Cherwin, C and Cho, TA and Brown, G and Ganesan, SM and Mangalam, AK},
title = {Multiple sclerosis patients exhibit oral dysbiosis with decreased early colonizers and lower hypotaurine level.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {199},
pmid = {41115930},
issn = {2055-5008},
support = {F31 DE033564/DE/NIDCR NIH HHS/United States ; 1RO1AI137075//National Institute of Allergy and Infectious Diseases/ ; P20 NR018081/NR/NINR NIH HHS/United States ; 1P20NR018081-01/NR/NINR NIH HHS/United States ; R03 DE030527/DE/NIDCR NIH HHS/United States ; R01 AI137075/AI/NIAID NIH HHS/United States ; T90 DE023520/DE/NIDCR NIH HHS/United States ; P30 ES005605/ES/NIEHS NIH HHS/United States ; T90DE023520/DE/NIDCR NIH HHS/United States ; I01 CX002212/CX/CSRD VA/United States ; F31DE033564/DE/NIDCR NIH HHS/United States ; 1I01CX002212//U.S. Department of Veterans Affairs/ ; R03DE030527/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; Adult ; *Taurine/analogs &amp; derivatives/analysis/metabolism ; Middle Aged ; Metagenomics ; *Mouth/microbiology ; *Multiple Sclerosis, Relapsing-Remitting/microbiology ; Metabolomics ; *Bacteria/classification/genetics/isolation &amp; purification ; Microbiota ; Fusobacterium nucleatum/isolation &amp; purification ; Metabolome ; *Multiple Sclerosis/microbiology ; Actinomyces/isolation &amp; purification ; Porphyromonas gingivalis/isolation &amp; purification ; },
abstract = {Although gut microbiome dysbiosis is implicated in the pathobiology of multiple sclerosis (MS), the role of the oral microbiome (OM), the second largest microbiome, remains poorly understood. Additionally, while the salivary metabolome has been linked to other neurodegenerative diseases; its role in people with Relapsing-Remitting MS (pwRRMS), the most prevalent form of MS, is unknown. Combining shotgun metagenomics with untargeted metabolomics, we identified a reduced abundance of several early colonizing species including Streptococcus and Actinomyces in pwRRMS and an enrichment of bacteria with pathogenic potential including Fusobacterium nucleatum, Porphyromonas gingivalis, and several Prevotella species. pwRRMS had an altered metabolite profile including a decreased hypotaurine compared to healthy controls. Thus we report altered oral microbiome and metabolome in pwRRMS which might contribute to MS pathobiology. These findings offer potential microbiome-metabolome based diagnostic biomarkers for MS and pave the way for novel therapeutic interventions to improve disease management and patient outcomes.},
}
@article {pmid41115834,
year = {2025},
author = {Facey, FSB and Maharjan, R and Dinh, H and Buchanan, JS and Connal, LA and Tay, AP and Paulsen, IT and Cain, AK},
title = {Characterising the Multiple-Plastic Degrading Strain of Bacillus subtilis GM_03 From the Galleria mellonella Microbiome.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70216},
pmid = {41115834},
issn = {1758-2229},
support = {W911NF2320155//US Department of Defense/ ; FT220100152//Australian Research Council Future Fellowship/ ; 20235185//FSBF was supported by Macquarie University Research Excellence Scholarship Programme/ ; },
mesh = {Animals ; *Bacillus subtilis/metabolism/genetics/isolation &amp; purification/classification ; Larva/microbiology ; *Moths/microbiology ; Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Polyethylene/metabolism ; Polyurethanes/metabolism ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Plastic waste is a mounting global problem with over 400 million tons of plastic produced annually and over 50% ending up in landfill after its intended use. Two types of plastics are particularly problematic and are difficult to recycle: low-density polyethylene (LDPE) and polyurethane (PU). Fortuitously, nature may offer a potential solution; Galleria mellonella larvae can digest various plastics, including LDPE, which is believed to be driven by microbes in their gut microbiome. Although some studies have examined their gut microbiota on a metagenomic level, little is known about their ability to degrade plastics. Here, we isolated six bacterial strains from G. mellonella larvae feeding on LDPE. One of them, identified as Bacillus subtilis GM_03, has the capacity to break down commercial PU (Impranil), in addition to LDPE. This bacterium encodes a suite of genes required for plastic degradation. Directed evolution was used to enhance this strain's plastic degrading rate by over six-fold. Sequencing of the evolved culture revealed four genes, srfAB, fadD, appA and citS, associated with this increased PU degradation rate. This is the first time that B. subtilis isolated from G. mellonella larvae has been shown to be capable of degrading multiple types of plastics.},
}
@article {pmid41114585,
year = {2025},
author = {Aries Marchington, M and Gasvoda, H and Michelotti, M and Rodriguez-Caro, F and Gooman, A and Perez, A and Hensley-McBain, T},
title = {APOE genotype and sex drive microbiome divergence after microbiome standardization in APOE-humanized mice.},
journal = {mSphere},
volume = {10},
number = {11},
pages = {e0042925},
pmid = {41114585},
issn = {2379-5042},
support = {P20 GM103474/GM/NIGMS NIH HHS/United States ; P20 GM152335/GM/NIGMS NIH HHS/United States ; R01 AG079224/AG/NIA NIH HHS/United States ; R01AG079224-01/NH/NIH HHS/United States ; },
mesh = {Animals ; Male ; Female ; *Gastrointestinal Microbiome/genetics ; Mice ; *Genotype ; Mice, Inbred C57BL ; *Apolipoproteins E/genetics ; Feces/microbiology ; Humans ; Sex Factors ; Bacteria/classification/genetics/isolation &amp; purification ; Mice, Transgenic ; Alzheimer Disease/microbiology/genetics ; Dysbiosis/microbiology ; },
abstract = {The APOE4 allele is the greatest known genetic factor for sporadic or late-onset Alzheimer's Disease (LOAD). Gut microbiome (GMB) dysbiosis can lead to poorer outcomes in disease. The intersection of sex, APOE genotype, inflammation, and gut microbiota is incompletely understood. Previous studies in humans and humanized APOE mice have demonstrated APOE-genotype-specific differences in the GMB. However, most of these studies were unable to resolve bacteria to the species level. It remains unclear how GMB changes with age and sex in the context of APOE genotype. In this study, humanized male mice with either APOE 2, 3, or 4 genotype were bred with the same two C57BL/6J sisters to standardize microbiomes across lines and monitor divergence based on APOE allele. Stool samples were collected at breeder set up and from the heterozygous (F1) and homozygous (F2) generations at wean and 6 months old. Stool was assessed via shallow shotgun sequencing to enable species and strain-level taxonomic resolution. The heterozygous pups' microbiome resembled each other at wean across all genotypes. However, the heterozygous pups and their homozygous offspring continued to diverge, particularly the APOE2 females. In homozygous mice, the GMB demonstrated significant divergence at 6 months of age based on sex and APOE genotype. In comparison to their APOE3 and APOE4 counterparts, APOE2 females and males demonstrated an increased quantity of bacteria associated with anti-inflammatory profiles, including in the Lachnospiraceae family (Lachnospiraceae bacterium UBA3401) and decreased quantities in the Turicibacteraceae family (higher levels are associated with LOAD).IMPORTANCEThe APOE4 allele is implicated as a significant risk factor for many diseases, including cardiovascular disease (responsible for more deaths than any other disease) and sporadic or late-onset Alzheimer's Disease (accounts for an estimated 60%-80% of all dementia cases). It is known that the gut microbiome (GMB) is affected by different genotypes and disease states. Mouse model studies have environmental and genetic controls, allowing a specific gene to be studied. This study aims at discovering key GMB species differences allowing for future therapeutic targets. The GMB of the experimental mice was standardized, and genotype and sex-specific divergence was observed with species and even strain level taxonomic resolution. Reported here are the first data demonstrating GMB divergence over time driven by APOE genotype from an inherited source and the first data to identify APOE genotype-specific bacteria species that may serve as therapeutic targets in APOE-driven disease.},
}
@article {pmid41114530,
year = {2025},
author = {Xiao, Y and Zhang, X and Shao, B and Wu, Z and Li, X and Yi, D and Li, T and Yang, T and Zhu, J and Huang, T and Deng, Y and Qiu, T and Yang, G and Sun, X and Wang, N},
title = {Hydroxytyrosol Improves Metabolic Dysfunction-Associated Fatty Liver Disease Dependent on the Modulation of Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {43},
pages = {27450-27468},
doi = {10.1021/acs.jafc.5c07003},
pmid = {41114530},
issn = {1520-5118},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Phenylethyl Alcohol/analogs &amp; derivatives/administration &amp; dosage ; Humans ; Animals ; Male ; Mice ; Bacteria/classification/genetics/isolation &amp; purification/drug effects/metabolism ; Middle Aged ; Female ; Adult ; *Fatty Liver/metabolism/drug therapy/microbiology ; Liver/metabolism/drug effects ; Feces/microbiology ; Fecal Microbiota Transplantation ; Mice, Inbred C57BL ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism/drug therapy ; },
abstract = {The global threat of metabolic dysfunction-associated fatty liver disease (MAFLD) is significant, but effective measures are still lacking. To explore the potential impact of hydroxytyrosol (HT), a plant polyphenol, in the metabolic outcomes of MAFLD and the mediating role of the gut microbiota, we performed an 8-week randomized placebo-controlled clinical trial in MAFLD patients and collected fecal bacteria for metagenomics analysis and targeted metabolomics. In this population-based trial, we have revealed that HT mitigates liver injury and steatosis in patients with MAFLD, as well as systemic glucolipid metabolism disorder. Through analysis of the differences in bacterial taxon and functional profiles, as well as correlation analysis between species and metabolic indicators, it was found that Fusicatenibacter saccharivorans (F. saccharivorans), the microbial species with the greatest difference after HT intervention, was also the most significantly correlated with metabolic parameters of MAFLD and showed a significant positive correlation with the content of fecal butanoic acid. Butanoic acid was further associated with MAFLD-related metabolic indexes. To confirm the potential causal relationship between alterations in gut microbiota induced by HT intervention and improved MAFLD metabolic phenotypes, fecal microbiota transplantation (FMT) was conducted using a model of pseudogerm-free mice. We have further demonstrated that the fecal microbiota from donors of MAFLD patients receiving HT supplementation can ameliorate liver and systemic phenotypes in western-diet-induced MAFLD mice, interpreting the robust action of gut microbiota remodeled by HT in improving MAFLD. Consequently, HT supplementation may represent a tactic for improving MAFLD by modulating the composition and functionality of the gut microbiota.},
}
@article {pmid41112778,
year = {2025},
author = {Dong, Y and Fan, S and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Li, Y and Wang, W},
title = {Comparative analysis of fecal DNA viromes in Large-billed crows and Northern ravens reveals diverse viral profiles.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20170},
pmid = {41112778},
issn = {2167-8359},
mesh = {Animals ; *Crows/virology ; *Feces/virology ; *Virome/genetics ; *DNA, Viral/genetics ; *DNA Viruses/genetics/isolation &amp; purification/classification ; Metagenomics ; },
abstract = {As facultative scavenger birds, crows carry various parasites, viruses, and bacteria, making them significant infection hosts and transmission vectors. In this study, we employed viral metagenomics to enrich viral particles from three fecal samples of the Northern ravens (Corvus corax) and four fecal samples of the Large-billed crows (Corvus macrorhynchos). Viral DNA was then extracted, and seven sequencing libraries were constructed. The composition and characteristics of the DNA viromes in the feces of these two facultative scavenging bird species were analyzed using the Illumina NovaSeq platform (PE150 mode). The results showed that the fecal DNA viruses carried by Northern ravens mainly belonged to Parvoviridae (31.49%), Caudoviricetes_Unclassified (21.91%), Microviridae (21.57%), and Genomoviridae (18.2%), while those carried by Large-billed crows were predominantly Genomoviridae (29.7%), Parvoviridae (26.15%), and Caudoviricetes_Unclassified (22.15%). Diversity analysis using Richness, Shannon, and Simpson indices showed no significant differences in viral composition between the two crow species. Additionally, principal coordinate analysis (PCoA) (F = 1.079, P = 0.155) and non-metric multidimensional scaling (NMDS) (F = 1.079, P = 0.154) analyses demonstrated no distinct separation between the two groups. Moreover, the KEGG-enriched pathways in both crow species were primarily associated with metabolic and genetic information processing functions. The selection of the Large-billed crows and Northern ravens in this study was based on their widespread distribution, close association with human settlements, and distinctive scavenging behavior. Comparative analysis of the diversity and composition of their DNA viral communities offers a basis for evaluating the zoonotic risks associated with these scavenger birds.},
}
@article {pmid41112578,
year = {2025},
author = {Chen, J and Xu, Q and Zhang, L and Zhang, D and Wu, X},
title = {Enrichment of prevotella melaninogenica in the lower respiratory tract links to checkpoint inhibitor pneumonitis and radiation pneumonitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1594460},
pmid = {41112578},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *Radiation Pneumonitis/microbiology ; *Prevotella/isolation &amp; purification/genetics/classification ; Microbiota ; Lung Neoplasms/drug therapy ; *Immune Checkpoint Inhibitors/adverse effects ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Pneumonia/microbiology ; Lung/microbiology ; },
abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) and radiation pneumonitis (RP) lead to anti-cancer therapy discontinuation and poor diagnosis. The human microbiome is related to various respiratory diseases. However, the role of the lung microbiome in CIP and RP remains unknown. Our study aimed to explore the lower respiratory tract (LRT) microbiome in CIP/RP patients.<br><br>METHODS: The study enrolled 61 patients with pneumonitis or pneumonia, including 23 with CIP/RP, and 38 with lung cancer with pneumonia (LC-P). Metagenomic next-generation sequencing (mNGS) was performed to identify the microbiota in bronchoalveolar lavage fluid (BALF), and bioinformatics methods were used to compare the microbial differences between CIP/RP and LC-P groups. Correlation analysis was conducted to explore the relationship between LRT microbiota and clinical features.<br><br>RESULTS: The Prevotella was the dominant genus in both groups. The Prevotella melaninogenica, which belongs to the Prevotella genus, was the dominant species in the CIP/RP group and the second most abundant species in the LC-P group. Compared to the LC-P group, the CIP/RP group had significantly high levels of Prevotella melaninogenica species and lymphocyte percentage in BALF but significantly low levels of lymphocytes, eosinophils and albumin in peripheral blood. In addition, the Prevotella melaninogenica species had a negative correlation with peripheral blood lymphocytes.<br><br>CONCLUSION: The enrichment of Prevotella melaninogenica species in LRT and a decreased level of peripheral blood lymphocytes are associated with CIP/RP.},
}
@article {pmid41112258,
year = {2025},
author = {Filippi Xavier, L and Gacesa, R and da Rocha, GHO and Broering, MF and Scharf, P and Lima, FDS and Faber, KN and Harmsen, H and Hoffmann, C and Farsky, SHP},
title = {Annexin A1 levels affect microbiota in health and DSS-induced colitis/inflammatory bowel disease development.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1679071},
pmid = {41112258},
issn = {1664-3224},
mesh = {Animals ; *Annexin A1/genetics/metabolism ; *Gastrointestinal Microbiome ; Humans ; Mice ; Mice, Knockout ; *Colitis/chemically induced/microbiology/metabolism ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; *Inflammatory Bowel Diseases/microbiology/metabolism ; Female ; Disease Models, Animal ; Dysbiosis ; Feces/microbiology ; Adult ; Middle Aged ; },
abstract = {BACKGROUND: Inflammatory Bowel Diseases (IBDs) are characterized by intestinal dysbiosis and immune dysregulation. Annexin A1 (AnxA1) promotes epithelial repair and inhibits immune responses during IBD. However, AnxA1's impact on gut microbiota during IBD remains unclear. Here, we experimentally investigated the microbiota profile during colitis in wild-type (WT) and AnxA1-deficient mice (AnxA1[-/-]), and evaluated an observational cohort in IBD patients with high or low AnxA1 expression.<br><br>METHODS: Colitis was induced in C57BL/6 WT and AnxA1 [[-]/[-]] mice via oral administration of 2% DSS for six days. Fecal samples were collected at baseline, peak inflammation (day 6), and during the recovery phase (day 10) for 16S rRNA sequencing. Human microbiota data from the Lifelines Dutch Microbiome Project cohort, including IBD and healthy subjects, were analyzed for AnxA1 expression using R software.<br><br>RESULTS: Healthy AnxA1[-/-] mice exhibited reduced microbial richness and a distinct gut microbiota composition, marked by increased Proteobacteria and Parasutterella, and reduced Deferribacterota, Campylobacterota, and Verrucomicrobiota. During DSS-induced colitis, AnxA1[-/-] mice showed greater weight loss and heightened inflammation, displaying earlier and more pronounced microbial shifts, including increased Proteobacteria, Cyanobacteria, Parabacteroides, Bacteroides, and Escherichia-Shigella. In contrast, WT mice exhibited delayed changes, with expansion of Alloprevotella, Akkermansia, and Faecalibaculum after day 6. In human IBD samples, Crohn's disease (CD) patients with low AnxA1 expression and active inflammation presented an altered microbiota enriched in Lachnoclostridium and Parabacteroides, while ulcerative colitis (UC) patients showed phylum-level shifts modulated by AnxA1 levels. Notably, non-inflamed CD and UC patients with low AnxA1 differed significantly in microbiota composition. Moreover, inflamed CD patients with high AnxA1 expression showed microbial profiles resembling those of healthy controls, while low AnxA1 expression was associated with a more pronounced dysbiotic state.<br><br>CONCLUSION: AnxA1 is implicated in microbiota control under healthy and IBD conditions. Accordingly, the microbiota of healthy AnxA1[-/-] mice, colitic AnxA1[-/-] mice, and IBD patients with low AnxA1 expression exhibit dysbiosis compared to their respective controls. Together, these unprecedented findings reveal AnxA1 as a potential regulatory protein in the immune-microbiota axis involved in IBD pathogenesis.},
}
@article {pmid41112045,
year = {2025},
author = {Zhang, Y and Gilbert, JA and Liu, X and Nie, L and Xu, X and Gao, G and Lyu, L and Ma, Y and Fan, K and Yang, T and Zhang, Y and Zhang, J and Chu, H},
title = {SynCom-mediated herbicide degradation activates microbial carbon metabolism in soils.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70058},
pmid = {41112045},
issn = {2770-596X},
abstract = {Extensive herbicide residues in the black soil of northeastern China are considered a significant agricultural pollution threat, yet effective bioremediation of this complex and persistent mixture remains a challenge. We identified 16 bacterial species that associated with these herbicide residues in situ, nine of which were culturable and could degrade multiple herbicides. From these strains, we constructed a four-member synthetic microbial community (SynCom) that degrades multiple herbicides, stabilizes colonization, increases soil bacterial biodiversity, and alters soil enzyme activity. Under laboratory conditions, the SynCom degraded eight herbicides within 48 h with >60% efficiency, and accumulated carbon on the cell surface of the constituent species. In black soil microcosm trials, the SynCom achieved 60%-99% degradation efficiency of the endogenous herbicides over 35 days and was able to consistently maintain biomass above 10[4] cfu/g soil. Additionally, SynCom application resulted in an accumulation of carbohydrate-active enzymes and microbial necromass-associated carbon, which suggests activation of soil microbial carbon metabolism. In support of this, metagenomic analyses identified a significant increase in the abundance of genes involved in the tricarboxylic acid cycle, pyruvate metabolism, and glycolysis. This SynCom represents a compelling bioremediation solution that simultaneously improves soil microbial carbon metabolism activity in polluted soils.},
}
@article {pmid41110780,
year = {2025},
author = {Sreekutti, S and Ndomondo, S and Sharma, P and Patel, R and Mevada, V},
title = {Forensic application of metagenomics: Methods and future directions.},
journal = {Journal of microbiological methods},
volume = {239},
number = {},
pages = {107300},
doi = {10.1016/j.mimet.2025.107300},
pmid = {41110780},
issn = {1872-8359},
mesh = {*Metagenomics/methods/trends ; Humans ; *Microbiota/genetics ; *Forensic Sciences/methods ; Bacteria/genetics/classification/isolation &amp; purification ; *Forensic Genetics/methods ; },
abstract = {The microbial communities are found commonly in our environment, making it impossible to touch any surface without interfering with them. The human microbiome, primarily bacteria in the saliva, skin, and gut, can be used for forensic purposes. Human-associated and environmental samples, such as soil, water, etc., carry the microbiome, which can be used for geolocation inference. These microbiomes have considerable potential for use in forensic investigations, including many instances of sexual violence, post-mortem examinations, individual identification, and location identification. Recent developments in metagenomic sequencing have greatly contributed to microbial analysis. Yet, because of certain issues and challenges, the forensic application of microbiomes is still in its infancy. This article reviewed the use of metagenomics in forensic science and some of the main obstacles that are faced by experts in this area. The first and foremost issues noted were the lack of standardization protocols and a poor reference database for research studies. Some limitations, such as storage sensitivity and limited samples, are also indicated. Future research studies should concentrate on more standardized investigations to overcome these difficulties and explore the enormous potential of microbiomes for beneficial applications in forensic contexts.},
}
@article {pmid41110566,
year = {2025},
author = {Wu, Z and He, Z and Dou, P and Wang, K and Zhang, Y},
title = {Study on the intestinal metabolism and absorption of polysaccharides from Dendrobium officinale.},
journal = {International journal of biological macromolecules},
volume = {331},
number = {Pt 2},
pages = {148390},
doi = {10.1016/j.ijbiomac.2025.148390},
pmid = {41110566},
issn = {1879-0003},
mesh = {*Dendrobium/chemistry ; *Polysaccharides/metabolism/chemistry/pharmacokinetics/pharmacology ; Gastrointestinal Microbiome/drug effects ; Animals ; *Intestinal Absorption ; Male ; *Intestinal Mucosa/metabolism ; Bacteroides/metabolism/genetics ; *Intestines/microbiology ; },
abstract = {Dendrobium officinale polysaccharide (DOP) is widely recognized for its excellent pharmacological activities, however, the in-depth pharmacokinetic characteristic remains unrevealed, significantly hindering its further development. It was hypothesized that Bacteroides predominantly mediates the in vivo metabolism of DOP via polysaccharide utilization loci (PULs), and the resulting oligosaccharides can be directly absorbed by the intestine. To verify this hypothesis, metagenomic sequencing analysis was first employed, confirming that DOP stimulates an upregulation of PULs associated with carbohydrate metabolism within the gut microbiota dominated by Bacteroides. The metabolized oligosaccharides were correlated with highly expressed endo-β-1,4-mannanase from Bacteroides. Further utilizing fluorescent labeling techniques, it was demonstrated that oligosaccharides derived from DOP metabolism are directly absorbed by intestinal tissues. Unabsorbed metabolites subsequently undergo disordered metabolism by gut microbiota into small molecules such as short-chain fatty acids. Collectively, these findings provide novel evidence for elucidating the pharmacological activities of DOP and offer new insights into pharmacokinetic research for other polysaccharides.},
}
@article {pmid41110291,
year = {2025},
author = {Liu, C and Liu, Y and Li, Y and Liu, M and Lu, H and Liu, X and Lu, M},
title = {Host-dominated oxidative cascades and transgenerational Cu transfer drive population collapse in Spodoptera frugiperda under chronic CuO nanoparticle exposure: Implications for nano-pesticide environmental risk assessment.},
journal = {Environment international},
volume = {205},
number = {},
pages = {109874},
doi = {10.1016/j.envint.2025.109874},
pmid = {41110291},
issn = {1873-6750},
mesh = {Animals ; *Copper/toxicity ; *Spodoptera/physiology/drug effects ; Risk Assessment ; *Metal Nanoparticles/toxicity ; Oxidative Stress/drug effects ; Gastrointestinal Microbiome/drug effects ; Nanoparticles/toxicity ; },
abstract = {The increasing use of CuO nanoparticles (NPs) in agriculture raises urgent concerns about their long-term ecological risks, particularly regarding transgenerational reproduction and gut microbiota in pest species. Here, we chronically exposed Spodoptera frugiperda to a sublethal concentration of CuO NPs (25 mg/kg). Population collapse occurred in the F4 generation (0 % survival), driven by pronounced oxidative stress (CAT and MDA activities increased up to 2.0-fold), substantial Cu accumulation in eggs (12 → 30 ng/mg) and gut tissue (25 → 750 ng/mg), and impaired reproductive output (33 % reduction in egg production with only 30 % hatching in F3). Although gut microbial diversity remained structurally stable (Shannon index, P > 0.05), metagenomic analysis revealed functional reprogramming, particularly in energy metabolism. Sterile larva inoculation assays confirmed that microbiota exacerbated toxicity, though direct NPs effects dominated. These findings highlight that current risk assessment frameworks, which are primarily focused on acute toxicity and microbial composition, severely underestimate the hazards of nanopesticides. We advocate for integrating multigenerational toxicity testing and metagenomic profiling into nano-pesticide risk evaluations to better capture population-level outcomes.},
}
@article {pmid41108937,
year = {2025},
author = {Yang, MT and Xie, LH and Wang, L and Gao, YQ and Liu, R and Ma, H and Lei, CC and Jiang, J and Su, JW and Zhang, XX and Ni, HB and Nan, FL},
title = {Metagenomic analysis of bile acid biotransformation by gut microbiota in wild birds.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105956},
pmid = {41108937},
issn = {1525-3171},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Bile Acids and Salts/metabolism ; *Birds/microbiology/metabolism ; Biotransformation ; Metagenomics ; Animals, Wild/microbiology/metabolism ; *Metagenome ; *Bacteria/metabolism/genetics/classification ; Phylogeny ; },
abstract = {Although gut microbiota-mediated bile acid (BA) metabolism is well characterized in mammals, its mechanisms in wild birds remain largely unknown, hindering our understanding of their ecological adaptation and health. In this study, metagenomic analysis was performed on 10,455 metagenome-assembled genomes (MAGs) derived from 718 wild bird gut samples, from which 1,034 high-quality non-redundant MAGs were selected for further analysis. Functional annotation analysis identified 755 MAGs encoding genes associated with BA biotransformation pathways, primarily derived from the phyla Bacillota_A, Bacteroidota, and Bacillota, with dominant genera including Helicobacter_G and Ligilactobacillus. Subsequent genomic analysis identified 379 MAGs encoding bile salt hydrolase (BSH), with phylogenetic classification demonstrating predominant affiliation to the Bacteroidota and Bacillota_A phyla. Compared to the BSH-producing microbiota in the human and chicken gut, the phylum Bacillota exhibited a notably higher relative abundance in wild birds. Within the wild bird gut microbiome, Helicobacter_G was identified as the predominant BSH-encoding genus, whereas its relative abundance was substantially lower in both humans and chickens. Moreover, migratory birds (MB) displayed significantly higher diversity of BA biotransformation genes than resident birds (RB), with Helicobacter_G being notably enriched at the genus level in MB, potentially associated with their heightened energy and nutritional demands during migration. Notably, in addition to residency status, host species emerged as the most influential factor shaping the compositional variation of BA biotransformation genes, followed by environmental factors and dietary habits. In summary, this study systematically elucidates the potential functions of gut microbiota in BA metabolism and their close associations with host ecological traits in wild birds, not only advancing our understanding of host-microbe interactions and metabolic adaptation mechanisms but also providing a theoretical foundation for future interventions targeting gut microbiota to improve wildlife health.},
}
@article {pmid41106786,
year = {2025},
author = {Guo, M and Zhao, H and Song, N and Huang, P and Li, M and Han, L and Zeng, KW and Lu, Z},
title = {Shenmai injection attenuates sepsis-associated acute lung injury by remodeling gut microbiota and restoring steroid hormone biosynthesis.},
journal = {Fitoterapia},
volume = {187},
number = {},
pages = {106935},
doi = {10.1016/j.fitote.2025.106935},
pmid = {41106786},
issn = {1873-6971},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/pharmacology ; *Acute Lung Injury/drug therapy/etiology/microbiology ; *Sepsis/complications ; Male ; Mice, Inbred C57BL ; Drug Combinations ; Panax/chemistry ; Ophiopogon/chemistry ; Cytokines ; *Steroids/biosynthesis ; },
abstract = {Sepsis-associated acute lung injury (SA-ALI), a critical complication of sepsis, is characterized by immune dysregulation-induced pulmonary dysfunction. Shenmai Injection (SMI) is a standardized herbal preparation consisting of Panax ginseng C.A.Mey (Hongshen) and Ophiopogon japonicus (Thunb.) Ker Gawl (Maidong), traditionally used for qi-replenishing, collapse-stabilizing, and lung-moistening therapy. Although clinically utilized in the management of SA-ALI, the specific mechanisms by which it acts against SA-ALI necessitate further investigation. The present study endeavors to comprehensively determine the therapeutic efficacy of SMI against SA-ALI through an integrated approach combining network pharmacology, metabolomics, metagenomic sequencing, and experimental validation. In this study, murine SA-ALI was established using lipopolysaccharide (LPS) and Poly(I:C). Results indicated that SMI administration significantly attenuated pulmonary inflammation, restored blood-gas barrier integrity, reduced serum pro-inflammatory cytokines and suppressed NF-κB pathway activation in SA-ALI mice. Network pharmacology elucidated the multi-targeted mechanism of SMI in modulating steroid hormone biosynthesis. Integrated metabolomics and target analysis revealed that ophiopogonin A/B and luteolin in SMI alleviates metabolic dysregulation by targeting key enzymes, including AKR1C3, HSD17B1/2, and SULT1E1. Metagenomic profiling demonstrated SMI-mediated gut microbiota remodeling, marked by suppression of pathogenic Chlamydiaceae (particularly Chlamydia abortus) and enrichment of commensal Lactobacillaceae. Correlation analysis showed that intestinal androstenedione and androsterone levels during SMI treatment recovery were negatively correlated with Chlamydia abortus abundance. In conclusion, SMI enhances the recovery from sepsis-associated SA-ALI by dual modulation of gut microbial ecology and host metabolic homeostasis, thereby establishing its potential as a multi-mechanistic therapeutic candidate for sepsis-related organ injury.},
}
@article {pmid41105996,
year = {2025},
author = {Chen, ZY and Gao, FZ and Bai, H and He, LY and Liu, YS and Ying, GG},
title = {Airborne free DNA in chicken farms: The overlooked traits in microbial diversity, viral composition, and antimicrobial resistance risk.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140144},
doi = {10.1016/j.jhazmat.2025.140144},
pmid = {41105996},
issn = {1873-3336},
mesh = {Animals ; Chickens ; *Air Microbiology ; Microbiota ; *Drug Resistance, Microbial/genetics ; Farms ; *DNA/analysis ; Bacteria/genetics ; Metagenomics ; },
abstract = {The enrichment of DNA from total suspended particulates (TSP) onto 0.22 µm pore size filters (intracellular DNA, iDNA) is a critical step in characterizing the airborne microbiome. However, free DNA (< 0.22 µm, fDNA) may harbor unrecognized microbial and genetic components. In this study, metagenomic analysis was employed to compare airborne fDNA and iDNA from eight chicken houses. Overall, the average concentration of fDNA was 5.6-fold higher than that of iDNA. A total of 587 genera spanning 28 phyla were identified in fDNA, including 162 genera absent from iDNA. Notably, 39.7 % of open reading frames were unique to fDNA, involving key metabolic and regulatory pathways. A total of 50.2 % viral contigs were only detected in fDNA, carrying mobile genetic elements, virulence factor genes, and resistance genes against antibiotics, biocides, and metals. The total absolute abundance of the antibiotic resistome was higher in fDNA, with 79.2 % of significantly varied genes enriched therein, including 16 high-risk genes. Metagenomic binning further supported that fDNA harbors broader microbial diversity and functional traits. These findings underscore airborne fDNA as an underexplored reservoir of microbial and genetic diversity, meriting further investigation for its ecological and public health implications.},
}
@article {pmid41104935,
year = {2025},
author = {Feijão, E and Duarte, IA and Pereira, M and Pascoal, P and Nunes, M and Tanner, SE and Dias, R and Duarte, B and Matos, AR and Figueiredo, A and Fonseca, VF},
title = {Gilthead sea bream gut bacteriome as a valuable tool for seafood provenance analysis.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {11},
pages = {e0150825},
pmid = {41104935},
issn = {1098-5336},
support = {https://doi.org/10.54499/2022.11916.BD//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; http://doi.org/10.54499/UIDB/04292/2020, http://doi.org/10.54499/UIDP/04292/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; http://doi.org/10.54499/LA/P/0069/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; http://doi.org/10.54499/UIDB/04046/2020, http://doi.org/10.54499/UIDP/04046/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; http://doi.org/10.54499/UIDB/00329/2020, http://doi.org/10.54499/UIDP/00329/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; http://doi.org/10.54499/LA/P/0121/2020//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Animals ; *Seafood/microbiology/analysis ; *Gastrointestinal Microbiome ; *Sea Bream/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Machine Learning ; Portugal ; },
abstract = {The increasing demand for high-quality seafood underscores the significant challenges posed by rampant seafood fraud. This study aimed to identify regional capture biomarkers by using the gut bacteriome of Sparus aurata specimens through state-of-the-art long-read sequencing allied to machine learning tools. The gut bacteriomes of animals from four different fishing areas on the Portuguese coast were sequenced. The alpha and beta diversity analyses were shown to enable Center-South gut bacteriome differentiation from other fishing areas due to higher abundance of species of the phyla Pseudomonadota, Bacteroidota, and Bacillota and classes such as Alphaproteobacteria, Betaproteobacteria, and Bacilli. The gradient boosting machine (GBM) model selected by the H2O automatic machine learning pipeline presented a high global accuracy during training and validation phases, identifying Center-South and South sample provenance with 100% and 71.1% accuracy, respectively. By integrating the most important OTUs to the GBM model with the regional biomarkers identified through point biserial correlation analysis (indicspecies packages), a reduced set of five provenance biomarkers was identified, belonging to Gammaproteobacteria, Betaproteobacteria, and Bacilli classes, possibly highlighting the anthropogenic activities surrounding the fishing areas and local environmental abiotic factors. This study highlights the extensive and valuable information obtained by long-read sequencing and couples it with the potential of machine learning algorithms to ultimately demonstrate its efficiency in providing efficient and highly accurate seafood provenance biomarkers. This study also reports the likely influence of industrial and recreational activities, population density, and water management facilities on the gut bacteriome of S. aurata.IMPORTANCEThis study significantly contributes to a topic of utmost importance-seafood provenance analysis and seafood fraud-by leveraging gut bacteriome profiling. Through the application of long-read sequencing and machine learning, it identifies reliable biomarkers that distinguish gilthead sea bream from different fishing areas. These findings enhance traceability methods by providing a robust tool to combat seafood fraud and ensure food authenticity, thereby protecting the supply chain, the consumer, and the environment. Additionally, this study explores the possible interactions between the gut bacteriome and the industrial, recreational, and environmental factors that could influence the identified biomarkers of regional provenance while also offering insights into the composition of the marine ecosystems surrounding the fishing areas. This approach has broader implications for fishery management, sustainable sourcing, and regulatory enforcement.},
}
@article {pmid41102734,
year = {2025},
author = {Lv, Y and Zhang, L and Zhang, Y},
title = {Clear niche partitioning of nitrite-oxidizing bacteria from the bottom and the slope of Mariana Trench.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {208},
pmid = {41102734},
issn = {2049-2618},
support = {42306104//National Natural Science Foundation of China/ ; 42122043//National Natural Science Foundation of China/ ; 2023M742237//China Postdoctoral Science Foundation/ ; HRSJ-ZSZX-008//Project of Hainan Research Institute/ ; 21TQ1400201//Shanghai Jiao Tong University, Shanghai Pilot Program for Basic Research-Shanghai Jiao Tong University/ ; 2023YFC2812800//National Key Research and Development Program of China/ ; },
mesh = {*Nitrites/metabolism ; Oxidation-Reduction ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Geologic Sediments/microbiology ; Metagenome ; Ecosystem ; Microbiota ; Metagenomics/methods ; Phylogeny ; Nitrogen Cycle ; },
abstract = {BACKGROUND: The hadal zone, characterized by extreme hydrostatic pressure and geographic isolation, hosts microbial communities uniquely adapted to these harsh conditions. While niche partitioning has been observed in other deep-sea environments, its existence within hadal trench ecosystems remains controversial. Focusing on the Mariana Trench, we investigated whether nitrite-oxidizing bacteria (NOB) exhibit depth-stratified ecological specialization between slope (6000-10,000 m) and bottom (> 10,000 m) sediments. By analysing the genomic features and ecological interactions of NOB, we aimed to resolve their functional roles in nitrogen cycling under distinct hadal microniches.<br><br>RESULTS: We reconstructed 8 high-quality NOB metagenome-assembled genomes (MAGs) from 58 sediment metagenomes, revealing stark niche differentiation between depth zones. Slope-dominant NOB harboured expanded genetic arsenals for antioxidation (e.g. superoxide dismutase) and osmoprotection (compatible solute transporters), Suggesting enhanced adaptive capacity to pressure-adjacent stresses. Metatranscriptomics revealed 1.48&#x2009;&#xd7;&#x2009;(nxrA) and 1.28&#x2009;&#xd7;&#x2009;(aclA) greater expression of nitrite oxidation and carbon fixation genes in slope communities than in their bottom counterparts. Network analysis identified slope NOB as keystone taxa with elevated among-module connectivity and intramodule linkages, in contrast with bottom NOB, which exhibited localized nitrate-production gene networks. Functional profiling revealed complementary biogeochemical roles: slope NOB primarily consumed nitrite, whereas bottom populations dominated nitrate synthesis.<br><br>CONCLUSION: Our multiomics analysis revealed depth-dependent niche partitioning among hadal NOB, with transcriptional and network evidence supporting distinct pressure adaptation strategies and biogeochemical functions. The slope-bottom differentiation in stress response systems and nitrogen transformation pathways highlights how micron-scale environmental gradients drive microbial specialization in Earth's deepest ecosystems. These findings establish NOB as critical mediators of hadal biogeochemical cycles and provide a framework for understanding microbial resilience in extreme biospheres. Video Abstract.},
}
@article {pmid41102233,
year = {2025},
author = {Kwak, MJ and Park, J and Park, H and Yoon, J and Lee, J and Hahnke, RL and Lee, SW and Kwon, SK and Song, JY and Kim, JF},
title = {Polyphasic and comparative genomic characterization of a novel Mariniflexile species in the rhizosphere microbiome of tomato resistant to bacterial wilt.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36158},
pmid = {41102233},
issn = {2045-2322},
support = {918011-4//Ministry of Agriculture, Food and Rural Affairs/ ; NRF-2023R1A2C3004496//Ministry of Science and ICT, South Korea/ ; NRF-2018R1A6A1A03025607//Ministry of Education, South Korea/ ; },
mesh = {*Solanum lycopersicum/microbiology ; *Rhizosphere ; Phylogeny ; *Plant Diseases/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Genome, Bacterial ; Ralstonia solanacearum ; Soil Microbiology ; Genomics ; Disease Resistance ; },
abstract = {A plethora of microbes resides in the plant rhizosphere, and some play roles in host health and disease. We previously isolated a Gram-negative, aerobic, rod-shaped rhizobacterium, TRM1-10, that contributes to bacterial wilt resistance of tomato caused by Ralstonia solanacearum. In this study, we characterized TRM1-10 through physiological and biochemical analyses, complemented by whole genome sequencing and comparative genomic analyses. Phylogenetic analysis using the 16S rRNA gene and genome sequences revealed that TRM1-10 belongs to the genus Mariniflexile and represents a new lineage. TRM1-10 also exhibits noticeable differences in physiological and biochemical characteristics compared to other Mariniflexile species. Thus, based on phylogenetic affiliation and chemotaxonomic characteristics, we propose this bacterium as a novel species in the genus, Mariniflexile rhizosphaerae sp. nov. (type strain TRM1-10[T] = KCTC 18646P[T] = DSM 33122[T]). Comparative genome analyses revealed that TRM1-10 harbors more genes linked to soil adaptation compared to other phylogenetically related Mariniflexile species, most of which are associated with marine habitats. The genomic features of TRM1-10 and other strains in the species may allow the taxon to adapt to the soil and rhizosphere, compete effectively with the resident soil microbiota, and contribute to plant health.},
}
@article {pmid41101029,
year = {2025},
author = {Ma, L and Liu, F and Zhou, M and Zhang, M and Zheng, J and Wang, Z and He, Z and Yan, Q and Wu, B and Wang, C and Shu, L},
title = {Amoebae contribute to the diversity and fate of antibiotic resistance genes in drinking water system.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109867},
doi = {10.1016/j.envint.2025.109867},
pmid = {41101029},
issn = {1873-6750},
mesh = {*Drinking Water/microbiology/parasitology ; *Amoeba/genetics/physiology ; *Drug Resistance, Microbial/genetics ; Symbiosis ; *Water Microbiology ; Bacteria/genetics ; Microbiota ; },
abstract = {Free-living amoebae represent a significant eukaryotic group that thrives in drinking water systems, posing considerable risks to water quality due to their inherent pathogenicity and associations with various microorganisms. However, the symbiotic microbial profiles of different amoeba species and the impact of amoeba-bacteria interactions on the antibiotic resistome within drinking water systems remain poorly understood. In this study, we obtained 24 amoeba isolates from tap water, encompassing diverse phyla within the amoeba lineage. Through metagenome sequencing, we uncovered variations in symbiotic microbiome composition across different amoeba species and strains. Notably, amoebae acted as vectors for human pathogens, including bacteria and viruses. The majority of symbionts carried multiple antibiotic-resistance genes and virulence factors. Furthermore, dominant symbiotic species could be cultured independently, underscoring the critical role of amoebae in preserving and transmitting antibiotic-resistant opportunistic pathogens in drinking water systems. Disinfection experiments demonstrated highly diverse viability of amoebae and their protective capabilities for symbionts against chlorine disinfection. Our findings expand the germplasm bank for amoebae and symbiotic bacteria derived from tap water and emphasize the necessity for further research on amoeba-bacteria symbiosis to ensure drinking water quality and public health safety.},
}
@article {pmid41100443,
year = {2025},
author = {Shi, F and Zou, D and Zhang, L and Guo, N and Yu, J and Degen, AA and Tang, X and Ren, S and Ru, Y and Zheng, S and Zhang, Y and Wang, D},
title = {Increased urea nitrogen salvaging by a remodeled gut microbiota helps nonhibernating pikas maintain protein homeostasis during winter.},
journal = {PLoS biology},
volume = {23},
number = {10},
pages = {e3003436},
pmid = {41100443},
issn = {1545-7885},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Nitrogen/metabolism ; *Urea/metabolism ; Seasons ; *Lagomorpha/metabolism/microbiology/physiology ; Homeostasis ; *Proteostasis/physiology ; Feces/microbiology ; Diet, Protein-Restricted ; Male ; Liver/metabolism ; Herbivory ; Fecal Microbiota Transplantation ; },
abstract = {Nitrogen balance is a major challenge for herbivores when consuming a low-nitrogen diet. Gut microbiota-mediated urea nitrogen recycling facilitates protein homeostasis during times of nitrogen deficiency, yet its relevance to wild nonhibernating small mammals remains unclear. Here, through a combination of isotope tracing, metagenomics, targeted short-chain fatty acid analysis, and fecal microbiota transplantation, we investigated the effects of protein restriction in winter on urea nitrogen recycling in plateau pikas (Ochotona curzoniae) of the Qinghai-Tibetan Plateau. Hepatic urea-cycle metabolism was downregulated during winter protein restriction, accompanied by increases in beneficial bacteria with ureolytic capacity (such as the genus Alistipes), gut urease activity, and urea transporters, and acetate production, with a consequent increase in nitrogen reincorporation into the pika's protein pool. Critically, supplementing a low-protein diet with yak fecal microbiota enhanced the ureolytic capacity by increasing Alistipes abundance, revealing a critical mechanism whereby interspecies horizontal microbial transfer between sympatric species enhances host protein homeostasis. Our results reveal a functional role for the gut microbiota in urea nitrogen recycling to maintain protein balance in winter-active herbivorous small mammals and contribute to our understanding of species coexistence and mammalian adaptation to high-altitude environments. Our findings establish that microbiota-driven urea nitrogen recycling is a key adaptive strategy for protein homeostasis in winter-active herbivores. This work provides new insights into the mechanisms of mammalian adaptation to high-altitude environments and the dynamics of interspecies coexistence.},
}
@article {pmid41099535,
year = {2025},
author = {Rusanova, A and Mamontov, V and Ri, M and Meleshko, D and Trofimova, A and Fedorchuk, V and Ezhova, M and Finoshin, A and Lyupina, Y and Isaev, A and Sutormin, D},
title = {Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level.},
journal = {mSystems},
volume = {10},
number = {11},
pages = {e0114725},
pmid = {41099535},
issn = {2379-5077},
support = {&#x2116; 0088-2024-0009//IDB RAS Government basic research program/ ; &#x2116; 0088-2024-0009//IDB RAS Government basic research program/ ; },
mesh = {*Symbiosis ; Animals ; *Porifera/microbiology/physiology/classification ; *Microbiota ; Arctic Regions ; Phylogeny ; Sympatry ; Bacteria/classification/genetics ; Gammaproteobacteria/genetics/classification ; },
abstract = {UNLABELLED: Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge-associated microbiomes contribute to the health of host organisms by defending them against invading bacteria and providing them with essential metabolites. Here, we describe the microbiomes of three sympatric species of cold-water marine sponges-Halichondria panicea, Halichondria sitiens, and Isodictya palmata-sampled at three time points over a period of 6 years in the White Sea. We identified the sponges as low microbial abundance species and detected stably associated bacteria that represent new taxa of sponge symbionts within Alpha- and Gammaproteobacteria. The sponges carried unique sets of unrelated species of symbiotic bacteria, illustrating the varying complexity of their microbiomes. At the community level, sponge-associated microbiomes shared common symbiotic features: they encoded multiple eukaryotic-like proteins, biosynthetic pathways and transporters of amino acids and vitamins essential for sponges. At the species level, however, different classes of eukaryotic-like proteins and pathways were distributed between dominant and minor symbionts, indicating specialization within microbiomes. Particularly, the taurine and sulfoacetate import and degradation pathways were associated exclusively with dominant symbionts in all three sponge species, suggesting that these pathways may represent symbiotic features. Our study indicates convergent evolution in the microbiomes of sympatric cold-water sponge species, as reflected by strong functional similarity despite the presence of distinct, taxonomically unrelated symbiotic communities.<br><br>IMPORTANCE: Sponges are regarded among the earliest multicellular organisms and the most ancient examples of animal-bacterial symbiosis. The study of host-microbe interactions in sponges has advanced rapidly due to the application of next-generation sequencing (NGS) technologies that help overcome the challenges of investigating their communities. However, many sponge species, particularly those from polar ecosystems, remain poorly characterized. Here, we demonstrate that three sympatric cold-water sponge species, including two analyzed for the first time, harbor distinct sets of bacterial symbionts, stably associated over 6 years. Using CORe contigs ITerative Expansion and Scaffolding, an algorithm developed in this study, we reconstructed high-quality symbiont genomes and revealed shared features indicative of convergent evolution toward symbiosis. Notably, we identified a potentially novel symbiotic feature-a gene cluster likely involved in sulfoacetate uptake and dissimilation. We also observed shifts in microbiome composition, associated with increasing water temperatures, raising concerns about the impact of global warming on cold-water ecosystems.},
}
@article {pmid41099510,
year = {2025},
author = {Wallace, BA and Varona, NS and Stiffler, AK and Vermeij, MJA and Silveira, C},
title = {High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral, Madracis mirabilis, in Curaçao's coral reefs.},
journal = {mSystems},
volume = {10},
number = {11},
pages = {e0120825},
pmid = {41099510},
issn = {2379-5077},
support = {UM PRA 2022-2547//University of Miami/ ; 2023353157//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; 2023349872//NSF | National Science Foundation Graduate Research Fellowship Program (GRFP)/ ; PG015171//University of Miami/ ; 2424579//NSF/ ; },
mesh = {Animals ; *Anthozoa/microbiology/virology ; *Coral Reefs ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Prophages/genetics ; Metagenomics/methods ; Metagenome ; Biodiversity ; },
abstract = {UNLABELLED: Coral reefs have undergone extensive coral loss and shifts in community composition worldwide. Despite this, some coral species appear naturally more resistant, such as Madracis mirabilis (herein Madracis). Madracis has emerged as the dominant hard coral in Curaçao, comprising 26% of coral cover in reefs that declined by 78% between 1973 and 2015. Although life history traits and competitive mechanisms contribute to Madracis's success, these factors alone may not fully explain it, as other species with similar traits have not shown comparable success. Here, we investigated the potential role of microbial communities in the success of Madracis on Curaçao reefs by leveraging a low-bias bacterial and viral enrichment method for metagenomic sequencing of coral samples, resulting in 77 unique bacterial metagenome-assembled genomes and 2,820 viral genomic sequences. Our analyses showed that Madracis-associated bacterial and viral communities are 12% and 20% richer than the communities of five sympatric coral species combined. The Madracis-associated bacterial community was dominated by Ruegeria and Sphingomonas, genera that have previously been associated with coral health, defense against pathogens, and bioremediation. These communities also displayed higher functional redundancy, which is often associated with ecological resilience. The viral community exhibited a 50% enrichment of proviruses relative to other corals. These proviruses had the genomic capacity to laterally transfer genes involved in antibiotic resistance, central metabolism, and oxidative stress responses, potentially enhancing the adaptive capacity of the Madracis microbiome and contributing to Madracis's success on Curaçao's reefs.<br><br>IMPORTANCE: Understanding why some coral species persist and thrive while most are in fast decline is critical. Madracis mirabilis is increasingly dominant on degraded reefs in Cura&#xe7;ao, yet the role of microbial communities in its success remains underexplored. This study highlights the potential role of Madracis-associated bacterial and viral communities in supporting coral resilience and competitive success. By identifying key microbial partners and viral genes that may enhance host stress tolerance and defense against pathogens, we broaden the understanding of how the coral holobiont contributes to species persistence under environmental stress. These insights are valuable for predicting key microbial community players in reef interactions and may inform microbiome-based strategies to support coral conservation and restoration.},
}
@article {pmid41097145,
year = {2025},
author = {Tuigunov, D and Sinyavskiy, Y and Nurgozhin, T and Zholdassova, Z and Smagul, G and Omarov, Y and Dolmatova, O and Yeshmanova, A and Omarova, I},
title = {Precision Nutrition and Gut-Brain Axis Modulation in the Prevention of Neurodegenerative Diseases.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
pmid = {41097145},
issn = {2072-6643},
support = {Grant No. AP23489983//This research is funded by the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; *Neurodegenerative Diseases/prevention &amp; control/microbiology ; *Gastrointestinal Microbiome/physiology ; *Brain ; *Precision Medicine/methods ; *Brain-Gut Axis/physiology ; Prebiotics/administration &amp; dosage ; Probiotics/administration &amp; dosage ; },
abstract = {In the recent years, the accelerating global demographic shift toward population aging has been accompanied by a marked increase in the prevalence of neurodegenerative disorders, notably Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and multiple sclerosis. Among emerging approaches, dietary interventions targeting the gut-brain axis have garnered considerable attention, owing to their potential to modulate key pathogenic pathways underlying neurodegenerative processes. This review synthesizes current concepts in precision nutrition and elucidates neurohumoral, immune, and metabolic regulatory mechanisms mediated by the gut microbiota, including the roles of the vagus nerve, cytokines, short-chain fatty acids, vitamins, polyphenols, and microbial metabolites. Emerging evidence underscores that dysbiotic alterations contribute to compromised barrier integrity, the initiation and perpetuation of neuroinflammatory responses, pathological protein aggregations, and the progressive course of neurodegenerative diseases. Collectively, these insights highlight the gut microbiota as a pivotal target for the development of precision-based dietary strategies in the prevention and mitigation of neurodegenerative disorders. Particular attention is devoted to key bioactive components such as prebiotics, probiotics, psychobiotics, dietary fiber, omega-3 fatty acids, and polyphenols that critically participate in regulating the gut-brain axis. Contemporary evidence on the contribution of the gut microbiota to the pathogenesis of Alzheimer's disease, Parkinson's disease, and multiple sclerosis is systematically summarized. The review further discusses the prospects of applying nutrigenomics, chrononutrition, and metagenomic analysis to the development of personalized dietary strategies. The presented findings underscore the potential of integrating precision nutrition with targeted modulation of the gut-brain axis as a multifaceted approach to reducing the risk of neurodegenerative diseases and preserving cognitive health.},
}
@article {pmid41094699,
year = {2025},
author = {Serrana, JM and Dessirier, B and Nascimento, FJA and Broman, E and Posselt, M},
title = {Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {204},
pmid = {41094699},
issn = {2049-2618},
support = {Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; },
mesh = {*Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Ecosystem ; Metagenome ; Petroleum/metabolism ; Microbiota ; Metagenomics/methods ; *Water Pollutants, Chemical/metabolism ; Oceans and Seas ; },
abstract = {BACKGROUND: The Baltic Sea receives petroleum hydrocarbons from various point sources. The degradation of these contaminants in the environment is typically facilitated by a variety of microorganisms that possess a range of genes and metabolic functions related to the degradation of various hydrocarbon substrates. However, our understanding of natural attenuation and the microbial capacity to degrade these contaminants within the Baltic Sea ecosystem remains limited. In this study, we compiled metagenomes from the benthic and pelagic ecosystems across the Baltic Sea to identify microorganisms and characterize their genes and metabolic functions involved in the degradation of hydrocarbon compounds.<br><br>RESULTS: Known hydrocarbon-degrading phyla, i.e., Pseudomonadota, Myxococcota A, Actinomycetota, and Desulfobacterota, were identified within the Baltic Sea metagenome-assembled genomes (MAGs). Notably, 80% of the MAGs exhibited multiple hydrocarbon degradation gene annotations (>&#x2009;10 reads per kilobase million). Aerobic degradation was the predominant pathway for hydrocarbon degradation across environmental samples. Hydrocarbon degradation gene abundances varied among samples and Baltic Sea subbasins, with long-chain alkanes and dibenzothiophene compounds being the preferred substrates. Species richness and diversity of both benthic and pelagic microorganisms positively correlated with hydrocarbon degradation gene diversity, with the pelagic ecosystem exhibiting significantly higher richness and diversity compared to the benthic ecosystem. Additionally, the composition of the hydrocarbon degradation genes across the Baltic Sea subbasins was influenced by oil spill history, with areas that experienced higher spill volumes showing lower microbial diversity, suggesting potential enrichment of specific hydrocarbon degraders. Among the environmental factors assessed, depth played a significant role in shaping the composition of genes involved in hydrocarbon degradation within the Baltic Sea.<br><br>CONCLUSIONS: Using metagenomics, we profiled the native microorganisms associated with hydrocarbon degradation in the Baltic Sea. This knowledge will aid in understanding the natural capacities of microbial communities, potentially linked to the natural attenuation of hydrocarbon pollutants in the area. Insights into microbial degradation potential can enhance predictions of petroleum pollutant persistence and accumulation, support mitigation strategies for marine pollution, and reveal the ecological resilience of native microbial communities in marine ecosystems. Video Abstract.},
}
@article {pmid41094135,
year = {2025},
author = {Dahlman, S and Avellaneda-Franco, L and Rutten, EL and Gulliver, EL and Solari, S and Chonwerawong, M and Kett, C and Subedi, D and Young, RB and Campbell, N and Gould, JA and Bell, JD and Docherty, CAH and Turkington, CJR and Nezam-Abadi, N and Grasis, JA and Lyras, D and Edwards, RA and Forster, SC and Barr, JJ},
title = {Isolation, engineering and ecology of temperate phages from the human gut.},
journal = {Nature},
volume = {647},
number = {8090},
pages = {698-705},
pmid = {41094135},
issn = {1476-4687},
support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Prophages/genetics/isolation &amp; purification/classification/physiology ; *Bacteriophages/isolation &amp; purification/genetics/classification/physiology ; Caco-2 Cells ; Lysogeny/genetics ; Virus Activation ; *Bacteria/virology/isolation &amp; purification ; Genome, Viral/genetics ; },
abstract = {Large-scale metagenomic and data-mining efforts have revealed an expansive diversity of bacteriophages (phages) within the human gut[1-3]. However, functional understanding of phage-host interactions within this complex environment is limited, largely due to a lack of cultured isolates available for experimental validation. Here we characterize 134 inducible prophages originating from 252 human gut bacterial isolates using 10 different induction conditions to expand the experimentally validated temperate phage-host pairs originating from the human gut. Importantly, only 18% of computationally predicted prophages could be induced in pure cultures. Moreover, we construct a 78-member synthetic microbiome that, when co-cultured in the presence of human colonic cells (Caco2), led to the induction of 35% phage species. Using cultured isolates, we demonstrate that human host-associated cellular products may act as induction agents, providing a possible link between gastrointestinal cell lysis and temperate phage populations[4,5]. We provide key insights into prophage diversity and genetics, including a genetic pathway for domestication, finding that polylysogeny was common and resulted in coordinated prophage induction, and that differential induction can be influenced by divergent prophage integration sites. More broadly, our study highlights the importance of culture-based techniques, alongside experimental validation, genomics and computational prediction, to understand the biology and function of temperate phages in the human gut microbiome. These culture-based approaches will enable applications across synthetic biology, biotechnology and microbiome fields.},
}
@article {pmid41093983,
year = {2025},
author = {Zhang, J and Sekela, JJ and Hutchinson, LE and Yang, J and Sellers, RS and Bhatt, AP and Redinbo, MR},
title = {Sex-dependent responses in mice to indomethacin-induced organ injury and gut microbiome-targeted alleviation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36025},
pmid = {41093983},
issn = {2045-2322},
support = {NIH R35 award GM152079/NH/NIH HHS/United States ; },
mesh = {Animals ; *Indomethacin/adverse effects/toxicity ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Anti-Inflammatory Agents, Non-Steroidal/adverse effects/toxicity ; Sex Factors ; Spleen/drug effects/pathology ; Liver/drug effects/pathology ; Colon/drug effects/pathology ; RNA, Ribosomal, 16S/genetics ; Glucuronidase/antagonists &amp; inhibitors/metabolism ; Sex Characteristics ; },
abstract = {Nonsteroidal anti-inflammatory drugs (NSAIDs) are used widely but produce gastrointestinal (GI) toxicities in both short- and long-term users. Previous studies have shown that the intestinal microbiota play an important role in gut damage and that gut microbial β-glucuronidase (GUS) inhibitors can alleviate NSAID-induced injury in male mice by blocking the GI reactivation of NSAID-glucuronides. Here, in both male and female C57BL/6 mice, we examine the effects of indomethacin alone and with the GUS inhibitor UNC10201652. Oral delivery of 5 mg/kg body weight indomethacin over 5 days decreased body weight, induced colonic and hepatic inflammatory cytokine gene expression, and enlarged the spleens of both male and female mice. However, sex-specific inflammatory responses to indomethacin were observed, with males demonstrating more colonic injury while females presented greater splenic and hepatic toxic responses. Females also showed a unique indomethacin-induced bloom of fecal Verrucomicrobia as measured by 16S rRNA metagenomic sequencing. UNC10201652 alleviated aspects of these indomethacin-induced toxicities, including features of the male-specific colonic damage and the female-specific compositional changes and spleen and liver toxicities. Thus, GI and non-GI tissues in male and female mice respond distinctly to indomethacin-induced damage. These findings advance our understanding of how sex impacts systemic responses to xenobiotic exposure and may lead to improved therapeutic outcomes with these widely used drugs.},
}
@article {pmid41093108,
year = {2025},
author = {Chandel, N and Patel, P and Somvanshi, PR and Verma, AK and Thakur, V},
title = {Inverse Association between Serum Vitamin B12 Level and Abundance of Potential B12-Producing Gut Microbes in Indian Children.},
journal = {The Journal of nutrition},
volume = {155},
number = {12},
pages = {4284-4295},
doi = {10.1016/j.tjnut.2025.10.021},
pmid = {41093108},
issn = {1541-6100},
mesh = {Humans ; *Vitamin B 12/blood/biosynthesis ; *Gastrointestinal Microbiome ; India ; *Vitamin B 12 Deficiency/blood/microbiology/epidemiology ; Male ; Female ; Feces/microbiology ; Child ; Child, Preschool ; Bacteria/classification/metabolism/genetics ; },
abstract = {BACKGROUND: The human gut microbiome is a natural source of essential micronutrients like B vitamins, which are used by both the host and other community members. The prevalence and abundance of known B-vitamin producers and B-vitamin biosynthesis pathways have already been reported in gut microbiome cohorts of a few countries including India.<br><br>OBJECTIVES: This study tested whether the presence of B-vitamin producers/biosynthetic pathways associates with serum B-vitamin levels, taking vitamin B12 as a case example.<br><br>METHODS: Fecal samples were collected from non-deficient (serum vitamin B12 level > 210 pg/mL; n = 29) and vitamin B12 deficient (serum vitamin B12 level < 210 pg/mL; n = 30) children from a tribal region of central India. Whole metagenomic DNA was extracted, sequenced, and analyzed for taxonomic profiling and diversity comparisons. Differentially abundant taxa between two groups were identified. The prevalence and abundance of potential vitamin B12 producers were compared, and their association with serum vitamin B12 level was established.<br><br>RESULTS: A comparison of within-sample diversity between the two groups did not show any difference; however, between-sample diversity was significantly less in the vitamin B12-deficient group. Differential abundance testing also showed different microbiome structure in the vitamin B12-deficient group, where a higher abundance of vitamin B12 transporter-carrying Bacteroides thetaiotaomicron, a few pathogenic species, and ten known vitamin B12 producers was observed. Potential vitamin B12 producers were also significantly prevalent and abundant in the deficient group. Their cumulative abundance was also significantly higher in the deficient group and showed a negative association with serum vitamin B12 levels.<br><br>CONCLUSIONS: A higher abundance of potential vitamin B12 producers in the deficient group suggest an adaptive mechanism by the gut microbiome to meet the community's vitamin B12 requirements, by selectively promoting the growth of vitamin B12 producers, but causality remains to be proved.},
}
@article {pmid41093042,
year = {2025},
author = {Noordzij, HT and Wortel, MT and Heintz-Buschart, A and Petrikonyte, P and de Muinck, EJ and Trosvik, P},
title = {Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids.},
journal = {Plasmid},
volume = {134},
number = {},
pages = {102761},
doi = {10.1016/j.plasmid.2025.102761},
pmid = {41093042},
issn = {1095-9890},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Plasmids/genetics ; Infant ; Feces/microbiology ; Infant, Newborn ; Bacteroides/genetics ; Longitudinal Studies ; Female ; Computational Biology/methods ; Male ; Clostridium/genetics ; },
abstract = {Little is known about the role of mobile genetic elements in natural ecosystems such as the infant gut microbiome. Here, we conduct the most comprehensive longitudinal study of the infant plasmidome to date by analyzing monthly fecal samples from 12 infants from birth to one year of age. We employ an assembly-based bioinformatic pipeline for the reconstruction and identification of full-length plasmids, including a novel approach for assigning putative plasmid hosts. We then investigated plasmid content and dynamics in the infant gut microbiome. After assembly and identification, we identified 620 unique circular plasmids in the infant cohort, including a number of novel sequences. Independent assembly of the same plasmids in several samples and infants helped corroborate the authenticity of the plasmids. Among the observed plasmids was the recently described ubiquitous and abundant Bacteroides plasmid pBI143. Overall, the genus Bacteroides had the highest plasmid carriage, while the highest plasmid diversity was observed in Clostridium, including 5 previously unknown widespread plasmids. Lastly, we leveraged the longitudinal nature of our dataset to investigate contemporaneous correlations between temporal variations in plasmid abundances and species dynamics. This enabled us to link co-residing plasmids and tightly linked plasmid-taxon pairs within each infant. These insights into plasmid ecology help us understand determinants driving plasmid distribution in complex microbial communities.},
}
@article {pmid41092906,
year = {2025},
author = {Wu, L and Li, Y and Wang, W and Deng, L and Ge, H and Cui, M and Bi, N},
title = {Gut microbiota predictive of the efficacy of consolidation immunotherapy and chemoradiotherapy toxicity in lung cancer.},
journal = {Med (New York, N.Y.)},
volume = {6},
number = {12},
pages = {100877},
doi = {10.1016/j.medj.2025.100877},
pmid = {41092906},
issn = {2666-6340},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung Neoplasms/therapy/mortality ; Female ; Male ; *Chemoradiotherapy/adverse effects ; Middle Aged ; Aged ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects ; *Immunotherapy/methods/adverse effects ; RNA, Ribosomal, 16S ; Prognosis ; Feces/microbiology ; Progression-Free Survival ; },
abstract = {BACKGROUND: Gut microbiota (GM) predict responses to immune checkpoint inhibitors (ICIs) in patients with advanced lung cancer. However, its role in patients with locally advanced lung cancer undergoing chemoradiotherapy (CRT) combined with consolidation ICIs remains unclear.<br><br>METHODS: A total of 177 fecal samples were collected pre- and post-CRT. Using 16S ribosomal RNA (16S rRNA) sequencing and metagenomic data from an internal cohort and published studies, the kinetics of microbiota were analyzed using the Wilcoxon signed-rank test, while prognostic factors for progression-free survival (PFS) were identified using Cox regression modeling and machine learning algorithms.<br><br>FINDINGS: The GM configuration was unaffected by traditional CRT. However, in cases of CRT with consolidation ICIs, patients with long-PFS showed a higher alpha diversity at baseline, followed by a reduction during treatment, contrasting with the stable diversity observed in the short-PFS group. Enrichment of the symbiotic microbe Akkermansia muciniphila (Akk) after CRT was observed, with its increased abundance correlating with extended distant metastasis-free survival in patients undergoing CRT with consolidation ICIs. Notably, the trend in Akk variation was a prognostic indicator of survival outcomes in patients undergoing CRT combined with ICIs. GM was also involved in the development of treatment-related pneumonia and was a promising predictive marker for severe pneumonia.<br><br>CONCLUSIONS: CRT with consolidation ICIs has more pronounced effects on the GM than CRT alone in patients with locally advanced lung cancer. The dynamic variation in Akk has predictive potential for patient survival in this context.<br><br>FUNDING: This study was supported by the National Science and Technology Major Project.},
}
@article {pmid41092847,
year = {2025},
author = {Zhang, Y and Su, K and Munir, F and Wang, W and Liang, X and Wang, J and Hua, J and Ma, W},
title = {Gut microbiome metagenomics in diarrheic and healthy Simmental cattle from Ningxia Province, China.},
journal = {Research in veterinary science},
volume = {197},
number = {},
pages = {105922},
doi = {10.1016/j.rvsc.2025.105922},
pmid = {41092847},
issn = {1532-2661},
mesh = {Animals ; Cattle ; China ; *Cattle Diseases/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Diarrhea/veterinary/microbiology ; Feces/microbiology ; Bacteria/genetics/classification ; },
abstract = {INTRODUCTION: The gut microbiome plays a crucial role in health and disease. This study aims to investigate the composition, characteristics, and functional diversity of the intestinal microbiome by performing metagenomic sequencing on fecal samples from diarrheic and healthy Simmental cattle.<br><br>RESULTS: This study compared the gut microbiome differences between two groups of Simmental cattle (5 diarrheic and 20 healthy) in Ningxia province, China. Metagenomic analysis revealed higher microbial heterogeneity in the diarrheic group, likely reflecting pathogen-driven ecological disruption, whereas the healthy group was dominated by butyrate-producing and fiber-degrading bacteria, maintaining intestinal homeostasis. Antibiotic resistance gene analysis detected glycopeptide resistance genes in both groups, but the healthy group also carried aminoglycoside/tetracycline resistance genes and poxtA. KEGG pathway analysis showed that the diarrheic group was enriched in purine synthesis-related pathways, while the healthy group exhibited dominant metabolic pathways such as glutamine synthase. Virulence factor analysis indicated that the diarrheic group had higher abundances of capsular polysaccharides and type IV secretion systems, potentially promoting bacterial colonization and immune evasion. In summary, diarrheic cattle harbored a gut microbiome dominated by opportunistic pathogens, accompanied by metabolic dysregulation and antimicrobial resistance risks, whereas healthy cattle maintained a microbial community rich in short-chain fatty acid producers. This study provides a theoretical foundation for gut microbiome modulation and antimicrobial resistance control in ruminants.<br><br>CONCLUSION: This study revealed distinct gut microbiome composition and function between diarrheic and healthy cattle through sequencing analysis. The findings offer insights for ruminant diarrhea management and provide a basis for developing more scientific antibiotic management strategies in animal husbandry.},
}
@article {pmid41091222,
year = {2025},
author = {Tajdozian, H and Seo, H and Kim, S and Rahim, MA and Park, HA and Sarafraz, F and Yoon, Y and Kim, H and Barman, I and Park, CE and Ghorbanian, F and Lee, S and Jeong, HR and Song, HY},
title = {Microbiome therapeutic PMC101 inhibits the translocation of carbapenem-resistant Klebsiella while enhancing eubiosis in antibiotic-induced dysbiosis mice.},
journal = {Medical microbiology and immunology},
volume = {214},
number = {1},
pages = {49},
pmid = {41091222},
issn = {1432-1831},
support = {No. RS-2023-00219563//Ministry of Science and ICT, South Korea/ ; P248400003//Korea Institute for Advancement of Technology/ ; },
mesh = {Animals ; *Dysbiosis/chemically induced/microbiology/therapy ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; *Klebsiella Infections/microbiology/therapy ; *Bacterial Translocation/drug effects ; Carbapenems/pharmacology ; Humans ; Mice, Inbred C57BL ; Feces/microbiology ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE), known for their extensive antibiotic resistance, pose a severe global medical threat. Therefore, developing novel therapeutics beyond conventional antibiotics is urgently needed, and the importance of microbiome therapeutics is increasingly being recognized. This study explores the expanded systemic efficacy of PMC101, a microbiome therapeutic, beyond intestinal CRE infections and investigates its mechanism of action from a microbiome perspective. First, the genetic characteristics of the novel strain were identified through whole-genome analysis, and a scalable cultivation process was established as part of the overall development of this microbiome therapeutic. PMC101 increased the survival rate to 100%, significantly reduced disease severity scores, and prevented weight loss in CRE-infected mice treated with antibiotics. These effects are attributed to the inhibition of CRE growth in stool and the reduced detection of CRE in the lungs and kidneys, indicating suppression of systemic translocation. Metagenomic analysis revealed that PMC101 prevented the reduction in microbial population caused by antibiotics and CRE infection, restored species diversity indices, and mitigated dysbiosis while promoting eubiosis. This CRE translocation suppression was closely associated with increased CRE translocation-microbiome index, defined as the ratio of Bacteroidetes to Proteobacteria. This relationship was further confirmed through simulations using a human intestinal microbial ecosystem model. Additionally, increases in short-chain fatty acids, reductions in excessive inflammatory responses, and decreases in tissue damage were observed, all of which contribute to preventing CRE translocation. Finally, pathogen inhibition effects and safety tests were conducted, confirming the prophylactic potential of PMC101 as a microbiome therapeutic. These findings strongly support PMC101 as a promising candidate for future microbiome-based therapies against CRE infections.},
}
@article {pmid41089454,
year = {2025},
author = {Hu, X and He, Z and Liu, C and Zhang, Y and Mu, D and Guskov, VY and Wang, K and Yao, Y and Jin, D and Lu, J and Ning, Y and Jiang, G},
title = {Revealing Amur tiger family pedigrees based on age identification using fecal microbiome and kinship analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1666201},
pmid = {41089454},
issn = {1664-302X},
abstract = {INTRODUCTION: The construction of a species' family pedigree is crucial for understanding population structure, assessing genetic diversity, and conserving the genetic resources of endangered species. However, developing non-invasive and reliable methods for age identification in wild individuals remains a significant challenge in family pedigree establishments.<br><br>METHODS: In this study, we employed 16S rRNA sequencing and metagenomic analysis to examine 30 fecal samples collected from captive Amur tigers across three distinct age groups, aiming to identify the age-specific biomarker, which could subsequently facilitate age determination of wild individuals and support the construction of species pedigree.<br><br>RESULTS: Our results demonstrate that, through 16S rRNA high-throughput sequencing, 16 potential microbial age biomarkers were identified in fecal samples from captive Amur tigers, and the ages of 17 captive individuals were distinguished. Notably, f_Erysipelotrichaceae_Unclassified and Paraclostridium, identified as potential age-associated bacterial markers in captive Amur tigers, were also detected in fecal samples from wild individuals of this species. To explore their potential application in age inference for Amur tigers, we integrated genetic relationship analysis with these potential age-specific biomarkers to construct a comprehensive pedigree of wild Amur tigers.<br><br>DISCUSSION: This study established a comprehensive scientific framework for pedigree reconstruction based on age determination in Amur tigers and developed a scalable, non-invasive methodology offering opportunities for population structure and promoting the precision of conservation for wild tigers.},
}
@article {pmid41088378,
year = {2025},
author = {Chen, Z and Jia, Y and Li, H and Fan, R and Cao, Y and Ni, L and Yang, L and Yuan, Z and Zhu, K and Gao, Y and Lin, Y},
title = {Effects of zacopride and multidimensional impacts of cross-kingdom symbiosis: gut microbiota modulates coronary microvascular dysfunction via the chlorophyll/heme-tryptophan metabolic axis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1097},
pmid = {41088378},
issn = {1479-5876},
support = {20210302123485//Fundamental Research Program of Shanxi Province/ ; BYJL065//Shanxi Province Higher Education "Billion Project" Science and Technology Guidance Project/ ; NSFC-82102104//National Natural Science Foundation of China/ ; 2021M702054//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Tryptophan/metabolism ; Male ; *Symbiosis/drug effects ; *Benzamides/pharmacology/therapeutic use ; *Coronary Vessels/drug effects/physiopathology ; *Microvessels/drug effects/physiopathology ; Rats ; *Microcirculation/drug effects ; },
abstract = {BACKGROUND: Coronary Microvascular Dysfunction (CMD) represents a critical pathological substrate for ischemic heart disease and is strongly associated with major adverse cardiovascular events. Zacopride, known for its dual cardiovascular regulatory properties targeting the 5-HT4 receptor and Kir2.1 channel, lacks evidence regarding its systemic impact on the gut microbiota-metabolism axis. Therefore, this study aims to elucidate the structural and metabolic characteristics of gut bacteria and fungi in CMD, and to explore the multidimensional therapeutic mechanisms of Zacopride through "microbial remodeling-metabolic regulation-microcirculation repair."<br><br>METHODS: Sixty Sprague-Dawley rats were randomized into three groups: coronary microvascular dysfunction (CMD), healthy control (NC), and Zacopride intervention (ZAC). CMD and ZAC groups received high-fat diet plus streptozotocin (STZ, 35&#xa0;mg/kg) for modeling. ZAC rats were orally administered 5&#xa0;mg/kg Zacopride daily for 7&#xa0;days. Transthoracic Doppler echocardiography measured left anterior descending coronary artery resting/stress peak flow velocity and coronary flow reserve (CFR). Ileocecal contents underwent bacterial-fungal metagenomic sequencing to identify differential metabolic pathways. Spearman's correlation assessed cross-kingdom ecological interactions. Nine machine learning algorithms constructed classification models, with Random Forest (RF) and an optimal model identifying key genera. Linear Discriminant Analysis Effect Size validated microbial biomarkers.<br><br>RESULTS: Zacopride partially restored the CFR in CMD rats, demonstrating a therapeutic effect, and exerted a beneficial influence on the structure and diversity of the gut microbiota. The CMD state significantly reduced the expression levels of the Chlorophyll a and tryptophan metabolic pathways in the gut microbiota. Zacopride specifically restored the Chlorophyll a pathway but did not significantly recover the tryptophan metabolic pathway. RF and Elastic Net (ENET) identified JC017, Chromelosporium, and Barnesiella as biomarker microbiota for CMD. Notably, JC017 primarily mediate the therapeutic effects of Zacopride via direct or indirect modulation of the Chlorophyll a metabolic pathway. Chromelosporium, acting as an interactive hub between fungi and bacteria, formed a cross-kingdom symbiotic relationship with Bradyrhizobium. Additionally, the reduction in Barnesiella abundance constitutes a distinctive feature of gut microbial dysbiosis in CMD.<br><br>CONCLUSION: This study provides the first evidence that the gut microbiota modulates the pathogenesis of CMD through the "chlorophyll/heme-tryptophan metabolic axis." Furthermore, we demonstrate that Zacopride exerts therapeutic effects by remodeling microbiota-host interactions and regulating this metabolic axis, revealing a novel mechanistic link between microbial metabolism and CMD progression.},
}
@article {pmid41088296,
year = {2025},
author = {Tang, A and Chen, Y and Ding, J and Li, Z and Xu, C and Hu, S and Lai, J},
title = {Gut microbiota remodeling and sensory-emotional functional disruption in adolescents with bipolar depression.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1083},
pmid = {41088296},
issn = {1479-5876},
support = {82201676//National Natural Science Foundation of China/ ; 82471542//National Natural Science Foundation of China/ ; No. JNL-2023001B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 2023YFC2506200//National Key Research and Development Program of China/ ; 2023ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; 2024ZFJH01-01//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Adolescent ; Female ; Humans ; Male ; *Bipolar Disorder/microbiology/physiopathology/drug therapy/psychology ; Brain/physiopathology/diagnostic imaging ; Case-Control Studies ; *Emotions ; *Gastrointestinal Microbiome/drug effects/physiology ; Magnetic Resonance Imaging ; Neuroimaging ; Quetiapine Fumarate/therapeutic use/pharmacology ; },
abstract = {BACKGROUND: Adolescence is the peak period of newly-onset bipolar disorder (BD). Accumulating studies have revealed disturbed gut microbiota can interfere with neurodevelopment in adolescents. In this study, we aimed to characterize the gut microbiota in adolescents with BD and its correlation with brain dysfunction.<br><br>METHODS: Thirty unmedicated BD adolescents within depressive episode were recruited and underwent four-week quetiapine treatment. Twenty-five age-, gender-, and BMI-matched healthy controls (HCs) were recruited. Fecal samples were collected from HCs and all BD adolescents before and after treatment and analyzed by metagenomic sequencing. Resting-state cranial functional magnetic images were collected from 21 BD adolescents before treatment. Random forest models were used to evaluate the discriminative power of gut microbiota and neuroimaging data for BD and the predictive power of treatment effect.<br><br>RESULTS: Although no significant difference was found in alpha-diversity, intra- and inter-group differences in beta-diversity were observed among HCs, pre- and post-treatment patients. Compared to HCs, unmedicated BD adolescents presented a differentiated gut microbial communities, which correlated to the short-chain fatty acids, choline, lipids, vitamins, polyamines, aromatic amino acids metabolic pathways. Four-week quetiapine treatment improved the abundance of specific genus, such as Odoribacter splanchnicus, Oribacterium sinus, Hafnia alvei, Fusobacterium periodonticum, Acidaminococcus interstini and Veillonella rogosae. Neuroimaging analysis revealed sensor-emotional brain regions were associated with BD severity. Finally, random forest models based on gut microbial biomarkers can well distinguish unmedicated BD from HCs (AUC&#x2009;=&#x2009;91.12%) and predict the treatment effect (AUC&#x2009;=&#x2009;91.84%). The random forest model integrating gut microbiota and neuroimaging data exhibited a better predictive efficacy than using microbiota data alone.<br><br>CONCLUSION: This study first characterized the gut microbiota architecture in adolescent BD. Combining gut microbiota and brain function biomarkers may benefit disease diagnosis and predict treatment outcome. Nonetheless, these findings should be carefully interpreted considering the limitations of a modest sample size and the absence of detailed mechanistic explorations. Trial registration NCT05480150. Registered 29 July 2022-Retrospectively registered, https://clinicaltrials.gov/study/NCT05480150 .},
}
@article {pmid41087898,
year = {2025},
author = {Zheng, N and Wang, D and Xing, G and Gao, Y and Li, S and Liu, J and Kang, J and Sha, S and Cheng, L and Fan, S and Yu, J and Yan, Q and Jiang, C},
title = {Characterization of the gut mycobiome in patients with non-alcoholic fatty liver disease and correlations with serum metabolome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {660},
pmid = {41087898},
issn = {1471-2180},
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology/blood/metabolism ; *Mycobiome ; *Gastrointestinal Microbiome ; *Metabolome ; Male ; Female ; Middle Aged ; *Fungi/classification/genetics/isolation &amp; purification ; Feces/microbiology ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Metagenomics ; },
abstract = {BACKGROUND: Emerging evidence suggests that the gut microbiome plays a key role in metabolic diseases such as non-alcoholic fatty liver disease, yet the contribution of the gut mycobiome remains largely overlooked.<br><br>METHODS: We performed a comprehensive analysis of publicly available fecal metagenomic sequencing data and matched serum metabolomic profiles from 90 non-alcoholic fatty liver disease patients and 90 healthy controls. A curated fungal genome database was constructed for taxonomic profiling. We integrated fungal, bacterial, and metabolomic data to assess taxon-specific associations, cross-kingdom interactions, and predictive potential.<br><br>RESULTS: Although overall fungal diversity showed no significant differences between groups, four fungal species-Pseudopithomyces sp. c174, Mucor sp. c176, Aspergillus sp. c25, and Ascochyta c213-were significantly enriched in non-alcoholic fatty liver disease patients. The gut mycobiome explained 38.2% of the variance in serum metabolomic profiles, with several species displaying strong correlations with non-alcoholic fatty liver disease relevant metabolites. For instance, Pseudopithomyces sp. c174 was positively associated with protective metabolites such as glycoursodeoxycholic acid and alpha-linolenic acid, while Aureobasidium c170 and Basipetospora c193 were linked to phenylacetic acid, a metabolite implicated in hepatic lipid accumulation. Network analysis revealed altered fungal-bacterial co-abundance patterns in non-alcoholic fatty liver disease, with fungal taxa such as Alternaria alternata c42 and Malassezia c303 emerging as key hubs. A random forest classifier integrating 42 bacterial and fungal features achieved an AUC of 0.772 for distinguishing non-alcoholic fatty liver disease from controls, highlighting the predictive value of the mycobiome.<br><br>CONCLUSIONS: Our findings reveal that gut fungal communities are functionally and ecologically altered in non-alcoholic fatty liver disease and contribute to shaping the host metabolic environment. These results underscore the need to incorporate the gut mycobiome into future microbiome-based strategies for non-alcoholic fatty liver disease diagnosis and treatment.},
}
@article {pmid41087864,
year = {2025},
author = {Chen, H and Wang, Z and Su, W and Li, S and Ye, Q and Zhang, G and Zhou, X},
title = {Helicobacter pylori infection impairs glucose homeostasis through gut microbiota dysbiosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {663},
pmid = {41087864},
issn = {1471-2180},
support = {82100594//National Natural Science Foundation of China,China/ ; },
mesh = {*Homeostasis ; *Helicobacter pylori/physiology ; *Helicobacter Infections/complications/metabolism/microbiology ; *Glucose/metabolism ; *Dysbiosis/metabolism/microbiology ; *Gastrointestinal Microbiome ; Male ; Animals ; Mice ; Mice, Inbred C57BL ; Fecal Microbiota Transplantation ; Diabetes Mellitus, Type 2/metabolism/microbiology ; Humans ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Diabetes Mellitus, Experimental/metabolism/microbiology ; Feces/microbiology ; Glucagon-Like Peptide 1/metabolism ; Colitis/metabolism/microbiology/therapy ; Retrospective Studies ; },
abstract = {BACKGROUND: Epidemiological data show that Helicobacter pylori (H. pylori) infection is not only the most important risk factor for gastric cancer, but is also associated with poor glycemic control in patients with diabetes. However, the direct causal and functional relationship between H. pylori infection and dysglycemia is unclear.<br><br>METHOD: A retrospective cohort study was conducted to examine the association between H. pylori infection and glycemic levels in individuals with Type 2 diabetes. C57BL/6 diabetic mice were infected with H. pylori, and the resulting changes in colonic inflammation and intestinal Glucagon-like peptide-1 (GLP-1) secretion were thoroughly examined using immunohistochemistry, RNA sequencing, metagenomic sequencing, and targeted metabolomics. The microbial and metabolomics profiles were analyzed and compared in antibiotic-treated mice through fecal transfer experiments.<br><br>RESULTS: H. pylori infection aggravated insulin resistance in diabetic individuals and mice. We identified a unique H. pylori-induced epithelial inflammation and reduced intestinal GLP-1 secretion in the colon. H. pylori infection also interrupts the normal microbial composition in the colon, leading to a decrease in SCFA-producing bacteria and a reduction in acetic and propionate acids. Similar changes were observed in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. In vitro studies revealed that the intestinal flora of H. pylori-positive diabetic mice inhibited proglucagon transcription, cAMP levels, and GLP-1 secretion in colonic endocrine cells, with SCFA supplementation reversing this effect on GLP-1 production. These microbial, metabolic, and GLP-1 alterations were also seen in antibiotic-treated mice after receiving fecal transplants from H. pylori-infected diabetic mice. H. pylori eradication with antibiotics improved glucose metabolism and GLP-1 secretion to levels comparable to uninfected controls.<br><br>CONCLUSION: Our studies offer evidence that H. pylori infection significantly contributes to the progression of glucose impairment and insulin resistance. Therefore, incorporating H. pylori status into preventive strategies for diabetes should be taken into account. (Chinese Clinical Trial Registry Center, ChiCTR2200063489, Registered 08 September 2022, https://www.chictr.org.cn/showproj.html?proj=178102).},
}
@article {pmid41087617,
year = {2025},
author = {Liu, M and Yang, L and Nan, D and Ma, L and Zhang, J and Liang, F and Yang, J and Liu, X},
title = {Hyperbaric oxygen treatment mitigates gut dysbiosis of mice with spinal cord injury.},
journal = {Journal of molecular medicine (Berlin, Germany)},
volume = {103},
number = {11-12},
pages = {1515-1532},
pmid = {41087617},
issn = {1432-1440},
support = {No. 82101964//National Natural Science Foundation of China/ ; No. 7202055//Natural Science Foundation of Beijing Municipality/ ; CYDXK 202208//Beijing Chao-Yang Hospital Multi-disciplinary Team Program/ ; },
mesh = {Animals ; *Spinal Cord Injuries/therapy/complications/metabolism/microbiology ; *Dysbiosis/therapy/etiology ; *Hyperbaric Oxygenation/methods ; *Gastrointestinal Microbiome ; Mice ; Disease Models, Animal ; Mice, Inbred C57BL ; Male ; Cytokines/metabolism ; Feces/microbiology ; },
abstract = {Gut dysbiosis impacts the recovery of neurological function after spinal cord injury (SCI). Hyperbaric oxygen (HBO) can alleviate SCI, but its effects on the gut microbiota post-SCI remain unclear. This study aimed to clarify the impact of HBO on SCI-induced gut dysbiosis and to explore the mechanisms of locomotor recovery in HBO-treated SCI mice. After establishing different groups of mouse models, bacterial cultures and Basso Mouse Scale (BMS) scores were performed at various time points post-SCI. Intestinal tissues were collected for intestinal permeability assay, histological analysis, immunofluorescence, and qPCR analysis. Flow cytometry and ELISA were used to detect immune-inflammatory cells and cytokines in intestinal tissue. The composition of gut microbiota in fecal samples from each group was also analyzed. Spinal cord tissues were collected for immunofluorescence and untargeted metabolomics analysis. Spearman correlation analysis was used to correlate differential microbiota with differential metabolites. Our results showed that the expression of tight junction proteins was increased after HBO treatment in SCI mice. Metagenomic analysis of the fecal DNA revealed that HBO altered intestinal bacterial composition. Differential metabolites were mainly enriched in pathways, such as glycerophospholipid metabolism, steroid biosynthesis, and glycolysis/gluconeogenesis. Moreover, differential microbiota showed a strong correlation with differential metabolites related to glycerophospholipids. HBO treatment significantly inhibited immune cells and inflammatory cytokines in the gut after SCI. In addition, HBO treatment significantly increased BMS scores and body weight, and repaired damaged cholinergic neurons. Antibiotic-induced gut dysbiosis impaired the recovery of locomotor function and exacerbated intraspinal pathology. However, these effects could be mitigated by HBO treatment. Overall, HBO treatment may improve neurological recovery through multiple regulatory mechanisms including alleviating gut dysbiosis, reducing intestinal inflammation, and rectifying glycerophospholipid metabolic disorders after SCI. These findings highlight HBO as a promising therapeutic strategy for SCI treatment and support its clinical application. KEY MESSAGES: The intestinal microbiota composition of mice changed after SCI. HBO treatment could preserve intestinal barrier integrity, modulate the composition of intestinal microbiota, rectify glycerophospholipid metabolic disorders, and reduce intestinal immune inflammatory responses. Intestinal microbiota identified as the target for HBO therapeutic in SCI recovery. Alleviating SCI-induced gut dysbiosis may be one of the mechanisms underlying the beneficial effect of HBO on neurological functions.},
}
@article {pmid41087549,
year = {2026},
author = {Chauhan, M and Maniya, H and Mori, P and Nagpal, R and Tirgar, P and Kumar, V},
title = {Assessment of multi-strain probiotics in regulating diet-induced obesity in Balb/c mice model.},
journal = {International journal of obesity (2005)},
volume = {50},
number = {1},
pages = {202-212},
pmid = {41087549},
issn = {1476-5497},
mesh = {Animals ; *Probiotics/therapeutic use/pharmacology ; *Obesity/prevention &amp; control ; Mice, Inbred BALB C ; Mice ; Male ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Gastrointestinal Microbiome ; },
abstract = {BACKGROUND/OBJECTIVES: This study investigated the efficacy of a novel multi-strain probiotic (MSP), composed of Limosilactobacillus fermentum BAB 7912, Bacillus rugosus PIC5CR, and Bacillus rugosus PIB9CR, in preventing and reverting diet-induced obesity in Balb/c male mice.<br><br>SUBJECTS/METHODS: This study used 8-week-old Balb/c mice. A total of 40 mice were divided into five groups namely control negative (CN), control with obesity (CO), and three treatment groups: microbial consortium treated (MCT), Healthy control 1 (HC1), and Healthy control 2 (HC2). Obesity was induced using a high-fat diet. MSP formulation developed indigenously as part of previous study, was fed to Balb/c mice at different time intervals to study its preventive and ameliorative potential. Animals were dissected for the collection of blood as well as various organs to study the effect of MSP feeding on obesity status. Results were validated using histopathological and metagenomic data.<br><br>RESULTS: The CN and other treatment groups gained significant weight at the end of 6 weeks, while no significant weight gain was observed among HC1 group animals that were fed with HFD and MSP together. This highlights the preventive effect of continuous MSP feeding in the HC1 animal group. Initial liver histopathology in the HC1 group revealed enlarged hepatocytes and fat droplets. By week 9, the MCT group, which received MSP with a basal diet, showed liver recovery towards normal, accompanied by body weight improvement from 28.02&#x2009;&#xb1;&#x2009;0.7&#x2009;g to 26.18&#x2009;&#xb1;&#x2009;0.96&#x2009;g. Metagenomic analysis revealed that MSP treatment increased the relative abundance of health-promoting bacteria, notably Lactobacillaceae (specifically Lactobacillus).<br><br>CONCLUSIONS: Findings indicated that continuous consumption of MSP contributes significantly in prevention of obesity and associated metabolic disorders. Future studies are needed to explore the mechanisms underlying these effects and to evaluate the potential of MSP for human health.},
}
@article {pmid41087370,
year = {2025},
author = {Balachandran, KRS and Mani, G and Sidharthan, AT and Mary Leema, JT and Senthilkumar, R and Gopal, D},
title = {Unearthing the genetic resources of Arabian sea seamount and metagenomic insights into phosphate cycling genes for next generation plant biostimulants.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35782},
pmid = {41087370},
issn = {2045-2322},
mesh = {*Metagenomics/methods ; *Metagenome ; *Phosphates/metabolism ; *Geologic Sediments/microbiology ; Bacteria/genetics ; Microbiota/genetics ; Phosphoric Monoester Hydrolases/genetics/metabolism ; },
abstract = {Deep-sea encompasses a wide diversity of microbiomes including bacteria, fungi and viruses which play crucial significant roles in nutrient biogeochemical cycling thereby imparting majorly to functional biodiversity of these hotspots. Sea mounts harboring microbes with extremophilic properties found in deep oceans could be conserved as living repository by functional metagenomics approach which is a potent source to screen bioactive compounds and novel enzymes thereby could address biological question on developing next generation plant biostimulants. This study outlines construction of fosmid metagenome library and adapted combined strategy of functional and nanopore sequence-based metagenomic screening to unveil phosphatase enzymes from Arabian Sea seamount sediment. About 9068 metagenomic clones were generated with an average insert size of 38 kb and stored in pools of 1024 clones, out of which 42 were found to be positive for phosphatase. Five clones with high phosphatase activity were further characterized and NIOT F41 showed the greatest specific activity for phosphatase (41.2 U/mg). Gluconic (1041 mg/L), oxalic (327 mg/L), and succinic acids (610 mg/L) were the predominant organic acids produced by recombinant clones. Fosmid DNA were extracted from five potential clones for nanopore-based metagenomics sequencing which generated an average of 6,00,786 reads. Taxonomic analysis revealed an abundance of Proteobacteria and Firmicutes phyla harboring phosphate-solubilising bacteria Pseudomonas aeruginosa, Bacillus subtilis and Staphylococcus warneri. Furthermore, functional annotation using phosphorus cycling database (PCycDB) predicted variation in relative abundance of phosphatase gene clusters encoding alkaline phosphatase (PhoD, PhoX and PhoA) and acid phosphatase (OlpA, PhoNand PhoC) produced by recombinant clones. In the pot assay, potential metagenomic clones exhibited positive impacts on shoot length (9.1 ± 1.1 cm, p < 0.05), root length (2.05 ± 0.05 cm, p < 0.05), wet biomass (39.3 ± 0.65 mg, p < 0.05), and dry biomass (5.1 ± 1.15 mg, p < 0.05) compared to the negative control indicating significant effect on promoting plant growth. The advanced nanopore sequencing and functional metagenomics methods employed in this study could serve as a marine biodiversity conservation approach for deep-sea microbes hidden in sea mount sediments towards harnessing potential next generation plant biostimulants with promising biotechnological application for sustainable agriculture.},
}
@article {pmid41086989,
year = {2026},
author = {Zheng, L and Yao, L and Zhu, B and Chen, S and Qian, J and Liu, S and Zhao, J and Chen, Z and Xiang, S and Xie, Z and Zhu, J and Wang, S and Wu, K and Chen, J and Zhang, S and Lu, X},
title = {Cross-kingdom gut microbiota signatures and their associations with clinical phenotypes in adolescents with bipolar depression.},
journal = {Journal of affective disorders},
volume = {394},
number = {Pt A},
pages = {120399},
doi = {10.1016/j.jad.2025.120399},
pmid = {41086989},
issn = {1573-2517},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Adolescent ; *Bipolar Disorder/microbiology ; Male ; Female ; Child ; Phenotype ; Feces/microbiology ; Archaea/genetics ; Bacteria ; Case-Control Studies ; },
abstract = {Emerging evidence highlights the pivotal role of the gut microbiota (GM) in mental health; however, investigations into its cross-kingdom composition in adolescent bipolar disorder remain critically limited. Most studies have focused solely on bacteria, overlooking the complex interactions involving archaea, viruses, and fungi. This study aimed to comprehensively characterize the taxonomic and functional alterations in the cross-kingdom gut microbiota of adolescents with bipolar depression and examine their associations with clinical parameters. We enrolled 60 adolescents aged 12-18 years, including 30 diagnosed with bipolar depression and 30 age- and sex-matched healthy controls. Fecal samples were collected alongside detailed clinical data, including psychiatric symptomatology, cognitive assessments, and dietary habits. Metagenomic sequencing was conducted to profile microbial taxa and functional gene pathways across domains. Statistical analyses assessed differences in alpha and beta diversity, differential abundance, and correlations with clinical phenotypes. Alpha diversity was significantly reduced in the viral and fungal domains among patients, while archaeal and bacterial diversity showed no significant differences. Beta diversity analysis did not reveal global community structural shifts across domains. Taxonomic profiling identified Methanohalobium evestigatum as significantly enriched in archaea, alongside increased abundance of several Firmicutes and Actinobacteria species in the bacterial domain. Viral analysis revealed elevated levels of Brussowvirus AlQ132, Orpheovirus IHUMI LCC2, Afonbuvirus coli, Carjivirus hominis, and Carjivirus communis in the patient group. LEfSe analysis uncovered 15 significantly altered metabolic pathways, including those involved in DNA repair, energy metabolism, and immune signaling. Notably, several taxa and pathways were significantly associated with clinical parameters such as symptom severity, cognitive flexibility, sleep quality, and dietary intake. Adolescents with bipolar depression exhibit distinct alterations in cross-kingdom gut microbiota composition and function, with specific microbial taxa and metabolic pathways correlating with key clinical phenotypes. These findings underscore the potential of gut microbiome signatures as biomarkers and therapeutic targets in early-onset mood disorders and highlight the importance of including archaea, fungi, and viruses in future microbiome-based mental health research.},
}
@article {pmid41086610,
year = {2026},
author = {Li, H and Gao, H and Chen, S and Li, X and Zhou, J},
title = {Intensive mariculture shifts microbial communities and life-history strategies in the semi-enclosed bay: Case study in Sansha Bay, China.},
journal = {Marine environmental research},
volume = {213},
number = {},
pages = {107607},
doi = {10.1016/j.marenvres.2025.107607},
pmid = {41086610},
issn = {1879-0291},
mesh = {China ; *Bays/microbiology ; *Microbiota ; *Aquaculture ; Eutrophication ; RNA, Ribosomal, 16S ; *Environmental Monitoring ; Animals ; },
abstract = {Coastal bays often experience significant disturbances from various mariculture activities, frequently leading to severe eutrophication. Yet, the ecological consequences of nutrient inputs derived from mariculture on bay-associated microbial communities remain insufficiently understood. Sansha Bay, known as the world's largest cage mariculture site for Larimichthys crocea, represents a characteristic semi-enclosed bay commonly utilized for studying the environmental impacts of intensive mariculture. In this study, we compared the highly eutrophic Sansha Bay with the relatively undisturbed natural East China Sea to investigate how intensive mariculture influences the bay microbial biosphere, focusing on community composition, assembly mechanisms, functional profiles, and life-history strategies. Amplicon sequencing and metagenomic analyses showed that Sansha Bay had a greater proportion of fast-growing microorganisms, nitrogen and carbon cycling microbes, and antibiotic-resistant bacteria. Null model analysis indicated that while natural coastal microbial assemblages were predominantly shaped by stochastic processes, deterministic selection became increasingly prominent as mariculture activities intensified. Correspondingly, microbial life-history traits, including 16S rRNA gene copy number, codon usage bias, predicted maximum growth rates, genome size, guanine-cytosine content, transposase abundance, and niche breadth, were consistently elevated in the eutrophic bay. These results suggest that eutrophication associated with mariculture drives a shift in life-history strategies from oligotrophs (K-strategists) to copiotrophs (r-strategists). Collectively, this study yields novel mechanistic understanding of how intensive mariculture reshapes microbial community structures, laying the groundwork for forecasting changes in coastal ecosystems subjected to ongoing human disturbances.},
}
@article {pmid41086517,
year = {2026},
author = {Obeten, AU and Avellán-Llaguno, RD and Huang, H and Yin, YH and Zhu, Y and Xu, XL and Chen, JY and Wang, Y and Ye, G and Pan, Z and Zhu, LT and Huang, Q},
title = {Decoding extracellular vesicles-mediated encapsulation of enveloped and nonenveloped gut viruses through phosphatidylserine affinity profiling.},
journal = {Virology},
volume = {613},
number = {},
pages = {110712},
doi = {10.1016/j.virol.2025.110712},
pmid = {41086517},
issn = {1096-0341},
mesh = {*Extracellular Vesicles/virology/metabolism ; *Phosphatidylserines/metabolism ; Humans ; Feces/virology ; Metagenomics ; Gastrointestinal Microbiome ; Virome ; *Viruses/genetics/classification/isolation &amp; purification/metabolism ; },
abstract = {Viruses are generally classified as enveloped viruses (EnVs) or nonenveloped viruses (non-EnVs), based on the presence of a lipid membrane, with membrane-mediated transmission traditionally attributed to EnVs. However, the composition and characteristics of viral populations encapsulated within extracellular vesicles (EVs) which are phospholipid bilayer nanoparticles released by all living organisms remain poorly understood. Here, we applied a phosphatidylserine (PS)-affinity enrichment strategy to isolate EV-encapsulated viral populations from human stool-derived extracellular viral-like particles (VLPs). Quantitative particle analysis revealed that EnVs exhibited an 11-fold higher PS affinity compared to free non-EnVs (fold change 2.79 vs 0.25). Metagenomic analysis revealed significant enrichment of non-EnVs within PS-positive fractions, including DNA viruses Salasmaviridae (3.84 ± 6.44 %) and RNA bacteriophage Fiersviridae (44.99 ± 32.80 %). Predicted Host-virus correlation analysis highlighted strong correlations between viral families Autographiviridae, Microviridae and host family Enterobacteriaceae. Functional annotation further showed enrichment of structural and replication-related genes in the EV-associated virome. These findings provide evidence for EVs-mediated encapsulation of non-EnVs, challenging the traditional dichotomy of viral classification. This noteworthy observation positions EVs encapsulation as a critical determinant in viral life cycles and underscores the need to revisit current viral taxonomy systems.},
}
@article {pmid41085703,
year = {2025},
author = {Sharma, N and Verma, A and Ambardar, S and Raj, S and Vakhlu, J},
title = {Comparative evaluation of MG-RAST, MEGAN6 and Kraken2 for whole metagenome analysis of saffron corms for bacterial community structure and function.},
journal = {Molecular genetics and genomics : MGG},
volume = {300},
number = {1},
pages = {97},
pmid = {41085703},
issn = {1617-4623},
support = {Rashtriya Uchchatar Shiksha Abhiyan//Rashtriya Uchchatar Shiksha Abhiyan/ ; JKST&amp;IC/J/14/2022/160//JKST&amp;IC-JKDST/ ; DST-INSPIRE/03/2022/004594//DST-INSPIRE/ ; BT/AIR01624/PACE-28/22//BIRAC-PACE/ ; },
mesh = {*Crocus/microbiology/genetics ; *Software ; *Metagenome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Algorithms ; },
abstract = {Taxonomic and functional analysis outcomes are greatly influenced by the algorithms and databases used by different software. The present study evaluated three widely used software; MG-RAST, MEGAN6 and Kraken2 for the analysis of the shotgun metagenomic data of saffron cormosphere. Kraken2 outperformed other two for taxonomy. It gave significantly higher alpha diversity values, indicating greater taxonomic diversity and evenness compared to MG-RAST and MEGAN6. The limitation of the Kraken2 is that it does not support functional analysis which both MG-RAST and MEGAN6 can do in addition to taxonomical analysis. Additionally, they can analyse sequence data generated by different sequencing methods such as Sanger, Illumina and PacBio. MG-RAST is comparatively easy to use and integrates large number of databases than MEGAN6, however data processing is relatively slow. Additionally, MEGAN6 has a feature of extraction of genes automatically, that allows user to study sub set of specific genes, though in MG-RAST, it can be done manually and the process is cumbersome. The difference in the outcome of these three software can be attributed to differences in the databases, algorithms, and parameters used by the three software. A combined approach using the results from more than one software can be considered to create a more comprehensive taxonomy and functional profile until a factotum software is developed.},
}
@article {pmid41084448,
year = {2025},
author = {Han, Z and Jin, LX and Wang, ZT and Yang, LQ and Li, L and Ruan, Y and Chen, QW and Yao, SH and Heng, XP},
title = {[Regulatory effects of Dangua Humai Oral Liquid on gut microbiota and mucosal barrier in mice with glucolipid metabolism disorder].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {50},
number = {15},
pages = {4315-4324},
doi = {10.19540/j.cnki.cjcmm.20250421.401},
pmid = {41084448},
issn = {1001-5302},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Intestinal Mucosa/drug effects/metabolism/microbiology ; Male ; *Drugs, Chinese Herbal/administration &amp; dosage ; Mice, Inbred C57BL ; Humans ; *Glycolipids/metabolism ; Lipid Metabolism/drug effects ; Administration, Oral ; Disease Models, Animal ; },
abstract = {The gut microbiota regulates intestinal nutrient absorption, participates in modulating host glucolipid metabolism, and contributes to ameliorating glucolipid metabolism disorder. Dysbiosis of the gut microbiota can compromise the integrity of the intestinal mucosal barrier, induce inflammatory responses, and exacerbate insulin resistance and abnormal lipid metabolism in the host. Dangua Humai Oral Liquid, a hospital-developed formulation for regulating glucolipid metabolism, has been granted a national invention patent and demonstrates significant clinical efficacy. This study aimed to investigate the effects of Dangua Humai Oral Liquid on gut microbiota and the intestinal mucosal barrier in a mouse model with glucolipid metabolism disorder. A glucolipid metabolism disorder model was established by feeding mice a high-glucose and high-fat diet. The mice were divided into a normal group, a model group, and a treatment group, with eight mice in each group. The treatment group received a daily gavage of Dangua Humai Oral Liquid(20 g·kg~(-1)), while the normal group and model group were given an equivalent volume of sterile water. After 15 weeks of intervention, glucolipid metabolism, intestinal mucosal barrier function, and inflammatory responses were evaluated. Metagenomics and untargeted metabolomics were employed to analyze changes in gut microbiota and associated metabolic pathways. Significant differences were observed between the indicators of the normal group and the model group. Compared with the model group, the treatment group exhibited marked improvements in glucolipid metabolism disorder, alleviated pathological damage in the liver and small intestine tissue, elevated expression of recombinant claudin 1(CLDN1), occluding(OCLN), and zonula occludens 1(ZO-1) in the small intestine tissue, and reduced serum levels of inflammatory factors lipopolysaccharides(LPS), lipopolysaccharide-binding protein(LBP), interleukin-6(IL-6), and tumor necrosis factor-α(TNF-α). At the phylum level, the relative abundance of Bacteroidota decreased, while that of Firmicutes increased. Lipid-related metabolic pathways were significantly altered. In conclusion, based on the successful establishment of the mouse model of glucolipid metabolism disorder, this study confirmed that Dangua Humai Oral Liquid effectively modulates gut microbiota and mucosal barrier function, reduces serum inflammatory factor levels, and regulates lipid-related metabolic pathways, thereby ameliorating glucolipid metabolism disorder.},
}
@article {pmid41083440,
year = {2025},
author = {Prasad, A and Pallujam, AD and Siddaganga, R and Suryanarayanan, A and Mazel, F and Brockmann, A and Yek, SH and Engel, P},
title = {Evolution of gut microbiota across honeybee species revealed by comparative metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9069},
pmid = {41083440},
issn = {2041-1723},
support = {225148//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Symbiosis ; Phylogeny ; Metagenome/genetics ; *Evolution, Molecular ; Biological Evolution ; },
abstract = {Studying gut microbiota evolution across animals is crucial for understanding symbiotic interactions but is hampered by the lack of high-resolution genomic data. Honeybees, with their specialized gut microbiota and well-known ecology, offer an ideal system to study this evolution. Using shotgun metagenomics on 200 worker bees from five honeybee species, we recover thousands of metagenome-assembled genomes and identify several novel bacterial species. While microbial communities were mostly host-specific, we found both specialists and generalists, even among closely related bacterial species, with notable variation between honeybee hosts. Some bacterial generalists emerged host-specific only at the strain level, suggesting recent host switches. While we found some signal of co-diversification between hosts and symbionts, this was not more than expected by chance and was much less pronounced than what has been observed for gut bacteria of hominids and small mammals. Instead, symbiont gains, losses, and replacements emerged as important factors for honeybees. This highly dynamic evolution of the specialized honey bee gut microbiota has led to taxonomic and functional differences across hosts, such as the ability to degrade pollen-derived pectin. Our results provide new insights into the evolutionary processes that govern gut microbiota diversity across closely related hosts and uncover the functional potential of the previously underexplored gut microbiota of these important pollinators.},
}
@article {pmid41082055,
year = {2025},
author = {Aderolu, AZ and Salam, LB and Lawal, MO and Kabiawu-Mutiu, LF and Bassey, ME and Shobande, MA},
title = {Microbial ecology and functional landscape of black soldier fly larval bioconversion of orange waste: A metataxonomic perspective.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {10},
pages = {377},
pmid = {41082055},
issn = {1573-0972},
mesh = {Animals ; Larva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Gastrointestinal Microbiome/genetics ; *Simuliidae/microbiology ; *Citrus sinensis/metabolism ; *Diptera/microbiology ; Nigeria ; Metagenome ; Metagenomics ; Phylogeny ; },
abstract = {The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate-gut-frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa's circular bioeconomy.},
}
@article {pmid41081627,
year = {2025},
author = {Yuan, Q and Yang, Y and Shen, Y and Sun, B and Chen, S and Zheng, C and Lou, Y and Zheng, M},
title = {Exploring the ocular microecology and its role in pterygium based on metagenomics.},
journal = {Microbiology spectrum},
volume = {13},
number = {11},
pages = {e0173025},
pmid = {41081627},
issn = {2165-0497},
support = {ZY2022018//WMSTB | Science and Technology Plan Project of Wenzhou Municipality ()/ ; },
mesh = {Humans ; *Pterygium/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Conjunctiva/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Male ; Female ; Middle Aged ; Aged ; Virulence Factors/genetics ; Adult ; Dysbiosis/microbiology ; },
abstract = {Pterygium is a chronic ocular surface condition marked by fibrovascular growth extending from the conjunctiva to the cornea. Emerging evidence suggests that microbial dysbiosis may play a role in its pathogenesis. To elucidate the microbial landscape associated with pterygium, we conducted metagenomic shotgun sequencing on conjunctival sac secretions from 24 patients with pterygium and 23 healthy controls, along with 19 pterygium tissue samples. We observed significantly higher microbial richness in the disease group, with distinct taxonomic profiles compared with healthy and tissue groups. Key species enriched in the disease group included Microbacterium proteolyticum and Bacillus cereus. Functional analyses revealed elevated bacterial motility, chemotaxis, and virulence genes, alongside a notable increase in antibiotic resistance genes such as tetB and AcrAB-TolC. In contrast, pterygium tissue samples showed limited microbial diversity and no detectable virulence or resistance genes. Importantly, the predominance of Vibrio phages in tissue samples, together with the frequent detection of their bacterial host Vibrio diabolicus, suggests a potential region-specific microbial risk factor, particularly relevant in coastal populations. These findings highlight distinct microbiome and functional profiles associated with pterygium, providing new insights into its pathogenesis and possible microbiome-based therapeutic targets.IMPORTANCEUnderstanding how microbial communities contribute to ocular diseases is crucial for advancing both diagnostics and therapy. This study provides the first integrated comparison of healthy ocular surfaces, diseased ocular surfaces, and pterygium tissues, revealing distinct microbial signatures and functional disruptions. The enrichment of specific bacterial taxa, virulence factors, and antibiotic resistance genes in diseased eyes underscores their potential role in shaping local immunity and driving disease progression. Meanwhile, the discovery of distinct viral elements in pterygium tissue expands current understanding of its microecological complexity. These findings lay a theoretical foundation for the development of microbiome-informed diagnostic tools and novel therapeutic interventions for pterygium.},
}
@article {pmid41081506,
year = {2025},
author = {Jiang, C and Wu, Y and Qiu, C and Zhu, S and Zhang, Y and Shui, W},
title = {Metagenomic insights into soil microbial diversity and antibiotic resistance genes in pristine karst tiankeng ecosystems.},
journal = {mSphere},
volume = {10},
number = {11},
pages = {e0034825},
pmid = {41081506},
issn = {2379-5042},
support = {41871198//National Natural Science Foundation of China/ ; 42471292//National Natural Science Foundation of China/ ; XRC-23078//Fuzhou University Reaserch Start-up Project/ ; },
mesh = {*Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; Archaea/genetics/classification ; *Bacteria/genetics/classification/drug effects ; Ecosystem ; Fungi/genetics/classification ; Microbiota ; Biodiversity ; Metagenome ; China ; },
abstract = {Surveys of microorganisms and antibiotic resistance genes (ARGs) in edaphic systems have centered on those in human-impacted environments, with relatively little information from primitive environments. The karst tiankeng (also known as sinkholes) is the largest negative terrain on the earth's surface, and the trapped terrain keeps the interior relatively pristine. In this study, three of the most representative tiankeng types (severely, moderately, and non-degraded tiankengs) were selected, and microbial composition, function, and their association with ARGs were determined using metagenetic techniques. The dominant phyla in karst tiankengs were Proteobacteria, Actinobacteria, and Acidobacteria; the dominant archaea were Crenarchaeota; and the dominant fungi were Ascomycota. The non-degrade tiankeng maintains a complex and stable microbial network. The major functional profiles of the microorganisms are involved in amino acid metabolism and carbohydrate metabolism. A total of 145 ARGs were annotated, and the dominant ARGs in karst tiankeng were CeoB, AcrB, and MexF. Paraburkholderia, Rhodococcus, Bradyrhizobium, and Agromyces were the main hosts of ARGs in karst tiankengs. Compared with ARGs, microorganisms were more influenced by soil factors. These results provide a novel insight into microbes and ARGs in unexplored karst tiankeng ecosystems. IMPORTANCE Currently, knowledge regarding the origin of antibiotic resistance genes (ARGs) in pristine soil environments remains limited, with some potentially linked to ancestral genetic diversity. In this study, metagenomics was employed to investigate the distribution of ARGs across nine relatively pristine karst tiankengs. We identified the predominant microbial communities and prevalent types of ARGs within these tiankengs. Soil factors primarily influenced the microbial community structure but had little effect on ARGs. This study offers insights for in-depth research on the microbial composition and risk assessment of antibiotic resistance genes within pristine karst tiankeng ecosystems.},
}
@article {pmid41080577,
year = {2025},
author = {Wang, Z and Yu, J and Liu, Y and Gong, J and Hu, Z and Liu, Z},
title = {Role of the microbiota-gut-lung axis in the pathogenesis of pulmonary disease in children and novel therapeutic strategies.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1636876},
pmid = {41080577},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Child ; *Lung/immunology/microbiology/metabolism ; *Lung Diseases/therapy/microbiology/immunology/etiology/metabolism ; Dysbiosis ; Animals ; Fatty Acids, Volatile/metabolism ; },
abstract = {Emerging evidence highlights the microbiota-gut-lung axis (MGLA) as a pivotal regulator of pediatric respiratory health, yet mechanistic insights are lacking and therapeutic applications remain unclear. This review synthesizes cutting-edge findings to delineate how gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs), orchestrate pulmonary immunity and disease pathogenesis in children. Leveraging multi-omics integration (metagenomics, metabolomics, transcriptomics), emerging studies have uncovered novel microbe-host interactions driving immune dysregulation in asthma, pneumonia, and cystic fibrosis. A comprehensive map of gut-lung crosstalk has been established across these conditions. Current studies suggest that early-life gut dysbiosis, shaped by delivery mode, antibiotics, and diet, disrupts SCFA-mediated immune homeostasis, amplifying T-helper 2 cell inflammation and impairing alveolar macrophage function. Crucially, we identified disease-specific microbial signatures (e.g., depletion of Lachnospira and Faecalibacterium in asthma) and demonstrated that fecal microbiota transplantation and probiotic interventions restore microbial balance, attenuating airway inflammation in preclinical models. This work pioneers the translation of MGLA insights into precision medicine strategies, highlighting dietary modulation and microbial therapeutics as viable alternatives to conventional treatments. By bridging microbial ecology and immune dynamics, our findings provide actionable biomarkers for early diagnosis and personalized interventions, addressing critical gaps in pediatric respiratory disease management. The integration of multi-omics frameworks not only advances mechanistic understanding but also positions the MGLA as a transformative target in reducing global childhood morbidity. Future research must prioritize longitudinal studies and clinical trials to validate these innovations, ultimately redefining therapeutic paradigms for GLA-driven pathologies.},
}
@article {pmid41077635,
year = {2025},
author = {Noel, S and Patel, SK and White, J and Verma, D and Menez, S and Raj, D and Parikh, C and Rabb, H and , },
title = {Metagenomic Profiling of Gut Microbiota in Kidney Precision Medicine Project Participants With CKD and AKI.},
journal = {Comprehensive Physiology},
volume = {15},
number = {5},
pages = {e70058},
doi = {10.1002/cph4.70058},
pmid = {41077635},
issn = {2040-4603},
support = {U01DK133081//KPMP/ ; U01DK133091//KPMP/ ; U01DK133092//KPMP/ ; U01DK133093//KPMP/ ; U01DK133095//KPMP/ ; U01DK133097//KPMP/ ; U01DK114866//KPMP/ ; U01DK114908//KPMP/ ; U01DK133090//KPMP/ ; U01DK133113//KPMP/ ; U01DK133766//KPMP/ ; U01DK133768//KPMP/ ; U01DK114907//KPMP/ ; U01DK114920//KPMP/ ; U01DK114923//KPMP/ ; U01DK114933//KPMP/ ; U24DK114886//KPMP/ ; UH3DK114926//KPMP/ ; UH3DK114861//KPMP/ ; UH3DK114915//KPMP/ ; UH3DK114937//KPMP/ ; R01DK104662/DK/NIDDK NIH HHS/United States ; R01DK123342/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Renal Insufficiency, Chronic/microbiology ; *Acute Kidney Injury/microbiology ; Metagenomics/methods ; Precision Medicine/methods ; Female ; Male ; Middle Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: The gut microbiome plays an important role in human health and disease. Kidney Precision Medicine Project (KPMP) is a well-phenotyped, kidney biopsy-proven cohort of AKI and CKD patients. Comprehensive profiling of gut microbiota can uncover novel mechanistic, diagnostic, and therapeutic strategies for CKD and AKI patients.<br><br>METHODS: We performed metagenomic whole genome sequencing (mWGS; >&#x2009;25 million reads) on KPMP stool samples. mWGS data of healthy controls from 4 published studies was used. Kraken2 and MetaPhlAn3 were used for taxonomic assignment, and HUMAnN3 for functional annotation.<br><br>RESULTS: Kraken2 analysis showed significantly higher abundance of Ruminococcus bicirculans in CKD (6.47) compared to AKI (1.82) and healthy individuals (2.42; p&#x2009;=&#x2009;0.01). Furthermore, the abundance of Gordonibacter pamelaeae increased in CKD (0.30) compared to AKI (0.07; p&#x2009;=&#x2009;0.05) and healthy individuals (0.03). The percent mean abundance of genus Chryseobacterium was slightly higher in CKD (0.07) compared to AKI (0.05; p&#x2009;=&#x2009;0.05) but reduced compared to healthy individuals (0.20; p&#x2009;<&#x2009;0.001). MetaPhlAn3 identified alterations in Gordonibacter, Bacteroides, and Faecalibacterium with a significant increase in Clostridium asparagiforme in AKI (11.68) compared to CKD (0.03; p&#x2009;=&#x2009;0.06) and healthy (0.01; p&#x2009;=&#x2009;0.001) individuals. Roseburia hominis, Roseburia intestinalis, Dorea longicatena, and Gemmiger formicilis were significantly reduced in AKI compared to CKD and healthy individuals. LDA/HUMAnN3 analysis showed a significant correlation between several metabolites and bacterial species in this KPMP population.<br><br>CONCLUSION: Kidney biopsy-proven CKD and AKI patients show a distinct gut microbiota profile compared to healthy individuals. This high-quality dataset is a valuable resource for developing microbiome-based diagnostics and therapies for CKD and AKI.},
}
@article {pmid41077176,
year = {2025},
author = {Agrawal, K and Hong, ASY and Cifuentes-González, C and Kumar, VS and Rojas-Carabali, W and Zhang, S and Wang, Q and de-la-Torre, A and Gijs, M and Gill, T and Rosenbaum, JT and Rajagopala, SV and Gangaputra, S and Conforti, A and Ross, RP and Yang, P and Wong, S and Agrawal, R},
title = {Microbiome signatures and their role in uveitis: Pathogenesis, diagnostics, and therapeutic perspectives.},
journal = {Progress in retinal and eye research},
volume = {109},
number = {},
pages = {101409},
doi = {10.1016/j.preteyeres.2025.101409},
pmid = {41077176},
issn = {1873-1635},
mesh = {Humans ; *Uveitis/microbiology/diagnosis/therapy/immunology ; Animals ; Dysbiosis ; *Microbiota/physiology ; *Gastrointestinal Microbiome/physiology ; },
abstract = {Non-infectious uveitis is a group of complex inflammatory eye diseases shaped by genetic susceptibility, immune dysregulation, and environmental cues. Among these, the mucosal microbiome-including gut, oral, and ocular surface microbial communities-has emerged as a key player in modulating systemic and ocular immune responses. Recent evidence supports a gut-eye axis wherein microbial dysbiosis alters intestinal barrier function, perturbs T cell homeostasis, and drives systemic immune activation that can breach ocular immune privilege. Specific taxa, such as Prevotella and Faecalibacterium, as well as microbial metabolites including short-chain fatty acids, have been implicated in promoting or mitigating ocular inflammation. Human leukocyte antigen (HLA) alleles, notably HLA-B27 and HLA-A29, influence both microbiome composition and disease phenotype, suggesting a gene-microbiome-immunity triad of interaction in uveitis pathogenesis. Drawing on insights from metagenomics, metabolomics, in vitro and in vivo experimental and murine models, this review delineates four key mechanisms-immune imbalance, antigenic mimicry, epithelial barrier disruption, and bacterial translocation-that underpin the key roles of microbiome in uveitis. We combine current literature and integrate findings from our research programs to highlight diagnostic and therapeutic opportunities. Microbiome-informed strategies, such as rational probiotic design, dietary modulation, and targeted microbial therapies, hold promise for complementing existing immunosuppressive regimens. Translating these insights into clinical practice requires robust multi-omic studies, longitudinal cohorts, mechanistic studies, and precision-guided intervention trials. By framing uveitis within a mucosal immunological context, this review proposes a future precision medicine roadmap for integrating microbiome science into ocular inflammatory disease management.},
}
@article {pmid41076729,
year = {2026},
author = {Burdon, IA and Psaltis, AJ},
title = {Changes in the sinus microbiome in health and chronic rhinosinusitis.},
journal = {Current opinion in otolaryngology &amp; head and neck surgery},
volume = {34},
number = {1},
pages = {8-15},
pmid = {41076729},
issn = {1531-6998},
mesh = {Humans ; *Sinusitis/microbiology ; *Rhinitis/microbiology ; Chronic Disease ; *Microbiota ; Dysbiosis/microbiology ; *Paranasal Sinuses/microbiology ; Rhinosinusitis ; },
abstract = {PURPOSE OF REVIEW: This article synthesises the recent sinus microbiome literature, identifying common themes in research findings as well as surveying the varied methodological approaches used across these studies.<br><br>RECENT FINDINGS: While there remains no clear consensus as to which microbes define dysbiosis in chronic rhinosinusitis (CRS), certain trends are emerging. Increasingly, the evidence points towards a pathogenic role in the overabundance of Moraxella , Haemophilus and Pseudomonas species, whilst the genera Cutibacterium, Anaerococcus and Dolosigranulum tend towards commensalism. However, the roles of the most common genera in the sinus microbiome, Staphylococcus and Corynebacterium, remain uncertain. Given the diversity and abundance of species within these genera, species and function-level analyses are needed to clarify their contributions to the aetiopathogenesis of CRS. Comprehensive study of the sinus microbiome in healthy individuals further shows that community composition shifts with age, suggesting that dysbiosis may manifest differently across the lifespan. Beyond bacteria, growing evidence highlights the importance of fungi and viruses, underscoring the need to incorporate these microbionts into future analyses.<br><br>SUMMARY: Progress towards a clinically meaningful consensus will require standardised approaches to sequencing, species-level resolution in these analyses, and consideration of the heterogeneous clinical and immunological subgroups of CRS.},
}
@article {pmid41075335,
year = {2025},
author = {Ghaffar, A and Liljebjelke, K and Checkley, SL and Farooq, M and Abdul-Careem, MF},
title = {Exploring the indoor airborne microbiome and resistome in layer barns across Alberta, Canada.},
journal = {Research in veterinary science},
volume = {196},
number = {},
pages = {105930},
doi = {10.1016/j.rvsc.2025.105930},
pmid = {41075335},
issn = {1532-2661},
mesh = {Alberta ; Animals ; *Microbiota ; *Housing, Animal ; *Air Microbiology ; *Chickens/microbiology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects/isolation &amp; purification ; Air Pollution, Indoor ; },
abstract = {The air in poultry barns carries a diverse range of microbial communities including potential opportunistic pathogens, which are important for both animal and human health. Bacteria carrying antimicrobial resistance genes (ARGs) can become airborne within poultry barns and be transmitted to animals and poultry workers, presenting a serious One Health concern. This study was aimed at characterizing the microbiome and resistome of bioaerosols sampled from layer chicken barns across Alberta. In total, 15 barns (9 cage housed and 6 floor housed) were sampled in this study using a microbial air sampler to characterize the microbiome and resistome using a shotgun metagenomic sequencing approach. The most abundant bacterial phyla found in the air of both housing systems for pullets were Bacilliota, Actinomycetota, and Bacteroidota. The respiratory pathogens such as Gallibacterium anatis, Ornithobacterium rhinotracheale, and Pasteurella multocida were relatively more abundant in the air of cage-housed barns, whereas Escherichia coli and Avibacterium paragallinarum were more prevalent in floor-housed barns. In total, 113 unique ARGs subtypes from 19 classes of antimicrobials were identified in this study. ARGs were significantly more abundant in the air of cage-housed barns compared to floor-housed barns. In particular, genes associated with resistance to tetracyclines, lincosamides, and macrolides were more frequently detected in cage-housed environments. Overall, both microbial and resistance gene levels were higher in the bioaerosols of cage-housed barns than in those from floor-housed pullet barns. The study results demonstrate the potential for air as a reservoir of ARGs and highlights microbial differences within cage and floor housing.},
}
@article {pmid41074949,
year = {2025},
author = {Malik, MZ and Nizam, R and Jacob, S and Al Alqaderi, H and Al-Mulla, F and Alqaderi, H},
title = {Microbial dysbiosis in oral cavity determines obesity status in adolescents.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {354},
pmid = {41074949},
issn = {1420-9071},
support = {Institutional Funding//Kuwait Foundation for the Advancement of Sciences/ ; },
mesh = {Humans ; Adolescent ; *Dysbiosis/microbiology ; Female ; Male ; *Mouth/microbiology ; *Obesity/microbiology ; Microbiota/genetics ; Saliva/microbiology ; Body Mass Index ; Kuwait ; },
abstract = {The prevalence of obesity is rapidly increasing among adolescents in Kuwait. The ecological and dynamic changes within the oral microbiota during this developmental stage remain elusive. This study aimed to investigate the impact of body mass index (BMI) on salivary microbiome diversity and composition in Kuwaiti adolescents by utilizing next-generation sequencing technologies. DNA was extracted from saliva samples of 62 Kuwaiti adolescents enrolled in the nationwide Kuwait Healthy Lifestyle Study, categorized as underweight, normal weight, overweight, and obese based on their BMI percentiles. The 16 S metagenomic profiling was performed to identify the key oral lineages and genera associated with obesity through comprehensive analysis involving taxonomic composition, co-occurrence networks, and key metabolic profiles. Our study reveals an inverse relationship between oral bacterial diversity and obesity status in Kuwaiti adolescents. The obese and overweight groups showed comparatively low microbial taxa compared to those of normal weight. We identified three potential microbial biomarkers linked to obesity and overweight: Prevotella melaninogenica, Veillonella dispar, and Veillonella parvula. The abundance of Neisseria subflava and Rothia mucilaginosa in normal weight adolescents indicates their role in weight homeostasis. In- silico analysis of differentially expressed microbiota revealed increased activity of major metabolic enzymes such as glucose- 6- phosphate dehydrogenase, pyruvate oxidase, and glycogen phosphorylase, along with oxidative stress- related enzymes including superoxide reductase and glutathione peroxidase in obese and over-weight adolescents. Conversely, normal weight adolescents exhibited heightened activity of pyruvate synthase and tRNA- methyltransferase, which are linked to antioxidative pathways and balanced energy metabolism. Our study highlights taxonomic and functional shifts in the oral microbiota of Kuwaiti adolescents across varying BMI categories, signifying key microbial markers that could pave the way for future research focused on microbiome- targeted interventions in obesity management.},
}
@article {pmid41074769,
year = {2025},
author = {Tucker, SJ and Freel, KC and Eren, AM and Rappé, MS},
title = {Habitat-specificity in SAR11 is associated with a few genes under high selection.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {41074769},
issn = {1751-7370},
support = {#989028//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; NA20NOS4200123//National Science Foundation Graduate Research/ ; 1842402//National Science Foundation Graduate Research/ ; #687269//Simons Foundation/ ; },
mesh = {*Ecosystem ; Phylogeny ; *Selection, Genetic ; *Seawater/microbiology ; Metagenome ; *Alphaproteobacteria/genetics/classification/isolation &amp; purification ; Metagenomics ; Genome, Bacterial ; Pacific Ocean ; Genetic Variation ; },
abstract = {The order Pelagibacterales (SAR11) is the most abundant group of heterotrophic bacteria in the global surface ocean, where individual sublineages likely play distinct roles in oceanic biogeochemical cycles. Yet, understanding the determinants of niche-partitioning within SAR11 has been a formidable challenge due to the high genetic diversity within individual SAR11 sublineages and the limited availability of high-quality genomes from both cultivation and metagenomic reconstruction. Through an integrated metapangenomic analysis of 71 new SAR11 isolate genomes and a time-series of metagenomes from the prominent source of isolation, we reveal an ecological and phylogenetic partitioning of metabolic traits across SAR11 genera. We resolve distinct habitat-preferences among genera for coastal or offshore environments of the tropical Pacific and identify a handful of genes involved in carbon and nitrogen metabolisms that appear to contribute to these contrasting lifestyles. Furthermore, we find that some habitat-specific genes experience high selective pressures, indicating that they are critical determinants of SAR11 fitness and niche differentiation. Together, these insights reveal the underlying evolutionary processes shaping niche-partitioning within sympatric and parapatric populations of SAR11 and demonstrate that the immense genomic diversity of SAR11 bacteria naturally segregates into ecologically and genetically cohesive units, or ecotypes, that vary in spatial distributions in the tropical Pacific.},
}
@article {pmid41074341,
year = {2025},
author = {Zhang, Z and Wang, Y and Yao, Y and Li, Y and Xu, X and Hou, Q and Hu, X and Mei, X and Guo, Z},
title = {Microbial and flavor dynamics of medium-high temperature Daqu: regional influences and implications for Daqu quality optimization.},
journal = {Food research international (Ottawa, Ont.)},
volume = {220},
number = {},
pages = {117155},
doi = {10.1016/j.foodres.2025.117155},
pmid = {41074341},
issn = {1873-7145},
mesh = {*Taste ; China ; *Hot Temperature ; *Wine/microbiology/analysis ; Odorants/analysis ; *Food Microbiology ; Bacteria/classification/genetics/metabolism ; Metagenomics ; Microbiota ; Fermentation ; Humans ; },
abstract = {Medium-high temperature Daqu (MHTD) plays a crucial role in Chinese strong-flavor Baijiu production, yet its microbial dynamics and the drivers of regional variation remain underexplored. In this study, we investigated the microbial community structure, enzyme activity, and flavor profiles of MHTD from three geographically adjacent regions in China, using metagenomic sequencing, E-sensory analysis, and multivariate statistics. Despite significant regional differences in microbial diversity, community composition, and taste, aroma profiles were relatively consistent. Redundancy analysis revealed that water content and acidity were the primary environmental drivers of microbial and flavor variation. Notably, increased water content was positively correlated with microbial richness, enzyme activity, and flavor complexity. Functional annotation of metagenomic data uncovered key microbial pathways for starch, cellulose, and lignin degradation, as well as for the biosynthesis of pyrazines and guaiacol derivatives. Limosilactobacillus fermentum, the dominant species across all samples, was found to possess the genetic potential to produce both compound classes-representing a novel finding. Fungal species such as Thermoascus sp. and Rasamsonia emersonii appeared to cooperate in guaiacol synthesis, while Acetobacter pasteurianus and A. oryzoeni in MHTD from Chuzhou City contributed to pyrazine production. These findings highlight the microbial and environmental basis of flavor formation in MHTD and offer practical implications for MHTD production. Specifically, moisture regulation during fermentation and selective enrichment of functional strains like L. fermentum and Acetobacter spp. may help optimize flavor development and product consistency.},
}
@article {pmid41073886,
year = {2025},
author = {Mao, K and Lu, G and Qiu, Q and Zang, Y and Ouyang, K and Zhao, X and Song, X and Xu, L and Liang, H and Qu, M and Li, Y},
title = {Influence of creatine pyruvate on newly received cattle: insights from metagenomics and metabolomics.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {658},
pmid = {41073886},
issn = {1471-2180},
support = {CARS-37//the China Agriculture Research System of MOF and MARA/ ; CARS-37//the China Agriculture Research System of MOF and MARA/ ; 20232BCJ23016//the Young Talents Training Program for Academic and Technical Leaders of Major Disciplines in Jiangxi Province/ ; },
mesh = {Animals ; Cattle/growth &amp; development/microbiology ; Rumen/microbiology/metabolism ; *Creatine/pharmacology/administration &amp; dosage ; Metabolomics ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; Metabolome/drug effects ; Animal Feed/analysis ; *Pyruvic Acid/pharmacology ; Bacteria/genetics/classification/metabolism ; },
abstract = {Transport stress is a critical factor affecting the health and growth performance of beef cattle, potentially leading to oxidative stress, inflammation, and metabolic disorders. Creatine pyruvate (CrPyr), as a potential stress alleviator, has unclear mechanisms of action. We monitored the growth of 17 Simmental calves (control, n = 8; CrPyr, n = 9) over 30 days post-transportation, collecting rumen and blood samples on days 1/4, and 30. This study aims to investigate the effects of CrPyr on the growth performance, rumen microbiome, and metabolome of calves subjected to transport stress. Results showed that CrPyr increased average daily gain and antioxidant capacity, while reducing the level of stress hormones and inflammation. In the 4 days post-transport, CrPyr mainly increases Ruminococcus abundance to boost ruminal nitrogen metabolism, providing substrates for microbial protein synthesis. CrPyr also provides energy for the proliferation of Ruminococcus by regulating ATP synthesis genes (ATPVC) and enriching purine metabolism products. Meanwhile, it strengthens the host's amino acid metabolism, especially aspartate, to enhance antioxidative capacity. By day 30, CrPyr primarily boosts Prevotella abundance to regulate VFA synthesis, supplying host energy. It regulates the ATP synthesis gene ATPF0A and enriches purine metabolism products, supporting Prevotella growth. Increased citric acid and ATP levels further aid host growth. The findings distinctly demonstrate that the mechanisms by which CrPyr alleviates transport stress through the regulation of the rumen microbiome and metabolome, and confirms that its effects are time-dependent. These findings provide a theoretical basis for the development of stress-alleviation strategies based on CrPyr and hold significant implications for enhancing the health and production performance of beef cattle.},
}
@article {pmid41073663,
year = {2025},
author = {Yoo, JS and Jung, DJ and Goh, B and Heo, K and Zheng, W and Lee, CC and Seo, JI and Geva-Zatorsky, N and Wu, M and Park, SB and Kasper, DL and Oh, SF},
title = {Human gut bacteria produce structurally related monoglycolipids with contrasting immune functions.},
journal = {Nature microbiology},
volume = {10},
number = {11},
pages = {2797-2807},
pmid = {41073663},
issn = {2058-5276},
support = {2021R1A6A3A14039202//National Research Foundation of Korea (NRF)/ ; RS-2023-00217123//National Research Foundation of Korea (NRF)/ ; 75N93022D00005/AI/NIAID NIH HHS/United States ; K01 DK102771/DK/NIDDK NIH HHS/United States ; 75N93023D00005/AI/NIAID NIH HHS/United States ; R01 AT010268/AT/NCCIH NIH HHS/United States ; 2021R1A6A3A14044113//National Research Foundation of Korea (NRF)/ ; 2014R1A3A2030423//National Research Foundation of Korea (NRF)/ ; RS-2024-00411992//National Research Foundation of Korea (NRF)/ ; 75N92020D00005/HL/NHLBI NIH HHS/United States ; 2012M3A9C4048780//National Research Foundation of Korea (NRF)/ ; RS-2024-00348702//National Research Foundation of Korea (NRF)/ ; R01-AT010268//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; 75N95020D00005/DA/NIDA NIH HHS/United States ; R01 AI165987/AI/NIAID NIH HHS/United States ; 75N99020D00005/OF/ORFDO NIH HHS/United States ; K01-DK102771//U.S. Department of Health &amp; Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes &amp; Digestive &amp; Kidney Diseases)/ ; R01-AI165987//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; Mice ; *Bacteroides fragilis/genetics/metabolism/immunology ; *Glycolipids/immunology/chemistry/metabolism/biosynthesis ; Natural Killer T-Cells/immunology ; Galactosyltransferases/metabolism/genetics ; Symbiosis ; Mice, Inbred C57BL ; Colon/immunology/microbiology ; Infant ; Galactosylceramides/metabolism/biosynthesis ; Female ; *Bacteria/metabolism/classification/genetics ; Lymphocyte Activation ; },
abstract = {Gut symbiont Bacteroides fragilis can produce α-galactosylceramides (BfaGCs), sphingolipids with immunomodulatory functions that regulate colonic natural killer T (NKT) cells. However, their synthesis pathway and whether other human gut bacteria can produce them are unclear. Here, using genetic and metabolomic approaches, we mapped the sphingolipid biosynthesis pathway of B. fragilis and determined that α-galactosyltransferase (agcT) is essential and sufficient for colonic NKT cell regulation in mice. The distribution of agcT is restricted to only a few species among Bacteroidales. However, structural homologues of AgcT, such as BgsB, are widely distributed in gut microbiota and produce α-glycosyldiacylglycerols (aGDGs), particularly in Enterococcus. Analysis of infant gut metagenomes revealed that B. fragilis predominantly accounts for agcT abundance regardless of the cohort, but bgsB-encoding bacteria were taxonomically diverse and showed dynamic changes with host age. In addition, aGDGs from bgsB-encoding species act as antagonistic ligands for BfaGC-mediated NKT cell activation in vitro and in vivo. Our findings highlight the distinct natures of immunoactive glycolipid-producing symbionts and their relevance in the human gut microbiome, particularly in early life.},
}
@article {pmid41072198,
year = {2025},
author = {Jamtsho, K and Lund, MA and Blake, D and Van Etten, E},
title = {Contrasting effects of impervious cover on riparian plant and soil bacterial communities in a rapidly urbanising Himalayan city.},
journal = {The Science of the total environment},
volume = {1003},
number = {},
pages = {180681},
doi = {10.1016/j.scitotenv.2025.180681},
pmid = {41072198},
issn = {1879-1026},
mesh = {*Soil Microbiology ; Bacteria/classification ; *Urbanization ; Bhutan ; Cities ; Biodiversity ; Plants ; Ecosystem ; *Environmental Monitoring ; Microbiota ; Soil/chemistry ; },
abstract = {Rapid urbanisation-particularly the expansion of impervious surfaces-is reshaping riparian landscapes worldwide. These areas are frequently targeted for development due to their favourable topography, abundant water resources, and aesthetic appeal. However, the impact of increasing impervious cover on soil bacterial communities in biodiverse urban riparian zones remains poorly understood, especially in developing countries, raising concerns about potential declines in essential ecosystem functions. In this study, we investigated the effects of impervious cover, quantified as the Percentage of Total Impervious Area (PTIA), on the taxonomic and functional diversity of riparian soil bacteria in Thimphu City, Bhutan. Using plot-based taxonomic profiling and metagenomic analysis across a PTIA gradient, we tested the hypothesis that bacterial diversity and functional pathways would decline beyond 40 % PTIA, mirroring patterns observed in riparian plant communities. Contrary to our hypothesis, plots with PTIA exceeding 40 % exhibited greater bacterial richness and functional diversity. These findings suggest opposing responses to impervious cover, with belowground microbial communities increasing in diversity while aboveground plant diversity declines. A significantly lower carbon-to‑nitrogen ratio in urban plots-likely driven by nutrient enrichment-emerged as the primary factor promoting bacterial diversity in high PTIA areas. This enrichment appeared to favour copiotrophic bacteria, enhancing both diversity and functional capacity. Our results suggest that bacterial communities may be effective bioindicators of riparian ecosystem health than plant communities. Incorporating microbial metrics into urban riparian management and monitoring could therefore provide valuable insights for sustaining ecosystem functions in rapidly urbanising regions.},
}
@article {pmid41069707,
year = {2025},
author = {Rubio-Portillo, E and Arias-Real, R and Rodríguez-Pérez, E and Bañeras, L and Antón, J and de Los Ríos, A},
title = {Short-term virus-host interactions and functional dynamics in recently deglaciated Antarctic tundra soils.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf157},
pmid = {41069707},
issn = {2730-6151},
abstract = {Long-term chronosequence studies have shown that, as glaciers retreat, newly exposed soils become colonized through primary succession. To determine the key drivers of this process and their vulnerability to climate change, the short-term responses of these pioneering microbial communities also need to be elucidated. Here, we investigated how the taxonomic and functional structure of microbial communities, including viruses, changed over a 7-year period in an Antarctic glacier forefield. Using metagenomics and metatranscriptomics we assessed the influence of both abiotic and biotic factors on these communities. Our results revealed a highly heterogeneous bacteria-dominated microbial community, with Pseudomonas as the most abundant genus, followed by Lysobacter, Devosia, Cellulomonas, and Brevundimonas. This community exhibited the capacity for aerobic anoxygenic phototrophy, carbon and nitrogen fixation, and sulfur cycling, processes vital for survival in nutrient-poor environments. 52 high-quality metagenome-assembled genomes (MAGs) were recovered, representing both transient and cosmopolitan taxa, some of which were able to rapidly respond to environmental changes. A diverse and highly dynamic collection of lytic and temperate viruses was identified across all samples, with high clonal viral genomes typically detected in only one of the eight samples analyzed. Metatranscriptomic analyses confirmed the activity of lytic viruses, while prophage genomes featured much lower expression levels. Prophages appeared to influence host fitness through the expression of genes encoding membrane transporters. Additionally, the abundance of genes linked to antimicrobial compound synthesis and resistance, along with antiphage defense systems, highlights the importance of biotic interactions in driving microbial community succession and shaping short-term responses to environmental fluctuations.},
}
@article {pmid41069107,
year = {2025},
author = {Ozel, B and Agirman, B and Simsek, O and Erten, H},
title = {Effects of Backslopping on Yeast Diversity and the Volatile Profile of Tarhana.},
journal = {Yeast (Chichester, England)},
volume = {42},
number = {11},
pages = {222-234},
doi = {10.1002/yea.70003},
pmid = {41069107},
issn = {1097-0061},
support = {//Cukurova University Academic Research Projects Unit (Project no: FDK-2017-7769)./ ; },
mesh = {*Volatile Organic Compounds/analysis/metabolism ; Fermentation ; *Yeasts/classification/genetics/metabolism/isolation &amp; purification ; Hydrogen-Ion Concentration ; *Biodiversity ; Temperature ; Food Microbiology ; *Fermented Foods/microbiology ; *Bread/microbiology/analysis ; },
abstract = {The primary challenge in tarhana production is the occurrence of spontaneous fermentation, which leads to non-standardized products. Thus, we investigated the effects of backslopping, a traditional method for inoculating fermented foods, on the yeast and volatile aroma compound diversity of tarhana dough. Backslopping fermentations were conducted at different temperatures (25°C and 30°C), pHs (3.70 and 4.00), and inoculation rates (5%, 10%, and 15%). The results revealed that the fermentation temperature and pH significantly influenced the diversity of yeast species and the volatile compound profile of the tarhana dough. However, despite some variations in the PCR-DGGE profiles, the metagenomic analysis revealed that the inoculation rate had minimal effect on yeast diversity, with species diversity remaining relatively constant over the cycles. Kazachstania humilis, Kazachstania bulderi, and Pichia kluyveri were the most prevalent yeast species across all experimental conditions. Pichia membranifaciens was exclusively detected in doughs fermented at 25°C and pH 4.00, whereas Saccharomyces cerevisiae was observed only in doughs fermented at 30°C. Tarhana doughs had a wide range of volatile compounds, the most abundant of which were terpenes and terpenoids, followed by esters, alcohols, aldehydes, and phenols. Doughs fermented at 25°C and pH 3.70 were differentiated from other groups, particularly for their content of esters (e.g., ethyl acetate, ethyl lactate, ethyl decanoate, and ethyl octanoate) and alcohols (e.g., ethyl alcohol, isobutyl alcohol, benzyl alcohol). This study highlights the direct influence of backslopping on yeast diversity and its indirect impact on the aroma profile of tarhana dough, providing insights into the optimization of fermentation conditions for improved product standardization.},
}
@article {pmid41068938,
year = {2025},
author = {Xu, J and Chen, X and Ren, J and Xu, J and Zhang, L and Yan, F and Liu, T and Zhang, G and Huws, SA and Yao, J and Wu, S},
title = {Multi-omics insights into microbiome-rumen epithelium interaction mechanisms underlying subacute rumen acidosis tolerance in dairy goats.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {345},
pmid = {41068938},
issn = {1474-760X},
support = {32272829//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; 2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; },
mesh = {Animals ; *Goats/microbiology ; *Rumen/microbiology/metabolism ; *Acidosis/veterinary/microbiology/metabolism ; *Gastrointestinal Microbiome ; Epithelium/metabolism/microbiology ; Fatty Acids, Volatile/metabolism ; Female ; *Goat Diseases/microbiology ; Hydrogen-Ion Concentration ; *Microbiota ; Transcriptome ; Multiomics ; },
abstract = {BACKGROUND: To address rising demand for dairy products, dairy goats are often fed high-concentrate diets, which lead to subacute rumen acidosis (SARA). The mechanisms behind individual variation in SARA tolerance are not well understood. This study aims to elucidate roles of rumen microbiome-host interactions in SARA-susceptibility and tolerance.<br><br>RESULTS: Goats susceptible or tolerant to SARA were selected by feeding diets with different levels of rumen degradable starch. SARA-susceptible goats present prolonged periods of rumen pH below 5.8 and volatile fatty acids (VFAs) accumulation. Metagenomic analysis reveals a decrease in cellulose- and hemicellulose-utilizing bacteria and enzymes, along with increased lysozymes, suggesting disrupted rumen homeostasis. Transcriptomic and single-nucleus transcriptome analyses reveal upregulated Th17 cells, IL-17 signalling, and inflammatory pathways in SARA-susceptible goats. In contrast, SARA-tolerant goats maintain stable pH levels and enhance VFAs absorption. Bifidobacterium adolescentis and other beneficial bacteria are enriched in the rumen of SARA-tolerant goats. These microbes are positively correlated with 3-methyl pyruvic acid, a key metabolite involved in branched-chain amino acid synthesis and epithelial cell proliferation. Both microbiome transplantation and B. adolescentis direct feeding experiments confirm the protective effects of SARA-tolerant microbiota including B. adolescentis, promoting rumen epithelial VFAs absorption and reducing ruminal inflammation.<br><br>CONCLUSIONS: This study highlights the importance of Th17-mediated immune responses in ruminal inflammation and the role of B. adolescentis in regulating rumen epithelial VFAs absorption. Modulating VFAs absorption in the rumen epithelium represents a promising strategy for improving animal health and enhancing rumen fermentation efficiency.},
}
@article {pmid41068590,
year = {2025},
author = {Chen, Y and Miao, Q and Bao, R and Qu, H and Shen, J and Li, N and Luan, S and Yin, X and Pan, J and Hu, B},
title = {Distinct lung microbiota community states are associated with pulmonary nontuberculous mycobacterial disease prognosis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {653},
pmid = {41068590},
issn = {1471-2180},
support = {2023ZSLC24//Zhongshan Hospital/ ; },
mesh = {Humans ; Male ; *Microbiota ; Female ; *Mycobacterium Infections, Nontuberculous/microbiology/diagnosis ; *Lung/microbiology ; Prognosis ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; *Nontuberculous Mycobacteria/genetics/isolation &amp; purification/classification ; Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Adult ; },
abstract = {BACKGROUND: The incidence of nontuberculous mycobacterial pulmonary disease (PNTM) is rising, but the available treatments have limitations. Currently, the understanding of the ecology of the airway microbiota in PNTM is limited, especially regarding community structure, dynamics, and their relationship with clinical outcomes.<br><br>METHODS: We used metagenomic sequencing to characterize the lung microbiota in bronchoalveolar lavage fluid (BALF). We evaluated the prognosis of patients with PNTM through respiratory specimen cultures and chest CT scans.<br><br>RESULTS: PNTM exhibit distinct airway microbiota characteristics compared to controls, however, no significant differences were observed in NTM species. A Dirichlet multinomial mixture model was used to identify two distinct community types (pneumotypes) and investigate their association with host immunity and prognosis. At the 13-month median follow-up, pneumotype 1 (including Mycobacterium, opportunistic pathogens, and anaerobes) presented a lower probability of sustained culture conversion (hazard ratio&#x2009;=&#x2009;0.29; 95% confidence interval&#x2009;=&#x2009;0.12-0.73; P&#x2009;=&#x2009;0.009) than pneumotype 2, indicating a worse prognosis. Based on microbial community abundance and interactions, Ralstonia (NetMoss score&#x2009;=&#x2009;1.0; log2FoldChange&#x2009;=&#x2009;3.6) and Dolosigranulum (NetMoss score&#x2009;=&#x2009;0.6; log2FoldChange&#x2009;=&#x2009;1.4) emerged as prominent taxa associated with the shift from pneumotype 1 to pneumotype 2, which correlated with differences in clinical outcomes.<br><br>CONCLUSION: Our research indicates that distinct baseline microbial characteristics in PNTM patients are associated with prognosis. Furthermore, we identified candidate microbes driving changes in the PNTM microbial community state, serving as potential therapeutic targets.},
}
@article {pmid41068306,
year = {2025},
author = {Shin, AS and Xing, Y and Waseem, MR and Siwiec, R and James-Stevenson, T and Rogers, N and Bohm, M and Wo, J and Lockett, C and Gupta, A and Kadariya, J and Toh, E and Anderson, R and Dong, A and Xu, H and Gao, X},
title = {Microbiota and short chain fatty acid relationships underlie clinical heterogeneity and identify key microbial targets in irritable bowel syndrome (IBS).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35375},
pmid = {41068306},
issn = {2045-2322},
support = {K23 DK122015/DK/NIDDK NIH HHS/United States ; R03 DK132446/DK/NIDDK NIH HHS/United States ; K23DK122015/DK/NIDDK NIH HHS/United States ; R03DK132446/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/metabolism ; Female ; *Gastrointestinal Microbiome ; Male ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Adult ; Middle Aged ; Bile Acids and Salts/metabolism ; Constipation/microbiology ; Metagenome ; Diarrhea/microbiology ; Bacteria/classification/genetics/metabolism ; },
abstract = {Short chain fatty acids (SCFA) are key microbial metabolites that modulate intestinal homeostasis and may influence irritable bowel syndrome (IBS) pathophysiology. We aimed to assess microbial features associated with SCFA and determine if features varied across IBS subtypes and endophenotypes. We analyzed stool microbial metagenomes, stool SCFA, and measurable IBS traits (stool bile acids, colonic transit, stool form) in 41 patients with IBS (IBS with constipation [IBS-C] IBS with diarrhea [IBS-D]) and 17 healthy controls. We used partial canonical correspondence analyses (pCCA), conditioned on transit, to quantify microbe-SCFA associations across groups. We further compared gut microbiome-encoded potential for substrate utilization across groups and within a subset of participants selected by their stool characteristics as well as stool microbiomes of patients with and without clinical bile acid malabsorption (BAM). Microbe-SCFA associations differed across groups and revealed key taxa including Dorea sp. CAG:317 and Bifidobacterium pseudocatenulatum in IBS-D and Akkermansia muciniphila and Prevotella copri in IBS-C that that could underlie subtype-specific microbially-mediated mechanisms. The greatest number of microbe-SCFA associations were observed in IBS-D. Several SCFA-producing species demonstrated inverse correlations with SCFA. Fewer bacterial taxa were associated with acetate to butyrate ratios in IBS compared to health. In participants selected by stool form, we demonstrated differential abundances of microbial genes/pathways for SCFA metabolism and degradation of carbohydrates and mucin across groups. SCFA-producing taxa were reduced in IBS-D patients with BAM. Keystone taxa responsible for SCFA production differ by IBS subtype and traits. IBS microbiomes appear exhibit reduced functional redundancy. Differences in substrate preferences are also linked to bowel functions. Focusing on taxa that drive SCFA profiles and stool form may be a rational strategy for identifying relevant microbial targets in IBS.},
}
@article {pmid41068233,
year = {2025},
author = {Giovannini, N and Limena, A and Ercolino, C and Uceda Renteria, SC and Strati, F and Giuffrè, MR and Maragno, P and Carbone, IF and Facciotti, F and Ceriotti, F and Ferrazzi, E and Lattuada, D},
title = {Nasopharyngeal and oral microbiota profiling in SARS-CoV-2 infected pregnant women.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35306},
pmid = {41068233},
issn = {2045-2322},
mesh = {Humans ; Female ; Pregnancy ; *COVID-19/microbiology/virology ; *Nasopharynx/microbiology ; Adult ; *Microbiota ; *Mouth/microbiology ; SARS-CoV-2/isolation &amp; purification ; *Pregnancy Complications, Infectious/microbiology/virology ; },
abstract = {Variations have been found in the upper respiratory tract microbiota in SARS-CoV-2 positive patients compared to healthy subjects, with different dominant species and diversity indexes detected, including a decrease in biodiversity and an increased abundance of bacterial pathogens. Moreover, these discrepancies were observed in patients with both mild and severe symptoms. Notably, the inflammatory state appears to be significantly influenced by the characteristics of the indigenous microbiota. This is particularly interesting in pregnant patients, as pregnancy involves an adaptive adjustment of the microbiota due to hormonal changes aimed at providing immune protection. The relationship between the microbiota of pregnant women and SARS-CoV-2 has not been deeply explored so far. The purpose of the present study is to investigate the relationship between SARS-CoV-2, nasopharyngeal and oral microbiota, and pregnancy. To our knowledge this is the first simultaneous investigation on both nasopharyngeal and oral microbiota in SARS-Cov-2 infected pregnant women. In this study, the nasopharyngeal and oral microbiota were analysed in 43 women in their third trimester of pregnancy enrolled from April 2020 to February 2021. The differential abundance of taxa was tested and alpha and beta diversity were evaluated. SARS-CoV-2 infected pregnant women showed an alteration of the nasopharyngeal and oral microbiota compared to healthy pregnant women. In both the nasopharyngeal and oral microbiota of the SARS-CoV-2 infected pregnant women, we found a variation in taxa, represented by an enrichment of pathobionts, which increased particularly with the severity of symptoms. Specifically, a significant reduction in microbial biodiversity has been identified within the nasopharyngeal microbiota of SARS-CoV-2 positive women. Furthermore, enrichment in pathobionts was noted in both asymptomatic and symptomatic women, with these changes being more pronounced in the nasopharyngeal microbiota compared to the oral one. The nasopharyngeal microbiota of asymptomatic and symptomatic SARS-CoV-2 infected women showed an enrichment of pathogens and pathobionts such as Corynebacterium, Fusobacterium, Neisseria, Streptococcus, Haemophilus, Mycobacterium and Porphyromonas compared with the control group. The oral microbiota showed an enrichment of pathobionts such as Neisseria, Fusobacterium and Streptococcus. A random forest classifier applied to metagenomic data from nasopharyngeal and oral swabs showed that the nasopharyngeal microbiota is the best sampling site to predict the patients' SARS-CoV-2 infection status. Gulbenkiania, Burkholderia and Actinomyces, all taxa significantly enriched in the control group compared to SARS-CoV-2 infected women, were the most important features selected by the classifier. Finally, correlations between the nasopharyngeal and oral microbiota and clinical parameters of pregnant women, particularly BMI and procalcitonin, were observed. SARS-CoV-2 infected pregnant women showed an alteration of the nasopharyngeal and oral microbiota compared to healthy pregnant women. We found a variation in taxa, represented by the enrichment of pathobionts in both the nasopharyngeal and oral microbiota of SARS-CoV-2 infected pregnant women, particularly increased in symptomatic individuals. The nasopharyngeal microbiota appears to be a better predictor of SARS-CoV-2 infection and its severity than the oral microbiota.},
}
@article {pmid41068119,
year = {2025},
author = {Liu, S and Feng, B and Zhang, Z and Miao, J and Lai, X and Zhao, W and Xie, Q and Ye, X and Cao, C and Yu, P and Sun, J and Guo, J and Wang, Z and Wang, Q and Zhang, Z and Pan, Y},
title = {UPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {196},
pmid = {41068119},
issn = {2055-5008},
support = {LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; LZ23C170003//Zhejiang Provincial Natural Science Foundation of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 2021YFD1200802,2023YFF1001100//National Key Research and Development Program of China/ ; 32272832//National Natural Science Foundation of China/ ; 32272832//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; *Archaea/genetics/classification/isolation &amp; purification ; Metagenome ; *Genome, Bacterial ; Interspersed Repetitive Sequences ; Phylogeny ; Metagenomics ; },
abstract = {The porcine gut microbiome is crucial for pig health and key to its production performance. However, genome-level analysis across multiple kingdoms remains limited. Here, we reconstructed the unified pig gastrointestinal genome (UPGG), including bacterial, archaeal, and annotated over 78 million non-redundant protein-coding genes using 5784 metagenome samples. We identified antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and the distribution of 72,056 metabolic gene clusters within existing populations. We have constructed pan-genomes of 436 high-quality microbial species and, using these as references, discovered intraspecies genomic variations that revealed 23,350,975 single-nucleotide variants (SNVs). Finally, through comparative analysis of gut microbiome genomes conducted in this study, we observed that pigs may serve as a more suitable model than other animals for investigating human gut microbiota composition and functional patterns. In summary, we constructed a comprehensive reference catalog of the porcine gut microbiome and enhanced the understanding of the host-microbe coevolution.},
}
@article {pmid41067450,
year = {2026},
author = {Liu, N and Zhang, Y and Zhang, Y and Yang, Y and Long, H and Huang, A and Zeng, Y and Xie, Z},
title = {Quorum sensing mediates spatiotemporal microbial community dynamics and nitrogen metabolism in biofloc-based Litopenaeus vannamei aquaculture systems.},
journal = {Bioresource technology},
volume = {440},
number = {},
pages = {133459},
doi = {10.1016/j.biortech.2025.133459},
pmid = {41067450},
issn = {1873-2976},
mesh = {*Quorum Sensing/physiology ; *Aquaculture/methods ; Animals ; *Penaeidae/microbiology/metabolism ; *Nitrogen/metabolism ; *Microbiota/physiology ; Nitrites/metabolism ; Ammonia/metabolism ; },
abstract = {Biofloc technology (BFT) enables sustainable aquaculture by leveraging microbial communities to enhance water quality and nutrient cycling. However, the role of quorum sensing (QS) in regulating microbial dynamics and metabolic functions within BFT systems remains poorly understood. This study examined how QS spatiotemporally regulates microbial succession and nutrient metabolism in a biofloc-based Litopenaeus vannamei aquaculture system over 82 days culture. Ammonia and nitrite concentrations shifted through four phases: initial (IP), rising (RP), declining (DP), and stabilization (SP). Notably, nitrite levels decreased rapidly from 1.21 mg/L to 0.03 mg/L during DP. Metagenomic analysis revealed Pseudomonadota, Actinomycetota, and Bacteroidota as the consistently dominant phyla, while dominant genera shifted over time. QS pathways displayed temporal heterogeneity: acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2) predominated during IP, whereas aromatic hydrocarbon kinases (AHKs) and cyclic dimeric guanosine monophosphate (c-di-GMP) were more enriched during SP. KEGG analysis indicated that nitrogen metabolism genes were more abundant in bioflocs than in the water. Genes associated with dissimilatory nitrate reduction and denitrification were significantly more abundant than those involved in other nitrogen metabolic processes (p < 0.05). Furthermore, QS signaling coordinated the complex interaction networks among 30 dominant bacterial genera (e.g., Amaricoccus and Ruegeria) involved in carbon, nitrogen, and sulfur metabolism, which is crucial for maintaining the stability and functionality of the biofloc system. This study elucidates the mechanisms through which microbial signaling orchestrates efficient nitrogen removal and sustains system stability, thereby providing a foundation for developing targeted bioaugmentation strategies to enhance sustainable aquaculture practices.},
}
@article {pmid41066275,
year = {2025},
author = {Mutafcilar Velioglu, E and Arslan, U and Kayis, SA and Maçin, S and Kamada, N and Hakki, SS},
title = {Correlation in the change of gut microbiota with clinical periodontal parameters in grade C periodontitis patients after non-surgical periodontal therapy.},
journal = {Journal of medical microbiology},
volume = {74},
number = {10},
pages = {},
pmid = {41066275},
issn = {1473-5644},
mesh = {*Gastrointestinal Microbiome ; *Periodontitis/complications/diagnosis/therapy ; Humans ; *Dysbiosis/complications ; Case-Control Studies ; Mouth/microbiology ; Male ; Female ; Adult ; Bacteria/classification ; },
abstract = {Introduction. Intestinal dysbiosis is associated with systemic health, and approaches targeting the microbiome can influence the host. Oral and intestinal microbiota are interrelated; therefore, we aimed to determine whether non-surgical periodontal treatment (NSPT) affects systemic health through its impact on the intestinal microbiota.Hypothesis/Gap Statement. Although the association between oral and gut microbiota has been suggested, there is limited evidence regarding how periodontal therapy may influence intestinal microbial composition. We hypothesized that NSPT in patients with periodontitis would lead to favourable changes in the gut microbiome, which may parallel improvements in clinical periodontal parameters.Aim. This study aimed to investigate the effect of NSPT on both oral and intestinal microbiota and to evaluate whether changes in gut microbial composition correlate with periodontal clinical outcomes.Methodology. Five systemically healthy individuals with grade C periodontitis and five systemically and periodontally healthy individuals were included. Saliva and stool samples were collected at baseline and 1 month after NSPT. DNA extractions were performed and subjected to 16S ribosomal RNA gene sequencing on the Illumina Novaseq at the V3-V4 hypervariable regions.Results. Grade C periodontitis patients displayed distinct oral and gut microbiomes compared to healthy individuals. NSPT resulted in a reduction in the diversity of both saliva and stool samples in healthy individuals (P>0.05). Salivary Fusobacteriota levels (P<0.05) and the gut Firmicutes/Bacteroides ratio decreased after NSPT. Moreover, changes in gut microbiota significantly correlated with improvements in periodontal probing depth and clinical attachment level in periodontitis patients.Conclusion. The improvement in clinical periodontal parameters after NSPT correlates with a positive shift in the gut microbiome towards health. Although the number of participants was limited, these findings support a strong relationship between periodontal and gut status. Further studies with larger cohorts and long-term follow-up are required to confirm these results.},
}
@article {pmid41066239,
year = {2025},
author = {Cook, RA and Ponsero, AJ and Telatin, A and Yang, Y and Liang, Z and Wang, F and Chen, R and Wang, Z and Adriaenssens, EM and Clokie, MRJ and Millard, AD and Brightling, CE},
title = {Bacteriophage diversity declines with COPD severity in the respiratory microbiome.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116413},
doi = {10.1016/j.celrep.2025.116413},
pmid = {41066239},
issn = {2211-1247},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/virology/pathology ; *Bacteriophages/genetics/physiology ; *Microbiota ; Female ; Male ; Middle Aged ; Aged ; Sputum/microbiology/virology ; Lung/microbiology/virology ; Severity of Illness Index ; },
abstract = {Chronic obstructive pulmonary disease (COPD) severity correlates with airway microbial dysbiosis, yet bacteriophage roles remain unexplored. We characterized the lung DNA virome by re-analyzing 135 sputum metagenomes from 99 COPD patients and 36 healthy controls. We identified 1,308 viral operational taxonomic units, revealing progressively lower viral diversity correlating with disease severity. While viral and bacterial diversity typically showed strong positive correlations, patients with frequent exacerbations uniquely exhibited decoupled viral-bacterial relationships, indicating disrupted ecological dynamics. Comparing all COPD patients to controls, phages infecting anaerobic oral bacteria showed disproportionately lower abundance-Porphyromonas phages were 40-fold less abundant, despite only 4-fold lower bacterial abundance-while pathogen-associated phages showed no significant differences. We detected virulence factor-encoding phages, including two neuA-carrying Haemophilus phages in 7.4% of Haemophilus-colonized patients, associated with 82-fold higher bacterial abundance. These findings establish altered bacteriophage ecology as an unrecognized feature of COPD pathobiology, with differential phage-bacteria relationships that reshape lung microbial ecosystems, offering new perspectives for microbiome-targeted interventions.},
}
@article {pmid41066109,
year = {2025},
author = {Zhou, T and Delgado-Baquerizo, M and Ren, C and He, N and Zhou, Z and He, Y},
title = {Soil microbial life history strategies covary with ecosystem multifunctionality across aridity gradients.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {41},
pages = {e2511071122},
pmid = {41066109},
issn = {1091-6490},
support = {202206600027//China Scholarship Council (CSC)/ ; 32522067//MOST | National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil Microbiology ; *Microbiota/physiology ; *Ecosystem ; *Desert Climate ; Soil/chemistry ; },
abstract = {Aridity thresholds shape ecosystem functions worldwide. Despite the importance of soil microbiomes in engineering ecosystem processes, the specific strategies employed by soil microbiomes to support ecosystem multifunctionality (EMF) across aridity gradients remain virtually unknown. Here, we investigated 474 soil samples across a continental-scale aridity gradient and identified an aridity threshold beyond which plot-level EMF declines sharply. Microbial habitat and decomposition functions were among the last to respond to aridity, with thresholds occurring under more arid conditions compared to plant productivity and soil fertility. Combining metagenomic sequencing with physiological assays to characterize microbial life history strategies of high yield (Y), resource acquisition (A), and stress tolerance (S), we introduce a microbial trait-based framework to mechanistically link community-level microbial life history strategies to EMF. Our results reveal that microbial Y-strategy is positively correlated with EMF across aridity gradients, A-strategy exhibits a negative association with EMF across aridity gradients, and S-strategy is negatively correlated with EMF in arid ecosystems. Collectively, this study offers empirical evidence and insights into how aridification interacts with soil microbiomes in shaping EMF, highlighting the pivotal role of microbial life history strategies in understanding the mechanisms behind EMF variation in an increasingly arid world.},
}
@article {pmid41065113,
year = {2025},
author = {Palacios, N and Gordon, S and Wang, T and Burk, R and Qi, Q and Huttenhower, C and Gonzalez, HM and Knight, R and De Carli, C and Daviglus, M and Lamar, M and Telavera, G and Tarraf, W and Kosciolek, T and Cai, J and Kaplan, RC},
title = {Gut microbiome and cognitive function in the Hispanic Community Health Study/Study of Latinos.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {108},
number = {1},
pages = {84-97},
doi = {10.1177/13872877251376911},
pmid = {41065113},
issn = {1875-8908},
mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; *Cognition/physiology ; Cohort Studies ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; *Hispanic or Latino/psychology ; },
abstract = {BackgroundThere is limited work on the association between the gut microbiome and Alzheimer's disease and related dementia (AD/ADRD) in Latinos.ObjectiveWe examined, within the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) cohort, the association between gut microbiome and cognitive function.MethodsWe analyzed the fecal metagenomes of 2471 HCHS/SOL participants to identify microbial taxonomic and functional features associated with global cognitive function. Omnibus (PERMANOVA) and feature-wise analyses (MaAsLin2) were conducted to identify microbiome-cognition associations, and specific microbial species and pathways (Kyoto Encyclopedia of Genes and Genomes (KEGG modules) associated with cognition.ResultsEubacterium species (E. siraeum and E. eligens), and C phoceensis, among other species were associated with better cognition. Several KEGG modules, most strongly Ornithine, Serine biosynthesis and Urea Cycle, were associated with worse cognition.ConclusionsIn a large Hispanic/Latino cohort, we identified several microbial taxa and KEGG pathways associated with cognition.},
}
@article {pmid41062579,
year = {2025},
author = {Wang, Y and Wang, Y and Hou, L and Zhong, L and Yang, H and Kang, X and Zhou, Y and Pan, J},
title = {Assessment of airborne and surface microbes on leather cultural relics in museums of arid regions represented by xinjiang, China.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35107},
pmid = {41062579},
issn = {2045-2322},
support = {2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; 2022YFF0904100//National Key Research and Development Program of China/ ; },
mesh = {China ; *Museums ; *Air Microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Microbiota ; },
abstract = {This study investigates the airborne microbial contamination in three museums located in the dry region of Xinjiang region, China-Bayingolin, Hami, and Turpan. Airborne microbial concentrations in these museums were found to be relatively low, ranging from 7.5 to 38.3 CFU/m[3], which is advantageous for the preservation of cultural relics, especially in comparison to humid regions where higher microbial concentrations have been reported. The microbial communities were dominated by bacteria, with Firmicutes being the most abundant phylum, followed by Proteobacteria and Bacteroidetes. Notably, Pseudomonas sp., Bacillus sp., and Staphylococcus hominis were identified as potential threats to the degradation of leather cultural relics. Additionally, Mycobacterium sp., Pantoea sp., and Priestia aryabhattai were first identified in the context of cultural heritage conservation. Metagenomic sequencing revealed a significant presence of salt-tolerant, spore-forming bacteria, which are characteristic of dry environments. Antibacterial tests showed that 0.5% K100 exhibited the best antimicrobial effect. This study provides valuable insights into the microbial ecology of museums in rid climates and suggests the need for targeted preservation strategies to mitigate microbial-induced biodeterioration, particularly through the use of antimicrobial agents and environmental management.},
}
@article {pmid41062543,
year = {2025},
author = {Prast-Nielsen, S and Granström, AL and Kiasat, A and Ahlström, G and Edfeldt, G and Rautiainen, S and Boulund, F and Andersson, FO and Lindberg, J and Schuppe-Koistinen, I and Gustafsson, UO and Engstrand, L},
title = {Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35039},
pmid = {41062543},
issn = {2045-2322},
mesh = {Humans ; *Bile Acids and Salts/blood ; *Gastrointestinal Microbiome ; *Crohn Disease/blood/microbiology ; *Colitis, Ulcerative/blood/microbiology ; Female ; Male ; Adult ; Biomarkers/blood ; Middle Aged ; *Inflammation/blood ; Case-Control Studies ; Feces/microbiology ; },
abstract = {Our study explores signatures for Crohn's disease (CD) and Ulcerative Colitis (UC) reflecting an interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ('CD' n = 64 and 'UC' n = 55), were age- and gender-matched to controls without findings during colonoscopy. Shotgun metagenomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls.In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.},
}
@article {pmid41062510,
year = {2025},
author = {Feng, S and Zhang, B and Wang, H and Xiong, Y and Tian, A and Yuan, X and Pan, C and Guo, X},
title = {Enhancing peptide identification in metaproteomics through curriculum learning in deep learning.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8934},
pmid = {41062510},
issn = {2041-1723},
support = {R01 AT011618/AT/NCCIH NIH HHS/United States ; R15 LM013460/LM/NLM NIH HHS/United States ; R01AT011618//U.S. Department of Health &amp; Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R15LM013460//U.S. Department of Health &amp; Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; },
mesh = {*Deep Learning ; *Proteomics/methods ; *Peptides/analysis ; Humans ; Gastrointestinal Microbiome ; Neural Networks, Computer ; Databases, Protein ; Metagenome ; },
abstract = {Metaproteomics offers a powerful window into the active functions of microbial communities, but accurately identifying peptides remains challenging due to the size and incompleteness of protein databases derived from metagenomes. These databases often contain vastly more sequences than those from single organisms, creating a computational bottleneck in peptide-spectrum match (PSM) filtering. Here we present WinnowNet, a deep learning-based method for PSM filtering, available in two versions: one using transformers and the other convolutional neural networks. Both variants are designed to handle the unordered nature of PSM data and are trained using a curriculum learning strategy that moves from simple to complex examples. WinnowNet consistently achieves more true identifications at equivalent false discovery rates compared to leading tools, including Percolator, MS[2]Rescore, and DeepFilter, and outperforms filters integrated into popular analysis pipelines. It also uncovers more gut microbiome biomarkers related to diet and health, highlighting its potential to support advances in personalized medicine.},
}
@article {pmid41062486,
year = {2025},
author = {Tu, Z and Sun, H and Wang, T and Liu, Y and Xu, Y and Peng, P and Qin, S and Tu, C and He, B},
title = {Node role of wild boars in virus circulation among wildlife and domestic animals.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8938},
pmid = {41062486},
issn = {2041-1723},
mesh = {Animals ; *Sus scrofa/virology ; *Animals, Wild/virology ; Swine/virology ; *Animals, Domestic/virology ; China/epidemiology ; Disease Reservoirs/virology ; Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation &amp; purification ; *Swine Diseases/virology ; Zoonoses/virology ; Phylogeny ; },
abstract = {Wild boars are considered pest animals in most of their distribution ranges, but their role as virus reservoirs has long been overlooked, with the circulation dynamics of their viruses rarely investigated. Here we prepared a data set, that is, BrCN-Virome, of 9281 viral metagenomes by pan-viromic analyses of 2535 organ and 274 blood samples from 466 healthy and 50 dead wild boars across 127 locations in 26 provincial regions of China. Compared to domestic pigs, BrCN-Virome shows different viromic composition, with a great expansion in the DNA virus diversity. Some wild boar viruses are traced to humans, domestic animals, wildlife, and arthropods, with several evidently or potentially related to epizootics or zoonoses. Pig pathogens spread widely in wild boars and are responsible for a substantial portion of wild boar mortality, with occurrences of co-infection with multiple African swine fever viruses. These results indicate that wild boars are a node animal connecting different animal taxa in the virus circulation network, and that their viruses not only pose a major threat to the pig industry but also challenge wildlife conservation and public health, highlighting the need for routine surveillance of wild boar viruses and active control of the wild boar population.},
}
@article {pmid41062001,
year = {2025},
author = {Ghaffar, T and Valeriani, F and Romano Spica, V},
title = {The sex related differences in health and Disease: A systematic review of sex-specific gut microbiota and Possible implications for microbial pathogenesis.},
journal = {Microbial pathogenesis},
volume = {209},
number = {},
pages = {108094},
doi = {10.1016/j.micpath.2025.108094},
pmid = {41062001},
issn = {1096-1208},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Female ; Male ; Sex Factors ; Mice ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; Sex Characteristics ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: The gut microbiota, a complex ecosystem influenced by various physiological and environmental factors, has been increasingly recognized for its role in health and disease. Emerging evidence suggests that sex differences, particularly mediated by sex hormones and physiological variations, significantly influence the composition and diversity of the gut microbiome. This systematic review aimed to evaluate and synthesize the current knowledge on sex-related variations in gut microbiota across human and animal studies.<br><br>METHODS: We conducted a systematic review of 24 eligible studies, selected from an initial 13,205 articles, focusing on healthy populations and next-generation sequencing-based microbiota profiling in both humans and animal models.<br><br>RESULTS: The results reveal sex-specific differences in microbial diversity and taxa abundance; however, the consistency and significance of these findings vary across studies, with females generally exhibiting higher levels of Akkermansia and Bifidobacterium, while males showed increased levels of Prevotella and Escherichia. These findings suggest that sex may be a contributing, but not necessarily dominant, biological variable shaping microbiome architecture across various species, including mice, pigs, deer, and humans, and highlight the influence of hormonal fluctuations, body composition, and lifestyle factors on gut microbial ecosystems.<br><br>CONCLUSION: Our findings underscore the importance of considering sex as a key biological variable in microbiome research and its potential implications for disease susceptibility, therapeutic interventions, and microbiome-targeted strategies in microbial pathogenesis. Moreover, evidence from human studies remains limited, especially those using 16S rRNA gene sequencing, which may lack the resolution to detect strain-level or functional differences. Incorporating multi-omics approaches such as metagenomics, metatranscriptomics, and metabolomics may offer deeper insights into sex-dependent microbial dynamics.However, these implications remain largely associative and require mechanistic validation in future studies.},
}
@article {pmid41061488,
year = {2026},
author = {Yang, M and Huang, Y and Liu, J and Wang, G and Mei, Y and Ge, L and Du, Q and Li, H and Zhao, N},
title = {Characterisation of microbial succession and exploration of the stability maintenance strategy of phage community on microbes in radish paocai.},
journal = {International journal of food microbiology},
volume = {444},
number = {},
pages = {111479},
doi = {10.1016/j.ijfoodmicro.2025.111479},
pmid = {41061488},
issn = {1879-3460},
mesh = {*Raphanus/microbiology/virology ; Fermentation ; *Bacteriophages/genetics/physiology/isolation &amp; purification/classification ; *Bacteria/virology/genetics/classification/isolation &amp; purification ; Food Microbiology ; Fermented Foods/microbiology/virology ; Fungi/isolation &amp; purification/genetics/classification/virology ; Microbiota ; },
abstract = {Previous research focused on the safety control of phages in food. In recent years, numerous phages have been extensively characterised in fermented foods, where they change along with fermentation process but do not compromise product quality. However, the potential roles of phages in fermented foods remain unclear. Microbial steady state is critical for maintaining normal radish paocai fermentation. To explore stability maintenance strategies for phages, their structure and interactions with microbes were investigated across two microbial structural systems during fermentation. Microbial counts showed the absence of fungi in the non-steady-state environment (NE), whereas high fungal levels (6.78 ± 0.09 log colony-forming units/mL) were detected in the steady-state environment (SE). Metagenomic analysis revealed that microbial structure remained stable in SE but changed markedly in NE. Pediococcus ethanolidurans and Lactococcus lactis were the species that differed significantly between SE and NE. Microbial succession exhibited a significant association with physicochemical environments in NE (P < 0.05), whereas microbial abundance fluctuations were unaffected by physicochemical stress in SE. Caudoviricetes was identified as the dominant viral class. Cluster analysis showed that NE systems displayed high variability with dramatic shifts across multiple viral genera (Clusters 3-6). In NE, 25 lytic and 226 lysogenic phages were identified, while 3 lytic and 29 lysogenic phages were found in SE. Phage host prediction indicated preferential targeting of harmful bacteria (e.g., Escherichia) in NE, contrasted with phage predation on fermentation-associated lactic acid bacteria in SE. Genomic analysis indicated that Lactiplantibacillus abundance and its corresponding phages remained stable in SE but increased sharply in NE on day 3. Lactiplantibacillus phages isolated from NE and SE displayed strict host specificity at the strain level and exhibited potent lytic activity across different fermented food matrices. This study advances our understanding of steady-state maintenance mechanisms in vegetable fermentation systems and offers new insight for cross-system phage applications.},
}
@article {pmid41060313,
year = {2025},
author = {Hays, MD and Fuchsman, CA},
title = {SAR11 ecotypes across ocean basins change with depth due to changes in light and oxygen.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {41060313},
issn = {1751-7370},
support = {R36 DP002021/DP/NCCDPHP CDC HHS/United States ; //Horn Point Laboratory/ ; },
mesh = {*Ecotype ; *Seawater/microbiology/chemistry ; Phylogeny ; Oceans and Seas ; *Light ; *Oxygen/metabolism ; *Bacteria/classification/genetics ; Phytoplankton ; Cyanobacteria ; },
abstract = {SAR11 bacteria are ubiquitous and abundant heterotrophs that are important mediators of marine biogeochemical cycles. Within the SAR11 clade smaller ecotypes inhabit different ecological niches. Using metagenomic read placement onto a phylogenetic tree of RNA polymerase (rpoB), we were able to determine the distribution of different ecotypes both geographically and by depth. Our method avoids biases from the absence of quality sequenced genomes for deep SAR11 ecotypes. Depth profiles that range from the surface to the bathypelagic were analyzed at 30 stations in six ocean basins. In the euphotic zone, changes in the dominant primary producer from eukaryotic algae to cyanobacteria, did not cause the abundance of SAR11 to shift between stations. However, specific SAR11 ecotypes did correlate with eukaryotic phytoplankton (1a.3 and 1a.4) or picocyanobacteria (1b.2, 1b.4, and IIaB). In the lower euphotic and mesopelagic zones, group IIb.x was overwhelmingly the dominant species but group 1c was also present, and we found several new deep subecotypes of 1b. The shift between the surface SAR11 community, dominated by 1a and surface 1b subecotypes, and the mesopelagic ecotype groups, corresponded to the maximum decrease in the light-dependent proteorhodopsin/rpoB ratio, indicating that many deep ecotypes did not possess proteorhodopsin. This ecotype switch repeatedly corresponded to the maximum in Low Light I Prochlorococcus, leading to the hypothesis that changes in light motivates the ecotype switch. Environmentally abiotic factors like light and temperature appear to be determining factors in the SAR11 ecotype distribution throughout the global oceans.},
}
@article {pmid41060304,
year = {2025},
author = {Bueno de Mesquita, CP and Olm, MR and Bissett, A and Fierer, N},
title = {High strain-level diversity of Bradyrhizobium across Australian soils.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {41060304},
issn = {1751-7370},
support = {//Bioplatforms Australia and the Integrated Marine Observing System/ ; //Australian Government's National Collaborative Research Infrastructure Strategy/ ; //Australian Government/ ; //BHP/ ; //CSIRO/ ; //Novo Nordisk Foundation/ ; //U.S. National Science Foundation/ ; //U.S. Army Research Office/ ; },
mesh = {*Bradyrhizobium/genetics/classification/isolation &amp; purification ; *Soil Microbiology ; Australia ; Phylogeny ; Metagenomics ; Genome, Bacterial ; Metagenome ; *Genetic Variation ; Soil/chemistry ; *Biodiversity ; },
abstract = {Global surveys of soil bacteria have identified several taxa that are nearly ubiquitous and often the most abundant members of soil bacterial communities. However, it remains unclear why these taxa are so abundant and prevalent across a wide range of soil types and environmental conditions. Here, we use genome-resolved metagenomics to test the hypothesis that strain-level differences exist in these taxa that are not adequately captured with standard marker gene sequencing, and that distinct strains harbor unique traits that reflect adaptations to different soil environments. We analyzed data from 331 natural soils spanning Australia to assess strain differentiation in Bradyrhizobium, a dominant soil bacterial genus of ecological importance. We developed a workflow for strain-level bacterial analyses of complex soil metagenomes, combining genomes from pre-existing databases with new genomes generated via targeted assembly from metagenomes to detect 181 Bradyrhizobium strains across the soil collection. In addition to a high degree of phylogenetic variation, we observed substantial variation in pangenome content and inferred traits, highlighting the breadth of diversity within this widespread genus. Although members of the genus Bradyrhizobium were detected in >80% of samples, most individual strains were restricted in their distributions. The overall strain-level community composition of Bradyrhizobium varied significantly across geographic space and environmental gradients, and was particularly associated with differences in temperature, soil pH, and soil nitrate and metal concentrations. Our work provides a general framework for studying the strain-level ecology of soil bacteria and highlights the ecological and pangenomic diversity within this dominant soil bacterial genus.},
}
@article {pmid41059690,
year = {2025},
author = {Venkatachalam, S and Granskog, MA and Gonçalves-Araujo, R and Divine, DV and Vipindas, PV and Jabir, T and Shereef, A and Jain, A},
title = {Distinct bacterial community structures with abundant carbon degradation and sulfur metabolisms found in different sea-ice types from the Central Arctic Ocean.},
journal = {Microbiology spectrum},
volume = {13},
number = {11},
pages = {e0129125},
pmid = {41059690},
issn = {2165-0497},
support = {PACER//National Centre for Polar and Ocean Research, Ministry of Earth Sciences/ ; SUDARCO//Norsk Polarinstitutt/ ; No. 4251-00058B//Denmark Research Fund/ ; },
mesh = {Arctic Regions ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Ice Cover/microbiology ; *Sulfur/metabolism ; *Carbon/metabolism ; *Seawater/microbiology ; *Microbiota ; Phylogeny ; Biodiversity ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Oceans and Seas ; },
abstract = {The rapid decline of sea ice in the relatively understudied Central Arctic Ocean has a significant impact on bacterial biodiversity and the ecological functions they support. We investigated the bacterial community composition and the associated metabolic functions from three geographically distinct sea-ice floes: first-year ice (FYI) at the North Pole and western Nansen Basin and second-year or multi-year ice (SYI/MYI) in the western Amundsen Basin. We resolved the sea-ice bacterial community diversity at species-level precision using a long-read amplicon (n = 18) and metagenomic (n = 3) sequencing approach. The amplicon sequencing highlighted marked differences in bacterial community structure driven by ice age, floe origin, and environmental factors, demonstrating pronounced vertical structuring among ice horizons. Bacterial taxa like Paraglaciecola psychrophila, Hydrogenophaga crassostreae, Octadecabacter arcticus, and Polaribacter irgensii mainly dominated the bottom layers of SYI/MYI, whereas species Actimicrobium antarcticum, Polaromonas cryoconiti, O. antarcticus, and Rhodoferax sp. dominated the FYI. Similarly, notable taxonomic differences were observed in bacterial taxa inhabiting the surface and interior layers of FYI and SYI/MYI (e.g., F. frigoris and Hydrogenophaga sp.). The metagenomic analysis showed the prevalence of sulfur cycling-associated (assimilatory and dissimilatory sulfur metabolism) and complex carbon degradation processes in sea ice. We also elucidated the potential ecological role of novel metagenome-assembled genomes belonging to the genus Aquiluna through phylogenomic and pangenomic analyses. Overall, our findings revealed novel insights on the distinct bacterial communities that inhabit ice horizons and their associated ecological functions correlating with sea-ice type, origin, and habitat characteristics in the Central Arctic Ocean.IMPORTANCEThe Arctic region is warming nearly four times faster than the global average, leading to the continuous replacement of its thick multi-year sea ice with thinner first-year ice. The reduction in Arctic sea-ice cover was previously shown to have cascading effects on sea-ice-associated microbial communities and their role in the functioning of the ecosystem. This study provides the first high-resolution, species-level insight into the bacterial community composition and metabolic potential across different sea-ice types in the Central Arctic Ocean-an understudied yet rapidly changing environment. By combining long-read amplicon and metagenomic sequencing, we uncover distinct bacterial assemblages and functional metabolic roles that were shaped by the ice age and other physicochemical properties. Our findings highlight the ecological importance of sea-ice associated bacterial communities and the prevalence of sulfur metabolism and carbon degradation processes in different sea-ice types found in the central Arctic Ocean through genome-resolved metagenomics.},
}
@article {pmid41059040,
year = {2025},
author = {Zhu, N and Gao, J and Wu, R and Jia, S and Guo, X and Sun, D and Guan, Q},
title = {Metagenomic insights into respiratory viral signatures in lower respiratory tract infections with and without respiratory failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1637352},
pmid = {41059040},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/virology/microbiology/complications ; *Metagenomics ; Male ; Middle Aged ; Female ; Bacteria/classification/genetics/isolation &amp; purification ; *Viruses/classification/genetics/isolation &amp; purification ; *Virome ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Microbiota ; Aged ; *Respiratory Insufficiency/virology/microbiology ; Adult ; },
