@article {pmid41345261,
year = {2025},
author = {Ma, J and Kim, N and Cha, JH and Kim, W and Kim, CY and Lee, YH and Kim, HS and Han, YD and Yong, D and Han, E and Yang, S and Beck, S and Lee, I},
title = {A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41345261},
issn = {2058-5276},
support = {2022M3A9F3016364//National Research Foundation of Korea (NRF)/ ; 2022R1A2C1092062//National Research Foundation of Korea (NRF)/ ; },
abstract = {Understanding the human gut microbiome requires comprehensive genomic catalogues, yet many lack geographic diversity and contain medium-quality metagenome-assembled genomes (MAGs) missing up to 50% of genomic regions, potentially distorting functional insights. Here we describe an enhanced Human Reference Gut Microbiome (HRGM2) resource, a catalogue of near-complete MAGs (≥90% completeness, ≤5% contamination) and isolate genomes. HRGM2 comprises 155,211 non-redundant near-complete genomes from 4,824 prokaryotic species across 41 countries, representing a 66% increase in genome count and a 50% boost in species diversity compared to the Unified Human Gastrointestinal Genome catalogue. It enabled improved DNA-based species profiling, resolution of strain heterogeneity and survey of the human gut resistome. The exclusive use of these genomes improved metabolic capacity assessment, enabling high-confidence, automated genome-scale metabolic models of the entire microbiota and revealing disease-associated microbial metabolic interactions. This resource will facilitate reliable functional insights into gut microbiomes.},
}

@article {pmid41345243,
year = {2025},
author = {Ste Marie, J and Mays, C and Guo, B and Radniecki, TS and Waite-Cusic, J and Navab-Daneshmand, T},
title = {Longitudinal replicated metagenomic analysis of biosolids-amended soils reveals enrichment of ARGs, virulence factors, and ESKAPE pathogens.},
journal = {npj antimicrobials and resistance},
volume = {3},
number = {1},
pages = {96},
pmid = {41345243},
issn = {2731-8745},
support = {2018-67017-27631//USDA National Institute of Food and Agriculture, Agricultural and Food Research Initiative Competitive Program, Agriculture Economics and Rural Communities/ ; },
abstract = {Biosolids land application introduces antibiotic resistance genes (ARGs) and clinically relevant pathogens into agricultural soils, raising concerns about long-term environmental and public health impacts. Despite growing interest in biosolids reuse, there remains a critical need for replicated, longitudinal studies to assess how biosolids amendments shape soil microbiomes and resistomes during crop cultivation. In this replicated longitudinal greenhouse study, we used shotgun metagenomics to characterize the impact of biosolids amendment on the soil microbiome, resistome, virulence factors, and ESKAPE pathogens during carrot cultivation. Biosolids-amended soils exhibited increased richness of microbial genera (e.g., Rhodanobacter, Dyella, and Thermomonas), ARG subtypes (resistance to sulfonamide, tetracycline, fosmidomycin, and macrolides), and virulence factors compared to pristine controls. Notably, all six ESKAPE pathogens, including Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp., were detected at elevated relative abundances (1.4- and 3.4-fold) in biosolids-amended soils and remained detectable throughout the 11-week cultivation period. Network analysis revealed statistically supported co-occurrences between microbial taxa and ARGs (with resistance to tetracyclines, beta-lactams, chloramphenicol, and multidrugs), suggesting possible host associations. These findings underscore the ecological and clinical relevance of biosolids amendment and highlight the need for integrated surveillance frameworks to mitigate antimicrobial resistance dissemination in agricultural environments.},
}

@article {pmid41345146,
year = {2025},
author = {Kar, S and Reddy, MK and Asthana, R and Srivastava, P and Dhaarani, R and Reddy, KVNS and Meghamala, V and Koduru, JR and Karri, RR},
title = {Synergistic effects of syzygium cumini sawdust biochar and poultry manure on soil quality enhancement, nitrogen, organic carbon dynamics, and Amaranthus cruentus growth.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-25003-6},
pmid = {41345146},
issn = {2045-2322},
support = {Ref. No-2022/0149//GITAM Research Seed Grants/ ; },
abstract = {The study aimed to evaluate the potential of incorporating biochar with poultry manure to address the constant challenges of sandy, loam soils due to poor water retention and low soil fertility, and their influence on the growth and yield of Amaranthus cruentus during the Rabi and Kharif seasons. The combined effect of manures on soil health over different seasons was unexplored, so the current research has been taken up to understand the impact of different treatments on physical, chemical, and microbial dynamics in the Rabi and Kharif seasons. Advanced statistical analysis was used to measure the soil and plant factor variations across seasons. Pre- and post-harvest results showed substantial progress in the soil bulk density, water-holding capacity (WHC), and nutrient retention in KR5 (biochar + poultry manure) treatment, where WHC displayed a strong positive correlation with organic matter (r > 0.82). Even chemical analysis indicated increased soil nitrogen, phosphorus, potassium, and carbon levels. Metagenomic analysis implied microbial diversity and abundance promoting nitrogen fixation and decomposition of organic matter. FTIR and SEM also revealed structural improvements that are beneficial for microbial colonization and nutrient retention. The combination of biochar and poultry manure showed higher growth, increasing plant height by 40 cm and yielding over 550 g/m[2] during the Kharif season. The results have revealed that the combination of biochar and poultry manure has improved soil fertility, microbial diversity, and yield of Amaranthus cruentus grown in sandy loam soils.},
}

@article {pmid41345123,
year = {2025},
author = {Tucker, SJ and Füssel, J and Freel, KC and Kiefl, E and Freel, EB and Ramfelt, O and Sullivan, CES and Gajigan, AP and Mochimaru, H and de Souza, MR and Quinn, M and Ratum, C and Tran, LL and Sobczyk, M and Miller, SE and Trigodet, F and Lolans, K and Morrison, HG and Fallon, B and Huettel, B and Pan, T and Rappé, MS and Eren, AM},
title = {A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1913},
pmid = {41345123},
issn = {2052-4463},
support = {687269//Simons Foundation/ ; 989028//Simons Foundation/ ; 989028//Simons Foundation/ ; 2019589//NSF | GEO | Division of Ocean Sciences (OCE)/ ; },
mesh = {*Metagenome ; Pacific Ocean ; *Transcriptome ; *RNA, Transfer/genetics ; *Seawater/microbiology ; Ecosystem ; Microbiota ; },
abstract = {The roles of marine microbes in ecosystem processes are inherently linked to their ability to sense, respond, and ultimately adapt to environmental change. Capturing the nuances of this perpetual dialogue and its long-term implications requires insight into the subtle drivers of microbial responses to environmental change that are most accessible at the shortest scales of time. Here, we present a multi-omics dataset comprising surface ocean metagenomes, metatranscriptomes, tRNA transcripts, and biogeochemical measurements, collected every 1.5 hours for 48 hours at two stations within coastal and adjacent offshore waters of the tropical Pacific Ocean. We expect that this integrated dataset of multiple sequence types and environmental parameters will facilitate novel insights into microbial ecology, microbial physiology, and ocean biogeochemistry and help investigate the different mechanisms of adaptation that drive microbial responses to environmental change.},
}

*Metagenome
Pacific Ocean
*Transcriptome
*RNA, Transfer/genetics
*Seawater/microbiology
Ecosystem
Microbiota

@article {pmid41345120,
year = {2025},
author = {Abad-Recio, IL and Rubel, V and Filker, S and Garate, L and Stoeck, T and Logares, R and Lanzén, A},
title = {The Basque Coast Estuarine Sediment Gene Catalogue.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1909},
pmid = {41345120},
issn = {2052-4463},
support = {Fi 2089/3-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; STO 414/19-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Estuaries ; *Geologic Sediments/microbiology ; Archaea/genetics ; Metagenomics ; Bacteria/genetics ; Biodiversity ; Ecosystem ; Eukaryota/genetics ; Viruses/genetics ; },
abstract = {Estuaries are critical transition zones that link marine, riverine, and terrestrial ecosystems, including habitats like intertidal mudflats and tidal marshes. These ecosystems are biodiversity hotspots providing essential ecological functions such as nutrient cycling and pollutant removal. Despite their importance, there is a significant knowledge gap regarding the ecological functioning of these habitats and how they are impacted by anthropogenic pressures. From intertidal estuarine benthos along the Basque Coast 92 microbial metagenomic assemblies were retrieved that allowed us to reconstruct 390 medium plus 81 high quality MAGs, along with 108 million putative genes from bacteria, archaea, eukaryotes, and viruses. This unique dataset will enhance our understanding of ecosystem functioning, biodiversity, and be useful to reveal biogeochemical processes and the role of unculturable biomass.},
}

*Estuaries
*Geologic Sediments/microbiology
Archaea/genetics
Metagenomics
Bacteria/genetics
Biodiversity
Ecosystem
Eukaryota/genetics
Viruses/genetics

@article {pmid41345102,
year = {2025},
author = {Pope, R and Visconti, A and Zhang, X and Louca, P and Baleanu, AF and Lin, Y and Asnicar, F and Bermingham, K and Wong, KE and Michelotti, GA and Wolf, J and Segata, N and Berry, SE and Spector, TD and Leeming, ER and Gibson, R and Menni, C and Falchi, M},
title = {Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10051},
pmid = {41345102},
issn = {2041-1723},
support = {27/2023//Chronic Disease Research Foundation (CDRF)/ ; },
mesh = {Humans ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome/physiology ; *Diet ; Male ; Female ; Metabolome ; Middle Aged ; Metabolomics/methods ; Aged ; Metagenomics ; Adult ; Machine Learning ; },
abstract = {The interplay between diet and gut microbiome composition is complex. Faecal metabolites, the end products of human and microbial metabolism, provide insights into these interactions. Here, we integrate faecal metabolomics, metagenomics, and habitual dietary data from 1810 individuals from the TwinsUK and 837 from the ZOE PREDICT1 cohorts. Using machine learning models, we find that faecal metabolites accurately predict reported intakes of 20 food groups (area under the curve (AUC) > 0.80 for meat, nuts and seeds, wholegrains, tea and coffee, and alcohol) and adherence to seven dietary patterns (AUC from 0.71 for the Plant-based Diet Index to 0.83 for the Dietary Approaches to Stop Hypertension score). Notably, the faecal metabolome is a stronger predictor of atherosclerotic cardiovascular disease risk (AUC = 0.86) than the Dietary Approaches to Stop Hypertension score (AUC = 0.66). We identify 414 associations between 19 food groups and 211 metabolites, that significantly correlate with microbial α-diversity and 217 species. Our findings reveal that faecal metabolites capture mediations between diet and the gut microbiome, advancing our understanding of diet-related disease risk and informing metabolite-based interventions.},
}

Humans
*Feces/chemistry/microbiology
*Gastrointestinal Microbiome/physiology
*Diet
Male
Female
Metabolome
Middle Aged
Metabolomics/methods
Aged
Metagenomics
Adult
Machine Learning

@article {pmid41344778,
year = {2026},
author = {Li, Z and Zhao, C and Mao, Z and Zhao, L and Penttinen, P and Zhang, S},
title = {Metagenomics insights into bacterial community, viral diversity and community-scale functions in fermented red pepper.},
journal = {Food microbiology},
volume = {135},
number = {},
pages = {104986},
doi = {10.1016/j.fm.2025.104986},
pmid = {41344778},
issn = {1095-9998},
mesh = {Fermentation ; *Capsicum/microbiology/virology ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism/virology ; *Fermented Foods/microbiology/virology ; Gene Transfer, Horizontal ; *Viruses/genetics/classification/isolation & purification ; Bacteriophages/genetics/classification/isolation & purification ; *Microbiota ; Food Microbiology ; },
abstract = {Fermented red peppers (FRPs) provide distinct flavor and possible health benefits, but understanding of their microbial functions, viral diversity, pathogenicity, and horizontal gene transfer (HGT) patterns remains limited. Integrated multi-method analysis revealed FRP's bacterial community was dominated by Bacillus (21.52 %), Lactobacillus sensu lato (14.27 %), and Pantoea (13.60 %). Bacillus drove core fermentation with an over 40 % contribution to carbon degradation and iron reduction. The virome was dominated by Caudoviricetes phages, yet 25.5 % of the functions of viral genes remained unknown. Critically, multidrug resistance genes were the most abundant ARGs, and beneficial bacteria served as major reservoirs for ARGs, co-occurring with potential opportunistic pathogens. Despite inhibitory conditions, these last dominated key metabolic nodes hydrogen generation and acetate oxidation. Counterintuitively, ARG profiles correlated with bacterial composition but not with mobile genetic elements or detected HGT events, challenging HGT as the primary ARG driver. These findings necessitate dual strategies: leveraging key microbes for fermentation efficiency while implementing stringent monitoring to mitigate pathogen and ARG related risks.},
}

Fermentation
*Capsicum/microbiology/virology
Metagenomics
*Bacteria/genetics/classification/isolation & purification/metabolism/virology
*Fermented Foods/microbiology/virology
Gene Transfer, Horizontal
*Viruses/genetics/classification/isolation & purification
Bacteriophages/genetics/classification/isolation & purification
*Microbiota
Food Microbiology

@article {pmid41344758,
year = {2026},
author = {Okoye, CO and Ezenwanne, BC and Olalowo, OO and Ajanwachukwu, OJ and Chukwudozie, KI},
title = {Microbial-mycotoxin interactions in food: A review of ecotoxicological implications and omics approaches for understanding detoxification mechanisms.},
journal = {Food microbiology},
volume = {135},
number = {},
pages = {104955},
doi = {10.1016/j.fm.2025.104955},
pmid = {41344758},
issn = {1095-9998},
mesh = {*Mycotoxins/metabolism/toxicity ; *Food Contamination/analysis ; *Fungi/metabolism/genetics ; *Food Microbiology ; Ecotoxicology ; Inactivation, Metabolic ; Animals ; Humans ; Genomics ; },
abstract = {Mycotoxins, toxic secondary metabolites produced by fungi such as Aspergillus, Fusarium, and Penicillium, frequently contaminate food supplies, posing risks to human health, animal welfare, and ecosystem stability. Mycotoxins like aflatoxins, ochratoxin A, fumonisins, trichothecenes, and zearalenone disrupt microbial communities, food chains, and environmental matrices, with synergistic interactions amplifying their toxicity. This review explores microbial-mycotoxin interactions in food systems, focusing on ecotoxicological implications and omics approaches for elucidating detoxification mechanisms. Microbial detoxification, through adsorption by cell wall components (e.g., β-glucans) or enzymatic biodegradation (e.g., lactonases, oxidoreductases), offers a sustainable alternative to physical and chemical methods. However, challenges include variable detoxification efficiency, mechanistic uncertainties, regulatory hurdles, and the detection of masked mycotoxins in complex food matrices. Omics technologies such as metagenomics, genomics, transcriptomics, and their integration provide comprehensive insights into microbial diversity, gene expression, enzyme activity, and metabolite transformations. In addition, omics integration enhances understanding of microbial-mycotoxin dynamics, supporting targeted biocontrol strategies. Future prospects include leveraging synthetic biology, CRISPR-based gene editing, and machine learning-assisted bioinformatics to optimize microbial strains and predict detoxification outcomes. By addressing these challenges, omics-driven approaches can mitigate mycotoxin contamination, ensure food safety, and reduce ecotoxicological impacts across global food systems.},
}

*Mycotoxins/metabolism/toxicity
*Food Contamination/analysis
*Fungi/metabolism/genetics
*Food Microbiology
Ecotoxicology
Inactivation, Metabolic
Animals
Humans
Genomics

@article {pmid41344333,
year = {2025},
author = {Cao, Y and Bowker, MA and Feng, Y and Delgado-Baquerizo, M and Xiao, B},
title = {The Great Wall of China harbors a diverse and protective biocrust microbiome.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.10.087},
pmid = {41344333},
issn = {1879-0445},
abstract = {The Great Wall of China, one of the most emblematic human heritage sites ever built, is largely covered by a living skin that has a potentially distinct microbiome compared with bare wall surfaces. However, the structure and function of this microbiome remain virtually unknown, which hampers any effort to understand the impacts of this microbiome on the long-term conservation of the Great Wall. Here, we investigated the microbiome of the Great Wall at six sampling sites along a 600-km section, which stretches across arid and semiarid climates and is covered by a mosaic of biological soil crusts (biocrusts) and exposed wall surfaces. We hypothesized that these biocrusts could establish a unique microhabitat and support a microbiome with a community structure and function potentially distinct from those on bare walls, thereby modulating the biodeterioration processes affecting the Great Wall. Our findings revealed that biocrust-covered sections exhibited a 12%-62% increase in abundance, diversity, and co-occurrence network complexity for bacterial and fungal communities compared with bare walls. Further metagenomic analyses indicated that the biocrust cover enhanced the abundance of overall functional genes and stress-resistance pathways within the microbiome by 4%-15%, while decreasing the metabolic pathways linked to heritage biodeterioration. Aridity was an additional determinant of the microbiome. Our work serves as a critical step toward understanding the microbiome of the Great Wall, which contributes to conserving this unparalleled human monument for future generations.},
}

@article {pmid41344255,
year = {2025},
author = {Chen, X and Wu, Y and Xue, B and You, Y and Yin, L and Wang, S and Zheng, J},
title = {Mechanism of flavor formation in Suansun fermented by Lactiplantibacillus plantarum during a three-stage flavor formation model.},
journal = {Food chemistry},
volume = {499},
number = {},
pages = {147316},
doi = {10.1016/j.foodchem.2025.147316},
pmid = {41344255},
issn = {1873-7072},
abstract = {This study employed an integrated multi-omics approach-metagenomics, metatranscriptomics, and metabolomics-to elucidate the flavor formation mechanism in Suansun, leading to the proposal of a three-stage flavor formation model. In the initial stage, Lactiplantibacillus plantarum dominates pyruvate metabolism, rapidly producing lactic acid and creating an acidic environment that drives microbial succession. This pH shift initiates the key flavor-forming stage, during which peak levels of Weissella cibaria align with linalool biosynthesis, suggesting strong temporal coordination. During the mid-to-late stages, the abundance of Clostridium species was strongly correlated with p-cresol generation via tyrosine catabolism, while Lactococcus and related taxa produce nonanal and ketones through fatty acid β-oxidation. Overall, the starter culture actively restructures the fermentation niche, sequentially activating metabolic pathways in successive microbial communities to shape a stable flavor profile. This staged model of flavor evolution provides a scientific foundation for optimizing and controlling Suansun fermentation quality.},
}

@article {pmid41344131,
year = {2025},
author = {Liu, T and Li, L and Chen, J and Cai, G and Meng, F and Jiao, Y and Mao, Y and Wang, Z and Zuo, W and Tian, Y and Sun, H},
title = {Real-world aged microplastics exacerbate antibiotic resistance genes dissemination in anaerobic sludge digestion via enhancing microbial metabolite communication-driven pilus conjugative transfer.},
journal = {Water research},
volume = {290},
number = {},
pages = {125056},
doi = {10.1016/j.watres.2025.125056},
pmid = {41344131},
issn = {1879-2448},
abstract = {The dissemination of antibiotic resistance genes (ARGs) facilitated by coexisting microplastics (MPs) in the "source-sink" hotspots of waste activated sludge (WAS) raises great concern. Despite real-world MPs undergoing aging, whether and how naturally aged microplastics (AMPs) affect ARG dissemination during sludge treatment remains largely unknown. Herein, we systematically explored the evolved effects and underlying mechanisms of environmentally relevant MPs (0, 3, and 30 mg/kg TS) aging on ARG propagation in anaerobic sludge digestion via multi-omics analyses. Specifically, microplastic exposure increased total ARG abundance by 2.59-15.31 % with enriched mobile genetic elements (MGEs, 0.22-16.71 %). These effects were escalated at higher microplastic dosages and aging degrees. Mechanistically, metagenomic and metaproteomic analyses revealed the drivers for ARG amplification in the sludge digester evolved from the pristine microplastics (PMPs)-induced higher oxidative stress and membrane permeability to AMPs-induced higher multidrug efflux coupled with pilus-mediated conjugation. Subsequently, metagenomic binning identified key multidrug-resistant hosts of Sedimentibacter, Alicycliphilus, and Sulfuricurvum genera. Moreover, high-resolution metabolomics and reactomics network analysis uncovered that AMPs stimulated microbial metabolite turnover, particularly of nitrogenous and sulfurous compounds, and enhanced the complexity and communication frequency of molecular transformation networks centered on lignin and protein nodes, thereby promoting ARG exchange. Finally, Mantel tests reconfirmed that reactive oxygen species level (Mantel's r = 0.93, p = 0.04) and metabolite network connectivity (Mantel's r = 0.82, p = 0.04) are paramount drivers of ARG spread. These findings offer novel insights into the ARG amplification risk driven by MPs aging, guiding targeted strategies to mitigate ARG spread and improve resource recovery in sludge bioengineering systems.},
}

@article {pmid41344128,
year = {2025},
author = {Xie, X and Li, E and Jiang, H and Pi, K and Yan, L and Shen, S},
title = {Methane biogeochemical turnover constrains arsenic transformation in groundwater systems: Organic molecular signatures and microbial functional networks.},
journal = {Water research},
volume = {290},
number = {},
pages = {125083},
doi = {10.1016/j.watres.2025.125083},
pmid = {41344128},
issn = {1879-2448},
abstract = {Arsenic (As) contamination of groundwater is primarily driven by microbially mediated redox processes and the dynamic evolution of dissolved organic matter (DOM). The influence of cycled methanogenesis and methane oxidation processes on As species transformation in geogenic As-contaminated groundwater, however, remain mechanistically elusive. In this study, quantitative relationships among DOM molecular characteristics, microbial functional networks, and As speciation were established using sediment microcosm experiments, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), and metagenomic sequencing. The results indicate that rates of methanogenesis and methane oxidation are regulated by thermodynamic properties of DOM. Labile DOM promoted As(III) mobilization at a rate of 1.04 μg kg[-1] d[-1] through methyl-related metabolism. Remarkably, enhanced methane oxidation further elevated the As(III) generation rate to 3.30 μg kg[-1] d[-1], underscoring the accelerating effect of methane cycling on As release. In contrast, humified DOM decoupled the geochemical linkage between iron and As. Microbial succession governed the redox transitions, as the proliferation of methanogens substantially increased methane production (up to 7.23 mg kg[-1] d[-1]), while methanotrophs enhanced oxidation rates from 94.99 to 190.76 mg kg[-1] d[-1]. This microbial progression coupled sulfate and As(V) reduction through the up-regulation of key functional genes (dsrAB, arsC). Energy conversion during DOM biodegradation governs As migration stages. These findings highlight the interactive constraints on As speciation dynamics by molecular characteristics of DOM and microbial functional networks during methane biotransformation processes in groundwater systems. This research provides new mechanistic insights into As biogeochemical cycling in geogenic contaminated groundwater.},
}

@article {pmid41342600,
year = {2025},
author = {Bauchinger, F and Berry, D},
title = {Metatranscriptomic-driven insights into mucosal glycan degradation by the human gut microbiota.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf118},
pmid = {41342600},
issn = {1574-6941},
abstract = {The secreted mucus layer in the human gastrointestinal tract constitutes both a protective boundary between gut lumen and epithelium as well as an important nutrient source for members of the gut microbiota. While many gut microbes possess the genetic potential to degrade mucin it is still unclear which species transcribe the respective genes. Here, we systematically analyzed publicly available metagenome and metatranscriptome datasets to characterize the gut microbial community involved in mucosal glycan degradation. We utilized co-occurrence network analysis and linear regression to elucidate the ecological strategies of, and relationship between, mucus degraders. We found that although approximately 60% of species carrying genes encoding for mucosal-glycan-degrading enzymes have detectable transcription of these genes, only 21 species prevalently transcribe more than 1 gene. Furthermore, the transcription of individual genes was frequently dominated by single species in individual samples. Transcription patterns suggested the presence of competitive mucosal glycan degraders characterized by abundance-driven transcription that were negative predictors for the transcription of other degraders as well as opportunistic species with decoupled abundance and transcription profiles. These findings provide insights into the ecology of the mucosal glycan degradation niche in the human gut microbiota.},
}

@article {pmid41341964,
year = {2025},
author = {Yao, J and Zhang, J and Zheng, L and Fang, W and Lang, Y},
title = {Coxiella burnetii Should Not Be Ignored: Two Cases of Q Fever Pneumonia Diagnosed by Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6227-6239},
pmid = {41341964},
issn = {1178-6973},
abstract = {BACKGROUND: Q fever is a globally distributed zoonotic disease caused by Coxiella burnetii (C. burnetii). As an obligate intracellular bacterium, C. burnetii is primarily transmitted from domestic animals to humans, with ticks also serving as potential vectors. The clinical manifestations of Q fever are often nonspecific and highly variable, making its diagnosis particularly challenging.

