@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 = {},
number = {},
pages = {127074},
doi = {10.1016/j.envpol.2025.127074},
pmid = {40914221},
issn = {1873-6424},
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 = {},
number = {},
pages = {102289},
doi = {10.1016/j.xcrm.2025.102289},
pmid = {40914165},
issn = {2666-3791},
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 = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.08.005},
pmid = {40914155},
issn = {1932-7420},
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 {pmid40914041,
year = {2025},
author = {Zhang, J and Li, W and Zhang, X and Wang, X and Guo, X and Bai, C and Lv, L},
title = {Higher chlorine dosage does not consistently enhance antibiotic resistance mitigation in the Cl2-UV process.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124534},
doi = {10.1016/j.watres.2025.124534},
pmid = {40914041},
issn = {1879-2448},
abstract = {Health problems arising from antibiotic resistance are a global concern. The Cl2-UV disinfection process has shown potential for controlling antibiotic resistance in water; however, the influence of disinfectant dosage on its effectiveness remains insufficiently understood. Can antibiotic resistance be controlled by simply increasing the disinfectant dosage? This study demonstrated that higher disinfectant levels improved antibiotic resistance gene (ARG) removal, with certain ARGs reaching 1.82 log removal under conventional conditions. Nevertheless, higher disinfectant dosages also led to an increase in the relative abundance of multidrug resistance genes (MRGs), aminoglycoside resistance genes (AmRGs), and fosmidomycin resistance genes (FRGs). Correlation analysis of ARGs with mobile genetic elements (MGEs) and ARG-host bacteria indicated that this enrichment was primarily driven by enhanced horizontal gene transfer (HGT). Notably, increases in UV fluence and chlorine dose had distinct impacts on the total relative abundance of ARGs: higher UV fluence reduced total relative abundance, whereas higher chlorine dose increased it. These contrasting trends are likely linked to differences in the dominant HGT pathways under each condition. Greater UV fluence tended to promote conjugative transfer among surviving bacteria, while higher chlorine dosages more effectively facilitated natural transformation. Considering both the absolute and relative abundances of ARGs, along with calculated health-risk indices for each treatment condition, the findings indicated that increasing UV fluence is more effective for controlling ARGs in water. These results provide valuable insights for optimizing the Cl2-UV disinfection process to better manage antibiotic resistance in aquatic environments.},
}

@article {pmid40914040,
year = {2025},
author = {Li, J and Wang, X and Zheng, J and Liu, Y and Zhang, D and Pan, X},
title = {Virulence-mediated colonization mechanism for TEP as a promising watershed-scale recorder and source-tracking indicator of human pathogens.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124537},
doi = {10.1016/j.watres.2025.124537},
pmid = {40914040},
issn = {1879-2448},
abstract = {Waterborne pathogens related diseases have been a global health concern. Precise source tracking of pathogens in rivers is crucial for understanding and reducing waterborne pathogens transmission risks. Current microbial source tracking techniques are still limited by identifying pathogen indicators at low concentrations, particularly in highly dynamic confluence zones of rivers where the coalescence of microbiomes exacerbates community disturbances. This study explored the potential of transparent exopolymeric particles (TEP) as effective carriers for pathogen source tracking, owing to their capacity to concentrate surrounding pathogenic bacteria as hitchhikers. The relative abundance of TEP-associated pathogenic bacteria (TAPs) was 1.61 times higher than that of overall pathogenic bacteria (OPs), which enhanced the detectability of pathogenic bacteria. Deterministic processes, particularly homogeneous selection, which accounts for 36 % of the variance, were found to govern the assembly of TAPs communities in contrast to OPs communities. In addition to nutrient and shelter functions of TEP, the selective enrichment of TAPs is mediated by virulence factors including adherence, motility, and biofilm-forming capacity, which are predominantly encoded within pathogenic bacteria. Furthermore, the relative stability of TAPs communities across watershed enabled them to record footprint of the hitchhiking pathogenic bacteria. Watershed-scale FEAST analysis confirmed superior capabilities of TAPs for source tracing than OPs, with fluctuations reduced by 0.11-32.02 %. This new MST technique based on TAPs can overcome some limitations with the traditional OPs-based methods and enables us to more precisely track pathogen sources and take evidence-based countermeasures to reduce pathogen transmission risk via rivers.},
}

@article {pmid40914035,
year = {2025},
author = {Ballén, V and Mondéjar, L and Gabasa, Y and Castellsagués, L and Alcalde-Rico, M and Pinar-Méndez, A and Vilaró, C and Galofré, B and Soto, SM},
title = {Integrated metagenomic, culture-based, and whole genome sequencing analyses of antimicrobial resistance in wastewater and drinking water treatment plants in Barcelona, Spain.},
journal = {International journal of hygiene and environmental health},
volume = {270},
number = {},
pages = {114664},
doi = {10.1016/j.ijheh.2025.114664},
pmid = {40914035},
issn = {1618-131X},
abstract = {The misuse and overuse of antimicrobials drive the emergence of antimicrobial resistance (AMR), a critical global health concern. While wastewater treatment plants (WWTPs) are essential for removing microorganisms and contaminants, they also serve as hotspots for antibiotic-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs), facilitating their persistence and dissemination. This study investigated AMR in two WWTPs and one drinking water treatment plant (DWTP) in the Baix Llobregat area of Barcelona, Spain. Four sampling campaigns were conducted during winter and summer 2023 across different treatment stages. Due to drought conditions, reclaimed water from the Baix Llobregat WWTP was discharged upstream of the DWTP intake to supplement water resources for indirect potable reuse. A total of 991 cultivable ARB were obtained, enabling phenotypic and genotypic characterisation. The most prevalent included Aeromonas spp. (44.3 %), Enterobacterales (27.9 %), Pseudomonas spp. (19.1 %), Acinetobacter spp. (4.8 %), Shewanella spp. (2.2 %), Stenotrophomonas spp. (1 %), and others (0.7 %). Among these, 57.3 % were multidrug-resistant and 2.7 % were extensively drug-resistant. Furthermore, 34.6 % produced extended-spectrum beta-lactamases, 14.1 % harboured carbapenemase genes, and 2.9 % exhibited colistin resistance. Shotgun metagenomic analysis revealed high taxonomic diversity, without dominant genera across treatment stages. The resistome was dominated by ARGs conferring resistance to beta-lactams, aminoglycosides, and macrolides, alongside genes linked to biocide resistance and heavy metal tolerance. Spearman correlation analysis of selected sequenced strains suggested a weak to moderate co-occurrence between ARGs and biocide or heavy metal tolerance genes. These findings underline WWTPs as AMR hotspots and reinforce the need to monitor DWTP source water within the One Health framework.},
}

@article {pmid40913922,
year = {2025},
author = {Uprety, T and Durazo, J and Paul, L and Metiner, K and Ruby, R and Loynachan, A and Janes, J and Kenndy, L and Cassone, L and Molly, E and Quick, M and Morgan, J and Beyhan, S and Erol, E},
title = {Detection of Neorickettsia risticii in antemortem fecal and postmortem fetal samples, with genomic insights from complete genome sequencing of a strain recovered from an aborted equine fetus.},
journal = {Veterinary microbiology},
volume = {310},
number = {},
pages = {110705},
doi = {10.1016/j.vetmic.2025.110705},
pmid = {40913922},
issn = {1873-2542},
abstract = {Neorickettsia risticii (N. risticii) is an obligatory intracellular bacterium that causes Potomac horse fever (PHF), a disease clinically characterized by diarrhea, pyrexia, and laminitis in horses. Although sporadic reports of N. risticii infection have been linked to abortion in mares, a detailed retrospective study, including genomic analysis of the pathogen from an aborted fetus, has not been published. This study examined 546 fecal samples from clinically ill horses (January 1, 2017-December 31, 2024) and 833 colon samples from aborted equine fetuses (September 20, 2018-December 31, 2024). Using real-time PCR, N. risticii was detected in 11.5 % of fecal samples and 1.08 % of fetal colon samples. Positive antemortem cases were detected between May and September, while fetal cases occurred from September to December. The fetuses were 5-8 months of gestational age, all showing microscopic evidence of colitis. A shotgun metagenomic approach was applied directly to an archived fetal colon sample using the MiSeq platform, yielding a complete genome of N. risticii (strain KY18-EqFetus) with 99.72 % nucleotide identity to the N. risticii strain Illinois reference genome. The genome was 879,923 bp with a GC content of 41.3 %, and 2024 variants (including indels and nucleotide polymorphisms) were identified. Notably, three genes coding for small hypothetical proteins present in the reference strain were absent in KY18-EqFetus. This study provides a comprehensive investigation of N. risticii in both antemortem and postmortem equine samples and reports the first complete genome assembly of the pathogen directly from an aborted equine.},
}

@article {pmid40913558,
year = {2025},
author = {Cai, TG and Lin, D and Ni, B and Zhang, TL and Wang, YF and Zhu, D},
title = {Microplastic Diversity as a Potential Driver of Soil Denitrification Shifts.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c04981},
pmid = {40913558},
issn = {1520-5851},
abstract = {Microplastics (MPs) are raising significant global concerns due to their environmental impacts. While most studies have focused on the effects of individual MP types, MPs in natural environments typically coexist as multiple types, and their combined effects remain poorly understood. In this study, we conducted a microcosm experiment with four levels of MP diversity (0, 1, 3, and 5 types) to investigate the effects of MP diversity on soil ecosystem functions using metagenomic sequencing. Our results revealed that increasing MP diversity significantly raised soil pH and organic carbon content while reducing available nitrogen. Notably, bacterial alpha diversity (Shannon and Invsimpson indices) increased significantly with higher MP diversity. Moreover, increasing MP diversity markedly shifted bacterial life-history strategies to adapt to the altered environment. Importantly, the abundance of nitrogen-related functional genes also increased with MP diversity. In particular, the abundance of denitrifying genes, predominantly driven by Rhodocyclaceae, was notably enhanced, resulting in a reduction of soil available nitrogen. Collectively, these findings offer valuable insights into the impact of MP diversity on soil function─especially within the nitrogen cycle─and have important implications for soil management strategies under MP stress.},
}

@article {pmid40912563,
year = {2025},
author = {Lu, Q and Qin, JX and Xie, SL and Chen, R and Xu, YQ and Ban, YM and Gao, CC and Li, PY and Wang, X and Tian, XZ},
title = {Effects of a commercial buckwheat rhizome flavonoid extract on milk production, plasma pro-oxidant and antioxidant, and the ruminal metagenome and metabolites in lactating dairy goats.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-26208},
pmid = {40912563},
issn = {1525-3198},
abstract = {Buckwheat is a common straw crop that contains an abundance of flavonoids and could be used as an antioxidant additive in animal diets. In this study, the effects of a commercial buckwheat rhizome flavonoid extract (BRFE) on milk production, plasma pro-oxidant and antioxidant, the ruminal metagenome, and ruminal metabolites in dairy goats were evaluated. Forty healthy, multiparous, nonpregnant Guanzhong dairy goats were blocked by DIM (122 ± 5.1 d), milk yield (1,461 ± 91 g/d), parity (3.80 ± 0.76 lactations), and BW (44.18 ± 2.47 kg), and were assigned to 1 of 4 diets. The control (CON) goats were fed the basal total mixed ratio, whereas the goats in treatment groups 1, 2, and 3 were fed the CON diet supplemented with 70, 140 (MB), and 210 mg/kg of a commercial BRFE (Shaanxi Haiyisi Biotechnology Co. Ltd., Xian, China) on a DM basis of the diet, respectively. The goats were fed these diets for a total of 63 d, with a 21-d adaptation period and a 42-d experimental period. Individual DMI and milk yield were recorded daily. Milk component samples were collected on d 6, 7, 13, 14, 20, 21, 27, 28, 34, 35, 41, and 42 of the experimental period; blood and ruminal fluid samples were collected on d 1, 21, and 42 of the experimental period. The results indicated that all milk production variables (milk yield, 3.5% FCM, fat, protein, lactose, and SNF yields) linearly and quadratically increased with increasing BRFE supplementation, and these variables were the highest in the MB group. The plasma total antioxidant capacity and superoxide dismutase increased linearly and quadratically with increasing BRFE supplementation. The plasma malondialdehyde and superoxide anion contents linearly and quadratically decreased with increasing dietary BRFE content. The ruminal fluid propionate content linearly and quadratically increased with BRFE supplementation. The ruminal acetate:propionate ratio linearly and quadratically decreased with increasing BRFE content. Compared with CON, feeding 140 mg/kg BRFE reduced the ruminal fluid abundances of Synergistetes at the phylum level and Quinella at the genus level. Dietary supplementation with BRFE increased the abundance of carbohydrate-digesting enzymes in ruminal fluid, among which glycoside hydrolase family 2 was the most dominant. Metabolomic analysis indicated that supplementation with BRFE enriched tryptophan metabolism in the rumen. Overall, this study revealed that dietary supplementation with BRFE increased plasma antioxidant capabilities and milk production and improved ruminal fermentation, the ruminal metagenome, and ruminal tryptophan metabolism in lactating dairy goats.},
}

@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 non-allergic with distinct biologic and microbiome traits.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.07.034},
pmid = {40912476},
issn = {1097-6825},
abstract = {BACKGROUND: Disentangling preschool wheezing heterogeneity in terms of clinical traits, temporal patterns, and collective healthcare burden is critical for precise and effective interventions.

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.

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, healthcare utilization, biological determinants, and clinical outcomes. Stool samples for shotgun metagenomic sequencing profiles from infant microbiomes collected at 3-months and 1-year were assessed for phenotype-specific biomarkers.

RESULTS: Six distinct respiratory phenotypes were identified from 2902 children that differed by temporal wheeze and allergic sensitization patterns. While allergic wheeze phenotypes (11·6% of participants) carried the highest asthma diagnosis risk, the more common non-allergic phenotypes (88·3% of participants) contributed to the majority of 5-year asthma diagnoses (61·4% of diagnoses). Most importantly, non-allergic phenotypes accounted for over 2/3 of healthcare utilization in this age group. Phenotypes differed by lung function, blood eosinophils, allergic comorbidities and weight-for-age z-score. Moreover, microbiome profiles from 1439 infants revealed largely non-overlapping microbial signatures at 1 year were associated with each phenotype.

CONCLUSION: We identified novel early childhood respiratory phenotypes to disentangle non-overlapping paths to preschool wheezing. Our findings highlight the continued clinical relevance of non-atopic wheeze phenotypes, which remain undertreated despite accounting for a substantial proportion of healthcare utilization and asthma diagnoses.},
}

@article {pmid40911772,
year = {2025},
author = {Li, Q and Yang, F and Zhou, CZ},
title = {Cyanophages: Billions of Years of Coevolution with Cyanobacteria.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-042924-095145},
pmid = {40911772},
issn = {1545-3251},
abstract = {Prevalent in marine and freshwater ecosystems, cyanophages compose a class of double-stranded DNA viruses that specifically infect cyanobacteria. During billions of years of coevolution, cyanophages and cyanobacteria have significantly contributed to the biogeochemical cycling and genetic diversity of aquatic ecosystems. As natural predators of cyanobacteria, cyanophages hold promise as eco-friendly agents against harmful cyanobacterial blooms. Recent technical advances in omics and cryo-electron microscopy have revealed the remarkable diversity of cyanophages in genome sequence and tail morphology. In this review, we summarize the genomic and metagenomic data, phylogenetic analyses, and diverse three-dimensional structures of cyanophages, in addition to their interplays with hosts. We also discuss the in vivo assembly processes of cyanophages, the exploration of uncultured cyanophages and host pairing, and the synthetic engineering and potential applications of cyanophages.},
}

@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 = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf226},
pmid = {40911291},
issn = {1365-2672},
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.

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 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.

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 = {},
doi = {10.1093/gigascience/giaf102},
pmid = {40910796},
issn = {2047-217X},
support = {DNRF143//Danmarks Grundforskningsfond/ ; CF20-0460//Carlsbergfondet/ ; 101066225//HORIZON EUROPE Framework Programme/ ; PD/BD/150645/2020//Agência Regional para o Desenvolvimento da Investigação, Tecnologia e Inovação/ ; 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.

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.

