@article {pmid40188788,
year = {2025},
author = {Lu, H and Miao, J and Zhang, N and Ji, J and Zhang, R and Zhu, S and Wei, X},
title = {Targeting regulation of nitrate removal and chlorophenol degradation through hydrogen/oxygen switching.},
journal = {Water research},
volume = {281},
number = {},
pages = {123581},
doi = {10.1016/j.watres.2025.123581},
pmid = {40188788},
issn = {1879-2448},
abstract = {Nitrate is a common co-contaminant with 2,4-dichlorophenol (2,4-DCP) in water, presenting a challenge for environmental remediation. Under anaerobic conditions, the ring cleavage of chlorophenol is inefficient, while under aerobic conditions, nitrate removal is hindered. In this study, a microbial consortium capable of hydrogenotrophic denitrification and 2,4-DCP degradation was cultured, aiming to achieve efficient nitrate removal and 2,4-DCP degradation by alternately switching between hydrogen (H2) and oxygen (O2). Under H2 conditions, nitrate removal exceeded 90 %, while under O2 conditions, 2,4-DCP degradation reached 100 %. Under H2 conditions, the abundance of the Nar gene which was involved in nitrate reduction was higher than that under O2 conditions, promoting hydrogenotrophic denitrification. In contrast, under O2 conditions, 2,4-DCP degradation occurred via hydroxylation, ring-cleavage, dechlorination, and mineralization through the TCA cycle. Metagenomic and metabolomic analysis was performed to explore microbial metabolic pathways and potential synergistic mechanisms involved in hydrogenotrophic denitrification and 2,4-DCP biodegradation. In the H2-atmosphere, microbes (Methylobacillus and Chromobacterium), genes (E3.1.1.45 and speG), and metabolites (Cytosine and Uridine) may play a crucial role in hydrogenotrophic denitrification. In the O2-atmosphere, the functional genus of Paracoccus and Aquamicrobium associated with genes (tfdB and tfdC) may contribute to 2,4-DCP and its metabolites 2-Chloromaleylacetate degradation. These findings confirmed the role of functional microbial communities through H2/O2 regulation. This work provides a promising technological reference for treating industrial wastewater containing phenols and nitrogen.},
}

@article {pmid40188743,
year = {2025},
author = {Deng, K and Wang, L and Nguyen, SM and Shrubsole, MJ and Cai, Q and Lipworth, L and Gupta, DK and Zheng, W and Shu, XO and Yu, D},
title = {A dietary pattern promoting gut sulfur metabolism is associated with increased mortality and altered circulating metabolites in low-income American adults.},
journal = {EBioMedicine},
volume = {115},
number = {},
pages = {105690},
doi = {10.1016/j.ebiom.2025.105690},
pmid = {40188743},
issn = {2352-3964},
abstract = {BACKGROUND: Excessive hydrogen sulfide in the gut, generated by sulfur-metabolising bacteria from foods, has been linked to intestinal inflammation and human diseases. We aim to investigate the interplay between diet and sulphur-metabolising bacteria in relation to mortality and circulating metabolites in understudied populations.

METHODS: In the Southern Community Cohort Study (SCCS), a prospective cohort of primarily low-income American adults, habitual diets were assessed using a food frequency questionnaire at baseline (2002-2009). A sulfur microbial diet score (SMDS) was developed among 514 Black/African American participants by linking habitual dietary intakes with the abundance of sulfur-metabolising bacteria profiled by faecal shotgun metagenomics. The SMDS was then constructed among all eligible SCCS participants (50,114 Black/African American and 23,923 non-Hispanic White adults), and its associations with mortality outcomes were examined by Cox proportional hazards model and Fine-Grey subdistribution hazard model. The association between SMDS and 1110 circulating metabolites was examined by linear regression among 1688 SCCS participants with untargeted metabolomic profiling of baseline plasma samples.

FINDINGS: Over an average 13.9-year follow-up, SMDS was associated with increased all-cause mortality (HR [95% CI] for the highest vs. lowest quartiles: 1.21 [1.15-1.27]) and cardiovascular disease (1.18 [1.08-1.29]), cancer (1.13 [1.02-1.25]), and gastrointestinal cancer-specific (1.22 [1.00-1.49]) mortality among Black/African American participants (all P-trend<0.05). The associations were largely consistent across participant subgroups. Similar results were observed among non-Hispanic White participants. The SMDS was associated with 112 circulating metabolites, which mediated 36.15% of the SMDS-mortality association (P = 0.002).

INTERPRETATION: A dietary pattern promoting sulfur-metabolising gut bacteria may contribute to increased total and disease mortality in low-income American adults.

FUNDING: This study was funded by the National Institutes of Health, United States, to Vanderbilt University Medical Center, United States, and Anne Potter Wilson Chair endowment to Vanderbilt University, United States.},
}

@article {pmid40188549,
year = {2025},
author = {Sun, J and Yang, W and Li, M and Zhang, S and Sun, Y and Wang, F},
title = {Metagenomic analysis reveals soil microbiome responses to microplastics and ZnO nanoparticles in an agricultural soil.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138164},
doi = {10.1016/j.jhazmat.2025.138164},
pmid = {40188549},
issn = {1873-3336},
abstract = {Both microplastics (MPs) and engineered nanoparticles are pervasive emerging contaminants that can produce combined toxicity to terrestrial ecosystems, yet their effects on soil microbiomes remain inadequately understood. Here, metagenomic analysis was employed to investigate the impacts of three common MPs [i.e., polyethylene (PE), polystyrene (PS), and polylactic acid (PLA)] and zinc oxide nanoparticles (nZnO) on soil microbiomes. Both MPs and nZnO significantly altered the taxonomic, genetic, and functional diversity of soil microbes, with distinct effects depending on dosage or type. Archaea, fungi, and viruses exhibited more pronounced responses compared to bacteria. Higher doses of MPs and nZnO reduced gene abundance for nutrient cycles like C degradation and N cycling, but enhanced CO2 fixation and S metabolism. nZnO consistently decreased the complexity, connectivity, and modularity of microbial networks; however, these negative effects could be mitigated by co-existing MPs, particularly at elevated doses. Notably, PLA (10 %, w/w) exhibited greater harm to fungal communities and increased negative interactions between microbes and nutrient-cycling genes, posing unique risks compared to PE and PS. These findings demonstrate that MPs and nZnO interact synergistically, complicating ecological predictions and emphasizing the need to consider pollutant interactions in ecological risk assessments, particularly for biodegradable MPs.},
}

@article {pmid40188455,
year = {2025},
author = {Li, Z and Xu, H and Zhang, L and Zhou, Y},
title = {Genome-Resolved Metagenomic and Metatranscriptomics Reveal Feammox Metabolism of Anaerobic Ammonia Oxidation Bacteria in Microaerobic Granular Sludge.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c13580},
pmid = {40188455},
issn = {1520-5851},
abstract = {Anammox is an energy-efficient nitrogen removal process in which anammox bacteria (AnAOB) oxidize NH4[+]-N to N2 using NO2[-]-N as the electron acceptor. Recent evidence suggests that AnAOB can perform extracellular electron transfer (EET), potentially coupling Fe(III) reduction with NH4[+]-N oxidation (Feammox). However, whether AnAOB directly participate in Feammox within complex wastewater treatment systems remains unclear. Here, we investigated the iron-mediated nitrogen metabolism pathways in a microaerobic granular sludge (MGS) reactor by integrating enzyme inhibition assays with analyses of gene dynamics and co-occurrence patterns of nitrogen- and iron-cycling genes. Results demonstrate that AnAOB contributed to Feammox activity. The iron reduction gene CT573071, coding a porin-cytochrome c protein complex associated with EET, co-occurred with hao, hzsABC, and hdh genes in Candidatus Kuenenia, suggesting its role in Feammox. Furthermore, four high-quality metagenome-assembled genomes (MAGs) affiliated with Kuenenia stuttgartiensis_A harbored CT573071, hao-like, hzsABC, and hdh genes, along with the hao-cluster, which catalyzes the oxidation of NH4[+]-N to hydroxylamine. This genomic evidence further supports their dual metabolic capacity. Metatranscriptomic analysis confirmed CT573071 upregulation and its coexpression with the hao, hzsABC, and hdh genes. These findings establish the potential role of K. stuttgartiensis_A in Feammox, providing novel insights into nitrogen removal in low-strength wastewater treatment systems.},
}

@article {pmid40187695,
year = {2025},
author = {Palumbo, S and Lucarelli, G and Lasorsa, F and Damiano, R and Autorino, R and Aveta, A and Spena, G and Perdonà, S and Russo, P and Giulioni, C and Cafarelli, A and Finati, M and Siracusano, S and Pandolfo, SD},
title = {Urobiome and Inflammation: A Systematic Review on Microbial Imbalances and Diagnostic Tools for Urinary Disorders.},
journal = {Urology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.urology.2025.03.050},
pmid = {40187695},
issn = {1527-9995},
abstract = {OBJECTIVE: To synthesize current knowledge on urobiome alterations, innovative diagnostic advancements, and emerging therapeutic strategies targeting urobiome dysbiosis in inflammatory urinary tract disorders, including urinary tract infections (UTIs), non-gonococcal urethritis (NGU), and interstitial cystitis.

METHODS: A systematic review was conducted by screening the most important scientific databases. The search included the keywords: (microbiome) OR (microbial) OR (bacteria) OR (bacterial profile) AND (urine) OR (urinary) AND (first-morning sample) OR (first void). Only original studies in English involving human specimens were considered.

RESULTS: Of the 760 articles initially identified, a final sample of 20 original studies met the inclusion criteria. Disruptions in the urobiome composition were associated with increased colonization by pathogens such as Escherichia coli and Mycoplasma genitalium, resulting in inflammation and recurrent urinary conditions. Advanced diagnostic techniques, including metaproteomics, metagenomics, and point-of-care assays like NG-LFA, demonstrated enhanced capabilities for rapid pathogen detection and differentiation of inflammatory conditions. Therapeutic interventions targeting urobiome dysbiosis, particularly probiotics (Lactobacillus rhamnosus, L. reuteri, L. crispatus), showed promising efficacy in reducing recurrence and inflammation in clinical trials.

CONCLUSIONS: Urobiome dysbiosis plays a critical role in inflammatory urinary tract disorders. Innovative diagnostic methods and targeted therapeutic approaches, especially probiotics, offer substantial potential to improve patient outcomes. Further research is warranted to refine these strategies and validate their clinical applicability.},
}

@article {pmid40187301,
year = {2025},
author = {Peng, Q and Wu, Z and Qian, D and Ren, H and Xie, G},
title = {Comprehensive multi-omics analysis of secondary distillate from fermented Huangjiu residue: Insights into flavor formation and microbial dynamics.},
journal = {Food chemistry},
volume = {482},
number = {},
pages = {144145},
doi = {10.1016/j.foodchem.2025.144145},
pmid = {40187301},
issn = {1873-7072},
abstract = {Huangjiu residue distillate, or Zaoshao, is a traditional Chinese liquor produced from the fermentation and distillation of Huangjiu lees. This study investigates the fermentation mechanisms and flavor formation of secondary Zaoshao, derived from the second round of Huangjiu lees fermentation, using flavoromics, amino acid and organic acid profiling, and metagenomics. Flavoromics identified ethyl octanoate, ethyl decanoate, ethyl dodecanoate, ethyl hexadecanoate, and ethyl (Z)-octadec-9-enoate as key flavor compounds. Amino acid and organic acid profiling showed continuous increases in amino acid content and significant changes in organic acids during fermentation. Metagenomics identified 9 dominant genera and 10 key species, with Saccharomyces, Saccharopolyspora, Aspergillus, Streptomyces, and Bacillus playing crucial roles in fermentation and flavor formation. These findings provide insights into microbial community functions and offer a foundation for regulating microbial consortia to enhance the flavor quality of secondary Zaoshao.},
}

@article {pmid40187295,
year = {2025},
author = {Coskuner-Weber, O and Alpsoy, S and Yolcu, O and Teber, E and de Marco, A and Shumka, S},
title = {Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing.},
journal = {Computational biology and chemistry},
volume = {118},
number = {},
pages = {108444},
doi = {10.1016/j.compbiolchem.2025.108444},
pmid = {40187295},
issn = {1476-928X},
abstract = {The burgeoning field of aquaculture has become a pivotal contributor to global food security and economic growth, presently surpassing capture fisheries in aquatic animal production as evidenced by recent statistics. However, the dense fish populations inherent in aquaculture systems exacerbate abiotic stressors and promote pathogenic spread, posing a risk to sustainability and yield. This study delves into the transformative potential of metagenomics, a method that directly retrieves genetic material from environmental samples, in elucidating microbial dynamics within aquaculture ecosystems. Our findings affirm that metagenomics, bolstered by tools in big data analytics, bioinformatics, and machine learning, can significantly enhance the precision of microbial assessment and pathogen detection. Furthermore, we explore quantum computing's emergent role, which promises unparalleled efficiency in data processing and model construction, poised to address the limitations of conventional computational techniques. Distinct from metabarcoding, metagenomics offers an expansive, unbiased profile of microbial biodiversity, revolutionizing our capacity to monitor, predict, and manage aquaculture systems with high accuracy and adaptability. Despite the challenges of computational demands and variability in data standardization, this study advocates for continued technological integration, thereby fostering resilient and sustainable aquaculture practices in a climate of escalating global food requirements.},
}

@article {pmid40187264,
year = {2025},
author = {Kwon, H and Li, B and Xu, M and Wang, Q and Maqbool, T and Lu, H and Winkler, M and Jiang, D},
title = {Minimizing byproduct formation in bioelectrochemical denitrification with anammox bacteria.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138110},
doi = {10.1016/j.jhazmat.2025.138110},
pmid = {40187264},
issn = {1873-3336},
abstract = {Autotrophic bioelectrochemical denitrification (BED) holds promise for nitrate remediation. However, the accumulation of byproducts such as NO2[-], N2O, and NH4[+], poses a significant challenge to effluent quality and climate adaptation. This study hypothesized that introducing anaerobic ammonium oxidation bacteria (anammox) to BED could alleviate this issue through synergy: a) anammox can utilize NH4[+] and NO2[-] from BED without producing N2O, as seen in canonical denitrification, and b) BED can recycle NO3[-] from the anammox anabolic pathway. Results showed that Anammox_BED reduced NO2[-] accumulation by two-thirds, lowered the relative abundance of N2O by 80 %, and eliminated NO. Metagenomic analysis revealed that the anammox species Ca. Brocadia sapporoensis tripled in abundance in the bulk sludge. Meanwhile, Pseudomonas stutzeri and Bosea robiniae, species capable of reducing nitrate via extracellular electron transfer (EET) and supplying NO2[-] to anammox, halved in relative abundance, while the abundance of Stenotrophomonas acidaminiphila, a non-EET, ammonia assimilation species, doubled following anammox introduction. Metatranscriptomic analysis found upregulation of denitrification-related functional genes in Anammox_BED biofilm and survival- and motility- related genes in bulk sludge, possibly due to insufficient substrate. Overall, BED-Anammox successfully diverted the rate-limiting EET nitrite reduction towards anammox-driven nitrite utilization thereby mitigating the generation of unwanted intermediates.},
}

@article {pmid40187012,
year = {2025},
author = {Khan, MM and Mushtaq, MA and Suleman, M and Ahmed, U and Ashraf, MF and Aslam, R and Mohsin, M and Rödiger, S and Sarwar, Y and Schierack, P and Ali, A},
title = {Fecal microbiota landscape of commercial poultry farms in Faisalabad, Pakistan: A 16S rRNA gene-based metagenomics study.},
journal = {Poultry science},
volume = {104},
number = {6},
pages = {105089},
doi = {10.1016/j.psj.2025.105089},
pmid = {40187012},
issn = {1525-3171},
abstract = {This study explores the microbiota of broiler and layer farms, aiming to understand how genetic breed, age, and farm type influence microbial communities in commercial settings. Fecal samples from 18 poultry farms (twelve layers and six broilers) in Faisalabad, Pakistan were analyzed using 16S rRNA gene sequencing of the V3-V4 region to evaluate bacterial composition. The dominant phylum, Firmicutes, accounted for 58.72 % of the microbial population, with Lactobacillus being the most abundant genus in both broilers and layers. The total abundance of potentially pathogenic genera was also assessed with Enterococcus and Corynebacterium being the most prevalent across all farms, regardless of bird type. Layers exhibited greater microbial richness and diversity than broilers, while the Karachi cage system (KCS) farm type showed higher richness than Floor system (FS). Although the breed significantly influenced microbial diversity, age was not a determining factor. Co-occurrence analyses revealed close interactions among phyla (Actinobacteriota, Proteobacteria, Firmicutes, Fusobacteriota, and Bacteroidota) and genera (Lactobacillus, Brevibacterium, Enterococcus), suggesting their pivotal roles within the microbial community. Additionally, functional analysis detected important metabolic pathways and traced microbial signatures of key pathogenic bacteria, enhancing our understanding of microbial contributions to poultry health. Despite limitations such as the need for broader geographic sampling and accounting for diet and medication, this study advances microbiome research in Pakistan's poultry sector, emphasizing consistent taxa and opening avenues for future investigations into microbiome manipulations for improved food safety and achieve better sustainable practices.},
}

@article {pmid40186063,
year = {2025},
author = {Saveetha, K and Somala, CS and Anand, T and Balamurugan, D and Vasudevan, V and Saravanan, KM and Senthil, R},
title = {Impact of Soil Microbiomes on Mung Bean Cultivation: Insights from 16S rRNA Metagenomics.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40186063},
issn = {1559-0305},
abstract = {Cyclic nutrient processes, soil health maintenance, and plant development are contingent upon soil microbiomes. The microbial makeup of the soil of Maruthupandiyar College, Thanjavur, is assessed using 16S rRNA gene sequencing. QIIME2, in conjunction with the SILVA database, analyzed the sequencing data to examine microbial diversity and composition. The experimental results revealed a diverse array of bacteria in soil physicochemical properties. The alpha and beta diversity assessment revealed significant microbial community complexity and distribution patterns disparities. The research revealed bacterial groups associated with biological nitrogen fixing, suggesting their potential to enhance mung bean growth. The current study illustrates the significance of microbial interactions in soil for sustaining soil fertility and enhancing crop output. Research findings provide essential insights into improving the sustainability of tropical agriculture through intentional microbial management to create sustainable soil health systems.},
}

@article {pmid40185904,
year = {2025},
author = {Wang, D and Gui, S and Pu, J and Zhong, X and Yan, L and Li, Z and Tao, X and Yang, D and Zhou, H and Qiao, R and Zhang, H and Cheng, X and Ren, Y and Chen, W and Chen, X and Tao, W and Chen, Y and Chen, X and Liu, Y and Xie, P},
title = {PsycGM: a comprehensive database for associations between gut microbiota and psychiatric disorders.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {40185904},
issn = {1476-5578},
support = {CSTB2024NSCQ-MSX1027//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; CSTB2024NSCQ-QCXMX0033//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; 82371526//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Psychiatric disorders pose substantial global burdens on public health, yet therapeutic options remain limited. Recently, gut microbiota is in the spotlight of new research on psychiatric disorders, as emerging discoveries have highlighted the importance of gut microbiome in the regulation of central nervous system via mediating the gut-brain-axis bidirectional communication. While metagenomics studies have accumulated for psychiatric disorders, few systematic efforts were dedicated to integrating these high-throughput data across diverse phenotypes, interventions, geographical regions, and biological species. To present a panoramic view of global data and provide a comprehensive resource for investigating the gut microbiota dysbiosis in psychiatric disorders, we developed the PsycGM, a manually curated and well-annotated database that provides the literature-supported associations between gut microbiota and psychiatric disorders or intervention measures. In total, PsycGM incorporated 559 studies from 31 countries worldwide, encompassing research involving humans, rats, mice, and non-human primates. PsycGM documented 8907 curated associations between 1514 gut microbial taxa and 11 psychiatric disorders, as well as 4050 associations between 869 taxa and 232 microbiota-based and non-microbiota-based interventions. Moreover, PsycGM provided a user-friendly web interface with comprehensive information, enabling browsing, retrieving and downloading of all entries. In the application of PsycGM, we panoramically depicted the intestinal microecological imbalance in depression. Additionally, we identified 9 microbial taxa consistently altered in patients with depression, with the most common dysregulations observed for Parabacteroides, Alistipes, and Faecalibacterium; in animal models of depression, consistent changes were observed in 21 microbial taxa, most frequently reported as Helicobacter, Lactobacillus, Roseburia, and the ratio of Firmicutes/Bacteroidetes. PsycGM is a comprehensive resource for future investigations on the role of gut microbiota in mental and brain health, and for therapeutic target innovations based on modifications of gut microbiota. PsycGM is freely accessed at http://psycgmomics.info .},
}

@article {pmid40185827,
year = {2025},
author = {Chornchoem, P and Tandhavanant, S and Saiprom, N and Preechanukul, A and Thongchompoo, N and Sensorn, I and Chantratita, W and Chantratita, N},
title = {Metagenomic evaluation, antimicrobial activities, and immune stimulation of probiotics from dietary supplements and dairy products.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11537},
pmid = {40185827},
issn = {2045-2322},
support = {220211/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Probiotics/pharmacology ; *Dietary Supplements/microbiology ; *Dairy Products/microbiology ; *Metagenomics/methods ; Humans ; Lactobacillus/genetics ; Killer Cells, Natural/immunology/drug effects ; Bifidobacterium/genetics ; Animals ; Macrophages/immunology/drug effects ; Anti-Bacterial Agents/pharmacology ; Cytokines/metabolism ; Mice ; },
abstract = {Probiotics are widely marketed as dietary supplements and dairy products for their purported antimicrobial and immunomodulatory activities, often with limited supporting evidence. We identified and isolated probiotics from commercial dietary supplements and dairy products using metagenomics and cultured-based methods. We assessed their anti-bacterial activity against diverse pathogens and investigated their immunomodulatory effects on phagocytes and natural killer (NK) cells. Metagenomic analysis revealed that Lactobacillus and Bifidobacterium were the predominant genera in dietary supplements, while Streptococcus spp. was dominated in dairy products. However, only 37% of the predominant microorganisms identified by metagenomics were accurately listed on product labels. Among 70 representative probiotic strains, 4.3-17.1% probiotic strains demonstrated strong antibacterial-effects against pathogenic bacteria. Notably, specific strains of Bifidobacterium longum and Lactobacillus plantarum exhibited strong antagonistic activity against extended-spectrum beta-lactamase-producing and carbapenem-resistant Escherichia coli. Some strains of Lactobacillus spp. significantly enhanced phagocytic activity in monocytes and increased IFN-γ production in NK cells, while members of Lactobacillus rhamnosus significantly suppressed TNF-α, IL-6, and IL-8 production in lipopolysaccharide-stimulated macrophages. In contrast, Bifidobacterium animalis stimulated the production of anti-inflammatory cytokines. This study highlights discrepancies in probiotic labeling and demonstrates the antimicrobial and immunomodulatory potential of specific probiotic strains, suggesting their utility in enhancing health and wellness.},
}

*Probiotics/pharmacology
*Dietary Supplements/microbiology
*Dairy Products/microbiology
*Metagenomics/methods
Humans
Lactobacillus/genetics
Killer Cells, Natural/immunology/drug effects
Bifidobacterium/genetics
Animals
Macrophages/immunology/drug effects
Anti-Bacterial Agents/pharmacology
Cytokines/metabolism
Mice

@article {pmid40185819,
year = {2025},
author = {Manzoor, M and Leskelä, J and Pietiäinen, M and Martinez-Majander, N and Könönen, E and Sinisalo, J and Putaala, J and Pussinen, PJ and Paju, S},
title = {Oral microbiome dysbiosis in cryptogenic ischemic stroke patients with high-risk patent foramen ovale.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {11535},
pmid = {40185819},
issn = {2045-2322},
support = {286246//Research Council of Finland/ ; 340750//Research Council of Finland/ ; 355532//Research Council of Finland/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; },
mesh = {Humans ; *Foramen Ovale, Patent/complications/microbiology ; Female ; Male ; *Ischemic Stroke/microbiology/etiology/complications ; *Dysbiosis/microbiology/complications ; *Microbiota ; Adult ; Middle Aged ; Saliva/microbiology ; Case-Control Studies ; *Mouth/microbiology ; Risk Factors ; },
abstract = {Patent foramen ovale (PFO) is the most common congenital heart abnormality of foetal origin and has been associated with cryptogenic ischemic stroke (CIS) through several mechanisms, with most theories supporting paradoxical embolism. Other possible but unknown contributing factors, such as the role of the microbiome in PFO-associated strokes, remain unclear. We analysed saliva metagenomes to study the differences in the oral microbiome between young-onset CIS patients with clinically relevant high-risk PFO (n = 52) and those without PFO (n = 52). Age- and sex-matched stroke-free controls (n = 16) with high-risk PFO were included for the comparison. Beta diversity was significantly different between patients and controls with high-risk PFO, but not between patients with and without high-risk PFO. The phylum Ascomycota and class Saccharomycetes were significantly more abundant in patients with high-risk PFO than in those without high-risk PFO. Additionally, the abundance of Lactococcus, including Lactococcus raffinolactis and L. cremoris, was higher in controls with high-risk PFO than in patients with high-risk PFO. These findings highlight that oral dysbiosis and high-risk PFO may form a critical but under-recognized combination in the aetiology of CIS. Future research should focus on elucidating the precise mechanisms of these interactions and developing targeted interventions.},
}

