@article {pmid41484024,
year = {2025},
author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and De Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L},
title = {Gut microbiome profiles and associated functional pathways are linked to Mediterranean diet adherence and blood glucose control in adults with type 1 diabetes mellitus.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {104487},
doi = {10.1016/j.numecd.2025.104487},
pmid = {41484024},
issn = {1590-3729},
abstract = {BACKGROUND AND AIMS: The Mediterranean diet (MD) has been associated with better glycaemic control in children with type 1 diabetes mellitus (T1DM) and favourable microbiome profiles in healthy individuals. However, it remains unclear whether MD adherence is associated with glycaemic control via microbiome. This study examined the relationships among MD adherence, gut microbiome, and glycaemic control in adults with T1DM and assessed the microbiome's ability to predict clinical and dietary outcomes.

METHODS AND RESULTS: In a cross-sectional study of 253 adults with T1DM, dietary intake was assessed using the EPIC food frequency questionnaire, and MD adherence was measured using the rMED score. Participants were stratified by adherence level (low, medium, high). Glycaemic control was evaluated using HbA1c and CGM metrics. Shotgun metagenomic sequencing of stool samples (n = 103) assessed the gut microbiome. Statistical analyses included ANOVA, PERMANOVA, LEfSe, and machine learning modeling. Higher MD adherence was associated with lower HbA1c levels (7.1 % vs 7.7 %; p < 0.001), greater time in range (67.0 % vs 59.4 %; p-trend = 0.03), and higher HDL cholesterol (1.62 vs 1.39 mmol/L; p = 0.01). High MD adherence was linked to a greater abundance of bacterial species such as Faecalibacterium prausnitzii. Both high MD adherence and lower HbA1c were associated with distinct microbiome functional pathways. Microbiome-based machine learning models predicted dietary patterns and clinical metrics.

CONCLUSIONS: In adults with T1DM, greater MD adherence is associated with better glycaemic control and a favourable gut microbiome. Specific microbial pathways may underlie these associations. Integrating diet and microbiome data supports personalized care. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.},
}

@article {pmid41483288,
year = {2026},
author = {Lema, NK and Gemeda, MT and Woldesemayat, AA},
title = {Uncovering resistomes in hospital and pharmaceutical industry wastes: insights from shotgun metagenomic profiling.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41483288},
issn = {1618-1905},
}

@article {pmid41482808,
year = {2026},
author = {Ip, YCA and Allan, EA and Hirsch, SL and Kelly, RP},
title = {Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade-Offs in Resource-Limited Settings.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70091},
pmid = {41482808},
issn = {1755-0998},
support = {GR042390//OceanKind/ ; GR016745//David and Lucile Packard Foundation/ ; },
mesh = {*Workflow ; Animals ; *DNA, Environmental/isolation & purification/genetics ; *Fishes/genetics/classification ; *Metagenomics/methods/economics ; Time Factors ; Sensitivity and Specificity ; Computational Biology/methods ; Biodiversity ; Resource-Limited Settings ; },
abstract = {Environmental DNA (eDNA) analysis enables biodiversity monitoring by detecting organisms from trace genetic material, but high reagent costs, cold-chain logistics and computational demands limit its broader use, particularly in resource-limited settings. To address these challenges and improve accessibility, we directly compared multiple workflow components, including four DNA extraction methods, two primer sets, three Nanopore basecalling models, and two demultiplexing pipelines. Across 48 workflow combinations tested in an aquarium with 15 fish species, we mapped trade-offs between cost, sensitivity, and processing speed to assess where time and resource savings are possible without compromising detection. Workflows using the Qiagen Blood and Tissue (BT) extraction kit and amplification using the MiFish-U primer set provided the highest sensitivity, detecting ≥ 12 of 15 species by ~3-5 h and reaching the 15-OTU plateau at ~8-10 h with Oxford Nanopore's high accuracy (HAC) basecalling model. Chelex, an alternative lower-cost extraction method, showed partial recovery only (≤ 9 OTUs by 61 h) even with extended sequencing, and did not recover all 15 OTUs. DirectPCR and QuickExtract offered field-friendly extraction alternatives that achieved comparable recovery in ~10-12 h, though their cost-effectiveness varied. While the MarVer1 primer was designed to broaden vertebrate detection, it recovered the same fish species as MiFish-U, though with fewer total reads. Real-time sequencing trials (0-61 h) revealed that high-efficiency workflows (BT + HAC) reached detection plateaus rapidly, indicating sequencing time can be reduced without sacrificing accuracy. The OBITools4 bioinformatics pipeline enabled automated demultiplexing but discarded more reads than an alternative, ONTbarcoder2.3, which retained low-abundance taxa at the cost of manual curation. Rather than identifying a single 'best' workflow, this study provides a transparent decision framework for prioritising cost, speed, and sensitivity in eDNA applications, supporting scalable, cost-effective eDNA monitoring in resource-limited settings.},
}

*Workflow
Animals
*DNA, Environmental/isolation & purification/genetics
*Fishes/genetics/classification
*Metagenomics/methods/economics
Time Factors
Sensitivity and Specificity
Computational Biology/methods
Biodiversity
Resource-Limited Settings

@article {pmid41482538,
year = {2026},
author = {Trigodet, F and Sachdeva, R and Banfield, JF and Eren, AM},
title = {Troubleshooting common errors in assemblies of long-read metagenomes.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41482538},
issn = {1546-1696},
abstract = {Assessing the accuracy of long-read assemblies, especially from complex environmental metagenomes that include underrepresented organisms, is challenging. Here we benchmark four state-of-the-art long-read assembly software programs, HiCanu, hifiasm-meta, metaFlye and metaMDBG, on 21 PacBio HiFi metagenomes spanning mock communities, gut microbiomes and ocean samples. By quantifying read clipping events, in which long reads are systematically split during mapping to maximize the agreement with assembled contigs, we identify where assemblies diverge from their source reads. Our analyses reveal that long-read metagenome assemblies can include >40 errors per 100 million base pairs of assembled contigs, including multi-domain chimeras, prematurely circularized sequences, haplotyping errors, excessive repeats and phantom sequences. We provide an open-source tool and a reproducible workflow for rigorous evaluation of assembly errors, charting a path toward more reliable genome recovery from long-read metagenomes.},
}

@article {pmid41482458,
year = {2026},
author = {Zhou, CB and Zhao, LC and Qin, Y and Yu, J and Li, W and Feng, Q and Tong, X and Abuduaini, R and Lu, SY and Tang, H and Zhang, YX and Cui, Y and Xiao, L and Song, LH and Ni, LK and Wu, K and Zhong, H and Jiang, YC and Zou, Y and Leng, XX and Wang, M and Zhao, WY and Wang, CJ and Liu, Q and Zhang, JQ and Hu, C and Chen, YX and Yao, YF and Zhu, S and Fang, JY},
title = {Streptococcus anginosus-derived methionine promotes gastric cancer progression.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336966},
pmid = {41482458},
issn = {1468-3288},
abstract = {BACKGROUND: Streptococcus anginosus has been linked with an increasing risk of gastric cancer (GC) and recognised as a signature for GC screening.

OBJECTIVE: To investigate the promotional effect of S. anginosus in terms of its metabolic interactions with the host.

DESIGN: We used the functional profiles of shotgun metagenomic sequencing from stools to detect bioactive molecules relevant to S. anginosus. In vivo and in vitro experiments were used to validate the facilitation of S. anginosus to GC progression. S. anginosus clinical strains were isolated and cultivated from cancerous tissues to verify its promotion of GC via methionine production. S. anginosus ΔmetE mutant strains were constructed to confirm the critical role of metE in methionine biosynthesis.

RESULTS: We verified S. anginosus facilitated GC progression in vivo and in vitro. Our functional analysis of metagenomes revealed a significant enrichment of bacterial methionine biosynthesis pathways in GC patients with high S. anginosus abundance. Methionine, identified here as one of the primary microbial metabolites derived from S. anginosus, contributed to GC progression in humans and mice. S. anginosus strains from cancerous tissues were found to promote GC via methionine production. We further observed a higher abundance and prevalence of metE gene in cancer stool metagenomes. By constructing an S. anginosus ΔmetE mutant strain, we confirmed the critical role of metE in methionine biosynthesis.

CONCLUSION: Our results elucidate the role of S. anginosus-derived methionine in GC progression, shedding light on intricate metabolic interplay between S. anginosus and host.},
}

@article {pmid41482085,
year = {2025},
author = {Yang, B and Xia, Q and Ji, X and Su, K and Yu, T and Xiao, Z and Shi, C and Luo, Z and Wang, X and Xu, W and Gao, Y and Hua, H and Shan, J},
title = {Ganjie Decoction protects against respiratory syncytial virus infection by activating PI3K/AKT-apoptosis axis and regulating gut microbiota metabolism.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121142},
doi = {10.1016/j.jep.2025.121142},
pmid = {41482085},
issn = {1872-7573},
abstract = {Ganjie Decoction (GJD), a traditional Chinese medicine (TCM) formula commonly used for respiratory diseases, has shown therapeutic potential against RSV pneumonia. However, its pharmacological mechanisms against respiratory syncytial virus (RSV) pneumonia are not fully understood.

AIM OF STUDY: This study aimd to characterize the active components of GJD and systematically investigate its therapeutic effects and underlying mechanisms in RSV-induced pneumonia.

MATERIALS AND METHODS: To evaluate the therapeutic efficacy of GJD in RSV-infected mice, we monitored body weight, performed qPCR, and conducted histopathological examination of lung tissues. The chemical constituents of GJD were characterized using UPLC-MS. Key bioactive compounds and their potential targets were predicted using network pharmacology and molecular docking. The underlying mechanisms were further elucidated using immunohistochemistry and western blotting. The interactions between GJD and the gut microbiota were explored using antibiotic depletion, fecal microbiota transplantation (FMT), metagenomic sequencing, and in vitro co-culture assays. Untargeted metabolomics was employed to assess GJD-induced metabolic alterations. Finally, the role of 4-hydroxyphenylacetic acid (4-HPA) was investigated through cell viability assays, immunofluorescence staining, and western blot analysis in vitro.

RESULTS: GJD significantly mitigated weight loss, attenuated pulmonary viral load, and suppressed inflammation in RSV-infected mice. Network pharmacology and molecular docking revealed that specific compounds in GJD target the PI3K/AKT signaling pathway. This finding was validated by western blotting and immunohistochemistry, which demonstrated that GJD suppresses PI3K/AKT pathway activation, thereby attenuating apoptosis and ameliorating RSV-induced pneumonia. Notably, these protective effects were markedly attenuated in mice with depleted gut microbiota. Furthermore, the therapeutic effects of GJD against RSV pneumonia were transferable via gut microbiota transplantation. GJD restored RSV-induced dysbiosis of the gut microbiota, with Lactobacillus reuteri emerging as one of the most enriched microbes following treatment. Metabolomics analysis identified 4-HPA as a microbiota-dependent metabolite significantly upregulated by GJD. Remarkably, administration of 4-HPA reproduced GJD's therapeutic effects in RSV-infected mice and activated the KEAP1/NRF2 antioxidant pathway, suggesting that 4-HPA functions as a key mediator of GJD's anti-RSV activity.

CONCLUSIONS: These findings suggest that GJD alleviates RSV pneumonia through a synergistic mechanism that modulates the PI3K/AKT-apoptosis pathway, restores gut microbial balance, and normalizes metabolic disturbances. This study systematically elucidates the mechanistic basis underlying the therapeutic effects of GJD against RSV pneumonia.},
}

@article {pmid41481471,
year = {2026},
author = {Regan, MD and Chiang, E and Grahn, M and Tonelli, M and Assadi-Porter, FM and Suen, G and Carey, HV},
title = {Host-microbiome mutualism drives urea carbon salvage and acetogenesis during hibernation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {1},
pages = {e2518978123},
doi = {10.1073/pnas.2518978123},
pmid = {41481471},
issn = {1091-6490},
support = {IOS-1558044//NSF (NSF)/ ; P41GM136463//HHS | NIH (NIH)/ ; DGE-1747503//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; RGPIN-2021-03109//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; 21HLSRM06//Canadian Space Agency (CSA)/ ; },
mesh = {Animals ; *Hibernation/physiology ; *Urea/metabolism ; *Sciuridae/microbiology/physiology/metabolism ; *Carbon/metabolism ; *Acetates/metabolism ; *Gastrointestinal Microbiome/physiology ; *Symbiosis/physiology ; Acetic Acid/metabolism ; Fatty Acids, Volatile/metabolism ; *Host Microbial Interactions/physiology ; },
abstract = {Hibernation is a seasonal survival strategy employed by certain mammals that, through torpor use, reduces overall energy expenditure and permits long-term fasting. Although fasting solves the challenge of winter food scarcity, it also removes dietary carbon, a critical biomolecular building block. Here, we demonstrate a process of urea carbon salvage (UCS) in hibernating 13-lined ground squirrels, whereby urea carbon is reclaimed through gut microbial ureolysis and used in reductive acetogenesis to produce acetate, a short-chain fatty acid (SCFA) of major value to the host and its gut microbiota. We find that urea carbon incorporation into acetate is more efficient during hibernation than the summer active season and that while both host and gut microbes oxidize acetate for energy supply throughout the year, the host's ability to absorb and oxidize acetate is highest during hibernation. Metagenomic analysis of the gut microbiome indicates that genes involved in the degradation of gut mucins, an abundant endogenous nutrient, are retained during hibernation. The hydrogen disposal associated with reductive acetogenesis from urea carbon helps facilitate this mucin degradation by providing a luminal environment that sustains fermentation, thereby generating SCFAs and other metabolites usable by both the host and its gut microbes. Our findings introduce UCS as a mechanism that enables hibernating squirrels and their gut microbes to exploit two key endogenous nutrient sources-urea and mucins-in the resource-limited hibernation season.},
}

Animals
*Hibernation/physiology
*Urea/metabolism
*Sciuridae/microbiology/physiology/metabolism
*Carbon/metabolism
*Acetates/metabolism
*Gastrointestinal Microbiome/physiology
*Symbiosis/physiology
Acetic Acid/metabolism
Fatty Acids, Volatile/metabolism
*Host Microbial Interactions/physiology

@article {pmid41481285,
year = {2026},
author = {Zhu, J and Huang, Z and Lin, Y and Zhu, J and Min, R and Wan, Z and Chen, Y and Zhu, J and Xing, L and Li, S and Olovo, CV and Wang, X and Li, G and Zhang, P},
title = {The potential immunological mechanisms of gut microbiota dysbiosis caused by antibiotics exacerbate the lethality of influenza viruses.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2609451},
doi = {10.1080/19490976.2025.2609451},
pmid = {41481285},
issn = {1949-0984},
mesh = {Animals ; *Dysbiosis/immunology/chemically induced/microbiology ; *Gastrointestinal Microbiome/drug effects/immunology ; *Anti-Bacterial Agents/adverse effects ; Mice ; *Orthomyxoviridae Infections/immunology/drug therapy/mortality/virology/microbiology ; Antiviral Agents/therapeutic use/pharmacology ; *Influenza A virus/drug effects/pathogenicity/immunology ; Lung/immunology/virology/pathology/drug effects ; Humans ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Antibiotics are not recommended to treat influenza A virus (IAV). However, antibiotic misuse for IAV persists worldwide. How to scientifically use antibiotics for IAV-infected patients remains a considerable challenge.

RESULTS: Here, we investigated the impact of antibiotics on viral pathogenicity, pulmonary-intestinal antiviral immunity, and antiviral drug efficacy. Our findings indicated that antibiotic intervention exacerbated IAV-caused mortality and lung injury in mice, manifested as increased mortality rates, shortened survival time, aggravated pulmonary injury, and excessive inflammatory responses. Furthermore, antibiotic pretreatment significantly diminished the efficacy of antivirals. Metagenomic sequencing revealed that antibiotics reduced the diversity and abundance of beneficial gut microbiota, including Lactobacillus and Bifidobacterium, while promoting the proliferation of pathogenic bacteria such as Klebsiella pneumoniae and Escherichia coli. Mechanistically, antibiotic intervention exacerbated IAV-caused excessive inflammatory responses by the blockage of pulmonary-intestinal antiviral immune pathways, which were caused by the upregulation of PKR, RIG-I, ISG15, and TRIM25 levels while downregulating IPS-1 mRNA levels. However, it is noteworthy that the combination of antibiotics and antiviral drugs effectively offset the adverse effects of antibiotic pretreatment on influenza mortality by upregulating IPS-1 levels and partially restoring pulmonary-intestinal immune homeostasis.

CONCLUSIONS: Pulmonary-intestinal immune homeostasis imbalance caused by antibiotic misuse can not only markedly exacerbate the lethality of IAV, but also significantly attenuate the efficacy of antiviral drugs. A mechanistic study confirmed that gut microbes dysbiosis caused by antibiotic pretreatment exacerbates the homeostasis imbalance of host antiviral immunity by blocking the RIG/MDA5/IPS-1 antiviral signaling pathway. However, combination therapy with antibiotics and antivirals effectively reversed the fatal outcome exacerbated by antibiotic pretreatment. Collectively, our findings not only provide a scientific explanation from the perspective of antiviral immunity as to why antibiotics should not be arbitrarily used to treat viral infections but also lay the scientific foundation for the rational clinical use of antivirals and antibiotics for treating influenza.},
}

Animals
*Dysbiosis/immunology/chemically induced/microbiology
*Gastrointestinal Microbiome/drug effects/immunology
*Anti-Bacterial Agents/adverse effects
Mice
*Orthomyxoviridae Infections/immunology/drug therapy/mortality/virology/microbiology
Antiviral Agents/therapeutic use/pharmacology
*Influenza A virus/drug effects/pathogenicity/immunology
Lung/immunology/virology/pathology/drug effects
Humans
Mice, Inbred C57BL

@article {pmid41481221,
year = {2026},
author = {Sun, S and Ning, Z and Xu, H and Peng, S and Gao, C and Hu, X},
title = {Diagnostic value of plasma cell-free DNA metagenomic next-generation sequencing in patients with suspected infections and exploration of clinical scenarios-a retrospective study from a single center.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2608531},
doi = {10.1080/07853890.2025.2608531},
pmid = {41481221},
issn = {1365-2060},
mesh = {Humans ; Retrospective Studies ; Female ; Male ; *High-Throughput Nucleotide Sequencing/methods ; *Cell-Free Nucleic Acids/blood/genetics ; Middle Aged ; *Metagenomics/methods ; Aged ; Adult ; Sensitivity and Specificity ; Blood Culture ; *Communicable Diseases/diagnosis/blood ; Coinfection/diagnosis/blood/microbiology ; },
abstract = {BACKGROUND: Plasma cell-free DNA metagenomic next-generation sequencing (mNGS) is a non-invasive comprehensive method for the etiological diagnosis of various infectious diseases. However, research on the early diagnosis and real-world clinical impact of plasma mNGS in patients with suspected infection are still limited.

MATERIALS AND METHODS: This study retrospectively included 140 patients with suspected infections who underwent early plasma mNGS and conventional culture testing. Referring to the clinical diagnosis of infectious diseases, the diagnostic performance of plasma mNGS and culture tests was compared, and the application scenarios and clinical effects of plasma mNGS were evaluated.

RESULTS: The positive rate of plasma mNGS was significantly higher than that of culture methods (55.71% vs 25.10%, p < 0.001) and blood cultures (55.71% vs 12.86%, p < 0.001). Regarding clinical diagnosis, the sensitivity of plasma mNGS was significantly higher than that of culture (58.27% vs 37.80%, p = 0.002). The combination of mNGS and culture achieved a higher detection sensitivity (69.29%), especially in patients with multi-site co-infections (73.68%) and blood infections (73.17%). Plasma mNGS demonstrated higher sensitivity in patients with procalcitonin (PCT) index > 5 ng/ml or human neutrophil lipocalin (HNL) index > 200 ng/ml. In terms of treatment, a total of 69 patients (54.33%) benefited from plasma mNGS.

CONCLUSION: This study highlights the significant improvement in pathogen detection performance by combining conventional culture with plasma mNGS detection, especially in patients with multi-site co-infections and blood infections. Early use of plasma mNGS as an adjunct to culture can better guide clinicians to initiate appropriate anti-infective therapy.},
}

Humans
Retrospective Studies
Female
Male
*High-Throughput Nucleotide Sequencing/methods
*Cell-Free Nucleic Acids/blood/genetics
Middle Aged
*Metagenomics/methods
Aged
Adult
Sensitivity and Specificity
Blood Culture
*Communicable Diseases/diagnosis/blood
Coinfection/diagnosis/blood/microbiology

@article {pmid41480976,
year = {2026},
author = {Rao, C and Su, X and Xia, Y and Li, N and Wan, Y and Lyu, H and Song, T and Dong, W and Shen, X},
title = {From Physical Architecture to Ecosystem Function: Tillage Exerts Indirect Control on Nitrogen Transformation by Restructuring Preferential Flow Paths.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12351},
pmid = {41480976},
issn = {1520-5851},
abstract = {How long-term tillage drives nitrogen (N) function succession by degrading vadose zone preferential flow paths remains unclear. This study investigated croplands across multiple tillage chronosequences by integrating dye tracing, [15]N isotope tracing, and metagenomic techniques. The study shows that tillage-induced degradation of preferential flow structures homogenizes the vadose zone and reshapes N-cycling communities, shifting denitrifiers from nirK- to nirS-dominated assemblages. Consistent with this community turnover, gross nitrification rates in shallow preferential paths are 30.8% higher than in the adjacent matrix in short-term tillage, whereas in deep layers matrix denitrification and DNRA rates exceed those in preferential paths by 37.9 and 76.1%, and anammox appears only in the matrix at medium- and long-term tillage, indicating a concentration of reductive N processes in the matrix. Path analysis further shows that tillage-driven alterations in hydraulic properties (path coefficient = -0.91, p < 0.01), together with these community and process-rate shifts, redirect the dominant N pathway from hotspot-driven nitrification in preferential channels to matrix-driven reductive N loss, converting a nitrate-leaching-prone system into one with higher gaseous emission potential. This establishes a mechanistic link linking soil hydraulic degradation to N functional succession and supports targeted, stage-dependent farmland nitrogen management.},
}

@article {pmid41480659,
year = {2026},
author = {Balbino, KP and Kravchychyn, ACP and Cândido, FG and Dias, MME and Mendes, TAO and Oliveira, LL and Castro, LCV and Bressan, J and de la Garza, AL and Milagro, FI and Zulet, MA and Hermsdorff, HHM},
title = {Precision nutrition in weight loss and neuroendocrine control of people with obesity: The study protocol of a factorial randomised controlled trial (GenON Programme).},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.70414},
pmid = {41480659},
issn = {1463-1326},
support = {444037/2023-3//National Council for Scientific and Technological Development - CNPq/ Brazilian Ministry of Health - MoH, Brazilian National Program of Genomics and Precision Health - Genomas Brasil/ ; Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {AIMS: Precision nutrition, guided by genetic testing, has emerged as a promising approach for managing obesity. However, robust clinical trials testing its effectiveness in real-world dietary interventions remain scarce. The GenOn Programme aims to evaluate whether tailoring nutritional care based on genetic risk for obesity enhances weight loss, satiety control, and metabolic outcomes in adults with overweight and obesity.

MATERIALS AND METHODS: The GenOn Programme is an 18-week, 2 × 2 factorial, randomised controlled trial including 120 adults classified as high or low genetic risk for obesity (variants: FTO rs9939609 and rs1121980; MC4R rs1782313; LEP rs7799039). Participants are randomised to standard or satiety-focused dietary counselling. Both groups receive five calorie-restricted (-500 kcal/day), nutritionally balanced meal plans. The satiety arm additionally includes a high-protein breakfast, daily granola supplementation and behavioural strategies. Assessments at baseline, Week 12, and Week 18 include weight loss, body composition, satiety perception, quality of life, cardiometabolic markers, (epi)genetics, inflammation, neuroendocrine regulation, and metagenomics.

RESULTS AND CONCLUSIONS: The GenOn Programme is a randomised controlled trial to test a precision nutrition approach for overweight and obesity, integrating genetics, dietary strategies, and behavioural support. Findings may inform dietitians and healthcare systems on the clinical value of genetically guided nutritional care to improve outcomes in the treatment of overweight and obesity.},
}

@article {pmid41480317,
year = {2025},
author = {Zakharzhevskaya, NB and Erdes, SI and Belousova, EA and Samolygo, IS and Manina, MA and Kondrashova, PV and Lomakina, EY and Kardonsky, DA and Vorobyeva, EA and Shagaleeva, OY and Silantyev, AA and Kazakova, VD and Kashatnikova, DA and Kalachnuk, TN and Kolesnikova, IV and Chaplin, AV and Markelova, MI and Grigoryeva, TV and Olekhnovich, EI and Veselovsky, VA and Morozov, MD and Zoruk, PY and Boldyreva, DI and Vanyushkina, AA and Efimov, BA},
title = {Combined metabolomic and metagenomic analysis reveals inflammatory bowel disease diversity in pediatric and adult patients.},
journal = {World journal of gastroenterology},
volume = {31},
number = {48},
pages = {112653},
pmid = {41480317},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metabolomics/methods ; *Colitis, Ulcerative/microbiology/diagnosis/metabolism ; *Crohn Disease/microbiology/diagnosis/metabolism ; Feces/microbiology ; Child ; Middle Aged ; Male ; Female ; *Metagenomics/methods ; Adolescent ; Child, Preschool ; Aged ; Biomarkers/metabolism/analysis ; Age Factors ; Adult ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; },
abstract = {BACKGROUND: The gut microbiota displays pronounced compositional differences between pediatric and adult populations, both under normal conditions and during the development of inflammatory bowel disease (IBD). These structural variations are accompanied by substantial changes in microbial metabolic activity.

