@article {pmid40053297,
year = {2025},
author = {Scholand, KK and Schaefer, L and Govindarajan, G and Yu, Z and Galletti, JG and de Paiva, CS},
title = {Aged regulatory T cells fail to control autoimmune lacrimal gland pathogenic CD4[+] T cells.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {40053297},
issn = {2509-2723},
support = {R01EY030447/EY/NEI NIH HHS/United States ; EY-002520/EY/NEI NIH HHS/United States ; EY021725/EY/NEI NIH HHS/United States ; EY007001/EY/NEI NIH HHS/United States ; R01EY035333/EY/NEI NIH HHS/United States ; P30CA125123/CA/NCI NIH HHS/United States ; CPRIT-RP180672//CPRIT/ ; CA125123//National Institutes of Health (US)/ ; RR024574//National Institutes of Health (US)/ ; 221859/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; PICT 2020-00138//Agencia Nacional de Promoción Científica y Tecnológica/ ; PICT 2021-00109//Agencia Nacional de Promoción Científica y Tecnológica/ ; },
abstract = {CD25KO mice are a model of Sjögren disease. CD25KO mice have severe inflammation and infiltrating lymphocytes to the lacrimal glands (LG). Whether the pathogenicity of CD25KO CD4[+] T cells can be controlled in vivo by Tregs is unknown. Eight-week-old B6 and CD25KO mice LGs were submitted for RNA bulk sequencing. A total of 3481 genes were differentially expressed in CD25KO LG compared to B6. Tear washing analysis identified CD25KO mice had elevated protein levels of TNF, IFN-γ, and CCL5 and decreased protein levels of IL-12p40 and VEGF-A. Co-adoptive transfer of CD25KO CD4[+] T cells with either young or aged B6 Tregs was performed in RAG1KO mice. Recipients of CD25KO CD4[+] T cells alone had higher LG inflammation than naive mice. However, in recipients of young B6 Tregs plus CD25KO CD4[+] T cells, LGs had significantly reduced inflammation. Recipients of CD25KO CD4[+] T cells with aged B6 Tregs had more inflamed LGs than young Tregs, suggesting aged Tregs have less suppressive capacity in vivo. Altogether, CD25KO mice have phenotypic and genetic changes resulting in increased inflammation and severe lymphocytic infiltration in the LGs. However, this autoimmunity can be controlled by the addition of young, but not aged, Tregs, suggesting that aging Tregs have dysfunctional suppression.},
}

@article {pmid40052570,
year = {2025},
author = {Shen, M and Gao, S and Zhu, R and Wang, W and Gao, W and Tao, L and Chen, W and Zhu, X and Yang, Y and Xu, T and Zhao, T and Jiao, N and Zhi, M and Zhu, L},
title = {Multimodal Metagenomic Analysis Reveals Microbial InDels as Superior Biomarkers for Pediatric Crohn's Disease.},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjaf039},
pmid = {40052570},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model.

METHODS: A total of 1,175 fecal metagenomic sequencing samples, predominantly from three cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms.

RESULTS: We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1,357 KO genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1,256 insertions/deletions (InDels), and 3,567 single nucleotide variants, with a considerable portion of these variants occurred in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an AUC of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC=0.996) and five other microbiome-associated pediatric cohorts.

CONCLUSIONS: Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of the non-invasive diagnostic tools and targeted therapies.},
}

@article {pmid40052474,
year = {2025},
author = {Bamigbade, GB and Abdin, M and Subhash, A and Arachchi, MP and Ullah, N and Gan, RY and Ali, A and Kamal-Eldin, A and Ayyash, M},
title = {Plant polysaccharide-capped nanoparticles: A sustainable approach to modulate gut microbiota and advance functional food applications.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {2},
pages = {e70156},
doi = {10.1111/1541-4337.70156},
pmid = {40052474},
issn = {1541-4337},
support = {//United Arab Emirates University/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; *Nanoparticles/chemistry ; *Polysaccharides/chemistry ; *Functional Food ; Humans ; Plants/chemistry ; },
abstract = {Plant-derived polysaccharides have emerged as sustainable biopolymers for fabricating nanoparticles (polysaccharide-based nanomaterials [PS-NPs]), presenting unique opportunities to enhance food functionality and human health. PS-NPs exhibit exceptional biocompatibility, biodegradability, and structural versatility, enabling their integration into functional foods to positively influence gut microbiota. This review explores the mechanisms of PS-NPs interaction with gut microbiota, highlighting their ability to promote beneficial microbial populations, such as Lactobacilli and Bifidobacteria, and stimulate the production of short-chain fatty acids. Key synthesis and stabilization methods of PS-NPs are discussed, focusing on their role in improving bioavailability, stability, and gastrointestinal delivery of bioactive compounds in food systems. The potential of PS-NPs to address challenges in food science, including enhancing nutrient absorption, mitigating intestinal dysbiosis, and supporting sustainable food production through innovative nanotechnology, is critically evaluated. Barriers such as enzymatic degradation and physicochemical stability are analyzed, alongside strategies to optimize their functionality within complex food matrices. The integration of PS-NPs in food systems offers a novel approach to modulate gut microbiota, improve intestinal health, and drive the development of next-generation functional foods. Future research should focus on bridging knowledge gaps in metagenomic and metabolomic profiling of PS-NPs, optimizing their design for diverse applications, and advancing their role in sustainable and health-promoting food innovations.},
}

*Gastrointestinal Microbiome/drug effects
*Nanoparticles/chemistry
*Polysaccharides/chemistry
*Functional Food
Humans
Plants/chemistry

@article {pmid40052450,
year = {2025},
author = {Qian, Z and Chen, S and Liao, X and Xie, J and Xu, Y and Zhong, H and Ou, L and Zuo, X and Xu, X and Peng, J and Wu, J and Cai, S},
title = {Decreased intestinal abundance of Akkermansia muciniphila is associated with metabolic disorders among people living with HIV.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2474730},
doi = {10.1080/07853890.2025.2474730},
pmid = {40052450},
issn = {1365-2060},
mesh = {Humans ; Male ; *HIV Infections/complications/microbiology ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; *Akkermansia ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; Prospective Studies ; Feces/microbiology ; Metagenomics/methods ; Hyperlipidemias/microbiology ; Metabolic Diseases/microbiology/epidemiology ; Verrucomicrobia/isolation & purification ; Overweight/microbiology/complications ; },
abstract = {BACKGROUND: Previous studies have shown changes in gut microbiota after human immunodeficiency virus (HIV) infection, but there is limited research linking the gut microbiota of people living with HIV (PLWHIV) to metabolic diseases.

METHODS: A total of 103 PLWHIV were followed for 48 weeks of anti-retroviral therapy (ART), with demographic and clinical data collected. Gut microbiome analysis was conducted using metagenomic sequencing of fecal samples from 12 individuals. Nonalcoholic fatty liver disease (NAFLD) was diagnosed based on controlled attenuation parameter (CAP) values of 238 dB/m from liver fibro-scans. Participants were divided based on the presence of metabolic disorders, including NAFLD, overweight, and hyperlipidemia. Akkermansia abundance in stool samples was measured using RT-qPCR, and Pearson correlation and logistic regression were applied for analysis.

RESULTS: Metagenomic sequencing revealed a significant decline in gut Akkermansia abundance in PLWHIV with NAFLD. STAMP analysis of public datasets confirmed this decline after HIV infection, while KEGG pathway analysis identified enrichment of metabolism-related genes. A prospective cohort study with 103 PLWHIV followed for 48 weeks validated these findings. Akkermansia abundance was significantly lower in participants with NAFLD, overweight, and hyperlipidemia at baseline, and it emerged as an independent predictor of NAFLD and overweight. Negative correlations were observed between Akkermansia abundance and both CAP values and body mass index (BMI) at baseline and at week 48. At the 48-week follow-up, Akkermansia remained a predictive marker for NAFLD.

CONCLUSIONS: Akkermansia abundance was reduced in PLWHIV with metabolic disorders and served as a predictive biomarker for NAFLD progression over 48 weeks of ART.},
}

Humans
Male
*HIV Infections/complications/microbiology
Female
*Gastrointestinal Microbiome
Middle Aged
Adult
*Akkermansia
*Non-alcoholic Fatty Liver Disease/microbiology/metabolism
Prospective Studies
Feces/microbiology
Metagenomics/methods
Hyperlipidemias/microbiology
Metabolic Diseases/microbiology/epidemiology
Verrucomicrobia/isolation & purification
Overweight/microbiology/complications

@article {pmid40052378,
year = {2025},
author = {Mise, K and Masuda, Y and Senoo, K and Itoh, H},
title = {Betaproteobacterial clade II nosZ activated under high N2O concentrations in paddy soil microcosms.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf055},
pmid = {40052378},
issn = {1365-2672},
abstract = {AIMS: Microbial communities in paddy soils act as potential sinks of nitrous oxide (N2O), a notorious greenhouse gas, but their potential to reduce external N2O is unclear. The direct observation of N2O reduction in submerged field soils is technically difficult. Here, we aimed to identify soil microbial clades that underpin the strong N2O mitigation capacity.

METHODS AND RESULTS: We constructed paddy soil microcosms with external N2O amendment that enabled the simultaneous evaluation of N2O reductase gene (nosZ) transcripts and N2O consumption. Although the amount of N2O amended was large, it was mostly consumed after 6-8 days of microcosm incubation. Metatranscriptomic sequencing revealed that betaproteobacterial nosZ, especially those classified as clade II nosZ belonging to the orders Rhodocyclales or Nitrosomonadales, occupied > 50% of the nosZ transcripts in three of the five paddy soils used. On the other hand, publicly available shotgun metagenomic sequences of 46 paddy soils were not dominated by betaproteobacterial clade II nosZ sequences, although they were ubiquitous. The same applied to the 16S rRNA sequences of Rhodocyclales or Nitrosomonadales.

CONCLUSIONS: The results indicated that betaproteobacterial N2O reducers potentially serve as powerful N2O sinks. Betaproteobacteria holding clade II nosZ can be targets of biostimulation, although further studies are required to understand their ecophysiology.},
}

@article {pmid40052334,
year = {2025},
author = {Lu, Y and Dong, Y and Zhang, M and Mao, L},
title = {Genome and Metagenome Skimming: Future Sequencing Methods for Environmental DNA (eDNA) Studies.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14095},
doi = {10.1111/1755-0998.14095},
pmid = {40052334},
issn = {1755-0998},
support = {2023YFF0805800//the National Key Research and Development Program of China/ ; BE2022792//Jiangsu Social Development Program/ ; },
abstract = {Genome skimming (GS), also referred to as low-coverage shotgun sequencing, is an efficient and cost-effective sequencing method that targets high-copy regions in genomes. It is most commonly used for species identification, phylogenetic analysis and expansion of reference libraries. GS can be applied to single species or composite DNA samples representing multiple species; the latter is termed metagenome skimming (MGS). GS/MGS shows promise as an effective approach for environmental DNA (eDNA) studies, but it is currently limited to ancient sedimentary samples. There is the potential to expand this methodology to other eDNA sources, including water, soil and airborne samples. In this paper, we introduce GS/MGS and briefly review its current applications. We also discuss the potential benefits and challenges of using GS/MGS to assay eDNA. eDNA GS/MGS is a promising technology that could broaden eDNA studies if some methodological challenges can be addressed.},
}

@article {pmid40052063,
year = {2025},
author = {Zheng, H and Peng, P and Wang, S and Zhang, B and Yang, L and Wang, Y and Li, L and Pang, G},
title = {Microbiological Diagnostic Performance and Clinical Effect of Metagenomic Next-Generation Sequencing for the Detection of Immunocompromised Patients With Community-Acquired Pneumonia.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1223-1236},
pmid = {40052063},
issn = {1178-6973},
abstract = {OBJECTIVE: Community-acquired pneumonia (CAP) presents a significant public health concern, necessitating timely and precise diagnosis. Metagenomic next-generation sequencing (mNGS) has shown promise as a powerful tool for pathogen identification in infectious diseases. This study aimed to evaluate the diagnostic efficacy and clinical applicability of mNGS for immunocompromised patients with CAP compared to the culture method.

METHODS: This study included 168 patients. We used both mNGS and conventional culture methods to identify the pathogen spectrum and evaluate diagnostic performance. Treatment regimens and clinical outcomes were meticulously documented.

RESULTS: The sensitivity of mNGS was greater than that of the culture method across all samples (79.05% vs 16.03%; p < 0.001). mNGS identified pathogens missed by culture in 59.52% of patients and detected polymicrobial infections that were not detected by culture in 47.62% of patients. Streptococcus pneumoniae, Candida albicans, and Human herpesvirus 4 at classification level emerged as the predominant pathogens identified in CAP patients through mNGS. When examining the mNGS results between groups, the proportions of immunocompromised patients with bacterial (p < 0.001), fungal (p < 0.001), viral (p < 0.05), and mixed infections (p < 0.001) were all significantly higher than those in immunocompetent patients. Treatment adjustments guided by mNGS were observed in 73.21% of patients. Specifically, a beneficial clinical effect was observed in 50.60% (85/168) of patients, treatment confirmation in 22.62% (38/168) of patients, and no clinical benefit in 26.80% (45/168) of patients based on mNGS-guided antibiotic treatment adjustments.

CONCLUSION: These findings highlight the diagnostic performance of mNGS for identifying pathogens, particularly in immunocompromised patients vulnerable to infections, offering valuable insights for clinical decision-making.},
}

@article {pmid40051621,
year = {2025},
author = {Chen, Y and Liang, S and Lu, Y and Zhou, X and Zheng, R and Chen, Y},
title = {Case Report: First report of Legionella micdadei pneumonia and organizing pneumonia in a patient with myelodysplastic and Sweet syndromes.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1510948},
pmid = {40051621},
issn = {1664-3224},
mesh = {Humans ; *Myelodysplastic Syndromes/complications ; *Sweet Syndrome/diagnosis/drug therapy ; Male ; Legionella ; Pneumonia, Bacterial/diagnosis/drug therapy/microbiology/immunology ; Immunocompromised Host ; Legionellosis/diagnosis/drug therapy/microbiology ; Aged ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; Glucocorticoids/therapeutic use ; Female ; Legionnaires' Disease/diagnosis/drug therapy/complications/immunology ; Organizing Pneumonia ; },
abstract = {The immunocompromised population is susceptible to Legionella pneumonia. The diagnosis and treatment of Legionella pneumonia in immunocompromised individuals are challenging clinical endeavors. Previous studies have identified Legionella pneumonia as a potential cause of organizing pneumonia (OP), however, the association between Legionella pneumonia and OP has not received enough clinical attention. We retrospectively evaluated a case involving Legionella micdadei infection and OP in a patient with myelodysplastic syndrome and concurrent Sweet syndrome. The diagnosis of Legionella micdadei pneumonia was confirmed through various methods: metagenomic next generation sequencing (mNGS), Giemsa-staining and fluorescence in situ hybridization of lung tissue, as well as serum immunofluorescence antibody testing. Histopathological analysis of lung tissue revealed OP. The patient was successfully treated with a combination of antibiotics and low-dose glucocorticoids. In immunocompromised individuals, mNGS was capable of detection non-Legionella pneumophila serogroup 1. The pathological examination is important for identifying secondary OP and provides the evidence for treatment with glucocorticoids.},
}

Humans
*Myelodysplastic Syndromes/complications
*Sweet Syndrome/diagnosis/drug therapy
Male
Legionella
Pneumonia, Bacterial/diagnosis/drug therapy/microbiology/immunology
Immunocompromised Host
Legionellosis/diagnosis/drug therapy/microbiology
Aged
Middle Aged
Anti-Bacterial Agents/therapeutic use
Glucocorticoids/therapeutic use
Female
Legionnaires' Disease/diagnosis/drug therapy/complications/immunology
Organizing Pneumonia

@article {pmid40051412,
year = {2025},
author = {Houttu, V and Boulund, U and Troelstra, M and Csader, S and Stols-Gonçalves, D and Mak, AL and Dijk, AV and Bouts, J and Winkelmeijer, M and Verdoes, X and van den Berg-Faay, S and Lek, D and Ronteltap, T and de Haan, F and Jorstad, H and Männistö, V and Savonen, K and Pentikäinen, H and Hanhineva, K and Babu, AF and Panagiotou, G and van Delden, O and Verheij, J and Doukas, M and Nederveen, A and Schwab, U and Grefhorst, A and Nieuwdorp, M and Holleboom, AG},
title = {Deep phenotyping of patients with MASLD upon high-intensity interval training.},
journal = {JHEP reports : innovation in hepatology},
volume = {7},
number = {3},
pages = {101289},
pmid = {40051412},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: Exercise is a key component of lifestyle management in patients with metabolic dysfunction-associated steatotic liver disease (MASLD), but neither its therapeutic effect on the active stage of the disease, that is metabolic dysfunction-associated steatohepatitis (MASH) nor the mediating mechanisms have been characterized. Therefore, we performed multi-omic phenotyping of patients with MASLD-MASH on an exercise program.

METHODS: Fifteen patients with MASLD conducted high-intensity interval training (HIIT) combined with home-based training for 12 weeks. MASLD was evaluated using histology, transient elastography, and multiparametric magnetic resonance imaging (MRI) before and after the intervention. Change in maximal oxygen consumption (VO2max) and MRI-determined liver fat were compared with a control group of patients with MASLD (n = 22). RNA sequencing was performed on liver, muscle, and fat biopsies of patients in the exercise group. Stool was analyzed by shotgun metagenomics and untargeted metabolomics was performed on plasma, urine, adipose, and stool.

RESULTS: HIIT increased VO2max by 10.1% and improved mitochondrial metabolism in skeletal muscle, indicating improved cardiorespiratory fitness and adherence. VO2max increased significantly in the exercise group compared with controls. Histologically, no reduction in steatosis, MASH, or liver fibrosis was observed; however, transient elastography tended to improve. MRI-determined liver fat did not change in the exercise group compared with controls. HIIT induced changes in mRNA expression of genes related to beiging of adipose tissue and fibrogenesis in liver. In addition, specific gut microbial taxa and metabolites changed.

CONCLUSIONS: HIIT increased cardiorespiratory fitness and induced beneficial gene expression changes in muscle, adipose tissue, and liver, but without translation into histological improvement of MASLD. Longer exercise intervention trials are warranted to validate or refute current recommendations for exercise as a cornerstone treatment for MASLD-MASH.

IMPACT AND IMPLICATIONS: Despite exercise being considered as a key component of lifestyle management for steatotic liver disease, neither the clinical effects nor the mechanisms involved are completely understood. We show that a high-intensity interval training (HIIT) program in 15 patients with metabolic dysfunction-associated steatotic liver disease (MASLD) improved cardiorespiratory fitness, compared with 22 control patients with MASLD who did not participate in an exercise program, however, it did not improve MASLD. HIIT induced a positive effect on fat tissue and muscle metabolism which was accompanied with changes in certain gut bacteria and metabolites in blood and urine. These findings improve our understanding of the effects of exercise on the whole-body metabolism in relation to steatotic liver disease. As such, this study provides a basis for future exercise interventions in patients with MASLD, required to thoroughly test current guideline advice for exercise as a cornerstone treatment for MASLD of all stages.

CLINICAL TRIAL REGISTRY: Dutch Trial Register (registration number NL7932).},
}

@article {pmid40050994,
year = {2025},
author = {Talat, A and Bashir, Y and Khalil, N and Brown, CL and Gupta, D and Khan, AU},
title = {Antimicrobial resistance transmission in the environmental settings through traditional and UV-enabled advanced wastewater treatment plants: a metagenomic insight.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {27},
pmid = {40050994},
issn = {2524-6372},
support = {BT/PR40148/BTIS/137/20/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {BACKGROUND: Municipal wastewater treatment plants (WWTPs) are pivotal reservoirs for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). Selective pressures from antibiotic residues, co-selection by heavy metals, and conducive environments sustain ARGs, fostering the emergence of ARB. While advancements in WWTP technology have enhanced the removal of inorganic and organic pollutants, assessing ARG and ARB content in treated water remains a gap. This metagenomic study meticulously examines the filtration efficiency of two distinct WWTPs-conventional (WWTPC) and advanced (WWTPA), operating on the same influent characteristics and located at Aligarh, India.

RESULTS: The dominance of Proteobacteria or Pseudomonadota, characterized the samples from both WWTPs and carried most ARGs. Acinetobacter johnsonii, a prevailing species, exhibited a diminishing trend with wastewater treatment, yet its persistence and association with antibiotic resistance underscore its adaptive resilience. The total ARG count was reduced in effluents, from 58 ARGs, representing 14 distinct classes of antibiotics in the influent to 46 and 21 in the effluents of WWTPC and WWTPA respectively. However, an overall surge in abundance, particularly influenced by genes such as qacL, blaOXA-900, and rsmA was observed. Numerous clinically significant ARGs, including those against aminoglycosides (AAC(6')-Ib9, APH(3'')-Ib, APH(6)-Id), macrolides (EreD, mphE, mphF, mphG, mphN, msrE), lincosamide (lnuG), sulfonamides (sul1, sul2), and beta-lactamases (blaNDM-1), persisted across both conventional and advanced treatment processes. The prevalence of mobile genetic elements and virulence factors in the effluents possess a high risk for ARG dissemination.

CONCLUSIONS: Advanced technologies are essential for effective ARG and ARB removal. A multidisciplinary approach focused on investigating the intricate association between ARGs, microbiome dynamics, MGEs, and VFs is required to identify robust indicators for filtration efficacy, contributing to optimized WWTP operations and combating ARG proliferation across sectors.},
}

@article {pmid40050500,
year = {2025},
author = {Dave, M and Tattar, R},
title = {Antimicrobial resistance genes in the oral microbiome.},
journal = {Evidence-based dentistry},
volume = {},
number = {},
pages = {},
pmid = {40050500},
issn = {1476-5446},
abstract = {A COMMENTARY ON: Sukumar S, Rahmanyar Z, El Jurf H Q et al. Mapping the oral resistome: a systematic review. J Med Microbiol 2024; https://doi.org/10.1099/jmm.0.001866 .

DESIGN: This systematic review, without meta-analysis, aimed to map the oral resistome by analysing clinical studies that detected bacterial antimicrobial resistance genes (ARGs) in the oral cavity using molecular techniques.

DATA SOURCES: The researchers used Medline, Embase, Web of Science, CINAHL and Scopus databases from January 2015 to August 2023.

STUDY SELECTION: This systematic review included cross-sectional or longitudinal clinical studies that detected ARGs using molecular techniques; specifically polymerase chain reaction (PCR) or next-generation sequencing (NGS) metagenomics for samples from the oral cavity (saliva, gingival biofilm, pulp, or oral mucosa). Studies were excluded if they were in vitro or animal studies, literature reviews and not focused on ARG detection.

DATA EXTRACTION AND SYNTHESIS: Five reviewers independently screened titles and abstracts based on inclusion criteria. Full-text reports were then independently assessed for eligibility by three reviewers. Extracted data encompassed publication details, sample size, country, molecular methods used, number of ARGs detected, participants' health status, antibiotic exposure, and sample location within the oral cavity.

RESULTS: Out of 580 initially identified studies, 15 met the inclusion criteria. These studies, published between 2015 and 2023 from 12 different countries, employed either PCR (n = 10) or NGS metagenomics (n = 5) to detect ARGs from a pool of 1486 participants (1 study did not report on the number of participants). PCR-based studies identified an average of 7 ARGs (range 1-20), while NGS studies identified an average of 34 ARGs (range 7-70). In total, 159 unique ARGs conferring resistance to 22 antibiotic classes were identified across six regions of the oral cavity. The supragingival biofilm and saliva exhibited the highest richness of ARGs, defined by the number of unique ARGs detected. Genes conferring resistance to 19 antibiotic classes were present in the supragingival biofilm. Notably, 49 ARGs, including tetracycline and macrolide resistance genes, were found across all sampled locations, indicating a widespread distribution within the oral cavity. Thirteen studies reported on bacterial species associated with ARGs. NGS studies identified a mean of 65 ARG-carrying bacterial species, compared to a mean of 4 species in PCR studies. Specifically, 25 ARG-carrying species were identified in PCR studies, while NGS studies identified 177 species. Four studies reported ARGs associated with streptococcal species implicated in distant-site infections such as infective endocarditis. ESKAPE pathogens (group of highly virulent multidrug-resistant bacteria) were detected with ARGs in various oral sites using both PCR and NGS methods. Comparisons between healthy and diseased states revealed that a healthy oral microbiome harbours a more diverse resistome at the antibiotic class level. The supragingival resistome demonstrated the richest composition in both health and disease, with tetracycline ARGs predominating in the supragingival and saliva resistomes in cases of dental caries.