Humans
*Foramen Ovale, Patent/complications/microbiology
Female
Male
*Ischemic Stroke/microbiology/etiology/complications
*Dysbiosis/microbiology/complications
*Microbiota
Adult
Middle Aged
Saliva/microbiology
Case-Control Studies
*Mouth/microbiology
Risk Factors

@article {pmid40185271,
year = {2025},
author = {Guajardo-Leiva, S and Díez, B and Rojas-Fuentes, C and Chnaiderman, J and Castro-Nallar, E and Catril, V and Ampuero, M and Gaggero, A},
title = {From sewage to genomes: expanding our understanding of the urban and semi-urban wastewater RNA virome.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121509},
doi = {10.1016/j.envres.2025.121509},
pmid = {40185271},
issn = {1096-0953},
abstract = {Wastewater is a hotspot for viral diversity, harboring various microbial, plant, and animal viruses, including those that infect humans. However, the dynamics, resilience, and ecological roles of viral communities during treatment are largely unknown. In this study, we explored RNA virus ecogenomics using metagenomics from influent and effluent samples across three wastewater catchment areas in Chile, with a population of 7.05 million equivalent inhabitants. We identified 14,212 RNA-dependent RNA polymerase (RdRP)-coding sequences from the Orthornavirae kingdom, clustering into 4,989 viral species. Using extensive databases of 14,150 family-level representative sequences, we classified 90% of our sequences at the family level. Our analysis revealed that treatment reduced viral richness and evenness (Shannon index), but phylogenetic diversity remained unchanged. Effluents showed lower richness and evenness than influents with similar phylogenetic diversity. Species turnover, influenced by catchment area and treatment, accounted for 54% of sample dissimilarities (Weighted Unifrac). Biomarker analysis indicated that families like Astroviridae and Fiersviridae were more abundant in influents, while Reoviridae and Virgaviridae dominated effluents. This suggests that viral resistance to treatment varies and cannot be solely attributed to genome type, size, or morphology. We traced viral genomes through time and space, identifying sequences like the Pepper Mild Mottle Virus (PMMoV) from the Virgaviridae family over large distances and periods, highlighting its wastewater marker potential. High concentrations of human pathogens, such as Rotavirus (Reoviridae) and Human Astrovirus (Astroviridae), were found in both influents and effluents, stressing the need for continuous monitoring, especially for treated wastewater reuse.},
}

@article {pmid40185197,
year = {2025},
author = {Jiang, Y and Yang, J and Liu, Y and Liu, Y and Zhou, W and Yang, B and Hu, B and Wu, H},
title = {A Neonate with Meningitis Caused by probiotic-related Clostridium butyricum.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {107900},
doi = {10.1016/j.ijid.2025.107900},
pmid = {40185197},
issn = {1878-3511},
abstract = {Clostridium butyricum (C. butyricum), a normal gut bacterium in humans, is commonly used as a probiotic. We described a 26-day-old premature neonate who was diagnosed with probiotic-related C. butyricum meningitis. Upon the admission, suppurative meningitis was considered based on cerebrospinal fluid (CSF) biochemical test and neuroimaging examination, and C. butyricum was subsequently identified by CSF metagenomic next-generation sequencing. Given the history of administrating living C. butyricum products before admission, probiotics-associated suppurative meningitis was considered a high possibility, leading to the confirmation of anti-infection treatment including vancomycin and meropenem. Following this therapy, the infant's CSF profiles demonstrated improvement. Additionally, further phylogenetic analysis confirmed the high homologous of C. butyricum from CSF with probiotics. This is the first report of C. butyricum infection in neonates, highlighting the importance for prudence in administrating probiotics for neonates, particularly in high-risk groups such as preterm infants, those with central venous catheters and intestinal diseases.},
}

@article {pmid40185186,
year = {2025},
author = {Liu, Y and Pei, Y and Wang, H and Yang, Z},
title = {Lead promoted bile acid deconjugation by modulating gut bacteria encoding bile salt hydrolase (BSH) in Rana chensinensis tadpoles.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126187},
doi = {10.1016/j.envpol.2025.126187},
pmid = {40185186},
issn = {1873-6424},
abstract = {Bile salt hydrolase (BSH) is produced by gut bacteria and is responsible for deconjugating amino acids from the aliphatic side chains of conjugated bile acids (BAs), initiating the critical first step in BAs metabolism. Lead (Pb) is known to cause gut microbial dysbiosis, but whether it affects BAs profiles by reshaping the gut microbiota remains elusive. Here, using targeted BAs metabolomics and metagenomics sequencing, we found that 200 μg/L Pb treatment led to a significant increase in the abundance of BSH-producing microbiota (e.g., Eubacterium and Yersinia), thus promoting the deconjugation of taurocholic acid (TCA) and taurochenodeoxycholic acid (TCDCA). Consequently, the accumulation of relatively hydrophobic BAs cholic acid (CA) and chenodeoxycholic acid (CDCA) may cause damage to enterocytes (e.g., reduced microvilli and enterocyte heights), which attenuated tadpole digestion and ultimately led to significant reductions in morphological parameters. The inhibition of tadpole growth by Pb toxicity may negatively affect their survival and even increase their risk of death. Overall, these results revealed for the first time the toxicological mechanism by which Pb reshapes the gut microbiota and thus disrupts the BAs profile, shedding new insights into the detrimental effects of Pb toxicity on amphibian growth.},
}

@article {pmid40185016,
year = {2025},
author = {Yang, M and Yang, H and Wang, W and Fang, H and Huang, L and Li, D and Fu, L and Ding, S and Li, XD and Liu, CQ and Wei, G and Li, D and Cui, G and Fan, Z and Zeng, F},
title = {Impact of particle-attached microbial denitrification on N2O production in an agricultural-urban watershed.},
journal = {Journal of environmental management},
volume = {381},
number = {},
pages = {125223},
doi = {10.1016/j.jenvman.2025.125223},
pmid = {40185016},
issn = {1095-8630},
abstract = {Anthropogenically influenced rivers are key hotspots for nitrous oxide (N2O) emissions. However, the seasonal and spatial heterogeneity of N2O emissions in subtropical riverine systems, particularly the role of particle-attached microbes (PAM) in regulating N2O production, remains poorly understood, contributing to uncertainties in global N2O estimates. This study investigates the potential impacts of PAM-driven nitrogen transformations on N2O production in the Dongjiang River under agricultural and urban influences. Water samples collected during the wet and dry seasons were analyzed for N2O concentrations, dual nitrogen-oxygen isotopes (δ[15]N-NO3[-], δ[18]O-NO3[-]), and metagenomic sequencing of PAM. All samples exhibited N2O supersaturation, with emissions significantly higher in the dry season than in the wet season. A linearly positive δ[15]N-δ[18]O correlation, accompanied by lower NO3[-] in the bottom layers than the surface layers in the dry season indicates active denitrification, leading to elevated N2O concentrations. PAM-driven denitrification was identified as the dominant nitrogen transformation process, supported by higher abundances of denitrification genes (nirKS, norBC, nosZ) relative to nitrification genes (amoABC). Despite aerobic water column conditions, low-oxygen microhabitats around suspended particles facilitated N2O production. A significantly positive correlation (p < 0.05, R[2] = 0.42) between N2O concentrations and the nirK/nosZ gene ratio suggests that gene expression imbalances contributed to net N2O accumulation. Additionally, the downstream urban area exhibited lower DO and higher DOC levels, enhancing denitrification and increasing N2O production by 4.7 % compared to the upstream agricultural region. Seasonal differences further influenced N2O dynamics: higher DOC/NO3[-] ratios in the dry season promoted heterotrophic denitrification, while elevated temperatures in the wet season favored complete denitrification, reducing N2O emissions. These findings provide critical insights into PAM-driven nitrogen cycling, informing strategies for mitigating N2O emissions and managing nitrogen pollution in subtropical riverine systems.},
}

@article {pmid40184966,
year = {2025},
author = {Tu, M and Lin, H and Zhang, X and Zhang, X and Yan, J},
title = {Elemental sulfur facilitates co-metabolism of Cr(VI) and nitrate by autotrophic denitrifiers in constructed wetlands.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138153},
doi = {10.1016/j.jhazmat.2025.138153},
pmid = {40184966},
issn = {1873-3336},
abstract = {The antagonistic microbial reduction of chromate and nitrate poses significant challenges for their simultaneous removal in autotrophic denitrifying systems. This study explored the treatment performance and mechanisms for the simultaneous removal of chromate (0, 2, and 10 mg·L[-1]) and nitrate (20 mg·L[-1]) in constructed wetland (CW) microcosms with elemental sulfur additions at 0-, 5-, and 25-times background levels. Results showed that sulfur-amended microcosms achieved chromate and nitrate removal up to 76.46 % and 28.12 % higher, respectively, than 0S groups. Notably, the nitrate removal rate constant was higher in the presence of chromate than its absence, exclusively in the 25S groups. In a sediment core assay, the 25S groups also exhibited substantially facilitating effect of chromate removal potential in the presence of nitrate. Metagenomic analyses revealed upregulations of denitrification and sulfur oxidation-related functional genes along with sulfur supplementation. Autotrophic denitrifiers including Dechloromonas, Thiobacillus, Sulfuricella, and Sulfuritalea made significant contributions to chromate and nitrate removal rates, as well as functional genes encoding sulfur, nitrogen, and chromium transformation, in response to sulfur addition. These findings shed first light on the co-metabolism of chromate and nitrate by sulfur-based autotrophic denitrifiers, emphasizing their pivotal role in denitrification systems, e.g., CWs, with chromate inputs.},
}

@article {pmid40184824,
year = {2025},
author = {Zhu, H and Mao, X and Sajnani, S and Yang, H and Li, T and Tan, S},
title = {Psychrophilic insights into petroleum degradation: Gene abundance dynamics.},
journal = {Enzyme and microbial technology},
volume = {188},
number = {},
pages = {110642},
doi = {10.1016/j.enzmictec.2025.110642},
pmid = {40184824},
issn = {1879-0909},
abstract = {Petroleum degradation by psychrophiles can be enhanced on the basis of omics analyses, which offer better sensitivity than traditional biochemical methods do. A metagenomic analysis focusing on gene abundance comparisons may provide new guidance to optimize soil decontamination under cold environmental conditions. The soil used in this study was sampled from Dalian, from which an indigenous consortium was isolated. The degradative soil systems, initially categorized into control (DLC) and experimental (DLD) groups, were kept at room temperature (20 ± 5 °C) for six weeks. The DLD group was subsequently transferred to a low-temperature environment (5-10 °C) for 90 days and renamed DDL. A petroleum removal rate of 74.59 % was achieved in the process from DLD to DDL groups. Each soil sample was subjected to analysis and metagenomic sequencing. The abundance of genes of interest was compared between pathways to determine trends. The findings demonstrate that psychrophilic degradation is more effective than natural remediation is. The soil microbial community structure displayed site specificity, with 802 genes in DDL associated with 249 pathways, indicating greater abundance of psychrophilic genes in DDL than in DLC. The abundance of key genes was at different orders of magnitude but showed similar trends. The abundance of genes associated with hydrocarbon-related metabolism surpassed that of genes associated with sphingolipid, fatty acid, or benzene metabolism. This study provides valuable insights into psychrophilic microbe-driven petroleum degradation and indicates the need for precise supplementation of biosurfactants to improve remediation efficiency.},
}

@article {pmid40184708,
year = {2025},
author = {He, D and Nong, Y and He, Y and Luo, Y and Li, C and Gao, J and Dang, C and Fu, J},
title = {Effect of pre-chlorination on bioelectricity production and stabilization of excess sludge by microbial fuel cell.},
journal = {Water research},
volume = {281},
number = {},
pages = {123564},
doi = {10.1016/j.watres.2025.123564},
pmid = {40184708},
issn = {1879-2448},
abstract = {Microbial fuel cell (MFC) is a technology that can generate electricity while degrading excess sludge. However, the complex components, intricate biological structures, and inhibitory compounds in sludge limit the application of MFC. Therefore, this study utilized chlorination as a sludge pretreatment method to improve the comprehensive performance of MFC in sludge treatment. Results showed that pre-chlorination at a dose of 0.2 mg/L increased output voltage of MFC by 500 % from approximately 100 mV to around 600 mV, and power density by 15.60 % from 3.15 W/m[3] to 3.64 W/m[3], and simultaneously increased the degradation of sludge MLSS (mixed liquor suspended solids), MLVSS (mixed liquor volatile suspended solids), EPS (extracellular polymeric substances) polysaccharide and protein by 9.64 %, 47.07 %, 18.63 % and 16.26 %, respectively. Molecular composition analysis of EPS in sludge by three-dimensional excitation emission matrix fluorescence spectroscopy (3D-EEM), Fourier transform infrared spectroscopy (FTIR) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) indicated pre-chlorination significantly promoted the molecular transformation in MFC. The microbiome analysis of anode biofilm in MFC by scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), metagenomics and metametabolomics revealed that pre-chlorination facilitated the development of biomass, enrichment of electricity-producing bacteria (EPB), enhancement of electricity-producing activity and metabolic activity. Moreover, the sludge EPS was the importance source for the microbial metabolites in MFC was validated by the joint analysis of FT-ICR-MS and metametabolomics.},
}

@article {pmid40184705,
year = {2025},
author = {Barrantes-Jiménez, K and Lejzerowicz, F and Tran, T and Calderón-Osorno, M and Rivera-Montero, L and Rodríguez-Sánchez, C and Wikmark, OG and Eiler, A and Grossart, HP and Arias-Andrés, M and Rojas-Jiménez, K},
title = {Anthropogenic imprint on riverine plasmidome diversity and proliferation of antibiotic resistance genes following pollution and urbanization.},
journal = {Water research},
volume = {281},
number = {},
pages = {123553},
doi = {10.1016/j.watres.2025.123553},
pmid = {40184705},
issn = {1879-2448},
abstract = {Plasmids are key determinants in microbial ecology and evolution, facilitating the dissemination of adaptive traits and antibiotic resistance genes (ARGs). Although the molecular mechanisms governing plasmid replication, maintenance, and transfer have been extensively studied, the specific impacts of urbanization-induced pollution on plasmid ecology, diversity, and associated ARGs in tropical regions remain underexplored. This study investigates these dynamics in a tropical aquatic ecosystem, providing novel insights into how pollution shapes plasmid composition and function. In contrast to the observed decrease in chromosomal diversity, we demonstrate that pollution associated with urbanization increases the diversity and taxonomic composition of plasmids within a bacterial community (plasmidome). We analyzed eighteen water and sediment metagenomes, capturing a gradient of pollution and ARG contamination along a tropical urban river. Plasmid and chromosomal diversity profiles were found to be anti-correlated. Plasmid species enrichment along the pollution gradient led to significant compositional differences in water samples, where differentially abundant species suggest plasmid maintenance within specific taxonomic classes. Additionally, the diversity and abundance of ARGs related to the plasmidome increased concomitantly with the intensity of fecal and chemical pollution. These findings highlight the critical need for targeted plasmidome studies to better understand plasmids' environmental spread, as their dynamics are independent of chromosomal patterns. This research is crucial for understanding the consequences of bacterial evolution, particularly in the context of environmental and public health.},
}

@article {pmid40184632,
year = {2025},
author = {Huang, Y and Mao, X and Zheng, X and Zhao, Y and Wang, D and Wang, M and Chen, Y and Liu, L and Wang, Y and Polz, MF and Zhang, T},
title = {Longitudinal dynamics and cross-domain interactions of eukaryotic populations in wastewater treatment plants.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf058},
pmid = {40184632},
issn = {1751-7370},
abstract = {Activated sludge is a large reservoir of novel microorganisms and microbial genetic diversity. While much attention has been given to the profile and functions of prokaryotes, the eukaryotic diversity remains largely unexplored. In this study, we analyzed longitudinal activated sludge samples spanning 13 years from the largest secondary wastewater treatment plants in Hong Kong, unveiling a wealth of eukaryotic taxa and 681 856 non-redundant protein-coding genes, the majority (416044) of which appeared novel. Ciliophora was the most dominant phylum with a significant increase after a transient intervention (bleaching event). Our metagenomic analysis reveals close linkage and covariation of eukaryotes, prokaryotes, and prokaryotic viruses (phages), indicating common responses to environmental changes such as transient intervention and intermittent fluctuations. Furthermore, high-resolution cross-domain relationships were interpreted by S-map, demonstrating a predatory role of Arthropoda, Ascomycota, Mucoromycota, and Rotifera. This high-resolution profile of microbial dynamics expands our knowledge on yet-to-be-cultured populations and their cross-domain interactions and highlights the ecological importance of eukaryotes in the activated sludge ecosystem.},
}

@article {pmid40184383,
year = {2025},
author = {Shen, C and Wedell, E and Pop, M and Warnow, T},
title = {TIPP3 and TIPP3-fast: Improved abundance profiling in metagenomics.},
journal = {PLoS computational biology},
volume = {21},
number = {4},
pages = {e1012593},
pmid = {40184383},
issn = {1553-7358},
mesh = {*Metagenomics/methods ; Algorithms ; *Software ; Computational Biology/methods ; Databases, Genetic ; Likelihood Functions ; Sequence Analysis, DNA/methods ; },
abstract = {We present TIPP3 and TIPP3-fast, new tools for abundance profiling in metagenomic datasets. Like its predecessor, TIPP2, the TIPP3 pipeline uses a maximum likelihood approach to place reads into labeled taxonomies using marker genes, but it achieves superior accuracy to TIPP2 by enabling the use of much larger taxonomies through improved algorithmic techniques. We show that TIPP3 is generally more accurate than leading methods for abundance profiling in two important contexts: when reads come from genomes not already in a public database (i.e., novel genomes) and when reads contain sequencing errors. We also show that TIPP3-fast has slightly lower accuracy than TIPP3, but is also generally more accurate than other leading methods and uses a small fraction of TIPP3's runtime. Additionally, we highlight the potential benefits of restricting abundance profiling methods to those reads that map to marker genes (i.e., using a filtered marker-gene based analysis), which we show typically improves accuracy. TIPP3 is freely available at https://github.com/c5shen/TIPP3.},
}

*Metagenomics/methods
Algorithms
*Software
Computational Biology/methods
Databases, Genetic
Likelihood Functions
Sequence Analysis, DNA/methods

@article {pmid40183829,
year = {2025},
author = {Moscona, R and Wagner, T and Geva, M and Bucris, E and Erster, O and Zuckerman, NS and Mor, O},
title = {Newly designed amplicons-based method for near-full-length genome (NFLG) sequencing of HIV-1 group M recombinant forms.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {362},
pmid = {40183829},
issn = {1573-4978},
mesh = {*HIV-1/genetics ; Humans ; *Genome, Viral/genetics ; Phylogeny ; HIV Infections/virology/genetics ; Recombination, Genetic/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Whole Genome Sequencing/methods ; Genotype ; },
abstract = {BACKGROUND: Over the years the spread of HIV-1 across the globe resulted in the creation of multiple subtypes and new recombinant forms (RFs). While the pol gene region of the HIV-1 genome is used for resistance mutations analysis and initial detection of RFs, whole genome sequencing analysis is required to determine recombination events across the viral genome. Here, we present a newly designed robust near-full length genome (NFLG) sequencing approach for the sequencing of HIV-1 genomes, out of clinical whole blood samples. This method has been successfully tested for various HIV-1 subtypes and RFs.

METHODS AND RESULTS: The method is based on an in-house developed set of 32 pan-genotypic primer pairs, divided into two pools, each containing 16 primer pairs covering the entire HIV-1 genome. Two parallel multiplex PCR reactions were used to generate 32 overlapping DNA fragments spanning the HIV-1 genome. Nextera XT protocol was used to obtain barcoded DNA libraries, which were sequenced with the Illumina Miseq platform using a V3 kit. A consensus sequence was determined for each sample and was used to define recombination events across the genome. For this aim, a combined analysis of several computational tools including HIV BLAST, phylogenetic analysis, RIP, SimPlot +  + and jpHMM were employed. Overall, plasma samples from 33 patients suspected to carry RFs and 2 different, known pure subtypes controls, were included in this study. Genome coverage varied between RFs, while the gag and pol genes were nearly fully covered, the highly variable env gene region was not. Yet, these NFLG analyses enabled the identification of recombination events genome wide.

CONCLUSIONS: In summary, we describe a methodology for HIV-1 NFLG sequencing, which is based on partially overlapping, multiple PCR fragments, spanning the HIV-1 genome. Additionally, this newly refined method was compared to HIV-1 NFLG results of PCR-free metagenomic sequencing and proved to obtain greater coverage of the HXB2 reference genome. Yet, further testing and validation on a larger cohort is required. Still, this method enables sequencing of 20 different patient samples in a single MiSeq sequencing run and was used for the characterization of different HIV-1 RFs and pure subtypes circulating in Israel.},
}

*HIV-1/genetics
Humans
*Genome, Viral/genetics
Phylogeny
HIV Infections/virology/genetics
Recombination, Genetic/genetics
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Whole Genome Sequencing/methods
Genotype

@article {pmid40183042,
year = {2025},
author = {Li, T and Shafiul Alam, M and Yang, Y and Mohammad Al-Amin, H and Rahman, M and Islam, F and Conte, MA and Price, DC and Hang, J},
title = {Metagenome analysis of viruses associated with Anopheles mosquitoes from Ramu Upazila, Cox's Bazar District, Bangladesh.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19180},
pmid = {40183042},
issn = {2167-8359},
mesh = {*Anopheles/virology ; Animals ; Bangladesh ; Phylogeny ; *Mosquito Vectors/virology ; *Metagenome ; Male ; Female ; High-Throughput Nucleotide Sequencing ; },
abstract = {Bangladesh has a warm climate and landscapes favourable for the proliferation of mosquitoes. Mosquito-borne pathogens including malaria and arthropod-borne viruses (arboviruses) remain a serious threat to the public health requiring constant vector control and disease surveillance. From November 2018 to April 2019, Anopheles mosquitoes were collected in three unions in the Ramu Upazila (sub-district) of Cox's Bazar District, Bangladesh. The mosquito specimens were combined into pools based on date of collection, household ID, and sex. Metagenome next-generation sequencing was conducted to elucidate diversity of virus sequences in each pool. Homology-based taxonomic classification and phylogenetic analyses identified a broad diversity of putative viruses from 12 known families, with additional unclassified viruses also likely present. Analysis of male mosquitoes showed some of these viruses are likely capable of being vertically transmitted. Moreover, many of the assembled virus sequences share homology and phylogenetic affinity with segments in sequenced Anopheles genomes, and may represent endogenous viral elements derived from a past evolutionary relationship between these putative viruses and their mosquito hosts.},
}

*Anopheles/virology
Animals
Bangladesh
Phylogeny
*Mosquito Vectors/virology
*Metagenome
Male
Female
High-Throughput Nucleotide Sequencing

@article {pmid40182804,
year = {2025},
author = {Sarwar, A and Aslam, B and Mahmood, S and Muzammil, S and Siddique, AB and Sarwar, F and Khurshid, M and Rasool, MH and Sasanya, J and Aljasir, SF},
title = {Distribution of multidrug-resistant Proteus mirabilis in poultry, livestock, fish, and the related environment: One Health heed.},
journal = {Veterinary world},
volume = {18},
number = {2},
pages = {446-454},
doi = {10.14202/vetworld.2025.446-454},
pmid = {40182804},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The emergence of multidrug-resistant (MDR) Proteus mirabilis in food-producing animals and their associated environments is a growing public health concern. The indiscriminate use of antimicrobials in animal husbandry exacerbates resistance development, posing significant threats to food safety and sustainability. This study investigates the distribution, antibiotic resistance patterns, and virulence-associated genes (VAGs) of P. mirabilis isolated from poultry, livestock, fish, and their environments in Pakistan under a One Health perspective.

MATERIALS AND METHODS: A total of 225 samples were collected from poultry (n = 100), livestock (n = 75), and aquatic sources (n = 50) from March 2023 to September 2024. Standard microbiological methods were employed for the isolation and identification of P. mirabilis. Polymerase chain reaction (PCR)-based detection of antibiotic resistance genes and VAGs was performed using specific primers. Antibiotic susceptibility was assessed through the disk diffusion method following Clinical and Laboratory Standards Institute 2022 guidelines. Statistical analyses, including analysis of variance and correlation models, were applied to assess the relationships between variables.

RESULTS: P. mirabilis was detected in 28.44% (64/225) of the total samples, with the highest occurrence observed in poultry (38%), followed by livestock (22.67%) and aquatic sources (18%). Resistance to ampicillin (100%), chloramphenicol (82%), cefepime (75%), and ciprofloxacin (75%) was widespread. PCR analysis revealed a high occurrence of extended-spectrum beta-lactamase-producing P. mirabilis carrying bla CTX-M (49%), bla OXA (54%), and bla TEM (25.67%) genes. In addition, VAGs such as zapA (39.53%), ucaA (34.88%), and hpmA (32.55%) were frequently identified. The presence of MDR P. mirabilis in fish and related environments (18%) is alarming, highlighting potential zoonotic and foodborne transmission risks.