CASE PRESENTATION: Two male pneumonia patients were hospitalized in Deqing People's Hospital, one was 73 years old, and the other one was 30 years old, both of them presented with hyperpyrexia without a clear epidemiological history. However, initial empirical treatment was ineffective and microbiological cultures were all negative, then bronchoscopy was conducted for them and bronchoalveolar lavage fluid (BALF) was sent for metagenomic next-generation sequencing (mNGS) test. Ultimately, two patients were diagnosed with Q fever pneumonia, and the symptoms of patients were significantly improved after timely treatment with the special drug doxycycline and moxifloxacin, and lung inflammation in both patients were effectively absorbed in the subsequent follow-up examination.

CONCLUSION: Two cases of Q fever pneumonia were diagnosed through mNGS. As a new detection method, mNGS has advantages in the diagnosis of unknown infectious pathogens. As a zoonotic pathogen, C. burnetii should not be ignored. The One Health approach may be suitable for Q fever prevention and control.},
}

@article {pmid41341958,
year = {2025},
author = {Chaves, M and Hashish, A and Goraichuk, IV and Casserta, LC and Mears, MC and Gadu, E and Bakre, A and Alexander Morris, ER and Shelkamy, MMS and Nadendla, S and Perez, DR and El-Gazzar, M},
title = {Nanopore sequencing in veterinary medicine: from concepts to clinical applications.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1701570},
pmid = {41341958},
issn = {2235-2988},
mesh = {*Nanopore Sequencing/methods/veterinary ; Animals ; *Veterinary Medicine/methods ; Computational Biology/methods ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Nanopores ; Genomics/methods ; },
abstract = {Oxford Nanopore Technologies (ONT) stands at the forefront of third-generation sequencing, utilizing a nanopore sequencing approach to achieve high-throughput DNA and RNA sequencing. This technology offers several key advantages, including real-time data generation, portability, and long-read capabilities, making it an increasingly valuable tool for a wide range of applications. This review will focus on the use of ONT in veterinary diagnostics exploring the evolving applications of ONT in veterinary medicine and its use in detecting viral and bacterial pathogens, antimicrobial resistance profiling, foodborne disease surveillance, and metagenomic analysis. We provide an overview of the diverse sequencing workflows available, from sample preparation to bioinformatics analysis, and highlight their advantages over traditional sequencing methods. While powerful, nanopore sequencing does present challenges such as error rates, barcode crosstalk, and workflow complexities. This review will address these issues and discuss potential future developments, as well as the long-term impact of ONT on the field of genomics. As nanopore sequencing technology continues to advance, its role in veterinary diagnostics is expected to expand significantly, leading to improvements in disease surveillance, outbreak response, and contributions to crucial One Health initiatives.},
}

*Nanopore Sequencing/methods/veterinary
Animals
*Veterinary Medicine/methods
Computational Biology/methods
*High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
Nanopores
Genomics/methods

@article {pmid41341954,
year = {2025},
author = {Fang, XZ and Liu, ZH and Duan, LM and Yao, L and Xu, JQ and Yang, XB and Ren, LH and Jiang, YX and Sun, SW and Shang, Y and Yuan, Y},
title = {Clinical features, pathogens, and prognosis of immunocompromised host pneumonia in patients with malignancies.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1646513},
pmid = {41341954},
issn = {2235-2988},
mesh = {Humans ; *Immunocompromised Host ; Male ; *Neoplasms/complications ; Female ; Middle Aged ; Prospective Studies ; Aged ; Prognosis ; Bronchoalveolar Lavage Fluid/microbiology/virology ; *Pneumonia/microbiology/mortality/diagnosis ; Coinfection/microbiology ; Adult ; Bacteria/isolation & purification/classification ; Metagenomics ; COVID-19 ; Aged, 80 and over ; SARS-CoV-2 ; },
abstract = {BACKGROUND: Cancer patients face elevated risks of severe pulmonary infections due to malignancy-related immunosuppression and anti-neoplastic therapy. Comprehensive data on the etiology and prognostic factors remain limited.

METHODS: This prospective cohort study enrolled 115 patients with malignancies and immunocompromised host pneumonia (ICHP) from July 2023 to July 2024. Pathogens were identified using clinical metagenomics of bronchoalveolar lavage fluid (BALF), supported by CT imaging and clinical evaluation.

RESULTS: Pathogens were detected in 92 patients (80.0%), with 158 potential pathogens detected. Etiologic diagnoses were established by BALF mNGS alone in 68 (73.9%), by combined mNGS plus standard microbiologic testing (SMT) in 24 (26.1%), and by SMT alone in 1 (1.1%). Pneumocystis jirovecii (32, 20.3%), SARS-CoV-2 (14, 8.9%), Aspergillus fumigatus (13, 8.2%), Klebsiella pneumoniae (12, 7.6%) and Haemophilus influenzae (10, 6.3%) were the five most common pathogens. Coinfections occurred in 36.5% of all enrolled patients. Death at 28 days, ICU admission, Death at ICU was more frequent among patients with polymicrobial infections than single pathogen infection, though this difference was not statistically significant. Use rate of vasoactive drugs was significantly higher in patients with coinfection than in patients with single-pathogen infection (39.1% vs. 16.0%). invasive mechanical ventilation (IMV) (OR = 22.86, p=0.047), vasopressor use (OR = 72.69, p=0.039), and higher Acute Physiology and Chronic Health Evaluation II (APACHE II) scores (OR = 1.46, p=0.016) were associated with increased 28-day all-cause mortality.

CONCLUSION: Patients with malignancies and evaluated for pulmonary infection were found to have unique microbiological profiles detected by BAL metagenomic sequencing. Co-detection of potential pathogens was high, and associated with high 28-day all-cause mortality.},
}

Humans
*Immunocompromised Host
Male
*Neoplasms/complications
Female
Middle Aged
Prospective Studies
Aged
Prognosis
Bronchoalveolar Lavage Fluid/microbiology/virology
*Pneumonia/microbiology/mortality/diagnosis
Coinfection/microbiology
Adult
Bacteria/isolation & purification/classification
Metagenomics
COVID-19
Aged, 80 and over
SARS-CoV-2

@article {pmid41341823,
year = {2025},
author = {Huang, W and Lai, HP and Yu, L and Jin, L and Lei, W},
title = {Case Report: Chronic Q fever mimicking malignancy and tuberculosis in a hemodialysis patient: multidisciplinary diagnosis guided by metagenomic next-generation sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1656891},
pmid = {41341823},
issn = {2296-858X},
abstract = {BACKGROUND: Q fever, caused by Coxiella burnetii, is a rare zoonosis whose clinical presentation is highly heterogeneous. Chronic Q fever can present with atypical systemic masses, creating significant diagnostic challenges as it lacks distinctive imaging features, often leading to misdiagnosis.

CASE PRESENTATION: We report a case of a 50-year-old woman on maintenance hemodialysis who presented with a one-month history of generalized myalgia and abdominal discomfort. Initial PET-CT imaging revealed multiple hypermetabolic abdominal lesions (SUV∼max∼ 7.1), mimicking metastatic malignancy. Histopathology of abdominal biopsies showed granulomatous inflammation with necrosis but lacked definitive microbiological evidence. Empirical anti-tuberculosis therapy was initiated based on clinical suspicion. Despite initial clinical improvement, the patient experienced recurrence of symptoms and radiological progression after 1 year. Re-evaluation with transesophageal echocardiography suggested the possibility of infective endocarditis. Crucially, metagenomic next-generation sequencing (mNGS) of a repeat biopsy identified Coxiella burnetii, confirming chronic Q fever. Targeted doxycycline therapy resulted in sustained clinical and radiological improvement, with lesion resolution confirmed at the 14-month follow-up.

CONCLUSION: This case underscores the diagnostic difficulty of chronic Q fever due to its non-specific presentation and imaging characteristics. PET-CT may suggest malignancy, but incorporating advanced molecular diagnostics such as mNGS is critical for accurate pathogen identification. Recognizing atypical manifestations and utilizing integrative diagnostic approaches can facilitate timely, targeted therapy, improving clinical outcomes in rare infectious diseases like Q fever.},
}

@article {pmid41341819,
year = {2025},
author = {Kong, M and Sun, J},
title = {Case Report: A case of Nocardia otitidiscaviarum pneumonia diagnosed by application of metagenome next-generation sequencing and a narrow literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1646940},
pmid = {41341819},
issn = {2296-858X},
abstract = {Nocardia is an opportunistic pathogen with relatively low incidence but high mortality. Recently, reports of Nocardia infections have increased; however, infections caused by Nocardia otitidiscaviarum (N. otitidiscaviarum) remain relatively rare. Due to its non-specific clinical manifestations and imaging features, N. ototidiscaviarum infections are frequently misdiagnosed or underdiagnosed, and no standardized guidelines currently exist for their diagnosis and treatment. In this study, we report a case of pulmonary infection caused by N. otitidiscaviarum, which was diagnosed using a combination of traditional microbial morphology and second-generation sequencing, and subsequently showed improvement following treatment with trimethoprim-sulfamethoxazole (TMP-SMZ) and linezolid. Additionally, we conducted a comprehensive literature review using PubMed to provide insights for improving the diagnosis and treatment of N. otitidiscaviarum infections.},
}

@article {pmid41341716,
year = {2025},
author = {Leutert, A and Zeckanovic, A and Huber, M and Meyer Sauteur, PM and Morscher, RJ},
title = {Recurrent vaccine-strain varicella zoster virus reactivation in a child with acute lymphatic leukemia.},
journal = {IDCases},
volume = {42},
number = {},
pages = {e02422},
pmid = {41341716},
issn = {2214-2509},
abstract = {This case illustrates recurrent herpes zoster (HZ) in a child with acute lymphatic leukemia. Interestingly, vaccine-strain HZ was confirmed by identifying the live-attenuated Oka vaccine strain (vOka) using metagenomic sequencing and sequence comparison at three loci that distinguish vOka from wild-type varicella zoster virus (VZV). Although vaccine-strain HZ is generally milder than HZ caused by wild-type VZV, prompt recognition and initiation of antiviral treatment is essential in immunocompromised patients, as fatal varicella due to disseminated vaccine-strain VZV has been reported in this high risk group.},
}

@article {pmid41341658,
year = {2025},
author = {Kriem, LS and King, N and Niemann, S and Vainshtein, Y and Sonntag, M},
title = {Molecular Identification of Human and Plant Pathogens in Municipal Domestic Wastewater for Hydroponic System Applications.},
journal = {International journal of microbiology},
volume = {2025},
number = {},
pages = {6958575},
pmid = {41341658},
issn = {1687-918X},
abstract = {Water is essential for human survival and socioeconomic development, yet its overconsumption threatens global food security and ecosystem integrity. This necessitates a 60% increase in food production, further straining water resources. Hydroponic systems represent a promising solution, utilizing up to 90% less water than traditional methods while providing optimal growing conditions for crops. This study was aimed at developing a PCR-based detection system for main human and plant pathogens in hydroponic systems using treated domestic wastewater. Metagenomic analysis of wastewater samples revealed significant microbial diversity, identifying human pathogens such as Pseudomonas aeruginosa and Yersinia enterocolitica, alongside plant pathogens including Rhodococcus fascians. Specific primer pairs for the most abundant species found in a domestic municipal wastewater sample of target pathogens (Streptococcus mutans, P. aeruginosa, Acinetobacter baumannii, Y. enterocolitica, Enterococcus faecalis, Pseudomonas viridiflava, R. fascians, Xanthomonas vesicatoria, and Pseudomonas syringae) were designed and validated, ensuring high specificity and efficiency. Future research should focus on enhancing detection methods and optimizing DNA extraction techniques to improve pathogen quantification and management in hydroponic systems. This approach is crucial for sustainable agricultural practices that minimize water usage while ensuring food safety and environmental health.},
}

@article {pmid41341495,
year = {2025},
author = {Rana, TS and Bansode, RR and Rana, JP and Williams, LL},
title = {A systematic review: polyphenol's effect on food allergy via microbiome modulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1673472},
pmid = {41341495},
issn = {1664-302X},
abstract = {INTRODUCTION: Food allergy is an increasing health concern worldwide. Microbes, food allergies, and polyphenols are found to be interrelated. However, studies relating polyphenols' effect on food allergy via microbiome modulation are scarce, and there is a lack of common signature microbiome modulation patterns. Thus, this review aims to summarize the effect of polyphenols on food allergy via microbiome modulation.

METHODS: Research articles were searched from Scopus, PubMed, ScienceDirect, and Web of Science database. The in vivo and in vitro studies were assessed via SYRCLE risk of bias and modified CONSORT checklist, respectively. The population characteristics and experimental details were extracted, and the data were synthesized narratively.

RESULTS: The included studies were free of selective reporting of results. The allergy of egg (ovalbumin), milk (𝛽-lactoglobulin), soybean (𝛽-conglycinin), and shrimp allergy contributed to 54%, 23%, 15%, and 8% of the total included studies, respectively. The used compounds were a different source or types of polyphenols such as cocoa, cyanidin-3-O-glucoside (C3G), avenanthramide's (AVA), rosmarinic acid (RA), neohesperidin, and fermented apple juice for egg allergy, luteolin, and green tea polyphenol (GTP) for soybean allergy, and flavonoids (Luteolin, myricetin and hyperoside), ferulic acid, and luteolin for milk allergy. Allergies of milk, egg, wheat, and shrimp occurred with the reduction of Lactobacillus, Alistipes, Odaribactor, Akkermansia, Bacteroides, and Lachnospiraceae_NK4A136_group and an increase of Prevotella, Alloprevotella, Faecalibaculum, Helicobactor, Blautia, Clostridium, and Staphylococcus. The polyphenols modulated these microbes in order to attenuate the food allergies.

DISCUSSION: The types of polyphenols, food allergies, animal model used, and taxonomic resolution of the microbiome studies lead to variation in the results. Thus, by increasing the studies on effect of polyphenols on individual food allergies, and combining with higher taxonomic resolution techniques such as shotgun metagenomics along with metabolomics would increase reliability of the results of the future studies.},
}

@article {pmid41341171,
year = {2025},
author = {Khan, N and Nasir, MM and Mushtaq, A and Kayani, MUR},
title = {SNPraefentia: a toolkit to prioritize microbial genome variants linked to health and disease.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf297},
pmid = {41341171},
issn = {2635-0041},
abstract = {MOTIVATION: Analysis of genomic variation in microbial genomes is crucial for understanding how microbes adapt, interact with their hosts, and influence health and disease. In metagenomic studies, where genetic material from entire microbial communities is sequenced, thousands of single-nucleotide polymorphisms can be detected across species and samples. However, identifying which of these variations has biologically or functionally relevant impacts remains a significant challenge.

RESULTS: To address this, we present SNPraefentia, a Python-based toolkit for prioritizing microbial SNPs based on their predicted functional relevance. The tool integrates multiple biologically meaningful parameters, including sequencing depth, physicochemical impact of amino acid substitutions, and the structural and functional context of mutations within annotated protein domains. SNPraefentia extracts variation depth and amino acid changes, annotates protein domains using UniProt, and computes individual impact scores. These are then integrated into a composite prioritization score that reflects the potential biological importance of each variant. Overall, SNPraefentia provides researchers with a systematic and reproducible approach to filter and rank microbial variants for downstream functional analysis or experimental validation.

The toolkit and test data are freely available at https://github.com/muneebdev7/SNPraefentia.},
}

@article {pmid41340567,
year = {2025},
author = {Ouradova, A and Ferrero, G and Bratova, M and Daskova, N and Bohdanecka, A and Dohnalova, K and Heczkova, M and Chalupsky, K and Kralova, M and Kuzma, M and Modos, I and Tichanek, F and Najmanova, L and Pardini, B and Pelantová, H and Tarallo, S and Videnska, P and Gojda, J and Naccarati, A and Cahova, M},
title = {A vegan diet signature from a multi-omics study on different European populations is related to favorable metabolic outcomes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593050},
doi = {10.1080/19490976.2025.2593050},
pmid = {41340567},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Vegan ; Male ; Female ; Adult ; Czech Republic ; Cross-Sectional Studies ; *Metabolome ; Middle Aged ; Italy ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Vegans ; Metagenome ; Multiomics ; },
abstract = {Vegan and omnivorous diets differ markedly in composition, but their effects on the gut microbiome, metabolome, and lipidome across populations remain insufficiently characterized. While both diet and country of origin influence these molecular layers, the relative contribution of diet versus country-specific factors has not yet been systematically evaluated within a multi-omics framework.In this cross-sectional, bicentric, observational study, we profiled healthy vegans (n = 100) and omnivores (n = 73) from the Czech Republic and Italy using integrated microbiome, metabolome, and lipidome analyses. Findings were subsequently validated in an independent cohort (n = 142).Significant differences across all omics layers were observed for both country and diet. The predictive models confirmed diet-associated separation, with validation cohort AUCs of 0.99 (lipidome), 0.89 (metabolome), and 0.87 (microbiome). Functional metagenome analysis revealed enrichment of amino acid biosynthesis, inositol degradation, and the pentose phosphate pathway in vegans, while omnivores presented greater potential for amino acid fermentation, fatty acid biosynthesis, and propanoate metabolism. Linear models identified a robust, country-independent "vegan signature" consisting of 27 lipid metabolites, five non-lipid metabolites, and 11 bacterial species. Several lipid features associated with an omnivorous diet were inversely related to the duration of vegan diet adherence. Some of the vegan-associated metabolites and bacteria have been previously linked to favorable cardiometabolic profiles, although causality remains to be established.These findings demonstrate that vegan diets are associated with reproducible, country-independent molecular and microbial signatures. Our results highlight diet-driven shifts in host-microbiota interactions and provide a framework for understanding how dietary patterns relate to host-microbiota interactions.},
}

Humans
*Gastrointestinal Microbiome
*Diet, Vegan
Male
Female
Adult
Czech Republic
Cross-Sectional Studies
*Metabolome
Middle Aged
Italy
*Bacteria/classification/metabolism/genetics/isolation & purification
Vegans
Metagenome
Multiomics

@article {pmid41340249,
year = {2025},
author = {Gluvić, Z and Zafirović, S and Sudar-Milovanović, E and Stanimirović, J and Soskić, S and Jevremović, D and Isenović, ER},
title = {Molecular insights into the gut-thyroid Axis: microbiota-driven biomarkers and diagnostic applications.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2025.2599225},
pmid = {41340249},
issn = {1744-8352},
abstract = {INTRODUCTION: New research has shown an intriguing link between the gut bacteria and the thyroid. A gut-thyroid relationship affects energy production, immunological function, and inflammation. As a result, disrupted gut flora harmony is associated with an increased/altered risk of thyroid dysfunction, autoimmune disorders, and metabolic imbalance. In addition to current diagnostic technology, understanding the gut flora-thyroid relationship could assist in the detection of thyroid-related conditions and modify patient treatment.

AREAS COVERED: This review explores state-of-the-art molecular techniques, e.g. metagenomics profiling and metabolomics, to uncover clinically relevant microbiota-driven biomarkers related to thyroid disorders.

EXPERT OPINION: Revealing potential microbiota-driven biomarker candidates is pivotal in enhancing our understanding of the mechanisms of thyroid disorders more precisely and identifying diagnostic and prognostic markers with clinical potential. Precisely, the individualization in the approach to patients with thyroid disorder, inevitably considering the harmonization of the gut microbiota-thyroid hormone relationship, is the basis of rational pharmacotherapy.},
}

@article {pmid41340151,
year = {2025},
author = {Kropp, DR and Glover, ME and Samanta, R and Unroe, KA and Clinton, SM and Hodes, GE},
title = {Perinatal citalopram exposure alters the gut composition and microbial metabolic profiles of Sprague-Dawley rat dams and female offspring but not male offspring.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-025-00794-5},
pmid = {41340151},
issn = {2042-6410},
support = {R01MH105447-01/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Selective serotonin reuptake inhibitors are widely prescribed during pregnancy. Their main route of administration is through the gut. However, their impact on the maternal and offspring gut microbiome and microbial metabolic pathways remains poorly understood. This study used metagenomic shotgun sequencing to examine the effects of perinatal citalopram exposure in rat dams and their offspring on gut composition and downstream metabolic pathways.

METHODS: We treated pregnant and nursing rat dams with either citalopram or vehicle (water). Their feces were collected, DNA from these samples was extracted and then sequenced using shotgun metagenomic sequencing. The BioBakery suite of microbiome analysis tools was utilized in tandem with RStudio to analyze the gut composition and microbial metabolic pathways of the rat dams and their offspring.

RESULTS: Pregnant and nursing dams treated with citalopram exhibited marked shifts in microbial community structure, including phylum-level alterations in Proteobacteria and Defferibacteria. Citalopram treated dams displayed significantly altered beta diversity. Species level alterations due to treatment were composed of five significantly altered microbes, two of which belong to the Proteobacteria phylum. These changes were highly diverse and were not congruent with microbe-level alterations observed in offspring. Alpha diversity of microbial metabolic pathways was compared using the Gini-Simpson index, which was significantly increased in dams suggesting greater metabolic functional diversity with age. Female offspring perinatally exposed to citalopram showed significant changes in gut beta diversity, with seven significant alterations at the microbe level. These microbial shifts were accompanied by twenty-one significantly altered microbial metabolic pathways. In contrast, male offspring showed no significant differences in microbial composition or beta diversity and only minor metabolic changes.

CONCLUSIONS: These findings demonstrate that maternal citalopram exposure during pregnancy and lactation has lasting, sex-specific impacts on the offspring's gut microbiome and microbial metabolic pathways. The pronounced alterations in female, but not male offspring, suggest that host sex may be a critical determinant in the developmental response to citalopram exposure. This work underscores the value of metagenomic approaches in uncovering complex host-microbiome interactions and highlights the need to consider offspring sex in evaluating the safety and long-term effects of antidepressant use during pregnancy.},
}

@article {pmid41340071,
year = {2025},
author = {Peng, J and Liu, X and Wang, J and Meng, N and Cai, R and Peng, Y and Han, Y and Liao, J and Li, C and Rubin-Blum, M and Ma, Q and Dong, X},
title = {Diverse quorum sensing systems regulate microbial communication and biogeochemical processes in deep-sea cold seeps.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02280-x},
pmid = {41340071},
issn = {2049-2618},
support = {1359/23//Israel Science Foundation/ ; 32170121//National Natural Science Foundation of China/ ; 92351304//National Natural Science Foundation of China/ ; 2023J06042//Natural Science Foundation of Fujian Province/ ; 3502Z202373076//Natural Science Foundation Project of Xiamen City/ ; 2022025//Scientific Research Foundation of Third Institute of Oceanography, MNR/ ; },
abstract = {BACKGROUND: Quorum sensing is a fundamental chemical communication mechanism that enables microorganisms to coordinate behavior and adapt to environmental conditions. However, its contribution in deep-sea cold seep ecosystems, where diverse microbial communities and frequent communication occur, remains poorly understood. In this study, we aimed to elucidate the occurrence and potential ecological roles of quorum sensing in cold seeps.