abstract = {OBJECTIVE: Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality worldwide, with the respiratory microbiome playing a pivotal role in disease pathogenesis. Comprehensive profiling of the lower respiratory tract virome allows investigation of potential differences between LRTIs and non-LRTIs, helps identify virus-associated taxa linked to pulmonary disease, and provides insights into virome-host interactions involved in respiratory health.<br><br>METHODS: In this study, we compared viral and bacterial microbiome characteristics of LRTI patients with non-LRTI controls by &#x3b1;-diversity, &#x3b2;-diversity (PCoA, NMDS, ANOSIM), and differential abundance (LEfSe) analyses using metagenomic sequencing of bronchoalveolar lavage fluids, and further performed these comparisons similarly in respiratory failure (RF) patients and non-RF patients in the LRTI group. In addition, virus-bacteria co-occurrence patterns, the correlations between viral and bacterial abundance profiles, and the associations between microbial features and host clinical indicators were assessed using Spearman correlation analysis.<br><br>RESULTS: Overall, no significant differences in viral and bacterial &#x3b1;- or &#x3b2;-diversity were detected between LRTI (n=39) and non-LRTI (n=9) groups. However, among LRTI patients with RF (n=5), distinct viral taxonomic signatures were observed, including enrichment of Phixviricota, Malgrandaviricetes, Petitvirales, and Microviridae lineages. Despite taxonomic shifts, overall viral diversity remained similar between RF and non-RF subgroups. Bacterial communities showed no notable stratification across clinical categories. Correlation analyses revealed that uncultured human fecal viruses were negatively associated with lymphocyte counts, while Streptococcus-related bacteriophages correlated positively with C-reactive protein (CRP) levels.<br><br>CONCLUSION: The overall composition and diversity of the respiratory microbiome were insufficient to distinguish LRTI from non-LRTI conditions. However, within the LRTI cohort, patients with RF exhibited distinct viral taxonomic profiles compared to non-RF individuals. Additionally, several viral taxa were correlated with host clinical indicators irrespective of clinical subgroup. These findings highlight virome compositional differences associated with RF within LRTI patients, but do not imply causal effects, and warrant further investigation.},
}
@article {pmid41058503,
year = {2025},
author = {Castro, M and Vida, R and Galeano, J and Cuesta, JA},
title = {Scarce data, noisy inferences and overfitting: the hidden flaws in ecological dynamics modelling.},
journal = {Journal of the Royal Society, Interface},
volume = {22},
number = {231},
pages = {20250183},
pmid = {41058503},
issn = {1742-5662},
support = {//Agencia Estatal de Investigaci&#xf3;n/ ; },
mesh = {*Models, Biological ; *Ecosystem ; Bayes Theorem ; *Microbiota ; Humans ; },
abstract = {Metagenomic data has significantly advanced microbiome research by employing ecological models, particularly in personalized medicine. The generalized Lotka-Volterra (gLV) model is commonly used to understand microbial interactions and predict ecosystem dynamics. However, gLV models often fail to capture complex interactions, especially when data are limited or noisy. This study critically assesses the effectiveness of gLV and similar models using Bayesian inference and a model reduction method based on information theory. We found that ecological data often leads to non-interpretability and overfitting due to limited information, noisy data and parameter sloppiness. Our results highlight the need for simpler models that align with the available data and propose a distribution-based approach to better capture ecosystem diversity, stability and competition. These findings challenge current bottom-up ecological modelling practices and aim to shift the focus towards a statistical mechanics view of ecology based on distributions of parameters.},
}
@article {pmid41058431,
year = {2025},
author = {Jiménez-Arroyo, C and Molinero, N and Del Campo, R and Delgado, S and Moreno-Arribas, MV},
title = {Human gut microbiome study through metagenomics: Recent advances and challenges for clinical implementation.},
journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)},
volume = {43},
number = {10},
pages = {698-708},
doi = {10.1016/j.eimce.2025.09.011},
pmid = {41058431},
issn = {2529-993X},
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Artificial Intelligence ; },
abstract = {Metagenomics has decisively advanced the study of the gut microbiome, enabling a better understanding of its importance for human health. Metataxonomics, based on the sequencing of the 16S rRNA gene, provides taxonomic profiles of prokaryotes, while shotgun metagenomics allows a comprehensive characterization of all DNA present in a sample. With adequate sequencing depth, the latter increases taxonomic resolution to the strain level and provides detailed information on the functional potential of the microbiota. However, the lack of standardization in sample collection and processing, sequencing technologies, and data management limits the comparability of results and their implementation in clinical laboratories. This review offers a practical and updated framework on metagenomic methodologies, data analysis, and the application of artificial intelligence tools, highlighting advances and best practices to facilitate the integration of functional microbiome analysis into clinical practice and to overcome current challenges.},
}
@article {pmid41056245,
year = {2025},
author = {Roongpiboonsopit, D and Wairit, S and Nithisathienchai, C and Pakdee, A and Cheibchalard, T and Sayasathid, J and Wilantho, A and Tongsima, S and Somboonna, N},
title = {Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0333676},
pmid = {41056245},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Dysbiosis/microbiology ; *Ischemic Attack, Transient/microbiology ; *Microbiota/genetics ; Middle Aged ; Case-Control Studies ; Aged ; *Ischemic Stroke/microbiology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; *Mouth/microbiology ; },
abstract = {Oral microbiome (bacterial community) may influence systemic inflammation and vascular health, which both are critical factors in a pathogenesis of ischemic stroke. This study aimed to evaluate differences in the saliva microbiome of acute ischemic stroke (AIS) and transient ischemic attack (TIA) patients compared with matched healthy controls, hypothesizing that AIS and TIA patients are associated with oral microbiome shift. A prospective case-control study was conducted in Naresuan University Hospital, Thailand, to compare the saliva microbiome of AIS and TIA stroke patients of Thai ethnic with matched healthy controls. Microbial profiles were analyzed by metagenomics combined 16S rRNA gene sequencing to assess microbial alpha diversity, taxonomic composition, beta diversity, and microbial functional pathways.Forty-one patients (31 AIS and 10 TIA) and 20 age- and sex-matched stroke-free healthy controls were included in this study. Baseline characteristics were comparable between groups, apart from higher rates of hypertension, diabetes, and smoking in the patient group. Patients exhibited significantly higher alpha-diversity genus richness by OTUs and Chao1 index than controls (p < 0.001), highlighting an altered microbial community structure. Phylum-level analysis revealed an increased abundance of Bacillota (p = 0.0285) in the patient group, with a statistically decreasing trend for Bacteroidota, Actinomycetota and Pseudomonadota (p < 0.05). At the genus level, Streptococcus was more significantly abundant in the patients (p = 0.0171), while Prevotella was reduced. The patient and control groups were statistically separated in beta-diversity analysis (PERMANOVA, p < 0.001), with species biomarker analysis by LEfSe (Linear discriminant analysis effect size) could suggest species markers for each group. Functional pathway analysis showed the patient group the significantly higher in functional categories of, for examples, xenobiotics biodegradation and metabolism, cardiovascular diseases, signal transduction, and membrane transport (Welch's t-test, p < 0.05). In conclusion, this study demonstrated the statistical alterations in the saliva microbiome of AIS and TIA patients, characterized by increased genus richness diversity and relatively distinct microbial shifts that may be associated with stroke-related inflammation. The findings suggest the saliva microbiome analysis as potential as a non-invasive biomarker for stroke risk and its role in stroke pathophysiology.},
}
@article {pmid41056240,
year = {2025},
author = {Brenner, LN and Huang, CY and Kim, M and Bringhurst, L and Richards, CJ and Sicilian, L and Neuringer, I and Putman, MS and Lai, PS},
title = {Dysglycemia and the airway microbiome in cystic fibrosis.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0331847},
pmid = {41056240},
issn = {1932-6203},
mesh = {Humans ; *Cystic Fibrosis/microbiology/complications ; *Microbiota ; Male ; Female ; Adult ; Sputum/microbiology ; *Diabetes Mellitus/microbiology/etiology ; Glucose Tolerance Test ; Young Adult ; Lung/microbiology ; Respiratory Function Tests ; Pseudomonas aeruginosa ; },
abstract = {BACKGROUND: Cystic fibrosis-related diabetes (CFRD) is one of the most common non-pulmonary complications in people living with cystic fibrosis (pwCF), seen in up to 50% of adults. Even when correcting for severity of CFTR mutations, those with CFRD have more pulmonary exacerbations, lower lung function, and increased mortality than those with normal glucose tolerance (NGT).<br><br>METHODS: Expectorated sputum samples were collected from 63 pwCF during routine outpatient visits (29 with CFRD, 12 with IGT and 22 with NGT). Oral glucose tolerance test results, A1c levels, and pulmonary function tests closest to the time of sputum collection were obtained from the medical record. Samples underwent metagenomics sequencing and raw reads were processed through the bioBakery workflow for taxonomic profiling at the species level as well as predicted functional profiling and antibiotic resistance profiling. Viral profiling was performed with Marker-MAGu. Differences in alpha diversity, beta diversity, and differential abundance were assessed. Microbiome and phage signatures of CFRD were generated using sparse partial least squares models which were subsequently used as a primary predictor of lung function using multivariate linear regression.<br><br>RESULTS: In linear models, CFRD status compared to NGT was associated with a lower alpha diversity (reciprocal Simpson -1.98 [-3.80,-0.16], p&#x2009;=&#x2009;0.033) and differences in microbial community composition (Bray Curtis dissimilarity PERMANOVA R2 0.17, p&#x2009;=&#x2009;0.011). Pseudomonas aeruginosa and Streptococcus gordonii had higher relative abundance in CRFD vs NGT participants (2.43 [0.027, 4.82], unadjusted p&#x2009;=&#x2009;0.056 and 1.11 [0.58, 1.64] unadjusted p=&#x2009;<&#x2009;.001 respectively). There were global differences between CFRD vs NGT in both functional pathways and antibiotic resistance genes. In multivariate models adjusting for age, sex, antibiotic use, and modulator therapies, virome but not microbiome signatures of CFRD were associated with lower FEV1 percent predicted (-6.4 [95% CI -10.2, -2.6]%, p&#x2009;=&#x2009;0.001 for each 10% increase in virome score).<br><br>CONCLUSION: Differences in the airway microbiome in those with dysglycemia in CF are associated with poorer lung function.},
}
@article {pmid41055380,
year = {2025},
author = {Du, J-Y and Zhang, Z-J and Tan, L and Yang, J-Y and Yang, R-N and Chen, Y-L and Tan, G-F and Li, J and Li, W-J and Yang, L and Cai, J and Shen, D-L and Zhu, H-R and Fan, Z-X and Yuan, M-L and Zhang, W},
title = {Gut microbiota dysbiosis and metabolic perturbations of bile/glyceric acids in major depressive disorder with IBS comorbidity.},
journal = {mBio},
volume = {16},
number = {11},
pages = {e0244725},
pmid = {41055380},
issn = {2150-7511},
support = {ZYJC21004//1.3.5 project for disciplines of excellence/ ; 82401769//National Natural Science Foundation of China/ ; 2025ZNSFSC//Department of Science and Technology of Sichuan Province/ ; 2023NSFSC1935//Sichuan science and technology program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Irritable Bowel Syndrome/microbiology/complications/metabolism/epidemiology ; *Dysbiosis/microbiology ; Female ; Male ; Adult ; *Major Depressive Disorder/microbiology/complications/metabolism/epidemiology ; *Bile Acids and Salts/metabolism ; Middle Aged ; Feces/microbiology ; Metagenomics ; Comorbidity ; Metabolomics ; },
abstract = {Major depressive disorder (MDD) and irritable bowel syndrome (IBS) exhibit high comorbidity, yet their shared pathophysiology remains unclear. Previous studies have primarily focused on the psychological health in the IBS population, without considering psychiatric diagnoses or stratifying different psychological states, potentially leading to biased findings. This study employed multi-omics approaches to characterize gut microbiota and serum metabolites in 120 MDD patients (47 with IBS and 73 without IBS) and 70 healthy controls (HCs). MDD with IBS patients showed significantly higher depression (Hamilton depression scale [HAMD-17]) and anxiety (Hamilton anxiety scale [HAMA-14]) scores than MDD-only patients (P < 0.05). Metagenomic sequencing of fecal samples revealed increased alpha diversity (Chao1/Shannon indices) and Firmicutes dominance in both MDD groups vs HC, while Actinobacteria enrichment specifically marked MDD with IBS. Functionally, MDD with IBS uniquely activated D-amino acid/glycerolipid metabolism pathways (Kyoto Encyclopedia of Genes and Genomes). Serum metabolomics identified comorbid-specific perturbations: downregulation of bile acids (CDCA, GCDCA, GCDCA-3S) and upregulation of glyceric acid/glutaconic acid. Our study also found that Eggerthella lenta and Clostridium scindens are differentially abundant bacteria that are involved in bile acid metabolism, and that microbial genes (e.g., K03738) are associated with glyceric acid production. These findings implicate gut microbiota-driven bile acid/glyceric acid dysregulation in MDD with IBS comorbidity, supporting the gut-brain axis as a therapeutic target for probiotics or microbiota transplantation.IMPORTANCEMajor depressive disorder (MDD) exhibits a high comorbidity rate with irritable bowel syndrome (IBS). Our study, conducted on 120 MDD patients (47 of whom were comorbid with IBS) and a control group of 70 individuals, revealed that MDD-IBS comorbid patients demonstrated significantly higher depression/anxiety scores. Multi-omics analysis indicated substantial alterations in the gut microbiota (e.g., Firmicutes, Actinobacteria) and serum metabolites (e.g., bile acids, glyceric acid) among MDD-IBS patients, which were associated with specific metabolic pathways. Therefore, the new aspect of this study was the inclusion of patients with MDD but without IBS symptoms, which provided a deeper understanding of the intestinal microbiota dysregulation associated with comorbid IBS and MDD. These findings suggest that there may be involvement of the gut-brain axis, providing new research directions for potential therapeutic targets.CLINICAL TRIALSThis study is registered with the Chinese Clinial Trial Registry as ChiCTR2100041598.},
}
@article {pmid41055333,
year = {2025},
author = {Sharma, S and Narahari, HP and Raman, K},
title = {Harnessing machine learning for metagenomic data analysis: trends and applications.},
journal = {mSystems},
volume = {10},
number = {11},
pages = {e0164224},
pmid = {41055333},
issn = {2379-5077},
mesh = {*Metagenomics/methods ; *Machine Learning ; Microbiota/genetics ; Humans ; Metagenome ; },
abstract = {Metagenomic sequencing has revolutionized our understanding of microbial ecosystems by enabling high-resolution profiling of microbes across diverse environments. However, the resulting data are high-dimensional, sparse, and noisy, posing challenges for downstream data analysis. Machine learning (ML) has provided an arsenal of tools to extract meaningful insights from such large and complex data sets. This review surveys the existing state of ML applications in metagenomic data analysis, from traditional supervised and unsupervised learning to time-series modeling, transfer learning, and newer directions such as causal ML and generative models. We highlight certain key challenges and delve into important issues like model interpretability, emphasizing the importance of explainable AI (XAI). We also compare ML with mechanistic models, commenting on their relative advantages, disadvantages, and prospects for synergy. Finally, we preview future directions, such as the incorporation of multi-omics data, synthetic data generation, and Agentic AI systems, highlighting the increasingly prominent role that AI and ML will play in the future of microbiome science.},
}
@article {pmid41053318,
year = {2025},
author = {Vitry, G and Angdisen, J and Sawant, MA and Arriaga, P and Irgen-Gioro, S and Peshette, P and Vuong, DC and Ilhardt, P and Fehr, J and Cwikla, B and Ponnaiya, B and Inman, JL and Snijders, AM and Hamid, S and Caballero-Lima, D and Garty, G and Apfeldorf, K and Laiakis, EC},
title = {Using a full thickness bioengineered human skin equivalent as a model for radiation biology research.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34702},
pmid = {41053318},
issn = {2045-2322},
support = {P30 CA051008/CA/NCI NIH HHS/United States ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; },
mesh = {Humans ; *Skin/radiation effects/microbiology/metabolism ; Animals ; Mice ; Microbiota/radiation effects ; Bioengineering ; Cell Proliferation/radiation effects ; Dose-Response Relationship, Radiation ; },
abstract = {Radiation exposure from radiological or nuclear events, medical treatments, or spaceflight poses significant health risks, yet human-specific models to investigate radiation effects on skin remain limited. This study establishes a novel in vitro platform using a full-thickness bioengineered human skin equivalent colonized with natural mixed human microbiota (coHSEs) to assess radiation-induced biological responses. We exposed coHSEs to acute doses of up to 4 Gy with x-rays and evaluated their viability, structural integrity, and molecular responses over 25 days. The coHSE model demonstrated sustained viability without dose-dependent opportunistic microbial overgrowth when procedural optimizations were applied. Radiation-induced epidermal remodeling did not compromise tissue architecture or swabbing-based sample collection. Cell proliferation analyses revealed dose- and time-dependent dynamics, with consistent dermal cell density maintained across radiation doses. Comparative multi-omic analyses, including untargeted metabolomics, targeted lipidomics, and 16 S metagenomics, revealed conserved metabolic and microbial responses to radiation in both coHSEs and skin from irradiated mice. Enriched pathways such as arachidonic acid and fatty acid metabolism, along with shifts in microbial taxa including Lachnospiraceae, support the translational relevance of the coHSE model. This system offers a scalable, ethical, and physiologically relevant platform for radiation biology, biodosimetry, and therapeutic development, advancing terrestrial health research with promising application for space research.},
}
@article {pmid41052982,
year = {2025},
author = {Cao, Y and Fan, X and Zang, T and Qiu, T and Fang, Q and Bai, J and Liu, Y},
title = {Prenatal depression-associated gut microbiota induces depressive-like behaviors and hippocampal neuroinflammation in germ-free mice.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {383},
pmid = {41052982},
issn = {2158-3188},
support = {2023AFB710//Natural Science Foundation of Hebei Province (Hebei Provincial Natural Science Foundation)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Hippocampus/metabolism/pathology/immunology ; Mice ; Pregnancy ; Fecal Microbiota Transplantation ; *Depression/microbiology/metabolism ; *Dysbiosis/microbiology/complications ; Humans ; Lipopolysaccharides/blood ; Germ-Free Life ; *Neuroinflammatory Diseases/metabolism/microbiology ; Microglia ; *Pregnancy Complications/microbiology ; Disease Models, Animal ; Behavior, Animal ; Interleukin-6/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {Numerous studies have described the role of the microbiome-gut-brain axis in depression. However, the molecular mechanisms underlying the involvement of gut microbiota in the development of prenatal depression are limited. In this study, fecal microbiota from women with prenatal depression was transplanted into germ-free mice to investigate the potential causal relationships between the gut microbiota and depressive phenotypes. Shotgun metagenomic sequencing and untargeted metabolomics approaches were used to investigate the characteristics of gut microbiota and microbial metabolites. The levels of neuroinflammation in the brain were detected using immunofluorescence and real-time quantitative PCR. We found significant changes in gut microbiota composition and metabolites in mice with fecal microbiota transplantation (FMT) from women with prenatal depression, including decreased Ligilactobacillus, increased Akkermansia, and abnormal glycerophospholipid metabolism. Besides, significant increase in plasma lipopolysaccharide (LPS) levels and significant proliferation of microglia in the hippocampus were observed in mice receiving FMT from women with prenatal depression, accompanied by a significant increase in the expression of nuclear factor-κB (NF-κB) p65, tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) mRNA. The gut microbiota and its metabolites were strongly associated with depressive-like behaviors, plasma LPS and neuroinflammation. Our study collectively demonstrates that dysbiosis of the gut microbiota may play a causal relationship in the development of prenatal depression. This process potentially involves the activation of neuroinflammation through the LPS-NF-κB signaling pathway.},
}
@article {pmid41052412,
year = {2026},
author = {Dias, ME and Breyer, GM and Torres, MC and Wuaden, CR and Rebelatto, R and Kich, JD and Dorn, M and Siqueira, FM},
title = {Overview of the microbiome and resistome of swine manure in commercial piglet farms and its application in grazing soils.},
journal = {Environmental technology},
volume = {47},
number = {1},
pages = {136-146},
doi = {10.1080/09593330.2025.2566429},
pmid = {41052412},
issn = {1479-487X},
mesh = {Animals ; *Manure/microbiology ; Swine ; *Soil Microbiology ; *Microbiota ; Farms ; Brazil ; Bacteria/genetics ; Fertilizers ; Agriculture ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Soil/chemistry ; },
abstract = {The environmental spread of antimicrobial resistance genes (ARGs) through the use of animal manure in agriculture has become a significant concern. This study investigated the impact of applying swine manure treated through biodigestion on the spread of ARGs in agricultural soils in the Midwest region of Brazil. Samples of untreated and treated manure, fertilized soil, and unfertilized soil were collected from three piglet production units. Bacterial communities and ARGs were characterized through metagenomic sequencing and bioinformatics. Bacterial profiles in fertilized and unfertilized soils were highly similar across all farms. In contrast, biodigestion reduced the total number of ARGs in treated manure. Of the 399 ARGs detected in fertilized soils, 67% were also found in unfertilized soils, and 12% were shared exclusively with treated manure. The presence of numerous ARGs in unfertilized soils highlights the role of environmental dissemination routes, such as runoff, dust, or wildlife, in shaping soil resistomes even in areas without manure application. These findings suggest a stable bacterial and resistome profile in soils, regardless of manure application. Although antimicrobial residues were not evaluated, the results reinforce the need for responsible antibiotic use and effective manure management to minimize environmental ARG dissemination.},
}
@article {pmid41052332,
year = {2025},
author = {Ni, G and Wang, M and Walker, N and Muetzel, S and Schmidt, O and Fischer, A and Stemmler, RT and Leung, PM and Zhang, X and Li, Q and Jain, S and Jespersen, M and Grinter, R and Archer, SDJ and Pacheco, D and Lowe, K and Pope, PB and Müller, V and Pitta, DW and Janssen, PH and Watson, M and Attwood, GT and Ver Loren van Themaat, E and Kindermann, M and Greening, C},
title = {Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {41},
pages = {e2514823122},
pmid = {41052332},
issn = {1091-6490},
support = {APP1178715//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Animals ; *Methane/metabolism/biosynthesis ; *Fermentation/drug effects ; *Rumen/microbiology/metabolism ; Cattle ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Animal Feed ; *Ruminants/microbiology/metabolism ; Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; },
abstract = {Rumen microbiota enable ruminants to grow on fibrous plant materials, but also produce methane, driving 5% of global greenhouse gas emissions and leading to a loss of gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropanol (3-NOP) decrease methane emissions in ruminants when supplemented in feed. Yet we lack a system-wide, species-resolved understanding of how the rumen microbiota remodels following inhibition and how this influences animal production. Here, we conducted a large-scale trial with 51 dairy calves to analyze microbiota responses to 3-NOP, pairing host performance, emissions, and nutritional profiles with genome-resolved metagenomic and metatranscriptomic data. 3-NOP supplementation decreased methane emissions by 62%, modulated short-chain fatty acid and H2 levels, and did not affect dietary intake or animal performance. We created a rumen microbial genome catalogue (27,884 genomes) that mapped to the meta-omic data at high rates. There was a strong reduction of methanogens and stimulation of reductive acetogens, primarily uncultivated lineages such as "Candidatus Faecousia." However, there was a shift in major fermentative communities away from acetate production in response to hydrogen gas accumulation. In vitro incubations recapitulated these results and showed an enrichment of acetate from reductive acetogenesis. Altogether, the divergent responses of the fermentative and hydrogenotrophic communities lead to net hydrogen build-up and limit potential productivity gains from methane reduction. By linking ruminant greenhouse gas emissions and productivity to specific microbial species, this study emphasizes the importance of microbiota-wide analysis for optimizing methane mitigation strategies and identifies promising strategies to simultaneously reduce emissions while increasing animal production.},
}
@article {pmid41050761,
year = {2025},
author = {Zhou, X and Yang, C and Liu, X and Wang, J and Li, Y and Pan, L and Peng, S and Yu, H and Deng, X},
title = {Clinical performance of metagenomic next-generation sequencing for distinction and diagnosis of Mucorales infection and colonization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1631960},
pmid = {41050761},
issn = {2235-2988},
mesh = {Humans ; *Mucormycosis/diagnosis/microbiology/drug therapy ; *Mucorales/genetics/isolation &amp; purification/classification ; Male ; Female ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; Adult ; ROC Curve ; Antifungal Agents/therapeutic use ; Microbiota ; },
abstract = {Mucormycosis is a lethal fungal infection disease with high mortality rate. However, investigations assessing the value of metagenomic next-generation sequencing (mNGS) for distinguishing Mucorales infection from colonization are currently insufficient. A retrospective analysis of clinical date from 71 patients at Sichuan Provincial People's Hospital from September 2021 to September 2024 was conducted. The performance of mNGS in distinguishing Mucorales infection from colonization, along with the differences in patients' characteristics, imaging characteristics, antimicrobial adjustment, and microbiota, were examined. Among the 71 patients, 51 were identified as Mucorales infection group (3 proven and 48 probable cases), and 20 were colonization group (possible cases). Receiver operating characteristic (ROC) curve for mNGS indicated an area under the curve of 0.7662 (95%CI: 0.6564-0.8759), with an optimal threshold value of 51 for discriminating Mucorales infection from colonization. The infection group exhibited a higher proportion of antimicrobial adjustments compared to the colonization group (64.71% vs. 35.00%, P < 0.05), with antifungal agent changed being more dominant (43.14% vs. 10.00%, P < 0.01). Mucorales RPTM value, length of hospital stays, hsCRP, immunocompromised, malignant blood tumor, and antifungal changed were significantly positively correlated with Mucorales infection. Rhizomucor pusillus showed significant differences between the two groups. The abundance of Torque teno virus significantly increased in the infection group, whereas the colonization group exhibited higher abundance of Rhizomucor delemar. mNGS is a valuable tool for differentiating colonization from infection of Mucorales. Malignant blood tumor, immunocompromised, length of hospital stays and hsCRP were significant different indicators between patients with Mucorales infection from colonization.},
}
@article {pmid41050671,
year = {2025},
author = {Duan, H and Xu, B and Luo, P and Chen, T and Zou, J},
title = {Microbial metabolites and their influence on the tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1675677},
pmid = {41050671},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/metabolism/therapy/microbiology ; Animals ; Immunotherapy ; *Microbiota/immunology ; Fatty Acids, Volatile/metabolism ; },
abstract = {While tumor immunotherapy has achieved remarkable progress in many hematological malignancies, its efficacy remains limited by key challenges, including the immunosuppressive microenvironment of solid tumors, metabolic abnormalities, and drug resistance. As a central mechanism underlying impaired immune function, metabolic reprogramming of immune cells has emerged as a pivotal focus for unraveling tumor immune evasion and therapeutic resistance. Advances in metagenomics have highlighted the significance of the human commensal microbiome as a 'second genome.' Microbial metabolites, whether circulating systemically or accumulating locally, serve as key messengers linking the microbiota to tumor immunometabolism. This review comprehensively examines the regulatory roles and metabolic mechanisms through which microbial metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, and lipopolysaccharides (LPS)-modulate tumor immunity and immunotherapeutic responses via immune cell metabolism. These metabolites shape the tumor immune microenvironment and influence immunotherapeutic efficacy by reprogramming immune cell metabolic and biosynthetic pathways. This review underscores the central regulatory role of microbial metabolites as the 'second genome' in tumor immunometabolism, offering a theoretical foundation and potential targets to elucidate mechanisms of immunotherapeutic resistance and advance microbiota metabolism-based precision interventions.},
}
@article {pmid41048389,
year = {2025},
author = {Kong, S and Abrams, E and Binik, Y and Cappelli, C and Chu, M and Cornett, T and Culbertson, I and Garcia, E and Henry, J and Lam, K and Lampman, DB and Morenko, G and Rivera, I and Swift, T and Torres, I and Velez, R and Waxman, E and Wessely, S and Yuen, A and Lardner, CK and Weissman, JL},
title = {Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20081},
pmid = {41048389},
issn = {2167-8359},
mesh = {New York City ; *Metagenome ; *Parks, Recreational ; Metagenomics ; Humans ; *Seawater/microbiology ; Microbiota/genetics ; *Water Microbiology ; },
abstract = {New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.},
}
@article {pmid41048034,
year = {2025},
author = {Wright, SL and Abdul-Aziz, M and Blaha, GN and Ta, CK and Gancz, A and Ademola-Popoola, IJ and Szécsényi-Nagy, A and Sereno, PC and Weyrich, LS},
title = {Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70054},
pmid = {41048034},
issn = {1755-0998},
mesh = {*DNA, Ancient/isolation &amp; purification ; *Microbiota/genetics ; Humans ; *Dental Calculus/microbiology ; *Metagenomics/methods ; Archaeology/methods ; *Mouth/microbiology ; *DNA, Bacterial/isolation &amp; purification/genetics ; *Gene Library ; *Specimen Handling/methods ; },
abstract = {Ancient DNA (aDNA) analysis of archaeological dental calculus has provided a wealth of insights into ancient health, demography and lifestyles. However, the workflow for ancient metagenomics is still evolving, raising concerns about reproducibility. Few systematic investigations have examined how DNA extraction methods and library preparation protocols influence ancient oral microbiome recovery, despite evidence from modern populations suggesting that they do. This leaves a gap in our understanding of how wet-lab protocols impact aDNA recovery from dental calculus. In this study, we apply two DNA extraction and two library preparation methods in the aDNA field on dental calculus samples from Hungary and Niger. Samples from each context have similar chronological ages, but differences in their levels of aDNA preservation are notable, providing additional insights into how the efficacy of wet-lab protocols is impacted by sample preservation. Several metrics were employed to assess intra- and inter-sample variability, such as DNA fragment length recovery, GC content, clonality, endogenous content, DNA deamination and microbial composition. Our findings indicate that both DNA extraction and library preparation protocols can considerably impact ancient DNA recovery from archaeological dental calculus. Furthermore, no single protocol consistently outperformed the others across all assessments, and the effectiveness of specific protocol combinations depended on the preservation of the sample. These findings highlight the challenges of meta-analyses and underscore the need to account for technical variability. Lastly, our study raises the question of whether the field should strive to standardise methods for comparability or optimise protocols based on sample preservation and specific research objectives.},
}
@article {pmid41044998,
year = {2025},
author = {Modin, O and Zheng, D and Schnürer, A and Lundwall, T and Bolanos, SE and Olsson, J},
title = {From Low-Loaded Mesophilic to High-Loaded Thermophilic Anaerobic Digestion: Changes in Reactor Performance and Microbiome.},
journal = {Microbial biotechnology},
volume = {18},
number = {10},
pages = {e70238},
pmid = {41044998},
issn = {1751-7915},
support = {//K&#xe4;ppalaf&#xf6;rbundet/ ; //The Swedish Research Council (VR)/ ; },
mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *Sewage/microbiology ; Methane/metabolism ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Temperature ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; },
abstract = {This study investigated temporal dynamics in reactor performance and microbial community structure during anaerobic digestion of sewage sludge when the temperature was changed from 37°C to 55°C, followed by an increase in organic loading rate (OLR). Performance instability was observed immediately following the temperature increase and in the end of the study when the OLR was 11.1 ± 0.3 kgVS m[-3]d[-1]. The specific methane production peaked at 0.31 ± 0.06 Nm[3] kg[-1] volatile solids (VS) during thermophilic operation and when the OLR was 3.5 ± 0.9 kgVS m[-3]d[-1]. Using metagenomic sequencing, 304 species-representative genome bins (SGB) were assembled. Network analysis revealed that 186 SGB were associated with thermophilic conditions and several new species putatively involved in key reactor functions were identified. When reactor function initially stabilised, two hydrogenotrophic and one aceticlastic methanogen (Methanothermobacter spp. and Methanosarcina thermophila), the hydrolytic Coprothermobacter proteolyticus, and putative syntrophic propionate oxidisers (e.g., Pelotomaculaceae) had high relative abundance. During the peak in specific gas production, the community was dominated by one hydrogenotrophic Methanothermobacter species coexisting with syntrophic acetate oxidising bacteria (Thermacetogenium phaeum and other species). Finally, when the reaction function deteriorated due to high OLR, new hydrolytic taxa emerged and the same aceticlastic methanogen as seen during the initial acclimatisation phase returned.},
}
@article {pmid41044404,
year = {2025},
author = {Rodríguez-Gijón, A and Pacheco-Valenciana, A and Milke, F and Dharamshi, JE and Hampel, JJ and Damashek, J and Wienhausen, G and Rodriguez-R, LM and Garcia, SL},
title = {Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34482},
pmid = {41044404},
issn = {2045-2322},
mesh = {*Fresh Water/microbiology ; Metagenome ; *Genome, Bacterial ; Genome Size ; Ecosystem ; *Bacteria/genetics/classification ; },
abstract = {Genome size is known to reflect the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to prokaryotic prevalence, relative abundance and co-occurrence. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems. Our study includes 80,561 medium-to-high quality genomes, from which we identified 9,028 species (ANI > 95%) present in a manually curated dataset of 636 freshwater metagenomes. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, network analyses revealed that the most prevalent prokaryotes have streamlined genomes that are found in co-occurrent cohorts potentially sustained by metabolic dependencies. Overall, species in these groups possess a diminished capacity for synthesizing different essential metabolites such as vitamins, amino acids and nucleotides, potentially fostering metabolic complementarities within the community. Moreover, we found the presence of the essential biosynthetic functions to be usage-dependent: nucleotide and amino acids biosynthesis are the most complete, whereas vitamin biosynthesis is most incomplete. Our results underscore genome streamlining as a central eco-evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.},
}
@article {pmid41044010,
year = {2026},
author = {Bleidorn, C and Sandberg, F and Martin, S and Vogler, AP and Podsiadlowski, L},
title = {The untapped potential of short-read sequencing in biodiversity research.},
journal = {Trends in genetics : TIG},
volume = {42},
number = {2},
pages = {137-149},
doi = {10.1016/j.tig.2025.09.001},
pmid = {41044010},
issn = {0168-9525},
mesh = {*Biodiversity ; Phylogeny ; *Genomics/methods ; *Sequence Analysis, DNA/methods ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; Genome ; Animals ; },
abstract = {The power of short-read DNA sequencing in biodiversity research and evolutionary genomics is rapidly growing due to advances in technology and bioinformatics. Short-read sequencing offers powerful solutions for taxonomic identification, biomass estimation, and phylogenetic reconstruction. Moreover, short-read data enable robust estimation of genome size and repeat content, offering valuable insights into genome evolution. Though growing in popularity, long-read genome assemblies are often not feasible with material from museum collections or raw biodiversity samples. With the growing demand for DNA-based approaches in biodiversity research, short-read genomics provides an easily generated universal data source spanning all levels from individual genomes to ecosystems, and including all species on Earth, to achieve the objectives of the Global Biodiversity Framework (GBF) for the preservation of biodiversity.},
}
@article {pmid41043307,
year = {2025},
author = {Ji, Z and Liu, S and Tian, Z and Guo, N and Wei, W and Jiang, Q},
title = {Tooth Loss-Induced Gut Dysbiosis Promotes Neuroinflammation via L-Asparagine-Mediated Neuronal Toxicity.},
journal = {International dental journal},
volume = {75},
number = {6},
pages = {103929},
pmid = {41043307},
issn = {1875-595X},
mesh = {Animals ; *Dysbiosis/etiology/metabolism ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/physiology ; Mice ; *Neuroinflammatory Diseases/etiology/metabolism ; *Tooth Loss/complications ; Male ; *Neurons/drug effects ; Disease Models, Animal ; },
abstract = {INTRODUCTION AND AIMS: Tooth loss is not only a dental issue but also affects gut microbial composition and downstream physiological responses. This study investigates how tooth loss-induced alterations in the gut microbiota influence metabolic and neural function. This study aimed to elucidate the mechanistic links between microbiota dysbiosis, metabolic imbalance, and neuroinflammation following tooth loss.<br><br>METHODS: Using a murine model, the first molars of C57BL/6 mice were extracted, followed by the collection of fecal samples, serum, and brain tissue for subsequent metagenomic sequencing, metabolomics, and transcriptomics. Pro-inflammatory markers (IL-6, TNF-&#x3b1;) and PSD95 expression were assessed. The neurotoxic effects of key metabolite L-Asparagine were validated using HT22 neuronal cell models.<br><br>RESULTS: Tooth loss induced gut microbiota dysbiosis, which subsequently mediated pathological alterations in brain tissue, characterised by a reduction in beneficial Butyribacter and an increase in pathogenic taxa. Corresponding shifts in systemic metabolism were observed, along with changes in brain gene expression, particularly in genes related to neuroinflammation. In vitro experiments further demonstrated that L-Asparagine directly induced neurotoxicity in HT22 hippocampal neurons through ROS overproduction, apoptosis, and inflammatory activation.<br><br>CONCLUSION: Tooth loss induced gut microbiota dysbiosis, systemic metabolic disruptions, and neuroinflammatory responses. Our findings demonstrated that tooth loss exacerbated neuroinflammation via gut-derived L-Asparagine, providing a mechanistic link in the oral-gut-brain axis.<br><br>CLINICAL RELEVANCE: This study demonstrated that molar extraction in mice disrupted gut microbiota and promoted neuroinflammation via L-Asparagine, suggesting that maintaining oral integrity might help preserve neurological health. This could open new avenues for microbiota-targeted interventions in neurodegenerative disease prevention.},
}
@article {pmid41043233,
year = {2025},
author = {Sun, C and Liu, X and Wang, M and Zhang, Q and Geng, H and Ji, X and Wang, H and Li, S and Jin, E and Zhang, F},
title = {Metagenome-metabolome responses to linarin alleviate hepatic inflammatory response, oxidative damage, and apoptosis in an ETEC-challenged weaned piglet model.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119145},
doi = {10.1016/j.ecoenv.2025.119145},
pmid = {41043233},
issn = {1090-2414},
mesh = {Animals ; Swine ; Oxidative Stress/drug effects ; Apoptosis/drug effects ; Enterotoxigenic Escherichia coli/physiology ; Gastrointestinal Microbiome/drug effects ; Liver/drug effects ; *Metabolome/drug effects ; *Metagenome/drug effects ; *Escherichia coli Infections/veterinary/drug therapy ; Inflammation ; Weaning ; },
abstract = {Enterotoxigenic Escherichia coli (ETEC), present in contaminated food, water, and environments, can induce hepatic injury via the gut-liver axis, posing a serious threat to ecological systems and public health. Linarin, a flavonoid extracted from Chrysanthemum indicum, exhibits anti-inflammatory and antioxidant properties, but its protective effects against ETEC-induced hepatic injury remain unclear. In this study, 24 weaned piglets were randomly assigned to four groups: BD+NB (basal diet + nutrient broth), LN+NB (basal diet + 150 mg/kg linarin + nutrient broth), BD+ETEC (basal diet + ETEC challenge), and LN+ETEC (basal diet + 150 mg/kg linarin + ETEC challenge). Dietary linarin significantly increased ADFI and the genes related to oxidative damage and bile acid metabolism, while decreasing F:G ratio, liver index, serum liver function-related parameters, and the genes related to inflammatory response and apoptosis. It also significantly altered the relative abundances of gut microbiota, which were closely associated with key hepatic metabolic pathways, including nicotinate and nicotinamide metabolism and fatty acid biosynthesis. Our study suggests that linarin alleviated ETEC-induced hepatic inflammation and apoptosis, enhanced antioxidant capacity, and regulated bile acid metabolism. The potential mechanism involves linarin modulating gut microbiota-mediated key hepatic metabolic pathways to exert protective effects. In contrast to previous flavonoid-ETEC studies that primarily focused on the gut, this study, based on the gut-liver axis, investigates the potential mechanisms by which linarin is associated with the alleviation of ETEC-induced hepatic injury through integrated analysis of gut microbiome metagenomics and liver metabolomics.},
}
@article {pmid41042593,
year = {2025},
author = {Varliero, G and Bauder, A and Stierli, B and Qi, W and Frey, B},
title = {Host-virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
pmid = {41042593},
issn = {2057-5858},
mesh = {*Ice Cover/microbiology/virology ; *Bacteria/genetics/virology/classification ; *Microbiota/genetics ; *Viruses/genetics/classification/isolation &amp; purification ; Switzerland ; Metagenomics/methods ; Ecosystem ; Host Specificity ; },
abstract = {Glaciers are retreating rapidly, altering ecosystem dynamics and increasing meltwater outflow into populated areas. Understanding microbial-virome interactions is crucial for predicting the consequences of this release. We sampled ice from four shallow pits in the weathering crust of the Rhonegletscher, Swiss Alps, and found a microbiome dominated by bacteria and microeukaryotes, alongside a metavirome infecting both groups. Viruses exhibited variable host specificity, with some targeting particular taxa and others showing a broader infectivity range. Variable genomic regions, including metagenomic and metaviromic islands, were enriched in genes related to replication, recombination, repair and transposable elements. Detected auxiliary metabolic genes were primarily involved in host coenzyme biosynthesis, uptake or utilization and in altering bacterial methylation patterns to evade detection. These findings underscore the major role of viruses in regulating microbial dynamics in glaciers and their potential downstream environmental impacts.},
}
@article {pmid41042396,
year = {2025},
author = {Wu, J and Zhou, J and Zhao, Q and Yang, C and Bai, Y},
title = {Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {212},
pmid = {41042396},
issn = {1432-0614},
support = {32072558//the Nature Science Foundation of China/ ; 2024-620-000-001-007//Hubei Agricultural Science and Technology Innovation Center Innovation Team Project/ ; },
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Soil Microbiology ; Metagenomics ; *Amorphophallus/microbiology ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Fungi/genetics/classification ; },
abstract = {Amorphophallus konjac, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic Rhizopus arrhizus and Rhizopus microsporus were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while Rhizopus spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance. KEY POINTS: • Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria. • Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links. • Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.},
}
@article {pmid41039256,
year = {2025},
author = {Jin, W and Zhang, Y and Su, X and Xie, Z and Wang, R and Wang, Y and Qiu, Y and He, Y},
title = {Effects of different land use on functional genes of soil microbial carbon and phosphorus cycles in the desert steppe zone of the Loess Plateau.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {607},
pmid = {41039256},
issn = {1471-2180},
support = {32072394//National Natural Science Foundation of China/ ; 23ZSCQ030//Gansu Province Intellectual Property Project/ ; 2022-01//Chinese Academy of Sciences regional development projects for young scholars/ ; },
mesh = {*Soil Microbiology ; *Phosphorus/metabolism ; China ; Soil/chemistry ; Grassland ; *Carbon/metabolism ; Desert Climate ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; Microbiota ; Metagenomics ; },
abstract = {Desert grassland ecosystems on China's Loess Plateau are characterized by diverse land use types and varying human disturbances. We aimed to evaluate how land use influences soil microbial communities and functional genes related to carbon (C) and phosphorus (P) cycling. To do this, we selected five representative land use types: natural grassland, 20-year abandoned farmland, 12-year alfalfa grassland, 5-year Lanzhou lily farmland, and 17-year Platycladus orientalis forest. High-throughput metagenomic sequencing and soil physicochemical analyses were conducted. Proteobacteria dominated the nutrient-rich lily soil, while Actinobacteria were more abundant in the other soils. Available phosphorus (AP) had the strongest influence on microbial community structure and gene composition (p < 0.01). The relative abundance of ppdK, rpiB, glpX, and epi (C fixation genes), and purS (purine metabolism) was significantly higher in forest soil than in abandoned farmland (p < 0.05). Similarly, forest soil showed elevated levels of mttB and acs (methanogenesis), sdhA (TCA cycle), pstS (P transport), and pps (pyruvate metabolism) compared to alfalfa soil. Lily soil exhibited significantly higher abundance of acr genes (involved in the hydroxypropionate-hydroxybutylate cycle) and phnE (an ATP-binding cassette transporter) than natural grassland and alfalfa soils (p < 0.05). Microbial networks involved in C and P cycling were simpler but more functionally specialized in forest soil. Positive microbial interactions related to C and P cycling were strongest in lily soil. These findings provide important insights into soil microbial functional adaptation and offer a foundation for sustainable land use management on the Loess Plateau.},
}
@article {pmid41039213,
year = {2025},
author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J},
title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {612},
pmid = {41039213},
issn = {1471-2180},
support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; Larva/microbiology/growth &amp; development ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Metagenome ; *Diptera/microbiology/growth &amp; development ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Diet ; Phylogeny ; Chickens ; },
abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.<br><br>RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.<br><br>CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.},
}
@article {pmid41039197,
year = {2025},
author = {Mpai, T and Diale, MO and Shargie, N and Gerrano, AS and Mtsweni, PN and Bopape, FL and Bairu, M and Hassen, AI},
title = {Functional and taxonomic profiles of soil microbial communities of tropical legume soils from smallholder farmers' fields in Tzaneen, Limpopo province, South Africa.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {601},
pmid = {41039197},
issn = {1471-2180},
support = {PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; },
mesh = {*Soil Microbiology ; South Africa ; *Bacteria/classification/genetics/isolation &amp; purification ; Soil/chemistry ; Metagenomics ; *Microbiota ; *Fabaceae/growth &amp; development/microbiology ; Agriculture ; Farmers ; Biodiversity ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Tropical Climate ; Vigna/growth &amp; development ; },
abstract = {BACKGROUND: Soil microorganisms play a vital role as the major indicators of soil health in sustainable agricultural farming systems. However, intensive cultivation and unrecommended farmers' soil management practices negatively affect the soil microbial communities, and hence that of the soil health. Here, we investigated the functional and taxonomic diversity of soil microorganisms on six selected smallholder farmers that grow Bambara groundnut (Vigna subterranea) and dry bean (Phaseolus vulgaris) in Limpopo Province, South Africa using metagenomics and phenotypic profiles studies. Five soil samples, randomly collected per farm and pooled into a single representative sample were used. Metagenomics raw read quality control, genome assembly and annotation were performed on the KBase platform while the community level physiological profile analysis was done using Biolog Ecoplates™.<br><br>RESULTS: The results indicated that the soil microbial communities in Chosen Generation farm had higher rates of carbon source utilization. Likewise, it showed greater microbial abundance of varying taxonomy in which Actinobacteria, Firmicutes and Proteobacteria were the predominant phyla while Bacillus, Streptomyces, Microvirga and Bradyrhizobium were the most represented genera.<br><br>CONCLUSIONS: This study reports that soils from the six farms studied are enriched with genetically and physiologically diverse microorganisms that are responsible for crop growth. While soil physico-chemical properties can be associated with microbial diversity in this study, further studies on farming practices such as fertilizer and irrigation are recommended to further explore their possible effects on soil microbes.},
}
@article {pmid41038565,
year = {2025},
author = {Habiba, U and Noor, M and Kayani, MUR and Huang, L},
title = {Horizontal gene transfers differentially shape the functional potential of the infant gut metagenome.},
journal = {Life sciences},
volume = {381},
number = {},
pages = {124006},
doi = {10.1016/j.lfs.2025.124006},
pmid = {41038565},
issn = {1879-0631},
mesh = {Humans ; *Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Infant ; Female ; Infant, Newborn ; *Metagenome/genetics ; Cesarean Section ; Male ; Delivery, Obstetric ; Feces/microbiology ; Pregnancy ; },
abstract = {Horizontal gene transfer (HGT) is a major driver of microbial evolution, influencing the metabolic potential of microbial communities. Despite its significance, the consequences of HGT in shaping the microbial metabolic potential remain poorly understood, particularly in complex environments such as the human gut. This study aimed to assess the impact of HGT in infant gut microbiome from Caesarean section (CSD) and vaginal delivery (VD) groups during the first year of life. At Month 0, CSD infants exhibited a higher number of HGT events than VD infants. However, the numbers converged around Month 2 and remained comparable until Month 9, with no significant differences between groups (p > 0.05). HGT in VD was primarily driven by Coprococcus catus and Ruminococcus sp_5_1_39BFAA, while in CSD, Salmonella enterica and Klebsiella pneumoniae were dominant donors and acceptors. Functional analysis revealed that HGT in VD enriched genes related to carbohydrate metabolism and immune responses, whereas CSD was enriched for metabolic processes and biofilm formation. Additionally, HGT events were associated with Neonatal Intensive Care Unit Admission and diet transitions. These results suggest that HGT events in the VD and CSD groups differently shape the functional potential of the infant gut microbiome, with possible health implications that require further investigation. However, experimental validation is needed to establish a causal link.},
}
@article {pmid41037127,
year = {2025},
author = {Arunrat, N and Mhuantong, W and Sereenonchai, S},
title = {Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {102},
pmid = {41037127},
issn = {1432-184X},
support = {MU-SRF-RS-21 B/67//Mahidol University (Strategic Research Fund: 2024)/ ; },
mesh = {*Soil Microbiology ; Thailand ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Soil/chemistry ; *Microbiota ; Nitrogen/metabolism ; Nitrification ; *Agriculture/methods ; Nitrogen Fixation ; Nitrogen Cycle ; },
abstract = {How land-use history-particularly in contrasting systems such as rotational shifting cultivation (RSC) and continuously fallow (CF) fields-influences soil microbial communities and their biogeochemical functions remains insufficiently understood. In this study, shotgun metagenomic sequencing was used to compare the taxonomic composition and functional gene profiles of soils under RSC and CF systems in Northern Thailand. The results revealed distinct microbial assemblages and metabolic potentials shaped by land-use legacy. RSC soils were characterized by a higher abundance of nitrifiers and nitrogen-fixing taxa, including Nitrosocosmicus and Streptomyces, along with enriched genes involved in nitrification (e.g., amoC_B, nxrB) and nitrogen fixation (nifD, nifK), reflecting an enhanced potential for nitrogen acquisition and retention. In contrast, CF soils showed enrichment in Bradyrhizobium, Halobaculum, and Russula, and exhibited higher expression of denitrification-related genes (norB, narJ), suggesting increased nitrogen loss via gaseous emissions. Functional genes related to phosphate metabolism (phoX, glpQ) and nutrient signal transduction were more abundant in RSC soils, indicating active nutrient cycling in response to recent disturbance. Conversely, CF soils demonstrated broader metabolic capabilities, including genes for sulfur oxidation and redox regulation, suggesting microbial adaptation to more stable but nutrient-limited conditions. These findings demonstrate that land-use legacies strongly influence microbial composition and function, with important implications for nutrient cycling and soil fertility restoration in shifting cultivation landscapes.},
}
@article {pmid41036845,
year = {2025},
author = {Du Plessis, I and Snyder, H and Calder, R and Rolando, JL and Kostka, JE and Weitz, JS and Dominguez-Mirazo, M},
title = {Viral community diversity in the rhizosphere of the foundation salt marsh plant Spartina alterniflora.},
journal = {mSphere},
volume = {10},
number = {10},
pages = {e0023425},
pmid = {41036845},
issn = {2379-5042},
mesh = {*Rhizosphere ; *Wetlands ; *Poaceae/virology ; Plant Roots/virology/microbiology ; Soil Microbiology ; *Virome ; *Viruses/classification/genetics/isolation &amp; purification ; Biodiversity ; Metagenome ; },
abstract = {Viruses of microorganisms impact microbial population dynamics, community structure, nutrient cycling, gene transfer, and genomic innovation. In wetlands, root-associated microbial communities mediate key biogeochemical processes important for plants involved in ecosystem maintenance. Nonetheless, the presence and role of microbial viruses in salt marshes remain poorly understood. In this study, we analyzed 24 metagenomes retrieved from the root zone of Spartina alterniflora, a foundation plant in salt marshes of the eastern and Gulf coasts of the U.S. The samples span three plant compartments-bulk sediment, rhizosphere, and root-and two cordgrass plant phenotypes: short and tall. We observed differentiation between phenotypes and increased similarity in viral communities between the root and rhizosphere, indicating that plant compartment and phenotype shape viral community composition. The majority of viral populations characterized are novel at the genus level, with a subset predicted to target microorganisms known to carry out key biogeochemical functions. The findings contribute to ongoing efforts to understand plant-associated viral diversity and community composition and to identify potential targets for exploring viral modulation of microbially mediated ecosystem functioning in intertidal wetlands.IMPORTANCESalt marshes are vital coastal ecosystems. Microbes in these environments drive nutrient cycling and support plant health, with Spartina alterniflora serving as a foundation species. This study explores viral communities associated with S. alterniflora, revealing how plant compartments and phenotypes shape viral composition. The discovery of numerous novel viruses, some potentially influencing microbes involved in key biogeochemical processes, highlights their ecological significance. Given the increasing pressures on coastal ecosystems, understanding virus-microbe-plant interactions is essential for predicting and managing ecosystem responses to environmental change.},
}
@article {pmid41036626,
year = {2025},
author = {Xia, Y and Liang, L and Wang, X and Chen, Z and Liu, J and Yang, Y and Xie, H and Ding, Z and Huang, X and Long, S and Wang, Z and Xu, X and Ding, C and Chen, Q and Feng, Q},
title = {MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis.},
journal = {Nucleic acids research},
volume = {53},
number = {18},
pages = {},
pmid = {41036626},
issn = {1362-4962},
support = {2022YFA1304100//National Key R&amp;D Program of China/ ; 82&#xa0;270&#xa0;980//National Natural Science Foundation of China/ ; 82071122//National Natural Science Foundation of China/ ; 82&#xa0;202&#xa0;539//National Natural Science Foundation of China/ ; 2023ZD0501406//National Science and Technology Major Program/ ; 2019//National Young Scientist Support Foundation/ ; ZR2021JQ29//Excellent Young Scientist Foundation of Shandong Province/ ; 2019//Taishan Young Scientist Project of Shandong Province/ ; 2021GXRC021//Periodontitis innovation team of Jinan City/ ; 2021SFGC0502//Major Innovation Projects in Shandong Province/ ; 2020KJK001//Oral Microbiome Innovation Team of Shandong Province/ ; 2021ZDSYS18//Shandong Province Key Research and Development Program/ ; #202412A001//horizontal cooperation project with Shenzhen 01 Life Institute/ ; #202112E401//horizontal cooperation project with Shenzhen 01 Life Institute/ ; },
mesh = {*Metagenomics/methods ; Workflow ; *Software ; *Metagenome/genetics ; *Microbiota/genetics ; Humans ; },
abstract = {Microbiomes play crucial roles in diverse ecosystems, spanning environmental, agricultural, and human health domains. However, in-depth metagenomic data analysis presents significant technical and resource challenges, particularly at scale. Existing computational pipelines are typically limited to either reference-based or reference-free approaches and exhibit inefficiencies in process large datasets. Here, we introduce MetaflowX (https://github.com/01life/MetaflowX), an open-resource workflow integrating both analytical paradigms for enhanced metagenomic investigations. This modular framework encompasses short-read quality control, rapid microbial profiling, hybrid contig assembly and binning, high-quality metagenome-assembled genome (MAG) identification, as well as bin refinement and reassembly. Benchmarking tests showed that MetaflowX completed full metagenomic analyses up to 14-fold faster and with 38% less disk usage than existing workflows. It also recovered the highest number of high-quality and taxonomically diverse MAGs. A dedicated reassembly module further improved MAG quality, increasing completeness by 5.6% and reducing contamination by 53% on average. Functional annotation modules enable detection of key features, including virulence and antibiotic resistance genes. Designed for extensibility, MetaflowX provides an efficient solution addressing current and emerging demands in large-scale metagenomic research.},
}
@article {pmid41035224,
year = {2025},
author = {Farini, A and Strati, F and Molinaro, M and Mostosi, D and Saccone, S and Tripodi, L and Troisi, J and Landolfi, A and Amoroso, C and Cassani, B and Blanco-Míguez, A and Leonetti, E and Bazzani, D and Bolzan, M and Fortunato, F and Caprioli, F and Facciotti, F and Torrente, Y},
title = {Immunoproteasome Inhibition Positively Impacts the Gut-Muscle Axis in Duchenne Muscular Dystrophy.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {16},
number = {5},
pages = {e70054},
pmid = {41035224},
issn = {2190-6009},
support = {M6/C2_CALL 2022//PNRR/ ; FRRB-2022//Unmet Medical Needs, Fondazione Regionale per la Ricerca Biomedica/ ; GJC21084//Cariplo Telethon Alliance GJC2021-2022/ ; //NextGenerationEU/ ; //MUR/ ; PR-0394//Gruppo familiari beta-sarcoglicanopatie/ ; PNC-E3-2022-23683266-CUP: C43C22001630001//Hub Life Science-Diagnostica Avanzata/ ; //Associazione Centro Dino Ferrari/ ; },
mesh = {Animals ; *Muscular Dystrophy, Duchenne/drug therapy/metabolism/pathology ; Mice ; Gastrointestinal Microbiome/drug effects ; *Proteasome Inhibitors/pharmacology/therapeutic use ; *Muscle, Skeletal/drug effects/metabolism ; Disease Models, Animal ; Mice, Inbred mdx ; Male ; *Proteasome Endopeptidase Complex/metabolism ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Duchenne Muscular Dystrophy (DMD) features immune-muscle crosstalk, where muscle fibre degeneration enhances pro-inflammatory macrophage infiltration, worsening inflammation and impairing regeneration.<br><br>METHODS: We investigated the impact of immunoproteasome (IP) inhibition on the gut-muscle axis in mdx mice, a well-established model of DMD. We employed microbiota perturbation models, including broad-spectrum antibiotic treatment (ABX) and faecal microbiota transplantation (FMT) from IP-inhibited mdx mice. IP inhibition effects were assessed by analysing gut microbiota composition, intestinal inflammation, muscle integrity and associated metabolic and inflammatory pathways.<br><br>RESULTS: IP inhibitor ONX-0914 significantly impacted the intestinal inflammatory microenvironment and gut microbiota of mdx mice. ONX-0914 treatment increased gastrointestinal transit (increased wet/dry faecal weights, p&#x2009;=&#x2009;0.0486 and p&#x2009;=&#x2009;0.0112, respectively) and partially restored intestinal barrier integrity (reduced FITC-dextran leakage, p&#x2009;=&#x2009;0.0449). JAM-A was significantly upregulated (p&#x2009;<&#x2009;0.0001). Colonic CD206+ M2 macrophages increased, while CD68&#x2009;+&#x2009;M1 cells partially decreased. ONX-0914 downregulated IP isoforms in macrophages (PSMB8: p&#x2009;=&#x2009;0.0022; PSMB9: p&#x2009;=&#x2009;0.0186) as well as FOXO-1 (p&#x2009;=&#x2009;0.0380) and TNF-&#x3b1; (p&#x2009;=&#x2009;0.0487). Antibiotic-induced microbiota depletion abrogated these effects. Metagenomic analysis revealed significant differences in microbiota composition between C57Bl controls and mdx mice (PERMANOVA p&#x2009;<&#x2009;0.001), with ONX-0914 inducing enrichment of stachyose degradation pathways. Metabolomic analysis showed enrichment of bacterial metabolites, fatty acid and sugar metabolism pathways, with increased glutathione, galactose, glycerol, glyceraldehyde and TCA cycle intermediates. ONX-0914 improved mitochondrial activity in skeletal muscle, as increased expression of ETC complexes (mdx vs. mdx+ONX: Complex II, p&#x2009;=&#x2009;0.0338; Complex IV, p&#x2009;=&#x2009;0.0023) and TCA enzymes (mdx vs. FTMmdx+ONX: IDH p&#x2009;=&#x2009;0.0258; FH p&#x2009;=&#x2009;0.0366). This led to a shift towards oxidative muscle fibres and improved muscle morphology (increased fibre size, p&#x2009;<&#x2009;0.0001 mdx vs. mdx+ONX and mdx vs. FTMmdx+ONX). Muscle performance was enhanced with reduced CPK levels (p&#x2009;=&#x2009;0.0015 mdx vs. mdx+ONX) and fibrosis (decreased TGF&#x3b2;: mdx vs. mdx+ONX, p&#x2009;=&#x2009;0.0248; mdx vs. FTMmdx+ONX, p&#x2009;=&#x2009;0.0279). ONX-0914 reduced CD68+ (mdx vs. mdx+ONX, p&#x2009;=&#x2009;0.0024; mdx vs. FTMmdx+ONX, p&#x2009;<&#x2009;0.0001) and increased CD206+ (mdx vs. FTMmdx+ONX: p&#x2009;=&#x2009;0.0083) macrophages in muscle, downregulated inflammatory genes (mdx vs. mdx+ONX: ccl2 p&#x2009;=&#x2009;0.0327, vcam-1p&#x2009;=&#x2009;0.0378) and reduced pro-inflammatory proteins (MCP1, mdx vs. mdx+ONX, p&#x2009;=&#x2009;0.0442). Inflammatory cytokines and endothelial vessel density in ONX-0914 treated mdx were restored to wild type mice. These data demonstrate that ONX-0914 enhances muscle function through microbiota-dependent mechanisms.<br><br>CONCLUSIONS: Our study advances the understanding of the role of dysbiosis in DMD disease and identifies IP inhibition as a potential therapeutic strategy to modulate the dystrophic gut-muscle axis, offering new perspectives for microbiota-targeted therapies.},
}
@article {pmid41034963,
year = {2025},
author = {Lewis, ZJ and Scott, A and Madden, C and Vik, D and Zayed, AA and Smith, GJ and Justice, SS and Rudinsky, A and Hokamp, J and Hale, VL},
title = {Evaluating urine volume and host depletion methods to enable genome-resolved metagenomics of the urobiome.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {199},
pmid = {41034963},
issn = {2049-2618},
support = {K08 ES034821/ES/NIEHS NIH HHS/United States ; 1K08ES034821-01A1/NH/NIH HHS/United States ; DBI 20222070//National Science Foundation/ ; Canine Intramural Grant//College of Veterinary Medicine, Ohio State University/ ; },
mesh = {*Metagenomics/methods ; Animals ; Dogs ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Humans ; Metagenome ; *Microbiota/genetics ; DNA, Bacterial/genetics ; *Urinary Tract/microbiology ; *Urine/microbiology ; Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: The gut microbiome has emerged as a clear player in health and disease, in part by mediating host response to environment and lifestyle. The urobiome (microbiota of the urinary tract) likely functions similarly. However, efforts to characterize the urobiome and assess its functional potential have been limited due to technical challenges including low microbial biomass and high host cell shedding in urine. Here, to begin addressing these challenges, we evaluate urine sample volume (100 ml-5 mL) and host DNA depletion methods and their effects on urobiome profiles in healthy dogs, which are a robust large animal model for the human urobiome. We collected urine from seven dogs and fractionated samples into aliquots. One set of samples was spiked with host (canine) cells to model a biologically relevant host cell burden in urine. Samples then underwent DNA extraction followed by 16S rRNA gene and shotgun metagenomic sequencing. We then assembled metagenome-assembled genomes (MAGs) and compared microbial composition and diversity across groups. We tested six methods of DNA extraction: QIAamp BiOstic Bacteremia (no host depletion), QIAamp DNA Microbiome, Molzym MolYsis, NEBNext Microbiome DNA Enrichment, Zymo HostZERO, and propidium monoazide.<br><br>RESULTS: In relation to urine sample volume,&#x2009;&#x2265;&#x2009;3.0&#xa0;mL resulted in the most consistent urobiome profiling. In relation to host depletion, individual (dog) but not extraction method drove overall differences in microbial composition. DNA Microbiome yielded the greatest microbial diversity in 16S rRNA sequencing data and shotgun metagenomic sequencing data and maximized MAG recovery while effectively depleting host DNA in host-spiked urine samples. As proof-of-principle, we then mined MAGs for select metabolic functions including central metabolism pathways and environmental chemical degradation.<br><br>CONCLUSIONS: Our findings provide guidelines for studying the urobiome in relation to sample volume and host depletion and lay the foundation for future evaluation of urobiome function in relation to health and disease. Video Abstract.},
}
@article {pmid41033626,
year = {2025},
author = {Kong, F and Guan, DX and Lu, L and Lu, S and Xu, J and Wang, H},
title = {Multi-element amendment reshaped rhizosphere microbiome: A microbially driven Fe/Mn/S synergistic action for Cd immobilization.},
journal = {Environmental research},
volume = {286},
number = {Pt 3},
pages = {122985},
doi = {10.1016/j.envres.2025.122985},
pmid = {41033626},
issn = {1096-0953},
mesh = {*Rhizosphere ; *Cadmium/metabolism ; *Microbiota/drug effects ; *Soil Pollutants/metabolism ; *Soil Microbiology ; Iron/metabolism ; Manganese/metabolism ; Oryza/microbiology ; Sulfur/metabolism ; Bacteria ; Environmental Restoration and Remediation/methods ; },
abstract = {Cadmium (Cd) contamination in soils threatens rice safety, necessitating effective remediation strategies. While the silicon-calcium-magnesium amendment (FSY) is known to reduce Cd bioavailability, its precise microbial mechanisms remain underexplored. This study integrated metagenomics and machine learning to investigate FSY's impact on the rice rhizosphere microbiome and to elucidate the biological drivers of Cd immobilization. FSY application and rice growth stage were the core factors that significantly reshaped bacterial and archaeal community structures, shifting archaeal community assembly toward deterministic processes, while the fungal community remained relatively stable. Co-occurrence network analysis revealed that FSY enhanced the complexity and stability of microbial interactions, strengthening the roles of key functional taxa. Crucially, functional profiling showed that FSY significantly upregulated genes related to multi-barrier systems (1) iron/manganese oxidation (e.g., feoB): associated with iron-manganese plaque (IP) formation (2) sulfate reduction (e.g., dsrA); linked to cadmium sulfide (CdS) precipitation; and (3) microbial Cd resistance (e.g., the czcA gene). Machine learning identified 14 core species, including key taxa in Campylobacterota and Thermoproteota, as the pivotal drivers of synergistic Fe/Mn/S-Cd interaction. These findings substantiated the microbially driven Fe/Mn/S synergistic model for Cd immobilization through three interconnected mechanisms: enhanced microbially mediated mineral fixation (IP thickening and CdS precipitation), and strengthened community-level Cd resistance. This research provided a deep mechanistic understanding of how chemical amendments induced microbial functions to mitigate heavy metal risks, thereby offering a scientifically-grounded strategy for remediation and safe use of Cd-contaminated field.},
}
@article {pmid41033498,
year = {2026},
author = {Saejung, C and Akkahat, S},
title = {Light color-based proliferation of purple phototrophic bacteria in a microbial consortium for sustainable wastewater treatment and bioproduct generation.},
journal = {Bioresource technology},
volume = {440},
number = {},
pages = {133411},
doi = {10.1016/j.biortech.2025.133411},
pmid = {41033498},
issn = {1873-2976},
mesh = {*Wastewater/microbiology ; *Microbial Consortia/radiation effects/physiology ; *Light ; Color ; *Water Purification/methods ; Biomass ; Biological Oxygen Demand Analysis ; Rhodopseudomonas/metabolism/growth &amp; development ; },
abstract = {Purple phototrophic bacteria (PPB) offer distinct advantages for wastewater treatment. However, the application of pure cultures of PPB in large-scale wastewater treatment is constrained by isolation challenges and microbial competition. Therefore, we investigated light color treatment as a tool to enrich PPB within a natural microbial consortium for integrated wastewater treatment and bioproduct generation. We used metagenomics to assess PPB population dynamics and measured bioproduct yields of pigments, protein, biomass, and polyhydroxybutyrate as well as chemical oxygen demand removal (COD). While an initial enrichment yielded low PPB abundance (12 %), subsequent exposure to specific light color greatly altered the community composition. White light (465 nm) enriched the consortium with 76 % PPB abundance, dominated by Rhodopseudomonas sp., which maximized bacterial biomass, polyhydroxybutyrate accumulation, and COD removal. Conversely, red light (616 nm) suppressed PPB proliferation but enhanced specific yields of photosynthetic pigments and protein, indicating a metabolic trade-off between growth and bioproduction. Thus, light color treatment may be a simple and powerful strategy to boost PPB abundance and performance within a microbial consortium, creating a cost-effective platform for wastewater biorefineries.},
}
@article {pmid41032862,
year = {2025},
author = {Ghosh Chowdhury, M and Singh, AA and Bhattacharyya, M and Muthukumar, V and Kapoor, S and Srivastava, A and Kumar, H and Shard, A},
title = {Thiazole-Based Tumor Pyruvate Kinase M2 Inhibitors: A Paradigm-Shifting Therapeutic Strategy Targeting Metabolic and Microbial Synergy in Colorectal Cancer.},
journal = {Journal of medicinal chemistry},
volume = {68},
number = {20},
pages = {21786-21806},
doi = {10.1021/acs.jmedchem.5c02169},
pmid = {41032862},
issn = {1520-4804},
mesh = {Animals ; Humans ; *Antineoplastic Agents/pharmacology/chemistry/chemical synthesis ; *Carrier Proteins/antagonists &amp; inhibitors/metabolism ; Cell Line, Tumor ; Cell Proliferation/drug effects ; *Colorectal Neoplasms/drug therapy/pathology/metabolism/microbiology ; *Enzyme Inhibitors/pharmacology/chemistry ; Gastrointestinal Microbiome/drug effects ; *Membrane Proteins/antagonists &amp; inhibitors/metabolism ; *Pyruvate Kinase/antagonists &amp; inhibitors/metabolism ; Structure-Activity Relationship ; *Thiazoles/pharmacology/chemistry/chemical synthesis ; Thyroid Hormone-Binding Proteins ; *Thyroid Hormones/metabolism ; },
abstract = {Colorectal cancer (CRC) remains a major global health burden, with current treatments primarily focused on eradicating cancer cells. However, chemotherapy-induced gut dysbiosis exacerbates inflammation and disease progression, necessitating innovative therapeutic strategies. While various metabolic inhibitors and microbiome-modulating approaches have been explored separately, no reported agent to date simultaneously targets both cancer cell survival and gut microbiome restoration. We designed thiazole-based pyruvate kinase M2 (PKM2) inhibitors, hypothesizing that selective modulation may suppress tumor growth while restoring gut microbial balance. 10j selectively inhibited PKM2 in a cell-free assay (0.01 ± 0.0009 μM) and in CRC cells (4.21 ± 0.04 μM), disrupting key pathways driving CRC progression. Remarkably, metagenomic analysis revealed that 10j restored gut microbiota balance. These findings suggest that dual-function anticancer agents, which kill cancer cells while simultaneously restoring gut microbiota, represent an unexplored therapeutic avenue. Thiazole-based PKM2 inhibitors are pioneering this novel strategy in CRC treatment.},
}
@article {pmid41032855,
year = {2025},
author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Pan, YP and Hua, ZS and Zhang, CJ and Li, M},
title = {Temporal and Spatial Dynamics of Microbial Community Composition and Functional Potential in Mangrove Wetlands over a Seven-Year Period.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {40},
pages = {21540-21554},
doi = {10.1021/acs.est.5c01564},
pmid = {41032855},
issn = {1520-5851},
mesh = {*Wetlands ; *Microbiota ; Archaea ; Bacteria ; China ; Ecosystem ; Metagenome ; },
abstract = {Microbial communities are essential to sustaining ecosystem functions in mangrove wetlands, yet their long-term responses to environmental changes remain poorly characterized. Here, we conducted a seven-year multiomics investigation (2017-2023) of microbial diversity, functionality, and evolutionary dynamics in the Futian Mangrove National Nature Reserve, Shenzhen, China. This region has experienced ecological degradation followed by phased restoration efforts since 2007. By analyzing 81 metagenomes, 8474 microbial metagenome-assembled genomes (MAGs) were successfully reconstructed, representing 13 archaeal phyla, 70 bacterial phyla, and up to 95% newly identified species. Community composition was primarily influenced by sediment depth and seasonal variations. Integrating 72 metatranscriptomes revealed marked temporal shifts in gene expression linked to carbon, nitrogen, and sulfur cycling, including enhanced transcription of genes involved in organic carbon oxidation, sulfate reduction, denitrification, and nitrogen fixation during later stages restoration. Evolutionary analyses demonstrated pervasive purifying selection across microbial lineages, with environmental fluctuations and genome size acting as key determinants of selective pressures. Additionally, a new class Candidatus Shennongiarchaeia within Thermoplasmatota was proposed, exhibited anaerobic, facultatively heterotrophic characteristics and bioactive compound synthesis potential. These findings demonstrate that microbial communities in restored mangrove wetlands undergo structural and functional reorganization, characterized by the enrichment of anaerobic lineages, upregulation of key metabolic pathways, and environmentally driven selective pressures. This long-term study deepens our understanding of microbial resilience and adaptation in mangrove ecosystems, with implications for future conservation and restoration strategies in coastal wetlands.},
}
@article {pmid41031025,
year = {2024},
author = {Waterworth, SC and Solomons, GM and Kalinski, JJ and Madonsela, LS and Parker-Nance, S and Dorrington, RA},
title = {The unique and enigmatic spirochete symbiont of latrunculid sponges.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41031025},
issn = {2692-8205},
abstract = {Bacterial symbionts are critical members of many marine sponge holobionts. Some sponge-associated bacterial lineages, such as Poribacteria, SAUL, and Tethybacterales appear to have broad host ranges and associate with a diversity of sponge species, while others are more species-specific, having adapted to the niche environment of their host. Host-associated spirochete symbionts that are numerically dominant have been documented in several invertebrates including termites, starfish, and corals. However, dominant spirochete populations are rare in marine sponges, thus far only observed in Clathrina clathrus and various species within the Latrunculiidae family, where they are co-dominant alongside Tethybacterales symbionts. This study aimed to characterize these spirochetes and their potential role in the host sponge. Analysis of metagenome-assembled genomes from eight latrunculid sponges revealed that these unusual spirochetes are relatively recent symbionts and are phylogenetically distinct from other sponge-associated spirochetes. Functional comparative analysis suggests that the host sponge may have selected for these spirochetes due to their ability to produce terpenoids and/or possible structural contributions.},
}
@article {pmid41030387,
year = {2025},
author = {Zheng-Qiang, L and Jun, L and Rui, A and Rui, L and Wei, D and Ping, M and Xu, Y and Rong, S and Xiao-Yan, Y and Wen, X},
title = {A probiotic for preventing microplastic toxicity: Clostridium dalinum mitigates microplastic-induced damage via microbiota-metabolism-barrier interactions.},
journal = {Current research in food science},
volume = {11},
number = {},
pages = {101200},
pmid = {41030387},
issn = {2665-9271},
abstract = {Microplastics (MPs) are widely distributed and accumulated in the environment, making it nearly impossible for humans to avoid ingestion. Their toxicity can cause serious health damage and pose a threat to human health. In this context, developing strategies to prevent and restore toxic damage from their ingestion is extremely urgent. This study comprehensively employs various techniques, including metagenomics and metabolomics, to explore the pre-protective and restorative effects of Clostridium dalinum, a potential probiotic with excellent antioxidant and anti-inflammatory capabilities, on damage induced by exposure to polystyrene microplastics (PS-MPs) in mice. The results show that exposure to PS-MPs leads to significant intestinal damage in mice; preemptive intake of C. dalinum for pre-protection, or post-exposure intake of C. dalinum for restorative treatment, both significantly reduced the damage caused by MPs exposure, as evidenced by changes in intestinal length (PS-MPs exposure vs C. dalinum pre-protection vs C. dalinum restoration vs control = 36.55 vs 39.94 vs 40.12 vs 41.05 cm), barrier protein content (27.12 % vs 97.28 % vs 97.73 % vs 100.00 %), and inflammation levels (284.56 % vs 101.05 % vs 98.17 % vs 100.00 %). Mechanistically, the pre-protective and restorative effects of C. dalinum both rely on upregulating the expression of barrier proteins such as ZO-1 and Occludin and inhibiting the TLR4/NF-κB inflammatory signaling pathway. Meanwhile, the two intervention modes also exhibit specific mechanisms: in the pre-protection mode, C. dalinum enhances lipid metabolic balance and antioxidant reserves by pre-activating the PPARγ/GPR43 pathway, and enriches the ABC transporters pathway to promote toxin efflux capacity, thereby preventing PS-MPs-induced damage; in the restoration mode, C. dalinum repairs intestinal damage by enriching the beneficial bacterium Lachnospiraceae NK4A136 and inhibiting the pro-inflammatory bacterium Desulfovibrio, and regulating intestinal metabolites. In summary, this study is the first to confirm that C. dalinum can effectively prevent and restore intestinal damage caused by PS-MPs exposure through the synergistic pathway of "microbiota-metabolism-barrier". Importantly, this study is the first to reveal the potential and unique mechanisms of probiotics in preventing and restoring MPs exposure toxicity, providing a theoretical basis for the future development of probiotic-based defense strategies.},
}
@article {pmid41029787,
year = {2025},
author = {Lemieux, &#xc9; and Monger, XC and Saucier, L and Charette, SJ and Guay, F and Pouliot, &#xc9; and Fournaise, S and Vincent, AT},
title = {Effect of an antibiotic and a probiotic on phage communities in the swine gut microbiota.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {402},
pmid = {41029787},
issn = {1756-0500},
support = {RGPIN-2022-03321//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; *Probiotics/pharmacology/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; Swine/microbiology ; *Bacteriophages/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology ; Feces/microbiology/virology ; Cross-Over Studies ; },
abstract = {OBJECTIVE: The impact of dietary treatments on the phage community of porcine intestinal microbiota is not well understood. An antibiotic (tylvalosin), a probiotic (Pediococcus acidilactici), and a combination of these were given to six cannulated pigs in a double crossover design study. Samples of ileal digesta and feces were collected and whole genome shotgun sequencing was performed. The variations in phage and bacterial communities were compared for each treatment and sample type.<br><br>RESULTS: The bacteriophages present in the gut microbiome exhibited greater variations in both &#x3b1;- and &#x3b2;-diversity between sample types (digesta, feces) than between treatments. &#x3b2;-diversity and differential abundance showed that the effect of the combined antibiotic and probiotic treatment was the same as with the antibiotic alone. However, the effects of the probiotic and antibiotic treatments were statistically significantly different in the fecal samples. &#x3b2;-diversity was different in those two treatments, and differential abundance analysis identified multiple phages as markers for each treatment. No significant variations in relative abundance were found in phage lifestyle (i.e., virulent, temperate) between treatments.},
}
@article {pmid41028378,
year = {2026},
author = {Sahil, R and Jain, M},
title = {A Multi-omics Approach for Microbiome Data Analysis in Legumes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2977},
number = {},
pages = {181-196},
pmid = {41028378},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Fabaceae/microbiology/genetics ; *Computational Biology/methods ; Data Analysis ; Metagenome ; Multiomics ; },
abstract = {Microbiome plays a crucial role in influencing the health and function of living beings as well as in regulating the biogeochemical cycles. The plant microbiome, in particular, has garnered significant research interest aimed at exploring the microbes that play a crucial role in regulating plant growth and nutrient acquisition. Recent advancements in omics sciences have played a crucial role in uncovering the complexities of these relationships. While techniques such as amplicon and shotgun metagenomics provide taxonomic profiling up to the species level and even the strain level, metatranscriptomics further elucidates the functional roles of these microbes. These techniques are being rapidly and widely adopted to understand the influence of microbes on the host. However, the challenge lies in their integration. Most studies to date rely on only one of these techniques, which limits the scope of holistic understanding of host-microbe interactions. Additionally, there is currently no well-established workflow that effectively combines these techniques to provide comprehensive biological insights. In this work, we describe an integrated approach for microbiome data analysis to provide biologically meaningful insights.},
}
@article {pmid41027803,
year = {2026},
author = {Blank, RB and Bu, K and Zhang, X and Chen, W and Cunningham, I and Sokolove, J and Lahey, L and Heguy, A and Medina, R and Ubeda, C and Nayak, RR and Hu, J and Cantor, A and Lee, J and Williams, FMK and Clemente, JC and Scher, JU},
title = {Short-chain fatty acids and their gut microbial pathways distinguish rheumatoid arthritis in discordant monozygotic twins.},
journal = {Annals of the rheumatic diseases},
volume = {85},
number = {2},
pages = {254-264},
doi = {10.1016/j.ard.2025.08.029},
pmid = {41027803},
issn = {1468-2060},
mesh = {Humans ; *Arthritis, Rheumatoid/microbiology/genetics/metabolism/diagnosis ; *Twins, Monozygotic ; *Fatty Acids, Volatile/metabolism/blood ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Middle Aged ; Biomarkers/metabolism ; Feces/chemistry/microbiology ; Adult ; Aged ; },
abstract = {OBJECTIVES: Although genetic risk factors, such as HLA-DRB1 alleles, contribute to the pathogenesis of rheumatoid arthritis (RA), the concordance rate in monozygotic (MZ) twins is low, suggesting that other factors are involved in disease development. Further, the relative contribution of nongenetic elements in identical twins has not been characterised. Here, we aimed to characterise host and microbial biomarkers of RA by studying MZ twins discordant for disease using a multiomics approach.<br><br>METHODS: Eight pairs of MZ twins discordant for RA (N = 16) were enrolled in the United States (US). The gut microbiome was assessed using shotgun metagenomic sequencing. Autoantibodies, cytokines, and plasma proteins were measured in both plasma and faeces. Levels of short-chain fatty acids (SCFAs) from serum and faeces were quantified using gas chromatography mass spectrometry (GC-MS). Metagenomic data from a UK twin registry (TwinsUK) (N = 14) were used to validate findings in the US population.<br><br>RESULTS: Although microbiome diversity and composition did not differ between twins, we observed a significant decrease in the SCFA-producing bacteria Blautia faecis and significantly lower concentrations of faecal butyrate and propionate in affected RA twins in the US. TwinsUK showed a similar reduction in the SCFA-producers Gemmiger formicilis and Faecalicatena fissicatena, as well as bacterial SCFA metabolism pathways.<br><br>CONCLUSIONS: Multiomics biomarkers differentiate MZ twins discordant for RA. Faecal butyrate and propionate, as well as SCFA-producing bacteria, were decreased in affected twins. We found a similar decrease in SCFA-producing taxa in affected twins in a geographically distinct cohort in the UK. Our results suggest that, if further validated in larger cohorts, multiomics approaches may improve our understanding of RA pathogenesis and, potentially, contribute to more accurate diagnostics and coadjuvant therapies.},
}
@article {pmid41026172,
year = {2025},
author = {Gao, H and Ma, X and Lu, M and Wang, Y and Liu, H and Hu, X and Nie, Y},
title = {Population and Spatial Features Impact the Gut Phageome-Bacteriome Structure and Interactions in a Mammal Species Living in Fragmented Habitats.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {98},
pmid = {41026172},
issn = {1432-184X},
support = {32225033//National Natural Science Foundation of China/ ; 2022YFF1301500//Ministry of Science and Technology of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/classification/physiology/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification/virology ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Antelopes/microbiology/virology ; Metagenome ; Feces/microbiology ; },
abstract = {The mammalian gut microbiome composition has been shown to promote host adaptation to ecological environments. However, the variation in the gut phageome and bacteriome composition at both the population level and spatial scale in wild animals has not been well investigated. Here, we used viral metagenomes and 16S rRNA gene sequencing to explore how these characteristics affect the gut microbiome of Przewalski's gazelle, an endangered group-living ungulate that lives in several fragmented habitats due to anthropogenic activities. The results revealed that population and habitat geographic characteristics collectively explained much more of the variation in phageome and bacteriome compositions than did host-associated factors. Both gut phage and bacterial diversity were positively associated with population size, and differentiation in gut microbiome diversity increased with geographic distance among populations. Additionally, the gut phage and the bacterial hosts displayed similar patterns in composition across habitats, indicating that the microbiome may exhibit complex interactions in response to the environment. For the first time, our study reveals the important roles of population and habitat geographic characteristics in driving spatial patterns of gut microbiome structures in wild animals and highlights the interactions between gut phages and the bacteriome in adaptation to living environments under the influence of human disturbances.},
}
@article {pmid41026152,
year = {2025},
author = {Nassirnia, S and Scherz, V and Greub, G and Caruana, G and Taffé, P and Jaton, K and Papis, S and Posfay-Barbe, KM and Mornand, A and Rochat-Guignard, I and Bertelli, C and Asner, SA},
title = {Concordance between upper and lower airway microbiota in children with cystic fibrosis.},
journal = {Journal of medical microbiology},
volume = {74},
number = {9},
pages = {},
doi = {10.1099/jmm.0.002079},
pmid = {41026152},
issn = {1473-5644},
mesh = {Humans ; *Cystic Fibrosis/microbiology ; *Sputum/microbiology ; *Microbiota ; Child ; *Pharynx/microbiology ; Male ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Adolescent ; Longitudinal Studies ; *Respiratory System/microbiology ; Metagenomics ; Infant ; },
abstract = {Introduction. Sputum is the most used sample type to monitor the lower respiratory tract microbiota in cystic fibrosis (CF), but young patients often cannot expectorate.Hypothesis. We hypothesized that throat swabs could reflect lower airway colonization and assessed the concordance of bacterial community composition between paired sputum and throat swab samples from children with CF.Aim. We aimed to compare bacterial community diversity and composition between sputum and throat swabs in the full cohort and in patients with paired samples from the same visit.Methodology. The prospective longitudinal multicentre MUCOVIB cohort included 379 samples from 61 CF children. Using V3-V4 16S rRNA amplicon metagenomics, we compared bacterial community diversity and composition between sputum and throat swabs in the full cohort and in 11 patients with paired samples from the same visit.Results. Sputum and throat swabs exhibited similar bacterial diversity, regardless of the exacerbation status, and presented a substantial agreement for detecting pathogens (Cohen's kappa: 0.6). Differences in bacterial abundance were observed (P=0.001), but not presence/absence (P=0.098). Community typing revealed three distinct community types, with 86% of paired samples falling into the same cluster, highlighting the homogeneity between sputum and throat swab microbiota. Network analysis demonstrated slight, non-random similarities in microbial interactions between sample types (adjusted Rand index=0.08 and 0.10). The average beta-diversity distances between samples collected from the same visit were shorter (0.505±0.056 95% confidence interval), compared with sputum (0.695±0.017) or throat swab (0.704±0.045) from the same patient collected during different visits.Conclusion. Throat swabs can provide representative information on lower respiratory microbiota. Clinicians should collect throat swabs rather than relying on sputum samples from previous visits to guide antibiotic prescriptions in CF children unable to expectorate.},
}
@article {pmid41026097,
year = {2025},
author = {Patyka, M and Wang, R and Honchar, A and Patyka, T and Khablak, S},
title = {Modulation of the rhizosphere microbiome structure and optimization of beneficial functions in winter wheat induced by Bacillus subtilis: a metagenomic and phenotypic study.},
journal = {FEMS microbiology ecology},
volume = {101},
number = {11},
pages = {},
pmid = {41026097},
issn = {1574-6941},
mesh = {*Triticum/microbiology/growth &amp; development ; *Rhizosphere ; *Bacillus subtilis/physiology ; *Microbiota ; *Soil Microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Indoleacetic Acids/metabolism ; Plant Roots/microbiology ; Phenotype ; },
abstract = {The rhizosphere microbiome critically determines plant health and productivity. This study investigated the impact of Bacillus subtilis H38 on the taxonomic and functional profiles of the winter wheat (Triticum aestivum L.) rhizosphere microbiome under typical chernozem conditions using 16S rRNA gene sequencing and shotgun metagenomics, complemented by plant phenotypic evaluation and targeted metabolite analysis. Inoculation with B. subtilis H38 significantly restructured the rhizosphere bacterial community, increasing alpha-diversity (Shannon index from 5.8 to 6.7) and showing distinct clustering in beta-diversity analysis. The relative abundance of putative plant-beneficial genera, including Bacillus, Pseudomonas, Azotobacter, and Streptomyces, was significantly elevated. Shotgun metagenomic analysis revealed enrichment of functional genes associated with nitrogen fixation, phosphorus mobilization, phytohormone biosynthesis, siderophore production, and synthesis of antimicrobial compounds. Targeted metabolomic analysis confirmed elevated levels of indole-3-acetic acid (IAA) and key siderophores. Concurrently, treated wheat plants exhibited an 18.0% increase in aboveground biomass and a 25.0% increase in root length under field conditions. These findings underscore the potential of B. subtilis to beneficially reshape the rhizosphere microbiome and its metagenome, leading to enhanced plant growth, and highlight its utility as a potent biofertilizer for improving wheat productivity. This research reinforces the potential of harnessing beneficial plant-microbe interactions to enhance agricultural productivity while minimizing dependence on synthetic agrochemicals.},
}
@article {pmid41025824,
year = {2025},
author = {Li, Z and Li, S and Han, C and Chen, Y and Zhen, H and Sun, Y and Zhou, X and Chen, Y and Zheng, Y and Han, L and Krutmann, J and Nie, C and Wang, J and Xia, J},
title = {A comprehensive reference catalog of human skin DNA virome reveals novel viral diversity and microenvironmental influences.},
journal = {Microbiology spectrum},
volume = {13},
number = {11},
pages = {e0117825},
pmid = {41025824},
issn = {2165-0497},
mesh = {Humans ; *Skin/virology/microbiology ; *Virome/genetics ; Microbiota/genetics ; *Viruses/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification/virology ; Metagenome ; Bacteriophages/genetics/classification/isolation &amp; purification ; *DNA, Viral/genetics ; Metagenomics ; },
abstract = {UNLABELLED: Human skin serves as a dynamic habitat for a diverse microbiome, including a complex array of viruses whose diversity and roles are not fully understood. A total of 2,760 skin metagenomes from 6 published skin studies were collected. A skin virome catalog was constructed using standard methods in the viromics field. Viral characteristics were identified through cross-cohort meta-analysis and used to characterize viral features across different skin environments. We identified 20,927 viral sequences, which clustered into 2,873 viral operational taxonomic units (vOTUs), uncovering a substantial breadth of viral diversity on human skin. The results also highlight significant differences in viral communities that are associated with varying skin microenvironments. The oily skin is enriched in Papillomaviridae, the dry skin area is enriched in Autographiviridae and Inoviridae, and the moist skin is enriched in Herelleviridae. We also investigated the relationship between bacteriophages and bacteria on the skin surface. We found that skin bacteria such as Pseudomonas, Klebsiella, and Staphylococcus are predicted to be infected by phages from the class Caudoviricetes. This comprehensive skin DNA viral catalog significantly advances our understanding of the virome's role within the skin ecosystem.<br><br>IMPORTANCE: This study presents a comprehensive reference catalog of the human skin DNA virome, constructed from 2,760 metagenomic datasets collected globally. It identified 20,927 viral sequences, with 90.85% representing previously unknown viruses, greatly expanding our understanding of skin viral diversity. The findings reveal significant differences in viral communities between distinct skin microenvironments (oily, dry, and moist) and highlight close interactions between bacteriophages and their bacterial hosts, suggesting a potential role for the virome in maintaining microbial balance and skin health. This extensive skin viral catalog constitutes a crucial resource for future epidemiological and therapeutic research, potentially facilitating the development of novel phage therapies and diagnostic markers for skin disorders.},
}
@article {pmid41025799,
year = {2025},
author = {Buckner, AM and Glendinning, L and Palma Hidalgo, JM and van Munster, JM and Stevens, M and Watson, M and Newbold, CJ},
title = {The selective culture and enrichment of major rumen bacteria on three distinct anaerobic culture media.},
journal = {Microbiology spectrum},
volume = {13},
number = {11},
pages = {e0056325},
pmid = {41025799},
issn = {2165-0497},
support = {BB/T00875X/1, BBS/E/RL/230001A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; UKSBS PR18037//Natural Environment Research Council/ ; },
mesh = {*Rumen/microbiology ; Animals ; *Bacteria/classification/isolation &amp; purification/growth &amp; development/genetics/metabolism ; *Culture Media/chemistry ; Anaerobiosis ; Methane/metabolism ; Gastrointestinal Microbiome ; Cattle ; Phylogeny ; },
abstract = {Ruminants play an important part in global food security, but also emit methane, which contributes to global warming. Rumen microbes strongly influence the energy retention efficiency from the host's plant-based diet and produce methane as a by-product. While thousands of novel microbial genomes have been assembled from metagenomic sequence data, their culturability is ill-defined. Here, different media (Med10, Med2, and MedTC) were used to isolate co-cultures of microbes from rumen fluid. Thirty-four OTUs were identified belonging to the phyla Bacillota (75.28 ± 6.34%), Bacteroidota (19.99 ± 4.85%), Pseudomonadota (2.46 ± 2.01%), and Actinomycetota (2.09 ± 1.07%). The most abundant genera were Selenomonas (28.08 ± 11.71%), Streptococcus (22.67 ± 6.06%), Prevotella (18.71 ± 4.02%), and unclassified Lachnospiraceae (11.50 ± 2.54%), and 31 significantly enriched on at least one medium, with each medium successfully culturing a distinct range of microbes. The composition of the source rumen fluid was vastly different from those cultured. Bacteroidota (52.53 ± 5.10%) predominated, with Bacillota (41.00 ± 3.96%), Methanobacteriota (5.12 ± 1.94%), Pseudomonadota (1.22 ± 0.78%), and Actinomycetota (0.12 ± 0.08%) comprising the rest. The most abundant genera were Prevotella (29.13 ± 4.16%), Butyrivibrio (18.21 ± 2.08%), Succiniclasticum (15.57 ± 5.03%), unclassified Bacteroidetes (13.91 ± 1.67%), and unclassified Prevotellaceae (9.50 ± 2.01%). These data further emphasize the importance of using defined media to select for different microbial taxa. This is essential to understand the complex workings of the rumen microbes to enhance digestion efficiency and reduce the loss of energy that could potentially be utilized by the host.IMPORTANCEThis research demonstrates that using a range of culture media, containing a wide variety of substrates, can lead to the culture of key rumen microbes. The knowledge of which of these microbes is selectively enriched on each medium is essential to understand how to grow these microbes in co-culture and isolate them in pure culture for further investigation. In addition, this research shows the stark disparity between the population of rumen microbes grown in co-culture and those found in the rumen itself. This further demonstrates the need for a targeted approach to growing and isolating these microbes. Learning how these microbes respond to culture media with different nutritional compositions will lead to a better understanding of the rumen microbiota, and this research provides a valuable insight into how selective media can target the enrichment of different microbes. This knowledge will contribute to increasing ruminant digestion efficiency and reducing methane production.},
}
@article {pmid41025782,
year = {2025},
author = {Boyd, AI and Kafer, LA and F Escapa, I and Kambal, A and Tariq, H and Hilsenbeck, SG and Nguyen-Phuc, H and Rajan, A and Lensmire, JM and Patras, KA and Piedra, PA and Blutt, SE and Lemon, KP},
title = {Nasal microbionts differentially colonize and elicit cytokines in human nasal epithelial organoids.},
journal = {mSphere},
volume = {10},
number = {10},
pages = {e0049325},
pmid = {41025782},
issn = {2379-5042},
support = {U19AI116497//National Institute of Allergy and Infectious Diseases/ ; U19AI144297//National Institute of Allergy and Infectious Diseases/ ; F31 AI172324/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; U19 AI144297/AI/NIAID NIH HHS/United States ; U19AI157981//National Institute of Allergy and Infectious Diseases/ ; U19 AI116497/AI/NIAID NIH HHS/United States ; F31AI172324//National Institute of Allergy and Infectious Diseases/ ; P30 ES030285/ES/NIEHS NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Cytokines/metabolism/immunology ; *Organoids/microbiology/immunology ; Streptococcus pneumoniae/growth &amp; development/immunology ; Staphylococcus aureus/growth &amp; development/immunology ; *Nasal Mucosa/microbiology/immunology ; *Microbiota ; Epithelial Cells/microbiology/immunology ; },
abstract = {UNLABELLED: Nasal colonization by Staphylococcus aureus or Streptococcus pneumoniae is associated with an increased risk of infection by these pathobionts, whereas nasal colonization by Dolosigranulum species is associated with health. Human nasal epithelial organoids (HNOs) differentiated at air-liquid interface (ALI) physiologically recapitulate human nasal respiratory epithelium with a robust mucociliary blanket. Due to their natural stem-like properties, HNO lines are a long-term experimental resource that offers genetic diversity based on the different donors. To develop HNOs as a new model system for bacterial nasal colonization, we reproducibly monocolonized HNOs differentiated at ALI with S. aureus, S. pneumoniae, or Dolosigranulum pigrum for up to 48 h with varying kinetics across species. HNOs tolerated bacterial monocolonization with localization of bacteria to the mucus layer and with minimal cytotoxicity compared to uncolonized HNOs. Human nasal epithelium exhibited both species-specific and general cytokine responses, without induction of type I interferons, which is consistent with colonization rather than infection. Only live S. aureus colonization robustly induced epithelial cell production of interleukin-1 family cytokines, suggestive of inflammasome signaling. D. pigrum and live S. aureus decreased CXCL10, whereas S. pneumoniae increased CXCL11, chemokines involved in antimicrobial responses to both viruses and bacteria. Overall, HNOs are a new model system for uncovering microbe-epithelial cell dynamics at the human nasal mucosa.<br><br>IMPORTANCE: Human nasal microbiota often includes highly pathogenic members, many of which are antimicrobial resistance threats, e.g., methicillin-resistant Staphylococcus aureus and drug-resistant Streptococcus pneumoniae. Preventing colonization by nasal pathobionts decreases infections and transmission. In contrast, nasal microbiome studies identify candidate beneficial bacteria that might resist pathobiont colonization, e.g., Dolosigranulum pigrum. Learning how these microbionts interact with the nasal epithelium and identifying new means to reduce pathobiont colonization are key goals in the field. As a tool to advance this research, we developed human nasal epithelial organoids (HNOs) differentiated at an air-liquid interface as a new model system of bacterial nasal colonization. HNOs accurately represent the mucosal surface of the human nasal passages, enabling exploration of bacterial-epithelial interactions, which is important since the epithelium is an instigator of the initial innate immune response to bacteria. Here, we identified differential epithelial cytokine responses to these three bacteria, setting the stage for future research.},
}
@article {pmid41025564,
year = {2025},
author = {Zeng, S and Wang, H and Zhang, L and Li, S and Yuan, Y and Tian, M and Qu, Y and Ying, J and Zhou, M and Hu, Y and Huang, J and Zou, R and Zhao, F and Su, X and Liu, Q and He, Y and Feng, J and Huang, W and Luo, Y and Zhou, Z and Shen, W and Mu, D and Wang, S},
title = {The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {45},
pages = {e05154},
pmid = {41025564},
issn = {2198-3844},
support = {2021YFC2701704//National Key Research and Development Program/ ; 2021YFC2701700//National Key Research and Development Program/ ; 82402025//National Natural Science Foundation of China/ ; 82241036//National Natural Science Foundation of China/ ; 82271749//National Natural Science Foundation of China/ ; 82371717//National Natural Science Foundation of China/ ; 82201905//National Natural Science Foundation of China/ ; 82571980//National Natural Science Foundation of China/ ; 82530056//National Natural Science Foundation of China/ ; 2025ZNSFSC1677//Department of Science and Technology of Sichuan Province/ ; SCU2023D006//Fundamental Research Funds for the Central University/ ; SZSM202311027//Sanming Project of Medicine in Shenzhen/ ; },
mesh = {Humans ; *Enterocolitis, Necrotizing/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; *Infant, Premature ; Infant, Newborn ; Female ; Male ; Metagenome/genetics ; Machine Learning ; },
abstract = {The accelerating threat from antimicrobial resistance (AMR) has become a global health issue. The properties of AMR in the gut microbiome of preterm infants and its clinical relevance with necrotizing enterocolitis (NEC) remain unknown. In-depth integrative analyses of 5,684 gut metagenomes are performed to build an AMR genes (ARGs) landscape. A subset of 107 preterm infants who developed NEC is sampled to examine the trajectory and predictive potential of ARGs preceding NEC onset. The variation and core set of ARGs, their higher burden and diversity, and potential ARGs-enriched gut bacteria in preterm infants compared to full-term infants are comprehensively discovered, reflecting a strain shift in genomic functions. Moreover, the gut resistome converged over 9 days before NEC onset is observed, which is driven by 24 ARGs. Machine learning analysis reveals potential usage of the gut resistome as an indicator for predicting NEC onset in an external validation preterm birth cohort (the area under the receiver operating characteristic curve, AU-ROC = 0.823), which is significantly higher than that based on the bacterial species (AU-ROC = 0.727). Overall, the findings can be referenced to mitigate the burden and spread of ARGs, and specific ARGs have potential for disease risk stratification to improve clinical management.},
}
@article {pmid41025248,
year = {2025},
author = {Park, YJ and Lim, JK and Lee, YJ and Kwon, KK},
title = {Protocol for efficient recovery of high-quality DNA from microbiome of marine invertebrates.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {63},
number = {9},
pages = {e2507003},
doi = {10.71150/jm.2507003},
pmid = {41025248},
issn = {1976-3794},
support = {EA0311//Ministry of Oceans and Fisheries/ ; KIMST 20210469//Ministry of Oceans and Fisheries/ ; },
mesh = {Animals ; *Microbiota/genetics ; *DNA, Bacterial/isolation &amp; purification/genetics ; *Aquatic Organisms/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; *Porifera/microbiology ; Symbiosis ; Republic of Korea ; *Invertebrates/microbiology ; Anthozoa/microbiology ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; },
abstract = {Marine organisms often form symbiotic relationships with various microorganisms to adapt and thrive in harsh environments. These symbiotic microbes contribute to host survival by providing nutrition, modulating the hosts' immune system, and supporting overall physiological stability. Advances in high-throughput sequencing technologies have enabled a deeper understanding of the structure and function of symbiotic microbial communities, as well as host-microbe interactions. Notably, symbiotic bacteria associated with marine invertebrates such as corals and sponges are recognized as a potential source of useful bioactive compounds, including antibiotics and enzymes. However, obtaining high-quality microbial DNA from host tissues still remains a technical challenge due to the presence of unknown substances. This study focuses on optimizing sample preparation and DNA extraction procedures and additional purification to improve the recovery of microbial DNA while minimizing host DNA contamination. Comparison between several methods was conducted using sponge samples to evaluate DNA quality and microbial recovery. A sample designated as 2110BU-001 was collected from the east coast of the Republic of Korea and used for culture-independent microbial cell isolation. Total bacterial DNA was extracted by using a manual Phenol-Chloroform protocol and three commercial kits. DNA extracted using the standard manual method showed both the highest yield and the largest fragment size. However, PCR (Polymerase chain reaction) test showed that quality of manually extracted DNA was not enough for sequencing. Therefore, the quality of DNA was improved through additional purification steps. Briefly, host eukaryotic cells were removed by mechanical process and almost only bacterial DNA was successfully obtained by combination of manual extraction method and further purification processes. The established protocol was successfully introduced to extraction of metagenomic DNA from mussel and jellyfish microbiomes, indicating that it can be widely applied to various marine organisms.},
}
@article {pmid41024767,
year = {2025},
author = {Ezzat, WM},
title = {Machine learning as an artificial intelligence application in management of chronic hepatitis B virus infection.},
journal = {World journal of gastroenterology},
volume = {31},
number = {35},
pages = {109776},
pmid = {41024767},
issn = {2219-2840},
mesh = {Humans ; *Hepatitis B, Chronic/therapy/microbiology/diagnosis/virology ; *Machine Learning ; *Gastrointestinal Microbiome ; *Hepatitis B virus/pathogenicity ; Algorithms ; Artificial Intelligence ; Antiviral Agents/therapeutic use ; Supervised Machine Learning ; },
abstract = {Let's review the role of gut microbiota in pathogenesis of chronic hepatitis B infection as addressed in by Zhu et al. Zhu et al used high-throughput technology to characterize the microbial ecosystems, which led to an explosion of various types of molecular profiling data, such as metagenomics, metatranscriptomics, and metabolomics. To analyze such data, machine learning (ML) algorithms have shown to be useful for identifying key molecular signatures, discovering potential patient stratifications, and, particularly, for generating models that can accurately predict phenotypes. Strong evidence suggests that such gut microbiome-based stratification could guide customized interventions to benefit human health. Supervised learning includes designing an algorithm to fix a pre-identified problem. To get an answer, ML software must access data that have been nominated. On the other hand, unsupervised learning does not address any pre-defined problems. Bias should be eliminated as much as possible. In unsupervised learning, an ML algorithm works to identify data patterns without any prior operator input. This can subsequently lead to elements being identified that could not be conceived by the operator. At the intersection between supervised and unsupervised learning is semi-supervised ML. Semi-supervised learning includes using a partially labeled data set. The ML algorithm utilizes unsupervised learning to label data (that has not yet been labelled) by drawing findings from the labeled data. Then, supervised techniques can be used to solve defined problems involving the labeled data. Reinforcement learning, which is similar to supervised learning in the meaning, is goal-oriented. Reinforcement learning does not need labeled data, instead, it is provided with a set of regulations on a problem. An algorithm will carry out operations to try to answer questions involving the problem. Based on obtained data of gut microbiota, various therapeutic modalities can be applied: Prebiotics, probiotics, postbiotics, engineered bacteria, bacteriophage, and novel microbe-materials therapeutic system and fecal transplantation. In conclusion, ML is an artificial intelligence application that helps in providing new perspectives on tailored therapy. Furthermore, assessing the impact of gut microbiota modification is a critical step in advanced liver disease management. These new artificial intelligence techniques although promising, still require further analysis and validation in future studies.},
}
@article {pmid41024212,
year = {2025},
author = {Wang, Y and Gong, L and Dong, D and Li, X},
title = {Metagenomic binning reveals community and functional characteristics of sulfur- and methane-oxidizing bacteria in cold seep sponge ground.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {122},
pmid = {41024212},
issn = {2524-6372},
support = {KEXUE2020GZ01//The Senior User Project of R/V Kexue/ ; 42176114//The National Natural Science Foundation of China/ ; ZR2023MD100//Natural Science Foundation of Shandong Province/ ; },
abstract = {BACKGROUND: Cold seep sponges typically reside in the carbonate rock areas surrounding the vents, often comprising only a few individuals of a limited number of species. Previous limited studies have indicated that sponges living in seeps or vents host chemolithotrophic microorganisms, including sulfur-oxidizing bacteria (SOB) and methane-oxidizing bacteria (MOB), regardless of their feeding habits. This suggests that they may utilize compounds from their environment. However, when multiple sponge species are found co-occurring in a single sponge ground sharing identical environmental and material conditions, it remains unclear how their symbiotic community structure will behave. Specifically, it is uncertain whether the community will exhibit greater similarity or, as seen in most studies, demonstrate host specificity.<br><br>RESULTS: We utilize metagenomics and binning analysis to characterize six new sponge species belonging to two classes and two distinct dietary habits, all discovered in the same cold seep. Our findings reveal that their associated microbial communities, primarily composed of SOB and MOB from the phylum Proteobacteria, exhibit a high abundance of groups with the same chemosynthetic functions. Binning recovered diverse, novel MAGs (metagenome-assembled genomes) primarily dominated by order PS1 (SOB) and order Methylococcales (MOB). This similarity extends beyond the dietary habits and higher taxonomic levels of the sponge hosts. Phylogenetic and abundance difference analyses of MAGs indicate significant host specificity in the selection of symbiotic microbial species among different sponge species. Notably, these MOB and SOB exhibit potential novelty within their clade compared to known taxa. Furthermore, the genomes of these SOB and MOB contain abundant functions related to their adaptation to the chemoautotrophic environment and symbiotic lifestyle within the cold seep.<br><br>CONCLUSIONS: The chemosynthetic environment shapes the high relative abundance of key functional groups that dominate the symbiotic community, while the species differences among host sponges determine the strain selection within these groups. The metabolic functions expressed by this "convergence with divergence" community structure collectively endow the holobionts with the ability to adapt to the cold seep environment.},
}
@article {pmid41023790,
year = {2025},
author = {Cao, L and Sun, H and Wang, Y and Wei, Z and Zhang, J and Wang, Y and Yan, J and Zhu, Y and Cheng, N and He, S and Liu, X and Li, T and Wang, M and Li, E},
title = {Comparative analysis of metagenomics between high- and medium-temperature daqu, and microbial succession in Jiang-Nong Jianxiang Baijiu fermentation.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {852},
pmid = {41023790},
issn = {1471-2164},
mesh = {*Fermentation ; *Metagenomics/methods ; *Alcoholic Beverages/microbiology ; *Microbiota ; *Bacteria/genetics/classification ; Temperature ; Phylogeny ; },
abstract = {BACKGROUND: The mixture of high-temperature Daqu and medium-temperature Daqu can be used to produce Chinese Jiang-Nong Jianxiang Baijiu. This study used metagenomic sequencing and physicochemical analysis to investigate the microbial community and functionality of high-temperature Daqu and medium-temperature Daqu. In addition, exploring the changes of microbial communities during the Jiang-Nong Jianxiang Baijiu fermentation process.<br><br>RESULTS: The results showed that Lichtheimia ramose and Saccharopolyspora rectivirgula were the significantly different species in high-temperature Daqu. However, Paecilomyces variotii, Aspergillus chevalieri, and Rasamsonia emersonii were the significantly different species in medium-temperature Daqu. The medium-temperature Daqu had higher saccharifying power (101.20&#x2009;&#xb1;&#x2009;1.85 U/g) than high-temperature Daqu (60.00&#x2009;&#xb1;&#x2009;0.58 U/g). And the protease activity of high-temperature Daqu (62.47&#x2009;&#xb1;&#x2009;5.84 U/mg) was significantly higher than medium-temperature Daqu (36.10&#x2009;&#xb1;&#x2009;1.13 U/mg). The community structure analysis results of the stack fermentation stage showed that the mixture of high-temperature Daqu and medium-temperature Daqu inherited the community advantages of both high-temperature Daqu and medium-temperature Daqu. With Jiang-Nong Jianxiang Baijiu fermentation, the significantly different species changed from Pichia sp., Acetobacter sp., and Lactobacillus sp. to Pediococcus sp., Lactobacillus sp., Lentilactobacillus sp., Saccharomyces sp., Thermoactinomyces sp., and Saccharopolyspora sp., implying the importance of acid-resistant and ethanol-resistant microorganisms for the production of flavor substances in the late Baijiu fermentation.<br><br>CONCLUSIONS: Our research revealed the difference in microbial communities between high-temperature Daqu and medium-temperature Daqu, and demonstrated the shifts and functionality of microbiota during Jiang-Nong Jianxiang Baijiu fermentation. This study provides a theoretical reference for utilizing core synergistic microbiota and their functional traits in Baijiu fermentation starters to improve Baijiu quality.},
}
@article {pmid41023192,
year = {2025},
author = {Vishal, V and Thakur, P and Tigga, SS and Lal, S},
title = {A metagenomic assessment of overburden dump of coal mine soil bacterial consortium from Jharkhand, India.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {10},
pages = {1161},
pmid = {41023192},
issn = {1573-2959},
mesh = {*Soil Microbiology ; India ; *Bacteria/classification/genetics ; *Coal Mining ; *Environmental Monitoring ; *Soil Pollutants/analysis ; Metagenomics ; Soil/chemistry ; *Microbial Consortia ; Biodegradation, Environmental ; RNA, Ribosomal, 16S ; Coal ; },
abstract = {Overburden dump (OBD) of coal mine waste soils is arguably a major source of heavy metals and metalloids, leading to both public health and ecological consequences. This study employed hypervariable V3-V4 region of 1.5 kbp 16S rDNA gene-based amplicon metagenomic sequencing to analyze unexplored bacterial diversity and its phenotypical and hypothetical functions, emphasizing the significance of these studies for assessing the potential of bioremediation. Triplicate coal OBD soil samples were collected from the coal dumping yard of Sarubera Colliery from Atna-Chainpur and agricultural soils from Ramgarh Cantonment, Jharkhand. There were 30 phyla And 320 operational taxonomic units (OTUs) recorded in coal OBD soil, while agricultural soil had 26 phyla And 240 OTUs. Proteobacteria were the predominant phylum in both environments. Firmicutes, Actinobacteria, and Bacteroidetes were the most prevalent phyla in the coal OBD soil, whereas Acidobacteria, Planctomycetes, and Nitrospirae were most frequently found in agricultural soil. Alphaproteobacteria and Gammaproteobacteria was the most abundant classes, and whereas the mesophilic Acinetobacter were the most abundant genus detected in coal OBD soil. The PICRUSt2 pipeline predicted hypothetical functional categories, identifying 2404 EC numbers, 7813 KO terms, And 442 MetaCyc pathways. The most enriched categories were RNA polymerase sigma-70 factor, ABC transporters, And 3-oxoacyl-[acyl-carrier-protein] reductase, aerobic respiration pathways, and pyruvate fermentation biosynthesis pathways. Taxonomy-to-phenotypic mapping was used to record phenotypic categories like oxygen requirement, temperature range, energy sources, biotic relationships, and Gram stain nature between the two habitats. The presence of nitrogen-fixing and phosphate-solubilizing bacteria in coal OBD soil offers their key roles of biodegrading polycyclic aromatic hydrocarbons (PAHs), speeding mineralization, and ameliorating environmental issues that threaten plant viability.},
}
@article {pmid41022942,
year = {2025},
author = {Halifu, S and Deng, X and Yang, L and Qian, L and Yang, L},
title = {Metagenomic analysis of pathogenicity of puccinia xanthii on invasive plant xanthium italicum.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33530},
pmid = {41022942},
issn = {2045-2322},
support = {KX031042//PhD research startup foundation of Shihezi University/ ; KX6107//a program of Shihezi University/ ; },
mesh = {*Plant Diseases/microbiology ; Plant Leaves/microbiology ; *Xanthium/microbiology ; *Metagenomics/methods ; *Puccinia/genetics/pathogenicity ; Introduced Species ; Photosynthesis ; China ; },
abstract = {Biological invasion refers to the establishment and proliferation of non-indigenous species in previously unoccupied areas, where they form wild populations. Xanthium italicum, an invasive species in Xinjiang, China, negatively affects local ecosystems, agriculture, and animal husbandry. In this study, we investigated the pathogenicity of Puccinia xanthii on the leaves of X. italicum by exploring the morphological characteristics of the pathogenic fungi, leaf enzyme activity measurement, photosynthesis measurement, and metagenomic sequencing. This study showed that P. xanthii infects the leaves of X. italicum, significantly reducing the activities of lyase, oxidoreductase, and antioxidant enzymes, including phenylalanine ammonia-lyase (PAL), superoxide dismutase (SOD), polyphenol oxidase (PPO), and catalase (CAT), as well as impairing photosynthesis. Furthermore, metagenomic analysis indicated that P. xanthii infection reduced the homogeneity and richness of phyllosphere microorganisms and increased the abundance of P. xanthii in the phyllosphere. Functional analysis also revealed that P. xanthii infection altered the diversity of microbial functions and eventually led to the development of disease symptoms and the demise of leaves through activated oxidative phosphorylation.},
}
@article {pmid41022706,
year = {2025},
author = {Füssy, Z and Lampe, RH and Arrigo, KR and Barry, K and Brisbin, MM and Brussaard, CPD and Decelle, J and de Vargas, C and DiTullio, GR and Elbourne, LDH and Frischer, ME and Goodstein, DM and Grigoriev, IV and Hayes, RD and Healey, AL and James, CC and Jenkins, JW and Juery, C and Kumar, M and Kustka, AB and Maumus, F and Novák Vanclová, AMG and Oborník, M and Paulsen, IT and Probert, I and Saito, MA and Schmutz, J and Skalický, T and Tec-Campos, D and Tomelka, H and Věchtová, P and Venepally, P and Wilson-Mortier, B and Zengler, K and Zheng, H and Allen, AE},
title = {Genome-resolved biogeography of Phaeocystales, cosmopolitan bloom-forming algae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8559},
pmid = {41022706},
issn = {2041-1723},
support = {NA15OAR4320071//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NA19NOS4780181//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; NSF OCE-1756884//National Science Foundation (NSF)/ ; 970820//Simons Foundation/ ; },
mesh = {Phylogeny ; *Haptophyta/genetics/classification/metabolism ; Phylogeography ; Gene Transfer, Horizontal ; Metagenome ; Oceans and Seas ; Genome ; Genomics ; },
abstract = {Phaeocystales, comprising the genus Phaeocystis and an uncharacterized sister lineage, are nanoplanktonic haptophytes widespread in the global ocean. Several species form mucilaginous colonies and influence key biogeochemical cycles, yet their underlying diversity and ecological strategies remain underexplored. Here, we present new genomic data from 13 strains, including three high-quality reference genomes (N50 > 30 kbp), and integrate previous metagenome-assembled genomes to resolve a robust phylogeny. Divergence timing of P. antarctica aligns with Miocene cooling and Southern Ocean isolation. Genomic traits reveal metabolic flexibility, including mixotrophic nitrogen acquisition in temperate waters and gene expansions linked to polar nutrient adaptation. Concordantly, transcriptomic comparisons between temperate and polar Phaeocystis suggest Southern Ocean populations experience iron and B12 limitation. We also identify signatures of horizontal gene transfer and endogenous giant virus/virophage insertions. Together, these findings highlight Phaeocystales as an ecologically versatile and geographically widespread lineage shaped by evolutionary innovation and adaptation to contrasting environmental stressors.},
}
@article {pmid41021050,
year = {2025},
author = {Kishk, M and Rahmeh, R and Asiri, F and Karam, H and Al-Muhanna, K and Hejji, AB and Shajan, A and Al-Salem, SM},
title = {Substrate-specific microbial community shifts during mesophilic biodegradation of polymers in compost amended soil.},
journal = {Biodegradation},
volume = {36},
number = {5},
pages = {93},
pmid = {41021050},
issn = {1572-9729},
support = {FB187K//Kuwait Institute for Scientific Research/ ; },
mesh = {*Biodegradation, Environmental ; *Polymers/analysis/metabolism ; *Composting ; Soil/chemistry ; *Soil Pollutants/analysis/metabolism ; Plastics/analysis/metabolism ; *Biodegradable Plastics/analysis/metabolism ; Soil Microbiology ; Microbial Consortia ; },
abstract = {Plastics are widely utilized across various industries, but their persistent accumulation in the environment has become a major ecological concern. Biodegradable alternatives offer a potential solution to plastic pollution; however, their degradation behavior under environmentally relevant conditions remains underexplored. This study evaluates the aerobic biodegradation of four polymer materials: starch, commercial thermoplastic starch of polyester origin (TPS1), linear low-density polyethylene (LLDPE), and a co-polyester thermoplastic starch (TPS2), over 180 days at 25 °C in a compost-soil matrix using the testing protocols of ASTM D5988-18 for carbon dioxide (CO2) evolution. Microbial community dynamics were profiled using 16S rRNA and ITS2 amplicon sequencing. TPS2 reached complete mineralization (~ 100%) in 28 days, followed by starch at 71.1% by day 180. TPS1 showed partial mineralization of 38.6%, while LLDPE showed minimal mineralization (21.9%) as expected. Alpha diversity revealed higher bacterial richness in starch treatments and a marked reduction in fungal diversity in TPS1 and LLDPE. Differential abundance testing revealed significant microbial shifts between treatments. Linear discriminant analysis Effect Size (LEfSe) identified polymer-specific microbial biomarkers, including Paenibacillus and Botryotrichum for starch, Acrophialophora and Mycothermus for TPS2, and the Mycobacterium for LLDPE. Subgroup 10 Acidobacteria was uniquely enriched in TPS2-treated samples. These taxa reflect substrate-driven microbial selection. Coupling CO2 mineralization with microbial profiling offers a practical framework to evaluate polymer biodegradability and guide the design of soil-degradable bioplastics. Overall, these findings demonstrate that polymer composition significantly influences microbial community structure and mineralization performance under mesophilic conditions.},
}
@article {pmid41020558,
year = {2025},
author = {Diallo, D and Sene, O and Ngom, D and Khoulé, A and Faye, ET and Dieng, I and Ndione, MHD and Faye, O and Simon-Lorière, E and Diagne, MM and Diallo, M and Sakuntabhai, A and Fall, G},
title = {Detection and genetic characterization of arboviruses and other viruses from mosquitoes collected in southeastern and central Senegal, October 2022.},
journal = {Medical and veterinary entomology},
volume = {39},
number = {4},
pages = {863-874},
doi = {10.1111/mve.70017},
pmid = {41020558},
issn = {1365-2915},
support = {U01AI151758//National Institute of Allergy and Infectious Diseases, National Institues of Health/ ; },
mesh = {Animals ; Senegal ; *Arboviruses/isolation &amp; purification/genetics ; *Culicidae/virology ; Phylogeny ; *Mosquito Vectors/virology ; *Virome ; },
abstract = {The knowledge of the distribution of viruses and their associated mosquito species is still incomplete in Senegal. Additionally, data on the genetic characterization of these viruses are limited. The aim was to update knowledge on the diversity, distribution and genetic relationships of mosquito-associated viruses in Senegal through entomological and molecular surveillance. Mosquitoes were collected in October 2022 across 10 districts in Senegal. Samples were identified morphologically and processed for virome characterization using qRT-PCR and next-generation sequencing. The most common species were Culex cinereus Theobald, 1901, Culex quinquefasciatus Say, 1823, Culex neavei Theobald, 1904, and Culex poicilipes Theobald, 1904 (Diptera: Culicidae). The number of mosquitoes collected varied by habitat and district. We detected 42 isolates of 7 viruses, including Bagaza (BAGV), Barkedji, Sindbis (SINV), Usutu (USUV), Dezidougou, Densovirus and Pestivirus A (PESVA), in 6 mosquito species (Mansonia uniformis, Cx. neavei Theobald, 1901, Anopheles coustani, Cx. cinereus Laveran, 1900, Aedes aegypti Linnaeus, 1762 and Aedes vexans Meigen, 1830) (Diptera: Culicidae). The viruses were mainly detected in mosquitoes collected near ponds (92.9%). BAGV and SINV were detected for the first time in southeastern Senegal. This is also the first association of PESVA with mosquitoes in the field. Phylogenetic analyses revealed that PESVA clustered with strains from Asia and Egypt, BAGV with strains from Senegal and Spain, USUV with strains from Senegal and SINV with strains from Spain and Kenya. This study expands the understanding of mosquito-virus associations in Senegal, revealing new geographic distributions and vectors for several viruses, with implications for arbovirus emergence and surveillance strategies.},
}
@article {pmid41017911,
year = {2025},
author = {Devarajalu, P and Attri, SV and Kumar, J and Dutta, S and Kabeerdoss, J},
title = {Characterization of gut microbiota signatures in Indian preterm infants with necrotizing enterocolitis: a shotgun metagenomic approach.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1649384},
pmid = {41017911},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant, Premature ; India/epidemiology ; Infant, Newborn ; *Enterocolitis, Necrotizing/microbiology/epidemiology ; Feces/microbiology ; *Metagenomics/methods ; Male ; Female ; Enterobacteriaceae/genetics/isolation &amp; purification/classification ; },
abstract = {INTRODUCTION: Necrotizing enterocolitis (NEC) is an inflammatory bowel disease that primarily affects preterm infants. Predisposing risk factors for NEC include prematurity, formula feeding, anemia, and sepsis. To date, no studies have investigated the gut microbiota of preterm infants with NEC in India.<br><br>METHOD: In the current study, shotgun metagenomic sequencing was performed on fecal samples from premature infants with NEC and healthy preterm infants (n = 24). Sequencing was conducted using the NovaSeq X Plus platform, generating 2 &#xd7; 150 bp paired-end reads. The infants were matched based on gestational age and postnatal age.<br><br>RESULT: The median time to NEC diagnosis was 9 days (range: 1-30 days). Taxonomic analysis revealed a high prevalence of Enterobacteriaceae at the family level, with the genera Klebsiella and Escherichia particularly prominent in neonates with NEC. No statistically significant differences in alpha or beta diversity were observed between stool samples from infants with and without NEC. Linear regression analysis demonstrated that Enterobacteriaceae were significantly more abundant in stool samples from infants with NEC than without NEC (q < 0.05). Differential abundance analysis using Linear Discriminant Analysis Effect Size (LEfSe) identified Klebsiella pneumoniae and Escherichia coli as enriched in the gut microbiota of preterm infants with NEC. Functional analysis revealed an increase in genes associated with lipopolysaccharide (LPS) O-antigen, the type IV secretion system (T4SS), the L-rhamnose pathway, quorum sensing, and iron transporters, including ABC transporters, in stool samples from infants with NEC.<br><br>CONCLUSION: The high prevalence of Enterobacteriaceae and enrichment of LPS O-antigen and T4SS genes may be associated with NEC in Indian preterm infants.},
}
@article {pmid41017909,
year = {2025},
author = {Maan, S and Batra, K and Rajendhran, J and Joseph, R and Singh, VK and Chaudhary, D and Sindhu, S and Kadian, V and Kumar, A and Maan, NS and Mor, S},
title = {Exploring viral diversity in diarrheic porcine feces: a metagenomic analysis from an Indian swine farm.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1653342},
pmid = {41017909},
issn = {2235-2988},
mesh = {Animals ; Swine ; *Feces/virology ; *Swine Diseases/virology/epidemiology ; *Metagenomics ; India/epidemiology ; *Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; *Diarrhea/veterinary/virology ; Farms ; Genome, Viral ; Virome ; *Virus Diseases/veterinary/virology ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Pig husbandry is a vital sector in India, providing nutritional security and employment for marginalized communities. Pigs are advantageous due to high reproduction rates and fecundity, shorter generation intervals, and efficient feed conversion, requiring minimal housing. However, the swine industry encounters significant disease challenges, particularly viral gastroenteritis, which poses serious public health risks, especially in developing countries. Pigs serve as natural reservoirs and amplifiers for numerous viruses with zoonotic potential, making disease surveillance essential.<br><br>MATERIALS: In this study, we conducted a metagenomic analysis of 15 fecal samples from diarrheic pigs on a farm in India, marking the first exploration of the fecal virome diversity in this region. Our next-generation sequencing approach has enabled the unbiased detection of multiple viral agents in the porcine fecal samples, detecting both known and novel viral agents without prior target knowledge.<br><br>RESULTS: The key and novel viruses obtained in our study were porcine circovirus, porcine parvovirus 7, porcine mamastrovirus 3, porcine sapelovirus A, and porcine enterovirus G. This work resulted in the generation of full genomes for multiple porcine viruses, including Circovirus, Enterovirus, Sapelovirus, and Mamastrovirus, along with partial genomes of Parvovirus, Picobirnavirus, Porcine stool-associated RNA virus (Porcine Posavirus), Kobuvirus, and Rotavirus, all subjected to phylogenetic analysis.<br><br>CONCLUSION: Our survey indicates frequent co-infections with diverse viruses, creating conducive environments for viral recombination and reassortment. Continuous surveillance of viral pathogens in animal populations is essential for understanding the dynamics of both known and novel viruses and for detecting emerging pathogens, along with their zoonotic and pathogenic potential.},
}
@article {pmid41016664,
year = {2025},
author = {Dong, Y and Zheng, JS and Yang, Y and Wang, T and Li, F and Wu, P and Lai, Y and Wang, Y and He, X and Zhang, P and Zhang, S and Wu, N and Li, S and Yuan, J and Shan, D and Liu, X and Liu, G and Hu, Y and Pan, A and Pan, XF},
title = {Associations between combined healthy lifestyle and adverse birth outcomes in 2 prospective cohorts: roles of gut microbiota and serum metabolites.},
journal = {The American journal of clinical nutrition},
volume = {122},
number = {6},
pages = {1735-1747},
doi = {10.1016/j.ajcnut.2025.09.036},
pmid = {41016664},
issn = {1938-3207},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Adult ; Prospective Studies ; Pregnancy ; Male ; *Healthy Lifestyle ; Infant, Newborn ; *Pregnancy Outcome ; Metabolome ; Cohort Studies ; Birth Cohort ; },
abstract = {BACKGROUND: Maternal lifestyle factors are reported to be associated with adverse birth outcomes (ABOs). These factors may also influence gut microbiota composition and serum metabolic profiles.<br><br>OBJECTIVES: The aim of this study was to investigate the associations between combined healthy lifestyle and ABOs, and the mediating roles of gut microbiota and serum metabolites.<br><br>METHODS: This study was conducted based on the Tongji-Huaxi-Shuangliu Birth Cohort (THSBC), comprising 1086 participants with repeated multiomics data collected at 3 time points. An independent validation was performed using 161 participants from the Huaxi Birth Cohort, with available multiomics data at 5 time points. Participants were classified into 3 lifestyle categories (unhealthy, low healthy, and highly healthy) according to diet, physical activity, smoking, drinking, sleep, and body mass index. Gut microbiota were characterized using 16S rRNA gene sequencing in the THSBC and metagenomics in the Huaxi Birth Cohort, whereas serum metabolites were profiled using untargeted liquid chromatography-mass spectrometry. Clinical data on birth outcomes, such as gestational age, birth weight, and sex, were collected in the THSBC.<br><br>RESULTS: A highly healthy lifestyle was associated with lower risks of macrosomia (MAC) [odds ratio (OR): 0.43; 95% confidence interval (CI): 0.33, 0.57], preterm birth (PTB) (OR: 0.60; 95% CI: 0.46, 0.79), and large for gestational age (LGA) (OR: 0.44; 95% CI: 0.35, 0.56). Among the identified mediators, gut microbiota and serum metabolites, including Eisenbergiella, Tyzzerella, Megamonas, pro-Ile, and 1-amino-1-cyclobutane-carboxylic acid, were negatively associated with a healthy lifestyle, whereas Lachnospiraceae NK4A136 group, 4-methoxyestrone, and lysophosphatidylcholine [LPC(0:0/18:3)] were positively associated. Mediation analyses showed that Eisenbergiella and 4-methoxyestrone explained 11.4% and 13.0% of the inverse association between a highly healthy lifestyle and PTB, respectively, whereas the other microbiota and metabolites mediated 5%-7% of the associations with MAC and LGA.<br><br>CONCLUSIONS: Maternal healthy lifestyle is associated with lower risk of ABOs, with gut microbiota and serum metabolites serving as important mediators in these relationships.},
}
@article {pmid41015602,
year = {2025},
author = {Nazrin, MRR and Pavan, JS and Gouda, MNR and Kumaranag, KM and Suroshe, SS and Kamil, D and Subramanian, S},
title = {Host-Driven Functional Divergence in Gut Microbiota of Honeybees Apis cerana and Apis mellifera: Implications for Pollination, Nutrition, and Sustainable Apiculture.},
journal = {Current microbiology},
volume = {82},
number = {11},
pages = {531},
pmid = {41015602},
issn = {1432-0991},
mesh = {Bees/microbiology/physiology ; Animals ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Pollination ; },
abstract = {Honeybees are indispensable in sustaining natural ecosystems and global crop production by pollinating key food crops. Understanding their gut microbiota is crucial for insights into their health, nutrition, and behavior, with broader ecological and agricultural relevance. This study compares the gut microbiota of Apis cerana and Apis mellifera, focusing on bacterial composition, diversity, and functional roles. Using culture-dependent and metagenomic methods, core bacteria such as Lactobacillus, Fructobacillus, Gilliamella apicola, Bartonella apis, and Snodgrassella alvi were identified, linked to carbohydrate and nitrogen metabolism, immune modulation, and polysaccharide degradation. A. mellifera exhibited greater microbial and functional diversity, reflected in higher Shannon (1.22 vs. 1.08) and Simpson (0.675 vs. 0.655) indices. Strong intraspecies correlations and weaker interspecies correlations (Pearson's r = 0.6486) indicated distinct microbial profiles, supported by PCA (75.3% variation) and Adonis test (P = 0.04, R[2] = 0.723). Functional analysis via MG-RAST and UniFrac-based PCoA showed species-specific differences in key metabolic pathways. Enzymatic profiling revealed Fructobacillus fructosus with high invertase activity (7.31 ± 0.30) and Apilactobacillus apinorum with strong pectinolytic activity (4.707 ± 0.36), enhancing honeybee nutrition. These findings have significant implications for pollination efficiency, probiotic development, and sustainable apiculture, ultimately supporting conservation strategies and the resilience of honeybee populations.},
}
@article {pmid41015591,
year = {2026},
author = {Raziq, K and Saleem, R and Zafar, S and Sanaullah, T and Nazir, MM and Ummara, UE and Abbasi, A},
title = {Environmental resistomes and antimicrobial resistance: integrating the One Health framework.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {399},
number = {2},
pages = {2081-2095},
pmid = {41015591},
issn = {1432-1912},
mesh = {Humans ; *One Health ; Animals ; *Drug Resistance, Bacterial/genetics ; *Microbiota ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/drug effects ; },
abstract = {Antimicrobial resistance (AMR) has emerged as a critical global health challenge, exacerbated by the interconnected dynamics of human, animal, and environmental health systems. The "One Health" approach, which integrates these domains, offers a comprehensive framework for addressing AMR at its roots. This review explores the environmental dimension of AMR by examining the role of environmental microbiomes as reservoirs and transmission vectors of antimicrobial resistance genes (ARGs). It highlights emerging evidence, transmission pathways, detection methodologies, and policy gaps, with an emphasis on low- and middle-income countries (LMICs). An in-depth literature synthesis was conducted across environmental, clinical, and molecular microbiology studies to understand the eco-evolutionary dynamics of resistance, routes of ARG transmission, and effectiveness of current surveillance models. Emphasis was placed on novel detection technologies and integrated policy frameworks. Environmental resistomes present in soil, water, air, and waste play a pivotal yet underappreciated role in ARG dissemination via horizontal gene transfer, mobile genetic elements, and co-selectors like heavy metals and biocides. The complexity of microbial communities in diverse ecological matrices fosters the persistence and evolution of resistance. Current surveillance systems often neglect environmental inputs, particularly in LMICs, limiting the effectiveness of AMR mitigation efforts. A paradigm shift is required to recognize the environmental microbiome as a central component of AMR. Integrated "One Health" strategies, improved environmental surveillance, policy reforms, and novel technological interventions are critical for global AMR control. Bridging the research-policy gap and empowering local surveillance infrastructure can significantly enhance resistance management and public health outcomes.},
}
@article {pmid41015376,
year = {2025},
author = {Zhao, JX and Wang, XY and Zhang, X and Tang, LY and Xie, SC and Lv, YH and Zheng, Z and Gao, YQ and Jiang, J and Zhang, XX and Ma, H},
title = {Toxoplasma gondii alters gut microbiota and systemic metabolism in cats: A multi-omics approach.},
journal = {Veterinary journal (London, England : 1997)},
volume = {314},
number = {},
pages = {106455},
doi = {10.1016/j.tvjl.2025.106455},
pmid = {41015376},
issn = {1532-2971},
mesh = {Animals ; Cats ; *Toxoplasmosis, Animal/metabolism/parasitology/microbiology ; *Gastrointestinal Microbiome ; *Toxoplasma/physiology ; *Cat Diseases/parasitology/metabolism/microbiology ; Female ; Metabolomics ; Male ; Feces/microbiology ; Host-Parasite Interactions ; Multiomics ; },
abstract = {Toxoplasma gondii (T. gondii) is an obligate intracellular parasite with a complex life cycle that culminates in cats-its only definitive host. While its immunological impact is well studied, how T. gondii shapes the feline gut microbiota and systemic metabolism remains largely unexplored. To investigate host-parasite-microbiome interactions, we performed a multi-omics study combining metagenomic sequencing and untargeted serum metabolomics in cats before and after T. gondii infection. Fecal samples were used to construct a comprehensive microbial gene catalog and assess functional shifts, while serum samples were analyzed via liquid chromatography-tandem mass spectrometry (LC-MS/MS) to capture systemic metabolic changes. Infection with T. gondii, particularly during its sexual replication phase, significantly disrupted gut microbial diversity, composition, and function. Functional annotation revealed downregulation of microbial genes involved in vitamin, cofactor, and energy metabolism, alongside upregulation of carbohydrate metabolism pathways. Concurrently, metabolomic profiling showed marked alterations in lipid profiles, amino acid pathways, and folate-mediated one-carbon metabolism. Integrated analysis uncovered strong correlations between specific microbial taxa-such as Bifidobacterium adolescentis and Ligilactobacillus animalis-and host metabolites, underscoring a tight link between microbial function and host metabolic responses to infection. To our knowledge, this is the first study to comprehensively map the microbiome and metabolic landscape of T. gondii infection in the feline host. Our findings reveal profound parasite-induced shifts in microbial function and systemic metabolism, offering new insights into the molecular interplay between host, parasite, and microbiota. These insights may inform future strategies for therapeutic modulation of host responses in toxoplasmosis.},
}
@article {pmid41015306,
year = {2026},
author = {Hou, DJ and Guo, WL and Yang, HW and Liu, QR and Fan, NS and Jin, RC},
title = {Behaviors and adaptive strategies of anammox microbiota in response to typical ionic liquid: Metabolic compensation and gene regulation.},
journal = {Bioresource technology},
volume = {439},
number = {},
pages = {133395},
doi = {10.1016/j.biortech.2025.133395},
pmid = {41015306},
issn = {1873-2976},
mesh = {*Ionic Liquids/pharmacology ; *Microbiota/drug effects/genetics ; *Ammonium Compounds/metabolism ; Wastewater/microbiology ; Oxidation-Reduction ; Anaerobiosis ; *Gene Expression Regulation, Bacterial/drug effects ; Bacteria/metabolism/genetics/drug effects ; Molecular Docking Simulation ; },
abstract = {Ionic liquids (ILs) have been used to replace organic solvents, thereby causing challenges for wastewater treatment. Anaerobic ammonium oxidation (anammox) had been recognized to treat high-strength ammonium wastewater, but its response to ILs remains unclear. Metagenomic sequencing, granule characterization and molecular docking simulation were employed to investigate the comprehensive effects of 1-ethyl-3-methylimidazolium acetate ([EMIM][Ac]) on anammox consortia. [EMIM][Ac] of 2 mg L[-1] reduced the specific anammox activity (SAA) by 46.0 %. [EMIM][Ac] also induced oxidative stress. The higher abundance of denitrifying bacteria and functional genes (nirK and nirS) compensated for the reduced nitrogen removal efficiency. In P2, the total abundance of nirK and nirS in R1 was 16.2 % higher than its initial value, and also 9.6 % higher than that in R0. This study elucidated how anammox microbiota resisted ILs via metabolic regulation and EPS secretion, providing a theoretical support for improving the feasibility and efficiency of anammox-based wastewater treatment systems.},
}
@article {pmid41015172,
year = {2025},
author = {Luo, S and Yuan, J and Song, Y and Qi, J and Zhu, M and Feng, H and Zhao, Y and Mei, W and Fu, F and Li, X and Song, C},
title = {Bacterial network complexity drives carbon, nitrogen and phosphorus metabolism potential under short-term soil water content changes in wetlands.},
journal = {Environmental research},
volume = {286},
number = {Pt 3},
pages = {122952},
doi = {10.1016/j.envres.2025.122952},
pmid = {41015172},
issn = {1096-0953},
mesh = {*Wetlands ; *Phosphorus/metabolism ; *Soil Microbiology ; *Nitrogen/metabolism ; *Carbon/metabolism ; Soil/chemistry ; China ; *Bacteria/metabolism ; Water/analysis ; Droughts ; Microbiota ; },
abstract = {Wetland soil microbial communities play pivotal roles in biogeochemical cycling; however, how their network complexity mediates carbon (C), nitrogen (N), and phosphorus (P) metabolism in response to soil water content (SWC) changes remains unclear. In this study, soil samples from the Zhalong, Momoge and Xianghai wetlands in Songnen Plain of China were incubated under natural (CK), drought (10 % SWC), and high SWC (50 % SWC) conditions, followed by metagenomic sequencing to evaluate the impact of SWC changes on bacterial community structure and function. The results showed that soil bacterial diversity and network complexity decreased under drought but recovered under high SWC, with Proteobacteria and Actinobacteria displaying divergent responses. C fixation pathways (rTCA and DC-HB cycles) were significantly enriched under 50 % SWC, which correlated strongly with enhanced bacterial interactions. The abundance of denitrification genes (norBC, nosZ) decreased under drought but increased under high SWC. P metabolism (purine metabolism and two-component systems) showed strong SWC dependence, with key genes (PstS, phnDC) increased in abundance under 50 % SWC. Notably, bacterial network complexity tightly coupled with metabolic pathways, indicating SWC driven community restructuring regulates wetland soil C, N and P cycling. These findings underscore the critical importance of hydrological management in maintaining bacterial-mediated nutrient cycling functions of wetland ecosystem under climate change.},
}
@article {pmid41015044,
year = {2025},
author = {Mukherjee, A and Mazumder, M and Verma, A and Tikariha, H and Bhattacharya, R and Ooi, QE and Swarup, S},
title = {A bacterial signal coordinates plant-microbe fitness trade-off to enhance sulfur deficiency tolerance in plants.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {10},
pages = {1748-1764.e6},
doi = {10.1016/j.chom.2025.09.007},
pmid = {41015044},
issn = {1934-6069},
mesh = {*Sulfur/deficiency/metabolism ; *Rhizosphere ; Soil Microbiology ; Microbiota ; *Glutathione/metabolism ; *Arabidopsis/genetics/growth &amp; development/microbiology ; Brassicaceae/genetics/growth &amp; development/microbiology ; Genetic Fitness ; Metagenome ; Plant Roots/microbiology ; },
abstract = {Plant-associated microorganisms interact with each other and with host plants via intricate chemical signals, offering multiple benefits, including enhanced nutrition. We report a mechanism through which the rhizosphere microbiome improves plant growth under sulfur (S) deficiency. Disruption of plant S homeostasis caused a coordinated shift in the composition and S-metabolism of the rhizosphere microbiome. Leveraging this, we developed an 18-membered synthetic rhizosphere bacterial community (SynCom) that rescued the growth of Arabidopsis and a leafy Brassicaceae vegetable under S-deficiency. This beneficial trait is taxonomically widespread among SynCom members, with bacterial pairs providing both synergistic and neutral effects on host growth. Notably, stronger competitive interactions among SynCom members conferred greater fitness benefits to the host, suggesting a trans-kingdom (plant-microbe) fitness trade-off. Finally, guided chemical screening, deletion knockout mutants, and targeted metabolomics identified and validated microbially released glutathione (GSH) as the necessary bioactive signal that coordinates the trans-kingdom fitness trade-off and improves plant growth under sulfur limitation.},
}
@article {pmid41014671,
year = {2025},
author = {Zhao, Y and Song, T and Ren, P and Wu, X and Luo, Q and Xie, J and Lai, H and Li, X and Wen, Y and Liao, X and Zhou, J},
title = {Integrating metagenomics, lipidomics and proteomics to explore the effect and mechanism of ginsenoside Rb1 on atherosclerosis co-depression disease.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157301},
doi = {10.1016/j.phymed.2025.157301},
pmid = {41014671},
issn = {1618-095X},
mesh = {Animals ; *Ginsenosides/pharmacology ; *Atherosclerosis/drug therapy/complications ; Proteomics ; Mice ; Lipidomics ; Male ; Gastrointestinal Microbiome/drug effects ; *Depression/drug therapy/complications ; Metagenomics ; Lipid Metabolism/drug effects ; Panax/chemistry ; Mice, Inbred C57BL ; Diet, High-Fat ; Disease Models, Animal ; },
abstract = {BACKGROUND: The comorbidity of atherosclerosis (AS) and depression presents a significant clinical challenge. Its pathogenesis entails complex abnormalities in inflammatory responses, lipid metabolism, and gut microbiota homeostasis. Ginsenoside Rb1 (GRb1)-a bioactive compound derived from the dried roots of Panax ginseng (Araliaceae)-demonstrates anti-inflammatory, antioxidant, lipid-lowering, and neuroprotective properties. However, GRb1's therapeutic potential and underlying mechanisms in AS co-depression remain inadequately characterized.<br><br>PURPOSE: This study aims to elucidate the mechanism of GRb1 in AS co-depression disease, identify potential therapeutic targets, and thereby develop novel therapeutic strategies for this condition.<br><br>METHODS: An AS co-depression comorbidity model was established using ApoE[&#x207b;/&#x207b;] mice fed a high-fat diet and subjected to chronic restraint stress. To evaluate GRb1's therapeutic efficacy, we assessed serum lipid profiles, performed aortic Oil Red O staining, and conducted behavioral tests for depressive-like phenotypes. Furthermore, we employed an integrated multi-omics approach-combining metagenomics, targeted lipid metabolomics, and proteomics-to identify key alterations in gut microbiota, lipid metabolites, and proteins, with subsequent correlation analysis. Key differential proteins and associated pathways identified through multi-omics were validated using both in vivo (AS co-depression mouse model) and in vitro (HT22 cells) experiments. Finally, GRb1's effects on ferroptosis and specific signaling pathways (CD44/Gls2, ACSL4/LPCAT3/ALOX15, SLC7A11/GPX4) were examined via Western blotting, immunofluorescence, and transmission electron microscopy in both mouse tissues and HT22 cells.<br><br>RESULTS: Proteobacteria, Helicobacter, and Helicobacter_typhlonius represent significant intestinal microbiota components. Their primary differential lipids include phosphatidylethanolamine (PE), phosphatidylcholine (PC), and lysophosphatidylcholine (LPC), while key differential proteins encompass CD44, Gls2, and Snrpf. Notably, a strong correlation exists among Helicobacter_typhlonius, PE, and CD44. GRb1 modulates PE metabolic dysregulation by reducing the relative abundance of Helicobacter_typhlonius, thereby inhibiting lipid peroxidation and ameliorating oxidative stress. Furthermore, GRb1 suppresses the CD44/Gls2 axis, ACSL4/LPCAT3/ALOX15 pathway, and activates the SLC7A11/GPX4-mediated ferroptosis pathway, thereby exerting its anti-AS co-depression effects through these multi-target mechanisms.<br><br>CONCLUSION: GRb1 regulates the intestinal microbiota, abnormal lipid metabolism, modulates protein function, inhibits lipid peroxidation, improves oxidative stress, inhibits ferroptosis, regulates the CD44/Gls2, ACSL4/LPCAT3/ALOX15, SLC7A11/ GPX4 signaling pathways, and prevents the progression of AS co-depression disease.},
}
@article {pmid41013611,
year = {2025},
author = {Kazarina, A and Sarkar, S and Adams, B and Vogt, B and Rodela, L and Pogranichny, S and Powell, S and Wiechman, H and Heeren, L and Reese, N and Thompson, D and Ran, Q and Hartung, E and Akhunova, A and Akhunov, E and Johnson, L and Jumpponen, A and Lee, STM},
title = {Interaction of plant-derived metabolites and rhizobiome functions enhances drought stress tolerance.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {310},
pmid = {41013611},
issn = {1474-760X},
support = {2020-67019-3180//National Institute of Food and Agriculture/ ; 2238633//National Science Foundation CAREER Award/ ; INV-004430/GATES/Gates Foundation/United States ; INV-004430/GATES/Gates Foundation/United States ; OIA-1656006//National Science Foundation Award/ ; },
mesh = {*Rhizosphere ; *Stress, Physiological ; *Plant Roots/microbiology/metabolism ; *Droughts ; Soil Microbiology ; *Microbiota ; },
abstract = {BACKGROUND: Plants have evolved alongside microbes, enabling plants to better cope with abiotic and biotic stress. Interactions between plant roots and local soil microbes are critical for environmental adaptation and plant health. Plants actively regulate the microbial community composition in their rhizospheres to recruit specific microorganisms that enhance their fitness in the ecosystem they inhabit. This study builds on prior research suggesting that plants exhibit a "home field advantage" by preferentially recruiting microbes unique to their native environments, likely through mutual recognition and selective recruitment mechanisms.<br><br>RESULTS: Using gene- and genome-centric approaches, we assess the functional potential of root-associated microbes and profile their host metabolites to uncover the metabolic outputs potentially regulating host&#x2012;microbe interactions in Andropogon gerardii. We find that plants adapted to drier environments experience less stress, producing fewer stress-related metabolites and impacting the recruitment of microbes with genes linked to stress relief pathways. In particular, plant-derived trimethyllysine is highly associated with microbial populations capable of improving nutrient uptake, producing plant growth-promoting compounds, and modulating stress responses.<br><br>CONCLUSIONS: This study highlights the critical interplay between host exudates and microbial substrate uptake as the primary mechanism of rhizosphere assembly. We demonstrate that plants actively produce metabolites to recruit microbial populations with the functional potential to enhance their ability to thrive in stressful environments. This research provides insights into the mechanisms of plant-microbe communication, rhizosphere recruitment, and the complex interplay of plant-microbe interactions. Furthermore, it highlights promising avenues for manipulating rhizosphere microbiomes to support conservation agriculture when coping with climate change.},
}
@article {pmid41013568,
year = {2025},
author = {Lei, Y and Zheng, Y and Yan, Y and Zhang, K and Sun, X and Yang, B and Ge, L and Meng, Z and Cao, X and Zhang, X and Yan, X and Xu, Y and Zhang, T and Shi, J and Chen, S and Qiu, Q and Chen, Y and Deng, L and Li, Z and Wang, X and Zhang, K},
title = {Deciphering functional landscapes of rumen microbiota unveils the role of Prevotella bryantii in milk fat synthesis in goats.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {311},
pmid = {41013568},
issn = {1474-760X},
support = {2022YFD1300203//the National Key Research and Development Program of China/ ; 2022ZD04014//the Biological Breeding-Major Projects/ ; CARS-39-03//the China Agricultural Research System/ ; 32402785//the National Natural Science Foundation of China/ ; 2024PT-ZCK-71-3//the Key Research and Development Program of Shaanxi Province/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Goats/microbiology ; *Milk/metabolism ; *Prevotella/genetics/metabolism ; Female ; *Gastrointestinal Microbiome ; Lactation ; *Microbiota ; Lipid Metabolism ; Niacinamide/metabolism ; },
abstract = {BACKGROUND: The rumen microbiome is critical for regulating milk synthesis in dairy livestock, yet the molecular mechanisms linking microbial functions to host lipid metabolism remain poorly understood. While host genetics and microbial composition have been studied, integrative analyses of the rumen-blood-mammary gland axis remain lacking.<br><br>RESULTS: Here, we present the goat rumen microbial reference gene catalog and 5514 metagenome-assembled genomes (MAGs) from 160 multi-breed rumen samples. Integrating this resource with lactation data from 177 Saanen dairy goats, we identify Prevotella spp. as keystone taxa driving concurrent increases in milk yield and fat percentage. Functional and metabolomic profiling reveals that Prevotella bryantii B14 synthesizes nicotinate, which is converted to nicotinamide in circulation. Using in vitro and in vivo models, we demonstrate that nicotinamide activates the mTORC1 pathway in mammary epithelial cells via GPR109A, which upregulates transcription factors SREBP and PPAR-&#x3b3; and the downstream lipogenic genes FASN, ACC&#x3b1;, and SCD1 to promote milk fat synthesis. In contrast, the relative deficiency of P. bryantii B14 and the associated reduction in nicotinamide levels in the rumen of poor lactating dairy goats may represent a significant contributor to impaired lactation performance. Additionally, the enhanced hydrogenotrophic methanogenesis activity may also adversely affect their lactation phenotype.<br><br>CONCLUSIONS: Our study establishes a causal link between rumen microbial metabolism and mammary lipid synthesis mediated by nicotinamide-mTORC1 signaling and identifies Prevotella abundance as a biomarker for precision breeding. These findings advance the understanding of microbiome-host crosstalk in lactation and provide actionable strategies for enhancing dairy productivity through microbiota-targeted interventions.},
}
@article {pmid41012703,
year = {2025},
author = {Johnson, ML and Boezen, D and Grum-Grzhimaylo, AA and van der Vlugt, RAA and de Visser, JAGM and Zwart, MP},
title = {Living Together Apart: Quantitative Perspectives on the Costs and Benefits of a Multipartite Genome Organization in Viruses.},
journal = {Viruses},
volume = {17},
number = {9},
pages = {},
pmid = {41012703},
issn = {1999-4915},
support = {016.VIDI.171.061/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Genome, Viral ; *Plant Viruses/genetics/physiology ; Host Specificity ; Metagenomics ; Plant Diseases/virology ; Plants/virology ; },
abstract = {BACKGROUND: Multipartite viruses individually package their multiple genome segments into virus particles, necessitating the transmission of multiple virus particles for effective viral spread. This dependence poses a cost in the form of reduced transmission compared to monopartite viruses, which only have a single genome segment. The notable cost of a multipartite genome organization has spurred debate on why multipartite viruses are so common among plant viruses, including a search for benefits associated with this organizational form.<br><br>METHODS: We investigated the costs and benefits of multipartite viruses with three approaches. First, we reanalyzed dose-response data to measure the cost of multipartition to between-host transmission for multipartite viruses. Second, we developed a simulation model to explore when the sharing of viral gene products between cells is beneficial. Third, we tested whether multipartite viruses have a broad host range by estimating the host range for plant viruses using metagenomics data.<br><br>RESULTS: We find that the observed cost to transmission exceeds theoretical predictions. We predict that a virus gene-product-sharing strategy only confers benefits under limited conditions, suggesting that this strategy may not be common. Our results suggest that multipartite and segmented viruses have broader host ranges than monopartite viruses.<br><br>CONCLUSIONS: Our analyses also suggest there is limited evidence for the costs and benefits of a multipartite organization, and we argue that the diversity of multipartite virus-host systems demands pluralistic explanatory frameworks.},
}
@article {pmid41012679,
year = {2025},
author = {Hernández, LHA and da Silva, FS and da Paz, TYB and Dias, DD and de Barros, BCV and Nunes, BTD and Casseb, LMN and da Silva, SP and da Costa Vasconcelos, PF and Cruz, ACR},
title = {Virome Analysis of Small Mammals from the Brazilian Amazon.},
journal = {Viruses},
volume = {17},
number = {9},
pages = {},
pmid = {41012679},
issn = {1999-4915},
support = {3286/2013//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 88887.636166/2021-00//Coordena&#xe7;&#xe3;o de Aperfeicoamento de Pessoal de N&#xed;vel Superior/ ; 310295/2021-1//National Council for Scientific and Technological Development/ ; 406490/2023-6//National Council for Scientific and Technological Development/ ; 314522/2021-2//National Council for Scientific and Technological Development/ ; 406360/2022-7//Instituto Nacional de Ci&#xea;ncia e Tecnologia em Viroses Emergentes e Reemergentes/ ; },
mesh = {Animals ; Brazil ; *Virome ; *Chiroptera/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Opossums/virology ; *Rodentia/virology ; Animals, Wild/virology ; *Mammals/virology ; },
abstract = {The municipalities of Peixe-Boi and Santa Bárbara do Pará, both in the Pará State (eastern Amazon), have more than half of their territory deforested. Understanding the viral diversity in wildlife that inhabits the surroundings of human communities contributes to strengthening surveillance. Samples from eleven bats, seven opossums, and eight rodents from the two locations were screened by high-throughput sequencing for virome analysis. Viral reads were assigned into twenty viral families, from which the most abundant was Retroviridae. Host order, tissue type, and season showed a significant effect on viral composition. Five viral genomes of bat ERVs with intact genes were recovered, showing the need to understand their endogenous nature. In addition, a new Buritiense virus (Hantaviridae) strain was also obtained, supporting its circulation in Santa Bárbara do Pará and expanding its genomic information. Together, these findings reinforce the need for continuous surveillance in wild animals, especially in the Amazon region, to anticipate potential threats to public health.},
}
@article {pmid41011853,
year = {2025},
author = {Saylam, E and Özden, &#xd6; and Yerlikaya, FH and Sivrikaya, A and Yormaz, S and Arslan, U and Topkafa, M and Maçin, S},
title = {Investigation of Intestinal Microbiota and Short-Chain Fatty Acids in Colorectal Cancer and Detection of Biomarkers.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
pmid = {41011853},
issn = {2076-0817},
support = {22401140//Sel&#xe7;uk University/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/microbiology/diagnosis/pathology/metabolism ; Male ; Female ; *Fatty Acids, Volatile/metabolism/analysis ; Middle Aged ; Feces/microbiology/chemistry ; Haptoglobins ; Aged ; Protein Precursors ; Acute-Phase Proteins/analysis ; Cholera Toxin/blood ; *Biomarkers, Tumor ; Carrier Proteins/blood ; Membrane Glycoproteins/blood ; Biomarkers ; Bacteria/classification/genetics/isolation &amp; purification ; Adult ; Lipopolysaccharide-Binding Protein ; },
abstract = {Colorectal cancer (CRC) is one of the most common cancers worldwide and a significant global health issue. The human gut microbiota, a complex ecosystem hosting numerous microorganisms such as bacteria, viruses, fungi, and protozoa, plays a crucial role. Increasing evidence indicates that gut microbiota is involved in CRC pathogenesis. In this study, the gut microbiota profiles, short-chain fatty acids, zonulin, and lipopolysaccharide-binding protein levels of newly diagnosed CRC patients were analyzed along with healthy controls to elucidate the relationship between CRC and the gut microbiota. The study included 16 newly diagnosed CRC patients and 16 healthy individuals. For microbiota analysis, DNA isolation from stool samples was performed using the Quick-DNA™ Fecal/Soil Microbe Miniprep Kit followed by sequencing using the MinION device. Data processing was conducted using Guppy software (version 6.5.7) and the Python (3.12) programming language. ELISA kits from Elabscience were utilized for analyzing LBP and zonulin serum levels. Fecal short-chain fatty acids were analyzed using GC-MS/MS equipped with a flame ionization detector and DB-FFAP column. Microbial alpha diversity, assessed using Shannon and Simpson indices, was found to be lower in CRC patients compared to healthy controls (p = 0.045, 0.017). Significant differences in microbial beta diversity were observed between the two groups (p = 0.004). At the phylum level, Bacteroidota was found to be decreased in CRC patients (p = 0.027). Potential biomarker candidates identified included Enterococcus faecium, Ruminococcus bicirculans, Enterococcus gilvus, Enterococcus casseliflavus, Segatella oris, and Akkermansia muciniphila. Serum zonulin levels were higher in CRC patients (CRC = 70.1 ± 26.14, Control = 53.93 ± 17.33, p = 0.048). There is a significant relationship between gut microbiota and CRC. A multifactorial evaluation of this relationship could shed light on potential biomarker identification and the development of new treatment options for CRC.},
}
@article {pmid41011835,
year = {2025},
author = {Ezzat, A and Abd El Wahed, A and Ceruti, A and El Asely, AM and Khalifa, MS and Winters, AD and Truyen, U and Shaheen, AA and Faisal, M},
title = {Exploring the Virome of Nile Tilapia (Oreochromis niloticus) Using Metagenomic Analysis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {9},
pages = {},
pmid = {41011835},
issn = {2076-0817},
mesh = {Animals ; *Cichlids/virology ; *Virome/genetics ; *Metagenomics/methods ; Phylogeny ; *Fish Diseases/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Egypt ; DNA Viruses/genetics/classification/isolation &amp; purification ; Metagenome ; },
abstract = {Nile tilapia (Oreochromis niloticus) is an indispensable source of high-quality protein worldwide. Along with the exponential expansion of tilapia aquaculture, several novel pathogenic viruses have emerged, and some cause significant economic losses. Unfortunately, there is scarce information on the biology and epidemiology of these viruses. This exploratory metagenomic study used Oxford Nanopore Technology (ONT) sequencing to profile the virome compositions of both wild and farmed Nile tilapia across five regions in Egypt. The Nile tilapia virome was dominated by two double-stranded DNA bacteriophages, Muvirus mu and M. sfmu, which constituted 79.8% of the detected sequences. Eukaryotic viruses, including members of the families Amnoonviridae, Peribunyaviridae, and Baculoviridae, were also identified. Two giant DNA viruses known to infect Acanthamoeba spp., Mollivirus sp., and Pandoravirus sp. were identified in the spleen virome of tilapia from a single sampling site. The diversity analysis showed no significant differences among tissue types or sampling sites. Phylogenetic analyses were performed on a single virus detected of potential pathogenicity, an amnoonvirus. The analyses demonstrated that the detected virus is a member of the family Amnoonviridae and placed it alongside members of the Tilapinevirus genus. The virus, however, was distinct from the other two members in the genus: T. tilapae and T. poikilos. This study underscores the usefulness of ONT in providing a foundational understanding of the Nile tilapia virome.},
}
@article {pmid41010985,
year = {2025},
author = {Petrelli, F and Ghidini, A and Dottorini, L and Ghidini, M and Zaniboni, A and Tomasello, G},
title = {Clinical Evidence for Microbiome-Based Strategies in Cancer Immunotherapy: A State-of-the-Art Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {9},
pages = {},
pmid = {41010985},
issn = {1648-9144},
mesh = {*Gastrointestinal Microbiome/immunology ; *Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; Drug Resistance, Neoplasm/immunology ; Symbiosis/immunology ; Progression-Free Survival ; *Neoplasms/immunology/mortality/therapy ; Fecal Microbiota Transplantation ; Humans ; Clinical Trials as Topic ; Probiotics/administration &amp; dosage ; },
abstract = {The gut microbiome has emerged as a critical determinant of immune-checkpoint inhibitor (ICI) efficacy. A narrative review of 95 clinical studies (2015-2025) shows that patients with greater gut microbial diversity and relative enrichment of commensals such as Akkermansia, Ruminococcus, and other short-chain fatty acid producers experience longer progression-free and overall survival, particularly in melanoma and non-small-cell lung cancer. Broad-spectrum antibiotics given within 30 days of ICI initiation and over-the-counter mixed probiotics consistently correlate with poorer outcomes. Early phase I/II trials of responder-derived fecal microbiota transplantation in ICI-refractory melanoma achieved objective response rates of 20-40%, while pilot high-fiber or plant-forward dietary interventions improved immunologic surrogates such as CD8[+] tumor infiltration. Machine-learning classifiers that integrate 16S or metagenomic profiles predict ICI response with an area under the ROC curve of 0.83-0.92. Methodological heterogeneity across sampling, sequencing, and clinical endpoints remains a barrier, underscoring the need for standardization and larger, well-powered trials.},
}
@article {pmid41010544,
year = {2025},
author = {Liu, Y and Kuang, W and Li, M and Wang, Z and Liu, Y and Zhao, M and Huan, H and Yang, Y},
title = {Cholesterol-Lowering Mechanism of Lactobacillus Bile Salt Hydrolase Through Regulation of Bifidobacterium pseudolongum in the Gut Microbiota.},
journal = {Nutrients},
volume = {17},
number = {18},
pages = {},
pmid = {41010544},
issn = {2072-6643},
support = {2024YFF0619500; no. BK20231280; CX(22)2019//National Key Research and Development Program of China; Natural Science Foundation of Jiangsu; Jiangsu Agriculture Science and Technology Innovation Fund/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; *Amidohydrolases/metabolism/pharmacology ; *Cholesterol/blood ; Mice ; Male ; *Bifidobacterium/growth &amp; development/drug effects/metabolism ; *Lactobacillus/enzymology ; *Hypercholesterolemia/blood/microbiology ; Cholesterol 7-alpha-Hydroxylase/metabolism ; Fibroblast Growth Factors/metabolism ; Mice, Inbred C57BL ; *Anticholesteremic Agents/pharmacology ; Bile Acids and Salts/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; Probiotics ; Receptor, Farnesoid X-Activated ; },
abstract = {Background: Cardiovascular diseases (CVDs) represent a major global health burden, and cholesterol reduction is a key strategy for their prevention and management. This study investigated the mechanism by which bile salt hydrolase (BSH) from Lactobacilli reduces cholesterol levels by modulating the growth of Bifidobacterium pseudolongum. Methods: The BSH-recombinant strain YB334 was administered to high-cholesterol-diet mice, and the cholesterol-lowering function of the strain was evaluated by assessing serum cholesterol parameters, including total cholesterol (TC), low-density lipoprotein (LDL) and high-density lipoprotein (HDL). Metagenomic sequencing was used to analyze the gut microbiota, leading to the screening and acquisition of the "responsive" strains affected by BSH. Subsequent investigations were conducted into their cholesterol-lowering effects and mechanisms of action. Results: Oral administration of the BSH-recombinant strain YB334 can effectively reduce serum cholesterol levels in hypercholesterolemic mice while simultaneously leading to a significant increase in the abundance of B. pseudolongum within the gut microbiota. In vitro experiments indicated that this increased abundance might be closely associated with the strain's high tolerance to CA, the catalytic product of the BSH enzyme. The BPL-4 strain, obtained through screening, demonstrated cholesterol-lowering efficacy. Mechanistically, BPL-4 altered bile acid pool composition and modulated the farnesoid X receptor (FXR) signaling axis: it suppressed ileal FXR-fibroblast growth factor 15 (FGF15) expression, thereby de-repressing hepatic cholesterol 7α-hydroxylase (CYP7A1) and accelerating cholesterol catabolism into bile acids. Conclusions: This study provides the first evidence that BSH from lactobacilli can shape the signature gut microbiota by modulating bile acid metabolism via the FXR-CYP7A1 axis, thereby demonstrating a mechanism for its cholesterol-lowering effects.},
}
@article {pmid41009770,
year = {2025},
author = {Pita-Galeana, MA and Ruhle, M and López-Vázquez, L and de Anda-Jáuregui, G and Hernández-Lemus, E},
title = {Computational Metagenomics: State of the Art.},
journal = {International journal of molecular sciences},
volume = {26},
number = {18},
pages = {},
pmid = {41009770},
issn = {1422-0067},
mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Computational Biology/methods ; Machine Learning ; Metagenome ; },
abstract = {Computational metagenomics has revolutionized our understanding of the human microbiome, enabling the characterization of microbial diversity, the prediction of functional capabilities, and the identification of associations with human health outcomes. This review provides a concise yet comprehensive overview of state-of-the-art computational approaches in metagenomics, alongside widely used methods and tools employed in amplicon-based metagenomics. It is intended as an introductory resource for new researchers, outlining key methodologies, challenges, and future directions in the field. We discuss recent advances in bioinformatics pipelines, machine learning (ML) models, and integrative frameworks that are transforming our understanding of the microbiome's role in health and disease. By addressing current limitations and proposing innovative solutions, this review aims to outline a roadmap for future research and clinical translation in computational metagenomics.},
}
@article {pmid41007466,
year = {2025},
author = {Godoy-Vitorino, F},
title = {Strengthening Integrative Microbiome Research Through Regional Leadership.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {9},
pages = {},
pmid = {41007466},
issn = {1660-4601},
support = {U54 MD007600/MD/NIMHD NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; 1P20GM156713-01/GM/NIGMS NIH HHS/United States ; P20 GM156713/GM/NIGMS NIH HHS/United States ; 2U54MD007600//Center for Collaborative Research in Minority Health and Health Disparities/ ; },
mesh = {*Microbiota ; Puerto Rico ; Leadership ; Humans ; Metagenomics ; Research/organization &amp; administration ; },
abstract = {Microbiome science has revolutionized modern biology, shifting the focus from pathogens to the essential roles of beneficial microbes in health, metabolism, and ecosystems. Advances in genomic technologies like metagenomics have rapidly expanded our understanding of microbial diversity and function. Despite this progress, global microbiome research remains concentrated in high-resource regions, limiting diverse perspectives and opportunities in places like the Caribbean. This communication discusses the establishment of the first Center for Microbiome Sciences in Puerto Rico, which addresses this gap by providing local researchers with access to advanced tools, training, and infrastructure through broader collaboration. Novelty, services, and ideas on the integration of activities among local centers for the scientific improvement of the region are addressed. Additionally, how the center is poised to contribute to improving public and environmental health is also highlighted.},
}
@article {pmid41006832,
year = {2025},
author = {Hug, LA and Hatzenpichler, R and Moraru, C and Soares, AR and Meyer, F and Heyder, A and , and Probst, AJ},
title = {A roadmap for equitable reuse of public microbiome data.},
journal = {Nature microbiology},
volume = {10},
number = {10},
pages = {2384-2395},
pmid = {41006832},
issn = {2058-5276},
support = {CTC 1439/2//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; MO3498/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; OCE-2049445//National Science Foundation (NSF)/ ; },
mesh = {*Microbiota/genetics ; *Information Dissemination/methods ; Humans ; },
abstract = {Science benefits from rapid open data sharing, but current guidelines for data reuse were established two decades ago, when databases were several million times smaller than they are today. These guidelines are largely unfamiliar to the scientific community, and, owing to the rapid increase in biological data generated in the past decade, they are also outdated. As a result, there is a lack of community standards suited to the current landscape and inconsistent implementation of data sharing policies across institutions. Here we discuss current sequence data sharing policies and their benefits and drawbacks, and present a roadmap to establish guidelines for equitable sequence data reuse, developed in consultation with a data consortium of 167 microbiome scientists. We propose the use of a Data Reuse Information (DRI) tag for public sequence data, which will be associated with at least one Open Researcher and Contributor ID (ORCID) account. The machine-readable DRI tag indicates that the data creators prefer to be contacted before data reuse, and simultaneously provides data consumers with a mechanism to get in touch with the data creators. The DRI aims to facilitate and foster collaborations, and serve as a guideline that can be expanded to other data types.},
}
@article {pmid41006795,
year = {2025},
author = {Aoyagi, LN and Wang, Y and Ohbayashi, T and Hirono, Y and Hayatsu, M and Tago, K},
title = {Diversity and characterization of the ammonia-oxidizing bacteria responsible for nitrification in tea field soils.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {33221},
pmid = {41006795},
issn = {2045-2322},
support = {JPNP18016//New Energy and Industrial Technology Development Organization (NEDO)/ ; 16K14874//MEXT KAKENHI/ ; 19H01156//MEXT KAKENHI/ ; 28004A//Science and Technology Research Promotion Program for Agriculture, Forestry, Fisheries, and Food Industry/ ; },
mesh = {*Nitrification ; *Ammonia/metabolism ; *Soil Microbiology ; Oxidation-Reduction ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Soil/chemistry ; Archaea/metabolism/genetics/classification ; Phylogeny ; *Tea/microbiology ; Biodiversity ; },
abstract = {Ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and comammox Nitrospira have been considered to coexist in acidic soils, oxidizing ammonia within their respective niches. However, their relative contributions to soil nitrification, as well as their properties and ecological roles in acidic soils, remain poorly understood. This study focused on AOB in acidic tea field soils, investigating their ecology and physiology through metagenomic analysis and the genomic and physiological characterization of AOB isolates. β-AOB were significantly more abundant than γ-AOB and AOA in soil layers with the highest potential for nitrification activity, indicating that β-AOB play a key role in acidic tea soil. Diversity analysis of this dominant group identified Nitrosospira as the major genus present in tea fields, and four pure strains representing some of the main operational taxonomic units in this environment were isolated. Physiological and genetic characterization of these isolates revealed some distinct traits compared to other species of the genus and closely related taxa, suggesting adaptations that may contribute to niche differentiation and survival in acidic soils. These findings provide new insights into the ecological role of β-AOB in acidic soils and may inform strategies to manage soil nitrification and reduce nitrogen loss in agricultural ecosystems.},
}
@article {pmid41006325,
year = {2025},
author = {Zhang, L and Zhou, DD and Feng, J and Liao, ZJ and Shu, XL and Yang, RM and Gao, YC and Zhou, HH and Zhang, W and Zou, Y and Liu, R},
title = {Intestinal fungal signatures and their impact on immune checkpoint inhibitor efficacy: a multi-cohort meta-analysis.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {188},
pmid = {41006325},
issn = {2055-5008},
support = {2021YFA1301200//the National Key Research and Development Program/ ; No. 82474022, 31801121, 82373961//the National Scientific Foundation of China/ ; 2022RC1022//the Hunan Provincial Science and Technology Innovation Plan Project/ ; },
mesh = {*Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects ; *Fungi/classification/genetics/isolation &amp; purification ; Animals ; Mice ; Feces/microbiology ; Cohort Studies ; *Neoplasms/drug therapy/microbiology ; },
abstract = {Gut microbiota influence on the effectiveness of immune checkpoint inhibitors (ICIs), but research on fungi-an essential component of the microbiome-has been limited. This multi-cohort meta-analysis of 976 fecal metagenomes across 8 cohorts, representing melanoma, non-small cell lung cancer (NSCLC), and renal cell carcinoma (RCC), identified fungal species associated with ICI efficacy. In melanoma, Rhizophagus irregularis and Debaryomyces hansenii were correlated with poor responses, whereas Aspergillus avenaceus was associated with great efficacy. In NSCLC, an increased abundance of Aspergillus pseudonomiae was associated with a favorable prognosis. Stronger bacterial-fungal interactions were observed in responders. The presence of certain fungi in fungal enterotypes, like Aspergillus or Saccharomyces, was linked to better efficacy to ICIs. Mouse models revealed Debaryomyces hansenii impaired ICI efficacy by reducing CD8+ T cells. Our findings highlight specific fungal signatures that may inform strategies to enhance ICI efficacy and encourage further research on microbial impacts on treatment outcomes.},
}
@article {pmid41005935,
year = {2026},
author = {Yang, W and Xin, X and Cao, X},
title = {Impacts of trace ofloxacin on autotrophic denitrification process driven by pyrite/sulfur: Performance, microbial community evolution and metagenomic analysis.},
journal = {Journal of environmental sciences (China)},
volume = {159},
number = {},
pages = {775-784},
doi = {10.1016/j.jes.2025.03.062},
pmid = {41005935},
issn = {1001-0742},
mesh = {*Denitrification/drug effects ; Autotrophic Processes ; *Water Pollutants, Chemical/toxicity/analysis ; Sulfides/chemistry ; *Ofloxacin/toxicity/analysis ; Sulfur/chemistry ; Iron/chemistry ; Metagenomics ; *Microbiota/drug effects ; Anti-Bacterial Agents/toxicity ; Bioreactors ; },
abstract = {In this work, ofloxacin (OFL), a kind of frequently detected antibiotic in groundwater, was selected to explore its impact (at ng/L-µg/L-level) on denitrification performance in an autotrophic denitrification system driven by pyrite/sulfur (FeS2/S[0]). Results showed that OFL restrained nitrate removal efficiency, and the inhibition degree was positively related to the concentration of OFL. After being exposed to increased OFL (200 ng/L-100 µg/L) for 69 days, higher inhibition of electron transport activity (ETSA), enzyme activities of nitrate reductase (NAR), and nitrite reductase (NIR) were acquired. Meanwhile, the extracellular protein (PN) content of sludge samples was remarkably stimulated by OFL to resist the augmented toxicity. OFL contributed to increased microbial diversity and sulfur/sulfide oxidation functional genes in ng/L-level bioreactors, whereas led to a decline in µg/L level experiments. With OFL at concentrations of 200 ng/L and 100 µg/L, the whole expression of 10 key denitrification functional genes was depressed, and the higher the OFL concentration, the lower the expression level. However, no significant proliferation of antibiotic resistance genes (ARGs) either in 200 ng/L-OFL or 100 µg/L-OFL groups was observed. Two-factor correlation analysis results indicated that Thiobacillus, Anaerolineae, Anaerolineales, and Nitrospirae might be the main hosts of existing ARGs in this system.},
}
@article {pmid41005808,
year = {2025},
author = {Purcell, M and Ackland, J and Staples, KJ and Freeman, A and Wilkinson, TMA},
title = {The respiratory tract virome: unravelling the role of viral dark matter in respiratory health and disease.},
journal = {European respiratory review : an official journal of the European Respiratory Society},
volume = {34},
number = {177},
pages = {},
pmid = {41005808},
issn = {1600-0617},
mesh = {Humans ; *Virome ; *Viruses/genetics/pathogenicity/immunology ; Host-Pathogen Interactions ; *Microbiota ; *Respiratory System/virology ; *Respiratory Tract Infections/virology ; Metagenomics ; *Respiratory Tract Diseases/virology/diagnosis ; Animals ; },
abstract = {The human respiratory tract virome is an underexplored component of the microbiome that includes eukaryotic viruses, bacteriophages and archaeal viruses. The respiratory virome represents a dynamic and heterogeneous ecosystem, shaped by host, environmental and microbial factors. Advances in metagenomic sequencing have expanded our understanding of virome composition, dynamics and potential roles in health and disease. Despite increasing interest, virome research remains fragmented and often secondary to bacteriome studies. Challenges in study design, genomic characterisation and interpretation limit consistent conclusions. This review summarises current knowledge of the respiratory virome in health and across acute and chronic respiratory diseases, including acute respiratory infection, asthma, COPD, cystic fibrosis and bronchiectasis. While each condition is distinct, they share features of airway inflammation and immune dysregulation where the virome may act as a modifier or marker. Across these syndromes, emerging evidence highlights the consistent detection of respiratory viruses including potential commensals, such as Anelloviridae, and the often-overlooked role of bacteriophages. We also discuss the concept of viral dark matter, where large proportions of sequence data remain unclassified, potentially representing novel viral taxa. Technical and conceptual challenges are evaluated, alongside recent methodological innovations such as meta-transcriptomics and viral enrichment protocols. We outline how standardised, multi-omic and longitudinal approaches are urgently needed to clarify the virome's functional role, interactions with immunity and microbial communities and its utility as a biomarker or therapeutic target.},
}
@article {pmid41005405,
year = {2025},
author = {Gomes, BM and de Oliveira, GS and de Melo, VS and Rossini, NO and Adriani, PP and Dias, MVB and Chambergo, FS},
title = {Structural and functional characterization of a bifunctional GH43 α-L-arabinofuranosidase/β-xylosidase from the metagenome of Pseudacanthotermes militaris gut.},
journal = {International journal of biological macromolecules},
volume = {329},
number = {Pt 2},
pages = {147909},
doi = {10.1016/j.ijbiomac.2025.147909},
pmid = {41005405},
issn = {1879-0003},
mesh = {*Glycoside Hydrolases/chemistry/metabolism/genetics ; *Xylosidases/chemistry/metabolism/genetics ; Substrate Specificity ; *Metagenome ; Animals ; *Isoptera/enzymology/genetics/microbiology ; Kinetics ; *Gastrointestinal Microbiome ; Models, Molecular ; Catalytic Domain ; Amino Acid Sequence ; },
abstract = {The pursuit of sustainable energy has intensified the search for efficient biocatalysts to convert lignocellulosic biomass. In this context, we characterized a novel bifunctional enzyme, TerARA, identified from the gut metagenome of the termite Pseudacanthotermes militaris. Belonging to the glycoside hydrolase 43 (GH43) family, TerARA was heterologously expressed in E. coli BL21 and purified. The enzyme demonstrated bifunctional activity toward synthetic substrates p-nitrophenyl-α-L-arabinofuranoside (pNP-Araf) (387.22 ± 74.2 U/mg) and p-nitrophenyl-β-D-xylopyranoside (pNP-Xyl) (330.82 ± 31.2 U/mg), with higher catalytic efficiency for pNP-Araf (9.14 s[-1]·mM[-1]), suggesting functional preference as an α-L-arabinofuranosidase. Activity modulation by metal ions revealed that Ca[2+] slightly improved efficiency toward pNP-Araf (to 9.58 s[-1]·mM[-1] at 1 mM), while Zn[2+] reduced efficiency for pNP-Xyl except at 5 mM (6.65 s[-1]·mM[-1]). Zn[2+] also enhanced enzymatic stability, maintaining 80 % activity in pNP-Xyl hydrolysis. Crystallographic analysis at 2.0 Å resolution revealed a 43 Glycosyl Hydrolase catalytic domain with a five-bladed β-propeller fold and two Ca[2+] ions and a Carbohydrate-Binding Module (CBM) domain with a β-sandwich fold likely involved in substrate interaction. Conserved catalytic residues, binding sites, and Ca[2+] stabilizing effects were identified. TerARA's bifunctionality and structural features support its application in hemicellulose degradation and biomass conversion.},
}
@article {pmid41005300,
year = {2025},
author = {Zhao, CN and Li, SS and Yau, T and Chen, WQ and Ji, R and Guan, XY and Kong, FS},
title = {Phocaeicola vulgatus induces immunotherapy resistance in hepatocellular carcinoma via reducing indoleacetic acid production.},
journal = {Cell reports. Medicine},
volume = {6},
number = {10},
pages = {102370},
pmid = {41005300},
issn = {2666-3791},
mesh = {Metagenomics ; *Gastrointestinal Microbiome/genetics/immunology ; *Carcinoma, Hepatocellular/drug therapy/immunology/microbiology/pathology ; Drug Resistance, Neoplasm/immunology ; *Liver Neoplasms/drug therapy/immunology/microbiology/pathology ; *Indoleacetic Acids/metabolism ; Fecal Microbiota Transplantation ; CD8-Positive T-Lymphocytes/immunology/metabolism ; *Bacteroides/genetics/immunology/isolation &amp; purification/metabolism ; *Dysbiosis/diagnosis/immunology/microbiology ; *Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; Programmed Cell Death 1 Receptor/antagonists &amp; inhibitors ; Metabolomics ; Feces/microbiology ; Disease Models, Animal ; Mice, Inbred C57BL ; Humans ; Animals ; Mice ; Male ; Female ; Middle Aged ; Aged ; },
abstract = {Immunotherapy has made remarkable achievements in various cancers, but response rates in hepatocellular carcinoma (HCC) remain highly variable. Understanding mechanisms behind this heterogeneity and identifying responsive patients are urgent clinical challenges. In this study, the metagenomic analysis of 65 HCC patients reveals distinct gut microbiota profiles distinguishing responders (Rs) from non-responders (NRs). These findings are further validated through fecal microbiota transplantation (FMT) in mouse models. Notably, Phocaeicola vulgatus (P. vulgatus) is enriched in NRs and diminishes anti-PD-1 efficacy in both syngeneic and orthotopic tumor models. Mechanistically, P. vulgatus suppresses the production of indoleacetic acid (IAA), thereby weakening interferon (IFN)-γ[+] and granzyme B (GzmB)[+]CD8[+] T cells and impairing the antitumor immune response. Furthermore, supplementation with IAA restores CD8[+] T cell cytotoxicity and counteracts the immune-suppressive effects of P. vulgatus. Our findings establish a causal relationship between P. vulgatus and anti-PD-1 resistance in HCC, highlighting IAA as a potential therapeutic target to enhance immunotherapy outcomes.},
}
@article {pmid41002268,
year = {2025},
author = {Aminu, S and Ascandari, A and Benhida, R and Daoud, R},
title = {GRUMB: a genome-resolved metagenomic framework for monitoring urban microbiomes and diagnosing pathogen risk.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {10},
pages = {},
pmid = {41002268},
issn = {1367-4811},
support = {//Mohammed VI Polytechnic University/ ; //African Supercomputing Center at UM6P/ ; },
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *Software ; *Metagenome ; Machine Learning ; Humans ; Cities ; },
abstract = {SUMMARY: Urban infrastructure hosts dynamic microbial communities that complicate biosurveillance and AMR monitoring. Existing tools rarely combine genome-resolved reconstruction with ecological modeling and batch-aware analytics tailored to infrastructure-scale studies. We present GRUMB (Genome-Resolved Urban Microbiome Biosurveillance), an open-source, SLURM-compatible pipeline that reconstructs high-quality metagenome-assembled genomes (MAGs) from shotgun sequencing reads and integrates taxonomic/functional annotation (CARD, VFDB), batch-aware normalization, ecological diagnostics and machine learning classification of environment types with uncertainty and risk scoring. GRUMB accepts either SRA project accessions or paired-end FASTQ files with metadata, and produces assemblies, MAGs, taxonomic and functional profiles, ecological outputs and risk-informed classification. Its modular design enables reproducible, infrastructure-scale biosurveillance across diverse environments.<br><br>GRUMB is freely available under the MIT License at: https://github.com/SuleimanAminu/genome-resolved-urban-microbiome-biosurveillance; Zenodo DOI: https://doi.org/10.5281/zenodo.15505402. Requirements: Linux (Ubuntu 20.04+), Python 3.11, R 4.2+, SLURM. Issues and feature requests are tracked on GitHub.},
}
@article {pmid41000006,
year = {2026},
author = {Hodgson, RJ and Cando-Dumancela, C and Davies, T and Dinsdale, EA and Doane, MP and Edwards, RA and Liddicoat, C and Peddle, SD and Ramesh, SA and Robinson, JM and Breed, MF},
title = {Contrasting Microbial Taxonomic and Functional Colonisation Patterns in Wild Populations of the Pan-Palaeotropical C4 Grass, Themeda triandra.},
journal = {Plant, cell &amp; environment},
volume = {49},
number = {1},
pages = {209-225},
pmid = {41000006},
issn = {1365-3040},
support = {//This metagenomics sequencing for this project was supported by the Flinders University Accelerator for Microbiome Exploration. We also received funding from the Holsworth Wildlife Research Endowment with the Ecological Society of Australia, the Conservation Biology Grant 2022 with the Biological Society of South Australia and Nature Conservation Society of South Australia and the Lirabenda Wildlife Research Fund from the Field Naturalists Society of South Australia. We also received support from the Australian Research Council (grant numbers LP190100051 and LP190100484) and the New Zealand Ministry of Business Innovation and Employment (grant UOWX2101)./ ; },
mesh = {*Soil Microbiology ; *Poaceae/microbiology ; Rhizosphere ; *Microbiota ; Plant Roots/microbiology ; Metagenomics ; Biodiversity ; },
abstract = {The interactions between native plants and soil microbiota are not well characterised, despite growing recognition of their importance for host plant fitness and ecological functioning. We used shotgun metagenomics to examine microbial taxonomic and functional colonisation patterns in wild populations of the pan-palaeotropical C4 grass, Themeda triandra, across a globally representative aridity gradient (aridity index 0.318-0.903). We investigated these patterns through the two-step selection process whereby microbes are recruited from bulk soils into rhizospheres (soil on the root surface), and root interiors (endospheres). We provide clear evidence of this process through decreasing microbial taxonomic diversity from bulk soil to T. triandra roots. Surprisingly, microbial functional potential showed the opposite trend: the diversity of potential functions (exponent of Shannon's diversity) increased from bulk soil to the rhizosphere and endosphere, but functional richness did not. Finally, we found that increasing aridity was associated with rhizospheres that were more compositionally similar, yet remained highly diverse in functional potential. Overall, aridity is strongly associated with the root-associated microbiome of T. triandra, selecting for microbiota that likely support plant resilience under dry conditions. Furthermore, microbial functional potential closely tracks taxonomic composition and aridity trends, highlighting how native plants can shape their microbial communities.},
}
@article {pmid40999698,
year = {2025},
author = {Elliott, L and Coissac, E},
title = {Can Amplicon Sequencing Be Replaced by Metagenomics for Biodiversity Inventories?.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70047},
pmid = {40999698},
issn = {1755-0998},
support = {819192//European Research Council (ERC)/ ; },
}
@article {pmid40998902,
year = {2025},
author = {Satpathy, SS and Pradhan, D},
title = {Unveiling community structure, antimicrobial resistance, and virulence factor of a wastewater sample of dairy farm located in mayurbhanj, odisha, India.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {32919},
pmid = {40998902},
issn = {2045-2322},
mesh = {*Wastewater/microbiology ; India ; *Virulence Factors/genetics ; *Dairying ; *Bacteria/genetics/drug effects/pathogenicity/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; Farms ; Animals ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Water Microbiology ; },
abstract = {Nutrient-rich dairy wastewater (DWW) is an excellent growing medium for microbes. Their antimicrobial resistance (AMR) genes and pathogenic roles remain in the DWW and even multiply in environmental settings, in contrast to many chemical toxins that break down over time. Necessary steps and standardized techniques for tracking AMR in DWW samples are desperately needed. In this context, a DWW sample was evaluated to assess the necessity of remediation and develop a suitable treatment technique. Physicochemical characterizations of the sample showed an elevated level of pollutants like proteins, fats, and carbohydrates that led to the water pollution and microbial diversity (e.g., 36 phyla, 72 classes, 111 orders, 168 families, 275 genera, and 347 species). The Shannon and Simpson indices showed that the DWW sample had a high level of microbial diversity of a few species. The gene ontology (GO) analysis revealed the functional categories with 2795 genes belonging to 11 virulence categories. Most of the identified AMR genes belonged to beta-lactamase, and the majority of them were linked to Escherichia coli, Mycobacterium tuberculosis, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, etc. The major bacterial phyla carrying AMR genes included Firmicutes (36%), Proteobacteria (31%), Actinobacteria (21%), and Bacteroidetes (5%).},
}
@article {pmid40998209,
year = {2025},
author = {Olsen, IA and Eggesbø, M and Trivedi, U and Timmermann, A},
title = {Per- and polyfluoroalkyl substances and the gut microbiota in infants: A scoping review.},
journal = {Environmental research},
volume = {286},
number = {Pt 2},
pages = {122937},
doi = {10.1016/j.envres.2025.122937},
pmid = {40998209},
issn = {1096-0953},
mesh = {Humans ; Infant ; Infant, Newborn ; *Environmental Exposure ; *Environmental Pollutants/toxicity ; *Fluorocarbons/toxicity ; *Gastrointestinal Microbiome/drug effects ; },
abstract = {Per-and polyfluoroalkyl substances (PFASs) are persistent environmental chemicals associated with adverse health effects. Emerging evidence suggests PFAS exposure may influence gut microbiota composition, which is a critical determinant of health particularly during infancy. A systematic search was conducted in PubMed to identify epidemiological studies investigating PFAS exposure and infant gut microbiota. Seven studies met the inclusion criteria, examining a range of PFASs derived from either breast milk, maternal blood, or umbilical cord blood and including from 30 to 789 subjects. These studies used either 16S rRNA sequencing or shotgun metagenomics to assess microbiota changes. Perfluorooctane sulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) were the most frequently examined PFASs. Across studies, exposure to PFASs was associated with both increased and decreased α-diversity. β-diversity shifts were also observed in some studies, suggesting altered microbial structures. PFAS exposure was associated with changes in the abundance of specific taxa, such as increased Enterococcus and decreased Faecalibacterium and Phocaeicola vulgatus. Functional pathway alterations were also reported, including disrupted bile acid metabolism. Variation in study design, covariate adjustment, and methodological approaches likely contribute to the inconsistencies in the observed associations between PFAS exposure and the infant gut microbiota. In conclusion, current evidence suggests that PFAS exposure may influence infant gut microbiota, but more and larger longitudinal studies are needed to better understand whether PFAS exposure is associated with altered gut microbiota composition in infants. This review synthesizes existing evidence on associations between PFAS exposure and gut microbiota composition in infants.},
}
@article {pmid40996787,
year = {2025},
author = {Bergner, L and Catalano, S and Nichols, J and Da Silva Felipe, A and Cao, X and Mair, D and Nankasi, A and Arinaitwe, M and Mubangizi, A and Pybus, OG and Standley, C and Faust, CL and Raghwani, J},
title = {Quantifying viral load and characterizing virus diversity in wildlife samples with target enrichment sequencing.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001513},
pmid = {40996787},
issn = {2057-5858},
mesh = {Animals ; *Viral Load ; *Metagenomics/methods ; Feces/virology ; *Animals, Wild/virology ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; *Viruses/genetics/classification/isolation &amp; purification ; RNA Viruses/genetics/isolation &amp; purification ; DNA Viruses/genetics/isolation &amp; purification ; Rodentia/virology ; },