CONCLUSION: The study underscores the widespread distribution of MDR P. mirabilis in animal-based food sources, raising significant concerns regarding food safety and antimicrobial resistance. The findings reinforce the need for stringent monitoring and regulatory policies to mitigate MDR bacterial dissemination across the food supply chain. Future research should employ metagenomic approaches for comprehensive surveillance and risk assessment.},
}

@article {pmid40182766,
year = {2025},
author = {Lazarevic, V and Gaïa, N and Pham, TT and de Lorenzi-Tognon, M and Girard, M and Mauffrey, F and Charretier, Y and Renzi, G and Huber, C and Schrenzel, J},
title = {Identification of causative agents of infective endocarditis by metagenomic next-generation sequencing of resected valves.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1532257},
doi = {10.3389/fcimb.2025.1532257},
pmid = {40182766},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Male ; Middle Aged ; Female ; *Heart Valves/microbiology/surgery ; Sensitivity and Specificity ; Aged ; *Endocarditis/microbiology/diagnosis/surgery ; Prospective Studies ; *Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics ; Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Infective endocarditis (IE) is a rare and life-threatening condition with considerable mortality rates. Diagnosis is often complicated by negative blood culture results, limiting the accurate identification of causative pathogens. This study aimed to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) of cardiac valve specimens compared to conventional clinical laboratory methods for identifying pathogens in IE.

METHODS: Nineteen patients with suspected IE who were scheduled for surgical valve removal were prospectively enrolled. The metagenomic workflow included bacterial DNA enrichment from resected valves using the Molzym Ultra-Deep Microbiome Prep, sequencing of metagenomic libraries using the Illumina MiSeq platform, and Kraken 2 taxonomic assignments based on read data.

RESULTS: Valve mNGS achieved a sensitivity of 82.4% and a specificity of 100% relative to the final adjudicated pathogen diagnosis. Blood culture, considered the reference standard, exhibited slightly higher sensitivity (88.2%) with comparable specificity (100%). In comparison, valve culture (sensitivity: 29.4%, specificity: 50.0%) and microscopy (sensitivity: 35.3%, specificity: 100%) showed lower diagnostic performance. Delays between blood culture negativization and valve resection impacted mNGS sensitivity, likely due to pathogen clearance. Notably, valves resected within 12 days from blood culture negativization achieved 100% diagnostic accuracy, emphasizing the importance of timing for optimal mNGS results.

CONCLUSION: This study underscores mNGS as a valuable diagnostic tool for detecting IE pathogens, complementing traditional diagnostic methods. The detection of antibiotic resistance genes and multi-locus sequence typing profiles in some samples further demonstrated its utility.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Male
Middle Aged
Female
*Heart Valves/microbiology/surgery
Sensitivity and Specificity
Aged
*Endocarditis/microbiology/diagnosis/surgery
Prospective Studies
*Bacteria/genetics/classification/isolation & purification
DNA, Bacterial/genetics
Adult
Aged, 80 and over

@article {pmid40182295,
year = {2025},
author = {Hou, J and Yin, H and Wang, D and Luo, J and Yang, W and Kang, T},
title = {The influence of rhizosphere soil microorganisms and environmental factors on gentiopicroside content in the roots and rhizomes of Gentiana scabra Bunge from Liaoning Province.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1554981},
doi = {10.3389/fmicb.2025.1554981},
pmid = {40182295},
issn = {1664-302X},
abstract = {BACKGROUND: Rhizosphere soil microorganisms, as the second genome of plants, play an important role in the formation of secondary metabolites of medicinal plants and are one of the key factors in the formation of the authenticity of medicinal materials.

METHODS: In this paper, the rhizosphere soils of Gentiana scabra Bunge from six producing areas in Liaoning Province were taken as the research objects. Through high-throughput sequencing technology, and with the help of PLS-DA and RDA, the impacts of rhizosphere soil microorganisms and environmental factors on the quality of G. scabra were explored in depth.

RESULTS: Alpha diversity shows that the diversity of bacterial communities varies significantly, while the regularity of fungi is weak; beta diversity shows that samples from different producing areas can be effectively grouped according to community structure. LDA effect shows that the differential species of bacteria and fungi vary among different producing areas. Indicator and random forest analysis show that Sphingomonas and Subgroup_2 are the main indicator species of the bacterial communities in the high-content group, which can increase the evenness of microbial communities and maintain or enhance species diversity. The regularity of fungal communities is relatively weak. Functional metagenomic analysis shows that the functions of soil microorganisms in the six producing areas are similar but the relative abundances are different. The main functions of bacteria are closely related to microbial metabolism in diverse environments, biosynthesis of secondary metabolites, metabolic pathways, etc.; fungi are mainly lichen parasite, plant saprotroph, and ericoid mycorrhizal. PLS-DA and RDA analysis show that properly adjusting the key environmental factors of Ca, pH, and rapidly available potassium, which have a great influence on G. scabra, can affect the abundances of microorganisms such as Subgroup_2, Burkholderia-Caballeronia-Paraburkholderia, Metarhizium, Bryobacter, Fusarium, Rhodanobacter, Cladophialophora, Sphingomonas and Trichoderma, and then regulate the content of gentiopicroside.

DISCUSSION: This study provides practical microbial approaches and strategies for improving gentiopicroside content in the roots and rhizomes of G. scabra, and lays a solid scientific foundation for ensuring the quality and safety of genuine medicinal materials and the stable and sustainable development of the G. scabra planting industry.},
}

@article {pmid40182288,
year = {2025},
author = {Lin, TS and Zhu, Z and Lin, X and Huang, HY and Li, LP and Li, J and Ni, J and Li, P and Chen, L and Tang, W and Liu, H and Se, X and Xie, M and Long, C and Chiu, CM and Fang, SH and Zhao, J and Lin, YC and Yu, X and Huang, HD},
title = {Enhancing bloodstream infection diagnostics: a novel filtration and targeted next-generation sequencing approach for precise pathogen identification.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1538265},
doi = {10.3389/fmicb.2025.1538265},
pmid = {40182288},
issn = {1664-302X},
abstract = {Bloodstream infections (BSIs) pose a significant diagnostic challenge, largely due to the limitations of traditional methods such as blood cultures. These methods often yield low positive rates, have lengthy processing times that delay treatment, and are limited in detecting only a narrow range of pathogens. Such delays and inaccuracies can critically impede timely clinical interventions, potentially compromising patient outcomes. Next-generation sequencing (NGS) is a powerful tool for rapid, precise pathogen identification. While metagenomic NGS (mNGS) offers broad pathogen coverage, it is often costly and complex. Targeted NGS (tNGS), however, focuses on key regions of clinically relevant pathogens, reducing costs and simplifying workflows while maintaining high sensitivity, making it more practical for routine diagnostics. In this study, we introduce a novel approach combining a human cell-specific filtration membrane with a multiplex tNGS panel to overcome these challenges. The filtration membrane, designed with surface charge properties to be electrostatically attractive to leukocytes for the selective capture of specific cells, demonstrated high efficiency in removing host cells and nucleic acids, achieving over a 98% reduction in host DNA and thereby minimizing background interference in pathogen detection. Additionally, we developed an effective multiplex tNGS panel targeting over 330 clinically relevant pathogens and verified its consistency with mNGS and blood culture results, demonstrating a significant improvement in detection sensitivity. By integrating these two methods, we achieved a synergistic enhancement in diagnostic capability, boosting pathogen reads by 6- to 8-fold, which enabled reliable identification even in cases of low-abundance pathogens. This approach provides faster, more accurate, and more sensitive detection of BSIs, enabling earlier identification of infections. This facilitates timely and targeted treatment, ultimately improving patient outcomes in critical care settings. Given the unique properties of the filtration membrane and the strengths of the tNGS panel, this approach shows promising applications in prenatal and genetic health support, as well as in advancing early cancer screening strategies.},
}

@article {pmid40182062,
year = {2025},
author = {Simon, SA and Soares, AR and Bornemann, TLV and Lange, A and Griesdorn, L and Fuentes, A and Dieckmann, M and Krok, BA and Ruff, SE and Hügler, M and Moraru, C and Probst, AJ},
title = {Inferring replication states of bacteria and viruses in enrichment cultures via long-read sequencing.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf041},
doi = {10.1093/ismeco/ycaf041},
pmid = {40182062},
issn = {2730-6151},
abstract = {Most microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes in enrichment cultures, no single technique can render simultaneous data on both metabolic capacities and mobile genetic elements. Here, we apply long-read sequencing to monitor the incorporation of non-canonical bases in genome-resolved metagenomic datasets and elucidate the replication patterns of both bacteria and phages. This technology enables the simultaneous reconstruction of both prokaryotic and viral genomes (alongside genomics downstream analyses like metabolic predictions), in addition to providing information regarding their replication in enrichment cultures. By spiking the base analog 5-bromo-2'-deoxyuridine (BrdU) into activated sludge microcosms, we determined that 114 of the 118 high-quality genomes recovered were actively replicating in enrichment cultures from activated sludge and identified both slow (low BrdU incorporation and change in abundance) and rapidly replicating organisms (high BrdU incorporation and change in abundance). Some of the genomes detected exhibited regions rich in BrdU that were predicted to represent prophages in their lytic cycle. Ultimately, this novel means of monitoring the replication responses of microbes, and deciphering their genomes and active mobile genetic elements will advance and empower strategies aimed at isolating previously uncultivated microbes in pure culture.},
}

@article {pmid40182061,
year = {2025},
author = {Cheung, S and Morando, M and Magasin, J and Cornejo-Castillo, FM and Zehr, JP and Turk-Kubo, KA},
title = {NifH gene amplicon sequencing and metagenomic approaches are complementary in assessing diazotroph diversity.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf038},
doi = {10.1093/ismeco/ycaf038},
pmid = {40182061},
issn = {2730-6151},
abstract = {Exploring the diversity of diazotrophs is key to understanding their role in supplying fixed nitrogen that supports marine productivity. A nested PCR assay using the universal primer set nifH1-nifH4, which targets the nitrogenase (nifH) gene, is a widely used approach for studying marine diazotrophs by amplicon sequencing. Metagenomics, direct sequencing of DNA without PCR, has provided complementary views of the diversity of marine diazotrophs. A significant fraction of the metagenome-derived nifH sequences (e.g. Planctomycete- and Proteobacteria-affiliated) were reported to have nucleotide mismatches with the nifH1-nifH4 primers, leading to the suggestion that nifH amplicon sequencing does not detect specific diazotrophic taxa and underrepresents diazotroph diversity. Here, we report that these mismatches are mostly located in a single-base at the 5'-end of the nifH4 primer, which does not impact detection of the nifH genes. This is demonstrated by the presence of nifH genes that contain the nucleotide mismatches in a recent compilation of global ocean nifH amplicon datasets, with high relative abundances detected in a variety of samples. While the metagenome- and metatranscriptome-derived nifH genes accounted for 4.4% of the total amplicon sequence variants from the global ocean nifH amplicon database, the corresponding amplicon sequence variants can have high relative abundances (accounting for 47% of the reads in the database). These analyses underscore that nifH amplicon sequencing using the nifH1-nifH4 primers is an important tool for studying diversity of marine diazotrophs, particularly as a complement to metagenomics which can provide taxonomic and metabolic information for some dominant groups.},
}

@article {pmid40181528,
year = {2025},
author = {Sun, Q and Teng, R and Shi, Q and Liu, Y and Cai, X and Yang, B and Cao, Q and Shu, C and Mei, X and Zeng, W and Hu, B and Zhang, J and Qiu, H and Liu, L},
title = {Clinical implement of Probe-Capture Metagenomics in sepsis patients: A multicentre and prospective study.},
journal = {Clinical and translational medicine},
volume = {15},
number = {4},
pages = {e70297},
doi = {10.1002/ctm2.70297},
pmid = {40181528},
issn = {2001-1326},
support = {2022YFC2504405//National Key Research and Development Program of China/ ; 82341032//National Natural Science Foundation of China/ ; 81930058//National Natural Science Foundation of China/ ; 82270083//National Natural Science Foundation of China/ ; LGY2022025//Second Level Talents of the '333 High Level Talents Training Project' in the sixth phase in Jiangsu/ ; ZDXYS202205//Jiangsu Provincial Medical Key Laboratory/ ; HMJH-2020-0005//Hongmian Plan' Project of Guangzhou/ ; },
mesh = {Humans ; *Sepsis/diagnosis/microbiology/blood/drug therapy ; *Metagenomics/methods ; Male ; Female ; Prospective Studies ; Aged ; Middle Aged ; Blood Culture/methods ; },
abstract = {BACKGROUND: Accurate pathogen identification is critical for managing sepsis. However, traditional microbiological methods are time-consuming and exhibit limited sensitivity, particularly with blood samples. Metagenomic sequencing of plasma or whole blood was highly affected by the proportion of host nucleic acid.

METHODS: We developed a Probe-Capture Metagenomic assay and established a multicentre prospective cohort to assess its clinical utility. In this study, 184 blood samples from patients suspected of sepsis were sent for blood culture and Probe-Capture Metagenomic sequencing before using antibiotics. The pathogen-positive rate and auxiliary abilities in diagnosis were compared among Probe-Capture Metagenomics, blood culture and real-time PCR (RT-PCR). Antibiotic therapy adjustments were based on the identification of pathogens, and changes in the Sequential Organ Failure Assessment (SOFA) score were monitored on days 0, 3 and 7 of admission.

RESULTS: A total of 184 sepsis patients were enrolled, with a mean age of 66 years (range 56-74). The Probe-Capture Metagenomics method, confirmed by RT-PCR, demonstrated a significantly higher pathogen detection rate than blood culture alone (51.6% vs. 17.4%, p < .001). When combining the results of blood culture and RT-PCR, Probe-Capture Metagenomics achieved a concordance rate of 91.8% (169/184), with a sensitivity of 100% and specificity of 87.1%. In terms of clinical impact, antibiotic therapy was adjusted for 64 patients (34.8%) based on the results from Probe-Capture Metagenomics, and 41 patients (22.3%) showed a > 2-point decrease in SOFA score following antibiotic adjustments.

CONCLUSION: Probe-Capture Metagenomics significantly enhances the ability of pathogen detection compared with traditional metagenomics. Compared to blood culture and RT-PCR in sepsis patients, it leads to improved antibiotic treatment and better patient outcomes. This study, for the first time, evaluates the clinical impact of metagenomic sequencing by integrating antibiotic adjustments and SOFA score changes, indicating that approximately one-fifth of sepsis patients benefit from this advanced diagnostic approach.

TRIAL REGISTRATION: This study has been registered in clinical trials (clinicaltrials.gov) on 30 November 2018, and the registration number is NCT03760315.

KEY POINTS: Probe-Capture Metagenome had a significantly higher positive rate than blood culture (51.6% vs. 17.4%, p < .001). Combining blood culture and RT-PCR results, Probe-Capture Metagenome achieved a consistency rate of 91.8%. Antibiotics were adjusted in 34.8% of patients based on Probe-Capture Metagenome results, and 22.3% of patients experienced a more than 2-point decrease in SOFA score.},
}

Humans
*Sepsis/diagnosis/microbiology/blood/drug therapy
*Metagenomics/methods
Male
Female
Prospective Studies
Aged
Middle Aged
Blood Culture/methods

@article {pmid40181443,
year = {2025},
author = {Xu, F and Chen, C and Lu, S and Xue, M and Ding, H and Song, Y and Zhang, Y and Sun, K and Tang, L and Wang, W and Wang, M and Tang, Y and Tan, D and Yao, C and Shi, D and Mao, E and Shao, M and Ying, Y and Zhou, C and Huang, L and Peng, H and Kuang, Z and Wang, S and Ma, Q and Sun, S and Guo, D and Gu, T and Yang, B and Ma, L and Gao, C and Lu, X and Zhang, H and Wang, R and Tong, C and Song, Z},
title = {Impact of metagenomics next-generation sequencing on etiological diagnosis and early outcomes in sepsis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {394},
pmid = {40181443},
issn = {1479-5876},
support = {2021YFC2501800//Key Technologies Research and Development Program/ ; 2023YFC0872500//Key Technologies Research and Development Program/ ; 2023YFC3043507//Key Technologies Research and Development Program/ ; 82072214//National Natural Science Foundation of China/ ; 23Y31900100//Science and Technology Commission of Shanghai Municipality/ ; 21MC1930400//Science and Technology Commission of Shanghai Municipality/ ; PWYts2021-17//Shanghai Pudong New Area Health Commission/ ; },
mesh = {Humans ; *Sepsis/diagnosis/microbiology/etiology/mortality ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; Aged ; Treatment Outcome ; Prognosis ; Prospective Studies ; Adult ; },
abstract = {BACKGROUND: Clinical implications of metagenomics next-generation sequencing (mNGS) in sepsis have not been fully evaluated. This study aimed to determine the diagnostic, therapeutic, and prognostic impacts of mNGS in sepsis.

METHODS: This multicenter prospective study was conducted at 19 sites in China from 2020 to 2021, and 859 adult patients hospitalized with sepsis were enrolled. The advantages, challenges, knowledge gaps and privacy risks of mNGS were carefully introduced to all participants, and participants chose on their own to either receive conventional microbiological test (CMT) alone (conventional-test-only group, n = 394) or receive mNGS test along with CMT (combined test group, n = 465). For prognostic analysis, the primary endpoint was 28-day mortality. Secondary endpoints included 7-day mortality and average per-day hospital cost. Inverse probability of treatment weighting was used to balance covariates between groups. Concurrent CMT and mNGS results from patients in the combined test group were used for diagnostic analyses. Therapeutic impact of mNGS was evaluated based on subsequent antibiotic adjustment.

RESULTS: Compared with composite reference standard, the positive percent agreement of mNGS among infected site samples was significantly higher than that of CMT (92.0% [95% CI, 88.7 to 94.5] vs. 51.1% [95% CI, 45.9 to 56.2], p < 0.001), while the negative percent agreement of mNGS was inferior to that of CMT (39.6% [95% CI, 29.5 to 50.4] vs. 69.2% [95% CI, 58.7 to 78.5], p < 0.001). The mNGS test identified causal microbes in 344 (74.0%) patients, and concomitant antibiotic changes occurred in 136 patients (29.2%). Death by day 7 occurred in 24 of 465 (5.2%) patients in the combined test group and in 34 of 394 (8.6%) patients in the conventional-test-only group (hazard ratio, 0.44 [95% CI, 0.26 to 0.77], p = 0.004). However, no significant difference in 28-day mortality was observed between two study groups (hazard ratio, 0.82 [0.56 to 1.20], p = 0.300).

CONCLUSIONS: The mNGS test of infected site samples exhibited 40% higher pathogen detection rate than CMT in patients with sepsis, which led to improved etiological diagnosis and tailored antibiotic therapy. Additional use of mNGS halved the risk of early death in 7 days, but did not improve 28-day survival in patients with sepsis.

TRIAL REGISTRATION: chictr.org.cn Identifier: ChiCTR2000031113. Registered 22 March 2020.},
}

Humans
*Sepsis/diagnosis/microbiology/etiology/mortality
Male
Female
*Metagenomics/methods
Middle Aged
*High-Throughput Nucleotide Sequencing
Aged
Treatment Outcome
Prognosis
Prospective Studies
Adult

@article {pmid40181255,
year = {2025},
author = {Mohammadzadeh, R and Mahnert, A and Shinde, T and Kumpitsch, C and Weinberger, V and Schmidt, H and Moissl-Eichinger, C},
title = {Age-related dynamics of predominant methanogenic archaea in the human gut microbiome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {193},
pmid = {40181255},
issn = {1471-2180},
support = {P 32697//Austrian Science Fund/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Aged ; *Archaea/classification/genetics/metabolism/isolation & purification ; *Methane/metabolism ; Feces/microbiology ; Aged, 80 and over ; Young Adult ; Female ; Male ; *Aging ; Age Factors ; Methanobrevibacter/genetics ; Metagenomics ; Phylogeny ; Bacteria/classification/genetics/metabolism ; },
abstract = {BACKGROUND: The reciprocal relationship between aging and alterations in the gut microbiota is a subject of ongoing research. While the role of bacteria in the gut microbiome is well-documented, specific changes in the composition of methanogens during extreme aging and the impact of high methane production in general on health remain unclear. This study was designed to explore the association of predominant methanogenic archaea within the human gut and aging.

METHODS: Shotgun metagenomic data from the stool samples of young adults (n = 127, Age: 19-59 y), older adults (n = 86, Age: 60-99 y), and centenarians (n = 34, age: 100-109 years) were analyzed.

RESULTS: Our findings reveal a compelling link between age and the prevalence of high methanogen phenotype, while overall archaeal diversity diminishes. Surprisingly, the archaeal composition of methanogens in the microbiome of centenarians appears more akin to that of younger adults, showing an increase in Methanobrevibacter smithii, rather than Candidatus Methanobrevibacter intestini. Remarkably, Ca. M. intestini emerged as a central player in the stability of the archaea-bacteria network in adults, paving the way for M. smithii in older adults and centenarians. Notably, centenarians exhibit a highly complex and stable network of these two methanogens with other bacteria. The mutual exclusion between Lachnospiraceae and these methanogens throughout all age groups suggests that these archaeal communities may compensate for the age-related drop in Lachnospiraceae by co-occurring with Oscillospiraceae.

CONCLUSIONS: This study underscores the dynamics of archaeal microbiome in human physiology and aging. It highlights age-related shifts in methanogen composition, emphasizing the significance of both M. smithii and Ca. M. intestini and their partnership with butyrate-producing bacteria for potential enhanced health.},
}

Humans
*Gastrointestinal Microbiome
Middle Aged
Adult
Aged
*Archaea/classification/genetics/metabolism/isolation & purification
*Methane/metabolism
Feces/microbiology
Aged, 80 and over
Young Adult
Female
Male
*Aging
Age Factors
Methanobrevibacter/genetics
Metagenomics
Phylogeny
Bacteria/classification/genetics/metabolism

@article {pmid40180917,
year = {2025},
author = {Schmitz, MA and Dimonaco, NJ and Clavel, T and Hitch, TCA},
title = {Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3204},
pmid = {40180917},
issn = {2041-1723},
support = {460129525//Massachusetts Department of Fish and Game (DFG)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; *Metagenomics/methods ; *Bacterial Proteins/genetics/metabolism ; *Bacteria/genetics/classification/metabolism ; Phylogeny ; Computational Biology/methods ; },
abstract = {Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.},
}

Humans
*Gastrointestinal Microbiome/genetics
Metagenome/genetics
*Metagenomics/methods
*Bacterial Proteins/genetics/metabolism
*Bacteria/genetics/classification/metabolism
Phylogeny
Computational Biology/methods

@article {pmid40180909,
year = {2025},
author = {Bedarf, JR and Romano, S and Heinzmann, SS and Duncan, A and Traka, MH and Ng, D and Segovia-Lizano, D and Simon, MC and Narbad, A and Wüllner, U and Hildebrand, F},
title = {A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson's Disease.},
journal = {NPJ Parkinson's disease},
volume = {11},
number = {1},
pages = {66},
pmid = {40180909},
issn = {2373-8057},
support = {BB/CCG2260/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
abstract = {Current treatment of Parkinson's Disease (PD) remains symptomatic, and disease-modifying approaches are urgently required. A promising approach is to modify intestinal microbiota and key metabolites of bacterial fermentation: short-chain fatty acids (SCFA), which are decreased in PD. A prospective, controlled pilot study (DRKS00034528) was conducted on 11 couples (PD patient plus healthy spouse as control (CO)). Participants followed a 4-week diet rich in dietary fibre, including intake of the prebiotic Lactulose. Gut metagenomes, faecal and urinary metabolites, and clinical characteristics were assessed. The dietary intervention significantly augmented faecal SCFA and increased Bifidobacteria spp., reducing PD-related gastrointestinal symptoms. The pre-existing bacterial dysbiosis in PD (depletion of Blautia, Dorea, Erysipelatoclostridium) persisted. Bacterial metabolite composition in faeces and urine positively changed with the intervention: Brain-relevant gut metabolic functions involved in neuroprotective and antioxidant pathways, including S-adenosyl methionine, glutathione, and inositol, improved in PD. These promising results warrant further investigation in larger cohorts.},
}

@article {pmid40180580,
year = {2025},
author = {Chiu, CY and Servellita, V and de Lorenzi-Tognon, M and Benoit, P and Sumimoto, N and Foresythe, A and Cerqueira, FM and Williams-Bouyer, N and Ren, P and Herrera, LNS and Gaston, DC and Sayyad, L and Whitmer, SL and Klena, J and Vikram, HR and Gold, JAW and Gade, L and Parnell, L and Misas, E and Chiller, TM and Griffin, IS and Basavaraju, SV and Smith, DJ and Litvintseva, AP and Chow, NA},
title = {Metagenomic Identification of Fusarium solani Strain as Cause of US Fungal Meningitis Outbreak Associated with Surgical Procedures in Mexico, 2023.},
journal = {Emerging infectious diseases},
volume = {31},
number = {5},
pages = {},
doi = {10.3201/eid3105.241657},
pmid = {40180580},
issn = {1080-6059},
abstract = {We used metagenomic next-generation sequencing (mNGS) to investigate an outbreak of Fusarium solani meningitis in US patients who had surgical procedures under spinal anesthesia in Matamoros, Mexico, during 2023. Using a novel method called metaMELT (metagenomic multiple extended locus typing), we performed phylogenetic analysis of concatenated mNGS reads from 4 patients (P1-P4) in parallel with reads from 28 fungal reference genomes. Fungal strains from the 4 patients were most closely related to each other and to 2 cultured isolates from P1 and an additional case (P5), suggesting that all cases arose from a point source exposure. Our findings support epidemiologic data implicating a contaminated drug or device used for epidural anesthesia as the likely cause of the outbreak. In addition, our findings show that the benefits of mNGS extend beyond diagnosis of infections to public health outbreak investigation.},
}