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.},
}

Animals
*Metagenomics/methods
*Metagenome
*Microbiota/genetics
Earth, Planet
*Vertebrates/genetics/microbiology
Databases, Genetic

@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 = {},
number = {},
pages = {e0158825},
doi = {10.1128/spectrum.01588-25},
pmid = {40910779},
issn = {2165-0497},
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 = {},
number = {},
pages = {e0054125},
doi = {10.1128/msystems.00541-25},
pmid = {40910778},
issn = {2379-5077},
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 {pmid40910361,
year = {2025},
author = {Mayr, MJ and Parra, SA and Connon, SA and Narayanan, AK and Murali, R and Crémière, A and Orphan, VJ},
title = {Distinct Microbial Communities Within and On Seep Carbonates Support Long-term Anaerobic Oxidation of Methane and Divergent pMMO Diversity.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf153},
pmid = {40910361},
issn = {1751-7370},
abstract = {At methane seeps worldwide, syntrophic anaerobic methane-oxidizing archaea and sulfate-reducing bacteria promote carbonate precipitation and rock formation, acting as methane and carbon sinks. Although maintenance of anaerobic oxidation of methane (AOM) within seep carbonates has been documented, its reactivation upon methane exposure remains uncertain. Surface-associated microbes may metabolize sulfide from AOM, maintain carbonate anoxia, contribute to carbonate dissolution, and support higher trophic levels; however, these communities are poorly described. We provide insights into microbial diversity, metabolism, activity, and resiliency within and on seep carbonates through amplicon and metagenomic sequencing, incubations, and non-canonical amino acid tagging combined with fluorescence in situ hybridization (BONCAT-FISH). Ca. Methanophaga (ANME-1) dominated the carbonate interiors in active and low activity seeps, co-occurring with Ca. Desulfaltia as main sulfate reducer, potentially a new syntrophic partner in AOM. Single-cell BONCAT-FISH revealed variability in ANME-1 activity, suggesting potential dormancy in carbonates from low activity seep sites. However, incubations with carbonates from low activity seeps (≥24 months) showed exponential AOM reactivation (~44-day doubling), suggesting these carbonates retain the potential as long-term methane sinks under dynamic seepage conditions. Surface-associated microbial communities were heterogeneous and distinct from the carbonate interior and other seep habitats. Anaerobic methane-oxidizing biofilms and sulfide-oxidizing mats were associated with carbonates with high and intermediate AOM rates potentially influencing carbonate precipitation/dissolution. Shared aerobic methanotrophs between carbonate surfaces and invertebrates indicated carbonate surfaces may represent animal epibiont reservoirs. Recovered particulate methane monooxygenases included both aerobic methanotrophs and divergent forms associated with the Methylophagaceae, suggesting a new function in this group.},
}

@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 = {},
number = {},
pages = {1-15},
doi = {10.1080/09593330.2025.2551907},
pmid = {40910191},
issn = {1479-487X},
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 {pmid40909844,
year = {2025},
author = {Hussain, FA and Bergerat, A and Kelly, J and Demidkina, BC and Worrall, D and Xu, J and Kannan, A and Brunner, T and Culler, N and Goldenberg, M and Arar, WE and Katukota, AV and Murthy, M and Elsherbini, J and Hussain, S and Dong, M and Kwon, DS and Mitchell, CM},
title = {Donation strain engraftment demonstrates feasibility of vaginal microbiota transplantation to prevent recurrent bacterial vaginosis.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.27.25334544},
pmid = {40909844},
abstract = {Although bacterial vaginosis (BV) affects 30% of women worldwide and is associated with adverse health outcomes, current standard-of-care antibiotics fail in over half of cases and treatments have not improved in over 40 years. Probiotics have been proposed as alternative treatments, but fail to restore an optimal lactobacilli-dominated microbiome in the vast majority of patients. Here, we present findings from a pilot clinical trial demonstrating the successful engraftment of vaginal microbiota transplantations (VMTs) after antibiotic treatment in individuals with recurrent BV. Following an investigational donation protocol under an FDA IND, we treated eight recipients with material from a single donor. Using 16S rRNA gene amplicon sequencing we show that VMT results in a shift toward an optimal, Lactobacillus crispatus -dominated microbial community in three out of four VMT recipients at one month post-transplant. In two successful transplantations, this shift lasted at least six months post-VMT. In contrast, no placebo recipients exhibited L. crispatus dominance. Bacterial culturing and whole genome sequencing combined with metagenomic sequencing from donations and recipient longitudinal samples revealed colonization by donor-derived strains of L. crispatus in VMT recipients. Additionally, we observed no increase in genital inflammatory markers or changes in endocervical immune cell proportions when comparing treatment to placebo, indicating transplant safety. Together, these findings support the hypothesis that transferring the entire vaginal microbiota can lead to a more complete restoration of the vaginal ecosystem compared to single strain probiotics and lay the foundation for designing novel microbial therapies for BV. Vaginal microbiota transplantations lead to stable L. crispatus engraftment in the microbiomes of certain patients with recurrent bacterial vaginosis.},
}

@article {pmid40909705,
year = {2025},
author = {Cumbo, F and Blankenberg, D},
title = {Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.25.672238},
pmid = {40909705},
issn = {2692-8205},
abstract = {UNLABELLED: Metagenomics has become a powerful tool for studying microbial communities, allowing researchers to investigate microbial diversity within complex environmental samples. Recent advances in sequencing technology have enabled the recovery of near-complete microbial genomes directly from metagenomic samples, also known as metagenome-assembled genomes (MAGs). However, accurately characterizing these genomes remains a significant challenge due to the presence of sequencing errors, incomplete assembly, and contamination. Here we present MetaSBT, a new tool for organizing, indexing, and characterizing microbial reference genomes and MAGs. It is able to identify clusters of genomes at all seven taxonomic levels, from the kingdom all the way down to the species level, using the Sequence Bloom Tree (SBT) data structure that relies on Bloom Filters (BFs) to index massive amounts of genomes based on their k-mers composition. We have built an initial set of databases composed of over 190 thousand viral genomes from NCBI GenBank and public sources grouped into sequence consistent clusters at different taxonomic levels, making it the first software solution for the classification of viruses at different ranks, including still unknown ones. This results in the definition of over 40 thousand species clusters where ∼80% do not match with any known viral species in reference databases to date. Furthermore, we show how our databases can be used as a new basis for existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. Finally, the framework is released open-source and, along with its public databases, is fully integrated into the Galaxy Platform enabling broad accessibility.

IMPORTANCE: The MetaSBT framework and its databases, together with its integration in the Galaxy Platform, provide a powerful resource for microbial research. MetaSBT provides a powerful and scalable approach for classifying microbial genomes, including previously unknown ones. This facilitates the discovery and characterization of novel taxa, a crucial feature for expanding our knowledge of microbial diversity and its implications within host health and environmental factors. Furthermore, MetaSBT databases can serve as a reference base for other state-of-the-art tools, enhancing their capabilities to identify, analyze, and classify unknown microbes in metagenomic samples.},
}

@article {pmid40909542,
year = {2025},
author = {Mahlich, Y and Sohi, H and Piehowski, P and McDermott, JE and Gosline, SJ},
title = {spammR: an R package designed for analysis and integration of spatial multi-omic measurements.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.26.672472},
pmid = {40909542},
issn = {2692-8205},
abstract = {SUMMARY: Spatial omics is a young and evolving field and as such shows rapid development of novel technologies and analysis methods to measure transcripts, proteins, metabolites, and post-translational modifications at high spatial resolution. These advances in technology have enabled the simultaneous generation of abundance profiles for multiple different omics types and associated microscopy imaging data, as well as their analysis in a spatial context. However, most analytical tools are designed for spatial transcriptomics platforms and are challenging to use in other contexts such as mass spectrometry-based measurements or metagenomics. To this end we present spammR (sp atial a nalysis of m ulti-omics m easurements in R), an R package that enables end-to-end analysis with a specific focus on mass-spectrometry derived spatial omics datasets with (1) smaller sample sizes and spatial sparsity of samples, (2) considerable missingness, and (3) no a-priori knowledge about proteins or genes of interest, relying on a fully data-driven approach.

spammR is implemented in R. The package is currently installable from GitHub (https://github.com/PNNL-CompBio/spammR).},
}

@article {pmid40909440,
year = {2025},
author = {Feng, M and Chai, Y and Li, J and Wang, Q and Zhang, D},
title = {A metagenome-wide association study of gut microbiota in hepatitis B virus-related cirrhosis in northwest China.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1619911},
pmid = {40909440},
issn = {1664-8021},
abstract = {BACKGROUND AND PURPOSE: In recent years, research on the relationship between hepatitis B virus-related cirrhosis (HBV-LC) and gut microbiota has grown, but studies focusing on the Northwest Chinese population are scarce. This study characterized the gut microbiota composition and function in HBV-LC patients vs. healthy individuals in Northwest China, aiming to provide a scientific basis for region-specific precision therapies.

MATERIALS AND METHODS: A cross-sectional study enrolled 43 HBV-LC patients and 43 age-/sex-matched healthy controls (HC) from Gansu Province. Clinical parameters including liver function, blood routine, coagulation function, blood biochemistry were measured. Shotgun metagenomic sequencing was conducted to analyze gut microbiota taxonomic composition and function.

RESULTS: HBV-LC patients showed significantly elevated alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), γ-glutamyl transferase (γ-GGT), prothrombin time, international normalized ratio (INR), and thrombin time, but reduced triglycerides (TG), total cholesterol (TC), erythrocytes, thrombocytes, total protein, albumin, and prothrombin time activity (PT-ratio). Alpha-diversity based on Shannon and Simpson indices was lower in HBV-LC. At the genus level, Bacteroides, Prevotella, Escherichia, Parabacteroides, Veillonella, and Klebsiella were enriched in HBV-LC, while Bifidobacterium, Faecalibacterium, Roseburia, Ruminococcus, Anaerostipes, Blautia, Eubacterium, and Fusicatenibacter were reduced. Species-level analysis identified distinct enrichment of Prevotella copri, Bacteroides vulgatus, Escherichia coli, Fusobacterium nucleatum, and Veillonella spp. in HBV-LC. Functional analysis revealed 482 metabolic pathways. HBV-LC showed enhanced lipid, amino acid, and nucleotide metabolism, menaquinol biosynthesis, and anaerobic energy metabolism, but reduced acetate/lactate production, lactose/galactose degradation, and peptidoglycan biosynthesis. Metagenome-wide association study revealed HBV-LC-enriched opportunistic species (e.g., E. coli, Veillonella spp.) correlated positively with hepatic enzymes and coagulation parameters, and negatively with TC, TG, and erythrocyte counts.

CONCLUSION: HBV-LC patients in Northwest China exhibit altered clinical indicators, gut microbial composition (reduced diversity, increased opportunistic pathogens, decreased beneficial species), and metabolic function. These findings highlight the potential of gut microbiome-targeted interventions for regional precision medicine of HBV-LC.},
}

@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 = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolome ; *HIV Infections/drug therapy/complications/microbiology ; Male ; Female ; *Brain/physiopathology/physiology ; Adult ; Biomarkers/blood ; Middle Aged ; Feces/microbiology ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; HIV-1/drug effects ; },
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).

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.

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.

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.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Metabolome
*HIV Infections/drug therapy/complications/microbiology
Male
Female
*Brain/physiopathology/physiology
Adult
Biomarkers/blood
Middle Aged
Feces/microbiology
Metagenomics
Bacteria/classification/genetics/isolation & purification
HIV-1/drug effects

@article {pmid40909218,
year = {2025},
author = {Tigrero-Vaca, J and Díaz, B and Gu, G and Cevallos-Cevallos, JM},
title = {Next-generation sequencing applications in food science: fundamentals and recent advances.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1638957},
pmid = {40909218},
issn = {2296-4185},
abstract = {Next-generation sequencing (NGS) has revolutionized food science, offering unprecedented insights into microbial communities, food safety, fermentation, and product authenticity. NGS techniques, including metagenetics, metagenomics, and metatranscriptomics, enable culture-independent pathogen detection, antimicrobial resistance surveillance, and detailed microbial profiling, significantly improving food safety monitoring and outbreak prevention. In food fermentation, NGS has enhanced our understanding of microbial interactions, flavor formation, and metabolic pathways, contributing to optimized starter cultures and improved product quality. Furthermore, NGS has become a valuable tool in food authentication and traceability, ensuring product integrity and detecting fraud. Despite its advantages, challenges such as high sequencing costs, data interpretation complexity, and the need for standardized workflows remain. Future research focusing on optimizing real-time sequencing technologies, expanding multi-omics approaches, and addressing regulatory frameworks is suggested to fully harness NGS's potential in ensuring food safety, quality, and innovation.},
}

@article {pmid40909207,
year = {2025},
author = {Li, D and Pan, J and Yang, M and Zhong, J and Ding, H and Chen, W and Zhang, J and Liao, G},
title = {Positive Metagenomic Next-Generation Sequencing of Renal Lavage Fluid Associates with Delayed Graft Function in Kidney Transplants from Donors After Circulatory Death: A Retrospective Study.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4579-4592},
pmid = {40909207},
issn = {1178-6973},
abstract = {BACKGROUND: Delayed graft function (DGF) is a major complication in kidney transplants from donation after circulatory death (DCD). This study assessed the association between metagenomic next-generation sequencing (mNGS) results and the occurrence of DGF during the perioperative period in DCD kidney transplant recipients.

METHODS: We analyzed 191 DCD kidney transplant recipients in this single-center retrospective cohort study. All recipients underwent routine mNGS testing of renal lavage fluid between July 2021 and July 2024. Demographic, clinical, and microbial data were collected. Associations between mNGS results and DGF were evaluated using logistic regression models adjusted for covariates.

RESULTS: The study revealed a strong association between mNGS positivity and DGF development. mNGS-positive recipients (n=97/191) showed significantly higher DGF incidence than mNGS-negative cases (30.9% vs 6.4%, p<0.001), highlighting the potential clinical utility of mNGS in predicting DGF. Multivariate analysis confirmed this association after adjusting for confounders (aOR=7.90, 95% CI 1.63-38.24). Bacterial pathogens constituted the majority of detected microorganisms (62.7%), with prevalent isolates including Enterococcus (37 cases) and Staphylococcus (29 cases) that harbored clinically relevant resistance genes.

CONCLUSION: Our findings demonstrate a significant association between mNGS positivity in renal lavage fluid and DGF development in DCD kidney recipients (aOR 7.90, 95% CI 1.63-38.24), These findings support further investigation into mNGS as a tool for early risk stratification and targeted antimicrobial therapy in DCD kidney recipients.},
}

@article {pmid40909168,
year = {2025},
author = {Siegwald, L and Cherta-Murillo, A and Christen, S and Boulangé, CL and Chou, CJ and Foata, F and Lahiry, A and Frézal, A and Giner, MP and Godin, JP and Sakwinska, O},
title = {The Impact of Low-Lactose, High Galacto-Oligosaccharides Milk on Gut Microbiome and Plasma Metabolome in Healthy Adults: A Randomized, Double-Blind, Controlled Clinical Trial Complemented by Ex Vivo Experiments.},
journal = {Current developments in nutrition},
volume = {9},
number = {9},
pages = {107506},
pmid = {40909168},
issn = {2475-2991},
abstract = {BACKGROUND: Galacto-oligosaccharides (GOS) intake has been linked to health benefits via modulation of the gut microbiome. Milk, where the majority of lactose is enzymatically converted to GOS (called here Novel or "N milk"), retains milk's nutritional value with reduced lactose and a high amount of prebiotic GOS.

OBJECTIVES: The aim of this study was to investigate the effect of N milk on the gut microbiome and related changes in health-related biomarkers, complemented by ex vivo fermentation experiments.

METHODS: In a 2-arm crossover, double-blind, randomized controlled clinical trial, 26 healthy adults consumed either N milk (containing 9 g GOS and 1.7 g of lactose per serving) or lactose-free milk (control), for 2 wk with a 2-wk washout period. Stool and fasting blood samples were collected at the start and the end of the intervention periods. Gut microbiome was analyzed using shotgun metagenomics, and metabolites using both targeted and untargeted methods. In addition, we tested lactose-free milk, N milk, and GOS in ex vivo colonic fermentation to obtain insights into the bacterial processing of substrates.