abstract = {Metagenomics is a powerful tool for characterizing viruses, with broad applications across diverse disciplines, from understanding the ecology and evolutionary history of viruses to identifying causative agents of emerging outbreaks with unknown aetiology. Additionally, metagenomic data contain valuable information about the amount of virus present within samples (i.e. viral load), which can provide insights into transmission potential, time since infection and, in turn, epidemic trajectories. However, before we can effectively use metagenomic data to inform transmission, we need to understand the general relationship between sequencing outputs and viral load. Here, using a commercially available probe panel targeting a wide diversity of viruses, we investigated the detection and recovery of virus genomes by spiking known concentrations of DNA and RNA viruses into wild rodent faecal samples. In total, 15 experimental replicates were sequenced with target enrichment sequencing and compared to shotgun sequencing of the same background samples. Target-enriched sequencing recovered all spike-in viruses at every concentration (10[2], 10[3] and 10[5]±1 log genome copies) and showed a log-linear relationship between spike-in concentration and mean read depth. Background viruses (including Kobuvirus and Cardiovirus) were recovered consistently across all biological and technical replicates and by shotgun sequencing, but genome coverage was variable between virus genera and likely reflected the composition of the target enrichment probe panel. Overall, our study highlights the strengths and weaknesses of using commercially available panels to quantify and characterize wildlife viromes and underscores the importance of probe panel design for accurately interpreting coverage and read depth. To advance the use of metagenomics for understanding virus transmission, further research will be needed to elucidate how sequencing strategy (e.g. library depth and pooling), virome composition and probe design influence viral read counts and genome coverage.},
}
@article {pmid40996703,
year = {2025},
author = {Sierra, MA and Ryon, K and Arikatla, MR and Elshafey, R and Bhaskar, H and Proszynski, J and Bhattacharya, C and Shaaban, H and Danko, DC and Ambrose, P and Spaulding, SA and Zambrano, MM and Consortium, TMD and Mason, CE},
title = {The Microbe Directory: a centralized database for biological interpretation of microbiome data.},
journal = {Database : the journal of biological databases and curation},
volume = {2025},
number = {},
pages = {},
pmid = {40996703},
issn = {1758-0463},
support = {U01DA053941/NH/NIH HHS/United States ; U54AG089334/NH/NIH HHS/United States ; R01AI151059/NH/NIH HHS/United States ; 80NSSC24K0728/NASA/NASA/United States ; 80NSSC24K1052/NASA/NASA/United States ; //WorldQuant Foundation/ ; },
mesh = {*Microbiota/genetics ; Humans ; *Databases, Genetic ; Data Curation ; Metadata ; Animals ; Metagenomics ; },
abstract = {The Microbe Directory (TMD) is a centralized database of metadata for microbes from all domains that helps with the biological interpretation of metagenomic data. The database comprises phenotypical and ecological traits of microorganisms, which have been verified by independent manual annotations. This effort has been possible by the help of a community of volunteer students worldwide who were trained in manual curation of microbiology data. To summarize this information, we have built an interactive browser that makes the database accessible to everyone, including non-bioinformaticians. We used the TMD data to analyse microbiome samples from different projects such as MetaSUB, TARA Oceans, Human Microbiome Project, and Sponge Microbiome Project, showcasing the utility of TMD. Furthermore, we compare our microbial annotations with annotations collected by artificial intelligence (AI) and demonstrate that despite the high speed of AI in reviewing and collecting microbial data, annotation requires domain knowledge and therefore manual curation. Collectively, TMD provides a unique source of information that can help to interpret microbiome data and uncover biological associations. Database URL: www.themicrobedirectory.com/.},
}
@article {pmid40996449,
year = {2026},
author = {Mimpen, IL and Battaglia, TW and Parra-Martinez, M and Toner-Bartelds, C and Zeverijn, LJ and Geurts, BS and Verkerk, K and Hoes, LR and van Renterghem, AWJ and Noë, M and Hofland, I and Broeks, A and van der Noort, V and Stigter, ECA and Gulersonmez, CMC and Burgering, BMT and van Gogh, M and de Zoete, MR and Gelderblom, H and Dijkstra, KK and Wessels, LFA and Voest, EE},
title = {Microbial Metabolic Pathways Guide Response to Immune Checkpoint Blockade Therapy.},
journal = {Cancer discovery},
volume = {16},
number = {1},
pages = {95-113},
doi = {10.1158/2159-8290.CD-24-1669},
pmid = {40996449},
issn = {2159-8290},
support = {//Mrs. Anneke Hoogendijk/ ; //Foundation Weteringschans/ ; 09150162210100//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; //Oncode Institute/ ; },
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Metabolic Networks and Pathways ; *Neoplasms/drug therapy/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome ; Riboflavin/metabolism ; },
abstract = {UNLABELLED: Studies have identified a link between specific microbiome-derived bacteria and immune checkpoint blockade (ICB) efficacy. However, these species lack consistency across studies, and their immunomodulatory mechanisms remain elusive. To understand the influence of the microbiome on ICB response, we studied its functional capacity. Using pan-cancer metagenomics data from ICB-treated patients, we showed that community-level metabolic pathways are stable across individuals, making them suitable for predicting ICB response. We identified several microbial metabolic processes significantly associated with response, including the methylerythritol 4-phosphate (MEP) pathway, which was associated with response and induced Vδ2 T cell-mediated antitumor responses in patient-derived tumor organoids. In contrast, riboflavin synthesis was associated with ICB resistance, and its intermediates induced mucosal-associated invariant T (MAIT) cell-mediated immune suppression. Moreover, gut metabolomics revealed that high riboflavin levels were linked to worse survival in patients with abundant intratumoral MAIT cells. Collectively, our results highlight the relevance of metabolite-mediated microbiome-immune cell cross-talk.<br><br>SIGNIFICANCE: Microbial metabolic pathways are highly conserved across individuals and therefore offer an opportunity to link the microbiome to immunotherapy efficacy. We identified specific microbial metabolic pathways associated with response to ICB and provided mechanistic insights into the immunomodulatory influence of these pathways on antitumor immunity.},
}
@article {pmid40996271,
year = {2025},
author = {Wong, MK and Armstrong, E and Heirali, AA and Schneeberger, PHH and Chen, H and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B},
title = {Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.},
journal = {mBio},
volume = {16},
number = {11},
pages = {e0190425},
pmid = {40996271},
issn = {2150-7511},
support = {UM1 CA186644/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Humans ; Feces/microbiology ; *Microbial Consortia ; Metagenomics ; Bacteroides ; Female ; Mice, Inbred C57BL ; Fecal Microbiota Transplantation ; Male ; Bacteria/classification/genetics/isolation &amp; purification ; Akkermansia ; },
abstract = {Composition and function of the gut microbiome are associated with diverse health conditions and treatment responses. Human microbiota-associated (HMA) mouse models are used to establish causal links for these associations but have important limitations. We assessed the fidelity of HMA mouse models in recapitulating ecological responses to a microbial consortium using stools collected from a human clinical trial. HMA mice were generated using different routes of consortium exposure, and their ecological features were compared to human donors by metagenomic sequencing. HMA mice resembled other mice more than their respective human donors in gut microbial composition and function, with taxa including Akkermansia muciniphila and Bacteroides spp. enriched in mouse recipients. A limited repertoire of microbes was able to engraft into HMA mice regardless of route of consortium exposure. In publicly available HMA mouse data sets from four distinct health conditions, we confirmed our observation that a taxonomically restricted set of microbes reproducibly engrafts in HMA mice and observed that stool microbiome composition of HMA mice was more like other mice than their human donor. Our data suggest that HMA mice are limited models for assessing the ecological impact of microbial consortia, with ecological effects in HMA mice being more strongly associated with host species than donor stool ecology or ecological responses to treatment in humans. Comparisons to published studies suggest this may be due to comparatively large host-species effects that overshadow ecological effects of treatments in humans that HMA models aim to recapitulate.IMPORTANCEHMA mice are models that better represent human gut ecology compared to conventional laboratory mice and are commonly used to test the effects of the gut microbiome on disease or treatment response. We evaluated the fidelity of using HMA mice as avatars of ecological response to a human microbial consortium, Microbial Ecosystem Therapeutic 4. Our results show that HMA mice in our cohort and across other published studies are more similar to each other than the human donors or inoculum they are derived from and harbor a taxonomically restricted gut microbiome. These findings highlight the limitations of HMA mice in evaluating the ecological effects of complex human microbiome-targeting interventions, such as microbial consortia.},
}
@article {pmid40996249,
year = {2025},
author = {Luo, Y and Xu, X and Qiao, R and Zhao, R-P and Zhou, Z-W and Li, D-A and Wen, Y and Song, J-M and Chen, L-L},
title = {Comparative analysis of rhizosphere microbiomes of cultivated and wild rice under contrasting field water regimes.},
journal = {Microbiology spectrum},
volume = {13},
number = {11},
pages = {e0026325},
pmid = {40996249},
issn = {2165-0497},
mesh = {*Oryza/microbiology/growth &amp; development ; *Rhizosphere ; Soil Microbiology ; *Microbiota/genetics ; Archaea/classification/genetics/isolation &amp; purification/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Water/metabolism ; Plant Roots/microbiology ; },
abstract = {UNLABELLED: Asian cultivated rice (Oryza sativa L.) is domesticated from the common wild rice (Oryza rufipogon Griff.). However, the increasing water stress caused by climate change in recent years has become a major threat to rice growth and yield. To explore the adaptive changes of rhizosphere microbiomes in annual cultivated and perennial wild rice under different water limitation conditions, we conducted metagenomic sequencing analysis on rice rhizosphere soil samples from natural environments with varying water conditions. In particular, the genus Pseudomonas plays a dominant role in the rhizosphere microbiome of wild rice under non-irrigated condition. For archaea, we found that, compared to non-irrigated condition, submergence condition enriched methanogenic Methanosarcina. In comparison to cultivated rice, wild rice showed significant enrichment of Nitrosarchaeum, as ammonia-oxidizing archaea play a key role in the nitrogen cycle, whereas cultivated rice tends to enrich methanogenic archaea (Methanosarcina), which may increase methane emissions and have adverse environmental impacts. The rhizosphere metabolites of wild rice also enriched DL-Norleucine, L-Phenylalanine, and Palmitic acid, which may enhance root water absorption and provide essential nutrients to help rice resist water-limiting stress. In terms of rhizosphere microbiome function, asnB and nirK were particularly enriched in wild rice under non-irrigated condition, suggesting that wild rice may exhibit higher ecological adaptability to water stress by enhancing nitrogen assimilation and denitrification processes. Excavating these microbiome communities and functional changes in rice rhizospheres is crucial for optimizing water-limiting resistance, protecting the environment, and improving rice yield.<br><br>IMPORTANCE: This study highlights the differences in rhizosphere microbiomes and metabolites between wild and cultivated rice, providing new insights into how water limitation impacts their interaction with the rhizosphere microbiome. These findings are crucial for advancing rice cultivation under submergence and non-irrigated conditions, offering strategies to optimize farming practices, manage water scarcity, and reduce methane emissions. In contrast to cultivated rice, wild rice may regulate its rhizosphere microbial community to enhance resistance to water stress. This discovery offers valuable theoretical support for improving rice growth and adaptation across diverse ecological environments.},
}
@article {pmid40996044,
year = {2025},
author = {Kwon, J and Correa, MA and Kong, Y and Pelletiers, W and Wade, M and Olson, D and Pettigrew, MM},
title = {Microbiome signatures of Clostridioides difficile toxin production and toxin gene presence: a shotgun metagenomic approach.},
journal = {mSphere},
volume = {10},
number = {10},
pages = {e0043525},
pmid = {40996044},
issn = {2379-5042},
support = {NU50CK000488/CC/CDC HHS/United States ; },
mesh = {Humans ; *Clostridioides difficile/genetics ; *Bacterial Toxins/genetics ; Female ; Male ; Metagenomics ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Feces/microbiology ; *Clostridium Infections/microbiology/diagnosis ; Aged ; Adult ; Anti-Bacterial Agents/therapeutic use ; Diarrhea/microbiology ; Aged, 80 and over ; },
abstract = {Clostridioides difficile is an opportunistic gastrointestinal pathogen capable of asymptomatic colonization and causes diseases ranging from diarrhea to pseudomembranous colitis. Accurate diagnosis of C. difficile infection (CDI) is challenging and critical for treatment and control. We hypothesized that gut microbiome profiles could help distinguish C. difficile colonized patients with diarrhea from those with true CDI. We analyzed 172 stool samples from individuals who tested glutamate dehydrogenase positive for C. difficile. Participants were categorized by toxin status (i.e., toxin positive or negative) and then further classified into three toxin groups based on the production of toxin, and if not produced, whether the C. difficile strain carried toxin-encoding genes. We examined associations between patient characteristics, prior antibiotics exposure, microbiome community structure and function, and toxin categories. Thirty-five percent of toxin-negative participants received antibiotics despite not meeting the criteria for true CDI. Enterococcus species were abundant in all groups. The relative abundance of E. faecalis was higher among individuals with prior antibiotics exposure. Alpha and beta diversity did not differ by toxin group. After controlling for prior antibiotics exposure and previous CDI episode, the abundance of Akkermansia muciniphila, Flavonifractor plautii, and Bifidobacterium adolescentis distinguished individuals with toxin-positive C. difficile. C. difficile abundance did not differentiate participants with true CDI from those who were colonized. We identified associations between the gut microbiome and C. difficile toxin gene presence and toxin production. These results highlight the potential for microbiome-informed diagnostics to improve CDI accuracy and guide treatment decisions.IMPORTANCEClostridioides difficile colonizes humans and causes diarrhea in community and hospital settings. C. difficile infection (CDI) is a toxin-mediated disease, and its diagnosis is challenging. The goal of this study was to determine whether differences in the gut microbiome could help distinguish between colonized individuals and those with CDI. We examined stool samples and data from 172 individuals categorized into three groups based on the detection of toxin and, if not detected, whether toxin-encoding genes were present in the C. difficile strain. We identified bacteria, such as Enterococcus faecalis, that were more abundant in people who had used antibiotics. While the diversity of the gut microbiome did not differ by toxin group, specific gut bacteria, antibiotic resistance genes, and metabolic pathways were associated with toxin group. Our findings suggest that considering the full gut microbiome and factors like past antibiotic use could help improve the diagnosis and treatment of CDI.},
}
@article {pmid40995781,
year = {2025},
author = {Hensen, T and Thiele, I},
title = {Metabolic modeling links gut microbiota to metabolic markers of Parkinson's disease.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2554195},
pmid = {40995781},
issn = {1949-0984},
support = {U19 AG063744/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/microbiology/metabolism/blood ; Male ; Female ; Biomarkers/blood/metabolism ; Middle Aged ; Aged ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics ; Leucine/metabolism/blood ; },
abstract = {Human gut microbiota have been implicated in metabolic disruptions in Parkinson's disease (PD). However, the underlying mechanisms linking gut microbiota to these disease-related metabolic changes remain largely unknown. In this study, we applied constraint-based metabolic modeling to identify potential causal links between compositional shifts in gut microbiota in PD and metabolic blood markers of PD. We personalized in silico whole-body metabolic models with gut metagenomics of 435 PD patients and 219 healthy controls and profiled in silico gut microbiome influences on 116 blood metabolites with replicated associations with PD diagnosis. Our analysis identified a reduced capacity of the PD host-microbiome co-metabolism to produce L-leucine and leucylleucine in blood. These metabolic predictions were traced back to lower L-leucine production of Roseburia intestinalis and higher L-leucine consumption by Methanobrevibacter smithii in PD microbiomes. We further predicted reduced host-microbiome production capacities of butyrate, myristic acid, and pantothenate in the blood of PD patients and linked these associations to reduced relative abundances of Faecalibacterium prausnitzii. Finally, lower nicotinic acid production capacities were predicted in PD patients, which were associated with increased relative abundances and increased nicotinic acid consumption of Ruthenibacterium lactatiformans in PD. In conclusion, we predicted that the gut microbiome can drive altered blood levels of six metabolites in PD and identified candidate microbial species that may influence these metabolic alterations. These findings may facilitate the development of novel therapies targeting the gut-brain axis in PD.},
}
@article {pmid40995227,
year = {2025},
author = {Lee, SH and Kim, EB and Park, SC and Nam, SJ and Cho, H and Jeon, HJ and Lee, SP},
title = {Evaluation of the gastric microbiota based on body mass index using 16S rRNA gene sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1651316},
pmid = {40995227},
issn = {2235-2988},
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Body Mass Index ; Female ; Male ; Middle Aged ; Obesity/microbiology ; *Gastrointestinal Microbiome/genetics ; Adult ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; DNA, Ribosomal/chemistry/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; *Stomach/microbiology ; Overweight/microbiology ; Metagenomics ; Phylogeny ; },
abstract = {INTRODUCTION: Obesity is a multifactorial condition influenced by various factors, including the gut microbiota. However, the relationship between the gastric microbiota and obesity remains poorly understood. This study aimed to investigate the composition of gastric microbiota, excluding Helicobacter pylori, in relation to body mass index (BMI) and metabolic indicators.<br><br>METHODS: Thirty participants undergoing health checkups were classified into three groups-normal weight (BMI 18.5-22.9), overweight (BMI 23.0-24.9), and obese (BMI &#x2265;25.0)-with ten individuals per group. Those with H. pylori infection, atrophic gastritis, or intestinal metaplasia were excluded. Gastric microbiota from four antral biopsies per subject were analyzed using 16S rRNA sequencing and functional profiling by metagenomic prediction.<br><br>RESULTS AND DISCUSSION: Alpha diversity (Gini-Simpson index) was significantly lower in the combined overweight/obese group than that in the normal group (P=0.049). Beta diversity analysis revealed clear group separation (Bray-Curtis, P=0.005; unweighted UniFrac, P=0.004). Significant species differences between the groups were observed; specifically, the abundances of Muribaculum gordoncarteri, Turicibacter bilis, and Duncaniella dubosii, were significantly reduced in the overweight/obese group. Functional predictions showed differential enrichment of pathways related to fatty acid, amino acid, vitamin, and carbohydrate metabolism across BMI categories. These findings suggest that alterations in the gastric microbiota may be linked to obesity and metabolic dysregulation.},
}
@article {pmid40993967,
year = {2025},
author = {Bibbò, S and Ahlström, G and Pes, GM and Graham, DY and Engstrand, L and Merola, E and Dore, MP},
title = {Resilience of the Gut Microbiome to Short Proton Pump Inhibitor Therapy With or Without High-Dosage L. reuteri in H. pylori-Infected Adults.},
journal = {Helicobacter},
volume = {30},
number = {5},
pages = {e70064},
pmid = {40993967},
issn = {1523-5378},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Limosilactobacillus reuteri/physiology/growth &amp; development ; *Helicobacter Infections/drug therapy/microbiology ; *Proton Pump Inhibitors/therapeutic use/administration &amp; dosage ; Female ; Male ; Middle Aged ; Double-Blind Method ; Adult ; Pantoprazole/therapeutic use ; *Probiotics/administration &amp; dosage ; Helicobacter pylori/drug effects ; Feces/microbiology ; Aged ; },
abstract = {BACKGROUND: Helicobacter pylori eradication therapy typically consists of a combination of antibiotics and an antisecretory drug. Probiotics may be added to reduce side effects and possibly improve outcomes.<br><br>MATERIALS AND METHODS: We conducted a double-blind, randomized trial of pantoprazole plus either Lactobacillus reuteri (Gastrus) (high dose) or a matching placebo to assess the impact on the gut microbiota of H. pylori-positive adults. Fecal samples were collected at baseline and after one and 2&#x2009;months for shotgun metagenomic sequencing.<br><br>RESULTS: A total of 26 patients were recruited and completed therapy. L. reuteri was only detected in the group that received supplemental L. reuteri and only at the 1-month post-treatment interval. L. reuteri failed to colonize for long-term&#xa0;the gut, and challenge with L. reuteri failed to alter alpha-diversity (Shannon index) or beta-diversity (community ordination) metrics at any time point. Machine learning (PLS-DA) analysis identified the presence of L. reuteri as the most distinguishing feature at 1 month. No other taxa showed a significant difference between groups.<br><br>CONCLUSION: Short-term administration of pantoprazole and L. reuteri had no lasting effects on gut microbial composition. While L. reuteri transiently bloomed during supplementation, the overall gut microbiota showed resilience, returning to baseline shortly after therapy.<br><br>TRIAL REGISTRATION: Identifier: NCT03404440.},
}
@article {pmid40993109,
year = {2025},
author = {Zeng, Y and Zhong, X and Chai, L and Zhang, X and Lu, Z and Liu, G and Tu, T and Lu, L and Zhang, R and Yu, H and Zhang, S and Wang, S and Shen, C and Shi, J and Xu, Z},
title = {Prokaryotic evolution shapes specialized communities in long term engineered pit mud ecosystem.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {186},
pmid = {40993109},
issn = {2055-5008},
support = {32201993//National Natural Science Foundation of China/ ; 31901658//National Natural Science Foundation of China/ ; 2024T170375//China Postdoctoral Science Foundation/ ; },
mesh = {*Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbial Consortia ; Ecosystem ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; Fermentation ; Phylogeny ; },
abstract = {Elucidating the temporal dynamics of complex microbial consortia is crucial for engineering robust microbiome. We investigated prokaryotic evolution in pit mud, a centuries-old engineered environment used in Chinese liquor fermentation. Metagenomic analysis of 120 pit mud samples across different ages revealed a transition from generalist-dominated to specialist-enriched communities. This shift was characterized by decreased hydrolytic potential and increased organic acid metabolism, with key taxonomic changes including declines in Proteiniphilum and Petrimonas, and increases in Methanobacterium and Caproicibacter. The mature specialist community accelerates the short-chain organic acids turnover through syntrophic fatty acid oxidation, methanogenesis, and carbon chain elongation, maintaining ecosystem stability. While nutrient availability primarily shapes early stages community interactions, environmental stress becomes a dominant factor in mature systems. These insights into long-term prokaryotic adaptation provide a foundation for the rational design of resilient, functionally optimized microbial communities for biotechnological applications.},
}
@article {pmid40992653,
year = {2025},
author = {Sharma, SP and Cha, MG and Kwon, GH and Song, SH and Park, JH and Kim, MJ and Eom, JA and Lee, KJ and Yoon, SJ and Park, H and Won, SM and Oh, KK and Ham, YL and Baik, GH and Kim, DJ and Suk, KT},
title = {Phocaeicola plebeius oral treatment improve fibrosis by reversing cirrhosis-related hepatic gene dysregulation.},
journal = {Life sciences},
volume = {381},
number = {},
pages = {123979},
doi = {10.1016/j.lfs.2025.123979},
pmid = {40992653},
issn = {1879-0631},
mesh = {Animals ; *Liver Cirrhosis/genetics/microbiology/drug therapy ; Humans ; Mice ; Male ; Gastrointestinal Microbiome/drug effects ; Female ; Gene Expression Regulation/drug effects ; Liver/metabolism/pathology ; Middle Aged ; Administration, Oral ; Dysbiosis ; *Bacteroidetes ; Feces/microbiology ; },
abstract = {BACKGROUND: Bacteroides-centric gut dysbiosis reported to exacerbates liver cirrhosis via inflammation and fibrosis, therefore utilizing Bacteroides species as microbiome-based therapeutic logical to mitigate disease progression.<br><br>MATERIALS AND METHODS: Feces were collected from 52 Healthy and 144 Liver cirrhosis individuals for V3-V4 dependent 16rRNA-bsed comparative metagenomics analysis, followed a by microbiome depleted and non-depleted DDC mice model to explain the role of Bacteroidetes phylum classified microbial species P. plebeius in liver fibrosis pathophysiological pathways.<br><br>RESULTS: Bacteroides presented cirrhosis-dependent decrease in human and animal microbiome, and negatively correlated to key molecular pattern associated with cirrhosis. P. plebeius significantly reduced in abundance and identified as a microbial biomarker for cirrhosis (AUC&#xa0;=&#xa0;0.73) and treatment with P. plebeius significantly improved the levels of cirrhosis-related phenotypical and biochemical markers in the microbiome-depleted cirrhosis group. P. plebeius decrease the expression of S100a9, CCR1, ADAM8, TREM2, ITGAM, and MYO5A which are primarily responsible for inducing inflammation in liver cirrhosis. P. plebeius downregulated the fibrosis related genes expression including CD51, PLAT, ITGA3, CXCR4, and TGFBR1 and gene related to extracellular matrix formation including COL1A1, LTBP2, S100A6, and SMCO2. Additionally, P. plebeius treatment decreased the expression of hepatotoxicity-related genes including LPL, KRT18, ALDOA, and MCM10, and increased the expression of FABP1 and RDX. Additionally, P. plebeius normalized the expression of genes connected to two pathophysiological process including TIMP4, TGFB3, S100A8, PLSCR1, MMP8, CXCL4, and BMP.<br><br>CONCLUSIONS: Our study revealed P. plebeius as a multifaceted bio-therapeutic candidate that normalized dysregulated gene expression and reversed hepatic inflammation, fibrogenesis, and hepatotoxicity.},
}
@article {pmid40990531,
year = {2026},
author = {Del Carratore, F and Breitling, R},
title = {Engineering microbiomes for natural product discovery and production.},
journal = {Natural product reports},
volume = {43},
number = {2},
pages = {301-312},
doi = {10.1039/d5np00038f},
pmid = {40990531},
issn = {1460-4752},
mesh = {*Biological Products/metabolism ; *Microbiota/genetics ; *Genetic Engineering ; Metabolomics ; Metagenomics ; },
abstract = {Covering: 2021 to 2025Microbial communities represent a vast and largely untapped source of natural products with potential applications in various fields, including medicine, agriculture, and the biomanufacturing industry. Secondary metabolites play a crucial role in mediating interspecies interactions within these communities, influencing their structure and function. Recent advances in microbial genetic engineering and multi-omics technologies have enabled the harnessing of these interactions for enhanced natural product discovery and production. These techniques, coupled with systems biology and mathematical modelling, allow for the rational design and manipulation of microbial consortia to elicit the expression of cryptic biosynthetic gene clusters and to optimize the production of desired compounds. Additionally, direct mining of microbiomes using metagenomics, metatranscriptomics, and metabolomics has revealed a wealth of novel biosynthetic gene clusters and secondary metabolites with potential therapeutic and industrial value. Despite the challenges associated with cultivating and characterizing diverse microbial species, ongoing advancements in computational tools and data analysis are rapidly expanding our ability to explore and exploit the seemingly inexhaustible reservoir of natural products hidden within microbial communities.},
}
@article {pmid40990171,
year = {2025},
author = {Sehgal, N and Pajuelo, MJ and Gilman, RH and Pickering, AJ and Earl, AM and Worby, CJ and Nadimpalli, ML},
title = {Effects of commonly used antibiotics on children's developing gut microbiomes and resistomes in peri-urban Lima, Peru.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {80},
number = {12},
pages = {3248-3256},
pmid = {40990171},
issn = {1460-2091},
support = {R01AI108695-01A/GF/NIH HHS/United States ; KL2TR002545/GF/NIH HHS/United States ; U19AI110818/GF/NIH HHS/United States ; 5T32ES012870/GF/NIH HHS/United States ; //Emory University/ ; //MP3 Initiative/ ; },
mesh = {Humans ; Peru ; *Gastrointestinal Microbiome/drug effects/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Infant ; Prospective Studies ; Feces/microbiology ; Male ; Female ; *Bacteria/drug effects/genetics/classification ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; },
abstract = {BACKGROUND: The effects of antibiotic use on children's gut microbiomes and resistomes are not well characterized in middle-income countries, where antibiotic consumption is exceptionally common.<br><br>OBJECTIVES: We characterized the effects of antibiotics commonly used by Peruvian children (i.e. amoxicillin, azithromycin, cefalexin, trimethoprim/sulfamethoxazole) on the &#x3b1;-diversity, &#x3b2;-diversity and abundance of gut genera and antibiotic resistance genes (ARGs) from 3 to 16&#x2005;months.<br><br>METHODS: This study included 54 children from a prospective cohort of enteric infections in peri-urban Lima, 2016-19. Stools collected at 3, 6, 7, 9, 12 and 16&#x2005;months underwent DNA extraction and short-read metagenomic sequencing. We profiled the taxonomy of stool metagenomes and assessed ARG abundance by aligning reads to the ResFinder database. We used daily surveillance data (40&#x200a;662 observations) to tabulate the number of antibiotic courses consumed in the 30&#x2005;days prior to stool sampling. Using linear mixed models, we examined associations of recent antibiotic use with richness, diversity and abundance of gut genera and ARGs over time.<br><br>RESULTS: Each additional recent antibiotic course decreased Bifidobacterium and Dialister abundance and increased Veillonella abundance, although gut richness and diversity were not affected. Recent use of amoxicillin, azithromycin, cefalexin or trimethoprim/sulfamethoxazole, specifically, did not impact gut microbiome measures. Amoxicillin, azithromycin and trimethoprim/sulfamethoxazole significantly enriched multiple ARGs and amoxicillin use significantly increased total ARGs.<br><br>CONCLUSIONS: Common antibiotics like amoxicillin and azithromycin appear to be key drivers of the paediatric gut resistome. Resistome perturbations appeared to be stronger, or persist for longer, than gut microbiome effects in this middle-income country setting.},
}
@article {pmid40989903,
year = {2025},
author = {Malygina, EV and Potapova, NA and Imidoeva, NA and Vavilina, TN and Belyshenko, AY and Morgunova, MM and Dmitrieva, ME and Shelkovnikova, VN and Vlasova, AA and Lipatova, OE and Zhilenkov, VM and Batalova, AA and Stoyanova, EE and Axenov-Gribanov, DV},
title = {Microbial communities inhabiting the surface and gleba of white (Tuber magnatum) and black (Tuber macrosporum) truffles from Russia.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20037},
pmid = {40989903},
issn = {2167-8359},
mesh = {Russia ; *Microbiota ; *Ascomycota/genetics/classification/isolation &amp; purification ; Symbiosis ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Phylogeny ; Mycorrhizae/genetics ; },
abstract = {The complex symbiotic relationships between truffles and their microbiota, coupled with their obligate mycorrhizal lifestyle, present significant challenges for obtaining axenic mycelium and achieving controlled cultivation. This study aimed to characterize the microbial communities within the surface and gleba of truffle ascomata using 16S and 18S rRNA gene sequencing and identify the taxonomic composition and ecological roles of these microbiota. Specimens of Tuber magnatum (white truffle) and Tuber macrosporum (smooth black truffle) were collected, with T. magnatum representing the first documented discovery of this species in Russia. Metabarcoding profiling identified both species-specific and shared microbial taxa, with the yeast-like fungus Geotrichum spp. emerging as a core symbiont in both truffle species. Its consistent detection in surface and gleba tissues suggests a critical role in mycorrhizal establishment and spore dispersal, potentially mediated by sulfur volatiles that attract mycophagous fauna. In T. magnatum, the bacterial community was dominated by Proteobacteria, particularly Alphaproteobacteria and Gammaproteobacteria, with the nitrogen-fixing genus Bradyrhizobium being especially abundant. The truffle microbiota predominantly comprised soil-derived microorganisms (e.g., nitrogen-fixing Rhizobiaceae spp., phenol-degrading Mycoplana spp.) and plant-associated symbionts (e.g., ectomycorrhizal Sebacina spp.), implicating these communities in nutrient cycling, xenobiotic degradation, and host plant interactions. By elucidating the taxonomic and functional profiles of truffle-associated microbiota, this study provides foundational insights into their ecological contributions. Chemical differences align with tissue-specific microbial communities, suggesting microenvironmental specialization in bioactive compound synthesis. These findings advance efforts to replicate critical symbiotic interactions in vitro, a prerequisite for developing sustainable cultivation protocols for T. magnatum and T. macrosporum under controlled conditions.},
}
@article {pmid40988537,
year = {2025},
author = {Tsamadou, V and Ohlsson, JA and Schnürer, A},
title = {Converge or Diverge? Exploring the Fate of Taxonomically Different Anaerobic Digestion Communities Under Uniform Growth Conditions.},
journal = {Microbial biotechnology},
volume = {18},
number = {9},
pages = {e70233},
pmid = {40988537},
issn = {1751-7915},
support = {310432//Energimyndigheten/ ; //Swedish Research Council (VR). The grant agreement corresponds to the Swedish Research Council./ ; //Sveriges Lantbruksuniversitet/Swedish University of Agricultural Sciencesarch Council through grant agreement no. 2022-06725/ ; },
mesh = {Anaerobiosis ; Culture Media/chemistry ; *Bacteria/classification/genetics/metabolism/growth &amp; development ; Sewage/microbiology ; Ammonia/metabolism ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Bioreactors/microbiology ; Biofuels ; DNA, Ribosomal/chemistry/genetics ; *Biota ; Sequence Analysis, DNA ; Metagenomics ; },
abstract = {Biogas inocula with distinct taxonomic compositions often converge to similar communities when fed the same substrate, indicating strong substrate-driven deterministic assembly. Nevertheless, stochastic processes have also been suggested as a critical element for microbial assembly in biogas systems. To date, assembly processes have mainly been investigated with undefined, non-sterile substrates, making it difficult to exclude the influence of external microorganisms. The aim of the present study was to investigate whether three taxonomically distinct anaerobic digestion (AD) communities would converge when exposed to uniform growth conditions during semi-continuous operation with a sterilised defined medium. The inocula originated from mesophilic processes using different substrates (food waste, sludge, and manure) and total ammonia levels (0.5-7.2 g/L). The medium was formulated to support all four main metabolic steps of AD: hydrolysis, fermentation, anaerobic oxidation, and methanogenesis. Taxonomic, phylogenetic, and functional analyses conducted via 16S and metagenomic sequencing showed that the substrate had no deterministic effect on microbial community taxonomic composition. Instead, the final community structure was dictated primarily by the initial inoculum, regardless of changes in substrate composition or ammonia levels. Despite taxonomic divergence, broad-level functionality and operational performance remained similar between communities.},
}
@article {pmid40987851,
year = {2025},
author = {Du, LF and Shi, W and Cui, XM and Fan, H and Jiang, JF and Bian, C and Ye, RZ and Wang, Q and Zhang, MZ and Yuan, TT and Xia, LY and Ruan, XD and Chang, QC and Du, CH and Que, TC and Wang, X and Han, XH and Yang, TC and Jiang, BG and Chen, JY and Wang, XR and Tan, LF and Liu, YW and Deng, LL and Liu, Y and Zhu, Y and Pan, YS and Wang, N and Lin, ZT and Li, LF and Li, C and Shen, SJ and Liu, YT and Tian, D and Han, XY and Wang, J and Wang, YF and Gao, WY and Li, YY and Xiong, T and Wang, TH and Shi, XY and Zhu, DY and Zhu, JG and Wang, CC and Shi, WQ and Zhan, L and Liu, ZH and Feng, D and Zhao, L and Sun, Y and , and Wang, J and Jia, N and Zhao, F and Cao, WC},
title = {Genome-resolved metagenomics reveals microbiome diversity across 48 tick species.},
journal = {Nature microbiology},
volume = {10},
number = {10},
pages = {2631-2645},
pmid = {40987851},
issn = {2058-5276},
support = {2019YFC1200501//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32025009//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Ticks/microbiology/classification/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; *Genome, Bacterial ; Phylogeny ; China ; Symbiosis ; Tick-Borne Diseases ; Genome-Wide Association Study ; Host Microbial Interactions/genetics ; Host-Pathogen Interactions/genetics ; },
abstract = {Ticks are arthropod vectors capable of transmitting a wide spectrum of pathogens affecting humans and animals. However, we have relatively limited information of their genomic characteristics and the diversity of associated microbiomes. Here we used long- and short-read sequencing on 1,479 samples from 48 tick species across eight genera from China to determine their genome and associated pathogens and microbiome. Through de novo assembly, we reconstructed 7,783 bacterial genomes representing 1,373 bacterial species, of which, 712 genomes represented 32 potentially pathogenic species. Computational analysis found nutritional endosymbionts to be prevalent and highly specific to tick genera. The microbiome genome-wide association study revealed host genetic variants linked to pathogen diversity, abundance and key biological pathways essential to tick biology, including blood-feeding and pathogen invasion. These findings provide a resource for studying the host-microbe interactions within ticks, paving the way for strategies to control tick populations and tick-borne diseases.},
}
@article {pmid40987427,
year = {2025},
author = {Hsu, BM and Chen, JS and Wang, WY and Chen, CJ and Fan, CW and Wu, CC and Hussain, B and Tsai, HC},
title = {An integral view of gut microbiome diversity and functional metabolic changes of a gut-brain axis associated with dementia based on metagenomic analysis.},
journal = {Physiology &amp; behavior},
volume = {302},
number = {},
pages = {115112},
doi = {10.1016/j.physbeh.2025.115112},
pmid = {40987427},
issn = {1873-507X},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; *Dementia/microbiology/metabolism ; Middle Aged ; Female ; Aged ; Aged, 80 and over ; Metagenomics ; *Brain/metabolism ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Brain-Gut Axis/physiology ; },
abstract = {BACKGROUND: Growing evidence highlights the vital role by gut microbiota in brain health through the gut-brain axis, which involves neural, immune, endocrine, and metabolic signaling pathways. Disruption of this axis through microbial dysbiosis is increasingly linked to cognitive disorders, including dementia. However, the specific taxa and pathways involved remain poorly characterized. This study investigates taxonomic and functional shifts in the gut microbiome across healthy individuals, mild dementia, and dementia patients, aiming to identify microbial signatures and metabolic alterations associated with cognitive decline.<br><br>METHODS: A total of 184 participants (aged 60-98) were recruited and grouped into healthy, mild dementia, and dementia categories based on Clinical Dementia Rating scores. Demographic and clinical data were collected through structured interviews. Fecal samples were collected from participants and DNA was extracted and subjected to 16S rRNA gene sequencing. Sequencing data were processed using QIIME2 and classified using the SILVA database. Alpha (Shannon, Inverse Simpson) and beta diversity (Bray-Curtis PCoA) were analyzed between participant groups. Functional prediction was performed with PICRUSt2 to estimate KEGG orthologs from normalized ASVs. Statistical analyses were conducted in R using Kruskal-Wallis and PERMANOVA tests to assess group-level differences.<br><br>RESULTS: Dementia patients exhibited the highest proportion of unique ASVs (32.1 %) but showed reduced alpha diversity compared to mild dementia and healthy controls. PCoA revealed distinct microbial clustering across groups, explaining 19.3 % of total variance, with dementia samples forming a unique cluster. Taxonomically, dementia samples were enriched in Firmicutes and pro-inflammatory genera such as Peptoclostridium and Scardovia, while healthy controls harbored more SCFA-producing taxa like Lachnospiraceae_UCG-001. Co-occurrence networks in dementia were more complex, with increased inter-species connectivity and key drivers including Dorea and Clostridium innocuum. Functionally, dementia samples showed enrichment of vanillate degradation pathways and depletion of neuroprotective pathways like ergothioneine and vitamin E biosynthesis, correlating with specific microbial signatures.<br><br>CONCLUSIONS: Cognitive decline was associated with reduced microbial diversity and selective enrichment of pro-inflammatory taxa, reflecting gut ecological instability due to dementia. Microbial composition shifted progressively with dementia severity, indicating disease-specific gut microbial restructuring. Moreover, the loss of key functional microbial metabolites such as neuroprotective and anti-inflammatory metabolites supports targeting such metabolites and their producing gut microbiota as a therapeutic strategy for dementia. Future studies should ensure generalization by recruiting multi-center participants with strict guidelines for monitoring confounders.},
}
@article {pmid40985733,
year = {2025},
author = {Romero, JL and Ratliff, JH and Carlson, CJ and Griffiths, DR and Miller, CS and Mosier, AC and Roane, TM},
title = {Community and functional stability in a working bioreactor degrading 1,4-dioxane at the Lowry Landfill Superfund Site.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {10},
pages = {e0057425},
pmid = {40985733},
issn = {1098-5336},
mesh = {*Dioxanes/metabolism ; Biodegradation, Environmental ; *Bioreactors/microbiology ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics/analysis ; Waste Disposal Facilities ; *Water Pollutants, Chemical/metabolism ; *Microbiota ; Phylogeny ; },
abstract = {UNLABELLED: 1,4-dioxane (dioxane) is an emerging contaminant that poses risks to human and environmental health. Bacterial dioxane degradation is increasingly being studied as a method to remove dioxane from contaminated water. However, there is a lack of studies on microbial community structures and functions within efficient, large-scale, biodegradation-based remediation technologies. The Lowry Landfill Superfund Site (Colorado, USA) uses an on-site, pump-and-treat facility to remove dioxane from contaminated groundwater by biodegradation. Here, 16S rRNA gene and shotgun metagenomic sequencing were used to describe microbial community composition, soluble di-iron monooxygenase (SDIMO) alpha hydroxylases, and potential for dioxane degradation and horizontal gene transfer in bioreactor support media from the facility. Support media showed diverse microbial communities dominated by Nitrospiraceae, Nitrososphaeraceae, and Nitrosomonadaceae. Pseudonocardia was also detected, suggesting a potential presence of known dioxane-degraders. Candidate SDIMOs belonged mostly to Group V, followed by Groups IV, II, and I (based on read depth). The most abundant Group V clade contained 38 proteins that were phylogenetically related to DxmA-like proteins, including that of Pseudonocardia dioxanivorans CB1190 (a known dioxane degrader). Seventeen Lowry contigs containing DxmA-like proteins contained protein-coding genes potentially involved in chemical degradation, transcriptional regulation, and chemical transport. Interestingly, these contigs also included evidence of potential horizontal gene transfer, including toxin-antitoxin proteins, phage integrase proteins, putative transposases, and putative miniature inverted-repeat transposable elements. These findings improve our understanding of potential dioxane biodegradation mechanisms in a functioning remediation system. Further studies are needed to definitively confirm microbial activity and enzymatic activity toward dioxane removal in this site.<br><br>IMPORTANCE: As an environmental contaminant, 1,4-dioxane poses risks for water quality and human health. Used as a solvent and chemical stabilizer in a variety of manufacturing and industrial applications, microbiological methods of detoxification and mitigation are of interest. The degradation of 1,4-dioxane by the bacterium Pseudonocardia spp. is the best understood example; however, these studies are largely based on single isolate, bench-scale, or in silico experiments. Consequently, a knowledge gap exists on bacterial degradation of 1,4-dioxane at environmentally relevant concentrations using functioning remediation technologies at scale. This study addresses this gap directly by describing microbial taxa, enzymes, and potential horizontal gene transfer mechanisms associated with an active treatment plant located on a 1,4-dioxane-impacted U.S. Environmental Protection Agency (EPA) superfund site. As 1,4-dioxane contamination gains more attention, these findings may prove useful for future facilities aiming to promote and optimize removal by biodegradation.},
}
@article {pmid40985550,
year = {2025},
author = {He, Y and Baltar, F and Wang, Y},
title = {Seasonal variability in community structure and metabolism of active deep-sea microorganisms.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40985550},
issn = {1751-7370},
support = {ZDSYS20230626091459009//Shenzhen Key Laboratory of Advanced Technology for Marine Ecology/ ; //National Natural Science Foundation of China/ ; },
mesh = {*Seasons ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; China ; *Microbiota ; Archaea/classification/metabolism/genetics ; Metagenome ; },
abstract = {Learning about the metabolic activities and adaptations of deep-sea microbes is challenging, as sample collection and retrieval often cause RNA degradation and microbial community shifts. Here, we employed an in situ DNA/RNA co-extraction device to collect 18 time-series nucleic acid samples during winter and summer in the South China Sea, minimizing sampling perturbation for metatranscriptome and metagenome analyses. Between the two seasons, the prokaryotic microbiota showed seasonal variations in species composition. Burkholderiales dominated in summer, whereas Pseudomonadales, Bacillales, and Rhodobacterales were enriched in winter. However, the dominant transcriptionally active taxa affiliated with Nitrososphaerales, MGIII, SAR324, UBA11654, Marinisomatales, and Poseidoniales remained largely stable across seasons. Among eukaryotes, Ciliophora were the most active, whereas Retaria were abundant but inactive. Despite the stable active prokaryotic community, metabolic profiles differed significantly between seasons. In the winter, autotrophic microorganisms, particularly Nitrososphaerales, exhibited higher CO2 fixation activity via the 3HP/4HB cycle, accompanied by enhanced ammonia oxidation for energy generation. In addition, CO oxidation activity was also elevated. In the summer, the primary source of energy originated from heterotrophic microorganisms capable of utilizing fatty acids, benzoate, and H2, likely relying on anaerobic respiration within organic particles. This may relate to nutrient source variations as reflected by the different levels of microbial network complexity between the two seasons. Altogether, our in situ metatranscriptomes revealed the metabolic activities and adaptations of active microbial groups across seasons, providing a basis for identifying the microbial contributors to elemental cycles in the deep ocean.},
}
@article {pmid40985325,
year = {2025},
author = {He, J and Xiao, J and Shen, X and Zhao, K and Lei, X and Zhang, H and Sun, C and Lu, H and Shao, Y},
title = {Multi-Habitat Landscape Promotes Microbial Diversity: Insights from the Traditional Agricultural Heritage and the Global Trend.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {46},
pages = {e06402},
pmid = {40985325},
issn = {2198-3844},
support = {518000-523500922002//Scientific Pre-research Fund of Zhejiang University/ ; CARS-18//Agriculture Research System of China/ ; 32022081//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; 31970483//National Outstanding Youth Science Fund Project of National Natural Science Foundation of China/ ; },
mesh = {*Ecosystem ; *Microbiota/genetics ; *Agriculture/methods ; Biodiversity ; Bacteria/genetics/classification ; Fungi/genetics ; Metagenomics ; },
abstract = {Ecosystems are interconnected networks of diverse habitat types, rather than isolated patches. However, the role of the multi-habitat landscape in influencing microbial diversity remains poorly understood. This study investigates bacterial and fungal communities within a 2500-year agricultural heritage system, the Mulberry-dyke and Fish-pond (MF), which integrates various terrestrial and aquatic habitats. Using amplicon sequencing, metagenomics, metatranscriptomics, and genomic analyses, these findings reveal a significant proportion of unclassified microbial taxa, underscoring the importance of MF systems as an untapped reservoir of microbial genetic resources. Moreover, single-nucleotide-level analyses demonstrate that a multi-habitat landscape enhances microbial diversity through ecosystem-wide assembly, facilitated by cross-habitat microbial dispersal. Taxa found across multiple habitats exhibit convergence in microdiversity and adaptive genetic traits, indicating both ecological and functional mechanisms underlying their adaptability. A global analysis of public microbiome datasets furthermore confirms that regions with higher habitat heterogeneity support significantly higher taxonomic and functional diversity of microbiomes. Overall, this study sheds new light on the overlooked microbial diversity in traditional agricultural heritages and emphasizes the value of ancestral ecological wisdom underlying multi-habitat integration for ecosystem management. These insights offer valuable guidance for developing sustainable agricultural strategies, enhancing microbial diversity, and reinforcing ecosystem resilience in the face of global change.},
}
@article {pmid40983948,
year = {2025},
author = {Zafeiropoulos, H and Delopoulos, EIM and Erega, A and Schneider, A and Geirnaert, A and Morris, J and Faust, K},
title = {microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {292},
pmid = {40983948},
issn = {1474-760X},
support = {101000309//Horizon 2020/ ; 101000309//Horizon 2020/ ; 9017//EMBO Scientific Exchange Grant/ ; },
mesh = {*Software ; *Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Metagenome ; Databases, Genetic ; *Microbiota ; },
abstract = {Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. Nodes, representing taxa, are enriched with phenotypic traits, while edges are enhanced with metabolic complementarities, highlighting potential cross-feeding relationships. microbetag's online version relies on microbetagDB, a database of 34,608 annotated representative genomes. microbetag can be applied to custom (metagenome-assembled) genomes via its stand-alone version. MGG, a Cytoscape app designed to support microbetag, offers a streamlined, user-friendly interface for network retrieval and visualization. microbetag effectively identified known metabolic interactions and serves as a robust hypothesis-generating tool.},
}
@article {pmid40982389,
year = {2025},
author = {Pizzini, JD and Midani, FS and Britton, RA},
title = {Updated Protocol for the Assembly and Use of the Minibioreactor Array (MBRA).},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {223},
pages = {},
doi = {10.3791/68788},
pmid = {40982389},
issn = {1940-087X},
mesh = {*Bioreactors/microbiology ; *Microbiota/physiology ; Humans ; },
abstract = {The human microbiome comprises diverse and dynamic microbial communities that play essential roles in host health. Understanding these communities and their responses to environmental factors is critical for advancing microbiome-based therapeutics. Traditional in vitro models for cultivating human-derived microbiota often lack scalability and require extensive technical expertise, limiting their accessibility and throughput. To address these limitations, we developed the Minibioreactor Array (MBRA) system -- a modular, single-stage, continuous-flow platform for high-throughput cultivation of microbial communities. This system enables parallel cultivation of up to 48 distinct microbial communities, supporting experimental flexibility while maintaining the stable growth of complex ecosystems. This protocol provides detailed guidance on MBRA fabrication, assembly, sterilization, and operation. The system's modular design allows for easy integration into anaerobic chambers and supports customization for a wide range of experimental applications. It has been used to study microbial responses to antibiotics, dietary compounds, and pathogen invasion, and to screen for pathogen-resistant communities. With its accessibility, scalability, and reproducibility, the MBRA represents a powerful model system for investigating microbial interactions and advancing microbiome research.},
}
@article {pmid40982108,
year = {2025},
author = {Saini, K and Kumar, SS and Kumar, V and Bajar, S},
title = {Demonstrated role of sulfate-reducing bacterial consortia in anaerobic paracetamol biodegradation.},
journal = {Biodegradation},
volume = {36},
number = {5},
pages = {91},
pmid = {40982108},
issn = {1572-9729},
support = {SR/PURSE/2022/126(G)//Department of Science and Technology (DST) PURSE Grant, New Delhi, India/ ; },
mesh = {*Acetaminophen/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; *Sulfates/metabolism ; Anaerobiosis ; *Bacteria/metabolism/genetics/classification ; *Water Pollutants, Chemical/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The escalating global production and usage of paracetamol (C8H9NO2), a widely administered analgesic and antipyretic pharmaceutical, has led to its ubiquitous presence in environmental matrices, including surface waters, municipal wastewater, and even potable water sources. Owing to its persistence and bioaccumulative potential, paracetamol poses a significant ecotoxicological threat, particularly through trophic transfer in aquatic ecosystems. Conventional wastewater treatment methods often fall short in completely eliminating such micropollutants. In this context, bioremediation offers a promising, sustainable, and cost-effective alternative for pharmaceutical remediation. This study investigates the anaerobic degradation potential of two sulfate-reducing bacterial consortia, designated Consortium I and Consortium II, isolated from Okhla landfill leachate and enriched with distinct Postgate media formulations. Paracetamol was introduced at varying concentrations (50-500 mg/L), with and without supplementation of an auxiliary carbon source, sodium lactate. Metagenomic profiling via 16S rRNA sequencing revealed that Consortium I was primarily composed of Clostridium (40.1%) and Acidipropionibacterium (31.2%), whereas Consortium II exhibited a dominant presence of Clostridium (80.3%) and Bacillus (7.99%). Consortium II exhibited superior degradation kinetics, achieving complete removal of 500 mg/L paracetamol in 48 h under lactate-free conditions. Conversely, the presence of sodium lactate significantly attenuated degradation efficiency, suggesting substrate competition and metabolic preference. Gas chromatography-mass spectrometry (GC-MS) identified 4-aminophenol and hydroquinone as transient intermediates, supporting a proposed anaerobic degradation pathway for paracetamol. These findings underscore the potential of native sulfate reducing bacterial consortia in the bioremediation of contaminants and provide mechanistic insight into anaerobic paracetamol degradation, offering a viable strategy for enhanced treatment efficacy of contaminated waste streams.},
}
@article {pmid40981429,
year = {2025},
author = {Ferretti, P},
title = {The gut remembers: the long-lasting effect of medication use on the gut microbiome.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0107625},
pmid = {40981429},
issn = {2379-5077},
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; Anti-Bacterial Agents/pharmacology/adverse effects ; Electronic Health Records ; Proton Pump Inhibitors/pharmacology ; Feces/microbiology ; },
abstract = {Growing evidence suggests that antibiotics and many human-targeted medications can alter the gut microbiome composition, but the persistence of these effects remains unclear. In their article, Aasmets and colleagues (O. Aasmets, N. Taba, K. L. Krigu, R. Andreson, et al., mSystems e00541-25, 2025, https://doi.org/10.1128/msystems.00541-25) leveraged electronic health records (EHR) and stool metagenomic data from 2,509 individuals to assess the impact of past medication use (up to 5 years prior to sampling) on the gut microbiome composition. They found that nearly half of the 186 tested drugs had long-term effects, with antibiotics, beta-blockers, benzodiazepine derivatives, proton-pump inhibitors, and antidepressants associated with microbiome changes that persisted for years after intake. For some medications, the effects were additive, with greater impact observed after repeated use. Overall, the authors highlight how medication use in the years preceding sample collection represents an often overlooked confounding factor in microbiome studies and emphasize the utility of combining EHR with microbiome data to assess the impact of past medication use.},
}
@article {pmid40981149,
year = {2025},
author = {Medina-Martínez, I and Gil-Gutiérrez, R and García-García, J and de la Hera-Fernández, FJ and Navarrete-Navarrete, N and Zamora-Pasadas, M and Ortego-Centeno, N and Callejas-Rubio, JL and García-García, F and Gálvez-Peralta, J and Rodríguez-Nogales, A and Correa-Rodríguez, M and Rueda-Medina, B},
title = {Association of Gut Dysbiosis with Disease Phenotype and Treatment in Systemic Lupus Erythematosus.},
journal = {Medical sciences (Basel, Switzerland)},
volume = {13},
number = {3},
pages = {},
pmid = {40981149},
issn = {2076-3271},
support = {20.000 &#x20ac;//B-CTS-100-UGR20, Consejer&#xed;a de Econom&#xed;a, Innovaci&#xf3;n y Ciencia de la Junta de Andaluc&#xed;a I+D+i Programa operativo FEDER Andaluc&#xed;a 2014-2020/ ; },
mesh = {Humans ; *Lupus Erythematosus, Systemic/microbiology/drug therapy/complications ; *Dysbiosis/microbiology/complications ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; Middle Aged ; Phenotype ; Feces/microbiology ; Case-Control Studies ; },
abstract = {Introduction: Gut dysbiosis has been associated with the development of autoimmune diseases, including systemic lupus erythematosus (SLE). Although previous studies suggest microbial alterations in SLE, evidence at the species level and its clinical relevance remain limited. This study aimed to characterise the gut microbiota at species level in SLE patients and evaluate its association with clinical features. Materials and methods: A total of 57 SLE patients and 57 matched controls were included. Faecal samples were collected using the OMNIgene-GUT kit, and microbial DNA was extracted with the Maxwell RSC PureFood GMO kit. Metagenomic sequencing was performed using the Illumina MiSeq platform, and the data was analysed with QIIME2. Microbial diversity and relative abundance were assessed using the phyloseq package, and differentially abundant taxa were identified using DESeq2. Clinical subgroups among SLE patients were identified via k-means clustering. Results: SLE patients exhibited significantly different beta diversity compared to controls (p = 0.001), with increased abundance of Pseudomonadota (3.81% vs. 6.80%, p < 0.05) and decreased Bacteroidota (53.42% vs. 38.04%, p < 0.05). Only 10 bacterial species were consistently present across all SLE samples, including Akkermansia muciniphila, Bacteroides dorei, and Lactobacillus gasseri. Hypertensive patients and those treated with corticosteroids presented a marked depletion of key microbial taxa. Conversely, Belimumab-treated patients displayed a distinct microbiota enriched in species such as Alistipes shahii and Prevotella corporis. Conclusions: This study confirms significant gut microbiota alterations in SLE and pinpoints microbial profiles associated with clinical subgroups. These findings suggest gut dysbiosis may contribute to SLE pathogenesis and indicate biomarkers for disease stratification.},
}
@article {pmid40980884,
year = {2025},
author = {Robinson, CRP and Dolezal, AG and Liachko, I and Newton, ILG},
title = {Hi-C-resolved metagenomics reveals host range variation among mobile genetic elements within the European honey bee.},
journal = {mBio},
volume = {16},
number = {11},
pages = {e0224325},
pmid = {40980884},
issn = {2150-7511},
support = {//Project Apis m. (PAm)/ ; 2005306//National Science Foundation/ ; 2022049//National Science Foundation/ ; },
mesh = {Animals ; Bees/microbiology ; *Metagenomics/methods ; *Interspersed Repetitive Sequences ; *Host Specificity/genetics ; Bacteriophages/genetics ; Metagenome ; Phylogeny ; Plasmids/genetics ; Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification ; Gene Transfer, Horizontal ; },
abstract = {Mobile genetic elements (MGEs), such as plasmids and bacteriophages, are major contributors to the ecology and evolution of host-associated microbes due to symbiotic interactions and gene flow via horizontal gene transmission. Antibiotic resistance genes (ARGs), which are frequently trafficked via MGEs, are known to be enriched within North American honey bee microbiomes due to decades of antibiotic exposure. While previous studies have identified nearly identical MGE-associated ARGs across geographically disparate honey bee colonies, our understanding of how ARGs are distributed and mobilized within and between individual microbiomes is limited. To address this limitation, we leverage Hi-C-resolved metagenomics with the honey bee worker gut microbiome and show that the worker gut contains dense, nested, and highly distinct MGE communities. We show that phage-microbe networks exhibit high variation among individual metagenomes and that phages show broad host range with respect to both the number and phylogenetic distance of their hosts. Comparisons of individual microbiomes reveal highly individualized plasmid communities that exhibit broad host range variation within microbiomes. Finally, we provide specific evidence that antibiotic resistance cassettes are being actively shuttled between honey bee microbes via plasmids and that these broad host range plasmids frequently recombine to share gene content. Our work corroborates early observations of ARG dispersal in honey bee colonies and provides evidence for how these genes are mobilized within and across honey bee-associated microbial communities.IMPORTANCEMobile genetic elements (MGEs) are found in every microbial community and often encode genes conferring antibiotic resistance (ARGs). Within the honey bee worker gut microbiome, ARGs are particularly frequent due to decades of antibiotic exposure. Previous studies have identified nearly identical ARGs in geographically disparate honey bee colonies, which suggests recent mobilization by MGEs into these colonies, but identifying how these ARGs are mobilized and distributed within honey bee colonies remains a challenging task, as most techniques rely on microbial culture. Applying metagenomic Hi-C, we describe how these ARGs are distributed among individual plasmid backbones and how those plasmids are distributed among host microbial populations. Remarkably, we find plasmids exhibit broad host range variation, although they encode nearly identical ARGs. Our work corroborates earlier observations of ARG dispersal in honey bee colonies and provides further evidence for how these ARGs are mobilized across vast geographic distance.},
}
@article {pmid40980873,
year = {2025},
author = {Lai, W and Alberdi, A and Leu, A and de Leon, AVP and Kobel, CM and Aho, VTE and Roehe, R and Pope, PB and Hvidsten, TR},
title = {Metabolic capabilities of key rumen microbiota drive methane emissions in cattle.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0060125},
pmid = {40980873},
issn = {2379-5077},
support = {0054575-SuPAcow//Novo Nordisk Fonden/ ; 101000213//HORIZON EUROPE European Research Council/ ; FT230100560//Australian Research Council/ ; },
mesh = {Animals ; Cattle/microbiology ; *Methane/metabolism ; *Rumen/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Animal Feed ; Bacteria/metabolism/genetics/classification ; },
abstract = {UNLABELLED: The rumen microbiome plays a critical role in determining feed conversion and methane emissions in cattle, with significant implications for both agricultural productivity and environmental sustainability. In this study, we applied a hierarchical joint species distribution model to predict directional associations between biotic factors and abundances of microbial populations determined via metagenome-assembled genomes (MAGs). Our analysis revealed distinct microbial differences, including 191 MAGs significantly more abundant in animals with a higher methane yield (above 24 g/kg dry matter intake [DMI]; high-emission cattle), and 220 MAGs more abundant in low-emission cattle. Interestingly, the microbiome community of the low-methane-emission rumen exhibited higher metabolic capacity but with lower functional redundancy compared to that of high-methane-emission cattle. Our findings also suggest that microbiomes associated with low methane yields are prevalent in specific functionalities such as active fiber hydrolysis and succinate production, which may enhance their contributions to feed conversion in the host animal. This study provides an alternate genome-centric means to investigate the microbial ecology of the rumen and identify microbial and metabolic intervention targets that aim to reduce greenhouse gas emissions in livestock production systems.<br><br>IMPORTANCE: Ruminant livestock are major contributors to global methane emissions, largely through microbial fermentation in the rumen. Understanding how microbial communities vary between high- and low-methane-emitting animals is critical for identifying mitigation strategies. This study leverages a genome-centric approach to link microbial metabolic traits to methane output in cattle. By reconstructing and functionally characterizing hundreds of microbial genomes, we observe that a low-methane-emission rumen harbors well-balanced, "streamlined" microbial communities characterized by high metabolic capacity and minimal metabolic overlap across populations (low functional redundancy). Our results demonstrate the utility of genome-level functional profiling in uncovering microbial community traits tied to climate-relevant phenotypes.},
}
@article {pmid40977701,
year = {2025},
author = {Ren, P and Zhao, Y and Li, X and Xie, J and Liao, X and Luo, Q and Liu, X and Li, J and Fan, Y and Cheng, X and Fu, X and Zhou, J and Wu, X},
title = {Comprehensive metagenomic and lipidomic analysis showed that baicalin could improve depressive behaviour in atherosclerotic mice by inhibiting nerve cell ferroptosis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1599570},
pmid = {40977701},
issn = {1664-3224},
mesh = {Animals ; *Flavonoids/pharmacology/therapeutic use ; *Ferroptosis/drug effects ; *Atherosclerosis/drug therapy/metabolism/complications ; Mice ; *Depression/drug therapy/metabolism/etiology ; *Neurons/drug effects/metabolism ; Metagenomics/methods ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Lipidomics/methods ; Disease Models, Animal ; Male ; Lipid Metabolism/drug effects ; Behavior, Animal/drug effects ; },
abstract = {BACKGROUND: Atherosclerosis (AS) concomitant depression is a serious clinical problem with unclear mechanisms of co-morbidity. Baicalin (BA) can resist atherosclerosis and depression by regulating intestinal flora and host lipid metabolism. Therefore, based on intestinal microorganisms and lipid metabolism, this study explored the mechanism of baicalin against AS concomitant depression.<br><br>METHODS: 16 C57BL/6 mice were fed with normal diet as blank control group. 48 ApoE[-/-]mice were randomly divided into 3 groups (model group and BAL, BAH two treatment groups). The mouse model of atherosclerosis concomitant depression was established by high-fat feeding combined with restraint stimulation for 16 weeks. Behavioural experiments and biochemical indexes were used to detect the antidepressant effect and anti-atherosclerosis effect of baicalin. Metagenomic sequencing technology combined with metabolomics analysis was used to detect the effects of BA on intestinal microflora structure and brain lipids in AS co-depressed mice. Erastin was used to induce HT-22 hippocampal neurons to construct a model of ferroptosis. The inhibition of baicalin on ferrotosis was verified by detecting the cell viability, ROS production, and expression levels of glutathione, SLC7A11, GPX4 and ACSL4 in each group.<br><br>RESULTS: Baicalin could effectively improve the indexes of AS co-depressed mice, and the results of metagenomics and lipidomics showed that there were disorders of intestinal flora represented by Helicobacter_typhlonius and Escherichia_coli and disorders of lipid metabolism represented by PE in the AS co-depressed model mice. The correlation analysis showed that the lipid metabolism disorders in the model mice were closely related to the intestinal flora disorders, and baicalin intervention could effectively improve the intestinal flora and lipid metabolism disorders in the AS co-depressed mice. Metabolic pathway enrichment analysis showed that differential lipid PEs were significantly enriched in the iron death pathway, and our further in vitro cellular experiments showed that baicalin could inhibit Erastin-induced Ferroptosis in the hippocampal neuronal cell line HT-22 by promoting the expression of SLC7A11, GSH, and GPX4, inhibiting the expression of ACSL4, and decreasing the cellular ROS.<br><br>CONCLUSION: Baicalin improves intestinal microbiota and brain lipid metabolism and inhibits ferroptosis of nerve cells, which possesses the application value of anti-atherosclerotic concomitant depression.},
}
@article {pmid40974529,
year = {2025},
author = {Tian, C and Tang, Z and Zhang, X and Yao, X and Li, Y and Zhuang, D and Luo, Y and Li, T and Bai, L and Zhao, F and Zhu, L and Shi, G and Jiang, P and Gong, Q and Zhou, H and Gao, H and Wu, Q and Sang, J and Liu, X and Li, X and Yu, L and Zhang, Z},
title = {Uncovering the gut microbiome and antibiotic resistome of mammals on the Tibetan Plateau.},
journal = {Science China. Life sciences},
volume = {68},
number = {12},
pages = {3646-3663},
pmid = {40974529},
issn = {1869-1889},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; Tibet ; *Mammals/microbiology ; Humans ; Metagenomics/methods ; Anti-Bacterial Agents/pharmacology ; Metagenome/genetics ; *Drug Resistance, Microbial/genetics ; Gene Transfer, Horizontal ; Bacteria/genetics/classification/drug effects ; },
abstract = {The mammalian species on the Tibetan Plateau are diverse and abundant, yet our understanding of their gut microbiome and antibiotic resistome remains limited. Here, we used metagenomics to analyse the gut microbiota of 2,561 mammals from the Tibetan Plateau, covering 14 species across six orders. Using de novo metagenome assembly, we reconstructed a total of 112,313 high- to medium-quality metagenomic assembly genomes (MAGs), representing 21,902 microbial species, 86% of which were unclassified. More than 8,000 nonredundant antibiotic resistance genes (ARGs) encompassing 28 types were identified in the gut microbiome of Tibetan Plateau mammals. We further conducted a risk assessment of these ARGs, identifying 334 nonredundant ARGs with high-risk characteristics related to human health. Importantly, seven cross-species horizontal gene transfer events involving high-risk ARGs were identified, three of which occurred between human and nonhuman mammalian gut microbiota. Additionally, we found that the abundance of ARGs in human gut microbiomes on the Tibetan Plateau was greater than that in those from eastern China, Europe, and the United States, whereas the abundance of ARGs in livestock gut microbiomes from the Tibetan Plateau was lower than that in livestock gut microbiomes from those regions. This study reveals that the gut microbiota of Tibetan Plateau mammals is a largely unexplored resource and a significant reservoir of ARGs, offering crucial insights into microbiome research and demonstrating potential public health implications.},
}
@article {pmid40974374,
year = {2025},
author = {Hemnani, M and Karatas, M and Cruz, AVS and da Silva, PG and Thompson, G and Poeta, P and Rebelo, H and Matthijnssens, J and Mesquita, JR},
title = {Metagenomic analysis of viral diversity in Portuguese bats.},
journal = {Veterinary research communications},
volume = {49},
number = {6},
pages = {319},
pmid = {40974374},
issn = {1573-7446},
mesh = {Animals ; *Chiroptera/virology ; Metagenomics ; Portugal/epidemiology ; Feces/virology ; *Coronavirus/genetics/isolation &amp; purification/classification ; Spike Glycoprotein, Coronavirus/metabolism/genetics ; *Coronavirus Infections/veterinary/virology/epidemiology ; Phylogeny ; },
abstract = {Bats are highly diverse mammals and known reservoirs of numerous zoonotic viruses. Their role in the ecology of emerging infectious diseases continues to be of significant interest. This study aimed to evaluate the occurrence of coronaviruses (CoVs) in Portuguese bats and predict the affinity of their spike proteins with the aminopeptidase N (APN) receptor of several host species. The study also explored the viral diversity in bat samples using metagenomic sequencing. Ten bats (five Myotis myotis and five Miniopterus schreibersii) were captured at an underground roost in 2022 (Central Portugal), and fecal samples, oral, and anal swabs were collected (n = 27). A Pan-CoV nested RT-PCR was used for initial screening, followed by viral metagenomic sequencing of all fecal samples and one CoV-positive buccal swab. In silico protein docking studies were performed between a Portuguese bat CoV spike protein and APNs of bats, pigs, and humans. Pan-CoV nested RT-PCR identified three positive samples: two fecal samples and one buccal sample. Metagenomic sequencing allowed us to determine two near complete CoV genomes. Protein docking predicted strong binding of this spike protein to bat, porcine, and human APN receptors. Metagenomics also identified picornaviruses, adenovirus, and dependoparvovirus in fecal samples. This study reports the first near complete genome sequences of two members of the Alphacoronavirus genus from a Portuguese bat The identification of other viral families highlights the diverse virome of these cave-dwelling bat species. Protein docking studies suggest a potential for cross-species transmission of this bat CoV between bats, porcines and humans, though further research is needed to confirm these interactions.},
}
@article {pmid40973961,
year = {2025},
author = {Lin, PT and Wu, YW},
title = {Highly-accurate prediction of colorectal cancer through low abundance uncultivated genomes recovered using metagenomic co-assembly and binning approach.},
journal = {BMC cancer},
volume = {25},
number = {Suppl 2},
pages = {1418},
pmid = {40973961},
issn = {1471-2407},
support = {MOST110-2221-E-038-019-MY3//Ministry of Science and Technology, Taiwan/ ; MOST111-2221-E-038-023-MY3//Ministry of Science and Technology, Taiwan/ ; grant TMU-NTUST-108-08//Taipei Medical University-National Taiwan University of Science and Technology Joint Research Program/ ; },
mesh = {Female ; Humans ; Male ; Asian People/genetics ; *Colorectal Neoplasms/microbiology/genetics/diagnosis ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; White People/genetics ; },
abstract = {BACKGROUND: Recent microbiome studies have established the association between the composition of gut microbiota and various diseases. Since 16S ribosomal RNA sequencing may suffer from problems such as lower taxonomic resolution or limited sensitivity, more and more studies embraced whole-metagenome approach, which has the potential of sequencing everything in the target microbiome, to conduct microbial association analysis. However, species profiling, which is the most popular analysis technique for whole-metagenome analysis, cannot detect uncultivated species. Since uncultivated species may also be indispensable in the gut environments, it is crucial to identify those uncultivated species and evaluate their importance in discerning disease samples from healthy ones.<br><br>RESULTS: After conducting de novo co-assembly and genome binning procedures on two colorectal cancer (CRC) cohorts, in which one of them was from the Asian population while the other was from the Caucasian population, we identified that the Asian and Caucasian cohorts shared a significant amount of microbial species in their microbiota. In addition we found that low abundance genomes may be more important in classifying disease and healthy metagenomes. By sorting the genomes based on their random forest importance scores in differentiating disease and healthy samples and cumulatively evaluating the genome subsets in predicting CRC status, we identified dozens of "important" genomes for each of the cohorts that were able to predict CRC with very high accuracy (0.90 and 0.98 AUROC for the Asian and Caucasian cohorts respectively). Uncultivated species were also identified among the selected genomes, highlighting the importance of including the uncultivated species in order to build better disease prediction models and evaluate the roles of the uncultivated species in the disease formation or progression. Finally we found that the "important" species for both cohorts did not overlap with each other, hinting that the species highly associated with CRC disease may be different between the Eastern and Western populations.<br><br>CONCLUSION: In this study we demonstrated the importance of recovering and analyzing low abundance uncultivated species to identify their associations with colorectal cancer. We hope this work shed new light on a more comprehensive understanding of how our gut microbes are correlated with diseases.},
}
@article {pmid40972887,
year = {2025},
author = {Hitch, TCA and Bosch, J and Bolsega, S and Deschamps, C and Etienne-Mesmin, L and Treichel, N and Blanquet-Diot, S and Ocvirk, S and Basic, M and Clavel, T},
title = {Function-based selection of synthetic communities enables mechanistic microbiome studies.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40972887},
issn = {1751-7370},
support = {CA23110//European Union, COST action INFOGUT/ ; 513892404//German Research Foundation/ ; 460129525//German Research Foundation/ ; NFDI4Microbiota//German Research Foundation/ ; 403224013//German Research Foundation/ ; SFB1382//German Research Foundation/ ; 395357507//German Research Foundation/ ; SFB1371//German Research Foundation/ ; 01KA2103//German Federal Ministry of Education and Research/ ; },
mesh = {Animals ; Mice ; Humans ; *Microbiota ; Inflammatory Bowel Diseases/microbiology ; *Host Microbial Interactions ; Metagenome ; Germ-Free Life ; *Gastrointestinal Microbiome ; Colitis/microbiology ; },
abstract = {Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynComs). We developed a functionally directed approach to generate SynComs by selecting strains that encode key functions identified in metagenomes. This approach enables the rapid construction of SynComs tailored to any ecosystem. To optimize community design, we implemented genome-scale metabolic models, providing in silico evidence for cooperative strain coexistence prior to experimental validation. Using this strategy, we designed multiple host-specific SynComs, including those for the rumen, mouse, and human microbiomes. By weighting functions differentially enriched in diseased versus healthy individuals, we constructed SynComs that capture complex host-microbe interactions. We designed an inflammatory bowel disease SynCom of 10 members that successfully induced colitis in gnotobiotic IL10-/- mice, demonstrating the potential of this method to model disease-associated microbiomes. Our study establishes a framework for designing functionally representative SynComs of any microbial ecosystem, facilitating mechanistic study.},
}
@article {pmid40972730,
year = {2026},
author = {Wang, X and Chen, M and Su, Y and Zhang, X and Chen, J and Huang, Z and Xie, J and Xie, Q and He, L and Su, L and Su, Z and Wang, H and Li, Y},
title = {A novel cholesterol-reducing mechanism of polygonati rhizoma: Dual action via Bacteroides-mediated cholesterol sulfonation and feedback inhibition of ACAT2 by sulfated metabolite.},
journal = {Journal of ethnopharmacology},
volume = {355},
number = {Pt A},
pages = {120619},
doi = {10.1016/j.jep.2025.120619},
pmid = {40972730},
issn = {1872-7573},
mesh = {Animals ; Mice ; Male ; *Cholesterol/metabolism/blood ; *Polygonatum/chemistry ; *Hypercholesterolemia/drug therapy ; Gastrointestinal Microbiome/drug effects ; Molecular Docking Simulation ; *Bacteroides/metabolism/drug effects ; *Anticholesteremic Agents/pharmacology/isolation &amp; purification ; *Phosphatidylcholine-Sterol O-Acyltransferase/antagonists &amp; inhibitors/metabolism ; Rhizome ; Disease Models, Animal ; *Plant Extracts/pharmacology ; Animals, Outbred Strains ; },
abstract = {Polygonati Rhizoma (PR) has the function of "invigorating spleen and tonifying kidney", and is historically applied as a homology of medicine and food to prevent and treat dyslipidemia in China. However, there is limited experimental evidence to support this application, and the underlying mechanism has not been fully deciphered.<br><br>AIM OF THE STUDY: To analyze the composition and illuminate the cholesterol-lowering potential and molecular mechanism of PR's aqueous extract (PRE) in high-fat emulsion (HFE)-induced hypercholesterolemia mouse model.<br><br>MATERIALS AND METHODS: Ion chromatograph was employed to determine the monosaccharide composition of PRE. HFE-induced Kunming mouse model was constructed to evaluate the anti-hypercholesterolemia effect of PRE. Metagenomic sequences and liquid chromatography-mass spectrometry (LC-MS) analysis were performed to elucidate the mechanism through which PR regulated cholesterol metabolism. Antibiotic cocktail (ABX) intervention and fecal microbiota transplantation (FMT) were used to validate whether PRE regulated cholesterol metabolism through the intestinal microbiota. The cholesterol-reducing effect of cholesterol sulfate (CS) was explored in poloxamer 407 (P407)-induced mouse model of dyslipidemia. Molecular docking and molecular dynamics (MD) simulation were also employed to elucidate the underlying mechanisms. Furthermore, a combination of qRT-PCR, Western blot, and surface plasmon resonance (SPR) were employed to delineate its mechanism.<br><br>RESULTS: Our study indicated that the polysaccharides of PRE were mainly composed of fructose (92.33&#xa0;%) and glucose (5.25&#xa0;%). PRE treatment effectively blocked body weight gain, significantly decreased serum and hepatic levels of triglycerides (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-C), and increased high-density lipoprotein cholesterol (HDL-C) level. Additionally, PRE ameliorated hepatic lipid accumulation in mice with HFE-elicited hypercholesterolemia. Notably, metagenomic sequencing and LC-MS analysis indicated that PRE markedly increased the abundance of intestinal genera Bacteroides and significantly elevated the fecal CS concentration in HFE mice. Genome-based functional analysis further indicated that cofactors of sulfonation (ATP sulfurylase CysD and CysN, BT0414-BT0415) were significantly upregulated after treatment with PRE. The cholesterol-lowering effect of PRE was largely contingent upon microbial conversion of cholesterol-to-CS mediated by Bacteroides, as validated by antibiotics-induced intestinal microbiota depletion in pseudo-germ-free model and restoration of gut microbiota through FMT. In vitro study also showed that PRE promoted the growth of Bacteroides thetaiotaomicron. Furthermore, CS markedly alleviated serum, hepatic, bile, and fecal levels of TG, TC, LDL-C, HDL-C, and TBA, indicative of appreciable lipid-lowering effect. MD simulation and SPR results indicated that CS directly bound to ACAT2. Consistent with this interaction, CS greatly downregulated the mRNA and protein expression of ACAT2 in small intestinal tissue.<br><br>CONCLUSION: These findings for the first time suggested that PR acted as a prebiotic agent to ameliorate hypercholesterolemia, at least in part, via dual mechanism involving modulation of Bacteroides-mediated sulfonation metabolic pathway and feedback inhibition of ACAT2 by CS, highlighting its therapeutic potential for cholesterol-related disorders. This work might also offer novel mechanistic insight and further buttressed the ethnopharmacological application of PR in the therapy of hypercholesterolemia.},
}
@article {pmid40972462,
year = {2026},
author = {Wang, X and Luo, Y and Gu, Y and Ren, T and Liu, Y and Wang, X and Zhao, N and Nie, X and Liu, D and Zhao, Z},
title = {Physicochemical properties, microbial diversity, metabolites and their potential relationships of traditional Chinese Zhacai fermented for different periods.},
journal = {International journal of food microbiology},
volume = {444},
number = {},
pages = {111447},
doi = {10.1016/j.ijfoodmicro.2025.111447},
pmid = {40972462},
issn = {1879-3460},
mesh = {Fermentation ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; *Fungi/metabolism/classification/isolation &amp; purification/genetics ; Food Microbiology ; *Fermented Foods/microbiology/analysis ; Amino Acids/analysis ; Biodiversity ; Hydrogen-Ion Concentration ; },
abstract = {In this study, we investigated the physicochemical properties, dominant microorganisms, non-volatile metabolites and their relationships of traditional Chinese Zhacai (TCZ) at the "second-time pickling and pressing" stage fermentation. pH and amino acid nitrogen contents exhibited an increasing and then decreasing trend. Metagenomics analysis revealed the dominant bacterial species Lactiplantibacillus (Lpb.) plantarum and Latilactobacillus (Lat.) sakei, and fungal species Debaryomyces (D.) hansenii. LEfSe analysis identified a total of 47 differentially abundant bacteria, including Lpb. plantarum and Lat. Sakei. Metabolomics analysis indicated organic acids and their derivatives, organic heterocyclic compounds, lipids and lipid-like molecules as the major differential metabolites. Spearman's correlation results showed significant correlations among differential bacteria, non-volatile metabolites and physicochemical properties. Unexpectedly, differential fungi were not observed in TCZ at this fermentation period. Pathway enrichment identified phenylpropanoid biosynthesis and tryptophan metabolism as dominant metabolic pathways, both influencing the TCZ flavor development. This study contributes to further understanding of quality formation of TCZ, providing a foundational resource for future optimization and industrial application.},
}
@article {pmid40972220,
year = {2026},
author = {Saha, S and Mondal, A and Bag, S and Ghosh, S and Mandal, AH and Saha, NC and Chatterjee, S and Sopjani, M and Multisanti, CR and Faggio, C},
title = {Are biopesticides really safe? Impacts on gut microbiota and intestinal health in freshwater fish.},
journal = {Journal of contaminant hydrology},
volume = {276},
number = {},
pages = {104727},
doi = {10.1016/j.jconhyd.2025.104727},
pmid = {40972220},
issn = {1873-6009},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Fishes/microbiology ; Fresh Water ; *Biological Control Agents/toxicity ; *Water Pollutants, Chemical/toxicity ; Aquaculture ; *Intestines/drug effects ; Pesticides/toxicity ; },
abstract = {The growing use of biopesticides as eco-friendly alternatives to chemical pesticides is reshaping pest control in agriculture and aquaculture. However, their potential effects on non-target aquatic species, particularly freshwater fish, remain underexplored. This review investigates how different biopesticides, such as microbial agents, biochemical compounds, and plant-incorporated protectants, affect the gut microbiota and intestinal health of freshwater fish. The gut microbiome plays a vital role in digestion, nutrient absorption, immunity, and overall fish health. Biopesticide exposure may disrupt microbial balance, leading to reduced diversity, changes in community composition, inflammation, and dysbiosis. These alterations can impair digestive efficiency, immune function, growth, and reproduction. Promising mitigation strategies include the use of probiotics, prebiotics, symbiotics, insect-based feeds and other non-bacterial dietary interventions to restore gut homeostasis and improve fish resilience. In addition, advanced techniques like metagenomics and metabolomics are enhancing our understanding of host-microbiome interactions under biopesticide exposure. This review emphasizes the importance of including gut microbiota health in environmental risk assessments for biopesticide use in aquaculture. Future studies should adopt a multidisciplinary approach combining toxicology, microbiology, nutrition, and environmental science to develop species-specific, long-term strategies that safeguard fish health in increasingly pesticide-influenced aquatic environments.},
}
@article {pmid40971838,
year = {2025},
author = {Guo, X and Liang, A},
title = {Rhizosphere-derived microbiome of Ailanthus altissima drives gut microbiome composition in Lycorma delicatula (Hemiptera: Fulgoridae).},
journal = {Journal of economic entomology},
volume = {118},
number = {6},
pages = {2771-2782},
doi = {10.1093/jee/toaf217},
pmid = {40971838},
issn = {1938-291X},
support = {32470469//National Natural Science Foundation of China/ ; 32070470//National Natural Science Foundation of China/ ; 31561163003//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Rhizosphere ; *Hemiptera/microbiology ; *Ailanthus/microbiology ; Bacteria/classification/isolation &amp; purification/genetics ; Soil Microbiology ; },
abstract = {The spotted lanternfly (SLF), Lycorma delicatula (White) (Hemiptera: Fulgoridae), a highly polyphagous invasive pest, preferentially feeds on tree-of-heaven (TOH), Ailanthus altissima (Mill.) Swingle (Sapindales: Simaroubaceae). However, the bacterial interactions between this pest and its host plant remain poorly understood. In this study, we investigated the bacterial community composition and functional profiles in the SLF gut, TOH leaves, and TOH rhizosphere soil using amplicon and metagenomic sequencing. This study showed that the bacterial alpha-diversity differed significantly among the 3 sample types (P < 0.05). Venn analysis identified 4 shared amplicon sequence variants (ASVs) between the TOH rhizosphere soil and SLF gut, suggesting potential bacterial interactions or transfer. Further source-tracking analysis indicated that most gut bacteria originated from the rhizosphere soil. However, the dominant taxa varied across compartments: Proteobacteria dominated both the SLF gut and TOH leaves, while Acidobacteria predominated in the TOH rhizosphere soil. Network analysis revealed significant correlations between gut and rhizosphere microbes, notably Candidatus Vidania and Fastidiosipila (P < 0.05, r = 1). Functional profiling showed that the rhizosphere microbiome was enriched in nitrogen cycling and carbon fixation pathways, whereas the gut microbiome was associated with carbohydrate metabolism and nutrient assimilation. These results provide new insights into the potential roles of microbiomes in mediating plant-insect interactions and underscore the rhizosphere as a critical microbial source for SLF. Understanding these microbial connections may support the development of innovative and sustainable pest management strategies.},
}
@article {pmid40971415,
year = {2026},
author = {Vermeer, E and Prins, FM and Hidding, IJ and Jagt, JZ and de Jonge, R and Benninga, MA and Gacesa, R and Weersma, RK and de Boer, NKH and de Meij, TGJ},
title = {Metagenomic Sequencing Reveals Distinct Gut Microbiome Profiles in Therapy-Naïve de Novo Pediatric Inflammatory Bowel Disease.},
journal = {Inflammatory bowel diseases},
volume = {32},
number = {2},
pages = {207-219},
pmid = {40971415},
issn = {1536-4844},
support = {WO 19-25//The Dutch Digestive Foundation (MLDS)/ ; WO 19-25//Right on Time/ ; //The Dutch Digestive Foundation/ ; },
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; Child ; Feces/microbiology ; *Metagenomics/methods ; Case-Control Studies ; Adolescent ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; Biomarkers/analysis ; Child, Preschool ; },
abstract = {BACKGROUND AND AIMS: Microbiome studies reveal distinct microbial differences in inflammatory bowel disease (IBD), indicating its potential role in pathophysiology and as a noninvasive diagnostic biomarker. This study aims to profile the gut microbiome in children with IBD, compared to both healthy controls (HC) and controls with gastrointestinal symptoms (CGI), and to assess the potential of microbiome profiles as noninvasive diagnostic markers for de novo treatment-naïve pediatric IBD, and as early predictive markers for therapy response.<br><br>METHODS: We analyzed baseline fecal samples and clinical data from 103 therapy-na&#xef;ve children with IBD, 75 CGI, and 356 age and sex matched HC. Metagenomic sequencing was performed, and prediction models assessed diagnostic potential and prediction of induction therapy response at 3 months.<br><br>RESULTS: Alpha diversity progressively decreased from HC to CGI (P&#x2009;<&#x2009;.001) and decreased even further in IBD patients (P&#x2009;=&#x2009;.0056). Beta diversity analysis showed significant clustering differences (P&#x2009;<&#x2009;.001, R2 = 0.045). Differential abundance analysis revealed 116 species differing between HC and IBD, and 30 species between CGI and IBD. Prediction models based on microbiome features accurately distinguished IBD from HC (area under the curve [AUC]&#x2009;=&#x2009;0.96) and from CGI (AUC&#x2009;=&#x2009;0.71). However, these models were outperformed by clinical features, such as fecal calprotectin. Microbiome-based prediction of response to induction therapy in general showed limited accuracy (AUC&#x2009;=&#x2009;0.63), as well as for response to nutritional induction therapy (AUC&#x2009;=&#x2009;0.67).<br><br>CONCLUSIONS: We observed profound gut microbiome differences between de novo, therapy-na&#xef;ve pediatric IBD patients and controls. While microbiome profiles hold promise for improving diagnostic precision, their predictive value for therapy response seems limited.},
}
@article {pmid40970702,
year = {2025},
author = {Hu, J and Blazier, JC and Gitter, A and Gregory, LF and Gentry, TJ},
title = {How sequencing technology shapes our understanding of river water microbiomes and resistomes: a comparative study.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {10},
pages = {e0172325},
pmid = {40970702},
issn = {1098-5336},
support = {8092-0//National Institute of Food and Agriculture/ ; 22-50//Texas State Water and Soil Conservation Board/ ; },
mesh = {*Rivers/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics/analysis ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Sequence Analysis, DNA/methods ; *Water Microbiology ; },
abstract = {UNLABELLED: River ecosystems are vital for supporting biodiversity and supplying freshwater, but are increasingly impacted by microbial pollution, including the spread of antibiotic resistance genes (ARGs), which poses growing public health concerns. While high-throughput sequencing technologies have advanced our ability to study microbial communities and resistomes, their varying capabilities and biases require comparative analysis. In this study, we compared three sequencing approaches-Illumina 16S rRNA amplicon, Illumina shotgun metagenomics, and Oxford Nanopore-based long-read metagenomics-to profile microbial communities, ARGs, and virulence factors (VFs) in 48 river water samples. All methods identified Proteobacteria and Actinobacteria as dominant phyla, but substantial differences emerged at finer taxonomic levels. Long-read metagenomics and 16S data showed greater consistency at the genus level, while Illumina metagenomics differed, detecting more potential pathogens and fewer native freshwater taxa. For ARG and VF profiling, unassembled Illumina data yielded higher diversity and abundance, but assembled Illumina data showed comparable results to long-read metagenomics data in terms of dominant genes and host associations. Although Illumina provides high sensitivity, the use of short reads and associated assembly limitations can compromise functional accuracy. In contrast, long-read metagenomics facilitates gene-level resolution and direct host linkage, providing a more comprehensive understanding of environmental microbiomes. Our findings highlight the strengths and limitations of each method and support Oxford Nanopore technology (ONT)-based long-read metagenomic sequencing as a cost-effective and informative tool for high-resolution taxonomic and functional analysis of complex environmental samples.<br><br>IMPORTANCE: Accurate characterization of microbial communities and their functional traits, such as antibiotic resistance, is essential for evaluating water quality and associated public health risks. However, the selection of sequencing methods can substantially influence the detection and interpretation of microbial community composition and functional potential in environmental samples. By directly comparing amplicon, short-read metagenomic, and long-read metagenomic sequencing across 48 freshwater samples collected across different sites and time points, this study builds upon earlier work that typically focused on only two methods or less complex communities. It provides a comparative evaluation of three widely used sequencing approaches, demonstrating how methodological differences affect the resolution and reliability of taxonomic and functional profiling in complex environmental microbiomes. By highlighting the strengths and limitations of each platform, these findings enhance our understanding of how sequencing strategy shapes environmental microbiome analyses and contributes to evidence-based method selection in environmental microbiology and antimicrobial resistance monitoring.},
}
@article {pmid40970218,
year = {2024},
author = {Finn, RD and Balech, B and Burgin, J and Chua, P and Corre, E and Cox, CJ and Donati, C and Dos Santos, VM and Fosso, B and Hancock, J and Heil, KF and Ishaque, N and Kale, V and Kunath, BJ and Médigue, C and Nogueira, T and Pafilis, E and Pesole, G and Richardson, L and Santamaria, M and Strepis, N and Van Den Bossche, T and Vizcaíno, JA and Zafeiropoulos, H and Willassen, NP and Pelletier, E and Batut, B},
title = {Establishing the ELIXIR Microbiome Community.},
journal = {F1000Research},
volume = {13},
number = {},
pages = {},
pmid = {40970218},
issn = {2046-1402},
mesh = {Computational Biology ; *Metagenomics/methods ; *Microbiota ; },
abstract = {Microbiome research has grown substantially over the past decade in terms of the range of biomes sampled, identified taxa, and the volume of data derived from the samples. In particular, experimental approaches such as metagenomics, metabarcoding, metatranscriptomics and metaproteomics have provided profound insights into the vast, hitherto unknown, microbial biodiversity. The ELIXIR Marine Metagenomics Community, initiated amongst researchers focusing on marine microbiomes, has concentrated on promoting standards around microbiome-derived sequence analysis, as well as understanding the gaps in methods and reference databases, and identifying solutions to the computational overheads of performing such analyses. Nevertheless, the methods used and the challenges faced are not confined to marine microbiome studies, but are broadly applicable to other biomes. Thus, expanding this Marine Metagenomics Community to a more inclusive ELIXIR Microbiome Community will enable it to encompass a broader range of biomes and link expertise across 'omics technologies. Furthermore, engaging with a large number of researchers will improve the efficiency and sustainability of bioinformatics infrastructure and resources for microbiome research (standards, data, tools, workflows, training), which will enable a deeper understanding of the function and taxonomic composition of the different microbial communities.},
}
@article {pmid40969555,
year = {2025},
author = {Zhang, Y and Zhang, Y and Xing, G and Mei, T and Wang, M and Huang, C and Yi, H and Zhan, Y and Yang, S and Yan, Q and Li, S and Chen, C},
title = {Characterization of the oral virome in patients with diabetes mellitus.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1607798},
pmid = {40969555},
issn = {2235-2988},
mesh = {Humans ; *Virome ; *Mouth/virology/microbiology ; Male ; Female ; *Diabetes Mellitus/virology/microbiology ; Middle Aged ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Microbiota ; Bacteria/classification/genetics ; Adult ; Aged ; Dysbiosis ; Metagenome ; },
abstract = {INTRODUCTION: Diabetes mellitus (DM), a globally prevalent chronic metabolic disorder characterized by persistent hyperglycemia, has been increasingly linked to dysbiosis of the oral microbiome. However, the relationship between the virome, a crucial component of the oral microbiome, and DM remains poorly understood.<br><br>METHODS: To explore the characteristics of the oral virome in DM patients, we analyze the oral viral communities of 45 DM patients and 40 healthy controls (HC) using a publicly available metagenomic dataset.<br><br>RESULTS: Our analysis revealed no significant differences in a-diversity between DM patients and HC. However, Podovirus was enriched in DM patients, whereas Microviridae was more prevalent in HC. A total of 1,131 virus signal was identified, primarily belonging to the Siphovirus and Myovirus taxa. Notably, HC-enriched vOTUs exhibited broader host tropism, predominantly infecting Prevotella, Fusobacterium, and Gemella, whereas DM-enriched vOTUs showed narrower specificity for Pauljensenia and Veillonella. Cross-kingdom network analysis suggested that certain viruses (HMP_1157.k81_309051) may have potential links to the development of DM, and the bacteria genus F0040 might play a significant role in maintaining oral health. Additionally, the random forest model based on viral markers effectively distinguished between HC and DM patients (AUC =90.8%), significantly outperforming the bacterial model.<br><br>DISCUSSION: This indicates that these unique viral markers could serve as potential targets for DM intervention. Taken together, our findings reveal distinct alterations in the oral virome of DM patients and highlight its promise as a novel diagnostic and therapeutic target in metabolic disease research.},
}
@article {pmid40969552,
year = {2025},
author = {Wang, J and Ren, W and Liu, S and Li, Z and Zeng, Y and Meng, J and Yao, X},
title = {Changes in antioxidant capacity and gut microbiota in mice after intake of camel milk.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1621031},
pmid = {40969552},
issn = {2235-2988},
mesh = {Animals ; Camelus ; *Gastrointestinal Microbiome ; *Antioxidants/metabolism/analysis ; *Milk/chemistry ; Mice ; Mice, Inbred ICR ; Liver/metabolism ; Bacteria/classification/genetics/isolation &amp; purification ; Colon/microbiology ; Metagenomics ; Male ; Fermentation ; Probiotics/administration &amp; dosage ; },
abstract = {Fermented camel milk offers significant nutritional benefits, enriched with probiotics that generate bioactive compounds advantageous to human health. In order to investigate the effects of camel milk with different treatments on Antioxidant Capacity and Gut Microbiota in mice, 32 ICR mice were selected and randomly divided into 4 groups, including gavage with 10 mL/kg body weight of distilled water (DW Group), camel milk (CM Group), fermented camel milk (FCM Group), and pasteurized fermented camel milk (PFCM Group) every morning, respectively. After 28 days, liver and colon samples were collected to assess liver antioxidant capacity, and metagenomic analysis was performed on alterations in microbial community structures. Results demonstrated that all camel milk treatments elevated liver total protein levels while reducing MDA and SOD activity. In addition, the PFCM group had the highest total antioxidant capacity and the lowest SOD content. In addition, the intestinal microorganisms of mice changed at the phylum, genus and species levels after being gavaged with camel milk of different treatments. A total of 4732 microorganisms were identified, of which 259, 222, 116 and 164 were unique to the DW, CM, FCM and PFCM groups, respectively. The relative abundances of Adlercreutzia caecimuris, Adlercreutzia mucosicola and Enterorhabdus sp. P55 were significantly higher in the CM, FCM and PFCM groups than in the DW group, and the relative abundances of Parvibacter caecicola, Adlercreutzia muris and Roseburia sp. 1XD42-69 were significantly higher in the CM and PFCM groups than in the DW group. In addition, the relative abundances of Faecalibaculum rodentium, Alistipes muris and Limosilactobacillus reuteri were different between the CM and FCM groups. The results of the correlation analysis between the relative abundance of microbial species and antioxidant indices showed that Adlercreutzia mucosicola, Adlercreutzia muris, Lactobacillus acidophilus, and Enterorhabdus sp. P55 were significantly correlated with the antioxidant indices of mice. Further functional annotations indicated that these microorganisms might modulate antioxidant activity via metabolic and organismal systems. In summary, camel milk and fermented camel milk can play a positive role in regulating the intestinal flora of mice, thereby regulating the antioxidant capacity of mice and alleviating the effects of oxidative stress on the body. This study provides a scientific foundation for the further exploration and utilization of camel milk.},
}
@article {pmid40968530,
year = {2026},
author = {Popov, IV and Chikindas, ML and Venema, K and Ermakov, AM and Popov, IV},
title = {KEGGaNOG: A Lightweight Tool for KEGG Module Profiling From Orthology-Based Annotations.},
journal = {Molecular nutrition &amp; food research},
volume = {70},
number = {1},
pages = {e70269},
doi = {10.1002/mnfr.70269},
pmid = {40968530},
issn = {1613-4133},
support = {23-14-00316//Russian Science Foundation/ ; },
mesh = {*Molecular Sequence Annotation ; Probiotics ; *Genome, Bacterial ; *Software ; Metagenome ; Microbiota ; },
abstract = {Functional interpretation of bacterial genomes and metagenomes is essential for applications ranging from microbial ecology to probiotic development. KEGGaNOG is a lightweight and scalable Python tool that enables pathway-level profiling by translating orthology-based annotations into KEGG module completeness scores. KEGGaNOG accepts input from eggNOG-mapper annotations and supports both individual genome and multi-sample analyses. It calculates completeness scores for KEGG modules using internally integrated KEGG-Decoder logic and offers a suite of visualization options, including heatmaps, grouped summaries, barplots, radar plots, and correlation networks. We demonstrate its use on 11 well-characterized bacterial genomes, including several probiotic strains. KEGGaNOG accurately captured core biosynthetic capabilities and highlighted functionally informative differences across samples, such as vitamin biosynthesis, stress-response pathways, and transport systems. KEGGaNOG provides a practical framework for high-throughput functional annotation and comparative metabolic profiling in bacterial genomics and microbiome research. It is particularly well suited for preliminary analysis of novel or uncharacterized strains and is applicable to both isolate and metagenome-derived data. In the context of probiotic research, KEGGaNOG supports mechanistic exploration and strain selection by linking genomic content to functional capacity in a reproducible and interpretable manner.},
}
@article {pmid40968486,
year = {2026},
author = {Hsu, PS and Lin, JA and Hung, YT and Wu, TH and Chen, YH and Wu, MC},
title = {Pollen beebreads as a source of probiotics: a metagenomic and biochemical characterization.},
journal = {Journal of the science of food and agriculture},
volume = {106},
number = {2},
pages = {842-853},
doi = {10.1002/jsfa.70209},
pmid = {40968486},
issn = {1097-0010},
support = {//National Scienece and Technology Council/ ; //Ministry of Agriculture/ ; },
mesh = {*Pollen/chemistry/microbiology/metabolism ; *Probiotics/analysis/chemistry/metabolism ; Antioxidants/analysis/chemistry/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Bees ; Brassica napus/chemistry/metabolism ; Animals ; Camellia sinensis/chemistry/metabolism/microbiology ; Microbiota ; Metagenomics ; Taiwan ; Phenols/analysis ; Nutritive Value ; Flavonoids/analysis ; },
abstract = {BACKGROUND: Pollen beebread, a fermented pollen stored in honeycombs, is a crucial food source for honey bees and holds promise as a nutraceutical for humans. This study investigated the nutritional composition, antioxidant properties, and microbiota of beebread derived from three major floral sources in Taiwan: rapeseed (Brassica napus, Bn), beggartick (Bidens pilosa var. radiata, Bp), and tea tree (Camellia sinensis, Cs).<br><br>RESULTS: Beebread from different floral sources exhibited significant differences in protein content (up to ~140&#x2009;mg bovine serum albumin equivalents (BSAE) g[-1] in Bn beebread vs. ~105&#x2009;mg BSAE g[-1] in Bp and Cs beebread), phenolic content (up to ~30&#x2009;mg gallic acid equivalents g[-1] in Bn beebread), flavonoid content (up to ~45&#x2009;mg quercetin equivalents g[-1] in Bn beebread), and antioxidant activity (up to ~130 &#x3bc;mol Trolox equivalents g[-1] in Bn beebread). A metagenomic analysis revealed distinct microbiota across samples, with differences in alpha diversity: Bn beebread exhibited higher species richness, whereas Cs beebread exhibited greater evenness. Firmicutes were the dominant phylum in Bn and Bp beebread (average relative abundances of 57.5% and 57.7%, respectively), whereas Proteobacteria predominated in Cs beebread (58.5%). Lactobacillus was the most abundant genus, with average relative abundances of 52.8% and 51.5%, respectively, in Bp and Bn beebread samples.<br><br>CONCLUSION: These findings highlight the influence of floral origin on the nutritional and microbial profiles of beebread and support its potential as a source of beneficial microbes and nutrients. &#xa9; 2025 Society of Chemical Industry.},
}
@article {pmid40968405,
year = {2025},
author = {Trubl, G and Probst, AJ},
title = {Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication.},
journal = {Environmental microbiology},
volume = {27},
number = {9},
pages = {e70177},
doi = {10.1111/1462-2920.70177},
pmid = {40968405},
issn = {1462-2920},
support = {SCW1632//U.S. Department of Energy Office of Biological and Environmental Research through the Genomic Science Program and the Lawrence Livermore National Laboratory/ ; CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; CRC 1439/2//Deutsche Forschungsgemeinschaft/ ; 426547801//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Communication ; *Ecology ; *Microbiology ; *Microbiota ; *Terminology as Topic ; },
abstract = {The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, including variations across different scientific disciplines, can lead to confusion and miscommunication within the scientific community. This article discusses the importance of precise terminology in microbiome research, highlighting examples where terms have been misused or redefined without clear justification. We also present a list of frequently used terms in microbial ecology along with their specific definitions. We argue that the misuse of terminology can hinder scientific progress by creating ambiguity and misunderstanding. To address this, we propose a set of guidelines for the consistent use of key terms and provide clear definitions for some of the most commonly misused or newly introduced terms in the field. The definitions provided herein will also function as a guide for young researchers new to the field of microbial ecology. Accurate and consistent use of terminology is crucial for effective communication and collaboration in microbiology research. By adhering to standardised definitions, researchers can ensure that their work is clearly communicated and contributes meaningfully to the progress of science.},
}
@article {pmid40967861,
year = {2025},
author = {Ma, Y and Si, JH and Sun, DJY and Yu, CQ and Pang, YJ and Lyu, J and Li, LM},
title = {[Progress in population-based research of human microbiome and cardiovascular diseases].},
journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi},
volume = {46},
number = {9},
pages = {1680-1687},
doi = {10.3760/cma.j.cn112338-20241219-00816},
pmid = {40967861},
issn = {0254-6450},
support = {2023ZD0510101, 2023ZD0510100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; },
mesh = {Humans ; *Cardiovascular Diseases/microbiology ; *Microbiota ; Metagenomics ; },
abstract = {The human microbiome encompasses a diverse array of microorganisms and their functional interactions within the human body. It exhibits a vast diversity of species and complex roles across various body environments. Advanced sequencing technologies, such as 16S amplicon sequencing and metagenomic sequencing, facilitate in-depth analysis on this microbial community. Recent researches have suggested that characteristics of the human microbiome (such as diversity and composition of microbiome, involving metabolic pathways and metabolites) might be associated with the onset and progression of cardiovascular diseases. These findings provide valuable insights into the etiology of chronic diseases and might aid in the development of novel disease biomarkers and intervention strategies. This paper summarizes the designs, current status and key findings of current population-based research in this field, and introduce the future development and analyze the existing critical problems that need further investigations.},
}
@article {pmid40967455,
year = {2025},
author = {Arffman, RK and Folch, BA and Leonés-Baños, I and Altmäe, S},
title = {Gut feelings-the gut microbiome as a regulator of mental health in polycystic ovary syndrome.},
journal = {Fertility and sterility},
volume = {124},
number = {5 Pt 2},
pages = {931-947},
doi = {10.1016/j.fertnstert.2025.09.014},
pmid = {40967455},
issn = {1556-5653},
mesh = {Humans ; *Polycystic Ovary Syndrome/psychology/microbiology ; *Gastrointestinal Microbiome/physiology ; Female ; *Mental Health ; *Emotions ; Animals ; },
abstract = {IMPORTANCE: Polycystic ovary syndrome (PCOS) is a common endocrine disorder associated with reproductive, metabolic, and mental health comorbidities. The exact mechanisms of PCOS-related psychological distress and the role of the microbiome in the process remain unclear.<br><br>OBJECTIVE: To systematically review the current literature on the gut microbiome's association with mental health in women with PCOS and to review the possible mechanisms.<br><br>EVIDENCE REVIEW: A comprehensive literature search across the PubMed database until July 2025. Studies were included if they met the following criteria: observational/intervention studies; assessing microbiome through 16S ribosomal ribonucleic acid amplicon/16S ribosomal ribonucleic acid gene sequencing/metagenomics; comparing microbiome between women with and without PCOS; published from 2007 until 2025, and articles available online. The exclusion criteria were: language other than English or Spanish; reviews; abstracts/posters; case reports; full text not available, and duplicates. Two independent reviewers screened all titles and abstracts to determine eligibility, and discrepancies were resolved through discussion. The methodological quality and the potential risk of bias were assessed following the Joanna Briggs Institute Critical Appraisal Checklist for Case-Control Studies.<br><br>FINDINGS: A total of 159 studies were identified and screened for title, abstract, and full text. Eight studies met the criteria (2 rodent, 6 human studies). The quality assessment indicated that half of the studies (4/8) presented a high risk of bias. Regardless of the limited number of studies and the low quality scores, all the studies highlighted the association of the gut microbiome in PCOS with mental health problems.<br><br>CONCLUSIONS AND RELEVANCE: Our review provides the first summary of the studies performed to date on the gut-brain axis in PCOS. Our review highlights that the current state of the research is rather preliminary, and the existing studies possess various limitations and often lack rigorous study design. Nevertheless, all the studies indicated an association between changes in gut microbiome and mental health indicators in PCOS. We also noted a consistent increase in Gram-negative bacteria in women with PCOS and mental health issues. More research is needed on humans with a bigger sample size, different ethnicities, and wider age groups to clarify the microbial patterns involved, and in parallel, the field should move from descriptive studies to mechanistic approaches.},
}
@article {pmid40967406,
year = {2026},
author = {Harwood, M and South, J and Dunn, AM and Stebbing, PD and Burgess, A and Bojko, J},
title = {Pathogen diversity of the non-native narrow-clawed crayfish (Pontastacus leptodactylus) in a UK water body.},
journal = {Journal of invertebrate pathology},
volume = {214},
number = {},
pages = {108458},
doi = {10.1016/j.jip.2025.108458},
pmid = {40967406},
issn = {1096-0805},
mesh = {Animals ; *Astacoidea/microbiology/parasitology/virology ; Introduced Species ; United Kingdom ; Symbiosis ; },
abstract = {Biological invasions are intrinsically linked to introducing associated symbiotic organisms, some of which can be parasitic or pathogenic. The pathogenic risk of an 'invasive parasite' (aka. exotic pathogen) stems from its potential to infect native hosts and induce behavioural change or mortality, with the pathogen potentially presenting a greater risk than the host. Conversely, parasites translocated by invasive hosts may also reduce the impact of their host, indirectly curbing the hosts impact on the invaded ecosystem. In this study, we develop a pathogen profile for the narrow-clawed crayfish, Pontastacus leptodactylus. This is a non-native species in the United Kingdom, and poses a possible risk as a sink for invasive parasites. We use histopathology, metagenomics and metratranscriptomics to outline the symbiotic diversity harboured by a P. leptodactylus population from West Yorkshire, England. We discovered several protozoan and bacterial species that appear to be putatively commensal with this invader, as well as several RNA viruses (Hepelivirales; Picornavirales; Nodaviridae, and others) that may be more pathogenic in nature. Microsporidia and Nudiviridae were absent in our population sample set, as were all metazoan obligate parasites, such as trematodes and acanthocephalans. Using the novel genomic and pathological data available to us, we have explored the evolutionary history of each symbiotic species and provided an initial assessment on the putative risk to native species.},
}
@article {pmid40967080,
year = {2025},
author = {Chen, J and Li, W and Yang, L and Li, J and Wang, S and Chen, Z and Xu, S and Wen, M and Liang, J and Hu, Z and Pan, F and He, L and Gu, L and Wang, Z and Chen, H and Guo, Z},
title = {Microbiota-derived butyrate potentiates MSLN CAR-T cell therapy by metabolic reprogramming and extracellular matrix remodeling.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {192},
number = {},
pages = {118560},
doi = {10.1016/j.biopha.2025.118560},
pmid = {40967080},
issn = {1950-6007},
mesh = {Humans ; *Immunotherapy, Adoptive/methods ; *Extracellular Matrix/metabolism/drug effects ; *Butyric Acid/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Receptors, Chimeric Antigen/metabolism/immunology ; Cell Line, Tumor ; *T-Lymphocytes/immunology/drug effects/metabolism ; Male ; *Butyrates ; Female ; Metabolic Reprogramming ; },
abstract = {Despite the success of chimeric antigen receptor (CAR)-T cell therapy in hematologic malignancies, its efficacy in solid tumors remains limited due to T cell dysfunction and immunosuppressive microenvironments. Emerging evidence suggests that gut microbiota-derived metabolites, particularly short-chain fatty acids (SCFAs), may enhance T cell function, but their role in CAR-T therapy is unexplored. Here, in a small patient cohort (n = 4), preliminary metagenomic and metabolomics data suggested an association between higher butyrate levels and improved CAR-T responses, motivating our investigation of sodium butyrate (NaB), a microbiota-derived short-chain fatty acid, as a potential enhancer of CAR-T cell function through integrated metabolic and transcriptional reprogramming. Functional screening showed that NaB treatment augmented CAR-T cell antitumor activity while promoting a memory-like phenotype and reducing exhaustion markers. Mechanistically, NaB amplified antigen-driven phosphorylation of signaling effectors (p-ERK1/2, p-ZAP-70, p-AKT), inducing dual activation of glycolytic and oxidative phosphorylation pathways, coupled with upregulation of extracellular matrix (ECM)-remodeling genes (MMPs, Collagens), thereby improving tumor homing capacity. These preliminary findings suggest NaB as a potential link between microbial metabolism and CAR-T cell efficacy, offering a promising yet exploratory strategy to optimize adoptive immunotherapy through signaling-metabolic-ECM crosstalk, pending validation in larger cohorts.},
}
@article {pmid40966609,
year = {2025},
author = {Wu, L and Bao, D and Liao, H and Yan, M and Ge, Y and Han, Z and Xia, X},
title = {Pore-scale mass transfer heterogeneity shapes nutrient accessibility and functional assembly in porous microbial ecosystems.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40966609},
issn = {1751-7370},
support = {2023YFF1103701//National Key Research and Development Program of China/ ; },
mesh = {*Ecosystem ; *Microbiota ; Porosity ; *Nutrients/metabolism ; *Bacteria/metabolism/genetics/classification ; Metagenomics ; Soil Microbiology ; Amino Acids/metabolism ; Biomass ; },
abstract = {Porous ecosystems represent ubiquitous microbial habitats across natural settings including soil, gut tract, and food matrices, where microscale spatial architecture critically shapes microbial colonization and interactions. Yet, the mechanisms of how pore-scale physical constraints influence microbial community assembly and metabolic performance remain poorly understood. Here, we employed a microfluidic platform with tunable inter-pillar spacings, coupled with a multi-omics approach including in situ imaging, exometabolomics, metagenomics, and metatranscriptomics, to investigate how pore-size modulates microbial community dynamics. Comparing representative small (50 μm) and large (150 μm) pore-sizes, we found that larger pore-sizes promoted greater biomass accumulation and significantly enhanced exometabolite production, particularly of amino acids. Microscopy and quantitative assays revealed that 150 μm pores facilitated more efficient substrate degradation, especially of carbohydrates. Taxonomic profiling showed that increasing pore-size reduced community evenness while enhancing richness, selectively enriching carbohydrate-degrading and amino acid-producing taxa, and promoting more complex, positively correlated co-occurrence networks. Metatranscriptomic analysis further demonstrated that larger pore-size significantly upregulated key functional genes involved in substrate degradation, amino acid biosynthesis, and stress response pathways. Fluorescent tracer assays revealed pronounced mass transfer heterogeneity, where smaller pores exhibited prolonged solute persistence and steeper chemical gradients, ultimately restricting substrate availability and microbial activity. Collectively, our results reveal that alleviation of microscale spatial constraints enhances nutrient accessibility, metabolic function, and community organization in porous ecosystems, underscoring the pivotal role of physical microstructure in regulating both the taxonomic composition and functional capacity of microbial ecosystems.},
}
@article {pmid40966389,
year = {2025},
author = {Yan, Y and Zhou, X and Liu, L and Cai, Z and Penuelas, J and Huang, X},
title = {Soil Nutrient Enrichment Induces Trade-Offs in Bacterial Life-History Strategies Promoting Plant Productivity.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {45},
pages = {e10066},
pmid = {40966389},
issn = {2198-3844},
support = {U21A20226//National Natural Science Foundation of China/ ; 42430701//National Natural Science Foundation of China/ ; KYCX24_1825//Graduate Research and Innovation Projects of Jiangsu Province/ ; CX(23)1038//Jiangsu Provincial Agricultural Science and Technology Independent Innovation Fund/ ; 2023YFD1902000//Key Technologies Research and Development Program/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; *Nutrients ; *Plant Development/physiology ; Microbiota ; },
abstract = {Despite the global prevalence of anthropogenic soil nutrient enrichment, its impacts on the trade-offs in microbial life-history strategies remain poorly understood, which is critical for agroecosystem productivity. Here, large-scale observational studies are integrated with controlled experiments to systematically evaluate how soil nutrient enrichment affects bacterial functional potential and growth-rate potential, ultimately determining microbial functions and plant productivity. These findings reveal stark contrasts between nutrient-poor open field (OF) and nutrient-rich greenhouse (GH) soils across multiple paired sites using 16S rRNA gene amplicon and metagenomic sequencing. OF microbial communities dominated by oligotrophs have higher taxonomic diversity, larger average genome sizes with abundant nutrient-cycling genes, but lower 16S ribosomal RNA gene operon copy numbers and predicted maximum growth rates. Conversely, GH communities dominated by copiotrophs have higher growth-rate potential, more plant-beneficial bacteria, and higher diversity of functional genes (e.g., biofilm formation, secondary metabolism, and bacterial chemotaxis), but lower bacterial functional potential. Controlled pot experiments demonstrate that GH-enriched microbial functions strongly promote plant growth, particularly under sufficient nutrients and abiotic stress. These findings reveal a nutrient-driven trade-off between bacterial functional potential and growth rate, with implications for optimizing nutrient management strategies in precision agriculture to enhance specific microbial functions and plant productivity.},
}
@article {pmid40966087,
year = {2025},
author = {Pu, Y and Qi, X and Huang, L and Wu, W and Zhou, X and Li, W and Yang, Z and Kong, M and Shen, J and Qi, W and Sun, Z and Mei, Z and Wang, Q and Yang, W and Gao, X and Wang, X and Liu, Z and Yuan, C and Zheng, Y},
title = {Gut metagenome and plasma metabolome profiles in older adults suggest pyruvate metabolism as a link between sleep quality and frailty.},
journal = {Cell reports},
volume = {44},
number = {10},
pages = {116297},
doi = {10.1016/j.celrep.2025.116297},
pmid = {40966087},
issn = {2211-1247},
mesh = {Humans ; Aged ; *Gastrointestinal Microbiome/genetics/physiology ; Female ; *Metabolome ; Male ; Middle Aged ; Aged, 80 and over ; *Metagenome ; *Sleep/physiology ; *Frailty/blood/microbiology/metabolism ; *Pyruvic Acid/metabolism ; },
abstract = {Poor sleep quality is associated with increased frailty in older adults, but the role of the gut microbiome in this relationship remains unclear. Here, gut metagenome and plasma metabolome were profiled in 1,225 individuals aged 62-96 years. Poor sleep quality was associated with reduced abundances of potential probiotics such as Faecalibacterium prausnitzii and elevated abundances of pathobionts. A gut microbiome sleep quality index (GMSI) was developed to quantify microbial balance related to better sleep quality; higher GMSI scores were inversely associated with frailty and related clinical traits. Pyruvate metabolism emerged as a key microbial pathway linking sleep quality to frailty, with features such as F. prausnitzii abundance and microbial pyridoxal 5'-phosphate biosynthesis implicated in this connection. These findings deepen our understanding of microbiome-metabolome pathways related to sleep quality and frailty in aging and provide a valuable resource for future longitudinal and interventional studies.},
}
@article {pmid40965271,
year = {2025},
author = {Dell'Acqua, AN and Scicchitano, D and Simoncini, N and Mercanti, I and Leuzzi, D and Turroni, S and Corlatti, L and Rampelli, S and Colonna, M and Corinaldesi, C and Candela, M and Palladino, G},
title = {Ski Tourism Shapes the Snow Microbiome on Ski Slopes in the Italian Central Alps.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70195},
pmid = {40965271},
issn = {1758-2229},
mesh = {Italy ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Skiing ; *Snow/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; *Tourism ; Humans ; Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Seasons ; },
abstract = {Winter sports exert significant anthropogenic pressures on the snow microbiome, affecting the entire alpine ecosystem. The massive usage of artificial snow, human occupation, and the release of xenobiotics like microplastics or ski wax components on ski tracks can profoundly alter snow microbial ecology. Here, we reconstructed the temporal dynamics of the snow microbiome at three sites in the Italian Alps: inside and outside a ski track at the impacted site of Santa Caterina Valfurva and near Cancano lake as an unimpacted control. Using epifluorescence microscopy, 16S rRNA amplicon sequencing, and inferred metagenomics, we found that the snow microbiome inside the track presented a higher load of prokaryotes and viruses. Notably, N2-fixing microorganisms from cryospheric environments and host-associated taxa, like Terrisporobacter, Clostridium sensu stricto, Enterococcus, and Muribaculaceae, and the opportunistic pathogen Citrobacter characterised the impacted site. These microorganisms could originate from the river water used to produce artificial snow during winter. Our findings highlight the complexity and multifunctionality of the snow microbiome, where microorganisms with different ecological propensities can coexist, and the detectable impact of ski tourism, which enriches host-associated and xenobiotic-degrading microorganisms. This underscores the need for systematic monitoring and protection of the snow microbiome in the Alpine environment from anthropogenic threats.},
}
@article {pmid40965138,
year = {2025},
author = {Barker, HA and Bhimani, S and Tirado, D and Canas, JJ and Lemos, LN and Roesch, LFW and Ferraro, MJ},
title = {Deficiency of cannabinoid receptors enhances host susceptibility to bacterial infection.},
journal = {mBio},
volume = {16},
number = {10},
pages = {e0208825},
pmid = {40965138},
issn = {2150-7511},
support = {//Consortium for Medical Marijuana Clinical Outcomes Research/ ; R01 AI158749/AI/NIAID NIH HHS/United States ; 5T32AI007110-38//National Institute of Allergy and Infectious Diseases/ ; T32 AI007110/AI/NIAID NIH HHS/United States ; AI158749-04//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Animals ; Mice ; *Disease Susceptibility/microbiology ; Salmonella typhimurium ; *Salmonella Infections/genetics ; Mice, Knockout ; Host-Pathogen Interactions ; *Receptor, Cannabinoid, CB2/genetics ; *Receptor, Cannabinoid, CB1/genetics ; Disease Models, Animal ; Inflammation ; Immunity, Mucosal ; Homeostasis ; Gastrointestinal Microbiome ; Macrophages/microbiology ; Mice, Inbred C57BL ; Male ; Female ; Dysbiosis ; },
abstract = {Host resilience to bacterial infection depends on tightly regulated immune responses, which can be shaped by metabolic cues, including the contribution from bioactive lipids. The endocannabinoid system (ECS), a lipid signaling network known for its neuromodulatory roles, also influences immunity; however, the receptor-specific contributions of cannabinoid receptor 1 (CB1R) and cannabinoid receptor 2 (CB2R) in host-pathogen interactions remain incompletely defined in this context. Using receptor-deficient mouse models, we investigated how CB1R and CB2R modify immune responses to Salmonella Typhimurium. CB1R-deficient (CB1R-KO) mice exhibited heightened systemic inflammation, impaired bacterial clearance, and reduced survival in systemic infection, associated with dysregulated macrophage polarization and diminished neutrophil recruitment. In contrast, CB2R-KO mice showed increased susceptibility in both systemic and mucosal infection models, marked by a pro-inflammatory macrophage profile, enhanced neutrophilia, and microbiota dysbiosis. Shotgun metagenomic analysis revealed a reduced abundance of specific protective commensals and altered microbial metabolic pathway profiles in CB2R-KO mice, suggesting a role for CB2R in maintaining mucosal immune-microbiota homeostasis. Collectively, these findings highlight non-redundant roles for CB1R and CB2R in regulating immune dynamics and salmonellosis disease severity, and they point to the ECS as a potential target for host-directed immunomodulatory therapies.IMPORTANCEEffective immunity against bacterial pathogens requires a delicate balance between microbial clearance and the containment of inflammatory damage encountered during many infections. The molecular pathways that regulate this equilibrium remain incompletely defined, and the involvement of bioactive lipid signaling mechanisms also needs to be better described. Here, we show that the endocannabinoid receptors CB1R and CB2R play non-redundant roles in host defense against Salmonella infection. CB1R deficiency results in exacerbated systemic inflammation, defective bacterial clearance, and dysregulated macrophage polarization. In contrast, CB2R deficiency leads post-infection to gut dysbiosis and has been found to negatively affect the outcome for the host in both systemic and mucosal infection with Salmonella. By describing cannabinoid receptor-specific contributions to immune regulation and microbiota dynamics, our findings reveal a previously underappreciated axis of host-pathogen interaction. This study broadens our understanding of lipid-mediated immune modulation and identifies CB1R and CB2R as potential targets for therapies aimed at restoring immune homeostasis and improving infectious disease outcomes.},
}
@article {pmid40964625,
year = {2025},
author = {López Clinton, S and Iwaszkiewicz-Eggebrecht, E and Miraldo, A and Goodsell, R and Webster, MT and Ronquist, F and van der Valk, T},
title = {Small Bugs, Big Data: Metagenomics for Arthropod Biodiversity Monitoring.},
journal = {Ecology and evolution},
volume = {15},
number = {9},
pages = {e72163},
pmid = {40964625},
issn = {2045-7758},
abstract = {Obtaining genome-wide data from complex samples, such as environmental material or bulk species collections, is increasingly feasible, yet inferring species presence and population genomic insights remains challenging. We applied metagenomic sequencing to 40 arthropod bulk samples collected with Malaise traps across Sweden and compared results with metabarcoding of the same material. Using a custom genome database, we achieved genus-level classification largely consistent with metabarcoding. While metagenomics detected all genera identified by metabarcoding, conservative filtering thresholds designed to minimise false positives also excluded some true signals, particularly for low-abundance taxa. Taxonomic overlap between methods was further constrained by limited reference database representation. Beyond taxonomic assignment, metagenomic sequencing yielded genome-level information: we inferred haplotype diversity, heterozygosity and geographic population structure for several abundant species, including variable degrees of hybrid origin in red wood ants and the genetic distinctiveness of Gotland bumblebees. Finally, by-catch plant DNA present in the bulk samples revealed plausible arthropod-plant interactions, several of which align with known ecological associations. Together, these results demonstrate the potential of metagenomics for biodiversity monitoring and population genomics, while underscoring the importance of filtering criteria and comprehensive reference databases.},
}
@article {pmid40963595,
year = {2025},
author = {Wang, Q and Luo, Y and Mao, C and Xiang, X and Chen, J},
title = {Combined metagenomic and metabolomic analyses reveal gut microbiota dysbiosis and metabolic dysfunction in pediatric neurodevelopmental disorders.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1645137},
pmid = {40963595},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; *Metabolomics/methods ; *Metagenomics/methods ; Child, Preschool ; *Dysbiosis/metabolism/microbiology ; *Neurodevelopmental Disorders/metabolism/microbiology/etiology ; Child ; Feces/microbiology ; Metabolome ; },
abstract = {INTRODUCTION: Neurodevelopmental disorders (NDDs) are chronic brain diseases linked to innate immune signaling abnormalities, affecting children with complex gut-brain axis etiologies and limited targeted therapies. While infant microbes/metabolites may predict childhood NDDs, their landscape and host-metabolism interactions in NDDchildren remain unclear.<br><br>METHODS: This study enrolled 40 NDDchildren (mean age: 5.18 &#xb1; 1.77, F:M = 11:29) and 60 healthy controls (HCs; mean age:5.11 &#xb1; 1.42, F:M = 25:35) from Gansu Province Hospital Rehabilitation Center. Shotgun metagenomics and untargeted metabolomics was used to analyze gut microbiota and fecal/plasma metabolites, multi-omics integration analysis was performed to explore host-microbe interactions.<br><br>RESULTS: Clinically, NDD children showed self-care, concentration, and social behavior deficits, with grandparents as primary caregivers, versus parents in HCs. Microbiome analysis revealed reduced gut diversity and dysregulation in NDDs: depleted beneficial taxa including Akkermansia muciniphila and Lactococcus lactis, but enriched GABA/lactateproducing bacteria; and disrupted pathways included polysaccharides/fatty acids/amino acid/purine ribonucleosides metabolism. Fecal metabolomics identified 100 enriched metabolites including polyamines and GABA in 45 pathways and 254 depleted metabolites including bile acids and butyrate in 57 pathways. Plasma metabolomics showed 321 enriched metabolites like free fatty acids in 143 pathways and 270 depleted metabolites including glycerophospholipids in 84 pathways. Notably, phenolic acids, arginine/proline metabolism, and HIF-1 signaling were enriched in both feces and plasma of NDDs children. Benzene derivatives, indoles, steroid hormone biosynthesis, and tryptophan/tyrosine/phenylalanine metabolism were increased in plasma but decreased in feces, while oxidized lipids, amino acids and derivatives, metabolism of glycine/serine/threonine, alanine/aspartate/glutamate, and cysteine/methionine showed the opposite pattern. Venn analysis identified 29 common metabolites, with eight in KEGG maps. 11-dehydrocorticosterone, LPC (17:0/0:0), adipic acid, and sucralose were decreased in feces but increased in plasma; 1-methylhistidine and trigonelline were decreased in both; L-asparagine anhydrous was increased in feces but decreased in plasma; and sarcosine increased in both. Microbe-metabolite correlation analyses linked these metabolites to NDDs depleted species A. muciniphila, L. lactis, A. butyriciproducens, and etc.<br><br>DISCUSSIONS: Collectively, our study presents the first integrated profile of gut microbiome, microbial metabolites, and host metabolome, reveals gut microbiota dysbiosis, functional impairment, and metabolic disturbance in pediatric NDDs. These findings provide a theoretical foundation for microbiotaand metabolite-targeted therapeutic strategies in childhood NDDs.},
}
@article {pmid40961652,
year = {2025},
author = {Gao, X and Ning, P and Luo, S and Wang, Y and Li, W and Fan, X and Li, X},
title = {Microbiome and pathogen identification, and associated antimicrobial resistance genes and virulence factors in seafood revealed by 16S rRNA amplicon and metagenomic sequencing.},
journal = {International journal of food microbiology},
volume = {443},
number = {},
pages = {111441},
doi = {10.1016/j.ijfoodmicro.2025.111441},
pmid = {40961652},
issn = {1879-3460},
mesh = {*Seafood/microbiology ; *Virulence Factors/genetics ; *Bacteria/genetics/isolation &amp; purification/drug effects/classification/pathogenicity ; Animals ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Fishes/microbiology ; *Microbiota ; Food Microbiology ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/pharmacology ; Shellfish/microbiology ; },
abstract = {16S rRNA amplicon sequencing and metagenomic next-generation sequencing (mNGS) were employed to comprehensively analyze the microbial communities, foodborne pathogens, antibiotic resistance genes (ARGs), and virulence factors (VFs) in four seafood categories: ready-to-eat fish (RET-fish), non-ready-to-eat fish (non-RTE-fish), shellfish, and shrimp. At the phylum level, Pseudomonadota dominated across all samples. The microbial community composition of shellfish exhibited significant distinctions compared to other seafood categories. Metagenomic profiling identified high-risk pathogens, such as pathogenic Vibrio, Salmonella enterica, and Listeria monocytogenes. ARGs and VFs displayed the highest relative abundance in RET-fish, while shellfish exhibited the lowest abundance with statistically significant differences compared to other groups. For ARGs carried hosts, Bacillus-associated tet(L) and Lactobacillus-associated Inu(A) in RTE-fish demonstrated elevated abundance. In contrast, Vibrio species in other groups carried high abundances of ARGs such as qnrS and tet(34). Additionally, Vibrio harbored high levels of VFs, such as flagella and EF-Tu. Furthermore, plasmid-derived contigs co-harboring ARGs and mobile genetic elements (MGEs) were identified, displaying broad host ranges and high homology with plasmids from previously isolated clinical pathogenic strains, which underscores the potential role of seafood as a critical reservoir for the dissemination of ARGs. High-throughput sequencing approaches, integrated with multi-tool bioinformatics pipelines, provided robust insights into microbial communities and associated safety risk factors. These findings highlight the urgent need for targeted surveillance of seafood products and stricter antibiotic regulations in aquaculture to mitigate public health risks posed by foodborne pathogens and antimicrobial resistance.},
}
@article {pmid40961576,
year = {2026},
author = {Sun, H and Guo, X and Sun, J and Zhou, W and Yu, Z and Li, M and Zhang, S and Liu, X and Zhao, Y and Zhang, Y},
title = {Metagenome assembled genomes revealed the influences of mariculture and seagrass species on the microbiomes in seawater and rhizosphere biotopes.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 1},
pages = {118703},
doi = {10.1016/j.marpolbul.2025.118703},
pmid = {40961576},
issn = {1879-3363},
mesh = {*Rhizosphere ; *Seawater/microbiology ; *Microbiota/genetics ; *Metagenome ; Bacteria/genetics/classification ; *Alismatales ; },
abstract = {Seagrasses provide critical ecosystem services, with their associated microbiomes playing vital roles in the health and adaptation of hosts. Metagenome sequencing has significantly advanced our understanding of seagrass-associated microbiomes; however, the application and interpretive reliability of metagenome-assembled genomes (MAGs) remain limited. This study presented a comparative analysis of high-quality MAGs from seawater and rhizosphere samples across five distinct marine habitats. A total of 93 dereplicated high-quality MAGs were obtained from seawater and rhizosphere samples and assigned to 5 and 11 phyla, respectively. Rhizosphere-derived MAGs were predominated by Desulfobacterota and exhibited enriched genes for carbon/nitrogen metabolism, dissimilatory sulfate reduction/oxidation, and glycopeptide antibiotic resistance. In contrast, MAGs from seawater primarily belonged to Pseudomonadota and Bacteroidota, with enriched genes in assimilatory sulfate reduction pathway and fluoroquinolone/tetracycline antibiotic resistance. Statistical analysis revealed that oyster culture had significantly elevated gene abundance of MAG functions linked to carbon metabolism, dissimilatory nitrate reduction, and nitrogen fixation processes in rhizosphere, while differences between seagrass species were minimal. Additionally, environmental factors, such as total organic carbon concentrations and particle sizes, exhibited closer interactions with functions of rhizosphere-associated MAGs compared to seawater samples. Our study provided novel insight into seagrass microbiome ecology, establishing a comparative genome-resolved framework to investigate functional adaptation of marine microbiome across distinct biotopes, and demonstrating the efficacy of MAG-based analysis for unrevealing environment-microbiome interactions in uncultured systems. These findings extend knowledge for developing microbial biomarkers of seagrass ecosystem health and offer methodological references for functional microbiome studies in coastal environments.},
}
@article {pmid40961238,
year = {2025},
author = {Shalash, A and Ezzeldin, S and Hashish, S and Salah, Y and Dawood, NL and Moustafa, A and Salama, M},
title = {Gut microbial shifts toward inflammation in Parkinson's disease: Insights from pilot shotgun metagenomics Egyptian cohort.},
journal = {Journal of Parkinson's disease},
volume = {15},
number = {8},
pages = {1540-1543},
doi = {10.1177/1877718X251370156},
pmid = {40961238},
issn = {1877-718X},
mesh = {Humans ; *Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics/physiology ; Pilot Projects ; Metagenomics ; Male ; Middle Aged ; Female ; Egypt ; Aged ; *Inflammation/microbiology ; Feces/microbiology ; Cohort Studies ; *Dysbiosis/microbiology ; },
abstract = {Gut microbiome alterations are increasingly linked to Parkinson's disease (PD), yet regional signatures remain underexplored. We performed shotgun metagenomic sequencing of stool samples from Egyptian PD patients and healthy controls. PD patients exhibited depletion of short-chain fatty acid-producing taxa, and enrichment of pathobionts. Our findings suggested a pro-inflammatory gut shift in PD and emphasized the need for geographically diverse microbiome studies. While limited in sample size (n = 7 PD patients and n = 6 controls), this pilot addressed a critical gap in African PD microbiome research.},
}
@article {pmid40960303,
year = {2025},
author = {Qie, J and Cao, M and Xu, M and Zhang, Y and Luo, L and Sun, C and Ke, D and Yuan, S and Jia, W and Qiu, T and Li, T and Du, X and Xiao, C and Hong, Z and Zhang, B},
title = {Multi-cohort analysis unveils novel microbial targets for the treatment of hyperuricemia and gout.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0109125},
pmid = {40960303},
issn = {2379-5077},
mesh = {Humans ; *Hyperuricemia/microbiology/therapy ; *Gout/microbiology/therapy ; *Gastrointestinal Microbiome/genetics ; Male ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Female ; Cohort Studies ; Uric Acid/metabolism ; Adult ; Aged ; Bacteria/genetics/classification ; Metagenomics ; },
abstract = {The gut microbiota plays a crucial role in the development of hyperuricemia (HUA) and gout. However, the variability in study designs and analytical methods has led to inconsistent conclusions across different studies. Here, we conducted a comprehensive analysis of the gut microbiota associated with HUA and gout by examining 368 16S rRNA sequencing data from four Chinese cohorts, including 159 healthy controls (HC), 136 HUA patients, and 73 gout patients. Our findings indicate that there were significant differences in the gut microbiota composition between the three groups. Specifically, the HUA and gout groups demonstrated an increased abundance of pro-inflammatory bacteria, such as Fusobacterium and Bilophila, while beneficial bacteria known for their anti-inflammatory properties and metabolic benefits, including Christensenellaceae R-7 group, Anaerostipes, and Collinsella, are relatively reduced. Additionally, we developed a predictive model using microbial markers that achieved a high accuracy (area under the curve [AUC] > 0.8) in distinguishing between the HC, HUA, and gout groups. Notably, further metagenomic analysis identified a species-level genome bin (SGB), designated as Phil1 sp00194085, belonging to the order Christensenellales. For the first time, we discovered that this SGB carries a uric acid metabolic gene cluster and possesses enzymes associated with purine metabolism, suggesting its potential role in uric acid metabolism. Overall, our study deepens the understanding of the gut microbiota's role in HUA and gout and lays a foundation for developing innovative therapeutic strategies to effectively control uric acid levels through gut microbiota modulation.In this study, we conducted a comprehensive analysis of gut microbiota across multiple cohorts, identifying distinct microbial signatures in healthy controls, hyperuricemia (HUA), and gout patients. We observed an increase in pro-inflammatory bacteria and a decrease in beneficial bacteria for host metabolism in both the HUA and gout groups. Additionally, we developed a predictive model with high accuracy (area under the curve [AUC] > 0.8) based on microbial markers and discovered a novel species with potential for uric acid metabolism, providing new therapeutic targets for HUA and gout.},
}
@article {pmid40960301,
year = {2025},
author = {Yan, Y and Zhao, X and Liang, X and Xue, Y and Niu, Q and Li, D and Zhou, X and Li, Y and Dong, S and Gai, Y},
title = {Global wastewater microbiome reveals core bacterial community and viral diversity with regional antibiotic resistance patterns.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0142824},
pmid = {40960301},
issn = {2379-5077},
support = {BLX202162//Central University Basic Research Fund of China/ ; },
mesh = {*Wastewater/microbiology/virology ; *Microbiota/genetics ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Drug Resistance, Microbial/genetics ; Humans ; Metagenome ; *Viruses/genetics/classification/isolation &amp; purification ; Metagenomics ; Drug Resistance, Bacterial ; Biodiversity ; },
abstract = {Municipal wastewater treatment plants (WWTPs) serve as global repositories for diverse and dynamic microbial communities, reflecting the complex interplay of human activities, environmental conditions, and public health challenges. Despite their importance, a comprehensive understanding of the global distribution, composition, and functional roles of these microbial ecosystems has remained elusive. Here, we present a comprehensive analysis of bacterial and viral diversities in global wastewater systems by examining 575 sampling sites across 74 cities in 60 countries. Through metagenomic analysis, we reconstructed 12,758 non-redundant bacterial metagenome-assembled genomes (MAGs) spanning 70 phyla, with 4,499 MAGs representing novel species. Despite considerable regional variation, we identified a consistent core microbiome present across 70% of global samples predominantly comprising Proteobacteria. We further assembled 1.7 million viral genomes, revealing unprecedented viral diversity with over 1.5 million species-level viral operational taxonomic units (vOTUs). Network analysis demonstrated that transport proteins play crucial roles in maintaining WWTP functional resilience against disturbances. Machine learning approaches effectively predicted continental origins of wastewater samples based on microbial signatures, confirming that microbial communities reflect local environmental and socioeconomic conditions while maintaining functional conservation. We observed significant variation in the antibiotic resistance gene (ARG) distribution, with elevated prevalence in certain African and Asian regions compared to Europe and North America. Our results establish wastewater microbiomes as important indicators of human activity and provide critical insights for advancing environmental monitoring, antimicrobial resistance surveillance, and wastewater-based epidemiology.IMPORTANCEIntensifying urbanization and human activities have dramatically increased global wastewater generation, creating complex microbial ecosystems that significantly impact environmental and public health. This study presents the first large-scale, comprehensive characterization of bacterial and viral communities in wastewater treatment systems worldwide. By analyzing samples from diverse geographical, climatic, and socioeconomic contexts, we reveal how wastewater microbiomes serve as microbial fingerprints of human society, reflecting regional characteristics while maintaining functional conservation. Our findings demonstrate that these communities function as ecological extensions of human gut microbiota in the external environment, with important implications for the spread of antibiotic resistance and pathogens. The identification of viruses as key metabolic regulators in these systems provides new perspectives on microbial community dynamics. This global-scale analysis advances our understanding of wastewater microbiology and offers valuable insights for improving wastewater management, enhancing environmental monitoring systems, and strengthening public health surveillance through wastewater-based epidemiology.},
}
@article {pmid40958540,
year = {2025},
author = {Wang, X and Wang, W and Deng, L and Li, T and Lei, S and Zhang, L and Liao, L and Song, Z and Liu, G and Zhang, C},
title = {Shifts in Genome Size and Energy Utilization Strategies Sustain Microbial Functions Along an Aridity Gradient.},
journal = {Global change biology},
volume = {31},
number = {9},
pages = {e70498},
doi = {10.1111/gcb.70498},
pmid = {40958540},
issn = {1365-2486},
support = {2023YFF1305103//National Key Research and Development Program of China/ ; 42130717//National Sciences Foundation of China/ ; 42177449//National Sciences Foundation of China/ ; 2024JC-JCQN-35//Shaanxi Provincial Science Fund for Distinguished Young Scholars/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; *Genome Size ; Desert Climate ; *Energy Metabolism ; *Bacteria/genetics/metabolism ; *Genome, Bacterial ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Microbes acquire energy to sustain their survival and function through the decomposition of organic carbon (C) or by oxidizing atmospheric trace gases (e.g., H2, CO, CH4). However, how these two microbial energy-acquisition strategies change along environmental gradients and the underlying mechanisms are unclear. This study investigated the energy strategies and genomic traits of soil microbiomes along a natural aridity gradient, ranging from semi-humid forests to arid deserts. By analyzing 374 metagenome-assembled genomes from 13 microbial phyla, we found that the most prevalent microbes are metabolically versatile aerobes that use atmospheric trace gases to support aerobic respiration, C fixation, and N, P, and S cycling. Soil microbes adapt genomic traits associated with reduced energy expenditure in more arid soils, including smaller genome sizes, lower GC content, and fewer 16S rRNA gene copies. Microbial communities in diverse arid habitats are capable of utilizing organic compounds and the oxidation of trace gases (e.g., H2, CO, CH4, and H2S) as energy sources. However, the utilization of organic energy decreased while reliance on trace gas oxidation increased with increasing aridity. Higher consumption rates of H2, CO, and CH4 in desert soils from ex situ culture experiments confirmed that increased aridity stimulates microbial oxidation of atmospheric trace gases. This shift in energy utilization was strongly correlated with declining soil organic C levels. As organic C decreased along the aridity gradient, the abundance of trace gas oxidizers (both specialized and multi-gas oxidizers) increased significantly, while that of non-oxidizers declined. Trace gas oxidizers exhibited smaller genomes, lower 16S rRNA operon copy numbers, and slower predicted growth rates, indicative of oligotrophic lifestyles. In contrast, copiotrophic non-oxidizers had larger genomes and faster growth rates. These findings reveal that microbial communities adapt their genomic traits and energy-acquisition strategies to sustain functionality across aridity gradients, enhancing our understanding of soil microbiome responses to climate change.},
}
@article {pmid40958166,
year = {2025},
author = {Ghaly, TM and Rajabal, V and Russell, D and Colombi, E and Tetu, SG},
title = {EcoFoldDB: Protein Structure-Guided Functional Profiling of Ecologically Relevant Microbial Traits at the Metagenome Scale.},
journal = {Environmental microbiology},
volume = {27},
number = {9},
pages = {e70178},
pmid = {40958166},
issn = {1462-2920},
support = {CE200100029//ARC Centre of Excellence in Synthetic Biology/ ; //Macquarie University Research Fellowship/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism ; Soil Microbiology ; Phylogeny ; *Microbiota/genetics ; Computational Biology/methods ; *Bacterial Proteins/genetics/chemistry ; *Databases, Protein ; Protein Conformation ; },
abstract = {Microbial communities are fundamental to planetary health and ecosystem processes. High-throughput metagenomic sequencing has provided unprecedented insights into the structure and function of these communities. However, functionally profiling metagenomes remains constrained due to the limited sensitivity of existing sequence homology-based methods to annotate evolutionarily divergent genes. Protein structure, more conserved than sequence and intrinsically tied to molecular function, offers a solution. Capitalising on recent breakthroughs in structural bioinformatics, we present EcoFoldDB, a database of protein structures curated for ecologically relevant microbial traits, and its companion pipeline, EcoFoldDB-annotate, which leverages Foldseek with the ProstT5 protein language model for rapid structural homology searching directly from sequence data. EcoFoldDB-annotate outperforms state-of-the-art sequence-based methods in annotating metagenomic proteins, in terms of sensitivity and precision. To demonstrate its utility and scalability, we performed structure-guided functional profiling of 32 million proteins encoded by 8000 high-quality metagenome-assembled genomes from the global soil microbiome. EcoFoldDB-annotate could resolve the phylogenetic partitioning of important nitrogen cycling pathways, from taxonomically restricted nitrifiers to more widespread denitrifiers, as well as identifying novel, uncultivated bacterial taxa enriched in plant growth-promoting traits. We anticipate that EcoFoldDB will enable researchers to extract ecological insights from environmental genomes and metagenomes and accelerate discoveries in microbial ecology.},
}
@article {pmid40958146,
year = {2025},
author = {Yang, Q and Liu, J and Lyu, S and Li, S and Han, Q and Ma, C and Du, Z and Zhang, T},
title = {Ovalbumin Peptides Restore Intestinal Barrier Integrity via Gut-Liver Axis Modulation of Bile Salt Hydrolase and Bile Acids Crosstalk.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {39},
pages = {24741-24752},
doi = {10.1021/acs.jafc.5c07236},
pmid = {40958146},
issn = {1520-5118},
mesh = {Animals ; *Bile Acids and Salts/metabolism ; Mice ; Gastrointestinal Microbiome/drug effects ; *Ovalbumin/chemistry/administration &amp; dosage ; *Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Male ; *Amidohydrolases/metabolism/genetics ; Humans ; *Intestinal Mucosa/metabolism/drug effects ; *Peptides/administration &amp; dosage/chemistry ; *Colitis/metabolism/drug therapy/microbiology/genetics ; Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Fibroblast Growth Factors/metabolism/genetics ; *Inflammatory Bowel Diseases/metabolism/drug therapy/microbiology/genetics ; Mucin-2/genetics/metabolism ; Tumor Necrosis Factor-alpha/genetics/metabolism ; Receptor, Farnesoid X-Activated ; },
abstract = {Inflammatory bowel disease (IBD) is characterized by intestinal barrier dysfunction and bile acid (BA) dysmetabolism. BA metabolism was a pivotal regulator in the "gut-liver axis" to maintain intestinal homeostasis. Ovalbumin-derived peptides (OVA-Ps) exhibit potential in barrier repair; however, their systemic mechanisms within the microbiota-BA-host network remain underexplored. This study investigates the therapeutic potential of the oligomer OVA-P in a DSS-induced colitis mouse model. OVA-P administration significantly alleviated colitis symptoms, restored colon length, reduced pro-inflammatory cytokines (tumor necrosis factor-α), and enhanced antioxidant markers (SOD). Mechanistically, the OVA-P reshaped gut microbiota composition, suppressed bile salt hydrolase (BSH), and elevated conjugated BAs (e.g., taurocholic acid) levels. These changes activated the farnesoid X receptor (FXR) pathway, upregulating tight junction protein (ZO-1), and mucin (MUC-2) expression, thereby restoring intestinal barrier integrity. Metabolomic and metagenomic analyses confirmed the OVA-P-mediated modulation of the gut-liver axis through FXR-SHP/FGF15 signaling, highlighting its role in maintaining BA homeostasis. These findings provide insights into the use of OVA-P as a dietary intervention for IBD by targeting microbiota-BA-FXR interactions, offering a foundation for high-value egg protein applications in functional foods.},
}
@article {pmid40957481,
year = {2025},
author = {Ren, Y and Fang, H and Gao, Y and Yin, G and He, X and Chen, N},
title = {Effects of exercise on gut microbiota in older people with sarcopenia: Study protocol for a randomised controlled trial.},
journal = {Experimental gerontology},
volume = {211},
number = {},
pages = {112898},
doi = {10.1016/j.exger.2025.112898},
pmid = {40957481},
issn = {1873-6815},
mesh = {*Sarcopenia/therapy/microbiology/physiopathology ; Humans ; *Gastrointestinal Microbiome/physiology ; Aged ; Single-Blind Method ; *Resistance Training/methods ; Male ; Female ; Randomized Controlled Trials as Topic ; Quality of Life ; Animals ; Mice ; Muscle Strength ; Muscle, Skeletal ; },
abstract = {BACKGROUND: Sarcopenia is an age-related disease imposing a substantial burden on individuals and healthcare systems. Resistance training (RT) is recommended as the primary non-pharmacological treatment, and Baduanjin (BDJ) has shown positive effects for sarcopenia. However, the mechanisms through which exercise improves sarcopenia remain unclear. Research has suggested that exercise may enhance sarcopenia through the gut-muscle axis. Therefore, the present study aims to evaluate the effects of BDJ-RT on the gut microbiota in older people with sarcopenia, identify potential target microbial taxa and explore related mechanisms.<br><br>METHODS: In this 12-week randomised, single-blind controlled trial, 30 older people with sarcopenia will be randomly assigned to the BDJ-RT group (n&#xa0;=&#xa0;15) or control group (n&#xa0;=&#xa0;15). The BDJ-RT group will undergo BDJ combined with RT, and the control group will receive health education. Muscle mass, strength, physical performance, quality of life, gut microbiota and short-chain fatty acids will be assessed at baseline, post-intervention and follow-up. Potential target gut microbiota related to sarcopenia will be identified through metagenomic sequencing. The identified strains will then be gavaged to sarcopenic mice to evaluate their effects on sarcopenia. Data will be analysed using an intention-to-treat approach.<br><br>DISCUSSION: This study will be the first to systematically investigate the effects of BDJ-RT on the gut microbiota in older people with sarcopenia. The findings will provide potential microbial targets and mechanistic insights into the gut-muscle axis underlying exercise-induced improvements in sarcopenia.<br><br>TRIAL REGISTRATION: This study was registered on the International Traditional Medicine Clinical Trial Registry, with registration number ITMCTR2025000036.},
}
@article {pmid40956094,
year = {2025},
author = {Carmichael, MM and Valls, RA and Soucy, S and Sanville, J and Madan, J and Surve, SV and Sundrud, MS and O'Toole, GA},
title = {Profiling bile acids in the stools of humans and animal models of cystic fibrosis.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0145125},
pmid = {40956094},
issn = {2165-0497},
support = {P20-GM130454/NH/NIH HHS/United States ; T32HL134598/NH/NIH HHS/United States ; P20 GM130454/GM/NIGMS NIH HHS/United States ; ES 033988-01A1/NH/NIH HHS/United States ; 75N92024C00008/HL/NHLBI NIH HHS/United States ; U01 AI163063/AI/NIAID NIH HHS/United States ; R01 ES033988/ES/NIEHS NIH HHS/United States ; P30 DK117469/DK/NIDDK NIH HHS/United States ; R01AI164772, U01AI163063, P30DK117469/NH/NIH HHS/United States ; 05912G223//Cystic Fibrosis Foundation/ ; R01 AI164772/AI/NIAID NIH HHS/United States ; T32 HL134598/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Child ; Female ; Humans ; Male ; Mice ; Bacteroidetes ; *Bile Acids and Salts/analysis/classification/metabolism ; *Cystic Fibrosis/metabolism ; Disease Models, Animal ; Dysbiosis ; *Feces/chemistry ; Ferrets ; Intestinal Absorption ; Microbiota ; Mice, Inbred C57BL ; },
abstract = {UNLABELLED: Cystic fibrosis (CF) is associated with aberrant bile acid (BA) metabolism. As little is known about BA in children with CF (cwCF), we performed both comprehensive (n = 89) and focused (n = 21) BA profiling in stool of children with or without CF. Our results reveal select BA species and metabolites are significantly different between cwCF and nonCF controls. Focused BA profiling revealed a significant increase in total BA levels and selected changes in a subset of BA classes for cwCF. Matched bacterial metagenomic analyses showed no change in alpha-diversity between groups in this small cohort, at odds with previous studies, whereas changes in relative abundance of Bacteroidetes (lower in cwCF) phylum are consistent with prior reports. A trend was noted toward reduced abundance of bsh gene families, a key rate-limiting enzyme required for bacterial synthesis of secondary BAs, in cwCF. Observed modest changes in both BAs and microbial BA metabolism-related gene abundances may suggest a possible combination of defects in host and microbial BA metabolic pathways in cwCF. Fecal BA profiles from both ferret and mouse CF models showed significant differences from human BA profiles, and while the ferret model reproduced significant differences between CF and nonCF animals, the nonCF animals showed higher levels of BA (opposite of what is observed in humans), indicating that neither model recapitulated BA in stool in the context of CF. Together, these results provide new insights into CF-related BA dysmetabolism in cwCF and highlight limitations of CF animal models for BA functional studies.<br><br>IMPORTANCE: Changes in the abundance and/or composition of intestinal BAs may contribute to dysbiosis and altered gastrointestinal physiology in CF. Here, we report shifts in select fecal BA classes and species for cwCF. Matched metagenomic analysis suggests possible defects in both host intestinal BA absorption and gut microbial BA metabolism. Additional analyses of mouse and ferret CF stool for BA composition suggest great care must be taken when interpreting BA functional studies using these animal models. Together, this work lays technical and conceptual foundations for interrogating BA-microbe interactions in cwCF.},
}
@article {pmid40956075,
year = {2025},
author = {Yu, D and Mai, Y and Zhang, L and Xiao, Y and Zhang, M and Shao, B and Chen, B and Wang, T and Zhang, K and Zhang, L and Gao, N and Zhang, J and Yan, J},
title = {Viral community succession during cadaver decomposition and its potential for estimating postmortem intervals.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {10},
pages = {e0145325},
pmid = {40956075},
issn = {1098-5336},
support = {82030058//National Natural Science Foundation of China/ ; 82101977//National Natural Science Foundation of China/ ; },
mesh = {Cadaver ; Animals ; Rats ; *Postmortem Changes ; *Viruses/classification/genetics/isolation &amp; purification ; *Microbiota ; Metagenomics ; },
abstract = {UNLABELLED: Microbial communities play a vital role in cadaver decomposition and serve as reliable tools for postmortem interval (PMI) estimation. However, current research focuses primarily on bacterial/fungal communities, though viruses-as Earth's most abundant biological entities-play key roles in biogeochemical cycles by regulating bacterial communities via lysis-lysogeny switching. Viral succession patterns during decomposition remain insufficiently characterized, and their PMI biomarker potential is unexamined. We present metagenomic analysis of viral succession during 35-day decomposition of buried rat cadavers, revealing stage-specific dynamics: early dominance of Peduoviridae (0-3 days), mid-stage proliferation of Herelleviridae (7-21 days), and late-stage resurgence of Peduoviridae (28-35 days). Viral α-diversity exhibits a fluctuating downward trend. β-Diversity analysis (PCoA, ANOSIM, PERMANOVA; P < 0.001) confirmed PMI as a major structural driver (27% variance explained). Nine viral families exhibited significant PMI correlations (P < 0.05): Zierdtviridae, Casjensviridae, Schitoviridae, and Ackermannviridae showed strong negative correlations (r = -0.82 to -0.78), while Straboviridae correlated positively (r = 0.59). Using integrated viral abundance data, our Extremely Randomized Trees model achieved exceptional PMI prediction accuracy (test set: R[2] = 0.96, MAE = 2.54 days). Spearman correlations between dominant bacterial phyla (Bacteroidota, Bacillota, etc.) and viral families, combined with Procrustes analysis (M[2] =0.3385, P = 0.001) and Mantel tests (r = 0.8059, P = 0.001), confirmed strong virus-bacteria community consistency. This indicates viruses may regulate decomposition by targeting bacteria for lysis, releasing nutrients (e.g., organic nitrogen/phosphorus) to drive bacterial succession. Our study establishes a novel virus-based PMI prediction tool and discusses ecological drivers of decomposition.<br><br>IMPORTANCE: We present a viral succession-based framework for estimating PMI in buried remains. Our study identifies stage-specific viral biomarkers and identified nine viral families significantly correlated with PMI. By combining metagenomics and machine learning, we developed an Extremely Randomized Trees (ERT) model that achieved a low prediction error (test set: R&#xb2; = 0.96, MAE = 2.54 days). Furthermore, our findings demonstrate that viral and bacterial communities exhibit significant consistency and correlation during cadaver decomposition. This study not only provides a novel tool for the accurate estimation of forensic PMI but also advances our insight into viral regulation of bacteria and their interactions during cadaver decomposition.},
}
@article {pmid40953724,
year = {2025},
author = {Lan, T and Zhang, Y and Xie, R and Wu, Q and Wang, H and Du, J and Guo, W},
title = {Aromatic hydrocarbon exposure alters soil microbial communities and redox-driven carbon metabolism.},
journal = {Environmental research},
volume = {286},
number = {Pt 2},
pages = {122845},
doi = {10.1016/j.envres.2025.122845},
pmid = {40953724},
issn = {1096-0953},
mesh = {*Soil Microbiology ; Oxidation-Reduction ; *Soil Pollutants/toxicity ; *Carbon/metabolism ; *Microbiota/drug effects ; *Hydrocarbons, Aromatic/toxicity ; Bacteria/drug effects ; Benzene Derivatives/toxicity ; },
abstract = {The environmental behavior and toxicological impacts of benzene, toluene, ethylbenzene, and xylene (BTEX) have been widely studied. Yet their concentration-dependent effects on soil microbial structure, redox dynamics, and metabolism remain insufficiently understood, constraining predictions of ecosystem responses and the development of targeted bioremediation strategies. Here, we explored how exposure to different concentrations of BTEX reshaped microbial community structure and metabolic function by integrating phased amplicon sequencing, metagenomic analysis, and metabolite profiling. BTEX exposure did not significantly alter the overall microbial richness or diversity across treatment groups but substantially changed the taxonomic composition (Stress = 0.096, R = 0.2284, P = 0.0500). It reduced the dominance of Bacillus and enriched various Clostridium spp. closely associated with acetate and butyrate production. At higher BTEX concentrations, Sporolactobacillus was selectively enriched, directing carbon flow toward lactate production. Functionally, BTEX inhibited early reactions in the pentose phosphate pathway (PPP), while increasing the abundance of genes involved in downstream glycolysis and PPP, leading to rapid pyruvate and NADH accumulation. Meanwhile, inhibition of NADH: ubiquinone oxidoreductase indicated a reduced capacity for respiratory NADH turnover. At slight BTEX concentrations, the redox imbalance increased NADH availability, thereby enhancing alcohol synthesis by 38.03 % (±29.18 %) (P < 0.05). Conversely, high BTEX concentrations enhanced lactate biosynthesis, redirecting carbon and reducing equivalents away from alcohol and acid accumulation (P < 0.05). These findings demonstrate that BTEX reshapes microbial redox dynamics and carbon allocation in a concentration-specific manner, providing mechanistic insights into soil microbiome responses to aromatic hydrocarbon pollution and a basis for designing and optimizing future bioremediation strategies.},
}
@article {pmid40953197,
year = {2025},
author = {Ogarkov, O and Orlova, E and Suzdalnitsky, A and Mokrousov, I},
title = {Microbiota of the Lung Tuberculoma: Paucibacillary Bacterial Community.},
journal = {International journal of mycobacteriology},
volume = {14},
number = {3},
pages = {209-218},
pmid = {40953197},
issn = {2212-554X},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification/classification ; *Microbiota ; *Tuberculoma/microbiology ; *Lung/microbiology/pathology ; *Tuberculosis, Pulmonary/microbiology ; },
abstract = {Caseum, the central necrotic material of tuberculous lesions, is a reservoir of drug-resistant persisting Mycobacterium tuberculosis (MTB). However, tubercle bacilli are not the only bacterial inhabitants of this necrosis. We discuss the available data on metagenomic and amplicon sequencing of 16S rRNA of caseous necrosis from surgically excised tuberculosis (TB) foci. This approach facilitated the characterization of the biodiversity and the potential biochemical pathways of these bacterial communities. We postulate that in terms of MTB content relative to satellite anaerobic lipophilic bacteria, caseum may present two distinct terminal states. "True" TB necrosis, containing 99.9% tubercle bacilli, and a polymicrobial community wherein anaerobic lipophilic bacteria predominate over MTB. Isolation from caseum and genomic characterization of several Corynebacterium and Staphylococcus species support this concept.},
}
@article {pmid40953029,
year = {2025},
author = {Park, R and Chevalier, C and Kieser, S and Marizzoni, M and Paquis, A and Armand, S and Scheffler, M and Allali, G and Assal, F and Momjian, S and Frisoni, GB},
title = {Gut microbiome signatures in iNPH: Insights from a shotgun metagenomics study.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0330251},
pmid = {40953029},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Male ; Female ; Aged ; *Hydrocephalus, Normal Pressure/microbiology ; Alzheimer Disease/microbiology ; Aged, 80 and over ; Dysbiosis/microbiology ; Case-Control Studies ; Middle Aged ; },
abstract = {Idiopathic normal pressure hydrocephalus (iNPH), a leading cause of reversible dementia in older adults, is marked by ventriculomegaly, gait disturbances, cognitive decline, and urinary incontinence. Emerging evidence suggests that gut dysbiosis (microbial imbalance) may influence neuroinflammation and cerebrospinal fluid dynamics, potentially contributing to glymphatic system dysfunction and ventricular enlargement. This study used shotgun metagenomics to analyze the gut microbiome in iNPH patients (n = 18) compared to healthy controls (n = 50), individuals with ventriculomegaly but no iNPH symptoms (n = 50), and Alzheimer's disease patients (n = 50). Microbiome analysis showed an enrichment of species previously linked to various disease states, such as Enterocloster bolteae and Ruminococcus gnavus, indicating general dysbiosis. In contrast, enrichment of specific taxa, including Evtepia gabavorous and Cuneatibacter sp., were specifically associated with iNPH clinical traits, pointing to possible disease-specific microbial markers. Functional analysis showed enrichment of pathways related to carbohydrate and amino acid metabolism, including the S-adenosyl-L-methionine superpathway, implicating inflammatory and immune processes. These findings suggest distinct gut microbiome signatures in iNPH, offering insights into potential gut-brain interactions that may contribute to the disorder's pathophysiology and highlighting possible targets for future therapeutic strategies.},
}
@article {pmid40952003,
year = {2025},
author = {Sun, T and Zheng, Q and Huang, R and Yang, L and Liu, Z and Zhang, Z and Liu, X and Yang, H and Li, X and Tong, J and Zhu, L},
title = {Exploring cervicovaginal microbiome differences between single and multiple endometrial polyps: implications for non-invasive classification.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0002325},
pmid = {40952003},
issn = {2379-5077},
support = {2022-PUMCH-A-264//National High Level Hospital Clinical Reasearch Fungding/ ; 2022-PUMCH-A-042//National High Level Hospital Clinical Reasearch Fungding/ ; L232074//Natural Science Foundation of Beijing Municipality/ ; 2021-12M-C&amp;TA-008//CAMS Innovation Funds for Medical Sciences/ ; 2022-PUMCH-C-031//National High Level Hospital Clinical Resarch Funding/ ; 2022-PUMCH-C-060//National High Level Hospital Clinical Research Funding/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology ; *Microbiota/genetics ; Adult ; *Polyps/microbiology/classification ; *Cervix Uteri/microbiology ; Metagenomics/methods ; Endometrium/microbiology/pathology ; Middle Aged ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Single and multiple endometrial polyps (EP) are common gynecological conditions with differing recurrence rates, influencing clinical treatment decisions. This study aimed to characterize the reproductive tract microbiome in both subtypes to support the development of methods for the non-invasive categorization of EPs. Using metagenomic sequencing, we analyzed vaginal and cervical samples from 27 reproductive-aged patients with single EP and 22 with multiple EP. Compared with controls and multiple EP cases, single EP vaginal and cervical samples exhibited a lower percentage of community state types (CST) I and II. Sneathia amnii was identified as a characteristic species in both the vagina (P = 0.0051) and cervix (P = 0.0398) of single EP patients compared with controls. Mesorhizobium sp. (vaginal P = 0.0110, cervical P = 0.0210), Acinetobacter baumannii (vaginal P = 8.0 × 10[-5], cervical P = 0.0314), and Pasteurella multocida (vaginal P = 0.0173, cervical P = 0.0210) were enriched in single EP compared with multiple EP. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of vaginal microbiome revealed unique pathways in single EP, including aminoacyl-tRNA biosynthesis, pantothenate and coenzyme A (CoA) synthesis, pyrimidine metabolism, glycolysis/gluconeogenesis, and biosynthesis of phenylalanine, tyrosine, and tryptophan. Using a random forest model, we further selected microbiota and clinical parameters to differentiate single and multiple EPs, thus achieving an area under curve (AUC) of 0.861. Our findings characterized the composition of the cervicovaginal microbiota of single and multiple EPs and proposed biomarkers for their non-invasive classification based on a random forest model.IMPORTANCEThe prevalence rate of endometrial polyps (EPs), a common gynecological condition, varies between 7.8% and 34.9%. Multiple EPs are associated with higher recurrence rates and chronic endometritis than single EPs and thus require more aggressive clinical interventions. However, only laparoscopic surgery can accurately identify single and multiple polyps. Non-invasive adjunctive diagnostic methods can aid in altering surgical indications preoperatively. Using metagenomic sequencing, we thoroughly analyzed the vaginal and cervical samples of 27 single EP and 22 multiple EP patients of reproductive age. We then identified distinct microbial patterns in the single and multiple samples, which were crucial for understanding EP pathogenesis and its association with gynecological health. Using a random forest model, key bacterial taxa that differentiate single and multiple EPs were identified with high accuracy. These could potentially serve as non-invasive diagnostic biomarkers. This research delineates the cervicovaginal microbiome of the reproductive tract in EP patients, offering a basis for developing non-invasive diagnostic tools and personalized treatment strategies.},
}
@article {pmid40952001,
year = {2025},
author = {Raich, SS and Majzoub, ME and Haifer, C and Paramsothy, S and Shamim, MMI and Borody, TJ and Leong, RW and Kaakoush, NO},
title = {Bacterial taxonomic and functional changes following oral lyophilized donor fecal microbiota transplantation in patients with ulcerative colitis.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0099125},
pmid = {40952001},
issn = {2379-5077},
support = {988415//Crohn's and Colitis Foundation/ ; APP2011047//National Health and Medical Research Council/ ; Investigator grant//National Health and Medical Research Council/ ; Scientia fellowship//University of New South Wales/ ; },
mesh = {Humans ; *Colitis, Ulcerative/therapy/microbiology ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Freeze Drying ; Female ; Male ; Administration, Oral ; Double-Blind Method ; Feces/microbiology ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; },
abstract = {UNLABELLED: Oral lyophilized fecal microbiota transplantation (FMT) can induce remission in patients with active ulcerative colitis (UC); however, our understanding of how this form of FMT alters the patient microbiome remains limited. Here, we analyzed data from a recent randomized, double-blind, placebo-controlled clinical trial of FMT in UC to assess donor species colonization and factors responsible for efficacy using this form of therapy. The gut microbiome of donors and patients was profiled longitudinally using deep shotgun metagenomic sequencing, and microbiome diversity, species-genome bin presence, functional profiles, and the resistome were studied. The gut microbiome of patients treated with oral lyophilized FMT significantly increased in species-genome bin richness and shifted in composition toward the donor profiles; this was not observed in patients receiving placebo. While species-genome bin richness was not associated with clinical response in this trial, we identified donor- and patient-specific features associated with the induction of remission and maintenance of response. However, the presence of a Clostridium species-genome bin, as well as L-citrulline biosynthesis contributed by Alistipes spp., was seen in responders treated by either donor. Several of the above outcomes were found to be consistent when data were analyzed at the level of metagenome-assembled genomes. FMT was also found to deplete the resistome within patients treated with antibiotics to levels lower than the UC baseline. Single donor oral lyophilized FMT substantially modifies taxonomic diversity and composition as well as microbiome function and the resistome in patients with UC, with several features identified as strongly linked to response regardless of the donor used.<br><br>IMPORTANCE: There is a limited amount of work examining the effects of oral lyophilized fecal microbiota transplantation (FMT) on the microbiome of patients with ulcerative colitis (UC), and less so studies examining species-level dynamics and functional changes using this form of FMT. We performed deep shotgun metagenomic sequencing to provide an in-depth species-genome bin-level analysis of the microbiome of patients with UC receiving oral lyophilized FMT from a single donor. We identified key taxonomic and functional features that transferred into patients and were associated with clinical response. We also determined how FMT impacts the resistome of patients with UC. We believe these findings will be important in ongoing efforts to not only improve the efficacy of FMT in UC but also allow for the transition to defined microbial therapeutics, foregoing the need for FMT donors.},
}
@article {pmid40951316,
year = {2025},
author = {Zhang, B and Sheng, Z and Bu, C and Wang, L and Lv, W and Wang, Y and Xu, Y and Yan, G and Gong, M and Liu, L and Hu, W},
title = {Whipworm infection remodels the gut microbiome ecosystem and compromises intestinal homeostasis in elderly patients revealed by multi-omics analyses.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663666},
pmid = {40951316},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome ; Animals ; Humans ; *Homeostasis ; RNA, Ribosomal, 16S/genetics ; Aged ; Metabolomics/methods ; Metagenomics ; *Trichuriasis/parasitology/microbiology ; *Trichuris ; Female ; Male ; Bacteria/classification/genetics/isolation &amp; purification ; Metabolic Networks and Pathways ; Aged, 80 and over ; Metabolome ; *Intestines/microbiology ; Multiomics ; },
abstract = {INTRODUCTION: Whipworm (Trichuris trichiura) coexists with symbiotic microbiota in the gastrointestinal ecosystem. There is a paucity of data on the association between whipworm infection and the gut microbiota composition in elderly individuals. This study was designed to investigate changes in gut microbiota and function and its metabolite profile in patients with whipworm infection.<br><br>METHODS: We used 16S rRNA gene sequencing to identify microbial signatures associated with whipworm infection. Subsequently, shotgun metagenomic sequencing revealed functional changes that highlighted disruptions in microbial gene expression and metabolic pathways influencing host health. Ultraperformance liquid chromatography-mass spectrometry metabolomics was used to characterize whipworm infectioninduced metabolic perturbations and elucidate metabolite dynamics linked to microbial activity. Collectively, this multi-omics approach deciphered structural, functional, and metabolic remodeling of the gut ecosystem that distinguished whipworm-infected patients from healthy controls.<br><br>RESULTS: Analyses of the gut microbiome in patients with whipworm infection revealed significantly increased observed species richness and ACE indices, along with an enrichment of Prevotella 9-driven enterotypes. Additionally, metagenomic and metabolomic analyses indicated enrichment in metabolic pathways related to amino acid, energy and carbohydrate metabolism. Metabolic network analysis further suggested that the upregulated Prevotella copri and Siphoviridae sp. were positively correlated with elevated levels of myristic acid and DL-dipalmitoylphosphatidylcholine.<br><br>CONCLUSION: These findings suggest that whipworm infection significantly remodels the gut microbiome ecosystem and compromises intestinal homeostasis.},
}
@article {pmid40950593,
year = {2025},
author = {Silva, ACP and Migliaccio, F and Barosa, B and Gallucci, L and Yücel, M and Foustoukos, D and Le Bris, N and Bartlett, SJ and D'Alessandro, V and Vetriani, C and Giovannelli, D},
title = {Hydrodynamic flow and benthic boundary layer interactions shape the microbial community in Milos shallow water hydrothermal vents.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1649514},
pmid = {40950593},
issn = {1664-302X},
abstract = {In shallow-water hydrothermal vents, the dynamic interface between the discharged reduced hydrothermal fluids and the oxidized seawater allows the establishment of gradients capable of supporting diverse and complex microbial mats. Due to their shallow depths and proximity to land masses, shallow vents are heavily influenced by dynamic forcing, tidal fluctuations, and episodic events (e.g., storms, tides, etc.). Although several studies have investigated the microbial communities inhabiting shallow vents in the last decades, less is known about how microbial communities respond to episodic events and how the complex interplay of physical and chemical drivers shapes the establishment and structure of microbial biofilms in these systems. Here we present data combining the taxonomic and functional diversity of the white microbial mats commonly found in sulfide rich shallow-water hydrothermal vents in Paleochori Bay (Milos Island, Greece), using a combined approach of 16S rRNA transcript amplicon sequencing (from RNA) and shotgun metagenomic sequencing (from which 16S rRNA genes were retrieved). We show that the white microbial mats of Milos shallow-water hydrothermal vents are dominated by Epsilonproteobacteria, now classified as Campylobacterota, with metabolic functions associated with chemolithoautotrophic lifestyles and exposed to a diverse array of viral communities. Taxonomic names follow the classification available at the time of analysis (2012). We explore how dynamic forcing and storm events influence microbial community restructuring and turn-over, and provide evidence that dynamic interactions with the benthic boundary layer play a key role in controlling the spatial distribution of taxa. Overall, our results show diverse processes through which geodynamic events influence microbial taxonomic and functional diversity.},
}
@article {pmid40948444,
year = {2025},
author = {Bryson, S and Sisson, Z and Nelson, B and Grove, J and Reister, E and Liachko, I and Auch, B and Graiziger, C and Khoruts, A},
title = {Use of proximity ligation shotgun metagenomics to investigate the dynamics of plasmids and bacteriophages in the gut microbiome following fecal microbiota transplantation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2559019},
pmid = {40948444},
issn = {1949-0984},
support = {R44 AI172703/AI/NIAID NIH HHS/United States ; },
mesh = {*Fecal Microbiota Transplantation ; Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteriophages/genetics/isolation &amp; purification/classification ; *Plasmids/genetics ; Feces/microbiology/virology ; *Clostridium Infections/therapy/microbiology ; *Bacteria/genetics/classification/virology/isolation &amp; purification ; Clostridioides difficile/genetics ; Male ; Female ; Middle Aged ; },
abstract = {Proximity ligation shotgun metagenomics facilitate the analysis of the relationships between mobile genetic elements, such as plasmids and bacteriophages, and their specific bacterial hosts. We applied this technique to investigate the changes in the fecal microbiome of patients receiving fecal microbiota transplantation (FMT) for recurrent Clostridioides difficile infections (rCDI). FMT was associated with successful engraftment of donor bacteria along with their associated bacteriophages. While fecal microbial diversity increased in all patients, the extent of specific bacterial taxa engraftment varied among individual patients. Interestingly, some donor bacteriophages remained closely linked to their original bacterial hosts, while others expanded their associations across different bacterial taxa. Notably, FMT partially reduced the content of vancomycin resistance and extended-spectrum beta-lactamase genes in the fecal microbiome of rCDI patients.},
}
@article {pmid40947719,
year = {2025},
author = {Wei, CR and Basharat, Z and Osama, M and Mah, K and Waheed, Y and Hassan, SS},
title = {An Overview of the Association of the Urinary Tract Microbiome with Various Diseases and Implications for Therapeutics.},
journal = {Mini reviews in medicinal chemistry},
volume = {25},
number = {18},
pages = {1420-1443},
pmid = {40947719},
issn = {1875-5607},
mesh = {Humans ; *Microbiota/drug effects ; *Urinary Tract/microbiology ; *Urinary Tract Infections/microbiology/therapy ; *Urologic Diseases/microbiology/therapy ; Probiotics/therapeutic use ; },
abstract = {The urinary tract (UT) was once considered sterile, but now it is known to host a diverse community of microorganisms, known as the urinary microbiome. The collective microbiota is made up of bacteria, fungi, and viruses, necessary for maintaining UT health. This review aims to synthesize current knowledge on the urinary microbiome and clarify its emerging role as a key modulator in both health and a wide spectrum of UT disorders. Dysbiosis within this microbial community has been linked to conditions such as urinary tract infections (UTIs), interstitial cystitis/ bladder pain syndrome (IC/BPS), urinary incontinence, urolithiasis, benign prostatic hyperplasia (BPH), and even urinary tract malignancies. Advances in methodologies, such as expanded quantitative urine culture and metagenomics, have provided valuable insights into microbial variability influenced by factors like age, sex, and disease conditions. Additionally, this review explores the therapeutic potential of probiotics and bacteriophages, as well as the association of urinary microbiota with autoimmune and inflammatory conditions. Special emphasis is placed on translational relevance, including emerging microbiome-targeted therapies and personalized interventions for UTIs. Ethical considerations allied with UT microbiome research, such as data privacy, informed consent, and equitable access to emerging therapies, are also discussed. Despite substantial progress, challenges such as methodological heterogeneity, a lack of longitudinal data, and unresolved causal relationships persist. The study concludes by identifying key knowledge gaps and proposing future directions for multidisciplinary research to advance therapeutic innovation in urological health.},
}
@article {pmid40946204,
year = {2025},
author = {Burnett, J and Buckley, D and Grinstead, DA and Oliver, HF},
title = {Microbial Community Associations With Listeria monocytogenes in Food Processing Environments: A Systematic Review and Meta-Analysis.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {5},
pages = {e70277},
pmid = {40946204},
issn = {1541-4337},
support = {//Diversey/ ; },
mesh = {*Listeria monocytogenes/growth &amp; development/physiology/isolation &amp; purification ; *Food Microbiology ; *Food Handling ; Microbiota ; Biofilms ; },
abstract = {Listeria monocytogenes persistence in food processing environments challenges current understanding of microbial community dynamics. This systematic review and meta-analysis examined peer-reviewed studies that screened for Listeria spp. and performed culture-independent metagenomics on FPE surface samples. Following PRISMA guidelines, we searched PubMed, Web of Science, and Food Science and Technology Abstracts databases, screening 464 studies, with 73 qualifying for full-text review. Seven studies met the inclusion criteria for final analysis, encompassing 1659 environmental samples from meat processing (n = 4 studies) and produce facilities (n = 3 studies). Meta-analysis using random effects models revealed no significant correlation between Listeria presence and overall microbial community alpha diversity (Shannon: z = -0.89, p = 0.40; inverse Simpson and Chao1 indices similarly non-significant). This finding challenges previous assumptions about the relationship between microbial diversity and pathogen persistence. Differential abundance analyses identified three genera most frequently associated with Listeria presence across multiple studies: Pseudomonas, Psychrobacter, and Acinetobacter. These Gammaproteobacteria are characterized as aerobic biofilm formers capable of growth at refrigeration temperatures. One study using rigorous mixed-effects modeling identified Veillonella as significantly associated with L. monocytogenes presence, suggesting potential anaerobic niche interactions within biofilm communities. Synthesis of metabolic capabilities reported in the literature suggests these associated genera may provide structural biofilm matrices and potentially complementary metabolic functions that could facilitate L. monocytogenes survival in FPE conditions. However, the genus-level resolution of 16S rRNA amplicon sequencing data and methodological variations across studies limit definitive conclusions about specific metabolic interactions. These findings indicate that L. monocytogenes persistence appears to be associated with specific microbial partners rather than overall community diversity metrics. Understanding these ecological relationships may inform targeted control strategies focusing on biofilm-forming genera that create favorable conditions for Listeria survival in food processing environments.},
}
@article {pmid40945093,
year = {2025},
author = {Niu, Y and Zhang, X and Jiao, M and Storey, KB and Shekhovtsov, SV},
title = {Metabolic plasticity and gut microbiome synergy underlie high-altitude adaptation in the plateau frog Rana kukunoris: A multi-omics perspective.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {119050},
doi = {10.1016/j.ecoenv.2025.119050},
pmid = {40945093},
issn = {1090-2414},
mesh = {Animals ; *Altitude ; *Gastrointestinal Microbiome/physiology ; *Ranidae/physiology/microbiology/metabolism ; *Adaptation, Physiological ; Metabolomics ; Liver/metabolism ; Acclimatization ; Muscle, Skeletal/metabolism ; Metabolome ; Multiomics ; },
abstract = {Life on the Qinghai-Tibet Plateau is exposed to extreme abiotic stressors, yet endemic frog species such as Rana kukunoris thrive due to specialized adaptations. However, the metabolic and gut microbial mechanisms that enable survival at high altitude remain unclear. Here, we used metabolomic analysis and metagenomic sequencing to compare metabolic profiles of liver and skeletal muscle, as well as gut microbial composition and function, between high- (3730 m) and low-altitude (1990 m) populations. Metabolomic profiling revealed significant altitude-driven shifts, including the down-regulation of glycolysis (fructose-1,6-bisphosphate and glyceraldehyde 3-phosphate decreased by 44.2 % and 40.7 %, respectively) and tricarboxylic acid (TCA) cycle intermediates (fumaric acid and malic acid reduced by 37.7 % and 35.9 %, respectively) in the liver, and enhanced oxidative phosphorylation efficiency via elevated flavins (flavin mononucleotide and flavin adenine dinucleotide increased 1.43- and 1.28-fold, respectively) in skeletal muscle. These findings suggest a conserved strategy of metabolic rate depression and tissue-specific metabolic regulation. Significantly differential metabolites were enriched in glycerophospholipid metabolism and glycosylphosphatidylinositol (GPI)-anchor biosynthesis, highlighting membrane remodeling as a key adaptive response to cold stress at high altitudes. Moreover, gut microbiomes of high-altitude frogs exhibited increased α-diversity and functional enrichment in the biosynthesis of secondary metabolites, cofactors, amino acids, and carbohydrate-active enzymes (GHs/GTs), all likely improving tolerance to stressful environments and maintaining homeostasis. Key microbial taxa, including Candidatus Udaeobacter, Desulfovibrio, Bradyrhizobium, and Akkermansia, showed a specific dominance in high-altitude frogs, which may support host energy homeostasis and fortify gut barrier function. Multi-omics data highlighted the convergence of protective mechanisms in high-altitude frogs, including autophagy and two-component/quorum sensing systems. This study reveals significant adaptive remodeling of metabolism and gut microbiota in high-altitude R. kukunoris, providing novel insights into host-microbe synergistic interactions under extreme environments.},
}
@article {pmid40944761,
year = {2025},
author = {Gundogdu, A and Nalbantoglu, OU and Ulgen, M and Sav, MA and Ekinci, G and Kelestimur, F and Türe, U},
title = {Unveiling gut microbiome divergence in sellar-parasellar masses and brain tumors: A link beyond the skull.},
journal = {Neurosurgical review},
volume = {48},
number = {1},
pages = {641},
pmid = {40944761},
issn = {1437-2320},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Middle Aged ; Adult ; *Brain Neoplasms/microbiology/metabolism ; Cross-Sectional Studies ; *Pituitary Neoplasms/microbiology/metabolism ; Aged ; },
abstract = {The gut microbiome is increasingly linked to systemic health and central nervous system disorders, including brain tumors. This study investigated gut microbiome composition and metabolic profiles in patients with sellar-parasellar tumors (SPTs), other brain tumor types (OBTs) and healthy controls (HCs) to identify microbial and metabolic biomarkers for brain tumor phenotypes. A cross-sectional study involving 56 participants (17 SPTs, 11 OBTs, 28 HCs) was conducted. Gut microbiota composition was analyzed with 16 S rRNA sequencing, and metabolic activity was inferred via metagenome-scale metabolic models. Multivariable regression and machine learning were used to evaluate microbial and metabolic differences across groups. Taxonomic and metabolic analyses revealed distinct profiles across these groups. The result showed that HCs exhibited higher levels of Lachnospira and Comamonadaceae, while tumor patients had an over-representation of Bacilli. OBT patients showed elevated metabolic exchange scores (MES) for amino acids (D-alanine, L-glutamic acid), carbohydrates (mucin-type O-glycans, alpha-lactose), and lipids (stearic acid, choline), most likely reflecting tumor-associated metabolic demands. Conversely, SPT patients had profiles closer to HCs, with lower MES and reduced systemic disruption. Key taxa such as Akkermansia, Faecalibacterium, and Lachnospira demonstrated tumor-specific adaptive metabolic outputs, emphasizing functional microbial contributions over purely taxonomic roles. These findings highlight the role of gut microbiota in brain tumor progression through altered metabolic pathways, suggesting potential biomarkers and therapeutic targets for neuro- oncology. The study integrates genome-scale metabolic modeling with 16 S profiling to show that functional metabolic divergence can exist even when taxonomic differences are subtle, revealing overlooked biomarkers of the gut-brain axis in neuro-oncology.},
}
@article {pmid40943646,
year = {2025},
author = {Kovenskiy, A and Katkenov, N and Ramazanova, A and Vinogradova, E and Jarmukhanov, Z and Mukhatayev, Z and Kushugulova, A},
title = {Bacteroides fragilis and Microbacterium as Microbial Signatures in Hashimoto's Thyroiditis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
pmid = {40943646},
issn = {1422-0067},
support = {AP19675503//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; *Bacteroides fragilis/genetics/isolation &amp; purification ; Adult ; Middle Aged ; Female ; Male ; *Gastrointestinal Microbiome ; *Hashimoto Disease/microbiology ; Young Adult ; Adolescent ; Aged ; Feces/microbiology ; Metagenomics/methods ; *Actinobacteria/genetics ; Case-Control Studies ; },
abstract = {Hashimoto's thyroiditis (HT) and alopecia areata (AA) are organ-specific autoimmune diseases that frequently co-occur, suggesting shared immunological and microbial pathways. The gut microbiome has emerged as a key modulator of immune function, yet disease-specific microbial signatures remain poorly defined. Fecal samples from 51 participants (HT: n = 16, AA: n = 17, healthy controls: n = 18) aged 18-65 years were analyzed using shotgun metagenomic sequencing followed by multivariate statistical analyses. While alpha and beta diversity did not differ significantly across groups, taxonomic profiling revealed disease-specific microbial patterns. Bacteroides fragilis was significantly enriched in HT, suggesting a potential role in immune modulation; although mechanisms such as polysaccharide A production and molecular mimicry have been proposed in previous studies, their involvement in HT remains to be confirmed. Microbacterium sp. T32 was elevated in both HT and AA, indicating its potential as a shared autoimmune marker. Functional analysis showed increased fermentation and amino acid biosynthesis in AA, contrasting with reduced metabolic activity and elevated carbohydrate biosynthesis in HT. HT and AA exhibit distinct gut microbial and metabolic signatures. Bacteroides fragilis and Microbacterium sp. T32 may serve as potential microbial correlates for autoimmune activity, offering new insights into disease pathogenesis and targets for microbiome-based interventions.},
}
@article {pmid40943581,
year = {2025},
author = {Gałęcki, R and Nowak, A and Szulc, J},
title = {Tenebrio molitor Meal-Induced Changes in Rat Gut Microbiota: Microbiological and Metagenomic Findings.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
pmid = {40943581},
issn = {1422-0067},
support = {LIDER/5/0029/ L-12/20/NCBR/2021//National Centre for Research and Development/ ; },
mesh = {Animals ; *Tenebrio/chemistry ; *Gastrointestinal Microbiome/genetics ; Rats ; Rats, Wistar ; *Metagenomics/methods ; *Animal Feed ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Male ; Feces/microbiology ; },
abstract = {As demand for sustainable protein sources grows, edible insects like Tenebrio molitor (yellow mealworm) are gaining attention as functional feed ingredients. This study investigated how dietary inclusion of T. molitor meal affects gut microbiota composition and diversity in laboratory rats. Wistar rats were divided into three diet groups: standard feed, 35% chicken meal, and 35% T. molitor meal. Fecal samples were collected at weeks 4, 6, and 8. Microbial populations were assessed using culture-based methods, and community structure was analyzed at week 9 via Illumina MiSeq 16S rRNA sequencing. Bioinformatic analyses evaluated microbial diversity and predicted functions. Rats fed T. molitor meal showed significantly reduced counts of total aerobic/anaerobic bacteria, fungi, and coagulase-positive staphylococci. Metagenomics revealed a Firmicutes-dominated microbiota, with enrichment of protein- and cholesterol-metabolizing taxa (e.g., Eubacterium coprostanoligenes, Oscillospiraceae, Ruminococcaceae), and a decline in fiber- and mucin-degrading bacteria like Akkermansia and Muribaculaceae. Functional predictions indicated upregulated amino acid metabolism and chitin degradation. Despite compositional shifts, microbial diversity remained stable, with no signs of dysbiosis. These findings suggest that T. molitor meal supports a safe, functional adaptation of gut microbiota to high-protein, chitin-rich diets, supporting its potential use in monogastric animal nutrition.},
}
@article {pmid40943165,
year = {2025},
author = {Wang, R and Ren, W and Liu, S and Li, Z and Li, L and Ma, S and Yao, X and Meng, J and Zeng, Y and Wang, J},
title = {Metagenomic Analysis Reveals the Anti-Inflammatory Properties of Mare Milk.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
pmid = {40943165},
issn = {1422-0067},
support = {2022A02007-1 and ZYYD2025JD02.//Xinjiang Uygur Autonomous Region Major Science and Technology Special Project and the Central Guidance for Local Science and Technology Development Fund/ ; },
mesh = {Animals ; Horses ; *Gastrointestinal Microbiome/drug effects/genetics ; *Milk/metabolism ; *Metagenomics/methods ; Mice ; *Anti-Inflammatory Agents/pharmacology ; Female ; Cytokines/metabolism ; },