AIM: To identify novel early diagnostic biomarkers of IBD, we performed an integrated multi-omics analysis that included assessing microbial community structure and profiling microbial metabolic activity in pediatric and adult cohorts with ulcerative colitis (UC) and Crohn's disease (CD).

METHODS: The study cohort consisted of two distinct age groups with confirmed IBD diagnoses: Adult patients (aged 45 to 70) and pediatric patients (aged 5 to 15), each diagnosed with either CD or UC. 16S rRNA gene sequencing was performed using the MinION™ Mk1B platform, with data acquisition carried out via MinKNOW software version 22.12.7 (Oxford Nanopore Technologies). Stool samples were analyzed using a Shimadzu QP2010 Ultra GC/MS system equipped with a Shimadzu HS-20 headspace extractor.

RESULTS: Comparative analysis revealed significant age-related differences in the abundance of Bacteroidota, with pediatric IBD patients showing a lower prevalence compared to adults. Microbial profiling identified Streptococcus salivarius and Escherichia coli as potential biomarkers for assessing IBD risk in children. Furthermore, metagenomic analysis uncovered five microbial signatures with diagnostic potential for CD: Ralstonia insidiosa, Stenotrophomonas maltophilia, Erysipelatoclostridium ramosum, Blautia spp., and Coprococcus comes. Using comprehensive metabolomic profiling, we developed and validated novel risk prediction algorithms for pediatric IBD. The CD risk stratification model identifies high-risk patients based on two key biomarkers: An elevated IBD risk coefficient score and reduced levels of 1H-indole-3-methyl. The UC risk prediction model incorporates three metabolic biomarkers indicative of increased disease risk: An elevated risk coefficient score, increased acetate levels, decreased pentanoic acid, and altered excretion of p-cresol (4-methylphenol).

CONCLUSION: Functional metabolomics holds transformative potential for IBD diagnostics across all age groups, with especially significant implications for pediatric patients. The distinct metabolic and metagenetic profiles observed in the pediatric cohort may represent primary alterations in IBD, providing valuable insights for exploring novel mechanisms underlying disease pathogenesis.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metabolomics/methods
*Colitis, Ulcerative/microbiology/diagnosis/metabolism
*Crohn Disease/microbiology/diagnosis/metabolism
Feces/microbiology
Child
Middle Aged
Male
Female
*Metagenomics/methods
Adolescent
Child, Preschool
Aged
Biomarkers/metabolism/analysis
Age Factors
Adult
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification

@article {pmid41480270,
year = {2025},
author = {Bustos-Caparros, E and Viver, T and Gago, JF and Venter, SN and Bosch, R and Konstantinidis, KT and Rodriguez-R, LM and Rossello-Mora, R},
title = {Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf228},
pmid = {41480270},
issn = {2730-6151},
abstract = {An unbiased and accurate estimation of intraspecies diversity, i.e. the extent of genetic diversity within species (or microdiversity), is crucial for clinical and environmental microbiome studies. Although it is well appreciated that sequencing depth (or coverage depth) below 10X can provide biased estimates of microdiversity, typically underestimating diversity due to the random sampling of alleles, there is a widely accepted convention that microdiversity estimates tend to be relatively stable at sequencing depth exceeding 10X. Therefore, discarding species with <10X or rarefying to 10-20X sequencing depth are generally used to compare microdiversity among taxa and samples. Our findings showed that these biases may persist even at depth levels above 50-200X for all popular sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. The biases mostly, but not always, represent an underestimation of diversity and were attributable to the incomplete recovery of Single Nucleotide Variants (SNVs) at lower sequencing depth levels. To address this issue, we recommend using rarefaction-based approaches to standardize data at least 50X, and ideally at 200X sequencing depth, which reduces differences between observed and expected microdiversity values to <0.5%. Furthermore, the Average Nucleotide Identity of reads (ANIr) metric is significantly less sensitive to sequencing depth variability than nucleotide diversity (π), making it a robust alternative for estimating microdiversity at sequencing depth close or exceeding 10X, without a need to rarefying data. Therefore, the sequencing depth thresholds proposed herein provide a more standardized framework for direct comparisons of microdiversity across samples and studies.},
}

@article {pmid41480265,
year = {2025},
author = {Ren, G and Gubry-Rangin, C and Wang, W and Liu, R and Liu, J and Liu, J and Zhang, XH and Liu, J},
title = {Purifying selection and low recombination facilitated sequential colonization of benthic and pelagic coastal ocean by ammonia-oxidizing archaea.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf234},
pmid = {41480265},
issn = {2730-6151},
abstract = {The evolutionary adaptation of archaea to ecologically diverse habitats remains poorly understood. Ammonia-oxidizing archaea (AOA) exhibit significant diversification across various environmental conditions; however, their ecological dynamics, diversification, and associated evolutionary processes are still largely unexplored in coastal environments, which contain extensive ecosystem heterogeneity. Combining newly assembled metagenomic data from Chinese marginal seas (2059 km coverage) with global datasets (spanning over 16 000 km), these knowledge gaps were explored across a continental-scale latitudinal gradient. It revealed that coastal AOA genomic diversity is latitude-dependent, with predicted optimum growth temperatures and substrate metabolic pathways explaining the geographical distribution. The two dominant genus-level clades exhibited significantly distinct benthic-pelagic niches, associated with specific genes involved in nutrient uptake and stress resistance. Phylogenomic reconstructions suggest that AOA initially colonized the coastal ocean sediments around 718 million years ago (Mya), and subsequent purifying selection and low recombination facilitated the AOA niche expansion into marine coastal environments. By revealing the evolutionary trajectories of Nitrososphaeria and their differential colonization patterns, our findings offer a novel perspective on the mechanisms of AOA diversification in the coastal ocean. This work advances our understanding of microbial diversification and niche differentiation of AOA in coastal ecosystems as well as the evolutionary forces shaping their global biogeography.},
}

@article {pmid41480263,
year = {2025},
author = {Ma, M and Wang, M and Liang, Y and Guo, Y and Zhang, H and Cao, L and Fu, L and Hu, G and Li, C and Mock, T and Li, C},
title = {Microbial communities and metabolic functions vary with spatial heterogeneity in cold-seep carbonates.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf232},
pmid = {41480263},
issn = {2730-6151},
abstract = {Cold-seep carbonates, formed through interactions among methane, fluid chemistry, and microbial chemosynthesis, represent biodiversity hotspots in the deep sea. Spatial heterogeneity within these carbonates arises from variations in methane flux, yet the microbial contributions to this heterogeneity remain underexplored. Here we combined remotely operated vehicle-based in situ measurements, X-ray imaging, metagenomics, qPCR, and [13]C-CH4 stable-isotope labeling to investigate microbial communities across carbonate habitats in the South China Sea. We found that methane flux linked to carbonate structural properties, shapes microbial metabolic interactions, notably anaerobic methane oxidation coupled with aragonite and FeS precipitation. These processes may contribute to self-sealing carbonate features, potentially reducing methane permeability and influencing geochemical gradients and geomorphology. Our findings reveal that microbiomes and their feedbacks play a significant role in shaping habitat-scale spatial heterogeneity of cold-seep carbonates, improving our understanding of methane cycling and carbonate ecosystem dynamics.},
}

@article {pmid41480114,
year = {2025},
author = {Robayo-Cuevas, C and Junca, H and Uribe, S and Gómez-Palacio, A},
title = {Detection of endosymbiotic, environmental, and potential bacterial pathogens in diverse mosquito taxa from Colombian tropical forests using RNAseq.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1727830},
pmid = {41480114},
issn = {1664-302X},
abstract = {INTRODUCTION: Mosquitoes of the subfamily Culicinae transmit pathogens of major medical and veterinary importance, particularly in tropical regions where urbanization and ecological change promote arbovirus circulation. In Colombia, rural Culicinae species are diverse and harbor microbiomes that may influence vector competence, yet their bacterial communities remain poorly characterized.

METHODS: We characterized the bacterial microbiota of multiple Culicinae species and morphotypes collected from two rural localities in Antioquia, Colombia, using an integrated metagenomic approach. Ribosomal 16S rRNA sequences were extracted from total RNA-seq datasets to infer bacterial community composition and assess α- and β-diversity. Diversity metrics (Chao1 and Shannon indices), Discriminant Analysis of Principal Components (DAPC), and Bray-Curtis ordination were used to evaluate community structure. In parallel, de novo assembled contigs were taxonomically annotated against the NCBI NR bacterial database to obtain complementary taxonomic and functional insights.

RESULTS: Culex morphotypes exhibited the highest richness and evenness, whereas Aedes and Trichoprosopon showed lower diversity. Ordination and DAPC analyses revealed partial clustering by species and tribe. Both the 16S and assembly-based analyses showed complex bacterial assemblages dominated by Wolbachia (up to 60% of reads in several Aedes and Culex morphotypes), followed by environmental genera such as Pseudomonas and Acinetobacter (10-20%). Lower-abundance taxa of medical and veterinary importance-including Salmonella, Borrelia, and Clostridium (<5%)-were also detected. Bacterial community structure differed among mosquito species; Aedes albopictus was enriched in lactic acid bacteria, while Culex morphotypes exhibited broader environmental and endosymbiotic profiles.

DISCUSSION: This study provides the first comprehensive metagenomic description of bacterial communities associated with rural Culicinae mosquitoes in Colombia. The predominance of symbionts such as Wolbachia and Spiroplasma, coupled with distinct bacterial signatures among host species, highlights the ecological complexity of these microbiomes and their potential relevance for microbiome-based strategies in sustainable arboviral disease management.},
}

@article {pmid41480112,
year = {2025},
author = {Fu, J and Bu, G and Aimaier, S and Yang, Y and Bao, Z and Wulasihan, M},
title = {Sex-specific association between gut Faecalibacterium prausnitzii and hypertension in male individuals.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1683587},
pmid = {41480112},
issn = {1664-302X},
abstract = {OBJECTIVE: While gut microbiota (GM) dysbiosis has been implicated in hypertension, the sexassociated microbial signatures and their underlying mechanisms remain poorly understood, particularly in populations living in unique geographical and climatic conditions.

DESIGN: Through an integrated approach combining 16S rRNA sequencing, shotgun metagenomics, and serum metabolomics, we systematically investigated the sex-associated characteristics of the gut microbiota in hypertension among a cohort of 200 participants from Xinjiang.

METHODS: An initial cohort analysis identified Faecalibacterium as a male-associated biomarker for hypertension. Subsequent species-level characterization revealed that Faecalibacterium prausnitzii (F. prausnitzii) showed significant negative correlations with systolic blood pressure (SBP). This male-specific association was consistently observed across both 16S rRNA sequencing and shotgun metagenomic datasets. Then, our integrated analysis suggested a potential pathway through which F. prausnitzii may be linked to systolic blood pressure in male individuals, with N-phenylacetylglutamine (PAGln) identified as a potential mediating metabolite.

CONCLUSION: Our study establishes a microbe-metabolite-clinical trait axis in the pathophysiology of sex-associated hypertension and significantly advances our understanding of sex-driven host-microbe interactions.},
}

@article {pmid41479870,
year = {2025},
author = {Ghosh, N and Sinha, K},
title = {Guardians within: Cross-talk between the gut microbiome and host immune system.},
journal = {World journal of gastrointestinal pathophysiology},
volume = {16},
number = {4},
pages = {111245},
pmid = {41479870},
issn = {2150-5330},
abstract = {The gut microbiome, a complex ecosystem of trillions of microorganisms, plays a crucial role in immune system regulation and overall health. This review explores the intricate cross-talk between the gut microbiota and the host immune system, emphasizing how microbial communities shape immune cell differentiation, modulate inflammatory responses, and contribute to immune homeostasis. Key interactions between innate and adaptive immune cells - including macrophages, dendritic cells, natural killer cells, innate Lymphoid cells, T cells, and B cells - and gut microbiota-derived metabolites such as short-chain fatty acids are discussed. The role of commensal bacteria in neonatal immune system development, mucosal barrier integrity, and systemic immunity is highlighted, along with implications for autoimmune diseases, inflammatory conditions, and cancer immunotherapy. Recent advances in metagenomics, metabolomics, and single-cell sequencing have provided deeper insights into the microbiota-immune axis, opening new avenues for microbiome-based therapeutic strategies. Understanding these interactions paves the way for novel interventions targeting immune-mediated diseases and optimizing health through microbiome modulation.},
}

@article {pmid41479581,
year = {2025},
author = {Komatsu, H},
title = {Comparison of three pediatric studies investigating acute hepatitis of unknown etiology.},
journal = {World journal of virology},
volume = {14},
number = {4},
pages = {110435},
pmid = {41479581},
issn = {2220-3249},
abstract = {Between 2021 and 2023, approximately 400 pediatric cases of acute hepatitis of unknown etiology (AHUE) were reported in European countries and the United States. In 2023, three pediatric studies revealed that adeno-associated virus serotype 2 (AAV-2) infection was associated with AHUE. This article presents a summary and comparison of the results of metagenomic sequencing, viral whole-genome sequencing, virus-specific real-time polymerase chain reaction (PCR) and histological analysis of the liver, all of which were among the common investigative methods used in the three pediatric studies. All three pediatric studies revealed 80% or greater rates of positivity for AAV-2 in cases of AHUE according to metagenomic sequencing. Moreover, on the basis of PCR results, two studies revealed high AAV-2 positivity rates (96.4% and 81.2%) among cases of AHUE. These findings suggest that AAV-2 is a pathogen in AHUE. Coinfection with AAV-2 and one or more helper viruses (human adenovirus, human herpesvirus 6B, Epstein-Barr virus, etc.), high viral loads of AAV-2 in blood, anti-AAV-2 IgM and human leukocyte antigen typing could be candidate diagnostic criteria for AHUE. AAV-2 infection should be incorporated into clinical guidelines for the management of acute liver failure. Cidofovir can be administered if coinfection with AAV-2 and HAdV is detected.},
}

@article {pmid41478956,
year = {2026},
author = {Halford, C and Moragues-Solanas, L and Weller, SA and Gilmour, M},
title = {Whole Genome Amplification of Microbial DNA from Host-Depleted Clinical Samples.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3003},
number = {},
pages = {175-186},
pmid = {41478956},
issn = {1940-6029},
mesh = {Humans ; *Metagenomics/methods ; *Nucleic Acid Amplification Techniques/methods ; *DNA, Bacterial/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Clinical metagenomics (CMg) involves the untargeted sequencing of the genetic content of samples collected from patients and is a highly promising method for the diagnosis of infectious disease. Depending on the sample type, CMg can be reliant on the removal of the host genetic material from the sample to support detection of microbial pathogens, and this selective process (or an otherwise low abundance of microbial cells in the sample) may result in concentrations of DNA too low for productive sequencing. Whole genome amplification (WGA), the nonselective amplification of the total DNA of a sample, can be applied to significantly increase the concentration of DNA and enable CMg sequencing. This chapter describes the methods for the amplification of microbial DNA extracted from host-depleted wound swab samples using the GenomiPhi[™] V3 Ready-To-Go[™] (Cytiva) DNA WGA kit and host-depleted whole blood samples using the REPLI-g[®] Single-Cell WGA kit (Qiagen). This is followed by the de-branching and bead-based clean-up of the amplified DNA, resulting in highly concentrated DNA ready for CMg DNA sequencing.},
}

Humans
*Metagenomics/methods
*Nucleic Acid Amplification Techniques/methods
*DNA, Bacterial/genetics/isolation & purification
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods

@article {pmid41478955,
year = {2026},
author = {Cruz-Flores, R and Cáceres-Martínez, J and Dhar, AK},
title = {Laser Microdissection and Near Single-Cell Whole Genome Amplification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3003},
number = {},
pages = {165-173},
pmid = {41478955},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; *Laser Capture Microdissection/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; *Nucleic Acid Amplification Techniques/methods ; *Genome, Viral ; Paraffin Embedding ; Tissue Fixation ; Genomics/methods ; DNA, Viral/genetics/isolation & purification ; },
abstract = {Laser microdissection (LMD) and whole genome amplification (WGA) are powerful techniques that integrate molecular and histological approaches to enable the precise selection of a minimal number of virus-infected cells-down to near single-cell resolution-and the subsequent generation of whole viral genomes with minimal host DNA interference. This chapter presents a detailed protocol for LMD and near single-cell WGA, specifically optimized for the recovery and sequencing of viral genomes from formalin-fixed paraffin-embedded (FFPE) tissues. The method allows for the targeted isolation of infected cells, thereby reducing host genomic background and enhancing the detection of pathogen-specific signals for downstream next-generation sequencing (NGS). The protocol includes steps for tissue section preparation, cell isolation via LMD, DNA extraction using the PicoPure DNA Extraction Kit, and unbiased genome amplification using the SeqPlex DNA Amplification Kit-ensuring high-quality nucleic acid recovery suitable for NGS workflows.},
}

*Single-Cell Analysis/methods
*Laser Capture Microdissection/methods
Humans
High-Throughput Nucleotide Sequencing/methods
*Nucleic Acid Amplification Techniques/methods
*Genome, Viral
Paraffin Embedding
Tissue Fixation
Genomics/methods
DNA, Viral/genetics/isolation & purification

@article {pmid41318438,
year = {2025},
author = {Liu, J and Wu, J and Zhang, W and Huang, H and Liao, D},
title = {Disseminated Talaromyces marneffei infection mimicking tuberculosis in an HIV-negative adult with anti-IFN-γ autoantibodies: a case report.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {1},
pmid = {41318438},
issn = {1471-2334},
support = {2024J0112//the Nature Science Foundation of Fujian Province of China/ ; },
abstract = {BACKGROUND: Talaromyces marneffei (TM) is an opportunistic fungus causing life-threatening disseminated infections in immunocompromised individuals. While classically associated with HIV, TM is increasingly reported in HIV-negative patients, often misdiagnosed due to nonspecific manifestations.

CASE PRESENTATION: A 38-year-old HIV-negative Chinese woman with a history of thyroid cancer presented with a three-month history of fever, cough, weight loss, and subcutaneous masses. Imaging revealed diffuse pulmonary nodules and osteolytic bone destruction. She was initially misdiagnosed with tuberculosis and received anti-TB therapy without improvement. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified TM, which was later confirmed by fungal culture. Anti–interferon-gamma autoantibodies (anti–IFN-γ auto-Abs) were markedly elevated (111.72 ng/mL). She was treated with liposomal amphotericin B(L-AmB) followed by itraconazole, achieving temporary remission. One month post-discharge, TM recurred with new Sweet syndrome–like skin lesions. Immunomodulatory therapy combined with antifungals led to disease control.

CONCLUSION: This case highlights three key clinical insights: (1) TM can closely mimic tuberculosis, especially in HIV-negative individuals; (2) mNGS is a valuable diagnostic tool when conventional tests fail; and (3) Anti–IFN-γ auto-Abs may underlie recurrent or refractory TM infections. Clinicians in endemic regions should consider TM and evaluate immune status early in atypical or treatment-resistant cases.},
}

@article {pmid41316171,
year = {2025},
author = {Meldrum, OW and Tiew, PY and Xu, H and Low, DY and Ivan, FX and Narayana, JK and Jaggi, TK and Ching, J and Chotirmall, SH},
title = {Integrated multi-omics profiling for risk stratification in Asians with COPD.},
journal = {Respiratory research},
volume = {27},
number = {1},
pages = {2},
pmid = {41316171},
issn = {1465-993X},
support = {(#020458-00001//LKCMedicine-ICL Fellowship/ ; MOH-001636//National Research Foundation Singapore under its Open Fund-Large Collaborative Grant and administered by the Singapore Ministry of Health's National Medical Research Council/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council under its Clinician-Scientist Individual Research Grant/ ; MOH-001855//Singapore Ministry of Health's National Medical Research Council under its Clinician-Scientist Award (CSA) Investigator (INV) category/ ; RT1/22//Singapore Ministry of Education under its AcRF Tier 1 Grant/ ; },
abstract = {BACKGROUND: Comorbidity-based risk stratification in Chronic Obstructive Pulmonary Disease (COPD) incompletely captures inherent biological heterogeneity, particularly in Asian populations that demonstrate high-risk clinical phenotypes including prior pulmonary tuberculosis. We investigated whether integrated sputum multi-omics could improve risk stratification in an Asian COPD cohort.

METHODS: We conducted a prospective, multicenter assessment of N = 56 Asians with established COPD, classified as high- (N = 25; cardiovascular or ex-tuberculosis) or low-risk (N = 31; diabetic or low-comorbidity) based on established co-morbidity phenotyping. Sputum was subjected to mucus analysis (MUC5AC, MUC5B, mucus solids, rheology), metabo-lipidomics (LC-MS/MS) and microbiome assessment (shotgun metagenomics). Multivariate statistics was employed to integrate datasets.

RESULTS: High-risk Asian COPD demonstrates abnormal mucus biochemistry characterized by elevated MUC5AC; extensive metabo-lipidomic alterations characterized by dysregulated tryptophan-kynurenine metabolism and lipid remodeling with enrichment of lysophosphatidylcholines and triacylglycerols. Microbial networks are disrupted in high-risk patients, typified by antagonistic interactions driven by K. pneumoniae, H. influenzae and Neisseria spp. Integrative assessment combining all datasets partitioned the cohort into two clusters: SNF 1 (N = 34) and SNF 2 (N = 22), the former representing an unfavorable group characterized by exacerbations, hospitalizations, mucus dysfunction, microbial pathogens and dysregulated metabo-lipidomic pathways. Remarkably, 42% (N = 13 of 31) of the originally classified low risk COPD exhibited the unfavorable SNF 1 endotype, distinguished by more severe exacerbations (hospitalizations), K. pneumoniae and elevated hypoxanthine, creatine, spermine and phosphatidylcholines.

