@article {pmid40902732,
year = {2025},
author = {Blecksmith, SE and Oliver, A and Alkan, Z and Lemay, DG},
title = {Gut microbiome genes involved in plant and mucin breakdown correlate with diet and gastrointestinal inflammation in healthy US adults.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.08.027},
pmid = {40902732},
issn = {1541-6100},
abstract = {BACKGROUND: Dietary carbohydrates shape the composition and function of gut microbes which may potentially influence human health. It is not known if these diet-microbiome relationships are relevant to healthy American adults.

OBJECTIVE: We hypothesized that intake of dietary fiber by healthy adults would be associated with the carbohydrate active enzyme (CAZyme) capacity of their gut microbiome and that this capacity would be negatively correlated with gastrointestinal (GI) inflammation.

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

RESULTS: CAZyme diversity varied across participants. Plant CAZyme diversity and abundance correlated significantly with fecal pH (Shannon: adjusted R[2] = 0.053, p < 0.001; Chao1: adjusted R[2] = 0.056, p < 0.001; abundance: adjusted R[2] = 0.036, p < 0.001) and habitual energy-adjusted total fiber (Shannon: adjusted R[2] = 0.015, p = 0.029; abundance: adjusted R[2] = 0.015, p = 0.010) and soluble fiber intake (Shannon: adjusted R[2] = 0.017, p = 0.019; abundance: adjusted R[2] = 0.015, p = 0.0010). The ratio of mucin-degrading CAZymes to plant-degrading enzymes, coined here as the metric Muc2Plant, varied across participants and differed by sex (Wilcoxon, p = 0.035) and BMI (adjusted R[2] = 0.028, p = 0.017). Muc2Plant positively correlated with GI inflammation (calprotectin: adjusted R[2] = 0.038, p = 0.001; neopterin: adjusted R[2] = 0.071, p < 0.001). ML classification models were used to identify specific foods (e.g. potatoes) and microbes (e.g. Lachnospiraceae) as predictors of low Muc2Plant.

CONCLUSION: These results support the relevance of diet-microbiome relationships even in healthy adults, and that reduction of Muc2Plant, via dietary and/or microbial interventions, would be a beneficial health target to potentially prevent dysbiosis and reduce GI inflammation.

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

@article {pmid40902606,
year = {2025},
author = {Zhang, D and Zou, Y and Shi, Y and Zhang, J and Liu, J and Wu, G and Zhang, J and Gao, Y and Chen, M and Li, YX},
title = {Systematically investigating and identifying bacteriocins in the human gut microbiome.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100983},
doi = {10.1016/j.xgen.2025.100983},
pmid = {40902606},
issn = {2666-979X},
abstract = {Human gut microbiota produces unmodified bacteriocins, natural antimicrobial peptides that protect against pathogens and regulate host physiology. However, current bioinformatic tools limit the comprehensive investigation of bacteriocins' biosynthesis, obstructing research into their biological functions. Here, we introduce IIBacFinder, a superior analysis pipeline for identifying unmodified class II bacteriocins. Through large-scale bioinformatic analysis and experimental validation, we demonstrate their widespread distribution across the bacterial kingdom, with most being habitat specific. Analyzing over 280,000 bacterial genomes, we reveal the diverse potential of human gut bacteria to produce these bacteriocins. Guided by meta-omics analysis, we synthesized 26 hypothetical bacteriocins from gut commensal species, with 16 showing antibacterial activities. Further ex vivo tests show minimal impact of narrow-spectrum bacteriocins on human fecal microbiota. Our study highlights the huge biosynthetic potential of unmodified bacteriocins in the human gut, paving the way for understanding their biological functions and health implications.},
}

@article {pmid40902595,
year = {2025},
author = {Guinet, B and Oskolkov, N and Moreland, K and Dehasque, M and Chacón-Duque, JC and Angerbjörn, A and Arsuaga, JL and Danilov, G and Kanellidou, F and Kitchener, AC and Muller, H and Plotnikov, V and Protopopov, A and Tikhonov, A and Termes, L and Zazula, G and Mortensen, P and Grigorieva, L and Richards, M and Shapiro, B and Lister, AM and Vartanyan, S and Díez-Del-Molino, D and Götherström, A and Pečnerová, P and Nikolskiy, P and Dalén, L and van der Valk, T},
title = {Ancient host-associated microbes obtained from mammoth remains.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.08.003},
pmid = {40902595},
issn = {1097-4172},
abstract = {Ancient genomic studies have extensively explored human-microbial interactions, yet research on non-human animals remains limited. In this study, we analyzed ancient microbial DNA from 483 mammoth remains spanning over 1 million years, including 440 newly sequenced and unpublished samples from a 1.1-million-year-old steppe mammoth. Using metagenomic screening, contaminant filtering, damage pattern analysis, and phylogenetic inference, we identified 310 microbes associated with different mammoth tissues. While most microbes were environmental or post-mortem colonizers, we recovered genomic evidence of six host-associated microbial clades spanning Actinobacillus, Pasteurella, Streptococcus, and Erysipelothrix. Some of these clades contained putative virulence factors, including a Pasteurella-related bacterium that had previously been linked to the deaths of African elephants. Notably, we reconstructed partial genomes of Erysipelothrix from the oldest mammoth sample, representing the oldest authenticated host-associated microbial DNA to date. This work demonstrates the potential of obtaining ancient animal microbiomes, which can inform further paleoecological and evolutionary research.},
}

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

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

@article {pmid40902348,
year = {2025},
author = {Zhou, N and Gu, T and Duan, M and Tian, Y and Chen, L and Zeng, T and Hou, X and Wang, X and Xu, Q and Zhang, Y and Lu, L},
title = {Gut microbiota dysbiosis exacerbates polystyrene microplastics-induced liver inflammation via activating LPS/TLR4 signaling pathway in ducks.},
journal = {Poultry science},
volume = {104},
number = {11},
pages = {105757},
doi = {10.1016/j.psj.2025.105757},
pmid = {40902348},
issn = {1525-3171},
abstract = {Ubiquitous microplastics can bioaccumulate in organisms, resulting in detrimental health impacts, such as liver inflammation. Nonetheless, the exact mechanism by which polystyrene microplastics (PS-MPs) trigger liver inflammation via the gut-liver axis in ducks remains unclear. The purpose of this study was to clarify the impact of PS-MPs exposure to liver inflammation through the gut-liver axis in ducks. Our investigation indicated that exposure to PS-MPs markedly upregulated the levels of MDA and ROS in the liver tissue and enhanced the release of pro-inflammatory cytokines (TNF-α, IL-6, and IL-1β). Additionally, PS-MPs exposure increased the LPS level, which ultimately triggered the TLR4/NF-κB signaling pathway. Notably, exposure to PS-MPs resulted in a marked change in the gut microbiota composition, primarily indicated by an increase in the relative abundance of Brachyspiraceae and a reduction in that of CAG-74 and Oscillospiraceae. Metabolome analysis further revealed that different expressed metabolites (DEMs) in the positive and negative mode were identified between the control and HMPs groups, including 1-methylhistamine, DL-Methionine sulfoxide, Guanidinoethyl sulfonate, l-Cysteic acid, Deoxyinosine, Camp. Both metagenomic and metabolome analyses showed enrichment in the lysosomal pathway. Correlation analysis suggested association among representative gut microbiota, serum LPS, oxidative stress factors, liver DEMs and key liver inflammatory indicators. Our study sheds light on the mechanism by which PS-MPs exposure induced liver inflammation in ducks via the modulation of the gut-liver axis. These findings improved our understanding of the underlying mechanisms that contribute to PS-MPs-induced hepatotoxicity in avian species.},
}

@article {pmid40901999,
year = {2025},
author = {Prabakaran, R and Bromberg, Y},
title = {Deciphering enzymatic potential in metagenomic reads through DNA language models.},
journal = {Nucleic acids research},
volume = {53},
number = {16},
pages = {},
doi = {10.1093/nar/gkaf836},
pmid = {40901999},
issn = {1362-4962},
support = {80NSSC18M0093//NASA Astrobiology Institute/ ; 2310114//National Science Foundation/ ; },
mesh = {*Metagenomics/methods ; Metagenome ; Molecular Sequence Annotation ; *Enzymes/genetics/metabolism ; Microbiota/genetics ; Software ; Sequence Analysis, DNA/methods ; },
abstract = {Microbial communities drive essential global processes, yet much of their functional potential remains unexplored. Metagenomics stands to elucidate this microbial "dark matter" by directly sequencing the microbial community DNA from environmental samples. However, the exploration of metagenomic sequences is mostly limited to establishing their similarity to curated reference sequences. A paradigm shift-language model (LM)-based methods-offers promising avenues for reference-free analysis of metagenomic reads. Here, we introduce two LMs, a pretrained foundation model REMME (Read EMbedder for Metagenomic Exploration), aimed at understanding the DNA context of metagenomic reads, and the fine-tuned REBEAN (Read Embedding-Based Enzyme ANnotator) for predicting the enzymatic potential encoded within the read-corresponding genes. By emphasizing function recognition over gene identification, REBEAN labels gene-encoded molecular functions of previously explored and new (orphan) sequences. Even though it was not trained to do so, REBEAN identifies the gene's function-relevant parts. It thus expands enzymatic annotation of unassembled metagenomic reads. Here, we present novel enzymes discovered using our models, highlighting model impact on our understanding of microbial communities.},
}

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

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

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

@article {pmid40901884,
year = {2025},
author = {Robes, JMD and Liebergesell, TCE and Beals, DG and Yu, X and Brazelton, WJ and Puri, AW},
title = {Inverse stable isotope probing-metabolomics (InverSIP) identifies an iron acquisition system in a methane-oxidizing bacterial community.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {36},
pages = {e2507323122},
doi = {10.1073/pnas.2507323122},
pmid = {40901884},
issn = {1091-6490},
support = {R35 GM147018/GM/NIGMS NIH HHS/United States ; 2339190//National Science Foundation (NSF)/ ; LS-ECIAMEE-00006628//Simons Foundation (SF)/ ; T32 AI055434/AI/NIAID NIH HHS/United States ; },
mesh = {*Methane/metabolism ; *Iron/metabolism ; *Metabolomics/methods ; Oxidation-Reduction ; Isotope Labeling/methods ; *Microbiota ; *Bacteria/metabolism/genetics ; Siderophores/metabolism ; Multigene Family ; },
abstract = {Methane is a potent greenhouse gas and a target for near-term climate change mitigation. In many natural ecosystems, methane is sequestered by microbial communities, yet little is known about how constituents of methane-oxidizing communities interact with each other and their environment. This lack of mechanistic understanding is a common issue for many important microbial communities, but it is difficult to draw links between available sequencing information and the metabolites that govern community interactions. Here, we develop and apply a technique called inverse stable isotope probing-metabolomics (InverSIP) to bridge the gap between metagenomic and metabolomic information and functionally characterize interactions in a complex methane-oxidizing community. Using InverSIP, we link a highly transcribed biosynthetic gene cluster in the community with its secondary metabolite product: methylocystabactin, a triscatecholate siderophore not previously observed in nature. We find that production of methylocystabactin is widespread among methanotrophic alphaproteobacteria and that it can be used by another methanotroph in the community that does not produce this siderophore itself. Functional assays reveal that methylocystabactin supports methanotroph growth and the activity of the methane-oxidizing enzyme soluble methane monooxygenase under conditions where bioavailable iron is limited, establishing an important molecular link between methane-oxidation and the insoluble iron found in many natural environments. These findings contribute to a molecular-level understanding of these environmentally important bacterial communities and establish InverSIP as a broadly applicable genomics-guided strategy for characterizing metabolites in microbial ecosystems.},
}

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

@article {pmid40901853,
year = {2025},
author = {Gómez-Palacio, A and Junca, H and Vivero-Gomez, RJ and Suaza, J and Moreno-Herrera, CX and Cadavid-Restrepo, G and Pieper, DH and Uribe, S},
title = {Metagenomic profiling of the insect-specific virome in non-urban mosquitoes (Culicidae: Culicinae) from Colombia's Northern inter-Andean valleys.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331552},
doi = {10.1371/journal.pone.0331552},
pmid = {40901853},
issn = {1932-6203},
mesh = {Animals ; Colombia ; *Virome/genetics ; *Culicidae/virology ; *Metagenomics/methods ; *Metagenome ; Phylogeny ; *Insect Viruses/genetics/classification ; },
abstract = {Hematophagous mosquitoes are major vectors of diverse pathogens and serve as bioindicators in tropical ecosystems, yet their virome in non-urban Neotropical regions remains poorly characterized. We analyzed the virome of 147 mosquitoes from two natural ecosystems in Colombia using a hybrid viral identification approach, combining high-confidence and less stringent methods. Most high-confidence viral contigs remained unclassified or unknown, as expected for metagenomic surveys in novel ecosystems. However, members for the Magrovirales and Ortervirales, and other six orders were detected at lower abundance. Using a complementary, less stringent approach, we identified 168 viral species from 68 genera and 22 families across four mosquito tribes (Aedini, Culicini, Orthopodomyiini, Sabethini), with dominance of Metaviridae, Retroviridae, Iridoviridae, and Poxviridae, though many sequences could not be taxonomically assigned. Insect-specific viruses predominated, while no medically relevant arboviruses were detected. Both methods consistently identified Trichoplusia ni TED virus, Cladosporium fulvum T-1 virus, Lymphocystis disease viruses, and Oryctes rhinoceros nudivirus among the most abundant and frequently detected taxa across samples. Alpha diversity indices revealed the highest virome diversity in Sabethini, followed by Orthopodmyiini, and substantially lower richness and diversity in Aedini and Culicini. These results provide a baseline for virome characterization in sylvatic mosquitoes from Colombia and highlight the need for further research on the ecological roles of the mosquito virome in pathogen transmission and microbiome evolution.},
}

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

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

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

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

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

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

@article {pmid40901000,
year = {2025},
author = {Huang, F and Li, J and Liu, D and Li, Y and Tang, J},
title = {Neonatal microbiome dysbiosis decoded by mNGS: from mechanistic insights to precision interventions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1642072},
doi = {10.3389/fcimb.2025.1642072},
pmid = {40901000},
issn = {2235-2988},
mesh = {Humans ; Infant, Newborn ; *Dysbiosis/microbiology/diagnosis/therapy ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Infant, Newborn, Diseases/microbiology/diagnosis/therapy ; Precision Medicine/methods ; *Microbiota/genetics ; },
abstract = {The neonatal period is a critical stage for microbial colonization and immune system development, with dynamic changes in the microbiome closely linked to the pathogenesis of various diseases. Traditional microbiological testing methods have low sensitivity and time-consuming limitations compared to metagenomic next-generation sequencing (mNGS), which makes it difficult to meet the diagnostic and therapeutic needs of critically ill neonates. mNGS analyzes the total DNA in a sample without bias, allowing comprehensive identification of bacteria, viruses, fungi, and parasites, and resolution of functional genes, providing new avenues for precision diagnosis and treatment of diseases such as neonatal sepsis, necrotizing enterocolitis, neonatal pneumonia, neonatal meningitis, neonatal jaundice, and other diseases. However, challenges remain, including the need to optimize sample processing workflows and develop portable devices to enhance clinical conversion potential. In this review, we summarize the application, efficacy, and limitations of mNGS in neonatal diseases. This approach paves the way for novel avenues in mechanistic research, early diagnosis, and personalized therapy for these conditions.},
}

Humans
Infant, Newborn
*Dysbiosis/microbiology/diagnosis/therapy
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Infant, Newborn, Diseases/microbiology/diagnosis/therapy
Precision Medicine/methods
*Microbiota/genetics

@article {pmid40900671,
year = {2025},
author = {Day, AS and Slater, R and Young, RB and Wheeler, RZ and Marcelino, VR and Maddigan, NK and Forster, SC and Costello, SP and Uylaki, W and Probert, CSJ and Andrews, JM and Yao, CK and Gibson, PR and Bryant, RV},
title = {Functional Profiling Demonstrates That a Sulfide-Reducing Diet Achieves Microenvironmental Targets in Ulcerative Colitis.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf177},
pmid = {40900671},
issn = {1536-4844},
support = {//Hospital Research Foundation/ ; //University of Adelaide/ ; },
abstract = {BACKGROUND: As a dietary approach to reducing inflammation in ulcerative colitis, the 4-SURE (4 Strategies to Sulfide Reduction) diet was designed to correct pathogenic alterations of excessive protein fermentation and hydrogen sulfide (H2S) production in the distal colon. We aimed to perform a deep functional analysis (microbial and metabolomic) of the feces of 28 adults with mild-moderately active ulcerative colitis who adhered to the 4-SURE diet over 8 weeks to explore whether the 4-SURE diet could modulate the intraluminal environment as intended.

METHODS: Fecal samples were collected at week 0 and 8 of dietary intervention, processed and aliquoted. Metagenomic sequencing was undertaken to identify changes in H2S-metabolizing genes, while gas chromatography-mass spectrometry was used to analyze fecal volatile organic compounds and H2S production.

RESULTS: The 4-SURE diet significantly increased alpha diversity between weeks 0 and 8. By random forest plot classifier, the abundance of taxonomic groups comprising known H2S-producing genera were markedly lower at week 8, specifically Odoribacter and Peptostreptococcaceae, and were of highest importance in discriminating between before- and after-diet samples. The capacity for bacterial H2S metabolism was altered with diet, with differences in 12 of 67 analyzed sulfur-metabolizing genes identified. H2S production and indole, a specific marker of protein fermentation, were significantly decreased due to the diet.