RESULTS: We analyzed 170 metagenomes and 33 metatranscriptomes from 17 global cold seep sites, identifying 299,355 quorum sensing genes from the cold seep non-redundant gene catalog. These genes represent 34 types across six quorum sensing systems, with distribution patterns influenced by sediment depth and seep type. A total of 32,500 quorum sensing genes were identified in 3576 metagenome-assembled genomes from 12 archaeal and 108 bacterial phyla, revealing a complex network of intraspecies and interspecies communication. Microbial groups involved in key metabolic processes, such as sulfate-reducing bacteria, anaerobic methanotrophic archaea, diazotrophs, and organohalide reducers, were extensively regulated by quorum sensing, influencing biogeochemical cycles in cold seeps. Phylogenetic analysis and protein domain identification highlighted the involvement of key quorum sensing-related proteins (e.g., PDE, RpfC/G, CahR, and LuxR) in modulating microbial behaviors, such as motility and chemotaxis. Heterologous expression further confirmed the activity of representative LuxI-R pairs, and metabolomic profiling suggested the presence of putative quorum sensing inhibitors in cold seep sediments.

CONCLUSIONS: Overall, these findings highlight the complexity and significance of quorum sensing in microbial interactions, ecological adaptation, and biogeochemical cycling within cold seep ecosystems, advancing our understanding of microbial communication in the deep biosphere. Video Abstract.},
}

@article {pmid41340070,
year = {2025},
author = {Jeilu, O and Sumner, JT and Moghadam, AA and Thompson, KN and Huttenhower, C and Catlett, C and Hartmann, EM},
title = {Metagenomic profiling of airborne microbial communities from aircraft filters and face masks.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {249},
pmid = {41340070},
issn = {2049-2618},
mesh = {*Air Microbiology ; *Metagenomics/methods ; Humans ; *Bacteria/genetics/classification/isolation & purification ; *Aircraft ; *Masks/microbiology ; *Microbiota/genetics ; *Air Filters/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Airborne microbial communities, although often challenging to study due to low biomass, play crucial roles in public health and pathogen transmission. Through shotgun metagenomics, this study utilizes non-invasive air sampling of face masks and aircraft cabin filters to investigate microbial diversity in environments with frequent human interactions, including hospitals and airplanes. A comprehensive sampling and analysis workflow was developed, incorporating environmental and enrichment protocols to enhance microbial DNA recovery and diversity profiling.

RESULTS: Despite limitations in biomass, optimized extraction methods allowed for the successful identification of 407 species, with dominant taxa including Cutibacterium acnes, Staphylococcus epidermidis, Sphingomonas hankookensis, and Methylobacterium radiotolerans. Enrichment processing resulted in greater metagenome-assembled genome (MAG) recovery and higher antimicrobial resistance gene (ARG) identification.

CONCLUSIONS: The findings highlight the presence of ARGs in high-occupancy public spaces, suggesting the importance of monitoring and the potential for mitigating airborne transmission risks in such environments. This study demonstrates the utility of combining environmental and enrichment sampling to capture comprehensive microbial and ARG profiles in confined spaces, providing a framework for enhanced pathogen monitoring in public health contexts. Video Abstract.},
}

*Air Microbiology
*Metagenomics/methods
Humans
*Bacteria/genetics/classification/isolation & purification
*Aircraft
*Masks/microbiology
*Microbiota/genetics
*Air Filters/microbiology
Metagenome

@article {pmid41339959,
year = {2025},
author = {McAdams, ZL and Campbell, EJ and Dorfmeyer, RA and Turner, G and Shaffer, S and Ford, T and Lawson, J and Terry, J and Raju, M and Coghill, L and Cresci, L and Lascola, K and Pridgen, T and Blikslager, A and Barrell, E and Banse, H and Paul, L and Gillen, A and Nott, S and VandeCandelaere, M and van Galen, G and Townsend, KS and Martin, LM and Johnson, PJ and Ericsson, AC},
title = {A novel dataset of 2,362 equine fecal microbiomes from veterinary teaching hospitals across three countries reveals effects of geography and disease.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {124},
pmid = {41339959},
issn = {2524-4671},
abstract = {BACKGROUND: Horses and other equids are reliant on the gut microbiome for health, and studies have reported associations between certain clinical conditions and features of the fecal microbiome. However, research to date on the equine fecal microbiome has often relied on small sample sizes collected from single and relatively localized geographic regions. Previous work also largely employs single timepoint analyses, or horses selected based on limited health criteria.

RESULTS: To address these limitations and expand our understanding of the core microbiome in health, and the changes associated with adverse outcomes, the Equine Gut Group (EGG) has collected and performed 16S rRNA sequencing on 2,362 fecal samples from 1,190 healthy and affected horses. This resource of 16S rRNA sequencing data with accompanying demographic and clinical metadata represent a diverse equine population in health and disease. We identified features making up the core microbiome of healthy equids and metadata factors influencing the relative abundance of those features. We then identified microbial markers of acute gastrointestinal disease at the community and taxonomic levels.

CONCLUSIONS: Here we present the EGG database and demonstrate its utility in characterizing the equine microbiome in health and acute gastrointestinal disease. The EGG 16S rRNA database is a valuable resource to study the equine microbiome and its role in equine health.},
}

@article {pmid41339940,
year = {2025},
author = {Parwin, N and Dixit, S and Das, S and Sahoo, RK and Subudhi, E},
title = {Metagenomic analysis of microbiome spatial dynamics in urban river confluence affected by city wastewater.},
journal = {Genomics & informatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s44342-025-00054-3},
pmid = {41339940},
issn = {1598-866X},
abstract = {BACKGROUND: Environmental pollutants have a profound impact on microbial dynamics. This study highlights the influence of anthropogenic activity on the shift in bacterial diversity in the catchment area compared to upstream and downstream at Kathajodi, using a metagenomic approach for the first time in River Kathajodi.

METHODS: Water samples were collected from upstream, catchment, and downstream locations and transported at 4°C to the laboratory for DNA extraction, library preparation, sequencing, and physicochemical analysis employing inductively coupled plasma. The extracted DNA was sequenced via the Illumina HiSeq platform and analyzed through MG-RAST for taxonomic and functional classification using KEGG and COG annotations. Statistical diversity analysis, including rarefaction curves, alpha- and beta-diversity indices, and Venn diagrams, provided insights into microbial composition and community variations across sites.

RESULTS: A significant abundance of pollution indicator members of phylum Bacteroidetes (29.82%) in the catchment (CM), highly contaminated with metals, fecal, and other organic pollutants, could be attributed to their high metabolic capabilities to degrade them. The pristine upstream (US) exhibited an abundance of Shewanella (25.04%), Pseudomonas (17.35%), and Synechococcus (5.62%). The CM, influenced by high anthropogenic activity, showed higher abundances of Flavobacterium (5.20%), Arcobacter (4.05%), and Bacteroides (3.88%). In contrast, downstream (DS), with fewer anthropogenic activities, displayed higher abundances of Aeromonas (4.40%), Acidovorax (0.52%), and Acidimicrobium (0.32%). The highest bacterial diversity of CM could be due to the influence of the physicochemical properties of city waste effluent. From the Venn diagram, 73 common OTUs at the genera level were observed in all three sites, which indicates that the native microflora of the river water niche remains unaffected irrespective of the temporary changes in the vicinity. The functional profiling through KEGG and COG revealed that CM was enriched in carbohydrate metabolism (12.11%), while DS exhibited higher contributions to amino acid metabolism, along with the highest relative abundance of general function prediction (R) (12.89%), all indicative of stress adaptation and metabolic flexibility under polluted conditions. The clean upstream is home to oxygen-loving helpful bacteria, the catchment supports nutrient-hungry and sewage-linked microbes, while the downstream is dominated by metal-tolerant and possibly harmful bacteria, showing the clear impact of human activities along the river.

CONCLUSIONS: The marked shift in bacterial diversity between US, CM, and DS regions highlights the ecological consequences of anthropogenic impact. These findings emphasize the need for effective environmental management to safeguard water quality and prevent undesirable health issues.},
}

@article {pmid41339801,
year = {2025},
author = {Yang, T and Wang, Y and Zhang, Y and Liu, C and Zeng, Y and Shi, P and Zhou, J and Li, Y and Wei, H},
title = {Haemophilus influenzae dominance in fungal ball microbiome revealed through multi-niche metagenomic sequencing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04546-8},
pmid = {41339801},
issn = {1471-2180},
support = {7222026//Natural Science Foundation of Beijing Municipality/ ; },
abstract = {OBJECTIVE: This study employed metagenomic sequencing to characterize the sinonasal microbiome in patients with unilateral maxillary sinus fungal ball (MSFB), with specific emphasis on bacterial-fungal interactions and functional pathways implicated in fungal ball pathogenesis.

METHODS: The study enrolled 30 MSFB patients and 30 healthy controls. Nasal secretion samples were obtained from three anatomical sites in MSFB cases: fungal ball cavity (FC), affected middle nasal meatus (AM), and contralateral unaffected middle nasal meatus (UM). And in the control group, samples were obtained from the healthy middle nasal meatus (HM). Metagenomic sequencing of microbial DNA was performed using the Illumina Novaseq platform. Taxonomic and functional analyses were conducted using Kraken2, Bracken, and HUMAnN2.

RESULTS: Bacteria dominated the microbiome in the FC group (98.53%), with Haemophilus influenzae identified as a key biomarker (LDA score > 5). A negative correlation between H. influenzae and Aspergillus flavus was observed in the FC group (r = -0.46, P = 0.013). Functional pathways enriched in the FC group included amino acid biosynthesis (map00290), lipopolysaccharide biosynthesis (map00540), and fatty acid biosynthesis (map00061), supporting H. influenzae survival and immune modulation. FC microbiota showed reduced diversity and distinct composition compared to other groups (PERMANOVA, P < 0.001). No significant differences were found in the composition of the microbiota between the bilateral middle nasal meatus groups of MSFB.

CONCLUSION: This study highlights H. influenzae as a critical bacterial biomarker in MSFB. The inverse relationship between H. influenzae and A. flavus may suggest competitive or immune-mediated interactions. These findings advance understanding of non-invasive fungal sinusitis. Future validation in larger fungal ball cohorts or invasive fungal sinusitis is warranted.},
}

@article {pmid41339548,
year = {2025},
author = {Singleton, CM and Jensen, TBN and Delogu, F and Knudsen, KS and Sørensen, EA and Jørgensen, VR and Karst, SM and Yang, Y and Sereika, M and Petriglieri, F and Knutsson, S and Dall, SM and Kirkegaard, RH and Kristensen, JM and Overgaard, CK and Woodcroft, BJ and Speth, DR and Aroney, STN and , and Wagner, M and Dueholm, MKD and Nielsen, PH and Albertsen, M},
title = {The Microflora Danica atlas of Danish environmental microbiomes.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41339548},
issn = {1476-4687},
abstract = {Over the past 20 years, there have been considerable advances in revealing the microbiomes that underpin processes in natural and human-associated environments. Recent large-scale metagenome surveys have recorded the variety of microbial life in the oceans[1], in the human gut[2] and on Earth[3], with compilations encompassing thousands of public datasets[4,5]. However, despite their broad scope, these studies often lack functional information, and their sample locations are frequently sparsely distributed, limited in resolution or lacking metadata. Here we present Microflora Danica-an atlas of Danish environmental microbiomes encompassing 10,683 shotgun metagenomes and 450 nearly full-length 16S and 18S rRNA datasets, linked to a five-level habitat classification scheme. We show that although human-disturbed habitats have high alpha diversity, species reoccur, revealing hidden homogeneity. This underlines the role of natural systems in maintaining total species (gamma) diversity and emphasizes the need for national baselines for tracking microbial responses to land-use and climate change. Consequently, we focused our dataset exploration on nitrifiers, a functional group closely linked to climate change and of major importance for Denmark's primary land use: agriculture. We identify several lineages encoding nitrifier key genes and reveal the effects of land disturbance on the abundance of well-studied, as well as uncharacterized, nitrifier groups, with potential implications for N2O emissions. Microflora Danica offers an unparalleled resource for addressing fundamental questions in microbial ecology about what drives microbial diversity, distribution and function.},
}

@article {pmid41339392,
year = {2025},
author = {Muratore, E and Conti, G and Fabbrini, M and Zama, D and Decembrino, N and Muggeo, P and Mura, R and Perruccio, K and Leardini, D and Barone, M and Zecca, M and Cesaro, S and Brigidi, P and Turroni, S and Masetti, R},
title = {Distinct functional and compositional properties in the gut microbiome of children with acute lymphoblastic leukaemia identified by shotgun metagenomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43082},
pmid = {41339392},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Child ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology ; Male ; Female ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Adolescent ; Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {Acute lymphoblastic leukaemia (ALL) represents the most common childhood malignancy, and emerging evidence underscores the impact of the gut microbiome (GM) on its pathogenesis. In this study, we used shotgun metagenomics to investigate the GM of 30 ALL patients at diagnosis-19 with B-ALL and 11 with T-ALL-and compared them to 176 healthy controls (HCs). When considered as a single ALL group versus HCs, clear compositional differences emerged: ALL patients exhibited higher relative abundances of Enterococcus faecium, oral commensals such as Rothia dentocariosa, and multiple opportunistic species, whereas HCs were enriched in short-chain fatty acid producers like Anaerostipes hadrus and Intestinibacter bartlettii. Functionally, the ALL GM relied more on protein and amino acid catabolism, while HCs possessed enhanced pathways for carbohydrate and folate metabolism. These findings broadly align with 16S rRNA-based analyses from previous publications, though some discrepancies highlight differences in technique-driven resolution. In contrast, comparing the two major molecular phenotypes-B-ALL and T-ALL-revealed only minimal taxonomic and functional differences, primarily confined to BAs metabolism pathways. Overall, our results indicate that children with ALL at the time of diagnosis already display a dysbiotic signature, bolstering the notion that a disturbance in GM development during childhood may be linked to the multistep pathogenesis model of ALL.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Child
*Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology
Male
Female
Child, Preschool
RNA, Ribosomal, 16S/genetics
Adolescent
Bacteria/genetics/classification
Case-Control Studies

@article {pmid41339358,
year = {2025},
author = {Li, H and Cao, Y and Liu, X and Ke, Z and Chen, L and Siame, BA and Yaron, S and Leung, KY},
title = {Reconstruction of 1,979 prokaryotic metagenome-assembled genomes from 37 global cave environments.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1896},
pmid = {41339358},
issn = {2052-4463},
support = {32373177//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32373177//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024LKSFG07//Li Ka Shing Foundation (Li Ka Shing Foundation Limited)/ ; 2024LKSFG07//Li Ka Shing Foundation (Li Ka Shing Foundation Limited)/ ; },
mesh = {*Caves/microbiology ; *Metagenome ; *Archaea/genetics/classification ; *Genome, Bacterial ; *Genome, Archaeal ; *Bacteria/genetics/classification ; },
abstract = {Cave microorganisms represent unique extremophiles that have evolved in isolated, nutrient-limited environments and harbor exceptional metabolic capabilities. However, knowledge of cave microbial diversity at genomic level remains limited. Previous studies have focused on individual caves and do not give a global picture. Here, we present the first prokaryotic cave metagenomic catalog from 37 geographical diverse cave environments. We employed an optimized genome reconstruction pipeline to recover 3,837 medium-to-high quality cave metagenome-assembled genomes (MAGs). These MAGs were dereplicated into 1,979 species-level representative clusters that spanned 67 phyla of Bacteria (n = 1,858) and Archaea (n = 121) domains. Classification of representative species showed that 98.7% did not match any existing genome taxonomy classification of named species at ≥ 95% average nucleotide identity (ANI). Most representative genomes harbored putative biosynthetic gene clusters (BGCs) (98.0%) and enzymatic antibiotic resistance genes (ARGs) (95.0%). This comprehensive MAGs catalog provides a foundational resource for exploring cave microbial diversity, secondary metabolism, and the evolutionary origins of antibiotic resistance in subterranean ecosystems.},
}

*Caves/microbiology
*Metagenome
*Archaea/genetics/classification
*Genome, Bacterial
*Genome, Archaeal
*Bacteria/genetics/classification

@article {pmid41339349,
year = {2025},
author = {Coe, A and Mullet, JI and Vo, NN and Berube, PM and Anjur-Dietrich, MI and Salcedo, E and Parker, SM and VonEmster, K and Bliem, C and Arellano, AA and Castro, KG and Becker, JW and Chisholm, SW},
title = {A curated protein dataset for taxonomic classification of Prochlorococcus and Synechococcus in metagenomes.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1895},
pmid = {41339349},
issn = {2052-4463},
support = {OCE-2048470//National Science Foundation (NSF)/ ; OCE-1153588//National Science Foundation (NSF)/ ; DBI-0424599//National Science Foundation (NSF)/ ; 984601//Simons Foundation/ ; 337262//Simons Foundation/ ; 329108//Simons Foundation/ ; GBMF495//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
mesh = {*Synechococcus/classification/genetics ; *Prochlorococcus/classification/genetics ; *Metagenome ; Phylogeny ; Genome, Bacterial ; Metagenomics ; *Bacterial Proteins/genetics ; },
abstract = {Prochlorococcus and Synechococcus are abundant marine picocyanobacteria that contribute significantly to ocean primary production. Recent genome sequencing efforts, including those presented here, have yielded a large number of high-quality reference genomes, enabling the classification of these picocyanobacteria in marine metagenomic sequence data at high phylogenetic resolution. When combined with environmental data, these classifications can guide cluster/clade/grade assignments and offer insights into niche differentiation within these populations. Here we present ProSynTax, a curated protein sequence dataset and accompanying classification workflow aimed at enhancing the taxonomic resolution of Prochlorococcus and Synechococcus classification. ProSynTax includes proteins from 1,260 genomes of Prochlorococcus and Synechococcus, including single-amplified genomes, high-quality draft genomes, and newly closed genomes. Additionally, ProSynTax incorporates proteins from 41,753 genomes of marine heterotrophic bacteria, archaea, and viruses to assess microbial and viral communities surrounding Prochlorococcus and Synechococcus. This resource enables accurate classification of picocyanobacterial clusters/clades/grades in metagenomic data - even when present at 0.15% of reads for Prochlorococcus or 0.03% of reads for Synechococcus.},
}

*Synechococcus/classification/genetics
*Prochlorococcus/classification/genetics
*Metagenome
Phylogeny
Genome, Bacterial
Metagenomics
*Bacterial Proteins/genetics

@article {pmid41339341,
year = {2025},
author = {Bellankimath, AB and Branders, S and Kegel, I and Ali, J and Asadi, F and Johansen, TEB and Imirzalioglu, C and Hain, T and Wagenlehner, F and Ahmad, R},
title = {Metagenomic sequencing enables accurate pathogen and antimicrobial susceptibility profiling in complicated UTIs in approximately four hours.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66865-8},
pmid = {41339341},
issn = {2041-1723},
support = {336420 and 352514//Norges Forskningsråd (Research Council of Norway)/ ; },
abstract = {Urinary tract infections (UTIs) affect 405 million people worldwide. Current diagnostics rely on cultures, which can take 2 to 4 days. This study evaluates eleven culture-independent methods for sample preparation from 78 complicated UTI patients, followed by real-time nanopore sequencing and data analysis. The metagenomic results are highly consistent with culture-based clinical routines (MALDI-TOF/VITEK-2). The optimized method demonstrated an accuracy score of 99% (100/101) for pathogen identification and 90% (589/653) for antimicrobial susceptibility profiling with 95% specificity. The method's robustness is highlighted by its ability to accurately identify pathogens with as few as 32 bacterial cells/µL and a low bacterial-to-host cell ratio limit of 0.5. Additionally, mNGS identified 13 pathogens that routine diagnostics missed, which were subsequently confirmed by Vivalytic or PCR. This method is up to 30% more economical than published studies and commercial kits. DNA yield and flow cytometry can be used for pre-screening to reduce costs, which is crucial for clinical adoption. This research highlights the rapid diagnosis of clinical UTIs using a cost-effective and scalable method that requires around four hours from sample collection to informed decision-making. Furthermore, it aims to improve antimicrobial and diagnostic stewardship by reducing empirical treatment and ensuring more judicious antibiotic use.},
}

@article {pmid41339319,
year = {2025},
author = {Harrison, LC and Allnutt, TR and Hanieh, S and Roth-Schulze, AJ and Ngui, KM and Stone, NL and Bandala-Sanchez, E and Backshell, L and Gurruwiwi, G and Gondarra, V and Couper, JJ and Craig, ME and Davis, EA and Huynh, T and Soldatos, G and Wentworth, JM and Vuillermin, P and Penno, MAS and Biggs, BA and , },
title = {Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9904},
pmid = {41339319},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Australia ; Female ; Male ; Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Infant, Newborn ; Indigenous Peoples ; Metagenome ; },
abstract = {Studies of traditional Indigenous compared to 'Western' gut microbiomes are underrepresented, and lacking in young children, limiting knowledge of early-life microbiomes in different cultural contexts. Here we analyze the gut metagenomes of 50 Indigenous Australian infants (median age }

Humans
*Gastrointestinal Microbiome/genetics
Infant
Australia
Female
Male
Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Infant, Newborn
Indigenous Peoples
Metagenome

@article {pmid41338553,
year = {2025},
author = {, and , },
title = {[The Chinese guidelines for the diagnosis and treatment of invasive fungal disease in patients with hematological disorders and cancers (the seventh revision)].},
journal = {Zhonghua nei ke za zhi},
volume = {64},
number = {12},
pages = {1155-1168},
doi = {10.3760/cma.j.cn112138-20250808-00468},
pmid = {41338553},
issn = {0578-1426},
mesh = {Humans ; *Invasive Fungal Infections/diagnosis/therapy/drug therapy ; *Hematologic Diseases/complications ; Antifungal Agents/therapeutic use ; *Neoplasms/complications ; Hematologic Neoplasms/complications ; *Mycoses/diagnosis/therapy ; China ; },
abstract = {In 2005, the Chinese Invasive Fungal Infection Working Group published the first guidelines for the diagnosis and treatment of invasive fungal disease (IFD) in patients with hematological disorders and cancers, with the sixth revision released in 2020. Numerous advances in the fields of hematological oncology treatment and the diagnosis and management of IFD have significantly influenced the corresponding strategies. Therefore, the Chinese Invasive Fungal Infection Working Group has reviewed key research advances from 2020 to 2024 and released the seventh revision of the Chinese guidelines. Major revisions include: changes in the epidemiology of IFD; evaluation of novel diagnostic methods (especially PCR and metagenomic next-generation sequencing); updated recommendations on therapeutic drug monitoring and in vitro drug sensitivity test; management of breakthrough IFD; targeted therapy of Pneumocystis jiroveci pneumonia and cryptococcosis; and updated recommendation on the duration of antifungal therapy.},
}

Humans
*Invasive Fungal Infections/diagnosis/therapy/drug therapy
*Hematologic Diseases/complications
Antifungal Agents/therapeutic use
*Neoplasms/complications
Hematologic Neoplasms/complications
*Mycoses/diagnosis/therapy
China