CONCLUSION: Integrative multi-omics profiling of Asian COPD significantly refines clinical risk stratification identifying a novel ‘high-risk’ biological endotype. Substantial proportions of clinically low-risk COPD exhibit this endotype, suggesting that clinical and co-morbidity profiling in Asians with COPD should be supplemented by molecular assessment to ensure accurate risk stratification.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12931-025-03440-1.},
}

@article {pmid41478953,
year = {2026},
author = {Lozano-Escobar, ED and Mateo-Cáceres, V and Mayoral-Campos, C and Redrejo-Rodríguez, M},
title = {Assessing Amplification Quality and Bias in MDA Methods Through Comparative Analysis of Short-Read Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3003},
number = {},
pages = {131-148},
pmid = {41478953},
issn = {1940-6029},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; Humans ; DNA Copy Number Variations ; *Nucleic Acid Amplification Techniques/methods/standards ; *Sequence Analysis, DNA/methods ; Genomics/methods ; Metagenome ; },
abstract = {Although high-throughput sequencing methods have greatly improved over the last few years, direct sequencing remains unfeasible when DNA quantity or quality is limited. In such instances, various whole genome or metagenome amplification (WGA) techniques can generate sufficient DNA for multiple analyses, albeit with some amplification bias. Competent WGA analysis is typically evaluated by sequence coverage, assessed through two key parameters: depth, referring to the number of reads containing each nucleotide, and breadth, indicating the proportion of nucleotides in the consensus sequence relative to the original sequence length at the obtained depth. Adequate coverage is essential for detailed genomic analysis and the detection of population variants, copy number variations (CNVs), and structural variants (SVs). This chapter outlines a pipeline for analyzing Illumina sequencing data of amplified samples compared to non-amplified samples to assess the performance of various WGA methods, starting from raw sequences.},
}

*High-Throughput Nucleotide Sequencing/methods
Humans
DNA Copy Number Variations
*Nucleic Acid Amplification Techniques/methods/standards
*Sequence Analysis, DNA/methods
Genomics/methods
Metagenome

@article {pmid41478678,
year = {2026},
author = {Wang, Y and He, L and Hu, X and Guan, Y and Chen, X and Du, J and Chen, J and Ma, C and Ye, L},
title = {Metagenomic and culture-based genomics reveal virulence and resistance risks in Manila clam microbiomes.},
journal = {Food microbiology},
volume = {136},
number = {},
pages = {105001},
doi = {10.1016/j.fm.2025.105001},
pmid = {41478678},
issn = {1095-9998},
mesh = {Animals ; *Bivalvia/microbiology ; Metagenomics ; *Bacteria/genetics/isolation & purification/pathogenicity/drug effects/classification ; *Microbiota ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence ; Genomics ; *Drug Resistance, Bacterial ; Vibrio/genetics/pathogenicity/isolation & purification/drug effects ; Shellfish/microbiology ; Phylogeny ; },
abstract = {Bivalves are important aquaculture products whose safety is shaped by their microbiomes. Here, we present the first comprehensive characterization of Manila clam (Ruditapes philippinarum) microbiomes using both shotgun metagenomics (6 clams) and culture-based genomics (169 isolates, 40 draft genomes), integrating community, functional, and antimicrobial resistance profiling. Communities were dominated by Proteobacteria (99.3-99.9 %), with Pseudoalteromonas and Vibrio collectively accounting for 74.9-99.7 % and showing strong inverse correlations, defining Pseudoalteromonas-dominated, Vibrio-dominated, and mixed states. Species richness ranged from 22 to 180 per sample. Recognized human pathogens occurred at low abundance (<0.3 %), including Vibrio parahaemolyticus, Vibrio alginolyticus, and Photobacterium damselae, while opportunistic vibrios expanded in some clams (e.g., Vibrio cyclitrophicus 57.9 %). We reconstructed 34 high-quality MAGs, seven resolved to species (Pseudoalteromonas tetraodonis, V. cyclitrophicus, Shewanella aquimarina), alongside unclassified lineages. Metagenomes encoded 14 virulence-factor categories with 2281 subtypes, and isolate genomes added 93 further subtypes, including high-virulence loci in Escherichia coli and type III secretion genes in V. parahaemolyticus. Resistomes spanned 18 antibiotic classes with 511 subtypes; isolates contributed 22 additional antibiotic resistance genes(ARGs), including extended-spectrum β-lactamases (blaCTX-M-102) and blaNDM-1. Four carbapenemase-producing isolates (three Shewanella algae, one V. parahaemolyticus) carried blaNDM-1 on IncC plasmids, with the V. parahaemolyticus plasmid transferable to E. coli. Two P. tetraodonis MAGs encoded RiPP-like and terpene biosynthetic clusters plus phage-defense systems, consistent with Vibrio suppression. These findings demonstrate that clam microbiomes fluctuate between protective (Pseudoalteromonas) and pathogenic (Vibrio-Shewanella) states, providing a first integrated framework for assessing microbial risk, antimicrobial resistance, and food safety interventions in bivalve aquaculture.},
}

Animals
*Bivalvia/microbiology
Metagenomics
*Bacteria/genetics/isolation & purification/pathogenicity/drug effects/classification
*Microbiota
Virulence Factors/genetics
Anti-Bacterial Agents/pharmacology
Virulence
Genomics
*Drug Resistance, Bacterial
Vibrio/genetics/pathogenicity/isolation & purification/drug effects
Shellfish/microbiology
Phylogeny

@article {pmid41478427,
year = {2025},
author = {Zhou, Z and Xu, M and Gao, C and Zheng, C and Bao, K and Ma, J},
title = {Metagenomic insights into N2O emission pathways shaped by arsenic and hydrological regimes in mangrove soils: An incubation study.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123658},
doi = {10.1016/j.envres.2025.123658},
pmid = {41478427},
issn = {1096-0953},
abstract = {Mangrove wetlands are characterized by an abundant and complex nitrogen cycling (N-cycling) process during periodic tidal flooding, and increasing arsenic (As) concentration profoundly influences microbial ecosystems and nitrogen (N) transformation. However, the combined impacts of As and hydrology on nitrous oxide (N2O) emissions remain unclear. Here, a soil microcosm experiment was conducted under two hydrological regimes (non-flooded and flooded) and with three As addition levels (50, 100, and 200 mg kg[-1]) to examine their effects on N2O fluxes and N transformation. The results demonstrated that As addition significantly enhanced N2O uptake, reducing fluxes by 1.29-26.47 % and 3.18-10.04 % relative to the control (CK) under non-flooded and flooded conditions, respectively. Notably, the N2O uptake flux under flooded conditions was 3.01 times that of non-flooded conditions on average. Furthermore, influencing mechanisms on N2O emission differ significantly between hydrological regimes. In non-flooded treatments, As primarily decreased NO3[-]-N availability and increased NH4[+]-N retention via upregulating nirBD and nrfAH genes to enhance the DNRA pathway, which reduced the production of N2O. Meanwhile, As promoted N2O reduction mainly through the upregulation of the nosZ gene, resulting in more N2O uptake. However, As predominantly existed as As(III) in flooded treatments, which stimulated the expression of As-resistance genes. This response helped alleviate As toxicity on microorganisms. Additionally, the enhanced decomposition of SOC served as the major energy source for microorganisms, maintaining and even increasing the abundance of partial N-cycling functional genes. Meanwhile, under nitrate-limited conditions, one possible explanation for the observed N2O uptake is that its reduction was stimulated because N2O could serve as an alternative terminal electron acceptor. The altered C and N availability under As contamination also shifted the microbial nitrogen transformation pathways toward processes that produce less N2O. These findings provided valuable insights about N-cycling and adaptations of N functional microorganisms in heavy metal-stressed mangrove wetland ecosystems.},
}

@article {pmid41478169,
year = {2025},
author = {Wang, W and Zhang, S and Wang, Y and Ge, J and Li, L},
title = {Metagenomic and cytotoxicity insights into the migration behavior and pathogenic potential of multi-medium microorganisms in a wastewater treatment plant.},
journal = {Water research},
volume = {292},
number = {},
pages = {125285},
doi = {10.1016/j.watres.2025.125285},
pmid = {41478169},
issn = {1879-2448},
abstract = {As important interphases between the human society and natural water environments, wastewater treatment plants (WWTPs) accumulate a variety of human activity-related microorganisms. The characteristics of potential pathogenic microorganisms associated with WWTPs have gradually become a research hotspot. In this study, the distribution characteristics and migration patterns of potential pathogenic genera in different processes, media and seasons were investigated via the metagenomic analysis of samples regularly collected at a typical WWTP in North China. The results obtained 112 pathogenic bacteria and 33 pathogenic fungi in the wastewater, sludge, and bioaerosol samples. Resistance mechanisms were dominated by antibiotic efflux with proportion of 62.63-63.53%. Functional genes encoding offensive virulence factors (VFs) including adherence, secretion system, toxin, invasion, and actin-based motility were the most common category in all the WWTP samples. Network analysis revealed the presence of core antibiotic resistance genes (including mtrA, bcrA, oleC, MexB, PmrE) and core VFs (including Type IV pili (VF0082), HIS-I (VF0334), LOS (CFV494), and Alginate (VF0091)) on multiple microbes, which increased the survival rate of microorganisms even under adverse conditions and enhanced the invasion potential to cause diseases. Additionally, cell exposure experiments confirmed the ability of Pseudomonas aeruginosa to induce inflammatory responses in Beas-2B cells. Based on these findings, which offer the insight of a comprehensive understanding of the potential pathogenicity of microorganisms in WWTPs, it is recommended to improve regulation of effluents from WWTPs a nd the implementation of measures to reduce the risk posed by airborne pathogenic microorganisms.},
}

@article {pmid41478124,
year = {2025},
author = {Xing, W and Gai, X and Cheng, X and Fang, Z and Chen, G},
title = {Rhizosphere microbiome drives Betula luminifera adaptation to antimony mining sites through functional traits and transcriptional reprogramming.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140972},
doi = {10.1016/j.jhazmat.2025.140972},
pmid = {41478124},
issn = {1873-3336},
abstract = {Rhizosphere microbiome are pivotal for plant adaptation to extreme environments. However, the regulatory mechanisms underlying their control of the ecological adaptation of native woody plants in mining areas remain unclear. Here, we integrated metagenomic and transcriptomic analyses to elucidate how the rhizosphere microbiome facilitates Betula luminifera adaptation to antimony (Sb) mining sites. Under sterile conditions, B. luminifera from mining sites prioritized shoot growth, whereas control-origin seedlings favored root development. Microbial inoculation mitigated this growth dichotomy, balancing above- and belowground biomass allocation. Notably, B. luminifera from control sites upregulated antioxidant biosynthesis genes (α- and β-tocopherol pathways), while B. luminifera from mining sites enhanced lignin synthesis under Sb stress. After inoculation with rhizosphere microbiome from the mining-site, genes related to Sb/As resistance (ACR3, arsB/C) and soil nutrient cycle (narG, phnM) were significantly enriched in the rhizosphere of B. luminifera, which were contributed by Proteobacteria and Actinobacteria. Transcriptional profiling revealed that microbial inoculation triggered systemic upregulation of phytohormone-related genes (auxin, cytokinin, abscisic acid), enhancing stress resilience and growth. These findings unveil a synergistic plant-microbe adaptation mechanism in Sb polluted soils in mining sites, highlighting microbial-mediated trait trade-offs and transcriptional plasticity as drivers of ecological success in extreme environments.},
}

@article {pmid41478064,
year = {2025},
author = {Zhang, H and Zhang, S and Li, X and Wang, W and Kuang, H},
title = {Bupleurum polysaccharide improves CUMS-induced depressive behavior in rats by regulating the "microbiota-gut-brain Axis": a mechanism study based on metabolomics and metagenomics.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1270},
number = {},
pages = {124905},
doi = {10.1016/j.jchromb.2025.124905},
pmid = {41478064},
issn = {1873-376X},
abstract = {This study aimed to comprehensively investigate the antidepressant mechanisms of Bupleurum polysaccharide (BP) through the microbiota-gut-brain axis, employing an integrated multi-omics approach. Using a chronic unpredictable mild stress (CUMS) rat model of depression, we evaluated BP's effects on depressive-like behaviors and analyzed its regulatory mechanisms on metabolites and gut microbiota through combined metabolomics and metagenomics. Structural characterization revealed that Bupleurum polysaccharide SPAP-1 is an acidic homogeneous polysaccharide with a molecular weight of approximately 100 kDa, primarily composed of glucose, mannose, rhamnose, and other monosaccharides. Pharmacodynamic assessments demonstrated that BP significantly ameliorated CUMS-induced depressive behaviors, including weight loss, reduced food intake, anhedonia, and behavioral despair (P < 0.05). Metabolomic analysis identified 19 differential metabolites, with BP reversing 11 of them, primarily involved in phenylalanine and tryptophan metabolism pathways. Western blot analysis confirmed BP's regulatory effects on key enzymes Got1 and Lta4h. Metagenomic results showed that BP remarkably reshaped gut microbiota structure, restored microbial diversity, optimized the Firmicutes/Bacteroidetes ratio, enriched beneficial genera (Agathobacter, Phocaeicola), and inhibited pathogenic genera (Ruminococcus). Crucially, integrated multi-omics analysis revealed significant microbiota-metabolite correlations, demonstrating that BP-promoted beneficial bacteria positively correlated with neurotransmitter precursors, while BP-inhibited pathogenic bacteria associated with pro-inflammatory mediators. Mediation analysis further established the "microbiota → metabolite → behavior" causal chain, with Ruminococcus → LTB4 → despair behavior accounting for 42.3 % of the mediation effect. In conclusion, Bupleurum polysaccharide ameliorates depressive-like behaviors through multi-target regulation of the metabolite-microbiota interaction network, highlighting its potential as an antidepressant agent or functional food and providing a novel research paradigm for understanding the multi-target characteristics of traditional Chinese medicine polysaccharides.},
}

@article {pmid41477534,
year = {2026},
author = {Vallejos, G and Kim, C and Holroyd, KB and Thakur, KT},
title = {Evaluating the Clinical Impact of Metagenomic Next-Generation Sequencing in CNS Infections: A Diagnostic Pathway and Resource Utilization Modeling Study.},
journal = {Open forum infectious diseases},
volume = {13},
number = {1},
pages = {ofaf743},
pmid = {41477534},
issn = {2328-8957},
abstract = {BACKGROUND: Diagnosing meningitis and encephalitis remains challenging due to nonspecific clinical presentations and the limitations of traditional microbiological methods. Metagenomic next-generation sequencing (mNGS) offers a broad approach to detect pathogens, but its real-world impact on clinical decision-making remains undefined.

METHODS: We used a cohort of patients with confirmed central nervous system infections and autoimmune encephalitis (AE) who underwent traditional microbiological cerebrospinal fluid testing at Columbia University Irving Medical Center. Using published sensitivity and specificity data for mNGS, we applied Bayes' theorem to calculate different etiology-specific pretest probabilities and model the potential impact in the diagnostic workflows including the number of lumbar punctures (LPs), additional etiologic tests potentially avoided, and time to diagnosis.

RESULTS: The cohort includes 54 patients in the infectious cohort and 29 patients with confirmed autoimmune encephalitis. In a modeled scenario, utilizing an mNGS test, such as Delve Detect, in patients with DNA viral infections (n = 23) could lead to a reduction of up to 88 microbiological tests, 145 days to diagnosis, and 2 LPs in total. For bacterial infections (n = 16), estimated impact included a reduction of 30 microbiological tests, 144 days to diagnosis, and 12 LPs (Table 1). Although fungal, RNA viral and parasitic infections were less common, with adjusted positive predictive values of 92.8%, 89.5%, and 84.6%, respectively. In the autoimmune cohort, a total of 2 LPs, 126 microbiological tests, and 297 days to diagnosis could have been avoided through the use of mNGS.

CONCLUSIONS: Our analysis suggests that an mNGS test, such as Delve Detect, could potentially streamline diagnostic and treatment pathways in meningitis and encephalitis of infectious or autoimmune origin.},
}

@article {pmid41477211,
year = {2025},
author = {Mankiewicz-Boczek, J and Font-Nájera, A and Gin, KY and Graham, JL and Strapagiel, D and Gorney, RM and Kok, JWK and Te, SH and Kluska, M and Skóra, M and Seweryn, M and López-Hun, F},
title = {Bacterial community diversity and potential eco-physiological roles in toxigenic blooms composed of Microcystis, Aphanizomenon or Planktothrix.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1655370},
pmid = {41477211},
issn = {1664-302X},
abstract = {Cyanobacterial toxicity, cyanotoxins, and their impact on aquatic ecosystems and human health are well documented. In comparison, less is known about bloom-associated bacterial communities. Co-occurring bacteria can influence bloom development, physiology and collapse, and may also provide a niche for pathogenic bacteria. Existing research focuses on the cyanosphere of Microcystis-dominated blooms, despite the increasing prevalence of filamentous genera (Aphanizomenon and Planktothrix). This pilot study aimed to broaden our understanding of the bacterial consortia attached to morphologically distinct cyanobacteria (coccoid and filamentous) dominating phytoplankton communities and to explore their potential roles in amplifying the impacts of cyanobacterial blooms. We investigated four shallow freshwater bodies across three continents and two climate zones: an urban pond in the USA, a dammed reservoir and a natural lake in Poland, and an urban water body in Singapore. Amplicon sequencing (16S rRNA gene) was used to characterize bacterial communities, while shotgun metagenomics identified nitrogen- and phosphorus-cycling genes to infer potential eco-physiological functions. Cyanobacteria dominated bacterioplankton assemblages at all sites (>35.6%), with bloom composition influencing toxigenic profiles. A mixed bloom of Microcystis, Snowella, and Aphanizomenon had the broadest range of cyanotoxin synthetase genes (mcyE, cyrJ, anaF and sxtA). Microcystis blooms correlated with increased Roseomonas, while Planktothrix co-occurred with Flavobacterium - both bacteria likely contribute to nutrient-cycling within blooms and represent potential opportunistic pathogens for aquatic organisms and humans. The Microcystis cyanosphere exhibited the highest number of significant positive correlations with bacteria (19 relations), compared to Planktothrix and Aphanizomenon (11 and 2 relations, respectively). Non-diazotrophic blooms of Microcystis and Planktothrix showed greater abundances of nitrogen - (ureB, glnA, narB, and narHZ) and phosphorus-cycling genes (phoBHPR and ppk1), indicating a strong dependence on associated bacteria for nutrient acquisition compared to diazotrophic Aphanizomenon. These findings suggest that Aphanizomenon-dominated blooms may be sustained by simpler microbiomes. Our results provide preliminary evidence of cyanosphere heterogeneity potentially shaped by the dominance or coexistence of three morphologically and eco-physiologically distinct genera of cyanobacteria. A comprehensive knowledge of the taxonomy and functional roles of bloom-associated microbiomes is therefore essential to understand bloom activity, evaluate the environmental threat, and develop effective strategies for prevention and mitigation.},
}

@article {pmid41477025,
year = {2025},
author = {Miao, H and Wang, Z and Chen, S and Wang, J and Ma, H and Liu, Y and Yang, H and Guo, Z and Wang, J and Cui, P},
title = {Application of machine learning in the discovery of antimicrobial peptides: exploring their potential for ulcerative colitis therapy.},
journal = {eGastroenterology},
volume = {3},
number = {4},
pages = {e100253},
pmid = {41477025},
issn = {2976-7296},
abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease with complex aetiology and limited treatment options. Antimicrobial peptides (AMPs), as endogenous immune effectors, have recently emerged as promising therapeutic agents in UC. However, systematic identification and functional evaluation of AMPs remain underexplored. We aimed to discover novel AMPs with potential therapeutic efficacy in UC by leveraging machine learning-based prediction and validating their impact in an experimental colitis model.

METHODS: We established a machine learning-driven pipeline to predict candidate AMPs based on their structural and functional features. Top-ranked peptides were synthesised and subjected to in vitro antibacterial assays and proteolytic stability tests. Their therapeutic potential was evaluated using a dextran sulfate sodium (DSS)-induced colitis mouse model, assessing clinical indicators, histopathology, inflammatory markers and gut microbiota alterations. Metagenomic and metabolomic analyses provided insights into microbial community dynamics and metabolic pathways. To probe the role of gut microbes in AMP-mediated gut homeostasis, we conducted Akkermansia (A.) muciniphila replenishment experiments.

RESULTS: Several AMPs identified by machine learning exhibited potent antimicrobial activity and resistance to proteolytic degradation. In vivo, AMP administration ameliorated DSS-induced colitis symptoms, including body weight loss, Disease Activity Index and histological damage. Treatment also modulated the gut microbiome, increasing the abundance of A. muciniphila and restoring microbial balance. Functional metagenomic profiling revealed enrichment of genes involved in mucosal barrier protection and immunoregulation. These findings were supported by improved inflammatory cytokine profiles and enhanced epithelial integrity.

CONCLUSIONS: Our findings demonstrate that machine learning-guided discovery of AMPs is a viable approach to identify promising therapeutic agents for UC. By integrating multi-omics analyses, we reveal potential microbiota-mediated mechanisms underlying AMP efficacy. These insights provide a strong foundation for advancing AMP-based strategies in UC management.},
}

@article {pmid41476341,
year = {2025},
author = {Njage, PMK and Becsei, Á and Marques, ARP and Muchiri, BW and Pedersen, JLM and Otani, S and Avot, BJP and Pruden, A and Calarco, J and Harwood, V and Meschke, JS and Gonzalez, R and Sozzi, E and Sobsey, M and McNamara, P and Beck, N and Clark, K and Ballash, G and Mollenkopf, D and Wittum, T and Smith, B and Maile-Moskowitz, A and Kang, S and Capone, D and Aarestrup, FM},
title = {Sociodemographic and Health Factors Are Associated with Antimicrobial Resistance across Eight States in the United States.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c07425},
pmid = {41476341},
issn = {1520-5851},
abstract = {Recent studies suggest that country-level socioeconomic factors may explain antimicrobial resistance (AMR) patterns better than antimicrobial usage (AMU), but it remains unclear whether this holds for sociodemographic and health variation within countries. We used metagenomic analysis of untreated sewage to cross-sectionally characterize the bacterial resistome as a proxy for AMR at 44 wastewater treatment plants across eight USA states between 2019 and 2020. We examined associations between AMR with site-specific sociodemographic and health indicators and AMU. Spatial autocorrelation analyses were used to identify clusters of AMR. Gradient-boosted multivariate regression trees were applied to evaluate individual and joint predictor effects on AMR. Outpatient AMU explained negligible variation in AMR, whereas predictors related to economy, income, preventive health care, access to health care, social welfare, housing, and racial/ethnic composition showed the strongest associations. These relationships were observed across individual resistance classes and their combinations and predicted AMR nonlinearly, with thresholds where AMR shows sharp increases (risk factors) or decreases (protective factors). Significant interannual differences in resistome and bacteriome composition were observed between 2019 and 2020. Although causal inference is limited, the findings suggest that local-level indicators of health, economic conditions, well-being, and development may play an important role in shaping AMR within countries.},
}

@article {pmid41476181,
year = {2025},
author = {Fedi, S and Ghezzi, D and Firrincieli, A and Lopo, E and Romeo, A and Sauro, F and Cappelletti, M},
title = {Taxonomy and functional profile of microbial communities across the depths of the Alpine Cenote Abyss ice cave.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29105-z},
pmid = {41476181},
issn = {2045-2322},
}

@article {pmid41476057,
year = {2025},
author = {Wu, Y and Wong, O and Chen, S and Wang, Y and Lu, W and Cheung, CP and Ching, JYL and Cheong, PK and Chan, S and Leung, P and Chan, FKL and Su, Q and Ng, SC},
title = {Distinct diet-microbiome associations in autism spectrum disorder.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67711-7},
pmid = {41476057},
issn = {2041-1723},
abstract = {Autism spectrum disorder (ASD) is linked to both altered gut microbiota and unhealthy diets; however, the mechanistic connections remain elusive. In this study, we conducted a systematic analysis of fecal microbiome metagenomic data, paired with granular dietary assessments and phenotypic profiles, across a cohort of 818 children (462 with ASD, 356 without ASD; mean age = 8.4 years; 27.3% female). By integrating dietary indices, nutrient intake, and food additive exposures, we uncovered ASD-specific linkages to the microbiome. Poor dietary quality correlated with aggregated core autistic symptoms, gastrointestinal complications, and atypical eating behaviors. Notably, children with ASD exhibited a more pronounced diet-microbiome interaction network compared to neurotypical peers, suggesting heightened microbial sensitivity to nutritional inputs. Furthermore, synthetic emulsifiers-specifically polysorbate-80 and carrageenan-were associated with disrupted microbial connectivity in ASD, a phenomenon attenuated in neurotypical children. Our findings elucidate the mechanistic links between dietary factors-particularly synthetic food additives-and microbiome dysregulation in ASD, urging a re-evaluation of dietary guidelines for ASD populations and laying the groundwork for personalized nutritional strategies.},
}

@article {pmid41475602,
year = {2025},
author = {Zhou, L and Zhang, M and Qiu, Y and Zhao, B and Li, H and Zhuang, WQ},
title = {'Protector' DNRA bacteria, shielding anammox systems from perfluorooctanoic acid by mitigating nitrite accumulation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133898},
doi = {10.1016/j.biortech.2025.133898},
pmid = {41475602},
issn = {1873-2976},
abstract = {The anaerobic ammonium oxidation (anammox) process is integral to nitrogen removal in wastewater treatment, but its effectiveness can be compromised by contaminants such as perfluorooctanoic acid (PFOA). This study revealed the protective mechanism of dissimilatory nitrate reduction to ammonium (DNRA) in protecting anammox bacteria from PFOA-induced toxicity in a lab-scale anaerobic membrane bioreactor (anammox-AnMBR), which operated for over 100 days. The system was exposed to stepwise PFOA increases (0.25, 0.5, and 0.75 mg/L). Nitrogen removal efficiency and extracellular polymeric substance (EPS) production were monitored. Microbial community dynamics were analyzed by metagenomic sequencing. Notably, increasing PFOA concentrations corresponded to stable NO2[-] levels and fluctuating NH4[+], suggesting a biphasic response to PFOA toxicity by the DNRA and anammox communities. Results indicate that DNRA bacteria were more tolerant to PFOA, even at high concentrations, than anammox bacteria. Metagenomic analysis further demonstrated the acute toxicity of high PFOA concentrations to anammox. The abundances of anammox functional genes (hzs, encoding hydrazine synthase; hdh, encoding hydrazine dehydrogenase) showed initial increases followed by declines at elevated PFOA concentrations. Concurrently, the increase in EPS (polysaccharides: 33.3 to 111.1 mg/g VSS; proteins: 3.0 to 247.6 mg/g VSS) indicated defense responses.},
}

@article {pmid41475601,
year = {2025},
author = {Tang, J and Liu, Y and Zhang, Q and Zhang, H and Ni, BJ and Lv, W},
title = {Multi-omics dissection of yeast-centric fungal-bacterial synergies in food-processing wastewater: insights from four full-scale treatment plants.},
journal = {Bioresource technology},
volume = {443},
number = {},
pages = {133911},
doi = {10.1016/j.biortech.2025.133911},
pmid = {41475601},
issn = {1873-2976},
abstract = {Fungal presence and ecological roles in activated sludge at municipal wastewater treatment plants are increasingly recognized, yet their diversity and functional contributions-especially of yeasts-in treating food-processing wastewater remain underexplored. High-throughput ITS and 16S rRNA sequencing and shotgun metagenomics, together with FUNGuild, were used to analyze microbial community structure, functional microorganisms, co-occurrence patterns, interkingdom interactions, functional pathways, and the distributions of degradation enzymes and functional genes for characteristic pollutants among four full-scale food-processing plants (seafood, pastry, orange-canning, and vegetable-oil refining). Community diversity and structural differences shaped by wastewater types, associated with metabolic traits and enzyme-secretion. Saccharomycetes emerged as the dominant fungal class; bacteria displayed more even class-level and genus-level distributions than fungi across plants, combining LEfSe (LDA > 4, p < 0.05) to reveal plant-specific environmental-driven taxa, mainly included members of Saccharomycetales among fungi. Module-based co-occurrence networks indicated symbiotic interactions among yeasts; predominant cooperation of fungal-bacterial interaction network, in which yeasts exhibited the highest degree among fungi; strong correlations between Saccharomycetales and functional genes. Metabolism was the most abundant functional pathway. "Undefined Saprotroph" was the most widespread fungal functional guild. We annotated 86 degradation enzymes and 150 functional genes targeting eight pollutant categories (proteins, lipids, starch, pectin, lignin, cellulose, hemicellulose, chitosan), elucidating plant-specific distributions and enzymatic synergies. These multi-plant comparisons disentangle conserved from plant-specific features of catabolism. Overall, this study elucidates microbial diversity, interactions, and functional potential in food-processing wastewater treatment, reveals yeasts as keystone microbes for pollutant degradation, and provides actionable insights for treatment strategies and process optimization.},
}

