@article {pmid40175821,
year = {2025},
author = {Takagi, K and Tamura, Y and Narita, N and Komatsu, S and Yamazaki, S and Matsumura, A and Kubota, K and Matsumiya, T and Sawada, K and Nakaji, S and Mikami, T and Kobayashi, W},
title = {Involvement of Megasphaera in the oral microbiome and dyslipidemia onset: evidence from a community-based study in Japan.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {40175821},
issn = {1874-9356},
support = {21K10202//Japan Society for the Promotion of Science/ ; 22K17281//Japan Society for the Promotion of Science/ ; 24K13233//Japan Society for the Promotion of Science/ ; JPMJCE 1302//Japan Science and Technology Agency/ ; JPMJCA　2201//Japan Science and Technology Agency/ ; JPMJPE 2210//Japan Science and Technology Agency/ ; },
abstract = {Dyslipidemia is a major risk factor for cardiovascular diseases and is influenced by genetic and environmental factors, including diet. Emerging research suggests a link between the gut microbiome and metabolic disorders. While the connection between the gut microbiota and dyslipidemia is well documented, the specific relationship between oral bacteria and dyslipidemia has not been thoroughly investigated. This study aimed to identify oral bacterial species associated with dyslipidemia in a community-based Japanese population. We conducted a metagenomic analysis on tongue coating samples from 763 participants in the Iwaki Health Promotion Project, which were collected during health checkups in 2017 and 2019. Dyslipidemia was diagnosed using standard lipid level criteria. The oral microbiome was analyzed via 16S rDNA amplicon sequencing. Statistical analyses included multiple regression and β diversity assessments. Our analysis revealed that the abundances of several bacterial genera, including Veillonella, Atopobium, Stomatobaculum, Tanneralla, and Megasphaera, are significantly associated with dyslipidemia. A higher relative abundance of Megasphaera was specifically observed in individuals with dyslipidemia. Moreover, Megasphaera abundance was closely associated with the onset of dyslipidemia (P = 0.038, odds ratio: 1.005, 95% confidence interval: 1.000-1.009), suggesting its role in metabolic regulation. This study revealed a significant association between the abundance of specific oral bacteria and dyslipidemia, suggesting the potential of using the oral microbiota as a biomarker for the early detection and management of dyslipidemia. Future research should explore the mechanisms through which oral bacteria influence lipid metabolism and the potential for microbioma-based therapies.},
}

@article {pmid40175737,
year = {2025},
author = {Sawhney, SS and Thänert, R and Thänert, A and Hall-Moore, C and Ndao, IM and Mahmud, B and Warner, BB and Tarr, PI and Dantas, G},
title = {Gut microbiome evolution from infancy to 8 years of age.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40175737},
issn = {1546-170X},
support = {R01AI155893//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01HD092414//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD092414//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; T32GM007067//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; MD-FR-2013-292//Children's Discovery Institute (CDI)/ ; 5P30 DK052574//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
abstract = {The human gut microbiome is most dynamic in early life. Although sweeping changes in taxonomic architecture are well described, it remains unknown how, and to what extent, individual strains colonize and persist and how selective pressures define their genomic architecture. In this study, we combined shotgun sequencing of 1,203 stool samples from 26 mothers and their twins (52 infants), sampled from childbirth to 8 years after birth, with culture-enhanced, deep short-read and long-read stool sequencing from a subset of 10 twins (20 infants) to define transmission, persistence and evolutionary trajectories of gut species from infancy to middle childhood. We constructed 3,995 strain-resolved metagenome-assembled genomes across 399 taxa, and we found that 27.4% persist within individuals. We identified 726 strains shared within families, with Bacteroidales, Oscillospiraceae and Lachnospiraceae, but not Bifidobacteriaceae, vertically transferred. Lastly, we identified weaning as a critical inflection point that accelerates bacterial mutation rates and separates functional profiles of genes accruing mutations.},
}

@article {pmid40175647,
year = {2025},
author = {Ahn, JS and Kim, S and Han, EJ and Hong, ST and Chung, HJ},
title = {Increasing spatial working memory in mice with Akkermansia muciniphila.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {546},
pmid = {40175647},
issn = {2399-3642},
support = {C512230//Korea Basic Science Institute (KBSI)/ ; RS-2023-00224099//National Research Foundation of Korea (NRF)/ ; },
abstract = {Recent research has shown the gut microbiome's impact on memory, yet limitations hinder the identification of specific microbes linked to cognitive function. We measured spatial working memory in individual mice before and after fecal microbiota transplantation (FMT) to develop a targeted analysis that identifies memory-associated strains while minimizing host genetic effects. Transplantation of human fecal into C57BL/6 mice yielded varied outcomes: some mice showed significant improvements while others had negligible changes, indicating that these changes are due to differences in FMT colonization. Metagenomic analysis, stratified by memory performance, revealed a positive correlation between the abundance of Akkermansia muciniphila and improved memory. Moreover, administering two A. muciniphila strains, GMB 0476 and GMB 2066, to wild-type mice elevated spatial working memory via BDNF activation. Our findings indicate that specific gut microbes, particularly A. muciniphila, may modulate memory and represent potential targets for therapeutic intervention in cognitive enhancement.},
}

@article {pmid40175554,
year = {2025},
author = {Ryan, FJ and Clarke, M and Lynn, MA and Benson, SC and McAlister, S and Giles, LC and Choo, JM and Rossouw, C and Ng, YY and Semchenko, EA and Richard, A and Leong, LEX and Taylor, SL and Blake, SJ and Mugabushaka, JI and Walker, M and Wesselingh, SL and Licciardi, PV and Seib, KL and Tumes, DJ and Richmond, P and Rogers, GB and Marshall, HS and Lynn, DJ},
title = {Bifidobacteria support optimal infant vaccine responses.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40175554},
issn = {1476-4687},
abstract = {Accumulating evidence indicates that antibiotic exposure may lead to impaired vaccine responses[1-4]; however, the mechanisms underlying this association remain poorly understood. Here we prospectively followed 191 healthy, vaginally born, term infants from birth to 15 months, using a systems vaccinology approach to assess the effects of antibiotic exposure on immune responses to vaccination. Exposure to direct neonatal but not intrapartum antibiotics was associated with significantly lower antibody titres against various polysaccharides in the 13-valent pneumococcal conjugate vaccine and the Haemophilus influenzae type b polyribosylribitol phosphate and diphtheria toxoid antigens in the combined 6-in-1 Infanrix Hexa vaccine at 7 months of age. Blood from infants exposed to neonatal antibiotics had an inflammatory transcriptional profile before vaccination; in addition, faecal metagenomics showed reduced abundance of Bifidobacterium species in these infants at the time of vaccination, which was correlated with reduced vaccine antibody titres 6 months later. In preclinical models, responses to the 13-valent pneumococcal conjugate vaccine were strongly dependent on an intact microbiota but could be restored in germ-free mice by administering a consortium of Bifidobacterium species or a probiotic already widely used in neonatal units. Our data suggest that microbiota-targeted interventions could mitigate the detrimental effects of early-life antibiotics on vaccine immunogenicity.},
}

@article {pmid40175522,
year = {2025},
author = {Gichuki, BM and Van Camp, AG and Shao, Y},
title = {A new strain of thought in gut metagenomics.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40175522},
issn = {1740-1534},
}

@article {pmid40175313,
year = {2025},
author = {Fortin, SG and Uhlig, K and Hale, RC and Song, B},
title = {Microplastic biofilms as potential hotspots for plastic biodegradation and nitrogen cycling: A metagenomic perspective.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf035},
pmid = {40175313},
issn = {1574-6941},
abstract = {Microplastics are an emerging contaminant worldwide, with the potential to impact organisms and facilitate the sorption and release of chemicals. Additionally, they create a novel habitat for microbial communities, forming biofilms known as the plastisphere. While the plastisphere has been studied in select aquatic environments, those in estuarine ecosystems merit additional attention due to their proximity to plastic debris sources. Additionally, the role plastisphere communities play in nutrient cycling has rarely been examined. This study used metagenomic analysis to investigate the taxonomic composition and functional genes of developing plastisphere communities living on petroleum-based (polyethylene and polyvinyl chloride) and biopolymer-based (polylactic acid) substrates. Isolated metagenome assembled genomes (MAGs) showed plastisphere communities have the genes necessary to perform nitrification and denitrification and degrade petroleum and biopolymer-based plastics. The functions of these plastispheres have implications for estuarine nitrogen cycling and provide a possible explanation for the plastisphere microbes' competitiveness in biofilm environments. Overall, microplastics in the estuarine system provide a novel habitat for microbial communities and associated nitrogen cycling, facilitating the growth of microbes with plastic degrading capabilities.},
}

@article {pmid40174744,
year = {2025},
author = {Liu, M and Wang, S and Zhou, H and Liu, H and Huang, D and Liu, L and Li, Q and Chen, H and Lei, Y and Jin, LN and Zhang, W},
title = {Thermal Environment Driving Specific Microbial Species to Form the Visible Biofilms on the UNESCO World Heritage Dazu Rock Carvings.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121510},
doi = {10.1016/j.envres.2025.121510},
pmid = {40174744},
issn = {1096-0953},
abstract = {The Dazu Rock Carvings, a UNESCO World Heritage site with over a millennium of history, are facing significant deterioration from microbial biofilms. However, the key microbial species responsible and the environmental factors driving their growth remain unclear. To address this gap, we conducted metagenomic sequencing to characterize the microbial community on the carvings, followed by correlation analyses with a variety of environmental factors in the surrounding air and within the rocks. Bacterial communities exhibited significantly higher richness and diversity than eukaryotic communities, though diversity metrics showed no significant differences between visibly colonized and uncolonized surfaces. We identified a distinctive consortium of 64 bacterial species, 35 fungal species, and 1 algal species specifically associated with visible biofilms, occurring at 9.56-fold higher relative abundance in colonized areas. These microorganisms contribute to characteristic green, brown-black, and white coloration on the carvings. Statistical analysis revealed absolute humidity and dew point temperature as key environmental factors influencing biofilm visibility, with thresholds of 21.00 g/m[3] and 23.4°C respectively, above which biofilms became visible. This study provides precise targets for conservation efforts and establishes critical environmental parameters to guide preservation strategies for this irreplaceable cultural heritage.},
}

@article {pmid40174653,
year = {2025},
author = {Balasundaram, G and Gahlot, P and Hafyan, RH and Tyagi, VK and Gadkari, S and Sahu, A and Barber, B and Mutiyar, PK and Kazmi, AA and Kleiven, H},
title = {Anaerobic digestion of thermal hydrolysis pretreated sludge: Process performance, metagenomic analysis, techno-economic and life cycle assessment.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132470},
doi = {10.1016/j.biortech.2025.132470},
pmid = {40174653},
issn = {1873-2976},
abstract = {This study assessed the potential of thermal hydrolysis process (THP) combined with anaerobic digestion (AD) for high solids sewage sludge treatment across various hydraulic retention times (HRTs). Optimal performance was achieved at a 10-day HRT (6 kg VS/m[3]·day), yielding 408 L CH4/kg VS added and 54 % volatile solids (VS) removal under THP conditions of 160 °C, 30 min, and 6 bar pressure. Microbial analysis revealed predominant acetoclastic and hydrogenotrophic methanogens. Four scenarios were designed and analyzed for environmental and economic performance: Scenario 1 (conventional AD-CHP), Scenario 2 (conventional AD-BioCNG), Scenario 3 (THP AD-BioCNG), and Scenario 4 (THP AD-CHP). The results showed that scenarios with CHP integration achieved better environmental performance by generating sufficient energy to meet demand, with energy consumption as a key factor. Notably, scenario 4 had the lowest global warming potential (GWP) at -0.0185 kg CO2-eq, outperforming conventional AD (Scenario 1) with CHP, which had a GWP of -0.00232 kg CO2-eq. However, profitability analysis showed that Scenario 3 was the most economically viable, with a net present value (NPV) of $4.3 million, an internal rate of return (IRR) of 10.21 %, and a 17-year payback period. Although it had higher capital ($58 million) and operational costs ($12.5 million/year) than Scenario 4 ($45 million and $8.6 million/year), its greater biomethane yield resulted in higher revenue ($20.7 million/year), making it the most profitable option. While Scenario 4 offered the best environmental benefits, Scenario 3 emerged as the most financially sustainable choice. These findings highlight the environmental and economic advantage of utilizing THP-AD process over conventional AD, suggesting that THP-AD optimizes methane production, solids reduction, and environmental impact, making the Bio CNG pathway a sustainable and economically viable option.},
}

@article {pmid40174641,
year = {2025},
author = {He, T and Zhang, X and Zhang, X},
title = {Thousands-years-old deep-sea DNA viruses reveal the evolution of human pathogenic viruses.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.03.057},
pmid = {40174641},
issn = {2090-1224},
abstract = {INTRODUCTION: In the last two decades, outbreaks of pathogenic viruses have led to significant human mortality and economic repercussions. Despite extensive investigations into tracing these viruses in terrestrial environments, their origins remain enigmatic.

OBJECTIVES: The Earth's biosphere encompasses both sunlight-dependent terrestrial and surface ocean ecosystems, as well as the sunlight-independent deep-sea ecosystem. However, the traceability of human pathogenic viruses in the deep sea has not been thoroughly explored. This study aimed to investigate the presence of human pathogenic viruses in the deep sea.

METHODS: In this study, we performed a viral metagenomic analysis using a global deep-sea sediment virome 2.0 dataset which contained 159 deep-sea sediment samples with geologic ages from 2,500 to 7,750 years.

RESULTS: A total of 554,664 viral operational taxonomic units (vOTUs) were identified and further obtained 2,254 potential pathogenic viruses of vertebrates. Among them, 23 vOTUs exhibited high homology with 12 species of human pathogenic viruses which belonged to 4 viral families. Notably, variola virus, the first human pathogenic virus eradicated from humans and now only found in laboratories, was discovered in the ancient deep-sea sediments. The evolution analysis showed that these DNA viruses might represent the ancestors or variants of human pathogenic viruses, suggesting that the deep sea could be a crucial reservoir for human pathogenic viruses.

CONCLUSION: Our findings present all the ancient pathogenic DNA viruses of humans found in the deep sea for the first time, highlighting the source of the future epidemics. It is imperative to implement the stringent virus monitoring and management measures for human activities in marine environments to address the emerging challenges of marine biosecurity and promote sustainable use of oceans.},
}

@article {pmid40174574,
year = {2025},
author = {Zeng, S and Almeida, A and Mu, D and Wang, S},
title = {Embracing the unknown: Proteomic insights into the human microbiome.},
journal = {Cell metabolism},
volume = {37},
number = {4},
pages = {799-801},
doi = {10.1016/j.cmet.2025.02.003},
pmid = {40174574},
issn = {1932-7420},
abstract = {Protein-level investigations into the human microbiome provide insights into active microbial functions. Recently, Valdés-Mas et al.[1] introduced a metagenome-informed metaproteomics approach to functionally explore species-level microbiome-host interactions and quantify the dietary exposome. Its potential has been implemented in mice and humans to uncover proteomic signatures of health and inflammatory bowel disease.},
}

@article {pmid40174565,
year = {2025},
author = {Krohn, C and Khudur, L and Biek, SK and Elliott, JA and Tabatabaei, S and Jiang, C and Wood, JL and Dias, DA and Dueholm, MKD and Rees, CA and O'Carroll, D and Stuetz, R and Batstone, DJ and Surapaneni, A and Ball, AS},
title = {Microbial population shifts during disturbance induced foaming in anaerobic digestion of primary and activated sludge.},
journal = {Water research},
volume = {281},
number = {},
pages = {123548},
doi = {10.1016/j.watres.2025.123548},
pmid = {40174565},
issn = {1879-2448},
abstract = {Foaming during anaerobic digestion (AD) of sewage sludge is poorly understood and remains an uncontrollable operational obstacle for sewage treatment systems globally, causing mechanical damage, increased hazards and reduced biogas recovery. Foams during AD commonly occur after process disturbances, such as organic loading shocks. However, it is still unclear whether these foam events are biologically driven and linked to the abundance of organisms like filamentous or hydrophobic bacteria. A time-series study was conducted, comparing digestion performance, microbial community succession, metagenomes, and metabolomes in six anaerobic continuous stirred-tank reactors (CSTRs): a control group fed normally (n = 3), and one treated group inhibited through organic shock loading of more than twice the steady state loading rate with glycerol (treatment, n = 3). As soon as microbial activity and methanogenesis recovered after inhibition, significant volumes of foam accumulated simultaneously in the reactor headspace of the three treated CSTRs. Microbial abundance profiles (16S rRNA, V3-V4) from 165 days of operation showed that filamentous or mycolic acid-producing organisms were not associated with this foam event. Shock loading led to acidification, biomass decline and microbial imbalance, contributing indirectly to the foam event. During that period, metabolomes and functional pathway abundances indicated that the stressed microbial biomass was enriched in long-chain fatty acids prior to foaming. This biomass, combined with pH changes, may have modified the physicochemical properties of sludge, leading to the fractionation of organic mass once gas production resumed. More research is needed to understand how abiotic and biotic interactions contribute to foam formation.},
}

@article {pmid40174457,
year = {2025},
author = {Han, Q and Wang, Y and Shi, C and Qian, Y and Wang, X and Wang, S and Sun, X and Yu, Q and Li, H},
title = {Urban landscape lakes with backwater hide higher antibiotic resistance risk than living water.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138101},
doi = {10.1016/j.jhazmat.2025.138101},
pmid = {40174457},
issn = {1873-3336},
abstract = {The pollution of antibiotic resistance genes (ARGs) in urban landscape lakes threatens the aquatic ecosystems and public health. However, a comprehensive understanding of the fate of ARGs in different types of park landscape lakes (i.e., backwater and living water) remains deficient. Here, we profiled the distribution, diversity, origin and potential spread risk to human of ARGs in backwater and living water using metagenomics and 16S rRNA gene sequencing. Our results showed higher antibiotic resistance risk presented in backwater due to higher ARG diversity, while higher resistance transfer risk occurred in living water due to higher mobile genetic elements (MGEs) diversity. Source tracking analysis revealed Yellow River water was the main the dominant source of ARGs in both backwater and living water, with an average contribution of 41.06 % and 65.82 %, respectively. Notably, nine high-risk ARGs (such as mdtM and msrA) significantly enriched in human feces, implying possible spread risk from environment to human. Metagenomics binning revealed that MAGs carrying ARGs mainly belong to Actinobacteria, while MAGs carrying MGEs belong to Proteobacteria. Our study highlights the significance of healthy management of park landscape lakes to prevent the spread of resistomes to the public.},
}

@article {pmid40174456,
year = {2025},
author = {Long, M and Zheng, CW and Zhou, C and Rittmann, BE},
title = {Mitigating chromate toxicity through concurrent denitrification in the H2-based membrane biofilm reactor.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138073},
doi = {10.1016/j.jhazmat.2025.138073},
pmid = {40174456},
issn = {1873-3336},
abstract = {High concentrations of hexavalent chromium (Cr(VI)) in industrial wastewaters pose significant environmental and health hazards. Biotranformation is a viable means to lower Cr(VI) toxicity, but research to date has focused on wastewaters with low concentrations (e.g., 2-5 mg/L Cr(VI)). This study evaluated the dynamics of biosorption and biotransformation of higher-concentration Cr(VI) by biofilms in the H2-based membrane biofilm reactor (MBfR). While the biofilm in an MBfR receiving Cr(VI) alone had limited capacity to remove Cr(VI) and Cr(VI) removal ceased in 30 days, an autotrophic denitrifying biofilms achieved 99 % reduction of over 20 mg/L Cr(VI) to less-toxic trivalent chromium (Cr(III)) in continuous long-term operation system over 4 months. Increasing the H2 pressure from 3 psig to 10 psig improved Cr(VI) removal from 87 % to 99 %, which occurred in parallel with over 95 % NO3[-] reduction to N2. Metagenomic analyses revealed the mechanisms of Cr(VI) bioreduction and highlighted the beneficial role of nitrate (NO3[-]) as the primary electron acceptor. For example, nitrite reductase NrfA could reduce Cr(VI), which lowered Cr(VI) caused oxidative stress. This research demonstrates the MBfR's effectiveness in reducing elevated levels of Cr(VI) and provides mechanistic understanding of the roles of denitrification in accelerating Cr(VI) reduction and detoxification.},
}

@article {pmid40174424,
year = {2025},
author = {Dai, Z and Li, Y and Zhang, Y and Xiang, T and Peng, J and Mao, X and Fan, Y and Wang, F and Yang, S and Cao, W},
title = {Nutrient enrichment by high aquaculture effluent input exacerbates imbalances between methane production and oxidation in mangrove sediments.},
journal = {Water research},
volume = {280},
number = {},
pages = {123552},
doi = {10.1016/j.watres.2025.123552},
pmid = {40174424},
issn = {1879-2448},
abstract = {Frequent aquaculture activities introduce substantial nutrients into mangrove ecosystems; however, the impact of this nutrient enrichment on methane (CH4) emissions and the associated microbial communities remains largely unexplored. In this study, we used the static chamber method, combined with 16S rRNA-based, metagenomic sequencing and binning techniques, to investigate the emission patterns of greenhouse gases (GHGs), with a particular focus on CH4, in mangroves subjected to different levels of effluents. The results showed that the effluent input decreased the mineral protection of sediment carbon (C) pools and increased C loss by more than double. In particular, high effluent input increased CH4 emissions by 243.3 %. Random forest analysis revealed that changes in methanogens were an important factor in explaining the variation of CH4 emissions. Amplicon data showed that the proportion of methylotrophic methanogens increased after effluent input, and metagenomic binning further attributed this change to the adaptability of methylotrophic methanogens to the substances transporting by the effluent. The enhanced hypoxia in sediments resulting from effluent input promoted the transition of methanotrophic communities from aerobic to anaerobic types and made anaerobic oxidation of CH4 more reliant on sulfur reduction rather than nitrate reduction. The PLS model further revealed that the nutrients brought by effluent input stimulated an increase in DOC content which induced an imbalance between CH4 production and oxidation in sediments by facilitating methanogens but inhibiting methanotrophs, ultimately resulting in an increase in CH4 fluxes. These findings underscore the significance of mangroves receiving effluent input as critical consequent reactors, highlighting the necessity to consider effects of high nutrient enrichment by aquaculture effluent input on GHG emissions and blue C potential in mangroves.},
}

@article {pmid40172536,
year = {2025},
author = {Madison, JD and Osborne, OG and Ellison, A and Garvey Griffith, CN and Gentry, L and Gross, H and Gratwicke, B and Grayfer, L and Muletz-Wolz, CR},
title = {Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0056924},
doi = {10.1128/iai.00569-24},
pmid = {40172536},
issn = {1098-5522},
abstract = {Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.},
}

@article {pmid40172519,
year = {2025},
author = {Chaves-Sierra, C and Botero-Rozo, D and Rodriguez-Cruz, MC and Montoya, C and Romero, HM},
title = {Detection and molecular characterization of 'Candidatus Liberibacter' in Colombian oil palms affected by Lethal Wilt Disease.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-10-24-2079-RE},
pmid = {40172519},
issn = {0191-2917},
abstract = {Lethal wilt (LW), also known as "Marchitez Letal (ML)" in Colombia, is an endemic disease affecting oil palms (Elaeis guineensis Jacq.) and is a leading cause of crop loss. The disease is characterized by the drying of leaflets from the tip to the base, primarily impacting the lower third of the plant and progressively moving upward. This progression leads to physiological disturbances, including necrosis at the tips of immature inflorescence bracts (spines) and the detachment of bunch fruits, ultimately causing wilting. As a phytosanitary measure, infected palms are eradicated to prevent further spread of the disease. The primary goal of this research was to identify the bacteria associated with LW and to validate a molecular detection method. A 16S amplicon-based analysis was employed to identify and compare the microbial diversity in LW-affected palm tissues with those of healthy plants. Among the 16 OTUs corresponding to different bacterial genera found in all LW samples, taxonomic classification and symptomatology suggested that the bacteria closely associated with LW belong to the genus Candidatus Liberibacter. Further phylogenetic analysis indicated that these bacteria are part of the Rhizobiaceae family, grouping closely with other species of the genus Candidatus. Liberibacter. The concentration of the pathogen in different oil palm tissues was determined using droplet digital PCR (ddPCR) and quantitative PCR (qPCR), expressed in copies/µL in the LW samples. This study represents the first report of 'Candidatus Liberibacter sp'. being associated with lethal wilt in oil palms of the Arecaceae family in Colombia. The findings from this research have the potential to contribute significantly to the development of effective management strategies to prevent crop losses.},
}