abstract = {This study aimed to assess the anti-inflammatory properties of mare milk by analyzing immune markers in mice following gavage of mare milk. Metagenomic sequencing was employed to examine variations in the composition and functional profiles of the intestinal microbiota across different experimental groups. Bacterial diversity, abundance, and functional annotations of gut microbiota were evaluated for each group. The results show that, compared to the control group, the mare milk group exhibited a significant decrease in the pro-inflammatory cytokine IL-6 levels and a significant increase in secretory immunoglobulin A (SIgA) levels (p < 0.05). The fermented mare milk group and the pasteurized fermented mare milk group demonstrated a significant downregulation of the pro-inflammatory cytokines TNF-α and IL-1β, along with a significant increase in the anti-inflammatory cytokine IL-10 levels (p < 0.05). Additionally, metagenomic analysis revealed that both the mare milk and fermented mare milk groups were able to regulate the imbalance of the intestinal microenvironment by improving the diversity of the gut microbiota and reshaping its structure. Specifically, the mare milk group enhanced gut barrier function by increasing the abundance of Bacteroides acidifaciens, while the fermented mare milk group increased the proportion of Bacillota and the relative abundance of beneficial bacterial genera such as Faecalibaculum and Bifidobacterium. KEGG pathway annotation highlighted prominent functions related to carbohydrate and amino acid metabolism, followed by coenzyme and vitamin metabolism activities. In conclusion, mare milk and its fermented products demonstrate anti-inflammatory effects, particularly in modulating immune responses and inhibiting inflammatory cascades. Additionally, the administration of mare milk enhances the composition and metabolic activity of intestinal microbiota in mice, supporting intestinal microecological balance and overall gut health, and offering valuable insights for the development of mare milk-based functional foods.},
}
@article {pmid40940575,
year = {2025},
author = {Abenaim, L and Mercati, D and Mandoli, A and Carpentier, J and Noël, G and Conti, B and Caparros Megido, R and Dallai, R},
title = {Exploring the plastivorous activity of Hermetia illucens (Diptera Stratiomyidae) larvae.},
journal = {Environmental science and pollution research international},
volume = {32},
number = {36},
pages = {21649-21665},
pmid = {40940575},
issn = {1614-7499},
mesh = {Animals ; Larva ; *Diptera ; Biodegradation, Environmental ; Gastrointestinal Microbiome ; },
abstract = {Hermetia illucens (Diptera Stratiomyidae), also known as Black Soldier Fly (BSF), is one of the insect species most investigated for biodegradation ability in its larvae. H. illucens larvae can biodegrade organic waste but also contaminants like pesticides, antibiotics, and mycotoxins. This study wants to investigate the ability of these larvae to degrade polystyrene (PS). Experiments evaluated the growth performance, survival rates, intestinal and intracellular morphological alterations, degradation by-product formation and intestinal microbiota alterations of larvae fed a PS-enriched diet. Despite the addition of PS microparticles, no significant differences in growth or survival were observed compared to the standard diet (p > 0.05). Confocal Laser Scanning Microscopy and Transmission Electron Microscopy confirmed the presence of PS microparticles in the larval gut, with potential signs of biodegradation. Metabolomic analyses identified styrene in the gut after 1 and 3 days of PS feeding, but its occurrence was likely due to thermal depolymerisation of the PS microparticles under GC-MS conditions. Metagenomic analysis revealed significant shifts in the intestinal microbiota. Notably, an enrichment of Corynebacterium, known for its role in aerobic PS degradation, and the abundance increase of other genera (Enterococcus, Enterobacteriaceae, Enterobacter, and Escherichia-Shigella) associated with synthetic polymer metabolism was observed. These results confirm the potential of BSF larvae to manage plastic waste through the interaction between their gut microbiota and synthetic materials. This study provides a foundation for future research focusing on isolating bacterial communities and enzymatic processes involved in polymer degradation, aiming to develop sustainable strategies for plastic waste management.},
}
@article {pmid40940504,
year = {2026},
author = {Ruiz-Malagón, AJ and Rodríguez-Sojo, MJ and García-García, J and Ho-Plagaro, A and García, F and Vezza, T and Redondo-Cerezo, E and Griñán-Lisón, C and Marchal, JA and Rodríguez-Cabezas, ME and Rodríguez-Nogales, A and Gálvez, J},
title = {Tigecycline suppresses colon cancer stem cells and impairs tumor engraftment by targeting SNAI1-regulated epithelial-mesenchymal transition.},
journal = {Acta pharmacologica Sinica},
volume = {47},
number = {1},
pages = {222-241},
pmid = {40940504},
issn = {1745-7254},
mesh = {*Epithelial-Mesenchymal Transition/drug effects ; Humans ; *Tigecycline/pharmacology/therapeutic use ; *Neoplastic Stem Cells/drug effects/metabolism/pathology ; Animals ; *Snail Family Transcription Factors/metabolism/antagonists &amp; inhibitors ; *Colonic Neoplasms/drug therapy/pathology/metabolism ; HCT116 Cells ; Mice ; Xenograft Model Antitumor Assays ; Cell Line, Tumor ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Cancer stem cells (CSCs) play a key role in the progression of colorectal cancer (CRC). The high heterogeneity of CSCs has hindered the clinical application of CSC-targeting therapies. Tetracyclines are drugs with therapeutic potentials beyond their antibiotic activity. We previously demonstrated the efficacy of tigecycline, a third-generation tetracycline, against a model of colitis-associated colorectal cancer, primarily focusing on its immunomodulatory role with a preliminary assessment of its impact on stemness. In this study we characterize the effects of tigecycline on colon CSCs in vitro and in a CRC xenograft model, with special attention on the signaling pathways involved and the modulation of the gut microbiota. We generated secondary colonospheres from two colon tumor cell lines HCT116 and CMT93, and evaluated the effect of tigecycline on CSCs properties. We showed that tigecycline (25, 50 μM) effectively reduced colon CD133[+]CD44[+]LGR5[+]ALDH[+] subpopulations and their viability, self-renewal and migratory capacity. Moreover, tigecycline treatment hindered epithelial-mesenchymal transition (EMT) process through targeting SNAI1 and β-catenin, resulting in an upregulation of epithelial markers (E-cadherin) and a downregulation of pluripotency and mesenchymal ones (Vimentin, N-cadherin, SOX2, NANOG, MIR155, MIR146). This effect was confirmed in two independent CRC-xenograft murine models in which tigecycline administration led to a reduction in tumor volume. Finally, CRC samples were taken from HCT116 xenograft model mice for analysis of CSCs-related signaling pathways and stools were collected for gut microbiome metagenomic analysis. We found that the antibiotic modulated gut dysbiosis by increasing the abundance of beneficial bacterial species such as Parabacteroides sp., which were involved in metabolic pathways that hindered SNAI1-Wnt-β-catenin signaling. These results reinforce the new role of tigecycline in the therapy of CRC and demonstrate for the first time the effect of tigecycline on colon CSCs and their malignancies.},
}
@article {pmid40940422,
year = {2025},
author = {Kumar Nath, A and da Silva, RR and Gauvin, CC and Akpoto, E and Dlakić, M and Lawrence, CM and DuBois, JL},
title = {Commensal gut bacteria employ de-chelatase HmuS to harvest iron from heme.},
journal = {The EMBO journal},
volume = {44},
number = {21},
pages = {6226-6252},
pmid = {40940422},
issn = {1460-2075},
support = {R35GM136390//HHS | National Institutes of Health (NIH)/ ; P30GM140963//HHS | National Institutes of Health (NIH)/ ; P30 GM140963/GM/NIGMS NIH HHS/United States ; R35 GM136390/GM/NIGMS NIH HHS/United States ; DBI-1828765//National Science Foundation (NSF)/ ; },
mesh = {*Heme/metabolism ; *Iron/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; *Bacteroides thetaiotaomicron/metabolism/enzymology/genetics ; Humans ; *Gastrointestinal Microbiome ; Cryoelectron Microscopy ; Models, Molecular ; Protoporphyrins/metabolism ; *Lyases/metabolism/genetics/chemistry ; },
abstract = {Iron is essential for almost all organisms, which have evolved different strategies for ensuring a sufficient supply from their environment and using it in different forms, including heme. The hmu operon, primarily found in Bacteroidota and ubiquitous in gastrointestinal tract metagenomes of healthy humans, encodes proteins involved in heme acquisition. Here, we provide direct physiological, biochemical, and structural evidence for the anaerobic removal of iron from heme by HmuS, a membrane-bound, NADH-dependent de-chelatase that deconstructs heme to protoporphyrin IX (PPIX) and Fe(II). Heme can serve as the sole iron source for the model gastrointestinal bacterium Bacteroidetes thetaiotaomicron, when active HmuS is present. Heterologously expressed HmuS was isolated with bound heme molecules under saturating conditions. Its cryo-EM structure at 2.6 Å resolution revealed binding of heme and a pair of cations at distant sites. These sites are conserved across the HmuS family and chelatase superfamily, respectively. The proposed structure-based mechanism for iron removal by HmuS is chemically analogous to the chelatases in both unrelated heme biosynthetic pathways and homologous enzymes in the biosynthetic pathways for chlorophyll and vitamin B12, although the reaction proceeds in the opposite direction. Taken together, our study identifies a widespread mechanism via which anaerobic bacteria can extract nutritional iron from heme.},
}
@article {pmid40939728,
year = {2025},
author = {de Souza, MA and Pereira, DE and da Silva, ECA and Medeiros, RG and Duarte, AM and Dutra, LMG and Araújo, DFS and de Araújo, WJ and de Oliveira, CJB and Guerra, GCB and Alves, AF and Viera, VB and Soares, JKB},
title = {Consumption of Brazilian palm fruit (Acrocomia intumescens drude) improves biochemical and gut microbiome parameters, reducing cardiovascular risk in exercised rats.},
journal = {Physiology &amp; behavior},
volume = {302},
number = {},
pages = {115102},
doi = {10.1016/j.physbeh.2025.115102},
pmid = {40939728},
issn = {1873-507X},
mesh = {Animals ; Male ; *Gastrointestinal Microbiome/drug effects/physiology ; *Physical Conditioning, Animal/physiology ; *Cardiovascular Diseases/prevention &amp; control ; Rats ; *Arecaceae ; Liver/metabolism/drug effects ; Oxidative Stress/drug effects ; Rats, Wistar ; Fruit ; Blood Glucose ; Cholesterol/blood ; Heart Disease Risk Factors ; },
abstract = {OBJECTIVE: This study aimed to evaluate the effects of macaiba pulp on physical, biochemical, intestinal health, and oxidative stress parameters in exercised rats.<br><br>METHODOLOGY: Forty-four male rats were divided into four groups (n= 11): sedentary control (CT), exercised control (CT-EX), sedentary macaiba (MC), and exercised macaiba (MC-EX). MC and MC-EX groups received 1000 mg/kg/day of macaiba pulp, while CT and CT-EX received distilled water for eight weeks. Exercised animals underwent swimming for five days a week, beginning with 10 min and progressing to 60 min. Blood was collected to measure cholesterol (TC, HDL, LDL, VLDL), glucose, urea, liver enzymes (AST, ALT), and cardiovascular risk factors. Liver samples were analyzed for malonaldehyde (MDA), total fat, and cholesterol, while feces were collected for metagenome analysis. Body fat and adiposity index were also measured.<br><br>RESULTS: Macaiba-treated groups showed improved gut microbiome balance, reduced TC, LDL, VLDL, glucose, urea, liver enzymes, cardiovascular risks, body fat, MDA, and liver fat, with an increase in HDL.<br><br>CONCLUSION: Macaiba pulp effectively improved biochemical parameters, reduced lipid peroxidation from exercise, and lowered adipose tissue and cardiovascular risks.},
}
@article {pmid40938427,
year = {2025},
author = {Sharma, S and Gajjar, B and Desai, C and Madamwar, D},
title = {Metagenomic analysis reveals the influence of wastewater discharge on the microbial community structures and spread of antibiotic-resistant bacteria at Mohar river, Gujarat.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {10},
pages = {1112},
pmid = {40938427},
issn = {1573-2959},
support = {GSBTM/JD(R&amp;D)/616/21-22/1236//Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat/ ; },
mesh = {*Wastewater/microbiology/chemistry ; *Rivers/microbiology ; *Bacteria/genetics/classification ; India ; *Environmental Monitoring ; *Drug Resistance, Bacterial ; Metagenomics ; Anti-Bacterial Agents/analysis ; Water Pollutants, Chemical/analysis ; *Water Microbiology ; *Microbiota ; },
abstract = {An extensive use of antibiotics has evolved bacterial antimicrobial resistance (AMR) and its spread through horizontal gene transfer within microbial communities of the natural environment. The water bodies receiving wastewater from sewage treatment plant (STP) serve as a conducive reservoir for the spread of antibiotic-resistant bacteria (ARB). This study revealed occurrence of multidrug-resistant and extended spectrum β-lactamase (ESBL) producing bacteria present in STP inlet (SI1), outlet (SO1), riverine environment receiving the STP wastewater (MP1), and control site (C1) of the river Mohar, Gujarat. Microbial community analysis revealed Proteobacteria and Firmicutes as dominating phyla in water samples of Mohar River sites. Shotgun analysis showed presence of antibiotic-degrading enzymes and pathways. The resistance profiling of ARBs showed the higher resistance towards cefotaxime at MP1 (77.4%), followed by SO1 (70.5%), SI1 (64.14%), and the least at C1 (57.13%). The highest ESBL isolates were observed at MP1 (96.42%), followed by SI1 (84.51%), SO1 (80.55%), and C1 (78.57%). Moreover, the RT-qPCR analysis for abundance of intI1 gene (responsible for HGT) showed a descending pattern from SI1 to the C1. The abundance of intI1 was found to correlate positively with mercury, chromium, and chlorine, and a negative correlation was observed with arsenic. The results obtained in this research suggest that AMR spreads and evolves in the water environment via discharge of wastewaters from STPs into the river ecosystems.},
}
@article {pmid40935925,
year = {2025},
author = {Zhou, Y and Wang, H and Sun, J and Wicaksono, WA and Liu, C and He, Y and Qin, Y and Berg, G and Li, L and Lin, H and Chai, Y and Bai, Y and Ma, Z and Cernava, T and Chen, Y},
title = {Phenazines contribute to microbiome dynamics by targeting topoisomerase IV.},
journal = {Nature microbiology},
volume = {10},
number = {10},
pages = {2396-2411},
pmid = {40935925},
issn = {2058-5276},
support = {LZ23C140004//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; U21A20219//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Phenazines/metabolism/pharmacology ; Rhizosphere ; *Microbiota/drug effects ; Bacillus subtilis/drug effects/genetics/enzymology ; *DNA Topoisomerase IV/metabolism/antagonists &amp; inhibitors/genetics ; Plant Diseases/microbiology/prevention &amp; control ; Soil Microbiology ; *Bacteria/genetics/classification/metabolism/drug effects ; Fusarium/drug effects ; Pseudomonas/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Genome, Bacterial ; DNA Damage/drug effects ; Metagenomics ; },
abstract = {Phenazines are highly prevalent, natural bioactive substances secreted by microbes. However, their mode of action and potential involvement in shaping microbiomes remain elusive. Here we performed a comprehensive analysis of over 1.35 million bacterial genomes to identify phenazine-producing bacteria distributed across 193 species in 34 families. Analysis of rhizosphere microbiome and public rhizosphere metagenomic datasets revealed that phenazines could shape the microbial community by inhibiting Gram-positive bacteria, which was verified by pairwise interaction assays using Phenazine-1-carboxamide (PCN)-producing Pseudomonas chlororaphis. PCN induced DNA damage in Bacillus subtilis, a model Gram-positive target, where it directly bound to the bacterial topoisomerase IV, inhibiting its decatenation activity and leading to cell death. A two-species consortium of phenazine-producing Pseudomonas and resistant B. subtilis exhibited superior synergistic activity in preventing Fusarium crown rot in wheat plants. This work advances our understanding of a prevalent microbial interaction and its potential for biocontrol.},
}
@article {pmid40935888,
year = {2025},
author = {Otani, K and Nakatsu, G and Fujimoto, K and Miyaoka, D and Sato, N and Nadatani, Y and Nishida, Y and Maruyama, H and Ominami, M and Fukunaga, S and Hosomi, S and Tanaka, F and Imoto, S and Uematsu, S and Watanabe, T and Fujiwara, Y},
title = {Development of gastric mucosa-associated microbiota in autoimmune gastritis with neuroendocrine tumors.},
journal = {Journal of gastroenterology},
volume = {60},
number = {12},
pages = {1481-1495},
pmid = {40935888},
issn = {1435-5922},
support = {JP22K08040//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; Male ; Middle Aged ; Female ; *Neuroendocrine Tumors/microbiology/pathology ; *Gastrointestinal Microbiome ; *Gastric Mucosa/microbiology/pathology ; Adult ; Aged ; *Autoimmune Diseases/microbiology/pathology/complications ; *Gastritis, Atrophic/microbiology ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; *Stomach Neoplasms/microbiology ; Metabolome ; },
abstract = {BACKGROUND: Autoimmune gastritis (AIG) is a chronic atrophic gastritis that affects the gastric corpus, leading to achlorhydria, hypergastrinemia, and a precursor of neuroendocrine tumors (NETs). This study aimed to elucidate the underlying mechanisms of gastric NET formation in AIG by analyzing gastric mucosa-associated microbiota and host tissue-derived metabolite profiles.<br><br>METHODS: A total of 19 patients diagnosed with AIG and 12 controls uninfected with Helicobacter pylori underwent gastric mucosal biopsies for microbiome analysis using next-generation sequencing with primers targeting the V3-V4 region of the 16S rRNA gene, and metabolome analysis using capillary electrophoresis time-of-flight mass spectrometry.<br><br>RESULTS: Microbiome analysis revealed significantly reduced &#x3b1;-diversity indices in patients with AIG when compared with the control group. &#x3b2;-Diversity analysis showed distinct microbial compositions among the control, NET-negative, and NET-positive groups. The NET-positive group exhibited a significantly higher abundance of Proteobacteria and Fusobacteriota, particularly Haemophilus parainfluenzae, Fusobacterium periodonticum, and Fusobacterium nucleatum, whereas Firmicutes, including Streptococcus salivarius and Veillonella atypica, were significantly decreased compared with the NET-negative group. Metabolome analysis revealed a shift away from glycolysis and tricarboxylic acid cycle activity toward alternative metabolic pathways in patients with AIG. Integrated analysis of gastric microbiota signatures (GMS) and tissue metabotypes demonstrated significant associations among GMS, tissue metabotypes, and NET diagnosis.<br><br>CONCLUSIONS: These findings highlight marked shifts in gastric mucosa-associated microbiota profiles in patients with AIG who developed gastric NETs. Tissue-specific metabolic alterations may precede mucosal dysbiosis in patients with AIG and promote the development of a microenvironment implicated in NET formation.},
}
@article {pmid40935093,
year = {2025},
author = {Marangi, M and Palladino, G and Valzano, F and Scicchitano, D and Turroni, S and Rampelli, S and Candela, M and Arena, F},
title = {Genetic characterization of enteric protozoan microorganisms in newly arrived migrants in Italy and correlation with the gut microbiome layout.},
journal = {Travel medicine and infectious disease},
volume = {67},
number = {},
pages = {102901},
doi = {10.1016/j.tmaid.2025.102901},
pmid = {40935093},
issn = {1873-0442},
mesh = {Humans ; Italy/epidemiology ; *Gastrointestinal Microbiome ; Adult ; Male ; *Transients and Migrants/statistics &amp; numerical data ; Female ; Blastocystis/genetics/isolation &amp; purification ; *Protozoan Infections/epidemiology/parasitology ; Entamoeba histolytica/genetics/isolation &amp; purification ; Feces/parasitology ; Prevalence ; Giardia lamblia/genetics/isolation &amp; purification ; Middle Aged ; Dientamoeba/genetics/isolation &amp; purification ; Young Adult ; Cryptosporidium parvum/genetics/isolation &amp; purification ; Africa/ethnology ; },
abstract = {The prevalence of the enteric protozoan microorganisms, its genetic characterization as well as its associated gut microbiome has been molecularly and 16S metagenomic characterized in a cohort of newly arrived migrants in Italy from African countries over the period 2022-2024. Out of 199 individuals, 92 (46.2%) were found to be carrier of protozoan microorganisms with a higher prevalence of Blastocystis sp. (15.5%), followed by Giardia duodenalis (12.6%), Dientamoeba fragilis (7.5%), Cryptosporidium parvum (6.5%), and Entamoeba histolytica (4%). Subtypes ST1, ST2 and ST3 were genetically characterized for Blastocystis sp., assemblages A and B for G. duodenalis, subtypes families IIa and IIc for C. parvum and genotype 1 for D. fragilis. High prevalence of Butyrivibrio, Lachnospiraceae UGC 10 and Paraprevotella, were identified in the protozoan non-carrier individual group. This work shed lights on the circulation of enteric protozoan microorganisms in apparently healthy migrants from African countries and the potential relationship with the host-microbiome composition. Moreover, these results give an overview of the importance of microbiological surveys among migrants and asylum seekers arriving to hosting countries in order to evaluate the reliable risk of several microorganisms introduction though migration. Ultimately, further investigation of interplays between the intestinal microbiota and protozoan microorganisms will provide new approaches in the diagnosis and treatment of intestinal infections.},
}
@article {pmid40933366,
year = {2025},
author = {Gutleben, J and Podell, S and Mizell, K and Sweeney, D and Neira, C and Levin, LA and Jensen, PR},
title = {Extremophile hotspots linked to containerized industrial waste dumping in a deep-sea basin.},
journal = {PNAS nexus},
volume = {4},
number = {9},
pages = {pgaf260},
pmid = {40933366},
issn = {2752-6542},
abstract = {Decaying barrels on the seafloor linked to DDT contamination have raised concerns about the public health implications of decades old industrial waste dumped off the coast of Los Angeles. To explore their contents, we collected sediment cores perpendicular to five deep-sea barrels. The concentration of DDT and its breakdown products were highly elevated relative to control sites yet did not vary with distance from the barrels, suggesting that they were not associated with the contamination. Sediment cores collected through white halos surrounding three barrels were enriched in calcite and had elevated pH. The associated microbial communities were low diversity and dominated by alkalophilic bacteria with metagenome-assembled genomes adapted to high pH. A solid concretion sampled between a white halo and barrel was composed of brucite, a magnesium hydroxide mineral that forms at high pH. Based on these findings, we postulate that leakage of containerized alkaline waste triggered the formation of mineral concretions that are slowly dissolving and raising the pH of the surrounding sediment pore water. This selects for taxa adapted to extreme alkalinity and drives the precipitation of "anthropogenic" carbonates forming white halos, which serve as a visual identifier of barrels that contained alkaline waste. Remarkably, containerized alkaline waste discarded >50 years ago represents a persistent pollutant creating localized mineral formations and microbial communities that resemble those observed at some hydrothermal systems. These formations were observed at one-third of the visually identified barrels in the San Pedro Basin and have unforeseen, long-term consequences for benthic communities in the region.},
}
@article {pmid40931350,
year = {2025},
author = {Ye, G and Hong, H and Li, T and Li, J and Wu, JQ and Jiang, S and Meng, ZT and Yuan, HT and Xue, W and Li, AL and Zhou, T and Li, TT and Li, T},
title = {MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {276},
pmid = {40931350},
issn = {1474-760X},
support = {No. 32100421//China National Natural Science Foundation/ ; No. 82341098//China National Natural Science Foundation/ ; No. 82130052//China National Natural Science Foundation/ ; No. NSS2021CI05002//Nanhu Laboratory/ ; No. 2024ZYYDSA400333//The Central Government Guides Local Science and Technology Development Fund Projects/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Databases, Genetic ; *Microbiota ; },
abstract = {Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .},
}
@article {pmid40930091,
year = {2025},
author = {Minich, JJ and Allsing, N and Din, MO and Tisza, MJ and Maleta, K and McDonald, D and Hartwick, N and Mamerto, A and Brennan, C and Hansen, L and Shaffer, J and Murray, ER and Duong, T and Knight, R and Stephenson, K and Manary, MJ and Michael, TP},
title = {Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition.},
journal = {Cell},
volume = {188},
number = {23},
pages = {6666-6686.e25},
doi = {10.1016/j.cell.2025.08.020},
pmid = {40930091},
issn = {1097-4172},
mesh = {Humans ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Genome-Wide Association Study ; Child, Preschool ; Child ; Male ; Infant ; Female ; *Malnutrition/microbiology/genetics ; Malawi ; Longitudinal Studies ; },
abstract = {The human gut microbiome is linked to child malnutrition, yet traditional microbiome approaches lack resolution. We hypothesized that complete metagenome-assembled genomes (cMAGs), recovered through long-read (LR) DNA sequencing, would enable pangenome and microbial genome-wide association study (GWAS) analyses to identify microbial genetic associations with child linear growth. LR methods produced 44-64× more cMAGs per gigabase pair (Gbp) than short-read methods, with PacBio (PB) yielding the most accurate and cost-effective assemblies. In a Malawian longitudinal pediatric cohort, we generated 986 cMAGs (839 circular) from 47 samples and applied this database to an expanded set of 210 samples. Machine learning identified species predictive of linear growth. Pangenome analyses revealed microbial genetic associations with linear growth, while genome instability correlated with declining length-for-age Z score (LAZ). This resource demonstrates the power of comparing cMAGs with health trajectories and establishes a new standard for microbiome association studies.},
}
@article {pmid40929881,
year = {2025},
author = {Liu, Y and Li, K and Xu, J and Shen, W and Li, Y and Ma, J and Wang, T and Liu, J and Li, T and Zhang, X and Tian, W and Tian, J and Wang, H and Zhang, X},
title = {Alpha-linolenic acid ameliorates T2DM via reshaping gut-liver axis and inflammatory GPR120-NF-κB/NLRP3 pathway in mouse and rat models.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {147},
number = {},
pages = {157214},
doi = {10.1016/j.phymed.2025.157214},
pmid = {40929881},
issn = {1618-095X},
mesh = {Animals ; *alpha-Linolenic Acid/pharmacology ; *Diabetes Mellitus, Type 2/drug therapy/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Liver/drug effects/metabolism ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; NF-kappa B/metabolism ; Rats ; Signal Transduction/drug effects ; Mice, Inbred C57BL ; Disease Models, Animal ; Insulin Resistance ; Inflammation/drug therapy ; },
abstract = {BACKGROUND: The gut-liver axis, pivotal in managing glucose balance and insulin responsiveness, is central to the development of type 2 diabetes mellitus (T2DM). Research has highlighted the regulatory effects of dietary alpha-linolenic acid (ALA), but it remains unclear how ALA modulates gut microbiota and liver inflammation in T2DM.<br><br>PURPOSE: This study aimed to systematically investigate ALA's influence on liver inflammation, intestinal barrier integrity, gut microbial composition, and metabolic homeostasis in T2DM, with a focus on the underlying molecular mechanisms.<br><br>STUDY DESIGN: A dual-model approach was employed using both db/db mouse model and the SCZ/NA-induced T2DM rat model to ensure robust species and model validation.<br><br>METHODS: Animals received oral ALA supplementation, followed by assessments of glucose tolerance, insulin sensitivity, hepatic histology, and inflammatory markers. Intestinal barrier function, permeability, and systemic LPS levels were evaluated. Mechanistic analysis focused on the GPR120-NF-&#x3ba;B/NLRP3 signaling pathway. Multi-omics profiling including fecal metagenomics, SCFA quantification, and plasma metabolomics were conducted to assess gut microbiota and host metabolic responses.<br><br>RESULTS: Our results revealed that ALA therapy significantly mitigated insulin resistance and glucose intolerance in db/db mice. Histopathological analysis revealed a decrease in hepatic steatosis following ALA administration, alongside a reduction in inflammatory markers indicative of T2DM. Importantly, our findings demonstrated that ALA mitigates liver inflammation by inhibiting the NF-&#x3ba;B/NLRP3 pathway, possibly via its interaction with GPR120. Beyond this, augmenting ALA bolstered intestinal integrity, minimized permeability, curbed lipopolysaccharide leakage, and suppressed pro-inflammatory cytokine expression within the intestines. Significantly, an integrated multi-omics investigation, encompassing fecal metagenomic sequencing, SCFA evaluation, and plasma non-targeted metabolomics, disclosed a potent correlation between ALA's hypoglycemic efficacy and the modulation of gut microbial community structure, elevation of SCFA synthesis, and enhancement of metabolic signatures.<br><br>CONCLUSION: Our study's initial insights indicated that dietary ALA modulates inflammation and metabolism in T2DM via the gut-liver axis, specifically through the GPR120-NF-&#x3ba;B/NLRP3 pathway. This elucidates ALA's dual function in reshaping the gut microbiota and combating systemic inflammation, positioning it as a potentially efficacious dietary component for managing T2DM.},
}
@article {pmid40929372,
year = {2025},
author = {Huereca, A and Allen, CCG and McMullin, RT and Simon, A and Belosokhov, A and Spribille, T},
title = {Evidence for extensive diversity in the pollen-parasitic genus Retiarius in western North America, including two new species associated with lichens.},
journal = {Mycologia},
volume = {117},
number = {6},
pages = {1148-1174},
doi = {10.1080/00275514.2025.2513197},
pmid = {40929372},
issn = {1557-2536},
mesh = {*Lichens/microbiology ; Phylogeny ; DNA, Fungal/genetics/chemistry ; North America ; *Pollen/microbiology ; *Ascomycota/genetics/classification/isolation &amp; purification/cytology ; DNA, Ribosomal Spacer/genetics/chemistry ; RNA, Ribosomal, 28S/genetics ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics/chemistry ; Molecular Sequence Data ; Canada ; *Biodiversity ; },
abstract = {Understanding the diversity of microscopic hyphomycetes is an ongoing effort, and many species remain undescribed. While studying lichen organismal composition in western Canada, metagenomic data revealed the presence of an unknown species of Retiarius (Orbiliaceae, Ascomycota), a genus of pollen-parasitic fungus with no previous records in the region. We developed genus-specific primers to amplify Retiarius DNA in lichen and adjacent substrate extractions, successfully detecting multiple lineages of Retiarius across a wide geographic range within North America. We proceeded to screen accumulations of pollen on the undersurface of lichen thalli to isolate any pollen-associated fungi. Using dilution series and PCR for identification, we isolated two specifically distinct strains of Retiarius with morphology unlike any described member of the genus. Inclusion of DNA from these strains in a multilocus phylogeny using the internal transcribed spacer regions ITS1-5.8S-ITS2 (ITS), partial nuc 28S rDNA (28S), and nuc small subunit (18S) confirmed their evolutionarily distinct position in the genus. We describe these two species here as Retiarius canadensis and R. crescentus. The former possesses trinacrium-shaped conidia, similar to those of R. bovicornutus and R. revayae but morphometrically different, and the latter is distinguished by its canoe-shaped conidia, a morphological character heretofore unknown from Retiarius.},
}
@article {pmid40929115,
year = {2025},
author = {Gonzalez, FL and Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Dussart, P and Héraud, JM and Brook, CE},
title = {Genomic characterization of novel bat kobuviruses in Madagascar: Implications for viral evolution and zoonotic risk.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331736},
pmid = {40929115},
issn = {1932-6203},
support = {DP2 AI171120/AI/NIAID NIH HHS/United States ; R01 AI129822/AI/NIAID NIH HHS/United States ; R25 GM066522/GM/NIGMS NIH HHS/United States ; },
mesh = {*Chiroptera/virology ; Animals ; Madagascar ; Phylogeny ; *Zoonoses/virology ; *Genome, Viral ; *Evolution, Molecular ; *Viral Zoonoses/virology ; Humans ; Genomics ; High-Throughput Nucleotide Sequencing ; *Picornaviridae Infections/virology/veterinary/epidemiology ; },
abstract = {Kobuviruses (family Picornaviridae, genus Kobuvirus) are enteric viruses that infect a wide range of both human and animal hosts. Much of the evolutionary history of kobuviruses remains elusive, largely due to limited screening in wildlife. Bats have been implicated as major sources of virulent zoonoses, including coronaviruses, henipaviruses, lyssaviruses, and filoviruses, though much of the bat virome still remains uncharacterized. While most bat virus research has historically focused on immediately recognizable zoonotic clades (e.g., SARS-related coronaviruses), a handful of prior reports catalog kobuvirus carriage in bats and posit the role of bats as progenitors of downstream kobuvirus evolution. As part of a multi-year study, we carried out metagenomic Next Generation Sequencing (mNGS) on fecal samples obtained from endemic, wild-caught Madagascar fruit bats to characterize potentially zoonotic viruses circulating within these populations. The wild bats of Madagascar represent diverse Asian and African phylogeographic histories, presenting a unique opportunity for viruses from disparate origins to mix, posing a significant public health threat. Here, we report detection of kobuvirus RNA in Malagasy fruit bats (Eidolon dupreanum) and undertake phylogenetic characterization of Malagasy kobuvirus sequences, which nest within the Aichivirus A clade - a kobuvirus clade known to infect a wide range of hosts including humans, rodents, canids, felids, birds, and bats. Given the propensity of kobuviruses for recombination and cross-species transmission, further characterization of this clade is critical for accurate evaluation of future zoonotic threats.},
}
@article {pmid40928232,
year = {2025},
author = {Allman, HM and Bernate, EP and Franck, E and Oliaro, FJ and Hartmann, EM and Crofts, TS},
title = {Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0103925},
pmid = {40928232},
issn = {2379-5077},
mesh = {*Metagenomics/methods ; *Gene Library ; *Drug Resistance, Microbial/genetics ; Metagenome ; Biomass ; Bacteria/genetics ; Humans ; Microbiota/genetics ; },
abstract = {A significant challenge in the field of microbiology is the functional annotation of novel genes from microbiomes. The increasing pace of sequencing technology development has made solving this challenge in a high-throughput manner even more important. Functional metagenomics offers a sequence-naive and cultivation-independent solution. Unfortunately, most methods for constructing functional metagenomic libraries require large input masses of metagenomic DNA, putting many sample types out of reach. Here, we show that our functional metagenomic library preparation method, METa assembly, can be used to prepare useful libraries from much lower input DNA quantities. Standard methods of functional metagenomic library preparation generally call for 5-60 µg of input metagenomic DNA. We demonstrate that the threshold for input DNA mass can be lowered at least to 30.5 ng, a 3-log decrease from prior art. We prepared functional metagenomic libraries using between 30.5 ng and 100 ng of metagenomic DNA and found that despite their limited input mass, they were sufficient to link MFS transporters lacking substrate-specific annotations to tetracycline resistance and capture a gene encoding a novel GNAT family acetyltransferase that represents a new streptothricin acetyltransferase, satB. Our preparation of functional metagenomic libraries from aquatic samples and a human stool swab demonstrates that METa assembly can be used to prepare functional metagenomic libraries from microbiomes that were previously incompatible with this approach.IMPORTANCEBacterial genes in microbial communities, including those that give resistance to antibiotics, are often so novel that sequencing-based approaches cannot predict their functions. Functional metagenomic libraries offer a high-throughput, sequence-naive solution to this problem, but their use is often held back due to their need for large quantities of metagenomic DNA. We demonstrate that our functional metagenomic library preparation method, METa assembly, can prepare these libraries using as little as ~30 ng of DNA, approximately 1,000-fold less than other methods. We use METa assembly to prepare functional metagenomic libraries from low-biomass aquatic and fecal swab microbiomes and show that they are home to novel tetracycline efflux pumps and a new family of streptothricin resistance gene, respectively. The efficiency of the METa assembly library preparation method makes many otherwise off-limits, low-biomass microbiome samples compatible with functional metagenomics.},
}
@article {pmid40928220,
year = {2025},
author = {Dong, L and Yang, J and Wu, H and Sun, Y and Liu, J and Yuan, H and Wang, M and Dai, Y and Teng, F and Jing, G and Yang, F},
title = {Metagenomic research on the structural difference of plaque microbiome from different caries stages and the construction of a caries diagnostic model.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0004425},
pmid = {40928220},
issn = {2379-5077},
support = {No. 81670979,No. 31300424//National Natural Science Foundation of China/ ; 24-4-4-zrjj-158-jch//Natural Science Foundation of Qingdao Municipality/ ; ZR2024MH235//Natural Science Foundation of Shandong Province/ ; tsqn201909126//Taishan Scholar Award For Young Expert/ ; 202408010669//Shandong Medical and Health Technology Development Project/ ; },
mesh = {*Dental Caries/microbiology/diagnosis ; Humans ; *Dental Plaque/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Child ; Female ; Male ; Child, Preschool ; },
abstract = {Development of dental caries is a dynamic process; yet, there is limited knowledge on microbial differences at various stages of caries at higher resolution. To investigate the shifting microbiome profiles across different caries stages, 30 children were enrolled in this study, including 15 caries-active patients and 15 caries-free individuals. Plaque samples were collected from the buccal surface of caries-free subjects, defined as confident health (CH; n = 15). For caries-active individuals, plaque samples were collected from non-cavitated surfaces (defined as relative health [RH], n = 15), enamel caries (EC; n = 15), and dentin caries samples (DC; n = 15). All the above samples were sequenced through the 2bRAD sequencing platform to reveal the microbial community structures in each group. We identified significant differences in microbial community structures from different caries stages. First, the CH group showed the highest species richness (P < 0.05), and then followed by the RH and EC groups with lower richness, and the lowest richness was found in the DC group, yet no significant difference was found among the last three groups (P > 0.05). Second, the microbial structure exhibited the greatest difference between CH and DC groups, followed by the distance between RH/EC and DC groups, and the smallest difference was found between RH and EC groups. Third, specific species were found with a significant difference during the different caries stages. Therefore, we developed a diagnostic model using deep learning methods based on neural networks to diagnose different caries stages with an AUC of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.IMPORTANCEThe diagnosis and treatment of dental caries are crucial for human oral health. Previous studies have focused on the microbial differences between caries and healthy teeth, but there was not enough knowledge on the microbial differences at different stages of dental caries. Our findings could provide a high-resolution understanding of the microbial divergencies among different stages of dental caries and thus build microbial-based diagnostic models for differentiating dental caries status using deep learning methods with an accuracy of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.},
}
@article {pmid40927879,
year = {2025},
author = {Wang, X and Wang, J and Chen, J and Bezemer, TM and Song, Z and Wanek, W and Liu, G and Zhang, C},
title = {Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.},
journal = {Molecular ecology},
volume = {34},
number = {20},
pages = {e70096},
doi = {10.1111/mec.70096},
pmid = {40927879},
issn = {1365-294X},
support = {2023YFF1305103//National Key Research and Development Program of China/ ; 42130717//National Sciences Foundation of China/ ; 42177449//National Sciences Foundation of China/ ; 2024JC-JCQN-35//Shaanxi Provincial Science Fund for Distinguished Young Scholars/ ; },
mesh = {*Soil Microbiology ; China ; *Stress, Physiological ; Bacteria/genetics/classification ; Fungi/genetics/classification ; *Microbiota/genetics ; Soil/chemistry ; Phylogeny ; Biodiversity ; Grassland ; Metagenomics ; Ecosystem ; },
abstract = {Increasing evidence indicates that the loss of soil microbial α-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial α-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal α- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal α-diversity declined under high environmental stress across three soil layers (0-20 cm, 20-40 cm and 40-60 cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.},
}
@article {pmid40927726,
year = {2025},
author = {Eiman, L and Moazzam, K and Anjum, S and Kausar, H and Sharif, EAM and Ibrahim, WN},
title = {Gut dysbiosis in cancer immunotherapy: microbiota-mediated resistance and emerging treatments.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1575452},
pmid = {40927726},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/therapy ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Animals ; *Drug Resistance, Neoplasm ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Tumor Microenvironment/immunology ; },
abstract = {Cancer is a multifaceted disease driven by a complex interplay of genetic predisposition, environmental factors and lifestyle habits. With the accelerating pace of cancer research, the gut microbiome has emerged as a critical modulator of human health and immunity. Disruption in the gut microbial populations and diversity, known as dysbiosis, has been linked with the development of chronic inflammation, oncogenesis, angiogenesis and metastasis. This review discusses the microbial species associated with various types of cancer and the pathways involved in their tumorigenic effect including mechanisms like inflammatory cytokine response, immune modulation, genotoxicity and modification of the tumor microenvironment. Diagnostic tools such as metagenomics, metabolomics, and the use of dysbiosis indexes help in the detection of gut bacterial imbalances, enabling early detection of cancer and potential intervention. Gut dysbiosis diminishes the efficacy of cancer treatments including immunotherapies, and creates immunotherapy resistance by altering drug metabolism and driving immunometabolic reprogramming, allowing tumor cells to evade immune attack. Immunometabolic reprogramming through gut microbiota modulation provides a new avenue to be explored that can restore anti-tumor immunity and reverse resistance to cancer treatments. This review also highlights the use of fecal microbiota transplantation and probiotics to mitigate chances of dysbiosis-related cancer progression. Through a comprehensive assessment of the role of gut microbiota in cancer, this review underscores the need for the use of gut microbial biomarkers for cancer detection and microbiome-targeting strategies to individualize cancer treatment.},
}
@article {pmid40926344,
year = {2025},
author = {Sarango Flores, S and Cordovez, V and Oyserman, BO and Arias Giraldo, LM and Stopnisek, N and Raaijmakers, JM and van 't Hof, P},
title = {Microbiome-Mediated Resistance of Wild Tomato to the Invasive Insect Prodiplosis longifila.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70190},
pmid = {40926344},
issn = {1758-2229},
support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Research Grant/ ; },
mesh = {Animals ; *Nematocera/physiology ; *Solanum lycopersicum/genetics/metabolism ; *Microbiota ; Soil ; Male ; Female ; Genotype ; Plant Leaves ; Rhizosphere ; *Soil Microbiology ; },
abstract = {Plant roots are colonised by diverse communities of microorganisms that can affect plant growth and enhance plant resistance to (a) biotic stresses. We investigated the role of the indigenous soil microbiome in the resistance of tomato to the invasive sap-sucking insect Prodiplosis longifila (Diptera: Cecidomyiidae). Native and agricultural soils were sampled from the Andes in Southern Ecuador and tested, in greenhouse bioassays, for leaf tissue damage caused by P. longifila on domesticated Solanum lycopersicum cv. Moneymaker and wild tomato S. pimpinellifolium. We observed no significant differences in insect damage between domesticated and wild tomatoes grown in live native or agricultural soils. However, when grown in sterilised native and agricultural soils, wild tomato was more severely affected by the insect than the domesticated tomato. Microbiome analyses revealed that soil sterilisation impacted overall rhizobacterial diversity and abundance in wild tomato. Particularly, Actinoplanes abundance was reduced upon sterilisation, which significantly correlated with loss of insect resistance. Metagenome analyses and genome assembly of Micromonosporaceae (Actinoplanes family) suggested a putative association between motility, chemotaxis, membrane transport, chorismate, and lanthipeptide biosynthesis and insect resistance. This indicates that wild S. pimpinellifolium, in contrast to domesticated S. lycopersicum, relies on specific members of the root-associated microbiome for P. longifila protection.},
}
@article {pmid40925458,
year = {2025},
author = {Zhao, Z and Gao, B and Henawy, AR and Ur Rehman, K and Ho, JW and Xue, Y and Wu, J and Jiménez, N and Subirats, J and Zheng, L and Huang, F and Yu, C and Zhang, J and Cai, M},
title = {Effects of chicken manure-derived black soldier fly organic fertilizer on soil carbon and nitrogen cycling: insights from metagenomic and microbial network analysis.},
journal = {Environmental research},
volume = {286},
number = {Pt 2},
pages = {122775},
doi = {10.1016/j.envres.2025.122775},
pmid = {40925458},
issn = {1096-0953},
mesh = {*Fertilizers/analysis ; *Manure/analysis ; Animals ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen Cycle ; Chickens ; Metagenomics ; Carbon ; *Diptera ; Nitrogen ; Microbiota ; },
abstract = {Black soldier fly (BSF) organic fertilizer is known to enhance soil fertility and promote plant growth. However, its effects on soil carbon (C) and nitrogen (N) cycling remains unclear. In this study, we established a BSF chicken manure bioconversion system to produce BSF organic fertilizer and investigate its impacts on soil C and N cycling, as well as microbial ecological networks through metagenomic analysis. Compared to the control, BSF organic fertilizer significantly increased soil organic matter by 16.1 % (p < 0.05) and total potassium by 11.0 % (p < 0.05). Metagenomic sequencing revealed that BSF organic fertilizer significantly enhanced soil C and N cycling. For instance, the abundance of carbon fixation genes such as Calvin-Benson-Bassham (CBB) cycle genes pyc, pycA, and pycB increased by 35.7 % (p < 0.01), 107.1 % (p < 0.001), and 14.6 % (p < 0.05), respectively. In nitrogen cycling, denitrification genes nirB, nirK, and nirS increased by 181.5 % (p < 0.001), 102.7 % (p < 0.001), and 25.9 % (p < 0.05), respectively. Furthermore, soils amended with BSF organic fertilizer displayed a 9.9 % higher proportion of positive microbial interactions, particularly enhancing synergistic associations between bacteria and fungi, suggesting improved microbial community stability. Importantly, bacteria and fungi were interdependent in regulating C and N cycling processes, together orchestrating soil ecosystem functions. Overall, BSF organic fertilizers effectively promoted soil C and N cycling and maintained the stability of microbial communities. These findings provide valuable insights for the rational selection of fertilizers and the optimization of fertilization management practices, thereby contributing to the sustainable development of agricultural production.},
}
@article {pmid40925130,
year = {2025},
author = {Sahu, KK and Yadav, K and Pradhan, M and Sharma, M and Dubey, A and Sucheta, and Kirubakaran, JJ},
title = {Pharmacological insights into gut microbiota modulation in systemic lupus erythematosus: Mechanisms, treatment strategies, and clinical implications.},
journal = {The Journal of pharmacology and experimental therapeutics},
volume = {392},
number = {9},
pages = {103659},
pmid = {40925130},
issn = {1521-0103},
mesh = {*Lupus Erythematosus, Systemic/microbiology/immunology/therapy/drug therapy ; Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; Animals ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation/methods ; Dysbiosis/immunology ; },
abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by widespread inflammation and immune system dysregulation. Recent research suggests that the gut microbiota may play a role in the development of SLE by modulating immune system responses, affecting cytokine production, and altering the activity of T and B cells lymphocytes. As a result, there is a growing interest in microbiota-targeted therapies, including probiotics, dietary changes, and fecal microbiota transplantation. These methods may help restore the balance of microbes and reduce disease activity, but there are still a number of problems to solve. For example, microbiota composition varies greatly from person to person, and it is not clear how dysbiosis causes disease onset. There are also safety concerns about fecal microbiota transplantation. Experimental and clinical studies have started to shed light on the complicated ways in which microbial communities and immune function affect each other in SLE. These studies provide useful information, but their results are often inconsistent. As research continues, integrative methods like metagenomics and metabolomics may help find microbial signatures linked to disease, helping create more accurate and personalized treatments. The gut microbiome is a promising yet still developing area of research that could help us learn more about autoimmune diseases and their treatment, such as SLE. SIGNIFICANCE STATEMENT: Grasping the complex interplay between gut microbiota and systemic lupus erythematosus (SLE) has provided an avenue for therapeutic intervention. This study emphasizes the importance of gut dysbiosis in immune dysregulation, with connections between microbial translocation, molecular mimicry, and inflammatory pathways as contributing factors to the progression of SLE. This work sets the stage for novel and targeted approaches to treating SLE and improving patient outcomes by investigating microbiota-centric treatment options, such as probiotics, dietary interventions, and fecal microbiota transplantation.},
}
@article {pmid40924621,
year = {2025},
author = {Liu, L and Hu, L and Kuzyakov, Y and Rillig, MC and Duan, G and Wei, G and Chen, C},
title = {Microbial Physiological Adaptation to Biodegradable Microplastics Drives the Transformation and Reactivity of Dissolved Organic Matter in Soil.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {37},
pages = {19856-19871},
doi = {10.1021/acs.est.5c09633},
pmid = {40924621},
issn = {1520-5851},
mesh = {*Soil/chemistry ; *Microplastics ; Soil Microbiology ; Biodegradation, Environmental ; Polyesters ; },
abstract = {The turnover of dissolved organic matter (DOM) in soil regulated by biodegradable microplastics (MPs) has garnered much attention due to its profound impact on the storage and stability of soil organic matter. However, the transformation and reactivity of plant-derived and microbially derived DOM by microorganisms adapted to biodegradable MPs, and the involved microbial physiological processes, remain nearly unknown. Here, we added virgin and aged polylactic acid (PLA) and polyhydroxyalkanoate (PHA) to agricultural soils and incubated for 56 days. Using stable isotope techniques, reactomics, and metagenomics, we found that the addition of both virgin and aged PLA induced hydroxylation, demethylation, and dehydrogenation of lignin-derived DOM, resulting in a 3-fold increase in their oxidation degree. PLA activated the enzymatic pathway for lignin-derived DOM decomposition and downregulated genes involved in bacterial anabolism, such as those related to protein, amino sugar, and peptidoglycan biosynthesis. In contrast, PHA increased the content of microbially derived DOM compounds such as proteins and amino sugars by 2.1-fold relative to the control with peptide chain elongation. PHA resulted in the degradation of lignin-derived DOM into pyruvate and acetyl-CoA, accelerated bacterial ATP synthesis, the de novo biosynthesis of proteins and peptidoglycan, and cell renewal and death, thereby increasing PHA- and soil organic matter-derived microbial necromass carbon. Our study provides new insights into the impact of biodegradable MPs on soil DOM transformation and underscores the importance of the microbial physiological processes involved.},
}
@article {pmid40923121,
year = {2025},
author = {Li, Z and Zhao, K and Liu, H and Liu, J and Chen, X and Hu, W and Wen, E and Zhang, K and Chen, L},
title = {Construction of Predictive Machine Learning Model of Glioma-Associated Gut Microbiota.},
journal = {Brain and behavior},
volume = {15},
number = {9},
pages = {e70843},
pmid = {40923121},
issn = {2162-3279},
support = {W2024SNKT13//the Research on Neurological Diseases and Nutritional Health at the Capacity Building and Continuing Education Center of the National Health Commission of China/ ; 82172680//the National Natural Science Foundation of China/ ; 82303586//the National Natural Science Foundation of China/ ; 82373220//the National Natural Science Foundation of China/ ; 82473264//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/physiology/genetics ; *Glioma/microbiology/diagnosis ; *Brain Neoplasms/microbiology/diagnosis ; Male ; Female ; Middle Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: The gut microbiota plays a crucial role in the development of glioma. With the evolution of artificial intelligence technology, applying AI to analyze the vast amount of data from the gut microbiome indicates the potential that artificial intelligence and computational biology hold in transforming medical diagnostics and personalized medicine.<br><br>METHODS: We conducted metagenomic sequencing on stool samples from 42 patients diagnosed with glioma after operation and 30 non-intracranial tumor patients and developed a Gradient Boosting Machine (GBM) machine learning model to predict the glioma patients based on the gut microbiome data.<br><br>RESULTS: The AUC-ROC for the GBM model was 0.79, indicating a good level of discriminative ability.<br><br>CONCLUSIONS: This method's efficacy in discriminating between glioma cells and normal controls underscores the potential of machine learning models in leveraging large datasets for clinical insights.},
}
@article {pmid40922218,
year = {2025},
author = {Di Gianvito, P and Englezos, V and Ferrocino, I and Cocolin, L and Rantsiou, K},
title = {Survey of a grapevine microbiome through functional metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {219},
number = {},
pages = {117000},
doi = {10.1016/j.foodres.2025.117000},
pmid = {40922218},
issn = {1873-7145},
mesh = {*Vitis/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Fungi/genetics/classification/isolation &amp; purification ; Rhizosphere ; Fruit/microbiology ; Plant Leaves/microbiology ; },
abstract = {Microorganisms colonizing grapevines possess diverse functional capabilities that influence the health, growth, productivity and, consequently, wine quality. In this study, spatial and temporal dynamics of the microbiome of Vitis vinifera cv. Barbera grapevine were determined by shotgun sequencing. Bacterial and fungal populations and functions were monitored in samples of rhizosphere, leaves, and grapes, collected at different stages from fruit development to harvest in a conventionally managed vineyard. A compartmental specificity of diverse species was observed within both bacterial and fungal communities. A core microbiome was also identified. LEfSe analysis revealed significantly discriminant taxa associated with each plant compartment, but not according to the sampling time. KEGG genes associated with carbohydrate metabolism were the most abundant in all samples, followed by genes related to amino acid metabolism, respectively involved in carbon and nitrogen metabolic pathways. Interestingly, differences were observed in the functions of rhizosphere and phyllosphere communities with additional differences observed between functions of bacterial and fungal communities. Pathways involved in critical functions like nutrient acquisition, stress resistance, metabolic flexibility, and interaction with the grapevine, were detected within the microbiome. The findings of this study unravel ecological and functional characteristics of the Barbera microbiome. This fundamental understanding is a prerequisite for the development of tailored strategies to protect vineyards and promote sustainability in grapevine production.},
}
@article {pmid40922213,
year = {2025},
author = {Zhang, Z and Guo, Z and Cao, L and Hou, Q and Liu, Z and Zhong, J and Liu, N and Mei, X and Wang, Y},
title = {Dissecting the microbial, physicochemical, and flavor dynamics of core and peel layers in Houhuo Daqu: Insights into quality regulation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {219},
number = {},
pages = {116992},
doi = {10.1016/j.foodres.2025.116992},
pmid = {40922213},
issn = {1873-7145},
mesh = {*Taste ; *Fruit/microbiology/chemistry ; Odorants/analysis ; *Food Microbiology ; *Microbiota ; Bacteria/classification/genetics ; Humans ; Amino Acids/analysis ; Metagenomics ; },
abstract = {Houhuo Daqu (HHD) exhibits significant heterogeneity between its core and peel layers, yet their differences remain underexplored. This study integrates metagenomic sequencing and electronic sensory technologies to compare the physicochemical properties, microbial communities, and flavor profiles of HHD's core and peel. Results reveal distinct microbial communities and diversity between the layers. Both are dominated by bacteria (>90 % relative abundance). The core shows significantly higher relative abundance of Bacillus licheniformis, Bacillus haynesii, and Bacillus paralicheniformis, while the peel has elevated levels of Streptomyces sp. NHF165, Pantoea agglomerans, and Lactiplantibacillus plantarum. Bacillus licheniformis is linked to acetic acid biosynthesis. Flavor analysis indicates both layers are rich in pyrazines, contributing to HHD's distinctive aroma. Enzyme activities differed markedly between the core and peel. Structural equation modeling, regression, and ENVFIT analyses show that amino acid nitrogen directly influences enzymatic activity and indirectly affects it by shaping microbial community and diversity. Additionally, amino acid nitrogen significantly impacts HHD's taste and aroma, modulated by starch and ash content. These findings highlight amino acid nitrogen as a key factor for controlling HHD quality in future production.},
}
@article {pmid40922105,
year = {2025},
author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C},
title = {Plastic-Microbial BioRemediation DB: A Curated Database for Multi-Omics Applications.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70178},
pmid = {40922105},
issn = {1758-2229},
mesh = {Biodegradation, Environmental ; *Plastics/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metagenomics ; Soil Microbiology ; Metagenome ; Genomics ; Multiomics ; },
abstract = {Plastic pollution is a major environmental challenge, with millions of tonnes produced annually and accumulating in ecosystems, causing long-term harm. Conventional disposal methods, such as landfilling and incineration, are often inadequate, emphasising the need for sustainable solutions like bioremediation. However, the bacterial biodiversity involved in plastic biodegradation remains poorly understood. To address this gap, we present the Plastic-Microbial BioRemediation (Plastic-MBR) database, a curated multi-omics resource that integrates publicly available genetic and enzymatic data related to putative plastic-degrading microorganisms. This database supports in silico analyses of metagenomic data from plastic-contaminated environments and comparative genomics, aiming to identify microbial taxa with potential plastic-degrading functions. We validated the functionality of the Plastic-MBR database by applying it to metagenomic datasets from plastic-contaminated soil and river water, successfully identifying numerous putative plastic-degrading genes across diverse microbial taxa. These results support the use of the Plastic-MBR database as a tool to identify candidate bacteria for future experimental validation, strain isolation, and functional studies, ultimately contributing to a deeper understanding of microbial potential in plastic bioremediation. While this study focuses on database development and computational validation, future studies will be essential to confirm and translate these genomic predictions into effective bioremediation strategies.},
}
@article {pmid40921745,
year = {2025},
author = {Zhang, X and Li, Y and Qin, Y and Liao, Z and Deng, C and Chen, Y and Li, Y and Qian, H and He, Y and Chen, S and Shi, G and Liu, Y},
title = {Vientovirus capsid protein mimics autoantigens and contributes to autoimmunity in Sjögren's disease.},
journal = {Nature microbiology},
volume = {10},
number = {10},
pages = {2591-2602},
pmid = {40921745},
issn = {2058-5276},
support = {82471833//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82101841//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82171779//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82371802//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023J06055//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; 2022XMSLCYX01//Xiamen Municipal Bureau of Science and Technology (Xiamen Science and Technology Bureau)/ ; },
mesh = {*Capsid Proteins/immunology/genetics ; *Sjogren's Syndrome/immunology/virology ; Humans ; *Autoantigens/immunology ; *Molecular Mimicry/immunology ; Animals ; Mice ; Female ; *Autoimmunity ; Saliva/virology ; Autoantibodies/immunology/blood ; Middle Aged ; Male ; Adult ; Virome ; },
abstract = {Viral infections are implicated in the pathogenesis of autoimmune diseases, including Sjögren's disease (SjD), but the mechanisms linking viral antigens to disease development remain poorly understood. To address this, we conducted shotgun metagenomic sequencing of saliva samples from 35 patients with SjD and 25 healthy controls. The salivary virome of the patients with SjD, particularly those with high disease activity, had an expansion of Siphoviridae bacteriophages and increased eukaryotic viral sequences, including Vientovirus. This virus was associated with lacrimal gland dysfunction and elevated anti-SSA/Ro52 autoantibody levels. Alignment analysis and cross-blocking assay identified molecular mimicry between the Vientovirus capsid protein and the autoantigen SSA/Ro52. Mice immunized with a Vientovirus capsid peptide developed anti-SSA/Ro52 antibodies and showed immunological features resembling those of patients with SjD. These findings highlight distinct virome profiles in SjD and provide mechanistic evidence supporting the role of Vientovirus in triggering autoimmunity through molecular mimicry.},
}
@article {pmid40920777,
year = {2025},
author = {Nendl, A and Raju, SC and Braadland, PR and Nordborg, A and Bratseth, V and Broch, K and Jørgensen, SF and Aukrust, P and Kristiansen, K and Hov, JR and Trøseid, M and Awoyemi, A},
title = {Circulating metabolites in patients with chronic heart failure are not related to gut leakage or gut dysbiosis.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331692},
pmid = {40920777},
issn = {1932-6203},
mesh = {Humans ; *Dysbiosis/blood/microbiology/metabolism ; *Heart Failure/blood/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; Feces/microbiology ; Chronic Disease ; Case-Control Studies ; Metabolomics ; Metabolome ; },
abstract = {BACKGROUND: The gut microbiota produces numerous metabolites that can enter the circulation and exert effects outside the gut. Several studies have reported altered gut microbiota composition and circulating metabolites in patients with chronic heart failure (HF) compared to healthy controls. Limited data is available on the interplay between dysbiotic features of the gut microbiota and altered circulating metabolites in HF patients. We aimed to examine differences in circulating metabolites between people with and without chronic HF, and their association with gut microbiota dysbiosis and cardiac function.<br><br>METHODS: We collected plasma, serum, and stool samples from 123 adult patients with stable chronic HF and left ventricular ejection fraction (LVEF) &#x2264;40%, and healthy controls (plasma: n&#x2009;=&#x2009;51, stool samples: n&#x2009;=&#x2009;69). Metabolomic and lipidomic profiling of plasma was performed using liquid chromatography with tandem mass spectrometry. Principal component analysis was used to explore differences in circulating profiles. Over-representation analysis was performed to identify pathways in which relevant metabolites were involved. Stool samples were sequenced using shotgun metagenomics. We calculated a dysbiosis index based on differential abundances of microbial taxa in patients vs. controls.<br><br>RESULTS: After adjusting for age, sex, and sampling location, we identified 67 enriched metabolites and 24 enriched lipids, and 115 depleted metabolites and 6 depleted lipids in HF patients compared to healthy controls. LVEF, N-terminal pro B-type natriuretic peptide, gut leakage markers, dysbiosis index, and fiber intake were not significantly related to any of the differentially abundant metabolites or lipids. Pathways related to energy metabolism differed most between HF patients and controls, however medication adjustment abolished all differences in circulating profiles.<br><br>CONCLUSIONS: Patients with chronic HF had distinct metabolomic and lipidomic profiles and energy metabolism differed significantly compared to healthy controls before adjusting for medication use. However, the alterations were not related to gut dysbiosis, gut leakage markers, cardiac function, or fiber intake.},
}
@article {pmid40919923,
year = {2025},
author = {Francis, JD and Yanaç, K and Uyaguari-Diaz, MI},
title = {Seasonal patterns of viromes in urban aquatic environments of Manitoba.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {10},
pages = {e0040824},
pmid = {40919923},
issn = {1098-5336},
support = {RGPIN-2022-04508//Natural Sciences and Engineering Research Council of Canada/ ; ALLRP 553987//Natural Sciences and Engineering Research Council of Canada/ ; 322388//University of Manitoba/ ; },
mesh = {Seasons ; Manitoba ; *Virome ; *Wastewater/virology ; *Rivers/virology ; *Water Microbiology ; Metagenomics ; *RNA Viruses/isolation &amp; purification/genetics/classification ; Cities ; *DNA Viruses/isolation &amp; purification/genetics/classification ; },
abstract = {UNLABELLED: Although wastewater treatment plants harbor many pathogens, traditional methods that monitor the microbial quality of surface water and wastewater have not changed since the early 1900s and often disregard the presence of other types of significant waterborne pathogens such as viruses. We used metagenomics and quantitative PCR to assess the taxonomy, functional profiling, and seasonal patterns of DNA and RNA viruses, including the virome distribution in aquatic environments receiving wastewater discharges. Environmental water samples were collected at 11 locations in Winnipeg, Manitoba, along the Red and Assiniboine rivers during the Spring, Summer, and Fall 2021. Samples were filtered and underwent skimmed milk flocculation for viral concentration. The taxonomy of classified DNA was primarily bacteriophages such as Autographiviridae, Kyanoviridae, and Peduoviridae, which were abundant to a lesser extent. Phage-related functionalities such as portal proteins and bacteriophage T4 major head proteins accounted for approximately 20%-40% of aquatic samples across seasons, which may possibly correspond to the DNA phages that were previously identified. RNA viruses went unclassified in the study; however, similar to DNA viruses, many were found to be non-enveloped or "naked viruses" such as Partiviridae, Picobirnaviridae, Tombusviridae, and Picornaviridae, which accounted for 3%-30% of RNA viruses in the study locations across season. Interestingly, aquatic samples were revealed to maintain an abundance of RNA phage-related functionalities such as long tail fiber protein and putative tail proteins, which accounted for approximately 2%-5% of aquatic samples during the Fall of 2021.<br><br>IMPORTANCE: Municipal wastewater effluents discharged into the Red and Assiniboine rivers of Winnipeg, Manitoba, rely on traditional methods that monitor the microbial quality of effluents and receiving surface waters focus solely on the detection of coliforms, which are not necessarily good indicators of viruses or other pathogens. There is also a lack of current wastewater system effluent regulations at the federal and provincial level. Furthermore, previous literature has shown that when viral DNA and RNA sequences are blasted against current genomic databases, approximately 50% of the viral reads are classified as unknown. The significance of our research in characterizing the virome distribution in aquatic environments addresses a knowledge gap in the current effluent guidelines and a need for regulatory practices. In the long run, fecal indicator bacteria, combined with the detection of enteric viruses, may complement assessment of water quality in effluents discharged into rivers.},
}
@article {pmid40919785,
year = {2025},
author = {Zou, Y-y and Yu, B-j and He, C and Ding, L and Xu, X and Wan, J-h and Lei, Y-p and Huang, X and Xiong, H-f and He, W-h and Luo, L-y and Xia, L and Lv, N-h and Zhu, Y},
title = {Rifaximin reduces gut-derived inflammation in severe acute pancreatitis: an experimental animal model and randomized controlled trial.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0129925},
pmid = {40919785},
issn = {2165-0497},
support = {No.82370661//National Natural Science Foundation of China/ ; YFYKCTDPY202202//Science and Technology Innovation Team Cultivation Project of the First Affiliated Hospital of Nanchang University/ ; },
mesh = {Animals ; *Rifaximin ; *Gastrointestinal Microbiome/drug effects ; Mice ; Male ; Humans ; Disease Models, Animal ; Female ; *Pancreatitis/drug therapy/microbiology/pathology ; Middle Aged ; *Inflammation/drug therapy ; Adult ; *Anti-Bacterial Agents/administration &amp; dosage/therapeutic use ; Mice, Inbred C57BL ; Dysbiosis/drug therapy ; },
abstract = {UNLABELLED: Severe acute pancreatitis (SAP) is characterized by systemic inflammation and intestinal barrier dysfunction and is often associated with gut microbiota dysbiosis. Rifaximin, a gut-specific non-absorbable antibiotic, is known to modulate the gut microbiota. Here, we investigated rifaximin's effects and mechanisms in SAP using murine models and a single-center, open-label, randomized controlled trial (Chinese Clinical Trial Registry: ChiCTR2100049794). In mice, rifaximin attenuated pancreatic injury and systemic inflammation and altered gut microbiota composition by decreasing mucin-degrading genera such as Akkermansia (P < 0.05). These protective effects persisted in antibiotic-treated and germ-free mice, suggesting mechanisms not solely dependent on gut microbiota modulation. In patients with predicted SAP (n = 60), rifaximin significantly reduced systemic inflammation compared with controls. WBC decreased from a median of 11.50 × 10[9]/L (IQR 8.76-15.68) to 8.49 × 10[9]/L (6.93-10.20; P = 0.04) and TNF-α from 15.05 pg/mL (12.73-19.75) to 11.00 pg/mL (8.74-15.40; P = 0.009). However, the incidence of culture-confirmed infection did not differ between the rifaximin and control groups (13.3% vs. 13.3%; RR, 1.00; 95% CI, 0.28-3.63). Adverse events were comparable between groups. Metagenomic analyses revealed suppression of mucin-degrading bacteria (e.g., Akkermansia, Bacteroides fragilis, and Hungatella hathewayi) (P < 0.05) and reductions in mucin-degrading carbohydrate-active enzymes, including sialidases and fucosidases. In conclusion, among patients with predicted SAP, rifaximin did not reduce culture-confirmed infectious complications within 90 days after randomization compared with standard care, despite significant improvements in systemic inflammatory markers and selected fecal microbiome features. Larger randomized controlled trials are warranted to validate these findings.<br><br>IMPORTANCE: Although rifaximin has been used to target gut-derived inflammation in other contexts, its role in SAP remains largely unexplored. In this study, rifaximin treatment was associated with reduced pancreatic injury and systemic inflammation in both murine models and patients with predicted SAP. Treatment also led to changes in gut microbial composition, notably a decrease in mucin-degrading taxa. Importantly, similar protective effects were also observed in antibiotic-treated and germ-free mice, indicating that rifaximin may act via microbiota-dependent and host-directed pathways. These findings offer novel insights into the gut-pancreas axis and suggest that rifaximin holds therapeutic potential by modulating gut microbial composition and host inflammatory responses in SAP.},
}
@article {pmid40918253,
year = {2025},
author = {McMahon, S and Franklin, S and Galloway-Peña, J},
title = {Utilization of machine learning to predict antibiotic resistant event outcomes in acute myeloid leukemia patients undergoing induction chemotherapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1629422},
pmid = {40918253},
issn = {2235-2988},
mesh = {Humans ; *Machine Learning ; *Leukemia, Myeloid, Acute/drug therapy/microbiology/complications ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Gastrointestinal Microbiome/drug effects ; Male ; Female ; Middle Aged ; *Induction Chemotherapy/adverse effects ; Bacteria/drug effects/genetics/classification ; Aged ; Adult ; Feces/microbiology ; Metagenomics ; *Drug Resistance, Bacterial ; },
abstract = {INTRODUCTION: Acute myeloid leukemia (AML) patients are highly susceptible to infection. Moreover, prophylactic and empirical antibiotic treatment during chemotherapy disrupts the gut microbiome, raising the risk for antibiotic-resistant (AR) opportunistic pathogens. There is limited data on risk factors for AR infections or colonization events in treated cancer patients, and no predictive models exist. This study aims to combine metagenomic and antibiotic administration data to develop a model predicting AR event outcomes.<br><br>METHODS: Baseline stool microbiome, antibiotic administration, resistome, and clinical metadata from 95 patients were utilized to build a Random Forest model to predict AR infection and colonization events by serious AR threats. Additionally, sparse canonical correlation analysis assessed correlations between microbiome and resistome data, while Spearman correlation networks identified direct associations with AR event outcomes and secondary variables.<br><br>RESULTS: AR-events were identified in 14 of the 95 included patients, with 8 developing AR infections and 9 identified as AR colonized. A Random Forest model predicted AR event outcomes (AUC = 0.73), identifying bacterial taxa and antibiotic resistance gene (ARG) classes as key variables of importance. Methanobrevibacter smithii, Clostridium leptum, and Bacteroides dorei were identified as key taxa associated with reduced risk of AR events, suggesting the potential roles of commensals in maintaining gut microbial resilience during chemotherapy. ARG classes, particularly those conferring resistance to lincosamides, macrolides, and streptogramins, were negatively associated with AR events.<br><br>CONCLUSION: These results underscore the value of integrating microbiome and resistome features to reveal potential protective mechanisms and improve risk prediction for AR outcomes in vulnerable patients.},
}
@article {pmid40916941,
year = {2025},
author = {Blecksmith, SE and Kalanetra, KM and Weng, CY and Suarez, C and Sitepu, IR and Tang, Y and Ehlers Cheang, S and Jiang, S and Cernioglo, K and Damian-Medina, K and Smilowitz, JT and Lebrilla, CB and Mills, DA and Lemay, DG},
title = {Fecal microbiomes from healthy adult consumers of fruits and vegetables exhibit fiber- and donor-specific fermentation: "5 a day" is not enough.},
journal = {Food &amp; function},
volume = {16},
number = {19},
pages = {7561-7577},
pmid = {40916941},
issn = {2042-650X},
support = {R01 DK124193/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Fruit/metabolism/microbiology ; *Feces/microbiology ; *Vegetables/metabolism/microbiology ; Fermentation ; Adult ; Male ; Female ; *Dietary Fiber/metabolism/analysis ; *Gastrointestinal Microbiome ; Middle Aged ; *Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Young Adult ; Fatty Acids, Volatile/metabolism ; },
abstract = {To determine the fermentation capacity of gut microbiomes with diverse plant carbohydrate active enzyme (CAZyme) repertoires, we collected fecal samples from 18 healthy adults who reported consuming at least 5 different fruits and vegetables daily and conducted shotgun metagenome analysis. Five fecal samples with the most diverse CAZymes were then fermented in vitro with 7 different fibers selected for their unique monosaccharide profiles-banana, kale,13-bean soup, flax, coconut flour, MS Prebiotic (resistant starch) and Sunfiber (guar gum)-for 72 hours. Samples were collected at 4 timepoints for 16S sequencing, and pH, SCFAs, and monosaccharide measurements. The largest changes in pH, microbial diversity, monosaccharides, and short chain fatty acids (SCFAs) occurred in the first 24 hours of fermentation. SCFA production was highest with flax and lowest with coconut flour. Fermentation patterns ranged from little change to primary degradation (liberated monosaccharides) to robust production of SCFAs. Abundance of Bifidobacteriaceae, Butyricicoccaceae, and Ruminococcaceae correlated with the highest fermentation, Clostridiaceae, Enterococcaceae, and Eggerthellaceae with the lowest. Samples from three of the participants were more responsive than the other two. The donor-specific and fiber-specific responses seen in our study indicate that dietary guidance to consume 5 servings of fruits and vegetables per day may not be enough to ensure that our gut microbiota is capable of unlocking all of fiber's benefits.},
}
@article {pmid40915974,
year = {2026},
author = {Ribeiro, MC and Colombo, APV and de Oliveira, AM and Lourenço, TGB and Honório, HM and de Freitas, EC and Messora, MR and Furlaneto, FAC},
title = {The Interplay Between Lifestyle and Oral/Faecal Microbial Profiles Among Periodontal Disease Patients: A Cross-Sectional Study.},
journal = {Journal of clinical periodontology},
volume = {53},
number = {1},
pages = {82-97},
pmid = {40915974},
issn = {1600-051X},
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; Anthropometry ; Brazil/epidemiology ; Cross-Sectional Studies ; Diet/adverse effects/statistics &amp; numerical data ; Discriminant Analysis ; Eating ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Life Style ; *Mouth/microbiology/physiology ; *Periodontitis/epidemiology/microbiology ; RNA, Ribosomal, 16S/isolation &amp; purification ; Sociodemographic Factors ; Biofilms ; },
abstract = {AIM: To characterise periodontal and faecal microbiomes of individuals with periodontal health (PH) and diseases, and evaluate associations with periodontal, sociodemographic, anthropometric, nutritional and lifestyle factors.<br><br>MATERIALS AND METHODS: Dental biofilm and faecal samples from individuals (n&#x2009;=&#x2009;24/group) with PH, gingivitis (GG) and periodontitis (PE) were sequenced (16S rRNA). Anthropometric data and questionnaires on demographics, lifestyle, diet and intestinal habits were collected. Data were statistically analysed (p&#x2009;<&#x2009;0.05).<br><br>RESULTS: GG and PE groups showed higher age, BMI, waist/abdominal circumferences and trans-fat intake and lower selenium and vitamin E intake compared to PH. Individuals with PE had higher hip circumference and lower income, education and intake of iron as well as vitamins A and B9. PE microbiomes (oral and faecal) showed distinct compositions, with the highest number of unique oral species. Faecal richness was lower in PE and GG compared to PH. Specific microbial taxa correlated with periodontal status and host factors.<br><br>CONCLUSION: Periodontal and faecal microbiomes vary across periodontal conditions. Discriminant analysis classified 77% of individuals by periodontal status, with key markers for PE including older age, poor dietary quality and distinct microbial oral and faecal signatures. These findings highlight the role of clinical, dietary and microbial factors in periodontal disease profiling.},
}
@article {pmid40915262,
year = {2025},
author = {Liu, S and Feng, K and Zhang, D and Liu, Y and Wang, J and Lu, B and Xing, D},
title = {Self-regulating adaptability of biofilm microbiomes enhances manganese and ammonia removal in microbial electrochemical filters under dioxane exposure.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139776},
doi = {10.1016/j.jhazmat.2025.139776},
pmid = {40915262},
issn = {1873-3336},
mesh = {*Biofilms ; *Ammonia/metabolism ; *Microbiota ; *Manganese/metabolism ; *Dioxanes ; *Water Pollutants, Chemical/metabolism ; Filtration ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; Electrochemical Techniques ; Water Purification/methods ; },
abstract = {Understanding the stability and assemblage of biofilm microbiomes under oligotrophic conditions is critical for improving groundwater bioremediation. In this study, a novel microbial electrochemical filter (MEF) was developed to explore the impact of weak electrical stimulation on functional adaptability of biofilms under oligotrophic and 1,4-dioxane exposure conditions. Under 20 mg/L 1,4-dioxane stress, the MEF achieved 94.72 % manganese removal and 27.27 % ammonia nitrogen removal, while the conventional biofilter exhibited 88.76 % manganese removal with negligible ammonia nitrogen removal. Metagenomics analyses revealed that dominant populations in the MEF included Nitrospira, Bradyrhizobium, and Nitrosomonas, with relative abundance of 6.23 -10.78 %, 5.81 -6.15 %, and 1.62 -5.58 %, respectively. Weak electrical stimulation enriched the manganese oxidation-associated genes cotA, mnxG, and mcoA, whose total relative abundances being 6.3 times that of the conventional biofilter before dioxane exposure and 2.0 times after exposure. Genes encoding ammonia monooxygenase (amoABC), hydroxylamine dehydrogenase (hao) increased by 2.4- and 1.9-fold, respectively, compared to the conventional biofilter. Additionally, genes involved in the reductive tricarboxylic acid cycle and nitrogen fixation were twice as abundant in the MEF than in the conventional biofilter, suggesting enhanced nutrients availability for heterotrophic bacteria during start-up. These findings demonstrated that weak electrical stimulation effectively regulated biofilm microbiomes and enhance pollutant removal in MEF under oligotrophic conditions.},
}
@article {pmid40915146,
year = {2025},
author = {Leonard, SR and Mammel, MK and Brassill, N and Champ, C and Lacher, DW and Saber, B and Kase, JA and Kataoka, A and Bell, RL and Brown, EW and Rock, CM and Musser, SM},
title = {Air microbiomes reveal presence of Shiga toxin-producing Escherichia coli in airborne cattle pen soil adjacent to large feedlot.},
journal = {The Science of the total environment},
volume = {1000},
number = {},
pages = {180375},
doi = {10.1016/j.scitotenv.2025.180375},
pmid = {40915146},
issn = {1879-1026},
mesh = {Animals ; Cattle ; *Shiga-Toxigenic Escherichia coli/isolation &amp; purification ; *Air Microbiology ; *Soil Microbiology ; *Microbiota ; *Environmental Monitoring ; Animal Husbandry ; },
abstract = {Cattle are a reservoir for the zoonotic human foodborne pathogen Shiga toxin-producing Escherichia coli (STEC), the causative agent of many disease outbreaks associated with contaminated fresh leafy greens. Concentrated animal feeding operations (CAFOs) housing cattle generate fugitive dust, however the potential risk of STEC movement by means of the aerosolized dust is not well known. In this investigation, we used metagenome sequencing of air samples collected in an agricultural setting to investigate airborne transfer of STEC from a large CAFO to the surrounding area. Shiga toxin genes and other E. coli virulence genes were observed in air metagenomes, and their presence was positively correlated with abundance of cattle mitochondrial DNA (mtDNA). Air bacterial community composition differed based on STEC presence, and source tracking utilizing the air metagenomes indicated that cattle feedlot soil contributed to the air bacterial communities. Moreover, a novel biomarker for cattle pen soil, Corynebacterium maris, was identified that correlated with both E. coli virulence gene presence and cattle mtDNA abundance. Overall, our results demonstrate a definitive link between aerosolized cattle feedlot dust and airborne STEC transfer to adjacent and nearby agricultural fields. This work highlights the importance of including the potential for airborne transmission of pathogens in risk assessments for contamination by human foodborne pathogens of fresh produce grown in proximity to CAFOs.},
}
@article {pmid40915037,
year = {2025},
author = {Baud, D and Peric, A and Vidal, A and Weiss, JM and Engel, P and Das, S and Stojanov, M},
title = {Genital microbiota in infertile couples.},
journal = {Reproductive biomedicine online},
volume = {51},
number = {5},
pages = {105056},
doi = {10.1016/j.rbmo.2025.105056},
pmid = {40915037},
issn = {1472-6491},
mesh = {Humans ; Female ; Male ; *Microbiota ; *Vagina/microbiology ; *Infertility/microbiology ; Adult ; Semen/microbiology ; Follicular Fluid/microbiology ; Penis/microbiology ; },
abstract = {RESEARCH QUESTION: What is the composition of bacterial communities at various genital sites and are there potential interactions between partners' microbiota?<br><br>DESIGN: This observational study involved metagenomic analyses of samples collected from male and female partners of couples undergoing fertility treatment. Samples included vaginal and penile swabs, as well as follicular fluid and semen, which were analysed using next-generation sequencing.<br><br>RESULTS: The bacterial community profiles of different genital tract niches were distinct, niche-specific compositions, with female samples predominantly featuring Lactobacillus species and male samples displaying greater microbial diversity, including genital-specific and skin-associated taxa. Significant differences were observed between the sample types and intra-couple comparisons, which suggested potential microbiota interactions between partners. Differential abundance analyses further identified genera specifically enriched in female versus male samples, and correlations between partner samples point towards possible microbial transmission or shared influences on genital microbiota composition.<br><br>CONCLUSIONS: Despite advances in reproductive medicine, many infertility cases remain idiopathic, prompting exploration into how the genital microbiota (both in female and male reproductive tracts) might influence reproductive success. Our findings reveal that, although female samples were predominantly colonized by Lactobacillus species, particularly in the lower genital tract, male samples had greater microbial diversity (including bacteria linked to bacterial vaginosis), with only limited evidence of inter-partner microbiota transmission, underscoring the need for further longitudinal studies on the effect of sexual activity on microbial dynamics.},
}
@article {pmid40914968,
year = {2025},
author = {Cho, Y and Kim, E and Kim, M and Rho, M},
title = {DeepMobilome: predicting mobile genetic elements using sequencing reads of microbiomes.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {5},
pages = {},
pmid = {40914968},
issn = {1477-4054},
support = {RS-2023-00217123//MSIT/ ; RS-2023-KH135226//Ministry of Health/ ; 2023ER210902/GF/NIH HHS/United States ; },
mesh = {*Microbiota/genetics ; *Interspersed Repetitive Sequences ; Metagenome ; Metagenomics/methods ; Humans ; Neural Networks, Computer ; Sequence Analysis, DNA ; Drug Resistance, Microbial/genetics ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {MOTIVATION: Mobile genetic elements (MGEs) play an important role in facilitating the acquisition of antibiotic resistance genes (ARGs) within microbial communities, significantly impacting the evolution of antibiotic resistance. Understanding the mechanism and trajectory of ARG acquisition requires a comprehensive analysis of the ARG-carrying mobilome-a collective set of MGEs carrying ARGs. However, identifying the mobilome within complex microbiomes poses considerable challenges. Existing MGE prediction methods, designed primarily for single genomes, exhibit substantial limitations when applied to metagenomic data, often producing high false positive rates in identifying target MGEs from metagenome sequencing data.<br><br>RESULTS: To address these challenges, we developed DeepMobilome, a novel approach for accurately identifying target MGEs within the microbiome. DeepMobilome leverages a convolutional neural network trained on read alignment data derived from sequence alignment map (SAM) files, providing superior accuracy in detecting MGEs. Trained on 364 647 cases, DeepMobilome achieved a high validation accuracy of 0.99. DeepMobilome consistently outperformed existing methods in discerning the presence of target MGE sequences across diverse test sets. In single-genome test scenarios, DeepMobilome showed an F1-score of 0.935, compared to 0.755 and 0.670 for MGEfinder and ISMapper, respectively, demonstrating its substantial improvements in prediction accuracy. Extensive evaluations across simulated microbiomes further validated the robustness and reliability of DeepMobilome in practical applications. In real microbiome data, DeepMobilome successfully identified six ARG-carrying MGEs across diverse populations. By addressing the limitations of current methods, DeepMobilome offers a powerful tool for advancing our understanding of ARG dissemination and supports targeted interventions in combating antibiotic resistance.},
}
@article {pmid40914221,
year = {2025},
author = {Geng, J and Zhang, W and Christie-Oleza, JA and Abdolahpur Monikh, F and Yang, Q and Yang, Y},
title = {Succession-driven potential functional shifts in microbial communities in the tire-plastisphere: Comparison of pristine and scrap tire.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {385},
number = {},
pages = {127074},
doi = {10.1016/j.envpol.2025.127074},
pmid = {40914221},
issn = {1873-6424},
mesh = {*Microbiota ; *Microplastics/analysis ; Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; Ecosystem ; Bacteria ; Lakes/microbiology ; },
abstract = {Tire microplastics (TMPs) represent a major contributor to microplastic pollution, posing threats to aquatic ecosystems. As carbon-rich substrates, TMPs influence microbial colonization and ecological functions. This study investigates the impacts of pristine (P-TMPs) and scrap (S-TMPs) TMPs from the same brand on microbial communities within the tire-plastisphere. We incubated wood particles, P-TMPs, and S-TMPs in situ in a lake environment for 60 days. Utilizing amplicon and metagenome sequencing, we analyzed structural and potential functional changes in microbial communities across five colonization time points. Our findings reveal that TMPs establish distinct ecological niches, functioning as hotspots of microbial activity in aquatic environments. Both niche specificity and colonization time significantly shape microbial community structure. During the early adaptation stage, we observed clustering patterns in both microbial composition and functional genes associated with the particles. Over time, divergent succession in community composition and potential function emerged, primarily driven by differences in substrate availability between niches. Notably, the substrate availability of S-TMPs promoted microbial community shifts, whereas the P-TMPs posed challenges to microbial adaptation. This study elucidates the long-term adaptive processes exhibited by microbial communities when colonizing the contrasting ecological niches represented by these two TMP states (pristine vs. scrap), documenting the progression from community structural change to functional adaptation. The results underscore the complexity of TMP impacts on microbial ecology and highlight the critical need for long-term monitoring to fully understand their environmental implications.},
}
@article {pmid40914165,
year = {2025},
author = {Anani, H and Destras, G and Bulteau, S and Castain, L and Semanas, Q and Burfin, G and Petrier, M and Martin, FP and Poulain, C and Dickson, RP and Bressollette-Bodin, C and Roquilly, A and Josset, L},
title = {Lung virome convergence precedes hospital-acquired pneumonia in intubated critically ill patients.},
journal = {Cell reports. Medicine},
volume = {6},
number = {9},
pages = {102289},
pmid = {40914165},
issn = {2666-3791},
mesh = {Aged ; Female ; Humans ; Male ; Middle Aged ; Bacteriophages ; Critical Illness ; *Cross Infection/microbiology/virology ; Dysbiosis/microbiology ; *Healthcare-Associated Pneumonia/virology/microbiology ; Intubation, Intratracheal ; *Lung/virology/microbiology ; Microbiota ; Streptococcus/virology ; *Virome ; Observational Studies as Topic ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; Clinical Trials, Phase II as Topic ; },
abstract = {Hospital-acquired pneumonia (HAP) is one of the most common nosocomial infections, leading to significant morbidity and mortality in critically ill patients. HAP is previously associated with dysbiosis of the microbiota. However, the composition of the lung virome and its role in HAP pathogenesis remain unclear. Here, we longitudinally analyze the endotracheal virome in 87 critically ill patients, including 48 with HAP. Within the virome dominated by Caudoviricetes, a decrease in viral beta-diversity toward a bacteriophage-dominated signature and a distinct viral-bacterial interactome is observed 5-4 days before HAP onset. Lung virome composition, viral convergence before HAP onset, and conservation of 18% of the bacteriophage signature are validated in an external cohort of 40 patients. In silico causal inference further identifies bacteriophages associated with Streptococcus and Prevotella as a key regulator of HAP onset. These findings suggest an uncovered pathophysiological mechanism of HAP with virome involvement in lung microbiota dysbiosis. The discovery and validation studies are registered at ClinicalTrials.gov (NCT02003196 and NCT04793568).},
}
@article {pmid40914155,
year = {2025},
author = {Muñoz, VR and Moreau, F and Soto, M and Watanabe, Y and Pham, LD and Zhong, J and Zimmerman, S and Brandao, BB and Girdhar, K and Avila, J and Pan, H and Dreyfuss, JM and Mi, MY and Gerszten, RE and Altindis, E and Kostic, A and Clish, CB and Kahn, CR},
title = {Portal vein-enriched metabolites as intermediate regulators of the gut microbiome in insulin resistance.},
journal = {Cell metabolism},
volume = {37},
number = {10},
pages = {2048-2065.e6},
pmid = {40914155},
issn = {1932-7420},
support = {R01 HL120393/HL/NHLBI NIH HHS/United States ; P30 DK036836/DK/NIDDK NIH HHS/United States ; R01 DK128429/DK/NIDDK NIH HHS/United States ; R01 DK121967/DK/NIDDK NIH HHS/United States ; K99 HL171844/HL/NHLBI NIH HHS/United States ; R01 DK031036/DK/NIDDK NIH HHS/United States ; U01 HL120393/HL/NHLBI NIH HHS/United States ; R01 DK081572/DK/NIDDK NIH HHS/United States ; HHSN268201800015I/HB/NHLBI NIH HHS/United States ; R37 DK031036/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Mice ; Diet, High-Fat/adverse effects ; Male ; Humans ; *Portal Vein/metabolism ; Gluconeogenesis ; Hepatocytes/metabolism/drug effects ; Vancomycin/pharmacology ; Liver/metabolism ; Obesity/metabolism ; Diabetes Mellitus, Type 2/metabolism ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Diet and obesity contribute to insulin resistance and type 2 diabetes, in part via the gut microbiome. To explore the role of gut-derived metabolites in this process, we assessed portal/peripheral blood metabolites in mice with different risks of obesity/diabetes, challenged with a high-fat diet (HFD) + antibiotics. In diabetes/obesity-prone C57BL/6J mice, 111 metabolites were portally enriched and 74 were peripherally enriched, many of which differed in metabolic-syndrome-resistant 129S1/129S6 mice. Vancomycin treatment of HFD-fed C57BL/6J mice modified the microbiome and the portal/peripheral ratio of many metabolites, including upregulating tricarboxylic acid (TCA) cycle-related metabolites, like mesaconate, in portal blood. Treatment of isolated hepatocytes with mesaconate, itaconate, or citraconate improved insulin signaling and transcriptionally regulated genes involved in gluconeogenesis, fatty acid oxidation, and lipogenesis in vitro and in vivo. In humans, citraconate levels are inversely correlated with plasma glucose. Thus, portal versus peripheral metabolites play important roles in mediating effects of the microbiome on hepatic metabolism and the pathogenesis of HFD-related insulin resistance.},
}
@article {pmid40912476,
year = {2025},
author = {Lu, Z and Petersen, C and Dai, R and Reyna, ME and Ahmadiankalati, M and Sifuentes, E and Dai, DLY and Hoskinson, C and Del Bel, KL and Miliku, K and Moraes, TJ and Mandhane, PJ and Becker, AB and Azad, MB and Simons, E and Lou, W and Ambalavanan, A and Duan, Q and Turvey, SE and Subbarao, P},
title = {Early-preschool wheeze trajectories are predominantly nonallergic with distinct biologic and microbiome traits.},
journal = {The Journal of allergy and clinical immunology},
volume = {156},
number = {6},
pages = {1556-1572},
doi = {10.1016/j.jaci.2025.07.034},
pmid = {40912476},
issn = {1097-6825},
mesh = {Humans ; *Respiratory Sounds/immunology ; Infant ; Female ; Male ; Child, Preschool ; *Asthma/diagnosis/epidemiology/microbiology/immunology ; Phenotype ; *Microbiota ; Cohort Studies ; Hypersensitivity ; },
abstract = {BACKGROUND: Disentangling preschool wheezing heterogeneity in terms of clinical traits, temporal patterns, and collective health care burden is critical for precise and effective interventions.<br><br>OBJECTIVE: We aimed to collectively define contributions and distinct characteristics of respiratory phenotypes based on longitudinal wheeze and atopic sensitization patterns in the first 5 years of life.<br><br>METHODS: Group-based trajectory analysis was performed in the CHILD Cohort Study to identify distinct wheeze and allergic sensitization trajectories. Trajectories were evaluated for associated risk factors, health care utilization, biologic determinants, and clinical outcomes. Stool samples for shotgun metagenomic sequencing profiles of infant microbiomes collected at ages 3 months and 1 year were assessed for phenotype-specific biomarkers.<br><br>RESULTS: A total of 6 distinct respiratory phenotypes were identified on the basis of samples from 2902 children; the phenotypes differed by temporal wheeze and allergic sensitization patterns. Although allergic wheeze phenotypes (found in 11.6% of participants) carried the highest risk of asthma diagnosis, the more common nonallergic phenotypes (in 88.3% of participants) contributed to the majority of 5-year asthma diagnoses (61.4% of diagnoses). Most importantly, nonallergic phenotypes accounted for more than two-thirds of health care utilization in this age group. Phenotypes differed by lung function, blood eosinophil counts, allergic comorbidities, and weight-for-age z score. Moreover, microbiome profiles developed from 1439 infants revealed that largely nonoverlapping microbial signatures at age 1 year are associated with each phenotype.<br><br>CONCLUSION: We identified novel early-childhood respiratory phenotypes to disentangle nonoverlapping paths to preschool wheezing. Our findings highlight the continued clinical relevance of nonatopic wheeze phenotypes, which remain undertreated despite accounting for a substantial proportion of health care utilization and asthma diagnoses.},
}
@article {pmid40911291,
year = {2025},
author = {Zhang, G and Yue, Y and Tu, L and Liu, Q and Zhang, Q and Shang, K},
title = {Responses of microbial communities during oilseed plant-based phytoremediation of heavy metal-contaminated soils.},
journal = {Journal of applied microbiology},
volume = {136},
number = {9},
pages = {},
doi = {10.1093/jambio/lxaf226},
pmid = {40911291},
issn = {1365-2672},
support = {G222408//Shanghai Landscaping and City Appearance Administration Bureau/ ; },
mesh = {Biodegradation, Environmental ; *Metals, Heavy/metabolism/analysis ; *Soil Pollutants/metabolism/analysis ; *Soil Microbiology ; Fungi/genetics/metabolism/isolation &amp; purification/classification ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Archaea/genetics/metabolism/isolation &amp; purification/classification ; *Microbiota ; Soil/chemistry ; },
abstract = {AIMS: Phytoremediation is an effective method of remediating soils contaminated with heavy metals. However, it has some limitations in practical applications with regard to rare plant species, poor environmental adaptability, and long growth cycles. The dynamic response mechanisms of soil microbial communities during phytoremediation are still unclear, which restricts the optimization and promotion of this approach.<br><br>METHODS AND RESULTS: No ethical approval was required for this study. In this study, soil bacterial, fungal, and archaeal communities during the remediation of Cu-, Pb-, and Zn-contaminated soils with five industrial oilseed plants [Xanthium strumarium (XS), Bidens pilosa (BP), Kosteletzkya virginica (KV), Sesbania cannabina (SC), and Commelina communis (CC)] were analyzed using metagenome sequencing. Compared with soil contaminated with heavy metals, remediation through five industrial oilseed plants significantly reduced the content of heavy metals in the soil, with soil Cu, Pb, and Zn decreasing by 44.01%, 46.32%, and 27.62%, respectively, and WSCu, WSPb, and WSZn content decreasing by 28.23%, 50.68%, and 75.26%, respectively. Microbial diversity analysis showed that the phytoremediation significantly affected the soil microbial communities, with a significant decrease in archaeal diversity. Variation partitioning analysis and Mantel tests revealed that heavy metals and soil physicochemical properties significantly affected microbial communities, and heavy metals exerted stronger effects on archaeal communities. Meanwhile, soil contaminated with heavy metals was mainly dominated by fungal-fungal interactions, whereas phytoremediation increased the complexity of microbial symbiotic networks.<br><br>CONCLUSION: Collectively, these results provide fundamental insights into the microbial community structure during phytoremediation of heavy metal-contaminated soil, which may aid in the bioregulation of phytoremediation.},
}
@article {pmid40910796,
year = {2025},
author = {Gaun, N and Pietroni, C and Martin-Bideguren, G and Lauritsen, J and Aizpurua, O and Fernandes, JM and Ferreira, E and Aubret, F and Sarraude, T and Perry, C and Wauters, L and Romeo, C and Spada, M and Tranquillo, C and Sutton, AO and Griesser, M and Warrington, MH and Pérez I de Lanuza, G and Abalos, J and Aguilar, P and de la Cruz, F and Juste, J and Alonso-Alonso, P and Groombridge, J and Louch, R and Ruhomaun, K and Henshaw, S and Cabido, C and Barrio, IG and Šunje, E and Hosner, P and Prates, I and While, GM and García-Roa, R and Uller, T and Feiner, N and Bonaccorso, E and Klein-Ipsen, P and Rotovnik, RM and Alberdi, A and Eisenhofer, R},
title = {The Earth Hologenome Initiative: Data Release 1.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40910796},
issn = {2047-217X},
support = {DNRF143//Danmarks Grundforskningsfond/ ; CF20-0460//Carlsbergfondet/ ; 101066225//HORIZON EUROPE Framework Programme/ ; PD/BD/150645/2020//Ag&#xea;ncia Regional para o Desenvolvimento da Investiga&#xe7;&#xe3;o, Tecnologia e Inova&#xe7;&#xe3;o/ ; 25925//Villum Fonden/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; Earth, Planet ; *Vertebrates/genetics/microbiology ; Databases, Genetic ; },
abstract = {BACKGROUND: The Earth Hologenome Initiative (EHI) is a global endeavor dedicated to revisit fundamental ecological and evolutionary questions from the systemic host-microbiota perspective, through the standardized generation and analysis of joint animal genomic and associated microbial metagenomic data.<br><br>RESULTS: The first data release of the EHI contains 968 shotgun DNA sequencing read files containing 5.2 TB of raw genomic and metagenomic data derived from 21 vertebrate species sampled across 12 countries, as well as 17,666 metagenome-assembled genomes reconstructed from these data.<br><br>CONCLUSIONS: The dataset can be used to address fundamental questions about host-microbiota interactions and will be available to the research community under the EHI data usage conditions.},
}
@article {pmid40910779,
year = {2025},
author = {Hanawa, S and Son, A and Kato, T and Matsuo, Y and Omae, T and Omori, Y and Yoshikawa, K and Yamanegi, K and Hirota, K and Ohno, H and Ogura, H and Ishido, S and Noguchi, K and Kishimoto, H},
title = {Identification of beneficial symbiont candidates in commensalism as potential oral gatekeepers.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0158825},
pmid = {40910779},
issn = {2165-0497},
support = {JP23H05357//Japan Society for the Promotion of Science/ ; JP22K09106//Japan Society for the Promotion of Science/ ; //Hyogo College of Medicine/ ; },
mesh = {Humans ; *Symbiosis ; *Mouth/microbiology ; Microbiota ; Male ; Female ; *Mouth Neoplasms/microbiology ; Middle Aged ; Probiotics ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; RNA, Ribosomal, 16S/genetics ; Healthy Volunteers ; Aged ; Dysbiosis/microbiology ; },
abstract = {The basis of the development of oral cancer has been reported to be inflammation (e.g., periodontitis) caused by dysbiosis of the oral microbiota (i.e., a decrease in beneficial oral symbionts). Since a decrease in beneficial symbionts is connected to oral cancer, restoring these bacteria may help prevent it. Based on this, oral probiotics using beneficial oral symbionts are under development. Therefore, it is necessary to understand how beneficial oral symbionts are maintained in a healthy oral cavity. We evaluated a cohort consisting of 42 healthy volunteers and 39 oral cancer patients via 16S metagenomic analysis. Beneficial symbiont candidates were mined by comparing the oral microbiota of healthy volunteers with that of oral cancer patients, and the interaction mode among the beneficial symbiont candidates was further examined. Cancer patients exhibited decreased relative abundance of the genera Rothia and Streptococcus. In addition, both bacterial genera further decreased in advanced cancer, highlighting them as beneficial candidates. Furthermore, these two bacterial genera demonstrated a positive correlation in terms of relative abundance. Rothia dentocariosa isolated from a representative healthy volunteer was suggested to support the survival of Streptococcus salivarius through possible syntrophic interaction. Thus, we report a potential syntrophic interaction between Streptococcus spp. and Rothia spp. as a possible mechanism underlying oral health maintenance. Given that S. salivarius is currently employed as an oral probiotic, our findings provide insights into the development of probiotics for oral cancer.IMPORTANCEPathobiont candidates associated with oral cancer are currently being thoroughly investigated. However, it is not clear which bacteria and how their interactions contribute to preventing the development of oral cancer. In this report, we demonstrate for the first time the presence of a potential syntrophic interaction between Rothia spp. and Streptococcus spp., both of which were identified as beneficial symbiont candidates in the oral cavity.},
}
@article {pmid40910778,
year = {2025},
author = {Aasmets, O and Taba, N and Krigul, KL and Andreson, R and , and Org, E},
title = {A hidden confounder for microbiome studies: medications used years before sample collection.},
journal = {mSystems},
volume = {10},
number = {10},
pages = {e0054125},
pmid = {40910778},
issn = {2379-5077},
support = {PRG1414//Eesti Teadusagentuur/ ; Installation grant 3573//European Molecular Biology Organization/ ; //Biocodex Microbiota Foundation/ ; 16-0125//Estonian Center of Genomics/Roadmap II/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Anti-Bacterial Agents/pharmacology/adverse effects ; Female ; Retrospective Studies ; Middle Aged ; Metagenomics/methods ; Adult ; Electronic Health Records ; Antidepressive Agents ; Aged ; Microbiota/drug effects ; },
abstract = {Medication usage is a known contributor to the inter-individual variability of the gut microbiome. However, medications are often used repeatedly and for long periods, a notion yet unaccounted for in microbiome studies. Recently, we and others showed that not only the usage of antibiotics and antidepressants at sampling, but also past consumption, is associated with the gut microbiome. This effect can be "additive"-the more a medication is used, the stronger the impact on the microbiome. Here, by utilizing retrospective medication usage data from the electronic health records and the observational Estonian microbiome cohort shotgun metagenomics data set (n = 2,509), we systematically evaluate the long-term effects of antibiotics and human-targeted medications on the gut microbiome. We show that past usage of medications is associated with the gut microbiome. For example, the effects of antibiotics, psycholeptics, antidepressants, proton pump inhibitors, and beta-blockers are detectable several years after use. Furthermore, by analyzing a subcohort (n = 328) with a second microbiome characterization, we show that similar changes in the gut microbiome occur after treatment initiation or discontinuation, possibly indicating causal effects.IMPORTANCEThis is the first study using detailed retrospective medication usage data from electronic health records to systematically assess the long-term effects of medication usage on the gut microbiome. We identified carryover and additive effects on the gut microbiome for a range of antibiotics and non-antibiotic medications, such as benzodiazepine derivatives, antidepressants and glucocorticoids, among others. These findings highlight a collateral effect of diverse drug classes on the gut microbiome, which warrants accounting for long-term medication usage history when assessing disease-microbiome associations.},
}
@article {pmid40910191,
year = {2025},
author = {Yehezkel-Cortes, AM and Ruiz-Ordaz, N and Galíndez-Mayer, J and González-Juárez, S and Gómez-Murcia, V},
title = {Modeling and simulation of a modified Ludzack-Ettinger wastewater treatment bioprocess based on the concept of multifunctional microbiota.},
journal = {Environmental technology},
volume = {46},
number = {28},
pages = {5680-5694},
doi = {10.1080/09593330.2025.2551907},
pmid = {40910191},
issn = {1479-487X},
mesh = {*Wastewater/microbiology ; *Bioreactors/microbiology ; *Waste Disposal, Fluid/methods ; *Microbiota ; Nitrogen/metabolism ; Phosphorus/metabolism/analysis ; Biological Oxygen Demand Analysis ; Models, Theoretical ; Biomass ; },
abstract = {This research investigates the behavior of key components within aerobic and anoxic bioreactors in Biological Nitrogen Removal (BNR) bioprocesses. A mathematical model based on the Modified Ludzack-Ettinger (MLE) configuration is proposed. The model comprises an ensemble of ten differential equations derived from mass balances in the MLE system, complemented with a set of biokinetic models. To reduce complexity and enhance applicability, the model treats all nitrogen and phosphorus compounds as atomic N and P, and aggregates carbon sources as Chemical Oxygen Demand (COD), eliminating the need for tuning complex compound-specific parameters. The model was calibrated and validated using analytical determinations of nitrogen, phosphorus, COD, dissolved oxygen, and biomass concentrations from experiments conducted with synthetic wastewater in aerobic and anoxic reactors. Complementing this, a metagenomic study characterized the diversity and relative abundance of taxonomic groups involved in nitrogen and phosphorus metabolism within the microbial communities. Utilizing biokinetic and stoichiometric parameters for the entire microbiota, the model can be solved for both transient and steady-state conditions across a range of operational variables. It enables the estimation of bioprocess resilience following disturbances and the subsequent recovery time to a new steady state. A one-at-a-time (OAT) sensitivity analysis identified the parameters most significantly affecting state variables. The experimental results confirm the model's validity and reliability in simulating BNR processes.},
}
@article {pmid40909338,
year = {2025},
author = {Borgognone, A and Prats, A and Sharma, AA and Martinez-Zalacaín, I and Soriano-Mas, C and Brander, C and Clotet, B and Moltó, J and Mothe, B and Sekaly, RP and Paredes, R and Muñoz-Moreno, JA},
title = {Interactions between gut microbiota, plasma metabolome and brain function in the setting of a HIV cure trial.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1629901},
pmid = {40909338},
issn = {2235-2988},
mesh = {*HIV Infections/blood/complications/drug therapy/microbiology ; Humans ; *Neurocognitive Disorders/etiology/microbiology ; *Gastrointestinal Microbiome ; Brain-Gut Axis ; *Depsipeptides/therapeutic use ; AIDS Vaccines/therapeutic use ; Desulfovibrio/isolation &amp; purification/metabolism ; Streptococcus thermophilus/isolation &amp; purification/metabolism ; Burkholderiales/isolation &amp; purification/metabolism ; Metabolic Networks and Pathways ; },
abstract = {BACKGROUND: The intestinal microbiota composition has been linked to neurocognitive impairment in people with HIV (PWH). However, the potential interplay of microbial species and related metabolites, particularly in the context of an HIV cure strategy remains underexplored. The BCN02 trial evaluated the impact of romidepsin (RMD), used as a HIV-1 latency reversing agent and with reported beneficial neurological effects, combined with the MVA.HIVconsv vaccine on virus control during 32-weeks of monitored antiretroviral treatment interruption (MAP) in early-treated HIV-infected individuals. Here, we analyzed longitudinal gut microbiome, plasma metabolome and brain functioning data to identify potential associations and novel putative biomarkers of HIV-associated neurocognitive disorders (HAND).<br><br>METHODS: Data from fecal shotgun metagenomics, plasma metabolome, cognitive (standardized neuropsychological test score covering 6 cognitive domains, NPZ-6), functional (neuropsychiatric symptoms) and neuroimaging assessments were obtained and evaluated in 18 participants before and after RMD administration, and at the study end (post-MAP follow-up) in the BCN02 trial.<br><br>RESULTS: Participants with neurocognitive impairment (Lower vs. Higher NPZ-6 score group) were enriched in bacterial species, including Desulfovibrio desulfuricans, Sutterella wadsworthensis and Streptococcus thermophilus, and showed higher 1,2-propanediol degradation microbial pathway levels, before RMD administration. A multi-omics profiling showed significant and positive correlations between these microbial features and lipid-related metabolic pathways, previously linked to neurological disorders (i.e., sphingolipid, ether lipid, and glycerophospholipid metabolism), in participants with neurocognitive impairment, before RMD administration. Three indices (microbial-, metabolite-based and combined) obtained from the discriminant features were assessed longitudinally, showing progressive similarities between NPZ-6 score groups over time. Furthermore, the three indices and related discriminant features correlated negatively with functional outcomes, such as quality of life and daily functioning, and positively with depression, stress and CNS-related symptoms before RMD administration, while these associations became less discernible at the subsequent timepoints.<br><br>CONCLUSIONS: While the direct effect of the intervention on the observed shifts cannot be conclusively determined in this study settings, these findings strengthen the link between gut bacteria, related metabolites, and neurocognitive function in PWH, and provide an analytical framework for future validation studies aimed at discovering predictive biomarkers for neurocognitive impairment in PWH.},
}
@article {pmid40908554,
year = {2025},
author = {Susilowati, A and Christita, M and Larekeng, SH and Lateef, AA and Ren, W and Azeez, AA and Simarmata, R and Khairina, Y and Khumairah, FH and Elfiati, D and Asiegbu, FO},
title = {Forest Type, Bark Wounding, and Tapping: Their Combined Influence on Bacteria Biota of Styrax Paralleloneurus in Natural and Community Forest.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70184},
pmid = {40908554},
issn = {1758-2229},
support = {353365//Research Council of Finland/ ; 13/UN5.2.3.1/PPM/KP-WCU/2022//Universitas Sumatera Utara/ ; },
mesh = {*Forests ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Plant Bark/microbiology ; Biodiversity ; Indonesia ; Phylogeny ; *Trees/microbiology ; DNA, Bacterial/genetics ; *Biota ; },
abstract = {Styrax paralleloneurus is a resin-producing tree native to Sumatra, Indonesia. This study investigated the effects of tapping, bark wounding and forest type on bacterial biota in the stem of styrax in natural and community forests. Amplicon metagenomic sequencing of the 16S rRNA region was deployed to identify the bacterial communities associated with tapped and untapped trees across various environmental and experimental conditions. The results of the study showed that tapped trees had lower abundance and diversity of Pseudomonas compared to untapped trees, largely due to their increased exposure to external microbe communities and environmental elements. Serratia and Pantoea were more abundant in natural forest than community forest, while Bradyrhizobium lablabi was found abundantly in untapped trees. Additionally, the taxonomic analysis revealed distinct responses of bacterial genera to tapping and forest type, indicating that community forests could play a significant role in promoting biodiversity in forest ecosystems. This finding underscores the importance of community forests in biodiversity conservation. These insights can inform future conservation and management strategies to enhance biodiversity and underscore the need for sustainable forest management practices to maintain forest health and productivity.},
}
@article {pmid40908532,
year = {2026},
author = {Wei, M and Mehravar, S and Leite, G and Naji, P and Barlow, GM and Hosseini, A and Rashid, M and Sanchez, M and Fajardo, CM and Pimentel, M and Mathur, R},
title = {Relationship Between Hypothyroidism, Risk of Small Intestinal Bacterial Overgrowth, and Duodenal Microbiome Alterations.},
journal = {The Journal of clinical endocrinology and metabolism},
volume = {111},
number = {3},
pages = {707-720},
doi = {10.1210/clinem/dgaf495},
pmid = {40908532},
issn = {1945-7197},
mesh = {Humans ; *Hypothyroidism/microbiology/complications/epidemiology ; Male ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; *Intestine, Small/microbiology ; *Duodenum/microbiology ; Incidence ; Case-Control Studies ; *Blind Loop Syndrome/epidemiology/microbiology/etiology ; Thyroiditis, Autoimmune/microbiology/complications/epidemiology ; Risk Factors ; RNA, Ribosomal, 16S/genetics ; Aged ; Prevalence ; Bacteria/growth &amp; development ; },
abstract = {CONTEXT: There is an association between hypothyroidism and small intestinal bacterial overgrowth (SIBO), but the exact mechanistic link between these 2 conditions is not fully elucidated.<br><br>OBJECTIVE: We evaluate the incidence and risks of subsequently developing SIBO, and changes in small bowel microbial populations, in subjects with hypothyroidism or autoimmune thyroiditis.<br><br>DESIGN AND OUTCOME MEASURES: Duodenal aspirates from REIMAGINE study subjects with a history of hypothyroidism (hypothyroid group, N = 49) and controls (N = 323) underwent 16S rRNA sequencing (MiSeq, Illumina); a subset also underwent metagenomic sequencing (NovaSeq6000, Illumina). Separately, the TriNetX Analytics platform was used to evaluate 10-year cumulative incidences and relative risk (RR) of developing SIBO in subjects with hypothyroidism (unspecified etiology [HUE]), and a subset with autoimmune thyroiditis, vs propensity score matched control groups.<br><br>RESULTS: Among REIMAGINE subjects, SIBO prevalence was higher in the hypothyroid group (32.65%) vs controls (15.17%). In the TriNetX analysis, 10-year cumulative incidences of SIBO were higher in HUE (RR = 2.20) and autoimmune thyroiditis (RR = 2.40) subjects vs matched controls. However, these risks appeared to be mitigated both in HUE (RR = 0.33) and autoimmune thyroiditis (RR = 0.78) subjects taking levothyroxine. Analyzing the duodenal microbiome, genus Neisseria was part of the core microbiome in the hypothyroid group (Hypo+/SIBO-, Hypo+/SIBO+) but not in nonhypothyroid subjects (Hypo-/SIBO-, Hypo-/SIBO+). Increased prevalence of Gram-negative coliforms occurred in both SIBO+ groups, but Escherichia/Shigella formed part of the core in nonhypothyroid subjects (Hypo-/SIBO+), whereas Klebsiella species were prevalent in hypothyroid group subjects with SIBO (Hypo+/SIBO+).<br><br>CONCLUSION: These findings suggest there is an increased risk for development of SIBO in individuals with a history of hypothyroidism that may be ameliorated by treatment, and may involve specific Gram-negative coliforms.},
}
@article {pmid40908508,
year = {2025},
author = {Boden, L and Bludau, D and Sieber, G and Deep, A and Baikova, D and David, GM and Hadžiomerović, U and Stach, TL and Buchner, D and Boenigk, J},
title = {Varying Responses to Heat Stress and Salinization Between Benthic and Pelagic Riverine Microbial Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {9},
pages = {e70173},
pmid = {40908508},
issn = {1462-2920},
support = {CRC 1439/1//Deutsche Forschungsgemeinschaft/ ; //Open Access Publication Fund of the University of Duisburg-Essen/ ; },
mesh = {*Salinity ; *Microbiota ; Geologic Sediments/microbiology ; Hot Temperature ; Ecosystem ; *Rivers/microbiology/chemistry ; Bacteria/genetics/classification/isolation &amp; purification ; *Heat-Shock Response ; Climate Change ; Archaea/genetics ; Fresh Water/microbiology ; },
abstract = {Microbial communities play a crucial role in the functioning of freshwater ecosystems but are continuously threatened by climate change and anthropogenic activities. Elevated temperatures and salinisation are particularly challenging for freshwater habitats, but little is known about how microbial communities respond to the simultaneous exposure to these stressors. Here, we use mesocosm experiments and amplicon sequencing data to investigate the responses of pelagic and benthic microbial communities to temperature and salinity increases, both individually and in combination. Our results highlight the varying responses of freshwater microbial communities, with sediment communities exhibiting greater stability in response to environmental changes compared to water column communities, and salinisation having a more pronounced impact on microeukaryotes compared to prokaryotes. Simultaneous exposure to elevated temperature and salinity reduced the impact of salinisation on prokaryotes, while microeukaryotes were similarly affected by the combined treatments and salinisation alone. These findings emphasise the complexity of microbial responses to single and multiple stressors, underscoring the need to consider both individual and interactive effects when predicting ecosystem responses to environmental changes.},
}
@article {pmid40905099,
year = {2026},
author = {Gem, H and Ebadi, M and Sebastian, G and Abasaeed, R and Lloid, M and Minot, SS and Dean, DR and Rashidi, A},
title = {Dental plaque microbiota following allogeneic hematopoietic cell transplantation and risk of chronic graft-versus-host disease.},
journal = {Haematologica},
volume = {111},
number = {2},
pages = {620-631},
pmid = {40905099},
issn = {1592-8721},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Graft vs Host Disease/etiology/diagnosis/microbiology ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Female ; Male ; Middle Aged ; Adult ; *Dental Plaque/microbiology ; *Microbiota ; Transplantation, Homologous ; Chronic Disease ; Aged ; Young Adult ; },
abstract = {Microbiota disruptions have been associated with short-term complications after allogeneic hematopoietic cell transplantation (alloHCT). However, only a few studies have examined the relationship between dysbiosis and chronic graft-versus-host disease (cGvHD), the main long-term immunologic toxicity of alloHCT. Considering the role of oral microbiota in systemic inflammatory diseases, we evaluated whether oral microbiota at day 28 post HCT corresponding to clinical recovery from the acute events after transplantation is associated with subsequent cGvHD. Shotgun metagenomic sequencing of 207 saliva and supragingival plaque samples collected longitudinally at baseline (pre-conditioning), day +28, and day +84 from 37 patients (11 with subsequent moderate/severe cGvHD) revealed a significant association between day +28 plaque microbiota composition and cGvHD. Two orthogonal statistical approaches demonstrated Streptococcus sanguinis and Prevotella loescheii in day +28 plaque to be associated with cGvHD. Metagenome-based functional analysis identified 4 microbial metabolic pathways associated with future cGvHD, 2 of which were highly attributed to S. sanguinis. These pathways - ethanolamine utilization and glycerol metabolism - increase bacterial fitness by providing an alternative carbon/nitrogen source and improving survival in inflamed tissues. Our findings propose a novel mechanism by which the early post-transplant dental biofilm may contribute to cGvHD months later, offering a potential target for early prophylactic intervention.},
}
@article {pmid40904108,
year = {2025},
author = {Meaden, S and Westra, ER and Fineran, PC},
title = {Phage defence-system abundances vary across environments and increase with viral density.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {380},
number = {1934},
pages = {20240069},
pmid = {40904108},
issn = {1471-2970},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; //James Cook Research Fellowship (RSNZ, Te Ap&#x101;rangi)/ ; //Philip Leverhulme/ ; //Bioprotection Aotearoa (Tertiary Education Commission, NZ)/ ; //UK Horizon Funding Guarantee/ ; },
mesh = {*Bacteriophages/physiology ; *Bacteria/virology/immunology ; *Microbiota ; *Metagenome ; *Virome ; },
abstract = {The defence systems bacteria use to protect themselves from their viruses are mechanistically and genetically diverse. Yet the ecological conditions that predict when defences are selected for remain unclear, as substantial variation in defence prevalence has been reported. Experimental work in simple communities suggests ecological factors can determine when specific defence systems are most beneficial, but applying these findings to complex communities has been challenging. Here, we use a comprehensive and environmentally balanced collection of metagenomes to survey the defence landscape across complex microbial communities. We also assess the association between the viral community and the prevalence of defence systems. We identify strong environmental effects in predicting overall defence abundance, with animal-host-associated environments and hot environments harbouring more defences overall. We also find a positive correlation between the density and diversity of viruses in the community and the abundance of defence systems. This study provides insights into the ecological factors that influence the composition and distribution of bacterial defence systems in complex microbial environments and outlines future directions for the study of defence-system ecology.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.},
}
@article {pmid40902732,
year = {2025},
author = {Blecksmith, SE and Oliver, A and Alkan, Z and Lemay, DG},
title = {Gut Microbiome Genes Involved in Plant and Mucin Breakdown Correlate with Diet and Gastrointestinal Inflammation in Healthy United States Adults.},
journal = {The Journal of nutrition},
volume = {155},
number = {11},
pages = {3757-3768},
doi = {10.1016/j.tjnut.2025.08.027},
pmid = {40902732},
issn = {1541-6100},
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Diet ; Dietary Fiber/administration &amp; dosage ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Inflammation/microbiology ; *Mucins/metabolism ; *Plants/metabolism ; United States ; },
abstract = {BACKGROUND: Dietary carbohydrates shape the composition and function of gut microbes, which may potentially influence human health. It is not known if these diet-microbiome relationships are relevant to healthy American adults.<br><br>OBJECTIVES: We hypothesized that intake of dietary fiber by healthy adults would be associated with the carbohydrate-active enzyme (CAZyme) capacity of their gut microbiome and that this capacity would be negatively correlated with gastrointestinal (GI) inflammation.<br><br>METHODS: We analyzed dietary data, GI inflammation, and CAZyme profiles from shotgun metagenomes of fecal samples in the US Department of Agriculture (USDA) Nutritional Phenotyping Study cohort of healthy United States adults (n = 330).<br><br>RESULTS: CAZyme diversity varied across participants. Plant CAZyme diversity and abundance correlated significantly with fecal pH (Shannon: adjusted R[2] = 0.053, P < 0.001; Chao1: adjusted R[2] = 0.056, P < 0.001; abundance: adjusted R[2] = 0.036, P < 0.001) and habitual energy-adjusted total fiber (Shannon: adjusted R[2] = 0.015, P = 0.029; abundance: adjusted R[2] = 0.015, P = 0.010) and soluble fiber intake (Shannon: adjusted R[2] = 0.017, P = 0.019; abundance: adjusted R[2] = 0.015, P = 0.0010). The ratio of mucin-degrading CAZymes to plant-degrading enzymes, coined here as the metric Muc2Plant, varied across participants and differed by sex (Wilcoxon, P = 0.035) and body mass index (adjusted R[2] = 0.028, P = 0.017). Muc2Plant positively correlated with GI inflammation (calprotectin: adjusted R[2] = 0.038, P = 0.001; neopterin: adjusted R[2] = 0.071, P < 0.001). Machine learning (ML) classification models were used to identify specific foods (e.g., potatoes) and microbes (e.g., Lachnospiraceae) as predictors of low Muc2Plant.<br><br>CONCLUSIONS: These results support the relevance of diet-microbiome relationships even in healthy adults, and that reduction of Muc2Plant, via dietary and/or microbial interventions, would be a beneficial health target to potentially prevent dysbiosis and reduce GI inflammation. This trial was registered at clinicaltrials.gov as NCT02367287.},
}
@article {pmid40902606,
year = {2025},
author = {Zhang, D and Zou, Y and Shi, Y and Zhang, J and Liu, J and Wu, G and Zhang, J and Gao, Y and Chen, M and Li, YX},
title = {Systematically investigating and identifying bacteriocins in the human gut microbiome.},
journal = {Cell genomics},
volume = {5},
number = {11},
pages = {100983},
pmid = {40902606},
issn = {2666-979X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Bacteriocins/analysis ; *Bacteria/chemistry/classification/genetics ; Metagenomics ; Software ; Genome, Bacterial ; },
abstract = {Human gut microbiota produces unmodified bacteriocins, natural antimicrobial peptides that protect against pathogens and regulate host physiology. However, current bioinformatic tools limit the comprehensive investigation of bacteriocins' biosynthesis, obstructing research into their biological functions. Here, we introduce IIBacFinder, a superior analysis pipeline for identifying unmodified class II bacteriocins. Through large-scale bioinformatic analysis and experimental validation, we demonstrate their widespread distribution across the bacterial kingdom, with most being habitat specific. Analyzing over 280,000 bacterial genomes, we reveal the diverse potential of human gut bacteria to produce these bacteriocins. Guided by meta-omics analysis, we synthesized 26 hypothetical bacteriocins from gut commensal species, with 16 showing antibacterial activities. Further ex vivo tests show minimal impact of narrow-spectrum bacteriocins on human fecal microbiota. Our study highlights the huge biosynthetic potential of unmodified bacteriocins in the human gut, paving the way for understanding their biological functions and health implications.},
}
@article {pmid40902595,
year = {2025},
author = {Guinet, B and Oskolkov, N and Moreland, K and Dehasque, M and Chacón-Duque, JC and Angerbjörn, A and Arsuaga, JL and Danilov, G and Kanellidou, F and Kitchener, AC and Muller, H and Plotnikov, V and Protopopov, A and Tikhonov, A and Termes, L and Zazula, G and Mortensen, P and Grigorieva, L and Richards, M and Shapiro, B and Lister, AM and Vartanyan, S and Díez-Del-Molino, D and Götherström, A and Pečnerová, P and Nikolskiy, P and Dalén, L and van der Valk, T},
title = {Ancient host-associated microbes obtained from mammoth remains.},
journal = {Cell},
volume = {188},
number = {23},
pages = {6606-6619.e24},
doi = {10.1016/j.cell.2025.08.003},
pmid = {40902595},
issn = {1097-4172},
mesh = {Animals ; *Mammoths/microbiology ; Phylogeny ; *DNA, Ancient/analysis ; *Microbiota/genetics ; *Fossils/microbiology ; Elephants/microbiology ; Erysipelothrix/genetics/isolation &amp; purification ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we analyzed ancient microbial DNA from 483 mammoth remains spanning over 1 million years, including 440 newly sequenced and unpublished samples from a 1.1-million-year-old steppe mammoth. Using metagenomic screening, contaminant filtering, damage pattern analysis, and phylogenetic inference, we identified 310 microbes associated with different mammoth tissues. While most microbes were environmental or post-mortem colonizers, we recovered genomic evidence of six host-associated microbial clades spanning Actinobacillus, Pasteurella, Streptococcus, and Erysipelothrix. Some of these clades contained putative virulence factors, including a Pasteurella-related bacterium that had previously been linked to the deaths of African elephants. Notably, we reconstructed partial genomes of Erysipelothrix from the oldest mammoth sample, representing the oldest authenticated host-associated microbial DNA to date. This work demonstrates the potential of obtaining ancient animal microbiomes, which can inform further paleoecological and evolutionary research.},
}
@article {pmid40902348,
year = {2025},
author = {Zhou, N and Gu, T and Duan, M and Tian, Y and Chen, L and Zeng, T and Hou, X and Wang, X and Xu, Q and Zhang, Y and Lu, L},
title = {Gut microbiota dysbiosis exacerbates polystyrene microplastics-induced liver inflammation via activating LPS/TLR4 signaling pathway in ducks.},
journal = {Poultry science},
volume = {104},
number = {11},
pages = {105757},
pmid = {40902348},
issn = {1525-3171},
mesh = {Animals ; *Ducks ; *Microplastics/toxicity/adverse effects ; Signal Transduction/drug effects ; *Gastrointestinal Microbiome/drug effects ; Toll-Like Receptor 4/metabolism/genetics ; *Polystyrenes/toxicity/adverse effects ; Lipopolysaccharides/metabolism ; *Dysbiosis/veterinary/chemically induced ; *Poultry Diseases/chemically induced/microbiology ; Liver/drug effects ; *Inflammation/veterinary/chemically induced ; Avian Proteins/metabolism/genetics ; },
abstract = {Ubiquitous microplastics can bioaccumulate in organisms, resulting in detrimental health impacts, such as liver inflammation. Nonetheless, the exact mechanism by which polystyrene microplastics (PS-MPs) trigger liver inflammation via the gut-liver axis in ducks remains unclear. The purpose of this study was to clarify the impact of PS-MPs exposure to liver inflammation through the gut-liver axis in ducks. Our investigation indicated that exposure to PS-MPs markedly upregulated the levels of MDA and ROS in the liver tissue and enhanced the release of pro-inflammatory cytokines (TNF-α, IL-6, and IL-1β). Additionally, PS-MPs exposure increased the LPS level, which ultimately triggered the TLR4/NF-κB signaling pathway. Notably, exposure to PS-MPs resulted in a marked change in the gut microbiota composition, primarily indicated by an increase in the relative abundance of Brachyspiraceae and a reduction in that of CAG-74 and Oscillospiraceae. Metabolome analysis further revealed that different expressed metabolites (DEMs) in the positive and negative mode were identified between the control and HMPs groups, including 1-methylhistamine, DL-Methionine sulfoxide, Guanidinoethyl sulfonate, l-Cysteic acid, Deoxyinosine, Camp. Both metagenomic and metabolome analyses showed enrichment in the lysosomal pathway. Correlation analysis suggested association among representative gut microbiota, serum LPS, oxidative stress factors, liver DEMs and key liver inflammatory indicators. Our study sheds light on the mechanism by which PS-MPs exposure induced liver inflammation in ducks via the modulation of the gut-liver axis. These findings improved our understanding of the underlying mechanisms that contribute to PS-MPs-induced hepatotoxicity in avian species.},
}
@article {pmid40901999,
year = {2025},
author = {Prabakaran, R and Bromberg, Y},
title = {Deciphering enzymatic potential in metagenomic reads through DNA language models.},
journal = {Nucleic acids research},
volume = {53},
number = {16},
pages = {},
pmid = {40901999},
issn = {1362-4962},
support = {80NSSC18M0093//NASA Astrobiology Institute/ ; 2310114//National Science Foundation/ ; },
mesh = {*Metagenomics/methods ; Metagenome ; Molecular Sequence Annotation ; *Enzymes/genetics/metabolism ; Microbiota/genetics ; Software ; Sequence Analysis, DNA/methods ; },
abstract = {Microbial communities drive essential global processes, yet much of their functional potential remains unexplored. Metagenomics stands to elucidate this microbial "dark matter" by directly sequencing the microbial community DNA from environmental samples. However, the exploration of metagenomic sequences is mostly limited to establishing their similarity to curated reference sequences. A paradigm shift-language model (LM)-based methods-offers promising avenues for reference-free analysis of metagenomic reads. Here, we introduce two LMs, a pretrained foundation model REMME (Read EMbedder for Metagenomic Exploration), aimed at understanding the DNA context of metagenomic reads, and the fine-tuned REBEAN (Read Embedding-Based Enzyme ANnotator) for predicting the enzymatic potential encoded within the read-corresponding genes. By emphasizing function recognition over gene identification, REBEAN labels gene-encoded molecular functions of previously explored and new (orphan) sequences. Even though it was not trained to do so, REBEAN identifies the gene's function-relevant parts. It thus expands enzymatic annotation of unassembled metagenomic reads. Here, we present novel enzymes discovered using our models, highlighting model impact on our understanding of microbial communities.},
}
@article {pmid40901884,
year = {2025},
author = {Robes, JMD and Liebergesell, TCE and Beals, DG and Yu, X and Brazelton, WJ and Puri, AW},
title = {Inverse stable isotope probing-metabolomics (InverSIP) identifies an iron acquisition system in a methane-oxidizing bacterial community.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {36},
pages = {e2507323122},
pmid = {40901884},
issn = {1091-6490},
support = {R35 GM147018/GM/NIGMS NIH HHS/United States ; T32 AI055434/AI/NIAID NIH HHS/United States ; 2339190//National Science Foundation (NSF)/ ; LS-ECIAMEE-00006628//Simons Foundation (SF)/ ; },
mesh = {*Methane/metabolism ; *Iron/metabolism ; *Metabolomics/methods ; Oxidation-Reduction ; Isotope Labeling/methods ; *Microbiota ; *Bacteria/metabolism/genetics ; Siderophores/metabolism ; Multigene Family ; },
abstract = {Methane is a potent greenhouse gas and a target for near-term climate change mitigation. In many natural ecosystems, methane is sequestered by microbial communities, yet little is known about how constituents of methane-oxidizing communities interact with each other and their environment. This lack of mechanistic understanding is a common issue for many important microbial communities, but it is difficult to draw links between available sequencing information and the metabolites that govern community interactions. Here, we develop and apply a technique called inverse stable isotope probing-metabolomics (InverSIP) to bridge the gap between metagenomic and metabolomic information and functionally characterize interactions in a complex methane-oxidizing community. Using InverSIP, we link a highly transcribed biosynthetic gene cluster in the community with its secondary metabolite product: methylocystabactin, a triscatecholate siderophore not previously observed in nature. We find that production of methylocystabactin is widespread among methanotrophic alphaproteobacteria and that it can be used by another methanotroph in the community that does not produce this siderophore itself. Functional assays reveal that methylocystabactin supports methanotroph growth and the activity of the methane-oxidizing enzyme soluble methane monooxygenase under conditions where bioavailable iron is limited, establishing an important molecular link between methane-oxidation and the insoluble iron found in many natural environments. These findings contribute to a molecular-level understanding of these environmentally important bacterial communities and establish InverSIP as a broadly applicable genomics-guided strategy for characterizing metabolites in microbial ecosystems.},
}
@article {pmid40901853,
year = {2025},
author = {Gómez-Palacio, A and Junca, H and Vivero-Gomez, RJ and Suaza, J and Moreno-Herrera, CX and Cadavid-Restrepo, G and Pieper, DH and Uribe, S},
title = {Metagenomic profiling of the insect-specific virome in non-urban mosquitoes (Culicidae: Culicinae) from Colombia's Northern inter-Andean valleys.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331552},
pmid = {40901853},
issn = {1932-6203},
mesh = {Animals ; Colombia ; *Virome/genetics ; *Culicidae/virology ; *Metagenomics/methods ; *Metagenome ; Phylogeny ; *Insect Viruses/genetics/classification ; },
abstract = {Hematophagous mosquitoes are major vectors of diverse pathogens and serve as bioindicators in tropical ecosystems, yet their virome in non-urban Neotropical regions remains poorly characterized. We analyzed the virome of 147 mosquitoes from two natural ecosystems in Colombia using a hybrid viral identification approach, combining high-confidence and less stringent methods. Most high-confidence viral contigs remained unclassified or unknown, as expected for metagenomic surveys in novel ecosystems. However, members for the Magrovirales and Ortervirales, and other six orders were detected at lower abundance. Using a complementary, less stringent approach, we identified 168 viral species from 68 genera and 22 families across four mosquito tribes (Aedini, Culicini, Orthopodomyiini, Sabethini), with dominance of Metaviridae, Retroviridae, Iridoviridae, and Poxviridae, though many sequences could not be taxonomically assigned. Insect-specific viruses predominated, while no medically relevant arboviruses were detected. Both methods consistently identified Trichoplusia ni TED virus, Cladosporium fulvum T-1 virus, Lymphocystis disease viruses, and Oryctes rhinoceros nudivirus among the most abundant and frequently detected taxa across samples. Alpha diversity indices revealed the highest virome diversity in Sabethini, followed by Orthopodmyiini, and substantially lower richness and diversity in Aedini and Culicini. These results provide a baseline for virome characterization in sylvatic mosquitoes from Colombia and highlight the need for further research on the ecological roles of the mosquito virome in pathogen transmission and microbiome evolution.},
}
@article {pmid40901000,
year = {2025},
author = {Huang, F and Li, J and Liu, D and Li, Y and Tang, J},
title = {Neonatal microbiome dysbiosis decoded by mNGS: from mechanistic insights to precision interventions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1642072},
pmid = {40901000},
issn = {2235-2988},
mesh = {Humans ; Infant, Newborn ; *Dysbiosis/microbiology/diagnosis/therapy ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Infant, Newborn, Diseases/microbiology/diagnosis/therapy ; Precision Medicine/methods ; *Microbiota/genetics ; },
abstract = {The neonatal period is a critical stage for microbial colonization and immune system development, with dynamic changes in the microbiome closely linked to the pathogenesis of various diseases. Traditional microbiological testing methods have low sensitivity and time-consuming limitations compared to metagenomic next-generation sequencing (mNGS), which makes it difficult to meet the diagnostic and therapeutic needs of critically ill neonates. mNGS analyzes the total DNA in a sample without bias, allowing comprehensive identification of bacteria, viruses, fungi, and parasites, and resolution of functional genes, providing new avenues for precision diagnosis and treatment of diseases such as neonatal sepsis, necrotizing enterocolitis, neonatal pneumonia, neonatal meningitis, neonatal jaundice, and other diseases. However, challenges remain, including the need to optimize sample processing workflows and develop portable devices to enhance clinical conversion potential. In this review, we summarize the application, efficacy, and limitations of mNGS in neonatal diseases. This approach paves the way for novel avenues in mechanistic research, early diagnosis, and personalized therapy for these conditions.},
}
@article {pmid40900671,
year = {2025},
author = {Day, AS and Slater, R and Young, RB and Wheeler, RZ and Marcelino, VR and Maddigan, NK and Forster, SC and Costello, SP and Uylaki, W and Probert, CSJ and Andrews, JM and Yao, CK and Gibson, PR and Bryant, RV},
title = {Functional Profiling Demonstrates That a Sulfide-Reducing Diet Achieves Microenvironmental Targets in Ulcerative Colitis.},
journal = {Inflammatory bowel diseases},
volume = {31},
number = {11},
pages = {3160-3171},
pmid = {40900671},
issn = {1536-4844},
support = {//Hospital Research Foundation/ ; //University of Adelaide/ ; //Gastrointestinal Society of Australia FICE/ ; //European Crohn's Colitis/ ; //Commonwealth Research Stipend/ ; },
mesh = {Humans ; *Colitis, Ulcerative/diet therapy/metabolism/microbiology ; *Hydrogen Sulfide/metabolism ; Male ; Female ; Adult ; Feces/microbiology/chemistry ; Middle Aged ; *Gastrointestinal Microbiome ; *Diet ; *Sulfides/metabolism ; Volatile Organic Compounds/analysis ; },
abstract = {BACKGROUND: As a dietary approach to reducing inflammation in ulcerative colitis, the 4-SURE (4 Strategies to Sulfide Reduction) diet was designed to correct pathogenic alterations of excessive protein fermentation and hydrogen sulfide (H2S) production in the distal colon. We aimed to perform a deep functional analysis (microbial and metabolomic) of the feces of 28 adults with mild-moderately active ulcerative colitis who adhered to the 4-SURE diet over 8 weeks to explore whether the 4-SURE diet could modulate the intraluminal environment as intended.<br><br>METHODS: Fecal samples were collected at week 0 and 8 of dietary intervention, processed and aliquoted. Metagenomic sequencing was undertaken to identify changes in H2S-metabolizing genes, while gas chromatography-mass spectrometry was used to analyze fecal volatile organic compounds and H2S production.<br><br>RESULTS: The 4-SURE diet significantly increased alpha diversity between weeks 0 and 8. By random forest plot classifier, the abundance of taxonomic groups comprising known H2S-producing genera were markedly lower at week 8, specifically Odoribacter and Peptostreptococcaceae, and were of highest importance in discriminating between before- and after-diet samples. The capacity for bacterial H2S metabolism was altered with diet, with differences in 12 of 67 analyzed sulfur-metabolizing genes identified. H2S production and indole, a specific marker of protein fermentation, were significantly decreased due to the diet.<br><br>CONCLUSIONS: Here, we demonstrate that the objectives of the 4-SURE diet were fulfilled. This application of deep functional analysis to a dietary intervention study is novel and highlights an exemplar framework for including microbial and metabolomic biomarkers of pathogenic relevance in the analysis of therapeutic diet strategies. (Australian New Zealand Clinical Trials Registry, Number: ACTRN12619000063112).},
}
@article {pmid40899487,
year = {2025},
author = {Gu, T and Zerry, Y and Zhang, B and Tan, J and Taft, DH},
title = {Influence of Resistant Starch-Added Meat Analogs on the Resistome of Fecal Fermentations Using Human Gut Microbiota.},
journal = {Journal of food science},
volume = {90},
number = {9},
pages = {e70430},
doi = {10.1111/1750-3841.70430},
pmid = {40899487},
issn = {1750-3841},
support = {//University of Florida/ ; //U.S. Department of Agriculture/ ; },
mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Fermentation ; *Starch/metabolism ; Bacteria/genetics/classification/isolation &amp; purification/drug effects/metabolism ; *Meat/analysis ; Adult ; Male ; Female ; *Resistant Starch ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Drug Resistance, Microbial ; Meat Substitutes ; },
abstract = {Meat analogs are emerging as a sustainable alternative to meat products, and novel meat analog products could potentially offer additional health benefits. Antimicrobial resistance (AMR) poses a serious threat to global human health. Dietary choices affect the composition of bacteria in the human gut microbiome and can influence the carriage of antimicrobial resistance genes (ARGs). Individuals with lower ARG carriage tend to consume more fiber, suggesting that novel fiber-rich meat analogs may help tackle the growing AMR crisis. We therefore hypothesized that adding resistant starch to meat analogs would reduce the number and abundance of ARGs in human gut microbial communities and tested this using in vitro fecal fermentation. Fecal samples were collected from three human donors. Meat analogs formulated from raw ingredients (pea, soy, and resistant starch)-including 100% pea, 90% pea and 10% resistant starch, 100% soy, and 90% soy and 10% resistant starch-served as the carbohydrate source for fecal fermentations. Whole metagenomic sequencing was performed on DNA from the fermentations. ANOVA showed significant differences in normalized ARG abundance by carbohydrate source (p = 0.021), though not in total ARG counts. Meat analogs with resistant starch resulted in a lower median normalized abundance of drug-resistant ARGs than meat analogs without resistant starch, but post-hoc testing could not determine which groups differed from each other due to limited sample size. Adding resistant starch to meat analogs is associated with reduced ARGs in human gut microbial communities, but more research is needed. PRACTICAL APPLICATIONS: Lowering the prevalence of antimicrobial resistance genes (ARGs) is an important public health goal, and emerging work suggests that diet may contribute to controlling the spread of ARGs. One association with diet and the resistome is a lower carriage of ARGs in individuals who consume more dietary fiber. This research therefore sought to pilot if adding resistant starch to meat analogs has the potential to reduce resistance gene carriage. The results found that adding resistant starch to plant-based meat products may help lower the abundance of antimicrobial resistance genes in the human gut microbiome. This provides the justification for larger scale studies and suggests that food manufacturers may be able to develop foods, including healthier meat alternatives, to assist in preserving the function of antibiotics for future generations.},
}
@article {pmid40897178,
year = {2025},
author = {Xu, T and Jiao, X and Liu, G and Chen, X and Luo, Q and Zhang, G and Li, B and Zhang, Y and Li, X and Cheung, Y and Chai, X and Huang, Y and Wu, H and Deng, F and Chen, F and Liang, G},
title = {Oral virome metagenomic catalog links Porphyromonas gingivalis phages to obesity and type 2 diabetes.},
journal = {Cell reports. Medicine},
volume = {6},
number = {9},
pages = {102325},
pmid = {40897178},
issn = {2666-3791},
mesh = {Humans ; *Porphyromonas gingivalis/virology ; *Diabetes Mellitus, Type 2/microbiology/virology ; *Virome/genetics ; *Bacteriophages/genetics ; *Obesity/microbiology/virology ; *Mouth/virology/microbiology ; *Metagenomics/methods ; *Metagenome ; Female ; Male ; Middle Aged ; Gastrointestinal Microbiome ; Microbiota ; },
abstract = {The human microbiota has a critical role in maintaining human microbiome homeostasis and health, yet the viral component of the oral microbiome remains largely unidentified. We establish the Human Oral Virome Database (HOVD) catalog, a freely accessible online resource cataloging 24,440 bacteriophage viral operational taxonomic units and 83 eukaryotic viral genomes. Utilizing HOVD, we investigate oral virome variation and its correlation with oral bacteria and gut virome in 220 obese individuals with or without type 2 diabetes mellitus (T2D). Obese individuals with T2D exhibit reduced oral viral diversity, lower correlations with clinical features, disrupted viral-bacterial correlations, and enhanced oral-gut virome transmission. Furthermore, we computationally identify bacteriophages that infect Porphyromonas gingivalis and screen six putative endolysins. Experimental validation reveals that a mixture of three endolysins significantly inhibits Porphyromonas gingivalis growth. These findings highlight the potential of phage-derived endolysins for periodontitis with T2D, offering a path toward oral and systemic disease intervention.},
}
@article {pmid40897099,
year = {2025},
author = {Ma, X and Zhai, T and Bao, X and Wu, Z and Yang, Y and Yin, R and Cai, C and Liu, G},
title = {Salinity-driven trade-offs between nitrogen removal and microbiome dynamics in Fe-C-CWs toward saline aquaculture tailwater management.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124519},
doi = {10.1016/j.watres.2025.124519},
pmid = {40897099},
issn = {1879-2448},
mesh = {*Salinity ; *Nitrogen ; *Microbiota ; *Aquaculture ; Iron ; Denitrification ; },
abstract = {Salinity-driven nitrogen removal mechanisms in iron-carbon CWs (Fe-C-CWs) remain poorly understood for aquaculture tailwater management. Through a 155-day trial under four salinities (designated as S0, S10, S20, and S30), result showed that S20 achieved optimal removals of total nitrogen (84.9 ± 3.1 %), nitrate (81.8 ± 2.5 %), and ammonium (79.3 ± 3.0 %), significantly outperforming other groups (P < 0.05). Metagenomics revealed that S20 significantly enriched denitrifying taxa (Halothiobacillus, Prolixibacter) and upregulated nitrogen cycling genes (nirB, nrfA, nrfH, hao) and iron cycling genes (feoA, feoB), highlighting the functional synergy between microbial composition and biogeochemical cycling processes. Dual isotope signatures (δ[15]NNO2/ δ[18]ONO2) first applied in Fe-C-CWs confirmed salinity-mediated pathway shifts: nitrite oxidation dominated in saline groups, especially in S20 versus reduction in S0. Enzymatic profiling substantiated the concurrent operation of nitrification, denitrification, and anammox pathways across all groups, with activities exhibiting significant salinity-dependent modulation. S20 demonstrated remarkable enzymatic potentiation, where core nitrogen-cycling enzymes including nitrite oxidoreductase (NXR: 8.79 ± 0.67 U/g), nitrate reductase (NAR: 18.13 ± 1.19 U/g), and nitrite reductase (NIR: 6.74 ± 0.47 U/g) showed 16.00∼32.18 % higher than S0 (P < 0.01). This enzymatic synergy suggests salinity-optimized coupling between dissimilatory iron reduction and nitrogen transformation processes. Ecological network analysis revealed significant interactions among microbial phyla, particularly between Proteobacteria and Planctomycetota. This study demonstrates that S20 can enhance interaction between Fe-C matrix and microorganisms, thereby improving the efficiency of Fe-C-CWs in removing nitrogen pollutants from aquaculture tailwater. These findings offer theoretical insights for further understanding the internal operational mechanisms of the Fe-C-CWs.},
}
@article {pmid40897066,
year = {2025},
author = {Slobodkina, GB and Merkel, AY and Kondrasheva, KV and Stroeva, AR and Bonch-Osmolovskaya, EA and Davranov, KD and Slobodkin, AI},
title = {Taxonomic and metabolic diversity of microbial communities in a thermal water stream in Uzbekistan and proposal of two new classes of uncultivated bacteria, Desulfocorpusculia class. nov. and Tepidihabitantia class. nov., named following the rules of SeqCode.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {5},
pages = {126650},
doi = {10.1016/j.syapm.2025.126650},
pmid = {40897066},
issn = {1618-0984},
mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; Uzbekistan ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Metagenomics ; Metagenome ; *Rivers/microbiology ; *Bacteria/classification/genetics/metabolism ; Groundwater/microbiology ; *Microbiota ; Geologic Sediments/microbiology ; Hot Springs/microbiology ; },
abstract = {Thermal ecosystems in Uzbekistan remain poorly characterized, particularly through culture-independent approaches. In this study, we performed 16S rRNA gene metabarcoding and metagenomic sequencing of microbial communities from a hot stream formed by the discharge of thermal artesian groundwater in the Navoiy region. The taxonomic composition of microbial communities varied with temperature and sample type, with the phylum Chloroflexota abundant in most samples. Members of Aquificota, Deinococcota, and Thermotogota dominated in sediments with temperatures around 60 °C, while Desulfobacterota and Cyanobacteriota were more abundant at lower temperatures. Metagenomic sequencing of the microbial community in sediment under orange-brown mat (54 °C) revealed a dominance of the phyla Chloroflexota, Armatimonadota, Aquificota, Ignavibacteriota, Desulfobacterota and Bacteroidota. Metagenomic data indicated that fermentation, aerobic degradation of organic matter, hydrogen oxidation, and sulfur cycling are the main metabolic processes. Two high-quality metagenome-assembled genomes (MAGs) were described as novel taxa named following the rules of SeqCode. Genome analysis suggests that both organisms are heterotrophic anaerobes capable of sulfate reduction or fermentation. We provide the description of Desulfocorpusculum asiaticum[Ts] gen. nov., sp. nov. affiliated with the novel family Desulfocorpusculaceae fam. nov., order Desulfocorpusculales ord. nov. and class Desulfocorpusculia class. nov.; and the description of the new species and genus Tepidihabitans asiaticus[Ts] gen. nov., sp. nov. affiliated with the novel family Tepidihabitantaceae fam. nov., order Tepidihabitantales ord. nov. and class Tepidihabitantia class. nov.},
}
@article {pmid40896895,
year = {2025},
author = {Jiang, Z and Yang, S and Pang, Q and Abdalla, M and Karbin, S and Qi, S and Hu, J and Qiu, H and Song, X and Smith, P},
title = {Metagenomic insights into the influence of soil microbiome on greenhouse gas emissions from paddy fields under varying irrigation and fertilisation regimes.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127129},
doi = {10.1016/j.jenvman.2025.127129},
pmid = {40896895},
issn = {1095-8630},
mesh = {*Greenhouse Gases ; Fertilizers ; *Agricultural Irrigation ; *Soil Microbiology ; Soil/chemistry ; *Microbiota ; China ; Agriculture ; Oryza ; Methane ; },
abstract = {Integration of diverse fertilisation strategies with water-saving irrigation techniques presents a promising sustainable agricultural practice, offering the potential to reduce greenhouse gases (GHGs) emissions, enhance carbon sequestration and boost crop yields. However, existing research on the influence of soil microorganisms on biogeochemical processes of GHGs is limited. Herein, we explored the microbial mechanisms influencing GHGs emissions through a 3-year field experiment and metagenomic sequencing conducted in southeastern China. We investigated two irrigation patterns (controlled irrigation [CI] and flooded irrigation [FI]) and three fertilisation strategies (chemical fertiliser [F], straw returning [S] and manure substitution [M]). Results indicated that irrigation patterns significantly affected the microbial community structure in paddy soil. The key environmental factors affecting microorganisms at the phylum level included soil pH, moisture content, total nitrogen content and CH4 emissions. Random forest analysis further identified Cyanobacteria, Nitrospirae, Kiritimatiellaeota, Proteobacteria, and Balneolaeota as dominant phyla driving the differences in microbial communities across treatments. Under CI, an increase in N2O emissions was observed, which was driven by key genes, such as nirS, nirK, nosZ and norB. Compared with CF (CI with F), S increased the abundance of nirS and nirK, leading to higher N2O emissions, whereas M increased the abundance of nosZ, thereby reducing N2O emissions. The genes mcrA, pmoA and pmoC were responsible for elevated CH4 emissions through straw incorporation and manure application. Structural equation model analysis revealed that the irrigation pattern significantly affected CH4 emissions and rice yield, while the fertilisation type mainly influenced soil pH and rice yield. Organic input, particularly manure, resulted in higher C emissions owing to the presence of more CH4-producing gene mcrA in the soil. Overall, the combination of CI and manure is recommended for reducing GHGs emissions, enhancing C sequestration and boosting rice yields.},
}
@article {pmid40895054,
year = {2025},
author = {Cárdenas-Hernández, V and Lemos-Lucumi, C and Toro-Perea, N},
title = {Uncovering tissue-specific endophytic microbiota composition and activity in Rhizophora mangle L.: a metagenomic and metatranscriptomic approach.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19728},
pmid = {40895054},
issn = {2167-8359},
mesh = {*Endophytes/genetics ; *Rhizophoraceae/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Plant Roots/microbiology ; Plant Leaves/microbiology ; Transcriptome ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {The interaction of mangrove trees with endophytic microorganisms contributes to the successful establishment of these plants in the challenging intertidal environment. The red mangrove, Rhizophora mangle L. (Rhizophoraceae), is one of the dominant species in mangrove ecosystems and is characterized by the provision of several ecologically relevant services. In this work, we integrated metagenomics and metatranscriptomics to perform a robust characterization of the community of endophytic microorganisms associated with R. mangle leaf and root tissues. The microbiota were characterized at taxonomic and functional levels, and abundance and gene expression profiles were compared between these two plant tissues. We found that the endophyte community consisted mainly of bacteria and eukaryotes, which were the most active groups at the transcriptional level, while archaea and viral groups were identified in lower abundance and expression. In addition, the results show that the community of endophytic microorganisms changes depending on the tissue type, with root-associated microorganisms being the most abundant at the metagenome level and active at the metatranscriptome level. It was also found that R. mangle endophytes actively contribute to key functions for adaptation to an intertidal ecosystem with high human intervention, such as salinity tolerance and degradation of heavy metals and xenobiotic compounds. Thus, according to the functions found and contributed by the endophyte community of red mangrove leaf and root tissues, it can be concluded that these microbial communities are crucial for the survival of R. mangle in the extreme environment of mangrove forests. This study provides a solid basis for future research aimed at understanding the role of plant-endophyte interactions.},
}
@article {pmid40892742,
year = {2025},
author = {Zhu, J and Chen, Y and Han, Y and Li, J},
title = {Mechanism of Huanglian Wendan Decoction in ameliorating non-alcoholic fatty liver disease via modulating gut microbiota-mediated metabolic reprogramming and activating the LKB1/AMPK pathway.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331303},
pmid = {40892742},
issn = {1932-6203},
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry ; Rats ; Male ; *AMP-Activated Protein Kinases/metabolism ; Rats, Sprague-Dawley ; Signal Transduction/drug effects ; *Protein Serine-Threonine Kinases/metabolism ; Lipid Metabolism/drug effects ; Liver/metabolism/drug effects/pathology ; AMP-Activated Protein Kinase Kinases ; Disease Models, Animal ; Carnitine O-Palmitoyltransferase/metabolism ; Metabolic Reprogramming ; },
abstract = {BACKGROUND: Huanglian Wendan Decoction (HLWDD), a classical traditional Chinese medicine (TCM) formula, has shown therapeutic promise in treating metabolic disorders. However, its underlying mechanisms against non-alcoholic fatty liver disease (NAFLD) remain unclear.<br><br>OBJECTIVE: This study aimed to elucidate the pharmacological mechanisms by which HLWDD ameliorates NAFLD, focusing on its impact on lipid metabolism, gut microbiota, and amino acid regulation.<br><br>METHODS: A NAFLD rat model was established by administering a high-sugar, high-fat, high-salt diet for 20 weeks. The core components of HLWDD were identified and quantified using UPLC-Q-TOF-MS/MS and HPLC, and further validated via network pharmacology and molecular docking. Therapeutic efficacy was assessed through analysis of body weight, serum lipid profiles, inflammatory cytokines, hepatic histology, and protein expression. Gut microbiota composition and liver-intestine metabolite profiles were evaluated using metagenomic sequencing and LC-MS/MS.<br><br>RESULTS: Seven key constituents, including quercetin and berberine, were quantified (15.11-164.37 &#x3bc;g/mL) and shown to interact with lipid metabolism targets such as liver kinase B1 (LKB1), AMP-activated protein kinase (AMPK), peroxisome proliferator-activated receptor alpha (PPAR&#x3b1;), and carnitine palmitoyltransferase 1A (CPT1A). HLWDD treatment significantly reduced body weight, hepatic lipid accumulation, and serum levels of triglycerides, total cholesterol, and low-density lipoprotein cholesterol, while increasing high-density lipoprotein cholesterol. Proinflammatory cytokines (IL-6, IL-1&#x3b2;, TNF-&#x3b1;) were notably suppressed. Mechanistically, HLWDD activated the LKB1/AMPK signaling pathway and modulated aspartic acid metabolism in association with increased abundance of Akkermansia in the gut. Metabolomic analysis identified 13 differential metabolites, with aspartic acid showing strong correlations with Akkermansia and LKB1/AMPK activity.<br><br>CONCLUSION: HLWDD exerts its anti-NAFLD effects by enhancing Akkermansia-mediated aspartate metabolism, thereby activating the LKB1/AMPK axis and promoting lipid oxidation via CPT1A and PPAR&#x3b1;. This study provides new mechanistic insight into the gut-liver axis in NAFLD and highlights HLWDD as a multi-targeted therapeutic approach for restoring metabolic balance.},
}
@article {pmid40890888,
year = {2025},
author = {Wang, S and Zhao, Z and Cheng, R and Cui, L and Wang, J and Rubin-Blum, M and Zhang, Y and Liu, B and Chen, X and Baltar, F and Cao, X and Wen, X and Alain, K and Chen, Z and Liao, J and Jiang, L and Shao, Z},
title = {Phylogenetically and metabolically diverse active carbon-fixing microbes reside in mangrove sediments.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {194},
pmid = {40890888},
issn = {2049-2618},
support = {42306127//National Natural Science Foundation of China/ ; 42306127//National Natural Science Foundation of China/ ; 42176134//National Natural Science Foundation of China/ ; 42030412//National Natural Science Foundation of China/ ; 2024002//Scientific Research Foundation of Third Institute of Oceanography/ ; 2019021//Scientific Research Foundation of Third Institute of Oceanography/ ; },
mesh = {*Geologic Sediments/microbiology ; *Carbon Cycle ; Wetlands ; Phylogeny ; China ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Carbon/metabolism ; Metagenomics/methods ; Gammaproteobacteria/metabolism/genetics/classification/isolation &amp; purification ; Microbiota ; },
abstract = {BACKGROUND: Mangroves are hotspots of carbon sequestration in transitional zones between marine and terrestrial ecosystems. Microbially driven dark carbon fixation (DCF) is prominent in sediments, yet our understanding of the DCF process across this continuum remains limited. In this study, we explored DCF activities and associated chemoautotrophs along the sediment depth of different mangrove sites in Fujian Province, China, using radiocarbon labeling and molecular techniques.<br><br>RESULTS: Our results showed that the DCF rates ranged from 0.02 to 3.27&#xa0;mmol C m[-2]&#xa0;day[-1] in all samples, showing a depth-dependent spatial variation. These rates of DCF were closely related to the environmental factors such as DIC, TS, AVS, NH4[+], NO3[-], and NO2[-]. Metagenomic analysis revealed six carbon-fixing pathways, with the Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl (WL) pathway being predominant. Further analysis of MAGs revealed that Gammaproteobacteria, Desulfobacteria, and Campylobacteria were the most abundant carbon-fixing groups. Intriguingly, some new lineages were found to have carbon-fixing potential, including two candidatus taxa JAJVIF01 and BMS3Abin14. Metatranscriptomic analyses confirmed that these carbon-fixing microbes were active in situ and occupied different niches. In the surface layers, Gammaproteobacteria with the CBB cycle played an important role in DCF, mainly driven by sulfur and hydrogen oxidation with oxygen reduction; in the deeper layers, Campylobacteria with the reductive tricarboxylic acid (rTCA) cycle and Desulfobacteria with the WL pathway were active members for DCF, mainly through sulfur, hydrogen, and CO oxidation. While in the deepest layers of 18-20&#xa0;cm, methane-producing archaea Methanosarcinia was the essential member driving DCF. In addition, most taxa containing the WL pathway displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies.<br><br>CONCLUSIONS: Overall, this study provides new insights into the understanding of biological carbon fixation and its ecological functions in mangrove sediments. Video Abstract.},
}
@article {pmid40890809,
year = {2025},
author = {Xue, S and Shi, T and Xie, J and Liu, W and Yao, S and Li, N and Liu, H and Kong, W and Gao, F},
title = {Integrated fecal macrogenomic and metabolomic analyses reveal celiac disease flora and metabolic profiles associated with Chinese populations.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {972},
pmid = {40890809},
issn = {1479-5876},
support = {2022D01C831//Natural Science Foundation of Xinjiang/ ; 82260116//National Natural Science Foundation of China/ ; 82460117//National Natural Science Foundation of China/ ; },
mesh = {Adolescent ; Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Case-Control Studies ; *Celiac Disease/ethnology/genetics/metabolism/microbiology ; China/ethnology ; *Feces/microbiology ; Gastrointestinal Microbiome ; *Metabolome ; *Metabolomics ; East Asian People ; },
abstract = {BACKGROUND AND AIMS: Genes and gluten intake are necessary but not sufficient to cause celiac disease (CeD), and altered intestinal flora is an additional risk factor for the development of CeD. The present study was conducted to investigate the intestinal flora and metabolic characteristics of CeD among the Chinese population, with the use of CeD patients from Xinjiang, China.<br><br>METHODS: Macrogenomic sequencing was performed to analyze the composition and differences of the intestinal flora of 40 CeD patients and 40 healthy subjects. Non-targeted metabolomics analysis was carried out using LC-MS metabolomics technology in 30 CeD patients and 30 control subjects. A model for CeD diagnosis was constructed based on differential flora and metabolites. Blood was collected from all subjects for HLA typing assay.<br><br>RESULTS: CeD-associated alterations were identified in the gut microbiome and metabolome. 15 differential bacterial strains (AUC&#x2009;=&#x2009;0.85) and 8 differential metabolites (AUC&#x2009;=&#x2009;0.9799) constructed a diagnostic panel that was effective in differentiating CeD patients from healthy subjects. Compared with non-CeD patients carrying HLA-DQ[&#xb1;], the abundances of Agathobacter_rectalis, Bifidobacterium_pseudocatenulatum, Clostridia_bacterium, Coprococcus_comes, and Fusicatenibacter_saccharivorans in CeD patients were significantly lower (P&#x2009;<&#x2009;0.05). Metabolomics analysis showed that Leoheteronin D, Pc (34:2), and GPEtn (18:1/16:0) were the major metabolites involved in multiple metabolic pathways in CeD patients.<br><br>CONCLUSION: Our study revealed specific alterations in the gut microbiome and metabolome of Chinese CeD patients through a multi-omics integration strategy. We found that CeD individuals carrying CeD risk genes may possess a unique intestinal flora composition, and this intestinal flora may, to some extent, explain the pathogenesis of CeD beyond the contributions of genes and gluten intake.},
}
@article {pmid40890565,
year = {2025},
author = {Ivanich, K and Yackzan, A and Flemister, A and Chang, YH and Xing, X and Chen, A and Yanckello, LM and Sun, M and Aware, C and Govindarajan, M and Kramer, S and Ericsson, A and Lin, AL},
title = {Ketogenic Diet Modulates Gut Microbiota-Brain Metabolite Axis in a Sex- and Genotype-Specific Manner in APOE4 Mice.},
journal = {Journal of neurochemistry},
volume = {169},
number = {9},
pages = {e70216},
pmid = {40890565},
issn = {1471-4159},
support = {R01 AG054459/AG/NIA NIH HHS/United States ; R56 AG079586/AG/NIA NIH HHS/United States ; RF1 AG062480/AG/NIA NIH HHS/United States ; RF1AG062480/AG/NIA NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Diet, Ketogenic/methods ; Female ; *Apolipoprotein E4/genetics ; Mice ; Male ; *Brain/metabolism ; *Sex Characteristics ; Genotype ; Mice, Inbred C57BL ; Apolipoprotein E3/genetics ; Mice, Transgenic ; },
abstract = {The apolipoprotein E4 (APOE4) allele is the strongest genetic risk factor for late-onset Alzheimer's disease (AD), associated with early brain metabolic dysfunction and gut microbiome alterations. Targeting these early changes through dietary interventions may reduce AD risk in asymptomatic carriers. This study evaluated whether a ketogenic diet (KD) could reshape the gut microbiome and enhance key brain metabolite levels in young APOE4 mice, using APOE3 mice as a neutral-risk comparison. Male and female APOE3 and APOE4 mice were fed either a control diet or KD for 16 weeks, starting at 12 weeks of age. We used shotgun metagenomics and targeted brain metabolomics to identify microbe-metabolite signatures linked to neuroprotection. KD increased beneficial species such as Lactobacillus johnsonii and Lactobacillus reuteri while reducing pathogenic Bacteroides intestinalis. These microbial shifts correlated with improved brain metabolites related to mitochondrial function, neurotransmitter balance, redox homeostasis, and lipid metabolism. Notably, Lactobacillus species and B. intestinalis exhibited inverse correlations with key brain metabolite levels, suggesting their roles as both modulators and biomarkers of brain health. APOE4 females showed the greatest benefits, including restored microbiome diversity and normalization of brain metabolite levels. In contrast, APOE3 mice showed microbiome changes but limited brain metabolic responses. These findings highlight KD's potential to reprogram the gut-brain axis in a genotype- and sex-dependent manner, supporting its use as a precision nutrition strategy to reduce AD risk, particularly in asymptomatic female APOE4 carriers.},
}
@article {pmid40890119,
year = {2025},
author = {Yuan, B and Wang, S},
title = {Microbiome data integration via shared dictionary learning.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8147},
pmid = {40890119},
issn = {2041-1723},
support = {DBI-2243257//National Science Foundation (NSF)/ ; DMS-2515171//National Science Foundation (NSF)/ ; DBI-2243257//National Science Foundation (NSF)/ ; DMS-2515171//National Science Foundation (NSF)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Metagenomics/methods ; Colorectal Neoplasms/microbiology/therapy ; Machine Learning ; Immunotherapy ; Gastrointestinal Microbiome ; Computational Biology/methods ; },
abstract = {Data integration is a powerful tool for facilitating a comprehensive and generalizable understanding of microbial communities and their association with outcomes of interest. However, integrating data sets from different studies remains a challenging problem because of severe batch effects, unobserved confounding variables, and high heterogeneity across data sets. We propose a new data integration method called MetaDICT, which initially estimates the batch effects by weighting methods in causal inference literature and then refines the estimation via novel shared dictionary learning. Compared with existing methods, MetaDICT can better avoid the overcorrection of batch effects and preserve biological variation when there exist unobserved confounding variables, data sets are highly heterogeneous across studies, or the batch is completely confounded with some covariates. Furthermore, MetaDICT can generate comparable embedding at both taxa and sample levels that can be used to unravel the hidden structure of the integrated data and improve the integrative analysis. Applications to synthetic and real microbiome data sets demonstrate the robustness and effectiveness of MetaDICT in integrative analysis. Using MetaDICT, we characterize microbial interaction, identify generalizable microbial signatures, and enhance the accuracy of outcome prediction in two real integrative studies, including an integrative analysis of colorectal cancer metagenomics studies and a meta-analysis of immunotherapy microbiome studies.},
}
@article {pmid40889848,
year = {2026},
author = {Lin, X and Deng, C and Shu, Y and Li, S and Song, Y and Kong, H and Liang, Z and Liu, L and Rao, Y},
title = {Ecological presence and functional role of bacteriophages in fermented vegetables.},
journal = {Food microbiology},
volume = {133},
number = {},
pages = {104884},
doi = {10.1016/j.fm.2025.104884},
pmid = {40889848},
issn = {1095-9998},
mesh = {*Vegetables/microbiology/virology ; *Bacteriophages/genetics/isolation &amp; purification/physiology/metabolism/classification ; Fermentation ; *Fermented Foods/virology/microbiology ; Microbiota ; *Bacteria/genetics/metabolism/virology/classification/isolation &amp; purification ; Food Microbiology ; },
abstract = {Fermented vegetables are widely favored by consumers for their distinctive flavors and nutritional value, with their quality attributes being closely associated with microbiome dynamics. Recent advances in high-throughput sequencing technologies have revealed abundant bacteriophage resources within the fermented vegetable microbiome. These viral components significantly influence fermentation processes and product characteristics by modulating microbial community structure and function. However, research on optimizing vegetable fermentation processes through bacteriophage-mediated regulation remains in its nascent stage. This study systematically summarizes the compositional characteristics and dynamic patterns of microbial communities in fermented vegetables. We review the latest research progress on bacteriophage diversity and functional properties in fermented vegetables. Furthermore, by integrating multi-omics data, we provide insights into the complex interaction network among bacteriophages, host microbiota, and metabolic products. The results demonstrate that bacteriophages precisely regulate the fermentation process by mediating microbial community succession via lytic-lysogenic cycles and participating in the biosynthesis of key flavor compounds through encoded auxiliary metabolic genes. Finally, we sort out an integrated technical framework combining metagenomics and culturomics. This research provides novel insights into understanding the functional mechanisms of bacteriophages in fermented vegetables, offers a theoretical foundation for developing precision fermentation technologies based on bacteriophage regulation.},
}
@article {pmid40889843,
year = {2026},
author = {Ren, F and Liu, M and Tan, B},
title = {Mycobiota of highly-preserved and easily-spoiled soybean pastes-what are their roles?.},
journal = {Food microbiology},
volume = {133},
number = {},
pages = {104876},
doi = {10.1016/j.fm.2025.104876},
pmid = {40889843},
issn = {1095-9998},
mesh = {*Glycine max/microbiology ; *Fungi/classification/genetics/isolation &amp; purification/metabolism ; *Mycobiome ; Food Preservation ; Biodiversity ; },
abstract = {Effective preservation of fermented soybean pastes is critically dependent on their microbial communities. In this study, the fungal assemblages of highly-preserved (HP) and easily-spoiled (ES) soybean paste samples were analyzed and compared mainly with Illumina sequencing of both mycobiota ITS amplicon and metagenomic functional annotation. The results showed that fungal communities of two types soybean pastes were distinct and had different α-diversity and β-diversity characteristics. The phylum Ascomycota was predominant in all samples, with Candida, Aspergillus, and Penicillium being the most abundant genera. The HP group exhibited greater richness and diversity compared to ES samples, and the relative abundance of specific fungal taxa varied significantly between the two groups. Additionally, functional annotation revealed differences in metabolic categories, with HP samples having higher levels of functions related to amino acid transport and metabolism, cell cycle control, and signal transduction mechanisms. These results enhance the understanding of the fungal diversity and functional differences of soybean pastes, providing insights that could improve preservation methods, optimize production and storage processes, and ensure the quality of the products.},
}
@article {pmid40889349,
year = {2025},
author = {Moraitou, M and Richards, JL and Bolyos, C and Saliari, K and Gilissen, E and Timmons, Z and Kitchener, AC and Pauwels, OSG and Sabin, R and Kokkini, P and Portela Miguez, R and Guschanski, K},
title = {Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70039},
pmid = {40889349},
issn = {1755-0998},
support = {2019-00275//Svenska Forskningsr&#xe5;det Formas/ ; },
mesh = {*Metagenomics/methods ; *Dental Calculus/microbiology ; *Mammals/microbiology/classification ; Animals ; *Microbiota ; *Gene Library ; Metagenome ; Computational Biology ; },
abstract = {Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.},
}
@article {pmid40888959,
year = {2025},
author = {Rajan, RJ and Sathyanathan, R and Rajnish, KN},
title = {Metabarcoding-Based Seasonal Assessment of Airborne Microbial Communities in PM10 Samples from a Semi-Urban Region in Tamil Nadu, India.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {9},
pages = {1069},
pmid = {40888959},
issn = {1573-2959},
mesh = {India ; *Air Microbiology ; Seasons ; *Environmental Monitoring/methods ; *Microbiota ; *Air Pollutants/analysis ; *Particulate Matter/analysis ; Bacteria/classification/genetics ; DNA Barcoding, Taxonomic ; Air Pollution/statistics &amp; numerical data ; },
abstract = {Airborne microbial communities show marked seasonal variability, with implications for both environmental processes and public health. In this study, metagenomic sequencing was applied to characterize airborne microbiota across four distinct seasons in India-winter (Sw), summer (Ss), southwest monsoon (Ssw), and northeast monsoon (Sne). Distinct shifts in dominant bacterial taxa were observed. Sne was dominated by Pseudomonas (42.3%) alongside sulfur-oxidizing Thiobacillus and Stenotrophomonas, likely influenced by lower temperatures and anthropogenic inputs. In Ss, Thiobacillus (72.9%) prevailed, followed by Pseudomonas (8.06%) and Sphingosinicella (6.68%), reflecting adaptation to arid, UV-intense conditions. Ssw featured Thiobacillus (58%) and Pseudomonas (18.5%) with additional plant-associated Lactobacillus and Clostridium, suggesting enhanced biogenic emissions. Sw was distinct for Enterococcus (21.9%) dominance and reduced Thiobacillus (16.2%), associated with high humidity and precipitation. Species richness followed the order Ssw > Sw > Ss > Sne, with the highest diversity during Ssw and Sw as indicated by Chao1, Fisher, Shannon, and Simpson indices. Kruskal-Wallis tests revealed no statistically significant differences in alpha diversity across seasons. Canonical Correspondence Analysis (CCA) highlighted strong seasonal structuring linked to environmental parameters such as temperature, humidity, and UV exposure. Dendrogram clustering showed greatest dissimilarity between Sne and Sw, while Ss and Ssw formed a closely related group. Ordination analyses (PCA, PCoA, NMDS) further confirmed seasonal distinctions. Seasonal variations in dominant bacterial taxa indicate potential public health risks in semi-urban tropical environments. Thiobacillus, prevalent in summer and the southwest monsoon, is generally non-pathogenic. In contrast, Pseudomonas species, abundant during the northeast monsoon and winter, are metabolically versatile, encompassing environmental strains and opportunistic pathogens known to cause respiratory and wound infections, especially in immunocompromised individuals. Winter also saw the presence of Enterococcus faecalis, a gut commensal and opportunistic pathogen linked to hospital-acquired infections and notable for multi-drug resistance. These seasonal shifts highlight varying exposure risks, emphasizing the need for public health attention to airborne microbial dynamics across different seasons.},
}
@article {pmid40888850,
year = {2026},
author = {Chasapi, MN and Chasapi, IN and Aplakidou, E and Baltoumas, FA and Karatzas, E and Iliopoulos, I and Stravopodis, DJ and Emiris, IZ and Buluç, A and Georgakopoulos-Soares, I and Kyrpides, NC and Pavlopoulos, GA},
title = {metagRoot: a comprehensive database of protein families associated with plant root microbiomes.},
journal = {Nucleic acids research},
volume = {54},
number = {D1},
pages = {D1733-D1742},
pmid = {40888850},
issn = {1362-4962},
support = {23592//Hellenic Foundation for Research and Innovation/ ; //European Union's Horizon 2020/ ; 945405//Marie Sk&#x142;odowska-Curie/ ; //Penn State College of Medicine/ ; //Huck Innovative and Transformational Seed/ ; //Huck Institutes of the Life Sciences/ ; 16718-PRPFOR//Hellenic Foundation for Research and Innovation/ ; TAEDR-0539180//Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//U.S. Department of Energy Office of Science/ ; //Nikos Kyrpides JGI-LBNL/ ; },
mesh = {*Plant Roots/microbiology ; *Microbiota/genetics ; *Databases, Protein ; Metagenomics ; Molecular Sequence Annotation ; Metagenome ; },
abstract = {The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences. These families are annotated with multiple sequence alignments, CRISPR elements, hidden Markov models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context. The database is available at https://pavlopoulos-lab.org/metagroot/ or https://www.metagroot.org.},
}
@article {pmid40888678,
year = {2025},
author = {Zhou, R and Ng, SK and Sung, JJY and Wong, SH and Goh, WWB},
title = {Detecting and mitigating doppelgänger bias in microbiome data: impacts on machine learning and disease classification.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2554196},
pmid = {40888678},
issn = {1949-0984},
mesh = {Humans ; *Machine Learning ; Clostridium Infections/microbiology ; Colorectal Neoplasms/microbiology ; Inflammatory Bowel Diseases/microbiology ; *Microbiota ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Obesity/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; },
abstract = {Highly similar microbiome samples - so-called "doppelgänger pairs" - can distort analysis outcomes, yet are rarely addressed in microbiome studies. Here, we demonstrate that even a small proportion of such pairs (1-10% of samples) can substantially inflate machine learning performance across diverse disease cohorts including colorectal cancer (CRC), inflammatory bowel diseases (IBD), Clostridioides difficile infection (CDI), and obesity. Doppelgänger pairs also bias statistical tests and distort microbial network topology. In predictive models, classification accuracy was artificially boosted by 15-30% points across KNN, SVM, and Random Forest classifiers. In association testing, doppelgängers increased false-positive rates and decreased effect size stability; their removal reduced bootstrap variance by up to 28.3%. Moreover, the removal of doppelgängers yielded more stable networks. These effects were consistently observed across 16S, shotgun metagenomic, and simulated datasets. By accounting for highly similar samples, we reduce analytical noise and false discoveries, ultimately enabling more accurate and biologically meaningful microbiome insights.},
}
@article {pmid40886575,
year = {2025},
author = {Agga, GE and Looft, T and Sistani, KR},
title = {Enrichment of soil microbiome and antimicrobial resistance genes following poultry litter application.},
journal = {The Science of the total environment},
volume = {999},
number = {},
pages = {180306},
doi = {10.1016/j.scitotenv.2025.180306},
pmid = {40886575},
issn = {1879-1026},
mesh = {*Soil Microbiology ; *Microbiota ; Animals ; Poultry ; *Drug Resistance, Microbial/genetics ; Fertilizers ; *Manure/microbiology ; Soil/chemistry ; },
abstract = {Poultry litter (PL) is often used for soil amendment as an alternative to chemical fertilizers. However, it may enrich microbial and antimicrobial resistance genes in applied soil. The objective of this study was to investigate changes in the soil microbiome and resistome profiles following PL application. Three treatments untreated control (UC), chemical fertilizer (CF), and PL were applied to corn plots in a completely randomized block design. Total soil (metagenomic) DNA (n = 72) obtained on d0, d7, and d28 were shotgun sequenced. A composite DNA sample pooled from PL samples (n = 8) was sequenced for comparison. While Actinomycetota and Pseudomonadota were the most prevalent phyla among the soil samples, their abundance was significantly higher in the PL amended soils. PL soil amendment shifted microbial composition (Gammaproteobacteria and fungal Saccharomycetes were enriched in PL amended soils), diversity, and abundance by differentially enriching several microbial species, functional pathway genes, virulence factor genes, and antimicrobial resistance genes. Macrolides-lincosamides-streptogramin (MLS) resistance genes were the most abundant genes enriched in PL amended soils. The PL microbiome was primarily composed of the phylum Bacillota with Virgibacillus alimentarius being the most abundant species, followed by Staphylococcus nepalensis and S. simulans. The PL resistome was dominated by MLS resistance genes. Virulence factor genes associated with the genera Bacteriodes, Enterococcus and Staphylococcus were the most prevalent. The study clearly showed that PL application enriches soil microbiome and resistome, the mechanism of which is more likely through nutrient enrichment rather than their direct transfer since PL and PL-amended soils had different microbiome profiles.},
}
@article {pmid40886530,
year = {2025},
author = {Miao, L and Ma, T and Qi, J and Deng, Y and Hong, Y and Gong, X and Zang, H and Cheng, Y and Li, C},
title = {Deciphering intrakingdom synergism in 17β-estradiol degradation through DNA-SIP coupled metagenomics: Metabolic cooperation and niche partitioning in bioaugmented soil microbiomes.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139709},
doi = {10.1016/j.jhazmat.2025.139709},
pmid = {40886530},
issn = {1873-3336},
mesh = {Metagenomics ; *Soil Microbiology ; Biodegradation, Environmental ; *Estradiol/metabolism ; *Microbiota ; Rhodococcus/metabolism/genetics ; *Soil Pollutants/metabolism ; Microbial Consortia ; RNA, Ribosomal, 16S/genetics ; },
abstract = {17β-Estradiol (17β-E2), a persistent endocrine-disrupting compound, threatens ecosystem health through bioaccumulation. While bioaugmentation offers promise for environmental remediation, mechanistic insights into interspecies interactions between exogenous and indigenous degraders remain underexplored. Here, a synthetic microbial consortium (EL) was constructed by combining Rhodococcus erythropolis D310-1 and Microbacterium oxydans ML-6, which reduced the 17β-E2 degradation half-life by 53.65 % compared with that of the noninoculated control while suppressing the accumulation of the toxic intermediate estrone (E1). Temporal 16S rRNA gene amplicon sequencing profiling with co-occurrence network analysis revealed that the consortium EL dynamically reinforced ecological synergies with indigenous functional microbiota, accelerating contaminant mineralization. DNA-stable isotope probing (DNA-SIP) coupled with metagenomics identified Rhodanobacter, Mycobacterium, Rhodococcus, Sphingomonas, and Microbacterium spp. as active 17β-E2 assimilators. Furthermore, high-performance liquid chromatography coupled with quadrupole timeflight mass spectrometry (HPLCQTOFMS) was used to predict three complementary degradation pathways in the assembled genomes, revealing related functional enzymes and addressing functional partitioning between exogenous inoculants and indigenous degraders. Two novel gene clusters responsible for 17β-E2 biodegradation were evaluated. This study pioneers DNA-SIP and metagenomics to track [13]C-labelled 17β-E2 fate within bioaugmented soil microbiota, resolving intrakingdom bacteria collaborations that drive 17β-E2 biodegradation in soil. The identification of cross-consortium metabolic handoffs provides a blueprint for engineering syntrophic partnerships targeting steroidal estrogens (SEs) pollutants.},
}
@article {pmid40885910,
year = {2025},
author = {Huang, W and Chai, Y and Li, X and Zhang, Q and Yan, Z and Wang, Y and Tao, X and Zhang, J and Qiu, F},
title = {Metagenomics and metabolomics to evaluate the potential role of gut microbiota and blood metabolites in patients with cerebral infarction.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {567},
pmid = {40885910},
issn = {1471-2180},
support = {2018YFA0108601//Clinical research on intracerebral precision transplantation of neural stem cells for stroke treatment/ ; L255012//The Huairou Innovation Joint Fund Project of Beijing Natural Science Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Cerebral Infarction/microbiology/blood/metabolism ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Middle Aged ; Female ; Aged ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Tandem Mass Spectrometry ; Adult ; Chromatography, High Pressure Liquid ; },
abstract = {Cerebral infarction, a cerebrovascular disorder, is characterized by the sudden onset of neurological deficits and clinical symptoms. It ranks among the leading causes of death and severe disability worldwide. The etiology of cerebral infarction is multifaceted, with common risk factors including dietary patterns, smoking, hypertension, and diabetes mellitus. In recent years, the role of the gut microbiota in systemic immunity and tumorigenesis has been intensively explored, thrusting the research on the gut-brain axis into the spotlight. However, there is a lack of literature investigating the relationship between the gut microbiota and blood metabolites in cerebral infarction. In this study, we employed 16S rRNA analysis and ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) for a comprehensive metagenomic and metabolomic analysis of fecal samples from cerebral infarction patients and the general population. Our results revealed a significant correlation between the gut microbiome and serum metabolites, highlighting the impact of the microbiome on metabolic pathways. Specifically, we found that 35 gut microbiome taxa, such as Actinobacteriota and Peptostreptococcales-Tissierellales, were significantly enriched in the control group (N group). Through Linear Discriminant Analysis Effect Size (LEfSe) analysis, 72 taxa showed significant differences between cerebral infarction patients and healthy individuals. Among them, 22 key taxa were identified as microbial biomarkers for differentiating patients from healthy controls. These findings suggest that variations in the microbiome and metabolites could potentially serve as biomarkers for future diagnostic and therapeutic strategies in cerebral infarction.},
}
@article {pmid40883297,
year = {2025},
author = {Chen, XP and Zhu, D and Liu, SY and Sun, MM and Ye, M and Wang, L and Lin, D and Zhang, TL and Rillig, MC and Zhu, YG},
title = {Unique plastisphere viromes with habitat-dependent potential for modulating global methane cycle.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8098},
pmid = {40883297},
issn = {2041-1723},
support = {42021005//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Methane/metabolism ; *Microbiota/genetics ; *Ecosystem ; *Virome/genetics ; Metagenomics/methods ; Soil Microbiology ; Bacteria/metabolism/genetics/virology ; },
abstract = {Plastispheres, novel niches in the Anthropocene, harbor microbial communities with unique functional signatures. As the most abundant biological entity on Earth, viruses are key regulators of microbial community composition and metabolism. However, little is known about viral communities and their functions in the plastisphere. Here, we investigate the composition and functional profile of plastisphere viral communities through microcosm experiments combined with global plastisphere metagenomics data. We find that the plastisphere recruits a distinct viral community with 86.9% novel viral operational taxonomic units compared to control substrates. The plastisphere viral community modulates host methane metabolism through auxiliary metabolic genes and distinctive interactions with hosts. These auxiliary metabolic genes for methane cycling are prevalent in global plastisphere viral communities. Notably, the plastisphere microbiome adopts the life history strategy of copiotrophs in the nutrient-poor water environment, making the water plastisphere a potential hot spot for methane emission compared to the soil plastisphere. Our phage transplantation experiments reveal that lysogenic viruses significantly contribute to enhancing the methanogenic capacity of microorganisms and promoting methane emission of the water plastisphere. Overall, we decipher the role of viruses in the plastisphere and reinforce the necessity of incorporating viral contributions when assessing the effects of plastisphere communities on global biogeochemical cycles.},
}
@article {pmid40871697,
year = {2025},
author = {Wang, B and Peters-Samuelson, BA and Luo, K and Cordero, C and Perreira, KM and Pirzada, A and Daviglus, ML and Li, Y and Kaplan, RC and Burk, RD and Qi, Q},
title = {Interplays of ADH1B Genotype, Alcohol Consumption, and Gut Microbiota in Relation to Insulin Resistance.},
journal = {Nutrients},
volume = {17},
number = {16},
pages = {},
pmid = {40871697},
issn = {2072-6643},
support = {R01-HL136266//National Heart Lung and Blood Institute/ ; R01-HL060712//National Heart Lung and Blood Institute/ ; R01 DK120870/DK/NIDDK NIH HHS/United States ; N01 HC065236/HL/NHLBI NIH HHS/United States ; R01-MD011389/MD/NIMHD NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; UM1-HG008898/HG/NHGRI NIH HHS/United States ; N01 HC065237/HL/NHLBI NIH HHS/United States ; R01 HL136266/HL/NHLBI NIH HHS/United States ; R01-DK126698/DK/NIDDK NIH HHS/United States ; R01-HL140976//National Heart Lung and Blood Institute/ ; R01 DK126698/DK/NIDDK NIH HHS/United States ; N01 HC065233/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; N01 HC065235/HL/NHLBI NIH HHS/United States ; R01 DK119268/DK/NIDDK NIH HHS/United States ; P30DK111022/DK/NIDDK NIH HHS/United States ; R01-DK119268/DK/NIDDK NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; N01 HC065234/HL/NHLBI NIH HHS/United States ; R01-DK120870/DK/NIDDK NIH HHS/United States ; R01 HL060712/HL/NHLBI NIH HHS/United States ; UM1 HG008898/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; *Alcohol Dehydrogenase/genetics ; *Insulin Resistance/genetics ; *Gastrointestinal Microbiome/genetics ; *Alcohol Drinking/genetics ; Male ; Female ; Cross-Sectional Studies ; Middle Aged ; *Genotype ; Adult ; Feces/microbiology ; Longitudinal Studies ; },
abstract = {BACKGROUND/OBJECTIVE: Alcohol consumption has been linked to alterations in gut microbiota and insulin resistance. The alcohol dehydrogenase 1B (ADH1B) gene plays a crucial role in alcohol catabolism, where rs1229984 variant carriers (CT/TT) catabolize ethanol at an 80-fold faster rate than non-carriers (CC). This study investigates the relationships between ADH1B gene rs1229984 mutation, alcohol consumption, gut microbiota, and insulin resistance.<br><br>METHODS: We performed cross-sectional analysis on fecal metagenomic sequencing data from diabetes-free participants in a longitudinal cohort of the Hispanic Community Health Study/Study of Latinos. We used Analysis of Composition of Microbiomes to identify gut microbial species associated with alcohol consumption in non-carriers (n = 1399) and carriers (n = 193). We constructed genotype-specific gut microbiome scores (GMSs) based on the identified species associated with alcohol consumption to examine how gut microbiota may influence the relationship between alcohol consumption and insulin resistance across ADH1B genotypes. Insulin resistance was defined as Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) > 2.5.<br><br>RESULTS: Distinct microbial species associated with alcohol consumption were identified in non-carriers (54 species) and carriers (16 species). In non-carriers, the genotype-specific GMS modified the relationship between alcohol consumption and insulin resistance (Pinteraction = 0.011). The odds ratios (OR) for insulin resistance with increasing alcohol consumption levels across low, moderate, and high tertiles of GMS were 0.75 (95%CI 0.58-0.96), 0.82 (0.67-1), and 1.13 (0.93-1.39), respectively. We identified that individual alcohol-related species, such as Prevotella copri, Ruminococcus callidus, and Erysipelatoclostridium ramosum, modified the relationship between alcohol consumption and insulin resistance in non-carriers.<br><br>CONCLUSIONS: This study suggests that the ADH1B gene rs1229984 mutation is associated with gut microbiota profiles altered by alcohol consumption. Our findings also suggest a potential role of gut microbiota in the protective association between alcohol consumption and insulin resistance in the ADH1B variant non-carriers.},
}
@article {pmid40867077,
year = {2025},
author = {Ebadi, M and Reddi, S and Senyshyn, L and Minot, SS and Gooley, T and Kabage, AJ and Lee, SJ and Hill, GR and Khoruts, A and Rashidi, A},
title = {Effect of fecal microbiota transplantation on gut microbiota functional profile in recipients of allogeneic hematopoietic cell transplantation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2551882},
pmid = {40867077},
issn = {1949-0984},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Fecal Microbiota Transplantation ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Female ; Adult ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Dysbiosis/therapy/microbiology ; Transplantation, Homologous ; Feces/microbiology ; Aged ; },
abstract = {Intestinal dysbiosis has been associated with both the effectiveness and toxicity of immunotherapy in cancer patients, inspiring multiple trials investigating fecal microbiota transplantation (FMT) in these patients. FMT restores microbial community structures damaged by antibiotics and enriches the microbiota with beneficial bacteria. However, the precise mechanism through which FMT exerts its effects and provides clinical benefits remains incompletely understood. Efforts to date have primarily focused on characterizing taxonomic changes following FMT. We hypothesized that FMT may also modify the functional pathways and metabolic capabilities of the gut microbiota, with possible clinical impact. To investigate this, we conducted a study involving 17 patients with blood disorders who received prophylactic FMT from one of the three healthy donors shortly after hematopoietic cell transplantation (HCT). By analyzing shotgun metagenomic profiles of the baseline, pre-FMT, and post-FMT gut microbiota, we demonstrate that FMT effectively restored pathways that had been depleted following HCT. However, it did not significantly reduce pathways that had expanded, indicating that FMT operates primarily through a restorative mechanism, reestablishing lost functional capabilities in the microbiota rather than suppressing overactive pathways. These findings highlight the potential for optimizing FMT protocols and identifying patient populations where FMT may be particularly beneficial.},
}
@article {pmid40844735,
year = {2025},
author = {Bhatt, P and Rajesh, P and Kukkar, D and Kim, KH},
title = {Metagenomic profiling of gut microbime: associating their role with the advancement of diabetic nephropathy.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {135},
pmid = {40844735},
issn = {1572-9699},
support = {DST/WISE-PhD/LS/2023/73/G//Department of Science and Technology, Ministry of Science and Technology, India/ ; EMDR/SG/13/2023-0756//Indian Council of Medical Research/ ; 2021R1A3B1068304//Ministry of Science, ICT and Future Planning/ ; 2022R1A6C101A779//National Center for Inter-University Research Facilities, Seoul National University/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Diabetic Nephropathies/microbiology ; *Metagenomics/methods ; Diabetes Mellitus, Type 2/microbiology/complications ; Disease Progression ; },
abstract = {Emerging evidence suggests that alterations in the gut microbiome should play a critical role in the development and progression of type 2 diabetes and its complication such as diabetic nephropathy (DN). Nevertheless, a considerable gap remains in our understanding of the interconnection between DN pathogenesis and gut microbiota arrangement. In this context, this review highlights recent research on the connection between the intestinal microbiota and DN risk, with a particular focus on the role of microbial metabolites in disease development. It also highlights recent advancements in metagenomic analyses of gut microbial communities and their potential contribution to the progression of DN. Further, it describes the challenges associated with the metagenomics-based analysis of intestinal microbiota and the advancement of therapeutics for DN. An exploration of the surveyed literature reveals the lack of any definitive correlation between gut microbiota and DN transition, even when assessed in view of widespread geographical and ethnic diversity. Future research in this domain should be conducted to address various issues like increasing the number of participants, intake patient diversity, logistical difficulties, and racial disparities. A critical assessment of these parameters will help improve our understanding of the potential contribution of gut microbiota to the DN progression.},
}
@article {pmid40886152,
year = {2025},
author = {Zemmel, ZM and Fan, X and Yu, Y and Markiewicz, E and Tsai, HM and Lu, L and Little, JC and Ramaswamy, R and Andrews, B and Claud, EC and Lu, J},
