@article {pmid41309379,
year = {2025},
author = {Kim, H and Jeon, HJ and Jeong, HM and Bang, WY and Lee, HB and Lee, KS and Moon, JS and Kwon, H and Lee, J and Yang, J and Jung, YH},
title = {Modulation of the Gut Microbiome and Metabolomes by Fermentation Using a Probiotic Complex in a Dysbiosis-Associated Fecal Model.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506014},
doi = {10.4014/jmb.2506.06014},
pmid = {41309379},
issn = {1738-8872},
mesh = {*Probiotics/pharmacology ; *Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome/drug effects ; Humans ; Fermentation ; *Feces/microbiology ; *Metabolome ; Inflammatory Bowel Diseases/microbiology ; Bifidobacterium/metabolism ; Lactobacillus/metabolism ; Bacteria/classification/genetics/metabolism/isolation & purification ; Streptococcus/metabolism ; },
abstract = {Inflammatory bowel disease (IBD), affecting up to 0.5% of the global population, is frequently associated with gut microbiota dysbiosis and metabolic imbalances, which contribute to chronic constipation and abdominal discomfort. This study investigated the modulatory effects of an eight-strain probiotic complex comprising Lactobacillus, Bifidobacterium, and Streptococcus species on the gut microbiome and metabolome using an in vitro fecal fermentation model derived from a single IBD patient with dysbiosis. Metagenomic analysis demonstrated that increased abundance of beneficial bacteria, such as Lacticaseibacillus rhamnosus, while suppressing opportunistic pathogens, such as Escherichia coli and Enterococcus faecium. Metabolomic profiling further revealed significant alterations in metabolite levels that may help alleviate gut dysbiosis-related symptoms. These included increases in 3-hydroxybutyric acid, ascorbic acid, cadaverine, L-hydroxyproline, and N-acetylornithine and decreases in lysine and 3-aminoalanine. Given the single-donor design and the use of technical replicates, findings are presented as preliminary and descriptive rather than confirmatory. Collectively, these findings support the potential of probiotic fermentation to modulate microbial composition and metabolic output in a dysbiosis-associated context.},
}

*Probiotics/pharmacology
*Dysbiosis/microbiology/therapy
*Gastrointestinal Microbiome/drug effects
Humans
Fermentation
*Feces/microbiology
*Metabolome
Inflammatory Bowel Diseases/microbiology
Bifidobacterium/metabolism
Lactobacillus/metabolism
Bacteria/classification/genetics/metabolism/isolation & purification
Streptococcus/metabolism

@article {pmid41309042,
year = {2025},
author = {Lin, QB and Xiao, S and Sheng, YZ and Shen, YX and He, Y and Liu, HY and Ye, YW and Chen, SD},
title = {Case report: Pulmonary extranodal mucosa-associated lymphoid tissue lymphoma with eosinophilia diagnosed via exclusion using metagenomic next-generation sequencing.},
journal = {The Journal of international medical research},
volume = {53},
number = {11},
pages = {3000605251399037},
doi = {10.1177/03000605251399037},
pmid = {41309042},
issn = {1473-2300},
mesh = {Humans ; Male ; *Lymphoma, B-Cell, Marginal Zone/diagnosis/genetics/complications/pathology ; *High-Throughput Nucleotide Sequencing ; *Lung Neoplasms/diagnosis/genetics/pathology/complications ; Adult ; *Eosinophilia/diagnosis/genetics/complications/pathology ; *Metagenomics/methods ; Tomography, X-Ray Computed ; Bronchoscopy ; Bronchoalveolar Lavage Fluid ; },
abstract = {Pulmonary extranodal mucosa-associated lymphoid tissue lymphoma (MALToma) is a slow-growing lymphoma often misdiagnosed or undiagnosed due to its nonspecific clinical symptoms. A man in his late 30s initially presented with cough, sputum production, and chest pain, which improved after antibiotic treatment. A definitive diagnosis of pulmonary MALToma was established via bronchoscopic biopsy. Following the exclusion of alternative diagnoses through metagenomic next-generation sequencing of bronchoalveolar lavage fluid, the marked eosinophilia and diverse chest computed tomography findings highlight the need for clinical awareness of this disease.},
}

Humans
Male
*Lymphoma, B-Cell, Marginal Zone/diagnosis/genetics/complications/pathology
*High-Throughput Nucleotide Sequencing
*Lung Neoplasms/diagnosis/genetics/pathology/complications
Adult
*Eosinophilia/diagnosis/genetics/complications/pathology
*Metagenomics/methods
Tomography, X-Ray Computed
Bronchoscopy
Bronchoalveolar Lavage Fluid

@article {pmid41308933,
year = {2025},
author = {Yue, J and Han, X and Yu, J},
title = {Multi-omics insights into ultra-rapid formation of aerobic granular sludge in 9 % salinity wastewater by filling of halotolerant loose mycelial pellets.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133705},
doi = {10.1016/j.biortech.2025.133705},
pmid = {41308933},
issn = {1873-2976},
abstract = {Salt-tolerant aerobic granular sludge (SAGS) had great potential in ultra-hypersaline wastewater treatment while slow and unstable formation hindered its application. Mycelial pellets (MPs) inoculation strategy could accelerate SAGS formation but collapse or peeling commonly occurred due to dense hyphal structures hindering microbial colonization in the connection layer between the shell and core. Besides, no MPs were reported to maintain structure under ultra-hypersaline environment. Herein, a novel strategy using newly-isolated ultra-high salt tolerant fungi Penicillium steckii NCSL-JXA6 with a loose MPs structure was applied for AGS start-up in 9 % salinity wastewater. Granulation completed on Day 1 and maintained stable for 97 days (D10 & D50 > 200 μm, SVI30/SVI5 = 1), which was the fastest under similar salinity. SEM and stained cross-sectional slides showed the loose MPs structure allowed early inner microbial colonization and dense connection layer and core formed before hyphae collapsed, enabling stable transition within 27 days without fragmentation or peeling. Extracellular polymeric substances (EPS) and acyl-homoserine lactone signals (AHLs) (mainly PN, C8-HSL, C12-HSL) increased during transition period, supporting rapid microbial colonization. High TOC and TN removal (∼93 % and ∼ 82 %, respectively) was obtained within only 5 days. Metaproteomic analysis identified Penicillium as module hub of community. Integrative metagenomics and metaproteomics revealed upregulated colonization-related pathways and further confirmed that Penicillium steckii NCSL-JXA6 probably facilitated microbial colonization through metabolic complementarity, adhesion sites, and a loose hyphal structure easily enabling bacterial sensing, motility, adhesion, and biofilm construction. This study proposed a novel loose MPs inoculation theory and achieved the fastest SAGS formation in ultra-hypersaline wastewater.},
}

@article {pmid41308930,
year = {2025},
author = {Wang, S and Dai, B and Wang, Z and Yang, S and Xia, S and Rittmann, BE},
title = {S[0] powder as biofilm carrier and electron donor enhances autotrophic nitrogen removal in sulfur-driven partial denitrification coupled with anammox.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133707},
doi = {10.1016/j.biortech.2025.133707},
pmid = {41308930},
issn = {1873-2976},
abstract = {Sulfur-driven partial denitrification coupled with anammox (SPD/A) has been proposed as an innovative strategy for nitrogen removal from wastewater. This study proposes a novel strategy that integrates 20-μm S[0] powders with anammox granules to establish S[0]-driven partial denitrification coupled with anammox (i.e., S[0]PD/A) for the simultaneous removal of NH4[+] and NO3[-] from wastewater. When the influent concentrations of NH4[+] and NO3[-] were maintained at 31 and 52 mg-N/L, respectively, the efficiency of total-nitrogen removal reached 92 %, with anammox, S[0]-driven denitrification, and sulfammox accounting for 71 %, 27.4 %, and 1.6 %, respectively. Microbial community analysis revealed that anammox bacteria and sulfur-oxidizing bacteria were dominant functional genera involved in the S[0]PD/A. Anammox bacteria were enriched in anammox granules, and sulfur-oxidizing bacteria were enriched in microgranules of S[0] powders and Candidatus Brocadia. These findings highlight distinct microbial niche differentiation, elucidate nitrogen-sulfur metabolic interactions, and offer insights into an autotrophic process for total-nitrogen removal.},
}

@article {pmid41308739,
year = {2025},
author = {Zhang, Y and Liu, J and Zhang, X and Cheng, S and Liu, S and Huang, A and Yu, Y and Liu, J and Chen, H and Shang, D and Yin, P and Ma, S},
title = {Rhein alleviates acute pancreatitis by inhibiting TMAO-mediated inflammatory signaling pathways and reducing acinar cell injury.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.11.056},
pmid = {41308739},
issn = {2090-1224},
abstract = {INTRODUCTION: Acute pancreatitis (AP) represents a significant global health challenge. Despite recent advances in medical treatment, the development of novel therapeutic strategies remains crucial.

OBJECTIVES: Rhein, a natural compound of the Chinese herb Rheum, shows promise in the treatment of AP. However, the exact mechanism underlying its therapeutic effect is still not fully understood.

METHODS: To investigate the association between the rhein-related gut microbiota and AP, we conducted antibiotic-mediated microbiota depletion experiments, fecal microbiota transplantation (FMT), and in vitro bacterial culture experiments. Concurrently, we performed 16S rRNA gene sequencing, metagenomic sequencing, and liquid chromatography‒mass spectrometry (LC‒MS) analyses on mouse fecal samples to characterize alterations in the microbiota and metabolome. Transcriptomic studies were also performed to elucidate the mechanisms underlying acinar cell inflammation.

RESULTS: Rhein alleviated AP by modulating the gut microbiota, as demonstrated by changes in the gut microbiota composition and improvements in AP after FMT in rhein-treated mice compared with those in cerulein-induced AP mice. Specifically, rhein is concentrated mainly in the stomach and intestines, where it exerts anti-inflammatory effects on acinar cells by antagonizing the TLR4/NF-κB/NLRP3 signaling pathway activated by trimethylamine-N-oxide (TMAO). This mechanism is associated with lipid peroxidation and necrosis mediated by oxidative stress. Clinically, disease severity in patients with AP is positively correlated with serum TMAO concentration.

CONCLUSION: Rhein alleviates AP by modulating the intestinal microbiota to reduce TMAO production, thereby suppressing TMAO-induced activation of the TLR4/NF-κB/NLRP3 signaling pathway and inhibiting acinar cell inflammation.},
}

@article {pmid41308447,
year = {2025},
author = {Yang, Z and Chen, B and Zhang, Q and Hu, X and Sun, L and Lu, T and Zhu, L and Ma, Y and Zhong, H and Ni, Y and Qian, H},
title = {Potential of traditional Chinese medicine as an antibiotic alternative for mitigating antibiotic resistance: A case study of Tetrastigma hemsleyanum.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140613},
doi = {10.1016/j.jhazmat.2025.140613},
pmid = {41308447},
issn = {1873-3336},
abstract = {The overuse of antibiotics in livestock production has accelerated the spread of antibiotic resistance genes (ARGs), posing a serious global public health threat. Identification of safe and effective alternatives to antibiotics has therefore become a research priority. Tetrastigma hemsleyanum (TH), a traditional Chinese medicine, modulates the intestinal microbiota; however, the mechanisms underlying its antibiotic-like effects are not fully understood. In this study, we investigated the anti-inflammatory effects of TH in a lipopolysaccharide-induced mouse model of intestinal inflammation. Metagenomic sequencing was used to evaluate its effects on intestinal microbiota composition and ARG abundance. TH effectively alleviated intestinal inflammation, significantly increased the abundance of beneficial microbes such as Lactobacillus, and suppressed the proliferation of major ARG-carrying pathogens, including Proteus and Shigella. Functional analysis revealed that TH treatment markedly enhanced the Wnt and TGF-β signaling pathways, which are associated with intestinal barrier repair and immune response regulation, respectively. Furthermore, TH supplementation restored ARG diversity, reduced the abundance of high-risk ARGs, and suppressed the spread of multidrug resistance genes, underscoring its potential for mitigating antibiotic resistance risks. These findings highlight the potential of TH as an alternative antibiotic and may be used as a feed additive to reduce antibiotic usage while enhancing animal health.},
}

@article {pmid41308344,
year = {2025},
author = {Mao, YL and Hu, Y and Wu, ZP and Sun, YP and Hou, J and Cui, HL},
title = {Natronorubrum marinum sp. nov., Natronorubrum amylolyticum sp. nov., Natronorubrum halobium sp. nov., and Natronorubrum salinum sp. nov., halophilic archaea from a coastal saline-alkali land and two saline lakes.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126680},
doi = {10.1016/j.syapm.2025.126680},
pmid = {41308344},
issn = {1618-0984},
abstract = {Four novel halophilic archaeal strains, DTA7[T], DTA28[T], FCH18a[T], and WLHS9[T], were isolated from a coastal saline-alkali land and two saline lakes in China. The metagenomic analyses revealed that the coastal saline-alkali land from Dongtai tidal flat the highest relative abundance of archaea compared to the saline sediment samples of Feicui Salt Lake and Wulanhushao Salt Lake. These four strains showed high sequence similarities to current species within the genus Natronorubrum judged by 16S rRNA gene and rpoB' gene sequence similarities, and formed tight clusters with current Natronorubrum species based on the phylogenies of these two house-keeping genes. Phylogenomic analysis confirmed the phylogenies based on 16S rRNA gene and rpoB' genes. Comparative genomic analysis revealed that the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values among these four strains and existing species of the genus Natronorubrum were 76.8-92.7 %, 22.8-52.7 %, and 73.4-94.7 %, respectively. These overall genome-related indexes were significantly below the thresholds for species delineation. These four strains showed optimal growth at 1.7-3.1 M NaCl, 37 °C, and pH 7.0-9.5. Strain WLHS9[T] was found to be a neutrophilic halophile, while the others exhibited alkaliphilic halophilic characteristics. The major phospholipids detected in these four strains included phosphatidic acid (PA), phosphatidylglycerol (PG), and phosphatidylglycerol phosphate methyl ester (PGP-Me). The glycolipid of strain WLHS9[T] was identical to that of the current neutrophilic species of Natronorubrum. Based on phylogenetic analysis, phenotypic characteristics, polar lipid profiles, and phylogenomic data, strains DTA7[T], DTA28[T], FCH18a[T], and WLHS9[T] represent four novel species within the genus, namely, Natronorubrum marinum sp. nov., Natronorubrum amylolyticum sp. nov., Natronorubrum halobium sp. nov., and Natronorubrum salinum sp. nov., respectively.},
}

@article {pmid41307726,
year = {2025},
author = {Ferreira, CM and de Affonseca, DB and Barbosa, FAS and Campos, AB and Menezes, R and Brait, L and Viana, PAB and Trindade-Silva, AE and Loiola, M and Azevedo, AR and Coutinho, FH and Assis, APA and Bruce, T and Ramos, PIP and Ara, A and Brouns, R and Andrade, RFS and Guimarães, PR and Meirelles, PM},
title = {Rare Phyla, Such as CPR and DPANN, Shape Ecosystem-Level Microbial Community Structure Dissimilarities.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02595-0},
pmid = {41307726},
issn = {1432-184X},
support = {88887-468244-2019-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 114693/2022-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; RYC2022-037094-I//Ministerio de Ciencia e Innovación/ ; Serra-1709-17818//Instituto Serrapilheira/ ; },
abstract = {Rare microbial lineages, such as members of the candidate phyla radiation (CPR) bacteria and Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota (DPANN) archaea, are increasingly recognized as key components of microbial communities in natural systems. Yet, their global distribution, biogeographic patterns, and broader role in shaping microbial community structure across diverse ecosystems remain poorly characterized. Here, we analyzed 2860 metagenomes spanning nine ecosystems using a curated reference database and a bias-aware taxonomic filtering approach to quantify the richness, relative abundance, and structural influence of low-abundance microbial taxa on community structure across a wide range of ecosystems. Our findings reveal that rare taxa, primarily CPR and DPANN, disproportionately shape microbial community dissimilarities across global ecosystems. We observed that the richness of these two groups, that drives community structure variation, increases with latitude, peaking in temperate regions, thereby contrasting classical latitudinal diversity patterns and suggesting unique biogeographic drivers. CPR and DPANN were predominantly enriched in free-living environments, particularly groundwater and soil, then in host-associated habitats, consistent with niche specialization shaped by environmental filtering and dispersal constraints. These findings challenge abundance-centric assumptions in microbial ecology and highlight the need to integrate low-abundance taxa into macroecological frameworks. Fully resolving their ecological functions, however, will require targeted experimental and multi-omics investigations.},
}

@article {pmid41307551,
year = {2025},
author = {Tamura, T and Ohsugi, Y and Katagiri, S and Kusano, A and Handa, T and Lin, P and Liu, A and Toyoshima, K and Takagi, S and Shiwaku, H and Sugihara, G and Takahashi, H},
title = {Oral Microbiota Associated With Cognitive Impairment in Schizophrenia: Composition and PICRUSt2-Predicted Functional Pathways.},
journal = {Schizophrenia bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1093/schbul/sbaf212},
pmid = {41307551},
issn = {1745-1701},
support = {24K18736//KAKENHI JP/ ; 24K12944//KAKENHI JP/ ; 24K02619//KAKENHI JP/ ; //Ministry of Education, Culture, Sports, Science and Technology of Japan/ ; //Enomoto Mental Health Association/ ; },
abstract = {BACKGROUND AND HYPOTHESIS: Cognitive impairment is a core disabling feature of schizophrenia (SZ). Changes in gut microbiota have been linked to cognitive dysfunction in SZ; however, changes in the oral microbiota in relation to immune dysregulation have only been recently reported, and their relevance to cognition remains unclear. The objective of this study was to explore the relationship between oral microbiota alterations and cognitive impairment in patients with SZ and to evaluate potential mediating mechanisms, including neuroinflammation and microbial functions.

STUDY DESIGN: In this cross-sectional study, we recruited 68 patients with SZ and 32 healthy controls (HC). Cognitive function was assessed using the Wechsler Adult Intelligence Scale-Fourth Edition. Oral microbiota composition was characterized by 16S rRNA gene sequencing, and microbial functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) based on the 16S profiles. Neuroinflammation was assessed using peripheral kynurenine (KYN) pathway activity as a proxy.

STUDY RESULTS: The patients with SZ exhibited significantly lower oral microbiota alpha diversity (driven by reduced evenness) and showed greater cognitive impairment and differences in the KYN pathway markers (neuroinflammation proxies) compared to HC. They also showed shifts in specific bacterial genera and the PICRUSt2-predicted functional pathways. Importantly, the oral microbiota alterations were significantly associated with cognitive impairment. Exploratory mediation analysis suggested that several pathways, including glycan biosynthesis and metabolism, may play a role in this association. In contrast, KYN pathway markers showed no significant association.

CONCLUSIONS: Our findings show an association between the oral microbiota alpha diversity and cognitive impairment in SZ, with the PICRUSt2-predicted functional pathways potentially implicated.},
}

@article {pmid41307322,
year = {2025},
author = {Baima, G and Dabdoub, S and Thumbigere-Math, V and Ribaldone, DG and Caviglia, GP and Tenori, L and Fantato, L and Vignoli, A and Romandini, M and Ferrocino, I and Aimetti, M},
title = {Multi-Omics Signatures of Periodontitis and Periodontal Therapy on the Oral and Gut Microbiome.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70055},
pmid = {41307322},
issn = {1600-0765},
support = {CUP B83C22004800006//Next Generation EU/ ; DM 1557 11.10.2022//Next Generation EU/ ; Prot. P2022YEX5R//Next Generation EU Program and the Italian Ministry of University and Research/ ; },
abstract = {AIM: To characterize the impact of periodontitis and of Steps I-II of periodontal therapy on microbiome composition, function, and metabolic output across the oral and gut environments.

METHODS: A multi-omics analysis was performed on saliva and stool samples collected from 50 systemically healthy individuals with and without Stage III-IV periodontitis. For participants with periodontitis, samples were analyzed both at baseline and 3 months after Steps I-II of periodontal therapy. High-throughput whole metagenome sequencing was used to profile microbial taxa and functional genes, NMR-based metabolomics profiled host-microbial metabolites. Single-omic differential abundance analysis between healthy samples and periodontitis samples was performed with MaAsLin2, while analysis between pre- and post-treatment was conducted with timeOmics. Variable selection and subsequent supervised multivariate analysis to determine group-separating markers utilized multi-level sparse Partial Least Squares Discriminant Analysis (sPLS-DA) through mixOmics. KEGG pathway enrichment was analyzed using clusterProfiler, whereas multi-omic data integration was performed with multi-block Partial Least Squares regression analysis.

RESULTS: Periodontitis was associated with significant compositional and functional changes in both saliva and stool, with increased abundance of pathobionts and loss of health-associated taxa in both niches. A subset of species was shared across oral and gut habitats, with detectable differences across clinical groups. As functional potential, periodontitis enriched microbial pro-inflammatory pathways (lipopolysaccharide biosynthesis, bacterial motility) and depleted beneficial short-chain fatty acid (SCFA)- and vitamin-producing functions. Metabolomic profiles revealed reduced SCFAs and amino acids in periodontitis, with elevated pro-inflammatory metabolites (succinate, trimethylamine) in both saliva and stool. Following therapy, microbial communities and their metabolic output partially reverted toward health-associated profiles, particularly in saliva. Stool samples showed subtler but consistent shifts, including a decrease in some typically oral species and decreased succinate and methylamine and restoration of amino acid and SCFA-related metabolites.

CONCLUSIONS: Periodontitis is associated with coordinated microbial and metabolic signatures across the oral and gut environments. Non-surgical periodontal therapy promotes partial ecological restoration in both niches, supporting the view of oral health as a modifiable target for influencing systemic microbial homeostasis.

TRIAL REGISTRATION: ClinicalTrials.gov identification number: NCT04826926.},
}

@article {pmid41306993,
year = {2025},
author = {Cai, X and Yi, H and Chen, K and Dai, J and Yi, J and Tu, B and Wang, Y and Li, J and Zhuang, J},
title = {Meta-Analysis of the Application Value of Metagenomic Next-Generation Sequencing Technology in the Diagnosis of Infectious Diseases of the Spine.},
journal = {JOR spine},
volume = {8},
number = {4},
pages = {e70134},
pmid = {41306993},
issn = {2572-1143},
abstract = {OBJECTIVE: To evaluate the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in infectious diseases of the spine (IDS).

METHODS: Systematic literature on the application of mNGS in the diagnosis of IDS was retrieved by two independent researchers from databases including Pubmed, China National Knowledge Infrastructure (CNKI), Wanfang, and VIP from the inception to 30 November 2024. Meta-analysis was conducted using Meta-Disc 1.4 and Stata 18.0 software.

RESULTS: The initial search identified 314 articles. After applying predefined inclusion and exclusion criteria, 15 studies were included, encompassing 1236 patients, of which 835 had confirmed IDS. Meta-analysis revealed that the pooled sensitivity and specificity of mNGS for IDS diagnosis were 0.95 (95% CI: 0.88-0.98) and 0.60 (95% CI: 0.48-0.71), respectively. The positive likelihood ratio was 2.3 (95% CI: 1.7-3.2), and the negative likelihood ratio was 0.09 (95% CI: 0.04-0.22). The pooled diagnostic odds ratio was 26 (95% CI: 9-75), with an area under the summary receiver operating characteristic curve of 0.85 (95% CI: 0.82-0.88).

CONCLUSION: The primary diagnostic value of mNGS lies in its ability to serve as a rapid screening tool for disease exclusion. However, for diagnosing IDS, it is essential to integrate other clinical indicators for a comprehensive assessment to confirm the diagnosis.},
}

@article {pmid41306730,
year = {2025},
author = {Nielsen, AB and Kvist-Hansen, A and Todberg, T and Zachariae, C and Pedersen, O and Skov, L},
title = {Dysbiosis of the Saliva Microbiota in Patients with Psoriasis: A Case-Control Study.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {16315-16330},
pmid = {41306730},
issn = {1178-7031},
abstract = {PURPOSE: Accumulating evidence supports the association between altered salivary microbiota and inflammatory diseases. The existing literature on the salivary microbiota in patients with psoriasis is limited. However, differences in the prevalence of Candida species and abundance of several bacterial taxa in saliva have been found between patients and controls. This study aimed to investigate the differences in the composition and functional potential of salivary microbiota in patients with psoriasis compared to their cohabiting partners and healthy controls.

PATIENTS AND METHODS: Samples from 115 of 123 individuals qualified for statistical analysis: patients with psoriasis who did not receive systemic anti-psoriatic treatment (n=47); cohabiting partners (n=21); and age-, sex-, and BMI-matched healthy controls (n=47). One saliva sample was collected from each participant and analysed by shotgun metagenomic sequencing.

RESULTS: A difference in the α-diversity of bacterial species was observed exclusively between patients and controls, with a lower diversity in patients (p=0.041). Variation in bacterial composition (β-diversity) was influenced by smoking (p=0.001) and diet (p=0.025) but not by group status. Using a linear regression model adjusted for smoking and diet, we identified four bacterial classes and five species that were significantly different between the patient, partner, and control groups. One Kyoto Encyclopedia of Genes and Genomes module differed significantly between patients with psoriasis and their partners. No differences in Candida species or abundance were found among the three groups.

CONCLUSION: Comparison of salivary microbiota at the levels of bacterial diversity, composition, and predicted function indicated that psoriasis cases are characterised by dysbiosis.},
}

@article {pmid41306593,
year = {2025},
author = {Xu, H and Xu, Y and Gu, J and Wang, X and Liao, B and Zhou, P and Wu, S and Tao, R and Fu, Y},
title = {Clinical characteristics of Treponema denticola-associated lung abscess diagnosed by metagenomic next-generation sequencing: a case series analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1688498},
pmid = {41306593},
issn = {2235-2988},
mesh = {Humans ; Male ; Middle Aged ; *Treponema denticola/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing ; *Lung Abscess/microbiology/diagnosis/drug therapy ; Retrospective Studies ; Female ; Aged ; Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; *Treponemal Infections/diagnosis/microbiology/drug therapy ; Adult ; },
abstract = {INTRODUCTION: Treponema denticola is an oral anaerobic bacterium commonly associated with periodontitis, but its role in lower respiratory tract infections (e.g., lung abscess) has long been overlooked. For bacteria that grow anaerobically, traditional culture methods exhibit low detection rates, which directly lead to the mis-diagnosis of anaerobic infection. With the ultilization of metagenomic next-generation sequencing (mNGS) in clinical practice, we studied the clinical features and treatment strategies of T. denticola-associated lung abscess.