@article {pmid40172478,
year = {2025},
author = {Wang, H and Zhao, X and Li, D and Meng, L and Liu, S and Zhang, Y and Huo, L},
title = {Marine Metagenome Mining Reveals Lanthipeptides Colwesin A-C, Exhibiting Novel Ring Topology and Anti-inflammatory Activity.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00057},
pmid = {40172478},
issn = {2161-5063},
abstract = {Marine natural products are promising sources for drug discovery due to their unique structures and diverse biological activities. The establishment of the Global Marine Microbiome Genome Catalogue (GOMC) has significantly expanded the repository of natural products derived from marine-associated bacteria. In this study, we identified the Class I lanthipeptide biosynthetic gene cluster col from Colwellia_A sp. based on the GOMC database. Through heterologous expression in Escherichia coli and subsequent structural analysis, we characterized three novel lanthipeptides, colwesins A-C, which possess unique cyclic structures characterized by an exceptionally large number of thioether rings. To the best of our knowledge, colwesin C is the first lanthipeptide simultaneously containing locked, nonoverlapped, and nested ring topologies. These findings highlight the robust ring-forming capacity of Class I lanthipeptide synthetases. Colwesins A-C were found to exhibit anti-inflammatory activity in lipopolysaccharide-induced mouse macrophage RAW264.7 cell lines without detectable cytotoxicity. Overall, our results broaden our understanding of the structural diversity of marine-derived lanthipeptides.},
}

@article {pmid40172215,
year = {2025},
author = {Brito Rodrigues, P and de Rezende Rodovalho, V and Sencio, V and Benech, N and Creskey, M and Silva Angulo, F and Delval, L and Robil, C and Gosset, P and Machelart, A and Haas, J and Descat, A and Goosens, JF and Beury, D and Maurier, F and Hot, D and Wolowczuk, I and Sokol, H and Zhang, X and Ramirez Vinolo, MA and Trottein, F},
title = {Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2486511},
doi = {10.1080/19490976.2025.2486511},
pmid = {40172215},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/virology/metabolism ; *Metagenomics ; *Metabolomics ; *Disease Models, Animal ; Cricetinae ; *SARS-CoV-2/genetics ; Aging ; Age Factors ; Dysbiosis/microbiology ; Male ; Bacteria/classification/genetics/metabolism/isolation & purification ; Mesocricetus ; Metabolome ; },
abstract = {Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium, Oscillospiraceae, Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.},
}

Animals
*Gastrointestinal Microbiome
*COVID-19/microbiology/virology/metabolism
*Metagenomics
*Metabolomics
*Disease Models, Animal
Cricetinae
*SARS-CoV-2/genetics
Aging
Age Factors
Dysbiosis/microbiology
Male
Bacteria/classification/genetics/metabolism/isolation & purification
Mesocricetus
Metabolome

@article {pmid40172109,
year = {2025},
author = {Tarracchini, C and Lordan, C and Milani, C and Moreira, LPD and Alabedallat, QM and de Moreno de LeBlanc, A and Turroni, F and Lugli, GA and Mancabelli, L and Longhi, G and Brennan, L and Mahony, J and LeBlanc, JG and Nilaweera, KN and Cotter, PD and van Sinderen, D and Ventura, M},
title = {Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0018423},
doi = {10.1128/mmbr.00184-23},
pmid = {40172109},
issn = {1098-5557},
abstract = {SUMMARYIn recent years, exhaustive efforts have been made to dissect the composition of gut-associated microbial communities and associated interactions with their human host, which are thought to play a crucial role in host development, physiology, and metabolic functions. Although such studies were initially focused on the description of the compositional shifts in the microbiota that occur between different health conditions, more recently, they have provided key insights into the functional and metabolic contributions of the gut microbiota to overall host physiology. In this context, an important metabolic activity of the human gut microbiota is believed to be represented by the synthesis of various vitamins that may elicit considerable benefits to human health. A growing body of scientific literature is now available relating to (predicted) bacterial vitamin biosynthetic abilities, with ever-growing information concerning the prevalence of these biosynthetic abilities among members of the human microbiota. This review is aimed at disentangling if and how cooperative trophic interactions of human microbiota members contribute to vitamin production, and if such, gut microbiota-mediated vitamin production varies according to different life stages. Moreover, it offers a brief exploration of how different diets may influence vitamin production by shaping the overall composition and metabolic activity of the human gut microbiota while also providing preliminary insights into potential correlations between human microbiota-associated vitamin production and the occurrence of human diseases and/or metabolic disorders.},
}

@article {pmid40171165,
year = {2025},
author = {Shi, H and Li, J},
title = {MAGs-based genomic comparison of gut significantly enriched microbes in obese individuals pre- and post-bariatric surgery across diverse locations.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1485048},
pmid = {40171165},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; *Bariatric Surgery ; Metagenome ; Metagenomics/methods ; Genomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; Gastric Bypass ; Computational Biology/methods ; Adult ; },
abstract = {INTRODUCTION: Obesity, a pressing global health issue, is intricately associated with distinct gut microbiota profiles. Bariatric surgeries, such as Laparoscopic Sleeve Gastrectomy (LSG), Sleeve Gastrectomy (SG), and Roux-en-Y Gastric Bypass (RYGB), induce substantial weight loss and reshape gut microbiota composition and functionality, yet their comparative impacts remain underexplored.

METHODS: This study integrated four published metagenomic datasets, encompassing 500 samples, and employed a unified bioinformatics workflow for analysis. We assessed gut microbiota α-diversity, identified species biomarkers using three differential analysis approaches, and constructed high-quality Metagenome-Assembled Genomes (MAGs). Comparative genomic, functional profiling and KEGG pathway analyses were performed, alongside estimation of microbial growth rates via Peak-to-Trough Ratios (PTRs).

RESULTS: RYGB exhibited the most pronounced enhancement of gut microbiota α-diversity compared to LSG and SG. Cross-cohort analysis identified 39 species biomarkers: 27 enriched in the non-obesity group (NonOB_Enrich) and 12 in the obesity group (OB_Enrich). Among the MAGs, 177 were NonOB_Enrich and 14 were OB_Enrich. NonOB_Enrich MAGs displayed enriched carbohydrate degradation profiles (e.g., GH105, GH2, GH23, GH43, and GT0 families) and higher gene diversity in fatty acid biosynthesis and secondary metabolite pathways, alongside significant enrichment in amino acid metabolism (KEGG analysis). Post-surgery, Akkermansia muciniphila and Bacteroides uniformis showed elevated growth rates based on PTRs.

DISCUSSION: These findings underscore RYGB's superior impact on gut microbiota diversity and highlight distinct microbial functional adaptations linked to weight loss, offering insights for targeted therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Obesity/microbiology
*Bariatric Surgery
Metagenome
Metagenomics/methods
Genomics
Bacteria/classification/genetics/isolation & purification/metabolism
Gastric Bypass
Computational Biology/methods
Adult

@article {pmid40170926,
year = {2025},
author = {Zhai, R and Zhao, C and Chang, L and Liu, J and Zhao, T and Jiang, J and Zhu, W},
title = {Diets shape thermal responses in Chinese giant salamanders by altering liver metabolism.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1546912},
pmid = {40170926},
issn = {1664-302X},
abstract = {Diet can influence the thermal performance of ectotherms, providing potential strategies for biological conservation in the context of global warming. The endangered Andrias davidianus is susceptible to heat stress due to energy deficiency in the liver when fed a worm-based diet rich in carbohydrates. A fish-based diet, rich in protein and lipids, improves their thermal performance, but the underlying physiological mechanisms remain unclear. In this study, we used metabolomics and metagenomics to examine the combined effects of temperature (15, 20, and 25°C) and diet (fish-based and worm-based) on liver metabolism and gut microbiota. Our results show that both temperature and diet shape liver metabolism, with several vital metabolic pathways (e.g., TCA cycle and sulfate metabolism) regulated by their combined effects. Notably, diet-dependent thermal responses in energy metabolism were observed, with fish-fed salamanders exhibiting a marked upregulation of the TCA cycle intermediates under heat stress, a response absent in worm-fed individuals. Given the role of TCA cycle in heat susceptibility of A. davidianus, these findings suggest that the TCA cycle likely mediates the interactive effects of temperature and diet on thermal performance. We then examined whether the gut microbiota is also a target of interactive effects or a mediator of the diet's influence on liver metabolism. While both temperature and diet shape microbiota composition, functional shifts occur only in response to temperature, indicating that the microbiota is not a major link between diet and liver metabolism. However, several bacterial groups (e.g., Thiosulfatimonas and Alcanivorax), jointly regulated by temperature and diet, correlate with liver metabolites, suggesting alternative, function-independent pathways through which dietary-related microbial changes may influence liver metabolism and even thermal tolerance. Overall, this study provides molecular insights into the dietary modulation of thermal performance in A. davidianus and highlight the potential of dietary microbial management strategies for amphibian conservation.},
}

@article {pmid40170918,
year = {2025},
author = {Hager, K and Luo, ZH and Montserrat-Diez, M and Ponce-Toledo, RI and Baur, P and Dahlke, S and Andrei, AS and Bulzu, PA and Ghai, R and Urich, T and Glatzel, S and Schleper, C and Rodrigues-Oliveira, T},
title = {Diversity and environmental distribution of Asgard archaea in shallow saline sediments.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549128},
pmid = {40170918},
issn = {1664-302X},
abstract = {In recent years, our understanding of archaeal diversity has greatly expanded, especially with the discovery of new groups like the Asgard archaea. These archaea show diverse phylogenetic and genomic traits, enabling them to thrive in various environments. Due to their close relationship to eukaryotes, a large number of metagenomic studies have been performed on Asgard archaea. Research on the fine scale distribution, diversity and quantification in saline aquatic sediments where they mostly occur, has, however, remained scarce. In this study, we investigated depths of shallow saline sediment cores from three distinct European environments: the Baltic Sea near Hiddensee, the coastal Lake Techirghiol in Romania, and an estuarine canal in Piran, Slovenia. Based on 16S rDNA amplicon sequencing, we observe variation in the relative abundance and occurrence of at least seven different Asgard groups that are distinct between the three environments and in their depth distribution. Lokiarchaeia and Thorarchaeia emerge as dominant Asgard groups across all sites, reaching maximal relative abundances of 2.28 and 2.68% of the total microbial communities respectively, with a maximal abundance of all Asgard reaching approx. 5.21% in Hiddensee. Quantitative PCR assays provide insights into the absolute abundance of Lokiarchaeia, supporting distinct patterns of distribution across depths in different sediments. Co-occurrence network analysis indicates distinct potential microbial partners across different Asgard groups. Overall, our study shows that Asgard archaea are found as a stable component in shallow sediment layers and have considerably diversified on macro- and microscales.},
}

@article {pmid40170844,
year = {2025},
author = {Zhou, Y and Han, W and Feng, Y and Wang, Y and Liu, X and Sun, T and Xu, J},
title = {Revealing gut microbiota biomarkers associated with melanoma immunotherapy response and key bacteria-fungi interaction relationships: evidence from metagenomics, machine learning, and SHAP methodology.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1539653},
pmid = {40170844},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Melanoma/therapy/immunology/microbiology ; *Metagenomics/methods ; *Immunotherapy/methods ; *Machine Learning ; Male ; *Bacteria/genetics/classification/immunology ; Female ; Fungi/immunology ; Middle Aged ; Skin Neoplasms/immunology/therapy/microbiology ; Biomarkers ; Aged ; Adult ; Treatment Outcome ; },
abstract = {INTRODUCTION: The gut microbiota is associated with the response to immunotherapy in cutaneous melanoma (CM). However, gut fungal biomarkers and bacterial-fungal interactions have yet to be determined.

METHODS: Metagenomic sequencing data of stool samples collected before immunotherapy from three independent groups of European ancestry CM patients were collected. After characterizing the relative abundances of bacteria and fungi, Linear Discriminant Analysis Effect Size (LEfSe) analysis, Random Forest (RF) model construction, and SHapley Additive exPlanations (SHAP) methodology were applied to identify biomarkers and key bacterial-fungal interactions associated with immunotherapy responders in CM.

RESULTS: Diversity analysis revealed significant differences in the bacterial and fungal composition between CM immunotherapy responders and non-responders. LEfSe analysis identified 45 bacterial and 4 fungal taxa as potential biomarkers. After constructing the RF model, the AUC of models built using bacterial and fungal data separately were 0.64 and 0.65, respectively. However, when bacterial and fungal data were combined, the AUC of the merged model increased to 0.71. In the merged model, the following taxa were identified as important biomarkers: Romboutsia, Endomicrobium, Aggregatilinea, Candidatus Moduliflexus, Colwellia, Akkermansia, Mucispirillum, and Rutstroemia, which were associated with responders, whereas Zancudomyces was associated with non-responders. Moreover, the positive correlation interaction between Akkermansia and Rutstroemia is considered a key bacterial-fungal interaction associated with CM immunotherapy response.

CONCLUSION: Our results provide valuable insights for the enrichment of responders to immunotherapy in CM patients. Moreover, this study highlights the critical role of bacterial-fungal interactions in CM immunotherapy.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Melanoma/therapy/immunology/microbiology
*Metagenomics/methods
*Immunotherapy/methods
*Machine Learning
Male
*Bacteria/genetics/classification/immunology
Female
Fungi/immunology
Middle Aged
Skin Neoplasms/immunology/therapy/microbiology
Biomarkers
Aged
Adult
Treatment Outcome

@article {pmid40170341,
year = {2025},
author = {Sorn, S and Matsuura, N and Honda, R},
title = {Metagenome-Assembled Genomes and Metatranscriptome Analysis of Perfluorooctane Sulfonate-Reducing Bacteria Enriched From Activated Sludge.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70087},
doi = {10.1111/1462-2920.70087},
pmid = {40170341},
issn = {1462-2920},
support = {19K22925//Japan Society for the Promotion of Science/ ; 22K19865//Japan Society for the Promotion of Science/ ; //Steel Foundation for Environmental Protection Technology/ ; },
mesh = {*Fluorocarbons/metabolism ; *Alkanesulfonic Acids/metabolism ; *Sewage/microbiology ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Biodegradation, Environmental ; *Metagenome ; *RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; Transcriptome ; Biotransformation ; Phylogeny ; },
abstract = {Per- and polyfluoroalkyl substances (PFAS) exhibit a widespread distribution across diverse global ecosystems throughout their lifecycle, posing substantial risks to human health. The persistence of PFAS makes biodegradation a challenging yet environmentally friendly solution for their treatment. In the authors' previous study, a bacterial consortium capable of reducing perfluorooctane sulfonate (PFOS) was successfully enriched from activated sludge. This study aimed to investigate the array of genes associated with PFOS reduction via biosorption and biotransformation to elucidate the metabolic pathways. Two metagenome-assembled genomes (MAGs) based on 16S rRNA sequences that share 99.86% and 97.88% similarity with Hyphomicrobium denitrificans and Paracoccus yeei, respectively were obtained. They were found to contain several genes encoding enzymes that potentially regulate biofilm formation of biosorption and facilitate the desulfonation and defluorination processes of biotransformation. Transcriptomic analysis demonstrated the high expression levels of these genes, including alkanesulfonate monooxygenase, catechol dioxygenase, (S)-2-haloacid dehalogenase and putative cytochrome P450, suggesting their involvement in PFOS biotransformation. The expression of these genes supports the presence of candidate metabolites of PFOS biotransformation detected in the previous study. These findings emphasise the significant potential of bacterial consortia and the crucial role played by genes encoding enzymes in facilitating the remediation of PFOS contaminants.},
}

*Fluorocarbons/metabolism
*Alkanesulfonic Acids/metabolism
*Sewage/microbiology
*Bacteria/genetics/metabolism/classification/isolation & purification
*Biodegradation, Environmental
*Metagenome
*RNA, Ribosomal, 16S/genetics
Genome, Bacterial
Transcriptome
Biotransformation
Phylogeny

@article {pmid40170118,
year = {2025},
author = {Li, J and Sun, W and Cao, Y and Wu, J and Duan, L and Zhang, M and Luo, X and Deng, Q and Peng, Z and Mou, X and Li, W and Wang, P},
title = {Increased temperature enhances microbial-mediated lignin decomposition in river sediment.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {89},
pmid = {40170118},
issn = {2049-2618},
support = {32200090//National Natural Science Foundation of China/ ; 91951205//National Natural Science Foundation of China/ ; 2023A1515012270//Guangdong Basic and Applied Basic Research Foundation, China/ ; },
mesh = {*Lignin/metabolism ; *Geologic Sediments/microbiology ; *Rivers/microbiology/chemistry ; *Temperature ; *RNA, Ribosomal, 16S/genetics ; Bacteria/metabolism/classification/genetics ; Carbon Dioxide/metabolism ; Carbon Cycle ; Metagenomics ; },
abstract = {BACKGROUND: Lignin, as the most abundant recalcitrant organic carbon in terrestrial ecosystems, plays a crucial role in the Earth's carbon cycle. After lignin entering aquatic environments, portion of it tends to accumulate in sediments, forming a stable carbon relatively reservoir. However, the increasing temperature caused by human activities may impact microbial-mediated lignin decomposition, thereby affecting sedimentary carbon reservoirs. Therefore, revealing how temperature affects microbial-mediated lignin decomposition in river sediment, a topic that remains elusive, is essential for comprehending the feedbacks between river carbon reservoirs and climate. To address this, we conducted stable isotope probing of river surface sediment using [13]C-lignin and [13]C-vanillin, and utilized a series of techniques, including CO2 production analysis, 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics, to identify the lignin-decomposing microbes and the effects of temperature on microbial-mediated lignin decomposition.

RESULTS: We found that elevated temperatures not only increased the total sediment respiration (total CO2) and the CO2 emissions from lignin/vanillin decomposition, but also enhanced priming effects. The [13]C-labled taxa, including Burkholderiales, Sphingomonadales, and Pseudomonadales, were identified as the main potential lignin/vanillin decomposers, and their abundances and activity significantly increased as temperature increased. Furthermore, we observed that increasing temperature significantly increased the activity of lignin decomposing pathways, including β-aryl ether fragments and 4,5-PDOG pathway. Additionally, as temperature increases, the transcriptional abundances of other carbon cycling related genes, such as pulA (starch decomposition) and xyla (hemicellulose decomposition), also exhibited increasing trends. Overall, our study elucidated the potential lignin-decomposing microbes and pathways in river sediment and their responses to temperature increasing.

CONCLUSIONS: Our study demonstrated that the temperature increasing can increase the rate of lignin/vanillin decomposition via affecting the activity of lignin-decomposing microbes. This finding indicates that the ongoing intensification of global warming may enhance the decomposition of recalcitrant organic carbon in river sediment, thereby impacting global carbon cycling. Video Abstract.},
}

*Lignin/metabolism
*Geologic Sediments/microbiology
*Rivers/microbiology/chemistry
*Temperature
*RNA, Ribosomal, 16S/genetics
Bacteria/metabolism/classification/genetics
Carbon Dioxide/metabolism
Carbon Cycle
Metagenomics

@article {pmid40169660,
year = {2025},
author = {Legrand, TPRA and Alexandre, PA and Wilson, A and Farr, RJ and Reverter, A and Denman, SE},
title = {Genome-centric metagenomics reveals uncharacterised microbiomes in Angus cattle.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {547},
pmid = {40169660},
issn = {2052-4463},
mesh = {Animals ; Cattle/microbiology ; *Metagenomics ; *Microbiota ; *Feces/microbiology ; Metagenome ; Saliva/microbiology ; Mouth/microbiology ; },
abstract = {Understanding the intricate nexus between cattle health and microbiome dynamics holds profound implications for enhancing animal productivity and welfare. However, our understanding of the role of these microbial communities is limited in beef cattle, especially in understudied body sites such as the oral and nasal microbiome. Here, using a genome-centric metagenomics approach, we recovered substantial metagenome-assembled genomes (MAGs) from the faecal, oral and nasal microbiome of Australian Angus cattle from different herds and life stages. The MAGs recovered from faecal samples were dominated by Bacillota and Bacteroidota, while the MAGs from saliva and nasal mucus samples were mainly associated with Pseudomonadota, Actinomycetota and Bacteroidota. Functional annotation of the MAGs revealed enriched pathways involved in the production of some amino acids, nucleic acids and short chain fatty acids (SCFA). The metabolic capacities of the MAGs were correlated with their taxonomy, notably at the phylum level. Overall, this study provides a comprehensive catalogue of MAGs to further our understanding of their role in the health and fitness of beef cattle.},
}

Animals
Cattle/microbiology
*Metagenomics
*Microbiota
*Feces/microbiology
Metagenome
Saliva/microbiology
Mouth/microbiology

@article {pmid40169555,
year = {2025},
author = {Li, H and Liu, P and Sun, T and Li, Y and Wu, J and Huang, Y and Yang, J and Yuan, M and Zhang, J and Yang, J and Wong, ML and Licinio, J and Zheng, P},
title = {Dynamic alterations of depressive-like behaviors, gut microbiome, and fecal metabolome in social defeat stress mice.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {115},
pmid = {40169555},
issn = {2158-3188},
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Stress, Psychological/metabolism/microbiology ; *Feces/microbiology/chemistry ; Male ; *Social Defeat ; *Metabolome ; *Disease Models, Animal ; *Depressive Disorder, Major/metabolism/microbiology ; *Behavior, Animal ; *Anhedonia ; Humans ; Mice, Inbred C57BL ; Female ; RNA, Ribosomal, 16S/genetics ; Depression/metabolism/microbiology ; },
abstract = {Gut microbiome is implicated in the onset and progression of major depressive disorder (MDD), but the dynamic alterations of depressive symptoms, gut microbiome, and fecal metabolome across different stages of stress exposure remain unclear. Here, we modified the chronic social defeat stress (CSDS) model to evaluate mice subjected to social defeat stress for 1, 4, 7, and 10 days. Behavioral tests, 16S rRNA, metagenomics, and fecal metabolomics were conducted to investigate the impact of stress exposure on behaviors, gut microbiota and fecal metabolites. We observed that depressive-like behaviors, such as anhedonia and social avoidance, worsened significantly as stress exposure increased. The microbial composition, function, and fecal metabolites exhibited distinct separations across the different social defeat stress groups. Mediation analysis identified key bacteria, such as Lachnospiraceae_UCG-001 and Bacteroidetes, and fecal metabolites like valeric acid and N-acetylaspartate. In our clinical depression cohort, we confirmed that fecal valeric acid levels, were significantly lower in depressive-like mice and MDD patients, correlating closely with stress exposure and anhedonia in mice. Further analysis of serum and brain metabolites in mice revealed sustained changes of N-acetylaspartate abundance in fecal, serum, and cortical samples following increasing stress exposure. Together, this study elucidated the characteristics of depressive-like behaviors, gut microbiome, and fecal metabolome across various social defeat stress exposure, and identified key bacteria and fecal metabolites potentially involved in modulating social defeat stress response and depressive-like behaviors, providing new insights into the pathogenesis and intervention of depression.},
}