CONCLUSIONS: Here, we demonstrate that the objectives of the 4-SURE diet were fulfilled. This application of deep functional analysis to a dietary intervention study is novel and highlights an exemplar framework for including microbial and metabolomic biomarkers of pathogenic relevance in the analysis of therapeutic diet strategies. (Australian New Zealand Clinical Trials Registry, Number: ACTRN12619000063112).},
}

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

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

@article {pmid40899487,
year = {2025},
author = {Gu, T and Zerry, Y and Zhang, B and Tan, J and Taft, DH},
title = {Influence of Resistant Starch-Added Meat Analogs on the Resistome of Fecal Fermentations Using Human Gut Microbiota.},
journal = {Journal of food science},
volume = {90},
number = {9},
pages = {e70430},
doi = {10.1111/1750-3841.70430},
pmid = {40899487},
issn = {1750-3841},
support = {//University of Florida/ ; //U.S. Department of Agriculture/ ; },
mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Fermentation ; *Starch/metabolism ; Bacteria/genetics/classification/isolation & purification/drug effects/metabolism ; *Meat/analysis ; Adult ; Male ; Female ; *Resistant Starch ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Drug Resistance, Microbial ; Meat Substitutes ; },
abstract = {Meat analogs are emerging as a sustainable alternative to meat products, and novel meat analog products could potentially offer additional health benefits. Antimicrobial resistance (AMR) poses a serious threat to global human health. Dietary choices affect the composition of bacteria in the human gut microbiome and can influence the carriage of antimicrobial resistance genes (ARGs). Individuals with lower ARG carriage tend to consume more fiber, suggesting that novel fiber-rich meat analogs may help tackle the growing AMR crisis. We therefore hypothesized that adding resistant starch to meat analogs would reduce the number and abundance of ARGs in human gut microbial communities and tested this using in vitro fecal fermentation. Fecal samples were collected from three human donors. Meat analogs formulated from raw ingredients (pea, soy, and resistant starch)-including 100% pea, 90% pea and 10% resistant starch, 100% soy, and 90% soy and 10% resistant starch-served as the carbohydrate source for fecal fermentations. Whole metagenomic sequencing was performed on DNA from the fermentations. ANOVA showed significant differences in normalized ARG abundance by carbohydrate source (p = 0.021), though not in total ARG counts. Meat analogs with resistant starch resulted in a lower median normalized abundance of drug-resistant ARGs than meat analogs without resistant starch, but post-hoc testing could not determine which groups differed from each other due to limited sample size. Adding resistant starch to meat analogs is associated with reduced ARGs in human gut microbial communities, but more research is needed. PRACTICAL APPLICATIONS: Lowering the prevalence of antimicrobial resistance genes (ARGs) is an important public health goal, and emerging work suggests that diet may contribute to controlling the spread of ARGs. One association with diet and the resistome is a lower carriage of ARGs in individuals who consume more dietary fiber. This research therefore sought to pilot if adding resistant starch to meat analogs has the potential to reduce resistance gene carriage. The results found that adding resistant starch to plant-based meat products may help lower the abundance of antimicrobial resistance genes in the human gut microbiome. This provides the justification for larger scale studies and suggests that food manufacturers may be able to develop foods, including healthier meat alternatives, to assist in preserving the function of antibiotics for future generations.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid40897178,
year = {2025},
author = {Xu, T and Jiao, X and Liu, G and Chen, X and Luo, Q and Zhang, G and Li, B and Zhang, Y and Li, X and Cheung, Y and Chai, X and Huang, Y and Wu, H and Deng, F and Chen, F and Liang, G},
title = {Oral virome metagenomic catalog links Porphyromonas gingivalis phages to obesity and type 2 diabetes.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102325},
doi = {10.1016/j.xcrm.2025.102325},
pmid = {40897178},
issn = {2666-3791},
abstract = {The human microbiota has a critical role in maintaining human microbiome homeostasis and health, yet the viral component of the oral microbiome remains largely unidentified. We establish the Human Oral Virome Database (HOVD) catalog, a freely accessible online resource cataloging 24,440 bacteriophage viral operational taxonomic units and 83 eukaryotic viral genomes. Utilizing HOVD, we investigate oral virome variation and its correlation with oral bacteria and gut virome in 220 obese individuals with or without type 2 diabetes mellitus (T2D). Obese individuals with T2D exhibit reduced oral viral diversity, lower correlations with clinical features, disrupted viral-bacterial correlations, and enhanced oral-gut virome transmission. Furthermore, we computationally identify bacteriophages that infect Porphyromonas gingivalis and screen six putative endolysins. Experimental validation reveals that a mixture of three endolysins significantly inhibits Porphyromonas gingivalis growth. These findings highlight the potential of phage-derived endolysins for periodontitis with T2D, offering a path toward oral and systemic disease intervention.},
}

@article {pmid40897099,
year = {2025},
author = {Ma, X and Zhai, T and Bao, X and Wu, Z and Yang, Y and Yin, R and Cai, C and Liu, G},
title = {Salinity-driven trade-offs between nitrogen removal and microbiome dynamics in Fe-C-CWs toward saline aquaculture tailwater management.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124519},
doi = {10.1016/j.watres.2025.124519},
pmid = {40897099},
issn = {1879-2448},
abstract = {Salinity-driven nitrogen removal mechanisms in iron-carbon CWs (Fe-C-CWs) remain poorly understood for aquaculture tailwater management. Through a 155-day trial under four salinities (designated as S0, S10, S20, and S30), result showed that S20 achieved optimal removals of total nitrogen (84.9 ± 3.1 %), nitrate (81.8 ± 2.5 %), and ammonium (79.3 ± 3.0 %), significantly outperforming other groups (P < 0.05). Metagenomics revealed that S20 significantly enriched denitrifying taxa (Halothiobacillus, Prolixibacter) and upregulated nitrogen cycling genes (nirB, nrfA, nrfH, hao) and iron cycling genes (feoA, feoB), highlighting the functional synergy between microbial composition and biogeochemical cycling processes. Dual isotope signatures (δ[15]NNO2/ δ[18]ONO2) first applied in Fe-C-CWs confirmed salinity-mediated pathway shifts: nitrite oxidation dominated in saline groups, especially in S20 versus reduction in S0. Enzymatic profiling substantiated the concurrent operation of nitrification, denitrification, and anammox pathways across all groups, with activities exhibiting significant salinity-dependent modulation. S20 demonstrated remarkable enzymatic potentiation, where core nitrogen-cycling enzymes including nitrite oxidoreductase (NXR: 8.79 ± 0.67 U/g), nitrate reductase (NAR: 18.13 ± 1.19 U/g), and nitrite reductase (NIR: 6.74 ± 0.47 U/g) showed 16.00∼32.18 % higher than S0 (P < 0.01). This enzymatic synergy suggests salinity-optimized coupling between dissimilatory iron reduction and nitrogen transformation processes. Ecological network analysis revealed significant interactions among microbial phyla, particularly between Proteobacteria and Planctomycetota. This study demonstrates that S20 can enhance interaction between Fe-C matrix and microorganisms, thereby improving the efficiency of Fe-C-CWs in removing nitrogen pollutants from aquaculture tailwater. These findings offer theoretical insights for further understanding the internal operational mechanisms of the Fe-C-CWs.},
}

@article {pmid40897066,
year = {2025},
author = {Slobodkina, GB and Merkel, AY and Kondrasheva, KV and Stroeva, AR and Bonch-Osmolovskaya, EA and Davranov, KD and Slobodkin, AI},
title = {Taxonomic and metabolic diversity of microbial communities in a thermal water stream in Uzbekistan and proposal of two new classes of uncultivated bacteria, Desulfocorpusculia class. nov. and Tepidihabitantia class. nov., named following the rules of SeqCode.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {5},
pages = {126650},
doi = {10.1016/j.syapm.2025.126650},
pmid = {40897066},
issn = {1618-0984},
abstract = {Thermal ecosystems in Uzbekistan remain poorly characterized, particularly through culture-independent approaches. In this study, we performed 16S rRNA gene metabarcoding and metagenomic sequencing of microbial communities from a hot stream formed by the discharge of thermal artesian groundwater in the Navoiy region. The taxonomic composition of microbial communities varied with temperature and sample type, with the phylum Chloroflexota abundant in most samples. Members of Aquificota, Deinococcota, and Thermotogota dominated in sediments with temperatures around 60 °C, while Desulfobacterota and Cyanobacteriota were more abundant at lower temperatures. Metagenomic sequencing of the microbial community in sediment under orange-brown mat (54 °C) revealed a dominance of the phyla Chloroflexota, Armatimonadota, Aquificota, Ignavibacteriota, Desulfobacterota and Bacteroidota. Metagenomic data indicated that fermentation, aerobic degradation of organic matter, hydrogen oxidation, and sulfur cycling are the main metabolic processes. Two high-quality metagenome-assembled genomes (MAGs) were described as novel taxa named following the rules of SeqCode. Genome analysis suggests that both organisms are heterotrophic anaerobes capable of sulfate reduction or fermentation. We provide the description of Desulfocorpusculum asiaticum[Ts] gen. nov., sp. nov. affiliated with the novel family Desulfocorpusculaceae fam. nov., order Desulfocorpusculales ord. nov. and class Desulfocorpusculia class. nov.; and the description of the new species and genus Tepidihabitans asiaticus[Ts] gen. nov., sp. nov. affiliated with the novel family Tepidihabitantaceae fam. nov., order Tepidihabitantales ord. nov. and class Tepidihabitantia class. nov.},
}

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

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

@article {pmid40896895,
year = {2025},
author = {Jiang, Z and Yang, S and Pang, Q and Abdalla, M and Karbin, S and Qi, S and Hu, J and Qiu, H and Song, X and Smith, P},
title = {Metagenomic insights into the influence of soil microbiome on greenhouse gas emissions from paddy fields under varying irrigation and fertilisation regimes.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127129},
doi = {10.1016/j.jenvman.2025.127129},
pmid = {40896895},
issn = {1095-8630},
abstract = {Integration of diverse fertilisation strategies with water-saving irrigation techniques presents a promising sustainable agricultural practice, offering the potential to reduce greenhouse gases (GHGs) emissions, enhance carbon sequestration and boost crop yields. However, existing research on the influence of soil microorganisms on biogeochemical processes of GHGs is limited. Herein, we explored the microbial mechanisms influencing GHGs emissions through a 3-year field experiment and metagenomic sequencing conducted in southeastern China. We investigated two irrigation patterns (controlled irrigation [CI] and flooded irrigation [FI]) and three fertilisation strategies (chemical fertiliser [F], straw returning [S] and manure substitution [M]). Results indicated that irrigation patterns significantly affected the microbial community structure in paddy soil. The key environmental factors affecting microorganisms at the phylum level included soil pH, moisture content, total nitrogen content and CH4 emissions. Random forest analysis further identified Cyanobacteria, Nitrospirae, Kiritimatiellaeota, Proteobacteria, and Balneolaeota as dominant phyla driving the differences in microbial communities across treatments. Under CI, an increase in N2O emissions was observed, which was driven by key genes, such as nirS, nirK, nosZ and norB. Compared with CF (CI with F), S increased the abundance of nirS and nirK, leading to higher N2O emissions, whereas M increased the abundance of nosZ, thereby reducing N2O emissions. The genes mcrA, pmoA and pmoC were responsible for elevated CH4 emissions through straw incorporation and manure application. Structural equation model analysis revealed that the irrigation pattern significantly affected CH4 emissions and rice yield, while the fertilisation type mainly influenced soil pH and rice yield. Organic input, particularly manure, resulted in higher C emissions owing to the presence of more CH4-producing gene mcrA in the soil. Overall, the combination of CI and manure is recommended for reducing GHGs emissions, enhancing C sequestration and boosting rice yields.},
}

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

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

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

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

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

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

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

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

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

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

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

@article {pmid40895054,
year = {2025},
author = {Cárdenas-Hernández, V and Lemos-Lucumi, C and Toro-Perea, N},
title = {Uncovering tissue-specific endophytic microbiota composition and activity in Rhizophora mangle L.: a metagenomic and metatranscriptomic approach.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19728},
doi = {10.7717/peerj.19728},
pmid = {40895054},
issn = {2167-8359},
abstract = {The interaction of mangrove trees with endophytic microorganisms contributes to the successful establishment of these plants in the challenging intertidal environment. The red mangrove, Rhizophora mangle L. (Rhizophoraceae), is one of the dominant species in mangrove ecosystems and is characterized by the provision of several ecologically relevant services. In this work, we integrated metagenomics and metatranscriptomics to perform a robust characterization of the community of endophytic microorganisms associated with R. mangle leaf and root tissues. The microbiota were characterized at taxonomic and functional levels, and abundance and gene expression profiles were compared between these two plant tissues. We found that the endophyte community consisted mainly of bacteria and eukaryotes, which were the most active groups at the transcriptional level, while archaea and viral groups were identified in lower abundance and expression. In addition, the results show that the community of endophytic microorganisms changes depending on the tissue type, with root-associated microorganisms being the most abundant at the metagenome level and active at the metatranscriptome level. It was also found that R. mangle endophytes actively contribute to key functions for adaptation to an intertidal ecosystem with high human intervention, such as salinity tolerance and degradation of heavy metals and xenobiotic compounds. Thus, according to the functions found and contributed by the endophyte community of red mangrove leaf and root tissues, it can be concluded that these microbial communities are crucial for the survival of R. mangle in the extreme environment of mangrove forests. This study provides a solid basis for future research aimed at understanding the role of plant-endophyte interactions.},
}

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

@article {pmid40894694,
year = {2025},
author = {Regan, MD and Chiang, E and Grahn, M and Tonelli, M and Assadi-Porter, FM and Suen, G and Carey, HV},
title = {Host-microbiome mutualism drives urea carbon salvage and acetogenesis during hibernation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.02.13.638127},
pmid = {40894694},
issn = {2692-8205},
abstract = {UNLABELLED: Hibernation is a seasonal survival strategy employed by certain mammals that, through torpor use, reduces overall energy expenditure and permits long-term fasting. Although fasting solves the challenge of winter food scarcity, it also removes dietary carbon, a critical biomolecular building block. Here, we demonstrate a process of urea carbon salvage (UCS) in hibernating 13-lined ground squirrels, whereby urea carbon is reclaimed through gut microbial ureolysis and used in reductive acetogenesis to produce acetate, a short-chain fatty acid (SCFA) of major value to the host and its gut microbiota. We find that urea carbon incorporation into acetate is more efficient during hibernation than the summer active season, and that while both host and gut microbes oxidize acetate for energy supply throughout the year, the host's ability to absorb and oxidize acetate is highest during hibernation. Metagenomic analysis of the gut microbiome indicates that genes involved in the degradation of gut mucins, an abundant endogenous nutrient, are retained during hibernation. The hydrogen disposal associated with reductive acetogenesis from urea carbon helps facilitate this mucin degradation by providing a luminal environment that sustains fermentation, thereby generating SCFAs and other metabolites usable by both the host and its gut microbes. Our findings introduce UCS as a mechanism that enables hibernating squirrels and their gut microbes to exploit two key endogenous nutrient sources - urea and mucins - in the resource-limited hibernation season.

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid40894065,
year = {2025},
author = {Chen, LX and Camargo, AP and Qin, Y and Wang, H and Zou, Y and Duan, Y and Li, H and Koonin, E},
title = {A prevalent huge phage clade in human and animal gut microbiomes.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7356405/v1},
pmid = {40894065},
issn = {2693-5015},
abstract = {Huge phages are widespread in the biosphere, yet their prevalence and ecology in the human gut remain poorly characterized. Here, we report Jug (Jumbo gut) phages with genomes of 360-402 kilobase pairs that comprise ~1.1% of the reads in human gut metagenomes, and are predicted to infect Bacteroides and/or Phocaeicola. Although three of the four major groups of Jug phages shared >90% genome-wide sequence identity, their large terminase subunits exhibited only 38-57% identity, suggesting horizontal acquisition from other phages. Over 1,500 genomes of Jug phages were recovered from human and animal gut metagenomes, revealing their broad distribution, with largely shared gene content suggestive of frequent cross-animal-host transmission. Jug phages displayed high gene transcription activities, including the gene for a calcium-translocating P-type ATPase not detected previously in phages. These findings broaden our understanding of huge phages and highlight Jug phages as potential major players in gut microbiome ecology.},
}

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

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

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

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

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

@article {pmid40892742,
year = {2025},
author = {Zhu, J and Chen, Y and Han, Y and Li, J},
title = {Mechanism of Huanglian Wendan Decoction in ameliorating non-alcoholic fatty liver disease via modulating gut microbiota-mediated metabolic reprogramming and activating the LKB1/AMPK pathway.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331303},
pmid = {40892742},
issn = {1932-6203},
mesh = {Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/microbiology/pathology ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry ; Rats ; Male ; *AMP-Activated Protein Kinases/metabolism ; Rats, Sprague-Dawley ; Signal Transduction/drug effects ; *Protein Serine-Threonine Kinases/metabolism ; Lipid Metabolism/drug effects ; Liver/metabolism/drug effects/pathology ; AMP-Activated Protein Kinase Kinases ; Disease Models, Animal ; Carnitine O-Palmitoyltransferase/metabolism ; Metabolic Reprogramming ; },
abstract = {BACKGROUND: Huanglian Wendan Decoction (HLWDD), a classical traditional Chinese medicine (TCM) formula, has shown therapeutic promise in treating metabolic disorders. However, its underlying mechanisms against non-alcoholic fatty liver disease (NAFLD) remain unclear.

OBJECTIVE: This study aimed to elucidate the pharmacological mechanisms by which HLWDD ameliorates NAFLD, focusing on its impact on lipid metabolism, gut microbiota, and amino acid regulation.

METHODS: A NAFLD rat model was established by administering a high-sugar, high-fat, high-salt diet for 20 weeks. The core components of HLWDD were identified and quantified using UPLC-Q-TOF-MS/MS and HPLC, and further validated via network pharmacology and molecular docking. Therapeutic efficacy was assessed through analysis of body weight, serum lipid profiles, inflammatory cytokines, hepatic histology, and protein expression. Gut microbiota composition and liver-intestine metabolite profiles were evaluated using metagenomic sequencing and LC-MS/MS.