@article {pmid40180222,
year = {2025},
author = {Yang, Y and Wang, D and Li, L and Song, J and Yang, X and Li, J},
title = {Evolution of enteric viruses in the progression of colorectal cancer via the adenoma-carcinoma sequence pathway.},
journal = {Virus research},
volume = {},
number = {},
pages = {199569},
doi = {10.1016/j.virusres.2025.199569},
pmid = {40180222},
issn = {1872-7492},
abstract = {The global incidence of colorectal cancer (CRC) is increasing. In the majority of CRC cases, colon cancer develops from alterations in the adenoma-carcinoma sequence pathway. Currently, there are few studies regarding the effects of enteric viruses on the adenoma-carcinoma sequence pathway, and subsequently, the progression and development of the CRC. Here, fecal and tissue samples from a normal control group, an adenomatous polyp group, and a colorectal adenocarcinoma group were collected to gain a deeper understanding of the variations in enteric viruses in CRC patients and to analyze their significance. With the progression of CRC from adenoma to adenocarcinoma, the number of DNA viruses in the virus-like particles (VLPs) of fecal and tissue samples gradually increased, and there were distinct differences in the composition of enteric viruses among the different groups. Multiple species correlation analysis revealed extensive interactions among viruses, bacteria, and fungi in fecal and tissue samples. Functional analysis also revealed that the functional pathways in fecal and tissue samples also underwent significant changes. In conclusion, the changes in the composition and function of enteric viruses in the progression of CRC via adenoma-carcinoma sequence pathway were analyzed in this study, and these changes hold certain importance for exploring the role of enteric viruses in the occurrence of this disease; however, their mode of action and specific mechanisms require further investigation.},
}

@article {pmid39930907,
year = {2025},
author = {Doorenspleet, K and Jansen, L and Oosterbroek, S and Kamermans, P and Bos, O and Wurz, E and Murk, A and Nijland, R},
title = {The Long and the Short of It: Nanopore-Based eDNA Metabarcoding of Marine Vertebrates Works; Sensitivity and Species-Level Assignment Depend on Amplicon Lengths.},
journal = {Molecular ecology resources},
volume = {25},
number = {4},
pages = {e14079},
doi = {10.1111/1755-0998.14079},
pmid = {39930907},
issn = {1755-0998},
support = {//European Regional Development Fund Interreg North Sea region GEANS/ ; TEWZ118017//Rijksdienst voor Ondernemend Nederland/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; North Sea ; *Vertebrates/classification/genetics ; *Aquatic Organisms/classification/genetics ; DNA Primers/genetics ; Biodiversity ; *Nanopore Sequencing/methods ; *Metagenomics/methods ; *DNA, Environmental/genetics ; Fishes/genetics/classification ; Sequence Analysis, DNA ; DNA, Mitochondrial/genetics ; },
abstract = {To monitor the effect of nature restoration projects in North Sea ecosystems, accurate and intensive biodiversity assessments are vital. DNA-based techniques and especially environmental (e)DNA metabarcoding is becoming a powerful monitoring tool. However, current approaches rely on genetic target regions under 500 bp, offering limited taxonomic resolution. We developed a method for long-read eDNA metabarcoding, using Nanopore sequencing of a longer amplicon and present DECONA, a read processing pipeline to enable improved identification of marine vertebrate species. We designed a universal primer pair targeting a 2 kb region of fish mitochondrial DNA and compared it to the commonly used MiFish primer pair targeting a ~ 170 bp region. In silico testing showed that 2 kb fragments improved accurate identification of closely related species. Analysing eDNA from a North Sea aquarium showed that sequences from both primer pairs could be assigned to most species, and additional species level assignments could be made through the 2 kb primer pair. Interestingly, this difference was opposite in eDNA from the North Sea, where not the 2 kb but the MiFish primer pair detected more species. This study demonstrates the feasibility of using long-read metabarcoding for eDNA vertebrate biodiversity assessments. However, our findings suggests that longer fragments are less abundant in environmental settings, but not in aquarium settings, suggesting that longer fragments may provide a more recent snapshot of the community. Thus, long-read metabarcoding can expand the molecular toolbox for biodiversity assessments by improving species-level identification and may be especially useful when the temporal origin of the eDNA signal is better understood.},
}

Animals
*DNA Barcoding, Taxonomic/methods
North Sea
*Vertebrates/classification/genetics
*Aquatic Organisms/classification/genetics
DNA Primers/genetics
Biodiversity
*Nanopore Sequencing/methods
*Metagenomics/methods
*DNA, Environmental/genetics
Fishes/genetics/classification
Sequence Analysis, DNA
DNA, Mitochondrial/genetics

@article {pmid40180172,
year = {2025},
author = {Li, VW and Dong, TS and Funes, D and Hernandez, L and Kushnir, NR and Nair, D and Jacobs, JP and Reddy, ST and Mayer, EA and Chang, L and Meriwether, D},
title = {Mass spectrometric profiling of primary estrogens and estrogen metabolites in human stool and plasma partially elucidates the role of the gut microbiome in estrogen recycling.},
journal = {Molecular and cellular endocrinology},
volume = {},
number = {},
pages = {112534},
doi = {10.1016/j.mce.2025.112534},
pmid = {40180172},
issn = {1872-8057},
abstract = {Primary estrogens and estrogen metabolites are commonly measured in human plasma and serum, but there exist almost no recent reports for human stool. This knowledge gap limits our understanding of the relationships between systemic and gut estrogens. We developed a highly sensitive liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS) method to determine, in human plasma and stool, the free and conjugated levels of estrone, estradiol, and estriol together with their additional hydroxyestrogen and methoxyestrogen metabolites. We investigated human stool and plasma estrogens in healthy control men; in follicular and luteal phase premenopausal women; and in postmenopausal women. Most estrogens were present in plasma and stool of all groups, while the plasma and stool levels of hydroxyestrogen and methoxyestrogen metabolites but not estrone were correlated. In stool, estrogens were higher in premenopausal women, with estrogens increasing across the menstrual cycle. We combined these LC-MS/MS measures with shotgun metagenomic sequencing of the stool microbiomes. Estrogen deconjugation enzyme gene copy numbers (β-glucuronidase and arylsulfatase) were higher in premenopausal women; while the gene copy number of β-glucuronidase + arylsulfatase, but not β-glucuronidase alone, correlated with deconjugated stool estrogens in all groups. Moreover, β-glucuronidase + arylsulfatase gene copy numbers correlated with combined plasma estrogens in men and with individual plasma estrogen metabolites in men and premenopausal women. These results support the hypothesis that gut microbial β-glucuronidase and arylsulfatase control the deconjugation of gut estrogens while modulating systemic levels through the uptake and recirculation of these deconjugated estrogens. The intestine may thus constitute an important additional compartment in estrogen physiology.},
}

@article {pmid40179782,
year = {2025},
author = {Chen, S and Xin, X and Wang, Z and Wang, H and Yan, W},
title = {Enhancing tetramethylammonium hydroxide degradation in anaerobic digestion: Neglected role of iron-based conductive materials in regulating degradation pathway.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138115},
doi = {10.1016/j.jhazmat.2025.138115},
pmid = {40179782},
issn = {1873-3336},
abstract = {The rapid expansion of TFT-LCD industry led to significant environmental challenges due to the highly corrosive and ecotoxic tetramethylammonium hydroxide (TMAH). This study explores a previously unrecognized role of iron-based conductive materials - nano magnetite (Fe3O4) and nano zero-valent iron (ZVI) - in enhancing TMAH degradation and regulating degradation pathways in anaerobic digestion systems. Results show these materials significantly enhance degradation efficiency as TMAH concentration increases. At the highest TMAH level (10 g/L), while the control group achieved only 78.41 % degradation efficiency, Fe3O4 and ZVI groups reached efficiencies of 97.36 % and 94.96 %, with methane yields increased by 89.00 % and 97.21 %. Mechanistic exploration revealed these materials promoted secretion of charged functional groups into extracellular polymeric substances that effectively shielded microbes from TMAH toxicity. Additionally, they stimulated flavin and riboflavin production, enhancing interspecies electron transfer rates by up to 46.14-fold for Fe3O4 and 9.00-fold for ZVI. Microbial and metagenomic analyses further uncovered these materials induced a shift in TMAH degradation from methylotrophic methanogenesis to syntrophic metabolism, facilitating a more efficient breakdown of TMAH through direct interspecies electron transfer. These findings unravel the effects of iron-based conductive materials in regulating degradation pathways, offering a promising approach to addressing environmental challenges posed by TFT-LCD industry.},
}

@article {pmid40179570,
year = {2025},
author = {Zhang, P and Liu, Y and Xu, M and Zhang, J and Xia, J and Shi, Y and Wang, J and Han, B and Feng, G},
title = {Gut microbiota characteristics and prognostic value in patients with aneurysmal subarachnoid hemorrhage: A clinical study.},
journal = {Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia},
volume = {136},
number = {},
pages = {111200},
doi = {10.1016/j.jocn.2025.111200},
pmid = {40179570},
issn = {1532-2653},
abstract = {BACKGROUND: This study aims to explore the characteristics of gut microbiota in the aneurysmal subarachnoid hemorrhage (aSAH) group and the healthy control group, as well as in the good prognosis group and the poor prognosis group. It also investigates the relationship between the severity of aSAH and gut microbiota, and the predictive value of gut microbiota for the prognosis outcome of patients with aSAH.

METHODS: Stool samples from 22 patients with aSAH and 11 healthy controls were subjected to metagenomic sequencing, and species annotations were obtained through the taxonomic information database corresponding to the NR database. The characteristics of the gut microbiota in the aSAH group versus the healthy control group, and the good prognosis group versus the poor prognosis group were analyzed.The correlations between differential microbiota and clinical hematology markers between the aSAH and control groups and between gut microbiota and aSAH severity were analyzed. The prognosis of patients with aSAH after three months was assessed. Finally, gut microbiota with significant effects were screened for potential as biomarkers, and the predictive value of gut microbiota for different prognostic outcomes in patients with aSAH was explored.

RESULTS: Gut microbiota composition, diversity, and abundance differed significantly between patients in the aSAH group and the control group. Additionally, the composition, diversity, and abundance differed between patients with good and poor prognosis. Five dominant genera--Bacillus, Eggerthia, Hominisplanchenecus, Carnobacterium, and Bifidobacterium were identified as potential biomarkers for predicting aSAH outcomes.

CONCLUSION: Patients with aSAH have altered gut microbiota composition, structure, and diversity compared with the healthy population. These alterations may be potential biomarkers for aSAH diagnosis and outcome prediction.},
}

@article {pmid40178790,
year = {2025},
author = {Yuan, J and Yang, J and Sun, Y and Meng, Y and He, Z and Zhang, W and Dang, L and Song, Y and Xu, K and Lv, N and Zhang, Z and Guo, P and Yin, H and Shi, W},
title = {An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP).},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40178790},
issn = {1869-1889},
abstract = {China's progressing space program, as evidenced by the formal operation of the China Space Station (CSS), has provided great opportunities for various space missions. Since microbes can present potential risks to human health and the normal operation of spacecraft, the study on space-microorganisms in the CSS is always a matter of urgency. In addition, the knowledge on the interactions between microorganisms, astronauts, and spacecraft equipment will shed light on our understanding of life activities in space and a closed environment. Here, we present the first comprehensive report on the microbial communities aboard the CSS based on the results of the first two survey missions of the CSS Habitation Area Microbiome Program (CHAMP). By combining metagenomic and cultivation methods, we have discovered that, in the early stage of the CSS, microbial communities are dominated by human-associated microbes, with strikingly large differences in both composition and functional diversity compared to those found on the International Space Station (ISS). While the samples from two missions of CHAMP possessed substantial differences in microbial composition, no significant difference in functional diversity was found, although signs of accumulating antibiotic resistance were evident. Meanwhile, strong bacteria co-occurrence was noted within the station's microbiota. At the strain level, environmental isolates from the CSS exhibited numerous genomic mutations compared to those from the Assembly, Integration, and Test (AIT) center, potentially linked to the adaptation to the unique conditions of space. Besides, the intraspecies variation within four high-abundance species suggests possible propagation and residency effects between sampling sites. In summary, this study offers critical insights that not only advance our understanding of space microbiology but also lay the groundwork for effective microbial management in future long-term human space missions.},
}

@article {pmid40178526,
year = {2025},
author = {Contreras-de la Rosa, PA and De la Torre-Zavala, S and O Connor-Sánchez, A and Prieto-Davó, A and Góngora-Castillo, EB},
title = {Exploring the microbial communities in coastal cenote and their hidden biotechnological potential.},
journal = {Microbial genomics},
volume = {11},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001382},
pmid = {40178526},
issn = {2057-5858},
mesh = {*Archaea/genetics/classification/metabolism/isolation & purification ; *Bacteria/genetics/classification/metabolism ; Biotechnology ; Secondary Metabolism/genetics ; Metagenomics/methods ; *Geologic Sediments/microbiology ; Multigene Family ; Polyketide Synthases/genetics ; *Microbiota/genetics ; Phylogeny ; },
abstract = {Bacterial secondary metabolites are crucial bioactive compounds with significant therapeutic potential, playing key roles in ecological processes and the discovery of novel antimicrobial agents and natural products. Cenotes, as extreme environments, harbour untapped microbial diversity and hold an interesting potential as sources of novel secondary metabolites. While research has focused on the fauna and flora of cenotes, the study of their microbial communities and their biosynthetic capabilities remains limited. Advances in metagenomics and genome sequencing have greatly improved the capacity to explore these communities and their metabolites. In this study, we analysed the microbial diversity and biotechnological potential of micro-organisms inhabiting sediments from a coastal cenote. Metagenomic analyses revealed a rich diversity of bacterial and archaeal communities, containing several novel biosynthetic gene clusters (BGCs) linked to secondary metabolite production. Notably, polyketide synthase BGCs, including those encoding ladderanes and aryl-polyenes, were identified. Bioinformatics analyses of these pathways suggest the presence of compounds with potential industrial and pharmaceutical applications. These findings highlight the biotechnological value of cenotes as reservoirs of secondary metabolites. The study and conservation of these ecosystems are essential to facilitate the discovery of new bioactive compounds that could benefit various industries.},
}

*Archaea/genetics/classification/metabolism/isolation & purification
*Bacteria/genetics/classification/metabolism
Biotechnology
Secondary Metabolism/genetics
Metagenomics/methods
*Geologic Sediments/microbiology
Multigene Family
Polyketide Synthases/genetics
*Microbiota/genetics
Phylogeny

@article {pmid40178319,
year = {2025},
author = {Herzog, E and Ishida, K and Scherlach, K and Chen, X and Bartels, B and Niehs, SP and Cheaib, B and Panagiotou, G and Hertweck, C},
title = {Antibacterial Siderophores of Pandoraea Pathogens and their Impact on the Diseased Lung Microbiota.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e202505714},
doi = {10.1002/anie.202505714},
pmid = {40178319},
issn = {1521-3773},
abstract = {Antibiotic-resistant bacteria of the genus Pandoraea, frequently acquired from the environment, are an emerging cause of opportunistic respiratory infections, especially in cystic fibrosis (CF) patients. However, their specialized metabolites, including niche and virulence factors, remained unknown. Through genome mining of environmental and clinical isolates of diverse Pandoraea species, we identified a highly conserved biosynthesis gene cluster (pan) that codes for a non-ribosomal peptide synthetase (NRPS) assembling a new siderophore. Using bioinformatics-guided metabolic profiling of wild type and a targeted null mutant, we discovered the corresponding metabolites, pandorabactin A and B. Their structures and chelate (gallium) complexes were elucidated by a combination of chemical degradation, derivatization, NMR, and MS analysis. Metagenomics and bioinformatics of sputum samples of CF patients indicated that the presence of the pan gene locus correlates with the prevalence of specific bacteria in the lung microbiome. Bioassays and mass spectrometry imaging showed that pandorabactins have antibacterial activities against various lung pathogens (Pseudomonas, Mycobacterium, and Stenotrophomonas) through depleting iron in the competitors. Taken together, these findings offer first insight into niche factors of Pandoraea and indicate that pandorabactins shape the diseased lung microbiota through the competition for iron.},
}

@article {pmid40177842,
year = {2025},
author = {Larnder, AH and Manges, AR and Murphy, RA},
title = {The estrobolome: Estrogen-metabolizing pathways of the gut microbiome and their relation to breast cancer.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.35427},
pmid = {40177842},
issn = {1097-0215},
support = {/CAPMC/CIHR/Canada ; //Weston Family Foundation/ ; },
abstract = {Increasing evidence links the gut microbiome to carcinogenesis. Disruptions in estrogen regulation by the estrobolome-gut microbiota with estrogen-related functions-may promote breast cancer. However, precise information on estrobolome targets and their underlying mechanisms is limited. This review identifies relevant targets for measuring the estrobolome, focusing on enzymes and microbial taxa involved in processing estrogens, precursors, metabolites, and phytoestrogens, to facilitate the exploration of potential links to breast cancer. Evidence from breast cancer case-control studies is synthesized to assess alignment with these targets, highlight gaps in the evidence, and suggest new paths forward. Findings from case-control studies were heterogeneous and showed limited alignment with estrobolome targets, with only Escherichia coli and Roseburia inulinivorans identified as differentially abundant and functionally relevant between cases and controls. The lack of compelling evidence for estrobolome-specific mechanisms may reflect measurement challenges or may suggest that broader ecological changes in the microbiome, which influence a network of interacting mechanisms, are more influential for carcinogenesis. To clarify the estrobolome's role in breast cancer, future research should use advanced sequencing techniques and methods such as metabolomics and transcriptomics, while considering clinical and behavioral factors that may modify estrobolome mechanisms.},
}

@article {pmid40177486,
year = {2025},
author = {Yang, S and Chen, J and Zheng, J and Mao, H and Deng, F and Wu, D and Chai, J},
title = {Feeding systems influence the rumen resistome in yaks by changing the microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1505938},
doi = {10.3389/fmicb.2025.1505938},
pmid = {40177486},
issn = {1664-302X},
abstract = {The rumen microbiome serves as a reservoir of antibiotic-resistance genes (ARGs) with significant implications for public health. This study aimed to investigate the effects of different feeding systems on the rumen resistome in yaks. Yaks that grazed naturally on pasture were used as controls, while the experimental yaks were housed in a high-density pen environment and fed a specially designed diet to optimally meet their nutritional requirements, with increased interactions with farm workers. Metagenomic analysis was performed to assess changes in the rumen microbiome and resistome. Dietary factors influencing changes in the rumen microbiome and resistome were identified. A greater variety of microbiomes associated with carbohydrate digestion was found in yaks under a house-feeding system, such as Stomatobaculum longum and Succiniclasticum ruminis. Although grazing yaks exhibited various dominant antibiotic resistance genes (ARGs) at the class level, house-fed yaks were mainly enriched with tetracycline-resistant genes. A random forest model identified specific ARG signatures for each group, such as Sent_cmlA and Sliv_cmlR (Phenicol) and vanHD (Glycopeptide) prevalent in grazing yaks, while tet44, tetW, tetW/N/W, and tet40 were abundant in house-fed yaks. ARG interactions varied by feeding system, with signature ARGs in each group showing distinct correlations. Nevertheless, strong correlations among ARGs existed regardless of the treatments, such as the positive correlation between tetW and tetW/N/W in both groups. The rumen microbiome was strongly associated with the resistome, especially regarding abundant microbiomes and ARGs. Proteobacteria carrying ARGs were observed in grazing yaks, while Firmicutes served as hosts for ARGs in yaks under a housed feeding system. The specific bacteria contributing to the distinct ARGs in each group were identified. For instance, members of Firmicutes (Clostridium tepidiprofundi) carried their ARG signatures, such as tet44. These findings emphasized that diet, along with environmental factors and farmworker interactions, contributed to changes in the rumen resistome of yaks. This study is the first to discuss how multiple factors within a feeding regime influence the gut resistome, highlighting the drawbacks of intensive feedings with respect to the gut resistome.},
}

@article {pmid40177475,
year = {2025},
author = {Tenea, GN and Reyes, P and Flores, C},
title = {Crosslinking bacterial postbiotics for microbial and quality control of strawberries postharvest: bacteriological and 16S amplicon metagenome evidence.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1570312},
doi = {10.3389/fmicb.2025.1570312},
pmid = {40177475},
issn = {1664-302X},
abstract = {INTRODUCTION: Strawberries are renowned for their exceptional flavor and nutritional properties but have a short shelf life due to rapid ripening and a high vulnerability to postharvest microbial decay. Postbiotic formulations (PBFs) derived from lactic acid bacteria (LAB) can be developed into effective preservation products, extending postharvest shelf life while maintaining fruit quality.

METHODS: This study aimed to assess the effects of postbiotic-based formulations (PBFs) consisting of two key components: (1) a precipitated peptide-protein extract (PP) from Weissella cibaria UTNGt21O, serving as the antimicrobial agent, and (2) an exopolysaccharide (EPS) from W. confusa UTNCys2-2, functioning as the biopolymer carrier. These formulations were tested against a multidrug-resistant Serratia liquefaciens P4StpC1 strain, isolated from ready-to-eat strawberries, and their potential mode of action was analyzed in vitro. Time-kill assays and electron microscopy were used to evaluate their impact on the target cells. Furthermore, the performance of PBFs was compared to a commercial disinfectant (C1) in terms of their effects on strawberry microbiota and fruit quality, employing bacteriological techniques and 16S amplicon metagenomic analysis.

RESULTS: The selected PBFs showed bacteriolytic effect on Serratia in vitro. The target cell viability was significantly reduced upon 1 h co-cultivation by inducing several morphological and ultrastructural modifications. Dipping strawberries at the ripe stage four in PBFs indicated no increase in total cell counts, thus the microorganisms colonization was retained during storage with refrigeration. The 16S metagenome analysis showed that the treatment impacted the fruit microbiota, significantly increasing Lactobacillus abundance (p < 0.001) by day eight compared to the disinfectant control. This suggests the formulation supports beneficial microbes, enhancing antimicrobial effects. Additionally, the postbiotic coating improved shelf-life, preserved fruit quality, and delayed deterioration in strawberries. The strawberries quality attributes were not affected by the treatment. Principal Component Analysis (PCA) revealed clear sample separation based on maturity stage, independent of the treatment.

CONCLUSION: The results highlight the potential of crosslinking of a peptide-protein fraction with EPS to prevent the colonization of undesirable microorganisms on postharvest strawberries while enhancing their safety and quality.},
}

@article {pmid40177465,
year = {2025},
author = {Krause, SMB and van den Berg, NI and Brenzinger, K and Zweers, H and Bodelier, PLE},
title = {Beyond methane consumption: exploring the potential of methanotrophic bacteria to produce secondary metabolites.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf030},
doi = {10.1093/ismeco/ycaf030},
pmid = {40177465},
issn = {2730-6151},
abstract = {Microbial methane-consuming communities significantly impact biogeochemical processes and greenhouse gas emissions. In this study, we explored secondary metabolites produced by methane-oxidizing bacteria (MOB) and their ecological roles. We analyzed the volatile profiles of four MOB strains under controlled conditions and conducted a meta-analysis using high-quality genomes from 62 cultured MOB strains and 289 metagenome-assembled genomes to investigate their potential for producing secondary metabolites. Results show species-specific volatile production, such as germacrene by Methylobacter luteus, which may play a role in the regulation of environmental methane consumption. The meta-analysis revealed that biosynthetic gene clusters (BGCs) for terpenes and β-lactones were more prevalent in the Methylocystaceae and/or Beijerinckiaceae families, while aryl polyene BGCs were dominant in the Methylococcaceae family, reflecting habitat-specific adaptations. These findings advance our understanding of the metabolic capabilities of MOB and underscore the importance of integrating experimental data with genomic and metabolomic analyses to elucidate their ecology, environmental interactions, and contributions to methane cycling.},
}

@article {pmid40177421,
year = {2025},
author = {Tian, Y and Yang, X and Yang, Y and Lin, T and Wang, G and Zhang, Y and Wu, H and Wang, J},
title = {Aeromonas veronii-induced septic arthritis of the hip in a child with acute lymphoblastic leukemia.},
journal = {Open life sciences},
volume = {20},
number = {1},
pages = {20221042},
doi = {10.1515/biol-2022-1042},
pmid = {40177421},
issn = {2391-5412},
abstract = {Septic arthritis of the hip (SAH) is a prevalent form of infectious arthritis in children that can lead to serious complications if not promptly diagnosed and treated. A 6-year 4-month-old female child with a 1-year history of acute lymphoblastic leukemia chemotherapy was admitted to our hospital due to a 1-day fever. After 1 week, the child experienced right inguinal pain and exhibited severe restriction in the flexion of the right lower limb and hip. Consequently, edema was observed in the right lower extremity and foot. SAH was initially diagnosed using computed tomography and magnetic resonance imaging examinations of both hip joints. Subsequently, incision and irrigation procedure were performed on the hip joint. Following the surgery, pus metagenomic next-generation sequencing (mNGS) were conducted promptly, and the mNGS analysis indicated an Aeromonas veronii infection. The diagnosis of A. veronii SAH was subsequently confirmed through polymerase chain reaction. The child's condition was successfully treated with a combination of amikacin and imipenem-cilastatin, leading to improvement and subsequent discharge in a satisfactory state. SAH caused by A. veronii is a rare occurrence, and the utilization of mNGS holds significant potential for the early detection of uncommon infections in immunosuppressed children.},
}

@article {pmid40177267,
year = {2025},
author = {Yan, Z and Sun, C and Tang, W and Cao, W and Lv, J and Liang, Z and Wei, S and Zhong, W and Zhao, Z and Zhao, Z and Li, Y},
title = {Application of the metagenomic next-generation sequencing technology to identify the causes of pleural effusion.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1525100},
doi = {10.3389/fmed.2025.1525100},
pmid = {40177267},
issn = {2296-858X},
abstract = {BACKGROUND: Pleural effusion (PE), frequently encountered in clinical practice, can arise from a variety of underlying conditions. Accurate differential diagnosis of PE is crucial, as treatment and prognosis are heavily dependent on the underlying etiology. However, diagnosing the cause of PE remains challenging, relying on mycobacteriological methods that lack sensitivity and are time-consuming, or on histological examinations that require invasive biopsies. The recent advancements in metagenomic next-generation sequencing (mNGS) have shown promising applications in the diagnosis of infectious diseases. Despite this, there is limited research on the utility of mNGS as a comprehensive diagnostic tool for simultaneously identifying the causes of PE, particularly in cases of tuberculosis or malignancy.