CONCLUSIONS: The analysis of the oral resistome from these 15 studies identified three ARGs present in all sites of the oral cavity, suggesting the presence of a core resistome. NGS studies provided greater insights compared to PCR studies; however, the overall research base is limited. Further comprehensive studies are necessary to fully map the oral resistome.},
}

@article {pmid39726137,
year = {2025},
author = {Schwesig, K and Zizka, V and Scherber, C and Hölzel, N},
title = {Comparing eDNA and Transect Methods for Aquatic Biodiversity Assessment in Lakes and Ponds.},
journal = {Molecular ecology resources},
volume = {25},
number = {3},
pages = {e14060},
doi = {10.1111/1755-0998.14060},
pmid = {39726137},
issn = {1755-0998},
support = {01UT2101C//Bundesministerium für Bildung und Forschung/ ; 01UT2101B//Bundesministerium für Bildung und Forschung/ ; },
mesh = {*Biodiversity ; Animals ; *Amphibians/genetics/classification ; *Ponds ; Germany ; *DNA Barcoding, Taxonomic/methods ; *Lakes ; Odonata/genetics/classification ; Metagenomics/methods ; DNA, Environmental/genetics ; Aquatic Organisms/genetics/classification ; },
abstract = {Biodiversity monitoring increasingly relies on molecular methods such as eDNA metabarcoding. However, sound applications have so far been only established for a limited number of taxonomic groups. More information on the strengths and weaknesses of eDNA methods, especially for poorly covered groups, is essential for practical applications to achieve the highest possible reliability. We compared amphibian and Odonata data from eDNA metabarcoding and traditional transect walks on N = 56 plots in 38 water bodies distributed over six extraction sites for building materials in Northwest Germany. The traditional amphibian assessment included visual encounters, dip netting and acoustic detection, while Odonata were assessed through exuviae. In total, both methods detected 8 out of 11 amphibian species, while the remaining three species were detected by eDNA only. We did not find differences in amphibian species numbers per plot, but mean detection probabilities were higher with metabarcoding. In contrast, both methods detected 10 out of 29 Odonata species, while the remaining 19 species were detected by exuviae only. Species numbers per plot were higher for exuviae and only 30% of species were detected with metabarcoding. The species identified by eDNA were those with high abundance, and their detection probabilities were similar to transect walks. The results for amphibians show equal suitability and high complementarity of the compared methods. Metabarcoding detected species more efficiently and therefore offers a suitable protocol for biodiversity monitoring. For Odonata, eDNA metabarcoding showed considerable gaps, implying the need for protocol evaluation and improvement in assessment of ecological communities based on eDNA.},
}

*Biodiversity
Animals
*Amphibians/genetics/classification
*Ponds
Germany
*DNA Barcoding, Taxonomic/methods
*Lakes
Odonata/genetics/classification
Metagenomics/methods
DNA, Environmental/genetics
Aquatic Organisms/genetics/classification

@article {pmid40050382,
year = {2025},
author = {Liu, C and Wang, H and Wang, Z and Liang, L and Li, Y and Liu, D and Lu, Q},
title = {Distinct assembly processes of intestinal and non-intestinal microbes of bark beetles from clues of metagenomic insights.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {7910},
pmid = {40050382},
issn = {2045-2322},
support = {32230071//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Coleoptera/microbiology/genetics ; Metagenome ; Bacteria/genetics/classification/metabolism ; Microbiota ; Symbiosis ; Weevils/microbiology/genetics ; Phylogeny ; },
abstract = {Ips (Curculionidae: Scolytinae) bark beetles (BBs) are ecologically and economically devastating coniferous pests in the Northern Hemisphere. Although the microbial diversity associated with these beetles has been well studied, mechanisms of community assembly and the functional roles of key microbes remain poorly understood. This study investigates the microbial community structures and functions in both intestinal and non-intestinal environments of five Ips BBs using a metagenomic approach. The findings reveal similar microbial community compositions, though the α-diversity of dominant taxa differs between intestinal and non-intestinal environments due to the variability in bark beetle species, host trees, and habitats. Intestinal microbial communities are predominantly shaped homogenizing dispersal (HD) and undominated processes (UP), whereas non-intestinal microbial communities are primarily driven by heterogeneous selection (HS). Functional analysis shows that genes and enzymes associated with steroid biosynthesis and oxidative phosphorylation are primarily found in non-intestinal fungal symbionts Ogataea, Wickerhamomyce, Ophiostoma, and Ceratocystis of Ips species. Genes and enzymes involved in degrading terpenoids, phenolic compounds, and polysaccharides are predominately found in the intestinal Acinetobacter, Erwinia, and Serratia. This study provides valuable and in-depth insights into the symbiotic relationships between Ips BBs and their microbial partners, enhancing our understanding of insect-microbe coevolution and suggesting new strategies for pest management.},
}

Animals
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Coleoptera/microbiology/genetics
Metagenome
Bacteria/genetics/classification/metabolism
Microbiota
Symbiosis
Weevils/microbiology/genetics
Phylogeny

@article {pmid40050078,
year = {2025},
author = {Zheng, YJ and Hou, JY and Zhong, J and Ye, XW},
title = {[A case of COVID-19-associated pulmonary aspergillosis combined with COVID-19-associated pulmonary mucormycosis].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {48},
number = {3},
pages = {267-271},
doi = {10.3760/cma.j.cn112147-20240809-00476},
pmid = {40050078},
issn = {1001-0939},
support = {82460015//National Natural Science Foundation of China/ ; 2019PT320003//Special Fund for Basic Scientific Research Operations of the Chinese Academy of Medical Sciences/ ; },
mesh = {Humans ; *Mucormycosis/diagnosis/complications ; *COVID-19/complications ; *Pulmonary Aspergillosis/complications/diagnosis ; Male ; Tomography, X-Ray Computed ; SARS-CoV-2/isolation & purification ; Lung Diseases, Fungal/diagnosis/complications ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Lung/pathology/diagnostic imaging/microbiology ; Antifungal Agents/therapeutic use ; },
abstract = {COVID-19-associated invasive fungal infections are fungal infections that develop during COVID-19, including pulmonary aspergillosis (CAPA) and pulmonary mucormycosis (CAPM). This report presents a case of a patient with recurrent COVID-19 infections who showed pulmonary cavities and pleural effusion on chest CT. A mixed diagnosis of CAPA and CAPM was confirmed by histopathological analysis of bronchoalveolar lavage fluid and metagenomic next-generation sequencing. This study highlights the importance of suspecting CAPA and CAPM in diabetic COVID-19 patients with unexplained radiological findings that cannot be attributed to common infections or pulmonary tumors. Prompt and thorough diagnostic investigations, including histopathology, microbiology, and molecular techniques, are essential for accurate diagnosis. Early and effective antifungal treatment can significantly improve patient outcomes.},
}

Humans
*Mucormycosis/diagnosis/complications
*COVID-19/complications
*Pulmonary Aspergillosis/complications/diagnosis
Male
Tomography, X-Ray Computed
SARS-CoV-2/isolation & purification
Lung Diseases, Fungal/diagnosis/complications
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology
Lung/pathology/diagnostic imaging/microbiology
Antifungal Agents/therapeutic use

@article {pmid40049907,
year = {2025},
author = {Jia, Z and Li, C and Zhang, S and Tang, Y and Ma, S and Liu, X and Zhang, J},
title = {Microbial inoculants modify the functions of soil microbes to optimize plant growth at abandoned mine sites.},
journal = {Journal of environmental sciences (China)},
volume = {154},
number = {},
pages = {678-690},
doi = {10.1016/j.jes.2024.10.002},
pmid = {40049907},
issn = {1001-0742},
mesh = {*Soil Microbiology ; *Mining ; *Plant Development ; *Soil/chemistry ; Phosphorus/metabolism ; Carbon/metabolism ; Biodegradation, Environmental ; Nitrogen/metabolism ; Microbiota ; Bacillus thuringiensis ; },
abstract = {Mining activities have caused significant land degradation globally, emphasizing the need for effective restoration. Microbial inoculants offer a promising solution for sustainable remediation by enhancing soil nutrients, enzyme activities, and microbial communities to support plant growth. However, the mechanisms by which inoculants influence soil microbes and their relationship with plant growth require further investigation. Metagenomic sequencing was employed for this study, based on a one-year greenhouse experiment, to elucidate the effects of Bacillus thuringiensis NL-11 on the microbial functions of abandoned mine soils. Our findings revealed that the application of microbial inoculants significantly enhanced the soil total carbon (TC), total sulfur (TS), organic carbon (SOC), available phosphorus (AP), ammonium (NH4[+]), urease, arylsulfatase, phosphatase, β-1,4-glucosidase (BG), β-1,4-N-acetylglucosaminidase (NAG). Moreover, this led to substantial improvements in plant height, as well as aboveground and belowground biomass. Microbial inoculants impacted functional gene structures without altering diversity. The normalized abundance of genes related to the degradation of carbon and nitrogen, methane metabolism, and nitrogen fixation were observed to increase, as well as the functional genes related to phosphorus cycling. Significant correlations were found between nutrient cycling gene abundance and plant biomass. Partial Least Squares Path Model analysis showed that microbial inoculants not only directly influenced plant biomass but also indirectly affected the plant biomass through C cycle modifications. This study highlights the role of microbial inoculants in promoting plant growth and soil restoration by improving soil properties and enhancing normalized abundance of nutrient cycling gene, making them essential for the recovery of abandoned mine sites.},
}

*Soil Microbiology
*Mining
*Plant Development
*Soil/chemistry
Phosphorus/metabolism
Carbon/metabolism
Biodegradation, Environmental
Nitrogen/metabolism
Microbiota
Bacillus thuringiensis

@article {pmid40049896,
year = {2025},
author = {Yu, Q and Hu, X and Qian, Y and Wang, Y and Shi, C and Qi, R and Heděnec, P and Nan, Z and Li, H},
title = {Virus communities rather than bacterial communities contribute more on nutrient pool in polluted aquatic environment.},
journal = {Journal of environmental sciences (China)},
volume = {154},
number = {},
pages = {550-562},
doi = {10.1016/j.jes.2024.08.026},
pmid = {40049896},
issn = {1001-0742},
mesh = {*Bacteria/metabolism/classification/genetics ; *Viruses ; Phosphorus/analysis ; RNA, Ribosomal, 16S/genetics ; Nitrogen/analysis ; Carbon/metabolism ; Water Microbiology ; Water Pollutants, Chemical/analysis ; Nutrients/analysis ; },
abstract = {The degradation of animal carcasses can lead to rapid waste release (e.g., pathogenic bacteria, viruses, prions, or parasites) and also result in nutrient accumulation in the surrounding environment. However, how viral profile responds and influences nutrient pool (carbon (C), nitrogen (N), phosphorus (P) and sulfur (S)) in polluted water caused by animal carcass decomposition had not been explored. Here, we combined metagenomic analysis, 16S rRNA gene sequencing and water physicochemical assessment to explore the response of viral communities under different temperatures (23 °C, 26 °C, 29 °C, 32 °C, and 35 °C) in water polluted by cadaver, as well as compare the contribution of viral/bacterial communities on water nutrient pool. We found that a total of 15,240 viral species were classified and mainly consisted of Siphoviridae. Both temperature and carrion reduced the viral diversity and abundance. Only a small portion of the viruses (∼8.8 %) had significant negative correlations with temperature, while most were not sensitive. Our results revealed that the viruses had lager contribution on nutrient pool than bacteria. Besides, viral-related functional genes involved in C, N, P and S cycling. These functional genes declined during carcass decomposition and covered part of the central nutrient cycle metabolism (including carbon sugar transformation, denitrification, P mineralization and extracelluar sulfate transfer, etc.). Our result implies that human regulation of virus communities may be more important than bacterial communities in regulating and managing polluted water quality and nutrition.},
}

*Bacteria/metabolism/classification/genetics
*Viruses
Phosphorus/analysis
RNA, Ribosomal, 16S/genetics
Nitrogen/analysis
Carbon/metabolism
Water Microbiology
Water Pollutants, Chemical/analysis
Nutrients/analysis

@article {pmid40049874,
year = {2025},
author = {Yao, W and Chang, R and Chen, K and Yang, C and Lu, Y and Wang, S and Dong, K and Huang, B and Jin, R},
title = {Performance and mechanism of enhanced phosphorus release and volatile fatty acid production from Fe-P sludge via co-fermenting with agricultural wastes.},
journal = {Journal of environmental sciences (China)},
volume = {154},
number = {},
pages = {290-299},
doi = {10.1016/j.jes.2024.07.019},
pmid = {40049874},
issn = {1001-0742},
mesh = {*Phosphorus/metabolism ; *Fatty Acids, Volatile/metabolism ; *Sewage ; *Fermentation ; *Agriculture/methods ; *Waste Disposal, Fluid/methods ; Iron/metabolism ; },
abstract = {Anaerobic fermentation is an efficient method to extract phosphorus from excess sludge, thereby facilitating its recovery and mitigating the phosphorus resource shortage. However, the prevalent metal-bound phosphorus species within sludge was difficult to release into the fermentation liquor. To address this, this study evaluated the enhanced phosphorus release performance from sludge containing iron-phosphorus compounds (Fe-P) via co-fermenting it with agriculture wastes. Specifically, protein-rich feather (Feather Group) and polysaccharide-rich tea residue (Tea Group) was respectively dosed into batch-scale fermentation jar. Results showed that the Feather Group exhibited significantly higher levels of released soluble phosphorus (2.1 folds) and volatile fatty acids (41.4 folds) compared to the Control Group, with concentrations reaching up to 280 mg/L and 9366 mg chemical oxygen demand /L, respectively. The activities of α-glucosidase, neutral protease and acetate kinase in the Feather group were increased by 11.1 %, 92.3 % and 37.6 %, respectively, compared with the Control group. Methanogen abundance decreased while hydrolytic acid-producing bacteria and iron-reducing bacteria increased significantly after supplying agricultural wastes. Metagenomic analysis demonstrated a significant increase in genes related to acetic acid synthesis. Mechanism elucidation suggested that increased iron-reducing bacteria abundance promoted Fe[3+] reduction into Fe[2+], thus enhancing phosphorus release from Fe-P compounds. This work may provide valuable information for developing effective strategy to extract phosphorus resource from complex environmental wastes.},
}

*Phosphorus/metabolism
*Fatty Acids, Volatile/metabolism
*Sewage
*Fermentation
*Agriculture/methods
*Waste Disposal, Fluid/methods
Iron/metabolism

@article {pmid40049354,
year = {2025},
author = {Sun, RZ and Pan, Y and Wang, J and Gao, T and Yu, HQ and Wang, J},
title = {Metabolic and Ecological Responses of Denitrifying Consortia to Different Carbon Source Strategies Under Fluctuating C/N Conditions.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121292},
doi = {10.1016/j.envres.2025.121292},
pmid = {40049354},
issn = {1096-0953},
abstract = {Frequent fluctuations in the carbon-to-nitrogen (C/N) ratio of urban wastewater influent can undermine denitrification performance, posing challenges for stable nitrogen removal. Although supplying additional carbon sources is a recognized strategy to mitigate these issues, the underlying microbial interactions and metabolic reconfigurations triggered by changing C/N ratios remain incompletely understood. Here, we employed methanol, glycerol, sodium acetate, and glucose in long-term denitrification reactors and integrated denitrification kinetics, 16S rRNA gene amplicon sequencing, metagenomic binning, and metabolic modeling to elucidate how these systems respond to a declining C/N ratio. Our results show that lower C/N ratios diminished denitrification efficiency in all treatments, with each carbon source eliciting distinct shifts in microbial assemblages. Fluctuations in the C/N ratio determine the extent of directional selection of microbial communities based on carbon source metabolism and induce significant changes in non-dominant microorganisms. Throughout the process, the synthesis potential of PHA is closely linked to the system's ability to withstand fluctuations. Notably, metabolic modeling indicated that heightened tricarboxylic acid (TCA) cycle activity in the methanol- and glucose-fed communities was associated with suboptimal nitrogen removal. These findings offer novel insights into the metabolic and ecological mechanisms governing carbon source-driven denitrification under fluctuating C/N conditions, providing a valuable framework for optimizing nitrogen removal in urban wastewater treatment systems.},
}

@article {pmid40049094,
year = {2025},
author = {Yu, C and He, Q and Nie, WB and Zhang, T and Wu, H and Yang, Y and Fu, S and Tan, X and Chen, Y},
title = {Effluent organic matter facilitates anaerobic methane oxidation coupled with nitrous oxide reduction in river sediments.},
journal = {Water research},
volume = {278},
number = {},
pages = {123415},
doi = {10.1016/j.watres.2025.123415},
pmid = {40049094},
issn = {1879-2448},
abstract = {Effluent organic matter (EfOM) from wastewater treatment plants (WWTPs) contains humic-like substances that function as electron shuttles, thereby facilitating microbially-mediated redox reactions. However, the mechanisms governing the coupled processes of anaerobic oxidation of methane (CH4) (AOM) and nitrous oxide (N2O) reduction in river sediments, which receive WWTPs effluents, remain poorly understood. In this study, an incubation experiment with anoxic river sediments was conducted to assess the impacts of EfOM on AOM and nitrous oxide reduction using different effluent dilution ratios. The results showed that EfOM significantly enhanced both processes. Specifically, the AOM rate increased from 8.1 to 14.3 μg gdw[-1] d[-1], while the N2O reduction rate increased from 29.2 to 56.5 μg gdw[-1] d[-1]. The results of batch tests demonstrated that AOM process enhanced N2O reduction in the presence of EfOM, highlighting the critical role of EfOM in linking these processes. Nitrate-dependent anaerobic methane oxidation (n-DAMO) archaea and denitrifying bacteria dominated the sediment incubated with EfOM. Metagenomic and metatranscriptomic analyses revealed that the denitrifying bacteria exclusively reduce N2O, confirming the role of EfOM in facilitating electron transfer between n-DAMO archaea and N2O reducers. This indicates that effluent discharge could be a potential factor driving the concurrent sinks of methane and nitrous oxide, offering a perspective for investigating the impacts of WWTPs effluent on greenhouse gas sinks in freshwater ecosystems.},
}

@article {pmid40048953,
year = {2025},
author = {Tamai, S and Okuno, M and Ogura, Y and Suzuki, Y},
title = {Genetic diversity of dissolved free extracellular DNA compared to intracellular DNA in wastewater treatment plants.},
journal = {The Science of the total environment},
volume = {970},
number = {},
pages = {178989},
doi = {10.1016/j.scitotenv.2025.178989},
pmid = {40048953},
issn = {1879-1026},
abstract = {Dissolved free extracellular DNA (free-exDNA) coexists with intracellular DNA (inDNA) in aquatic environments. Free-exDNA can be taken up by bacteria through transformation, and wastewater treatment plants (WWTPs) are positioned as potential hot spots for genetic contamination. However, studies comparing the composition of free-exDNA and inDNA is limited. This study employed colloidal adsorption and foam concentration method to recover free-exDNA from different WWTP stages and compared its diversity with inDNA via metagenomic analysis. Free-exDNA concentrations were observed to increase after chlorination. Genetic analysis revealed a higher abundance of specific genes following chlorination, suggesting that free-exDNA in effluent originated from bacterial death in secondary treated water. This result indicates that free-exDNA, which increases due to chlorination, is subsequently released into the catchment. Additionally, several high-risk antibiotic-resistance genes (ARGs) were detected that colocalized with mobile genetic elements. These ARGs were expected to have a high potential for gene transfer via transformation, and the risk was highlighted. Overall, these findings deepen our understanding of horizontal gene transfer risks in WWTPs.},
}

@article {pmid40048849,
year = {2025},
author = {Bargheet, A and Noordzij, HT and Ponsero, AJ and Jian, C and Korpela, K and Valles-Colomer, M and Debelius, J and Kurilshikov, A and Pettersen, VK},
title = {Dynamics of gut resistome and mobilome in early life: a meta-analysis.},
journal = {EBioMedicine},
volume = {114},
number = {},
pages = {105630},
doi = {10.1016/j.ebiom.2025.105630},
pmid = {40048849},
issn = {2352-3964},
abstract = {BACKGROUND: The gut microbiota of infants harbours a higher proportion of antibiotic resistance genes (ARGs) compared to adults, even in infants never exposed to antibiotics. Our study aims to elucidate this phenomenon by analysing how different perinatal factors influence the presence of ARGs, mobile genetic elements (MGEs), and their bacterial hosts in the infant gut.

METHODS: We searched MEDLINE and Embase up to April 3rd, 2023, for studies reporting infant cohorts with shotgun metagenomic sequencing of stool samples. The systematic search identified 14 longitudinal infant cohorts from 10 countries across three continents, featuring publicly available sequencing data with corresponding metadata. For subsequent integrative bioinformatic analyses, we used 3981 high-quality metagenomic samples from 1270 infants and 415 mothers.

FINDINGS: We identified distinct trajectories of the resistome and mobilome associated with birth mode, gestational age, antibiotic use, and geographical location. Geographical variation was exemplified by differences between cohorts from Europe, Southern Africa, and Northern America, which showed variation in both diversity and abundance of ARGs. On the other hand, we did not detect a significant impact of breastfeeding on the infants' gut resistome. More than half of detected ARGs co-localised with plasmids in key bacterial hosts, such as Escherichia coli and Enterococcus faecalis. These ARG-associated plasmids were gradually lost during infancy. We also demonstrate that E. coli role as a primary modulator of the infant gut resistome and mobilome is facilitated by its increased abundance and strain diversity compared to adults.

INTERPRETATION: Birth mode, gestational age, antibiotic exposure, and geographical location significantly influence the development of the infant gut resistome and mobilome. A reduction in E. coli relative abundance over time appears as a key factor driving the decrease in both resistome and plasmid relative abundance as infants grow.

FUNDING: Centre for Advanced Study in Oslo, Norway. Centre for New Antibacterial Strategies through the Tromsø Research Foundation, Norway.},
}

@article {pmid40048707,
year = {2025},
author = {Hernández-Verdin, I and Kirasic, E and Mokhtari, K and Barillot, N and Rincón de la Rosa, L and Sourdeau, E and Abada, Y and Le Tarff-Tavernier, M and Nichelli, L and Rozenblum, L and Kas, A and Mathon, B and Choquet, S and Houillier, C and Hoang-Xuan, K and Alentorn, A},
title = {Gut microbiome modulates the outcome in primary central nervous system lymphoma patients undergoing chemotherapy: an ancillary study from the BLOCAGE trial.},
journal = {Neuro-oncology},
volume = {},
number = {},
pages = {},
doi = {10.1093/neuonc/noaf059},
pmid = {40048707},
issn = {1523-5866},
abstract = {BACKGROUND: Primary central nervous system lymphoma (PCNSL) treatment relies on a high-dose methotrexate based chemotherapy (HD-MTX-based CT) regimen; however, whether there is a specific microbiota composition association with treatment response and clinical outcomes remains incompletely understood.

METHODS: We conducted a prospective study of PCNSL patients, included in the clinical trial NCT02313389 and the ancillary study NCT04253496 from 2020 to 2023, where patients were treated with first line HD-MTX-based polychemotherapy without a consolidation treatment. Stool (n=52), cerebrospinal fluid (CSF, n=52), and plasma samples (n=35) were collected before and/or after therapy initiation to perform metagenomic, flow cytometry, and metabolomic analyses. Plasma metabolomic data of 90 patients also included in the BLOCAGE clinical trial was subsequently used as a validation cohort.

RESULTS: Unsupervised clustering of microbial data identified two distinct gut microbial communities, differing in Parabacteroides distasonis abundance, which correlated with progression-free survival and overall survival in both uni- and multivariate analyses. Higher P. distasonis levels were linked to increased plasma betaine/valine metabolites and enhanced CD8 T cell infiltration in the CSF, suggesting a connection between gut microbiota and immune regulation. Stratifying the validation cohort by betaine/valine content confirmed these clinical associations.

CONCLUSIONS: Our findings suggest that gut microbiome communities modulate clinical outcomes in PCNSL patients undergoing standard treatment. Moreover, after future validation in external cohorts, the quantification of Parabacteroides distasonis could potentially provide a basis for patient stratification and guide personalized therapeutic strategies in the near future.},
}

@article {pmid40047424,
year = {2025},
author = {Li, N and Li, M and Zhang, H and Bai, Z and Fei, Z and Dong, Y and Zhang, X and Xiao, P and Sun, X and Zhou, D},
title = {Effects of post-adulthood environmental hygiene improvement on gut microbiota and immune tolerance in mice.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0247724},
doi = {10.1128/aem.02477-24},
pmid = {40047424},
issn = {1098-5336},
abstract = {UNLABELLED: Changes in diet, cleanliness, stress, and exercise patterns may contribute to the disappearance of various gut microbes in humans who relocate to developed countries from developing countries. To explore the impact of environmental cleanliness on the gut microbiota, adult mice housed in a general animal room were divided into three groups. The control group was subjected to an unchanged living environment, SPF mice were moved to a specific pathogen-free (SPF) animal room with higher environmental cleanliness, and SPFL (specific pathogen-free specific with a fecal leakage grid) mice were moved to the SPF animal room and reared in cages with the function of preventing mice from eating feces as much as possible. Metagenome sequencing results showed that the gut microbial diversity decreased after the environmental change, accompanied by a substantial loss in gut microbiota, including genera known to have protective effects against allergies and those involved in short-chain fatty acid production. Additionally, the abundance of functional genes involved in short-chain fatty acid metabolism, amino acid synthesis, vitamin metabolism, flagellar assembly, and bacterial chemotaxis decreased. The environmental hygiene improvement also resulted in significant increases in total serum IgE, IL-4, IL-5, and IL-13 levels in mice with artificially induced chronic inflammatory dermatosis. Compared with SPF mice, preventing mice from eating feces as much as possible decreased the gut microbial diversity but did not markedly change functional gene expression or total serum cytokine levels.