METHODS: A retrospective analysis was conducted on patients confirmed with T. denticola lung abscess by mNGS from October 2023 to October 2024. Routine aerobic bacterial culture and stains were used. Histopathological analysis and Warthin-Starry silver staining was completed on samples from lung tissue. A literature review was performed using PubMed and CNKI (up to June 2025).

RESULTS: Seven patients were diagnosed with T. denticola lung abscess under mNGS. The cohort predominantly comprised elderly males (mean age 62.3 years), all of whom had underlying oral diseases. Clinical manifestations featured chronic cough (mean symptom duration 3.6 months) and frequent hemoptysis (85.7%), with notably mild systemic inflammation (only one febrile case). Characteristic CT findings included mass-like lesions with necrosis (100%) and cavitation (71.4%), without air-fluid levels. Conventional cultures were overwhelmingly negative, whereas mNGS detected T. denticola in all seven cases. Among the seven patients, one showed clinical improvement after two months of amoxicillin-clavulanate therapy, and another responded well to seven months of doxycycline treatment. The remaining five patients initially treated with levofloxacin or moxifloxacin demonstrated poor responses, with three cases ultimately requiring surgical resection of the lesions.

DISCUSSION: T. denticola lung abscess is most commonly seen in individuals with poor oral hygiene. It presents as an indolent, chronic course and a high incidence of hemoptysis. Typical CT findings include a mass-like lesion with cavitation but no air-fluid level. Traditional microbiological detection often yield false negative results, making mNGS a critical diagnostic tool. First-line therapy should include β-lactams or tetracyclines, and surgery is warranted for refractory cases or massive hemoptysis.},
}

Humans
Male
Middle Aged
*Treponema denticola/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing
*Lung Abscess/microbiology/diagnosis/drug therapy
Retrospective Studies
Female
Aged
Metagenomics/methods
Anti-Bacterial Agents/therapeutic use
*Treponemal Infections/diagnosis/microbiology/drug therapy
Adult

@article {pmid41306589,
year = {2025},
author = {Yu, HL and Liu, R and Wang, HT and Hou, QY and Qin, Y and Yang, X and Gao, ZQ and Yang, LH and Zhao, Q and Ma, H},
title = {Metagenomic analysis of gut microbiota composition and function in wild mice (Rattus flavipectus) infected with Enterocytozoon bieneusi.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1708266},
pmid = {41306589},
issn = {2235-2988},
mesh = {Animals ; *Enterocytozoon ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Microsporidiosis/microbiology/veterinary ; Feces/microbiology ; Mice ; China ; Animals, Wild/microbiology ; Virome ; Bacteria/classification/genetics/isolation & purification ; *Murinae/microbiology ; },
abstract = {BACKGROUND: Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that infects a variety of hosts, including wild mice, potentially influencing their gut microbiota. This study aims to explore how E. bieneusi infection influences the gut microbiota composition and function in wild mice.

METHODS: Fecal samples were collected from 20 wild mice (Rattus flavipectus) in September 2023 in Yunnan Province, China. The PCR results showed that 10 were infected with E. bieneusi and 10 were uninfected, with no samples testing positive for Cryptosporidium spp., Blastocystis, Giardia, Cyclospora or Balantioides coli. DNA was extracted and subjected to metagenomic sequencing using Illumina HiSeq. Gut microbiota composition was assessed using MetaPhlAn4 for species-level annotation. The contigs were used to construct a gene catalog and perform functional annotation. Additionally, viral sequences were identified by analyzing the contigs with software, such as CheckV and Vibrant.

RESULTS: The gut microbiota diversity showed no significant difference between mice infected with E. bieneusi and the control group, with the dominant phyla being Firmicutes and Bacteroidetes. Virome analysis identified 18,192 high-quality viral sequences, with the E. bieneusi group exhibiting higher viral species diversity. Furthermore, significant differences were observed in 178 viral operational taxonomic units (vOTUs) between the two groups, with 161 vOTUs enriched in the E. bieneusi group. Functional analysis demonstrated significant enrichment of several metabolic pathways in the gut microbiota of wild mice infected with E. bieneusi, particularly in the metabolism of terpenoids and polyketides, digestive system, biosynthesis of other secondary metabolites and metabolism of cofactors and vitamins. Notably, unique virus-bacteria correlations were observed in the E. bieneusi group.

CONCLUSIONS: E. bieneusi infection significantly alters the gut virome in wild mice, affecting microbial composition and interactions. The infection appears to drive adaptive changes in microbial functions, especially in metabolic processes, suggesting a host response to infection-related stress.},
}

Animals
*Enterocytozoon
*Gastrointestinal Microbiome/genetics
Metagenomics
*Microsporidiosis/microbiology/veterinary
Feces/microbiology
Mice
China
Animals, Wild/microbiology
Virome
Bacteria/classification/genetics/isolation & purification
*Murinae/microbiology

@article {pmid41306406,
year = {2025},
author = {Hongbin, W and Jing, X and Xianwei, W and Hui, G and Xutao, F},
title = {Successful Treatment of Escherichia coli-Related Spondylitis With an Extended Meropenem Infusion Time for a 72-Year-Old Woman: A Case Report.},
journal = {Clinical case reports},
volume = {13},
number = {12},
pages = {e71531},
pmid = {41306406},
issn = {2050-0904},
abstract = {Escherichia coli (E. coli) causes spinal infections relatively rarely and is often closely associated with parenteral infections. E. coli spondylitis can cause fever and local pain and, in severe cases, can lead to bone destruction, abscess formation, and even the risk of high paraplegia. Therefore, timely and precise diagnosis and effective treatment are crucial. We report successful conservative management of E. coli spondylitis in a 72-year-old female using metagenomic sequencing-guided prolonged meropenem infusion. Extending the infusion time of meropenem achieved clinical resolution without surgery, demonstrating this strategy's efficacy for carbapenem-sensitive spinal infections.},
}

@article {pmid41306274,
year = {2025},
author = {Xue, N and Xia, M and Hu, B and Gong, X and Wang, Z and Zhao, X},
title = {Factors influencing the spatial distributions of river microbial communities at the watershed scale: a case study involving the Wuding River Basin.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1667966},
pmid = {41306274},
issn = {1664-302X},
abstract = {Microbial communities regulate water quality and biogeochemical cycling in rivers, but their responses to geomorphological factors remain unclear. Water samples were collected in August 2024 (summer wet season) from the Wuding River, and metagenomic sequencing was used to investigate microbial community changes and the influences of geomorphological factors. Environment (nutrients, etc.,) exhibited significant spatial heterogeneity with temperature (p < 0.01), total organic carbon (TOC, p < 0.001), dissolved organic carbon (DOC, p < 0.001), chemical oxygen demand (COD, p < 0.05), total phosphorus (TP, p < 0.001) and suspended solids (SS, p < 0.001), which were significantly higher downstream than upstream. Pseudomonadota, Cyanobacteriota, and Actinomycetota were the most important microbial phyla, and Cyanobacteriota (p = 0.016) was significantly more abundant upstream than downstream. The linear discriminant analysis effect size (LEfSe) revealed 8 and 10 biomarkers upstream and downstream, respectively. Upstream microbial communities were adapted to oligotrophic and high-light environments, whereas heterotrophic, carbon-metabolizing communities occurred downstream. Significantly higher ACE (p < 0.05), Chao1 (p < 0.05), Shannon (p < 0.001), and Pielou's evenness (p < 0.001) indices were observed downstream than upstream. The relative abundance of genes associated with carbon cycling (the methane metabolism pathway, TCA cycle, and rTCA cycle) was greater downstream than upstream, as was the relative abundance of nitrogen functional genes. Elevation affected the upstream microbial communities, whereas temperature, TP, TOC, and nitrate nitrogen (NO3-N) affected the downstream communities. The results improve our understanding of how geomorphology drives the environmental factors and then governs the microbial community and their carbon and nitrogen cycling pathways.},
}

@article {pmid41306264,
year = {2025},
author = {Shi, Y and Wang, X and Mao, X and Mi, L and Liu, W and Wang, N},
title = {Severe mitral valve papillary muscle rupture of isolated Whipple's endocarditis: a case report and review of the literature.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1669997},
pmid = {41306264},
issn = {2297-055X},
abstract = {BACKGROUND: Tropheryma whipplei endocarditis (TWE) is rarely reported. Diagnosis is particularly challenging when it occurs as isolated TWE without classical manifestations of Whipple's disease.

CASE PRESENTATION: A 35-year-old Asian female with systemic lupus erythematosus presented with acute heart failure secondary to mitral valve papillary muscle rupture as her sole symptom, requiring emergent veno-arterial extracorporeal membrane oxygenation support and urgent valve replacement. Intraoperative absence of vegetations and negative conventional microbiological examination preliminarily ruled out infective endocarditis. However, on postoperative day (POD) 3, her condition rapidly deteriorated into septic shock. Follow-up chest CT revealed bilateral asymmetric pulmonary infiltrates inconsistent with cardiogenic pulmonary edema alone. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected T. whipplei, providing a crucial diagnostic breakthrough. Subsequent periodic acid-Schiff staining of the resected valve confirmed the definitive diagnosis of isolated TWE. Targeted meropenem therapy for 5 days resulted in significant improvement in both pneumonia and septic shock, permitting ECMO discontinuation. The patient was successfully extubated by POD 12 and discharged on POD 22 with oral co-trimoxazole and doxycycline in a stable condition.

CONCLUSION: We present the first case of isolated TWE in a young Asian female, notable for its atypical clinical presentation, fulminant progression, and profound diagnostic challenges. Clinicians should maintain a high vigilance for blood culture-negative endocarditis. Timely diagnosis and appropriate treatment are crucial for improving prognosis. mNGS analysis of samples from suspected disseminated sites may yield crucial diagnostic breakthrough.},
}

@article {pmid41305954,
year = {2025},
author = {Osei Sekyere, J},
title = {Next-Generation Sequencing in Infectious-Disease Diagnostics: Economic, Regulatory, and Clinical Pathways to Adoption.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70104},
doi = {10.1002/mbo3.70104},
pmid = {41305954},
issn = {2045-8827},
support = {//The author received no specific funding for this study./ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/economics/methods ; *Communicable Diseases/diagnosis ; *Molecular Diagnostic Techniques/economics/methods ; Whole Genome Sequencing/economics/methods ; Polymerase Chain Reaction/economics/methods ; },
abstract = {Next-generation sequencing (NGS) has emerged as a transformative tool for infectious disease diagnosis, offering broad pathogen detection, antimicrobial resistance profiling, and syndromic panel testing. However, widespread clinical adoption remains hindered by insurance reimbursement challenges, high costs, and regulatory barriers. Unlike polymerase chain reaction (PCR), which enjoys well-established Current Procedural Terminology (CPT) codes and reimbursement pathways, many NGS-based tests lack standardized billing mechanisms, discouraging laboratories from integrating NGS into routine diagnostics. This article explores the economic, clinical, and technological considerations of targeted amplicon sequencing (tNGS) versus PCR and whole-genome sequencing (WGS), demonstrating how optimized multiplexing strategies, emerging NGS platforms, and regulatory advancements can enhance feasibility. It is argued that insurance policies must evolve to recognize NGS's superior clinical utility in detecting polymicrobial infections, emerging pathogens, and antimicrobial resistance determinants, ultimately improving patient outcomes and reducing healthcare costs. Current reagent-only costs now average US $65 per microbial genome, US $600 per 30× human genome, and US $130-600 per metagenomic sample when multiplexed; these figures continue to fall with higher multiplexing. To accelerate equitable adoption, we recommend near-term payer coverage pilots for clearly defined clinical indications, dedicated CPT pathways for infectious-disease sequencing (including metagenomic assays), and pragmatic validation frameworks that acknowledge genotype-phenotype limits while leveraging multiplexing and centralized reference workflows.},
}

Humans
*High-Throughput Nucleotide Sequencing/economics/methods
*Communicable Diseases/diagnosis
*Molecular Diagnostic Techniques/economics/methods
Whole Genome Sequencing/economics/methods
Polymerase Chain Reaction/economics/methods

@article {pmid41305578,
year = {2025},
author = {Rehner, J and Gund, M and Becker, SL and Hannig, M and Rupf, S and Schattenberg, JM and Keller, A and The Imagine Consortium, and Molano, LG and Keller, V},
title = {Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223527},
pmid = {41305578},
issn = {2072-6643},
support = {469073465//DFG/ ; },
mesh = {Humans ; *Saliva/microbiology ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Mouth/microbiology ; Male ; Female ; Biomarkers/analysis ; Middle Aged ; Adult ; Dental Plaque/microbiology ; *Bacteria/isolation & purification/classification/genetics ; Metagenome ; },
abstract = {Background: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. Methods: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen types (dental plaque (n = 143; 65 non-obese, 78 obese), saliva (n = 166; 75 non-obese, 91 obese), and stool (n = 109; 57 non-obese, 52 obese)) to compare site-specific microbial shifts between obese (BMI > 30 kg/m[2]) and non-obese individuals. Differential abundance was assessed with ANCOM-BC; effect sizes were summarized as Cohen's d. Results: Across all samples, we detected 240 bacterial species in plaque, 229 in saliva, and 231 in stool, with 46 species present across all three sites. Absolute effect sizes were significantly larger in plaque (mean |d| = 0.26) and saliva (0.25) than in stool (0.21; p = 9 × 10[-3]). Several taxa showed an opposite directionality between oral and gut sites, including Streptococcus salivarius and Bifidobacterium longum, indicating site-specific associations. Notably, Actinomyces sp. and Streptococcus sp. exhibited promising effect sizes as diagnostic markers. Conclusions: The oral and gut microbiomes capture complementary obesity-related signals, with stronger shifts observed in oral sites. We suggest that integrating oral and gut profiling could enhance diagnostic and therapeutic strategies in obesity.},
}

Humans
*Saliva/microbiology
*Obesity/microbiology
*Gastrointestinal Microbiome
Feces/microbiology
*Mouth/microbiology
Male
Female
Biomarkers/analysis
Middle Aged
Adult
Dental Plaque/microbiology
*Bacteria/isolation & purification/classification/genetics
Metagenome

@article {pmid41305529,
year = {2025},
author = {Dong, Y and Fan, S and Zhu, L and Sharshov, K and Wang, W},
title = {Viromic Insights into Gut RNA Virus Diversity Among Three Corvid Species.},
journal = {Viruses},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/v17111508},
pmid = {41305529},
issn = {1999-4915},
support = {grant No. 2022-HZ-812//the program of science and technology international cooperation project of Qinghai province/ ; grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; },
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Metagenomics ; *Crows/virology ; *Gastrointestinal Microbiome ; *Virome ; *Birds/virology ; Genome, Viral ; Tibet ; Genetic Variation ; },
abstract = {As viromics advances, the diversity and ecological significance of RNA viruses in global ecosystems are gaining growing recognition. Nevertheless, studies on RNA viruses in wildlife, especially non-model avian species, are still relatively scarce. This study employed viral metagenomics to systematically characterize the gut RNA viromes of three widely distributed corvid species on the Qinghai-Tibet Plateau: the Red-billed chough (Pyrrhocorax pyrrhocorax), Daurian jackdaw (Coloeus dauuricus), and Rook (Corvus frugilegus). These three corvid species are closely associated with human-inhabited areas on the Qinghai-Tibet Plateau and display distinctive scavenging behaviors that may lower their exposure to environmental pathogens while concurrently elevating their risk of viral infection, rendering them key targets for viral surveillance and research into zoonotic disease transmission. The analysis annotated viral communities into 4 phyla and 8 classes, with Pisuviricota and Kitrinoviricota emerging as the predominant phyla in all samples. Alpha diversity analysis indicated no significant differences among groups, while beta diversity showed significant compositional differences. KEGG annotation revealed that enriched functional pathways were mainly concentrated in "Global and overview maps", "Drug resistance: antimicrobial", and "Biosynthesis of other secondary metabolites". Furthermore, 4 antibiotic resistance genes and 13 putative virulence factor genes were identified. Phylogenetic analysis further indicated that several identified viruses have the potential for cross-species transmission, underscoring the pivotal role of wild birds in viral ecosystems and disease spread. This study uncovered multi-faceted features of the gut RNA viromes in the three crow species, spanning structural, functional, and evolutionary dimensions. These results offer novel perspectives on the viromes of wild corvids and their potential contributions to viral emergence and dissemination in the Qinghai-Tibet Plateau ecosystem.},
}

Animals
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
Metagenomics
*Crows/virology
*Gastrointestinal Microbiome
*Virome
*Birds/virology
Genome, Viral
Tibet
Genetic Variation

@article {pmid41305512,
year = {2025},
author = {Storms, S and Lim, A and Savard, C and Olivera, YR and Kayastha, S and Wang, L},
title = {Identification of Hunnivirus in Bovine and Caprine Samples in North America.},
journal = {Viruses},
volume = {17},
number = {11},
pages = {},
doi = {10.3390/v17111491},
pmid = {41305512},
issn = {1999-4915},
support = {1U18FD006673//Food and Drug Administration Veterinary Laboratory Investigation and Response Network/ ; },
mesh = {Animals ; Cattle ; Goats/virology ; Phylogeny ; Feces/virology ; Genome, Viral ; *Cattle Diseases/virology ; North America/epidemiology ; *Goat Diseases/virology ; High-Throughput Nucleotide Sequencing ; *Diarrhea/veterinary/virology ; Sheep ; Metagenomics ; },
abstract = {Diarrhea in young ruminants is a global issue and causes significant economic losses worldwide. In addition to common pathogens like rotavirus, coronavirus, and astrovirus, new viruses can be identified through unbiased next-generation sequencing (NGS) techniques. Here, we report the initial identification of a hunnivirus from a one-month-old goat with diarrhea using shotgun metagenomic NGS. A complete hunnivirus genome was recovered. Phylogenetic tree analysis revealed that this goat hunnivirus was more closely related to cattle hunnivirus than to small ruminant hunnivirus strains, suggesting a prior cross-species transmission event. The genome was used to design primers/probes for the conserved 3D[pol] RdRP gene for real-time RT-PCR to screen banked ruminant fecal samples. Screening of 144 ruminant fecal samples showed that 9 of 38 goat, 22 of 96 cattle, and 0 of 8 sheep samples were positive for hunnivirus. Sequencing of the 3D[po] region was performed on selected positive samples and revealed two lineages of hunnivirus circulating in North America. Our study highlights the importance of further investigation and monitoring of fecal samples using unbiased metagenomic tools to identify potential pathogens or co-infections in ruminants.},
}

Animals
Cattle
Goats/virology
Phylogeny
Feces/virology
Genome, Viral
*Cattle Diseases/virology
North America/epidemiology
*Goat Diseases/virology
High-Throughput Nucleotide Sequencing
*Diarrhea/veterinary/virology
Sheep
Metagenomics

@article {pmid41305373,
year = {2025},
author = {Pham, TTN and Dao, TK and Nguyen, TVH and Phung, TBT and Nguyen, HD and Nguyen, TQ and Le, TTH and Do, TH},
title = {Diversity and Functional Predictions of Gut Microbiota in Vietnamese Children Aged 6-24 Months with Persistent Diarrhea of Unknown Etiology.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/pathogens14111136},
pmid = {41305373},
issn = {2076-0817},
support = {ĐTĐLCN.63/22//Ministry of Science and Technology/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; *Diarrhea/microbiology ; Male ; Female ; Feces/microbiology ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; *Bacteria/classification/genetics/isolation & purification ; Vietnam ; Biodiversity ; DNA, Bacterial/genetics ; Metagenomics/methods ; Southeast Asian People ; },
abstract = {Persistent diarrhea remains a significant cause of morbidity in young children, yet the role of gut microbiota has not been fully clarified. This prospective study evaluated the diversity and predicted functions of the gut microbiota in 30 children aged 6-24 months with persistent diarrhea of unknown etiology (patient group, PG) and 30 healthy controls (healthy group, HG). Nearly full-length 16S rRNA genes from fecal bacterial metagenomic DNA were sequenced and taxonomically annotated. Subsequently, all downstream analyses, including diversity assessment, differential abundance and functional prediction analyses, and data visualization, were performed using R software (version 4.5.0, 2025). The PG showed lower Shannon and higher Simpson indices than the HG (p < 0.05), reflecting reduced microbial diversity. At the phylum level, Firmicutes predominated in the PG, whereas Actinobacteriota, Bacteroidota, and Verrucomicrobiota were more abundant in the HG (|log2FC| > 1 and FDR < 0.05). At the genus and species levels, the PG exhibited a marked depletion of essential commensals such as Bifidobacterium longum, Faecalibacterium, Lactobacillus, and Eubacterium, alongside an enrichment of opportunistic taxa including Klebsiella, Enterococcus lactis, and Streptococcus spp. (FDR < 0.05). Functional predictions using PICRUSt2 indicated an enrichment of carbohydrate metabolism and reductions in amino acid metabolism, B-vitamin pathways, and the biosynthesis of endogenous antibiotics (FDR < 0.05). These findings suggest that the PG harbors a dysbiotic gut microbiota characterized by reduced diversity, depletion of key commensal taxa, expansion of opportunistic bacteria, and potentially adverse shifts in metabolic functions.},
}

Humans
*Gastrointestinal Microbiome/genetics
Infant
*Diarrhea/microbiology
Male
Female
Feces/microbiology
Child, Preschool
RNA, Ribosomal, 16S/genetics
Prospective Studies
*Bacteria/classification/genetics/isolation & purification
Vietnam
Biodiversity
DNA, Bacterial/genetics
Metagenomics/methods
Southeast Asian People

@article {pmid41304932,
year = {2025},
author = {Hasan, GM and Mohammad, T and Shamsi, A and Sohal, SS and Hassan, MI},
title = {Applications of Genome Sequencing in Infectious Diseases: From Pathogen Identification to Precision Medicine.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {18},
number = {11},
pages = {},
doi = {10.3390/ph18111687},
pmid = {41304932},
issn = {1424-8247},
support = {PSAU/2025/RV/7//Prince Sattam Bin Abdulaziz University/ ; },
abstract = {Background: Genome sequencing is transforming infectious-disease diagnostics, surveillance, and precision therapy by enabling rapid, high-resolution pathogen identification, transmission tracking, and genomic-informed antimicrobial stewardship. Methods: We review contemporary sequencing platforms (short- and long-read), targeted and metagenomic approaches, and operational workflows that connect laboratory outputs to clinical and public health decision-making. We highlight strengths and limitations of genomic AMR prediction, the role of plasmids and mobile elements in resistance and virulence, and practical steps for clinical translation, including validation, reporting standards, and integration with electronic health records. Results: Comparative and population genomics reveal virulence determinants and host-pathogen interactions that correlate with clinical outcomes, improving risk stratification for high-risk infections. Integrating sequencing with epidemiological and clinical metadata enhances surveillance, uncovers cryptic transmission pathways, and supports infection control policies. Despite these advances, clinical implementation faces technical and interpretative barriers, as well as challenges related to turnaround time, data quality, bioinformatic complexity, cost, and ethical considerations. These issues must be addressed to realize routine, point-of-care sequencing. Conclusions: Emerging solutions, including portable sequencing devices, standardized pipelines, and machine-learning models, promise faster, more actionable results and tighter integration with electronic health records. The widespread adoption of sequencing in clinical workflows has the potential to shift infectious disease management toward precision medicine, thereby improving diagnostics, treatment selection, and public health responses.},
}

@article {pmid41304632,
year = {2025},
author = {Wang, B and Meng, F and Cheng, T and Niu, J and Rao, D and Han, Z and Zhang, W and Zhang, Z},
title = {Comprehensive Responses of Physiology and Rhizosphere Microbiome to Saline-Alkaline Stress in Soybean Seedlings with Different Tolerances.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/plants14223480},
pmid = {41304632},
issn = {2223-7747},
support = {2023YFD2300100//National Key Research and Development Program of China/ ; CARS-04-PS15//China Agriculture Research System/ ; JLARS-2025030101//Jilin Agriculture Research System/ ; },
abstract = {Soil salinization severely threatens global crop production. Understanding the relationship between crop saline-alkaline tolerance physiology and the rhizosphere microbiome, and leveraging beneficial microorganisms to enhance crop stress resistance, holds importance for sustainable agricultural development. This study investigated the physiological and rhizosphere microbial responses of two soybean cultivars with different saline-alkaline tolerance to stress. Under saline-alkaline conditions, the tolerant cultivar exhibited superior physiological performance, including higher chlorophyll content, photosynthetic efficiency, and elevated activities of antioxidant enzymes (SOD, POD, and CAT), alongside reduced oxidative damage (MDA) and greater biomass accumulation. Combined metagenomic and physiological analyses revealed significant correlations of Bradyrhizobium and Solirubrobacter with key physiological indicators, including dry weight, PIABS, φpo, and MDA. The tolerant cultivar selectively enriched distinct marker microbes, such as Bradyrhizobium sp. and Bradyrhizobium liaoningense, in its rhizosphere. We conclude that the tolerant cultivar exhibits strong intrinsic physiological resistance. This resistance is further enhanced by a beneficially assembled rhizosphere microbiome, while the host plant's physiology remains the dominant factor.},
}

@article {pmid41304493,
year = {2025},
author = {Sun, H and Li, J and Zhuang, L and Zhang, Y and Zhou, Z and Sun, J and Wang, D and Ren, Y and Xu, X and He, J and Xue, Y},
title = {Ultrasonic Cavitation Transforms Organic Matter to Achieve Reduction of Excess Sludge and Recycling of Carbon Sources.},
journal = {Toxics},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/toxics13110941},
pmid = {41304493},
issn = {2305-6304},
support = {BK20240983//Natural Science Foundation of Jiangsu Province/ ; 52500021//National Natural Science Foundation of China/ ; SJCX24_1645//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; },
abstract = {Reducing the generation of excess sludge and achieving resource recovery are crucial for enhancing the economic efficiency and environmental sustainability of wastewater treatment plants (WWTPs). This study utilizes ultrasonic cavitation technology to transform organic matter into excess sludge to achieve sludge reduction and carbon source recovery. To this end, we systematically investigated the effects of various ultrasonic cavitation conditions on sludge reduction, organic matter conversion, and denitrification efficiency. The results showed that the optimal sludge reduction effect occurs at an original mixed liquid suspended solids (MLSS) of 10 g/L, under neutral and non-aerated conditions, reaching 15.07%. Ultrasonic cavitation treatment significantly enhanced the conversion efficiency of organic matter in the sludge, greatly increasing the concentration of organic matter in the supernatant, with soluble chemical oxygen demand (SCOD) maintained around 900 mg/L, thereby significantly improving the denitrification process. Furthermore, through magnetic-nanoparticle mediated isolation (MMI) and metagenomic sequencing analysis, the dominant denitrifying bacteria and their functional genes that utilize organic matter in the supernatant of ultrasonically treated sludge as a carbon source were identified. Finally, long-term pilot-scale operations further validated the practical application potential of ultrasonic cavitation technology for excess sludge reduction and resource utilization.},
}