@article {pmid41338123,
year = {2025},
author = {Huang, S and Yang, P and Wang, X and Zhang, K and Li, L and Yao, S and Qian, L and Liu, C and Guo, J and Shi, L and Liu, F and Xie, W and Guo, Y},
title = {Integrated metagenome and metabolome analysis reveals a disease signature of gut microbiota and the key gut microbiota-associated metabolite proline in schizophrenia.},
journal = {Journal of psychiatric research},
volume = {193},
number = {},
pages = {223-235},
doi = {10.1016/j.jpsychires.2025.11.029},
pmid = {41338123},
issn = {1879-1379},
abstract = {Schizophrenia (SCZ) is a multifaceted psychiatric condition with a complex set of etiological factors. Recent studies have revealed that gut microbiota play a significant role in the neurobiology associated with SCZ. Utilizing metagenomic sequencing and analysis techniques, we obtained composition and functional information of the gut microbiota from 68 SCZ patients and 61 healthy control (HC) subjects. We identified 72 inter-group differential species, 49 differential metabolic pathways, and 1987 differential functional genes. A. odontolyticus and F. prausnitzii were the core species enriched in the SCZ group and the HC group, respectively. Arginine and proline metabolism were the most significant differential metabolic pathways, with K00286 being the differential functional gene catalyzing the synthesis of L-proline in this pathway. Notably, a strong disease classification model was developed based on the gut microbiota data, achieving an outstanding AUC of 0.94, outperforming earlier models, the model achieved AUC values of 0.745 and 0.845 in two separate external datasets, respectively. Furthermore, insights into mechanisms were investigated by analyzing the relationships between microbial species and their associated metabolic pathways. Future research is essential to clarify causal connections, detail specific molecular pathways-particularly those involving functional proteins such as K00286-and to explore the communication processes between the gut microbiota and the brain. Our results underscore the potential for microbiota-based biomarkers and therapeutic targets in SCZ, emphasizing the essential role of gut microbiota in this intricate disorder.},
}

@article {pmid41339745,
year = {2025},
author = {Zhang, L and Marfil-Sánchez, A and Kuo, TH and Seelbinder, B and van Dam, L and Depetris-Chauvin, A and Jahn, LJ and Sommer, MOA and Zimmermann, M and Ni, Y and Panagiotou, G},
title = {Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41339745},
issn = {2058-5276},
support = {Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; Excellent Young Scientists Fund (project ID 24HAA01325)//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Food, especially plant-based diet, has complex chemical diversity. However, large-scale phytonutrient-metabolizing activities of gut bacteria are largely unknown. Here we integrated and systematically analysed multiple databases containing information on enzymatic reactions and food health benefits, and 3,068 global public human microbiomes. Transformation of 775 phytonutrients from edible plants was associated with enzymes encoded by diverse gut microbes. In vitro assays validated the biotransformation activity of gut species, for example, Eubacterium ramulus. The biotransformation of phytonutrients demonstrated high interpersonal and geographical variability. Machine learning models based on 2,486 public case-control microbiomes, using the abundances of enzymes associated with modification of phytonutrients present in health-associated foods, discriminated the health status of individuals in multiple disease contexts, suggesting altered biotransformation potential in disease. We validated the association of microbiome-encoded enzymes with the anti-inflammatory activity of common edible plants by combining metagenomics and metatranscriptomics analysis in specific-pathogen-free and germ-free mice. These findings have implications for designing precise, personalized diets to guide an individual towards a healthy state.},
}

@article {pmid41339710,
year = {2025},
author = {Pacheco-Valenciana, A and Tausch, A and Veseli, I and Dharamshi, JE and Bergland, F and Delgado, LF and Rodríguez-Gijón, A and Andersson, AF and Garcia, SL},
title = {Microbial model communities exhibit widespread metabolic interdependencies.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09306-y},
pmid = {41339710},
issn = {2399-3642},
support = {grant 2022-03077//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-03077//Vetenskapsrådet (Swedish Research Council)/ ; grant 2018-05973//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-06725//Vetenskapsrådet (Swedish Research Council)/ ; grant 2022-03077//Science for Life Laboratory (SciLifeLab)/ ; },
abstract = {Microorganisms thrive in complex communities shaped by intricate interactions, yet the extent and ecological implications of biosynthetic dependencies in natural communities remain underexplored. Here, we used a dilution approach to cultivate 204 microbial model communities from the Baltic Sea and recovered 527 metagenome-assembled genomes (MAGs) that dereplicated into 72 species-clusters (>95% average nucleotide identity, ANI). Of these species, at least 70% represent previously uncultivated lineages. Combined with 1073 MAGs from Baltic Sea metagenomes, we generated a genomic catalog of 701 species-clusters. Our results show that cultures with more than three species included microorganisms with smaller genome sizes, lower biosynthetic potential for amino acids and B vitamins, and higher prevalence and abundance in the environment. Moreover, the taxa found together in the same model communities had complementary biosynthetic gene repertoires. Our results demonstrate that cultivating bacteria in dilution model communities facilitates access to previously uncultivated but abundant species that likely depend on metabolic partners for survival. Together, our findings highlight the value of community-based cultivation for unraveling ecological strategies. Finally, we confirm that metabolic interdependencies and genome streamlining are widespread features of successful environmental microorganisms.},
}

@article {pmid41338426,
year = {2025},
author = {Yan, L and Su, Y and Xie, X and Peng, K and Zhang, P and Deng, Y and Gan, Y and Li, Q and Zhang, Y},
title = {Decoding Microbial-Mediated Sulfur Transformation Pathways in Mangrove Wetland: Metagenomic and Hydrogeochemical Insights.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123472},
doi = {10.1016/j.envres.2025.123472},
pmid = {41338426},
issn = {1096-0953},
abstract = {Sulfur (S) cycling is essential to the ecological function of mangrove wetlands, but how microbial processes and gene-level patterns respond to environmental gradients remains poorly understood. Here, we integrated high-resolution hydrogeochemical profiling with metagenomic sequencing to characterize depth-resolved microbial communities and S-cycling genes in the mangrove wetlands of Dongzhai Harbor, Hainan, China. The results revealed pronounced differences in microbial community composition between zones, with Escherichia dominating mangrove sediments (4.22-20.07%) and Salmonella prevailing in mudflat sediments (23.87-60.98%). The abundance of S-cycling genes (e.g., tusA, soeA, aprA, dsrAB, sat) declined markedly with depth. Spatial variation in biogeochemical conditions shaped functional gene distributions: oxidative genes (aprA, soeA) were more abundant in mudflat profiles, whereas sat dominated reductive pathways in mangrove sediments. Environmental gradients structured microbial communities, with salinity, pH, total nitrogen (TN), and total organic carbon (TOC) showing negative correlations, and total sulfur (TS), total phosphorus (TP), SO4[2-] acting as positive drivers. Co-occurrence network analysis indicated tighter microbial associations in surface layers compared to deeper strata. The thiosulfate oxidation pathway was confined to the 5-10 cm interval in mudflat sediments and appeared at both 5-10 cm and 15-20 cm in mangrove sediments, while direct sulfite oxidation occurred in both zones. Moreover, methanogenesis, nitrification, and denitrification were more prominent in mudflat sediments, whereas methane oxidation prevailed in mangrove profiles. These findings advance our understanding of how microbial functional stratification and S metabolic pathways respond to environmental gradients, with implications for biogeochemical coupling in coastal wetland ecosystems.},
}

@article {pmid41338072,
year = {2025},
author = {Jose, S and Lohith Kumar, DH and Malla, MA and Featherston, J and Bux, F and Kumari, S},
title = {Insights into microbial community, nitrogen‑phosphorus metabolism from metagenomic and metabolomic analysis of microalgal-cyanobacterial consortium-based bioinoculants.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181092},
doi = {10.1016/j.scitotenv.2025.181092},
pmid = {41338072},
issn = {1879-1026},
abstract = {The intensification of agriculture through chemical fertilizers has led to severe environmental consequences. This study provides a comprehensive investigation on chemical fertilizer, vermiculite and on microalgal-cyanobacterial consortia (bioinoculants) influencing soil microbial community. Chemical fertilizer application significantly altered the microbial community, suppressing the dominant phylum Proteobacteria to 48.3 % abundance from 60.9 % in the control soil. The bioinoculant treatments maintained a high Proteobacteria abundance (58.9 %-59.7 %) and fostered a growth-oriented, anabolic strategy. The 50:50 mix treatment uniquely promoted the fungal phylum Basidiomycota to 18.2 % abundance and showed the highest investment in the Glycolysis/Gluconeogenesis pathway (23.0 %). Chemical fertilizer treatment upregulated genes for rapid nitrogen assimilation (glnA, Log2FC = 0.60) and phosphorus starvation response (phoB, Log2FC = 0.65; pstS, Log2FC = 0.83). The enhanced energy production and conversion (11.83 %), amino acid transport and metabolism (11.20 %), and fatty acid biosynthesis (45.3 %) was observed in bioinoculant treatment. Unlike chemical fertilizer treatment, bioinoculant treatment led to the accumulation of the osmoprotectant trehalose and structural membrane lipids, while the 50:50 mix was uniquely characterized by a higher abundance of xylose. These findings demonstrate that the microalgal-cyanobacterial consortium can enhance nutrient recycling, and potentially boost soil health by reshaping the soil microbiome and metabolic functions, offering a promising strategy for sustainable agriculture.},
}

@article {pmid41335477,
year = {2025},
author = {Riskumäki, M and Ruuskanen, MO and Mäenpää, K and Ruokolainen, L and Mäkelä, MJ and Jousilahti, P and Vartiainen, E and Ottman, N and Laatikainen, T and Haahtela, T and Alenius, H and Fyhrquist, N and Sinkko, H},
title = {Shotgun metagenomics reveals distinct skin microbial species in allergen-sensitized individuals.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001527},
pmid = {41335477},
issn = {2057-5858},
mesh = {Humans ; *Metagenomics/methods ; *Allergens/immunology ; *Skin/microbiology/virology ; Finland ; Adolescent ; *Microbiota/genetics ; Male ; Russia ; Female ; *Hypersensitivity/microbiology/immunology ; Malassezia/genetics/isolation & purification ; Immunoglobulin E/immunology ; Bacteria/genetics/classification ; Child ; },
abstract = {The Karelian region, which spans the border between Finland and Russia, presents distinct environmental exposures and lifestyles on either side of the governmental border. In the more urbanized Finnish Karelia, allergic diseases are markedly more prevalent than in the more rural Russian Karelia. Prior studies, based on amplicon sequencing, have demonstrated major differences in skin microbiotas between the two populations. However, compositional differences in microbiota between sensitized and non-sensitized (NS) individuals have not been characterized. Here, in a selected population of 112 allergen-sensitized and NS adolescents, we used shotgun metagenomics to characterize the prokaryotic, eukaryotic and viral species in the skin potentially involved in allergic sensitization via distinct environmental exposures. In the more urban Finnish Karelia, the microbiome species composition was associated with IgE-mediated allergen sensitization status, while in the more rural Russian Karelia, the composition was associated with exposure to furry pets. Finnish participants showing high IgE-mediated sensitization to common allergens (allergen-specific IgE >7.5 kU/L) had less Cutibacterium acnes and Malassezia in their skin and displayed weaker interconnectedness of the microbial co-occurrence network compared with NS participants. Moreover, Malassezia restricta strain-level differences were related to allergen sensitization in both Finnish and Russian participants. In summary, we found distinct skin microbiomes between allergen-sensitized and NS participants and tracked the bacterial and fungal species associated with the degree of allergic sensitization in the more urbanized part of the Karelian region. These findings provide new insights into the factors that shape the human skin microbiome and influence allergic diseases.},
}

Humans
*Metagenomics/methods
*Allergens/immunology
*Skin/microbiology/virology
Finland
Adolescent
*Microbiota/genetics
Male
Russia
Female
*Hypersensitivity/microbiology/immunology
Malassezia/genetics/isolation & purification
Immunoglobulin E/immunology
Bacteria/genetics/classification
Child

@article {pmid41335476,
year = {2025},
author = {Docter, J and Mansfeldt, C},
title = {Environmental Census: Modeling Synthetic Biology Ecological Risk with Metagenomic Enzymatic Data and High-Performance Computing.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00618},
pmid = {41335476},
issn = {2161-5063},
abstract = {Engineered microorganisms in biotechnology present biosafety and environmental management challenges. As the synthetic biology market develops and deploys new technologies, these engineered organisms may escape into unintended environments. Improved predictive computational tools are necessary to assess the potential establishment risk and environmental location of these escaped engineered microorganisms, assisting their design and management. Here, we present EnCen, a risk assessment Python software package that predicts the environmental range of engineered microorganisms through annotated functional one-hot-encoded similarity between the engineered microorganism and resident microorganisms of a given environment. EnCen utilizes publicly available composite metagenomes as representatives of microbial environments that occur along an agriculture-water cycle and can be customized for any additional target environment. This tool was deployed against case studies reported in the literature and to reassess commercially available bacterial biopesticides, highlighting both the successful recapture of previously reported dynamics and the identification of select commercial products that pose a wider establishment risk in multiple environments. When further utilizing EnCen to investigate the receiving environments comprising the central database, key enzyme classes are mapped as characteristics to select environments, prioritizing certain modifications likely leading to a greater risk (or effectiveness) of establishment. The results demonstrate that EnCen meaningfully summarizes publicly available metagenomic data, prioritizes environments to monitor for adverse effects, and analyzes potential impacts on microbial community composition and functioning. Overall, this study demonstrates a computational approach to managing engineered microorganisms, aiding in the safe deployment and benefit of industrial synthetic biology.},
}

@article {pmid41335362,
year = {2025},
author = {Jia, Y and Shi, Y and Wang, J and Liu, H and Wang, H and Huang, Y and Liu, Y and Chen, P and Peng, J},
title = {Astragalin attenuates caerulein-induced acute pancreatitis by targeting the NLRP3 signaling pathway and gut microbiota.},
journal = {Bioresources and bioprocessing},
volume = {12},
number = {1},
pages = {139},
pmid = {41335362},
issn = {2197-4365},
support = {82170661//National Natural Science Foundation of China/ ; 2023DK2002//Key Project of Research and Development Plan of Hunan Province/ ; 2025JJ60669//Hunan Provincial Natural Science Foundation of China/ ; 2024M763719//China Postdoctoral Science Foundation/ ; GZC20242045//Postdoctoral Fellowship Program of CPSF/ ; },
abstract = {BACKGROUND: Acute pancreatitis (AP) has caused great concern worldwide due to its serious threat to human health. Astragalin is a bioactive natural flavonoid compound with several pharmacological activities, but it remains unclear about its effect on AP. The objective of this experiment was to explore the mitigating efficacy of astragalin on caerulein-induced AP model and examine the underlying mechanisms.

METHODS: Following the assessment of astragalin's direct effects on pancreatic acinar cells using an in vitro AP model, an in vivo mouse model was established to further validate its efficacy and elucidate the underlying mechanisms. Pancreatic histopathology, amylase, and lipase levels of mice were observed to determine the optimal therapeutic dose of astragalin. The network pharmacology and RNA sequencing technology were used to reveal the possible targets and pathways. Subsequent molecular docking and western blot were conducted to validate the association between astragalin and key target molecules, as well as the NLRP3 signaling pathway. Combined with metagenomics and metabolomics analysis, the astragalin effective gut microbiota-metabolite-gene network was constructed. Moreover, fecal microbiota transplantation experiments were performed to clarify the importance of gut microbiota in astragalin-mediated alleviation of AP.

RESULTS: The results showed that astragalin attenuated caerulein-induced injury in AR42J cells in vitro. Consistent with these findings, in vivo experiments revealed that astragalin treatment significantly improved pancreatic pathological injury, cell apoptosis, and systemic inflammatory response in AP mice, particularly at high doses. The integrated analysis of network pharmacology and transcriptomics revealed that the NLRP3 signaling pathway was a key molecular pathway, which was further validated using western blot. Docking analysis showed that 12 target genes had good docking activity with astragalin. More intriguingly, it was found that astragalin could reverse gut microbiota dysbiosis by restoring microbial diversity, altering bacterial community composition, and modulating key metabolic pathways. Specifically, astragalin-effective correlation networks were constructed with Lachnoclostridium sp. YL32, Roseburia intestinalis, Ruminococcus gnavus, Lachnospiraceae bacterium Choco86, Anaerobutyricum hallii, etc. as the core strains, 22 metabolites, including 5-Methoxytryptophan, D-Serine, L-Tryptophan, L-Methionine, etc. as core metabolites, and NLRP3 pathway-related genes as the main regulatory targets. Furthermore, fecal microbiota transplantation experiments confirmed the involvement of gut microbiota in AP remission.

CONCLUSION: Collectively, these findings identify astragalin as a promising therapeutic agent for AP, targeting both the NLRP3 signaling cascade and gut microbial homeostasis.},
}

@article {pmid41334926,
year = {2025},
author = {Shulman, HB and Pyle, JAM and Classen, AT and Inouye, DW and Simberloff, R and Sorensen, PO and Thomas, W and Rudgers, JA and Kivlin, SN},
title = {Nutrient limitation shapes functional traits of mycorrhizal fungi and phosphorus-cycling bacteria across an elevation gradient.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0052325},
doi = {10.1128/msystems.00523-25},
pmid = {41334926},
issn = {2379-5077},
abstract = {In nutrient-limited high-elevation ecosystems, plants rely on arbuscular mycorrhizal (AM) fungi to provide mineral phosphorus (P) in the form of phosphate (PO4[3-]). AM fungi gather these nutrients from phosphorus-cycling bacteria (PCBs) that can mineralize PO4[3-] from organic matter and solubilize mineral-bound P. How climate, soil factors, and nutrient limitation influence AM fungi and PCB assembly remains unclear. We collected soil from montane meadows across a 1,000-m elevation gradient on three replicate mountainsides and analyzed AM fungal marker genes, P-cycling genes from shotgun metagenomes, and edaphic measurements. High-elevation soils had nearly 50-fold less soil PO4[3-] and 60% more AM fungal hyphae than low-elevation soils. AM fungal turnover was linked to changes in pH, organic carbon, and PO4[3][-]. The composition of 198 P-cycling genes was influenced by the AM fungal community structure. Drivers of individual PCB functional genes, including pH and organic carbon, varied with gene phylogeny. We found a trade-off in P-cycling strategies across elevation: P-rich, low-elevation soils supported root-colonizing AM fungi and organic P-mineralizing bacteria. P-poor, high-elevation soils were dominated by stress-tolerant AM fungi and mineral P-solubilizing bacteria. Our results suggest that AM fungi and PCB community turnover across elevation are both shaped by pH, organic carbon, and P availability. With continued climate warming, the structure and function of mountaintop ecosystems might shift to resemble lower elevations, disrupting long-established and specialized microbial assemblages, with consequences for P-cycling dynamics and the total P available to plant communities.IMPORTANCEPhosphorus (P) limits plant productivity in high-elevation ecosystems, yet the microbial networks that mobilize P, including arbuscular mycorrhizal (AM) fungi and phosphorus-cycling bacteria (PCBs), remain under-characterized in these nutrient-poor soils. We show that across a 10,00-m elevation gradient, AM fungi and P-cycling gene assemblages shift predictably with pH, organic carbon, and phosphate availability. Higher elevations, with less available P, select for stress-tolerant AM fungal taxa and PCB strategies geared toward mineral solubilization, while low-elevation sites favor root colonization by AM fungi and organic P mineralization. These results suggest that nutrient limitation can constrain microbial community assembly in consistent ways across landscapes. High mountain soils are low in P and rely on a network of underground AM fungi and PCB to deliver nutrients to plants. This study shows how those underground relationships reorganize with elevation and how climate change could collapse long-standing microbial strategies by pushing high-elevation ecosystems toward lowland conditions. As soils warm and dry, the microbial scaffolding that supports alpine plant life may become increasingly unstable.},
}

@article {pmid41334911,
year = {2025},
author = {Kandathil, AJ and Clipman, SJ and Anantharam, R and Duchen, D and Cox, AL and Larman, HB and Thomas, DL},
title = {Antibody-mediated control of anellovirus infection: evidence from people who inject drugs.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0161225},
doi = {10.1128/jvi.01612-25},
pmid = {41334911},
issn = {1098-5514},
abstract = {Infections with viruses belonging to the family Anelloviridae are widespread among humans. Although generally considered a commensal, there is evidence to suggest that these infections may be controlled by host immune responses. However, the mechanism of immune control remains unclear. Previous research has also suggested a possible role of anellovirus capsid spikes in immune evasion. To investigate the role of antibodies in controlling infection, we used AnelloScan to profile plasma collected every 6 months over 2 years from 10 persons who inject drugs (PWID). Participants were selected based on viremia patterns: persistent (n = 6) versus intermittent (n = 4). Long-read metagenomic sequencing revealed a higher median number of alphatorquevirus (TTV) species in participants with persistent viremia compared to those with intermittent viremia (P < 0.0001). AnelloScan detected TTV-specific antibodies among all study participants. No significant differences were observed between the two groups when all antibody-reactive peptides located in the capsid were included. However, among participants with intermittent viremia, antibodies were more frequently reactive to peptides located in the amino acid variable region of the capsid spike domain (P = 0.0429). These findings suggest that among PWID, antibodies targeting the sequence variable region of the spike domain appear to be associated with control of anellovirus infection. Additionally, anelloviruses might be susceptible to pre-existing immunity, and the amino acid variable region of the spike protein may play a role in viral infectivity.IMPORTANCEAnelloviruses are highly diverse and are recognized as the major component of the blood virome in healthy humans. Despite this, little is known about their interactions with their hosts. In this study, we found that anelloviruses can elicit antibody responses. Notably, antibodies that targeted a sequence variable region on spikes present on viral capsids were associated with truncation of plasma viremia. These data suggest a possible mechanism of immune control of anellovirus infections while also indicating a role of the capsid spikes in viral infectivity.},
}

@article {pmid41334589,
year = {2025},
author = {Li, J and Xu, Y and Wang, M and Lin, J and Sun, J and Ma, J and Zhang, H},
title = {Dual-source DPP4 drives intestinal fibrosis in Crohn's disease: synergistic therapeutic targeting of host and microbiota pathways.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593119},
doi = {10.1080/19490976.2025.2593119},
pmid = {41334589},
issn = {1949-0984},
mesh = {Animals ; Humans ; *Dipeptidyl Peptidase 4/metabolism/genetics ; *Crohn Disease/pathology/drug therapy/microbiology/metabolism ; Mice ; Fibrosis ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Male ; Myofibroblasts/metabolism ; Dipeptidyl-Peptidase IV Inhibitors/pharmacology ; *Intestines/pathology ; Sitagliptin Phosphate/pharmacology ; Mice, Inbred C57BL ; Female ; Dextran Sulfate ; },
abstract = {Crohn's disease (CD), a chronic inflammatory bowel disorder, often progresses to intestinal fibrosis and stricture, yet no effective anti-fibrotic treatments exist. This study reveals dipeptidyl peptidase 4 (DPP4) as a pivotal driver of fibrosis through bioinformatics analysis, clinical samples, and experimental models. Elevated DPP4 expression was observed in stenotic intestinal tissues of CD patients and dextran sodium sulfate (DSS)-induced fibrotic mice. Mechanistically, both membrane-bound DPP4 and soluble DPP4 (sDPP4) activated human intestinal myofibroblasts (HIMFs) via the PI3K-AKT pathway, stimulating migration, proliferation, and extracellular matrix deposition. Importantly, metagenomic sequencing revealed enrichment of microbial Dpp4 genes in fecal samples from CD patients with stenosis, and in vivo colonization with engineered E. coli overexpressing microbial DPP4 exacerbated fibrotic remodeling, confirming microbiota-derived DPP4 (mDPP4) as a pathogenic driver. Furthermore, pharmacological inhibition of host DPP4 (sitagliptin) or selective blockade of mDPP4 (Dau-d4) attenuated fibrosis in murine models, with combined therapy showing enhanced efficacy. These findings underscore the roles of DPP4, originating from both host and microbiota, and existing in membrane-bound and soluble forms, in promoting CD-associated intestinal fibrosis. This study identifies DPP4 as a novel therapeutic target, proposing dual-source inhibition as a promising strategy to prevent stricture formation in CD patients, thereby addressing a critical unmet clinical need.},
}

Animals
Humans
*Dipeptidyl Peptidase 4/metabolism/genetics
*Crohn Disease/pathology/drug therapy/microbiology/metabolism
Mice
Fibrosis
*Gastrointestinal Microbiome/drug effects
Disease Models, Animal
Male
Myofibroblasts/metabolism
Dipeptidyl-Peptidase IV Inhibitors/pharmacology
*Intestines/pathology
Sitagliptin Phosphate/pharmacology
Mice, Inbred C57BL
Female
Dextran Sulfate

@article {pmid41334206,
year = {2025},
author = {Yang, L and Liu, Y and Guo, S and Li, T and Nie, Q and Zhang, Y and Zeng, S and Wang, F and Liu, L},
title = {Mechanism of tobacco-sweet potato intercropping in suppressing Ralstonia solanacearum in flue-cured tobacco.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1688379},
pmid = {41334206},
issn = {1664-462X},
abstract = {Tobacco bacterial wilt (Ralstonia solanacearum) is a fatal pathogen of tobacco, causing severe losses annually. Intercropping has been proposed as a sustainable strategy to mitigate soil-borne pathogens through rhizosphere interactions. However, the mechanisms by which tobacco-sweet potato intercropping specifically affects the microecological environment and suppresses R. solanacearum remain poorly understood. To investigate the effect of the TSP model on the soil-borne pathogen of bacterial wilt (Ralstonia solanacearum) in tobacco-growing soil, this study compared and analyzed the characteristics and differences in bacterial wilt incidence, Ralstonia solanacearum content, phenolic acid components, metabolome, and metagenome between (T) and (TSP) systems. The results showed that compared to the T treatment, the TSP treatment reduced the incidence of bacterial wilt in flue-cured tobacco and significantly decreased the abundance of R. solanacearum in the soil by 21.4%, while increasing the total phenolic acid content by 21.9%. The total phenolic content in the TSP soil was increased by 21.9% compared to T. Differentially abundant metabolites between TSP and T were primarily enriched in carbohydrate metabolic pathways, such as nucleotide sugar biosynthesis, fructose, and mannose metabolism. The content of substances such as rhamnose, D-allose, and mannitol in T-treated soil was 2.14-6.62 times higher than that in TSP-treated soil, with new tobacco alkaloids being up to 91.09 times higher. Compared to the T treatment, the TSP treatment significantly increased the relative abundances of Acidobacteriota, Chloroflexota, Bradyrhizobium, Pseudolabrys, and Sphingomonas by 64.08%, 18.86%, 23.55%, 21.80%, and 12.98%, respectively. The content of Ralstonia solanacearum in the soil was positively correlated with differential metabolites such as mannitol, rhamnose, and D-allose (r = 0.8), while negatively correlated with phenolic acids such as syringic acid, ferulic acid, caffeic acid, and gallic acid, as well as microorganisms such as Chloroflexota, Gemmatimonadota, Acidobacteriota, and Sphingomonas. In summary, TSP can regulate soil metabolites, phenolic acids, and beneficial microorganisms, forming a synergistic network to suppress the content of Ralstonia solanacearum and reduce the risk of tobacco bacterial wilt. This provides a theoretical basis for regulating soil microecology and enhancing crop disease resistance in intercropping systems.},
}

@article {pmid41333806,
year = {2025},
author = {Al Bataineh, MT and Dash, NR and Mysara, M and Saeed, O and Alkhayyal, N and Talaat, IM and Bendardaf, R and Saber-Ayad, M},
title = {Metagenomic analysis of gut microbiota in colorectal adenocarcinoma in the MENA region.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1634631},
pmid = {41333806},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Male ; Female ; Middle Aged ; *Adenocarcinoma/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; DNA, Bacterial/genetics/chemistry ; Middle East ; Feces/microbiology ; Phylogeny ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {BACKGROUND: Growing evidence suggests that gut microbiota plays a role in the development of colorectal cancer (CRC), and a few bacterial strains have been linked to carcinogenesis. Contrary to the Western population, the relationship between pro-cancer microorganisms and CRC among Middle Eastern individuals remains largely unexplored. Ninety-eight samples from Middle Eastern individuals with and without CRC were subjected to microbial profiling based on the 16S rRNA gene.