METHODS: This study aimed to assess the efficacy of mNGS in detecting tuberculous pleural effusion (TPE) and malignant pleural effusion (MPE). A total of 35 patients with PE were included, and their PE samples were analyzed using mNGS.

RESULTS: Among the participants, 8 were ultimately diagnosed with TPE, and 10 were diagnosed with MPE, with lung adenocarcinoma being the most prevalent pathological type (50%, 5/10), according to established diagnostic criteria. Additionally, 7 patients were diagnosed with non-infectious PE. However, mNGS identified only 2 cases of TPE and 8 cases of MPE. The sensitivity of mNGS for detecting Mycobacterium tuberculosis was 25% (2/8), while the specificity was 100%. For tumor detection, mNGS demonstrated a sensitivity of 80%, a specificity of 92.6%, and an AUC of 0.882.

CONCLUSION: mNGS is effective in distinguishing MPE from non-MPE, but is not suitable for diagnosing TPE.},
}

@article {pmid40177264,
year = {2025},
author = {Kananen, K and Veseli, I and Quiles Pérez, CJ and Miller, SE and Eren, AM and Bradley, PH},
title = {Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf039},
doi = {10.1093/bioadv/vbaf039},
pmid = {40177264},
issn = {2635-0041},
abstract = {MOTIVATION: Gene function annotation in microbial genomes and metagenomes is a fundamental in silico first step toward understanding metabolic potential and determinants of fitness. The Kyoto Encyclopedia of Genes and Genomes publishes a curated list of profile hidden Markov models to identify orthologous gene families (KOfams) with roles in metabolism. However, the computational tools that rely upon KOfams yield different annotations for the same set of genomes, leading to different downstream biological inferences.

RESULTS: Here, we apply three open-source software tools that can annotate KOfams to genomes of phylogenetically diverse bacterial families from host-associated and free-living biomes. We use multiple computational approaches to benchmark these methods and investigate individual case studies where they differ. Our results show that despite their fundamental similarities, these methods have different annotation rates and quality. In particular, a method that adaptively tunes sequence similarity thresholds substantially improves sensitivity while maintaining high accuracy. We observe particularly large improvements for protein families with few reference sequences, or when annotating genomes from nonmodel organisms (such as gut-dwelling Lachnospiraceae). Our findings show that small improvements in annotation workflows can maximize the utility of existing databases and meaningfully improve in silico characterizations of microbial metabolism.

Anvi'o is available at https://anvio.org under the GNU GPL license. Scripts and workflow are available at https://github.com/pbradleylab/2023-anvio-comparison under the MIT license.},
}

@article {pmid40176261,
year = {2025},
author = {Sim, BZ and Mah, JK and Heldman, MR and Stanly, KL and Hanson, KE and Caliendo, AM and Andes, D and Ostroskly-Zeichner, L and Wingard, JR and Alexander, BD},
title = {Plasma microbial cell-free DNA Metagenomic Sequencing for Diagnosis of Invasive Fungal Diseases Among High Risk Outpatient and Inpatient Immunocompromised Hosts.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciaf170},
pmid = {40176261},
issn = {1537-6591},
abstract = {BACKGROUND: New and minimally-invasive tools to aid the diagnosis of invasive fungal diseases (IFD) are urgently needed as the immunocompromised population at highest risk increases. Advancements in molecular technology have rendered new diagnostics more readily available for clinical use.

METHODS: This case-control study utilized prospectively collected, archived plasma specimens and data from the Aspergillus Technology Consortium (AsTeC) Repository to investigate the diagnostic performance of microbial cell free DNA (mcfDNA) sequencing as a minimally-invasive diagnostic for IFDs in a population of high-risk immunocompromised hosts including hematologic malignancy, stem cell and solid organ transplants patients. The 2008 Mycoses Study Group/European Organization for the Research and Treatment of Cancer diagnostic criteria served as the gold standard for test performance.

RESULTS: Sixty-five adult subjects with proven or probable IFD and 65 controls without IFD were included. Among IFD episodes Aspergillus was the most common pathogen (70.8%, 46/65), followed by Mucorales (10.8%, 7/65). Overall, sensitivity was 47.7% and specificity was 100%. Sensitivity varied based on disease certainty and pathogen; sensitivity was higher in proven versus probable IFD (60.0% vs 37.1%, respectively) and higher for subjects with invasive mucormycosis (100%) compared with aspergillosis (45.7%).

CONCLUSIONS: A positive result by mcfDNA sequencing may reduce the need for invasive sampling in patients with suspected IFD. In this exploratory analysis, its high sensitivity and specificity for invasive mucormycosis suggests it could be useful for early treatment and intervention of this IFD. Future studies should focus on understanding how specific factors impact the sensitivity of mcfDNA sequencing for invasive aspergillosis.},
}

@article {pmid40176190,
year = {2025},
author = {Xing, J and Niu, T and Yu, T and Zou, B and Shi, C and Wang, Y and Fan, S and Li, M and Bao, M and Sun, Y and Gao, K and Qiu, J and Zhang, D and Wang, N and Jiang, Y and Huang, H and Cao, X and Zeng, Y and Wang, J and Zhang, S and Hu, J and Zhang, D and Sun, W and Yang, G and Yang, W and Wang, C},
title = {Faecalibacterium prausnitzii-derived outer membrane vesicles reprogram gut microbiota metabolism to alleviate Porcine Epidemic Diarrhea Virus infection.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {90},
pmid = {40176190},
issn = {2049-2618},
support = {U21A20261//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Swine ; *Porcine epidemic diarrhea virus/physiology ; *Gastrointestinal Microbiome ; *Swine Diseases/virology/microbiology ; *Faecalibacterium prausnitzii/metabolism/physiology ; *Coronavirus Infections/veterinary/virology/microbiology ; Probiotics/administration & dosage ; Feces/microbiology ; *Bacterial Outer Membrane/metabolism ; },
abstract = {BACKGROUND: The Porcine Epidemic Diarrhea Virus (PEDV) is one of the major challenges facing the global pig farming industry, and vaccines and treatments have proven difficult in controlling its spread. Faecalibacterium prausnitzii (F.prausnitzii), a key commensal bacterium in the gut, has been recognized as a promising candidate for next-generation probiotics due to its potential wide-ranging health benefits. A decrease in F.prausnitzii abundance has been associated with certain viral infections, suggesting its potential application in preventing intestinal viral infections. In this study, we utilized a piglet model to examine the potential role of F.prausnitzii in PEDV infections.

RESULTS: A piglet model of PEDV infection was established and supplemented with F.prausnitzii, revealing that F.prausnitzii mitigated PEDV infection. Further studies found that outer membrane vesicles (OMVs) are the main functional components of F.prausnitzii, and proteomics, untargeted metabolomics, and small RNA-seq were used to analyze the composition of OMVs. Exhaustion of the gut microbiota demonstrated that the function of Fp. OMVs relies on the presence of the gut microbiota. Additionally, metagenomic analysis indicated that Fp. OMVs altered the gut microbiota composition, enhancing the abundance of Faecalibacterium prausnitzii, Prevotellamassilia timonensis, and Limosilactobacillus reuteri. Untargeted metabolomics analysis showed that Fp. OMVs increased phosphatidylcholine (PC) levels, with PC identified as a key metabolite in alleviating PEDV infection. Single-cell sequencing revealed that PC altered the relative abundance of intestinal cells, increased the number of intestinal epithelial cells, and reduced necroptosis in target cells. PC treatment in infected IPEC-J2 and Vero cells alleviated necroptosis and reduced the activation of the RIPK1-RIPK3-MLKL signaling axis, thereby improving PEDV infection.

CONCLUSION: F.prausnitzii and its OMVs play a critical role in mitigating PEDV infections. These findings provide a promising strategy to ameliorate PEDV infection in piglets. Video Abstract.},
}

Animals
Swine
*Porcine epidemic diarrhea virus/physiology
*Gastrointestinal Microbiome
*Swine Diseases/virology/microbiology
*Faecalibacterium prausnitzii/metabolism/physiology
*Coronavirus Infections/veterinary/virology/microbiology
Probiotics/administration & dosage
Feces/microbiology
*Bacterial Outer Membrane/metabolism

@article {pmid40176137,
year = {2025},
author = {Sommer, F and Bernardes, JP and Best, L and Sommer, N and Hamm, J and Messner, B and López-Agudelo, VA and Fazio, A and Marinos, G and Kadibalban, AS and Ito, G and Falk-Paulsen, M and Kaleta, C and Rosenstiel, P},
title = {Life-long microbiome rejuvenation improves intestinal barrier function and inflammaging in mice.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {91},
pmid = {40176137},
issn = {2049-2618},
support = {SO1141/10-1//Deutsche Forschungsgemeinschaft/ ; CRC1182//Deutsche Forschungsgemeinschaft/ ; miTARGET//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Mice ; RNA, Ribosomal, 16S/genetics ; *Fecal Microbiota Transplantation ; *Aging/physiology ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; *Intestinal Mucosa/microbiology/metabolism ; *Inflammation/microbiology ; Mice, Inbred C57BL ; *Rejuvenation ; Permeability ; *Intestines/microbiology ; Metagenomics ; Intestinal Barrier Function ; },
abstract = {BACKGROUND: Alterations in the composition and function of the intestinal microbiota have been observed in organismal aging across a broad spectrum of animal phyla. Recent findings, which have been derived mostly in simple animal models, have even established a causal relationship between age-related microbial shifts and lifespan, suggesting microbiota-directed interventions as a potential tool to decelerate aging processes. To test whether a life-long microbiome rejuvenation strategy could delay or even prevent aging in non-ruminant mammals, we performed recurrent fecal microbial transfer (FMT) in mice throughout life. Transfer material was either derived from 8-week-old mice (young microbiome, yMB) or from animals of the same age as the recipients (isochronic microbiome, iMB) as control. Motor coordination and strength were analyzed by rotarod and grip strength tests, intestinal barrier function by serum LAL assay, transcriptional responses by single-cell RNA sequencing, and fecal microbial community properties by 16S rRNA gene profiling and metagenomics.

RESULTS: Colonization with yMB improved coordination and intestinal permeability compared to iMB. yMB encoded fewer pro-inflammatory factors and altered metabolic pathways favoring oxidative phosphorylation. Ecological interactions among bacteria in yMB were more antagonistic than in iMB implying more stable microbiome communities. Single-cell RNA sequencing analysis of intestinal mucosa revealed a salient shift of cellular phenotypes in the yMB group with markedly increased ATP synthesis and mitochondrial pathways as well as a decrease of age-dependent mesenchymal hallmark transcripts in enterocytes and TA cells, but reduced inflammatory signaling in macrophages.

CONCLUSIONS: Taken together, we demonstrate that life-long and repeated transfer of microbiota material from young mice improved age-related processes including coordinative ability (rotarod), intestinal permeability, and both metabolic and inflammatory profiles mainly of macrophages but also of other immune cells. Video Abstract.},
}

Animals
*Gastrointestinal Microbiome/physiology
Mice
RNA, Ribosomal, 16S/genetics
*Fecal Microbiota Transplantation
*Aging/physiology
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Male
*Intestinal Mucosa/microbiology/metabolism
*Inflammation/microbiology
Mice, Inbred C57BL
*Rejuvenation
Permeability
*Intestines/microbiology
Metagenomics
Intestinal Barrier Function

@article {pmid40175903,
year = {2025},
author = {Cao, L and Sun, H and Xu, Z and Xu, X and Shi, G and Zhang, J and Liang, C and Li, T and Liu, C and Wang, M and Tian, S and Li, E},
title = {Metagenomic and physicochemical profiling reveal microbial functions in pit mud for Jiang-Nong Jianxiang Baijiu fermentation.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {190},
pmid = {40175903},
issn = {1471-2180},
mesh = {*Fermentation ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; China ; Food Microbiology ; *Metagenome ; Microbiota ; *Alcoholic Beverages/microbiology ; },
abstract = {BACKGROUND: The unique flavour and quality of Baijiu, a treasure of traditional Chinese culture, has attracted increasing attention. The pit mud is a key component for forming the unique flavour styles of different Baijiu brands. Hence, conducting in-depth research on the microbial colonies present in pit mud is paramount for enhancing the intricate bouquets of Baijiu flavours.

RESULTS: This study conducts a comprehensive metagenomic examination of the microbial ecosystem within Chinese Jiang-Nong Jianxiang Baijiu fermentation pit mud. Within the pit mud walls, six prominent species, each accounting for more than 1% of the average relative abundance, emerged as key contributors: Lentilactobacillus buchneri, Secundilactobacillus silagincola, Clostridium tyrobutyricum, Lentilactobacillus parafarraginis, Ligilactobacillus acidipiscis, and Lactobacillus acetotolerans. Conversely, at the pit mud bases, four species surpassed this threshold: Petrimonas sp. IBARAKI, Methanosarcina barkeri, Methanofollis ethanolicus, and Proteiniphilum propionicum. Notably, the abundance of Clostridium in the pit mud walls impart superior saccharifying capabilities compared with those at the bases. The consistently high relative abundance of enzymes belonging to the glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) across both the pit mud walls and the bases highlight their importance in fermentation.

CONCLUSIONS: The microbial composition analysis results underscore the important role of pit mud microorganisms in facilitating starch saccharification, ethyl caproate and ethyl butyrate production, among other aromatic compounds. Microbes residing in the pit mud walls may be exhibited a heightened propensity for lactic acid generation, whereas those inhabiting the bases may be displayed a stronger inclination towards caproic acid production. This research serves as a valuable reference for future endeavours aimed at harnessing microbial resources to refine and optimize Baijiu fermentation methodologies.},
}

*Fermentation
*Metagenomics/methods
*Bacteria/genetics/classification/metabolism/isolation & purification
China
Food Microbiology
*Metagenome
Microbiota
*Alcoholic Beverages/microbiology

@article {pmid40175854,
year = {2025},
author = {Abuzahrah, SS},
title = {Exploring the microorganisms biodiversity associated with sponge species in the red sea through 18S ribosomal RNA gene sequencing.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {60},
pmid = {40175854},
issn = {2191-0855},
abstract = {Around the world, sponges play a significant role in marine ecosystems, and a wide variety of sponge species can be found in the coast of Red Sea of Saudi Arabia. The unique environmental conditions of the Red Sea, including warm, oligotrophic water and high salinity, have encouraged the growth of abundant sponge fauna. Our study aims to investigate the biodiversity, taxonomic composition, and phylogenetic relationships of eukaryotic organisms linked with sponges in the Red Sea off the coast of Saudi Arabia and infer the possible ecological roles and functional contributions of the identified eukaryotic taxa to sponge health and ecosystem functioning. The study investigated the microbial diversity, focusing on the genera Hyalosynedra sp., Navicula sp., Papiliocellulus sp., Psammodictyon sp., Pynococcus sp., Ostreococcus sp., Micromonas sp., and other unclassified species. Our metagenomic analysis and phylogenetic evaluation revealed a deep and diverse microbial community, with each genus performing significant ecological roles, including nutrient cycling, primary production, and contributing to marine food networks. Moreover, these genera display promising biotechnological prospects, including uses in bioremediation, biofuel production, and the synthesis of high-value biomolecules. Comparative analysis with other marine regions has focused on both the similarities and unique aspects of the Red Sea microbial community, which are influenced by its distinct environmental conditions. The gained findings contribute to a deeper understanding of the ecological dynamics in the Red Sea and open new avenues for biotechnological exploration in marine ecosystems.},
}

@article {pmid40175821,
year = {2025},
author = {Takagi, K and Tamura, Y and Narita, N and Komatsu, S and Yamazaki, S and Matsumura, A and Kubota, K and Matsumiya, T and Sawada, K and Nakaji, S and Mikami, T and Kobayashi, W},
title = {Involvement of Megasphaera in the oral microbiome and dyslipidemia onset: evidence from a community-based study in Japan.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {40175821},
issn = {1874-9356},
support = {21K10202//Japan Society for the Promotion of Science/ ; 22K17281//Japan Society for the Promotion of Science/ ; 24K13233//Japan Society for the Promotion of Science/ ; JPMJCE 1302//Japan Science and Technology Agency/ ; JPMJCA　2201//Japan Science and Technology Agency/ ; JPMJPE 2210//Japan Science and Technology Agency/ ; },
abstract = {Dyslipidemia is a major risk factor for cardiovascular diseases and is influenced by genetic and environmental factors, including diet. Emerging research suggests a link between the gut microbiome and metabolic disorders. While the connection between the gut microbiota and dyslipidemia is well documented, the specific relationship between oral bacteria and dyslipidemia has not been thoroughly investigated. This study aimed to identify oral bacterial species associated with dyslipidemia in a community-based Japanese population. We conducted a metagenomic analysis on tongue coating samples from 763 participants in the Iwaki Health Promotion Project, which were collected during health checkups in 2017 and 2019. Dyslipidemia was diagnosed using standard lipid level criteria. The oral microbiome was analyzed via 16S rDNA amplicon sequencing. Statistical analyses included multiple regression and β diversity assessments. Our analysis revealed that the abundances of several bacterial genera, including Veillonella, Atopobium, Stomatobaculum, Tanneralla, and Megasphaera, are significantly associated with dyslipidemia. A higher relative abundance of Megasphaera was specifically observed in individuals with dyslipidemia. Moreover, Megasphaera abundance was closely associated with the onset of dyslipidemia (P = 0.038, odds ratio: 1.005, 95% confidence interval: 1.000-1.009), suggesting its role in metabolic regulation. This study revealed a significant association between the abundance of specific oral bacteria and dyslipidemia, suggesting the potential of using the oral microbiota as a biomarker for the early detection and management of dyslipidemia. Future research should explore the mechanisms through which oral bacteria influence lipid metabolism and the potential for microbioma-based therapies.},
}

@article {pmid40175737,
year = {2025},
author = {Sawhney, SS and Thänert, R and Thänert, A and Hall-Moore, C and Ndao, IM and Mahmud, B and Warner, BB and Tarr, PI and Dantas, G},
title = {Gut microbiome evolution from infancy to 8 years of age.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40175737},
issn = {1546-170X},
support = {R01AI155893//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01HD092414//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; R01HD092414//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; T32GM007067//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; MD-FR-2013-292//Children's Discovery Institute (CDI)/ ; 5P30 DK052574//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; },
abstract = {The human gut microbiome is most dynamic in early life. Although sweeping changes in taxonomic architecture are well described, it remains unknown how, and to what extent, individual strains colonize and persist and how selective pressures define their genomic architecture. In this study, we combined shotgun sequencing of 1,203 stool samples from 26 mothers and their twins (52 infants), sampled from childbirth to 8 years after birth, with culture-enhanced, deep short-read and long-read stool sequencing from a subset of 10 twins (20 infants) to define transmission, persistence and evolutionary trajectories of gut species from infancy to middle childhood. We constructed 3,995 strain-resolved metagenome-assembled genomes across 399 taxa, and we found that 27.4% persist within individuals. We identified 726 strains shared within families, with Bacteroidales, Oscillospiraceae and Lachnospiraceae, but not Bifidobacteriaceae, vertically transferred. Lastly, we identified weaning as a critical inflection point that accelerates bacterial mutation rates and separates functional profiles of genes accruing mutations.},
}

@article {pmid40175647,
year = {2025},
author = {Ahn, JS and Kim, S and Han, EJ and Hong, ST and Chung, HJ},
title = {Increasing spatial working memory in mice with Akkermansia muciniphila.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {546},
pmid = {40175647},
issn = {2399-3642},
support = {C512230//Korea Basic Science Institute (KBSI)/ ; RS-2023-00224099//National Research Foundation of Korea (NRF)/ ; },
abstract = {Recent research has shown the gut microbiome's impact on memory, yet limitations hinder the identification of specific microbes linked to cognitive function. We measured spatial working memory in individual mice before and after fecal microbiota transplantation (FMT) to develop a targeted analysis that identifies memory-associated strains while minimizing host genetic effects. Transplantation of human fecal into C57BL/6 mice yielded varied outcomes: some mice showed significant improvements while others had negligible changes, indicating that these changes are due to differences in FMT colonization. Metagenomic analysis, stratified by memory performance, revealed a positive correlation between the abundance of Akkermansia muciniphila and improved memory. Moreover, administering two A. muciniphila strains, GMB 0476 and GMB 2066, to wild-type mice elevated spatial working memory via BDNF activation. Our findings indicate that specific gut microbes, particularly A. muciniphila, may modulate memory and represent potential targets for therapeutic intervention in cognitive enhancement.},
}

@article {pmid40175554,
year = {2025},
author = {Ryan, FJ and Clarke, M and Lynn, MA and Benson, SC and McAlister, S and Giles, LC and Choo, JM and Rossouw, C and Ng, YY and Semchenko, EA and Richard, A and Leong, LEX and Taylor, SL and Blake, SJ and Mugabushaka, JI and Walker, M and Wesselingh, SL and Licciardi, PV and Seib, KL and Tumes, DJ and Richmond, P and Rogers, GB and Marshall, HS and Lynn, DJ},
title = {Bifidobacteria support optimal infant vaccine responses.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40175554},
issn = {1476-4687},
abstract = {Accumulating evidence indicates that antibiotic exposure may lead to impaired vaccine responses[1-4]; however, the mechanisms underlying this association remain poorly understood. Here we prospectively followed 191 healthy, vaginally born, term infants from birth to 15 months, using a systems vaccinology approach to assess the effects of antibiotic exposure on immune responses to vaccination. Exposure to direct neonatal but not intrapartum antibiotics was associated with significantly lower antibody titres against various polysaccharides in the 13-valent pneumococcal conjugate vaccine and the Haemophilus influenzae type b polyribosylribitol phosphate and diphtheria toxoid antigens in the combined 6-in-1 Infanrix Hexa vaccine at 7 months of age. Blood from infants exposed to neonatal antibiotics had an inflammatory transcriptional profile before vaccination; in addition, faecal metagenomics showed reduced abundance of Bifidobacterium species in these infants at the time of vaccination, which was correlated with reduced vaccine antibody titres 6 months later. In preclinical models, responses to the 13-valent pneumococcal conjugate vaccine were strongly dependent on an intact microbiota but could be restored in germ-free mice by administering a consortium of Bifidobacterium species or a probiotic already widely used in neonatal units. Our data suggest that microbiota-targeted interventions could mitigate the detrimental effects of early-life antibiotics on vaccine immunogenicity.},
}

@article {pmid40175522,
year = {2025},
author = {Gichuki, BM and Van Camp, AG and Shao, Y},
title = {A new strain of thought in gut metagenomics.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40175522},
issn = {1740-1534},
}

@article {pmid40175313,
year = {2025},
author = {Fortin, SG and Uhlig, K and Hale, RC and Song, B},
title = {Microplastic biofilms as potential hotspots for plastic biodegradation and nitrogen cycling: A metagenomic perspective.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf035},
pmid = {40175313},
issn = {1574-6941},
abstract = {Microplastics are an emerging contaminant worldwide, with the potential to impact organisms and facilitate the sorption and release of chemicals. Additionally, they create a novel habitat for microbial communities, forming biofilms known as the plastisphere. While the plastisphere has been studied in select aquatic environments, those in estuarine ecosystems merit additional attention due to their proximity to plastic debris sources. Additionally, the role plastisphere communities play in nutrient cycling has rarely been examined. This study used metagenomic analysis to investigate the taxonomic composition and functional genes of developing plastisphere communities living on petroleum-based (polyethylene and polyvinyl chloride) and biopolymer-based (polylactic acid) substrates. Isolated metagenome assembled genomes (MAGs) showed plastisphere communities have the genes necessary to perform nitrification and denitrification and degrade petroleum and biopolymer-based plastics. The functions of these plastispheres have implications for estuarine nitrogen cycling and provide a possible explanation for the plastisphere microbes' competitiveness in biofilm environments. Overall, microplastics in the estuarine system provide a novel habitat for microbial communities and associated nitrogen cycling, facilitating the growth of microbes with plastic degrading capabilities.},
}