RESULTS: N milk intake led to a 3-fold increase in median gut bifidobacteria (P < 0.0001) and significant increases in plasma acetate, octanoic acid, β-alanine, and nicotinamide (all P < 0.05). Untargeted plasma metabolomics revealed a shift in amino acid metabolism, with an increase in 3-indole propionate, accompanied by a decrease in 2 uremic toxins, p-cresol sulfate, and indoxyl-sulfate (P < 0.05 without false discovery rate adjustment). Ex vivo fermentation experiments supported the results of the clinical study, whereby N milk increased bifidobacteria accompanied by higher production of short-chain fatty acids and a shift in microbial tryptophan metabolism, and indicated unique effects of N milk compared with GOS.

CONCLUSIONS: N milk resulted in a significant increase in gut bifidobacteria, along with changes in plasma metabolites previously associated with immune and metabolic health benefits.This study was registered at clinicaltrials.gov as NCT05207839.},
}

@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},
doi = {10.1111/1758-2229.70184},
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 & 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.},
}

*Forests
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Plant Bark/microbiology
Biodiversity
Indonesia
Phylogeny
*Trees/microbiology
DNA, Bacterial/genetics
*Biota

@article {pmid40908532,
year = {2025},
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 = {},
number = {},
pages = {},
doi = {10.1210/clinem/dgaf495},
pmid = {40908532},
issn = {1945-7197},
abstract = {CONTEXT: There is an association between hypothyroidism and small intestinal bacterial overgrowth (SIBO), but the exact mechanistic link between these two conditions is not fully elucidated.

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.

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 ten-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 (PSM) control groups.

RESULTS: Among REIMAGINE subjects, SIBO prevalence was higher in the hypothyroid group (32.65%) vs. controls (15.17%). In the TriNetX analysis, ten-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 non-hypothyroid 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 non-hypothyroid subjects (Hypo-/SIBO+), whereas Klebsiella species were prevalent in hypothyroid group subjects with SIBO (Hypo+/SIBO+).

CONCLUSION: These findings suggest there is an increased risk for development of SIBO in individuals with a history of hypothyroidism which 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 & 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.},
}

*Salinity
*Microbiota
Geologic Sediments/microbiology
Hot Temperature
Ecosystem
*Rivers/microbiology/chemistry
Bacteria/genetics/classification/isolation & purification
*Heat-Shock Response
Climate Change
Archaea/genetics
Fresh Water/microbiology

@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.},
}

*Bioelectric Energy Sources/microbiology
*Denitrification/drug effects
Electrodes
*Ferrosoferric Oxide/pharmacology
Oxygen
*Water Purification/methods
Metagenome
Ammonium Compounds/metabolism
*Microbiota

@article {pmid40907413,
year = {2025},
author = {Nono, JKN and Ayemele, AG and Fotsidie, HG and Tang, H and Li, Y and Huang, X and Hu, N and Li, X and Xu, J},
title = {Manganese accumulation characteristics and rhizosphere decontamination mechanisms of Phytolacca icosandra L.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118970},
doi = {10.1016/j.ecoenv.2025.118970},
pmid = {40907413},
issn = {1090-2414},
abstract = {The role of microbial metagenomics in understanding ecological changes associated with rhizosphere heavy metal decontamination by plants has often been overlooked. The aim of this study was to scrutinize the structural, enzymological and metagenomic mechanisms leading to manganese (Mn) decontamination in the rhizosphere by Phytolacca icosandra. Seedlings of P. icosandra were planted for three months under six sets of Mn treatment (addition of 0, 250, 500, 100, 2500, and 5000 µg/g Mn in original soils) using a complete randomized block design. When Mn addition increased to 2500 and 5000 µg/g, the shoot biomass of P. icosandra was reduced by 3.14% and 51.85% respectively, while root biomass was reduced by 5.91% and 47.29% respectively. When Mn uptake increased in the roots/shoots and leaves after the addition of 5000 µg/g Mn, plant chlorophyll a, and malondialdehyde (MDA) concentrations decreased by 4% and 17% respectively. As a result, lipids in the cell membranes of the leaves were no longer destroyed and cell membrane degradation was inhibited by Mn gradients. With addition of 2500-5000 µg/g Mn, the overall weight and height biomasses of P. icosandra was reduced in size to absorb excess Mn. Soil N bioavailability decreased the most at the highest Mn concentration. Above 2500 µg/g Mn, rhizosphere acidification increased (pH < 7). The abundances of rhizosphere bacteria Ramlibacter sp. and Planctomycetaceae bacterium LX124 decreased when soil Mn concentration increased, while those of Tumebacillus avium, Devosia riboflavina, and Flavobacterium fevense increased, paving the way towards microbial biomarkers of soil Mn decontamination. These findings provide valuable knowledge on remediating heavy metal-contaminated agricultural soils.},
}

@article {pmid40907321,
year = {2025},
author = {Lv, H and Chi, Q and Wang, J and Xu, Y and Li, M and Jiang, X and Shen, J},
title = {Electron transfer mediates position-dependent hydrolytic dichlorination during dichlorophenols biodegradation under nitrate-reducing conditions.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139753},
doi = {10.1016/j.jhazmat.2025.139753},
pmid = {40907321},
issn = {1873-3336},
abstract = {Polychlorinated phenols (PCPs) are persistent pollutants due to strong C-Cl bonds and toxicity, posing challenges for bioremediation. Although electron acceptor activation can facilitate degradation, the effect of chlorine-substituent positions on isomer-specific biodegradability remains unclear. To address this gap, dichlorophenols (DCPs) were selected as chlorine substitution patterns shape degradation kinetics and microbial responses. Six UASB bioreactors were operated under nitrate-reducing conditions for 130 days to investigate isomer-specific degradation behaviors. The results revealed complete removal (100 %) of ortho-substituted DCPs (2,6-/2,4-DCP) versus limited removal (27.86 ± 2.26 %) of 3,4-DCP (meta-para), establishing a reactivity hierarchy among DCP isomers: dual ortho (2,6) > ortho-para (2,4) > ortho-meta (2,3/2,5) > meta substituted (3,4/3,5). Metagenomic analysis indicated that dehalogenators (Gordonia, Chryseobacterium) were enriched in 2,4-/2,3-DCP systems, nitrate-reducing Pseudomonas dominated the 3,5-DCP system, and Desulfovibrio contributed to electron transfer in the 2,3-DCP system. Molecular docking confirmed that badk (PDB ID: 7P98) and paaF (PDB ID: 6IJK) hydratases regulated degradation kinetics through substrate-specific binding, with computed affinities strongly correlating with observed removal efficiencies. Collectively, these findings demonstrate that chlorine substituent positions fundamentally govern the biodegradability of halogenated aromatics, underscoring the importance of structure-specific bioremediation strategies for effective wastewater treatment.},
}

@article {pmid40907234,
year = {2025},
author = {Shi, X and Zhang, J and Chen, X and Li, Q and Hui, Y and Han, J and Jin, X and Jin, P},
title = {Impact of bacteriophage MS2 adsorption on biofilm microbial communities, metabolic pathways, and protein expression in sewer systems.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126998},
doi = {10.1016/j.jenvman.2025.126998},
pmid = {40907234},
issn = {1095-8630},
abstract = {The stability of microbial communities within sewer systems is essential for maintaining effluent quality and infrastructure longevity. However, the functional consequences of viral interactions with biofilms remain poorly characterised. This study examines the effects of bacteriophage MS2 adsorption on biofilm structure, metabolism, and pathogenic potential in a simulated 1 km sewer pipeline. Quartz crystal microbalance with dissipation monitoring (QCM-D) revealed irreversible phage adsorption onto extracellular polymeric substances (EPS), inducing a biphasic viscoelastic response. During the first 24 h, the ΔD/Δf slope increased from 0.204 to 0.420, indicating initial loosening of the EPS matrix. This was followed by a compaction phase, with the slope decreasing to 0.102 by 96 h. Metagenomic profiling indicated a shift in community functionality, with sulphur-metabolising Chlorobium decreasing by 27.8 % and the pathogenic genus Novosphingobium increasing by 4.87 %. Corresponding trends were observed in enzymatic activity: sulphate reduction genes (e.g., EC 2.7.7.4) declined to 10 % of baseline levels at 24 h, before recovering to 14542 annotations at 96 h. Metaproteomic analysis revealed divergent regulatory responses, with acetyl-CoA synthetase (EC 6.2.1.1) transcriptionally upregulated, while phosphate acetyltransferase (EC 2.3.1.8) increased independently of gene expression, indicating potential post-translational control. These findings demonstrate that phage adsorption perturbs biofilm integrity and reprogrammes microbial metabolism, underscoring the need for virus-informed strategies in sewer monitoring and pathogen management.},
}

@article {pmid40906991,
year = {2025},
author = {Norman, RS and Granger, CO and Cochran, KH and Isanovic, M and Self, S and Klein, E and Richardson, SD},
title = {Aerosolization of Azithromycin, Ofloxacin, and Co-occurring Antibiotic Resistance Genes during Municipal Wastewater Treatment.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c08502},
pmid = {40906991},
issn = {1520-5851},
abstract = {To effectively combat antibiotic resistance, it is critical to understand antibiotic usage patterns and their environmental dissemination. Wastewater treatment plants (WWTPs) are well-documented sources of antibiotics discharged into aquatic environments, but their role in releasing antibiotics via bioaerosols has not previously been investigated. In this study, seasonal air and liquid samples were collected throughout 2019 from a midsize WWTP employing both mechanical surface agitation and fine bubble aeration of activated sludge. Azithromycin and ofloxacin were detected in bioaerosols collected near aeration tanks at concentrations ranging from below detection limits up to 29 pg L[-1] air, suggesting that bioaerosols may represent a previously underappreciated route of environmental and occupational antibiotic exposure. Metagenomic analysis confirmed the co-occurrence of antibiotic resistance genes (ARGs) conferring resistance to macrolides and fluoroquinolones in both air and liquid samples. These findings highlight bioaerosols as an important yet overlooked pathway for the dissemination of antibiotics and ARGs, emphasizing the necessity of integrating airborne pathways into environmental antibiotic resistance surveillance programs, especially given the global scale of WWTP operations.},
}

@article {pmid40906773,
year = {2025},
author = {Liu, Z and Ji, S and Chang, Q and Wang, J and Galon, EM and Xu, Y and Yin, G and Li, J and Gao, X and Tian, W and Han, Z and Li, C and Xu, Z and Du, R and Xue, S},
title = {Surveillance of tick-borne viruses in the border regions of the Tumen River Basin: Co-circulation in ticks and livestock.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {9},
pages = {e0013500},
doi = {10.1371/journal.pntd.0013500},
pmid = {40906773},
issn = {1935-2735},
abstract = {BACKGROUND: The unique eco-geographical patterns and climatic conditions of the China-Tumen River border region, combined with frequent cross-border tourism and trade activities, collectively establish this area as a recognized hotspot for tick-borne disease outbreaks. However, critical knowledge gaps persist regarding the eco-epidemiology of emerging tick-borne viruses and the distribution of their potential reservoir hosts within this trinational ecosystem spanning China, North Korea, and Russia.

METHODS: We collected a total of 2,004 ticks from the study area, along with blood samples obtained from 42 sheep and 45 cattle. Following viral metagenomic analysis of the ticks, dual verification of target pathogens in all samples was performed using qRT-PCR and RT-PCR assays. Phylogenetic trees were constructed and nucleotide sequences were analyzed to delineate relationships between the obtained virus strains and reference sequences.

RESULTS: Viral metagenomics identified three viruses in ticks: Dabieshan tick virus (DBTV), Songling virus (SGLV), and Yanggou tick virus (YGTV). PCR analysis detected DBTV exclusively in Hunchun ticks (minimum infection rates, MIR:4.73%) and YGTV in Antu specimens (MIR:0.97%). Conversely, SGLV was detected in ticks from all four regions, with MIR of 1.68% (Helong), 0.74% (Hunchun), 1.61% (Antu), and 4.79% (Longjing). Concurrently, SGLV was detected in 19 sheep blood samples from Longjing, yielding a positivity rate of 45.24%, while YGTV was identified in 13 cattle blood samples from Antu, with a positivity rate of 28.89%. Phylogenetically, the DBTV strain clustered with previously reported DBTV and Yongjia tick virus 1 isolates. Sheep-derived SGLV strains shared close evolutionary ties with tick-borne SGLV, whereas YGTV from cattle and ticks formed a distinct cluster with Russian strains but diverged into two branches from Chinese variants, suggesting evolutionary instability.

CONCLUSION: These findings address critical knowledge gaps in the transmission dynamics and genetic diversity of emerging arboviruses while providing vital insights for developing cross-border surveillance strategies with significant public health implications.},
}

@article {pmid40906457,
year = {2025},
author = {Rahube, TO and Selvarajan, R and Nduna, B and Nthaba, B and Molwalefhe, L and Shemang, E},
title = {Evaluation of Bacterial Population Changes and Ecological Dynamics in Oil-Impacted Soils Using 16S rRNA Amplicon Sequencing.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14081074},
pmid = {40906457},
issn = {2079-7737},
support = {BIUST//Botswana International University of Science and Technology/ ; },
abstract = {Soils are vibrant and diverse natural entities situated at the juncture between Earth, air, water, and life [...].},
}

@article {pmid40906400,
year = {2025},
author = {Zeng, Q and Wang, Z and Shen, Z and Li, W and Luo, K and Qin, Q and Li, S and Gu, Q},
title = {Microbiome Diversity and Dynamics in Lotus-Fish Co-Culture Versus Intensive Pond Systems: Implications for Sustainable Aquaculture.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14081092},
pmid = {40906400},
issn = {2079-7737},
support = {2023YFD2400902//National Key Research and Development Program of China/ ; 2023YFD2401605//National Key Research and Development Plan Program/ ; 23B0073//Scientific Research Foundation of Hunan Provincial Education Department/ ; },
abstract = {The lotus-fish co-culture (LFC) system leverages plant-fish symbiosis to optimize aqua-culture environments, enhancing both economic and ecological yields. However, the eco-logical mechanisms of microbial communities in LFC systems remain poorly understood, particularly regarding the functional roles of fungi, archaea, and viruses. This study compared microbiota (viruses, archaea, fungi) in water, sediment, and fish (crucian carp) gut of LFC and intensive pond culture (IPC) systems using integrated metagenomic and environmental analyses. Results demonstrated that LFC significantly reduced concentrations of total nitrogen, total phosphorus, and nitrite nitrogen and chemical oxygen demand in water, and organic matter and total nitrogen in sediment compared to IPC. Community diversity analysis, LefSe, and KEGG annotation revealed suppressed viral diversity in LFC, yet increased complexity and stability of intestinal virus communities compared to IPC. Archaeal and functional analyses revealed significantly enhanced ammonia oxidation and OM decomposition in LFC versus IPC, promoting methane metabolism equilibrium and sediment organic matter decomposition. Moreover, crucian carp intestines in LFC harbored abundant Methanobacteria, which contributed to maintaining a low hydrogen partial pressure, suppressing facultative anaerobes and reducing intestinal infection risk. The abundance of fungi in sediment and crucian carp intestine in LFC was significantly higher than that in IPC, showing higher ecological self-purification ability and sustainability potential in LFC. Collectively, LFC's optimized archaeal-fungal networks strengthened host immunity and environmental resilience, while viral community suppression reduced pathogen risks. These findings elucidate microbiome-driven mechanisms underlying LFC's ecological advantages, providing a framework for designing sustainable aquaculture systems through microbial community modulation.},
}