title = {Early-life gut microbiome maturity regulates blood-brain barrier and cognitive development.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2551879},
pmid = {40886152},
issn = {1949-0984},
support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R01 HD105234/HD/NICHD NIH HHS/United States ; R21 NS121432/NS/NINDS NIH HHS/United States ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Blood-Brain Barrier/metabolism/physiology/growth &amp; development ; Mice ; Female ; Humans ; *Cognition/physiology ; Pregnancy ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Mice, Inbred C57BL ; Brain/growth &amp; development/metabolism ; Male ; Germ-Free Life ; },
abstract = {The gut microbiome is an emerging factor in the neurobiology of disease. Blood-brain barrier (BBB) integrity is essential for proper brain function. However, the role the initial microbiome plays in BBB and brain development is unclear. In this study, we colonized germ-free pregnant mice with human full-term- or preterm-infant-derived gut microbiota, thereby establishing these communities in the resulting offspring. We discovered that mice harboring a full-term-associated microbiome exhibited stronger memory and learning capabilities and dramatically decreased early-life BBB permeability when compared to those with a prematurity-associated microbiome. Whole-brain single-cell RNA sequencing revealed downregulation of synaptic signaling genes in BBB cell types of mice with the prematurity-associated microbiome, indicating that microbiome maturity influences BBB transcriptional programs that support cognitive development. Comprehensive metagenomics and metabolomics uncovered bacterial populations and genomic pathways corresponding with decreased levels of circulating long-chain acylcarnitines and lysophosphatidylcholines in mice with the full-term-associated microbiome. Our findings highlight the microbiome as a therapeutic target for improving long-term neurodevelopmental outcomes due to its effect on the early-life BBB.},
}
@article {pmid40885737,
year = {2025},
author = {Chatzigiannidou, I and Johansen, PL and Dehli, RK and Moll, JM and Eriksen, C and Myers, PN and Roager, HM and Yang, L and Stokholm, J and Sørensen, SJ and Krogfelt, KA and Laursen, MF and Trivedi, U and Scheynius, A and Kristiansen, K and Mie, A and Alm, J and Brix, S},
title = {Temporal dynamics and microbial interactions shaping the gut resistome in early infancy.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8139},
pmid = {40885737},
issn = {2041-1723},
support = {2012-3011//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; 0171-00006B//Det Frie Forskningsr&#xe5;d (Danish Council for Independent Research)/ ; 4203-00005B//Innovationsfonden (Innovation Fund Denmark)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; Infant ; Escherichia coli/genetics/drug effects/growth &amp; development ; Female ; Infant, Newborn ; Bifidobacterium/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Microbial Interactions/genetics ; *Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Metagenomics ; Male ; },
abstract = {Despite the critical role of the gut resistome in spreading of antimicrobial resistance (AMR), strategies to reduce the abundance of antibiotic resistance genes (ARGs) during microbiota development in infancy remain underexplored. Using longitudinal quantitative metagenomic data, we here show that ARGs are present in the gut microbiota from the first week of life, with a peak in absolute ARG abundance and richness at 6 months. Delivery mode significantly affects early ARG dynamics, and vaginally delivered infants exhibit higher ARG abundance due to maternal transmission of Escherichia coli strains harbouring extensive resistance repertoires. The abundance of E. coli and other ARG-rich taxa inversely correlates with aromatic lactic acid-producing bifidobacteria, and aromatic lactic acids strongly inhibit the in vitro growth of E. coli and other opportunistic ARG-rich taxa. Our results highlight temporal and critical microbial interactions shaping the gut resistome in early infancy, pointing to potential interventions to curb AMR during this vulnerable developmental window by promoting colonization of aromatic lactic acid-producing bifidobacteria.},
}
@article {pmid40885659,
year = {2026},
author = {Klier, KM and Anantharaman, K},
title = {An updated view of metabolic handoffs in microbiomes.},
journal = {Trends in microbiology},
volume = {34},
number = {1},
pages = {98-112},
doi = {10.1016/j.tim.2025.07.009},
pmid = {40885659},
issn = {1878-4380},
mesh = {Humans ; *Microbiota/physiology ; Ecosystem ; *Bacteria/metabolism/genetics/classification ; Biodiversity ; *Microbial Interactions/physiology ; Gastrointestinal Microbiome ; },
abstract = {From the human gut to the deep ocean, diverse microbial communities underpin essential ecosystem processes. Limited understanding of the dynamics and interactions that shape these communities, however, constrains efforts to culture, investigate, and harness their potential. Further, these knowledge gaps restrict the ability to predict microbial responses to broader biodiversity declines and global change. Among the numerous types of microbial interactions, metabolite exchanges, or 'metabolic handoffs', are a well-documented phenomenon. Recent methodological advances have uncovered a broader spectrum of metabolic handoffs than previously appreciated. Varying in both mechanism and ecological role, metabolic handoffs influence diverse natural environments. In this review, we define two major types of metabolic handoffs, examine their potential drivers and benefits, and highlight emerging research that underscores their widespread occurrence and importance in complex microbial ecosystems.},
}
@article {pmid40885432,
year = {2026},
author = {Kwon, M and Kwon, SH and Jang, H and Oh, H and Sun, S and Jung, C and Kil, EJ},
title = {Landscape-scale virome analysis uncovers endemic and emerging honey bee viruses in the Silk-Road hub of Uzbekistan.},
journal = {Journal of invertebrate pathology},
volume = {214},
number = {},
pages = {108436},
doi = {10.1016/j.jip.2025.108436},
pmid = {40885432},
issn = {1096-0805},
mesh = {Animals ; Bees/virology ; *Virome ; Uzbekistan ; *RNA Viruses/isolation &amp; purification/genetics ; Phylogeny ; *Insect Viruses/genetics/isolation &amp; purification ; Genome, Viral ; },
abstract = {Honey bee health is increasingly threatened worldwide by a complex and evolving viral landscape; however, this aspect in Central Asia remains understudied despite the region being strategically positioned along historic and modern trade routes. In 2024, we conducted a nationwide virome survey of Apis mellifera across 32 cities in 11 regions of Uzbekistan, combining the metagenomic data of 14 pooled RNA-seq libraries with RT-PCR validation and phylogenetic analyses. High-quality sequencing yielded an average of approximately 60 million reads per pool. We recovered 30 viral species from 162 genomic sequences (131 complete sequences), including 11 honey bee-associated and 19 plant-infecting viruses. All samples harbored deformed wing virus type A (DWV-A), and co-infection with DWV-B predominated. Our findings provided the first full-length DWV-B genomes from Central Asia, revealing that it had > 97 % identity to European strains. New variants of the Sacbrood virus (partial sequence, approximately 4.7 kb) and Lake Sinai virus UZB were also detected. The chronic bee paralysis virus was sequenced in full for the first time in Uzbekistan, and varroa orthomyxovirus-1 exhibited segment-specific divergence. Additionally, we identified two novel plant viruses: Gulistan nepovirus 1 and Arpa carmo-like virus 1. Phylogenetic patterns of the identified viruses indicate that Uzbekistan serves as a genetic corridor connecting European and Asian virus populations. These findings fill critical geographical gaps, underscore the need for transboundary surveillance, and provide a genomic baseline for future diagnostics, epidemiology, and control strategies aimed at safeguarding pollinator and ecosystem health.},
}
@article {pmid40885278,
year = {2025},
author = {Bastón-Paz, N and Moreno-Blanco, A and Palacios, E and Olavarrieta, L and Galeano, J and Garriga, M and Máiz, L and Vicente-Santamaría, S and Oteo-Iglesias, J and López-Causapé, C and Fuentes, I and Oliver, A and Cantón, R and Del Campo, R and de Dios-Caballero, J},
title = {Exploring the complexities of intestinal and pulmonary microbiota in cystic fibrosis: A multi-omics approach.},
journal = {Respiratory medicine},
volume = {248},
number = {},
pages = {108331},
doi = {10.1016/j.rmed.2025.108331},
pmid = {40885278},
issn = {1532-3064},
mesh = {Humans ; *Cystic Fibrosis/microbiology/physiopathology ; Male ; Female ; Feces/microbiology ; Sputum/microbiology ; Adult ; *Gastrointestinal Microbiome/genetics ; *Lung/microbiology ; Metagenomics/methods ; Adolescent ; Fatty Acids, Volatile/metabolism/analysis ; Child ; Young Adult ; *Microbiota ; Multiomics ; },
abstract = {BACKGROUND: We aimed to elucidate the cystic fibrosis (CF) microbiota composition (shotgun metagenomics) and functionality (short-chain fatty acids, SCFAs).<br><br>METHODS: Fecal and sputum samples were recruited from 39 clinically stable CF subjects.<br><br>RESULTS: Bacillota and Pseudomonadota were dominant in both gut and lung compartments, whereas Ascomycota were the most abundant fungi in feces, and Basidiomycota, especially Malassezia globosa, in sputum. Viruses accounted for 0.4&#xa0;% of the relative abundance in the gut and 0.6&#xa0;% in lungs. Mycobacteroides abscessus was genetically identified in 10 individuals, although only 2 had positive cultures. Patients with higher levels of Pseudomonas filamentous phages had negative cultures for P. aeruginosa. The protozoan Toxoplasma gondii was detected in all sputum samples, accounting for 0.25&#xa0;% of the metagenomic reads, with further PCR-confirmation in 50&#xa0;% of subjects, including children. No correlation was found between SCFA and lung function or microbial composition. The resistome of the fecal compartment was higher than that of the lungs, and a greater abundance of SCFAs in the intestine was associated with poorer lung function.<br><br>CONCLUSIONS: Patients with normal-mild lung function had higher alpha diversity in the respiratory microbiota; however, beta diversity in the stool was statistically different compared with the group with poorer lung function. Although there were no differences in SCFA concentrations, butyrate-producing bacteria were more abundant in the sputum of the group with better lung function. In fecal samples, resistome to tetracyclines, glycopeptides, and aminoglycosides predominated, whereas in sputum an enrichment of ARGs related to tetracyclines, beta-lactams, and macrolides was observed.},
}
@article {pmid40883413,
year = {2025},
author = {Manzoor, M and Pussinen, PJ and Saarela, RKT and Hiltunen, K and Mäntylä, P},
title = {Metagenomic analysis of the denture-associated oral microbiome in patients with denture stomatitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31913},
pmid = {40883413},
issn = {2045-2322},
support = {1340750//Research Council of Finland/ ; },
mesh = {Humans ; Female ; Male ; *Stomatitis, Denture/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Aged, 80 and over ; Aged ; *Mouth/microbiology ; Dysbiosis/microbiology ; *Dentures/microbiology ; Metagenome ; Bacteria/genetics/classification ; },
abstract = {Denture stomatitis (DS) is an inflammatory condition that affect denture wearers and is characterized by erythema of the mucosa opposing the denture. DS is often associated with oral microbiome dysbiosis. We used shotgun metagenomics to investigate the association between the denture-associated oral microbiome (DAOM) and DS in older adults living in long-term care facilities. We included participants with DS (n = 28) and age-and sex-matched removable denture wearers without signs of DS (n = 28). Clinical oral examinations were performed, and demographic and medical data were obtained from medical records. Median (interquartile range) age of participants was 88 (9) years; 75% were females. Beta diversity differed between the DS and non-DS groups (Bray-Curtis dissimilarity, p = 0.01; Jaccard index, p = 0.004). Two phyla, nine genera, and 15 species differed significantly between groups, with the genera Candida and Scardovia, and species Candida albicans, Aggregatibacter actinomycetemcomitans, and Scardovia inopinata being enriched in DS. Network analysis revealed strongly interconnected microbial communities and more prominent bacterial-fungal co-occurrence in DS than in non-DS. These findings indicate that DS is associated with significant alterations in the DAOM, which may contribute to inflammation. Microbiome-targeted strategies are needed for the management of DS.},
}
@article {pmid40883308,
year = {2025},
author = {Chen, T and Xiong, Y and Zhang, J and Zhang, Q and Wu, J and Xu, N and Liu, T},
title = {Temporal dynamics, microdiversity, and ecological functions of viral communities during cyanobacterial blooms in Lake Taihu.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {178},
pmid = {40883308},
issn = {2055-5008},
support = {20220808011114001//Shenzhen Natural Science Fund/ ; },
mesh = {*Lakes/microbiology/virology ; *Cyanobacteria/virology/growth &amp; development ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; China ; Biodiversity ; Eutrophication ; *Harmful Algal Bloom ; *Virome ; },
abstract = {Harmful cyanobacterial blooms pose severe threats to aquatic ecosystems. Bloom-forming cyanobacteria form cyanobacterial aggregates (CAs) that create a phycosphere supporting diverse microbial interactions. Here, longitudinal metagenomics and metatranscriptomics were employed to explore the temporal variation of CA-attached viral communities throughout cyanobacterial blooms in Lake Taihu. Viral communities, represented by 5613 viral operational taxonomic units, showed increased relative abundance (RPKM) with the expansion of bloom areas. Among 1791 virus‒host linkages, host shifts followed the succession of two dominant cyanobacterial genera, Microcystis and Dolichospermum. Viruses demonstrated high virus‒host abundance ratios within all host genera and showed elevated transcriptional activities infecting Dolichospermum during the late bloom stage. Viruses featured high microdiversity and positively selected replication-associated genes in response to abundant host genera and variable trophic status. This study uncovered diverse active viral auxiliary metabolism associated with photosynthesis, biochemical cycling, and DNA biosynthesis, and highlighted the significant role of phycosphere-associated viruses during cyanobacterial blooms.},
}
@article {pmid40882788,
year = {2026},
author = {Wu, J and Li, X and Huang, X and Zhu, Y and Yu, H and Xia, Y and Guo, S and Wang, X and Dong, T and Keung Tsim, KW and Zhu, Y},
title = {Kai-Xin-San, an ancient herbal mixture for anti-depression, mitigates the fluoxetine-induced gut dysbiosis and intestinal damage in chronic unpredictable mild stressed mice.},
journal = {Journal of ethnopharmacology},
volume = {354},
number = {},
pages = {120484},
doi = {10.1016/j.jep.2025.120484},
pmid = {40882788},
issn = {1872-7573},
mesh = {Animals ; *Fluoxetine/adverse effects/toxicity ; *Dysbiosis/chemically induced/drug therapy ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Male ; Mice ; *Stress, Psychological/drug therapy ; *Depression/drug therapy/microbiology ; *Antidepressive Agents/pharmacology ; Intestines/drug effects/pathology ; Behavior, Animal/drug effects ; Disease Models, Animal ; },
abstract = {The gut microbiome plays a crucial role in the pathology of depression. The intestinal dysbiosis associated with prolonged use of antidepressants, such as fluoxetine, can adversely affect the efficacy of these medications. Kai-Xin-San (KXS), a traditional Chinese herbal decoction, has been utilized to treat mental disorders with a long history in China. The modulation of the gut microbiome by KXS could underlie its antidepressant effect. In the context of combining with fluoxetine, KXS could potentially mitigate fluoxetine-associated intestinal side effects during depression treatment.<br><br>AIM OF THE STUDY: This study investigates the impact of KXS on the gut of depressive mice, with a particular emphasis on its potential to mitigate fluoxetine-induced intestinal side effects.<br><br>MATERIALS AND METHODS: A high dose of fluoxetine was applied to the chronic unpredictable mild stress (CUMS)-induced mice, alone or in combination with KXS. Behavior tests were conducted to confirm the anti-depressant efficiencies. The feces of mice were collected and subjected to 16S rDNA and metagenomic sequencing. The gastrointestinal morphology and functions were assessed. The potential mechanistic action of KXS on alleviating the intestinal dysbiosis was probed.<br><br>RESULTS: Notable imbalance of microbiome and disruption of intestinal barrier were observed in CUMS mice. The intake of fluoxetine exacerbated the dysbiosis, as evidenced by the increased ratio of Firmicutes/Bacteroidetes and the elevated abundance of antibiotic-resistant genes in the gut microbiome. In addition, fluoxetine treatment further compromised the intestinal integrity and functions. Significantly, KXS treatment effectively mitigated the impairment of intestinal barrier induced by fluoxetine. These protective effects appeared to be mediated through multiple mechanisms, including the restoration of microbial homeostasis and the direct cytoprotective action on intestinal epithelial cells.<br><br>CONCLUSIONS: These findings particularly provide support for the combined usage of KXS and fluoxetine in depression treatment.},
}
@article {pmid40878918,
year = {2025},
author = {Liu, X and Xie, Y and Yang, S and Jiang, C and Shang, K and Luo, J and Zhang, L and Hu, G and Liu, Q and Yue, B and Fan, Z and He, Z and Li, J},
title = {Multi-omics investigation of spontaneous T2DM macaque emphasizes gut microbiota could up-regulate the absorption of excess palmitic acid in the T2DM progression.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {40878918},
issn = {2050-084X},
support = {2021YJ0136//Science and Technology Foundation of Sichuan Province/ ; 32171607//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/microbiology/pathology/metabolism ; *Palmitic Acid/metabolism ; Macaca mulatta ; Mice ; Disease Models, Animal ; Male ; Gene Expression Profiling ; Metabolome ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; Multiomics ; },
abstract = {Although gut microbiota and lipid metabolites have been suggested to be closely associated with type 2 diabetes mellitus (T2DM), the interactions between gut microbiota, lipid metabolites, and the host in T2DM development remains unclear. Rhesus macaques may be the best animal model to investigate these relationships given their spontaneous development of T2DM. We identified eight spontaneous T2DM macaques and conducted a comprehensive study investigating the relationships using multi-omics sequencing technology. Our results from 16 S rRNA, metagenome, metabolome, and transcriptome analyses identified that gut microbiota imbalance, tryptophan metabolism and fatty acid β oxidation disorders, long-chain fatty acid (LCFA) accumulation, and inflammation occurred in T2DM macaques. We verified the accumulation of palmitic acid (PA) and activation of inflammation in T2DM macaques. Importantly, mice transplanted with spontaneous T2DM macaque fecal microbiota and fed a high PA diet developed prediabetes within 120 days. We determined that gut microbiota mediated the absorption of excess PA in the ileum, resulting in the accumulation of PA in the serum, consequently leading to T2DM in mice. In particular, we demonstrated that the specific microbiota composition was probably involved in the process. This study provides new insight into interactions between microbiota and metabolites and confirms causative effect of gut microbiota on T2DM development.},
}
@article {pmid40872157,
year = {2025},
author = {Nityagovsky, NN and Ananev, AA and Suprun, AR and Dneprovskaya, AA and Kiselev, KV and Aleynova, OA},
title = {Endophytic Bacterial and Fungal Communities of Spruce Picea jezoensis in the Russian Far East.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {16},
pages = {},
pmid = {40872157},
issn = {2223-7747},
support = {22-74-10001//Russian Science Foundation/ ; 124012200181-4//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {A wide range of microorganisms, including endophytes, frequently interact with forest trees. The role of endophytes in industrial conifers has not been fully investigated. The Yezo spruce Picea jezoensis is widely used for logging in Russia and Japan. In this work, the endophytic communities of bacteria and fungi in healthy needles, branches, and fresh wood of P. jezoensis from Primorsky Territory were analyzed using metagenomic analysis. The results indicate that the diversity of endophytic communities in P. jezoensis is predominantly influenced by the specific tree parts (for both bacteria and fungi) and by different tree specimens (for fungi). The most abundant bacterial classes were Alphaproteobacteria, Gammaproteobacteria and Actinobacteria. Functional analysis of KEGG orthologs (KOs) in endophytic bacterial community using PICRUSt2 and the PLaBAse PGPT ontology revealed that 59.5% of the 8653 KOs were associated with plant growth-promoting traits (PGPTs), mainly, colonization, stress protection, bio-fertilization, bio-remediation, vitamin production, and competition. Metagenomic analysis identified a high abundance of the genera Pseudomonas and Methylobacterium-Methylorubrum in P. jezoensis, which are known for their potential growth-promoting activity in other coniferous species. The dominant fungal classes in P. jezoensis were Dothideomycetes, Sordariomycetes, and Eurotiomycetes. Notably, the genus Penicillium showed a pronounced increase in relative abundance within the fresh wood and needles of Yezo spruce, while Aspergillus displayed elevated abundance specifically in the fresh wood. It is known that some of these fungi exhibit antagonistic activity against phytopathogenic fungi. Thus, our study describes endophytic communities of the Yezo spruce and provides a basis for the production of biologicals with potential applications in forestry and agriculture.},
}
@article {pmid40884577,
year = {2025},
author = {Kumar, V and Sandil, S and Verma, P and Ameen, F},
title = {Decoding microbial ecology and functions: metagenomic profiling of activated sludge contaminated with chlorolignin compounds in a pulp-paper mill treatment system.},
journal = {Archives of microbiology},
volume = {207},
number = {10},
pages = {247},
pmid = {40884577},
issn = {1432-072X},
support = {ORF-2025-364//The authors extend their appreciation to the ongoing research funding program, (ORF-2025-364), King Saud University, Riyadh, Saudi Arabia./ ; },
mesh = {*Sewage/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Metagenomics ; *Water Pollutants, Chemical/analysis ; Microbiota ; Metals, Heavy/analysis ; Industrial Waste/analysis ; },
abstract = {This study aimed to profile the dynamics of indigenous bacterial communities in activated sludge, assess the pollutant load, and unlock the functional genes involved during the activated sludge treatment process. The physicochemical analyses of activated sludge revealed high amounts of phosphate, sulfate, chloride, and lignin, along with heavy metals like Fe, Zn, Cu, Ni, and Pb. Simultaneously, the GC-MS/MS technique identified decane, 1 bromo-2-methyl, pentadecanoic acid, methyl ester, benzene dicarboxylic acid, stigmasterol, borinic acid, diethyl, 2-hydroxymethyl cyclopropane, 2-methoxy-4-ethyl-phenol, 3,4,5-trichlorophenol, octadecanoic acid, and tetracosanic acid as major compounds. Furthermore, taxonomic classification of operational taxonomic unit (OTU) data revealed that Proteobacteria was the most abundant phylum, comprising 44.54% of the microbial community. In addition, other phyla, such as Bacteriodetes, Acidobacteria, Planctomycetes, Chlorolfexi, Actinobacteria, and Verrucomicrobia were also recorded within a range between 13.27 and 4.1% in the sludge. At the genus and species levels, the dominant organisms were unclassified (3.62%) and belonged to the family Rhodospirillacea. Further, PICRUSt2-based KEGG Orthology (KO) analysis showed enriched energy metabolism as the most abundant category, driven by oxidative phosphorylation and the TCA cycle. Furthermore, the MetaCyc analysis revealed a robust and adaptable microbial community with the dominant pathways of aerobic respiration I (cytochrome c) and fatty acid biosynthesis pathways, such as cis-vaccenate biosynthesis. The EC assignments highlighted a broad range of enzymatic functions, with a strong emphasis on oxidoreductases and transferases involved in energy production and biosynthesis. This research offers valuable insights into microbial community dynamics in wastewater treatment processes and identifies their functional role in a chlorolignin waste-polluted environment.},
}
@article {pmid40883892,
year = {2025},
author = {Kanaan, G and Deming, JW},
title = {Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40883892},
issn = {1751-7370},
support = {//Benjamin Hall Conservation Genetics/ ; 325405//Research Council of Norway BREATHE project/ ; },
mesh = {*DNA Methylation ; *Bacteria/genetics/classification ; *Ice Cover/microbiology/virology ; *Microbiota ; Metagenome ; Arctic Regions ; *Viruses/genetics ; DNA, Viral/genetics ; DNA, Bacterial/genetics ; Seawater/microbiology ; Epigenesis, Genetic ; },
abstract = {Despite growing evidence for the role of DNA methylation in bacterial acclimation to environmental stress, this epigenetic mechanism remains unexplored in sea-ice microbial communities known to tolerate multiple stressors. This study presents a first analysis of DNA methylation patterns in bacterial communities and associated viruses across the vertical thickness of sea-ice. Using a novel stepped-sackhole method, we collected sea-ice brines from distinct horizons of an Arctic ice floe, capturing microbial communities that had been exposed to different environmental conditions. Through Oxford Nanopore sequencing, we characterized methylation patterns in bacterial and associated viral DNA, analysing for methylation motifs and differences between ice horizons. We identified 22 unique bacterial methylation motifs and 27 viral motifs across three nucleotide methylation types (5mC, 6 mA, and 4mC), with evidence of differential methylation between upper and lower ice. Analysis of metagenome-assembled genomes revealed the regulatory potential of methylation in both ice-adapted (Psychromonas and Polaribacter) and nonadapted bacteria (Pelagibacter); e.g. in Pelagibacter, differential methylation of the GANTC motif between upper and lower ice affected genes involved in core cellular processes. Viral methylation patterns showed evidence of recent infection. We also identified orphan methyltransferases in sea-ice phages, suggesting a mechanism for bypassing host restriction-modification systems and regulating host genes. Our findings reveal that DNA methylation serves functions in sea-ice beyond traditional restriction-modification systems that protect against foreign DNA, opening new avenues for research on the role of epigenetic mechanisms not only in acclimation to the cryosphere but also more generally in microbial ecology and evolution.},
}
@article {pmid40883605,
year = {2025},
author = {Yi, H and Lu, X and Chang, Q},
title = {MetaKSSD: boosting the scalability of the reference taxonomic marker database and the performance of metagenomic profiling using sketch operations.},
journal = {Nature computational science},
volume = {5},
number = {10},
pages = {884-897},
pmid = {40883605},
issn = {2662-8457},
mesh = {*Metagenomics/methods ; *Databases, Genetic ; Humans ; Microbiota/genetics ; Metagenome ; Software ; Computational Biology/methods ; Cluster Analysis ; },
abstract = {The performance of metagenomic profiling is constrained by the diversity of taxa present in the reference taxonomic marker database (MarkerDB) used. However, continually updating MarkerDB to include newly determined taxa using existing approaches faces increasing difficulties and will soon become impractical. Here we introduce MetaKSSD, which redefines MarkerDB construction and metagenomic profiling using sketch operations, enhancing MarkerDB scalability and profiling performance. MetaKSSD encompasses 85,202 species in its MarkerDB using just 0.17 GB of storage and profiles 10 GB of data within seconds. Leveraging its comprehensive MarkerDB, MetaKSSD substantially improves profiling results. In a microbiome-phenotype association study, MetaKSSD identified more effective associations than MetaPhlAn4. We profiled 382,016 metagenomic runs using MetaKSSD, conducted extensive sample clustering analyses and suggested potential yet-to-be-discovered niches. MetaKSSD offers functionality for instantaneous searching of similar profiles. It enables the swift transmission of metagenome sketches over the network and real-time online metagenomic analysis, facilitating use by non-expert users.},
}
@article {pmid40882565,
year = {2025},
author = {Cheng, S and Hu, Y and Gu, X and Xu, X and Duan, X and Li, X and Liu, Z and Jian, Q and Oleskowicz-Popiel, P and Shen, P and Zhou, A and Xue, G and Makinia, J},
title = {Magnetite-enhanced chain elongation via endogenous electron donors through a novel fungi-bacteria microbiome.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124478},
doi = {10.1016/j.watres.2025.124478},
pmid = {40882565},
issn = {1879-2448},
mesh = {*Microbiota ; Bacteria/metabolism ; *Ferrosoferric Oxide ; Fungi/metabolism ; Fermentation ; Fatty Acids/metabolism ; },
abstract = {Anaerobic fermentation of organic waste stream into medium-chain fatty acids (MCFA) through chain elongation (CE) has emerged as a sustainable and eco-friendly approach for resource recovery. Co-culture of yeast with chain elongator achieved a promising endogenous electron donor (ED)-driven CE but was limited by the weak yeast-bacteria synergy. This study presents a novel approach to optimizing the CE process through the regulation of magnetite (0-15 g/L). Results indicated that the 5 g/L of magnetite (Mag-5) achieved MCFA production at 8.42±0.67 g COD/L, which was 2.01 times greater than the blank. In-situ ethanol and lactate served as the ED to drive the CE. Under the optimal condition (Mag-5), Streptococcus (55.83%) and Candida (57.52%) were the dominant ED-producing microorganisms, and Clostridium_sensu_stricto_12 (22.70%) was the dominant chain elongator. In addition, metagenome analysis demonstrated the enhancement in reverse β-oxidization for MCFA production. Furthermore, the truncated tricarboxylic acid cycle was enhanced by magnetite amendment to provide more reduced energy, potentially accelerating the electron transfer within the mixed fungi-bacteria consortia. Finally, the constructed network of fungi and bacteria discerned the substrate competition between yeast and bacteria, and the cooperation among chain elongators, yeast, and mold. This study first proposed to regulate the mixed fungi-bacteria microbiome with magnetite to enhance the in-situ ED-driven CE process, providing a viable approach to the bioconversion of organic streams into high-value products.},
}
@article {pmid40882554,
year = {2025},
author = {Balamurugan, J and Jagadeesan, H and Vijayakumar, M},
title = {A metagenomic approach to predict the role of microbiome in a plant-microbe system for degrading the model azo dye methyl red.},
journal = {Journal of contaminant hydrology},
volume = {275},
number = {},
pages = {104703},
doi = {10.1016/j.jconhyd.2025.104703},
pmid = {40882554},
issn = {1873-6009},
mesh = {*Azo Compounds/metabolism ; Biodegradation, Environmental ; *Microbiota ; Metagenomics ; *Plants/microbiology/metabolism ; *Coloring Agents/metabolism ; *Water Pollutants, Chemical/metabolism ; Bacteria/metabolism/genetics ; },
abstract = {Azo dye contamination poses significant environmental challenges due to its persistence and toxicity. Plant-microbe integrated systems offer a sustainable solution for dye bioremediation, yet the functional roles of microbial communities and their interactions within community and with host plants during bioremediation remain underexplored. This study presents an integrated, multi omics approach to dissect the microbial diversity, functional potential, and plant-microbe interactions within a plant-microbe integrated bioremediation system for model azo dye, methyl red degradation. The microbial diversity of various organisms enriched under different treatment conditions for effective azo dye treatment was explored. A read-based approach using HUMAnN 3 pipeline was adopted to extract metabolic information from the shotgun metagenomic reads. Diversity analysis showed the enrichment of microorganisms capable of growing in the presence of the pollutant methyl red in an oligotrophic condition. The metabolic potential of the enriched organisms in dye removal was studied. Based on the enzymatic abundance, a pathway for the degradation of methyl red is proposed. Endophytic bacteria such as Klebsiella pneumoniae and Klebsiella varicola were responsible for encoding major dye-degrading enzymes in plant-integrated systems. In the plant-microbe integrated system both endophytic and intestinal microorganisms such as Kluyvera intestini and Escherichia coli are among the top 5 contributors of genes encoding downstream aromatic compound degradation enzymes. Notably Enterococcus casseliflavus showed highest enzyme abundance for azobenzene reductase in plant -microbe integrated strategy with 11.5-fold greater abundance than the treatment system containing only microbial inoculum. Metabolomics data from root exudates experiment revealed the role of root exudates in selective recruitment of microbial community. The role of biofilm and quorum sensing pathways in enhancing the bioremediation potential of the microbiome and the potential microbe-microbe and plant-microbe interaction was analysed. Deciphering the metabolic contribution of each microorganism and the microbiome as a whole is crucial to design engineered bioremediation systems. ENVIRONMENTAL IMPLICATIONS: Understanding the potential of microorganisms, their enrichments, and survival will help in designing specific consortia for effective degradation of pollutants. Metagenomic analysis reveal that the functional complementation in the microbiome is responsible for the pollutant degradation and the presence of plants through the root exudates, provide the nutrients lacking in the oligotrophic conditions observed in many waste streams, thereby enriching suitable microorganisms. This metagenomic study along with the metabolomics component, provides the justification for the efficiency of the plant microbe treatment of model dye methyl red and this could be exploited in real time situations.},
}
@article {pmid40882374,
year = {2025},
author = {Chen, Y and Zhang, Y and Li, J and Li, Y and Chen, Z and Qin, J and Deng, Z and Wang, X},
title = {Fe(Ⅱ)-mediated detoxification mitigates low-dose rare earth elements-induced stress on anammox consortia for mining tailwater treatment.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139681},
doi = {10.1016/j.jhazmat.2025.139681},
pmid = {40882374},
issn = {1873-3336},
mesh = {Mining ; *Metals, Rare Earth/toxicity ; *Water Pollutants, Chemical/toxicity/metabolism ; Bioreactors ; *Microbial Consortia/drug effects ; Wastewater ; *Ferrous Compounds/chemistry ; Biodegradation, Environmental ; Waste Disposal, Fluid/methods ; Oxidation-Reduction ; Water Purification/methods ; *Iron ; },
abstract = {Rare earth mining activities cause severe nitrogen pollution in watersheds, yet the residual hazardous rare earth elements (REEs) toxicity in tailings wastewater challenges biological nitrogen removal technology. This work demonstrated that introducing low-dose Fe(II) into partial denitrification/anammox (PD/A) system significantly alleviated REEs-induced stress on anammox consortia via detoxification and physical barrier reinforcement. The PD/A bioreactor with 15 mg/L Fe(II) (R1) was compared against a control without Fe(II) for real rare earth tailings wastewater treatment. Metagenomic analysis identified 1.14-fold upregulation of hydrazine (N2H4) dehydrogenase alongside substantial 5.82-fold downregulation of N2H4 synthase in R1, indicating a critical metabolic reconfiguration that expedited the degradation of toxic intermediates and alleviated REEs-mediated cytotoxicity. Electrons with lower redox potential released from N2H4 oxidation were more effectively utilized for carbon fixation, as evidenced by the upregulated electron transport complexes and Wood-Ljungdahl pathway. Concurrent biosynthetic modulation stimulated lipopolysaccharide production (module M00063) and carbohydrate storage (module M00064), collectively reinforcing microbial stress resilience through both defensive metabolites (lipopolysaccharides and trehalose) and hydrophobicity-driven aggregation. Moreover, modified 2-P logistic modeling confirmed elevated REEs inhibition thresholds under Fe(II) mediation. This study reveals the defense mechanism of Fe(II)-enhanced anammox consortia against REEs stress, providing new insights for sustainable bioremediation in rare earth mining areas.},
}
@article {pmid40877975,
year = {2025},
author = {Xu, L and Jiao, JY and Ling, C and Du, RB and Wu, Q and Xu, Y and Li, WJ},
title = {Mobilome-mediated transcriptional activation of biosynthetic gene clusters and its impact on strain competitiveness in food fermentation microbiomes.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {191},
pmid = {40877975},
issn = {2049-2618},
support = {32172175//National Natural Science Foundation of China/ ; No. 111-2-06//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
mesh = {Fermentation ; *Microbiota/genetics ; *Multigene Family ; Metagenome ; *Bacteria/genetics/classification/metabolism ; *Transcriptional Activation ; Gene Transfer, Horizontal ; Metagenomics/methods ; *Interspersed Repetitive Sequences ; *Food Microbiology ; Bacillota/genetics ; *Fermented Foods/microbiology ; Microbial Interactions/genetics ; },
abstract = {BACKGROUND: Microbial interactions are critical for maintaining the stability of food fermentation microbiomes, and mobile genetic elements (MGEs) significantly influence these interactions by horizontal gene transfer events. Although MGEs are known to facilitate horizontal gene transfer, their distribution among microorganisms and specific effects on microbial interactions remain poorly understood.<br><br>RESULTS: We analyzed 590 metagenomic and 42 metatranscriptomic samples from food fermentations, recovering 1133 metagenome-assembled genomes (MAGs). Our analysis revealed that MGEs were widely distributed in food fermentation microbiomes, with higher occurrence rates in Firmicutes (Bacillota: 0.71&#x2009;~&#x2009;11.85%) and Proteobacteria (Pseudomonadota: 0.47&#x2009;~&#x2009;11.05%). MGEs tended to be located adjacent to functional genes, particularly biosynthetic gene clusters (BGCs), with co-occurrence rates ranging from 9.41 to 23.99%. Furthermore, the transcriptional activity of BGCs was significantly correlated with the number of MGEs that were co-located with BGCs, which might enhance the competitiveness of strains. Variability in the diversity of MGEs that were co-located with BGCs was also evident at the strain level. Using Lactiplantibacillus plantarum as a case, we revealed that the strain-level differences in MGEs that were co-located with BGCs are positively correlated with the transcription of BGCs and competitiveness of strains within the species.<br><br>CONCLUSIONS: This study highlighted the role of MGEs in enhancing transcription of BGCs and facilitating strain competitiveness, providing new insights into how MGEs enhance the adaptability of microbial communities. Video Abstract.},
}
@article {pmid40877311,
year = {2025},
author = {Wilson, BC and Zuppi, M and Derraik, JGB and Albert, BB and Tweedie-Cullen, RY and Leong, KSW and Beck, KL and Vatanen, T and O'Sullivan, JM and Cutfield, WS and , },
title = {Long-term health outcomes in adolescents with obesity treated with faecal microbiota transplantation: 4-year follow-up.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7786},
pmid = {40877311},
issn = {2041-1723},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Adolescent ; Male ; Female ; Follow-Up Studies ; Double-Blind Method ; *Pediatric Obesity/therapy ; Treatment Outcome ; Body Composition ; Body Mass Index ; Gastrointestinal Microbiome ; *Obesity/therapy ; Metabolic Syndrome/therapy ; Feces/microbiology ; },
abstract = {Faecal microbiota transplantation (FMT) has been explored as a potential treatment for obesity, but its long-term effects on metabolic health remain unclear. Here, we report 4-year follow-up findings from a double-blind, randomised, placebo-controlled trial assessing FMT in adolescents with obesity (ACTRN12615001351505, Australian New Zealand Clinical Trials Registry). This unblinded follow-up study evaluated 63% (55/87) of the original participants (27 FMT, 28 placebo). There was no difference in BMI between the two groups, after adjusting for sex, age, diet, and physical activity (-3.6 kg/m[2], p = 0.095). However, FMT recipients showed clinical improvements in body composition and metabolic health compared to the placebo group. Specifically, FMT recipients had smaller waist circumference (-10.0 cm, p = 0.026), total body fat (-4.8%, p = 0.024), metabolic syndrome severity score (-0.58, p = 0.003), and systemic inflammation (-68% hs-CRP, p = 0.002) and higher levels of HDL cholesterol (0.16 mmol/L, p = 0.037). No group differences were observed in glucose markers, or other lipid parameters. Shotgun metagenomic sequencing revealed sustained long-term alterations in gut microbiome richness, composition and functional capacity, with persistence of donor-derived bacterial and bacteriophage strains. These findings highlight the potential relevance of FMT as a microbiome-augmenting intervention for obesity management and metabolic health, warranting further investigation.},
}
@article {pmid40872269,
year = {2025},
author = {Britto Martins de Oliveira, J and Barbieri, M and Corrêa-Junior, D and Schmitt, M and Santos, LLR and Bahia, AC and Parente, CET and Frases, S},
title = {Urban Mangroves Under Threat: Metagenomic Analysis Reveals a Surge in Human and Plant Pathogenic Fungi.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
pmid = {40872269},
issn = {2076-0817},
support = {CNE//FAPERJ/ ; 001//CAPES/ ; BP//CNPQ/ ; },
mesh = {*Metagenomics/methods ; *Fungi/genetics/classification/isolation &amp; purification ; Humans ; *Wetlands ; Ecosystem ; Biodiversity ; Mycobiome ; Geologic Sediments/microbiology ; },
abstract = {Coastal ecosystems are increasingly threatened by climate change and anthropogenic pressures, which can disrupt microbial communities and favor the emergence of pathogenic organisms. In this study, we applied metagenomic analysis to characterize fungal communities in sediment samples from an urban mangrove subjected to environmental stress. The results revealed a fungal community with reduced richness-28% lower than expected for similar ecosystems-likely linked to physicochemical changes such as heavy metal accumulation, acidic pH, and eutrophication, all typical of urbanized coastal areas. Notably, we detected an increase in potentially pathogenic genera, including Candida, Aspergillus, and Pseudoascochyta, alongside a decrease in key saprotrophic genera such as Fusarium and Thelebolus, indicating a shift in ecological function. The fungal assemblage was dominated by the phyla Ascomycota and Basidiomycota, and despite adverse conditions, symbiotic mycorrhizal fungi remained present, suggesting partial resilience. A considerable fraction of unclassified fungal taxa also points to underexplored microbial diversity with potential ecological or health significance. Importantly, this study does not aim to compare pristine and contaminated environments, but rather to provide a sanitary alert by identifying the presence and potential proliferation of pathogenic fungi in a degraded mangrove system. These findings highlight the sensitivity of mangrove fungal communities to environmental disturbance and reinforce the value of metagenomic approaches for monitoring ecosystem health. Incorporating fungal metagenomic surveillance into environmental management strategies is essential to better understand biodiversity loss, ecological resilience, and potential public health risks in degraded coastal environments.},
}
@article {pmid40869994,
year = {2025},
author = {Peña, N and Lafuente, I and Sevillano, E and Feito, J and Allendez, G and Muñoz-Atienza, E and Crispie, F and Cintas, LM and Cotter, PD and Hernández, PE and Borrero, J},
title = {Exploring the Functional Potential of the Broiler Gut Microbiome Using Shotgun Metagenomics.},
journal = {Genes},
volume = {16},
number = {8},
pages = {},
pmid = {40869994},
issn = {2073-4425},
support = {2018-T1/BIO-10158//Comunidad de Madrid/ ; 2022-5A/BIO-24232//Comunidad de Madrid/ ; PEJ-2020-AI/BIO-17758//Comunidad de Madrid/ ; PID2019-104808RAI00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
mesh = {Animals ; *Chickens/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Antimicrobial Peptides/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; Cecum/microbiology ; },
abstract = {Background/Objectives: Antimicrobial peptides (AMPs) have emerged as promising alternatives to conventional antibiotics in livestock, offering a sustainable strategy for controlling bacterial pathogens in food production systems. In addition to their direct antimicrobial effects, AMPs play a key role in modulating host-associated microbiomes, influencing both microbial composition and function. Advances in metagenomic sequencing and bioinformatic tools now enable comprehensive exploration of AMP diversity and activity within complex microbial ecosystems. Methods: In this study, we employed Illumina-based next-generation sequencing (NGS) to analyze intestinal contents from six gut sections of broiler chickens obtained from a Spanish slaughterhouse. Results: Through de novo assembly and bioinformatic annotation, we identified biosynthetic gene clusters (BGCs) encoding ribosomally synthesized and post-translationally modified peptides (RiPPs), other specialized bioactive secondary metabolites, antimicrobial resistance genes (ARGs), virulence factor genes (VFGs), and a diverse microbial community. Among all gut sections, the cecum exhibited the highest genetic richness, characterized by a high diversity of RiPP-like clusters and antimicrobial resistance determinants. Conclusions: These findings highlight the poultry gut, particularly the cecum, as a significant reservoir of antimicrobial peptides (AMPs) with potential implications in antibiotic-free poultry production and enhanced food safety.},
}
@article {pmid40869080,
year = {2025},
author = {Moiseenko, F and Kechin, A and Koryukov, M and Boyarskikh, U and Gabina, A and Oganesian, A and Belukhin, S and Makarkina, M and Elsakova, E and Artemeva, E and Myslik, A and Volkov, N and Bogdanov, A and Kuligina, E and Aleksakhina, S and Iyevleva, A and Ivantsov, A and Bogdanov, A and Sidorenko, S and Gostev, V and Komissarov, A and Dudurich, V and Danilov, L and Imyanitov, E and Moiseyenko, V},
title = {Interconnection of Gut Microbiome and Efficacy of Immune Checkpoint Inhibitors in Inoperable Non-Small-Cell Lung Cancer.},
journal = {International journal of molecular sciences},
volume = {26},
number = {16},
pages = {},
pmid = {40869080},
issn = {1422-0067},
support = {125041005115-5//Russian state-funded project for ICBFM SB RAS/ ; },
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy/microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Lung Neoplasms/drug therapy/microbiology/pathology ; Male ; Female ; Aged ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; Tumor Microenvironment/drug effects ; },
abstract = {The efficacy of immune checkpoint inhibitors (ICIs) in non-small-cell lung cancer (NSCLC) varies widely across patients. Growing evidence indicates that the gut microbiome, through its interaction with the tumor microenvironment, may influence the response to immunotherapy. To investigate this, we analyzed fecal and tumor samples from 63 patients with inoperable NSCLC undergoing ICI therapy. Based on microbiome profiling using 16S rRNA sequencing, patients were grouped according to treatment benefit, defined as progression-free survival (PFS) of six months or longer. Associations between α-diversity indices, microbial composition at the genus and phylum levels, and a composite Sum Index of Binary Abundance (SIBA) were examined in relation to clinical outcomes. Higher microbial α-diversity was linked to improved response to ICIs (p-value = 0.0078 for the Chao1 index). Multiple specific taxa, such as Ruminococcus gauvreauii (p-value = 2 × 10[-4]), Ruminiclostridium 9 (p-value = 8 × 10[-4]), and [Eubacterium] ventriosum (p-value = 9 × 10[-4]), were enriched in patients with favorable outcomes, whereas Oscillibacter and the Eubacterium hallii group were associated with disease progression (p-value = 2 × 10[-3] and 9 × 10[-3], respectively). The SIBA index, which reflects the absence of multiple beneficial bacterial taxa, proved to be a stronger predictor of treatment response than individual taxa alone. Median SIBA values were 18 vs. 24 in patients benefiting from IO therapy compared to non-responders (p-value = 9 × 10[-7]). These findings suggest that gut microbiome diversity and composition are closely tied to immunotherapy outcomes in NSCLC. Composite microbial metrics like SIBA may enhance predictive accuracy and inform personalized treatment approaches.},
}
@article {pmid40882272,
year = {2025},
author = {Wang, K and Xu, J and Luo, X and Yu, Z and Tang, A and Peng, K and Song, J and Chen, X and Ren, M},
title = {Insights into microalgal-bacterial consortia in sustaining denitrification via algal-derived organic matter in harsh low-C/N wastewater.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127108},
doi = {10.1016/j.jenvman.2025.127108},
pmid = {40882272},
issn = {1095-8630},
mesh = {*Denitrification ; *Wastewater/chemistry ; *Microalgae/metabolism ; Carbon ; Nitrates ; Bacteria/metabolism ; Nitrogen ; Microbial Consortia ; },
abstract = {Conventional nitrate removal processes are often hampered by insufficient carbon sources for remediating low-C/N wastewater. Herein, a microalgal-bacterial (MB) consortia system was constructed to leverage algal-derived organic matter for sustaining denitrification. The system demonstrated superior nitrate removal performance when assisted by algal-derived organic matter, achieving a 168.62 ± 4.17 % enhancement in nitrate removal capacity compared to the sole bacterial system. Furthermore, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) analysis of algal-derived organic matter revealed that specific components facilitating nitrate elimination included unsaturated aliphatic compounds, aliphatic/peptide-like/amino sugars, lignin-like, and tannin-like substances. Notably, the consortia showed preferential utilization of unsaturated aliphatic (35.21 %) and aliphatic/amino sugars over aliphatic/peptide-like/amino acids (31.05 %) and aliphatic/peptide-like compounds (31.31 %) within the CHO, CHON, CHON2, and CHON3 classes, respectively. Metagenomic analysis identified notable disparities in microbial community composition between the bacterial and MB consortia systems. Moreover, the MB consortia exhibited higher abundances of genes encoding nitrate removal enzymes, including those involved in denitrification, assimilatory/dissimilatory reduction, and L-glutamate synthesis pathways. Genes associated with lignin degradation were also detected, suggesting potential indirect contributions to nitrate elimination. Besides, the MB symbiotic microspheres were successfully fabricated and achieved efficient nitrate removal. These findings provide novel insights into the development of innovative MB symbiotic systems for nitrate removal under harsh carbon-limited conditions.},
}
@article {pmid40882267,
year = {2025},
author = {Davis, BC and Linz, D and McMinn, BR and Korajkic, A},
title = {Limited ARG removal but stable resistome dynamics in a surface flow constructed wetland.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126986},
doi = {10.1016/j.jenvman.2025.126986},
pmid = {40882267},
issn = {1095-8630},
mesh = {*Wetlands ; Wastewater/microbiology ; Bacteria/genetics ; Microbiota ; Anti-Bacterial Agents ; },
abstract = {Improperly treated wastewater and surface runoff can degrade water quality by introducing microbial contaminants, including antibiotic-resistant bacteria (ARB) and their genes (ARGs). Constructed treatment wetlands (CTWs) offer a low-resource solution for managing impaired watersheds. However, their ability to mitigate microbial contaminants, particularly ARGs, requires further study. In this study, 62 water samples from Banklick Creek CTW (BCTW) were shotgun sequenced to assess ARG dynamics and removal characteristics. Results showed minimal resistome attenuation, likely due to the wetland's horizontal surface flow design with short, variable hydraulic residence times (0.48-3.1 days). Despite this, 198 low-abundance ARGs were removed, accounting for a median of 0.52 % (0-3.1 %) of total ARG abundance upstream. The core resistome, comprising 95.6 ± 1.9 % of total ARG abundance, was stable and mainly consisted of multidrug efflux systems carried by bacterioplankton and macrophyte symbionts, indicating a native resistome reflective of regional pollution history. Resistome and microbiome structures were highly correlated (R[2] = 0.808), with ARGs rarely co-occurring with mobile genetic elements, indicating limited intercellular transfer potential. No significant correlations were found between resistome dynamics and human fecal (HF183, crAssphage) or avian (GFD) biomarkers. Although several class-one integron-integrase (intI1) contigs were enriched in treatment channels, gene cassette cargo was void of ARGs. As detection of intI1 via qPCR is generally considered indicative of resistome mobility potential, this finding carries important implication for intI1 qPCR assay selection (i.e., targeting clinical intI1 mosaics) and over-interpretation of ARG spread in the environment.},
}
@article {pmid40880127,
year = {2025},
author = {Milnitsky, BP and Junior, HLP and Chaúque, BJM and Corção, G},
title = {Successful establishment of a model of the piglet gastrointestinal microbiota and its' modulation by prebiotics.},
journal = {Journal of applied microbiology},
volume = {136},
number = {9},
pages = {},
doi = {10.1093/jambio/lxaf216},
pmid = {40880127},
issn = {1365-2672},
support = {//National Council for Scientific and Technological Development/ ; //Universidade Federal do Rio Grande do Sul/ ; },
mesh = {Animals ; *Prebiotics ; Swine/microbiology ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology ; *Bacteria/drug effects/classification/isolation &amp; purification/genetics ; Microbial Sensitivity Tests ; Butyric Acid/pharmacology ; Anti-Bacterial Agents/pharmacology ; Oligosaccharides/pharmacology ; *Gastrointestinal Tract/microbiology ; },
abstract = {AIMS: This study proposed an in-house in vitro model to investigate the effects of two prebiotic treatments on the gastrointestinal microbiota of piglets.<br><br>METHODS AND RESULTS: The model involved suspending piglet feces in a culture medium to simulate the ileum and proximal colon regions of the swine gastrointestinal tract. The prebiotics tested were mannanoligosaccharides (MOS) and sodium butyrate. Metabarcoding and culturomics were used to assess the impact of prebiotics on bacterial species composition. Minimum inhibitory concentration tests were conducted to examine bacterial susceptibility patterns. Key bacterial phyla identified included firmicutes, proteobacteria, bacteroidetes, and actinobacteria. Culturomics detected families and several species not identified by metabarcoding. In the simulated proximal colon, MOS increased the abundance of certain species and reduced bacteria with type I fimbriae. Butyric acid promoted beneficial host-associated bacteria and decreased pathogenic species. However, the prebiotics did not significantly affect bacterial susceptibility to antibiotics.<br><br>CONCLUSION: The in-house model successfully mimicked piglet intestinal microbiota, allowing for detailed analysis. Both prebiotics positively influenced the piglets microbiota, providing insights into how these treatments potentially influenced the microbiota.},
}
@article {pmid40880079,
year = {2025},
author = {Tang, Y and Oliver, A and Alkan, Z and Korf, I and Huang, L and Kable, ME and Lemay, DG},
title = {Association of lactose intake and lactase persistence genotype with microbial taxa and function in healthy multi-ethnic U.S. adults.},
journal = {Food &amp; function},
volume = {16},
number = {18},
pages = {7393-7407},
doi = {10.1039/d5fo01640a},
pmid = {40880079},
issn = {2042-650X},
mesh = {Humans ; *Lactose/metabolism ; *Lactase/genetics/metabolism ; Male ; Female ; Adult ; Genotype ; Middle Aged ; Feces/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; United States ; Polymorphism, Single Nucleotide ; Yogurt ; Diet ; Lactose Intolerance/genetics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; },
abstract = {Lactase persistence is a genetically inherited trait that enables continued lactose digestion into adulthood. Lactase non-persistence (LNP) individuals often experience incomplete lactose digestion, allowing undigested lactose to reach the colon, where it may shape microbial composition and function. We investigated the relationship between the lactase persistence (LP) genotype, lactose consumption, and the taxonomic and functional profiles of the fecal microbiome. Participants from the USDA Nutritional Phenotyping Study, a cross-sectional observational study designed to assess how dietary factors impact human health, whose fecal microbiome profile was measured using shotgun metagenomic sequencing (n = 330) were included in this analysis. Fecal SCFA levels were measured using GC-MS. Fecal microbiome taxonomy and gene abundance were quantified using shotgun metagenomic sequencing. Lactose consumption and yogurt intake were estimated based on Automated Self-Administered 24h Dietary Assessment Tool (ASA24®) dietary recalls or Food Frequency Questionnaire. The LP/LNP genotype was determined by a single nucleotide polymorphism (SNP ID: rs4988235). Several genera of lactic acid bacteria (Veillonella, Lactobacillus, Lacticaseibacillus, and Lactococcus) were differentially abundant between recent high-lactose consuming (>10.0 g lactose per day) and low-lactose consuming (<3.3 g lactose per day) individuals. Among the LNP participants who self-identified as Caucasian or Hispanic, high-lactose consumers (>10.0 g per day via 24-h recall) had significantly higher relative abundances of lactic acid bacteria and lactate-utilizing bacteria (Lacticaseibacillus, Lactobacillus, Megamonas, and Veillonella) than low-lactose consumers (<3.3 g per day). Independent of lactose intake, LNP participants had a higher abundance of fecal microbial β-galactosidase genes than LP participants. Among the LNP participants, those with high recent lactose consumption also showed a significant shift towards more fecal propionate. The abundance of the yogurt-associated microbe, Streptococcus thermophilus, was positively associated with yogurt intake independent of the genotype. Alternative milk consumption was significantly negatively associated with fecal SCFAs both in the full cohort and the Caucasian/Hispanic subset, regardless of the genotype. Our results suggest that functional and persistent host lactase enzymes may work to competitively exclude lactic acid bacteria, contributing to a smaller realized niche for lactic acid bacteria in LP individuals compared to LNP individuals. However, regardless of the host genotype, consumption of alternative milk may be associated with reduced production of health-promoting intestinal metabolites, such as SCFAs.},
}
@article {pmid40879860,
year = {2025},
author = {Liu, Y and Wang, Q and Zhang, Y and Duo, R and Bian, X and Tian, J and Hao, J and Zheng, J and Shen, H},
title = {Multi-omics characterization of gut microbiota and fecal and plasma metabolites in patients with primary Sjögren's syndrome.},
journal = {Clinical rheumatology},
volume = {44},
number = {10},
pages = {4103-4118},
pmid = {40879860},
issn = {1434-9949},
support = {CY2021-QN-A10//the Cuiying Scientific and Technological Innovation Program of Lanzhou University Second Hospital/ ; 2022-ZD-101//Science and Technology Program of Lanzhou city/ ; GSWSKY2023-08//Health Industry Scientific Research Project of Gansu Province/ ; },
mesh = {Humans ; *Sjogren's Syndrome/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Female ; *Feces/microbiology/chemistry ; Middle Aged ; Male ; Adult ; Metabolomics ; *Metabolome ; Case-Control Studies ; Metagenomics ; Aged ; Multiomics ; },
abstract = {INTRODUCTION: Accumulating evidence has implicated gut microbiota and their metabolites in primary Sjögren's syndrome (pSS) pathogenesis. However, no study simultaneously explores the gut microbiome, microbial, and plasma metabolome in pSS patients.<br><br>METHOD: Thirty pSS patients and 60 healthy controls (HCs) were recruited. Shotgun metagenomic sequencing and untargeted metabolomics were performed on stool and plasma samples.<br><br>RESULTS: pSS patients exhibited significant reduction in microbial richness and diversity. Bacteroidetes and Firmicutes accounted for over 80% of all phyla. Four phyla, 48 genera, and 106 species with significant differences were identified (P&#x2009;<&#x2009;0.05). Proteobacteria, Ascomycota, Fusobacteria, and 31 genera (e.g., Escherichia, Veillonella, Prevotella, Klebsiella) were enriched in pSS, while Actinobacteria, Bifidobacterium, Dorea, and Blautia were depleted. Opportunistic pathogens (e.g., Escherichia coli, Prevotella copri, Streptococcus oralis, Klebsiella pneumoniae, Enterococcus faecalis) and pathogenic Clostridium bolteae and Fusobacterium nucleatum were more abundant in pSS, whereas beneficial Bifidobacterium longum and butyrate-producing Eubacterium hallii and Anaerostipes hadrus were in HCs. Notably, Lactobacillus spp. were enriched in pSS. Of 298 differential functional pathways, 239 pSS-enriched pathways were focused on nutrient and energy metabolism, while amino acid biosynthesis in HCs. During 881 differential fecal metabolites (pSS: HCs&#x2009;=&#x2009;631:250), fatty acyls were enriched in pSS, and glycerophospholipids in HCs. Among the 712 differential plasma metabolites (pSS: HCs&#x2009;=&#x2009;438:274), heterocyclic compounds and benzene derivatives were more abundant in pSS, while fatty acyls and glycerophospholipids prevailed in HCs. Amino acids and organic acids were predominant in both samples.<br><br>CONCLUSIONS: This study characterized gut microbiome and fecal/plasma metabolome in pSS patients, providing theoretical support for regional pSS prevention and treatment. Key Points &#x2022; This is the first study to systematically characterize the gut microbiome and fecal and plasma metabolomes of primary Sj&#xf6;gren's syndrome (pSS) patients in Northwest China via multi-omics integration analysis. &#x2022; Significant reduction in gut microbial diversity and probiotic bacteria, enrichment of opportunistic and infectious pathogens, and microbial dysfunction were observed in pSS patients. &#x2022; Much more differential fecal and plasma metabolites were observed in pSS patients, with amino acids, organic acids and derivatives, nucleotides, and metabolites being the main altered metabolites in both samples.},
}
@article {pmid40879288,
year = {2025},
author = {Hao, Y},
title = {Gut microbiota-immune axis in the regulation of rheumatoid arthritis: from mechanism to precision probiotic strategies.},
journal = {Modern rheumatology},
volume = {36},
number = {1},
pages = {1-14},
doi = {10.1093/mr/roaf081},
pmid = {40879288},
issn = {1439-7609},
mesh = {*Arthritis, Rheumatoid/immunology/microbiology/therapy ; *Gastrointestinal Microbiome/immunology ; *Probiotics/therapeutic use ; Humans ; Animals ; Dysbiosis/microbiology ; Intestinal Barrier Function/immunology ; Precision Medicine ; },
abstract = {Rheumatoid Arthritis (RA) is a progressive autoimmune disorder with substantial global health and economic impacts. Despite advancements in conventional therapies, biologics, and targeted drugs, challenges such as adverse effects, cost, and interindividual heterogeneity underscore the need for safer, precision-based treatments. Notably, emerging evidence highlights the pivotal role of the gut microbiota-immune axis in RA pathogenesis. Affected individuals typically exhibit gut dysbiosis, marked by increased pro-inflammatory taxa and reduced anti-inflammatory species, which disrupts immune homeostasis through Th17/Treg imbalance, molecular mimicry, and compromised gut barrier integrity. These processes drive systemic inflammation, exacerbating both articular destruction and extra-articular manifestations. Probiotics demonstrate therapeutic potential by modulating this axis via microbiota restoration, barrier reinforcement, and immune regulation. Strain-specific effects have been documented in both preclinical and clinical studies, although efficacy varies depending on host genetics, baseline microbiota composition, and intervention protocols-a variability underscoring the need for personalized probiotic selection. This review consolidates current knowledge on gut microbiota-immune crosstalk in RA and explores probiotics as precision therapeutics. Integrating multi-omics (metagenomics, metabolomics) with targeted probiotic strategies could enable the development of personalized interventions. While translational obstacles persist, including mechanistic complexity and limited clinical validation, the gut microbiota-immune axis offers a novel paradigm for RA management. Future priorities include large-scale trials, biomarker discovery, and combinatorial approaches to advancing microbiome-guided precision medicine in autoimmune diseases.},
}
@article {pmid40874749,
year = {2025},
author = {Gao, J and Han, W and Jiang, X and Xi, Y and Chen, Y and Huang, S and Huang, X and Zhang, Y and Zhang, T and Zhang, M and Zhang, W and Ni, B},
title = {Unexplored viral diversity in Siberian cranes and wild geese: metagenomic insights from a global wintering haven.},
journal = {mSystems},
volume = {10},
number = {9},
pages = {e0075625},
pmid = {40874749},
issn = {2379-5077},
support = {2023YFD1801302//National Key Research and Development Program of China/ ; 2024YFF1307203//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Geese/virology ; Metagenomics/methods ; *Birds/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Feces/virology ; China ; Biodiversity ; Seasons ; Animals, Wild/virology ; Phylogeny ; Animal Migration ; },
abstract = {Migratory birds are critical global carriers and vectors of various viruses, potentially driving the mutation and transmission of novel pathogens, especially zoonotic viruses. Despite advancements in sequencing technologies, the viral diversity in wintering Siberian cranes (Leucogeranus leucogeranus) and wild geese (Anser spp.) remains poorly understood. In this study, we conducted a viral metagenomic survey of fecal samples from 320 Siberian cranes and wild geese wintering in Poyang Lake, China. Through this approach, we identified 183 novel viruses associated with known and putative vertebrate-infecting viruses, including a novel coronavirus, parvoviruses, picornaviruses, picobirnaviruses, anelloviruses, and CRESS-DNA viruses. Furthermore, we detected evidence of cross-species transmission and identified viruses with zoonotic potential, such as picobirnaviruses and picornaviruses. These findings highlight the significant public health risks posed by migratory birds and provide new insights into the viral diversity within these populations, contributing to a better understanding of their role in viral evolution and transmission.IMPORTANCEUnderstanding the diversity of enteroviruses in Siberian cranes and geese is essential for biodiversity conservation and ecosystem stability. As migratory birds, these species play key roles in ecological networks while carrying intestinal viruses that may spread along migration routes, which could pose potential risks to wildlife, poultry, and human health. This study systematically analyzed enterovirus diversity and the genetic characteristics of novel viruses in wintering Siberian cranes and geese at Poyang Lake using metagenomic sequencing. We identified viral sequences distantly related to known viruses and those with potential cross-species transmission risks. These findings highlight the diversity of migratory bird viruses and their public health implications, providing data to evaluate transmission risks and monitor emerging threats, supporting strategies for wildlife conservation and disease prevention.},
}
@article {pmid40873785,
year = {2025},
author = {Bei, Q and Williams, NLR and Furtado, LE and Blasi, DD and Williams, J and Brotas, V and Tarran, G and Rees, AP and Bowler, C and Fuhrman, JA},
title = {Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf131},
pmid = {40873785},
issn = {2730-6151},
abstract = {High-throughput sequencing has provided unprecedented insights into microbial biodiversity in marine and other ecosystems. However, most sequencing-based studies report only relative (compositional) rather than absolute abundance, limiting their application in ecological modeling and biogeochemical analyses. Here, we present a metagenomic protocol incorporating genomic internal standards to quantify the absolute abundances of prokaryotes and eukaryotic phytoplankton, which together form the base of the marine food web, in unfractionated seawater. We applied this method to surface waters collected across 50°N to 40°S during the 29[th] Atlantic Meridional Transect. Using the single-copy recA gene, we estimated an average bacterial abundance of 1.0 × 10[9] haploid genome equivalents per liter. Leveraging a recent report that the psbO gene is typically single-copy in phytoplankton, we also quantified eukaryotic phytoplankton. Metagenomic estimates closely aligned with flow cytometry data for cyanobacteria (slope = 1.03, Pearson's r = 0.89) and eukaryotic phytoplankton (slope = 0.72, Pearson's r = 0.84). Compared to flow cytometry, taxonomic resolution for nano- and picoeukaryotes was greatly improved. Estimates for diatoms, dinoflagellates, and Trichodesmium were considerably higher than microscopy counts, likely reflecting microscopy undercounts and potential ploidy variation. These findings highlight the value of absolute quantification by metagenomics and offer a robust framework for quantitative assessments in microbial oceanography.},
}
@article {pmid40872213,
year = {2025},
author = {Raza, A and Ling, SJ and Wei, YL and Bahadur, S and Ren, MX},
title = {Facilitation in the Dry Season: Species Interactions Between a Limestone-Endemic Plant and Moss Altered by Precipitation Dynamics.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {16},
pages = {},
pmid = {40872213},
issn = {2223-7747},
support = {ZDYF2023RDYL01//Hainan Tropical Rainforest Conservation/ ; 42371054//National Natural Science Foundation of China/ ; },
abstract = {Plant-to-plant interactions are essential for structuring plant communities and supporting adaptation in nutrient-poor, seasonally dry environments. This study examined the interactions between moss Leucobryum aduncum Dozy &amp; Molk and Oreocharis hainanensis by analyzing microbial communities and physicochemical parameters across various sample types. These included soil [bare (B), O. hainanensis (O), moss (M), and moss + O. hainanensis (MO)], rhizosphere soil [O. hainanensis (ORS), moss (MRS), and moss + O. hainanensis (MORS)], and root [O. hainanensis (OHR), moss (MR), and moss + O. hainanensis (MOR)] using metagenomics sequencing across dry and wet seasons in limestone habitats on Hainan Island. During the dry season, combined plant samples MOR, MO, and MORS showed higher nutrients, supported by microbes that enhance nutrient turnover, which may indicate facilitation. Conversely, during the wet season, increased moisture leads to decreased nutrient levels and microbial communities shift, associated with slower nutrient turnover in combined plant samples, which may reflect competition. According to KEGG analysis, an increase in oxidative phosphorylation and ABC transporters in the dry season supported the facilitative interaction, while quorum sensing and two-component systems supported the competitive interaction in the wet season. These findings show how shifts between facilitation and competition arise from seasonal conditions and microbes in the limestone ecosystem.},
}
@article {pmid40865528,
year = {2025},
author = {Shi, Y and Li, Y and Li, H and Haerheng, A and Marcelino, VR and Lu, M and Lemey, P and Tang, J and Bi, Y and Pettersson, JH and Bohlin, J and Klaps, J and Wu, Z and Wan, W and Sun, B and Kang, M and Holmes, EC and He, N and Su, S},
title = {Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance.},
journal = {Cell},
volume = {188},
number = {23},
pages = {6591-6605.e14},
doi = {10.1016/j.cell.2025.08.016},
pmid = {40865528},
issn = {1097-4172},
mesh = {Animals ; *Mammals/microbiology/virology ; Humans ; *Public Health Surveillance ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Microbiota/genetics ; Animals, Wild/microbiology/virology ; Metagenomics ; Feces/microbiology/virology ; Animals, Domestic/microbiology/virology ; Viruses/genetics/isolation &amp; purification ; Phylogeny ; },
abstract = {Non-traditional farmed and wild mammals are often neglected in pathogen surveillance. Through metagenomic and metatranscriptomic sequencing of fecal and tissue samples from 973 asymptomatic mammals, we identified 128 viruses (30 novel), including a new coronavirus genus, 10,255 bacterial species (over 7,000 undescribed), 201 fungi, and 7 parasites. Farmed and wild mammals shared 13.3% of virus species, including canine coronavirus in Asiatic black bears and Getah virus in rabbits, while the 2.3.4.4b clade of H5N1 avian influenza virus was found in a wild leopard cat. We identified potential bacterial pathogen transmission between farmed and wild mammals and bacterial strains with high genetic similarity to those found in humans. We observed 157 clinically prioritized antibiotic resistance genes (ARGs) in mammalian microbiomes with greater than 99% identity to ARGs from human microbiomes, often co-occurring with mobile genetic elements. Overall, this work highlights cross-species risks at the human-animal interface.},
}
@article {pmid40865218,
year = {2025},
author = {Yang, H and Fu, H and Zhao, Y and Li, R and Cao, M and Liu, Y and Ni, Y and Song, W and Liang, Y and Cai, P and Chang, W and Tao, F and Wang, H and Liu, K},
title = {Antibiotic resistance genes in multi-matrices of Chaohu Lake: Spatiotemporal variation and correlation with pesticides and PPCPs.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139604},
doi = {10.1016/j.jhazmat.2025.139604},
pmid = {40865218},
issn = {1873-3336},
mesh = {*Lakes/microbiology/chemistry ; *Water Pollutants, Chemical/analysis ; *Pesticides/analysis ; *Drug Resistance, Microbial/genetics ; Environmental Monitoring ; *Genes, Bacterial ; Geologic Sediments/microbiology ; Animals ; Pharmaceutical Preparations/analysis ; Microbiota ; Spatio-Temporal Analysis ; Fishes ; China ; },
abstract = {This study explored the spatiotemporal distributions of microorganisms and antibiotic resistance genes (ARGs) in the surface water, sediments, and fish intestinal contents (IC) of Chaohu Lake, and further revealed the pharmaceuticals and personal care products (PPCPs), pesticides in lake water and their relationships with ARGs. 53 types of pesticides and 25 types of PPCPs were identified in the river-lake system basin, with the highest concentrations observed for tebuconazole (1142.36 ng/L) and amantadine (851.41 ng/L). Higher concentrations of these target contaminants were detected in the western part of the lake and during the wet season. No significant east-west differences in ARGs and microbiota across the three environmental matrices were found, whereas seasonal variations impacted lake water and IC more profoundly than sediments. Significant correlations between microbiota and ARGs in the lake water and IC, while those in sediments showed weaker associations. Co-occurrence network analysis showed, among three environmental media, β-lactam and multidrug-resistant genes were widespread found, and Proteobacteria were identified as a stable host. Non-antibiotic pollutants, such as amantadine and terbuthylazine, displayed significant positive correlations with ARGs, similar to sulfamethoxazole and clindamycin. Our findings highlight the important roles of seasonal hydrological changes and non-antibiotic pollutants in the dissemination of ARGs.},
}
@article {pmid40863630,
year = {2025},
author = {Hu, GA and Sun, HY and Yin, QJ and Wang, H and Liu, SY and Wang, BG and Wang, H and Li, X and Wei, B},
title = {Exploring the Biosynthetic Potential of Microorganisms from the South China Sea Cold Seep Using Culture-Dependent and Culture-Independent Approaches.},
journal = {Marine drugs},
volume = {23},
number = {8},
pages = {},
pmid = {40863630},
issn = {1660-3397},
support = {2022YFC2804700//National Key Research and Development Program/ ; 42276137//National Natural Science Foundation of China/ ; RF-A2022013//Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; },
mesh = {China ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Secondary Metabolism/genetics ; *Microbiota/genetics ; *Bacteria/genetics/metabolism ; *Seawater/microbiology ; Ecosystem ; Oceans and Seas ; },
abstract = {Cold seep ecosystems harbor unique microbial communities with potential for producing secondary metabolites. However, the metabolic potential of cold seep microorganisms in the South China Sea remains under-recognized. This study employed both culture-dependent and culture-independent approaches, including 16S rRNA amplicon sequencing and metagenomics, to investigate microbial communities and their potential for secondary metabolite production in the South China Sea cold seep. The results indicate microbial composition varied little between two non-reductive sediments but differed significantly from the reductive sediment, primarily due to Planctomycetes and Actinobacteria. Predicting the Secondary Metabolism Potential using Amplicon (PSMPA) predictions revealed 115 strains encoding more than 10 biosynthetic gene clusters (BGCs), with lower BGC abundance in reductive sediment. Culture-dependent studies showed Firmicutes as the dominant cultivable phylum, with strains from shallow samples encoding fewer BGCs. Metagenomic data confirmed distinct microbial compositions and BGC distributions across sediment types, with cold seep type having a stronger influence than geographic location. Certain BGCs showed strong correlations with sediment depth, reflecting microbial adaptation to nutrient-limited environments. This study provides a comprehensive analysis of the metabolic capabilities of South China Sea cold seep microorganisms and reveals key factors influencing their secondary metabolic potential, offering valuable insights for the efficient exploration of cold seep biological resources.},
}
@article {pmid40863548,
year = {2025},
author = {García-Muñoz, A and Pino-Bodas, R},
title = {Evaluating the Assembly Strategy of a Fungal Genome from Metagenomic Data: Solorina crocea (Peltigerales, Ascomycota) as a Case Study.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {8},
pages = {},
pmid = {40863548},
issn = {2309-608X},
support = {CNS2022-135904//Agencia Estatal de Investigaci&#xf3;n/ ; 2020-T1/AMB-19852//CAM Atracci&#xf3;n de Talento program/ ; },
abstract = {The advent of next-generation sequencing technologies has given rise to considerably diverse techniques. However, integrating data from these technologies to generate high-quality genomes remains challenging, particularly when starting from metagenomic data. To provide further insight into this process, the genome of the lichenized fungus Solorina crocea was sequenced using DNA extracted from the thallus, which contains the genome of the mycobiont, along with those of the photobionts (a green alga and a cyanobacterium), and other associated microorganisms. Three different strategies were assessed for the assembly of a de novo genome, employing data obtained from Illumina and PacBio HiFi technologies: (1) hybrid assembly based on metagenomic data; (2) assembly based on metagenomic long reads and scaffolded with filtered mycobiont long and short reads; (3) hybrid assembly based on filtered mycobiont short and long reads. Assemblies were compared according to contiguity and completeness criteria. Strategy 2 achieved the most continuous and complete genome, with a size of 55.5 Mb, an N50 of 148.5 kb, and 519 scaffolds. Genome annotation and functional prediction were performed, including identification of secondary metabolite biosynthetic gene clusters. Genome annotation predicted 6151 genes, revealing a high number of genes associated with transport, carbohydrate metabolism, and stress response.},
}
@article {pmid40863514,
year = {2025},
author = {Alcaíno, J and Veloso, C and Coche, M and Troncoso, D and Baeza, M},
title = {Fungi in the Chilean Altiplano: Analyses of Diversity and Yeasts with Applied Enzymatic Potential.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {8},
pages = {},
pmid = {40863514},
issn = {2309-608X},
support = {Fondecyt 1230427//Agencia Nacional de Investigacion y Desarrollo de Chile/ ; },
abstract = {Fungal communities in high plateau ecosystems remain understudied despite their crucial roles in soil ecosystems, and yeasts inhabiting extreme regions have potential for industrial and biotechnological applications. We studied the fungal diversity in soils across 14 Chilean Altiplano sites using amplicon-based metagenomics and isolation of yeasts to assess their growth under various conditions and hydrolytic enzyme secretion. Using the metagenomic approach, the Ascomycota and Basidiomycota phyla were found to be the most abundant (85% and 8%, respectively). Unclassified families and genera prevailed at six and ten sites, respectively. At the other sites, the most abundant families included Cladosporiaceae, Teratosphaeriaceae, and Sporormiaceae, and the genera Oleoguttula, Coniochaeta, and Peziza. Biodiversity indices did not correlate with the soil's geographic origin, organic matter content, humidity, or pH. Most isolated yeasts belong to the Naganishia, Holtermanniella, and Vishniacozyma genera, growing at temperatures ranging from 4 °C to 26 °C. Most isolates could use glucose, sucrose, and maltose as carbon sources and exhibited amylase, esterase, pectinase, and protease activities at 30 °C and below. Our results indicate that the evaluated soil physicochemical parameters do not explain the fungal distribution in the Altiplano and highlight the region as a reservoir of unknown fungi, including yeasts with industrially relevant enzymes.},
}
@article {pmid40859872,
year = {2025},
author = {Bunka, L and Rozenberga, M and Silamiķelis, I and Saksis, R and Birzniece, L and Megnis, K and Fedulovs, A and Pahirko, L and Zaļizko, P and Krustiņš, E and Kloviņš, J and Sokolovska, J and Elbere, I},
title = {Dual-approach analysis of gut microbiome in patients with type 1 diabetes and diabetic kidney disease.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2531254},
pmid = {40859872},
issn = {1365-2060},
mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology/complications ; *Diabetic Nephropathies/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Feces/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Middle Aged ; Disease Progression ; Metagenomics/methods ; Biopsy ; Young Adult ; Bacteroides/isolation &amp; purification/genetics ; },
abstract = {BACKGROUND: Type 1 diabetes (T1D) is a multifactorial autoimmune disease mediated by genetic, epigenetic, and environmental factors. Diabetic kidney disease (DKD) is a major complication of diabetes mellitus which affects 30-40% of T1D patients. Increasing evidence suggests the significant role of the microbiome in the progression of both T1D and DKD.<br><br>MATERIALS AND METHODS: Here we recruited 76 T1D patients and 22 healthy controls and combined data from sigmoid colon biopsy samples analysed with V3-V4 region amplification of 16S rRNA gene and shotgun metagenomics data obtained from faecal samples. Additionally, we compared T1D patients with and without progression of DKD.<br><br>RESULTS: We observed significant differences within both sample types at various taxonomic and functional levels. T1D patient microbiota detected using biopsy samples had a lower abundance of the Bacteroides genus when compared to healthy controls. Significantly, despite only a few taxonomic differences patients with and without DKD progression were vastly different at the functional pathway level within the faecal samples - we observed 2 and 61 enriched pathways in these groups. respectively, with several of these pathways linked to the mediation of renal function.<br><br>CONCLUSION: Altogether, we present novel data about microbial signatures relevant to T1D and DKD progression, which partly supports previous data and also presents possible tissue type or population-specific elements. DKD progression is characterized with significant differences within the functional level of the gut microbiome.},
}
@article {pmid40859318,
year = {2025},
author = {Lin, Z and Jiang, Y and Liu, H and Yang, J and Yang, B and Zhang, K and Tang, P and Xiang, B and Sun, B},
title = {Airway microbiota and immunity associated with chronic obstructive pulmonary disease severity.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {962},
pmid = {40859318},
issn = {1479-5876},
support = {GMUCR2024-02009//Major clinical research project of Guangzhou Medical University/ ; 2023B110008//Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases/ ; },
mesh = {*Pulmonary Disease, Chronic Obstructive/immunology/microbiology/pathology/genetics ; Humans ; *Microbiota ; *Severity of Illness Index ; Male ; Female ; Aged ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *Immunity ; Cohort Studies ; Biomarkers/metabolism ; Dysbiosis ; Reproducibility of Results ; *Respiratory System/microbiology ; Metagenomics ; Bacteria ; },
abstract = {BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is characterized by progressive airflow limitation and chronic inflammation. Although airway microbes and host immunity are known contributors, the molecular mechanisms underlying disease severity remain unclear. This study explores microbial dysbiosis and host immune responses across varying COPD severities.<br><br>METHODS: We conducted integrated metagenomic and transcriptomic analyses on bronchoalveolar lavage fluid from two cohorts: a discovery cohort and a validation cohort. We investigated microbial diversity, pathogenic bacterial enrichment, and host gene expression patterns. Functional metagenomics was used to assess antibiotic resistance genes. Host-microbe network analyses explored correlations between pathogens and immune-metabolic pathways. Diagnostic models utilizing microbial-immune biomarkers were developed, trained on a subset of the discovery cohort, tested on remaining discovery samples, and validated by quantitative polymerase chain reaction (qPCR) in the validation cohort to distinguish COPD from controls and stratify disease severity.<br><br>RESULTS: Severe COPD exhibited reduced microbial diversity and an increased presence of pathogenic bacteria, including Moraxella osloensis and Streptococcus species. These pathogens were associated with dysregulated inflammatory signaling, and significant neutrophil activity, evidenced by the formation of Neutrophil Extracellular Traps (NETs), and oxidative stress, which correlated with airway remodeling and a decline in lung function. Functional metagenomics showed a significant increase in antibiotic resistance genes in severe cases, linked to chronic treatment pressures. Host-microbe network analyses revealed strong correlations between these pathogens and disrupted immune-metabolic pathways, such as altered energy metabolism and inflammatory cascades, consistent across both cohorts. Diagnostic models based on microbial-immune biomarkers demonstrated high accuracy in differentiating COPD patients from controls and in stratifying disease severity.<br><br>CONCLUSIONS: This study identifies microbial and immune signatures associated with COPD severity, providing mechanistic insights into its pathophysiology. The findings may inform precision medicine strategies by targeting airway dysbiosis and immune dysregulation. While causal relationships could not be established in this cross-sectional study, the findings provide a foundation for future mechanistic investigations using advanced in vitro and in vivo models.},
}
@article {pmid40858544,
year = {2025},
author = {Zou, X and Cao, H and Hong, L and Suo, L and Wang, C and Chang, K and Ni, Y and Liu, B and Cao, B},
title = {Enrichment of Streptococcus oralis in respiratory microbiome enhance innate immunity and protects against influenza infection.},
journal = {Signal transduction and targeted therapy},
volume = {10},
number = {1},
pages = {272},
pmid = {40858544},
issn = {2059-3635},
mesh = {Humans ; *Immunity, Innate/genetics/immunology ; Mice ; Animals ; *Influenza, Human/immunology/microbiology/genetics ; Female ; Male ; *Streptococcus oralis/immunology/pathogenicity/genetics ; Middle Aged ; *Microbiota/immunology/genetics ; Gastrointestinal Microbiome/immunology/genetics ; Aged ; Probiotics ; },
abstract = {Respiratory microbial dysbiosis has been implicated in the occurrence and progression of community-acquired pneumonia (CAP). However, the dynamic variation in the respiratory microbiota and its interaction with the host response remain poorly understood. Here, we performed metagenomic analysis of respiratory and gut microbiota, along with blood transcriptomics, using longitudinally collected samples from 38 CAP patients. CAP patients presented disrupted sputum microbiota at the early, middle, and late stages of hospitalization. Microbial pathways involved in peptidoglycan biosynthesis and immune evasion, particularly contributed by the Streptococcus genus, were enriched in CAP patients. Additionally, several Streptococcus strains demonstrated correlation between respiratory and gut microbiota in CAP patients. By incorporating host response data, we revealed that Streptococcus oralis (SOR) was associated with host pathways involved in the innate immune response to infection, and this microbe‒host interaction was reproduced in a newly enrolled CAP cohort consisting of 22 patients with influenza infection. The host-SOR interaction was validated in a mouse model, where SOR demonstrated protective efficacy against influenza virus infection comparable to that of the well-established respiratory probiotic Lactobacillus rhamnosus GG. Preaspiration of SOR in mice significantly mitigated body weight loss, reduced lung inflammation, and lowered viral loads following influenza virus challenge. Host response profiling indicated that SOR priming activated a greater innate immune response at the early stage of infection and that this response resolved timely as the host began to recover. These findings suggest that respiratory commensals play an immune-protective role by inducing a timely innate immune response to prevent CAP progression.},
}
@article {pmid40855532,
year = {2025},
author = {Babalola, OO and Ogundeji, FO and Akanmu, AO},
title = {Dataset of 16S rRNA and ITS gene amplicon sequencing of celery and parsley rhizosphere soils.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {60},
pmid = {40855532},
issn = {2730-6844},
support = {UID123634 and UID132595//National Research Foundation/ ; },
mesh = {*Rhizosphere ; *RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Bacteria/genetics/classification ; Fungi/genetics/classification ; *Apium/microbiology ; Metagenomics ; Microbiota ; Phylogeny ; },
abstract = {OBJECTIVES: This amplicon metagenomic study examines the relative abundance, taxonomic profiles and community structure of bacterial and fungal communities associated with the roots of parsley (Petroselinum crispum) and celery (Apium graveolens) under monocropping and intercropping systems. The study aims to provide a baseline understanding of how intercropping influences rhizosphere microbial dynamics.<br><br>DATA DESCRIPTION: The dataset provides insight into the effects of parsley-celery intercropping system on soil microbial richness, diversity and community structure. Amplicon metagenomic sequencing was performed on the DNA samples, targeting the 16S rRNA gene (V3-V4 region) and the ITS region for bacterial and fungal communities, respectively. The quantified libraries were pooled and sequenced using Illumina platforms, and the raw sequences were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.) pipeline. The resulting Amplicon Sequence Variant (ASV) profiles revealed Actinobacteria and Protobacteria as the most predominant bacteria phyla, followed by Bacteroidota, Gemmatimonadota and Acidobacteriaota. The most predominant taxonomic distribution of fungi at the phylum level includes Ascomycota and Mortierellomycota. The dataset includes raw sequence reads in FASTQ format (.fastq.gz), which have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) under the Bioproject Accession numbers; SRP540554 (16S rRNA) and SRP540675 (ITS).},
}
@article {pmid40855409,
year = {2025},
author = {Graeber, E and Tysha, A and Nisar, A and Wind, D and Mendling, W and Finzer, P and Dilthey, A},
title = {Shallow shotgun metagenomic sequencing of vaginal microbiomes with the Oxford Nanopore technology enables the reliable determination of vaginal community state types and broad community structures.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {544},
pmid = {40855409},
issn = {1471-2180},
mesh = {Female ; Humans ; *Vagina/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Vaginosis, Bacterial/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Adult ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Nanopore Sequencing/methods ; Sequence Analysis, DNA/methods ; Young Adult ; DNA, Bacterial/genetics ; Cohort Studies ; Nanopores ; },
abstract = {BACKGROUND: The vaginal microbiome plays an important role in female health; it is associated with reproductive success, susceptibility to sexually transmitted infections, and, importantly, the most prevalent vaginal condition in reproduction-age women, bacterial vaginosis (BV). Traditionally, 16S rRNA gene sequencing-based approaches have been used to characterize the composition of vaginal microbiomes, but shallow shotgun metagenomic sequencing (SMS) approaches, in particular when implemented with the Oxford Nanopore Technologies, have important potential advantages with respect to cost effectiveness, speed of data generation, and the availability of flexible multiplexing schemes.<br><br>RESULTS: Based on a study cohort of n&#x2009;=&#x2009;52 women, of which 23 were diagnosed with BV, we evaluated the applicability of Nanopore-based SMS for the characterization of vaginal microbiomes in direct comparison to Illumina 16S-based sequencing. We observed perfect agreement between the two approaches with respect to detecting the dominance of individual samples by either Lactobacilli, vaginosis-associated, or other taxa; very high concordance (92%) with respect to community state type (CST) classification; and a high degree of concordance with respect to the overall clustering structures of the sequenced microbiomes. Comparing the inferred abundances of individual species in individual samples, we observed significant differences (Wilcoxon signed-rank test p&#x2009;<&#x2009;0.05) between the two approaches for 12 of the 20 species most abundant in our cohort, indicating differences in the fine-scale characterization of vaginal microbiomes. Higher overall abundance of Gardnerella vaginalis, associated with an increased number of CST IV detections, in the Nanopore shallow SMS data indicated potentially increased sensitivity of this approach to dysbiotic states of the vaginal microbiome. Nanopore shallow SMS also enabled the methylation-based quantification of different human cell types in the characterized samples as well as the detection of non-prokaryotic species, including Lactobacillus phage and Candida albicans in study participants with microscopically detected Candida. One important potential limitation of the evaluated Nanopore-based SMS approach was marked variation in sequencing yields.<br><br>CONCLUSION: Our study demonstrated the successful application and potential advantages of Nanopore-based shallow SMS for the characterization of vaginal microbiomes and paves the way for its application in larger-scale research or diagnostic settings.},
}
@article {pmid40862625,
year = {2025},
author = {Ao, J and Tang, X and Li, Z and Tang, Z},
title = {Shrub encroachment alters microbial community composition and soil carbon and nitrogen cycling functional genes in northern peatlands.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0054225},
pmid = {40862625},
issn = {2165-0497},
support = {2023YFF1304604-3//National Key Research and Development Program of China/ ; XZ202401ZY0110//Key R&amp;D Program of Tibet Autonomous Region, China/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism/analysis ; *Soil/chemistry ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Nitrogen Cycle/genetics ; Nitrogen/metabolism ; Wetlands ; *Microbiota/genetics ; Fungi/genetics/classification/metabolism/isolation &amp; purification ; Carbon Cycle/genetics ; Nitrogen Fixation/genetics ; Ecosystem ; },
abstract = {Changes in vegetation, such as shrub encroachment in grassland and wetland ecosystems, significantly influence soil microbial communities and biogeochemical processes. However, the specific impact of shrub encroachment on peatland ecosystems remains poorly understood. This study used a "space-for-time" approach, collecting soil samples from three encroachment stages-uninvaded, shrub invasion, and shrub invasion expansion-at two depths (0-30 cm and 30-60 cm). Metagenomic sequencing was used to assess the microbial community composition and functional gene dynamics. Shrub encroachment significantly alters soil physicochemical properties, nutrient availability, and microbial communities. Alpha diversity of bacteria and fungi was influenced by shrub encroachment and depth, whereas beta diversity varied mainly with depth. Functional carbon fixation genes (korA and pps) increased during shrub encroachment, while methane oxidation (hdrA2) and carbon degradation genes (GH31 and GH51) decreased before increasing. In addition, functional genes linked to nitrogen cycling (nifD, nifH, amoA, and amoC) declined, indicating a reduction in nitrogen fixation and nitrification pathways. Correlation and Mantel tests revealed that the total soil carbon content was the primary driver of these functional changes. These findings highlight the dynamic microbial responses to shrub encroachment and offer insights into the soil carbon and nitrogen-cycling mechanisms in peatlands.IMPORTANCEShrub encroachment is transforming peatlands and altering their ecological and biogeochemical functions. This study provides critical insights into how shrub invasion affects microbial communities and functional genes responsible for carbon and nitrogen cycling in peatland soils. By revealing the underlying genetic mechanisms, this study enhances our understanding of the consequences of vegetation shifts on ecosystem processes. These findings are essential for predicting and managing peatland responses to environmental changes, helping to preserve their role as vital carbon and nutrient reservoirs.},
}
@article {pmid40862113,
year = {2025},
author = {Wang, W and Wang, L and Chen, J and Yang, X and Guo, Q and Zhang, Z and Liang, J and Gu, P and Shao, J},
title = {The gut microbiome: a vital link to hyperuricemia, gout and acute flares?.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1643566},
pmid = {40862113},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Hyperuricemia/microbiology ; *Gout/microbiology ; Male ; Middle Aged ; Female ; Adult ; Uric Acid/blood ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; Feces/microbiology ; Bacteria/genetics/classification ; },
abstract = {OBJECTIVES: To explore the associations between the gut microbiome and asymptomatic hyperuricemia, as well as acute gout flares.<br><br>METHODS: Forty-three Chinese participants were divided into healthy and hyperuricemic groups according to serum uric acid (SUA) levels. The hyperuricemia group were further separated into asymptomatic hyperuricemia (HUA) and gout patients on the basis of their clinical symptoms. In addition, the gout group was further divided into intercritical gout and acute gout groups on the basis of the claim of joint pain and relevant clinical parameters. 16S rRNA sequencing was used to evaluate the microbiome composition of all the groups.<br><br>RESULTS: A dramatic decreasing trend in microbial richness and diversity was observed in hyperuricemic patients compared with healthy controls. The same decreasing trend in microbial relative abundance was also observed. The butyrate-producing genera Faecalibacterium, Coprococcus and Enterococcus were markedly decreased in hyperuricemic patients. Moreover, opportunistic pathogens, such as the phylum Proteobacteria and genus Fusobacterium, were enriched in the hyperuricemia group. Furthermore, the gut microbiota of gout patients also exhibited significantly reduced microbial diversity compared with asymptomatic hyperuricemic patients, characterized by decreased richness of the genera Dialister, Ruminococcus, and Faecalibacterium. Greater differences in microbial richness and diversity can still be observed when gout flares occur. The abundances of Bacteroides and Lachnospira genera decreased in the acute gout stage.<br><br>CONCLUSION: Our study revealed that community richness and diversity change during the process of gout or HUA, especially during acute gout flares. Metagenomic species were significantly altered during different stages of hyperuricemia.},
}
@article {pmid40857949,
year = {2025},
author = {Jin, L and Yuan, L and Bürgmann, H and Ju, F},
title = {Wastewater treatment plant effluent drives coupled changes of viral and bacterial community structure and function in impacted rivers.},
journal = {Environment international},
volume = {203},
number = {},
pages = {109737},
doi = {10.1016/j.envint.2025.109737},
pmid = {40857949},
issn = {1873-6750},
mesh = {*Rivers/microbiology/virology ; *Wastewater/microbiology/virology ; *Bacteria/classification ; *Waste Disposal, Fluid ; Viruses/classification ; *Water Microbiology ; Microbiota ; },
abstract = {The discharge of wastewater treatment plant (WWTP) effluent containing bacteria and viruses has significant ecological and public health implications for aquatic ecosystems. While viruses infecting bacterial hosts are abundant and diverse in wastewater, their environmental fate, host association, and functional impact in affected river ecosystems remain poorly understood. Using a metagenomic approach, we characterized double-stranded DNA viral communities across nine WWTPs and impacted riverine habitats, including water, suspended particles, sediment, and epilithic biofilm. River water was the most affected habitat by WWTP effluent, with viral diversity increasing by 22 % (±15 %) downstream. In contrast, no significant differences were observed in either viral or bacterial community structures across locations in biofilm or sediment. Among 38,826 viral operational taxonomic units (vOTUs) recovered from 148 metagenomes, 18 % were shared exclusively between effluent and downstream habitats, primarily with river water (99 % of the vOTUs). These wastewater-associated vOTUs were predicted to infect key bacterial taxa involved in carbon and nitrogen cycling (e.g., Nitrosomonas and Methylomonadaceae) and potential human pathogens (e.g., Vibrio and Ralstonia). Additionally, WWTP effluent increased the diversity of virus-encoded auxiliary metabolic genes, especially those involved in carbon, nutrient, and drug metabolism, suggesting potential roles in shaping host fitness and environmental adaptation. Overall, our findings demonstrate that WWTP effluent drives coupled changes in viral and bacterial communities in river water, highlighting the potential ecological consequences of virus-host interactions in wastewater-impacted aquatic environments.},
}
@article {pmid40854874,
year = {2025},
author = {Kaelin, EA and Mitchell, C and Soria, J and La Rosa, A and Ticona, E and Coombs, RW and Frenkel, LM and Bull, ME and Lim, ES},
title = {Longitudinal cervicovaginal bacteriome and virome alterations associate with discordant shedding and ART duration in women living with HIV in Peru.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7904},
pmid = {40854874},
issn = {2041-1723},
support = {R01 AI071212/AI/NIAID NIH HHS/United States ; R00 DK107923/DK/NIDDK NIH HHS/United States ; R01 AI091550/AI/NIAID NIH HHS/United States ; R00DK107923//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; P30 AI027757/AI/NIAID NIH HHS/United States ; UM1 AI106701/AI/NIAID NIH HHS/United States ; },
mesh = {Female ; Humans ; Peru ; *HIV Infections/drug therapy/virology/microbiology ; *Virome/genetics ; *Virus Shedding/drug effects ; Adult ; *Vagina/microbiology/virology ; *Cervix Uteri/microbiology/virology ; *Microbiota/genetics ; Longitudinal Studies ; HIV-1/physiology ; Middle Aged ; CD4 Lymphocyte Count ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Viral Load ; Anti-HIV Agents/therapeutic use ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {Despite successful suppression of plasma HIV replication by antiretroviral therapy (ART), some women living with HIV (WLHIV) can still experience genital HIV shedding (discordant shedding). Female genital tract (FGT) bacterial and viral microbiome (bacteriome and virome) community dynamics during long-term ART in WLHIV are poorly understood but might contribute to discordant HIV shedding, as the bacteriome and virome are known to influence FGT health. Here, using metagenomic next-generation sequencing, we characterize the bacteriome and virome in 125 cervicovaginal specimens collected over two years from 31 WLHIV in Lima, Peru, and show that FGT bacteriome instability is associated with discordant HIV shedding, while longitudinal changes in FGT virome composition are associated with ART duration. Intrapersonal bacteriome variation is higher in discordant HIV shedders compared to non-shedders. Cervicovaginal virome composition changes over time, particularly in non-shedders. Specifically, anellovirus relative abundance is inversely associated with ART duration and CD4 counts. Our results suggest that discordant HIV shedding is linked with FGT bacteriome instability, and immune recovery during ART influences FGT virome composition.},
}
@article {pmid40856764,
year = {2025},
author = {Sharma, P and Iqbal, MZ and Chandra, R},
title = {Bacterial allies in chromium hyperaccumulation: native rhizobacterial dynamics of profusely growing Dactyloctenium aegyptium in highly tainted tannery sludge.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {9},
pages = {314},
pmid = {40856764},
issn = {1573-0972},
support = {IF210284//Department of Science and Technology, Ministry of Science and Technology, India/ ; },
mesh = {*Chromium/metabolism ; Biodegradation, Environmental ; *Sewage/microbiology/chemistry ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Plant Roots/microbiology/metabolism ; Soil Pollutants/metabolism ; Tanning ; Soil Microbiology ; Microbiota ; Rhizosphere ; Industrial Waste ; },
abstract = {Tannery sludge has highly toxic heavy metals like chromium (Cr), posing environmental and health risks. This research investigates the potential of Dactyloctenium aegyptium (L.) Willd. and the associated rhizobacterial communities for bacterial-assisted phytoremediation of tannery sludge, having 6403.16 ± 0.71 mg/kg Cr. The analyses of culturable bacterial communities resulted in the exploration of two highly potent plant growth-promoting strains (CRB2 and CRB5), out of the six culturable strains obtained. SEM imaging depicted robust bacterial colonization on the plant root surface, confirming active plant-microbe interaction. D. aegyptium showed significant Cr accumulation (4936 ± 1.34 mg/kg) within the tissues, followed by substantial translocation to shoots and leaves (TF = 1.01). With a BCF of 1.66 for Cr, D. aegyptium bespeaks evident hyperaccumulation potential. TEM imaging revealed the granular metal deposition in the plant tissues. Post-plant growth, the sludge exhibited an 80.3% reduction in Cr concentration, alongside enhanced physicochemical properties (reduced pH, increased organic matter, reduced metal content). Furthermore, metagenomics analyses showed that the growth of D. aegyptium drastically changed rhizobacterial communities, decreasing species richness and increasing functional pathways associated with stress responses and metal tolerance. Important genes (copA, czcA, nirA), enzymes (dioxygenases, trimethylamine-N-oxide reductase), and proteins (CsgE, DsbG), essential for the nitrogen cycle, chromium detoxification, and plant-microbe associations, were found to be involved in metabolic pathways. The study amalgamates morphophysiological and advanced metagenomic approaches to put forth an understanding of species-specific plant-microbe interactions for the development of scalable and sustainable remediation and engineering of rhizospheric microbiomes for eco-restoration of heavy metal-polluted industrial sites.},
}
@article {pmid40856172,
year = {2025},
author = {de-Dios, T and Bonucci, B and Barbieri, R and Kushniarevich, A and D'Atanasio, E and Dittmar, J and Cessford, C and Solnik, A and Robb, JE and Warinner, C and Oras, E and Scheib, CL},
title = {Bone Adhered Sediments as a Source of Target and Environmental DNA and Proteins.},
journal = {Molecular biology and evolution},
volume = {42},
number = {9},
pages = {},
pmid = {40856172},
issn = {1537-1719},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *Geologic Sediments/chemistry ; Humans ; *Bone and Bones/chemistry ; Rats ; *DNA, Ancient/analysis ; Archaeology ; Metagenomics ; Fossils ; Gastrointestinal Microbiome/genetics ; },
abstract = {In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, however, sediments are not always collected during excavation. In this study, we analyzed an overlooked but abundant resource in archaeological collections - sediments adhered to bone. We performed metagenomics and metaproteomics analysis on sediment from several human skeletal elements, originating from Neolithic to Medieval sites in England. We were able to reconstruct a partial human genome, the genetic profile of which matches that recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular, we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material that is usually ignored or discarded, can be used to reveal information about the individual and the environmental conditions at the time of their death.},
}
@article {pmid40855911,
year = {2025},
author = {Wei, L and Wu, H and Wen, L and Chen, M and Cui, B and Wang, X and Wu, T and Cheng, Y},
title = {Rice protein peptides alleviate lipid accumulation via modulating liver metabolism and remodeling the gut microbiota in HFD-induced mice.},
journal = {Food &amp; function},
volume = {16},
number = {18},
pages = {7266-7282},
doi = {10.1039/d5fo01536g},
pmid = {40855911},
issn = {2042-650X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Oryza/chemistry ; *Lipid Metabolism/drug effects ; *Liver/metabolism/drug effects ; Male ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; *Peptides/pharmacology ; *Hyperlipidemias/metabolism/drug therapy ; *Plant Proteins/pharmacology/chemistry ; },
abstract = {Hyperlipidemia is a significant risk factor for lipid metabolism disorder and gut health impairment. Rice protein peptides (RPs) have emerged as promising interventions for hyperlipidemia management, owing to their safety profile, bioavailability, and cost-effectiveness. However, comprehensive investigations into their anti-hyperlipidemic effects and underlying mechanisms remain insufficiently explored. This study aimed to investigate the efficacy of RPs in alleviating hyperlipidemia and hepatic lipid accumulation by lipidomic and microbiome analyses. Results revealed that RP administration significantly ameliorated lipid metabolism disorders by reducing fat accumulation, normalizing blood lipid levels, and inhibiting lipase activity. Additionally, RPs exhibited hepatoprotective effects by increasing antioxidant enzyme activity and decreasing pro-inflammatory cytokines. Lipidomic analysis further revealed that RPs altered lipid metabolic patterns, identifying 10 differentially regulated lipid species that may serve as potential biomarkers for hyperlipidemia. Furthermore, RP supplements significantly regulated the mRNA levels of gene expression (HMGR, SREBP2, CYP7A1, LDLR, PPARα, PPARγ, FAS, and ACS) involved in hepatic lipid metabolism. Metagenomic analysis demonstrated that RPs reversed gut microbiota dysbiosis by reducing the Firmicutes/Bacteroidetes ratio and increasing the abundance of beneficial genera such as Akkermansia, Muribaculaceae, Clostridia_UCG-014, and Blautia. Furthermore, RP intervention significantly elevated fecal short-chain fatty acid (SCFA) content, particularly butyrate, isobutyrate, and isovalerate, suggesting a link between microbial modulation and metabolic improvement. These findings suggested RPs as an effective strategy for improving lipid metabolism and the gut microbiota composition, offering a promising dietary intervention for hyperlipidemia management.},
}
@article {pmid40851072,
year = {2025},
author = {Zhang, L and Wang, S and Wong, MCS and Mok, CKP and Ching, JYL and Mak, JWY and Chen, C and Huo, B and Yan, S and Cheung, CP and Chiu, EOL and Fung, EYT and Cheong, PK and Chan, FKL and Ng, SC},
title = {The resident gut microbiome modulates the effect of synbiotics on the immunogenicity after SARS-COV-2 vaccination in elderly and diabetes patients.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {171},
pmid = {40851072},
issn = {2055-5008},
support = {COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; NCI202346//New Cornerstone Science Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Aged ; *Synbiotics/administration &amp; dosage ; SARS-CoV-2/immunology ; Female ; Male ; *COVID-19/prevention &amp; control/immunology ; *COVID-19 Vaccines/immunology/administration &amp; dosage ; Feces/microbiology ; Bifidobacterium ; *Immunogenicity, Vaccine ; *Diabetes Mellitus/immunology/microbiology ; Vaccination ; BNT162 Vaccine/immunology ; Middle Aged ; Antibodies, Viral/blood ; },
abstract = {The study aims to tackle the seed and soil microbiome and mechanisms that contribute to the effect of synbiotics in enhancing immunogenicity after SARS-CoV-2 vaccination in elderly and diabetic patients. Among 369 subjects who received 3 months of SIM01, a gut microbiota-derived synbiotic formula of three Bifidobacterium strains (B. adolescentis, B. bididum, and B. longum) or a placebo after the SARS-CoV-2 vaccines (mRNA vaccine BNT162b2 (Pfizer-BioNTech) or the inactivated vaccine Sinovac-CoronaVac), we performed metagenomic sequencing in stool samples of 280 vaccinees collected at baseline and 3-month postvaccination and metabonomic sequencing in 276 vaccinees collected at baseline and 1-month postvaccination. The open niche of autochthonous gut microbiota (lower levels of Bifidobacterium and decreased functional potential for carbohydrate metabolism) was associated with enhancing SIM01-contained species. The enrichment of three bifidobacterial species after 3 months of SIM01 intervention (BABBBL_fc) was positively correlated with the level of neutralizing antibodies to the BNT162b2 vaccine at 6-month postvaccination. The fold change of benzoic acid was positively correlated with BABBBL_fc in the BNT162b2 vaccinees, which was also implicated with SARS-CoV-2 surrogate virus neutralization test (sVNT)% levels at 1-month postvaccination. Importantly, SIM01 strain engraftment assessed by StrainPhlAn (A metagenomic strain-level population genomics tool) was associated with a higher fold change of three bifidobacterial species and could be predicted based on the baseline gut microbiome. Therefore, the resident gut microbiome affected the SIM01 engraftment, which was associated with the immunogenicity of SARS-CoV-2 BNT162b2 vaccines.},
}
@article {pmid40850953,
year = {2025},
author = {Tang, M and Li, C and Ge, X and Kuang, Y and Qiu, L and Chan, KC and Chen, Z and Guo, L and Zhao, Z and Zhang, B and Liu, S and Zhou, X},
title = {Honeybee-Gilliamella synergy in carbohydrate metabolism enhances host thermogenesis in cold acclimation.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {172},
pmid = {40850953},
issn = {2055-5008},
support = {RDF-23-01-067//Research Development Fund of Xi'an Jiaotong-Liverpool University/ ; 2023YFD2201804//Program of the Ministry of Science and Technology of China/ ; 2023YFD2201804//Program of the Ministry of Science and Technology of China/ ; 32470455//National Natural Science Foundation of China/ ; 2023IOZ0104//program from Institute of Zoology, Chinese Academy of Sciences/ ; No.SYND-2021-30//Program from the Sanya Institute of China Agricultural University/ ; },
mesh = {Animals ; Bees/microbiology/physiology ; *Carbohydrate Metabolism ; Cold Temperature ; *Acclimatization ; *Thermogenesis ; Gastrointestinal Microbiome ; Glucose/metabolism ; Symbiosis ; Metagenomics ; Metabolomics ; Pyruvic Acid/metabolism ; },
abstract = {How gut symbionts contribute to host adaptation remains largely elusive. Studying co-diversified honeybees and gut bacteria across climates, we found cold-adapted species (Apis mellifera, A. cerana) exhibit enhanced genomic capacity for glucose, pyruvate, lipid and glucuronate production versus tropical species. Metagenomics revealed Gilliamella as the most enriched gut bacterium in cold-adapted bees. Germ-free honeybees inoculated with the Gilliamella from A. cerana showed increased activity, body temperature and fat storage upon cold exposure. Saccharide metabolomics demonstrated higher hindgut glucose levels in Gilliamella-colonized A. mellifera versus germ-free bees, and in A. cerana versus three sympatric tropical species. Although Gilliamella can hydrolyze β-glucan into glucose, cultural experiments suggest it preferentially degrades glucuronate to pyruvate. In turn, monocolonized bees upregulated hindgut glucose/pyruvate utilization while increasing glucuronate provision, suggesting nutritional complementarity. Gilliamella's transporter genes predominantly target ascorbate (a glucuronate derivative), which is elevated in inoculated hindguts. Accordingly, Gilliamella converts ascorbate to D-xylulose-5P (promoting lipogenesis), while showing reduced growth on glucuronate/ascorbate versus glucose, potentially minimizing glucose competition with hosts. We revealed a highly coordinated host-symbiont metabolic synergy enhancing host energy acquisition for cold adaptation.},
}
@article {pmid40849632,
year = {2025},
author = {Jang, S and Lee, EJ and Park, S and Lim, H and Ahn, B and Huh, Y and Koh, H and Park, YR},
title = {Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {189},
pmid = {40849632},
issn = {2049-2618},
mesh = {Humans ; *Crohn Disease/microbiology/genetics/pathology ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Child ; Male ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; *Ileum/microbiology/pathology ; Prospective Studies ; Adolescent ; Transcriptome ; Gene Expression Profiling ; Metagenome ; Computational Biology/methods ; *Host Microbial Interactions/genetics ; },
abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory bowel disease involving complex relationships between the gut microbiome and host immune system. However, the spatial relationships between tissue-resident bacteria and host cells in CD pathogenesis remain poorly understood. We developed a spatial host-microbiome profiling approach to simultaneously detect host transcriptomics and bacterial species at high taxonomic resolution in pediatric ileal CD tissues.<br><br>RESULTS: In this prospective case-control study, we analyzed 14 terminal ileal tissue samples from six pediatric patients with ileal CD and two controls. Spatial host-microbiome sequencing, combined spatial transcriptomics and in-situ polyadenylation, and bulk shotgun metagenome sequencing were performed. We developed a comprehensive bioinformatics pipeline to identify bacterial species and analyze host-microbiome interactions at cellular resolution, resulting in 13,876 analyzed cells. Our approach revealed increased bacterial abundance in CD tissues compared with controls. The extent of bacterial infiltration at diagnosis correlated with disease prognosis and severity of endoscopic findings. We identified 16 potentially beneficial and nine pathogenic microbiome members in ileal CD, including several newly discovered risk-modulating bacterial species. Cell-type-specific host gene expression analysis revealed transcriptome alterations related to bacterial defense mechanisms in the presence of various bacterial species.<br><br>CONCLUSIONS: Our spatial host-microbiome profiling approach enables simultaneous species-level identification of bacteria and host transcriptomics. It reveals the intricate interactions between host cells and bacteria, providing cellular-level insights into CD pathogenesis. Our approach offers a powerful tool for investigating host-microbiome interactions in various microbiome-associated diseases to direct new strategies for microbiome-based therapeutics and prognostic markers. Video Abstract.},
}
@article {pmid40849482,
year = {2025},
author = {Zhang, Y and Liao, YT and Liu, F and Li, RW and Wu, VCH},
title = {Impact of diet in shaping gut virome of grain-fed and grass-fed beef cattle revealed by a comparative metagenomic study.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {190},
pmid = {40849482},
issn = {2049-2618},
support = {2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; },
mesh = {Animals ; Cattle ; *Virome/genetics ; Metagenomics/methods ; *Animal Feed/analysis ; *Gastrointestinal Microbiome/genetics ; Feces/virology ; *Viruses/classification/genetics/isolation &amp; purification ; *Poaceae ; *Diet/veterinary ; *Edible Grain ; },
abstract = {BACKGROUND: In the United States beef industry, grain-feeding and grass-feeding are the two most common types of cattle feeding. Different feeding methods are likely to affect gut microbiota compositions and subsequently change microbial adaptation and cattle metabolism. However, there is limited information regarding the impact of diet on cattle gastrointestinal virome. This study examined the composition of fecal virome from grain-fed and grass-fed beef cattle and identified unique virome features to understand the relationship between these two feeding types.<br><br>RESULTS: Six grain-fed and six grass-fed Angus beef cattle were weighed, and their fecal samples were collected for further viral metagenomic sequencing. The difference in animal growth revealed a significantly higher post-weaning weight in grain-fed cattle than in grass-fed cattle after day 56. Furthermore, the analysis of the fecal viral population showed that approximately 795 and 1266 predicted viral sequences were obtained in the grain-fed and grass-fed samples, respectively. Among those, 54.3% of the grain-fed and 26.3% of the grass-fed viral sequences were identified as known viruses. The taxonomic classification showed that viruses belonging to the order Caudovirales, mostly bacteriophages, dominated the cattle virome in both sample groups, followed by the order Cremeviriles and Petitvirales. At the family level, 13 and 16 different viral families were detected in the grain and grass-fed groups, respectively. The comparison of virome features from the two groups indicated that the viral population from the kingdom Bamfordvirae had a significantly higher abundance in the grain-fed group than in the grass-fed cattle virome. In contrast, the kingdom Heunggongvirae had a significantly higher abundance in the grass-fed group than in the grain-fed cattle virome. Moreover, the viruses, belonging to the order Caudovirales and the family Podoviridae, had significantly higher abundances in the grass-fed virome than in the grain-fed virome.<br><br>CONCLUSIONS: The findings indicate the influence of animal feeds on the changes in gastrointestinal viral compositions and their potential association with cattle weight gain. The current outcome can contribute to further understanding of&#xa0;phage-bacterial interactions and their underlying mechanisms in regulating the animal host's metabolism and feed efficiency. Video Abstract.},
}
@article {pmid40847279,
year = {2025},
author = {Azmi, MAI and William-Dee, J and Morni, MA and Azhar, NAA and Sabarudin, NA and Jinggong, ER and Zolkapley, S and Baharom, NIM and Haqeem, MD and Sien, VL and Mohamad Azmi, AH and Adrus, M and Tan, CS and Khan, FAA},
title = {Metagenomic insights into host-specific gastroenteritis bacteria in forest rodents of Sarawak, Borneo: implications for one health surveillance of rodent-borne pathogens.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {531},
pmid = {40847279},
issn = {1471-2180},
support = {GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; F07/PGRG/2046/2020//Postgraduate Research Grant, UNIMAS/ ; },
mesh = {Animals ; *Gastroenteritis/microbiology/veterinary ; Borneo/epidemiology ; Feces/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Forests ; *Rodentia/microbiology ; Humans ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; One Health ; Host Specificity ; Phylogeny ; Zoonoses/microbiology ; DNA, Bacterial/genetics ; Disease Reservoirs/microbiology ; *Rodent Diseases/microbiology ; },
abstract = {Rodents are known to act as reservoirs for zoonotic diseases due to their widespread distribution and synanthropic nature. Among these, foodborne pathogens capable of causing gastroenteritis in humans are of particular concern, as rodents can facilitate their transmission through contamination of food sources. Forest-dwelling rodents may harbour bacterial taxa native to their habitat, posing a risk of zoonotic spillover to nearby human settlements. This risk is further heightened by the growing prevalence of ecotourism activities, particularly in tropical countries like Malaysia. In this study, rodent trapping was conducted in selected forested areas adjacent to human settlements across Sarawak. Nanopore sequencing of the full-length 16 S rRNA gene was conducted on faecal DNA from 46 rodent individuals representing seven different species (Maxomys surifer, M. tajuddinii, M. whiteheadi, Niviventer cremoriventer, Rattus tanezumi, R. tiomanicus and Sundamys muelleri). A total of ten bacterial species associated with gastroenteritis were successfully detected. Notable findings in this study include Campylobacter, Salmonella and Shigella species, which are known to cause bacterial gastroenteritis in humans. Also, the presence of certain bacterial taxa in specific rodent genera suggests potential host specificity of foodborne pathogens. This study highlights the potential public health risks caused by rodent-borne bacterial transmission and the importance of monitoring forest rodents as potential reservoirs of zoonotic pathogens.},
}
@article {pmid40846880,
year = {2025},
author = {Kotrbová, L and Grabicová, K and Švecová, H and Staňová, AV and Petrlíková, M and Grabic, R and Kodešová, R and Chroňáková, A},
title = {The effect of WWTP products amendments on Phaseolus vulgaris rhizosphere and its ability to inactivate clarithromycin.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30950},
pmid = {40846880},
issn = {2045-2322},
support = {QK21020080//Ministerstvo Zem&#x11b;d&#x11b;lstv&#xed;/ ; QK21020080//Ministerstvo Zem&#x11b;d&#x11b;lstv&#xed;/ ; QK21020080//Ministerstvo Zem&#x11b;d&#x11b;lstv&#xed;/ ; QK21020080//Ministerstvo Zem&#x11b;d&#x11b;lstv&#xed;/ ; QK21020080//Ministerstvo Zem&#x11b;d&#x11b;lstv&#xed;/ ; QK21020080//Ministerstvo Zem&#x11b;d&#x11b;lstv&#xed;/ ; QK21020080//Ministerstvo Zem&#x11b;d&#x11b;lstv&#xed;/ ; 063/2023/P//Grantov&#xe1; agentura Jiho&#x10d;esk&#xe9; univerzity v &#x10c;esk&#xfd;ch Bud&#x11b;jovic&#xed;ch/ ; },
mesh = {*Phaseolus/microbiology ; *Rhizosphere ; *Wastewater/chemistry ; Agricultural Irrigation ; Soil Microbiology ; *Clarithromycin/analysis ; Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Water Pollutants/analysis ; },
abstract = {With increasing efforts to reuse wastewater treatment plant (WWTP) products in agriculture, assessing their impact on soil-plant systems is crucial, while the effects of accompanying antibiotic residues on soil microbial communities have not yet been adequately studied. This study focuses on clarithromycin (CLR), highly present in wastewater, and investigates the CLR-degradation potential of plant-associated microorganisms. Phaseolus vulgaris plants were grown in raised beds filled with Haplic Cambisol and amended with or without WWTP products (treated wastewater, biosolid, or composted biosolid), as a source of CLR residues. The rhizosphere microbiomes after biosolid amendments was significantly enriched by Pseudomonadaceae as assessed by 16S rRNA metagenomics and cultures enriched by CLR revealed dominance of Proteobacteria. However, no degradation of CLR by microbial consortia or enrichment cultures was observed, suggesting the multiplication of CLR-resistant bacteria with other resistance mechanisms. Cultivation-based approach combined with antibiotic modulation assays and subsequent LC-MS analysis confirmed the complete CLR removal by seven phylogenetic groups of actinomycetes in vitro. The proportion of isolates indicated that the rhizosphere is a natural reservoir for CLR-inactivating microorganisms; however, the amendment of soils with WWTP products can significantly increase their abundance and diversity.},
}
@article {pmid40846855,
year = {2025},
author = {Zhang, M and Wang, X and Yao, H and Shen, Y and Teng, Y and Garber, PA and Pan, H and Li, M},
title = {Plasticity of the gut microbiome of golden snub-nosed monkeys (Rhinopithecus roxellana) in response to seasonal variation in diet.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {169},
pmid = {40846855},
issn = {2055-5008},
support = {32330015, 31821001//National Natural Science Foundation of China/ ; 32070404//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Seasons ; *Gastrointestinal Microbiome ; *Diet ; *Colobinae/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Feces/microbiology ; },
abstract = {The effects of seasonal fluctuations in food availability on gut microbiome composition, diversity, and function present significant challenges to animals with hard-to-digest diets. Here, we investigate seasonal variation the gut microbiome of wild golden snub-nosed monkeys (Rhinopithecus roxellana), a foregut fermenting primate, using metagenomics and metatranscriptomics data. We reconstructed 578 metagenome-assembled genomes (MAGs), 76.5% of which did not have exact matches in reference databases, highlighting the novelty of their gut microbiota. The gut microbiome of wild golden snub-nosed monkeys exhibited high diversity and enrichment in plant secondary compound metabolism during summer, while in winter it was enriched with enzymes that function in lichen polysaccharide degradation and Lachnospiraceae, which is important for energy balance. Captive monkeys on a consistent diet showed minimal seasonal variation in gut microbiome composition. Habitat changes also affected golden snub-nosed monkey microbiota community assembly and carbon cycling pathways. These findings underscore the gut microbiome's plasticity in meeting host dietary needs under varying environmental conditions.},
}
@article {pmid40841555,
year = {2025},
author = {Wang, T and Zhang, P and Anantharaman, K and Wang, H and Zhang, H and Zhang, M and Xu, J},
title = {Metagenomic analysis reveals how multiple stressors disrupt virus-host interactions in multi-trophic freshwater mesocosms.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7806},
pmid = {40841555},
issn = {2041-1723},
support = {42377469//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32001151//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Metagenomics/methods ; Microbiota/genetics ; Lakes/microbiology/virology ; *Fresh Water/microbiology/virology ; Ecosystem ; Metagenome ; *Viruses/genetics/classification ; *Bacteria/genetics/virology ; Pesticides ; *Host Microbial Interactions/genetics ; Stress, Physiological ; Climate Change ; },
abstract = {Virus-host interactions are vital to microbiome ecology and evolution, yet their responses to environmental stressors under global change remain poorly understood. We perform a 10-month outdoor mesocosm experiment simulating multi-trophic freshwater shallow lake ecosystems. Using a fully factorial design comprising eight treatments with six replicates each, we assess the individual and combined effects of climate warming, nutrient loading, and pesticide loading on DNA viral communities and their interactions with microbial hosts. Metagenomic sequencing recovers 12,359 viral OTUs and 1628 unique prokaryotic metagenome-assembled genomes. Our analysis shows that combined nutrient and pesticide loading causes significant disruption by synergistically reducing viral alpha diversity while altering beta diversity and predator-prey linkages. Stressors lead to the simplification of virus-bacteria cross-kingdom networks, with nutrient-pesticide combinations exerting the strongest influence, although warming impacts diminish in the presence of pesticides. Stressor-driven changes also affect the abundance and composition of viral auxiliary metabolic genes, leading to complex shifts in virus-mediated metabolic pathways under multiple stress conditions. These findings underscore the importance of understanding the regulatory role of viruses on microbial communities to effectively address the challenges posed by global change.},
}
@article {pmid40852940,
year = {2025},
author = {Philip, M and Nilsen, T and Majaneva, S and Pettersen, R and Stokkan, M and Ray, JL and Keeley, N and Rudi, K and Snipen, LG},
title = {A Targeted Reference Database for Improved Analysis of Environmental 16S rRNA Oxford Nanopore Sequencing Data.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70036},
doi = {10.1111/1755-0998.70036},
pmid = {40852940},
issn = {1755-0998},
support = {320076//Norges Forskningsr&#xe5;d/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; Norway ; *Nanopore Sequencing/methods ; *Geologic Sediments/microbiology ; Metagenomics/methods ; *Bacteria/classification/genetics ; Sequence Analysis, DNA/methods ; *Databases, Genetic ; Computational Biology/methods ; },
abstract = {The Oxford Nanopore Technologies (ONT) sequencing platform is compact and efficient, making it suitable for rapid biodiversity assessments in remote areas. Despite its long reads, ONT has a higher error rate compared to other platforms; necessitating high-quality reference databases for accurate taxonomic assignments. However, the absence of targeted databases for underexplored habitats, such as the seafloor, limits ONT's broader applicability for exploratory analysis. To address this, we propose an approach for building environmentally targeted databases to improve 16S rRNA gene (16S) analysis using Oxford Nanopore Technologies (ONT), using seafloor sediment samples from the Norwegian coast as an example. We started by using Illumina short-read data to create a database of full-length or near full-length 16S sequences from seafloor samples. Initially, amplicons are mapped to the SILVA database, with matches added to our database. Unmatched amplicons are reconstructed using METASEED and Barrnap methodologies with amplicon and metagenome data. Finally, if the previous strategies did not succeed, we included the short-read sequences in the database. This resulted in AQUAeD-DB, which contains 14,545 16S sequences clustered at 95% identity. Comparative database analysis reveals that AQUAeD-DB provides consistent results for both Illumina and Nanopore read assignments (median correlation coefficient: 0.50), whereas a standard database showed a substantially weaker correlation. These findings also emphasise its potential to recognise both high and low abundance taxa, which could be key indicators in environmental studies. This work highlights the necessity of targeted databases for environmental analysis, especially for ONT-based studies, and lays the foundations for future extension of the database.},
}
@article {pmid40849730,
year = {2025},
author = {Zhou, SY and Lie, Z and Lei, C and Zhang, Q and Liu, X and Wu, G and Neilson, R and Huang, FY and Chu, G and Meng, Z and Zhu, D and Tissue, DT and Peñuelas, J and Liu, J},
title = {Multi-scale evidence for declining microbial carbon fixation along forest succession gradients.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40849730},
issn = {1751-7370},
support = {42477132//National Natural Science Foundation of China/ ; 42207158//National Natural Science Foundation of China/ ; 32101342//National Natural Science Foundation of China/ ; 2022B1111230001//Key-Area Research and Development Program of Guangdong Province/ ; 2024B1212080005//Science and Technology Program of Guangdong/ ; 2024B1212070012//Science and Technology Program of Guangdong/ ; TED2021-132627//Spanish Government/ ; B-I00//Spanish Government/ ; PID2022-140808NB-I00//Spanish Government/ ; AEI/10.13039/501100011033//Spanish Government/ ; SGR 2021-1333//European Union Next Generation EU/PRTR/ ; },
mesh = {*Forests ; *Soil Microbiology ; *Carbon Cycle ; *Bacteria/metabolism/classification/genetics ; *Fungi/metabolism/classification/genetics ; Carbon/metabolism ; Metagenomics ; Carbon Dioxide/metabolism ; Microbiota ; Isotope Labeling ; Carbon Isotopes/metabolism ; Soil/chemistry ; },
abstract = {Although soil carbon accumulates during subtropical forest succession, changes in microbial communities and their carbon fixation capacity remain unclear. Using an integrative approach that combines field experimentation, extensive global metagenomic data, and isotope labelling, we analysed 84 soil microbiomes from a long-term successional site and 755 global metagenomes to investigate microbial community dynamics and their role in carbon fixation. Based on field data, bacteria, fungi, and protists had synchronous succession with vegetation; however, the relative abundance of carbon fixation genes declined significantly in later successional stages. To further investigate this outcome, we analysed global data from planted and mature natural forests and found significantly higher carbon fixation potential in planted forests, predominantly driven by Pseudomonadota and Actinomycota members. Field-based 13C labelling results further confirmed a significant decline in microbial CO2 fixation rates with forest succession. These findings underscore the ecological importance of microbial carbon fixation in early forest succession, emphasizing its foundational role in initiating soil carbon accumulation and shaping long-term carbon cycling trajectories.},
}
@article {pmid40848995,
year = {2025},
author = {Wang, J and Xue, L and Zhang, M and Shen, P and Zhao, W and Tong, Q and Wu, S and Dai, W and Yang, X and Wang, H},
title = {Colonoscopic fecal microbiota transplantation for Mild-to-Moderate Parkinson's Disease: A randomized controlled trial.},
journal = {Brain, behavior, and immunity},
volume = {130},
number = {},
pages = {106086},
doi = {10.1016/j.bbi.2025.106086},
pmid = {40848995},
issn = {1090-2139},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; Middle Aged ; *Parkinson Disease/therapy/microbiology ; Aged ; Double-Blind Method ; Quality of Life ; *Colonoscopy/methods ; Feces/microbiology ; Treatment Outcome ; Gastrointestinal Microbiome/physiology ; Constipation ; },
abstract = {OBJECTIVE: Growing evidence supports the efficacy and safety of fecal microbiota transplantation (FMT) in treating Parkinson's disease (PD). Fecal microbiota are commonly transplanted via oral capsules, a nasojejunal tube, or colonoscopy, but freezing often decreases the diversity and viability of transplanted microbiota. This single-center, double-blind, randomized, placebo-controlled trial aims to explore the efficacy and safety of fresh FMT via colonoscopy in dealing with PD.<br><br>METHODS: Thirty patients with mild-to-moderate PD (Hoehn-Yahr stage I-III) were randomly assigned into the FMT group (fresh FMT via colonoscopy) and placebo group (saline injection via colonoscopy) in a 1:1 ratio. Motor and non-motor symptoms, constipation, quality of life, cognitive function, emotional state and sleep quality were assessed using relevant scales. Fecal samples were harvested before and at 4, 8 and 12&#xa0;weeks after treatment for metagenomic and metabolomics analyses.<br><br>RESULTS: A total of 30 patients with mild-to-moderate PD were enrolled in the present study, involving 18 males and 12 females with a median age of 68&#xa0;years, a median age of onset of 63.5&#xa0;years, and a median disease duration of 3&#xa0;years. At 12&#xa0;weeks, scores of the UPDRS &#x2162; (group&#xa0;&#xd7;&#xa0;time effect, B&#xa0;=&#xa0;&#xa0;-&#xa0;8.80 [-13.79, -3.81]), PAC-QOL (group&#xa0;&#xd7;&#xa0;time effect, B&#xa0;=&#xa0;&#xa0;-&#xa0;29.67 [-45.35, -13.98]), UPDRS &#x2161; (group&#xa0;&#xd7;&#xa0;time effect, B&#xa0;=&#xa0;&#xa0;-&#xa0;5.07 [-8.85, -1.28]), NMSS (group&#xa0;&#xd7;&#xa0;time effect, B&#xa0;=&#xa0;&#xa0;-&#xa0;35.60 [-53.59, -17.61]), PDQ-39 (group&#xa0;&#xd7;&#xa0;time effect, B&#xa0;=&#xa0;&#xa0;-&#xa0;17.80 [-28.21, -7.39]), HAMA (group&#xa0;&#xd7;&#xa0;time effect, B&#xa0;=&#xa0;&#xa0;-&#xa0;1.66 [-2.92, -0.40]), and HAMD (group&#xa0;&#xd7;&#xa0;time effect, B&#xa0;=&#xa0;&#xa0;-&#xa0;1.33 [-2.49, -0.16]) were significantly reduced in the FMT group, while CSBM per week (group&#xa0;&#xd7;&#xa0;time effect, B&#xa0;=&#xa0;3.03 [1.42, 4.63]) and the Bristol Stool Scale score (group&#xa0;&#xd7;&#xa0;time effect, B&#xa0;=&#xa0;1.95 [0.12, 3.79]) significantly increased (all P&#xa0;<&#xa0;0.05). Significant alterations were seen in the gut microbiota and fecal metabolites in the FMT group. No adverse events were observed during the follow-up period.<br><br>CONCLUSION: Fresh FMT via colonoscopy is a safe and well-tolerated procedure for treating mild-to-moderate PD. It effectively alleviates motor and non-motor symptoms, thus facilitating defecation and improving the quality of life. These effects can be maintained for a minimum of 12&#xa0;weeks and may be attributed to the optimization of gut microbiota and fecal metabolites.},
}
@article {pmid40848874,
year = {2025},
author = {Fonnes, S and Mollerup, S and Paulsen, SJ and Petersen, AM and Holzknecht, BJ and Westh, H and Rosenberg, J},
title = {A prospective cohort study of the rectal microbiome in patients with suspected appendicitis.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {49},
number = {8},
pages = {102675},
doi = {10.1016/j.clinre.2025.102675},
pmid = {40848874},
issn = {2210-741X},
mesh = {Humans ; *Appendicitis/microbiology/diagnosis/surgery ; Prospective Studies ; Male ; Adult ; Female ; *Rectum/microbiology ; *Microbiota ; Middle Aged ; Appendectomy ; Cohort Studies ; Aged ; Young Adult ; },
abstract = {PURPOSE: Diagnosing appendicitis is difficult. An infectious origin has been proposed, therefore signals from the microbiome could be a potential diagnostic measure. The aim was to evaluate the diagnostic potential of the rectal microbiome in patients with suspected appendicitis.<br><br>METHODS: We included adult Danish patients with suspected appendicitis undergoing appendectomy in a prospective, observational cohort study. Patients were first grouped as patients with and without appendicitis according to histopathological findings, and second, as having uncomplicated or complicated appendicitis according to the surgical report. Rectal swabs were analysed with shotgun metagenomics. The outcomes were alpha diversity, beta diversity, and differential abundance of bacteria.<br><br>RESULTS: Rectal swabs from 220 patients were analysed: 49 patients without appendicitis, 111 patients with uncomplicated and 60 patients with complicated appendicitis, respectively. Across all groups, both the alpha and beta diversity were similar. The relative abundance of bacterial genera and species was also similar across all groups. Thus, the three groups of patients had similar rectal microbiomes.<br><br>CONCLUSION: The rectal microbiome in adult patients with suspected appendicitis was similar and does not seem to have the potential to be used to diagnose neither appendicitis nor the severity of appendicitis preoperatively.<br><br>TRIAL REGISTRATION: NCT03349814 (clinicaltrials.gov).},
}
@article {pmid40848630,
year = {2025},
author = {Zhang, L and Zhang, Y and Huang, J and Zhou, R and Wu, C},
title = {Temperature-driven functional microbial interactions in soy sauce fermentation: Effects of Zygosaccharomyces rouxii and Wickerhamiella versatilis on flavor enrichment and biogenic amine reduction.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111399},
doi = {10.1016/j.ijfoodmicro.2025.111399},
pmid = {40848630},
issn = {1879-3460},
mesh = {Fermentation ; *Soy Foods/microbiology/analysis ; *Biogenic Amines/metabolism/analysis ; *Zygosaccharomyces/metabolism ; Temperature ; *Flavoring Agents/metabolism ; Food Microbiology ; Taste ; *Microbial Interactions ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Microbiota ; Amino Acids/metabolism ; Odorants/analysis ; Saccharomycetales ; },
abstract = {This study elucidates the temperature-dependent interactions between halotolerant yeasts and microbial communities during secondary fortified soy sauce fermentation (SFFSS) and their implications for flavor enhancement and safety. A dual-mode fermentation system compared natural temperature fermentation (NTF) and controlled temperature fermentation (CTF, 30 °C), each with and without co-inoculation of Zygosaccharomyces rouxii and Wickerhamiella versatilis (ZC). Multi-omics analyses integrating amplicon sequencing, metagenomics, and metabolomics revealed that CTF control elevated amino acid nitrogen and aroma compounds, while increasing biogenic amines (BA) by 47.88 %. In both NTF and CTF modes, the ZC pattern significantly reduced lactic acid while enhancing succinic acid, umami/sweet free amino acids, and key aroma compounds (e.g., 4-ethylguaiacol, 5-ethyl-4-hydroxy-2-methyl-3(2H)-furanone), alongside enriching functional bacteria (Staphylococcus, Weissella), stabilizing fungal communities, and suppressing Tetragenococcus and Ligilactobacillus pobuzihii. Mechanistically, ZC pattern promoted tricarboxylic acid cycle flux and amino acid metabolism, synergistically enhancing volatile phenolics, esters, and alcohols, and reduced BA by >87 % via dual modulation of decarboxylase inhibition and oxidase activation. Network analyses linked microbial composition shifts to targeted flavor metabolite synthesis, providing a mechanistic framework for microbial community engineering. These findings highlight yeast-mediated, temperature-driven modulation of microbiota-metabolite networks as a viable strategy for producing high-quality, safe soy sauce with optimized flavor complexity.},
}
@article {pmid40848515,
year = {2025},
author = {Ni, J and Fu, L and Xiao, J and Li, C and Wu, X and Yuan, Z and Wang, J and Tang, S and Deng, F and Shen, S},
title = {Metagenomic evidence of viral secretion from tick salivary glands to saliva: implications for potential horizontal transmission.},
journal = {Ticks and tick-borne diseases},
volume = {16},
number = {5},
pages = {102540},
doi = {10.1016/j.ttbdis.2025.102540},
pmid = {40848515},
issn = {1877-9603},
mesh = {Animals ; *Saliva/virology ; Salivary Glands/virology ; *Ixodidae/virology ; China ; *Viruses/genetics/isolation &amp; purification/classification ; *Virome ; Metagenomics ; Female ; *Metagenome ; },
abstract = {Ticks transmit diverse viral pathogens to hosts during blood-feeding via saliva secretion. This study characterized viral compositions in salivary glands and saliva from adults of four tick species (Ixodes persulcatus, Rhipicephalus microplus, Haemaphysalis longicornis, and Haemaphysalis concinna) collected in China. Meta-transcriptomic analysis revealed distinct viromes across species, with Flaviviridae dominant in R. microplus, Nairoviridae in H. concinna and I. persulcatus, and Phenuiviridae in H. longicornis and I. persulcatus. Among 27 viruses detected in salivary glands, 14 were identified in saliva, indicating horizontal transmission potential. Viruses with higher abundance (transcripts per thousand bases per million, TPM) in salivary glands were more likely to be secreted in saliva. Genomic sequences of eight viruses, including severe fever with thrombocytopenia syndrome virus (SFTSV), tick-borne encephalitis virus (TBEV), Jingmen tick virus (JMTV), Songling virus (SGLV), Wetland virus (WELV), Beiji nairovirus (BJNV), Mukawa virus (MKWV), and Wuhan tick virus 2 (WHTV2), which are associated with human diseases or possess spillover potentials, were fully assembled from salivary glands and confirmed in saliva. Notably, SFTSV in H. longicornis; MKWV, Sichuan tick hepe-like virus, and Jilin luteo-like virus 2 in I. persulcatus; and JMTV in R. microplus showed significantly increased abundance in saliva, indicating an enhanced secretion of these viruses into saliva. Conversely, TBEV, BJNV, and Sara tick phlebovirus in I. persulcatus, SGLV and WELV in H. concinna, and WHTV2 in R. microplus exhibited reduced salivary abundance despite glandular presence. These findings demonstrate differential secretion capabilities of tick-borne viruses (TBVs) from glands to saliva, advancing understanding of horizontal transmission risks for pathogens affecting human health.},
}
@article {pmid40848105,
year = {2025},
author = {Proskynitopoulos, PJ and Woltemate, S and Rhein, M and Böke, I and Molks, J and Schröder, S and Schneider, HU and Bleich, S and Frieling, H and Geffers, R and Glahn, A and Vital, M},
title = {The effect of alcohol withdrawal therapy on gut microbiota in alcohol use disorder and its link to inflammation and craving.},
journal = {Alcohol, clinical &amp; experimental research},
volume = {49},
number = {9},
pages = {1912-1923},
pmid = {40848105},
issn = {2993-7175},
support = {//Hetzler Foundation for Addiction Research and Prevention/ ; },
mesh = {Humans ; *Craving/physiology/drug effects ; *Gastrointestinal Microbiome/drug effects/physiology ; Male ; Female ; Middle Aged ; *Alcoholism/microbiology/therapy ; Adult ; *Substance Withdrawal Syndrome/microbiology ; *Inflammation ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; },
abstract = {BACKGROUND: Alcohol use disorder (AUD) is linked to changes in the function and composition of the human gut microbiome (GM). The GM affects inflammation by producing anti-inflammatory molecules such as short-chain fatty acids (SCFA), in particular butyrate, which are linked to appetite regulation, a mechanism involved in alcohol craving. This study investigates changes in GM composition and functional capacity to produce SCFA during alcohol withdrawal and their link to inflammation and craving.<br><br>METHODS: Sixty-three patients (mean age 48, SD&#x2009;=&#x2009;12) with AUD were enrolled. We collected stool (n&#x2009;=&#x2009;63) and blood (n&#x2009;=&#x2009;48) during the first 48&#x2009;h (timepoint A) of withdrawal therapy and between Days 10-14 (timepoint B). Microbiota were analyzed using shotgun metagenomics along with bacterial load determinations. TNF-&#x3b1;, IL-6, IL-8, and IL-10 were measured in plasma.<br><br>RESULTS: Bacterial diversity (species richness, Shannon Index) did not change significantly throughout withdrawal, while overall bacterial load increased. Abundances of several taxa changed, and the overall community composition during withdrawal was approaching those of healthy controls; the potential to synthesize butyrate, a key SCFA, increased. However, it remained at lower levels compared with controls. Both diversity parameters correlated with cell concentrations and the butyrate pathway at baseline. The latter was negatively associated with IL-6 at baseline. IL-8 and IL-10 levels decreased significantly during withdrawal, as did craving, which was linked to abundance alterations of six species and IL-8.<br><br>CONCLUSIONS: Alcohol withdrawal affected GM composition and increased concentration of the butyrate pathway along with overall bacterial load. Changes in bacterial composition and the butyrate production capacity demonstrate a shift toward healthier microbiota during withdrawal therapy. Changes in some species and IL-8 were linked to alcohol craving, replicating findings of previous studies. Our study adds new findings helping to understand the microbiome-gut-brain axis.},
}
@article {pmid40848091,
year = {2025},
author = {Dong, Y and Fan, S and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Li, Y and Wang, W},
title = {RNA-viromics unveils diverse RNA viral communities in Large-billed crows and Northern Ravens.},
journal = {Virus genes},
volume = {61},
number = {6},
pages = {657-667},
pmid = {40848091},
issn = {1572-994X},
support = {grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; grant No. 2022-HZ-812//program of science and technology international cooperation project of Qinghai province/ ; },
mesh = {Animals ; *Crows/virology ; *RNA Viruses/genetics/classification/isolation &amp; purification ; *Virome/genetics ; Metagenomics ; Feces/virology ; RNA, Viral/genetics ; Phylogeny ; },
abstract = {Birds have historically served as key vectors for viruses causing significant diseases. Corvid birds, often living in close proximity to livestock, poultry, and humans, provide substantial opportunities for cross-species viral transmission. Such transmission can occur through their feces or via ectoparasites (such as ticks, mites, and fleas) on their bodies, thereby releasing viruses into the environment. Despite the development of viral metagenomics, an increasing number of RNA viruses are being characterized across different species. RNA viruses in birds' gut microbial communities remain poorly studied. Here we report an extensive analysis of an RNA virome in fecal samples from Large-billed crows (Corvus macrorhynchos) and Northern Ravens (Corvus corax), both of which are common Corvus species found in the high-altitude forest and grassland regions of the Qinghai-Tibetan Plateau. This study aims to assess the RNA viruses present in the intestines of these corvids and provides the first comprehensive characterization of the diversity of gut-colonizing viruses in these two crow species.},
}
@article {pmid40847462,
year = {2025},
author = {Ma, H and Wang, M and Feng, Y and Zhang, W and Wang, W and Xie, Y and Kong, G and Feng, J and Wang, P and Wang, Q and Huang, X},
title = {Microbial profile of the appendix niche in acute appendicitis: a novel sampling approach.},
journal = {FEBS open bio},
volume = {15},
number = {12},
pages = {2001-2020},
pmid = {40847462},
issn = {2211-5463},
support = {GSWSKY2020-50//Gansu Provincial Health Commission, Provincial Health Industry Research Project/ ; 20240050058//Lanzhou University Student Innovation and Entrepreneurship Action Plan Project/ ; CY2023-QN-B17//Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University in 2023/ ; },
mesh = {Humans ; *Appendicitis/microbiology ; Male ; Female ; *Appendix/microbiology ; Adult ; Metagenomics/methods ; Middle Aged ; Bacteria/genetics/classification/isolation &amp; purification ; Gastrointestinal Microbiome/genetics ; },
abstract = {Relatively little is known about the microbial variations within the human appendix niche. To overcome this knowledge gap, we employed endoscopic retrograde appendicitis treatment (ERAT) technology to collect microbial samples from the appendix lumen, followed by shotgun metagenomic sequencing on participants with acute appendicitis without antibiotic treatment. Compared to the cecum and terminal ileum, the appendix had a higher abundance at the genus level of Sphingobium, Leptotrichia and Oribacterium, as well as a significant increase in species-level abundance of oral bacteria, including Streptococcus sanguinis, Streptococcus australis, Streptococcus sp. A12, Leptotrichia sp. oral taxon 215, Veillonella dispar, Veillonella infantium and Oribacterium sinus. Pearson correlation analysis showed that bacterial species abundant in the appendix, such as Acinetobacter johnsonii, Sphingobium yanoikuyae and Agrobacterium tumefaciens, had negative correlations with the top five most abundant Gene Ontology (GO) categories (molecular function, biological process and cellular component). Conversely, species underrepresented in the appendix, including Mogibacterium diversum, Streptococcus sanguinis, Megasphaera micronuciformis and Actinomyces graevenitzii, had significant positive correlations with these GO categories. Our results show that ERAT technology can be used to improve sampling and microbiome profiling in the appendix. Furthermore, this in-depth microbial characterization could inform clinicians during antibiotic prescription. However, further large sample size studies are required to validate these results.},
}
@article {pmid40846661,
year = {2025},
author = {Qin, Q and Zhu, Y and Yang, L and Guo, R and Song, L and Wang, D and Li, W},
title = {Oral microbiome between patients with non-obstructive and obstructive hypertrophic cardiomyopathy.},
journal = {Chinese medical journal},
volume = {138},
number = {18},
pages = {2308-2315},
pmid = {40846661},
issn = {2542-5641},
mesh = {Humans ; *Cardiomyopathy, Hypertrophic/microbiology ; Female ; Male ; *Microbiota/physiology/genetics ; Middle Aged ; Cross-Sectional Studies ; Adult ; *Mouth/microbiology ; Aged ; },
abstract = {BACKGROUND: The profile and clinical significance of the oral microbiome in patients with non-obstructive hypertrophic cardiomyopathy (noHCM) and obstructive hypertrophic cardiomyopathy (oHCM) remain unexplored. The objective of this study was to evaluate the difference of oral microbiome between noHCM and oHCM patients.<br><br>METHODS: This cross-sectional study enrolled 18 noHCM patients and 26 oHCM patients from Fuwai Hospital, Chinese Academy of Medical Sciences between 2020 and 2021. Clinical and periodontal evaluations were conducted, and subgingival plaque samples were collected. Metagenomic sequencing and subsequent microbial composition and functional analyses were performed.<br><br>RESULTS: Compared to oHCM patients, those with noHCM had higher systolic blood pressure (138.1 &#xb1; 18.8 mmHg vs . 124.2 &#xb1; 13.8 mmHg, P = 0.007), a larger body circumference (neck circumference: 39.2 &#xb1; 4.0 cm vs . 35.1 &#xb1; 3.7 cm, P = 0.001; waist circumference: 99.7 &#xb1; 10.5 cm vs . 92.2 &#xb1; 10.8 cm, P = 0.027; hip circumference: 102.5 &#xb1; 5.6 cm vs . 97.5 &#xb1; 9.1 cm, P = 0.030), a greater left ventricular end-diastolic diameter (46.6 &#xb1; 4.9 mm vs . 43.1 &#xb1; 4.9 mm, P = 0.026), and a lower left ventricular ejection fraction (64.1 &#xb1; 5.7 % vs . 68.5 &#xb1; 7.8%, P = 0.048). While overall biodiversity and general microbial composition were similar between the noHCM and oHCM groups, ten taxa displayed significant differences at the genus and species levels, with Porphyromonas gingivalis showing the highest abundance and greater enrichment in noHCM (relative abundance: 7.79535 vs . 4.87697, P = 0.043). Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis identified ten distinct pathways, with pathways related to energy and amino acid metabolism being enriched in oHCM patients, and those associated with genetic information processing less abundant in the oHCM group. Metabolic potential analysis revealed ten significantly altered metabolites primarily associated with amino sugar and nucleotide sugar metabolism, porphyrin metabolism, pentose and glucuronate interconversion, and lysine degradation.<br><br>CONCLUSIONS: The higher abundance of Porphyromonas gingivalis , which is known to impact cardiovascular health, in noHCM patients may partially account for clinical differences between the groups. Pathway enrichment and metabolic potential analyses suggest microbial functional shifts between noHCM and oHCM patients, potentially reflecting inherent metabolic changes in HCM.},
}
@article {pmid40846194,
year = {2025},
author = {Han, Y and Cui, J and Guo, P and Yang, S},
title = {Remediation effects of straw combined with microbial agents on cinnamon soils with varying degradation based on metagenomics and untargeted metabolome.},
journal = {Environmental research},
volume = {285},
number = {Pt 5},
pages = {122649},
doi = {10.1016/j.envres.2025.122649},
pmid = {40846194},
issn = {1096-0953},
mesh = {*Soil Microbiology ; Metagenomics ; *Cinnamomum zeylanicum ; *Metabolome ; Soil/chemistry ; Biodegradation, Environmental ; *Environmental Restoration and Remediation/methods ; *Soil Pollutants/metabolism ; Microbiota ; },
abstract = {Microbial agents show potential for improving soil quality and crop yield. However, in the context of different soil degraded degrees, the effects of straw combined with microbial agents on soil microbial communities and their associated metabolic processes remain insufficiently explored. Here, we conducted pot experiments using cinnamon soils at three degradation levels (highly, moderately, and non-degraded), applying straw alone or straw combined with microbial agents during alfalfa cultivation. In this study, we combined metagenomic sequencing and untargeted metabolomics to study the effects of straw and straw combined with microbial agents on soil quality and plant biomass, and metabolites as well as on the network complexity and stability of soil microbial communities. Our findings showed that both straw and straw-microbial agent combinations enhanced the soil quality and alfalfa yield, as well as on the complexity and stability of bacterial networks in highly degraded soils. Meanwhile, the straw-microbial agent combination significantly altered key metabolic pathways (e.g., steroid hormone biosynthesis, cofactor biosynthesis, and nucleotide metabolism) and differentially regulated metabolites (e.g., amino acids/peptides, organosulfur compounds, and alkaloids) compared to straw alone, with distinct effects observed across degradation levels. Overall, the microbial community and their metabolites shaped by straw and straw combined with microbial agents promoted the remediation of degraded soils, ultimately enhancing soil quality and plant biomass. These findings advance the understanding of straw and microbial agents as a synergistic remediation strategy for modulating soil microbial communities and offer practical insights for soil health restoration.},
}
@article {pmid40845638,
year = {2025},
author = {Bai, X and Bi, J and Li, A and Zhu, X and Zhao, Z and Hu, H and Pan, H},
title = {Phylosymbiosis of antibiotic resistance genes in pig feces and potential transmission to piggery workers.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118907},
doi = {10.1016/j.ecoenv.2025.118907},
pmid = {40845638},
issn = {1090-2414},
mesh = {Animals ; *Feces/microbiology ; Swine/microbiology ; *Drug Resistance, Microbial/genetics ; Gastrointestinal Microbiome/genetics ; Phylogeny ; *Symbiosis ; Humans ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Animal feces are recognized as reservoirs of antibiotic resistance genes (ARGs) that threaten public health and environmental safety. However, it remains unclear whether livestock breeds affect ARGs in feces and how they are transferred from animals to workers. Here, an approach integrated with metagenomics and whole-genome resequencing was used to study Saba (SB) and Large White (LW) pigs on the same pig farm. Higher abundance of both gut bacterial and viral communities and lower abundance of tetracycline and aminoglycoside resistance genes were observed in SB pigs. Gut bacterial communities control the shape of the antibiotic resistome in pig feces. The co-occurrence network showed a close association between ARGs, mobile genetic elements, and gut microbiota in SB pigs. By integrating whole-genome resequencing, an apparent phylosymbiosis was revealed in the antibiotic resistome in pig feces. The structural equation model revealed that host phylogeny primarily directly controlled the antibiotic resistome in pig feces, with additional indirect effects mediated by gut bacterial communities. The flow of ARGs, including pig feces, sludge, flies, and worker feces, between pig farms was further investigated. The findings revealed a direct contribution of pig feces to the ARGs in worker feces, while flies played only a minor role in the transfer of ARGs to pig workers. These findings are essential for developing effective measures to combat antimicrobial resistance in pigs and potential threats to public health.},
}
@article {pmid40845582,
year = {2025},
author = {Li, Y and Zhang, C and Meng, Z and You, M and Shi, H},
title = {Microbial dysbiosis induced in Cyprinus carpio by tetrabromobisphenol A exposure: Mediation through gut barrier impairment and oxidative stress.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {56},
number = {},
pages = {101609},
doi = {10.1016/j.cbd.2025.101609},
pmid = {40845582},
issn = {1878-0407},
mesh = {Animals ; *Carps/microbiology ; *Oxidative Stress/drug effects ; *Dysbiosis/chemically induced/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Polybrominated Biphenyls/toxicity ; *Water Pollutants, Chemical/toxicity ; *Fish Diseases/microbiology/chemically induced ; },
abstract = {The frequent detection of Tetrabromobisphenol A (TBBPA) in environmental media has elicited considerable scientific concern. The ecotoxicological impacts of TBBPA on intestinal health in the common carp (Cyprinus carpio) were systematically investigated through integrated histopathological, biochemical, and metagenomic analyses. Fish were exposed to environmentally relevant TBBPA concentrations (0, 0.005, 0.05, and 0.5 mg/L) for a 14-day duration. Dose-dependent intestinal damage was induced by TBBPA exposure, manifested as villus fusion and atrophy, oxidative stress (diminished SOD/CAT activities and elevated MDA levels), and downregulated expression of tight junction proteins (ZO-1, Claudin-3, Occludin). This collectively compromised barrier integrity and triggered pro-inflammatory cytokine upregulation of TNF-α alongside anti-inflammatory IL-10 suppression. Significant intestinal microbial dysbiosis was detected via 16S rRNA sequencing. Alpha diversity indices were reduced at low concentrations (0.005 mg/L) of TBBPA but elevated at higher concentrations (0.05-0.5 mg/L). TBBPA exposure induced gut microbiota perturbations, characterized by depletion of beneficial taxa (Cetobacterium) and enrichment of opportunistic pathogens (Legionella and Thermomonas). Functional prediction analyses indicated that these microbial alterations may influence carbohydrate metabolism, and vitamin biosynthesis within the intestinal tract of common carp. Collectively, these findings demonstrated that TBBPA disrupted intestinal health via synergistic mechanisms involving oxidative stress, histopathological damage, and microbiota-mediated dysregulation. This investigation addresses a critical knowledge gap regarding the impacts of TBBPA on fish gut microbiota, while providing provided a reference for assessing the potential ecological risks of TBBPA in the environment.},
}
@article {pmid40841874,
year = {2025},
author = {Dinçer, S and Ülger, Y and Delik, A},
title = {Mucosal microbiota signatures reveal diagnostic insights in chronic liver disease.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {607},
pmid = {40841874},
issn = {1471-230X},
support = {CUBAP-FBA-2021-13667//Cukurova University Scientific Research Projects Unit/ ; CUBAP-FBA-2021-13667//Cukurova University Scientific Research Projects Unit/ ; CUBAP-FBA-2021-13667//Cukurova University Scientific Research Projects Unit/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Middle Aged ; *Intestinal Mucosa/microbiology/pathology ; Female ; Case-Control Studies ; Metagenomics ; *Colon/microbiology/pathology ; Adult ; *Liver Diseases/microbiology/diagnosis ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S ; Aged ; Chronic Disease ; Biopsy ; High-Throughput Nucleotide Sequencing ; Principal Component Analysis ; },
abstract = {PURPOSE: Chronic liver disease (CLD) and complications of cirrhosis are responsible for the deaths of approximately two million people per year worldwide. Abnormal intestinal permeability in the intestinal-liver axis and development of intestinal dysbiosis increase disease progression contributing to chronic systemic inflammation in CLD patients. The intestinal microbiota acts as a bioreactor for autonomous metabolic and immunological functions in regulating the host's response to external stimuli in the intestinal microbiota. The study aimed to analyze the gut microbiota profile from colonic mucosal biopsy materials in CLD patients using a metagenomic application.<br><br>MATERIALS AND METHODS: CLD and control groups were formed based on predefined inclusion and exclusion criteria from the study. In the metagenomic study, colonic mucosal biopsy material was studied from a total of 40 individuals, 20 with CLD and 20 healthy controls. We analyzed gut microbiota by 16&#xa0;S rRNA metagenomic next-generation sequencing (NGS) method from colonic mucosal biopsy samples in CLD and healthy individuals. Metagenomic results were analyzed by Principal Component Analysis (PCA).<br><br>RESULTS: Significant differences were observed between the CLD and control groups across multiple taxonomic levels. At the phylum level, Proteobacteria were significantly enriched in CLD patients, while Firmicutes predominated in controls. Class-level analysis showed increased Gammaproteobacteria in CLD, the former associated with inflammatory pathways. At the order level, Enterobacterales were significantly higher in CLD (OR: 1.89, p&#x2009;=&#x2009;0.04), whereas Clostridiales were more abundant in controls. Family-level comparisons revealed elevated Enterobacteriaceae in CLD, while Ruminococcaceae and Veillonellaceae were relatively preserved in controls. At the genus level, Prevotella and Streptococcus were increased in controls. Alpha diversity indices (Shannon, Chao1) were significantly lower in the CLD group (p&#x2009;<&#x2009;0.001), indicating reduced microbial richness. Beta diversity analysis (PCoA, Bray-Curtis) showed distinct clustering between groups, supporting compositional divergence. Integration of metagenomic findings with biochemical markers (e.g.<br><br>, GGT: OR 0.79, p&#x2009;=&#x2009;0.03) further underscored group-specific microbial signatures.<br><br>CONCLUSION: We observed a significant compositional shift in the gut microbiota of patients with CLD. Notably, pro-inflammatory taxa were increased and a decrease in beneficial bacterial groups involved in maintaining microbial homeostasis. Diversity analyses indicated a reduction in microbial richness in the CLD group. These findings may aid in identifying CLD-specific microbial signatures. Furthermore, integrating metagenomic data with biochemical parameters may contribute to improved diagnostic strategies.},
}
@article {pmid40841038,
year = {2025},
author = {Tang, Z and Zhang, Y and Shangguan, H and Xie, A and Xu, X and Jiang, Y and Breed, MF and Sun, X},
title = {Urban organic manure application enhances antibiotic resistance gene diversity and potential human pathogen abundance in invasive giant African snails.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {610-620},
doi = {10.1016/j.jes.2025.02.028},
pmid = {40841038},
issn = {1001-0742},
mesh = {Animals ; *Manure ; *Drug Resistance, Microbial/genetics ; *Snails/microbiology ; Humans ; Introduced Species ; Gastrointestinal Microbiome ; Soil Microbiology ; Environmental Monitoring ; RNA, Ribosomal, 16S ; Feces/microbiology ; },
abstract = {The giant African snail (Achatina fulica) is an invasive species served as potential vectors for antibiotic resistance genes (ARGs) and potential human bacterial pathogens. Currently, urban green spaces receive extensive organic manure additions as part of their management, may intensify the biological contamination potential of these snail vectors, thereby increasing the risk of biological pollution in green spaces. However, the specific impacts of this practice on the microbial ecology of these invasive species remain poorly understood. Here, we investigated the effects of organic manure application on the gut microbiome of giant African snails, focusing on ARGs, bacterial community structure, and potential human bacterial pathogens. Microcosm experiments compared snail gut microbiomes in different treatments (Soil: soil samples collected after manure amendment, before any snail exposure. Feces: fecal samples collected from snails that lived on manure-amended soil. Control: fecal samples collected from snails that lived on unamended soil) using 16S rRNA high-throughput sequencing and metagenomic analysis. Our results show that manure application significantly altered gut bacterial community structure and increased ARG diversity by enriching specific high-risk ARGs (such as sul1 and sul2 in the Feces group increased by 2.89 and 2.43 times, respectively, compared to the Control group), and the introduction of eight novel ARG subtypes, despite decreasing overall ARG abundance. Moreover, the relative abundance of potential human pathogens, particularly Pseudomonadaceae, was greatly increased by manure application. These findings reveal that organic manure application in urban green spaces can potentially enhances their role as reservoirs and vectors of ARGs and human pathogens.},
}
@article {pmid40841030,
year = {2025},
author = {Nie, E and He, P and Zhang, H and Lü, F},
title = {Genome-centric metagenomic analysis unveils the influence of temperature on the microbiome in anaerobic digestion.},
journal = {Journal of environmental sciences (China)},
volume = {158},
number = {},
pages = {516-526},
doi = {10.1016/j.jes.2024.10.007},
pmid = {40841030},
issn = {1001-0742},
mesh = {Anaerobiosis ; *Microbiota ; Metagenomics ; *Temperature ; *Metagenome ; Archaea/genetics ; Bacteria/genetics ; },
abstract = {Temperature plays a crucial role in shaping microbial ecosystems during anaerobic digestion. However, the specific microbial communities and their functions across a wide temperature range still remain elusive. This study employed a genome-centric metagenomic approach to explore microbial metabolic pathways and synergistic networks at temperatures of 35, 44, 53, 55, and 65 °C. A total of 84 metagenome assembled genomes (MAGs) were assembled, with over 65 % of these MAGs corresponding to novel bacterial and archaeal species (including Firmicutes, Chloroflexota, Bacteroidia and Methanobacteriota), greatly enhancing our current comprehension anaerobic digestion process. Notably, functional annotation identified that 44_bin.2 (Methanothrix_A sp. 001602645) harbors enzymes associated with hydrogenotrophic metabolism. Additionally, this microorganism exhibited diverse metabolic capabilities at 44 °C, a temperature commonly employed in industrial practice yet less explored in bench studies. Consequently, it implies a promising potential for conducting anaerobic digestion at a moderate thermophilic temperature, as opposed to the conventional mesophilic range. The microorganism exhibited a variety of metabolic capabilities at 44 °C, a temperature frequently employed in industrial applications but underexplored in laboratory investigations. The findings suggest that anaerobic digestion carried out at moderate thermophilic temperatures may have a higher potential for methane production.},
}
@article {pmid40840192,
year = {2025},
author = {Yang, SB and Lu, ZM and Shen, HJ and Fu, JJ and Yang, Y and Zhang, XJ and Chai, LJ and Wang, ST and Zhang, SY and Shen, CH and Shi, JS and Xu, ZH},
title = {Unraveling Qu-aroma variation between inner and outer layers of medium-temperature Daqu: A multi-omics and sensory approach.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111392},
doi = {10.1016/j.ijfoodmicro.2025.111392},
pmid = {40840192},
issn = {1879-3460},
mesh = {*Volatile Organic Compounds/analysis/metabolism/chemistry ; Fermentation ; *Odorants/analysis ; Gas Chromatography-Mass Spectrometry ; Microbiota ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Humans ; Temperature ; Metagenomics ; Metabolic Networks and Pathways ; Edible Grain/microbiology/chemistry ; Taste ; Multiomics ; },
abstract = {Solid-state fermentation heterogeneity causes microenvironmental differences, shaping diverse microbial communities and metabolite compositions. Here, we aimed to investigate the variations in Qu-aroma between the inner (I-) and outer (O-) layers of medium-temperature Daqu (MT-Daqu) starter, and to analyze the differences in microbial communities as well as the associated metabolic pathways related to Qu-aroma volatile organic compounds (VOCs). Firstly, quantitative descriptive analysis revealed that the I-layer exhibited intensified rancid-roasted notes, whereas the O-layer showed stronger grain and woody notes. Secondly, a total of 225 VOCs were identified from 88 inner and outer layer samples using HS-SPME-GC-MS, among which 43 differential VOCs were confirmed between the layers (VIP > 1, P < 0.05, and Fold change ≥1.5 or ≤0.67). Thin film (TF)-SPME-GC-O/MS revealed 52 and 47 odors with corresponding VOCs in the I- and O-layers, respectively. Subsequently, cross-referencing metagenomic and metabolic databases revealed that 37 aroma-active VOCs were functionally linked to six metabolic modules within the MT-Daqu microbial metabolic network. Finally, integrated metagenomic and amplicon sequencing identified potential functional microorganisms associated with specific metabolic modules. Five genera, including Kroppenstedtia and Thermomyces, were identified as characteristic of the I-layer, while 22 genera, such as Lactobacillus and Saccharomycopsis, were characteristic of the O-layer. Notably, Kroppenstedtia, Thermomyces, Lactobacillus, Saccharomycopsis, and Weissella were ubiquitously associated with all six metabolic modules across both layers of MT-Daqu. This study delivers a perspective for clarifying the spatial heterogeneity of Qu-aroma and its microbial drivers.},
}
@article {pmid40838847,
year = {2025},
author = {Gao, X and Zheng, Y and Chang, H and Liu, J and Sun, X and Ren, Y and Li, L and Zhao, G and Cheng, Y and Ma, S and Zhao, J and Deng, J and Kang, T and Qiao, Z and Zhao, H and Xie, D and Wang, T and Li, S and Shi, H and Shi, A and Zhang, P},
title = {Metagenomic Analysis of the Tonsil Virome Highlights Its Diagnostic Potential for Rheumatoid Arthritis.},
journal = {Journal of medical virology},
volume = {97},
number = {8},
pages = {e70570},
doi = {10.1002/jmv.70570},
pmid = {40838847},
issn = {1096-9071},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; *Virome ; *Arthritis, Rheumatoid/diagnosis/virology ; *Metagenomics ; Male ; Female ; Middle Aged ; *Palatine Tonsil/virology ; Adult ; *Viruses/genetics/classification/isolation &amp; purification ; Aged ; Microbiota ; },
abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune disease whose exact pathogenesis remains unclear, despite links to genetics, environmental factors, and microbial dysbiosis. Recent studies have highlighted the role of the microbiome in RA, yet the contribution of the tonsil virome remains unexplored. This study aims to investigate whether changes in the tonsil virome are associated with RA progression and assess its diagnostic potential. Using metagenomic data from 32 RA patients and 30 healthy controls (HCs), we identified 45 782 viral operational taxonomic units (vOTUs), with 14 341 classified as core vOTUs. RA patients exhibited significantly reduced virome richness and diversity, whereas Siphoviridae and Microviridae dominated both groups. Statistical analysis identified 235 RA-associated viral markers, including 13 enriched in RA and 222 in HCs. RA-enriched markers were primarily bacteriophages infecting Streptococcaceae, whereas HCs displayed more diverse viral-host interactions. Random forest models demonstrated strong discriminatory power of viral markers in distinguishing RA patients from HCs, achieving an AUC of 0.960, outperforming bacterial markers. Correlation analyses further linked viral markers to immune cell subsets, suggesting that tonsil virome alterations may influence immune dysregulation in RA. This study reveals significant changes in the tonsil virome of RA patients, highlighting its potential as a diagnostic tool and offering new insights into RA pathogenesis. These findings pave the way for future research into the virome's role in autoimmune diseases and therapeutic development.},
}
@article {pmid40836310,
year = {2025},
author = {Wang, X and Dong, Q and Huang, P and Yang, S and Gao, M and Zhang, C and Zhang, C and Deng, Y and Huang, Z and Ma, B and Jiao, Y and Zhou, Y and Wu, T and Zou, H and Shi, J and Sheng, Y and Wang, Y and Consortium, C and Tang, L and Hu, S and Duan, Y and Sun, W and Chen, W and Zhai, Q and Kong, X and Chen, L},
title = {The genetic diversity and populational specificity of the human gut virome at single-nucleotide resolution.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {188},
pmid = {40836310},
issn = {2049-2618},
support = {32270077//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome/genetics ; Genome, Viral ; Feces/virology/microbiology ; *Genetic Variation ; *Polymorphism, Single Nucleotide ; *Viruses/genetics/classification/isolation &amp; purification ; China ; Bacteria/genetics/classification ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Large-scale characterization of gut viral genomes provides strain-resolved insights into host-microbe interactions. However, existing viral genomes are mainly derived from Western populations, limiting our understanding of global gut viral diversity and functional variations necessary for personalized medicine and addressing regional health disparities.<br><br>RESULTS: Here, we introduce the Chinese Gut Viral Reference (CGVR) set, consisting of 120,568 viral genomes from 3234 deeply sequenced fecal samples collected nationwide, covering 72,751 viral operational taxonomic units (vOTUs), nearly 90% of which are likely&#xa0;absent from current databases. Analysis of single-nucleotide variations (SNVs) in 233 globally prevalent vOTUs revealed that 18.9% showed significant genetic stratification between Chinese and non-Chinese populations, potentially linked to bacterial infection susceptibility. The predicted bacterial hosts of population-stratified viruses exhibit distinct genetic components associated with health-related functions, including multidrug resistance. Additionally, viral strain diversity at the SNV level correlated with human phenotypic traits, such as age and gastrointestinal issues like constipation. Our analysis also indicates that the human gut bacteriome is specifically shaped by the virome, which mediates associations with human phenotypic traits. Video Abstract CONCLUSIONS: Our analysis&#xa0;underscores the unique genetic makeup of the gut virome across populations and emphasizes the importance of recognizing gut viral genetic heterogeneity for deeper insights into regional health implications.},
}
@article {pmid40835198,
year = {2025},
author = {Liu, Q and Wang, M and Xie, JW and Du, YT and Yin, ZG and Cai, JH and Zhao, MH and Jiang, YT and Zhang, HD},
title = {Macrogenome analysis of rodents from Heilongjiang Province, China.},
journal = {Acta tropica},
volume = {270},
number = {},
pages = {107789},
doi = {10.1016/j.actatropica.2025.107789},
pmid = {40835198},
issn = {1873-6254},
mesh = {Animals ; China ; *Viruses/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; *Rodentia/microbiology/virology ; *Murinae/microbiology/virology ; *Arvicolinae/microbiology/virology ; *Microbiota ; Phylogeny ; *Metagenome ; Disease Reservoirs/virology/microbiology ; Zoonoses ; },
abstract = {Rodents are carriers and hosts of numerous zoonotic pathogens, analysing the diversity of viruses and bacteria carried by rodents is important for predicting and reducing the risk of future outbreaks of zoonotic diseases. Heilongjiang is a border province in China with rich ecological resources. In this study, we characterized the zoonotic microbiota (viruses and bacteria) in wild rodents. Sixty-seven rodents representing two species (20 Apodemus peninsulae; 47 Myodes rufocanus) were collected in Hengdaohezi Town, Heilongjiang Province, China. Metagenomic sequencing was employed to characterize pathogen carriage in these reservoirs. The sequencing results showed that the annotated viruses covered 21 viral families, including family Arenaviridae and family Hantaviridae. The annotated bacteria cover 1051 bacterial genera, including genus Salmonella and genus Yersinia. Results of de novo assembly of extracted viral sequences using Megahit showed that 154 contigs were assembled from these two hosts, and 110 of these contigs were mapped to 19 viruses from eight families, including Rat arterivirus1, Amur virus and Lassa mammarenavirus, these results can provide a certain reference for the monitoring and control of rodents in Heilongjiang Province.},
}
@article {pmid40835054,
year = {2025},
author = {Wu, Y and Tao, S and Xiao, L and Zhang, J and Tang, Y and Zhang, M and Liu, S and Huang, Y and Liu, Y and Xie, M and Zhao, Z and Lv, Q and Cai, J and Pei, K and Ma, Q and Yin, Y and Dai, M and Wei, M and Chen, Y and Wang, Q},
title = {Gut virome alterations in schizophrenia: identifying viral biomarkers associated with schizophrenia and treatment response.},
journal = {Brain, behavior, and immunity},
volume = {130},
number = {},
pages = {106080},
doi = {10.1016/j.bbi.2025.106080},
pmid = {40835054},
issn = {1090-2139},
mesh = {Humans ; *Schizophrenia/virology/drug therapy/microbiology ; Male ; Female ; Adult ; *Gastrointestinal Microbiome/physiology ; *Virome/physiology ; Feces/virology ; Biomarkers ; Treatment Outcome ; Young Adult ; Antipsychotic Agents/therapeutic use ; },
abstract = {BACKGROUND: The gut virome is an important component of the microbiome with potential implications for schizophrenia. However, its role in disease pathology and treatment response remains unclear.<br><br>METHODS: We performed metagenomic sequencing on fecal samples from 49 first-episode schizophrenia patients and 49 healthy controls. Viral diversity and taxonomic profiles were compared between groups. Within patients, we assessed associations between viral alpha diversity and symptom severity, as well as between specific viral taxa and treatment outcomes, including short- and long-term PANSS reduction and response trajectories. Response trajectories were identified by clustering patients based on the longitudinal PANSS reduction patterns.<br><br>RESULTS: There were no significant differences in alpha diversity between schizophrenia patients and healthy controls. Among patients, higher viral diversity was associated with more severe negative symptoms. Although several viral taxa showed nominal associations with schizophrenia, none remained significant after FDR correction. Regarding treatment outcomes, the abundance of Brigitvirus was negatively associated with the 6-week symptom reduction rate (FDR&#xa0;=&#xa0;0.012), and two viral species were reduced in the low-response trajectory group.<br><br>CONCLUSIONS: Although virome differences between patients with schizophrenia and healthy controls were modest, associations between viral features and both symptom severity and treatment response indicate potential clinical relevance.},
}
@article {pmid40834728,
year = {2025},
author = {Bains, A and Dahal, S and Manna, B and Lyte, M and Yang, L and Singhal, N},
title = {L-norepinephrine induces community shift, oxidative stress response, metabolic reprogramming, and virulence potential in wastewater microbiomes.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124353},
doi = {10.1016/j.watres.2025.124353},
pmid = {40834728},
issn = {1879-2448},
mesh = {*Oxidative Stress/drug effects ; *Wastewater/microbiology ; Virulence/drug effects ; *Microbiota/drug effects ; *Bacteria/drug effects/pathogenicity/genetics/metabolism ; },
abstract = {Neuroendocrine compounds discharged into wastewater systems represent an emerging challenge at the intersection of human physiology and environmental microbiology. l-norepinephrine (L-NE), which has been recognized to potentiate growth of human and animal bacterial pathogens, is discharged in sewage through urine and faeces. While extensive pure culture studies have established l-NE's capacity to modulate bacterial virulence through iron acquisition and quorum sensing pathways, its impact on complex microbial communities, where intricate metabolic networks and interspecies interactions dominate, remains largely unexplored. This knowledge gap is particularly critical as urbanization drives increasing neuroendocrine compound loads in wastewater influents in metropolitan areas. Through parallel treatments of l-NE (1 × 10[-5] M to 1 × 10[-4] M), dextrose, and H2O2 in municipal and agricultural wastewater communities, we uncovered sophisticated metabolic and regulatory mechanisms that challenge the conventional understanding of microbial substrate utilization. Despite containing 10-fold less carbon, l-NE treatments achieved superior growth (10[8] CFU mL[-1]) while maintaining Pseudomonadaceae-dominated communities. Targeted metaproteomics revealed coordinated upregulation of oxidative stress genes (oxyR, soxRS) and antioxidant enzymes, while proteome-constrained metabolic modeling demonstrated distinct pathway modulation in central carbon and nitrogen metabolism. Notably, when compared to dextrose-supplemented controls, representing typical carbon substrate utilization, l-NE treatments showed similar taxonomic profiles without preferential enrichment of known pathogenic families. However, l-NE significantly enhanced autoinducer gene (luxS, qseC) expression, suggesting increased virulence potential through community-level metabolic reprogramming. These findings reveal l-NE as a potent modulator of microbial community dynamics in engineered ecosystems, with important implications for treatment process stability and downstream environmental impacts.},
}
@article {pmid40834570,
year = {2025},
author = {Ansari, SA and Ramteke, A and Sawarkar, R and Kumar, T and Khan, D and Agashe, A and Patil, MP and Singh, L},
title = {"Innovative approaches in microbial community engineering for food waste management: A comprehensive review".},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127000},
doi = {10.1016/j.jenvman.2025.127000},
pmid = {40834570},
issn = {1095-8630},
mesh = {*Waste Management/methods ; Biodegradation, Environmental ; *Microbial Consortia ; Metabolic Engineering ; Fermentation ; },
abstract = {Food waste (FW) is a critical global issue, exacerbating environmental degradation and resource scarcity. Traditional FW management methods are often inefficient and unsustainable. This review highlights advances in microbial community engineering for FW valorization, focusing on synthetic biology, metagenomics, metabolic engineering, and electro-fermentation. Engineered microbial consortia enhance the breakdown of complex organics while producing bioenergy, bioplastics, and organic acids. Metagenomics enables precise metabolic optimizations, and electro-fermentation improves bioconversion yields. These systems outperform conventional methods in reducing greenhouse gases, recovering nutrients, and promoting a circular bioeconomy. Challenges persist, including microbial stability, scalability, and incomplete knowledge of interspecies interactions. Future research should integrate AI and machine learning to design robust synthetic consortia and optimize metabolic pathways. Scaling electrochemical technologies (e.g., microbial electrosynthesis) requires further validation. Standardized biosafety protocols, techno-economic analyses, and supportive policies are essential for industrial adoption. Interdisciplinary collaboration is crucial to address these gaps. In conclusion, microbial engineering offers a sustainable FW management solution, improving biodegradation efficiency and resource recovery. Future efforts must prioritize scalable, stable systems with real-time monitoring and ecological safety. Overcoming these challenges will enable engineered microbes to mitigate environmental impacts, generate renewable energy, and advance a resource-efficient future.},
}
@article {pmid40834509,
year = {2025},
author = {Poshvina, DV and Balkin, AS and Dilbaryan, DS and Vasilchenko, AS},
title = {Unravelling the response of the soil microbiome to macrolactin A: A metagenomic study.},
journal = {Chemosphere},
volume = {387},
number = {},
pages = {144645},
doi = {10.1016/j.chemosphere.2025.144645},
pmid = {40834509},
issn = {1879-1298},
mesh = {*Soil Microbiology ; *Microbiota/drug effects ; *Macrolides/pharmacology ; Metagenomics ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Rhizosphere ; Soil/chemistry ; },
abstract = {The development of environmentally sustainable biopreparations for crop protection requires comprehensive assessment of their microbiome impacts. This study investigates how macrolactin A (McA)-a polyketide antibiotic produced by plant-beneficial Bacillus velezensis-shapes soil microbial communities and antibiotic resistance gene (ARG) profiles under various agricultural scenarios. Using high-throughput metagenomics and network analysis, we compared untreated soils with those exposed to two McA concentrations: a high dose (10 mg/kg soil, representing potential point-source accumulation) and a low dose (1 mg/kg, mimicking natural rhizosphere levels). While overall ARG α- and β-diversity remained stable, we observed significant taxonomic restructuring, with Pseudomonadota increasing by 1.36-2.15 % and Actinomycetota declining by 1.14-1.74 % across treatments. Resistome analysis showed dose-dependent ARG selection: control soils favored target alteration mechanism, whereas McA promoted efflux, inactivation, and protection mechanisms. Network analysis demonstrated disruption of complex ARG-host associations, as control-dominant genera belonging to Actinomycetota (Conexibacter, Baekduia, and Capillimicrobium) maintaining 16-21 ARGs per genome decreased, while genera belonging to Pseudomonadota (Bradyrhizobium, Mesorhizobium, Paraburkholderia, and Piscinibacter) with streamlined resistomes (1-2 ARGs) became prevalent. Functional gene profiling (COGs) and annotation of MAGs revealed dose-dependent restructuring: low-dose McA enriched chemotaxis systems and broad-spectrum efflux pumps, facilitating motile escape and energy-efficient resistance, whereas high-dose exposure selected for secondary metabolite synthesis, metal transporters, and cell wall remodeling genes, indicating defensive countermeasures. These findings demonstrate McA's biphasic selection: low doses favor avoidance strategies (efflux/motility), while high doses enforce biosynthetic defenses and structural resilience. The results support the hypothesis that narrow-spectrum antibiotics act as ecosystem engineers through metabolic trade-offs, highlighting the need to evaluate resistome restructuring in biocontrol agent risk assessments.},
}
@article {pmid40833800,
year = {2025},
author = {Kaspersen, HP and Estensmo, EL and Slettemeås, JS and Haverkamp, THA and Sjurseth, SK and Granstad, S and Sekse, C and Frederiksen, RF and Urdahl, AM},
title = {Monensin phase-out in Norwegian turkey production decreases Bifidobacterium spp. abundance while enhancing microbial diversity.},
journal = {Microbial genomics},
volume = {11},
number = {8},
pages = {},
pmid = {40833800},
issn = {2057-5858},
mesh = {Animals ; *Monensin/pharmacology ; *Turkeys/microbiology ; *Bifidobacterium/drug effects/genetics/classification/isolation &amp; purification ; Poultry Diseases/prevention &amp; control/microbiology ; Cecum/microbiology ; *Gastrointestinal Microbiome/drug effects ; Norway ; Female ; Male ; Coccidiosis/veterinary/prevention &amp; control ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; *Coccidiostats/pharmacology ; },
abstract = {Intestinal tissue damage caused by coccidiosis is an important predisposing factor for necrotic enteritis in turkeys, and both diseases are common health issues in turkey production. In Norway, the in-feed ionophore coccidiostat monensin has been used as a preventive measure to combat coccidiosis since the late 1980s. In 2022, however, preventive use of monensin was phased out, which led to an undesired increase in antibiotic treatments among turkey flocks, largely due to necrotic enteritis. The aim of this study was to investigate the overall effects of the preventive monensin use and antibiotic treatment on the turkey caecal microbiota. A total of 102 flock samples from the Norwegian turkey population were included, and metagenomic datasets were generated through shotgun sequencing. All datasets were processed with the Taxprofiler pipeline, followed by diversity, redundancy and differential abundance analyses in R. A significant decrease in alpha and beta diversity was observed for the caecal samples from turkeys exposed to monensin, compared with the non-exposed. An increased abundance of Bifidobacterium spp. was observed in the samples from monensin-exposed turkeys, including Bifidobacterium pullorum, Bifidobacterium longum, Bifidobacterium pseudolongum, Bifidobacterium pseudocatenulatum and Bifidobacterium animalis. Additionally, a decrease in Megamonas and Megasphaera species was detected in these samples. Further, species within the Clostridium genus were higher in abundance among the samples from female turkeys compared with male turkeys. The results indicate that the use of monensin seems to decrease the overall diversity and promote the abundance of Bifidobacterium spp. in the caecum of turkeys, while decreasing the abundance of Megamonas and Megasphaera species. The use of monensin may be beneficial for the gut microbiota due to an increase in favourable Bifidobacterium spp. In contrast, treatment with phenoxymethylpenicillin (penicillin V) early in the turkey life cycle does not seem to cause long-term changes in the caecal microbiota composition. However, further studies are needed to investigate the effects of a decreased abundance of Bifidobacterium spp. and increased gut microbiota diversity in turkeys in the absence of monensin use.},
}
@article {pmid40833852,
year = {2025},
author = {Vander Donck, L and Victor, M and Van Beeck, W and Van Rillaer, T and Dillen, J and Ahannach, S and Wittouck, S and Allonsius, CN and Lebeer, S},
title = {Host-independent synergism between Lactobacillus crispatus and other vaginal lactobacilli.},
journal = {Cell reports},
volume = {44},
number = {9},
pages = {116171},
pmid = {40833852},
issn = {2211-1247},
mesh = {Female ; Humans ; *Vagina/microbiology ; *Lactobacillus crispatus/physiology/genetics ; Microbiota ; *Lactobacillus/physiology/genetics ; },
abstract = {The human vagina is a unique microbiome, typically predominated by Lactobacillus species in healthy women. However, we currently lack an understanding of why lactobacilli predominate in this environment and how these bacteria interact, aspects that are crucial for developing microbiome-based therapeutics. In this study, we used cost-efficient synthetic communities (SynComs) to investigate the stability and dynamics of Lactobacillus-predominated vaginal communities from healthy women independent of host influence. Reproducible communities of Lactobacillus crispatus co-occurring with Limosilactobacillus species and Lactobacillus jensenii were established in top-down experiments. Co-occurrence was verified with compositional correlation patterns in metagenome sequencing data and reproduced through a bottom-up approach. This co-occurrence pattern was independent of strain selection, host factors, and inoculation ratio. Genome-scale metabolic models predicted potential cross-feeding involving amino acids (e.g., L-arginine, L-lysine, and γ-aminobutyric acid [GABA]) and vitamins as mechanisms mediating their co-occurrence. This study provides a framework for developing reproducible synthetic vaginal Lactobacillus communities and informs future microbiome-based therapies.},
}
@article {pmid40833454,
year = {2025},
author = {Fong, GY and Chan, KG and Goh, WL and Yap, ML},
title = {Metagenomic profiling of pigeon faecal microbiota: insights into microbial diversity, pathogens, and antimicrobial resistance genes.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {134},
pmid = {40833454},
issn = {1572-9699},
support = {IPSR/RMC/UTARRF/2022-C1/Y01//Universiti Tunku Abdul Rahman/ ; },
mesh = {Animals ; *Columbidae/microbiology/virology ; *Feces/microbiology/virology ; *Bacteria/genetics/classification/isolation &amp; purification/drug effects ; Metagenomics ; Viruses/genetics/classification/isolation &amp; purification ; Fungi/genetics/classification/isolation &amp; purification/drug effects ; Metagenome ; Malaysia ; *Microbiota ; Biodiversity ; Phylogeny ; *Drug Resistance, Microbial/genetics ; },
abstract = {Rock pigeon (Columba livia) droppings harbour diverse microorganisms, including potential pathogens. This study utilised shotgun metagenomic sequencing to analyse pigeon faecal microbiota and identify potential pathogens. Fresh faecal samples (273) were collected within Universiti Tunku Abdul Rahman Kampar campus, Malaysia. Total genome and viral genomes were extracted and sequenced using the Illumina NovaSeq 6000 platform. Taxonomic assignment, antimicrobial resistance (AMR) gene detection, and viral genome assembly were conducted using the CZ ID platform. The microbial diversity was predominated by bacteria, followed by eukaryotic viruses and fungi, with no archaea were detected. Pseudomonadota (84.44%) and Bacillota (15.26%) were the predominant bacterial phyla, with Pseudomonadota being 5.5 times more abundant, indicating potential enteric-like issues within the pigeon flocks. Approximately 5.11% of the bacterial community (comprising 38 species), was identified as potential pathogens, could primarily cause human enteric and respiratory infections. Nineteen AMR genes were detected, primarily associated with pathogenic Shigella, Salmonella, and Klebsiella. The presence of AMR genes and possible co-circulation among pathogenic bacteria impose the risk of emergence of multidrug-resistant bacteria. Nine avian virus species were detected. The predominant DNA virus, pigeon circovirus (73.23%) could cause immunosuppression, predisposing pigeons to secondary infections by E. coli, K. pneumoniae, and rotaviruses. The predominant RNA virus, rotaviruses (80.43%) could cause enteric diseases in both humans and birds. The fungal community comprised Kazachstania (94.11%) and Trichosporon (3.56%), with K. bovina and T. asahii identified as human pathogens. This study highlights the compelling need for effective pigeon control in dining areas, ventilation systems, and healthcare facilities.},
}
@article {pmid40833093,
year = {2025},
author = {Lai, Z-L and Su, Y-D and Lin, H-H and Wang, S-Y and Lin, Y and Liang, S and Chen, W-C and Hsueh, P-R},
title = {Deciphering the impact of contaminating microbiota in DNA extraction reagents on metagenomic next-generation sequencing workflows.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0311924},
pmid = {40833093},
issn = {2165-0497},
mesh = {*Metagenomics/methods/standards ; Humans ; *High-Throughput Nucleotide Sequencing/methods/standards ; *DNA Contamination ; *Microbiota/genetics ; Workflow ; *DNA, Bacterial/genetics/isolation &amp; purification ; Indicators and Reagents ; Bacteria/genetics/classification/isolation &amp; purification ; },
abstract = {UNLABELLED: The widespread adoption of metagenomic next-generation sequencing has revolutionized microbial detection, yet contaminating DNA in laboratory reagents poses significant challenges for result interpretation. This study investigated microbial contamination profiles across four commercial DNA extraction reagent brands (M, Q, R, and Z) and assessed batch-to-batch variability. Extraction blanks were generated using molecular-grade water or ZymoBIOMICS Spike-in Control I as input materials. Analysis revealed distinct background microbiota profiles between brands, with some containing common pathogenic species that could affect clinical interpretation. Notably, background contamination patterns varied significantly between different lots of the same brand, highlighting the need for lot-specific microbiota profiling. Site-specific environmental contaminants were identified through analysis of 30 control samples from a single study site. Additionally, comparison of blood samples from healthy individuals with control samples suggested no evidence of a consistent blood microbiome, suggesting that "extraction blanks" may serve as negative controls in clinical metagenomic testing of sterile liquid biopsy samples. These findings emphasize the importance of including negative controls in every run and underscore the need for manufacturers to provide comprehensive background microbiota data for each reagent lot to optimize clinical interpretation and minimize false-positive results.<br><br>IMPORTANCE: Metagenomic next-generation sequencing (mNGS) has revolutionized pathogen detection and microbiome studies, but contamination from DNA extraction reagents remains a critical challenge. This study highlights the significant variability in background microbiota profiles across reagent brands and manufacturing lots, emphasizing the need for manufacturers to provide detailed contamination profiles. Our findings underscore the importance of implementing extraction blanks as standard controls and incorporating bioinformatics tools to account for background noise. These measures are essential to enhance the reliability of mNGS results and prevent diagnostic errors, particularly in clinical settings where contamination could mask or mimic pathogen signals. Additionally, our confirmation that healthy blood lacks a consistent microbiome helps streamline control selection in clinical testing protocols, potentially reducing costs and complexity in clinical mNGS workflows.},
}
@article {pmid40832979,
year = {2025},
author = {Zhou, W and Fan, Y and Zhang, X and Liu, M and Jiang, S and Shang, E and Duan, J},
title = {Amelioration of Guishao Yigong Decoction on Colorectal Cancer Through the Integration of 16S rRNA Sequencing and Fecal Metabolomics.},
journal = {Biomedical chromatography : BMC},
volume = {39},
number = {10},
pages = {e70198},
doi = {10.1002/bmc.70198},
pmid = {40832979},
issn = {1099-0801},
support = {ZDXM-3-9//Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization/ ; },
mesh = {*Drugs, Chinese Herbal/administration &amp; dosage/pharmacology ; *Colorectal Neoplasms/microbiology/therapy ; Metabolomics ; *RNA, Ribosomal, 16S/genetics ; *Feces/chemistry/microbiology ; Animals ; Mice ; *Gastrointestinal Microbiome/drug effects/genetics ; Sequence Analysis, RNA ; *Dysbiosis/microbiology/therapy ; Thiamine Pyrophosphate/metabolism ; Pentanes/metabolism ; Propionates/metabolism ; Levodopa/metabolism ; Stearic Acids/metabolism ; Mice, Inbred C57BL ; Male ; },
abstract = {Guishao Yigong Decoction (GYD), a classical formula, has been used to treat colorectal cancer (CRC) in clinical practices. However, its mechanism is still unclear. Increasing evidence suggests that the gut microbiota may serve as a potential target for treating CRC. Therefore, this study aims to elucidate the amelioration and potential mechanism of GYD on CRC by comprehensively analyzing the metagenome of gut microbiota and fecal metabolome. The results indicated that GYD significantly reduced the number and size of adenomas in the mouse colon, decreased spleen index, alleviated mouse emaciation and rectal bleeding, and protected the colonic barrier. 16S rRNA gene sequencing analysis revealed that GYD could markedly improve the dysbiosis of gut microbiota in CRC mice, increasing the abundance of beneficial bacteria and decreasing the abundance of pathogenic bacteria. Furthermore, the disordered fecal metabolic profiling of CRC mice was notably reversed by GYD. Following GYD administration, metabolites such as thiamine pyrophosphate, 3-methylpentanoic acid, and propanoic acid significantly increased, whereas 2-hydroxy-2-methylpropanoic acid, levodopa, and stearic acid remarkably decreased. Correlation analysis further indicated a close relationship between differential gut microbiota and metabolites. In conclusion, the amelioration of GYD on CRC might involve the regulation of gut microbiota and its metabolism.},
}
@article {pmid40832781,
year = {2025},
author = {Tian, Y and Xu, Q and Wu, Z and Wang, H and Hu, X and He, N and Li, H and Liu, B and Zhong, Y and Zhang, H and Wang, M and Xiao, L and Li, S and Zou, Y},
title = {Ameliorating Effect of Bifidobacterium breve CM02-09T on High-Fat Diet-Induced Nonalcoholic Fatty Liver Disease in Mice.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {16},
pages = {e70957},
doi = {10.1096/fj.202501250RR},
pmid = {40832781},
issn = {1530-6860},