Animals
*Gastrointestinal Microbiome
Mice
*Stress, Psychological/metabolism/microbiology
*Feces/microbiology/chemistry
Male
*Social Defeat
*Metabolome
*Disease Models, Animal
*Depressive Disorder, Major/metabolism/microbiology
*Behavior, Animal
*Anhedonia
Humans
Mice, Inbred C57BL
Female
RNA, Ribosomal, 16S/genetics
Depression/metabolism/microbiology

@article {pmid40169141,
year = {2025},
author = {Zhang, J and Ying, X and Hu, R and Huang, Y and Wang, R and Wu, L and Han, D and Ma, R and He, K},
title = {Metagenomic and metabolomic analysis of gut microbiome's role in spinal cord injury recovery in rats.},
journal = {Biomolecules & biomedicine},
volume = {},
number = {},
pages = {},
doi = {10.17305/bb.2025.12164},
pmid = {40169141},
issn = {2831-090X},
abstract = {Spinal cord injury (SCI) induces profound systemic changes, including disruptions in gut microbiome composition and host metabolism. This study aimed to investigate the impact of SCI on gut microbial diversity and serum metabolites in rats, and to explore potential microbiome-metabolite interactions that may influence recovery. Male Sprague-Dawley (SD) rats were assigned to either SCI or sham-operated groups. Fecal samples were collected for whole-genome metagenomic sequencing, and serum samples were analyzed using untargeted metabolomics. Gut microbial composition and diversity were assessed using α- and β-diversity indices, while Linear discriminant analysis effect size (LEfSe) identified differentially abundant taxa. Metabolomic pathway analysis was performed to detect significant changes in serum metabolites, and Spearman's correlation was used to evaluate associations between gut microbes and metabolites. SCI significantly altered gut microbiota composition, with increased proportions of Ligilactobacillus and Staphylococcus, and decreased proportions of Lactobacillus and Limosilactobacillus. Metabolomic analysis revealed disrupted energy metabolism and elevated oxidative stress in SCI rats, as indicated by increased serum levels of pyruvate and lactic acid. Correlation analysis further identified significant associations between specific gut bacteria and key metabolites, suggesting microbiome-driven metabolic dysregulation following SCI. These findings highlight significant interactions between the gut microbiota and host metabolism after SCI and suggest that microbiome-targeted interventions may hold therapeutic potential for improving recovery by modulating metabolic function and oxidative stress responses.},
}

@article {pmid40156868,
year = {2025},
author = {Yang, W and Luyten, Y and Reister, E and Mangelson, H and Sisson, Z and Auch, B and Liachko, I and Roberts, RJ and Ettwiller, L},
title = {Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.},
journal = {Nucleic acids research},
volume = {53},
number = {6},
pages = {},
pmid = {40156868},
issn = {1362-4962},
support = {//New England Biolabs, Inc./ ; R44AI172703/GF/NIH HHS/United States ; //Bill & Melinda Gates Foundation/ ; },
mesh = {*Methyltransferases/metabolism/genetics ; *Microbiota/genetics ; DNA Methylation ; Bacteriophages/genetics/enzymology ; High-Throughput Nucleotide Sequencing ; Bacteria/genetics/enzymology ; Substrate Specificity ; Bacterial Proteins/metabolism/genetics ; Sequence Analysis, DNA/methods ; DNA, Viral/genetics/metabolism ; },
abstract = {Methylation patterns in bacteria can be used to study restriction-modification or other defense systems with novel properties. While m4C and m6A methylation are well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 (rapid identification of methyltransferase specificity sequencing) on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on bacteriophage DNA and compared with host DNA, strengthening evidence for phage-host interactions. Applied to three different microbiomes, the method unveiled over 1900 motifs that were deposited in REBASE. The motifs include a novel eight-base recognition site (CATm5CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5C methyltransferase specificities, providing insights into bacterial biology and biotechnological applications.},
}

*Methyltransferases/metabolism/genetics
*Microbiota/genetics
DNA Methylation
Bacteriophages/genetics/enzymology
High-Throughput Nucleotide Sequencing
Bacteria/genetics/enzymology
Substrate Specificity
Bacterial Proteins/metabolism/genetics
Sequence Analysis, DNA/methods
DNA, Viral/genetics/metabolism

@article {pmid40169073,
year = {2025},
author = {Sun, L and Yin, Y and Guo, Y and Chen, H and Wang, H},
title = {Metagenomic Next-Generation Sequencing Enhances the Diagnosis of Q Fever: A Retrospective Observational Study.},
journal = {Travel medicine and infectious disease},
volume = {},
number = {},
pages = {102845},
doi = {10.1016/j.tmaid.2025.102845},
pmid = {40169073},
issn = {1873-0442},
abstract = {BACKGROUND: Q fever, a global zoonosis, poses a significant challenge for public health due to its varied and nonspecific clinical presentations, making diagnosis difficult. Metagenomic next-generation sequencing (mNGS) is a potential tool for diagnosing Q fever.

METHODS: This retrospective observational study was conducted on patients with Q fever admitted to Peking University People's Hospital, from May 2023 to November 2024. mNGS was performed using the patient's peripheral blood, and the qPCR of Coxiella burnetii was also adopted. Subsequently, the clinical data of patients diagnosed with Q fever were systematically evaluated.

RESULTS: Twelve peripheral blood samples of 12 patients were detected Coxiella burnetii positive by mNGS. Most patients were male (10, 83.33%). Fever (12, 100%), muscle soreness (8, 66.7%), and headache (4, 33.3%) were the most common clinical manifestations. Specific qPCR of Coxiella burnetii was detected positive in 8 patients. Chronic Q fever was diagnosed in two patients, who had aortic valve replacement, and their immunological markers, like anti-nuclear were elevated. Once the diagnosis was clear, proper antibiotics were used, and all patients were discharged in better health.

CONCLUSION: Metagenomic next-generation sequencing enhances the diagnosis of Q fever, especially for patients displaying atypical and various clinical symptoms and having unclear epidemiological data or histories of antibiotic use.},
}

@article {pmid40169018,
year = {2025},
author = {Wallace, MA and Wille, M and Geoghegan, J and Imrie, RM and Holmes, EC and Harrison, XA and Longdon, B},
title = {Making sense of the virome in light of evolution and ecology.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2044},
pages = {20250389},
doi = {10.1098/rspb.2025.0389},
pmid = {40169018},
issn = {1471-2954},
support = {//Leverhulme Trust/ ; //National Health and Medical Research Council (NHMRC)/ ; //Royal Society/ ; /WT_/Wellcome Trust/United Kingdom ; //Webster Family Chair in Viral Pathogenesis/ ; //New Zealand Royal Society Rutherford Discovery Fellowship/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; },
mesh = {*Virome ; *Viruses/genetics ; Biological Evolution ; Metagenomics ; Ecology ; Ecosystem ; Phylogeny ; },
abstract = {Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.},
}

*Virome
*Viruses/genetics
Biological Evolution
Metagenomics
Ecology
Ecosystem
Phylogeny

@article {pmid40168930,
year = {2025},
author = {Tang, GX and Huang, YH and Feng, LW and Hu, YC and Wei, JL and Lü, H and Liu, LH and Zhao, HM and Xiang, L and Li, H and Mo, CH and Li, YW and Cai, QY},
title = {New insights into rhizosphere bacterial community shaped by lettuce genotypes for divergent degradation efficiencies of phthalates.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138077},
doi = {10.1016/j.jhazmat.2025.138077},
pmid = {40168930},
issn = {1873-3336},
abstract = {Rhizosphere dissipation of organic pollutants benefits safe utilization of the polluted agricultural soil. Nevertheless, dissipation variation of phthalates (PAEs) in rhizosphere among different vegetable genotypes and the related microbial mechanisms remain unknown. Here, twelve lettuce cultivars with different genetic relationships identified by 18S rRNA gene sequencing were cultivated in soil spiked with di-(2-ethylhexyl) phthalate (DEHP). Bacterial communities and function genes in rhizosphere of lettuce were analyzed by 16S rRNA gene and metagenomic sequencing. Results showed significant variations in DEHP concentrations of roots (2.8-15.3 mg/kg) and shoots (0.70-1.8 mg/kg) among 12 cultivars. Notably, cultivars L11 and L12 showed the lowest DEHP accumulation in roots and shoots, being lower by 82 % and 58 % than the highest accumulators (cultivars L5 and L6), respectively. This accumulation variation was closely connected with their genetic relationships and exhibited genotype-dependent trait. The significantly different bacterial community diversities and structures were recorded in rhizosphere among 12 cultivars. Especially, bacterial communities in rhizosphere of cultivars L11 and L12 (low-DEHP accumulators with high DEHP dissipation) strengthened their adaptation by enriching pollutant-resistant taxa, increasing extracellular polymeric substance contents and biofilm formation, as well as constructing complex ecological networks under DEHP pollution. Moreover, PAE-degrading bacteria and genes (e.g., hydrolase65, phtAb, and pcaI) in rhizosphere were enriched by low-DEHP accumulators, which benefited DEHP removal and subsequently safe agricultural products. This study provides new insights into microbial mechanisms on rhizosphere DEHP degradation and its correlation with accumulation variation among different crop genotypes.},
}

@article {pmid40168814,
year = {2025},
author = {Harish, J and Prasannakumar, MK and Venkateshbabu, G and Karan, R and Mahesh, HB and Devanna, P and Sarangi, AN and Patil, SS and Tejashwini, V and Lohithaswa, HC and Kagale, S},
title = {Molecular and genomic insights into the pathogenicity of Sarocladium zeae causing maize stalk rot disease.},
journal = {Microbiological research},
volume = {296},
number = {},
pages = {128146},
doi = {10.1016/j.micres.2025.128146},
pmid = {40168814},
issn = {1618-0623},
abstract = {Post-flowering stalk rot (PFSR) of maize has been traditionally associated with Fusarium verticillioides. Conversely, this study reveals Sarocladium zeae as a new phytopathogen responsible for the disease. This research was conducted to gain a comprehensive understanding of S. zeae by investigating its pathogenic mechanisms, profiling its metabolome, and deciphering its genomic characteristics. Maize stalks displaying stalk rot symptoms were collected from various regions of India. S. zeae was isolated and characterized using ITS and TEF-1α sequencing. Cultures of S. zeae exhibited slower growth on PDA medium compared to F. verticillioides, which dominated due to its rapid growth rate. Pathogenicity was confirmed through a toothpick inoculation assay. The symptoms induced by S. zeae was characterized by powdery, dry, pale brown-black discoloration, were distinct from the typical dark-brown lesions of Fusarium stalk rot. Enzymatic assays revealed increased activity of β-glucosidase, cellulase, and pectate lyase in infected stalks, while qPCR analysis showed the upregulation of endoglucanase and β-glucosidase genes in infected stalks underscored the critical roles of cellulase and β-glucosidase in pathogenicity Metagenomic analysis identified S. zeae as the predominant species in infected stalk samples. Genome assembly revealed the pathogen's complete genetic repertoire, including genes encoding effector proteins and CAZymes involved in cell wall degradation. Moreover, we have demonstrated that the S. zeae as a causal agent of maize stalk rot and further shedding light on its transition from an endophytic to a pathogenic lifestyle. Taken together, this research represents the first report to attribute maize stalk rot to S. zeae and to present its complete genome assembly, significantly advancing the understanding of its biology and pathogenic potential.},
}

@article {pmid40168753,
year = {2025},
author = {Ji, X and Yu, X and Xu, Y and Wu, Q and Madadi, M and Khaneghah, AM},
title = {Initial acidity regulates microbial sulfur metabolism in the spontaneous fermentation of sesame flavor-type baijiu.},
journal = {International journal of food microbiology},
volume = {435},
number = {},
pages = {111182},
doi = {10.1016/j.ijfoodmicro.2025.111182},
pmid = {40168753},
issn = {1879-3460},
abstract = {Volatile sulfur compounds play a crucial role in fermented foods, however, their metabolism during spontaneous food fermentation remains underexplored. With 3-(methylthio)-1-propanal as a case, we revealed the effect of initial acidity on the sulfur metabolism during sesame flavor-type baijiu fermentation. Results showed that the content of 3-(methylthio)-1-propanal reached 383.29 μg/kg with 1.8 mmol/10 g of the initial acidity, and it decreased to 320.54 μg/kg when the initial acidity increased to 2.4 mmol/10 g. Metagenomic analysis identified 11 core microbes associated with sulfur metabolism, characterized by gene abundance (> 0.5 %) and catalytic enzyme distribution frequency (> 10 %). Saccharomyces was the main producer of sulfur compounds. Lactobacillus was an important player in the methyl cycle pathway of sulfur metabolism. Low initial acidity increased the abundance of Lactobacillus and the content of genes associated with the methyl cycle pathway (P < 0.05). This resulted in a significant increase of methionine (253.26 mg/kg) (P < 0.05) and 3-(methylthio)-1-propanal contents (383.29 μg/kg) (P < 0.05). In simulated fermentation, the content of 3-(methylthio)-1-propanal significantly increased by 2.91 folds when Saccharomyces cerevisiae was cocultured with Lactobacillus acetotolerans (P < 0.05), and the transcription of genes related to sulfur metabolism significantly increased by 33.71 folds (P < 0.05). Results indicated that low initial acidity increased the abundance of Lactobacillus, which mediates the methyl cycle pathway in the sulfur metabolism, thereby increasing the contents of methionine and volatile sulfur compounds. This work provided insight into the regulation of metabolic mechanisms of volatile sulfur compounds in baijiu fermentation.},
}

@article {pmid40168325,
year = {2025},
author = {Yun, H and Seo, JH and Kim, YK and Yang, J},
title = {Examining the bacterial diversity including extracellular vesicles in air and soil: implications for human health.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0320916},
doi = {10.1371/journal.pone.0320916},
pmid = {40168325},
issn = {1932-6203},
mesh = {*Extracellular Vesicles/metabolism ; *Soil Microbiology ; Humans ; *Bacteria/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Air Microbiology ; Microbiota ; Biodiversity ; Metagenomics/methods ; },
abstract = {As the significance of human health continues to rise, the microbiome has shifted its focus from microbial composition to the functional roles it plays. In parallel, interest in ultrafine particles associated with clinically important impact has been increasing. Bacterial extracellular vesicles (BEVs), involved in systemic microbiome activity, are nano-sized spherical vesicles (20 - 100 nm in diameter) containing DNA, RNA, proteins, and lipids. They are known to be absorbed into the body potentially through air and soil, circulate in the blood, and directly impact diseases by affecting organs. Therefore, the aim of this study is to examine the biodiversity of bacteria and BEVs and predicted functional pathways. We sampled air and soil samples in Seoul, Korea and analyzed metagenomics based on 16S rRNA sequencing. At the phylum levels, Firmicutes in BEVs from soil and air were significantly higher than in bacteria, and Acidobacteria in both bacteria and BEVs from soil were significantly higher than from air (p < 0.05). The most dominant genera were Pseudomonas in bacteria from air and soil; and Escherichia-Shigella in BEVs from air and soil. In addition, Two-component system (ko02020) and ATP-binding cassette transporters (ko02010) were dominant functional pathways in both air and soil. The most functional pathways and orthologous groups were significantly different between air and soil (p < 0.05). In conclusion, human health can be affected differently depending on type of environment. Future study is necessary to have a better understanding of human health effects from environmental microbiota.},
}

*Extracellular Vesicles/metabolism
*Soil Microbiology
Humans
*Bacteria/genetics/classification/metabolism
*RNA, Ribosomal, 16S/genetics
Air Microbiology
Microbiota
Biodiversity
Metagenomics/methods

@article {pmid40167463,
year = {2025},
author = {Sun, C and Liu, H and Teng, J and Feng, W and Wang, D and Wang, X and Zhao, J and Wang, Q},
title = {Impact of Microplastic Exposure on Sand Crab Scopimera globosa Behavior: Implications for Microplastic Transport and Sulfur Cycling through Bioturbation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01192},
pmid = {40167463},
issn = {1520-5851},
abstract = {The accumulation of microplastics (MPs) in estuarine regions and their ecological consequences have become global environmental concerns. Estuarine sediments function as major sinks for MPs and hotspots for critical biogeochemical processes, which are significantly influenced by benthic bioturbation. However, the impacts of MPs on the behavior of highly mobile benthic organisms and the ecological effects of bioturbation activities remain poorly understood. This study utilized laboratory simulation experiments, AI-based behavioral tracking, and metagenomic sequencing to systematically examine the effects of sand crab bioturbation on MPs migration, sediment physicochemical properties and sulfur cycling processes. Results demonstrated that sand crab bioturbation substantially enhanced the vertical migration of MPs, with fluxes to surface layers and the overlying water increasing by 27-fold compared to undisturbed conditions. Exposure to PE-MPs reduced sand crabs' surface foraging intensity and induced behavioral abnormalities. The crabs actively avoided MPs, exhibiting a preference for burrowing and residing in deeper sediment layers. This behavioral shift significantly altered microbial community distributions, with an increase of Pseudomonadota abundance and a decline of sulfate-reducing bacteria Thermodesulfobacteriota abundance. Furthermore, bioturbation accelerated sulfate oxidation in deeper sediments while inhibited dissimilatory sulfate reduction. This study is the first to identify the role of bioturbation in promoting the upward migration of MPs in sediments. Altered sand crab bioturbation will impact sediment biogeochemistry, estuarine function, and coastal resilience.},
}

@article {pmid40167332,
year = {2025},
author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF},
title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14105},
doi = {10.1111/1755-0998.14105},
pmid = {40167332},
issn = {1755-0998},
support = {CEEC/0482/2020//Fundação para a Ciência e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Fundação para a Ciência e a Tecnologia/ ; LA/P/0069/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Fundação para a Ciência e a Tecnologia/ ; UID/04292/2020//Fundação para a Ciência e a Tecnologia/ ; UID/BIA/00329/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; },
abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.},
}

@article {pmid40166061,
year = {2025},
author = {Zhang, L and Guo, Y and Wang, X and Gai, W and Liu, L},
title = {Severe adenovirus pneumonia complicated by acute respiratory distress syndrome in immunocompetent patients: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1524783},
pmid = {40166061},
issn = {2296-858X},
abstract = {BACKGROUND: Human adenovirus (HAdV) is one of the most important pathogens detected in acute respiratory illness in pediatric and immunocompromised patients, but it is relatively rare to develop severe pneumonia in immunocompetent patients. We analyzed the clinical features, as well as the diagnosis and treatment processes, to provide a reference for clinical practice.

CASE PRESENTATION: We report a case of severe pneumonia caused by HAdV, complicated by acute respiratory distress syndrome (ARDS), in an immunocompetent patient with no underlying conditions. Chest computed tomography (CT) revealed consolidation in the right lower lung. Conventional microbial tests were negative, but metagenomic next-generation sequencing (mNGS) identified a large number of HAdV sequences in blood and sputum. Together with the clinical symptoms, this confirmed the diagnosis of severe pneumonia caused by HAdV. The patient was discharged after timely treatment with cidofovir.

CONCLUSION: In our study, we described a rare case of severe pneumonia caused by HAdV, complicated by ARDS, in an immunocompetent patient. mNGS proves to be an effective diagnostic tool for guiding treatment decisions.},
}

@article {pmid40165946,
year = {2025},
author = {Guo, Z and Wang, X and Li, Y and Zhang, Y and Guo, P and Zhang, J and Zhang, Z and Ma, X},
title = {Evaluation of the therapeutic effect of pomegranate peel ginger ultrafine powder on chronic enteritis in mice by regulating intestinal microbiota.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1563225},
pmid = {40165946},
issn = {1664-3224},
mesh = {Animals ; Mice ; *Pomegranate/chemistry ; *Zingiber officinale ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Enteritis/drug therapy/microbiology/veterinary ; *Aquaporins/metabolism/genetics ; Cytokines/metabolism ; Chronic Disease ; Disease Models, Animal ; Powders ; Plant Extracts/pharmacology/administration & dosage ; Aquaporin 3 ; Aquaporin 4 ; },
abstract = {To explore the efficacy and mechanism of Pomegranate peel Ginger ultrafine powder (PG) in treating chronic enteritis in mice. Sixty SPF-grade mice were randomly divided into a blank group, a model group, loperamide hydrochloride group (5 mg/kg), a high-dose PG group (100 mg/kg), a medium-dose group (50 mg/kg), and a low-dose group (25 mg/kg), with 10 mice in each group and an equal number of males and females. A chronic enteritis mouse model was established using a multifactorial method of low temperature + ice water + castor oil. The blank group was given an equal amount of physiological saline intragastrically, while the other groups were intervened with corresponding drugs for 7 consecutive days. After 7 days, samples were collected, and Enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of interleuckin 1β (IL-1β), IL-6, and Tumor necrosis factorα(TNF-α) in mouse serum. HE staining was used to examine the pathological changes in the small intestine. oxidative reagent kits were used to detect the content of total superoxide dismutase(T-SOD) and Malondialdehyde (MDA) in the small intestine. Western blot was used to detect the expression of Aquaporin 8(AQP8) proteins in the small intestine. Real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to detect the expression of AQP3, AQP4, AQP8, and Sodium/hydrogen exchanger 8 (NHE8) genes in the small intestine. metagenomics was used to detect the gut microbiota in mouse feces. Compared with the model group, all doses of PG groups reduced the levels of IL-1β, IL-6, and TNF-α in mouse serum (P<0.05), improved pathological changes in the small intestine, increased the content of T-SOD in the small intestine tissue, reduced the content of MDA, increased the expression of AQP4 and AQP8 mRNA, and decreased the expression of AQP3 and NHE8 mRNA (P<0.05), increased the expression of AQP8 protein. PG could improve the pathological changes of chronic enteritis in mice, enhance antioxidant capacity, and alleviate diarrhea caused by chronic enteritis by downregulating the expression of intestinal epithelial transport proteins and acute-phase proteins, and altering gut microbiota.},
}

Animals
Mice
*Pomegranate/chemistry
*Zingiber officinale
*Gastrointestinal Microbiome/drug effects
Male
Female
*Enteritis/drug therapy/microbiology/veterinary
*Aquaporins/metabolism/genetics
Cytokines/metabolism
Chronic Disease
Disease Models, Animal
Powders
Plant Extracts/pharmacology/administration & dosage
Aquaporin 3
Aquaporin 4

@article {pmid40165815,
year = {2025},
author = {Battur, M and Aaqil, M and Zheng, J and Lin, HX and Chuluunotgon, B and Zorigtbaatar, T and Zhao, C and Tian, Y},
title = {Exploring the effects of milk-enriched walnut soy sauce: Insights from GC-IMS and metagenomics approach to flavor and microbial shifts.},
journal = {Food chemistry: X},
volume = {27},
number = {},
pages = {102364},
pmid = {40165815},
issn = {2590-1575},
abstract = {This study investigates the impact of milk addition on the fermentation of walnut soy sauce, using Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) and metagenomics to analyze flavor profiles and microbial dynamics. GC-IMS analysis showed significant increases in volatile compounds such as esters (ethyl acetate), aldehydes (hexanal), and alcohols (isoamyl alcohol), enhancing the aroma and taste. Metagenomic analysis revealed that milk increased microbial diversity, with Weissella and Lactobacillus dominating early fermentation. The milk-enriched soy sauce (SYM) exhibited higher amino acid nitrogen (2.67 g/L), and total nitrogen (7.18 g/L) compared to the control, indicating improved nutritional quality. Protease activity peaked at 2438.5 U/g for neutral protease, supporting efficient protein hydrolysis. Relative Odor Activity Value (ROAV) analysis identified 29 key flavor compounds, including 3-methyl butanol and ethyl 2-methyl butyrate, which contributed fruity and buttery notes to SYM. These results suggest that milk enhances microbial growth and improves both flavor and nutritional quality of walnut soy sauce.},
}

@article {pmid40165787,
year = {2025},
author = {Huang, Z and Wang, J and He, X and Zhang, M and Ren, X and Yu, W and Yao, S and Ji, K},
title = {Divergent profiles of rhizosphere soil carbon and nitrogen cycling in Pinus massoniana provenances with different types of carbon storage.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537173},
pmid = {40165787},
issn = {1664-302X},
abstract = {INTRODUCTION: In subtropical China, P. massoniana is a timber tree species which have a great potential for carbon sequestration. However, few studies have investigated how varying levels of carbon storage in P. massoniana provenances affect the soil microbial functional potential related to nutrient cycling within the rhizosphere.