@article {pmid41304327,
year = {2025},
author = {Li, X and Ma, X and Wu, L and Mo, Z and Chen, Z and Zhang, R and Xing, M},
title = {Metagenomic Analysis of Gut Microbiota Structure and Function in Adults with Subclinical Hypothyroidism: A Cross-Sectional Study in China.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112643},
pmid = {41304327},
issn = {2076-2607},
support = {2025JK158//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; 2025JK151//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; 2025KY758//Zhejiang Provincial Project for Medical Research and Health Sciences/ ; 2024KY910//Zhejiang Provincial Project for Medical Research and Health Sciences/ ; 25TJYX05//Research Project of Zhejiang Provincial Bureau of Statistics/ ; 2025ZL254//Zhejiang Province Traditional Chinese Medicine Science and Technology Plan Project/ ; 2023-B-04//Zhejiang CDC Science and Technology Talent Incubation Project/ ; },
abstract = {Subclinical hypothyroidism (SCH) is a condition characterized by thyroid hormone dysregulation, often associated with subtle clinical symptoms and metabolic disturbances. Emerging evidence suggests that the gut microbiota plays a crucial role in modulating thyroid function, but the microbiota-thyroid axis in SCH remains poorly understood. This study systematically investigates the gut microbiota composition, functional characteristics, and their correlation with thyroid hormone profiles in SCH patients. Using metagenomic sequencing and thyroid function assessments, we identified significant alterations in the gut microbiota of SCH patients, including a depletion of beneficial microbes such as Blautia and Bifidobacterium, and an enrichment of opportunistic pathogens like Bacteroides and Escherichia. Notably, Blautia depletion was negatively correlated with TSH levels, while Bacteroides abundance positively correlated with TSH levels, further highlighting the role of gut microbiota in thyroid dysfunction. Moreover, functional gene analysis revealed significant alterations in microbial metabolic pathways, with key pathways demonstrating correlations with thyroid hormone levels (free triiodothyronine (FT3) and triiodothyronine (T3)). Our findings suggest that gut microbial dysbiosis is closely associated with SCH. The study provides novel insights into the gut-thyroid axis and its role in SCH, offering new targets for early diagnosis, risk stratification, and intervention strategies in thyroid diseases.},
}

@article {pmid41304325,
year = {2025},
author = {Garzon, A and Portillo-Gonzalez, R and Habing, G and Weimer, BC and Schlesener, C and Silva-Del-Rio, N and Karle, BM and Miramontes, C and Pereira, RV},
title = {Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112641},
pmid = {41304325},
issn = {2076-2607},
support = {2018-68003-27466//USDA National Institute of Food and Agriculture/ ; },
abstract = {Antimicrobial resistance (AMR) poses a critical public health threat, with rising multidrug resistance cases compromising treatment effectiveness. Knowledge about the resistome in dairy production systems remains limited, particularly regarding lactating cows. This study investigated the microbiome and resistome across the hospital, fresh, and mid-lactation pens on 18 conventional dairy farms in California and Ohio using shotgun metagenomic sequencing of pooled fecal samples. Pooled fecal pat samples were collected as part of a larger field study using a quasi-experimental design that assigned farms to the training intervention group (six per state) or the control group (three per state). For the training intervention group, farm worker(s), identified as having the task of diagnosing and treating adult cows on the farm, participated in a training program on antimicrobial stewardship practices. Pooled fecal samples (n = 7) were collected at enrollment and 3 months after the intervention was completed on each participating farm (n = 18). A total of 10,221 bacterial species and 345 AMR genes conferring resistance to 22 antimicrobial classes were identified. The hospital pen exhibited a higher AMR gene diversity compared to fresh and mid-lactation pens (p < 0.05). Several AMR genes showed bimodal distribution, suggesting complex transmission mechanisms. Network analysis revealed distinct gene correlation profiles across pens, with the hospital pen showing fewer gene interactions. Our findings suggest that farm-level antimicrobial drug use may not be the sole or primary driver of resistome composition in pooled fecal samples from dairy cattle, highlighting the need to investigate other factors influencing AMR dynamics in livestock systems.},
}

@article {pmid41304316,
year = {2025},
author = {Hu, P and Carr, AN and Parlov, M and Swift, D and Tiesman, JP and Ramji, N and Schoch, JJ and Teufel, AG},
title = {Metagenomics Investigation on Baby Diaper Area Microbiome and Its Association with Skin pH and Dermatitis in the Diapered Area.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112632},
pmid = {41304316},
issn = {2076-2607},
abstract = {Dermatitis in the diapered area (DDA) is the most common skin condition in infants and can cause significant pain and discomfort, leading to disturbed sleep, changes in temperament, and heightened concern and anxiety for caregivers. This study investigates the relationship between skin pH, microbiome composition, and DDA severity in 158 infants from China, the US, and Germany, focusing on the buttocks, perianal, and thigh regions. Significant variations in DNA biomass and microbiota profiles were noted. Escherichia coli and Veillonella atypica were linked to higher rash scores and elevated skin pH, while Bifidobacterium longum showed a negative correlation with buttocks pH and rash severity but not with perianal rash. Correlation patterns emerged for other species, like Enterococcus faecalis, between perianal and buttocks rashes. Functional analysis identified key categories, including lipid and fatty acid metabolism, cofactor, amino acid, and carbohydrate metabolism, homeostasis and osmolarity stress, and microbial virulence and oxidative stress response, which are vital for skin health, DDA, and pH regulation in infants. These findings underscore the importance of maintaining a mildly acidic skin pH and minimizing fecal and urine residues for optimal infant skin health, suggesting that microbiota significantly influence DDA development, and provide insights for future preventive strategies and therapeutic interventions.},
}

@article {pmid41304309,
year = {2025},
author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN},
title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112625},
pmid = {41304309},
issn = {2076-2607},
support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; },
abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.},
}

@article {pmid41304302,
year = {2025},
author = {Xiao, H and Jing, Y and Ma, K and Wang, Y and Xu, C and Yu, X},
title = {Spring Rest-Grazing Time Influenced Soil Phosphorus Fractions by Altering the Abundance of Genes Involved in Phosphorus Cycling in a Subalpine Meadow.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112618},
pmid = {41304302},
issn = {2076-2607},
support = {GAU-KYQD-2021-01//Scientific Research Start-up Funds for Openly-recruited Doctors, China/ ; GSAU-DKZY-2025-004//China Agricultural University Collaborative Research Support Fund, China/ ; 32460356, 32301509//National Natural Science Foundation of China/ ; },
abstract = {Soil phosphorus (P) availability is a critical factor limiting plant growth and ecosystem productivity that can be strongly influenced by land use factors, such as grazing by livestock. Seasonal grazing management can benefit grassland productivity and soil nutrient cycling in alpine meadows, but its effects on soil P availability and the microbial processes driving P transformation remain poorly understood. To address this, a long-term field experiment was conducted with five different spring rest-grazing periods, where soil P fractions were examined and metagenomic sequencing was employed to assess the functional profiles of microbial genes involved in P cycling. Early spring rest-grazing led to higher concentrations of labile P fractions (Resin-P and NaHCO3-Pi), indicating improved soil P availability. Moreover, rest-grazing in early spring significantly reduced HCl-Pi concentration while increased the concentration of conc. HCl-Po. Metagenomic analysis revealed that early spring rest-grazing may have contributed to a higher relative abundance of the organic P mineralization gene phnA but decreasing the relative abundance of inorganic P solubilization genes ppa, and P-uptake and transport gene pstB. The dominant microbial genera involved in P cycling were Rhodopseudomonas and Mesorhizobium. Soil temperature and water infiltration rate, both affected by early rest-grazing, were identified as the main environmental variables correlated with P-cycling functional gene composition. These influenced taxa with functional genes involving organic P mineralization, inorganic P solubilization, and P-uptake and transport, which may associate with enhancing soil labile P. This study provides insights into potential microbial processes under grazing management in grassland ecosystems.},
}

@article {pmid41304301,
year = {2025},
author = {Martinez, A and St-Pierre, B},
title = {Metagenomic Identification and Characterization of Novel Vitamin B12 Synthesizers from the Rumen of Beef Cattle Fed High-Lipid Inclusion Diets.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112617},
pmid = {41304301},
issn = {2076-2607},
support = {SD00H866-26//South Dakota State University Agricultural Experiment Station Hatch funds (USDA National In-stitute of Food and Agriculture)/ ; },
abstract = {Beef production in intensive systems requires optimal nutrition to maximize growth and profitability. While triglycerides contain twice the energy per unit weight compared to polysaccharides, they are not nearly as commonly used as a supplemental source of energy compared to starch, largely in part due to their negative effects on rumen physiology when their inclusion levels are too high. To gain further insights into the response of rumen microbial communities to elevated dietary lipid levels, we took advantage of rumen samples collected as part of a previously published study that tested high inclusion (4% and 8%) of tallow or linseed oil in beef cattle as part of a 5 × 5 Latin square design, with corn used as a base dietary ingredient. Using a 16S rRNA gene-based profiling approach, two uncharacterized candidate rumen bacterial Operational Taxonomic Units (OTUs), referred to as Bt-995 and Bt-1367, were found to be in higher abundance in rumen samples collected from steers when they were fed diets with higher inclusion of linseed oil. Using a metagenomics approach to assemble contigs corresponding to genomic regions of these OTUs, various predicted metabolic functions were found to be shared. Consistent with the dietary treatments of the original animal study, functions associated with starch utilization and triglyceride metabolism were identified. Unexpectedly, however, contig sets from both OTUs also encoded genes predicted to be involved in vitamin B12 biosynthesis, as well as ethanolamine utilization, a function that is dependent on vitamin B12 as a co-factor. Together, these results indicate that vitamin B12-related functions may provide an advantage to rumen bacteria under conditions of high dietary triglyceride inclusion.},
}

@article {pmid41304286,
year = {2025},
author = {Wu, Y and Liu, C and Qiu, Q and Zhao, X},
title = {Xylo-Oligosaccharide Production from Wheat Straw Xylan Catalyzed by a Thermotolerant Xylanase from Rumen Metagenome and Assessment of Their Probiotic Properties.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112602},
pmid = {41304286},
issn = {2076-2607},
support = {20224ACB205007, 20242BAB20309, 20252BAC240121//Natural Science Foundation of Jiangxi Province/ ; 20252ZDF030003//Central Leading Local Science and Technology Development Special Project/ ; 2024H-100160//Ji'an Municipal Science and Technology Plan Project/ ; },
abstract = {A novel xylanase gene (RuXyn854) was identified from the rumen metagenome and was heterologously expressed in Escherichia coli to produce xylo-oligosaccharides (XOSs) as a prebiotic in this study. RuXyn854, a member of glycosyl hydrolase family 10, demonstrated peak enzymatic activity at pH 7.0 and 50 °C. RuXyn854 retains more than 50% of its activity after treatment at 100 °C for 10 min, highlighting the enzyme's excellent heat resistance. RuXyn854 showed a preferential hydrolyzation of xylan, especially rice straw xylan. RuXyn854 activity was significantly increased in the presence of 15 mM Mn[2+], 0.25% Tween-20, and 0.25% Triton X-100 (125%, 20%, and 26%, respectively). The reaction temperature (30, 40, and 50 °C), dosage (0.20, 0.27, and 0.34 U), and time (90, 120, and 150 min) of RuXyn854 affected the XOS yield and composition, with a higher yield at 0.27 U, 50 °C, and 120-150 min. Xylobiose, xylotriose, and xylotetraose were characterized as the predominant XOS products resulting from the enzymatic hydrolysis of wheat straw xylan by RuXyn854, with xylose present at a mere 0.49% of the total yield. The prebiotic potential of XOSs was assessed through in vitro fermentation with established probiotic strains of Bifidobacterium bifidum and Lactobacillus brevis. The results showed that, regardless of incubation time, XOSs stimulated the growth and xylanolytic enzyme secretion of the two probiotics compared to the controls. These results demonstrate that the feature of RuXyn854 to withstand temperatures up to 100 °C is impressive, and its ability to hydrolyze wheat xylan into XOSs promotes the growth of probiotics.},
}

@article {pmid41304279,
year = {2025},
author = {Zhou, M and Li, Q and Han, Y and Wang, Q and Yang, H and Li, H and Hu, C},
title = {Sulfur Cycling and Life Strategies in Successional Biocrusts Link to Biomass Carbon in Dryland Ecosystems.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112594},
pmid = {41304279},
issn = {2076-2607},
support = {32370125//National Natural Science Foundation of China/ ; 41877419//National Natural Science Foundation of China/ ; 41877339//National Natural Science Foundation of China/ ; XDA17010502//Strategic Priority Research Program at the Chinese Academy of Science/ ; },
abstract = {Examining the changing patterns and underlying mechanisms of soil biomass carbon stocks constitutes a fundamental aspect of soil biology. Despite the potential influence of the sulfur cycle and the life strategies of organisms on community biomass, these factors have rarely been studied in tandem. Biocrusts are model systems for studying soil ecosystems. In this study, metagenomic analysis of biocrusts related to different life strategies from five batches over four consecutive years demonstrated that, in free-living communities, microbial biomass carbon (MBC) synthesis, via assimilatory sulfate reduction (ASR), is primarily coupled with the 3-hydroxypropionate/4-hydroxybutyrate and Calvin-Benson-Bassham cycles. These pathways are affected by the oxidation-reduction potential (Eh), pH, electrical conductivity, and nutrient levels. The decomposition of organic carbon (OC) via dissimilatory sulfate reduction (DSR) was accompanied by the production of dimethyl sulfide (DMS), which was influenced by the C/S ratio and moisture, whereas the synthesis of MBC by symbiotic communities was found to be affected by Eh and pH, and decomposition was affected by the C/S ratio. The MBC stock was influenced by all strategies, with resource strategies having the greatest impacts during the growing season, and the contribution of chemotrophic energy was most significant in free-living communities. In conclusion, the MBC in biocrusts is associated with both ASR and DSR and is facilitated by the A-, S-, and P-strategies under the regulation of the stoichiometric C/S ratio. The exploration of microbial life strategies and sulfur cycling in biocrusts within arid ecosystems in this study offers a new perspective on the patterns of change in soil biomass carbon stocks.},
}

@article {pmid41304278,
year = {2025},
author = {Qiao, T and Zhu, Z},
title = {Multi-Kingdom Gut Microbiome Interaction Characteristics Predict Immune Checkpoint Inhibitor Efficacy Across Pan-Cancer Cohorts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112595},
pmid = {41304278},
issn = {2076-2607},
support = {2025A04J5264//Guangzhou Basic and Applied Basic Research Project/ ; 2023A1515010744//Guangdong Basic and Applied Basic Research Foundation/ ; },
abstract = {An increasing number of studies have confirmed that the gut microbiota, especially bacteria, is closely related to the efficacy of immune checkpoint inhibitor (ICI) therapy. However, the effectiveness of multi-kingdom microbiota and their interactions in predicting the therapeutic effect of ICI therapy remains uncertain. We integrated extensive gut metagenomic databases, including 1712 samples of 10 cohorts from 7 countries worldwide, to conduct rigorous differential analysis and co-occurrence network analysis targeting multi-kingdom microbiota (bacteria, fungi, archaea, and virus). We ultimately identified two subtypes (C1 and C2) by employing a weighted similarity network fusion (WSNF) method. Subtype C2 exhibited higher microbial diversity, better treatment response, and improved prognosis compared to subtype C1. Notably, subtype C2 was associated with higher abundance of beneficial genera such as Bacteroides and Kluyveromyces, while subtype C1 contained potentially detrimental taxa like Malassezia. A multi-kingdom model incorporating 32 genera demonstrated superior predictive accuracy for ICI therapy efficacy compared to single-kingdom models. Co-occurrence network analysis revealed a more robust and interconnected microbiome in subtype C2, suggesting a stable gut environment correlates with effective ICI therapy efficacy. This study highlights the potential of a multi-kingdom signature in predicting the efficacy of ICI therapy, offering a novel perspective for personalized therapy in oncology.},
}

@article {pmid41304274,
year = {2025},
author = {Li, J and Hou, L and Liu, Y and Sun, Y and Li, Y and He, B and Tu, C and Zhou, X},
title = {Metagenomic Sequencing Reveals the Viral Diversity of Bactrian Camels in China.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112589},
pmid = {41304274},
issn = {2076-2607},
support = {32130104//National Natural Science Foundation of China/ ; 32460902//National Natural Science Foundation of China/ ; 2021GKLRLX10//Ningxia Hui Autonomous Region Science and Technology Innovation Leading Talents Cultivation Project/ ; Ning Ren She Han [2024] No. 106//Ningxia Hui Autonomous Region Young Top-notch Talents Cultivation Project/ ; },
abstract = {The Bactrian camel is a key economic livestock species in China and around the world. It yields meat and milk (high-quality functional foods), and the milk reports health benefits. Dromedary camels, as intermediate hosts of MERS-CoV, have garnered significant public health attention. In contrast, viral surveillance in Bactrian camels from the same genus as dromedaries has received limited attention, with only sporadic or regionally confined reports available. Systematic investigations into the virome of viral species, viral diversity, and novel viruses in Bactrian camels are lacking. In this study, swabs were collected from 701 Bactrian camels in China. Through metagenomics, 3262 viral contigs were classified into 16 viral phyla, 29 viral families, and an unclassified group. The different landforms were found to influence viral diversity and composition in Bactrian camels, with mountainous area exerting the greatest impact. The viral composition significantly differed between captive and free-ranging camels. The study identified at least 12 viruses with zoonotic potential, and phylogenetic analysis indicated cross-species transmission in some of them. Additionally, picornavirus, circular Rep-encoding single-stranded (CRESS) DNA virus, and polyomavirus from Bactrian camels may represent novel species or genotypes. To summarize, in this study, we described the baseline virome profile of Chinese Bactrian camels, investigated the ecological factors influencing the viral distribution of Bactrian camels, identified key potential viral risks, and provided a scientific basis for the prevention, control, and early warning of critical viral diseases in Bactrian camels from China.},
}

@article {pmid41304268,
year = {2025},
author = {Bednarska, NG and Reitlo, LS and Beisvag, V and Stensvold, D and Haberg, AK},
title = {Microbial Signatures Mapping of High and Normal Blood Glucose Participants in the Generation 100 Study.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112582},
pmid = {41304268},
issn = {2076-2607},
abstract = {Intestinal dysbiosis has been linked to metabolic disorders, including insulin resistance and type 2 diabetes mellitus (T2DM). T2DM typically follows a prediabetic stage, during which insulin resistance develops. During the early stages of T2DM, its development can be corrected, thus potentially preventing or delaying the onset of the disease. This secondary, exploratory, cross-sectional comparison study aimed to contrast the gut microbiome of individuals with elevated fasting blood glucose to that of individuals with glucose levels within the normal range. This study involved 65 older adults (ages 76-83 years) enrolled from the randomized controlled trial entitled the "Generation 100 Study", all of whom consented to provide their gut microbiome samples. We employed a high-throughput sequencing of the bacterial 16S rRNA gene to obtain metagenomic microbial profiles for all participants. These profiles were then correlated with clinical measures. Overall, microbial alpha diversity was significantly reduced in the high glucose group. We have also observed distinct patterns of microbial beta diversity between high and normal glucose groups. At the phylum level, we found that Synergistes, Elusimicobia, Euryarchaeota, Verrucomicrobia, and Proteobacteria were all significantly decreased in participants with high blood glucose. Additionally, P. copri (ASV 909561) was significantly elevated (10-fold increase) in the high glucose groups, suggesting that it may serve as an early T2DM marker. In contrast to prior reports on the Fusobacterium genus, we found that it was significantly increased in the normal glucose group, with a significant 151-fold increase compared to the high glucose group. Directly linking gut microbiota profiles with clinical indicators such as fasting blood glucose and T2DM diagnosis allows the identification of specific microbial features associated with glucose dysregulation, providing preliminary population-level evidence to guide future translational research. Our results indicate significant changes in the microbiome that may provide valuable insights for early intervention in pre-diabetic states.},
}

@article {pmid41304199,
year = {2025},
author = {Zhang, J and Jiang, F and Li, X and Song, P and Zhang, T},
title = {Metagenome-Based Functional Differentiation of Gut Microbiota and Ecological Adaptation Among Geographically Distinct Populations of Przewalski's Gazelle (Procapra przewalskii).},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112513},
pmid = {41304199},
issn = {2076-2607},
support = {QHEG-2024-04//the 2023 award fund of Qinghai Provincial Key Laboratory of Animal Ecological Genomics/ ; 2024-ZZ-14//Independent Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Univer-sity/ ; 2024T170992//the China Postdoctoral Science Foundation/ ; },
abstract = {Przewalski's gazelle (Procapra przewalskii) is an endangered ungulate endemic to the Qinghai-Tibet Plateau, with a small population size and exposure to multiple ecological pressures. Its gut microbiota may play a crucial role in host environmental adaptation. To investigate the functional divergence of gut microbial communities, we performed high-throughput metagenomic sequencing on 105 wild fecal samples collected from 10 geographic regions around Qinghai Lake. The results revealed significant regional differentiation in key functional modules related to metabolism, antibiotic resistance mechanisms, and virulence-associated pathways. All populations showed enrichment in core metabolic pathways such as carbohydrate and amino acid metabolism, with carbohydrate-active enzymes dominated by glycoside hydrolases (GHs) and glycosyltransferases (GTs), exhibiting overall functional conservation. Although populations shared many antibiotic- and virulence-related reference genetic markers, the marker composition associated with distinct resistance mechanisms and pathogenic processes exhibited clear population-specific patterns, suggesting differential microbial responses to local environmental pressures. Correlation network analysis further identified core taxa (e.g., Arthrobacter and Oscillospiraceae/Bacteroidales lineages) as key genera linking community structure with core metabolic, resistance-related, and virulence-associated marker functions. Overall, the gut microbiota of Przewalski's gazelle exhibits a complex spatially structured functional differentiation, reflecting host-microbiome co-adaptation under region-specific ecological pressures. These findings provide critical methodological and theoretical support for microecological health assessment and regionally informed conservation management of this endangered species.},
}

@article {pmid41304195,
year = {2025},
author = {Wen, L and Luo, H and Li, C and Cheng, K and Shi, L and Liu, L and Wang, K and Tang, H},
title = {Substituting Chemical by Organic Fertilizer Improves Soil Quality, Regulates the Soil Microbiota and Increases Yields in Camellia oleifera.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112509},
pmid = {41304195},
issn = {2076-2607},
support = {U21A20187//National Natural Science Foundation of China/ ; 2022tfs201//Director Fund of Hunan Soil and Fertilizer Institute/ ; XDA0440404//Strategic Priority Research Program of Chinese Academy of Sciences/ ; },
abstract = {The partial substitution of chemical fertilizer with organic fertilizer has been regarded as an effective strategy for enhancing crop yield and soil quality. Nevertheless, its effects on soil properties and microbes remain contentious. In this study, we examined the effects of four different fertilization strategies (including without fertilizer (CK), 100% chemical fertilizer (NPK), 30% organic fertilizer + 70% chemical fertilizer (LOM) and 60% organic fertilizer + 40% chemical fertilizer (HOM)) on soil nutrients and microbial communities through metagenomic sequencing in a Camellia oleifera field experiment. Compared to CK and NPK, HOM significantly increased SOC, TN, TP, AK and AN contents. The substitution of organic fertilizer notably increased Camellia oleifera yield, with the highest increase of 93.35% observed in HOM relative to NPK. Soil bacterial and fungal communities responded inconsistently to fertilization patterns. Bacteria predominated as the main soil microorganisms, and higher rates of organic fertilizer substitution facilitated a shift from bacterial to fungal communities. Organic fertilizer substitution significantly increased soil bacteria diversity and fungal richness, particularly in the HOM. Soil bacterial community structure was more sensitive to fertilization regimes than soil fungi. High rates of organic fertilizer substitution substantially suppressed oligotrophic and increased copiotrophic bacterial communities. Mucoromycota emerged as the dominant fungal group, with a considerable increment in HOM soils. SOC and TN were the main factors affecting Camellia oleifera yield and shaping soil bacteria and fungal diversity and composition. This study provided crucial insights into the ecological implications of organic fertilizer application and the potential of managing soil microorganisms for sustainable Camellia oleifera productivity.},
}

@article {pmid41304167,
year = {2025},
author = {Vitezić, BM and Franović, B and Renko, I and Kuiš, D and Begić, G and Blašković, M and Gabrić, D and Nikolić, M and Vranić, TŠ and Veljanovska, D and Cvijanović Peloza, O},
title = {Microbiome Profiling of Biofilms Formed on d-PTFE Membranes Used in Guided Bone Regeneration.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112478},
pmid = {41304167},
issn = {2076-2607},
support = {2170-137-08-24-19//UNIRI-biomed/ ; IP-2020-02-7875//the Croatian Science Foundation/ ; },
abstract = {In guided bone regeneration (GBR) procedures, d-PTFE membranes are often used as a barrier to promote alveolar ridge regeneration. The aim of this randomized clinical trial was to examine the microbial diversity and structure of biofilms on two types of d-PTFE membranes, Permamem[®] and Cytoplast™, over four-week oral cavity exposure periods. Bacterial biofilm analysis was performed using 16S rRNA next-generation sequencing (NGS) on 36 samples (20 Permamem[®] and 16 Cytoplast™). The results showed significant differences in the microbial profiles: Cytoplast™ membranes showed reduced microbial diversity and an enhanced proportion of pathobionts like Selenomonas, Segatella, Fusobacterium and Parvimonas, which are associated with periodontal and peri-implant diseases and alveolar bone loss. Permamem[®] membranes promoted colonization by bacteria associated with healthy oral conditions, such as the genera Streptococcus, Kingella and Corynebacterium. Overall, our results showed that Cytoplast™ membranes generate a specific type of biofilm, leading to reduction in health-related bacterial species and facilitating growth conditions for dysbiosis shift. Further research and patient follow-ups are essential to thoroughly evaluate the clinical implications of different d-PTFE membranes used in guided bone regeneration.},
}