@article {pmid41475238,
year = {2025},
author = {Xin, H and Chen, S and Li, X and Chen, Z and Fan, Q and Luo, H and Liu, G and Mai, W},
title = {High-level chloramphenicol degradation in mariculture wastewater via cathodic nitro-reduction in a single-chamber bioelectrochemical system.},
journal = {Water research},
volume = {291},
number = {},
pages = {125174},
doi = {10.1016/j.watres.2025.125174},
pmid = {41475238},
issn = {1879-2448},
abstract = {The aim of this study was to investigate the mechanism of high-level chloramphenicol (CAP) degradation in mariculture wastewater using a single chamber bioelectrochemical system (BES). The reactor was assembled with carbon-brush electrodes and operated with sea mud as inoculum. Nearly complete removal of 200 mg/L CAP was achieved within 36 h when 2 g/L glucose was supplied as a co-substrate. With 200 mg/L CAP as the sole carbon source, BES at the close circuit achieved 28 ± 3% higher CAP removal than that at the open circuit within 72 h. CAP removal declined from 100 ± 5% to 45 ± 4% as the initial concentration increased from 200 to 600 mg/L within 36 h. High CAP concentration markedly inhibited sulfate-reducing bacteria (SRB), reducing the relative abundance of Desulfobulbus from 28.7% to < 0.5%, and decreasing sulfate removal from 90 ± 5% to < 56 ± 3% compared with the control. Nitro-reduction of CAP at the cathodic biofilm was determined as the predominant pathway among the three degradation routes in the BES. Metagenomic analysis revealed that 200 mg/L CAP significantly inhibited both multidrug efflux pump genes and key operons involved in dissimilatory sulfate reduction in the cathodic biofilm. Our results could be useful for eliminating high concentrations of antibiotic contaminants from seawater.},
}

@article {pmid41475234,
year = {2025},
author = {Wang, N and Lv, K and Guo, S and Peng, D},
title = {Functional imbalance between Thauera and anammox governs PD/A pathway stability under contrasting reactor modes.},
journal = {Water research},
volume = {291},
number = {},
pages = {125201},
doi = {10.1016/j.watres.2025.125201},
pmid = {41475234},
issn = {1879-2448},
abstract = {Partial denitrification coupled with anammox (PD/A) is a promising energy-efficient alternative for mainstream nitrogen removal, yet its stability under different reactor modes remains unclear. This study systematically compared sequencing batch (RS) and continuous-flow (RC) PD/A systems using performance monitoring, activity assays, and metagenomic analyses. RC maintained superior long-term stability, achieving >80% nitrogen removal with anammox contributing above 90%, whereas RS remained less stable (∼65% NRE, ∼75% anammox contribution) and relied more on complete denitrification. Activity assays revealed that PD activity in RS was 5.03 times that of anammox, favoring complete denitrification. In contrast, RC maintained balanced activities, with PD activity being 0.89 times that of anammox, supporting cooperative PD/A interactions. Metagenomic analysis further revealed that Thauera-associated Nir/Nor/Nos genes were markedly enriched in RS, indicating a stronger potential for complete denitrification. These findings demonstrate that reactor mode regulates PD/A interactions through distinct stabilization mechanisms, with continuous-flow operation enhancing microbial cooperation and system resilience. This study provides mechanistic insights and practical guidance for the stable implementation of mainstream PD/A processes.},
}

@article {pmid41475142,
year = {2025},
author = {Gallego-Cartagena, E and Morillas, H and Maguregui, M},
title = {Biodeterioration of built heritage in the context of climate change and atmospheric pollution: Toward transdisciplinary conservation strategies.},
journal = {The Science of the total environment},
volume = {1013},
number = {},
pages = {181313},
doi = {10.1016/j.scitotenv.2025.181313},
pmid = {41475142},
issn = {1879-1026},
abstract = {The built heritage -encompassing monuments, historic buildings and sculptural ensembles- is increasingly threatened by the synergistic impacts of climate change, atmospheric pollution and biological activity. This review critically analyses current understanding of the mechanisms driving the biodeterioration of built heritage, focusing on calcareous materials (e.g., limestone, marble and lime-based mortars), which are both widespread in built heritage and highly susceptible to degradation. We examine how environmental drivers -such as elevated humidity, temperature fluctuations, and pollutant deposition (SOₓ, NOₓ, particulate matter)-trigger complex physicochemical and biochemical reactions that compromise structural stability and aesthetic integrity. The review explores the metabolic strategies of biodeteriative organisms (fungi, algae, cyanobacteria), the interactions of pollutants and mineral substrates, and the consequent formation of salts, black crusts and corrosion products. We highlight the role of biomonitoring as a methodological and interpretive bridge linking atmospheric pollution to biodeterioration processes. In addition, we discuss emerging interdisciplinary methodologies - including functional metagenomics, microbial network analysis, and metabolomic profiling -and introduce the Function-Based Biodegradation Risk Assessment model, extended into a Multi-Level Risk Assessment Framework that connects microbial functionality, material diagnostics, and climate modeling. We contend that safeguarding built heritage in a changing climate requires transitioning from static, material-centred diagnostics to integrated, predictive frameworks that link microbial ecology, materials science, and climate dynamics, providing the basis for adaptive and anticipatory conservation strategies.},
}

@article {pmid41474788,
year = {2025},
author = {Wong, KX and Chen, ST and Ong, JJ and Gan, WY and Abdul Murad, NA and Chong, CW and Ramzi, NH},
title = {Exploring gut microbiome and nutritional status among children with Autism Spectrum Disorder (MY-ASD Microbiome): A study protocol.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0338801},
pmid = {41474788},
issn = {1932-6203},
mesh = {Humans ; *Autism Spectrum Disorder/microbiology ; *Gastrointestinal Microbiome ; Child ; Male ; Child, Preschool ; *Nutritional Status ; Case-Control Studies ; Feces/microbiology ; Saliva/microbiology ; Malaysia ; Female ; },
abstract = {BACKGROUND: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterised by persistent deficits in social communication and the presence of restricted, repetitive behaviours or interests. Previous literature has identified a link between the gut and ASD; however, the underlying mechanisms remain unclear. Gut microbiota dysbiosis has been extensively reported in cohort studies of ASD, and specific microbial metabolites or by-products may serve as potential biomarkers for ASD. Additionally, children with ASD often exhibit food refusal, have a limited food repertoire and display a tendency to consume the same foods frequently; thus, these behaviours increase their risk of malnutrition (over-nutrition or under-nutrition) compared to typically developing (TD) healthy children. This study primarily aims to identify oral and gut microbiota among children with ASD and TD healthy children. The secondary aim is to determine the associations between oral and gut microbiota with nutritional status among children with ASD. The findings will enhance understanding of the aetiology of ASD and inform early intervention strategies to mitigate disease severity and early identification of malnutrition in genetically at-risk children.

METHODS AND ANALYSIS: This observational, age-matched, case-control study is conducted in Malaysia among 40 male children with ASD and age-matched with 40 TD healthy controls aged 4-10 years. The dependent variables include the microbiota profile, identified through metagenomic sequencing analysis of saliva and faecal samples, and autism severity, assessed through validated questionnaires. Independent variables include nutritional status, determined through Subjective Global Nutrition Assessment (SGNA), anthropometry and dietary measurements, gastrointestinal symptoms, eating behaviour, behavioural profile, and sleep quality. Data collection is expected to be completed by June 2026. The study nature may limit causality establishment. Analyses will use chi-square/ANOVA for group comparisons, SparCC for microbiota correlations, and mixed-effects logistic regression to model associations.

CONCLUSION: This study advances understanding of ASD-related microbiota, guiding personalised nutrition and precision healthcare in Malaysia.},
}

Humans
*Autism Spectrum Disorder/microbiology
*Gastrointestinal Microbiome
Child
Male
Child, Preschool
*Nutritional Status
Case-Control Studies
Feces/microbiology
Saliva/microbiology
Malaysia
Female

@article {pmid41474524,
year = {2025},
author = {Luo, S and Li, Z and Peng, Y and Xie, X and Zeng, Y and Dai, L and Zhang, X},
title = {Comparative metagenomics reveals the differential gut microbiota involved in bile acid metabolism in patients with crohn's disease.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {1},
pages = {21},
pmid = {41474524},
issn = {1573-0972},
support = {32101368//National Natural Science Foundation of China/ ; 2022YFE0119600//National Key Research and Development Program of China/ ; 2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; },
mesh = {Humans ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/genetics ; *Crohn Disease/microbiology/metabolism ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Male ; Female ; Adult ; Feces/microbiology ; Middle Aged ; },
abstract = {Gut microbiota plays a critical role in bile acid (BA) metabolism within healthy populations, yet the differential species involved in BA metabolism in patients with Crohn's disease (CD) remains poorly characterized. To address this knowledge gap, we conducted a comparative metagenomics for nine CD patients and nine healthy controls. Integrated metagenomic species profiling and functional annotation, accompanied with species-function network analysis, reduced abundance in metabolism-associated genes and lower species-function correlation were predicted, suggesting a possible imbalance of microbial communities in CD group. Focused on functional genes involved in BA metabolism and their associated bacterial taxa, our results revealed that Anaerostipes hadrus-like (P = 0.001317), Roseburia intestinalis-like (P = 0.03542), and Coprococcus catus-like (P = 0.0005787), the microbial species related to bile salt hydrolase-coding gene, showed significantly lower abundance in CD patients. Conversely, Ruminococcus gnavus-like, related to 3α-hydroxysteroid dehydrogenase (3α-HSDH)- and 3β-HSDH-coding genes, demonstrated relatively higher abundance (P = 0.0257). Escherichia coli-like, the species for 7α-HSDH-coding genes, also exhibited higher abundance in CD group (P = 0.01044). Further network correlation analysis indicated that there was a potential association between these differential species with other co-occurring gut microbiota. Collectively, the findings identify and characterize the differential gut microbiota involved in BA metabolism in CD patients, which may provide the possible target microorganisms for future therapeutic interventions.},
}

Humans
*Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome/genetics
*Crohn Disease/microbiology/metabolism
*Metagenomics/methods
*Bacteria/genetics/classification/metabolism/isolation & purification
Male
Female
Adult
Feces/microbiology
Middle Aged

@article {pmid41474055,
year = {2025},
author = {Mehar, K and K, KP and Sen, AP and Paliwal, RK and M, BK and Kalidhas, AM and Mohapatra, TK and Samrat, A and Jayabal, R},
title = {Next-Generation Eco-Omics: Integrating Microbial Function Into Predictive Ecosystem Models.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.70121},
pmid = {41474055},
issn = {1470-8744},
abstract = {Microorganisms drive essential ecosystem functions by mediating carbon, nitrogen, sulfur, and phosphorus transformations that regulate productivity and shape climate feedbacks. Rapid methodological advances now allow precise linkage of microbial identity, in situ activity, and ecosystem processes across spatial and temporal scales. High-resolution approaches-including long-read metagenomics and Hi-C-generate near-complete metagenome-assembled genomes (MAGs) from diverse environments, enabling reconstruction of microbial and viral-host interaction networks. Activity-resolved tools such as quantitative stable isotope probing (qSIP) and bioorthogonal non-canonical amino acid tagging (BONCAT), combined with fluorescence-activated cell sorting (FACS), yield taxon-specific growth and substrate assimilation rates within hours. Single-cell isotope techniques, including Raman-SIP and nanoSIMS, deliver nanometer-scale metabolic insights. Spatial meta-omics platforms, such as MetaFISH and MALDI-MSI, map metabolites alongside microbial identities with micrometer-level precision. Meanwhile, autonomous sequencing systems, including environmental sample processors and nanopore adaptive sampling, enable real-time (<24 h) ecological surveillance. Integrating these multimodal datasets into trait-based frameworks has reduced uncertainty in carbon flux predictions by nearly 20%. This review synthesizes these innovations, outlines optimized analytical pipelines, and proposes a framework for embedding eco-omics into predictive ecosystem and climate models, supporting evidence-driven management aligned with Climate Action and Life on Land.},
}

@article {pmid41473771,
year = {2025},
author = {Mao, X and Hu, X and Fang, J},
title = {Gut microbiota-metabolite interactions in drug-induced liver injury: mechanisms, biomarkers, and therapeutic perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1737234},
pmid = {41473771},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Chemical and Drug Induced Liver Injury/microbiology/metabolism/therapy ; Biomarkers/metabolism ; Dysbiosis ; Animals ; Liver/metabolism ; },
abstract = {Drug-induced liver injury (DILI) remains a major obstacle in clinical pharmacotherapy and a leading cause of acute liver failure and drug withdrawal worldwide. Conventional mechanistic models centered on hepatic xenobiotic metabolism, oxidative stress, and immune injury cannot fully account for the substantial interindividual variability and the unpredictable nature of idiosyncratic DILI. Increasing evidence shows that the gut microbiota and its metabolites critically shape hepatic susceptibility through modulation of drug metabolism, inflammatory signaling, and intestinal barrier integrity. This review summarizes current understanding of the gut-liver axis in DILI pathogenesis, with a focus on microbial enzymes such as β-glucuronidase that reactivate detoxified drug conjugates, microbial dysbiosis that disrupts bile acid homeostasis, and depletion of short chain fatty acids and indole derivatives that normally support epithelial defenses and immunologic tolerance. Drug-specific microbial patterns are discussed, including acetaminophen, amoxicillin-clavulanate, anti-tuberculosis regimens, and immune checkpoint inhibitors. We introduce the concept of metabotype-dependent hepatotoxicity, which emphasizes that individual microbial metabolic profiles influence DILI risk. Advances in metagenomics, metabolomics, and integrative multi-omics enable the identification of microbial biomarkers and functional pathways associated with DILI susceptibility. Emerging therapeutic strategies include restoration of microbial homeostasis, selective inhibition of microbial enzymes, and supplementation of hepatoprotective metabolites. Finally, we outline key challenges and future directions toward translating microbiome-based insights into clinical prediction and precision prevention of DILI. Importantly, this review integrates microbial metabolic functions with precision hepatology concepts, highlighting how metabotype-driven variability can be leveraged for individualized DILI risk assessment.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Chemical and Drug Induced Liver Injury/microbiology/metabolism/therapy
Biomarkers/metabolism
Dysbiosis
Animals
Liver/metabolism

@article {pmid41473686,
year = {2025},
author = {Yao, X and Zou, X and Cao, B},
title = {The Human Respiratory Virome in Health and Disease: Interactions, Dysbiosis, and Methodological Challenges.},
journal = {Advanced genetics (Hoboken, N.J.)},
volume = {6},
number = {4},
pages = {e00022},
pmid = {41473686},
issn = {2641-6573},
abstract = {The human respiratory virome is an underexplored component of the microbiome that includes diverse DNA and RNA viruses such as eukaryotic viruses, bacteriophages, and archaeal viruses. Recent advances in metagenomics have revealed the complexity and dynamic nature of the human respiratory virome, which interacts closely with the host and the bacterial microbiome to influence respiratory health and disease. In healthy individuals, the virome is characterized by low biomass and high temporal variability, with Anelloviruses predominant in the upper airways, whereas Streptococcus phages and herpesviruses are most commonly detected in the lower airways. Common respiratory viruses, such as respiratory syncytial virus, human rhinovirus, and influenza A virus, can persist after acute infection and modulate host immunity. The respiratory virome also plays a significant role in chronic respiratory diseases. Despite its importance, research on the respiratory virome is hampered by technical challenges, including low viral abundance and limited reference databases. This review summarizes current understanding of the composition and determinants of the respiratory virome in healthy individuals, describes its interactions with the host and respiratory microbiota, including the potential modulatory roles of bacteriophages, outlines virome alterations in respiratory diseases, examines methodological challenges, and highlights potential clinical applications and future research directions.},
}

@article {pmid41473253,
year = {2025},
author = {Wagner, ES and Oliphant, K and D'Souza, M and Cruz-Ayala, W and Azzam, RK and Andrews, B and Claud, EC},
title = {Fecal Microbiome and Bile Acid Profiles Differ in Preterm Infants with Parenteral Nutrition-associated Cholestasis.},
journal = {Journal of clinical and translational hepatology},
volume = {13},
number = {12},
pages = {1036-1045},
pmid = {41473253},
issn = {2310-8819},
abstract = {BACKGROUND AND AIMS: Parenteral nutrition (PN)-associated cholestasis (PNAC) is frequently diagnosed in premature infants; however, not all PN-exposed infants develop PNAC. We propose that, in premature infants receiving PN and varying amounts of enteral feeds, differences in the gut microbiome and fecal bile acid content are associated with PNAC development. This study aimed to examine the fecal microbiome and bile acid content of premature infants on PN to determine if there is a relationship with the development of PNAC.

METHODS: Twenty-two preterm infants had serial bilirubin measurements and fecal samples collected during their neonatal intensive care unit admission. Fecal samples underwent 16S rRNA gene sequencing and bile acid analysis. Binomial regression, adjusting for postmenstrual age with feed amount as a moderator, was used to assess the impact of the fecal microbiome and bile acids on PNAC development.

RESULTS: Cholestatic patients (n = 11) had greater PN and antibiotic exposure (p = 0.020; p = 0.010) and longer neonatal intensive care unit stays (p = 0.0038) than non-cholestatic patients. Microbiome richness was higher in non-cholestatic infants (p < 2E-16), with no difference in β diversity (p = 1.0). Cholestatic infants had a significantly higher abundance of Proteobacteria and Fusobacteriota and a lower abundance of Bacteroidota (p < 2E-16). Akkermansia was abundant in all infants on low feeds; as feed volume increased, Akkermansia abundance significantly increased in non-cholestatic infants (p < 2E-16). Bile acid analysis demonstrated significantly lower deoxycholic acid concentrations in cholestatic infants (p < 2E-16). Metagenomic analysis revealed an increase in Proteobacteria requiring augmented stress responses in non-cholestatic infants.

CONCLUSIONS: This is the first study to directly explore the relationship between PNAC susceptibility, the microbiome, and fecal bile acids in preterm infants. The microbiome and bile acid patterns identified here may inform the development of targeted therapeutics for this vulnerable population.},
}

@article {pmid41472855,
year = {2025},
author = {Wu, D and Wang, AJ and Bu, DC and Sun, YY and Li, CH and Hong, YM and Zhang, S and Chen, SY and Zhou, JA and Zhang, TY and Yu, MH and Ma, YJ and Wang, XL and Xu, J and He, W and Heeschen, C and Chen, JF and Mao, WJ and Ding, H and Wu, WJ and Zhao, Y and Wang, H and Liu, NN},
title = {The interplay between tissue-resident microbiome and host proteins by integrated multi-omics during progression of colorectal adenoma to carcinoma.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70090},
pmid = {41472855},
issn = {2770-596X},
abstract = {The intratumoral microbiome is an emerging hallmark of cancer, yet its multi-kingdom host-microbiome ecosystem in colorectal cancer (CRC) remains poorly characterized. Here, we conducted an integrated analysis using deep shotgun metagenomics and proteomics on 185 tissue samples, including adenoma (A), paired tumor (T), and para-tumor (P). We identified 4057 bacterial, 61 fungal, 108 archaeal, and 374 viral species in tissues and revealed distinct intratumor microbiota dysbiosis, indicating a CRC-specific multi-kingdom microbial ecosystem. Proteomic profiling uncovered four CRC subtypes (C1-C4), each with unique clinical prognoses and molecular signatures. We further discovered that host-microbiome interactions are dynamically reorganized during carcinogenesis, where different microbial taxa converge on common host pathways through distinct proteins. Leveraging this interplay, we identified 14 multi-kingdom microbial and 8 protein markers that strongly distinguished A from T samples (area under the receiver operating characteristic curve (AUROC) = 0.962), with external validation in two independent datasets (AUROC = 0.920 and 0.735). Moreover, we constructed an early- versus advanced-stage classifier using 8 microbial and 4 protein markers, which demonstrated high diagnostic accuracy (AUROC = 0.926) and was validated externally (AUROC = 0.659-0.744). Functional validation in patient-derived organoids and murine allograft models confirmed that enterotoxigenic Bacteroides fragilis and Fusobacterium nucleatum promoted tumor growth by activating Wnt/β-catenin and NF-κB signaling pathways, corroborating the functional potential of these biomarkers. Together, these findings reveal dynamic host-microbiome interactions at the protein level, tracing the transition from adenoma to carcinoma and offering potential diagnostic and therapeutic targets for CRC.},
}

@article {pmid41472852,
year = {2025},
author = {Liu, J and Xing, W and Zhang, X and Xu, N and Xu, R and Gong, J and Zhang, J and Yang, F and Gao, S and Hou, Y and Shan, Y and Liu, B and Yuan, Q and Wang, A and Ren, N and Huang, C},
title = {Metagenomics and digital cell modeling facilitate targeted high-throughput sorting of anaerobic hydrogen-producing microorganisms.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70082},
pmid = {41472852},
issn = {2770-596X},
abstract = {This study proposes a novel strategy that prioritizes functional recognition, followed by targeted high-throughput sorting, to enable the comprehensive, rapid, and efficient acquisition of target microorganisms. Using metagenomic sequencing and binning analysis, we identified 215 potential anaerobic hydrogen-producing strains from 12 large-scale biogas samples. Digital cell models were subsequently constructed from metagenome-assembled genomes, which guided the design of 14 selective culture media for enriching these hydrogen-producing bacteria. Flow cytometry-based high-throughput sorting successfully isolated 81 potential anaerobic hydrogen-producing strains, achieving a target acquisition rate above 37% and a survival rate exceeding 70%. This method holds broad potential for the discovery and sorting of functional microorganisms across diverse environments and may ultimately facilitate the development of synthetic microbiomes for industrial applications.},
}

@article {pmid41472849,
year = {2025},
author = {Xiao, Z and Ding, K and Guo, X and Zhao, Y and Li, X and Jiang, D and Zhu, D and Chen, Q and Jong, MC and Graham, DW and Li, G and Zhu, YG},
title = {Soil-borne legacy facilitates the dissemination of antibiotic resistance genes in soil-plant continua.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70094},
pmid = {41472849},
issn = {2770-596X},
abstract = {Antimicrobial resistance (AMR) disseminates throughout the soil-plant continuum via complex microbial interactions. Plants shape root- and leaf-associated microbiomes that sustain plant health; however, soil-borne legacies-enriched with antibiotic-producing microbes and resistance genes-govern AMR dynamics across agroecosystems. Using 16S rRNA gene sequencing, shotgun metagenomics, and high-throughput quantitative PCR, we profiled antibiotic resistance genes (ARGs), mobile genetic elements, and virulence factor genes across bulk soil, rhizosphere, phyllosphere, and root endosphere within soil-tomato and soil-strawberry continua. Recurrent bacterial wilt amplified the resistome, particularly polypeptide resistance genes, thereby establishing the rhizosphere as a major hotspot of ARG accumulation. Multidrug-resistant Ralstonia solanacearum (R. solanacearum) strains acted as major ARG reservoirs, harboring resistance determinants on both chromosomes and megaplasmids. Collectively, these findings demonstrate that pathogen-driven restructuring of the plant microbiome accelerates ARG dissemination, establishing soil-borne diseases as critical amplifiers of AMR across agricultural ecosystems.},
}

@article {pmid41472846,
year = {2025},
author = {Wang, G and Zhao, L and Shi, Y and Qu, F and Ding, Y and Liu, W and Liu, C and Luo, G and Li, M and Bai, X and Li, L and Wang, L and Wong, CC and Ho, YP and Yu, J},
title = {High-throughput generic single-entity sequencing using droplet microfluidics.},
journal = {iMeta},
volume = {4},
number = {6},
pages = {e70087},
pmid = {41472846},
issn = {2770-596X},
abstract = {Single-cell sequencing has revolutionized our understanding of cellular heterogeneity by providing a micro-level perspective in the past decade. While heterogeneity is fundamental to diverse biological communities, existing platforms are primarily designed for eukaryotic cells, leaving significant gaps in the study of other single biological entities, such as viruses and bacteria. Current methodologies for single-entity sequencing remain limited by low throughput, inefficient lysis, and highly fragmented genomes. Here, we present the Generic Single-Entity Sequencing (GSE-Seq), a versatile and high-throughput framework that overcomes key limitations in single-entity sequencing through an integrated workflow. GSE-Seq combines (1) one-step generation of massive barcodes, (2) degradable hydrogel-based in situ sample processing and whole genome amplification, (3) integrated in-droplet library preparation, and (4) long-read sequencing. We applied GSE-Seq to profile viral communities from human fecal and marine sediment samples, generating thousands of high-quality single-entity genomes and revealing that most are novel. GSE-Seq identified not only dsDNA and ssDNA viruses, but also hard-to-detect giant viruses and crAssphages. GSE-Seq of bacterial genomes also revealed putative novel bacterial species, validating the versatility of this platform across different microbial kingdoms. Collectively, GSE-Seq represents a robust framework that addresses persistent challenges in high-throughput profiling for generic applications and holds immense promise for single-cell deconvolution of diverse biological entities.},
}

@article {pmid41472810,
year = {2025},
author = {Lan, B and Liang, Y and Zhou, Z and Liu, J},
title = {Gut microbiome dysbiosis implicates the gut-bone axis in Modic changes: a metagenomic case-control study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1702357},
pmid = {41472810},
issn = {1664-302X},
abstract = {INTRODUCTION: Modic changes (MCs) are vertebral endplate lesions strongly associated with discogenic low back pain (LBP), though their pathogenesis remains poorly understood. Emerging evidence implicates gut microbial dysbiosis in systemic inflammation and musculoskeletal disorders, yet its potential role in MCs has not been investigated. This study aimed to characterize the gut microbiome in patients with MCs and identify microbial and metabolic features linked to disease severity.