IMPORTANCE: Research has indicated that the human gut microbial diversity gradually decreases, while the prevalence of allergic diseases increases after movement from developing countries to developed countries. A healthy gut microbiota is necessary for proper human immune function. Movement from undeveloped to developed regions is often accompanied by an increase in environmental cleanliness. However, whether changes in environmental cleanliness are an important factor contributing to the decreased gut microbial diversity and increased prevalence of allergic diseases has not been reported. This study demonstrates the impact of increased environmental cleanliness on gut microbiota and susceptibility to allergic diseases and contributes to a better understanding of the increased incidence rate of various chronic diseases.},
}

@article {pmid40047330,
year = {2025},
author = {Gong, S and Li, M and Gao, J and Huang, S and Song, W and Sun, L},
title = {Cucumaria frondosa intestines and ovum hydrolysates intervention ameliorates the symptoms of dextran sulfate sodium-induced colitis by modulating gut microbiota and its metabolites.},
journal = {Journal of food science},
volume = {90},
number = {3},
pages = {e70106},
doi = {10.1111/1750-3841.70106},
pmid = {40047330},
issn = {1750-3841},
support = {42106111//National Natural Science Foundation of China/ ; ZR2021QD030//Natural Science Foundation of Shandong Province/ ; NYJG202303//Fund of Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, China/ ; 2023KJ241//Program for Scientific Research Innovation Team of Young Scholar in Colleges and Universities of Shandong Province/ ; R20076//Doctoral Startup Project of Guangdong Ocean University funded by W.S/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colitis/chemically induced ; *Dextran Sulfate ; Mice ; Male ; Disease Models, Animal ; Mice, Inbred C57BL ; Colon/metabolism/microbiology/drug effects ; Cytokines/metabolism ; Intestines/microbiology/drug effects ; },
abstract = {Colitis, a troublesome inflammatory disease that significantly impacts daily life, has garnered considerable attention in recent times. Protolysates play a crucial role in the treatment of colitis, and the intestines and ovum of Cucumaria frondosa represent a readily available source of these hydrolysates. However, the effects of C. frondosa intestines and ovum hydrolysates (CFHs) on colitis have not been thoroughly investigated. We initially examined the molecular weight distribution of CFHs and found that the fraction of molecules with a weight less than 1000 Da accounted for 86.98%, indicating that the hydrolysis primarily produced oligopeptides. Subsequently, we employed a dextran sulfate sodium-induced experimental colitis model to assess the therapeutic potential of CFHs. The findings indicated that preventive administration of CFHs dramatically attenuated the pathological manifestations associated with colitis in mice, including weight loss, colon shortening, and tissue damage. Furthermore, CFHs suppressed the secretion of pro-inflammatory cytokines IL-6, TNF-α, and IL-1β, as well as MPO in colon tissue. Metagenomic sequencing demonstrated that CFHs could restore balance to the dysregulated gut microbiota by reinforcing Bacteroidota and suppressing Verrucomicrobia populations, impacting various microbial functions. Metabolomic analyses further revealed that CFHs exhibited a more efficacious modulatory effect on DSS-induced metabolic abnormalities, including amino acid biosynthesis, linoleic acid metabolism, and dopaminergic synapses. In conclusion, CFHs showed promise in alleviating colitis, laying the groundwork for the development and application of CFHs as functional food for colitis relief.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Colitis/chemically induced
*Dextran Sulfate
Mice
Male
Disease Models, Animal
Mice, Inbred C57BL
Colon/metabolism/microbiology/drug effects
Cytokines/metabolism
Intestines/microbiology/drug effects

@article {pmid40047235,
year = {2025},
author = {Garg, RK},
title = {Tuberculosis of the central nervous system: current concepts in diagnosis and treatment.},
journal = {Current opinion in neurology},
volume = {},
number = {},
pages = {},
pmid = {40047235},
issn = {1473-6551},
abstract = {PURPOSE OF REVIEW: The outcome of central nervous system (CNS) tuberculosis has shown little improvement over several decades, with diagnosis remaining unconfirmed in nearly half of the cases. This review highlights current insights and advancements in the diagnosis and treatment of CNS tuberculosis.

RECENT FINDINGS: Miliary pulmonary tuberculosis is often linked to CNS tuberculosis and is associated with a worse prognosis. Complications, such as, optochiasmatic arachnoiditis, strokes, and transverse myelitis severely affect prognosis and quality of life. Nearly half of tuberculous meningitis patients exhibited impaired cognition. Diagnosing CNS tuberculosis is challenging because of the low accuracy of standard tests. Advanced techniques like metagenomic and nanopore sequencing enhance detection but are hindered by high costs and limited access. Treatment outcomes remain suboptimal but approaches such as higher drug doses, novel medications, and host-directed therapies are being explored. Drug-resistant tuberculous meningitis is increasingly recognized, posing significant challenges to both diagnosis and treatment. Artificial intelligence (AI) enhances care by enabling early diagnosis, disease monitoring, and personalized treatments, improving outcomes.

SUMMARY: CNS tuberculosis diagnosis faces challenges due to limited sensitivity and delayed results of available tests. Treatments remain suboptimal, with multidrug-resistant cases posing high mortality risks. AI aids in early diagnosis and personalized care.},
}

@article {pmid40046986,
year = {2025},
author = {Zhang, D and Deng, M and Li, F and Shen, R},
title = {A Report of Primary Pyogenic Ventriculitis Caused by Streptococcus Constellatus Diagnosed by Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1209-1214},
pmid = {40046986},
issn = {1178-6973},
abstract = {BACKGROUND: Primary ventriculitis is a rare but serious brain infection characterized by inflammation of the ependyma and purulence within the ventricular system. Due to the challenges in early diagnosis and the potential for suboptimal treatment, this condition carries a significant risk of complications such as recurrence, hydrocephalus, and death. Metagenomic next-generation sequencing (mNGS) enables the rapid and broad-spectrum identification of pathogens, facilitating timely and precise diagnosis.

CASE REPORT: This study presents the first reported case of primary ventriculitis caused by Streptococcus constellatus. An 81-year-old female patient with hydrocephalus and clinical signs of central nervous system infection was diagnosed with primary ventriculitis based on brain magnetic resonance imaging (MRI) and cerebrospinal fluid (CSF) analysis using mNGS. The patient underwent external ventricular drainage (EVD) and received a five-week course of ceftriaxone and linezolid. Following timely and targeted therapy, she demonstrated significant clinical improvement and was discharged without residual symptoms.

CONCLUSION: Key insights from this case include: 1) mNGS is an invaluable tool for the early and accurate diagnosis of primary ventriculitis; 2) MRI is indispensable for identifying characteristic radiological features of the condition; 3) prompt initiation and completion of appropriate antibiotic regimens significantly improve clinical outcomes.},
}

@article {pmid40046887,
year = {2025},
author = {Kim, M and Damronglerd, P and Molina Garcia, S and Yetmar, ZA and Razi, S and Ranganath, N and Mahmood, M and Abu Saleh, OM},
title = {Illuminating the Challenges and Diagnostic Utility of Plasma Microbial Cell-Free DNA Sequencing in Suspected Infective Endocarditis: A Retrospective Observational Cohort Study.},
journal = {Open forum infectious diseases},
volume = {12},
number = {3},
pages = {ofaf099},
pmid = {40046887},
issn = {2328-8957},
abstract = {BACKGROUND: Infective endocarditis (IE) is a life-threatening infection often challenging to diagnose, particularly in culture-negative cases. Plasma microbial cell-free DNA (mcfDNA) sequencing has shown potential for detecting pathogens in IE. However, its clinical utility, diagnostic impact, and limitations remain debated. This study evaluates its use in diagnosing and managing IE in a tertiary care setting.

METHODS: This single-center retrospective cohort study included adult patients (≥18 years) who underwent mcfDNA sequencing via the Karius test for suspected IE at Mayo Clinic Rochester between December 2019 and February 2024. Diagnostic classification followed the 2023 Duke-International Society of Cardiovascular Infectious Diseases criteria. Data on demographics, clinical features, routine microbiologic workup, and mcfDNA sequencing results were collected. Statistical analysis was conducted to evaluate diagnostic utility and treatment impact.

RESULTS: Among 141 patients, 66 had a diagnosis of IE, with mcfDNA sequencing identifying pathogens in 60.6% of them, compared with 39.4% with routine workup. mcfDNA sequencing was the sole microbiologic test with positive results in 33.3% of patients, leading to antimicrobial adjustments in 50.0% of that group. Clinically insignificant mcfDNA sequence detection occurred in 28.6% of patients without a diagnosis of IE.

CONCLUSIONS: mcfDNA sequencing is a valuable adjunctive tool for diagnosing culture-negative IE and guiding antimicrobial therapy when clinical suspicion is high. However, its utility depends on appropriate clinical context, highlighting the need for careful test interpretation and further prospective studies to assess patient-centered outcomes and cost-effectiveness.},
}

@article {pmid40046856,
year = {2025},
author = {Tan, L and He, Z and Liang, Y and Wang, K and Chen, X},
title = {Correlation analysis between the severity of respiratory syncytial virus pneumonia and the expression levels of inflammatory cytokines in bronchoalveolar lavage fluid among infants and young children.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1482029},
pmid = {40046856},
issn = {2296-2360},
abstract = {PURPOSE: RSV is the primary cause of lower respiratory tract infections in infants and young children. Current study aims to investigate the correlation between the severity of respiratory syncytial virus pneumonia (RSVP) in infants and young children and the number of RSV infection sequences as well as the levels of cytokines in bronchoalveolar lavage fluid (BALF).

METHODS: Metagenomics next-generation sequencing (mNGS) and enzyme-linked immunosorbent assay (ELISA) were used to detect the number of RSV infection sequences and the levels of related inflammatory cytokines in BALF samples. Comparisons between groups and Logistic regression analysis were performed to examine the differences in RSV infection sequences and inflammatory cytokine levels between the sRSVP and nsRSVP groups. Spearman's correlation coefficient was used to analyze the correlations among PCIS, RSV infection sequences, and inflammatory cytokines. Finally, ROC curve analysis was conducted to assess the diagnostic performance of inflammatory cytokines as biomarkers in determining the severity of RSVP.

RESULTS: A total of 49 infants and young children diagnosed with RSV infection were enrolled and divided into severe RSVP (sRSVP) and non-severe RSVP (nsRSVP) groups based on the pediatric critical illness score (PCIS) scale. The levels of Interleukin (IL)-6, IL-8, IL-10, tumor necrosis factor α (TNF-α), IL-17A, and monocyte chemotactic protein 1 (MCP-1) as well as the number of RSV sequences in BALF were significantly higher in the sRSVP group than in the nsRSVP group. Additionally, elevated levels of IL-6, IL-10, TNF-α, IL-17A, and the number of RSV sequences were identified as risk factors for the severity of RSVP. Spearman's correlation analysis revealed significant negative correlations between the levels of IL-6, IL-10, TNF-α, IL-17A, and MCP-1 in BALF with PCIS, and significant positive correlations with the number of RSV sequences. Furthermore, a significant negative correlation was observed between RSV sequence count and PCIS. ROC curve analysis showed that the levels of IL-6, IL-10, TNF-α, IL-17A, and MCP-1, as well as their combined diagnostic approach, exhibited high diagnostic performance in determining the severity of RSVP.

CONCLUSION: The levels of inflammatory cytokines and RSV sequences in BALF are significantly correlated with the severity of RSVP in infants and young children. The levels of IL-6, IL-10, TNF-α, IL-17A, and MCP-1 can serve as potential biomarkers for diagnosing the severity of RSVP.},
}

@article {pmid40046438,
year = {2025},
author = {Lin, K and Lin, W and Guo, Z and Chen, C and Chen, L and Cai, X},
title = {Plasma exosomal miRNA expression and gut microbiota dysbiosis are associated with cognitive impairment in Alzheimer's disease.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1545690},
pmid = {40046438},
issn = {1662-4548},
abstract = {INTRODUCTION: The gut microbiota composition and the expression profiles of microRNAs (miRNAs) in the brain tissue, cerebrospinal fluid, and blood of patients with Alzheimer's disease (AD) differ significantly from those with normal cognition function. The study aimed to initially explore the relationship between plasma exosomal microRNAs, gut microbiota, and cognitive impairment, providing insights into the pathogenesis and treatment of AD.

METHODS: The study enrolled 8 participants with AD and 8 participants with normal cognition. The Mini-Mental State Examination (MMSE) was utilized to evaluate cognitive function. High-throughput sequencing was used to identify differentially expressed miRNAs in plasma exosomes, while metagenomic sequencing was employed to detect differences in the abundance of gut microbiota. Furthermore, the associations among them were analyzed.

RESULTS: Four exosomal miRNAs and 14 microbiota taxa, which exhibited differential expression and abundance, respectively, in comparison between AD group and normal cognition group, were identified to be significantly associated with MMSE scores. Notably, the abundance of potential probiotics, including Faecalibacterium prausnitzii, Roseburia intestinalis and Roseburia inulinivorans, which was decreased in AD patients, exhibited positive correlations with specific exosomal miRNAs: Roseburia intestinalis correlated with miR-3120-3p and miR-6529-5p; Roseburia inulinivorans correlated with miR-3120-3p, miR-6529-5p and miR-124-3p; Faecalibacterium prausnitzii correlated with miR-3120-3p.

DISCUSSION: The study revealed a close association among gut microbiota, plasma exosomal miRNAs, and cognitive impairment in AD, and suggested that specific components of gut microbiota and exosomal miRNAs may serve as potential biomarkers and therapeutic targets for AD on the microbiota-gut-brain axis.},
}

@article {pmid40046298,
year = {2025},
author = {Sun, W and Li, M and Zhu, X},
title = {Bordetella pertussis bacteremia in infants co-infected with cytomegalovirus and respiratory syncytial virus.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1544935},
pmid = {40046298},
issn = {1664-302X},
abstract = {INTRODUCTION: Hematogenous infections caused by Bordetella pertussis are rare. This study aimed to increase clinicians' knowledge of B. pertussis bacteremia.

METHODS: We described a case of an infant with B. pertussis bacteremia, searched and reviewed for B. pertussis bacteremia-related literatures published in the PubMed database between 1946 to 2022.

RESULTS: A 3-month-old male infant was admitted to the hospital with a respiratory tract infection. Respiratory pathogen testing indicated the presence of B. pertussis, cytomegalovirus, and respiratory syncytial viruses. Blood metagenomic next-generation sequencing (mNGS) confirmed B. pertussis bacteremia. After 32 days of anti-infective treatment and supportive therapy, the patient's condition improved, and he was discharged. The literature review found that B. pertussis bacteremia is rare, often with fever as the first symptom, and is most common in individuals with underlying diseases or prolonged immunosuppressive therapy.

DISCUSSION: In infants lacking specific protective antibodies against B. pertussis, B. pertussis bacteremia should be considered when bacteremia-associated clinical manifestations are present and the causative organism remains undetected. Timely refinement of mNGS can help clarify the diagnosis.},
}

@article {pmid40046038,
year = {2025},
author = {Bird, E and Pickens, V and Molik, D and Silver, K and Nayduch, D},
title = {BALROG-MON: a high-throughput pipeline for Bacterial AntimicrobiaL Resistance annOtation of Genomes-Metagenomic Oxford Nanopore.},
journal = {microPublication biology},
volume = {2025},
number = {},
pages = {},
pmid = {40046038},
issn = {2578-9430},
abstract = {BALROG-MON is a Nextflow pipeline for automated analysis of metagenomic long-read data to detect pathogens, annotate antimicrobial resistance genes (ARGs), link ARGs to specific pathogens, predict ARG origin (e.g., plasmid, chromosomal) and optionally perform steps like community analysis. With both assembly-based and assembly-free workflows, BALROG-MON is applicable to a wide range of sample types with low or high coverage, varying complexities and origins. Optional genome binning provides a comprehensive overview of ARGs within the dataset. BALROG-MON additionally presents results in summarized reports, overall serving as a flexible analysis tool for exploring diverse metagenomic samples for pathogens and antibiotic resistance.},
}

@article {pmid40045326,
year = {2025},
author = {Zhang, R and Yu, J and Shang, X and Wang, Z and Li, H and Cao, B},
title = {Heterogeneity in clinical patterns of adult lung abscess patients: an 8-year retrospective study in a tertiary hospital.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {101},
pmid = {40045326},
issn = {1471-2466},
support = {NO. 82030002/H0102//National Natural Science Foundation of China/ ; NO.20220484049//Beijing Nova Program of Science and Technology under grant/ ; No. ZRJY2021-QM09//National High Level Hospital Clinical Research Funding, the Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; },
mesh = {Humans ; *Lung Abscess/microbiology ; Male ; Retrospective Studies ; Female ; Middle Aged ; China/epidemiology ; *Tertiary Care Centers ; Aged ; *Tomography, X-Ray Computed ; Adult ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Hospital Mortality ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: The widespread use of broad-spectrum antibiotics has led to changes in both the microbiological and clinical characteristics of lung abscesses. It is necessary to re-evaluate the bacterial spectrum associated with these infections. As a novel method for pathogen detection, metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical practice. There is limited research evaluating the use of mNGS in patients with lung abscesses.

METHODS: A retrospective analysis was conducted on patients with lung abscess who were hospitalized between July 2015 and July 2023 at a teaching hospital in China. Patients who underwent both computerized tomography (CT) imaging and conventional pathogen testing were included in the study. The efficacy of pathogen detection using conventional methods was compared with that of mNGS. Additionally, the clinical and radiological features were analyzed to provide a comprehensive understanding of the disease patterns.

RESULTS: A total of 782 patients with lung abscess were included in the study and hematogenous abscess accounting for 7.16% (56/782) of cases. The overall hospital mortality rate was 1.53%. The mean age of the patients with lung abscess was 60 years, with a male predominance (80.2%). A significant proportion of patients had comorbid conditions, including diabetes (29.7%) and cardiovascular disease (18.2%). Lung abscesses were predominantly located in the right lung, and pleural effusion was more commonly observed in the deceased group. The detection rate of pathogen via conventional test was lower at 41.8% (327/782). Among patients with positive mNGS results, only 51.9% had pathogens identified through conventional testing methods. Klebsiella pneumoniae was the most frequently detected pathogen by conventional culture, while mNGS identified was Parvimonas micra. Infections caused solely by anaerobic bacteria or facultative anaerobes were associated with shorter hospital stays. Patient infected with Gram-negative bacilli (GNB) had a higher proportion of liver abscesses (11.8%).

CONCLUSION: Compared to conventional testing methods, mNGS demonstrates superior performance in detecting anaerobic and facultative anaerobic bacteria. The low detection rate of conventional tests may result in an underestimation of the clinical significance of anaerobic bacteria infections. In patients with lung abscess caused by GNB, hematogenous dissemination, liver abscess and diabetes were more commonly observed and these patients tended to have longer hospital stays.},
}

Humans
*Lung Abscess/microbiology
Male
Retrospective Studies
Female
Middle Aged
China/epidemiology
*Tertiary Care Centers
Aged
*Tomography, X-Ray Computed
Adult
High-Throughput Nucleotide Sequencing
Metagenomics
Hospital Mortality
Anti-Bacterial Agents/therapeutic use

@article {pmid40045185,
year = {2025},
author = {Freund, L and Hung, C and Topacio, TM and Diamond, C and Fresquez, A and Lyons, TW and Aronson, EL},
title = {Diversity of sulfur cycling halophiles within the Salton Sea, California's largest lake.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {120},
pmid = {40045185},
issn = {1471-2180},
support = {NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NIH 1U54MD013368-01A1/NH/NIH HHS/United States ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; NSF EAR-2012878//National Science Foundation, United States/ ; },
mesh = {California ; *Sulfur/metabolism ; *Microbiota ; *Lakes/microbiology ; *Seawater/microbiology/chemistry ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Seasons ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Biodiversity ; },
abstract = {BACKGROUND: Microorganisms are the biotic foundation for nutrient cycling across ecosystems, and their assembly is often based on the nutrient availability of their environment. Though previous research has explored the seasonal lake turnover and geochemical cycling within the Salton Sea, California's largest lake, the microbial community of this declining ecosystem has been largely overlooked. We collected seawater from a single location within the Salton Sea at 0 m, 3 m, 4 m, 5 m, 7 m, 9 m, 10 m, and 10.5 m depths in August 2021, December 2021, and April 2022.

RESULTS: We observed that the water column microbiome significantly varied by season (R[2] = 0.59, P = 0.003). Temperature (R[2] = 0.27, P = 0.004), dissolved organic matter (R[2] = 0.13, P = 0.004), and dissolved oxygen (R[2] = 0.089, P = 0.004) were significant drivers of seasonal changes in microbial composition. In addition, several halophilic mixotrophs and other extremotolerant bacteria were consistently identified in samples across depths and time points, though their relative abundances fluctuated by season. We found that while sulfur cycling genes were present in all metagenomes, their relative coverages fluctuated by pathway and season throughout the water column. Sulfur oxidation and incomplete sulfur oxidation pathways were conserved in the microbiome across seasons.

CONCLUSIONS: Our work demonstrates that the microbiome within the Salton Seawater has the capacity to metabolize sulfur species and utilize multiple trophic strategies, such as alternating between chemorganotrophy and chemolithoautrophy, to survive this harsh, fluctuating environment. Together, these results suggest that the Salton Sea microbiome is integral in the geochemical cycling of this ever-changing ecosystem and thus contributes to the seasonal dynamics of the Salton Sea. Further work is required to understand how these environmental bacteria are implicated relationship between the Salton Sea's sulfur cycle, dust proliferation, and respiratory distress experienced by the local population.},
}

California
*Sulfur/metabolism
*Microbiota
*Lakes/microbiology
*Seawater/microbiology/chemistry
*Bacteria/classification/genetics/metabolism/isolation & purification
*Seasons
Phylogeny
RNA, Ribosomal, 16S/genetics
Ecosystem
Biodiversity

@article {pmid40045177,
year = {2025},
author = {Torshizi Esfahani, A and Zafarjafarzadeh, N and Vakili, F and Bizhanpour, A and Mashaollahi, A and Karimi Kordestani, B and Baratinamin, M and Mohammadpour, S},
title = {Gut Microbiome in Colorectal Cancer: Metagenomics from Bench to Bedside.},
journal = {JNCI cancer spectrum},
volume = {},
number = {},
pages = {},
doi = {10.1093/jncics/pkaf026},
pmid = {40045177},
issn = {2515-5091},
abstract = {Colorectal cancer (CRC) is a major global health challenge. Emerging research highlights the pivotal role of the gut microbiota in influencing CRC risk, progression, and treatment response. Metagenomic approaches, especially high-throughput shotgun sequencing, have provided unprecedented insights into the intricate connections between the gut microbiome and CRC. By enabling comprehensive taxonomic and functional profiling, metagenomics has revealed microbial signatures, activities, and biomarkers associated with colorectal tumorigenesis. Furthermore, metagenomics has shown a potential to guide patient stratification, predict treatment outcomes, and inform microbiome-targeted interventions. Despite remaining challenges in multi-omics data integration, taxonomic gaps, and validation across diverse cohorts, metagenomics has propelled our comprehension of the intricate gut microbiome-CRC interplay. This review underscores the clinical relevance of microbial signatures as potential diagnostic and prognostic tools in CRC. Furthermore, it discusses personalized treatment strategies guided by this omics' approaches.},
}

@article {pmid40044917,
year = {2025},
author = {Štůsková, K and Vavřiník, A and Hakalová, E and Čechová, J and Gramaje, D and Eichmeier, A},
title = {Arbuscular mycorrhizal fungi strongly influence the endorhizosphere of grapevine rootstock with soil type as a key factor.},
journal = {Mycorrhiza},
volume = {35},
number = {2},
pages = {17},
pmid = {40044917},
issn = {1432-1890},
support = {CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; CZ.02.1.01/0.0/0.0/16_025/0007314//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; IGA-ZF/2022-ST2-004//Internal Grant Agency, Mendel university in Brno/ ; },
mesh = {*Mycorrhizae/physiology ; *Vitis/microbiology ; *Soil Microbiology ; *Soil/chemistry ; Czech Republic ; Plant Roots/microbiology ; Mycobiome ; Basidiomycota/genetics/physiology ; Rhizosphere ; Phosphorus/metabolism/analysis ; },
abstract = {Arbuscular mycorrhizal fungi (AMF) play a crucial role in enhancing the health and productivity of host plants, including grapevine. By forming symbiotic relationships with plant roots, AMF significantly improve water uptake and nutrient absorption, particularly phosphorus (P) and nitrogen (N). This study evaluated the microbiome composition and AMF colonization in the grapevine endorhizosphere across five wine-growing sub-regions in the Czech Republic. In all five sub-regions, in terms of composition of the fungal microbiome, the phyla Ascomycetes and Basidiomycetes were most numerous. Additionally, the study confirmed that LSU primers are more sensitive than ITS primers for AMF sequencing. While the representation of the phylum Glomeromycetes ranged from 0.07% to 5.65% in the ITS library, it was significantly higher, ranging from 83.74% to 98.71%, in the LSU library. The most significant difference compared to other sub-regions was observed in the Slovácko sub-region, where the soil had a low pH, a different texture (sandy loam), reduced micronutrient concentration, and low organic matter. The application of chemical plant protection products to grapevines also could have played a significant role, with 49 applications recorded in the Slovácko sub-region during the three years preceding sample collection. In other sub-regions, chemical treatments were conducted only 19-26 times. These factors resulted in only trace amounts of AMF being detected in Slovácko. Furthermore, it was demonstrated that AMF positively influenced the phosphorus concentration in the soil and reduced the presence of certain fungal pathogens.},
}

*Mycorrhizae/physiology
*Vitis/microbiology
*Soil Microbiology
*Soil/chemistry
Czech Republic
Plant Roots/microbiology
Mycobiome
Basidiomycota/genetics/physiology
Rhizosphere
Phosphorus/metabolism/analysis

@article {pmid40044690,
year = {2025},
author = {Zheng, K and Sun, J and Liang, Y and Kong, L and Paez-Espino, D and Mcminn, A and Wang, M},
title = {VITAP: a high precision tool for DNA and RNA viral classification based on meta-omic data.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2226},
pmid = {40044690},
issn = {2041-1723},
support = {41976117//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42176111//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*RNA, Viral/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; *DNA Viruses/genetics/classification ; *DNA, Viral/genetics ; Software ; Phylogeny ; Genome, Viral/genetics ; Metagenomics/methods ; Virome/genetics ; Computational Biology/methods ; },
abstract = {The rapid growth in the number of newly identified DNA and RNA viral sequences underscores the need for an accurate and comprehensive classification system for all viral realms at different taxonomic levels. Here, we establish the Viral Taxonomic Assignment Pipeline (VITAP), which addresses classification challenges by integrating alignment-based techniques with graphs, offering high precision in classifying both DNA and RNA viral sequences and providing confidence level for each taxonomic unit. This tool automatically updates its database in sync with the latest references from the International Committee on Taxonomy of Viruses (ICTV), efficiently classifying viral sequences as short as 1,000 base pairs to genus level. VITAP possesses good generalization capabilities, maintaining accuracy comparable to other pipelines while achieving higher annotation rates across most DNA and RNA viral phyla. Its application in deep-sea viromes has led to significant taxonomic updates, providing comprehensive diversity information of viruses from deep-sea. VITAP is available at https://github.com/DrKaiyangZheng/VITAP .},
}

*RNA, Viral/genetics
*RNA Viruses/genetics/classification/isolation & purification
*DNA Viruses/genetics/classification
*DNA, Viral/genetics
Software
Phylogeny
Genome, Viral/genetics
Metagenomics/methods
Virome/genetics
Computational Biology/methods