@article {pmid40906131,
year = {2025},
author = {Yuan, J and Sun, Z and Sun, R and Wang, J and Wu, C and Liu, B and Zhao, X and Li, Q and Zhao, J and Cai, K},
title = {A Spatiotemporal Atlas of the Gut Microbiota in Macaca mulatta brevicaudus: Implications for Health and Environment.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14080980},
pmid = {40906131},
issn = {2079-7737},
abstract = {The gut microbiota of macaques, highly homologous to humans in biological characteristics and metabolic functions, serves as an ideal model for studying the mechanisms of human intestinal diseases and therapeutic approaches. A comprehensive characterization of the macaque gut microbiota provides unique insights into human health and disease. This study employs metagenomic sequencing to assess the gut microbiota of wild M. mulatta brevicaudus across various ages, sexes, and physiological states. The results revealed that the dominant bacterial species in various age groups included Segatella copri and Bifidobacterium adolescentis. The predominant bacterial species in various sexes included Alistipes senegalensis and Parabacteroides (specifically Parabacteroides merdae, Parabacteroides johnsonii, and Parabacteroides sp. CT06). The dominant species during lactation and non-lactation periods were identified as Alistipes indistinctus and Capnocytophaga haemolytica. Functional analysis revealed significant enrichment in pathways such as global and overview maps, carbohydrate metabolism and amino acid metabolism. This study enhances our understanding of how age, sex, and physiological states shape the gut microbiota in M. mulatta brevicaudus, offering a foundation for future research on (1) host-microbiome interactions in primate evolution, and (2) translational applications in human health, such as microbiome-based therapies for metabolic or immune-related disorders.},
}

@article {pmid40906071,
year = {2025},
author = {Zeng, X and Chen, J and Liu, G and Zhou, Y and Wang, L and Zhang, Y and Liu, S and Shao, Z},
title = {Host Shaping Associated Microbiota in Hydrothermal Vent Snails from the Indian Ocean Ridge.},
journal = {Biology},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/biology14080954},
pmid = {40906071},
issn = {2079-7737},
support = {2023YFC2812903, 2021YFF0501304, and 2018YFC0310702.//National Key R&D Program of China/ ; },
abstract = {Snails at hydrothermal vents rely on symbiotic bacteria for nutrition; however, the specifics of these associations in adapting to such extreme environments remain underexplored. This study investigated the community structure and metabolic potential of bacteria associated with two Indian Ocean vent snails, Chrysomallon squamiferum and Gigantopelta aegis. Using microscopic, phylogenetic, and metagenomic analyses, this study examines bacterial communities inhabiting the foot and gland tissues of these snails. G. aegis exhibited exceptionally low bacterial diversity (Shannon index 0.14-0.18), primarily Gammaproteobacteria (99.9%), including chemosynthetic sulfur-oxidizing Chromatiales using Calvin-Benson-Bassham cycle and methane-oxidizing Methylococcales in the glands. C. squamiferum hosted significantly more diverse symbionts (Shannon indices 1.32-4.60). Its black variety scales were dominated by Campylobacterota (67.01-80.98%), such as Sulfurovum, which perform sulfur/hydrogen oxidation via the reductive tricarboxylic acid cycle, with both Campylobacterota and Gammaproteobacteria prevalent in the glands. The white-scaled variety of C. squamiferum had less Campylobacterota but a higher diversity of heterotrophic bacteria, including Delta-/Alpha-Proteobacteria, Bacteroidetes, and Firmicutes (classified as Desulfobacterota, Pseudomomonadota, Bacteroidota, and Bacillota in GTDB taxonomy). In C. squamiferum, Gammaproteobacteria, including Chromatiales, Thiotrichales, and a novel order "Endothiobacterales," were chemosynthetic, capable of oxidizing sulfur, hydrogen, or iron, and utilizing the Calvin-Benson-Bassham cycle for carbon fixation. Heterotrophic Delta- and Alpha-Proteobacteria, Bacteroidetes, and Firmicutes potentially utilize organic matter from protein, starch, collagen, amino acids, thereby contributing to the holobiont community and host nutrition accessibility. The results indicate that host species and intra-species variation, rather than the immediate habitat, might shape the symbiotic microbial communities, crucial for the snails' adaptation to vent ecosystems.},
}

@article {pmid40905761,
year = {2025},
author = {Abbasi, E},
title = {Forensic Entomology in Criminal Investigations: Advances in Insect-Mediated Postmortem Interval Estimation, Species Identification, and Environmental Influences.},
journal = {The American journal of forensic medicine and pathology},
volume = {},
number = {},
pages = {},
doi = {10.1097/PAF.0000000000001067},
pmid = {40905761},
issn = {1533-404X},
abstract = {Forensic entomology is a crucial discipline in forensic investigations, primarily used for postmortem interval (PMI) estimation, species identification, and crime scene reconstruction. Recent advancements in molecular techniques, computational models, and climate-adaptive forensic entomology have enhanced the field's forensic applications. However, challenges related to methodological standardization, environmental variability, and legal admissibility persist. This comprehensive review examines recent developments in forensic entomology, focusing on molecular methodologies, AI-assisted species identification, and environmental influences on forensic insect succession. Literature was sourced from Scopus, Web of Science, and PubMed, emphasizing peer-reviewed studies published in the last 2 decades. Key themes include PMI estimation advancements, forensic insect ecology, and legal challenges in forensic entomology. Findings highlight improved accuracy in PMI estimation through genetic and computational approaches, the expansion of forensic molecular entomology applications, and the impact of climate change on forensic insect activity. While AI and molecular forensics have revolutionized species identification, standardization and legal frameworks remain insufficient. The study underscores the need for globally harmonized forensic entomology protocols, forensic training programs, and ethical guidelines. Future research should integrate metagenomics, forensic AI, and climate-adaptive forensic models to enhance forensic accuracy and reliability.},
}

@article {pmid40905099,
year = {2025},
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 = {},
number = {},
pages = {},
doi = {10.3324/haematol.2025.288279},
pmid = {40905099},
issn = {1592-8721},
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, two 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 {pmid40904740,
year = {2025},
author = {Sapthanakorn, T and Choopong, P and Sermsripong, W and Boriboonhirunsarn, C and Khamwachirapitak, C and Krasaesin, A and Sutthiboonyaphan, P and Siripaiboonpong, N and Mahanonda, R and Wiriyakijja, P and Pelekos, G and Porntaveetus, T and Srithanyarat, SS},
title = {Functional and taxonomic dysbiosis of the supragingival plaque metagenome in Behçet's disease.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2552165},
pmid = {40904740},
issn = {2000-2297},
abstract = {BACKGROUND: Behçet's Disease (BD), a complex autoinflammatory disorder, is increasingly linked to microbial dysbiosis, yet the specific microbial signatures and their functional consequences remain incompletely characterized. Elucidating these alterations is crucial for understanding BD pathogenesis.

OBJECTIVE: To identify distinct microbial community structures and functional potentials in supragingival plaque microbiomes of BD patients versus healthy controls (HC) using high-resolution shotgun metagenomic sequencing.

METHODS: Supragingival plaque from 18 BD patients and 22 HCs was subjected to shotgun metagenomics. Analyses included alpha/beta diversity, taxonomic composition, and MetaCyc pathway abundance, with statistical comparisons.

RESULTS: Despite similar age and clinical attachment levels, BD patients exhibited significantly increased alpha diversity and distinct beta diversity compared to HCs. Differential abundance analysis revealed an enrichment of anaerobic and opportunistic taxa in BD (implicating 4 phyla and 28 genera), alongside 19 significantly altered MetaCyc pathways, indicating substantial functional reprogramming within the BD oral microbiome.

CONCLUSION: This high-resolution metagenomic analysis reveals profound oral microbiome dysbiosis in Behçet's Disease, characterized by altered diversity, a distinct taxonomic signature enriched with pathobionts, and significant functional shifts. These comprehensive microbial alterations are implicated in contributing to the local and systemic inflammatory processes driving BD pathogenesis, offering potential avenues for diagnostic biomarkers and targeted therapies.},
}

@article {pmid40904363,
year = {2025},
author = {Zeng, W and Feng, X and Liang, B and Ou, X},
title = {Good syndrome presenting with multiple pulmonary infections: a case report involving metagenomic sequencing diagnosis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1649584},
pmid = {40904363},
issn = {2296-858X},
abstract = {Good syndrome (GS), alternatively termed thymoma with immunodeficiency, is a rare adult-onset immunodeficiency disorder characterized by concurrent thymoma and hypogammaglobulinemia, accompanied by defects in both B-cell-mediated immunity and T-cell-mediated immunity. Owing to the non-specific clinical presentation, diagnosis is frequently delayed, resulting in poor prognosis and elevated mortality. In this study, we report the case of a 69-year-old man with GS who presented with symptoms of recurrent cough and productive sputum. Metagenomic next-generation sequencing (mNGS) of oropharyngeal swabs detected multiple microorganisms, including SARS-CoV-2 (35,047 reads), Epstein-Barr virus (7,236 reads), Micromonas pusilla (3,674 reads), Bacillus spp. (3,284 reads), cytomegalovirus (1,203 reads), and herpes simplex virus type 1 (575 reads). Following a comprehensive clinical evaluation-including recurrent pulmonary infections, history of thymoma, and lymphopenia with immunodeficiency-the diagnosis of GS was confirmed. This patient received an intensified anti-infective regimen, with broad-spectrum carbapenem, meropenem, as the backbone therapy, combined with antifungal agents and antiviral treatment (IV ganciclovir and oral molnupiravir). After aggressive anti-infection therapy, the patient experienced clinical improvement, and chest CT demonstrated significant radiographic improvement. Although intravenous immunoglobulin (IVIG) is foundational in GS, intensive antimicrobial therapy is also critical for clinical outcomes.},
}

@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 Apārangi)/ ; //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'.},
}

*Bacteriophages/physiology
*Bacteria/virology/immunology
*Microbiota
*Metagenome
*Virome

@article {pmid40903950,
year = {2025},
author = {Liu, Y and Tang, T and Cai, H and Liu, Z},
title = {Bidirectional communication between the gut microbiota and the central nervous system.},
journal = {Neural regeneration research},
volume = {},
number = {},
pages = {},
doi = {10.4103/NRR.NRR-D-25-00434},
pmid = {40903950},
issn = {1673-5374},
abstract = {In recent years, an increasing number of researchers have become interested in the bidirectional communication between the gut microbiota and the central nervous system. This communication occurs through the microbiota-gut-brain axis. As people age, the composition of the gut microbiota undergoes considerable changes, which are now known to play an important role in the development of many neurodegenerative diseases. This review aims to investigate the complex bidirectional signaling pathways between the gut and the brain. It summarizes the latest research findings on how the gut microbiota and its metabolites play critical roles in regulating inflammation, maintaining gut health, and influencing the development of neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. The review also analyzes the current clinical applications of gut microbiota-based treatments for neurological disorders, including fecal microbiota transplantation, probiotics, and prebiotics. Many studies show that the gut microbiota affects the brain in several ways. For example, it can produce substances such as short-chain fatty acids and activate inflammatory pathways. Studies involving animals and laboratory models have demonstrated that adjusting the gut microbiota can help improve behavior and reduce neurological problems. Recent metagenomic and metabolomics studies have shown that the microbiota plays a crucial role in maintaining the organism's health. Microorganisms primarily colonize the gut and are involved in host nutrient metabolism, maintaining the structural integrity of the intestine, preserving the intestinal mucosal barrier, and modulating the immune system. The gut microbiota communicates with the brain through a bidirectional microbiota-gut-brain axis. The composition of the gut flora changes considerably with age, and ecological dysregulation has been recognized as one of the twelve most recent hallmarks of aging. Recent studies have linked these changes to a variety of age-related neurological disorders, including Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease, multiple sclerosis, and Huntington's disease. Specifically, the gut microbiota influences the brain through the production of key metabolites such as short-chain fatty acids and the activation of inflammatory and other relevant signaling pathways. In preclinical studies, targeted modulation of the gut microbiota, through methods such as fecal microbiota transplantation, probiotics, and prebiotics, has demonstrated potential in improving host behavioral outcomes. Therefore, gut microbiotabased treatments offer new hope for the treatment of nervous system diseases. However, due to the complexity of the gut microbiota and the potential adverse reactions associated with these therapies, researchers need to carefully assess their safety and efficacy before widespread clinical application.},
}

@article {pmid40903035,
year = {2025},
author = {Hou, Y and Wu, H and Zhang, Z and Wang, J and Chen, Q and Lian, C and He, D and Li, Z and Wei, W and Lin, X and Sun, D and Cao, B and Xu, T and Cai, M and Wang, G and Zhang, X and Duan, L and Hao, H and Zheng, X},
title = {Bacteroides intestinalis mediates the sensitivity to irinotecan toxicity via tryptophan catabolites.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-334699},
pmid = {40903035},
issn = {1468-3288},
abstract = {BACKGROUND: Late-onset diarrhoea remains a poorly managed concern for clinical irinotecan therapy. Although bacterial β-glucuronidases (β-GUS) mediated SN-38 production is prevailingly thought to mediate intestinal toxicity, β-GUS inhibitors confer limited benefits in the clinic.

OBJECTIVE: This study aimed to explore the role and mechanism of endogenous bacterial metabolites in susceptibility to irinotecan toxicity.

DESIGN: Gut microbiota profiles and metabolites in patients with colorectal cancer (CRC) with or without diarrhoea were investigated via 16S rRNA sequencing, shotgun metagenomics and metabolomics. The role of microbial metabolites was investigated in mice by metabolic bioengineering and intestinal organoid culture. The mechanism of microbial metabolites on intestinal stem cells was investigated by transcriptional profiling and chemical intervention.

RESULTS: Gut microbial configuration was differentially remodelled in diarrhoea and non-diarrhoea patients with irinotecan therapy, and the susceptibility was transmissible to recipient mice via transplantation of baseline faecal microbiome. Bacteroides intestinalis (B. intestinalis) was notably expanded in the diarrhoea-prone cohorts as well as in irinotecan-treated mice. B. intestinalis colonisation sensitised intestinal epithelia to irinotecan-induced chemical injury, partially via tryptophan metabolite indole-3-acetate (IAA). Both B. intestinalis and bioengineered bacteria that produce IAA exacerbated irinotecan-induced intestinal epithelial injury in mice. Mechanistically, IAA suppressed PI3K-Akt signalling, thereby impairing the renewal of intestinal epithelia under the insult of irinotecan. In clinical patients receiving irinotecan therapy, faecal IAA level was closely associated with the diarrhoea severity.

CONCLUSION: Our study uncovers the mechanism of endogenous bacterial metabolite in shaping the individual susceptibility to irinotecan toxicity and suggests IAA as a potential predictive biomarker.},
}

@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 US adults.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.08.027},
pmid = {40902732},
issn = {1541-6100},
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.

OBJECTIVE: 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.

METHODS: We analyzed dietary data, GI inflammation and CAZyme profiles from shotgun metagenomes of fecal samples in the USDA Nutritional Phenotyping Study cohort of healthy US adults (n=330).

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 BMI (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). ML classification models were used to identify specific foods (e.g. potatoes) and microbes (e.g. Lachnospiraceae) as predictors of low Muc2Plant.

CONCLUSION: 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.