METHODS: In a case-control study, shotgun metagenomic sequencing was performed on fecal samples from 31 patients with MCs (16 Type 1, 15 Type 2) and 25 age- and sex-matched healthy controls. Microbial community structure was assessed via alpha and beta diversity analyses. Differential taxa and predictive biomarkers were identified using linear discriminant analysis effect size (LEfSe) and Random Forest modeling. Functional potential was evaluated via Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Associations between microbial features and clinical markers (C-reactive protein [CRP], Pfirrmann grade) were also examined.

RESULTS: Patients with MCs showed significantly reduced gut microbial alpha diversity compared to controls (Chao1 index: p = 0.005; Shannon index: p = 0.034; Simpson index: p = 0.042), with the most pronounced reduction in Type 1 MCs. Beta diversity analysis revealed distinct microbial communities between groups (PERMANOVA, p = 0.001). Key discriminative taxa included unclassified_Parabacteroides (AUC = 0.895) and Bacteroides uniformis (AUC = 0.889). Metabolic pathway analysis identified 52 differentially abundant pathways, with significant enrichment of quorum sensing (p < 0.001) and glycerolipid metabolism (p < 0.001) in MC patients, both strongly correlated with elevated CRP and higher Pfirrmann grade (p < 0.001).

DISCUSSION: Gut microbial dysbiosis is associated with MCs, marked by reduced diversity, specific bacterial biomarkers, and altered metabolic pathways related to inflammation and tissue degeneration. These results suggest a potential role of the gut-bone axis in MC pathogenesis and highlight novel targets for diagnostic and therapeutic strategies in LBP.},
}

@article {pmid41472461,
year = {2025},
author = {Xu, ST and Qian, ZY and Tao, Y},
title = {Chinese Expert Consensus on the Application of Metagenomic Sequencing Technology in Ocular Infectious Diseases: A Delphi Method.},
journal = {Biomedical and environmental sciences : BES},
volume = {38},
number = {12},
pages = {1550-1557},
doi = {10.3967/bes2025.156},
pmid = {41472461},
issn = {2214-0190},
}

@article {pmid41472301,
year = {2025},
author = {Yagi, K and Ethridge, AD and Asai, N and Malinczak, CA and Arzola Martinez, L and Rasky, AJ and Morris, SB and Falkowski, NR and Fonseca, W and Huffnagle, GB and Lukacs, NW},
title = {Changes in Microbiome Correspond with Diminished Lung Pathophysiology Following Early-Life Respiratory Syncytial Virus Infection or Antibiotic Treatment: Microbiome Following RSV Infection.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
pmid = {41472301},
issn = {1999-4915},
mesh = {*Respiratory Syncytial Virus Infections/microbiology/physiopathology/drug therapy/virology ; Animals ; *Lung/physiopathology/microbiology/virology/drug effects ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Mice ; Mice, Inbred BALB C ; Dysbiosis ; *Microbiota/drug effects ; Gastrointestinal Microbiome/drug effects ; Animals, Newborn ; Disease Models, Animal ; Ampicillin/pharmacology ; Respiratory Syncytial Viruses ; Humans ; Female ; },
abstract = {Early-life respiratory syncytial virus (EL-RSV) infection has been implicated in long-term pulmonary disease in children. In these studies, neonatal BALB/c mice were infected at day 7 of life, leading to >35% losses in critical lung function, airway mucus metaplasia, and transcriptional hallmarks of mucus hypersecretion four weeks after RSV infection. While EL-RSV minimally reshaped the resident lung microbiota, it led to significant gut dysbiosis, including a long-term reduction of Proteobacteria that can be a source of protective metabolites related to barrier and immune function. Subsequent studies assessing whether a common infant antibiotic (ampicillin) could mitigate EL-RSV-induced lung alterations revealed further severe gut microbiome alterations and, on its own, later in life, recapitulated the full spectrum of RSV-associated alterations in lung function. Metagenomic inference showed that both RSV and ampicillin administered during early life reduced biosynthetic pathways for microbiome-derived metabolites, which are known to reinforce tight junctions, regulate inflammation, and preserve extracellular matrix elasticity. The shared loss of these metabolic programs provides a mechanistic bridge linking distinct early-life exposures to the microbiome changes and airway mechanical deficits later in life. Collectively, the data suggest that RSV and/or antibiotic-triggered gut dysbiosis is the primary insult that likely promotes improper lung maturation/repair through a metabolite-mediated mechanism and may suggest metabolite restoration as a strategy to promote proper developmental lung function.},
}

*Respiratory Syncytial Virus Infections/microbiology/physiopathology/drug therapy/virology
Animals
*Lung/physiopathology/microbiology/virology/drug effects
*Anti-Bacterial Agents/pharmacology/therapeutic use
Mice
Mice, Inbred BALB C
Dysbiosis
*Microbiota/drug effects
Gastrointestinal Microbiome/drug effects
Animals, Newborn
Disease Models, Animal
Ampicillin/pharmacology
Respiratory Syncytial Viruses
Humans
Female

@article {pmid41472294,
year = {2025},
author = {Mandal, E and Noirungsee, N and Disayathanoowat, T and Kil, EJ},
title = {TSWV Infection Differentially Reshapes the Symbiotic Microbiome of Two Frankliniella Thrips Species.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
pmid = {41472294},
issn = {1999-4915},
support = {0//Gyeongkuk National University/ ; },
mesh = {*Thysanoptera/microbiology/virology ; Animals ; *Symbiosis ; *Microbiota ; *Tospovirus/physiology ; Serratia/genetics ; Bacteria/classification/genetics/isolation & purification ; Insect Vectors/virology/microbiology ; Metagenomics ; Plant Diseases/virology ; Wolbachia/genetics ; },
abstract = {Vectoring tomato spotted wilt virus (TSWV) by two well-known thrips species, Frankliniella occidentalis Pergande and F. intonsa Trybom (Thysanoptera: Thripidae), is facilitated in different ways. Symbiotic bacteria positively influence thrips fitness, but the interaction between these bacteria and tospovirus inside the thrips' body remains unknown. Metagenomic profiling of symbionts in nonviruliferous and viruliferous Frankliniella thrips was performed to elucidate the interactions between symbiotic bacteria and the virus. A total of 97 operational taxonomic units (OTUs) were identified by profiling the microbes, where Proteobacteria was the most abundant phylum, with a high richness in Serratia spp. F. occidentalis showed lower variation in bacterial diversity between nonviruliferous and viruliferous treatments than F. intonsa. RT-qPCR validation for Serratia and Escherichia revealed opposite abundance patterns between the two thrips species. In contrast, Enterobacteriaceae and Pantoea showed similar patterns with higher abundance in nonviruliferous conditions. Wolbachia was detected exclusively in F. intonsa, with a higher bacterial titer in the viruliferous sample. Our findings suggest that TSWV association may influence the abundance of different bacterial symbionts within the thrips' body, potentially via induction of antimicrobial peptides in response to viral invasion, and to our knowledge this is the first report addressing this tripartite interaction. These findings improve our understanding of how virus-symbiont association contributes to thrips vector competence.},
}

*Thysanoptera/microbiology/virology
Animals
*Symbiosis
*Microbiota
*Tospovirus/physiology
Serratia/genetics
Bacteria/classification/genetics/isolation & purification
Insect Vectors/virology/microbiology
Metagenomics
Plant Diseases/virology
Wolbachia/genetics

@article {pmid41472225,
year = {2025},
author = {Dos Santos, MM and Salles, TS and de Campos, GM and Brcko, IC and Lima, ARJ and Sampaio, SC and Elias, MC and Giovanetti, M and Slavov, SN},
title = {Acute Respiratory Infections (ARIs): Current Etiological Perspectives and Advances in Viral Metagenomics-A Review.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/v17121554},
pmid = {41472225},
issn = {1999-4915},
support = {17/23205-8, 23/12155-0, 21/11944-6, 23/07688-0//FAPESP/ ; 403075/2023-8, 305111/2022-1//CNPq/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Respiratory Tract Infections/virology/diagnosis/etiology ; *Viruses/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing ; *Virus Diseases/virology/diagnosis ; Acute Disease ; Genome, Viral ; },
abstract = {Acute respiratory infections (ARIs) remain a leading cause of global morbidity and mortality, disproportionately affecting vulnerable populations such as children, the elderly, and immunocompromised individuals. Despite the availability of traditional diagnostic tools, including viral culture and highly elaborated PCR respiratory panels, many cases of ARI remain without an identified etiological agent. This is due to the vast diversity of viral agents that can be involved in cases of ARI, which represents a major limitation of the targeted diagnosis. In this context, viral metagenomics has emerged as a powerful, unbiased approach for detecting both known and novel pathogens directly from clinical samples. This review highlights the application of metagenomic next-generation sequencing for the investigation of etiological causes of ARIs, emphasizing its relevance in complex cases-particularly among immunocompromised patients-where standard methods might fail. We highlight the main viruses involved in respiratory infections, the strengths and limitations of metagenomic next-generation sequencing approaches, their role in genomic surveillance of respiratory viruses, and their potential to build public health responses to potentially emerging respiratory threats. Ultimately, integrating viral metagenomics into clinical and surveillance frameworks could enhance the early detection and control of respiratory viral diseases worldwide.},
}

*Metagenomics/methods
Humans
*Respiratory Tract Infections/virology/diagnosis/etiology
*Viruses/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing
*Virus Diseases/virology/diagnosis
Acute Disease
Genome, Viral

@article {pmid41472209,
year = {2025},
author = {Galeeva, J and Kuzmichenko, P and Manolov, A and Lukashev, A and Ilina, E},
title = {Bioinformatics Tools and Approaches for Virus Discovery in Genomic Data: A Systematic Review.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/v17121538},
pmid = {41472209},
issn = {1999-4915},
support = {075-15-2025-530//Russian Ministry of Education and Science/ ; },
mesh = {*Viruses/genetics/classification/isolation & purification ; *Computational Biology/methods ; *Genome, Viral ; *Metagenomics/methods ; *Genomics/methods ; High-Throughput Nucleotide Sequencing ; Machine Learning ; Humans ; },
abstract = {The exponential growth of viral metagenomic data has created an urgent need for accurate and scalable tools for virus discovery, yet the extreme diversity, rapid evolution, and limited reference databases for viruses pose unique computational challenges that traditional sequence comparison methods struggle to address. This systematic review, conducted in accordance with PRISMA 2020, examines current trends and methodological advances in virus discovery tools from 1990 to 2025. As virus discovery is a broad and multi-dimensional topic, this review focuses on the first-line tools used to analyze the results of high-throughput sequencing. The review was conducted using the PubMed database with a snowballing approach, with over 54 key studies selected for the analysis. These studies encompass the following approaches: alignment-based methods, rapid similarity estimation techniques, profile hidden Markov model methods, combination pipelines, k-mer-based approaches, and machine learning-based methods. The transition from alignment-based to machine learning methods has dramatically improved the detection of divergent viruses, yet challenges remain in interpreting model decisions and handling incomplete viral genomes. This review summarizes current knowledge and potential future directions for the development of virus detection capabilities.},
}

*Viruses/genetics/classification/isolation & purification
*Computational Biology/methods
*Genome, Viral
*Metagenomics/methods
*Genomics/methods
High-Throughput Nucleotide Sequencing
Machine Learning
Humans

@article {pmid41472203,
year = {2025},
author = {Lapshina, VK and Guskova, NI and Stetsenko, IF and Luong, MT and Tran, TV and Matsvay, AD and Shipulin, GA and Yudin, SM and Skvortsova, VI},
title = {Characterizing the Bat Virome of Vietnam: A Systematic Review of Viral Diversity and Zoonotic Potential.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/v17121532},
pmid = {41472203},
issn = {1999-4915},
support = {388-00084-24-00//Federal Medical Biological Agency/ ; },
mesh = {*Chiroptera/virology ; Vietnam/epidemiology ; Animals ; *Virome ; *Zoonoses/virology/epidemiology ; Humans ; *Viruses/genetics/classification/isolation & purification ; Disease Reservoirs/virology ; Biodiversity ; Viral Zoonoses/virology ; Genetic Variation ; },
abstract = {Bats have been identified as reservoir hosts for an exceptional diversity of viruses, including multiple taxa of high zoonotic concern. Over a hundred bat species inhabit Vietnam, which, combined with significant biodiversity, carry high risk of zoonotic spillover due to dense human-animal interfaces, extensive wildlife trade, and proximity to recent outbreak epicenters. This review systematically synthesizes data on the bat virome in Vietnam and neighboring Southeast Asian countries, assessing viral diversity, host species involvement, and zoonotic potential. By prioritizing virus groups with established zoonotic capacity and pandemic potential, the systematic search identified studies reporting viruses from 32 families across 13 bat families. Based on the WHO 2024 risk classification, seven of these viral families were categorized as high-risk, three as medium-risk, and twelve as low-risk. The comparatively higher viral diversity reported in neighboring countries suggests that the current study likely represents an underestimation of the true virome present in Vietnamese bat populations. We emphasize the urgent need for expanded virological studies integrating metagenomic sequencing, serological surveys, and ecological modeling to improve early detection of emerging threats, as the comparatively higher viral diversity reported in neighboring countries suggests existing research likely represents an underestimation of the true virome present in Vietnamese bat populations. Strengthening regional collaboration is critical for establishing proactive pandemic prevention strategies in this high-risk zoonotic hotspot.},
}

*Chiroptera/virology
Vietnam/epidemiology
Animals
*Virome
*Zoonoses/virology/epidemiology
Humans
*Viruses/genetics/classification/isolation & purification
Disease Reservoirs/virology
Biodiversity
Viral Zoonoses/virology
Genetic Variation

@article {pmid41472198,
year = {2025},
author = {Koutsakos, M and Parry, RH and Wille, M},
title = {Mounting Evidence for an Expanded Host Range of Influenza B Viruses.},
journal = {Viruses},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/v17121528},
pmid = {41472198},
issn = {1999-4915},
mesh = {Animals ; *Influenza B virus/physiology/genetics/classification ; *Host Specificity ; Humans ; *Orthomyxoviridae Infections/virology/veterinary ; Influenza, Human/virology ; Phylogeny ; },
abstract = {Influenza B viruses (IBV) belong to the family of Orthomyxoviridae and circulate annually in humans causing respiratory illness. Although they are considered an exclusively human pathogen, there is evidence of IBV infections in animals, including wildlife, companion animals and livestock. In addition, metagenomic studies have identified novel orthomyxoviruses in amphibians and fish that appear related to IBV, suggesting influenza viruses, including IBV, have been associated with vertebrates across their evolutionary history. In this review, we summarise our current knowledge of potential IBV and IBV-like infections in animals. These collectively suggest that the ecology of IBV extends beyond humans and warrants further investigations.},
}

Animals
*Influenza B virus/physiology/genetics/classification
*Host Specificity
Humans
*Orthomyxoviridae Infections/virology/veterinary
Influenza, Human/virology
Phylogeny

@article {pmid41472072,
year = {2025},
author = {Cheng, H and Chong, H and Yuan, M and Ren, C and Wang, J and Zhao, F},
title = {Soil Microbial Life History Strategies Drive Microbial Carbon Use Efficiency Following Afforestation.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472072},
issn = {2076-2607},
support = {42277322, 31570440//National Natural Science Foundation of China/ ; },
abstract = {Soil microbial carbon use efficiency (CUE) is the core of the soil carbon (C) cycle that captures a dual microbial control point between soil organic C (SOC) accumulation and loss. The interpretation of these patterns and drivers of microbial CUE after long-term afforestation remains, however, a major scientific challenge. In particular, there are major uncertainties about the role of microbial traits in driving CUE. Here, we compared sites along a 45-year afforestation chronosequence and combined the novel [18]O-H2O tracer method with metagenomic analysis to quantify CUE and explore the mechanisms underlying microbe-mediated C dynamics. The results showed that soil microbial CUE significantly increased following afforestation and showed a positive relationship with SOC, which suggested that microbial CUE could promote C accumulation in afforested ecosystems. We further found the critical role of microbial traits in the regulation of CUE through altering microbial life history strategies: microbial CUE was positively and significantly correlated with resource acquisition (A) genes, but showed a negative and significant correlation with stress tolerance (S) strategy genes. These results suggested that soil microbes reduce investment in S strategies and shift to A and high yield (Y) strategies, thereby increasing CUE. This knowledge is important because it advances our understanding of the microbial physiological and evolutionary tradeoffs mediating soil C cycling in the context of human-induced land use change.},
}

@article {pmid41472057,
year = {2025},
author = {Yamaguchi, J and Orf, GS and Malinauskas, J and Mata, M and Weiss, SL and Forberg, K and Meyer, TV and Wiebe, PO and Mowerman, I and Piotrowski, SJ and Glownia, D and Rodgers, MA and Hackett, J and Suputtamongkol, Y and Phoompoung, P and Gomathi, S and Pradeep, A and Solomon, SS and Bbosa, N and Kaleebu, P and Ahouidi, AD and Mboup, S and Sequeira, AF and Tojo, A and Cloherty, GA and Berg, MG},
title = {teamNGS Balances Sensitivity for Viruses with Comprehensive Microbial Detection in Clinical Specimens.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472057},
issn = {2076-2607},
support = {N/A//Abbott Laboratories/ ; },
abstract = {Probe-based capture represents a highly sensitive and cost-effective approach for overcoming host background and enriching viruses in metagenomic NGS (mNGS) libraries. Using clinical specimens collected globally from patients with fever or respiratory illness, we generated mNGS libraries by random priming and Nextera XT tagmentation, followed by target enrichment (teNGS) with Comprehensive Viral Research Panel (CVRP) probes. Capture pool sizes and total reads were optimized, and libraries were initially sequenced separately. Using only 3-4% of reads required for standard mNGS, teNGS achieved increased sensitivity, 100-10,000× increases in depth, and >50% genome coverage for pathogens with titers ≥ 1000 cp/mL. Application to >2000 clinical specimens from various matrices and to contrived samples containing viruses absent from the CVRP probe set enabled detection of diverse viral families and established a minimum 65% nucleotide identity for hybridization, respectively. To save time and resources, teNGS and mNGS libraries were then combined into one sequencing run: teamNGS. In addition to streamlining the workflow, teamNGS also improved genome recovery. Coupling methods maintain the sensitivity and coverage for viruses achieved by enrichment alone while also ensuring comprehensive recovery of non-viral microbes. teamNGS has the potential to improve patient management and lower the rates of unnecessary testing and antibiotic use.},
}

@article {pmid41472033,
year = {2025},
author = {Gladkov, GV and Kimeklis, AK and Orlova, OV and Lisina, TO and Aksenova, TS and Kichko, AA and Pinaev, AG and Andronov, EE},
title = {Taxonomic and Metagenomic Survey of a Peat-Based Straw Degrading Biofertilizer.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472033},
issn = {2076-2607},
support = {23-16-00147//Russian Science Foundation/ ; },
abstract = {The mobilization of complex microbial communities from natural resources can be a valuable alternative to the use of single-species biofertilizers when it comes to the decomposition of plant residues. However, the functioning and interaction of microorganisms within these communities remain largely unexplored. Our task was to investigate the cellulose-degrading community using the biofertilizer BAGS (peat-based compost with straw) as an example and define its active component. For this, we monitored the succession of the biofertilizer's taxonomic composition during two consecutive rounds of its six-month composting process, varying in the applied mineral fertilization. The amount of added nitrogen significantly affected the performance of the biofertilizer, contributing to its high cellulolytic activity. Based on the network analysis, the biofertilizer's mature phase was determined, and its characteristic ASVs (amplicon sequence variants) were described. Metagenomic analysis of this phase revealed MAGs (metagenome-assembled genomes) corresponding to these ASVs, which contained genes for cellulose and aromatics degradation, as well as genes for nitrogen and sulfur pathways, including anaerobic nitrate reduction and thiosulfate oxidation. Thus, we propose that the cellulose-decomposing bacterial component of BAGS, associated with the mature phase, occupied different trophic niches, not limited to cellulose degradation, which should be considered when designing natural or artificial microbial systems for the decomposition of plant residues.},
}

@article {pmid41472032,
year = {2025},
author = {Li, M and Chen, P and Liu, C and Wang, S and Zhang, H and Li, J and Karrow, NA and Mao, Y and Yang, Z},
title = {Gut Microbiome and Metabolome Signatures Associated with Heat Tolerance in Dairy Cows.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472032},
issn = {2076-2607},
support = {2022YFF1001200//National Key Research and Development Program of China/ ; BK20241934//Natural Science Foundation of Jiangsu Province/ ; 32172686//National Natural Science Foundation of China/ ; },
abstract = {Heat stress significantly impairs dairy cow health and productivity, highlighting the need to understand the gut microbiome-metabolite interactions that contribute to heat tolerance. Here, we integrated metagenomic sequencing and untargeted metabolomics in twelve holstein cows selected from a previously phenotyped herd of 120 individuals, including six heat-tolerant (HT) and six heat-sensitive (HS) cows identified using entropy-weighted TOPSIS scoring. HT cows were enriched in genera such as Faecalimonas and UBA737, which were functionally linked to pathways of energy and lipid metabolism, whereas, HS cows harbored taxa associated with bacterial lipopolysaccharide and glycosphingolipid biosynthesis. A total of 135 metabolites were differentially abundant between groups. Among them, glycerol 2-phosphate and 24(28)-dehydroergosterol showed perfect classification performance (AUC = 1.000), and were mainly involved in membrane lipid remodeling and redox regulation. Integrated analysis revealed coordinated microbial-metabolite networks, exemplified by the Faecalimonas-LysoPS (16:0/0:0) and UBA737-Glycerol 2-phosphate axes, suggesting functional coupling between microbial composition and metabolic adaptation. Together, these findings demonstrate that HT cows harbor gut microbiota and metabolites favoring energy balance, membrane remodeling, and oxidative stress resilience, while HS cows display stress-related metabolic patterns. This study elucidates the microbial-metabolic mechanisms underlying thermal resilience and highlights potential biomarkers and metabolic pathways that could be applied in heat-tolerance breeding and precision management of dairy cattle.},
}

@article {pmid41472029,
year = {2025},
author = {Dhakal, R and Guo, W and Vieira, RAM and Guan, L and Neves, ALA},
title = {Advances in Lignocellulose-Degrading Enzyme Discovery from Anaerobic Rumen Fungi.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472029},
issn = {2076-2607},
abstract = {Anaerobic fungi (phylum Neocallimastigomycota) play a crucial role in degrading forages and fibrous foods in the gastrointestinal tract of mammalian herbivores, particularly ruminants. Currently, they are classified into twenty-two genera; however, recent research suggests the occurrence of several novel taxa that require further characterization. Anaerobic rumen fungi play a pivotal role in lignocellulose degradation due to their unique enzymatic capabilities. This review explores the enzymatic systems of rumen anaerobic fungi, highlighting their ability to produce a diverse array of carbohydrate-active enzymes (CAZymes), such as cellulases, hemicellulases, and pectinases. These enzymes facilitate the breakdown of complex plant polymers, making anaerobic fungi essential contributors to fiber degradation in the rumen ecosystem and valuable resources for biotechnological applications. This review summarizes the structural and functional diversity of fungal CAZymes, and the mechanical disruption of plant cell walls by fungal rhizoidal networks is discussed, showcasing the ability of fungi to enhance substrate accessibility and facilitate microbial colonization. Recent studies using genomic, transcriptomic, and biochemical approaches have uncovered several novel CAZymes in anaerobic fungi, including multifunctional xylanases, β-glucosidases, and esterases. These findings highlight the continued expansion of fungal enzyme repertoires and their potential for biotechnology and feed applications. Continued research in this field will enhance our understanding of microbial ecology and enzyme function, paving the way for applications that address global challenges in energy, food security, and environmental sustainability.},
}