RESULTS: The CRC group exhibited a more complex gut microbiota with clusters that were significantly distinct from those of the control group. The taxonomic orders Caulobacterales, Rhizobiales, Sphingomonadales, and Burkholderiales, along with the genera Recibecterium and Sphingobium, were overrepresented in the CRC samples based on differential abundance testing between the CRC and control groups. Utilizing 16S-based functional prediction, we identified a significant enrichment of pathways vital for pentose and glucuronate interconversions, metabolism of terpenoids and polyketides, spliceosome, and dTMP kinase pathways within the CRC group. Moreover, we observed a link between Herbaspirillum huttiense and the pathways regulating the actin cytoskeleton; this intriguing connection may provide insights into the molecular mechanisms underlying cytoskeletal rearrangement and carcinogenesis triggered by H. huttiense.

CONCLUSIONS: The findings of this study support the connection between gut microbiota and the development of CRC and highlight region-specific microbial signatures that may serve as non-invasive diagnostic biomarkers or predictive tools for early screening in Middle Eastern populations, where CRC is increasingly diagnosed at advanced stages. These insights could inform the development of microbiome-based screening panels and personalized prevention strategies adapted to the MENA region's unique genetic, dietary, and environmental profiles.},
}

Humans
*Colorectal Neoplasms/microbiology
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
*Metagenomics
Male
Female
Middle Aged
*Adenocarcinoma/microbiology
*Bacteria/classification/genetics/isolation & purification
Aged
DNA, Bacterial/genetics/chemistry
Middle East
Feces/microbiology
Phylogeny
DNA, Ribosomal/genetics/chemistry

@article {pmid41333777,
year = {2025},
author = {Zhang, Q and Gong, Q and Sun, X and Zhu, H},
title = {Massive hemoptysis as the sentinel symptom: a case report of pulmonary nocardiosis in an immunocompetent patient.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1677156},
pmid = {41333777},
issn = {2296-858X},
abstract = {Pulmonary nocardiosis is frequently missed or misdiagnosed due to its atypical clinical symptoms and non-specific imaging findings. Moreover, delayed diagnosis and treatment can lead to high mortality rates, underscoring the need to enhance etiological diagnosis. Here, we report a 55-year-old immunocompetent woman who developed pulmonary Nocardia cyriacigeorgica infection with massive hemoptysis as the initial symptom. The patient had no history of chronic respiratory diseases. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid collected via bronchoscopy was performed, which confirmed the diagnosis. After targeted therapy with oral sulfamethoxazole-trimethoprim and linezolid, the patient achieved significant symptomatic and radiological improvement, accompanied by normalization of white blood cell count and neutrophil count. No recurrence was observed during follow-up.},
}

@article {pmid41333773,
year = {2025},
author = {Li, Q and Sun, X and Lei, W and Zhu, Y and Du, W and Jiang, X and Su, N},
title = {Psittacosis chlamydia pneumonia complicated with organizing pneumonia: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1670456},
pmid = {41333773},
issn = {2296-858X},
abstract = {BACKGROUND: Secondary organizing pneumonia (SOP) may develop following infections. Psittacosis, caused by Chlamydia psittaci (C. psittaci), is a zoonotic disease transmitted from birds to humans. It can present with a wide spectrum of symptoms, ranging from mild flu-like illness to life-threatening severe pneumonia. Cases of C. psittaci infection complicated by organizing pneumonia (OP) are rarely reported, and delayed treatment may pose a life-threatening risk.

METHODS: We report a case of C. psittaci pneumonia complicated by OP. To identify additional cases and clarify the clinical features of this condition, a literature search was conducted using the PubMed and Embase databases for the period from January 1995 to May 2025. The search included the following keywords: "psittacosis," "Chlamydia psittaci," "chlamydia," "organizing pneumonia," and "bronchiolitis obliterans with organizing pneumonia."

RESULTS: A 66-year-old male with a history of poultry farming presented with fever, cough, sputum production, and hemoptysis. Empirical antimicrobial therapy with ceftizoxime was ineffective. To identify the etiology of the pulmonary lesions, bronchoscopy was performed, and C. psittaci infection was confirmed by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Although the lesions partially resolved after moxifloxacin therapy, the patient experienced recurrent episodes. Chest CT revealed migratory lesions, which are uncommon in C. psittaci pneumonia. Further pathological examination of the specimen confirmed the diagnosis of OP. The patient's condition improved following corticosteroid therapy. A review of the literature indicated that none of the three previously reported cases were definitively diagnosed at initial admission; all presented primarily with fever and cough. One case progressed to severe pneumonia and resulted in death.

CONCLUSION: OP caused by C. psittaci pneumonia presents with non-specific symptoms and signs, making early diagnosis challenging. During treatment of C. psittaci pneumonia, if empirical anti-infective therapy shows no response after three days, or if imaging reveals features such as consolidation, migratory lesions, or a reverse halo sign, the possibility of concurrent OP should be considered. Pathological examination is recommended in such cases to avoid missed diagnosis and to ensure timely intervention.},
}

@article {pmid41333054,
year = {2025},
author = {Kravchuk, OI and Finoshin, AD and Nikishina, YO and Melnikova, VI and Kublanov, IV and Sutormin, DA and Rusanova, AN and Ri, MT and Isaev, AB and Mikhailov, KV and Ziganshin, RH and Adameyko, KI and Anashkina, AA and Ignatyuk, VM and Gornostaev, NG and Voronezhskaya, EE and Sokolova, AM and Mikhailov, VS and Lyupina, YV},
title = {Evolutionary conservation of dopamine-mediated cellular plasticity in Arctic sponges (Porifera).},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1671771},
pmid = {41333054},
issn = {2296-889X},
abstract = {Dopamine is an evolutionarily ancient signaling molecule implicated in stress responses across the tree of life. The role of dopamine is well-documented in the nervous system of animals, yet in the early-branching animal lineage of sponges its utility is poorly understood. Arctic marine sponges inhabiting the tidal zone of the White Sea, with fluctuating seasonal ice cover and solute concentrations, exhibit remarkable physiological plasticity, making them ideal models for studying conserved stress-response mechanisms. We investigated the dopamine signaling in two sponge species, Sycon ciliatum (class Calcarea) and Halisarca dujardini (class Demospongiae), using metagenomics, transcriptomics, high performance liquid chromatography, mass spectrometry, molecular docking, and immunofluorescence. S. ciliatum expresses an aromatic amino acid decarboxylase-like enzyme and efficiently converts L-DOPA to dopamine, whereas H. dujardini lacks this canonical biosynthetic enzyme, but accumulates dopamine, likely via its symbionts. During morphogenetic transitions in H. dujardini, genes involved in dopamine turnover, including tyrosinase, dopamine β-hydroxylase, and G protein-coupled receptors (GPCRs), showed dynamic expression. Molecular docking revealed that GPCR affinity for dopamine is modulated by cellular redox status. Notably, we report the first evidence of post-translational dopaminylation of cytoskeleton proteins in a non-bilaterian animal. Fluctuations in cellular dopamine levels and actin dopaminylation correlated with structural remodeling of the aquiferous system throughout the sponge life cycle. These findings demonstrate that dopamine regulates cellular plasticity through both transcriptional and post-translational mechanisms. The discovery of dopaminylation in sponges expands the evolutionary scope of catecholamine signaling and underscores the ancient role of dopamine in the regulatory interactions of animal cells.},
}

@article {pmid41332906,
year = {2025},
author = {Zhao, Z and Lu, L and Yi, Y and Gao, N and Hu, J and Han, G and Ma, X},
title = {Gut microbiota signature in a cohort of Chinese patients with rosacea.},
journal = {Biochemistry and biophysics reports},
volume = {44},
number = {},
pages = {102361},
pmid = {41332906},
issn = {2405-5808},
abstract = {BACKGROUND: Rosacea is a chronic inflammatory skin disease characterized by diverse symptoms and variable clinical progression, which can significantly impair patients' quality of life and mental health. The exact etiology of rosacea remains elusive. It has been hypothesized that specific microorganisms may trigger symptom onset and play crucial roles in the pathogenesis of the disease.

OBJECTIVE: We performed a case-control study to investigate the gut microbiome of rosacea patients compared to controls matched by age, sex in China.

METHODS: The study cohort comprised eight patients diagnosed with rosacea and eight age- and sex-matched healthy controls residing in Beijing. Metagenomic sequencing was performed using on a llumina Novaseq 6000 platform. Hospital Anxiety and Depression Scale was used to evaluate the severity of anxiety and depression of rosacea patients. Skindex-16 score was used to assess dermatology-specific health-related quality of life (HrQoL) in patients with rosacea. The clinical evaluation of acne was done using the ECLA score.

RESULTS: The rosacea patients showed higher HADS and Skindex-16 score (15.375 ± 1.302 and 46 ± 9.75 respectively) vs healthy controls (3.425 ± 1.308 and 0 respectively). A clear distinction was observed between the rosacea group and the control group, characterized by a significant increase in the abundance of Turicibacter_sp._TJ11, Turicibacter_sp._H121,Turicibacter_sp._TA25,Turicibacter_sp._T129,Ruminococcus_sp._AF18-22,Ruminococcus_sp._CAG:379,Ruminococcus_sp._AM2829LB,Ruminococcus_callidus, Ruminococcus_sp._AM36-18,Ruminococcus_sp._AF43-11,Ruminococcus_sp._AM28-41,Streptococcus sp. 23.2,Streptococcus infantarius, Streptococcus vestibularis, Streptococcus salivarius, Streptococcus gordonii, Clostridium_sp._CAG:798, Clostridium_tertium, Alistipes_sp._Z76 and Lachnospiraceae_bacterium_XBB2008in the rosacea group. In contrast, reduced levels were detected in the rosacea group for Clostridium_sp._AF12-41, Clostridium_sp._CAG:299, Clostridium_sp._OM05-5BH,Clostridium_sp._AF24-2LB, Clostridium_sp._AM18-55, Clostridium_sp._CAG:43, Clostridium_sp._OM047,Clostridium_sp._TF1113AC,Clostridium_sp._OF134,Clostridium_disporicum, Butyrivibrio_sp._CB08,Butyrivibrio_sp._INlla14, Roseburia_sp._CAG:50 (p < 0.05). Pearson correlation analysis revealed that Gemmiger_sp._An120 was positively correlated with Skindex-16 and negatively correlated with ECLA score (P < 0.05). Clostridium_sp._CAG:299 was negatively correlated with HADS scores and positive correlation with ECLA score (P < 0.05). KEGG pathway analysis found KO05034, KO04024 and KO00920 pathways exhibited increased activity in the Rosacea group (P < 0.05).

CONCLUSIONS: The gut microbiota in individuals with rosacea displayed changed from that of healthy control. These microbial alterations may contribute to the pathogenesis of rosacea through multiple mechanisms, including impairment of the intestinal barrier function, induction of pro-inflammatory cytokine release, and modulation of neurotransmitter synthesis. By integrating taxonomic shifts with functional alterations, this study provides deeper insights into the gut ecosystem changes associated with systemic inflammation in rosacea.},
}

@article {pmid41332561,
year = {2025},
author = {Ahmed, MA and John, J and Campbell, BJ},
title = {Ecological distribution, environmental roles and drivers of Actinobacteriota in two Mid-Atlantic estuaries.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.21.689735},
pmid = {41332561},
issn = {2692-8205},
abstract = {Actinobacteriota, a bacterial phylum renowned for members that produce bioactive compounds (e.g., antibiotics), has key roles in terrestrial and aquatic ecosystems. Although soil and marine/freshwater Actinobacteriota are well studied, functions and activities of their estuarine counterparts are poorly understood. We characterized 67 metagenome-assembled genomes (MAGs) belonging to 12 Actinobacteriota families from Chesapeake and Delaware Bay water samples across different seasons, salinities, and size fractions. MAGs from four dominant families, Ilumatobacteraceae, Nanopelagicaceae, Microbacteriaceae, and S36-B12, were examined in depth for their abundance, functional potential, estimated growth rates, and gene expression among samples. Actinobacteriota were most abundant in low- to medium-salinity samples during spring and summer. Their abundance patterns were strongly influenced by combinations of salinity, temperature, and phosphate, nitrate and silicate concentrations. Notably, many exhibited high estimated growth rates under low and medium salinities in summer. Members of the four major families showed a range of metabolic capacities from generalist to specialist, and all encoded biosynthetic gene clusters (BGCs) for secondary metabolites, particularly terpenes and betalactones, that were differentially expressed across conditions. Bay, salinity and size fraction were the primary drivers of gene expression differences. Distinct secondary metabolite genes were expressed between bays, with higher expression generally observed in medium compared to low salinities. These findings underscore the metabolic versatility and environmental responsiveness of Actinobacteriota, highlighting their active role in estuarine microbial communities and their contributions to biogeochemical cycling in dynamic coastal ecosystems.},
}

@article {pmid41332430,
year = {2025},
author = {Li, L and Zhou, N and Wang, Z and Wang, T and Wang, Y and Qiao, F and Du, ZY and Zhang, ML},
title = {Intestinal microbiota contributes to the heterogeneity of fat deposition by promoting mitochondrial fatty acid β-oxidation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593076},
doi = {10.1080/19490976.2025.2593076},
pmid = {41332430},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Fatty Acids/metabolism ; Carnitine/biosynthesis/metabolism ; Oxidation-Reduction ; *Mitochondria/metabolism ; Zebrafish ; Lipid Metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Male ; Humans ; Feces/microbiology ; },
abstract = {The gut microbiota plays a crucial role in lipid metabolism in both humans and animals. However, the specific contributions of gut microbiota and their associated metabolites to fat deposition, as well as the underlying mechanisms, remain largely unexplored. In this study, we demonstrated that the intestinal microbiota mediated the heterogeneity of mesenteric fat index (MFI), as evidenced by fecal microbiota transplantation (FMT) experiments. Notably, analysis of the 16S rRNA gene amplicon sequencing of 44 samples revealed a significantly higher abundance of Cetobacterium somerae in the Low MFI group, with a positive correlation to reduced MFI. Serum metabolomics analysis confirmed that L-Carnitine emerged as the most differentially abundant metabolite in the Low MFI group and exhibited a strong positive correlation with C. somerae abundance. Metagenomic analysis showed that microbial genes related to L-Carnitine biosynthesis were significantly enriched in the Low MFI group. Further, C. somerae was isolated and cultured, and its subsequent monocolonization in germ-free zebrafish and tilapia demonstrated its lipid-lowering effects by enhancing mitochondrial fatty acid β-oxidation. Whole genome sequencing demonstrated C. somerae could encode the [EC:1.2.1.3] gene, which promotes the production of 4-trimethylammoniobutanoate, a precursor of L-Carnitine, thereby enhancing L-Carnitine biosynthesis by the host and gut microbiota, leading to the reduced fat deposition in Nile tilapia. In conclusion, C. somerae, a core gut microbe with high abundance in aquatic teleost intestines, plays an important role in host lipid metabolism. This study advances our understanding of how core gut microbes shape host phenotypes and provides novel insights into manipulating core gut colonizers to reduce fat deposition.},
}

*Gastrointestinal Microbiome/physiology
Animals
*Fatty Acids/metabolism
Carnitine/biosynthesis/metabolism
Oxidation-Reduction
*Mitochondria/metabolism
Zebrafish
Lipid Metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Fecal Microbiota Transplantation
RNA, Ribosomal, 16S/genetics
Male
Humans
Feces/microbiology

@article {pmid41331875,
year = {2025},
author = {Kong, L and Mao, Y and Zheng, R and Feng, Y and Chen, B and Wu, X and Zhu, Q and Feng, J and Liu, S},
title = {Overlooked siderophore producers favor ammonium oxidation in global wastewater treatment plants.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02290-9},
pmid = {41331875},
issn = {2049-2618},
support = {523B2095//National Natural Science Foundation of China/ ; Nos. 52270016//National Natural Science Foundation of China/ ; 2022YFC3203003//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Iron is essential for biological nitrogen removal in wastewater treatment plants (WWTPs), as a significant portion of microbial nitrogen-transforming enzymes require iron. However, iron bioavailability is a global challenge for nitrogen removal microbes in WWTPs, where it often exists in insoluble forms due to its complexation with various wastewater constituents.

RESULTS: Combined laboratory experiment and metagenomic analysis of 52 global WWTPs, we found that siderophore-producing bacteria (SPB) were previously uncharacterized dominant members in activated sludge. SPB enhance the iron uptake of activated sludge microbial communities by facilitating the transport of iron ions from insoluble sources into the cells. Of the 1328 total recovered metagenome-assembled genomes (MAGs) from global WWTPs, 6.2% were identified as SPB, while 79.3% of MAGs could utilize siderophores, indicating widespread sharing of siderophores in WWTPs. Interestingly, nearly all ammonium-oxidizing bacteria (AOB) from WWTPs lacked siderophore-producing capacity, and exogenous siderophore (20 µM pyochelin) addition boosted ammonium oxidation rates by 28.2%. Moreover, strong indications were found for an association between AOB and the SPB in global WWTPs, suggesting their symbiotic interaction is a common and critical process to maintain ammonium oxidation performance. SPB in WWTPs were predominantly aerobic or facultative anaerobic heterotrophic bacteria, exhibiting low taxonomic diversity but high abundance.

CONCLUSIONS: This study reveals SPB as previously overlooked but crucial contributors to biological nitrogen removal in global WWTPs, providing foundational insights into iron-based microbial cooperation within engineered systems. Modulating SPB activity based on their metabolic characteristics is a promising strategy to cope with low iron bioavailability issue for biological processes in WWTPs. Video Abstract.},
}

@article {pmid41331807,
year = {2025},
author = {Rouzban, T and Goudarzi, R and Motamedi, E and Ghollasi, M and Zeinalabedini, M and Ariaeenejad, S},
title = {Metagenomic laccase-catalyzed crosslinking of wheat proteins for enhanced soybean meal nutritional value: applications in poultry feed and food industry.},
journal = {BMC biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12896-025-01081-2},
pmid = {41331807},
issn = {1472-6750},
support = {0//Agricultural Biotechnology Research Institute of Iran (ABRII)/ ; },
}

@article {pmid41331687,
year = {2025},
author = {Abedi, Z and Sheikh Beig Goharrizi, MA and Abbasi, A and Sadat Soleimani Zakeri, N and Jangi, H},
title = {Metagenomic insights into microbial community alterations and co-occurrence networks in infective endocarditis.},
journal = {Genomics & informatics},
volume = {23},
number = {1},
pages = {25},
pmid = {41331687},
issn = {1598-866X},
abstract = {BACKGROUND: Infective endocarditis (IE) is a serious infection of the heart valves, and standard culture methods often miss the bacteria responsible, especially in culture-negative cases. To address this, we used 16S rRNA gene-based next-generation sequencing (NGS) on heart valve tissue. This approach allowed us to map out the bacterial communities present and evaluate their potential role in IE.

RESULT: We identified six key bacterial genera-Enterococcus, Streptococcus, Coxiella, Staphylococcus, Haemophilus, and Cutibacterium-plus three specific species: Streptococcus troglodytae, Haemophilus parainfluenzae, and Coxiella burnetii. Our co-occurrence analysis showed that these bacteria tend to exist independently within infected valve tissue, with no significant correlations between them.

CONCLUSION: We detected bacterial taxa, including Cutibacterium and Streptococcus troglodytae. Although S. troglodytae is rarely associated with IE, and Cutibacterium comprises low-abundance bacteria not typically linked to this condition. These findings demonstrate the value of NGS in identifying pathogens that standard culture methods may overlook. As these results are based on computational analyses, further laboratory validation is required. Incorporating NGS into diagnostic protocols may enhance pathogen detection in culture-negative IE and support more targeted treatment and prevention strategies.},
}

@article {pmid41331561,
year = {2025},
author = {Tian, J and Wang, X and Zhu, Y and Kong, F and Sun, J},
title = {Diagnosis of esophageal pleural fistula via metagenomic next-generation sequencing of pleural effusion: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1689},
pmid = {41331561},
issn = {1471-2334},
}

@article {pmid41331462,
year = {2025},
author = {Xu, W and Wang, W and Liu, Q},
title = {Identification of a novel pegivirus in reindeer (Rangifer tarandus valentinae) in Northeastern China.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-025-05167-z},
pmid = {41331462},
issn = {1746-6148},
support = {2024YFD1800103//This study was financially supported by the National Key Research and Development Program of China ./ ; },
abstract = {BACKGROUND: Pegiviruses (family Flaviviridae), associated with persistent infections in diverse mammalian and avian hosts, are increasingly recognized for their evolutionary significance. Reindeer (Rangifer tarandus valentinae), semi-domesticated in northeastern China's Greater Khingan Mountains, are critical reservoirs for zoonotic pathogens and face growing human contact due to tourism. This study aims to investigate the viral diversity in reindeer, identify potential viruses of public health or veterinary significance, and highlight the need for viral surveillance at the human-animal interface.