@article {pmid40174744,
year = {2025},
author = {Liu, M and Wang, S and Zhou, H and Liu, H and Huang, D and Liu, L and Li, Q and Chen, H and Lei, Y and Jin, LN and Zhang, W},
title = {Thermal Environment Driving Specific Microbial Species to Form the Visible Biofilms on the UNESCO World Heritage Dazu Rock Carvings.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121510},
doi = {10.1016/j.envres.2025.121510},
pmid = {40174744},
issn = {1096-0953},
abstract = {The Dazu Rock Carvings, a UNESCO World Heritage site with over a millennium of history, are facing significant deterioration from microbial biofilms. However, the key microbial species responsible and the environmental factors driving their growth remain unclear. To address this gap, we conducted metagenomic sequencing to characterize the microbial community on the carvings, followed by correlation analyses with a variety of environmental factors in the surrounding air and within the rocks. Bacterial communities exhibited significantly higher richness and diversity than eukaryotic communities, though diversity metrics showed no significant differences between visibly colonized and uncolonized surfaces. We identified a distinctive consortium of 64 bacterial species, 35 fungal species, and 1 algal species specifically associated with visible biofilms, occurring at 9.56-fold higher relative abundance in colonized areas. These microorganisms contribute to characteristic green, brown-black, and white coloration on the carvings. Statistical analysis revealed absolute humidity and dew point temperature as key environmental factors influencing biofilm visibility, with thresholds of 21.00 g/m[3] and 23.4°C respectively, above which biofilms became visible. This study provides precise targets for conservation efforts and establishes critical environmental parameters to guide preservation strategies for this irreplaceable cultural heritage.},
}

@article {pmid40174653,
year = {2025},
author = {Balasundaram, G and Gahlot, P and Hafyan, RH and Tyagi, VK and Gadkari, S and Sahu, A and Barber, B and Mutiyar, PK and Kazmi, AA and Kleiven, H},
title = {Anaerobic digestion of thermal hydrolysis pretreated sludge: Process performance, metagenomic analysis, techno-economic and life cycle assessment.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132470},
doi = {10.1016/j.biortech.2025.132470},
pmid = {40174653},
issn = {1873-2976},
abstract = {This study assessed the potential of thermal hydrolysis process (THP) combined with anaerobic digestion (AD) for high solids sewage sludge treatment across various hydraulic retention times (HRTs). Optimal performance was achieved at a 10-day HRT (6 kg VS/m[3]·day), yielding 408 L CH4/kg VS added and 54 % volatile solids (VS) removal under THP conditions of 160 °C, 30 min, and 6 bar pressure. Microbial analysis revealed predominant acetoclastic and hydrogenotrophic methanogens. Four scenarios were designed and analyzed for environmental and economic performance: Scenario 1 (conventional AD-CHP), Scenario 2 (conventional AD-BioCNG), Scenario 3 (THP AD-BioCNG), and Scenario 4 (THP AD-CHP). The results showed that scenarios with CHP integration achieved better environmental performance by generating sufficient energy to meet demand, with energy consumption as a key factor. Notably, scenario 4 had the lowest global warming potential (GWP) at -0.0185 kg CO2-eq, outperforming conventional AD (Scenario 1) with CHP, which had a GWP of -0.00232 kg CO2-eq. However, profitability analysis showed that Scenario 3 was the most economically viable, with a net present value (NPV) of $4.3 million, an internal rate of return (IRR) of 10.21 %, and a 17-year payback period. Although it had higher capital ($58 million) and operational costs ($12.5 million/year) than Scenario 4 ($45 million and $8.6 million/year), its greater biomethane yield resulted in higher revenue ($20.7 million/year), making it the most profitable option. While Scenario 4 offered the best environmental benefits, Scenario 3 emerged as the most financially sustainable choice. These findings highlight the environmental and economic advantage of utilizing THP-AD process over conventional AD, suggesting that THP-AD optimizes methane production, solids reduction, and environmental impact, making the Bio CNG pathway a sustainable and economically viable option.},
}

@article {pmid40174641,
year = {2025},
author = {He, T and Zhang, X and Zhang, X},
title = {Thousands-years-old deep-sea DNA viruses reveal the evolution of human pathogenic viruses.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.03.057},
pmid = {40174641},
issn = {2090-1224},
abstract = {INTRODUCTION: In the last two decades, outbreaks of pathogenic viruses have led to significant human mortality and economic repercussions. Despite extensive investigations into tracing these viruses in terrestrial environments, their origins remain enigmatic.

OBJECTIVES: The Earth's biosphere encompasses both sunlight-dependent terrestrial and surface ocean ecosystems, as well as the sunlight-independent deep-sea ecosystem. However, the traceability of human pathogenic viruses in the deep sea has not been thoroughly explored. This study aimed to investigate the presence of human pathogenic viruses in the deep sea.

METHODS: In this study, we performed a viral metagenomic analysis using a global deep-sea sediment virome 2.0 dataset which contained 159 deep-sea sediment samples with geologic ages from 2,500 to 7,750 years.

RESULTS: A total of 554,664 viral operational taxonomic units (vOTUs) were identified and further obtained 2,254 potential pathogenic viruses of vertebrates. Among them, 23 vOTUs exhibited high homology with 12 species of human pathogenic viruses which belonged to 4 viral families. Notably, variola virus, the first human pathogenic virus eradicated from humans and now only found in laboratories, was discovered in the ancient deep-sea sediments. The evolution analysis showed that these DNA viruses might represent the ancestors or variants of human pathogenic viruses, suggesting that the deep sea could be a crucial reservoir for human pathogenic viruses.

CONCLUSION: Our findings present all the ancient pathogenic DNA viruses of humans found in the deep sea for the first time, highlighting the source of the future epidemics. It is imperative to implement the stringent virus monitoring and management measures for human activities in marine environments to address the emerging challenges of marine biosecurity and promote sustainable use of oceans.},
}

@article {pmid40174574,
year = {2025},
author = {Zeng, S and Almeida, A and Mu, D and Wang, S},
title = {Embracing the unknown: Proteomic insights into the human microbiome.},
journal = {Cell metabolism},
volume = {37},
number = {4},
pages = {799-801},
doi = {10.1016/j.cmet.2025.02.003},
pmid = {40174574},
issn = {1932-7420},
abstract = {Protein-level investigations into the human microbiome provide insights into active microbial functions. Recently, Valdés-Mas et al.[1] introduced a metagenome-informed metaproteomics approach to functionally explore species-level microbiome-host interactions and quantify the dietary exposome. Its potential has been implemented in mice and humans to uncover proteomic signatures of health and inflammatory bowel disease.},
}

@article {pmid40174565,
year = {2025},
author = {Krohn, C and Khudur, L and Biek, SK and Elliott, JA and Tabatabaei, S and Jiang, C and Wood, JL and Dias, DA and Dueholm, MKD and Rees, CA and O'Carroll, D and Stuetz, R and Batstone, DJ and Surapaneni, A and Ball, AS},
title = {Microbial population shifts during disturbance induced foaming in anaerobic digestion of primary and activated sludge.},
journal = {Water research},
volume = {281},
number = {},
pages = {123548},
doi = {10.1016/j.watres.2025.123548},
pmid = {40174565},
issn = {1879-2448},
abstract = {Foaming during anaerobic digestion (AD) of sewage sludge is poorly understood and remains an uncontrollable operational obstacle for sewage treatment systems globally, causing mechanical damage, increased hazards and reduced biogas recovery. Foams during AD commonly occur after process disturbances, such as organic loading shocks. However, it is still unclear whether these foam events are biologically driven and linked to the abundance of organisms like filamentous or hydrophobic bacteria. A time-series study was conducted, comparing digestion performance, microbial community succession, metagenomes, and metabolomes in six anaerobic continuous stirred-tank reactors (CSTRs): a control group fed normally (n = 3), and one treated group inhibited through organic shock loading of more than twice the steady state loading rate with glycerol (treatment, n = 3). As soon as microbial activity and methanogenesis recovered after inhibition, significant volumes of foam accumulated simultaneously in the reactor headspace of the three treated CSTRs. Microbial abundance profiles (16S rRNA, V3-V4) from 165 days of operation showed that filamentous or mycolic acid-producing organisms were not associated with this foam event. Shock loading led to acidification, biomass decline and microbial imbalance, contributing indirectly to the foam event. During that period, metabolomes and functional pathway abundances indicated that the stressed microbial biomass was enriched in long-chain fatty acids prior to foaming. This biomass, combined with pH changes, may have modified the physicochemical properties of sludge, leading to the fractionation of organic mass once gas production resumed. More research is needed to understand how abiotic and biotic interactions contribute to foam formation.},
}

@article {pmid40174457,
year = {2025},
author = {Han, Q and Wang, Y and Shi, C and Qian, Y and Wang, X and Wang, S and Sun, X and Yu, Q and Li, H},
title = {Urban landscape lakes with backwater hide higher antibiotic resistance risk than living water.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138101},
doi = {10.1016/j.jhazmat.2025.138101},
pmid = {40174457},
issn = {1873-3336},
abstract = {The pollution of antibiotic resistance genes (ARGs) in urban landscape lakes threatens the aquatic ecosystems and public health. However, a comprehensive understanding of the fate of ARGs in different types of park landscape lakes (i.e., backwater and living water) remains deficient. Here, we profiled the distribution, diversity, origin and potential spread risk to human of ARGs in backwater and living water using metagenomics and 16S rRNA gene sequencing. Our results showed higher antibiotic resistance risk presented in backwater due to higher ARG diversity, while higher resistance transfer risk occurred in living water due to higher mobile genetic elements (MGEs) diversity. Source tracking analysis revealed Yellow River water was the main the dominant source of ARGs in both backwater and living water, with an average contribution of 41.06 % and 65.82 %, respectively. Notably, nine high-risk ARGs (such as mdtM and msrA) significantly enriched in human feces, implying possible spread risk from environment to human. Metagenomics binning revealed that MAGs carrying ARGs mainly belong to Actinobacteria, while MAGs carrying MGEs belong to Proteobacteria. Our study highlights the significance of healthy management of park landscape lakes to prevent the spread of resistomes to the public.},
}

@article {pmid40174456,
year = {2025},
author = {Long, M and Zheng, CW and Zhou, C and Rittmann, BE},
title = {Mitigating chromate toxicity through concurrent denitrification in the H2-based membrane biofilm reactor.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138073},
doi = {10.1016/j.jhazmat.2025.138073},
pmid = {40174456},
issn = {1873-3336},
abstract = {High concentrations of hexavalent chromium (Cr(VI)) in industrial wastewaters pose significant environmental and health hazards. Biotranformation is a viable means to lower Cr(VI) toxicity, but research to date has focused on wastewaters with low concentrations (e.g., 2-5 mg/L Cr(VI)). This study evaluated the dynamics of biosorption and biotransformation of higher-concentration Cr(VI) by biofilms in the H2-based membrane biofilm reactor (MBfR). While the biofilm in an MBfR receiving Cr(VI) alone had limited capacity to remove Cr(VI) and Cr(VI) removal ceased in 30 days, an autotrophic denitrifying biofilms achieved 99 % reduction of over 20 mg/L Cr(VI) to less-toxic trivalent chromium (Cr(III)) in continuous long-term operation system over 4 months. Increasing the H2 pressure from 3 psig to 10 psig improved Cr(VI) removal from 87 % to 99 %, which occurred in parallel with over 95 % NO3[-] reduction to N2. Metagenomic analyses revealed the mechanisms of Cr(VI) bioreduction and highlighted the beneficial role of nitrate (NO3[-]) as the primary electron acceptor. For example, nitrite reductase NrfA could reduce Cr(VI), which lowered Cr(VI) caused oxidative stress. This research demonstrates the MBfR's effectiveness in reducing elevated levels of Cr(VI) and provides mechanistic understanding of the roles of denitrification in accelerating Cr(VI) reduction and detoxification.},
}

@article {pmid40174424,
year = {2025},
author = {Dai, Z and Li, Y and Zhang, Y and Xiang, T and Peng, J and Mao, X and Fan, Y and Wang, F and Yang, S and Cao, W},
title = {Nutrient enrichment by high aquaculture effluent input exacerbates imbalances between methane production and oxidation in mangrove sediments.},
journal = {Water research},
volume = {280},
number = {},
pages = {123552},
doi = {10.1016/j.watres.2025.123552},
pmid = {40174424},
issn = {1879-2448},
abstract = {Frequent aquaculture activities introduce substantial nutrients into mangrove ecosystems; however, the impact of this nutrient enrichment on methane (CH4) emissions and the associated microbial communities remains largely unexplored. In this study, we used the static chamber method, combined with 16S rRNA-based, metagenomic sequencing and binning techniques, to investigate the emission patterns of greenhouse gases (GHGs), with a particular focus on CH4, in mangroves subjected to different levels of effluents. The results showed that the effluent input decreased the mineral protection of sediment carbon (C) pools and increased C loss by more than double. In particular, high effluent input increased CH4 emissions by 243.3 %. Random forest analysis revealed that changes in methanogens were an important factor in explaining the variation of CH4 emissions. Amplicon data showed that the proportion of methylotrophic methanogens increased after effluent input, and metagenomic binning further attributed this change to the adaptability of methylotrophic methanogens to the substances transporting by the effluent. The enhanced hypoxia in sediments resulting from effluent input promoted the transition of methanotrophic communities from aerobic to anaerobic types and made anaerobic oxidation of CH4 more reliant on sulfur reduction rather than nitrate reduction. The PLS model further revealed that the nutrients brought by effluent input stimulated an increase in DOC content which induced an imbalance between CH4 production and oxidation in sediments by facilitating methanogens but inhibiting methanotrophs, ultimately resulting in an increase in CH4 fluxes. These findings underscore the significance of mangroves receiving effluent input as critical consequent reactors, highlighting the necessity to consider effects of high nutrient enrichment by aquaculture effluent input on GHG emissions and blue C potential in mangroves.},
}

@article {pmid40172536,
year = {2025},
author = {Madison, JD and Osborne, OG and Ellison, A and Garvey Griffith, CN and Gentry, L and Gross, H and Gratwicke, B and Grayfer, L and Muletz-Wolz, CR},
title = {Probiotic colonization of Xenopus laevis skin causes short-term changes in skin microbiomes and gene expression.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0056924},
doi = {10.1128/iai.00569-24},
pmid = {40172536},
issn = {1098-5522},
abstract = {Probiotic therapies have been suggested for amelioration efforts of wildlife disease such as chytridiomycosis caused by Batrachochytrium spp. in amphibians. However, there is a lack of information on how probiotic application affects resident microbial communities and immune responses. To better understand these interactions, we hypothesized that probiotic application would alter microbial community composition and host immune expression in Xenopus laevis. Accordingly, we applied three amphibian-derived and anti-Batrachochytrium bacteria strains (two Pseudomonas spp. and one Stenotrophomonas sp.) to X. laevis in monoculture and also as a cocktail. We quantified microbial community structure using 16S rRNA gene sequencing. We also quantified genes involved in X. laevis immune responses using quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) and skin transcriptomics over 1 and 3-week periods. All probiotic treatments successfully colonized X. laevis skin for 3 weeks, but with differential amplicon sequence variant (ASV) sequence counts over time. Bacterial community and immune gene effects were most pronounced at week 1 post-probiotic exposure and decreased thereafter. All probiotic treatments caused initial changes to bacterial community alpha and beta diversity, including reduction in diversity from pre-exposure anti-Batrachochytrium bacterial ASV relative abundance. Probiotic colonization by Pseudomonas probiotic strain RSB5.4 reduced expression of regulatory T cell marker (FOXP3, measured with RT-qPCR) and caused the greatest gene expression changes detected by transcriptomics. Single bacterial strains and mixed cultures, therefore, altered amphibian microbiome-immune interactions. This work will help to improve our understanding of the role of the microbiome-immune interface underlying both disease dynamics and emergent eco-evolutionary processes.IMPORTANCEAmphibian skin microbial communities have an important role in determining disease outcomes, in part through complex yet poorly understood interactions with host immune systems. Here we report that probiotic-induced changes to the Xenopus laevis frog skin microbial communities also result in significant alterations to these animals' immune gene expression. These findings underscore the interdependence of amphibian skin immune-microbiome interactions.},
}

@article {pmid40172519,
year = {2025},
author = {Chaves-Sierra, C and Botero-Rozo, D and Rodriguez-Cruz, MC and Montoya, C and Romero, HM},
title = {Detection and molecular characterization of 'Candidatus Liberibacter' in Colombian oil palms affected by Lethal Wilt Disease.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-10-24-2079-RE},
pmid = {40172519},
issn = {0191-2917},
abstract = {Lethal wilt (LW), also known as "Marchitez Letal (ML)" in Colombia, is an endemic disease affecting oil palms (Elaeis guineensis Jacq.) and is a leading cause of crop loss. The disease is characterized by the drying of leaflets from the tip to the base, primarily impacting the lower third of the plant and progressively moving upward. This progression leads to physiological disturbances, including necrosis at the tips of immature inflorescence bracts (spines) and the detachment of bunch fruits, ultimately causing wilting. As a phytosanitary measure, infected palms are eradicated to prevent further spread of the disease. The primary goal of this research was to identify the bacteria associated with LW and to validate a molecular detection method. A 16S amplicon-based analysis was employed to identify and compare the microbial diversity in LW-affected palm tissues with those of healthy plants. Among the 16 OTUs corresponding to different bacterial genera found in all LW samples, taxonomic classification and symptomatology suggested that the bacteria closely associated with LW belong to the genus Candidatus Liberibacter. Further phylogenetic analysis indicated that these bacteria are part of the Rhizobiaceae family, grouping closely with other species of the genus Candidatus. Liberibacter. The concentration of the pathogen in different oil palm tissues was determined using droplet digital PCR (ddPCR) and quantitative PCR (qPCR), expressed in copies/µL in the LW samples. This study represents the first report of 'Candidatus Liberibacter sp'. being associated with lethal wilt in oil palms of the Arecaceae family in Colombia. The findings from this research have the potential to contribute significantly to the development of effective management strategies to prevent crop losses.},
}

@article {pmid40172478,
year = {2025},
author = {Wang, H and Zhao, X and Li, D and Meng, L and Liu, S and Zhang, Y and Huo, L},
title = {Marine Metagenome Mining Reveals Lanthipeptides Colwesin A-C, Exhibiting Novel Ring Topology and Anti-inflammatory Activity.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.5c00057},
pmid = {40172478},
issn = {2161-5063},
abstract = {Marine natural products are promising sources for drug discovery due to their unique structures and diverse biological activities. The establishment of the Global Marine Microbiome Genome Catalogue (GOMC) has significantly expanded the repository of natural products derived from marine-associated bacteria. In this study, we identified the Class I lanthipeptide biosynthetic gene cluster col from Colwellia_A sp. based on the GOMC database. Through heterologous expression in Escherichia coli and subsequent structural analysis, we characterized three novel lanthipeptides, colwesins A-C, which possess unique cyclic structures characterized by an exceptionally large number of thioether rings. To the best of our knowledge, colwesin C is the first lanthipeptide simultaneously containing locked, nonoverlapped, and nested ring topologies. These findings highlight the robust ring-forming capacity of Class I lanthipeptide synthetases. Colwesins A-C were found to exhibit anti-inflammatory activity in lipopolysaccharide-induced mouse macrophage RAW264.7 cell lines without detectable cytotoxicity. Overall, our results broaden our understanding of the structural diversity of marine-derived lanthipeptides.},
}

@article {pmid40172215,
year = {2025},
author = {Brito Rodrigues, P and de Rezende Rodovalho, V and Sencio, V and Benech, N and Creskey, M and Silva Angulo, F and Delval, L and Robil, C and Gosset, P and Machelart, A and Haas, J and Descat, A and Goosens, JF and Beury, D and Maurier, F and Hot, D and Wolowczuk, I and Sokol, H and Zhang, X and Ramirez Vinolo, MA and Trottein, F},
title = {Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2486511},
doi = {10.1080/19490976.2025.2486511},
pmid = {40172215},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *COVID-19/microbiology/virology/metabolism ; *Metagenomics ; *Metabolomics ; *Disease Models, Animal ; Cricetinae ; *SARS-CoV-2/genetics ; Aging ; Age Factors ; Dysbiosis/microbiology ; Male ; Bacteria/classification/genetics/metabolism/isolation & purification ; Mesocricetus ; Metabolome ; },
abstract = {Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium, Oscillospiraceae, Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.},
}

Animals
*Gastrointestinal Microbiome
*COVID-19/microbiology/virology/metabolism
*Metagenomics
*Metabolomics
*Disease Models, Animal
Cricetinae
*SARS-CoV-2/genetics
Aging
Age Factors
Dysbiosis/microbiology
Male
Bacteria/classification/genetics/metabolism/isolation & purification
Mesocricetus
Metabolome

@article {pmid40172109,
year = {2025},
author = {Tarracchini, C and Lordan, C and Milani, C and Moreira, LPD and Alabedallat, QM and de Moreno de LeBlanc, A and Turroni, F and Lugli, GA and Mancabelli, L and Longhi, G and Brennan, L and Mahony, J and LeBlanc, JG and Nilaweera, KN and Cotter, PD and van Sinderen, D and Ventura, M},
title = {Vitamin biosynthesis in the gut: interplay between mammalian host and its resident microbiota.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0018423},
doi = {10.1128/mmbr.00184-23},
pmid = {40172109},
issn = {1098-5557},
abstract = {SUMMARYIn recent years, exhaustive efforts have been made to dissect the composition of gut-associated microbial communities and associated interactions with their human host, which are thought to play a crucial role in host development, physiology, and metabolic functions. Although such studies were initially focused on the description of the compositional shifts in the microbiota that occur between different health conditions, more recently, they have provided key insights into the functional and metabolic contributions of the gut microbiota to overall host physiology. In this context, an important metabolic activity of the human gut microbiota is believed to be represented by the synthesis of various vitamins that may elicit considerable benefits to human health. A growing body of scientific literature is now available relating to (predicted) bacterial vitamin biosynthetic abilities, with ever-growing information concerning the prevalence of these biosynthetic abilities among members of the human microbiota. This review is aimed at disentangling if and how cooperative trophic interactions of human microbiota members contribute to vitamin production, and if such, gut microbiota-mediated vitamin production varies according to different life stages. Moreover, it offers a brief exploration of how different diets may influence vitamin production by shaping the overall composition and metabolic activity of the human gut microbiota while also providing preliminary insights into potential correlations between human microbiota-associated vitamin production and the occurrence of human diseases and/or metabolic disorders.},
}

@article {pmid40171165,
year = {2025},
author = {Shi, H and Li, J},
title = {MAGs-based genomic comparison of gut significantly enriched microbes in obese individuals pre- and post-bariatric surgery across diverse locations.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1485048},
pmid = {40171165},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; *Bariatric Surgery ; Metagenome ; Metagenomics/methods ; Genomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; Gastric Bypass ; Computational Biology/methods ; Adult ; },
abstract = {INTRODUCTION: Obesity, a pressing global health issue, is intricately associated with distinct gut microbiota profiles. Bariatric surgeries, such as Laparoscopic Sleeve Gastrectomy (LSG), Sleeve Gastrectomy (SG), and Roux-en-Y Gastric Bypass (RYGB), induce substantial weight loss and reshape gut microbiota composition and functionality, yet their comparative impacts remain underexplored.

METHODS: This study integrated four published metagenomic datasets, encompassing 500 samples, and employed a unified bioinformatics workflow for analysis. We assessed gut microbiota α-diversity, identified species biomarkers using three differential analysis approaches, and constructed high-quality Metagenome-Assembled Genomes (MAGs). Comparative genomic, functional profiling and KEGG pathway analyses were performed, alongside estimation of microbial growth rates via Peak-to-Trough Ratios (PTRs).

RESULTS: RYGB exhibited the most pronounced enhancement of gut microbiota α-diversity compared to LSG and SG. Cross-cohort analysis identified 39 species biomarkers: 27 enriched in the non-obesity group (NonOB_Enrich) and 12 in the obesity group (OB_Enrich). Among the MAGs, 177 were NonOB_Enrich and 14 were OB_Enrich. NonOB_Enrich MAGs displayed enriched carbohydrate degradation profiles (e.g., GH105, GH2, GH23, GH43, and GT0 families) and higher gene diversity in fatty acid biosynthesis and secondary metabolite pathways, alongside significant enrichment in amino acid metabolism (KEGG analysis). Post-surgery, Akkermansia muciniphila and Bacteroides uniformis showed elevated growth rates based on PTRs.