@article {pmid40044673,
year = {2025},
author = {Wood, JR and Zhou, C and Cole, TL and Coleman, M and Anderson, DP and Lyver, PO and Tan, S and Xiang, X and Long, X and Luo, S and Lou, M and Southon, JR and Li, Q and Zhang, G},
title = {Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1798},
pmid = {40044673},
issn = {2041-1723},
mesh = {Animals ; Antarctic Regions ; *Spheniscidae/genetics ; *DNA, Mitochondrial/genetics ; *Geologic Sediments ; Phylogeny ; Seals, Earless ; Metagenome ; Ecosystem ; Diet ; },
abstract = {We report 156 sediment metagenomes from Adélie penguin (Pygoscelis adeliae) colonies dating back 6000 years along the Ross Sea coast, Antarctica, and identify marine and terrestrial eukaryotes, including locally occurring bird and seal species. The data reveal spatiotemporal patterns of Adélie penguin diet, including spatial patterns in consumption of cnidarians, a historically overlooked component of Adélie penguin diets. Relative proportions of Adélie penguin mitochondrial lineages detected at each colony are comparable to those previously reported from bones. Elevated levels of Adélie penguin mitochondrial nucleotide diversity in upper stratigraphic samples of several active colonies are consistent with recent population growth. Moreover, the highest levels of Adélie penguin mitochondrial nucleotide diversity recovered from surface sediment layers are from the two largest colonies, indicating that sedaDNA could provide estimates for the former size of abandoned colonies. SedaDNA also reveals prior occupation of the Cape Hallett Adélie penguin colony site by southern elephant seal (Mirounga leonina), demonstrating how terrestrial sedaDNA can detect faunal turnover events in Antarctica driven by past climate or sea ice conditions. Low rates of cytosine deamination indicate exceptional sedaDNA preservation within the region, suggesting there is high potential for recovering much older sedaDNA records from local Pleistocene terrestrial sediments.},
}

Animals
Antarctic Regions
*Spheniscidae/genetics
*DNA, Mitochondrial/genetics
*Geologic Sediments
Phylogeny
Seals, Earless
Metagenome
Ecosystem
Diet

@article {pmid40043990,
year = {2025},
author = {Lou, D and Xiao, S and Cui, J and Duan, J and Duan, H and Cao, Y and Wang, D and Zhou, B and Tan, J},
title = {Discovery and characterization of the first hyperthermophilic 3-quinuclidinone reductase from hot-spring metagenomes.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {141706},
doi = {10.1016/j.ijbiomac.2025.141706},
pmid = {40043990},
issn = {1879-0003},
abstract = {Extremozymes play an essential part in the biosynthesis of pharmaceuticals (intermediates). In this study, a mixed assembly was performed for five metagenomes from hot springs. Via a series of procedures, including homology analysis, heterologous expression, and catalytic property characterization, the first hyperthermophilic 3-quinuclidinone reductase (SbQR) was successfully identified. The SbQR exhibits an optimal temperature of ≥95 °C and demonstrates remarkable thermal stability, with over 80 % of its activity retained following a 48-hour incubation at 50 °C. At particular concentrations, Mg[2+], Na[+], and Mn[2+] can substantially enhance the enzymatic activity. However, no significant influence of K[+] on the activity of SbQR was detected within the concentration range of 0-400 mM. Employing AlphaFold2, the three-dimensional structure of SbQR was predicted, which presents the typical traits of the Rossmann fold and is classified as a member of the short-chain dehydrogenases/reductases (SDR) superfamily. Molecular dynamics simulations were carried out and the results showed that when the temperature was increased to 390 K, the flexibility of residues 90-104 and the C-terminal increased significantly. This increase might lead to the destruction of the three-dimensional structure of the enzyme. In conclusion, this study identified the first hyperthermophilic 3-quinuclidinone reductase, providing a potential biocatalyst for the biopreparation of (R)-3-quinuclidinol.},
}

@article {pmid40043973,
year = {2025},
author = {Liu, N and Dai, S and Fan, X and Li, B and Chen, M and Gong, P and Chen, X},
title = {In vitro fermentation of Auricularia auricula polysaccharides and their regulation of human gut microbiota and metabolism.},
journal = {International journal of biological macromolecules},
volume = {306},
number = {Pt 4},
pages = {141714},
doi = {10.1016/j.ijbiomac.2025.141714},
pmid = {40043973},
issn = {1879-0003},
abstract = {Auricularia auricula is abundant in polysaccharides that received increasing attention due to their variety biological activities and prebiotic potential. In order to explore the role of A. auricula polysaccharides (AAP) in regulating human gut microbiota and metabolic health, this study employed metagenomic and metabolomic analyses to examine the impact of AAP on the gut microbiota via in vitro fecal fermentation experiments. After in vitro fermentation, the data indicated that gut microbiota utilized AAP to produce rich short-chain fatty acids (SCFAs) including acetic acid, propionic acid, butyric acid and modulate gut microbiota structure, such as increasing the proportion of Bacteroidetes to Firmicutes, elevating the abundance of beneficial bacteria, including Bacteroides, especially the Parabacteroides, and inhibiting the abundance of harmful bacteria such as Bilophila, Morganella, and Escherichia-Shigella. Furthermore, the metabolomic analysis indicated that AAP utilization by gut microbes substantially alters the metabolic profile, in which 26 potential biological biomarkers were found and affects tryptophan, bile acids, purines, and butyric acid pathways to promote host health. In conclusion, this research indicated that AAP has a prebiotic potential, which can regulate the gut microbiota and promote host health. Moreover, this study provided scientific evidence for using AAP as a functional food with prebiotic effect.},
}

@article {pmid40043931,
year = {2025},
author = {Li, HQ and Wang, WL and Shen, YJ and Su, JQ},
title = {Mangrove Plastisphere as a Hotspot for High-Risk Antibiotic Resistance Genes and Pathogens.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121282},
doi = {10.1016/j.envres.2025.121282},
pmid = {40043931},
issn = {1096-0953},
abstract = {Microplastics (MPs) are critical vectors for the dissemination of antibiotic resistance genes (ARGs); however, the prevalence and ecological risks of high-risk ARGs in mangrove ecosystems-globally vital yet understudied coastal habitats-remain poorly understood. To address this gap, this study investigated polyethylene, polystyrene, and polyvinyl chloride incubated in mangrove sediments for one month, focusing on high-risk ARGs, virulence gene (VGs), and pathogenic antibiotic-resistant bacteria within the mangrove plastisphere. High-throughput PCR and metagenomic analyses revealed that high-risk ARGs, VGs, and mobile genetic elements (MGEs) were significantly enriched on MPs compared to surrounding sediments. Pathogenic bacteria and MGEs were also more abundant in the plastisphere, highlighting its role as a hotspot for ARG dispersal. Metagenome-assembled genome analysis identified Pseudomonas and Bacillus as key hosts for ARGs, MGEs, and VGs, particularly multidrug resistance genes, integrase genes, and adherence factors. Notably, polystyrene harbored the highest abundance of pathogenic bacteria carrying ARGs, MGEs, and VGs, and mangrove root exudates were found to amplify horizontal gene transfer on MPs, uncovering a previously overlooked mechanism driving antibiotic resistance in coastal ecosystems. These findings not only elucidate how MPs accelerate the spread of ARGs, but also underscore the urgent need for targeted mitigation strategies to address the adverse impacts microplastic pollution on human, animal, and environmental health.},
}

@article {pmid40043916,
year = {2025},
author = {Yang, H and Zhu, X and Zhan, Z and Wu, X and Mou, S and Zhou, P and Peng, Q and Wang, W and Teng, H and Tang, H},
title = {Metagenomic Analysis of Pathogenic Microorganisms in Bloodstream Infections Following Venomous Snakebites.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {},
number = {},
pages = {108304},
doi = {10.1016/j.toxicon.2025.108304},
pmid = {40043916},
issn = {1879-3150},
abstract = {PURPOSE: This study aimed to investigate the biometric characterization of pathogenic microorganisms associated with bloodstream infections in patients bitten by venomous snakes, and to determine whether the composition of these microorganisms influences the effects of snake venom.

METHODS: The composition and relative abundance of microorganisms were statistically analyzed using metagenomic next-generation sequencing (mNGS) on blood samples from patients with varying degrees of snakebite injuries. These patients were admitted to the our study.

RESULTS: In the light injury group (group L), the dominant phylum and genus were Pseudomonadota (73.31%) and Pseudomonas (35.32%). In the moderate injury group (group M), the predominant phylum was Bacillota (56.74%) and Aerococcus (45.45%). There was no statistically significant difference in the microbial composition between group L and group M based on α- and β- diversity analyses. LEfSe differential analysis revealed that the absolute abundances of Actinomycetota and Actinomycetes were higher in group L, while Pseudomonas aeruginosa emerged as a significantly differential species in Group M.

CONCLUSION: The study found that differences in bacterial bloodstream infections due to venomous snakebite may enhance the effects of snake venom, leading to more severe injuries. The mNGS technique can rapidly detect pathogens related to venomous snakebites and has the potential for broader clinical use.},
}

@article {pmid40043765,
year = {2025},
author = {Yang, Y and Wu, X and Xu, Y and Shuang, Q and Xia, YN},
title = {Influence of Feeding Systems on the Microbial Community and Flavor Characteristics of Raw Milk: A Comparative Analysis.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25959},
pmid = {40043765},
issn = {1525-3198},
abstract = {This study analyzed the composition of the microbial community in raw milk and its effects on flavor compounds by comparing samples from cows raised on pasture (PXN) and in housing (HXN). In August 2023, 9 raw milk samples from Holstein cows were collected from a pasture in the Xilin Gol League, Inner Mongolia, China, and labeled as the PXN group. Simultaneously, 9 raw milk samples were collected from Holstein cows raised by individual farmers in the region and labeled as the HXN group. Metagenomic sequencing technology was used to detect and analyze the dynamics of microbial community in milk samples. At the same time, headspace solid phase microextraction, electronic nose and electronic tongue technology were used to monitor the flavor characteristics of raw milk under the 2 feeding conditions and to analyze the correlations between them. The results showed that raw milk protein (PXN 3.43%; HXN 3.36%) and fat (PXN 4.01%; HXN 3.79%) content in pasture group were higher than that in the housed group, while lactose content (PXN 4.98%; HXN 5.12%) and total solid content (PXN 4.98%; HXN 5.12%) were lower than that under the housed system. However, there was no significant difference between non-milk fat solid contents of the 2 groups. W1C, W5C, W5S, W2S sensors of electronic nose played an important role in distinguishing the 2 groups of samples. The sour taste of raw milk in pasture group was different from that in house feeding group. There were significant differences in the microbial communities of the 2 groups, with Macrococcus caseolyticus (39.85%) in PXN group and Lactococcus lactis (49.59%) in HXN group being the dominant bacteria. The volatile compounds of raw milk in PXN and HXN groups were detected by headspace solid phase microextraction method. A total of 62 and 53 flavor compounds were detected in PXN and HXN groups, respectively. Terpenoids, esters and aldehydes were dominant in PXN group, while acids were dominant in HXN group. The saturated fatty acid (SFA) content in HXN group (76.13%) was higher than that in PXN group (72.47%). The gamma-linolenic acid (GLA) content in PXN group (3.56 g/100g) was higher than that in HXN group (1.32 g/100g). The dominant strains, i.e., Macrococcus caseolyticus, Lactococcus lactis and Lactococcus cremoris, in both PXN and HXN groups exhibited positive effects on the formation of alcohols, esters, phenols and unsaturated fatty acids. In addition, Macrococcus caseolyticus in PXN group showed significant positive correlation with calcium lactate (CAL). This study comprehensively elaborates the microbial community structure and flavor quality of raw milk under different feeding methods, which may serve as a reference to control the quality of raw milk.},
}

@article {pmid40043731,
year = {2025},
author = {Wang, M and Liu, YB and Tong, WM and Leung, WK and He, LL and Xu, X and Xu, D and Zhou, Q},
title = {Periodontitis History Shapes the Early Peri-Implant Microbiome Formation: A Metagenomic Analysis.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14147},
pmid = {40043731},
issn = {1600-051X},
support = {32270188//National Natural Science Foundation of China/ ; 32070134//National Natural Science Foundation of China/ ; 2023-YBSF-162//Key Research and Development Program of Shaanxi Province, China/ ; //National Training Program of Innovation and Entrepreneurship for Undergraduates/ ; },
abstract = {AIM: This study aims to investigate the early alterations in microbiome construction and succession around dental implants in both periodontally healthy individuals and patients with a history of periodontitis during the first month after implant-crown placement.

MATERIALS AND METHODS: Ninety-five subgingival plaque samples were collected from 10 periodontally compromised patients (PCP) and nine periodontally healthy patients (PHP) at four time points with a 1-week interval and analysed using dynamic metagenomic analysis. The study compared the formation and temporal change in the peri-implant microbiome in the PCP and PHP groups during the first month after the implant crown placement. A two-year follow-up examination was conducted to assess the clinical outcomes of early peri-implant dysbiosis.

RESULTS: The results showed that PCP groups exhibited distinctively dysbiotic features in their peri-implant microbiome upon initial establishment, with an earlier and elevated emergence of periodontopathogens. This dysbiosis in the PCP group was associated with significantly higher modified sulcus bleeding index (mBI) scores compared with the PHP group. Neisseria was identified as a key driver of early peri-implant dysbiosis in patients with a periodontitis history.

CONCLUSIONS: This study established the first microbial link between periodontitis history and early peri-implant dysbiosis, highlighting the importance of early prevention strategies against peri-implant diseases in patients with a periodontitis history.},
}

@article {pmid40043574,
year = {2025},
author = {Wang, B and Chen, X and Wen, G and Duan, Z and Xue, P and Gao, H},
title = {Treating nitrobenzene (NB) wastewater via an enhanced iron‒manganese oxides electron transfer strategy: Methods and mechanisms.},
journal = {Water research},
volume = {278},
number = {},
pages = {123407},
doi = {10.1016/j.watres.2025.123407},
pmid = {40043574},
issn = {1879-2448},
abstract = {Nitrobenzene (NB) is widely used in the fine chemical, pharmaceutical, and textile industries, but its toxicity and resistance to degradation present challenges, and traditional treatment methods are limited due to costs and a lack of efficiency. In this study, using a three-dimensional biofilm electrode reactor (3D-BER) enhanced with iron-manganese oxide catalysts was explored for the treatment of NB wastewater. Modifying polyurethane (PU) sponge fillers with Fe3O4 and Mn3O4 improved the conductivity and microbial electron transfer of the 3D-BER, significantly enhancing organic compound degradation, nitrogen and phosphorus removal. At the optimal voltage of 6 V and hydraulic retention time (HRT) of 24 h, the reactor achieved CODCr and ammonia nitrogen removal rates of 93.04 % and 86.25 %, respectively, which were more than 20 % higher than those in the control group. The iron and manganese present facilitated increased microbial activity and electron transfer efficiency, and metagenomic sequencing revealed shifts in the microbial communities and the enrichment of specific functional genes related to NB degradation. This integrated bioelectrochemical approach offers an effective and low-cost solution for treating NB wastewater, with broader implications for organic chemical wastewater management.},
}

@article {pmid40043404,
year = {2025},
author = {Pang, L and Chen, J and Li, W and Chatzisymeon, E and Xu, K and Yang, P},
title = {Particle size of zero-valent iron affects the risks from antibiotic resistance genes in waste activated sludge during anaerobic digestion.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137785},
doi = {10.1016/j.jhazmat.2025.137785},
pmid = {40043404},
issn = {1873-3336},
abstract = {Zero-valent iron (ZVI) is the promising enhancer for sludge anaerobic digestion (AD) performance and for mitigating the proliferation of antibiotic resistance genes (ARGs). However, concerns about its size effects in shifting the behavior and risk of ARGs in sludge, during the AD process. Here, the metagenomics-based profile of ARGs, along with their potential (pathogenic) hosts in sludge were investigated, during mesophilic AD enhanced by ZVI with three different sizes. Results showed that the size of ZVI affected the profiles of ARGs, with nano-ZVI (nZVI, 50 nm) demonstrating the most significant reduction in abundance (by 45.0 %) and diversity (by 8.6 %) of total ARGs, followed by micron-ZVI (150 μm) and iron scrap (1 mm). Similar trends were also observed for high-risk ARGs, pathogens, and potential pathogenic hosts for ARGs. Notably, nZVI achieved the greatest reductions in the abundance of risk ARGs and potential pathogenic hosts (superbugs) by 58.8 % and 53.9 %, respectively. Correlation and redundancy analyses revealed that, the size of ZVI induced concentration differences in ammonium nitrogen, pH, carbonaceous matters, iron, and potential microbial hosts were the main reasons for the variation in the risk of ARGs. Moreover, the down-regulation of genes involved in oxidative stress contributed to the lower risk of ARGs in the three ZVI groups, especially in nZVI. This study provides insights into AD processes of solid wastes using ZVI enhancers.},
}

@article {pmid40043390,
year = {2025},
author = {Li, F and Zeng, Z and Wu, Y and Wang, Y and Shen, L and Huang, X and Wang, X and Sun, Y},
title = {Characteristics of microplastics in typical poultry farms and the association of environment microplastics colonized-microbiota, waterfowl gut microbiota, and antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {490},
number = {},
pages = {137808},
doi = {10.1016/j.jhazmat.2025.137808},
pmid = {40043390},
issn = {1873-3336},
abstract = {Microplastics (MPs) pollution is a growing global environmental concern. MPs serve as ecological niches for microbial communities, which may accelerate the spread of antibiotic resistance genes (ARGs), posing risks to the breeding industry. While studies on MPs in aquatic organisms are common, research on farmed poultry is limited. This study investigates MPs in poultry farm environments and waterfowl intestines for the first time. MPs were isolated via density separation and analyzed for characterization in soil, pond water, and waterfowl intestines. Metagenomics was used to investigate the association between environment MPs colonized-microbiota and waterfowl gut microbiota. Our findings reveal that MPs are abundant in soil (6.75 ± 2.78 items/g d.w.), pond water (0.94 ± 0.28 items/g w.w.), and poultry intestines (45.35 ± 19.52 items/g w.w.), primarily appearing as fragmented particles sized 20-50 μm. MPs abundance in intestines correlates with environmental levels. Colonized-microbiota on MPs are linked to poultry intestinal microbiota, with greater diversity and microbial functions. Network analysis reveals that Corynebacterium plays a key role in MPs and poultry intestinal. Polymyxin resistance exhibits high clustering. Procrustes analysis reveals correlations between MPs, bacteria, and ARGs in the farming environment. Overall, MPs in poultry farms may facilitate pathogen and ARGs transmission, posing risks to animal gut health.},
}

@article {pmid40043057,
year = {2025},
author = {Mercado-Juárez, RA and Valdespino-Castillo, PM and Merino Ibarra, M and Batista, S and Mac Cormack, W and Ruberto, L and Carpenter, EJ and Capone, DG and Falcón, LI},
title = {What defines a photosynthetic microbial mat in western Antarctica?.},
journal = {PloS one},
volume = {20},
number = {3},
pages = {e0315919},
pmid = {40043057},
issn = {1932-6203},
mesh = {Antarctic Regions ; *Bacteria/genetics/classification/isolation & purification ; Photosynthesis ; Archaea/genetics/classification/isolation & purification ; Biodiversity ; Phylogeny ; Microbiota ; },
abstract = {Antarctic microbial mats, with their significant biodiversity and key role in biogeochemical cycling, were the focus of our study. We employed a metagenomic approach to analyze 14 microbial mats from meltwater streams of western Antarctica, covering the Maritime, Peninsula, and Dry Valleys regions. Our findings revealed that the taxonomic compositional level of the microbial mat communities is characterized by similar bacterial groups, with diatoms being the main distinguishing factor between the rapidly warming Maritime Antarctica and the other mats. Bacteria were found to be the predominant component of all microbial mats (>90%), followed by Eukarya (>3%), Archaea (<1%), and Viruses (<0.1%). The average abundance of the main phyla composing Antarctic microbial mats included Bacteroidota (35%), Pseudomonadota (29%), Cyanobacteriota (19%), Verrucomicrobiota (3%), Bacillariophyta (2%), Planctomycetota (2%), Acidobacteriota (2%), Actinomycetota (2%), Bacillota (1%), and Chloroflexota (1%). We also identified some microeukaryotes that could play essential roles in the functioning of Antarctic microbial mats. Notably, all mats were found in sites with varied environmental characteristics, showed N-limitation, and shared functional patterns.},
}

Antarctic Regions
*Bacteria/genetics/classification/isolation & purification
Photosynthesis
Archaea/genetics/classification/isolation & purification
Biodiversity
Phylogeny
Microbiota

@article {pmid40042766,
year = {2025},
author = {Kumar, A and Saini, S and Anvikar, A and Mishra, N and Misra, G},
title = {Evolving Landscape of Emerging Virus Diagnosis: Challenges and Innovations.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40042766},
issn = {1559-0305},
abstract = {Emerging and re-emerging viruses (like Spanish flu, SARS-CoV-2, etc.) have substantially impacted global public health since the early twentieth century. These outbreaks are unpredictable and novel viruses are difficult to understand due to emerging variations. Advanced virology and diagnostic technologies have revolutionized viral diagnostics, enabling accurate early identification and successful treatment and containment. Next-generation sequencing (NGS) technologies, such as metagenomics and whole-genome sequencing, have played a crucial role in the detection and monitoring of emerging viruses, such as SARS-CoV-2 and its variants. Advanced diagnostic methods, such as digital PCR, CRISPR-based tools, and serological techniques like ELISA, enhance viral detection's sensitivity, specificity, and speed. Research has shown that innovations such as lateral flow immunoassays, biosensors, and aptamers have the potential to significantly enhance diagnostic accuracy in various fields. The integration of AI in diagnostics aids researchers in understanding viral evolution and outbreak management, offering new avenues for rapid response. This review aims to examine the latest advancements in virus diagnosis technologies, identify unresolved accuracy and detection issues, and discuss emerging ideas that are transforming the future of viral diagnostics. It is important to improve early identification, rendering the system more cost-effective and adaptable to new viral threats.},
}

@article {pmid39902625,
year = {2025},
author = {Pelosi, JA and Sorojsrisom, ES and Barbazuk, WB and Sessa, EB},
title = {Population genomics of the gametophyte-only fern Vittaria appalachiana provides insights into clonal plant evolution.},
journal = {The New phytologist},
volume = {246},
number = {1},
pages = {349-364},
doi = {10.1111/nph.20433},
pmid = {39902625},
issn = {1469-8137},
support = {2024-67012-43394//National Institute of Food and Agriculture/ ; 1701708//Division of Environmental Biology/ ; 1754911/2310485//Division of Integrative Organismal Systems/ ; //Department of Biology, University of Florida/ ; //Southern Appalachian Botanical Society/ ; },
mesh = {*Germ Cells, Plant/physiology ; *Ferns/genetics/physiology ; *Genetic Variation ; *Biological Evolution ; Reproduction, Asexual/genetics ; Genome, Plant ; Metagenomics ; Genetics, Population ; Mutation/genetics ; Clone Cells ; },
abstract = {How asexually reproducing organisms maintain genetic diversity and adaptive potential is a long-standing question in evolutionary biology. Asexual lineages have historically been thought of as evolutionary dead ends, yet some exhibit remarkable persistence through time. The gametophyte-only fern Vittaria appalachiana is a clonal eukaryote, the focus of extensive study due to its peculiar habit and life history, and is an excellent system to explore the consequences of asexuality. Using reduced representation sequencing and life cycle simulations, we assess theoretical expectations for genomic consequences of long-term asexual reproduction and test hypotheses about its origin and demographic history. We show that V. appalachiana colonies are not patches of single genotypes but are mosaics of genetic diversity, and the accumulation of mutations in the absence of recombination plays an important role in driving this diversity. We identify increased genomic variation, excess heterozygosity, decreased population differentiation, and increased effective population size, all of which are consistent with the expectations for prolonged clonality. Our analyses support the hypothesis that the loss of sexual reproduction in V. appalachiana occurred during the Last Glacial Maximum. Our results from empirical and simulation-based analyses illuminate how an asexual eukaryote generates, retains, and partitions genomic diversity.},
}

*Germ Cells, Plant/physiology
*Ferns/genetics/physiology
*Genetic Variation
*Biological Evolution
Reproduction, Asexual/genetics
Genome, Plant
Metagenomics
Genetics, Population
Mutation/genetics
Clone Cells

@article {pmid40042720,
year = {2025},
author = {Zhang, H and Zhang, H and Du, H and Zhang, Y and Zhang, M and Yu, X and Xu, Y},
title = {Unraveling the multiple interactions between phages, microbes and flavor in the fermentation of strong-flavor Baijiu.},
journal = {Bioresources and bioprocessing},
volume = {12},
number = {1},
pages = {14},
pmid = {40042720},
issn = {2197-4365},
abstract = {The fermentation process of strong-flavor Baijiu represents a complex and unique ecosystem, characterized by the involvement of various microorganisms that drive intricate biochemical reactions, ultimately contributing to the distinct flavor profile of the Baijiu. Viruses may affect the succession of microorganisms and thus affect the style and quality of the product. However, the interaction between viruses and microorganisms during the fermentation of Baijiu is still unclear. Here we combined viral metagenomics and amplicon sequencing, physicochemical analysis, and GC-MS detection with temporal sampling to study the dynamics of viral and microbial communities, physicochemical properties, and flavor compounds during strong-flavor Baijiu fermentation. Viral metagenomic analysis revealed 513 viral operational taxonomic units (vOTUs), encompassing 34 viral families. Principal coordinates analysis (PCoA) demonstrated significant differences in vOTUs at different fermentation stages. Notably, the microbial community exhibited distinct succession patterns at various fermentation stages; it changed rapidly during the initial five days, with similarities observed between days 10 and 20. Volatile profile analysis identified 38 flavor components in fermented grains, comprising 16 ester compounds, 11 alcohols, and 8 acids, with the majority formed between days 10 and 30. The Spearman's rank correlation analysis revealed that Peduoviridae exhibited a negative correlation with Gluconobacter. Genomoviridae showed a negative correlation with Issatchenkia, Penicillium, and Monascus. These findings highlight the potential for complex interactions between viruses and microbial communities during Baijiu fermentation, underscoring the importance of considering viral communities in studies of the microbial ecology of fermented foods.},
}

@article {pmid40042334,
year = {2025},
author = {Venturini, AM and Gontijo, JB and Berrios, L and Rodrigues, JLM and Peay, KG and Tsai, SM},
title = {Linking soil microbial genomic features to forest-to-pasture conversion in the Amazon.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156124},
doi = {10.1128/spectrum.01561-24},
pmid = {40042334},
issn = {2165-0497},
abstract = {Amazonian soil microbial communities are known to be altered by land-use change. However, attempts to understand these impacts have focused on broader community alterations or the response of specific microbial groups. Here, we recovered and characterized 69 soil bacterial and archaeal metagenome-assembled genomes (MAGs) from three forests and three pastures of the Eastern Brazilian Amazon and evaluated the impacts of land conversion on their genomic features. Pasture MAGs had significantly higher GC content (64.9% vs 60.2%), genome size (4.0 vs 3.1 Mbp), and number of coding sequences (4,058 vs 3,306) compared to forest genomes. Taxonomically, MAGs belonged to eight phyla; however, most (90%) had low similarity to previously known species, indicating potentially novel taxa at multiple levels. We also observed that the functional profiles associated with biogeochemical cycling and carbohydrate-active enzyme genes were impacted by forest conversion, with pasture MAGs exhibiting a notably higher number of both gene groups. Together, these data constitute the largest single-sourced genomic data set from upland soils of the Brazilian Amazon to date and increase the known MAG richness in these soils by 78%. Our data, therefore, not only add to a neglected yet emerging field but, importantly, highlight that land-use change has drastic impacts on the genomic characteristics and functional traits of dominant soil microbes.IMPORTANCEThe Brazilian Amazon is facing unprecedented threats, including increasing deforestation and degradation, which together impact half of the original forest area. Soil microorganisms are sensitive indicators of land-use change, linked to a rise in microbial methane emissions and antibiotic-resistance genes in the Amazon. However, most Amazonian soil microbes remain unknown, and little attention has been given to their genomes. Using sequencing and bioinformatics, we recovered and characterized 69 soil bacterial and archaeal genomes (metagenome-assembled genomes). These abundant members of the microbial communities diverged across forests and pastures in terms of taxonomic and functional traits. Forest conversion favors organisms with specific genomic features - increased GC content, genome size, and gene number - selecting for microorganisms that can thrive under altered conditions. Our paper helps us understand the intricate relationships between microbes and the environment, which are crucial pieces of information for comprehensive soil health assessments and future policy formulation.},
}

@article {pmid40042126,
year = {2025},
author = {Hayden, HS and Nelson, MT and Ross, SE and Verster, AJ and Bouzek, DC and Eng, A and Waalkes, A and Penewit, K and Kopp, BT and Siracusa, C and Rock, MJ and Salipante, SJ and Hoffman, LR and Sanders, DB},
title = {Effects of Therapeutic Antibiotic Exposure on the Oropharyngeal and Fecal Microbiota in Infants With Cystic Fibrosis.},
journal = {Pediatric pulmonology},
volume = {60},
number = {3},
pages = {e71024},
doi = {10.1002/ppul.71024},
pmid = {40042126},
issn = {1099-0496},
support = {//This work was supported by the Cystic Fibrosis Foundation (CFF; SANDER16Y5, SANDER18A0-I) and the National Institutes of Health (NIH; NIH NHLBI K24HL141669)./ ; },
mesh = {Humans ; *Cystic Fibrosis/microbiology/drug therapy ; *Feces/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; Infant ; *Oropharynx/microbiology ; Male ; Female ; *Microbiota/drug effects ; beta-Lactams/pharmacology/therapeutic use ; Bacterial Load/drug effects ; Longitudinal Studies ; },
abstract = {BACKGROUND: Systemic antibiotics can impact all microbes inhabiting patients, regardless of the intended target organism(s). We studied the simultaneous effects on respiratory and fecal microbiomes of β-lactam antibiotics administered for respiratory symptoms in infants with cystic fibrosis (IWCF).