@article {pmid41472016,
year = {2025},
author = {Li, H and Yang, K and Liu, H and Cao, S and Bao, Y and Feng, L and Zhang, L and Niu, J and Tian, T},
title = {Effects of Long-Term Heavy Metal Exposure on Oral Microbial Antibiotic Resistance Genes of Residents in the Mining and Smelting Area.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472016},
issn = {2076-2607},
support = {lzujbky-2023-34//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {Growing evidence highlights the role of heavy metals in driving the co-selection of an-tibiotic resistance genes (ARGs), and the human oral cavity is an important reservoir of ARGs. This cross-sectional study investigated the effects of heavy metal exposure on human oral microbiota and ARGs, collecting buccal mucosal and blood samples from residents in a heavy metal-contaminated area (Baiyin City) and a non-contaminated area (Yuzhong County, Lanzhou City). The results showed heavy metal exposure is associated with altered alpha and beta diversity of bacteria and ARGs in human oral cavities, with bacterial compositional shifts being the main factor in ARG variation. Metagenomic analysis revealed heavy metal exposure is linked to modifying the interactions in the bacterial community and between ARGs and metal resistance genes (MRGs), shown by simplified topological structures in bacterial and resistome networks, along with enhanced positive correlations among nodes. Neisseria, Haemophilus, Morococcus, Streptococcus, Staphylococcus, and Mycobacteroides as potential hosts for resistance genes in human oral cavity. Furthermore, blood metal quantification revealed distinct associations with resistance patterns. This study demonstrates significant associations between environmental heavy metal exposure and the oral resistome and emphasizes the role of bacterial community composition.},
}

@article {pmid41472002,
year = {2025},
author = {Cheng, H and Yuan, M and Ren, C and Zhao, F and Wang, J},
title = {Soil Nitrogen Mineralization Is Driven by Functional Microbiomes Across a North-South Forest in China.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41472002},
issn = {2076-2607},
support = {2023YFF1305103//National Key Research and Development Program of China/ ; },
abstract = {Nitrogen (N) mineralization is a complex microbial-driven process that controls the supply of N for plants and microbes. The relative contribution of different microbial N-cycling species/genes to the variation in N mineralization rate (NMR) across contrasting forest biomes was unclear. Here, we investigate the linkages between soil metagenomes and N mineralization rates across 10 contrasting forest biomes (covering temperate, subtropical, and tropical forests) along a 3425 km north-south forest in China. We found that the NMR was higher in subtropical forests, and the variation in NMR can be explained by climate and soil environments, particularly for soil substrate NH4[+]. Similar to NMR, microbial N-cycling genes/species were also higher in subtropical forests, suggesting that the higher microbial N-cycling traits in warm regions may drive higher NMR. We also quantified the contribution of microbial N-cycling gene pathways to NMR across forest biomes and found that the microbial N-denitrification pathway (genes like norZ, narG, nirK, and norB) and nitrification pathway (genes like nxr) explained more variation in NMR than other pathways, such as N ammonification. Collectively, our work demonstrates the importance of microbial N-cycling traits to explain soil N mineralization rates across forest biomes and suggests that this information can be used to help improve the management of the N cycle in forests across biomes.},
}

@article {pmid41471973,
year = {2025},
author = {Pang, Z and Guo, J and Xu, H and Li, Y and Chen, C and Zhang, G and Lu, A and Shao, X and Kan, H},
title = {Inter-Row Grassing Reshapes Nitrogen Cycling in Peach Orchards by Influencing Microbial Pathways in the Rhizosphere.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471973},
issn = {2076-2607},
support = {KJCX20230220//Beijing Academy of Agricultural and Forestry Sciences (BAAFS)/ ; KJCX20240319//Beijing Academy of Agricultural and Forestry Sciences (BAAFS)/ ; KJCX 20230305//Beijing Academy of Agricultural and Forestry Sciences (BAAFS)/ ; },
abstract = {Traditional clean tillage in peach orchards leads to soil degradation and nitrogen (N) loss. While inter-row grassing can optimize N cycling, the specific rhizosphere microbial mechanisms involved have not been fully understood. This study investigated how different inter-row grassing modes influence N availability through microbial communities in a peach orchard. The experiment included a monoculture of Trifolium repens L. (Tr), a monoculture of Lolium perenne L. (Pr), their mixture (TPr), and clean tillage (CK). By combining soil physicochemical analyses, metagenomic sequencing, functional gene quantification, and multivariate statistics, the study systematically examined the impacts of inter-row grassing modes on soil N cycling. The results showed that inter-row grassing modes played a significant role in reshaping N processes. Pr enhanced mineralization and nitrification, increasing inorganic N through specific genes (amoA, hao). Tr, on the other hand, promoted diazotrophs (Bradyrhizobium) and dissimilatory nitrate-reducing bacteria, enhancing biological N fixation and retention. TPr combined these benefits, leading to enhanced nitrification, increased labile carbon, and elevated enzyme activities, creating a complex microbe-gene network that mediated nitrification and denitrification. Overall, inter-row grassing modulates rhizosphere functions by enhancing N cycling through a "carbon input-microbial regulation" mechanism, offering an effective strategy for improving N use efficiency and promoting sustainable orchard management.},
}

@article {pmid41471959,
year = {2025},
author = {Wang, C and Yu, Y and Feng, W and Xu, Y and Deng, T and Cai, W and Liang, W and Wang, H},
title = {The Microbial Community Succession Drives Stage-Specific Carbon Metabolic Shifts During Agaricus bisporus Fermentation: Multi-Omics Reveals CAZymes Dynamics and Lignocellulose Degradation Mechanisms.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471959},
issn = {2076-2607},
support = {No. 2021C02073-9//Zhejiang Science and Technology Major Program on Agriculture New Variety Breeding/ ; },
abstract = {This study integrates metagenomic and metabolomic data to systematically analyze the microbial community succession and carbon source metabolism transitions during the third fermentation cycle of Agaricus bisporus, with the aim of optimizing fermentation efficiency and lignocellulose degradation strategies. Principal Coordinate Analysis (PcoA) based on Bray-Curtis dissimilarity reveals significant microbial community separation across the stages of the first mushroom fruiting cycle. The overall pattern of "stage-specific differentiation" is consistent with the "cellulose hydrolysis" turn to the degradation of complex polysaccharides via carbohydrate-active enzymes (CAZymes). In the microbial network analysis showed that different microbe group controlled the stage-specific differentiation. These findings highlight a phase-dependent metabolic shift during the fermentation process: the early stages of fruiting rely more on cellulose-degrading microbes and their enzymatic systems, while later stages are driven by the degradation of complex polysaccharides and lignin derivatives, with Planctomycetota leading the degradation. This provides new mechanistic insights into agricultural waste resource utilization and the directional regulation of fermentation processes.},
}

@article {pmid41471954,
year = {2025},
author = {Cui, G and Cui, J and Zhang, M and Zhang, B and Huang, Y and Wang, Y and Feng, W and Zhou, J and Liu, Y and Li, T},
title = {Study on the Source and Microbial Mechanisms Influencing Heavy Metals and Nutrients in a Subtropical Deep-Water Reservoir.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471954},
issn = {2076-2607},
support = {42403018//National Natural Science Foundation of China/ ; },
abstract = {Reservoirs are hotspots for the coupling of nutrients and heavy metals, and they substantially modify the compositions and spatiotemporal distributions of microorganisms in fluvial systems. However, relatively few studies have been performed that investigate the microbial mechanisms driving interactions among heavy metals and nutrients in reservoirs. The Goupitan Reservoir, a seasonal stratified reservoir located within the Wujiang River catchment, was chosen as the research subject. The temporal and spatial variations in heavy metals and nutrients, and the metagenomic composition of the reservoir water were analyzed in January, April, July, and October 2019. The results revealed that As, Ni, Co, and Mn were derived primarily from mine wastewater, whereas Zn, Pb, Cd, and Cr were related to domestic and agricultural wastewater discharge. The study area was dominated by Proteobacteria, Actinobacteria, Cyanobacteria, and Bacteroidetes, with the proportion of dominant phyla reaching 90%. Decreases in the dissolved oxygen (DO) concentration and pH in the bottom water during July and October were conducive to increases in the abundance of the anaerobic bacterial groups Planctomycetes and Acidobacteria. The functional genes norBC and nosZ associated with denitrification (DNF), the key gene nrfAH involved in the dissimilatory nitrate reduction to ammonium (DNRA) process, the functional genes aprAB and dsrAB responsible for sulfate reduction/sulfide oxidation, as well as the thiosulfate oxidation complex enzyme system SOX, all exhibit high abundance in hypoxic water bodies and peak in the redoxcline, highlighting the significance of related nitrogen (N) and sulfur (S) metabolic processes. In addition, the concentrations of heavy metals significantly affected the spatial differentiation of the planktonic bacterial community structure, with Mn, Co, Fe, Ni, As, and Cu making relatively high individual contributions (p < 0.01). This study is important for elucidating the sources and microbiological mechanisms influencing heavy metals and nutrients in seasonally stratified subtropical reservoirs.},
}

@article {pmid41471939,
year = {2025},
author = {Luo, Z and Zhou, Y and Wang, X and He, L and Jia, T},
title = {Effects of Endophytic Fungi and Arbuscular Mycorrhizal Fungi on Microbial Community Function and Metabolic Pathways in the Rhizosphere Soil of Festuca rubra.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471939},
issn = {2076-2607},
abstract = {Numerous studies have shown that there are many uncertainties associated with the interactions of nitrogen with plants and microorganisms. In particular, the effects of symbioses between plants and various microorganisms on soil microbial community function remain unclear. Metagenomic sequencing was used to explore the changes in microbial community composition, function and metabolic pathways in rhizosphere soil and the associated influencing factors under different nitrogen levels caused by arbuscular mycorrhizal fungi (AMF) inoculation of F. rubra infected with endophytic fungi and nonendophytic fungi. Plant nutrient allocation (aboveground/belowground), soil pH, and enzymatic activities significantly modulated the functional profiles of the bacterial, fungal, and archaeal communities within these rhizospheres. Soil β-glucosidase activity had the greatest effect on the cluster of orthologous groups of proteins (COG) function of the rhizosphere soil bacterial community, and soil L-leucine aminopeptidase had the greatest effect on the COG function of the rhizosphere soil fungal and archaeal communities. The contributions of AMF colonization to the kyoto encyclopedia of genes and genomes (KEGG) functions of bacteria and archaea in the rhizosphere soil were greater than those of F. rubra infection with endophytic fungi, and AMF colonization improved the metabolic pathways, secondary metabolite biosynthesis, microbial metabolism, amino acid biosynthesis and carbon metabolism of bacterial and archaeal communities in the rhizosphere soil of F. rubra. The effects of endophytic fungi and AMFs on the function and metabolic pathways of symbiotic rhizosphere soil microbial communities were heterogeneous. This study revealed that considering both biotic and abiotic factors is essential for predicting the maintenance of soil ecosystem function by plant-fungal symbionts.},
}

@article {pmid41471929,
year = {2025},
author = {Han, D and Zhao, R and Yang, X and Wang, T and Li, Z and Zhu, M and Yang, Q and Qu, Y and Chen, X and Chen, Z},
title = {Comparative Analysis of Environmental and Host-Associated Microbiome in Odorrana schmackeri (Auran: Ranidae): Insights into Tissue-Specific Colonization and Microbial Adaptation.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471929},
issn = {2076-2607},
support = {ZC (Grant no. 32270440), XHC (Grant no. U21A20192) and YFQ (32171498)//National Natural Science Foundation of China/ ; },
abstract = {Amphibian microbial communities are known to be shaped by host physiology and environmental factors, yet the relative roles of sexual dimorphism and tissue specialization remain poorly understood. Using 16S rRNA gene sequencing, we compared the gastrointestinal and integumentary microbiomes of a monomorphic Chinese frog population, Odorrana schmackeri, inhabiting identical montane streams. Our results showed distinct phylogenetic stratification between niches: Proteobacteria dominated both environmental microbiota and O. schmackeri gut and skin microbiotas but with differential sub-phylum specialization. The soil microbiota was dominated by unclassified_Vicinamibacteraceae, the water microbiota was Limnohabitans-dominated, the skin microbiota was dominated by Bordetella, and the gut microbiota was led by Acinetobacter. Alpha diversity analysis revealed significant tissue- and environmental-based divergences but no sexual differentiation, a pattern confirmed by beta diversity assessments showing stronger microbial community separation by tissue and environmental compartmentalization than by sex. Functional metagenomic prediction indicated convergent enrichment of metabolic pathways across host-associated and environmental communities. These results suggest that microbial community structure in O. schmackeri is principally governed by tissue-specific ecological selection pressures rather than host sexual characteristics. Our findings enhance understanding of microbiome assembly rules in vertebrate ectotherms and identify potential connections between microbiota in different ecological niches.},
}

@article {pmid41471911,
year = {2025},
author = {Zhang, Z and Islam, MS and Noman, M and Hao, Z and Chai, R and Qiu, H and Wang, J and Cai, Y and Wang, Y and Wang, J},
title = {Enhanced Mesophilic Degradation of Rice Straw by Microbial Consortium SXJG15 Through Coordinated Enzymatic Activity and Community Reshaping.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471911},
issn = {2076-2607},
support = {2023C02018//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; 2023SNJF033//"Three Agriculture and Nine organizations" Science and Technology Cooperation Program of Zhejiang Province/ ; },
abstract = {The sustainable utilization of rice straw is challenged by its recalcitrant lignocellulosic structure, especially under low-to-moderate field temperatures. In this study, a novel microbial consortium (SXJG15) mainly containing Sphingobacterium, Azospirillum, and Pseudomonas was enriched from overwintering rice stubble in Zhejiang, China, and evaluated for its rice straw degradation efficiency at 25 °C. Over an 18-day cultivation period, SXJG15 achieved a 52.5% degradation of total rice straw, including 60.2% cellulose, 76.3% hemicellulose, and 40.7% lignin. High extracellular enzymatic activities, including cellulases (up to 80.3 U/mL) and xylanases (up to 324.8 U/mL), were observed during the biodegradation process. 16S rRNA gene sequencing and metagenomics analyses revealed a succession of dominant taxa, including Sphingobacterium, Azospirillum, and Cellulomonas. Further, CAZy annotation indicated that the SXJG15 enzyme system was rich in glycoside hydrolases (42.7%) and glycosyltransferases (34.2%), demonstrating its high potential for lignocellulose degradation. This study uniquely demonstrates the mesophilic (moderate temperature 25 °C) efficiency of SXJG15 in lignocellulose breakdown, provides new insights into the microbial mechanisms of straw decomposition, and lays a foundation for bioenergy and soil fertility applications for developing a sustainable agriculture system.},
}

@article {pmid41471909,
year = {2025},
author = {Cui, Y and Wang, S and Zhao, W and Du, Y and Wang, L and Han, B and Zhang, M and Xu, X and Wang, S and Ma, X and Xu, X and Zhao, Y and Liu, S and Wang, Y and Tuo, H},
title = {Shared Gut Microbial and Functional Signatures Linking Parkinson's Disease and Type 2 Diabetes Revealed by Function-Anchored Metagenomics.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471909},
issn = {2076-2607},
support = {82071257, 82371254//National Natural Science Foundation of China/ ; JX2023YJ021//Tongzhou District, Beijing Medical and Health Industry Development Project/ ; tsqn202306029//Taishan Young Scholars/ ; },
abstract = {Parkinson's disease (PD) and type 2 diabetes mellitus (T2DM) exhibit increasing comorbidity, yet the shared contribution of gut microbiota remains unclear. To investigate parallel microbial and functional alterations underlying PD, T2DM, and PD with diabetes (PDDM), we performed fecal metagenomic sequencing in 156 PD, 41 T2DM, and 44 PD with diabetes (PDDM) patients and 83 healthy controls (HC). PD and T2DM showed highly concordant microbial shifts, with 22 genera and 91 species consistently altered across disease groups compared with HC. Functional enrichment highlighted common perturbations in taurine and hypotaurine metabolism, retinol metabolism, the hypoxia-inducible factor-1 (HIF-1) pathway, and xenobiotic degradation, implicating disrupted oxidative stress responses, neuro-metabolic regulation, and detoxification. Key taxa, including Limosilactobacillus fermentum, Lactobacillus porci, and Lactobacillus delbrueckii, were increased and showed moderate positive correlations (|ρ| ≥ 0.3) with antioxidant/retinol-HIF-1, taurine-hypotaurine, and xenobiotic degradation pathways. Bifidobacterium breve (unadjusted analysis) was increased in PD and further enriched in PDDM, correlating with multiple beneficial pathways. Bifidobacterium simiarum (covariate-adjusted analyses) showed the broadest positive pathway associations, while selected Bacteroides species (e.g., B. acidifaciens) exhibited negative correlations with insulin-resistance pathways and positive correlations with steroid hormone biosynthesis. By contrast, Butyricimonas vaginalis showed negative correlations with HIF-1 and insulin signaling and with cytochrome P450-related drug metabolism. These findings provide the first systematic evidence of parallel taxonomic and functional dysbiosis in PD and T2DM, supporting gut microbiota as a shared mediator and potential therapeutic target in comorbidity.},
}

@article {pmid41471883,
year = {2025},
author = {Ji, J and Jiang, X and Song, P and Yang, Q and Sun, M and Dong, Z and Lu, Y and Dou, S and Dong, L},
title = {Multi-Omics Insights into Microbial Interactions and Fermented Food Quality.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471883},
issn = {2076-2607},
support = {2014020134//Natural Science Foundation of Liaoning Province/ ; JYTMS2023037//Liaoning Provincial Department of Education University Basic Scientific Research Surface Project/ ; },
abstract = {The quality, flavor, and functional attributes of fermented foods are intrinsically shaped by the composition and metabolic dynamics of their microbial communities. This systematic review explores the structural organization, successional patterns, and mechanistic roles of these communities in influencing food quality, with a specific focus on core functional groups-including lactic acid bacteria (LAB), yeasts, and molds-and their interplay through key metabolic pathways. By integrating multi-omics approaches, such as metagenomics and metabolomics, we elucidate the underlying relationships between microbial activity and the formation of volatile flavor compounds, nutritional metabolites, and bioactive substances. These insights offer a scientific basis for the targeted regulation and functional enhancement of fermented food products.},
}

@article {pmid41471878,
year = {2025},
author = {Qi, X and Han, Z and Meng, J and Zhao, H and Zhou, M and Wang, M and Kang, S and Shi, Q and Li, H and Lu, F and Zhao, H},
title = {Integrated Metagenomic and Lipidomic Profiling Reveals Dysregulation of Facial Skin Microbiome in Moderate Acne Vulgaris.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471878},
issn = {2076-2607},
support = {32402248//the National Natural Science Foundation of China/ ; No. 24JCQNJC00880//the Natural Science Foundation of Tianjin/ ; },
abstract = {Acne vulgaris is a prevalent chronic inflammatory dermatosis primarily affecting the pilosebaceous units. Current therapeutic approaches often exhibit limited efficacy and high recurrence rates. To investigate the microbiome-related mechanisms of acne vulgaris, facial skin samples from 19 patients with moderate acne and 20 healthy individuals were analyzed using an integrated metagenomic and lipidomic profiling strategy. Metagenomic analysis revealed a significant reduction in microbial diversity (Chao index) in acne-affected skin compared to healthy controls (p < 0.001). The relative abundance of Staphylococcus, particularly Staphylococcus epidermidis, was significantly elevated in acne group (p < 0.05), while Cutibacterium acnes levels remained unchanged. Carbon metabolism pathways were enriched in the acne group (p < 0.05), predominantly driven by Cutibacterium, whereas other enriched metabolic pathways, such as ABC transporters and glycine, serine, and threonine metabolism (p < 0.05), showed a greater contribution from Staphylococcus. Virulence factors enriched in acne samples were primarily offensive in nature and largely attributed to Staphylococcus. Moreover, acne-associated microbiome exhibited a significantly higher prevalence of resistance genes against fluoroquinolones, fosfomycin, and triclosan (p < 0.05). Untargeted lipidomic analysis demonstrated significantly elevated total serum and triglyceride levels, along with a reduction in fatty acid chain length and a higher degree of saturation compared to the healthy group (p < 0.01). Specific triglycerides significantly enriched in the acne group, such as TG (15:0_14:0_16:0) + NH4, exhibited a significant positive correlation with Staphylococcus. This correlation is associated with elevated clinical erythema and melanin indices, suggesting that Staphylococcus is implicated in the development of acne-related inflammation. Additionally, Thermus exhibits negative correlations with acne-associated lipids and inflammatory parameters, potentially exerting a protective role. These findings suggest that Cutibacterium and Staphylococcus play differential yet synergistic roles in acne pathogenesis. The observed skin microbiome dysbiosis and lipid metabolic alterations provide novel insights into the pathophysiology of acne vulgaris, which may inform the development of targeted therapeutic strategies.},
}

@article {pmid41471876,
year = {2025},
author = {Wang, Y and Gong, L and Gao, Z and Dong, D and Li, X},
title = {Comparative Analysis of Sponge-Associated, Seawater, and Sediment Microbial Communities from Site F Cold Seep in the South China Sea.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471876},
issn = {2076-2607},
support = {42176114//National Natural Science Foundation of China/ ; ZR2023MD100//the Shandong Provincial Natural Science Foundation/ ; CAS-TAX-24-30//Biological Resources Programme, Chinese Academy of Sciences/ ; },
abstract = {Microbial communities at Site F cold seep, ubiquitous in both the environment and the associated fauna, demonstrate clear habitat-specific partitioning. Metagenomic sequencing and binning demonstrated a striking partitioning of microbial taxa at the cold seep: whereas the sponge-associated microbiome was distinctly enriched with specialized sulfur- and methane-oxidizing bacteria that were rare in the environment, it simultaneously exhibited a significantly reduced archaeal content, lower α-diversity, and a simpler overall community structure compared to the sediment and seawater communities. Distinct evolutionary lineages and varying abundances were observed among the microbiomes from seawater, sediment, and sponges. Furthermore, their Metagenome-Assembled Genomes (MAGs) exhibited significant differences in genomic features, including genome size and GC content. The sponge-associated microbiome exhibits lower diversity but maintains a high abundance of key functional genes, particularly those involved in sulfur cycling (e.g., apr, dsr, metZ), indicating enhanced metabolic efficiency in energy conservation and nutrient acquisition. This study reveals that the seawater, sediment, and sponge-associated microbiomes exhibit genome simplification and functional specialization in the cold seep environment, with varying lifestyles driving structural optimization and functional remodeling of the symbiotic microbiomes.},
}

@article {pmid41471869,
year = {2025},
author = {Brouwir, L and KleinJan, H and Balent, C and Quabron, G and Salmerón, I and Venditti, S and Gritten, F},
title = {Fate and Removal of Antibiotics and Antibiotic Resistance Genes in a Rural Wastewater Treatment Plant: A Microbial Perspective of Nature-Based Versus Advanced Technologies.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471869},
issn = {2076-2607},
abstract = {Antibiotics (ATBs), antibiotic-resistant bacteria (ARB), and antibiotic resistance genes (ARGs) present an increasing threat/challenge to our environment and human health, resulting in increasingly strict wastewater management regulations through the revised Urban Wastewater Treatment Directive (UWWTD, 2024/3019/EU). This study evaluates a vertical-flow constructed wetland (CW) as a nature-based solution for removing ATBs, ARB, and ARGs from urban wastewater. The CW operated alongside two conventional quaternary treatments: granular activated carbon (GAC) and ozonation combined with GAC (O3 + GAC). Hydraulic conditions were kept stable across seasonal variations. Three antibiotics were quantified (through LC-MS/MS) in parallel to ARGs (through qPCR and metagenomics) and bacterial profiling (metabarcoding and plate counts). Results indicate that under the conditions tested (rural environment; UWWTP 13.000 p.e.), the CW achieves effective and stable removal of ATBs and ARGs. This study highlights the potential of nature-based solutions to match advanced quaternary treatments in removal performance and operational reliability, offering a sustainable and cost-effective means to reduce the spread of ATBs and ARGs via wastewater.},
}

@article {pmid41471853,
year = {2025},
author = {Tkaczyk, M},
title = {Biofilm as a Key Element in the Bacterial Pathogenesis of Forest Trees: A Review of Mechanisms and Ecological Implications.},
journal = {Microorganisms},
volume = {13},
number = {12},
pages = {},
pmid = {41471853},
issn = {2076-2607},
abstract = {Bacterial diseases of forest trees represent an increasing threat to ecosystem health and the sustainability and resilience of forest management, particularly under changing climate conditions. One of the key yet still insufficiently understood adaptive mechanisms of pathogens is biofilm formation-a structured community of bacterial cells embedded in a matrix of extracellular polymeric substances (EPS), which provides protection against stress factors, biocides, and the host's defensive responses such as antimicrobial compounds or immune reactions. This paper presents a comprehensive review of current knowledge on the role of biofilms in the bacterial pathogenesis of forest trees, covering their formation mechanisms, molecular regulation, and ecological significance. Four key stages of biofilm development are discussed-adhesion, microcolony formation, EPS production, and dispersion-along with the roles of quorum sensing systems and c-di-GMP-based signaling in regulating these processes. Examples of major tree pathogens are presented, including Pseudomonas syringae, Erwinia amylovora, Xylella fastidiosa, the Brenneria-Gibbsiella complex associated with Acute Oak Decline (AOD) and Lonsdalea populi. Biofilm formation is shown to play a crucial role in the colonization of xylem, leaf surfaces, and tissues undergoing necrosis, where biofilms may stabilize decomposition zones and support saprophytic-pathogenic transitions. In the applied section, the concept of "biofilm-targeted control" is discussed, encompassing both chemical and biological strategies for disrupting biofilm structure-from quorum-sensing inhibitors and EPS-degrading enzymes to the use of biosurfactants and antagonistic microorganisms. The need for in situ research in forest environments and the adaptation of advanced imaging (CLSM, micro-CT) and metagenomic analyses to tree systems is also emphasized. This review concludes that biofilms are not merely a physiological form of bacterial organization but a complex adaptive system essential for the survival and virulence of pathogens in forest ecosystems. Understanding their functions is fundamental for developing sustainable and ecologically safe phytosanitary strategies for forest protection.},
}