DISCUSSION: These findings underscore RYGB's superior impact on gut microbiota diversity and highlight distinct microbial functional adaptations linked to weight loss, offering insights for targeted therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Obesity/microbiology
*Bariatric Surgery
Metagenome
Metagenomics/methods
Genomics
Bacteria/classification/genetics/isolation & purification/metabolism
Gastric Bypass
Computational Biology/methods
Adult

@article {pmid40170926,
year = {2025},
author = {Zhai, R and Zhao, C and Chang, L and Liu, J and Zhao, T and Jiang, J and Zhu, W},
title = {Diets shape thermal responses in Chinese giant salamanders by altering liver metabolism.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1546912},
pmid = {40170926},
issn = {1664-302X},
abstract = {Diet can influence the thermal performance of ectotherms, providing potential strategies for biological conservation in the context of global warming. The endangered Andrias davidianus is susceptible to heat stress due to energy deficiency in the liver when fed a worm-based diet rich in carbohydrates. A fish-based diet, rich in protein and lipids, improves their thermal performance, but the underlying physiological mechanisms remain unclear. In this study, we used metabolomics and metagenomics to examine the combined effects of temperature (15, 20, and 25°C) and diet (fish-based and worm-based) on liver metabolism and gut microbiota. Our results show that both temperature and diet shape liver metabolism, with several vital metabolic pathways (e.g., TCA cycle and sulfate metabolism) regulated by their combined effects. Notably, diet-dependent thermal responses in energy metabolism were observed, with fish-fed salamanders exhibiting a marked upregulation of the TCA cycle intermediates under heat stress, a response absent in worm-fed individuals. Given the role of TCA cycle in heat susceptibility of A. davidianus, these findings suggest that the TCA cycle likely mediates the interactive effects of temperature and diet on thermal performance. We then examined whether the gut microbiota is also a target of interactive effects or a mediator of the diet's influence on liver metabolism. While both temperature and diet shape microbiota composition, functional shifts occur only in response to temperature, indicating that the microbiota is not a major link between diet and liver metabolism. However, several bacterial groups (e.g., Thiosulfatimonas and Alcanivorax), jointly regulated by temperature and diet, correlate with liver metabolites, suggesting alternative, function-independent pathways through which dietary-related microbial changes may influence liver metabolism and even thermal tolerance. Overall, this study provides molecular insights into the dietary modulation of thermal performance in A. davidianus and highlight the potential of dietary microbial management strategies for amphibian conservation.},
}

@article {pmid40170918,
year = {2025},
author = {Hager, K and Luo, ZH and Montserrat-Diez, M and Ponce-Toledo, RI and Baur, P and Dahlke, S and Andrei, AS and Bulzu, PA and Ghai, R and Urich, T and Glatzel, S and Schleper, C and Rodrigues-Oliveira, T},
title = {Diversity and environmental distribution of Asgard archaea in shallow saline sediments.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1549128},
pmid = {40170918},
issn = {1664-302X},
abstract = {In recent years, our understanding of archaeal diversity has greatly expanded, especially with the discovery of new groups like the Asgard archaea. These archaea show diverse phylogenetic and genomic traits, enabling them to thrive in various environments. Due to their close relationship to eukaryotes, a large number of metagenomic studies have been performed on Asgard archaea. Research on the fine scale distribution, diversity and quantification in saline aquatic sediments where they mostly occur, has, however, remained scarce. In this study, we investigated depths of shallow saline sediment cores from three distinct European environments: the Baltic Sea near Hiddensee, the coastal Lake Techirghiol in Romania, and an estuarine canal in Piran, Slovenia. Based on 16S rDNA amplicon sequencing, we observe variation in the relative abundance and occurrence of at least seven different Asgard groups that are distinct between the three environments and in their depth distribution. Lokiarchaeia and Thorarchaeia emerge as dominant Asgard groups across all sites, reaching maximal relative abundances of 2.28 and 2.68% of the total microbial communities respectively, with a maximal abundance of all Asgard reaching approx. 5.21% in Hiddensee. Quantitative PCR assays provide insights into the absolute abundance of Lokiarchaeia, supporting distinct patterns of distribution across depths in different sediments. Co-occurrence network analysis indicates distinct potential microbial partners across different Asgard groups. Overall, our study shows that Asgard archaea are found as a stable component in shallow sediment layers and have considerably diversified on macro- and microscales.},
}

@article {pmid40170844,
year = {2025},
author = {Zhou, Y and Han, W and Feng, Y and Wang, Y and Liu, X and Sun, T and Xu, J},
title = {Revealing gut microbiota biomarkers associated with melanoma immunotherapy response and key bacteria-fungi interaction relationships: evidence from metagenomics, machine learning, and SHAP methodology.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1539653},
pmid = {40170844},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Melanoma/therapy/immunology/microbiology ; *Metagenomics/methods ; *Immunotherapy/methods ; *Machine Learning ; Male ; *Bacteria/genetics/classification/immunology ; Female ; Fungi/immunology ; Middle Aged ; Skin Neoplasms/immunology/therapy/microbiology ; Biomarkers ; Aged ; Adult ; Treatment Outcome ; },
abstract = {INTRODUCTION: The gut microbiota is associated with the response to immunotherapy in cutaneous melanoma (CM). However, gut fungal biomarkers and bacterial-fungal interactions have yet to be determined.

METHODS: Metagenomic sequencing data of stool samples collected before immunotherapy from three independent groups of European ancestry CM patients were collected. After characterizing the relative abundances of bacteria and fungi, Linear Discriminant Analysis Effect Size (LEfSe) analysis, Random Forest (RF) model construction, and SHapley Additive exPlanations (SHAP) methodology were applied to identify biomarkers and key bacterial-fungal interactions associated with immunotherapy responders in CM.

RESULTS: Diversity analysis revealed significant differences in the bacterial and fungal composition between CM immunotherapy responders and non-responders. LEfSe analysis identified 45 bacterial and 4 fungal taxa as potential biomarkers. After constructing the RF model, the AUC of models built using bacterial and fungal data separately were 0.64 and 0.65, respectively. However, when bacterial and fungal data were combined, the AUC of the merged model increased to 0.71. In the merged model, the following taxa were identified as important biomarkers: Romboutsia, Endomicrobium, Aggregatilinea, Candidatus Moduliflexus, Colwellia, Akkermansia, Mucispirillum, and Rutstroemia, which were associated with responders, whereas Zancudomyces was associated with non-responders. Moreover, the positive correlation interaction between Akkermansia and Rutstroemia is considered a key bacterial-fungal interaction associated with CM immunotherapy response.

CONCLUSION: Our results provide valuable insights for the enrichment of responders to immunotherapy in CM patients. Moreover, this study highlights the critical role of bacterial-fungal interactions in CM immunotherapy.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Melanoma/therapy/immunology/microbiology
*Metagenomics/methods
*Immunotherapy/methods
*Machine Learning
Male
*Bacteria/genetics/classification/immunology
Female
Fungi/immunology
Middle Aged
Skin Neoplasms/immunology/therapy/microbiology
Biomarkers
Aged
Adult
Treatment Outcome

@article {pmid40170341,
year = {2025},
author = {Sorn, S and Matsuura, N and Honda, R},
title = {Metagenome-Assembled Genomes and Metatranscriptome Analysis of Perfluorooctane Sulfonate-Reducing Bacteria Enriched From Activated Sludge.},
journal = {Environmental microbiology},
volume = {27},
number = {4},
pages = {e70087},
doi = {10.1111/1462-2920.70087},
pmid = {40170341},
issn = {1462-2920},
support = {19K22925//Japan Society for the Promotion of Science/ ; 22K19865//Japan Society for the Promotion of Science/ ; //Steel Foundation for Environmental Protection Technology/ ; },
mesh = {*Fluorocarbons/metabolism ; *Alkanesulfonic Acids/metabolism ; *Sewage/microbiology ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Biodegradation, Environmental ; *Metagenome ; *RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; Transcriptome ; Biotransformation ; Phylogeny ; },
abstract = {Per- and polyfluoroalkyl substances (PFAS) exhibit a widespread distribution across diverse global ecosystems throughout their lifecycle, posing substantial risks to human health. The persistence of PFAS makes biodegradation a challenging yet environmentally friendly solution for their treatment. In the authors' previous study, a bacterial consortium capable of reducing perfluorooctane sulfonate (PFOS) was successfully enriched from activated sludge. This study aimed to investigate the array of genes associated with PFOS reduction via biosorption and biotransformation to elucidate the metabolic pathways. Two metagenome-assembled genomes (MAGs) based on 16S rRNA sequences that share 99.86% and 97.88% similarity with Hyphomicrobium denitrificans and Paracoccus yeei, respectively were obtained. They were found to contain several genes encoding enzymes that potentially regulate biofilm formation of biosorption and facilitate the desulfonation and defluorination processes of biotransformation. Transcriptomic analysis demonstrated the high expression levels of these genes, including alkanesulfonate monooxygenase, catechol dioxygenase, (S)-2-haloacid dehalogenase and putative cytochrome P450, suggesting their involvement in PFOS biotransformation. The expression of these genes supports the presence of candidate metabolites of PFOS biotransformation detected in the previous study. These findings emphasise the significant potential of bacterial consortia and the crucial role played by genes encoding enzymes in facilitating the remediation of PFOS contaminants.},
}

*Fluorocarbons/metabolism
*Alkanesulfonic Acids/metabolism
*Sewage/microbiology
*Bacteria/genetics/metabolism/classification/isolation & purification
*Biodegradation, Environmental
*Metagenome
*RNA, Ribosomal, 16S/genetics
Genome, Bacterial
Transcriptome
Biotransformation
Phylogeny

@article {pmid40170118,
year = {2025},
author = {Li, J and Sun, W and Cao, Y and Wu, J and Duan, L and Zhang, M and Luo, X and Deng, Q and Peng, Z and Mou, X and Li, W and Wang, P},
title = {Increased temperature enhances microbial-mediated lignin decomposition in river sediment.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {89},
pmid = {40170118},
issn = {2049-2618},
support = {32200090//National Natural Science Foundation of China/ ; 91951205//National Natural Science Foundation of China/ ; 2023A1515012270//Guangdong Basic and Applied Basic Research Foundation, China/ ; },
mesh = {*Lignin/metabolism ; *Geologic Sediments/microbiology ; *Rivers/microbiology/chemistry ; *Temperature ; *RNA, Ribosomal, 16S/genetics ; Bacteria/metabolism/classification/genetics ; Carbon Dioxide/metabolism ; Carbon Cycle ; Metagenomics ; },
abstract = {BACKGROUND: Lignin, as the most abundant recalcitrant organic carbon in terrestrial ecosystems, plays a crucial role in the Earth's carbon cycle. After lignin entering aquatic environments, portion of it tends to accumulate in sediments, forming a stable carbon relatively reservoir. However, the increasing temperature caused by human activities may impact microbial-mediated lignin decomposition, thereby affecting sedimentary carbon reservoirs. Therefore, revealing how temperature affects microbial-mediated lignin decomposition in river sediment, a topic that remains elusive, is essential for comprehending the feedbacks between river carbon reservoirs and climate. To address this, we conducted stable isotope probing of river surface sediment using [13]C-lignin and [13]C-vanillin, and utilized a series of techniques, including CO2 production analysis, 16S rRNA gene amplicon sequencing, metagenomics, and metatranscriptomics, to identify the lignin-decomposing microbes and the effects of temperature on microbial-mediated lignin decomposition.

RESULTS: We found that elevated temperatures not only increased the total sediment respiration (total CO2) and the CO2 emissions from lignin/vanillin decomposition, but also enhanced priming effects. The [13]C-labled taxa, including Burkholderiales, Sphingomonadales, and Pseudomonadales, were identified as the main potential lignin/vanillin decomposers, and their abundances and activity significantly increased as temperature increased. Furthermore, we observed that increasing temperature significantly increased the activity of lignin decomposing pathways, including β-aryl ether fragments and 4,5-PDOG pathway. Additionally, as temperature increases, the transcriptional abundances of other carbon cycling related genes, such as pulA (starch decomposition) and xyla (hemicellulose decomposition), also exhibited increasing trends. Overall, our study elucidated the potential lignin-decomposing microbes and pathways in river sediment and their responses to temperature increasing.

CONCLUSIONS: Our study demonstrated that the temperature increasing can increase the rate of lignin/vanillin decomposition via affecting the activity of lignin-decomposing microbes. This finding indicates that the ongoing intensification of global warming may enhance the decomposition of recalcitrant organic carbon in river sediment, thereby impacting global carbon cycling. Video Abstract.},
}

*Lignin/metabolism
*Geologic Sediments/microbiology
*Rivers/microbiology/chemistry
*Temperature
*RNA, Ribosomal, 16S/genetics
Bacteria/metabolism/classification/genetics
Carbon Dioxide/metabolism
Carbon Cycle
Metagenomics

@article {pmid40169660,
year = {2025},
author = {Legrand, TPRA and Alexandre, PA and Wilson, A and Farr, RJ and Reverter, A and Denman, SE},
title = {Genome-centric metagenomics reveals uncharacterised microbiomes in Angus cattle.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {547},
pmid = {40169660},
issn = {2052-4463},
mesh = {Animals ; Cattle/microbiology ; *Metagenomics ; *Microbiota ; *Feces/microbiology ; Metagenome ; Saliva/microbiology ; Mouth/microbiology ; },
abstract = {Understanding the intricate nexus between cattle health and microbiome dynamics holds profound implications for enhancing animal productivity and welfare. However, our understanding of the role of these microbial communities is limited in beef cattle, especially in understudied body sites such as the oral and nasal microbiome. Here, using a genome-centric metagenomics approach, we recovered substantial metagenome-assembled genomes (MAGs) from the faecal, oral and nasal microbiome of Australian Angus cattle from different herds and life stages. The MAGs recovered from faecal samples were dominated by Bacillota and Bacteroidota, while the MAGs from saliva and nasal mucus samples were mainly associated with Pseudomonadota, Actinomycetota and Bacteroidota. Functional annotation of the MAGs revealed enriched pathways involved in the production of some amino acids, nucleic acids and short chain fatty acids (SCFA). The metabolic capacities of the MAGs were correlated with their taxonomy, notably at the phylum level. Overall, this study provides a comprehensive catalogue of MAGs to further our understanding of their role in the health and fitness of beef cattle.},
}

Animals
Cattle/microbiology
*Metagenomics
*Microbiota
*Feces/microbiology
Metagenome
Saliva/microbiology
Mouth/microbiology

@article {pmid40169555,
year = {2025},
author = {Li, H and Liu, P and Sun, T and Li, Y and Wu, J and Huang, Y and Yang, J and Yuan, M and Zhang, J and Yang, J and Wong, ML and Licinio, J and Zheng, P},
title = {Dynamic alterations of depressive-like behaviors, gut microbiome, and fecal metabolome in social defeat stress mice.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {115},
pmid = {40169555},
issn = {2158-3188},
mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Stress, Psychological/metabolism/microbiology ; *Feces/microbiology/chemistry ; Male ; *Social Defeat ; *Metabolome ; *Disease Models, Animal ; *Depressive Disorder, Major/metabolism/microbiology ; *Behavior, Animal ; *Anhedonia ; Humans ; Mice, Inbred C57BL ; Female ; RNA, Ribosomal, 16S/genetics ; Depression/metabolism/microbiology ; },
abstract = {Gut microbiome is implicated in the onset and progression of major depressive disorder (MDD), but the dynamic alterations of depressive symptoms, gut microbiome, and fecal metabolome across different stages of stress exposure remain unclear. Here, we modified the chronic social defeat stress (CSDS) model to evaluate mice subjected to social defeat stress for 1, 4, 7, and 10 days. Behavioral tests, 16S rRNA, metagenomics, and fecal metabolomics were conducted to investigate the impact of stress exposure on behaviors, gut microbiota and fecal metabolites. We observed that depressive-like behaviors, such as anhedonia and social avoidance, worsened significantly as stress exposure increased. The microbial composition, function, and fecal metabolites exhibited distinct separations across the different social defeat stress groups. Mediation analysis identified key bacteria, such as Lachnospiraceae_UCG-001 and Bacteroidetes, and fecal metabolites like valeric acid and N-acetylaspartate. In our clinical depression cohort, we confirmed that fecal valeric acid levels, were significantly lower in depressive-like mice and MDD patients, correlating closely with stress exposure and anhedonia in mice. Further analysis of serum and brain metabolites in mice revealed sustained changes of N-acetylaspartate abundance in fecal, serum, and cortical samples following increasing stress exposure. Together, this study elucidated the characteristics of depressive-like behaviors, gut microbiome, and fecal metabolome across various social defeat stress exposure, and identified key bacteria and fecal metabolites potentially involved in modulating social defeat stress response and depressive-like behaviors, providing new insights into the pathogenesis and intervention of depression.},
}

Animals
*Gastrointestinal Microbiome
Mice
*Stress, Psychological/metabolism/microbiology
*Feces/microbiology/chemistry
Male
*Social Defeat
*Metabolome
*Disease Models, Animal
*Depressive Disorder, Major/metabolism/microbiology
*Behavior, Animal
*Anhedonia
Humans
Mice, Inbred C57BL
Female
RNA, Ribosomal, 16S/genetics
Depression/metabolism/microbiology

@article {pmid40169141,
year = {2025},
author = {Zhang, J and Ying, X and Hu, R and Huang, Y and Wang, R and Wu, L and Han, D and Ma, R and He, K},
title = {Metagenomic and metabolomic analysis of gut microbiome's role in spinal cord injury recovery in rats.},
journal = {Biomolecules & biomedicine},
volume = {},
number = {},
pages = {},
doi = {10.17305/bb.2025.12164},
pmid = {40169141},
issn = {2831-090X},
abstract = {Spinal cord injury (SCI) induces profound systemic changes, including disruptions in gut microbiome composition and host metabolism. This study aimed to investigate the impact of SCI on gut microbial diversity and serum metabolites in rats, and to explore potential microbiome-metabolite interactions that may influence recovery. Male Sprague-Dawley (SD) rats were assigned to either SCI or sham-operated groups. Fecal samples were collected for whole-genome metagenomic sequencing, and serum samples were analyzed using untargeted metabolomics. Gut microbial composition and diversity were assessed using α- and β-diversity indices, while Linear discriminant analysis effect size (LEfSe) identified differentially abundant taxa. Metabolomic pathway analysis was performed to detect significant changes in serum metabolites, and Spearman's correlation was used to evaluate associations between gut microbes and metabolites. SCI significantly altered gut microbiota composition, with increased proportions of Ligilactobacillus and Staphylococcus, and decreased proportions of Lactobacillus and Limosilactobacillus. Metabolomic analysis revealed disrupted energy metabolism and elevated oxidative stress in SCI rats, as indicated by increased serum levels of pyruvate and lactic acid. Correlation analysis further identified significant associations between specific gut bacteria and key metabolites, suggesting microbiome-driven metabolic dysregulation following SCI. These findings highlight significant interactions between the gut microbiota and host metabolism after SCI and suggest that microbiome-targeted interventions may hold therapeutic potential for improving recovery by modulating metabolic function and oxidative stress responses.},
}

@article {pmid40156868,
year = {2025},
author = {Yang, W and Luyten, Y and Reister, E and Mangelson, H and Sisson, Z and Auch, B and Liachko, I and Roberts, RJ and Ettwiller, L},
title = {Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.},
journal = {Nucleic acids research},
volume = {53},
number = {6},
pages = {},
pmid = {40156868},
issn = {1362-4962},
support = {//New England Biolabs, Inc./ ; R44AI172703/GF/NIH HHS/United States ; //Bill & Melinda Gates Foundation/ ; },
mesh = {*Methyltransferases/metabolism/genetics ; *Microbiota/genetics ; DNA Methylation ; Bacteriophages/genetics/enzymology ; High-Throughput Nucleotide Sequencing ; Bacteria/genetics/enzymology ; Substrate Specificity ; Bacterial Proteins/metabolism/genetics ; Sequence Analysis, DNA/methods ; DNA, Viral/genetics/metabolism ; },
abstract = {Methylation patterns in bacteria can be used to study restriction-modification or other defense systems with novel properties. While m4C and m6A methylation are well characterized mainly through PacBio sequencing, the landscape of m5C methylation is under-characterized. To bridge this gap, we performed RIMS-seq2 (rapid identification of methyltransferase specificity sequencing) on microbiomes composed of resolved assemblies of distinct genomes through proximity ligation. This high-throughput approach enables the identification of m5C methylated motifs and links them to cognate methyltransferases directly on native microbiomes without the need to isolate bacterial strains. Methylation patterns can also be identified on bacteriophage DNA and compared with host DNA, strengthening evidence for phage-host interactions. Applied to three different microbiomes, the method unveiled over 1900 motifs that were deposited in REBASE. The motifs include a novel eight-base recognition site (CATm5CGATG) that was experimentally validated by characterizing its cognate methyltransferase. Our findings suggest that microbiomes harbor arrays of untapped m5C methyltransferase specificities, providing insights into bacterial biology and biotechnological applications.},
}

*Methyltransferases/metabolism/genetics
*Microbiota/genetics
DNA Methylation
Bacteriophages/genetics/enzymology
High-Throughput Nucleotide Sequencing
Bacteria/genetics/enzymology
Substrate Specificity
Bacterial Proteins/metabolism/genetics
Sequence Analysis, DNA/methods
DNA, Viral/genetics/metabolism

@article {pmid40169073,
year = {2025},
author = {Sun, L and Yin, Y and Guo, Y and Chen, H and Wang, H},
title = {Metagenomic Next-Generation Sequencing Enhances the Diagnosis of Q Fever: A Retrospective Observational Study.},
journal = {Travel medicine and infectious disease},
volume = {},
number = {},
pages = {102845},
doi = {10.1016/j.tmaid.2025.102845},
pmid = {40169073},
issn = {1873-0442},
abstract = {BACKGROUND: Q fever, a global zoonosis, poses a significant challenge for public health due to its varied and nonspecific clinical presentations, making diagnosis difficult. Metagenomic next-generation sequencing (mNGS) is a potential tool for diagnosing Q fever.

METHODS: This retrospective observational study was conducted on patients with Q fever admitted to Peking University People's Hospital, from May 2023 to November 2024. mNGS was performed using the patient's peripheral blood, and the qPCR of Coxiella burnetii was also adopted. Subsequently, the clinical data of patients diagnosed with Q fever were systematically evaluated.

RESULTS: Twelve peripheral blood samples of 12 patients were detected Coxiella burnetii positive by mNGS. Most patients were male (10, 83.33%). Fever (12, 100%), muscle soreness (8, 66.7%), and headache (4, 33.3%) were the most common clinical manifestations. Specific qPCR of Coxiella burnetii was detected positive in 8 patients. Chronic Q fever was diagnosed in two patients, who had aortic valve replacement, and their immunological markers, like anti-nuclear were elevated. Once the diagnosis was clear, proper antibiotics were used, and all patients were discharged in better health.