OBJECTIVE: To compare the magnitude and duration of intended (respiratory) and unintended (fecal) antimicrobial action by analyzing oropharyngeal (OP) and fecal microbiota in IWCF.

DESIGN: Shotgun metagenomic sequencing and qPCR were performed on OP and fecal samples collected longitudinally from 14 IWCF (ages 1-17 months) during ("On Antibiotics") and after ("Off Antibiotics") β-lactam therapy, and from 5 IWCF (3-16 months) never treated with antibiotics.

RESULTS: Total bacterial loads (TBL) for On Antibiotics samples were lower than for both Never (OP and fecal) and Off Antibiotics samples (fecal only). α-diversities (within-sample) for OP On Antibiotics samples were lower than for Never and Off Antibiotics samples but did not differ between fecal sample groups. β-diversity (between-sample) differed between all OP sample groups and between fecal On and Never Antibiotics and Off and Never antibiotics samples; however, fecal On and Off Antibiotics sample β-diversities did not differ. Patterns of change in antibiotic resistance gene abundances reflected shifts in microbial community composition.

CONCLUSIONS: β-lactam antibiotic exposure was followed by marked alterations in both OP and fecal microbiota. While microbiota appeared to rebound after treatment in both sample types, our results suggest that fecal microbiota recovered less than OP. The clinical consequences of these findings should be studied in IWCF and other populations frequently treated with antibiotics.},
}

Humans
*Cystic Fibrosis/microbiology/drug therapy
*Feces/microbiology
*Anti-Bacterial Agents/therapeutic use/pharmacology
Infant
*Oropharynx/microbiology
Male
Female
*Microbiota/drug effects
beta-Lactams/pharmacology/therapeutic use
Bacterial Load/drug effects
Longitudinal Studies

@article {pmid40041876,
year = {2025},
author = {Zhang, Y and Peng, J and Wang, Z and Zhou, F and Yu, J and Chi, R and Xiao, C},
title = {Metagenomic analysis revealed the bioremediation mechanism of lead and cadmium contamination by modified biochar synergized with Bacillus cereus PSB-2 in phosphate mining wasteland.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1529784},
pmid = {40041876},
issn = {1664-302X},
abstract = {INTRODUCTION: Phosphate mining wasteland is contaminated with heavy metals, such as lead (Pb) and cadmium (Cd), which pose significant environmental risks. Ecological restoration of these lands is crucial, but limited research has focused on the remediation of heavy metal-contaminated soils using modified biochar and functional microorganisms.

METHODS: In this study, we investigated the bioremediation of phosphate mining wasteland soil using modified biochar in combination with the phosphate-solubilizing bacterium Bacillus cereus. The effects of this synergistic approach on soil nutrient content, heavy metal immobilization, and microbial community structure were assessed.

RESULTS AND DISCUSSION: The results indicated that the available phosphate content in the soil increased by 59.32%. The content of extractable state Pb[2 +] and Cd[2 +] decreased by 65.06 and 71.26%, respectively. And the soil nutrient conditions were significantly improved. Synergistic remediation can significantly increase the diversity and abundance of soil microbial communities (p < 0.05). Janibacter, Lysobacter, Ornithinimicrobium, Bacillus, and Salinimicrobium were the main functional flora during soil remediation, with significant correlations for the promotion of Pb[2 +] and Cd[2 +] immobilization and the increase of available phosphate and organic matter. ZitB, czcD, zntA, and cmtR are the major heavy metal resistance genes and regulate metabolic pathways to make microbial community function more stable after soil remediation in phosphate mining wasteland.},
}

@article {pmid40041864,
year = {2025},
author = {Brick, S and Niggemann, J and Reckhardt, A and Könneke, M and Engelen, B},
title = {Interstitial microbial communities of coastal sediments are dominated by Nanoarchaeota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1532193},
pmid = {40041864},
issn = {1664-302X},
abstract = {Microbial communities in subsurface coastal sediments are highly diverse and play an important role in nutrient cycling. While the major fraction of microorganisms in sandy sediments lives as epipsammon (attached to sand grains), only a small fraction thrives in the interstitial porewaters. So far, little is known about the composition of these free-living microbial communities. In the subsurface of the sandy beach, investigated in this study, we compared the archaeal and bacterial community structures within sediments and corresponding porewaters applying 16S rRNA gene sequencing. We found that the free-living prokaryotes only had a proportion of about 0.2-2.3% of the bulk communities, depending on the pore space. The interstitial microbial communities showed a small overlap with the attached fraction of 4-7% ASVs, and comprised a unique composition of 75-81% ASVs found exclusively in the porewaters. They were more diverse than the respective sediment-attached fraction and showed a much higher archaea-to-bacteria ratio. The archaea were mainly affiliated to Nanoarchaeota of the DPANN superphylum, with a relative abundance up to 50% of the interstitial communities. The bacterial fraction included several species related to the Candidate Phyla Radiation (CPR). Both prokaryotic lineages are known to have small cell sizes, comprising not-yet cultured species with unidentified metabolic functions. Our findings were supported by the investigation of an adjacent tidal flat, showing a similar trend. Thus, our results indicate the presence of distinct interstitial microbial communities in the subsurface of coastal sediments. This natural enrichment of not-yet cultured Nanoarchaeota and members of the CPR provides the opportunity for targeted metagenomic analyses or even isolating members of these groups for further metabolic characterization.},
}

@article {pmid40041703,
year = {2025},
author = {Sato, Y},
title = {Rumen DNA virome in beef cattle reveals an unexplored diverse community with potential links to carcass traits.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf021},
pmid = {40041703},
issn = {2730-6151},
abstract = {Rumen deoxyribonucleic acid viruses that infect and replicate within bacteria and archaea are key modulators of the prokaryotic community. These viruses influence prokaryotic community abundance, composition, and function impacting host productivity and methane production. In this study, viral genomes were assembled from the rumen of 37 Japanese Black cattle using virus-like particle metagenome sequencing, providing insights into viral diversity, functional potential, and virus-host interactions. The relationship between the rumen deoxyribonucleic acid virome and carcass traits, particularly carcass weight and marbling, was also investigated. A total of 22 942 viral operational taxonomic units of medium-quality or higher (≥5 kb length and ≥ 50% completeness), referred to as Japanese Black Rumen Viral genomes, were reconstructed. Among these, 5973 putative novel genera were identified, significantly expanding the catalog of rumen viral genomes. Hosts were predicted for 2364 viral operational taxonomic units, including carbohydrate-degrading bacteria and methanogens. Additionally, 27 auxiliary metabolic genes were categorized as glycosyl hydrolases which are responsible for the degradation of cellulose, hemicellulose, and oligosaccharides, suggesting that rumen viruses may enhance the breakdown of complex carbohydrates during infection. Furthermore, the rumen virome differed considerably between high vs low carcass weight cattle and high vs low marbling cattle. Viruses associated with Methanobrevibacter were linked to higher carcass weight. This database and the insights from this study provide primary information for the development and improvement of beef production.},
}

@article {pmid40041700,
year = {2025},
author = {Wang, X and Cao, D and Zhang, H and Chen, W and Sun, J and Hu, H},
title = {Utilizing metagenomic profiling and machine learning model to identify bacterial biomarkers for major depressive disorder.},
journal = {Frontiers in psychiatry},
volume = {16},
number = {},
pages = {1539596},
pmid = {40041700},
issn = {1664-0640},
abstract = {BACKGROUND: Major depressive disorder (MDD) is highly heterogeneous, which provides a significant challenge in the management of this disorder. However, the pathogenesis of major depressive disorder is not fully understood. Studies have shown that depression is highly correlated with gut flora. The objective of this study was to explore the potential of microbial biomarkers in the diagnosis of major depressive disorder.

METHODS: In this study, we used a metagenomic approach to analyze the composition and differences of gut bacterial communities in 36 patients with major depressive disorder and 36 healthy individuals. We then applied a Support Vector Machine Recursive Feature Elimination (SVM-RFE) machine learning model to find potential microbial markers.

RESULTS: Our results showed that the alpha diversity of the intestinal flora did not differ significantly in major depressive disorder compared to healthy populations. However, the beta diversity was significantly altered. Machine learning identified 8 MDD-specific bacterial biomarkers, with Alistipes, Dysosmobacter, Actinomyces, Ruthenibacterium, and Thomasclavelia being significantly enriched, while Faecalibacterium, Pseudobutyrivibrio, and Roseburia were significantly reduced, demonstrating superior diagnostic accuracy (area under the curve, AUC = 0.919). In addition, the gut bacteria performed satisfactorily in the validation cohort with an AUC of 0.800 (95% CI: 0.6334-0.9143).

CONCLUSION: This study reveals the complex relationship between gut microbiota and major depressive disorder and provides a scientific basis for the development of a microbiota-based diagnostic tool for depression.},
}

@article {pmid40041441,
year = {2025},
author = {Xu, C and Shen, Y and Chen, S and Liu, T and Chen, X and Yu, Y and Liu, L and Ma, R and Zhang, L and Liu, X and Zhou, L and Zhu, G and Feng, S},
title = {Effect of Interpretation of Positive Metagenomic Next-Generation Sequencing Reports on the Infection Diagnosis in Patients With Hematological Disorders.},
journal = {Open forum infectious diseases},
volume = {12},
number = {2},
pages = {ofaf076},
pmid = {40041441},
issn = {2328-8957},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has become a crucial diagnostic tool for infectious diseases in patients with hematological disorders. However, despite the abundant microbial information provided by positive mNGS reports, interpreting these results remains challenging due to the lack of standardized criteria.

METHODS: We surveyed 92 clinicians to identify common challenges in understanding mNGS reports. Microbiologists then provided additional "report interpretation cards" (RICs) for positive mNGS results alongside original reports. The aim of using RICs was to determine whether each detected microorganism was likely cause of infection. After a 3-month period, a panel of clinical experts retrospectively reviewed 281 cases, involving 728 detected microorganisms, to assess RIC accuracy.

RESULTS: In total, 82.6% of clinicians (76 of 92) experienced difficulties in interpreting mNGS reports. After receiving RICs, 97.8% of clinicians (90 of 92) reported satisfaction. The overall concordance rates between interpretation and adjudication in the 281 cases was 79.0% (222 of 281). In 203 cases in which multiple microorganisms were detected, 37.9% (77 of 203) and 37.4% (76 of 203) were interpreted and adjudicated as mixed infections. Among the 728 microorganisms, interpretation and adjudication revealed concordance rates of 93.9% (154 of 164), 95.7% (88 of 92), and 72.3% (339 of 469) for bacterial, fungal, and viral infections, respectively. In 68.7% of the cases (193 of 281), mNGS positively influenced pathogen diagnosis.

CONCLUSIONS: Not all microorganisms detected by mNGS are responsible for infection, and appropriate interpretation is essential. The provision of interpretations by microbiologists aids clinicians in accurately using mNGS for infection diagnosis.},
}

@article {pmid40040800,
year = {2025},
author = {He, J and Ye, L and Xu, H and Yang, H and Shen, J and Li, M and Weng, S and Jiao, D and Chu, C and Liao, Q and Zou, H and Zhu, J and Wang, C and Xu, X},
title = {Multi-omics analysis reveals a novel NFE2L3 variant impairing choroidal vasculature development in high myopia and myopic maculopathy.},
journal = {National science review},
volume = {12},
number = {2},
pages = {nwae291},
pmid = {40040800},
issn = {2053-714X},
}

@article {pmid40040609,
year = {2025},
author = {Liu, FQ and An, ZY and Cui, LJ and Xiao, MY and Wu, YJ and Li, W and Zhang, BS and Yu, L and Feng, J and Liu, ZG and Feng, R and Jiang, ZX and Huang, RB and Jing, HM and Ren, JH and Zhu, XY and Cheng, YF and Li, YH and Zhou, HB and Gao, D and Liu, Y and Yu, F and Wang, X and Qiao, JL and Hu, DH and Wang, LL and Zang, MT and Chen, Q and Qu, QY and Zhou, JY and Li, ML and Chen, YX and Huang, QS and Fu, HX and Li, YY and Wang, QF and Huang, XJ and Zhang, XH and , },
title = {Correlation Between Fecal Microbiota and Corticosteroid Responsiveness in Primary Immune Thrombocytopenia: an Exploratory Study.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2410417},
doi = {10.1002/advs.202410417},
pmid = {40040609},
issn = {2198-3844},
support = {2023YFC2507803//Key Technologies Research and Development Program/ ; 82300149//National Natural Science Foundation of China/ ; 82130008//National Natural Science Foundation of China/ ; 82230004//National Natural Science Foundation of China/ ; 82350004//National Natural Science Foundation of China/ ; 82430006//National Natural Science Foundation of China/ ; 2024M761208//China Postdoctoral Science Foundation/ ; 2023ZB182//Department of Human Resources and Social Security of Jiangsu Province/ ; 2022-1-4082//Capital Health Research and Development of Special Fund/ ; 7242154//Natural Science Foundation of Beijing Municipality/ ; 7232188//Natural Science Foundation of Beijing Municipality/ ; 71003Y3035//Peking University Medicine/ ; },
abstract = {Corticosteroids (CSs) are the initial therapy for immune thrombocytopenia (ITP); however, their efficacy is not adequately predicted. As a novel biomarker, the composition of the gut microbiota is non-invasively tested and altered in patients with ITP. This study aims to develop a predictive model that leverages gut microbiome data to predict the CS response in patients with ITP within the initial four weeks of treatment. Metagenomic sequencing is performed on fecal samples from 212 patients with ITP, 152 of whom underwent CS treatment and follow-up. Predictive models are trained using six machine-learning algorithms, integrating clinical indices and gut microbiome data. The support vector machine (SVM) algorithm-based model has the highest accuracy (AUC = 0.80). This model utilized a comprehensive feature set that combined clinical data (including sex, age, duration, platelet count, and bleeding scales) with selected microbial species (including Bacteroides ovatus, Bacteroides xylanisolvens, and Parabacteroides gordonii), alpha diversities, KEGG pathways, and microbial modules. This study will provide new ideas for the prediction of clinical CS efficacy, enabling informed decision-making regarding the initiation of CS or personalized treatment in patients with ITP.},
}

@article {pmid40040342,
year = {2025},
author = {Ren, M and Hu, A and Zhao, Z and Yao, X and Kimirei, IA and Zhang, L and Wang, J},
title = {Trait-environmental relationships reveal microbial strategies of environmental adaptation.},
journal = {Ecology},
volume = {106},
number = {3},
pages = {e70047},
doi = {10.1002/ecy.70047},
pmid = {40040342},
issn = {1939-9170},
support = {BK20240111//Basic Research Program of Jiangsu/ ; 067GJHZ2023034MI//the International Collaboration Program of Chinese Academy of Sciences/ ; 151542KYSB20210007//the International Collaboration Program of Chinese Academy of Sciences/ ; SAJC202403//the International Collaboration Program of Chinese Academy of Sciences/ ; 42002304//National Natural Science Foundation of China/ ; 42107445//National Natural Science Foundation of China/ ; 42225708//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; 92251304//National Natural Science Foundation of China/ ; 92351303//National Natural Science Foundation of China/ ; },
mesh = {*Lakes/microbiology ; *Adaptation, Physiological ; *Bacteria/classification/genetics ; Bacterial Physiological Phenomena ; Microbiota ; Hydrogen-Ion Concentration ; },
abstract = {Microbial trait variation along environmental gradients is crucial to understanding their ecological adaptation mechanisms. With the increasing availability of microbial genomes, making full use of the genome-based traits to decipher their adaptation strategies becomes promising and urgent. Here, we examined microbial communities in water and sediments of 20 East African lakes with pH values ranging from 7.2 to 10.1 through taxonomic profiling and genome-centric metagenomics. We identified functional traits important for microbial adaptation to the stresses of alkalinity and salinity based on the significant trait-environment relationships (TERs), including those involved in cytoplasmic pH homeostasis, compatible solute accumulation, cell envelope modification, and energy requisition. By integrating these significant traits, we further developed an environmental adaptation index to quantify the species-level adaptive capacity for environmental stresses, such as high pH environments. The adaptation index of pH showed consistently significant positive relationships with species pH optima across regional and global genomic datasets from freshwater, marine, and soda lake ecosystems. The generality of the index for quantifying environmental adaptation was demonstrated by showing significant relationships with the species niche optima for the gradients of soil temperature and seawater salinity. These results highlight the importance of TERs in facilitating the inference of microbial genomic-based adaptation mechanisms and expand our understanding of ecological adaptive strategies along environmental gradients.},
}

*Lakes/microbiology
*Adaptation, Physiological
*Bacteria/classification/genetics
Bacterial Physiological Phenomena
Microbiota
Hydrogen-Ion Concentration

@article {pmid40038896,
year = {2025},
author = {Zhang, H and Ruan, Y and Kuzyakov, Y and Sun, H and Huang, Q and Guo, S and Shen, Q and Ling, N},
title = {Viruses Facilitate Energy Acquisition Potential by Their Bacterial Hosts in Rhizosphere of Grafted Plants.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15458},
pmid = {40038896},
issn = {1365-3040},
support = {//This study was supported by the National Nature Science Foundation of China (32302670) and Nanjing Agricultural University (XUEKEN2023039)./ ; },
abstract = {Viruses alter the ecological and evolutionary trajectories of bacterial host communities. Plant grafting is a technique that integrates two species or varietiies and have consequences on the rhizosphere functioning. The grafting effects on the taxonomic and functional assembly of viruses and their bacterial host in the plant rhizosphere remain largely elusive. Using shotgun metagenome sequencing, we recover a total of 1441 viral operational taxonomic units from the rhizosphere of grafted and ungrafted plants after 8-year continuous monoculture. In the grafted and ungrafted rhizosphere, the Myoviridae, Zobellviridae and Kyanoviridae emerged as the predominant viral families, collectively representing around 40% of the viral community in each respective environment. Grafting enriched the members in viral family Kyanoviridae, Tectiviridae, Peduoviridae and Suoliviridae, and auxiliary metabolic genes related to pyruvate metabolism and energy acquisition (e.g., gloB, DNMT1 and dcyD). The virus-bacterial interactions increased the rapid growth potential of bacteria, which explains the strong increase in abundance of specific bacterial hosts (i.e., Chitinophagaceae, Cyclobacteriaceae and Spirosomaceae) in the grafted-plant rhizosphere. Overall, these results deepen our understanding of microbial community assembly and ecological services from the perspective of virus-host interactions.},
}

@article {pmid40038838,
year = {2025},
author = {Thiruppathy, D and Moyne, O and Marotz, C and Williams, M and Navarro, P and Zaramela, L and Zengler, K},
title = {Absolute quantification of the living skin microbiome overcomes relic-DNA bias and reveals specific patterns across volunteers.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {65},
pmid = {40038838},
issn = {2049-2618},
support = {S10 OD026929/NH/NIH HHS/United States ; S10 OD026929/NH/NIH HHS/United States ; },
mesh = {Humans ; *Skin/microbiology ; *Microbiota/genetics ; *DNA, Bacterial/genetics ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Bacterial Load ; Healthy Volunteers ; Adult ; Female ; Male ; },
abstract = {BACKGROUND: As the first line of defense against external pathogens, the skin and its resident microbiota are responsible for protection and eubiosis. Innovations in DNA sequencing have significantly increased our knowledge of the skin microbiome. However, current characterizations do not discriminate between DNA from live cells and remnant DNA from dead organisms (relic DNA), resulting in a combined readout of all microorganisms that were and are currently present on the skin rather than the actual living population of the microbiome. Additionally, most methods lack the capability for absolute quantification of the microbial load on the skin, complicating the extrapolation of clinically relevant information.

RESULTS: Here, we integrated relic-DNA depletion with shotgun metagenomics and bacterial load determination to quantify live bacterial cell abundances across different skin sites. Though we discovered up to 90% of microbial DNA from the skin to be relic DNA, we saw no significant effect of this on the relative abundances of taxa determined by shotgun sequencing. Relic-DNA depletion prior to sequencing strengthened underlying patterns between microbiomes across volunteers and reduced intraindividual similarity. We determined the absolute abundance and the fraction of population alive for several common skin taxa across body sites and found taxa-specific differential abundance of live bacteria across regions to be different from estimates generated by total DNA (live + dead) sequencing.

CONCLUSIONS: Our results reveal the significant bias relic DNA has on the quantification of low biomass samples like the skin. The reduced intraindividual similarity across samples following relic-DNA depletion highlights the bias introduced by traditional (total DNA) sequencing in diversity comparisons across samples. The divergent levels of cell viability measured across different skin sites, along with the inconsistencies in taxa differential abundance determined by total vs live cell DNA sequencing, suggest an important hypothesis for certain sites being susceptible to pathogen infection. Overall, our study demonstrates a characterization of the skin microbiome that overcomes relic-DNA bias to provide a baseline for live microbiota that will further improve mechanistic studies of infection, disease progression, and the design of therapies for the skin. Video Abstract.},
}

Humans
*Skin/microbiology
*Microbiota/genetics
*DNA, Bacterial/genetics
*Bacteria/classification/genetics/isolation & purification
*Metagenomics/methods
Sequence Analysis, DNA/methods
Bacterial Load
Healthy Volunteers
Adult
Female
Male

@article {pmid40038823,
year = {2025},
author = {Liu, F and Yang, J and Shen, W and Fu, J and Meng, J and Zhang, Y and Li, J and Yuan, Z},
title = {Effects of drainage and long-term tillage on greenhouse gas fluxes in a natural wetland: insights from microbial mechanisms.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {26},
pmid = {40038823},
issn = {2524-6372},
support = {No. ES202308//Open Project of State Key Laboratory of Urban Water Resource and Environment/ ; No. 2024M763244//China Postdoctoral Science Foundation/ ; No. 242300421652//Natural Science Foundation of Henan Province/ ; No. 30501300//Top Talent Foundation of Henan Agricultural University/ ; },
abstract = {BACKGROUND: The conversion of natural wetlands to agricultural land through drainage contributes to 62% of the global wetland loss. Such conversion significantly alters greenhouse gas (GHG) fluxes, yet the underlying mechanisms of GHG fluxes resulting from drainage and long-term tillage practices remain highly uncertain. In this study, we measured GHG fluxes of a natural reed wetland (referred to as "Wetland") and a drained wetland that used as farmland (referred to as "Dryland").