METHODS: In this investigation, metagenomic sequencing was employed to explore the differences in carbon and nitrogen cycling capabilities among rhizosphere microbial communities within P. massoniana provenances, categorized by high, medium, and low levels of carbon storage.

RESULTS: Our findings revealed a significant increase in the relative abundance of Acidobacteriota and Ascomycota by 23 and 61%, respectively, whereas Basidiomycota significantly decreased by 8% in the rhizosphere of P. massoniana provenances with high carbon storage compared with those with low carbon storage. The variability in carbon storage among P. massoniana provenances was linked to marked disparities in the presence of key genes essential for carbon and nitrogen cycling within their rhizosphere soils.

DISCUSSION: Notably, in P. massoniana provenances characterized by high carbon storage, the rhizosphere presented a significantly elevated presence of genes associated with carbon decomposition, carbon assimilation, methane generation, and denitrification, in stark contrast to provenances with medium and low carbon storage. Furthermore, P. massoniana provenances with high carbon storage rates presented increased transformation and availability of soil carbon and nitrogen, along with increased potential for ecological restoration. Moreover, the rhizosphere soil nitrification of P. massoniana provenances with low carbon storage surpassed that of other provenances, leading to increased available nitrogen content and elevated nitrate leaching risk. In the P. massoniana rhizosphere, critical soil factors, including soil organic carbon (SOC), total nitrogen (TN), pH, and nitrate nitrogen (NO3 [-]-N) content, significantly shape the functionality of genes associated with carbon and nitrogen cycling. In conclusion, our study lays a scientific foundation for establishing P. massoniana plantations and identifying P. massoniana provenances with superior ecological value and potential.},
}

@article {pmid40165255,
year = {2025},
author = {Xie, B and Dong, C and Zhao, X and Qu, L and Lv, Y and Liu, H and Xu, J and Yu, Z and Shen, H and Shang, Y and Zhao, X and Zhang, J},
title = {Structural and functional alteration of the gut microbiomes in ICU staff: a cross-sectional analysis.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {141},
pmid = {40165255},
issn = {1466-609X},
support = {82402568//National Natural Science Foundation of China/ ; 82472223//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/physiology ; *Intensive Care Units/organization & administration/statistics & numerical data ; Male ; Female ; Prospective Studies ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Cohort Studies ; Feces/microbiology ; Health Personnel/statistics & numerical data ; },
abstract = {BACKGROUND: 16S rRNA sequencing has revealed structural alterations in the gut microbiomes of medical workers, particularly those working in intensive care unit (ICU). This study aims to further compare the taxonomic and functional characteristics of gut microbiomes between ICU staff and non-medical individuals using metagenomic sequencing.

METHODS: A prospective cross-sectional cohort study was conducted, fecal samples from 39 individuals in each group-ICU staff and non-medical subjects were analyzed using metagenomic sequencing. PERMANOVA (using the adonis function) was employed to analyze the genus-level profiles and assess the impact of individual parameters on the gut microbiome. Multiple databases were utilized to annotate and compare the functional differences in gut microbiomes between the two groups.

RESULTS: We observed that ICU staff exhibited a significant decrease in gut microbiome diversity, characterized by a marked decline in Actinobacteria and a substantial increase in Bacteroides and Bacteroidaceae. CAZy annotation revealed a notable increase in carbohydrate-active enzymes within the ICU staff cohort. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further indicated an elevated risk of endocrine and metabolic disorders, along with enhanced glycan biosynthesis and metabolism. Additionally, KEGG pathway enrichment analysis highlighted significant enrichment in cancer-related pathways. Analysis using the Virulence Factor Database (VFDB) showed a higher abundance of virulence factors associated with immune modulation, invasion, and antimicrobial activity/competitive advantage among ICU staff. Notably, no discernible difference in the presence of antibiotic resistance genes within the gut microbiomes was observed between the two groups. Importantly, all aforementioned differences demonstrated clear gender disparities.

CONCLUSIONS: Our findings indicated that ICU staff exhibited a reduction in gut microbiome diversity which was associated with an increase in virulence factors and carbohydrate-active enzymes, as well as with a heightened susceptibility to endocrine and metabolic diseases and cancers.},
}

Humans
Cross-Sectional Studies
*Gastrointestinal Microbiome/physiology
*Intensive Care Units/organization & administration/statistics & numerical data
Male
Female
Prospective Studies
Adult
Middle Aged
RNA, Ribosomal, 16S/analysis/genetics
Cohort Studies
Feces/microbiology
Health Personnel/statistics & numerical data

@article {pmid40165201,
year = {2025},
author = {Lin, L and Peng, X and Chen, L and Dong, L and Zhong, L},
title = {Case report: novel NFKB2 variant associated with pediatric eosinophilic granulomatosis with polyangiitis (EGPA) in the COVID-19 pandemic.},
journal = {Pediatric rheumatology online journal},
volume = {23},
number = {1},
pages = {35},
pmid = {40165201},
issn = {1546-0096},
mesh = {Humans ; Female ; *COVID-19/complications ; Child ; *NF-kappa B p52 Subunit/genetics ; SARS-CoV-2 ; Churg-Strauss Syndrome/genetics/diagnosis ; Granulomatosis with Polyangiitis/genetics/diagnosis ; },
abstract = {BACKGROUND: Childhood-onset eosinophilic granulomatosis with polyangiitis (cEGPA) is a rare type of systemic autoimmune disorder. Variants in the NFKB2 gene can manifest as common variable immunodeficiency or combined immunodeficiency, often accompanied by autoimmunity and ectodermal dysplasia. Here, we report a case of a Chinese patient who carries NFKB2 variants that coexist with cEGPA, a novel combination which, to our knowledge, has not been previously published.

CASE PRESENTATION: We reported a 9-year and 10-month-old girl who presented with cough, wheezing, dyspnea, hypereosinophilia, and vasculitis. Notably, she had significant bilateral pulmonary interstitial lesions. We performed metagenomic next-generation sequencing (mNGS), bronchoscopy and immunological analysis. She was considered to have refractory cEGPA after six months of corticosteroid and immunosuppressive treatment. Tapering off corticosteroids posed a challenge, and multiple immunosuppressive agents were ineffective. Our patient suffered from recurrent fever, wheezing, dyspnea and perianal abscess, along with life-threatening infections, including pneumocystis jirovecii pneumonia (PJP) and severe coronavirus disease 2019 (COVID-19) pneumonia during the pandemic. Her cytokines and inflammatory markers showed a profound collapse. She developed significant hypoxemia, which necessitated mechanical ventilation. Primary immunodeficiency gene panel testing revealed a novel de novo variant in NFKB2 (c.2578 + 2 dup) that was classified as pathogenic. Despite treatment with antibacterial, antiviral, and antifungal agents, biologics, and plasma exchange, she ultimately succumbed to respiratory failure.

CONCLUSIONS: This case report establishes a novel link between NFKB2 variants and EGPA, particularly in the context of the COVID-19 pandemic. This study expands the spectrum of NFKB2 variants and vividly illustrates the complex interrelationships among autoimmunity, infection, and immunodeficiency.},
}

Humans
Female
*COVID-19/complications
Child
*NF-kappa B p52 Subunit/genetics
SARS-CoV-2
Churg-Strauss Syndrome/genetics/diagnosis
Granulomatosis with Polyangiitis/genetics/diagnosis

@article {pmid40165140,
year = {2025},
author = {Trivett, H and Darby, AC and Oyebode, O},
title = {Academic and clinical perspectives of metagenome sequencing as a diagnostic tool for infectious disease: an interpretive phenomenological study.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {448},
pmid = {40165140},
issn = {1471-2334},
mesh = {Humans ; *Metagenome ; *Communicable Diseases/diagnosis ; *COVID-19/diagnosis ; Metagenomics/methods ; SARS-CoV-2/genetics ; England ; },
abstract = {BACKGROUND: Effective infectious disease diagnostics (IDD) are vital for informing clinical decision-making regarding the treatment and patient management of disease and infections. In England, conventional clinical methods rely upon culture-dependent techniques, and there has been little shift in the acceptance and integration of culture-independent sequencing methods into routine clinical IDD. This study explored stakeholders' experiences within IDD, including those working in clinical settings and those conducting research at the forefront of microbial genomics. From the participants' experiences, the study aimed to identify barriers and facilitators driving the development and implementation of metagenome sequencing as a routine diagnostic.

METHODS: Virtual semi-structured interviews were conducted with purposively selected individuals involved in IDD. The interviews explored the experiences of implementing metagenome sequencing as a diagnostic tool and decisions about which diagnostics are used for identifying bacteria-causing infections. Thematic analysis was used to analyse the data, and an Interpretive Phenomenological approach was used throughout.

RESULTS: Ten individuals were interviewed between July 2021 and October 2021, including clinical scientists, consultants, and professors in academia. Their experience ranged from limited knowledge of metagenome sequencing to an expert understanding of the phenomenon. The thoughts and perspectives of participants of the study could be grouped into five themes: Availability of diagnostics for infectious diseases; Clinical laboratory infrastructure; Ethical Data Sharing: Enhancing metagenomics through Open Access; Case study in action: COVID-19; and The importance of communication to improve developments of new diagnostics. Participants recognised the need for new diagnostics to be implemented to overcome the limitations of current diagnostic approaches but highlighted the barriers to integrating new diagnostics into clinical settings, such as the impact on clinical decision-making, accreditation, and cost. Further, participants felt that lessons could be learnt from using metagenomics in COVID-19 and how other diagnostic platforms have been integrated into clinical settings over the last 20 years.

CONCLUSIONS: The study provided insights into stakeholders' perspectives and opinions to address the knowledge gap in current literature and identified barriers and facilitators which drive the implementation of metagenome sequencing as a routine IDD in clinical settings. Knowledge of new and upcoming genomic diagnostic testing is not equally distributed throughout the UK, impacting the understanding and drive to integrate metagenome sequencing into routine clinical diagnostics. Improvements in access to new diagnostics could improve patient treatment and management and positively impact population health.},
}

Humans
*Metagenome
*Communicable Diseases/diagnosis
*COVID-19/diagnosis
Metagenomics/methods
SARS-CoV-2/genetics
England

@article {pmid40165002,
year = {2025},
author = {Wang, H and Su, Q and Sun, H and Meng, Y and Xing, X and Zheng, H and Li, Y},
title = {Unexpected Microbial and Genetic Diversity in the Gut of Chinese Giant Salamander.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12976},
pmid = {40165002},
issn = {1749-4877},
abstract = {The gut microbiome is crucial for animal health, yet the diversity of the critically endangered Chinese giant salamander's gut microbiota remains largely uncharacterized. In this study, we first conducted a comprehensive landscape survey of the gut microbiome of the Chinese giant salamander using 16S rRNA sequencing across a wide geographic range, identifying a distinct microbial cluster within its habitat. Subsequently, using shotgun metagenomes, we recovered 1518 metagenome-assembled genomes. Notably, 85% of the newly identified genomes could not be assigned to any known bacterial species, indicating a significant presence of novel taxa in Chinese giant salamander intestines. We observed substantial species-level variations in the gut microbiome across different age groups, with some novel species uniquely enriched in specific age populations. From the gut symbionts, we established a gene catalog comprising 3 278 107 non-redundant protein-coding genes, of which 7733 were annotated into recognized KEGG orthology groups. Additionally, we found that the gut microbiota of the Chinese giant salamander exhibits enhanced functional capacities explicitly in lipid metabolism and assimilatory sulfate reduction. Significant variations in the abundance of related enzyme-encoding genes across age groups suggest the unique roles of microbial metabolism in salamander health. By identifying microbial genomes and constructing an integrated gene catalog from metagenomic data, we significantly expand the resources available for research on the gut microbiome of the Chinese giant salamander, paving the way for further investigations into its ecological and health-related implications.},
}

@article {pmid40164980,
year = {2025},
author = {Otani, S and Louise Jespersen, M and Brinch, C and Duus Møller, F and Pilgaard, B and Egholm Bruun Jensen, E and Leekitcharoenphon, P and Aaby Svendsen, C and Aarestrup, AH and Sonda, T and Sylvina, TJ and Leach, J and Piel, A and Stewart, F and Sapountzis, P and Kazyoba, PE and Kumburu, H and Aarestrup, FM},
title = {Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2484385},
doi = {10.1080/19490976.2025.2484385},
pmid = {40164980},
issn = {1949-0984},
mesh = {Animals ; *Diet ; *Hominidae/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome ; *Life Style ; Humans ; Adaptation, Physiological ; Pan troglodytes/microbiology ; Metagenome ; Phylogeny ; Africa ; },
abstract = {In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza and wild chimpanzees, identified similar bacterial richness and diversity surpassing those of westernized populations. While hominids share core bacterial communities, they also harbor distinct, population-specific bacterial taxa tailored to specific diets, ecology and lifestyles, differentiating non-indigenous and indigenous humans and chimpanzees. Even amongst shared bacterial communities, several core bacteria have co-diversified to fulfil unique dietary degradation functions within their host populations. These co-evolutionary trends extend to non-bacterial elements, such as mitochondrial DNA, antimicrobial resistance, and parasites. Our findings indicate that microbiome-host co-adaptations have led to both taxonomic and within taxa functional displacements to meet host physiological demands. The microbiome, in turn, transcends its taxonomic interchangeable role, reflecting the lifestyle, ecology and dietary history of its host.},
}

Animals
*Diet
*Hominidae/microbiology
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome
*Life Style
Humans
Adaptation, Physiological
Pan troglodytes/microbiology
Metagenome
Phylogeny
Africa

@article {pmid40164860,
year = {2025},
author = {Adawiah, A and Meryandini, A and Ridwan, R and Fidriyanto, R and Sarwono, KA and Wiryawan, KG},
title = {The rumen microbiome and metabolome profile of Ongole crossbreed cattle fed probiotics and protected amino acids.},
journal = {Tropical animal health and production},
volume = {57},
number = {3},
pages = {148},
pmid = {40164860},
issn = {1573-7438},
mesh = {Animals ; *Rumen/microbiology/metabolism ; Cattle ; *Amino Acids/metabolism ; *Animal Feed/analysis ; Male ; *Metabolome ; *Diet/veterinary ; *Gastrointestinal Microbiome/drug effects ; *Probiotics/administration & dosage/pharmacology ; Cross-Over Studies ; Dietary Supplements/analysis ; Bacteria/classification/metabolism/genetics ; },
abstract = {This study aimed to investigate the microbial population dynamics and metabolite profiles of Ongole crossbreed cattle (OCC) fed a combination of feed additives using metagenomic and metabolomic analyses. A crossover design was employed, involving four 3-year-old fistulated OCC bulls, each receiving four distinct dietary treatments per experimental period, followed by a washout phase with a basal diet. The treatments consisted of a basal diet (G1) as control, and the addition of feed additives as follows: G2: probiotics (Lactiplantibacillus plantarum); G3: premix; G4: G2 + G3 + amino acids lysine and methionine; and G5: G2 + G3 + amino acids protected with tannin. Rumen fluid was collected for the analysis of microbiome dynamics and metabolite profiles. The bacterial communities in diets G1, G2, G3, and G5 exhibited similar compositions, dominated by Bacteroidota, particularly the genus Prevotella. The G5 diet successfully suppressed the population of archaea, notably Methanosarcinales and Methanobacteriales, which are associated with methane production. A total of 28 significant metabolites (VIP > 1) was identified in rumen fluid, including lipid prenols, phenolic compounds, indoles and derivatives, saturated and unsaturated hydrocarbons, fatty acyls, benzene derivatives, and organooxygen compounds. The volatile compounds profile of rumen fluid showed a marked increase in prenol lipid compounds, especially in the G5 diet. Additionally, Methanosarcinales and Methanobacteriales were negatively correlated with prenol lipid levels. The inclusion of probiotics and protected amino acids alters the microbiome community structure and metabolites, positively affecting ruminant productivity.},
}

Animals
*Rumen/microbiology/metabolism
Cattle
*Amino Acids/metabolism
*Animal Feed/analysis
Male
*Metabolome
*Diet/veterinary
*Gastrointestinal Microbiome/drug effects
*Probiotics/administration & dosage/pharmacology
Cross-Over Studies
Dietary Supplements/analysis
Bacteria/classification/metabolism/genetics

@article {pmid40164832,
year = {2025},
author = {Litichevskiy, L and Considine, M and Gill, J and Shandar, V and Cox, TO and Descamps, HC and Wright, KM and Amses, KR and Dohnalová, L and Liou, MJ and Tetlak, M and Galindo-Fiallos, MR and Wong, AC and Lundgren, P and Kim, J and Uhr, GT and Rahman, RJ and Mason, S and Merenstein, C and Bushman, FD and Raj, A and Harding, F and Chen, Z and Prateek, GV and Mullis, M and Deighan, AG and Robinson, L and Tanes, C and Bittinger, K and Chakraborty, M and Bhatt, AS and Li, H and Barnett, I and Davenport, ER and Broman, KW and Levy, M and Cohen, RL and Botstein, D and Freund, A and Di Francesco, A and Churchill, GA and Li, M and Thaiss, CA},
title = {Gut metagenomes reveal interactions between dietary restriction, ageing and the microbiome in genetically diverse mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40164832},
issn = {2058-5276},
abstract = {The gut microbiome changes with age and has been proposed to mediate the benefit of lifespan-extending interventions such as dietary restriction. However, the causes and consequences of microbiome ageing and the potential of such interventions remain unclear. Here we analysed 2,997 metagenomes collected longitudinally from 913 deeply phenotyped, genetically diverse mice to investigate interactions between the microbiome, ageing, dietary restriction (caloric restriction and fasting), host genetics and a range of health parameters. Among the numerous age-associated microbiome changes that we find in this cohort, increased microbiome uniqueness is the most consistent parameter across a second longitudinal mouse experiment that we performed on inbred mice and a compendium of 4,101 human metagenomes. Furthermore, cohousing experiments show that age-associated microbiome changes may be caused by an accumulation of stochastic environmental exposures (neutral theory) rather than by the influence of an ageing host (selection theory). Unexpectedly, the majority of taxonomic and functional microbiome features show small but significant heritability, and the amount of variation explained by host genetics is similar to ageing and dietary restriction. We also find that more intense dietary interventions lead to larger microbiome changes and that dietary restriction does not rejuvenate the microbiome. Lastly, we find that the microbiome is associated with multiple health parameters, including body composition, immune components and frailty, but not lifespan. Overall, this study sheds light on the factors influencing microbiome ageing and aspects of host physiology modulated by the microbiome.},
}

@article {pmid40164697,
year = {2025},
author = {Jia, L and Ke, Y and Zhao, S and Liu, J and Luo, X and Cao, J and Liu, Y and Guo, Q and Chen, WH and Chen, F and , and Wang, J and Wu, H and Ding, J and Zhao, XM},
title = {Metagenomic analysis characterizes stage-specific gut microbiota in Alzheimer's disease.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {40164697},
issn = {1476-5578},
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder with a decade-long preclinical pathological period that can be divided into several stages. Emerging evidence has revealed that the microbiota-gut-brain axis plays an important role in AD pathology. However, the role of gut microbiota in different AD stages has not been well characterized. In this study, we performed fecal shotgun metagenomic analysis on a Chinese cohort with 476 participants across five stages of AD pathology to characterize stage-specific alterations in gut microbiota and evaluate their diagnostic potential. We discovered extensive gut dysbiosis that is associated with neuroinflammation and neurotransmitter dysregulation, with over 10% of microbial species and gene families showing significant alterations during AD progression. Furthermore, we demonstrated that microbial gene families exhibited strong diagnostic capabilities, evidenced by an average AUC of 0.80 in cross-validation and 0.75 in independent external validation. In the optimal model, the most discriminant gene families are primarily involved in the metabolism of carbohydrates, amino acids, energy, glycan and vitamins. We found that stage-specific microbial gene families in AD pathology could be validated by an in vitro gut simulator and were associated with specific genera. We also observed that the gut microbiota could affect the progression of cognitive decline in 5xFAD mice through fecal microbiota transplantation, which could be used for early intervention of AD. Our multi-stage large cohort metagenomic analysis demonstrates that alterations in gut microbiota occur from the very early stages of AD pathology, offering important etiological and diagnostic insights.},
}

@article {pmid40164638,
year = {2025},
author = {Mills, S and Ijaz, UZ and Lens, PNL},
title = {Environmental instability reduces shock resistance by enriching specialist taxa with distinct two component regulatory systems.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {54},
pmid = {40164638},
issn = {2055-5008},
support = {15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; 15/RP/2763//Science Foundation Ireland (SFI)/ ; 16/RI/3401//Science Foundation Ireland (SFI)/ ; EP/P029329/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/V030515/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bioreactors/microbiology ; *Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification ; Microbiota ; High-Throughput Nucleotide Sequencing ; Microbial Consortia/genetics ; Methane/metabolism ; Metagenome ; Phylogeny ; },
abstract = {Different microbial communities are impacted disproportionately by environmental disturbances. The degree to which a community can remain unchanged under a disturbance is referred to as resistance[1]. However, the contributing ecological factors, which infer a community's resistance are unknown. In this study, the impact of historical environmental stability on ecological phenomena and microbial community resistance to shocks was investigated. Three separate methanogenic bioreactor consortia, which were subjected to varying degrees of historical environmental stability, and displayed different levels of resistance to an organic loading rate (OLR) shock were sampled. Their community composition was assessed using high throughput sequencing of 16S rRNA genes and assembly based metagenomics. The effect environmental instability on ecological phenomena such as microbial community assembly, microbial niche breadth and the rare biosphere were assessed in the context of each reactor's demonstrated resistance to an OLR shock. Additionally, metagenome assembled genomes were analysed for functional effects of prolonged stability/instability. The system which was subjected to more environmental instability experienced more temporal variation in community beta diversity and a proliferation of specialists, with more abundant two component regulatory systems. This community was more susceptible to deterministic community assembly and demonstrated a lower degree of resistance, indicating that microbial communities experiencing longer term environmental instability (e.g. variations in pH or temperature) are less able to resist a large disturbance.},
}

*RNA, Ribosomal, 16S/genetics
*Bioreactors/microbiology
*Metagenomics/methods
Bacteria/genetics/classification/isolation & purification
Microbiota
High-Throughput Nucleotide Sequencing
Microbial Consortia/genetics
Methane/metabolism
Metagenome
Phylogeny

@article {pmid39812462,
year = {2025},
author = {Kamel, K and Sardo Infirri, S and Riddell, A and Chowdary, P and Batty, P},
title = {Factor VIII Antibodies Demonstrate Type I or Type II Kinetics in Acquired Haemophilia A.},
journal = {Haemophilia : the official journal of the World Federation of Hemophilia},
volume = {31},
number = {2},
pages = {313-318},
pmid = {39812462},
issn = {1365-2516},
mesh = {*Hemophilia A/immunology/blood ; Humans ; *Factor VIII/immunology ; Kinetics ; Male ; Retrospective Studies ; *Autoantibodies/immunology/blood ; Aged ; Middle Aged ; Female ; Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Acquired haemophilia A (AHA) is an acquired bleeding disorder resulting from autoantibodies against Factor VIII (FVIII). Previous studies have reported differences in FVIII inhibitor kinetics (type I or type II) in AHA compared to severe haemophilia A.