CLINICAL TRIALS REGISTRY: NCT02367287, ClinicalTrials.gov.},
}

@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 = {},
number = {},
pages = {100983},
doi = {10.1016/j.xgen.2025.100983},
pmid = {40902606},
issn = {2666-979X},
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 = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.08.003},
pmid = {40902595},
issn = {1097-4172},
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 {pmid40902558,
year = {2025},
author = {Chen, A and Li, J and Yao, A and Du, G and Li, J and Chen, J},
title = {Advancing kombucha fermentation: Microbial interactions, functional metabolites, and innovative optimization strategies.},
journal = {Food chemistry},
volume = {494},
number = {},
pages = {146121},
doi = {10.1016/j.foodchem.2025.146121},
pmid = {40902558},
issn = {1873-7072},
abstract = {Kombucha is a fermented tea beverage that has attracted increasing attention due to its diverse microbial ecosystem and potential health benefits. This review presents a comprehensive and innovative perspective on kombucha fermentation by integrating recent advances in microbial interactions, functional metabolite production, and emerging biotechnological approaches. The synergistic roles of bacteria and yeasts in shaping its physicochemical and bioactive properties are explored, with a focus on how multi-omics techniques, including metagenomics and metabolomics, are redefining microbial dynamics. Additionally, advancements in precision fermentation, engineered microbial consortia, and AI-assisted fermentation optimization offer novel insights into improving product consistency, metabolic efficiency, and functional enhancement. By bridging traditional fermentation knowledge with modern biotechnological innovations, this review establishes a foundation for future research and industrial applications, positioning kombucha as a highly customizable functional beverage.},
}

@article {pmid40902385,
year = {2025},
author = {Zhang, C and Zhang, Z and Zhang, S and Chen, Y and Li, D and Li, Y},
title = {Methionine-based insights into C-S-Fe-P transformations in anaerobic co-digestion of sludge containing iron-phosphorus compounds.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124458},
doi = {10.1016/j.watres.2025.124458},
pmid = {40902385},
issn = {1879-2448},
abstract = {Anaerobic co-digestion of sulfur-containing organic wastes with waste-activated sludge containing iron-phosphorus compounds (FePs) was recently suggested as an environment-friendly strategy to promote phosphate release, energy recovery, and hydrogen sulfide (H2S) control. Nevertheless, the mechanistic coupling between FePs speciation and the concurrent transformation of carbon, sulfur, iron, and phosphorus within this system remains to be fully elucidated. To address this knowledge gap, methionine, a typical hydrolysis product of sulfur-containing organics, and five FePs prevalent in sludge (ferric-phosphate tetrahydrate (FePO4⋅4H2O), ferric-phosphate dihydrate (FePO4⋅2H2O), vivianite (Fe3(PO4)2·8H2O), phosphate coprecipitated with Fe(III) (COP-P), and phosphate adsorption on hydrous ferric oxide (HFO-P)) were selected to elucidate C-S-Fe-P transformations in this study. The results showed that the H2S and methyl mercaptan productions decreased by >96 % and >99 %, respectively, while the methane production rate increased by 51.60-103.9 % in the presence of FePs. The reaction between FePs and sulfide promoted the transformation of gaseous H2S and aqueous S[2-] to solid sulfur species (elemental sulfur and iron sulfide precipitates), while simultaneously promoting the release of PO4[3-] from FePs. The formation of Fe(II) species derived from both abiotic sulfide-driven reduction and microbial-mediated iron reduction processes. The reduction rates of FePO4⋅2H2O and FePO4⋅4H2O were higher than those of COP-P and HFO-P, owing to their higher thermodynamic favorability. A negative correlation was observed between the Fe/P molar ratio and PO4[3-] release efficiency. FePO4 (FePO4⋅2H2O and FePO4⋅4H2O) with the lowest Fe/P molar ratio achieved the highest P release efficiency (89.83-91.01 %). Metagenomics analysis revealed that the SELENBP1 gene related to the degradation of methanethiol to sulfide was upregulated by 21.12-51.72 % in the presence of FePs, and the genes involved in propionate metabolism, methylotrophic, and hydrogenotrophic methanogenesis were up-regulated concurrently. This study provides an in-depth understanding of C-S-Fe-P interactions and transformations during the anaerobic co-digestion of sulfur-containing organic wastes with FePs-containing sludge, helping to enhance methane production and the recovery of phosphorus and sulfur.},
}

@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},
doi = {10.1016/j.psj.2025.105757},
pmid = {40902348},
issn = {1525-3171},
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 = {},
doi = {10.1093/nar/gkaf836},
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.},
}

*Metagenomics/methods
Metagenome
Molecular Sequence Annotation
*Enzymes/genetics/metabolism
Microbiota/genetics
Software
Sequence Analysis, DNA/methods

@article {pmid40901934,
year = {2025},
author = {Witsø, IL and Baral, A and Llarena, AK and Aspholm, M and Myrmel, M and Wasteson, Y},
title = {Plastispheres as reservoirs of antimicrobial resistance: Insights from metagenomic analyses across aquatic environments.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0330754},
doi = {10.1371/journal.pone.0330754},
pmid = {40901934},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; *Bacteria/genetics/drug effects ; Wastewater/microbiology ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Humans ; Metagenome ; Water Microbiology ; Fresh Water/microbiology ; Drug Resistance, Microbial/genetics ; },
abstract = {Evidence suggests that plastic particles from various environments can accumulate harmful microorganisms and carry bacteria with antimicrobial resistance genes (ARGs). The so-called "plastisphere" might facilitate the spread of pathogens and antimicrobial resistance across environments, posing risks to human and animal health. This study aimed to analyze the diversity and abundance of ARGs found in plastispheres from various aquatic environments, identify clinically relevant pathogenic species, and ascertain bacterial hosts carrying ARGs. We present data from 36 metagenomes collected from plastispheres in different environments (freshwater, raw wastewater, and treated wastewater). The diversity and abundance of ARGs in the resistome of the plastispheres were analyzed through metagenomic methods. A total of 537 high-quality metagenomic-assembled genomes (MAGs) were constructed to identify clinically relevant pathogens and to link the detected ARGs to their bacterial hosts. The results show that the environment has the greatest influence on the abundance and diversity of ARGs in the plastispheres resistome, with the wastewater plastisphere containing a resistome with the highest diversity of ARGs. Resistance to beta-lactams, aminoglycosides, and tetracyclines were the most abundant resistance mechanisms detected in the different plastispheres. The construction of MAGs identified potential pathogens and environmental bacteria that confer resistance to one or several drug classes, with beta-lactams being the most pervasive form of AMR detected. This work enhances our understanding of the plastisphere's role in antimicrobial resistance dissemination and its ecological and public health risks.},
}

*Metagenomics/methods
*Bacteria/genetics/drug effects
Wastewater/microbiology
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Humans
Metagenome
Water Microbiology
Fresh Water/microbiology
Drug Resistance, Microbial/genetics

@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},
doi = {10.1073/pnas.2507323122},
pmid = {40901884},
issn = {1091-6490},
support = {R35 GM147018/GM/NIGMS NIH HHS/United States ; 2339190//National Science Foundation (NSF)/ ; LS-ECIAMEE-00006628//Simons Foundation (SF)/ ; T32 AI055434/AI/NIAID NIH HHS/United States ; },
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.},
}

*Methane/metabolism
*Iron/metabolism
*Metabolomics/methods
Oxidation-Reduction
Isotope Labeling/methods
*Microbiota
*Bacteria/metabolism/genetics
Siderophores/metabolism
Multigene Family

@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},
doi = {10.1371/journal.pone.0331552},
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.},
}

Animals
Colombia
*Virome/genetics
*Culicidae/virology
*Metagenomics/methods
*Metagenome
Phylogeny
*Insect Viruses/genetics/classification

@article {pmid40901820,
year = {2025},
author = {Ergunay, K and Golubiani, G and Kirkitadze, G and Reinbold-Wasson, DD and Bourke, BP and Phelps, CA and Kotorashvili, A and Kotaria, N and Hulseberg, CE and Chunashvili, T and Sydenstricker, A and Shubashishvili, A and Musich, TA and Linton, YM},
title = {Ongoing circulation of emerging tick-borne viruses in Poland, Eastern Europe.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0330544},
doi = {10.1371/journal.pone.0330544},
pmid = {40901820},
issn = {1932-6203},
mesh = {Poland/epidemiology ; Animals ; Phylogeny ; Genome, Viral ; *Tick-Borne Diseases/virology/epidemiology ; *Ixodes/virology ; *Dermacentor/virology ; Humans ; Europe, Eastern/epidemiology ; },
abstract = {In order to investigate previously reported expansion of tick-borne pathogenic viruses in Eastern Europe, we conducted this study using pooled ticks collected from various locations in Poland, utilizing Sequence Independent Single Primer Amplification (SISPA) and metagenomic sequencing. We processed 575 Dermacentor reticulatus and Ixodes ricinus ticks and generated 280 virus assemblies in 20 pools. Viruses representing 28 species or strains classified in 12 families or higher taxonomic ranks were observed. We identified four tick-borne human pathogens including Alongshan virus (ALSV), Tacheng tick virus 1 (TcTV-1), Tacheng tick virus 2 (TcTV-2) and Nuomin virus (NUMV), in 55% of the pools, comprising 19.2% of the assemblies. We detected ALSV in I. ricinus ticks, with virus genome segments in complete or near-complete forms, comprising the initial reporting of ALSV from Poland. Further analyses revealed phylogenomic clustering with ALSV strains from Europe and lack of recombination signals among virus genomes. TcTV-1 was detected in 35% of the pools comprising D. reticulatus and I. ricinus ticks, implicating I. ricinus in TcTV-1 transmission for the first time. Maximum likelihood analyses on TcTV-1 and TcTV-2 genome segments indicated separate clustering patterns suggesting geographically-segregated clades. Evidence for NUMV or a closely-related chuvirus in I. ricinus ticks was further noted. In conclusion, we identified persistence of previously-documented tick-borne pathogens in Poland as well as additional viruses such as ALSV. Assessment of temporal and spatial patterns for virus circulation and diagnostic assays for these agents is needed. The distribution and public health impact of these pathogens throughout Europe require further investigation.},
}

Poland/epidemiology
Animals
Phylogeny
Genome, Viral
*Tick-Borne Diseases/virology/epidemiology
*Ixodes/virology
*Dermacentor/virology
Humans
Europe, Eastern/epidemiology

@article {pmid40901081,
year = {2025},
author = {Dong, W and Peng, Y and Ma, J and Hu, Y and Chen, S and Zhao, S},
title = {Yeasts in traditional Baijiu fermentation: diversity, functions, microbial interactions and applications.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1652173},
doi = {10.3389/fmicb.2025.1652173},
pmid = {40901081},
issn = {1664-302X},
abstract = {Baijiu is a traditional distilled liquor unique to China. Its distinctive flavor is shaped by the synergistic activity of complex microbial communities, among which yeasts play a central role in sugar metabolism, ethanol fermentation, and aroma synthesis. In recent years, the advancement of isolation and cultivation techniques, high-throughput sequencing, metagenomics, and multi-omics technologies has deepened our understanding of yeast community compositions, succession patterns, and functional characteristics during Baijiu brewing. Among these, Saccharomyces cerevisiae was recognized as the core ethanol-producing species and has been extensively studied for its metabolic traits and stress tolerance in Baijiu fermentation. Studies have shown that, in addition to S. cerevisiae, non-Saccharomyces yeasts such as Pichia, Wickerhamomyces, Saccharomycopsis, Kazachstania, and Candida et al. are widely distributed across strong-, sauce-, and light-flavor Baijiu and their respective starters (Daqu), exhibiting robust ester-producing capacities and stress resistance. These yeasts occupy distinct ecological niches throughout fermentation stages and engage in dynamic and environment-dependent interactions with lactic acid bacteria, molds, and other microbes. This review systematically summarizes yeast diversity, community structure, metabolic traits, key functional genes, microecological interactions, recent discoveries of novel yeast species, and advances in genetic engineering in Baijiu brewing. It further highlights future research priorities, including multi-omics integration, functional exploration of non-Saccharomyces yeasts, and synthetic biology-guided strain development, with the goal of supporting high-quality and intelligent Baijiu production.},
}

@article {pmid40901069,
year = {2025},
author = {Xu, C and Lin, R and Bai, Y and Han, Y and Hu, J and Hu, J and Hu, Y and Huang, F and Huang, X and Ji, C and Li, X and Liang, A and Lu, P and Ma, J and Mei, H and Niu, T and Ouyang, J and Qian, W and Shi, J and Song, Y and Sun, A and Tan, Y and Wang, H and Wang, J and Wang, Y and Wu, D and Xiao, Z and Yang, T and Zhang, C and Zhang, X and Zhang, X and Zhao, W and Zheng, Z and Zhu, Z and Feng, S and Liu, Q},
title = {China Expert consensus on the application of metagenomic next-generation sequencing for the etiological diagnosis of infections in hematological disorders (2024).},
journal = {Blood science (Baltimore, Md.)},
volume = {7},
number = {3},
pages = {e00241},
doi = {10.1097/BS9.0000000000000241},
pmid = {40901069},
issn = {2543-6368},
abstract = {Infections are frequent complications in patients with hematological disorders, and pathogen diagnosis remains challenging. Metagenomic next-generation sequencing (mNGS) is an unbiased high-throughput technology that has been widely applied in the diagnosis of infectious diseases. However, to date, there are no established international guidelines or expert consensuses regarding the use of mNGS to diagnose infections in patients with hematologic disorders. The Anti-Infection Study Group of the Chinese Society of Hematology invited experts in the fields of hematology, microbiology, and mNGS technology to draft an expert consensus focused on clinical indications, sample collection, quality control, and interpretation of results. This consensus will likely contribute to clarifying the medical indications for mNGS testing, optimizing the interpretation of reports, and becoming an inspiration for global practice.},
}

@article {pmid40901009,
year = {2025},
author = {Shao, M and Ni, L and Jiang, L and Hou, J and Xu, S and Lin, Y and Xie, X},
title = {A Case Report of Refractory Mycobacterium wolinskyi Knee Infection in a Metabolic Syndrome Patient: mNGS Diagnosis and Pharmacist-Guided Therapy.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4427-4434},
doi = {10.2147/IDR.S542439},
pmid = {40901009},
issn = {1178-6973},
abstract = {Mycobacterium wolinskyi (M. wolinskyi), which is a rare rapidly growing mycobacterium (RGM), and the infections it causes are predominantly linked to surgery or invasive procedures. We detailed a case of refractory surgical site infection (SSI) caused by M. wolinskyi. The causative pathogen was identified by metagenomic next-generation sequencing (mNGS) analysis, 16S rRNA and rpoB gene sequencing. What renders this case particularly remarkable is the complexity introduced by a series of antibiotic-induced adverse effects, which seem to be deeply intertwined with the patient's underlying metabolic syndrome. With the meticulous pharmaceutical guidance provided by the clinical pharmacist, the patient experienced a substantial improvement in his knee joint infection.},
}

@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},
doi = {10.3389/fcimb.2025.1642072},
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.},
}

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

@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 = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf177},
pmid = {40900671},
issn = {1536-4844},
support = {//Hospital Research Foundation/ ; //University of Adelaide/ ; },
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.

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.

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.

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 {pmid40900113,
year = {2025},
author = {Wendling, CC and Vasse, M and Wielgoss, S},
title = {Phage quest: a beginner's guide to explore viral diversity in the prokaryotic world.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {5},
pages = {},
pmid = {40900113},
issn = {1477-4054},
support = {PZ00P3_179743/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {*Bacteriophages/genetics/classification ; *Computational Biology/methods ; Metagenomics/methods ; *Prokaryotic Cells/virology ; Machine Learning ; *Bacteria/virology ; Genome, Viral ; },
abstract = {The increasing interest in finding new viruses within (meta)genomic datasets has fueled the development of computational tools for virus detection and characterization from environmental samples. One key driver is phage therapy, the treatment of drug-resistant bacteria with tailored bacteriophage cocktails. Yet, keeping up with the growing number of automated virus detection and analysis tools has become increasingly difficult. Both phage biologists with limited bioinformatics expertise and bioinformaticians with little background in virus biology will benefit from this guide. It focuses on navigating routine tasks and tools related to (pro)phage detection, gene annotation, taxonomic classification, and other downstream analyses. We give a brief historical overview of how detection methods evolved, starting with early sequence-composition assessments to today's powerful machine-learning and deep learning techniques, including emerging language models capable of mining large, fragmented, and compositionally diverse metagenomic datasets. We also discuss tools specifically aimed at detecting filamentous phages (Inoviridae), a challenge for most phage predictors. Rather than providing an exhaustive list, we emphasize actively maintained and state-of-the-art tools that are accessible via web or command-line interfaces. This guide provides basic concepts and useful details about automated phage analysis for researchers in different biological and medical disciplines, helping them choose and apply appropriate tools for their quest to explore the genetic diversity and biology of the smallest and most abundant replicators on Earth.},
}

*Bacteriophages/genetics/classification
*Computational Biology/methods
Metagenomics/methods
*Prokaryotic Cells/virology
Machine Learning
*Bacteria/virology
Genome, Viral

@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 & 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.},
}

Humans
*Feces/microbiology
*Gastrointestinal Microbiome
Fermentation
*Starch/metabolism
Bacteria/genetics/classification/isolation & purification/drug effects/metabolism
*Meat/analysis
Adult
Male
Female
*Resistant Starch
Drug Resistance, Bacterial/genetics
Middle Aged
Drug Resistance, Microbial
Meat Substitutes

@article {pmid40899150,
year = {2025},
author = {Ürel, H and Benassou, S and Marti, H and Reska, T and Sauerborn, E and Pinheiro Alves De Souza, Y and Perlas, A and Rayo, E and Biggel, M and Kesselheim, S and Borel, N and Martin, EJ and Venegas, CB and Schloter, M and Schröder, K and Mittelstrass, J and Prospero, S and Ferguson, JM and Urban, L},
title = {Nanopore- and AI-empowered microbial viability inference.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf100},
pmid = {40899150},
issn = {2047-217X},
support = {//Helmholtz Principal Investigator Grant/ ; HIDSS-006//Munich School for Data Science/ ; BB/M010996/1//BBSRC/ ; //STFC Food Network+ Scoping Grant/ ; //Helmholtz Association Initiative and Networking Fund/ ; 1336/2004//Vontobel-Stiftung/ ; //University of Zurich/ ; },
mesh = {*Microbial Viability ; *Nanopores ; *Artificial Intelligence ; *Nanopore Sequencing/methods ; Metagenomics/methods ; Escherichia coli/genetics ; Computational Biology/methods ; },
abstract = {BACKGROUND: The ability to differentiate between viable and dead microorganisms in metagenomic data is crucial for various microbial inferences, ranging from assessing ecosystem functions of environmental microbiomes to inferring the virulence of potential pathogens from metagenomic analysis. Established viability-resolved genomic approaches are labor-intensive as well as biased and lacking in sensitivity.