RESULTS: The results demonstrated that annual cumulative N2O and CO2 fluxes in Dryland were 282.77% and 53.79% higher than those in Wetland, respectively. However, CH4 annual cumulative fluxes decreased from 12,669.45 ± 564.69 kg·ha[- 1] to 8,238.40 ± 207.72 kg·ha[- 1] in Dryland compared to Wetland. The global warming potential (GWP) showed no significant difference between Dryland and Wetland, with comparable average rates of 427.50 ± 48.83 and 422.21 ± 73.59 mg·CO2-eq·m[- 2]·h[- 1], respectively. Metagenomic analysis showed a decrease in the abundance of acetoclastic methanogens and their functional genes responsible for CH4 production. Functional genes related to CH4 oxidation (pmoA) and gene related to N2O reduction (nosZ) exhibited a substantial sensitivity to variations in TOC concentration (p < 0.05). Candidatus Methylomirabilis, belonging to the NC10 phylum, was identified as the dominant methanotroph and accounted for 49.26% of the methanotrophs. Its relative abundance was significantly higher in Dryland than in Wetland, as the nitrogenous fertilizer applied in Dryland acted as an electron acceptor, with the nearby Wetland produced CH4 serving as an electron donor. This suggests that Dryland may act as a CH4 sink, despite the significant enhancement in CO2 and N2O fluxes.

CONCLUSIONS: In conclusion, this study provides insights into the influence of drainage and long-term tillage on GHG fluxes in wetlands and their contribution to global warming.},
}

@article {pmid40038809,
year = {2025},
author = {Reyes, G and Betancourt, I and Andrade, B and Pozo, Y and Sorroza, L and Trujillo, LE and Bayot, B},
title = {Genomic sequence data of Thiohalocapsa marina: a sulfur-oxidizing bacterium prevalent in treated municipal wastewater and commercial shrimp hatchery effluents.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {97},
pmid = {40038809},
issn = {1756-0500},
mesh = {*Wastewater/microbiology ; Animals ; *Genome, Bacterial ; *Sulfur/metabolism ; Oxidation-Reduction ; Biodegradation, Environmental ; Chlorobi/genetics/metabolism ; Aquaculture ; Penaeidae/microbiology ; Phylogeny ; },
abstract = {OBJECTIVES: This study highlighted the gap in the genetic characterization of marine bacteria, specifically within the genus Thiohalocapsa. This genus thrives in contaminated environments with high concentrations of sulfide, such as treated municipal wastewater. Thc. marina is a phototrophic purple bacterium known for its role in sulfur oxidation and bioremediation in marine aquaculture systems. To date, only one Thc. marina genome has been published in the GenBank database. This study enhances the understanding of the ecological adaptation and bioremediation capabilities of Thc. marina in treated municipal wastewater effluents.

DATA DESCRIPTION: We present a draft genome of Thc. marina LNA26 recovered from treated municipal wastewater effluents using shotgun metagenomic sequencing. The genome of Thc. marina LNA26 harbors 4,356,720 bp and contains 4,032 genes (3,936 CDSs, 50 RNA genes, and 46 pseudogenes), some of them involved in sporulation, siderophores biosynthesis, arsenate bioremediation, sulfide metabolism, capacity for nitrogen fixation, the biosynthesis of PHA, and NHPL bacteriocins. Thc. marina LNA26 exhibits 3 CRISPR Arrays and a high abundance of COGs in signal transduction, energy production, and cell wall biogenesis, indicating advanced environmental responsiveness, energy efficiency, and cellular robustness.},
}

*Wastewater/microbiology
Animals
*Genome, Bacterial
*Sulfur/metabolism
Oxidation-Reduction
Biodegradation, Environmental
Chlorobi/genetics/metabolism
Aquaculture
Penaeidae/microbiology
Phylogeny

@article {pmid40038603,
year = {2025},
author = {Gao, M and Zhong, S and Han, G and Kuang, D and Yun, C and Fu, C},
title = {Atypical rat bite fever associated with knee joint infection in a Chinese patient: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {312},
pmid = {40038603},
issn = {1471-2334},
mesh = {*Rat-Bite Fever/microbiology/diagnosis/drug therapy ; Humans ; *Streptobacillus/isolation & purification/genetics ; *Knee Joint/microbiology/pathology ; Animals ; Male ; *Anti-Bacterial Agents/therapeutic use ; *RNA, Ribosomal, 16S/genetics ; Synovial Fluid/microbiology ; Arthroscopy ; China ; Middle Aged ; Rats ; East Asian People ; },
abstract = {BACKGROUND: Rat bite fever (RBF) is a rare zoonosis transmitted from rodents to humans through bites and scratches. However, diagnosis and treatment of atypical clinical cases can be challenging.

CASE PRESENTATION: Herein, we report an atypical case of RBF with unilateral knee joint infection caused by Streptobacillus moniliformis. Streptobacillus moniliformis was isolated from the knee synovial fluid of the patient via microbiological culture and metagenomic next-generation sequencing (mNGS). After treatment with antibiotics and arthroscopic surgery, the patient reported symptom alleviation and was subsequently discharged home. This is the first reported detection of intraarticular histopathological changes caused by Streptobacillus moniliformis during knee arthroscopy.

CONCLUSIONS: In atypical cases, importantly, clinical healthcare professionals should promptly obtain microbiological culture results. When culture is negative, 16S ribosomal RNA gene polymerase chain reaction (16S rRNA PCR) or mNGS can be considered for identification, with inquiring about the patient's disease history, including any contact with rodents. Surgical interventions, such as arthroscopy, may be included in treatment. Streptobacillus moniliformis infection should be considered when considerable fibrous connective tissue and capillary proliferation are observed under arthroscopic guidance.},
}

*Rat-Bite Fever/microbiology/diagnosis/drug therapy
Humans
*Streptobacillus/isolation & purification/genetics
*Knee Joint/microbiology/pathology
Animals
Male
*Anti-Bacterial Agents/therapeutic use
*RNA, Ribosomal, 16S/genetics
Synovial Fluid/microbiology
Arthroscopy
China
Middle Aged
Rats
East Asian People

@article {pmid40038315,
year = {2025},
author = {Chen, Y and Chen, S and Tao, J and Li, M and Wang, W and Chen, M and Fang, X and Kong, L and Wang, Y and Pereira, O and Zhang, C},
title = {Multi-omic stock of surface ocean microbiome built by monthly, weekly and daily sampling in Dapeng Bay, China.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {378},
pmid = {40038315},
issn = {2052-4463},
support = {32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42321004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92351301//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32393974//National Natural Science Foundation of China (National Science Foundation of China)/ ; RCBS20221008093229035//Shenzhen Science and Technology Innovation Commission/ ; 92351301//École Nationale d'Ingénieurs de Saint-Etienne (National Engineering School of Saint-Étienne)/ ; },
mesh = {China ; *Microbiota ; *Archaea/genetics ; *Bacteria/genetics/classification ; *Bays ; Seawater/microbiology ; Metagenome ; Multiomics ; },
abstract = {The coastal ocean is the dynamic interface where terrestrial, atmospheric, and marine systems converge, acting as a hotspot for microbial activity, which underpins the intricate web of carbon and nitrogen cycling. Dapeng Bay, a typical semi-enclosed bay along the southern coastline of China, is strongly influenced by monsoon climates and human activities. Despite its ecological importance, long-term observations and investigations into the microbial community structure in this region are notably lacking. To address this gap, we conducted a two-year continuous sampling from May 2021 to June 2023 to explore shifts in nearshore surface microbial communities and assess the long-term effects of environmental stressors. This study presents comprehensive amplicon, metagenomic, and metatranscriptomic information. We identified 3,600 amplicon sequence variants and recovered 1,216 high-quality metagenome-assembled MAGs, representing 17 bacterial and 3 archaeal phyla. Additionally, 587 MAGs were correlated with transcriptional activity, comprising 539 bacterial and 48 archaeal populations. This dataset is anticipated to provide a multi-dimensional perspective, enhancing our understanding of the complexity, dynamics, and adaptability of microbial communities in coastal environments.},
}

China
*Microbiota
*Archaea/genetics
*Bacteria/genetics/classification
*Bays
Seawater/microbiology
Metagenome
Multiomics

@article {pmid38892504,
year = {2024},
author = {Duysburgh, C and Govaert, M and Guillemet, D and Marzorati, M},
title = {Co-Supplementation of Baobab Fiber and Arabic Gum Synergistically Modulates the In Vitro Human Gut Microbiome Revealing Complementary and Promising Prebiotic Properties.},
journal = {Nutrients},
volume = {16},
number = {11},
pages = {},
pmid = {38892504},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome ; *Prebiotics ; *Gum Arabic/therapeutic use ; *Adansonia ; *Plant Preparations/therapeutic use ; Metabolome ; Metagenome ; Colon/microbiology ; },
abstract = {Arabic gum, a high molecular weight heteropolysaccharide, is a promising prebiotic candidate as its fermentation occurs more distally in the colon, which is the region where most chronic colonic diseases originate. Baobab fiber could be complementary due to its relatively simple structure, facilitating breakdown in the proximal colon. Therefore, the current study aimed to gain insight into how the human gut microbiota was affected in response to long-term baobab fiber and Arabic gum supplementation when tested individually or as a combination of both, allowing the identification of potential complementary and/or synergetic effects. The validated Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]), an in vitro gut model simulating the entire human gastrointestinal tract, was used. The microbial metabolic activity was examined, and quantitative 16S-targeted Illumina sequencing was used to monitor the gut microbial composition. Moreover, the effect on the gut microbial metabolome was quantitatively analyzed. Repeated administration of baobab fiber, Arabic gum, and their combination had a significant effect on the metabolic activity, diversity index, and community composition of the microbiome present in the simulated proximal and distal colon with specific impacts on Bifidobacteriaceae and Faecalibacterium prausnitzii. Despite the lower dosage strategy (2.5 g/day), co-supplementation of both compounds resulted in some specific synergistic prebiotic effects, including a biological activity throughout the entire colon, SCFA synthesis including a synergy on propionate, specifically increasing abundance of Akkermansiaceae and Christensenellaceae in the distal colon region, and enhancing levels of spermidine and other metabolites of interest (such as serotonin and ProBetaine).},
}

*Gastrointestinal Microbiome
*Prebiotics
*Gum Arabic/therapeutic use
*Adansonia
*Plant Preparations/therapeutic use
Metabolome
Metagenome
Colon/microbiology

@article {pmid40038282,
year = {2025},
author = {Li, Z and Riley, WJ and Marschmann, GL and Karaoz, U and Shirley, IA and Wu, Q and Bouskill, NJ and Chang, KY and Crill, PM and Grant, RF and King, E and Saleska, SR and Sullivan, MB and Tang, J and Varner, RK and Woodcroft, BJ and Wrighton, KC and , and Brodie, EL},
title = {A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {2186},
pmid = {40038282},
issn = {2041-1723},
support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; SCW1746//DOE | Office of Science (SC)/ ; DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; (#FP00005182//DOE | Office of Science (SC)/ ; 2022070//National Science Foundation (NSF)/ ; },
mesh = {*Ecosystem ; *Methane/metabolism ; *Genomics/methods ; *Microbiota/genetics ; Arctic Regions ; Metagenomics/methods ; Wetlands ; Greenhouse Gases/metabolism ; Climate Change ; Bacteria/genetics/metabolism/classification ; },
abstract = {Microbes drive the biogeochemical cycles of earth systems, yet the long-standing goal of linking emerging genomic information, microbial traits, mechanistic ecosystem models, and projections under climate change has remained elusive despite a wealth of emerging genomic information. Here we developed a general genome-to-ecosystem (G2E) framework for integrating genome-inferred microbial kinetic traits into mechanistic models of terrestrial ecosystems and applied it at a well-studied Arctic wetland by benchmarking predictions against observed greenhouse gas emissions. We found variation in genome-inferred microbial kinetic traits resulted in large differences in simulated annual methane emissions, quantitatively demonstrating that the genomically observable variations in microbial capacity are consequential for ecosystem functioning. Applying microbial community-aggregated traits via genome relative-abundance-weighting gave better methane emissions predictions (i.e., up to 54% decrease in bias) compared to ignoring the observed abundances, highlighting the value of combined trait inferences and abundances. This work provides an example of integrating microbial functional trait-based genomics, mechanistic and pragmatic trait parameterizations of diverse microbial metabolisms, and mechanistic ecosystem modeling. The generalizable G2E framework will enable the use of abundant microbial metagenomics data to improve predictions of microbial interactions in many complex systems, including oceanic microbiomes.},
}

*Ecosystem
*Methane/metabolism
*Genomics/methods
*Microbiota/genetics
Arctic Regions
Metagenomics/methods
Wetlands
Greenhouse Gases/metabolism
Climate Change
Bacteria/genetics/metabolism/classification

@article {pmid40038255,
year = {2025},
author = {Cui, B and Luo, H and He, B and Liu, X and Lv, D and Zhang, X and Su, K and Zheng, S and Lu, J and Wang, C and Yang, Y and Zhao, Z and Liu, X and Wang, X and Zhao, Y and Nie, X and Jiang, Y and Zhang, Z and Liu, C and Chen, X and Cai, A and Lv, Z and Liu, Z and An, F and Zhang, Y and Yan, Q and Kelley, KW and Xu, G and Xu, L and Liu, Q and Peng, F},
title = {Gut dysbiosis conveys psychological stress to activate LRP5/β-catenin pathway promoting cancer stemness.},
journal = {Signal transduction and targeted therapy},
volume = {10},
number = {1},
pages = {79},
pmid = {40038255},
issn = {2059-3635},
support = {82373096//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82473131//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82273480//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Low Density Lipoprotein Receptor-Related Protein-5/genetics/metabolism ; Animals ; Mice ; *Gastrointestinal Microbiome ; Humans ; *Dysbiosis/genetics/microbiology/metabolism ; Female ; *beta Catenin/genetics/metabolism ; *Stress, Psychological/genetics/microbiology/metabolism ; Neoplastic Stem Cells/metabolism/pathology ; Wnt Signaling Pathway/genetics ; Breast Neoplasms/genetics/metabolism/pathology/microbiology ; },
abstract = {Psychological stress causes gut microbial dysbiosis and cancer progression, yet how gut microbiota determines psychological stress-induced tumor development remains unclear. Here we showed that psychological stress promotes breast tumor growth and cancer stemness, an outcome that depends on gut microbiota in germ-free and antibiotic-treated mice. Metagenomic and metabolomic analyses revealed that psychological stress markedly alters the composition and abundance of gut microbiota, especially Akkermansia muciniphila (A. muciniphila), and decreases short-chain fatty acid butyrate. Supplement of active A. muciniphila, butyrate or a butyrate-producing high fiber diet dramatically reversed the oncogenic property and anxiety-like behavior of psychological stress in a murine spontaneous tumor model or an orthotopic tumor model. Mechanistically, RNA sequencing analysis screened out that butyrate decreases LRP5 expression to block the activation of Wnt/β-catenin signaling pathway, dampening breast cancer stemness. Moreover, butyrate as a HDAC inhibitor elevated histone H3K9 acetylation level to transcriptionally activate ZFP36, which further accelerates LRP5 mRNA decay by binding adenine uridine-rich (AU-rich) elements of LRP5 transcript. Clinically, fecal A. muciniphila and serum butyrate were inversely correlated with tumoral LRP5/β-catenin expression, poor prognosis and negative mood in breast cancer patients. Altogether, our findings uncover a microbiota-dependent mechanism of psychological stress-triggered cancer stemness, and provide both clinical biomarkers and potential therapeutic avenues for cancer patients undergoing psychological stress.},
}

*Low Density Lipoprotein Receptor-Related Protein-5/genetics/metabolism
Animals
Mice
*Gastrointestinal Microbiome
Humans
*Dysbiosis/genetics/microbiology/metabolism
Female
*beta Catenin/genetics/metabolism
*Stress, Psychological/genetics/microbiology/metabolism
Neoplastic Stem Cells/metabolism/pathology
Wnt Signaling Pathway/genetics
Breast Neoplasms/genetics/metabolism/pathology/microbiology

@article {pmid40038232,
year = {2025},
author = {Gohar, M and Shaheen, N and Goyal, SM and Mor, SK and Rodriguez-R, LM and Imran, M},
title = {Probiotic Potential of Yeast, Mold, and Intermediate Morphotypes of Geotrichum candidum in Modulating Gut Microbiota and Body Physiology in Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40038232},
issn = {1867-1314},
support = {No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; No: 1-8/HEC/HRD/2020/10594//Higher Education Commission (HEC), Pakistan/ ; MPC-2022-02167//OeAD-GmbH, Austria ́s Agency for Education and Internationalization/ ; MPC-2022-02167//OeAD-GmbH, Austria ́s Agency for Education and Internationalization/ ; No. PSF/CRP/C-QU/T-Helix (70)//Pakistan Science Foundation (PSF) Research/ ; },
abstract = {Geotrichum candidum, a polymorphic fungus, exists in yeast, mold, and intermediate morphotypes, each with varying genome sizes and phenotypic traits. While G. candidum has been studied as a probiotic in dairy cattle and aquaculture, the differential probiotic potential of its morphotypes has not been fully investigated; therefore, the current study was designed to investigate their impact on the modulation of physiological and gut microbial diversity in BALB/c male mice. In this study, four strains of G. candidum were used, comprising two yeast morphotypes (QAUGC01 and UCMA3730), one mold morphotype (UCMA103), and one intermediate morphotype (UCMA91). BALB/c male mice were administered G. candidum yeast, intermediate, and mold morphotypes via drinking water for 4 weeks. After 4 weeks of experimentation, the yeast morphotype (QAUGC01) notably facilitated healthy weight gain compared to other groups. This was accompanied by significant increases in red blood cell count (p = 0.01). Importantly, QAUGC01 showed no detrimental effects on kidney function, as evidenced by significantly reduced CPK levels (77.25 ± 4.87 U/L) and low cholesterol levels (64.75 ± 0.83 mg/dL). Metagenomic analysis revealed that Firmicutes, Bacteroidetes, and Proteobacteria were predominant bacterial phyla, while Ascomycota and Basidiomycota dominated the fungal populations. Lactobacillus and Bifidobacterium were prominent in the gastrointestinal tract of QAUGC01-treated mice, while Lactococcus correlated with intermediate and mold morphotypes. Predictive functional annotation (PICRUSt2) has revealed the maximum relative abundance of metabolic pathways in mold and intermediate-supplemented mice gut. In contrast, the yeast morphotype (UCMA3730) exhibited a higher metabolic pathway activity in the large intestine. Conclusively, yeast morphotypes increase beneficial bacterial diversity, including Brevibacillus and Bacillus, particularly lactic acid bacteria throughout the gastrointestinal tract. These findings suggest that different G. candidum morphotypes have distinct probiotic potentials, with implications for enhancing gut health in food and feed applications.},
}

@article {pmid40038088,
year = {2025},
author = {Leung, MBW and Chan, DYL and Fok, EKL and Yim, HCH and Jiang, X and Li, TC},
title = {Semen metagenomics and spent culture media in patients undergoing conventional in vitro fertilisation: abridged secondary publication.},
journal = {Hong Kong medical journal = Xianggang yi xue za zhi},
volume = {31 Suppl 1},
number = {1},
pages = {45-47},
pmid = {40038088},
issn = {1024-2708},
}

@article {pmid40037896,
year = {2025},
author = {Chen, N and Kishida, K and Stari, L and Moriuchi, R and Ohtsubo, Y and Damborsky, J and Nagata, Y},
title = {Haloalkane dehalogenases other than LinB can contribute to the γ-hexachlorocyclohexane utilization.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbaf022},
pmid = {40037896},
issn = {1347-6947},
abstract = {Haloalkane dehalogenases (HLDs) convert halogenated compounds to corresponding alcohols by a simple hydrolytic mechanism. Although many bacterial strains possess HLDs or HLD homologues, LinB is the only HLD known to be involved in the utilization of γ-hexachlorocyclohexane (γ-HCH), a man-made chlorinated pesticide. In this study, to gain insight into the functional evolution of HLDs toward the γ-HCH utilization, the linB gene in γ-HCH-degrading Sphingobium japonicum strain UT26 was replaced by 7 other HLD or HLD homologous genes, including 3 putative ancestral enzymes. Interestingly, strains carrying genes for DmmA from marine metagenome or Rluc_anc, an ancestor of Renilla-luciferin 2-monooxygenase (Rluc) and LinB, produced 2,5-dichlorophenol and 2,5-dichlorohydroquinone from γ-HCH, which are indicators of LinB activity, and grew in minimal medium supplied with γ-HCH as a sole carbon source. These results indicated that other HLDs in addition to LinB can play roles in the γ-HCH utilization.},
}

@article {pmid40037607,
year = {2025},
author = {Antaliya, K and Godhaniya, M and Galawala, J and Vansia, A and Mangrola, A and Ghelani, A and Patel, R},
title = {Microbial community transition in Surti buffalo-based fermented formulations sustainably enhances soil fertility and plant growth.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf030},
pmid = {40037607},
issn = {1472-765X},
abstract = {This study investigates the role of microbial dynamics during the fermentation of Buffalo dung and urine-fermented plant growth-promoting formulation, a natural biofertilizer, and its impact on plant growth and soil health. This formulation was prepared using Surti buffalo dung, urine, jaggery, gram flour, and soil and fermented for up to 14 days. Metagenomic analysis revealed microbial succession from a diverse initial community to a Bacillus-dominated population, especially the Lactic Acid Bacteria, after eight days of fermentation. The changes were accompanied by increases in the plant growth-promoting genes related to nutrient acquisition, phytohormone production, and stress resistance. The pot experiment revealed a significant increase in mung bean growth, with the maximum effect obtained from the 8th-day fermented formulation. The experiment showed considerable improvement in the physicochemical properties of soil, including increased organic carbon and nutrient availability. These findings underscore the ecological importance of microbial input preparation in enhancing soil fertility and plant growth sustainably. Future research should delve deeper into the specific mechanisms these microbes facilitate nutrient cycling and resilience in various agroclimatic conditions.},
}

@article {pmid40037564,
year = {2025},
author = {Miller, SJ and Zhang, F and Taylor, S and Woodman, R and Shoubridge, AP and Papanicolas, LE and Rogers, GB},
title = {Oropharyngeal Staphylococcus aureus is linked to higher mortality in long-term aged care residents.},
journal = {Age and ageing},
volume = {54},
number = {3},
pages = {},
doi = {10.1093/ageing/afaf042},
pmid = {40037564},
issn = {1468-2834},
support = {//Australian Medical Research Future Fund/ ; GNT1152268//Australian Department of Health/ ; //Australian Department of Health/ ; GNT119378//National Health and Medical Research Council/ ; //Matthew Flinders Professorial Fellowship/ ; GNT2008625//NHMRC Emerging Leadership/ ; },
mesh = {Humans ; Male ; Female ; *Staphylococcal Infections/mortality/microbiology/diagnosis ; Aged, 80 and over ; Aged ; *Staphylococcus aureus/isolation & purification ; *Oropharynx/microbiology ; *Homes for the Aged/statistics & numerical data ; Risk Factors ; South Australia/epidemiology ; Nursing Homes/statistics & numerical data ; Age Factors ; Long-Term Care/statistics & numerical data ; Carrier State/microbiology/diagnosis ; Time Factors ; Metagenomics ; Microbiota ; Comorbidity ; Cause of Death ; Risk Assessment ; Methicillin-Resistant Staphylococcus aureus/isolation & purification ; },
abstract = {BACKGROUND: Biological ageing, healthcare interactions, and pharmaceutical and environmental exposures in later life alter the characteristics of the oropharyngeal (OP) microbiome. These changes, including an increased susceptibility to colonisation by pathobiont species, have been linked with diverse health outcomes.

OBJECTIVES: To investigate the relationship between OP microbiome characteristics and all-cause mortality in long-term aged care residents.

METHODS: OP swabs were collected from 190 residents of five aged care facilities in South Australia. Microbiota composition was assessed by shotgun metagenomics and related to health outcomes during a 12-month follow-up period. OP carriage of Staphylococcus aureus and methicillin resistance was confirmed by qPCR.

RESULTS: OP carriage of S. aureus was identified in 13 (6.8%) residents. Detection of S. aureus was significantly associated with an increased risk of mortality (adjusted HR [95% CI]: 9.7 [3.8-24.9], P < .0001), compared with non-carriers, independent of methicillin resistance. Staphylococcus aureus carriage demonstrated a stronger association with mortality risk than the total number of comorbidities at the univariate level (S. aureus HR [95% CI]: 7.2 [3.4-15.5], P < .0001 vs. comorbidity count HR [95% CI]: 1.1 [1.0-1.3], P = .03), and remained significant after multivariable adjustment. Staphylococcus aureus detection was significantly associated with total number of comorbidities (adjusted OR [95% CI]: 1.4 [1.0-2.0], P = .04).

