@article {pmid40543441,
year = {2025},
author = {Hong, WL and Yao, LY and Zhong, Z and Meng, FJ and Zhang, WY and Lu, K and She, ZY},
title = {Successful management of Nocardia farcinica brain abscess in an immunocompetent adult with trimethoprim/sulfamethoxazole hypersensitivity: A case report and review.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {2},
pages = {116954},
doi = {10.1016/j.diagmicrobio.2025.116954},
pmid = {40543441},
issn = {1879-0070},
abstract = {BACKGROUND: Nocardia farcinica brain abscesses are rare in immunocompetent individuals. Trimethoprim/sulfamethoxazole (TMP/SMX) is first-line therapy, but hypersensitivity reactions necessitate alternative regimens. This report details successful management in a TMP/SMX-allergic patient.

CASE REPORT: A 38-year-old immunocompetent male presented with recurrent seizures. MRI revealed expanding left frontal lobe lesions. Surgical excision and metagenomic next-generation sequencing (mNGS) confirmed N. farcinica. Due to hypersensitivity to TMP/SMX, an alternative antibiotic regimen consisting of intravenous imipenem/cilastatin for 18 days and amikacin for 7 days was administered, followed by oral amoxicillin for 435 days and minocycline for 252 days. This therapeutic approach resulted in effective infection control, as evidenced by sustained clinical improvement over a 28-month follow-up period.

CONCLUSION: N. farcinica brain abscess can occur in immunocompetent adults, posing therapeutic challenges with TMP/SMX intolerance. This case demonstrates that alternative regimens-imipenem/cilastatin, amikacin, amoxicillin, and minocycline-can achieve sustained remission. Individualized therapy based on drug susceptibility and patient factors is critical.},
}

@article {pmid40543402,
year = {2025},
author = {Aziz, T and Shabbir, MA and Sarwar, A and Khan, AA and Zhao, L and Yang, Z and Shami, A and Alwethaynani, MS and Al-Asmari, F and Alghamdi, AM and Al-Joufi, FA},
title = {Exploring the multifaceted probiotic potential of Lactiplantibacillus plantarum NMGL2, investigating its antimicrobial resistance profiles and bacteriocin production.},
journal = {Journal of microbiological methods},
volume = {236},
number = {},
pages = {107178},
doi = {10.1016/j.mimet.2025.107178},
pmid = {40543402},
issn = {1872-8359},
abstract = {BACKGROUND: Lactiplantibacillus plantarum is widely recognized for its probiotic and antimicrobial properties, making it a valuable candidate for food and clinical applications. Genomic characterization provides deeper insight into its potential health benefits and safety profile.

AIM: This study aimed to sequence and analyze the genome of L. plantarum NMGL2 to evaluate its antimicrobial resistance, probiotic potential, and genetic suitability for biotechnological applications.

METHODS: The genomic DNA of L. plantarum NMGL2 was extracted and sequenced using Illumina technology. Genome assembly and annotation were performed, followed by gene prediction using Prokka and identification of antimicrobial resistance genes, virulence factors, and probiotic markers via BLAST. Metagenomic analysis of gut microbiota samples and phylogenetic analysis were conducted to assess strain relationships with other L. plantarum isolates.

RESULTS: The genome analysis revealed approximately 3000 protein-coding genes, including those encoding bile salt hydrolase, antimicrobial peptides, and antibiotic resistance determinants. Phylogenetic analysis showed that NMGL2 is closely related to other probiotic L. plantarum strains, supporting its probiotic characteristics and its potential role in combating pathogens.

CONCLUSION: L. plantarum NMGL2 demonstrates promising probiotic traits and carries genes that support its application in food safety and clinical contexts. Further, in vivo studies are needed to validate its health benefits and ensure safety, particularly in treating gastrointestinal disorders.},
}

@article {pmid40543345,
year = {2025},
author = {Li, S and Jiang, Y and Wang, J and Bartlam, M and Wang, Y},
title = {Chiral naproxen enhances horizontal transfer of antibiotic resistance genes in biofilms: Molecular docking reveals stereoselective mechanisms.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138980},
doi = {10.1016/j.jhazmat.2025.138980},
pmid = {40543345},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) is a growing global health concern. This study investigates how the chiral enantiomers of the non-antibiotic drug naproxen (NAP) influence ARG dissemination in biofilms. Metagenomic sequencing and binning analyses revealed that NAP enantiomers selectively enriched ARGs and their bacterial hosts, enhancing resistance to specific antibiotics. Notably, the stereoselective effects of NAP enantiomers not only shaped microbial community composition but also affected the potential for ARG spread. Mechanistically, exposure to R-NAP, in comparison to S-NAP, resulted in a 1.53-fold increase in reactive oxygen species (ROS) production, an 18.20 % enhancement in cell membrane permeability, and a 1.93-fold rise in the abundance of genes associated with the type IV secretion system (T4SS). These physiological and genetic changes promoted microbial aggregation and DNA conjugation, particularly enhancing the transfer of the sul1 gene within the Aquabacter genus through the coordinated action of T4SS, two-component systems (TCS), and quorum sensing (QS). Molecular docking and qRT-PCR analyses further revealed that the stereoselectivity of NAP enantiomers stemmed from their distinct binding interactions with proteins involved in horizontal gene transfer, shedding light on the molecular mechanisms underlying ARG dissemination under chiral NAP exposure.},
}

@article {pmid40543204,
year = {2025},
author = {Yang, J and Kim, JS and Jeon, HW and Lee, J and Seo, JH},
title = {Integrated culture-based and metagenomic profiling of airborne and surface-deposited bacterial communities in residential environments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {382},
number = {},
pages = {126703},
doi = {10.1016/j.envpol.2025.126703},
pmid = {40543204},
issn = {1873-6424},
abstract = {Indoor environments host diverse microbial communities, where airborne and surface-deposited bacteria contribute to human exposure and potential health risks. This study applies metagenomic analysis to examine bacterial diversity in residential apartments, focusing on four key indoor spaces: kitchens, living rooms, toilets, and bedrooms. Airborne bacteria were collected using a culture-based air sampler and surface-deposited bacteria were collected via swabbing of high-contact areas; both were analyzed through 16S rRNA gene sequencing and bioinformatics processing. Airborne bacterial communities were primarily composed of Staphylococcus, Bacillus, and Enhydrobacter, whereas surface-deposited bacteria varied by location, with Streptococcus and Staphylococcus being most common on high-contact surfaces. Overall, surface-deposited bacterial diversity was greater than that of airborne communities, highlighting their distinct but interconnected roles in indoor microbial ecosystems. Functional pathway analysis suggested that indoor bacterial communities may harbor metabolic functions, as well as antibiotic resistance and virulence-related pathways, pointing to potential health concerns. Principal component analysis (PCA) showed clear distinctions between airborne and surface-deposited bacterial communities. These findings highlight the need for space-specific microbial management strategies, such as improved ventilation and surface hygiene, to reduce exposure risks and promote healthier indoor environments.},
}

@article {pmid40542451,
year = {2025},
author = {Ji, S and Ahmad, F and Peng, B and Yang, Y and Su, M and Zhao, X and Vatanen, T},
title = {Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {149},
pmid = {40542451},
issn = {2049-2618},
support = {U22A20365//Joint Funds of National Natural Science Foundation of China/ ; T2341019//National Natural Science Foundation of China/ ; 2023A1515012429//Natural Science Foundation of Guangdong Province/ ; 2024B03J1343//Guangzhou Science and Technology Plan Project/ ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is widely used to treat severe infections and investigated for the treatment of complex diseases. The therapeutic efficacy of FMT is related to the successful engraftment of bacteriophages from healthy donors to recipients. However, gut bacteriophage contributions to FMT engraftment and treatment outcomes remain unclear.

METHODS: The gut phageome from previously published metagenomes of donors and recipients across 23 FMT studies was assembled and functionally annotated for a meta-analysis.

RESULTS: Gut phageome profiles of FMT recipients, especially those with recurrent Clostridioides difficile infection (rCDI), shifted toward donor phageomes, accompanied by increased phageome alpha diversity. Engraftment of donor phages varied between recipient conditions with the highest engraftment rate, overrepresented by putative temperate phage, in patients with rCDI. Consistently, a higher proportion of auxiliary metabolic genes (AMGs), with the potential to support and modulate bacterial metabolism, were annotated on putative temperate phages.

CONCLUSIONS: FMT leads to significant taxonomic, functional, and lifestyle shifts in recipient phageome composition. Future FMT studies should include gut phageome characterization and consider it as a potential factor in microbial community shifts and treatment outcomes. Video Abstract.},
}

@article {pmid40542420,
year = {2025},
author = {Yu, M and Chu, Y and Wang, Y and Mo, L and Tan, X and Guo, S and Yuan, S and Ma, Y},
title = {Metagenomic analysis reveals gut phage diversity across three mammalian models.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {146},
pmid = {40542420},
issn = {2049-2618},
support = {2024YFA0919400//National Key Research and Development Program of China/ ; 2024YFA0919400//National Key Research and Development Program of China/ ; 2024YFA0919400//National Key Research and Development Program of China/ ; B2302023//Shenzhen Medical Research Fund/ ; B2302023//Shenzhen Medical Research Fund/ ; KJZD20230923115859008//Shenzhen Science and Technology Program/ ; KJZD20230923115859008//Shenzhen Science and Technology Program/ ; },
abstract = {BACKGROUND: The gut virome plays a pivotal role in shaping the host's microbiota. However, gut viruses across different mammalian models, and their connections with the human gut microbiota remain largely unknown.

RESULTS: We identified 977 high-confidence species-level viral operational taxonomic units (vOTUs) in mice (hcMGV), 12,896 in pigs (hcPGV), and 1480 in cynomolgus macaques (hcCMGV) from metagenomes, respectively. Clustering these vOTUs at approximately genus level uncovered novel clades with high prevalence across animal guts (> = 60%). In particular, crAss-like phages and cas-harboring jumbophages were characterized. Comparative analysis revealed that hcCMGV had a closer relationship with hcPGV than hcMGV, despite the animal-specific characteristics, and that 55.88% hcCMGV had connections with the human microbiota.

CONCLUSIONS: Our findings shed light on the diversity of gut viruses across these three animals, contributing to future gut microbial studies using model animals. Video Abstract.},
}

@article {pmid40542368,
year = {2025},
author = {Liu, F and Zhuang, Y and Huang, X and Papazian, L and Cai, H and Shao, H and Chen, Q and Xie, C and Tang, K and Li, K and Wang, M and Xu, Y and Shen, P and Wang, Q and He, X and Wang, N and Wang, H and Dai, M and Xiong, Y and Zhong, L and Pan, Y and Chu, L and Yang, B and Zhang, G and Zhou, H and Xu, J and Jiang, C and Huang, L},
title = {The Landscape of lower respiratory tract herpesviruses in severe pneumonia patients: a multicenter, retrospective study with prospective validation.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {254},
pmid = {40542368},
issn = {1466-609X},
support = {82202356, 82341109, and 82173645//National Natural Science Foundation of China/ ; LTGY24H190001//Zhejiang Provincial Natural Science Fund/ ; 2025C02090//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; },
abstract = {OBJECTIVE: Herpesviruses are widely distributed in the lower respiratory tract, yet no study has comprehensively characterized their clinical features and prognostic impact in severe pneumonia.

METHOD: In this multicenter, retrospective study, we included severe pneumonia patients who underwent bronchoalveolar lavage fluid (BALF) metagenomic testing in intensive care units across 17 medical centers from January 2019 to June 2023. Based on metagenomic results, patients were categorized into herpesvirus-negative, HSV-1, EBV, CMV, HHV-6B, and HHV-7 groups. Propensity score matching and multivariable Cox regression were used to compare mortality between herpesvirus-positive and -negative patients. Interaction analyses were conducted to assess the impact of co-detection of different herpesviruses. Besides, main findings were validated using data from a prospective multicenter cohort.

RESULTS: Among 1,737 enrolled patients, the 28-day mortality rate was 41.3% (718/1,737). Herpesviruses were detected in 828 patients. Detection frequencies were: HSV-1 (26.8%), CMV (17.8%), EBV (16.6%), HHV-7 (5.3%), HHV-6B (2.2%), and VZV (0.5%). Clinical characteristics varied across herpesvirus groups. No single herpesvirus was independently associated with increased mortality compared to the negative group. However, co-detection of HSV-1 and CMV was significantly associated with higher 28-day mortality (vs. both negative: adj-HR = 1.439, 95% CI: 1.093-1.894, P = 0.009). This finding was validated in a prospective cohort (adj-HR = 1.656, 95% CI: 1.061-2.585, P = 0.026).

CONCLUSIONS: Herpesviruses are frequently detected in the lower respiratory tract of patients with severe pneumonia, with distinct clinical features across virus types. Co-detection of HSV-1 and CMV was associated with increased 28-day mortality.},
}

@article {pmid40542287,
year = {2025},
author = {Fierer, N and Leung, PM and Lappan, R and Eisenhofer, R and Ricci, F and Holland, SI and Dragone, N and Blackall, LL and Dong, X and Dorador, C and Ferrari, BC and Goordial, J and Holmes, SP and Inagaki, F and Korem, T and Li, SS and Makhalanyane, TP and Metcalf, JL and Nagarajan, N and Orsi, WD and Shanahan, ER and Walker, AW and Weyrich, LS and Gilbert, JA and Willis, AD and Callahan, BJ and Shade, A and Parkhill, J and Banfield, JF and Greening, C},
title = {Guidelines for preventing and reporting contamination in low-biomass microbiome studies.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40542287},
issn = {2058-5276},
support = {SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; APP1178715//Department of Health | National Health and Medical Research Council (NHMRC)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; RGY0058/2022//Human Frontier Science Program (HFSP)/ ; },
abstract = {Numerous important environments harbour low levels of microbial biomass, including certain human tissues, the atmosphere, plant seeds, treated drinking water, hyper-arid soils and the deep subsurface, with some environments lacking resident microbes altogether. These low microbial biomass environments pose unique challenges for standard DNA-based sequencing approaches, as the inevitability of contamination from external sources becomes a critical concern when working near the limits of detection. Likewise, lower-biomass samples can be disproportionately impacted by cross-contamination and practices suitable for handling higher-biomass samples may produce misleading results when applied to lower microbial biomass samples. This Consensus Statement outlines strategies to reduce contamination and cross-contamination, focusing on marker gene and metagenomic analyses. We also provide minimal standards for reporting contamination information and removal workflows. Considerations must be made at every study stage, from sample collection and handling through data analysis and reporting to reduce and identify contaminants. We urge researchers to adopt these recommendations when designing, implementing and reporting microbiome studies, especially those conducted in low-biomass systems.},
}

@article {pmid40541587,
year = {2025},
author = {Pletsch, EA and Smith, AD and Ragonese, JS and Narrowe, AB and Cheung, L and Chen, CT and Wang, TTY and Dawson, HD},
title = {Broccoli consumption alters microbial diversity, metatranscriptome and host transcriptome in mice fed a Total Western Diet.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.05.041},
pmid = {40541587},
issn = {1541-6100},
abstract = {BACKGROUND: Cruciferous vegetables (CV) are a source of dietary fiber and phytochemicals that alter the microbiome in animals and humans. Constituent CV compounds, such as glucosinolates, have demonstrated anti-inflammatory properties in animal models, though often using doses and basal diets that are not relevant to humans. The mechanism(s) are unclear, but the gut microbiota may metabolize these compounds into bioactive molecules that influence immune pathways.

OBJECTIVE: We investigated the effects of a broccoli powder-supplemented Total Western Diet (TWD) on changes in the gut microbiome, the host transcriptome and the metatranscriptome at levels relevant to the human diet to understand how these changes affect metabolic and immune functions.

METHODS: C57BL/6 male mice (n = 40) were fed a TWD control diet for six weeks followed by supplementation with 0, 0.5, 1 or 2.5% broccoli powder (BP) (reflecting a human intake from ¼ -1 cup per day) for three weeks. Microbial communities from cecal contents were taxonomically profiled using 16S rRNA amplicon and shotgun metagenomic sequencing, and metatranscriptomics was used to assess functionality of the microbial communities. The host cecal transcriptome was also assessed.

RESULTS: Beta diversity was significantly higher (p = 1.20E-03) for mice fed the 2.5% BP diet compared to the control group at the species level. Lachnospiraceae MD335 was significantly more abundant in mice fed higher levels of broccoli, and analysis of bacterial RNA transcripts indicated a dose-dependent increase in transcription of genes associated with butyrate and acetate production, plant cell wall degradation and carbohydrate utilization. Activation of the aryl hydrocarbon receptor pathway in the cecum was evident.