RESULTS: We here introduce a new fully computational framework that leverages nanopore sequencing technology to assess microbial viability directly from freely available nanopore signal data. Our approach utilizes deep neural networks to learn features from such raw nanopore signal data that can distinguish DNA from viable and dead microorganisms in a controlled experimental setting of UV-induced Escherichia cell death. The application of explainable artificial intelligence (AI) tools then allows us to pinpoint the signal patterns in the nanopore raw data that allow the model to make viability predictions at high accuracy. Using the model predictions as well as explainable AI, we show that our framework can be leveraged in a real-world application to estimate the viability of obligate intracellular Chlamydia, where traditional culture-based methods suffer from inherently high false-negative rates. This application shows that our viability model captures predictive patterns in the nanopore signal that can be utilized to predict viability across taxonomic boundaries. We finally show the limits of our model's generalizability through antibiotic exposure of a simple mock microbial community, where a new model specific to the killing method had to be trained to obtain accurate viability predictions.

CONCLUSIONS: While the potential of our computational framework's generalizability and applicability to metagenomic studies needs to be assessed in more detail, we here demonstrate for the first time the analysis of freely available nanopore signal data to infer the viability of microorganisms, with many potential applications in environmental, veterinary, and clinical settings.},
}

*Microbial Viability
*Nanopores
*Artificial Intelligence
*Nanopore Sequencing/methods
Metagenomics/methods
Escherichia coli/genetics
Computational Biology/methods

@article {pmid40898498,
year = {2025},
author = {Liu, Y and Yue, X and Zhou, Y and Wang, J and Yang, F and Jin, Y and Zhang, G},
title = {Recurrent breast abscess caused by Lawsonella clevelandensis: A case report and literature review.},
journal = {Medicine},
volume = {104},
number = {35},
pages = {e44218},
doi = {10.1097/MD.0000000000044218},
pmid = {40898498},
issn = {1536-5964},
support = {202501AY070001-203//Joint Special Fund for Basic Research of Yunnan Provincial Department of Science and Technology and Kunming Medical University/ ; },
mesh = {Humans ; Female ; Middle Aged ; *Abscess/microbiology/diagnosis/drug therapy/therapy ; Recurrence ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; *Breast Diseases/microbiology ; *Gram-Positive Bacterial Infections/microbiology/diagnosis/drug therapy ; },
abstract = {RATIONALE: Lawsonella clevelandensis is a gram-positive bacterium, partially acid-fast, strictly anaerobic, nonspore-forming, and catalase-positive. This microorganism was once overlooked in clinical microbiology due to its stringent growth requirements in laboratory cultures, but it has recently attracted recognition as a potential pathogen. Available reports implicate Lawsonella clevelandensis infection with abscess formation, including breast, spinal, abdominal, and deep soft tissue abscesses. Here, we present a case of recurrent breast abscess caused by Lawsonella clevelandensis infection.

PATIENT CONCERNS: A 46-year-old female patient had a history of left breast abscess for 6 years, with recurrent episodes and persistent symptoms.

DIAGNOSES: Three milliliters of pus obtained from abscess puncture were examined. The results were negative for tuberculosis, interferon-γ, the rifampicin resistance gene rpoB, and Mycobacterium tuberculosis complex. The Kingfield metagenomics capture (MetaCAP) test identified Lawsonella clevelandensis (sequence number 17,296) with a 99% confidence level and no detected resistance genes.

INTERVENTIONS: Following abscess puncture and irrigation under ultrasound guidance, intravenous infusion of "piperacillin-tazobactam (4.5 g q8h)" was administered for 16 days, resulting in an improvement in the patient's condition. Oral treatment with "amoxicillin-clavulanate 2.0 g bid and metronidazole 1.2 g tid" was continued after discharge.

OUTCOMES: One month after discharge, color Doppler ultrasound showed a significant reduction in the abscess size. At the 3-month telephone follow-up, the patient reported that she had not taken the medication for over a month and had experienced no symptoms of redness, swelling, or pain in the left breast.

LESSONS: The clinical manifestations of Lawsonella clevelandensis infection are similar to those of other acid-fast bacilli (e.g., Nocardia and Mycobacterium tuberculosis), potentially leading to misdiagnosis and mistreatment, thereby delaying resolution of the condition. The methods used for treating infections by bacterial pathogens differ significantly, as do the prognoses, indicating the importance of precise diagnosis. Lawsonella clevelandensis should be included in the differential diagnosis of infections caused by acid-fast bacteria. Due to the extreme difficulty in culturing this bacterium in vitro, gene sequencing is used primarily for diagnosis. Overall, the prognosis of patients with Lawsonella clevelandensis infection is good. Timely debridement and drainage, combined with antibiotic treatment, can usually lead to a cure.},
}

Humans
Female
Middle Aged
*Abscess/microbiology/diagnosis/drug therapy/therapy
Recurrence
Anti-Bacterial Agents/therapeutic use/administration & dosage
*Breast Diseases/microbiology
*Gram-Positive Bacterial Infections/microbiology/diagnosis/drug therapy

@article {pmid40897609,
year = {2025},
author = {Visioli, F and Urbistondo, DM and Gkipalis, S and Vidal-Ostos De Lara, F and Ruiz-Saavedra, A and Leon, M and Beddar Chaib, F and Hernández, AH and Landecho Acha, MF and Laparra, M and Vizmanos, B and Ramos-Lopez, O and Yannakoulia, M and Martínez, JA},
title = {Translational biomarkers for integrated cardiovascular disease risk assessment: A multidisciplinary review with applications in precision medicine.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {104215},
doi = {10.1016/j.numecd.2025.104215},
pmid = {40897609},
issn = {1590-3729},
abstract = {AIMS: Cardiovascular disease (CVD) continues to be a leading cause of morbidity and mortality, significantly impacting healthcare systems and individual lives. This pragmatic review focuses on the assessment of CVD utilizing traditional and emerging risk factors that provide a basis for personalized medicine and precision nutrition, highlighting the knowledge and application of these insights for accurate risk diagnosis, individualized interventions, and precise outcome/evaluation prognosis.

DATA SYNTHESIS: Critical biochemical markers such as lipid metabolism signatures, inflammatory molecules, endocrine mediators, homeostatic signals (including omics data), and lifestyle factors such as unhealthy dietary habits, physical inactivity, smoking, alcohol abuse, along with anthropometric variables and body composition measurements, play a pivotal role in assessing and managing CVD. This progression starts with early vascular and cardiac dysfunctions, advancing to atherosclerosis, and ultimately leading to cardiovascular events. Major adverse cardiovascular events, including myocardial infarction, stroke, and heart failure, highlight the need for effective and accurate risk stratification and objective assessment. Various CVD risk scores, such as the Framingham Risk Score, SCORE, and the Atherosclerotic Cardiovascular Disease Risk Calculator, provide valuable global frameworks for predicting individual risk based on recognized conventional factors. Additionally, omics markers-which encompass genomic, transcriptomic, epigenomic, proteomic, metabolomic, and metagenomic data-offer deeper insights into the molecular mechanisms underlying CVD, alongside novel lipidomic and immunomic determinants.

CONCLUSIONS: Integrating these various determinants and risk factors through a comprehensive approach is essential for advancing and implementing precision medicine and nutrition in the management of CVD.},
}

@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 = {},
number = {},
pages = {102325},
doi = {10.1016/j.xcrm.2025.102325},
pmid = {40897178},
issn = {2666-3791},
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},
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},
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 {pmid40896938,
year = {2025},
author = {Qiao, K and Wang, WX},
title = {Subtle biogeochemical consequences of biodegradable and conventional microplastics in estuarine blue carbon systems.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139705},
doi = {10.1016/j.jhazmat.2025.139705},
pmid = {40896938},
issn = {1873-3336},
abstract = {Blue carbon ecosystems act as critical sinks for microplastics (MPs), yet field-based evidence of their biogeochemical consequences remains scarce. In this study, we conducted in situ exposures of estuarine mangroves to environmentally relevant concentrations of polypropylene (PP) and polylactic acid (PLA) MPs for 30 and 100 days. Metagenomic analyses revealed stable microbial community composition across treatments. However, PLA exposure transiently induced significant functional disturbances in carbon, nitrogen, and phosphorus cycling processes. These responses also increased the sediment total organic carbon by 52.8 % and available phosphorus by 86.5 % under PLA exposure. Simultaneously, enhanced carbon decomposition and inhibited methane oxidation potentially exacerbate greenhouse gas emissions. PP amendments triggered no comparable functional shifts. Intriguingly, long-term exposure indicated microbial functional resilience and restored metabolic pathways, while PLA exposure remained associated with a 54.9 % increase in sediment available phosphorus. Two-dimensional diffusive gradients in thin films further suggested that PP may have restructured redox gradients, while PLA-driven acidification likely mobilized phosphorus, increasing labile phosphorus concentrations by 98.6 % and 64.4 %, respectively. These findings demonstrate that ostensibly low-impact MPs can subtly disrupt biogeochemical networks. Notably, biodegradable MPs pose unexpected long-term risks of phosphorus leakage, underscoring the need to consider conventional and biodegradable plastics in sustainable coastal ecosystem management.},
}

@article {pmid40896934,
year = {2025},
author = {Zhang, S and Chen, X and Gu, W and Fang, Y and Qu, Y and Bai, J and Xu, Y},
title = {Metagenomic and molecular simulation insights into plastic degradation: Microenvironmental matching and the key role of residue Phe392.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139706},
doi = {10.1016/j.jhazmat.2025.139706},
pmid = {40896934},
issn = {1873-3336},
abstract = {Due to their chemical inertness, polyethylene (PE) and polystyrene (PS) persistently accumulate in the environment. This study integrates metagenomics, degradation profiling, and molecular simulations to elucidate their divergent microbial degradation pathways. PE degradation was dominated by Burkholderia (97 %), with selective C-C bond cleavage causing a 29.8 % reduction in weight-average molecular weight (Mw) and a 35.46 % degradation rate. PS degradation relied on multispecies cooperation, primarily involving Acinetobacter (52 %), Bacillus (21 %), and Achromobacter (17 %), resulting in random main-chain cleavage, a 9.0 % reduction in number-average molecular weight (Mn), and an 18.63 % degradation rate. Molecular docking and dynamics simulations showed that PS-degrading enzymes exhibit higher binding affinity (-8.0 kcal/mol) via π-π stacking and cation-π interactions, outperforming the hydrophobic interaction-dominated PE-degrading enzymes (-5.4 kcal/mol). Residue Phe392 exhibited dual functionality in PS degradation for the first time. These findings reveal a divergence in microbial strategies: single-species dominance in PE degradation versus functional consortia for PS. The underlying mechanism is the structural compatibility between polymer substrates and enzyme active sites. This work provides a mechanistic framework for understanding microbial plastic degradation and offers insights for engineering microbial consortia and enzymes for efficient bioremediation of mixed plastic pollution.},
}

@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},
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 {pmid40896389,
year = {2025},
author = {Li, D and Liu, H and Wang, Y and Guo, W and Wen, H and Yang, J and Dai, Q and Jia, S and Zhang, J},
title = {A patient with severe fever with thrombocytopenia syndrome complicated with intracranial and pulmonary aspergillosis.},
journal = {IDCases},
volume = {41},
number = {},
pages = {e02347},
doi = {10.1016/j.idcr.2025.e02347},
pmid = {40896389},
issn = {2214-2509},
abstract = {Some patients with severe fever with thrombocytopenia syndrome (SFTS) develop complications including viral encephalitis and fungal infections, with a mortality rate reaching 44.7 %. In this case, the patient was admitted on Day 5 of illness, with symptoms of apathy and a delayed response. Computed tomography (CT) scans of the head and lungs revealed no abnormalities. After admission, the patient was diagnosed with SFTS. Following treatment, the patient's body temperature returned to normal, and laboratory tests revealed increased white blood cell and platelet counts and decreased myocardial enzymes. However, on Day 10 of illness, the patient experienced convulsions and somnolence. Enhanced brain magnetic resonance imaging (MRI) revealed multiple nodular abnormal signal shadows in the skull. Cerebrospinal fluid metagenomic sequencing revealed Aspergillus fumigatus infection. The patient also developed respiratory symptoms, and a chest CT revealed inflammatory changes. As the patient was suspected to have both intracranial and pulmonary Aspergillus infections, antifungal treatment was initiated. The patient's condition gradually improved with antifungal therapy, and the patient is currently receiving oral treatment with isavuconazole.},
}

@article {pmid40895792,
year = {2025},
author = {Yu, HL and Hou, XW and Zhao, JX and Liu, GH and Meng, JX and Wei, YJ and Cai, Y and Liu, J and Shang, KM and Ni, HB and Liu, R and Ma, H and Nan, FL and Zhang, XX and Chen, BN and Yang, X},
title = {Insights from metagenomics on microbial biosynthesis of vitamins B and K2 in chicken gut microbiota.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1646825},
doi = {10.3389/fvets.2025.1646825},
pmid = {40895792},
issn = {2297-1769},
abstract = {INTRODUCTION: The chicken gut microbiome plays a pivotal role in nutrient absorption and overall health, contributing to the biosynthesis of essential vitamins. However, the biosynthesis of vitamins B and K2 by the whole gut microbiome, as well as their abundances across different gut regions, remains largely unknown.

METHODS: We employed both metagenomic sequencing and culture-based techniques, collecting a total of 25,825 genomes (25,764 metagenome-assembled genomes and 61 isolated genomes). After quality assessment and average nucleotide identity (ANI), 13,734 genomes were retained for downstream analysis.

RESULTS: Whole-genome clustering analysis identified 2,675 species-level genome bins (SGBs), predominantly from the phyla Bacillota, Bacteroidota, Pseudomonadota, and Actinomycetota. A gene catalog comprising 9.69 million genes revealed that 195,517 genes are involved in the biosynthesis of vitamins B and K2, exhibiting significant regional variation. The large intestine exhibited greater species richness and evenness compared to the small intestine. From the 13,734 genomes, we discovered 3,063 high-quality ones capable of synthesizing at least one vitamin. Genomic analysis revealed that a mere 8.2% of genomes were capable of producing five or more vitamins, while almost half were limited to synthesizing just one. Comparative genomics of cobalamin (B12) biosynthesis highlighted the predominance of the anaerobic pathway. Additionally, changes in microbial abundance were observed, such as increased abundance of the genera Phocaeicola and Faecalibacterium during bacterial infections, and Limisoma during parasitic infections.