CONCLUSION: Metagenomic next-generation sequencing enhances the diagnosis of Q fever, especially for patients displaying atypical and various clinical symptoms and having unclear epidemiological data or histories of antibiotic use.},
}

@article {pmid40169018,
year = {2025},
author = {Wallace, MA and Wille, M and Geoghegan, J and Imrie, RM and Holmes, EC and Harrison, XA and Longdon, B},
title = {Making sense of the virome in light of evolution and ecology.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2044},
pages = {20250389},
doi = {10.1098/rspb.2025.0389},
pmid = {40169018},
issn = {1471-2954},
support = {//Leverhulme Trust/ ; //National Health and Medical Research Council (NHMRC)/ ; //Royal Society/ ; /WT_/Wellcome Trust/United Kingdom ; //Webster Family Chair in Viral Pathogenesis/ ; //New Zealand Royal Society Rutherford Discovery Fellowship/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; },
mesh = {*Virome ; *Viruses/genetics ; Biological Evolution ; Metagenomics ; Ecology ; Ecosystem ; Phylogeny ; },
abstract = {Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.},
}

*Virome
*Viruses/genetics
Biological Evolution
Metagenomics
Ecology
Ecosystem
Phylogeny

@article {pmid40168930,
year = {2025},
author = {Tang, GX and Huang, YH and Feng, LW and Hu, YC and Wei, JL and Lü, H and Liu, LH and Zhao, HM and Xiang, L and Li, H and Mo, CH and Li, YW and Cai, QY},
title = {New insights into rhizosphere bacterial community shaped by lettuce genotypes for divergent degradation efficiencies of phthalates.},
journal = {Journal of hazardous materials},
volume = {492},
number = {},
pages = {138077},
doi = {10.1016/j.jhazmat.2025.138077},
pmid = {40168930},
issn = {1873-3336},
abstract = {Rhizosphere dissipation of organic pollutants benefits safe utilization of the polluted agricultural soil. Nevertheless, dissipation variation of phthalates (PAEs) in rhizosphere among different vegetable genotypes and the related microbial mechanisms remain unknown. Here, twelve lettuce cultivars with different genetic relationships identified by 18S rRNA gene sequencing were cultivated in soil spiked with di-(2-ethylhexyl) phthalate (DEHP). Bacterial communities and function genes in rhizosphere of lettuce were analyzed by 16S rRNA gene and metagenomic sequencing. Results showed significant variations in DEHP concentrations of roots (2.8-15.3 mg/kg) and shoots (0.70-1.8 mg/kg) among 12 cultivars. Notably, cultivars L11 and L12 showed the lowest DEHP accumulation in roots and shoots, being lower by 82 % and 58 % than the highest accumulators (cultivars L5 and L6), respectively. This accumulation variation was closely connected with their genetic relationships and exhibited genotype-dependent trait. The significantly different bacterial community diversities and structures were recorded in rhizosphere among 12 cultivars. Especially, bacterial communities in rhizosphere of cultivars L11 and L12 (low-DEHP accumulators with high DEHP dissipation) strengthened their adaptation by enriching pollutant-resistant taxa, increasing extracellular polymeric substance contents and biofilm formation, as well as constructing complex ecological networks under DEHP pollution. Moreover, PAE-degrading bacteria and genes (e.g., hydrolase65, phtAb, and pcaI) in rhizosphere were enriched by low-DEHP accumulators, which benefited DEHP removal and subsequently safe agricultural products. This study provides new insights into microbial mechanisms on rhizosphere DEHP degradation and its correlation with accumulation variation among different crop genotypes.},
}

@article {pmid40168814,
year = {2025},
author = {Harish, J and Prasannakumar, MK and Venkateshbabu, G and Karan, R and Mahesh, HB and Devanna, P and Sarangi, AN and Patil, SS and Tejashwini, V and Lohithaswa, HC and Kagale, S},
title = {Molecular and genomic insights into the pathogenicity of Sarocladium zeae causing maize stalk rot disease.},
journal = {Microbiological research},
volume = {296},
number = {},
pages = {128146},
doi = {10.1016/j.micres.2025.128146},
pmid = {40168814},
issn = {1618-0623},
abstract = {Post-flowering stalk rot (PFSR) of maize has been traditionally associated with Fusarium verticillioides. Conversely, this study reveals Sarocladium zeae as a new phytopathogen responsible for the disease. This research was conducted to gain a comprehensive understanding of S. zeae by investigating its pathogenic mechanisms, profiling its metabolome, and deciphering its genomic characteristics. Maize stalks displaying stalk rot symptoms were collected from various regions of India. S. zeae was isolated and characterized using ITS and TEF-1α sequencing. Cultures of S. zeae exhibited slower growth on PDA medium compared to F. verticillioides, which dominated due to its rapid growth rate. Pathogenicity was confirmed through a toothpick inoculation assay. The symptoms induced by S. zeae was characterized by powdery, dry, pale brown-black discoloration, were distinct from the typical dark-brown lesions of Fusarium stalk rot. Enzymatic assays revealed increased activity of β-glucosidase, cellulase, and pectate lyase in infected stalks, while qPCR analysis showed the upregulation of endoglucanase and β-glucosidase genes in infected stalks underscored the critical roles of cellulase and β-glucosidase in pathogenicity Metagenomic analysis identified S. zeae as the predominant species in infected stalk samples. Genome assembly revealed the pathogen's complete genetic repertoire, including genes encoding effector proteins and CAZymes involved in cell wall degradation. Moreover, we have demonstrated that the S. zeae as a causal agent of maize stalk rot and further shedding light on its transition from an endophytic to a pathogenic lifestyle. Taken together, this research represents the first report to attribute maize stalk rot to S. zeae and to present its complete genome assembly, significantly advancing the understanding of its biology and pathogenic potential.},
}

@article {pmid40168753,
year = {2025},
author = {Ji, X and Yu, X and Xu, Y and Wu, Q and Madadi, M and Khaneghah, AM},
title = {Initial acidity regulates microbial sulfur metabolism in the spontaneous fermentation of sesame flavor-type baijiu.},
journal = {International journal of food microbiology},
volume = {435},
number = {},
pages = {111182},
doi = {10.1016/j.ijfoodmicro.2025.111182},
pmid = {40168753},
issn = {1879-3460},
abstract = {Volatile sulfur compounds play a crucial role in fermented foods, however, their metabolism during spontaneous food fermentation remains underexplored. With 3-(methylthio)-1-propanal as a case, we revealed the effect of initial acidity on the sulfur metabolism during sesame flavor-type baijiu fermentation. Results showed that the content of 3-(methylthio)-1-propanal reached 383.29 μg/kg with 1.8 mmol/10 g of the initial acidity, and it decreased to 320.54 μg/kg when the initial acidity increased to 2.4 mmol/10 g. Metagenomic analysis identified 11 core microbes associated with sulfur metabolism, characterized by gene abundance (> 0.5 %) and catalytic enzyme distribution frequency (> 10 %). Saccharomyces was the main producer of sulfur compounds. Lactobacillus was an important player in the methyl cycle pathway of sulfur metabolism. Low initial acidity increased the abundance of Lactobacillus and the content of genes associated with the methyl cycle pathway (P < 0.05). This resulted in a significant increase of methionine (253.26 mg/kg) (P < 0.05) and 3-(methylthio)-1-propanal contents (383.29 μg/kg) (P < 0.05). In simulated fermentation, the content of 3-(methylthio)-1-propanal significantly increased by 2.91 folds when Saccharomyces cerevisiae was cocultured with Lactobacillus acetotolerans (P < 0.05), and the transcription of genes related to sulfur metabolism significantly increased by 33.71 folds (P < 0.05). Results indicated that low initial acidity increased the abundance of Lactobacillus, which mediates the methyl cycle pathway in the sulfur metabolism, thereby increasing the contents of methionine and volatile sulfur compounds. This work provided insight into the regulation of metabolic mechanisms of volatile sulfur compounds in baijiu fermentation.},
}

@article {pmid40168325,
year = {2025},
author = {Yun, H and Seo, JH and Kim, YK and Yang, J},
title = {Examining the bacterial diversity including extracellular vesicles in air and soil: implications for human health.},
journal = {PloS one},
volume = {20},
number = {4},
pages = {e0320916},
doi = {10.1371/journal.pone.0320916},
pmid = {40168325},
issn = {1932-6203},
mesh = {*Extracellular Vesicles/metabolism ; *Soil Microbiology ; Humans ; *Bacteria/genetics/classification/metabolism ; *RNA, Ribosomal, 16S/genetics ; Air Microbiology ; Microbiota ; Biodiversity ; Metagenomics/methods ; },
abstract = {As the significance of human health continues to rise, the microbiome has shifted its focus from microbial composition to the functional roles it plays. In parallel, interest in ultrafine particles associated with clinically important impact has been increasing. Bacterial extracellular vesicles (BEVs), involved in systemic microbiome activity, are nano-sized spherical vesicles (20 - 100 nm in diameter) containing DNA, RNA, proteins, and lipids. They are known to be absorbed into the body potentially through air and soil, circulate in the blood, and directly impact diseases by affecting organs. Therefore, the aim of this study is to examine the biodiversity of bacteria and BEVs and predicted functional pathways. We sampled air and soil samples in Seoul, Korea and analyzed metagenomics based on 16S rRNA sequencing. At the phylum levels, Firmicutes in BEVs from soil and air were significantly higher than in bacteria, and Acidobacteria in both bacteria and BEVs from soil were significantly higher than from air (p < 0.05). The most dominant genera were Pseudomonas in bacteria from air and soil; and Escherichia-Shigella in BEVs from air and soil. In addition, Two-component system (ko02020) and ATP-binding cassette transporters (ko02010) were dominant functional pathways in both air and soil. The most functional pathways and orthologous groups were significantly different between air and soil (p < 0.05). In conclusion, human health can be affected differently depending on type of environment. Future study is necessary to have a better understanding of human health effects from environmental microbiota.},
}

*Extracellular Vesicles/metabolism
*Soil Microbiology
Humans
*Bacteria/genetics/classification/metabolism
*RNA, Ribosomal, 16S/genetics
Air Microbiology
Microbiota
Biodiversity
Metagenomics/methods

@article {pmid40167463,
year = {2025},
author = {Sun, C and Liu, H and Teng, J and Feng, W and Wang, D and Wang, X and Zhao, J and Wang, Q},
title = {Impact of Microplastic Exposure on Sand Crab Scopimera globosa Behavior: Implications for Microplastic Transport and Sulfur Cycling through Bioturbation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01192},
pmid = {40167463},
issn = {1520-5851},
abstract = {The accumulation of microplastics (MPs) in estuarine regions and their ecological consequences have become global environmental concerns. Estuarine sediments function as major sinks for MPs and hotspots for critical biogeochemical processes, which are significantly influenced by benthic bioturbation. However, the impacts of MPs on the behavior of highly mobile benthic organisms and the ecological effects of bioturbation activities remain poorly understood. This study utilized laboratory simulation experiments, AI-based behavioral tracking, and metagenomic sequencing to systematically examine the effects of sand crab bioturbation on MPs migration, sediment physicochemical properties and sulfur cycling processes. Results demonstrated that sand crab bioturbation substantially enhanced the vertical migration of MPs, with fluxes to surface layers and the overlying water increasing by 27-fold compared to undisturbed conditions. Exposure to PE-MPs reduced sand crabs' surface foraging intensity and induced behavioral abnormalities. The crabs actively avoided MPs, exhibiting a preference for burrowing and residing in deeper sediment layers. This behavioral shift significantly altered microbial community distributions, with an increase of Pseudomonadota abundance and a decline of sulfate-reducing bacteria Thermodesulfobacteriota abundance. Furthermore, bioturbation accelerated sulfate oxidation in deeper sediments while inhibited dissimilatory sulfate reduction. This study is the first to identify the role of bioturbation in promoting the upward migration of MPs in sediments. Altered sand crab bioturbation will impact sediment biogeochemistry, estuarine function, and coastal resilience.},
}

@article {pmid40167332,
year = {2025},
author = {Curto, M and Veríssimo, A and Riccioni, G and Santos, CD and Ribeiro, F and Jentoft, S and Alves, MJ and Gante, HF},
title = {Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e14105},
doi = {10.1111/1755-0998.14105},
pmid = {40167332},
issn = {1755-0998},
support = {CEEC/0482/2020//Fundação para a Ciência e a Tecnologia/ ; DL 57/2016/CP1440/CP1646/CT0001//Fundação para a Ciência e a Tecnologia/ ; LA/P/0069/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/BIA-CBI/31644/2017//Fundação para a Ciência e a Tecnologia/ ; UID/04292/2020//Fundação para a Ciência e a Tecnologia/ ; UID/BIA/00329/2020//Fundação para a Ciência e a Tecnologia/ ; UIDP/50027/2020//Fundação para a Ciência e a Tecnologia/ ; LA/P/0048/2020//Fundação para a Ciência e a Tecnologia/ ; 857251//Horizon 2020 Framework Programme/ ; STG/21/044//KU Leuven/ ; },
abstract = {Environmental DNA (eDNA) metagenomics sequences all DNA molecules present in environmental samples and has the potential of identifying virtually any organism from which they are derived. However, due to unacceptable levels of false positives and negatives, this approach is underexplored as a tool for biodiversity monitoring across the tree of life, particularly for non-microscopic eukaryotes. We present SeqIDist, a framework that combines multilocus BLAST matches against several reference databases followed by an analysis of sequence identity distribution patterns to disentangle false positives while revealing new biodiversity and increasing the accuracy of metagenomic approaches. We tested SeqIDist on an eDNA metagenomic dataset from a riverine site and compared the results to those obtained with an eDNA metabarcoding approach for benchmarking purposes. We start by characterising the biological community (~2000 taxa) across the tree of life at low taxonomic levels and show that eDNA metagenomics has a higher sensitivity than eDNA metabarcoding in discovering new diversity. We show that limited representation of whole genome sequences in reference databases can lead to false positives. For non-microscopic eukaryotes, eDNA metagenomic data often consist of a few sparse, anonymous sequences scattered across the genome, making metagenome assembly methods unfeasible. Finally, we infer eDNA source and residency time using read length distributions as a measure of decay status. The higher accuracy of SeqIDist opens the discussion of the potential of eDNA metagenomics for archived samples and its implementation in long-term biodiversity monitoring at a planetary scale.},
}

@article {pmid40166061,
year = {2025},
author = {Zhang, L and Guo, Y and Wang, X and Gai, W and Liu, L},
title = {Severe adenovirus pneumonia complicated by acute respiratory distress syndrome in immunocompetent patients: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1524783},
pmid = {40166061},
issn = {2296-858X},
abstract = {BACKGROUND: Human adenovirus (HAdV) is one of the most important pathogens detected in acute respiratory illness in pediatric and immunocompromised patients, but it is relatively rare to develop severe pneumonia in immunocompetent patients. We analyzed the clinical features, as well as the diagnosis and treatment processes, to provide a reference for clinical practice.

CASE PRESENTATION: We report a case of severe pneumonia caused by HAdV, complicated by acute respiratory distress syndrome (ARDS), in an immunocompetent patient with no underlying conditions. Chest computed tomography (CT) revealed consolidation in the right lower lung. Conventional microbial tests were negative, but metagenomic next-generation sequencing (mNGS) identified a large number of HAdV sequences in blood and sputum. Together with the clinical symptoms, this confirmed the diagnosis of severe pneumonia caused by HAdV. The patient was discharged after timely treatment with cidofovir.

CONCLUSION: In our study, we described a rare case of severe pneumonia caused by HAdV, complicated by ARDS, in an immunocompetent patient. mNGS proves to be an effective diagnostic tool for guiding treatment decisions.},
}

@article {pmid40165946,
year = {2025},
author = {Guo, Z and Wang, X and Li, Y and Zhang, Y and Guo, P and Zhang, J and Zhang, Z and Ma, X},
title = {Evaluation of the therapeutic effect of pomegranate peel ginger ultrafine powder on chronic enteritis in mice by regulating intestinal microbiota.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1563225},
pmid = {40165946},
issn = {1664-3224},
mesh = {Animals ; Mice ; *Pomegranate/chemistry ; *Zingiber officinale ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Enteritis/drug therapy/microbiology/veterinary ; *Aquaporins/metabolism/genetics ; Cytokines/metabolism ; Chronic Disease ; Disease Models, Animal ; Powders ; Plant Extracts/pharmacology/administration & dosage ; Aquaporin 3 ; Aquaporin 4 ; },
abstract = {To explore the efficacy and mechanism of Pomegranate peel Ginger ultrafine powder (PG) in treating chronic enteritis in mice. Sixty SPF-grade mice were randomly divided into a blank group, a model group, loperamide hydrochloride group (5 mg/kg), a high-dose PG group (100 mg/kg), a medium-dose group (50 mg/kg), and a low-dose group (25 mg/kg), with 10 mice in each group and an equal number of males and females. A chronic enteritis mouse model was established using a multifactorial method of low temperature + ice water + castor oil. The blank group was given an equal amount of physiological saline intragastrically, while the other groups were intervened with corresponding drugs for 7 consecutive days. After 7 days, samples were collected, and Enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of interleuckin 1β (IL-1β), IL-6, and Tumor necrosis factorα(TNF-α) in mouse serum. HE staining was used to examine the pathological changes in the small intestine. oxidative reagent kits were used to detect the content of total superoxide dismutase(T-SOD) and Malondialdehyde (MDA) in the small intestine. Western blot was used to detect the expression of Aquaporin 8(AQP8) proteins in the small intestine. Real time quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to detect the expression of AQP3, AQP4, AQP8, and Sodium/hydrogen exchanger 8 (NHE8) genes in the small intestine. metagenomics was used to detect the gut microbiota in mouse feces. Compared with the model group, all doses of PG groups reduced the levels of IL-1β, IL-6, and TNF-α in mouse serum (P<0.05), improved pathological changes in the small intestine, increased the content of T-SOD in the small intestine tissue, reduced the content of MDA, increased the expression of AQP4 and AQP8 mRNA, and decreased the expression of AQP3 and NHE8 mRNA (P<0.05), increased the expression of AQP8 protein. PG could improve the pathological changes of chronic enteritis in mice, enhance antioxidant capacity, and alleviate diarrhea caused by chronic enteritis by downregulating the expression of intestinal epithelial transport proteins and acute-phase proteins, and altering gut microbiota.},
}

Animals
Mice
*Pomegranate/chemistry
*Zingiber officinale
*Gastrointestinal Microbiome/drug effects
Male
Female
*Enteritis/drug therapy/microbiology/veterinary
*Aquaporins/metabolism/genetics
Cytokines/metabolism
Chronic Disease
Disease Models, Animal
Powders
Plant Extracts/pharmacology/administration & dosage
Aquaporin 3
Aquaporin 4

@article {pmid40165815,
year = {2025},
author = {Battur, M and Aaqil, M and Zheng, J and Lin, HX and Chuluunotgon, B and Zorigtbaatar, T and Zhao, C and Tian, Y},
title = {Exploring the effects of milk-enriched walnut soy sauce: Insights from GC-IMS and metagenomics approach to flavor and microbial shifts.},
journal = {Food chemistry: X},
volume = {27},
number = {},
pages = {102364},
pmid = {40165815},
issn = {2590-1575},
abstract = {This study investigates the impact of milk addition on the fermentation of walnut soy sauce, using Gas Chromatography-Ion Mobility Spectrometry (GC-IMS) and metagenomics to analyze flavor profiles and microbial dynamics. GC-IMS analysis showed significant increases in volatile compounds such as esters (ethyl acetate), aldehydes (hexanal), and alcohols (isoamyl alcohol), enhancing the aroma and taste. Metagenomic analysis revealed that milk increased microbial diversity, with Weissella and Lactobacillus dominating early fermentation. The milk-enriched soy sauce (SYM) exhibited higher amino acid nitrogen (2.67 g/L), and total nitrogen (7.18 g/L) compared to the control, indicating improved nutritional quality. Protease activity peaked at 2438.5 U/g for neutral protease, supporting efficient protein hydrolysis. Relative Odor Activity Value (ROAV) analysis identified 29 key flavor compounds, including 3-methyl butanol and ethyl 2-methyl butyrate, which contributed fruity and buttery notes to SYM. These results suggest that milk enhances microbial growth and improves both flavor and nutritional quality of walnut soy sauce.},
}

@article {pmid40165787,
year = {2025},
author = {Huang, Z and Wang, J and He, X and Zhang, M and Ren, X and Yu, W and Yao, S and Ji, K},
title = {Divergent profiles of rhizosphere soil carbon and nitrogen cycling in Pinus massoniana provenances with different types of carbon storage.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1537173},
pmid = {40165787},
issn = {1664-302X},
abstract = {INTRODUCTION: In subtropical China, P. massoniana is a timber tree species which have a great potential for carbon sequestration. However, few studies have investigated how varying levels of carbon storage in P. massoniana provenances affect the soil microbial functional potential related to nutrient cycling within the rhizosphere.

METHODS: In this investigation, metagenomic sequencing was employed to explore the differences in carbon and nitrogen cycling capabilities among rhizosphere microbial communities within P. massoniana provenances, categorized by high, medium, and low levels of carbon storage.

RESULTS: Our findings revealed a significant increase in the relative abundance of Acidobacteriota and Ascomycota by 23 and 61%, respectively, whereas Basidiomycota significantly decreased by 8% in the rhizosphere of P. massoniana provenances with high carbon storage compared with those with low carbon storage. The variability in carbon storage among P. massoniana provenances was linked to marked disparities in the presence of key genes essential for carbon and nitrogen cycling within their rhizosphere soils.

DISCUSSION: Notably, in P. massoniana provenances characterized by high carbon storage, the rhizosphere presented a significantly elevated presence of genes associated with carbon decomposition, carbon assimilation, methane generation, and denitrification, in stark contrast to provenances with medium and low carbon storage. Furthermore, P. massoniana provenances with high carbon storage rates presented increased transformation and availability of soil carbon and nitrogen, along with increased potential for ecological restoration. Moreover, the rhizosphere soil nitrification of P. massoniana provenances with low carbon storage surpassed that of other provenances, leading to increased available nitrogen content and elevated nitrate leaching risk. In the P. massoniana rhizosphere, critical soil factors, including soil organic carbon (SOC), total nitrogen (TN), pH, and nitrate nitrogen (NO3 [-]-N) content, significantly shape the functionality of genes associated with carbon and nitrogen cycling. In conclusion, our study lays a scientific foundation for establishing P. massoniana plantations and identifying P. massoniana provenances with superior ecological value and potential.},
}

@article {pmid40165255,
year = {2025},
author = {Xie, B and Dong, C and Zhao, X and Qu, L and Lv, Y and Liu, H and Xu, J and Yu, Z and Shen, H and Shang, Y and Zhao, X and Zhang, J},
title = {Structural and functional alteration of the gut microbiomes in ICU staff: a cross-sectional analysis.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {141},
pmid = {40165255},
issn = {1466-609X},
support = {82402568//National Natural Science Foundation of China/ ; 82472223//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/physiology ; *Intensive Care Units/organization & administration/statistics & numerical data ; Male ; Female ; Prospective Studies ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/analysis/genetics ; Cohort Studies ; Feces/microbiology ; Health Personnel/statistics & numerical data ; },
abstract = {BACKGROUND: 16S rRNA sequencing has revealed structural alterations in the gut microbiomes of medical workers, particularly those working in intensive care unit (ICU). This study aims to further compare the taxonomic and functional characteristics of gut microbiomes between ICU staff and non-medical individuals using metagenomic sequencing.

METHODS: A prospective cross-sectional cohort study was conducted, fecal samples from 39 individuals in each group-ICU staff and non-medical subjects were analyzed using metagenomic sequencing. PERMANOVA (using the adonis function) was employed to analyze the genus-level profiles and assess the impact of individual parameters on the gut microbiome. Multiple databases were utilized to annotate and compare the functional differences in gut microbiomes between the two groups.

RESULTS: We observed that ICU staff exhibited a significant decrease in gut microbiome diversity, characterized by a marked decline in Actinobacteria and a substantial increase in Bacteroides and Bacteroidaceae. CAZy annotation revealed a notable increase in carbohydrate-active enzymes within the ICU staff cohort. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further indicated an elevated risk of endocrine and metabolic disorders, along with enhanced glycan biosynthesis and metabolism. Additionally, KEGG pathway enrichment analysis highlighted significant enrichment in cancer-related pathways. Analysis using the Virulence Factor Database (VFDB) showed a higher abundance of virulence factors associated with immune modulation, invasion, and antimicrobial activity/competitive advantage among ICU staff. Notably, no discernible difference in the presence of antibiotic resistance genes within the gut microbiomes was observed between the two groups. Importantly, all aforementioned differences demonstrated clear gender disparities.

CONCLUSIONS: Our findings indicated that ICU staff exhibited a reduction in gut microbiome diversity which was associated with an increase in virulence factors and carbohydrate-active enzymes, as well as with a heightened susceptibility to endocrine and metabolic diseases and cancers.},
}

Humans
Cross-Sectional Studies
*Gastrointestinal Microbiome/physiology
*Intensive Care Units/organization & administration/statistics & numerical data
Male
Female
Prospective Studies
Adult
Middle Aged
RNA, Ribosomal, 16S/analysis/genetics
Cohort Studies
Feces/microbiology
Health Personnel/statistics & numerical data

@article {pmid40165201,
year = {2025},
author = {Lin, L and Peng, X and Chen, L and Dong, L and Zhong, L},
title = {Case report: novel NFKB2 variant associated with pediatric eosinophilic granulomatosis with polyangiitis (EGPA) in the COVID-19 pandemic.},
journal = {Pediatric rheumatology online journal},
volume = {23},
number = {1},
pages = {35},
pmid = {40165201},
issn = {1546-0096},
mesh = {Humans ; Female ; *COVID-19/complications ; Child ; *NF-kappa B p52 Subunit/genetics ; SARS-CoV-2 ; Churg-Strauss Syndrome/genetics/diagnosis ; Granulomatosis with Polyangiitis/genetics/diagnosis ; },
abstract = {BACKGROUND: Childhood-onset eosinophilic granulomatosis with polyangiitis (cEGPA) is a rare type of systemic autoimmune disorder. Variants in the NFKB2 gene can manifest as common variable immunodeficiency or combined immunodeficiency, often accompanied by autoimmunity and ectodermal dysplasia. Here, we report a case of a Chinese patient who carries NFKB2 variants that coexist with cEGPA, a novel combination which, to our knowledge, has not been previously published.

CASE PRESENTATION: We reported a 9-year and 10-month-old girl who presented with cough, wheezing, dyspnea, hypereosinophilia, and vasculitis. Notably, she had significant bilateral pulmonary interstitial lesions. We performed metagenomic next-generation sequencing (mNGS), bronchoscopy and immunological analysis. She was considered to have refractory cEGPA after six months of corticosteroid and immunosuppressive treatment. Tapering off corticosteroids posed a challenge, and multiple immunosuppressive agents were ineffective. Our patient suffered from recurrent fever, wheezing, dyspnea and perianal abscess, along with life-threatening infections, including pneumocystis jirovecii pneumonia (PJP) and severe coronavirus disease 2019 (COVID-19) pneumonia during the pandemic. Her cytokines and inflammatory markers showed a profound collapse. She developed significant hypoxemia, which necessitated mechanical ventilation. Primary immunodeficiency gene panel testing revealed a novel de novo variant in NFKB2 (c.2578 + 2 dup) that was classified as pathogenic. Despite treatment with antibacterial, antiviral, and antifungal agents, biologics, and plasma exchange, she ultimately succumbed to respiratory failure.

CONCLUSIONS: This case report establishes a novel link between NFKB2 variants and EGPA, particularly in the context of the COVID-19 pandemic. This study expands the spectrum of NFKB2 variants and vividly illustrates the complex interrelationships among autoimmunity, infection, and immunodeficiency.},
}

Humans
Female
*COVID-19/complications
Child
*NF-kappa B p52 Subunit/genetics
SARS-CoV-2
Churg-Strauss Syndrome/genetics/diagnosis
Granulomatosis with Polyangiitis/genetics/diagnosis