CONCLUSION: OP S. aureus carriage predicts all-cause mortality in long-term aged care. We speculate that S. aureus carriage represents a marker of general health, including prior healthcare exposures. OP S. aureus carriage could contribute to estimations of general health in older individuals and thereby inform care strategies.},
}

Humans
Male
Female
*Staphylococcal Infections/mortality/microbiology/diagnosis
Aged, 80 and over
Aged
*Staphylococcus aureus/isolation & purification
*Oropharynx/microbiology
*Homes for the Aged/statistics & numerical data
Risk Factors
South Australia/epidemiology
Nursing Homes/statistics & numerical data
Age Factors
Long-Term Care/statistics & numerical data
Carrier State/microbiology/diagnosis
Time Factors
Metagenomics
Microbiota
Comorbidity
Cause of Death
Risk Assessment
Methicillin-Resistant Staphylococcus aureus/isolation & purification

@article {pmid40037293,
year = {2025},
author = {Delherbe, NA and Gomez, O and Plominsky, AM and Oliver, A and Manzanera, M and Kalyuzhnaya, MG},
title = {Atmospheric methane consumption in arid ecosystems acts as a reverse chimney and is accelerated by plant-methanotroph biomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf026},
pmid = {40037293},
issn = {1751-7370},
abstract = {Drylands cover one-third of the Earth's surface and are one of the largest terrestrial sinks for methane. Understanding the structure-function interplay between members of arid biomes can provide critical insights into mechanisms of resilience toward anthropogenic and climate-change-driven environmental stressors-water scarcity, heatwaves, and increased atmospheric greenhouse gases. This study integrates in situ measurements with culture-independent and enrichment-based investigations of methane-consuming microbiomes inhabiting soil in the Anza-Borrego Desert, a model arid ecosystem in Southern California, United States. The atmospheric methane consumption ranged between 2.26 to 12.73 μmol m2 h-1, peaking during the daytime at vegetated sites. Metagenomic studies revealed similar soil-microbiome compositions at vegetated and unvegetated sites, with Methylocaldum being the major methanotrophic clade. Eighty-four metagenome-assembled genomes were recovered, six represented by methanotrophic bacteria (three Methylocaldum, two Methylobacter, and uncultivated Methylococcaceae). The prevalence of copper-containing methane monooxygenases in metagenomic datasets suggests a diverse potential for methane oxidation in canonical methanotrophs and uncultivated Gammaproteobacteria. Five pure cultures of methanotrophic bacteria were obtained, including four Methylocaldum. Genomic analysis of Methylocaldum isolates and metagenome-assembled genomes revealed the presence of multiple stand-alone methane monooxygenase subunit C paralogs, which may have functions beyond methane oxidation. Furthermore, these methanotrophs have genetic signatures typically linked to symbiotic interactions with plants, including tryptophan synthesis and indole-3-acetic acid production. Based on in situ fluxes and soil microbiome compositions, we propose the existence of arid-soil reverse chimneys, an empowered methane sink represented by yet-to-be-defined cooperation between desert vegetation and methane-consuming microbiomes.},
}

@article {pmid40037072,
year = {2025},
author = {Meng, JX and Li, MH and Wang, XY and Li, S and Zhang, Y and Ni, HB and Ma, H and Liu, R and Yan, JC and Li, XM and Sun, YZ and Yang, X and Zhang, XX},
title = {Temporal variability in the diversity, function and resistome landscapes in the gut microbiome of broilers.},
journal = {Ecotoxicology and environmental safety},
volume = {292},
number = {},
pages = {117976},
doi = {10.1016/j.ecoenv.2025.117976},
pmid = {40037072},
issn = {1090-2414},
abstract = {Understanding the dynamic and stability of gut microbiota over the course of production cycle of broiler chicken can help identify microbial features that associate with better health and productivity. In the present study, we profile the changes in the composition and stability of gut microbiota of commercially raised broilers at nine distinct time points using shotgun metagenomics and culturomics approaches. We demonstrate, within the first week post-hatching, a rapid decline in relative abundance of 122 pioneer microbial species including Bacteroides fragilis, Lachnospira eligens and Ruminococcus gnavus, accompanied by a substantial decrease in both microbial richness and diversity. This was followed by a gradual increase and stabilization in the microbial diversity and population structure that persisted until the broilers reached the marketing age. Throughout the production cycle, key bacterial families such as Lachnospiraceae, Bacteroidaceae, and Ruminococcaceae were identified. However, significant shifts at the lower taxonomic levels occurred at different production stages, influencing the functional capacities and resistance profiles of the microbiota. During the rapid growth phase, enzymes crucial to vitamin and amino acid metabolism dominated, whereas enzymes associated with carbohydrate and energy metabolism were notably more abundant during the fattening stage. Many predicted antibiotic resistance genes were detected in association with typical commensal bacterial species in the gut microbiota, indicating a sustained resistance of the gut microbiota to antibiotic classes such as aminoglycosides and tetracyclines, which persist even in the absence of antibiotic selection pressure. Our research carries important implications for the management and health surveillance of broiler production.},
}

@article {pmid40036691,
year = {2025},
author = {Gao, Y and Luo, H and Lyu, H and Yang, H and Yousuf, S and Huang, S and Liu, YX},
title = {Benchmarking short-read metagenomics tools for removing host contamination.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf004},
pmid = {40036691},
issn = {2047-217X},
support = {2024M753580//China Postdoctoral Science Foundation/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; },
mesh = {*Metagenomics/methods ; *Benchmarking ; Microbiota/genetics ; Humans ; DNA Contamination ; Metagenome ; Software ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Reproducibility of Results ; },
abstract = {BACKGROUND: The rapid evolution of metagenomic sequencing technology offers remarkable opportunities to explore the intricate roles of microbiome in host health and disease, as well as to uncover the unknown structure and functions of microbial communities. However, the swift accumulation of metagenomic data poses substantial challenges for data analysis. Contamination from host DNA can substantially compromise result accuracy and increase additional computational resources by including nontarget sequences.

RESULTS: In this study, we assessed the impact of computational host DNA decontamination on downstream analyses, highlighting its importance in producing accurate results efficiently. We also evaluated the performance of conventional tools like KneadData, Bowtie2, BWA, KMCP, Kraken2, and KrakenUniq, each offering unique advantages for different applications. Furthermore, we highlighted the importance of an accurate host reference genome, noting that its absence negatively affected the decontamination performance across all tools.

CONCLUSIONS: Our findings underscore the need for careful selection of decontamination tools and reference genomes to enhance the accuracy of metagenomic analyses. These insights provide valuable guidance for improving the reliability and reproducibility of microbiome research.},
}

*Metagenomics/methods
*Benchmarking
Microbiota/genetics
Humans
DNA Contamination
Metagenome
Software
Sequence Analysis, DNA/methods
Computational Biology/methods
High-Throughput Nucleotide Sequencing/methods
Reproducibility of Results

@article {pmid40036505,
year = {2025},
author = {Langenfeld, K and Hegarty, B and Vidaurri, S and Crossette, E and Duhaime, MB and Wigginton, KR},
title = {Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.},
journal = {Nucleic acids research},
volume = {53},
number = {5},
pages = {},
doi = {10.1093/nar/gkaf118},
pmid = {40036505},
issn = {1362-4962},
support = {1 545 756//NSF/ ; //University of Michigan Integrated Training in Microbial Systems (ITiMS)/ ; //University of Michigan/ ; //NSF/ ; //ITiMS/ ; //Burroughs Wellcome Fund/ ; },
mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Humans ; Wastewater/virology/microbiology ; DNA Viruses/genetics ; DNA, Viral/genetics ; Bacteriophages/genetics ; Genome, Viral/genetics ; Viruses/genetics ; },
abstract = {Quantitative metagenomic methods are maturing but continue to lack clearly-defined analytical limits. Here, we developed a computational tool, QuantMeta, to determine the absolute abundance of targets in metagenomes spiked with synthetic DNA standards. The tool establishes (i) entropy-based detection thresholds to confidently determine the presence of targets, and (ii) an approach to identify and correct read mapping or assembly errors and thus improve the quantification accuracy. Together this allows for an approach to confidently quantify absolute abundance of targets, be they microbial populations, genes, contigs, or metagenome-assembled genomes. We applied the approach to quantify single- and double-stranded DNA viruses in wastewater viral metagenomes, including pathogens and bacteriophages. Concentrations of total DNA viruses in wastewater influent and effluent were >108 copies/ml using QuantMeta. Human-associated DNA viruses were detected and quantifiable with QuantMeta thresholds, including polyomavirus, papillomavirus, and crAss-like phages, at concentrations similar to previous reports that utilized quantitative polymerase chain reaction (PCR)-based assays. Our results highlight the higher detection thresholds of quantitative metagenomics (approximately 500 copies/μl) as compared to PCR-based quantification (approximately 10 copies/μl) despite a sequencing depth of 200 million reads per sample. The QuantMeta approach, applicable to both viral and cellular metagenomes, advances quantitative metagenomics by improving the accuracy of measured target absolute abundances.},
}

*Metagenomics/methods
*Metagenome/genetics
Humans
Wastewater/virology/microbiology
DNA Viruses/genetics
DNA, Viral/genetics
Bacteriophages/genetics
Genome, Viral/genetics
Viruses/genetics

@article {pmid40036345,
year = {2025},
author = {Hemeda, AA and Zahran, SA and Tammam, MA and Ewida, MA and Kashef, MT and Yassin, AS and Mitra, A and Youssef, NH and Elshahed, MS},
title = {Metagenomic mining unveils a novel GH130 enzyme with exclusive xylanase activity over a wide temperature and pH ranges.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jimb/kuaf006},
pmid = {40036345},
issn = {1476-5535},
abstract = {The equine gut harbours a diverse microbial community and represents a rich source of carbohydrate-active enzymes (CAZymes). To identify and characterize potentially novel CAZymes from a horse's hindgut metagenome, shotgun metagenomic sequencing was performed on DNA extracted from a stool sample of a male horse followed by CAZyme annotation. Here, we report on the characterization of a novel enzyme (AH2) that was identified, synthesized, cloned and characterized from the obtained CAZyme dataset. AH2 was identified as a GH130 family member and displayed an exclusive xylanase activity, a trait hitherto unreported in prior characterization of GH130 CAZymes. AH2 displayed an optimal activity at a pH of 5.6 and a temperature of 50°C. AH2 maintained significant activity across a pH range of 4 to 10 (62 -72%) and temperatures of 30 to 70°C (77-86%). The enzyme had remarkable stability, with minimal reductions in activity across a temperature range of 4 to 70°C and pH levels of 3, 7, and 9. Docking studies identified AH2's amino acids (Glu90 and Glu149) to be involved in substrate binding. Molecular dynamics simulation confirmed the structural stability of AH2 at pH 5.6 and 50°C, further supporting its resilience under these conditions. Our results expand on the known activities associated with the GH130 CAZyme family and demonstrate that the horse gut metagenome represents an unexplored source of novel CAZymes.},
}

@article {pmid40035787,
year = {2025},
author = {Tappauf, N and Lamers, Y and Sham, HP and Piper, HG},
title = {Multiomics profiling and parenteral nutrition weaning in pediatric patients with intestinal failure: A longitudinal cohort study.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.2742},
pmid = {40035787},
issn = {1941-2444},
support = {//This study was funded through a 2021-2022 Healthy Starts Catalyst Grant, awarded by the BC Children's Hospital Research Institute in Vancouver, Canada./ ; },
abstract = {BACKGROUND: Intestinal failure (IF) is a life-limiting condition that includes a variety of intestinal pathologies. Currently, there are few clinical biomarkers that reflect intestinal function or a patient's potential to wean off parenteral nutrition (PN), making it difficult to predict the clinical trajectory. By associating gut microbiome taxonomic and functional features and blood analytes with the proportion of daily energy delivered via PN-a proxy for intestinal function-our study aimed to discover potential predictors of intestinal function and PN weaning potential.

METHODS: In this longitudinal multiomics cohort study, we followed 18 pediatric patients with IF and PN support for ≤1.5 years. Fecal and stoma samples were analyzed using metagenomic shotgun sequencing to assess bacterial taxonomy and function and internal transcribed spacer 2 ribosomal RNA sequencing to characterize the fungal community. Targeted metabolomics was used to quantify 257 blood analytes. Linear mixed models were used to analyze the associations of PN dependence with microbiome features and blood analytes.

RESULTS: The bacterial and fungal taxonomic composition exhibited substantial interpatient and intrapatient variability, with no link to PN dependence. In contrast, bacterial functional analysis revealed 63 MetaCyc pathways significantly associated with PN dependence. Additionally, 32 blood analytes were associated with PN dependence.

CONCLUSION: In this exploratory study, we found that functional microbiome features and blood metabolomic profiles-particularly urea cycle metabolites, creatinine, asparagine, and tryptophan-derived metabolites-show promise for predicting intestinal function. Furthermore, they may have therapeutic implications for promoting intestinal adaptation. Confirmatory trials with larger sample sizes are needed to validate these findings.},
}

@article {pmid40034816,
year = {2024},
author = {Liu, Z and Jiang, A and Ma, D and Liu, D and Han, X and Zhao, M and Zhou, C and Tan, Z},
title = {The impact of rumen microbial composition on apparent digestibility, rumen fermentation and metabolism in Sanhe cows and Holstein cows of different parities under identical dietary conditions.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1463209},
pmid = {40034816},
issn = {2297-1769},
abstract = {Previous studies have discussed the association between serum metabolism and lactation performance among Sanhe and Holstein cows of different parities and found that the metabolic profiles of these two breeds vary differently with parity. Since the rumen is the central organ for nutrient absorption and production transformation in dairy cows, it remains unknown whether the differences observed under the same dietary conditions are related to the structure of the rumen microbiome. This study measured the apparent digestibility and rumen fermentation parameters of Sanhe cows (S1/S2/S3/S4) and Holstein cows (H1/H2/H3/H4) across four parities and generated a comprehensive rumen microbiome dataset using high-throughput sequencing technology. Significant differences in dry matter digestibility (p = 0.001) and ammonia nitrogen (p = 0.024) were observed among the S groups, with higher trends of various VFA contents in S1 (0.05 < p < 0.1). The H group showed significant differences in crude protein digestibility (p = 0.001), higher isovaleric acid content in H1 (p = 0.002), and the lowest acetate to propionate ratio (p = 0.002) in H3. Metagenomic sequencing results indicated consistency between rumen microbiome patterns and metabolic changes, with S1 distinctly different from S2/S3/S4, and H1 and H2 different from H3 and H4. The species composition of the rumen microbiome was similar between Sanhe and Holstein cows, but differences in abundance were noted. Rhizophagus , Neocallimastix, and Piromyces were more abundant in S1, H1, and H2, and pathways such as autophagy-animal, plant-pathogen interaction, and endocytosis were significantly enriched in these parities. Multiparous Sanhe cows had higher abundances of ATP-binding cassette transporters pathways. Additionally, CAZymes such as GH84 and GH37 were significantly associated with differential physiological indicators and milk traits. In conclusion, this study reveals the complex relationship between rumen microbiota and metabolic characteristics in Sanhe and Holstein cows of different parities, indicating that changes in the structure of the rumen microbiome may be key factors affecting lactation performance and metabolic differences in dairy cows.},
}

@article {pmid40034572,
year = {2025},
author = {Phillips, R and Fisher, BT and Ladas, EJ and Patel, P and Robinson, PD and Dupuis, LL and Ammann, RA and Beauchemin, MP and Carlesse, F and Castagnola, E and Davis, BL and Efremov, K and Elgarten, CW and Groll, AH and Haeusler, GM and Koenig, C and Morris, A and Santolaya, ME and Spinelli, D and Tissing, WJE and Wolf, J and Sung, L and Lehrnbecher, T},
title = {Use of food restrictions to prevent infections in paediatric patients with cancer and haematopoietic cell transplantation recipients: a systematic review and clinical practice guideline.},
journal = {EClinicalMedicine},
volume = {81},
number = {},
pages = {103093},
pmid = {40034572},
issn = {2589-5370},
abstract = {BACKGROUND: Food restrictions during periods of neutropenia have been widely used in oncology settings to prevent infections. As there is a lack of clearly demonstrated effectiveness, this strategy is being increasingly questioned.

METHODS: A multi-national panel of 23 individuals was convened to develop a clinical practice guideline (CPG) on the use of food restrictions to prevent infections in paediatric patients with cancer and haematopoietic cell transplantation (HCT) recipients. It included representation from persons with lived experience and physicians, dieticians, nurses, pharmacists and guideline methodologists working in paediatric oncology/HCT or infectious diseases. Panel members (female n = 15; 65%) were from North America (12, 52%), Europe (8, 35%), South America (2, 9%) and Australia (1, 4%). The Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach was used to formulate the CPG recommendations based on a systematic review of randomised controlled trials (RCTs). MEDLINE, MEDLINE in-Process and Embase databases were searched from January 1, 1980, to May 7, 2024, with a broad strategy which combined subject headings and text words relating to neutropenia, infection and diet.

FINDINGS: The systematic review, which provided the evidence base for the CPG recommendations, identified 4312 unique citations, of which 52 were retrieved for full-text evaluation. Eight RCTs met the eligibility criteria and informed panel deliberations. Although there was clinical heterogeneity in the food restrictions evaluated, data were consistent in suggesting that food restrictions lack clinically significant benefit in preventing infections. The panel made two conditional recommendations against the use of food restrictions in a) paediatric patients with cancer receiving chemotherapy and b) in the setting of allogeneic and autologous HCT. The panel developed a good practice statement to emphasise the importance of health care organisations and families adhering to local food safety practices.

INTERPRETATION: This CPG provides the first evidence-based recommendations on use of food restrictions to prevent infections in children and adolescents undergoing chemotherapy and paediatric haematopoietic cell transplant recipients.

FUNDING: This CPG was funded and developed through the POGO Guidelines Program.},
}

@article {pmid40034495,
year = {2025},
author = {Zhao, SY and Meng, YL and Yang, ZH and Li, BL and Li, YY and Han, H and Liu, L and Duan, PF and Chen, ZJ},
title = {Rhizosphere microbiome metagenomics in PGPR-mediated alleviation of combined stress from polypropylene microplastics and Cd in hybrid Pennisetum.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549043},
pmid = {40034495},
issn = {1664-302X},
abstract = {The simultaneous presence of microplastics (MPs) and heavy metals in soil may result in heightened toxicity, causing more significant adverse effects on plant growth. Plant growth-promoting rhizobacteria (PGPR) have demonstrated significant capacities in alleviating the toxic stress caused by the combined pollution of heavy metals and other contaminants. However, research on the impacts and processes of PGPR in alleviating stress induced by the combined pollution from MPs and heavy metals is still insufficient. This study involved a pot experiment to evaluate the ability of PGPR to mitigate stress induced by the combined pollution from polypropylene microplastic (PP MPs) particles of different sizes (6.5 μm and 830 μm) and the heavy metal cadmium (Cd) in the bioenergy plant hybrid Pennisetum. Moreover, metagenomic analysis was used to examine the effects of PGPR on the rhizospheric microbial community and function. The cocontamination of PP and Cd affected the growth of the hybrid Pennisetum differently depending on the size of the MPs particles, with the aboveground and underground lengths of the 6.5 μm PP + Cd experimental group being smaller than those of the 830 μm PP + Cd group. The PGPRs (Bacillus sp. Y-35, Bacillus sp. Y-62, Bacillus sp. Y-S, and Enterobacter sp. Y-V) successfully alleviated the stress caused by the combined pollution of PP and Cd, resulting in increases of 8.24 and 42.21% in the plant height and dry weight, respectively. The metagenomic studies indicated that the cocontamination of PP and Cd, along with PGPR inoculation, altered the composition of the rhizospheric bacterial community, leading to changes in microbial diversity indices and the composition of dominant groups such as Pseudomonadota, Actinomycetota, and Acidobacteriota. The functional analysis revealed that the main functional groups involved glucose metabolism, energy metabolism, signal transduction, and nucleotide metabolism. The MPs particle size and different PGPR significantly affected functions such as the pentose phosphate pathway, benzoate degradation, and amide biosynthesis. This study provides essential data and scientific evidence on the ecotoxicological effects of simultaneous contamination by MPs and heavy metals, as well as insights into potential bioremediation methods.},
}

@article {pmid40033444,
year = {2025},
author = {Dias, BDC and Lamarca, AP and Machado, DT and Kloh, VP and de Carvalho, FM and Vasconcelos, ATR},
title = {Metabolic pathways associated with Firmicutes prevalence in the gut of multiple livestock animals and humans.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {20},
pmid = {40033444},
issn = {2524-4671},
support = {88887.508687/2020-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 88887.677436/2022-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; E-26/200.200/2024//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 302023/2024-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Dynamic interspecific interactions and environmental factors deeply impact the composition of microbiotic communities in the gut. These factors intertwined with the host's genetic background and social habits cooperate synergistically as a hidden force modulating the host's physiological and health determinants, with certain bacterial species being maintained from generation to generation. Firmicutes, one of the dominant bacterial phyla present across vertebrate classes, exhibits a wide range of functional capabilities and colonization strategies. While ecological scenarios involving microbial specialization and metabolic functions have been hypothesized, the specific mechanisms that sustain the persistence of its microbial taxa in a high diversity of hosts remain elusive. This study fills this gap by investigating the Firmicutes metabolic mechanisms contributing to their prevalence and heritability in the host gut on metagenomes-assembled bacterial genomes collected from 351 vertebrate samples, covering 18 food-producing animals and humans, specific breeds and closely-related species. We observed that taxa belonging to Acetivibrionaceae, Clostridiaceae, Lachnospiraceae, Ruminococcaceae, and the not well understood CAG-74 family were evolutionarily shared across all hosts. These prevalent taxa exhibit metabolic pathways significantly correlated with extra-host survival mechanisms, cell adhesion, colonization and host transmission, highlighted by sporulation, glycan biosynthesis, bile acid metabolism, and short-chain fatty acid encoded genes. Our findings provide a deeper understanding of the ecological foundations governing distinct transmission modes, effective colonization establishment, and maintenance of Firmicutes, offering new perspectives on both well-known and poorly characterized species.},
}

@article {pmid40032396,
year = {2025},
author = {Zimmermann, P and Kurth, S and Giannoukos, S and Stocker, M and Bokulich, NA},
title = {NapBiome trial: Targeting gut microbiota to improve sleep rhythm and developmental and behavioural outcomes in early childhood in a birth cohort in Switzerland - a study protocol.},
journal = {BMJ open},
volume = {15},
number = {3},
pages = {e092938},
doi = {10.1136/bmjopen-2024-092938},
pmid = {40032396},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome ; Switzerland ; Infant ; Infant, Newborn ; *Sleep/physiology ; Double-Blind Method ; Child Development ; Infant, Premature ; Child, Preschool ; Brain-Gut Axis ; Female ; Randomized Controlled Trials as Topic ; Male ; Probiotics/therapeutic use ; Multicenter Studies as Topic ; },
abstract = {INTRODUCTION: The gut-brain axis plays a crucial role in the regulation and development of psychological and physical processes. The first year of life is a critical period for the development of the gut microbiome, which parallels important milestones in establishing sleep rhythm and brain development. Growing evidence suggests that the gut microbiome influences sleep, cognition and early neurodevelopment. For term-born and preterm-born infants, difficulties in sleep regulation may have consequences on health. Identifying effective interventions on the gut-brain axis in early life is likely to have long-term implications for the health and development of at-risk infants.

METHODS AND ANALYSES: In this multicentre, four-group, double-blinded, placebo (PLC)-controlled randomised trial with a factorial design, 120 preterm-born and 260 term-born infants will be included. The study will investigate whether the administration of daily synbiotics or PLC for a duration of 3 months improves sleep patterns and neurodevelopmental outcomes up to 2 years of age. The trial will also: (1) determine the association between gut microbiota, sleep patterns and health outcomes in children up to 2 years of age; and (2) leverage the interactions between gut microbiota, brain and sleep to develop new intervention strategies for at-risk infants.

ETHICS AND DISSEMINATION: The NapBiome trial has received ethical approval by the Committee of Northwestern and Central Switzerland and Canton Vaud, Switzerland (#2024-01681). Outcomes will be disseminated through publication and will be presented at scientific conferences. Metagenomic data will be shared through the European Nucleotide Archive.

TRIAL REGISTRATION NUMBER: The US National Institutes of Health NCT06396689.},
}

Humans
*Gastrointestinal Microbiome
Switzerland
Infant
Infant, Newborn
*Sleep/physiology
Double-Blind Method
Child Development
Infant, Premature
Child, Preschool
Brain-Gut Axis
Female
Randomized Controlled Trials as Topic
Male
Probiotics/therapeutic use
Multicenter Studies as Topic

@article {pmid40032028,
year = {2025},
author = {Ismaiah, MJ and Kwan Lo, EK and Chen, C and Shing-Jie Tsui, J and Johnson-Hill, WA and Felicianna, and Zhang, F and Matthew Leung, HK and Oger, C and Durand, T and Chung-Yung Lee, J and El-Nezami, H},
title = {Alpha-aminobutyric acid administration suppressed visceral obesity and modulated hepatic oxidized PUFA metabolism via gut microbiota modulation.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2025.02.029},
pmid = {40032028},
issn = {1873-4596},
abstract = {BACKGROUND: High-fat diet (HFD) is associated with visceral obesity due to disruption in the lipid metabolism and gut dysbiosis. These symptoms may contribute to hepatic steatosis and the formation of oxidized polyunsaturated fatty acids (PUFAs). Alpha-aminobutyric acid (ABA) is an amino-acid derived metabolite, and its concentration has been correlated with several metabolic conditions and gut microbiome diversity while its direct effects on visceral obesity, lipid metabolism and the gut microbiota are not well understood. This study was designed to investigate the effect of physiological dose of ABA on diet-induced visceral obesity and lipid metabolism dysregulation by examining the fatty acids and oxidized PUFAs profile in the liver as well as the gut microbiota.

RESULTS: ABA administration reduced visceral obesity by 28% and lessened adipocyte hypertrophy. The expression of liver Cd36 was lowered by more than 50% as well as the saturated and monounsaturated FA concentration. Notably, the desaturation index for C16 and C18 FAs that are correlated with adiposity were reduced. The concentration of several DHA-derived oxidized PUFAs were also enhanced. Faecal metagenomics sequencing revealed enriched abundance of Leptogranulimonas caecicola and Bacteroides sp. ZJ-18 and were positively correlated with several DHA- and ALA-derived oxidized PUFAs in ABA group.