AIM: To characterise inhibitor kinetics in AHA and evaluate the proportions displaying type I, II or indeterminate kinetics.

METHODS: Single-centre retrospective study of inhibitor kinetics in adults with AHA. Type I kinetics were defined as linear FVIII inhibition with ≥ 97% FVIII inactivation. Type II kinetics were defined as non-linear kinetics and inability to completely neutralise FVIII. Inhibitor titres were calculated using two methods outlined by the International Council for Standardisation in Haematology.

RESULTS: Baseline samples from 34 patients were included. Fifteen samples (44.1%) exhibited type I kinetics, 16 samples (47.1%) exhibited type II kinetics and 3 (8.8%) were indeterminate. Plateau mean residual FVIII:C was higher for inhibitors displaying type II compared to type I kinetics (18.6 vs. 2.9 IU/dL, p < 0.0001). Non-linear regression using a dose-response curve without categorisation for kinetics type yielded a poor fit (R[2] = 38%), which improved with refitting using categories of type I or II kinetics that explained 87% and 85% of the variability. The median difference in inhibitor titre between the two reporting methods was 5% and 15% in the type I and II kinetics groups, respectively.

CONCLUSION: FVIII autoantibodies demonstrate either type I or type II kinetics. Greater discrepancy in reported inhibitor titres depending on the method used is seen for inhibitors with type II kinetics.},
}

*Hemophilia A/immunology/blood
Humans
*Factor VIII/immunology
Kinetics
Male
Retrospective Studies
*Autoantibodies/immunology/blood
Aged
Middle Aged
Female
Adult
Aged, 80 and over

@article {pmid40164558,
year = {2025},
author = {Zhou, HY and Zhang, J and Weng, DD},
title = {[One case of recurrent infection with chlamydia psittaci pneumonia].},
journal = {Zhonghua lao dong wei sheng zhi ye bing za zhi = Zhonghua laodong weisheng zhiyebing zazhi = Chinese journal of industrial hygiene and occupational diseases},
volume = {43},
number = {3},
pages = {237-240},
doi = {10.3760/cma.j.cn121094-20240109-00008},
pmid = {40164558},
issn = {1001-9391},
mesh = {Humans ; *Chlamydophila psittaci/isolation & purification ; Male ; Bronchoalveolar Lavage Fluid/microbiology ; Psittacosis/microbiology ; Recurrence ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {This paper analyzed the clinical data of a patient with recurrent infection of chlamydia psittaci pneumonia within 7 months. The patient had a clear history of contact with live poultry, and the clinical manifestations were dry cough, persistent fever, and respiratory failure. Chest CT imaging changes showed lobar consolidation of infected lung lobes, ground-glass shadows, bronchial air-filling signs, and pleural effusion. The two infections were detected in bronchoalveolar lavage fluid by metagenomic next-generation sequencing (mNGS) and pathogen targeted next-generation sequencing (tNGS), respectively, to achieve early diagnosis of chlamydia psittaci pneumonia. New tetracycline drugs were used as the core of treatment for both infections, and rapid improvement was achieved after anti-infection treatment.},
}

Humans
*Chlamydophila psittaci/isolation & purification
Male
Bronchoalveolar Lavage Fluid/microbiology
Psittacosis/microbiology
Recurrence
Middle Aged
High-Throughput Nucleotide Sequencing
Anti-Bacterial Agents/therapeutic use

@article {pmid40163992,
year = {2025},
author = {Lei, H and Zhou, N and Zhang, J and Lin, R and Chen, T and Wu, J and Su, L and Liu, S and Liu, T},
title = {Salinity as a key factor affects viral structure, function, and life strategies in lakes from arid and semi-arid regions.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138075},
doi = {10.1016/j.jhazmat.2025.138075},
pmid = {40163992},
issn = {1873-3336},
abstract = {Salinity impacts lake microorganisms in arid and semiarid zones, affecting climate change. Viruses regulate community structure, facilitate gene transfer, and mediate nutrient cycling. However, studies on the diversity and functional differences of viruses in lakes of varying salinity are limited. Thus, we investigated metagenomic data from 20 lakes in Xinjiang Province, China, to determine viral distribution, virus-host linkage, function, and drivers in lakes of varying salinity. The results showed that salinity shaped the distribution of viral community composition, and Hafunaviridae was the dominant virus in high-salinity lakes. All the metagenome-assembled genomes (MAGs) belonging to Halobacteriota were predicted as hosts, with a lysogenic lifestyle predominating the life strategy, implying their potential protection in salt lakes. Moreover, some auxiliary metabolic genes (AMGs), such as cpeT and PTOX, were related to antioxidant and stress responses, which might help the host survive high salinity stress-induced peroxidation. Notably, the main antibiotic resistance genes (ARGs) carried by viruses, which conferred resistance to polymyxin and trimethoprim, related to the local use of veterinary antibiotics, suggesting that they are potential vehicles for the transmission of ARGs. Overall, these findings suggest that lake systems include unique viral varieties that may influence microbial ecosystems and host metabolism related to environmental adaptability.},
}

@article {pmid40163955,
year = {2025},
author = {Du, R and Cui, L and Feng, Y and Lv, X and Gao, Y and Li, A and Wang, Q and Ma, Y},
title = {Enhancing the decomposition and composting of food waste by in situ directional enzymatic hydrolysis: performance, ARGs removal and engineering application.},
journal = {Waste management (New York, N.Y.)},
volume = {200},
number = {},
pages = {114774},
doi = {10.1016/j.wasman.2025.114774},
pmid = {40163955},
issn = {1879-2456},
abstract = {This research utilized food waste (FW) as substrate, innovatively developed a directional multienzyme applied for accelerating FW hydrolysis and composting, and an in situ enzymatic hydrolysis combining in composting has been developed to manage FW. Results showed that the composting was achieved at 4 days and the humification index was increased by 2.60 compared with that of without enzymatic hydrolysis. FTIR analysis revealed that following multienzyme pretreatment, the primary constituents of FW, including protein, starch and lipid, underwent structural breakdown, among which protein exhibited the higher susceptibility to multienzyme action and was the first to disintegrated, and the structure also became looser. Moreover, the total antibiotic resistance gene (ARGs) was reduced more than 90 % in the proposed composting process. Analysis of microbial communities and metagenomes showed that multienzyme pretreatment reshaped microbial communities towards favoring FW hydrolysis and humification. The engineering application analysis further implied that the proposed composting approach is scale flexible, engineering applicable, economic viability and environmentally sustainability. It was anticipated that this study has the potential to trigger a paradigm shift in future in-situ treatment of FW to achieve full resource recovery towards zero solid discharge.},
}

@article {pmid40163458,
year = {2025},
author = {Vendrell-Fernández, S and Beamud, B and Abou Haydar, Y and Am de Sousa, J and Burlaud-Gaillard, J and Kornobis, E and Raynal, B and Vinh, J and Bikard, D and Ghigo, JM},
title = {Incomplete lytic cycle of a widespread Bacteroides bacteriophage leads to the formation of defective viral particles.},
journal = {PLoS biology},
volume = {23},
number = {3},
pages = {e3002787},
doi = {10.1371/journal.pbio.3002787},
pmid = {40163458},
issn = {1545-7885},
mesh = {*Bacteriophages/physiology/genetics ; *Virion/ultrastructure ; *Bacteroides/virology/genetics ; *Lysogeny ; Phylogeny ; Retroelements/genetics ; DNA, Viral/genetics ; Genome, Viral ; },
abstract = {Advances in metagenomics have led to the identification of new intestinal temperate bacteriophages. However, their experimental characterization remains challenging due to a limited understanding of their lysogenic-lytic cycle and the common lack of plaque formation in vitro. In this study, we investigated the hankyphage, a widespread transposable phage of prominent Bacteroides symbionts. Hankyphages spontaneously produced virions in laboratory conditions even in the absence of inducer, but virions did not show any evidence of infectivity. To increase virion production and raise the chances of observing infection events, we identified a master repressor of the hankyphage lytic cycle, RepCHP, whose silencing amplified hankyphage gene expression, and enhanced replicative transposition and virion production. However, attempts to infect or lysogenize new host cells with different capsular types remained unsuccessful. Transmission electron microscopy and capsid DNA sequencing revealed an abnormal virion morphology and incomplete DNA packaging of the hankyphage, suggesting that it cannot complete its assembly in laboratory conditions for reasons that are yet to be identified. Still, metavirome and phylogenetic analyses were suggestive of hankyphage horizontal transmission. We could also detect the activity of diversity-generating retroelements (DGRs) that mutagenize the hankyphage tail fiber, and likely contribute to its broad host range. This study sheds light on the life cycle of this abundant intestinal bacteriophage and highlights important gaps in our understanding of the factors required for the completion of its life cycle. Elucidating this puzzle will be critical to gain a better understanding of the hankyphage biology and ecological role.},
}

*Bacteriophages/physiology/genetics
*Virion/ultrastructure
*Bacteroides/virology/genetics
*Lysogeny
Phylogeny
Retroelements/genetics
DNA, Viral/genetics
Genome, Viral

@article {pmid40163416,
year = {2025},
author = {Tordoff, J and Alfonse, LE and Makarova, KS and Ornstein, A and Garrity, AJ and Yan, WX and Scott, DA and Koonin, EV and Cheng, DR},
title = {Initial Characterization of 12 New Subtypes and Variants of Type V CRISPR Systems.},
journal = {The CRISPR journal},
volume = {},
number = {},
pages = {},
doi = {10.1089/crispr.2024.0100},
pmid = {40163416},
issn = {2573-1602},
abstract = {Type V CRISPR systems are highly diverse in sequence, mechanism, and function. Although recent efforts have greatly expanded our understanding of their evolution, the diversity of type V systems remains to be completely explored, and many clades have not been experimentally characterized. In this work, we mined metagenomic databases to identify three new subtypes and nine new variants of Cas12, the effector of Type V systems, and provide experimental and computational characterization of their Protospacer-Adjacent Motif (PAM), interference activity, loci architecture, and tracrRNA dependence. Half of the new Cas12s are found in phages or prophages. New subtypes Cas12o and Cas12p lack the canonical RuvC catalytic residues, suggesting they interfere with the target without cleavage, possibly by blocking transcription or replication. One variant, Cas12f10, displays substantial activity on PAM-less targets. Our work expands the diversity of the functionally characterized Cas12 effectors and provides some promising candidates for genome engineering tools.},
}

@article {pmid40162776,
year = {2025},
author = {Haft, DH and Tolstoy, I},
title = {Novel selenoprotein neighborhoods suggest specialized biochemical processes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0141724},
doi = {10.1128/msystems.01417-24},
pmid = {40162776},
issn = {2379-5077},
abstract = {UNLABELLED: Prokaryotic genomes encode selenoproteins sparsely, roughly one protein per 5,000. Finding novel selenoprotein families can expose unknown biological processes that are enabled, or at least enhanced, by having a selenium atom replace a sulfur atom in some cysteine residues. Here, we report the discovery of 18 novel selenoprotein families or second selenocysteine sites in previously unrecognized extensions of protein translations. Most of these families had some confounding factors-too small a family, too few selenoproteins in the family, selenocysteine (U) too close to one end, a skew toward understudied or uncultured lineages, and consequently were missed previously. Discoveries were triggered by observations during the ongoing construction of protein family models for the National Center for Biotechnology Information's RefSeq and Prokaryotic Gene Annotation Pipeline or made by targeted searches for novel selenoproteins in the vicinity of known ones, rather than by any broadly applied genome mining method. Unrelated families TsoA, TsoB, TsoC, and TsoX are adjacent in tso (three selenoprotein operon) loci in the bacterial phylum Thermodesulfobacteriota. TrsS (third radical SAM selenoprotein) occurs strictly in the context of a molybdopterin-dependent aldehyde oxidoreductase. A short carboxy-terminal motif, U-X-X-stop (UXX-star), occurs in selenoproteins with various architectures, usually providing the second U in the protein. The multiple new selenocysteine insertion sites, selenoprotein families, and selenium-dependent operons we curated manually suggest that many more proteins and pathways remain to be discovered; once improved computational methods are applied comprehensively to the latest collections of microbial genomes and metagenomes, they may reveal surprising new biochemical processes.

IMPORTANCE: Next-generation DNA sequencing and assembly of metagenome-assembled genomes (MAGs) for uncultured species of various microbiomes adds a vast "dark matter" of hard-to-decipher protein sequences. Selenoproteins, optimized by natural selection to encode selenocysteine where cysteine might have been encoded much more easily, carry a strong clue to their function-some specialized aspect of binding or catalysis. Operons with multiple adjacent, but otherwise unrelated, selenoproteins should provide even more vivid information. In this study, efforts in protein family construction and curation, aimed at improving the PGAP genome annotation pipeline, generated multiple novel selenoprotein-containing genomic contexts that may lead to the future characterization of several systems of proteins. Past observations suggest roles in the metabolic handling of trace elements (mercury, tungsten, arsenic, etc.) or of organic compounds refractory to simpler enzymatic pathways. In addition, the work significantly expands the truth set of validated selenoproteins, which should aid future, more automated genome mining efforts.},
}

@article {pmid40162769,
year = {2025},
author = {Dickter, JK and Zhao, Y and Parekh, V and Ma, H and Modi, BG and Li, W-Y and Armenian, SH and Wu, X and Abdulla, FR},
title = {Mining metagenomes and metatranscriptomes unveils viruses associated with cutaneous squamous cell carcinoma in hematopoietic stem cell transplant recipients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0005325},
doi = {10.1128/spectrum.00053-25},
pmid = {40162769},
issn = {2165-0497},
abstract = {UNLABELLED: We investigated the presence of viral DNA and RNA in cutaneous squamous cell carcinoma (cSCC) tumor and normal tissues from nine individuals with a history of hematopoietic stem cell transplantation (HCT). Microbiome quantification through DNA and RNA sequencing (RNA-seq) revealed the presence of 18 viruses in both tumor and normal tissues. DNA sequencing (DNA-seq) identified Torque teno virus, Saimiriine herpesvirus 1, Merkel cell polyomavirus, Human parvovirus B19, Human gammaherpesvirus-4, Human herpesvirus-6, and others. RNA-seq revealed additional viruses such as Tobamovirus, Pinus nigra virus, Orthohepadnavirus, Human papillomavirus-5, Human herpesvirus-7, Human gammaherpesvirus-4, Gammaretrovirus, and others. Notably, DNA-seq indicated that tumor samples exhibited low levels of Escherichia virus in three out of nine subjects and elevated levels of Human gammaherpesvirus-4 in one subject, while normal samples frequently contained Gammaretrovirus and occasionally Escherichia virus. A comparative analysis using both DNA- and RNA-seq captured three common viruses: Abelson murine leukemia virus, Murine type C retrovirus, and Human gammaherpesvirus-4. These findings were corroborated by an independent data set, supporting the reliability of the viral detection methods utilized. The study provides insights into the viral landscape in post-HCT patients, emphasizing the need for comprehensive viral monitoring in this vulnerable population.

IMPORTANCE: This study is important because it explores the potential role of viruses in the development of cSCC in individuals who have undergone allogeneic HCT. cSCC is common in this population, particularly in those with chronic graft-versus-host disease on long-term immunosuppression. By using advanced metagenomic and metatranscriptomic next-generation sequencing, we aimed to identify viral pathogens present in tumor and adjacent normal tissue. The results could lead to targeted preventive or therapeutic interventions for these high-risk people, potentially improving their outcomes and management of cSCC.},
}

@article {pmid40162572,
year = {2025},
author = {Wu, H and Zhang, H and Dong, T and Li, Z and Guo, X and Chen, H and Yao, Y},
title = {Overcoming Extreme Ammonia Inhibition on Methanogenesis by Artificially Constructing a Synergistically Community with Acidogenic Bacteria and Hydrogenotrophic Archaea.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2502743},
doi = {10.1002/advs.202502743},
pmid = {40162572},
issn = {2198-3844},
support = {2024YFD1700500//National Key R&D Program of China/ ; A279021901//Shaanxi Youth Thousand Talents/ ; 2024CY2-GJHX-74//Shaanxi Key R&D Program of China/ ; 2452021112//Chinese Universities Scientific Fund/ ; JCYJ20220530161408019//Shenzhen Natural Science Foundation/ ; 2023KCXTD038//Guangdong Provincial University Innovation Team Project/ ; 2022-K32//Foundation of State Key Laboratory of High-efficiency Utilization of Coal and Green Chemical Engineering/ ; Z111021902//Northwest A&F University Young Talent Project/ ; },
abstract = {High total ammonia nitrogen (TAN) inhibits anaerobic digestion (AD) and cannot be completely eliminated by merely enhancing a stage of AD. This study incorporates TAN-tolerant inoculum into substrates hydrolyzed by Rhizopus mixed agents to simultaneously enhance hydrolysis-acidogenesis-methanogenesis. The results show a 16.46-fold increase in CH4 production under TAN-inhibited (6870.97 mg L-1) conditions, even exceeding the AD without TAN by 21.10%. Model substrates sodium acetate and mixed H2 confirm hydrogenotrophic methanogenesis is the main pathway, with reduced TAN inhibition. Furthermore, a synergistic metabolic microbial community dominated by hydrolytic bacteria JAAYGG01 sp. and DTU014 sp., acidogenic bacteria DTU015 sp., DTU013 sp., and JAAYLO01 sp., and methanogens Methanosarcina mazei and an unclassified species in the Methanoculleus is reconstructed to resist TAN inhibition. Metagenomic combined with metatranscriptomic sequencing identifies that this microbial community carries xynD and bglB to regulate substrate hydrolysis, leading to acetate production through glycolysis, butyrate, and pyruvate metabolism with high acetate kinase activity, thereby CH4 produced primarily via hydrogenotrophic methanogenesis with high coenzyme F420 activity, facilitated by efficient mass transfer processes and quorum sensing regulation. This cleaner strategy obtains higher economic benefit (US$149.02) than conventional AD and can increase 154.64-fold energy production of a 24 000 m3 biogas plant, guided by machine learning.},
}

@article {pmid40162034,
year = {2025},
author = {Huang, L and Zheng, D and Li, T and Li, X and Kong, J and Wang, K and Wang, S and Cao, C},
title = {Disseminated Histoplasmosis Due to Anti-IFN-γ Autoantibodies-Associated Immunodeficiency.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1605-1609},
doi = {10.2147/IDR.S513750},
pmid = {40162034},
issn = {1178-6973},
abstract = {BACKGROUND: Disseminated histoplasmosis caused by the temperature-dependent dimorphic fungus Histoplasma capsulatum is an invasive fungal disease rarely reported in southern China. Here, we report a case of disseminated histoplasmosis due to anti-IFN-γ autoantibodies (AIGA)- associated immunodeficiency.

CASE PRESENTATION: We present the case of a 57-year-old HIV-negative female patient with disseminated histoplasmosis in southern China. The patient showed progressively enlarging multiple clavicular, neck, and upper chest skin nodules and dyspnea, which led to the initial suspicion of pulmonary tuberculosis or lung cancer. Bacterial cultures results were negative. Histopathology of a skin tissue showed infectious granulomas. Disseminated histoplasmosis was diagnosed via next-generation sequencing (mNGS) and fungal culture. Furthermore, enzyme-linked immunosorbent assay results from a peripheral blood confirmed that the patient had a high-titer of AIGA.

CONCLUSION: This case prompts clinicians to consider histoplasmosis an important differential diagnosis in a region where talaromycosis is highly endemic. This case report emphasizes that clinicians should be vigilant for immunodeficiency and consider testing for AIGA in HIV-negative patients who are suspected of having complex opportunistic infections.},
}

@article {pmid40161798,
year = {2025},
author = {Zeamer, AL and Lai, Y and Sanborn, V and Loew, E and Tracy, M and Jo, C and Ward, DV and Bhattarai, SK and Drake, J and McCormick, BA and Bucci, V and Haran, JP},
title = {Microbiome functional gene pathways predict cognitive performance in older adults with Alzheimer's disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.06.641911},
pmid = {40161798},
issn = {2692-8205},
abstract = {Disturbances in the gut microbiome is increasing correlated with neurodegenerative disorders, including Alzheimer's Disease. The microbiome may in fact influence disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby driving disease pathology along the "microbiota-gut-brain-axis". Currently, drivers of cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (age 60+) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiomes. Subjects were classified as healthy controls or as having mild cognitive impairment based on cognitive performance. Those with a diagnosis of Alzheimer's Diseases with confirmed using serum biomarkers. Using metagenomic sequencing, we found that relative species abundances correlated well with cognition status (MCI or AD). Furthermore, gene pathways analyses suggest certain microbial metabolic pathways to either be correlated with cognitive decline or maintaining cognitive function. Specifically, genes involved in the urea cycle or production of methionine and cysteine predicted worse cognitive performance. Our study suggests that gut microbiome composition may predict AD cognitive performance.},
}

@article {pmid40161742,
year = {2025},
author = {Wong, MK and Armstrong, E and Heirali, AA and Schneeberger, PHH and Chen, H and Cochrane, K and Sherriff, K and Allen-Vercoe, E and Siu, LL and Spreafico, A and Coburn, B},
title = {Assessment of ecological fidelity of human microbiome-associated mice in observational studies and an interventional trial.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.11.642547},
pmid = {40161742},
issn = {2692-8205},
abstract = {UNLABELLED: Composition and function of the gut microbiome is associated with diverse health conditions and treatment responses. Human microbiota-associated (HMA) mouse models are used to establish causal links for these associations but have important limitations. We assessed the fidelity of HMA mouse models to recapitulate ecological responses to a microbial consortium using stools collected from a human clinical trial. HMA mice were generated using different routes of consortium exposure and their ecological features were compared to human donors by metagenomic sequencing. HMA mice were more similar in gut composition to other mice than their respective human donors, with taxa including Akkermansia muciniphila and Bacteroides species enriched in mouse recipients. A limited repertoire of microbes was able to engraft into HMA mice regardless of route of consortium exposure. In publicly available HMA mouse datasets from four distinct health conditions, we confirmed our observation that a taxonomically restricted set of microbes reproducibly engrafts in HMA mice and observed that stool microbiome composition of HMA mice were more like other mice than their human donor. Our data suggest that HMA mice are limited models to assess the ecological impact of microbial consortia, with ecological effects in HMA mice being more strongly associated with host species than donor stool ecology or ecological responses to treatment in humans. Comparisons to published studies suggest this may be due to comparatively large host-species effects that overwhelm ecological effects of treatment in humans that HMA models aim to recapitulate.