RESULTS: The metagenomic sequencing analysis identified a novel pegivirus, Rangifer tarandus pegivirus (RPgV), in reindeer serum from Inner Mongolia. The near-complete genome (10,367 nucleotides; GenBank OQ164633) encodes a polyprotein (3,249 amino acids) processed into four structural (Y, E1, E2, X) and six non-structural (NS2-NS5B) proteins. RPgV shares 57.3% nucleotide and 60.6% amino acid identity with its closest relative, equine pegivirus (EPgV), but exceeds species demarcation thresholds for NS3 (p-distance: 0.340) and NS5B (p-distance: 0.408). Phylogenetic analyses placed RPgV within the equine pegivirus clade, while cophylogenetic models revealed strong host specificity and co-divergence over evolutionary timescales. With a 9.5% prevalence (2/21) in sampled reindeer, RPgV represents the first pegivirus detected in Cervidae, underscoring its potential role in wildlife virome dynamics.

CONCLUSION: This study identified a novel pegivirus, which expands its host range, geographic distribution, and genetic diversity. This discovery highlights the need for enhanced surveillance of understudied viral families in regions where human-wildlife interfaces amplify zoonotic risks.},
}

@article {pmid41331251,
year = {2025},
author = {Zhao, Y and Chen, H and Huang, J and Chistoserdova, L and Yu, Z},
title = {The gut methanotroph Methylocystis intestini modulates intestinal peristalsis and fat metabolism via reducing methane levels.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66596-w},
pmid = {41331251},
issn = {2041-1723},
support = {32300051//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Methane, a predominant component of human intestinal gas, has been reported to be associated with a reduction in intestinal transit speed, as well as correlations with elevated body mass index. While the gut methanogenic archaea that produce this gas have been studied, the countervailing role of methane-consuming bacteria (methanotrophs) within the human gut ecosystem remains a critical, under-explored area. The potential for these bacteria to act as a built-in sink for intestinal methane and thereby mitigate its negative physiological effects is unknown. Here, we isolate an unreported methanotroph from human fecal samples, classified as Methylocystis intestini. Using a mouse model, we observe that methane challenge is associated with gastrointestinal motility and fat metabolism. We then demonstrate that the administration of Methylocystis intestini effectively reverses these dysfunctional processes, restoring motility and metabolic parameters. Additional analysis of methane-oxidation genes abundance in 1207 public metagenomic sequences from individuals with varying health statuses, including obesity and constipation, provides consistent correlative support for our experimental conclusions. Expanding this view to a global scale, we conducted a metagenomic survey of 550 human fecal samples from populations across five continents. This broader analysis reveals that methane-oxidizing genes are not a rarity but a common feature of the human gut microbiome, being detectable in over 91% of samples. This ubiquity underscores their fundamental role in human biology. Collectively, our findings establish gut methanotrophs as key mediators of intestinal methane level. Their presence is widespread across global populations, and their functional capacity can balance the effects of methane on host physiology. This work elucidates a crucial component of gut homeostasis and opens a promising avenue for developing microbiome-based therapeutic strategies aimed at managing methane-related gastrointestinal disorders by harnessing the power of these native methane-consuming bacteria.},
}

@article {pmid41333904,
year = {2024},
author = {Choi, CH and Lee, M and Lee, SE and Shin, H and Choi, MM and Kim, JW and Yi, H and Chung, YS},
title = {[Monkeypox Virus Genomic Analysis in the Republic of Korea: A Comparison of Metagenomic- and Probe Hybridization Capture Sequencing Methods].},
journal = {Jugan geon-gang gwa jilbyeong},
volume = {17},
number = {20},
pages = {859-873},
pmid = {41333904},
issn = {2586-0860},
abstract = {Monkeypox virus (MPXV) whole-genome from specimens of individuals diagnosed with mpox in the Republic of Korea (ROK) between May 2022 and November 2023 was analyzed comprehensively. An infectious disease originating in Africa, mpox gained global significance after the first case was confirmed in the UK in May 2022, subsequently spreading worldwide. In the ROK, 155 infection cases were recorded, predominantly transmitted through close contact with symptomatic individuals. MPXV, consisting of approximately 197,000 base pairs of double-stranded DNA, encompasses approximately 191 genes consisting of inverted terminal repeats at both ends and a central conserved region. The virus is categorized as Clade I (Central African type) and Clade II (West African type), with Clade I and II reporting fatality rates of 1-10% and less than 1%, respectively. Two sequencing methods, metagenomic and hybridization capture sequencing, were used to perform a thorough whole-genome analysis. Compared to metagenomic sequencing, hybridization capture sequencing demonstrated superior efficiency in generating MPXV read sequences. The proportion of virus reads varied based on specimen type, informing the selection of targets for whole-genome analysis. Genomic phylogenetic analysis revealed that the MPXV in the ROK belonged to lineage C.1, indicating sustained domestic transmission and providing crucial insights for national and international responses to MPXV variants. This information will contribute to understanding infection pathways and improving strategies for disease response and prevention.},
}

@article {pmid41330454,
year = {2025},
author = {Zhao, D and Zou, B and Do, QL and Wu, SK and Shen, Y and Yang, Y and Kang, J and Su, KP and Wang, B},
title = {Circadian rhythms and gut microbiota Dysbiosis: emerging gut-brain axis pathways in insomnia pathophysiology and Therapeutics.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106203},
doi = {10.1016/j.bbi.2025.106203},
pmid = {41330454},
issn = {1090-2139},
abstract = {Insomnia, a widespread sleep disorder, significantly impacts mental and physical health. Emerging research highlights the crucial role of gut microbiota (GM) in modulating circadian rhythms (CR), which regulate sleep-wake cycles. This review explores the interplay between GM dysbiosis, CR disruptions, and insomnia, synthesizing findings from human and animal studies. GM dysbiosis is linked to reduced microbial diversity and altered abundance of key taxa, such as short-chain fatty acid-producing bacteria, which influence clock gene expression and hormonal rhythms. CR disruption exacerbates GM imbalances, forming a feedback loop that impairs sleep regulation through both central and peripheral pathways. We also examine the therapeutic potential of probiotics in restoring GM balance and synchronizing CR. Clinical trials suggest that specific probiotic strains improve sleep quality by modulating microbial metabolites and their downstream effects on the circadian system. However, inconsistencies in outcomes underscore the need for precision interventions. The review concludes by identifying gaps in the current literature, emphasizing the necessity of integrative approaches combining metagenomics and personalized medicine to optimize GM-targeted therapies. These insights pave the way for novel, safer, and more effective strategies to manage insomnia by addressing its biological underpinnings.},
}

@article {pmid41330298,
year = {2025},
author = {Huang, Y and Li, R and Dai, Y and Ren, Z and Wu, J},
title = {Migration characteristics of ARGs from pig manure in compost - soil - lettuce.},
journal = {Ecotoxicology and environmental safety},
volume = {308},
number = {},
pages = {119447},
doi = {10.1016/j.ecoenv.2025.119447},
pmid = {41330298},
issn = {1090-2414},
abstract = {This study aims to reveal the contamination patterns, persistence characteristics, and fate dynamics of ARGs during aerobic composting of swine manure with different carbon-nitrogen ratios (C/N = 15:1, 25:1, 35:1) and their subsequent dissemination in soil-plant systems following fertilization. The absolute abundances of 101 ARGs of six categories ranged from 10[5] to 10[14] copies/g during the composting process. The tetracyclines, macrolides and β-lactams ARGs were effectively reduced by the maturation phase. Among them, the β-lactam ARGs had the highest abatement efficiency (73-89 %). Quinolones, aminoglycosides and sulfonamides ARGs had relatively high residues during the maturation phase. Composting treatments with higher C/N (25:1 and 35:1) exhibited superior performance in ARGs reduction. Metagenomic analysis revealed the compost microbial community succession from Firmicutes to Proteobacteria and Actinobacteria. Luteimonas may be potential hosts for high-residual ARGs in compost, while Acinetobacter exhibited strong associations with β-lactam and macrolide ARGs that can be easily reduced. The ARGs in the fertilized soil increased significantly. ARGs such as floR, tetG-01, sul1 and sul2 have the highest abundance in the soil where lettuce is grown. The ARGs reduction is better in C/N 25:1 group, and the ARGs abundance of the soil is lower after fertilization with compost products. The sulfonamide sul1 and sul2 genes have always maintained a high abundance in compost, soil and lettuce. This study provides a theoretical basis for controlling the residue and spread of ARGs by regulating the C/N of compost to drive changes in microbial community.},
}

@article {pmid41330199,
year = {2025},
author = {Li, S and Wang, XR and Han, JR and Lian, WH and Ali, M and Liu, YH and Liu, J and Huang, J and He, HH and Govindan, R and Abdalla Abdelshafy Mohamad, O and Fang, BZ and Dong, L and Li, WJ},
title = {Genome-centric culture-enriched metagenomics reveals temperature-driven reassembly and functional stratification in culturable desert soil bacteria.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128411},
doi = {10.1016/j.micres.2025.128411},
pmid = {41330199},
issn = {1618-0623},
abstract = {Desert ecosystems cover nearly one-third of Earth's land surface and face rising temperatures and climatic variability. Soil microbiomes underpin biogeochemical cycling and ecosystem resilience in these arid landscapes, yet the genome-resolved temperature responses of their culturable fraction remain poorly understood. Here, we employed genome-centric culture-enriched metagenomics (CE-MGS) to rhizosphere and bulk desert soils from the Gurbantunggut Desert incubated at 15°C, 30°C, and 45°C. From 90 culture-enriched metagenomes, we reconstructed 1184 cultivated metagenome-assembled genomes (cMAGs), including 218 putative novel genomospecies across 73 bacterial genera, substantially expanding the genomic representation of desert bacteria. Temperature influenced both community composition and interactions, with Actinomycetota, Pseudomonadota, and Bacillota dominating at 15°C, 30°C, and 45°C, respectively. Co-occurrence networks showed that lower temperatures and rhizosphere soils supported more interconnected consortia of culturable bacteria and that key hub taxa shifted across thermal regimes, reflecting temperature-driven reorganization of interactions within the culturable microbial community. Functional profiling revealed that temperature selected for specialized taxa, with elevated temperatures favoring redox-efficient pathways and more energy-efficient resource use. While representing only the culturable fraction of desert soil microbiomes, CE-MGS enables genome reconstruction of experimentally tractable microbes, linking identity, function, and thermal adaptation. These results provide a genome-resolved view of temperature responses, extend understanding of desert microbial adaptation beyond previous culture-independent studies, and establish CE-MGS as a practical approach to access ecologically relevant microbes for conservation and biotechnological applications under a warming climate.},
}

@article {pmid41330099,
year = {2025},
author = {Barman, P and Paul, A and Sinha, S and Saha, T and Mondal, N and Dutta, S and Chatterjee, S and Ghosh, W and Chakraborty, R},
title = {Microbial-viral synergy in Eisenia fetida gut supports earthworm survival, detoxification, and functional resilience.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181101},
doi = {10.1016/j.scitotenv.2025.181101},
pmid = {41330099},
issn = {1879-1026},
abstract = {The ecological success of Eisenia fetida within decomposer food webs is closely linked to the functional diversity of its gut microbiome. This study integrates 16S rRNA gene profiling, whole-metagenome sequencing, and virome analysis to elucidate how microbial and viral communities within the earthworm gut contribute to nutrient biosynthesis, xenobiotic degradation, and environmental adaptation. Earthworms reared on compost feed enriched with Quisqualis indica plant matter showed selective enrichment of bacterial genera such as Ohtaekwangia, Nocardioides, and Steroidobacter, which are associated with hydrocarbon degradation and aromatic compound detoxification. Functional annotation of the gut metagenome revealed complete biosynthetic pathways for riboflavin, lysine, and methionine, and degradation routes for 3-nitropropionic acid (3-NPA) and aromatic pollutants. The gut virome, dominated by Siphoviridae and Myoviridae, carried auxiliary metabolic genes (AMGs) related to redox and xenobiotic metabolism, highlighting viral contributions to microbial adaptability. Reconstruction of metagenome-assembled genomes (MAGs), including a high-quality Flavobacterium MAG encoding both riboflavin biosynthesis and denitrification genes, underscored metabolic specialization within the gut. Collectively, these findings demonstrate that bacterial-viral metabolic synergy underpins E. fetida survival and ecological resilience, suggesting new microbiome-informed strategies for biowaste valorization and soil health restoration through vermicomposting.},
}

@article {pmid41329990,
year = {2025},
author = {Choi, HI and Cha, JM},
title = {Non-invasive colorectal cancer screening: emerging tools and clinical evidence.},
journal = {Clinical endoscopy},
volume = {},
number = {},
pages = {},
doi = {10.5946/ce.2025.246},
pmid = {41329990},
issn = {2234-2400},
abstract = {The fecal immunochemical test (FIT) is a widely used non-invasive screening method for colorectal cancer (CRC) in many countries, valued for its simplicity, affordability, and reasonable sensitivity. Typically recommended on an annual or biennial basis, the FIT is effective in reducing CRC incidence and mortality by facilitating early detection. Stool DNA tests, including multitarget DNA tests and DNA methylation assays, demonstrate higher sensitivity than FIT for CRC and advanced adenomas, although they have slightly lower specificity and higher cost. These tests are generally performed at longer intervals, such as every 3 years, and are useful alternatives for individuals who are unwilling or unable to undergo a colonoscopy. Emerging non-invasive CRC screening tools, such as liquid biopsy, microRNA, microbiome tests, and urine-based tests, are being developed to improve patient compliance and test convenience. In particular, liquid biopsy offers a minimally invasive option that may be more acceptable to populations hesitant to undergo stool-based tests. Furthermore, the integration of machine learning with metagenomic sequencing data has shown promise in distinguishing patients with CRC from healthy individuals. As CRC screening evolves, these novel approaches may enable the development of more personalized, accessible, and effective screening strategies, ultimately improving adherence and reducing CRC-related mortality.},
}

@article {pmid41328758,
year = {2026},
author = {Plewnia, A and Hoenig, BD and Lötters, S and Heine, C and Erens, J and Böning, P and Bending, GD and Krehenwinkel, H and Williams, MA},
title = {The Emergence of a CRISPR-Cas Revolution in Ecology: Applications, Challenges, and an Ecologist's Overview of the Toolbox.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70086},
doi = {10.1111/1755-0998.70086},
pmid = {41328758},
issn = {1755-0998},
support = {//University of Warwick/ ; NE/S010270/1//Natural Environment Research Council/ ; },
mesh = {*CRISPR-Cas Systems ; *Ecology/methods ; *Gene Editing/methods ; },
abstract = {CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated nucleases) systems allow researchers to detect, capture, and even alter parts of an organism's genome. However, while the use of CRISPR-Cas has revolutionised many fields in the life sciences, its full potential remains underutilised in ecology and biodiversity research. Here we outline the emerging applications of CRISPR-Cas in ecological contexts, focusing on three main areas: nucleic acid detection, CRISPR-enhanced sequencing, and genome editing. CRISPR-based nucleic acid detection of environmental DNA samples is already reshaping species monitoring, providing highly sensitive and non-invasive tools for both scientists and the public alike, with reduced costs and minimal experience required. Further, CRISPR-enhanced sequencing, including Cas-mediated target enrichment, enables efficient recovery of ecologically relevant loci and supports diverse applications such as amplification-free metagenomics. Finally, while genome editing on wild species remains largely theoretical in ecology, these tools are already being used in controlled settings to study adaptation and resilience in the face of ongoing global stressors. Together, the applications of CRISPR-Cas are paving the way for more affordable, accessible, and impactful applications for species conservation, and promise to improve our ability to tackle the ongoing global biodiversity crisis.},
}

*CRISPR-Cas Systems
*Ecology/methods
*Gene Editing/methods

@article {pmid41328492,
year = {2025},
author = {Knoll, RL and Podlesny, D and Fortmann, I and Göpel, W and Zemlin, M and Lynch, S and Bork, P and Gehring, S and Härtel, C},
title = {Staphylococcus aureus colonization and bloodstream infection in very preterm infants.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2592423},
doi = {10.1080/19490976.2025.2592423},
pmid = {41328492},
issn = {1949-0984},
mesh = {Humans ; *Staphylococcal Infections/epidemiology/microbiology ; Infant, Newborn ; Feces/microbiology ; *Staphylococcus aureus/isolation & purification/genetics/growth & development/classification ; Female ; Male ; Infant, Premature ; *Bacteremia/microbiology/epidemiology ; Gastrointestinal Microbiome ; Germany/epidemiology ; Infant ; Cohort Studies ; Infant, Very Low Birth Weight ; Metagenomics ; Incidence ; Gestational Age ; },
abstract = {BACKGROUND: Staphylococcus (S.) aureus remains a frequent pathogen for neonatal late-onset bloodstream infections (BSIs). The impact of colonization screening on BSI incidence is less understood.

METHODS: We assessed the epidemiology of late-onset S. aureus BSI in two independent multicenter cohorts of preterm infants born at < 33 weeks' gestation, the German Neonatal Network (GNN, very low birth weight infants) and PRIMAL (infants with a gestational age 28-32 weeks). In the PRIMAL cohort, we determined S. aureus colonization in fecal samples by culture and shotgun metagenomic sequencing (metaG) during the first year of life. In addition, we integrated publicly available metaG data from preterm infant cohorts born at 23-34 weeks' gestation.

RESULTS: Late-onset S. aureus BSI was noted in 1.5% (336/21491) in preterm infants in the GNN cohort and 0.5% (3/638) in the PRIMAL cohort, respectively. At day 30 of life, 7.6% (42/553) of fecal samples were positive for S. aureus, while available metaG data of corresponding samples revealed S. aureus positivity in 36.6% (159/434). Every 10-fold increase in S. aureus relative abundance (metaG) was associated with a 2.9-fold higher odds of S. aureus detection in blood culture. We also confirmed S. aureus detection in 22% (393/1782) of samples across several published cohorts of preterm infants by metaG, while 95 samples carried at least one Staphylococcus-specific virulence gene (SVG).

CONCLUSION: Our study demonstrates that metagenomic quantification of pathobionts such as S. aureus in intestinal samples provides a stronger predictor of colonization than culture. Future prevention strategies should focus on promoting S. aureus colonization resistance through microbiome-informed approaches.},
}

Humans
*Staphylococcal Infections/epidemiology/microbiology
Infant, Newborn
Feces/microbiology
*Staphylococcus aureus/isolation & purification/genetics/growth & development/classification
Female
Male
Infant, Premature
*Bacteremia/microbiology/epidemiology
Gastrointestinal Microbiome
Germany/epidemiology
Infant
Cohort Studies
Infant, Very Low Birth Weight
Metagenomics
Incidence
Gestational Age

@article {pmid41328416,
year = {2025},
author = {Ueira-Vieira, C and Santos, ACC and Araújo, TN and Augusto, SC and de Avila, NB and Bonetti, AM and Dos Santos, AR},
title = {A Deep Metagenomic Snapshot as a Proof-of-Concept for Resource Generation: Simultaneous Assembly of Host, Food, and Microbiome Genomes From Stingless Bee Larval Food.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72546},
pmid = {41328416},
issn = {2045-7758},
abstract = {Characterizing the complex web of ecological interactions is a central challenge in molecular ecology. Shotgun metagenomics of environmental samples offers a powerful, high-resolution approach, yet its potential for simultaneously generating multiple genomic resources from different trophic levels remains underexplored. This study serves as a proof-of-concept, using deep sequencing of a single, complex sample-the larval food of the stingless bee Tetragonisca angustula-to demonstrate the method's capacity to recover genomic information across varying template abundances. We successfully assembled three genomes of different completeness levels: a near-complete bacterial genome (Acetilactobacillus jinshanensis, 2,097,977 bp with 0.002% ambiguous bases), a draft mitochondrial genome (T. angustula, 15,498-15,549 bp), and a fragmented chloroplast genome (Lactuca sativa, 130,532 bp with 23.47% ambiguous bases). The assembly quality gradient, observed from complete to fragmented, directly reflects the relative abundance of each DNA template in the environmental sample, demonstrating the method's sensitivity and ecological informativeness. Beyond these genomic resources, the data provided a comprehensive biodiversity profile, revealing DNA from seven major taxonomic groups, including 209 bacterial genera, 123 plant families, and 55 insect taxa. Additionally, genomic comparisons using Average Nucleotide Identity (ANI) and digital DNA-DNA Hybridization (dDDH) analyses suggest that the dominant bacterial strain represents a putative novel species within the genus Acetilactobacillus. This approach simultaneously provided insights into host genetics, food sources, and microbial communities, illustrating the potential of single metagenomic datasets to generate multiple valuable genomic resources for molecular ecology research.},
}

@article {pmid41328415,
year = {2025},
author = {Long, D and Zhao, W and Li, X and Sun, Q and Li, J and Lin, X},
title = {Rhizosphere Effect Enhances Belowground Competition of Coastal Invasive Spartina alterniflora With Mangroves.},
journal = {Ecology and evolution},
volume = {15},
number = {12},
pages = {e72565},
pmid = {41328415},
issn = {2045-7758},
abstract = {Spartina alterniflora has severely invaded mangroves in China. In order to explore the possible belowground interspecific interaction along with its invasion, the rhizosphere effect enhancing the competition of S. alterniflora neighboring mangroves was hypothesized. Here, both rhizosphere soil of S. alterniflora and bulk soil were collected from the center of S. alterniflora marsh and border sites where S. alterniflora was adjacent to Kandelia obovata and Aegiceras corniculatum, respectively, in both vigorous growth and senescent periods. Soil nutrient properties, rhizospheric low-molecular-weight organic acids (LMWOAs), soil microbiomes, and microbial functional genes were analyzed. Soil total carbon and total nitrogen contents of S. alterniflora neighboring mangroves were increased, and its LMWOAs were altered when adjacent to mangroves in both vigorous growth and senescent periods. These changes were significantly correlated with variation in the composition of S. alterniflora rhizosphere microbiome. Microbial interkingdom co-occurrence networks were simplified when S. alterniflora neighbored mangroves, while network modularity significantly increased. Metagenomics indicated that genes involved in methanogenesis (ackA, mvhD, etc.) and nitrogen fixation (nifH, nifK, etc.) were significantly enriched in those S. alterniflora neighboring K. obovata, and genes related to phosphate transporter (pstA, pstB, etc.) were significantly enriched in those S. alterniflora neighboring A. corniculatum. These results demonstrated that the rhizosphere effect intensified the belowground interspecific competition of S. alterniflora adjacent to mangroves by altering root exudates, changing the soil microbial composition, and modulating strategies for core nutrient metabolism.},
}

@article {pmid41328248,
year = {2025},
author = {Rossi, E and Pato, U and Ayu, DF and Melia, S and Sukma, A and Rahmayuni, R and Salman, AN},
title = {Bacterial biodiversity and metagenomic study of dadih, traditional fermented buffalo milk from Kampar district, Riau, Indonesia.},
journal = {Journal of advanced veterinary and animal research},
volume = {12},
number = {3},
pages = {717-727},
pmid = {41328248},
issn = {2311-7710},
abstract = {OBJECTIVE: This study aimed to investigate the metagenomic and microbial diversity of dadih in Kampar District, Riau, Indonesia.

MATERIALS AND METHODS: The dadih samples were collected from dadih producers in three villages, namely Limau Manis (LM), Rumbio (RB), and Muaro Jalai (MJ). DNA samples were extracted and sequenced through Oxford Nanopore Technology (ONT), operated by MinKNOW software version 23.04.5. Library preparations were conducted using kits from ONT.