CONCLUSIONS: Consumption of a broccoli-supplemented TWD induces changes in the gut microbiome, host and microbial gene expression that affect immune health and inflammation in the gut at levels that are achievable in the human diet.},
}

@article {pmid40541578,
year = {2025},
author = {Tian, J and Hu, J and Xiong, Y and Deng, X and Fang, Y and Wang, G and Chi, R and Xiao, C},
title = {Metagenomic and metabolomic insights into microalgal-bacterial symbiosis under low carbon-to-nitrogen ratios.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132849},
doi = {10.1016/j.biortech.2025.132849},
pmid = {40541578},
issn = {1873-2976},
abstract = {Microalgal-bacterial symbiotic system (MBSS) is expected to efficiently treat ammonia nitrogen (NH4[+]-N) wastewater at low carbon-to-nitrogen ratio (CNR). In this study, MBSS was constructed and operated at CNRs of 0, 2, and 4 for 36 days, named as L (low CNR), M (medium CNR), and H (high CNR). Microbial interaction mechanisms were explored through metagenomics and non-targeted metabolomics. The average NH4[+]-N removal efficiencies of L, M, and H were 9.2 ± 4.3 %, 33.6 ± 10.9 %, and 51.6 ± 14.1 %, respectively. CNR significantly influenced NH4[+]-N removal. Metagenomics and metabolomics showed that bacteria dominate MBSS, with phylum Pseudomonadota having a large advantage. Addition of simple organic carbon sources may inhibit the generation of complex organic compounds by microalgae, consequently leading to bacteria utilizing simple carbon sources. Certain key microorganisms, genes, and metabolites respond to different CNRs to regulate MBSS performance. This study provides new insights into MBSS nitrogen removal at low CNR.},
}

@article {pmid40541123,
year = {2025},
author = {Jiao, Y and Xiao, D and Li, X and Jiang, M and Li, H},
title = {Integrative fMRI and multiomics reveal neuroprotective mechanisms of Astragalus membranaceus in sleep deprivation-induced depression.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {156959},
doi = {10.1016/j.phymed.2025.156959},
pmid = {40541123},
issn = {1618-095X},
abstract = {BACKGROUND: Sleep deprivation (SD) is a significant public health concern and a risk factor for neuropsychiatric disorders, including depression. SD disrupts the gut-brain axis, causing dysbiosis and neuroinflammation. Astragalus membranaceus (AST) exhibits antidepressant and anti-inflammatory properties, including modulation of the gut microbiota; however, its neuroprotective effects on SD-induced neuropsychiatric disturbances remain largely unexplored. This study investigates the potential of AST using an innovative integrative multiomics approach.

PURPOSE: This study was conducted to investigate the neuroprotective effects of AST against SD-induced depression-like behavior and to explore the mechanism underlying its regulatory effects on the gut-brain axis.

METHODS: We established a chronic SD mouse model that was subjected to AST intervention and employed a pioneering integrative multiomics approach-combining resting-state functional magnetic resonance imaging for brain function, metagenomics for microbiota profiling, metabolomics for metabolic alterations, and transcriptomics for gene expression in key brain regions. Behavioral tests and cytokine assays complemented these analyses to comprehensively evaluate the therapeutic effects of AST.

RESULTS: SD induced depression-like behavior, neuroinflammation (IL-1β, IL-6, and TNF-α secretion), gut dysbiosis (Proteobacteria expansion, loss of beneficial microbes), and disrupted metabolic pathways. AST alleviated behavioral deficits, normalized brain connectivity, and reduced the levels of proinflammatory cytokines. It also reshaped microbiota, enriching Muribaculum and Butyricicoccus, and restored metabolic profiles, increasing the levels of short-chain fatty acids and promoting bile acid pathways. Integrated analysis linked microbiota restoration to reduced neuroinflammation and improved neuroprotection.

CONCLUSION: AST modulates the gut-brain axis to counteract SD-induced dysbiosis, neuroinflammation, and metabolic imbalance, alleviating depression-like symptoms. These findings offer novel mechanistic insights into the therapeutic potential of AST for SD-related neuropsychiatric conditions.},
}

@article {pmid40540838,
year = {2025},
author = {Conti Taguali, S and Pöter, R and Aloi, F and Fernández-Trujillo, C and Acedo, A and La Spada, F and Li Destri Nicosia, MG and Pane, A and Schena, L and Cacciola, SO},
title = {Influence of environmental and agronomic variables on soil microbiome in citrus orchards: A comparative analysis of organic and conventional farming system.},
journal = {Microbiological research},
volume = {299},
number = {},
pages = {128260},
doi = {10.1016/j.micres.2025.128260},
pmid = {40540838},
issn = {1618-0623},
abstract = {Crop health and productivity depend on the structure and functionality of soil microbiota associated with the root system of plants. The agricultural policy of the European Union promotes organic farming systems to ensure environmental sustainability and food safety. The objective of this study was to investigate the impact of organic farming on soil microbiome in citrus orchards. The soil microbiota of eight conventionally and seven organically managed commercial citrus orchards across eastern Sicily was characterised using Illumina sequencing and BeCrop® primers for PCR amplification. The structure (diversity and relative abundance) and functionality of soil bacterial and fungal communities depended primarily on the sampling site. Other variables influencing the soil microbiome included soil total carbon content, seasonality, rootstock genotype, soil tillage and irrigation system. The latter three exerted differential effects on either bacterial or fungal communities. Conversely, age and visible health status of the tree had negligible influence on both communities. The differences between organically and conventionally managed citrus orchards accounted for a significant proportion of the variability, indicating a relevant effect of the farming system on soil microbiome. Organically managed orchards compared to those managed conventionally exhibited higher microbial diversity and a unique composition of nutrient-cycling microbes. In particular, organic farming promoted beneficial microbial functions, such as nitrogen fixation and phosphorus solubilization. Findings provide insights into the dynamic and complex interactions between environmental variables and soil microbial communities in citrus orchards, confirming the potential of microbial diversity as an indicator of sustainability in agricultural systems.},
}

@article {pmid40540566,
year = {2025},
author = {Woods, PH and Speth, DR and Laso-Pérez, R and Utter, DR and Ruff, SE and Orphan, VJ},
title = {Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea.},
journal = {Science advances},
volume = {11},
number = {25},
pages = {eadq5232},
pmid = {40540566},
issn = {2375-2548},
abstract = {Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, "Candidatus Methanovorans" (ANME-3), to identify evolutionary processes and innovations at work in ANME, which may be obscured in earlier evolved lineages. We identified horizontal transfer of hdrA homologs and convergent evolution in carbon and energy metabolic genes as potential early steps in Methanovorans evolution. We also identified the erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multiheme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a globally important metabolic niche.},
}

@article {pmid40540222,
year = {2025},
author = {Xiao, YY and Lu, AL and Mo, HY and He, ZD and Wen, JL and Yin, X},
title = {Clinical value of metagenomic next-generation sequencing in patients with connective tissue diseases co-infections: a single-center study from southern hospital in China.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {40540222},
issn = {1434-9949},
support = {81760298//National Natural Science Foundation of China/ ; 2021JJA140699//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; (Grant No. YYZS2023005).//the First Afliated Hospital of Guangxi Medical University/ ; },
abstract = {OBJECTIVES: This study aimed to assess the clinical value of metagenomic next-generation sequencing (mNGS) in patients with connective tissue diseases (CTDs) co-infections, thereby establishing a foundation for early infection identification and the development of anti-infective regimens.

METHODS: This retrospective study analyzed 304 CTD patients with suspected infections at the First Affiliated Hospital of Guangxi Medical University between October 2020 and April 2024. The study compared the diagnostic efficacy between mNGS and conventional microbiological testing (CMT), examined pathogen detection rates across different periods and pathogen types, and evaluated the clinical outcomes of mNGS-guided antimicrobial regimen adjustments.

RESULTS: Among the 180 confirmed infections (Group I), mNGS demonstrated superior diagnostic performance compared to conventional microbiological testing (CMT). mNGS exhibited significantly higher sensitivity (89.6% vs. 57.0%; OR = 6.5, 95% CI: 3.7-11.0, p < 0.001), with a specificity of 81.5%, positive predictive value (PPV) of 97.2%, and negative predictive value (NPV) of 52.4%. mNGS outperformed CMT in detecting bacterial and viral pathogens (p < 0.05). Viral infections were the most common. Compared to prior studies, mNGS exhibited improved pathogen detection rates. mNGS-guided treatment optimization significantly enhanced clinical outcomes, with higher cure rates, lower mortality, and shorter hospital stays.

CONCLUSION: Current evidence suggests that while mNGS demonstrates superior diagnostic performance over CMT for detecting infections in CTD patients, their combined use provides optimal pathogen identification accuracy and enhanced clinical management. Key Points • This is the larger-scale retrospective study of mNGS application in patients with CTDs co-infections following the Coronavirus Disease 2019 (COVID-19). • We found that the distribution of pathogens and positivity rates have changed in recent years, especially after the COVID-19. • The clinical value of mNGS was further demonstrated through its impact of mNGS results on antibiotic regimens and the analysis of negative samples.},
}

@article {pmid40539808,
year = {2025},
author = {Sun, H and Chen, Q and Zhang, D and Hu, L and Li, S and Lu, M and Wang, Y and Su, H and Gao, Y and Guo, J and Zhao, Y and Du, J and Liu, C and Xia, H and Xu, Y and Ge, X and Yang, Q},
title = {Integrative study of pulmonary microbiome and clinical diagnosis in pulmonary tuberculosis patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156324},
doi = {10.1128/spectrum.01563-24},
pmid = {40539808},
issn = {2165-0497},
abstract = {UNLABELLED: This study investigated the diagnostic potential of mNGS for detecting MTB in pulmonary tuberculosis patients. We analyzed pulmonary microbiome data to assess its impact on mNGS diagnostic accuracy and explored the association between microbiome profiles and clinical diagnosis. Bronchoalveolar lavage fluid samples were collected from 236 patients with pulmonary infections, and the diagnostic performance of mNGS was compared with traditional methods in detecting MTB. Furthermore, the incidence of false negatives and false positives, as well as the characteristics of the lung microbiota in TB patients, was analyzed to improve the diagnostic precision of mNGS. We observed that among all detection methods, mNGS showed the highest sensitivity (73.33%), followed by X-pert (60.00%), culture (53.33%), RT-PCR (53.33%), and sputum smear (23.33%). Notably, mNGS produced 3 false positive results in 236 samples, yielding a specificity of 98.54%. Analysis of the pulmonary microbiome revealed significant differences in both α-diversity and β-diversity between patients with TB and uninfected controls (P<0.05). Shannon index and Chao1 index were identified as significant predictors associated with MTB infection. ROC curve analysis demonstrated an AUC of 0.765, indicating good discriminatory performance. This study suggested that integrating wet-laboratory techniques with bioinformatics analysis can further enhance the diagnostic accuracy of mNGS for TB. Furthermore, microbiome analysis holds significant potential for the diagnosis of MTB infection.

IMPORTANCE: This study focuses on the application of next-generation sequencing (NGS) technology in detecting Mycobacterium tuberculosis in bronchoalveolar lavage fluid and explores the impact of M. tuberculosis infection on the pulmonary microbiome. By optimizing the methods and conducting microbial analyses, the accuracy of metagenomic NGS for detecting M. tuberculosis has been improved.},
}

@article {pmid40539782,
year = {2025},
author = {Qi, Y-H and Ye, Z-X and Feng, K-H and Ma, X-W and Zhang, C-X and Hu, M-H and Shi, M and Chen, J-P and Li, J-M},
title = {Diversity and evolutionary history of RNA viruses among different horseshoe crab species.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0016425},
doi = {10.1128/jvi.00164-25},
pmid = {40539782},
issn = {1098-5514},
abstract = {Horseshoe crabs (Xiphosura: Limulidae) are the sole surviving species of the class Merostomata, with only four extant species remaining today. Recent advances in metagenomic next-generation sequencing have unveiled a vast diversity of RNA viruses and non-retroviral endogenous RNA viral elements (nrEVEs) in invertebrates. This raises intriguing questions about the RNA virome and nrEVEs in horseshoe crabs as "living fossils," potentially offering insights into the evolutionary relationships between RNA viruses and these ancient organisms. In this study, 22 novel RNA viruses were identified across the four horseshoe crab species by screening 117 data sets, including picornaviruses, totiviruses, a flavivirus, a rhabdovirus, as well as a plant-associated tombusvirus and a fungi-associated narnavirus. Additionally, 20 nrEVEs were identified in the genomes of the four horseshoe crab species (hcEVEs), with most sharing homology with the viral family Chuviridae (N = 11), supporting the hypothesis that modern negative-sense RNA viruses may trace their origins to ancient oceanic chuviruses. A time-scaled phylogenetic tree based on hcEVEs suggests that at least two independent ancient chuvirus infections and genome integration events occurred in the common ancestor of horseshoe crab species. Interestingly, transcriptional analyses indicated that hcEVE-containing transcripts display typical exon-intron structures in the three Asian horseshoe crab species, suggesting that these hcEVEs may have been co-opted by horseshoe crabs during coevolution. These findings advance our understanding of the RNA viruses associated with horseshoe crabs and shed light on the potential role of RNA viruses in shaping the evolutionary history of this "living fossil" arthropod host.IMPORTANCERecent studies have discovered abundant RNA viruses in invertebrates, revealing that viral genomes may integrate into host genomes, creating a genetic record of past infections. In this study, we explored the evolutionary relationship between RNA viruses and the four extant horseshoe crab species-the last representatives of the class Merostomata, often termed "living fossils"-by analyzing viral sequences embedded in their genomes. The presence of chuvirus-like sequences in the genomes of these horseshoe crabs suggests that modern negative-sense RNA viruses may trace their origins back to ancient chuviruses from the ocean. Furthermore, we identified at least two independent ancient integrations of chuviruses in the evolutionary history of horseshoe crabs, with one orthologous gene containing a chuvirus-derived G protein gene/coding sequence potentially inherited from a common ancestor of the three Asian species before their divergence. Our findings contribute to a deeper understanding of the long-term coevolution between RNA viruses and their arthropod hosts.},
}

@article {pmid40539777,
year = {2025},
author = {Olmsted, CN and Gahler, M and Roden, E and Peterson, B and Lazarcik, J and Tran, PQ and Berg, M and Bryant, DA and Goudeau, D and Malmstrom, RR and Qin, M and McMahon, KD},
title = {Cryptic cycling by electroactive bacterioplankton in Trout Bog Lake.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0178924},
doi = {10.1128/aem.01789-24},
pmid = {40539777},
issn = {1098-5336},
abstract = {The potential for extracellular electron transfer (EET) is a prevailing genomic feature of humic lake bacterioplankton. However, there has been little evidence for the substantial ecological contribution predicted by genetics. We hypothesized that anoxygenic phototrophic electrotrophs and accompanying heterotrophic electrogens cycle dissolved organic matter (DOM) between oxidized and reduced states. We predicted that such bacterioplankton would exhibit diel-scale oscillations due to the light dependency of photosynthesis. Using Trout Bog Lake in Wisconsin, USA, as our model ecosystem, we profiled the water column with depth-discrete metagenomic, physiochemical, and electrochemical analyses. We observed variation in oxidation reduction potential (ORP) in response to sunlight, initiating at depths populated by anoxygenic phototrophs with EET genes. We developed an automated buoy to measure electric current flow between many pairs of electrodes simultaneously, observing correlation in electron consumption to sunlight. Our results, combined with published metatranscriptomic analysis, indicate the occurrence of electron cycling between phototrophic oxidation (electrotrophic metabolism) by Chlorobium and anaerobic respiration (electrogenic metabolism) by Geothrix, involving DOM. We also repeatedly observed gradual seasonal increases in hypolimnion ORP throughout summer. These diel and seasonal patterns imply that electroactive DOM mediates the ecology of electroactive bacteria in lakes, controlling humic lake methane emissions.IMPORTANCEWe investigated the physical, chemical, and redox characteristics of a bog lake and electrodes hung therein to test the hypothesis that dissolved organic matter is being cycled between oxidized and reduced states by electroactive bacterioplankton powered by phototrophy. To do so, we performed field-based analyses on multiple timescales using both established and novel instrumentation. We paired these analyses with recently developed bioinformatics pipelines for metagenomics data to investigate genes that enable electroactive metabolism and accompanying metabolisms. Our results are consistent with our hypothesis and yet upend some of our other expectations. Our findings have implications for understanding greenhouse gas emissions from lakes, including electroactivity as an integral part of lake metabolism throughout more of the anoxic parts of lakes and for a longer portion of the summer than expected. Our results also give a sense of what electroactivity occurs at given depths and provide a strong basis for future studies.},
}

@article {pmid40539111,
year = {2025},
author = {Ma, Y and Wu, Q and Wang, X and Sui, W and Zhang, X},
title = {Carbon components in organic amendments drive nitrogen metabolism in one-year-long anaerobic soil microcosms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1588169},
pmid = {40539111},
issn = {1664-302X},
abstract = {INTRODUCTION: Long-term studies on the dynamic changes in nitrogen metabolism and functional microbial communities under anaerobic conditions, particularly those driven by organic amendments, remain scarce.

METHODS: We conducted a year-long anaerobic microcosm experiment using three organic amendments-aerobically fermented pig-manure digestate (ACM), compost (ACP) and straw powder (ACS)-alongside an inorganic fertilizer-only control (ACN).

RESULTS: Temporal shifts revealed that organic amendments drove distinct nitrogen metabolism pathways. Amendments of digestate and compost promoted the proliferation of nitrogen-mineralizing bacteria such as Ramlibacter and Lysobacter, leading to significant ammonium accumulation. After 12-month incubation, the ACM treatment caused a 75.6-fold increase in ammonium, a 43.4% rise in total nitrogen (TN), and a 27.0% increase in total organic carbon (TOC). In contrast, the ACS treatment exhibited superior nitrogen fixation, with an average of 1.69-fold higher rate than ACM and 5.30 fold higher than ACP The ACS treatment enriched cellulolytic nitrogen-fixing bacteria, including Clostridium, and nitrogen-fixing archaea.

DISCUSSION: This study provides profound insights in to the unique nitrogen metabolism pathways influenced by organic amendments under anoxic conditions, ultimately offering valuable insights into improved soil fertility and sustainable nitrogen management practices in agricultural systems.},
}

@article {pmid40539103,
year = {2025},
author = {Lin, ZY and He, SS and Mo, ZT and Liao, XT and Feng, ZS and Kong, J and Zhu, L and Li, Y and Tan, HY and Su, ZW and Jia, CH and Wu, F},
title = {Integrated analysis of serum metabolomics and fecal microbiome in infants with necrotizing enterocolitis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1584041},
pmid = {40539103},
issn = {1664-302X},
abstract = {BACKGROUND: Necrotizing enterocolitis (NEC), a lethal gastrointestinal disorder in preterm infants, remains poorly understood in its pathology, and early diagnosis are critically limited. Multi-omics approaches present unprecedented opportunities to elucidate NEC pathogenesis and identify clinically translatable biomarkers.