IMPORTANCE: Human microbiota-associated (HMA) mice are models that better represent human gut ecology compared to conventional laboratory mice and are commonly used to test the effect of the gut microbiome on disease or treatment response. We evaluated the fidelity of using HMA mice as avatars of ecological response to a human microbial consortium, MET4. Our results show that HMA mice in our cohort and across other published studies are more similar to each other than the human donors or inoculum they are derived from and harbour a taxonomically restricted gut microbiome. These findings highlight the limitations of HMA mice in evaluating the ecological effects of complex human microbiome-targeting interventions, such as microbial consortia.},
}

@article {pmid40161675,
year = {2025},
author = {Secaira-Morocho, H and Jiang, X and Zhu, Q},
title = {Augmenting microbial phylogenomic signal with tailored marker gene sets.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.13.643052},
pmid = {40161675},
issn = {2692-8205},
abstract = {Phylogenetic marker genes are traditionally selected from a fixed collection of whole genomes evenly distributed across major microbial phyla, covering only a small fraction of gene families. And yet, most microbial diversity is found in metagenome-assembled genomes that are unevenly distributed and harbor gene families that do not fit the criteria of universal orthologous genes. To address these limitations, we systematically evaluate the phylogenetic signal of gene families annotated from KEGG and EggNOG functional databases for deep microbial phylogenomics. We show that markers selected from an expanded pool of gene families and tailored to the input genomes improve the accuracy of phylogenetic trees across simulated and real-world datasets of whole genomes and metagenome-assembled genomes. The improved accuracy of trees compared to previous markers persists even when metagenome-assembled genomes lack a fraction of open reading frames. The selected markers have functional annotations related to metabolism, cellular processes, and environmental information processing, in addition to replication, translation, and transcription. We introduce TMarSel, a software tool for automated, systematic, free-from-expert opinion, and tailored marker selection that provides flexibility in the number of markers and annotation databases while remaining robust against uneven taxon sampling and incomplete genomic data.},
}

@article {pmid40161639,
year = {2025},
author = {Williams, A and Ravel, J and Kaul, R and Armstrong, E and Huibner, S and Holm, JB},
title = {Temporal Dynamics of the Vaginal Microbiome and Host Immune Markers Before, During, and After Metronidazole Treatment for Bacterial Vaginosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.03.13.643085},
pmid = {40161639},
issn = {2692-8205},
abstract = {UNLABELLED: This study analyzed metagenomic and immune marker profiles of seven individuals before, during, and after a 7-day course of metronidazole treatment for bacterial vaginosis (BV). Treatment reduced BV-associated bacteria and immune marker levels, with distinct early (days 1-4) and late (days 5-7) phases. Post-treatment, variability in microbial and immune marker profiles demonstrated a rapid resurgence of certain BV associated bacteria, highlighting the need for additional strategies like probiotics to maintain a healthy vaginal microbiome. The study found significant host and microbial influences on immune response variance, with IP-10 and sEcad highly correlated with the vaginal microbiome. The findings identify optimal timing for administering live biotherapeutics to restore D-lactic acid-producing Lactobacillus species dominance and underscore the complexity of BV infection and treatment response among different people.

IMPORTANCE: Bacterial vaginosis (BV), a common condition associated with an increased risk of preterm birth and sexually transmitted infections among others, is characterized by a dysbiotic vaginal microbiome associated with dominance of a diverse assortment of anaerobic bacterial species. Metronidazole is the first-line treatment recommended by the CDC for BV when patients report symptoms. Despite treatment, BV recurrence is common. There is limited data regarding the effects of oral metronidazole on the vaginal microbiome starting at initiation of treatment as most studies have compared measurements taken before and after treatment completion. This study utilized metagenomic sequencing, pan-bacterial qPCR, and immune marker measurements to analyze the longitudinal dynamics of the vaginal microbiome and host immune response before, during and after metronidazole treatment.},
}

@article {pmid40160274,
year = {2025},
author = {Naushad, S and Gao, R and Duceppe, MO and Dupras, AA and Reiling, SJ and Merks, H and Dixon, B and Ogunremi, D},
title = {Metagenomic detection of protozoan parasites on leafy greens aided by a rapid and efficient DNA extraction protocol.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1566579},
doi = {10.3389/fmicb.2025.1566579},
pmid = {40160274},
issn = {1664-302X},
abstract = {INTRODUCTION: Infections with protozoan parasites associated with the consumption of fresh produce is an on-going issue in developed countries but mitigating the risk is hampered by the lack of adequate methods for their detection and identification.

MATERIALS AND METHODS: We developed a metagenomic next-generation sequencing (mNGS) assay using a MinION sequencer for the identification of parasites in intentionally contaminated lettuce to achieve a more accurate and rapid method than the traditional molecular and microscopy methods commonly used for regulatory purposes. Lettuce (25 g) was spiked with varying numbers of Cryptosporidium parvum oocysts, and microbes washed from the surface of the lettuce were lysed using the OmniLyse device. DNA was then extracted by acetate precipitation, followed by whole genome amplification. The amplified DNA was sequenced by nanopore technology and validated with the Ion Gene Studio S5, and the generated fastq files raw reads were uploaded to the CosmosID webserver for the bioinformatic identification of microbes in the metagenome. To demonstrate the ability of the procedure to distinguish other common food and waterborne protozoan parasites, lettuce was also spiked with C. hominis, C. muris, Giardia duodenalis and Toxoplasma gondii individually or together.

RESULTS: The efficient lysis of oocysts and cysts was a prerequisite for the sensitive detection of parasite DNA and was rapidly achieved within 3 min. Amplification of extracted DNA led to the generation of 0.16-8.25 μg of DNA (median = 4.10 μg), sufficient to perform mNGS. Nanopore sequencing followed by bioinformatic analysis led to the consistent identification of as few as 100 oocysts of C. parvum in 25 g of fresh lettuce. Similar results were obtained using the Ion S5 sequencing platform. The assay proved useful for the simultaneous detection of C. parvum, C. hominis, C. muris, G. duodenalis and T. gondii.

DISCUSSION: Our metagenomic procedure led to the identification of C. parvum present on lettuce at low numbers and successfully identified and differentiated other protozoa either of the same genus or of different genera. This novel mNGS assay has the potential for application as a single universal test for the detection of foodborne parasites, and the subtyping of parasites for foodborne outbreak investigations and surveillance studies.},
}

@article {pmid40160273,
year = {2025},
author = {Liu, Y and Ying, Y and Li, Y and Zhang, W and Shu, J},
title = {Symbiotic bacteria associated with different species of Curculio (Coleoptera: Curculionidae) and their host plants.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1531847},
doi = {10.3389/fmicb.2025.1531847},
pmid = {40160273},
issn = {1664-302X},
abstract = {Bacteria often play important roles in the host adaptation of phytophagous insects. Beetles of the genus Curculio (Coleoptera: Curculionidae) include pest species that bore into the seeds of trees in the family Fagaceae and damage the cotyledons. At present, there are few studies of the taxonomic diversity and functional effects of symbiotic bacteria involved in changes in host ranges and host adaptation of Curculio. Here, we used 16S rRNA gene Illumina and metagenomic sequencing to compare the composition and functions of the bacterial communities of three species of host plants and several Curculio species combinations: Curculio bimaculatus feeding on Castanopsis sclerophylla, C. bimaculatus feeding on Castanopsis tibetana, and Curculio davidi feeding on Ca. tibetana. The host plants influenced the diversity of symbiotic bacteria, while the Curculio species influenced the community structure of the symbiotic bacteria. Functional predictions showed that symbiotic bacteria contributed to the metabolism of the hosts. However, consistent with the variation in bacteria, the major metabolism-related bacterial genera varied among the treatment groups. Comparisons of metabolic enzymes based on KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation revealed differences in the enzymes involved in insect development and detoxification of plant secondary compounds among the three groups, and the patterns were influenced by the dominance of the Curculio species on the host plants. This study provides valuable insights into the possible role of symbiotic bacteria in Curculio as host insects.},
}

@article {pmid40160271,
year = {2025},
author = {Yang, B and Feng, C and Jiang, H and Chen, Y and Ding, M and Dai, H and Zhai, Z and Yang, M and Liang, T and Zhang, Y},
title = {Effects of long-term continuous cropping on microbial community structure and function in tobacco rhizosphere soil.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1496385},
doi = {10.3389/fmicb.2025.1496385},
pmid = {40160271},
issn = {1664-302X},
abstract = {As is well known, continuous cropping can lead to a decrease in crop yield and quality. Despite this, continuous cropping remains prevalent in practical agricultural production, particularly in the case of tobacco cultivation, owing to its high economic value. The samples for this study were collected from a flue-cured tobacco planting base located in Huili County, Liangshan Yi Autonomous Prefecture, Sichuan Province, China. After years of continuous planting, the yield of tobacco in this base has significantly decreased. In order to explain the microecological causes of this phenomenon, we collected non-continuous cropping, continuous cropping for 5 years, and continuous cropping for 10 years of tobacco rhizosphere soil, and analyzed the effects of long-term continuous cropping on nutrients, enzyme activities, microbial community structure, and function of tobacco rhizosphere soil. The results showed that with the continuous cropping, the majority nutrients (except for phosphorus and manganese) in rhizosphere soil decreased significantly, and the rhizosphere microbial community structure changed significantly. Correlation network analysis results showed that changes in the rhizosphere microbial community of tobacco were closely related to soil urease, active organic carbon, and available iron content. The results of functional analysis based on microorganisms and genes showed that the rhizosphere microbiota may change the content of soil nutrients through iron_respiration, sulfur_respiration, and Carbon fixation in prokaryotes pathways. The results of the correlation network analysis and the functional analysis mutually confirmed each other, both emphasizing the important role of soil carbon and iron in shaping the structure of the tobacco rhizosphere microbial community. Based on the results of this study, we propose to improve the microbial community structure of tobacco rhizosphere soil by increasing the levels of readily oxidizable organic carbon, available iron, and soil urease activity in the future, so as to alleviate the negative impact of continuous cropping on crop yield. The results of this study provide theoretical support for modifying the rhizosphere microbial environment through nutrient regulation, thereby enhancing plant growth in the context of continuous tobacco cropping.},
}

@article {pmid40160267,
year = {2025},
author = {Kragh, ML and Scheel, NH and Leekitcharoenphon, P and Truelstrup Hansen, L},
title = {Repeated biocide treatments cause changes to the microbiome of a food industry floor drain biofilm model.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1542193},
doi = {10.3389/fmicb.2025.1542193},
pmid = {40160267},
issn = {1664-302X},
abstract = {There is a concern about the development of microbial tolerance and resistance to biocides due to their repeated use within the food industry. This study aimed to develop a floor drain biofilm model and test whether repeated biocide treatment would result in increased tolerance to biocides. Culturomics and shotgun metagenomic analysis of 14 drains and 214 bacterial isolates from three industrial food production environments revealed microbiomes with great diversity and complexity, but with the dominance of a few highly abundant taxa, including Pseudomonas. A representative drain biofilm was created (3 days, 15°C) using 31 whole genome sequenced bacterial isolates from 24 genera. The biofilm model represented 47-58% and 76-81% of the microbial abundance observed in the metagenome and viable microbiota, respectively. The biofilm model was exposed on days 3 and 6 to water or different industrial concentrations of benzalkonium chloride (BC), peracetic acid (PAA), or sodium hypochlorite (SH). Analysis of the viable survivors using MALDI-TOF MS and the regrowing biofilms using 16S rRNA amplicon sequencing showed how the diversity of the biofilm decreased but without any change in biocide tolerance as seen in log reductions (CFU/cm[2]). The use of different biocides did, however, exert significantly different selective pressures on the microbiomes as Citrobacter, Acinetobacter, Aeromonas, and Pseudomonas dominated the biofilm after treatments with SH or PAA, while Serratia and Moraxella dominated after treatments with BC. The dominance of Serratia marcescens could be explained by the carriage of a BC efflux pump (oqxB) and the highest (20 mg/L BC) minimum inhibitory concentration (MIC) result of the drain isolates. In contrast, despite carrying a BC efflux pump (qacH), Listeria monocytogenes ST121 did not show increased survival or presence in the biofilm after BC treatments. Only the highest tested concentration of PAA was able to completely eradicate L. monocytogenes. The developed biofilm model and the repeated biocide treatments enabled a better understanding of how biocides affect the biofilm microbiome. Future research should involve testing biocide rotation strategies to control biofilm regrowth and inactivation of persistent foodborne pathogens in floor drains.},
}

@article {pmid40159059,
year = {2025},
author = {Shang, SY and Li, XP and Xu, J and Li, Y and Cao, LQ and Ye, H},
title = {[A case of acute pseudomembranous necrotizing tracheobronchitis in an adult].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {48},
number = {4},
pages = {385-388},
doi = {10.3760/cma.j.cn112147-20240828-00510},
pmid = {40159059},
issn = {1001-0939},
mesh = {Humans ; *Tracheitis/diagnosis/microbiology ; *Bronchitis/microbiology/diagnosis ; *Staphylococcal Infections/diagnosis ; Male ; Staphylococcus aureus/isolation & purification ; Bronchoscopy ; Influenza B virus/isolation & purification ; Adult ; Necrosis ; Influenza, Human/complications ; Middle Aged ; Linezolid/therapeutic use ; },
abstract = {This study presented a rare case of secondary Staphylococcus aureus (S. aureus) infection following influenza B virus infection, resulting in diffuse airway injury and hemorrhagic pneumonia. The patient initially underwent bronchial artery embolization (BAE) due to persistent hemoptysis refractory to conventional hemostatic therapy. Although the hemoptysis was resolved postoperatively, severe hypoxemia persisted. Bronchoscopy revealed diffuse yellow plaques with mucosal erosion and necrosis in the airways. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified S. aureus harboring the Panton-Valentine leukocidin (PVL) genes. Histopathological examination revealed severe acute inflammatory changes consistent with necrotizing airway pathology. A diagnosis of IBV-associated S. aureus infection leading to acute pseudomembranous necrotizing tracheobronchitis and hemorrhagic pneumonia was made. The patient responded favorably to linezolid therapy. Follow-up bronchoscopy revealed multiple granulation tissues in the airways, which were subsequently removed under endoscopic guidance. After ruling out persistent infection, the patient was treated with low-dose oral prednisone, which resulted in significant clinical improvement.},
}

Humans
*Tracheitis/diagnosis/microbiology
*Bronchitis/microbiology/diagnosis
*Staphylococcal Infections/diagnosis
Male
Staphylococcus aureus/isolation & purification
Bronchoscopy
Influenza B virus/isolation & purification
Adult
Necrosis
Influenza, Human/complications
Middle Aged
Linezolid/therapeutic use

@article {pmid40158829,
year = {2025},
author = {Liu, Y and Zhang, Q and Lu, L and Qian, Y and Wu, Y and Hu, D and Xu, Y and Xu, H and Ji, G},
title = {Huang-qin Decoction alleviates Deoxycholic Acid-induced Colorectal Cancer in Mice by Regulating Gut Microbiota.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {119715},
doi = {10.1016/j.jep.2025.119715},
pmid = {40158829},
issn = {1872-7573},
abstract = {Huangqin Decoction (HQD), a traditional Chinese medicine (TCM) formula documented in Shang Han Lun, has demonstrated safety and efficacy in the treatment of ulcerative colitis (UC). Recent studies also suggest that HQD exerts therapeutic effects on colorectal cancer (CRC). However, the underlying mechanisms remain unclear.

AIMS OF THE STUDY: This study aimed to investigate the therapeutic effects of HQD on CRC and explore its potential mechanisms of action.

METHODS: The active ingredients and potential targets of HQD were identified through network pharmacology-based analyses. The CRC-related targets were compared with those of HQD. Shared targets were subjected to Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses, and a protein-protein interaction (PPI) network was constructed. Additionally, APC[min/+] mice were treated with 0.2% deoxycholic acid (DCA) and gavaged with low or high doses of HQD. Tumor morphology was assessed using hematoxylin and eosin (HE) staining. Immunohistochemical staining was performed to evaluate the expression of Ki-67, Caspase-3, and MUC2 in the intestine. Periodic acid-Schiff (PAS) and PAS-alcian blue (PAS-AB) staining were utilized to detect mucin distribution and the number of goblet cells in the intestines of the mice. The mRNA expression levels of interleukin 6 (IL-6), mitogen-activated protein kinase 8 (MAPK8), vascular endothelial growth factor A (VEGFA), epidermal growth factor receptor (EGFR), albumin (ALB), and Caspase 3 (CASP3) were quantified using quantitative reverse-transcription PCR (qRT-PCR). Immunofluorescence was employed to assess the degree of apoptosis. Additionally, 16S ribosomal RNA gene sequencing, sequence curation and annotation, and metagenomic sequencing were performed to analyze changes in the composition of the mouse intestinal microbiota and related functions and signaling pathways.

RESULTS: The active ingredients of HQD were identified. GO and KEGG pathway enrichment analyses indicated that the shared targets were primarily involved in tumor suppression. HQD effectively treated DCA-induced CRC in mice. Furthermore, positive PAS and PAS-AB staining was significantly increased in the intestines of mice treated with HQD. HQD enhanced the abundance of Lachnospiraceae, Firmicutes, Fusobacteria, and Clostridium, while reducing the abundance of Eggerthellales. Additionally, HQD modulated secondary bile acid metabolism, carbohydrate synthesis, and other energy metabolism pathways, which may underlie its therapeutic effects.

CONCLUSION: HQD effectively treated CRC in mice, and its mechanisms of action may be related to the regulation of the gut microbiota.},
}

@article {pmid40158299,
year = {2025},
author = {Borkakoti, N and Ribeiro, AJM and Thornton, JM},
title = {A structural perspective on enzymes and their catalytic mechanisms.},
journal = {Current opinion in structural biology},
volume = {92},
number = {},
pages = {103040},
doi = {10.1016/j.sbi.2025.103040},
pmid = {40158299},
issn = {1879-033X},
abstract = {In this perspective, we analyse the progress made in our knowledge of enzyme sequences, structures and functions in the last 2 years. We review how much new enzyme data have been garnered and annotated, derived from the study of proteins using structural and computational approaches. Recent advances towards capturing 'Catalysis in silico' are described, including knowledge and predictions of enzyme structures, their interactions and mechanisms. We highlight the flood of enzyme data, driven by metagenomic sequencing, the improved enzyme data resources, the high coverage in Protein Data Bank of E.C. classes and the AI-driven structure prediction techniques that facilitate the accurate prediction of protein structures. We note the focus on disordered regions in the context of enzyme regulation and specificity and comment on emerging bioinformatic approaches that capture reaction mechanisms computationally for comparing and predicting enzyme mechanisms. We also consider the drivers of progress in this field in the next five years.},
}

@article {pmid40158160,
year = {2025},
author = {Zhu, M and Wang, Q and Yang, Y and Liu, X and Zhang, J and Li, G and Liu, W and Xiang, X and Chen, J},
title = {Multiomics approach reveals the comprehensive interactions between nutrition and children's gut microbiota, and microbial and host metabolomes.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {50},
pmid = {40158160},
issn = {1475-2891},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Child ; Male ; Cross-Sectional Studies ; *Metabolome/physiology ; Female ; Child, Preschool ; *Feces/microbiology ; China ; *Diet/methods ; Metabolomics/methods ; Nutritional Status ; Multiomics ; },
abstract = {The gut microbiome can modulate nutrient metabolism to produce many metabolites interacting with the host. However, the intricate interactions among dietary intake, the gut microbiome and metabolites, and host metabolites need to be further explored although some studies have been devoted to it. Here, in a cross-sectional studies, 88 children aged 2-12 years were enrolled from northwestern China. The dietary intake data were collected via a designed food frequency questionnaire to calculate plant-based diet indices (PDIs). Stool and plasma samples were collected for metagenomic and broad-targeted metabolomic analysis. Spearman's rank correlation was used to describe the associations between nutrients/PDIs and the gut microbiota and metabolites. PDI was significantly positively associated with Bilophila wadsworthia, Bacteroides thetaiotaomicron, and Alistipes indistinctus, etc., but was obviously negatively correlated with Roseburia intestinalis, Faecalibacterium prausnitzii, etc. However, these species showed no significant associations with either healthy PDI (hPDI) or unhealthy PDI (uPDI). Interestingly, hPDI was significantly positively related to species, including Ruminococcus bicirculans, and was significantly negatively associated with uPDI, and vice versa. The above correlation trends were also observed between PDIs and predicted gut microbial functional pathways, microbial metabolites and the host metabolome. Notably, the significantly related pathways were focused mainly on substances and energy metabolism. PDI was significantly positively associated with the fecal contents of P-aminobenzoate, chenodeoxycholic acid, 4,6-dihydroxyquinoline, quinoline-4,8-diol, etc., but was significantly negatively associated with those of TMAO, FFA, creatine phosphate, etc. In plasma, PDI was significantly positively associated with sarcosine, ornithine, L-histidine, etc., but was distinctly negatively correlated with FFAs, carnitine C2:0, etc. Strikingly, the healthy plant-based diet index (hPDI) is correlated with increased levels of metabolites related to tryptophan metabolism, whereas the unhealthy PDI (uPDI) is linked to increased levels of metabolites associated with tyrosine and sphingolipid metabolism, which are pathways commonly associated with Western diets. Our studies provide reliable data support and a comprehensive understanding of the effects of dietary intake on the gut microbiome and microbial and host metabolites and lay a foundation for further studies of the diet-gut microbiota-microbial metabolites and host metabolism.},
}

*Gastrointestinal Microbiome/physiology
Humans
Child
Male
Cross-Sectional Studies
*Metabolome/physiology
Female
Child, Preschool
*Feces/microbiology
China
*Diet/methods
Metabolomics/methods
Nutritional Status
Multiomics

@article {pmid40158141,
year = {2025},
author = {Jiang, Y and Aton, M and Zhu, Q and Lu, YY},
title = {Modeling microbiome-trait associations with taxonomy-adaptive neural networks.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {87},
pmid = {40158141},
issn = {2049-2618},
support = {RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; RGPIN-03270-2023//Canadian NSERC Discovery Grant/ ; },
mesh = {Humans ; *Neural Networks, Computer ; *Microbiota ; Metagenomics/methods ; Bacteria/classification/genetics ; Computer Simulation ; },
abstract = {The human microbiome, a complex ecosystem of microorganisms inhabiting the body, plays a critical role in human health. Investigating its association with host traits is essential for understanding its impact on various diseases. Although shotgun metagenomic sequencing technologies have produced vast amounts of microbiome data, analyzing such data is highly challenging due to its sparsity, noisiness, and high feature dimensionality. Here, we develop MIOSTONE, an accurate and interpretable neural network model for microbiome-disease association that simulates a real taxonomy by encoding the relationships among microbial features. The taxonomy-encoding architecture provides a natural bridge from variations in microbial taxa abundance to variations in traits, encompassing increasingly coarse scales from species to domains. MIOSTONE has the ability to determine whether taxa within the corresponding taxonomic group provide a better explanation in a data-driven manner. MIOSTONE serves as an effective predictive model, as it not only accurately predicts microbiome-trait associations across extensive simulated and real datasets but also offers interpretability for scientific discovery. Both attributes are crucial for facilitating in silico investigations into the biological mechanisms underlying such associations among microbial taxa. Video Abstract.},
}

Humans
*Neural Networks, Computer
*Microbiota
Metagenomics/methods
Bacteria/classification/genetics
Computer Simulation

@article {pmid40157594,
year = {2025},
author = {Wang, C and Fan, S and Li, M and Ye, Y and Li, Z and Long, W and Li, Y and Huang, Z and Jiang, Q and Yang, W and Yang, R and Tang, D},
title = {A 7-year feed study on the long-term effects of genetically modified maize containing cry1Ab/cry2Aj and EPSPS genes on gut microbiota and metabolite profiles across two generations of cynomolgus macaques.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {115419},
doi = {10.1016/j.fct.2025.115419},
pmid = {40157594},
issn = {1873-6351},
abstract = {The health implications of genetically modified (GM) crops remain controversial relative to their non-GM counterparts, particularly regarding long-term dietary exposure. Although the gut microbiome is a key health indicator, studies investigating the impact of GM crop consumption on intestinal microbiota remain limited. This study presents a comprehensive 7-year evaluation of GM maize expressing cry1Ab/cry2Aj and G10evo-EPSPS proteins through metagenomic and metabolomic analyses. We assessed the effects of GM maize consumption on gut microbiota diversity and metabolite profiles in cynomolgus macaques (Macaca fascicularis) compared with non-GM maize. Three diet regimens were implemented: a conventional compound feed (CK group), diet formulation containing 70% non-GM maize (Corn group), and diet formulation containing 70% GM maize (Tg group). The results demonstrated that feeding GM maize to the first (F0) and second (F1) generations of monkeys did not substantially affect the composition, community structure, or function of the intestinal microbiome, as indicated by species composition and diversity analyses. Minor differences in intestinal metabolites were observed but were not directly linked to transgenic maize consumption. Collectively, long-term intake of maize with cry1Ab/cry2Aj and g10evo-epsps genes had no adverse effects on macaques or their offspring.},
}