@article {pmid41304165,
year = {2025},
author = {Tong, F and Feng, X and Yuan, H and Chen, Y and Chen, P},
title = {Oyster Aquaculture Impacts on Environment and Microbial Taxa in Dapeng Cove.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112480},
pmid = {41304165},
issn = {2076-2607},
support = {SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)/ ; 2023TD06//Central Public-interest Scientific Institution Basal, Research Fund, CAFS/ ; 2024YFD2401405; 2024YFB4206600//National Key Research and Development Program of China/ ; },
abstract = {Environmental physicochemical factors and microorganisms play critical roles in the health of oysters. However, the impact of high-density oyster farming-a highly efficient filter-feeding bivalve system-on environmental conditions and microbial community structure and function remains poorly understood. This study conducted four-season monitoring of the water and sediment parameters in a semi-enclosed bay commercial oyster aquaculture (OA) system and a control area (CT), coupled with 16S rRNA amplicon sequencing of the environmental microbiota. Oyster aquaculture caused negligible disruption to water column parameters but significantly increased the concentrations of total organic carbon (TOC, annual mean OA vs. CT:1.15% vs. 0.56%), sulfides (annual mean OA vs. CT:67.72 vs. 24.99 mg·kg[-1]), and heavy metals (Cd, Pb, Cu, Zn, and Cr) in the sediment. α-diversity (Shannon and Chao indices) exhibited minimal overall perturbation, with significant inter-regional differences observed only in winter for both water and sediment. The bacterial community structure of the water column was significantly altered only in winter, whereas sediment communities showed structural shifts in spring, summer, and autumn. Water microbiota were primarily influenced by turbidity, dissolved oxygen, salinity, the Si/N ratio, and silicates. Sediment microbiota were correlated with Pb, Cu, Zn, TOC, Cr, and sediment particle size. Water bacterial functions displayed only four significantly divergent biogeochemical processes annually (sulfur compound respiration; OA vs. CT). In contrast, sediment bacteria exhibited 29 significantly disrupted functions annually, with the greatest seasonal divergence in winter (11/67 functions). Spring, summer, and autumn sediment functions showed distinct patterns. Understanding these environmental-microbial interactions is essential for sustainable oyster aquaculture and ecological optimization.},
}

@article {pmid41304105,
year = {2025},
author = {Zhong, Y and Wu, C and Yao, Z and Li, X and Chi, H and Wu, T and Du, X},
title = {Metagenomic Analysis of Distribution Characteristics and Driving Mechanisms of Antibiotic Resistance Genes, Virulence Factors, and Microbial Communities in Rice Seedling Cultivation Soils.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112419},
pmid = {41304105},
issn = {2076-2607},
abstract = {The extensive utilization of antibiotics in both healthcare and agricultural sectors has precipitated an exponential surge in antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) within environmental matrices, thereby posing formidable threats to ecosystem stability and human health. Given soil's pivotal role as a primary reservoir for ARGs and the inherent potential for these genes to translocate into agricultural produce, this study endeavors to evaluate the distribution patterns of ARGs and virulence factors (VFs) in soils designated for rice seedling cultivation. This study employed metagenomic sequencing to analyze antibiotic resistance genes (ARGs), virulence factors (VFs), and microbial communities in four rice seedling cultivation soils. The results revealed significant variations in microbial alpha diversity, community structure, ARGs, and VFs across soils, with multidrug resistance, glycopeptide resistance, and tetracycline resistance genes predominating. The inclusion of organic matter increased the complexity of the microbial network by increasing the levels of ARGs and VFs. Neutral community model analysis revealed that stochastic processes predominantly governed the assembly of microbial taxa, ARGs, and VFs, though ARGs were subject to stronger deterministic pressures. These communities were shaped by the pH, nitrogen, organic carbon content, electrical conductivity, and salinity of the soil. The core Actinobacteria genera acted as key vectors for ARGs and VFs dissemination. Our findings elucidate the complex interactions between microbes, ARGs, and VFs in cultivation soils and highlight that organic matter amendment, while enhancing fertility, can also increase the potential spread of microbial risk genes, underscoring the need for monitoring and managing ARGs and VFs in agricultural soils to mitigate public health risks.},
}

@article {pmid41302874,
year = {2025},
author = {Berlanga, M and Miñana-Galbis, D and Guerrero, R},
title = {Disentangling Gut Bacterial Community Patterns in Cryptocercus punctulatus and Comparing Their Metagenomes with Other Xylophagous Dyctioptera Insects.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111128},
pmid = {41302874},
issn = {2075-4450},
support = {project PID2021-123735OB-C22.//MCIN/ ; },
abstract = {Gut microbiota enable wood-feeding insects to digest recalcitrant diets. Two DNA-based analyses were performed. Amplicon sequencing of gut microbiota samples from Cryptocercus punctulatus showed inter-individual heterogeneity with visually distinct ordination patterns; however, no statistically significant differences were detected. Shotgun metagenomics was used to compare the taxonomic and functional profiles of C. punctulatus gut microbiota with those of other xylophagous Dictyoptera. Despite taxonomic differences, C. punctulatus microbiota revealed functional convergence with termites (Mastotermes darwiniensis and Nasutitermes sp.). Carbohydrate metabolism was performed by different bacterial phyla across all insects. All insect species possessed metabolic potential for cellulose, hemicellulose, pectin, and starch digestion, but lignin degradation capabilities were not detected. Termites showed higher abundance of chitin and xylan degradation pathways and nitrogen fixation genes, though nitrogen fixation was also present in Cryptocercus cockroaches. Genes for oxidative stress tolerance were present across all species but were most abundant in cockroaches, particularly, Cryptocercus. All insects harbored antibiotic resistance genes, with highest levels found in cockroaches. These findings indicate that metabolic requirements for wood digestion shape gut microbial community assembly across xylophagous insects, with distinct microbial taxa contributing to cellulose and hemicellulose breakdown. Moreover, the widespread presence of antibiotic resistance genes raises concerns about the potential transmission of antibiotic resistance within insect-associated microbiomes.},
}

@article {pmid41301629,
year = {2025},
author = {Wang, Y and Li, L and Liang, Y and Xu, K and Ye, Y and He, M},
title = {Phage Therapy for Acinetobacter baumannii Infections: A Review on Advances in Classification, Applications, and Translational Roadblocks.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111134},
pmid = {41301629},
issn = {2079-6382},
support = {82302568//National Natural Science Foundation of China/ ; 2308085QH283//Anhui Provincial National Science Foundation/ ; 2022xkjT012//Basic and Clinical Collaboration Enhancement Program Foundation of Anhui Medical University/ ; },
abstract = {The global spread of carbapenem-resistant Acinetobacter baumannii (CRAB) poses a severe public health threat, driving growing interest in phage-based precision antibacterial strategies. This systematic review synthesizes recent advances in the field of A. baumannii phage. Modern taxonomy, based on whole-genome phylogeny, has reclassified the majority of A. baumannii phages into the class Caudoviricetes, revealing distinct evolutionary clades that correlate with host tropism and biological properties, superseding the traditional morphological families (Myoviridae, Siphoviridae, Podoviridae). To overcome limitations of natural phage therapy, such as narrow host range, cocktail therapies (ex vivo resistance mutation rates < 5%) and phage-antibiotic synergism (enabling antibiotic efficacy at 1/4 minimum inhibitory concentration) have significantly enhanced antibacterial efficacy. Preclinical models demonstrate that phage therapy efficiently clears pathogens in pneumonia models and promotes the healing of burn wounds and diabetic ulcers via immunomodulatory mechanisms. Technical optimizations include nebulized inhalation delivery achieving 42% alveolar deposition, and thermosensitive hydrogels enabling sustained release over 72 h. Genetic engineering approaches, such as host range expansion through tail fiber recombination and CRISPR/Cas-mediated elimination of lysogeny, show promise. However, the genetic stability of engineered phages requires further validation. Current challenges remain, including limited host spectrum, the absence of clinical translation standards, and lagging regulatory frameworks. Future efforts must integrate metagenomic mining and synthetic biology strategies to establish a precision medicine framework encompassing resistance monitoring and personalized phage formulation, offering innovative solutions against CRAB infections.},
}

@article {pmid41301609,
year = {2025},
author = {Abi Younes, JN and McLeod, L and Otto, SJG and Chai, Z and Lacoste, S and McCarthy, EL and Links, MG and Herman, EK and Stothard, P and Gow, SP and Campbell, JR and Waldner, CL},
title = {Evaluating the Diagnostic Performance of Long-Read Metagenomic Sequencing Compared to Culture and Antimicrobial Susceptibility Testing for Detection of Bovine Respiratory Bacteria and Indicators of Antimicrobial Resistance.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111114},
pmid = {41301609},
issn = {2079-6382},
support = {Not applicable//Genome Prairie/ ; Not applicable//Genome Canada/ ; Not applicable//Genome Alberta/ ; Not applicable//Saskatchewan Agriculture Development Fund/ ; },
abstract = {Background/Objectives: Long-read metagenomic sequencing can detect bacteria and antimicrobial resistance genes (ARGs) from bovine respiratory samples, providing an alternative to culture and antimicrobial susceptibility testing (C/S). This study applied Bayesian latent class models (BLCMs) to estimate the sensitivity (Se) and specificity (Sp) of long-read metagenomic sequencing compared to C/S for detecting Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni, as well as associated macrolide and tetracycline resistance potential. Methods: Deep nasopharyngeal swabs were collected from fall-placed feedlot calves at arrival, 13, and 36 days on feed across two years and two metaphylaxis protocols. Samples underwent C/S and long-read metagenomic sequencing. BLCMs were used to estimate Se and Sp for the detection of bacteria and potential for antimicrobial resistance (AMR). Results: Se and Sp for detecting respiratory bacteria by metagenomics were not significantly different than culture, with four exceptions. For the 2020 samples, Se for M. haemolytica was lower than culture, and Sp for H. somni was lower, while in both 2020 and 2021 samples, Se for P. multocida was higher for metagenomics than culture. The estimated Se and Sp of metagenomics for the detection of msrE-mphE, EstT, and tet(H) within bacterial reads were either not significantly different or were lower than AST, with Sp > 95% with one exception. Conclusions: This study provided BLCM-based estimates of clinical Se and Sp of metagenomics and C/S without assuming a gold standard in a large pen research setting. These findings demonstrate the potential of long-read metagenomics to support bovine respiratory disease diagnostics, AMR surveillance, and antimicrobial stewardship in feedlot cattle.},
}

@article {pmid41301606,
year = {2025},
author = {Aguilar-Rangel, EJ and Paredes-Cárcamo, F and Andrade, MD and Contreras-Sánchez, D and Rain-Medina, V and Campanini-Salinas, J and Medina, DA},
title = {Hospital Wastewater as a Reservoir of Contaminants of Emerging Concern: A Study Report from South America, Chile.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111111},
pmid = {41301606},
issn = {2079-6382},
support = {Proyectos Colaborativos 2024 #3557//San Sebastián University/ ; Fondecyt Iniciación #11230295//Agencia Nacional de Investigación y Desarrollo de Chile/ ; },
abstract = {Background/Objectives: Hospital wastewater is a complex effluent containing a wide range of biological and chemical contaminants, including pharmaceuticals, pathogens, and antimicrobial resistance determinants. These discharges pose a growing threat to aquatic ecosystems and public health, particularly in regions where wastewater treatment is insufficient. This study aimed to characterize the chemical and microbiological composition of untreated effluent from a tertiary care hospital in southern Chile, focusing on contaminants of emerging concern. Methods: Wastewater samples were collected at the hospital outlet before any treatment. The presence of two commonly used pharmaceutical compounds, paracetamol and amoxicillin, was quantified using high-performance liquid chromatography (HPLC). Bacterial isolation was performed using selective media, and antibiotic susceptibility testing was conducted via the disk diffusion method following CLSI guidelines. In addition, metagenomic DNA was extracted and sequenced to assess microbial community composition and functional gene content, focusing on the identification of resistance genes and potential pathogens. Results: A total of 42 bacterial isolates were recovered, including genera with known pathogenic potential such as Aeromonas, Klebsiella, and Enterococcus. Antibiotic susceptibility tests revealed a high prevalence of multidrug-resistant strains. Metagenomic analysis identified the dominance of Bacillota and Bacteroidota, together with 56 antimicrobial-resistance gene (ARG) families and 38 virulence-factor families. Functional gene analysis indicated the presence of efflux-pump systems, β-lactamases, and mobile genetic elements, suggesting that untreated hospital effluents serve as potential sources of resistance and virulence determinants entering the environment. Paracetamol was detected in all samples, with an average concentration of 277.4 ± 10.7 µg/L; amoxicillin was not detected, likely due to its instability and rapid degradation in the wastewater matrix. Conclusions: These findings highlight the complex microbiological and chemical burden of untreated hospital wastewater and reinforce the need for continuous monitoring and improved treatment strategies to mitigate environmental dissemination of antibiotic resistance.},
}

@article {pmid41301593,
year = {2025},
author = {Abi Younes, JN and McLeod, L and Lacoste, SR and Chai, Z and Herman, EK and McCarthy, EL and Campbell, JR and Gow, SP and Stothard, P and Links, MG and Otto, SJG and Waldner, CL},
title = {Respiratory Bacteria and Antimicrobial Resistance Genes Detected by Long-Read Metagenomic Sequencing Following Feedlot Arrival, Subsequent Treatment Risk and Phenotypic Resistance in Feedlot Calves.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antibiotics14111098},
pmid = {41301593},
issn = {2079-6382},
support = {NA//Genome Canada/ ; NA//Genome Prairie/ ; NA//Genome Alberta/ ; NA//Saskatchewan Agriculture Development Fund/ ; },
abstract = {Background/Objectives: Long-read metagenomic sequencing can assign antimicrobial resistance genes (ARGs) to speciated bacterial reads. This study evaluated whether metagenomic data from respiratory bacteria derived from feedlot calves sampled in the early feeding period were associated with subsequent bovine respiratory disease (BRD) treatment and phenotypic antimicrobial resistance (AMR) at treatment. Methods: Deep nasopharyngeal swabs (DNPSs) obtained at arrival processing (1 day on feed; DOF), 13 DOF, and the time of BRD treatment were cultured and subjected to antimicrobial susceptibility testing (AST) and long-read metagenomic sequencing. Analyses focused on macrolide (mphE-msrE, EstT) and tetracycline (tet(H)) ARGs within reads assigned to Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, or Bibersteinia trehalosi. Generalized estimating equations assessed associations between metagenomic results from 1 and 13 DOF and subsequent BRD treatment risk and AST outcomes at treatment, at both the individual animal (calf) and pen levels. Results: Calf-level detection of H. somni at 13 DOF was associated with a greater BRD treatment risk between 14 and 45 DOF. An increased pen prevalence of either M. haemolytica or P. multocida at 13 DOF was associated with a greater BRD treatment risk from 14 to 45 DOF. At 13 DOF, detections of mphE-msrE, EstT, or tet(H) in target bacteria were associated with corresponding phenotypic AMR at BRD treatment. Similarly, a higher pen-level prevalence of mphE-msrE or EstT at 13 DOF was also associated with increased macrolide resistance at BRD treatment. Conclusions: The results from long-read metagenomic sequencing of DNPSs collected at 13 DOF were associated with both BRD risk and AMR at treatment. These findings align with prior culture-based results and support the potential utility of pen-level metagenomic testing for AMR surveillance and informing antimicrobial selection in feedlots.},
}

@article {pmid41301447,
year = {2025},
author = {Rehman, Y and Kim, Y and Tong, M and Blaby, IK and Blaby-Haas, CE and Beatty, JT},
title = {Mining Thermophile Photosynthesis Genes: A Synthetic Operon Expressing Chloroflexota Species Reaction Center Genes in Rhodobacter sphaeroides.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111529},
pmid = {41301447},
issn = {2218-273X},
support = {DE-AC02-05CH11231//United States Department of Energy/ ; DE-AC02-05CH11231//United States Department of Energy/ ; RGPIN 2018-03898//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN 2025-04928//Natural Sciences and Engineering Research Council of Canada/ ; 3-1/PDFP/HEC/2022(B-3)/2339/02//Higher Education Commission/ ; },
mesh = {*Rhodobacter sphaeroides/genetics/metabolism ; *Operon ; *Photosynthesis/genetics ; *Photosynthetic Reaction Center Complex Proteins/genetics/metabolism ; *Chloroflexi/genetics ; Bacterial Proteins/genetics/metabolism ; },
abstract = {Photosynthesis is the foundation of the vast majority of life systems, and is therefore the most important bioenergetic process on earth. The greatest diversity of photosynthetic systems is found in microorganisms. However, our understanding of the biophysical and biochemical processes that transduce light into chemical energy is derived from a relatively small subset of proteins from microbes that are amenable to cultivation, in contrast to the huge number of predicted proteins that catalyze the initial photochemical reactions deposited in databases, such as from metagenomics. We describe the use of a Rhodobacter sphaeroides laboratory strain for the expression of heterologous photosynthesis genes to demonstrate the feasibility of mining this resource, focusing on hot spring Chloroflexota gene sequences. Using a synthetic operon of genes, we produced a photochemically active complex of reaction center proteins in our biological system. We also present bioinformatic analyses of anoxygenic type II reaction center sequences from metagenomic samples collected from hot (42-90 °C) springs available through the JGI IMG database, to generate a resource of diverse sequences that are potentially adapted to photosynthesis at such temperatures. These data provide a view into the natural diversity of anoxygenic photosynthesis, through a lens focused on high-temperature environments. The approach we took to express such genes can be applied for potential biotechnology purposes as well as for studies of fundamental catalytic properties of these heretofore inaccessible protein complexes.},
}

*Rhodobacter sphaeroides/genetics/metabolism
*Operon
*Photosynthesis/genetics
*Photosynthetic Reaction Center Complex Proteins/genetics/metabolism
*Chloroflexi/genetics
Bacterial Proteins/genetics/metabolism

@article {pmid41301445,
year = {2025},
author = {Zhang, J and Xu, G and Yi, Z and Tang, X},
title = {Efficient Mining and Characterization of Two Novel Keratinases from Metagenomic Database.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111527},
pmid = {41301445},
issn = {2218-273X},
support = {2024YFC2815900//National Key R\&D Program of China/ ; SOA: 2017002//Scientific Research Foundation of Third Institute of Oceanography/ ; 23CZB005HJ08//Xiamen Southern Oceanographic Center/ ; 2021J02015//Fujian Provincial Natural Science Foundation of China/ ; },
mesh = {*Peptide Hydrolases/genetics/metabolism/chemistry ; Phylogeny ; Keratins/metabolism ; Animals ; Enzyme Stability ; *Metagenomics ; Data Mining ; *Metagenome ; Feathers ; Kinetics ; Substrate Specificity ; Amino Acid Sequence ; Databases, Genetic ; },
abstract = {Keratin is a fibrous structural protein found in various natural materials such as hair, feathers, and nails. Its high stability and cross-linked structure make it resistant to degradation by common proteases, leading to the accumulation of keratinous waste in various industries. In this study, we developed and validated an effective bioinformatics-driven strategy for mining novel keratinase genes from the Esmatlas (ESM Metagenomic Atlas) macrogenomic database. Two candidate genes, ker820 and ker907, were identified through sequence alignment, structural modeling, and phylogenetic analysis, and were subsequently heterologously expressed in Escherichia coli Rosetta (DE3) with the assistance of a solubility-enhancing chaperone system. Both enzymes belong to the Peptidase S8 family. Enzymatic characterization revealed that GST-tagged ker820 and ker907 exhibited strong keratinolytic activity, with optimal conditions at pH 9.0 and temperatures of 60 °C and 50 °C, respectively. Both enzymes showed significant degradation of feather and cat-hair keratin. Kinetic analysis showed favorable catalytic parameters, including Km values of 9.81 mg/mL (ker820) and 5.25 mg/mL (ker907), and Vmax values of 120.99 U/mg (ker820) and 89.52 U/mg (ker907). Stability tests indicated that GST-ker820 retained 70% activity at 60 °C for 120 min, while both enzymes remained stable at 4 °C for up to 10 days. These results demonstrate the high catalytic capacity, thermal stability, and substrate specificity of the enzymes, supporting their classification as active keratinases. This study introduces a promising strategy for efficiently discovering novel functional enzymes using an integrated computational and experimental approach. Beyond keratinases, this methodology could be extended to screen for enzymes with potential applications in environmental remediation.},
}

*Peptide Hydrolases/genetics/metabolism/chemistry
Phylogeny
Keratins/metabolism
Animals
Enzyme Stability
*Metagenomics
Data Mining
*Metagenome
Feathers
Kinetics
Substrate Specificity
Amino Acid Sequence
Databases, Genetic

@article {pmid41301179,
year = {2025},
author = {Liu, D and Kuo, J and Lin, CH},
title = {Computational Investigation of Smooth Muscle Cell Plasticity in Atherosclerosis and Vascular Calcification: Insights from Differential Gene Expression Analysis of Microarray Data.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/bioengineering12111223},
pmid = {41301179},
issn = {2306-5354},
abstract = {The dedifferentiation of smooth muscle cells (SMCs) is the main cause of atherosclerosis and vascular calcification. This study integrated the gene expression data of multiple microarrays to identify relevant marker molecules. A total of 72 Gene Expression Omnibus (GEO) samples (GSM) were collected from 10 gene expression data series (GSE) and divided into five groups: non-SMC, SMC, atherosclerotic SMC (SMC-ath), calcified SMC (SMC-calc), and treated SMC (SMC-t). The SMC-t group included synthetic SMCs that had undergone treatment to inhibit proliferation, migration, or inflammation. The gene expression data were merged, normalized, and batch effects were removed before differential gene expression (DGE) analysis was performed via linear models for microarray data (limma) and statistical analysis of metagenomic profiles (STAMPs). The genes with expressions that significantly differed were subsequently subjected to protein-protein interaction (PPI) and functional prediction analyses. In addition, the random forest method was used for classification. Twelve proteins that may be marker molecules for SMC differentiation and dedifferentiation were identified, namely, Proprotein convertase subtilisin/kexin type 1 (PCSK1), Transforming growth factor beta-induced (TGFBI), Complement C1s (C1S), Phosphomannomutase 1 (PMM1), Claudin 7 (CLDN7), Calcium binding and coiled-coil domain 2 (CALCOCO2), SAC3 domain-containing protein 1 (SAC3D1), Natriuretic peptide B (NPPB), Monoamine oxidase A (MAOA), Regulator of the Cell Cycle (RGCC), Alpha-crystallin B Chain (CRYAB), and Alcohol dehydrogenase 1B (ADH1B). Finally, their possible roles in SMCs are discussed. This study highlights the feasibility of bioinformatics analysis for studying SMC dedifferentiation.},
}

@article {pmid41301089,
year = {2025},
author = {Ostos, I and Ruiz, I and Cruz, D and Flórez-Pardo, LM},
title = {Methane Concentration Prediction in Anaerobic Codigestion Using Multiple Linear Regression with Integrated Microbial and Operational Data.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/bioengineering12111133},
pmid = {41301089},
issn = {2306-5354},
support = {No. DGI-01-2025//Dirección General de Investigaciones of Universidad Santiago de Cali/ ; },
abstract = {Anaerobic codigestion of organic residues is a proven strategy for enhancing methane recovery. However, the complexity of microbial interactions and variability in operational conditions make it difficult to estimate methane concentration in real time, particularly in rural contexts. This study developed a multiple linear regression model to predict methane concentration using operational data and microbial community profiles derived from 16S rRNA gene sequencing. The system involved the codigestion of cassava by-product and pig manure in a two-phase anaerobic reactor. Predictor variables were selected through a hybrid approach combining statistical correlation with microbial functional relevance. The final model, trained on 70% of the dataset, demonstrated satisfactory generalization capability on the other 30 test set, achieving a coefficient of determination (R[2]) of 0.92 and a mean relative error (MRE) of 6.50%. Requiring only a limited set of inputs and minimal computational resources, the model offers a practical and accessible solution for estimating methane levels in decentralized systems. The integration of microbial community data represents a meaningful innovation, improving prediction by capturing biological variation not reflected in operational parameters alone. This approach can support local decision making and contribute to Sustainable Development Goal 7 by promoting reliable and affordable technologies for clean energy generation in rural and resource-constrained settings.},
}

@article {pmid41300910,
year = {2025},
author = {Jin, X and Shen, H and Zhou, P and Yang, J and Yang, S and Ni, H and Yu, Y and Zhang, Z},
title = {Research Progress on Sepsis Diagnosis and Monitoring Based on Omics Technologies: A Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/diagnostics15222887},
pmid = {41300910},
issn = {2075-4418},
support = {2023YFC3603104//China National Key Research and Development Program/ ; Nos. 82472243 and 82272180//National Natural Science Foundation of China/ ; LHDMD24H150001//Huadong Medicine Joint Funds of the Zhejiang Provincial Natural Science Foundation of China/ ; 2024C03240//the Key Research & Development Project of Zhejiang Province/ ; No. GZY-ZJ-KJ-24082//a collaborative scientific project co-established by the Science and Technology Department of the National Administration of Traditional Chinese Medicine and the Zhejiang Provincial Administration of Traditional Chinese Medicine/ ; No. 2024KY1099//the General Health Science and Technology Program of Zhejiang Province/ ; No. ZJDXLQCXZCJBGS2024016//the Project of Zhejiang University Longquan Innovation Center/ ; 320.6750.2024-23-07//Wu Jieping Medical Foundation Special Research Grant/ ; },
abstract = {Sepsis poses a significant global health burden, with millions of cases and high mortality rates annually, largely due to challenges in early diagnosis and monitoring. Traditional methods, reliant on nonspecific clinical manifestations and limited biomarkers like C-reactive protein and procalcitonin, often fail to distinguish infection from non-infectious inflammation or capture disease heterogeneity. This review synthesizes recent progress in omics technologies-genomics, transcriptomics, proteomics, and metabolomics-for advancing sepsis management. Genomics, via metagenomic next-generation sequencing, enables rapid pathogen identification and genetic variant analysis for susceptibility and prognosis. Transcriptomics reveals molecular subtypes and immune dynamics through RNA sequencing and single-cell approaches. Proteomics and metabolomics uncover protein and metabolite profiles linked to immune imbalance, organ damage, and metabolic disorders. Multi-omics integration, enhanced by artificial intelligence and machine learning, facilitates biomarker discovery, patient stratification, and predictive modeling, bridging laboratory findings to bedside applications like rapid diagnostic tools and clinical decision support systems. Despite advancements, challenges including data heterogeneity, high costs, and ethical concerns persist. Future directions emphasize single-cell and spatial omics, AI-driven personalization, and ethical frameworks to transform sepsis care from reactive to proactive, ultimately improving outcomes.},
}