RESULTS: Seven key constituents, including quercetin and berberine, were quantified (15.11-164.37 μg/mL) and shown to interact with lipid metabolism targets such as liver kinase B1 (LKB1), AMP-activated protein kinase (AMPK), peroxisome proliferator-activated receptor alpha (PPARα), and carnitine palmitoyltransferase 1A (CPT1A). HLWDD treatment significantly reduced body weight, hepatic lipid accumulation, and serum levels of triglycerides, total cholesterol, and low-density lipoprotein cholesterol, while increasing high-density lipoprotein cholesterol. Proinflammatory cytokines (IL-6, IL-1β, TNF-α) were notably suppressed. Mechanistically, HLWDD activated the LKB1/AMPK signaling pathway and modulated aspartic acid metabolism in association with increased abundance of Akkermansia in the gut. Metabolomic analysis identified 13 differential metabolites, with aspartic acid showing strong correlations with Akkermansia and LKB1/AMPK activity.

CONCLUSION: HLWDD exerts its anti-NAFLD effects by enhancing Akkermansia-mediated aspartate metabolism, thereby activating the LKB1/AMPK axis and promoting lipid oxidation via CPT1A and PPARα. This study provides new mechanistic insight into the gut-liver axis in NAFLD and highlights HLWDD as a multi-targeted therapeutic approach for restoring metabolic balance.},
}

Animals
*Non-alcoholic Fatty Liver Disease/drug therapy/metabolism/microbiology/pathology
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/pharmacology/therapeutic use/chemistry
Rats
Male
*AMP-Activated Protein Kinases/metabolism
Rats, Sprague-Dawley
Signal Transduction/drug effects
*Protein Serine-Threonine Kinases/metabolism
Lipid Metabolism/drug effects
Liver/metabolism/drug effects/pathology
AMP-Activated Protein Kinase Kinases
Disease Models, Animal
Carnitine O-Palmitoyltransferase/metabolism
Metabolic Reprogramming

@article {pmid40890888,
year = {2025},
author = {Wang, S and Zhao, Z and Cheng, R and Cui, L and Wang, J and Rubin-Blum, M and Zhang, Y and Liu, B and Chen, X and Baltar, F and Cao, X and Wen, X and Alain, K and Chen, Z and Liao, J and Jiang, L and Shao, Z},
title = {Phylogenetically and metabolically diverse active carbon-fixing microbes reside in mangrove sediments.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {194},
pmid = {40890888},
issn = {2049-2618},
support = {42306127//National Natural Science Foundation of China/ ; 42306127//National Natural Science Foundation of China/ ; 42176134//National Natural Science Foundation of China/ ; 42030412//National Natural Science Foundation of China/ ; 2024002//Scientific Research Foundation of Third Institute of Oceanography/ ; 2019021//Scientific Research Foundation of Third Institute of Oceanography/ ; },
mesh = {*Geologic Sediments/microbiology ; *Carbon Cycle ; Wetlands ; Phylogeny ; China ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Carbon/metabolism ; Metagenomics/methods ; Gammaproteobacteria/metabolism/genetics/classification/isolation & purification ; Microbiota ; },
abstract = {BACKGROUND: Mangroves are hotspots of carbon sequestration in transitional zones between marine and terrestrial ecosystems. Microbially driven dark carbon fixation (DCF) is prominent in sediments, yet our understanding of the DCF process across this continuum remains limited. In this study, we explored DCF activities and associated chemoautotrophs along the sediment depth of different mangrove sites in Fujian Province, China, using radiocarbon labeling and molecular techniques.

RESULTS: Our results showed that the DCF rates ranged from 0.02 to 3.27 mmol C m[-2] day[-1] in all samples, showing a depth-dependent spatial variation. These rates of DCF were closely related to the environmental factors such as DIC, TS, AVS, NH4[+], NO3[-], and NO2[-]. Metagenomic analysis revealed six carbon-fixing pathways, with the Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl (WL) pathway being predominant. Further analysis of MAGs revealed that Gammaproteobacteria, Desulfobacteria, and Campylobacteria were the most abundant carbon-fixing groups. Intriguingly, some new lineages were found to have carbon-fixing potential, including two candidatus taxa JAJVIF01 and BMS3Abin14. Metatranscriptomic analyses confirmed that these carbon-fixing microbes were active in situ and occupied different niches. In the surface layers, Gammaproteobacteria with the CBB cycle played an important role in DCF, mainly driven by sulfur and hydrogen oxidation with oxygen reduction; in the deeper layers, Campylobacteria with the reductive tricarboxylic acid (rTCA) cycle and Desulfobacteria with the WL pathway were active members for DCF, mainly through sulfur, hydrogen, and CO oxidation. While in the deepest layers of 18-20 cm, methane-producing archaea Methanosarcinia was the essential member driving DCF. In addition, most taxa containing the WL pathway displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies.

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

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

@article {pmid40890809,
year = {2025},
author = {Xue, S and Shi, T and Xie, J and Liu, W and Yao, S and Li, N and Liu, H and Kong, W and Gao, F},
title = {Integrated fecal macrogenomic and metabolomic analyses reveal celiac disease flora and metabolic profiles associated with Chinese populations.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {972},
pmid = {40890809},
issn = {1479-5876},
support = {2022D01C831//Natural Science Foundation of Xinjiang/ ; 82260116//National Natural Science Foundation of China/ ; 82460117//National Natural Science Foundation of China/ ; },
mesh = {Adolescent ; Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Case-Control Studies ; *Celiac Disease/ethnology/genetics/metabolism/microbiology ; China/ethnology ; *Feces/microbiology ; Gastrointestinal Microbiome ; *Metabolome ; *Metabolomics ; East Asian People ; },
abstract = {BACKGROUND AND AIMS: Genes and gluten intake are necessary but not sufficient to cause celiac disease (CeD), and altered intestinal flora is an additional risk factor for the development of CeD. The present study was conducted to investigate the intestinal flora and metabolic characteristics of CeD among the Chinese population, with the use of CeD patients from Xinjiang, China.

METHODS: Macrogenomic sequencing was performed to analyze the composition and differences of the intestinal flora of 40 CeD patients and 40 healthy subjects. Non-targeted metabolomics analysis was carried out using LC-MS metabolomics technology in 30 CeD patients and 30 control subjects. A model for CeD diagnosis was constructed based on differential flora and metabolites. Blood was collected from all subjects for HLA typing assay.

RESULTS: CeD-associated alterations were identified in the gut microbiome and metabolome. 15 differential bacterial strains (AUC = 0.85) and 8 differential metabolites (AUC = 0.9799) constructed a diagnostic panel that was effective in differentiating CeD patients from healthy subjects. Compared with non-CeD patients carrying HLA-DQ[±], the abundances of Agathobacter_rectalis, Bifidobacterium_pseudocatenulatum, Clostridia_bacterium, Coprococcus_comes, and Fusicatenibacter_saccharivorans in CeD patients were significantly lower (P < 0.05). Metabolomics analysis showed that Leoheteronin D, Pc (34:2), and GPEtn (18:1/16:0) were the major metabolites involved in multiple metabolic pathways in CeD patients.

CONCLUSION: Our study revealed specific alterations in the gut microbiome and metabolome of Chinese CeD patients through a multi-omics integration strategy. We found that CeD individuals carrying CeD risk genes may possess a unique intestinal flora composition, and this intestinal flora may, to some extent, explain the pathogenesis of CeD beyond the contributions of genes and gluten intake.},
}

Adolescent
Adult
Female
Humans
Male
Middle Aged
Young Adult
Case-Control Studies
*Celiac Disease/ethnology/genetics/metabolism/microbiology
China/ethnology
*Feces/microbiology
Gastrointestinal Microbiome
*Metabolome
*Metabolomics
East Asian People

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

@article {pmid40890565,
year = {2025},
author = {Ivanich, K and Yackzan, A and Flemister, A and Chang, YH and Xing, X and Chen, A and Yanckello, LM and Sun, M and Aware, C and Govindarajan, M and Kramer, S and Ericsson, A and Lin, AL},
title = {Ketogenic Diet Modulates Gut Microbiota-Brain Metabolite Axis in a Sex- and Genotype-Specific Manner in APOE4 Mice.},
journal = {Journal of neurochemistry},
volume = {169},
number = {9},
pages = {e70216},
doi = {10.1111/jnc.70216},
pmid = {40890565},
issn = {1471-4159},
support = {RF1AG062480/AG/NIA NIH HHS/United States ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Diet, Ketogenic/methods ; Female ; *Apolipoprotein E4/genetics ; Mice ; Male ; *Brain/metabolism ; *Sex Characteristics ; Genotype ; Mice, Inbred C57BL ; Apolipoprotein E3/genetics ; Mice, Transgenic ; },
abstract = {The apolipoprotein E4 (APOE4) allele is the strongest genetic risk factor for late-onset Alzheimer's disease (AD), associated with early brain metabolic dysfunction and gut microbiome alterations. Targeting these early changes through dietary interventions may reduce AD risk in asymptomatic carriers. This study evaluated whether a ketogenic diet (KD) could reshape the gut microbiome and enhance key brain metabolite levels in young APOE4 mice, using APOE3 mice as a neutral-risk comparison. Male and female APOE3 and APOE4 mice were fed either a control diet or KD for 16 weeks, starting at 12 weeks of age. We used shotgun metagenomics and targeted brain metabolomics to identify microbe-metabolite signatures linked to neuroprotection. KD increased beneficial species such as Lactobacillus johnsonii and Lactobacillus reuteri while reducing pathogenic Bacteroides intestinalis. These microbial shifts correlated with improved brain metabolites related to mitochondrial function, neurotransmitter balance, redox homeostasis, and lipid metabolism. Notably, Lactobacillus species and B. intestinalis exhibited inverse correlations with key brain metabolite levels, suggesting their roles as both modulators and biomarkers of brain health. APOE4 females showed the greatest benefits, including restored microbiome diversity and normalization of brain metabolite levels. In contrast, APOE3 mice showed microbiome changes but limited brain metabolic responses. These findings highlight KD's potential to reprogram the gut-brain axis in a genotype- and sex-dependent manner, supporting its use as a precision nutrition strategy to reduce AD risk, particularly in asymptomatic female APOE4 carriers.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Diet, Ketogenic/methods
Female
*Apolipoprotein E4/genetics
Mice
Male
*Brain/metabolism
*Sex Characteristics
Genotype
Mice, Inbred C57BL
Apolipoprotein E3/genetics
Mice, Transgenic

@article {pmid40890119,
year = {2025},
author = {Yuan, B and Wang, S},
title = {Microbiome data integration via shared dictionary learning.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8147},
pmid = {40890119},
issn = {2041-1723},
support = {DBI-2243257//National Science Foundation (NSF)/ ; DMS-2515171//National Science Foundation (NSF)/ ; DBI-2243257//National Science Foundation (NSF)/ ; DMS-2515171//National Science Foundation (NSF)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Metagenomics/methods ; Colorectal Neoplasms/microbiology/therapy ; Machine Learning ; Immunotherapy ; Gastrointestinal Microbiome ; Computational Biology/methods ; },
abstract = {Data integration is a powerful tool for facilitating a comprehensive and generalizable understanding of microbial communities and their association with outcomes of interest. However, integrating data sets from different studies remains a challenging problem because of severe batch effects, unobserved confounding variables, and high heterogeneity across data sets. We propose a new data integration method called MetaDICT, which initially estimates the batch effects by weighting methods in causal inference literature and then refines the estimation via novel shared dictionary learning. Compared with existing methods, MetaDICT can better avoid the overcorrection of batch effects and preserve biological variation when there exist unobserved confounding variables, data sets are highly heterogeneous across studies, or the batch is completely confounded with some covariates. Furthermore, MetaDICT can generate comparable embedding at both taxa and sample levels that can be used to unravel the hidden structure of the integrated data and improve the integrative analysis. Applications to synthetic and real microbiome data sets demonstrate the robustness and effectiveness of MetaDICT in integrative analysis. Using MetaDICT, we characterize microbial interaction, identify generalizable microbial signatures, and enhance the accuracy of outcome prediction in two real integrative studies, including an integrative analysis of colorectal cancer metagenomics studies and a meta-analysis of immunotherapy microbiome studies.},
}

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

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

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

@article {pmid40889848,
year = {2026},
author = {Lin, X and Deng, C and Shu, Y and Li, S and Song, Y and Kong, H and Liang, Z and Liu, L and Rao, Y},
title = {Ecological presence and functional role of bacteriophages in fermented vegetables.},
journal = {Food microbiology},
volume = {133},
number = {},
pages = {104884},
doi = {10.1016/j.fm.2025.104884},
pmid = {40889848},
issn = {1095-9998},
mesh = {*Vegetables/microbiology/virology ; *Bacteriophages/genetics/isolation & purification/physiology/metabolism/classification ; Fermentation ; *Fermented Foods/virology/microbiology ; Microbiota ; *Bacteria/genetics/metabolism/virology/classification/isolation & purification ; Food Microbiology ; },
abstract = {Fermented vegetables are widely favored by consumers for their distinctive flavors and nutritional value, with their quality attributes being closely associated with microbiome dynamics. Recent advances in high-throughput sequencing technologies have revealed abundant bacteriophage resources within the fermented vegetable microbiome. These viral components significantly influence fermentation processes and product characteristics by modulating microbial community structure and function. However, research on optimizing vegetable fermentation processes through bacteriophage-mediated regulation remains in its nascent stage. This study systematically summarizes the compositional characteristics and dynamic patterns of microbial communities in fermented vegetables. We review the latest research progress on bacteriophage diversity and functional properties in fermented vegetables. Furthermore, by integrating multi-omics data, we provide insights into the complex interaction network among bacteriophages, host microbiota, and metabolic products. The results demonstrate that bacteriophages precisely regulate the fermentation process by mediating microbial community succession via lytic-lysogenic cycles and participating in the biosynthesis of key flavor compounds through encoded auxiliary metabolic genes. Finally, we sort out an integrated technical framework combining metagenomics and culturomics. This research provides novel insights into understanding the functional mechanisms of bacteriophages in fermented vegetables, offers a theoretical foundation for developing precision fermentation technologies based on bacteriophage regulation.},
}

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

@article {pmid40889843,
year = {2026},
author = {Ren, F and Liu, M and Tan, B},
title = {Mycobiota of highly-preserved and easily-spoiled soybean pastes-what are their roles?.},
journal = {Food microbiology},
volume = {133},
number = {},
pages = {104876},
doi = {10.1016/j.fm.2025.104876},
pmid = {40889843},
issn = {1095-9998},
mesh = {*Glycine max/microbiology ; *Fungi/classification/genetics/isolation & purification/metabolism ; *Mycobiome ; Food Preservation ; Biodiversity ; },
abstract = {Effective preservation of fermented soybean pastes is critically dependent on their microbial communities. In this study, the fungal assemblages of highly-preserved (HP) and easily-spoiled (ES) soybean paste samples were analyzed and compared mainly with Illumina sequencing of both mycobiota ITS amplicon and metagenomic functional annotation. The results showed that fungal communities of two types soybean pastes were distinct and had different α-diversity and β-diversity characteristics. The phylum Ascomycota was predominant in all samples, with Candida, Aspergillus, and Penicillium being the most abundant genera. The HP group exhibited greater richness and diversity compared to ES samples, and the relative abundance of specific fungal taxa varied significantly between the two groups. Additionally, functional annotation revealed differences in metabolic categories, with HP samples having higher levels of functions related to amino acid transport and metabolism, cell cycle control, and signal transduction mechanisms. These results enhance the understanding of the fungal diversity and functional differences of soybean pastes, providing insights that could improve preservation methods, optimize production and storage processes, and ensure the quality of the products.},
}

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

@article {pmid40889721,
year = {2025},
author = {Gao, R and Liu, Z and Li, W and Lou, L and Xu, T and Shi, L and Cao, J and Fang, J and Liu, G},
title = {Novel compound bacterial agent effects on pig farm wastewater denitrification and nitrogen transformation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133232},
doi = {10.1016/j.biortech.2025.133232},
pmid = {40889721},
issn = {1873-2976},
abstract = {This research involved the screening and combination of Escherichia coli, Acinetobacter radioresistens, and Klebsiella michiganensis to create a novel compound bacterial agent known as SSF-1. The efficacy of SSF-1 in treating real pig farm wastewater was assessed, focusing on its impact on nitrogen transformation, the structure of bacterial communities, and functional genes. SSF-1 demonstrated stable ammonia nitrogen conversion under both weakly acidic and weakly alkaline conditions, exhibiting superior environmental adaptability compared to individual strains. Under optimal conditions, the ammonia nitrogen conversion rate in simulated wastewater reached 98.4 ± 0.2 %. Furthermore, SSF-1 was found to synergistically treat wastewater with functional bacteria in the sludge. Metagenomic analysis revealed that SSF-1 enhanced nitrogen transformation and the reduction of nitrate/nitrite by upregulating key nitrogen metabolism genes. This discovery expands the application potential of compound bacterial agent in actual environments and contributes to the sustainable utilization of water resources.},
}

@article {pmid40889349,
year = {2025},
author = {Moraitou, M and Richards, JL and Bolyos, C and Saliari, K and Gilissen, E and Timmons, Z and Kitchener, AC and Pauwels, OSG and Sabin, R and Kokkini, P and Portela Miguez, R and Guschanski, K},
title = {Host Traits Impact the Outcome of Metagenomic Library Preparation From Dental Calculus Samples Across Diverse Mammals.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70039},
doi = {10.1111/1755-0998.70039},
pmid = {40889349},
issn = {1755-0998},
support = {2019-00275//Svenska Forskningsrådet Formas/ ; },
abstract = {Dental calculus metagenomics has emerged as a valuable tool for studying the oral microbiomes of humans and a few select mammals. With increasing interest in wild animal microbiomes, it is important to understand how widely this material can be used across the mammalian tree of life, refine the related protocols and understand the expected outcomes and potential challenges of dental calculus sample processing. In this study, we significantly expand the breadth of studied host species, analysing laboratory and bioinformatics metadata of dental calculus samples from 32 ecologically and phylogenetically diverse mammals. Although we confirm the presence of an oral microbiome signature in the metagenomes of all studied mammals, the fraction recognised as oral varies between host species, possibly because of both biological differences and methodological biases. The overall success rate of dental calculus processing, from extractions to sequencing, was ~74%. Although input sample weight was positively associated with the number of produced library molecules, we identify a negative impact of enzymatic inhibition on the library preparation protocol. The inhibition was most prevalent in herbivores and frugivores and is likely diet-derived. In contrast, hosts with an animalivore diet posed fewer challenges during laboratory processing and yielded more DNA relative to sample weight. Our results translate into recommendations for future studies of dental calculus metagenomics from a variety of host species, identifying required sample amounts, and emphasising the utility of dental calculus in exploring the oral microbiome in relation to broader ecological and evolutionary questions.},
}