METHODS: Infants with Bell stage II-III NEC and gestational age-matched controls were enrolled. Serum/stool samples from NEC patients at acute (NEC-D) and recovery (NEC-R) phases, and controls (non-NEC) were collected. Fecal metagenomic sequencing and serum untargeted metabolomic profiling were performed. Clinical parameters were compared.

RESULTS: The study comprised seven NEC and seven non-NEC infants. Baseline neonatal characteristics and maternal perinatal parameters showed no significant differences between NEC-D and non-NEC except for markedly lower leukocyte counts in NEC infants. Fecal metagenomics revealed severely diminished alpha diversity in NEC-D versus both non-NEC controls and NEC-R, characterized with lower Chao1 index. NEC-D exhibited elevated Escherichia coli relative abundance alongside reduced Staphylococcus haemolyticus, Staphylococcus aureus, Staphylococcus epidermidis, and Lactobacillus paracasei. Correspondingly, KEGG functional gene analysis demonstrated impaired metabolism in NEC-D. Serum metabolomics identified significantly decreased ornithine, DL-arginine, L-threonine, leucine, and D-proline in NEC-D versus non-NEC. NEC-D also showed lower taurodeoxycholic acid, glycocholic acid, and chenodeoxycholic acid compared to NEC-R. Integrative analysis revealed a positive correlation between the metabolites D-proline and ornithine and the Lactobacillus paracasei, Staphylococcus epidermidis, and Staphylococcus aureus abundance.

CONCLUSION: NEC is characterized by gut microbiota dysbiosis with reduced diversity, altered functional gene expression, and disrupted host-microbiota metabolic crosstalk. The identified serum metabolite-microbiome correlations provide mechanistic insights into NEC pathogenesis and potential diagnostic biomarkers.},
}

@article {pmid40538825,
year = {2025},
author = {Hofman, J and Brenerova, P and Borilova Linhartova, P},
title = {State-of-the-art approaches in the investigation of human seminal bacteriome using metagenomic methods.},
journal = {Frontiers in reproductive health},
volume = {7},
number = {},
pages = {1557912},
pmid = {40538825},
issn = {2673-3153},
abstract = {Although the understanding of the causes of infertility is the key to its successful treatment, recent studies have shown that as many as 50% of male-caused infertility cases are considered idiopathic. The microbial colonization of the male reproductive system was shown to be associated with reduced male reproductive fitness. Investigation of the seminal microbiome, however, remains challenging. This article aimed to improve this situation by creating the first comprehensive review of literature on the metagenomic methods (including the pre-analytical and analytical approaches) used in the research on human seminal bacteriome (total bacterial DNA in the matrix), published in 2018-2024. A total of 29 studies addressing the analysis of the human seminal bacteriome were identified. The analysis typically involved DNA extraction from the supernatant using commercial kits, amplification of the gene for 16S rRNA, and sequencing of amplicons. Where the separation of seminal plasma was performed, centrifugation was the dominant method used for this purpose. The significant heterogeneity in individual steps of methodological approaches in the analysis of the human seminal bacteriome complicates the comparison of results among studies and the establishment of standard procedures, hindering clinical advancements. For this reason, a protocol for the analysis of the human seminal plasma bacteriome is proposed here, which could lead to improved comparability of results among studies and make future research more efficient. This protocol is founded on rigorous quality control measures, compliance with the WHO laboratory manual for sample collection, extensive pretreatment involving mechanical and enzymatic lysis, DNA extraction using the QIAamp DNA Mini Kit (Qiagen), and short-read sequencing conducted on the MiSeq platform (Illumina).},
}

@article {pmid40538739,
year = {2025},
author = {Zou, ZL and Shen, ZH},
title = {Amoebic liver abscess co-infected with bacterial liver abscess: A rare case in an immunocompromised patient.},
journal = {IDCases},
volume = {41},
number = {},
pages = {e02279},
pmid = {40538739},
issn = {2214-2509},
abstract = {We present a complex case of a 43-year-old HIV-positive Chinese male with co-infection of amoebic liver abscess (ALA) and bacterial liver abscess caused by Salmonella enterica subsp. enterica serotype Typhi (abbreviated as Salmonella Typhi). The patient presented with fever and abdominal pain. Initial bacterial cultures identified Salmonella Typhi, but targeted antibiotic therapy failed to resolve his symptoms, prompting to further investigation. Metagenomic next-generation sequencing (mNGS) of pleural and liver abscess drainage fluids revealed sequences of Entamoeba histolytica, confirming a dual infection. The patient was treated with combination therapy, resulting in clinical improvement. This case highlights diagnostic challenges in immunocompromised patients and underscores the critical role of mNGS in identifying co-infections and guiding treatment. Early recognition and timely intervention are essential for achieving optimal outcomes in such complex cases.},
}

@article {pmid40538403,
year = {2025},
author = {Chengsupanimit, T and Mahajan, A and Farhadian, S and Machiavello Roman, F},
title = {Case Report: Spinal cord abscess due to Nocardia farcinica presenting as longitudinally extensive transverse myelitis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1613770},
pmid = {40538403},
issn = {2296-858X},
abstract = {A middle-aged man, renal transplant recipient, was admitted with lower extremity paralysis, loss of sensation and urinary retention. The initial diagnostic workup revealed extensive inflammatory spinal changes on imaging, consistent with longitudinally extensive transverse myelitis. Cerebrospinal fluid testing demonstrated neutrophilic pleocytosis; routine tests for bacterial and viral pathogens were negative. The patient received high-dose steroids for presumed autoimmune myelitis, but his condition worsened. Repeat spinal imaging revealed an intramedullary spinal cord abscess and a loculated collection in the cauda equina. Nocardia farcinica was isolated from spinal biopsy tissue cultures and metagenomic sequencing of cerebrospinal fluid. He received treatment with trimethoprim-sulfamethoxazole and linezolid, with subsequent improvement of the radiological abnormalities. At outpatient follow-up two months after initiating antimicrobials, the patient endorsed improved upper extremity strength, though remained paraplegic. This case report highlights the protean manifestations of central nervous system nocardiosis and the benefits of using metagenomic sequencing to diagnose complex central nervous system infections.},
}

@article {pmid40537892,
year = {2025},
author = {Kang, J and Choi, Y and Keum, GB and Doo, H and Kwak, J and Kim, H and Chae, Y and Lee, S and Yang, H and Kim, S and Sun, X and Kim, HB and Yoo, SJ},
title = {Effect of Diet and Lifestyle Changes on Gut Microbial Diversity in Healthy Adolescents.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2503018},
doi = {10.4014/jmb.2503.03018},
pmid = {40537892},
issn = {1738-8872},
abstract = {The human gut microbiome is a complex ecosystem shaped by both intrinsic and extrinsic factors, with external elements such as diet and exercise significantly influencing its diversity and composition. In this study, we evaluated gut microbiome shifts in adolescents participating in a four-week camp with controlled diets, lifestyle, and a healthy living environment. Stool samples were collected before and after the camp period and analyzed through 16S rRNA gene sequencing to assess changes in microbial composition and diversity. Post-intervention, gut microbiome diversity increased significantly, with notable changes in the relative abundance of taxa such as Lachnospira, Alistipes, and Barnesiella, which are associated with enhanced immune function and gut health. Additionally, functional prediction using PICRUSt indicated an increase in genes associated with energy production and metabolism, suggesting a broader functional impact of lifestyle modifications on gut microbial functionalities. These findings revealed the potential causal relationships between lifestyle modifications and gut microbiome shifts, providing valuable insights into the interactions between environment, diet, and the gut microbiota.},
}

@article {pmid40537881,
year = {2025},
author = {Linghu, Y and Hu, RS and Tang, XM and Li, RT and Li, WY and Wu, JH},
title = {Unveiling viral diversity and dynamics in mosquitoes through metagenomic analysis in Guizhou Province, China.},
journal = {Infectious diseases of poverty},
volume = {14},
number = {1},
pages = {51},
pmid = {40537881},
issn = {2049-9957},
support = {Qian Ke He Platform Talent-GCC [2022] 033-1//The Training Project for High-Level Innovative talents in Guizhou Province, China/ ; Qian Ke He Platform Talent-CXTD [2022] 004//The Science and Technology Innovation Talent team of Guizhou Province, China/ ; Project Contract Number: Xiao Bo He J Zi [2023] 44//The Scientific Research Foundation for Advanced Talents, Guizhou Medical University/ ; NO. 2024GCC16Z//The High-level Talent Research Start-up Project of Sichuan University of Arts and Science/ ; },
abstract = {BACKGROUND: Poverty, disease, and vector ecology intersect to present ongoing health threats, particularly in ecologically sensitive regions. Guizhou Province in China, with its complex karst topography and rich biodiversity, offers a unique environment to study mosquito-borne viral transmission. Despite over 5000 reported cases of Japanese encephalitis in the past two decades and the detection of Zika virus in 2016, the virological landscape of this region remains poorly understood. This study aims to characterize the mosquito-associated virome, assess viral diversity, and identify factors influencing transmission dynamics in Guizhou Province.

METHODS: Between 2021 and 2022, we conducted a 2-year mosquito surveillance across eight ecologically distinct regions in Guizhou Province. Adult mosquitoes were collected using a variety of methods, including BG Mosquitaire CO2 traps, mosquito-killing lamps, manual collection, human bait traps, and oviposition traps. To investigate the virome diversity and dynamics within mosquito populations, we performed metagenomic sequencing and bioinformatics analysis on pooled mosquito samples collected from geographically diverse sampling sites.

RESULTS: We collected more than 40,000 adult mosquitoes, primarily belonging to four genera: Aedes, Anopheles, Armigeres, and Culex. Dominant species included Aedes albopictus, Anopheles sinensis, Armigeres subalbatus, and Culex tritaeniorhynchus. Notably, we report the first provincial record of the Anopheles baileyi complex, expanding the known distribution of mosquito vector in this region. Viral metagenomic sequencing, coupled with bioinformatic analysis, identified 162 viral contigs, including 140 known and 22 previously uncharacterized viruses. We experimentally confirmed the genotypes of three medically important zoonotic viruses: Japanese encephalitis virus (JEV-GI), Getah virus (GETV-GIII) and Banna virus (BAV-A2). Comparative analysis of viral abundance across mosquito species revealed that Aedes albopictus populations in Guizhou harbor a distinct virome composition, diverging from those reported in other geographic regions.

CONCLUSIONS: This study presents the comprehensive characterization of the mosquito-associated virome in Guizhou Province, providing critical insights into viral diversity, vector competence, and transmission dynamics within karst ecosystems. The detection of multiple zoonotic viruses highlights the need for strengthened surveillance and targeted public health interventions in this region.},
}

@article {pmid40537478,
year = {2025},
author = {Sommer, AJ and Skarlupka, JH and Teseo, S and Otani, S and Suen, G and Coon, KL and Sapountzis, P},
title = {Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {111},
pmid = {40537478},
issn = {2055-5008},
support = {WIS04039//United States Department of Agriculture | National Institute of Food and Agriculture (NIFA)/ ; },
abstract = {Dairy farms are major reservoirs of zoonotic bacterial pathogens, which harbor antimicrobial resistance genes (ARGs), and raise critical questions about their dissemination on and off the farm environment. Here, we investigated the role of coprophagous muscid flies (Diptera: Muscidae) as carriers of zoonotic pathogens and antimicrobial resistance. We collected cow manure and flies on a dairy farm and used shotgun metagenomics to identify the presence of clinically relevant bacteria, virulence factors, and ARGs in both environments. Our results reveal that, although the fly microbiome is largely composed of manure-associated taxa, they also harbor specific insect-associated bacteria, which may be involved in nutrient provisioning to the host. Furthermore, we identifed shared ARGs, virulence factors, and zoonotic pathogens enriched within the fly gastrointestinal tract (GIT). Our study illustrates the potential flow of pathogenic microorganisms from manure to coprophagous flies, suggesting that flies may pose an important zoonotic threat on dairy farms.},
}

@article {pmid40537448,
year = {2025},
author = {Rudi, K and Nilsen, T and Pettersen, R and Keeley, NB and Ray, JL and Majaneva, S and Stokkan, M and Hervik, A and Angell, IL and Philip, M and Martin, J and Sundt, MØ and Snipen, LG},
title = {The Coastal Seafloor Microbiota Is Structured by Local Selection of Cosmopolitan Taxa.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70123},
doi = {10.1111/1758-2229.70123},
pmid = {40537448},
issn = {1758-2229},
support = {320076//Norges Forskningsråd/ ; },
abstract = {Understanding the assembly processes of the coastal seafloor microbiota is crucial for gaining insights into how ocean ecosystems work. In our study, we addressed the question about how local selection affects the global distribution of coastal seafloor microorganisms. We identified two main clusters of samples by examining the geographical distribution of 356 high-quality prokaryote metagenome-assembled genomes (MAGs) from 94 coastal samples collected along the Norwegian and Icelandic coasts. There was no identifiable correlation between the abundance of MAGs and the geographic distance between them central to the identified clusters (no distance decay). In contrast, noncentral MAGs demonstrate a pronounced distance decay. We also observed significant functional differences between the two sample clusters. One cluster showed enrichment in functions such as dissimilatory nitrate reduction to ammonium (DNRA), acetoclastic methanogenesis, thiosulphate conversion and acetate and butyrate metabolism. The other cluster was enriched in propionate metabolism, nitrite oxidation to nitrate and cobalamin-dependent carbon fixation. These results suggest that localised environmental selection acts on cosmopolitan taxa to shape seafloor microbiota. Our findings therefore profoundly impact the understanding of seafloor ecological processes and their management.},
}

@article {pmid40536635,
year = {2025},
author = {Zhang, X and Feng, Y and Shi, X and Zhang, Y and Wang, W},
title = {Degradable plastic of high-density polyethylene (HDPE)-CaCO3 reduced the abundance of antibiotic resistance genes in soil.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {7},
pages = {773},
pmid = {40536635},
issn = {1573-2959},
support = {20170031//Henan Normal University Outstanding Youth Science Fund/ ; 20170031//Henan Normal University Outstanding Youth Science Fund/ ; 20170031//Henan Normal University Outstanding Youth Science Fund/ ; 41907121//National Natural Science Foundation of China/ ; },
mesh = {*Polyethylene/chemistry ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Calcium Carbonate/chemistry ; *Biodegradable Plastics ; *Soil Pollutants/analysis ; Soil/chemistry ; Biodegradation, Environmental ; Plastics ; },
abstract = {A large number of degradable plastics have entered the market because traditional plastics are not easy to degrade. However, degradable plastics have problems such as inability to be completely degraded in time. Therefore, evaluating whether degradable plastics pose environmental harm is both urgent and crucial. High-density polyethylene (HDPE) disposable degradable plastic bags which were filled with CaCO3 have been widely circulated in the market. But there has been no reported research on whether HDPE/CaCO3 degradable plastics are harmful to the environment. Therefore, in this study, HDPE-CaCO3 degradable plastics circulated in the market were taken as the research objects, and the antibiotic resistance genes (ARG), a new type of environmental pollution indicator, were used as the evaluation indicators. The HDPE/CaCO3 degradable plastics were made into plastic pieces less than 10 mm in size and then evenly mixed with soil. After 30 days, metagenomic sequencing was performed on the soil microorganisms, and the soil microbial community structure and the abundance of ARGs in the soil were analyzed to evaluate the potential environmental risks of HDPE/CaCO3 degradable plastics. The results showed that comparing with HDPE, the HDPE/CaCO3 degradable plastics could reduce the abundance of soil ARGs and change the soil microbial community structure. Our results indicated that HDPE/CaCO3 degradable plastics imposed a reduced environmental impact compared to conventional HDPE plastics.},
}

*Polyethylene/chemistry
*Soil Microbiology
*Drug Resistance, Microbial/genetics
*Calcium Carbonate/chemistry
*Biodegradable Plastics
*Soil Pollutants/analysis
Soil/chemistry
Biodegradation, Environmental
Plastics

@article {pmid40535544,
year = {2025},
author = {Wang, X and Cao, D and Chen, W and Sun, J and Hu, H},
title = {Metagenomics reveals unique gut mycobiome biomarkers in major depressive disorder - a non-invasive method.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1582522},
pmid = {40535544},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Depressive Disorder, Major/microbiology/diagnosis ; *Mycobiome ; Biomarkers/analysis ; Male ; Female ; Adult ; *Metagenomics/methods ; *Fungi/classification/genetics/isolation & purification ; Middle Aged ; Machine Learning ; Support Vector Machine ; Case-Control Studies ; Feces/microbiology ; },
abstract = {BACKGROUND: An increasing amount of evidence suggests a potential link between alterations in the intestinal microbiota and the onset of various psychiatric disorders, including depression. Nevertheless, the precise nature of the link between depression and the intestinal microbiota remains largely unknown. A significant proportion of previous research has concentrated on the study of gut bacterial communities, with relatively little attention paid to the link between gut mycobiome and depression.

METHODS: In this research, we analyzed the composition and differences of intestinal fungal communities between major depressive disorder (MDD) and healthy controls. Subsequently, we constructed a machine learning model using support vector machine-recursive feature elimination to search for potential fungal markers for MDD.

RESULTS: Our findings indicated that the composition and beta diversity of intestinal fungal communities were significantly changed in MDD compared to the healthy controls. A total of 22 specific fungal community markers were screened out by machine learning, and the predictive model had promising performance in the prediction of MDD (area under the curve, AUC = 1.000). Additionally, the intestinal fungal communities demonstrated satisfactory performance in the validation cohort, with an AUC of 0.884 (95% CI: 0.7871-0.9476) in the Russian validation cohort, which consisted of 36 patients with MDD and 36 healthy individuals. The AUC for the Wuhan validation cohort was 0.838 (95% CI: 0.7403-0.9102), which included 40 patients with MDD and 42 healthy individuals.