DISCUSSION: This study provides detailed metagenomic insights into the capacity of chicken gut microbiome for vitamins B and K2 biosynthesis, revealing significant regional and taxonomic variations. These results suggest a collaborative microbial effort in vitamin biosynthesis, with potential implications for optimizing poultry health and nutrition through targeted microbial interventions.},
}

@article {pmid40895484,
year = {2025},
author = {Liu, S and Chen, Y and Zhang, K and Tang, D and Zhang, J and Wang, Y and Zhao, J and Li, D and Wang, T},
title = {Exploring vaginal microbiome: from traditional methods to metagenomic next-generation sequencing-a systematic review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1578681},
doi = {10.3389/fmicb.2025.1578681},
pmid = {40895484},
issn = {1664-302X},
abstract = {Recent research has highlighted the vaginal microbiome as a crucial factor in women's health and fertility. The growing recognition of its significance has intensified the focus on studying the female reproductive tract's microbial ecosystem. While various analytical methods exist for examining the vaginal microbiome, metagenomic next-generation sequencing (mNGS) has emerged as an auspicious approach. This study examines how mNGS technology can be applied to analyze vaginal microbiota. We begin by exploring the relationship between vaginal bacterial communities and women's health, followed by a comparative analysis of metagenomics against other detection methods, highlighting their respective strengths and limitations. The paper systematically reviews different detection techniques, examining their fundamental principles, constraints, and advantages. Several factors can affect data quality, including sampling procedures, contamination issues, and PCR amplification errors. We suggest implementing third-generation sequencing (TGS) to address these challenges to enhance reproducibility and read length, utilizing single-molecule sequencing (SMS) to eliminate PCR amplification-related errors, and integrating multiple analytical approaches to provide comprehensive insights. In summary, mNGS technology allows us to collect valuable information at a lower cost, and it remains a leading method for detecting female reproductive tract microbes. The goal of this review is to describe the principle, benefits and drawbacks, and application areas of mNGS, as well as to serve as a reference for research into female reproductive tract microbial detection methods, promote the improvement of mNGS in the detection of female reproductive tract microbial technology, and ensure the health of the female reproductive tract.},
}

@article {pmid40895312,
year = {2025},
author = {Wang, G and Chen, W and Chen, X and Hou, H and Zhang, J and Han, Z},
title = {Detection of Ureaplasma parvum in amniotic fluids via reanalysis of prenatal copy number variation sequencing data: an exploratory study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1579049},
doi = {10.3389/fcimb.2025.1579049},
pmid = {40895312},
issn = {2235-2988},
abstract = {BACKGROUND: Detecting microbes in amniotic fluids via amniocentesis represents the standard method for diagnosing intrauterine infections. Given its similarity to metagenomic next-generation sequencing, copy number variation sequencing (CNV-seq) data may also contain microbial sequences. This exploratory study aimed to investigate the feasibility of prenatal CNV-seq for detecting Ureaplasma parvum (U. parvum) in amniotic fluids and to evaluate the pregnancy outcomes in U. parvum-positive cases.

METHODS: This retrospective study enrolled 2419 singleton pregnant women who underwent genetic amniocentesis for fetal CNV-seq testing and completed the follow-up with documented pregnancy outcomes. The CNV-seq data were reanalyzed to extract the read counts of U. parvum from each sample's raw data, and reads per million (RPM) was used to quantify its relative abundance.

RESULTS: The prevalence of asymptomatic intrauterine U. parvum positivity in this cohort was 1.4% (33/2419), with read counts ranging 1 to 30423 and RPM from 0.09 to 3580.65 by reanalysis of CNV-seq data. There was a statistically significantly higher risk for early spontaneous preterm labor (<32 gestational weeks; P<0.001) and preterm premature rupture of the membranes (P<0.001) in women with positive U. parvum compared to negative cases. Among U. parvum positive cases, six cases (6/33, 18.2%) had relatively higher read counts ranging from 2483 to 30423, with corresponding RPM of 406.45 to 3580.65. Adverse pregnancy outcomes were exclusively observed among women with high reads of U. parvum as opposed to those with low reads. Four cases with high U. parvum reads in amniotic fluids, not treated with antibiotics, showed a latency period of 6 to 10 weeks from positive detection to the onset of clinical manifestations.

CONCLUSIONS: CNV-seq may be a feasible method for detecting intraamniotic U. parvum infection. High abundance of asymptomatic U. parvum in amniotic fluids are statistically associated with adverse pregnancy outcomes, highlighting its importance in preliminary screening.},
}

@article {pmid40895097,
year = {2025},
author = {Jin, Y and Wang, H and Song, J},
title = {Gut-brain axis modulation in remote rehabilitation of Parkinson's disease: reconstructing the fecal metabolome and nigral network connectivity.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1644490},
doi = {10.3389/fneur.2025.1644490},
pmid = {40895097},
issn = {1664-2295},
abstract = {The pathogenesis of Parkinson's disease (PD) is gradually evolving from a central neurodegeneration-centered concept to a multi-pathway pathological model at the gut-brain system level. Studies have shown that PD patients commonly exhibit dysbiosis, reduced short-chain fatty acids (SCFAs; microbial fermentation products of dietary fiber that play key roles in host metabolism and immune regulation), abnormal tryptophan metabolism, and impaired gut barrier function. These alterations may contribute to dopaminergic neuronal damage through mechanisms including neuroinflammation, oxidative stress, and α-synuclein (α-syn) aggregation. The vagus nerve plays a critical role in bidirectional gut-brain signaling, and its dysfunction may represent a key route for pathological protein transmission from the periphery to the brain. In response, remote rehabilitation and gut-targeted interventions-including probiotics, prebiotics, dietary modulation, fecal microbiota transplantation (FMT), and transcutaneous vagus nerve stimulation (tVNS)-have shown potential in improving neurological function and inflammation in both animal and clinical studies. Multimodal data analyses have revealed significant associations between SCFA levels in fecal metabolomics and brain imaging features. Despite ongoing challenges in mechanistic extrapolation, biomarker sensitivity, and translational implementation, the integration of metagenomics, metabolomics, neuroimaging, and digital therapeutics-collectively referred to as multi-omics and digital profiling techniques-represents an emerging research direction with the potential to inform future clinical paradigms for precision remote management of PD.},
}

@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},
doi = {10.7717/peerj.19728},
pmid = {40895054},
issn = {2167-8359},
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 {pmid40894769,
year = {2025},
author = {Shih, J and Bloom, SM and Xu, J and Mitchell, CM and Elsherbini, J and Kwon, DS},
title = {StrainFacts accurately quantifies both endogenous and live biotherapeutic product strain abundances in simulated and clinical vaginal microbiota samples.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.15.670563},
pmid = {40894769},
issn = {2692-8205},
abstract = {Live biotherapeutic products (LBPs) deliver microbial strains to modulate the host microbiota in order to promote health or treat and prevent disease. Since endogenous strains are already present, accurately evaluating LBP efficacy and mechanism of action requires distinguishing administered from endogenous strains. Although computational tools exist for inferring strains from short-read metagenomic data, few have been rigorously tested in the context of LBP treatment. Here, we assess the ability of StrainFacts, a computational tool for inferring strains from short-read metagenomic data, to estimate strain abundances and genotypes of endogenous and administered strains. We performed a simulation study of a single-strain LBP trial, modeling serial samples across a range of administered strain abundance, co-occurring endogenous strains, and sequencing depths. We found that StrainFacts accurately estimated both LBP and endogenous strain abundances and genotypes within simulated samples. We further validated methods using human vaginal microbiota samples spiked with CTV-05, the Lactobacillus crispatus strain contained in the LBP LACTIN-V, which has been shown to reduce recurrent bacterial vaginosis. Our findings demonstrate that StrainFacts can robustly assess LBP and endogenous strain colonization, abundance, and dynamics in simulated and experimental microbiota samples, supporting its utility as an analysis tool for vaginal LBP therapeutic trial data.},
}

@article {pmid40894694,
year = {2025},
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 = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.13.638127},
pmid = {40894694},
issn = {2692-8205},
abstract = {UNLABELLED: 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.

SIGNIFICANCE STATEMENT: 3. When food becomes scarce during winter, hibernating mammals induce torpor to minimize energy demands and enable monthslong fasting. However, fasting eliminates the intake of essential nutrients such as carbon. We identified a two-step microbial-host interaction in ground squirrels - urea carbon salvage (UCS) - which counters carbon limitation by salvaging carbon from waste urea. Through activities of ureolytic and acetogenic bacteria, urea-derived CO 2 is reduced by free hydrogen to form acetate, whose oxidation provides energy for gut microbes and the host. This process also helps maintain a permissive environment for fermentation of other host-derived, energy-dense compounds such as mucins. UCS broadens our understanding of host-microbe mutualism under extreme nutritional constraints and may represent a widespread adaptation among fasting mammals.},
}

@article {pmid40894501,
year = {2025},
author = {Monteiro, E and Baptista, P and Silva, S and Carvalho, M and Bragança, R and Guinan, KJ and Sujeeth, N and Cortez, I and Gonçalves, B and Castro, I},
title = {Metagenomic analysis of the effects of plant- and yeast-based formulations on the grapevine leaf microbiome of cv. 'Touriga Franca'.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1637143},
doi = {10.3389/fpls.2025.1637143},
pmid = {40894501},
issn = {1664-462X},
abstract = {INTRODUCTION: Grapevine is highly susceptible to fungal diseases such as downy mildew and powdery mildew, which are traditionally managed through the intensive use of chemical fungicides. However, in the context of increasingly sustainable viticulture, biofungicides derived from plant and yeast extracts are gaining attention. Despite this, their impact on the grapevine leaf microbiome, crucial for plant health and disease resilience, remains underexplored.

MATERIAL AND METHODS: This study evaluated the effects of foliar applications of biofungicides (nettle extract, Japanese knotweed extract, and a yeast-based formulation - T66 and T90) in comparison with conventional chemical treatments and control (no treatment). Over two consecutive growing seasons, high-throughput sequencing was used to assess the diversity and composition of fungal and bacterial communities on grapevine leaves.

RESULTS: Bacterial communities were more sensitive to treatments and interannual variability than fungal communities, which remained relatively stable. Conventional treatment (CT) showed the highest influence on fungal and bacterial composition, reducing the diversity of both. Some important fungal (Aureobasidium and Sporobolomyces) and bacterial (Pseudomonas and Sphingomonas) genera associated with the promotion of plant growth, health, and biocontrol were detected.

DISCUSSION: These findings reinforce the potential of new treatments with putative fungicide effects to modulate the leaf microbiome, particularly bacterial communities, without disrupting the natural fungal balance. Thus highlight their relevance for developing sustainable viticultural practices aimed at improving plant protection.},
}

@article {pmid40894332,
year = {2025},
author = {Zhai, J and Choi, Y and Yang, X and Chen, Y and Knox, K and Twigg, HL and Won, JH and Zhou, H and Zhou, JJ},
title = {DeepBiome: A Phylogenetic Tree Informed Deep Neural Network for Microbiome Data Analysis.},
journal = {Statistics in biosciences},
volume = {17},
number = {1},
pages = {191-215},
doi = {10.1007/s12561-024-09434-9},
pmid = {40894332},
issn = {1867-1764},
abstract = {Evidence linking the microbiome to human health is rapidly growing. The microbiome profile has the potential as a novel predictive biomarker for many diseases. However, tables of bacterial counts are typically sparse, and bacteria are classified within a hierarchy of taxonomic levels, ranging from species to phylum. Existing tools focus on identifying microbiome associations at either the community level or a specific, pre-defined taxonomic level. Incorporating the evolutionary relationship between bacteria can enhance data interpretation. This approach allows for aggregating microbiome contributions, leading to more accurate and interpretable results. We present DeepBiome, a phylogeny-informed neural network architecture, to predict phenotypes from microbiome counts and uncover the microbiome-phenotype association network. It utilizes microbiome abundance as input and employs phylogenetic taxonomy to guide the neural network's architecture. Leveraging phylogenetic information, DeepBiome is applicable to both regression and reduces the need for extensive tuning of the deep learning architecture, minimizes overfitting, and, crucially, enables the visualization of the path from microbiome counts to disease. It classification problems. Simulation studies and real-life data analysis have shown that DeepBiome is both highly accurate and efficient. It offers deep insights into complex microbiome-phenotype associations, even with small to moderate training sample sizes. In practice, the specific taxonomic level at which microbiome clusters tag the association remains unknown. Therefore, the main advantage of the presented method over other analytical methods is that it offers an ecological and evolutionary understanding of host-microbe interactions, which is important for microbiome-based medicine. DeepBiome is implemented using Python packages Keras and TensorFlow. It is an open-source tool available at https://github.com/Young-won/DeepBiome.},
}

@article {pmid40894237,
year = {2025},
author = {Fissel, JA and Bergman, Y and Campodónico, VL and Walsh, DM and Fanelli, B and Arogyaswamy, K and Kwon, JH and Milstone, AM and Tamma, PD and Simner, PJ},
title = {Microbiome and resistome characterization of patients colonized with carbapenem-resistant Enterobacterales by long-read metagenomic next-generation sequencing of rectal swabs.},
journal = {JAC-antimicrobial resistance},
volume = {7},
number = {4},
pages = {dlaf152},
doi = {10.1093/jacamr/dlaf152},
pmid = {40894237},
issn = {2632-1823},
abstract = {OBJECTIVES: Evaluation of differences in the intestinal microbiome and resistome among high-risk patients (i.e. intensive care, oncology, transplant recipients) who are and are not colonized with carbapenem-resistant Enterobacterales (CRE).

METHODS: One hundred and twelve rectal swabs were obtained from 85 patients with known CRE colonization status and cohorted. Long-read metagenomic next-generation sequencing (mNGS) was performed on rectal swabs. Microbiome and resistome analysis were performed by assessing α-diversity, β-diversity, relative abundance assessment and linear discriminant analysis effect size (LEfSe), comparing patients colonized (CRE positive) and not colonized (CRE negative) with CRE. Longitudinal analysis of sequential swabs collected over multiple hospital encounters on a subset of patients was performed at the patient level.

RESULTS: The microbiomes of cohorts were similar when comparing α- and β-diversity measures and relative abundance. LEfSe analysis identified Gram-negative pathobionts enriched among CRE-positive samples and Gram-positive taxa enriched among CRE-negative samples. α-Diversity of the resistome differed at class, gene and allele levels. Relative abundance and LEfSe analysis demonstrated enrichment of genes conferring β-lactam resistance among CRE-positive patients; LEfSe also demonstrated enrichment of antimicrobial resistance genes to multiple antimicrobial classes. At the patient level, fluctuations in the microbiome and resistome among longitudinally collected swabs were associated with antibiotic exposure.