@article {pmid41471192,
year = {2025},
author = {Liu, P and Wang, D and Zhang, F and Wang, T and Han, J and Zou, Q},
title = {Seasonal Metagenomic Survey of Pathogenic Microorganisms in Non-Human Primates in Mayanghe National Nature Reserve, China.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/pathogens14121237},
pmid = {41471192},
issn = {2076-0817},
mesh = {Animals ; Seasons ; China ; *Metagenomics/methods ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Understanding the diversity of pathogenic microorganisms in wild primates is essential for assessing their health and zoonotic risks. In this study, metagenomic sequencing was applied to investigate the composition and seasonal dynamics of potential pathogenic microorganisms in the feces of François' langurs. A total of 77 potential pathogenic taxa were identified, mainly belonging to Bacillota and Pseudomonadota. The most abundant genera were Streptococcus, Staphylococcus, Salmonella, Listeria, and Pseudomonas, while dominant species included Staphylococcus aureus, Streptococcus pneumoniae, Salmonella enterica, Listeria monocytogenes, and Escherichia coli. Significant seasonal differences were detected in both α- and β-diversity indices, with higher microbial diversity in spring and distinct community structures across seasons. Several genera and species, including Vibrio, Chlamydia, Mycobacteroides, Vibrio cholerae, Yersinia enterocolitica, Chlamydia trachomatis, and Mycobacteroides abscessus, showed marked seasonal fluctuations. The findings reveal that the pathogenic microbial community of François' langurs is strongly shaped by seasonal environmental factors. The detection of multiple zoonotic pathogens suggests a potential risk of cross-species transmission, providing valuable baseline data for primate disease ecology and conservation health management.},
}

Animals
Seasons
China
*Metagenomics/methods
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification

@article {pmid41471117,
year = {2025},
author = {Shuvo, MSH and Kim, S and Jo, S and Rahim, MA and Barman, I and Hossain, MS and Yoon, Y and Tajdozian, H and Ahmed, I and Atashi, A and Jeong, G and Suh, HS and You, J and Sung, C and Kim, M and Seo, H and Song, HY},
title = {Flavonifractor plautii as a Next-Generation Probiotic Enhancing the NGP F/P Index in a Simulated Human Gut Microbiome Ecosystem.},
journal = {Pharmaceutics},
volume = {17},
number = {12},
pages = {},
doi = {10.3390/pharmaceutics17121603},
pmid = {41471117},
issn = {1999-4923},
support = {No. RS-2023-00219563//Ministry of Science and ICT/ ; Bio Workforce Training Program//Ministry of Trade, Industry, and Energy/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; },
abstract = {Background/Objectives: Traditionally consumed fermented foods and lactic acid bacteria (LAB)-based products have primarily been investigated for their nutritional and health-promoting benefits as dietary supplements. More recently, research has advanced toward exploring their therapeutic potential in pharmaceutical development. However, reliance on conventional LAB strains despite their established safety and efficacy has led to saturation at the strain level, underscoring the need for next-generation probiotics (NGPs) with novel therapeutic potential. In this context, we identified Flavonifractor plautii from human feces as a candidate NGP and investigated its effects on the human gut microbiota. Methods: Whole-genome sequencing revealed distinct genetic features that supported its uniqueness, and the strain was designated PMC93. A human gut microbial ecosystem simulator was used to administer F. plautii daily for one week, after which microbial community changes were evaluated using 16S rRNA gene-based metagenomic sequencing. Results: The administration did not induce significant changes in alpha or beta diversity, suggesting that F. plautii does not disrupt overall bacterial community structure, thereby supporting its microbial community safety. Taxonomic analysis demonstrated a significant increase in the Firmicutes-to-Proteobacteria ratio (NGP F/P index). The improvement surpassed that of conventional LAB treatments and was consistently maintained under supplementation with commonly encountered pharmaceutical compounds and nutrients. The shift was associated with an increase in short-chain fatty acid (SCFA)-producing beneficial taxa and a decrease in pro-inflammatory and potentially pathogenic groups. Functional outcomes, including elevated SCFA levels and downregulation of inflammation-related gene expression, further corroborated these compositional changes. The strain also demonstrated safety in in vivo models. Conclusions: Collectively, these findings suggest that strain PMC93 is a promising NGP candidate with substantial therapeutic potential for microbiota-associated health and disease modulation, particularly due to its ability to enhance the NGP F/P index.},
}

@article {pmid41470606,
year = {2025},
author = {Karpova, D and Belkina, D and Porotikova, E and Yurchenko, E and Vinogradova, S},
title = {Metagenomic Study of the Grapevine Decline Detected a Cocktail of Fungi Associated with Grapevine Trunk Diseases.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {24},
pages = {},
pmid = {41470606},
issn = {2223-7747},
support = {23-16-00232//Russian Science Foundation/ ; 00000//Ministry of Education and Science of Russian Federation/ ; },
abstract = {This study analyzed the microbiome of three varieties differing in genotype and technical purpose: Cristal, Riesling, and Avgustin, all exhibiting decline symptoms of unknown etiology. A total of 92 symptomatic and asymptomatic grapevines were analyzed using ITS and 16S rRNA amplicon sequencing and molecular genetic methods. Phytoplasmas and the pathogenic bacteria Xylella fastidiosa and Xylophilus ampelinus were not present in the samples. The decline symptoms were associated with a cocktail of fungal pathogens that cause grapevine trunk diseases. In particular, the analysis revealed the causative agents of Botryosphaeria dieback (Sphaeropsis spp. and Botryosphaeria spp.), fungi associated with the Esca complex (Phaeomoniella spp., Phaeoacremonium spp., Inonotus spp., Seimatosporium spp., Stereum spp., and Cadophora spp.), and the causative agents of Phomopsis dieback (Diaporthe spp.). The symptoms of decline may be increased by several facultative grapevine pathogens that have been identified in microbiome (genera Stemphylium, Alternaria, Aspergillus, Penicillium, Talaromyces, and Fusarium). The metagenomic data of the grapevine microbiome provides opportunities for developing disease control strategies, which is important for the sustainable management of vineyards.},
}

@article {pmid41469598,
year = {2025},
author = {Mbabazi, M and Kateete, DP and Nakazzi, F and Wandera, JN and Mutesi, N and Ocan, M and Biraro, IA and Abaasa, A and Johnson, WE and Wee, B and Muwonge, A},
title = {The impact of tuberculosis and its treatment on the lung and gut microbiota: a global systematic review, meta-analysis, and amplicon-based metagenomic meta-analysis.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-12369-1},
pmid = {41469598},
issn = {1471-2334},
}

@article {pmid41469026,
year = {2025},
author = {Yao, L and Solania, A and Luissint, AC and Balana, AT and Zhang, H and Sangaraju, D and Lai, Z and Kuo, J and Storek, KM and Wolan, DW},
title = {The Secreted Metabolite Isopentenyladenine from Faecalibacterium prausnitzii Is Anti-inflammatory with Barrier-Protective Properties.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00771},
pmid = {41469026},
issn = {2373-8227},
abstract = {Colonic microbiome dysbiosis is correlated with inflammatory bowel disease (IBD), and depletion of the commensal bacterium Faecalibacterium prausnitzii (F. prausnitzii) is routinely observed in the metagenomic analyses of IBD patient microbiome samples. F. prausnitzii is likely beneficial to hosts, as oral administration of F. prausnitzii strain A2-165 has anti-inflammatory properties in murine models of colitis. Previous studies attribute the anti-inflammatory effects of F. prausnitzii A2-165 to production of the short-chain fatty acid butyrate, as well as a secreted protein known as microbial anti-inflammatory molecule (MAM). Here, we verified that oral dosing of strain A2-165 protects against DSS-induced murine colitis and further showed that the aqueous-soluble secreted fraction of overnight cultures from a collection of F. prausnitzii strains inhibits inflammatory signatures, including the activation of the host's NF-κB pathway, production of IL-8, and differentiation of naïve T cells into the TH17 lineage. Our findings against a panel of in vitro assays suggested that the anti-inflammatory responses were attributable to secreted small-molecule or peptide metabolites, as both heat-inactivated and proteinase K-treated F. prausnitzii culture supernatants retained activity. Untargeted and targeted mass spectrometry metabolomics analyses on the soluble anti-inflammatory secretome yielded several unique F. prausnitzii metabolites, including isopentenyladenine. We demonstrated that isopentenyladenine independently modulates host cellular signaling and immune responses and suggest that this newly identified metabolite with human immunomodulatory properties may be useful toward the discovery of IBD-focused therapeutics.},
}

@article {pmid41468749,
year = {2025},
author = {Liu, X and Ma, T and Khan, I and Chen, L and Zhang, H},
title = {Age-dependent variations in aerosol-borne particulates and microbial communities in multi-tier broiler housing systems: A metagenomics environmental health risk assessment.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106308},
doi = {10.1016/j.psj.2025.106308},
pmid = {41468749},
issn = {1525-3171},
abstract = {By investigating the temporal dynamics of airborne microbial communities associated with particulate matter in multi‑tier broiler housing, this study offers a systematic reference for understanding how environmental microbiota shift with broiler age. Fine particulate matter (PM2.5) and total suspended particulate (TSP) were collected from the housing environment at three growth stages: D10 (10-day-old), D24 (24-day-old), and D38 (38-day-old). The concentration and LPS content of the collected TSP and PM2.5 samples from each stage were measured, followed by metagenomic sequencing. Results revealed that the concentrations of TSP and PM2.5 peaked at D24 (P < 0.05), showing a trend of first increasing and then decreasing, and the change trend of mortality in the early stage was similar. Metagenomic results identified that Faecalibacterium, Pseudomonas, and Acinetobacter were the dominant genera at D24, whereas Enterococcus and Macrococcus were the dominant genera at D10 and D38, respectively. Correlation analysis further indicated that TSP was positively associated with mortality and g_Pseudomonas, while PM2.5 was positively associated with g_Faecalibacterium. Significant enrichment was observed in metabolic pathways such as glycosyltransferase 35 and glycoside hydrolase 23, macB, LOS(CVF494), and other antibiotic resistance and virulence genes in TSP and PM2.5 (P < 0.05). Collectively, these findings elucidate the stage‑specific dynamics of environmental microbiota in broiler housing and underscore particulate matter as a potential driver of both microbial shifts and health outcomes, thereby providing evidence to inform interventions aimed at improving environmental and flock health.},
}

@article {pmid41468674,
year = {2025},
author = {Feng, W and Ma, R and Guo, Y and Zhang, B and Lan, J and Liu, J and Chen, S},
title = {Rhizosphere metagenomics and metabolomes provide new insights into the relationship between rhizosphere microecology and early bolting of Angelica dahurica.},
journal = {Microbiological research},
volume = {305},
number = {},
pages = {128435},
doi = {10.1016/j.micres.2025.128435},
pmid = {41468674},
issn = {1618-0623},
abstract = {Angelica dahurica is a medicinal and edible plant with a wide range of pharmaceutical and food applications. However, the early bolting, which leads to reduced yield and loss of bioactive constituents, has become a major obstacle to the industrial development of A. dahurica. Rhizosphere microecology affects plant growth and secondary metabolite accumulation, but the association of rhizosphere microecology with the early bolting of A. dahurica is not fully understood. This study integrated metagenomic and metabolomic analyses to systematically characterize the differences in rhizosphere microecology of non-bolting and early bolting A. dahurica plants. Results revealed significant disparities in soil physicochemical properties, root exudate profiles, and microbial community composition between two groups, all of which exhibited correlations with the coumarin compounds content, the primary pharmacologically active constituents of A. dahurica. Integrated analysis suggested that root-derived acyl-homoserine lactone (AHL) quorum-sensing signals, as the primary chemical signals of the prevalent Gram-negative bacteria, may participate in regulating the microbial community structure and soil properties, thereby influencing the bolting and flowering process. This study proposes a potential complex regulatory network of "rhizosphere microbiome - quorum-sensing signals - soil nitrogen cycle - bolting and flowering" linking the rhizosphere microecology to early bolting in A. dahurica, thereby addressing a key knowledge gap in this area. The findings offer a scientific foundation and innovative strategy for the simultaneous prevention of early bolting and quality improvement in A. dahurica through soil microecological management, which is of significant importance for promoting the sustainable commercial development of the A. dahurica industry.},
}

@article {pmid41468660,
year = {2025},
author = {Yu, X and Huang, S and Tang, J and Peng, C and Wen, Q and Chen, S and Lei, L and Yang, C and Liu, Y and Xiang, W and Zhang, Q and Lin, H and Zhang, M},
title = {Multi-omics reveals efficient thiamethoxam biodegradation but altered flavor profile by native microbiota during Pixian broad bean paste fermentation.},
journal = {International journal of food microbiology},
volume = {449},
number = {},
pages = {111600},
doi = {10.1016/j.ijfoodmicro.2025.111600},
pmid = {41468660},
issn = {1879-3460},
abstract = {Thiamethoxam (TH), a systemic neonicotinoid insecticide, poses food safety risks due to its persistence and uptake in crops. Microbial degradation during fermentation offers a promising decontamination strategy, but the underlying mechanisms and impact on food quality remain unclear. This study investigated TH and its toxic metabolite clothianidin biodegradation in Pixian broad bean paste (PBP) fermentation, assessed the impact of residue dissipation on product quality, and revealed microbial responses and metabolic adaptations under pesticide stress. Results demonstrated that TH and clothianidin were nearly completely degraded in the PBP fermentation system within 16 days, with a half-life of 3.25 days. Metagenomic analysis revealed that TH stress enriched pollutant-degrading microbes (e.g., Aspergillaceae, Desulfobacterota) and upregulated xenobiotic degradation genes (e.g., drug metabolism). However, volatile flavor compounds analysis indicated that TH treatment altered the flavor profile by reducing esters and phenols while increasing ketones and acids. Integrated metabolomics demonstrated that TH may disrupt organic acid metabolism during early fermentation, suppressing downstream flavonoid transformation and amino acid biosynthesis, ultimately compromising nutritional quality and flavor attributes. Multi-omics integration revealed that TH stress reshaped microbial community structure and enabled dual regulation of pesticide degradation and fermentation pathways through coordinated gene expression, ultimately altering PBP fermentation quality. Therefore, these findings demonstrate that the native microbial community in PBP efficiently degrades neonicotinoid pesticides, providing a novel strategy for the bioremediation of fermented foods and serving as an emerging reservoir of potential safe degrading bacteria, while highlighting the necessity for optimized microbial interventions to minimize adverse effects on product quality.},
}

@article {pmid41467811,
year = {2025},
author = {Ha, LH and On, YY and Pohan, C and Lee, J and How, SHC and Teo, Y-Y and Seedorf, H and Gounot, J-S and Nagarajan, N},
title = {High-throughput single-cell isolation of Bifidobacterium strains from the human gut microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0303325},
doi = {10.1128/spectrum.03033-25},
pmid = {41467811},
issn = {2165-0497},
abstract = {UNLABELLED: Bifidobacterium represents a diverse genus of commensal gut bacteria with key roles in human health, from metabolizing indigestible fibers to protecting against pathogens. While metagenomic studies have highlighted significant strain diversity for Bifidobacterium species within individuals, their systematic isolation and phenotypic characterization can be hampered by the significant effort and biases inherent in traditional culturomics. Here, we explored the utility of a high-throughput single-cell dispensing system (B.SIGHT)-based workflow for accelerating the process of isolating diverse Bifidobacterium strains from fecal samples. Systematic assessment of this workflow revealed a high single-cell dispensing frequency (>88%) and the ability to preserve species diversity when a pool of Bifidobacterium strains was dispensed. Culturing-related factors including the use of an effective selection medium, such as the Bifidus Selective Medium supplemented with mupirocin, and the length of pre-dispensing incubation were found to be critical in determining isolation success. Leveraging this workflow, we obtained a total of 622 viable isolates from five Singaporean fecal samples, of which >98% were found to be from Bifidobacterium species. Whole-genome sequencing of 96 isolates identified six different Bifidobacterium species with both inter- and intra-subject strain and lineage diversity, and the majority (>66%) were novel relative to large public genomic databases. Our findings highlight the ability of this high-throughput culturomics workflow to accelerate the recovery of diverse and novel Bifidobacterium strains, enabling further interrogation of their functional characteristics and advancing our understanding of important bacterial species in the gut microbiome.

IMPORTANCE: The field of high-throughput microbial culturomics is still in its early stages. Enhancing our ability to isolate and phenotypically test bacterial strains from complex communities is crucial for advancing microbiome research and healthcare development. Given the time and cost inefficiencies of traditional culturing methods, a more efficient, high-throughput approach to obtain isolates is needed. In the present study, we assessed a single-cell dispensing platform and developed a workflow to isolate diverse Bifidobacterium strains from fecal samples. We demonstrated here the capability of this novel technology to efficiently obtain hundreds of isolates of a targeted group, covering both species and strain diversities. This generalizable and scalable method can potentially allow for the high-throughput recovery of microbes from other taxonomic groups, providing a fundamental step in improving the culturomics framework to complement metagenomic approaches and enable isolate-level functional studies of important microbes.},
}

@article {pmid41467786,
year = {2025},
author = {McParland, EL and Wittmers, F and Bolaños, LM and Carlson, CA and Curry, R and Giovannoni, SJ and Michelsen, M and Parsons, RJ and Kido Soule, MC and Swarr, GJ and Temperton, B and Vergin, K and Worden, AZ and Longnecker, K and Kujawinski, EB},
title = {Seasonal patterns of DOM molecules are linked to microbial functions in the oligotrophic ocean.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0154025},
doi = {10.1128/msystems.01540-25},
pmid = {41467786},
issn = {2379-5077},
abstract = {Hundreds of thousands of individual microbe-molecule interactions regulate the flux, transformation, and fate of carbon stored in the climatically important reservoir of marine dissolved organic matter (DOM). While marine microbial communities have been characterized at high resolution for over a decade, observations of the molecules cycled by the microbial-chemical network at similar resolution are limited. In addition, bulk characterizations of DOM can mask the complex network of interactions comprised of rich chemical diversities. Here, we present a three-year, depth-resolved, molecular time-series of DOM and prokaryoplankton at the Bermuda Atlantic Time-series Study (BATS) site. Both time-series exhibited seasonality that was compositionally distinct and primarily endemic to one sampling depth. We also putatively identified four exometabolites (gonyol, glucose-6-sulfate, succinate, and trehalose) that exhibit seasonal accumulation. We hypothesize these patterns result from environmental conditions that alter community composition on a seasonal timescale and thus shift the relative proportions of microbial functions that produce and consume the substrates. Critically, we observed the interannual composition of seasonal DOM molecules to be more stable than the taxonomy of the microbial community. This points to an important role of functional redundancy in regulating DOM composition. We tested this observation by querying metagenomes for pathways that utilize metabolic by-products putatively identified in the DOM time-series. We find that core microbial metabolisms, either those required by all or by a subset of marine microbes, are important predictors of DOM composition. The molecular-level characterization of DOM herein highlights the potential imprint of microbial activity on seasonal DOM composition.IMPORTANCEMarine dissolved organic matter (DOM) is a major carbon reservoir that acts as a critical control on the Earth's climate. DOM dynamics are largely regulated by a complex web of chemical-microbial interactions, but the mechanisms underpinning these processes are not well understood. In a three-year time-series, we found that the identity of the microbes is more likely to change between years than the composition of the DOM molecules. The taxonomic variability suggests that metabolisms shared across taxa, encoded by genes that conduct core microbial functions, are responsible for the more stable composition of DOM. While more than three decades of marine prokaryoplankton time-series are available, a similar reference for DOM molecules was missing. This time-series provides an improved understanding of the different responses of DOM molecules and microbes to seasonal environmental changes.},
}

@article {pmid41467315,
year = {2025},
author = {Sun, Y and Li, P and Wang, X and Jiang, D and Shao, Y},
title = {Gut dysbiosis in early severe burns contributes to acute lung injury by impairing neutrophil chemotaxis.},
journal = {Journal of leukocyte biology},
volume = {118},
number = {1},
pages = {},
doi = {10.1093/jleuko/qiaf169},
pmid = {41467315},
issn = {1938-3673},
support = {82302800//National Natural Science Foundation of China/ ; 2024M751108//China Postdoctoral Science Foundation/ ; SDCX-ZG-202400032//Postdoctoral Innovation Program in Shandong Province/ ; },
mesh = {Animals ; *Dysbiosis/complications/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Acute Lung Injury/etiology/pathology/microbiology/immunology ; *Neutrophils/immunology/pathology ; Humans ; Mice ; *Burns/complications/microbiology/pathology/immunology ; *Chemotaxis, Leukocyte ; Male ; Female ; Mice, Inbred C57BL ; Butyrates/pharmacology ; Disease Models, Animal ; Neutrophil Infiltration ; Chemotaxis ; },
abstract = {Severe burns complicated by acute lung injury are critical causes of respiratory failure and multiple organ dysfunction syndrome. Neutrophils extensively infiltrate lung tissues early postburn to mediate pulmonary damage, but the underlying mechanisms remain unclear. We analyzed gut microbiota of severe burn patients via metagenomics and metabolomics, assessed neutrophil chemotaxis using a self-developed in vitro agarose model, and validated Faecalibacterium prausnitzii and butyrate's effects on restoring neutrophil chemotaxis in gut microbiota-depleted mice via oral gavage (plus in vivo validation with small animal imaging). Bronchoalveolar lavage fluid biomarkers and pulmonary function tests evaluated pulmonary injury from impaired neutrophil chemotaxis. Early postburn, F. prausnitzii and its metabolite butyrate were significantly depleted in patients, concurrent with impaired neutrophil chemotaxis-restored by butyrate supplementation. In murine burn models, F. prausnitzii or butyrate rescued neutrophil chemotaxis, reduced pulmonary neutrophil infiltration, and attenuated lung injury. Mechanistically, butyrate restored neutrophil function in a severe burn patient plasma-stimulated model by downregulating P2X1 receptor expression and suppressing myosin light chain phosphorylation. Our findings indicate postburn gut microbiota dysbiosis and metabolite alterations disrupt neutrophil chemotaxis, causing excessive pulmonary neutrophil infiltration/activation. This highlights gut microbiota-derived metabolites as potential therapeutics for mitigating neutrophil-driven lung injury early postsevere burns.},
}

Animals
*Dysbiosis/complications/immunology/microbiology
*Gastrointestinal Microbiome/immunology
*Acute Lung Injury/etiology/pathology/microbiology/immunology
*Neutrophils/immunology/pathology
Humans
Mice
*Burns/complications/microbiology/pathology/immunology
*Chemotaxis, Leukocyte
Male
Female
Mice, Inbred C57BL
Butyrates/pharmacology
Disease Models, Animal
Neutrophil Infiltration
Chemotaxis

@article {pmid41467083,
year = {2022},
author = {Kulohoma, BW and Ng'eno, I},
title = {NOMAD: metagenomic characterisation of the viral pathogen composition in outbreaks of non-malaria acute febrile illness cases.},
journal = {Open research Africa},
volume = {5},
number = {},
pages = {24},
doi = {10.12688/openresafrica.13406.2},
pmid = {41467083},
issn = {2752-6925},
abstract = {The clinical importance of non-malaria febrile acute illness (NM-AFI) in patients with a negative parasitological test has become apparent, with the progressive reduction in malaria transmission in endemic regions. Bacterial pathogens, for example Streptococcus pneumoniae and Haemophilus influenzae, which contribute disproportionally to febrile illness, are now preventable by vaccines. However, there are no vaccines, and little is known about viral NM-AFI prevalence, proliferation, virulence, and transmission chains between hosts. Although the predominant viral causes of NM-AFI are established, it is unclear if there are other NM-AFI associated emerging infectious viral pathogens that previously remained undetectable by conventional diagnostic strategies, for example severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Presumptive broad-spectrum antibiotic prescriptions to aparasitaemic patients not only drive drug resistance, but also lead to poor treatment outcomes. We hypothesized that insights on NM-AFI etiology, and consequently case management, could be improved by exploiting viral sequence diversity to identify viral pathogens present within metagenomics samples. We exploited simulated and existing infectious disease (Ebola, hepatitis C, chikungunya, and mosquito-borne arboviruses) metagenomic datasets to determine the composition of viral pathogens present, by implementing profile Hidden Markov Models derived from Swiss-Prot viral reference sequences for accurate pathogen detection and classification. Our analysis identified a combination of sequences from multiple viral etiological agents within the same disease sample. This approach provides a granular perspective of multiple viral etiological agents present within a single intra-host disease episode. It highlights prevalent viral strains that can subsequently be routinely detected using directed diagnostic tests to improve disease surveillance in endemic regions.},
}

@article {pmid41467046,
year = {2025},
author = {Sharma, S and Gupta, N and Kaur, S and Kumawat, KC and Chakkal, AS},
title = {Soil microbial resources: Unlocking sustainable strategies for crop productivity and soil health.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100468},
pmid = {41467046},
issn = {2666-5174},
abstract = {Using efficient rhizospheric microbes as bio-inoculants is a key factor in promoting agricultural sustainability, as these microbes have been shown to enhance plant growth promotion and crop productivity. Soil microbial communities offer numerous benefits to crops, including improved nutrient uptake efficiency, phytohormone production, improved soil structure, nutrient balance, enhanced plant and soil health, protection against soil borne phyto-pathogens and increased plant resilience to abiotic and biotic stresses. These characteristics of rhizospheric microbes have attracted researcher's attention, as using these microbes individually or in consortia has enhanced soil fertility as well as soil heatlh in a eco-friendly manner. Further, the utilization of multi-omics techniques for exploring the hidden potential of beneficial plant growth promoting microbes is one of the novel approaches that can result in the generation of new biological formulations under changing climatic conditions. This review is therefore focused on the diversity of microbes, their contributions for plant growth promotion and yield with advances in techniques for screening and development of efficient bio-inoculant with a special emphasis on promoting sustainable agriculture practices.},
}

@article {pmid41467044,
year = {2025},
author = {Fernandes, P and Cano-Díaz, C and Pinto, R and Mourão, I and Brito, LM and Moura, L},
title = {The composition and structure of bacterial and fungal communities in kiwifruit are influenced by photoselective nets.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100424},
pmid = {41467044},
issn = {2666-5174},
abstract = {Photoselective nets in agriculture are typically designed to modify the light spectrum, intensity, and microclimate around crops, influencing plant growth, productivity, and quality. However, knowledge regarding their impact on the microbiota of plants and fruits remains limited. This study assessed the impact of pearl, grey, and yellow photoselective nets on the microbial communities present on kiwifruit surfaces using amplicon high-throughput sequencing of ITS and 16S metagenomic DNA. Kiwifruit pathogens associated with postharvest rot, such as Alternaria, Didymella, and Cladosporium, were significantly more prevalent on kiwis grown without nets. Additionally, different net types influenced microbial diversity, richness, and network structure. Pearl nets promoted bacterial richness and fungal diversity, while yellow nets enhanced overall diversity and resilience in both microbial communities. Grey nets resulted in evenness in fungal communities but led to less robust bacterial networks. Kiwifruit yield increased under photoselective nets compared to outside. At harvest, fruit dry matter, firmness, pH, total soluble solids, and titratable acidity were similar across treatments. However, fruits under yellow and grey nets showed significantly lower firmness compared to other treatments. Understanding these effects may contribute to optimizing fruit production and shelf-life management.},
}

@article {pmid41466423,
year = {2025},
author = {Chen, L and Tang, C and Hu, D and Yu, S and Liao, P},
title = {Brevilin a reverses colitis of inflammatory bowel disease via modulation of TNF-α signaling and microbiome dysregulation.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00792-3},
pmid = {41466423},
issn = {1757-4749},
support = {2024000003-09//Middle-aged Backbone Talents in the Province/ ; },
abstract = {BACKGROUND: Brevilin A (Br) has shown potential in modulating inflammatory bowel disease (IBD). Our study aims to explore its mechanism of anti-inflammatory action.