@article {pmid40889140,
year = {2025},
author = {Elton, L and Mateos, AD and Frosini, SM and Jepson, R and Rofael, S and McHugh, TD and Wey, EQ},
title = {A metagenomic approach to One Health surveillance of antimicrobial resistance in a UK veterinary centre.},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
pmid = {40889140},
issn = {2057-5858},
mesh = {Animals ; *Metagenomics/methods ; One Health ; *Drug Resistance, Bacterial/genetics ; Dogs ; Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/isolation & purification/classification ; Plasmids/genetics ; Hospitals, Animal ; Microbial Sensitivity Tests ; United Kingdom ; Humans ; London ; },
abstract = {There are currently no standardized guidelines for genomic surveillance of One Health antimicrobial resistance (AMR). This project aimed to utilize metagenomics to identify AMR genes present in a companion animal hospital and compare these with phenotypic results from bacterial isolates from clinical specimens from the same veterinary hospital. Samples were collected from sites within a primary care companion animal veterinary hospital in London, UK. Metagenomic DNA was sequenced using Oxford Nanopore Technologies MinION. The sequencing data were analysed for AMR genes, plasmids and clinically relevant pathogen species. These data were compared to phenotypic speciation and antibiotic susceptibility tests of bacterial isolates from patients. The most common resistance genes identified were aph (n=101 times genes were detected across 48 metagenomic samples), sul (84), bla CARB (63), tet (58) and bla TEM (46). In clinical isolates, a high proportion of isolates were phenotypically resistant to β-lactams. Rooms with the greatest mean number of resistance genes identified per swab site were the medical preparation room, dog ward and surgical preparation room. Twenty-four and four plasmids typically associated with Gram-positive and Enterobacteriaceae, respectively, were identified. Sequencing reads matched with 14 out of 22 (64%) of the phenotypically isolated bacterial species. Metagenomics identified AMR genes, plasmids and species of relevance to human and animal medicine. Communal animal-handling areas harboured more AMR genes than areas animals did not frequent. When considering infection prevention and control measures, adherence to, and frequency of, cleaning schedules, alongside potentially more comprehensive disinfection of animal-handling areas, may reduce the number of potentially harmful bacteria present.},
}

Animals
*Metagenomics/methods
One Health
*Drug Resistance, Bacterial/genetics
Dogs
Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/isolation & purification/classification
Plasmids/genetics
Hospitals, Animal
Microbial Sensitivity Tests
United Kingdom
Humans
London

@article {pmid40888959,
year = {2025},
author = {Rajan, RJ and Sathyanathan, R and Rajnish, KN},
title = {Metabarcoding-Based Seasonal Assessment of Airborne Microbial Communities in PM10 Samples from a Semi-Urban Region in Tamil Nadu, India.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {9},
pages = {1069},
pmid = {40888959},
issn = {1573-2959},
mesh = {India ; *Air Microbiology ; Seasons ; *Environmental Monitoring/methods ; *Microbiota ; *Air Pollutants/analysis ; *Particulate Matter/analysis ; Bacteria/classification/genetics ; DNA Barcoding, Taxonomic ; Air Pollution/statistics & numerical data ; },
abstract = {Airborne microbial communities show marked seasonal variability, with implications for both environmental processes and public health. In this study, metagenomic sequencing was applied to characterize airborne microbiota across four distinct seasons in India-winter (Sw), summer (Ss), southwest monsoon (Ssw), and northeast monsoon (Sne). Distinct shifts in dominant bacterial taxa were observed. Sne was dominated by Pseudomonas (42.3%) alongside sulfur-oxidizing Thiobacillus and Stenotrophomonas, likely influenced by lower temperatures and anthropogenic inputs. In Ss, Thiobacillus (72.9%) prevailed, followed by Pseudomonas (8.06%) and Sphingosinicella (6.68%), reflecting adaptation to arid, UV-intense conditions. Ssw featured Thiobacillus (58%) and Pseudomonas (18.5%) with additional plant-associated Lactobacillus and Clostridium, suggesting enhanced biogenic emissions. Sw was distinct for Enterococcus (21.9%) dominance and reduced Thiobacillus (16.2%), associated with high humidity and precipitation. Species richness followed the order Ssw > Sw > Ss > Sne, with the highest diversity during Ssw and Sw as indicated by Chao1, Fisher, Shannon, and Simpson indices. Kruskal-Wallis tests revealed no statistically significant differences in alpha diversity across seasons. Canonical Correspondence Analysis (CCA) highlighted strong seasonal structuring linked to environmental parameters such as temperature, humidity, and UV exposure. Dendrogram clustering showed greatest dissimilarity between Sne and Sw, while Ss and Ssw formed a closely related group. Ordination analyses (PCA, PCoA, NMDS) further confirmed seasonal distinctions. Seasonal variations in dominant bacterial taxa indicate potential public health risks in semi-urban tropical environments. Thiobacillus, prevalent in summer and the southwest monsoon, is generally non-pathogenic. In contrast, Pseudomonas species, abundant during the northeast monsoon and winter, are metabolically versatile, encompassing environmental strains and opportunistic pathogens known to cause respiratory and wound infections, especially in immunocompromised individuals. Winter also saw the presence of Enterococcus faecalis, a gut commensal and opportunistic pathogen linked to hospital-acquired infections and notable for multi-drug resistance. These seasonal shifts highlight varying exposure risks, emphasizing the need for public health attention to airborne microbial dynamics across different seasons.},
}

India
*Air Microbiology
Seasons
*Environmental Monitoring/methods
*Microbiota
*Air Pollutants/analysis
*Particulate Matter/analysis
Bacteria/classification/genetics
DNA Barcoding, Taxonomic
Air Pollution/statistics & numerical data

@article {pmid40888850,
year = {2025},
author = {Chasapi, MN and Chasapi, IN and Aplakidou, E and Baltoumas, FA and Karatzas, E and Iliopoulos, I and Stravopodis, DJ and Emiris, IZ and Buluç, A and Georgakopoulos-Soares, I and Kyrpides, NC and Pavlopoulos, GA},
title = {metagRoot: a comprehensive database of protein families associated with plant root microbiomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf862},
pmid = {40888850},
issn = {1362-4962},
support = {23592//Hellenic Foundation for Research and Innovation/ ; //European Union's Horizon 2020/ ; 945405//Marie Skłodowska-Curie/ ; //Penn State College of Medicine/ ; //Huck Innovative and Transformational Seed/ ; //Huck Institutes of the Life Sciences/ ; 16718-PRPFOR//Hellenic Foundation for Research and Innovation/ ; TAEDR-0539180//Hellenic Foundation for Research and Innovation/ ; DE-AC02-05CH11231//U.S. Department of Energy Office of Science/ ; //Nikos Kyrpides JGI-LBNL/ ; },
abstract = {The plant root microbiome is vital in plant health, nutrient uptake, and environmental resilience. To explore and harness this diversity, we present metagRoot, a specialized and enriched database focused on the protein families of the plant root microbiome. MetagRoot integrates metagenomic, metatranscriptomic, and reference genome-derived protein data to characterize 71 091 enriched protein families, each containing at least 100 sequences. These families are annotated with multiple sequence alignments, CRISPR elements, hidden Markov models, taxonomic and functional classifications, ecosystem and geolocation metadata, and predicted 3D structures using AlphaFold2. MetagRoot is a powerful tool for decoding the molecular landscape of root-associated microbial communities and advancing microbiome-informed agricultural practices by enriching protein family information with ecological and structural context. The database is available at https://pavlopoulos-lab.org/metagroot/ or https://www.metagroot.org.},
}

@article {pmid40888678,
year = {2025},
author = {Zhou, R and Ng, SK and Sung, JJY and Wong, SH and Goh, WWB},
title = {Detecting and mitigating doppelgänger bias in microbiome data: impacts on machine learning and disease classification.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2554196},
doi = {10.1080/19490976.2025.2554196},
pmid = {40888678},
issn = {1949-0984},
mesh = {Humans ; *Machine Learning ; Clostridium Infections/microbiology ; Colorectal Neoplasms/microbiology ; Inflammatory Bowel Diseases/microbiology ; *Microbiota ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Obesity/microbiology ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Highly similar microbiome samples - so-called "doppelgänger pairs" - can distort analysis outcomes, yet are rarely addressed in microbiome studies. Here, we demonstrate that even a small proportion of such pairs (1-10% of samples) can substantially inflate machine learning performance across diverse disease cohorts including colorectal cancer (CRC), inflammatory bowel diseases (IBD), Clostridioides difficile infection (CDI), and obesity. Doppelgänger pairs also bias statistical tests and distort microbial network topology. In predictive models, classification accuracy was artificially boosted by 15-30% points across KNN, SVM, and Random Forest classifiers. In association testing, doppelgängers increased false-positive rates and decreased effect size stability; their removal reduced bootstrap variance by up to 28.3%. Moreover, the removal of doppelgängers yielded more stable networks. These effects were consistently observed across 16S, shotgun metagenomic, and simulated datasets. By accounting for highly similar samples, we reduce analytical noise and false discoveries, ultimately enabling more accurate and biologically meaningful microbiome insights.},
}

Humans
*Machine Learning
Clostridium Infections/microbiology
Colorectal Neoplasms/microbiology
Inflammatory Bowel Diseases/microbiology
*Microbiota
*Gastrointestinal Microbiome
Metagenomics/methods
Obesity/microbiology
Bacteria/classification/genetics/isolation & purification

@article {pmid40888465,
year = {2025},
author = {Li, Q and Wang, R and Zhou, X and Li, S and Zhang, S and Zhang, X and Wang, W and Jiao, J and Janssen, PH and Ungerfeld, EM and Müller, V and Conrad, R and Greening, C and Tan, Z and Fu, B and Wang, M},
title = {Metabolic versatility enables acetogens to colonize ruminants with diet-driven niche partitioning.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf183},
pmid = {40888465},
issn = {1751-7370},
abstract = {Enteric methane emissions are energy losses from farmed ruminants and contribute to global warming. Diverting electrons and H2 flow toward beneficial fermentation products would mitigate ruminal methane emissions while improving feed efficiency. Acetogens can direct H2 and electrons to acetate production via the Wood-Ljungdahl pathway, but methanogens have more competitive H2 affinities. Thus, it is unclear how acetogenesis subsists in the rumen. An analysis of 2102 globally derived rumen metagenomes from multiple ruminant species revealed that putative acetogens were phylogenetically diverse and capable of using carbohydrates or H2 as electron donors. The metabolic versatility of these acetogens may enable them to outcompete methanogens with lower versatility. Through animal trials, in vitro experiments, and DNA stable isotope probing, we verified the presence of diverse acetogens in beef cattle rumens and revealed that their niche partitioning is driven by contrasting fiber-rich and starch-rich diets. A fiber-rich diet enriched heterotrophic acetogens, which increased acetate formation while decreasing methane production. Overall, this study highlights the overlooked heterotrophy of acetogens in the rumen and their potential for mitigating enteric methane emissions.},
}

@article {pmid40886575,
year = {2025},
author = {Agga, GE and Looft, T and Sistani, KR},
title = {Enrichment of soil microbiome and antimicrobial resistance genes following poultry litter application.},
journal = {The Science of the total environment},
volume = {999},
number = {},
pages = {180306},
doi = {10.1016/j.scitotenv.2025.180306},
pmid = {40886575},
issn = {1879-1026},
abstract = {Poultry litter (PL) is often used for soil amendment as an alternative to chemical fertilizers. However, it may enrich microbial and antimicrobial resistance genes in applied soil. The objective of this study was to investigate changes in the soil microbiome and resistome profiles following PL application. Three treatments untreated control (UC), chemical fertilizer (CF), and PL were applied to corn plots in a completely randomized block design. Total soil (metagenomic) DNA (n = 72) obtained on d0, d7, and d28 were shotgun sequenced. A composite DNA sample pooled from PL samples (n = 8) was sequenced for comparison. While Actinomycetota and Pseudomonadota were the most prevalent phyla among the soil samples, their abundance was significantly higher in the PL amended soils. PL soil amendment shifted microbial composition (Gammaproteobacteria and fungal Saccharomycetes were enriched in PL amended soils), diversity, and abundance by differentially enriching several microbial species, functional pathway genes, virulence factor genes, and antimicrobial resistance genes. Macrolides-lincosamides-streptogramin (MLS) resistance genes were the most abundant genes enriched in PL amended soils. The PL microbiome was primarily composed of the phylum Bacillota with Virgibacillus alimentarius being the most abundant species, followed by Staphylococcus nepalensis and S. simulans. The PL resistome was dominated by MLS resistance genes. Virulence factor genes associated with the genera Bacteriodes, Enterococcus and Staphylococcus were the most prevalent. The study clearly showed that PL application enriches soil microbiome and resistome, the mechanism of which is more likely through nutrient enrichment rather than their direct transfer since PL and PL-amended soils had different microbiome profiles.},
}

@article {pmid40886530,
year = {2025},
author = {Miao, L and Ma, T and Qi, J and Deng, Y and Hong, Y and Gong, X and Zang, H and Cheng, Y and Li, C},
title = {Deciphering intrakingdom synergism in 17β-estradiol degradation through DNA-SIP coupled metagenomics: Metabolic cooperation and niche partitioning in bioaugmented soil microbiomes.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139709},
doi = {10.1016/j.jhazmat.2025.139709},
pmid = {40886530},
issn = {1873-3336},
abstract = {17β-Estradiol (17β-E2), a persistent endocrine-disrupting compound, threatens ecosystem health through bioaccumulation. While bioaugmentation offers promise for environmental remediation, mechanistic insights into interspecies interactions between exogenous and indigenous degraders remain underexplored. Here, a synthetic microbial consortium (EL) was constructed by combining Rhodococcus erythropolis D310-1 and Microbacterium oxydans ML-6, which reduced the 17β-E2 degradation half-life by 53.65 % compared with that of the noninoculated control while suppressing the accumulation of the toxic intermediate estrone (E1). Temporal 16S rRNA gene amplicon sequencing profiling with co-occurrence network analysis revealed that the consortium EL dynamically reinforced ecological synergies with indigenous functional microbiota, accelerating contaminant mineralization. DNA-stable isotope probing (DNA-SIP) coupled with metagenomics identified Rhodanobacter, Mycobacterium, Rhodococcus, Sphingomonas, and Microbacterium spp. as active 17β-E2 assimilators. Furthermore, high-performance liquid chromatography coupled with quadrupole timeflight mass spectrometry (HPLCQTOFMS) was used to predict three complementary degradation pathways in the assembled genomes, revealing related functional enzymes and addressing functional partitioning between exogenous inoculants and indigenous degraders. Two novel gene clusters responsible for 17β-E2 biodegradation were evaluated. This study pioneers DNA-SIP and metagenomics to track [13]C-labelled 17β-E2 fate within bioaugmented soil microbiota, resolving intrakingdom bacteria collaborations that drive 17β-E2 biodegradation in soil. The identification of cross-consortium metabolic handoffs provides a blueprint for engineering syntrophic partnerships targeting steroidal estrogens (SEs) pollutants.},
}

@article {pmid40886152,
year = {2025},
author = {Zemmel, ZM and Fan, X and Yu, Y and Markiewicz, E and Tsai, HM and Lu, L and Little, JC and Ramaswamy, R and Andrews, B and Claud, EC and Lu, J},
title = {Early-life gut microbiome maturity regulates blood-brain barrier and cognitive development.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2551879},
doi = {10.1080/19490976.2025.2551879},
pmid = {40886152},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Blood-Brain Barrier/metabolism/physiology/growth & development ; Mice ; Female ; Humans ; *Cognition/physiology ; Pregnancy ; Bacteria/classification/genetics/isolation & purification/metabolism ; Mice, Inbred C57BL ; Brain/growth & development/metabolism ; Male ; Germ-Free Life ; },
abstract = {The gut microbiome is an emerging factor in the neurobiology of disease. Blood-brain barrier (BBB) integrity is essential for proper brain function. However, the role the initial microbiome plays in BBB and brain development is unclear. In this study, we colonized germ-free pregnant mice with human full-term- or preterm-infant-derived gut microbiota, thereby establishing these communities in the resulting offspring. We discovered that mice harboring a full-term-associated microbiome exhibited stronger memory and learning capabilities and dramatically decreased early-life BBB permeability when compared to those with a prematurity-associated microbiome. Whole-brain single-cell RNA sequencing revealed downregulation of synaptic signaling genes in BBB cell types of mice with the prematurity-associated microbiome, indicating that microbiome maturity influences BBB transcriptional programs that support cognitive development. Comprehensive metagenomics and metabolomics uncovered bacterial populations and genomic pathways corresponding with decreased levels of circulating long-chain acylcarnitines and lysophosphatidylcholines in mice with the full-term-associated microbiome. Our findings highlight the microbiome as a therapeutic target for improving long-term neurodevelopmental outcomes due to its effect on the early-life BBB.},
}

*Gastrointestinal Microbiome/physiology
Animals
*Blood-Brain Barrier/metabolism/physiology/growth & development
Mice
Female
Humans
*Cognition/physiology
Pregnancy
Bacteria/classification/genetics/isolation & purification/metabolism
Mice, Inbred C57BL
Brain/growth & development/metabolism
Male
Germ-Free Life