@article {pmid41300336,
year = {2025},
author = {Liu, Y and Xie, J and He, Y and Shi, Q and Gong, Q and Zhao, W and Qin, C and Zhou, C},
title = {Metabolome and Metagenome Signatures Underlying the Differential Resistance of Percocypris pingi, Crucian Carp, and Yellow Catfish to Ichthyophthirius multifiliis Infection.},
journal = {Biology},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/biology14111546},
pmid = {41300336},
issn = {2079-7737},
support = {2023M732476//China Postdoctoral Science Foundation/ ; NJTCSC24-3//Open Project of Sichuan Provincial Key Laboratory of Fish Resources Conservation and Utilization in the Upper Reaches of the Yangtze River/ ; 2023YFH0046//Sichuan Science and Technology Program/ ; },
abstract = {Ichthyophthirius multifiliis poses a significant threat to global aquaculture, yet some fish species exhibit remarkable resistance. This study employed a combined LC-MS-based metabolomics and 16S rRNA gene sequencing approach to investigate the intrinsic mechanisms underlying the differential susceptibility of Percocypris pingi, crucian carp, and yellow catfish. Our results revealed distinct skin molecular and microbial profiles in P. pingi associated with its enhanced resilience. Metabolomic analysis identified a significant upregulation of key antioxidants (L-Glutathione reduced, L-Glutathione oxidized, L-Cysteine-glutathione gisulfide, Uric acid, Histamine, N-Acetylhistamine, and scorbic acid) in P. pingi, most notably L-Glutathione reduced, which was 31- and 59-fold higher than in yellow catfish and crucian carp, respectively. Functional enrichment further highlighted the critical role of enhanced antioxidant capacity (centered on glutathione metabolism) and immune/inflammatory responses in the resistance to I. multifiliis of P. pingi. Concurrently, skin microbiome analysis showed that P. pingi hosted a microbial community distinct from the other two species, with significantly higher α-diversity. Notably, P. pingi skin was significantly depleted of the parasitic bacteria Candidatus_Megaira and Candidatus_Midichloria, which were highly abundant in the susceptible species. Furthermore, predicted metagenomic functions indicated that P. pingi's microbiota was enriched in fundamental metabolic pathways, whereas the microbiota of crucian carp and yellow catfish was skewed towards disease- and immune-related pathways. In conclusion, our findings demonstrate that the superior resistance of P. pingi to I. multifiliis is likely conferred by a synergistic effect of a robust skin antioxidant capacity (primarily driven by glutathione) and a protective skin microbiome that excludes specific parasites. This study provides novel insights into the multi-faceted mechanisms of disease resistance in fish.},
}

@article {pmid41300008,
year = {2025},
author = {Rajah Kumar, M and Amankwaa, AO and Razali, NS and Mohamad, NE and Khalid, M and Abdullah, JO and Masarudin, MJ and Osman, MA and Abd Rahman, NMAN and Alitheen, NB},
title = {Preliminary Evaluation of the Gut Microbiota Modulatory Potential of Malaysian Kefir Water in Ageing Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/foods14223851},
pmid = {41300008},
issn = {2304-8158},
support = {FRGS-777 MRSA/1/2018/SKK10/UPM/02/1//Fundamental Research Grant Scheme (FRGS) by the Malaysian Ministry of Higher Education (MoHE)/ ; },
abstract = {Ageing is often accompanied by gut microbiota alterations that contribute to dysbiosis-a recognised hallmark of ageing and a risk factor for neurodegenerative diseases. Probiotic interventions offer a promising approach to restore microbial homeostasis. This preliminary study explored the potential modulatory effects of Malaysian kefir water, a Lactobacillus-enriched fermented beverage with previously reported antioxidant and neuroprotective properties in D-galactose-induced ageing mice. Kefir water was administered as both a pre-treatment and co-treatment, and gut microbiota changes were assessed using 16S rRNA metagenomic sequencing of faecal samples. Alpha and beta diversity analyses showed a stable microbial diversity across treatments. However, preliminary descriptive trends suggested that kefir water may influence specific bacterial populations. Increases were observed in Muribaculaceae and Lactobacillaceae, along with apparent decreases in Lachnospiraceae and Prevotellaceae. Both kefir treatments tended to increase the abundance of Ligilactobacillus, with the co-treatment group appearing to restore the Firmicutes/Bacteroidota ratio toward control levels, while the pre-treatment group showed a tendency to further reduce this ratio. Collectively, these findings provide preliminary indications that kefir water may hold potential as a dietary approach to modulate gut microbial changes associated with ageing. However, confirmation through studies with larger sample sizes and broader analytical coverage is necessary to substantiate these initial observations.},
}

@article {pmid41299763,
year = {2025},
author = {Manrique-de-la-Cuba, MF and López-Rodríguez, M and Abades, S and Trefault, N},
title = {Cold adaptation and horizontal gene transfer shape Antarctic sponge microbiomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02262-z},
pmid = {41299763},
issn = {2049-2618},
support = {Fondecyt 1230758//Agencia Nacional de Investigación y Desarrollo/ ; DG_02-22//Instituto Antartico Chileno/ ; },
abstract = {BACKGROUND: Marine sponges exhibit wide distribution in tropical, temperate, and polar environments. They host diverse microbiomes important to their survival and ecological roles. Antarctic sponges, thriving in extreme cold environments, harbor unique microbial communities. However, functional differences distinguishing Antarctic sponge microbiomes have been poorly investigated. In this study, we investigated how the functional composition of the microbiomes of Antarctic sponges differs from that of their counterparts in other environments, with a particular focus on functions related to cold adaptation. We also assessed the role of horizontal gene transfer (HGT) in driving these functional adaptations.

RESULTS: Antarctic sponge microbiomes displayed a unique functional signature characterized by significantly higher proportions of genes related to cold adaptation, such as cold shock proteins, chaperones, heat shock proteins, and osmoprotectants, compared to their tropical and temperate counterparts, and antioxidants compared to the surrounding seawater. HGT was prevalent in Antarctic sponge symbionts, particularly in the dominant Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia, contributing equally to metabolic functions and cold adaptation, with an important fraction of the latter exhibiting long-distance horizontal gene transfer (HGT). Conjugation, primarily mediated by integrative and conjugative elements (ICE), is a proposed crucial mechanism driving horizontal gene transfer (HGT) in Antarctic sponge symbionts. The cold shock protein C (CspC), linked to cold adaptation, was restricted to Proteobacteria and identified as a potential horizontally acquired gene exclusive to sponge symbionts compared to free-living bacteria in the Antarctic marine ecosystem.

CONCLUSIONS: Antarctic sponge microbiomes exhibit higher proportions of functional adaptations for cold environments facilitated by horizontal gene transfer (HGT). These findings highlight the evolutionary importance of HGT mechanisms in shaping microbial symbioses in extreme environments. Further exploration of HGT dynamics and the role of specific symbionts in cold adaptation could reveal novel insights into microbial evolution and host-symbiont interactions in polar ecosystems. Video Abstract.},
}

@article {pmid41299634,
year = {2025},
author = {Meawad, M and Singh, D and Deng, A and Sonthalia, R and Cai, E and Dumeaux, V},
title = {Functional archetypes in the human gut microbiome reveal metabolic diversity, stability, and influence disease-associated signatures.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {241},
pmid = {41299634},
issn = {2049-2618},
support = {Vector Scholarship in Artificial Intelligence//Vector Institute/ ; Globalink Summer Internship Award//MITACS/ ; 391682//Natural Sciences and Engineering Research Council of Canada/ ; 43481//Canadian Foundation for Innovation J. Evans Leaders Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metagenomics/methods ; Adult ; Metagenome ; Female ; Male ; },
abstract = {BACKGROUND: Understanding the functional diversity of the gut microbiome is critical for elucidating its roles in human health and disease. While traditional approaches focus on taxonomic composition, functional configurations of the microbiome remain understudied. This study introduces a deep-learning framework combined with archetypal analysis to identify and characterize functional archetypes in the adult human gut microbiome. This approach aims to provide insights into interindividual variability, function-driven microbiome stability, and the potential confounding role of functional diversity in disease-associated microbial signatures.

RESULTS: Analyzing 9838 whole-genome metagenomic samples from healthy adults across 29 countries, we identified three distinct functional archetypes that define the boundaries of the gut microbiome's functional space. Each archetype is characterized by unique metabolic potentials: Archetype 1 is enriched in sugar metabolism, branched-chain amino acid biosynthesis, and cell wall synthesis; Archetype 2 is dominated by fatty acid metabolism and TCA cycle pathways; and Archetype 3 is defined by amino acid and nitrogen metabolism. While most gut microbiome communities are a blend of these archetypes, some align closely with a single archetype, potentially reflecting adaptation to host factors such as distinct dietary patterns. Proximity to these archetypes correlates with microbiome stability, with Archetype 2 representing the most resilient state, likely due to its metabolic flexibility and diversity. Functional archetypes emerged as a potential confounder in disease-associated microbial signatures, including in type-2 diabetes, colorectal cancer, and inflammatory bowel disease (IBD). In IBD, archetype-specific shifts were observed: Archetype 1-dominant samples exhibited increased carbohydrate metabolism, while Archetype 3-dominant samples showed enrichment in inflammatory pathways. These findings highlight the potential for archetype-specific functional changes to inform microbiome-targeted interventions.

CONCLUSIONS: The identified functional archetypes provide a robust framework for addressing interindividual variability and potential confounding in gut microbiome-based disease studies. By incorporating archetypes as potential confounders or stratification factors, researchers can reduce variability, uncover novel pathways, and improve the precision of microbiome-targeted interventions. The deep-learning framework can be applied to other host-associated microbial ecosystems, providing new insights into microbial functional dynamics and their implications for the host's health.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Bacteria/classification/metabolism/genetics/isolation & purification
Metagenomics/methods
Adult
Metagenome
Female
Male

@article {pmid41299624,
year = {2025},
author = {Zhang, XA and Zhang, MQ and Liu, YW and Lin, L and Zhang, JT and George, T and Jalloh, MB and Sevalie, S and Kargbo, KB and Jiang, BG and Mi, ZQ and Wang, SC and Si, GQ and Zhang, L and Fang, LQ and Chen, WW and Dong, G and Huang, WJ and Liu, W},
title = {Virome characterization of wild small mammals provides new insight into zoonotic pathogens in West Africa.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {242},
pmid = {41299624},
issn = {2049-2618},
support = {81825019//National Science Fund for Distinguished Young Scholars/ ; },
mesh = {Animals ; *Virome/genetics ; *Zoonoses/virology/transmission ; Metagenomics/methods ; Chiroptera/virology ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; Africa, Western ; Humans ; Shrews/virology ; Genome, Viral ; *Animals, Wild/virology ; Disease Reservoirs/virology ; *Mammals/virology ; Rodentia/virology ; *Viral Zoonoses/virology/transmission ; },
abstract = {BACKGROUND: A significant number of infectious diseases affecting humans have been associated with zoonotic viruses. Wild small mammals, such as bats, rodents, and shrews, serve as natural reservoirs for a multitude of zoonotic viruses, particularly in Africa, where zoonosis is prevalent. Nevertheless, our knowledge of the virome composition within these hosts remains limited, impeding a more profound understanding of spillover events into human populations.

RESULTS: We employed a viral metagenomics approach to characterize the virome in 846 wild small mammals sampled from Sierra Leone. Based on the complete RNA-dependent RNA polymerase genome, a total of 39 RNA viruses infecting mammals were identified, comprising 13 known viruses and 26 novel viruses. Notably, the Paramyxoviridae family exhibited the highest diversity of viral species across all three orders of wild mammal. The animal species Hipposideros jonesi and Lophuromys chrysopus were found to harbor the highest viral richness. Among these viral species, 15 were identified as cross-species transmitted viruses shared among different animal species, 3 were classified as zoonotic (Encephalomyocarditis virus, Rocahepevirus sp., and Lassa virus), while 3 others posed a potential risk for spillover (melian virus, Rodent hepacivirus, Hunnivirus A). Cross-species transmission analysis revealed that rodents played central roles in virus sharing, while cross-order viral transmission was less likely to occur in bats. Among 26 newly identified viruses, four viruses (Bat ledantevirus 2, Rattus rattus jeilongvirus, Miniopterus inflatus ribovirus, and Rat mamastrovirus) were predicted to have high zoonotic potential. Among them, Bat ledantevirus 2 exhibited the highest zoonotic potential and phylogenetic relatedness to the known human-infecting virus (Le Dantec virus). Further seroepidemiological analysis in patients, using single-round infectious virus particles as antigens, revealed the presence of neutralizing antibodies against Bat ledantevirus 2, a novel virus belonging to the Rhabdoviridae family.

CONCLUSIONS: These findings highlight the critical need for enhanced surveillance at the human-animal interface in order to identify viruses with cross-species transmission potential prior to their spillover into human population. Video Abstract.},
}

Animals
*Virome/genetics
*Zoonoses/virology/transmission
Metagenomics/methods
Chiroptera/virology
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
Africa, Western
Humans
Shrews/virology
Genome, Viral
*Animals, Wild/virology
Disease Reservoirs/virology
*Mammals/virology
Rodentia/virology
*Viral Zoonoses/virology/transmission

@article {pmid41299512,
year = {2025},
author = {Kansou, E and Aubry, A and Brochot, E and Priam, A and Cabry-Goubet, R and Bosquet, D and Demey, B},
title = {Human papillomavirus seminal carriage alters virome diversity and male fertility: a case-control study.},
journal = {Reproductive biology and endocrinology : RB&E},
volume = {23},
number = {1},
pages = {154},
pmid = {41299512},
issn = {1477-7827},
mesh = {Humans ; Male ; Case-Control Studies ; *Virome/genetics ; Adult ; *Semen/virology ; Retrospective Studies ; *Papillomavirus Infections/virology/complications ; *Infertility, Male/virology ; *Papillomaviridae/genetics/isolation & purification ; *Fertility/physiology ; Spermatozoa/virology ; Human Papillomavirus Viruses ; },
abstract = {BACKGROUND: A link between idiopathic male infertility and viral infections exhibiting seminal carriage has emerged recently. In this respect, human papillomavirus (HPV) appears to be the most prevalent sexually transmitted agent worldwide. The viruses present in the genital environment comprise the genital virome. HPV infection reportedly disrupts homeostasis of the virome in women but this topic has not previously been studied in men.

METHODS: This was a retrospective study of males attending the fertility clinic at Amiens University Medical Center (Amiens, France). Men with a multiple-type HPV infection in the sperm (n = 15) were considered to be cases, and men with no detectable HPV in the sperm were considered to be controls (n = 13). The molecular virome in cases and controls was described via metagenomic next-generation sequencing. The cases and controls were compared with regard to genomic, clinical and sperm-related characteristics.

RESULTS: The seminal virome analysis revealed the predominance of Papillomaviridae in cases (63.4%). Other virus families found in both groups (albeit with lower proportions of reads in cases than in controls) were Herpesviridae (6.9% vs. 40.5%, respectively), Polyomaviridae (11.3% vs. 17.8%, respectively), and other viral sequences (18.4% vs. 40%, respectively). There was no difference in viral diversity between the two groups (p = 0.0692). Viral diversity was correlated with the semen sample volume, progressive sperm motility, total motility, and sperm vitality in cases but not in controls. Univariate and multivariate comparative analyses did not reveal significant differences in sperm parameters between cases and controls.

CONCLUSIONS: The male seminal virome mainly comprises viruses from the Papillomaviridae, Herpesviridae and Polyomaviridae families. The correlation between viral diversity and sperm parameters in HPV-positive patients suggests that HPV-specific interactions within the seminal virome are responsible for variations in sperm parameters. Hence, alterations in the seminal virome (due mostly to HPV infection) might impact sperm parameters and thus male fertility.},
}

Humans
Male
Case-Control Studies
*Virome/genetics
Adult
*Semen/virology
Retrospective Studies
*Papillomavirus Infections/virology/complications
*Infertility, Male/virology
*Papillomaviridae/genetics/isolation & purification
*Fertility/physiology
Spermatozoa/virology
Human Papillomavirus Viruses

@article {pmid41299356,
year = {2025},
author = {Shen, A and Xu, X and Xu, L and Nie, X and Ai, J and Chen, W},
title = {Clinical utility of metagenomic next-generation sequencing (mNGS) and a novel PCR-based point-of-care testing (POCT) for pathogen detection in pulmonary infections: a retrospective study.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-11814-5},
pmid = {41299356},
issn = {1471-2334},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) and multiple point-of-care testing (POCT) techniques have demonstrated significant potential in pathogen detection. However, neither technology fully meets all clinical diagnostic needs for pulmonary infections. This study aimed to evaluate the complementary detection performance and clinical applicability of POCT and mNGS in pulmonary infections, using conventional culture as a reference.

METHODS: This study enrolled forty-five patients with suspected lower respiratory tract infections for concurrent evaluation using POCT and mNGS. The detection performance of traditional culture methods, POCT, and mNGS was subsequently analyzed and compared.

RESULTS: Both molecular methods showed high positive detection rates, surpassing that of the culture method. When conventional culture was used as the gold standard, the sensitivity and positive predictive value (PPV) within the detection range of the PM Easy Lab Respiratory Panel (RP) were 97.1% and 80.5%, respectively, whereas for mNGS, these values were 90.2% and 92.5%, respectively. A comparison of the PM Easy Lab RP and mNGS results revealed that the PM Easy Lab was faster (100 min vs. 24 h) and more sensitive (88 vs. 63 pathogens) within its detection range, whereas mNGS offered a broader spectrum of pathogen detection. The overall consistency between PM Easy Lab RP and mNGS was 88.9%. Klebsiella pneumoniae and Acinetobacter baumannii were identified as the most prevalent bacterial infections by all three detection methods. Moreover, both PM Easy Lab RP and mNGS demonstrated enhanced capability over culture in detecting mixed infections (57.8%, 84.4% vs. 15.6%, all P < 0.01), uncovering a substantial number of viral and bacterial-viral co-infections that are undetectable by conventional culture methods. The most common combination of mixed infections in the PM Easy Lab RP was mixed bacterial infections (76.9%, 20/26), whereas in mNGS, it was bacterial-fungal-viral mixed infections (36.8%, 14/38).

CONCLUSIONS: The findings indicate that PM Easy Lab RP and mNGS offer distinct yet complementary value. PM Easy Lab has potential advantages in speed, sensitivity, and efficiency in detecting pathogens within its panel, and it could be considered for rapid, frontline testing, while mNGS provides a broad-spectrum detection capability, making it more suitable for comprehensive investigation of complex cases, though careful clinical interpretation is required to distinguish pathogenic from colonizing or contaminating organisms. Understanding their respective strengths can guide the development of optimized, hierarchical diagnostic pathways.},
}

@article {pmid41299229,
year = {2025},
author = {Thurimella, K and Mohamed, AMT and Li, C and Vatanen, T and Graham, DB and Owens, RM and La Rosa, SL and Plichta, DR and Bacallado, S and Xavier, RJ},
title = {Protein language models uncover carbohydrate-active enzyme function in metagenomics.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {285},
pmid = {41299229},
issn = {1471-2105},
mesh = {*Metagenomics/methods ; Humans ; *Enzymes/metabolism/chemistry/genetics ; Carbohydrate Metabolism ; Molecular Sequence Annotation ; },
abstract = {BACKGROUND: The functional annotation of uncharacterized microbial enzymes from metagenomic data remains a significant challenge, limiting our understanding of microbial metabolic dynamics. Traditional annotation methods often rely on sequence homology, which can fail to identify remote homologs or enzymes with structural rather than sequence conservation. To address this gap, we developed CAZyLingua, the first annotation tool to use protein language models (pLMs) for the accurate classification of carbohydrate-active enzyme (CAZyme) families and subfamilies.

RESULTS: CAZyLingua demonstrated high performance, maintaining precision and recall comparable to state-of-the-art hidden Markov model-based methods while outperforming purely sequence-based approaches. When applied to a metagenomic gene catalog from mother/infant pairs, CAZyLingua identified over 27,000 putative CAZymes missed by other tools, including horizontally-transferred enzymes implicated in infant microbiome development. In datasets from patients with Crohn's disease and IgG4-related disease, CAZyLinuga uncovered disease-associated CAZymes, highlighting an expansion of carbohydrate esterases (CEs) in IgG4-related disease. A CE17 enzyme predicted to be overabundant in Crohn's disease was functionally validated, confirming its catalytic activity on acetylated manno-oligosaccharides.

CONCLUSIONS: CAZyLingua is a powerful tool that effectively augments existing functional annotation pipelines for CAZymes. By leveraging the deep contextual information captured by pLMs, our method can uncover novel CAZyme diversity and reveal enzymatic functions relevant to health and disease, contributing to a further understanding of biological processes related to host health and nutrition.},
}

*Metagenomics/methods
Humans
*Enzymes/metabolism/chemistry/genetics
Carbohydrate Metabolism
Molecular Sequence Annotation

@article {pmid41299176,
year = {2025},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Long-read metagenomics reveals phage dynamics in the human gut microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41299176},
issn = {1476-4687},
abstract = {Gut bacteriophages profoundly impact microbial ecology and health[1-3]; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although most prophages remained stably integrated into their hosts, approximately 5% of phages were dynamically gained or lost from persistent bacterial hosts. Within a sample, we found that bacterial hosts with and without a given prophage coexisted simultaneously. Furthermore, phage induction, when detected, occurred predominantly at low levels (1-3× coverage compared to the host region), in line with theoretical expectations[4]. We identified multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phages are specific to a host of a given species or strain[5]. Finally, we describe a new class of 'IScream phages', which co-opt bacterial IS30 transposases to mediate their mobilization, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity.},
}

@article {pmid41299116,
year = {2025},
author = {Akhtar, S and Malik, A},
title = {Integrated physicochemical and metagenomic analysis of the Ganges River water.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41299116},
issn = {1614-7499},
abstract = {The perennial River Ganges, one of India's most vital freshwater resources, is increasingly threatened by growing human activities. The present study provides an integrated assessment of water quality, heavy metal pollution, antibiotic resistance, and microbial community dynamics along a culturally important section of the river. Physicochemical parameters showed seasonal variations, with higher pH, TDS, nitrate, and sulfate levels, indicating significant human activities. ICP-AES analysis of heavy metals revealed high levels of Cr and Cd, with a contamination degree of 38.25, indicating a very high pollution level. Antibiotic susceptibility testing of 84 bacterial isolates demonstrated 64.28% multidrug resistance, mainly against β-lactam antibiotics. Although the Water Quality Index was 43.43 (classified as good), microbial and metal contamination indicated hidden ecological risks. 16S rRNA gene-based metagenomic profiling showed dominance of pollution-tolerant bacterial groups, especially Pseudomonadota, Bacillota, and Fusobacteriota. Genera like Brevundimonas, Methylobacterium, Pseudomonas, and Acinetobacter were most common, indicating microbial shifts due to ongoing human activities. Functional predictions (KEGG) suggested enrichment in pathways for xenobiotic degradation, energy production, and environmental information processing. These findings highlight the importance of comprehensive monitoring that combines chemical, microbiological, and genomic tools to better assess the river pollution and efforts to reduce public health risks.},
}

@article {pmid41298564,
year = {2025},
author = {Qu, T and Koch, L and Mukherjee, R and Tu, Y and Seidel, AL and Püttmann, LD and Winkel, A and Yang, I and Grischke, J and Liu, D and Wolkers, WF and Kittler, S and Chichkov, B and Stiesch, M and Szafrański, SP},
title = {Laser-assisted microbial culturomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10614},
pmid = {41298564},
issn = {2041-1723},
support = {German Cluster of Excellence Ex62/2 Rebirth//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; SFB/TRR 298 SIIRI - Project-ID 426335750//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2155 - project number 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Laser-Tissue-Perfude, 101054009//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {Biofilms/growth & development ; Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/isolation & purification/classification/growth & development ; *Lasers ; Dental Plaque/microbiology ; Bioprinting/methods ; Metagenomics/methods ; },
abstract = {Even though metagenomics have revolutionized the characterization of the human microbiome, detailed mechanistic studies are impracticable, as there is a dearth of robust culture collections. We now describe the development and use of a laser-assisted culturomics platform, incorporating the elements of a bioprinter, the culture conditions, the methods to characterize the microorganisms and a biobank. With laser-assisted bioprinting, the microorganisms can be rapidly and precisely transferred from clinical biofilms to highly organized arrays of microbial colonies, which are suitable for co-culturing and molecular analyses. The presented technique has propagated 99 of 100 microbial species and recovered 79% of abundant species from dental plaque in accordance with full 16S rRNA gene profiling of 691,199 sequences. Microscopy, spectroscopy and enzyme assays have been used to guide isolations. Processing of oral biofilms from four individuals has yielded 249 representative isolates, from 14 classes and 124 species in total. Functional profiling with bioprinting has indicated commensals which could potentially contribute to disease development. Isolates from peri-implantitis cover 85.4% of the transcriptionally active clinical biofilms at genus level. Taken together, this work provides the basis for generating on-demand culture collections and biofilms for research and clinical use.},
}

Biofilms/growth & development
Humans
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Bacteria/genetics/isolation & purification/classification/growth & development
*Lasers
Dental Plaque/microbiology
Bioprinting/methods
Metagenomics/methods