METHODS: Colitis was induced in C57BL/6 mice with dextran sulfate sodium (DSS), followed by treatment with or without Br(20 mg/kg). Fecal microbiota and metabolites were profiled by metagenomic sequencing and liquid chromatography-mass spectrometry (LC-MS), respectively. Furthermore, to delineate the essential role of the gut microbiota, we employed antibiotic-treated (microbiota-depleted) mice in our investigation of Br's mechanism of action.

RESULTS: Br significantly alleviated DSS-induced colitis and modulated the gut microbiota profile. Specifically, Br enriched beneficial bacteria such as Lactobacillus, while suppressing pathogenic bacteria including Escherichia coli and Clostridium perfringens. Metabolomic analysis revealed that Br significantly altered bacterial metabolites, including 7-Oxolithocholic Acid, Kudinoside A, Veratrine, and Soyasaponin. These metabolites were linked to key pathways such as GPCR signaling, DNA damage response, aminoacyl-tRNA biosynthesis, riboflavin metabolism, and central carbon metabolism in cancer. Transcriptomic profiling indicated that Br inhibited the TNF-α signaling pathway, and this inhibition was confirmed as TNF-α overexpression reversed its anti-inflammatory effects. Furthermore, the therapeutic effects of Br were partially recapitulated in microbiota-depleted mice through fecal microbiota transplantation from Br-treated donors.

CONCLUSION: Br's ability to regulate gut microbiota and metabolites, improve gut barrier function, and eliminate inflammation by inhibiting TNF-α highlights its potential as a novel therapeutic medicine for IBD. Future research should focus on further exploring its mechanisms and clinical applications.},
}

@article {pmid41466385,
year = {2025},
author = {Zhao, L and Li, M and Wang, Y and Chen, L},
title = {Combined effects of sound and temperature on the composition and function of bacterial and fungal communities in loess.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {803},
pmid = {41466385},
issn = {1471-2180},
support = {31920250052; 22YF7FA172; Z2101707; 31560120//the Fundamental Research Funds for the Central Universities; the Key Research and Development Program of Gansu Province; Talent Introduction Program of Northwest Minzu University; National Natural Science Foundation of China/ ; },
mesh = {*Fungi/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; *Temperature ; *Soil Microbiology ; China ; *Sound ; Biodiversity ; *Mycobiome ; Metagenomics ; Phylogeny ; Soil/chemistry ; *Microbiota ; },
abstract = {In Northwest China, the dominant soil type is loess, which is highly susceptible to various environmental factors. Of these, limited research has focused on the impacts of sound disturbance and temperature fluctuations on the microbial communities in loess. An orthogonal experiment was conducted by varying sound intensity (70 dB, 90 dB, 110 dB), sound duration (2 h, 4 h, 6 h), and temperature (- 5 °C, 15 °C, 35 °C). Metagenomic sequencing was then applied to investigate the effects of sound and temperature on the composition and function of bacterial and fungal communities in loess. Our results show that under the combined effects of sound and temperature, the dominant phyla and genera of bacteria and fungi have different responses and preferences to temperature and sound decibels. Alpha diversity analysis revealed that the Shannon index of the bacterial community differed significantly under the 90 dB treatment at - 5 °C and under the 110 dB treatment at 15 °C (P < 0.05). For the fungal community, both the Simpson and Shannon indices showed significant differences under the 70 dB treatment at - 5 °C and under the 110 dB treatment at 15 °C (P < 0.05). Notably, the richness of rare fungal taxa and overall species richness in the loess fungal community were significantly enhanced at 90 dB compared with the control and other treatment groups, while these indices were significantly reduced at 110 dB. In the loess microbial treatment groups subjected to the combined effects of sound and temperature, the gene abundance of CAZy family genes was lowest under high decibel (110 dB) sound stimulation. Among the six enzyme-encoding gene categories within the CAZy family, the highest number of annotated species was observed in Group A (2 h, 70 dB, - 5 °C), whereas the lowest was recorded in Group C (6 h, 110 dB, - 5 °C). Among the metabolic pathway functional genes annotated in the KEGG database, the abundance of metabolic genes in Group C (6 h, 110 dB, - 5 °C) was significantly lower than that in other treatment groups.},
}

*Fungi/classification/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
*Temperature
*Soil Microbiology
China
*Sound
Biodiversity
*Mycobiome
Metagenomics
Phylogeny
Soil/chemistry
*Microbiota

@article {pmid41466331,
year = {2025},
author = {Li, J and Zhang, X and Zhao, X and Gong, G and Li, J and Dalai, B and Mo, Z and Xu, X and Jia, X and Li, Y and Lai, J and Wang, P and Sun, L and Liu, Y and Luo, X},
title = {Characterising gut microbiome dysbiosis in diarrhoea calves from multiple farms in Inner Mongolia using 16S and metagenomics.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {259},
pmid = {41466331},
issn = {2049-2618},
support = {2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2021GG0171//Key Technology Project of Inner Mongolia Science and Technology Department/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Special Project/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; 2022LJRC0009//Science and Technology Leading Talent Team in Inner Mongolia Autonomous Region/ ; },
mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/genetics ; *Diarrhea/microbiology/veterinary/epidemiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; China/epidemiology ; *Dysbiosis/microbiology/veterinary ; *Cattle Diseases/microbiology/epidemiology ; Feces/microbiology ; Escherichia coli/genetics/isolation & purification/pathogenicity ; *Bacteria/classification/genetics/isolation & purification ; Farms ; },
abstract = {BACKGROUND: The pathogenesis of neonatal calf diarrhoea (NCD), a critical disease that contributes to neonatal mortality in calves, remains nebulous.

RESULTS: Inner Mongolia, a key region for cattle farming in China, was selected as a study area to provide a comprehensive overview of the epidemiology and treatment of calf diarrhoea. No significant correlation was found between the incidence of diarrhoea and sampling points or medications. The severity of diarrhoea cases was stratified into five levels based on faecal characteristics. To elucidate the pathogenesis of NCD, 16S rRNA gene and metagenomic sequencing analyses were performed across severity levels. Microbial diversity analyses revealed distinct variations in microbial communities at different severity levels. Employing binning and LEfSe methodologies, two potential bacterial pathogens were identified: Escherichia coli (bin.216), leveraging non-canonical virulence mechanisms; and Streptococcus ruminantium (bin.338), an uncharacterised diarrhoeagenic bacterium. Furthermore, the viral agent Escherichia phage VpaE1_ev108 was significantly associated with disease progression. Gene function enrichment analysis revealed a broad spectrum of antibiotic resistance genes even in farms without direct antibiotic treatment, underscoring the pervasive prevalence of drug resistance.

CONCLUSIONS: The findings of this study revealed significant gut microbial dysbiosis in calves with severe diarrhoea, through which two putative NCD-associated pathogens were identified: E. coli (bin.216) and S. ruminantium (bin.338). Marked enrichment of Bacteroides spp. and Methanobrevibacter_A sp. 900313645 was observed in healthy cohorts, suggesting their potential protective roles. Therapeutic strategies employing phage-mediated pathogen targeting combined with probiotic transplantation have demonstrated dual benefits, potentially reducing antimicrobial dependency and preserving microbial homeostasis through ecological network reconstruction. Video Abstract.},
}

Animals
Cattle
*Gastrointestinal Microbiome/genetics
*Diarrhea/microbiology/veterinary/epidemiology
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
China/epidemiology
*Dysbiosis/microbiology/veterinary
*Cattle Diseases/microbiology/epidemiology
Feces/microbiology
Escherichia coli/genetics/isolation & purification/pathogenicity
*Bacteria/classification/genetics/isolation & purification
Farms

@article {pmid41466328,
year = {2025},
author = {Thirumaran, S and George, C and Kortheerakul, C and Khunthong, N and Bhunjun, CS and Phukhamsakda, C and Chan, KG and Chang, Y and Tan, EJ and Daroch, M and Hyde, KD and Goh, KM and Waditee-Sirisattha, R and Pointing, SB},
title = {Fungi dominate eukaryotic microbial assemblages in hot spring biofilms of East and Southeast Asia.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {156},
pmid = {41466328},
issn = {2524-6372},
support = {MOE-T2EP30123-0007//Ministry of Education - Singapore/ ; },
abstract = {Terrestrial hot springs are globally distributed extreme environments, and these systems have long served as natural laboratories for studying microbial life under thermal stress. While much of the research to date has focused on thermophilic bacteria and archaea, there is a growing appreciation for the diversity and ecological significance of eukaryotic microorganisms in these habitats. In this study, we used metagenomic sequencing to assess inter-domain microbial diversity in biofilms from 47 circumneutral hot springs across East and Southeast Asia, with a specific focus on resolving eukaryotic taxa and their ecology. Whilst all biofilm communities were dominated by bacteria, the microbial eukaryotes represented approximately 10% of the taxonomic diversity and accounted for 1.3% of overall taxa abundance, indicating a small but significant presence. We provide the first comprehensive inter-domain checklist of over 14,500 microbial taxa in hot springs. Patterns in diversity were significantly correlated with temperature, hydrogen sulfide, and pH in hot springs. Fungi emerged as the most abundant and prevalent eukaryotic group, indicating an important role as eukaryotic saprotrophs, with Ascomycota yeasts comprising the most individually abundant taxa. Among other microbial eukaryotic phyla, the photosynthetic Chlorophyta and Bacillariophyta were most abundant. Predatory/grazing microbial eukaryotes were relatively less diverse and abundant. Network co-occurrence analysis was used to indicate extensive and specific biotic interactions between eukaryotes and bacteria in biofilms. We further employed metatranscriptomics to identify putatively active taxa, revealing that most detected eukaryotes were transcriptionally active. While fungi accounted for most transcripts, the highest RNA:DNA ratios were observed among predatory and photosynthetic taxa, suggesting elevated activity in these functional groups. Overall, our findings highlight the diversity, interactions, and activity of eukaryotes in Southeast Asian hot spring biofilms, underscoring their potential importance in shaping microbial community structure and function in extreme environments.},
}

@article {pmid41466105,
year = {2025},
author = {Zhang, H and Shen, C and Lei, W and Wang, J and Liu, J and Qiu, Z},
title = {Pilot Clinical Trial of Fecal Microbiota Transplantation for Constipation in Parkinson's Disease.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2509029},
doi = {10.4014/jmb.2509.09029},
pmid = {41466105},
issn = {1738-8872},
mesh = {Humans ; *Constipation/therapy/etiology/microbiology ; *Fecal Microbiota Transplantation/methods ; *Parkinson Disease/complications/therapy/microbiology ; Aged ; Pilot Projects ; Middle Aged ; Male ; Gastrointestinal Microbiome ; Female ; Prospective Studies ; Feces/microbiology ; Treatment Outcome ; Dysbiosis/therapy ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {The purpose of this study was to evaluate the safety and efficacy of fecal microbiota transplantation in patients with constipation due to parkinson's disease. Gut dysbiosis has long been associated with parkinson's and recent studies have shown that FMT can restore the normal flora of the gut. Therefore, this clinical trial aimed to test the therapeutic efficacy of FMT in 5 patients aged 55 to 71 diagnosed with PD who presented with constipation. The study was conducted as an open label, prospective trial and consisted of FMT performed every 3 days via nasojejunal tube placement followed by 8 weeks of patient follow-up to evaluate response to drug therapy and to assess neurological function using UPDRS-III OFF scores, and improvement in constipation assessed with Wexner scores. Samples taken before and after FMT were collected for shotgun metagenomic sequencing to analyze the composition of the microbial communities present in patients. Untargeted non-targeted metabolomic studies were performed to investigate the impact of FMT on metabolome changes due to FMT. The results indicate an improvement in constipation and neurological functioning following FMT, and significant alteration of the gut microbiota. Significant increases in Bifidobacteria bifidus, Alistipes shahi, Anaerotruncus coli, and uncharacterized Flavonifractor were found post-treatment compared to the baseline. Many of the other strains present prior to treatment, including Acinetobacter sp. and Proteobacteria sp., had significantly decreased after the FMT. The metabolomic studies found shifts in metabolic pathways involved with unsaturated fatty acid synthesis and amino acid metabolism due to FMT. FMT may be an effective treatment option for constipation and neurological symptoms associated with PD.},
}

Humans
*Constipation/therapy/etiology/microbiology
*Fecal Microbiota Transplantation/methods
*Parkinson Disease/complications/therapy/microbiology
Aged
Pilot Projects
Middle Aged
Male
Gastrointestinal Microbiome
Female
Prospective Studies
Feces/microbiology
Treatment Outcome
Dysbiosis/therapy
Bacteria/classification/genetics/isolation & purification

@article {pmid41466004,
year = {2025},
author = {Li, S and Zhang, M},
title = {Mycobacterium chelonae infection treated with combined medication and surgical therapy: A case report.},
journal = {Medicine},
volume = {104},
number = {52},
pages = {e46692},
pmid = {41466004},
issn = {1536-5964},
mesh = {Humans ; *Mycobacterium Infections, Nontuberculous/therapy/drug therapy/etiology/diagnosis/surgery ; *Mycobacterium chelonae/isolation & purification ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; Female ; Levofloxacin/administration & dosage/therapeutic use ; Rifampin/administration & dosage/therapeutic use ; *Skin Diseases, Bacterial/therapy ; Combined Modality Therapy ; Drug Therapy, Combination ; *Cosmetic Techniques/adverse effects ; Adult ; },
abstract = {RATIONALE: The misuse of antibiotics and immunosuppressive agents has led to an increase in the incidence of infections caused by opportunistic pathogens, and even rare microbial infections such as Mycobacterium chelonae (MC) have emerged. Currently, there are very few reported cases of MC infection globally, and clinical experience in treating this disease is limited. This case report focuses on the treatment methods for infections caused by this bacterium, aiming to accumulate experience for clinicians in the diagnosis and treatment of this condition.

PATIENT CONCERNS: This study reports a case of MC infection that occurred following an invasive cosmetic injection treatment. Due to the progression of the condition, medical intervention was required. The patient underwent combined medication and surgical therapy, and the treatment outcomes were subsequently tracked.

DIAGNOSES: Histopathological examination of the skin lesion, fungal culture, and metagenomic detection of the infectious pathogen suggested MC infection.

INTERVENTIONS: The patient underwent excision of the skin lesion, along with intravenous infusion of levofloxacin hydrochloride and sodium chloride injection at a dose of 0.4 g once daily and oral administration of rifampicin capsules at a dose of 0.45 g once daily. Complete lesion resolution was achieved at 1 month postoperatively.

OUTCOMES: At the 1-month postoperative follow-up, the patient's rash had healed completely.

LESSONS: This case fills a gap in domestic and international reports of MC infection following cosmetic filler injections. By employing metagenomic next-generation sequencing, the pathogen was rapidly identified within a short timeframe, significantly reducing the diagnostic delay associated with conventional bacterial culture and identification methods. Early radical lesion excision combined with a dual-antibiotic regimen (levofloxacin-rifampin) achieved complete resolution within 1 month, establishing a replicable treatment paradigm for cutaneous MC infections. Further multicenter prospective studies are warranted to optimize surgical margins and antimicrobial treatment duration.},
}

Humans
*Mycobacterium Infections, Nontuberculous/therapy/drug therapy/etiology/diagnosis/surgery
*Mycobacterium chelonae/isolation & purification
*Anti-Bacterial Agents/therapeutic use/administration & dosage
Female
Levofloxacin/administration & dosage/therapeutic use
Rifampin/administration & dosage/therapeutic use
*Skin Diseases, Bacterial/therapy
Combined Modality Therapy
Drug Therapy, Combination
*Cosmetic Techniques/adverse effects
Adult

@article {pmid41465859,
year = {2025},
author = {Angelova, B and Boteva, S and Traykov, I and Tsvetkov, M and Kenarova, A},
title = {Bacterial Community Composition and Structure in the Littoral of Rila Mountains Glacial Lakes.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {41465859},
issn = {2075-1729},
support = {KP-06-M71/2//The Bulgarian National Science Fund/ ; },
abstract = {High-mountain lakes are biodiversity hotspots sensitive to increasing regional and global climate warming. However, their microbial communities remain insufficiently characterized due to their remoteness and limited accessibility. This study aimed to determine how seasonal environmental parameters shape the composition, structure and diversity of littoral bacterial communities in three glacial lakes in Rila Mountains (Bulgaria). Water samples were collected during ice-free periods in 2023 and 2024, and bacterial taxonomic composition was analysed by Next-generation sequencing. A total of 1158 bacterial OTUs were identified encompassing 18 phyla and 165 families. Actinomycetota, Pseudomonadota, and Bacteroidota were dominant at the phylum level, and Sporichthyaceae, Comamonadaceae, Chitinophagaceae and Mycobacteriaceae were most abundant among the families. Community richness and diversity peaked in June, immediately after ice melting, particularly in the highest-altitude lake (Sulzata Lake), and declined during the warm season (August), when the relative abundances of Sporichthyaceae and Mycobacteriaceae (Actinomycetota) increased. Seasonal restructuring occurred across phyla and families even in a single taxon, with water temperature and organic carbon availability identified as the main environmental drivers. The findings have improved our understanding of temperature-driven bacterial responses. They have also highlighted the vulnerability of cold-adapted taxa to regional climate warming which may contribute to more effective biodiversity conservation strategies for these unique ecosystems.},
}

@article {pmid41465696,
year = {2025},
author = {Jin, JX and Wang, Y and Zhang, GF and Ye, ZC and Liu, B and Yao, DD and Jiang, ZC and He, YF},
title = {Diversity and Functional Analysis of Gut Microbiota in the Adult of Lissorhoptrus oryzophilus (Coleoptera: Curculionidae) by Metagenome Sequencing.},
journal = {Insects},
volume = {16},
number = {12},
pages = {},
pmid = {41465696},
issn = {2075-4450},
abstract = {The gut microbiota of insects plays a fundamental role in modulating host physiology, including nutrition, development, and adaptability to environmental challenges. The rice water weevil, Lissorhoptrus oryzophilus Kuschel (Coleoptera: Curculionidae), is a major invasive pest of rice worldwide, yet the composition and functional profile of its gut microbial community remain poorly characterized. Here, we employed metagenome sequencing on the Illumina NovaSeq X Plus platform to explore the gut microbial diversity and predicted functions in adults of L. oryzophilus. Our results revealed a rich microbial community, comprising 26 phyla, 42 classes, 72 orders, 111 families, and 191 genera. The bacterial microbiota was overwhelmingly dominated by the phylum Proteobacteria (85.13% of total abundance). At the genus level, Pantoea (48.86%) was the most predominant taxon, followed by Wolbachia (14.57%) and Rickettsia (11.81%). KEGG analysis suggested that the gut microbiota is primarily associated with metabolic pathways such as membrane transport, carbohydrate and amino acid metabolism, cofactor and vitamin metabolism, energy metabolism, and signal transduction. eggNOG annotation further highlighted significant gene representation in amino acid and carbohydrate transport and metabolism, while CAZy annotation revealed glycosyl transferases (GTs) and glycoside hydrolases (GHs) as the dominant carbohydrate-active enzymes. This study provides the first comprehensive insight into the gut microbiome of L. oryzophilus adults, highlighting its potential role in the ecological success of this invasive pest. Our findings lay groundwork for future research aimed at developing novel microbial-based strategies for the sustainable management of L. oryzophilus.},
}

@article {pmid41465567,
year = {2025},
author = {Zhao, H and Wang, H and Zhao, X and Song, Y and Liang, D and Ma, Y and Xu, Z},
title = {Bifidobacterium adolescentis Strengthens Gut Barrier in Post-Voyage Functional Constipation.},
journal = {International journal of molecular sciences},
volume = {26},
number = {24},
pages = {},
pmid = {41465567},
issn = {1422-0067},
support = {2024QN019//University-level research project of the Naval Medical University/ ; },
mesh = {*Constipation/microbiology/therapy/etiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Bifidobacterium adolescentis/physiology ; *Probiotics ; Mice, Inbred C57BL ; Feces/microbiology ; Male ; Humans ; Gastrointestinal Motility ; },
abstract = {Prolonged periods of sailing may contribute to the development of functional constipation, which can significantly impair an individual's work efficiency. Currently, the efficacy of Bifidobacteria in treating functional constipation is gaining recognition. However, since the therapeutic effects of Bifidobacteria are strain-specific, further research is required on strains isolated from pre-voyage fecal samples. This study examines the role of gut microbiota in post-stroke constipation, aiming to identify specific microbial biomarkers for the development of targeted therapeutic strategies. B. adolescentis was identified through metagenomic analysis and subsequently isolated for validation. In the experimental group (EG), C57BL/6J mice received fecal suspension treatment following a 12-day navigation period, which was subsequently followed by a 12-day oral administration of B. adolescentis. After treatment, EG significantly improved fecal volume, intestinal motility, and goblet cells; reversed microbial ecological imbalance; reduced pathogens (E. coli and Klebsiella) by restoring arginine/bile acid metabolism, decreasing Tauro-ursodeoxycholic acid (TUDCA) content, 5-Hydroxytryptamine 4 Receptor (5-HT4R)/Slc8a1 signaling, and Ca[2+] signaling pathway; and restoring beneficial species (B. adolescentis, Pseudomonas aeruginosa). This study provides new insights into probiotics in improving human intestinal health.},
}

*Constipation/microbiology/therapy/etiology
Animals
*Gastrointestinal Microbiome
Mice
*Bifidobacterium adolescentis/physiology
*Probiotics
Mice, Inbred C57BL
Feces/microbiology
Male
Humans
Gastrointestinal Motility