@article {pmid40885910,
year = {2025},
author = {Huang, W and Chai, Y and Li, X and Zhang, Q and Yan, Z and Wang, Y and Tao, X and Zhang, J and Qiu, F},
title = {Metagenomics and metabolomics to evaluate the potential role of gut microbiota and blood metabolites in patients with cerebral infarction.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {567},
pmid = {40885910},
issn = {1471-2180},
support = {2018YFA0108601//Clinical research on intracerebral precision transplantation of neural stem cells for stroke treatment/ ; L255012//The Huairou Innovation Joint Fund Project of Beijing Natural Science Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Cerebral Infarction/microbiology/blood/metabolism ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Middle Aged ; Female ; Aged ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Tandem Mass Spectrometry ; Adult ; Chromatography, High Pressure Liquid ; },
abstract = {Cerebral infarction, a cerebrovascular disorder, is characterized by the sudden onset of neurological deficits and clinical symptoms. It ranks among the leading causes of death and severe disability worldwide. The etiology of cerebral infarction is multifaceted, with common risk factors including dietary patterns, smoking, hypertension, and diabetes mellitus. In recent years, the role of the gut microbiota in systemic immunity and tumorigenesis has been intensively explored, thrusting the research on the gut-brain axis into the spotlight. However, there is a lack of literature investigating the relationship between the gut microbiota and blood metabolites in cerebral infarction. In this study, we employed 16S rRNA analysis and ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) for a comprehensive metagenomic and metabolomic analysis of fecal samples from cerebral infarction patients and the general population. Our results revealed a significant correlation between the gut microbiome and serum metabolites, highlighting the impact of the microbiome on metabolic pathways. Specifically, we found that 35 gut microbiome taxa, such as Actinobacteriota and Peptostreptococcales-Tissierellales, were significantly enriched in the control group (N group). Through Linear Discriminant Analysis Effect Size (LEfSe) analysis, 72 taxa showed significant differences between cerebral infarction patients and healthy individuals. Among them, 22 key taxa were identified as microbial biomarkers for differentiating patients from healthy controls. These findings suggest that variations in the microbiome and metabolites could potentially serve as biomarkers for future diagnostic and therapeutic strategies in cerebral infarction.},
}

Humans
*Gastrointestinal Microbiome
*Cerebral Infarction/microbiology/blood/metabolism
*Metabolomics/methods
*Metagenomics/methods
Male
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Middle Aged
Female
Aged
*Bacteria/classification/genetics/isolation & purification/metabolism
Tandem Mass Spectrometry
Adult
Chromatography, High Pressure Liquid

@article {pmid40885737,
year = {2025},
author = {Chatzigiannidou, I and Johansen, PL and Dehli, RK and Moll, JM and Eriksen, C and Myers, PN and Roager, HM and Yang, L and Stokholm, J and Sørensen, SJ and Krogfelt, KA and Laursen, MF and Trivedi, U and Scheynius, A and Kristiansen, K and Mie, A and Alm, J and Brix, S},
title = {Temporal dynamics and microbial interactions shaping the gut resistome in early infancy.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8139},
pmid = {40885737},
issn = {2041-1723},
support = {2012-3011//Vetenskapsrådet (Swedish Research Council)/ ; 0171-00006B//Det Frie Forskningsråd (Danish Council for Independent Research)/ ; 4203-00005B//Innovationsfonden (Innovation Fund Denmark)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; Infant ; Escherichia coli/genetics/drug effects/growth & development ; Female ; Infant, Newborn ; Bifidobacterium/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; *Microbial Interactions/genetics ; *Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Metagenomics ; Male ; },
abstract = {Despite the critical role of the gut resistome in spreading of antimicrobial resistance (AMR), strategies to reduce the abundance of antibiotic resistance genes (ARGs) during microbiota development in infancy remain underexplored. Using longitudinal quantitative metagenomic data, we here show that ARGs are present in the gut microbiota from the first week of life, with a peak in absolute ARG abundance and richness at 6 months. Delivery mode significantly affects early ARG dynamics, and vaginally delivered infants exhibit higher ARG abundance due to maternal transmission of Escherichia coli strains harbouring extensive resistance repertoires. The abundance of E. coli and other ARG-rich taxa inversely correlates with aromatic lactic acid-producing bifidobacteria, and aromatic lactic acids strongly inhibit the in vitro growth of E. coli and other opportunistic ARG-rich taxa. Our results highlight temporal and critical microbial interactions shaping the gut resistome in early infancy, pointing to potential interventions to curb AMR during this vulnerable developmental window by promoting colonization of aromatic lactic acid-producing bifidobacteria.},
}

Humans
*Gastrointestinal Microbiome/genetics/drug effects
Infant
Escherichia coli/genetics/drug effects/growth & development
Female
Infant, Newborn
Bifidobacterium/genetics/drug effects
Anti-Bacterial Agents/pharmacology
*Microbial Interactions/genetics
*Drug Resistance, Bacterial/genetics
Feces/microbiology
Metagenomics
Male

@article {pmid40885659,
year = {2025},
author = {Klier, KM and Anantharaman, K},
title = {An updated view of metabolic handoffs in microbiomes.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.07.009},
pmid = {40885659},
issn = {1878-4380},
abstract = {From the human gut to the deep ocean, diverse microbial communities underpin essential ecosystem processes. Limited understanding of the dynamics and interactions that shape these communities, however, constrains efforts to culture, investigate, and harness their potential. Further, these knowledge gaps restrict the ability to predict microbial responses to broader biodiversity declines and global change. Among the numerous types of microbial interactions, metabolite exchanges, or 'metabolic handoffs', are a well-documented phenomenon. Recent methodological advances have uncovered a broader spectrum of metabolic handoffs than previously appreciated. Varying in both mechanism and ecological role, metabolic handoffs influence diverse natural environments. In this review, we define two major types of metabolic handoffs, examine their potential drivers and benefits, and highlight emerging research that underscores their widespread occurrence and importance in complex microbial ecosystems.},
}

@article {pmid40885534,
year = {2025},
author = {Gagnon, DJ and Burkholder, KM and Weissman, AJ and Riker, RR and Ryzhov, S and May, TL and DiPalazzo, J and deKay, JT and Knudsen, L and Moore, MW and Pozzessere, NA and Weatherbee, M and Kelly, M and Nigatu, AS and Sevigny, JL and Simpson, S and Thomas, WK and Callaway, CW and Geller, BJ and Sawyer, DB and Seder, DB},
title = {Ceftriaxone to prevent early-onset pneumonia in comatose patients after out-of-hospital cardiac arrest: a pilot randomized controlled trial and resistome assessment (PROTECT).},
journal = {Chest},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chest.2025.08.007},
pmid = {40885534},
issn = {1931-3543},
abstract = {BACKGROUND: Antibiotic prophylaxis after out-of-hospital cardiac arrest (OHCA) reduces early-onset pneumonia, but has uncertain impact on mortality and non-infectious outcomes, with ongoing concerns about the subsequent development of antibiotic resistance.

RESEARCH QUESTION: Does prophylactic ceftriaxone reduce the incidence of early-onset pneumonia without increasing the acquisition of antibiotic resistance genes after OHCA?

STUDY DESIGN: and Methods: Comatose survivors of OHCA treated with targeted temperature management without a clinical diagnosis of pneumonia at admission were randomized to ceftriaxone 2 gm or matching placebo every 12 hours for three days. The primary outcome was early-onset pneumonia occurring ≤4 days after intubation confirmed by blinded adjudicators. Abundance of antibiotic resistance genes recovered from rectal swabs before-and-after study drug administration were analyzed with metagenomic sequencing.

RESULTS: 411 subjects were screened, 53 (13%) were randomized, and one subject withdrew, leaving 26 in each group in the final analysis. Early-onset pneumonia was diagnosed in 10 (38%) subjects receiving ceftriaxone and 18 (69%) subjects receiving placebo (RR 0.57, 95% CI 0.21-1.001; p=0.05). Open-label antibiotics were administered to 14 (54%) subjects receiving ceftriaxone and 22 (85%) receiving placebo (RR 0.64, 95%CI 0.43-0.94), most of which were broad-spectrum (93% and 100%, respectively). After adjusting for differences in abundance of antibiotic resistance genes prior to study drug administration, subjects randomized to ceftriaxone acquired significantly fewer antibiotic resistance genes to frequently used antibiotics in the ICU compared to those randomized to placebo (IRR 0.30, 95% CI 0.13-0.70). Serious adverse drug effects were not reported in either treatment group.

INTERPRETATION: This trial was inconclusive regarding the impact of ceftriaxone prophylaxis to reduce the incidence of EOP after OHCA but ceftriaxone was associated with less frequent administration of open-label antibiotics, and reduced acquisition of ARGs to frequently used antibiotics in the ICU.

CLINICAL TRIAL REGISTRATION: National Library of Medicine at www.

CLINICALTRIALS: gov (NCT04999592).},
}

@article {pmid40885432,
year = {2025},
author = {Kwon, M and Kwon, SH and Jang, H and Oh, H and Sun, S and Jung, C and Kil, EJ},
title = {Landscape-scale virome analysis uncovers endemic and emerging honey bee viruses in the Silk-Road hub of Uzbekistan.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108436},
doi = {10.1016/j.jip.2025.108436},
pmid = {40885432},
issn = {1096-0805},
abstract = {Honey bee health is increasingly threatened worldwide by a complex and evolving viral landscape; however, this aspect in Central Asia remains understudied despite the region being strategically positioned along historic and modern trade routes. In 2024, we conducted a nationwide virome survey of Apis mellifera across 32 cities in 11 regions of Uzbekistan, combining the metagenomic data of 14 pooled RNA-seq libraries with RT-PCR validation and phylogenetic analyses. High-quality sequencing yielded an average of approximately 60 million reads per pool. We recovered 30 viral species from 162 genomic sequences (131 complete sequences), including 11 honey bee-associated and 19 plant-infecting viruses. All samples harbored deformed wing virus type A (DWV-A), and co-infection with DWV-B predominated. Our findings provided the first full-length DWV-B genomes from Central Asia, revealing that it had > 97 % identity to European strains. New variants of the Sacbrood virus (partial sequence, approximately 4.7 kb) and Lake Sinai Virus UZB were also detected. The chronic bee paralysis virus was sequenced in full for the first time in Uzbekistan, and Varroa orthomyxovirus-1 exhibited segment-specific divergence. Additionally, we identified two novel plant viruses: Gulistan nepovirus 1 and Arpa carmo-like virus 1. Phylogenetic patterns of the identified viruses indicate that Uzbekistan serves as a genetic corridor connecting European and Asian virus populations. These findings fill critical geographical gaps, underscore the need for transboundary surveillance, and provide a genomic baseline for future diagnostics, epidemiology, and control strategies aimed at safeguarding pollinator and ecosystem health.},
}

@article {pmid40885278,
year = {2025},
author = {Bastón-Paz, N and Moreno-Blanco, A and Palacios, E and Olavarrieta, L and Galeano, J and Garriga, M and Máiz, L and Vicente-Santamaría, S and Oteo-Iglesias, J and López-Causapé, C and Fuentes, I and Oliver, A and Cantón, R and Del Campo, R and de Dios-Caballero, J},
title = {Exploring the Complexities of Intestinal and Pulmonary Microbiota in Cystic Fibrosis: A Multi-Omics Approach.},
journal = {Respiratory medicine},
volume = {},
number = {},
pages = {108331},
doi = {10.1016/j.rmed.2025.108331},
pmid = {40885278},
issn = {1532-3064},
abstract = {BACKGROUND: We aimed to elucidate the cystic fibrosis (CF) microbiota composition (shotgun metagenomics) and functionality (short-chain fatty acids, SCFAs).

METHODS: Fecal and sputum samples were recruited from 39 clinically stable CF subjects.

RESULTS: Bacillota and Pseudomonadota were dominant in both gut and lung compartments, whereas Ascomycota were the most abundant fungi in feces, and Basidiomycota, especially Malassezia globosa, in sputum. Viruses accounted for 0.4% of the relative abundance in the gut and 0.6% in lungs. Mycobacteroides abscessus was genetically identified in 10 individuals, although only 2 had positive cultures. Patients with higher levels of Pseudomonas filamentous phages had negative cultures for P. aeruginosa. The protozoan Toxoplasma gondii was detected in all sputum samples, accounting for 0.25% of the metagenomic reads, with further PCR-confirmation in 50% of subjects, including children. No correlation was found between SCFA and lung function or microbial composition. The resistome of the fecal compartment was higher than that of the lungs, and a greater abundance of SCFAs in the intestine was associated with poorer lung function.

CONCLUSIONS: Patients with normal-mild lung function had higher alpha diversity in the respiratory microbiota; however, beta diversity in the stool was statistically different compared with the group with poorer lung function. Although there were no differences in SCFA concentrations, butyrate-producing bacteria were more abundant in the sputum of the group with better lung function. In fecal samples, resistome to tetracyclines, glycopeptides, and aminoglycosides predominated, whereas in sputum an enrichment of ARGs related to tetracyclines, beta-lactams, and macrolides was observed.},
}

@article {pmid40885195,
year = {2025},
author = {Grujcic, V and Mehrshad, M and Vigil-Stenman, T and Lundin, D and Foster, RA},
title = {Stepwise genome evolution from a facultative symbiont to an endosymbiont in the N2-fixing diatom-Richelia symbioses.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.08.003},
pmid = {40885195},
issn = {1879-0445},
abstract = {A few genera of diatoms that form stable partnerships with N2-fixing filamentous cyanobacteria Richelia spp. are widespread in the open ocean. A unique feature of the diatom-Richelia symbioses is the symbiont cellular location spans a continuum of integration (epibiont, periplasmic, and endobiont) that is reflected in the symbiont genome size and content. In this study, we analyzed genomes derived from cultures and environmental metagenome-assembled genomes of Richelia symbionts, focusing on characters indicative of genome evolution. Our results show an enrichment of short-length transposases and pseudogenes in the periplasmic symbiont genomes, suggesting an active and transitionary period in genome evolution. By contrast, genomes of endobionts exhibited fewer transposases and pseudogenes, reflecting advanced stages of genome reduction. Pangenome analyses identified that endobionts streamline their genomes and retain most genes in the core genome, whereas periplasmic symbionts and epibionts maintain larger flexible genomes, indicating higher genomic plasticity compared with the genomes of endobionts. Functional gene comparisons with other N2-fixing cyanobacteria revealed that Richelia endobionts have similar patterns of metabolic loss but are distinguished by the absence of specific pathways (e.g., cytochrome bd ubiquinol oxidase and lipid A) that increase both dependency and direct interactions with their respective hosts. In conclusion, our findings underscore the dynamic nature of genome reduction in N2-fixing cyanobacterial symbionts and demonstrate the diatom-Richelia symbioses as a valuable and rare model to study genome evolution in the transitional stages from a free-living facultative symbiont to a host-dependent endobiont.},
}

@article {pmid40885069,
year = {2025},
author = {Li, B and Feng, L and Zhang, J and Giannakis, S},
title = {PFOA and a dash of aluminum: The perfect recipe for growing drug-resistant biofilms in urban water supply.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139660},
doi = {10.1016/j.jhazmat.2025.139660},
pmid = {40885069},
issn = {1873-3336},
abstract = {This study investigated the impact of perfluorooctanoic acid (PFOA) and aluminum (Al(III)) on the proliferation of drug-resistant pathogenic bacteria in drinking water distribution system (DWDS) biofilms, and their combined effect. Experimental simulations of stagnant residential water conditions, analyzed via comprehensive metagenomics, revealed a significant increase in bacterial biomass, extracellular polymeric substances (EPS), and the abundance of pathogenic bacteria and antibiotic resistance genes (ARGs). Biofilm formation was markedly enhanced in the presence of PFOA and Al(III), creating protective niches that facilitated the proliferation of pathogenic bacteria and ARGs. Key observations included increases in Legionella pneumophila and Pseudomonas aeruginosa, along with a shift in ARG profiles towards antibiotic efflux and target protection mechanisms. Critically, this study identified the presence and dynamics of priority drug-resistant pathogens within these biofilms, providing essential insights into pollutant-influenced risks and transmission pathways. These findings highlight the significant public health implications of PFOA and Al(III) co-contamination in drinking water systems.},
}

@article {pmid40884577,
year = {2025},
author = {Kumar, V and Sandil, S and Verma, P and Ameen, F},
title = {Decoding microbial ecology and functions: metagenomic profiling of activated sludge contaminated with chlorolignin compounds in a pulp-paper mill treatment system.},
journal = {Archives of microbiology},
volume = {207},
number = {10},
pages = {247},
pmid = {40884577},
issn = {1432-072X},
support = {ORF-2025-364//The authors extend their appreciation to the ongoing research funding program, (ORF-2025-364), King Saud University, Riyadh, Saudi Arabia./ ; },
mesh = {*Sewage/microbiology/chemistry ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Metagenomics ; *Water Pollutants, Chemical/analysis ; Microbiota ; Metals, Heavy/analysis ; Industrial Waste/analysis ; },
abstract = {This study aimed to profile the dynamics of indigenous bacterial communities in activated sludge, assess the pollutant load, and unlock the functional genes involved during the activated sludge treatment process. The physicochemical analyses of activated sludge revealed high amounts of phosphate, sulfate, chloride, and lignin, along with heavy metals like Fe, Zn, Cu, Ni, and Pb. Simultaneously, the GC-MS/MS technique identified decane, 1 bromo-2-methyl, pentadecanoic acid, methyl ester, benzene dicarboxylic acid, stigmasterol, borinic acid, diethyl, 2-hydroxymethyl cyclopropane, 2-methoxy-4-ethyl-phenol, 3,4,5-trichlorophenol, octadecanoic acid, and tetracosanic acid as major compounds. Furthermore, taxonomic classification of operational taxonomic unit (OTU) data revealed that Proteobacteria was the most abundant phylum, comprising 44.54% of the microbial community. In addition, other phyla, such as Bacteriodetes, Acidobacteria, Planctomycetes, Chlorolfexi, Actinobacteria, and Verrucomicrobia were also recorded within a range between 13.27 and 4.1% in the sludge. At the genus and species levels, the dominant organisms were unclassified (3.62%) and belonged to the family Rhodospirillacea. Further, PICRUSt2-based KEGG Orthology (KO) analysis showed enriched energy metabolism as the most abundant category, driven by oxidative phosphorylation and the TCA cycle. Furthermore, the MetaCyc analysis revealed a robust and adaptable microbial community with the dominant pathways of aerobic respiration I (cytochrome c) and fatty acid biosynthesis pathways, such as cis-vaccenate biosynthesis. The EC assignments highlighted a broad range of enzymatic functions, with a strong emphasis on oxidoreductases and transferases involved in energy production and biosynthesis. This research offers valuable insights into microbial community dynamics in wastewater treatment processes and identifies their functional role in a chlorolignin waste-polluted environment.},
}