CONCLUSION: To summarize, our research revealed the characterization of intestinal fungal communities in MDD and developed a prediction model based on specific intestinal fungal communities. Although MDD has well-established diagnostic criteria, the strategy based on the model of gut fungal communities may offer predictive biomarkers for MDD.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Depressive Disorder, Major/microbiology/diagnosis
*Mycobiome
Biomarkers/analysis
Male
Female
Adult
*Metagenomics/methods
*Fungi/classification/genetics/isolation & purification
Middle Aged
Machine Learning
Support Vector Machine
Case-Control Studies
Feces/microbiology

@article {pmid40535541,
year = {2025},
author = {Kato-Kogoe, N and Tsuda, K and Kudo, A and Sakaguchi, S and Omori, M and Komori, E and Ohmichi, M and Hamada, W and Nakamura, S and Nakano, T and Tamaki, J and Ueno, T},
title = {Salivary microbiota and IgA responses are different in pre-diabetic individuals compared to normoglycemic controls.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1591285},
pmid = {40535541},
issn = {2235-2988},
mesh = {Humans ; *Saliva/microbiology/immunology ; Female ; Male ; *Immunoglobulin A/analysis/immunology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Microbiota/immunology ; *Prediabetic State/immunology/microbiology ; Adult ; Bacteria/classification/genetics/isolation & purification ; Diabetes Mellitus, Type 2/immunology/microbiology ; Aged ; Metagenomics ; DNA, Bacterial/genetics/chemistry ; },
abstract = {INTRODUCTION: In recent years, changes in the oral microbiota of patients with type 2 diabetes mellitus (T2DM) have been increasingly recognized. The salivary microbiota may also be altered in pre-diabetes, which is the earliest stage of abnormal blood glucose regulation and a reversible stage preceding T2DM; however, its characteristics are poorly understood. Salivary immunoglobulin A (IgA) is a host defense factor central to the oral immune system and may play an important role in regulating the salivary microbiota. Given that alterations in immunoreactivity are observed in pre-diabetes, we hypothesized that the salivary IgA response may also be altered; however, limited knowledge exists regarding this. Therefore, in the present study, we aimed to evaluate the characteristics of salivary microbiota and IgA responses against salivary microbiota in individuals with pre-diabetes, comparing them to those in individuals with normoglycemia.

METHODS: Saliva samples were collected from 101 pre-diabetic individuals (PreDM group) and 101 age- and sex-matched normoglycemic controls (Normal group). Further, 16S rRNA metagenomic analysis was performed to compare bacterial microbiota composition. For each of the 19 saliva samples from the PreDM and Normal groups, IgA-enriched and IgA-nonenriched fractions were separated via magnetic-activated cell sorting, followed by 16S rRNA metagenomic analysis. The IgA index was calculated to evaluate the difference in the IgA response to each bacterium between the PreDM and Normal groups.

RESULTS: Bacterial species richness was significantly lower in the PreDM group than in the Normal group (observed operational taxonomic unit index, p = 0.042), and a difference between these groups was noted in the overall salivary microbiota structure (unweighted UniFrac distances, p = 0.009). Salivary IgA responses against several bacterial genera differed between the PreDM and Normal groups. Significantly higher IgA responses were noted against Haemophilus in the PreDM group, with lower responses against Capnocytophaga, Corynebacterium, and Streptococcus relative to those in the Normal group.

CONCLUSIONS: Salivary microbiota and IgA responses differ between pre-diabetic individuals and normoglycemic controls. The current findings advance our understanding of the interaction between oral bacteria and host immune responses in patients with a poor glycemic status.},
}

Humans
*Saliva/microbiology/immunology
Female
Male
*Immunoglobulin A/analysis/immunology
Middle Aged
RNA, Ribosomal, 16S/genetics
*Microbiota/immunology
*Prediabetic State/immunology/microbiology
Adult
Bacteria/classification/genetics/isolation & purification
Diabetes Mellitus, Type 2/immunology/microbiology
Aged
Metagenomics
DNA, Bacterial/genetics/chemistry

@article {pmid40535168,
year = {2025},
author = {Huang, J and Ren, W and Hu, W and Ni, J},
title = {Diagnosis of secondary tuberculosis infection in an asymptomatic elderly with cancer using next-generation sequencing: Case report.},
journal = {Open life sciences},
volume = {20},
number = {1},
pages = {20251123},
pmid = {40535168},
issn = {2391-5412},
abstract = {In recent years, there has been a notable increase in the prevalence of tumors and tuberculosis (TB), particularly among elderly and immunocompromised populations. Early diagnosis and treatment are crucial for significantly improving patient outcomes. However, traditional diagnostic methods exhibit certain limitations. The rapid advancement of metagenomic next-generation sequencing (mNGS) has shown promising applications in the field of infectious diseases. We describe an 88-year-old male with multiple comorbidities, including newly diagnosed localized prostate cancer, who presented asymptomatically. Routine mNGS screening unexpectedly identified Mycobacterium tuberculosis, suggesting that malignancy may foster immune conditions favoring latent TB reactivation. This case emphasizes mNGS's role as a rapid, sensitive diagnostic adjunct for occult infections in high-risk populations.},
}

@article {pmid40535082,
year = {2025},
author = {Wang, C and Hu, B and Liang, Q and Jiang, H and Yuan, L and Li, S},
title = {Oral microbiome and risk of lung cancer: results from a two-sample mendelian randomization analysis.},
journal = {Translational lung cancer research},
volume = {14},
number = {5},
pages = {1715-1723},
pmid = {40535082},
issn = {2218-6751},
abstract = {BACKGROUND: Numerous studies have suggested that the oral microbiome may function as a biomarker for lung cancer screening. However, the relationship between oral microbiome and lung cancer has not been thoroughly investigated. Consequently, investigating the causal relationship between oral microbiome and lung cancer was the primary goal of this study.

METHODS: We conducted a two-sample Mendelian randomization (MR) analysis to investigate the causal relationship between the oral microbiome and lung cancer. Summary statistics for the oral microbiomes were obtained from large-scale metagenome-genome-wide association studies (mgGWAS), while genome-wide association study (GWAS) summary statistics for lung cancer were sourced from the IEU-OpenGWAS online platform. We employed inverse variance weighted (IVW) analysis and Wald ratio methods to evaluate the causal associations between the oral microbiome and lung cancer. Finally, we performed MR Steiger's test to strengthen the validity of the causal associations.

RESULTS: Three oral microbiomes were causally associated with lung cancer. Gemella haemolysans (pheno.388) from saliva and an unclassified species (pheno.844) of Clostridia from saliva were protective factors for lung cancer, and an unclassified species (pheno.1354) of Prevotella from tongue was a risk factor for lung cancer. And there is no bidirectional association of causality between oral microbiomes and lung cancer.

CONCLUSIONS: The oral microbiomes, Gemella haemolysans (pheno.388) from saliva, an unclassified species (pheno.844) of Clostridia from saliva and an unclassified species (pheno.1354) of Prevotella from tongue, were causally associated with lung cancer. Oral microbiology holds significant potential for clinical applications in etiologic exploration, early screening, prevention, and enhancing survival in lung cancer. Regarding treatment, personalized therapy based on oral flora may provide novel therapeutic strategies for lung cancer.},
}

@article {pmid40535022,
year = {2025},
author = {Blaustein, RA and Smith, JE and Toro, M and Pachepsky, Y and Stocker, MD},
title = {Water metagenomes reflect physicochemical water quality throughout a model agricultural pond.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1535096},
pmid = {40535022},
issn = {1664-302X},
abstract = {Agricultural ponds are essential irrigation resources, though may also serve as reservoirs for pathogens and antimicrobial resistance (AMR) genes. While monitoring microbiological water quality is critical for food safety, the influence of sampling factors (e.g., when and where to collect samples) in making risk assessments and potential applications for using environmental covariates as indicators remain unclear. Here, we explored the hypothesis that metagenomes of agricultural waters change with spatiotemporal shifts in physicochemical water quality, i.e., across water depths over time. Water samples and underlying sediments were collected at a model pond at the surface and within the water column (0, 1, 2 m depths) throughout one day (i.e., 9:00, 12:00, 15:00). All samples were processed for shotgun metagenomic sequencing analysis and enumeration of various water quality parameters (e.g., temperature, nutrient concentrations, turbidity, pH, culturable Escherichia coli). At the pond surface, Microcystis aeruginosa and members of Cyanobacteria, along with genes encoding pathways related to photosynthesis and nucleotide biosynthesis, were enriched throughout the day. In contrast, within the water column (1-2 m depths) and sediments, diverse members of Proteobacteria and Actinobacteria were more dominant, along with encoded pathways related to respiration and amino acid biosynthesis. Various aspects of water quality (i.e., chlorophyll dissolved organic matter, ammonia, E. coli concentrations) correlated with water metagenome diversity, albeit not with any specific AMR genes or virulence factors. Nevertheless, de novo assembly of sequenced reads uncovered 22 unique strains encoding several AMR, virulence, or stress response genetic elements, thus linking metagenome functional potential to key taxa. Overall, our findings highlight distinctions in agricultural pond water metagenomes at the surface and in the water column and demonstrate the potential for metagenomic surveillance in water quality monitoring to support food safety.},
}

@article {pmid40535021,
year = {2025},
author = {Chen, Z and Li, Q and Li, F and Yin, L and Wang, L and Ye, T and Wang, Y and Fu, S and Wang, W and Huang, X},
title = {Evolution in a plant matrix: adaptive reshaping of kefir grains microbiota and function during long-term soymilk culture.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1614639},
pmid = {40535021},
issn = {1664-302X},
abstract = {To explore the adaptability of kefir grains in long-term subculture in soymilk, this study tracked the succession and functional changes of its microbial community over 4 months. High-throughput sequencing results showed that the microbial community structure was drastically reshaped, mainly manifested in the relative abundance of Lacticaseibacillus kefiranofaciens decreasing from 95.00 to 15.70%, while Lacticaseibacillus paracasei increased from 0.32 to 76.94%, becoming the dominant bacteria. Metagenomic analysis indicated that L. paracasei possesses key enzymes for metabolizing raffinose, stachyose and sucrose, which is the basis for its efficient utilization of soymilk oligosaccharides and its competitive advantage. The decrease in the abundance of L. kefiranofaciens was associated with a decrease in the synthesis of extracellular polysaccharides (EPS), which in turn caused a reduction in the diameter of kefir grains, an increase in surface viscosity and a partial collapse of the gel matrix structure. The pH and free amino acid content of fermented soymilk did not fluctuate much during the passage process, but the sensory acceptance, antioxidant capacity and angiotensin converting enzyme (ACE) inhibitory activity all showed a downward trend. This work reveals the adaptive evolution mechanism of kefir grains in a plant matrix environment and provides a theoretical basis for the optimization of soymilk fermentation based on limited strains.},
}

@article {pmid40535015,
year = {2025},
author = {Chen, Y and Jiang, X and Zhao, J and Yang, M and Chen, Y and Ling, H and Liu, Y and Deng, F and Wang, Z},
title = {Microbial response under sulfate stress in a sulfur-based autotrophic denitrification system.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1615317},
pmid = {40535015},
issn = {1664-302X},
abstract = {This study investigated the responses of the bacterial community structure and metabolic pathways in a sulfur-based autotrophic denitrification filter (SADF) system to fast elevated sulfate salinity, from 0.04 to 1.2% in 30 days. Results showed that the SADF system exhibited robust sulfate salinity stress tolerance at low nitrate concentrations. In the context of sulfate scenarios, the genus Thiobacillus significantly proliferated and was identified as the dominant sulfur-oxidizing player in the SADF system, achieving a relative abundance of 63.79% under 1.2% sulfate salinity. Cooperative and competitive interactions were found in the SADF-related microorganisms, promoting stable denitrification performance under high salinity. Surprisingly, with a low hydraulic retention time (HRT) of 60 min, metagenomic sequencing revealed a upregulated abundance of functional genes encoding for enzymes associated with nitrogen and sulfur metabolism, while positive correlations were observed between these two pathways in response to sulfate salinity. Furthermore, global wastewater treatment plants were thoroughly explored for the distribution of the SADF-related microorganisms identified in this study. Interestingly, one-way ANOVA analysis showed that the SADF-related microorganisms were widely distributed globally, demonstrating their universality in potential engineering applications worldwide.},
}

@article {pmid40535009,
year = {2025},
author = {He, S and Qi, Y},
title = {The microbiota, the malarial parasite, and the mice-a three-sided relationship.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1615846},
pmid = {40535009},
issn = {1664-302X},
abstract = {In recent years, the role of gut microbiota in modulating malaria susceptibility and infection progression has emerged as a pivotal focus in interdisciplinary research. While existing reviews have delineated mechanisms by which mosquito-associated gut microbiota regulate Plasmodium development, a systematic synthesis of the tripartite interplay among host gut microbiota, Plasmodium and host immunometabolic networks remains absent. Compared with previous studies predominantly focusing on single species or unitary mechanisms, this review fills the gap in cross-species integrated analysis of host-microbiota-pathogen interactions. By consolidating metagenomic, metabolomic, and immunological data, this review transitions from unitary mechanistic explanations to multi-omics-driven systematic analyses, demonstrating that murine microbiota suppresses Plasmodium proliferation through adaptive immune activation and metabolic product regulation. Meanwhile, Plasmodium infection induces decreased microbial diversity and functional pathway deviation in murine microbiota, exacerbating host immunometabolic imbalance. These advancements not only elucidate core biological principles governing "microbiota-host-pathogen" interactions but also transcend traditional pathogen-centric perspectives by pioneering precise intervention strategies based on microbiota homeostasis restoration. This provides theoretical foundation for developing microbiome-targeted precision prevention approaches, which will continue to make substantial contributions to malaria research.},
}

@article {pmid40535002,
year = {2025},
author = {Xamxidin, M and Zhang, X and Zheng, G and Chen, C and Wu, M},
title = {Metagenomics-assembled genomes reveal microbial metabolic adaptation to athalassohaline environment, the case Lake Barkol, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1550346},
pmid = {40535002},
issn = {1664-302X},
abstract = {Salt-tolerant and halophilic microorganisms are critical drivers of ecosystem stability and biogeochemical cycling in athalassohaline environments. Lake Barkol, a high-altitude inland saline lake, provides a valuable natural setting for investigating microbial community dynamics and adaptation mechanisms under extreme salinity. In this study, we employed high-throughput metagenomic sequencing to characterize the taxonomic composition, metabolic potential, and ecological functions of microbial communities in both water and sediment samples from Lake Barkol. We reconstructed 309 metagenome-assembled genomes (MAGs), comprising 279 bacterial and 30 archaeal genomes. Notably, approximately 97% of the MAGs could not be classified at the species level, indicating substantial taxonomic novelty in this ecosystem. Dominant bacterial phyla included Pseudomonadota, Bacteroidota, Desulfobacterota, Planctomycetota, and Verrucomicrobiota, while archaeal communities were primarily composed of Halobacteriota, Thermoplasmatota, and Nanoarchaeota. Metabolic reconstruction revealed the presence of diverse carbon fixation pathways, including the Calvin-Benson-Bassham (CBB) cycle, the Arnon-Buchanan reductive tricarboxylic acid (rTCA) cycle, and the Wood-Ljungdahl pathway. Autotrophic sulfur-oxidizing bacteria, alongside members of Cyanobacteria and Desulfobacterota, were implicated in primary production and carbon assimilation. Nitrogen metabolism was predominantly mediated by Gammaproteobacteria, with evidence for both nitrogen fixation and denitrification processes. Sulfur cycling was largely driven by Desulfobacterota and Pseudomonadota, contributing to sulfate reduction and sulfur oxidation pathways. Microbial communities exhibited distinct osmoadaptation strategies. The "salt-in" strategy was characterized by ion transport systems such as Trk/Ktr potassium uptake and Na[+]/H[+] antiporters, enabling active intracellular ion homeostasis. In contrast, the "salt-out" strategy involved the biosynthesis and uptake of compatible solutes including ectoine, trehalose, and glycine betaine. These strategies were differentially enriched between water and sediment habitats, suggesting spatially distinct adaptive responses to local salinity gradients and nutrient regimes. Additionally, genes encoding microbial rhodopsins were widely distributed, suggesting that rhodopsin-based phototrophy may contribute to supplemental energy acquisition under osmotic stress conditions. The integration of functional and taxonomic data highlights the metabolic versatility and ecological roles of microbial taxa in sustaining biogeochemical processes under hypersaline conditions. Overall, this study reveals extensive taxonomic novelty and functional plasticity among microbial communities in Lake Barkol and underscores the influence of salinity in structuring microbial assemblages and metabolic pathways in athalassohaline ecosystems.},
}

@article {pmid40533851,
year = {2025},
author = {Rahman, N and McCullough, T and Orozco, DF and Walkowiak, S and Farzan, A and Shekarriz, S and Surette, MG and Cicek, N and Derakhshani, H},
title = {Genomic characterization of antimicrobial resistance and mobile genetic elements in swine gut bacteria isolated from a Canadian research farm.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {66},
pmid = {40533851},
issn = {2524-4671},
support = {(RGPIN-2023-04359)//NSERC Discovery Grant/ ; },
abstract = {INTRODUCTION: The widespread use of antimicrobials in the livestock industry has raised global concerns regarding the emergence and spread of antimicrobial resistance genes (ARGs). Comprehensive databases of ARGs specific to different farm animal species can greatly improve the surveillance of ARGs within the agri-food sector and beyond. In particular, defining the association of ARGs with mobile genetic elements (MGEs)-the primary agents responsible for the spread and acquisition of resistant phenotypes among bacterial populations-could help assess the transmissibility potential of clinically relevant ARGs. Recognizing the gut microbiota as a vast reservoir of ARGs, we aimed to generate a representative isolate collection and genome database of the swine gut microbiome, enabling high-resolution characterization of ARGs in relation to bacterial host range and their association with MGEs.