@article {pmid40157532,
year = {2025},
author = {Pienaar, RD and Herrero, S and Cerqueira de Araujo, A and Krupa, F and Abd-Alla, AMM and Herniou, EA},
title = {High-throughput screening reveals high diversity and widespread distribution of viruses in black soldier flies (Hermetia illucens).},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108322},
doi = {10.1016/j.jip.2025.108322},
pmid = {40157532},
issn = {1096-0805},
abstract = {Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (Hermetia illucens, BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the orders Ghabrivirales and Bunyavirales, as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. A high-throughput pipeline allowed the simultaneous investigation of 203 next generation sequencing datasets. This revealed the presence of seven viruses belonging to the families Dicistroviridae, Iflaviridae, Rhabdoviridae, Solinviviridae, Inseviridae, Lebotiviridae, and an unclassified Bunyavirales. Here we describe five viruses, which were detected in BSF from multiple origins, outlining the diversity of naturally occurring viruses associated with BSF colonies. As this viral community may also include BSF pathogens, we developed molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.},
}

@article {pmid40157487,
year = {2025},
author = {Li, J and Zhu, L and Li, X and Han, X and Yi, J and Wu, Y and Wang, M},
title = {Characterization and Risk-quantification of Antibiotic Resistome in Grain-based and Non-grain Cropping Soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126147},
doi = {10.1016/j.envpol.2025.126147},
pmid = {40157487},
issn = {1873-6424},
abstract = {Microbial contamination in soils, encompassing human bacterial pathogens (HBPs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs), poses a significant threat to human health via the food chain. Currently, there is a lack of comprehensive assessments of microbial contamination and associated health risks of ARGs in agricultural soils. In this study, metagenomic sequencing was used to evaluate microbial contamination in grain-based cropping soils (rice cultivation) and non-grain cropping soils (vegetable cultivation and aquaculture). The results showed that the diversity and abundance of HBPs and VFGs were significantly higher in non-grain soils. Further resistome analysis revealed higher abundances of high-risk (from 0.014 to 0.018 - 0.023) and "last-resort" ARGs (from 0.007 to 0.034 - 0.046) in non-grain soils. Besides ARGs abundance, health risk quantification revealed that non-grain soils exhibited 1.49 to 2.14-fold greater ARG-related risks than grain-based soils. Additionally, stronger network associations were found between HBPs, ARGs, and mobile genetic elements (MGEs) in non-grain soils. This study indicated that the non-grain cropping pattern of soils elevated the risk of microbial contamination and ARGs health risk, which provided an important basis for accurately quantifying the risk of microbial contamination in different agricultural soils.},
}

@article {pmid40157184,
year = {2025},
author = {Qiao, X and Kong, X and Zhou, H and Fan, X and Yuan, J and Zhang, Y},
title = {Deciphering the inhibitory mechanisms of polystyrene microplastics on thermophilic methanogens from the insights of microbial metabolite profiling and metagenomic analyses.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138054},
doi = {10.1016/j.jhazmat.2025.138054},
pmid = {40157184},
issn = {1873-3336},
abstract = {Due to the utilization of food packaging bags, a substantial amount of polystyrene microplastics (PS MPs) are introduced into the food waste (FW) treatment system during the pre-treatment process, potentially impacting the subsequent biochemical treatment system. In order to investigate the mechanism by which PS MPs affect anaerobic methanogenesis metabolism in thermophilic condition, this study analyzed the characteristics of methanogenesis in thermophilic anaerobic digestion (AD) of FW under different concentrations of PS MPs (100 μm, 10-200 mg/L). The results revealed a negative correlation between PS MPs concentration and methane (CH4) yield from FW. When the concentration of PS MPs reached 200 mg/L, CH4 yield decreased by 47.8 %. Further mechanistic investigations revealed that while the presence of PS MPs at lower concentrations could alleviate its adverse impact on methanogenesis by enhancing EPS content, the accumulation of reactive oxygen species (ROS) persisted with increasing PS MPs concentration, thereby inhibiting the activities of key enzymes involved in solubilization and acidification metabolisms (e.g., acetate kinase and F420). Metagenomics analysis indicated that the presence of PS MPs down-regulate abundance of genes for quorum sensing and CH4 metabolism pathways. These findings not only unveil potential detrimental effects of PS MPs on AD systems but also provide novel insights into comprehending and controlling the impact of MPs pollution on environmental preservation and energy recovery processes.},
}

@article {pmid40157173,
year = {2025},
author = {Weiting, S and Chen, W and Xiao, L and Yanqiu, H},
title = {Enhanced acid reduction in lactic acid bacteria: Breeding through irradiation-induced mutation and functional assessment.},
journal = {International journal of food microbiology},
volume = {435},
number = {},
pages = {111161},
doi = {10.1016/j.ijfoodmicro.2025.111161},
pmid = {40157173},
issn = {1879-3460},
abstract = {High concentrations of citric acid (CA), malic acid (MA), and tartaric acids (TA) are the primary contributors to the sour taste of fruit and fruit products. However, lactic acid bacteria that are capable of efficiently degrading these organic acids are scarce. Here, three brands of sauerkraut (Xinxi, X; Yuyuan, Y; and Zou Youcai, Z) with various doses of [60]Co γ-irradiation could be treated to induce mutations in their associated lactic acid bacteria and then the abilities of the resulting microbial communities to degrade CA, MA, and TA were evaluated. Sauerkraut X treated with 0.4 kGy irradiation demonstrated the greatest ability of acid reduction. Metagenomic analyses of irradiated (0.4 kGy) and non-irradiated bacterial communities from sauerkraut X revealed a slight decrease in microbial diversity due to irradiation, with a substantial decline in the relative abundance of Lactiplantibacillus xiangfangensis. Concurrently, the relative abundance of dominant acid-reducing lactic acid bacteria such as Levilactobacillus brevis, Pediococcus ethanolidurans, and Lentilactobacillus parafarraginis increased. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed an increase in metabolism-related genes after irradiation, indicating that fatty acid synthesis and aspartate metabolism might be key pathways involved in the enhanced degradation of CA, MA, and TA. Analysis using the Carbohydrate-Active enzymes Database (CAZy) database revealed that glycoside hydrolase (GH) and glycosyltransferase (GT) genes were the most abundant carbohydrate-associated enzyme genes in the bacterial community of sauerkraut X. This finding proved that the oligosaccharides and monosaccharides produced by GH and GT might indirectly affect rates of organic acid degradation. Three highly effective acid-reducing lactic acid bacteria from the microbial community of irradiated sauerkraut X a were isolated and identified via 16S rRNA sequencing as Pediococcus ethanolidurans, Levilactobacillus brevis, and Loigolactobacillus coryniformis. The individual strains showed degradation rates as high as 92.02 % for citric acid (Pediococcus ethanolidurans), 83.04 % for malic acid (Levilactobacillus brevis), and 90.33 % for TA (Loigolactobacillus coryniformis). This study provides a theoretical basis and technical support for the development of enhanced microbial strains that can reduce the acid content of fruit materials.},
}

@article {pmid40156973,
year = {2025},
author = {Zhong, S and Li, B and Chen, Q and Zhang, J and Cai, H and An, R and Liu, G and Zhou, S},
title = {Identifying groundwater anthropogenic disturbances and their predominant impact on microbial nitrogen cycling at a former contamination site adjacent to Baiyangdian Lake.},
journal = {Water research},
volume = {280},
number = {},
pages = {123544},
doi = {10.1016/j.watres.2025.123544},
pmid = {40156973},
issn = {1879-2448},
abstract = {Groundwater ecosystems face increasing threat from declining water quality due to intensified urbanization, agricultural, and industrial activities. Accurately identifying anthropogenic disturbances remains challenging, and their effects on microbial nitrogen cycling are still largely unknown. Here, by collecting 64 groundwater samples from an aquifer beneath the Tanghe sewage reservoir in the North China Plain, we conducted a full-spectrum screening of 228 physiochemical indices, 47 nitrogen cycling genes (NCGs) and 2182 metagenome-assembled genomes (MAGs) harboring NCGs. Unmix model identified antibiotic usage, industrial manufacturing, and agricultural practices as the predominant pollution sources, explaining 49.6-92.2 % (averaged 81.0 %) of the variations in aquifer attributes. These activities were primary drivers governing distributions of groundwater NCGs and NCG-hosts, with fragmented denitrification processes being prevalent. Antibiotic usage and industrial activities were probably associated with suppressed nitrogen cycling, while agriculture had a positive effect. Notably, we observed enhanced mutualistic interactions within NCG-hosts and increased enrichment of NCG-antibiotic resistance gene (ARG), NCG-mental resistance gene (MRG), and NCG-ARG-MRG co-hosts under high anthropogenic stresses, suggesting microbial adaptation to optimize nutrient and energy metabolism. This study provided new insight into how groundwater nitrogen cycling responds to anthropogenic disturbances, offering valuable information for developing groundwater management and pollution control strategies.},
}

@article {pmid40156579,
year = {2025},
author = {Sanghani, A and Antaliya, K and Patel, R and Dave, S and Tipre, D},
title = {Revealing Microbial Functionalities and Ecological Roles in Rajpardi Lignite Mine: Insights from Metagenomics Analysis.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf048},
pmid = {40156579},
issn = {1472-765X},
abstract = {The present study employs a metagenomics approach to evaluate microbial communities' ecological functions and potential within the Rajpardi lignite mine of Gujarat, India. Through whole genome shotgun sequencing on the Illumina Miseq platform, we obtained 10,071,318 sequences, which unveiled a diverse and abundant microbial community primarily composed of Proteobacteria, Acidobacteria, and Nitrospirae. Comprehensive taxonomic profiling and gene prediction was carried out using the SqueezeMeta pipline, which highlighted significant contributions to carbohydrate, amino acid, and energy metabolism. The detection of antimicrobial resistance (AMR) and stress resistance genes, such as blaTEM and merA, suggests that these microbes possess the ability to adapt to harsh environmental conditions. Genome binning revealed species such as Acidiphilum sp. 20-67-58, emphasising the nature of these communities as they adapted to an acidic environment. This finding highlights the crucial role of microbes in biogeochemical cycles, emphasizing their potential in bioremediation, pollutant degradation, and ecosystem restoration.},
}

@article {pmid40156577,
year = {2025},
author = {Kop, LFM and Koch, H and Martins, PD and Suarez, C and Karačić, S and Persson, F and Wilén, BM and Hagelia, P and Jetten, MSM and Lücker, S},
title = {High diversity of nitrifying bacteria and archaea in biofilms from a subsea tunnel.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf032},
pmid = {40156577},
issn = {1574-6941},
abstract = {Microbial biofilm formation can contribute to the accelerated deterioration of steel-reinforced concrete structures and significantly impact their service life, making it critical to understand the diversity of the biofilm community and prevailing processes in these habitats. Here, we analyzed 16S rRNA gene amplicon and metagenomics sequencing data to study the abundance and diversity of nitrifiers within biofilms on the concrete surface of the Oslofjord subsea road tunnel in Norway. We showed that the abundance of nitrifiers varied greatly in time and space, with a mean abundance of 24.7±15% but a wide range between 1.2-61.4%. We hypothesize that niche differentiation allows the coexistence of several nitrifier groups and that their high diversity increases the resilience to fluctuating environmental conditions. Strong correlations were observed between the nitrifying families Nitrosomonadaceae and Nitrospinaceae, and the iron-oxidizing family Mariprofundaceae. Metagenome-assembled genome (MAG) analyses suggested that early Mariprofundaceae colonizers may provide a protected environment for nitrifiers in exchange for nitrogen compounds and vitamin B12, but further studies are needed to elucidate the spatial organization of the biofilms and the cooperative and competitive interactions in this environment. Together, this research provides novel insights into the diverse communities of nitrifiers living within biofilms on concrete surfaces and establishes a foundation for future experimental studies of concrete biofilms.},
}

@article {pmid40156536,
year = {2025},
author = {Sarker, S and Klukowski, N and Talukder, S and Athukorala, A and Uddin, MJ},
title = {Opportunistic sampling from the near-threatened Alexandrine parakeet uncovers genomes of a novel parvovirus and beak and feather disease virus.},
journal = {Australian veterinary journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/avj.13442},
pmid = {40156536},
issn = {1751-0813},
support = {DE200100367//Australian Research Council/ ; },
abstract = {Birds are known to harbour a wide range of pathogenic viruses, including the beak and feather disease virus (BFDV; species, Circovirus parrot), which poses a significant threat to the conservation of endangered avian species. This study reports the genomic identification and characterisation of a novel psittaciform chaphamaparvovirus (PsChPV-6) and BFDV, sequenced from the faecal samples of healthy Alexandrine parakeets (Psittacula eupatria). PsChPV-6 is a linear, single-stranded DNA virus consisting of 4232 nucleotides (nt) with a high A + T content and five predicted open reading frames (ORFs). Key proteins encoded by PsChPV-6, such as the nonstructural protein 1 (NS1) and major capsid protein VP1, demonstrate strong sequence similarities to other avian parvoviruses, with conserved motifs in NS1 crucial for viral replication. The presence of a previously uncharacterised ORF1 region suggests strain-specific viral features that warrant further exploration. BFDV is a circular single-stranded DNA virus in the Circoviridae family and was also identified in the samples. Phylogenetic analysis positioned PsChPV-6 within the Chaphamaparvovirus genus, closely related to parvoviruses from diverse avian species, whereas BFDV was grouped with strains from Australian cockatoos and other nonpsittacine birds, suggesting potential cross-species transmission. These findings contribute to a deeper understanding of the genetic diversity and evolutionary dynamics of these viral pathogens in bird populations, underscoring the importance of ongoing surveillance to evaluate their ecological and veterinary impacts.},
}

@article {pmid40156205,
year = {2025},
author = {Huyghe, CET and Fages, A and Ronco, F and Indermaur, A and Schedel, FDB and Kimirei, I and Makasa, L and Tschopp, P and Salzburger, W},
title = {Metagenomic Insights Into the Dietary Diversity of the Adaptive Radiation of Cichlid Fishes in Lake Tanganyika.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17743},
doi = {10.1111/mec.17743},
pmid = {40156205},
issn = {1365-294X},
support = {189970//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {Diet specialisation is a main driver of diversification in many adaptive radiations. Therefore, identifying diet items is essential to characterise trophic specialisations and to understand the dynamics of dietary adaptations. In this study, we explored the trophic niches of 56 species from the adaptive radiation of cichlid fishes in Lake Tanganyika, encompassing all major phylogenetic lineages and feeding specialisations. We employed a metagenomic sequencing approach to identify the food sources of the investigated species at high taxonomic resolution, sequencing over 400 digestive content samples from wild-caught individuals at around 50 million paired-end read depth per sample. Our analyses revealed Arthropoda, Chordata (fishes), Bacillariophyta and Streptophyta as the primary diet phyla of the Tanganyikan cichlids. Moreover, we confirmed the presence of other food sources and identified taxa not previously documented to be part of the cichlids' diet. Based on their dietary compositions, the Tanganyikan cichlids can be grouped into herbivores, invertivores, piscivores and mixed feeders. Further, we showed that trophic disparity in the radiation is shaped by rapid divergence and documented cases of dietary niche convergence. Diet composition correlated with carbon and nitrogen stable isotope values, gut length, and body morphology. Differences in diet-such as the consumption of diatoms, streptophytes and chlorophytes versus fish and arthropods-were associated with changes in body, upper oral jaw and lower pharyngeal jaw shape. Collectively, this study presents a comprehensive and detailed diet classification of the Tanganyikan cichlids, highlighting the power of metagenomic approaches in delineating dietary adaptations.},
}

@article {pmid40155949,
year = {2025},
author = {Song, J and Lin, LA and Tang, C and Chen, C and Yang, Q and Zhang, D and Zhao, Y and Wei, HC and Linghu, K and Xu, Z and Chen, T and He, Z and Liu, D and Zhong, Y and Zhu, W and Zeng, W and Chen, L and Song, G and Chen, M and Jiang, J and Zhou, J and Wang, J and Chen, B and Ying, B and Wang, Y and Geng, J and Lin, JW and Chen, L},
title = {DEMINERS enables clinical metagenomics and comparative transcriptomic analysis by increasing throughput and accuracy of nanopore direct RNA sequencing.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {76},
pmid = {40155949},
issn = {1474-760X},
mesh = {*Metagenomics/methods ; Humans ; *Nanopore Sequencing/methods ; *Sequence Analysis, RNA/methods ; COVID-19/virology/genetics ; Gene Expression Profiling/methods ; Transcriptome ; Glioma/genetics ; High-Throughput Nucleotide Sequencing/methods ; SARS-CoV-2/genetics ; Software ; Malaria ; },
abstract = {Nanopore direct RNA sequencing (DRS) is a powerful tool for RNA biology but suffers from low basecalling accuracy, low throughput, and high input requirements. We present DEMINERS, a novel DRS toolkit combining an RNA multiplexing workflow, a Random Forest-based barcode classifier, and an optimized convolutional neural network basecaller with species-specific training. DEMINERS enables accurate demultiplexing of up to 24 samples, reducing RNA input and runtime. Applications include clinical metagenomics, cancer transcriptomics, and parallel transcriptomic comparisons, uncovering microbial diversity in COVID-19 and m[6]A's role in malaria and glioma. DEMINERS offers a robust, high-throughput solution for precise transcript and RNA modification analysis.},
}

*Metagenomics/methods
Humans
*Nanopore Sequencing/methods
*Sequence Analysis, RNA/methods
COVID-19/virology/genetics
Gene Expression Profiling/methods
Transcriptome
Glioma/genetics
High-Throughput Nucleotide Sequencing/methods
SARS-CoV-2/genetics
Software
Malaria

@article {pmid40155846,
year = {2025},
author = {Zhang, Z and Tian, L},
title = {Validation of mNGS results using extensive lab and clinical data.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {173},
pmid = {40155846},
issn = {1471-2180},
mesh = {Humans ; Retrospective Studies ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Mycoplasma pneumoniae/genetics/isolation & purification ; Male ; Adult ; Middle Aged ; Female ; Tuberculosis/microbiology/diagnosis ; Aged ; Adolescent ; Young Adult ; Child ; },
abstract = {PURPOSE: Interpreting the results of metagenomic next-generation sequencing (mNGS) presents a significant challenge in both clinical and laboratory contexts.

METHODS: A retrospective analysis was conducted to validate mNGS findings, with a particular emphasis on Mycobacterium tuberculosis, Mycoplasma pneumoniae, and Pneumocystis jirovecii as representative pathogens, examined from both clinical and laboratory perspectives.

RESULTS: Based on a comprehensive clinical analysis, the mNGS demonstrated detection accuracies for M. tuberculosis, M. pneumoniae, and P. jirovecii of 87.0% (60 out of 69; 95% confidence interval [CI], 77.04%-92.99%), 97.6% (81 out of 83; 95% CI, 91.63%-99.34%), and 78.9% (45 out of 57; 95% CI, 66.72%-87.53%), respectively. Conversely, when incorporating laboratory confirmation from a variety of detection methodologies, the accuracy rates for mNGS in identifying M. tuberculosis, M. pneumoniae, and P. jirovecii were 92.7% (51 out of 55; 95% CI, 82.74%-97.14%), 82.3% (51 out of 62; 95% CI, 70.96%-89.80%), and 83.9% (26 out of 31; 95% CI, 67.36%-92.91%), respectively. Additionally, our analysis revealed no statistically significant difference in read counts and relative abundances between mNGS results deemed clinically as false positives and those considered true positives (P < 0.05).

CONCLUSION: In contemporary clinical practice, the detection of positive results from mNGS is notably high from both laboratory and clinical standpoints. Nonetheless, the interpretation of results with low read counts presents significant challenges for both clinical and laboratory environments under current conditions.},
}

Humans
Retrospective Studies
*Mycobacterium tuberculosis/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Mycoplasma pneumoniae/genetics/isolation & purification
Male
Adult
Middle Aged
Female
Tuberculosis/microbiology/diagnosis
Aged
Adolescent
Young Adult
Child

@article {pmid40155693,
year = {2025},
author = {Refahi, M and Sokhansanj, BA and Mell, JC and Brown, JR and Yoo, H and Hearne, G and Rosen, GL},
title = {Enhancing nucleotide sequence representations in genomic analysis with contrastive optimization.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {517},
pmid = {40155693},
issn = {2399-3642},
support = {1936791//National Science Foundation (NSF)/ ; 1919691//National Science Foundation (NSF)/ ; 2107108//National Science Foundation (NSF)/ ; },
mesh = {*Genomics/methods ; Sequence Analysis, DNA/methods ; Base Sequence ; Algorithms ; Metagenomics/methods ; },
abstract = {Analysis of genomic and metagenomic sequences is inherently more challenging than that of amino acid sequences due to the higher divergence among evolutionarily related nucleotide sequences, variable k-mer and codon usage within and among genomes of diverse species, and poorly understood selective constraints. We introduce Scorpio (Sequence Contrastive Optimization for Representation and Predictive Inference on DNA), a versatile framework designed for nucleotide sequences that employ contrastive learning to improve embeddings. By leveraging pre-trained genomic language models and k-mer frequency embeddings, Scorpio demonstrates competitive performance in diverse applications, including taxonomic and gene classification, antimicrobial resistance (AMR) gene identification, and promoter detection. A key strength of Scorpio is its ability to generalize to novel DNA sequences and taxa, addressing a significant limitation of alignment-based methods. Scorpio has been tested on multiple datasets with DNA sequences of varying lengths (long and short) and shows robust inference capabilities. Additionally, we provide an analysis of the biological information underlying this representation, including correlations between codon adaptation index as a gene expression factor, sequence similarity, and taxonomy, as well as the functional and structural information of genes.},
}

*Genomics/methods
Sequence Analysis, DNA/methods
Base Sequence
Algorithms
Metagenomics/methods

@article {pmid40155620,
year = {2025},
author = {Kazarina, A and Wiechman, H and Sarkar, S and Richie, T and Lee, STM},
title = {Recovery of 679 metagenome-assembled genomes from different soil depths along a precipitation gradient.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {521},
pmid = {40155620},
issn = {2052-4463},
support = {2020-67019-31803//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; 2238633//National Science Foundation (NSF)/ ; OIA-1656006//National Science Foundation (NSF)/ ; },
mesh = {*Soil Microbiology ; *Metagenome ; Metagenomics ; Bacteria/genetics/classification ; Kansas ; Soil/chemistry ; Archaea/genetics ; },
abstract = {Soil contains a diverse community of organisms; these can include archaea, fungi, viruses, and bacteria. In situ identification of soil microorganisms is challenging. The use of genome-centric metagenomics enables the assembly and identification of microbial populations, allowing the categorization and exploration of potential functions living in the complex soil environment. However, the heterogeneity of the soil-inhabiting microbes poses a tremendous challenge, with their functions left unknown, and difficult to culture in lab settings. In this study, using genome assembling strategies from both field core samples and enriched monolith samples, we assembled 679 highly complete metagenome-assembled genomes (MAGs). The ability to identify these MAGs from samples across a precipitation gradient in the state of Kansas (USA) provided insights into the impact of precipitation levels on soil microbial populations. Metabolite modeling of the MAGs revealed that more than 80% of the microbial populations possessed carbohydrate-active enzymes, capable of breaking down chitin and starch.},
}

*Soil Microbiology
*Metagenome
Metagenomics
Bacteria/genetics/classification
Kansas
Soil/chemistry
Archaea/genetics