*Sewage/microbiology/chemistry
*Bacteria/genetics/classification/isolation & purification/metabolism
Metagenomics
*Water Pollutants, Chemical/analysis
Microbiota
Metals, Heavy/analysis
Industrial Waste/analysis

@article {pmid40883892,
year = {2025},
author = {Kanaan, G and Deming, JW},
title = {Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf198},
pmid = {40883892},
issn = {1751-7370},
abstract = {Despite growing evidence for the role of DNA methylation in bacterial acclimation to environmental stress, this epigenetic mechanism remains unexplored in sea-ice microbial communities known to tolerate multiple stressors. This study presents a first analysis of DNA methylation patterns in bacterial communities and associated viruses across the vertical thickness of sea ice. Using a novel stepped-sackhole method, we collected sea-ice brines from distinct horizons of an Arctic ice floe, capturing microbial communities that had been exposed to different environmental conditions. Through Oxford Nanopore sequencing, we characterized methylation patterns in bacterial and associated viral DNA, analysing for methylation motifs and differences between ice horizons. We identified 22 unique bacterial methylation motifs and 27 viral motifs across three nucleotide methylation types (5mC, 6mA, and 4mC), with evidence of differential methylation between upper and lower ice. Analysis of metagenome-assembled genomes revealed the regulatory potential of methylation in both ice-adapted (Psychromonas and Polaribacter) and non-adapted bacteria (Pelagibacter); e.g., in Pelagibacter, differential methylation of the GANTC motif between upper and lower ice affected genes involved in core cellular processes. Viral methylation patterns showed evidence of recent infection. We also identified orphan methyltransferases in sea-ice phages, suggesting a mechanism for bypassing host restriction-modification systems and regulating host genes. Our findings reveal that DNA methylation serves functions in sea ice beyond traditional restriction-modification systems that protect against foreign DNA, opening new avenues for research on the role of epigenetic mechanisms not only in acclimation to the cryosphere but also more generally in microbial ecology and evolution.},
}

@article {pmid40883783,
year = {2025},
author = {Lei, H and Du, S and Tong, X and Chan, WL and Leung, MHY and Bøifot, KO and Bezdan, D and Butler, DJ and Danko, DC and Green, DC and Hernandez, MT and Kelly, FJ and Lucaci, AG and Meydan, C and Nieto-Caballero, M and Ryon, K and Tierney, B and Udekwu, KI and Young, BG and Mason, CE and Dybwad, M and Lee, PKH},
title = {Global biogeography of airborne viruses in public transit systems and their host interactions.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {193},
pmid = {40883783},
issn = {2049-2618},
support = {SLL 20160933//Stockholm Health Authority/ ; R01AI151059 and U01DA053941//Igor Tulchinsky and the WorldQuant Foundation, US National Institutes of Health/ ; OPP1151054//Bill and Melinda Gates Foundation/ ; R1016-20F//Research Impact Fund, Hong Kong Research Grants Council/ ; 11214721 and 11206224//General Research Fund, Hong Kong Research Grants Council/ ; },
mesh = {*Viruses/genetics/classification/isolation & purification ; *Air Microbiology ; Metagenomics/methods ; Genome, Viral ; Metagenome ; CRISPR-Cas Systems ; *Host Microbial Interactions/genetics ; Humans ; Phylogeography ; Cities ; },
abstract = {BACKGROUND: There is a diverse assemblage of microbes in air in built environments (BEs), but our understanding of viruses and their interactions with hosts in BEs remains incomplete. To address this knowledge gap, this study analyzed 503 metagenomes isolated from air samples from public transit systems in six global cities, namely Denver, Hong Kong, London, New York City, Oslo, and Stockholm. Viral genomes were recovered from samples via metagenomic binning, and viruses' taxonomy, functional potential, and microbial hosts were determined. The study also investigated correlations between virus and host abundances, the coevolution of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems and anti-CRISPR (Acr) proteins, and the potential impacts of auxiliary metabolic genes (AMGs) on hosts.

RESULTS: Airborne viruses in global BEs exhibited biogeographical variations in diversity, composition, function, and virus-host interactions. Nearly half of the vOTUs analyzed were from the Caulimoviridae family, while 31.8% of them could not be taxonomically classified. Diverse functions were identified within the vOTUs, together with antimicrobial resistance genes with the potential to confer resistance to various antibiotics and antimicrobial agents. Strong correlations were observed between vOTU and host abundances, with clear distinctions between virulent and temperate viruses. However, there was limited co-evolution of CRISPR-Cas systems and Acr proteins, which was likely due to the oligotrophic and physical conditions in the BEs and the dominance of vOTUs with a virulent lifestyle. Phage-encoded AMGs appeared to have the potential to enhance host fitness. These findings highlight biogeographical variations in airborne viruses in BEs and that physical and oligotrophic conditions in BEs drive virus survival strategies and virus-host coevolution.

CONCLUSION: There are biogeographical variations in airborne viruses in BEs in global cities, as physical and oligotrophic conditions in BEs drive virus survival strategies and virus-host coevolution. Moreover, the characteristics of airborne viruses in BEs are distinct from those of viruses found in other, more nutrient-rich ecosystems. Video Abstract.},
}

*Viruses/genetics/classification/isolation & purification
*Air Microbiology
Metagenomics/methods
Genome, Viral
Metagenome
CRISPR-Cas Systems
*Host Microbial Interactions/genetics
Humans
Phylogeography
Cities

@article {pmid40883605,
year = {2025},
author = {Yi, H and Lu, X and Chang, Q},
title = {MetaKSSD: boosting the scalability of the reference taxonomic marker database and the performance of metagenomic profiling using sketch operations.},
journal = {Nature computational science},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43588-025-00855-0},
pmid = {40883605},
issn = {2662-8457},
abstract = {The performance of metagenomic profiling is constrained by the diversity of taxa present in the reference taxonomic marker database (MarkerDB) used. However, continually updating MarkerDB to include newly determined taxa using existing approaches faces increasing difficulties and will soon become impractical. Here we introduce MetaKSSD, which redefines MarkerDB construction and metagenomic profiling using sketch operations, enhancing MarkerDB scalability and profiling performance. MetaKSSD encompasses 85,202 species in its MarkerDB using just 0.17 GB of storage and profiles 10 GB of data within seconds. Leveraging its comprehensive MarkerDB, MetaKSSD substantially improves profiling results. In a microbiome-phenotype association study, MetaKSSD identified more effective associations than MetaPhlAn4. We profiled 382,016 metagenomic runs using MetaKSSD, conducted extensive sample clustering analyses and suggested potential yet-to-be-discovered niches. MetaKSSD offers functionality for instantaneous searching of similar profiles. It enables the swift transmission of metagenome sketches over the network and real-time online metagenomic analysis, facilitating use by non-expert users.},
}

@article {pmid40883585,
year = {2025},
author = {Banerjee, A and Samanta, MK and Kanwar, M and Maiti, S and Mondal, KC and Thatoi, H and Das Mohapatra, PK},
title = {Characterization and Evolutionary Study of Fungal Nitrate Reductase Through Bioinformatics and Partial Gene Amplification from Aspergillus niger PKA16 employing Degenerate Primers.},
journal = {The protein journal},
volume = {},
number = {},
pages = {},
pmid = {40883585},
issn = {1875-8355},
support = {F.11-114/2008(BSR)//University Grants Commission/ ; },
abstract = {Nitrate contamination in water sources creates major health risks that primarily affect infants by causing methemoglobinemia ("blue baby syndrome") while also leading to congenital defects and cancer development. The human body absorbs nitrates mainly through drinking contaminated water. Enzyme nitrate reductase (NR) produced by microorganisms, functions as a key factor in nitrate detoxification. A partial NR gene (GenBank accession: MN833805) from Aspergillus niger PKA16 (KY907172.1) was amplified by employing degenerate primers in this research. The primer sequences were designed based on conserved protein motifs and orthologous diversity analysis of 399 NR protein sequences spanning 127 fungal genera. The NR proteins exhibited an extensive range which demonstrated extensive intra- and interspecies diversity. The multiple conserved domains included nine motifs which remained consistent despite the observed sequence variability. Two highly conserved sequences RLTGKHPFN and PDHGYPLRLV were validated through degenerate-PCR which demonstrated their effectiveness for partial NR gene detection and amplification. In the present study, the developed degenerate primers enable researchers to detect and amplify NR genes from majority of known and unknown fungal strains including those identified through metagenomic studies also. This research establishes fundamental principles for using biotechnology to amplify bioremediatory enzyme nitrate reductase from fungal origin to clean up water and food that contains nitrates, to reduce the risk of 'blue baby' disease and cancer.},
}

@article {pmid40883484,
year = {2025},
author = {Havenga, B and Jacobs, K},
title = {South African Myxococcota: an untapped resource for microbial ecolo gy and biotechnology.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {192},
pmid = {40883484},
issn = {1432-0614},
support = {PSTD23032387009//National Research Foundation/ ; },
mesh = {South Africa ; *Biotechnology/methods ; *Myxococcales/genetics/classification/metabolism/isolation & purification ; Secondary Metabolism ; Metagenomics ; Metagenome ; Genome, Bacterial ; },
abstract = {An extraordinary multicellular life cycle, ecological versatility, and prolific production of bioactive secondary metabolites characterise the phylum Myxococcota. While research has predominantly focused on Myxococcota in Asia, Europe, and North America, their potential occurrence in Sub-Saharan Africa remains largely unexplored. To date, only one study has isolated Myxococcota in South Africa, with additional findings limited to incidental detection through metagenomic studies. Considering South Africa's ecological diversity, its biomes may represent promising but under-examined environments for systematic bioprospecting aimed at discovering novel Myxococcota with ecological or biotechnological potential. The recent reclassification of Myxococcota from the former Deltaproteobacteria has provided a more coherent taxonomic framework to guide future ecological and systematic studies. This review presents an overview of the taxonomic revision and explores the potential occurrence of Myxococcota in South African biomes. It covers the challenges associated with conventional culture-based isolation methods and highlights potential genome- and metagenome-based approaches, including the use of metagenome-assembled genomes (MAGs) to identify cryptic biosynthetic gene clusters (BGCs), while acknowledging current limitations. Considering the increasing resistance to chemical fungicides in South African agriculture, this review further explores the potential of Myxococcota-derived secondary metabolites as candidate bioprotective alternatives. By identifying current research gaps, it aims to support future efforts towards systematic bioprospecting to investigate the ecological and biotechnological potential of Myxococcota in South Africa. KEY POINTS: • South African biomes may harbour novel Myxococcota with biosynthetic potential. • Genome mining could reveal cryptic biosynthetic gene clusters (BGCs). • Myxococcota metabolites may help control resistant fungal phytopathogens.},
}

South Africa
*Biotechnology/methods
*Myxococcales/genetics/classification/metabolism/isolation & purification
Secondary Metabolism
Metagenomics
Metagenome
Genome, Bacterial

@article {pmid40883419,
year = {2025},
author = {Oh, J and Voigt, AY},
title = {Author Correction: The human skin microbiome: from metagenomes to therapeutics.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41579-025-01238-y},
pmid = {40883419},
issn = {1740-1534},
}

@article {pmid40883413,
year = {2025},
author = {Manzoor, M and Pussinen, PJ and Saarela, RKT and Hiltunen, K and Mäntylä, P},
title = {Metagenomic analysis of the denture-associated oral microbiome in patients with denture stomatitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {31913},
pmid = {40883413},
issn = {2045-2322},
support = {1340750//Research Council of Finland/ ; },
mesh = {Humans ; Female ; Male ; *Stomatitis, Denture/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; Aged, 80 and over ; Aged ; *Mouth/microbiology ; Dysbiosis/microbiology ; *Dentures/microbiology ; Metagenome ; Bacteria/genetics/classification ; },
abstract = {Denture stomatitis (DS) is an inflammatory condition that affect denture wearers and is characterized by erythema of the mucosa opposing the denture. DS is often associated with oral microbiome dysbiosis. We used shotgun metagenomics to investigate the association between the denture-associated oral microbiome (DAOM) and DS in older adults living in long-term care facilities. We included participants with DS (n = 28) and age-and sex-matched removable denture wearers without signs of DS (n = 28). Clinical oral examinations were performed, and demographic and medical data were obtained from medical records. Median (interquartile range) age of participants was 88 (9) years; 75% were females. Beta diversity differed between the DS and non-DS groups (Bray-Curtis dissimilarity, p = 0.01; Jaccard index, p = 0.004). Two phyla, nine genera, and 15 species differed significantly between groups, with the genera Candida and Scardovia, and species Candida albicans, Aggregatibacter actinomycetemcomitans, and Scardovia inopinata being enriched in DS. Network analysis revealed strongly interconnected microbial communities and more prominent bacterial-fungal co-occurrence in DS than in non-DS. These findings indicate that DS is associated with significant alterations in the DAOM, which may contribute to inflammation. Microbiome-targeted strategies are needed for the management of DS.},
}

Humans
Female
Male
*Stomatitis, Denture/microbiology
*Metagenomics/methods
*Microbiota/genetics
Aged, 80 and over
Aged
*Mouth/microbiology
Dysbiosis/microbiology
*Dentures/microbiology
Metagenome
Bacteria/genetics/classification

@article {pmid40883363,
year = {2025},
author = {Xiong, X and Liu, S and Huang, J and Feng, L and Liu, W},
title = {236 metagenome-assembled microbial genomes from rivers along a latitudinal gradient.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1516},
pmid = {40883363},
issn = {2052-4463},
support = {U24A20641//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32401363//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023M733714//China Postdoctoral Science Foundation/ ; 2025AFB983//Natural Science Foundation of Hubei Province (Hubei Provincial Natural Science Foundation)/ ; },
mesh = {*Metagenome ; *Rivers/microbiology ; China ; Bacteria/genetics/classification ; Archaea/genetics ; Soil Microbiology ; Wetlands ; *Genome, Microbial ; },
abstract = {Rivers are dynamic ecosystems that play a crucial role in supporting microbial diversity and sustaining a wide range of ecological functions. Here, we used metagenomic sequencing datasets of channel sediments, riparian bulk soils, and riparian rhizosphere soils to construct metagenome-assembled genomes (MAGs) from 30 river wetlands along a latitudinal gradient in China. We identified 236 MAGs with completeness ≥ 50% and contamination ≤ 10%, including 225 bacteria and 11 archaea. Among these, 24.2% showed a completeness of 80% or higher. The dominant taxa were assigned to Pseudomonadota (78 MAGs), Actinomycetota (47 MAGs), and Bacteroidota (29 MAGs), which were particularly prevalent in riparian soils. These draft genomes provide valuable insights into microbial diversity and biogeochemical potential in river wetlands, enhancing our understanding of how microorganisms have evolved to adapt to the complex environments of rivers and latitudinal variation.},
}

*Metagenome
*Rivers/microbiology
China
Bacteria/genetics/classification
Archaea/genetics
Soil Microbiology
Wetlands
*Genome, Microbial

@article {pmid40883308,
year = {2025},
author = {Chen, T and Xiong, Y and Zhang, J and Zhang, Q and Wu, J and Xu, N and Liu, T},
title = {Temporal dynamics, microdiversity, and ecological functions of viral communities during cyanobacterial blooms in Lake Taihu.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {178},
pmid = {40883308},
issn = {2055-5008},
support = {20220808011114001//Shenzhen Natural Science Fund/ ; },
mesh = {*Lakes/microbiology/virology ; *Cyanobacteria/virology/growth & development ; *Viruses/classification/genetics/isolation & purification ; Metagenomics ; China ; Biodiversity ; Eutrophication ; *Harmful Algal Bloom ; *Virome ; },
abstract = {Harmful cyanobacterial blooms pose severe threats to aquatic ecosystems. Bloom-forming cyanobacteria form cyanobacterial aggregates (CAs) that create a phycosphere supporting diverse microbial interactions. Here, longitudinal metagenomics and metatranscriptomics were employed to explore the temporal variation of CA-attached viral communities throughout cyanobacterial blooms in Lake Taihu. Viral communities, represented by 5613 viral operational taxonomic units, showed increased relative abundance (RPKM) with the expansion of bloom areas. Among 1791 virus‒host linkages, host shifts followed the succession of two dominant cyanobacterial genera, Microcystis and Dolichospermum. Viruses demonstrated high virus‒host abundance ratios within all host genera and showed elevated transcriptional activities infecting Dolichospermum during the late bloom stage. Viruses featured high microdiversity and positively selected replication-associated genes in response to abundant host genera and variable trophic status. This study uncovered diverse active viral auxiliary metabolism associated with photosynthesis, biochemical cycling, and DNA biosynthesis, and highlighted the significant role of phycosphere-associated viruses during cyanobacterial blooms.},
}

*Lakes/microbiology/virology
*Cyanobacteria/virology/growth & development
*Viruses/classification/genetics/isolation & purification
Metagenomics
China
Biodiversity
Eutrophication
*Harmful Algal Bloom
*Virome