RESULTS: We generated a biobank of bacteria from different sections of the gastrointestinal tracts of four clinically healthy pigs housed at a research farm in Ontario, Canada. The culturing was performed under anaerobic conditions using both selective and general enrichment media to ensure the capture of a diverse range of bacterial families within the swine gut microbiota. We sequenced the genomes of 129 unique isolates encompassing 44 genera and 25 distinct families of the swine gut microbiome. Approximately 85.3% (110 isolates) contained one or more ARGs, with a total of 246 ARGs identified across 38 resistance gene families. Tetracycline and macrolide resistance genes were the most prevalent across different lineages of the swine gut microbiota. Additionally, we observed a wide range of MGEs, including integrative conjugative elements, plasmids, and phages, frequently associated with ARGs, indicating that the swine gut ecosystem is conducive to the horizontal transfer of ARGs. High-throughput alignment of the identified ARG-MGE complexes to large-scale metagenomics datasets of the swine gut microbiome suggests the presence of highly prevalent and conserved resistome sequences across diverse pig populations.

CONCLUSION: Our findings reveal a highly diverse and relatively conserved reservoir of ARGs and MGEs within the gut microbiome of pigs. A deeper understanding of the microbial host range and potential transmissibility of prevalent ARGs in the swine microbiome can inform development of targeted antimicrobial resistance surveillance and disease control programs.},
}

@article {pmid40533761,
year = {2025},
author = {Hosch, S and Hamelin, B and Haslbauer, JD and Field, CM and Heim, A and Boeck, L and Savic Prince, S and Gradistanac, TA and Gander, AE and Keller, PM and Leuzinger, K and Mertz, KD},
title = {Human mastadenovirus pneumonia in two immunocompetent patients.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {198},
pmid = {40533761},
issn = {1743-422X},
mesh = {Humans ; Female ; Lung/pathology/virology/diagnostic imaging ; *Mastadenovirus/isolation & purification/genetics/classification ; *Pneumonia, Viral/pathology/virology/diagnosis ; Middle Aged ; Switzerland ; Tomography, X-Ray Computed ; *Adenovirus Infections, Human/pathology/virology/diagnosis ; Immunocompetence ; Histocytochemistry ; Whole Genome Sequencing ; Aged ; },
abstract = {BACKGROUND: Human adenoviruses (hAdV) are common pathogens associated with acute respiratory tract infections. Mastadenovirus blackbeardi (hAdV-B) has been linked to severe pneumonia and disseminated disease, primarily in immunocompromised patients. The histopathological and clinical features of adenoviral pneumonia remain poorly characterized.

CASE PRESENTATION: We report two cases of hAdV-B pneumonia in immunocompetent female patients with a history of smoking. Both patients are of Caucasian origin and reside in Switzerland. They presented with persistent respiratory symptoms, pulmonary infiltrates on CT scans, and necrotizing granulomatous inflammation in lung tissue. After excluding other pathogens, metagenomic whole-genome sequencing identified hAdV-B in both cases. Both patients recovered fully following wedge resection of the affected lung tissue, without the need for additional therapy.

CONCLUSIONS: These two cases demonstrated a remarkably similar clinical and histopathological profile, characterized by chronic granulomatous lung inflammation. The findings suggest a prolonged inflammatory response leading to persistent tissue damage. Our observations highlight the potential of hAdV-B to cause chronic pneumonia even in otherwise healthy individuals.},
}

Humans
Female
Lung/pathology/virology/diagnostic imaging
*Mastadenovirus/isolation & purification/genetics/classification
*Pneumonia, Viral/pathology/virology/diagnosis
Middle Aged
Switzerland
Tomography, X-Ray Computed
*Adenovirus Infections, Human/pathology/virology/diagnosis
Immunocompetence
Histocytochemistry
Whole Genome Sequencing
Aged

@article {pmid40533170,
year = {2025},
author = {Kumari Nawarathna, TNT and Fujii, N and Yamamoto, K and Kuroda, K and Narihiro, T and Ozaki, N and Ohashi, A and Kindaichi, T},
title = {Metagenomic Insights into Candidatus Scalindua in a Long-term Cultivated Marine Anammox Consortium: The Important Role of Tetrahydrofolate-mediated Carbon Fixation.},
journal = {Microbes and environments},
volume = {40},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME25007},
pmid = {40533170},
issn = {1347-4405},
mesh = {*Bacteria/metabolism/genetics/classification/isolation & purification ; *Carbon Cycle ; Metagenomics ; *Microbial Consortia/genetics ; *Ammonia/metabolism ; Folic Acid/metabolism/biosynthesis ; *Seawater/microbiology ; Metagenome ; Bioreactors/microbiology ; Metabolic Networks and Pathways ; Phylogeny ; Genome, Bacterial ; Wastewater/microbiology ; Carbon/metabolism ; },
abstract = {Marine anammox bacteria have been an exciting research area in recent years due to their high effectiveness in treating ammonia-containing saline wastewater. However, their direct implementation in the wastewater industry faces challenges due to slow growth, difficulty obtaining pure cultures, and their tendency to exist as part of an anammox consortium, interacting symbiotically with other bacteria. In the present study, 91 draft genome metagenome-assembled genomes (MAGs) from a long-term-operated reactor were recovered to clarify detailed symbiotic interactions within an anammox consortium. One marine anammox bacterial MAG, identified as Candidatus Scalindua, was successfully recovered and was abundant within the sampled microbial community. A comprehensive metabolic pathway ana-lysis revealed that Ca. Scalindua exhibited the complete anammox pathway and the Wood-Ljungdahl pathway for carbon fixation. The folate biosynthesis pathway in Ca. Scalindua was incomplete, lacking dihydrofolate reductase, a key enzyme for tetrahydrofolate (THF) production. The folate biopterin transporter, essential for transporting folate-related metabolites among coexisting bacteria, was identified exclusively in Ca. Scalindua. In addition, the impact of exogenously supplied THF on microbial activity and carbon uptake rates was investigated in batch experiments using [14]C-labeled bicarbonate. The results obtained revealed that 2‍ ‍mg L[-1] of exogenous THF resulted in a 43% increase in the carbon uptake rate, while anammox activity remained unaffected. The present results suggest that THF is a key intermediate for carbon fixation in Ca. Scalindua and may be essential for their growth.},
}

*Bacteria/metabolism/genetics/classification/isolation & purification
*Carbon Cycle
Metagenomics
*Microbial Consortia/genetics
*Ammonia/metabolism
Folic Acid/metabolism/biosynthesis
*Seawater/microbiology
Metagenome
Bioreactors/microbiology
Metabolic Networks and Pathways
Phylogeny
Genome, Bacterial
Wastewater/microbiology
Carbon/metabolism

@article {pmid40532861,
year = {2025},
author = {Biswas, I and Mitra, D and Mallik, C and Das Mohapatra, PK},
title = {Characterization and toxicity assessment of metabiotic produced through natural tannin fermentation by newly isolated probiotic Lactiplantibacillus plantarum PKI15 and study of its effect on gut microbiome through metagenomics approach.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107815},
doi = {10.1016/j.micpath.2025.107815},
pmid = {40532861},
issn = {1096-1208},
abstract = {Metabiotic fabrication has been done by mixed plant fermentation of Terminalia bellirica and Phyllanthus emblica fruit extract with probiotic bacteria Lactiplantibacillus plantarum PKI15 and showed considerable tannase (0.36 U/ml), gallic caid and pyrogallol production. Fermentative end-product analysis through FTIR, LC-MS and GC-MS analysis result indicates the presence of several bioactive compounds confirming the presence of gallic acid and pyrogallol respectively. Molecular docking analysis of the identified bioactive compounds with the protein myeloperoxidase denotes quercetin-3β-D-glucoside as the best ligand showing a binding score of -9.5 Kcal/mol. The formulated metabiotic revealed potential antibacterial and antioxidant properties activities. In-vivo toxicity assessment was done on the laboratory rats. Results revealed reduced body weight, urea content and creatinine level. Increase in superoxide dismutase, catalase activity and reduced content of conjugated diene, glutamate pyruvate transaminase and glutamic-oxaloacetic transaminase further supports the antioxidative potential of the metabiotic. Further study through histological sectioning of liver, kidney and spleen showed no structural abnormalities. Finally, metagenomics analysis of the gut microbiome of the experimental rats was done to check the influence of the formulated metabiotic on the gut commensals and it was found that species of Bifidobacterium and Pseudomonas are the most prevalent members of the examined groups, while, the relative proportion of other bacterial genera, such as Lactobacillus, Lactococcus, and Bacillus, were found to vary among the groups. Thus, both the in vivo and in silico studies proved that the formulated metabiotic is non-toxic and safe in use.},
}

@article {pmid40532815,
year = {2025},
author = {Pan, D and Sun, H and Liu, Y and Wang, J and Kuang, Y and Shi, T and Zhang, H},
title = {Mobilome dominates fomesafen-responsive dissemination of antibiotic resistome in manure-amended agricultural soils.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126686},
doi = {10.1016/j.envpol.2025.126686},
pmid = {40532815},
issn = {1873-6424},
abstract = {Pesticides are increasingly perceived as emerging drivers in the spread of antibiotic resistance genes (ARGs) within agroecosystems. Pesticides with longer half-lives tend to impose persistent stresses on soil microbiomes, yet the selection for ARG dissemination remains overlooked. Focusing on a widely used long residual herbicide fomesafen, we examined recommended dose-based selection on the dissemination of ARGs in agricultural soils with or without manure amendment. The degradation half-lives of fomesafen in the blank soils and manure-amended soils were 35.77-124.00 and 20.00-73.27 d, respectively. After 42d exposure, the total abundances of ARGs in the fomesafen-treated manure-amended soils at exposure concentrations of 1 and 5 mg/kg were 1.20- and 1.36-fold higher than that in the controls, with the changes of mobile genetic elements (MGEs) reaching 1.24-2.22 folds; while no significant changes were observed in the blank soils. Furthermore, no significant changes were observed in either bacterial communities or ARG-carrying metagenome-assembled genomes in both manure-amended soils and blank soils under fomesafen selection. Variation partition analysis suggested that 24.42%-25.41% of the variations in ARGs could be individually explained by MGEs, while only 13.47%-13.75% by bacterial communities. Overall, these findings demonstrate that MGE-mediated horizontal transfer predominates fomesafen-responsive dissemination of ARGs in manure-amended agriculture soils and underscores the urgency of re-evaluating agricultural practices involving co-application of manures and long residual herbicides.},
}

@article {pmid40532696,
year = {2025},
author = {Er, YX and Lee, SC and Aneke, C and Conlan, S and Muslim, A and Deming, C and Che, Y and Yap, NJ and Tee, MZ and Abdull-Majid, N and Shahrizal, S and Leong, KF and Han, J and Shen, Z and Than, LTL and Park, M and Mohd Sayed, I and , and Seyedmousavi, A and Kong, HH and Loke, P and Segre, JA and Lim, YAL},
title = {Trichophyton concentricum fungal infections and skin microbiomes of Indigenous Peninsular Malaysians.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.034},
pmid = {40532696},
issn = {1097-4172},
abstract = {Recent outbreaks of multidrug-resistant fungi infecting human skin emphasize the importance of understanding fungal pathophysiology and spread. In efforts to address health concerns with various Indigenous Peninsular Malaysians (Orang Asli [OA]), tinea imbricata-a Trichophyton concentricum fungal skin infection-emerged as a particular concern. We investigated the etiology and transmission of tinea imbricata by culturing, testing antifungal sensitivities, and sequencing T. concentricum isolates in remote OA villages. Among regionally conserved isolates, we identified the emergence of terbinafine-resistant T. concentricum microbiologically and genomically. Investigating the skin microbiomes of 82 Indigenous OA, we found unique microbiota and lower relative abundances of bacterial commensals (Cutibacterium acnes, Staphylococcus epidermidis) among OA versus Malaysian and US urban populations, emphasizing how understudied populations provide unprecedented knowledge on host-microbiome co-evolution. These findings provide valuable insights into clinical, microbiological, and genomic features of chronic fungal skin infections, offering the potential to inform strategies to address drug resistance and effective therapy.},
}

@article {pmid40532535,
year = {2025},
author = {Wang, Z and He, Y and Luo, M and Liu, S and Hou, J and Cao, B and An, X},
title = {Transfer toxicity of polystyrene microplastics in vivo: Multi-organ crosstalk.},
journal = {Environment international},
volume = {202},
number = {},
pages = {109604},
doi = {10.1016/j.envint.2025.109604},
pmid = {40532535},
issn = {1873-6750},
abstract = {The accumulation of microplastics (MPs) within the environment caused serious ecological and health problems. Nevertheless, its systemic toxicity to organisms and its mechanisms lack effective evidence. This study established a model of MP exposure through the gavage of polystyrene (PS)-MPs particles to maternal mice on days 1 to 21 of lactation. The results demonstrated that PS-MPs were distributed widely in maternal mice, occurring mainly in the feces, colon, liver and mammary glands. Further experiments revealed that the gut and blood-milk barriers were disrupted, and pathological injury and inflammatory reactions were observed in the liver, gut, and mammary glands. Metabolomic and metagenome analysis indicated abnormalities in hepatic bile acid metabolism and significant alterations in the gut microbiota after exposure to PS-MPs. These alterations led to increased disruption of the intestine-liver axis. Notably, with fecal microbiota transplantation and antibiotic experiments, we observed that elimination of the intestinal microbiota reduced tissue inflammation and improved gut and blood-milk barrier leakage. These findings demonstrated that PS-MPs exaggerated intestine-liver axis disorders by inducing colonic injury, intestinal ecological dysregulation and abnormal hepatic bile acid metabolism. Furthermore, PS-MPs translocated via the intestine-liver axis and exerted broader toxic effects on mammary tissue. Overall, our study uncovered the transfer toxicity of PS-MPs in mice, proposing the possibility of a gut-liver-mammary axis.},
}

@article {pmid40532529,
year = {2025},
author = {Parab, AS and Ghose, M and Manohar, CS},
title = {Metagenomic reconstruction of microbial genomes and biogeochemical pathways: insights into carbon and nitrogen flux dynamics in the eastern Arabian Sea.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107292},
doi = {10.1016/j.marenvres.2025.107292},
pmid = {40532529},
issn = {1879-0291},
abstract = {The eastern Arabian Sea (EAS) experiences seasonal nutrient availability and productivity shifts driven by the Indian monsoon, influencing microbial contributions to biogeochemical cycles. This study explores carbon, nitrogen and sulfur cycling using metagenome-assembled genomes (MAGs) from water samples collected at chlorophyll maxima (C-Max) depths during non-monsoon and monsoon seasons. A total of 49 high-quality MAGs were reconstructed from 12 metagenomic samples, including four novel lineages from the phyla Pseudomonadota and Bacteroidota. These MAGs revealed distinct seasonal shifts in microbial composition and function. During the non-monsoon season, microbial communities dominated by Idiomarina and Marinobacter showed increased gene abundance for C1 compound metabolism, nitrogen cycling and sulfur oxidation, processes essential for managing climate-active gases such as carbon dioxide (CO2) and nitrous oxide (N2O), while also preventing toxic sulfide accumulation. In contrast, monsoon conditions enhanced organic matter influx, promoting nitrogen retention pathways driven by Sinimarinibacterium and Oleibacter, raising concerns about potential nutrient buildup and localized hypoxia. Despite seasonal variations, functional redundancy ensured the stability of nutrient cycling processes. PERMANOVA analysis (p < 0.001) confirmed that microbial functional gene distribution was primarily shaped by taxonomic structure, with genus-level composition playing a dominant role. The study highlights microbial adaptability and resilience, ensuring ecosystem stability in the dynamic EAS environment. Understanding microbial processes at C-Max depths has enhanced our understanding of biogeochemical cycling in the EAS. Although focused on oxygenated depths, these findings offer insights relevant to microbial functions in the OMZ, reflecting the distinct environmental conditions of EASs.},
}

@article {pmid40532377,
year = {2025},
author = {Deng, Y and Li, J and Taherzadeh, MJ and Lu, H and Kong, D and Ma, B and Hu, Y and Chen, G and Ruan, Y},
title = {Metagenomics reveal the mechanisms of integrated heterotrophic and sulfur autotrophic denitrification (HSAD) using PBAT/starch as carbon source.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138943},
doi = {10.1016/j.jhazmat.2025.138943},
pmid = {40532377},
issn = {1873-3336},
abstract = {The accumulation of nitrate in recirculating aquaculture system constrains the sustainable development of aquaculture industry. This study evaluated the performance of two heterotrophic sulfur autotrophic denitrification (HSAD) reactors packed with PBAT/starch granules and supplemented with thiosulfate in the influent, operating at salinities of 0 ‰ (Reactor I) and 25 ‰ (Reactor II) over a 163-day period. Reactor I achieved an average nitrate removal rate of 0.17 kg/m[3]/d with minimal accumulation of nitrite, total ammonia nitrogen (TAN) and dissolved organic carbon (DOC). In contrast, Reactor II exhibited a slower start-up, a lower denitrification rate of 0.08 kg/m[3]/d, and higher fluctuations in water quality parameters. Over time, both reactors transitioned from heterotrophic to sulfur autotrophic denitrification, as evidenced by increased effluent sulfate concentration, acidification and a decline in microbial biomass. Metagenomics and metatranscriptomics analyses revealed the coexistence of autotropic and heterotrophic denitrifying bacteria, with salinity inhibiting the abundance of denitrifying bacteria and expression of functional genes associated with nitrogen and sulfur metabolism. Network analysis further identified positive correlations among microorganisms involved in carbon, nitrogen and sulfur cycling. This study provides insights into the microbial mechanisms in HSAD process and offers a promising approach for the treatment of nitrate-rich aquaculture wastewater.},
}