@article {pmid41298464,
year = {2025},
author = {Ricci, F and Bay, SK and Nauer, PA and Wong, WW and Ni, G and Jimenez, L and Jirapanjawat, T and Leung, PM and Bradley, JA and Eate, VM and Hall, M and Stubbusch, AKM and Fernández-Marín, B and de Los Ríos, A and Cook, PLM and Schroth, MH and Chiri, E and Greening, C},
title = {Metabolically flexible microorganisms rapidly establish glacial foreland ecosystems.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66734-4},
pmid = {41298464},
issn = {2041-1723},
support = {APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE230101346//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; 101115755//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; PID2019-105469RB-C22//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; },
abstract = {An overriding question in ecology is how new ecosystems form. This question can be tested by studying colonisation of environments with little to no pre-existing life. Here, we investigated the functional basis of microbial colonisation in the forelands of a maritime Antarctic and an alpine Swiss retreating glacier, by integrating quantitative ecology, metagenomics, and biogeochemical measurements. Habitat generalists and opportunists rapidly colonise both forelands and persist across soil decadal chronosequences serving as proxies for temporal community dynamics. These microbes are metabolically flexible chemotrophic aerobes that overcome oligotrophic conditions by using organic and inorganic compounds, including atmospheric trace gases and sulphur substrates, for energy and carbon acquisition. They co-exist with metabolically flexible early-colonising opportunists and metabolically restricted later-colonising specialists, including Cyanobacteria, ammonia-oxidising archaea, and obligate predatory and symbiotic bacteria, that exhibit narrower habitat distributions. Analysis of 589 species-level metagenome-assembled genomes reveals early colonisation by generalists and opportunists is strongly associated with metabolic flexibility. Field- and laboratory-based biogeochemical measurements reveal the activity of metabolically flexible microbes rapidly commenced in the forelands. Altogether, these findings suggest primary succession in glacial foreland soils is driven by self-sufficient metabolically flexible bacteria that mediate chemosynthetic primary production and likely provide a more hospitable environment for subsequent colonisation.},
}

@article {pmid41298409,
year = {2025},
author = {Thorpe, AC and Busi, SB and Warren, J and Hunt, LH and Walsh, K and Read, DS},
title = {National-scale biogeography and function of river and stream bacterial biofilm communities.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10571},
pmid = {41298409},
issn = {2041-1723},
support = {SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; SC220034//Environment Agency (EA)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015777/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015777/1//RCUK | Natural Environment Research Council (NERC)/ ; NE/X015947/1//RCUK | Natural Environment Research Council (NERC)/ ; BB/X011089/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {*Biofilms/growth & development ; *Rivers/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; England ; Ecosystem ; Biodiversity ; Metagenomics ; Metagenome ; Microbiota/genetics ; Phylogeny ; },
abstract = {Biofilm-dwelling microorganisms coat the surfaces of stones in rivers and streams, forming diverse communities that are fundamental to biogeochemical processes and ecosystem functioning. Flowing water (lotic) ecosystems face mounting pressures from changes in land use, chemical pollution, and climate change. Despite their ecological importance, the taxonomic and functional diversity of river biofilms and their responses to environmental change are poorly understood at large spatial scales. We conducted a national-scale assessment of bacterial diversity and function using metagenomic sequencing from rivers and streams across England. We recovered 1,014 metagenome-assembled genomes (MAGs) from 450 biofilms collected across England's extensive river network. Substantial taxonomic novelty was identified, with ~20% of the MAGs representing novel genera. Here we show that biofilm communities, dominated by generalist bacteria, exhibit remarkable functional diversity and metabolic versatility, and likely play a significant role in nutrient cycling with the potential for contaminant transformation. Measured environmental drivers collectively explained an average of 71% of variation in the relative abundance of bacterial MAGs, with geology and land cover contributing most strongly. These findings highlight the importance of river biofilms and establish a foundation for future research on the roles of biofilms in ecosystem health and resilience to environmental change.},
}

*Biofilms/growth & development
*Rivers/microbiology
*Bacteria/genetics/classification/metabolism/isolation & purification
England
Ecosystem
Biodiversity
Metagenomics
Metagenome
Microbiota/genetics
Phylogeny

@article {pmid41298355,
year = {2025},
author = {Holcik, L and von Haeseler, A and Pflug, FG},
title = {Genomic GC bias correction improves species abundance estimation from metagenomic data.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {10523},
pmid = {41298355},
issn = {2041-1723},
mesh = {*Metagenomics/methods ; Humans ; Algorithms ; *Gastrointestinal Microbiome/genetics ; Base Composition/genetics ; Colorectal Neoplasms/microbiology ; *Metagenome ; Bacteria/genetics/classification ; Microbiota/genetics ; },
abstract = {Metagenomic sequencing measures the species composition of microbial communities and has revealed the crucial role of microbiomes in the etiology of a range of diseases such as colorectal cancer. Quantitative comparisons of microbial communities are, however, affected by GC-content-dependent biases. Here, we present GuaCAMOLE, a computational method to detect and remove GC bias from metagenomic sequencing data. The algorithm relies on comparisons between individual species in a single sample to estimate the sequencing efficiency at levels of GC content, and outputs unbiased species abundances. GuaCAMOLE thus works regardless of the specific amount or direction of GC-bias present in the data and does not rely on calibration experiments or multiple samples. Applying our algorithm to 3435 gut microbiomes of colorectal cancer patients from 33 individual studies reveals that the type and severity of GC bias vary considerably between studies. In many studies, we observe a clear bias against GC-poor species in the abundances reported by existing methods. GuaCAMOLE successfully removes this bias and corrects the abundance of clinically relevant GC-poor species such as F. nucleatum (28% GC) by up to a factor of two. GuaCAMOLE thus contributes to a better quantitative understanding of microbial communities by improving the accuracy and comparability of species abundances across experimental setups.},
}

*Metagenomics/methods
Humans
Algorithms
*Gastrointestinal Microbiome/genetics
Base Composition/genetics
Colorectal Neoplasms/microbiology
*Metagenome
Bacteria/genetics/classification
Microbiota/genetics

@article {pmid41298327,
year = {2025},
author = {Wang, BW and Liu, YF and Chen, LG and Wang, B and Qian, ZH and Yang, F and Cai, JC and Zhou, L and Yang, SZ and Gu, JD and Mu, BZ},
title = {Microbial Community Composition and Function in Jiangsu Oil Reservoir Cores, China.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70229},
doi = {10.1111/1758-2229.70229},
pmid = {41298327},
issn = {1758-2229},
support = {52074129//National Natural Science Foundation of China/ ; 42061134011//National Natural Science Foundation of China/ ; 42173076//National Natural Science Foundation of China/ ; 42473082//National Natural Science Foundation of China/ ; 21ZR1417400//Natural Science Foundation of Shanghai Municipality/ ; JKJ01231714//Fundamental Research Funds for the Central Universities/ ; //Research Program of the State Key Laboratory of Bioreactor Engineering/ ; },
mesh = {China ; *Oil and Gas Fields/microbiology ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Petroleum/microbiology ; Hydrocarbons/metabolism/analysis ; *Microbiota ; Phylogeny ; Metagenomics ; },
abstract = {Shale oil reservoirs are typically characterised by elevated temperatures, confined spaces and oligotrophic conditions. Understanding the role of microorganisms in shale oil reservoirs is essential for elucidating biogeochemical cycles and the origins of life. However, the composition and metabolic functions of microbial communities in shale oil reservoirs remain elusive. In this study, shale core samples were collected from the HY1-1 and HY7 wells in the Jiangsu Oilfield. A combination of X-ray fluorescence, powder X-ray diffraction and scanning electron microscope analyses revealed that the samples contained various transition metals, abundant clay minerals and numerous pores with diameters greater than 1 μm. Fractionation of extracted crude oil fractions revealed that HY1-1 and HY7 contained 60% and 74% saturated hydrocarbons, primarily comprising C11-C35 n-alkanes. Various hydrocarbon-degrading microorganisms, including Marinobacter, Alcanivorax, Alkanindiges and Nocardioides were present in HY1-1 or HY7 samples. Metagenomic analysis showed the presence of genes associated with aerobic hydrocarbon degradation, denitrification and DNRA in the HY7 sample, suggesting that microorganisms may utilise crude oil for growth and participate in the subsurface carbon and nitrogen cycle. This study elucidates the microbial community structure and functional gene profiles in shale core samples, providing critical insights for harnessing in situ microorganisms in shale oil reservoir development.},
}

China
*Oil and Gas Fields/microbiology
*Bacteria/classification/genetics/metabolism/isolation & purification
*Petroleum/microbiology
Hydrocarbons/metabolism/analysis
*Microbiota
Phylogeny
Metagenomics

@article {pmid41298270,
year = {2025},
author = {Zou, J and Xu, H and Qin, B and Lan, C and Li, J and Zhang, B and Zhang, H and Guo, C and Chen, H and Fang, Z and Zhao, Q and Wang, W and Fang, C and Zhang, Z and Lin, W},
title = {Ratoon Season Rice Reduces Methane Emissions by Limiting Acetic Acid Transport to the Rhizosphere and Inhibiting Methanogens.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e07916},
doi = {10.1002/advs.202507916},
pmid = {41298270},
issn = {2198-3844},
support = {32001109//Nature Science Foundation of China/ ; 31871542//national Nature Science Foundation of China/ ; 31871556//national Nature Science Foundation of China/ ; 2017YFE0121800//National Key Research and Development Project of China/ ; 2018YFD0301105//National Key Research and Development Project of China/ ; BQW [2024]001//Innovative Talent Team in Rice Crop Science and Technology in Karst Mountainous Areas of Guizhou Province/ ; 2023//Key Laboratory of Molecular Breeding for Grain and Oil Crops in Guizhou Province/ ; (2023) 007//Key Laboratory of Functional Agriculture of Guizhou Provincial Higher Education Institutions/ ; Key Laboratory of Functional Agriculture of Guizhou Provincial Higher Education Institutions (//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Qianjiaoji//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; (2023)007)//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Xiligongmi//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Innovative Talent Workstation of Guizhou Province(Qian-//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; Ke//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; -He-Platform-talent KXJZ(2024)038)//Chongqing Municipal Key Laboratory of Institutions of Higher Education/ ; (Qian-//Key Laboratory of Microbial Resources and Drug Development in Guizhou Province/ ; Ke//Key Laboratory of Microbial Resources and Drug Development in Guizhou Province/ ; -He YWZ(2024(004)//Key Laboratory of Microbial Resources and Drug Development in Guizhou Province/ ; },
abstract = {Rice paddies are a major, persistent source of atmospheric methane (CH4), emission rates depend on the partitioning of photosynthate carbon between the rice plant and the rhizosphere microbiome. Although ratoon season rice (RR) is shown to emit far less CH4 than main-crop rice (MC), the mechanisms have remained unresolved. This work conducts a 2-year field experiment in which RR is compared with MC and with late rice (LR) synchronized to the RR heading stage. Relative to MC and LR, RR lowers daily CH4 flux by 91%, raises daily grain yield by 34%-57%, and increases net economic return by 90%-136%. Mechanistically, [13]C-labelling reveals that RR diverted more newly fixed carbon to the grain and less to the rhizosphere, thereby restricting acetate availability for methanogens. Rhizosphere metagenomics show reduced abundance of Methanobacteriaceae and down-regulation of methanogenic genes in RR. This carbon-reallocation pattern is underpinned by an abscisic acid (ABA)-mediated interaction between OsCIPK2 and OsSWEET1A, which simultaneously curtailed carbon efflux from roots and enhanced grain filling. This study is the first to establish a comprehensive framework of "ABA regulation-carbon allocation-microbial function-emission reduction and efficiency enhancement." It provides targetable strategies for carbon allocation and microbial management within climate-smart rice farming systems.},
}

@article {pmid41298102,
year = {2025},
author = {Ammer-Herrmenau, C and Meier, R and Antweiler, KL and Asendorf, T and Cameron, S and Capurso, G and Damm, M and Dang, L and Frost, F and Hamm, J and Hoffmeister, A and Kocheva, Y and Meinhardt, C and Nawacki, L and Nunes, V and Panyko, A and Ruiz-Rebollo, ML and Flórez-Pardo, C and Phillip, V and Pukitis, A and Vaselane, D and Rinja, E and Sandru, V and Schaefer, A and Scholz, R and Seelig, J and Sirtl, S and Ellenrieder, V and Neesse, A},
title = {Gut microbiota predict development of postdischarge diabetes mellitus in acute pancreatitis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336715},
pmid = {41298102},
issn = {1468-3288},
abstract = {BACKGROUND: Postdischarge morbidity and mortality is high in acute pancreatitis (AP) and pathophysiological mechanisms remain poorly understood.

OBJECTIVES: We aim to investigate the composition of gut microbiota and clinical long-term outcomes of prospectively enrolled patients with AP to predict postdischarge complications.

DESIGN: In this long-term follow-up study, we analysed clinical and microbiome data of 277 patients from the prospective multicentre Pancreatitis-Microbiome As Predictor of Severity trial. The primary endpoint was the association of the microbial composition with postdischarge mortality, recurrent AP (RAP), progression to chronic pancreatitis, pancreatic exocrine insufficiency, diabetes mellitus (DM) and pancreatic ductal adenocarcinoma.

RESULTS: Buccal (n=238) and rectal (n=249) swabs were analysed by 16S rRNA and metagenomics sequencing using Oxford Nanopore Technologies. Median follow-up was 2.8 years. Distance-based redundancy analysis with canonical analysis of principal coordinates showed significant differences for β-diversity (Bray-Curtis) for postdischarge mortality (p=0.04), RAP (p=0.02) and DM (p=0.03). A ridge regression model including 11 differentially abundant species predicted postdischarge DM with an area under the receiving operating characteristic of 94.8% and 86.2% in the matched and entire cohort, respectively. Using this classifier, a positive predictive value of 66.6%, a negative predictive value of 96% and an accuracy of 95% was achieved.

CONCLUSION: Our data indicate that the admission microbiome of patients with AP correlates with postdischarge complications independent from multiple risk factors such as AP severity, smoking or alcohol. Microbiota at admission show excellent capacity to predict postdischarge DM and may thus open new stratification tools for a tailored risk assessment in the future.

TRIAL REGISTRATION NUMBER: NCT04777812.},
}

@article {pmid41298101,
year = {2025},
author = {Liu, CS and Merrick, B and Taboun, ZS and Mullish, BH and Goldenberg, SD and Terveer, EM and Porcari, S and Bradbury, RS and Ianiro, G and Ng, SC and , and Kao, D and Kuijper, E},
title = {Towards optimising and standardising donor screening for faecal microbiota transplantion.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336532},
pmid = {41298101},
issn = {1468-3288},
abstract = {Rigorous donor screening is fundamental for the safe and effective delivery of faecal microbiota transplantion (FMT) services, whether in the treatment of Clostridioides difficile infection or within microbiome intervention clinical trials. Donor screening is of paramount importance given the potential risk of pathogen transmission-a feared complication. While rare in practice, documented cases of FMT-associated infections have resulted in significant morbidity and even mortality. Despite the importance of screening, evidence-based approaches to developing donor-screening protocols are lacking. Inadequate screening for transmissible pathogens may lead to infections in recipients, while overly cautious screening for pathogens with negligible transmission potential could strain healthcare resources and unnecessarily exclude donors, who are already in limited supply. This review aimed to evaluate the evidence underpinning current FMT donor screening protocols. We began by comparing protocols from major FMT guidelines and manufacturers, highlighting their differences in lists of screened pathogens, laboratory assays and clinical characteristics used for donor selection. We critically appraised the existing literature on transmission dynamics for pathogens. These findings were incorporated into a Delphi process with an expert panel group to develop a rational and streamlined screening approach. We further emphasised the importance of maintaining transparency with regard to donor recruitment, screening, monitoring and traceback record keeping. Finally, we explored future directions in donor screening, including approaches to monitoring emerging pathogens and the potential for integration of new technologies, such as metagenomic assays, to enhance and refine donor selection.},
}

@article {pmid41297753,
year = {2025},
author = {Zhong, Z and Ye, W and Li, B and Al-Dhabi, NA and Zhao, J and Li, S and Sun, Y and Zhang, H and Tang, W and Chen, S},
title = {Phosphate-Iron Modified Enteromorpha Prolifera Hydrochar Enhances Dry Anaerobic Digestion of Food Waste: Synergistic Mechanisms of Electron Transfer Network, Microbial Consortia Remodeling, and Metagenomic Insights.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123385},
doi = {10.1016/j.envres.2025.123385},
pmid = {41297753},
issn = {1096-0953},
abstract = {The dual pressures of marine ecological disasters and urban solid waste treatment pose severe challenges to sustainable development. However, current research mostly focuses on single waste treatment, lacking coordinated governance strategies. This study innovatively proposes a "marine-urban" solid waste collaborative treatment strategy, converting Enteromorpha Prolifera into phosphate - iron composite modified hydrothermal carbon (P-MEPHC) via hydrothermal carbonization technology, and systematically analyzes its enhancement mechanisms in dry anaerobic digestion of food waste. Characterization results indicate that P-MEPHC possesses high electrical conductivity (488 S/m), a hierarchical mesoporous structure (BET specific surface area of 15.15 m[2]/g, average pore size of 10.57 nm), and abundant Fe-P-O active sites. Engineering verification showed that the addition of 52 mg/g VSS (volatile suspended solids) P-MEPHC increased the cumulative methane production to 99.25 mL/g VS (volatile solids), representing a 50.6% improvement over the control group. Concurrently, the peak value of soluble chemical oxygen demand (SCOD) was elevated to 111.53 g/L, while the inhibition intensity of ammonia nitrogen was reduced by 32%. Metagenomics indicated that it achieves process enhancement through dual regulatory mechanisms: at the community structure level, it enriches syntrophic acid-producing bacteria Sporanaerobacter (+7.9%) and hydrogenotrophic methanogens Methanoculleus (+17.7%); at the metabolic function level, it significantly upregulates the expression of core methanogenic metabolic genes such as acetyl-CoA synthase (ACSS1_2, +255%), thereby activating the direct interspecies electron transfer pathway. This research provides a technically feasible paradigm with both environmental and economic benefits for the coordinated resource utilization of near - shore algal bloom biomass and organic solid waste, and promotes the closed - loop integration of blue carbon sinks and urban metabolic systems.},
}

@article {pmid41297621,
year = {2025},
author = {Houmenou, CT and Sokhna, C and Fenollar, F and Mediannikov, O},
title = {Advancements and challenges in bioinformatics tools for microbial genomics in the last decade: Toward the smart integration of bioinformatics tools, digital resources, and emerging technologies for the analysis of complex biological data.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105859},
doi = {10.1016/j.meegid.2025.105859},
pmid = {41297621},
issn = {1567-7257},
abstract = {Over the past decade, microbial genomics has been transformed by advances in sequencing technologies and bioinformatics, enabling the transition from targeted gene markers to complete genome assemblies and ecological scale metagenomic surveys. This review presents a comprehensive overview of the bioinformatics pipelines that structure this field, from sample preparation, PCR amplification, and next-generation sequencing (NGS) to read preprocessing, genome assembly, polishing, structural and functional annotation, and submission to public databases. We highlight the major tools that have become standards at each stage, including FastQC, SPAdes, Prokka, Bakta, CARD, GTDB-Tk, QIIME 2, and Kraken2, while also emphasizing recent innovations such as hybrid assemblers, ontology-driven annotation frameworks, and automated workflows (nf-core, Bactopia). Applications extend across microbiology, from antimicrobial resistance surveillance and phylogenetic classification to ecological studies, exemplified here by three case studies: termite gut microbiota profiling by 16S metabarcoding, the description of new Bartonella species from bats, and the genomic characterization of rare Salmonella enterica serovars from primates. Despite these advances, persistent challenges remain, including incomplete and biased reference databases, computational bottlenecks, and economic disparities in sequencing and storage capacities. In response, international initiatives increasingly promote open, interoperable, and reusable bioinformatics infrastructures. Conforming to the Findable, Accessible, Interoperable, Reusable (FAIR) principles and global frameworks such as Global Alliance for Genomics and Health (GA4GH), these efforts are driving greater standardization, transparency, and data sharing across the microbial genomics community. Future perspectives point toward the integration of artificial intelligence, long-read and telomere-to-telomere (T2T) sequencing, cloud-native infrastructures, and even quantum computing, paving the way for a predictive, reproducible, and globally inclusive microbial genomics.},
}

@article {pmid41297516,
year = {2025},
author = {Xu, L and Zhang, J and Xiao, Y and Jin, P and Zhang, J},
title = {High-fat diet promotes colorectal tumorigenesis through gut microbiota-mediated metabolic reprogramming and M2 macrophage polarization.},
journal = {Biochemical and biophysical research communications},
volume = {794},
number = {},
pages = {153014},
doi = {10.1016/j.bbrc.2025.153014},
pmid = {41297516},
issn = {1090-2104},
abstract = {BACKGROUND: High-fat diet (HFD) drives colorectal cancer (CRC) progression through gut microbiota dysbiosis and M2 macrophage polarization, yet the microbiota-immunity crosstalk remains mechanistically unresolved.

METHODS: APC[min/+] (CRC model, n = 8) and wild-type controls (n = 7) received 12-weeks HFD. We employed integrated metagenomic sequencing (Illumina NovaSeq) and immunohistochemistry (targeting CD206+ M2 macrophages) to investigate the linkages between the gut microbiota and the host.

RESULTS: CRC mice exhibited colonic adenocarcinoma with increased M2 macrophages. Gut microbiota in CRC mice showed enrichment of pro-inflammatory taxa (e.g., Bacteroides massiliensis, Vampirovibrion) and upregulated pathways (carbohydrate metabolism, mucin degradation). Strikingly, the relative abundances of Bacteroides massiliensis and Vampirovibrion showed significant positive correlations with CD206+ M2 macrophage infiltration levels.

CONCLUSION: HFD induces microbiota-directed metabolic reprogramming and M2 polarization, synergistically accelerating CRC. Notably, targeting key pro-inflammatory taxa (e.g., B. massiliensis) or glycan hydrolysis pathways (e.g. GH95 enzyme) may provide mechanism-guided anti-CRC strategies.},
}

@article {pmid41297400,
year = {2025},
author = {Chen, S and Liu, Q and Li, D},
title = {Engineering the composting microbiome with a synthetic microbial community to accelerate lignocellulose degradation and humus synthesis.},
journal = {Journal of environmental management},
volume = {396},
number = {},
pages = {128088},
doi = {10.1016/j.jenvman.2025.128088},
pmid = {41297400},
issn = {1095-8630},
abstract = {Bioaugmentation with synthetic microbial communities (SynComs) presents a promising engineering strategy to overcome the bottleneck of lignocellulose recalcitrance in organic waste valorization. However, the mechanisms by which SynComs modulate indigenous microbial networks and steer metabolic fluxes remain elusive. Here, we deconstruct these mechanisms by investigating the impact of a rationally designed five-member bacterial-fungal SynCom on the co-composting of cattle manure and mulberry branches. Through an integrated multi-omics approach, we reveal that SynCom inoculation acts as a potent ecological engineer, accelerating the process by significantly elevating pile temperatures and shortening the maturation period by accelerating entry into the maturation phase by approximately 7 days. Compared with the control, the SynCom treatment enhanced the overall degradation rates of lignin, cellulose, and hemicellulose by 19.3 %, 7.9 %, and 12.0 %, respectively, and boosted humus content by 34.4 %. Metagenomics revealed that the SynCom profoundly restructured the native microbiome, enriching for key functional genera such as Thermobifida and Actinomadura. This engineered community possessed an enhanced genetic toolkit, with a significantly increased abundance of crucial carbohydrate-active enzymes (CAZymes), including cellulases (GH5, GH12), hemicellulases (CE1, CE3), and lignin-modifying auxiliary activity enzymes (AA1, AA6). Untargeted metabolomics further identified a distinct metabolic footprint in the SynCom treatment, characterized by the enrichment of key humification precursors like protocatechuic acid and sinapic acid. Integrated Procrustes and correlation analyses confirmed a tight coupling between the engineered microbiome, its functional gene repertoire and metabolic output. This study deciphers the multi-layered mechanism by which a designed SynCom enhances biowaste valorization and provides a mechanistic blueprint for engineering microbial consortia for advanced biotechnology applications in sustainable agriculture.},
}

@article {pmid41297255,
year = {2025},
author = {Lindstedt, K and Osińska, A and Bargheet, A and Sørum, H and Wick, RR and Holt, KE and Pettersen, VK and Sundsfjord, A and Wasteson, Y},
title = {Microbiota and resistome dynamics in untreated and treated wastewater: A ten-month study leveraging RNA-probe capture and subspecies-level metagenomics.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140566},
doi = {10.1016/j.jhazmat.2025.140566},
pmid = {41297255},
issn = {1873-3336},
abstract = {Wastewater is regarded as a hotspot for the acquisition and dissemination of antimicrobial resistance genes (ARGs) in bacteria, and wastewater treatment plants are key sites for studying and monitoring these phenomena. This study employed metagenomic approaches, with and without targeted ARG enrichment, to investigate the composition and dynamics of the microbiota, resistome, and mobilome in untreated (UWW) and treated (TWW) wastewater from a full-scale treatment plant serving municipal and hospital wastewater in Oslo, Norway. Over a ten-month period, we observed that wastewater treatment led to a significant reduction in the relative abundance of human gut-associated bacterial species and total load of coliform bacteria, alongside an increase in environmental bacterial taxa. This shift correlated with a significant reduction in the relative abundance and richness of ARGs and mobile genetic elements. Despite this, the effect of treatment on the relative abundance of key AMR-associated pathogens was highly inconsistent. Further subspecies analysis revealed several Escherichia coli and Klebsiella pneumoniae lineages persisted in UWW and TWW over multiple months, suggesting stable colonization and survival despite treatment processes. Targeted RNA probe-hybridisation enrichment detected clinically important ARGs in both UWW and TWW samples, including genes encoding extended-spectrum β-lactamases, carbapenemases, glycopeptide resistance, and colistin resistance. Most of these were undetectable by shotgun metagenomics alone, demonstrating the strength of this technique in high-sensitivity ARG surveillance. These findings highlight the value of combined metagenomic methods in wastewater AMR surveillance, the potential for monitoring high-risk bacterial lineages, and high-sensitivity detection of clinically important ARGs, in a low AMR prevalence setting.},
}

@article {pmid41297254,
year = {2025},
author = {Hatwar, N and Qureshi, A},
title = {Biodegradation of PVC by novel bacterial consortia isolated from municipal solid waste dumpsite.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140589},
doi = {10.1016/j.jhazmat.2025.140589},
pmid = {41297254},
issn = {1873-3336},
abstract = {In view of environmental issues related to Polyvinyl chloride (PVC), attempts have been made in the present study, to enrich and isolate novel bacteria from landfill dumpsites, capable of degrading PVC with reduced emissions. A potential bacterial consortium (NH_AQ) was designed, which comprised of Lysinibacillus spp., Bacillus spp., Staphylococcus spp., Exiguobacterium spp., and Arthrobacter spp. Metagenomic analysis of landfill soils indicated predominance of these bacterial species, which ensured that the culturable bacteria could be isolated from landfill sites for PVC degradation. This study was carried out at three temperatures (ambient, 37°C and 50°C). The percentage weight reduction of PVC films was 31.45 % ± 2 at 37°C. SEM-EDX showed external erosion and changes in chemical element composition, due to growth of bacteria as biofilms on PVC films at 37 °C. FTIR study confirmed oxidation and dechlorination happening during PVC utilization. TGA analysis indicated PVC thermal shifts in presence of consortia and ion chromatography too showed a significant reduction in chlorine content. Overall findings demonstrated that the designed NH_AQ consortium could degrade PVC effectively, offering a promising and sustainable approach to mitigate PVC pollution through microbial action in future.},
}