@article {pmid40883297,
year = {2025},
author = {Chen, XP and Zhu, D and Liu, SY and Sun, MM and Ye, M and Wang, L and Lin, D and Zhang, TL and Rillig, MC and Zhu, YG},
title = {Unique plastisphere viromes with habitat-dependent potential for modulating global methane cycle.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8098},
pmid = {40883297},
issn = {2041-1723},
support = {42021005//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Methane/metabolism ; *Microbiota/genetics ; *Ecosystem ; *Virome/genetics ; Metagenomics/methods ; Soil Microbiology ; Bacteria/metabolism/genetics/virology ; },
abstract = {Plastispheres, novel niches in the Anthropocene, harbor microbial communities with unique functional signatures. As the most abundant biological entity on Earth, viruses are key regulators of microbial community composition and metabolism. However, little is known about viral communities and their functions in the plastisphere. Here, we investigate the composition and functional profile of plastisphere viral communities through microcosm experiments combined with global plastisphere metagenomics data. We find that the plastisphere recruits a distinct viral community with 86.9% novel viral operational taxonomic units compared to control substrates. The plastisphere viral community modulates host methane metabolism through auxiliary metabolic genes and distinctive interactions with hosts. These auxiliary metabolic genes for methane cycling are prevalent in global plastisphere viral communities. Notably, the plastisphere microbiome adopts the life history strategy of copiotrophs in the nutrient-poor water environment, making the water plastisphere a potential hot spot for methane emission compared to the soil plastisphere. Our phage transplantation experiments reveal that lysogenic viruses significantly contribute to enhancing the methanogenic capacity of microorganisms and promoting methane emission of the water plastisphere. Overall, we decipher the role of viruses in the plastisphere and reinforce the necessity of incorporating viral contributions when assessing the effects of plastisphere communities on global biogeochemical cycles.},
}

*Methane/metabolism
*Microbiota/genetics
*Ecosystem
*Virome/genetics
Metagenomics/methods
Soil Microbiology
Bacteria/metabolism/genetics/virology

@article {pmid40882798,
year = {2025},
author = {Fu, Q and Yuan, B and Wang, XY and Luo, S and Zhang, XH and Zhang, MY},
title = {Behavioural response and physiological adaptation of captive sub-adult giant pandas in response to a short-term social environment.},
journal = {Physiology & behavior},
volume = {},
number = {},
pages = {115077},
doi = {10.1016/j.physbeh.2025.115077},
pmid = {40882798},
issn = {1873-507X},
abstract = {During ex-situ conservation, giant pandas inevitably transition from their natural wild habitats to captive environments. The living conditions of captive giant pandas differ significantly from those in the wild. For instance, during the sub-adult stage, solitary giant pandas are human-reared in groups. What impact does the captive social environment have on solitary giant pandas? Does it lead to changes in behavioral expression patterns? Is this pattern associated with physiological responses for environmental adaptation? To address these questions, we allocated six giant pandas into a group-housed group and a solitary-housed group, with each group consisting of three pandas. By observing their behaviors and performing analyses of urinary and fecal metabolomics, as well as metagenomics, we intended to explore the welfare status of the two groups under different management approaches. The results showed that group-housed sub-adult giant pandas exhibited significantly more playing behavior compared to those in solitary conditions. Further analysis revealed that the majority of the playing behavior involved playful interactions with companions. Additionally, we did not observe stereotyped behaviors in group-housed giant pandas. Through an exploration of the omics data, it was found that urinary metabolites associated with positive emotions, such as dopamine, along with related metabolic pathways like the dopamine synthesis system, were significantly upregulated and activated in group-housed giant pandas. Meanwhile, fecal metabolites associated with neurotransmitter synthesis and mood regulations, as well as the abundance of beneficial intestinal flora, were significantly higher in the feces of the group-housed pandas than those of the solitary-housed group. These findings indicated that short-term group housing does have an impact on the behavioral expression patterns of captive sub-adult giant pandas. Moreover, compared with those housed individually, short-term sub-adult giant pandas kept in groups seem to experience less stress. This reveals the behavioral response and physiological adaption of captive sub-adult giant pandas to group living environments.},
}

@article {pmid40882788,
year = {2025},
author = {Wu, J and Li, X and Huang, X and Zhu, Y and Yu, H and Xia, Y and Guo, S and Wang, X and Dong, T and Keung Tsim, KW and Zhu, Y},
title = {Kai-Xin-San, an ancient herbal mixture for anti-depression, mitigates the fluoxetine-induced gut dysbiosis and intestinal damage in chronic unpredictable mild stressed mice.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {120484},
doi = {10.1016/j.jep.2025.120484},
pmid = {40882788},
issn = {1872-7573},
abstract = {The gut microbiome plays a crucial role in the pathology of depression. The intestinal dysbiosis associated with prolonged use of antidepressants, such as fluoxetine, can adversely affect the efficacy of these medications. Kai-Xin-San (KXS), a traditional Chinese herbal decoction, has been utilized to treat mental disorders with a long history in China. The modulation of the gut microbiome by KXS could underlie its antidepressant effect. In the context of combining with fluoxetine, KXS could potentially mitigate fluoxetine-associated intestinal side effects during depression treatment.

AIM OF THE STUDY: This study investigates the impact of KXS on the gut of depressive mice, with a particular emphasis on its potential to mitigate fluoxetine-induced intestinal side effects.

MATERIALS AND METHODS: A high dose of fluoxetine was applied to the chronic unpredictable mild stress (CUMS)-induced mice, alone or in combination with KXS. Behavior tests were conducted to confirm the anti-depressant efficiencies. The feces of mice were collected and subjected to 16S rDNA and metagenomic sequencing. The gastrointestinal morphology and functions were assessed. The potential mechanistic action of KXS on alleviating the intestinal dysbiosis was probed.

RESULTS: Notable imbalance of microbiome and disruption of intestinal barrier were observed in CUMS mice. The intake of fluoxetine exacerbated the dysbiosis, as evidenced by the increased ratio of Firmicutes/Bacteroidetes and the elevated abundance of antibiotic-resistant genes in the gut microbiome. In addition, fluoxetine treatment further compromised the intestinal integrity and functions. Significantly, KXS treatment effectively mitigated the impairment of intestinal barrier induced by fluoxetine. These protective effects appeared to be mediated through multiple mechanisms, including the restoration of microbial homeostasis and the direct cytoprotective action on intestinal epithelial cells.

CONCLUSIONS: These findings particularly provide support for the combined usage of KXS and fluoxetine in depression treatment.},
}

@article {pmid40882565,
year = {2025},
author = {Cheng, S and Hu, Y and Gu, X and Xu, X and Duan, X and Li, X and Liu, Z and Jian, Q and Oleskowicz-Popiel, P and Shen, P and Zhou, A and Xue, G and Makinia, J},
title = {Magnetite-enhanced chain elongation via endogenous electron donors through a novel fungi-bacteria microbiome.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124478},
doi = {10.1016/j.watres.2025.124478},
pmid = {40882565},
issn = {1879-2448},
abstract = {Anaerobic fermentation of organic waste stream into medium-chain fatty acids (MCFA) through chain elongation (CE) has emerged as a sustainable and eco-friendly approach for resource recovery. Co-culture of yeast with chain elongator achieved a promising endogenous electron donor (ED)-driven CE but was limited by the weak yeast-bacteria synergy. This study presents a novel approach to optimizing the CE process through the regulation of magnetite (0-15 g/L). Results indicated that the 5 g/L of magnetite (Mag-5) achieved MCFA production at 8.42±0.67 g COD/L, which was 2.01 times greater than the blank. In-situ ethanol and lactate served as the ED to drive the CE. Under the optimal condition (Mag-5), Streptococcus (55.83%) and Candida (57.52%) were the dominant ED-producing microorganisms, and Clostridium_sensu_stricto_12 (22.70%) was the dominant chain elongator. In addition, metagenome analysis demonstrated the enhancement in reverse β-oxidization for MCFA production. Furthermore, the truncated tricarboxylic acid cycle was enhanced by magnetite amendment to provide more reduced energy, potentially accelerating the electron transfer within the mixed fungi-bacteria consortia. Finally, the constructed network of fungi and bacteria discerned the substrate competition between yeast and bacteria, and the cooperation among chain elongators, yeast, and mold. This study first proposed to regulate the mixed fungi-bacteria microbiome with magnetite to enhance the in-situ ED-driven CE process, providing a viable approach to the bioconversion of organic streams into high-value products.},
}

@article {pmid40882554,
year = {2025},
author = {Balamurugan, J and Jagadeesan, H and Vijayakumar, M},
title = {A metagenomic approach to predict the role of microbiome in a plant-microbe system for degrading the model azo dye methyl red.},
journal = {Journal of contaminant hydrology},
volume = {275},
number = {},
pages = {104703},
doi = {10.1016/j.jconhyd.2025.104703},
pmid = {40882554},
issn = {1873-6009},
abstract = {Azo dye contamination poses significant environmental challenges due to its persistence and toxicity. Plant-microbe integrated systems offer a sustainable solution for dye bioremediation, yet the functional roles of microbial communities and their interactions within community and with host plants during bioremediation remain underexplored. This study presents an integrated, multi omics approach to dissect the microbial diversity, functional potential, and plant-microbe interactions within a plant-microbe integrated bioremediation system for model azo dye, methyl red degradation. The microbial diversity of various organisms enriched under different treatment conditions for effective azo dye treatment was explored. A read-based approach using HUMAnN 3 pipeline was adopted to extract metabolic information from the shotgun metagenomic reads. Diversity analysis showed the enrichment of microorganisms capable of growing in the presence of the pollutant methyl red in an oligotrophic condition. The metabolic potential of the enriched organisms in dye removal was studied. Based on the enzymatic abundance, a pathway for the degradation of methyl red is proposed. Endophytic bacteria such as Klebsiella pneumoniae and Klebsiella varicola were responsible for encoding major dye-degrading enzymes in plant-integrated systems. In the plant-microbe integrated system both endophytic and intestinal microorganisms such as Kluyvera intestini and Escherichia coli are among the top 5 contributors of genes encoding downstream aromatic compound degradation enzymes. Notably Enterococcus casseliflavus showed highest enzyme abundance for azobenzene reductase in plant -microbe integrated strategy with 11.5-fold greater abundance than the treatment system containing only microbial inoculum. Metabolomics data from root exudates experiment revealed the role of root exudates in selective recruitment of microbial community. The role of biofilm and quorum sensing pathways in enhancing the bioremediation potential of the microbiome and the potential microbe-microbe and plant-microbe interaction was analysed. Deciphering the metabolic contribution of each microorganism and the microbiome as a whole is crucial to design engineered bioremediation systems. ENVIRONMENTAL IMPLICATIONS: Understanding the potential of microorganisms, their enrichments, and survival will help in designing specific consortia for effective degradation of pollutants. Metagenomic analysis reveal that the functional complementation in the microbiome is responsible for the pollutant degradation and the presence of plants through the root exudates, provide the nutrients lacking in the oligotrophic conditions observed in many waste streams, thereby enriching suitable microorganisms. This metagenomic study along with the metabolomics component, provides the justification for the efficiency of the plant microbe treatment of model dye methyl red and this could be exploited in real time situations.},
}

@article {pmid40882431,
year = {2025},
author = {Xu, Y and He, J and Jin, P and Fei, M and Cheng, S},
title = {Beyond the lungs: a case report of disseminated cutaneous aspergillosis highlighting clinical dilemmas in invasive fungal infections of critically ill patients.},
journal = {Journal de mycologie medicale},
volume = {35},
number = {4},
pages = {101573},
doi = {10.1016/j.mycmed.2025.101573},
pmid = {40882431},
issn = {1773-0449},
abstract = {With opportunistic fungal pathogens increasingly recognized as a global public health threat, the population at high risk for invasive fungal infections (IFIs) has expanded beyond traditionally immunocompromised individuals-such as those with malignancies, organ transplantation, diabetes mellitus, or acquired immunodeficiency syndrome (AIDS)-to include critically ill patients in intensive care units (ICUs) receiving invasive support and immunomodulatory therapies. Invasive aspergillosis (IA) is one of the most lethal opportunistic infections in this population, characterized by insidious onset, clinical heterogeneity, and a lack of specific signs, often resulting in delayed diagnosis. Disseminated or breakthrough aspergillosis carries an exceedingly high mortality rate. We report the case of a female patient admitted to the ICU with fulminant myocarditis who required extracorporeal membrane oxygenation (ECMO), continuous renal replacement therapy (CRRT), and immunomodulation. Her hospitalization was complicated by a progressive pulmonary infection, and metagenomic next-generation sequencing (mNGS) of respiratory specimens identified Candida albicans, Aspergillus spp. and Staphylococcus hominis, prompting an adjustment in antimicrobial therapy. Subsequently, the patient developed multiple cutaneous nodules, which tissue biopsy and mNGS confirmed as invasive cutaneous aspergillosis. Despite aggressive antifungal treatment with isavuconazole and amphotericin B, her condition deteriorated rapidly, leading to disseminated cutaneous necrosis, irreversible septic shock and multiorgan failure. This case highlights the clinical importance of recognizing atypical IFI presentations. Heightened clinical suspicion for disseminated fungal disease is warranted in critically ill patients with extrapulmonary lesions. Prompt microbiological diagnosis and antifungal resistance surveillance are essential for effective antifungal therapy.},
}

@article {pmid40882424,
year = {2025},
author = {Zheng, Z and Li, X and Huang, S and Wang, X and Jia, X and Wang, H and Zhou, J and Ma, L},
title = {Novel insights into microbial strategies for antimony (Sb) transformation coupled with carbon utilization in groundwater ecosystem.},
journal = {Environment international},
volume = {203},
number = {},
pages = {109752},
doi = {10.1016/j.envint.2025.109752},
pmid = {40882424},
issn = {1873-6750},
abstract = {Microbial-mediated antimony (Sb) metabolism and its coupling with bio-essential elements cycles are not only crucial to the biogeochemistry of Sb-contaminated groundwater but also have potential implications for human health. However, the ways in which Sb contamination affects microbial carbon, nitrogen, and sulfur metabolism, particularly carbon-utilization strategies, remain poorly understood and lack direct experimental confirmation. Herein, well and spring water samples were collected from the Xikuangshan (XKS) mine to investigate microbial responses and functional adaptations. The results showed that microbial communities in well and spring became similar during the wet season, with total Sb identified as a major shaping force in this complex environment. Communities in low-Sb samples harbored a higher potential functional diversity, whereas those in high-Sb samples exhibited convergent metabolic potential, with enrichment in genes for pyruvate metabolism. Metagenome-assembled genomes (MAGs) in low-Sb samples harbored more pathways for inorganic carbon utilization, including cynT, pycA, PRK, rbcL, and rbcS genes, primarily derived from the phyla Bdellovibrionota and Eremiobacterota. Microcosm cultivation confirmed a preference for inorganic carbon (NaHCO3) in low-Sb samples and organic carbon sources (pyruvate) in high-Sb samples. These findings provide new genomic insights and experimental evidence for the coupling between Sb transformation and carbon utilization in contaminated aquifers.},
}

@article {pmid40882374,
year = {2025},
author = {Chen, Y and Zhang, Y and Li, J and Li, Y and Chen, Z and Qin, J and Deng, Z and Wang, X},
title = {Fe(Ⅱ)-mediated detoxification mitigates low-dose rare earth elements-induced stress on anammox consortia for mining tailwater treatment.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139681},
doi = {10.1016/j.jhazmat.2025.139681},
pmid = {40882374},
issn = {1873-3336},
abstract = {Rare earth mining activities cause severe nitrogen pollution in watersheds, yet the residual hazardous rare earth elements (REEs) toxicity in tailings wastewater challenges biological nitrogen removal technology. This work demonstrated that introducing low-dose Fe(II) into partial denitrification/anammox (PD/A) system significantly alleviated REEs-induced stress on anammox consortia via detoxification and physical barrier reinforcement. The PD/A bioreactor with 15 mg/L Fe(II) (R1) was compared against a control without Fe(II) for real rare earth tailings wastewater treatment. Metagenomic analysis identified 1.14-fold upregulation of hydrazine (N2H4) dehydrogenase alongside substantial 5.82-fold downregulation of N2H4 synthase in R1, indicating a critical metabolic reconfiguration that expedited the degradation of toxic intermediates and alleviated REEs-mediated cytotoxicity. Electrons with lower redox potential released from N2H4 oxidation were more effectively utilized for carbon fixation, as evidenced by the upregulated electron transport complexes and Wood-Ljungdahl pathway. Concurrent biosynthetic modulation stimulated lipopolysaccharide production (module M00063) and carbohydrate storage (module M00064), collectively reinforcing microbial stress resilience through both defensive metabolites (lipopolysaccharides and trehalose) and hydrophobicity-driven aggregation. Moreover, modified 2-P logistic modeling confirmed elevated REEs inhibition thresholds under Fe(II) mediation. This study reveals the defense mechanism of Fe(II)-enhanced anammox consortia against REEs stress, providing new insights for sustainable bioremediation in rare earth mining areas.},
}

@article {pmid40882289,
year = {2025},
author = {Bature, I and Liang, Z and Xiaohu, W and Yang, F and Yang, Y and Dong, P and Ding, X},
title = {Isolation, cloning, and characterization of a novel GH5 cellulase from yak rumen metagenome for enhanced lignocellulose hydrolysis in biofuel production and ruminant feed utilization.},
journal = {Enzyme and microbial technology},
volume = {191},
number = {},
pages = {110737},
doi = {10.1016/j.enzmictec.2025.110737},
pmid = {40882289},
issn = {1879-0909},
abstract = {Lignocellulosic biomass is a promising feedstock for biofuel production, but its complex structure, including cellulose and hemicellulose, challenges efficient enzymatic hydrolysis. CelyA, a novel cellulase from the yak rumen, has potential for improving biomass degradation and biofuel production. The CelyA gene was cloned, expressed, and purified. Biochemical characterization included assessments of pH, temperature, and salt tolerance. The enzyme's substrate specificity was tested on crystalline cellulose, CMC, and other polysaccharides. In vitro rumen fermentation was performed to evaluate its effect on fiber digestibility and microbial community composition. Biofuel production was tested by hydrolyzing maize, rice, and wheat straw. CelyA demonstrated optimal activity at pH 6.0 and 40.0 °C and maintained moderate stability across a wide pH range (3.0-12.0), retaining measurable activity even under strongly acidic and alkaline conditions. The enzyme demonstrated excellent salt tolerance, retaining 91.0 % activity in 1.0 M NaCl. CelyA efficiently degraded maize straw in hydrolysis assays, producing 7.2 µmol/L of reducing sugars. In vitro rumen fermentation with CelyA increased fiber digestibility by 8.3 % for maize straw, 14.5 % for rice straw, and 2.7 % for wheat straw. Gas production also increased significantly, with maize straw showing a 91.3 % increase. 16S rRNA sequencing revealed selective enrichment of Ruminococcus and Prevotella, key cellulolytic microbes. CelyA demonstrates strong potential for biofuel production, efficiently hydrolyzing lignocellulosic biomass and enhancing ruminal fiber digestibility. Its stability, salt tolerance, and substrate specificity make it a valuable enzyme for biofuel production and livestock feed optimization.},
}