@article {pmid40531665,
year = {2025},
author = {Phithakrotchanakoon, C and Kitikhun, S and Siriarchawatana, P and Charoenyingcharoen, P and Jeennor, S and Nilsakha, T and Chanpet, A and Vorajinda, T and Mayteeworakoon, S and Yukphan, P and Ingsriswang, S},
title = {Flavobacterium mekongense sp. nov., isolated from the Mekong River in Thailand.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {6},
pages = {},
doi = {10.1099/ijsem.0.006815},
pmid = {40531665},
issn = {1466-5034},
mesh = {Thailand ; *Flavobacterium/classification/genetics/isolation & purification ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rivers/microbiology ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Base Composition ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Vitamin K 2/analogs & derivatives/chemistry/analysis ; Nucleic Acid Hybridization ; Genome, Bacterial ; Phospholipids/analysis/chemistry ; *Water Microbiology ; },
abstract = {Two Gram-stain-negative, aerobic, non-motile, non-gliding, rod-shaped bacterial strains, designated as TBRC 19031[T] and TBRC 19032, were isolated from water samples collected from the Mekong River, Thailand. Strain TBRC 19031[T] was obtained from Chiang Saen in the upstream section near the borders with China and Myanmar, while TBRC 19032 originated from Khong Chiam, in the downstream section where the river exits Thailand. Colonies of both strains were circular, smooth and deep yellow on Reasoner's 2A agar and did not produce flexirubin-type pigments. Phylogenetic analysis with 16S rRNA gene sequences placed both strains within the genus Flavobacterium, showing the highest sequence similarity to Flavobacterium cheonhonense ARSA-15[T] (98.29% for TBRC 19031[T] and 98.22% for TBRC 19032). However, whole-genome comparisons between the strains and F. cheonhonense ARSA-15[T] revealed average nt identity (89.39% and 89.29%), average aa identity (92.84% and 92.95%) and digital DNA-DNA hybridization (35.00% and 34.70%). The predominant fatty acids were iso-C15:1, iso-C15:0 and iso-C15:0 3-OH, and menaquinone MK-6 was the major respiratory quinone. The major polar lipids of both strains included phosphatidylethanolamine, steryl ester and diacylglycerol. The genome sizes were 3.02 and 3.04 Mbp, with G+C contents of 38.3% and 38.2% for TBRC 19031[T] and TBRC 19032, respectively. Comparative genomic analyses revealed the absence of genes involved in sulphate reduction and denitrification pathways and the presence of a gene encoding phosphatidylinositol synthase, distinguishing them from other Flavobacterium within the clade. Ecological profiling using public metagenomic datasets showed that both strains were associated with lotic freshwater environments. This study not only introduces Flavobacterium mekongense sp. nov. as a new species but also provides broader insights into the ecology, metabolism and environmental distribution of freshwater Flavobacterium. The genomic features identified here offer promising leads for future studies in microbial ecology, comparative genomics and functional gene mining in aquatic ecosystems. The type strain is TBRC 19031[T] (TBRC 19031[T]=NBRC 117006[T]).},
}

Thailand
*Flavobacterium/classification/genetics/isolation & purification
*Phylogeny
RNA, Ribosomal, 16S/genetics
*Rivers/microbiology
Fatty Acids/chemistry/analysis
DNA, Bacterial/genetics
Base Composition
Bacterial Typing Techniques
Sequence Analysis, DNA
Vitamin K 2/analogs & derivatives/chemistry/analysis
Nucleic Acid Hybridization
Genome, Bacterial
Phospholipids/analysis/chemistry
*Water Microbiology

@article {pmid40530883,
year = {2025},
author = {Ganote, CL and Caesar, L and Rice, DW and Whitaker, RJ and Newton, ILG},
title = {Evolutionary trends in Bombella apis CRISPR-Cas systems.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0016625},
doi = {10.1128/msystems.00166-25},
pmid = {40530883},
issn = {2379-5077},
abstract = {UNLABELLED: Bacteria and archaea employ a rudimentary immune system, CRISPR-Cas, to protect against foreign genetic elements such as bacteriophage. CRISPR-Cas systems are found in Bombella apis. B. apis is an important honey bee symbiont, found primarily in larvae, queens, and hive compartments. B. apis is found in the worker bee gut but is not considered a core member of the bee microbiome and has therefore been understudied with regard to its importance in the honey bee colony. However, B. apis appears to play beneficial roles in the colony, by protecting developing brood from fungal pathogens and by bolstering their development under nutritional stress. Previously, we identified CRISPR-Cas systems as being acquired by B. apis in its transition to bee association, as they are absent in a sister clade. Here, we assess the variation and distribution of CRISPR-Cas types across B. apis strains. We found multiple CRISPR-Cas types, some of which have multiple arrays, within the same B. apis genomes and also in the honey bee queen gut metagenomes. We analyzed the spacers between strains to identify the history of mobile element interaction for each B. apis strain. Finally, we predict interactions between viral sequences and CRISPR systems from different honey bee microbiome members. Our analyses show that the B. apis CRISPR-Cas systems are dynamic; that microbes in the same niche have unique spacers, which supports the functionality of these CRISPR-Cas systems; and that acquisition of new spacers may be occurring in multiple locations in the genome, allowing for a flexible antiviral arsenal for the microbe.

IMPORTANCE: Honey bee worker gut microbes have been implicated in everything from protection from pathogens to breakdown of complex polysaccharides in the diet. However, there are multiple niches within a honey bee colony that host different groups of microbes, including the acetic acid bacterium Bombella apis. B. apis is found in the colony food stores, in association with brood, in worker hypopharyngeal glands, and in the queen's digestive tract. The roles that B. apis may serve in these environments are just beginning to be discovered and include the production of a potent antifungal that protects developing bees and supplementation of dietary lysine to young larvae, bolstering their nutrition. Niche specificity in B. apis may be affected by the pressures of bacteriophage and other mobile elements, which may target different strains in each specific bee environment. Studying the interplay between B. apis and its mobile genetic elements (MGEs) may help us better understand microbial community dynamics within the colony and the potential ramifications for the honey bee host.},
}

@article {pmid40530822,
year = {2025},
author = {Wu, H and Sun, B and Li, J},
title = {Metagenomics research on PAH biodegradation in the lower reaches of the Shiwuli River in Chaohu, China.},
journal = {Environmental science. Processes & impacts},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5em00025d},
pmid = {40530822},
issn = {2050-7895},
abstract = {Metagenomics is a powerful tool for investigating functional microorganisms, molecular mechanisms and genes involved in the degradation of polycyclic aromatic hydrocarbons (PAHs) in situ complex environments. In this study, we selected three land use types in the lower reaches of the Shiwuli River in Chaohu and applied metagenomics technology. The results revealed that Rhodoplanes and Bradyrhizobium were the abundant PAH-degrading microorganisms across the three land use types. Based on the functional annotation and PAH degradation pathway, it was found that the in situ microbial communities of the three land use types shared common metabolic pathways for phenanthrene degradation. In addition, a unique metabolic pathway for PAH degradation was identified in the agricultural land. Only Patulibacter contributed to flnE (KO14604) in the agricultural land, which was involved in the metabolic pathway of fluorene degradation. Results of this study suggested that the in situ degradation of PAHs was not completed by a single genus, and it involved the synergy effects of different PAH-degrading microorganisms. There was no significant difference between the compositions and relative abundances of PAH-degrading microorganisms in the three land use types and those presented in the Kyoto Encyclopedia of Genes and Genomes Orthology (KO). However, the same microorganism contributed to different functional genes in different samples. Genes encoding protocatechuic acid 4,5-dioxygenase were widely distributed and relatively abundant. Therefore, this gene may serve as an indicator of PAH degradation potential. Among all the factors, the total organic carbon and nitrate nitrogen contents exhibited significant influences on the functional genes (KO) related to PAH degradation (p < 0.05).},
}

@article {pmid40530648,
year = {2025},
author = {Alam, I and Najar, F and Fathepure, B},
title = {Metagenome-assembled genomes of two salt-tolerant methylotrophs enriched from a sulfur-rich Zodletone spring in Oklahoma, USA.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0046125},
doi = {10.1128/mra.00461-25},
pmid = {40530648},
issn = {2576-098X},
abstract = {We obtained metagenome-assembled genomes (MAGs) of two salt-tolerant methylotrophic bacteria, Methylohalobius sp. strain ZOD2 and Methyloligella sp. strain ZOD6, from an enrichment culture derived from sediment collected at a sulfur-rich spring in Oklahoma, USA. These MAGs offer insights into the methane oxidation capabilities of these bacteria under high-salinity conditions.},
}

@article {pmid40530272,
year = {2025},
author = {Jia, Y and Wang, J and Lin, X and Liang, T and Dai, H and Wu, B and Yang, M and Zhang, Y and Li, R},
title = {Integrated metabolomics and metagenomics reveal plant-microbe interactions driving aroma differentiation in flue-cured tobacco leaves.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1588888},
pmid = {40530272},
issn = {1664-462X},
abstract = {Current research on tobacco aroma predominantly focuses on single-omics approaches. In this study, we conducted a comprehensive investigation of the relationships between tobacco metabolite profiles, microbial communities, and aroma characteristics. Untargeted metabolomics and metagenomic analyses were performed on flue-cured upper tobacco leaves to compare light aromatic tobacco (LAT) and strong aromatic tobacco (SAT). The results showed that sugar metabolite levels in LAT were significantly higher than those in SAT, whereas levels of specific acids and amino acid metabolites in SAT exceeded those in LAT. Redundancy analysis (RDA) and metabolomic correlation analyses indicated that the genera Methylorubrum and Pseudomonas may promote sugar metabolite accumulation, while Pseudokineococcus potentially regulates both sugar and acid metabolites. In contrast, Methylobacterium and Sphingomonas were associated with acid and amino acid metabolism, with Methylobacterium additionally exhibiting inhibitory effects on sugar metabolism. Metagenomic analysis revealed that Methylorubrum, Pseudomonas, and Pseudokineococcus were abundant in LAT, whereas Methylobacterium and Sphingomonas dominated in SAT. Notably, the bidirectional regulation of aromatic metabolites by microbial genera such as Pseudokineococcus highlights the universality of plant-microbe interactions in shaping metabolic networks-a mechanism potentially applicable to other crop systems. These findings reveal conserved microbial functional traits (e.g., metabolic pathway modulation) that may drive plant phenotypic differentiation beyond tobacco, offering insights into microbiome-mediated crop quality improvement. The results provide theoretical guidance for tobacco aging and aroma regulation and underscore the broader significance of microbial community engineering in agriculture for manipulating plant metabolic outputs.},
}

@article {pmid40529498,
year = {2025},
author = {Zhu, L and Han, R and He, L and Pan, B and Zhong, W and Li, Y and Liu, X},
title = {Innovative strategies for post-stroke depression: integrating traditional Chinese medicine with neurobiological insights, including the gut-brain axis.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1539357},
pmid = {40529498},
issn = {1663-9812},
abstract = {Post-stroke depression (PSD) is a debilitating condition affecting more than one-third of stroke survivors, leading to significant impairments in mood, cognitive function, and overall quality of life. While conventional treatments like selective serotonin reuptake inhibitors (SSRIs) are commonly used, their efficacy is often limited, and they are associated with adverse side effects. Emerging research underscores the critical roles of neuroinflammation, neurotransmitter imbalances, and disruptions in the gut-brain axis in the development and progression of PSD, suggesting that targeting these pathways could lead to more effective therapeutic outcomes. Traditional Chinese Medicine (TCM) presents a promising multi-faceted approach, addressing these complex biological mechanisms by regulating neurotransmitter systems, modulating immune responses, and restoring gut microbiota balance. Key herbs such as Salvia miltiorrhiza Bunge (Lamiaceae; Dan Shen) and Bupleurum chinense DC. (Apiaceae; Chai Hu) have shown significant potential in modulating neurotransmitter levels, reducing neuroinflammation, and providing neuroprotection. Additionally, TCM formulations like Chaihu Shugan Powder (CSP) and Shugan Jieyu Capsules (SG) further enhance these effects by promoting gut microbiota homeostasis and restoring metabolic balance. This review delves into the biological mechanisms underlying PSD, with a particular focus on neuroinflammation, neurotransmitter dysregulation, and gut-brain axis dysfunction. It also explores the potential of integrating TCM with advanced multi-omics technologies-such as metabolomics, metagenomics, and transcriptomics-to develop personalized treatment strategies for PSD. By combining the holistic principles of TCM with modern Western medicine and cutting-edge omics technologies, this integrative approach offers a comprehensive framework for managing PSD, with the potential to significantly improve recovery outcomes and enhance the quality of life for stroke survivors.},
}

@article {pmid40529430,
year = {2025},
author = {Chen, R and Li, R and Jiang, J and Zhou, L and Zhao, S and Zhang, Y and Xia, Q and Yang, Z},
title = {Coconut oil derived medium-chain triglycerides ameliorated memory deficits via promoting neurite outgrowth and maintaining gut homeostasis in 5×FAD mice.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1585640},
pmid = {40529430},
issn = {2296-861X},
abstract = {Alzheimer's disease (AD) is a prevalent neurodegenerative disorder characterized by neurite atrophy, neuronal loss, and memory impairment. Medium-chain triglycerides (MCT), a type of fatty acid predominantly found in coconut oil, have been shown to improve metabolic syndrome as well as cognitive performance via ketone production in humans. Here, we investigated the protective effects of MCT on neurite atrophy and memory deficits in 5×FAD mice and elucidated the underlying mechanisms. First, virgin coconut oil (VCO), refined, bleached, and deodorized coconut oil (RBDCO), and MCT were orally administered to 6-8 months old 5×FAD mice for 9 consecutive weeks, the effects on cognition were then evaluated. MCT demonstrated superior effects compared to RBDCO and VCO in reducing Aβ levels, inhibiting hyperactivated microglia and astroglia, protecting neurons, and mitigating memory decline. Further, metagenomic analysis and RT-qPCR results revealed that MCT intervention increased the relative abundance of Akkermansia, reduced intestinal permeability, and elevated the concentration of short-chain fatty acids in the brain. Additionally, MCT treatment significantly protected primary cortical neurons against Aβ25-35-induced apoptosis and promoted neurite regeneration. Transcriptome and RT-qPCR data suggested that Ucp1 and Flor1 may be potential targets through which MCT exerts its neuroprotective effects. Our findings suggest that MCT may help prevent the progression of AD by promoting neurite outgrowth and maintaining gut homeostasis in 5×FAD mice, offering a theoretical foundation for the development of dietary therapies for AD.},
}

@article {pmid40528946,
year = {2025},
author = {Miao, Y and Sun, M and Huo, R and Chen, Y and Xie, J and Dong, T and Zhang, M},
title = {Metagenomics and volatile metabolomics reveal microbial succession and flavor formation mechanisms during fermentation of Novel Pasture-style Laozao.},
journal = {Food chemistry: X},
volume = {28},
number = {},
pages = {102598},
pmid = {40528946},
issn = {2590-1575},
abstract = {Novel Pasture-style Laozao (NPLZ) is a local specialty fermented food with unique flavor and mouthfeel. This study investigated the dynamic changes of physicochemical properties, volatile flavor substances and microbial community succession during the fermentation of NPLZ and revealed their interactions through the joint analysis of metagenomics and volatile metabolomics. Differences in the contents of 52 characteristic flavor substances were the main reasons for the changes in aroma. Saccharomyces cerevisiae, Pseudomonas oryzihabitans, and Pantoea vagans were the dominant microbial communities during fermentation. Under symbiotic conditions, five species including Paenibacillus piri and Methyloversatilis thermotolerans were found to be crucial in influencing microbial community succession. The accumulation of organic acids was identified as the primary environmental factor driving changes in microbial community structure. Through correlation analysis, eight microbial species were identified as core microorganisms affecting flavor differences, and the metabolic networks of key flavor metabolites were reconstructed in conjunction with the KEGG database.},
}

@article {pmid40528807,
year = {2025},
author = {Ding, X and Wang, J and Zhu, W},
title = {The hydrogenation metabolism process of rosmarinic acid by microbial enzymes in chickens.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70000},
pmid = {40528807},
issn = {1097-0010},
support = {2017YFE0135200//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: The gut microbiota plays a critical role in the metabolism of rosmarinic acid (RA) through converting RA to caffeic acid (CA), danshensu (DSS), and m-coumaric acid. However, the gut environment and microbiota may have complicated metabolic converting RA processes. This study aimed to investigate the metabolism of RA in gastrointestinal tract of chickens through liquid chromatography-tandem mass spectrometry (LC-MS/MS) and metagenomic analysis.

RESULTS: Through in vivo and in vitro studies, RA was found to be hydrogenated into dihydrorosmarinic acid, then hydrolyzed into DSS and dihydrocaffeic acid (DHCA). DSS and DHCA could be further converted to 3-hydroxyphenylpropionic acid. But RA remained stable in the stomach, duodenum, jejunum, and ileum, as well as in the cecum of antibiotic-treated chickens. This indicated that the degradation of RA was mainly mediated by cecal microbiota. Furthermore, the metagenomic analysis of cecal microbiota revealed that reductases and hydrolases from Clostridium spp., Alistipes spp., and other microbiota were involved in these processes. NADH:flavin oxidoreductase and 3-oxoacyl-[acyl-carrier-protein] reductase participated in the hydrogenation reaction of RA, and BaiCD involved in dehydroxylation reaction of RA.