@article {pmid41297084,
year = {2025},
author = {Cameron, CC and Gebbie, W and Bowman, C and Waters, ER and Kalyuzhnaya, MG},
title = {Characterization and description of plant-growth-promoting methanotrophic bacteria belonging to the genus of Methylocaldum.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126670},
doi = {10.1016/j.syapm.2025.126670},
pmid = {41297084},
issn = {1618-0984},
abstract = {Arid soil microbiomes present untapped resources of microbial diversity. Here, we describe twelve isolates, all belonging to the Methylocaldum genus. Based on metagenomic studies, the isolates represent the major clades of methanotrophic bacteria inhabiting the arid biomes of Southern California, comprising up to 0.03 % of the total soil microbiota. Phenotyping of isolates indicates that they are obligate methanotrophic bacteria, some capable of methanol utilization. All strains can fix nitrogen, use nitrate and ammonia as a N-source, and have key genetic signatures of autotrophy, methylotrophy, and N2O assimilation. Based on the 16S rRNA phylogeny and whole -genome analyses, all strains are assigned to the species M. gracile. Three isolates from the rhizosphere of native Californian plants (Strains 0917, YM2 and S3V3) and GT1B-W are set apart from the other M. gracile strains, despite sharing <98 % of average nucleotide identity. Microbes isolated from plant rhizosphere display 150 unique genetic features and a series of tandem gene duplications predicted to contribute to their interactions with plants, including the 20-gene polyketide biosynthesis cluster and the TRAP C4-dicarboxylate transport system. Consistent with the genetic properties that may indicate an enhancement of plant-cooperation functions, the rhizosphere isolates support the survival of plants, Boechera depauperata and Arabidopsis thaliana, under drought conditions. Based on genetic and phenotypic characteristics, we propose to designate strains 0917, YM2, S3V3, and GT1B-W as a new subspecies of Methylocaldum gracile - Methylocaldum gracile subspecies dēsertum, L.n. dēsertum - a desert, to represent the native habitat of the species. The amended description of the M.gracile species is provided.},
}

@article {pmid41297027,
year = {2025},
author = {Palanisamy, H and Vidyalakshmi, S},
title = {Deciphering the Interrelation of Gut Microbiota and BMI in Atherosclerosis: A Metagenomic Approach.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0075},
pmid = {41297027},
issn = {1480-3275},
abstract = {Atherosclerotic Cardiovascular Disease (ASCVD) is a global health concern, leading to higher rates of morbidity and mortality. Gut microbial dysbiosis significantly contributes to obesity related ASCVD. However the interrelation of gut microbiome in driving obesity or overweight mediated ASCVD has not been sufficiently investigated. To unravel this complex interplay, we have compared the gut microbial shotgun metagenome data of ASCVD subjects across normal BMI (Body Mass Index) and overweight/obese (OW/OB) BMI categories. We identified a distinct gut microbial composition and function in normal and OW/OB ASCVD subjects. Using gut microbial abundance, a machine learning model was built to predict ASCVD in the normal and OW/OB samples. The gut microbiome based signature for ASCVD discrimination was achieved with an AUC of 0.87 and 0.83 for distinguishing control and ASCVD in normal and OW/OB BMI groups respectively. In addition, we have also identified that Pseudoflavonifractor capillosus could act as a prognostic organism in identifying OW/OB associated ASCVD. Therefore, an appropriate diet could modifying the ASCVD contributing gut microbiome, hence minimizing the risk of ASCVD in OW/OB individuals.},
}

@article {pmid41296543,
year = {2025},
author = {Podlesny, D and Kim, CY and Robbani, SM and Schudoma, C and Fullam, A and Reimer, LC and Koblitz, J and Schober, I and Iyappan, A and Van Rossum, T and Schiller, J and Grekova, A and Kuhn, M and Bork, P},
title = {metaTraits: a large-scale integration of microbial phenotypic trait information.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1241},
pmid = {41296543},
issn = {1362-4962},
support = {460129525//Deutsche Forschungsgemeinschaft/ ; RS-2023-00240807//National Research Foundation of Korea/ ; //Ministry of Science, Research and the Arts Baden-Württemberg (MWK)/ ; },
abstract = {Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is dispersed across multiple databases and is largely unavailable for taxa that remain uncultured. Here, we present metaTraits, a unified and accessible trait resource that integrates culture-derived trait information from BacDive, BV-BRC, JGI IMG, and GOLD with genome-based predictions for medium and high-quality isolate and metagenome-assembled genomes (MAGs) from proGenomes and SPIRE. metaTraits covers over 2.2 million genomes and >140 harmonized traits mapped to standardized ontologies, spanning cell morphology (e.g. shape, size, and Gram staining), physiology (e.g. motility and sporulation), metabolic and enzymatic activities, environmental preferences (e.g. temperature, salinity, and oxygen tolerance), and lifestyle categories. All records are linked to the original evidence, and species are cross-linked to NCBI and GTDB taxonomies. The interactive metaTraits website provides search and visualization tools, taxonomy-level summaries, and two workflows for annotating user-submitted genomes or community profiles. metaTraits substantially advances accessibility and interoperability of microbial trait data, enabling comprehensive trait-based analyses of microbiomes across diverse environments. metaTraits is accessible via https://metatraits.embl.de.},
}

@article {pmid41296394,
year = {2025},
author = {Albaijan, D and Albaijan, D and Akbar, A},
title = {Intestinal Microbial Profiles of Wild Zobaidy (Pampus argenteus) Fish Characterized by 16S rRNA Next Generation Sequencing.},
journal = {Current issues in molecular biology},
volume = {47},
number = {11},
pages = {},
doi = {10.3390/cimb47110890},
pmid = {41296394},
issn = {1467-3045},
abstract = {Pampus argenteus (Zobaidy) is an important fish in Kuwait and the Gulf region due to its economic value in the fish industry. Analyzing the gut microbiome of Zobaidy can help determine the health status of the fish and its responses to environmental changes. In this study, we investigated the microbiome composition of the intestinal tract among seven wild-caught silver pomfret specimens sampled in the Arabian gulf. The 16S rRNA was sequenced using the Illumina platform; then, sequences were analyzed using several bioinformatics tools to identify the microbial diversity, taxonomical status, and functional aspects. The results were 5933 operational taxonomic units (OTUs) categorized into 35 phyla. Proteobacteria, Firmicutes, Bacteroidota, and Actinobacterota were most abundant in the Zobaidy and water samples. At the genus level, we found high relative abundances of Acinetobacter. The results indicated that Lactococcus piscium, Enterococcus cecorum, Psychrobacter arenosus, Vagococcus salmoninarum, and Carnobacterium maltaromaticum are the most commonly present species in the analyzed Zobaidy samples. A heatmap analysis indicated notable differences in the functional categories of intestinal microflora within the Zobaidy2 sample compared to other Zobaidy samples. It should be noted that microbiome studies can provide novel ways to enhance the overall welfare of fish, strengthen disease prevention, and increase sustainability in aquaculture production.},
}

@article {pmid41296232,
year = {2025},
author = {Jalal, D and Lotfi, M and Ziad, GA and Mahfouz, S and Madney, Y and Bayoumi, A and Hassanain, O and Tolba, M and Hashem, M and Elanany, M and Sayed, AA and Shalaby, L},
title = {Dual Transmission Dynamics of Carbapenem Resistance in Pediatric Oncology: Plasmid-Mediated and Clonal Spread of blaNDM-5 Enterobacterales.},
journal = {Infectious diseases and therapy},
volume = {},
number = {},
pages = {},
pmid = {41296232},
issn = {2193-8229},
support = {54699605//Pfizer/ ; },
abstract = {INTRODUCTION: Carbapenem-resistant Enterobacterales (CRE) pose a major threat to immunocompromised pediatric oncology patients. However, the routes of resistance spread in this vulnerable population remain poorly understood, despite their importance for guiding infection control.

METHODS: We analyzed 189 CRE bloodstream isolates (106 Escherichia coli, 72 Klebsiella pneumoniae, and 11 other Enterobacterales) collected at the Children's Cancer Hospital Egypt 57357 (August 2021-October 2022). Whole genome sequencing was used to assess sequence types, resistance genes, virulence factors, plasmid content, and transmission dynamics.

RESULTS: Carbapenem resistance was primarily mediated by blaNDM-5, carried on species-specific plasmids: IncFIA/IncFII in E. coli and IncFIB/IncHIB megaplasmids in K. pneumoniae, frequently co-harboring additional aminoglycoside, sulfonamide, and fluoroquinolone resistance genes. The most common sequence types were ST361, ST167, and ST405 in E. coli, and ST11, ST383, and ST147 in K. pneumoniae. Clonal clustering was observed in 62.5% of K. pneumoniae but only 17% of E. coli. Plasmid phylogenetics and patient movement data indicated extensive horizontal plasmid transfer across unrelated lineages and patients, including ICU cases. A nonfunctional rmpA variant was found in 30 K. pneumoniae isolates, but no hypermucoviscous phenotype was observed.

CONCLUSION: CRE bloodstream infections in pediatric oncology patients are driven by both clonal expansion and plasmid-mediated dissemination, with plasmids playing a dominant role, especially in E. coli. These findings highlight the limitations of strain-based surveillance and the need for integrated genomic and plasmid-level monitoring to inform infection control in high-risk hospital settings. A Graphical Abstract is available for this article.},
}

@article {pmid41295733,
year = {2025},
author = {O'Donoghue, S and Waters, SM and Morris, DW and Earley, B},
title = {A Comprehensive Review: Molecular Diagnostics and Multi-Omics Approaches to Understanding Bovine Respiratory Disease.},
journal = {Veterinary sciences},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/vetsci12111095},
pmid = {41295733},
issn = {2306-7381},
support = {16/RD/US-ROI/11//Department of Agriculture, Food and the Marine (DAFM) US-Ireland R&D partnership call/ ; 2018US-IRL200//the US- Ireland Tri Partite Grant/ ; No. 101000213//European Union Horizons 2020, HoloRuminant project/ ; },
abstract = {Bovine respiratory disease (BRD) is a multifactorial syndrome and a leading cause of morbidity and economic loss in global cattle production. Next-generation sequencing (NGS) platforms, including Illumina and Oxford Nanopore Technologies (ONT), have enabled high-resolution profiling of the bovine respiratory microbiome and virome, revealing novel viral contributors such as bovine rhinitis A virus (BRAV) and influenza D virus (IDV). Transcriptomic approaches, including RNA sequencing (RNA-Seq) and microRNA (miRNA) profiling, provide insights into host immune responses and identify potential biomarkers for disease prediction. Traditional diagnostic methods-culture, ELISA, and immunohistochemistry-are increasingly complemented by PCR-based and metagenomic techniques, improving sensitivity and specificity. Despite technological progress, gaps remain in virome characterization, miRNA function, and the integration of multi-omics data. Standardized protocols and longitudinal studies are needed to validate microbial signatures and support field-deployable diagnostics. Advances in bioinformatics, particularly network-based integrative pipelines, are becoming essential for harmonizing multi-omics datasets and revealing complex host-pathogen interactions. The objective of this comprehensive review was to synthesize current understanding of the bovine transcriptomic response to BRD as well as the respiratory microbiome and virome, emphasizing how advanced sequencing technologies have transformed microbial profiling and molecular diagnostics in BRD.},
}

@article {pmid41295660,
year = {2025},
author = {Ren, Q and Lu, W and Zhang, T and Hao, S and Wang, J and Xu, X and Wang, F and Huang, Z and Lei, X and Cao, S and Chen, D and Li, Y},
title = {Comparative Analysis of Bacterial Diversity and Composition in Oral Fluid from Pigs of Different Ages and Water Pipe Wall Biofilms.},
journal = {Veterinary sciences},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/vetsci12111022},
pmid = {41295660},
issn = {2306-7381},
support = {No. 32372957//National Natural Science Foundation of China/ ; },
abstract = {Drinking water pipe biofilms, comprising viable microorganisms, microbial residues, and organic/inorganic particulates, pose significant risks to water safety by promoting the proliferation of opportunistic pathogens, pipe corrosion, and degradation of water quality. Their formation is strongly influenced by environmental conditions within the piping system. However, there is a lack of systematic research investigating the potential correlations between biofilm microbiota and the oral microbiomes of intensively farmed swine, as well as the age-dependent regulatory mechanisms shaping aquatic microbial communities. This pioneering study conducted a comparative analysis of biofilm microbiota from swine house water pipes and oral microbiomes across three growth stages (30-day BBF, 70-day NBF, and 110-day FBF groups), yielding three key findings. First, the biofilm biomass and dominant bacterial genera (e.g., Brevibacterium in BBF vs. Brevundimonas in FBF) exhibited stage-specific variations associated with swine age. Second, while the oral microbiomes showed no significant taxonomic divergence at the phylum or genus level, they shared characteristic phyla, including Actinobacteria and Bacteroidetes, with pipe biofilms, indicating potential cross-habitat microbial interactions. Third, the antibiotic resistance gene (ARG) adeF was consistently detected at high prevalence across all biofilm groups. These findings offer new insights into microbial transmission dynamics and inform risk mitigation strategies for livestock water supply systems.},
}

@article {pmid41295321,
year = {2025},
author = {Liu, X and Fu, C and Gao, Q and Zhang, H and Shi, T and Li, G and Wang, Y and Shang, Y},
title = {Effect of Tryptophan Supplementation Levels on the Cecal Microbial Composition, Growth Performance, Immune Function and Antioxidant Capacity in Broilers.},
journal = {Metabolites},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/metabo15110736},
pmid = {41295321},
issn = {2218-1989},
support = {ZR2024QC376//Shandong Provincial Natural Science Foundation/ ; CXGC2025F10//Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences/ ; CXGC2025B03//Agricultural Science and Technology Innovation Project of Shandong Academy of Agricultural Sciences/ ; 202228037//Jinan Introductory Innovation Team Project/ ; TSCX202306046//Taishan Industry Experts Program/ ; },
abstract = {BACKGROUND: Tryptophan (Trp) is a limiting amino acid in poultry nutrition. Dietary supplementation of Trp not only enhances production performance, but also supports intestinal barrier integrity, alleviates stress, and boosts immunity, in which the derivatives from gut Trp-metabolizing commensal microbes play crucial roles. However, research on how excessive Trp affects poultry growth, metabolism, and gut microbiota composition remains limited.

METHODS: In this study, we investigated the effects of varying Trp levels (0.23%, 0.29%, 0.35%) on broiler production performance, immune function, and antioxidant levels through controlled feeding trials. These host responses were further correlated with cecal microbiota metagenomic sequencing data using multivariate analysis.

RESULTS: Compared with the basal 0.23% Trp level, a 0.35% of Trp addition significantly impaired broiler body weight gain and feed intake, and 0.29% Trp could increase thymus index and serum superoxide dismutase (SOD) level without affecting the growth performance; neither of these two levels affected the feed conversion rate. The cecal microbial metagenomic data further revealed that Trp supplementation reduced the abundance of harmful bacteria, while increasing the abundance of beneficial bacteria and Trp-metabolizing microorganisms. Correlation analysis showed that Trp supplementation was negatively correlated with body weight (BW) but positively correlated with thymus index and SOD level, with similar trends observed between the abundance of specific Trp-utilizing microorganisms and these indicators. Functional analysis revealed an increase in the abundance of KEGG orthology (KO) related to Trp metabolism from the aforementioned microbes.

CONCLUSIONS: An appropriate addition of Trp (0.29%) can enhance certain metabolic levels without affecting production performance, which might be achieved through relevant metabolic pathways of intestinal microorganisms.},
}

@article {pmid41295300,
year = {2025},
author = {Bai, H and Luo, K and Jin, Y and Sun, X and Zhang, X and Zhao, Y and Muhammad, Y and Huang, A and Yin, P and Zhang, G},
title = {Integrated Metagenomic and Metabolomic Analyses Reveal a Microbiota-Metabolite Axis Associated with Gallstone Pathogenesis.},
journal = {Metabolites},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/metabo15110714},
pmid = {41295300},
issn = {2218-1989},
support = {82174136//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND/OBJECTIVES: Gallstone disease is a prevalent digestive disorder worldwide, with incidence increasingly linked to obesity, insulin resistance, and dyslipidemia. Emerging evidence suggests that intestinal microbial communities and their bioactive compounds play a central role in pathogenesis. Here, we aimed to clarify whether diet-related microbial alterations and circulating metabolites contribute to gallstone formation.

METHODS: We integrated dietary inflammatory index (DII) evaluation, genetic analyses of large-scale cohorts, and a cholesterol gallstone mouse model induced by a lithogenic diet (LD). Serum and fecal samples were subjected to metabolomic and metagenomic profiling, followed by multi-omics integration to identify links between microbial taxa, metabolites, and gallstone risk.

RESULTS: Higher DII scores were associated with increased gallstone risk. Genetic evidence supported bile acid and amino acid metabolism as potential mediating pathways, with Akkermansia muciniphila linked to decreased N-acetylarginine levels and CAG-448 showing an inverse association with glycodeoxycholate (GDCA). In LD-fed mice, shotgun metagenomics revealed enrichment of lithogenic taxa such as Bacteroides stercorirosoris and Enterocloster, whereas protective taxa, including Akkermansia muciniphila and CAG-448, were markedly depleted. Untargeted metabolomics confirmed elevations of GDCA and N-acetylarginine together with broader bile acid imbalance, amino acid stress, and long-chain acylcarnitine accumulation. Correlation analyses further showed that protective taxa were inversely associated with risk metabolites, whereas gallstone-enriched microbes displayed the opposite pattern.

CONCLUSIONS: This study provides evidence consistent with a contributory role of gut microbiota-metabolite dysregulation in gallstone pathogenesis. Specific taxa (A. muciniphila, CAG-448) and metabolites (GDCA, N-acetylarginine) may serve as potential biomarkers or targets for microbiota- and diet-based prevention strategies.},
}

@article {pmid41295156,
year = {2025},
author = {Zou, R and Zhang, Y and Zhang, L and Chen, M and Xin, L and Zhang, L},
title = {The Effect of Pseudomonas putida on the Microbial Community in Casing Soil for the Cultivation of Morchella sextelata.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/jof11110775},
pmid = {41295156},
issn = {2309-608X},
support = {XJBS-202445; QNYC-202515; Young talent program//Special Fund for Anhui Agricultural Research System; Agricultural Sciences Academy of Anhui Province Talent Project; Science and Technology Innovation Team Project of Anhui Academy of Agricultural Sciences/ ; },
abstract = {Morels are a rare edible and medicinal fungus. A major factor contributing to difficulties with their continuous cropping is alteration in soil microbial communities. Pseudomonas putida is a key microorganism in morel cultivation soils; it has garnered significant attention due to its ability to degrade 1-aminocyclopropane-1-carboxylic acid (ACC), a precursor of ethylene. However, the interaction between Pseudomonas putida and morels remains unclear. This study evaluated the growth-promoting potential of P. putida KT2440 by measuring the casing soil ACC content and assessing its ACC utilization capacity. Metagenomic sequencing was performed to assess the changes in soil microbial composition and function. The results indicated that ACC accumulated in the soil following morel cultivation and that P. putida KT2440 was capable of utilizing ACC as its sole nitrogen source for growth on plates. Inoculation enhanced the depletion of available nitrogen, phosphorus, and potassium; increased bacterial diversity; improved the stability of the soil microbial community; and caused the mycelium of morels to grow earlier. These processes occurred along with a decline in the abundance of the Streptomyces genus. Furthermore, a positive correlation was identified between the abundance of P. putida and ACC deaminase activity in the soil. Overall, this study examined the role of Pseudomonas putida inoculation in modulating the soil microbial community and metabolic processes within casing soil during Morchella sextelata cultivation. The findings indicate that P. putida inoculation promotes Morchella growth through ACC decomposition and microbial restructuring, offering a potential strategy for mitigating ethylene-related suppression in continuous cropping systems.},
}

@article {pmid41294637,
year = {2025},
author = {Ionaș, TH and Ionaș, M and Chicea, R and Dădârlat, DA and Ștef, L},
title = {Assessing the Oral Microbiome in Women of Reproductive Age: A Narrative Review.},
journal = {Clinics and practice},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/clinpract15110206},
pmid = {41294637},
issn = {2039-7275},
abstract = {The oral microbiome may be an indicator of oral pathologies and hormonal fluctuations. Consequently, the proper identification of methods for studying microbial factors is essential. Because more than half of the components of the oral microbiome belong to species that are very difficult or even impossible to cultivate in the laboratory, the assessment of the oral microbiome nowadays is based on genetic sequencing, using techniques such as DNA hybridization, 16S rRNA sequencing, and metagenomics, mainly analyzing saliva and subgingival plaque. Variations in results may be caused by differences in sample type, analysis methods, accuracy in determining cycle phases, and biases introduced by DNA extraction techniques and technical variations. Choosing the right primers for the 16S rRNA gene and reference databases (like HOMD, Greengenes2) is essential for accurately identifying microorganisms. Metagenomic sequencing offers greater taxonomic and functional detail, but it is costlier and presents bioinformatics challenges, including contamination with human DNA. When the patients under study are women, we have to take into consideration the cyclical changes in the menstrual cycle. Studies suggest that estrogen influences local immune and inflammatory responses and can worsen existing gingival inflammation. Certain oral bacteria can even utilize estradiol and progesterone as growth factors. The composition of the oral microbiome is also affected by hormonal contraceptives, carbohydrate intake, smoking, age, body mass index, genetics, and oral hygiene-all factors that need to be controlled for in future studies. Interpreting the biological significance of the reported cyclic changes requires careful examination of the specific methods used in each study.},
}

@article {pmid41294355,
year = {2025},
author = {O'Connor, JB and Fouquier, J and Neff, CP and Sterrett, JD and Marden, T and Fiorillo, S and Siebert, JC and Schneider, J and Nusbacher, N and Noe, AT and Fennimore, B and Higgins, J and Campbell, TB and Palmer, BE and Lozupone, C},
title = {Agrarian diet improves metabolic health in HIV-positive men with Prevotella-rich microbiomes: results from a randomized trial.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0118525},
doi = {10.1128/msystems.01185-25},
pmid = {41294355},
issn = {2379-5077},
abstract = {UNLABELLED: This study aimed to assess the impact of a high-fiber/low-fat agrarian diet (AD) on inflammation and metabolic outcomes in HIV-positive men who have sex with men (MSM). Since the gut microbiomes of MSM resemble those of individuals in agrarian cultures, including being Prevotella-rich and Bacteroides-poor, we hypothesized that they would have particularly strong health benefits from consumption of a diet matched to their microbiome type. Sixty-six participants, including 36 HIV-positive MSM [HIV(+)MSM], 21 HIV-negative MSM, and 9 HIV-negative men who have sex with women, were randomized to either an AD or a high-fat/low-fiber western diet (WD) for 4 weeks. Plasma, fecal, and colonic biopsy samples were obtained. Metabolic and inflammatory markers were measured in plasma. 16S ribosomal RNA sequencing was performed on fecal and biopsy samples, and shotgun metagenomic sequencing was performed on fecal samples. The AD reduced plasma low-density lipoprotein cholesterol (LDL-C) in HIV(+)MSM, with median reductions of 0.4138 mmoL/L at 2 weeks and 0.2845 mmol/L at 4 weeks. Greater LDL-C reductions were predicted by Prevotella-rich/Bacteroides-poor microbiomes with increased starch utilization potential, emphasizing the importance of personalized microbiome-dietary matching. The AD also reduced T cell exhaustion and pro-inflammatory intermediate monocytes and altered host transcription in the colonic mucosa.