CONCLUSIONS: Differences between the microbiomes of CRE-positive- and CRE-negative-colonized patients at the cohort level were relatively muted, whereas statistically significant differences were observed among their resistomes. In patients followed longitudinally, shifts in microbiome and resistome composition were dramatic in between encounters and antibiotic exposures.},
}

@article {pmid40894205,
year = {2025},
author = {Narsing Rao, MP and Quadri, SR and Sathish, M and Quach, NT and Li, WJ and Thamchaipenet, A},
title = {Exploring omics strategies for drug discovery from Actinomycetota isolated from the marine ecosystem.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1634207},
doi = {10.3389/fphar.2025.1634207},
pmid = {40894205},
issn = {1663-9812},
abstract = {Marine Actinomycetota are prolific producers of diverse bioactive secondary metabolites, making them vital for drug discovery. Traditional cultivation and bioassay-guided isolation techniques often lead to the rediscovery of the same compounds, revealing the limitations of these traditional approaches and emphasizing the need for more advanced methods. The emergence of omics technologies such as genomics, metagenomics, transcriptomics, and metabolomics has dramatically enhanced the ability to investigate microorganisms by providing detailed insights into their biosynthetic gene clusters, metabolic pathways, and regulatory mechanisms. These comprehensive tools facilitate the discovery and functional analysis of new bioactive compounds by revealing the genetic blueprints underlying their biosynthesis. Omics and function-driven techniques like heterologous expression, analytical techniques (including high-resolution mass spectrometry and nuclear magnetic resonance spectroscopy), and culture condition optimization have enabled access to previously silent or cryptic gene clusters, expanding the chemical diversity available for exploration. This review emphasizes the integration of omics-based insights with function-driven methodologies and innovative culture techniques, forming a holistic approach to unlock the extensive biosynthetic capabilities of marine Actinomycetota. Combining these strategies holds great promise for discovering new marine-derived compounds with potential therapeutic applications.},
}

@article {pmid40894109,
year = {2025},
author = {Lopez, JV and Pomponi, SA and Hentschel, U and Erpenbeck, D and Pruzinsky, N and Fiore, C and Mulheron, R 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 giant barrel sponge, Xestospongia muta Schmidt 1870 and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {336},
doi = {10.12688/wellcomeopenres.24173.1},
pmid = {40894109},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Xestospongia muta (Caribbean barrel sponge; Porifera; Demospongiae; Haplosclerida; Petrosiidae). The genome sequence has a total length of 158.52 megabases. Most of the assembly (99.56%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.99 kilobases in length. Several symbiotic bacterial genomes were assembled as MAGs, including Candidatus Poribacteria species, Candidatus Latescibacteria, Acidobacteriota, Actinomycetota Gemmatimonadota, multiple Chloroflexota and the archaeon Nitrosopumilus. Gene annotation of this assembly on Ensembl identified 20,220 protein-coding genes.},
}

@article {pmid40894108,
year = {2025},
author = {de Goeij, JM and Mueller, B and Achlatis, M and Campana, S and Hudspith, M and Kornder, NA 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 scaffold-level genome sequence of an encrusting sponge, Halisarca caerulea Vacelet & Donadey, 1987, and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {344},
doi = {10.12688/wellcomeopenres.24281.1},
pmid = {40894108},
issn = {2398-502X},
abstract = {We present a scaffold-level genome assembly from a Halisarca caerulea specimen (encrusting sponge; Porifera; Demospongiae; Chondrillida; Halisarcidae). The genome sequence is 195.70 megabases in span. The mitochondrial genome has also been assembled and is 19.15 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,722 protein-coding genes. The metagenome of the specimen was also assembled and four binned bacterial genomes related to the relevant sponge symbiont clades Alphaproteobacteria bacterium GM7ARS4 and Gammaproteobacteria bacterium AqS2 ((Tethybacterales) were identified.},
}

@article {pmid40894065,
year = {2025},
author = {Chen, LX and Camargo, AP and Qin, Y and Wang, H and Zou, Y and Duan, Y and Li, H and Koonin, E},
title = {A prevalent huge phage clade in human and animal gut microbiomes.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7356405/v1},
pmid = {40894065},
issn = {2693-5015},
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 360-402 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 38-57% identity, suggesting horizontal acquisition from other phages. Over 1,500 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 {pmid40893472,
year = {2025},
author = {Xu, T and Huang, D and Huang, T and Wang, Y and Chen, W and Chen, S and Qian, Y and Yue, H},
title = {Gene Surfing: An efficient and versatile tool for targeted enzyme mining in metagenomics.},
journal = {Synthetic and systems biotechnology},
volume = {10},
number = {4},
pages = {1377-1387},
doi = {10.1016/j.synbio.2025.07.006},
pmid = {40893472},
issn = {2405-805X},
abstract = {Microbial community studies have established enzymes' pivotal catalytic roles in ecosystem metabolism, yet cultivation-dependent methods fail to exploit uncultured microbial enzyme resources. Metagenomics overcomes this by directly accessing microbial genetic information, but its massive data generation challenges precise enzyme identification: (1) Restricted applicability across varied sample types. (2) Narrow functional scope in target enzyme discovery. To address this, we developed Gene Surfing, a bioinformatics workflow platform based on Snakemake. It integrates modules for data quality control (Fastp), genome assembly (MEGAHIT), assembly evaluation (QUAST and MetaQUAST), functional annotation (Prokka), and homologous sequence retrieval (MMseqs2). Gene Surfing offers scalability, reproducibility, and efficiency, addressing key challenges in enzyme identification. Validation results include: Cellulose-degrading enzymes (GH5 family): 1,311,316 potential lignocellulolytic enzyme sequences were identified, with 127 sequences functionally validated (84.25 % activity rate); Polyethylene-degrading enzymes: 705 candidate sequences were found, 38 of which were heterologously expressed, showing an 81.5 % activity rate (31/38); Endonucleases (HNH superfamily): 585 potential sequences were retrieved, with 4 out of 7 tested showing activity (57.1 % success rate).},
}

@article {pmid40893417,
year = {2025},
author = {Liu, T and Zhang, C and Ming, M and Chen, L and Chen, W and Xu, Y and Shen, M and Liu, J and Ou, Q and Bao, H and Chen, X and Lu, G and Yan, G},
title = {A Case of Measles Virus-caused Subacute Sclerosing Panencephalitis Diagnosed by Molecular and Clinical Analysis.},
journal = {Open forum infectious diseases},
volume = {12},
number = {8},
pages = {ofaf453},
doi = {10.1093/ofid/ofaf453},
pmid = {40893417},
issn = {2328-8957},
abstract = {Subacute sclerosing panencephalitis (SSPE) is a rare and lethal neurodegenerative encephalitis caused by persistent measles virus infection. We report an SSPE case in a patient infected at 6 months old, diagnosed using clinical methods and metagenomic sequencing, highlighting the benefits of combining clinical and molecular techniques for improved diagnosis.},
}

@article {pmid40892879,
year = {2025},
author = {Liu, W and Xie, S and Zhu, G and Qin, S and Li, M and Yin, S and Lai, W and Lu, C and Chen, Q and Feng, P},
title = {Concurrent chromoblastomycosis and eumycetoma: a unique case of dual neglected tropical fungal diseases in Asia.},
journal = {PLoS neglected tropical diseases},
volume = {19},
number = {9},
pages = {e0013484},
doi = {10.1371/journal.pntd.0013484},
pmid = {40892879},
issn = {1935-2735},
abstract = {Chromoblastomycosis (CBM) and mycetoma, as implantation mycoses, have been listed as neglected tropical diseases (NTDs) by the World Health Organization. The concurrent occurrence of these two NTDs in a single patient is extremely rare. A 69-year-old female patient presented with papules on the dorsum of her left hand for over 5 months and nodules on the left lower limb accompanied by ulceration and pain for 20 days. Histopathological examination of the papule on the dorsum of the left hand revealed muriform cells and fungal culture of the tissue identified Fonsecaea monophora. Microscopic examination of the purulent secretion from the ulcer on the left lower calf revealed the presence of grains, and the tissue culture result was Scedosporium apiosperma complex, with metagenomic next-generation sequencing further identifying S. dehoogii as the predominant pathogen. The clinical diagnosis was CBM caused by F. monophora combined with eumycetoma due to S. dehoogii. The patient was treated with voriconazole at a dosage of 200 mg twice daily for 4 weeks, after which the papules on the dorsum of the left hand and the ulcer on the left lower calf showed gradual improvement. This case represents the first reported instance of concurrent CBM caused by F. monophora and eumycetoma due to S. dehoogii, providing a novel perspective on the clinical manifestations and early identification of neglected implantation mycoses.},
}

@article {pmid40892803,
year = {2025},
author = {Haugum, K and Ravi, A and Afset, JE and Ås, CG},
title = {Evaluation of shotgun metagenomics as a diagnostic tool for infectious gastroenteritis.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331288},
pmid = {40892803},
issn = {1932-6203},
mesh = {*Metagenomics/methods ; Humans ; *Gastroenteritis/diagnosis/microbiology ; Feces/microbiology ; Polymerase Chain Reaction ; Bacteria/genetics/isolation & purification ; },
abstract = {Infectious gastroenteritis is a significant health issue globally. Identifying the causative pathogen is crucial for treatment, infection control and epidemiological surveillance. While PCR-based analyses are fast and sensitive, they only detect known pathogens. Clinical metagenomics can potentially identify novel or unexpected pathogens. This study aimed to evaluate shotgun metagenomics for detecting diarrhoeal pathogens in faecal samples from patients with infectious gastroenteritis and spiked samples from healthy donors, compared to PCR. DNA from clinical faecal samples (n = 12), spiked samples (n = 36), and control samples (n = 7) were analysed by PCR and shotgun metagenomics sequencing. Reads were taxonomically assigned, assembled, and binned into MAGs. MAGs were taxonomically assigned, and virulence genes were detected in bacterial assemblies and MAGs. Pathogens detected by PCR were also identified by taxonomic assignment of reads, though with lower sensitivity. Taxonomic assignment of MAGs identified 50% of bacterial pathogens and HAdV-F. Additional potential pathogens were observed in most samples. More bacterial virulence genes were detected in assemblies than in MAGs. In spiked samples, C. jejuni and HAdV-F were detected by both PCR and metagenomics, with significant correlation between Cq values and reads. Parasites were detected by few reads. Metagenomics has lower sensitivity compared to PCR but can provide supplementary information relevant for treatment. Challenges include additional potential pathogens, background microbiome, and introduced kitome, necessitating optimized extraction methods and strict quality controls.},
}

*Metagenomics/methods
Humans
*Gastroenteritis/diagnosis/microbiology
Feces/microbiology
Polymerase Chain Reaction
Bacteria/genetics/isolation & purification

@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.

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.

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.

RESULTS: Seven key constituents, including quercetin and berberine, were quantified (15.11-164.37 μg/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 (PPARα), 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-1β, TNF-α) 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.

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 PPARα. 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.},
}

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

@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 & purification ; Carbon/metabolism ; Metagenomics/methods ; Gammaproteobacteria/metabolism/genetics/classification/isolation & 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.

RESULTS: Our results showed that the DCF rates ranged from 0.02 to 3.27 mmol C m[-2] 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 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.

CONCLUSIONS: Overall, this study provides new insights into the understanding of biological carbon fixation and its ecological functions in mangrove sediments. Video Abstract.},
}

*Geologic Sediments/microbiology
*Carbon Cycle
Wetlands
Phylogeny
China
*Bacteria/classification/metabolism/genetics/isolation & purification
Carbon/metabolism
Metagenomics/methods
Gammaproteobacteria/metabolism/genetics/classification/isolation & purification
Microbiota

@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.

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.

RESULTS: CeD-associated alterations were identified in the gut microbiome and metabolome. 15 differential bacterial strains (AUC = 0.85) and 8 differential metabolites (AUC = 0.9799) constructed a diagnostic panel that was effective in differentiating CeD patients from healthy subjects. Compared with non-CeD patients carrying HLA-DQ[±], the abundances of Agathobacter_rectalis, Bifidobacterium_pseudocatenulatum, Clostridia_bacterium, Coprococcus_comes, and Fusicatenibacter_saccharivorans in CeD patients were significantly lower (P < 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.

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.},
}

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

@article {pmid40890622,
year = {2025},
author = {Demiralay, B and Can, T},
title = {Effective primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {223},
pmid = {40890622},
issn = {1471-2105},
abstract = {Identification of microorganisms in a biological sample is a crucial step in diagnostics, pathogen screening, biomedical research, evolutionary studies, agriculture, and biological threat assessment. While progress has been made in studying larger organisms, there is a need for an efficient and scalable method that can handle thousands of whole genomes for organisms with high mutation rates and genetic diversity such as single stranded viruses. In this study, we developed a novel method to identify subsequences for detection of a given species/subspecies in a (meta)genomic sample using the Polymerase Chain Reaction (PCR) method. Species detection in any analysis depends highly on the measurement method and since thermodynamic interactions are critical in PCR, thermodynamics is the main driving force in the proposed methodology. Our method is parallelized in multiple steps and involves extracting all oligonucleotides from target genomes. We then locate the target sites for each oligonucleotide using the constructed suffix array and local alignment followed by thermodynamic interaction assessment. An important requirement for subspecies identification is to avoid amplifying a non-target set of genomes and our method addresses this. We applied our method to three highly divergent viruses; (1) Hepatitis C virus (HCV), where the subtypes differ in 31-33% of nucleotide sites on average, (2) Human immunodeficiency virus (HIV), for which, 25-35% between-subtype and 15-20% within-subtype variation is observed, and (3) the Dengue virus, whose respective genomes (only DENV 1-4) share 60% sequence identity to each other. Using our method, we were able to select oligonucleotides that can identify in silico 99.9% of 1657 HCV genomes, 99.7% of 11,838 HIV genomes, and 95.4% of 4016 Dengue genomes. We also show subspecies identification on genotypes 1-6 of HCV and genotypes 1-4 of the Dengue virus with more than 99.5% true positive and less than 0.05% false positive rate, on average. None of the state-of-the-art methods can produce oligonucleotides with this specificity and sensitivity on highly divergent viral genomes like the ones studied in this article.},
}

@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},
doi = {10.1111/jnc.70216},
pmid = {40890565},
issn = {1471-4159},
support = {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.},
}

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

@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.},
}

Humans
*Microbiota/genetics
Metagenomics/methods
Colorectal Neoplasms/microbiology/therapy
Machine Learning
Immunotherapy
Gastrointestinal Microbiome
Computational Biology/methods

@article {pmid40889931,
year = {2025},
author = {Sun, XY and Qi, RT and Li, HX and Zheng, LX},
title = {Soil ammonia oxidation process and its driving factors in the riparian zone of drainage ditch in saline-alkali area of Ningxia, Northwest China.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {7},
pages = {2201-2212},
doi = {10.13287/j.1001-9332.202507.033},
pmid = {40889931},
issn = {1001-9332},
mesh = {China ; *Ammonia/metabolism/chemistry ; Soil/chemistry ; Nitrification ; Oxidation-Reduction ; *Soil Microbiology ; Bacteria/metabolism ; Alkalies ; Archaea/metabolism ; *Ecosystem ; Rivers ; },
abstract = {Ammonia oxidation plays a critical role in nitrogen cycling within riparian zones. To investigate this process in saline-alkali soils of the Yinbei region, northern Yinchuan, Ningxia, we selected five distinct riparian types along the Third Drainage Ditch: gravel-reed mixed zone, reed zone, high-salt Bassia scoparia zone, Iris lactea embankment zone and bare soil zone. We quantified soil potential nitrification rates (PNR), environmental factors, and analyzed ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities via me-tagenomics and qPCR targeting amoA genes. The results showed that the total potential nitrification rate (PNRtotal) in the riparian zones ranged from 0.47 to 1.37 μmol N·g[-1]·d[-1], with PNRAOA (potential nitrification rate of AOA) being higher than PNRAOB (potential nitrification rate of AOB). The copy number of AOA amoA genes (2.63×10[6]-2.06×10[7] copies·g[-1]) was significantly higher than AOB amoA genes (7.14×10[5]-9.55×10[6] copies·g[-1]). The PNR and amoA gene copy number in the reed zone, gravel-reed mixed zone, and I. lactea embankment zone were higher than those in the high-salt B. scoparia zone and bare soil zone, indicating that nitrification in the riparian zones was dominated by AOA. AOA were affiliated with the phylum Nitrososphaerota, with the dominant genera being unclassified_f__Nitrososphaeraceae and Candidatus Nitrosocosmicus. The physicochemical factors, including ammonium, nitrite, nitrate, electrical conductivity, total organic carbon, and total nitrogen exhibited significant differences among different riparian zones. PNRAOA and PNRtotal were significantly influenced by ammonium, total nitrogen, total organic carbon and pH, and PNRtotal showed a highly significant positive correlation with amoA gene copy number. Structural equation modeling (SEM) results indicated that pH and total organic carbon were the primary factors affecting nitrification in the riparian zones and that AOA amoA gene copy number showed significant positive correlation with nitrification rate.},
}

China
*Ammonia/metabolism/chemistry
Soil/chemistry
Nitrification
Oxidation-Reduction
*Soil Microbiology
Bacteria/metabolism
Alkalies
Archaea/metabolism
*Ecosystem
Rivers

@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 & purification/physiology/metabolism/classification ; Fermentation ; *Fermented Foods/virology/microbiology ; Microbiota ; *Bacteria/genetics/metabolism/virology/classification/isolation & 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.},
}

*Vegetables/microbiology/virology
*Bacteriophages/genetics/isolation & purification/physiology/metabolism/classification
Fermentation
*Fermented Foods/virology/microbiology
Microbiota
*Bacteria/genetics/metabolism/virology/classification/isolation & purification
Food Microbiology

@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 & 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.},
}

*Glycine max/microbiology
*Fungi/classification/genetics/isolation & purification/metabolism
*Mycobiome
Food Preservation
Biodiversity