CONCLUSION: The hydrogenation process by microbial enzymes was an important metabolic pathway of RA. These hydrogenation products contribute to improving the biological function of RA. © 2025 Society of Chemical Industry.},
}

@article {pmid40528698,
year = {2025},
author = {Bonilla-Espadas, M and Lifante-Martínez, I and Camacho, M and Orgilés-Calpena, E and Arán-Aís, F and Bertazzo, M and Bonete, MJ},
title = {Chromium-Tanned Leather and Microbial Consortia: Identification of Taxa With Biodegradation Potential and Chromium Tolerance.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70134},
doi = {10.1111/1758-2229.70134},
pmid = {40528698},
issn = {1758-2229},
support = {IMDEEA/2021/11//European Union through the European Regional Development Fund within the Operational Programme of the Valencian Community 2014-2020/ ; UAIND21-02B//Universidad de Alicante/ ; },
mesh = {*Chromium/metabolism/toxicity ; *Microbial Consortia ; Biodegradation, Environmental ; Biofilms/growth & development ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Microscopy, Electron, Scanning ; Tanning ; },
abstract = {Chromium-tanned leather waste poses significant environmental challenges due to its resistance to degradation and heavy metal content. This study investigates the potential of naturally selected microbial consortia to initiate the degradation of chromium-tanned leather and identifies key bacterial genera capable of tolerating chromium and producing enzymes relevant to collagen breakdown. A novel multidisciplinary approach combining gravimetric assays, metagenomic sequencing, and scanning electron microscopy (SEM) was applied to characterise both microbial composition and degradation dynamics. Dominant genera such as Bacillus, Microbacterium, and Acinetobacter were associated with collagen degradation and metal tolerance, with Bacillus-rich communities showing the most pronounced mass loss (up to 3%). SEM analysis revealed the formation of robust biofilms and extensive matrix disruption, indicating enzymatic activity and structural breakdown of the leather. The formation of exopolysaccharide-rich biofilms was found to be critical for microbial adhesion and biodegradation efficacy. These findings provide initial insights into microbial mechanisms involved in the degradation of chromium-tanned leather and suggest potential applications for microbial consortia in future sustainable leather waste management strategies.},
}

*Chromium/metabolism/toxicity
*Microbial Consortia
Biodegradation, Environmental
Biofilms/growth & development
*Bacteria/metabolism/classification/genetics/isolation & purification
Microscopy, Electron, Scanning
Tanning

@article {pmid40528272,
year = {2025},
author = {Guitart-Matas, J and Vera-Ponce de León, A and Pope, PB and Hvidsten, TR and Fraile, L and Ballester, M and Ramayo-Caldas, Y and Migura-Garcia, L},
title = {Multi-omics surveillance of antimicrobial resistance in the pig gut microbiome.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {65},
pmid = {40528272},
issn = {2524-4671},
support = {10385//European Molecular Biology Organization/ ; RYC2019-027244-I//Ministerio de Ciencia e Innovación/ ; RTI2018-095586-B-C22//Ministerio de Economía y Competitividad/ ; },
abstract = {BACKGROUND: High-throughput sequencing technologies play an increasingly active role in the surveillance of major global health challenges, such as the emergence of antimicrobial resistance. The post-weaning period is of critical importance for the swine industry and antimicrobials are still required when infection occurs during this period. Here, two sequencing approaches, shotgun metagenomics and metatranscriptomics, have been applied to decipher the effect of different treatments used in post-weaning diarrhea on the transcriptome and resistome of pig gut microbiome. With this objective, a metagenome-assembled genome (MAG) catalogue was generated to use as a reference database for transcript mapping obtained from a total of 140 pig fecal samples in a cross-sectional and longitudinal design to study differential gene expression. The different treatments included antimicrobials trimethoprim/sulfamethoxazole, colistin, gentamicin, and amoxicillin, and an oral commercial vaccine, a control with water acidification, and an untreated control. For metatranscriptomics, fecal samples from pigs were selected before weaning, three days and four weeks post-treatment.

RESULTS: The final non-redundant MAGs collection comprised a total of 1396 genomes obtained from single assemblies and co-assemblies per treatment group and sampling time from the metagenomics data. Analysis of antimicrobial resistance genes (ARGs) at this assembly level considerably reduced the total number of ARGs identified in comparison to those found at the reads level. Besides, from the metatranscriptomics data, half of those ARGs were detected transcriptionally active in all treatment groups. Differential gene expression between sampling times after treatment found major number of differential expressed genes (DEGs) against the group treated continuously with amoxicillin, with DEGs being correlated with antimicrobial resistance. Moreover, at three days post-treatment, a high number of significantly downregulated genes was detected in the group treated with gentamicin. At this sampling time, this group showed an altered expression of ribosomal-related genes, demonstrating the rapid effect of gentamicin to inhibit bacterial protein synthesis.

CONCLUSIONS: Different antimicrobial treatments can impact differently the transcriptome and resistome of microbial communities, highlighting the relevance of novel sequencing approaches to monitor the resistome and contribute to a more efficient antimicrobial stewardship.},
}

@article {pmid40528256,
year = {2025},
author = {Viver, T and Knittel, K and Amann, R and Orellana, LH},
title = {Comparative metagenomics indicates metabolic niche differentiation of benthic and planktonic Woeseiaceae.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {74},
pmid = {40528256},
issn = {2524-6372},
abstract = {BACKGROUND: Benthic microbiomes exhibit remarkable temporal stability, contrasting with the dynamic, substrate-driven successions of bacterioplankton. Nonetheless, understanding their role in carbon cycling and interactions between these two microbial communities is limited due to the complexity of benthic microbiomes.

RESULTS: Here, we used a long-reads (LRs) metagenomic approach to examine benthic microbiomes and compared them to the microbiomes in the overlaying water column and on particles, sampled at the same site and time off the island Heligoland in the North Sea. Although the diversity is vast in marine sediments, we recovered high quality metagenome assembled genomes (MAGs). Based on taxonomy and metabolic annotation of predicted proteins, benthic microbiomes are distinctly different from pelagic microbiomes. When comparing the 270 MAGs from free living and particle attached microbes from the water column to 115 MAGs from sediments only 2 MAGs affiliated to Acidimicrobiia and Desulfocapsaceae were shared at species level. Although, we recovered MAGs with the same taxonomic annotation in pelagic and benthic microbiomes, their metabolic potentials were different. A prominent example was the family Woeseiaceae that was among the most abundant taxa in the sediments. In benthic Woeseiaceae MAGs, we found polysaccharide utilization loci (PULs), predicted to target laminarin, alginate, and α-glucan. In contrast, pelagic Woeseiaceae MAGs were only recovered in the particle attached but not in the free-living fraction, and lacked PULs. They encoded a significantly more sulfatases and peptidases genes. Additionally, while genes involved in iron acquisition, gene regulation, and iron storage were widespread in Woeseiaceae MAGs, genes linked to dissimilatory iron reduction were mostly restricted to benthic Woeseiaceae, suggesting niche-specific adaptations to sediment redox conditions. Both, benthic and pelagic particle-attached Woeseiaceae MAGs encoded pilus TadA genes, which are essential for adhesion, colonization, and biofilm formation.

CONCLUSIONS: LR sequencing is currently the most valuable tool for analyzing highly diverse benthic microbiomes. The small overlap of MAGs from water column and sediments indicated a limited bentho-pelagic coupling. The data suggest that Woeseiaceae have habitat-specific metabolic specialization: while benthic Woeseiaceae possess the metabolic capabilities to utilize fresh organic compounds like laminarin derived from algae blooms, and to perform dissimilatory nitrate, nitrite and iron reduction for gain energy, particle attached Woeseiaceae from the water column may be specialized in degrading protein-rich and sulfated organic matter likely reflecting adaptation to the different types of organic matter and redox conditions in sediments vs. the water column.},
}

@article {pmid40528221,
year = {2025},
author = {Gao, L and Liao, H and Chen, Y and Ye, C and Huang, L and Xu, M and Du, J and Zhang, J and Huang, D and Cai, S and Dong, H},
title = {Airway microbiota associated D-phenylalanine promotes non-small cell lung cancer metastasis through epithelial mesenchymal transition.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {673},
pmid = {40528221},
issn = {1479-5876},
support = {82170032//National Natural Science Foundation of China/ ; 82470058//National Natural Science Foundation of China/ ; 82270024//National Natural Science Foundation of China/ ; YZ2022ZX04//President Foundation of The Fifth Affiliated Hospital, Southern Medical University/ ; 2023A1515110216//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023M731546//China Postdoctoral Science Foundation/ ; },
mesh = {*Epithelial-Mesenchymal Transition/drug effects ; Humans ; *Carcinoma, Non-Small-Cell Lung/pathology/microbiology ; *Lung Neoplasms/pathology/microbiology ; Animals ; Male ; Neoplasm Metastasis ; Female ; *Microbiota ; *Phenylalanine/metabolism/pharmacology/administration & dosage ; Middle Aged ; Bronchoalveolar Lavage Fluid/chemistry ; Cell Line, Tumor ; Mice ; Aged ; *Respiratory System/microbiology ; },
abstract = {BACKGROUND: Lung cancer is the leading cause of cancer-related death worldwide, and patients with distant metastasis have a poor prognosis. Various studies have reported that microbiota and metabolites significantly differ between healthy individuals and lung cancer patients. However, the effects of metabolites on tumor formation and metastasis are unclear. Therefore, our study aimed to determine the correlation between airway metabolites and microbiota, along with their respective roles in lung cancer metastasis.

METHODS: Bronchoalveolar lavage fluid (BALF) samples were collected from 30 non-small cell lung cancer (NSCLC) patients, including 11 patients without metastasis (M0) and 19 patients with metastasis (M1). Integrated pathogenic metagenomic and Liquid chromatography-mass spectrometry (LC‒MS) analyses were employed to explore differences between two groups. The omics data were analyzed and integrated via Spearman's correlation coefficient. Specific metabolites were subsequently used to intervene in lung cancer cells and animal models to assess their influence on tumor metastasis.

RESULTS: A total of 801 metabolites were identified in the BALF of all patients. Compared with those in the M0 group, 48 metabolites in the M1 group were significantly different. D-phenylalanine was notably upregulated in M1 and was positively related to Metamycoplasma salivarium. Intranasal administration of D-phenylalanine promoted tumor intrapulmonary metastasis and induced epithelial mesenchymal transition (EMT) process in NSCLC mouse models. Moreover, D-phenylalanine promotes the proliferation of non-small cell lung cancer cells and facilitates their migration and invasion via EMT.

CONCLUSION: The airway microbiota associated D-phenylalanine could promote lung cancer metastasis via EMT, which could be a new predictor for the diagnosis of tumor metastasis in NSCLC patients.},
}

*Epithelial-Mesenchymal Transition/drug effects
Humans
*Carcinoma, Non-Small-Cell Lung/pathology/microbiology
*Lung Neoplasms/pathology/microbiology
Animals
Male
Neoplasm Metastasis
Female
*Microbiota
*Phenylalanine/metabolism/pharmacology/administration & dosage
Middle Aged
Bronchoalveolar Lavage Fluid/chemistry
Cell Line, Tumor
Mice
Aged
*Respiratory System/microbiology

@article {pmid40528214,
year = {2025},
author = {Zhang, Y and Luo, J and Chen, K and Li, N and Luo, C and Di, S and Qin, J and Zhang, F and Chen, H and Dai, M},
title = {Cross-cohort analysis identifies shared gut microbial signatures and validates microbial risk scores for colorectal cancer.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {676},
pmid = {40528214},
issn = {1479-5876},
support = {2022-I2M-1-0031//Institute of Chinese Materia Medica, China Academy of Chinese Medical Science/ ; 82173606//National Natural Science Foundation of China/ ; 82273726//National Natural Science Foundation of China/ ; 20230484397//Beijing Nova Program of Science and Technology/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Risk Factors ; Risk Assessment ; Reproducibility of Results ; Male ; Female ; Middle Aged ; Metagenomics ; Case-Control Studies ; },
abstract = {BACKGROUND: Microbiome-wide association studies showed links between colorectal cancer (CRC) and gut microbiota. However, the clinical application of gut microbiota in CRC prevention has been hindered by the diversity of study populations and technical variations. We aimed to determine CRC-related gut microbial signatures based on cross-regional, cross-population, and cross-cohort metagenomic datasets, and elucidate its application value in CRC risk assessment.

METHODS: We used the MMUPHin tool to perform a meta-analysis of our own cohort and seven publicly available metagenomics datasets to identify gut microbial species associated with CRC across different cohorts, comprising of 570 CRC cases and 557 controls. Based on differential species sets, we constructed the microbial risk score (MRS) using α-diversity of the sub-community (MRSα), weighted/unweighted summation methods and machine learning algorithms. Cohort-to-cohort training and validation were performed to demonstrate the transferability.

RESULTS: We found that MRSα of core species was better validated and more interpretable than those constructed with summation methods or machine learning algorithms. Six species, including Parvimonas micra, Clostridium symbiosum, Peptostreptococcus stomatis, Bacteroides fragilis, Gemella morbillorum, and Fusobacterium nucleatum, were included in MRSα constructed by half or more of the cohorts. The AUC of MRSα, calculated based on the sub-community of six species, varied between 0.619 and 0.824 across the eight cohorts.

CONCLUSION: We identified six CRC-related species across regions, populations, and cohorts. The constructed MRSα could contribute to the risk prediction of CRC in different populations.},
}

Humans
*Colorectal Neoplasms/microbiology
*Gastrointestinal Microbiome/genetics
Cohort Studies
Risk Factors
Risk Assessment
Reproducibility of Results
Male
Female
Middle Aged
Metagenomics
Case-Control Studies

@article {pmid40527424,
year = {2025},
author = {Liu, Z and Tang, S and Ren, Y and Chen, P and Ma, D and Si, B and Jiang, W and Lu, H and Zhang, Y},
title = {Biohydrogen production from food waste using a novel rotational drum reactor integrated with milli-magnetite.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132822},
doi = {10.1016/j.biortech.2025.132822},
pmid = {40527424},
issn = {1873-2976},
abstract = {Dark fermentation, regarded as a promising path for sustainable hydrogen production from food waste, is hindered by slow hydrolysis and low hydrogen yield. This study presented a novel rotational drum reactor integrated with milli-magnetite (RD-M) to enhance hydrogen production, using potato peel as feedstock. The RD-M designed to simultaneously achieve grinding and biochemical stimulation. To verify the promoting performance and elucidate the underlying mechanisms, a drum reactor with sand (RD-S) and one without additives (RD-C) were used as controls. Enhanced hydrolysis in RD-M was confirmed from a smaller dominant particle size distribution (100-500 µm), accelerated production of organic acids (e.g., acetate, butyrate), and increased volatile solids degradation (by 23.6 %) compared to RD-C. Notably, hydrogen production in RD-M increased by 97.04 %. The RD-M system induced a shift in fermentation to an acetate-butyrate pathway, associated with an enrichment of butyrate-producing Clostridium. Metagenomic analysis further revealed that milli-magnetite established an efficient electron transfer chain that improved electron utilization and hydrogen yield. Additives were shown to promote direct interspecies electron transfer by upregulating genes encoding flagella and cytochrome-c synthesis. Furthermore, intracellular electron bifurcation at pyruvate ferredoxin directed electrons into the butyrate pathway, while enhanced iron metabolism explained the fermentation shift observed in RD-M. This study highlights the combined mechanical and biochemical benefits of RD-M, offering a promising solution for sustainable biohydrogen production from solid waste.},
}

@article {pmid40527400,
year = {2025},
author = {Clodfelter, EB and Doña, J and Walden, KKO and Johnson, KP},
title = {Metagenomic analyses reveal three supergroups of Wolbachia in a single genus of feather-feeding lice (Penenirmus).},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108387},
doi = {10.1016/j.ympev.2025.108387},
pmid = {40527400},
issn = {1095-9513},
abstract = {Insects with nutritionally limited diets often harbor bacterial endosymbionts that supplement their nutritional requirements. However, not all interactions between bacteria and insects are mutually beneficial. Wolbachia is a genus of bacteria that frequently causes cytoplasmic incompatibility and other reproductive parasitic effects on many of its arthropod hosts. In nematodes and some insects, however, Wolbachia is a nutritional mutualist. A lineage of Wolbachia closely related to mutualist strains has previously been identified in parasitic lice, including the louse genus Penenirmus (Ischnocera), which specializes in feeding on feathers. In this study, we used genome-resolved metagenomics to examine the diversity of Wolbachia across the genus Penenirmus, with a focus on evidence of long term associations with their hosts, which could indicate a mutualistic relationship. Phylogenomic analysis of over 100 genes from Wolbachia provided a well-resolved phylogeny of this bacterial genus. Across diverse species of the louse genus Penenirmus, genome-resolved metagenomic assemblies of Wolbachia from these insects revealed the presence of three different supergroups (B, F, and V). Supergroup V had not previously been known from lice. Cophylogenetic analysis revealed significant congruence between the Wolbachia and louse trees, although some branches showed incongruence. The Wolbachia in Penenirmus species from supergroups F and B showed evidence of potential mutualism by having long branches, cophylogenetic congruence with their louse hosts, and comparatively smaller genome sizes. Long branch attraction may be affecting the phylogenetic position of two lineages of Wolbachia, but the relative position of all other samples was comparatively stable.},
}

@article {pmid40527211,
year = {2025},
author = {Ghosh, S and Nath, S and Chakraborty, A and Bhowmick, S and Majumdar, KK and Mukherjee, S and Pramanik, S},
title = {Long-term arsenic exposure perturbs gut microbial diversity, composition and predicts metabolic dysregulation.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138836},
doi = {10.1016/j.jhazmat.2025.138836},
pmid = {40527211},
issn = {1873-3336},
abstract = {The present study documents significant alterations in human gut microbial composition in arsenic exposed populations of West Bengal, India through amplicon sequencing of human stool metagenomic DNA. A notable reduction in α-diversity underscored a reduced species richness and an altered predominance. β- diversity analysis revealed prominent inter-individual differences. Among the 26 phyla detected, significant perturbation was noted in Bacteroidetes, Actinobacteria, Proteobacteria, and Firmicutes. Species analysis identified significant increase in Bifidobacterium adolescentis, B.longum, Blautia luti, B.wexlerae, Clostridium saudiense, Romboutsia timonensis and Streptococcus salivarius whereas members of Faecalibacterium prausnitzii, Megasphaera elsdenii, Prevotella copri and P. stercorea were found to be highly diminished due to As stress. PICRUSt analysis predicted significant upregulation (pT-test< 0.05) in gene families associated with carbohydrate, amino acid, nucleotide and lipid metabolism along with fermentation and secondary metabolite/ vitamin synthesis pathways in exposed group confirmed through Linear Discriminant Analysis. B.longum, B.luti and S.salivarius were found to be associated with obesity and ulcerative colitis. Network interactions were also characterized with major disruptions in keystone species interaction. The major findings of this study shall drive future studies like community-based metagenomics, metabolomics and in-vitro microbial verifications for designing of microbial therapeutics targeting gut health to combat the harmful impact of As exposure.},
}