support = {32100009//National Natural Science Foundation of China-Guangdong Joint Fund/ ; },
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/etiology/microbiology/metabolism/pathology/therapy ; *Diet, High-Fat/adverse effects ; Male ; *Probiotics/pharmacology ; Mice, Inbred C57BL ; Mice ; *Bifidobacterium breve/physiology ; *Gastrointestinal Microbiome ; Liver/metabolism/pathology ; },
abstract = {Evidences have demonstrated that the regulation of gut microbiota by probiotics can be utilized to prevent nonalcoholic fatty liver disease (NAFLD); Bifidobacterium was widely used as a potential therapeutic alternative for metabolic diseases. In this study, the probiotic functions of Bifidobacterium breve CM02-09T and its effects on NAFLD were investigated through genome annotation and high-fat diet (HFD)-induced mouse model. The genome of B. breve CM02-09T consists of a single circular chromosome of 2 372 890 bp. Eighteen male C57BL/6J mice were fed a normal chow diet (NCD), a high-fat diet, and a high-fat diet (HFD) with B. breve CM02-09T separately for 12 weeks. Histopathology, lipid content, biochemical markers in the liver and blood, and metagenomics were assessed and compared. Our results indicate that supplementation with B. breve CM02-09T alleviated liver damage, reduced fat accumulation in the liver and epididymal adipose tissue, decreased TNF-α concentration, and improved NAFLD activity scores. Metagenomic analysis revealed that administration of B. breve CM02-09T promoted a decreased Firmicutes/Bacteroidetes ratio (F/B), an increase in beneficial bacteria, and enhanced lipid metabolism functions. Correlation analysis between the differential species and NAFLD-related indicators suggested that the anti-NAFLD effect of B. breve CM02-09T is related to the gut microbiota. Therefore, B. breve CM02-09T attenuates NAFLD by modulating the gut microbiota and could be used as an alternative therapeutic strategy.},
}
@article {pmid40830497,
year = {2025},
author = {Marialva, EF and Martins-Campos, KM and Ramos de Almeida, V and Ríos-Velasquez, CM and Tempone, AJ and Pessoa, FAC and Traub-Cseko, YM},
title = {Investigation of bacterial microbiota variability in two allopatric populations of Nyssomyia umbratilis, susceptible and nonsusceptible to Leishmania (Viannia) guyanensis infection in the Amazon region.},
journal = {Parasites &amp; vectors},
volume = {18},
number = {1},
pages = {354},
pmid = {40830497},
issn = {1756-3305},
mesh = {Animals ; *Psychodidae/microbiology/parasitology ; Brazil ; Female ; *Leishmania guyanensis/physiology ; *Insect Vectors/microbiology/parasitology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Humans ; },
abstract = {BACKGROUND: Sand flies of the species Nyssomyia umbratilis (Diptera: Psychodidae: Phlebotominae) are vectors of the parasite Leishmania (Viannia) guyanensis, one of the etiological agents of cutaneous leishmaniasis in the Amazon region. In addition, Ny. umbratilis is a cryptic species, with populations showing differences in their ability to transmit the parasite. For instance, populations of Ny. umbratilis from the Manacapuru municipality (MAN), located on the south bank of the Negro river, in the Amazonas state of Brazil, shows refractoriness to Leishmania infection, while populations from Rio Preto da Eva municipality (RPE), located on the north bank of the Negro river, are susceptible to infection. This lack of vectorial capacity may be caused by several factors, including the intestinal bacterial microbiota of sand flies.<br><br>METHODS: In this work, we carried out a metagenomic study of the intestinal microbiota of Ny.&#xa0;umbratilis populations from MAN and RPE. Ny.&#xa0;umbratilis females were collected in forested areas, sand&#xa0;fly midguts were dissected, DNA was extracted, and the 16&#xa0;S rRNA gene sequenced to identify the bacterial composition of the microbiota.<br><br>RESULTS: In total, 16 phyla, 33 classes, 49 orders, 93 families, and 112 genera of bacteria were identified. The phylum Proteobacteria was the most frequent (85.9%) in both localities, followed by the phyla Bacteroidetes, Actinobacteria, and Firmicutes with, 9.9%, 4.9%, and 4.4%, respectively. In MAN, 84 genera were identified and 79 in RPE, with MAN having a greater richness compared with RPE. Among these, the genera Rickettsia, Prevotella, Porphyromonas, Peptostreptococcus, and Caulobacter were the most prevalent in MAN, and the genera Rickettsia, Prevotella, Cryocola, Porphyromonas, and Caulobacter were the most prevalent in RPE.<br><br>CONCLUSIONS: Bacterial microbiota from MAN insects presents a greater diversity in relation to the RPE insects. Some of the identified bacteria have the potential to be used in alternative transmission control approaches as the development of transgenic vectors, and also, bacteria found exclusively in MAN sand&#xa0;flies may be candidates for a future transmission control approach to combat leishmaniasis in the Amazon region.},
}
@article {pmid40829558,
year = {2025},
author = {Huang, WC and Spang, A},
title = {DPANN archaea.},
journal = {Current biology : CB},
volume = {35},
number = {16},
pages = {R791-R794},
doi = {10.1016/j.cub.2025.06.038},
pmid = {40829558},
issn = {1879-0445},
mesh = {*Archaea/genetics/physiology/classification/metabolism ; *Symbiosis ; Phylogeny ; *Genome, Archaeal ; Biological Evolution ; },
abstract = {Archaea are one of the two primary domains of life alongside Bacteria. Extant archaea play an important role in global nutrient cycles and comprise members that were crucial for the evolution of life on Earth including the origin of eukaryotic cells through a symbiotic integration of an archaeal and bacterial partner. Despite their importance in ecology and evolution, our knowledge of archaeal diversity and function remains limited in part because it has proven challenging to cultivate archaea in the laboratory. Over the last two decades, the use of novel cultivation-independent approaches such as metagenomics has not only led to the discovery of a vast diversity of previously unknown archaeal lineages but also provided a window into their genomic content, allowing researchers to make predictions about metabolic functions and lifestyles. For example, by combining genomics approaches with phylogenetic analyses (that is, the reconstruction of species trees) researchers have uncovered several phylum-level lineages of putative genome-reduced archaea referred to as the 'DPANN' archaea, whose members were shown to have limited metabolic capabilities, indicating their dependency on symbiotic partners. These findings are consistent with observations from cultivation-based studies that have succeeded in enriching some of these small-cell symbionts in co-cultures with their hosts. Although they were initially discovered in extreme environments, DPANN archaea have now been shown to be widespread across a variety of environments and may thus play an important role in not only host evolution but also ecology. Herein, we aim to highlight DPANN archaea by providing an overview of their diversity, genomic and metabolic features, unique cell biology and interactions, and evolutionary origins. We also underscore several fascinating topics that remain underexplored.},
}
@article {pmid40828642,
year = {2025},
author = {Davies, RG and Wood, LA and Hengist, A and O'Donovan, C and Barton, W and Crispie, F and Walhin, JP and Valdivia-Garcia, MA and Garcia-Perez, I and Frost, G and O'Sullivan, O and Cotter, PD and Gonzalez, JT and Betts, JA and Koumanov, F and Thompson, D},
title = {Effects of a combined energy restriction and vigorous-intensity exercise intervention on the human gut microbiome: A randomised controlled trial.},
journal = {The Journal of physiology},
volume = {603},
number = {24},
pages = {7731-7750},
pmid = {40828642},
issn = {1469-7793},
support = {MR/P002927/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Exercise/physiology ; *Caloric Restriction ; *Obesity/microbiology/therapy/metabolism ; Adult ; Aged ; Muscle, Skeletal/metabolism ; Feces/microbiology ; },
abstract = {Metabolic health improvements in response to exercise and energy restriction may be mediated by the gut microbiome, yet causal evidence in humans remains limited. We used a 3-week exercise and energy restriction intervention to examine changes to the gut microbiome in otherwise healthy sedentary men and postmenopausal women with overweight/obesity. Intervention participants (n = 18) reduced habitual energy intake by 5000 kcal/week and expended 2000 kcal/week in addition to habitual physical activity through treadmill walking at 70% V̇O2Peak. Control participants (n = 12) maintained their usual lifestyle. Participants underwent dual-energy X-ray absorptiometry (DEXA), and samples of faeces, fasted venous blood, subcutaneous adipose tissue and skeletal muscle were collected. Faecal DNA was sequenced and profiled using shotgun metagenomics, Kraken2/Bracken and Human Microbiome Project Unified Metabolic Analysis Network 2 (HUMAnN2). The intervention significantly reduced body mass (mean Δ ± SD: -2.6 ± 1.5 kg), fat mass (-1.5 ± 1.3 kg), fasted insulin (-23.5 ± 38.1 pmol/l), leptin (-10.6 ± 7.3 ng/ml) and total cholesterol (-0.70 ± 0.42 mmol/l) concentrations, and also improved insulin sensitivity (HOMA2%S (homeostatic model of assessment)). Despite these significant metabolic changes the gut microbiome was unchanged in terms of α and β diversity and relative abundance. Thus, despite clinically meaningful improvements in body composition and metabolic health, we found no evidence for changes to the gut microbiome. In conclusion early metabolic changes with weight loss in humans are unlikely to be mediated by changes to the gut microbiome. KEY POINTS: Changes to the gut microbiome could contribute to metabolic improvements associated with weight loss in humans, but there have been limited attempts to address this question using robust randomised controlled trials (RCTs). We used a parallel-group RCT to examine whether a 3-week combined energy intake restriction and vigorous-intensity exercise intervention in people with overweight and obesity was temporally associated with changes to gut microbiome taxonomic composition and functional potential, short-chain fatty acid concentrations and expression of genes related to host-microbiome interactions in skeletal muscle and subcutaneous adipose tissue. We found that the human gut microbiome remains unchanged in the face of an intensive energy intake restriction and vigorous exercise intervention that significantly improved body composition and metabolic health in people with overweight/obesity. These findings indicate that early metabolic changes with weight loss in humans are unlikely to be mediated by changes to the gut microbiome.},
}
@article {pmid40828281,
year = {2025},
author = {Enciso Garcia, JS and Chignola, M and Ragionieri, L and Rey, F and Fluch, M and Borruso, L and Corretto, E and Schuler, H},
title = {High-Throughput Amplicon Sequencing for Analyzing Microbial Communities of Insects.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {237-258},
pmid = {40828281},
issn = {1940-6029},
mesh = {Animals ; *Insecta/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Insects represent more than 80% of all described species on the planet. This diversity is a result of millions of years of evolution, during which insects have colonized nearly every habitat. Their success is partly due to their ability to form symbiotic relationships with a wide variety of other organisms, especially microorganisms. Identifying and characterizing associated microorganisms are crucial to understanding the complexity and dynamics of these symbiotic relationships. To date, advancements in sequencing technologies that provide large sequence data sets have become ideal tools for characterizing insect microbiomes, including information about non-cultivable microorganisms commonly found in insects. Despite the growing number of studies focused on insect microbiome characterization, there are few protocols detailing methodological procedures for fieldwork, DNA extraction, and data processing. Here, we present an overview of the characterization of insect-associated bacterial communities. We cover best practices for data interpretation and visualization, including alpha and beta diversity analyses, community composition profiling, and statistical testing to identify microbial associations of insects.},
}
@article {pmid40827925,
year = {2025},
author = {Caffrey, EB and Olm, MR and Kothe, CI and Wastyk, HC and Evans, JD and Sonnenburg, JL},
title = {MiFoDB, a workflow for microbial food metagenomic characterization, enables high-resolution analysis of fermented food microbial dynamics.},
journal = {mSystems},
volume = {10},
number = {9},
pages = {e0014125},
pmid = {40827925},
issn = {2379-5077},
support = {F32-DK128865//U.S. Department of Health and Human Services/ ; R01-DK085025//Bill and Melinda Gates Foundation/ ; F32 DK128865/DK/NIDDK NIH HHS/United States ; R01 DK085025/DK/NIDDK NIH HHS/United States ; NNF20CC0035580//Novo Nordisk/ ; },
mesh = {*Metagenomics/methods ; *Fermented Foods/microbiology ; *Food Microbiology/methods ; Workflow ; Fermentation ; Microbiota/genetics ; Metagenome ; Humans ; Bacteria/genetics/classification ; },
abstract = {Fermented foods, which contain a diversity of microbes and microbial metabolites, have been used for millennia to increase food security, flavor, and nutritional content; more recently, they have been recognized as potential mediators of human health. Metagenomics is a powerful approach to characterize microbes in fermented foods, providing high taxonomic resolution and functional insights. Here, we introduce the Microbial Food DataBase, a metagenomics-based approach designed for the identification of fermentation-associated microbes. Using this primary database of metagenome-assembled genomes and relevant deposited genomes of prokaryotes, eukaryotes, and common food-relevant substrates, we investigated 89 fermented food samples. We present a streamlined high-confidence characterization of microbial diversity in fermented food, identifying previously undiscovered genomes and facilitating strain-level tracking across food environments. The easy and robust functionality of the workflow has significant implications for advancing food safety, promoting desired microbial communities, and increasing sustainability in food production.IMPORTANCEFermented foods have microbial communities that influence food safety, flavor, and human health. Microbial Food DataBase (MiFoDB), an alignment-based sequencing workflow and database, addresses the limitations of existing tools by enabling strain-level resolution, identifying novel genomes, and providing functional insights into microbial communities. Applying MiFoDB to fermented food samples, we demonstrate its ability to uncover novel species, track microbial strains across substrates, and integrate functional annotations. Additionally, the outlined workflow is highly customizable and can be used to generate alignment-based databases for other microbial ecosystems. This work highlights the importance of fermentation-specific workflows for studying microbial food ecosystems, advancing food safety, sustainability, and innovation in fermented food research.},
}
@article {pmid40827869,
year = {2025},
author = {Allen, JM},
title = {Rediscovering the wild: MiFoDB brings fermented food microbiomes into focus.},
journal = {mSystems},
volume = {10},
number = {9},
pages = {e0059925},
pmid = {40827869},
issn = {2379-5077},
mesh = {Humans ; *Fermented Foods/microbiology ; *Microbiota/genetics ; *Food Microbiology/methods ; *Metagenomics/methods ; Fermentation ; },
abstract = {Fermented foods have sustained human societies for thousands of years, with their microbial communities subtly shaping flavor, nutrient preservation, and health. Yet despite this long-standing relationship, much of the microbial complexity within fermented foods remains unresolved. In recent work, Caffrey et al. (E. B. Caffrey, M. R. Olm, C. I. Kothe, H. C. Wastyk, et al., mSystems 10:e00141-25, 2025, https://doi.org/10.1128/msystems.00141-25) put forth a new tool, MiFoDB, a metagenomic workflow that offers a promising alternative for advancing food microbiome science. By enabling strain-level resolution, functional gene annotation, and microbial tracking across substrates and time, MiFoDB provides a clearer view into the ecological and functional landscape of the fermented food microbiota. This work also bridges gaps between food and human microbiome research and brings us closer to a mechanistic understanding of how fermented foods influence health, helping transform ancient dietary practices into actionable and targeted nutritional strategies for improving human health and well-being.},
}
@article {pmid40827090,
year = {2025},
author = {Mulligan, C and Gold, DA},
title = {A Reassessment of the Coprostane Biomarker in the Ediacaran With Implications for Dickinsonia.},
journal = {Geobiology},
volume = {23},
number = {4},
pages = {e70029},
pmid = {40827090},
issn = {1472-4669},
support = {2044871//National Science Foundation/ ; },
mesh = {Animals ; *Fossils/microbiology ; Biomarkers/analysis ; *Cholestanes/analysis ; *Bacteria/genetics/metabolism ; Gastrointestinal Microbiome ; },
abstract = {The discovery of cholestane in animal fossils from the Ediacaran (571-541 million years ago) has generated much excitement, but it is not the only interesting biomarker recovered. Coprostane, a geologically stable form of coprostanol, has also been found in Ediacaran rocks. This is surprising, since coprostanol is typically used in modern settings as an environmental biomarker for humans and other mammals, who produce the compound with help from bacteria in their gut. The prevailing hypothesis is that an abundance of coprostane in some Ediacaran fossils-particularly Dickinsonia-represents the degradation of the organism's cholesterol by bacteria in the microbial mat, comparable to what is seen in modern vertebrate corpses as they decompose. However, this hypothesis assumes coprostanol-producing bacteria were absent in the guts of Ediacaran organisms, and to date no one has tested whether such bacteria exist in modern invertebrates. In this study, we assembled 115 metagenomes to look for evidence of coprostanol-producing enzymes in invertebrate microbiomes. Ultimately, we did not find any evidence for the enzyme in any invertebrate microbiomes, supporting the hypothesis that coprostane is not a gut biomarker for Ediacaran animals. However, a reassessment of coprostane/cholestane ratios shows Dickinsonia was unique in coprostanol enrichment, with ratio levels comparable to waste polluted marine waters and modern vertebrate feces. While we cannot rule out the possibility of contamination, we prefer a novel interpretation of the coprostane signature in dickinsoniomorph fossils, where the elevated level of coprostanol comes from digestion of the microbial mat and concentration of the biologically inert compound. If correct, the elevated coprostanol signal provides new insights into the feeding strategy of these enigmatic animals.},
}
@article {pmid40826150,
year = {2025},
author = {Dang, HT and Phung, TTB and Tran, DM and Bui, ATP and Vu, YH and Luong, MT and Nguyen, HM and Trinh, HT and Vo, HTN and Nguyen, TTT and Nguyen, AH and Tung, PD and Tran, LH and Van Nguyen, AT},
title = {High-dose multi-strain Bacillus probiotics enhance treatment and reduce antibiotic usage in children with persistent diarrhea through immune and microbiota modulation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30231},
pmid = {40826150},
issn = {2045-2322},
support = {ANABIO/RG-2022-06//ANABIO R&amp;D Ltd. Company, Viet Nam/ ; },
mesh = {Child ; Child, Preschool ; Female ; Humans ; Infant ; Male ; *Anti-Bacterial Agents/therapeutic use ; *Bacillus ; Cytokines/blood ; *Diarrhea/diet therapy/drug therapy/immunology/microbiology ; Double-Blind Method ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration &amp; dosage ; Treatment Outcome ; },
abstract = {Persistent diarrhea remains medical challenge to date regarding both its etiology and therapeutic interventions. Here, we conducted a randomized, double-blind, controlled clinical trial to evaluate the effectiveness of high-dose multi-strain Bacillus spore probiotics (LiveSpo DIA30) containing B. subtilis, B. clausii, and B. coagulans at 5 billion CFU/5 mL ampoule, in the supportive treatment of persistent diarrhea in children. Our findings revealed a significant 3-day shorter recovery period, 1.60-fold enhanced efficacy, and a 9.47-fold increase in odds (all p-values < 0.0001) for effectively resolving diarrhea by day 5 with the Bacillus spores. Notably, the group receiving LiveSpo DIA30 (Dia30 group) experienced a reduction in antibiotic treatment duration by 2 days compared to the Control group, equivalent to a 25% decrease in antibiotic usage. After 5 days of treatment, LiveSpo DIA30 demonstrated significant reductions in elevated blood pro-inflammatory cytokines, including IL-17 (26.62%; p = 0.0178), IL-23 (25.13%; p = 0.0256), TNF-α (19.09%; p = 0.038), and in fecal sIgA (24.24%; p = 0.0433). Analysis of 16S rRNA metagenome revealed that Dia30 group exhibited a notable increase in density of Actinomycetota and Bacillota phylum, along with Actinomycetaceae, Lactobacillaceae, and Streptococaceae families. Lacticaseibacillus rhamnosus, a beneficial gut species, was not detectable at day 0 but reached a density of 0.91% (p = 0.015) in Dia30 group by day 5. Additionally, Dia30 group showed a significant reduction in density of the Proteobacteria phylum, Enterobacteriaceae family, and harmful species Escherichia fergusoni (682.8-fold; p = 0.011). In conclusion, this clinical trial presents robust clinical evidence, supported by laboratory testing data, demonstrating the efficacy of multi-strain and high-concentration Bacillus spore probiotics in rapidly alleviating symptoms and reducing antibiotic usage in children with persistent diarrhea. This is archived by improving the native gut microbiota and modulating immunological responses.Trial registration: ClinicalTrials.gov, Identifier No: NCT05812820, 14/4/2023.},
}
@article {pmid40825877,
year = {2025},
author = {Xu, Y and Liu, Y and Leng, Y and Qian, J and Yang, Q and Zhu, J and Li, G and Peng, Y},
title = {Signature of oral microbial dysbiosis in different periodontitis risk levels.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {186},
pmid = {40825877},
issn = {1432-0614},
support = {XDYC-YLWS-2023-0048//Xingdian Talents Support Program/ ; 202401AU070088//Natural Science Foundation of Yunnan Province/ ; EYQ2024001//National Key Clinical Specialty Development Project of Pediatric Dentistry Division of China/ ; 202501AY070001-052//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; 202401AY070001-365//the Joint Fund of Yunnan Provincial Science and Technology Office and Kunming Medical University/ ; },
mesh = {Humans ; *Periodontitis/microbiology ; *Dysbiosis/microbiology ; Metagenomics ; Female ; *Microbiota ; Middle Aged ; Male ; *Bacteria/classification/genetics/isolation &amp; purification ; Saliva/microbiology ; Adult ; *Mouth/microbiology ; },
abstract = {Individuals categorized into distinct periodontitis risk levels often demonstrate substantial disparities not only in the likelihood of developing periodontitis but also in the rate at which the disease progresses. However, the oral microbial communities and their functional characteristics corresponding to different periodontitis risk levels remain to be further explored. Therefore, 52 subjects with periodontitis were selected and categorized into different periodontitis risk groups based on the periodontal risk calculator (PRC). Unstimulated saliva was collected, and metagenomics sequencing was performed to compare microbial diversity, taxonomy, and functional annotation among groups. There was no significant difference in species richness and evenness between the very high risk group and the high risk group, but beta diversity increased in the former group. A higher abundance of Filifactor alocis, Streptococcus cristatus, Klebsiella pneumoniae, and Streptococcus anginosus was attributed to the very high risk group, while Pseudopropionibacterium propionicum and Abiotrophia defectiva were found in higher abundance in the high risk group. Functional annotation revealed that biosynthesis of amino acids (lysine biosynthesis; phenylalanine, tyrosine and tryptophan biosynthesis; valine, leucine, and isoleucine biosynthesis), citrate cycle (TCA cycle), carbon fixation pathways in prokaryotes, oxidative phosphorylation, lipopolysaccharide biosynthesis, fatty acid biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, pantothenate and CoA biosynthesis, and glutathione metabolism were enriched in the very high risk group. The combined results indicate that the periodontal pathogens associated with a higher risk of periodontitis and the regulation of their related functional pathways increase the risk and likelihood of periodontitis development. KEY POINTS : • There were differences in microbial diversity among different periodontitis risk-level groups. • Some previously overlooked species and pathogenic pathways were linked to periodontitis risk differences. • Combining PRC with metagenomic sequencing revealed more potential pathogens.},
}
@article {pmid40825855,
year = {2025},
author = {Gopaulchan, D and Moore, C and Ali, N and Sukha, D and Florez González, SL and Herrera Rocha, FE and Yang, N and Lim, M and Dew, TP and González Barrios, AF and Umaharan, P and Salt, DE and Castrillo, G},
title = {A defined microbial community reproduces attributes of fine flavour chocolate fermentation.},
journal = {Nature microbiology},
volume = {10},
number = {9},
pages = {2130-2152},
pmid = {40825855},
issn = {2058-5276},
support = {133788//Innovate UK/ ; },
mesh = {*Chocolate/microbiology/analysis ; *Fermentation ; *Cacao/microbiology/metabolism ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; *Microbiota ; Fungi/metabolism/genetics/classification/isolation &amp; purification ; Colombia ; Hydrogen-Ion Concentration ; *Flavoring Agents/metabolism ; *Microbial Consortia ; Metagenomics ; Temperature ; Taste ; Food Microbiology ; },
abstract = {Cocoa (Theobroma cacao L.) bean fermentation is a spontaneous process involving interactions between abiotic and biotic factors that contribute to the final flavours of chocolate. Understanding these underlying interactions could enable desired flavour profiles to be reproduced under controlled conditions. Here, using bean fermentation samples from Colombian farms, we established that pH, temperature and microbiota composition, including both bacteria and fungi, influence key flavour attributes of premium chocolate. Genome-resolved metagenomics revealed that metabolic traits necessary for the development of the flavour profile of chocolate are redundantly present in the fermentation microbial community. Using a defined and metabolically competent microbial consortium, the feasibility of replicating fine flavour attributes of chocolate under controlled conditions was confirmed via omics, metabolic networks and a trained tasting panel. Our results provide the basis for the design of fermentation starters to robustly reproduce fine chocolate characteristics.},
}
@article {pmid40825816,
year = {2025},
author = {Kaushal, M and Kolombia, YA and Alakonya, AE and Masso, C},
title = {Comparing soil microbial diversity in smallholder plantain backyard gardens and main farms in Western and Central Africa.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30220},
pmid = {40825816},
issn = {2045-2322},
support = {HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; HRST/ST/AURG-II/CALL2/2018//African Union Research Grants/ ; },
mesh = {*Soil Microbiology ; Biodiversity ; *Bacteria/genetics/classification ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Africa, Central ; Africa, Western ; Microbiota ; Farms ; Gardens ; },
abstract = {In sub-Saharan Africa (SSA), plantains (Musa spp.) are a staple crop and a vital source of income for smallholder farmers. Despite their importance, the microbial diversity of soils in plantain-growing agroecologies remains poorly understood-particularly how it may influence plant performance and resilience through soil-plant interactions. In this study, we used Illumina MiSeq-based 16S rDNA sequencing to characterize bacterial communities in the rhizosphere of plantains cultivated under two distinct agroecological settings: Backyard gardens and main farms. Analyses of alpha and beta diversity (Sobs, Chao1, ACE, Shannon-Wiener, and Simpson indices; P < 0.05) revealed significant differences in species richness and community structure between the two agroecologies. Actinobacteria (55%) emerged as the dominant phylum, followed by Proteobacteria (21%) and Acidobacteria (15%). Beneficial genera such as Bacillus, Streptomyces, Bradyrhizobium, and Paenibacillus were also detected. Functional predictions based on COG and KEGG databases indicated notable differences in microbial functional potential between the two settings. These results suggest that agroecological context and habitat type strongly influence rhizosphere microbial diversity, with important implications for enhancing plant-microbe interactions and supporting crop resilience in SSA's resource-limited smallholder systems.},
}
@article {pmid40825123,
year = {2025},
author = {Park, JD and Lee, SR and Dhennezel, C and Taylor, N and Dame, A and Kadoki, M and Pishchany, G and Graham, DB and Xavier, RJ and Seyedsayamdost, MR},
title = {Elucidating the role of Campylobacter concisus-derived indole metabolites in gut inflammation and immune modulation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {34},
pages = {e2514071122},
pmid = {40825123},
issn = {1091-6490},
support = {2023A004123//Leona M. and Harry B. Helmsley Charitable Trust (Helmsley Charitable Trust)/ ; },
mesh = {*Indoles/metabolism ; Animals ; *Gastrointestinal Microbiome/immunology ; *Campylobacter/metabolism/immunology ; Mice ; *Inflammation/immunology/microbiology/metabolism ; Humans ; Macrophages/immunology ; Cytokines/metabolism ; Mice, Inbred C57BL ; Inflammatory Bowel Diseases/microbiology/immunology ; },
abstract = {The gut microbiota plays a pivotal role in maintaining human health with dysbiosis linked to a variety of diseases. Metagenome sequencing and robust statistical analysis have linked specific strains, including the gut bacterium Campylobacter concisus, to Crohn's disease and ulcerative colitis, together known as inflammatory bowel disease (IBD). However, the roles of this and other strains in disease progression remain to be investigated. Herein, we assess the contribution of C. concisus secondary metabolites to inflammation. Through untargeted metabolomics, we identified a diverse array of nineteen indole-containing metabolites produced by C. concisus, including trisindoline, previously isolated from a marine bacterium. Collectively, these metabolites modulate inflammatory responses by significantly inducing the release of proinflammatory cytokines interleukin (IL)-1β, IL-6, IL-8, and MCP-1. The metabolites act through the aromatic hydrocarbon receptor arylhydrocarbon receptor and in vivo intravital imaging revealed a marked increase in the recruitment and activation of immune cells, specifically neutrophils and macrophages, following the administration of trisindoline. Several indole metabolites also exhibited antimicrobial activity against commensal strains that facilitate a proper immune response. Our study provides a possible rationale for the association of C. concisus with IBD and underscores the complex interplay between gut bacteria and host immunity. The identification of indole-derived secondary metabolites as key modulators of inflammation offers new avenues for therapeutic intervention.},
}
@article {pmid40824084,
year = {2025},
author = {Li, J and Liang, L and Ye, J and Miao, Y and Zhao, K and Tian, Y and Li, X and Li, X and Chen, X and Wen, B and He, Y and Chen, B and Qin, L and Wang, Y and Fu, X},
title = {Gastric microbiota transplantation enhanced the eradication of refractory Helicobacter pylori infection by modulating the gastric microbiota: a pilot study.},
journal = {Microbiology spectrum},
volume = {13},
number = {10},
pages = {e0326324},
pmid = {40824084},
issn = {2165-0497},
support = {2024ZYD0144 and 24ZYZYTS0389//Central Government-Directed Project for Local Science and Technology Development/ ; 24WXXT05//Health Commission of Sichuan Province/ ; },
mesh = {Humans ; *Helicobacter Infections/therapy/microbiology ; Pilot Projects ; *Helicobacter pylori ; Male ; Middle Aged ; Female ; Adult ; Gastric Mucosa/microbiology ; *Gastrointestinal Microbiome ; Gastritis, Atrophic/therapy/microbiology ; *Stomach/microbiology ; Aged ; Dysbiosis/therapy/microbiology ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {UNLABELLED: Dysbiosis of the gastric microecology is implicated in various gastric diseases, with Helicobacter pylori (H. pylori) infection serving as a pivotal factor influencing the gastric microecological balance and vice versa. In this study, we investigated the novel effects of gastric microbiota transplantation (GMT) on gastric microecology and the potential of this treatment to enhance H. pylori eradication. We performed a metagenomic analysis of the microecological systems across different regions of the stomach, including the gastric fluid (GF), the gastric mucus layer (GML), and the gastric mucosa (GM). We initiated a clinical GMT intervention by transplanting microbial communities from healthy individuals' GML into patients exhibiting refractory H. pylori infection and chronic atrophic gastritis. Our findings demonstrated significant disparities in species richness among the GF, GML, and GM, with the GML exhibiting the highest diversity of unique microbial genera. H. pylori infection primarily influenced the relative species abundance within the GML community, without altering its fundamental composition. Clinically, GMT was well-tolerated by all recipients and showed substantial synergistic efficacy against refractory H. pylori infection, achieving a 100% eradication rate in all patients, and significantly alleviating symptoms in individuals with H. pylori-positive atrophic gastritis (P < 0.05). Compared with the gastric microbiota of H. pylori-negative patients, the gastric microbiota of H. pylori-positive patients treated with GMT exhibited closer alignment with those of healthy donors. In conclusion, GMT utilizing GML enhanced the eradication rate of refractory H. pylori infection and improved symptoms in patients with H. pylori-positive atrophic gastritis through modulating the gastric microbiota.<br><br>IMPORTANCE: Dysbiosis of the gastric microecology is implicated in various gastric diseases, with Helicobacter pylori (H. pylori) infection serving as a pivotal factor influencing the gastric microecological balance and vice versa. We investigated the novel effects of gastric microbiota transplantation (GMT) on gastric microecology and the potential of this treatment to enhance H. pylori eradication. GMT significantly enhanced the eradication rate of refractory H. pylori infection and improved symptoms in patients with H. pylori-positive atrophic gastritis. GMT demonstrated improvements in the cure rate of refractory H. pylori infection, potentially offering a new clinical treatment approach. This finding provides new insights and a potential therapeutic direction for treating dysbiosis related chronic gastric diseases.},
}
@article {pmid40823805,
year = {2025},
author = {Kim, L and Lavrinienko, A and Sebechlebska, Z and Stoltenberg, S and Bokulich, NA},
title = {Tier-based standards for FAIR sequence data and metadata sharing in microbiome research.},
journal = {Nucleic acids research},
volume = {53},
number = {15},
pages = {},
pmid = {40823805},
issn = {1362-4962},
support = {2020-2024//ETH Domain's Open Research Data (ORD)/ ; 2021-362//ETH Domain's Open Research Data (ORD)/ ; //Strategic Focus Area "Personalized Health and Related Technologies (PHRT)/ ; //ETH Zurich/ ; //ETH Read and Publish OA/ ; },
mesh = {*Metadata/standards ; Humans ; *Information Dissemination/methods ; *Microbiota/genetics ; Metagenome/genetics ; *Metagenomics/standards/methods ; Gastrointestinal Microbiome/genetics ; Software ; },
abstract = {Microbiome research is a growing, data-driven field within the life sciences. While policies exist for sharing microbiome sequence data and using standardized metadata schemes, compliance among researchers varies. To promote open research data best practices in microbiome research and adjacent communities, we (i) propose two tiered badge systems to evaluate data/metadata sharing compliance, and (ii) developed an automated evaluation tool to determine adherence to data reporting standards in publications with amplicon and metagenome sequence data. In a systematic evaluation of publications (n = 2929) spanning human gut microbiome research, and case studies of soil and gut microbiota (n = 370), we found nearly half do not meet minimum standards for sequence data availability. Moreover, poor standardization of metadata creates a high barrier to harmonization and cross-study comparison. Using this badge system and evaluation tool, our proof-of-concept work exposes (i) the ineffectiveness of sequence data availability statements and (ii) the lack of consistent metadata reporting. We highlight the need for improved practices and infrastructure that reduce barriers to data submission and maximize reproducibility in microbiome research. We anticipate that our tiered badge framework will promote dialogue regarding data sharing practices and facilitate data reuse, supporting best practices that make microbiome data Findable, Accessible, Interoperable, and Reusable (FAIR).},
}
@article {pmid40822586,
year = {2025},
author = {Dharmalingam, D and Semalaiyappan, J and Thirumal, S and Kuttiatt, VS},
title = {Unveiling Facklamia: detection of an emerging microbe in the skin microbiome of patients with filarial lymphedema.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1624288},
pmid = {40822586},
issn = {2235-2988},
mesh = {Humans ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; *Elephantiasis, Filarial/microbiology ; *Lymphedema/microbiology ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; *Skin/microbiology ; Skin Microbiome ; },
abstract = {Facklamia is an emerging pathogen in human beings and only a few clinical cases were reported in the literature. We detected the presence of this unusual microbe among the skin flora of three patients with filarial lymphedema in a 16S rRNA-based metagenomic study on the skin microbiome. To our knowledge, this is the first report of detection of this microbe in patients affected with filarial lymphedema. Further investigations are required to elucidate the role of Facklamia in secondary skin and soft tissue infection of filarial lymphedema patients.},
}
@article {pmid40822578,
year = {2025},
author = {Wu, X and Zhu, H and Hu, Y and Zhang, L and Huang, L},
title = {Meta-analysis of H. pylori and the gut microbiome interactions and clinical outcomes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1610523},
pmid = {40822578},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Helicobacter pylori/genetics ; *Helicobacter Infections/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Gastritis/microbiology ; Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Stomach Neoplasms/microbiology ; },
abstract = {INTRODUCTION: Helicobacter pylori is a globally prevalent gastric pathogen associated with chronic gastritis, peptic ulcers, and gastric cancer. Its interaction with the gut microbiome (GM), a dynamic microbial community within the gastrointestinal tract, plays a critical role in modulating host immune responses and disease progression. This study aimed to investigate the complex interactions between H. pylori infection and the GM and to evaluate how microbiome alterations relate to clinical outcomes such as gastritis, ulcers, and gastric cancer.<br><br>METHODS: A meta-analysis was conducted using publicly available 16S rRNA and shotgun metagenomic datasets. Microbiome composition differences were assessed using differential abundance analysis, alpha- and beta-diversity metrics, and principal component analysis (PCA). Random forest models were employed to predict the clinical outcomes based on microbiome and clinical data. Hyperparameter tuning and cross-validation were applied to ensure model robustness.<br><br>RESULTS: The analysis revealed significant microbial shifts associated with H. pylori infection, including enrichment of Proteobacteria, Fusobacterium spp., and Prevotella spp., and depletion of beneficial taxa like Lactobacillus spp. and Faecalibacterium prausnitzii. Microbial diversity declined progressively with disease severity. Predictive models demonstrated high accuracy (89.3%) in classifying the disease states and identifying key microbial biomarkers such as Fusobacterium spp. and Bacteroides fragilis with strong predictive power.<br><br>DISCUSSION: This study highlights the critical role of GM dysbiosis in H. pylori-related disease progression. The identified microbial signatures and predictive models offer promising tools for early diagnosis, risk stratification, and personalized treatment of H. pylori-associated gastrointestinal disorders. Future integration of multi-omics data may further unravel the microbial mechanisms and support microbiome-based precision medicine.},
}
@article {pmid40819273,
year = {2025},
author = {Puranik, S and Mekali, J and Damodaram, KJP},
title = {Seed Biopriming From Basics to Omics: Relieving Plants From Biotic Stress Through the Microbial Way.},
journal = {Journal of basic microbiology},
volume = {65},
number = {10},
pages = {e70083},
doi = {10.1002/jobm.70083},
pmid = {40819273},
issn = {1521-4028},
mesh = {*Seeds/microbiology/growth &amp; development ; *Stress, Physiological ; *Crops, Agricultural/microbiology/growth &amp; development ; Plant Diseases/prevention &amp; control/microbiology ; Rhizosphere ; Animals ; Metabolomics ; Proteomics ; Microbiota ; Plant Development ; *Agricultural Inoculants/physiology ; Metagenomics ; Plant Growth Regulators/metabolism ; },
abstract = {From seed to harvest, cultivated crops face numerous biotic stresses, including insects, nematodes, and diseases, which significantly hinder their growth and vigor, resulting in substantial crop losses. In contrast to use of toxic agrochemicals, seed biopriming with microbial inoculants has emerged as an effective and eco-friendly alternative against pathogens and pests. Seed biopriming involves coating seeds with beneficial microorganisms that enhance protection and immunity against a variety of harmful pests and pathogens. These microbial agents colonize the seeds and establish themselves in the rhizosphere, reducing the impact of biotic stresses while fostering a healthier environment for plant growth. They are known to exhibit several mechanisms against pathogens and pests, like production of cell wall degrading enzymes, antibiosis, competition, induced systemic resistance, chelation of iron etc. Additionally, these microorganisms regulate phytohormone levels, further optimizing the physiological and metabolic characteristics of plants. This approach not only promotes robust plant growth but also enhances tolerance to deleterious bacteria, fungi, nematodes and arthropods, ensuring healthier crops. These interactions can further be well studied and expressed by using different omics approaches like metagenomics (of seed microbiome), proteomics, transcriptomics, metabolomics and differential gene expression. This review highlights the role and benefits of seed biopriming as a sustainable strategy to manage biotic stresses effectively, and the importance of omics for better understanding of complex processes during such interactions, contributing to resilient agricultural production systems and environmental sustainability.},
}
@article {pmid40819131,
year = {2025},
author = {Tang, B and Li, S and Li, X and He, J and Zhou, A and Wu, L and Xiao, X and Wang, S and Jiang, H and Jian, J and Hou, Z and Ge, Y and Lei, Y and Zhou, J and Tu, D and Lu, C and Yang, M and Yang, S},
title = {Cholecystectomy-related gut microbiota dysbiosis exacerbates colorectal tumorigenesis.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7638},
pmid = {40819131},
issn = {2041-1723},
support = {82030020//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82172958//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology/genetics ; *Colorectal Neoplasms/microbiology/etiology/pathology/metabolism ; *Dysbiosis/microbiology/etiology ; Humans ; Mice ; *Carcinogenesis/pathology/metabolism/drug effects ; *Cholecystectomy/adverse effects ; Receptors, Cytoplasmic and Nuclear/metabolism/agonists ; Chenodeoxycholic Acid/analogs &amp; derivatives/pharmacology ; Bile Acids and Salts/metabolism ; Male ; Mice, Inbred C57BL ; Taurochenodeoxycholic Acid/metabolism ; Female ; Fecal Microbiota Transplantation ; beta Catenin/metabolism ; Disease Models, Animal ; Ruminococcus ; Receptor, Farnesoid X-Activated ; },
abstract = {Cholecystectomy represents the most prevalent biliary surgical procedure for gallbladder abnormalities. Growing evidence suggests that cholecystectomy is associated with an elevated risk of colorectal cancer. However, the underlying mechanism remains elusive. Here we show that cholecystectomy exacerbates colorectal tumorigenesis in both AOM/DSS and APC[min/+] mice models. Metagenomic sequencing and targeted metabolomics show that cholecystectomy leads to a decrease of Bifidobacterium breve (B. breve) and an increase of Ruminococcus gnavus (R. gnavus), along with increased levels of glycoursodeoxycholic acid (GUDCA) in human and tauroursodeoxycholic acid (TUDCA) in mice. Fecal microbiota transplantation, single bacterial colonization and bile acid supplementation demonstrate that cholecystectomy-related gut microbiota perturbations promote the production of TUDCA and facilitate colorectal tumorigenesis. RNA-sequencing and co-immunoprecipitation reveal that the compromised bile acid metabolism inhibits farnesoid X receptor (FXR) signaling, disrupts the FXR/β-catenin interaction, and ultimately exacerbates colorectal tumorigenesis. Significantly, FXR agonist obeticholic acid (OCA) averts cholecystectomy-related colorectal tumorigenesis. The gut microbiota holds a crucial position in cholecystectomy-induced colorectal tumorigenesis, and modulation of the gut microbiota-bile acid-FXR axis represents a promising preventive strategy.},
}
@article {pmid40817325,
year = {2025},
author = {Star-Shirko, B and Pangga, GM and McKenna, A and Corcionivoschi, N and Richmond, A and Ijaz, UZ and Gundogdu, O},
title = {Investigating microbial population structure and function in the chicken caeca and large intestine over time using metagenomics.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {355},
pmid = {40817325},
issn = {1756-0500},
support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Cecum/microbiology ; *Intestine, Large/microbiology ; Metagenome ; },
abstract = {OBJECTIVES: Although taxonomic variations in chicken gut microbiota have been previously documented, their functional capacity remain poorly understood. To gain a better understanding, we incorporated whole genome shotgun metagenomics to analyse microbial communities of two different organs: the caeca and the large intestine.<br><br>RESULTS: Using 24 samples obtained from the caeca and the large intestine of commercial chickens, we assembled Metagenome-Assembled Genomes (MAGs) and characterise their functional profiles. Afterwards, using 8 samples, we integrated this sequencing data with chicken performance metadata body weight (BW), weight gain, feed intake (FI), feed conversion ratio (FCR) and age. MAGs belonging to specific families were found to be positively associated with changes in performance parameters. Functional analyses suggest changes in nutrient geochemical cycles including hydrogen generation within the carbon-cycle. Furthermore, 108 CAZymes were identified for MAGs belonging to two major families - glycoside hydrolase (GH) and polysaccharide lyase (PL), which are important for breakdown of dietary carbohydrates and fibres. A total of 13 polysaccharide lyases were identified functioning on day 20 with enzymes were specific to organs. Overall, our results provide a deeper understanding of microbial-mediated metabolism concerning key performance parameters in chicken production.},
}
@article {pmid40817175,
year = {2025},
author = {Yang, JX and Peng, Y and Yang, JJ and Zhang, YH and Dong, Q and Li, QS and Han, XG and Gao, C},
title = {Nitrogen addition alters arbuscular mycorrhizal fungi and soil bacteria networks without promoting phosphorus mineralization in a semiarid grassland.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1229},
pmid = {40817175},
issn = {2399-3642},
mesh = {*Mycorrhizae/genetics/drug effects/metabolism ; *Phosphorus/metabolism ; *Nitrogen/metabolism/pharmacology ; *Soil Microbiology ; *Grassland ; *Bacteria/genetics/metabolism/classification/drug effects ; Soil/chemistry ; Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Mycorrhiza interplays with the microbiome in adaptation to environmental fluctuation, yet how arbuscular mycorrhizal fungi (AMF) and the associated microbiome respond to nitrogen addition remains poorly understood. Here, we addressed this gap by conducting amplicon sequencing of AMF 18S rRNA and bacterial 16S rRNA operons, along with shotgun metagenome sequencing, using soil samples collected from a semiarid grassland that has received nitrogen inputs for 11 years at different levels. We found that the nitrogen response of the AMF community was characterized by a negative association whereby increasing nitrogen addition leads to higher beta diversity and lower alpha diversity. Multiple co-inertia analyses revealed a coordinated response of the AMF community, bacterial community, and bacterial functions to nitrogen addition, which as a whole was strongly related to soil phosphorus availability. Besides, through network analysis of AMF with bacteria and bacterial functional genes, we found that nitrogen addition selected Actinobacteria and enriched functions of transporters, amino acid synthesis and metabolism, and replication repair, whereas there was no evidence for the enrichment of phosphorus mineralization functions.},
}
@article {pmid40817036,
year = {2025},
author = {Chen, Y and Huang, S and Lu, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Zhang, W},
title = {Viral metagenomics reveals parvovirus dark matter of herbivorous wildlife from the Qinghai-Tibet Plateau.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {508},
pmid = {40817036},
issn = {1471-2180},
support = {82341106//National Natural Science Foundation of China/ ; 2023YFD1801300 and 2022YFC2603801//National Key Research and Development Programs of China/ ; },
mesh = {Animals ; *Metagenomics ; Phylogeny ; *Animals, Wild/virology ; Feces/virology ; *Parvovirus/genetics/classification/isolation &amp; purification ; Tibet ; Parvoviridae Infections/veterinary/virology ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: As one of the birthplaces of modern biodiversity, the Qinghai-Tibet Plateau is home to a rich variety of unique animal groups. Herbivorous wildlife constitutes a vital component of the plateau's ecosystems, yet current research on parvoviruses in these species remains limited. With the development of viral metagenomics and next-generation sequencing technology, more and more novel viruses have been detected.<br><br>RESULTS: In this study, we collected 741 fecal samples from herbivorous wildlife across three distinct habitats on the Qinghai-Tibet Plateau and employed metagenomics analysis technology to characterize the parvovirus dark matter. We identified 32 parvoviruses by analysis, of which 13 were closely related to the members of Bocapavovirus, Dependoparvovirus and Protoparvovirus in the subfamily of Parvovirinae, 5 belonging to the Densovirinae subfamily, and 5 were classified into the newly proposed subfamily of Hamaparvovirinae. Additionally, 9 parvoviruses remain unclassified and cannot be assigned to any existing subfamily. We conducted a phylogenetic analysis based on the non-structural proteins of the viruses to explore the evolutionary relationships among parvoviruses, and found that some viruses could not be clustered with known parvoviruses.<br><br>CONCLUSIONS: These results enrich our understanding of parvovirus and viral dark matter, and reveal that these wild animals carry a large number of unknown new viruses that may have implications for the ecological balance of the Qinghai-Tibet Plateau.},
}
@article {pmid40816543,
year = {2025},
author = {Amarlapudi, MR and Balasubramaniam, C and Akash, and Singh, H and Yadav, A and Hirikyathanahalli Vishweswaraiah, R and Pradhan, D and Kumar, N and Dhotre, D and Kolte, AP and Hogarehalli Mallappa, R},
title = {Microbiome and antibiotic resistance profile of milk and faeces from cattle in an organized dairy production system.},
journal = {International journal of antimicrobial agents},
volume = {66},
number = {6},
pages = {107590},
doi = {10.1016/j.ijantimicag.2025.107590},
pmid = {40816543},
issn = {1872-7913},
mesh = {Animals ; Cattle ; *Feces/microbiology ; *Milk/microbiology ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Microbiota ; Dairying ; Metagenomics ; Metagenome ; Microbial Sensitivity Tests ; Female ; },
abstract = {Antimicrobial resistance (AMR) represents a critical public health challenge, responsible for over one million fatalities each year. Livestock, particularly dairy cattle, significantly contribute to the AMR crisis due to the extensive use of antibiotics in the animal health sector. This study aimed to characterize the antibiotic resistome of dairy cattle by analyzing their fecal and milk metagenomes. We collected 36 milk and 36 fecal samples from three different organized dairy farms and extracted metagenomic DNA, yielding 2.58 and 2.81 billion total reads contributing 200.4 and 206.5 GB data, respectively. The majority of these reads mapped to bacterial genomes, revealing 37 bacterial phyla within the dairy production system, with greater phylum-level diversity observed in feces compared to milk. The predominant phyla identified were Bacillota (53.3%), Pseudomonadota (24.7%), Bacteroidota (11.0%), and Actinomycetota (8.4%). The most abundant genera found were Clostridium in milk and Bifidobacterium in feces. In total, we identified 290 distinct antibiotic-resistant genes spanning 27 diverse drug classes and 12 resistance mechanisms. The abundance of antibiotic-resistant genes was higher in feces than in milk, with 229 distinct antibiotic-resistant genes found in milk. Overall, aminoglycoside-resistant genes were the most prevalent and abundant in both fecal and milk metagenomes of cattle from organized dairy production systems.},
}
@article {pmid40816430,
year = {2025},
author = {Kong, Z and Wang, H and Man, S and Yan, Q},
title = {Magnetite modulates bacterial cooperation during cathodic nitrogen removal in bioelectrochemical systems under trace dissolved oxygen.},
journal = {Bioresource technology},
volume = {437},
number = {},
pages = {133147},
doi = {10.1016/j.biortech.2025.133147},
pmid = {40816430},
issn = {1873-2976},
mesh = {*Bioelectric Energy Sources/microbiology ; *Denitrification/drug effects ; Electrodes ; *Ferrosoferric Oxide/pharmacology ; Oxygen ; *Water Purification/methods ; Metagenome ; Ammonium Compounds/metabolism ; *Microbiota ; },
abstract = {Nitrate and ammonium co-contamination poses a major challenge for sustainable nitrogen removal, especially under microoxic conditions. This study investigated the effect of magnetite on microbial nitrogen metabolism and nitrite accumulation in biocathodes of bioelectrochemical systems under 0.25 mg/L dissolved oxygen. Magnetite improved total nitrogen removal by 22.8 %, reduced peak nitrite levels by 22.6 %, and lowered residual ammonium by 49.2 %. Magnetite promoted interspecies cooperation, driving modular specialization in nitrite reduction while suppressing dissimilatory nitrate reduction to ammonium. Concurrently, it stimulated ammonia-oxidizing bacteria activity, accelerating ammonium conversion and mitigating nitrite accumulation through enhanced denitrification. A cooperative microbial pattern emerged, with dominant species such as Hanamia sp. and Moheibacter sp. carrying out nitrite reduction, while less abundant species performed single nitrogen metabolic processes. This study highlights the role of magnetite in integrating aerobic and anaerobic nitrogen pathways, offering a sustainable strategy for controlling complex nitrogen pollution.},
}
@article {pmid40816065,
year = {2025},
author = {Kim, E and Song, TC and Yang, SM and Kim, J and Kim, HY},
title = {Comparative analysis of microbial diversity and fatty acids in raw milk from different production systems.},
journal = {Food chemistry},
volume = {493},
number = {Pt 3},
pages = {145899},
doi = {10.1016/j.foodchem.2025.145899},
pmid = {40816065},
issn = {1873-7072},
mesh = {*Milk/microbiology/chemistry ; Animals ; *Fatty Acids/analysis/metabolism/chemistry ; *Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Cattle ; Microbiota ; },
abstract = {This study investigated how differences in raw milk obtained from different milk production practices, such as conventional, antibiotic-free, and organic, influence microbial community structure and fatty acid profiles, potentially affecting milk quality. Microbial diversity revealed no significant differences among the three milk production practices. However, Pseudomonas was dominant across all milk types, with organic milk demonstrating significantly higher relative abundances of Lactococcus, Acinetobacter, and Carnobacterium. Fatty acid profiling revealed significantly higher levels of essential polyunsaturated fatty acids (PUFAs) in organic milk, probably due to easier access to pasture-based diets. Correlation and network analyses demonstrated associations between PUFAs and microbial genera predominantly present in organic milk, such as Serratia with C18:2n-6 and Lactococcus with C20:4n-6, suggesting a potential relationship between microbial composition and fatty acid metabolism influenced by production practices. These data emphasize the impact of production practices on milk quality and microbial dynamics.},
}
@article {pmid40815468,
year = {2025},
author = {Gao, Y and Wang, D and Lu, T and Liu, K and Li, S and Kang, J and Sha, S and Xing, G and Cheng, L and Fan, S and Yang, W and Yan, Q and Ding, Y and Xu, D},
title = {Cross-cohort microbiome-wide study reveals consistent alterations in the gut bacteriome, but not the gut mycobiome, in patients with hypertension.},
journal = {mSystems},
volume = {10},
number = {9},
pages = {e0065725},
pmid = {40815468},
issn = {2379-5077},
support = {82370563//National Natural Science Foundation of China/ ; 2021024//Dalian Municipal Dengfeng Clinical Medicine Grant Support/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Male ; *Hypertension/microbiology ; Middle Aged ; *Mycobiome ; Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenome ; Aged ; Fungi/classification/genetics ; Cohort Studies ; Adult ; Case-Control Studies ; },
abstract = {UNLABELLED: Hypertension, one of the most prevalent cardiovascular diseases, has been linked to the gut microbiota. However, there is a lack of well-defined, cross-population validated gut microbial signatures associated with hypertension, particularly at both the bacterial and fungal levels. To address this gap, we conducted a metagenome-wide analysis of fecal samples from 159 hypertensive patients and 101 healthy controls, using two publicly available data sets from the Beijing and Dalian regions. Our results showed that hypertensive patients exhibit a significant reduction in gut bacterial diversity, accompanied by substantial alterations in bacterial composition. A total of 61 bacterial species were identified with significantly different relative abundance between patients and controls across both regions (combined P < 0.05, q = 0.25). Hypertension-enriched species included Lachnospiraceae (Clostridium symbiosum, Enterocloster bolteae) and Clostridium sp. AT4, while Lachnospiraceae bacterium, Firmicutes bacterium, and Clostridium sp. AM49 4BH were significantly decreased in hypertensive patients. In contrast, no significant differences were observed in gut fungal diversity between hypertensive patients and healthy controls, and only minor differences in fungal composition were noted. Specifically, six fungal species were identified as potentially significant in the combined data set (P < 0.05, q = 0.73), but they only Blastomyces emzantsi c231 meet the same consistency across the two cohorts as the bacterial signatures. Furthermore, we developed classification models using gut bacterial and fungal signatures to distinguish hypertension patients from healthy controls. The bacterium-based models achieved area under the curves (AUCs) greater than 0.70 in cross-cohort classification and validation, while the fungus-based models only achieved AUCs between 0.55 and 0.57. In summary, our study identifies cross-cohort gut bacterial and fungal signatures associated with hypertension, suggesting that the gut bacteriome may serve as a more reliable target for hypertension intervention compared to the gut mycobiome.<br><br>IMPORTANCE: Hypertension (HTN) represents a global health burden affecting billions of individuals worldwide; however, the relationship between HTN and gut microbial ecosystems remains inadequately characterized. This study presents the first cross-cohort microbiome analysis revealing significant alterations in the gut bacteriome of HTN patients, with limited changes observed in the mycobiome. These findings highlight the critical role of the gut bacteriome in the pathogenesis of HTN and provide new microbial biomarkers for early diagnosis. Furthermore, the identification of bacterial species establishes a foundation for future intervention approaches, enhancing the applicability of microbiome research in cardiovascular health and opening new avenues for related studies in this field.},
}
@article {pmid40815091,
year = {2025},
author = {Garcia-Pichel, F and Farias, J and Fernandes, V and Roush, D and Swenson, TL and Kosina, SM and Northen, TR and Cao, H and Jaunin, S and Kandel, R and Gaxiola, R},
title = {Swift microbiome-mediated phenotype transfer from transgenic plants.},
journal = {Journal of environmental quality},
volume = {54},
number = {6},
pages = {1368-1382},
pmid = {40815091},
issn = {1537-2537},
mesh = {*Plants, Genetically Modified/microbiology ; *Arabidopsis/microbiology/genetics/physiology ; *Microbiota ; Phenotype ; Plant Roots/microbiology ; Soil Microbiology ; Butylene Glycols/metabolism ; },
abstract = {The expression of an organism's genes determines its own characteristics in any given environment. In this study, we demonstrate that the phenotypic traits of genetically modified transgenic Arabidopsis thaliana plants, designed for nutrient efficiency and enhanced yield, can be naturally and readily transferred to neighboring wild-type plants. Our findings reveal that the transgenic plants significantly influence the populational, compositional, and functional traits of their root-associated microbiome (RAM), resulting in a larger population, with distinct composition and high functional potential compared to wild-type plants, regardless of soil type. This phenomenon appears to stem from altered metabolite exudation patterns, which enhance root recruitment. Notably, the RAM plays a dual role: it not only contributes to the robust phenotype of the transgenic plants but also facilitates the transfer of these traits to adjacent wild-type plants. Upon transplanting wild-type plants into the presence of transgenics, we observed the induction of transgenic-like phenotypes. Metagenomic and compositional analyses indicate that this transfer is linked to an increase in 2,3-butanediol (2,3-BD) fermenting bacteria. Furthermore, exposure to 2,3-BD alone was sufficient to elicit transgenic phenotypes in wild-type plants. These results suggest that factors external to plant tissues, such as root-associated bacteria and their volatile metabolic products, play a crucial role in the transferability of plant phenotypes to neighboring plants. Our findings underscore the importance of evaluating microbiome interactions in the context of transgenic organisms and open new avenues for alternative agricultural practices that may reduce reliance on genetic modification.},
}
@article {pmid40813371,
year = {2025},
author = {Kiu, R and Darby, EM and Alcon-Giner, C and Acuna-Gonzalez, A and Camargo, A and Lamberte, LE and Phillips, S and Sim, K and Shaw, AG and Clarke, P and van Schaik, W and Kroll, JS and Hall, LJ},
title = {Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7569},
pmid = {40813371},
issn = {2041-1723},
support = {100974/C/13/Z//Wellcome Trust (Wellcome)/ ; BB/R012490/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/X011054/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/S017941/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Probiotics/administration &amp; dosage/pharmacology ; *Infant, Very Low Birth Weight ; *Anti-Bacterial Agents/pharmacology/therapeutic use/adverse effects ; Infant, Newborn ; Infant, Premature ; Feces/microbiology ; Female ; Male ; Gene Transfer, Horizontal ; Metagenomics ; Milk, Human ; Enterococcus/genetics/drug effects ; Metagenome ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Preterm infants (<37 weeks' gestation) are commonly given broad-spectrum antibiotics due to their risk of severe conditions like necrotising enterocolitis and sepsis. However, antibiotics can disrupt early-life gut microbiota development, potentially impairing gut immunity and colonisation resistance. Probiotics (e.g., certain Bifidobacterium strains) may help restore a healthy gut microbiota. In this study, we investigated the effects of probiotics and antibiotics on the gut microbiome and resistome in two unique cohorts of 34 very-low-birth-weight, human-milk-fed preterm infants - one of which received probiotics. Within each group, some infants received antibiotics (benzylpenicillin and/or gentamicin), while others did not. Using shotgun metagenomic sequencing on 92 longitudinal faecal samples, we reconstructed >300 metagenome-assembled genomes and obtained ~90 isolate genomes via targeted culturomics, allowing strain-level analysis. We also assessed ex vivo horizontal gene transfer (HGT) capacity of multidrug-resistant (MDR) Enterococcus using neonatal gut models. Here we show that probiotic supplementation significantly reduced antibiotic resistance gene prevalence, MDR pathogen load, and restored typical early-life microbiota profile. However, persistent MDR pathogens like Enterococcus, with high HGT potential, underscore the need for continued surveillance. Our findings underscore the complex interplay between antibiotics, probiotics, and HGT in shaping the neonatal microbiome and support further research into probiotics for antimicrobial stewardship in preterm populations.},
}
@article {pmid40813370,
year = {2025},
author = {Rakoff-Nahoum, S and Debelius, J and Valles-Colomer, M and Noordzij, HT and Esteban-Torres, M and Zhernakova, A and Brusselaers, N and Pettersen, VK},
title = {A reconceptualized framework for human microbiome transmission in early life.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7546},
pmid = {40813370},
issn = {2041-1723},
mesh = {Humans ; *Microbiota/physiology/genetics ; Metagenomics/methods ; },
abstract = {Human development and physiology are fundamentally linked with the microbiome. This is particularly true during early life, a critical period for microbiome assembly and its impact on the host. Understanding microbial acquisition in early life is thus central to both our basic understanding of the human microbiome and strategies for disease prevention and treatment. Here, we review the historical approaches to categorize microbial transmission originating from the fields of infectious disease epidemiology and evolutionary biology and discuss how this lexicon has influenced our approach to studying the early-life microbiome, often leading to confusion and misinterpretation. We then present a conceptual framework to capture the multifaceted nature of human microbiome acquisition based on four key components: what, where, who, and when. We present ways these parameters may be assigned, with a particular focus on the 'transmitted strain' through metagenomics to capture these elements. We end with a discussion of approaches for implementing this framework toward defining each component of microbiome acquisition.},
}
@article {pmid40813051,
year = {2025},
author = {An, FJ and Niu, ZR and Liu, TN and Su, YZ},
title = {[Structure and Metabolic Function Characteristics of Soil Bacterial Communities under Different Vegetation Types in Arid Region].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {8},
pages = {5360-5368},
doi = {10.13227/j.hjkx.202407230},
pmid = {40813051},
issn = {0250-3301},
mesh = {*Soil Microbiology ; *Desert Climate ; China ; *Bacteria/metabolism/classification ; *Ecosystem ; Soil/chemistry ; Biodiversity ; Plants/classification ; Plant Development ; },
abstract = {The aim of this study was to explore the effects of different vegetation types on soil bacterial community structure and metabolic function in an oasis-desert ecotone and provide scientific theoretical basis for species allocation and management of vegetation reconstruction in arid desert ecosystem. Nitraria sphaerocarpa Maxim and Calligonum mongolicum Turcz are the main natural vegetation, Haloxylon ammodendron Bunge, and Hedysarum scoparium Fisch are the primary artificial vegetation, and Ha-Cm are the main mixed community in an oasis-desert ecotone in northwest China. Understanding soil microbial community structure and function under typical vegetation types is crucial for accurate management and sustainable use of desert vegetation. We used high-throughput sequencing technology to explore the effects of different vegetation types on the structure, diversity, and metabolic pathways of soil bacteria and to investigate the key factors driving the change of soil bacterial community structure. The results showed that the growth of artificial vegetation and natural vegetation significantly increased the richness and diversity of the soil bacterial community, but no significant difference was observed. Metagenomic analysis showed that the same dominant bacterial phyla existed in all soils, but the proportions were different. Actinobacteriota, Proteobacteria, and Chloroflexi were the absolute dominant bacterial phyla, accounting for 65.12%-78.68% of the total bacteria. Principal co-ordinates analysis showed significant differences in soil bacterial community structure in the planted forest but similarities in the natural forest. The metabolic pathways of soil bacteria in different vegetation communities were similar. Soil organic carbon （SOC）, available phosphorus （AP）, and pH were important abiotic factors affecting the functional structure of bacteria. The findings are helpful for furthering the understanding of plant-soil interaction in ecologically fragile deserts.},
}
@article {pmid40812707,
year = {2025},
author = {Wu, J and Chen, Y and Zhao, J and O'Brien, JW and Coin, L and Hai, FI and Sanderson-Smith, M and Jiang, G},
title = {Impact of human lifestyle on the pathogenic potential of urban wastewater.},
journal = {Environmental research},
volume = {286},
number = {Pt 1},
pages = {122591},
doi = {10.1016/j.envres.2025.122591},
pmid = {40812707},
issn = {1096-0953},
mesh = {*Wastewater/microbiology ; Humans ; *Life Style ; Australia ; Virulence Factors/genetics ; *Bacteria/pathogenicity/genetics ; Cities ; *Microbiota ; },
abstract = {Domestic wastewater has been known for its pathogenic potential including the presence of pathogenic bacteria, virulence factor genes (VFGs) and antibiotic resistance genes (ARGs). While previous studies have investigated regional differences in microbial communities, the influence of population lifestyle factors on the pathogenic potential of wastewater microbiomes remains poorly understood. In this study, we analyzed ten Australian wastewater treatment plants (WWTPs) using Nanopore metagenomic sequencing to profile pathogens, ARGs, and VFGs, and examined their associations with health-related behaviors such as smoking, alcohol consumption, and obesity. A total of 196 pathogenic species, 951 ARG subtypes, and 380 VFGs were detected. Staphylococcus aureus was the most abundant pathogen, macB the dominant ARG, and lipooligosaccharides (LOS) the most prevalent VFG. While pathogen and ARG profiles were relatively stable across sites and showed limited association with lifestyle variables, VFG profiles demonstrated significant correlations with smoking rates, alcohol consumption, and nicotine levels in wastewater. Co-occurrence network analysis revealed strong interconnectivity among VFGs and between VFGs and ARGs, suggesting potential co-selection. Principal component analysis and diversity metrics further confirmed distinct patterns in VFG distribution across sites. These findings suggest VFGs as potentially sensitive indicators of behavioral health risks in wastewater-based epidemiology.},
}
@article {pmid40812705,
year = {2025},
author = {Gao, H and Guo, Z and Huang, F and Li, S and He, X and Fernio, JU and Lv, W and Zhou, L and Du, S and Shen, M and Xu, R},
title = {Core microbiota with antimonite oxidation coupled nitrogen fixation traits persist in the rhizosphere of pioneer plants in antimony tailings.},
journal = {Environmental research},
volume = {285},
number = {Pt 4},
pages = {122586},
doi = {10.1016/j.envres.2025.122586},
pmid = {40812705},
issn = {1096-0953},
mesh = {*Antimony/metabolism ; *Rhizosphere ; *Nitrogen Fixation ; *Microbiota ; Oxidation-Reduction ; *Soil Pollutants/metabolism ; *Soil Microbiology ; *Poaceae/microbiology ; Mining ; Bacteria ; },
abstract = {Antimony (Sb) tailings pose a dual challenge to plant colonization, combining high metal(loid) toxicity with nitrogen (N) limitation, both of which constrain pioneer plant establishment and hinder ecological restoration. Rhizosphere microbiota, particularly Sb(III) oxidation coupled with nitrogen fixation (SbNF) taxa, are critical in mitigating such stresses. However, the composition and persistence of these functional microbes may vary across plant species, leading to untargeted selection. Here, we investigated the rhizosphere microbiomes of two pioneer species-Miscanthus sinensis (herbaceous) and Boehmeria nivea (shrubby)-in Sb tailings. A shared core microbiota (>20 % of the genera) was identified, within which certain taxa exhibited SbNF capabilities with plant growth-promoting (PGP) potential. Through integrated metagenomic binning, culture-based isolation, and functional validation, we identified core genera, such as Pseudomonas and Streptomyces, that were consistently enriched across plant types and exhibited robust SbNF capacities, versatile PGP traits, and community assembly interactions. These findings reveal a conserved assembly mechanism of functional rhizobacteria in Sb-stressed environments and offer promising microbial candidates for the development of bioinoculants to support phytoremediation in metalloid-contaminated ecosystems.},
}
@article {pmid40812483,
year = {2025},
author = {Han, Q and Xia, S and Huang, X and He, J and Yin, Y and Yin, J},
title = {Age-Related Differences in the Gut Microbiota of Pigs Influence Fat Deposition in the Mouse.},
journal = {The Journal of nutrition},
volume = {155},
number = {10},
pages = {3547-3561},
doi = {10.1016/j.tjnut.2025.07.022},
pmid = {40812483},
issn = {1541-6100},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; Swine ; Feces/microbiology ; Age Factors ; Lipid Metabolism ; *Adipose Tissue/metabolism ; RNA, Ribosomal, 16S/genetics ; *Aging ; Male ; Fecal Microbiota Transplantation ; },
abstract = {BACKGROUND: The gut microbiota significantly influences lipid metabolism, but the impact of its developmental patterns at different growth stages on fat deposition remains unclear.<br><br>OBJECTIVES: This study aimed to explore the dynamic changes in microbial diversity and composition during the growth of pig models and assess their involvement in fat deposition.<br><br>METHODS: Forty-five Duroc-Landrace-Yorkshire (DLY) crossbred pigs were killed at 5 ages: 90, 120, 150, 180, and 210 d of age (n = 9). Fecal samples were collected 1 and 15 d before each killing, and the fecal microbiota were detected by 16S rRNA sequencing. The backfat thickness, serum lipid concentrations, intramuscular fat, and fatty acid content in the longissimus dorsi muscle of pigs were measured to assess lipid metabolism. Fecal microbiota transplantation (FMT) from DLY pigs of different ages to antibiotics-challenged mice (n = 8) was used to confirm the effects of microbial development on fat deposition. Metagenomic sequencing was conducted on feces from pigs aged 150 and 180 d and their corresponding transplanted mice to identify key strains involved in fat deposition.<br><br>RESULTS: We observed marked alterations and an increase in intestinal microbial &#x3b1;-diversity with age, peaking at 150 d of age in DLY pigs (P < 0.05). Spearman correlation analyses indicated that 20 genera significantly correlated with the muscle fatty acid contents (P < 0.05). FMT further confirmed that the developmental patterns of the gut microbiota affected host fat deposition, with notable differences observed between the fecal microbiota at day 150 and 180 of age in pigs. Schaalia canis was identified as a potential key microbial strain involved in the developmental patterns of the gut microbiota-governed fat deposition, and its colonization in mice reduced fat deposition by downregulating of LXR&#x3b1;/&#x3b2; gene expressions (P < 0.05).<br><br>CONCLUSIONS: Gut microbiota development impacts fat deposition in pigs, with S canis capable of inhibiting fat deposition.},
}
@article {pmid40812303,
year = {2025},
author = {Huang, Y and Zhang, X and Yu, C and Liu, Y and Kang, H and Liu, Y and Ni, Y and Xia, Y and Jiang, Z and Chen, J and Zhao, K and Han, L and Zou, X and Wang, J and Lei, T and Gan, C and Zhang, H},
title = {Lactobacillus acidophilus promotes cognitive function recovery via regulating microglial peroxisomal function in cerebral ischemia.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {9},
pages = {1484-1501.e12},
doi = {10.1016/j.chom.2025.07.018},
pmid = {40812303},
issn = {1934-6069},
mesh = {Animals ; Female ; Humans ; Male ; Mice ; Middle Aged ; *Brain Ischemia/therapy/microbiology ; *Cognition/physiology ; Cognitive Dysfunction ; Disease Models, Animal ; Gastrointestinal Microbiome ; *Lactobacillus acidophilus/physiology ; Mice, Inbred C57BL ; *Microglia/metabolism ; *Peroxisomes/metabolism ; Probiotics ; Reactive Oxygen Species/metabolism ; Randomized Controlled Trials as Topic ; },
abstract = {Cerebral ischemia causes significant mortality and is accompanied by inflammatory reactions that exacerbate damage. While the gut microbiota is linked to clinical outcomes, specific treatments and mechanisms remain unclear. Our metagenomics linked low Lactobacillus abundance to cognitive decline in patients with cerebral ischemia. L. acidophilus supplementation alleviated post-ischemic deficits in murine middle cerebral artery occlusion and bilateral carotid artery stenosis models. The neuroprotective effects of L. acidophilus were driven by enhanced gut absorption of linoleic acid (LinA). L. acidophilus-induced LinA activates peroxisomes in microglia, triggering microglial reprogramming to an anti-inflammatory state via reactive oxygen species (ROS) scavenging and β-oxidation-mediated epigenetic changes. These L. acidophilus-driven effects are lost upon dietary deficits in LinA, microglia depletion, or peroxisome disruption. A randomized clinical trial showed that L. acidophilus improved cognition and cerebral blood flow in ischemic patients. This study was registered at ClinicalTrials.gov (NCT05845983). Collectively, these findings reveal a therapeutic axis whereby L. acidophilus drives microglial reprogramming, providing a basis for microbiome-targeted neurotherapies.},
}
@article {pmid40812187,
year = {2025},
author = {Tričković, M and Kieser, S and Zdobnov, EM and Trajkovski, M},
title = {Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {8},
pages = {1446-1458.e4},
doi = {10.1016/j.chom.2025.07.015},
pmid = {40812187},
issn = {1934-6069},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Colorectal Neoplasms/microbiology/diagnosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Machine Learning ; Species Specificity ; },
abstract = {Microbial strains within a single species can exhibit distinct functional characteristics due to variations in gene content and often show individual specificity, which can obscure unbiased associations and hinder deductive research. Here, we comprehensively define the human gut microbiota at a consistently annotated operational subspecies unit (OSU) resolution in an unbiased, cohort-independent manner, demonstrating that this approach can generalize across diverse global populations while maintaining specificity and improving interstudy reproducibility. We develop panhashome-a sketching-based method for rapid subspecies and species quantification and identification of genes that drive intraspecies variations-and show that subspecies carry implicit information undetectable at the species level. We identify subspecies associated with colorectal cancer (CRC) whose sibling subspecies or species are not, while a machine-learning CRC diagnostic algorithm based on subspecies outperformed species-level methods. This subspecies catalog allows identification of genes that drive functional differences between subspecies as a fundamental step in mechanistically understanding microbiome-phenotype interactions.},
}
@article {pmid40811873,
year = {2025},
author = {Simpson, AM and Chase, AB and Rodríguez-Verdugo, A and Martiny, JB},
title = {Investigating bacterial evolution in nature with metagenomics.},
journal = {Current opinion in microbiology},
volume = {87},
number = {},
pages = {102654},
doi = {10.1016/j.mib.2025.102654},
pmid = {40811873},
issn = {1879-0364},
mesh = {*Metagenomics ; *Biodiversity ; Biological Evolution ; *Bacteria/classification/genetics ; *Environmental Microbiology ; },
abstract = {Metagenomic sequencing has revolutionized our ability to capture the vast genetic diversity of microbiomes. The technique provides an especially detailed characterization of intraspecific diversity, and a growing number of studies are using that information to investigate bacterial evolution in nature. Here, we review how these studies operationally define evolution, the sampling approaches and metrics used, and the interpretation of the observed evolutionary signatures. Current studies address three main themes: (1) the mechanisms that generate genetic diversity, (2) the spatiotemporal structure of that diversity, and (3) the evolutionary processes that determine its fate. While metagenomics provides enormous potential to investigate in situ evolution, the approach also introduces new questions, including whether populations defined by read mapping are meaningful proxies for biological units of evolution. Addressing these questions will facilitate investigation of the role of evolution relative to ecological shifts in shaping a microbiome's response to environmental change.},
}
@article {pmid40811063,
year = {2025},
author = {Qu, EB and Baker, JS and Markey, L and Khadka, V and Mancuso, C and Tripp, AD and Lieberman, TD},
title = {Intraspecies associations from strain-rich metagenome samples.},
journal = {Cell reports},
volume = {44},
number = {8},
pages = {116134},
pmid = {40811063},
issn = {2211-1247},
support = {DP2 GM140922/GM/NIGMS NIH HHS/United States ; R35 GM156282/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Metagenome/genetics ; Phylogeny ; *Microbiota/genetics ; Female ; *Metagenomics/methods ; Vagina/microbiology ; Skin/microbiology ; },
abstract = {Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides information on all strains in a sample, current strain-resolved analysis methods face a tradeoff: de novo genotyping approaches can detect novel strains but struggle when applied to strain-rich or low-coverage samples, while reference database methods work robustly across sample types but are insensitive to novel diversity. We present PHLAME, a method that bridges this divide by combining the advantages of reference database approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutation-based framework to quantify novelty from the nearest reference. By applying PHLAME to publicly available human skin and vaginal metagenomes, we find clade associations with coexisting species, geography, and host age. The ability to characterize intraspecies associations and dynamics in previously inaccessible environments will enable strain-level insights from accumulating metagenomic data.},
}
@article {pmid40810759,
year = {2025},
author = {Frere Martiniuc, C and de Assis Leite, DC and Seldin, L and Jurelevicius, D},
title = {Viral Diversity in Polar Hydrocarbon-Contaminated Soils: A Transect Study from King George Island, Antarctica.},
journal = {Food and environmental virology},
volume = {17},
number = {3},
pages = {43},
pmid = {40810759},
issn = {1867-0342},
mesh = {Antarctic Regions ; *Soil Microbiology ; *Viruses/classification/genetics/isolation &amp; purification ; *Soil Pollutants/analysis/metabolism ; *Hydrocarbons/analysis/metabolism ; Polycyclic Aromatic Hydrocarbons/analysis/metabolism ; Soil/chemistry ; Metagenomics ; Biodiversity ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Phylogeny ; Metagenome ; },
abstract = {Viruses are key components of soils, influencing microbial dynamics and biogeochemical cycles. Here, we used shotgun metagenomics to analyze the virome of hydrocarbon-contaminated and uncontaminated soils from King George Island, Antarctica. Viral sequences were obtained from metagenomes of all soils; however, the relative abundance of viruses was higher in hydrocarbon-contaminated soils compared to uncontaminated soils. Our results indicate that viral distribution correlates with polycyclic aromatic hydrocarbons (PAHs) in King George Island soil (p = 0.05). Taxonomic analysis of viral contigs revealed viruses from realms Duplodnaviria, Varidnaviria, Monodnaviria, and Riboviria. While Caudoviricetes (realm Duplodnaviria) represented more than 90% of the relative abundance of viruses found in hydrocarbon-contaminated soils, this class represented less than 62% of the viruses of uncontaminated soils. Most viral hosts detected in King George Island soils belonged to hydrocarbon-degrading bacterial genera from the phyla Pseudomonadota and Actinomycetota. Hydrocarbon contamination resulted in the enrichment of well-characterized viruses at the expense of previously uncharacterized viral taxa, which were predominantly detected in non-contaminated soils. Among them, Gordonia-related Stormageddonvirus was the most abundant viral entity identified in King George Island soil. Viral auxiliary metabolic genes (AMGs) associated with nitrogen and phosphate cycles were found in different Caudoviricetes-related contigs. Our results further indicate that Caudoviricetes abundance is correlated with the carbon: phosphate (C:P) ratio in King George Island soils. We propose the Caudoviricetes may actively contribute to microbial competition for phosphorus in hydrocarbon-contaminated soils. These findings shed light on the intricate interplay between viruses, microbial hosts, and environmental contamination in Antarctic soils.},
}
@article {pmid40810220,
year = {2025},
author = {Ni, Z and Yanxi, C and Lianqun, J and Xinya, LI and Yixin, MA},
title = {Huayu Qutan formula can improve platelet aggregation in acute coronary syndrome rats by regulating gut microbes to drive trimethylamine/flavin containing monooxygenase 3/trimethylamine N-oxide pathway.},
journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan},
volume = {45},
number = {4},
pages = {747-758},
pmid = {40810220},
issn = {2589-451X},
support = {82104841//National Natural Science Foundation of China Project: based on the Theory of "the Heart is in Harmony with the Small Intestine" to Explore the Influence and Mechanism of Gut Microbes on High Platelet Reactivity of Acute Coronary Syndrome with Phlegm and Blood Stasis Syndrome/ ; L202039//Education Department of Liaoning Province Young Science and Technology Talents "Seedling" Project: to Explore the Effect and Mechanism of Huayu Qutan Formula on Platelet Function in Acute Coronary Syndrome Patients with Phlegm and Blood Stasis Syndrome after Percutaneous Coronary Intervention based on Intestinal Microbiome/ ; },
mesh = {Animals ; *Methylamines/metabolism ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Drugs, Chinese Herbal/administration &amp; dosage ; Male ; *Platelet Aggregation/drug effects ; *Acute Coronary Syndrome/drug therapy/microbiology/metabolism/physiopathology ; *Oxygenases/metabolism/genetics ; Rats, Sprague-Dawley ; Bacteria/classification/isolation &amp; purification/genetics/metabolism/drug effects ; Humans ; },
abstract = {OBJECTIVE: To investigate the effects of gut microbes regulation of the trimethylamine (TMA)/flavin containing monooxygenase 3 (FMO3)/trimethylamine N-oxide (TMAO) pathway on platelet aggregation in acute coronary syndrome (ACS) rats and the intervention of Huayu Qutan formula.<br><br>METHODS: The ACS rats with syndrome of phlegm and blood stasis rats were established. Platelet, platelet aggregation, platelet activation markers and TMA/FMO3/ TMAO pathway were detected. Metagenomics technology was employed to analyze the characteristics of the gut microbiota.<br><br>RESULTS: Huayu Qutan formula and gut microbes could inhibit high platelet reactivity and regulate the TMA/ FMO3/TMAO pathway. The dominant bacteria in ACS rats including but not limited to the major phyla, Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria, also including some low abundance phyla, Fusobacteria, Verrucomicrobia, Spirochaetes, and Deferribacteres. The dominant bacteria in the Huayu Qutan formula group were Synergistetes, Deferribacteres, Deferribacteraceae, Faecalibacterium and Mucispirillum. In the Huayu Qutan formula combined with fecal bacteria enema group, the dominant bacteria were Verrucomicrobia, Verrucomicrobiae, Akkermansia and Verrucomicrobium. These gut microbiota were correlated with pathways such as Riboflavin metabolism and Arachidonic acid metabolism.<br><br>CONCLUSION: Huayu Qutan formula may prevent ACS by modulating gut microbes Synergistetes, Faecalibacterium and Allobaculum, regulating the iron metabolism of Deferribacteres, and driving the TMA/FMO3/TMAO pathway to regulate gut microbiota function, and improving platelet aggregation. Akkermansia may serve as a promising probiotic, which could drive TMA/FMO3/ TMAO pathway to regulate Arachidonic acid metabolism to improve platelet aggregation. The findings of this study provide a theoretical basis for the theory of "the heart is connected with the small intestine".},
}
@article {pmid40810199,
year = {2026},
author = {Lin, YT and Sayols-Baixeras, S and Graells, T and Dekkers, KF and Baldanzi, G and Nguyen, D and Larsson, A and Feldreich, TR and Nielsen, N and Eklund, AC and Holm, JB and Nielsen, HB and Bergström, G and Smith, JG and Malinovschi, A and Engström, G and Orho-Melander, M and Fall, T and Ärnlöv, J},
title = {Identification of Gut Microbiome Signatures and Metabolites Associated With Albuminuria in Type 2 Diabetes.},
journal = {The Journal of clinical endocrinology and metabolism},
volume = {111},
number = {3},
pages = {e927-e936},
doi = {10.1210/clinem/dgaf453},
pmid = {40810199},
issn = {1945-7197},
support = {ERC- STG-2018-801965 (T.F.)/ERC_/European Research Council/International ; ERC-CoG-2014-649021/ERC_/European Research Council/International ; ERC-STG-2015-679242/ERC_/European Research Council/International ; VR 2019-01471//Swedish Research Council/ ; 2018-02784//Swedish Research Council/ ; 2018-02837//Swedish Research Council/ ; 2021-03291//Swedish Research Council/ ; EXODIAB 2009-1039//Swedish Research Council/ ; 2019-01015//Swedish Research Council/ ; 2020-00243//Swedish Research Council/ ; 2019-01236//Swedish Research Council/ ; 2021-02273//Swedish Research Council/ ; 20200711//Swedish Heart-Lung Foundation/ ; 20180343//Swedish Heart-Lung Foundation/ ; 20210357//Swedish Heart-Lung Foundation/ ; 20200173//Swedish Heart-Lung Foundation/ ; 20190526//Swedish Heart-Lung Foundation/ ; NNF20OC0063886//Novo Nordic Foundation/ ; DIA 2018-375//Swedish Diabetes Foundation/ ; //Swedish Foundation for Strategic Research/ ; //Center for Clinical Research, Region Dalarna Sweden/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 2/complications/microbiology/metabolism ; *Albuminuria/microbiology/metabolism/etiology ; Male ; Female ; Middle Aged ; Aged ; Feces/microbiology ; *Diabetic Nephropathies/microbiology/metabolism ; Sweden/epidemiology ; },
abstract = {CONTEXT: Type 2 diabetes is a growing global concern with serious complications, including kidney damage and cardiovascular morbidity and mortality. Monitoring albuminuria, which is associated with these complications, is crucial in optimal diabetes management. Gut microbiota composition has been suggested to impact albuminuria, but large studies with granular data are lacking.<br><br>METHODS: We investigated the relationship between 1002 gut microbial species, 1308 plasma metabolites, and albuminuria in 752 participants with type 2 diabetes from the Swedish CArdioPulmonary BioImage Study (SCAPIS). To determine the relative abundance of species, we employed deep shotgun metagenomic sequencing of fecal samples. Plasma metabolites were analyzed using mass spectrometry-based methods.<br><br>RESULTS: We identified 3 species that were associated with albuminuria, including Sellimonas intestinalis, Eggerthellales sp., and Ellagibacter isourolithinifaciens. Two of these species were replicated in an independent prediabetic population (n = 3423) in SCAPIS. In total, 36 annotated metabolites were associated with the 3 albuminuria-signature species. Functional mapping of the signature species suggests a role in the regulation of the metabolites of imidazole propionate and trigonelline, which have previously been reported to play roles in the progression of albuminuria.<br><br>CONCLUSION: These findings provide additional evidence of the potential impact of microbial species and contribute to our understanding of the complex relationship between the gut microbiome, plasma metabolites, and albuminuria in individuals with diabetes.},
}
@article {pmid40808637,
year = {2025},
author = {Ferhaoui, N and Sebaihia, M and Sekizuka, T and Kuroda, M},
title = {Shotgun Metagenomic Investigation of the Microbiome in Diabetic Foot Infections Compared to Healthy Skin.},
journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society},
volume = {33},
number = {4},
pages = {e70074},
doi = {10.1111/wrr.70074},
pmid = {40808637},
issn = {1524-475X},
support = {//Algerian Ministry of Higher Education and Scientific Research (DGRSDT/MESRS)/ ; JP23fk0108666j0401//Research Program on Emerging and Reemerging Infectious Diseases of the Japan Agency for Medical Research and Development/ ; },
mesh = {Humans ; *Diabetic Foot/microbiology ; Male ; Female ; Middle Aged ; *Microbiota/genetics ; *Skin/microbiology ; Metagenomics ; Aged ; Adult ; Wound Healing ; },
abstract = {Diabetic foot infection (DFI) is a major complication of diabetes, causing significant morbidity and mortality. Host factors and microorganisms in DFI can disrupt healing processes, leading to chronic, non-healing wounds. The aim of this study was to characterise the microbiome of DFIs and contralateral healthy foot skin (CHFS). Thirty-two diabetic patients were enrolled in this study. Samples were obtained from DFIs and CHFS from the same patient. The microbiome was profiled using metagenomic shotgun sequencing. All the samples were polymicrobial, with a predominance of the obligate anaerobes belonging to Bacteroidetes in PEDIS 4. While PEDIS 3 and 2 were dominated by Proteobacteria. CHFS showed similar bacterial composition across all grades of severity, and the most abundant genera detected were Corynebacterium, Staphylococcus, Pseudomonas, and Cutibacterium. The CHFS was more diverse than DFIs in PEDIS 3 and 4. However, DFIs and CHFS in PEDIS 2 present similar diversity. In addition, DFIs of this grade exhibited a high proportion of Corynebacterium as well as CHFS. PCoA analysis demonstrated that the community structure of DFIs was different from that of CHFS, with Prevotella, Bacteroides, and Porphyromonas the main contributors to the clustering. Neighbour-Net analyses revealed that DFIs exhibited lower diversity compared to CHFS and harboured a more homogeneous dominant bacterial community. Our study revealed a high abundance of obligate anaerobes, including Bacteroides, Prevotella, Morganella, and Porphyromonas, in more severe infections; along with a decrease in microbial diversity. Additionally, there was a decrease in the abundance of key bacteria from the normal skin microbiota.},
}
@article {pmid40803594,
year = {2025},
author = {Wenderlein, J and Burkhardt, W and Dietrich, S and Trefflich, I and Penczynski, K and Thomas, K and Salzinger, C and Abraham, K and Malorny, B and Weikert, C and Ansorge, R and Grützke, J},
title = {Beyond the plate: A pilot study exploring the microbial landscape of omnivores and vegans through 16S rRNA gene amplicon sequencing and metagenomics.},
journal = {Clinical nutrition ESPEN},
volume = {69},
number = {},
pages = {551-565},
doi = {10.1016/j.clnesp.2025.08.008},
pmid = {40803594},
issn = {2405-4577},
mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Male ; Female ; Adult ; *Vegans ; Middle Aged ; *Diet, Vegan ; Diet ; Diet, Vegetarian ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND &amp; AIMS: Previous studies have described benefits and risks on human health associated with a vegan diet. Although it is recognized that diet affects the gut microbiota, there is no consensus on the effects of a vegan diet compared to omnivorous diet on the gut microbiota. We have conducted a pilot study to assess the differences between the gut microbiome of vegans and omnivores in 2017 and 2021.<br><br>METHODS: Fecal samples of 23 vegans and 23 omnivores (n = 46) were collected in 2017 and 2021 together with more than 300 dietary, lifestyle, and health related characteristics. The fecal microbiome was assessed comparing both amplicon sequencing and metagenome sequencing, to determine robust signals agnostic of sequencing approaches.<br><br>RESULTS: Dietary grouping itself explained a small (&#x223c;4 %) but significant proportion of the individual variation between microbiota. Natural clustering of microbiomes explained an even larger proportion. We found Ruminococcus torques to be relatively enriched in omnivores compared to vegans across methods and years. Interestingly, this species has been previously associated with unfavorable health outcomes. Despite a low sample size, we found some consistent differences between microbiota of individuals consuming either a vegan or omnivorous diet.<br><br>CONCLUSIONS: These results were consistent with recently published gut microbiome signatures of vegans and omnivores across three different countries. Therefore, this small dataset allows a first insight into the gut microbiota of another county's omnivores and vegans whereby detailed and relevant dietary, lifestyle and health related characteristics collected in this study aid in understanding of the connection between respective diets and the microbiome.},
}
@article {pmid40803134,
year = {2025},
author = {Wu, F and Campbell, BC and Greenfield, P and Hose, GC and Midgley, DJ and George, SC},
title = {There and back again: Genomic insights into microbial life in a recirculating petroleum refinery wastewater biotreatment system.},
journal = {Microbiological research},
volume = {301},
number = {},
pages = {128299},
doi = {10.1016/j.micres.2025.128299},
pmid = {40803134},
issn = {1618-0623},
mesh = {*Wastewater/microbiology ; *Petroleum/metabolism ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; China ; Metagenome ; Phylogeny ; Genome, Bacterial ; Nitrogen/metabolism ; Microbiota/genetics ; Biodegradation, Environmental ; Carbon/metabolism ; Metabolic Networks and Pathways/genetics ; CRISPR-Cas Systems ; },
abstract = {Petroleum refinery wastewater biotreatment relies on microbes to remediate carbon, nitrogen, and sulfur compounds, yet their life strategies and ecological roles remain unclear. This study characterises the ecological functions of 20 metagenome-assembled genomes (MAGs) from a full-scale petroleum refinery wastewater treatment plant in southern China. The taxonomic identity, nutrient metabolism genes (including C/N/S cycling), carbohydrate-active enzymes, and CRISPR-Cas systems of these MAGs were analysed. The recovered MAGs represented bacteria primarily from the Pseudomonadota and Bacteroidota phyla. The major carbon sources for the represented organisms are likely aromatic and aliphatic compounds, as well as carbohydrates including peptidoglycan, chitin, and starch. Almost all MAGs contained genes for nitrate or nitrite reduction, while metabolic pathways for sulfur metabolism were generally less prevalent. Meiothermus sp. bin.89 was the most metabolically versatile MAG. This organism possessed genes that allowed it to recycle biomass, break down aliphatic and monoaromatic compounds, and perform anaerobic respiration using nitrate. However, it was likely the most susceptible to viral predation, as indicated by the high abundance of CRISPR spacers. Overall, the results revealed that stress-tolerant ecological traits were common among organisms in this microbiome, showcasing the ability of the microbes to obtain carbon from aromatic and aliphatic compounds. This study provides a substantial contribution towards future efforts in optimising microbiome stability for pollutant removal in petroleum refinery wastewater biotreatment systems.},
}
@article {pmid40801952,
year = {2025},
author = {Eckl-Dorna, J and Pjevac, P},
title = {[Principles of microbiome research].},
journal = {HNO},
volume = {73},
number = {9},
pages = {605-609},
pmid = {40801952},
issn = {1433-0458},
mesh = {*Microbiota/genetics ; Humans ; *Metagenomics/methods ; },
abstract = {Microbiome research in the ear nose and throat (ENT) field has substantially gained in importance in recent decades. Modern sequencing methods have largely replaced traditional cultivation. Standardized protocols are essential to ensure reliable and comparable data. The article explains key terms, such as microbiome (the entire microbial community and its environment) and microbiota (only living microorganisms), along with the microbial taxonomy. Important measures for microbiome assessment include the alpha-diversity (species richness and distribution within a sample) and beta-diversity (differences between samples). A differentiation is made between two main approaches to microbiome sequencing: 1) 16S rRNA gene amplicon sequencing (identifies microbial community composition by sequencing the PCR product of a specific gene), 2) metagenomic sequencing (sequences the entire genomic material of a sample, allowing deeper insights). As nasal microbiome biomass is low, careful study design and controls are crucial. Microbiome research is a rapidly growing field with great potential but it requires meticulous planning and bioinformatics expertise for meaningful results.},
}
@article {pmid40801302,
year = {2026},
author = {Guzman, JPMD and Mwamburi, SM and Lurkpranee, S and Koiwai, K and Kondo, H and Hirono, I},
title = {Machine Learning-Aided Meta-Analysis Reveals Changes in Penaeus vannamei Gut Bacterial Communities Upon Dietary Supplementation-Induced Immunostimulation.},
journal = {Journal of fish diseases},
volume = {49},
number = {2},
pages = {e70043},
doi = {10.1111/jfd.70043},
pmid = {40801302},
issn = {1365-2761},
support = {22H00379//Japan Society for the Promotion of Science/ ; JPMJSA1806//Japan Science and Technology Agency/ ; },
mesh = {Animals ; *Penaeidae/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; *Machine Learning ; RNA, Ribosomal, 16S/genetics/analysis ; *Adjuvants, Immunologic/pharmacology/administration &amp; dosage ; Animal Feed/analysis ; Bacteria/classification/genetics ; Diet/veterinary ; },
abstract = {Gut bacterial communities play a key role in shrimp health; thus, their modulation has been a target of dietary supplements which also function in enhancing disease and stress resistance of shrimp. However, this also raised the question of whether immunostimulants yield distinct changes in the gut bacterial composition or whether there are consistent features across all treatments. Here, we performed a machine learning-aided meta-analysis of 16S rRNA gut bacterial community studies of immunostimulants for Penaeus vannamei. Sequence reads from the selected studies were obtained and processed through bioinformatics tools. While beta diversity analysis suggests similarities between the normal, infected and stimulated shrimp, alpha diversity indices showed higher species richness in the gut bacterial communities of shrimp fed with immunostimulants. Specific beneficial taxa were enriched upon immunostimulation, while potentially pathogenic taxa decreased in abundance. Random forest modelling also identified key predictor taxa which may be used to classify gut bacterial communities based on immune status, type of immunostimulant and the specific immunostimulant. Despite some shared patterns in differential abundance-having decreased relative abundances of Photobacterium and other members of Gammaproteobacteria-the influence of immunostimulation on gut bacterial community composition was type- and treatment-specific, as evident in the distinct abundance profiles of the predictor taxa. Functional prediction analysis also showed distinct pathways enriched in immunostimulated shrimp, as influenced by the type of the immunostimulant. This study highlighted the specific impacts of dietary supplementation-induced immunostimulation on gut bacterial communities and identified key features in immunostimulated shrimp which provide a novel perspective on the interplay between gut bacterial community and immunity.},
}
@article {pmid40797468,
year = {2025},
author = {Guo, T and Chang, L and Huang, PW and Yao, JP and Zhang, YC and Ren, CY and Bao, CQ},
title = {Investigating the mediating effect of plasma metabolites on the gut microbiome in influencing Behçet disease: A multi-omics validated Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {32},
pages = {e42698},
pmid = {40797468},
issn = {1536-5964},
support = {Z202213//Wuxi Municipal Health Commission's research project/ ; },
mesh = {Humans ; *Behcet Syndrome/microbiology/blood/genetics ; *Gastrointestinal Microbiome/physiology/genetics ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Male ; Female ; Multiomics ; },
abstract = {Although an established correlation between gut microbiota (GM) and Behçet syndrome exists, the potential mediating involvement of plasma metabolites remains unclear. Using the most recent statistical data from genome-wide association studies conducted in 2024, we investigated the causal relationships between 473 GM taxa, 233 circulating metabolites, and Behçet syndrome (Behçet disease [BD]) through a 2-sample Mendelian randomization approach. This analysis was further supported by incorporating transcriptome and metagenomic data related to BD. A 2-step methodology was employed to evaluate the extent to which the effect of GM on BD is mediated through plasma metabolites. These results were subsequently validated in a separate validation set. Our Mendelian randomization results demonstrated correlations between various GM and the risk of Behçet syndrome. The potential link between GM and BD risk may be mediated through plasma circulating metabolite levels. Specifically, for every standard deviation, an increase in the abundance of Turicibacter sp001543345 was correlated with a 403% increase in BD risk (odds ratio : 5.03 [95% confidence interval, 1.77-14.25]). Meanwhile, the cholesteryl esters to total lipids ratio in large very low-density lipoprotein and the total cholesterol to total lipids ratio in very large very low-density lipoprotein increased by 4%. The proportion of indirect effects is 3.026% and 3.338%, respectively. Our study established a causal link between distinct GM and BD and quantified the proportion of effects mediated through plasma metabolites. These findings provide further insights for the treatment of BD.},
}
@article {pmid40797356,
year = {2025},
author = {Rashwan, HH and Ali, MH and Mostafa, MM and Ramadan, R and Mysara, M},
title = {Insights into the tripartite relationship between cervical cancer, human papillomavirus, and the vaginal microbiome: a mega-analysis.},
journal = {Human genomics},
volume = {19},
number = {1},
pages = {89},
pmid = {40797356},
issn = {1479-7364},
mesh = {Humans ; Female ; *Microbiota/genetics ; *Uterine Cervical Neoplasms/microbiology/virology/genetics/pathology ; *Vagina/microbiology/virology ; RNA, Ribosomal, 16S/genetics ; *Papillomavirus Infections/microbiology/virology/complications/genetics ; Dysbiosis/microbiology ; *Papillomaviridae/pathogenicity/genetics ; Case-Control Studies ; Adult ; Human Papillomavirus Viruses ; },
abstract = {BACKGROUND: Cervical cancer (CC) is the fourth most prevalent malignancy among women worldwide, where 99.7% of the cases are linked to persistent human papillomavirus (HPV) infections. While emerging evidence suggests a role for vaginal microbiome dysbiosis in HPV-driven CC, the specific microbial alterations and their functional implications remain unclear. However, inconsistencies in identifying specific microbial signatures-largely due to heterogeneous study designs, targeted 16S rRNA regions, and data processing methods-have limited the generalizability of existing findings. To address these challenges, we conducted a standardized mega-analysis using a compositionality-aware approach to ensure consistency and minimize technical bias across studies.<br><br>RESULTS: Our mega-analysis consolidates findings from five case-control 16S rRNA ampilicon sequencing studies, encompassing 215 samples. Compared to healthy controls, CC patients exhibited significantly higher alpha diversity (Shannon index, p&#xa0;<0.005)&#xa0;and a shift from a Lactobacillus-dominant to a polymicrobial vaginal microbiome.&#xa0;This microbial dysbiosis was&#xa0;characterized by an increased abundance&#xa0;of Porphyromonadaceae, particularly Porphyromonas asaccharolytica, and other anaerobic bacterial species&#xa0;such as&#xa0;Campylobacter ureolyticus, Peptococcus niger, and Anaerococcus obesiensis (FDR&#xa0;<0.05).&#xa0;Functional profiling of the altered microbiome revealed enrichment in pathways associated with chronic inflammation, fatty acid biosynthesis, amino acid metabolism, cellular proliferation, invasion, and metastasis.<br><br>CONCLUSIONS: This mega-analysis presents the most methodologically homogeneous study to date of CC-associated vaginal microbiome using publicly available 16S datasets. Our findings not only deepen our understanding of microbial influences on CC but also pave the way for novel diagnostic and therapeutic approaches potentially enhancing patient outcomes in CC care. These insights open new avenues for clinical interventions that extend beyond conventional HPV-centric&#xa0;strategies.},
}
@article {pmid40796374,
year = {2025},
author = {Pan, S and Du, H and Zheng, R and Zhang, C and Pan, J and Yang, X and Wang, C and Lin, X and Li, J and Liu, W and Zhou, H and Yu, X and Mo, S and Zhang, G and Zhao, G and He, Z and Tian, Y and Jiang, C and Qu, W and Liu, Y and Li, M},
title = {A holistic genome dataset of bacteria and archaea of mangrove sediments.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40796374},
issn = {2047-217X},
support = {2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; 92251306//National Natural Science Foundation of China/ ; 92051102//National Natural Science Foundation of China/ ; 92251307//National Natural Science Foundation of China/ ; 92351303//National Natural Science Foundation of China/ ; 32370055//National Natural Science Foundation of China/ ; 32200099//National Natural Science Foundation of China/ ; 32070108//National Natural Science Foundation of China/ ; 32225003//National Natural Science Foundation of China/ ; 31970105//National Natural Science Foundation of China/ ; 42303064//National Natural Science Foundation of China/ ; 42430707//National Natural Science Foundation of China/ ; JCYJ20200109105010363//Shenzhen Science and Technology Program/ ; KCXFZ20201221173404012//Shenzhen Science and Technology Program/ ; JCYJ20230808105711023//Shenzhen Science and Technology Program/ ; 20220809161641002//Shenzhen Science and Technology Program/ ; SML2023SP218/SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory/ ; 2022B002//Shenzhen University/ ; },
mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification ; Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; *Genome, Bacterial ; China ; Microbiota/genetics ; *Genome, Archaeal ; Wetlands ; },
abstract = {BACKGROUND: Mangroves are one of the most productive marine ecosystems with high ecosystem service value. The sediment microbial communities contribute to pivotal ecological functions in mangrove ecosystems. However, the study of mangrove sediment microbiomes is limited.<br><br>FINDINGS: Here, we applied metagenome sequencing analysis of microbial communities in mangrove sediments across Southeast China from 2014 to 2020. This genome dataset includes 966 metagenome-assembled genomes with &#x2265;50% completeness and &#x2264;10% contamination generated from 6 groups of samples. Phylogenomic analysis and taxonomy classification show that mangrove sediments are inhabited by microbial communities with high species diversity. Thermoplasmatota, Thermoproteota, and Asgardarchaeota in archaea, as well as Proteobacteria, Desulfobacterota, Chloroflexota, Acidobacteriota, and Gemmatimonadota in bacteria, dominate the mangrove sediments across Southeast China. Functional analyses suggest that the microbial communities may contribute to carbon, nitrogen, and sulfur cycling in mangrove sediments.<br><br>CONCLUSIONS: These combined microbial genomes provide an important complement of global mangrove genome datasets and may serve as a foundational resource for enhancing our understanding of the composition and functions of mangrove sediment microbiomes.},
}
@article {pmid40796349,
year = {2025},
author = {Huang, WC and Probst, M and Hua, ZS and Szánthó, LL and Szöllősi, GJ and Ettema, TJG and Rinke, C and Williams, TA and Spang, A},
title = {Phylogenomic Analyses Reveal that Panguiarchaeum Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia.},
journal = {Molecular biology and evolution},
volume = {42},
number = {9},
pages = {},
pmid = {40796349},
issn = {1537-1719},
support = {947317//European Union's Horizon 2020/ ; 714774//European Union's Horizon 2020/ ; GBMF9741//Gordon and Betty Moore Foundation/ ; 735929LPI//Simons Foundation/ ; 63451//John Templeton Foundation/ ; },
mesh = {*Phylogeny ; *Archaea/genetics/classification ; *Genome, Archaeal ; Evolution, Molecular ; },
abstract = {The Asgard archaea are a diverse archaeal phylum important for our understanding of cellular evolution because they include the lineage that gave rise to eukaryotes. Recent phylogenomic work has focused on characterizing the diversity of Asgard archaea in an effort to identify the closest extant relatives of eukaryotes. However, resolving archaeal phylogeny is challenging, and the positions of 2 recently described lineages-Njordarchaeales and Panguiarchaeales-are uncertain, in ways that directly bear on hypotheses of early evolution. In initial phylogenetic analyses, these lineages branched either with Asgards or with the distantly related Korarchaeota, and it has been suggested that their genomes may be affected by metagenomic contamination. Resolving this debate is important because these clades include genome-reduced lineages that may help inform our understanding of the evolution of symbiosis within Asgard archaea. Here, we performed phylogenetic analyses revealing that the Njordarchaeales and Panguiarchaeales constitute the new class Njordarchaeia within Asgard archaea. We found no evidence of metagenomic contamination affecting phylogenetic analyses. Njordarchaeia exhibit hallmarks of adaptations to (hyper-)thermophilic lifestyles, including biased sequence compositions that can induce phylogenetic artifacts unless adequately modeled. Panguiarchaeum is metabolically distinct from its relatives, with reduced metabolic potential and various auxotrophies. Phylogenetic reconciliation recovers a complex common ancestor of Asgard archaea that encoded the Wood-Ljungdahl pathway. The subsequent loss of this pathway during the reductive evolution of Panguiarchaeum may have been associated with the switch to a symbiotic lifestyle, potentially based on H2-syntrophy. Thus, Panguiarchaeum may contain the first obligate symbionts within Asgard archaea besides the lineage leading to eukaryotes.},
}
@article {pmid40796326,
year = {2025},
author = {Patel, SM and Farirai, J and Patel, MZ and Boiditswe, S and Tawe, L and Lekalake, S and Matshaba, M and Steenhoff, AP and Arscott-Mills, T and Feemster, KA and Shah, SS and Thielman, N and Cunningham, CK and David, LA and Murdoch, DM and Kelly, MS},
title = {Alterations of the Upper Respiratory Microbiome Among Children Living With HIV Infection in Botswana.},
journal = {The Journal of infectious diseases},
volume = {232},
number = {4},
pages = {815-825},
pmid = {40796326},
issn = {1537-6613},
support = {//Duke University Center for AIDS Research/ ; D43 TW009337/TW/FIC NIH HHS/United States ; //NIH/ ; K23-HL166022//NIH Career Development Award/ ; K23 HL166022/HL/NHLBI NIH HHS/United States ; L30 HL170390/HL/NHLBI NIH HHS/United States ; K23-AI135090//NIH-funded program/ ; 5P30-AI064518//NIH-funded program/ ; T32 HL 007538//Institutional Training Grant in Pulmonary and Critical Care Medicine/ ; P30-AI045008//Penn Center for AIDS Research/ ; },
mesh = {Humans ; *HIV Infections/microbiology/complications ; Botswana/epidemiology ; Female ; Male ; Cross-Sectional Studies ; *Microbiota ; *Nasopharynx/microbiology ; Child, Preschool ; *Respiratory Tract Infections/microbiology/epidemiology ; Infant ; },
abstract = {Children living with HIV (CLWH) are at high risk of colonization and infection by respiratory pathogens, though this risk can be reduced by other microbes in the upper respiratory microbiome. The impact of HIV infection on the pediatric upper respiratory microbiome is poorly understood, and we sought to address this knowledge gap by identifying associations between HIV infection and the nasopharyngeal microbiomes of Batswana children. We enrolled Batswana CLWH (<5 years) and age- and sex-matched HIV-exposed, uninfected and HIV-unexposed, uninfected children in a cross-sectional study. We used shotgun metagenomic sequencing to compare nasopharyngeal microbiomes by HIV status. Among the 143 children in this study, HIV and HIV-associated immunosuppression were associated with alterations in nasopharyngeal microbiome composition, including lower abundances of Corynebacterium species associated with resistance to bacterial pathogen colonization. These findings suggest that the upper respiratory microbiome may contribute to the high risk of respiratory infections among CLWH.},
}
@article {pmid40795932,
year = {2025},
author = {Teng, ZJ and Yuan, XJ and Liu, R and Xu, SC and Chen, XL and Chen, Y and Zhang, YZ},
title = {Inositol phosphates as an overlooked phosphorous source in marine ecosystems.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40795932},
issn = {1751-7370},
mesh = {*Phosphorus/metabolism ; *Seawater/chemistry/microbiology ; *Inositol Phosphates/metabolism/analysis ; *Ecosystem ; *Aquatic Organisms/metabolism ; 6-Phytase/genetics/metabolism ; Metagenome ; Bacteria/metabolism/genetics/classification ; Hydrolysis ; },
abstract = {Inositol phosphates, common phosphorus storage compounds that are also crucial for eukaryotic cell signaling, constitute a significant portion of dissolved organic phosphorus in coastal waters. The hydrolysis of inositol phosphates could be an important contributor to phosphorus cycling in phosphorus-limited marine ecosystems, yet this process remains poorly understood in marine contexts. In this study, we reveal substantial concentrations of inositol phosphates in marine macrophytes, including green, brown, and red algae as well as common seagrasses, suggesting that these organisms are likely major biological sources of inositol phosphates in the oceans. A comprehensive analysis of genes involved in inositol phosphates hydrolysis in global marine metagenomes and metatranscriptomes identified key roles for γ-, α-, and δ-proteobacteria, with additional contributions from Flavobacteriia. The degradation of marine inositol phosphates was predominantly mediated by alkaline β-propeller phytases, though genes associated with acidic cysteine phytases and purple acid phytases were also widely present. Community structure and functional traits linked to inositol phosphates degradation were shaped largely by stochastic processes. Further examination of enzyme activity at the protein and community levels indicated that phytate metabolism by marine microbes is likely a widespread phenomenon in the ocean. Overall, this study highlights inositol phosphates hydrolysis as an essential yet overlooked adaptation by marine microorganisms to address phosphorus limitations in ocean ecosystems.},
}
@article {pmid40795737,
year = {2025},
author = {Zhao, J and Kou, X and Liu, H and Wu, T and Li, J and Wang, Y and Xie, H and Wang, M and Wu, L and Wen, L and Wang, L},
title = {Microbial community responses and functional shifts in carbon degradation driven by water-salt gradients in lakeshore wetlands of semi-arid lakes.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126893},
doi = {10.1016/j.jenvman.2025.126893},
pmid = {40795737},
issn = {1095-8630},
mesh = {*Wetlands ; *Lakes ; *Carbon/metabolism ; Soil/chemistry ; Salinity ; Soil Microbiology ; Microbiota ; Ecosystem ; },
abstract = {Wetlands, especially lakeshore ecosystems, play an essential role in global carbon (C) cycling and are strongly influenced by dynamic water-salt gradients. However, the mechanisms by which these gradients shape microbial communities and affect soil organic C (SOC) degradation remain incompletely understood. Here, we aimed to elucidate microbial mechanisms driving C degradation shifts along water-salt gradients. We investigated microbially mediated SOC degradation potential in Daihai Lake wetlands by metagenomic profiling of carbohydrate-active enzyme (CAZyme) genes. Our results demonstrated a significant shift in CAZyme gene abundances across the gradients. Genes involved in plant-derived C (cellulose, hemicellulose, lignin) degradation decreased with increasing soil salinity and moisture, while those related to microbial-derived C (chitin, peptidoglycan, glucans) decomposition were significantly enriched. Concurrently, the microbial community composition shifted toward greater abundance of salt-tolerant taxa, notably Proteobacteria and Bacteroidetes, while Actinobacteria and Firmicutes declined under higher water-salt conditions. Statistical analyses revealed strong correlations between key environmental factors (soil salinity (EC), soil moisture (SM), and pH) and both microbial community structure and CAZyme gene abundances (p < 0.001). Random Forest analysis further identified EC and SM as primary factors influencing C-degrading microbial functions. This study highlights the importance of water-salt gradients in regulating microbial-mediated C cycling in wetlands, providing critical insights into microbial adaptation strategies and their implications for wetland C dynamics under environmental change.},
}
@article {pmid40795730,
year = {2025},
author = {D'Ugo, E and Mukherjee, A and Resitano, M and Giuseppetti, R and Fortini, D and Bruna Matturro, and Chirico, M and Pisanu, ME and Tucci, M and Pozzi, R and Lovecchio, N and Slawomir, O and Iosi, F and Villa, L and Iorio, E and Aulenta, F and Viggi, CC and Bertuccini, L and Magurano, F},
title = {Fishing out microorganisms for bioremediation using metagenomics: Isolation and whole-genome sequencing of the metabolically versatile Rhodococcus erythropolis LP27217 strain from oil spill lake.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139463},
doi = {10.1016/j.jhazmat.2025.139463},
pmid = {40795730},
issn = {1873-3336},
mesh = {*Rhodococcus/genetics/metabolism/isolation &amp; purification ; Biodegradation, Environmental ; *Petroleum Pollution ; *Lakes/microbiology ; *Water Pollutants, Chemical/metabolism ; Metagenomics ; Whole Genome Sequencing ; Polycyclic Aromatic Hydrocarbons/metabolism ; RNA, Ribosomal, 16S/genetics ; Hydrocarbons/metabolism ; Genome, Bacterial ; Petroleum/metabolism ; Thiophenes ; },
abstract = {Isolating microorganisms from oil spill-contaminated environments is essential for advancing bioremediation strategies and discovering novel bioprocesses for hydrocarbon degradation. In this study, we report the isolation of a novel strain, Rhodococcus erythropolis LP27217, from Pertusillo Lake (Italy) on february 2017. Water samples were collected during an oil spill event and microbial community was previously characterized using 16S rRNA gene-targeted metagenomic analysis and functional prediction. The Rhodococcus genus was identified as the dominant member of this microbiome, and functional predictive analyses guided the isolation of the R. erythropolis LP27217 strain under various growth conditions, including the presence of hydrocarbons and in Liquid Microbial Fuel Cell (L-MFC) systems. This strain exhibits a versatile hydrocarbon-degrading and transforming metabolism, effectively addressing pollutants such as crude oil, polycyclic aromatic hydrocarbons (PAHs), and dibenzothiophene (DBT), even under psychrophilic conditions. Additionally, R. erythropolis LP27217 demonstrated the ability to produce lipopeptide biosurfactants and lipophilic polymers, with the latter being associated with the formation of an electrogenic hydrocarbonoclastic biofilm at the anoxic oil-water interface. Overall, this study demonstrated that R. erythropolis LP27217 is a promising candidate for sustainable applications, including in situ bioremediation of oil spills in lake ecosystems and the biosynthesis of innovative polymers and biosurfactants for biotechnological and environmental purposes. Furthermore, its ability to operate across oxic and hypoxic conditions, at the oil-water interface and within the water column, highlights a novel microbial mechanism with significant ecological and industrial potential.},
}
@article {pmid40795725,
year = {2025},
author = {Zhang, FL and Li, AY and Zhu, KX and Zhang, K and Tian, Z and Wang, T and Zhang, XH and Zang, J and Sun, XF and Shen, W and Li, L},
title = {Integrated multi-omics analysis uncovers Zearalenone-induced ovarian and intestinal inflammation is mediated by the tumor necrosis factor-α.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139476},
doi = {10.1016/j.jhazmat.2025.139476},
pmid = {40795725},
issn = {1873-3336},
mesh = {*Zearalenone/toxicity ; Animals ; Female ; *Tumor Necrosis Factor-alpha/genetics/metabolism ; *Inflammation/chemically induced/metabolism/genetics ; *Ovary/drug effects/pathology/metabolism ; Mice ; Gastrointestinal Microbiome/drug effects ; *Intestines/drug effects/pathology ; Mice, Knockout ; Mice, Inbred C57BL ; Dysbiosis/chemically induced ; Cell Line ; Multiomics ; },
abstract = {As a widely encountered foodborne mycotoxin, Zearalenone (ZEN) has the potential to accumulate along the food chain, posing threats to public health and safety. However, the precise mechanisms by which ZEN causes tissue damage remain incompletely understood. Here, we established in vivo (40 μg/kg) and in vitro (30 μM) models to elucidate the underlying processes of ZEN-induced damage to the ovary and intestine. Our results demonstrated that, following ZEN exposure, pro-inflammatory signaling factors, including NLR family pyrin domain containing 3 (NLRP3) and Interleukin 6 (IL6), were significantly elevated in both ovarian and intestines. Metagenomic analysis revealed dysbiosis of the gut microbiota, which was closely associated with tumor necrosis factor (TNF)-α signaling pathway. Transcriptomic results further indicated that inflammatory response are intricately linked to TNF signaling pathway. Additionally, the Tnf-α knockout mouse model showed a marked resistance to ZEN-induced ovarian and intestinal injuries. In vitro, RNA interference targeting TNF-α attenuated the inflammatory response in IPEC-J2 cells. Moreover, dysregulated expression of the hormone synthesis genes, including KISS-1 metastasis suppressor (Kiss1) and gonadotropin releasing hormone 1 (Gnrh1), was observed, suggesting that ZEN-induced microbial dysbiosis and ovary damage may be interconnected through hormonal disruption. In summary, our results emphasize the role of TNF-α in causing ovarian and intestinal damage after ZEN exposure.},
}
@article {pmid40795332,
year = {2025},
author = {Aguilera-Campos, KI and Boisard, J and Törnblom, V and Jerlström-Hultqvist, J and Behncké-Serra, A and Cotillas, EA and Stairs, CW},
title = {Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40795332},
issn = {1751-7370},
mesh = {Anaerobiosis ; *Microbiota ; Hydrogen/metabolism ; *Bacteria/metabolism/classification/genetics ; *Eukaryota/growth &amp; development ; Metagenomics ; Symbiosis ; },
abstract = {Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.},
}
@article {pmid40795028,
year = {2025},
author = {Park, HS and Chavarria, X and Shatta, A and Kang, D and Oh, S and Choi, DY and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY},
title = {Distinct microbial communities of drain flies (Clogmia albipunctata) across sites with differing human influence.},
journal = {FEMS microbiology letters},
volume = {372},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf078},
pmid = {40795028},
issn = {1574-6968},
support = {RS-2024-00456300//National Research Foundation of Korea/ ; //Korea Health Industry Development Institute/ ; RS-2024-00406488//Ministry of Health and Welfare/ ; },
mesh = {Animals ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Humans ; Republic of Korea ; *Diptera/microbiology ; Phylogeny ; DNA, Bacterial/genetics ; Metagenomics ; },
abstract = {Drain flies (Clogmia albipunctata) are insects that thrive in humid urban environments such as bathrooms drains and sewage systems. While their role in pathogen transmission has been suggested, little is known about their microbiome or ecology in non-clinical contexts. Using 16S rRNA gene metabarcoding, we characterized the bacterial communities of drain flies from three locations in South Korea, public bathrooms from a college in Seoul, a rural port in Ulleungdo island, and a highly frequented public park in Yeouido. In total, we obtained 221 families and 1 474 features. We found significant differences in microbiome composition and diversity as well as a small core microbiome shared among locations, with environmental bacteria such as Pseudomonas and Ralstonia being the dominant taxa across samples. The majority of the detected amplicon sequence variants (ASV) were not shared among locations. These findings suggest drain fly transport a location-specific environmental bacteria. Notably, we also identified ASVs of potential clinical relevance, including Mycobacterium, Acinetobacter baumanii, Providencia, and Nocardia. This is the first metagenomic insight into the microbiome of this species and adds to a renewed interest in the role that non-hematophagous insects play in urban microbial ecology and the spread of microbes.},
}
@article {pmid40794955,
year = {2025},
author = {Dai, Y and Qian, Y and Qu, Y and Guan, W and Xie, J and Wang, D and Butler, C and Dashper, S and Carroll, I and Divaris, K and Liu, Y and Wu, D},
title = {Decoding longitudinal microbiome trajectories: an interpretable machine learning approach for biomarker discovery and prediction.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
pmid = {40794955},
issn = {1477-4054},
support = {R03 DE034507/DE/NIDCR NIH HHS/United States ; U01 DE025046/DE/NIDCR NIH HHS/United States ; U01DE025046/NH/NIH HHS/United States ; 1R03DE034507-01/NH/NIH HHS/United States ; },
mesh = {Humans ; *Machine Learning ; *Biomarkers ; *Microbiota ; Longitudinal Studies ; Gastrointestinal Microbiome ; },
abstract = {Information generated from longitudinally sampled microbial data has the potential to illuminate important aspects of development and progression for many human conditions and diseases. Identifying microbial biomarkers and their time-varying effects can not only advance our understanding of pathogenetic mechanisms, but also facilitate early diagnosis and guide optimal timing of interventions. However, longitudinal predictive modeling of highly noisy and dynamic microbial data (e.g. metagenomics) poses analytical challenges.To overcome these challenges, we introduce a robust and interpretable machine-learning-based longitudinal microbiome analysis framework, LP-Micro, that encompasses (i) longitudinal microbial feature screening via a polynomial group lasso, (ii) disease outcome prediction implemented via machine learning methods (e.g. XGBoost, deep neural networks), and (iii) interpretable association testing between time points, microbial features, and disease outcomes via permutation feature importance. We demonstrate in simulations that LP-Micro can not only identify incident disease-related microbiome taxa, but also offers improved prediction accuracy compared with existing approaches. Applications of LP-Micro in two longitudinal microbiome studies with clinical outcomes of childhood dental disease and weight loss following bariatric surgery yield consistently high prediction accuracy. Moreover, LP-Micro highlights critical time points and associated microbial changes: oral microbial changes, including Streptococcus mutans, are most informative for predicting childhood dental disease at around 39 months of age, while gut microbial changes shortly after bariatric surgery strongly predict future weight loss. These findings are both informative and aligned with clinical expectations. The tool LP-Micro can be seen at https://github.com/IV012/LPMicro.},
}
@article {pmid40794939,
year = {2025},
author = {Kannan, EP and Venkatachalam, P and Gopal, J and Sarkaraisamy, P and Muthu, M},
title = {Temporal shift of bacterial communities in poultry litter during the course of broiler chicken rearing: a 16S rRNA-based metagenomic study.},
journal = {Journal of applied microbiology},
volume = {136},
number = {8},
pages = {},
doi = {10.1093/jambio/lxaf199},
pmid = {40794939},
issn = {1365-2672},
support = {//DRDO/ ; },
mesh = {Animals ; *Chickens/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenomics ; India ; DNA, Bacterial/genetics ; *Manure/microbiology ; *Microbiota ; Soil Microbiology ; Phylogeny ; },
abstract = {AIM: To decipher the bacterial community transitions of poultry litter at various time frames over a 6-week rearing cycle in a commercial broiler chicken poultry farm in Marakanam, Tamil Nadu, India.<br><br>METHODS AND RESULTS: The bacterial consortia of poultry litter were elucidated using the 16S rRNA-based metagenomic Oxford nanopore sequencing method, followed by taxonomic assignment using the Kraken2 tool. Our findings unveiled the varied dominance patterns of bacteria in poultry litter (P1-P6) with Sphingobacterium sp. 21 (53%) in P1, Amphibacillus xylanus dominated in P2 (&#x223c;12%), Oceanimonas sp. GK1 in P3 (&#x223c;14%) and P6 (>50%), Anaerococcus prevotii in P4 (&#x223c;10%) and Marinobacter hydrocarbonoclasticus (&#x223c;15%) in P5. Importantly various bacteria involved in key biogeochemical cycles, including Nitrosomonas eutropha (nitrogen cycle), Bacillus subtilis (phosphorous cycle), and Acidithiobacillus caldus (sulphur cycle) were detected indicating a strong potential of utilizing the poultry litter as an effective biofertilizer. On the other hand, harmful human pathogens, including Mycobacterium tuberculosis, Escherichia coli, Salmonella enterica, and Streptococcus pneumoniae were also detected indicating significant public health concern associated with the application of poultry litter as fertilizer.<br><br>CONCLUSIONS: This study offers knowledge to both leverage the usefulness of poultry litter as biofertilizer and to mitigate transmission of harmful pathogens harboured by poultry litter.},
}
@article {pmid40794845,
year = {2025},
author = {Heber, K and Tian, S and Betancurt-Anzola, D and Koo, H and Bisanz, JE},
title = {StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {8},
pages = {},
pmid = {40794845},
issn = {1367-4811},
support = {R00 AI147165/AI/NIAID NIH HHS/United States ; R35 GM151045/GM/NIGMS NIH HHS/United States ; },
mesh = {Mice ; Animals ; *Software ; *Metagenomics/methods ; *Microbiota/genetics ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Sequence Analysis, DNA/methods ; },
abstract = {MOTIVATION: Synthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level and other methods such as quantitative polymerase chain reaction (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes.<br><br>RESULTS: Both in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy and efficiency than other tools utilizing shotgun metagenomic sequencing reads. We demonstrate that StrainR2's accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification.<br><br>Software is available at GitHub and implemented in C, R, and Bash. Software is supported on Linux and MacOS, with packages available on Bioconda or as a Docker container. The source code at the time of publication is also available on figshare at the doi: 10.6084/m9.figshare.29420780.},
}
@article {pmid40794770,
year = {2025},
author = {Chia, M and Pop, M and Salzberg, SL and Nagarajan, N},
title = {Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.},
journal = {Cancer research},
volume = {85},
number = {19},
pages = {3584-3595},
pmid = {40794770},
issn = {1538-7445},
support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; OFYIRG21nov-0024//National Medical Research Council (NMRC)/ ; R35-GM130151//National Institute of General Medical Sciences (NIGMS)/ ; R01-HG006677//National Human Genome Research Institute (NHGRI)/ ; NRFI09-0015//National Research Foundation Singapore (NRF)/ ; },
mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; },
abstract = {The study of cancer-associated microbiomes has gained significant attention in recent years, spurred by advances in high-throughput sequencing and metagenomic analysis. Microbiome research holds promise for identifying noninvasive biomarkers and possibly new paradigms for cancer treatment. In this review, we explore the key computational challenges and opportunities in analyzing cancer-associated microbiomes (in tumor/normal tissues and other body sites, e.g., gut, oral, and skin), focusing on sequencing-driven strategies and associated considerations for taxonomic and functional characterization. The discussion covers the strengths and limitations of current analysis tools for identifying contamination, determining compositional bias, and resolving species and strains, as well as the statistical, metabolic, and network inferences that are essential to uncover host-microbiome interactions. Several key considerations are required to guide the choice of databases used for metagenomic analysis in such studies. Recent advances in spatial and single-cell technologies have provided insights into cancer-associated microbiomes, and Artificial Intelligence-driven protein function prediction might enable rapid advances in this field. Finally, we provide a perspective on how the field can evolve to manage the ever-growing size of datasets and generate robust and testable hypotheses. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI .},
}
@article {pmid40794299,
year = {2025},
author = {El-Halim, HMA and El-Hadidi, M and Fouad, N and Hamed, RR and Megid, IA and Taha, MH and Radwan, KH},
title = {Metagenomic insight into drought-induced changes in the Egyptian wheat rhizosphere microbiome.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {8},
pages = {310},
pmid = {40794299},
issn = {1573-0972},
mesh = {*Triticum/microbiology ; *Rhizosphere ; *Droughts ; Egypt ; *Microbiota/genetics ; Soil Microbiology ; Phylogeny ; *Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification ; Stress, Physiological ; RNA, Ribosomal, 16S/genetics ; Metagenome ; },
abstract = {Wheat is one of the most important cereal crops and an important source of food for billions of people worldwide. However, drought stress can pose a real threat to its productivity and lead to significant yield losses, especially in Egypt. The rhizospheric microbiome of wheat can play an important role in drought stress and help wheat to respond to this abiotic stress. Understanding this microbiome is therefore also important to improve drought stress resilience and productivity. In this study, a metagenomic analysis was performed to investigate how the composition and diversity of microbial communities associated with the wheat rhizosphere change under drought. Taxonomic and phylogenetic analyses revealed a shift in microbial abundance, with Actinobacteria, Bacteroidetes, Proteobacteria and Verrucomicrobia being the four most abundant phyla of the ethnic microbiota. Remarkably, other classes, including Alphaproteobacteria and Cytophagia, were significantly enriched under drought, which could be a promising enhancement of plant stress altruism. Differential abundance analysis showed that the control samples had higher abundance of microbial taxa such as OD1, WS2, Chlorobi, ABY1 and SHA-109 compared to the drought-treated genotypes. Functional prediction analysis using PICRUSt showed that an uncharacterized ATP-binding protein within the AAA + superfamily is overrepresented under drought conditions. This suggests that these genes may play a role in stress adaptation, possibly via energy-dependent regulation of cellular processes involved in plant survival. Our results expand our understanding of the complexity of responses of the wheat rhizosphere microbiome to drought and have practical implications for the development of microbial target combinations to improve wheat tolerance and productivity in the context of climate change challenges.},
}
@article {pmid40793873,
year = {2025},
author = {Manning, S and Hackney, E and Dunneram, Y and Hull, MA and Mitra, S and Stewart, CJ and Louca, P and Meader, N and Sharp, L and Rees, C},
title = {Systematic Review: The Relationship Between the Faecal Microbiome and Colorectal Neoplasia in Shotgun Metagenomic Studies.},
journal = {Alimentary pharmacology &amp; therapeutics},
volume = {62},
number = {6},
pages = {568-584},
pmid = {40793873},
issn = {1365-2036},
support = {//Guts UK/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Reproducibility of Results ; },
abstract = {BACKGROUND: The human gut microbiome is of academic and clinical interest. Associations between certain organisms and colorectal neoplasia have been reported, but findings have limited reproducibility in different populations.<br><br>METHODS: We performed a systematic review of whole metagenome shotgun sequencing studies using faecal samples from patients with colorectal neoplasia and control populations. Searches were performed on 30th June 2023. We identified 26 studies, reporting on 22 study populations (13 from Asia, five from Europe and four from North America). Study size ranged from 14 to 971 individuals (mean 170).<br><br>RESULTS: Some reproducible data were identified, such as the significant enrichment of Fusobacterium nucleatum and Parvimonas micra in colorectal cancer patients compared to controls (in 10 and nine studies, respectively). However, 21 out of 26 studies scored poorly on quality appraisal, specifically surrounding selection of cases and controls. Definitions of controls varied; some studies used individuals with normal endoscopic investigations, some used 'healthy' individuals where no colonoscopy was performed, and one used those with non-neoplastic findings (haemorrhoids). There was even less reproducibility of data in studies where individuals with colorectal polyps were compared to controls, possibly because of heterogeneity in these patient groupings as a variety of definitions for 'polyp cases' were used.<br><br>CONCLUSIONS: Heterogeneity and potential for bias indicates that findings should be interpreted with caution. Standardised protocols to ensure robust methodology and allow pooling of large-scale data are required before these findings can be used in clinical practice (PROSPERO: CRD42023431977).},
}
@article {pmid40793781,
year = {2025},
author = {Cifuentes, SG and Graham, J and Trueba, G and Cárdenas, PA},
title = {Hi-C untangles the temporal dynamics of the children's gut resistome and mobilome, highlighting the role of transposable elements.},
journal = {mBio},
volume = {16},
number = {9},
pages = {e0113425},
pmid = {40793781},
issn = {2150-7511},
support = {D43 TW010540/TW/FIC NIH HHS/United States ; R01 AI135118/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *DNA Transposable Elements ; Feces/microbiology ; Ecuador ; Metagenomics ; Child ; Child, Preschool ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Female ; Gene Transfer, Horizontal ; Male ; Plasmids/genetics ; },
abstract = {Many metagenomic studies lack the ability to measure the temporal dynamics of the intestinal resistome (the collection of antibiotic resistance genes [ARGs]) and mobilome (the collection of all mobile genetic elements that enable their transfer) and link the genetic features to specific species in the gut. We applied Hi-C sequencing and shotgun metagenomics to study fecal matter from children (n = 15) living in semi-rural communities of Quito, Ecuador. We sampled at three different periods, with a 4- to 6-month interval between each sample collection. To understand the dynamics of ARGs from different genetic perspectives, we focused on identifying classes of mobile ARGs that are classified as high risk to human health. We selected those ARGs that appeared at least twice across sampling periods in the same child and focused the longitudinal analysis on the subset of children (n = 6) where these high-risk ARGs were consistently detected. The study demonstrated the temporal dynamics of these mobile ARGs from the taxonomic, plasmid, and transposable element perspectives, including insertion sequences and transposons. Our findings reveal that while plasmid composition fluctuates over time, transposons play a crucial role in the stability and dissemination of ARGs. Specifically, aph(3″)-Ib and aph(6)-Id genes were consistently mobilized by transposons across multiple multidrug-resistant Escherichia coli strains. These results highlight the importance of transposons in shaping the gut resistome and suggest that tracking regionally significant transposons could improve our understanding of ARG transmission in small geographic areas.IMPORTANCEAntibiotic resistance (ABR) is a growing global challenge, and particularly high-risk antibiotic resistance genes (ARGs) are a threat to public health. While plasmids are often considered the cornerstone of the spread of ARGs, our study emphasizes the critical role of transposons in the persistence and mobility of ARGs within the gut microbiota. By integrating Hi-C sequencing and shotgun metagenomics, we show that transposons mediate the transfer and persistence of ARGs across different Escherichia coli lineages, while plasmid composition changes over time. Recognizing the impact of transposons on resistome dynamics can help refine strategies to mitigate ABR transmission, particularly in regions where the impact of resistance is most significant, such as low- and middle-income countries. Our findings provide new insights into the mechanisms driving the persistence of ABR in the human gut, which are essential for developing more effective public health interventions and incorporating transposable elements into surveillance efforts.},
}
@article {pmid40792105,
year = {2025},
author = {Han, W and Zhou, Y and Wang, Y and Liu, X and Sun, T and Xu, J},
title = {Exploring fecal microbiota signatures associated with immune response and antibiotic impact in NSCLC: insights from metagenomic and machine learning approaches.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1591076},
pmid = {40792105},
issn = {2235-2988},
mesh = {Humans ; *Machine Learning ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Metagenomics/methods ; *Feces/microbiology ; *Carcinoma, Non-Small-Cell Lung/immunology/microbiology/drug therapy/therapy ; *Lung Neoplasms/immunology/microbiology/therapy/drug therapy ; Immunotherapy ; Male ; Female ; Middle Aged ; Aged ; Bacteria/classification/genetics/drug effects ; },
abstract = {BACKGROUND: Substantial interstudy heterogeneity in cancer immunotherapy-associated biomarkers has hindered their clinical applicability. To address this challenge, we performed a comprehensive integration of publicly available global metagenomic datasets. By leveraging metagenomic profiling and machine learning approaches, this study aimed to elucidate gut microbial signatures associated with immune response in lung cancer (LC) and to evaluate the modulatory effects of antibiotic exposure.<br><br>METHODS: A systematic literature search was conducted to identify relevant datasets, resulting in the inclusion of 209 fecal metagenomic samples: 154 baseline samples (45 responders, 37 non-responders, and 72 healthy controls) and 55 longitudinal samples collected during immunotherapy. We performed taxonomic and functional characterization of gut microbiota (GM) differentiating responders from non-responders, delineated microbiome dynamics during treatment, and assessed the impact of antibiotics on key microbial taxa. Among eight machine learning algorithms evaluated, the optimal model was selected to construct a predictive framework for immunotherapy response.<br><br>RESULTS: Microbial &#x3b1;-diversity was significantly elevated in responders compared to non-responders, with antibiotic administration further amplifying this difference-most notably at the species level. Integrative multi-omics analysis identified two pivotal microbial biomarkers, s_Bacteroides caccae and s_Prevotella copri, which were strongly associated with immunotherapy efficacy. A random forest-based classifier achieved robust predictive performance, with area under the curve (AUC) values of 0.82 and 0.79 at the species and genus levels, respectively. Notably, P. copri was further enriched in responders with poor progression-free survival (PFS <3 months), indicating a potential deleterious role. Antibiotic exposure significantly influenced the abundance and functional potential of these key taxa. KEGG-based functional analysis revealed the enrichment of amino acid metabolism pathways in responders. Additionally, CARD database annotation demonstrated that the majority of antibiotic resistance genes were associated with Bacteroidetes and Proteobacteria, implicating these taxa in shaping microbial-mediated therapeutic responses.<br><br>CONCLUSIONS: This study represents the first large-scale, cross-cohort integration of metagenomic data to identify reproducible GM signatures predictive of immune checkpoint inhibitor efficacy in LC. The findings not only underscore the prognostic relevance of specific taxa but also establish a foundation for developing microbiome-informed, personalized immunotherapeutic strategies.},
}
@article {pmid40790223,
year = {2025},
author = {Ren, Y and Zhang, P and Yu, H and Li, S and Jiang, H},
title = {Metagenome-based characterization of the gut virome in patients with schizophrenia.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {895},
pmid = {40790223},
issn = {1479-5876},
support = {82170755//National Natural Science Foundation of China/ ; LHYYKYQD20240307//Scientif Research Foudation of People's Hospital of Longhua of Shenzhen/ ; },
mesh = {Humans ; *Schizophrenia/virology/microbiology ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; Male ; *Metagenome/genetics ; Female ; Adult ; Feces/virology/microbiology ; Middle Aged ; Case-Control Studies ; },
abstract = {BACKGROUND: Schizophrenia (SCZ) is a multifactorial psychiatric disorder increasingly linked to gut microbial dysbiosis. While bacterial alterations have been widely studied, the role of the gut virome in SCZ remains largely unexplored. This study aimed to characterize the gut virome in SCZ and identify potential viral biomarkers associated with the disease.<br><br>METHODS: We analyzed fecal metagenomic data from 171 individuals (90 SCZ patients and 81 controls) using the Chinese Gut Virus Catalog (cnGVC). We assessed gut virome diversity, identified SCZ-associated vOTUs, explored virus-bacteria correlations, and evaluated diagnostic potential using random forest models. In addition, we examined follow-up samples from SCZ patients to assess the impact of antipsychotic treatment on the gut virome.<br><br>RESULTS: We identified 171 vOTUs that differed significantly between SCZ patients and controls, with 124 enriched in SCZ-mainly from Siphoviridae and Flandersviridae. Correlation analysis revealed altered virus-bacteria interactions in SCZ, including disease-specific associations with Akkermansia and Clostridia. A random forest classifier based on virome features achieved an AUC of 93.2%, outperforming the bacterial model. External validation using ASD and PD cohorts yielded lower AUCs (61.2-67.0%), suggesting disease specificity. In follow-up samples collected after three months of treatment, we observed partial changes in alpha diversity, while beta diversity remained stable, indicating that antipsychotic therapy may alter specific viral taxa without broadly reshaping the overall gut virome structure.<br><br>CONCLUSIONS: This study provides evidence of distinct gut virome alterations in SCZ and identifies specific viral markers with strong diagnostic potential. These findings highlight the underappreciated role of the gut virome in psychiatric disorders and support its utility as a non-invasive biomarker for SCZ diagnosis and future therapeutic development.},
}
@article {pmid40790086,
year = {2025},
author = {Wu, L and Lian, W and Bai, R and Chen, H and Wu, J and Li, H and Zhao, L},
title = {METTL3 facilitates colorectal cancer growth through altering the abundance of intestinal Akkermansia muciniphila.},
journal = {Cancer gene therapy},
volume = {32},
number = {10},
pages = {1098-1106},
pmid = {40790086},
issn = {1476-5500},
support = {82203607//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2022M721540//China Postdoctoral Science Foundation/ ; 2021A1515111186//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; 2024A04J6605//Guangzhou Municipal Science and Technology Project/ ; },
mesh = {*Colorectal Neoplasms/pathology/genetics/metabolism/microbiology ; Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; *Methyltransferases/metabolism/genetics ; Akkermansia ; Cell Line, Tumor ; },
abstract = {Colorectal cancer (CRC) is a prevalent malignant tumor that poses a significant threat to human health; however, the precise mechanism underlying its onset remains elusive. In this study, we utilized metagenomic sequencing to reveal the dysregulation of intestinal microbiota caused by CRC. Single-cell sequencing data showed elevated mRNA expression of methyltransferase-like protein 3 (METTL3) in CRC, which was correlated with the abundance of intestinal microbiota. Furthermore, we found that METTL3 promotion of CRC progression is microbiota-dependent. Using induced METTL3[fl/fl] Vil1-cre[+/-] mice, we identified the microbiota regulated by METTL3 in CRC. Our research indicates that METTL3 leads to high expression of HIF1α, which promotes the expression of lipocalin 2 (LCN2) in CRC cells, inhibiting the abundance of Akkermansia muciniphila, thereby promoting CRC progression.},
}
@article {pmid40790024,
year = {2025},
author = {Kiguchi, Y and Hamamoto, N and Kashima, Y and Runtuwene, LR and Ishizaka, A and Kuze, Y and Enokida, T and Tanaka, N and Tahara, M and Kageyama, SI and Fujisawa, T and Yamashita, R and Kanai, A and Tuda, JSB and Mizutani, T and Suzuki, Y},
title = {Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7397},
pmid = {40790024},
issn = {2041-1723},
support = {22fk0108538s0201//Japan Agency for Medical Research and Development (AMED)/ ; },
mesh = {Humans ; Saliva/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; *Mouth/microbiology ; Female ; Male ; Colorectal Neoplasms/microbiology ; Head and Neck Neoplasms/microbiology ; Metagenome ; Adult ; DNA, Bacterial/genetics ; *Bacteria/genetics ; Middle Aged ; Streptococcus/genetics ; },
abstract = {Survival strategy of bacteria is expanded by extrachromosomal elements (ECEs). However, their genetic diversity and functional roles for adaptability are largely unknown. Here, we discover a novel family of intracellular ECEs using 56 saliva samples by developing an efficient microbial DNA extraction method coupled with long-read metagenomics assembly. Even though this ECE family was not hitherto identified, our global prevalence analysis using 476 salivary metagenomic datasets elucidates that these ECEs reside in 74% of the population. These ECEs, which we named, "Inocles", are giant plasmid-like circular genomic elements of 395 kb in length, including Streptococcus as a host bacterium. Inocles encode a series of genes that contribute to intracellular stress tolerance, such as oxidative stress and DNA damage, and cell wall biosynthesis and modification involved in the interactions with oral epithelial cells. Moreover, Inocles exhibit significant positive correlations with immune cells and proteins responding to microbial infection in peripheral blood. Intriguingly, we examine and find their marked reductions among 68 patients of head and neck cancers and colorectal cancers, suggesting its potential usage for a novel biomarker of gastrointestinal cancers. Our results suggest that Inocles potentially boost the adaptive capacity of host bacteria against various stressors in the oral environment.},
}
@article {pmid40789383,
year = {2025},
author = {Rout, AK and Rout, SS and Panda, A and Tripathy, PS and Kumar, N and Parida, SN and Dey, S and Dash, SS and Behera, BK and Pandey, PK},
title = {Potential applications and future prospects of metagenomics in aquatic ecosystems.},
journal = {Gene},
volume = {967},
number = {},
pages = {149720},
doi = {10.1016/j.gene.2025.149720},
pmid = {40789383},
issn = {1879-0038},
mesh = {*Metagenomics/methods ; *Ecosystem ; Microbiota/genetics ; *Water Microbiology ; Environmental Monitoring/methods ; Computational Biology/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; },
abstract = {Metagenomics plays a vital role in advancing our understanding of microbial communities and their functional contributions in various ecosystems. By directly sequencing DNA from environmental samples such as soil, water, air, and the human body. Metagenomics enables the identification of previously uncultivable or unknown microorganisms, offering key insights into their ecological functions. Beyond taxonomic classification, metagenomic analyses reveal functional genes and metabolic pathways, facilitating the discovery of enzymes, bioactive compounds, and other molecules with applications in agriculture, biotechnology, and medicine. This review discusses the broad applications of metagenomics in environmental monitoring, encompassing sample collection, high-throughput sequencing, data analysis and interpretation. We review different sequencing platforms, library preparation methods, and advanced bioinformatics tools used for quality control, sequence assembly, and both taxonomic and functional annotation. Special focus is given to the role of metagenomics in evaluating microbial responses to environmental stress, contaminant degradation, disease emergence, and climate change. The use of microbial bioindicators for aquatic ecosystem monitoring and toxicological assessments is also examined. A comprehensive evaluation of current bioinformatics pipelines is provided for their effectiveness in processing large-scale metagenomic datasets. As global environmental pressures intensify, integrative meta-omics approaches, including whole-genome metagenomics, will become crucial for understanding the complexity, functions, and dynamics of microbiomes in both natural and affected ecosystems.},
}
@article {pmid40789238,
year = {2025},
author = {Geng, B and Zhu, C and Cui, Z and Chen, Y and Zhang, Q and Shi, H and Min, L and Zhu, S and Zhang, W and Zhao, M and Zhang, S and Xu, J},
title = {Maslinic acid alleviates ulcerative colitis by inhibiting the colitis-aggravating pathogen Clostridium perfringens and modulating gut microbiota.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {146},
number = {},
pages = {157144},
doi = {10.1016/j.phymed.2025.157144},
pmid = {40789238},
issn = {1618-095X},
mesh = {Animals ; *Clostridium perfringens/drug effects/pathogenicity ; *Gastrointestinal Microbiome/drug effects ; *Colitis, Ulcerative/drug therapy/microbiology ; Mice ; *Triterpenes/pharmacology ; Mice, Inbred C57BL ; Disease Models, Animal ; Male ; Humans ; Dextran Sulfate ; Oleanolic Acid/analogs &amp; derivatives ; },
abstract = {BACKGROUND: Ulcerative colitis (UC), a prevalent form of inflammatory bowel disease, continues to pose therapeutic challenges due to the limitations of conventional drugs and their inability to prevent relapse. Emerging evidence highlights the crucial role of gut microbiota dysbiosis in UC pathogenesis, yet our understanding of specific harmful microbes and their contributions to disease development remains limited.<br><br>PURPOSE: This study aims to (1) investigate the therapeutic potential of maslinic acid (MA), a food-derived natural compound, in colitis mice models; (2) elucidate the previously underestimated pathogenic role of Clostridium perfringens in UC development; and (3) reveal the molecular mechanisms underlying both C. perfringens pathogenesis and MA-mediated protection.<br><br>METHODS: We examined the therapeutic effect of MA using DSS-induced colitis model and performing metagenomic sequencing; elucidated the pathogenic role of C. perfringens using GMrepo database, clinical stool samples, and in vivo infection models. Additionally, we revealed its mechanism using inhibitors and markers of various cell death and inflammation pathways. The bactericidal effect of MA on C. perfringens was studied through in vitro experiments and two in vivo colitis models.<br><br>RESULTS: MA alleviates DSS-induced colitis and restores gut microbiota. C. perfringens is enriched following DSS administration while significantly decreased after treatment with MA. C. perfringens contributes to the development of colitis and induces ZBP1-mediated PANoptosis in intestinal epithelial cells, while stimulates inflammation through NOD2 activation. MA has direct bactericidal activity against C. perfringens through ROS induction. It can almost completely rescue the exacerbation of colitis-related pathological and physiological phenotypes caused by C. perfringens in two mice colitis models.<br><br>CONCLUSIONS: Our study reveals that MA effectively mitigates DSS-induced colitis by inhibiting the colitis-aggravating pathogen C. perfringens and modulating gut microbiota. Furthermore, it elucidates the previously underestimated role and mechanism of C. perfringens in the development of UC. It also highlights the therapeutic potential of MA in preventing and treating UC, particularly in patients who are C. perfringens positive.},
}
@article {pmid40788706,
year = {2025},
author = {Israel, A and Israel, S and Weizman, A and Ashkenazi, S and Vinker, S and Magen, E and Merzon, E},
title = {Atovaquone-proguanil and reduced digestive cancer risk: a Toxoplasma gondii connection.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2545412},
pmid = {40788706},
issn = {1949-0984},
mesh = {Humans ; Middle Aged ; *Atovaquone/therapeutic use/pharmacology ; *Toxoplasma/isolation &amp; purification/drug effects/genetics ; Adult ; Male ; Aged ; Female ; Retrospective Studies ; *Proguanil/therapeutic use/pharmacology ; Drug Combinations ; Gastrointestinal Microbiome/drug effects ; Feces/parasitology/microbiology ; *Colorectal Neoplasms/epidemiology/prevention &amp; control/parasitology ; Toxoplasmosis ; Incidence ; Metagenomics ; },
abstract = {Emerging evidence suggests microbial pathogens contribute to digestive cancer risk. Atovaquone - proguanil (A-P), an antimalarial with antiparasitic activity, has been associated with a reduced risk of colorectal cancer (CRC). We conducted a retrospective cohort study using the TriNetX US Collaborative Network, including over 100,000 individuals aged 40-69 years who received A-P, matched 1:1 to controls who received other medications. Incident digestive cancers were analyzed using Cox proportional hazards models. Additionally, we performed a metagenomic analysis of 1,044 fecal samples from 156 individuals to assess the abundance of Toxoplasma gondii in CRC-associated microbiota. A-P use was associated with a significant reduction in digestive cancer incidence across all age groups: hazard ratios (HRs) ranged from 0.49 to 0.53 (all p < 0.001). Protective associations extended to pancreatic cancer (HR range, 0.50-0.72). In metagenomic analysis, T. gondii was the most discriminatory microbial species for CRC (p = 1.8 × 10[-16]), detected above threshold in 22.6% of CRC samples versus 1.6% of controls (odds ratio 18.2, 95% CI, 8.2-47.6, p = 2.3 × 10[-22]). These findings suggest T. gondii may be an overlooked microbial risk factor for digestive cancers, and that A-P may offer chemopreventive effects through antiparasitic activity. Prospective studies are needed to evaluate its preventive potential.},
}
@article {pmid40787979,
year = {2025},
author = {Liu, Y and Zhao, X and Feng, X and Zhu, W and Feng, S and Ren, M and Tu, Y and Niu, G and Zhu, Y},
title = {Diversity and evolutionary analysis of viruses carried by mosquitoes in Shandong, China.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0101825},
pmid = {40787979},
issn = {2165-0497},
support = {KY202422//the Suqian Science and Technology Program/ ; },
mesh = {Animals ; China ; Phylogeny ; *Culicidae/virology/classification ; *Mosquito Vectors/virology ; *Arboviruses/genetics/classification/isolation &amp; purification ; High-Throughput Nucleotide Sequencing ; Virome ; *Viruses/classification/genetics/isolation &amp; purification ; Genetic Variation ; Biodiversity ; Evolution, Molecular ; Genome, Viral ; },
abstract = {UNLABELLED: Arboviruses represent a growing threat to global public health, as climate change is exacerbating the spread of these vectors and thereby increasing the transmission potential of arboviruses. As primary vectors, mosquitoes harbor remarkably diverse virus populations, broadly classified into mosquito-borne viruses and mosquito-specific viruses. Although metagenomic sequencing has revolutionized viral discovery, geographical variations in mosquito viromes remain poorly characterized. In this study, we conducted comprehensive viral surveillance on 5,051 mosquitoes representing six medically important species (grouped into 14 taxonomic units) collected from Shandong, China, in 2021. Using next-generation sequencing, we generated 3.7 billion clean reads and identified 10 distinct virus species spanning eight virus families. Phylogenetic analyses revealed substantial genomic diversity and complex evolutionary relationships, including two completely novel virus species and several incompletely characterized known viruses. Notably, Culex quinquefasciatus mosquitoes exhibited significantly greater viral diversity than other species, although we observed considerable overlap in viral communities across mosquito taxa, suggesting non-host-specific viral maintenance. The presence of two novel viruses in field populations was confirmed by RT-qPCR screening, wherein minimum infection rates of 0.16% and 0.38% were established. Our findings substantially expand the known diversity of mosquito-associated viruses in East Asia and provide critical baseline data for arbovirus surveillance programs. This work highlights the value of systematic virome characterization for predicting emerging arboviral threats and understanding virus-mosquito ecology in changing environments.<br><br>IMPORTANCE: Ten viruses, including two novel ones, were found in a study performed on mosquitoes in Shandong, China. It shows viral diversity and coexistence in different species, highlighting host impact on viral communities. The new viruses are prevalent locally, with infection rates of 0.38% and 0.16%. This work advances viral ecology understanding and has public health significance. This study sheds light on the circulation of the identified viruses in Shandong.},
}
@article {pmid40785530,
year = {2025},
author = {Liang, J and He, J and Zhao, J and Yang, Y and Xu, W},
title = {Decline in the Relative Abundance of Antibiotic Resistance Genes in Long-Term Fertilized Soil and Its Driving Factors.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {33},
pages = {20710-20718},
doi = {10.1021/acs.jafc.5c03478},
pmid = {40785530},
issn = {1520-5118},
mesh = {Soil Microbiology ; *Fertilizers/analysis ; *Bacteria/genetics/drug effects/isolation &amp; purification/classification/metabolism ; Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *Bacterial Proteins/genetics/metabolism ; Microbiota ; Metals, Heavy/analysis ; },
abstract = {The changes in antibiotic resistance genes (ARGs) in long-term fertilized soil remain controversial. We aimed to analyze the variation characteristics of ARGs in long-term fertilized soil using metagenomic sequencing. The relative abundance of ARGs did not increase significantly after 7 years of fertilization. However, a clear decline in the relative abundance of ARGs was observed compared to the data from the 4th year. Microbial adaptation strategies in response to changes in the ARG abundance were associated with shifts in microbiome composition and function. Among these, bacterial abundance was the primary driving factor. Additionally, total heavy metal content might serve as the most significant co-selective pressure influencing ARG number. We believe that increasing the selective pressure from heavy metals and antibiotics might result in the loss of certain microbial species and a decrease in ARG abundance. This study provides novel insights into the variations of soil resistance genes under long-term fertilization.},
}
@article {pmid40785047,
year = {2025},
author = {Shi, H and Wu, M and Wu, X and Liu, Z and Jiang, S and Li, G and Yang, Y and Fu, Y and Wang, Q and Zhang, G and Cheng, L},
title = {Multi-omics integration reveals functional signatures of gut microbiome in atherosclerosis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2542384},
pmid = {40785047},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Atherosclerosis/microbiology/genetics/metabolism ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Transcriptome ; Metabolomics ; Multiomics ; },
abstract = {Atherosclerosis (AS), a predominant contributor to global cardiovascular disease burden, exhibits complex interplay with gut microbiota dysbiosis. While the associations between microbial imbalance and AS pathogenesis are well-documented, the pathophysiological mechanisms governing microbe-host crosstalk remain incompletely characterized. Current research limitations stem from methodological heterogeneity across studies and the absence of consensus regarding disease-specific microbial signatures. In this study, we conducted an integrated multi-omics analysis to characterize the functional signatures of gut microbiome in AS. We collected all public AS-related 6 microbiome datasets and 8 peripheral blood host transcriptomic datasets from across the world, comprising 456 metagenomic samples and 111 16S rRNA gene sequencing samples for microbial profiling, alongside 118 RNA-Seq samples and 302 microarray samples. We systematically characterized AS microbial taxa and computationally inferred the metabolic potential for the gut microbiome using metabolomic-related data. Metabolite-host gene interactions were further predicted based on the synergistic effects between microbiome and host transcriptome in AS. Five "microbe-metabolite-host gene" tripartite associations related to AS were identified involving 5 microbial genera (Actinomyces, Bacteroides, Eisenbergiella, Gemella, and Veillonella), 2 metabolites (Ethanol and H2O2), and 2 host genes (FANCD2 and GPX2), and the reliability of these associations was validated. Five microbial genera demonstrated robust diagnostic potential as noninvasive biomarkers, with 5-fold cross-validation, study-to-study transfer validation, and leave-one-study-out (LOSO) validation confirming good diagnostic performance. Additionally, the specificity of the biomarkers was validated against hypertension, inflammatory bowel disease (IBD), diabetes, and obesity cohorts. Our study unveiled the functional characteristics of gut microbiota interacting with AS host genes and highlighted the potential of gut microbiota as both diagnostic biomarkers and therapeutic targets for AS. However, the findings should be interpreted considering the inherent heterogeneity of the integrated datasets and the preliminary diagnostic value of the biomarkers.},
}
@article {pmid40784769,
year = {2025},
author = {Kim, HS and Kim, BH and Nam, B and Oh, SJ and Park, SK and Lee, SW and Lee, JY and Jo, S and Lee, YA and Lee, JY and Park, DI and Kim, TH and Lee, CK},
title = {Oral-gut microbiome axis in a Korean cohort with inflammatory bowel disease and ankylosing spondylitis (INTEGRATE): a prospective and observational study protocol.},
journal = {BMJ open},
volume = {15},
number = {8},
pages = {e092075},
pmid = {40784769},
issn = {2044-6055},
mesh = {Adult ; Female ; Humans ; Male ; *Colitis, Ulcerative/microbiology ; *Crohn Disease/microbiology ; Dysbiosis ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Mouth/microbiology ; Observational Studies as Topic ; Prospective Studies ; Republic of Korea ; RNA, Ribosomal, 16S ; Saliva/microbiology ; *Spondylitis, Ankylosing/microbiology ; },
abstract = {INTRODUCTION: The global burden of chronic immune-mediated inflammatory diseases (IMIDs) is increasing, and rising prevalence rates significantly affect socioeconomic factors and quality of life. Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), along with ankylosing spondylitis (AS), are prominent chronic IMIDs that share overlapping pathophysiological mechanisms. Recent research has highlighted the importance of the gut microbiota in the pathogenesis of these diseases, suggesting that shared microbial dysbiosis may contribute to their development. Comprehensive research focusing on the gut and oral microbial characteristics and environmental factors is essential to elucidate the fundamental pathophysiology and develop personalised management strategies for IBD and AS. In-depth analyses and insights based on multiomics approaches are required to achieve these objectives.<br><br>METHODS AND ANALYSIS: This protocol describes a nationwide prospective observational study of CD, UC and AS in a Korean population. Over 5 years, we aim to recruit at least 900 patients with IBD and 200 first-degree relatives (FDRs), 500 patients with AS and 200 of their FDRs, and 2244 healthy controls. We will systematically collect clinical data and biological samples, including saliva, stool, blood and tissue biopsies, for integrative multiomics analyses focusing primarily on the microbiome. Highly advanced full-length 16S ribosomal RNA gene sequencing and shotgun metagenomics will be used to characterise the microbial composition of saliva and stool samples. Quantitative microbiome profiling will be used to address the pathological, physiological and ecological differences between microbial groups that may be masked by their relative abundance. Metabolomic analyses will be conducted on saliva, stool and plasma samples to assess functional metabolic profiles. Culturomics will be used to isolate, identify and characterise the diversity of microbial species, including rare or previously unrecognised species, to provide a comprehensive understanding of the microbiota associated with these diseases.<br><br>ETHICS AND DISSEMINATION: Ethical approval was obtained from the Ethics Committee of Kyung Hee University Hospital, Hanyang University Hospital, Kangbuk Samsung Hospital, Yeungnam University Hospital, Kyungpook National University Hospital, Chonnam National University Hospital, Wonkwang University Hospital, Catholic University Daejeon St. Mary's Hospital, Soon Chun Hyang University Hospital Cheonan, Chung-Ang University Hospital, Inje University Haeundae Paik Hospital, Dankook University Hospital, Hanyang University Guri Hospital, Kyung Hee University Hospital at Gangdong, Chung-Ang University Gwangmyeong Hospital and Keimyung University Dongsan Hospital. Our research team will provide detailed information about the study, including an information sheet explaining its aims and procedures, prior to enrolment. Prospective participants will be informed that they have the right to withdraw from the study at any time, without penalty. Participants will be assured of the anonymity and confidentiality of any data they provide throughout the study, using participant numbers and the storage of sensitive data in locked cabinets. Participants will be enrolled in the study only after providing written informed consent to the research staff. The results of this study will be disseminated to healthcare and academic professionals through publications in peer-reviewed journals and presentations at international conferences.<br><br>TRIAL REGISTRATION NUMBER: This prospective observational study is registered at ClinicalTrials.gov ((ID: NCT06124833, data first posted: 9 November 2023); (ID: NCT06076083, data first posted: 21 November 2023) and (ID: NCT06183697, data first posted: 27 December 2023)).},
}
@article {pmid40784283,
year = {2025},
author = {Zhao, J and Wang, Q and Zhao, Y and Guo, J and Ji, Z and Huang, Y and Shen, Q and Liu, Y and Bai, Y and Qi, W and Liu, H and Chen, Y},
title = {Chronic exposure to environmentally-relevant sulfamethoxazole alters ammonia-oxidizing microbial communities in managed aquifer recharge systems.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124298},
doi = {10.1016/j.watres.2025.124298},
pmid = {40784283},
issn = {1879-2448},
mesh = {*Sulfamethoxazole/pharmacology ; *Ammonia/metabolism ; *Groundwater/microbiology ; Archaea/drug effects ; Oxidation-Reduction ; Bacteria/metabolism/drug effects ; Anti-Bacterial Agents ; Microbiota/drug effects ; },
abstract = {Managed aquifer recharge (MAR) is a critical technology for water resource management and purification, yet its capacity to remove antibiotics remains limited. Understanding the response of ammonia-oxidizing microorganisms (AOMs) to antibiotics exposure is essential for optimizing MAR-based antibiotic mitigation strategies. This study investigated the long-term effects of sulfamethoxazole (SMX, ∼500 ng/L) on AOM communities through a 20-month controlled MAR column experiment. Results showed that AOMs (0.4-3.7 % of total microbial abundance) were dominated by ammonia-oxidizing archaea (AOA, 10.2-82.9 %) and complete ammonia oxidizers (comammox, 15.4-89.7 %), with negligible ammonia-oxidizing bacteria (AOB, <2.4 %). Chronic effects of SMX resulted in a 60-67 % reduction in amoA genes across AOA, AOB, and comammox populations, indicating a significant threat to nitrogen cycling. Specifically, SMX suppressed 2-7 AOA metagenome-assembled genomes (MAGs) (e.g., Nitrosotenuis) by 57-95 % and 4-5 comammox MAGs (e.g., Nitrospira) by 23-82 %. Conversely, SMX increased 4-7 AOA MAGs (e.g., Nitrosarchaeum) by 1.4-24.3-fold and 2 comammox MAGs (e.g., Nitrospira) by 1.9-2.0-fold, revealing taxon-specific tolerance. Notably, AOA lineages demonstrated superior resilience to SMX compared to comammox. These findings advance our understanding of antibiotic-driven microbial community dynamics in MAR systems and provide valuable insights for enhancing their performance in antibiotic-polluted environments.},
}
@article {pmid40784097,
year = {2025},
author = {Lin, Y and Wang, X and Zhao, D and Zhou, H and Wang, Y and Gao, Y and Lin, Y and Xu, G and Ni, K and Yang, F},
title = {Waterlogging-induced restructuring of phyllosphere microbiota associated with mycotoxin accumulation.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118821},
doi = {10.1016/j.ecoenv.2025.118821},
pmid = {40784097},
issn = {1090-2414},
mesh = {*Zea mays/microbiology ; Plant Leaves/microbiology ; *Microbiota ; *Mycotoxins/metabolism ; Fungi/genetics ; },
abstract = {As waterlogging events intensify and become more frequent in the future, understanding their impact on plant physiology and associated microbes is crucial for alleviating stress in vulnerable species and ecosystems. Despite its importance, our understanding of how phyllosphere microbiota react to waterlogging stress remains limited. This study utilized metagenomic sequencing to assess the effects of waterlogging on microbial diversity and functional activities in different tissues of the maize phyllosphere, focusing specifically on leaves and ears. Our findings indicated that waterlogging significantly affected the maize phyllosphere microbial communities. Also, waterlogging altered the microbial interaction networks by increasing network complexity, enhancing negative interactions, and shifting the relative abundance of key bacterial and fungal genera. Moreover, metagenomic analysis revealed upregulated signaling pathways and oxidative stress responses, particularly within the fungal communities associated with maize ears. Crucially, we identified a higher abundance of genes related to mycotoxin production under waterlogged conditions, leading to elevated mycotoxin levels in ear tissues. These results suggest that waterlogging-induced changes in fungal communities may heighten the risk of mycotoxin contamination in maize. The distinct microbial responses noted between maize leaves and ears further highlight the tissue-specific dynamics of these communities.},
}
@article {pmid40784060,
year = {2025},
author = {Zhang, H and Wang, C and Gong, Y and Zhu, Y and Zhang, M and Li, D and Tian, Y and Han, R and Guo, Y and Zhang, Y and Kang, X and Jiang, R},
title = {Changes in pathogenicity of gut microbiota during fasting-induced molting in laying hens and their impact on spleen immune function.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105526},
pmid = {40784060},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/immunology/microbiology ; *Gastrointestinal Microbiome/physiology ; Female ; *Molting ; *Spleen/immunology ; Random Allocation ; *Fasting ; Food Deprivation ; },
abstract = {Fasting-induced molting (FIM) leverages the natural molting mechanism of aging laying hens to enhance their egg production and egg quality. However, fasting may also increase the risk of pathogen infection and activate immune regulation in the spleen. Understanding the specific types of pathogen infections triggered during FIM and their impacts on the spleen's immune regulation mechanisms is crucial for enhancing the immunological resilience of poultry. A total of 90, aged 60 weeks, late-laying hens were randomly assigned to undergo FIM. During FIM, hens kept regular feed and 16 hours light initially. A 3-day fast with 8 hours light followed. Then, they gradually resumed water and feed, increasing from 30 g to 120 g daily, with light returning to 16 hours. This study investigates the effects of FIM on the gut microbiota and metabolites through metagenomic sequencing and metabolomics. Additionally, blood routine tests and ELISA assays were conducted to measure serum Ig concentrations. Real-time quantitative PCR and ELISA were used to detect the expression of inflammatory factors and immune cell markers in the spleen. The study also analyzed gene expression levels in the PI3K/AKT pathway, systematically exploring fasting's regulatory impact on gut-spleen immunity. Results showed that during FIM, the abundance of pathogens utilizing non-carbohydrates as an energy source initially increased and then decreased, while the abundance of pathogens relying on carbohydrates as an energy source declined. Correspondingly, with beneficial metabolites initially decreased before increasing, while harmful metabolites exhibited the opposite trend. During fasting, the concentration of eosinophilic leukocytes in serum significantly increased (P < 0.05), while the concentration of IgA significantly decreased (P < 0.05). In the spleen, significant increase in the expression of immune-related metabolites, including NF-κB, IFN-β, iNOS, IL-1β, and IFN-α, were observed, along with significant increases in the secretion of TNF-α, TGF-β, IL-1, and IL-8, suggesting a significant activation of the immune response. After refeeding, these factors in serum and spleen returned to pre-fasting levels. Notably, the PI3K/AKT signaling pathway was significantly activated during fasting, indicating that fasting exerts broad effects on the immune system via the PI3K/AKT pathway. This study holds significant theoretical and practical value for enhancing the immunity of molting laying hens, reducing pathogenic bacterial infections, and optimizing production performance.},
}
@article {pmid40783881,
year = {2025},
author = {Maldonado-Gómez, JC and Rincón-Molina, FA and Rincón-Rosales, R and Manzano-Gómez, LA and Gen-Jiménez, A and Rincón-Molina, CI},
title = {Diversity and plant growth-promoting properties of rhizospheric and endophytic bacteria associated with Agave americana.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {56},
number = {4},
pages = {2777-2790},
pmid = {40783881},
issn = {1678-4405},
support = {21914.25-P//Tecnol&#xf3;gico Nacional de M&#xe9;xico/ ; 22004.25-P//Tecnol&#xf3;gico Nacional de M&#xe9;xico/ ; },
mesh = {*Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Endophytes/classification/genetics/isolation &amp; purification/metabolism ; *Agave/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; Biodiversity ; Indoleacetic Acids/metabolism ; Plant Growth Regulators/metabolism ; Phylogeny ; Plant Roots/microbiology/growth &amp; development ; Plant Development ; },
abstract = {Plant-microbe interactions play a critical role in maintaining plant health, enhancing soil fertility, and sustaining ecosystem functionality. Agave americana (Asparagales, Asparagaceae, L.), a crassulacean acid metabolism (CAM) species known for its remarkable drought tolerance and diverse industrial uses, represents a valuable model for exploring the ecological and functional dynamics of these associations. This study explores the diversity and functional potential of bacterial communities associated with A. americana and their role in promoting plant growth. A combination of culture-dependent techniques and metagenomic sequencing was employed to isolate and characterize rhizospheric and endophytic bacteria. Prominent bacterial genera identified included Acinetobacter, Bacillus, Rhizobium/Mesorhizobium, and Microbacterium. Metagenomic analyses revealed a high abundance of Actinobacteria, Proteobacteria, and Chloroflexi, highlighting their roles in nutrient cycling and organic matter decomposition. Plant growth-promoting assays demonstrated that Rhizobium sp. 34 A produced significant levels of indole-3-acetic acid (IAA), enhancing nutrient availability and plant growth. Mesorhizobium sp. 28 A had the greatest overall impact, significantly increasing total fresh weight, chlorophyll content, and sugar profiles, surpassing the effects of chemical fertilizers. Furthermore, Bacillus sp. T12C12, in combination with other plant growth-promoting bacteria (PGPB), exhibited the highest nitrogenase activity, as measured through acetylene reduction assays (ARA). These findings suggest that bacterial inoculants can enhance the nutritional and agronomic value of Agave species, which are of significant agro-industrial and food importance, providing a sustainable alternative to chemical fertilizers. This study offers valuable insights into sustainable agricultural practices by leveraging microbial communities to enhance crop productivity and resilience.},
}
@article {pmid40783398,
year = {2025},
author = {Shen, Y and Sun, D and Chen, K and Jiang, J and Shao, D and Yang, L and Sun, C and Liu, D and Ke, Y and Wu, C and Walsh, TR and Shen, J and Lv, Z and Wang, Y},
title = {High-fat and low-fiber diet elevates the gut resistome: a comparative metagenomic study.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {156},
pmid = {40783398},
issn = {2055-5008},
support = {81991535//National Natural Science Foundation of China/ ; 32141002//National Natural Science Foundation of China/ ; 2022YFD1800400//National Key Research and Development Program of China/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Dietary Fiber/administration &amp; dosage ; *Diet, High-Fat ; Mice ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Metagenomics/methods ; Male ; Humans ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; Interspersed Repetitive Sequences ; Female ; },
abstract = {Antimicrobial resistance (AMR) is a global health challenge. The gut microbiome, a major reservoir for AMR, is influenced by dietary habits. However, the specific impact of dietary patterns on gut resistome remains poorly understood. This study aimed to assess the effects of high-fat/low-fiber and high-fiber/low-fat diets on the development of AMR in the gut microbiome. The shift from a normal diet to a high-fat/low-fiber or a high-fiber/low-fat diet in mice resulted in corresponding increases and decreases in the relative abundance of the resistome (0.14 to 0.25, p < 0.001 vs. 0.14 to 0.09 p < 0.05), virulence genes (VGs) (0.56 to 0.91, p < 0.001 vs. 0.58 to 0.50, p < 0.05), and mobile genetic elements (MGEs) (0.20 to 1.66, p < 0.001 vs. 0.22 to 0.13, p < 0.05), respectively. Network analyses identified bacteria such as Bacteroides, Parabacteroides, and Alistipes as hosts of ARGs and VGs, with changes in their abundance closely associated with shifts in ARG and VG levels. Mobile genetic elements such as Tn916, ISBf10, IS91, and intl1 were linked to these variations, including genes conferring resistance to vancomycin and capsule-related VGs. In humans, a similar trend was observed, with high-fat diets correlating with higher resistome levels, while high-fiber diets were associated with lower resistome levels compared to a normal diet group. ARGs were more prevalent in pathogenic genera such as Enterococcus spp., Klebsiella spp., Pseudomonas spp., and Staphylococcus spp. The high-fat/low-fiber diet increased the bacterial resistome and VG abundance compared to a high-fiber/low-fat diet. Therefore, adopting a high-fiber/low-fat diet may be an effective strategy to reduce the AMR burden in the human gut, providing a valuable insight for public health recommendations.},
}
@article {pmid40782151,
year = {2026},
author = {Kumari, P and Tripathi, BM and Eo, KY and Kimura, J and Yamamoto, N},
title = {Spatioseasonal Comparison of Fecal Resistome and Pathogenome of Raccoon Dogs in Korea.},
journal = {EcoHealth},
volume = {23},
number = {1},
pages = {71-83},
pmid = {40782151},
issn = {1612-9210},
support = {2021R1F1A1060259//National Research Foundation of Korea/ ; },
mesh = {Animals ; *Raccoon Dogs/microbiology ; *Feces/microbiology ; Republic of Korea ; Seasons ; *Drug Resistance, Bacterial/genetics ; Gastrointestinal Microbiome ; },
abstract = {The raccoon dog (Nyctereutes procyonoides) is a medium-sized omnivore native to Asia. Because they live close to human habitation, and therefore, there is likely bidirectional influence between raccoon dogs and humans, it is important to investigate their potential risks. Here, to identify potential risks of carriage of antimicrobial resistance (AMR) and human pathogens by raccoon dogs, we investigated spatioseasonal patterns of fecal resistome (collection of antimicrobial resistance genes: ARGs), pathogenome (collection of virulence factor genes: VFGs), and microbiome (collection of bacterial species) of raccoon dogs inhabiting an urban forest area and a rural rice paddy area in Korea. Metagenomic sequencing revealed that the compositions of fecal resistome, pathogenome, and microbiome were all patterned by season, and we hypothesize that the observed patterns are due to seasonal changes in the diet of omnivorous raccoon dogs. Furthermore, although less pronounced than the seasonal differences, we also observed the geographical differences in the resistome, with aminoglycoside resistance genes being more prevalent in the rural area, which may reflect the geographical difference in selective pressures for AMR emergence, such as the use of manure that may contain antimicrobials in rice cultivation in agricultural areas. Additionally, our network analysis revealed that specific antimicrobial resistance genes were linked to specific bacterial pathogens, e.g., tetA-P to Clostridium. Overall, our study successfully revealed for the first time that not only the microbiome, but also the resistome and pathogenome of wild animals change spatioseasonally, and that the risk of AMR in bacterial pathogens laden by raccoon dogs is spatioseasonal.},
}
@article {pmid40782126,
year = {2025},
author = {Andeta, AF and Lema, NK and Debel, GL and Misganaw, FW and Ifa, AC},
title = {Evaluating food safety of traditionally fermented kocho: microbial profiling through classical methods and PacBio SMRT sequencing technology.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {127},
pmid = {40782126},
issn = {1572-9699},
support = {CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; },
mesh = {*Fermented Foods/microbiology ; *Food Safety ; *Bacteria/classification/genetics/isolation &amp; purification ; *Food Microbiology ; Ethiopia ; Fermentation ; Cross-Sectional Studies ; Fungi/isolation &amp; purification/classification/genetics ; Microbiota ; },
abstract = {Enset (Ensete ventricosum) serves as a staple or co-staple food crop for over 20 million people in Southern, Southwestern, and Central Ethiopia, significantly contributing to regional food security. Despite its importance, food safety concerns surrounding its fermented product, kocho, remain largely unaddressed. This study aimed to evaluate the food safety of traditionally fermented kocho samples collected from districts in the Gamo Zone using a cross-sectional study design. The microbial community composition was analyzed through both culture-based methods and PacBio sequencing. The physicochemical properties exhibited slight variations in acidity, fermentation stage, and moisture content among samples from different districts. Culture-based microbiological analysis indicated total viable aerobic counts ranging from 5.76 to 7.13 log CFU/g, yeast and mold counts between 5.20 to 8.53 log CFU/g, and Enterobacteriaceae counts ranging from 5.03 to 6.13 log CFU/g. Metagenomic analysis revealed that Proteobacteria and Firmicutes were the predominant phyla, with Acetobacter and Lactobacillus as the most prevalent genera. Notably, potential pathogenic bacteria, including Klebsiella pneumoniae, Klebsiella terrigena, Dysgonomonas capnocytophagoides, and Clostridium paraputrificum, were identified. The coexistence of beneficial microorganisms and potential pathogens underscores the urgent need for enhanced food safety measures in the traditional production of kocho.},
}
@article {pmid40782046,
year = {2025},
author = {Bradley, ES and Stansky, C and Zeamer, AL and Huang, Z and Cincotta, L and Lopes, A and Potter, L and Fontes, T and Ward, DV and Bucci, V and McCormick, BA and Haran, JP},
title = {The urinary microbiome distinguishes symptomatic urinary tract infection from asymptomatic older adult patients presenting to the emergency department.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2546063},
pmid = {40782046},
issn = {2150-5608},
mesh = {Humans ; Aged ; Emergency Service, Hospital ; Female ; Male ; *Urinary Tract Infections/microbiology/diagnosis/urine ; Aged, 80 and over ; *Microbiota ; *Asymptomatic Infections ; Bacteria/classification/genetics/isolation &amp; purification ; Bacteriuria/microbiology/diagnosis ; Urinalysis ; *Urine/microbiology ; Middle Aged ; },
abstract = {Older adults suffer from a high rate of asymptomatic bacteriuria (ASB), in which urinalysis may appear positive (presence of bacteria, white blood cells, and nitrates), often triggering initiation of antibiotics in acute care settings, without actual urinary tract infection (UTI) present. To investigate the urinary microbiome of older adults being tested for UTI, we enrolled a convenience sample of 250 older adult Emergency Department patients who had microscopic urinalysis ordered as part of their routine clinical care. Urinalysis results were classified as positive or negative, and patients were classified as being symptomatic or asymptomatic based on established diagnostic guidelines. We sought to determine if features of the urinary microbiome differed between positive and negative urinalysis (UAs) and symptomatic and asymptomatic patients with positive UAs. The same urine sample used for clinical testing was sequenced and analyzed for bacterial taxa, metabolic pathways, and known bacterial virulence factors. After exclusion of anatomical abnormalities and filtering for sequencing quality, 152 samples were analyzed (5 negative UAs, 147 positive UAs, among which 68 were asymptomatic, and 79 symptomatic). Positive UA samples showed significantly lower alpha diversity (2.29 versus 0.086, p < 0.01) and distinct community composition based on beta-diversity (PERMANOVA on Bray-Curtis distance p < 0.01). Alpha and beta diversity did not significantly differ between asymptomatic and symptomatic patients. Machine learning classifiers combining clinical covariates other than specific signs and symptoms and microbiome features (taxa, metabolic pathways, or virulence factors) revealed mostly microbiome features as predictive of symptomatic UTI over clinical features.},
}
@article {pmid40780971,
year = {2025},
author = {Boulanger, N},
title = {Tick and host microbiotas: immunomodulators in tick-borne diseases?.},
journal = {Trends in parasitology},
volume = {41},
number = {9},
pages = {796-805},
doi = {10.1016/j.pt.2025.07.009},
pmid = {40780971},
issn = {1471-5007},
mesh = {Animals ; *Tick-Borne Diseases/microbiology/immunology/prevention &amp; control ; *Microbiota/immunology ; *Ticks/microbiology/immunology ; Humans ; },
abstract = {Vector-borne diseases have a growing impact on human and animal health. Metagenomics has been largely used to characterize the microbiome and has highlighted the key role of the microbiota in modulating the vector competence of insects. Currently, an integrated approach combining vector control, vaccine prevention, and drug treatment is being developed to limit the transmission of insect-borne pathogens. This is more complex for tick-associated diseases, considering the biology of the tick and the possibility of modifications of its microbiota in vector control. Conversely, because the skin is an essential interface in tick-borne diseases, an in-depth study of the precise role of the tick and host microbiota during tick bite and pathogen inoculation opens up new prospects for controlling these diseases.},
}
@article {pmid40780374,
year = {2025},
author = {Mao, Z and Liu, C and Ni, J and Huang, M and Qu, W and Chen, W and Shen, Y and Qin, T and Gao, M and Zheng, S and Chen, Y},
title = {Gut derived (S)-Equol mitigates influenza viral pneumonia by modulating macrophage polarization via Nrf2 mediated AKT/ERK/NF-κb signaling pathways.},
journal = {Free radical biology &amp; medicine},
volume = {239},
number = {},
pages = {457-471},
doi = {10.1016/j.freeradbiomed.2025.08.004},
pmid = {40780374},
issn = {1873-4596},
mesh = {Animals ; *NF-E2-Related Factor 2/metabolism/genetics ; Mice ; NF-kappa B/metabolism/genetics ; Proto-Oncogene Proteins c-akt/metabolism/genetics ; *Gastrointestinal Microbiome/drug effects ; *Macrophages/drug effects/immunology/metabolism ; Signal Transduction/drug effects ; Humans ; *Pneumonia, Viral/drug therapy/pathology/metabolism/virology/immunology ; *Orthomyxoviridae Infections/drug therapy/virology/pathology ; *Influenza, Human/virology/drug therapy ; Male ; Influenza A virus/pathogenicity ; Disease Models, Animal ; Mice, Inbred C57BL ; Female ; },
abstract = {Respiratory virus including influenza A virus (IAV) infection induces alterations in gut microbiota structure and function, which in turn plays an essential role in the pathogenic process. Alterations in gut microbiota are usually accompanied with changes in metabolites. The specific relationship between dynamic changes in gut microbiota and serum metabolites in influenza remains unclear. In this study, we depicted dynamic changes in composition of gut microbiota by using metagenomic sequencing in an influenza mouse model. Through mass spectrometry based metabolomic, we identified (S)-Equol as a notable protective metabolite derived from intestinal flora. Serum (S)-Equol level decreased from the initial infection phase and increased gradually during the convalescence phase, which was positively associated with the changes in some Eggerthella and Bifidobacterium species. Antibiotic treatment reduced serum (S)-Equol level and exacerbated lung pathological damage. Oral administration of (S)-Equol relieved disease severity and controlled inflammatory infiltration. Mechanistically, (S)-Equol activated Nrf2 in macrophages, thereby inhibited AKT, ERK and NF-κB phosphorylation. The inhibition of these signaling pathways ultimately restrained pro-inflammatory cytokines release and repressed pro-inflammatory macrophage polarization. Moreover, serum (S)-Equol level was lower in influenza patients at progressed phase and was negatively correlated with serum levels of IL-6, IL-1β, and TNF-α. Collectively, our data highlighted gut derived (S)-Equol a promising postbiotic for alleviating influenza pneumonia.},
}
@article {pmid40779866,
year = {2025},
author = {Lin, XQ and Li, ZL and Chen, XQ and Wang, L and Yu, L and Wang, AJ},
title = {Microbial synergistic metabolic mechanism of enhanced tetrabromobisphenol A removal by bio-electrochemical system coupled constructed wetland.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139382},
doi = {10.1016/j.jhazmat.2025.139382},
pmid = {40779866},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; *Bioreactors/microbiology/statistics &amp; numerical data ; Desulfovibrio/metabolism ; Geobacter/metabolism ; Metagenome ; *Microbiota ; Nitrates/metabolism ; *Polybrominated Biphenyls/metabolism ; *Water Pollutants, Chemical/metabolism ; *Water Purification/methods/statistics &amp; numerical data ; Wetlands ; Electrochemical Techniques ; },
abstract = {The widespread existence of tetrabromobisphenol A (TBBPA) in the aquatic environment requires efficient treatment technology. The feasibility and related molecular mechanisms for the simultaneous deep removal of nitrate and TBBPA in a bio-electrochemical system coupled with a constructed wetland (BES-CW) are unclear. This study fabricated the BES-CW to achieve simultaneously deep removal of nitrate and TBBPA. TBBPA majorly went through reductive debromination, hydrolytic debromination, ring-cleavage, and oxidation in the open and closed circuits of BES-CW. Electricity activated key genes encoded in oxidoreductase (pflA, pflX) and oxygenase (dmpB, pobA) from electroactive bacteria (Geobacter and Desulfovibrio), accelerating TBBPA metabolites' oxidation and mineralization. Nitrate enriched the Acinetobacter and stimulated genes encoded in hydrolytic dehalogenase, inducing TBBPA hydrolytic debromination and further mineralization. Electricity and nitrate synergistically enhance TBBPA degradation and mineralization, guiding the advanced treatment of emerging pollutants in the aquatic environment.},
}
@article {pmid40779699,
year = {2025},
author = {Bao, Y and Ho, YW and Shen, Z and Lam, EY and Fang, JKH and Leung, KMY and Lee, PKH},
title = {Ecological Roles and Shared Microbes Differentiate the Plastisphere from Natural Particle-Associated Microbiomes in Urban Rivers.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {32},
pages = {17298-17309},
pmid = {40779699},
issn = {1520-5851},
mesh = {*Rivers/microbiology ; *Microbiota ; Microplastics ; Ecosystem ; },
abstract = {The "plastisphere," comprising microbes associated with microplastics (MPs), may have substantial ecological impacts on riverine ecosystems. However, little is known about how the microbiomes associated with anthropogenic MPs compare with those associated with natural particles (NPs) in urban rivers with varying MP pollution levels. We therefore conducted a comparative analysis of the metagenomes associated with MPs and NPs (100-5000 μm) and river water (RW) across 10 urban river systems. Although we found similarities in taxonomic and functional compositions between the microbiomes associated with MPs and NPs, the plastisphere exhibited distinct associations with specialized taxa and life-history strategies. These unique traits enhanced the potential of the plastisphere for complex carbohydrate and plastic degradation, nitrate and nitric oxide reduction, and antibiotic resistance and virulence compared with the NP or RW microbiomes. Furthermore, MPs supported the sharing of unique microbes with the surrounding RW; these shared microbes possessed enhanced horizontal gene transfer capabilities and potentially could disperse traits of the plastisphere into the broader RW microbiomes. This study highlights the distinct ecological roles and shared microbes of the plastisphere, indicating that MP pollution may substantially and uniquely impact the function and health of riverine ecosystems.},
}
@article {pmid40778433,
year = {2025},
author = {Li, W and Pan, S and Qian, J and Xia, Y and Han, G and Liu, J and Wang, Y and Peng, L and Huang, S and Chen, Y and Xie, Y and Xu, J and Zhang, W and Zhou, C},
title = {Comparisons of blood, upper respiratory tract and gut viromes from patients with lung cancer and healthy persons.},
journal = {International journal of cancer},
volume = {157},
number = {9},
pages = {1924-1938},
doi = {10.1002/ijc.70075},
pmid = {40778433},
issn = {1097-0215},
support = {TZKY20230204//Clinical Research Project of Taizhou Clinical Medical College, Nanjing Medical University/ ; TZKY20230305//Key Research Project of Taizhou Clinical Medical College, Nanjing Medical University/ ; 24142202800//Shanghai Science and Technology Innovation Action Plan/ ; 82341106//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Lung Neoplasms/virology/blood ; Male ; Female ; *Virome/genetics ; Middle Aged ; Aged ; Case-Control Studies ; Metagenomics/methods ; *Respiratory System/virology ; Adult ; *Viruses/genetics/classification/isolation &amp; purification ; },
abstract = {Lung cancer is the leading cause of cancer-related mortality globally. Although some studies have proposed a potential association between viral infections and lung cancer pathogenesis, the evidence remains inconclusive. This study characterized the virome in blood, upper respiratory tract, and gut samples from 200 lung cancer patients and 75 healthy controls, with the goal of identifying potential microbial biomarkers for lung cancer, using viral metagenomics. Significant differences in viral diversity and composition were observed between cancer and healthy groups, with lower similarities in blood, respiratory, and gut viromes. Notably, LUSC and LUAD groups showed high similarity, with LUAD exhibiting the most diverse virome. In blood, Anelloviridae dominated in cancer patients, while Retroviridae was more abundant in specific subgroups. The upper respiratory tract virome in cancer patients was enriched with Siphoviridae and Myoviridae, contrasting with Retroviridae in healthy individuals. Gut viromes were dominated by Podoviridae and Virgaviridae in cancer patients, with Virgaviridae showing higher abundance compared to healthy controls. Alpha and beta diversity analyses indicated significant differences in blood and respiratory viromes but not in gut viromes. STAMP and LEfSe analyses identified Anelloviridae and Siphoviridae as potential biomarkers for lung cancer. Additionally, 242 anelloviruses with complete ORF1 were isolated, revealing high genetic diversity. These findings highlight distinct virome profiles in lung cancer patients, offering insights into potential diagnostic and therapeutic targets.},
}
@article {pmid40777923,
year = {2025},
author = {Ramos, SF and Siguenza, N and Zhong, W and Mohanty, I and Lingaraju, A and Richter, RA and Karthikeyan, S and Lukowski, AL and Zhu, Q and Nunes, WDG and Zemlin, J and Xu, ZZ and Hasty, J and Dorrestein, PC and Panda, S and Knight, R and Zarrinpar, A},
title = {Metatranscriptomics Uncover Diurnal Functional Shifts in Bacterial Transgenes with Profound Metabolic Effects.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {7},
pages = {1057-1072},
pmid = {40777923},
issn = {1934-6069},