RESULTS: The next-generation sequencing analysis on three dadih from Kampar identified two bacterial phyla, Bacillota and Pseudomonadota. Furthermore, there was a slight variation in dadih's microbiota composition between LM, RB, and MJ. The Bacillota phylum dominated the dadih microbiota in LM and RB villages, with a relative abundance of 60%-80%. The dadih from MJ was dominated by the phylum Pseudomonadota, which reached 55%. The dominant species found in all three dadih was Lactococcus lactis, with an abundance of 53.80, 80.80, and 40.31% for dadih LM, RB, and MJ, respectively.

CONCLUSION: Dadih MJ had the highest Simpson's value (~0.8), showing a relatively even abundance of species in the sample. Furthermore, dadih LM had a high Simpson's value (~0.75), indicating similar conditions to dadih MJ. Dadih RB had the lowest Simpson's value (~0.4), confirming that the microbiota in the sample tends to be dominated by certain species with a less even distribution.},
}

@article {pmid41328030,
year = {2025},
author = {Hickman, B and Korpela, K},
title = {Impact of data compositionality on the detection of microbiota responses.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2590841},
doi = {10.1080/19490976.2025.2590841},
pmid = {41328030},
issn = {1949-0984},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Humans ; Computer Simulation ; *Gastrointestinal Microbiome ; Computational Biology/methods ; *Metagenomics/methods ; },
abstract = {Next-generation sequencing (NGS) data usage is widespread, but its compositional nature poses challenges. We evaluated four normalization methods (relative abundance, CLR, TMM, DESeq2) for identifying true signals in compositional microbiota data using simulations. Two experiments were conducted: one with only increases in specific taxa, and a 1:1 increase/decrease in specific taxa. Simulated sequencing produced compositional data, which were normalized using the four methods. The study compared absolute abundance data and the normalized compositional data using variance explained and false discovery rates. All normalization methods showed decreased variance explained and increased false positives and negatives compared to absolute abundance data. CLR, TMM, and DESeq2 did not improve over relative abundance data and sometimes worsened false discovery rates. The study highlights that false positives and negatives are common in compositional NGS datasets, and current normalization methods do not consistently address these issues. Compositionality artefacts should be considered when interpreting NGS results and obtaining absolute abundances of features/taxa is recommended to distinguish biological signals from artefacts.},
}

*High-Throughput Nucleotide Sequencing/methods
*Bacteria/classification/genetics/isolation & purification
*Microbiota
Humans
Computer Simulation
*Gastrointestinal Microbiome
Computational Biology/methods
*Metagenomics/methods

@article {pmid41328016,
year = {2025},
author = {Fresno, C and Oropeza-Valdez, JJ and Alvarado-Luis, PI and Peña-González, P and Tovar, AR and Torres, N and Diener, C and Gibbons, S and Resendis-Antonio, O},
title = {MICOMWeb: a website for microbial community metabolic modeling of the human gut.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2587968},
doi = {10.1080/19490976.2025.2587968},
pmid = {41328016},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Internet ; *Gastrointestinal Tract/microbiology/metabolism ; Models, Biological ; Software ; Computer Simulation ; Computational Biology/methods ; },
abstract = {MICOMWeb is a user-friendly website for modeling microbial community metabolism in the human gut. This website tackles three constraints when generating in silico metagenome-scale metabolic models: i) the prior Python user knowledge for metabolic modeling using flux balance analysis with the MICOM Python package, ii) predefined and user-defined diets to generate ad hoc metabolic models, and iii) the high-throughput computational infrastructure required to obtain the simulated growth and metabolic exchange fluxes, using real abundance from metagenomic shotgun or 16S amplicon sequencing; we present MICOMWeb's features to easily run in silico experiments as a functional hypothesis generator for experimental validation on three previously published databases. MICOMWeb has a constant run-time independent of the number of samples provided and database complexity. In practical terms, this behavior is upper-bounded by the sample with the greatest microbiota diversity, i.e., the sample with the largest metabolic reconstruction model size. The evidence suggests that the bigger the database, the better the MICOMWeb performs compared to MICOM in terms of consumed RAM (from 3.52 up to 7.13 folds) and total execution time (from 10.87 up to 205.05 folds).},
}

Humans
*Gastrointestinal Microbiome
Internet
*Gastrointestinal Tract/microbiology/metabolism
Models, Biological
Software
Computer Simulation
Computational Biology/methods

@article {pmid41327872,
year = {2025},
author = {Zhang, Y and Zhang, Z and Chen, Z and Yang, B and Cai, S and Chen, J and Guo, J and Zhang, W},
title = {2-line Ferrihydrite Enhance Microbial Synthesis of Plant Biostimulants in Composted Biosolid by Regulating Phyla Pseudomonadota and Actinomycetota.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e06502},
doi = {10.1002/advs.202506502},
pmid = {41327872},
issn = {2198-3844},
support = {U24A20193,52270141//The National Natural Science Foundation of China/ ; 2024BCA006//Hubei Province Technological Innovation Plan Project/ ; 122-G1323522145//Fundamental Research Funds for the central Universities, China University of Geosciences/ ; },
abstract = {The discovery of plant biostimulants (PBs) in sewage sludge offers a promising avenue for biosolids valorization. Here, the study investigates how two mineral additives, including 2-line ferrihydrite (a disordered iron oxide) and disordered birnessite (a manganese oxide), modulate microbial activity and molecular pathways to enhance PB production during aerobic sludge composting. Application of 2-line ferrihydrite significantly promotes the synthesis of growth-promoting PBs, including arginine, valine, decanoic acid, and indoleacetic acid (IAA), while disordered birnessite primarily enhances resistance-related PBs, such as decanoic acid, L-pyroglutamate, and trans-aconitic acid. In pot trials, composted biosolids amended with 2-line ferrihydrite significantly improve plant biomass and leaf area compared to mineral-free and birnessite treatments. Metagenomic profiling reveals that PB biosynthesis is dominated by members of the phyla Pseudomonadota and Actinomycetota, with temporal niche partitioning across the thermophilic and maturation stages. 2-line ferrihydrite enhances the abundance of critical biosynthetic genes (e.g., trpA/C/D/E/F), particularly within taxa such as Xanthomonadaceae, Sphingomonadaceae, and Streptosporangiaceae. Additionally, genes involved in IAA and indole biosysnthesis (ALDH, DDC, and tnaA) are enriched, supporting enhanced tryptophan-to-IAA conversion. This study provides a mechanistic link between iron oxide-mediated microbial modulation and PB production in composted biosolids, offering a sustainable approach for upgrading waste into high-value agricultural inputs.},
}

@article {pmid41327491,
year = {2025},
author = {Wu, H and Sun, Z and Chen, B and Hu, X and Li, Y},
title = {Enhanced nitrogen load improved soil phosphorus availability by regulating P-cycling microbial genes in a typical subtropical estuary (Min River), Southeast China.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {151},
pmid = {41327491},
issn = {2524-6372},
support = {No. 42371105//the National Natural Science Foundation of China/ ; No. 2023J02012//the Key Program of Natural Science Foundation of Fujian Province/ ; },
abstract = {BACKGROUND: Enhanced nitrogen (N) load was considered a critical factor influencing phosphorus (P) availability and P-cycling in marsh soils. However, information on the links between soil P availability and microbial genes involved in P-cycling processes under N enrichment conditions remains scarce.

METHODS: A field N load experiment with four treatments (N0, Nlow, Nmedium, and Nhigh) was conducted in Cyperus malaccensis marsh of the Min River estuary, and soil P availability, the relative abundances of P-cycling functional genes and their regulatory roles on P availability were investigated.

RESULTS: The total phosphorus (TP) contents in soils were significantly positively correlated with N load levels (p < 0.05). Compared with the N0 treatment, the TP in the Nlow, Nmedium and Nhigh treatments increased by 8.97%, 17.34% and 15.21%, respectively. With increasing N load levels, the proportions of easily- and moderately-available P in TP contents noticeably increased, suggesting that N additions enhanced soil P availability. Metagenomic sequence analyses showed that N enrichment markedly altered the relative abundances of P-cycling functional genes. Briefly, the abundances of inorganic P solubilization genes (particularly ppa and ppx) increased substantially with increasing N load levels. The total abundances of organic P mineralization genes in the Nlow and Nmedium treatments decreased markedly, while those in the Nhigh treatment increased greatly. The abundances of genes coding for phytase (phy and appA) markedly increased with increasing N load levels, implying that phytase was more sensitive to N enrichment. Furthermore, enhanced N load noticeably reduced the abundances of genes participated in P transportation (particularly ugpABEC) and those involved in P-assimilating process (e.g., phoR, phoB, pstABCS and pit). As affected by enhanced N load, the contents of easily-available P showed strong correlations with the abundances of genes involved in inorganic P solubilization while those of moderately-available P (particularly Sonic-Pi, Sonic-Po and NaOH-Pi) were positively correlated with the abundances of genes involved in P regulation and transportation, indicating strong linkages between P-cycling functional genes and soil P availability.

CONCLUSIONS: This paper found that, under N enrichment conditions, the increased inorganic P solubilization potential and the weakened microbial P immobilization capacity were beneficial to increasing soil P availability.},
}

@article {pmid41327449,
year = {2025},
author = {Zhao, Y and Duanmu, X and Hu, Z and Fan, Y and Mao, R and Zhang, Y and Zhang, X},
title = {Temperature seasonality constrains soil T4-like bacteriophage abundance at large spatial scale.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00824-0},
pmid = {41327449},
issn = {2524-6372},
support = {U21A20188//National Natural Science Foundation of China/ ; jxsq2023102216//Double Thousand Plan of Jiangxi Province/ ; },
abstract = {BACKGROUND: Viruses play key roles in regulating soil microbial dynamics and biogeochemical cycles. T4-like bacteriophages, one of the best-studied viral groups, are abundant in soils, but their biogeographical patterns and ecological drivers remain poorly understood. In this study, we performed the first large-scale assessment of soil T4-like bacteriophages based on metagenomic data using viral hallmark genes, revealing broad spatial structure, identifying dominant environmental factors, and projecting shifts under future climate scenarios.

RESULTS: We analyzed two viral hallmark genes, gene 20 (g20) and gene 23 (g23), retrieved from global soil metagenomes, and National Center for Biotechnology Information (NCBI) reference sequences, yielding 2,385 and 2,928 full-length sequences clustered into 1,211 and 1,269 operational taxonomic units (OTUs), respectively. Phylogenetic analysis revealed that only a small fraction of soil-derived sequences could be assigned to established viral families, with most remaining unclassified below the class Caudoviricetes. The relative abundances of g20 and g23 were assessed at 116 sites spanning 14 biomes across six continents. Consistent biogeographic patterns were observed for both genes, with higher relative abundance in tropical climates and lower levels in polar and dry regions, indicating strong climatic influence. Temperature seasonality (BIO4) was identified as the primary environmental driver, showing a significant negative correlation with the relative abundance of both genes. Using an extreme gradient boosting (XGBoost) model, we predicted global distribution patterns based on extrapolation, revealing concordant global trends, with lower relative abundances in regions with greater seasonal temperature variation. Future projections of BIO4 and viral gene abundance further supported this significant negative correlation.

CONCLUSIONS: Our findings reveal that temperature seasonality constrains the abundance of soil T4-like bacteriophages, which serve as sensitive indicators of climate-driven environmental shifts and play important ecological roles within soil microbial communities.},
}

@article {pmid41327428,
year = {2025},
author = {Zorea, A and Moraïs, S and Pellow, D and Gershoni-Yahalom, O and Probst, M and Nadler, S and Shamir, R and Rosental, B and Elia, N and Mizrahi, I},
title = {ProFiT-SPEci-FISH: a novel approach for linking plasmids to hosts in complex microbial communities at the single-cell level.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02238-z},
pmid = {41327428},
issn = {2049-2618},
support = {ISF 1947/19//Israel Science Foundation/ ; ISF 1947/19//Israel Science Foundation/ ; 2476/2-1//German-Israeli Project Cooperation (DIP)/ ; ERC 866530//the European Research Council/ ; },
abstract = {BACKGROUND: Plasmids are influential drivers of bacterial evolution, facilitating horizontal gene transfer and shaping microbial communities. Current knowledge on plasmid persistence and mobilization in natural environments is derived from community-level studies, neglecting the single-cell level, where these dynamic processes unfold. Pinpointing specific plasmids within their natural environments is essential to unravel the dynamics between plasmids and their bacterial hosts.

RESULTS: Here, we overcame the technical hurdle of natural plasmid detectability in single cells by developing SPEci-FISH (Short Probe EffiCIent Fluorescence In Situ Hybridization), a novel molecular method designed to detect and visualize plasmids, regardless of their copy number, directly within bacterial cells, enabling their precise identification at the single-cell level. To complement this method, we created ProFiT (PRObe FInding Tool), a program facilitating the design of sequence-based probes for targeting individual plasmids or plasmid families.

CONCLUSIONS: We have successfully applied these methods, combined with high-resolution microscopy, to investigate the dispersal and localization of natural plasmids within a clinical isolate, revealing various plasmid spatial patterns within the same bacterial population. Importantly, bridging the technological gap in linking plasmids to hosts in native complex microbial environments, we demonstrated that our method, when combined with fluorescence-activated cell sorting (FACS), can track plasmid-host dynamics in a human fecal sample. This approach identified multiple potential bacterial hosts for a conjugative plasmid that we assembled from this fecal sample's metagenome. Our integrated approach offers a significant advancement toward understanding plasmid ecology in complex microbiomes. Video Abstract.},
}

@article {pmid41327409,
year = {2025},
author = {Jin, J and Wang, X and Zhang, X and Mei, J and Zheng, W and Guo, L and Sun, H and Zhang, L and Liu, C and Ye, W and Guo, L},
title = {Grapevine phyllosphere pan-metagenomics reveals pan-microbiome structure, diversity, and functional roles in downy mildew resistance.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02287-4},
pmid = {41327409},
issn = {2049-2618},
support = {ZR2024QC241//Shandong Provincial Natural Science Foundation Youth Project/ ; 2024CXPT031//Key R&D Program of Shandong Province/ ; ZR2023JQ010//Natural Science Foundation for Distinguished Young Scholars of Shandong Province/ ; },
abstract = {BACKGROUND: Grapevines are among the most economically important fruit crops, and the microbiome profoundly influences their health, yield, and quality. However, mechanistic insights into microbiome-orchestrated grapevine biology remain limited.

RESULTS: Here, we conduct large-scale pan-metagenomic and pan-metatranscriptomic analyses of the phyllosphere microbiome from 107 grapevine accessions spanning 34 Vitis species. We show that the grapevine core microbiome is dominated by phyla Bacillota and Pseudomonadota. Leveraging PacBio sequencing, we assembled 19 high-quality metagenome-assembled genomes (MAGs) from the grapevine pan-microbiome, representing the first MAG reconstruction in plant-associated microbial communities using PacBio reads. These MAGs encode genes associated with antibiotic resistance, secondary metabolism, and carbohydrate-active enzymes (CAZymes), which could potentially influence grapevine biology. During downy mildew (DM) infection, DM-resistant grapevines exhibit significantly higher microbial network complexity than susceptible counterparts. Among the key taxa contributing to this complexity, Bacillota emerged as the dominant phylum, displaying strong abundance correlations with phylum Euglenozoa and Cyanobacteriota, and an isolated Bacillota species from the grapevine leaves, Bacillus cereus, demonstrated potent biocontrol activity against DM infection. Pan-metatranscriptomic analysis further revealed significant upregulation of eukaryotic microbial genes involved in primary and secondary metabolism.

CONCLUSIONS: This pan-metagenomic study offers unprecedented insights into the complex structure, diversity, and functional roles of the grapevine phyllosphere microbiome and presents valuable genomic and microbial resources for microbiome research and engineering to enhance viticulture productivity and quality. Video Abstract.},
}

@article {pmid41327304,
year = {2025},
author = {Zhang, X and Li, Y and Xiong, Z and Zheng, N and Wang, J and Zhao, S},
title = {Biochanin A improves nitrogen utilization efficiency by regulating ruminal microbial community in dairy goats.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02275-8},
pmid = {41327304},
issn = {2049-2618},
support = {32402768//National Natural Science Foundation of China/ ; 2004DA125184G2108//State Key Laboratory of Animal Nutrition and Feeding/ ; CARS-36//Earmarked Fund for CARS/ ; 2022YFD1301000//National Key R&D Program of China/ ; CAAS-ZDRW202304//Agricultural Science and Technology Innovation Program/ ; },
abstract = {BACKGROUND: Rumen microbial nitrogen metabolism is crucial for animal health, productivity, and environmental sustainability in ruminants. Natural products like biochanin A are garnering interest as potential feed additives due to their beneficial effects and safety profiles. Here, we collected total mixed diet, plasma, milk, urine, and feces samples of dairy goats to evaluate the impact of biochanin A on nitrogen metabolism and elucidated regulatory mechanisms of nitrogen metabolism using multi-omics approaches by analyzing plasma metabolites and ruminal microbial communities.

RESULTS: Supplementation with biochanin A significantly enhanced nitrogen utilization efficiency of dairy goats. Plasma metabolomics revealed that biochanin A altered pathways related to amino acid biosynthesis/metabolism and glycolysis/gluconeogenesis. In the rumen, biochanin A enriched microbial strains from the families Selenomonadaceae and Aminobacteriaceae. Up-regulated proteins predominantly associated with glycolysis were identified by metaproteomics. Integrated metagenomic and metaproteomic analyses demonstrated that biochanin A positively influenced carbohydrate metabolism, amino acid metabolism, and energy metabolism pathways.

CONCLUSION: Biochanin A enhances nitrogen metabolism by regulating rumen microbial community function, supporting its potential as a natural feed additive to improve nitrogen utilization of ruminants. Video Abstract.},
}

@article {pmid41327286,
year = {2025},
author = {Xu, W and Top, J and Viveen, MC and Slyzkyi, A and Hermans, N and van Erp, S and Eiloz, D and Anthony, R and Kremer, K and Schürch, AC},
title = {Limited value of Nanopore adaptive sampling in a long-read metagenomic profiling workflow of clinical sputum samples.},
journal = {BMC medical genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12920-025-02272-8},
pmid = {41327286},
issn = {1755-8794},
support = {LSHM22031//Health~Holland/ ; },
abstract = {BACKGROUND: Oxford Nanopore adaptive sampling (NAS) is a method by which the long-read sequencing flowcell accepts or rejects DNA molecules that are actively being sequenced based on their initial ~ 500 bp sequences, selectively increasing target data output. NAS promises up to 5-10 × enrichment of target sequencing yield without additional sample preparation, but this optimal performance is dependent on ideal sample parameters which may be difficult to achieve under many real-world use-cases. We evaluated the use of NAS for profiling clinical sputum metagenomes.

METHODS: We sequenced DNA extracted from clinical sputa and spike-in controls of a mock community of bacterial respiratory pathogens, using the current R10.4.1 MinION flowcell chemistry.

RESULTS: We achieved at best 3.1 × enrichment of bacterial sequence output with NAS due to the shorter read lengths (~ 2.5 kb) from the PCR amplification necessary to compensate for low DNA extraction yields. More critically, we encountered rapid pore loss during our runs that reduced total sequencing yield by an estimated 80%. We were unable to mitigate the pore loss despite extensive attempts to reduce contaminant carry-over, and we could not determine its cause but ruled out NAS and pore underloading as contributing factors.

CONCLUSIONS: We conclude that the utility of NAS is often limited by the characteristics of the metagenomic sample studied, and that the factors contributing to pore loss need to be resolved before ONT sequencing can be reliably applied to long-read metagenomics.},
}

@article {pmid41327021,
year = {2025},
author = {Chen, B and Shu, W and Le, J and Jin, D},
title = {Application of metagenomic next-generation sequencing technology in hematologic malignancy patients with sepsis following antibiotic use.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1678},
pmid = {41327021},
issn = {1471-2334},
}

@article {pmid41327018,
year = {2025},
author = {Gajjar, K and Patel, S and Chaudhary, M and Agrawal, D and Maniyar, R and Chaudhary, D and Patel, CK and Joshi, C and Joshi, M and Dharajiya, D},
title = {Metagenomic insights reveal the impact of natural farming on soil nutrients, enzyme activities, microbial communities, and yield in turmeric cultivation.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-025-07781-3},
pmid = {41327018},
issn = {1471-2229},
support = {GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission/ ; },
}

@article {pmid41326768,
year = {2025},
author = {Polizel, GHG and Cánovas, Á and Diniz, WJS and Ramírez-Zamudio, GD and Cesar, ASM and Fukumasu, H and Fernandes, AC and Furlan, É and de Almeida Santana, MH},
title = {Unveiling long-term prenatal nutrition biomarkers in beef cattle via multi-tissue and multi-OMICs analysis.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {1},
pages = {8},
pmid = {41326768},
issn = {1573-3890},
support = {23/09113-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 17/12105-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307593/2021-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; Cattle ; Female ; Pregnancy ; *Biomarkers/metabolism/analysis ; *Metabolomics/methods ; Male ; Liver/metabolism ; Transcriptome ; *Maternal Nutritional Physiological Phenomena ; *Prenatal Nutritional Physiological Phenomena ; Multiomics ; },
abstract = {INTRODUCTION: Maternal nutrition during gestation plays a crucial role in shaping offspring development, metabolism, and long-term health, yet the underlying molecular mechanisms remain poorly understood.

OBJECTIVES: This study investigated potential biomarkers through multi-OMICs and multi-tissue analyses in offspring of beef cows subjected to different gestational nutrition regimes.

METHODS: A total of 126 cows were allocated to three groups: NP (control, mineral supplementation only), PP (protein-energy supplementation in the last trimester), and FP (protein-energy supplementation throughout gestation). Post-finishing phase, samples (blood, feces, ruminal fluid, fat, liver, and longissimus muscle/meat) were collected from 63 male offspring. RNA sequencing was performed on muscle and liver, metabolomics on plasma, fat, liver, and meat, and 16S rRNA sequencing on feces and ruminal fluid. Data were analyzed via DIABLO (mixOmics, R).

RESULTS: The muscle transcriptome showed strong cross-block correlations (|r| > 0.7), highlighting its sensitivity to maternal nutrition. Plasma glycerophospholipids (PC ae C30:0, PC ae C38:1, lysoPC a C28:0) were key biomarkers, particularly for FP. The PP group exhibited liver-associated markers (IL4I1 gene, butyrylcarnitine), reflecting late-gestation effects, while NP had reduced ruminal Clostridia (ASV151, ASV241), suggesting impaired microbial energy metabolism.