@article {pmid40155586,
year = {2025},
author = {Bebawy, AS and Saad, BT and Saad, MT and Mosaad, GS and Gomaa, FAM and Alshahrani, MY and Aboshanab, KM},
title = {Evaluation of the taxonomic classification tools and visualizers for metagenomic analysis using the Oxford nanopore sequence database.},
journal = {Journal of applied genetics},
volume = {},
number = {},
pages = {},
pmid = {40155586},
issn = {2190-3883},
abstract = {Microbial metagenomic identification is generally attributed to the specificity and type of the bioinformatic tools, including classifiers and visualizers. In this study, the performance of two major classifiers, Centrifuge and Kraken2, and two visualizers (Recentrifuge and Krona) has been thoroughly investigated for their efficiency in the identification of the microorganisms using the Whole-Genome Sequence (WGS) database and four targeted databases including NCBI, Silva, Greengenes, and Ribosomal Database Project (RDP). Two standard DNA metagenomic library replicates, Zymo and Zymo-1, were used as quality control. Results showed that Centrifuge gave a higher percentage of Pseudomonas aeruginosa, Escherichia coli, and Salmonella enterica identification than Kraken2. Compared to Recentrifuge, Kraken2 was more accurate in identifying Staphylococcus aureus, Listeria monocytogenes, Bacillus subtilis, and Cryptococcus neoformans. The results of the rest of the detected microorganisms were generally consistent with the two classifiers. Regarding visualizers, both Recentrifuge and Krona provided similar results regarding the abundance of each microbial species regardless of the classifier used. The differences in results between the two mentioned classifiers may be attributed to the specific algorithms each method uses and the sequencing depth. Centrifuge uses a read mapping approach, while Kraken2 uses a k-mer-based system to classify the sequencing reads into taxonomic groups. In conclusion, both Centrifuge and Kraken2 are effective tools for microbial classification. However, the choice of classifier can influence the accuracy of microbial classification and, therefore, should be made carefully, depending on the desired application, even when the same reference database is used.},
}

@article {pmid40154870,
year = {2025},
author = {Yang, JT and Zhang, Y and Xiong, SY and Wei, HJ and Zhang, WT and Lian, XL and Xu, XL and Jiang, HX and Sun, J},
title = {Microplastics Reduced the Natural Attenuation of Antibiotic Resistance Genes in Fertilized Soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126144},
doi = {10.1016/j.envpol.2025.126144},
pmid = {40154870},
issn = {1873-6424},
abstract = {The prolonged application of mulch and manure in agriculture has led to significant microplastic (MP) pollution in fertilized soils, raising global concerns about its potential impacts on soil health and ecosystem function. However, the effects of MP exposure on antibiotic resistance genes (ARGs) and microbial communities in fertilized soils are unknown. Therefore, we comprehensively explored the trends and drivers of ARGs during their natural abatement under the stress of conventional and biodegradable MP addition in fertilized soils using a soil microcosm experiment and metagenomic. The findings indicated that the presence of polybutylene succinate MPs (PBS-MPs) reduced the natural attenuation rate of ARGs in fertilized soils while increasing the fraction of high-risk ARGs in soils. Microbial communities and mobile genetic elements (MGEs) mainly drove the inhibitory effect of MPs on ARG abatement. Interestingly, most potential hosts for the coexistence of ARGs, metal resistance genes (MRGs), and MGEs were annotated as pathogens, such as Escherichia spp., Salmonella spp., and Klebsiella spp. In addition, MP stress in fertilized soil may lead to long-term contamination by highly virulent and antibiotic-resistant Escherichia coli. MPs influence the distribution of carbon sources, which in turn reduces the diversity and stability of soil microbial communities, while simultaneously promoting the colonization of crucial ARG hosts, like Dyella spp. This ultimately prolonged the high-risk state for ARG proliferation in the soil. This study highlights the significant risk posed by MPs to the persistence and spread of ARGs in fertilized soils. These results provide valuable insights for managing MP contamination in agricultural systems, emphasizing the need for sustainable practices to mitigate the long-term environmental risks associated with MP pollution.},
}

@article {pmid40154751,
year = {2025},
author = {Jiang, X and Zhao, Y and Zhang, W and Zheng, Q and Li, D and Zhang, G and Zhou, T},
title = {Chlorotetracycline-driven modulation of substrate utilization and metabolic traits in sludge anaerobic fermentation for optimized methane production.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132449},
doi = {10.1016/j.biortech.2025.132449},
pmid = {40154751},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) is a highly efficient and promising method for treating waste activated sludge (WAS). Nevertheless, the presence of chlortetracycline (CTC) in WAS introduced uncertainty into the AD process. This study revealed thatthe cumulative methane yield was increased by 27.5 % with the CTC concentration at 50 mg/kg dry sludge by enhancing hydrolysis, acidification and methanogenesis during which specific microbial communities were enriched and related functional genes were enhanced. Subsequent investigations foundthe accumulation of extracellular polymeric substances (EPS) was improved and methane-producing microorganisms (e.g., Bacteroidetes and Euryarchaeota) were also enriched under CTC exposure. Metagenomic analysis further elucidated thatCTC significantly increased functional genes related to bacterial secretion system and metabolism of organic matter for methane production (e.g., pyruvate metabolism and methane metabolism). This study shed light on the substantial impact of CTC on the AD of WAS and provided a promising strategy for improvements in anaerobic fermentation.},
}

@article {pmid40154110,
year = {2025},
author = {Alameer, RM and Tayeb, H and Magrashi, A and Alqasabi, A and Nazmi, A and Yamani, A and Almaghrabi, RS},
title = {Diagnosis of donor-derived Malassezia restricta &Aspergillus species invasive fungal infection in renal transplant recipient using next generation sequencing - A report of 2 cases and literature review.},
journal = {Journal of infection and public health},
volume = {18},
number = {5},
pages = {102742},
doi = {10.1016/j.jiph.2025.102742},
pmid = {40154110},
issn = {1876-035X},
abstract = {Diagnosing donor-derived fungal infection in solid organ transplant recipients can be particularly challenging and is associated with high mortality. Here, we report two cases of Malassezia restricta and Aspergillus spp donor-derived fungal infection in renal transplant recipients leading to graft loss. Fortunately, both patients achieved full recovery with the administration of antifungal therapy.},
}

@article {pmid40154057,
year = {2025},
author = {Chen, H and Zhong, S and Liu, Z and Hu, Z and Wang, C and Zhou, Y and Xu, N and Zhao, F and Li, D and Hu, Y},
title = {Microbiome-metabolomic insights into the systemic regulation in Fangxian Huangjiu fermentation.},
journal = {Food chemistry},
volume = {481},
number = {},
pages = {143980},
doi = {10.1016/j.foodchem.2025.143980},
pmid = {40154057},
issn = {1873-7072},
abstract = {Metabolic forces drive microecological succession in Huangjiu fermentation. This study investigates the dynamic metabolic-microbial interplay during Fangxian Huangjiu fermentation. Temporal changes of metabolome and microbiome revealed a syntropic relationship that purified the microbial community with convergent metabolic patterns. With species turnover driving microbial community structure, early-stage microbiomes exhibited great functional diversity. Functions related to energy and molecular building blocks were enriched at the end of early stage, and contributed greatly to microbial adaptation, highlighting the importance of metabolic forces in shaping community structure. Proteobacteria were identified as key facilitators of diverse metabolic activities, and Enterobacter emerged as a fundamental microbial community particularly for materials transformation. Correlation analysis enriched amino acid metabolism pathways. Further, Pantoea ananatis and Wickerhamomyces anomalus were isolated to enhance sphingosine-1-phosphate, γ-aminobutyric acid, and creatine levels without altering physicochemical properties. The study offers insights into the regulation of Huangjiu fermentation, and suggested potential micobiome manipulation to optimize characteristics.},
}

@article {pmid40154039,
year = {2025},
author = {Li, J and Huang, Z and Zhang, R},
title = {Unmasking Prototheca wickerhamii: A rare case of cutaneous infection and its implications for clinical practice.},
journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases},
volume = {29},
number = {3},
pages = {104525},
doi = {10.1016/j.bjid.2025.104525},
pmid = {40154039},
issn = {1678-4391},
abstract = {Prototheca, an opportunistic pathogenic algae widely found in nature, has emerged as a potential public health concern. Most cases occur in immunocompromised individuals, with infections in immunocompetent patients being relatively rare. Due to their non-specific clinical presentation and limited awareness among clinicians, Prototheca infections are often misdiagnosed, resulting in delayed treatment. Recent advances in species identification and antifungal susceptibility testing have provided important tools for diagnosis and therapy. Here, we report a case of recurrent facial infection in a 76-year-old immunocompetent man. Skin biopsy revealed an infectious granuloma, and fungal culture identified yeast-like colonies. Fluorescence staining and scanning electron microscopy revealed abundant spores, while metagenomic sequencing confirmed the infection as Prototheca wickerhamii. The patient was successfully treated with long-term itraconazole and dipotassium glycyrrhizinate capsules. This case highlights the importance of early and accurate diagnosis in the management of Prototheca skin infections and reviews the therapeutic strategies used.},
}

@article {pmid40153957,
year = {2025},
author = {Huang, M and Mu, G and Mai, F and Zhou, Y and Li, X and Yang, Q and Shao, B and Wang, J and Tong, Y},
title = {Methane cycling in typical emerging proglacial lakes on the Tibetan Plateau: Insights into the metabolic mechanisms mediated by microorganisms.},
journal = {Water research},
volume = {280},
number = {},
pages = {123533},
doi = {10.1016/j.watres.2025.123533},
pmid = {40153957},
issn = {1879-2448},
abstract = {A large number of high-latitude emerging proglacial lakes have formed on the Tibetan Plateau (TP) due to the global warming and deglaciation. These lakes have the potential to emit methane (CH4) because of the exposure of cryopreserved organic carbon, leading to their significance in regional carbon turnover and cycling. However, previous studies have focused more on human-impacted lakes (e.g., eutrophic lakes), resulting in limited research on the mechanisms of CH4 cycling in the proglacial lakes. In this study, we demonstrated that three typical emerging high-latitude proglacial lakes (∼5500 m a.s.l.) on the TP exhibited a diffusive emission flux of 32.39 ± 11.66 μmol/m[2]/d during the summer. The δ[13]C-CH4 values (-50.10 ± 0.56‰) suggested a biogenic origin of CH4 through the acetoclastic pathway in the lakes. Metagenome sequencing further showed that microbes involved in methanogenesis were dominated by Methanosarcina (36.74 ± 0.07 % of total methanogens). Significant CH4 consumption was observed in the proglacial lakes. The microbes involved in the CH4 consumption were dominated by Methylobacter (48.50 ± 0.17 % of total methanotrophs). A Mantel test demonstrated that dissolved iron (Fe) was a key factor controlling the structure of the CH4 cycling microbial communities. Functional gene and co-occurrence network analyses indicated that members of Pseudomonadota, Bacteroidota, and Actinomycetota may be involved in CH4 cycling by providing methanogenic substrates (i.e., acetyl coenzyme A) and consuming CH4 oxidative intermediates (i.e., methanol, formaldehyde, and formic acid). This study emphasized the ecological significance of emerging proglacial lakes in CH4 releases. It broadened the current understanding of cryophilic CH4 cycling microbes and their mechanisms, that enhances our knowledge of the carbon cycle on the TP.},
}

@article {pmid40153355,
year = {2025},
author = {Klištincová, N and Koreňová, J and Rešková, Z and Čaplová, Z and Burdová, A and Farkas, Z and Polovka, M and Drahovská, H and Pangallo, D and Kuchta, T},
title = {Bacterial consortia of ewes´ whey in the production of bryndza cheese in Slovakia.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf047},
pmid = {40153355},
issn = {1472-765X},
abstract = {Whey from previous production is often used as a natural starter in the technology of traditional cheeses, including bryndza-cheese in Slovakia. Therefore, studying its bacterial community and isolating new potential natural starters is important for improving the characterisitics of final product. Composition of bacterial consortia of fresh and fermented whey in the production of raw ewes´ milk-based bryndza-cheese from 8 small or medium-sized producers was analysed. Culture-based microbiological analysis and culture-independent analysis based on 16S rRNA gene sequencing by MiSeq and MinION were used. Results showed the dominance of lactococci or streptococci, with 3 - 8 log CFU ml-[1] of Lactobacillus sensu lato in all whey samples. Potential natural starters comprising Lacticaseibacillus paracasei/casei, Lactiplantibacillus plantarum, Lentilactobacillus parabuchneri, Lactobacillus helveticus, Lactobacillus diolivorans, Levilactobacillus brevis, Limosilactobacillus fermentum, Lactobacillus delbrueckii, Lactobacillus gasseri and Lentilactobacillus otakiensis were isolated. Coliforms were also present in all samples, with no consistently lower values in fermented whey samples. Some samples contained pseudomonads and/or acinetobacters. Coagulase positive staphylococci were present at relevant levels in samples from 4 producers. The results revealed that whey is a source of natural starters due to the presence of lactobacilli.},
}

@article {pmid40153196,
year = {2025},
author = {Erickson, I and Davidson, S and Choi, H and Rho, S and Guignet, M and Peagler, K and Thummel, K and Ericsson, A and Barker-Haliski, M},
title = {Intestinal dysbiosis alters acute seizure burden and antiseizure medicine activity in Theiler's virus model of encephalitis.},
journal = {Epilepsia},
volume = {},
number = {},
pages = {},
doi = {10.1111/epi.18395},
pmid = {40153196},
issn = {1528-1167},
support = {//University of Washington/ ; },
abstract = {OBJECTIVE: Brain infection with Theiler's murine encephalomyelitis virus (TMEV) in C57BL/6J mice produces an etiologically relevant model of acquired seizures. Dietary changes can modify seizure presentation following TMEV brain infection and influence intestinal microbiome diversity and composition. Intestinal dysbiosis may thus similarly affect seizure burden and antiseizure medicine (ASM) activity in this model, independent of pharmacokinetic effects. We thus sought to define the influence of antibiotic (ABX)-induced gut dysbiosis on acute seizure presentation, anticonvulsant activity of carbamazepine (CBZ), and CBZ pharmacokinetics with TMEV infection.

METHODS: Male C57BL/6J mice (4-5 weeks old) received oral ABX or saline (SAL) once daily beginning on arrival through day 7 after TMEV infection (postinfection [p.i.]). Mice were infected with TMEV or phosphate-buffered saline on day 0. Mice received intraperitoneal (20 mg/kg) CBZ or vehicle (VEH) twice daily on days 3-7 p.i. and were assessed for handling-induced seizures 30 min after treatment. Plasma was collected on day 7 p.i. at 15 and 60 min after CBZ administration for bioanalysis.

RESULTS: TMEV infection induced acute seizures, but ABX-induced gut dysbiosis altered seizure presentation. There were 75% SAL-VEH, 35% SAL-CBZ, 35% ABX-VEH, and 72% ABX-CBZ mice with seizures during the 7-day monitoring period. There was a significant pretreatment × ASM interaction (p = .0001), with differences in seizure burden in SAL- versus ABX-pretreated mice (p = .004). CBZ significantly increased latency to seizure presentation, an effect absent in ABX-CBZ mice. Plasma CBZ concentrations did not differ between SAL and ABX pretreatment groups, suggesting that ABX did not influence CBZ pharmacokinetics.

SIGNIFICANCE: ABX-induced gut dysbiosis markedly altered acute disease trajectory with TMEV-induced encephalitis, reflecting a novel contribution of the gut microbiome to seizure presentation. ABX-induced gut dysbiosis also significantly changed acute seizure control by CBZ, but did not influence plasma CBZ concentrations. The gut-brain axis is thus an underrecognized contributor to TMEV infection-induced seizures, ASM activity, and disease burden.},
}

@article {pmid40152616,
year = {2025},
author = {Yao, J and Zeng, Y and Hong, X and Wang, M and Zhang, Q and Chen, Y and Gou, M and Xia, Z-Y and Tang, Y-Q},
title = {Phages-bacteria interactions underlying the dynamics of polyhydroxyalkanoate-producing mixed microbial cultures via meta-omics study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0020025},
doi = {10.1128/msystems.00200-25},
pmid = {40152616},
issn = {2379-5077},
abstract = {The dynamics of the structure of polyhydroxyalkanoate-producing mixed microbial cultures (PHA-MMCs) during enrichment and maintenance is an unsolved problem. The effect of phages has been proposed as a cause of dynamic changes in community structure, but evidence is lacking. To address this question, five PHA-MMCs were enriched, and biological samples were sampled temporally to study the interactions between phage and bacterial members by combining metagenomics and metatranscriptomics. A total of 963 metagenome-assembled genomes (MAGs) and 4,294 phage operational taxonomic units (pOTUs) were assembled from bulk metagenomic data. The dynamic changes in the structure of phage and bacterial communities were remarkably consistent. Structural equation modeling analysis showed that phages could infect and lyse dominant species to vacate ecological niches for other species, resulting in a community succession state in which dominant species alternated. Seven key auxiliary metabolic genes (AMGs), phaC, fadJ, acs, ackA, phbB, acdAB, and fadD, potentially contributing to PHA synthesis were identified from phage sequences. Importantly, these AMGs were transcribed, indicating that they were in an active expression state. The meta-analysis provides the first catalog of phages in PHA-MMCs and the AMGs they carry, as well as how they affect the dynamic changes in bacterial communities. This study provides a reference for subsequent studies on understanding and regulating the microbial community structure of open microbial systems.IMPORTANCEThe synthesis of biodegradable plastic PHA from organic waste through mixed microbial cultures (PHA-MMCs), at extremely low cost, has the potential for expanded production. However, the dynamics of dominant species in PHA-MMCs are poorly understood. Our results demonstrate for the first time the impact of phages on the structure of bacterial communities in the PHA-MMCs. There are complex interactions between the PHA producers (e.g., Azomonas, Paracoccus, and Thauera) and phages (e.g., Casadabanvirus and unclassified Hendrixvirinae). Phage communities can regulate the activity and structure of bacterial communities. In addition, the AMGs related to PHA synthesis may hitchhike during phage-host infection cycles, enabling their dissemination across bacterial communities, and phages may act as a critical genetic reservoir for bacterial members, facilitating access to PHA synthesis-related functional traits. This study highlights the impact of phages on bacterial community structure, suggesting that phages have the potential to be used as a tool for better controlling the microbial community structure of PHA-MMCs.},
}

@article {pmid40152185,
year = {2025},
author = {Allos, H and Hasbun, R},
title = {Aseptic meningitis: a foundation review.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000001105},
pmid = {40152185},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: This review addresses the multifaceted nature of aseptic meningitis, a condition with diverse infectious and noninfectious etiologies. Despite its common presentation in clinical settings, over half of the cases remain without an identified cause, necessitating a comprehensive examination of diagnostic and management strategies. The increasing availability of advanced molecular diagnostics and the challenge of distinguishing bacterial from nonbacterial cases make this an opportune time to explore its implications for clinical practice.

RECENT FINDINGS: The literature highlights the pivotal role of advanced molecular diagnostics, such as multiplex PCR and metagenomic sequencing, in improving the identification of pathogens in aseptic meningitis. Enteroviruses remain the leading cause, but pathogens like Herpesviridae, arboviruses, and nonviral agents such as fungi and spirochetes also contribute significantly. New diagnostic algorithms and clinical models are emerging to distinguish bacterial from viral meningitis, reducing unnecessary treatments.

SUMMARY: Aseptic meningitis management is evolving with advancements in diagnostic technologies that allow for earlier pathogen identification, improving patient outcomes and minimizing healthcare costs. These findings underscore the importance of timely and accurate diagnostics and tailored therapeutic strategies in both clinical and research settings. Enhanced awareness of noninfectious causes is also crucial for comprehensive care.},
}

@article {pmid40152095,
year = {2025},
author = {Wu, S and Luo, Y and Wei, F and Li, Y and Fan, J and Chen, Y and Zhang, W and Li, X and Xu, Y and Chen, Z and Xia, C and Hu, M and Li, P and Gu, Q},
title = {Lactic acid bacteria target NF-κB signaling to alleviate gastric inflammation.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo06308b},
pmid = {40152095},
issn = {2042-650X},
abstract = {Helicobacter pylori (H. pylori) infection and the resulting gastric inflammation are major contributors to gastric cancer development. Probiotics, particularly Lactobacillus, are promising for their anti-inflammatory potential, yet their exact mechanisms in inhibiting H. pylori-induced inflammation are unclear. In our previous study, Lactiplantibacillus plantarum ZJ316 (L. plantarum ZJ316) demonstrated strong anti-inflammatory effects against H. pylori infection in vivo, but its precise mechanisms were not fully understood. Here, we aimed to investigate how L. plantarum ZJ316 inhibits the inflammatory response to H. pylori infection. Our results demonstrated that L. plantarum ZJ316 effectively reduced the expression of pro-inflammatory cytokines in H. pylori-infected AGS cells. Mechanistically, L. plantarum ZJ316 inhibited the NF-κB signaling pathway by preventing the degradation of IκBα, suppressing p65 phosphorylation, and blocking the nuclear translocation of phosphorylated p65. Treatment with the NF-κB inhibitor BAY 11-7082 further decreased tumor necrosis factor-α (TNF-α), interleukin-8 (IL-8), and interleukin-1β (IL-1β) levels, confirming the inhibitory effect of L. plantarum ZJ316 on the NF-κB pathway. In H. pylori-infected mice, oral administration of L. plantarum ZJ316 significantly alleviated inflammatory cell infiltration, reduced TNF-α and pepsinogen II (PGII) levels, and increased interleukin-10 (IL-10) levels in serum. A comparative metagenomic analysis of the gastric microbiota revealed a decrease in Prevotella and Desulfovibrio, alongside an increase in Ligilactobacillus and Akkermansia, supporting the protective effects of L. plantarum ZJ316 and correlating with their decreased inflammatory response. In summary, administration of L. plantarum ZJ316 demonstrated robust anti-inflammatory effects against H. pylori infection by suppressing NF-κB signaling and promoting favorable changes in the gastric microbiota composition. Therefore, L. plantarum ZJ316 holds promise as a novel functional food for protecting the body against H. pylori infection.},
}

@article {pmid40151642,
year = {2025},
author = {Cai, X and Cho, JY and Chen, L and Liu, Y and Ji, F and Salgado, K and Ge, S and Yang, D and Yu, H and Shao, J and Futreal, PA and Sepesi, B and Gibbons, D and Chen, Y and Wang, G and Cheng, C and Wu, M and Zhang, J and Hsiao, A and Xia, T},
title = {Enriched pathways in gut microbiome predict response to immune checkpoint inhibitor treatment across demographic regions and various cancer types.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112162},
pmid = {40151642},
issn = {2589-0042},
abstract = {Understanding the effect of gut microbiota function on immune checkpoint inhibitor (ICI) responses is urgently needed. Here, we integrated 821 fecal metagenomes from 12 datasets to identify differentially abundant genes and construct random forest models to predict ICI response. Gene markers demonstrated excellent predictive performance, with an average area under the curve (AUC) of 0.810. Pathway analyses revealed that quorum sensing (QS), ABC transporters, flagellar assembly, and amino acid biosynthesis pathways were enriched between responders (R) and non-responders (NRs) across 12 datasets. Furthermore, luxS, manA, fliC, and trpB exhibited consistent changes between R and NR across 12 datasets. Follow-up microbiota transplant experiments showed that inter-species signaling by different QS autoinducer-2 (AI-2) molecules (synthesized by luxS) can act on overall community function to promote the colonization of Akkermansia muciniphila, which is associated with superior ICI responses. Together, our data highlight the role of gut microbiota function in modulating the microbiome and antitumor immunity.},
}