@article {pmid40882272,
year = {2025},
author = {Wang, K and Xu, J and Luo, X and Yu, Z and Tang, A and Peng, K and Song, J and Chen, X and Ren, M},
title = {Insights into microalgal-bacterial consortia in sustaining denitrification via algal-derived organic matter in harsh low-C/N wastewater.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127108},
doi = {10.1016/j.jenvman.2025.127108},
pmid = {40882272},
issn = {1095-8630},
abstract = {Conventional nitrate removal processes are often hampered by insufficient carbon sources for remediating low-C/N wastewater. Herein, a microalgal-bacterial (MB) consortia system was constructed to leverage algal-derived organic matter for sustaining denitrification. The system demonstrated superior nitrate removal performance when assisted by algal-derived organic matter, achieving a 168.62 ± 4.17 % enhancement in nitrate removal capacity compared to the sole bacterial system. Furthermore, Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) analysis of algal-derived organic matter revealed that specific components facilitating nitrate elimination included unsaturated aliphatic compounds, aliphatic/peptide-like/amino sugars, lignin-like, and tannin-like substances. Notably, the consortia showed preferential utilization of unsaturated aliphatic (35.21 %) and aliphatic/amino sugars over aliphatic/peptide-like/amino acids (31.05 %) and aliphatic/peptide-like compounds (31.31 %) within the CHO, CHON, CHON2, and CHON3 classes, respectively. Metagenomic analysis identified notable disparities in microbial community composition between the bacterial and MB consortia systems. Moreover, the MB consortia exhibited higher abundances of genes encoding nitrate removal enzymes, including those involved in denitrification, assimilatory/dissimilatory reduction, and L-glutamate synthesis pathways. Genes associated with lignin degradation were also detected, suggesting potential indirect contributions to nitrate elimination. Besides, the MB symbiotic microspheres were successfully fabricated and achieved efficient nitrate removal. These findings provide novel insights into the development of innovative MB symbiotic systems for nitrate removal under harsh carbon-limited conditions.},
}

@article {pmid40882267,
year = {2025},
author = {Davis, BC and Linz, D and McMinn, BR and Korajkic, A},
title = {Limited ARG removal but stable resistome dynamics in a surface flow constructed wetland.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126986},
doi = {10.1016/j.jenvman.2025.126986},
pmid = {40882267},
issn = {1095-8630},
abstract = {Improperly treated wastewater and surface runoff can degrade water quality by introducing microbial contaminants, including antibiotic-resistant bacteria (ARB) and their genes (ARGs). Constructed treatment wetlands (CTWs) offer a low-resource solution for managing impaired watersheds. However, their ability to mitigate microbial contaminants, particularly ARGs, requires further study. In this study, 62 water samples from Banklick Creek CTW (BCTW) were shotgun sequenced to assess ARG dynamics and removal characteristics. Results showed minimal resistome attenuation, likely due to the wetland's horizontal surface flow design with short, variable hydraulic residence times (0.48-3.1 days). Despite this, 198 low-abundance ARGs were removed, accounting for a median of 0.52 % (0-3.1 %) of total ARG abundance upstream. The core resistome, comprising 95.6 ± 1.9 % of total ARG abundance, was stable and mainly consisted of multidrug efflux systems carried by bacterioplankton and macrophyte symbionts, indicating a native resistome reflective of regional pollution history. Resistome and microbiome structures were highly correlated (R[2] = 0.808), with ARGs rarely co-occurring with mobile genetic elements, indicating limited intercellular transfer potential. No significant correlations were found between resistome dynamics and human fecal (HF183, crAssphage) or avian (GFD) biomarkers. Although several class-one integron-integrase (intI1) contigs were enriched in treatment channels, gene cassette cargo was void of ARGs. As detection of intI1 via qPCR is generally considered indicative of resistome mobility potential, this finding carries important implication for intI1 qPCR assay selection (i.e., targeting clinical intI1 mosaics) and over-interpretation of ARG spread in the environment.},
}

@article {pmid40881965,
year = {2024},
author = {Fox, JD and Sims, A and Ross, M and Bettag, J and Wilder, A and Natrop, D and Borsotti, A and Kolli, S and Mehta, S and Verma, H and Kurashima, K and Manithody, C and Verma, A and Jain, A},
title = {Bioinformatic Methodologies in Assessing Gut Microbiota.},
journal = {Microbiology research},
volume = {15},
number = {4},
pages = {2554-2574},
doi = {10.3390/microbiolres15040170},
pmid = {40881965},
issn = {2036-7473},
abstract = {Bioinformatic methodologies play a crucial role in the assessment of gut microbiota, offering advanced tools for analyzing complex microbial communities. These methodologies involve high-throughput sequencing technologies, such as 16S rRNA gene sequencing and metagenomics, which generate vast amounts of data on microbial diversity and functional potential, as well as whole-genome sequencing, which, while being more costly, has a more expansive potential. Bioinformatics tools and algorithms process these data to identify microbial taxa and quantify and elucidate their roles within the microbiome. Advanced statistical and computational models further enable the identification of microbiota patterns associated with various diseases and health conditions. Overall, bioinformatic approaches are essential for deciphering the complexities of gut microbiota so that, in the future, we may be able to discover treatments and technologies aimed at restoring or optimizing the microbiome. The goal of this review is to describe the differences in methodology and utilization of 16S versus whole-genome sequencing to address the increased understanding of the role that the gut microbiome plays in human physiology and pathology.},
}

@article {pmid40881292,
year = {2025},
author = {Daddy Gaoh, S and Alusta, P and Lee, YJ and Hussong, D and Marasa, B and Ahn, Y},
title = {A metagenomic analysis coupled with oligotrophic enrichment approach for detecting specified microorganisms in potable groundwater samples.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1645324},
doi = {10.3389/fmicb.2025.1645324},
pmid = {40881292},
issn = {1664-302X},
abstract = {In pharmaceutical manufacturing, there is a significant need for the detection and identification of specified microorganisms (i.e., Burkholderia cepacia complex (BCC), E. coli, Pseudomonas aeruginosa, Salmonella enterica, Staphylococcus aureus, Clostridium sporogenes, Candida albicans, and Mycoplasma), which are often missed or not identified by traditional culture-dependent methods. We employed a metagenomic analysis coupled with oligotrophic enrichment to identify specified microorganisms and evaluate tryptic soy broth (TSB) and 1/10 strength TSB for the recovery of specific microorganisms in potable groundwater samples. A total of 589-996 genera were identified in 12 water samples taken from a cold water fountain, with Bacillus spp. (97%) in TSB and Stenotrophomonas spp. (97%) in 1/10 strength TSB, representing the primary recovered genera after a 72-h pre-enrichment at 23°C. Likewise, we also detected lower abundance of specific organisms, Clostridium spp., Burkholderia spp., and Staphylococcus spp. (0.04-0.07%) in TSB and Burkholderia spp., Pseudomonas spp., Salmonella spp., Staphylococcus spp. and Escherichia spp. (0.01-1.73%) in 1/10 strength TSB. Co-inoculation with Burkholderia cepacia complex (BCC) yielded a higher recovery rate of Pseudomonas spp. compared to uninoculated controls in 1/10 strength TSB. Further functional analyses indicated that, toluene degradation (PWY-5180 and PWY-5182) was chiefly contributed by BCC in co-cultures of TSB + BCC-24 h and TSB + BCC-48 h. Our results demonstrate the potential value of the metagenomic approach during enrichment in detecting specified microorganisms, including oligotrophs such as BCC in non-sterile pharmaceutical products.},
}

@article {pmid40880127,
year = {2025},
author = {Milnitsky, BP and Junior, HLP and Chaúque, BJM and Corção, G},
title = {Successful establishment of a model of the piglet gastrointestinal microbiota and its' modulation by prebiotics.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf216},
pmid = {40880127},
issn = {1365-2672},
abstract = {AIMS: This study proposed an in-house in vitro model to investigate the effects of two prebiotic treatments on the gastrointestinal microbiota of piglets.

METHODS AND RESULTS: The model involved suspending piglet feces in a culture medium to simulate the ileum and proximal colon regions of the swine gastrointestinal tract. The prebiotics tested were mannanoligosaccharides (MOS) and sodium butyrate. Metabarcoding and culturomics were used to assess the impact of prebiotics on bacterial species composition. Minimum inhibitory concentration tests were conducted to examine bacterial susceptibility patterns. Key bacterial phyla identified included Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Culturomics detected families and several species not identified by metabarcoding. In the simulated proximal colon, MOS increased the abundance of certain species and reduced bacteria with type I fimbriae. Butyric acid promoted beneficial host-associated bacteria and decreased pathogenic species. However, the prebiotics did not significantly affect bacterial susceptibility to antibiotics.

CONCLUSION: The in-house model successfully mimicked piglet intestinal microbiota, allowing for detailed analysis. Both prebiotics positively influenced the piglets microbiota, providing insights into how these treatments potentially influenced the microbiota.},
}

@article {pmid40880079,
year = {2025},
author = {Tang, Y and Oliver, A and Alkan, Z and Korf, I and Huang, L and Kable, ME and Lemay, DG},
title = {Association of lactose intake and lactase persistence genotype with microbial taxa and function in healthy multi-ethnic U.S. adults.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01640a},
pmid = {40880079},
issn = {2042-650X},
abstract = {Lactase persistence is a genetically inherited trait that enables continued lactose digestion into adulthood. Lactase non-persistence (LNP) individuals often experience incomplete lactose digestion, allowing undigested lactose to reach the colon, where it may shape microbial composition and function. We investigated the relationship between the lactase persistence (LP) genotype, lactose consumption, and the taxonomic and functional profiles of the fecal microbiome. Participants from the USDA Nutritional Phenotyping Study, a cross-sectional observational study designed to assess how dietary factors impact human health, whose fecal microbiome profile was measured using shotgun metagenomic sequencing (n = 330) were included in this analysis. Fecal SCFA levels were measured using GC-MS. Fecal microbiome taxonomy and gene abundance were quantified using shotgun metagenomic sequencing. Lactose consumption and yogurt intake were estimated based on Automated Self-Administered 24h Dietary Assessment Tool (ASA24®) dietary recalls or Food Frequency Questionnaire. The LP/LNP genotype was determined by a single nucleotide polymorphism (SNP ID: rs4988235). Several genera of lactic acid bacteria (Veillonella, Lactobacillus, Lacticaseibacillus, and Lactococcus) were differentially abundant between recent high-lactose consuming (>10.0 g lactose per day) and low-lactose consuming (<3.3 g lactose per day) individuals. Among the LNP participants who self-identified as Caucasian or Hispanic, high-lactose consumers (>10.0 g per day via 24-h recall) had significantly higher relative abundances of lactic acid bacteria and lactate-utilizing bacteria (Lacticaseibacillus, Lactobacillus, Megamonas, and Veillonella) than low-lactose consumers (<3.3 g per day). Independent of lactose intake, LNP participants had a higher abundance of fecal microbial β-galactosidase genes than LP participants. Among the LNP participants, those with high recent lactose consumption also showed a significant shift towards more fecal propionate. The abundance of the yogurt-associated microbe, Streptococcus thermophilus, was positively associated with yogurt intake independent of the genotype. Alternative milk consumption was significantly negatively associated with fecal SCFAs both in the full cohort and the Caucasian/Hispanic subset, regardless of the genotype. Our results suggest that functional and persistent host lactase enzymes may work to competitively exclude lactic acid bacteria, contributing to a smaller realized niche for lactic acid bacteria in LP individuals compared to LNP individuals. However, regardless of the host genotype, consumption of alternative milk may be associated with reduced production of health-promoting intestinal metabolites, such as SCFAs.},
}

@article {pmid40879860,
year = {2025},
author = {Liu, Y and Wang, Q and Zhang, Y and Duo, R and Bian, X and Tian, J and Hao, J and Zheng, J and Shen, H},
title = {Multi-omics characterization of gut microbiota and fecal and plasma metabolites in patients with primary Sjögren's syndrome.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {40879860},
issn = {1434-9949},
support = {CY2021-QN-A10//the Cuiying Scientific and Technological Innovation Program of Lanzhou University Second Hospital/ ; 2022-ZD-101//Science and Technology Program of Lanzhou city/ ; GSWSKY2023-08//Health Industry Scientific Research Project of Gansu Province/ ; },
abstract = {INTRODUCTION: Accumulating evidence has implicated gut microbiota and their metabolites in primary Sjögren's syndrome (pSS) pathogenesis. However, no study simultaneously explores the gut microbiome, microbial, and plasma metabolome in pSS patients.

METHOD: Thirty pSS patients and 60 healthy controls (HCs) were recruited. Shotgun metagenomic sequencing and untargeted metabolomics were performed on stool and plasma samples.

RESULTS: pSS patients exhibited significant reduction in microbial richness and diversity. Bacteroidetes and Firmicutes accounted for over 80% of all phyla. Four phyla, 48 genera, and 106 species with significant differences were identified (P < 0.05). Proteobacteria, Ascomycota, Fusobacteria, and 31 genera (e.g., Escherichia, Veillonella, Prevotella, Klebsiella) were enriched in pSS, while Actinobacteria, Bifidobacterium, Dorea, and Blautia were depleted. Opportunistic pathogens (e.g., Escherichia coli, Prevotella copri, Streptococcus oralis, Klebsiella pneumoniae, Enterococcus faecalis) and pathogenic Clostridium bolteae and Fusobacterium nucleatum were more abundant in pSS, whereas beneficial Bifidobacterium longum and butyrate-producing Eubacterium hallii and Anaerostipes hadrus were in HCs. Notably, Lactobacillus spp. were enriched in pSS. Of 298 differential functional pathways, 239 pSS-enriched pathways were focused on nutrient and energy metabolism, while amino acid biosynthesis in HCs. During 881 differential fecal metabolites (pSS: HCs = 631:250), fatty acyls were enriched in pSS, and glycerophospholipids in HCs. Among the 712 differential plasma metabolites (pSS: HCs = 438:274), heterocyclic compounds and benzene derivatives were more abundant in pSS, while fatty acyls and glycerophospholipids prevailed in HCs. Amino acids and organic acids were predominant in both samples.

CONCLUSIONS: This study characterized gut microbiome and fecal/plasma metabolome in pSS patients, providing theoretical support for regional pSS prevention and treatment. Key Points • This is the first study to systematically characterize the gut microbiome and fecal and plasma metabolomes of primary Sjögren's syndrome (pSS) patients in Northwest China via multi-omics integration analysis. • Significant reduction in gut microbial diversity and probiotic bacteria, enrichment of opportunistic and infectious pathogens, and microbial dysfunction were observed in pSS patients. • Much more differential fecal and plasma metabolites were observed in pSS patients, with amino acids, organic acids and derivatives, nucleotides, and metabolites being the main altered metabolites in both samples.},
}

@article {pmid40879375,
year = {2025},
author = {Munguti, F and Nyaboga, EN and Holton, T and Kreuze, J and Maina, S},
title = {Genomics insight on passion fruit viral disease complexity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0034425},
doi = {10.1128/spectrum.00344-25},
pmid = {40879375},
issn = {2165-0497},
abstract = {Passion fruit viral diseases pose a significant threat to Kenya's passion fruit industry. To unravel the complexity of these diseases, comprehensive virus surveys were conducted across major passion fruit-growing counties. Passion fruit woodiness disease symptoms, like fruit hardening, chlorotic mottling, and leaf distortion, were prevalent. The study unveiled the first 23 complete genomes of Ugandan passiflora virus (UPV) and two East Asian passiflora distortion virus (EAPDV) in Kenya. UPV showed 99% nucleotide (nt) match to a UPV genome from Uganda and 66% nt identity match to EAPDV. In addition, UPV variants and two partial passion fruit green spot virus sequences and partial (passiflora emaravirus) segment RNA1-5 (novel allexivirus and an emaravirus, respectively) were detected. Phylogenetic analysis revealed distinct lineages (I-III), indicating potential multiple introductions into Kenya. Recombination analysis detected no significant breakpoints. However, the study proposed the renaming of EAPDV to passiflora distortion virus (PDV) and UPV to passiflora virus (PV) for neutral nomenclature, without geographical association. Additionally, the study highlighted the role of coinfections in symptom expression, suggesting a potential synergistic relationship between PV, PDV, and other viruses. The results recommend stringent management strategies and enhanced surveillance to mitigate the economic impact of these viruses on the Kenyan passion fruit industry. The findings from this study underscore the need to strengthen nursery certification programs and pest diagnostic protocols in Kenya. Additionally, enhanced pest surveillance and import regulations are critical to preventing the introduction and spread of emerging plant viral diseases, thereby safeguarding the country's horticultural productivity and biosecurity. To our knowledge, this is the first comprehensive study of viral diseases of passion fruit in Kenya.IMPORTANCEThis study presents the first comprehensive survey of viral pathogens affecting passion fruit in Kenya, identifying Ugandan passiflora virus (UPV) and East Asian passiflora distortion virus (EAPDV) as major contributors. Through genomic sequencing, 23 complete genomes of UPV and two of EAPDV were characterized, revealing a 99% nucleotide (nt) similarity between UPV strains from Uganda and Kenya, and 66% nt match with EAPDV. Phylogenetic analysis identified distinct lineages, suggesting possible multiple viral introductions in Kenya. The study also highlights potential synergistic coinfections between UPV, EAPDV, and other viruses, leading to more severe disease symptoms. In light of these findings, the study proposes renaming EAPDV as passiflora distortion virus and UPV as passiflora virus for a more neutral name classification. The research underscores the urgent need for enhanced surveillance, stringent phytosanitary measures, and improved management strategies to mitigate the threat of viral diseases, to safeguard the Kenyan passion fruit industry, and elsewhere.},
}