support = {R01 EB030134/EB/NIBIB NIH HHS/United States ; R01 HL148801/HL/NHLBI NIH HHS/United States ; I01 BX005707/BX/BLRD VA/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 CA236352/CA/NCI NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; R01 AI163483/AI/NIAID NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 CA265719/CA/NCI NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; R01 DK136117/DK/NIDDK NIH HHS/United States ; R01 CA258221/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Circadian Rhythm ; Mice ; Cecum/microbiology ; *Transgenes ; Escherichia coli/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; *Transcriptome ; Diet, High-Fat ; Metagenomics ; Metagenome ; Mice, Inbred C57BL ; Male ; *Bacteria/genetics/metabolism ; Gene Expression Profiling ; },
abstract = {Diurnal rhythmicity in the gut maintains gut integrity, circadian rhythms, and metabolic homeostasis. However, existing studies focus on microbial composition rather than transcriptional activity. To understand microbial functional dynamics, we characterize diurnal fluctuations in the mouse cecal metatranscriptome and metagenome under high-fat diet and time-restricted feeding (TRF). We show that metatranscriptomics uncover TRF-induced time-dependent microbial functional shifts that are undetectable with metagenomics alone. We also found bile salt hydrolase (bsh) from Dubosiella newyorkensis exhibits diurnal expression in the TRF group. Engineering this bsh, along with other candidates, into a native E. coli chassis reveals distinct differences in deconjugation and amidation activities, underscoring functional specificity. In vivo, a D. newyorkensis bsh improves insulin sensitivity, glucose tolerance, and body composition, suggesting a direct role in TRF metabolic benefits. This study highlights how coupling metatranscriptomics with engineered bacterial systems is a powerful approach for uncovering time-dependent bacterial functions related to health and disease.},
}
@article {pmid40776036,
year = {2025},
author = {Upadhyay, U and Dhar, E and Bomrah, S and Syed-Abdul, S},
title = {Unraveling the Role of Gut Microbiota in Colorectal Cancer: A Global Perspectives and Biomarkers as Early Screening Tool for Colorectal Cancer.},
journal = {Studies in health technology and informatics},
volume = {329},
number = {},
pages = {1145-1149},
doi = {10.3233/SHTI251018},
pmid = {40776036},
issn = {1879-8365},
mesh = {*Colorectal Neoplasms/diagnosis/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Early Detection of Cancer/methods ; *Biomarkers, Tumor ; Metagenomics ; },
abstract = {Colorectal cancer (CRC), the second deadliest cancer globally, is closely tied to gut microbiota, opening doors for early detection and treatment. This review of 45 studies (2018-2024) highlights microbial biomarkers like Fusobacterium nucleatum, Bacteroides fragilis, and Parvimonas micra, with strong diagnostic accuracy (AUC >80%) across populations. Techniques like 16S rRNA sequencing, metagenomics, and shotgun sequencing revealed these links. Gut-based diagnostics offer a non-invasive, cost-effective alternative to colonoscopy and FIT for spotting early CRC and precancerous lesions. Yet, regional microbial differences and inconsistent methods-sample processing and sequencing-hinder comparability. Standardizing approaches and exploring fungi and viruses are key to unlocking microbiota's full potential in CRC prevention, diagnosis, and therapy.},
}
@article {pmid40775451,
year = {2025},
author = {Crognale, S and Amalfitano, S and Casentini, B and Di Pippo, F and Fazi, S and Tonanzi, B and Rossetti, S},
title = {Microbial signature of groundwater mixing in geothermal areas: insights from the Cimino-Vico volcanic system (central Italy).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28941},
pmid = {40775451},
issn = {2045-2322},
support = {CN_00000033//Ministero dell'Universit&#xe0; e della Ricerca/ ; CN_00000033//Ministero dell'Universit&#xe0; e della Ricerca/ ; },
mesh = {*Groundwater/microbiology ; Italy ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; *Water Microbiology ; *Hot Springs/microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The complex structure and dynamics of geothermal ecosystems strongly affect the spatial distribution and activity of aquatic microbial communities. The interactions between groundwaters and thermal waters represent an additional selective factor. A deeper understanding of microbial diversity, metabolic potential, and ecological interactions in groundwater mixing zones is essential for evaluating their impact on biogeochemical cycles (such as sulfur, nitrogen, and carbon) and predicting the ecological consequences of water mixing on ecosystem functioning. In this study, the taxonomic diversity and metabolic potentialities of microbial communities in groundwater and thermal waters revealed the occurrence of novel thermophiles able to cope with extreme physical-chemical conditions and high concentrations of toxic elements, such as arsenic, characteristics of the studied area. Furthermore, a core microbiome composed of the families Burkholderiaceae, Caulobacteraceae, Halothiobacillaceae, and Sulfurovaceae was identified as markers of the interaction between the two water compartments. Our findings emphasize the key role of microbial communities in S-, As-, and N-related biogeochemical cycles of geothermal areas.},
}
@article {pmid40774824,
year = {2025},
author = {Lee, I and Kim, BS and Suk, KT and Lee, SS},
title = {Gut Microbiome-Based Strategies for the Control of Carbapenem-Resistant Enterobacteriaceae.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2406017},
pmid = {40774824},
issn = {1738-8872},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; Humans ; Fecal Microbiota Transplantation ; *Enterobacteriaceae Infections/prevention &amp; control/microbiology/therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Animals ; Carbapenems/pharmacology ; Antimicrobial Stewardship ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) represent a critical antimicrobial resistance threat due to their resistance to last-resort antibiotics and high transmission potential. While conventional strategies-such as infection control, antimicrobial stewardship, and novel antibiotic development-remain essential, growing attention has shifted toward the gut microbiome, which plays a central role in mediating colonization resistance against CRE. Disruption of the intestinal microbiota-primarily driven by antibiotic exposure and further exacerbated by non-antibiotic drugs such as proton pump inhibitors-reduces microbial diversity and impairs functional integrity, facilitating CRE acquisition, prolonged carriage, and horizontal transmission. In response, microbiome-based strategies-including microbiome disruption indices (MDIs), fecal microbiota transplantation (FMT), and rationally designed symbiotic microbial consortia-are being explored as novel approaches for CRE prevention and decolonization. Mechanistic studies have shown that colonization resistance is mediated by both direct mechanisms (e.g., nutrient competition, short-chain fatty acid production) and indirect mechanisms (e.g., immune modulation via IL-36 signaling). Advances in metagenomics, metabolomics, and culturomics have enabled high-resolution profiling of gut microbial communities and their functional roles. Emerging preclinical and clinical evidence supports the potential of microbiome-informed interventions to predict infection risk, enhance antimicrobial stewardship, and guide the development of next-generation probiotics targeting CRE. Longitudinal studies continue to evaluate the efficacy of FMT and synthetic microbial consortia in eradicating intestinal CRE colonization. Collectively, these insights underscore the promise of gut microbiome science as a complementary and innovative strategy for CRE control in the post-antibiotic era.},
}
@article {pmid40774558,
year = {2025},
author = {Li, Y and Dai, L and Zhang, L and Shen, X and Zhang, X and Yang, Y and Guan, Y},
title = {Metagenomic insights into the changes of runoff water quality in a deep tunnel drainage system.},
journal = {Environmental research},
volume = {285},
number = {Pt 3},
pages = {122509},
doi = {10.1016/j.envres.2025.122509},
pmid = {40774558},
issn = {1096-0953},
mesh = {*Water Quality ; China ; Water Pollutants, Chemical/analysis ; Rain ; Metagenomics ; Environmental Monitoring ; Microbiota ; *Water Microbiology ; *Metagenome ; Nitrogen ; },
abstract = {Deep tunnel retrofitting of conventional urban drainage systems represents a pivotal strategy for mitigating stormwater pollution and combating flooding. While microbial-driven biogeochemical cycles in stormwater are constrained by taxonomic diversity and environmental variability, the interplay between hydrogeochemical dynamics and microbial functional genes during storage remains poorly characterized. In this study, an in situ stormwater self-purification system was constructed to investigate seasonal water quality evolution, microbial community dynamics, and functional gene regulation in Shenzhen, China. Compared with continuous rainfall events, initial postdrought stormwater events resulted in significantly elevated pollutant loads. Dissolved organic matter analysis revealed that endogenous contaminants accounted for 76 % of the total contaminants, characterized by high microbial bioavailability and low humification after 14 days of storage. The storage of samples favors the enrichment of functional microorganisms such as Plancomycetota, Verrucomicrobiota and Proteobacteria. A quantitative assessment of 62 functional genes linked to carbon (C)/nitrogen (N)/sulfur (S) cycling identified temperature, oxidation‒reduction potential ammonia nitrogen, chemical oxygen demand and total nitrogen as critical drivers of microbial community succession and gene abundance. N cycle genes presented heightened sensitivity to environmental fluctuations, with increased stability and metabolic activity observed in wet season samples. Comparative analysis demonstrated that deep tunnel samples presented more stable functional gene profiles and enriched microbial consortia relative to their surface counterparts. These findings elucidate the mechanistic relationships between hydrogeochemical variables and microbial functional resilience in stormwater storage systems. This work advances the process-level understanding of biochemical cycles mediated by C, N and S transformations, offering actionable insights for optimizing urban drainage infrastructure and microbial-mediated pollution control strategies.},
}
@article {pmid40773868,
year = {2025},
author = {Kim, SY and Woo, SY and Kim, HR and Kim, NY and Kim, HL and Chang, Y and Ryu, S and Kim, HN},
title = {Shotgun metagenomics reveals alteration of gut microbiota and metabolic pathways in adults with poor sleep quality.},
journal = {Psychoneuroendocrinology},
volume = {180},
number = {},
pages = {107565},
doi = {10.1016/j.psyneuen.2025.107565},
pmid = {40773868},
issn = {1873-3360},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Female ; Adult ; Middle Aged ; *Metabolic Networks and Pathways/genetics/physiology ; Feces/microbiology ; Metagenomics/methods ; *Sleep Quality ; *Sleep Wake Disorders/microbiology/metabolism ; Metagenome/genetics ; },
abstract = {INTRODUCTION: Emerging evidence suggests that the gut microbiome plays a role in sleep disturbance. This study explored the characteristics of the gut microbiome and the functional metabolic pathways related to sleep quality.<br><br>METHODS: A total of 588 participants were recruited. Sleep quality was assessed using the Pittsburgh Sleep Quality Index, employing a cutoff score of 8.5. Based on this criterion, 42 individuals with poor sleep quality (PSQ) and 546 healthy controls with good sleep quality (GSQ) were identified. The fecal microbiome was analyzed using shotgun whole-metagenome sequencing, and groups were compared based on diversity metrics, differentially abundant species, metabolic pathways and metabolites.<br><br>RESULTS: No significant differences in alpha and beta diversity indices were observed between individuals experiencing subjective sleep disturbances and those who did not. Klebsiella pneumoniae was more abundant in the PSQ group (&#x3b2; = 0.476; q = 0.017). Additionally, the following metabolic pathways were enriched in the PSQ group: octane oxidation (coefficient = 0.495, q =&#x202f;0.033), the superpathway of acetyl-CoA biosynthesis (coefficient =&#x202f;0.377, q =&#x202f;0.025), superpathway of (Kdo)2-lipid A biosynthesis (coefficient =&#x202f;0.367, q =&#x202f;0.026), petroselinate biosynthesis (coefficient = 0.353, q =&#x202f;0.034), and superpathway of histidine, purine, and pyrimidine biosynthesis (coefficient =&#x202f;0.349, q =&#x202f;0.042). When metabolites levels associated with poor sleep quality were inferred using MelonnPan, higher xanthine levels were observed in the PSQ group (coefficient =&#x202f;0.018; q =&#x202f;0.025).<br><br>CONCLUSION: In summary, this study poses significant questions regarding the relationship between the gut microbiome and poor sleep quality.},
}
@article {pmid40772864,
year = {2025},
author = {Richter, TKS and Kauffman, M and Mammel, MK and Lacher, DW and Rajashekara, G and Leonard, SR},
title = {Long-term impacts of untreated dairy manure on the microbiome and Shiga toxin-producing Escherichia coli persistence in agricultural soil.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {9},
pages = {e0044725},
pmid = {40772864},
issn = {1098-5336},
mesh = {*Manure/microbiology/analysis ; *Soil Microbiology ; *Shiga-Toxigenic Escherichia coli/genetics/isolation &amp; purification/physiology ; *Microbiota ; Animals ; Ohio ; Agriculture ; Soil/chemistry ; },
abstract = {Biological soil amendments of animal origin (BSAAO) improve the soil health of agricultural fields for plant growth. However, as natural reservoirs for bacterial foodborne pathogens, BSAAO application can introduce and support microbes of public health concern, such as pathogenic Shiga toxin-producing Escherichia coli (STEC), in agricultural soils. Using shotgun metagenomic sequencing, this project investigated the microbiome of soil with and without BSAAO, focusing on STEC and the E. coli population over time alongside changes in the soil microbiome and soil abiotic properties. Two farms in Ohio, one using an untreated dairy manure amendment and one that does not use a BSAAO, were sampled for over a year for metagenomic analysis of the soil microbiome. All manure samples were positive for stx genes, indicating the presence of STEC. Impacts of the manure on the soil lasted four weeks by several measures including higher E. coli diversity and more frequent STEC detection. Outside of these four weeks post-amendment, Shiga toxin genes (stx) were identified periodically in both fields throughout the year. STEC detection significantly correlated with higher in silico E. coli O-serogroup diversity, as well as lower soil cation exchange capacity and concentrations of calcium, magnesium, and organic nitrogen. Differential abundance analysis of the soil metagenomes identified several taxa influenced by amendment but did not identify taxa correlated with detection of stx genes. This work provides insights into the timing of and ecological factors associated with STEC persistence in the agricultural environment.IMPORTANCEShiga toxin-producing E. coli (STEC), including E. coli O157:H7, is a major etiological agent of foodborne human disease outbreaks associated with fresh produce and can be transferred to produce via contaminated agricultural soil. Given the devastating impacts of foodborne STEC outbreaks on public health and growers, it is necessary to understand the longevity of the impacts of manure application on the pathogen risk in the soil as well as better understand the ecological and environmental conditions that contribute to STEC survival in the agricultural soil environment. This work expands upon the knowledge of conditions that support STEC persistence in the produce-growing environment and its longevity following amendment in commercial fields with naturally occurring STEC contamination.},
}
@article {pmid40772811,
year = {2025},
author = {Ascari, R and Migliorati, S and Ongaro, A},
title = {A New Dirichlet-Multinomial Mixture Regression Model for the Analysis of Microbiome Data.},
journal = {Statistics in medicine},
volume = {44},
number = {18-19},
pages = {e70220},
pmid = {40772811},
issn = {1097-0258},
support = {2022CLTYP4//Ministero dell'Universit&#xe0; e della Ricerca/ ; },
mesh = {Regression Analysis ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; *Microbiota/genetics ; Computer Simulation ; Monte Carlo Method ; Multivariate Analysis ; Bayes Theorem ; Computational Biology ; Humans ; *Data Interpretation, Statistical ; },
abstract = {Motivated by the challenges in analyzing gut microbiome and metagenomic data, this paper introduces a novel mixture distribution for multivariate counts and a regression model built upon it. The flexibility and interpretability of the proposed distribution accommodate both negative and positive dependence among taxa and are accompanied by numerous theoretical properties, including explicit expressions for inter- and intraclass correlations, thereby providing a powerful tool for understanding complex microbiome interactions. Furthermore, the regression model based on this distribution facilitates the clear identification and interpretation of relationships between taxa and covariates by modeling the marginal mean of the multivariate response (i.e., taxa counts). Inference is performed using a tailored Hamiltonian Monte Carlo estimation method combined with a spike-and-slab variable selection procedure. Extensive simulation studies and an application to a human gut microbiome dataset highlight the proposed model's substantial improvements over competing models in terms of fit, interpretability, and predictive performance.},
}
@article {pmid40772758,
year = {2025},
author = {Yu, J-H and Lugli, GA and Ventura, M and van der Vaart, R and Nauta, A and Mahony, J and van Sinderen, D},
title = {Distinct shifts in bacteriophage diversity and abundance during various stages of Gouda-type cheese production.},
journal = {Applied and environmental microbiology},
volume = {91},
number = {9},
pages = {e0065125},
pmid = {40772758},
issn = {1098-5336},
support = {EPSPG/2020/42//Irish Research Council/ ; 20/FFP-P/8864/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {*Cheese/microbiology/virology ; *Bacteriophages/genetics/classification/isolation &amp; purification/physiology ; Fermentation ; Phylogeny ; Genome, Viral ; *Lactococcus/virology ; Virome ; Food Microbiology ; },
abstract = {Bacteriophage (or phage) infection is known to disrupt milk fermentation processes involving lactic acid bacteria (LAB). This highlights the need to understand the dynamics of phage infection, particularly in fermentations involving undefined complex starter cultures, where conventional phage detection methodologies that rely on host bacteria come with limitations. Here, a metagenomic approach combined with microbiological methods was employed to assess the presence, diversity, and compositional changes in lactococcal phages within an industrial cheese production process. The virome data sets of ingredients and samples taken at various stages of the fermentation process were analyzed, revealing 12 presumptive lactococcal phage genomes belonging to either the Skunavirus genus or the P335 group phages. Phylogenetic analysis of the receptor-binding protein (RBP) sequence from these identified Skunavirus phages enabled us to predict the cell wall polysaccharide (CWPS) types of their bacterial hosts. This prediction was partially validated through host-range assays of three isolated phages, which matched phage genome contigs identified in the virome. Furthermore, alignment of their RBP-encoding gene sequences against virome data, along with real-time quantitative PCR targeting the Skunavirus genus, revealed a significant shift in the abundance and diversity of Skunavirus phages infecting different CWPS type strains throughout the production regime. Overall, our study revealed fluctuations in phage abundance and diversity during a cheese production cycle, underscoring the potential risk of inconsistent product quality due to phage proliferation and the need for effective strategies to mitigate phage contamination.IMPORTANCEThis study investigated dairy samples collected during a full fermentation cycle in a Gouda-type cheese facility to assess the prevalence, abundance, diversity, and dynamics of bacteriophages (phages) infecting starter culture components using a combination of metagenomic and microbiological assays. Also, by predicting the cell wall polysaccharide (CWPS) type of the host bacteria based on receptor-binding protein (RBP) sequences, the possible impact of bacteriophages on starter culture composition was evaluated. These findings highlight the need for tracking strategies to monitor bacteriophage dynamics in order to ensure robust and reliable fermentations.},
}
@article {pmid40772734,
year = {2025},
author = {Wei, Z and Meng, L and Du, S and Wang, F and Jiang, A and Lu, R and Liu, K and Wang, X and Xu, Q and Mu, X and Meng, L and Shao, C},
title = {Metabolic potentials of the gut microbes in Antarctic krill (Euphausia superba).},
journal = {mSystems},
volume = {10},
number = {9},
pages = {e0037725},
pmid = {40772734},
issn = {2379-5077},
support = {4240060500//National Science Foundation for Young Scientists of China/ ; 2022YFC2807505//National Key Research and Development Program of China/ ; ZR2024QD165//National Science Foundation for Young Scientists of Shandong, China/ ; 2023TD19//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; 2022QNLM030004//Marine S&amp;T Fund of Shandong Province for Pilot National Laboratary for Marine Science and Technology (Qingdao)/ ; ZDKC-2022-03//Technological Innovation Projects of Qingdao West New Area/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Euphausiacea/microbiology/metabolism ; Antarctic Regions ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Metagenome ; Metagenomics/methods ; Bacteria/metabolism/genetics/classification ; },
abstract = {Antarctic krill (Euphausia superba) plays crucial roles in the Southern Ocean biological system, yet the ecological functions of their gut microbiota remain poorly understood. The study investigated the composition and diversity of the gut microbiota in E. superba using 16S rRNA gene sequencing, revealing a highly diverse and tissue-specific microbiota. Further investigation through direct metagenomics and culture-enriched metagenomics identified 12 metagenome-assembled genomes (MAGs), which might represent novel species based on their phylogenetic positions, average nucleotide identity (ANI), average amino acid identity (AAI), and relative evolutionary divergence (RED) values. These MAGs were grouped into two distinct clusters according to their completeness of metabolic modules. Although MAGs in cluster 2 showed lower read relative abundance compared to those in cluster 1, they exhibited a greater number of amino acid synthesis modules. The synthesis of glutathione, heme, ubiquinone, vitamins, and betaine by MAGs suggested potential roles in enhancing survival of E. superba in extreme environment. Moreover, the functional genes in the 12 MAGs had abundant transcripts indicating they exhibited high metabolic activity in the E. superba gut microbiota. These findings shed new light on the metabolic contributions of gut microbiota in E. superba.IMPORTANCEThis study provided a comprehensive characterization of the gut microbiome of Euphausia superba, revealing its diverse and functionally distinct microbial community. Furthermore, 12 metagenome-assembled genomes (MAGs) representing novel species were successfully identified. The metabolic analysis demonstrated that these microbes contribute to host nutrient acquisition by synthesizing essential amino acids and vitamins. The identification of antioxidant and osmoregulatory compound synthesis modules suggested that gut microbiota might facilitate the survival of E. superba in the harsh Antarctic environment. Those findings elucidated the host-microbe interactions in polar marine ecosystems and provided new insights into microbial contributions to host nutrient cycling and environmental adaptation in the Southern Ocean.},
}
@article {pmid40772300,
year = {2025},
author = {Li, S and Huang, W and Ma, B and Xia, L and Hu, H and Sun, Y and Ni, H and Yuan, MM and Zhou, J and Zhang, J and Liang, Y},
title = {Viral Diversity Mediates Carbon Allocation for Ecosystem Multifunctionality Across Biomes.},
journal = {Global change biology},
volume = {31},
number = {8},
pages = {e70412},
doi = {10.1111/gcb.70412},
pmid = {40772300},
issn = {1365-2486},
support = {42425703//National Natural Science Foundation of China/ ; 2024QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; YSBR-108//CAS (Chinese Academy of Sciences) Project for Young Scientists in Basic Research/ ; ISSASIP2201//Innovation Program of Institute of Soil Science/ ; 2022ZB467//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; },
mesh = {*Carbon/metabolism ; *Soil Microbiology ; *Ecosystem ; *Viruses/classification/genetics ; Metagenome ; Soil/chemistry ; Biodiversity ; },
abstract = {Viral diversity is essential for regulating the stability of ecosystem function by modulating the biochemical cycles via alterations in the survival and metabolic processes of host organisms. However, how viral survival strategies impact ecosystem function remains unresolved. Here, we analyzed 1824 metagenomes from soils across eight biomes, revealing that lytic viruses constituted a dominant proportion (88%) of the viral communities, with Siphoviridae (35.34%) being the most abundant lytic viral group. Viral communities significantly impacted soil organic carbon dynamics, while ecosystem multifunctionality was notably influenced by microbial necromass carbon, microbial biomass carbon, and various environmental factors. Microbial carbon use efficiency was the primary driver of ecosystem multifunctionality, with significant modulation by lytic and lysogenic viral communities, and lytic viruses contributed more directly to ecosystem multifunctionality (3%) compared to lysogenic viruses (1%). Our study underscores the pivotal role of viral communities, particularly lytic viruses, in shaping global carbon dynamics and ecosystem function, thereby providing a novel framework for future carbon management.},
}
@article {pmid40770776,
year = {2025},
author = {Kauer, L and Sapountzis, P and Imholt, C and Berens, C and Kuehn, R},
title = {Microbial exchange at the wildlife-livestock interface: insights into microbial composition, antimicrobial resistance and virulence factor gene dynamics in grassland ecosystems.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {84},
pmid = {40770776},
issn = {2524-4671},
abstract = {The transmission of antimicrobial resistance genes (ARGs) and virulence factors (VFs) between wildlife and livestock is an emerging concern for animal and human health, especially in shared ecosystems. ARGs enhance bacterial survival against antibiotics, while VFs contribute to infection processes, and the microbiome composition influences host health. Understanding microbial exchange at the wildlife-livestock interface is essential for assessing risks to both animal and human health. This study addresses the gap in knowledge by investigating the microbial composition, ARGs, and VFs in fecal matter from livestock (Bos taurus, Ovis aries) and wildlife (Microtus arvalis) cohabiting grassland pastures. Sampling was conducted within the DFG Biodiversity Exploratories, which provides valuable and extensive long-term ecological datasets and enables the study of diverse environmental parameters. Using metagenomic sequencing and 16 S rRNA amplicon analysis, we compared bacterial diversity, antimicrobial resistance profiles, and virulence gene presence across the three host species. Metagenomic analysis revealed host-specific differences in bacterial community composition. Livestock samples exhibited higher microbial diversity than those from M. arvalis, likely due to greater environmental exposure and management practices. The most common VFs in livestock were associated with immune modulation, whereas motility-related VFs were prevalent in M. arvalis. ARG profiles differed among hosts, suggesting rare events rather due to environmental acquisition than direct transmission between the hosts. The limited numbers of ARGs and VFs shared between the species indicate that horizontal gene transfer events between wildlife and livestock are infrequent. Notably, M. arvalis harbored diverse ARGs, including resistance to tetracycline and vancomycin, which were likely acquired from the environment rather than from direct livestock contact. These findings highlight the significant role of environmental reservoirs in shaping microbial communities and the spread of resistance. This research underscores the need for enhanced surveillance and ecosystem management strategies to mitigate the risk associated with antimicrobial resistance and the potential impacts on both animal and human health.},
}
@article {pmid40770684,
year = {2025},
author = {Winand, R and D'hooge, E and Van Uffelen, A and Bogaerts, B and Van Braekel, J and Hoffman, S and Roosens, NHCJ and Becker, P and De Keersmaecker, SCJ and Vanneste, K},
title = {Investigating fungal diversity through metabarcoding for environmental samples: assessment of ITS1 and ITS2 Illumina sequencing using multiple defined mock communities with different classification methods and reference databases.},
journal = {BMC genomics},
volume = {26},
number = {1},
pages = {729},
pmid = {40770684},
issn = {1471-2164},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Fungi/genetics/classification ; *High-Throughput Nucleotide Sequencing ; *Biodiversity ; *DNA, Ribosomal Spacer/genetics ; Databases, Genetic ; Software ; Computational Biology/methods ; DNA, Fungal/genetics ; Sequence Analysis, DNA ; },
abstract = {An important challenge in taxonomic classification of environmental samples is capturing the real diversity by identifying all species present in a sample. Metabarcoding approaches are often employed to identify species in complex samples. The internal transcribed spacer (ITS) region is the official, widely adopted, barcode for identifying fungal species. Metabarcoding can be done in many different ways with multiple choices at different steps of the workflow. We present a comparative evaluation of the sequenced region (ITS1 and/or ITS2), two different reference databases (UNITE versus BCCM/IHEM), two different bioinformatics software packages (BLAST versus mothur), and the considered taxonomic level (species versus genus level), to accurately capture the diversity using 37 fungal defined mock communities (DMCs). The DMCs cover a broad range of fungal diversity, including 42 Ascomycota species (26 genera), 4 Basidiomycota species (4 genera), and 5 Mucoromycota species (5 genera), all commonly found in indoor environments in Western Europe. Classification performance was first evaluated using ITS1 and ITS2 sequences of all species in the DMCs, generated by Sanger sequencing, to evaluate the discriminatory power of ITS and set a baseline for subsequent comparison with Illumina sequencing. Classification performance was found to be variable depending on all considered variables (sequencing technology, taxonomic level, ITS region, software, database) with 56-100% of species correctly assigned. Sanger sequencing showed that neither ITS1 nor ITS2 resulted in optimal performance due to its low discriminatory power within certain genera. Compared to Sanger sequencing, Illumina sequencing generally resulted in lower precision but comparable recall. Classification performance was generally good at genus but not at species level, although intermediate taxonomic levels could present adequate alternatives. ITS2 typically resulted in slightly better precision and comparable recall compared to ITS1. The employed reference database had a marked effect, with BCCM/IHEM performing better than UNITE due to the difference in number of sequences in each database. BLAST resulted in better performance, but required expert curation, whereas mothur performed better when using an automated workflow. Estimating species abundances using Illumina sequencing read counts generally performed only poorly, although read abundance filtering could increase the precision of ITS1, but not ITS2. Each approach comes with its own advantages and inconveniences and should be carefully selected based on the objectives of the analysis. Our results highlight the power of metabarcoding using Illumina sequencing for investigating fungal diversity in complex samples and can guide scientists in selecting the most appropriate setup for their own purposes.},
}
@article {pmid40770608,
year = {2025},
author = {Babalola, OO and Shittu, OE and Enagbonma, BJ},
title = {Unveiling the Allium ampeloprasum rhizosphere microbiome and its functional dataset under different fertilization systems.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {54},
pmid = {40770608},
issn = {2730-6844},
support = {CRP/ZAF22-03//NRF, South Africa and ICGEB, Italy/ ; },
mesh = {*Rhizosphere ; *Allium/microbiology ; *Microbiota ; Metagenomics ; Fertilizers ; Soil Microbiology ; Bacteria/genetics/classification ; },
abstract = {Leek (Allium ampeloprasum) is a nutritious vegetable popularly cultivated in South Africa and most regions of the world. It is generally recognised as a source of vitamins and vegetables. Nevertheless, little is known about its rhizosphere microbiome and its microbial functional dataset under various fertilization systems. Therefore, this study intended to unveil the rhizosphere microbiome of Allium ampeloprasum and their functional datasets through shotgun metagenomics sequencing analysis.},
}
@article {pmid40770383,
year = {2025},
author = {Zhou, Z and Niu, Y and Ma, Y and Zhang, D and Wang, Y and Ji, R and Zhao, J and Ma, C and Zhu, H and Liu, Y and Tu, L and Lu, J and Zhang, B and Zhang, H and Ma, X and Chen, P},
title = {Lipid accumulation inhibition strategies alleviate Fusobacterium nucleatum-infected colorectal cancer.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {181},
pmid = {40770383},
issn = {2049-2618},
support = {24ZDFA001//Gansu Provincial Science and Technology Major Project/ ; 2024-8-27//The Lanzhou Municipal Science and Technology Program/ ; 20250260006//the College Students' Innovation and Entrepreneurship Program of Lanzhou University, China/ ; },
mesh = {*Fusobacterium nucleatum/drug effects ; Animals ; Humans ; *Colorectal Neoplasms/microbiology/metabolism/pathology/drug therapy ; Mice ; Feces/microbiology ; *Fusobacterium Infections/microbiology ; Bifidobacterium/genetics ; *Lipid Metabolism/drug effects ; Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Male ; Amidohydrolases/metabolism/genetics ; Bile Acids and Salts/metabolism ; Female ; Cell Proliferation ; Escherichia coli/genetics ; Cell Line, Tumor ; Disease Models, Animal ; },
abstract = {BACKGROUND: Fusobacterium nucleatum (F. nucleatum) is prevalent in colorectal cancer (CRC), and it can promote proliferation and induce chemoresistance via multiple pathways. The development of treatment strategies for F. nucleatum-infected CRC is of great importance.<br><br>METHODS: Shotgun metagenomic and metabolomic analyses of human feces, as well as metabolomic analysis of human blood, were performed to reveal the dysbiosis and metabolic dysregulation in CRC. Furthermore, the effects of Bifidobacterium animalis (B. animalis) on F. nucleatum and CRC were assessed in vitro and in vivo. Using a mouse CRC model, the function of bile salt hydrolase (BSH) in B. animalis was verified through heterologous expression in Escherichia coli (E. coli). Bile acids and drug library screening experiments were performed to inhibit F. nucleatum and tumor proliferation.<br><br>RESULTS: We identified an increase in F. nucleatum, enrichment of lipid metabolites, and depletion of Bifidobacterium in CRC patients. Furthermore, B. animalis inhibited F. nucleatum and CRC cells growth in an acid-dependent manner and reduced F. nucleatum-induced tumor increasement in mice. Mechanistically, F. nucleatum caused lipid accumulation, exacerbated inflammation, and intestinal barrier disruption, whereas B. animalis alleviated these changes, increased the Simpson diversity index, reduced lipid metabolites, and altered secondary bile acid composition in mice. Moreover, E. coli-BSH and ursodeoxycholic acid (UDCA) inhibited F. nucleatum-induced lipid accumulation and FASN/CPT1/NF-&#x3ba;B upregulation. Additionally, they alleviated F. nucleatum-related intestinal tumorigenesis in vivo. Targeting F. nucleatum-infected CRC cells and subcutaneous tumors in mice, penfluridol or the combination of orlistat and 5-FU exhibited superior inhibitory effects compared to 5-FU alone.<br><br>CONCLUSIONS: F. nucleatum and lipid metabolites are enriched in CRC patients. Furthermore, BSH-expressing E. coli, UDCA, and penfluridol can alleviate F. nucleatum-induced lipid accumulation and tumor growth in mice. Video Abstract.},
}
@article {pmid40769940,
year = {2025},
author = {De Corte, D and Dlugosch, L and Srivastava, A and Simon, M and Hansell, DA and Bercovici, S and Orellana, M},
title = {Taxonomic and Functional Features of Surface to Deep-Sea Prokaryotic Communities in the Eastern North Pacific Ocean.},
journal = {Environmental microbiology reports},
volume = {17},
number = {4},
pages = {e70170},
pmid = {40769940},
issn = {1758-2229},
support = {CO 2218/2-1//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; OCE-1634009//National Science Foundation/ ; OCE-1634250//National Science Foundation/ ; },
mesh = {Pacific Ocean ; *Seawater/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Archaea/classification/genetics/isolation &amp; purification/metabolism ; Phylogeny ; *Microbiota ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Metagenome ; },
abstract = {Biogeochemical cycles in the ocean are strongly influenced by microbial activity, which affects nutrient and organic matter cycling. These processes, influenced by factors such as temperature, salinity, density and inorganic nutrients, drive the vertical stratification of microbial communities, which subsequently influence the chemistry at different depth layers. Sequencing technology has expanded our understanding of oceanic prokaryotic communities' taxonomic and functional potential. However, there is limited information on how these communities vary across gradients. In this study, we conducted metagenomic analyses on samples from the eastern North Pacific, collected across a longitudinal transect around 45°N and throughout the entire water column. We assessed taxonomic and functional classification, focusing on the roles of prokaryotic communities in biogeochemical cycling. Our results revealed that the surface community was dominated by the SAR11 clade, followed by Flavobacterales and Rhodobacterales. The deep layers harboured a more diverse community, where Thaumarchaeota accounted for the most significant proportion. This clear taxonomic stratification led to variations in the communities' functional capabilities across different depth layers. Photosynthesis and heterotrophy dominated the surface layers, whereas the deeper layers exhibited a mix of metabolic features, allowing organisms to potentially utilise both inorganic and organic carbon sources.},
}
@article {pmid40768422,
year = {2025},
author = {Pan, S and Li, W and Zhao, X and Wang, H and Liu, J and Zhang, W and Zhou, C and Xie, Y},
title = {Blood virome profiling reveals subtype-specific viral signatures and reduced diversity in non-Hodgkin lymphoma.},
journal = {Virulence},
volume = {16},
number = {1},
pages = {2542457},
pmid = {40768422},
issn = {2150-5608},
mesh = {Humans ; *Virome ; *Lymphoma, Non-Hodgkin/virology/blood ; Middle Aged ; Male ; Female ; Aged ; Adult ; *Viruses/classification/genetics/isolation &amp; purification ; Metagenomics ; Aged, 80 and over ; },
abstract = {Non-Hodgkin lymphoma (NHL), a heterogeneous lymphoid malignancy, demonstrates molecular diversity linked to genetic and immune factors, with emerging roles for viral infections in pathogenesis. Yet, the blood virome's composition and dynamics in NHL remain poorly characterized. This study characterizes the blood virome in NHL subtypes using viral metagenomic sequencing of serum from 217 patients (B-cell: BCL, T-cell: TCL, NK-cell: NKCL) and 40 healthy controls. Bioinformatic analysis identified 45 viral families, revealing subtype-specific viromic signatures. BCL exhibited a dominance of Anelloviridae, which accounted for 86% of eukaryotic viruses, compared with only 3% in controls, correlating with immunosuppression. Additionally, picobirnavirus, an opportunistic pathogen particularly in hosts with compromised immune systems, also showed a significant difference compared to controls. NKCL showed Flaviviridae enrichment, accounting for 82% of eukaryotic viruses, with nearly all of them being human pegivirus-1 (HPgV-1). Compared with healthy controls, patients with NHL exhibited significantly lower blood virome α-diversity at the genus level, and T-cell lymphomas showed the lowest species-level richness (140 vs. 332 in controls). Beta diversity highlighted BCL-specific viral heterogeneity, contrasting conserved T/NKCL viral profiles. Anelloviridae and Picobirnavirus expansion aligns with immune dysfunction, whereas NKCL-restricted HPgV-1 prevalence underscores biomarker potential. These findings implicate blood virome alterations marked by viral family predominance and diversity loss in NHL pathogenesis via immune modulation or oncogenesis. This first comprehensive NHL virome profile identifies subtype-specific signatures (Anelloviridae/Picobirnavirus/HPgV-1) for potential diagnostic and therapeutic targeting. Validation of these biomarkers may refine NHL subtyping and elucidate virome-lymphomagenesis mechanisms.},
}
@article {pmid40768327,
year = {2025},
author = {Gilbert, E and Binks, S and Damato, V and Uy, C and Colmenero, P and Kelly, M and Khalil, MI and O'Brien, M and Claesson, MJ and Cryan, JF and Delanty, N and Irani, SR and Cavalleri, GL},
title = {The gut microbiome associated with LGI1-antibody encephalitis.},
journal = {Epilepsia},
volume = {66},
number = {11},
pages = {4411-4424},
pmid = {40768327},
issn = {1528-1167},
support = {MRCG-2018-005//Medical Research Charities Group/ ; 104079/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; 16/RC/3948/SFI_/Science Foundation Ireland/Ireland ; MR/V007173/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Female ; Male ; *Intracellular Signaling Peptides and Proteins/immunology ; *Encephalitis/immunology/microbiology/genetics ; *Autoantibodies/immunology ; Adult ; Middle Aged ; Young Adult ; Aged ; },
abstract = {OBJECTIVE: Autoimmune encephalitis is a cause of brain inflammation characterized by auto-antibodies, which target cell surface neuronal proteins and lead to neuronal dysfunction. The most common form is associated with auto-antibodies to leucine-rich glioma-inactivated 1 (LGI1) protein, the presentation of which includes frequent focal seizures. The exact cause of these auto-antibodies remains unknown, but established predispositions include overrepresented human leukocyte antigen (HLA) alleles. Yet, these HLA alleles are themselves common in the healthy ancestry-matched population. One potential etiological hypothesis is that an environmental trigger, such as the gut microbiome, interacts with a genetically predisposed individual.<br><br>METHODS: To investigate this, we studied 42 patients with LGI1-antibody encephalitis (LGI1-Ab-E) and 27 familial/environmentally matched controls, and performed metagenomic shotgun sequencing, to describe the compositional and functional differences in the gut microbiome.<br><br>RESULTS: We observed that LGI1-Ab-E gut microbiomes exhibited a significant reduction in the ratio of Firmicutes (or Bacillota) and Bacteroidetes phyla, which is associated with the dosage of HLA susceptibility allele count in patients with LGI1-Ab-E. Furthermore, we identified differences in functional gene profiles in the gut microbiome that led to a reduction of neuroinflammatory protective short-chain fatty acids (SCFAs) in LGI1-Ab-E patients.<br><br>SIGNIFICANCE: Taken together, our results suggest that a compositional shift in the gut microbiome of LGI1-Ab-E associates with a neuroinflammatory state, possibly through the reduction of SCFA production. Our study highlights the potential of the gut microbiome to explain some of the complex condition and unravel etiological questions. Validation studies with greater sample sizes are recommended.},
}
@article {pmid40767981,
year = {2025},
author = {Jena, R and Singh, NA and Ahmed, N and Choudhury, PK},
title = {Bifidobacteria in antibiotic-associated dysbiosis: restoring balance in the gut microbiome.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {8},
pages = {297},
pmid = {40767981},
issn = {1573-0972},
mesh = {*Dysbiosis/chemically induced/microbiology/therapy ; Humans ; *Probiotics/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Bifidobacterium/physiology ; *Anti-Bacterial Agents/adverse effects ; Animals ; Prebiotics ; },
abstract = {Antibiotic-associated dysbiosis disrupts the gut's microbial balance, leading to reduced diversity, overgrowth of antibiotic-resistant strains, and compromised gut homeostasis. This can result in inflammation, increased intestinal permeability, impaired immunity, and heightened susceptibility to infections. In this context, probiotics have been highlighted as a promising remedy in alleviating this antibiotic-induced gut microbiome aberrations with subsequent decrease of the detrimental effects. Bifidobacteria, a prominent bacterial group with promising probiotic attributes, have shown effectiveness in restoring the gut microbiome by strong adherence to the colon's mucosal lining and enhancing the immune response through increased anti-inflammatory cytokines. They also play a crucial role as key producers of acetic acid, which supports butyric acid-producing bacteria essential for colonocyte health during dysbiosis. The synergistic use of bifidobacteria with other probiotic species or prebiotic substrates has further enhanced their survival, colonization capacity, and overall impact on gut microbial restoration. Advanced metagenomic analyses have begun to reveal strain-specific functions, paving the way for personalized probiotic therapies tailored to an individual's unique microbiome profile. Despite encouraging progress, critical research gaps persist, particularly regarding strain-specific efficacy, formulation stability, long-term outcomes, underlying mechanisms, systemic interactions, and the distinct and specific role of bifidobacteria. Addressing these gaps through targeted clinical investigations is essential to fully harness their therapeutic potential and develop optimized strategies for restoring the microbial balance in the gut microbiome.},
}
@article {pmid40767409,
year = {2025},
author = {Liu, WS and Liu, CD and Liu, C and van der Ent, A and Cao, Y and Chao, YQ and Qiu, RL and Tang, YT},
title = {Microbial Phosphate Solubilization Promotes Rare Earth Element Accumulation in the Hyperaccumulator Dicranopteris linearis from China.},
journal = {Environmental science &amp; technology},
volume = {59},
number = {32},
pages = {17092-17102},
doi = {10.1021/acs.est.5c05746},
pmid = {40767409},
issn = {1520-5851},
mesh = {China ; Rhizosphere ; *Phosphates/metabolism ; Soil/chemistry ; *Metals, Rare Earth/metabolism ; Phosphorus ; Soil Microbiology ; Microbiota ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Plant and rhizosphere soil samples of the rare earth element (REE) hyperaccumulator plant Dicranopteris linearis were collected across tropical and subtropical China to elucidate how rhizosphere microbiota drive soil REE solubilization and accumulation in this species. The results show that this facultative REE hyperaccumulator species grows under severe phosphorus deficiency conditions, with soil available phosphorus concentrations ∼2 mg kg[-1] and a leaf nitrogen-to-phosphorus ratio >20. The core rhizosphere microbiota comprise 111 OTUs (occupancy >95%, relative abundance >0.1%), with community structure primarily correlated with soil phosphorus availability, rather than with geographical location or climatic variables. Foliar phosphorus and REE concentrations are positively associated with soil total phosphorus concentrations and glucose dehydrogenase (GCD) gene abundance─a key biomarker of microbial phosphate solubilization activity─but exhibit no significant association with soil available phosphorus or soil extractable REE concentrations. Combined 16S rRNA sequencing and metagenomic analyses further reveal abundant phosphate-solubilizing microbes within the core microbiome. These results show that REE mineral weathering in the rhizosphere soil and subsequent accumulation in D. linearis are side effects of phosphate solubilization promoted by the rhizosphere microbiome under phosphorus deficiency conditions.},
}
@article {pmid40766845,
year = {2025},
author = {Zheng, N and Yu, HL and Zhang, BJ and Wang, D and Ji, YL and Dai, LL and Li, W and Li, SH and Hu, ZL and Zheng, YS},
title = {Metagenomic next-generation sequencing-based characterization of the viral spectrum in clinical pulmonary and peripheral blood samples of patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1562965},
pmid = {40766845},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Bronchoalveolar Lavage Fluid/virology ; *Virome/genetics ; *Viruses/genetics/classification/isolation &amp; purification ; Female ; Male ; Middle Aged ; Adult ; Aged ; *Lung/virology ; *Blood/virology ; Bacteria/classification/genetics/isolation &amp; purification ; *Virus Diseases/virology ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables comprehensive profiling of viral communities in clinical samples. However, comparative analyses of the virome across anatomical compartments and disease states remain limited. This study aims to characterize the virome in bronchoalveolar lavage fluid (BALF) and peripheral blood samples from patients with various clinical conditions using mNGS.<br><br>METHODS: A total of 338 clinical samples-including 240 BALF and 69 blood samples for DNA sequencing, and 18 BALF and 11 blood samples for RNA sequencing-underwent shotgun metagenomic sequencing. Following removal of host-derived reads, high-quality non-human sequences were aligned to a viral reference database. Virome composition was assessed through alpha and beta diversity metrics. Principal coordinates analysis was used to evaluate disease-related variation, and virus-bacteria associations in BALF were investigated via Spearman correlation.<br><br>RESULTS: Sequencing yielded an average of 51 million raw reads per sample, resulting in approximately 8 million non-human reads after host filtering. Distinct virome profiles were observed between BALF and blood samples. Bacteriophages dominated all groups, with Siphoviridae and Myoviridae as the most abundant families, although only 13.6% of viral abundance could be assigned to known families. Diversity analyses revealed significant differences between BALF and peripheral blood, and DNA-sequenced BALF samples showed disease-specific viral signatures in pulmonary infections. In contrast, tumor presence had no significant effect on virome composition in either BALF or blood. Network analysis identified complex virus-bacteria correlations in BALF, with genera such as Haemophilus, Megasphaera, and Treponema as key bacterial hosts.<br><br>CONCLUSIONS: This study reveals pronounced differences in virome composition between the respiratory and circulatory systems and highlights the specific influence of pulmonary disease-but not tumors-on the pulmonary virome. The observed virus-bacteria networks provide novel insights into pulmonary microbial ecology and underscore the importance of integrating host and disease context in virome studies.},
}
@article {pmid40765405,
year = {2025},
author = {Dai, G and Zhang, Y and Shen, C and Jiao, Y and Shen, W and Yu, F and Liu, R and Wang, D and Yuan, G and Jia, J},
title = {Luteolin Treats Obese Rats With Polycystic Ovary Syndrome by Improving Liver Lipid Metabolism and Regulating the Gut Microbiota.},
journal = {Phytotherapy research : PTR},
volume = {39},
number = {9},
pages = {4171-4180},
doi = {10.1002/ptr.70043},
pmid = {40765405},
issn = {1099-1573},
support = {JLY2021209//Clinical Medical Science and Technology Development Foundation of Jiangsu University/ ; BK20231251//Natural Science Foundation of Jiangsu Province/ ; JDY2022005//Key project for Medical Education Collaborative Innovation Fund of Jiangsu University/ ; BE2023757//Social Development Project of Jiangsu Province/ ; BRA2022008//the sixth phase 333 second level talent training project of Jiangsu Province (tackling bottleneck technology)/ ; jdfyRC2020010//Doctoral Research Initiation Fund/ ; BGYCA202207//Beigu Talent Cultivation Program of Affiliated Hospital of Jiangsu University/ ; SS202204-KFB05//open project of clinical medical research center of Gynecology and Traditional Chinese Medicine of Zhenjiang/ ; MS2024142//Science and Technology Development Program for Traditional Chinese Medicine of Jiangsu Province/ ; },
mesh = {Animals ; *Luteolin/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Female ; *Polycystic Ovary Syndrome/drug therapy/complications/metabolism ; *Obesity/drug therapy/complications ; *Lipid Metabolism/drug effects ; *Liver/metabolism/drug effects ; Rats ; Rats, Sprague-Dawley ; Body Weight/drug effects ; Disease Models, Animal ; },
abstract = {Polycystic ovary syndrome (PCOS) and obesity share a bidirectional relationship. While previous studies have indicated the anti-obesity effects of luteolin, its role in PCOS exacerbated by obesity remains unclear. This study aimed to investigate the ameliorative effects of luteolin on obese rats with PCOS and explore its underlying mechanisms. We established a rat model of PCOS with obesity and administered luteolin to evaluate its mitigating effects on the metabolic phenotype. Liver transcriptomics and fecal metagenomics were employed to analyze potential targets and alterations in the gut microbiota composition associated with luteolin's effects. Results showed that luteolin reduced body weight, improved estrous cycles, polycystic ovarian morphology, and glucose tolerance, and lowered serum levels of triglycerides (TG), total cholesterol (TC), and low-density lipoprotein cholesterol (LDL-c) in the model rats. Importantly, luteolin significantly alleviated hepatic steatosis and reversed the expression of 138 key differentially expressed genes (DEGs) in the liver, including UQCRC2, IRS2, NFIX, and ALDH6A1. In addition, luteolin significantly increased the alpha diversity of the gut microbiota and modulated its composition, specifically increasing the relative abundance of Bacteroidota and decreasing that of Firmicutes. Our findings suggest that luteolin exerts beneficial effects on PCOS with obesity, potentially mediated through the improvement of hepatic lipid metabolism and the restoration of gut microbiota homeostasis. Luteolin emerges as a promising therapeutic candidate for managing PCOS with obesity.},
}
@article {pmid40764903,
year = {2025},
author = {Jingwen, J and Jingran, F and Liye, M and Yu, H and Yancen, M and Jingya, Z},
title = {The role of cervical microbiome in cervical incompetence: insights from 16 S rRNA metagenomic sequencing.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {486},
pmid = {40764903},
issn = {1471-2180},
support = {No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; No.20241295//This study was supported by Hebei Province 2024 Medical Research Project Plan./ ; },
mesh = {Female ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Pregnancy ; Metagenomics ; Adult ; *Uterine Cervical Incompetence/microbiology/immunology ; *Bacteria/classification/genetics/isolation &amp; purification ; *Cervix Uteri/microbiology ; NF-kappa B/metabolism ; Toll-Like Receptor 2/metabolism/genetics ; Toll-Like Receptor 4/metabolism/genetics ; Cervix Mucus/microbiology ; },
abstract = {Cervical incompetence (CI) is recognized as a critical factor contributing to mid-pregnancy miscarriage and preterm delivery, significantly affecting pregnancy outcomes. Despite this, the specific role of the microbiome in this pathological process remains inadequately understood. This study seeks to elucidate the core microbiome associated with CI in pregnant women and explore its potential biological mechanisms. Utilizing 16 S rRNA metagenomic sequencing, we examined the cervical mucus microbiota of women with CI both pre-operatively (PreOp) and post-operatively (PostOp). Subsequently, the immunomodulatory effects of these microbial communities on the immune system were systematically assessed using quantitative real-time PCR, Western blotting, and enzyme-linked immunosorbent assay. The findings revealed a significant reduction in microbial diversity and richness in PostOp cervical mucus, alongside notable alterations in microbiota composition. The genera Lactobacillus, Bifidobacterium, Gardnerella, Streptococcus, and Anaerococcus were identified as predominant. Further analysis demonstrated that treatment with 25% Lactobacillus crispatus (L. crispatus) supernatants, in comparison to 25% Group B Streptococcus (GBS) supernatants, resulted in high cell viability and normal morphology in HcerEpic cells. Importantly, the combination of 25% L. crispatus and 25% GBS supernatants significantly reduced the mRNA and protein expression levels of Toll-like receptor 4 (TLR4), Toll-like receptor 2 (TLR2), and nuclear factor kappa B (NF-κB) in vitro. These results indicate that L. crispatus may play a role in modulating cervical inflammation in CI by suppressing the TLR/NF-κB signaling pathway, potentially contributing to a more stable cervical microenvironment during pregnancy.},
}
@article {pmid40764207,
year = {2026},
author = {Jiang, H and Zhang, J and Li, S and Kwok, T and Ng, SC and Lee, ATC and Xu, Z},
title = {Dietary index for gut microbiota (DI-GM) and cognitive function: NHANES findings and validation in a Hong Kong cohort with metagenomic data.},
journal = {The journal of prevention of Alzheimer's disease},
volume = {13},
number = {1},
pages = {100319},
pmid = {40764207},
issn = {2426-0266},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Hong Kong ; Male ; Female ; *Cognition/physiology ; Aged ; *Diet ; Nutrition Surveys ; Cohort Studies ; Metagenomics ; Middle Aged ; *Cognitive Dysfunction ; Neuropsychological Tests ; },
abstract = {BACKGROUND: The diet-gut-microbiota-brain axis is critical for maintaining brain health. The Dietary Index for Gut Microbiota (DI-GM), comprising beneficial and unfavorable components, may serve as a proxy for this connection, yet its association with cognition remains underexplored.<br><br>METHODS: This study examined the relationship between DI-GM, its components, and cognitive function in older adults using data from the National Health and Nutrition Examination Survey (NHANES). Findings were validated in an independent Hong Kong osteoporosis cohort (OS cohort) with gut metagenomic data to assess of microbiota's mediating role in diet-cognition relationship. Cognitive assessment in NHANES utilized the Consortium to Establish a Registry for Alzheimer's Disease (CERAD), Animal Fluency Test (AFT), and Digit Symbol Substitution Test (DSST), while the OS cohort employed the Hong Kong version of the Montreal Cognitive Assessment (HK-MoCA). DI-GM was calculated from 24-hour dietary recalls. The diet-cognition associations were assessed by weighted multivariate regressions, supplemented by restricted cubic spline (RCS), subgroup, correlation network, and mediation analyses.<br><br>RESULTS: Higher DI-GM was significantly associated with better performance on DSST (OR=0.90; 95 % CI: 0.82, 0.99; p = 0.033). The beneficial-to-gut-microbiota score (BGMS) associated with lower psychometric mild cognitive impairment (p-MCI) risk (OR=0.88; 95 % CI: 0.80, 0.98; p = 0.022) and better CERAD immediate and delayed recall and DSST (all p < 0.05). The beneficial-to-gut-microbiota components like dietary fiber demonstrated protective effects across cognitive domains, while refined grains was associated with poorer cognition. In the OS cohort, higher dietary fiber intake correlated with higher HK-MoCA score (p < 0.05) and increased abundance of fermenting bacteria. Among these species, Eubacterium ventriosum mediated the beneficial effect of dietary fiber intake on dementia risk reduction, with an indirect effect of -0.014 (95 % CrI: -0.040, -0.001), accounting for approximately 12.7 % of the total effect.<br><br>CONCLUSION: Higher adherence to beneficial-to-gut-microbiota dietary patterns, as reflected by DI-GM, was associated with better cognitive function in older adults. These findings highlight the importance of a gut-microbiota-targeted diet in maintaining cognitive health.},
}
@article {pmid40763732,
year = {2025},
author = {Zhou, Z and Jiang, A and Jiang, X and Hatzios, SK},
title = {Metabolic cross-feeding of a dietary antioxidant enhances anaerobic energy metabolism by human gut bacteria.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {8},
pages = {1321-1332.e9},
pmid = {40763732},
issn = {1934-6069},
support = {R35 GM137952/GM/NIGMS NIH HHS/United States ; ZIA LM202010/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Humans ; *Energy Metabolism ; *Antioxidants/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology ; Anaerobiosis ; Ergothioneine/metabolism ; Colorectal Neoplasms/microbiology ; *Bacteria/metabolism ; Bacteroides/metabolism ; *Gastrointestinal Tract/microbiology ; Oxidation-Reduction ; Diet ; Adenosine Triphosphate/biosynthesis ; },
abstract = {The degradation of complex carbohydrates and other macromolecules by human gut bacteria generates metabolites that are used by neighboring microbes for anaerobic respiration. However, it is largely unknown whether cross-feeding of other dietary compounds can drive energy-yielding redox reactions in the gut. We show that gut bacteria from different phyla cross-feed a common dietary antioxidant to produce energy under anaerobic conditions. Clostridium symbiosum encodes ergothionases that transform ergothioneine, a mushroom-derived antioxidant, into the electron acceptor thiourocanic acid (TUA). TUA is reduced by Bacteroides xylanisolvens, increasing bacterial ATP synthesis and growth. Furthermore, TUA is selectively produced and consumed by certain human fecal microbial communities. Consistent with emerging links between intestinal ergothioneine homeostasis and colorectal cancer, ergothionase is significantly enriched in fecal metagenomes from colorectal cancer patients. Together, these results illustrate how commensalistic cross-feeding of an antioxidant nutrient enhances microbial energy metabolism, which may contribute to interpersonal differences in disease risk.},
}
@article {pmid40763378,
year = {2025},
author = {Mollick, SA},
title = {Genetic sex prediction from human gut shotgun metagenomic data: An ethical appraisal.},
journal = {Forensic science international},
volume = {376},
number = {},
pages = {112585},
doi = {10.1016/j.forsciint.2025.112585},
pmid = {40763378},
issn = {1872-6283},
mesh = {Humans ; Male ; Female ; *Metagenomics ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome/genetics ; Machine Learning ; *Metagenome ; Sequence Analysis, DNA ; Chromosomes, Human, Y ; High-Throughput Nucleotide Sequencing ; Forensic Genetics ; },
abstract = {Human DNA inadvertently captured during gut shotgun metagenomic sequencing is typically treated as background contamination, yet it can reveal sensitive personal traits, raising ethical and forensic concerns. In this study, fecal metagenomes from 626 individuals were processed using four DNA extraction protocols and both paired and single-end sequencing, to evaluate the extent of identifiable human information. Host-derived reads exhibited uniform chromosomal coverage, enabling the accurate prediction of genetic sex based on the Y-to-X read-depth ratio. A machine learning model trained on this metric achieved over 92 % accuracy with the detection threshold (-β0/β1) = 0.34 across different protocols and sequencing configurations, demonstrating the method's robustness and general applicability. These findings highlight that even low levels of residual human DNA in microbiome datasets are sufficient to infer individual traits, such as sex, which can compromise participant anonymity. Given that such reads are often retained in public repositories, the risk of re-identification persists despite microbiome-focused study designs. This work serves as both a technical demonstration and an ethical imperative. Host-DNA masking should become standard before data sharing; ethics boards and data custodians must recognize the potential for unintentional disclosure; and informed consent procedures must reflect the realities of high-throughput sequencing. While the Y-to-X depth ratio offers a scalable quality control and forensic tool, its application must be balanced with rigorous privacy safeguards to uphold research integrity and participant trust.},
}
@article {pmid40761666,
year = {2025},
author = {Zhou, H and Mu, X and Hu, H and Zhao, S and Hu, N and Yang, M and Jiang, J},
title = {DHLCA Alleviates Diabetic Kidney Disease via TGR5/FXR Activation and Gut Microbiota Remodeling.},
journal = {Drug design, development and therapy},
volume = {19},
number = {},
pages = {6469-6485},
pmid = {40761666},
issn = {1177-8881},
mesh = {*Receptors, G-Protein-Coupled/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Diabetic Nephropathies/drug therapy/metabolism ; Animals ; Mice ; Male ; Humans ; *Receptors, Cytoplasmic and Nuclear/metabolism/agonists ; *Diabetes Mellitus, Type 2/drug therapy/metabolism ; Middle Aged ; Diabetes Mellitus, Experimental/drug therapy/metabolism ; Mice, Inbred C57BL ; Female ; *Lithocholic Acid/analogs &amp; derivatives/pharmacology ; Disease Models, Animal ; Receptor, Farnesoid X-Activated ; },
abstract = {PURPOSE: Diabetic kidney disease (DKD) is a major contributor to chronic kidney disease worldwide. Bile acids (BAs) are increasingly recognized as key regulators of glucose metabolism and kidney function. This study aimed to investigate the role of BA metabolism in the progression of DKD.<br><br>METHODS: Plasma BA profiles were measured in healthy controls (HC), patients with type 2 diabetes mellitus (T2DM), and patients with DKD using ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). After identifying potential BA biomarkers in the clinical cohort, in vivo validation was conducted using dehydrolithocholic acid (DHLCA) intervention in DKD mouse model. Kidney injury markers, as well as the expression of Takeda G protein-coupled receptor 5 (TGR5) and farnesoid X receptor (FXR), were evaluated. In addition, gut microbiota (GM) composition was analyzed via metagenomic sequencing following DHLCA treatment.<br><br>RESULTS: The plasma DHLCA levels were significantly lower in DKD with macroalbuminuria group compared to T2DM group and DKD with microalbuminuria group (P < 0.01). Partial Spearman correlation analysis adjusted for age and diabetes duration showed that DHLCA levels were negatively correlated with urine albumin (&#x3c1; = -0.347; 95% CI, -0.531 to -0.135; q = 0.008) and urine albumin-to-creatinine ratio (UACR) (&#x3c1; = -0.332; 95% CI, -0.499 to -0.155; q = 0.010). In vivo, DHLCA administration significantly reduced UACR and fasting blood glucose (FBG) levels (P < 0.01), and improved liver function (ALT, P < 0.05) in DKD mice. DHLCA treatment attenuated renal tubular injury, restored TGR5 and FXR expression in kidney tissue, and decreased levels of kidney injury molecule-1 (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL). Metagenomic analysis revealed an enrichment of Lachnospiraceae bacterium following DHLCA treatment.<br><br>CONCLUSION: DHLCA may represent a promising therapeutic candidate for DKD by targeting the TGR5/FXR signaling pathway and GM remodeling. Its metabolic and kidney benefits, along with an improved hepatic profile and absence of hepatotoxicity, support further translational investigation.},
}
@article {pmid40760050,
year = {2025},
author = {Oh, J and Voigt, AY},
title = {The human skin microbiome: from metagenomes to therapeutics.},
journal = {Nature reviews. Microbiology},
volume = {23},
number = {12},
pages = {771-787},
pmid = {40760050},
issn = {1740-1534},
mesh = {Humans ; *Skin/microbiology ; *Microbiota/genetics ; *Metagenome ; Bacteria/genetics/classification ; Metagenomics ; Fungi/genetics ; Skin Microbiome ; },
abstract = {The skin microbiome is composed of a diverse community of microorganisms, including bacteria, fungi, viruses and mites. These microorganisms have a crucial role in maintaining skin health, protecting against pathogens and modulating immune responses. In recent years, our understanding of the skin microbiome has expanded substantially with the deployment of metagenomic sequencing. This technology, by reconstructing microbial species, strains and gene pathways in the microbiomes of different cohorts, has led to identification of numerous therapeutic targets and thus propelled the development of therapeutic approaches that are aimed at leveraging these microorganisms to treat skin conditions and to improve skin health. In this Review, we discuss the composition, ecology, functions and therapeutic horizons of the human skin microbiome, presenting examples of studies that highlight potential therapeutic targets in the skin microbiome, ongoing progress in the development of skin microbiome-based therapeutics and challenges.},
}
@article {pmid40759346,
year = {2025},
author = {Zhao, C and Song, Y and Chen, H and Li, Y and Lei, A and Wu, Q and Zhu, L and He, Q},
title = {Study on the selective regulation of microbial community structure in microbial fuel cells by magnetic field-coupled magnetic carbon dots.},
journal = {Bioresource technology},
volume = {437},
number = {},
pages = {133065},
doi = {10.1016/j.biortech.2025.133065},
pmid = {40759346},
issn = {1873-2976},
mesh = {*Bioelectric Energy Sources/microbiology ; *Carbon/chemistry ; *Magnetic Fields ; RNA, Ribosomal, 16S/genetics ; Electricity ; Bacteria/genetics/metabolism ; *Quantum Dots/chemistry ; *Microbiota ; },
abstract = {Microbial fuel cells (MFCs), as a green energy technology that simultaneously enables electricity generation and wastewater treatment, exhibit performance that is highly dependent on the structural distribution of the microbial community. In this study, we investigated the effect of magnetic field (MF)-coupled magnetic carbon dots (N-CD/Fe3O4) as a selective pressure on the structure of mixed microbial communities in an intermittent pulsating fluidized-bed bioelectrochemical reactor. Under a moderate magnetic field (15 mT), N-CD/Fe3O4 were effectively adsorbed onto microbial cells and subsequently aggregated, significantly enhancing electron transfer within the community. The maximum power density reached 38.43 mW/m[2], which is about 5.07 times that of the blank control group. 16S rRNA and metagenomic analyses showed that the MF (15 mT) group exhibited significant enrichment of typical electroactive bacteria (40.32 %), such as Geobacter, which directly contributed to improved power production performance. In contrast, under a stronger magnetic field (60 mT), the abundance of typical electroactive bacteria (17.94 %) decreased, while atypical electroactive (38 %) and metabolically complementary bacteria that facilitate syntrophic cooperation (42.85 %) showed adjusted abundances, forming a functionally more balanced microbial community with improved adaptability to real wastewater conditions. This study demonstrates that by tuning magnetic field intensity and coupling with magnetic carbon dots, the structure and function of microbial communities can be directionally regulated, providing an effective strategy for developing electroactive inocula with enhanced power generation and wastewater adaptability.},
}
@article {pmid40757481,
year = {2025},
author = {Bustos-Caparros, E and Viver, T and Gago, JF and Avontuur, JR and Amiour, S and Baxter, BK and Llames, ME and Mutlu, MB and Oren, A and Ramírez, AS and Stott, MB and Venter, SN and Santos, F and Antón, J and Rodriguez-R, LM and Bosch, R and Hedlund, BP and Konstantinidis, KT and Rossello-Mora, R},
title = {Global dominance of Haloquadratum walsbyi by a single genomovar with distinct gene content and viral cohorts from close relatives.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40757481},
issn = {1751-7370},
support = {80NSSC18M0027/NASA/NASA/United States ; PID2021-126114NB-C41//Spanish Ministry of Science, Innovation and Universities/ ; PID2024-158829NB-C42//Spanish Ministry of Science, Innovation and Universities/ ; PID2021-126114NB-C42//Spanish Ministry of Science, Innovation and Universities/ ; PGC2018-096956-B-C41//Spanish Ministry of Science, Innovation and Universities/ ; },
mesh = {Metagenome ; Phylogeny ; Salinity ; *Halobacteriaceae/virology/genetics ; Ecosystem ; *Viruses/genetics/classification/isolation &amp; purification ; },
abstract = {Haloquadratum walsbyi is generally the dominant species in hypersaline ecosystems at salt saturation conditions. Here, we followed the dynamics of its genomovars and associated viruses during recurrent evaporation-dilution disturbances of varying intensities at the mesocosm scale over 813 days. The diversity observed within a single mesocosm was also compared with that in a global-scale inventory of hypersaline environments of thalassohaline origin. The 140 binned metagenome assembled genomes (MAGs) together with the genomes of the (only) two available of H. walsbyi isolates grouped into four highly related (98.25% > Average Nucleotide Identity [ANI] > 99.5%) dominant genomovars (intra-genomovar ANI > 99.5%). In mesocosm experiments, moderate disturbances (i.e. recurrent dilution from saturation to 20% salts) enhanced the abundance of the already-dominant genomovar Hqrw1, resulting in reduced intraspecific diversity. This genomovar also dominated in almost all sites sampled around the globe. In contrast, more intense disturbance (i.e. recurrent dilution from saturation to 13% salts) decreased the abundance of Hqrw1 to lower levels than genomovar Hqrw2 by the end of the incubation, which seems to resist better osmotic changes. Further, our results showed that genomovars were followed by their viral cohorts, who play a significant role in the global dominance of the four H. walsbyi genomovars and their replacement under unfavorable conditions. We propose that the global dominance of H. walsbyi in thalassohaline hypersaline sites is enabled by both the success of Hqrw1 in high but stable salinities and the larger resistance of Hqrw2 to extreme osmotic stress, safeguarding the presence of the species in the system.},
}
@article {pmid40755755,
year = {2025},
author = {Vicente-Valor, J and Tesolato, S and Gómez-Garre, D and Paz-Cabezas, M and Ortega-Hernández, A and Fernández-Hernández, C and de la Serna, S and Domínguez-Serrano, I and Dziakova, J and Rivera, D and Rupérez, FJ and García, A and Torres, A and Iniesta, P},
title = {Identification of clinically relevant profiles in colorectal cancer through integrated analysis of bacterial DNA and metabolome in serum.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1562416},
pmid = {40755755},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/blood/diagnosis/microbiology/metabolism ; Male ; Female ; Middle Aged ; *Metabolome ; *DNA, Bacterial/blood/genetics ; Aged ; Cross-Sectional Studies ; *Biomarkers, Tumor/blood ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome ; Metabolomics/methods ; Adult ; Bacteria/genetics ; },
abstract = {INTRODUCTION: There is increasing evidence demonstrating the relationship between microbiota and colorectal cancer. Several studies have been published analyzing microbiota in tissues and feces from cancer patients; however, there are only a few publications investigating the clinical utility of serum microbiome from colorectal cancer patients. Our aim was to advance in the search for serum biomarkers for the diagnosis of colorectal cancer.<br><br>METHODS: We conducted a cross-sectional study assessing bacterial DNA and metabolomic profiles in 64 serum samples from subjects affected by colorectal cancer and controls. A metagenomic analysis of the bacterial 16S rRNA gene in serum was established, and serum metabolites were detected through an untargeted metabolic study based on Gas Chromatography-Quadruple Time-Of-Flight Mass Spectrometry with accurate mass.<br><br>RESULTS AND DISCUSSION: After integrating the data resulting from the bioinformatics and statistical analyses, we obtained different profiles in colorectal cancer population and controls, regardless of the subjects' age, gender and body mass index. Serum levels of Firmicutes and threonic acid were the most relevant characteristics that could help differentiate both groups, achieving an excellent predictive accuracy in this discovery cohort (area under the ROC curve = 0.95). Although these results should be validated in other cohorts through multicenter studies, we consider that our data could be relevant and applicable to the early diagnosis of colorectal cancer.},
}
@article {pmid40755247,
year = {2025},
author = {Nadimpalli, ML and Sehgal, N and Rojas-Salvatierra, L and Gilman, RH and Earl, AM and Worby, CJ and Schwab, M and Pickering, AJ and Pajuelo, MJ},
title = {Role of the gut microbiome in frequent gut colonization with extended-spectrum β lactamase-producing Enterobacterales among Peruvian children.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2541029},
pmid = {40755247},
issn = {1949-0984},
support = {KL2 TR002545/TR/NCATS NIH HHS/United States ; R01 AI108695/AI/NIAID NIH HHS/United States ; T32 ES012870/ES/NIEHS NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Peru/epidemiology ; *beta-Lactamases/metabolism/genetics ; Infant ; Feces/microbiology ; Male ; *Enterobacteriaceae/genetics/enzymology/isolation &amp; purification/classification ; Female ; Child, Preschool ; *Enterobacteriaceae Infections/microbiology/epidemiology ; Metagenomics ; },
abstract = {Gut colonization with extended-spectrum beta lactamase-producing Enterobacterales (ESBL-E) is increasingly common among children in low- and middle-income countries. Some children nevertheless remain never or rarely colonized during early life. Understanding how this protection is conferred could be helpful for designing future interventions to protect children's health. Here, we investigated whether differences in gut microbiome development could underlie differential susceptibility to ESBL-E gut colonization over time among children in peri-urban Lima. Weekly stool and daily surveys were collected from 345 children < 3 years old during a 2016-19 study of enteric infections. A subset of children (n = 12) was rarely gut-colonized with ESBL-E from 1-16 months of age. We performed short-read metagenomic sequencing of stool collected at 3, 6, 7, 9, 12, and 16 months from these children and a random subset of 42 frequently colonized children, and characterized differences in their exposures and gut microbiomes. No differences in gut taxa or functional pathways were identified over time, though children harbored differentially abundant taxa, more unique E. coli strains, and a higher abundance of blaCTX-M gene copies at ESBL-E-positive versus negative timepoints. Differing patterns of ESBL-E colonization over time among children in peri-urban Lima do not appear to be related to differences in gut microbiome development.},
}
@article {pmid40755225,
year = {2025},
author = {Pan, Z and Walsh, CJ and Feehily, C and Nori, SRC and McAuliffe, FM and Cotter, PD and MacSharry, J and van Sinderen, D},
title = {Breastfeeding and the milk resistome shape the establishment and transmission of antibiotic resistance genes in the infant gut microbiome.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2541033},
pmid = {40755225},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Breast Feeding ; *Milk, Human/microbiology ; Infant ; Female ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; },
abstract = {The infant resistome, the collection of antimicrobial resistance genes (ARGs) of newborns, is critical for gut microbiota establishment. Using metagenomic sequencing data, we analyzed various 1-week and 1-month postpartum samples to study infant resistome establishment, ARG transmission, and its impact on functional redundancy of the microbiota. A total of 431 samples were analyzed; infant stools (1-week, n = 119; 1-month, n = 119), maternal stools (1-month postpartum, n = 120), and breastmilk (1-month postpartum, n = 73). Breastfeeding correlated with increased functional redundancy and altered bacterial-ARG co-occurrence networks in the infant resistome. Escherichia coli dominated early resistome dynamics with a higher abundance correlating with reduced functional redundancy. Bifidobacterium longum exhibited a consistent negative association with 21 ARGs at one-month in breastfed infants, while four negative relationships between ARGs and Bifidobacterium bifidum were observed in formula-fed infants. ARG transmission via breastmilk appears to be gene-specific, with the quinolone resistance gene sdrM likely transmitted under maternal antibiotic use. Delivery mode modulated the microbial environment in ways that interact with resistome structure and changing functional redundancy, particularly through genera like Staphylococcus and Streptococcus. These findings highlight the role of early feeding practices in resistome development and propose functional redundancy as a key ecological framework for understanding infant gut resistome dynamics.},
}
@article {pmid40755083,
year = {2025},
author = {Koseki, Y and Takeshima, H and Yoneda, R and Katayanagi, K and Ito, G and Yamanaka, H},
title = {gmmDenoise: A New Method and R Package for High-Confidence Sequence Variant Filtering in Environmental DNA Amplicon Analysis.},
journal = {Molecular ecology resources},
volume = {25},
number = {8},
pages = {e70023},
pmid = {40755083},
issn = {1755-0998},
support = {JP21K12329//Japan Society for the Promotion of Science/ ; JP22K14908//Japan Society for the Promotion of Science/ ; JP25K02038//Japan Society for the Promotion of Science/ ; },
mesh = {*DNA, Environmental/genetics ; *DNA Barcoding, Taxonomic/methods ; *Computational Biology/methods ; *Genetic Variation ; *Metagenomics/methods ; *Software ; Sequence Analysis, DNA/methods ; },
abstract = {Assessing and monitoring genetic diversity is vital for understanding the ecology and evolution of natural populations but is often challenging in animal and plant species due to technically and physically demanding tissue sampling. Although environmental DNA (eDNA) metabarcoding is a promising alternative to the traditional population genetic monitoring based on biological samples, its practical application remains challenging due to spurious sequences present in the amplicon data, even after data processing with the existing sequence filtering and denoising (error correction) methods. Here we developed a novel amplicon filtering approach that can effectively eliminate such spurious amplicon sequence variants (ASVs) in eDNA metabarcoding data. A simple simulation of eDNA metabarcoding processes was performed to understand the patterns of read count (abundance) distributions of true ASVs and their polymerase chain reaction (PCR)-generated artefacts (i.e., false-positive ASVs). Based on the simulation results, the approach was developed to estimate the abundance distributions of true and false-positive ASVs using Gaussian mixture models and to determine a statistically based threshold between them. The developed approach was implemented as an R package, gmmDenoise and evaluated using single-species metabarcoding datasets in which all or some true ASVs (i.e., haplotypes) were known. Example analyses using community (multi-species) metabarcoding datasets were also performed to demonstrate how gmmDenoise can be used to derive reliable intraspecific diversity estimates and population genetic inferences from noisy amplicon sequencing data. The gmmDenoise package is freely available in the GitHub repository (https://github.com/YSKoseki/gmmDenoise).},
}
@article {pmid40753386,
year = {2025},
author = {AlHilli, MM and Sangwan, N and Myers, A and Tewari, S and Lindner, DJ and Cresci, GAM and Reizes, O},
title = {The effects of dietary fat on gut microbial composition and function in a mouse model of ovarian cancer.},
journal = {Journal of ovarian research},
volume = {18},
number = {1},
pages = {174},
pmid = {40753386},
issn = {1757-2215},
support = {K12 CA076917/CA/NCI NIH HHS/United States ; K12CA076917//NIH K12CA076917 Clinical Oncology Training Program/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/drug effects ; *Ovarian Neoplasms/microbiology/pathology ; Mice ; Disease Models, Animal ; Humans ; *Dietary Fats/pharmacology ; Diet, Ketogenic ; Cell Line, Tumor ; Mice, Inbred C57BL ; Diet, High-Fat ; },
abstract = {OBJECTIVES: The gut microbiome (GM) is pivotal in regulating inflammation, immune responses, and cancer progression. This study investigates the effects of a ketogenic diet (KD) and a high-fat/low-carbohydrate (HF/LC) diet on GM alterations and tumor growth in a syngeneic mouse model of high-grade serous ovarian cancer (EOC).<br><br>METHODS: Thirty female C57BL/6&#xa0;J mice injected with KPCA cells were randomized into KD, HF/LC, and low-fat/high-carbohydrate (LF/HC) diet groups. Tumor growth was monitored with live, in vivo imaging. Stool samples were collected at the time of euthanasia and analyzed by 16SrRNA sequencing and shotgun metagenomic sequencing was performed to identify differential microbial taxonomic composition and metabolic function.<br><br>RESULTS: Our findings revealed that KD and HF/LC diets significantly accelerated EOC tumor growth compared to the LF/HC diet in a xenograft model. GM diversity was markedly reduced in KD and HF/LC-fed mice, correlating with increased tumor growth, whereas LF/HC-fed mice showed higher GM diversity. Metagenomic analyses identified distinct alterations in microbial taxa including Bacteroides, Lachnospiracae bacterium, Bacterium_D16_50, and Enterococcus faecalis predominantly abundant in HF/LC-fed mice, Dubsiella_newyorkensis predominantly abundant in LF/HC-fed, and KD fed mice showing a higher abundance of Akkermansia and Bacteroides. Functional pathways across diet groups indicated polyamine biosynthesis and fatty acid oxidation pathways were enriched in HF/LC-fed mice.<br><br>CONCLUSIONS: These results highlight the intricate relationship between diet andthe gut microbiome in promoting EOC growth. The potential role of dietary interventions in cancer prevention and treatment warrants further investigation.},
}
@article {pmid40753152,
year = {2025},
author = {Jiang, W and Li, Y and Yang, J and Tan, X and Tian, R and Ma, G and Wu, J and Zhang, J and Huang, Y and Liu, P and Yuan, M and Song, X and Luo, L and Zhou, X and Zuo, H and Wong, ML and Licino, J and Zheng, P},
title = {Chronic stress in mice: how gut bacteria influence gene activity in key brain neurons.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {262},
pmid = {40753152},
issn = {2158-3188},
support = {2024MD754023//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology/genetics ; Mice ; *Stress, Psychological/microbiology/metabolism/genetics ; *Neurons/metabolism ; *Hypothalamus/metabolism ; Male ; Disease Models, Animal ; Transcriptome ; RNA, Ribosomal, 16S/genetics ; *Major Depressive Disorder/microbiology ; Mice, Inbred C57BL ; },
abstract = {Major depressive disorder (MDD) is a serious mental disorder. Increasing evidence suggests that changes of gut microbiota are involved in pathogenesis of depression, yet the underlying mechanisms remains unknown. Here, chronic unpredictable mild stress (CUMS) mice model was constructed to mimic depression. We characterized the microbial composition and function of control, bedding exchange, and CUMS mice through 16S rRNA gene and metagenomic sequencing. Additionally, single-nucleus RNA sequencing (snRNA-seq) was used to compare the transcriptomic changes in the hypothalamus of these three groups. We found that replacing the bedding of CUMS mice with that of control mice could reverse the depressive-like behaviors. The microbial signatures of bedding exchange group trended towards the control group at the genus level. The abundance of g_norank_f_Muribaculaceae significantly increased in the bedding exchange group compared to CUMS group. Meanwhile, we found that the CUMS mice were characterized by cell-specific transcriptomic changes in hypothalamus. Notably, the transcriptomes of excitatory neurons in the hypothalamus were mainly affected, and these changes could be effectively reversed by bedding exchange treatment. The gene modules analysis revealed that the gut microbiota mainly modulated glyoxylate and dicarboxylate metabolism as well as arginine biosynthesis in hypothalamic excitatory neurons. Our findings provide new insights into the pathogenesis of depression.},
}
@article {pmid40752853,
year = {2025},
author = {Santiwijai, M and Taoka, Y},
title = {Effect of Bacillus subtilis and fungal enzymes on immune responses and gut microbiota of masu salmon (Oncorhynchus masou masou).},
journal = {Developmental and comparative immunology},
volume = {170},
number = {},
pages = {105424},
doi = {10.1016/j.dci.2025.105424},
pmid = {40752853},
issn = {1879-0089},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Bacillus subtilis/immunology ; *Probiotics/administration &amp; dosage ; Muramidase/blood/metabolism ; *Salmon/immunology/microbiology ; *Aspergillus ; Fish Proteins/metabolism/genetics ; },
abstract = {The effects of oral administration of probiotics Bacillus subtilis (BS) and Aspergillus sojae-fermented materials (AFM) supplementation on immune responses and the gut microbiome of masu salmon Oncorhynchus masou masou were evaluated. Masu salmon (44.07 ± 7.1 g) were individually raised on a commercial diet without supplementation (control group), with B. subtilis strain DB9011 at 1.0 × 10[6] cfu/g-feed (BS group), and with A. sojae-fermented materials supplementation at 0.2 % (AFM group) for 24 days. Lysozyme activity in fish serum was determined using turbidimetric assays. Immune-related gene expression and gut microbiota were analyzed through real-time PCR and metagenomics analysis with a next-generation sequencer, respectively. Both the BS and AFM groups showed higher lysozyme activity but lower serum protein concentrations compared to the control group without significant different. The gut bacterial composition in the BS and AFM groups was dramatically different compared to that in the control group. The alpha diversity of the BS group showed significantly greater richness in terms of Chao1, faith_pb, and shannon_entropy. Conversely, the alpha diversity of the AFM group showed significantly greater richness only on faith_pb. The expression of immune-related genes such as TNF-α and IFN-γ was upregulated in the treatment group compared to the control group. IL1-β was upregulated in the AFM group. Regarding IL1-β, no differences were observed between the control and BS group. Thus, results indicated that oral administration of the BS and AFM modify gut microbiota and stimulated the expression of immune-gene expression.},
}
@article {pmid40752224,
year = {2025},
author = {Carrillo-Barragán, P and Cassola, GE and Burkhardt-Holm, P},
title = {Microbial colonisation of polyethylene in offshore marine environments: Insights from the Southern and South Atlantic Oceans.},
journal = {The Science of the total environment},
volume = {996},
number = {},
pages = {180189},
doi = {10.1016/j.scitotenv.2025.180189},
pmid = {40752224},
issn = {1879-1026},
mesh = {*Polyethylene/analysis/metabolism ; Atlantic Ocean ; RNA, Ribosomal, 16S/analysis ; Seawater/microbiology ; *Water Pollutants, Chemical/analysis/metabolism ; *Microbiota ; Bacteria ; },
abstract = {Plastic debris is a pervasive environmental pollutant, with polyethylene (PE) among the most abundant floating polymers in marine environments. While microbial colonisation of marine plastics has been extensively documented, most studies focus on coastal waters in the Northern Hemisphere, leaving colonisation dynamics in remote Southern Hemisphere regions poorly understood. Here, we investigate early microbial colonisation of PE films incubated during two oceanographic transects across the Southern Ocean and South Atlantic Ocean. Using 16S rRNA gene amplicon sequencing and shotgun metagenomics, we assessed how geographic location, incubation regime (aquarium vs ship deck), and environmental factors (UV exposure, temperature, and salinity) shape microbial community structure and functional potential. Community composition was primarily influenced by transect location and incubation conditions, rather than material type. Dominant taxa included Cyanobacteria, Pseudomonadota, and Bacteroidota, taxa often associated with phototrophy, hydrocarbon degradation, and early surface colonisation. Functional analyses revealed enrichment in pathways related to biofilm formation, hydrocarbon degradation, lipid oxidation, and iron metabolism. These findings highlight how environmental conditions shape early plastisphere assembly and metabolic capabilities in understudied oceanic regions of the Southern Hemisphere.},
}
@article {pmid40752173,
year = {2025},
author = {Li, WJ and Ghaly, TM and Tetu, SG and Huang, FY and Li, HZ and Li, H},
title = {Effects of agricultural inputs on soil virome-associated antibiotic resistance and virulence: A focus on manure, microplastic and pesticide.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139380},
doi = {10.1016/j.jhazmat.2025.139380},
pmid = {40752173},
issn = {1873-3336},
mesh = {*Manure ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Pesticides/toxicity ; *Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Virome/drug effects ; Agriculture ; Virulence/genetics ; Virulence Factors/genetics ; Bacteria/genetics ; Soil/chemistry ; },
abstract = {Soil viruses are increasingly recognized as crucial mediators of horizontal gene transfer, yet their role in disseminating antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) under agricultural disturbances remains poorly understood. Here, we characterized the viromes and associated ARGs and VFGs in agricultural soils treated with low- and high-dose manures, microplastics, and pesticides. Using metagenomic sequencing coupled with advanced viral identification tools, we found that manure fertilization markedly altered viral community composition and increased viral diversity. Manure also enhanced the abundance of ARGs and VFGs in viromes by 2.0-9.8-fold and 2.0-8.1-fold, respectively, while microplastics and pesticides had limited impacts. Additionally, gene pathways related to human diseases and environmental adaptation were enriched in soil viromes treated with manures and high-dose pesticides. Virus-host prediction revealed that Actinomycetia dominated bacterial hosts of both ARG- and VFG-carrying viruses, with some VFG-carrying viruses linked to potential human pathogens, e.g., Escherichia albertii and Klebsiella pneumoniae. Co-occurrence network analysis indicated that these disturbances strengthened connections between bacteria, viruses, and ARGs (or VFGs). Our study provides a comprehensive profile of viromes and associated risks in agricultural soil under three disturbances, highlighting the role of viruses in spread of antibiotic resistance and pathogenic risks in agricultural soil.},
}
@article {pmid40752126,
year = {2025},
author = {Hong, W and Yang, S and Shu, W and Price, G and Song, L},
title = {Spatiotemporal dynamics of multi-kingdom microbiome interactions drive CNPS cycling in landfills.},
journal = {Waste management (New York, N.Y.)},
volume = {206},
number = {},
pages = {115048},
doi = {10.1016/j.wasman.2025.115048},
pmid = {40752126},
issn = {1879-2456},
mesh = {*Microbiota ; *Waste Disposal Facilities ; Phosphorus/metabolism/analysis ; Soil Microbiology ; Nitrogen/metabolism/analysis ; *Refuse Disposal ; Bacteria/metabolism ; Carbon/metabolism/analysis ; Solid Waste/analysis ; Sulfur/metabolism ; },
abstract = {Landfill ecosystems represent significant terrestrial carbon sinks, where municipal solid waste (MSW) undergoes decomposition and transformation through biochemical reactions mediated by multi-kingdom microbiome. However, the spatial and temporal characterization of microbial interactions and collaboration within these multi-kingdom microbiomes remain largely unknown. In this study, we reveal the hierarchical and collaborative mechanisms by which multi-kingdom microbiomes drive carbon, nitrogen, phosphorus, and sulfur cycling across a 30-meter landfilling depth, corresponding to a landfilling age of 1 to 4 years. Through integration of metagenomics and network analyses, we elucidated vertical succession patterns in microbial community structure and function. The surface layer (1-2 years) was centered on bacterial-dominated primary metabolism, with Enterococcus aquimarinus and Brevundimonas bullata inferred to mediate metabolic coupling through fermentation, nitrogen fixation andphosphorus solubilization. Concurrently, phage-driven host lysis may contribute to the suppression of acidification. In the middle layer (2-3 years), co-occurrence patterns between archaea and fungi suggest mutualistic interaction supporting methanogenesis, wherein fungi such as Anaeromyces robustus would supply key substrates for methanogens such as Methanofollis ethanolicus. In the bottom layer (3-4 years), fungi, bacteria, and viruses collaborate under nutrient-limited conditions, with phages employing a "kill-the-winner" approach to sustain ecosystem function and stability. Collectively, our findings indicate that key microbial connectors across kingdoms contribute to elemental cycling through cross-kingdom interaction, including substrate exchange and nutrient supply. This study advances our understanding of multi-kingdom microbial dynamics during MSW decomposition and offers a conceptual framework for enhancing biogeochemical cycling efficiency within landfill ecosystems.},
}
@article {pmid40751372,
year = {2025},
author = {Bryant, JA and Straub, TJ and Pardi, DS and Litcofsky, KD and Kelly, CR and Chafee, ME and Cohen, SH and Khanna, S and Berenson, CS and Wortman, J and Sims, M and Ford, CB and Lombardo, MJ and McGovern, BH and von Moltke, L and Kraft, CS and Henn, MR and Hasson, BR},
title = {Comparability of Gastrointestinal Microbiome and Bile Acid Profiles in Patients With First or Multiply Recurrent Clostridioides difficile Infection.},
journal = {The Journal of infectious diseases},
volume = {232},
number = {5},
pages = {e733-e740},
pmid = {40751372},
issn = {1537-6613},
support = {//Seres Therapeutics/ ; },
mesh = {Humans ; *Bile Acids and Salts/analysis/metabolism ; *Gastrointestinal Microbiome ; *Clostridium Infections/microbiology/drug therapy/therapy ; Male ; Female ; Feces/microbiology/chemistry ; Middle Aged ; *Clostridioides difficile ; Aged ; Recurrence ; Anti-Bacterial Agents/therapeutic use ; Adult ; Fecal Microbiota Transplantation ; },
abstract = {BACKGROUND: Clostridioides difficile infection (CDI) treatment guidelines suggest varied approaches for patients with first (frCDI) or multiply recurrent CDI (mrCDI). Low microbial diversity, elevated primary bile acids (BA), and low secondary BA concentrations favor germination of C. difficile spores into toxin-producing bacteria and are believed to increase rCDI risk. Greater understanding of the gastrointestinal (GI) microbiome in rCDI may inform management of the disease. We describe a post hoc comparison of GI microbiome and bile acid profiles between patients with frCDI and mrCDI in a Phase 3 open-label trial, ECOSPOR IV, of fecal microbiota spores, live-brpk (VOWST®; VOS, formerly SER-109), an orally-administered live microbiome therapeutic.<br><br>METHODS: Patients received VOS following symptom resolution after standard-of-care antibiotics. Pretreatment baseline (within 3 days following antibiotic completion) and Week 1 post-dosing stool samples were collected for whole metagenomic sequencing and metabolomics. Diversity was calculated from MetaPhlAn2 species profiles. Concentrations of primary and secondary BAs were measured via targeted LC-MS/MS.<br><br>RESULTS: rCDI rates through Week 8 were similarly low in both frCDI and mrCDI patients (6.5% versus 9.7%, respectively). Baseline microbial diversity was similarly low between frCDI and mrCDI subgroups (P > .05). Diversity and secondary BA concentrations increased in both subgroups, whereas primary BA concentrations declined following VOS dosing, leading to few differences between subgroups at Week 1.<br><br>CONCLUSIONS: These data suggest commonalities in microbiome disruption in patients with frCDI and mrCDI that contribute to recurrence and suggest that antibiotics followed by a live microbiome therapy may be an optimal treatment strategy for rCDI, regardless of number of prior CDI recurrences.},
}
@article {pmid40751224,
year = {2025},
author = {Reinoso-Peláez, EL and Saura, M and González, C and Ramón, M and Calvo, JH and Serrano, M},
title = {The influence of vaginal microbiota on ewe fertility: a metagenomic and functional genomic approach.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {177},
pmid = {40751224},
issn = {2049-2618},
support = {RTI-2018-096487-R-C33//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; },
mesh = {Female ; Animals ; *Vagina/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Sheep/microbiology ; *Fertility ; *Bacteria/classification/genetics/isolation &amp; purification ; Pregnancy ; Genomics ; Metagenome ; },
abstract = {BACKGROUND: Despite advancements in artificial insemination, sheep fertility rates remain suboptimal. Recent studies in other species highlight the critical role of reproductive microbiota in influencing fertility outcomes. This research explores the relationship between ovine vaginal microbiota, associated functional pathways, and fertility using advanced nanopore long-reading metagenomic sequencing on 297 ewes from three Spanish breeds across four herds. The study aimed to describe a core vaginal microbiota, analyse the complex interactions with herd, breed, age, and parity factors, and identify taxa and genes associated with reproductive success by artificial insemination.<br><br>RESULTS: The study identified Staphylococcus, Escherichia, and Histophilus as the most abundant genera. Microbial communities varied considerably between breeds and herds, with high predictive accuracy (>&#x2009;90%) in classification models. Differential abundance analysis revealed that the genera Histophilus, Fusobacterium, Bacteroides, Campylobacter, Streptobacillus, Gemella, Peptoniphilus, Helococcus, Treponema, Tissierella, and Phocaeicola were more abundant in non-pregnant ewes. Some of these taxa were also associated with four COG entries and one KEGG orthologue significantly linked to non-pregnancy, primarily involving carbohydrate metabolism, defence mechanisms, and structural resilience. Age and parity were also associated with microbiota composition, particularly in ewes older than five&#xa0;years or with more than three parturitions, suggesting that cumulative physiological changes may contribute to microbial shifts over time.<br><br>CONCLUSIONS: The ewe's vaginal microbiome appears to be&#xa0;mainly influenced by both herd and breed, though distinguishing genetic from environmental factors is challenging within our study design. While the overall microbiota showed a subtle effect on pregnancy, certain genera had a significant negative impact, likely due to pathogenic or inflammatory properties that disrupt reproductive health. The metagenomic approach used here enabled not only comprehensive taxonomic classification but also detailed functional analysis, providing deeper insights into the microbiome's role in reproductive outcomes. Video Abstract.},
}
@article {pmid40750823,
year = {2025},
author = {Adebayo, AA and Enagbonma, BJ and Babalola, OO},
title = {Comparative metagenomics on community structure and diversity of rhizomicrobiome associated with monoculture and soybean precedent carrot.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28161},
pmid = {40750823},
issn = {2045-2322},
mesh = {*Daucus carota/microbiology/growth &amp; development ; *Glycine max/microbiology/growth &amp; development ; Rhizosphere ; *Metagenomics/methods ; Soil Microbiology ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Plant Roots/microbiology ; Biodiversity ; Agriculture/methods ; },
abstract = {Several studies have explored the impact of cropping systems, including monoculture and crop rotation, on the plant rhizosphere - an essential dynamic in designing strategies for optimizing soil health and crop productivity. It remains largely unknown how these agricultural practices drive the diversity and community structure of the microbiome in the carrot rhizosphere. Thus, this study aims to profile the core rhizo-microbiome of carrots grown under a monoculture system and those grown after soybean cultivation. The microbial DNA extracted from 12 soil samples collected from monoculture carrot rhizosphere (MCR), soybean-precedent carrot rhizosphere (SCR), and uncultivated land (bulk soils) (BS) were analyzed via shotgun metagenomics sequencing. Findings show that bacterial phyla were the most dominant taxa across the sampling points. Principal Component Analysis (PCA) revealed that Pseudomonadota, Bacillota, and Actinomycetota are significantly enriched in soybean-precedent carrot rhizosphere, monoculture carrot rhizosphere, and bulk soil, respectively. Furthermore, genera Bradyrhizobium and Agromyces were significantly enriched, and Rhodococcus was exclusively present in soybean-precedent carrot rhizosphere. Alpha and Beta diversity analyses indicated that the microbial community composition was unique within and between the sampling sites (genus level). Redundancy Analysis (RDA) demonstrated that soil properties like silt (contributing 84.2%), total nitrogen (contributing 83.2%), organic carbon (contributing 81.0%), and sand texture (contributing 75.8%) explained the variance in microbiome composition. This study provides fundamental insight into how cropping systems influence carrot rhizo-microbiome. Crop rotation practice with soybeans was found to increase microbial composition and diversity in carrot plantations.},
}
@article {pmid40749888,
year = {2025},
author = {Carella, F and Correggia, M and Cordone, A and Iacovino, O and Maresca, F and Villari, G and Roque, A and Vico, G},
title = {Bald disease in a natural population of the purple sea urchin Paracentrotus lividus of the Mediterranean Sea: From spines to tissues.},
journal = {Journal of invertebrate pathology},
volume = {213},
number = {},
pages = {108415},
doi = {10.1016/j.jip.2025.108415},
pmid = {40749888},
issn = {1096-0805},
mesh = {Animals ; *Paracentrotus/microbiology ; Mediterranean Sea ; Microbiota ; },
abstract = {Recently, unusual mortality outbreaks have been reported in the echinoderm populations over broad geographic regions. The present work used different diagnostic approaches to unravel the Bald Sea Urchin Disease (BSUD) causes in a natural population of Paracentrotus lividus from the Gulf of Naples sampled in 2021. Symptomatic individuals displayed the typical signs such as test discoloration and ulceration, loss of spines and pedicellariae and visceral hyperpigmentation. Scanning electron microscopy of diseased individuals (stage 2 and stage 3) revealed a bare exoskeleton with multiplying bacteria penetrating the damaged test, and histopathology revealed inflammatory lesions and phagocytosis only in stages 2 and 3, with Gram negative and positive bacteria at stage 3. Metagenomics revealed an increase in DNA virus and Proteobacteria during disease progression. Microbial community analyses failed to reveal a single putative pathogen associated with symptoms, but microbiome analysis showed higher diversity in asymptomatic individuals compared to the symptomatic. Different Vibrio spp. belonging to the Splendidus clade were also isolated, with V. crassostreae as the most represented in advanced stages of disease. We cannot confirm that the observed microorganisms were associated with tissue damage and their contribution to the disease outcome remains unclear as they could be just opportunistic in the lesions. This preliminary study on a wild population highlights the importance of morphological analysis (histopathology and SEM) coupled with microbiome and metagenome analyses in sea urchin disease investigations. Moreover, we suggest also performing transmission electron microscopy (TEM), experimental challenges and in situ hybridization methods (ISH) to provide morphological evidence of potential infective agents. Future studies should also include histopathology of the test.},
}
@article {pmid40749752,
year = {2025},
author = {Von Tönnemann Pilati, G and da Silva Grisard, HB and Dorighello, RC and Filho, VB and Dahmer, M and Savi, BP and Elois, MA and Salles, GBC and Muniz, EC and Fongaro, G},
title = {Protocol for virome characterization in low-volume respiratory samples from broiler chickens.},
journal = {Journal of virological methods},
volume = {338},
number = {},
pages = {115233},
doi = {10.1016/j.jviromet.2025.115233},
pmid = {40749752},
issn = {1879-0984},
mesh = {Animals ; *Chickens/virology ; *Virome ; *Metagenomics/methods ; Brazil ; *Poultry Diseases/virology ; *Viruses/isolation &amp; purification/genetics/classification ; Ultracentrifugation ; Trachea/virology ; Genome, Viral ; },
abstract = {The poultry industry is a major global source of animal protein but remains vulnerable to immunosuppressive viral infections that compromise bird health and productivity. This study evaluated five viral purification methods for metagenomic analysis of respiratory samples from broiler chickens in Santa Catarina, Brazil. Tracheal swabs from ten flocks (one per farm) were pooled, and 50 µL of a herpes simplex virus type 2 (HSV-2) and murine norovirus (MNV-1) mix was added as an internal positive control. The sample was centrifuged (2000 × g for 30 min), filtered (0.45 μm), and subjected to five purification methods. The filtrate was subjected to five different purification methods. Method 1 (M1) was based on nucleic acid direct genomic extraction of the supernatant. Method 2 (M2): a pre-treatment with DNase was used, followed by genomic extraction. Method 3 (M3) was performed using ultracentrifugation at 100,000 × g / 3 h at 4 °C, followed by genomic extraction. In Method 4 (M4), the sample was submitted to ultracentrifugation on a 25 % sucrose cushion at 100,000 × g / 3 h at 4 °C, followed by genomic extraction. Finally, in Method 5 (M5), the sample was ultracentrifuged on a 25 % sucrose cushion at 100,000 × g / 3 h at 4 °C, and the pellet was treated with DNase followed by genomic extraction. All genomic extractions were performed using the RNeasy Mini kit. Samples were reverse transcribed into cDNA and sequenced by the MiSeq Sequencing System. The efficiency of M1-5 was evaluated based on the yield of viral genetic material. All methodologies employed demonstrated varying rates of genome recovery from viruses identified in poultry production. Notable viruses included avian gyrovirus 2 (AGV-2), avian leukosis virus (ALV), and the avian endogenous retrovirus EAV-HP found within chicken genomes. However, M5 showed the best performance, recovering 9.32 % of viral sequences, 44 % of HSV-2, as internal viral control, 32 % of EAV-HP, 8 % of ALV, and 7 % of AGV-2. In conclusion, this study successfully evaluated and compared five distinct viral purification methods, contributing significantly to the characterization of avian viromes and enhancing comprehension of viral ecology.},
}
@article {pmid40749656,
year = {2025},
author = {Asghar, MU and Zhai, Y and Liu, T and Fan, P and Ain, NU and Zaidi, AH and Tariq, M and Mainar-Jaime, RC and Jeong, KC},
title = {A metagenomics-based approach to understanding the transmission of healthcare-associated antimicrobial resistance in Pakistan.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139384},
doi = {10.1016/j.jhazmat.2025.139384},
pmid = {40749656},
issn = {1873-3336},
mesh = {Pakistan ; *Metagenomics ; *Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Humans ; Bacteria/genetics/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Cross Infection/microbiology/transmission ; Microbiota ; },
abstract = {Hospital environments are critical yet underexamined reservoirs for hazardous antimicrobial resistance (AMR), particularly in lower-middle-income countries (LMICs) where resource constraints often hinder comprehensive surveillance. In this study, we employed 16S rRNA gene sequencing and shotgun metagenomics to characterize the microbiome, resistome, and potential transmission routes across five clinical environments within a hospital in Pakistan: the intensive care unit (ICU), surgical ward (SW), cardiac surgery ward (CSW), cardiac ward (CW), and operating theater (OT). Microbial community analysis revealed compositional similarities among the ICU, SW, and OT, with the ICU emerging as a primary source of microbial dissemination. Species-level profiling identified hospital-associated pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, and Enterobacter cloacae, and metagenome-assembled genome (MAG) analysis enabled the linkage of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) to specific bacterial hosts. ARGs and MGEs displayed setting-specific patterns, with the SW harboring the highest abundance of ARGs, particularly those conferring resistance to β-lactams and biocides. Insertion sequences were the most prevalent MGEs and were commonly linked to ARGs, indicating potential horizontal gene transfer. Co-occurrence network analysis identified Staphylococcus, Enterococcus, and Escherichia as central hub taxa within the microbial communities of the ICU, SW, and OT, indicating their critical roles in potential ARG transmission. These findings provide critical insights into the environmental transmission dynamics of AMR in LMIC healthcare settings and underscore the urgent need for metagenomics-informed infection control strategies.},
}
@article {pmid40749338,
year = {2025},
author = {Le, MH and Lee, HJ and Justine, EE and Tran, THM and Kim, YJ},
title = {Bacillus velezensis GV1 polysaccharides enhance immune function in cyclophosphamide-induced immunosuppressed mice via gut microbiota modulation and metabolic pathway regulation.},
journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie},
volume = {190},
number = {},
pages = {118387},
doi = {10.1016/j.biopha.2025.118387},
pmid = {40749338},
issn = {1950-6007},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Cyclophosphamide ; *Bacillus/chemistry ; *Polysaccharides/pharmacology/isolation &amp; purification ; Mice ; *Metabolic Networks and Pathways/drug effects ; Male ; Cytokines/metabolism ; Mice, Inbred BALB C ; Colon/drug effects/pathology/immunology ; Immunosuppressive Agents ; *Immunocompromised Host/drug effects ; },
abstract = {In this study, we investigated the immunomodulatory effects of Bacillus velezensis GV1 polysaccharides (BPS) on gut microbial regulation in a cyclophosphamide (CTX)-induced immunosuppressed mouse model. BPS treatment significantly restored immune function, as evidenced by improvements in spleen and thymus indices and increased cytokine expression levels, including IL-6, TNF-α, IFN-γ, and IL-2. Additionally, BPS administration effectively alleviated the CTX-induced histopathological damage to the colon, enhanced tissue repair, and maintained epithelial integrity. The beneficial effects of BPS were associated with the selective modulation of the gut microbiota, and notably enhanced beneficial bacterial taxa, including PAC001112_g, PAC001074_g (Muribaculaceae), Monoglobus, PAC001500_g (Peptococcaceae), and PAC002153_g (Lachnospiraceae). Metagenomic analysis further revealed key metabolic pathways affected by BPS, such as folate biosynthesis, fructose and mannose metabolism, and pentose and glucuronate interconversion, involving essential enzymes such as xylulokinase, triosephosphate isomerase (TIM), and fructan beta-fructosidase. Collectively, these findings indicate that BPS effectively alleviates CTX-induced immunosuppression by modulating gut microbiota composition, underscoring its potential as a valuable supplementary or functional agent with immune-enhancing effects.},
}
@article {pmid40748897,
year = {2025},
author = {Ségurel, L and Ulaganathan, TS and Mathieu, S and Loiodice, M and Poulet, L and Drouillard, S and Cygler, M and Helbert, W},
title = {The porphyran degradation system is complete, phylogenetically and geographically diverse across the gut microbiota of East Asian populations.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0329457},
pmid = {40748897},
issn = {1932-6203},
mesh = {Humans ; Asia, Eastern/ethnology ; Bacterial Proteins/genetics/metabolism ; *Bacteroides/enzymology/genetics ; *East Asian People/statistics &amp; numerical data ; *Gastrointestinal Microbiome/genetics ; *Gene Transfer, Horizontal ; Genetic Variation ; Glycoside Hydrolases/genetics/metabolism ; Metagenome ; Phylogeny ; *Polysaccharides, Bacterial/metabolism ; *Porphyra/microbiology ; Sepharose/analogs &amp; derivatives ; },
abstract = {The human gut microbiota can acquire new catabolic functions by integrating genetic material coming from the environment, for example from food-associated bacteria. An illustrative example of that is the acquisition by the human gut microbiota of Asian populations of genes coming from marine bacteria living on the surface of red algae that are incorporated into their diet when eating maki-sushi. To better understand the function and evolution of this set of algal genes corresponding to a polysaccharide utilization locus (PUL) dedicated to the degradation of porphyran, the main polysaccharide of the red algae Porphyra sp., we characterized it biochemically, assessed its genetic diversity and investigated its geographical distribution in large public worldwide datasets. We first demonstrated that both methylated and unmethylated fractions are catabolized without the help of external enzymes. By scanning the genomic data of more than 10,000 cultivated isolates as well as metagenomic data from more than 14,000 worldwide individuals, we found that the porphyran PUL is present in 17 different Phocaeicola/Bacteroides species (including 12 species that were not known to carry it), as well as in two Parabacteroides species and two genera from the Bacillota phylum, highlighting multiple lateral transfers within the gut microbiota. We then analyzed the prevalence of this porphyran PUL across 32 countries and showed that it exists in appreciable frequencies (>1%) only in East Asia (Japan, China, Korea). Finally, we identified three major PUL haplotypes which frequencies significantly differ between these East Asian countries. This geographic structure likely reflects the rate of bacterial horizontal transmission between individuals.},
}
@article {pmid40748490,
year = {2025},
author = {He, T and Wang, Y and Zhao, L and Che, Y and Zhang, L and Zeng, Y and Shen, H and Hao, H and Cao, L},
title = {Integrated Microbiota-Bile Acid Analysis as Potential NonInvasive Biomarkers for Ulcerative Colitis Staging Diagnose.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {39},
number = {15},
pages = {e70859},
doi = {10.1096/fj.202501078R},
pmid = {40748490},
issn = {1530-6860},
support = {2021YFA1301300//the National Key Research and Development Program of China/ ; 2022YFF1100601//the National Key Research and Development Program of China/ ; 82173886//the National Natural Science Foundation of China/ ; 82373886//the National Natural Science Foundation of China/ ; 82404997//the National Natural Science Foundation of China/ ; G20582017001//111 Plan | Overseas Expertise Introduction Project for Discipline Innovation/ ; SKLNMZZ202402//the Project of State Key Laboratory of Natural Medicines, China Pharmaceutical University/ ; },
mesh = {Humans ; *Colitis, Ulcerative/diagnosis/microbiology/metabolism/blood ; *Bile Acids and Salts/metabolism/blood/analysis ; Male ; Biomarkers/metabolism/blood ; Adult ; Female ; Feces/microbiology/chemistry ; Middle Aged ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Clinical staging diagnosis and progression tracking for ulcerative colitis (UC) is as challenging as poor patient compliance with endoscopic biopsy. We perform a study that integrates metabolomic profiling, 16S rRNA, and metagenomic sequencing on serum and fecal samples from 23 active state UC patients, 24 remission state UC patients, and 20 healthy volunteers from China, aiming to explore a non-invasive integrative biochemical index to quantitatively track and monitor pathological activity of UC. Besides the known associations of microbes such as Fusobacterium nucleatum and Clostridium symbiosum with UC, we found several bile acid-transforming species, including 7α-dehydroxygenase and 7α/β-dehydrogenase expressing microbiota, were significantly correlated with UC pathological activity. We identified 2 bacterial gene markers related to secondary bile acid synthesis besides Clostridium scindens that differentiated active and remission stage UC and healthy control microbiomes. Relevantly, reduced serum deoxycholic acid (DCA)/cholic acid (CA) species ratio and increased fecal ursodeoxycholic acid (UDCA)/chenodeoxycholic acid (CDCA) ratio were associated with the pathological activity of UC. Moreover, receiver operating characteristic analysis based on serum/fecal bile acid ratios was much more accurate in the prediction of active and remission stage outcomes. This species-specific temporal change and bile acid dysregulation pattern linked to disease severity indicate that integrated microbiome-bile acid profiles may be implied for disease activity prediction and that targeting microbiome-mediated gut flora and bile acid homeostasis may be implicative of therapy efficacy. These insights will help improve clinical diagnosis and optimize existing medical treatments.},
}
@article {pmid40748195,
year = {2025},
author = {Bai, S and Wang, Z and Guo, Y and Xu, H and Li, J and Peng, X},
title = {Iron is an important influence of volcanic ash input on the evolution of deep-sea ecosystems.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0071525},
pmid = {40748195},
issn = {2165-0497},
mesh = {*Oceans and Seas ; *Biological Evolution ; *Volcanic Eruptions/analysis ; *Iron/metabolism/pharmacology ; *Microbiota/drug effects ; Water Microbiology ; *Seawater/microbiology ; Geologic Sediments/microbiology ; Metagenome ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {UNLABELLED: Volcanoes, originating from deep-seated magmatic activity, serve as crucial conduits connecting Earth's interior and surface. Volcanic eruptions, a primary manifestation of this connection, exert profound influence across Earth's surface systems. Volcanic ash, a significant product of these eruptions, has long been a focal point of Earth science research due to its far-reaching impacts. However, the challenges associated with deep-sea sampling and a relative lack of interdisciplinary collaboration have hindered our understanding of how volcanic ash deposition affects the abyssal environment. Here, leveraging a combined geological and microbiological approach, we investigated sediments within the Kermadec Trench impacted by rhyolitic volcanic ash. Our findings demonstrate that iron availability is the primary driver of microbial community structure in these ash-influenced deep-sea sediments. The mantel test analysis further revealed that four key categories of iron-related functional genes involved in iron acquisition (heme transport, iron transport, and siderophore transport) and iron storage significantly shape the resident microbial communities. Furthermore, metagenomic binning yielded numerous refined metagenome-assembled genomes (MAGs) from these deep-sea sediments, all of which harbored iron-related functional genes. Viral metagenomic analysis suggests that viruses in these sediments do not directly influence abyssal prokaryote-mediated iron cycling through the carriage of iron-related auxiliary genes. Instead, viral lysis of iron-cycling prokaryotes appears to be a key regulatory mechanism. These results provide critical new data and insights into microbial iron cycling in the deep sea under the influence of volcanic ash deposition.<br><br>IMPORTANCE: Volcanic eruptions emit vast amounts of ash, which eventually settle in the deep ocean. This study explores how the deposition of volcanic ash influences deep-sea microbial communities, primarily through iron enrichment. Our findings highlight the pivotal role of iron-related genes in shaping these communities, while viruses may play an indirect role in modulating iron cycling. These insights enhance our understanding of how volcanic activity affects deep-sea ecosystems and biogeochemical cycles. By elucidating the intricate link between volcanic ash, iron availability, and microbial dynamics, this research provides a novel perspective on how geological processes drive life in the deep ocean. Ultimately, this knowledge contributes to a deeper understanding of global nutrient cycles.},
}
@article {pmid40746878,
year = {2025},
author = {Xu, F and Li, W and Zheng, XJ and Hao, Y and Yang, YH and Yang, H and Zhang, S and Cao, WX and Li, XX and Zhang, X and Du, GH and Ji, TF and Wang, JH},
title = {3-O-Acetyl-11-Keto-β-Boswellic Acid Suppresses Colitis-Associated Colorectal Cancer by Inhibiting the NF-Kb Signaling Pathway and Remodeling Gut Microbiota.},
journal = {Oncology research},
volume = {33},
number = {8},
pages = {1969-1989},
pmid = {40746878},
issn = {1555-3906},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; Humans ; *Triterpenes/pharmacology ; *NF-kappa B/metabolism ; Signal Transduction/drug effects ; *Colitis-Associated Neoplasms/drug therapy/pathology/metabolism/microbiology ; Cell Proliferation/drug effects ; Apoptosis/drug effects ; *Colorectal Neoplasms/drug therapy/pathology ; *Colitis/complications/drug therapy ; Disease Models, Animal ; Cell Line, Tumor ; Male ; HCT116 Cells ; },
abstract = {OBJECTIVES: Colorectal cancer (CRC) is one of the most common cancers all over the world. The progression of CRC is associated with inflammation and disruptions in intestinal flora. 3-O-Acetyl-11-keto-β-boswellic acid (AKBA) has been noted for its potent anti-inflammatory properties. However, the effect of AKBA on colon cancer caused by inflammation and its mechanism are not unclear. The study is to explore the effect of AKBA on CRC and its mechanism.<br><br>MATERIALS AND METHODS: Cell proliferation, (5-ethynyl-2[']-deoxyuridine, EdU)-DNA synthesis assay and colony formation were used to assess the effect of AKBA on the proliferation of CRC cells. Flow cytometry was employed to analyze the cell cycle and apoptosis rate of cells treated with AKBA. RNA sequencing was done to explore the underlying mechanisms of AKBA. Western blot was used to assess the expression of key proteins in the nuclear factor kappa-B (NF-&#x3ba;B) signaling pathway after the treatment of AKBA. Real-time quantitative PCR (RT-qPCR), enzyme-linked immunosorbent assay (ELISA), and Meso Scale Discovery (MSD) assays were employed to check the anti-inflammation effects of AKBA on Lipopolysaccharide (LPS)-induced RAW264.7 cells and LPS-induced mouse model. Additionally, the Azoxymethane/Dextran sulfate sodium (AOM/DSS)-induced colitis-associated CRC model was used to evaluate the anti-CRC effect of AKBA. Gut microbiota profiling of fecal samples from CRC mice, both with and without AKBA treatment, was conducted through metagenomic sequencing analysis.<br><br>RESULTS: Our results showed that AKBA reduced the proliferation of HCT116 and SW620 cells, increased apoptosis of cells, and arrested the cell cycle at the G2/M phase. Results from RNA-seq showed that AKBA inhibited CRC by inhibiting the NF-&#x3ba;B signaling pathway and reducing cellular inflammation. Furthermore, AKBA reduced the levels of inflammatory cytokines, including tumor necrosis factor-&#x3b1; (TNF-&#x3b1;), Interferon-&#x3b3; (IFN-&#x3b3;), Interleukin-IL-12p70 (IL-12p70), Interleukin-1&#x3b2; (IL-1&#x3b2;), and tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) in both the spleen and serum of LPS-induced acute inflammation mice. Additionally, AKBA inhibited the development of AOM/DSS-induced colitis-associated colon cancer in mice and positively influenced gut microbiota.<br><br>CONCLUSION: This study highlights the inhibitory effect of AKBA on colitis-associated CRC and reveals a novel aspect of its role in the remodeling of gut microbiota. These findings suggest that AKBA may be used as a potential therapeutic agent for CRC.},
}
@article {pmid40745465,
year = {2025},
author = {Popova, A and Rācenis, K and Brīvība, M and Saksis, R and Saulīte, M and Šlisere, B and Berga-Švītiņa, E and Oļeiņika, K and Saulīte, AJ and Seilis, J and Kroiča, J and Čerņevskis, H and Pētersons, A and Kloviņš, J and Lejnieks, A and Kuzema, V},
title = {Reduced butyrate-producing bacteria and altered metabolic pathways in the gut microbiome of immunoglobulin A nephropathy patients.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28011},
pmid = {40745465},
issn = {2045-2322},
support = {lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; lzp-2019/1-0139//Latvian Council of Science/ ; },
mesh = {Humans ; *Glomerulonephritis, IGA/microbiology/metabolism/pathology ; Female ; *Butyrates/metabolism ; Male ; Adult ; *Gastrointestinal Microbiome ; Middle Aged ; *Metabolic Networks and Pathways ; Cross-Sectional Studies ; Feces/microbiology ; *Bacteria/metabolism/genetics/classification ; Prospective Studies ; Immunoglobulin A/metabolism ; Case-Control Studies ; },
abstract = {Gut-associated lymphoid tissue is central to the production of galactose-deficient IgA1 (Gd-IgA1), a key factor in immunoglobulin A nephropathy (IgAN). Although no major differences in gut microbiome diversity have been reported across IgAN cohorts, functional alterations in microbial composition may contribute to disease pathogenesis. The study was designed as a cross-sectional study with an embedded prospective cohort component. Forty-eight adults with biopsy-confirmed IgAN-categorized as progressors (eGFR decline > 5 ml/min/1.73 m[2]/year, n = 23) or nonprogressors (n = 23)-and 23 healthy controls (HC) were recruited. Stool samples underwent metagenomic and functional profiling. Alpha diversity did not differ significantly between IgAN patients and HC. However, butyrate-producing bacteria (Butyrococcus, Agathobacter rectalis) were less abundant in IgAN patients. The sulfoquinovose degradation I pathway, associated with these bacteria, was also reduced. Nucleotide- and nucleoside-biosynthesis pathways were elevated in IgAN. Gd-IgA1 levels correlated with variations in metabolic pathways. Progressors demonstrated enhanced activity in isopropanol biosynthesis, biotin biosynthesis II, and phospholipid biosynthesis pathways. IgAN patients show reduced butyrate-producing bacteria and distinct functional changes in the gut microbiome suggestive of immune activation and inflammation. Progressors exhibit additional metabolic shifts linked to bacterial membrane stabilization.},
}
@article {pmid40744923,
year = {2025},
author = {Grossegesse, M and Horn, F and Kurth, A and Lasch, P and Nitsche, A and Doellinger, J},
title = {vPro-MS enables identification of human-pathogenic viruses from patient samples by untargeted proteomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7041},
pmid = {40744923},
issn = {2041-1723},
mesh = {Humans ; *Proteomics/methods ; *SARS-CoV-2/isolation &amp; purification/genetics ; *COVID-19/virology/diagnosis ; *Viruses/genetics/isolation &amp; purification/classification ; Viral Proteins/metabolism ; Workflow ; *Virus Diseases/virology/diagnosis ; Genome, Viral ; Algorithms ; Peptide Library ; Virome ; Sensitivity and Specificity ; Metagenomics/methods ; Nasopharynx/virology ; },
abstract = {Viral infections are commonly diagnosed by the detection of viral genome fragments or proteins using targeted methods such as PCR and immunoassays. In contrast, metagenomics enables the untargeted identification of viral genomes, expanding its applicability across a broader spectrum. In this study, we introduce proteomics as a complementary approach for the untargeted identification of human-pathogenic viruses from patient samples. The viral proteomics workflow (vPro-MS) is based on an in-silico derived peptide library covering the human virome in UniProtKB (331 viruses, 20,386 genomes, 121,977 peptides). A scoring algorithm (vProID score) is developed to assess the confidence of virus identification from proteomics data (https://github.com/RKI-ZBS/vPro-MS). In combination with diaPASEF-based data acquisition, this workflow enables the analysis of up to 60 samples per day. The specificity is determined to be >99,9% in an analysis of 221 plasma, swab and cell culture samples covering 17 different viruses. The sensitivity of this approach for the detection of SARS-CoV-2 in nasopharyngeal swabs corresponds to a PCR cycle threshold of 27 with comparable quantitative accuracy to metagenomics. vPro-MS enables the integration of untargeted virus identification in large-scale proteomic studies of biofluids such as human plasma to detect previously undiscovered virus infections in patient specimens.},
}
@article {pmid40744840,
year = {2025},
author = {Zhan, J and Cheng, B and Guo, K and Tao, X and Cai, X and Li, Z and Tang, Z and Zhan, J and Wu, C},
title = {Absolute quantitative metagenomic analysis reveals unique gut bacteria underlying berberine and metformin's anti-metabolic disorders effects.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0008425},
pmid = {40744840},
issn = {2165-0497},
mesh = {*Berberine/pharmacology ; *Gastrointestinal Microbiome/drug effects/genetics ; *Metformin/pharmacology ; Animals ; Mice ; *Metagenomics/methods ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Metabolic Diseases/drug therapy/microbiology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Feces/microbiology ; },
abstract = {This study aimed to evaluate the potential functional bacteria in the efficacy of two drugs in ameliorating diet-induced metabolic disorder model using absolute and relative quantification methods and to evaluate the benefit of absolute quantification compared with relative quantification. The gut microbiota is implicated in the pathogenesis of various chronic diseases, including diet-induced metabolic disorder model. Berberine (BBR) and metformin (MET) are commonly used in the clinical management of metabolic disorder, yet their effects on gut microbiota regulation differ. This study employs both relative and absolute quantitative methods to assess the differential impacts of these drugs on the modulation of gut microbiota in metabolic disorder mice. Both BBR and MET effectively ameliorate the condition of metabolic disorder. While some relative quantitative sequencing results contradicted the absolute sequencing data, the latter was more consistent with the actual microbial community composition. Absolute quantitative sequencing provides a more accurate reflection of the drug's effects. Notably, both absolute and relative quantitative sequencing demonstrated an upregulation of Akkermansia.IMPORTANCEOur study underscores the importance of absolute quantitative analysis in accurately representing the true microbial counts in a sample and evaluating the modulatory effects of drugs on the microbiome, which plays a vital role in the study of the microbiome.},
}
@article {pmid40744013,
year = {2025},
author = {Arnoldini, M and Sharma, R and Moresi, C and Chure, G and Chabbey, J and Slack, E and Cremer, J},
title = {Quantifying the varying harvest of fermentation products from the human gut microbiota.},
journal = {Cell},
volume = {188},
number = {19},
pages = {5332-5342.e16},
pmid = {40744013},
issn = {1097-4172},
support = {R01 GM149611/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Fermentation ; Bacteria/metabolism/genetics ; Dietary Carbohydrates/metabolism ; Metagenomics ; Diet ; Mucins/metabolism ; },
abstract = {Fermentation products released by the gut microbiota provide energy and regulatory functions to the host. Yet, little is known about the magnitude of this metabolic flux and its quantitative dependence on diet and microbiome composition. Here, we establish orthogonal approaches to consistently quantify this flux, integrating data on bacterial metabolism, digestive physiology, and metagenomics. From the nutrients fueling microbiota growth, most carbon ends up in fermentation products and is absorbed by the host. This harvest varies strongly with the amount of complex dietary carbohydrates and is largely independent of bacterial mucin and protein utilization. It covers 2%-5% of human energy demand for Western diets and up to 10% for non-Western diets. Microbiota composition has little impact on the total harvest but determines the amount of specific fermentation products. This consistent quantification of metabolic fluxes by our analysis framework is crucial to elucidate the gut microbiota's mechanistic functions in health and disease.},
}
@article {pmid40743118,
year = {2025},
author = {Ozturk, S and Ekmen, FG and Ekmen, H and Ünal, EM and Er, A and Keskin, E and Arbuckle, BS},
title = {Decoding past microbial life and antibiotic resistance in İnonü Cave's archaeological soil.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0326358},
pmid = {40743118},
issn = {1932-6203},
mesh = {*Soil Microbiology ; *Archaeology ; *Bacteria/genetics/classification/drug effects ; *Caves/microbiology ; RNA, Ribosomal, 16S/genetics ; Humans ; *Drug Resistance, Microbial/genetics ; Microbiota/genetics ; Turkey ; },
abstract = {This study, which bridges the disciplines of archaeology and microbiology, examines the ancient bacterial communities and antibiotic-resistance genes in soil samples collected from İnönü Cave in Zonguldak, Turkiye. Our aim is to provide a comprehensive understanding of historical human activities and their influence on microbial communities. Soil samples were gathered from four distinct cultural levels from the Chalcolithic Age to the Early Iron Age. The microbial communities were characterized, and antibiotic-resistance genes were identified using high-throughput sequencing of 16S rRNA genes and metagenomic studies. This interdisciplinary approach not only enriches our understanding of ancient microbial communities but also opens up new avenues for research and collaboration. The results of our study showed a wide range of microorganisms, including prominent bacterial groups such as Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, Cyanobacteria, Firmicutes, Myxococcota, and Proteobacteria. The study identified the presence of the tetracycline resistance gene tetA in Chalcolithic samples, the class 1 integron intl1 in Early Bronze Age samples, and the oxacillinase gene OXA58 in Late Bronze Age samples. These findings underscore the long-term impact of human activities on microbial communities, as antibiotic-resistance genes have been present and have remained over various historical periods, perhaps influenced by both human activities and environmental variables. This knowledge is crucial for understanding the resilience and adaptability of microbial communities in the face of human-induced changes. The coexistence of these resistance genes and alterations in the microbial population suggest substantial connections between human activities and soil microbiota. This study, which draws on the fields of archaeology, microbiology, and environmental science, offers valuable insights into the ancient microbial ecology and underscores the enduring presence of antibiotic resistance. It emphasizes the necessity of a comprehensive, interdisciplinary approach, spanning multiple fields, to comprehend microbial communities' evolution and resistance mechanisms in archaeological settings.},
}
@article {pmid40742667,
year = {2025},
author = {Liang, M and Wu, WJ and Li, L and Qin, H and Li, SN and Zheng, GL and Hou, DM and Huang, Q and Cheng, L and Jie, HQ and Lu, JR and He, JC and Yang, J and Wei, W},
title = {Characteristics of the microbiota in the nasopharynx and nasal cavity of healthy children before and during the COVID-19 pandemic.},
journal = {World journal of pediatrics : WJP},
volume = {21},
number = {8},
pages = {836-845},
pmid = {40742667},
issn = {1867-0687},
support = {81800903//National Natural Science Foundation of China/ ; 82171135//National Natural Science Foundation of China/ ; 82371140//National Natural Science Foundation of China/ ; 81970881//National Natural Science Foundation of China/ ; 82271160//National Natural Science Foundation of China/ ; 21Y31900504//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; 2024YFC2511100//National Key R&amp;D Program of China/ ; },
mesh = {Humans ; *COVID-19/epidemiology ; *Nasopharynx/microbiology ; *Nasal Cavity/microbiology ; *Microbiota ; Male ; Female ; Child ; SARS-CoV-2 ; Pandemics ; Child, Preschool ; Infant ; },
abstract = {BACKGROUND: Microbial colonization in the nasopharynx and nasal cavity plays a defensive role in children. The coronavirus disease 2019 (COVID-19) pandemic may have an influence on the nasopharynx and nasal cavity microbiota. This study aimed to identify and compare the microbiota in the nasopharynx and nasal cavity before and during the COVID-19 pandemic in a healthy pediatric population.<br><br>METHODS: Separate mucosal swabs were collected from the nasopharynx and nasal cavity of healthy children before and during the COVID-19 pandemic. A 16S ribosomal RNA-based metagenomic approach was employed to characterize and analyze alterations in the nasopharyngeal and nasal microbiota to determine whether isolation measures, such as mask wearing, influence microbial ecology.<br><br>RESULTS: The richness and diversity of the nasopharyngeal and nasal microbiota decreased during the COVID-19 pandemic compared with before the pandemic. Firmicutes and Proteobacteria were the most abundant phyla in the nasopharyngeal and nasal microbiota, respectively, both before and during the pandemic. Corynebacterium and Moraxella were the dominant genera in the nasopharyngeal and nasal microbiota during the COVID-19 pandemic, whereas Pseudomonas and Corynebacterium were dominant before the pandemic. Compared with pre-pandemic conditions, microbial colonization differed significantly for Cyanobacteria/Chloroplast and Bacteroidetes in the nasopharynx and for Planctomycetes in the nasal cavity during the COVID-19 pandemic.<br><br>CONCLUSIONS: This study revealed a lower microbiota diversity during COVID-19, possibly accompanied by microbiota dysbiosis, increased risk of respiratory infections and inflammatory responses in healthy children. This study underscores the importance of reestablishing microbiota balance and highlights the need for personalized treatment and prophylactic strategies in routine public health practice. Supplementary file3 (MP4 150533 KB).},
}
@article {pmid40742180,
year = {2025},
author = {Tang, G and Carr, AV and Perez, C and Ramos Sarmiento, K and Levy, L and Lampe, JW and Diener, C and Gibbons, SM},
title = {Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization.},
journal = {mSystems},
volume = {10},
number = {8},
pages = {e0098425},
pmid = {40742180},
issn = {2379-5077},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; R01 DK133468/DK/NIDDK NIH HHS/United States ; R01DK133468//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Feces/microbiology ; Biomass ; *Bacteria/genetics/isolation &amp; purification ; *Metagenome ; Animals ; Host Microbial Interactions/genetics ; },
abstract = {Absolute bacterial biomass estimation in the human gut is crucial for understanding microbiome dynamics and host-microbe interactions. Current methods for quantifying bacterial biomass in stool, such as flow cytometry, quantitative polymerase chain reaction (qPCR), or spike-ins, can be labor-intensive, costly, and confounded by factors like water content, DNA extraction efficiency, PCR inhibitors, and other technical challenges that add bias and noise. We propose a simple, cost-effective approach that circumvents some of these technical challenges: directly estimating bacterial biomass from metagenomes using bacterial-to-host (B:H) read count ratios. We compared B:H ratios to the standard methods outlined above, demonstrating that B:H ratios are useful proxies for bacterial biomass in stool and possibly in other host-associated substrates. B:H ratios in stool were correlated with bacterial-to-diet (B:D) read count ratios, but B:D ratios exhibited a substantial number of outlier points. Host read depletion methods reduced the total number of human reads in a given sample, but B:H ratios were strongly correlated before and after host read depletion, indicating that host read depletion did not reduce the utility of B:H ratios. B:H ratios showed expected variation between health and disease states and were generally stable in healthy individuals over time. Finally, we showed how B:H and B:D ratios can be used to track antibiotic treatment response and recovery. B:H ratios offer a convenient alternative to other absolute biomass quantification methods, without the need for additional measurements, experimental design considerations, or machine learning, enabling robust absolute biomass estimates directly from stool metagenomic data.IMPORTANCEIn this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, additional experimental biomass measurements, or training data. The approach assumes that the contribution of host DNA to stool is more constant or stable than biologically relevant fluctuations in bacterial biomass. We find that host read normalization is an effective method for detecting variation in gut bacterial biomass. Absolute bacterial biomass is a key metric that often gets left out of gut microbiome studies, and empowering researchers to include this measure more broadly in their metagenomic analyses should serve to improve our understanding of host-microbiota interactions.},
}
@article {pmid40742167,
year = {2025},
author = {Fan, P and Ma, J and Shen, Q and Ouyang, Y and Zhang, T and Shen, J and Luo, Z-C and Liu, Z and Ouyang, F},
title = {Gut microbiota development, antibiotic resistome, and related perinatal factors in early infancy.},
journal = {mSystems},
volume = {10},
number = {8},
pages = {e0050225},
pmid = {40742167},
issn = {2379-5077},
support = {81961128023,81673178//National Natural Science Foundation of China/ ; 2017YFE0124700//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Male ; Infant ; Infant, Newborn ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; Bacteria/genetics/classification/drug effects ; Delivery, Obstetric ; Pregnancy ; *Drug Resistance, Microbial/genetics ; Cesarean Section ; },
abstract = {Early life is a critical window for gut microbiota development and antibiotic resistome. We aimed to investigate the microbiota longitudinal change during the first 6 months of life and the differences associated with assisted reproductive technology (ART) treatment, mode of delivery, and infant sex. Gut microbiota was measured by metagenomic sequencing of fecal samples repeatedly collected within 3 days after birth, at 42 days, 3 months, and 6 months in 155 Chinese infants. Among infants born by vaginal delivery, the ACE, Chao, and Sobs indexes increased with age. Accordingly, the relative abundance of Actinobacteria phylum increased from 43% ± 37% (mean ± SD) to 57% ± 36% and Proteobacteria phylum decreased from 48% ± 36% to 17% ± 25%; and Bifidobacterium and Klebsiella genus increased and Escherichia genus decreased, from the first 3 days to 6 months. The dominant antibiotic resistance genes were macB and msbA. Boys and girls had similar features. Infants born by cesarean section exhibited a similar gut microbiota developmental trajectory, but with a slower increase in alpha diversity over time, and lower Bacteroidetes phylum and Bacteroides genus at each age point. Compared with non-ART infants, ART infants had slightly higher alpha diversity indexes of ACE, Chao, Sobs, Shannon, and Pielou's evenness at age 42 days among infants born by vaginal delivery. Our findings confirm increasing diversity and composition evolution of gut microbiota in the first 6 months of life. Both modes of delivery and ART conception are associated with early gut microbiota alteration.IMPORTANCEGut microbiota plays an important role in various aspects of human health. Early life is a critical period for the development of gut microbiota. In this prospective study, we observed that the diversity and antibiotic resistance genes of gut microbiota increased gradually with age in the first 6 months of life. Boys and girls had similar features of gut microbiota. Cesarean section was associated with a lower abundance of Bacteroidetes phylum and Bacteroides genus. Compared with non-ART infants (spontaneous conception), ART infants had slightly higher alpha diversity indexes of ACE, Chao, Sobs, Shannon, and Pielou's evenness at age 42 days among infants born by vaginal delivery. This study presents gut microbiota development with age, antibiotic resistome, and related perinatal factors in early infancy.},
}
@article {pmid40742122,
year = {2025},
author = {Wu, H and Jiang, X and Xi, Y and Ning, S and Wu, H and Xin, W and Peng, W and Wang, S and Zhang, W},
title = {Genetic characterization of the marmot gut virome in high-altitude Qinghai Province and identification of novel viruses with zoonotic potential.},
journal = {mSphere},
volume = {10},
number = {8},
pages = {e0029725},
pmid = {40742122},
issn = {2379-5042},
mesh = {Animals ; China ; *Virome/genetics ; Phylogeny ; *Marmota/virology ; Altitude ; Genome, Viral ; *Viruses/genetics/classification/isolation &amp; purification ; Humans ; Metagenomics ; Zoonoses/virology ; },
abstract = {The high-altitude ecosystems of Qinghai Province, China, harbor unique viral communities shaped by extreme environmental conditions and host adaptations. This study presents a comprehensive genetic characterization of the marmot gut virome, revealing novel viral strains with zoonotic potential. Using viral metagenomics, we analyzed intestinal contents from 70 marmots collected from Chengduo and Maqin counties. Sequencing on the Illumina NovaSeq 6000 platform identified 19 viral genomes belonging to four major families: Adenoviridae, Astroviridae, Parvoviridae, and Picornaviridae, along with four novel circular Rep-encoding single-stranded DNA (CRESS DNA) viruses. Phylogenetic analyses demonstrated close relationships between marmot-derived strains and viruses from humans, bats, and other mammals, highlighting potential cross-species transmission risks. Notably, bat-associated adenoviruses showed closer phylogenetic proximity to human strains, while novel parvoviruses formed a distinct clade within the Dependoparvovirus genus. The discovery of a novel astrovirus with low sequence similarity to known genera underscores the need for taxonomic reclassification. Additionally, a novel picornavirus related to Sapelovirus and four divergent CRESS DNA viruses were identified, expanding our understanding of viral diversity in high-altitude rodents. These findings emphasize the role of marmots as viral reservoirs and highlight the importance of high-altitude ecosystems as hotspots for zoonotic pathogen emergence. This study provides critical insights into viral evolution, host adaptation, and zoonotic risks, advocating for integrated surveillance strategies to mitigate future spillover events.IMPORTANCEViruses are the most abundant and diverse biological entities on Earth, yet their presence in wildlife from extreme environments remains poorly understood. High-altitude ecosystems, shaped by harsh conditions like intense UV radiation and low oxygen levels, create unique settings for virus evolution. This study is the first to comprehensively profile the gut virome of marmots in Qinghai Province, uncovering novel viral strains and highlighting how extreme environments drive viral diversity. Marmots, as key species in these regions, can act as bridges for virus transmission among wildlife, livestock, and humans, posing zoonotic risks. Understanding these viral communities is essential for predicting and preventing future outbreaks. Our findings emphasize the urgent need for integrated, One Health-based surveillance strategies to safeguard both public health and biodiversity in fragile high-altitude ecosystems.},
}
@article {pmid40739184,
year = {2025},
author = {Tang, HB and Si, YX and Li, HD and Dang, W and Lu, HL},
title = {Intestinal microbial dysbiosis under nitrite stress in juvenile three-keeled pond turtles, Mauremys reevesii.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {466},
pmid = {40739184},
issn = {1471-2180},
support = {32471577//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Turtles/microbiology ; *Nitrites/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/microbiology/veterinary/chemically induced ; *Bacteria/classification/genetics/drug effects/isolation &amp; purification ; Stress, Physiological ; Intestines/microbiology ; *Water Pollutants, Chemical/toxicity ; Aquaculture ; },
abstract = {BACKGROUND: Nitrite is one of the primary pollutants in high-density aquaculture systems, and may cause various toxic effects (e.g., oxidative damage, metabolic and immune dysregulation, histological inflammation, etc.) on economically important aquaculture species, such as echinoderms, crustaceans and fish. Nitrite can also disrupt the intestinal function and microbiota in some fish and amphibians. However, intestinal physiological and microbial responses of cultured turtles under nitrite stress were rarely explored.<br><br>METHOD: Twenty Mauremys reevesii juveniles were exposed to different nitrite levels and fed with a commercial diet. Their intestinal content samples were analyzed for microbial diversity and composition.<br><br>RESULTS: Nitrite exposure reduced intestinal microbial diversity, with lower &#x3b1;-diversity values in higher-concentration exposed turtles. It also changed the microbial composition. After exposure, the abundances of Bacteroidetes and Firmicutes decreased, but that of Proteobacteria increased at the phylum level. Similarly, abundances of some potentially beneficial bacterial genera, e.g., Prevotella_1, Christensenellaceae_R-7, Muribaculaceae_ge, were shown to decrease, but those of putatively pathogenic genera, e.g., Halomonas, Nesterenkonia, increased at the genus level. Furtherly, potentially altered metabolic pathways (e.g., biosynthesis of ansamycins and vancomycin group antibiotics) were revealed by functional predictions of intestinal microbiota.<br><br>CONCLUSION: This study highlighted intestinal microbial dysbiosis and prevalence of putatively pathogenic bacteria in cultured turtles under nitrite stress. Excessive levels of nitrite would alter the health status of aquatic animals by disrupting their intestinal microbiome.},
}
@article {pmid40739125,
year = {2025},
author = {Jiang, W and Xiong, M and Feng, S and Liu, Q and Chen, Y and Zou, S and Kang, D},
title = {Water content alters soil organic carbon metabolism via microbial traits in Tibetan alpine peatlands.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27793},
pmid = {40739125},
issn = {2045-2322},
support = {No. 2023NSFSC0143//the Natural Science Foundation of Sichuan Provence/ ; No. 31800458//the National Natural Science Foundation of China/ ; No. 2019-ZL-19//Sichuan Province Transportation Science and Technology Project: Research and Demonstration on Crucial Technologies of Wetland Eco-environment Protection Under the Influence of Highway Engineering on the Western Sichuan Plateau/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; Tibet ; *Water/analysis ; Carbon Cycle ; Archaea/metabolism/genetics ; Bacteria/metabolism/genetics ; Fungi/metabolism/genetics ; Microbiota ; },
abstract = {Alpine peatlands on the eastern Tibetan Plateau are vital carbon sinks, with soil moisture playing a key role in peatland carbon cycling. However, they face disruptions in their carbon balance due to drought, which reduces soil water content. Therefore, this study investigated microbially driven water-carbon interactions through field surveys, laboratory incubations, and metagenomics. Soil drying contributes to changes in both the metabolic quotient (qCO2) and the microbial quotient (Cmic: Corg), as well as the microbial abundance. As the soil water content decreased, both qCO2 and Cmic: Corg exhibited an overall increasing trend. Moreover, soil water content had a more significant effect on soil bacteria, while its effect on fungi and archaea was minimal. Soil microbial carbon decomposition genes were also influenced by changes in soil water content. Next, we used RDA to analyze the relationship between soil respiration quotient values and microbial traits. The results revealed that Actinobacteria were strongly negatively correlated with qCO2, whereas Archaea and Candidatus_R were positively correlated with qCO2. Additionally, Cmic: Corg was closely linked to fungi, and both Proteobacteria and Acidobacteria exhibited positive correlations. qCO2 had a strong negative correlation with genes involved in the degradation of monosaccharides and hemicellulose, whereas Cmic: Corg was positively correlated with genes related to the degradation of cellulose and lignin. Moreover, droughts affected microbial residue carbon and associated carbon metabolic pathways. Therefore, changes in soil water content may be an important factor influencing carbon metabolism processes in peatlands. This study deepens our understanding of the effects of drought on soil metabolism and microbial dynamics in alpine peatlands and provides new insights into the microecological mechanisms of soil carbon cycling in these ecosystems in the context of global change.},
}
@article {pmid40738886,
year = {2025},
author = {Wang, S and Zhang, Z and Zhao, J and Yang, K and Zhang, W and Wang, Z and Liang, Z and Zhang, Y and Zhang, Y and Liu, J and Zhang, L},
title = {Metaproteomic Insights into Bioenergy Conversion Enzymes of Bathypelagic Microbial Communities in the South China Sea.},
journal = {Journal of proteome research},
volume = {24},
number = {9},
pages = {4780-4791},
doi = {10.1021/acs.jproteome.5c00551},
pmid = {40738886},
issn = {1535-3907},
mesh = {China ; *Proteomics/methods ; *Seawater/microbiology ; *Microbiota ; Energy Metabolism ; Metagenomics ; Metagenome ; Archaea/enzymology/genetics ; Oceans and Seas ; Bacteria/enzymology/genetics ; *Bacterial Proteins/metabolism/genetics ; Carbon Cycle ; },
abstract = {Marine microorganisms inhabiting the bathypelagic zone (1000-4000 m) exhibit distinctive environmental adaptability and serve as a valuable reservoir of bioenzymes. However, a limited understanding of deep-sea microbial community composition and metabolic activities hinders the broad application of their enzymatic potential. In this study, we employed a metaproteomic approach to investigate the protein profiles of microbial communities in the bathypelagic layers of the South China Sea (SCS), and we compared them with the corresponding metagenomic data. Our findings revealed a strong phylum-level correlation between metaproteomic and metagenomic datasets, along with a significant enrichment of proteins associated with inorganic ion metabolism and energy conversion. Deep-sea microbial communities are characterized by unique dominant taxa, such as Propionibacteriales, and exhibit diverse strategies for energy utilization. Notably, we identified several enzymes involved in energy conversion, including RuBisCO and carbon monoxide dehydrogenase in Proteobacteria and ammonia monooxygenase in Thaumarchaeota for carbon fixation. These enzymes catalyze reactions utilizing various inorganic substrates as energy sources. Additionally, the deep-sea environment significantly enhanced the expression of methane monooxygenase in methylotrophs, suggesting that such conditions may promote the development of methane-utilizing cell factories. This study not only deepens our understanding of energy conversion mechanisms in deep-sea microorganisms but also offers valuable enzymatic resources for the development of novel bioenergy technologies.},
}
@article {pmid40738384,
year = {2025},
author = {Liang, T and Jiang, T and Liang, Z and Chen, Y and Chen, T and Dong, B and Xie, X and Gu, B and Wu, Q},
title = {Lactiplantibacillus plantarum strain 84-3-derived l-glutamine ameliorates glucose homeostasis via AMPK/PPARγ signaling pathway activation in type 2 diabetes.},
journal = {Metabolism: clinical and experimental},
volume = {172},
number = {},
pages = {156357},
doi = {10.1016/j.metabol.2025.156357},
pmid = {40738384},
issn = {1532-8600},
mesh = {*Glutamine/metabolism/pharmacology ; *Diabetes Mellitus, Type 2/metabolism ; Animals ; Rats ; Homeostasis/drug effects ; Signal Transduction/drug effects ; Humans ; Male ; *AMP-Activated Protein Kinases/metabolism ; Case-Control Studies ; *PPAR gamma/metabolism ; *Lactiplantibacillus plantarum/metabolism ; *Glucose/metabolism ; Gastrointestinal Microbiome ; Probiotics ; Diabetes Mellitus, Experimental/metabolism ; Blood Glucose/metabolism ; Rats, Sprague-Dawley ; Middle Aged ; Adult ; Female ; },
abstract = {BACKGROUND: Gut microbiota and their metabolites play an essential role in type 2 diabetes (T2D). However, contributions of individual bacterial strains and their metabolites to T2D pathogenesis remain poorly understood. We investigated T2D regulation by Lactobacillus in various animal models to understand its therapeutic effects.<br><br>METHODS AND RESULTS: We performed a case-control study of Chinese adults using metabolome profiling and identified an inverse correlation between l-glutamine and T2D serum concentrations. The glnA and GLUL genes encoding glutamine synthetase (GS) in L. plantarum 84-3 were also identified. L. plantarum 84-3 treatment significantly decreased serum inflammation and improved metabolic phenotypes in streptozotocin- or tetraoxypyrimidine-induced T2D rats, including blood glucose, glucose tolerance, insulin resistance, and lipids. We confirmed elevated serum l-glutamine levels in the L. plantarum 84-3 group. RNA sequencing analysis demonstrated that L. plantarum 84-3-derived l-glutamine is a vital bioactive molecule, improving glucose homeostasis by activating the liver AMPK/PPAR signaling pathway and ameliorating T2D. We conducted co-culture fermentation experiments in vitro and in vivo, and metagenomic and metabolomic analyses revealed that resistance starch combined with L. plantarum 84-3 significantly enriched of Lactobacillus abundance and increased the l-glutamine level, affecting of alanine, aspartate, and glutamate metabolism pathways, which was confirmed in vivo in rats. The reduced L. plantarum and l-glutamine levels were validated in a human T2D cohort.<br><br>CONCLUSIONS: These findings revealed a novel therapeutic effect of L. plantarum in alleviating T2D-related glucose homeostasis by increasing circulating l-glutamine, which suggests viable preventive and therapeutic strategies for metabolic disorders.},
}
@article {pmid40738105,
year = {2025},
author = {Rodriguez-Rodriguez, L and Pfister, J and Schuck, L and Martin, AE and Mercado-Santiago, LM and Tagliabracci, VS and Forsberg, KJ},
title = {Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {8},
pages = {1381-1395.e7},
pmid = {40738105},
issn = {1934-6069},
support = {DP2 AI154402/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Bacteriophages/physiology ; *Metagenomics ; Escherichia coli/virology/genetics ; *Bacteria/genetics/virology/classification ; Soil Microbiology ; *Metagenome ; },
abstract = {To prevent phage infection, bacteria have developed an arsenal of antiphage defenses. Evidence suggests that many examples in nature have not been described. Using plasmid libraries expressing small DNA inserts and functional selections for antiphage defense in Escherichia coli, we identified over 200 putative defenses from 14 bacterial phyla in 9 human and soil microbiomes. Many defenses were unrecognizable based on sequence or predicted structure and thus could only be identified via functional assays. In mechanistic studies, we show that some defenses encode nucleases that distinguish phage DNA via diverse chemical modifications. We also identify outer membrane proteins that prevent phage adsorption and a set of unknown defenses with diverse antiphage profiles and modalities. Most defenses acted against at least two phages, indicating that broadly acting systems are widely distributed. Collectively, these findings highlight the diversity and interoperability of antiphage defense systems.},
}
@article {pmid40736894,
year = {2025},
author = {Child, HT and Barber, DG and Maneein, S and Clayton, J and Love, J and Tennant, RK},
title = {Laboratory and In-Field Metagenomics for Environmental Monitoring.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {71-88},
doi = {10.1007/978-1-0716-4702-8_5},
pmid = {40736894},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Environmental Monitoring/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Gene Library ; },
abstract = {Direct sequencing of DNA from environmental samples (eDNA) is increasingly utilized to provide a census of natural and industrial habitats. The methodology required to perform metagenomics can be divided into three distinct stages: DNA Purification, Library Preparation and Sequencing, and Bioinformatic Analysis. Here we demonstrate an end-to-end protocol that can be utilized either in the field or laboratory for metagenomic analysis of environmental samples utilizing the Oxford Nanopore Technologies MinION sequencing platform.},
}
@article {pmid40736175,
year = {2025},
author = {Shi, Q and Wei, Z and Pang, J and Qudsi, AI and Wei, M and Zhang, Z and Zhang, Y and Wang, Z and Chen, K and Xu, X and Lu, X and Liang, Q},
title = {Achromobacter in the Conjunctival Sac Microbiota: Potential Association With Acanthamoeba Keratitis Related to Orthokeratology Lenses.},
journal = {Investigative ophthalmology &amp; visual science},
volume = {66},
number = {9},
pages = {71},
pmid = {40736175},
issn = {1552-5783},
mesh = {Humans ; Male ; Female ; *Microbiota ; *Acanthamoeba Keratitis/microbiology/etiology ; *Conjunctiva/microbiology ; Adult ; *Achromobacter/isolation &amp; purification/genetics/physiology ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S/genetics ; *Orthokeratologic Procedures/adverse effects/instrumentation ; Acanthamoeba ; *Contact Lenses/adverse effects ; Young Adult ; DNA, Bacterial/genetics/analysis ; Dysbiosis/microbiology ; Middle Aged ; },
abstract = {PURPOSE: Acanthamoeba keratitis (AK) is a severe infection linked to orthokeratology lens use, whereas the involvement of conjunctival microbiota in AK remains poorly understood. This study investigates microbiota dysbiosis in AK pathogenesis to inform microbiota-based interventions.<br><br>METHODS: Conjunctival swabs from 14 patients with AK and 10 healthy controls underwent 16S rRNA sequencing. Microbiome analysis compared diversity, taxa, and metabolic pathways. Functional assays quantified Achromobacter-enhanced Acanthamoeba adhesion and migration. Metagenomics and fluorescence in situ hybridization (FISH) with species-specific probes confirmed endosymbiosis.<br><br>RESULTS: Patients with AK showed reduced bacterial diversity compared with the healthy controls (P < 0.001) but similar richness. Relative abundance of Achromobacter in the AK group was higher compared to the healthy control group (P < 0.001). Achromobacter dominated microbiota among the AK group, being identified as a key biomarker via the linear discriminant analysis effect size (LEfSe). In vitro, Achromobacter increased Acanthamoeba adhesion (P = 0.007) and the migration area (P < 0.05). Metagenomic analysis and FISH further showed Achromobacter spp. as potential endosymbionts of Acanthamoeba. Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed upregulated phenylalanine, fatty acid, and propanoate metabolism in the AK group (all P < 0.001). MetaCyc highlighted enriched pyruvate fermentation to isobutanol, aerobic respiration I, and L-isoleucine biosynthesis II in the AK group (P < 0.001).<br><br>CONCLUSIONS: AK-associated conjunctival dysbiosis features Achromobacter dominance, reduced diversity, and altered metabolism. Achromobacter is associated with enhanced adhesion and migration of Acanthamoeba, indicating a possible symbiotic interaction and its potential as a biomarker and therapeutic target.},
}
@article {pmid40735808,
year = {2025},
author = {Maffei, VJ and Bertoni, AG and Wood, AC and Rotter, JI and Crago, O and Chen, YI and Petrosino, JF and Hoffman, KL and Goodarzi, MO and Jensen, ET},
title = {Menopause factors and alterations in gut microbiota and insulin homeostasis: A cross-sectional analysis of the microbiome and insulin longitudinal evaluation study (MILES).},
journal = {Diabetes, obesity &amp; metabolism},
volume = {27},
number = {10},
pages = {5444-5454},
pmid = {40735808},
issn = {1463-1326},
support = {R01-DK109588/DK/NIDDK NIH HHS/United States ; P30-DK063491/DK/NIDDK NIH HHS/United States ; UL1 TR001420/TR/NCATS NIH HHS/United States ; UL1-TR001420/TR/NCATS NIH HHS/United States ; UL1-TR001881/TR/NCATS NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; 58-3092-5-001//Agricultural Research Service/ ; P30 DK063491/DK/NIDDK NIH HHS/United States ; R01 DK109588/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; Female ; Middle Aged ; *Gastrointestinal Microbiome/physiology ; Longitudinal Studies ; Cross-Sectional Studies ; *Insulin Resistance/physiology ; *Menopause/physiology/metabolism ; Homeostasis/physiology ; *Insulin/metabolism/blood ; *Dysbiosis/microbiology/metabolism ; Adult ; Feces/microbiology ; Glucose Tolerance Test ; },
abstract = {AIM: To assess the risk for impaired insulin homeostasis as a function of menopause-related factors and gut microbiota dysbiosis in non-diabetic, post-menopausal women.<br><br>MATERIALS AND METHODS: Baseline data (n&#x2009;=&#x2009;175 women) from the Microbiome and Insulin Longitudinal Evaluation Study (MILES) were used, including insulin and dysglycaemia indices calculated from a 2-h oral glucose tolerance test, untargeted peripheral metabolomics, targeted peripheral short chain fatty-acid levels and faecal bacterial microbiota surveyed by whole-metagenomic sequencing.<br><br>RESULTS: After adjustment for covariates, menopause age&#x2009;<50&#x2009;years and use of hormone replacement therapy (HRT) were associated with lower Matsuda et al. insulin sensitivity index levels (&#x3b2;&#x2009;=&#x2009;-0.232, confidence interval (CI)&#x2009;=&#x2009;[-0.450, -0.014] and &#x3b2;&#x2009;=&#x2009;-0.275, CI&#x2009;=&#x2009;[-0.444, -0.107], respectively) but not pre-menopausal gynaecologic surgery. Pre-menopausal gynaecologic surgery was significantly associated with faecal microbiota beta diversity driven by a relative increase in diabetogenic Ruminococcus gnavus and Clostridium species and a decrease in protective Alistipes species and Akkermansia muciniphila relative abundances. A reduction in two glycerophospholipids in the plasmalogen class significantly statistically mediated an inverse association between gynaecologic surgery before menopause and insulin sensitivity.<br><br>CONCLUSIONS: Menopause age and history of HRT are more strongly associated with insulin resistance than gynaecologic surgery before menopause. However, gynaecologic surgery is associated with shifts in gut microbial composition and plasma metabolite levels with a potential to contribute to future diabetes risk.},
}
@article {pmid40732945,
year = {2025},
author = {Kulecka, M and Jaworski, P and Zeber-Lubecka, N and Bałabas, A and Piątkowska, M and Czarnowski, P and Frączek, B and Tarnowski, W and Mikula, M and Ostrowski, J},
title = {The Gut Microbiome Obesity Index: A New Analytical Tool in the Metagenomics Workflow for the Evaluation of Gut Dysbiosis in Obese Humans.},
journal = {Nutrients},
volume = {17},
number = {14},
pages = {},
pmid = {40732945},
issn = {2072-6643},
support = {2018/29/B/NZ7/00809//National Science Center/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; Male ; Female ; *Metagenomics/methods ; Adult ; Feces/microbiology ; *Dysbiosis/microbiology/diagnosis ; Body Mass Index ; Middle Aged ; Bacteria/classification/genetics ; Workflow ; Case-Control Studies ; Young Adult ; },
abstract = {Background/Objectives: Our aim was to create a new method for analyzing metagenomics data, named the gut microbiome obesity index, using a set of taxa/biological functions that correlated with BMI. Methods: A total of 109 obese patients (73 women and 36 men, median BMI 43.0 kg/m[2]), 87 healthy control (HC) individuals (39 females and 48 males, median BMI 22.7 kg/m[2]), and 109 esports players (five females and 104 males, median BMI 23.0 kg/m[2]) were included in the study. To conduct metagenomic and metabolomic analyses, DNA and selected metabolites were isolated from fecal samples and used for whole-genome shotgun sequencing and gas chromatography/mass spectrometry, respectively. Results: Compared with HCs and esports players, obese patients with a BMI > 40 kg/m[2] had a significantly higher alpha diversity, as analyzed by the Shannon index, and significant dissimilarities in beta diversity. Both richness and diversity measures were correlated with BMI. Compared with HCs and esports players, 12 differential bacteria were found in the overall obesity group and 42 were found in those with a BMI > 40 kg/m[2]. Most of the altered species belonged to the Lachnospiraceae family. When the logarithmic relationship of the sums of the bacteria correlated with BMI was calculated to establish a taxonomic health index, it better differentiated between the obesity groups than a standard analytical pipeline; however, it did not differentiate between the HC and the BMI < 35 kg/m[2] obesity group. Therefore, we created a functional index based on BMI-associated biological pathways, which differentiated between all obesity groups. Conclusions: Of the obesity indices used to distinguish between healthy and obese microbiota analyzed in this study, a function-based index was more useful than a taxonomy-based index. We believe that gut microbiome indexes could be useful as part of routine metagenomics evaluations. However, an index developed in one geographical area might not be applicable to individuals in a different region and, therefore, further studies should develop separate indices for different populations or geographical regions rather than relying on a single index.},
}
@article {pmid40731978,
year = {2025},
author = {Garcia, M and Bruna, P and Duran, P and Abanto, M},
title = {Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
pmid = {40731978},
issn = {2076-2607},
abstract = {Soil degradation has been accelerating globally due to climate change, which threatens food production, biodiversity, and ecosystem balance. Traditional soil restoration strategies are often expensive, slow, or unsustainable in the long term. In this context, cyanobacteria have emerged as promising biotechnological alternatives, being the only prokaryotes capable of performing oxygenic photosynthesis. Moreover, they can capture atmospheric carbon and nitrogen, release exopolysaccharides (EPSs) that stabilize the soil, and facilitate the development of biological soil crusts (biocrusts). In recent years, the convergence of multi-omics tools, such as metagenomics, metatranscriptomics, and metabolomics, has advanced our understanding of cyanobacterial dynamics, their metabolic potential, and symbiotic interactions with microbial consortia, as exemplified by the cyanosphere of Microcoleus vaginatus. In addition, recent advances in bioinformatics have enabled high-resolution taxonomic and functional profiling of environmental samples, facilitating the identification and prediction of resilient microorganisms suited to challenging degraded soils. These tools also allow for the prediction of biosynthetic gene clusters and the detection of prophages or cyanophages within microbiomes, offering a novel approach to enhance carbon sequestration in dry and nutrient-poor soils. This review synthesizes the latest findings and proposes a roadmap for the translation of molecular-level knowledge into scalable biotechnological strategies for soil restoration. We discuss approaches ranging from the use of native biocrust strains to the exploration of cyanophages with the potential to enhance cyanobacterial photosynthetic activity. By bridging ecological functions with cutting-edge omics technologies, this study highlights the critical role of cyanobacteria as a nature-based solution for climate-smart soil management in degraded and arid ecosystems.},
}
@article {pmid40731321,
year = {2025},
author = {Rech de Laval, V and Dainat, B and Engel, P and Robinson-Rechavi, M},
title = {The BeeBiome data portal provides easy access to bee microbiome information.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {198},
pmid = {40731321},
issn = {1471-2105},
mesh = {Bees/microbiology ; Animals ; *Microbiota/genetics ; Metagenomics/methods ; *Databases, Genetic ; Metagenome ; },
abstract = {Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition, genomic content, and gene expression of bee-associated microbial communities. While each of these datasets by itself has provided important insights, the integration of such datasets provides an unprecedented opportunity to obtain a global picture of the microbes associated with bees and their link to bee health. The challenge of such an approach is that datasets are difficult to find within large generalist repositories and are often not readily accessible, which hinders integrative analyses. Here we present a publicly-available online resource, the BeeBiome data portal (https://www.beebiome.org), which provides an overview of and easy access to currently available metagenomic datasets involving bee-associated microbes. Currently the data portal contains 33,678 Sequence Read Archive (SRA) experiments for 278 Apoidea hosts. We present the content and functionalities of this portal. By providing access to all bee microbiomes in a single place, with easy filtering on relevant criteria, BeeBiome will allow faster progress of applied and fundamental research on bee biology and health. It should be a useful tool for researchers, academics, funding agencies, and governments, with beneficial impacts for stakeholders.},
}
@article {pmid40731267,
year = {2025},
author = {Xu, X and Qin, D and Qin, X and Gao, X and Li, C and Liu, X and Wu, G},
title = {Sustainable management of soil-borne disease: integrating fumigation with Andrographis paniculata residues to rebuild rhizosphere function.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {460},
pmid = {40731267},
issn = {1471-2180},
support = {32060639//the National Natural Science Foundation of China/ ; 202105AC160037, 202205AC160077//the Reserve Talents Project for Yunnan Young and Middle-aged Academic and Technical Leaders/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; *Fumigation/methods ; *Andrographis/chemistry ; *Plant Diseases/microbiology/prevention &amp; control ; *Plant Extracts/pharmacology/chemistry ; Metabolomics ; Fusarium/drug effects ; Soil/chemistry ; Microbiota/drug effects ; Metagenomics ; },
abstract = {Continuous pepper cropping induces soil-borne diseases and disrupts rhizosphere microecological balance. This study employed untargeted metabolomics and metagenomics to investigate treatment effects on rhizosphere metabolic reprogramming and microbe-metabolite interactions. Aqueous and ethanolic extracts of Andrographis paniculata residues (TCMR) were rich in flavonoids, terpenoids, and phenolic acids, exhibiting significant inhibition against soil-borne pathogens (Fusarium oxysporum, Fusarium solani, and others; >70% inhibition at high doses). While single fumigation (W1, M1) transiently suppressed pathogens, it disrupted rhizosphere metabolic homeostasis. In contrast, combined fumigation-TCMR treatments (WC, MC) enhanced plant stress resistance, stabilized membrane integrity, and reshaped microbial communities by modulating amino acid, lipid, and phenylpropanoid biosynthesis pathways. Microbe-metabolite network analysis revealed that coupling carbon-nitrogen cycling with redox homeostasis drives soil microecological optimization. This integrated strategy provides a sustainable solution for continuous cropping obstacles through synergistic metabolic reprogramming and microbiome reconstruction.},
}
@article {pmid40730965,
year = {2025},
author = {Clark-Boucher, D and Coull, BA and Reeder, HT and Wang, F and Sun, Q and Starr, JR and Lee, KH},
title = {Group-wise normalization in differential abundance analysis of microbiome samples.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {196},
pmid = {40730965},
issn = {1471-2105},
support = {U01 HD052104/HD/NICHD NIH HHS/United States ; T32 GM135117/GM/NIGMS NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; T32GM135117/GM/NIGMS NIH HHS/United States ; R03 DE027486/DE/NIDCR NIH HHS/United States ; P30ES000002/ES/NIEHS NIH HHS/United States ; R01 GM126257/GM/NIGMS NIH HHS/United States ; U01 HD052102/HD/NICHD NIH HHS/United States ; R03DE027486/DE/NIDCR NIH HHS/United States ; P01 HD103133/HD/NICHD NIH HHS/United States ; R01GM126257/GM/NIGMS NIH HHS/United States ; P30 ES000002/ES/NIEHS NIH HHS/United States ; U01 CA176726/CA/NCI NIH HHS/United States ; },
mesh = {*Microbiota/genetics ; Metagenome ; Algorithms ; *Metagenomics/methods ; Humans ; },
abstract = {BACKGROUND: A key challenge in differential abundance analysis (DAA) of microbial sequencing data is that the counts for each sample are compositional, resulting in potentially biased comparisons of the absolute abundance across study groups. Normalization-based DAA methods rely on external normalization factors that account for compositionality by standardizing the counts onto a common numerical scale. However, existing normalization methods have struggled to maintain the false discovery rate in settings where the variance or compositional bias is large. This article proposes a novel framework for normalization that can reduce bias in DAA by re-conceptualizing normalization as a group-level task. We present two new normalization methods within the group-wise framework: group-wise relative log expression (G-RLE) and fold-truncated sum scaling (FTSS).<br><br>RESULTS: G-RLE and FTSS achieve higher statistical power for identifying differentially abundant taxa than existing methods in model-based and synthetic data simulation settings. The two novel methods also maintain the false discovery rate in challenging scenarios where existing methods suffer. The best results are obtained from using FTSS normalization with the DAA method MetagenomeSeq.<br><br>CONCLUSION: Compared with other methods for normalizing compositional sequence count data prior to DAA, the proposed group-level normalization frameworks offer more robust statistical inference. With a solid mathematical foundation, validated performance in numerical studies, and publicly available software, these new methods can help improve rigor and reproducibility in microbiome research.},
}
@article {pmid40730483,
year = {2025},
author = {Zhong, H and Song, Y and Hu, S and Zhang, C and Li, L},
title = {Metagenomics-Metabolomics Reveals the Alleviation of Indole-3-Ethanol on Radiation-Induced Enteritis in Mice.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2502037},
pmid = {40730483},
issn = {1738-8872},
mesh = {Animals ; *Indoles/pharmacology/metabolism ; *Enteritis/drug therapy/etiology/metabolism/microbiology/pathology ; Mice ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Anti-Inflammatory Agents/pharmacology ; Colon/pathology/drug effects/radiation effects ; Cytokines/metabolism ; Interleukin-17/metabolism ; },
abstract = {Indole-3-ethanol (IEt), a small molecule metabolite from intestinal microbial tryptophan metabolism, has been established to have anti-inflammatory properties. However, its effect on radiation-induced enteritis has not been reported. Here, we aim to explore the effects and potential mechanisms of IEt on radiation enteritis. C57BL/6J mice were orally administered an IEt solution before radiation exposure. Inflammatory factors, including IL-17A, IFN-γ, IL-6 and IL-1β, were detected using enzyme-linked immunosorbent assay. Colonic histopathology was assessed through H&amp;E staining. Subsequently, gut microbiota and its metabolites were analyzed using metagenomics and metabolomics. The results suggested that IEt alleviated radiation-induced enteritis, as evidenced by improved colonic structural integrity, decreased levels of pro-inflammatory factors like IL-17A, and the restoration of intestinal microecological and metabolic balance. IEt enriched the abundance of Lachnospiraceae family members, particularly the genus Roseburia - a known anti-inflammatory commensal. In addition, IEt upregulated the levels of metabolites with anti-inflammatory effects such as indole-3-carbinol, pteridine, and pyropheophorbide-a. Furthermore, Roseburia was significantly positively correlated with indole-3-carbinol and negatively correlated with the pro-inflammatory factor IL-17A. Therefore, IEt may alleviate radiation enteritis through Roseburia-indole-3-carbinol and Roseburia-IL-17A axes. This study revealed the potential mechanisms by which IEt alleviated radiation enteritis, providing a potential protective candidate for radiation enteritis.},
}
@article {pmid40730159,
year = {2025},
author = {Che, Y and Han, J and Harkins, CP and Hou, P and Conlan, S and Deming, C and Amirkhani, A and Bingham, MA and Holmes, CJ and Englander, H and Shen, Z and , and Castelo-Soccio, L and Dimitrova, D and Kanakry, JA and Bergerson, JRE and Notarangelo, LD and Pittaluga, S and Zhao, C and Dell'Orso, S and Pai, SY and Hickstein, DD and Holland, SM and Brownell, I and Nagao, K and Gonzalez, CE and Shah, NN and Freeman, AF and Su, HC and Segre, JA and Kong, HH},
title = {Restoration of the human skin microbiome following immune recovery after hematopoietic stem cell transplantation.},
journal = {Cell host &amp; microbe},
volume = {33},
number = {8},
pages = {1412-1427.e5},
pmid = {40730159},
issn = {1934-6069},
support = {ZIA AR041218/ImNIH/Intramural NIH HHS/United States ; Z99 AR999999/ImNIH/Intramural NIH HHS/United States ; ZIA AR041219/ImNIH/Intramural NIH HHS/United States ; ZIA AR041217/ImNIH/Intramural NIH HHS/United States ; ZIA BC011558/ImNIH/Intramural NIH HHS/United States ; ZIA BC010938/ImNIH/Intramural NIH HHS/United States ; },
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation ; *Skin/microbiology/virology/immunology ; *Microbiota/immunology ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Adult ; Young Adult ; Metagenomics ; Child ; Adolescent ; Bacteria/classification/genetics/isolation &amp; purification ; Child, Preschool ; Skin Microbiome ; },
abstract = {The human skin microbiome is intricately intertwined with host immunity. While studies have elucidated microbial influences on immunity, understanding how immune alterations modulate this equilibrium remains limited. We investigated the dual impact of immune deficiency and hematopoietic stem cell transplantation (HSCT) on the skin microbiome in 24 patients with dedicator of cytokinesis 8 (DOCK8) deficiency, a rare inborn error of immunity. Analyzing 590 metagenomic and 534 16S rDNA sequencing samples across eight skin sites, we observed disrupted microbiota pre-HSCT (median eukaryotic viruses 67.6% vs. 0.04% in controls), with extremely diverse human papillomaviruses (HPVs) and polyomaviruses-including oncogenic viruses. Specific bacterial species markedly changed, including decreased Staphylococcus aureus post-HSCT. DNA eukaryotic viruses dramatically decreased (79.7% ± 28.3% to 4.9% ± 8.6%; p < 0.01) 12 months post-HSCT. Recovered microbial communities remained relatively stable through 1-year follow-up with clearance of oncogenic HPV and no convergence with transplant donors. These results highlight the immune system's critical role in restoring microbial balance and skin health.},
}
@article {pmid40728669,
year = {2025},
author = {Priyadarsini, M and Dhoble, AS},
title = {Combination of flow cytometry and metagenomics to monitor the effect of raw vs digested manure on microbial diversity in anaerobic digestion of Napier grass.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {8},
pages = {963},
pmid = {40728669},
issn = {1573-2959},
support = {SPARC/2019-2020/P1570/SL//Scheme for Promotion of Academic and Research Collaboration (SPARC)/ ; },
mesh = {*Manure/microbiology ; Flow Cytometry ; Metagenomics ; *Poaceae/microbiology ; Anaerobiosis ; *Microbiota ; Biofuels ; Bacteria ; Archaea ; Animals ; },
abstract = {Microbiomes play a crucial role in anaerobic digestion (AD), by degrading the complex lignocellulosic biomass leading to biomethane production. This study emphasizes the role of microbial diversity and its impact on the digester's performance with raw (CD) and digested manure (ADS) as a source of microbiome and Napier grass (NG) as feedstock. The integration of flow cytometry and metagenomics provides a novel perspective on microbial dynamics during anaerobic digestion. Initially, the inocula (ADS and CD) had 354 bacterial and 8 archaeal genera in common that decreased to 39 bacteria and 1 archaeon at the end of experiment, indicating significant shift in microbial diversity during the process. Metagenome sequencing showed that Clostridium was the most abundant genera in NG digested with ADS, while Prevotella was in NG digested with CD. An approximately 2.45% increase in Clostridium in NG digested with ADS led to VFA accumulation and pH drop, inhibiting methanogens and lower biogas production. Most of the flow cytometric populations showed positive correlation with Prevotella suggesting its key role in breaking down of complex substrate. The population 2, 3, and 5 positively correlated to biogas production. NG digested with CD produced nearly twice biogas yield (1064.33 ± 119.97 mL) compared to ADS (508 ± 20.95 mL) which corresponds to the enhanced microbial activity in CD. These findings suggest that microbiome of CD might be better acclimatized for NG degradation than ADS as NG is often used as cattle fodder.},
}
@article {pmid40728577,
year = {2025},
author = {Raziq, MF and Manzoor, H and Kayani, MUR},
title = {Non-small Cell Lung Cancer, Immunotherapy and the Influence of Gut Microbiome.},
journal = {Current microbiology},
volume = {82},
number = {9},
pages = {419},
pmid = {40728577},
issn = {1432-0991},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology/immunology ; *Immunotherapy/methods ; *Lung Neoplasms/therapy/microbiology/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Animals ; },
abstract = {Lung cancer remains the second most commonly diagnosed cancer and the leading cause of cancer-related deaths worldwide. Non-small cell lung cancer (NSCLC), accounting for approximately 85% of lung cancer cases, is the most prevalent form. Treatment options for NSCLC include surgery, radiation therapy, chemotherapy, immunotherapy, and targeted drug therapies. Among these, immune checkpoint inhibitors targeting PD-1/PD-L1 have demonstrated significant potential, particularly in improving treatment outcomes. However, their clinical efficacy is impeded by challenges such as toxicity, resistance development, and variable patient responses. Emerging evidence highlights the critical role of the gut microbiome as an important modulator of immune responses in NSCLC, particularly in the context of anti-PD-1/PD-L1 therapies. Specific gut microbes, such as Akkermansia muciniphila, have been associated with improved responses to immunotherapy, suggesting that modulation of the gut microbiome may enhance treatment outcomes. This review discusses the current understanding of the influence of gut microbiome on NSCLC and its potential to improve the clinical efficacy of anti-PD-1/PD-L1 therapies. By integrating microbiome-based insights into personalized treatment strategies, we can overcome the limitations of current immunotherapy approaches and optimize patient outcomes. This review aims to serve as a resource for the scientific community by providing insights into how modulation of gut microbiome may enhance treatment outcomes in NSCLC patients receiving anti-PD-1/PD-L1 immunotherapy.},
}
@article {pmid40728316,
year = {2025},
author = {Armitage, DW and Alonso-Sánchez, AG and Coy, SR and Cheng, Z and Hagenbeek, A and López-Martínez, KP and Phua, YH and Sears, AR},
title = {Adaptive pangenomic remodeling in the Azolla cyanobiont amid a transient microbiome.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40728316},
issn = {1751-7370},
support = {2018-07819//USDA NIFA Postdoctoral Fellowship/ ; //Rice University Department of BioSciences/ ; CSP-503794//US Department of Energy Joint Genome Institute Community Science Program/ ; },
mesh = {*Symbiosis ; *Microbiota ; *Genome, Bacterial ; *Cyanobacteria/genetics/physiology ; Metagenome ; Phylogeny ; Nitrogen Fixation ; *Ferns/microbiology ; Plant Leaves/microbiology ; },
abstract = {Plants fix nitrogen in concert with diverse microbial symbionts, often recruiting them from the surrounding environment each generation. Vertical transmission of a microbial symbiont from parent to offspring can produce extreme evolutionary consequences, including metabolic codependence, genome reduction, and synchronized life cycles. One of the few examples of vertical transmission of N-fixing symbionts occurs in Azolla ferns, which maintain an obligate mutualism with the cyanobacterium Trichormus azollae-but the genomic consequences of this interaction, and whether the symbiosis involves other vertically transmitted microbial partners, are currently unknown. We generated high-coverage metagenomes across the genus Azolla and reconstructed metagenome assembled genomes to investigate whether a core microbiome exists within Azolla leaf cavities, and how the genomes of T. azollae diverged from their free-living relatives. Our results suggest that T. azollae is the only consistent symbiont across all Azolla accessions, and that other bacterial groups are transient or facultative associates. Pangenomic analyses of T. azollae indicate extreme pseudogenization and gene loss compared to free-living relatives-especially in defensive, stress-tolerance, and secondary metabolite pathways-yet, the key functions of nitrogen fixation and photosynthesis remain intact. Additionally, differential codon bias and intensified positive selection on photosynthesis, intracellular transport, and carbohydrate metabolism genes suggest ongoing evolution in response to the unique conditions within Azolla leaf cavities. These findings highlight how genome erosion and shifting selection pressures jointly drive the evolution of this unique mutualism, while broadening the taxonomic scope of genomic studies on vertically transmitted symbioses.},
}
@article {pmid40726432,
year = {2025},
author = {Hua, R and Ding, N and Hua, Y and Wang, X and Xu, Y and Qiao, X and Shi, X and Bai, T and Xiong, Y and Zhuo, X and Fan, C and Zhou, J and Wu, Y and Liu, J and Yuan, Z and Li, T},
title = {Ligilactobacillus Murinus and Lactobacillus Johnsonii Suppress Macrophage Pyroptosis in Atherosclerosis through Butyrate-GPR109A-GSDMD Axis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {38},
pages = {e01707},
pmid = {40726432},
issn = {2198-3844},
support = {2021YFA1301201//National Key R&amp;D Program of China/ ; 2021YFA0805400//National Key R&amp;D Program of China/ ; 2024YFA1307004//National Key R&amp;D Program of China/ ; 82000474//National Science Foundation of China/ ; 82370458//National Science Foundation of China/ ; 82370875//National Science Foundation of China/ ; 82430019//National Science Foundation of China/ ; 2021KJXX-04//Innovative Talents Promotion Plan of Shaanxi Province of China/ ; xzy012019093//Xi'an&#xa0;Jiaotong University/ ; 2020JM-383//Natural Science Foundation of Shaanxi Province/ ; },
mesh = {*Atherosclerosis/metabolism/microbiology ; Animals ; Mice ; *Receptors, G-Protein-Coupled/metabolism/genetics ; *Pyroptosis/drug effects/physiology ; Gastrointestinal Microbiome/physiology ; *Butyrates/metabolism ; *Macrophages/metabolism ; Probiotics/pharmacology ; Humans ; *Lactobacillus johnsonii/metabolism ; Mice, Inbred C57BL ; *Lactobacillus/metabolism ; Male ; Disease Models, Animal ; },
abstract = {Gut microbiota and their metabolites are remarkable regulators in atherosclerosis. Oral drugs such as aspirin have recently been found to modulate the gut microbiome. However, the roles of drug-microbiota-metabolite interactions in atherosclerosis have not been explored. Herein, two gut probiotics, Ligilactobacillus murinus (L. murinus) and Lactobacillus johnsonii (L. johnsonii), are identified from mouse models and human cohorts, which are positively correlated with aspirin usage. Specifically, the eradication of these two species eliminated aspirin's anti-atherosclerotic effects, while their transplantation exhibited therapeutic effects against atherosclerosis. Integrative analysis of metagenomic and metabolomic data showed that elevated levels of butyrate are associated with these two species. Mechanically, L. murinus and L. johnsonii form symbiotic networks with butyrate-producing bacteria such as Allobaculum. This study confirmed that gut microbes produce butyrate, which helps preserve the gut barrier and prevents the leakage of lipopolysaccharides. By integrating molecular biology and single-cell sequencing data, G protein-coupled receptor 109A (GPR109A) is confirmed as the direct target of butyrate. Through the activation of GPR109A, butyrate produced by L. murinus and L. johnsonii suppressed the expression of Gasdermin D (GSDMD) in the pyroptosis of macrophages during atherosclerosis. These findings offer novel insights into the drug-microbiota axis that can be targeted to improve the treatment of atherosclerosis.},
}
@article {pmid40726156,
year = {2025},
author = {Yang, S and Huang, X and Li, X and Feng, J and Chen, P and Cao, Z and He, L and Li, C and Li, Z and Xie, M},
title = {Aloe vera polysaccharides mitigate high-fat high-cholesterol diet-induced atherosclerosis in ApoE[-/-] mice via regulation of lipid metabolism and gut microbiota.},
journal = {Food &amp; function},
volume = {16},
number = {16},
pages = {6671-6686},
doi = {10.1039/d5fo01995h},
pmid = {40726156},
issn = {2042-650X},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Atherosclerosis/drug therapy/metabolism/etiology ; Diet, High-Fat/adverse effects ; Mice ; *Lipid Metabolism/drug effects ; *Aloe/chemistry ; Male ; *Polysaccharides/pharmacology/administration &amp; dosage ; Apolipoproteins E/genetics ; Mice, Inbred C57BL ; RAW 264.7 Cells ; Disease Models, Animal ; },
abstract = {Cardiovascular diseases are leading causes of death globally, often manifesting after years of atherosclerosis (AS) progression. In this study, we investigated the atheroprotective effects of three different sources of glucomannan, Dendrobium officinale polysaccharide, Konjac glucomannan, and Aloe vera polysaccharide (AVP), using an in vitro ox-LDL-induced foam cell model and an in vivo high-fat high-cholesterol diet-fed ApoE[-/-] mouse model. Both settings indicate that AVP exerts the most significant atheroprotective effects. It inhibits lipid absorption and enhances the regulation of lipid homeostasis by the liver X receptor, thereby suppressing the formation of foam cells. It can also alleviate ox-LDL-induced oxidative stress and apoptosis in RAW 264.7 cells. Animal experiments show that AVP can prevent the formation of atherosclerotic plaques and coronary artery fibrosis, while also reducing circulating IL-1β levels. Furthermore, liver transcriptomic analysis shows that AVP inhibits inflammation and promotes bile acid excretion and transport by upregulating the farnesoid X receptor. Additionally, metagenomic analysis indicates that AVP can significantly reverse the microbial alterations associated with AS. Specific gut microbes, such as Prevotella, may partially mediate the effects of AVP through the gut-liver axis. This is the first study to report the atheroprotective effects of AVP, demonstrating that it alleviates atherosclerosis by restoring lipid metabolism homeostasis and modulating the gut microbiome.},
}
@article {pmid40724992,
year = {2025},
author = {Rušanac, A and Škibola, Z and Matijašić, M and Čipčić Paljetak, H and Perić, M},
title = {Microbiome-Based Products: Therapeutic Potential for Inflammatory Skin Diseases.},
journal = {International journal of molecular sciences},
volume = {26},
number = {14},
pages = {},
pmid = {40724992},
issn = {1422-0067},
support = {NPOO.C3.2.R3-I1.04.0240//European Regional Development Fund/ ; KK.01.2.1.02.0137//European Regional Development Fund/ ; IP.1.1.03.0157//European Regional Development Fund/ ; },
mesh = {Humans ; *Microbiota/drug effects ; Probiotics/therapeutic use ; Prebiotics/administration &amp; dosage ; *Skin Diseases/microbiology/therapy ; Dysbiosis/microbiology/therapy ; Skin/microbiology ; Animals ; Psoriasis/microbiology/therapy ; Dermatitis, Atopic/microbiology/therapy ; },
abstract = {Maintaining a balanced skin microbiota is essential for skin health, whereas disruptions in skin microbiota composition, known as dysbiosis, can contribute to the onset and progression of various skin disorders. Microbiota dysbiosis has been associated with several inflammatory skin conditions, including atopic dermatitis, seborrheic dermatitis, acne, psoriasis, and rosacea. Recent advances in high-throughput sequencing and metagenomic analyses have provided a deeper understanding of the skin microbial communities in both health and disease. These discoveries are now being translated into novel therapeutic approaches aimed at restoring microbial balance and promoting skin health through microbiome-based interventions. Unlike conventional therapies that often disrupt the microbiota and lead to side effects or resistance, microbiome-based products offer a more targeted strategy for preventing and managing inflammatory skin diseases. These products, which include probiotics, prebiotics, postbiotics, and live biotherapeutic agents, are designed to modulate the skin ecosystem by enhancing beneficial microbial populations, suppressing pathogenic strains, and enhancing immune tolerance. As a result, they represent a promising class of products with the potential to prevent, manage, and even reverse inflammatory skin conditions. However, realizing the full therapeutic potential of microbiome-based strategies in dermatology will require continued research, robust clinical validation, and clear regulatory frameworks.},
}
@article {pmid40723458,
year = {2025},
author = {Penalba-Iglesias, D and Robas-Mora, M and González-Reguero, D and Fernández-Pastrana, VM and Probanza, A and Jiménez-Gómez, PA},
title = {Use of Bacillus pretiosus and Pseudomonas agronomica for the Synthesis of a Valorized Water Waste Treatment Plant Waste as a Biofertilizer Intended for Quercus pyrenaica L. Fertigation.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
pmid = {40723458},
issn = {2079-7737},
support = {TED2021-132285A-I00//Next Generation Funds/ ; },
abstract = {The loss of hectares of forest areas has become a global issue that has worsened over recent years due to unsustainable human activities. In a context of limited availability of productive land, it is urgent to adopt efficient strategies to recover the affected natural areas. Actions based on a circular economy, such as the use of organic chemical matrices recovered from water waste treatment plant waste, have proven to be effective. In this regard, the addition of plant growth-promoting bacteria (PGPB), such as Bacillus pretiosus and Pseudomonas agronomica, can contribute to the chemical treatment, favoring the recovery of soils, accelerating the recovery of vegetation cover, and inducing an increase in biodiversity. In this research, the effect of bio-fertigation under controlled laboratory conditions in Quercus pyrenaica is evaluated. After a thirty-six-week trial, the biometric and nutritional parameters of the plants were harvested and measured, and the diversity and composition of the metagenomes of their rhizospheres were evaluated. As well, the cenoantibiogram and the metabolic diversity were measured. The results showed that the use of these biofertilizers increased the variables related to plant production, quality of plant composition as an indirect means of their resilience, as well as an increase in rhizospheric microbial diversity and a reduction in their MIC resistance to the most widely used antibiotics. For all these reasons, the use of the biofertilizer result of the combination of WWTP waste, Bacillus pretiosus, and Pseudomonas agronomica is postulated as an environmentally friendly strategy that can contribute to the recovery of potential oak forest areas.},
}
@article {pmid40722249,
year = {2025},
author = {Hilberath, J and Busch, A and Schoppmeier, U and Schmauder, K and Oberhettinger, P and Marschal, M and Slavetinsky, C and Sturm, E and Peter, S and D'Alvise, P},
title = {Small intestinal bacterial overgrowth and dysbiosis in children with intestinal failure: A descriptive cohort study.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {49},
number = {8},
pages = {964-974},
pmid = {40722249},
issn = {1941-2444},
mesh = {Humans ; *Dysbiosis/microbiology ; Female ; Male ; *Intestine, Small/microbiology ; Child, Preschool ; Child ; *Gastrointestinal Microbiome ; Infant ; Prospective Studies ; Cohort Studies ; *Intestinal Failure/microbiology/complications ; Bacteria/growth &amp; development ; Short Bowel Syndrome/microbiology ; Feces/microbiology ; },
abstract = {BACKGROUND: Small intestinal bacterial overgrowth (SIBO) is a clinical and diagnostic challenge in pediatric intestinal failure. This study aimed to assess SIBO and dysbiosis in children with intestinal failure and to analyze clinical characteristics as well as cultural and metagenomic sequencing results from different sampling methods.<br><br>METHODS: Descriptive, single-center cohort study in intestinal failure patients with prospective collection of intraluminal aspirate, epithelial brush swab, mucosal biopsy, and small bowel stoma stool for SIBO diagnosis, defined as &#x2265;10[3]&#x2009;CFU/ml of enteric, colonic-type bacteria, and microbiome analysis via whole-genome sequencing. Statistical testing included receiver operating characteristic analysis, chi-square test, and independent samples t test.<br><br>RESULTS: Forty-four children with intestinal failure were analyzed (median age 58 months; female 48%; short bowel syndrome 70%). Sixty-six percent of samples were positive for SIBO. In 93%, all three endoscopic sampling methods showed congruent results. SIBO-positive cases were associated (P&#x2009;<&#x2009;0.05) with small bowel dilatation, proton pump inhibitor use, intestinal inflammation, elevated direct bilirubin and hepatocellular enzyme levels, and a history of liver fibrosis and central venous catheter infections. Metagenomic sequencing revealed microbial dysbiosis in intestinal failure patients, with SIBO-positive cases showing higher microbial reads, lower alpha diversity, and increased abundance of Enterobacteriaceae and enteric anaerobes.<br><br>CONCLUSION: SIBO and dysbiosis are common in children with intestinal failure and associated with liver injury, central line-associated bloodstream infections, and intestinal inflammation. Cultural diagnosis of SIBO using mucosal biopsies or brush swabs are alternatives to small bowel aspirates. Metagenomic sequencing is feasible, and high microbial read numbers are indicative of SIBO.},
}
@article {pmid40721426,
year = {2025},
author = {Yang, Y and Ye, M and Song, Y and Xing, W and Zhao, X and Li, Y and Shen, J and Zhou, J and Arikawa, K and Wu, S and Song, Y and Xu, N},
title = {Gut microbiota and SCFAs improve the treatment efficacy of chemotherapy and immunotherapy in NSCLC.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {146},
pmid = {40721426},
issn = {2055-5008},
support = {2020YFC2003700//National Key R&amp;D Plan/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; 20Z11901000, 20DZ2261200, 20XD1401200, 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; SHDC2020CR5010-002//Clinical Research Plan of SHDC/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; ZY(2021-2023)-0207-01//Shanghai Municipal Health Commission and Shanghai Municipal Administrator of Traditional Chinese Medicine/ ; 81401877, 82130001, and 82272243//National Natural Science Foundation of China/ ; 81401877, 82130001, and 82272243//National Natural Science Foundation of China/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology/drug therapy ; *Immunotherapy/methods ; Animals ; *Lung Neoplasms/therapy/microbiology/drug therapy ; Mice ; *Fatty Acids, Volatile/metabolism ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Female ; Male ; Metagenomics ; Middle Aged ; Aged ; Dysbiosis/microbiology ; Antineoplastic Agents/therapeutic use ; },