CONCLUSIONS: This integrative multi-OMICs approach provided deeper insights than single-layer analyses, distinguishing nutritional groups and revealing tissue- and OMIC-specific patterns. These findings demonstrate the value of combining transcriptomic, metabolomic, and microbiome data to identify biomarkers linked to maternal nutrition in beef cattle.},
}

Animals
Cattle
Female
Pregnancy
*Biomarkers/metabolism/analysis
*Metabolomics/methods
Male
Liver/metabolism
Transcriptome
*Maternal Nutritional Physiological Phenomena
*Prenatal Nutritional Physiological Phenomena
Multiomics

@article {pmid41326588,
year = {2025},
author = {Yadav, MK and Ranjan, R and Verma, P and Sharma, R},
title = {Discovery and characterization of an enantioselective family VIII esterase from effluent treatment plant sludge metagenome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29625-8},
pmid = {41326588},
issn = {2045-2322},
support = {BSC0124//Council of Scientific and Industrial Research (CSIR), India/ ; },
}

@article {pmid41326129,
year = {2026},
author = {Wu, M and Lu, P and Feng, Y and He, S and Han, G and Hu, S},
title = {Construction and functional characterization of a synthetic consortium for synergistic degradation of dimethachlon.},
journal = {Pesticide biochemistry and physiology},
volume = {216},
number = {Pt 1},
pages = {106807},
doi = {10.1016/j.pestbp.2025.106807},
pmid = {41326129},
issn = {1095-9939},
mesh = {Biodegradation, Environmental ; *Microbial Consortia ; Aniline Compounds/metabolism ; Animals ; Pseudomonas/metabolism/genetics ; *Soil Pollutants/metabolism/toxicity ; Zebrafish ; *Fungicides, Industrial/metabolism/toxicity ; Soil Microbiology ; },
abstract = {The residual dicarboximide fungicide dimethachlon and its primary metabolite 3,5-dichloroaniline entail significant health and ecological risks. Microbial degradation effectively mitigates associated environmental risks. The microbial degradation of organic contaminants is a complex process, typically facilitated by microbial consortia rather than individual species. However, research on the biodegradation of dimethachlon by synergistic microbial consortia is limited. In this study, an enriched bacterial consortium designated as JHJ-2 capable of degrading dimethachlon was obtained. A synthetic consortium was constructed, comprising Bosea sp. S6, which transforms dimethachlon to 3,5-dichloroaniline, and Pseudomonas sp. KH-1, which degrades 3,5-dichloroaniline; both strains were isolated from the enriched consortium JHJ-2 and synergistically degrade dimethachlon. Toxicity assays using the zebrafish showed that dimethachlon is converted into non-toxic products by the synthetic consortium (strains S6 and KH-1). Bioaugmentation with the synthetic consortium led to the complete removal of dimethachlon and its highly toxic metabolite 3,5-dichloroaniline from contaminated soil. In addition, 16 bins were successfully recovered by metagenomic binning, including bin 12 (Bosea sp.) and bin 15 (Pseudomonas sp.), and several potential degradation enzymes were hypothesized in the genomes of bins 12 and 15. Overall, the developed synthetic consortium exhibits significant potential for the enhanced bioremediation and detoxification of dimethachlon-contaminated sites.},
}

Biodegradation, Environmental
*Microbial Consortia
Aniline Compounds/metabolism
Animals
Pseudomonas/metabolism/genetics
*Soil Pollutants/metabolism/toxicity
Zebrafish
*Fungicides, Industrial/metabolism/toxicity
Soil Microbiology

@article {pmid41325946,
year = {2025},
author = {Yin, Z and Ma, J and Bian, R and Wang, Y and Zhang, K and Ma, Y and Zhang, X and Ye, L},
title = {Xenobiotic degradation promotes enrichment but not dissemination of antibiotic resistance genes in activated sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133748},
doi = {10.1016/j.biortech.2025.133748},
pmid = {41325946},
issn = {1873-2976},
abstract = {Activated sludge in wastewater treatment bioreactors plays a pivotal role in xenobiotic degradation but is also regarded as a hotspot for the dissemination of antibiotic resistance genes (ARGs). Yet, it remains unclear whether pollutant degradation itself also creates conditions that facilitate ARG spread. To address this, we developed a xenobiotic degradation gene (XDG) database covering 22 degradation pathways. Using this database, we analyzed over 30,000 complete bacterial genomes and identified widespread co-occurrence of ARGs and XDGs, particularly within Pseudomonadota and Campylobacterota. Metagenomic profiling of 119 activated sludge samples further revealed strong positive correlations (Pearson's r > 0.8) between XDG and intrinsic ARGs, especially, modules involved in aromatic ring cleavage showed the highest correlations with ARGs. However, only 30.9 % of ARG-HGT events were found in MAGs carrying XDGs, and genome-level proximity analysis indicated that such microorganisms did not exhibit higher horizontal transfer potential. Cultivation-based experiments revealed that Pseudomonas strains with high degradation capacity carried intrinsic but not mobile ARGs. Together, these results demonstrate that xenobiotic degradation promotes ARG enrichment primarily through shifts in community composition rather than by enhancing gene mobility, highlighting that environmental AMR risk assessments based solely on ARG abundance may be misleading, and should avoid misestimation in future research.},
}

@article {pmid41324463,
year = {2025},
author = {Furman, O and Sorek, G and Moraïs, S and Levin, L and Tovar-Herrera, OE and Winkler, S and Mizrahi, I},
title = {Persistent auxiliary microbiome of early novel colonizers in the developing rumen with lasting functional significance.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf252},
pmid = {41324463},
issn = {1751-7370},
abstract = {The early life assembly of the rumen microbiome is a critical process with lasting implications for host development and function. Using high-resolution longitudinal metagenomics in calves tracked from birth to three years (∼800 days) of age, we reconstructed 2873 high-quality metagenome-assembled genomes (MAGs), including 517 novel genomes primarily detected in early life. These novel genomes, spanning 274 genera and largely classified as non-core taxa, reveal a diverse and functionally distinct auxiliary microbiome. Unlike in other ecosystems, this early microbial community persists into adulthood, retaining ecological and functional relevance despite a decline in abundance. Temporal clustering revealed strong associations between auxiliary taxa and dietary transitions, with functional enrichments in environmental sensing, nutrient biosynthesis, and volatile fatty acid metabolism. Metabolic network analyses showed that auxiliary genomes complement non-auxiliary community members in key functions, with potential effects on the host. Our findings suggest that early colonizers act as ecosystem engineers, with the potential to shape the developmental trajectory of the rumen microbiome. This study thus positions the early microbiome not as a transient feature of colonization, but as a structured, functionally coherent auxiliary community that interacts with the mature rumen ecosystem.},
}

@article {pmid41324436,
year = {2025},
author = {Gu, H and Liu, Z and Liu, S and Hu, X and Yu, Z and Li, Y and Li, L and Sui, Y and Jin, J and Liu, X and Jia, Z and Sun, L and Adams, JM and van der Heijden, MGA and Liu, J and Wang, G},
title = {Land conversion to cropland homogenizes variation in soil biota, gene assemblages and ecological strategies on local and regional scales.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf264},
pmid = {41324436},
issn = {1751-7370},
abstract = {It is widely considered that conversion of natural landscapes to agriculture results in biotic homogenization. A recent study comparing soil biota of 27 paired natural steppe soil (NS) and agricultural soil (AS) sites across 900km in north-eastern China found that conversion to agriculture had increased spatial gradients in soil functional genes. Using the same shotgun metagenome samples, and bacterial amplicon data, we instead analyzed total observed variation at the between-site and within-site level. We found that from the perspective of community taxonomic composition, archaeal and fungal community variation was decreased in AS compared to NS at both within- and between-site scales. In contrast, the bacterial and metazoal community was homogenized only at the local scale. Total functional KEGG gene assemblage was homogenized in AS at both the local and regional scale, whereas "Y-A-S" strategies in bacteria were homogenized at the local scale but not the between-site scale. Overall, these results show a clear homogenizing effect of agriculture with respect to multiple aspects of soil taxonomic and functional diversity, though varying by scale. Certain abiotic soil properties showed homogenization in AS at within-site and between-site scales may explain this homogenization, and uniformity of plant cover in croplands likely contribute to the effect. These findings confirm and extend global-scale studies showing homogenization of soil biota in agricultural environments, revealing that effects extend to functional genes and the broad taxonomic spectrum of life - with potential loss of soil ecosystem resilience to environmental change resulting from agriculture.},
}

@article {pmid41324077,
year = {2025},
author = {Mah, JK and Hogan, JI and Kothadia, S and Keenan, JE and Berger, J and Carugati, M},
title = {Application of plasma cell-free metagenomic next-generation sequencing for the identification of Aspergillus fumigatus donor-derived infections among solid organ transplant recipients.},
journal = {Medical mycology case reports},
volume = {50},
number = {},
pages = {100751},
pmid = {41324077},
issn = {2211-7539},
abstract = {A cluster of Aspergillus fumigatus donor-derived infections (DDI) was rapidly diagnosed using plasma metagenomic next-generation sequencing (mNGS) among solid organ transplant recipients. The heart recipient, experiencing marginal hemodynamics, underwent an endomyocardial biopsy, which was concerning for a fungal infection on histopathology. Plasma mNGS was performed, identifying A. fumigatus two days prior to conventional diagnostics. This timely diagnosis enabled prompt nephrectomies in the kidney recipients, who survived. This report represents the first published use of mNGS in the diagnosis of Aspergillus fumigatus DDI, highlighting the utility of this novel, underutilized assay for early diagnosis of donor-derived infections.},
}

@article {pmid41323881,
year = {2025},
author = {Aini, N and Wahyuningsih, SPA and Achhlam, DH and Fatimah, and Amin, MHF and Do, HDK},
title = {Modulation of Gut Microbiota, Intestinal Physiology, and Digestive Enzyme Levels by Duo-Strain Probiotics in African Catfish (Clarias gariepinus) Challenged With Aeromonas hydrophila.},
journal = {Aquaculture nutrition},
volume = {2025},
number = {},
pages = {6624613},
pmid = {41323881},
issn = {1365-2095},
abstract = {This study aimed to determine the effect of dual-strains probiotic (DSP) consisting of Lactobacillus casei and Bacillus subtilis on bacterial metagenomic profile, gut physiology, and digestive enzyme levels of African catfish (Clarias gariepinus) infected by Aeromonas hydrophila. The ratio between L. casei and B. subtilis was 1:1 each with a density of 10[8] CFU/mL. Catfish (n = 8 fish per tank, three replicates per treatment) were fed diets supplemented with 0%, 5%, 10%, or 15% DSP for 42 days. On the 35th day, selected groups were intraperitoneally challenged with A. hydrophila at a dose of 0.1 mL × 10[8] CFU/mL. The observed parameters included bacterial counts and microbial profile in the gastrointestinal tract (analyzed using next-generation sequencing [NGS]), gut physiology, and digestive enzyme levels (amylase, lipase, and protease). The results showed that DSP supplementation increased both the abundance and diversity of gastrointestinal microbes, elevated digestive enzyme levels, and enhanced the number of goblet cells in the intestinal lining. The dominant microbial phyla observed in the control group were Fusobacteria and Pseudomonadota.},
}

@article {pmid41323829,
year = {2025},
author = {Luo, A and Liu, L and Shi, S and Liu, X and Hu, B},
title = {Analysis of Microbial Community Structure and Functional Genes for Volatile Flavor in Stinky Tofu.},
journal = {Food science & nutrition},
volume = {13},
number = {12},
pages = {e71257},
pmid = {41323829},
issn = {2048-7177},
abstract = {The distinctive flavor of stinky tofu arises from intricate microbial metabolic networks during traditional fermentation, yet the genetic mechanisms linking microbial community structure to flavor formation remain incompletely resolved. This study employed metagenomic sequencing (Illumina NovaSeq 6000, Q30 > 92%) to generate 7.32 Gb of high-quality data, integrated with functional annotations from KEGG, eggNOG, and CAZy databases, to systematically dissect core microbial taxa and metabolic genes driving flavor biosynthesis. Dominant genera included Pseudomonas (relative abundance: 74.3%), Acinetobacter (14.4%), and Enterobacter (5%), with Pseudomonas putida (12.5%) and Pseudomonas fluorescens (3.2%) orchestrating carbohydrate metabolism (68.22% KEGG pathways) and amino acid degradation via glycoside hydrolases (GHs, 73% of CAZy-annotated enzymes) and dehydrogenases (e.g., 125 lactate dehydrogenase genes). Key flavor compounds, such as diacetyl (379 α-acetolactate synthase genes) and 3-methylbutanoic acid, were synthesized through synergistic pathways. Additionally, Lactococcus and Kluyvera contributed to ester and short-chain fatty acid production via α-keto acid dehydrogenase complexes (55 genes). A total of 410,231 non-redundant genes were identified, annotated to 4690 microbial species, establishing a multi-layered microbial-gene-metabolite regulatory network. This work elucidates the molecular basis of stinky tofu flavor formation and provides a framework for optimizing traditional fermentation processes through targeted microbial engineering.},
}

@article {pmid41323686,
year = {2025},
author = {Shi, X and Fan, C and Hui, M and Tian, Q and Zhang, F and Pan, C},
title = {Multiomics analysis of microbial succession and flavor formation mechanism during the fermentation process of Maotai-flavour Baijiu.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103236},
pmid = {41323686},
issn = {2590-1575},
abstract = {This study employed metagenomics and metabolomics techniques to investigate the complex relationship between microbial succession and the formation of flavor compounds during the fermentation process of Maotai-flavour Baijiu. Results demonstrated that stacking fermentation, characterized by Weissella, Pichia, and Aspergillus, which secreted amylases and proteases to hydrolyze starch and proteins. Pitting fermentation facilitated the enrichment of anaerobic microbes such as Acetilactobacillus and Pichia, significantly promoting the synthesis of key flavor compounds, including esters, alcohols, and acids, through Glycosyltransferase and Esterification activities. Volatile compound analysis revealed distinct stage-specific profiles, with acids, alcohols, and esters accumulating predominantly in pitting fermentation. These findings elucidate the stage-specific microbial metabolic networks and synergistic mechanisms underlying flavor formation, providing a scientific basis for optimizing traditional Baijiu fermentation processes.},
}

@article {pmid41323679,
year = {2025},
author = {He, Y and Qiao, M and Zhang, H and Xiao, D and Guo, X},
title = {Microbial community, metabolic, and flavor differences among high-temperature Daqu with varying Douchi aroma intensities: a comprehensive metagenomic and metabolomic analysis.},
journal = {Food chemistry: X},
volume = {32},
number = {},
pages = {103265},
pmid = {41323679},
issn = {2590-1575},
abstract = {The Douchi aroma is widely regarded as a key quality marker of high-quality high-temperature Daqu, but the compounds related to Douchi aroma formation and the key aroma-producing microorganisms remain unclear, which this study seeks to clarify. Therefore, metagenomic and metabolomic approaches were employed to decode the characteristic compounds and core microbial contributors in high-temperature Daqu samples no (NF), light (LF), and strong (SF) Douchi aroma. Esters were the most abundant volatiles across all groups, while acids increased with aroma intensity. Lentibacillus daqui, enriched in SF, showed strong positive correlations with isocetic, phenylacetic, and nonanoic acids. In contrast, Lichtheimia ramosa and Monascus purpureus were dominant in NF and LF, respectively. Furthermore, functional prediction and KEGG analysis further revealed potential biosynthetic pathways for phenylacetic and acetic acid. These findings clarify the molecular and microbial basis of Douchi aroma formation and provide a scientific reference for targeted quality regulation in Daqu production.},
}

@article {pmid41322275,
year = {2025},
author = {Dong, R and Liu, Y and Wang, N and Tan, KKY and Ji, M},
title = {The distribution of antibiotic resistance and virulence factor genes in the sediment of Inexpressible Island, East Antarctica.},
journal = {Marine life science & technology},
volume = {7},
number = {4},
pages = {978-988},
pmid = {41322275},
issn = {2662-1746},
abstract = {UNLABELLED: Inexpressible Island is a small rocky island in Terra Nova Bay, Victoria Land, Antarctica, which is an area with limited human activities. Understanding the distribution of antibiotic-resistance genes (ARGs) and virulence factor genes (VFGs) in this environment can provide key information on their potential risks to humans and their roles for microbial survival. In this study, we investigated the ARGs and VFGs in lake sediments from Inexpressible Island using metagenomic sequencing. We identified 11,502,071 open-reading frames (ORFs), with 1,749 classified as ARGs and 6,838 as VFGs. The dominant ARGs were associated with antibiotic target alteration and efflux pump mechanisms, while the VFGs were related to adherence and immune modulation functions. While associated within microbial genomes, these ARGs and VFGs were mobile genetic elements like viruses and insertion sequences, distinct from ecosystems with strong human influence. We identified 974 metagenome-assembled genomes (MAGs), with 465 being medium-to-high quality. Of these, 325 (69.9%) contained ARGs, primarily affiliated with Actinomycetota and Pseudomonadota. Additionally, 269 MAGs contained VFGs, with 174 MAGs carrying both ARGs and VFGs, highlighting significant microbial antibiotic resistance and pathogenic potential. Our findings highlight the need for ongoing monitoring of ARGs and VFGs in Antarctica, particularly in light of increasing human activity and climate change.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00323-8.},
}

@article {pmid41322254,
year = {2025},
author = {Al, MA and Wang, Y and Huang, J and Yu, Y and Juneau, P and He, Z and Yan, Q},
title = {Anammox and denitrifying bacteria and their nitrogen removal potential in lake sediments mediated by environmental changes.},
journal = {Marine life science & technology},
volume = {7},
number = {4},
pages = {670-681},
pmid = {41322254},
issn = {2662-1746},
abstract = {UNLABELLED: Anammox and denitrification are key processes for nitrogen removal in lake sediments. However, how environmental changes mediate the community structure and functional genes of nitrogen removal bacteria in lakes remain unclear. Using metagenome and amplicon sequencing, we investigated the anammox and denitrifying bacteria and their nitrogen removing potentials in lakes experiencing significant spatiotemporal and environmental variations. The community structure of anammox and denitrifying bacteria exhibited stronger lake-wide spatial variations than that of seasonality, while only the denitrification-related functional genes showed substantial variations in both lakes. Anammox genes (e.g., hzsA/B/C and hdh) showed no significant spatial variations. However, the abundances of anammox and denitrifying genes were significantly higher in winter than in summer. The mesotrophic Lake Weishan demonstrated a greater capacity for complete denitrification in winter, while the eutrophic Lake Donghu exhibited a higher potential of anammox in summer. Differences in functional gene abundances between lakes were more pronounced than variations in phylogenetic diversity, indicating clear functional adaptations to local environments. The coupled nitrogen removal potentials also reflected ecological interactions among anammox and denitrifying genes. Importantly, anammox and denitrifying bacterial communities and their functional genes were primarily driven by dissolved organic carbon, total phosphorous and zinc (Zn). The dissimilarities of anammox and denitrifying bacterial communities increased with geographic distance, indicating a clear distance-decay effect. This study highlights the anammox and denitrifying bacteria and their nitrogen removal potentials in lake sediments that are mediated by both spatial and seasonal environmental changes.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00310-z.},
}

@article {pmid41322233,
year = {2025},
author = {Chen, X and Yu, X and Deng, J and Yang, J and Chen, P},
title = {Case Report: Blood and cerebrospinal fluid mNGS-assisted diagnosis Toxoplasma gondii infection-associated with hemophagocytic syndrome and systemic lupus erythematosus.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1674391},
pmid = {41322233},
issn = {2296-858X},
abstract = {BACKGROUND: Reactivation of latent Toxoplasma gondii (T. gondii) infection is more prevalent than primary infection in patients with autoimmune diseases. We present a rare case of systemic lupus erythematosus (SLE) and hemophagocytic syndrome (HPS) associated with T. gondii infection.

CASE PRESENTATION: We describe the case of a young girl with SLE and HPS who presented with fever, dyspnea, and pancytopenia. The patient's T. gondii infection was diagnosed through the detection of double-positive IgM and IgG antibodies. Metagenomic next-generation sequencing (mNGS) analysis of both plasma and cerebrospinal fluid (CSF) samples revealed a high concentration of T. gondii DNA. The patient demonstrated a positive response to a combined treatment regimen consisting of anti-Toxoplasma medications and glucocorticoids.

CONCLUSIONS: Co-infection with uncommon pathogens is not uncommon in patients with autoimmune diseases. In individuals with immune disorders and positive T. gondii IgM antibodies, mNGS analysis of peripheral blood samples proves valuable in diagnosing disseminated T. gondii infection.},
}

@article {pmid41322208,
year = {2025},
author = {Duan, J and Li, X and Hu, Y and Pang, F and Cao, Y and You, Z},
title = {Case Report: Next-generation metagenomic sequencing in the diagnosis of Brucella-associated joint infections-a case series analysis and comprehensive literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1688037},
pmid = {41322208},
issn = {2296-858X},
abstract = {BACKGROUND: The application of next-generation metagenomic sequencing (mNGS) in the diagnosis of human brucellosis, particularly in cases of joint brucellosis infection, remains under-explored, with rarely no case reports available in the literature. We present the first case series focusing on the application of mNGS in the diagnosis of Brucella joint infections. The results indicate that mNGS plays a crucial role in diagnosing Brucella joint infections, serving as a valuable complement, particularly for culture-negative patients.

CASE PRESENTATION: This study presents a comprehensive analysis of four cases of human joint brucellosis diagnosed using mNGS on the BGI sequencing platform, involving three male and one female patients aged from 42 to 63 years, all of whom had documented epidemiological exposure histories. mNGS successfully identified Brucella sequences in all cases, with additional diagnostic findings including a positive Brucella agglutination test in Patient 1, positive joint fluid cultures in Patients 3 and 4, and no positive results in Patient 2. Following surgery and targeted antibiotic therapy, all patients exhibited clinical improvement and favorable follow-up outcomes.

CONCLUSION: These findings underscore the utility of mNGS as a critical diagnostic tool for joint brucellosis infections and highlight its potential as a complementary approach in cases of culture-negative joint infections. In cases where clinical suspicion of joint infection persists despite the absence of identifiable etiological evidence, the implementation of mNGS is strongly advised to facilitate timely and accurate clinical decision-making.},
}

@article {pmid41321514,
year = {2025},
author = {Liu, Z and Jiang, A and Kong, Z and Lv, X and Zhang, J and Wu, J and Zhou, C and Tan, Z},
title = {Multi-omics analysis reveals the mechanism of rosemary extract supplementation in increasing milk production in Sanhe dairy cows via the "rumen-serum-milk" metabolic pathway.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {396-414},
pmid = {41321514},
issn = {2405-6383},
abstract = {Rosemary extract (RE) has shown potential as a plant-derived feed additive, but its effects on Sanhe dairy cows are still unknown. In this study, 30 multiparous Sanhe dairy cows (days in milk 171 ± 17 days) with similar body condition were randomly divided into two groups: the RE group (n = 15) was fed the basal diet plus 20 g RE/d, and the CON group (n = 15) was fed only the basal diet. The experiment lasted for 57 days, including a one-week adaptation period. Compared with the CON group, milk yield (P = 0.022) increased significantly with RE supplementation, while milk fat (P = 0.071) also tended to increase. Milk urea nitrogen (P = 0.003) and serum urea nitrogen (P = 0.013) contents were significantly reduced in the RE group compared with the CON group. In rumen fermentation, the content of butyric acid (P = 0.035) in RE group was significantly increased, while valeric acid (P = 0.080) content had an increasing trend. In addition, RE supplementation improved the antioxidant capacity of Sanhe dairy cows by significantly increasing the serum total antioxidant capacity (P < 0.001), superoxide dismutase activity (P = 0.001), immunoglobulin A content (P < 0.001), and immunoglobulin G content (P = 0.005), while decreasing serum malondialdehyde content (P < 0.001), to improve immunity and also affect the composition of serum free amino acids. Metabolomic results showed that a total of 13 co-differential metabolites were identified in rumen and serum, including ursolic acid, a major component of RE, which was higher in both rumen and serum. The milk metabolome analysis identified glycerides, glycerophospholipids, and sphingolipids as the three lipid types that exhibited higher identification intensity in RE. Rumen metagenomic results showed that RE supplementation affected the composition of rumen microorganisms, and differential microbial Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses revealed that the RE group was significantly enriched in the fatty acid biosynthesis pathway and the glycerophospholipid metabolism pathway; two pathways related to lipid synthesis. By associating the genus-level differential microorganisms in the rumen with the "rumen-serum-milk" metabolome and mapping the correlation network, it was found that g_Sharpea, g_Tistlia, and g_Acetobacter, which were more abundant in RE, correlated with more differential metabolites and clustered in the same module. Among the 10 microbial biomarkers screened in the rumen, g_Acetobacter and g_Prevotella were more abundant in the RE, and Mantel's analysis showed that they correlated with rumen fermentation parameters and oxidative and immunological indicators in serum. These results reveal the regulatory mechanism of RE supplementation feeding to enhance milk production and improve milk quality by improving oxidative stress capacity and immunity and reducing nitrogen loss in Sanhe dairy cows, suggesting that RE has the potential as a feed additive for dairy cows.},
}