IMPORTANCE: Our findings suggest tailoring diet interventions to baseline microbiome types can promote metabolic health in Prevotella-rich/Bacteroides-poor MSM, a significant portion of people living with HIV at risk for metabolic syndrome.This study was registered at NCT02610374.},
}

@article {pmid41294346,
year = {2025},
author = {Bodourian, CS and Imran, M and Georgakis, ND and Papageorgiou, AC and Labrou, NE},
title = {Structural and functional characterization of a metagenomically derived γ-type carbonic anhydrase and its engineering into a hyperthermostable esterase.},
journal = {Protein science : a publication of the Protein Society},
volume = {34},
number = {12},
pages = {e70396},
doi = {10.1002/pro.70396},
pmid = {41294346},
issn = {1469-896X},
mesh = {*Carbonic Anhydrases/chemistry/genetics/metabolism ; *Esterases/chemistry/metabolism/genetics ; Crystallography, X-Ray ; Enzyme Stability ; Models, Molecular ; Protein Engineering ; Amino Acid Sequence ; Escherichia coli/genetics ; Molecular Sequence Data ; },
abstract = {The 16S microbial community profiling of a metagenomics library from geothermal spring at Lisvori (Lesvos island, Greece) enabled the identification of a putative sequence exhibiting 95% identity to the γ-type carbonic anhydrase (γ-CA) from Caloramator australicus (γ-CaCA). The sequence of γ-CaCA was amplified by PCR, cloned, and expressed in E. coli. Activity assays showed that γ-CaCA possesses very low, but detectable, anhydrase activity, while exhibiting no measurable esterase activity. Differential scanning fluorimetry (DSF) revealed that the enzyme shows high thermal stability with a melting temperature (Tm) approximately 65-75°C in the pH range between 5.5 and 9.0. The structure of γ-CaCA was determined by X-ray crystallography at 1.11 Å resolution, the highest resolution reported so far for a γ-CA. The enzyme was crystallized as a trimer in the crystallographic asymmetric unit and contains three zinc-binding sites, one at each interface of neighboring subunits of the trimer. Structure-based rational design enabled the design and creation of a mutant enzyme (γ-CaCAmut) which possessed a heptapeptide insertion at the active-site loop and two-point mutations. Kinetic analysis demonstrated that γ-CaCAmut was successfully converted into a catalytically active esterase indicating successful activity gain through structure-guided engineering. The thermostability of γ-CaCAmut was significantly increased, aligning with the thermostability typically observed in hyperthermostable enzymes. X-ray crystallographic analysis of the γ-CaCAmut structure at 2.1 Å resolution, provided detailed structural insights into how the mutations impact the overall enzyme structure, function, and thermostability. These findings provide valuable structural and functional insights into γ-CAs and demonstrate a strategy for converting an inactive enzyme into a catalytically active form through rational design.},
}

*Carbonic Anhydrases/chemistry/genetics/metabolism
*Esterases/chemistry/metabolism/genetics
Crystallography, X-Ray
Enzyme Stability
Models, Molecular
Protein Engineering
Amino Acid Sequence
Escherichia coli/genetics
Molecular Sequence Data

@article {pmid41293880,
year = {2025},
author = {Damian, D},
title = {Metagenomic Applications in the Early Detection of Human Viral Threats.},
journal = {Viral immunology},
volume = {},
number = {},
pages = {},
doi = {10.1177/08828245251400169},
pmid = {41293880},
issn = {1557-8976},
abstract = {The rapid evolution of viral pathogens presents significant challenges for global health, as traditional methods for virus detection often fail to identify novel or genetically diverse viruses. The emergence and reemergence of viral pathogens necessitate more advanced and inclusive diagnostic approaches. This review aims to explore the role of metagenomics in overcoming the limitations of traditional viral detection methods and to assess its impact on the discovery, characterization, and surveillance of viral pathogens. A comprehensive review of recent studies employing metagenomic approaches to viral detection was conducted. High-throughput sequencing technologies and bioinformatics tools were highlighted as key components in enabling broad-spectrum viral identification and characterization. Metagenomic approaches have successfully identified novel pathogens, including new arboviruses and reemerging strains of known viruses. These techniques provide a more complete understanding of viral diversity and dynamics, surpassing the limitations of targeted assays and culturing methods. Key findings emphasize the capability of metagenomics to detect viruses previously undetected by conventional methods, improving the scope of surveillance. Metagenomics offers transformative advantages for viral surveillance and outbreak management. It enhances early detection, allows for better-informed responses to viral threats, and contributes to more effective strategies for managing emerging and reemerging viral pathogens. Integration of metagenomic techniques into public health practices is crucial for combating the evolving landscape of viral diseases.},
}

@article {pmid41293547,
year = {2025},
author = {Paul, D and Paasisalo, I and Putkinen, A and Jones, CM and Kohl, L and Hallin, S and Pihlatie, M and Siljanen, HMP},
title = {Microorganisms in the phyllosphere of Norway spruce controlling nitrous oxide dynamics.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf196},
pmid = {41293547},
issn = {2730-6151},
abstract = {Current climate change assessments and greenhouse gas flux models often lack information on the microbiological processes that consume atmospheric nitrous oxide (N2O), a potent greenhouse gas. There is limited understanding of phyllospheric microorganisms controlling N2O exchange. In this study, we determined the microbial potential for N2O consumption in aboveground vegetation in boreal forests. For this, we collected shoot samples from upland spruce forests in Finland and used a novel targeted metagenomics approach with a hybridization capture of gene-specific probes. Most of the samples contained nosZ genes, encoding the N2O reductase. Phylogenetic placement showed a significantly higher relative abundance (P < .01) of nosZ Clade I than nosZ Clade II. Bacterial members such as Comamonadaceae, Hydrogenophaga, and Paracoccus, which all harbor nosZ Clade I, were found in high relative abundance in the spruce shoots across the sites, suggesting they play a role in N2O consumption capabilities in the spruce phyllosphere. Anoxic incubations, utilizing gas chromatography for N2O analyses, showed potential N2O consumption activity across the spruce samples. The presence of nirK and nirS suggests potential for denitrification, possibly resulting in N2O production. Our finding provides evidence of microbial communities in spruce canopies with potential for N2O exchange. Given the vast coverage of boreal forests globally, understanding the role of phyllospheric microorganisms in N2O exchange is crucial for improving the accuracy of greenhouse gas models and enhancing climate prediction reliability.},
}

@article {pmid41293456,
year = {2025},
author = {Li, Z and Zhu, P and Zhang, Z and Li, Z and Liu, P and Meng, L and Yang, Q and Yang, Z and Song, J},
title = {Metavirome Identification and Pathogenicity Evaluation of Tibet Orbivirus in Pigs.},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {6628384},
pmid = {41293456},
issn = {1865-1682},
mesh = {Animals ; Swine ; *Swine Diseases/virology ; *Reoviridae Infections/veterinary/virology ; Tibet/epidemiology ; *Orbivirus/pathogenicity/genetics/isolation & purification ; Virulence ; Viremia/veterinary/virology ; Phylogeny ; },
abstract = {Tibet orbivirus (TIBOV) is an orbivirus transmitted by mosquitoes and Culicoides, despite specific neutralizing antibodies being detected in pigs, but the molecular genetic characteristics of TIBOV strains in infected pigs are completely uncharted, and their pathogenicity in piglets is poorly elucidated. This study aimed to investigate the genetic characteristics of TIBOV in infected pigs and evaluate the pathogenicity of TIBOV in weaned piglets. Through viral metagenomic sequencing, seven segments (VP1-VP4, VP6, NS1, and NS2) of TIBOV were obtained from swine tissues, and the sequences showed high identity with TIBOVs isolated from Culicoides, mosquitos, and cattle. After infection with TIBOV, the body temperature, appetite, and behavior of the piglets were normal, whereas hemorrhage nodes were observed on the hooves of all piglets and on the abdominal skin of one pig. Viremia was first detected at 2 days postinfection (dpi), peaked at 6 dpi, and remained high until 21 dpi. The virus was distributed in multiple organs, and the highest viral load and strongest viral nucleic acid signals were observed in the spleen. The most severe lesion was observed in the spleen with white pulp atrophy, a decreased number of lymphocytes, and widened septa of the medullary cord, indicating that the spleen was the most important target organ of TIBOV infection. The levels of inflammatory cytokines, including interleukin (IL)-18, tumor necrosis factor-α (TNF-α), interferon (IFN)-α, and IFN-λ3 in peripheral blood lymphocytes decreased significantly from 2 to 6 dpi, and interferon-stimulated gene-15 (ISG-15) and IFN regulatory factor 7 (IRF-7) expression levels declined significantly from 2 to 9 dpi, suggesting that the host immune response was inhibited within 6 dpi. Our findings confirmed that TIBOV elicited long-term viremia with mild clinical symptoms in piglets, the spleen was the target organ of TIBOV proliferation, and the host immune response may be slightly inhibited in the early stage of viral infection.},
}

Animals
Swine
*Swine Diseases/virology
*Reoviridae Infections/veterinary/virology
Tibet/epidemiology
*Orbivirus/pathogenicity/genetics/isolation & purification
Virulence
Viremia/veterinary/virology
Phylogeny

@article {pmid41293056,
year = {2025},
author = {Lee, JA and Won, D and Lee, EH and Lee, ST and Park, KK and Shin, S and Jeong, SJ},
title = {Utilization of cell-free DNA metagenomic analysis for early detection and microbial identification in prosthetic joint infections: a prospective cohort study in Korea.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663857},
pmid = {41293056},
issn = {2235-2988},
mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; Prospective Studies ; Synovial Fluid/microbiology/chemistry ; Female ; Male ; Aged ; Middle Aged ; *Cell-Free Nucleic Acids/genetics/analysis ; *Metagenomics/methods ; Republic of Korea ; Early Diagnosis ; *Bacteria/genetics/isolation & purification/classification ; Aged, 80 and over ; Arthroplasty, Replacement, Knee/adverse effects ; },
abstract = {BACKGROUND: Prosthetic joint infection (PJI) is a severe complication of hip or knee arthroplasty, often necessitating invasive intervention and posing a high risk of adverse outcomes. Early diagnosis and tailored antibiotic therapy are critical for the effective management of PJI. This study evaluated the utility of cell-free deoxyribonucleic acid (cfDNA) extracted from synovial fluid to diagnose PJI and identify the causative pathogens.

METHODS: This prospective, single-center study included a PJI group consisting of patients with confirmed infections based on the European Bone and Joint Infection Society criteria and a non-PJI group comprising patients without suspected PJIs who underwent joint surgery or aspiration. Synovial fluid samples were collected from all patients, and various culture methods, including conventional synovial fluid, sonication, and tissue and blood cultures, were applied along with cfDNA analysis.

RESULTS: A total of 35 patients were included, with 20 diagnosed with PJI and 15 classified as non-PJI. The median cfDNA concentration in synovial fluid was significantly higher in the PJI group (4.560 ng/μl, interquartile range (IQR) [3.320-6.348]) compared with the non-PJI group (0.028 ng/μl, IQR [0.009-0.273]) (p < 0.001). The Youden index identified a cfDNA concentration ≥ 1.59 ng/μl as strong likelihood of PJI. Culture positivity rates in the PJI group were as follows: synovial culture (10/20, 50.0%), sonication culture (8/9, 88.9%), tissue culture (2/8, 25.0%), and blood culture (2/12, 16.7%). The bacterial detection rate of cfDNA was 65.0% (13/20).

CONCLUSION: cfDNA concentration was significantly higher in the PJI group, with synovial cultures showing substantial agreement. Additionally, cfDNA sequencing detected pathogens in patients who had received prior antibiotic therapy and identified multiple pathogens in polymicrobial infections. These findings highlight cfDNA analysis as a valuable diagnostic tool for PJI, with the potential to enhance current diagnostic approaches.},
}

Humans
*Prosthesis-Related Infections/diagnosis/microbiology
Prospective Studies
Synovial Fluid/microbiology/chemistry
Female
Male
Aged
Middle Aged
*Cell-Free Nucleic Acids/genetics/analysis
*Metagenomics/methods
Republic of Korea
Early Diagnosis
*Bacteria/genetics/isolation & purification/classification
Aged, 80 and over
Arthroplasty, Replacement, Knee/adverse effects

@article {pmid41292684,
year = {2025},
author = {Liu, J and Sha, Y and Dang, R and Zhou, L and Zhou, M and Tan, Y and Wang, J and Ran, G and Xie, W and Xia, D and Wang, L and Zhao, X and Goi, BM and Yu, J and Xiao, L},
title = {Acetate-based syntrophy enhances methane production potential of ruminant feces.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1706620},
pmid = {41292684},
issn = {1664-302X},
abstract = {Livestock feces contribute to approximately 32% of global methane emissions. Although ruminants are generally believed to have a higher methane production potential than non-ruminants, the dominant pathways and key regulatory processes underlying methane generation in ruminants remain poorly understood, impeding effective manure management and accurate livestock emission assessments. In this study, metagenomic and carbon isotope techniques were employed to investigate methane production potential and key pathways in sheep, pig, chicken, and duck feces. Methane production potential of ruminant sheep feces was significantly higher (approximately threefold) compared to that of non-ruminants. Isotopic analysis of methane sources revealed that sheep feces primarily produce methane through the acetoclastic pathway, whereas the other three likely rely on CO2 reduction. Metagenomic analysis of methanogenic pathways further indicated that the abundance of functional genes associated with acetoclastic methanogenesis is significantly higher in sheep feces compared to the other three. Moreover, the co-occurrence network analysis highlighted a tightly coordinated, cross-species partnership between fermentative acetogenic bacteria and methanogenic archaea in the sheep fecal microbiome. Together, our findings provide insights into some key methanogenic pathways, such as acetoclastic methanogenesis, contributing to high methane production from ruminant feces.},
}

@article {pmid41292560,
year = {2025},
author = {Li, X and Wang, Y and Ma, F and Zhao, C and Zhang, Y and Zhu, Y and Zhang, Y and Hou, S and Li, B and Yang, F and Hao, L and Zhu, T},
title = {Chaperone-mediated thermotolerance in hyperthermophilic composting: Molecular-Level protein remodeling of microbial communities.},
journal = {Environmental science and ecotechnology},
volume = {28},
number = {},
pages = {100630},
pmid = {41292560},
issn = {2666-4984},
abstract = {Hyperthermophilic composting (HC) represents a promising approach for converting organic solid waste into valuable resources by leveraging extreme temperatures to enhance microbial degradation and detoxification processes. In this high-temperature environment, microbial communities undergo dynamic succession, where thermophilic bacteria dominate and drive efficient organic matter transformation through adapted metabolic pathways and stress responses. These adaptations include the stabilization of cellular structures and enzymes, often mediated by heat shock proteins (HSPs) that prevent protein misfolding under thermal stress. However, the integrated mechanisms linking community-level functional shifts to molecular-level protein remodeling in thermophiles during HC remain poorly understood. Here we show a coordinated interaction of functional succession and molecular adaptations within thermophilic bacteria in HC, which collectively achieve heat resistance. This interaction encompasses enhanced metabolic and genetic modules, accounting for 97 % of the variance observed in thermophile abundance. Metagenomic analyses revealed upregulation of translation, transcription, amino acid metabolism, and cell wall biosynthesis, coupled with suppression of mobilome functions to maintain genomic stability, as confirmed by partial least squares path modeling and Boruta analyses. Molecular dynamics simulations of key enzymes from the thermophile Truepera further demonstrated intrinsic structural rigidity, reduced hydrophobic exposure, and hierarchical chaperone activity involving DNAJ, DNAK, and GroEL for protein repair. These findings enhance our comprehension of microbial thermotolerance and establish a foundation for optimizing composting efficiency and advancing heat-resistant microbial applications in biotechnology and waste management. Additionally, they offer insights into the evolution of thermophiles, protein engineering, and stress adaptation across various biological and industrial systems, thereby promoting the integration of environmental engineering and systems biology.},
}

@article {pmid41291881,
year = {2025},
author = {Binod, M and Chang, L and Hung, MW and Dong, TS and Kilpatrick, LA and Tomasevic, A and Choy, M and Shin, A and Mayer, EA and Church, A},
title = {Multi-omics analysis reveal clinical-gut-brain interactions in female ibs patients with adverse childhood experiences.},
journal = {Biology of sex differences},
volume = {16},
number = {1},
pages = {101},
pmid = {41291881},
issn = {2042-6410},
support = {T32DK007180/GF/NIH HHS/United States ; U54 DK123755/GF/NIH HHS/United States ; R01 MD015904/GF/NIH HHS/United States ; },
mesh = {Humans ; Female ; *Irritable Bowel Syndrome/physiopathology/microbiology/psychology/diagnostic imaging ; *Adverse Childhood Experiences ; *Gastrointestinal Microbiome ; Adult ; *Brain/diagnostic imaging/physiopathology ; Middle Aged ; *Brain-Gut Axis ; Magnetic Resonance Imaging ; Young Adult ; Multiomics ; },
abstract = {BACKGROUND: The brain-gut system, which involves bidirectional communication between the central nervous system and the gut, plays a central role in stress responses. Its dysregulation is implicated in irritable bowel syndrome (IBS), a stress-sensitive, female-predominant disorder characterized by abdominal pain and altered bowel habits. Adverse childhood experiences (ACE) increase the risk and severity of IBS, likely by amplifying stress responsiveness and gut-brain dysfunction in females. However, the mechanisms involved are unknown.

AIM: This study aimed to identify a multi-omic signature linking ACE exposure to IBS females via clinical, neuroimaging, and gut microbiome features as compared to healthy control (HC) females.

METHODS: Data was analyzed from participants with Rome positive IBS and HCs. Four subgroups were created based on IBS diagnosis and ACE score with high ACE defined as ≥2 and low as ACE 0-1. Validated questionnaires assessed clinical variables. Biological markers included multimodal brain MRI, and gut microbial function using metagenomics. eXtreme gradient boosting (XGBoost) identified key differentiating features between the groups. Connectograms visualized relationships across mutli-omics data within each group.

RESULTS: Among 188 female participants, the four groups included IBS with high ACE (n=37), IBS with low ACE (n=55), HCs with high ACE (n=19), and HCs with low ACE (n=77). Key findings include: 1. High ACE participants with IBS versus their HC counterparts showed increased depression and anxiety symptoms, GI-symptom related anxiety, perceived stress, somatic symptom severity, and poorer physical and mental health scores. 2. High ACE participants with IBS had negative associations between key bacteria such as Akkermansia (a beneficial bacteria) and somatic symptom severity, and between Bifidobacterium and ACE parental divorce/separation and alterations in the salience and central autonomic networks. 3. The ensemble model accurately distinguished IBS patients with high ACE (AUC of 0.87), demonstrating strong predictive performance with an overall model accuracy of 78%.

CONCLUSIONS: Our findings highlight the unique microbiota and brain networks contributing to a complex interplay of chronic stress as measured by early life adversity, the brain-gut-microbiome system, and IBS pathophysiology which can inform therapeutic targets aimed at mitigating the long-term impacts of early life stress in female IBS patients.},
}

Humans
Female
*Irritable Bowel Syndrome/physiopathology/microbiology/psychology/diagnostic imaging
*Adverse Childhood Experiences
*Gastrointestinal Microbiome
Adult
*Brain/diagnostic imaging/physiopathology
Middle Aged
*Brain-Gut Axis
Magnetic Resonance Imaging
Young Adult
Multiomics

@article {pmid41291846,
year = {2025},
author = {Ding, J and Yang, W and Li, X and Liu, X and Zhao, J and Sun, T and Liu, H},
title = {The microbial community metabolic regime adapts to hydraulic disturbance in river-lake systems with high-frequency regulation.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00821-3},
pmid = {41291846},
issn = {2524-6372},
support = {National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; National Key Research and Development Program of China (No. 2023YFC3209003)//Wei YANG/ ; },
abstract = {BACKGROUND: River-lake ecosystems are crucial for the rational allocation of water resources, but frequent water diversion can destabilize water quality due to hydraulic disturbance. Microbial communities can respond rapidly to such external perturbations and influence these systems through the effects on nutrient metabolism. Therefore, understanding how microbial communities respond to hydraulic shocks in aquatic systems and whether they can adapt to such disturbances is essential for maintaining the health of river-lake systems. We used 16S rRNA and metagenomic sequencing technologies to examine the metabolic regimes of microbial communities during water regulation and non-regulation periods in river-lake systems.

RESULTS: We found that hydraulic disturbance tended to drive the microbial community toward homogenized selection, thereby weakening its stability. Flow velocity (V) and the nitrate (NO3[-]-N) concentration significantly affected microbial community composition and abundance, with clear threshold effects. We established low (V = 0.284 m/s, NO3[-]-N = 0.031 mg/L) and high (V = 0.461 m/s, NO3[-]-N = 0.055 mg/L) thresholds. These thresholds categorize microbial communities into three distinct regimes: regime1 (R1), regime 2 (R2), and regime 3 (R3). The microbial abundances in R1 and R3 were significantly higher than those in R2 (p < 0.01), while the community in R3 exhibited a strong denitrification capacity. In R3, the microbial community enhanced its denitrification metabolism by promoting the growth of denitrifying microbial genera (e.g., Pseudomonas and Flavobacterium) to counterbalance the impact of high V and NO3[-]-N. These strains contributed the denitrification-related genes nasA, narB, nirB, and nirD to the community, thereby promoting the NO3[-]-N metabolism and reducing environmental NO3[-]-N concentrations. In addition, we predicted microbial community abundance using an artificial neural network to validate the thresholds we identified.

CONCLUSIONS: Our study provides theoretical support for understanding how microbial communities adapt to high-frequency hydraulic disturbances and offer valuable insights for managers to adjust water diversion strategies in a timely manner, thereby safeguarding the integrity of river-lake ecosystems.},
}

@article {pmid41291642,
year = {2025},
author = {Xie, Q and Li, D and Ren, C and Shen, Y and Lin, S and Chen, W},
title = {Metabolomic and metagenomic analyses reveal distinct microenvironmental signatures between clear aligner-associated and tooth surface dental plaque.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07231-4},
pmid = {41291642},
issn = {1472-6831},
support = {No. 2023J01643//the Fujian Provincial Natural Science Foundation of China/ ; },
}

@article {pmid41291413,
year = {2025},
author = {Zhang, J and Zhao, Y and Li, W and Xu, J and Chen, Y and Yang, S and Wu, P and Li, Y and Zhou, C and Zhang, W},
title = {Viromic analysis of cerebrospinal fluid (CSF) samples identified an unclassified RNA virus exhibiting an atypical genomic architecture.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {776},
pmid = {41291413},
issn = {1471-2180},
mesh = {Humans ; *Genome, Viral ; Phylogeny ; Open Reading Frames ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; *RNA Viruses/genetics/classification/isolation & purification ; *Cerebrospinal Fluid/virology ; *Meningoencephalitis/virology/cerebrospinal fluid ; Metagenomics ; Viral Proteins/genetics ; Male ; RNA-Dependent RNA Polymerase/genetics ; },
abstract = {The central nervous system (CNS) is highly susceptible to infections that can lead to severe neurological morbidity and mortality. Despite advances in diagnostic technologies, a significant proportion of encephalitis and meningitis cases remain etiologically undiagnosed, underscoring the need for novel pathogen discovery approaches. Here, we report the identification of a novel unclassified RNA virus, provisionally named hucaurvirus ("human CSF-associated unclassified RNA virus"), in the cerebrospinal fluid (CSF) of a pediatric patient with unexplained meningoencephalitis, using metagenomic next-generation sequencing (mNGS). The hucaurvirus exhibits a monopartite, positive-sense RNA genome of 6.5 kb which contains two overlapping open reading frames (ORFs), which was confirmed by conventional PCR amplification and Sanger sequencing. The large ORF encodes a polyprotein containing a capsid domain, while the small ORF overlaps within the large ORF and encodes the RNA-dependent RNA polymerase (RdRp) protein. BLASTp search based on the amino acid sequence of RdRp showed that hucaurvirus had the highest sequence identity and query coverage of 39.2% and 90%, respectively, to a noda-like virus (GenBank no. MT138110). Phylogenetic analysis showed that hucaurvirus was closely related to four viruses annotated as noda-like viruses, forming a cluster that is adjacent to the cluster of the Carmotetraviridae family and appears to form a new viral family within the order Tolivirales. PCR screening confirmed the presence of hucaurvirus in one of ten CSF samples, validating its detection. Our findings emphasize the utility of mNGS in uncovering novel pathogens and expanding our understanding of viral diversity in CNS infections.},
}

Humans
*Genome, Viral
Phylogeny
Open Reading Frames
RNA, Viral/genetics
High-Throughput Nucleotide Sequencing
*RNA Viruses/genetics/classification/isolation & purification
*Cerebrospinal Fluid/virology
*Meningoencephalitis/virology/cerebrospinal fluid
Metagenomics
Viral Proteins/genetics
Male
RNA-Dependent RNA Polymerase/genetics

@article {pmid41291216,
year = {2025},
author = {Jurado, J and Garcia-Vega, A and Vasquez, Y and Villegas-Plazas, M and Roldan, F},
title = {Field-Scale AMD Remediation: Microbial Community Dynamics and Functional Insights in Biochemical Passive Reactors.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02628-8},
pmid = {41291216},
issn = {1432-184X},
abstract = {Acid mine drainage (AMD) generated during coal mining activities is characterized by low pH, high concentrations of dissolved metals and metalloids, and elevated sulfate levels, all of which significantly impact surrounding ecosystems. Scaling up biochemical passive reactor (BPR) systems represents a promising approach for the in situ bioremediation of AMD. While numerous laboratory-scale studies have described the taxonomic and functional composition of microbial communities in BPRs, typically dominated by (ligno)cellulolytic organisms and sulfate-reducing bacteria (SRB), it remains unclear whether this composition is maintained at the field-pilot scale under environmental conditions. To address this gap, 16S rRNA gene metabarcoding and shotgun metagenomics analyses were performed to characterize the taxonomic and functional diversity of microbial communities in the BPRs within a multi-unit field-pilot system. The results revealed that bioremediation effectiveness was driven by syntrophic interactions among hydrolytic, fermentative, and sulfate-reducing bacteria, aligning with laboratory-scale observations. While community composition shifts altered specific taxa, core operational dynamics remained preserved.},
}

@article {pmid41291200,
year = {2025},
author = {Zha, Y and Fan, L and Shen, T and Zhang, Y and Ren, H},
title = {Triptolide ameliorates LPS-induced acute lung injury in Balb/c mice through gut-lung axis-mediated regulation of bile acid metabolism and gut microbiota.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29758-w},
pmid = {41291200},
issn = {2045-2322},
support = {PW2022A-21//the Scientific Research Program of Shanghai Pudong New Area Health Commission/ ; },
abstract = {Acute lung injury (ALI) associated with pulmonary edema is a severe clinical condition characterized by acute inflammation, disrupted lung barrier function, and high mortality. Current therapeutic strategies remain limited, highlighting the need for exploring novel agents and their underlying mechanisms. Triptolide (TP), an active component derived from Tripterygium wilfordii, has shown anti-inflammatory and tissue-protective properties[1,2], but its specific role in alleviating ALI and the involvement of the lung-gut axis in metabolic regulation remain poorly understood. This study aims to investigate the therapeutic effects of TP on LPS-induced ALI, focusing on its impact on pulmonary edema and inflammatory injury. By analyzing the lung-gut axis using multi-omics approaches, we seek to clarify the metabolic network regulatory mechanisms through which TP exerts its effects. LPS-induced ALI model was established in Balb/c mice, with TP administered as the therapeutic intervention. Histopathological examination of lung tissues and detection of pro-inflammatory cytokines were performed to assess lung injury. Untargeted metabolomics via LC-MS/MS was used to identify differential metabolites in lung tissues and serum, while metagenomic sequencing analyzed changes in gut microbiota composition. Integrated multi-omics analysis was applied to explore associations between gut microbiota alterations, serum metabolites, and pulmonary bile acid levels. TP administration significantly reduced histopathological damage in lung tissues of ALI mice and decreased pro-inflammatory cytokine levels. Metabolomics profiling revealed distinct changes in key metabolites, including bile acids, amino acid derivatives, and energy metabolism intermediates, in both lung tissues and serum after TP treatment. Metagenomic analysis showed that TP restructured gut microbiota composition, with functional enrichment in glycolysis and thiamine metabolism pathways. Integrated analysis confirmed strong correlations between dynamic microbiota changes, serum metabolite profiles, and pulmonary bile acid levels, indicating a regulatory role of the lung-gut axis. This study demonstrates that TP alleviates pulmonary edema and inflammatory injury in ALI by modulating gut microbial ecology and function, which drives bile acid metabolic reprogramming and regulates metabolite interactions within the lung-gut axis. These findings provide novel insights into TP's therapeutic mechanism and support its potential application in ALI treatment.},
}