CONCLUSION: Our study revealed the modulatory effect of physiological dose of ABA on attenuating visceral obesity, reducing hepatic steatosis, and promoting the production of anti-inflammatory oxidized PUFAs that were potentially mediated by the gut microbiota.},
}

@article {pmid40030240,
year = {2024},
author = {Xiao, Z and Sun, H and Wei, A and Zhao, W and Jiang, X},
title = {A Novel Framework for Predicting Phage-Host Interactions Via Host Specificity-Aware Graph Autoencoder.},
journal = {IEEE journal of biomedical and health informatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/JBHI.2024.3500137},
pmid = {40030240},
issn = {2168-2208},
abstract = {Due to the abuse of antibiotics, some pathogenic bacteria have developed resistance to most antibiotics, leading to the emergence of antibiotic-resistant superbugs. Therefore, researchers resort to phage therapy for bacterial infections. For phage therapy, the fundamental step is to accurately identify phage-host interactions. Although various methods have been proposed, the existing methods suffer from the following two shortcomings: 1) they fail to make full use of genetic information including both genome and protein sequence of phages; 2) host specificity of phages is not explicitly utilized when learning representations of phages and bacteria. In this paper, we present an efficient computational method called PHISGAE for predicting phage-host interactions, in which the host specificity is explicitly employed. Firstly, initial phage-phage connections are efficiently constructed via utilizing phage genome and protein sequence. Then, the refined heterogeneous network is derived by applying K-nearest neighbor strategy, keeping relatively more meaningful local semantics among phages and bacteria. Finally, a host specificity-aware graph autoencoder is proposed to learn high-quality representations of phages and bacteria for predicting phage-host interactions. Experimental results show that PHISGAE outperforms the state-of-the-art methods on predicting phage-host interactions at both species level and genus level (AUC values of 94.73% and 96.32%, respectively). Moreover, results of case study demonstrate that PHISGAE is able to identify candidate hosts with high probability for previously unseen phages identified from metagenomics, effectively predicting potential phage-host interactions in real-world applications.},
}

@article {pmid40030030,
year = {2025},
author = {Ghimire, S and Lehman, PC and Aguilar Meza, LS and Shahi, SK and Hoang, J and Olalde, H and Paullus, M and Cherwin, C and Wang, K and Gill, C and Cho, T and Mangalam, AK},
title = {Specific microbial ratio in the gut microbiome is associated with multiple sclerosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {10},
pages = {e2413953122},
doi = {10.1073/pnas.2413953122},
pmid = {40030030},
issn = {1091-6490},
support = {R01AI137075//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1I01CX002212//U.S. Department of Veterans Affairs (VA)/ ; P30 ES005605/ES/NIEHS NIH HHS/United States ; T32AI007260//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
mesh = {*Gastrointestinal Microbiome ; *Multiple Sclerosis/microbiology ; Animals ; Humans ; Mice ; Female ; *Dysbiosis/microbiology ; *Feces/microbiology ; Male ; Akkermansia ; Adult ; Encephalomyelitis, Autoimmune, Experimental/microbiology ; Middle Aged ; Bifidobacterium ; Prevotella/isolation & purification ; Mice, Inbred C57BL ; Case-Control Studies ; },
abstract = {Gut microbiota dysbiosis is associated with multiple sclerosis (MS), but the causal relationship between specific gut bacteria and MS pathogenesis remains poorly understood. Therefore, we profiled the stool microbiome of people with MS (PwMS) and healthy controls (HC) using shotgun metagenomic sequencing. PwMS showed a distinct microbiome compared to HC, with Prevotella copri (PC) and Blautia species as drivers of microbial communities in HC and PwMS, respectively. Administration of MS-driving Blautia species (Blautia wexlerae; BW) to mice resulted in increased levels of gut inflammatory markers and altered microbiota with increased capacity to induce proinflammatory cytokines. Utilizing experimental autoimmune encephalomyelitis (EAE), an animal model of MS, we identified a lower gut Bifidobacterium to Akkermansia ratio as a hallmark of the disease. BW-administered mice also showed a lower Bifidobacterium to Akkermansia ratio pre-EAE induction which correlated with increased disease severity post-EAE induction. The importance of the Bifidobacterium to Akkermansia ratio at the species level, lower Bifidobacterium adolescentis to Akkermansia muciniphila (BA:AM), was validated in our MS cohort and a large International Multiple Sclerosis Microbiome Study. Thus, our findings highlight the BA:AM ratio as a potential gut microbial marker in PwMS, opening avenues for microbiome-based diagnosis, prognosis, and therapy in MS.},
}

*Gastrointestinal Microbiome
*Multiple Sclerosis/microbiology
Animals
Humans
Mice
Female
*Dysbiosis/microbiology
*Feces/microbiology
Male
Akkermansia
Adult
Encephalomyelitis, Autoimmune, Experimental/microbiology
Middle Aged
Bifidobacterium
Prevotella/isolation & purification
Mice, Inbred C57BL
Case-Control Studies

@article {pmid39882942,
year = {2025},
author = {Tran Lu Y, A and Ruault, S and Daguin-Thiebaut, C and Le Port, AS and Ballenghien, M and Castel, J and Gagnaire, PA and Bierne, N and Arnaud-Haond, S and Poitrimol, C and Thiebaut, E and Lallier, F and Broquet, T and Jollivet, D and Bonhomme, F and Hourdez, S},
title = {Comparative Population Genomics Unveils Congruent Secondary Suture Zone in Southwest Pacific Hydrothermal Vents.},
journal = {Molecular biology and evolution},
volume = {42},
number = {2},
pages = {},
doi = {10.1093/molbev/msaf024},
pmid = {39882942},
issn = {1537-1719},
support = {ANR-17-CE02-0003//ANR CERBERUS project/ ; },
mesh = {*Hydrothermal Vents ; *Phylogeography ; Pacific Ocean ; Gene Flow ; Genetic Variation ; Metagenomics ; },
abstract = {How the interplay of biotic and abiotic factors shapes current genetic diversity at the community level remains an open question, particularly in the deep sea. Comparative phylogeography of multiple species can reveal the influence of past climatic events, geographic barriers, and species life history traits on spatial patterns of genetic structure across lineages. To shed light on the factors that shape community-level genetic variation and to improve our understanding of deep-sea biogeographic patterns, we conducted a comparative population genomics study on seven hydrothermal vent species co-distributed in the Back-Arc Basins of the Southwest Pacific region. Using ddRAD-seq, we compared the range-wide distribution of genomic diversity across species and discovered a shared phylogeographic break. Demogenetic inference revealed shared histories of lineage divergence and a secondary contact. Low levels of asymmetric gene flow probably occurred in most species between the Woodlark and North Fiji basins, but the exact location of contact zones varied from species to species. For two species, we found individuals from the two lineages co-occurring in sympatry in Woodlark Basin. Although species exhibit congruent patterns of spatial structure (Eastern vs. Western sites), they also show variation in the degree of divergence among lineages across the suture zone. Our results also show heterogeneous gene flow across the genome, indicating possible partial reproductive isolation between lineages and early speciation. Our comparative study highlights the pivotal role of historical and contemporary factors, underscoring the need for a comprehensive approach-especially in addressing knowledge gaps on the life history traits of deep-sea species.},
}

*Hydrothermal Vents
*Phylogeography
Pacific Ocean
Gene Flow
Genetic Variation
Metagenomics

@article {pmid40028749,
year = {2025},
author = {Salahi, A and Abd El-Ghany, WA},
title = {A Spotlight on Archaea in Humans, Livestock and Poultry: A Review.},
journal = {Veterinary medicine and science},
volume = {11},
number = {2},
pages = {e70263},
doi = {10.1002/vms3.70263},
pmid = {40028749},
issn = {2053-1095},
mesh = {Animals ; *Archaea/physiology ; Humans ; *Poultry ; Livestock ; Gastrointestinal Microbiome ; },
abstract = {The microbiota includes prokaryotes (archaea and bacteria) and eukaryotes. Archaea are single-celled prokaryotes and essential part of gut microbiome. Researches on archaea in ruminants and humans are more than mono-gastric. The low abundance of archaea in the gut depends on the method used (metagenomics or meta-transcriptomic) and age of people or poultry. The lack of complete recognition of archaea is due to their small number and method of identifying them (16S rRNA gene primers). The uses of archaea include analytical kit, reduce oil pollution, archaeosomes or drugs production, vaccines agents, lipid carriers in the pharmaceutical industry and molybdenum extraction in the nuclear industry. The nutritional functions of methanogenic archaea including feed utilization (ruminants) and efficiency, hydrogen reducing (human), fat deposition and enhancement of energy harvesting in mice, CAZymes genes, cecal fermentation, syntrophic potential, carotenoid source and improved transit time and appetite and SCFAs production. Archaea acting as antibiotics (produce archaeocins, sulfolobicins and halocin KPS1) and as probiotics (archaeobiotics) can reduce TMAU (trimethylaminuria) disease, cardiovascular diseases (CVDs), and atherosclerosis, brain abscess, cancer, colorectal cancer, inflammatory bowel disease (IBD), constipation, obesity, food allergies, asthma and anti-inflammation which can be prevented by using archaea, and other functions include energy homeostasis, heat shock protein (HSP) production and reducing aging.},
}

Animals
*Archaea/physiology
Humans
*Poultry
Livestock
Gastrointestinal Microbiome

@article {pmid40028600,
year = {2025},
author = {Lu, K and Wang, Y and Wang, Y and Zhang, Q and Zhu, Y and Yu, X and Niu, G},
title = {Chijiahe virus, a novel mosquito-associated virus of the Iflaviridae family found in Shandong Province, China.},
journal = {Heliyon},
volume = {11},
number = {4},
pages = {e42532},
pmid = {40028600},
issn = {2405-8440},
abstract = {Climate change is increasing the threat of arboviruses globally, amplifying their geographic distribution and virulence. This poses a grave risk to public health as mosquito-transmitted viral infections resurge and spread. Unbiased metagenomics plays a crucial role in identifying unknown pathogens and monitoring significant ones. Using this approach, a novel mosquito-associated virus, named Chijiahe virus, was discovered. We collected 2910 mosquitoes and divided them into 65 pools based on species and collection site. To ascertain the existence of Chijiahe virus, we utilized nested PCR alongside real-time quantitative reverse transcription PCR (RT-qPCR). Further analysis of the virus's genomic characteristics and phylogenetic relationships revealed its detection in 10 out of 65 mosquito pools, yielding a minimum infection rate (MIR) of 0.34 %. The virus genome consists of a 9654-nucleotide single-stranded RNA, containing an open reading frame (ORF) that encodes essential proteins, including the capsid protein, RNA helicase, and RNA-dependent RNA polymerase (RdRp). Pairwise distance analysis revealed high nucleotide identity among all obtained sequences. Phylogenetic analysis demonstrated Chijiahe virus's close relationship to Arthropod iflavirus, a member of the family Iflaviridae. Additional analyses confirmed Chijiahe virus as a novel member of Iflaviridae.},
}

@article {pmid40028274,
year = {2025},
author = {Veluz, JT and Mallari, LAN and Gloria, PCT and Siringan, MAT},
title = {Exploring the taxonomical and functional profiles of marine microorganisms in Submarine Groundwater Discharge vent water from Mabini, Batangas, Philippines through metagenome-assembled genomes.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1522253},
pmid = {40028274},
issn = {1664-8021},
}

@article {pmid40027914,
year = {2025},
author = {Huang, M and Wang, Y and Lu, Y and Qu, W and Zou, Q and Zhang, D and Shen, Y and Han, D and Yu, F and Zheng, S},
title = {Clinical Characteristics and Predicting Disease Severity in Chlamydia psittaci Infection Based on Metagenomic Next-Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1171-1181},
pmid = {40027914},
issn = {1178-6973},
abstract = {INTRODUCTION: Psittacosis pneumonia, as a zoonotic infection, is induced by the pathogen Chlamydia psittaci. In the present study, we sought to characterize the clinical manifestations and prognosticate the severity of psittacosis pneumonia.

METHODS: We retrospectively verified instances of psittacosis pneumonia in Zhejiang province, China, from January 2021 to April 2024. Relevant data pertaining to epidemiological, clinical, and laboratory aspects were compiled and evaluated.

RESULTS: Among a total of 110 individuals enrolled who were diagnosed with psittacosis pneumonia, the median age being 62.0 years (IQR, 53-69 years). The most common comorbidities were hypertension (36.4%) and diabetes mellitus (17.3%). Patients categorized as having severe disease (n=68) were significantly older than those with mild disease (n=42). Most patients had notable elevations in aspartate aminotransferase (AST), creatine kinase (CK), creatine kinase-MB (CK-MB), lactate dehydrogenase (LDH), D-dimer, C-reactive protein (CRP), procalcitonin, total bilirubin (TBil), and interleukin-6, as along with significant reductions in lymphocytes, monocytes, albumin, and interleukin-4. Chest CT scans showed bilateral lung involvement in 70 cases. In the cohort of patients having received empirical antibiotic therapy, 57.3% had their antibacterial medication adjusted in light of the mNGS findings. mNGS results indicated that 31.8% (35/110) had suspected coinfections. The random forest classifiers based upon the clinical and laboratory characteristics attained AUC values of 0.822.

DISCUSSION: The study underscores the efficacy of mNGS as a robust diagnostic tool for detecting Chlamydia psittaci, which can simultaneously detect other pathogens and guide clinical treatment. Severe patients exhibit significant inflammatory imbalances and lymphocyte depletion. A predictive model based on clinical and laboratory data at admission can effectively guide early clinical intervention.},
}

@article {pmid40027489,
year = {2025},
author = {Bai, D and Chen, T and Xun, J and Ma, C and Luo, H and Yang, H and Cao, C and Cao, X and Cui, J and Deng, YP and Deng, Z and Dong, W and Dong, W and Du, J and Fang, Q and Fang, W and Fang, Y and Fu, F and Fu, M and Fu, YT and Gao, H and Ge, J and Gong, Q and Gu, L and Guo, P and Guo, Y and Hai, T and Liu, H and He, J and He, ZY and Hou, H and Huang, C and Ji, S and Jiang, C and Jiang, GL and Jiang, L and Jin, LN and Kan, Y and Kang, D and Kou, J and Lam, KL and Li, C and Li, C and Li, F and Li, L and Li, M and Li, X and Li, Y and Li, ZT and Liang, J and Lin, Y and Liu, C and Liu, D and Liu, F and Liu, J and Liu, T and Liu, T and Liu, X and Liu, Y and Liu, B and Liu, M and Lou, W and Luan, Y and Luo, Y and Lv, H and Ma, T and Mai, Z and Mo, J and Niu, D and Pan, Z and Qi, H and Shi, Z and Song, C and Sun, F and Sun, Y and Tian, S and Wan, X and Wang, G and Wang, H and Wang, H and Wang, H and Wang, J and Wang, J and Wang, K and Wang, L and Wang, SK and Wang, X and Wang, Y and Xiao, Z and Xing, H and Xu, Y and Yan, SY and Yang, L and Yang, S and Yang, Y and Yao, X and Yousuf, S and Yu, H and Lei, Y and Yuan, Z and Zeng, M and Zhang, C and Zhang, C and Zhang, H and Zhang, J and Zhang, N and Zhang, T and Zhang, YB and Zhang, Y and Zhang, Z and Zhou, M and Zhou, Y and Zhu, C and Zhu, L and Zhu, Y and Zhu, Z and Zou, H and Zuo, A and Dong, W and Wen, T and Chen, S and Li, G and Gao, Y and Liu, YX},
title = {EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research.},
journal = {iMeta},
volume = {4},
number = {1},
pages = {e70001},
pmid = {40027489},
issn = {2770-596X},
abstract = {Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in-depth analysis of microbial communities at both the high-resolution taxonomic and functional levels. This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user-friendly pipeline that supports multiple analysis methods, including quality control and host removal, read-based, assembly-based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third-generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at https://github.com/YongxinLiu/EasyMetagenome.},
}

@article {pmid40027486,
year = {2025},
author = {Zhao, Y and Hu, J and Wang, J and Yao, X and Zhang, T and Hu, B},
title = {Comammox Nitrospira act as key bacteria in weakly acidic soil via potential cobalamin sharing.},
journal = {iMeta},
volume = {4},
number = {1},
pages = {e271},
pmid = {40027486},
issn = {2770-596X},
abstract = {The discovery of comammox Nitrospira in low pH environments has reshaped the ammonia oxidation process in acidic settings, providing a plausible explanation for the higher nitrification rates observed in weakly acidic soils. However, the response of comammox Nitrospira to varying pH levels and its ecological role in these environments remains unclear. Here, a survey across soils with varying pH values (ranging from 4.4 to 9.7) was conducted to assess how comammox Nitrospira perform under different pH conditions. Results showed that comammox Nitrospira dominate ammonia oxidation in weakly acidic soils, functioning as a K-strategy species characterized by slow growth and stress tolerance. As a key species in this environment, comammox Nitrospira may promote bacterial cooperation under low pH conditions. Genomic evidence suggested that cobalamin sharing is a potential mechanism, as comammox Nitrospira uniquely encode a metabolic pathway that compensates for cobalamin imbalance in weakly acidic soils, where 86.8% of metagenome-assembled genomes (MAGs) encode cobalamin-dependent genes. Additionally, we used DNA stable-isotope probing (DNA-SIP) to demonstrate its response to pH fluctuations to reflect how it responds to the decrease in pH. Results confirmed that comammox Nitrospira became dominant ammonia oxidizers in the soil after the decrease in pH. We suggested that comammox Nitrospira will become increasingly important in global soils, under the trend of soil acidification. Overall, our work provides insights that how comammox Nitrospira perform in weakly acidic soil and its response to pH changes.},
}

@article {pmid40027485,
year = {2025},
author = {Liu, Y and Li, H and Sun, T and Sun, G and Jiang, B and Liu, M and Wang, Q and Li, T and Cao, J and Zhao, L and Xiao, F and Zhao, F and Cui, H},
title = {Gut microbiome and metabolome characteristics of patients with cholesterol gallstones suggest the preventive potential of prebiotics.},
journal = {iMeta},
volume = {4},
number = {1},
pages = {e70000},
pmid = {40027485},
issn = {2770-596X},
abstract = {Cholesterol gallstones (CGS) still lack effective noninvasive treatment. The etiology of experimentally proven cholesterol stones remains underexplored. This cross-sectional study aims to comprehensively evaluate potential biomarkers in patients with gallstones and assess the effects of microbiome-targeted interventions in mice. Microbiome taxonomic profiling was conducted on 191 samples via V3-V4 16S rRNA sequencing. Next, 60 samples (30 age- and sex-matched CGS patients and 30 controls) were selected for metagenomic sequencing and fecal metabolite profiling via liquid chromatography-mass spectrometry. Microbiome and metabolite characterizations were performed to identify potential biomarkers for CGS. Eight-week-old male C57BL/6J mice were given a lithogenic diet for 8 weeks to promote gallstone development. The causal relationship was examined through monocolonization in antibiotics-treated mice. The effects of short-chain fatty acids such as sodium butyrate, sodium acetate (NaA), sodium propionate, and fructooligosaccharides (FOS) on lithogenic diet-induced gallstones were investigated in mice. Gut microbiota and metabolites exhibited distinct characteristics, and selected biomarkers demonstrated good diagnostic performance in distinguishing CGS patients from healthy controls. Multi-omics data indicated associations between CGS and pathways involving butanoate and propanoate metabolism, fatty acid biosynthesis and degradation pathways, taurine and hypotaurine metabolism, and glyoxylate and dicarboxylate metabolism. The incidence of gallstones was significantly higher in the Clostridium glycyrrhizinilyticum group compared to the control group in mice. The grade of experimental gallstones in control mice was significantly higher than in mice treated with NaA and FOS. FOS could completely inhibit the formation of gallstones in mice. This study characterized gut microbiome and metabolome alterations in CGS. C. glycyrrhizinilyticum contributed to gallstone formation in mice. Supplementing with FOS could serve as a potential approach for managing CGS by altering the composition and functionality of gut microbiota.},
}

@article {pmid40026814,
year = {2025},
author = {Zhang, X and Yin, H and Yang, X and Kang, J and Sui, N},
title = {Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics.},
journal = {International journal of general medicine},
volume = {18},
number = {},
pages = {1007-1022},
pmid = {40026814},
issn = {1178-7074},
abstract = {PURPOSE: To explore the mechanism of Zhuyang Tongbian Decoction (ZTD) in treating functional constipation (FC) by observing its effects on intestinal flora composition, the metabolic function of gut microbiota, fecal short-chain fatty acid (SCFA) levels, and serum concentrations of TLR4, NF-κB, TNF-α, and IL-6 in patients with FC.

PATIENTS AND METHODS: 40 patients with FC were randomly divided into the control group and the treatment group, 20 cases in each group. And 20 healthy volunteers were recruited during the same period. The control group was administered lactulose, while the treatment group was treated with ZTD. 16s RNA sequencing technology was used to compare the changes in the structure and diversity of the intestinal flora of patients before and after treatment. Changes in the levels of SCFAs in faeces and the levels of TLR4, NF-κB, TNF-α and IL-6 in serum were analysed. Metagenomics sequencing assessed microbiota metabolic functions.

RESULTS: The treatment group showed a significant increase in the relative abundance of beneficial bacteria, including Bifidobacterium, Lactobacillus, and Faecalibacterium_prausnitzii (P < 0.05), whereas Desulfobacterota and Ruminococcus were significantly reduced (P < 0.05). Notably, fecal acetic and propionic acid levels were significantly higher in the treatment group (P < 0.05). Serum biomarkers TLR4, NF-κB, TNF-α, and IL-6 decreased significantly (P < 0.05). Metagenomics sequencing showed that Carbohydrate metabolism, Metabolism of cofactors and vitamins, and C5- Branched dibasic acid metabolism were significantly increased in functional abundance (P < 0.05).

CONCLUSION: ZTD notably improves intestinal flora composition and gut microbiota metabolic function, regulates SCFA levels, and reduces inflammation markers in FC patients. The strain Faecalibacterium_prausnitzii shows significant potential in regulation of intestinal inflammation and may play a crucial role in the treatment efficacy of ZTD for FC.},
}

@article {pmid40026575,
year = {2025},
author = {Shen, W and Wang, D and Li, J and Liu, Y and Wang, Y and Yang, X and Peng, X and Xie, B and Su, L and Wei, Z and He, Q and Wang, Z and Feng, K and Du, W and Deng, Y},
title = {Developing a microfluidic-based epicPCR reveals diverse potential hosts of the mcrA gene in marine cold seep.},
journal = {mLife},
volume = {4},
number = {1},
pages = {70-82},
pmid = {40026575},
issn = {2770-100X},
abstract = {Anaerobic methanotrophic (ANME) microbes play a crucial role in the bioprocess of anaerobic oxidation of methane (AOM). However, due to their unculturable status, their diversity is poorly understood. In this study, we established a microfluidics-based epicPCR (Emulsion, Paired Isolation, and Concatenation PCR) to fuse the 16S rRNA gene and mcrA gene to reveal the diversity of ANME microbes (mcrA gene hosts) in three sampling push-cores from the marine cold seep. A total of 3725 16S amplicon sequence variants (ASVs) of the mcrA gene hosts were detected, and classified into 78 genera across 23 phyla. Across all samples, the dominant phyla with high relative abundance (>10%) were the well-known Euryarchaeota, and some bacterial phyla such as Campylobacterota, Proteobacteria, and Chloroflexi; however, the specificity of these associations was not verified. In addition, the compositions of the mcrA gene hosts were significantly different in different layers, where the archaeal hosts increased with the depths of sediments, indicating the carriers of AOM were divergent in depth. Furthermore, the consensus phylogenetic trees of the mcrA gene and the 16S rRNA gene showed congruence in archaea not in bacteria, suggesting the horizontal transfer of the mcrA gene may occur among host members. Finally, some bacterial metagenomes were found to contain the mcrA gene as well as other genes that encode enzymes in the AOM pathway, which prospectively propose the existence of ANME bacteria. This study describes improvements for a potential method for studying the diversity of uncultured functional microbes and broadens our understanding of the diversity of ANMEs.},
}

@article {pmid40026326,
year = {2024},
author = {Laço, J and Martorell, S and Gallegos, MDC and Gomila, M},
title = {Yearlong analysis of bacterial diversity in hospital sink drains: culturomics, antibiotic resistance and implications for infection control.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1501170},
pmid = {40026326},
issn = {1664-302X},
abstract = {Hospitals can carry high levels of bacterial diversity from all types of origins, such as human skin, outside environment and medical equipment. Sink drains in clinical settings are considered reservoirs for pathogenic bacteria and potential sources of hospital-acquired infections (HAI's) and antibiotic resistance genes (ARGs). Therefore, infection control measures are crucial to minimizing the risks associated with these reservoirs. Recent research has focused primarily on intensive care units (ICUs) and known pathogens, often employing metagenomic approaches that do not include bacterial isolation. This study aims to evaluate bacterial diversity using culturomics, extending the investigation beyond the ICU to identify antibiotic-resistant bacteria. A total of four samplings were conducted over 1 year (March 2022 to March 2023) in five different hospital wards [ICU, General Medicine (GM), Hematology (H), Short stay unit (UCE), and Microbiology laboratory (MS)]. All samples were cultured on selective and non-selective culture media, resulting in 1,058 isolates identified using MALDI-TOF MS, with a subset confirmed through 16S rRNA gene sequencing. Isolates retrieved from antibiotic supplemented agar were subjected to antibiotic susceptibility testing. The highest bacterial diversity, as measured by the Shannon index, was observed in the ICU and GM wards, posing significant risks to patients in these areas. While bacterial genera were largely similar across wards and sampling times, with Pseudomonas and Stenotrophomonas being the most prevalent, different species were detected in each sampling, indicating no loss of diversity. This suggests that these environments undergo dynamic changes over time, influenced by their surroundings. The results also indicate a relationship between human activity and drain usage and the presence of Pseudomonas aeruginosa, the most commonly found species across most wards. Antibiotic susceptibility testing revealed that all tested isolates, except for one, were multi-resistant, including clinically relevant species, such as P. aeruginosa and K. pneumoniae. Hospital drains may serve as reservoirs for both known and emerging pathogens exhibiting high antibiotic resistance phenotypes. Their dynamic nature may provide insights into strategies for preventing the colonization of these environments by such species.},
}

@article {pmid40025421,
year = {2025},
author = {Sun, J and Ru, J and Cribbs, AP and Xiong, D},
title = {PyPropel: a Python-based tool for efficiently processing and characterising protein data.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {70},
pmid = {40025421},
issn = {1471-2105},
support = {MR/V010182/1//UKRI Medical Research Council (MRC) career development fellowship/ ; MR/V010182/1//UKRI Medical Research Council (MRC) career development fellowship/ ; },
mesh = {*Software ; *Proteins/chemistry/metabolism ; *Computational Biology/methods ; Databases, Protein ; Machine Learning ; Sequence Analysis, Protein/methods ; },
abstract = {BACKGROUND: The volume of protein sequence data has grown exponentially in recent years, driven by advancements in metagenomics. Despite this, a substantial proportion of these sequences remain poorly annotated, underscoring the need for robust bioinformatics tools to facilitate efficient characterisation and annotation for functional studies.

RESULTS: We present PyPropel, a Python-based computational tool developed to streamline the large-scale analysis of protein data, with a particular focus on applications in machine learning. PyPropel integrates sequence and structural data pre-processing, feature generation, and post-processing for model performance evaluation and visualisation, offering a comprehensive solution for handling complex protein datasets.

CONCLUSION: PyPropel provides added value over existing tools by offering a unified workflow that encompasses the full spectrum of protein research, from raw data pre-processing to functional annotation and model performance analysis, thereby supporting efficient protein function studies.},
}

*Software
*Proteins/chemistry/metabolism
*Computational Biology/methods
Databases, Protein
Machine Learning
Sequence Analysis, Protein/methods