abstract = {The role of gut dysbiosis in shaping immunotherapy responses is well-recognized, yet its effect on the therapeutic efficacy of chemotherapy and immunotherapy combinations remains poorly understood. We analyzed gut microbiota in non-small cell lung cancer (NSCLC) patients treated with chemo-immunotherapy, comparing responders and non-responders using 16S rRNA sequencing. Responders showed higher microbial richness and abundance of specific genera like Faecalibacterium and Subdoligranulum, and the phylum Firmicutes. Support vector machine (SVM), a machine learning model based on microbial composition, predicted treatment efficacy with the area under the curve (AUC) values of 0.763 for genera and 0.855 for species. Metagenomic analysis revealed significant differences in metabolic pathways, with responders exhibiting higher short-chain fatty acids (SCFAs) production. Fecal microbiota transplantation (FMT) and SCFAs supplementation in mouse models enhanced treatment efficacy by promoting effector T cell activity in tumors. Our study suggests that gut microbiota, through SCFAs production, regulates chemo-immunotherapy efficacy, offering new strategies to improve NSCLC treatment outcomes.},
}
@article {pmid40716139,
year = {2025},
author = {Lemos-Lucumi, CA and Cárdenas-Hernández, V and Toro-Perea, N},
title = {Metagenomic and metatranscriptomic exploration of Avicennia germinans L.: Endophytic microbiome of leaves and roots.},
journal = {Microbiological research},
volume = {300},
number = {},
pages = {128287},
doi = {10.1016/j.micres.2025.128287},
pmid = {40716139},
issn = {1618-0623},
mesh = {*Endophytes/genetics/classification/isolation &amp; purification ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; *Avicennia/microbiology ; *Microbiota ; Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification ; Gene Expression Profiling ; Transcriptome ; Metagenome ; },
abstract = {Mangroves are productive coastal ecosystems with extreme environmental conditions of temperature, salinity and anthropogenic pollution. Their associated microbiota plays an essential role in plant survival, yet their functional dynamics remain poorly understood. This study characterizes the endophytic microbiome of Avicennia germinans L. in the Buenaventura Bay mangrove ecosystem (Colombia), using a combined metagenomic and metatranscriptomic approach. Distinct microbial communities were observed in leaves and pneumatophores. Root-associated endophytes exhibited higher taxonomic richness and greater transcriptional activity. Functional gene expression revealed enrichment of pathways related to osmotic and oxidative stress responses, hydrocarbon degradation, nitrogen metabolism, and ion homeostasis. The expression of efflux pumps, NADH dehydrogenase, cytochromes, chaperones, H[+]-ATPases, and H[+]/Na[+] antiporters suggest active microbial participation in salinity, heavy metal, xenobiotics and stress resistance. These findings highlight the adaptive versatility of the endophytic microbiome in A. germinans and support its potential for biotechnological applications in stress resistance and bioremediation.},
}
@article {pmid40720840,
year = {2025},
author = {Slizovskiy, IB and Gaire, TN and Ferm, PM and Odland, CA and Dee, SA and Nerem, J and Bravo, JE and Kimball, AD and Boucher, C and Noyes, NR},
title = {Reducing skin microbiome exposure impacts through swine farm biosecurity.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40720840},
issn = {2047-217X},
support = {R01 AI141810/AI/NIAID NIH HHS/United States ; U54 OH010170/OH/NIOSH CDC HHS/United States ; 1R01AI141810-01//National Institute of Allergy and Infectious Diseases/ ; 5U54OH010170-13A/OH/NIOSH CDC HHS/United States ; /NH/NIH HHS/United States ; },
mesh = {*Microbiota ; *Skin/microbiology ; Animals ; Swine/microbiology ; Humans ; Farms ; *Biosecurity ; *Occupational Exposure ; Female ; Male ; Adult ; Bacteria/genetics/classification/isolation &amp; purification ; Longitudinal Studies ; Animal Husbandry ; Skin Microbiome ; },
abstract = {BACKGROUND: Livestock work is unique due to worker exposure to animal-associated microbiomes within the workplace. Swine workers are a unique cohort within the US livestock labor force, as they have direct daily contact with pigs and undertake mandatory biosecurity interventions. However, investigating this occupational cohort is challenging, particularly within tightly regulated commercial swine operations. Thus, little is known about the impacts of animal exposure and biosecurity protocols on the swine worker microbiome. We obtained unique samples from US swine workers, using a longitudinal study design to investigate temporal microbiome dynamics.<br><br>RESULTS: We observed a significant increase in bacterial DNA load on worker skin during the workday, with concurrent changes in the composition and abundance of microbial taxa, resistance genes, and mobile genetic elements. However, mandatory showering at the end of the workday partially returned the skin's microbiome and resistome to their original state.<br><br>CONCLUSIONS: These novel results from a human cohort demonstrate that existing biosecurity practices can ameliorate work-associated microbiome impacts.},
}
@article {pmid40719990,
year = {2025},
author = {Naqvi, SAH and Umar, UUD and Rehman, AU},
title = {Beneficial communities from core bacterial microbiota of Oryza sativa L. soil and leaves perform dynamic role in growth promotion and suppression of bacterial leaf blight.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {41},
number = {8},
pages = {285},
pmid = {40719990},
issn = {1573-0972},
mesh = {*Oryza/microbiology/growth &amp; development ; *Soil Microbiology ; *Plant Leaves/microbiology/growth &amp; development ; Xanthomonas/pathogenicity/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; *Plant Diseases/microbiology/prevention &amp; control ; *Microbiota/genetics ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Pakistan ; Biological Control Agents ; Soil/chemistry ; Metagenomics ; Phylogeny ; },
abstract = {Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), severely threatens global rice production, highlighting the urgent need for sustainable alternatives to chemical pesticides. This study investigates the rhizosphere and phyllosphere microbiomes of Oryza sativa in Punjab, Pakistan, to identify native biocontrol agents (BCAs) with potential to suppress BLB. Using 16S rRNA amplicon sequencing (V3-V9 regions), we analyzed soil and leaf samples from 10 agricultural districts. Microbial diversity, community structure, and functional potential were assessed via bioinformatics tools (QIIME 2, DADA2, PICRUSt2), with a focus on taxa antagonistic to Xoo. Healthy rhizospheres exhibited significantly higher alpha diversity (Shannon index: 6.8 vs. 4.2 in leaves; *p* < 0.001), dominated by copiotrophic taxa (Proteobacteria, Bacteroidetes) linked to organic inputs and root exudates. Diseased soils favored oligotrophic Actinobacteria and Chloroflexi. Functional metagenomics revealed enrichment of siderophore biosynthesis, antibiotic production, and nutrient-cycling genes in healthy soils. Antagonistic genera (Bacillus, Pseudomonas, Streptomyces) demonstrated chitinase and surfactin activity against Xoo, while diseased samples showed elevated Xanthomonas and Erwinia abundances correlating with BLB severity. Native BCAs outperformed non-native strains in colonization and nutrient competition, highlighting their adaptability to local agroecological conditions. Our findings position native BCAs as pivotal tools for BLB suppression and sustainable agriculture, reducing reliance on synthetic chemicals. Field trials confirmed that microbial consortia formulations reduced BLB incidence by 40% and increased yield by 18%. These findings highlight the potential of microbiome-driven strategies to mitigate BLB, reduce chemical reliance, and foster sustainable agricultural practices. Future work should integrate multi-omics approaches to optimize microbial solutions for climate resilience and scale their adoption through policy frameworks.},
}
@article {pmid40719501,
year = {2025},
author = {Keskey, R and Bluiminck, S and Sangwan, N and Meltzer, R and Lam, A and Thewissen, R and Zaborin, A and van Goor, H and Zaborina, O and Alverdy, J},
title = {Dietary impact on the gut resistome: western diet independently increases the prevalence of antibiotic resistance genes within the gut microbiota.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0276624},
pmid = {40719501},
issn = {2165-0497},
support = {R01GMO62344-22//HHS | NIH | OSC | Common Fund (NIH Common Fund)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Anti-Bacterial Agents/pharmacology ; *Diet, Western/adverse effects ; Cecum/microbiology ; *Bacteria/genetics/drug effects/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; Mice, Inbred C57BL ; Male ; },
abstract = {Approximately half of surgical site infections are caused by pathogens resistant to the antibiotics used for prophylaxis. We recently demonstrated that when mice are fed a western diet (WD) that is high in fat and low in fiber, exposed to antibiotics, and undergo an otherwise recoverable surgery, they develop lethal sepsis associated with dissemination of multi-drug-resistant pathogens. Here, we hypothesized that a WD alone can drive the intestinal microbiome to become populated by antibiotic-resistant bacteria independent of exposure to antibiotics. The cecal microbiota response to antibiotics was determined utilizing Biolog Phenotype Microarrays in the presence of 48 different antibiotics. WD-fed mice had a significant increase in antibiotic resistance within their microbiome compared to mice on a standard low-fat, high-fiber diet (SD) including aminoglycosides, tetracyclines, cephalosporins, fluoroquinolones, and sulfamethoxazole. By metagenomic sequencing, there was an increase in the antibiotic resistance genes (ARGs) within the WD cecal microbiota, including CfxA2, ErmG, TetQ, and LnuC. After just 7 days of WD, the ARGs ErmG and CfxA2 were detectable within the stool. WD independent of antibiotic exposure increases the presence of ARGs within the gut microbiota independent of antibiotic exposure.IMPORTANCEAntibiotic resistance is a major challenge in healthcare and results in significant morbidity and mortality. Currently, half of surgical site infections are caused by pathogens resistant to antibiotics used for prophylaxis. In this study, we demonstrate that a western diet alone has the ability to increase the presence of antibiotic resistance genes within the gut microbiome. By understanding dietary influences on the gut resistome, we may improve our understanding of infections with antibiotic-resistant organisms and one day develop personalized antibiotic regimens based on an individual's gut resistome.},
}
@article {pmid40719460,
year = {2025},
author = {Tang, J and Baker, JL},
title = {The salivary virome during childhood dental caries.},
journal = {mSphere},
volume = {10},
number = {8},
pages = {e0019825},
pmid = {40719460},
issn = {2379-5042},
support = {R00 DE029228/DE/NIDCR NIH HHS/United States ; S10 OD034224/OD/NIH HHS/United States ; R00-DE029228/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Dental Caries/virology/microbiology ; *Saliva/virology ; *Virome ; Child ; Male ; Female ; Child, Preschool ; Metagenomics ; Metagenome ; Genome, Viral ; *Viruses/classification/genetics/isolation &amp; purification ; Bacteriophages/genetics/classification ; Bacteria ; Microbiota ; },
abstract = {While many studies have examined the bacterial taxa associated with dental caries, the most common chronic infectious disease, little is known about the caries-associated virome. In this study, the salivary viromes of 21 children with severe caries (>2 dentin lesions) and 23 children with healthy dentition were examined. A total of 2,485 viral metagenome-assembled genomes (vMAGs) were identified, binned, and quantified from the metagenomic assemblies. These vMAGs were mostly phages and represented 1,865 unique species-level viral operational taxonomic units (vOTUs), of which 478 appear to be novel. The metagenomes were also queried for all 3,858 unique species-level vOTUs of DNA viruses with a human host on NCBI Virus; however, all but Human betaherpesvirus 7 were at very low abundance in the saliva. The oral viromes of the children with caries exhibited significantly different beta diversity compared to the oral virome of the children with healthy dentition; several vOTUs predicted to infect Haemophilus and Neisseria were strongly correlated with health, and five vOTUs predicted to infect Saccharibacteria, Prevotella, and Veillonella were correlated with caries. Co-occurrence analysis indicated that the phage typically co-occurred with both their predicted hosts and with bacteria that were themselves associated with the same disease status. Overall, this study provided the sequences of 35 complete or nearly complete novel oral phages and illustrated the potential significance of the oral virome in the context of dental caries, which has been largely overlooked. This work represents an important step toward the identification and study of phage therapy candidates that treat or prevent caries pathogenesis.IMPORTANCEDental caries is the most common chronic infectious disease worldwide and is caused by dysbiosis of the oral microbiome featuring an increased abundance of acid-tolerant, acid-producing, and biofilm-forming bacteria. The oral microbiome also contains viruses; however, very little is known about the caries-associated virome. In this study, the salivary virome of children with severe caries was compared to the salivary virome of children with healthy dentition. The metagenomes contained a total of 1,865 unique species-level viral operational taxonomic units (vOTUs), of which 478 appeared to be novel. The viromes from the children with caries were significantly different than the viromes from the children with healthy teeth, and several health- and disease-associated vOTUs were identified. This study illustrated the potential importance of the oral virome in the context of dental caries and serves as a step towards a better understanding of oral inter-kingdom interactions and identification of potential phage-based caries therapeutics.},
}
@article {pmid40719366,
year = {2025},
author = {Wang, X and Wang, N and Gao, T and Zhang, Y and Fu, Z and Zhao, Y and Huang, Y and Zheng, X and Gao, X and Lu, L and Yang, L},
title = {Symptom-specific gut microbial and metabolic profiles in ADHD reveal SCFA deficiency as a Key pathogenic mechanism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2537755},
pmid = {40719366},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; *Attention Deficit Disorder with Hyperactivity/microbiology/metabolism ; Animals ; Humans ; Mice ; Male ; Female ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Fecal Microbiota Transplantation ; Child ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metabolome ; Adolescent ; Metabolomics ; },
abstract = {Previous evidence links gut microbiota to attention-deficit/hyperactivity disorder (ADHD) through the gut-brain axis. However, the specific microbiota contributing to symptoms remain unclear. To characterize the gut microbial profile related to different symptoms and explore the mediation mechanism between microbiota alterations and the core ADHD symptoms, we conducted shotgun metagenomic sequencing and fecal metabolomics analysis on 94 ADHD patients and 94 age- and gender-matched controls. Microbial characteristics of three subgroups exhibiting different ADHD core symptom presentations were analyzed. We developed a metabolic model and conducted causal mediation analyses to examine how metabolites connect the microbiota to the symptoms. Fecal microbiota transplantation in mice was employed to validate the findings. The redundancy analysis identified ADHD symptoms as environmental gradients and explained the changes in beta diversity (F = 1.345, pFDR = 0.015). Greater gut microbial alterations were observed in combined presentations (ADHD-C). Several beneficial bacteria involved in short-chain fatty acid synthesis were found to be downregulated, with Lactobacillus sanfranciscensis notably linked to all three core symptoms (p.adj = 1.04E-13; p.adj = 5.07E-07; p.adj = 2.61E-05). Various taxa, functional pathways, and metabolites associated with specific ADHD symptom domains were identified. Imidazoleacetic acid partially mediated the effects between Lactobacillus sanfranciscensis and inattention (p = 0.012). In mice subjected to feces from ADHD patients with a low abundance of Lactobacillus sanfranciscensis, treatment with this strain greatly improved both hyperactivity (t = 2.665, p = 0.0237) and inattention (t = 2.389, p = 0.0380), while acetate supplementation only alleviated inattention (t = 2.362, p = 0.0398). Our findings suggest that different ADHD symptoms were related to common and different gut microbiota and metabolites. Fecal microbiota transplantation in mice validated the hypothesis that gut microbial composition affects ADHD symptoms through metabolic alterations. This study provides more insight into the mechanisms underlying metabolic disturbances in ADHD and elucidates the role of gut microbiota in these processes.},
}
@article {pmid40719338,
year = {2025},
author = {Louca, S and Mullin, CE},
title = {Effects of Vacuum-Heat-Assisted Sample Desiccation on Microbiome Surveys.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e70020},
pmid = {40719338},
issn = {1755-0998},
support = {2243038//US National Science Foundation/ ; },
mesh = {*Desiccation/methods ; Animals ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Specimen Handling/methods ; Vacuum ; Feces/microbiology ; Hot Temperature ; Metagenomics/methods ; Soil Microbiology ; },
abstract = {Sample preservation in the field and during transport can be a logistical challenge for microbiome surveys, particularly in remote areas. Sample desiccation eliminates the need for complicated cold chains and dangerous preservatives. However, the effects of desiccation on modern microbiome workflows such as gene-centric metagenomic profiling and metagenome-assembled genome (MAG) binning, remain poorly understood. In addition, most common desiccation tools such as lyophilisation cannot easily be deployed in the field. Here, we describe a proof-of-principle sample desiccator using vacuum and heat, specifically built for deployment in the field and exhibiting low power consumption and cost. We then test the effects of vacuum-heat-assisted sample desiccation followed by storage at room temperature, in comparison to conventional freezing, on multiple soil and animal faecal samples, via metagenomic and 16S rRNA amplicon sequencing. We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG construction, as well as effects on inferred microbial community composition. We find that the impact of drying on considered success metrics was almost always either minor, non-significant or positive. For a subset of source materials we observed moderate but statistically significant differences in terms of inferred microbial taxonomic and genetic composition. We conclude that vacuum- and heat-assisted desiccation can be a useful, practical and cost-effective tool for microbiome field surveys, when a high consistency with frozen samples is not required.},
}
@article {pmid40715814,
year = {2025},
author = {Xiong, R and Aiken, E and Caldwell, R and Vernon, SD and Kozhaya, L and Gunter, C and Bateman, L and Unutmaz, D and Oh, J},
title = {AI-driven multi-omics modeling of myalgic encephalomyelitis/chronic fatigue syndrome.},
journal = {Nature medicine},
volume = {31},
number = {9},
pages = {2991-3001},
pmid = {40715814},
issn = {1546-170X},
support = {R01 AR078634/AR/NIAMS NIH HHS/United States ; U19 AI142733/AI/NIAID NIH HHS/United States ; DP2 GM126893-01//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; U54 NS105539/NS/NINDS NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; DP2 GM126893/GM/NIGMS NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; },
mesh = {Humans ; *Fatigue Syndrome, Chronic/metabolism/microbiology/genetics/immunology/blood ; Male ; Female ; Metabolomics/methods ; Adult ; Biomarkers/blood/metabolism ; Gastrointestinal Microbiome/genetics ; Middle Aged ; *Artificial Intelligence ; Metabolome ; Neural Networks, Computer ; Longitudinal Studies ; Metagenomics ; Multiomics ; },
abstract = {Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic illness with a multifactorial etiology and heterogeneous symptomatology, posing major challenges for diagnosis and treatment. Here we present BioMapAI, a supervised deep neural network trained on a 4-year, longitudinal, multi-omics dataset from 249 participants, which integrates gut metagenomics, plasma metabolomics, immune cell profiling, blood laboratory data and detailed clinical symptoms. By simultaneously modeling these diverse data types to predict clinical severity, BioMapAI identifies disease- and symptom-specific biomarkers and classifies ME/CFS in both held-out and independent external cohorts. Using an explainable AI approach, we construct a unique connectivity map spanning the microbiome, immune system and plasma metabolome in health and ME/CFS adjusted for age, gender and additional clinical factors. This map uncovers altered associations between microbial metabolism (for example, short-chain fatty acids, branched-chain amino acids, tryptophan, benzoate), plasma lipids and bile acids, and heightened inflammatory responses in mucosal and inflammatory T cell subsets (MAIT, γδT) secreting IFN-γ and GzA. Overall, BioMapAI provides unprecedented systems-level insights into ME/CFS, refining existing hypotheses and hypothesizing unique mechanisms-specifically, how multi-omics dynamics are associated to the disease's heterogeneous symptoms.},
}
@article {pmid40715695,
year = {2025},
author = {Yu, L and Guo, Q and Gu, X and Wang, Z and Li, J and Wang, X and Xu, Z and Wang, Y and Zhang, Y and Zhang, Y and Ding, Y and Chen, Z and Chen, K and Ding, Y},
title = {Impact of gut microbiome on radiotherapy and immunotherapy efficacy in microsatellite-stable colorectal cancer: role of propionic acid and B. fragilis.},
journal = {British journal of cancer},
volume = {133},
number = {7},
pages = {956-969},
pmid = {40715695},
issn = {1532-1827},
mesh = {*Colorectal Neoplasms/therapy/microbiology/immunology/genetics/pathology ; *Gastrointestinal Microbiome/immunology/drug effects ; Animals ; Mice ; *Immunotherapy/methods ; *Propionates/metabolism/pharmacology ; Microsatellite Instability ; *Bacteroides fragilis ; Humans ; Tumor Microenvironment/immunology ; Female ; CD8-Positive T-Lymphocytes/immunology ; Combined Modality Therapy ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer-related deaths worldwide. While immunotherapy is effective in microsatellite instability-high (MSI-H) CRC, its benefits in microsatellite-stable (MSS) CRC are limited. Radiotherapy may modify the immune microenvironment in MSS-CRC, enhancing immunotherapy efficacy, but individual responses vary.<br><br>METHODS: We employed MSS-CRC mouse models to examine the effects of combined radiotherapy and immunotherapy, with and without antibiotics (ABX). Various analyses, including metagenomic, nontargeted metabolomic, and gas chromatography-mass spectrometry (GC-MS), were performed to identify factors influencing treatment outcomes. Flow cytometry, immunohistochemistry and in vivo antibody blockade experiments assessed the role of metabolites and bacteria on CD8[+] T cell infiltration and treatment responses, complemented by transcriptomic sequencing and molecular biology experiments.<br><br>RESULTS: Our analyses identified propionic acid and Bacteroides fragilis (B. fragilis) as crucial factors enhancing the efficacy of combined therapies in MSS-CRC. Both propionic acid and B. fragilis improved CD8[+] T cell infiltration and treatment outcomes, with molecular assays indicating that propionic acid facilitates H3K14 acetylation, activating the Meox1-Cxcr6/Ccl5 axis.<br><br>CONCLUSIONS: This study highlights the pivotal role of the gut microbiome, specifically propionic acid and B. fragilis, in modulating the efficacy of combined radiotherapy and immunotherapy in MSS-CRC.},
}
@article {pmid40715283,
year = {2025},
author = {Tan, JH and Liew, KJ and Sani, RK and Samanta, D and Pointing, SB and Chan, KG and Goh, KM},
title = {Microbial diversity and metabolic predictions of high-temperature streamer biofilms using metagenome-assembled genomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27297},
pmid = {40715283},
issn = {2045-2322},
mesh = {*Biofilms/growth &amp; development ; *Hot Springs/microbiology ; *Metagenome ; Hot Temperature ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Biodiversity ; Genome, Bacterial ; Metagenomics/methods ; Malaysia ; },
abstract = {High-temperature streamer biofilm communities (SBCs) are often dominated by Aquificota, which can comprise over 90% of the microbial population in shallow water channels, such as those found at Mammoth hot springs of Yellowstone National Park and the Rehai hot springs in China. This study examines SBCs from the Dusun Tua (DT) hot spring in Malaysia (75 °C, pH 7.6), where Aquificota accounted for only ~ 35% of the total amplicon sequence variants. Amplicon and hybrid metagenomic sequencing revealed a more balanced microbial community, co-dominated by Aquificota, Chloroflexota, Desulfobacterota, Bacteroidota, Deinococcota, and Candidatus Hydrothermae, along with Thermoproteota and Micrarchaeota. To our knowledge, the co-dominance of Aquificota and Chloroflexota in SBCs has not been previously reported. The unexpected abundance of Chloroflexota may stem from dispersal from upstream Cyanobacteriota-Chloroflexota biofilms, contributing to community diversification. Genome-resolved analyses identified more than 60 medium- to high-quality metagenome-assembled genomes (MAGs), suggesting that biofilm formation was initially driven by chemoautotrophic sulfur oxidation and CO2 fixation, followed by the gradual integration of heterotrophic taxa. Nitrogen cycling and hydrogen oxidation are likely to contribute additional sources of energy. The presence of diverse CAZymes suggests that plant litter may serve as an additional carbon source. Genome-centric analyses across multiple phyla indicated that extracellular polymeric substances (EPS), curli fibers, and other matrix components contribute to the biofilm matrix, enhancing structural resilience and supporting persistence under harsh conditions. Overall, this study highlights the distinct microbial ecology of the DT SBC and broader metabolic roles beyond Aquificota dominance. The genes identified in this study may hold biotechnological potential and serve as a valuable resource for future enzyme discovery and functional screening.},
}
@article {pmid40715043,
year = {2025},
author = {Duchesneau, K and Aldeguer-Riquelme, B and Petro, C and Makke, G and Green, M and Tfaily, M and Wilson, R and Roth, SW and Johnston, ER and Kluber, LA and Schadt, CW and Trejo, JB and Callister, SJ and Purvine, SO and Chanton, JP and Hanson, PJ and Tringe, S and Eloe-Fadrosh, E and Glavina Del Rio, T and Konstantinidis, KT and Kostka, JE},
title = {Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6869},
pmid = {40715043},
issn = {2041-1723},
support = {DE-SC0023297//U.S. Department of Energy (DOE)/ ; DE-SC0012088//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Microbiota/genetics/physiology ; Methane/metabolism ; Metagenome ; Carbon/metabolism ; Climate Change ; Bacteria/metabolism/genetics/classification ; Global Warming ; Ecosystem ; Electrons ; },
abstract = {The response of microbial communities that regulate belowground carbon turnover to climate change drivers in peatlands is poorly understood. Here, we leverage a whole ecosystem warming experiment to elucidate the key processes of terminal carbon decomposition and community responses to temperature rise. Our dataset of 697 metagenome-assembled genomes (MAGs) represents the microbial community from the surface (10 cm) to 2 m deep into the peat column, with only 3.7% of genomes overlapping with other well-studied peatlands. Community composition has yet to show a significant response to warming after 3 years, suggesting that metabolically diverse soil microbial communities are resistant to climate change. Surprisingly, abundant and active methanogens in the genus Candidatus Methanoflorens, Methanobacterium, and Methanoregula show the potential for both acetoclastic and hydrogenotrophic methanogenesis. Nonetheless, the predominant pathways for anaerobic carbon decomposition include sulfate/sulfite reduction, denitrification, and acetogenesis, rather than methanogenesis based on gene abundances. Multi-omics data suggest that organic matter cleavage provides terminal electron acceptors, which together with methanogen metabolic flexibility, may explain peat microbiome composition resistance to warming.},
}
@article {pmid40714398,
year = {2025},
author = {Wu, L and Yan, M and Huang, X and Liao, H and Bao, D and Ge, Y and Wang, S and Xia, X},
title = {Temperature-mediated shift from competitive to facilitative interactions between lactic acid bacteria and bacillus species in daqu fermentation: Insights from metagenomics, dual RNA-seq, and coculture analysis.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111352},
doi = {10.1016/j.ijfoodmicro.2025.111352},
pmid = {40714398},
issn = {1879-3460},
mesh = {Fermentation ; *Bacillus/genetics/metabolism/physiology/growth &amp; development ; Temperature ; Metagenomics ; *Lactobacillales/genetics/metabolism/physiology ; *Microbial Interactions ; Coculture Techniques ; Lactic Acid/metabolism ; RNA-Seq ; *Fermented Foods/microbiology ; Food Microbiology ; },
abstract = {Daqu, a pivotal starter that defines the flavor profile and quality of Baijiu, undergoes dynamic temperature changes during its production, significantly influencing the microbial community structure and function. Although the importance of fermentation temperature in shaping microbial biodiversity is well-recognized, its impact on microbial interaction dynamics and the underlying mechanisms remains poorly understood. This study integrates metagenomics, dual RNA-seq, and coculture experiments to elucidate temperature-dependent microbial interactions during Daqu fermentation. Metagenomic analysis revealed that lactic acid bacteria (LAB) and Bacillus are dominant genera with distinct thermal preferences that nevertheless coexist throughout the fermentation process. Elevated temperature stress was found to enhance positive microbial interactions within the Daqu ecosystem. Dual RNA-seq analysis uncovered temperature-responsive gene expression patterns associated with oxidative stress, metabolic capacity, and environmental information processing in representative LAB and Bacillus strains. Guided by these multi-omics findings, co-culture assays demonstrated a temperature-dependent shift in microbial interaction modes. At 30 °C, Lactococcus lactis secretes lactic acid that inhibits the growth of Bacillus subtilis, whereas at 50 °C, B. subtilis alleviates oxidative stress in L. lactis by producing cobalamin, thereby enabling short-term rescue and sustained coexistence over serial transfers. These findings provide critical insights into the temperature-driven modulation of microbial interactions, enhancing the precision and manageability of the Daqu fermentation process.},
}
@article {pmid40713905,
year = {2025},
author = {Zhou, J and Zhang, CJ and Zou, D and Gu, C and Li, M},
title = {Magnetite drives microbial community restructuring and stimulates aceticlastic methanogenesis of type II Methanosarcina in mangrove sediments.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {174},
pmid = {40713905},
issn = {2049-2618},
support = {42207144//National Natural Science Foundation of China/ ; 32225003, 32393971, and 32393970//National Natural Science Foundation of China/ ; 2024A1515010843//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; KCXFZ20240903092800002//Shenzhen Science and Technology Program/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; },
mesh = {*Methane/metabolism/biosynthesis ; *Ferrosoferric Oxide/pharmacology/metabolism ; *Geologic Sediments/microbiology ; Wetlands ; *Methanosarcina/metabolism/genetics/classification/isolation &amp; purification/drug effects ; *Microbial Consortia/drug effects ; *Microbiota/drug effects ; Acetates/metabolism ; Lactic Acid/metabolism ; },
abstract = {BACKGROUND: Mangrove wetlands are critical hotspots of methane emissions, yet the role of naturally occurring minerals in shaping their microbial communities and methanogenic processes is poorly understood. Magnetite, a common iron mineral in soils and sediments, has been reported to enhance aceticlastic methanogenesis and facilitate syntrophic methanogenesis. In this study, we integrated multi-omic profiling with cultivation-based approaches to investigate the impact of magnetite on methanogenesis of microbial consortia derived from mangrove sediments, using lactate as a substrate.<br><br>RESULTS: Across five serial transfers, mangrove microbial consortia converted lactate to propionate and acetate, which were subsequently degraded into methane. Magnetite addition significantly stimulated methane production, leading to notable changes in community structure, particularly for aceticlastic methanogens, with Methanosarcina predominating in the magnetite-amended cultures and Methanothrix in controls. Four Methanosarcina strains T3, T4, T13, and MeOH were subsequently isolated from magnetite-amended cultures. Combined analyses of metagenome-assembled genomes and the genomes of these isolates revealed that the enriched Methanosarcina in magnetite-amended cultures belonged to type II deficient in hydrogenotrophic methanogenesis pathway. Metatranscriptomic analyses suggested that magnetite addition stimulated aceticlastic methanogenesis of type II Methanosarcina and hydrogenotrophic methanogenesis of Methanomicrobiales in the consortia. Furthermore, pure culture experiments confirmed that magnetite stimulated aceticlastic methanogenesis by Methanosarcina sp. T3, although its gene expression patterns differed from those observed in the microbial consortia. Additionally, Methanofastidiosales, an uncultured archaeal lineage possessing H2-dependent methylotrophic methanogenesis, was detected in all transfers.<br><br>CONCLUSIONS: Our findings demonstrate that magnetite alters methanogenic consortia in mangrove sediments, selectively stimulating aceticlastic methanogenesis of type II Methanosarcina and modulating hydrogenotrophic activity in Methanomicrobiales. By integrating multi-omics analyses with pure culture validation, we demonstrate, for the first time, that magnetite directly enhances the aceticlastic methanogenesis of type II non-hydrogenotrophic Methanosarcina. This study provides new insights into the influence of magnetite on complex microbial consortia, offers a deeper understanding of the physiology of type II non-hydrogenotrophic Methanosarcina, and advances knowledge of mineral-mediated regulation of methanogenic networks in anoxic environments. Video Abstract.},
}
@article {pmid40713701,
year = {2025},
author = {Bhardwaj, K and Niharika, and Garg, A and Jain, A and Kumar, M and Datt, M and Singh, V and Vrati, S},
title = {Identification and profiling of novel metagenome assembled uncultivated virus genomes from human gut.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {254},
pmid = {40713701},
issn = {1743-422X},
support = {BT/PR18657/BIC/101/507/2016//Department of Biotechnology, Ministry of Science and Technology, India/ ; JCB/2021/000015//Science and Engineering Research Board/ ; },
mesh = {Humans ; *Genome, Viral ; *Metagenome ; Feces/virology ; *Virome ; Metagenomics ; *Gastrointestinal Tract/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Gastrointestinal Microbiome ; Phylogeny ; },
abstract = {Metagenomics has revealed an unprecedented viral diversity in human gut although, most of the sequence data remains uncharacterized. In this study, we mined a collection of 1090 metagenome assembled "high quality" viral genomes (> 90% completeness, as determined by CheckV) derived from human fecal samples. Sequence analysis revealed eight new species spanning seven genera within the class, Caudoviricetes and nineteen new species from fourteen genera within the ssDNA virus family, Microviridae. Additionally, four "high quality" genomes were not found in any of the four major viral databases, NCBI viral RefSeq, IMG-VR, Gut Phage Database (GPD) and Gut Virome Database (GVD). Further, annotation and KEGG pathway analysis of the "high-quality" genomes identified seven core genes (antB, dnaB, DNMT1, DUT, xlyAB, xtmB and xtmA) associated with metabolism and fundamental viral processes. Moreover, genes for virulence, host-takeover, drug resistance, tRNA, tmRNA and CRISPR elements were also detected. Host prediction analysis suggest bacterial hosts for approximately 40% of the genomes. Overall, this study reports the discovery of novel viral genomes and provides a comprehensive genome profiling of human gut viruses in a subpopulation from India. These findings serve as a foundation for future biological investigations to elucidate the role of these viruses in host physiology.},
}
@article {pmid40712732,
year = {2025},
author = {Pérez-Molina, JA and Moreno, E and Crespillo-Andújar, C and Chamorro-Tojeiro, S and Arsuaga, M and Olavarrieta, L and Martín, O and Monge-Maillo, B and Norman, F and Lanza, VF and Serrano-Villar, S},
title = {Chagas disease induces gut microbial metabolic stress: Disruption of energy and nucleotide pathways and partial reversal by antiparasitic therapy (TRIPOBIOME-2 study).},
journal = {Travel medicine and infectious disease},
volume = {67},
number = {},
pages = {102881},
doi = {10.1016/j.tmaid.2025.102881},
pmid = {40712732},
issn = {1873-0442},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Chagas Disease/drug therapy/microbiology/metabolism ; Adult ; Male ; Female ; Middle Aged ; *Nitroimidazoles/therapeutic use ; Feces/microbiology ; Energy Metabolism ; *Nucleotides/metabolism ; Aged ; Trypanosoma cruzi ; Stress, Physiological ; },
abstract = {Chagas disease (CD) can alter gut microbiota composition, although its functional impact is poorly defined. We conducted whole-genome metagenomic sequencing of stool samples from 55 adults with chronic CD (23 treated with benznidazole) and 17 non-infected controls. Functional pathways were annotated with HUMAnN 3, and their differential abundance was assessed using ANCOM-BC2. Diversity metrics (Chao1/ACE indices and multidimensional scaling) and sPLS-DA modelling were used to explore community structure. No significant group differences were observed for alpha- and beta-diversity of bacterial functions; only 6-7 % of variance was attributable to infection status or prior benznidazole therapy. Nevertheless, chronic CD produced a distinctive functional signature marked by depletion of energy-yielding pathways (reductive and canonical tricarboxylic-acid cycles, fatty-acid β-oxidation, haem and 2-methylcitrate metabolism) and modest enrichment of purine and pyrimidine biosynthetic routes. These shifts may imply a microbiome adapting to hypoxia, nutrient scarcity, and metabolic competition with Trypanosoma cruzi. Compared with untreated patients and controls, benznidazole-treated individuals exhibited partial metabolic restoration, namely, up-regulated nucleotide and carbohydrate-degradation pathways, enhanced (5Z)-dodecenoate synthesis, and reduced reliance on the reductive tricarboxylic acid cycle, suggesting renewed microbial growth and improved short-chain-fatty-acid potential. Collectively, our results seem to portray a resource-limited, metabolically stressed gut ecosystem in chronic CD whose functional imbalance is partially reversible with antiparasitic therapy. The affected pathways, particularly those governing energy and nucleotide metabolism, could be used as candidate surrogate markers for disease monitoring and therapeutic response and as targets for microbiota-directed adjuvant strategies.},
}
@article {pmid40712359,
year = {2025},
author = {Liu, Y and Li, S and Song, X and Bartlam, M and Wang, Y},
title = {Differential responses of bacterial and archaeal communities to biodegradable and non-biodegradable microplastics in river.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139327},
doi = {10.1016/j.jhazmat.2025.139327},
pmid = {40712359},
issn = {1873-3336},
mesh = {*Archaea/drug effects/genetics ; *Microplastics/toxicity ; *Bacteria/drug effects/genetics ; *Water Pollutants, Chemical/toxicity ; *Rivers/microbiology ; Biodegradation, Environmental ; Polyvinyl Chloride/toxicity ; Microbiota/drug effects ; Polyesters ; Drug Resistance, Microbial/genetics ; },
abstract = {Microplastics are widespread environmental pollutants that pose risks to ecosystems, yet their effects on bacterial and archaeal communities in aquatic ecosystems remain understudied. In this study, we performed a 14-day microcosm experiment combined with metagenomic sequencing to compare bacterial and archaeal responses to a biodegradable microplastic (polylactic acid, PLA) and a non-biodegradable microplastic (polyvinyl chloride, PVC). Microplastics selectively enriched distinct microbial assemblages, with Pseudomonadota and Euryarchaeota identified as the dominant bacterial and archaeal phyla, accounting for 67.83 % and 15.95 %, respectively. Archaeal community in surrounding water were more sensitive to colonization time than bacterial community. Compared to the surrounding water, the plastisphere displayed simpler and more loosely connected microbial networks. Notably, co-occurrence networks of both bacteria and archaea in the PVC plastisphere were predominantly shaped by symbiotic interactions. Both bacteria and archaea carried diverse antibiotic resistance genes (ARGs), but PLS-PM indicated that bacteria were the primary drivers of ARG dissemination (path coefficient = 0.952). While the PVC plastisphere showed higher ARG abundance than the PLA plastisphere, elevated intI1 expression in the PLA plastisphere suggests a potentially greater risk of ARG dissemination associated with PLA microplastics. These findings reveal the distinct effects of PLA and PVC microplastics on microbial communities and highlight the role of microplastics in ARG dissemination, emphasizing their ecological risks in aquatic ecosystems.},
}
@article {pmid40711892,
year = {2025},
author = {Turner, D and Adriaenssens, EM and Amann, RI and Bardy, P and Bartlau, N and Barylski, J and Błażejak, S and Bouzari, M and Briegel, A and Briers, Y and Carrillo, D and Chen, X and Claessen, D and Cook, R and Crisci, MA and Dechesne, A and Deptula, P and Dutilh, BE and Ely, B and Fieseler, L and Fogg, PCM and Fukudome, A and Ganjoor, MS and Gientka, I and Holmfeldt, K and Kalatzis, PG and Kauffman, KM and Kempff, A and Knezevic, P and Koonin, EV and Kropinski, AM and Krupovic, M and Kurtböke, I and Lambon, K and Lavigne, R and Lehman, SM and Liu, HT and Lood, C and Lurz, R and Mäntynen, S and Matrishin, CB and Middelboe, M and Millard, AD and Moraru, C and Nielsen, DS and Nobrega, FL and Nunoura, T and Oksanen, HM and Ongenae, V and Parra, B and Pas, C and Pogliano, J and Poranen, MM and Potipimpanon, S and Prichard, A and Pye, HV and Rothschild-Rodriguez, D and Rozen, DE and Santini, JM and Sha, Y and Shymialevich, D and Sokołowska, B and Soleimani-Delfan, A and Średnicka, P and Tavares, P and Telatin, A and Tolstoy, I and Urayama, SI and van Neer, V and Vogensen, FK and Wen, Q and Wichels, A and Wójcicki, M and Ictv Taxonomy Summary Consortium, and , },
title = {Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025.},
journal = {The Journal of general virology},
volume = {106},
number = {7},
pages = {},
pmid = {40711892},
issn = {1465-2099},
support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R03 DE030987/DE/NIDCR NIH HHS/United States ; T32 DE023526/DE/NIDCR NIH HHS/United States ; U24 AI162625/AI/NIAID NIH HHS/United States ; },
mesh = {*Viruses/classification/genetics ; *Bacteria/virology ; Phylogeny ; *Classification/methods ; },
abstract = {This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species. These proposals mark significant progress in refining the taxonomy of bacterial viruses. Key updates include the creation of new orders and families that include existing taxa to better reflect genomic and evolutionary relationships. As sequencing and bioinformatics approaches continue to advance, further expansion and refinements in viral taxonomy can be anticipated in the coming years.},
}
@article {pmid40711419,
year = {2025},
author = {Licata, AG and Zoppi, M and Dossena, C and Rossignoli, F and Rizzo, D and Marra, M and Gargari, G and Mantegazza, G and Guglielmetti, S and Bergamaschi, L and Nigro, O and Chiaravalli, S and Massimino, M and De Cecco, L},
title = {QIIME2 enhances multi-amplicon sequencing data analysis: a standardized and validated open-source pipeline for comprehensive 16S rRNA gene profiling.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0167325},
pmid = {40711419},
issn = {2165-0497},
support = {//Bain Capital Children's Fund Europe/ ; ID NET-2019-12371188//Italian Ministry of Health/Regione Lombardia/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; Humans ; Feces/microbiology ; Software ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Child ; Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; Sequence Analysis, DNA/methods ; Reproducibility of Results ; *Computational Biology/methods ; },
abstract = {Multi-amplicon sequencing is a cost-effective method for profiling multiple regions of the 16S rRNA gene, offering a more comprehensive view of microbial diversity. However, implementing such pipelines on open-source platforms (e.g., QIIME2) is often hindered by limited documentation and lack of validation against established tools. This lack of standardization poses challenges for researchers, particularly in clinical and experimental settings. This study aims to: (i) develop and benchmark a standardized, open-source QIIME2- and R-based pipeline for 16S rRNA gene profiling using semiconductor-based sequencing, comparing it with a commercial, closed-source software; and (ii) validate its effectiveness in a pediatric cancer cohort to examine parental influence on the microbiome and child-caregiver microbial relationships. We generated 16S rRNA profiles from 5 mock communities and 12 child-caregiver fecal sample pairs. Benchmarking against commercial software showed that the multi-region (V2-9) approach produced microbial profiles nearly identical to proprietary outputs, with higher sequencing depth and improved taxonomic resolution compared to single-region analyses. Both approaches demonstrated similar microbial richness, accurate mock community reconstruction, and high reproducibility (R = 0.99, P < 0.0001). These findings were further validated using fecal samples. Application of the pipeline to pediatric samples revealed distinct, differentially abundant Bifidobacterium bifidum and Bifidobacterium adolescentis variants in children whose microbiota closely resembled that of their caregivers. Overall, this study presents a validated, open-source QIIME2 and R pipeline for multi-amplicon sequencing, providing a standardized and reproducible framework for 16S rRNA gene profiling in clinical and research contexts.IMPORTANCEMulti-amplicon sequencing comprehensively characterizes microbial communities by targeting multiple regions of the 16S rRNA gene. However, analytical workflows and reference databases provided by commercial library preparation kits frequently rely on proprietary primers and closed-source pipelines, which can limit transparency, reproducibility, and adaptability. To address these limitations, we developed and validated an open-source bioinformatics pipeline utilizing QIIME2 and R. Our pipeline integrates data from all targeted 16S regions, generating microbial profiles comparable to those produced by proprietary software. Validation was performed using mock samples and fecal samples collected from pediatric cancer patients and their caregivers, confirming the pipeline's reliability and broad applicability. Furthermore, our pipeline enables detailed analysis of microbial variants, surpassing traditional genus-level restrictions and fully leveraging the enhanced coverage offered by multi-amplicon sequencing. Our findings highlight the necessity of adopting open-source solutions to ensure scientific reproducibility and adaptability to emerging methodologies.},
}
@article {pmid40709814,
year = {2025},
author = {Labisa-Morais, F and Valente, D and Blanco-Míguez, A and Manghi, P and Garcia-Valiente, A and Andriamaniraka, H and Armanini, F and Asnicar, F and De Gregorio, C and Golzato, D and Manara, S and Modesto, M and Piperni, E and Punčochář, M and Scarafile, D and Torti, V and Borruso, L and Mattarelli, P and Giacoma, C and Sandri, C and Spiezio, C and Segata, N and Valles-Colomer, M},
title = {Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40709814},
issn = {1751-7370},
support = {BG22/00172//Spanish Ministry of Universities to MV-C/ ; PID2022-139328OA-I00//Knowledge Generation Project/ ; ERC-CoG microTOUCH-101045015/ERC_/European Research Council/International ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Lemur/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Metagenome ; Endangered Species ; Female ; Social Behavior ; Social Group ; },
abstract = {The Indri indri is a critically endangered lemur species that has not successfully been maintained or bred under human care. Investigating this lemur's virtually unexplored gut microbiome will deepen our understanding of the species' health determinants and inform conservation efforts. Through metagenomic assembly and integration into an updated reference database, we found the I. indri fecal microbiome remains largely uncultivated (cultivated species representing <0.1% relative abundance) and is largely specific to this primate species. After reconstructing 342 metagenome-assembled genomes encompassing 48 candidate species from a total of 22 samples (18 of which newly sequenced), we substantially improved microbiome mappability to 85% on average and found evidence for a proportionally large core microbiome. Social group membership emerged as the main determinant of both their taxonomic and functional gut microbiome composition. Using strain-level profiling, we detected extensive microbiome transmission within social groups, suggesting physical interaction is key in promoting microbiome acquisition. Strain sharing rates were highest between mothers and their offspring. Intergroup strain sharing was minimal and inversely correlated with geographical distance, aligning with the rare intergroup interactions and stable territory occupancy coupled with ongoing habitat fragmentation. No evidence of microbiome acquisition through geophagy was detected. These findings underscore the profound influence of social structure on microbiome transmission and composition in I. indri, and highlight the importance of considering social dynamics into research and conservation strategies.},
}
@article {pmid40707990,
year = {2025},
author = {Drevland, OM and de Muinck, EJ and Trosvik, P and Hammerstad, M and Kvitne, KE and Midtvedt, K and Åsberg, A and Robertsen, I},
title = {Microbiome-derived reactivation of mycophenolate explains variations in enterohepatic recirculation in kidney transplant recipients.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {169},
pmid = {40707990},
issn = {2049-2618},
support = {315792//Norges Forskningsr&#xe5;d/ ; 315792//Norges Forskningsr&#xe5;d/ ; },
mesh = {*Mycophenolic Acid/pharmacokinetics/analogs &amp; derivatives/metabolism ; *Kidney Transplantation ; Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Immunosuppressive Agents/pharmacokinetics/therapeutic use ; Middle Aged ; Feces/microbiology ; Adult ; Transplant Recipients ; Glucuronidase/metabolism/genetics ; Glucuronides/metabolism ; Metagenomics/methods ; *Enterohepatic Circulation ; },
abstract = {BACKGROUND: The pivotal role of microbes in drug metabolism is increasingly recognized, as variation in the gut microbiome composition between individuals has been shown to impact systemic drug exposure, efficacy and toxicity. Mycophenolate mofetil (MMF) is a cornerstone in immunosuppressive therapy following solid organ transplantation. However, dosing and tolerance are challenged by significant pharmacokinetic variability among patients, largely due to variable degrees of enterohepatic recirculation of mycophenolic acid (MPA), the active moiety of MMF. It is hypothesized that the variability in MPA recirculation is driven by gut microbiome-derived β-glucuronidase (β-GUS) mediated cleavage of MPA-glucuronide (MPAG) excreted in the bile. Here, we investigated the bidirectional interaction between MPA and the gut microbiome in kidney transplant recipients, using a combination of in vivo and in vitro data.<br><br>RESULTS: We compared the fecal microbiomes of kidney transplant recipients (n&#x2009;=&#x2009;21) both pre- and post-transplantation to healthy individuals (n&#x2009;=&#x2009;15) using shotgun metagenomic sequencing. We also determined the individual microbiome-derived reactivation rate of MPAG to MPA and show a strong positive correlation between this reactivation rate and the degree of MPA enterohepatic recirculation in vivo. Through metagenomic analysis, the reactivation rate of MPA was linked to specific gut microbial species. In particular, specific &#x3b2;-GUS gene variants associated with Faecalibacterium prausnitzii showed a strong impact on the conversion of MPAG to MPA. Furthermore, our study confirmed a significant shift in microbial composition post-transplantation and revealed notable fluctuations in species such as F. prausnitzii and Akkermansia muciniphila across different time points after transplantation. Lastly, we provide evidence that the microbiome-derived reactivation rate of MPA is linked to specific beta-glucuronidase alleles.<br><br>CONCLUSIONS: We highlight for the first time that the ex vivo determined reactivation rate of MPA explains the variation of enterohepatic recirculation, emphasizing the important role of F. prausnitzii in this process. More broadly, our findings suggest that the gut microbiome significantly influences the degree of enterohepatic recirculation of MPA, providing valuable insights that could be relevant for optimizing individualized immunosuppressive drug dosing in transplant patients. Video Abstract.},
}
@article {pmid40707831,
year = {2025},
author = {Sereika, M and Mussig, AJ and Jiang, C and Knudsen, KS and Jensen, TBN and Petriglieri, F and Yang, Y and Jørgensen, VR and Delogu, F and Sørensen, EA and Nielsen, PH and Singleton, CM and Hugenholtz, P and Albertsen, M},
title = {Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats.},
journal = {Nature microbiology},
volume = {10},
number = {8},
pages = {2018-2030},
pmid = {40707831},
issn = {2058-5276},
support = {130690//Villum Fonden (Villum Foundation)/ ; 50093//Villum Fonden (Villum Foundation)/ ; },
mesh = {*Soil Microbiology ; Phylogeny ; Metagenomics/methods ; *Genome, Bacterial ; *Bacteria/genetics/classification/isolation &amp; purification ; Geologic Sediments/microbiology ; *Biodiversity ; Ecosystem ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Nanopore Sequencing ; Sequence Analysis, DNA/methods ; },
abstract = {The emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the terrestrial microbial genome catalogue has been challenging due to the enormous complexity of these environments. Here we performed deep, long-read Nanopore sequencing of 154 soil and sediment samples collected during the Microflora Danica project, yielding genomes of 15,314 previously undescribed microbial species, recovered using our custom mmlong2 workflow. The recovered microbial genomes span 1,086 previously uncharacterized genera and expand the phylogenetic diversity of the prokaryotic tree of life by 8%. The long-read assemblies also enabled the recovery of thousands of complete ribosomal RNA operons, biosynthetic gene clusters and CRISPR-Cas systems. Furthermore, the incorporation of the recovered genomes into public genomic databases substantially improved species-level classification rates for soil and sediment metagenomic datasets. These findings demonstrate that long-read sequencing allows cost-effective recovery of high-quality microbial genomes from highly complex ecosystems, which remain an untapped source of biodiversity.},
}
@article {pmid40707808,
year = {2025},
author = {Liu, Y and Shen, J and Zhang, X and Ping, F and Qyu, K and Shen, X},
title = {Xiaoyao Pill Regulates Gut Microbiota and Tryptophan Metabolism to Alleviate Depression Induced by Chronic Stress in Rats.},
journal = {Chinese journal of integrative medicine},
volume = {31},
number = {12},
pages = {1087-1096},
pmid = {40707808},
issn = {1993-0402},
mesh = {Animals ; *Tryptophan/metabolism ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Depression/drug therapy/microbiology/etiology/metabolism/blood ; Male ; *Stress, Psychological/complications/drug therapy ; Behavior, Animal/drug effects ; Rats ; Chronic Disease ; Hippocampus/pathology/drug effects ; },
abstract = {OBJECTIVE: To investigate the antidepressant effects of Xiaoyao Pill (XYP) by exploring its interactions with gut microbiota and tryptophan metabolism.<br><br>METHODS: Utilizing network pharmacology, the functional substance groups, key targets, and pathways of XYP in the treatment of depression were identified. The chronic unpredictable mild stress (CUMS) protocol was implemented in male Sprague-Dawley rats to establish depression model. Thirty rats were randomly divided into 3 groups according to their body weight (10 for each): control, CUMS and XYP groups (1.8 g/kg). After 28-day interventions, behavioral phenotyping including sucrose preference test (SPT) and open field test (OFT) were performed. Biochemical validation encompassed enzyme-linked immunosorbent assay for serum cortisol, hematoxylin-eosin histopathology, and immunohistochemistry. Liquid chromatography-mass spectrometry was utilized to profile serum metabolites, while fecal samples underwent metagenomic sequencing for gut microbiota characterization.<br><br>RESULTS: Network pharmacology studies predicted that key components can protect the nervous system by regulating inflammatory pathways through the blood-brain barrier. SPT and OFT showed that XYP treatment significantly ameliorated depressive-like behaviors (all P<0.05). XYP treatment also restored hippocampal neuronal density, increased serum neurotransmitter levels of neurotransmitters such as 5-hydroxytryptamine and vasoactive intestinal peptide, and while suppressing inflammatory markers such as tumor necrosis factor-alpha, interleukin-1 beta (IL-1 &#x3b2;), and IL-6 (all P<0.05). Metagenomics revealed significant restructuring of gut microbiota, notably the regulation of Parabacteroides distasonis (P<0.05). Non-targeted metabolomics analysis showed that the level of metabolites in the tryptophan and kynurenine pathway significantly changed (variable importance in the projection >1, P<0.05), and the change of metabolic flux was significantly correlated with behavioral improvement (P<0.05).<br><br>CONCLUSIONS: XYP exerts antidepressant effects by increasing neurotransmitter levels, reducing inflammatory makers and modulating Parabacteroides distasonis. Through further exploration of metabolomics, we found that XYP may play a protective role in depression by regulating tryptophan metabolism.},
}
@article {pmid40707722,
year = {2025},
author = {Mangnier, L and Bodein, A and Mariaz, M and Mathieu, A and Scott-Boyer, MP and Vashist, N and Bramble, MS and Droit, A},
title = {A systematic benchmark of integrative strategies for microbiome-metabolome data.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1100},
pmid = {40707722},
issn = {2399-3642},
support = {K01 TW011772/TW/FIC NIH HHS/United States ; },
mesh = {Humans ; *Metabolomics/methods ; *Metabolome ; *Gastrointestinal Microbiome ; Benchmarking ; *Metagenomics/methods ; *Microbiota ; Computational Biology/methods ; },
abstract = {The rapid advancement of high-throughput sequencing technologies has enabled the integration of various omic layers into computational frameworks. Among these, metagenomics and metabolomics are increasingly studied for their roles in complex diseases. However, no standard currently exists for jointly integrating microbiome and metabolome datasets within statistical models. We benchmarked nineteen integrative methods to disentangle the relationships between microorganisms and metabolites. These methods address key research goals, including global associations, data summarization, individual associations, and feature selection. Through realistic simulations, we identified the best-performing methods and validated them on real gut microbiome datasets, revealing complementary biological processes across the two omic layers. Practical guidelines are provided for specific scientific questions and data types. This work establishes a foundation for research standards in metagenomics-metabolomics integration and supports future methodological developments, while also providing guidance for designing optimal analytical strategies tailored to specific integration questions.},
}
@article {pmid40707492,
year = {2025},
author = {Villette, R and Novikova, PV and Laczny, CC and Mollenhauer, B and May, P and Wilmes, P},
title = {Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson's disease.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {142},
pmid = {40707492},
issn = {2055-5008},
support = {863664//HORIZON EUROPE European Research Council/ ; 863664//HORIZON EUROPE European Research Council/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; },
mesh = {*Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Gene Regulatory Networks ; Metagenomics ; Gene Expression Profiling ; Male ; Female ; Aged ; Middle Aged ; },
abstract = {Gut microbiome alterations are linked to various diseases, including neurodegeneration, but their ecological and functional impacts remain unclear. Using integrated multi-omics (metagenomics and metatranscriptomics), we analyse microbiome gene co-expression networks in Parkinson's disease (PD) and healthy controls (HC). We observe a significant depletion of hub genes in PD, including genes involved in secondary bile acid biosynthesis, bacterial microcompartments (BMCs), polysaccharides transport and flagellar assembly (FA). Blautia, Roseburia, Faecalibacterium and Anaerobutyricum genera are the main contributors to these functions, showing significantly lower expression in PD. Additionally, we identify a strong correlation between BMC and FA expression, and an apparent dysregulation in cross-feeding between commensals in PD. Finally, PD also exhibits reduced gene expression diversity compared to HC, whereby higher gene expression correlates with greater diversity. We identify disruptions in gut metabolic functions, at both taxonomic and functional level, and microbiome-wide ecological features, highlighting targets for future gut microbiome restoration efforts.},
}
@article {pmid40707215,
year = {2025},
author = {Li-Hau, F and Nakagawa, M and Kakegawa, T and Ward, LM and Ueno, Y and McGlynn, SE},
title = {Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan.},
journal = {Microbes and environments},
volume = {40},
number = {3},
pages = {},
pmid = {40707215},
issn = {1347-4405},
mesh = {*Hot Springs/microbiology/chemistry ; Japan ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Archaea/classification/metabolism/genetics/isolation &amp; purification ; Oxidation-Reduction ; Phylogeny ; Nitrogen Fixation ; Oceans and Seas ; Iron/metabolism ; *Biodiversity ; Carbon Cycle ; RNA, Ribosomal, 16S/genetics ; Nitrogen Cycle ; Hydrogen/metabolism ; },
abstract = {Circumneutral iron-rich hot springs may represent analogues of Neoarchean to Paleoproterozoic oceans of early Earth, potentially providing windows into ancient microbial ecology. Here we sampled five Japanese hot springs to gain insights into functional processes and taxonomic diversity in these analog environments. Amplicon and metagenomic sequencing confirm a hypothesis where taxonomy is distinct between sites and linked to the geochemical setting. Metabolic functions shared among the springs include carbon fixation via the reductive pentose phosphate cycle, nitrogen fixation, and dissimilatory iron oxidation/reduction. Among the sites, Kowakubi was unique in that it was dominated by Hydrogenophilaceae, a group known for performing hydrogen oxidation, motivating a hypothesis that H2 as an electron donor may shape community composition even in the presence of abundant ferrous iron. Evidence for nitrogen cycling across the springs included N2 fixation, dissimilatory nitrate reduction to ammonia (DNRA), and denitrification. The low-salinity springs Furutobe and OHK lacked evidence for ammonium oxidation by ammonia monooxygenase, but evidence for complete nitrification existed at Kowakubi, Jinata, and Tsubakiyama. In most sites, the microaerophilic iron-oxidizing bacteria from the Zetaproteobacteria or Gammaproteobacteria classes had higher relative abundances than Cyanobacteria. Microaerophilic iron oxidizers may outcompete abiotic Fe oxidation, while being fueled by oxy-phototrophic Cyanobacteria. Our data provide a foundation for considering which factors may have controlled productivity and elemental cycling as Earth's oceans became oxygenated at the onset of the Great Oxidation Event.},
}
@article {pmid40706488,
year = {2025},
author = {Tong, Y and Wang, Y and Zhang, J and Guo, Y and Yuan, T and Chen, H and Zhang, H and Zhan, K and Zhao, L and Ma, Q and Huang, S},
title = {Comprehensive study on the impact of ginger extract on laying performance, egg quality, inflammatory responses, intestinal barrier function, and cecal microbiome and resistome in laying hens.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105448},
pmid = {40706488},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/microbiology/immunology ; *Gastrointestinal Microbiome/drug effects ; Female ; *Zingiber officinale/chemistry ; Animal Feed/analysis ; Dietary Supplements/analysis ; Diet/veterinary ; *Plant Extracts/administration &amp; dosage/metabolism ; Random Allocation ; Ovum/physiology/drug effects ; Inflammation/veterinary ; Cecum/microbiology ; *Reproduction/drug effects ; Intestines/drug effects/physiology ; *Immunity, Innate/drug effects ; Eggs/analysis ; Intestinal Barrier Function ; },
abstract = {Experimental models have been extensively used to explore the effects of ginger extract (GE) on oxidative stress and immune response. However, the influence of GE dietary supplementation on gut microbial composition, function, and the resistome in laying hens remains not fully understood. This research investigated the impact of GE supplementation on laying performance, egg quality, metabolism, inflammation, and the gut microbiome and resistome in laying hens. Thirty healthy, 35-week-old Jingfen No.6 laying hens with consistent body weight and laying rate were randomly allocated to either the control group (Con; basal diet) or the ginger extract supplementation group (Con-G; basal diet with 5 g/kg GE), each with fifteen replicates (one hen per replicate). The pre-feeding period lasted one week, followed by an eight-week trial. The results revealed that average laying rate (P = 0.051) and egg mass (P < 0.05) significantly increased, while feed conversion efficiency improved (P < 0.05) in the GE-supplemented group during the study period. Additionally, egg quality, host metabolism, serum antioxidant levels, and histological assessments of the jejunum, ileum, and cecum tissues were positively affected by GE (P < 0.05). Notably, GE supplementation significantly decreased (P < 0.05) serum pro-inflammatory cytokines (IL-6, IL-1β, and TNF-α) and increased (P < 0.05) IgA, IgG, and IL-10 levels. LEfSe analysis revealed that the relative abundance of genera such as Ligilactobacillus salivarius, Limosilactobacillus vaginalis, Butyricimonas virosa, and Limosilactobacillus alvi were significantly increased (P < 0.05) in the Con-G group. Furthermore, ginger extract significantly enhanced (P < 0.05) the production of short-chain fatty acids(including acetate, propionate, butyrate, isovalerate, valerate, and lactate) in the cecum, modulated the expression profile of antibiotic resistance genes in the intestines of laying hens, and inhibited pathogen colonization. The study concludes that ginger extract supplementation in laying hen diets improves laying performance, egg quality, host metabolism, and immune responses, positively alters gut microbiota composition and functionality, and modulates the poultry resistome. Metagenomic analysis underscores the potential of GE as a safe and effective additive.},
}
@article {pmid40706155,
year = {2025},
author = {Wang, YC and He, LY and Wu, HY and Qiao, LK and Huang, Z and Bai, H and Gao, FZ and Shi, YJ and Zhao, JL and Liu, YS and Ying, GG},
title = {High-risk plasmid-borne resistance genes from swine farm environments infiltrate deep soil and interact with the human gut microbiome via horizontal transfer.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139281},
doi = {10.1016/j.jhazmat.2025.139281},
pmid = {40706155},
issn = {1873-3336},
mesh = {Animals ; *Gene Transfer, Horizontal ; Swine ; *Gastrointestinal Microbiome/genetics ; *Plasmids/genetics ; Humans ; Farms ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Swine farms serve as critical reservoirs of antibiotic resistance genes (ARGs), yet the frequency of horizontal gene transfer (HGT) remains poorly understood. In this study, we explored the gene exchange within the "swine farm-human-pig" network and assessed its risks. We identified 16,612 plasmid contigs from 107 field samples, revealing a significant presence of previously uncharacterized plasmid types. Notably, 52.88 % of acquired ARGs were located on plasmids, with 71.22 % containing at least one mobile genetic element (MGE). We quantified HGTs at the microbial community level among the human gut, pig gut, and swine farm environments. Among 4687 metagenome-assembled genomes (MAGs), 3008 were involved in 11,250 HGTs. HGT linkages were most frequently identified between microbial genomes from the swine farm and the human gut microbiome. ARGs were involved in 91 HGT events, with 645 events linked to MGEs and 16 related to virulence factors, suggesting potential cross-species transmission of clinical pathogens. The detection of 32 Rank I ARGs and the identification of increased resistome risks underscore the extensive dispersion of livestock-related contaminants into more distant environmental compartments. This study elucidates the complexities of gene exchange networks in swine farm environments, underscoring the urgent need for strategies to mitigate risks associated with the antibiotic resistome.},
}
@article {pmid40704918,
year = {2025},
author = {Pan, J and Tian, X and Wu, K and Ji, J and Dong, M and Sun, T and Lv, D and Yao, P and Lv, L and Yao, H},
title = {Gut microbiota-associated non-cholesterol sterol dysregulation modulates immune reconstitution during antiretroviral therapy in people living with HIV.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0140425},
pmid = {40704918},
issn = {2165-0497},
support = {2024YFC2309900//National Key Research and Development Program of China/ ; 2022R52029//Zhejiang Plan for the Special Support fort Top-notch Talents/ ; 2022ZFJH003//Fundamental Research Funds for the Central Universities/ ; SYS202202//Shandong Provincial Laboratory Project/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *HIV Infections/drug therapy/immunology/microbiology ; Male ; Leukocytes, Mononuclear/immunology ; Adult ; Female ; *Sterols/metabolism ; Middle Aged ; CD4-Positive T-Lymphocytes/immunology ; Dysbiosis/microbiology/immunology ; Phytosterols/metabolism ; },
abstract = {Non-cholesterol sterol metabolism plays a crucial role in immune regulation. However, the non-cholesterol sterol profiles, its association with gut dysbiosis, and its impact on the CD4[+] T cell recovery in people living with HIV (PLWH) are yet to be elucidated. In this study, we recruited 37 PLWH and 50 healthy controls to characterize non-cholesterol sterol profiles and gut microbiota composition using targeted liquid chromatography-mass spectrometry and metagenomic analysis. Correlations between sterol profiles and immune cell subsets were assessed. In vitro peripheral blood mononuclear cell (PBMC) model was used to validate key findings. We identified a distinct dysregulation of non-cholesterol sterol metabolism in PLWH, characterized by elevated levels of cholesterol precursors and metabolites and depleted levels of plant sterols, which were linked to gut dysbiosis. Our study results highlighted Oscillibacter spp. as the key regulator of sterol metabolism. Specifically, plant sterols (e.g., brassicasterol and campesterol) were found to be associated with impaired CD4[+] T cell recovery during antiretroviral therapy (ART). These findings were validated using ex vivo PBMC models, which revealed that brassicasterol stimulates T cell abnormal activation and pro-inflammatory cytokine release, whereas lathosterol dampens immune activation and inflammation. In summary, our study highlights the interplay between gut dysbiosis and sterol dysregulation in PLWH, demonstrating that higher brassicasterol levels impair immune recovery post-ART by promoting CD4[+] T cell hyperactivation. Hence, targeting microbial sterol metabolism-through Oscillibacter spp. enrichment or plant sterol modulation-may offer novel therapeutic strategies to optimize ART outcomes by balancing immune activation and resolution.IMPORTANCEThis study is the first to integrate non-cholesterol sterol profiling with gut microbiota analysis in people living with HIV (PLWH), uncovering a unique sterol dysregulation characterized by elevated cholesterol precursors and depleted plant sterols in this population. We demonstrate that Oscillibacter spp. were associated with these metabolic shifts and that specific sterols differentially affect immune recovery: plant sterols such as brassicasterol impede CD4[+] T cell restoration by promoting hyperactivation, whereas the cholesterol derivative lathosterol mitigates inflammation and supports immune reconstitution. These insights reveal novel microbiome-sterol interactions that can be leveraged to develop targeted microbiome- and sterol-based interventions aimed at enhancing antiretroviral therapy efficacy and long-term immune health in PLWH.},
}
@article {pmid40703671,
year = {2025},
author = {Wang, Y and Lu, J and Dai, W and Yang, S},
title = {Jian-Pi-Yi-Shen formula improves kidney function by regulating gut microbiome in rats with chronic kidney disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1526863},
pmid = {40703671},
issn = {2235-2988},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Renal Insufficiency, Chronic/drug therapy/microbiology ; *Drugs, Chinese Herbal/pharmacology/administration &amp; dosage ; Rats ; *Kidney/drug effects/physiopathology ; Disease Models, Animal ; Feces/microbiology ; Male ; Creatinine/blood ; Rats, Sprague-Dawley ; Metagenomics ; Medicine, Chinese Traditional ; },
abstract = {INTRODUCTION: Recent studies have underscored the role of interactions between Traditional Chinese Medicine (TCM) and the gut microbiome (GM) in mediating therapeutic effects. Jian-Pi-Yi-Shen Formula (JPYSF) has shown efficacy in ameliorating chronic kidney disease (CKD) symptoms, but its mechanisms via GM modulation remain unclear.<br><br>METHODS: In this study, 8-week-old rats were assigned to three groups after a two-week acclimation: C (normal diet for six weeks), M (adenine diet for four weeks then normal diet for two weeks), and T (same as M, with JPYSF administered during the final three weeks). Fecal samples were collected at three timepoints (T1: post-acclimation; T2: after three weeks on respective diets; T3: after three weeks of JPYSF treatment) for metagenomic sequencing. Serum creatinine (SCR) was measured at T2 and T3.<br><br>RESULTS: At T2, adenine-fed rats showed elevated SCR (C: 28.4&#x202f;&#xb1;&#x202f;1.5&#x202f;&#xb5;mol/L; M: 189.6&#x202f;&#xb1;&#x202f;25.8&#xb5;mol/L; T: 186.4&#x202f;&#xb1;&#x202f;32.5&#xb5;mol/L; p&#x202f;<&#x202f;0.001). By T3, SCR decreased more in T (86.0&#x202f;&#xb1;&#x202f;14.9&#xb5;mol/L) than in M (119.6&#x202f;&#xb1;&#x202f;16.3&#xb5;mol/L; p&#x202f;=&#x202f;0.012), with C remaining stable (30.8&#x202f;&#xb1;&#x202f;4.4&#xb5;mol/L). Adenine feeding induced significant GM shifts, evidenced by increased Aitchison distance (p&#x202f;<&#x202f;0.01) and altered co-abundance interaction groups (CIGs): CIG3, 6, 9, 10 increased; CIG1, 2, 4, 12 decreased (all p&#x202f;<&#x202f;0.05). After JPYSF treatment, only CIG4 significantly rebounded (T3 vs. M, p&#x202f;=&#x202f;0.0079), and T3-T1 dissimilarity was lower in T than M (p&#x202f;<&#x202f;0.05). SCR levels were significantly lower in T than M after returning to a normal diet, suggesting a renoprotective effect of JPYSF. Co-occurrence analysis linked SCR positively with toxin-associated CIGs (CIG3, 6, 7, 9, 10) and pathways (purine metabolism, toluene degradation), and negatively with CIG4.<br><br>DISCUSSION: These results demonstrate that JPYSF lowers SCR and selectively modulates GM modules, particularly CIG4, which inversely correlates with uremic toxin-producing pathways, suggesting improved renal function and specific gut microbiota modulation in CKD rats.},
}
@article {pmid40702703,
year = {2025},
author = {Liu, X and Kong, J and Shan, Y and Yang, Z and Miao, J and Pan, Y and Luo, T and Shi, Z and Wang, Y and Gou, Q and Yang, C and Li, H and Li, C and Li, S and Zhang, X and Sun, Y and Holmes, EC and Guo, D and Shi, M},
title = {SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
pmid = {40702703},
issn = {1477-4054},
support = {82341118//National Natural Science Foundation of China/ ; KQTD20200820145822023//Shenzhen Science and Technology Program/ ; MRP/071/20X//Hong Kong Innovation and Technology Fund/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; GZNL2023A01008//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province 'Pearl River Talent Plan' Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; },
mesh = {*Genome, Viral ; *RNA Viruses/genetics ; Animals ; *Computational Biology/methods ; Metagenomics/methods ; *Software ; RNA, Viral/genetics ; },
abstract = {Metagenomic sequencing has expanded the ribonucleic acid (RNA) virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed a new bioinformatic tool-SegFinder-that identifies virus genome segments based on their common co-occurrence at similar abundance within segmented viruses. SegFinder successfully re-discovered all segments from a test data set of individual mosquito transcriptomes, which was also used to establish parameter thresholds for reliable segment identification. Using these optimal parameters, we applied SegFinder to 858 libraries from eight metagenomic sequencing projects, including vertebrates, invertebrates, plants, and environmental samples. Excluding the RdRP segment, we identified 106 unique viral genome segments from these samples. Among them, 53 were novel, including 30 segments that showed no recognizable sequence homology to any known viruses. However, the viral origin of these highly divergent segment was supported by the presence of conserved terminal sequences. SegFinder identifies segmented genome structures in viruses previously considered to be predominantly unsegmented, and in doing so expanded the number of known families and orders of segmented RNA viruses, making it a valuable tool in an era of large-scale parallel sequencing.},
}
@article {pmid40701508,
year = {2025},
author = {Chen, WJ and Wang, JP and Zhou, JR and He, Y and An, DQ and Tian, TT and Liang, MT and Aikepa, D and Kahaer, M and Sun, YP},
title = {Efficacy and mechanisms of compound Bai Mao Yin in regulating uric acid transport and improving the intestinal microbiota to alleviate hyperuricemia via the enterorenal axis.},
journal = {Microbial pathogenesis},
volume = {207},
number = {},
pages = {107922},
doi = {10.1016/j.micpath.2025.107922},
pmid = {40701508},
issn = {1096-1208},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Humans ; *Uric Acid/metabolism/blood ; Mice ; *Hyperuricemia/drug therapy/metabolism/microbiology ; Male ; Fecal Microbiota Transplantation ; Disease Models, Animal ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Middle Aged ; Feces/microbiology ; Female ; Metagenomics ; Kidney/metabolism/drug effects ; RNA, Ribosomal, 16S/genetics ; Signal Transduction/drug effects ; Biological Transport/drug effects ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: The compound Bai Mao Yin (BMY) has demonstrated therapeutic efficacy in reducing uric acid (UA) levels; however, its underlying mechanisms remain unclear.<br><br>METHODS: The UA-lowering effects of BMY were evaluated in a cohort of 40 patients with hyperuricemia (HUA) who received BMY treatment for 90 days. Fecal samples were collected at baseline (day 0), mid-treatment (day 30), and post-treatment (day 90) for metagenomic sequencing to analyze changes in gut microbiota and identify potential BMY targets in HUA. These clinical findings were validated in a hyperuricemic mouse model induced by xanthine and potassium oxonate. Mouse fecal samples were analyzed via 16S rDNA (V3-V4 region) sequencing to assess microbiota shifts. Additionally, fecal microbiota transplantation (FMT) from BMY-treated mice to HUA mice and in vitro cell experiments using HK2 cells were conducted to investigate the roles of BMY and the reconstructed microbiota in UA metabolism, renal UA transport, and inflammation through upstream signaling pathways.<br><br>RESULTS: Clinical cohort studies demonstrated that the BMY effectively lowers UA levels in patients with HUA without inducing hepatorenal toxicity. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of metagenomic data revealed that BMY modulates the gut microbiota and influences ATP-binding cassette transporters and UA metabolism-related pathways. In animal models, BMY increased the relative abundance of beneficial gut bacteria, reduced intestinal permeability, and regulated UA transporters in both intestinal and renal systems, contributing to UA reduction. In vitro assays showed that BMY directly decreased UA levels in the cell supernatant and suppressed interleukin-1&#x3b2; (IL-1&#x3b2;) and interleukin-6 (IL-6) expression by downregulating the TLR4/MYD88/NF&#x3ba;B signaling pathway, thereby alleviating inflammation.<br><br>CONCLUSIONS: Compound BMY was found to improve the intestinal microenvironment and modulate UA transport via the enterorenal axis, effectively reducing HUA.},
}
@article {pmid40701001,
year = {2025},
author = {Shang, H and Gou, W and Liu, S and Yuan, W and Cao, Z and Guo, Y and Zhang, N},
title = {Integrated metagenomics and metabolomic to reveal the effects of dietary comfrey polysaccharides on the oxidative stability and fatty acid composition of egg yolks in laying hens.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105553},
pmid = {40701001},
issn = {1525-3171},
mesh = {Animals ; *Chickens/physiology/metabolism ; Diet/veterinary ; Female ; Animal Feed/analysis ; *Fatty Acids/metabolism/chemistry ; *Egg Yolk/chemistry/drug effects ; *Polysaccharides/metabolism/administration &amp; dosage ; Metagenomics ; Oxidation-Reduction ; Metabolomics ; Dietary Supplements/analysis ; Gastrointestinal Microbiome/drug effects ; Random Allocation ; Antioxidants/metabolism ; },
abstract = {This study investigated the influences of comfrey (Symphytum officinale L.) polysaccharides (CPs) in the diet of laying hens on the oxidation stability and fatty acid composition of the egg yolks based on metagenomic and metabolomics techniques. Dietary CPs improved the total phenolic content in fresh and stored eggs. The activity of superoxide dismutase was increased, and the content of malondialdehyde was reduced in the stored eggs of the 1.0 % group of CPs. Dietary supplementation with 1.0 % CPs increased some polyunsaturated fatty acid (PUFA) contents in stored egg yolk, including dihomo-γ-linolenic acid (C20:3n6), arachidonic acid (C20:4n6), and docosahexaenoic acid (C22:6n3). The abundances of Methanobrevibacter, Parabacteroides, and Merdibacter in the caecum were increased in the 1.0 % group of CPs. The content of melatonin was increased, and the contents of palmitic acid and myristic acid in the caecum were decreased by CPs. These results suggested that CPs could improve the antioxidant status and fatty acid composition of egg yolks.},
}
@article {pmid40700599,
year = {2025},
author = {Mofidifar, S and Tefagh, M},
title = {Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {7},
pages = {},
pmid = {40700599},
issn = {1367-4811},
mesh = {*Phylogeny ; *Models, Biological ; *Microbiota ; *Metagenomics/methods ; *Computational Biology/methods ; Computer Simulation ; },
abstract = {MOTIVATION: Metabolic modeling has emerged as a powerful tool for predicting community functions. However, current modeling approaches face significant challenges in balancing the metabolic trade-offs between individual and community-level growth. In this study, we investigated the effect of metabolic relatedness among taxa on growth rate calculations by merging related taxa based on their metabolic similarity, introducing this approach as PhyloCOBRA.<br><br>RESULTS: This approach enhanced the accuracy and efficiency of microbial community simulations by combining genome-scale metabolic models (GEMs) of closely related organisms, aligning with the concepts of niche differentiation and nestedness theory. To validate our approach, we implemented PhyloCOBRA within the MICOM and OptCom package (creating PhyloMICOM and PhyloOptCom, respectively), and applied it to metagenomic data from 186 individuals and four-species synthetic community (SynCom). Our results demonstrated significant improvement in the accuracy and reliability of growth rate predictions compared to the standard methods. Sensitivity analysis revealed that PhyloMICOM models were more robust to random noise, while Jaccard index calculations showed a reduction in redundancy, highlighting the enhanced specificity of the generated community models. Furthermore, PhyloMICOM reduced the computational complexity, addressing a key concern in microbial community simulations. This approach marks a significant advancement in community-scale metabolic modeling, offering a more stable, efficient, and ecologically relevant tool for simulating and understanding the intricate dynamics of microbial ecosystems.<br><br>PhyloCOBRA implementations are available as extensions to the MICOM packages and can be accessed at https://github.com/sepideh-mofidifar/PhyloCOBRA.},
}
@article {pmid40698938,
year = {2025},
author = {Lei, L and Li, X and Xiong, Z and Li, J and Liu, L and Chen, L and Zhong, Q and Jiang, H and Cheng, Z and Xiao, S},
title = {Distinctive structure of endophytic microbial communities in two species of wild and cultivated rice.},
journal = {Microbiology spectrum},
volume = {13},
number = {9},
pages = {e0297824},
pmid = {40698938},
issn = {2165-0497},
support = {202205AR070001-01//Yunnan seed Laboratory/ ; 202205AM340037//Science and technology personnel/ ; 2021YFD1200100//National Key Research and Development Program of China/ ; SKL-KF-202325//Open Research Fund of State Key Laboratory of Bioelectronics/ ; },
mesh = {*Oryza/microbiology/classification/growth &amp; development ; *Endophytes/classification/genetics/isolation &amp; purification ; *Bacteria/classification/genetics/isolation &amp; purification ; *Microbiota/genetics ; China ; Plant Leaves/microbiology ; Metagenomics ; Phylogeny ; },
abstract = {Endophytic microbial communities play an important role in plant development, nutrient acquisition, and oxidative stress tolerance. Oryza officinalis and Oryza meyeriana are unique wild rice varieties in China with many high-quality resistance genes, rich endophyte diversity, and potential resources for sustainable agriculture. In the present study, the endophytic microbial community structures of O. officinalis, O. meyeriana, and cultivated rice were compared using metagenomic sequencing. Dechloromonas, Salmonella, Klebsiella, and Listeria were the core microbial groups in wild and cultivated rice. The relative abundances of Ligilactobacillus, Escherichia, and Bradyrhizobium in O. meyeriana were higher than those in cultivated rice. The relative abundances of Listeria, Acinetobacter, Escherichia, and Dechloromonas in O. officinalis were also higher. Compared to that of cultivated rice, the microbiota of wild rice had a more complex and stable community network. At the pathway level 2 based on the Kyoto Encyclopedia of Genes and Genomes classification system, the relative abundance of metabolic categories was dominant. Most pathways showed that the O. officinalis relative abundance was higher than those of the other two species. Our study revealed differences in the leaf endophyte community structure and function between wild and cultivated rice in the same habitat, demonstrating the potential of wild rice in recruiting specific microorganisms to improve crop performance and promote safe and sustainable food production.IMPORTANCEUnder the current climate change environment, plant-beneficial endophytes are of great significance for promoting food production. Modern cultivars may have lost many beneficial endophytes compared to their ancestors. However, relatively few studies have been conducted on the community structure and function of modern ancestral crop endophytes. In this study, the composition and function of the microbial communities of two wild rice species were analyzed; the differences between them and cultivated rice were determined; and the patterns of microbial interactions and their core microbiomes were determined. Our findings can aid in the exploration of the beneficial endophytes in wild rice and use them to improve crop stress resistance and sustainability. These results provide relevant insights into the role of endophytes in the mechanism of high-stress resistance in wild rice.},
}
@article {pmid40698936,
year = {2025},
author = {Maghini, DG and Kiguchi, Y and Darling, AE and Monahan, LG and Halpern, AL and Burke, CM and Jaeger, E and Statham, A and Truong, T and Ying, K and Bruinsma, SP and Schroth, GP and Bhatt, AS},
title = {Illumina complete long read assay yields contiguous bacterial genomes from human gut metagenomes.},
journal = {mSystems},
volume = {10},
number = {8},
pages = {e0153124},
pmid = {40698936},
issn = {2379-5077},
support = {//Stand Up To Cancer/ ; //Allen Foundation/ ; //Stanford Medicine Children's Health Center for IBD and Celiac Disease/ ; R01 AI143757/AI/NIAID NIH HHS/United States ; //Chan Zuckerberg Initiative/ ; P30 CA124435, R01 AI143757, 1S10OD02014101, R01 AI148623/NH/NIH HHS/United States ; P30 CA124435/CA/NCI NIH HHS/United States ; //Alfred P. Sloan Foundation/ ; R01 AI148623/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Genome, Bacterial/genetics ; *Metagenomics/methods ; *Metagenome/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; Sequence Analysis, DNA/methods ; Nanopore Sequencing ; },
abstract = {Metagenomics enables direct investigation of the gene content and potential functions of gut bacteria without isolation and culture. However, metagenome-assembled genomes are often incomplete and have low contiguity due to challenges in assembling repeated genomic elements. Long-read sequencing approaches have successfully yielded circular bacterial genomes directly from metagenomes, but these approaches require high DNA input and can have high error rates. Illumina has recently launched the Illumina Complete Long Read (ICLR) assay, a new approach for generating kilobase-scale reads with low DNA input requirements and high accuracy. Here, we evaluate the performance of ICLR sequencing for gut metagenomics for the first time. We sequenced a microbial mock community and 10 human gut microbiome samples with standard, shotgun 2 × 150 paired-end sequencing, ICLR sequencing, and nanopore long-read sequencing and compared performance in read lengths, assembly contiguity, and bin quality. We find that ICLR human metagenomic assemblies have higher N50 (119.5 ± 24.8 kilobases) than short read assemblies (9.9 ± 4.5 kilobases; P = 0.002), and comparable N50 to nanopore assemblies (91.0 ± 43.8 kilobases; P = 0.32). Additionally, we find that ICLR draft microbial genomes are more complete (94.0% ± 20.6%) than nanopore draft genomes (85.9% ± 23.0%; P ≤ 0.001), and that nanopore draft genomes have truncated gene lengths (924.6 ± 114.7 base pairs) relative to ICLR genomes (954.6 ± 71.5 base pairs; P ≤ 0.001). Overall, we find that ICLR sequencing is a promising method for the accurate assembly of microbial genomes from gut metagenomes.IMPORTANCEMetagenomic sequencing allows scientists to directly measure the genome content and structure of microbes residing in complex microbial communities. Traditional short-read metagenomic sequencing methods often yield fragmented genomes, whereas advanced long-read sequencing methods improve genome assembly quality but often suffer from high error rates and are logistically limited due to high input requirements. A new method, the Illumina Complete Long Read (ICLR) assay, is capable of generating highly accurate kilobase-scale sequencing reads with minimal input material. To evaluate the utility of ICLR in metagenomic contexts, we applied short-read, long-read, and ICLR methods to simple and complex microbial communities. We found that ICLR outperforms short-read methods and yields comparable metagenomic assemblies to standard long-read approaches while requiring less input material. Overall, ICLR represents an additional option for assembling complete genomes from complex metagenomes.},
}
@article {pmid40697984,
year = {2025},
author = {Hebbar, P and Han, OB and Yan, NX and Kay, D and Chu, KY and Woon, JS and Lun, PK and Kabekkodu, SP and Prasad, ASB and Prakash, B and Nograles, N and Kanakal, MM and Goodson, M and Nagaraja, S and Mascarenhas, R},
title = {Characterization of microbiome diversity unveils substantial microbial variation in mangrove soil sediments from coastal regions of Malaysia.},
journal = {Access microbiology},
volume = {7},
number = {6},
pages = {},
pmid = {40697984},
issn = {2516-8290},
abstract = {The mangrove ecosystems are of great ecological importance found in tropical and subtropical coasts, including Malaysia. The microbial communities in the mangrove sediments play an indispensable role in maintaining homeostasis and supporting biodiversity. However, mangroves are facing various threats due to increasing anthropogenic activities. Thus, it is important to monitor the microbial community to improve our understanding of anthropogenic pressure on reshaping these ecosystems. This study examines the microbial community diversity in mangrove sediments of southern peninsular Malaysia. High-throughput MinION sequencing of the 16S rRNA gene was performed to compare the soil microbiome diversity in 35 samples from 8 different mangroves representing Sungai Sedili Kecil and Sungai Sedili Besar that flow into the South China Sea; Sungai Pulai, Sungai Melayu, Sungai Danga, Sungai Skudai and Sungai Johor that join the Straits of Johor; and Pulau Kukup from the Straits of Malacca. The metagenomic classification performed with 16S rRNA showed 2,573 taxa comprising 32 phyla. Total abundance analysis showed Pseudomonadota (67-69%), Bacteroidota (6-8%), Bacillota (5-8%), Campylobacterota (4-5%), Acidobacteriota (3-4%), Planctomycetota (2-4%) and Actinomycetota (1-2%) as the relatively common phyla. Alpha diversity indices revealed significantly higher richness in samples from mangroves of the South China Sea. Further, the 'Shannon' index showed a significant difference in diversity between Sungai Melayu and Sungai Pulai. Higher abundance of Burkholderiaceae, Bacillaceae and Enterobacteriaceae suggests a difference in the microbial community structure. This study stands as the first comprehensive analysis of microbial communities for future monitoring and conservation in these mangroves.},
}
@article {pmid40696437,
year = {2025},
author = {Ashton, PM and Mageiros, L and Meiring, JE and Chunga-Chirambo, A and Khanam, F and Dongol, S and Banda, H and Karkey, A and Preciado-Llanes, L and Thomaides-Brears, H and Gibani, M and Rajib, NH and Rahman, N and Biswas, PK and Bhuiyan, MAI and Kay, S and Auger, K and Seret, O and Thomson, NR and Pollard, AJ and Baker, S and Basnyat, B and Clemens, JD and Dolecek, C and Dunstan, SJ and Dougan, G and Heyderman, RS and Pitzer, VE and Qadri, F and Gordon, MA and Holt, KE and Darton, TC and , },
title = {Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {168},
pmid = {40696437},
issn = {2049-2618},
mesh = {Humans ; *Typhoid Fever/microbiology/epidemiology ; *Gastrointestinal Microbiome ; *Salmonella typhi/pathogenicity ; Prospective Studies ; Male ; Female ; Malawi/epidemiology ; Adult ; Bangladesh/epidemiology ; Nepal/epidemiology ; Adolescent ; Child ; Feces/microbiology ; Young Adult ; Endemic Diseases ; Fatty Acids, Volatile/metabolism ; Middle Aged ; Child, Preschool ; },
abstract = {BACKGROUND: Typhoid fever is a systemic infection caused by Salmonella enterica serovar Typhi (S. Typhi) invasion from the gut lumen. Transmission between people occurs through ingestion of contaminated food and water, particularly in settings with poor water and sanitation infrastructure, resulting in over 10 million illnesses annually. As the pathogen invades via the gastrointestinal tract, it is plausible that the gut microbiome may influence the outcome of S. Typhi exposure. There is some evidence that bacteria producing short-chain fatty acids (SCFAs) may create an environment unfavourable to invasive Salmonella, but data from humans is limited.<br><br>METHODS: To investigate the association between the gut microbiome and typhoid fever, we analysed samples collected from three all-age cohorts enrolled in a prospective surveillance study conducted across three settings where typhoid fever is endemic (Dhaka, Bangladesh; Blantyre, Malawi; and Kathmandu, Nepal). Cohorts consisted of acute typhoid fever patients (n&#x2009;=&#x2009;92), asymptomatic household contacts of typhoid fever patients (representing individuals who were likely exposed to S. Typhi but did not develop the disease, n&#x2009;=&#x2009;97) and asymptomatic serosurvey participants with high Vi antibody titres (representing individuals who were exposed to S. Typhi and may be carriers, n&#x2009;=&#x2009;69). The stool microbiomes of each cohort were characterised using shotgun metagenomics, and bacterial diversity, composition and function were compared.<br><br>RESULTS: We identified 4 bacterial species that were significantly lower in abundance in typhoid fever patients compared with household contacts (i.e. probably exposed), in two of the three participant populations (Bangladesh and Malawi). These bacteria may represent taxa that provide protection against the development of clinical infection upon exposure to S. Typhi and include the inflammation-associated species Prevotella copri clade A and Haemophilus parainfluenzae. Our functional analysis identified 28 specific metabolic gene clusters (MGCs) negatively associated with typhoid fever in Bangladesh and Malawi, including seven MGCs involved in SCFA metabolism. The putative protection provided by microbiome SCFA metabolism was supported by data from a controlled human infection model conducted in a UK population, in which participants who did not develop typhoid fever following ingestion of S. Typhi had a higher abundance of a putative SCFA-metabolising MGC (q-value&#x2009;=&#x2009;0.22).<br><br>CONCLUSIONS: This study identified the same protective associations between taxonomic and functional microbiota characteristics and non-susceptibility to typhoid fever across multiple human populations. Future research should explore the potential functional role of SCFAs and inflammation-associated bacteria in resistance to S. Typhi and other enteric infections. Video Abstract.},
}
@article {pmid40695901,
year = {2025},
author = {Awad, N and Larson, PJ and Sissoko, CA and Bond, LL and Dion, GR},
title = {Metagenomic whole genome shotgun analysis of the airway microbiome in laryngotracheal stenosis: a pilot study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26570},
pmid = {40695901},
issn = {2045-2322},
mesh = {Humans ; Pilot Projects ; *Microbiota/genetics ; *Laryngostenosis/microbiology ; *Tracheal Stenosis/microbiology ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Metagenome ; Adult ; Tracheostomy ; Whole Genome Sequencing ; RNA, Ribosomal, 16S/genetics ; Shotgun Sequencing ; },
abstract = {The airway microbiome has been implicated in the pathogenesis of laryngotracheal stenosis (LTS), yet prior studies using 16 S rRNA sequencing have limited sub-genus level resolution. Metagenomic whole genome shotgun sequencing (mWGS) allows for strain-level taxonomic and functional genomic analysis, providing detailed insights into specific organisms and pathways. A pilot study was conducted to explore the advantages and challenges of mWGS in investigating the airway metagenome in LTS. mWGS was conducted on 12 intraoperative swab samples from 8 LTS patients, divided into tracheostomy-dependent (n = 3) and non-tracheostomy (n = 5) groups, and 4 controls. Patient comorbidities, antibiotic use, and medications were documented. Biobakery workflows were used for taxonomic and functional profiling. Species-specific reference databases were constructed for 6 abundant species for strain-level analyses. LTS samples had decreased taxonomic diversity and were dominated by species with previously described roles in other chronic inflammatory processes such as Staphylococcus aureus, Streptococcus parasanguinis, Streptococcus mitis, and Corynebacterium pseudogenitalium. LTS samples were enriched for pathways involved in fatty acid biosynthesis and formaldehyde metabolism. Our results identified tracheostomy as an important potential confounder in airway metagenomics but show mWGS techniques are promising in uncovering microbiota correlates in LTS that could reveal disease-specific biomarkers, comorbidity links, and therapeutic targets.},
}
@article {pmid40695592,
year = {2025},
author = {Welsch, EC and Barron, MR and Storage, KM and Kazen, AB and Aboulalazm, FA and Kirby, JR and Kindel, TL},
title = {Gut microbiome and bile acid changes after male rodent sleeve gastrectomy: what comes first?.},
journal = {American journal of physiology. Regulatory, integrative and comparative physiology},
volume = {329},
number = {3},
pages = {R410-R421},
pmid = {40695592},
issn = {1522-1490},
support = {HL072483//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; T35 HL072483/HL/NHLBI NIH HHS/United States ; Clowes Career Development Award//American College of Surgeons (ACS)/ ; R01HL158900//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R01 HL158900/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Bile Acids and Salts/metabolism ; *Gastrectomy/methods ; Male ; Mice, Inbred C57BL ; *Liver/metabolism ; Mice ; Fecal Microbiota Transplantation ; },
abstract = {Understanding how a sleeve gastrectomy (SG) achieves metabolic improvement is challenging due to the complex relationship between the liver, bile acid (BA) pool, and gut microbiome. We hypothesized that SG alters the gut microbiome, which then increases the BA pool, leading to metabolic efficacy. We performed fecal material transfer (FMT) from SG or sham mice to surgically naïve mice with an intact microbiome. We evaluated the effect of surgery and FMT on BA-related liver enzymes, BA concentrations, and gut microbiome composition via 16S and metagenomic analysis. SG significantly deflected weight gain compared with sham surgery, 5 ± 2 g versus 10 ± 3 g, respectively (P = 0.004). SG significantly increased the BA pool and decreased liver transcription of slc10a1 (P = 0.04) and cyp8b1 (P = 0.03). Random forest analysis identified several features with significantly increased relative abundance in SG compared with sham mice, including Lactobacillus. Examination of metabolic profiles with metagenomic analysis revealed a BA salt hydrolase produced by the Ligilactobacillus species. FMT of SG stool to surgically naïve mice significantly decreased the BA pool compared with sham FMT (P = 0.034). Unlike SG surgery, we found no effect of SG or sham FMT on bile acid-related enzymes in the liver after 14 wk of treatment. Overall, we propose that the metabolic benefits of SG surgery are related to decreased liver transcription of cyp8b1 and slc10a1 with subsequent increases in the systemic and enterohepatic BA pool, including lithocholic acid. The gut microbiome adapts to the altered BA pool with associated increases in Ligilactobacillus and bile salt hydrolase production.NEW &amp; NOTEWORTHY We propose that the metabolic benefits of sleeve gastrectomy are initiated by decreased liver transcription of cyp8b1 and slc10a1. A notable downstream effect includes changes in systemic bile acid composition and circulation, including increased LCA. An altered gut microbiome after surgery includes increases in Ligilactobacillus that was shown to express a bile salt hydrolase, which could be a contributor to the post-sleeve gastrectomy gut microbiome changes.},
}
@article {pmid40695364,
year = {2025},
author = {Kabil, AK and Liu, LT and Xu, C and Nayyar, N and González, L and Chopra, S and Brassard, J and Beaulieu, MJ and Li, Y and Damji, A and Zandstra, PW and Blanchet, MR and Hughes, MR and McNagny, KM},
title = {Microbial dysbiosis sculpts a systemic ILC3/IL-17 axis governing lung inflammatory responses and central hematopoiesis.},
journal = {Mucosal immunology},
volume = {18},
number = {5},
pages = {1139-1158},
doi = {10.1016/j.mucimm.2025.07.002},
pmid = {40695364},
issn = {1935-3456},
mesh = {Animals ; *Dysbiosis/immunology ; Mice ; *Interleukin-17/metabolism ; *Th17 Cells/immunology ; *Hematopoiesis ; *Lung/immunology ; Mice, Inbred C57BL ; Streptomycin ; Disease Models, Animal ; Microbiota ; Immunity, Innate ; },
abstract = {Advancements in vaccination and sanitation have significantly reduced the prevalence and burden of infectious diseases; however, these benefits have coincided with a marked rise in autoimmune and allergic disorders. Recent studies have investigated these linked trends through the lens of host-microbiome alterations, proposing these shifts as a potential explanatory mechanism. Previously, we demonstrated that vancomycin-induced depletion of short-chain fatty acid (SCFA) producing bacteria results in hyperactivation of ILC2s and exacerbated allergic responses. Here we investigate the effects of low-dose streptomycin on innate and adaptive immune cell populations and their activation states. Although streptomycin-treated mice exhibit normal allergic responses, they display heightened susceptibility to Th1/Th17-mediated disease, specifically hypersensitivity pneumonitis (HP). This is characterized by a two-fold increase in ILC3s and Th17 cells in the lungs, alongside activation of antigen-presenting cells (APCs) at steady state, an effect that is further amplified upon exposure to HP-inducing agents. Shotgun metagenomic analysis revealed that streptomycin-induced dysbiosis reduces microbial diversity, depletes bile acid-metabolizing bacteria, and enriches for metabolic pathways involved in branched-chain amino acid biosynthesis, including leucine, a known activator of mTORC1. Strikingly, administration of the secondary bile acid metabolite isolithocholic acid (an inverse agonist of RORγt), or an IL-23 neutralizing antibody, reverses the enhanced susceptibility to HP. Inhibition of mTORC1 also significantly reduced Th17/ILC3 responses and histopathology. Our findings underscore microbial equilibrium as a key determinant of susceptibility to HP and uncover a positive feedback loop between IL-23-producing APCs and ILC3/Th17 cells that mechanistically links dysbiosis to sustained type 3 inflammation; and we identify a simple, actionable means of intervention.},
}
@article {pmid40695175,
year = {2025},
author = {Federico, S and Esposito, R and De Rosa, M and Sonnessa, M and Reddel, S and Laurenzi, G and Bertolino, M and Giovine, M and Pozzolini, M and Zupo, V and Costantini, M},
title = {Comparative metagenomic analyses of the microbiome from three Mediterranean sponges to identify genes involved in biosynthesis of bioactive compounds.},
journal = {Marine genomics},
volume = {82},
number = {},
pages = {101202},
doi = {10.1016/j.margen.2025.101202},
pmid = {40695175},
issn = {1876-7478},
mesh = {Animals ; *Porifera/microbiology ; *Microbiota/genetics ; Metagenomics ; *Bacteria/genetics/metabolism/classification ; *Metagenome ; },
abstract = {Marine sponges host a range of microorganisms and among them, bacteria represent a significant part of their biomass. Furthermore, bacteria are promising sources of natural products to be applied in various fields. Often the study their biotechnological potential is relented by low grow rates. For this reason, such cultivation-independent approaches, as metagenomics tools applied to sponges is obtaining wide success. For the first time, here we aimed at having an almost complete information about taxonomic and functional diversity of bacteria associated to three sponges, Agelas oroides, Haliclona (Halichoclona) vansoesti and Geodia cydonium, previously reported as candidate sources of bioactive compounds for pharmacological, nutraceutical and cosmeceutical purposes. Comparative metagenomic analyses were applied, sequencing DNA from the three sponges by ONT GridION X5 Mk1 sequencer. Our findings revealed for all the analyzed sponges the presence of genes/enzymes responsible for the synthesis of vitamins, fatty acids, antioxidant glutathione, terpenes, steroids and carotenoids. Consequently, we demonstrated the three sponges under analysis and their associated microorganisms could be considered good candidates for the isolation and identification of bioactive compounds for biotechnological application in the field of pharmacology, nutraceuticals and cosmeceuticals as well as environmental biotechnologies. Overall, metagenomic data represent a useful tool exploitable to sustainably develop bioactive products.},
}
@article {pmid40694475,
year = {2025},
author = {Pfeifer, E and d'Humières, C and Lamy-Besnier, Q and Oñate, FP and Denisé, R and Dion, S and Condamine, B and Touchon, M and Ma, L and Burdet, C and Mentré, F and Denamur, E and Rocha, EPC and , },
title = {Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages.},
journal = {Cell reports},
volume = {44},
number = {8},
pages = {116020},
doi = {10.1016/j.celrep.2025.116020},
pmid = {40694475},
issn = {2211-1247},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Bacteriophages/drug effects/pathogenicity/genetics ; *Anti-Bacterial Agents/pharmacology ; Female ; Male ; Adult ; Virulence/drug effects ; Cephalosporins/pharmacology ; },
abstract = {Antibiotic use disrupts the gut microbiota, posing risks of long-term health issues and resistance. To study its impact on gut phages, we followed 22 healthy individuals 2 weeks before and up to 6 months after a 3-day course of 3[rd]-generation cephalosporins. Our results show that gut phages rarely encode antibiotic resistance genes and are mostly temperate, including many phage plasmids. Furthermore, phage populations remain individual-specific even after microbiome perturbation. Yet, we report a 20% decline in phage diversity the day after treatment, alongside blooms of a few, mostly virulent, phages. We suggest that some of these phages contribute to the recovery of bacterial diversity via "kill-the-winner" dynamics. This is supported by (temporarily) dominant phages targeting Parabacteroides distasonis, a bacterium that thrives post-treatment only in the absence of these phages. Our findings suggest gut phages are crucial to the microbiome response to antibiotics, aiding the restoration of balance and diversity.},
}
@article {pmid40694261,
year = {2025},
author = {Tay, DD and Kumar, VS and Shapawi, R and Shah, MD and Ahmad, HF and Mazlan, N},
title = {The Relationship Between the Gut Microbiome and the Aqua Cultured Fish, General Prospects Toward Fish Health: A Systematic Review.},
journal = {Applied biochemistry and biotechnology},
volume = {197},
number = {10},
pages = {6314-6357},
pmid = {40694261},
issn = {1559-0291},
support = {Grant Agensi Kerajaan HIC2404//Ministry of Higher Education, Malaysia/ ; },
mesh = {*Gastrointestinal Microbiome ; Animals ; *Fishes/microbiology ; *Aquaculture ; },
abstract = {Aquaculture allows the cultivation of aquatic life outside its normal origins which can provide work opportunities, seafood security, as well as conservation efforts for endangered fish species. Numerous factors influence the health of aquaculture fish, with the gut microbiome playing a pivotal role. Research indicates that an imbalance or dysbiosis in the gut microbiome can significantly affect the overall well-being and health outcome of these fish. Despite extensive research utilizing metagenomics across diverse environments and controlled conditions, a clear consensus on the characteristic of "healthy" or "optimal" gut microbiome in domesticated fish has yet to be established. This review will cover 28 studies, which further discusses the findings of the gut microbiome within fish and attempts to provide a general outline of how the gut bacteria may interact and affect fish health within aquaculture environments. The indices as well as pathogens and beneficial bacteria of each study are also listed. This review aims to provide readers with an enhanced understanding of the complex dynamics of the gut microbiome in aquaculture fish, while offering insights that could inform the design of future studies in this field.},
}
@article {pmid40693750,
year = {2025},
author = {Sant, DG and Smith, TP and Wong, ELY and Cohen, J and King, KC and Bell, T and Barraclough, TG},
title = {Eco-evolutionary robustness of wild bacterial communities to experimental perturbation.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {40693750},
issn = {1751-7370},
support = {NE/V011596/1//National Environment Research Council/ ; },
mesh = {*Bacteria/genetics/classification ; *Biological Evolution ; Ecosystem ; Biodiversity ; *Microbiota ; Metagenome ; Polymorphism, Single Nucleotide ; Fagus/microbiology ; },
abstract = {Most knowledge about bacterial evolution and ecological interactions comes from laboratory studies. One difference between the wild and most laboratory experiments is the diversity of bacterial taxa present. Understanding how wild bacteria respond to perturbation therefore requires consideration of how ecological sorting, colonization, and genetic changes of constituent species interact. Ecological sorting of species might reduce evolutionary rates and make communities robust to disturbance, or it could amplify selection pressures and lead to unstable co-evolutionary cascades. Even estimates of basic rates of ecological sorting, dispersal, and genetic change are rare. Here, we addressed these knowledge gaps by liming wild decomposer communities living in beech tree holes and tracking ecological and evolutionary responses for 12 weeks. Overall, tree hole communities were extremely robust to liming involving short-term pulses up to 4 pH units and long-term increases up to 2 pH units. Species diversity and composition displayed significant but small changes in treatment tree holes compared to control ones. New bacterial taxa colonized at a low rate that did not vary with liming. Genetic changes in the frequency of single nucleotide polymorphisms in metagenome assembled genomes occurred at rates that were both comparable to and correlated with ecological changes in the same metagenome assembled genomes, but the rate of genetic changes did not vary between limed and control tree holes. Analysis of rates of genetic change estimated low effective population size (~104) and generation times of roughly 1 day. Our study provides estimates of rates of ecological and evolutionary processes in wild bacterial communities, which displayed remarkable robustness to our experimental perturbation.},
}
@article {pmid40692682,
year = {2025},
author = {Qin, X and Xi, L and Zhao, L and Han, J and Qu, H and Xu, Y and Weng, W},
title = {Exploring the distinctive characteristics of gut microbiota across different horse breeds and ages using metataxonomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1590839},
pmid = {40692682},
issn = {2235-2988},
mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Age Factors ; Metagenomics/methods ; DNA, Bacterial/genetics ; Biodiversity ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Gut microbiota exerts a pivotal function in host nutrient metabolism and maturation of the mucosal immunity. Analyzing the reciprocal interaction between horses and gut microbiota constitutes a crucial aspect of scientific feeding practices. This study aims to investigate the differences in gut microbiota among Hequ horses, Mongolian horses, and Thoroughbred horses, as well as between Thoroughbred horses at two age stages.<br><br>METHODS AND RESULTS: Paired-end sequencing with a read length of 2&#xd7;250 bp targeting the V3-V4 region of the 16S rRNA gene in fecal samples was carried out. Subsequently, differences in the diversity, composition, and metabolic pathways of the gut microbiota among the groups were analyzed. The results showed that: (1) Horse breeds were associated with variations in the gut microbiota. Microbial diversity, the proportion of commensal bacteria from Bacillota and Bacteroidota, and bacterial communities involved in dietary fiber metabolisms were significantly higher in the gut of the Hequ horses than in the gut of the Mongolian and Thoroughbred horses. The highest Bacillota to Bacteroidota (B/B) ratio and enrichment of bacterial communities involved in the metabolism of bile acids, lipids, and amino acids in the gut of the Mongolian horses resulted in significantly higher lipid metabolism and amino acid metabolism than in the other two breeds. The bacterial communities enriched in the gut of Thoroughbred horses were primarily involved in carbohydrate metabolism, but the level of energy metabolism was significantly lower than in Hequ horses. (2) The results also showed an association between age and gut microbiota of Thoroughbred horses. The alpha diversity, B/B ratio, and 83.33% of metabolic pathways did not differ significantly between younger and older Thoroughbred horses. However, there were significant differences between the two age groups in beta diversity, composition of glycolytic bacteria, metabolism of cofactors and vitamins, and energy metabolism of gut microbiota.<br><br>CONCLUSIONS: Collectively, these results point to an association between the breed of horses or the age of Thoroughbred horses with variations in gut microbiota. The current findings will serve as a reference for improving feeding strategies for horses.},
}
@article {pmid40692127,
year = {2025},
author = {Vipindas, PV and Venkatachalam, S and Jabir, T and Yang, EJ and Cho, KH and Jung, J and Lee, Y and Moon, JK and Jain, A},
title = {Distribution of Surface-Layer Prokaryotes in the Western Arctic Ocean: Responses to Pacific Water Inflow and Sea Ice Melting.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70154},
doi = {10.1111/1462-2920.70154},
pmid = {40692127},
issn = {1462-2920},
support = {//National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Govt. of India/ ; //Korea Polar Research Institute/ ; //The Ministry of Oceans and Fisheries, Republic of Korea/ ; },
mesh = {Arctic Regions ; *Ice Cover/microbiology ; *Archaea/genetics/classification/isolation &amp; purification ; *Seawater/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Pacific Ocean ; Microbiota ; Metagenome ; },
abstract = {Here, we evaluated how microbial community composition and functions vary along the path of Pacific water inflow, starting from the Bering Sea via the Chukchi Sea to the central Arctic Ocean. Our findings reveal that the inflow of Pacific water and sea ice melt significantly influence the environmental settings of the western Arctic Ocean, resulting in distinct prokaryotic communities with varied distribution patterns between the open Chukchi Sea and the Ice-covered central Arctic Ocean. The heterotrophic populations reliant on phytoplankton predominated in the Bering Sea and Southern Chukchi Sea, while in the Central Arctic Ocean, chemoautotrophic bacteria and archaea contributed equally with heterotrophic populations adapted to oligotrophic conditions. Although no specific functional genes were universally enriched across the metagenome libraries of prokaryotic communities, the relative abundance of functional genes varied among oceanic sectors. The assembly processes of prokaryotic communities in the western Arctic Ocean were found to be influenced by both deterministic and stochastic factors, with deterministic processes playing a more significant role. Thus, the ongoing increases in Pacific inflow and sea ice melt could lead to the displacement of native chemoautotrophic and oligotrophic populations in the Arctic Ocean by fast-growing heterotrophic populations better adapted to elevated nutrient concentrations and temperatures.},
}
@article {pmid40691525,
year = {2025},
author = {Abdelkader, A and Ferdous, NA and El-Hadidi, M and Burzykowski, T and Mysara, M},
title = {metaGEENOME: an integrated framework for differential abundance analysis of microbiome data in cross-sectional and longitudinal studies.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {189},
pmid = {40691525},
issn = {1471-2105},
mesh = {Longitudinal Studies ; *Microbiota/genetics ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Humans ; Metagenome ; },
abstract = {BACKGROUND: Detecting biomarkers is a key objective in microbiome research, often done through 16S rRNA amplicon sequencing or shotgun metagenomic analysis. A critical step in this process is differential abundance (DA) analysis, which aims to pinpoint taxa whose abundance significantly differs between groups. However, DA analysis remains challenging due to high dimensionality, compositionality, sparsity, inter-taxa correlations, uneven abundance distributions, and missing values-all which hinder our ability to model the data accurately. Despite the availability of many DA tools, balancing high statistical power with effective false discovery rate (FDR) control remains a major limitation.<br><br>RESULTS: Here, we introduce a novel approach for DA analysis that integrates counts adjusted with Trimmed Mean of M-values (CTF) normalization and Centered Log Ratio (CLR) transformation with Generalized Estimating Equation (GEE) model. We benchmarked our approach against eight widely used tools employing both simulated and real datasets in cross-sectional and longitudinal settings. While several tools (e.g. MetagenomeSeq, edgeR, DESeq2 and Lefse) achieved high sensitivity, they often failed to adequately control the FDR. In contrast, our method demonstrated high sensitivity and specificity when compared to other approaches that successfully controlled the FDR, including ALDEx2, limma-voom, ANCOM, and ANCOM-BC2.<br><br>CONCLUSIONS: Our approach effectively addresses key challenges in microbiome data analysis across both cross-sectional and longitudinal designs. Integrated into the R package metaGEENOME (https://github.com/M-Mysara/metaGEENOME), our framework provides a flexible, scalable and statistically robust solution for DA analysis, offering improved FDR control and enhanced performance for biomarker discovery in microbiome studies.},
}
@article {pmid40691449,
year = {2025},
author = {Vázquez-Castellanos, JF and Maciel, LF and Wauters, L and Gregory, A and Van Oudenhove, L and Geboers, K and Verbeke, K and Smokvina, T and Tack, J and Vanuytsel, T and Derrien, M and Raes, J},
title = {Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {140},
pmid = {40691449},
issn = {2055-5008},
mesh = {Humans ; *Probiotics/administration &amp; dosage ; *Gastrointestinal Microbiome/drug effects ; *Stress, Psychological/microbiology ; *Students/psychology ; Male ; Female ; *Lacticaseibacillus rhamnosus/physiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Adult ; Feces/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Anxiety ; Metagenomics ; },
abstract = {Probiotics have been widely tested for their effect on mental well-being, albeit with heterogeneous outcomes. Direct and indirect effects through the gut microbiome might lie at the basis of these observations. Here, in a post-hoc analysis, we assessed the effect of 4-week consumption of a probiotic candidate strain on the gut microbiome in students exposed to academic stress. Healthy students were randomized to consume a fermented milk product with Lacticaseibacillus rhamnosus CNCM I-3690 (N = 39) or an acidified non-fermented milk product (N = 40) twice daily for 4 weeks before academic exams. The gut microbiome was analysed by Quantitative Microbiome Profiling based on 16S rRNA gene amplicon and shotgun metagenomic sequencing. Stress and anxiety were assessed using both objective and self-reported markers. Changes of alpha-diversity markers and community shifts from baseline (beta diversity) were lower in L. rhamnosus treated individuals over controls, suggesting lower overall changes of gut microbiota during psychological stress in the Probiotic group. The intake of L. rhamnosus CNCM I-3690 induced differential abundance of some species, such as the maintenance of the quantitative abundance of Ruminococcus bicirculans, and co-varied with species, which differed according to visits (i.e., stress level), suggesting a potential beneficial effect of the strain before the highest increase of stress level. The higher quantitative abundance of F. prausnitzii induced by the probiotic intake was associated with lowered self-reported anxiety levels before the exam. Functional analysis revealed minor changes upon intake of the probiotic strain. Taken together, using a quantitative framework, we found that L. rhamnosus CNCM I-3690 has a potential effect on gut microbiome response to stress, although further studies are needed to better understand the precise interaction.},
}
@article {pmid40691354,
year = {2026},
author = {Roux, S and Coclet, C},
title = {Viromics approaches for the study of viral diversity and ecology in microbiomes.},
journal = {Nature reviews. Genetics},
volume = {27},
number = {1},
pages = {32-46},
pmid = {40691354},
issn = {1471-0064},
mesh = {*Microbiota/genetics ; *Viruses/genetics/classification ; *Virome/genetics ; Humans ; Metagenomics/methods ; Ecosystem ; Genetic Variation ; Biodiversity ; Animals ; Genome, Viral ; },
abstract = {Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.},
}
@article {pmid40691217,
year = {2025},
author = {Leung, HKM and Lo, EKK and Chen, C and Zhang, F and Felicianna, and Ismaiah, MJ and El-Nezami, H},
title = {Theabrownin combined with zearalenone suppresses colitis-associated colorectal cancer by inhibiting PI3K/AKT pathway and enhancing microbial propionate production.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26386},
pmid = {40691217},
issn = {2045-2322},
mesh = {*Zearalenone/pharmacology/administration &amp; dosage ; Animals ; Mice ; *Proto-Oncogene Proteins c-akt/metabolism ; *Phosphatidylinositol 3-Kinases/metabolism ; Gastrointestinal Microbiome/drug effects ; *Propionates/metabolism ; Signal Transduction/drug effects ; *Colorectal Neoplasms/drug therapy/etiology ; *Colitis-Associated Neoplasms/drug therapy/metabolism/pathology ; Male ; Cytokines/metabolism ; Fluorouracil/pharmacology ; *Colitis/complications ; Mice, Inbred C57BL ; },
abstract = {Colorectal cancer (CRC) is both a leading cause of cancer-related mortality and one of the most frequently diagnosed cancers. Previous studies have shown that zearalenone and theabrownin each exert anti-CRC effects. Here, we aimed to evaluate the anti-tumor properties of theabrownin and zearalenone mixture (TZ) and to assess whether supplementing TZ with 5-FU, a commonly used chemotherapeutic drug, could further suppress CRC tumorigenesis. Our results revealed that TZ significantly attenuated AOM/DSS-induced colorectal tumorigenesis. TZ improved survival rate, reduced tumor count, preserved colon length, and mitigated colonic inflammation in AOM/DSS mice. In addition, the concentration of pro-inflammatory cytokines IL-6, TNF-α and IL-17 A/F and proliferative PI3K/AKT were significantly reduced. Metagenomic analyses revealed that TZ modulated the gut microbiota and mycobiota composition and increased the fecal acetate and propionate levels. Furthermore, the enrichment of the bacterial Desulfovibrionaceae bacterium LT0009, Helicobacter sp. MIT 03-1616 and fungal Xylariaceae sp. FL0594 was associated with the reduction of tumor multiplicity and pro-inflammatory cytokines. No additional benefits were observed with combining TZ with 5-FU. Taken together, TZ presented remarkable inhibitory effects on colorectal tumorigenesis, indicating its potential as a novel therapeutic candidate for CRC.},
}
@article {pmid40689619,
year = {2025},
author = {Tambovtseva, RS and Arslan, LA and Grigoryeva, TA and Abdulkhakov, SR and Doludin, YV and Stoma, IO and Rizvanov, AA and Miftakhova, RR and Gabdoulkhakova, AG},
title = {Narrative review on bacteria-derived metabolites in the pathogenesis of ulcerative colitis.},
journal = {Clinical microbiology reviews},
volume = {38},
number = {3},
pages = {e0021024},
pmid = {40689619},
issn = {1098-6618},
support = {FZSM-2023-0011//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Colitis, Ulcerative/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome ; *Bacteria/metabolism ; },
abstract = {SUMMARYThe pathogenesis of ulcerative colitis (UC) is heterogeneous; the causes are considered to be external factors such as stress, infections, antibiotics, and other medications, diet, and intrinsic factors such as genetic predisposition. The aim of this narrative review is to analyze data on intestinal flora and bacteria-derived metabolites in inflammatory bowel diseases and ulcerative colitis in particular. The main focus is on proteolytic, saccharolytic, mucin-degrading, and bile acid-metabolizing bacteria. What types of metabolites are beneficial for intestinal integrity and the patient's health? How can dietary preferences trigger disease and cause complications? What kind of changes in the microbiome promote the disease? We consider what targets/receptors metabolites act on and their physiological role. The knowledge accumulated over the past years on the gut metagenome, metabolome, and signaling mechanisms may allow, in the future, modulating the composition of the intestinal microbiome and suppressing the growth of pathogenic flora without the use of antibiotics, but due to pro- and prebiotics, products of bacterial metabolism, including quorum sensing molecules.},
}
@article {pmid40686474,
year = {2025},
author = {Lledós, M and Prats-Sánchez, L and Muiño, E and Cullell, N and Llucià-Carol, L and Cárcel-Márquez, J and Gallego-Fabrega, C and Martín-Campos, JM and Marín, R and Aguilera-Simón, A and Guasch-Jiménez, M and Ezcurra-Díaz, G and Camps-Renom, P and Del Mar Freijo, M and Martí-Fàbregas, J and Fernández-Cadenas, I},
title = {Influence of the Gut Microbiota on Acute Ischemic Stroke Functional Outcomes at Three Months.},
journal = {European journal of neurology},
volume = {32},
number = {7},
pages = {e70265},
pmid = {40686474},
issn = {1468-1331},
support = {RD21/0006/0006//RICORS-ICTUS/ ; AC19/00106//ERA-Net NEURON/ ; CD20/00043//Instituto de Salud Carlos III/ ; FI19/00309//Instituto de Salud Carlos III/ ; PI18/01338//Instituto de Salud Carlos III/ ; PI20/00925//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Ischemic Stroke/microbiology/physiopathology ; Male ; Female ; Aged ; Middle Aged ; *Recovery of Function/physiology ; Genome-Wide Association Study ; },
abstract = {BACKGROUND: Functional recovery from ischemic stroke (IS), the main cause of adult disability worldwide, is influenced by many factors, and a portion of interindividual variability remains unexplained.<br><br>METHODS: Observational study in a tertiary stroke centre of patients with IS analyzed using shotgun metagenomic sequencing (January 2020-March 2022). Functional outcomes were assessed according to modified Rankin Scale (mRS) scores 3-months post-IS, considering 0-2 favorable and 3-6 unfavorable. The causal relationship between several bacteria and post-IS outcomes was explored via two-sample Mendelian randomization (MR) analyses using Genome-Wide Association Analysis (GWAS) summary statistics.<br><br>RESULTS: Comparing 128 patients with favorable and unfavorable post-IS functional outcomes, &#x3b2;-diversity analysis showed a separation in microbial structure, and &#x3b1;-diversity measures revealed greater bacterial richness in the favorable outcomes group. Taxonomic profiling of the samples showed that a greater abundance of pathogenic bacteria (e.g., Pseudomonas, Finegoldia, Porphyromonas) was associated with an unfavorable outcome. Functional profiling of the samples revealed differences in the ethylbenzene degradation pathway and in 16S rRNA (uracil1498-N3)-methyltransferase. MR confirmed increased pyruvate levels to be causally associated with post-IS favorable outcomes (&#x3b2;&#x2009;=&#x2009;-0.50, 95% CI: -0.91, -0.10).<br><br>CONCLUSIONS: Our study points to gut microbiota differences in patients with unfavorable versus favorable 3-month post-IS outcomes. Patients with unfavorable outcomes presented gut microbiota dysbiosis and alterations in multiple metabolic pathways.<br><br>TRIAL REGISTRATION: This study was registered on 3 October 2021 with https://clinicaltrials.gov. Access number: NCT04795687.},
}
@article {pmid40685922,
year = {2025},
author = {Chen, QY and Shao, MM and Dong, SF and Shi, HZ and Yi, FS},
title = {Metagenomic and Metabolomic Profiling Reveals the Impact of High-Fat Diet on Malignant Pleural Effusion.},
journal = {Thoracic cancer},
volume = {16},
number = {14},
pages = {e70126},
pmid = {40685922},
issn = {1759-7714},
support = {7232066//Natural Science Foundation of Beijing Municipality/ ; 82200111//National Natural Science Foundation of China/ ; 048//Beijing Scholars Program/ ; QML20230303//Beijing Hospitals Authority Youth Program/ ; Ggyfz202314//Reform and Development Program of Beijing Institute of Respiratory Medicine/ ; Ggyfz202330//Reform and Development Program of Beijing Institute of Respiratory Medicine/ ; Ggyfz202416//Reform and Development Program of Beijing Institute of Respiratory Medicine/ ; },
mesh = {Animals ; Mice ; *Diet, High-Fat/adverse effects ; *Metabolomics/methods ; *Metagenomics/methods ; *Pleural Effusion, Malignant/etiology/metabolism/pathology ; Male ; Gastrointestinal Microbiome ; Humans ; *Metabolome ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Malignant pleural effusion (MPE) is a common complication in the advanced stage of cancer. High-Fat Diet (HFD)-induced obesity has become a common metabolic background in cancer patients. Recent studies have demonstrated that HFD induces gut dysbiosis, resulting in alterations in metabolites and immune responses. However, its role in MPE remains unclear.<br><br>METHODS: We established an MPE mouse model under both normal chow and HFD conditions. Metagenomic sequencing of fecal samples and untargeted metabolomics of plasma were performed to assess alterations in gut microbiota and systemic metabolites, respectively. Bioinformatic and statistical analyses were conducted to identify significant microbial taxa and metabolic pathways.<br><br>RESULTS: HFD-fed mice exhibited increased pleural effusion. Metagenome data of the intestinal microbiome and metabolome profiles of plasma metabolites revealed key taxa-Akkermansiaceae, Parabacteroides, and Muribaculaceae-as well as significant metabolic pathways involved in sphingolipid metabolism, glycerophospholipid metabolism, and steroid hormone biosynthesis.<br><br>CONCLUSION: These findings suggest that HFD may accelerate the MPE progression through modulation of gut microbiota and plasma metabolites, providing new strategies for prevention and treatment.},
}
@article {pmid40685618,
year = {2025},
author = {Morsy, Y and Walberg, &#xc5; and Wawrzyniak, P and Hubeli, B and Truscello, L and Mamie, C and Niechcial, A and Gueguen, E and Manzini, R and Gottier, C and Lang, S and Scharl, S and Blümel, S and Biedermann, L and Rogler, G and Turina, M and Ramser, M and Petrowsky, H and Arnold, IC and Zeissig, S and Zamboni, N and Egli, A and Niess, JH and Hruz, P and Knuth, A and Fritsch, R and Manz, MG and Wawrzyniak, M and Scharl, M},
title = {Blood-borne immune cells carry low biomass DNA remnants of microbes in patients with colorectal cancer or inflammatory bowel disease.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2530157},
pmid = {40685618},
issn = {1949-0984},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/immunology/blood ; *Inflammatory Bowel Diseases/microbiology/immunology/blood ; *Leukocytes, Mononuclear/microbiology/immunology ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/isolation &amp; purification ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *DNA, Bacterial/genetics ; Metagenomics ; Adult ; Bacterial Translocation ; Aged ; },
abstract = {The involvement of the intestinal microbiome in the pathogenesis of inflammatory bowel disease (IBD) and colorectal cancer (CRC), is well-established. Bacteria interact with immune cells at sites of intestinal inflammation, but also in the CRC tumor microenvironment. We hypothesized that bacterial remnants translocate within peripheral blood mononuclear cells (PBMCs) into the circulation and thus explored the composition of the detectable microbiome in PBMCs of patients with CRC or IBD compared to healthy controls. The PBMC microbiome profiles partially align with the tumor-derived or intestinal tissue-derived microbiome signatures obtained from the same patients with CRC or IBD, respectively. Our metagenomics data, supported by 16S-rRNA-FISH-Flow, imaging flow cytometry and species-specific qPCR, revealed the presence of translocated bacterial genetic sequences in the patients with CRC and IBD. Thus, our data suggest that in patients with intestinal barrier leakage, there is the potential for the translocation of bacterial remnants into the circulation via PBMCs.},
}
@article {pmid40684088,
year = {2025},
author = {Kreisinger, J and Kaňková, &#x160; and Dlouhá, D and Ullmann, J and Nouzová, K and Hrbáčková, H and Schmiedová, L and Takács, L},
title = {Associations between psychological or biological stress indicators and gut microbiota in pregnant women - findings from a prospective longitudinal study.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {442},
pmid = {40684088},
issn = {1471-2180},
support = {21-23288S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky,Czechia/ ; 21-23288S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky,Czechia/ ; 21-23288S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky,Czechia/ ; 21-23288S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky,Czechia/ ; 21-23288S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky,Czechia/ ; 21-23288S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky,Czechia/ ; 21-23288S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky,Czechia/ ; 21-23288S//Grantov&#xe1; Agentura &#x10c;esk&#xe9; Republiky,Czechia/ ; CZ.02.01.01/00/22_008/0004597//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; CZ.02.01.01/00/22_008/0004597//Ministerstvo &#x160;kolstv&#xed;, Ml&#xe1;de&#x17e;e a T&#x11b;lov&#xfd;chovy/ ; },
mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Longitudinal Studies ; Prospective Studies ; Adult ; RNA, Ribosomal, 16S/genetics ; Anxiety/microbiology ; *Stress, Psychological/microbiology ; Depression/microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Hydrocortisone/blood ; Young Adult ; Surveys and Questionnaires ; Pregnant People/psychology ; Postpartum Period ; },
abstract = {BACKGROUND: The perinatal period has been linked with higher vulnerability to stress and symptoms of depression and anxiety, as well as with dynamic changes in the composition of maternal gut microbiota. While recent studies indicated significant associations between stress, depression, or anxiety, and alterations in gut microbiota in pregnant women, research in this avenue is still emerging, with existing studies often being limited by small sample sizes.<br><br>METHOD: We conducted a prospective longitudinal study of 171 women, collecting gut microbiota samples in each trimester of pregnancy and in the early postpartum, questionnaire data (perceived stress via the Perceived Stress Scale, symptoms of depression via the Edinburgh Postnatal Depression Scale, and anxiety via the 6-item State-Trait Anxiety Inventory) twice in each trimester and twice in the early postpartum period, and blood samples for cortisol levels analysis in the first and third pregnancy trimesters. Gut microbiota samples were analyzed by amplicon sequencing of 16S rRNA gene.<br><br>RESULTS: Perceived stress and symptoms of depression and anxiety showed moderate temporal changes and a high consistency at the individual level over the study period. Cortisol levels rose significantly from the first to the third trimester. There were significant temporal changes in microbiota composition between the first and second trimesters, and between the first and third trimesters. After controlling for false positive findings due to multiple testing, we found no significant associations between stress-related variables (perceived stress, cortisol levels, symptoms of depression and anxiety) and gut microbiota diversity, microbial community composition, or relative abundances of individual bacterial taxa.<br><br>CONCLUSIONS: The present study results contradict previous research that indicated significant associations between emotions and gut microbiota in the perinatal period. Although we cannot provide an ultimate explanation for this discrepancy, we propose it can lie in insufficient control for false positives in the differential abundance analyses in most previous studies.},
}
@article {pmid40683926,
year = {2025},
author = {Zafeiropoulou, K and Voermans, B and Ngo, H and Moreno, J and Lee, D and Derikx, JPM and Luyer, M and Zwinderman, AH and Nieuwdorp, M and de Goffau, M and de Jonge, WJ and Levin, E},
title = {Application of image guided analyses to monitor fecal microbial composition and diversity in a human cohort.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26237},
pmid = {40683926},
issn = {2045-2322},
support = {09150182010020//Amsterdam University Medical Centers/ ; 101141346/ERC_/European Research Council/International ; },
mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Cohort Studies ; Adult ; Smartphone ; *Bacteria/genetics/classification ; Metagenomics/methods ; Middle Aged ; },
abstract = {The critical role of gut microbiota in human health and disease has been increasingly illustrated over the past decades, with a significant amount of research demonstrating an unmet need for self-monitor of the fecal microbial composition in an easily-accessible, rapid-time manner. In this study, we employed a tool for Smartphone Microbiome Evaluation and Analysis in Rapid-time (SMEAR) that uses images of fecal smears to predict microbial compositional characteristics in a human cohort. A subset of human fecal samples was randomly retrieved from the second wave of data collection in the Healthy Life in an Urban Setting (HELIUS) study cohort. Per sample, 16S rRNA gene sequencing data was generated in addition to an image of a fecal smear, spread on a standard A4 paper. Metagenomics-paired pictures were used to validate a computer vision-based technology to classify whether the sample is of low or high relative abundance of the 50 most abundant genera, and α-diversity (Shannon-index). In total, 888 fecal samples were used as an application of the SMEAR technology. SMEAR gave accurate predictions whether a fecal sample is of low or high relative abundance of Sporobacter, Oscillibacter and Intestinimonas (very good performance, AUC > 0.8, p-value < 0.001, for all models), as well as Neglecta, Megasphaera, Lachnospira, Methanobrevibacter, Harryflintia, Roseburia, and Dialister (good performance, AUC > 0.75, p-value < 0.001, for all models). Likewise, SMEAR could classify whether a fecal sample was of low or high α-diversity (AUC = 0.83, p-value < 0.001). Our study demonstrates that SMEAR robustly predicts microbial composition and diversity from digital images of fecal smears in a human cohort. These findings establish SMEAR as a new benchmark for rapid, cost-effective microbiome diagnostics and pave the way for its direct application in research settings and clinical validation.},
}
@article {pmid40683886,
year = {2025},
author = {Wu, T and Guo, SZ and Zhang, Y and Zhao, XZ and Ran, CG and Liu, FL and Wang, RH and Li, DF and Zhu, HZ and Jiang, CY and Shen, XH and Liu, SJ},
title = {The engineering of TBBPA-degrading synthetic microbiomes with integrated strategies.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {139},
pmid = {40683886},
issn = {2055-5008},
support = {41991333//National Natural Science Foundation of China/ ; 41991333//National Natural Science Foundation of China/ ; 41991333//National Natural Science Foundation of China/ ; 41991333//National Natural Science Foundation of China/ ; 32270084//National Natural Science Foundation of China/ ; 41991333//National Natural Science Foundation of China/ ; 2019YFA0905500//National Key Research and Development Program of China/ ; 2019YFA0905500//National Key Research and Development Program of China/ ; 2019YFA0905500//National Key Research and Development Program of China/ ; 2019YFA0905500//National Key Research and Development Program of China/ ; 2019YFA0905500//National Key Research and Development Program of China/ ; },
mesh = {Biodegradation, Environmental ; *Polybrominated Biphenyls/metabolism ; *Microbiota ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Soil Microbiology ; Metagenomics ; Soil Pollutants/metabolism ; },
abstract = {The capability to understand and construct synthetic microbiomes is crucial in biotechnological innovation and application. Tetrabromobisphenol A (TBBPA) is an emerging pollutant, and the understanding of its biodegradation is very limited. Here, a top-down approach was applied for the enrichment of TBBPA-degrading microbiomes from natural microbiomes. Ten keystone taxa correlated to TBBPA degradation and their co-occurrence interactions were identified by the dissection of the degrading microbiomes. Those keystone taxa were targeted and cultivated, and the genomic information was obtained by genome sequencing of strains and metagenomic binning. The keystone bacterial strains showed efficient degradation of TBBPA, and L-amino acids were important co-metabolic substrates to promote the degradation. Guided by this knowledge, a bottom-up approach was applied to design and construct a simplified synthetic consortium SynCon2, that consisted of four strains. The SynCon2 demonstrated efficient TBBPA degradation activity and soil bioremediation. Our study demonstrates the importance of the application of multiple tools in understanding the functions of microbiomes and provides an integrated top-down and bottom-up strategy for the construction of synthetic microbiomes with various applications.},
}
@article {pmid40683476,
year = {2025},
author = {Díaz-Moreno, N and Lobos, C and Carvajal, A and Poblete, I and Cantera, S and Lebrero, R},
title = {Valorization of aromatic hydrocarbons into polyhydroxyalkanoates: advances towards sustainable waste gas treatment.},
journal = {Bioresource technology},
volume = {436},
number = {},
pages = {132991},
doi = {10.1016/j.biortech.2025.132991},
pmid = {40683476},
issn = {1873-2976},
mesh = {*Hydrocarbons, Aromatic/chemistry/metabolism ; *Polyhydroxyalkanoates/chemistry/metabolism ; *Waste Management ; *Bioreactors/microbiology ; Sustainable Development ; Gases/chemistry/metabolism ; Pseudonocardia/metabolism ; Rhodococcus/metabolism ; Microbial Consortia ; Nitrogen/metabolism ; *Biopolymers/biosynthesis ; },
abstract = {Benzene, toluene, ethylbenzene, xylene and styrene (BTEXS) are priority gaseous pollutants due to their widespread release and health risks. This study demonstrates an efficient BTEXS bioconversion process into polyhydroxyalkanoates (PHA) using a specialized mixed microbial culture dominated by Pseudonocardia and Rhodococcus. The consortium achieved simultaneous degradation rates of 15.1 ± 3.9 g m[-3]h[-1] for toluene and 17.6 ± 5.7 g m[-3]h[-1] for ethylbenzene, with removal efficiencies over 90 %. The operating strategy promoted PHA accumulation up to 21.4 % gPHA gDCW[-1]. A two-step process was successfully implemented consisting of an initial reactor for biomass growth followed by a second reactor under nitrogen deprivation. PHA analysis revealed the synthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) copolymer with a dynamic increase in 3-hydroxyvalerate content under prolonged nitrogen starvation. Metagenomics provided insights into the microbial networks and metabolic pathways involved in the process. This research offers a sustainable solution for mitigating BTEXS pollution while producing valuable bioplastics.},
}
@article {pmid40683452,
year = {2025},
author = {Timilsina, M and Chundru, D and Pradhan, AK and Blaustein, RA and Ghanem, M},
title = {Benchmarking Metagenomic Pipelines for the Detection of Foodborne Pathogens in Simulated Microbial Communities.},
journal = {Journal of food protection},
volume = {88},
number = {9},
pages = {100583},
doi = {10.1016/j.jfp.2025.100583},
pmid = {40683452},
issn = {1944-9097},
mesh = {*Metagenomics/methods ; Food Microbiology ; Animals ; Benchmarking ; Listeria monocytogenes/isolation &amp; purification ; Chickens ; Campylobacter jejuni/isolation &amp; purification ; Cronobacter sakazakii/isolation &amp; purification ; Food Contamination/analysis ; Microbiota ; },
abstract = {Foodborne pathogens pose a significant public health threat worldwide, despite modern advances in food safety. While molecular detection of pathogens in complex food matrices has gained attention to support tracking and preventing outbreaks, thorough benchmarking is needed to optimize workflows for specific scenarios. This study evaluated the performance of four metagenomic classification tools: Kraken2, Kraken2/Bracken, MetaPhlAn4, and Centrifuge, for estimating pathogen presence and abundance in simulated microbial communities representing three food products. Specifically, we evaluated workflow performance in predicting varying levels of Campylobacter jejuni, Cronobacter sakazakii, and Listeria monocytogenes in metagenomes of chicken meat, dried food, and milk products. Metagenomes were simulated to include the respective pathogen at defined relative abundance levels (0%-control, 0.01%, 0.1%, 1%, and 30%) within the respective food microbiome. Performance evaluations demonstrated that Kraken2/Bracken achieved the highest classification accuracy, with consistently higher F1-scores across all food metagenomes, whereas Centrifuge exhibited the weakest performance. MetaPhlAn4 also performed well, particularly in predicting C. sakazakii in dried food metagenomes, but was limited in detecting pathogens at the lowest abundance level (0.01%). Overall, Kraken2/Bracken and Kraken2 exhibited the broadest detection range, correctly identifying pathogen sequence reads down to the 0.01% level, whereas MetaPhlAn4 and Centrifuge had higher limits of detection. Our results highlight Kraken2/Bracken as an effective tool for pathogen detection, with MetaPhlAn4 serving as a valuable alternative depending on pathogen prevalence. These findings provide crucial insights for selecting metagenomic tools for applications in food safety and pathogen surveillance applications.},
}
@article {pmid40682875,
year = {2025},
author = {Beltrán de Heredia, I and Sbaffi, T and González-Gaya, B and Di Cesare, A and Sabatino, R and Alkorta, I and Ruiz-Romera, E},
title = {Comparative analysis of planktonic and sessile microbiomes and associated resistomes in a freshwater ecosystem impacted by municipal wastewater treatment plant discharge.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139250},
doi = {10.1016/j.jhazmat.2025.139250},
pmid = {40682875},
issn = {1873-3336},
mesh = {*Microbiota/drug effects ; *Wastewater ; Biofilms ; *Plankton/drug effects ; *Fresh Water/microbiology ; Rivers/microbiology ; Ecosystem ; Waste Disposal, Fluid ; Water Microbiology ; Bacteria/genetics/drug effects ; *Water Pollutants, Chemical ; },
abstract = {Wastewater treatment plants (WWTPs) disrupt freshwater ecosystems and are recognised as hotspots for antimicrobial resistance. This study assessed the effect of treated municipal wastewater discharge on both planktonic and sessile freshwater microbial communities. A monitoring network was established in a Spanish urban river basin during 2022 dry season, with sampling points upstream and downstream of a WWTP. Artificial glass-based substrates enabled biofilm colonisation, while river water and effluent samples were collected during biofilm harvesting. Chemical exposure was assessed by characterising nutrients and antimicrobial concentrations in water, while shotgun metagenomics revealed taxonomic composition and resistome pools in both matrices. River water exhibited greater genus richness and pathobiome diversity than biofilms. Wastewater discharge shaped microbial composition, leading to shifts in less dominant groups, with partial attenuation of this effect downstream. Resistome richness was higher in river water compared to biofilm, though the latter displayed greater total abundances and distinct resistance profiles suggesting their role as genetic reservoirs. While no consistent resistome trends were linked to sampling location, higher total resistance abundances occurred in river water at sites impacted by wastewaters. Background resistance levels found upstream likely persisted downstream due to pollutant-driven selection. Lower resistome richness in effluent water suggests downstream abundances may also result from microbiome shifts and environmental factors. Assembly-based analysis revealed resistance genetic contexts and indicators of gene dissemination.},
}
@article {pmid40681522,
year = {2025},
author = {Xiang, X and Li, Y and Ye, J and Li, B and He, G and Zhu, M and Zhang, J and Zhang, B and Miao, M and Yang, Y},
title = {Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {136},
pmid = {40681522},
issn = {2055-5008},
support = {Z191100008619006//Beijing Municipal Science and Technology Commission/ ; CASNHP-MJN2023-04//the Chinese Association for Student Nutrition &amp; Health Promotion-Mead Johnson Nutritionals (China) Joint Fund/ ; 21JZD039//Major Research Project on Philosophy and Social Sciences of the Ministry of Education/ ; 2021YFC2600501//National Key R&amp;D Program Project of the Ministry of Science and Technology/ ; },
mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; China ; Fermentation ; *Fermented Foods/microbiology ; Food Microbiology ; *Gastrointestinal Microbiome ; Gene Transfer, Horizontal ; Glycine max/microbiology ; *Metagenomics/methods ; *Microbiota ; *Soy Foods/microbiology ; Humans ; },
abstract = {Fermented foods are a longstanding part of the Chinese diet and have been recognized for promoting gut microbial diversity. However, their microbial composition remains poorly defined, raising concerns about potential exposure to pathogens and antibiotic resistance genes (ARGs). Using shotgun metagenomics, we examined microbiota of 93 representative samples spanning three major categories of traditional Chinese fermented soybean products. We identified distinct microbial and functional profiles across food types, with antagonism between beneficial taxa (Bacillales and Lactobacillales) and harmful Enterobacterales. Comparative analysis with public Chinese gut microbiomes revealed species- and strain-sharing between fermented foods and human gut microbiota, identifying certain products as sources of clinically relevant pathogens, including Klebsiella pneumoniae and Klebsiella quasipneumoniae. Horizontal gene transfer analysis highlighted potential transfer of ARGs (e.g., efflux pump genes) from food microbes to gut microbiota. Our findings underscore the need to integrate microbial surveillance into traditional fermentation to balance health benefits with food safety.},
}
@article {pmid40680679,
year = {2025},
author = {Ni, H and Wang, J and Wu, H and Chan, BK and Chen, K and Wang, H and Chan, EW and Li, F and Chen, S},
title = {Exposure to the growth promoter tylosin elicits gut microbiota disruption and metabolic imbalance in mouse model.},
journal = {Environment international},
volume = {202},
number = {},
pages = {109684},
doi = {10.1016/j.envint.2025.109684},
pmid = {40680679},
issn = {1873-6750},
mesh = {*Tylosin/toxicity/adverse effects ; Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Anti-Bacterial Agents/toxicity/adverse effects ; Mice, Inbred C57BL ; Male ; *Growth Substances/toxicity ; },
abstract = {The environmental risk associated with the usage of the antibiotic tylosin as an animal growth promoter (AGPs) needs to be assessed because such agents are used in abundance and contamination of the environment is common, yet their effects on the physiology and gut microbiota composition of animals and humans are poorly understood. In this work, we performed metagenomic analysis and revealed that tylosin significantly disrupted the gut microbiota structure of animals, reduced species diversity, and caused the increase in the relative abundance of Blautia (60.95%). Enrichment of multiple contigs containing ARGs was observed, indicating that tylosin promotes antimicrobial resistance (AMR) development. Transcriptomic analyses of ileum tissues revealed perturbation in gene expression patterns suggestive of mitochondrial dysfunction and energy metabolism imbalance. These alterations might compromise nutrient absorption and utilization in the GI tract, and heighten the risk of development of obesity and non-alcoholic fatty liver disease (NAFLD). Furthermore, downregulation of immune-related gene expression was observed, indicating that tylosin caused immunosuppression and increased susceptibility to microbial infections when used over extended periods. Integrated omics analysis of the liver also showed significant disturbances in metabolism through activation of the arachidonic acid metabolism pathway, exacerbating inflammatory responses, and precipitating the occurrence of metabolic disorders such as type 2 diabetes mellitus (T2DM) and NAFLD. Our findings unveil the detrimental effects of tylosin on animal gut microbiota and metabolic functions and highlight the potential health risks to wildlife and humans when released into the environment. These findings highlight a need for cautious use of AGPs and the development of safer alternatives.},
}
@article {pmid40680146,
year = {2025},
author = {Li, B and Sakaguchi, T and Tani, H and Ito, T and Murakami, M and Okumura, R and Kobayashi, M and Okuzaki, D and Motooka, D and Ikeuchi, H and Ogino, T and Mizushima, T and Hirota, S and Otake-Kasamoto, Y and Kishikawa, T and Nakamura, S and Kobiyama, K and Ishii, KJ and Hashiguchi, T and Kawai, T and Kuroda, E and Shinzaki, S and Ise, W and Kurosaki, T and Kikuchi, A and Tomofuji, Y and Okada, Y and Takeda, K and Kayama, H},
title = {OTUD3 prevents ulcerative colitis by inhibiting microbiota-mediated STING activation.},
journal = {Science immunology},
volume = {10},
number = {109},
pages = {eadm6843},
doi = {10.1126/sciimmunol.adm6843},
pmid = {40680146},
issn = {2470-9468},
mesh = {Animals ; *Colitis, Ulcerative/immunology/microbiology/prevention &amp; control/genetics/pathology ; Mice ; Humans ; *Membrane Proteins/metabolism/immunology ; *Gastrointestinal Microbiome/immunology ; Mice, Inbred C57BL ; Fibroblasts/metabolism/immunology ; Male ; Female ; Nucleotides, Cyclic/metabolism ; Mice, Knockout ; STING Protein ; },
abstract = {Ulcerative colitis (UC) develops through a complicated interaction between the host and microbiota. Intestinal fibroblasts are believed to play crucial roles in the pathogenesis of UC, but the influence of the host-microbiota interaction on the pathophysiology of intestinal fibroblasts remains poorly understood. Here, we demonstrate that OTU deubiquitinase 3 (OTUD3) suppresses pathologic activation of fibroblasts exposed to microbial cyclic GMP-AMP (3'3'-cGAMP) in the colon by deubiquitinating stimulator of interferon genes (STING). Mice harboring a UC risk missense variant in the Otud3 gene showed pathological features of UC in the colon after transplantation of a fecal microbiota with the potential to produce excessive cGAMP from patients with UC. Collectively, these results highlight a mechanism of the interaction between OTUD3 in host fibroblasts and STING-activating microbiota in UC development.},
}
@article {pmid40679638,
year = {2025},
author = {Fulke, AB and Sharma, N and Nadekar, J},
title = {Darkness to Discovery: A Comprehensive Mini-Review on Culturable and Non-Culturable Microbial Diversity from Deep Sea.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {77},
pmid = {40679638},
issn = {1432-184X},
support = {OLP2009//National Institute of Oceanography, India/ ; OLP2009//National Institute of Oceanography, India/ ; OLP2009//National Institute of Oceanography, India/ ; },
mesh = {*Seawater/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification/growth &amp; development ; *Microbiota ; *Biodiversity ; Metagenomics/methods ; Ecosystem ; Hydrothermal Vents/microbiology ; Oceans and Seas ; },
abstract = {Microorganisms are essential players in Earth's ecosystems, demonstrating remarkable adaptability to harsh conditions including arctic ice caps, deep-sea hydrothermal vents, and high-pressure oceanic zones. While the study of these extremophiles has long been constrained by challenges in culturing, recent advances in metagenomic techniques have enabled a deeper understanding of microbial diversity in these extreme habitats. This review explores both culturable and non-culturable microbial communities, focusing on the diverse strategies employed by microorganisms to thrive in harsh conditions, including high pressure, temperature, salinity, and nutrient limitations. Traditional cultivation methods often fail to capture the full spectrum of deep-sea microbiota due to the unique growth requirements of many organisms. In the omic era, however, microbial cultivation and the function of microbial resources are important. Non-culturable methods, like metagenomic studies and environmental DNA sequencing, have uncovered hitherto unknown microbial taxa and metabolic pathways, offering important new information on microbial ecology and biogeochemistry. The complex microbial interactions and adaptive methods that support these ecosystems are highlighted by case studies, including as studies on hydrothermal plumes and hadal deposits. The expanding significance of non-culturable techniques in microbial research is highlighted in this review, which also highlights how they might help us better understand microbial life in harsh conditions and how they may be used in biotechnology and environmental management.},
}
@article {pmid40678348,
year = {2025},
author = {Köhler, M and Castro Sánchez-Bermejo, P and Hähn, G and Ferlian, O and Eisenhauer, N and Wubet, T and Haider, S and Bruelheide, H},
title = {Foliar Endophytic Fungal Communities Are Driven by Leaf Traits-Evidence From a Temperate Tree Diversity Experiment.},
journal = {Ecology and evolution},
volume = {15},
number = {7},
pages = {e71691},
pmid = {40678348},
issn = {2045-7758},
abstract = {Fungal endophyte communities are mainly driven by host plant identity and geographic location. However, little is known about interactions between endophytes and characteristics of the host plant such as leaf functional traits, which vary both among and within host species. Previous studies focused on a limited number of host plant species and did not control for varying conditions in the host's neighborhood, which affect leaf functional traits and, in turn, might affect fungal endophyte communities. Using a tree diversity experiment in which all trees grow under standardized conditions, we were able to assess the contributions of host tree identity, host neighborhood species richness, and host community composition as well as the variation of leaf traits caused by these factors on taxonomic richness and community composition of foliar fungal endophytes. We used next-generation amplicon sequencing to analyze the fungal endophyte community and visible-near infrared spectrometry data to predict the mean values and the intra-individual variation of leaf traits in individual trees. We found both mean trait values and intra-individual trait variation to have significant effects on endophyte richness. Mean trait values of leaf dry matter content, leaf carbon, leaf nitrogen, and leaf carbon-to-nitrogen ratio exhibited negative effects on endophyte richness, whereas specific leaf area and leaf phosphorus content increased endophyte richness. Additionally, intra-individual leaf-trait variation generally had positive effects on richness. Overall endophyte community composition was influenced by mean leaf dry matter content and specific leaf area. Ascomycota were influenced by the specific leaf area, whereas Basidiomycota responded to leaf dry matter content. We demonstrate that functional leaf traits affect foliar endophyte communities, with positive diversity effects of host leaf nutrients that are essential, and likely limiting, for fungal endophytes. Although our study emphasizes the role of leaf traits in shaping fungal communities, we also acknowledge that these dynamic interactions could lead to traits being influenced by microbes through microbe-plant interactions.},
}
@article {pmid40677913,
year = {2025},
author = {Piro, VC and Reinert, K},
title = {ganon2: up-to-date and scalable metagenomics analysis.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {3},
pages = {lqaf094},
pmid = {40677913},
issn = {2631-9268},
mesh = {*Metagenomics/methods ; *Software ; Humans ; Microbiota/genetics ; Algorithms ; },
abstract = {The fast growth of public genomic sequence repositories greatly contributes to the success of metagenomics. However, they are growing at a faster pace than the computational resources to use them. This challenges current methods, which struggle to take full advantage of massive and fast data generation. We propose a generational leap in performance and usability with ganon2, a sequence classification method that performs taxonomic binning and profiling for metagenomics analysis. It indexes large datasets with a small memory footprint, maintaining fast, sensitive, and precise classification results. Based on the full NCBI RefSeq and its subsets, ganon2 indices are on average 50% smaller than state-of-the-art methods. Using 16 simulated samples from various studies, including the CAMI 1+2 challenge, ganon2 achieved up to 0.15 higher median F1-score in taxonomic binning. In profiling, improvements in the F1-score median are up to 0.35, keeping a balanced L1-norm error in the abundance estimation. ganon2 is one of the fastest tools evaluated and enables the use of larger, more diverse, and up-to-date reference sets in daily microbiome analysis, improving the resolution of results. The code is open-source and available with documentation at https://github.com/pirovc/ganon.},
}
@article {pmid40676575,
year = {2025},
author = {Wei, F and Wu, Z and Li, G and Sun, X and Shi, X and Tan, L and Ai, T and Qu, L and Zheng, S},
title = {Ensemble learning for microbiome-based caries diagnosis: multi-group modeling and biological interpretation from salivary and plaque metagenomic data.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {1188},
pmid = {40676575},
issn = {1472-6831},
mesh = {Humans ; *Dental Caries/diagnosis/microbiology ; *Dental Plaque/microbiology ; *Saliva/microbiology ; *Microbiota/genetics ; *Machine Learning ; Child ; *Metagenomics ; Child, Preschool ; Female ; Male ; RNA, Ribosomal, 16S ; Neural Networks, Computer ; Ensemble Learning ; },
abstract = {BACKGROUND: Oral microbiota is a major etiological factor in the development of dental caries. Next-generation sequencing techniques have been widely used, generating vast amounts of data which is underexplored. The advancement of artificial intelligence (AI) technologies has made it possible to mine information from these large datasets. This study aimed to develop AI-driven diagnostic models and identify key microbial features for caries.<br><br>METHODS: We collected raw metagenomic and full-length 16&#xa0;S rRNA gene sequencing data from previous studies on saliva and plaque to construct a caries AI training dataset comprising nearly 600 samples. Samples were grouped based on age, sequencing and sampling method. Through systematic comparison of seven machine learning architectures, including Logistic Regression, Random Forest, Support Vector Machines, Gradient Boosting, Convolutional Neural Networks, Feedforward Neural Networks, and Transformer models, we developed subgroup-specific caries diagnostic models, with subsequent ensemble learning integration to enhance generalizability.<br><br>RESULTS: The caries diagnostic model achieved a maximum AUC value of 1 (accuracy of 100%) for children under 6 years old in both saliva and plaque groups. The consistency of top features (species and metabolic pathways) contributing to the models was demonstrated through intra- and inter-group analyses. Key caries-associated species included Streptococcus salivarius, Streptococcus parasanguinis and Veillonella dispar. Veillonella parvula exhibits higher abundance in caries plaque samples, while being elevated in healthy saliva samples. Metabolic pathways like geranylgeranyl diphosphate and fructan biosynthesis were enriched in caries, whereas Bifidobacterium shunt and peptidoglycan biosynthesis were depleted.<br><br>CONCLUSION: The current work provided reliable diagnostic models for early childhood caries, and established a robust computational framework for AI-driven microbiome analysis. This study, by focusing on the characteristics of the oral microbiome, offers novel perspectives for data mining and validation of existing data through the application of AI modelling.},
}
@article {pmid40674970,
year = {2025},
author = {Göçer, S and Arı, O and Göçer, C and Durmaz, R},
title = {Metagenomic analysis of the middle ear microbiome: A next-generation sequencing approach in pediatric patients with and without effusion.},
journal = {International journal of pediatric otorhinolaryngology},
volume = {196},
number = {},
pages = {112487},
doi = {10.1016/j.ijporl.2025.112487},
pmid = {40674970},
issn = {1872-8464},
mesh = {Humans ; Male ; Female ; Child ; Child, Preschool ; *Microbiota/genetics ; *Ear, Middle/microbiology ; *Metagenomics/methods ; *Otitis Media with Effusion/microbiology ; *High-Throughput Nucleotide Sequencing ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; },
abstract = {OBJECTIVES: Otitis media with effusion (OME) is one of the most common causes of reversible hearing loss in childhood. In recent years, host-microbiota interactions and alterations in microbiota composition associated with health and disease have gained increasing attention in the context of OME. This study aimed to investigate the bacterial microbiota composition of middle ear cavity (MEC) samples obtained from pediatric patients with and without OME. Microbiome differences were analyzed according to clinical groups and variables such as age and gender.<br><br>METHODS: 16S rRNA-based metagenomic sequencing was performed on MEC samples (n&#xa0;=&#xa0;80) and nasopharyngeal samples (n&#xa0;=&#xa0;20) obtained from 80 children-40 diagnosed with bilateral or unilateral OME (OME group) and 40 undergoing cochlear implant surgery without any history of otitis media (control group). The study cohort included 37 males and 43 females, aged between 2 and 11 years (mean age: 5.2 years).<br><br>RESULTS: Sequencing analysis revealed that the phyla Firmicutes and Proteobacteria were dominant in MEC samples. In the OME group, Firmicutes were significantly more abundant, whereas Proteobacteria levels were reduced. At the genus level, Alloiococcus was significantly enriched in the OME group, while genera considered potentially protective, such as Lactobacillus and Propionibacterium, were significantly decreased. Age was not significantly associated with microbial richness or evenness, suggesting stability of microbiota composition across age groups. However, a significantly higher relative abundance of Ralstonia was observed in female patients, suggesting that gender-related hormonal or immunological differences may influence the middle ear microbiota.<br><br>CONCLUSION: This study identifies a distinct microbiota profile associated with OME and suggests that host factors, particularly gender, may contribute to shaping the microbial and immunological landscape of the middle ear. These findings also indicate that the microbial environment in OME may shift toward a low-diversity, pathobiont-dominant state.},
}
@article {pmid40674393,
year = {2025},
author = {Mubaraki, FA},
title = {Extensive novel diversity and phenotypic associations in the dromedary camel microbiome are revealed through deep metagenomics and machine learning.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0328194},
pmid = {40674393},
issn = {1932-6203},
mesh = {*Camelus/microbiology ; Animals ; *Metagenomics/methods ; *Machine Learning ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Phenotype ; *Microbiota ; },
abstract = {The dromedary camel, also known as one-humped camel or Arabian camel, is iconic and economically important to Arabian society. Its contemporary importance in commerce and transportation, along with the historical and modern use of its milk and meat products for dietary health and wellness, make it an ideal subject for scientific scrutiny. The gut microbiome has recently been associated with numerous aspects of health, diet, lifestyle, and disease in livestock and humans alike, as well as serving as an exploratory and diagnostic marker of many physical characteristics. Our initial pilot analysis of 55 camel gut microbiomes from the Fathi Camel Microbiome Project uses deep metagenomic shotgun sequencing to reveal substantial novel species-level microbial diversity, for which we have generated an extensive catalog of prokaryotic metagenome-assembled microorganisms (MAGs) as a foundational microbial reference database for future comparative analysis. Exploratory correlation analysis shows substantial correlation structure among the collected subject-level metadata, including physical characteristics. Machine learning using these novel microbial markers, as well as statistical testing, demonstrates strong predictive performance of microbial taxa to distinguish between multiple dietary and lifestyle characteristics of dromedary camels. We present strongly predictive machine learning models for camel age, diet (especially wheat intake), and level of captivity. These findings and resources represent substantial strides toward understanding the camel microbiome and pave the way for a deeper understanding of the nuanced factors that shape camel health.},
}
@article {pmid40674041,
year = {2025},
author = {Bisson, G and Comuzzi, C and FitzGerald, JA and Mukherjee, A and Renoldi, N and Innocente, N and Beresford, T and Mathur, H and Cotter, PD and Marino, M},
title = {Development of a bio-functional fermented soy beverage supplemented with microbial exopolysaccharides and its effect on the human gut microbiome in vitro.},
journal = {Food &amp; function},
volume = {16},
number = {15},
pages = {6203-6212},
doi = {10.1039/d5fo01288k},
pmid = {40674041},
issn = {2042-650X},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Fermentation ; Feces/microbiology ; *Polysaccharides, Bacterial/metabolism/pharmacology ; Prebiotics ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Glycine max/metabolism ; *Soy Foods/microbiology/analysis ; Male ; Fermented Foods/microbiology ; Leuconostoc mesenteroides/metabolism ; Adult ; },
abstract = {The gut microbiome plays a key role in modulating human health and well-being. Exopolysaccharides (EPS) produced by lactic acid bacteria (LAB) are emerging as novel polymers that could exert a prebiotic effect via modification of this microbiome. Thus, incorporation of EPS to enhance food functionality is of interest. This study investigates the impact of a fermented soy beverage, supplemented with EPS produced by Leuconostoc mesenteroides DSA_O or DSA_F, on the faecal microbiota as assessed using an ex vivo model of the human distal colon. The soy beverage (SM) was prepared by fermentation with Lactiplantibacillus paraplantarum GB3 followed by supplementation with EPS_O (SMO) or EPS_F (SMF). Faecal samples from healthy donors were inoculated into a faecal fermentation medium with SM, SMO and SMF and incubated anaerobically at 37 °C for 24 h. After incubation, samples were subjected to shotgun metagenomic and short-chain fatty acid (SCFA) analysis. SMO and SMF were more effective than SM at enhancing the alpha diversity of the faecal microbiota after 24 h incubation. In addition, SMO promoted the growth of the health-associated species Bifidobacterium longum and Faecalibacterium prausnitzii, the latter of which is considered a next-generation probiotic. Butyrate and propionate levels were higher in faecal samples fermented with SMO and SMF than in SM. Taken together, these preliminary results indicate a potential role of EPS produced by Leuc. mesenteroides to be used as a functional food ingredient, modulating the gut microbiome as well as increasing the levels of SCFAs.},
}
@article {pmid40671669,
year = {2025},
author = {Sánchez-Terrón, G and Martínez, R and Morcuende, D and Estévez, M},
title = {Deciphering the Physiological Responses to the Intake of Plant-Based Meat Analogues: On the Track of Microbiota and Biomarkers in Serum and Urine.},
journal = {Journal of agricultural and food chemistry},
volume = {73},
number = {36},
pages = {22698-22713},
pmid = {40671669},
issn = {1520-5118},
mesh = {Animals ; Rats, Wistar ; Rats ; *Gastrointestinal Microbiome ; Male ; *Biomarkers/urine/blood ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Triticum/metabolism ; *Meat/analysis ; Cattle ; Humans ; Urine/chemistry ; Glycine max/metabolism ; },
abstract = {Growing concerns about the alleged negative outcomes of the consumption of animal-based foods (ABF) lead a number of consumers to demand so-called plant-based meat analogues (PBMAs), which are designed to replicate the sensory and nutritional characteristics of genuine meat. This study aimed to characterize the physiological effects of long-term PBMA consumption by comparing their specific influence on both gut microbiota and fluids (i.e., plasma and urine) with those of conventional beef in a rodent model by using metagenomic and metabolomic tools. Twenty-one Wistar rats were divided into groups and consumed diets made with either wheat- and soy-based meat analogues or beef. The microbiota of PBMA-fed animals showed increased amounts of the harmful genus of gut bacteria, while their metabolomes reflected disturbances in the nitrogen-containing compound metabolism and the presence of potentially harmful metabolites. These results should raise concern and prompt further research into the long-term impact of consumption of PBMAs on health.},
}
@article {pmid40671648,
year = {2025},
author = {Maiello, G and Lippert, MR and Neave, EF and Hanson, EA and Palumbi, SR and Mariani, S},
title = {Multi-Tool Marine Metabarcoding Bioassessment for Baselining and Monitoring Species and Communities in Kelp Habitats.},
journal = {Molecular ecology resources},
volume = {25},
number = {7},
pages = {e70010},
pmid = {40671648},
issn = {1755-0998},
support = {//The Pew Charitable Trusts under the Lenfest Ocean Program/ ; //The Gordon and Betty Moore Foundation/ ; //Oceankind Labs/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Kelp ; Ecosystem ; California ; Animals ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Biota ; },
abstract = {The astonishing biological diversity found in Californian kelp forests requires efficient and robust monitoring tools to better understand ecological trends and mitigate against loss or disruption of ecosystem services due to human pressure and climate changes. With environmental DNA (eDNA) metabarcoding becoming a popular biodiversity assessment approach, we set out to evaluate a combination of powerful, rapid and sustainable eDNA solutions for characterising marine community composition in kelp-dominated habitats along the central California coast, in the newly proposed Chumash Heritage National Marine Sanctuary. We employed and compared the efficiency of several eDNA collection approaches, including 'traditional' surface water filtration, the collection of organisms encrusting cobble rocks and various deployments of an artificial passive sampler, the metaprobe (i.e., attached to divers, dangled from a boat and cast from the shore using a fishing rod). By combining the information from fish specific (Tele02 12S) and universal metazoan (COI) markers, we 'captured' 501 unique marine taxa, belonging to at least 36 phyla, over 400 of which were identified to genus/species level, and including 52 vertebrate species typical of Californian kelp forest ecosystems. Despite differences in the type of biodiversity returned by the tested sampling methods, the overall community structure of the surveyed area was highly spatially structured and strongly influenced by the biogeographic break around Point Conception (Humqaq). We discuss the benefits of integrating eDNA metabarcoding in existing monitoring programs and devising a reproducible approach to monitor faunal changes in kelp forest habitats and beyond.},
}
@article {pmid40671255,
year = {2025},
author = {Bartsch, S and Kreutz, C and Scholz, KJ and Kohnert, E and Hertel, J and Wolf, M and Jakubovics, N and Al-Ahmad, A and Cieplik, F},
title = {Culturomics: Deciphering the Microbial Dark Matter in the Oral Cavity.},
journal = {Journal of dental research},
volume = {104},
number = {11},
pages = {1171-1180},
doi = {10.1177/00220345251346781},
pmid = {40671255},
issn = {1544-0591},
mesh = {*Mouth/microbiology ; Humans ; *Microbiota ; *Bacteria/classification/isolation &amp; purification/genetics ; Archaea/isolation &amp; purification/classification/genetics ; },
abstract = {The idea of the tree of life originated in the 19th century and has steadily evolved since then. In the last 20 y, high-throughput sequencing methods have revolutionized microbial ecology and expanded our understanding of this tree of life tremendously. However, this has led to a sharp increase in what is known as microbial dark matter, consisting of bacterial and archaeal taxa that are only known by sequencing and have not yet been cultivated. The lack of ecologic information about these species poses a major challenge. This has led to the need for other approaches to supplement the DNA sequence-based findings. The term "culturomics"-which describes the large-scale isolation, culture, and identification of species from an environment-was introduced in 2012 with a focus on the human gut microbiota. The cultivation of new species, which had been neglected for many years, is now firmly back in the spotlight since strains are required for experimental studies to complement the knowledge obtained from microbial DNA sequences. Laboratory culture is essential to gain knowledge of microbial physiology, assign functions to novel genes and proteins, identify resistance profiles, and better understand the impact of different microorganisms on human health. While many culturomics studies have focused on gut microbiota, significant progress has been made in oral microbiology, with the enrichment of Candidatus Nanosynbacter lyticus representing one of the greatest achievements. This review gives a comprehensive overview of the oral microbial community regarding the microbial dark matter and summarizes the work carried out to date on the oral microbiota using culturomics. The capability and challenges of metagenomics and culturomics and the potential use of artificial intelligence are examined, with insights from extensive culturomics research on gut microbiota, which promises applicability to the field of oral microbiology.},
}
@article {pmid40671160,
year = {2025},
author = {Wang, S and Kong, F and Zhang, X and Dai, D and Li, C and Cao, Z and Wang, Y and Wang, W and Li, S},
title = {Disruption of hindgut microbiome homeostasis promotes postpartum energy metabolism disorders in dairy ruminants by inhibiting acetate-mediated hepatic AMPK-PPARA axis.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {167},
pmid = {40671160},
issn = {2049-2618},
support = {32130100//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/physiology ; Cattle ; *Energy Metabolism ; *AMP-Activated Protein Kinases/metabolism ; *Liver/metabolism ; Homeostasis ; *Postpartum Period/metabolism ; *PPAR alpha/metabolism/genetics ; *Acetates/metabolism ; 3-Hydroxybutyric Acid/blood ; Ruminants/microbiology ; },
abstract = {BACKGROUND: Postpartum energy metabolism disorders pose a significant challenge to the health and productivity of dairy ruminants, yet their underlying pathogenesis remains poorly understood. The critical role of the gut microbiota in regulating host metabolic processes via the "gut-liver axis" has garnered increasing attention, but its specific mechanisms in dairy ruminant energy metabolism disorders are still unclear. This study uses dairy cows as a model and employs a large-scale case-control analysis to systematically investigate the pathophysiological basis of postpartum energy metabolism disorders through the lens of the "gut-liver axis."<br><br>RESULTS: Postpartum energy metabolism disorders in dairy cows are characterized by elevated blood &#x3b2;-hydroxybutyrate (BHB) and aspartate aminotransferase (AST) levels, and hepatic steatosis. A random forest model based on gut microbiota effectively predicts disease occurrence (AUC&#x2009;=&#x2009;0.74). Multi-omics (metagenomics, metabolomics, and transcriptomics) analysis further identified key microbes, including Faecousia species (sp017465625 and sp017380435), Methanosphaera species (sp016282985), and Bifidobacterium globosum. These microbes regulate acetate concentration in the gut, which is significantly correlated with key genes in the hepatic PPAR and PI3K-AKT pathways, as well as with blood BHB levels. Primary hepatocyte culture experiments further confirmed that sodium acetate effectively inhibits hepatic fat deposition induced by mixed fatty acids through the hepatic AMPK-PPARA axis and reduces the production of BHB in the culture medium.<br><br>CONCLUSION: This study demonstrates that key gut microbes and their metabolic product (acetate) inhibit the occurrence of metabolic disorders through the hepatic AMPK-PPARA axis. These findings provide new insights and potential therapeutic targets for understanding and mitigating postpartum metabolic disorders in dairy&#xa0;ruminants. Video Abstract.},
}
@article {pmid40670379,
year = {2025},
author = {Shi, W and Lv, M and Wang, R and Saleem, M and Wang, L and Li, M and Wang, B and Lin, R and Xu, B and Yang, C and Ning, T and Zhou, B and Gao, Z},
title = {Geocaulosphere soil bacterial community drives potato common scab outcomes beyond pathogen abundance.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {134},
pmid = {40670379},
issn = {2055-5008},
support = {2024M751875//China Postdoctoral Science Foundation/ ; 42407427//National Natural Science Foundation of China/ ; 42377309//National Natural Science Foundation of China/ ; 2023YFD20014003//Shandong Provincial "811" Project of First-class Discipline Construction, the National Key R&amp;D Program of China/ ; 2023BCF01015//Key R&amp;D Program of Ningxia Hui Autonomous Region of China/ ; M2023-07//State Key Natural Science Foundations of China Laboratory of Microbial Technology Open Projects Fund/ ; SDAIT-16-01//Potato Innovation Program for the Chief Expert of Shandong Province/ ; 2021CXGC010804//Shandong Province Key R&amp;D Program/ ; },
mesh = {*Solanum tuberosum/microbiology ; *Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; Metagenomics ; Soil/chemistry ; },
abstract = {The assembly mechanisms of soil microbiome during plant disease progression remain incomplete. This study linked potato common scab (PCS) severity to destabilized soil microbiome dynamics in potato geocausphere soil (GS) through integrated metagenomic analysis and culture-based experiments. Across four Shandong fields, PCS-infected GS exhibited an 11.66% reduction in bacterial α-diversity (Shannon index) and elevated stochastic community assembly. Bacterial community structure explained 39.28% (GS) and 15.96% (bulk soil) of PCS variance, outperforming pathogen abundance contributions (14.39% GS, 7.33% BS). Two microbial interaction patterns emerged in GS: 1) synchronized shifts between pathogens and beneficial taxa as PCS intensified; 2) stochastic assembly governing entire communities but deterministic processes dominating specialized subgroups. These results propose a microbial stability framework connecting soil microbiome structural rules to plant disease progression, emphasizing community-level dynamics over pathogen-centric explanations.},
}
@article {pmid40670173,
year = {2025},
author = {Ai, S and Gao, D and Zhai, Z and Wang, S and Xue, Y and Liu, Z and Yan, X},
title = {[Effect mechanism of electroacupuncture on diabetic peripheral neuropathy in rats based on gut microbiota and metabolomics].},
journal = {Zhongguo zhen jiu = Chinese acupuncture &amp; moxibustion},
volume = {45},
number = {7},
pages = {945-956},
doi = {10.13703/j.0255-2930.20250225-k0005},
pmid = {40670173},
issn = {0255-2930},
mesh = {Animals ; *Electroacupuncture ; Male ; *Gastrointestinal Microbiome ; *Diabetic Neuropathies/therapy/metabolism/microbiology ; Rats, Sprague-Dawley ; Rats ; Metabolomics ; Humans ; Acupuncture Points ; },
abstract = {OBJECTIVE: To explore the effect mechanism of electroacupuncture (EA) for ameliorating diabetic peripheral neuropathy (DPN) based on the analysis of gut microbiota and metabolomics.<br><br>METHODS: Thirty SPF-grade male SD rats were randomly divided into a normal group, a model group, and an EA group, with 10 rats in each one. Except in the normal group, the intraperitoneally injection with streptozotocin was used to induce diabetes mellitus model in the rest groups. In the EA group, acupuncture was delivered at bilateral "Zusanli" (ST36), "Sanyinjiao" (SP6), "Pishu" (BL20) and "Shenshu" (BL23), and electric stimulation was attached to "Zusanli" (ST36)-"Sanyinjiao" (SP6) and "Pishu" (BL20)-"Shenshu" (BL23), on the same side, with continuous wave and a frequency of 2 Hz, for 10 min in each intervention. The intervention measure of each group was delivered once every 2 days, 3 times a week, for 8 consecutive weeks. Body weight, random blood glucose (RBG), thermal withdrawal latency (TWL), and mechanical withdrawal threshold (MWT) before intervention, and in 4 and 8 weeks of intervention, separately, as well as sensory nerve conduction velocity (SCV) and motor nerve conduction velocity (MCV) of the sciatic nerve after intervention were measured. Metagenomic sequencing (MS) was used to analyze gut microbiota and screen for differential species. Liquid chromatography-mass spectrometry (LC-MS) was employed to detect the differential metabolites in plasma, and the metabolic pathway enrichment analysis was performed on the differential metabolites. Spearman correlation analysis was adopted to assess the relationship between gut microbiota and metabolomics.<br><br>RESULTS: After 4 and 8 weeks of intervention, when compared with the model group, the EA group showed the increase in body weight, TWL, MWT (P<0.01), and the decrease in RBG (P<0.01). Compared with the normal group, SCV and MCV, as well as Chao1 index were dropped in the model group (P<0.01), and those were elevated in the EA group when compared with those in the model group (P<0.01). The dominant bacterial phyla of each group were Firmicutes (F) and Bacteroidota (B), the ratio of them (F/B) in the model group was lower than that of the normal group (P<0.05), and F/B in the EA group was higher when compared with that in the model group (P<0.05). In comparison with the normal group, the relative abundance increased in Prevotella, Segatella, Prevotella-hominis and Segatella-copri (P<0.05); and it decreased in Ligilactobacillus, Eubacterium, Pseudoflavonifractor, Ligilactobacillus-murinus (P<0.05) in the model group. Compared with the model group, the relevant abundance of the above mentioned gut bacteria was all ameliorated in the EA group (P<0.05, P<0.01). Among the three groups, 120 differential metabolites were identified and enriched in 28 key metabolic pathways, such as glycerophospholipid and linoleic acid, of which, glycerophospholipid was the most significantly affected pathway in EA intervention. Spearman correlation analysis showed that 6 phosphatidylcholine metabolites were significantly positively correlated with Pseudoflavonifractor and were negatively with Prevotella, Segatella, Prevotella-hominis, Segatella-copri; 5 phosphatidylethanolamine metabolites were significantly negatively correlated with Pseudoflavonifractor and positively correlated with Prevotella, Segatella, Prevotella-hominis, Segatella-copri.<br><br>CONCLUSION: EA may regulate metabolic pathways such as glycerophospholipid, modulate specific gut microbiota such as Pseudoflavonifractor, Prevotella, and Segatella, and the co-expressed differential metabolites like phosphatidylcholine and phosphatidylethanolamine, thereby reducing blood glucose and protecting nerve function, so as to relieve the symptoms of DPN of rats.},
}
@article {pmid40669611,
year = {2025},
author = {Song, S and Li, F and Zhao, B and Xu, Y and Liu, Z and Liu, J and Hou, Q and Chen, J and Chen, M and Liu, Z and Zhou, M and Wu, X and Wang, X},
title = {Sparfloxacin ameliorates DSS-induced ulcerative colitis by suppressing cellular senescence, JAK/NF-κB signaling pathway and modulation of the gut microbiota-metabolite axis.},
journal = {Biochemical pharmacology},
volume = {241},
number = {},
pages = {117167},
doi = {10.1016/j.bcp.2025.117167},
pmid = {40669611},
issn = {1873-2968},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/physiology ; Mice ; *NF-kappa B/metabolism/antagonists &amp; inhibitors ; *Cellular Senescence/drug effects/physiology ; *Fluoroquinolones/pharmacology/therapeutic use ; Signal Transduction/drug effects/physiology ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism ; Mice, Inbred C57BL ; *Dextran Sulfate/toxicity ; Male ; Humans ; },
abstract = {The progression of ulcerative colitis (UC) involves immune dysregulation, intestinal barrier dysfunction, and microbial dysbiosis while existing targeted therapies present challenges, including adverse effects and economic burdens. UC is characterized by persistent intestinal inflammation, manifesting as abdominal pain, hematochezia, and malnutrition. Prolonged uncontrolled inflammation may lead to colorectal cancer or severe complications, significantly impairing quality of life. Recent studies have revealed a significant correlation between pathological accumulation of senescent cells and UC pathogenesis, suggesting anti-senescence therapeutics as potential interventions. In this study, we identified sparfloxacin (SPA), a fluoroquinolone antibiotic, through high-throughput screening as an effective senolytic agent that markedly alleviates DSS-induced murine colitis. Mechanistically, combining cellular and animal experiments with transcriptomic, untargeted metabolomic, and metagenomic analyses, we demonstrated sparfloxacin's tripartite therapeutic effects: ① Senescence inhibition via downregulation of p16/p21 expression; ② Effective suppression of aberrant JAK/NF-κB signaling activation with a concomitant reduction in pro-inflammatory cytokines (TNF-α, IL-6); ③ Gut microbiota remodeling characterized by increased probiotic abundance and elevated levels of beneficial metabolites. This study for the first time elucidates the molecular mechanism whereby SPA ameliorates UC through coordinated multi-target actions involving senescence inhibition, anti-inflammatory effects, and microbiome restoration. Our findings not only expand the clinical applications of fluoroquinolones but also provide a theoretical foundation for developing integrated UC treatment strategies targeting cellular senescence.},
}
@article {pmid40669466,
year = {2025},
author = {Ghiotto, G and Xirostylidou, A and Gaspari, M and Kougias, PG and Campanaro, S and Treu, L},
title = {Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.},
journal = {Cell genomics},
volume = {5},
number = {9},
pages = {100949},
pmid = {40669466},
issn = {2666-979X},
mesh = {*Metagenomics/methods ; Anaerobiosis ; *Ecosystem ; *Adaptation, Physiological/genetics ; *Microbiota/genetics ; *Methanobacteriaceae/genetics/metabolism ; Methane/metabolism ; Carbon Dioxide/metabolism ; Mutation ; },
abstract = {Genetic heterogeneity exists within all microbial populations, with sympatric cells of the same species often exhibiting single-nucleotide variations that influence phenotypic traits, including metabolic efficiency. However, the evolutionary dynamics of these strain-level differences in response to environmental stress remain poorly understood. Here, we present a first-of-its-kind study tracking the adaptive evolution of an anaerobic, carbon-fixing microbiota under a controlled engineered ecosystem focused on carbon dioxide bioconversion into methane. Leveraging strain-resolved metagenomics with an ad hoc variant calling and phasing approach, we mapped mutation trajectories and observed that the two dominant Methanothermobacter species maintained distinct sweeping haplotypes over time, most likely due to niche-specific metabolic roles. By combining population genetic statistics and peptide reconstruction, mer and mcrB genes emerged as potential drivers of archaeal strain-level competition. These findings pave the way for targeted engineering of microbial communities to enhance bioconversion efficiency, with significant implications for sustainable energy and carbon management in anaerobic systems.},
}
@article {pmid40669445,
year = {2025},
author = {Omary, L and Canfora, EE and Puhlmann, ML and Gavriilidou, A and Rijnaarts, I and Holst, JJ and Op den Kamp-Bruls, YMH and de Vos, WM and Blaak, EE},
title = {Intrinsic chicory root fibers modulate colonic microbial butyrate-producing pathways and improve insulin sensitivity in individuals with obesity.},
journal = {Cell reports. Medicine},
volume = {6},
number = {7},
pages = {102237},
pmid = {40669445},
issn = {2666-3791},
mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Butyrates/metabolism ; *Cichorium intybus/chemistry ; *Colon/microbiology/metabolism ; Diabetes Mellitus, Type 2 ; *Dietary Fiber ; *Gastrointestinal Microbiome/drug effects ; *Insulin Resistance ; *Obesity/microbiology/metabolism/diet therapy ; Plant Roots/chemistry/metabolism ; Triglycerides/blood ; },
abstract = {Type 2 diabetes and obesity have become major public health concerns. Growing evidence suggests that increased dietary fiber intake, through its interaction with the gut microbiota, may help prevent these diseases. Here, we demonstrate in a 12-week randomized, placebo-controlled trial in individuals at risk for type 2 diabetes that intake of an intrinsic fiber product, consisting of entire plant cells, tended to improve peripheral insulin sensitivity (p = 0.085), increased whole-body insulin sensitivity (p = 0.032), reduced circulating triglycerides (p = 0.049), and tended to reduce intrahepatic lipid content (p = 0.063), along with an increased proportion of small adipocytes (p = 0.008). Phylogenetic and metagenomic analysis revealed that these outcomes coincided with increased levels of fiber-degrading Bifidobacterium spp. and butyrate-producing Anaerostipes spp. and a functional shift toward a distal butyrogenic trophic chain while the best responding individuals had increased levels of pectin degraders that may produce propionate. Our findings demonstrate the pivotal role of slowly fermented, intrinsic plant cell fibers in improving cardiometabolic health. This study was registered at ClinicalTrials.gov (NCT04714944).},
}
@article {pmid40669246,
year = {2025},
author = {Liu, S and Chen, Q and Dong, C and Qiu, X and Li, W and Tang, K},
title = {Impact of coastal deoxygenation on antibiotic resistance gene profiles in size-fractionated bacterial communities.},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118445},
doi = {10.1016/j.marpolbul.2025.118445},
pmid = {40669246},
issn = {1879-3363},
mesh = {*Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; China ; *Oxygen ; Anti-Bacterial Agents ; Seawater/chemistry/microbiology ; Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Oxygen loss disrupts marine ecosystems, threatening biodiversity and causing mass mortality of marine life. Antibiotic resistance genes (ARGs) pose a significant threat to human health by promoting the spread of resistant pathogens, making infections harder to treat and increasing mortality risks. However, the interplay between deoxygenation and ARG dynamics remains poorly understood. In this study, we employed time-series metagenomics to investigate the responses of ARG profiles in free-living (FL) and particle-associated (PA) fraction to oxygen loss during a 22-day summer deoxygenation event in the East China Sea. In total, we identified 1,186 ARG subtypes and 2,279 mobile genetic element (MGE) subtypes. The most dominant resistance classes of antibiotics were multidrug (23.5%), followed by tetracycline (15%), macrolide-lincosamide-streptogramin (13.4%), peptide (10.3%), glycopeptide (8.7%), aminoglycoside (7.3%), and beta-lactam (4.9%). We found that ARG richness in FL fraction increased with declining oxygen levels, particularly for beta-lactam and multidrug class, while no significant relationship was observed in the PA fraction. Although the total relative abundance of ARGs in both fraction showed no significant oxygen dependence, beta-lactam and multidrug resistance genes in FL fraction significantly increased with oxygen loss. Co-occurrence network analysis revealed stronger positive associations between ARGs and MGEs in the FL fraction, suggesting enhanced gene transfer among environmental bacteria. Furthermore, neutral community model analysis indicated that stochastic processes also played an interactive role in shaping ARG composition dynamics in both bacterial fractions. Our findings provide evidence that coastal deoxygenation preferentially enriches high-risk ARGs (e.g., beta-lactamase genes) in FL bacteria through MGE-mediated transfer, highlighting escalating antibiotic resistance risks that threaten both ecosystem and human health under climate warming. This study offers a framework for size-fractionated ARG monitoring and targeted mitigation strategies in coastal ecosystems.},
}
@article {pmid40668000,
year = {2025},
author = {Jiang, D and Hurst, JH and Mohamed, G and Kelly, MS and Roper, J and Surana, NK},
title = {Decreased Microbiota-Driven Tyrosine Metabolism Is Associated With Symptomatic COVID-19 in Children.},
journal = {The Journal of infectious diseases},
volume = {232},
number = {4},
pages = {796-805},
doi = {10.1093/infdis/jiaf325},
pmid = {40668000},
issn = {1537-6613},
mesh = {Humans ; *COVID-19/microbiology/metabolism ; *Tyrosine/metabolism ; *Gastrointestinal Microbiome/physiology ; Child ; Male ; Female ; Child, Preschool ; SARS-CoV-2 ; Feces/microbiology ; Prospective Studies ; Adolescent ; Cytokines/blood ; Infant ; },
abstract = {BACKGROUND: The gut microbiota has been implicated in driving coronavirus disease 2019 (COVID-19) disease severity, but the underlying mechanisms remain unknown. We investigated the relationship between the gut microbiota and development of symptomatic COVID-19 in children.<br><br>METHODS: We prospectively collected stool and plasma samples from 229 children who were exposed to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), including 45 COVID-19 negative, 57 with asymptomatic COVID-19, and 127 with symptomatic COVID-19. We performed shotgun metagenomic sequencing on the stool samples to characterize the microbial taxa and functional profiles. Plasma cytokine levels were measured in SARS-CoV-2-infected individuals.<br><br>RESULTS: Children with symptomatic COVID-19 had reduced microbial biodiversity and decreased functional capacity for several metabolic pathways, including a reduction in the tyrosine biosynthesis pathway, as compared to SARS-CoV-2-uninfected children or those with asymptomatic infection. The abundance of the tyrosine biosynthesis pathway was associated with plasma levels of interferon alpha (IFN-&#x3b1;), which were lower in children with symptomatic COVID-19.<br><br>CONCLUSIONS: Our findings highlight a relationship between the ability of the gut microbiota to metabolize tyrosine and the development of COVID-19 symptoms in children. More generally, our study suggests that the gut microbiota may help protect against more severe forms of COVID-19, potentially by modulating IFN-&#x3b1;.},
}
@article {pmid40667647,
year = {2025},
author = {Yan, C and Li, XN and Peng, ZL and Wu, W and Wang, Z and Zhu, ZR and Liu, JC and Wang, Y and Ren, JL and Zhang, ZY and Li, JT},
title = {Hologenomics Reveals Specialized Dietary Adaptations in the Mengla Snail-Eating Snake.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {12},
number = {40},
pages = {e09999},
pmid = {40667647},
issn = {2198-3844},
support = {2024NSFSC1181//Sichuan Science and Technology Program/ ; 2024YFHZ0294//Sichuan Science and Technology Program/ ; 32325011//National Natural Science Foundation of China/ ; 32220103004//National Natural Science Foundation of China/ ; 32370449//National Natural Science Foundation of China/ ; 32300351//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Adaptation, Physiological/genetics ; Snails ; Gastrointestinal Microbiome/genetics ; *Diet ; Genomics/methods ; *Snakes/genetics/physiology ; Biological Evolution ; },
abstract = {Serpents, as highly adaptable vertebrates, provide robust models for studying the mechanisms of dietary specialization. Using an integrative multi-omics approach, encompassing host genomic, transcriptomic, proteomic, gut metagenomic, and enzymatic analyses, the mechanisms underlying dietary adaptations in the Mengla snail-eating snake (Pareas menglaensis), a species specialized in consuming snails is investigated. Adaptations supporting this diet included evolution of infralabial glands secreting toxin homologs and digestive enzymes, facilitating molluscan predation and digestion. This specialization has driven adaptive evolution in the host genome and shaped the gut microbiota, addressing both nutritional challenges (e.g., lipid deficiency) and digestive requirements (e.g., mucus degradation) associated with snail consumption. Notably, the functional convergence in microbial gene functions between reptiles and mammals highlights parallel evolutionary pathways in dietary specialization. These findings elucidate the genomic foundations of dietary specialization in P. menglaensis, offering broader insights into evolutionary adaptation within a holobiome framework.},
}
@article {pmid40667420,
year = {2025},
author = {Orejudo, M and Gómez, MJ and Riestra, S and Rivero, M and Gutiérrez, A and Rodríguez-Lago, I and Fernández-Salazar, L and Ceballos, D and Benítez, JM and Aguas, M and Bastón-Rey, I and Bermejo, F and Casanova, MJ and Lorente-Poyatos, RH and Ber, Y and Ginard, D and Esteve, M and de Francisco, R and García, MJ and Francés, R and Rodríguez, A and Alcaide Suárez, N and Guerra Del Río, E and Soto, P and Nos, P and Barreiro-de Acosta, M and Guerra, I and Hervías Cruz, D and Domínguez Cajal, M and Royo, V and Aceituno, M and Aldars-García, L and Garre, A and Ramírez, C and Soleto, I and Schuppe-Koistinen, I and Engstrand, L and Baldán-Martín, M and Sánchez-Cabo, F and Gisbert, JP and Chaparro, M},
title = {Exploration of fecal microbiota in newly diagnosed patients with inflammatory bowel disease using shotgun metagenomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1595884},
pmid = {40667420},
issn = {2235-2988},
mesh = {Humans ; *Feces/microbiology ; *Metagenomics/methods ; Female ; Male ; Adult ; Middle Aged ; *Inflammatory Bowel Diseases/microbiology/diagnosis ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Crohn Disease/microbiology ; Colitis, Ulcerative/microbiology ; Young Adult ; Aged ; Computational Biology ; Bacteria/classification/genetics/isolation &amp; purification ; Biodiversity ; },
abstract = {INTRODUCTION: Dysbiosis is a key mechanism in inflammatory bowel disease (IBD) pathophysiology. Previous microbiota studies in IBD generally have involved patients treated with immunosuppressive agents, which can affect the results. We aimed to elucidate the fecal microbiota composition in newly diagnosed treatment-naïve IBD patients.<br><br>METHODS: Microbiota from stool samples were investigated using shotgun metagenomics sequencing and subsequent bioinformatics analysis.<br><br>RESULTS: A total of 103 patients with Crohn's disease (CD), 144 with ulcerative colitis (UC), and 49 healthy controls (HC) were included. CD patients had significantly lower species-level diversity than those with UC and HC. CD subgroups with Ileocolonic location and stricturing behavior showed reduced diversity compared to HC. A negative correlation was observed between endoscopic severity and microbial diversity in CD patients. UC patients had similar microbial d