@article {pmid40527192,
year = {2025},
author = {Yin, Y and Xiao, K and Wang, YF and Cao, JM and Dong, JP and Zhu, D and Zhu, YG},
title = {Nanoplastics released from textile washing enrich antibiotic resistance and virulence genes in sewage sludge microbiomes.},
journal = {Environment international},
volume = {202},
number = {},
pages = {109611},
doi = {10.1016/j.envint.2025.109611},
pmid = {40527192},
issn = {1873-6750},
abstract = {The washing of synthetic textiles is a major source of microplastic pollution, contributing to the widespread presence of nanoplastics (NPs) in wastewater treatment plants (WWTPs). However, the role of laundry-released NPs in shaping microbial communities and facilitating the spread of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in sludge remains unclear. Here, we quantified the concentration and size distribution of NPs released during the washing of polyamide (PA), polypropylene (PP), and polyethylene terephthalate (PET) textiles using nanoparticle tracking analysis. Substantial NP release was observed, with concentrations ranging from 3.4 × 10[7] to 1.7 × 10[8] particles mL[-1], and sizes between 130 and 240 nm. We then evaluated their impact on ARG and VFG profiles, as well as bacterial communities in anaerobic sludge through metagenomic and 16S rRNA gene sequencing. Laundry-released NPs significantly increased the abundance of ARGs, VFGs, and mobile genetic elements (MGEs) in sludge, with D8A-2 and Halomonas identified as potential ARG and VFG hosts. Notably, the mechanisms driving ARG enrichment varied by NP type. PA-released NPs elevated reactive oxygen species levels in bacterial communities, facilitating horizontal gene transfer via MGEs, while PP- and PET-released NPs enhanced ARG enrichment through both horizontal gene transfer and shifts in bacterial community composition. These findings highlight the risks posed by laundry-released NPs accumulating in WWTPs, emphasizing the urgent need for improved wastewater management strategies to mitigate their environmental and public health impacts.},
}

@article {pmid40526465,
year = {2025},
author = {Zhang, J and Yuan, B and Peng, R and Zhang, P and Liu, X and Qu, Y and Xiao, G and Li, Y and Zhang, X and Hong, J},
title = {Etiology of Iridocorneal Endothelial Syndrome: Viral Infection and Immune Suppression.},
journal = {Cornea},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICO.0000000000003911},
pmid = {40526465},
issn = {1536-4798},
support = {82371027//National Natural Science Foundation of China/ ; },
abstract = {PURPOSE: Iridocorneal endothelial (ICE) syndrome is a rare ocular disease affecting the anterior segment, leading to cornea edema and glaucoma. Its unclear etiology limits clinical management to symptomatic interventions. This study uses diverse methodologies to explore potential viral sequences in patients' samples and to elucidate the transcriptomic profiles of ICE cells.

METHODS: We used a convenience sampling method, including all eligible patients for analysis. We reviewed polymerase chain reaction (PCR) results for herpes viruses across all samples obtained from ICE syndrome patients at our institution. To further delve into potential pathogenic involvement, we used metagenomic sequencing and whole-genome sequencing techniques on samples. We used smart-seq2 RNA sequencing to explore the transcriptomic features of ICE cells compared with normal cells.

RESULTS: In our PCR tests involving 141 samples, only two positive results were detected in the aqueous humor. Furthermore, the application of metagenomic sequencing on three aqueous humor samples and three corneal endothelium samples, along with whole-genome sequencing on one corneal endothelium sample, yielded no evidence of viral sequences. RNA sequencing revealed upregulated cell growth and neuronal death in ICE cells, alongside downregulated expression in extracellular matrix composition, cell adhesion, and immune response functions.

CONCLUSIONS: Our findings from multiple sequencing assays consistently indicate the absence of compelling evidence supporting viral infection in patients with ICE syndrome. Furthermore, the transcriptional analysis of ICE cells reveals a distinct profile characterized by upregulated cell growth and suppressed immune response. Future studies are necessary to validate these findings and improve the generalizability of the results.},
}

@article {pmid40525868,
year = {2025},
author = {Wang, H and Xue, W and Cheng, J and He, Y and Song, Y and Hu, D and Peng, A and Li, C and Bao, H},
title = {Altered fecal microbial and metabolic profiles reveal potential mechanisms underlying anemia in patients with chronic renal failure.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0316624},
doi = {10.1128/spectrum.03166-24},
pmid = {40525868},
issn = {2165-0497},
abstract = {The gut microbiomes communicate with the kidney and may play a crucial role in the development of anemia in patients with chronic renal failure (CRF). However, the alterations in microbiota and their association with functional metabolites remain unclear. We performed metagenomics and untargeted metabolomics in a cohort of 30 patients with anemia of CRF and 20 healthy controls (HCs) to identify the characteristics of the gut microbiome and explore its potential interactions with the host. Decreased microbiota diversity and significant compositional differences were observed in the patients with anemia of CRF. We identified six gut microbiotas significantly changed in the patients with anemia of CRF, particularly Faecalibacterium prausnitzii, Prevotella copri, and Escherichia coli, which were closely correlated with hemoglobin (Hb) levels and estimated glomerular filtration rate (eGFR). These changes were accompanied by functional alterations in distinctive microbial pathways. Further fecal and serum metabolomics revealed fecal 12-KETE-LTB4 in arachidonic acid metabolism, uracil and L-aspartic acid in beta-alanine metabolism, gulonic acid in ascorbate and aldarate metabolism, accompanied by the top 15 differential serum metabolites that were closely correlated with Hb levels. Furthermore, we observed a complex co-occurrence between anemia of CRF-related gut microbiota species and the characterized metabolites. Moreover, a non-invasive model incorporating Faecalibacterium prausnitzii and Prevotella copri, combined with fecal 12-KETE-LTB4, uracil, L-aspartic acid, and gulonic acid, distinguished the patients with anemia of CRF from HCs (area under the curve: 0.879). Collectively, our results suggest that a disordered gut microbiome associated with functional metabolites may be a non-invasive diagnostic and therapeutic target for anemia of CRF.IMPORTANCEAnemia is a prevalent complication in patients with chronic renal failure (CRF), which is associated with a high burden of morbidity and adverse clinical outcomes. Various evidence suggests that gut microbiota dysbiosis may contribute to the pathogenesis of anemia in CRF, although the mechanism is still obscure. This work provides substantial evidence identifying the specific characteristics of the gut microbiomes accompanied by functional alterations in anemia of CRF. We highlight the intricate interactions among the anemia of CRF-related gut microbiome and the functional metabolites, which may regulate toxic accumulation, oxidative stress, and immune-inflammatory responses to induce and exacerbate anemia in patients with CRF. Furthermore, we found that evaluating the gut microbiota and fecal metabolites in combination might be a non-invasive prognostic indicator of CRF-induced anemia. These findings provide important insights into the role of gut microbiota in the mechanism of anemia in CRF.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05543291.},
}

@article {pmid40525692,
year = {2025},
author = {Jarrett, ZS and Xia, H and O'Neil, ER and Lonergan, TP and Gonzales, M and Sobieszczyk, M and Gibbons, TF and Marcus, JE},
title = {Characterizing Microbiome Changes in Veno-Venous Extracorporeal Membrane Oxygenation: A Case Report of Multidrug-Resistant Bacteremia.},
journal = {ASAIO journal (American Society for Artificial Internal Organs : 1992)},
volume = {},
number = {},
pages = {},
doi = {10.1097/MAT.0000000000002479},
pmid = {40525692},
issn = {1538-943X},
support = {//Clinical Investigations & Research Support (CIRS)/ ; },
abstract = {Microbiome analysis using metagenomics next-generation sequencing (mNGS) is rarely performed in patients receiving extracorporeal membrane oxygenation (ECMO). Patient body sites were swabbed within 72 hours of ECMO cannulation and weekly during ECMO course. Specimens underwent 16S sequencing to identify the microbiome along with mNGS to determine antimicrobial resistance genes. Fifty-two year old male who suffered polytraumatic injuries and developed acute respiratory syndrome was placed on veno-venous (VV) ECMO to treat severe respiratory failure. On ECMO day 1, the patient was undergoing treatment for urinary tract infection due to susceptible Pseudomonas aeruginosa (PsA). On ECMO day 22, the patient developed fulminant septic shock and tracheal aspirate and blood cultures both grew MDR PsA and Enterobacter cloacae complex (ECC) and ultimately died on day 23. There were significant microbiome and antimicrobial resistance changes that preceded sepsis on day 22, as evidenced by the increase in oral PsA colonization and expansion of resistance genes, such as KPC and OXA-50, which suggest several possible reservoirs for infection outside of the circuit. Further application of these methods is needed to understand microbiome changes in ECMO and ultimately guide infection prevention efforts.},
}

@article {pmid40525681,
year = {2025},
author = {Reinhardt, CR and Kastner, DW and Kulik, HJ},
title = {Role of Active Site Residues and Weak Noncovalent Interactions in Substrate Positioning in N,N-Dimethylformamidase.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.5c00207},
pmid = {40525681},
issn = {1520-4995},
abstract = {N,N-Dimethylformamide (DMF) is a solvent that can be metabolized naturally by DMF-utilizing microorganisms via a nonheme iron enzyme N,N-dimethylformamidase (DMFase). DMF is a small molecule with very few hydrogen bond donors or acceptors, and thus must be bound in the active site through other noncovalent interactions. We investigated the unusual protein fold, role of active site residues, and substrate positioning by performing molecular dynamics (MD) simulations and studying DMF binding. Our docking studies support idea that the DMF substrate directly coordinates the iron center through its carbonyl group, with Fe-DMF distances consistent with structures of inorganic complexes. DMF binding is predominantly stabilized by weak noncovalent interactions with nearby phenylalanine residues, which also serve to control access of solvent to the active site according to cavity analysis of crystal structures and MD snapshots. Based on noncovalent interactions sampled in our simulations and on sequence conservation, we ascribe roles to active site residues E657β, H519β, N547β, F611β, and F693β'. We perform sequence and structural alignments to identify putative DMFases and active site geometries in protein structures predicted from metagenomic DNA. These analyses suggest common conserved residues among putative DMFases and relate them to catalytic function, providing guidance for future experimental studies or characterization of new DMFases for DMF bioremediation.},
}

@article {pmid40524271,
year = {2025},
author = {Serrano-Gómez, G and Yañez, F and Soler, Z and Pons-Tarin, M and Mayorga, L and Herrera-deGuise, C and Borruel, N and Rodriguez-Sinovas, A and Consegal, M and Manjón, I and Vega-Abellaneda, S and Manichanh, C},
title = {Microbiome multi-omics analysis reveals novel biomarkers and mechanisms linked with CD etiopathology.},
journal = {Biomarker research},
volume = {13},
number = {1},
pages = {85},
pmid = {40524271},
issn = {2050-7771},
support = {72190278//Agencia Nacional de Investigación y Desarrollo/ ; FI21/00262//Instituto de Salud Carlos III/ ; PI20/00130//Instituto de Salud Carlos III/ ; 2021 SGR 00459//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; 2021 SGR 00459//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; 2021 SGR 00459//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; },
abstract = {BACKGROUND: The gut microbiome plays a key role in the development of inflammatory bowel disease (IBD), as imbalances in microbial composition are associated with immune dysfunction. However, the specific mechanisms by which certain microorganisms contribute to this process remain unclear.

METHODS: Here, we employed a multi-omics approach on fecal samples to identify novel microbiome markers and elucidate mechanisms underlying IBD. Shotgun metagenomics was applied to 212 samples (850 in total with validation cohort), shotgun metatranscriptomics to 103 samples and metabolomics to 105 samples. Machine learning techniques were used to predict disease and the three omics data were integrated to propose a mechanistic role of the microbiota.

RESULTS: Metagenomic analysis identified Crohn's disease (CD)-specific microbiome signatures, including a panel of 20 species that achieved a high diagnostic performance, with an area under the ROC curve (AUC) of 0.94 in an external validation set. Metatranscriptomic analysis revealed significant alterations in microbial fermentation pathways in CD, but not in ulcerative colitis (UC), highlighting disruptions that explain the depletion of butyrate-a key anti-inflammatory metabolite-observed in metabolomics analysis. Integrative multi-omics analyses further identified active virulence factor genes in CD, predominantly originating from the adherent-invasive Escherichia coli (AIEC). Notably, these findings unveiled novel mechanisms, including E. coli-mediated aspartate depletion and the utilization of propionate, which drives the expression of the ompA virulence gene, critical for bacterial adherence and invasion of the host's macrophages. Interestingly, these microbiome alterations were absent in UC, underscoring distinct mechanisms of disease development between the two IBD subtypes.

CONCLUSIONS: In conclusion, our study not only identifies promising novel biomarkers with strong diagnostic potential, which could be valuable in challenging clinical scenarios, but also offers an integrated multi-omics perspective on the microbial mechanisms underlying inflammation and virulence in Crohn's disease.},
}

@article {pmid40524224,
year = {2025},
author = {Jaffe, AL and Salcedo, RSR and Dekas, AE},
title = {Abundant and metabolically flexible bacterial lineages underlie a vast potential for rubisco-mediated carbon fixation in the dark ocean.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {167},
pmid = {40524224},
issn = {1474-760X},
support = {Postdoctoral Research Fellowship//Division of Ocean Sciences/ ; OCE-1634297//Division of Ocean Sciences/ ; },
mesh = {*Ribulose-Bisphosphate Carboxylase/metabolism/genetics ; *Carbon Cycle/genetics ; Metagenome ; *Seawater/microbiology ; *Bacteria/genetics/metabolism/classification/enzymology ; Oceans and Seas ; Phylogeny ; },
abstract = {BACKGROUND: Rubisco is among the most abundant enzymes on Earth and is a critical conduit for inorganic carbon into the biosphere. Despite this, the full extent of rubisco diversity and the biology of organisms that employ it for carbon fixation are still emerging, particularly in unlit ecosystems like the deep sea.

RESULTS: We generate fifteen metagenomes along a spatially resolved transect off the California coast and combine them with globally distributed public data to examine the diversity, distribution, and metabolic features of rubisco-encoding organisms from the dark water column. Organisms with the form I and/or form II rubisco are detected in the vast majority of all samples and comprise up to around 20% of the binned microbial community. At 150 m and below, the potential for autotrophic carbon fixation via rubisco is dominated by just two orders of gammaproteobacteria and SAR324, encoding either the form I or II rubisco. Many of these organisms also possess genes for the oxidation of reduced sulfur compounds, which may energetically support carbon fixation. Transcriptomic profiling in the epi- and mesopelagic suggests that all major forms of rubisco (I, II, and III) can be highly expressed in the deep water column but are not done so constitutively, consistent with metabolic flexibility.

CONCLUSIONS: Our results demonstrate that the genetic potential to fix carbon via rubisco is significant and spatially widespread in the dark ocean. We identify several rubisco-encoding species that are particularly abundant and cosmopolitan, highlighting the key role they may play in deep-sea chemoautotrophy and the global marine carbon cycle.},
}

*Ribulose-Bisphosphate Carboxylase/metabolism/genetics
*Carbon Cycle/genetics
Metagenome
*Seawater/microbiology
*Bacteria/genetics/metabolism/classification/enzymology
Oceans and Seas
Phylogeny

@article {pmid40523923,
year = {2025},
author = {Zhang, M and Liang, C and Li, B and Jiang, F and Song, P and Gu, H and Gao, H and Cai, Z and Zhang, T},
title = {Gut microbiome and diet contribute to ecological niche differentiation between argali (Ovis ammon hodgsoni) and blue sheep (Pseudois nayaur) on the Qinghai-Tibet Plateau.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {930},
pmid = {40523923},
issn = {2399-3642},
mesh = {Animals ; *Gastrointestinal Microbiome ; Tibet ; *Diet/veterinary ; Sheep/microbiology ; Ecosystem ; Herbivory ; },
abstract = {The gut microbiota plays a critical role in plant digestion, nutrient absorption, and ecological adaptation in herbivores. However, how gut microbiota and diet jointly influence ecological niche differentiation in sympatric species remains unclear. Here, we use metagenomic sequencing and plant trnL (UAA) fragment sequencing to examine the gut microbiota and dietary composition of sympatric Tibetan argali (Ovis ammon hodgsoni) and blue sheep (Pseudois nayaur) in the Kunlun Mountains of the Qinghai-Tibet Plateau. Despite inhabiting similar environments, the two species harbor distinct microbial compositions and functional profiles. Interestingly, higher dietary diversity does not correspond to higher microbial diversity. Tibetan argali, despite having a simpler diet, possesses a more diverse and flexible gut microbiome. In contrast, blue sheep show broader dietary preferences and stronger microbial metabolic adaptation to glycan biosynthesis and metabolism. These findings reveal significant associations between gut microbiota composition, function, and diet, supporting a microbial contribution to trophic niche differentiation. Our results highlight distinct microbial-dietary strategies in sympatric herbivores and underscore the role of the gut microbiome in ecological adaptation and species coexistence.},
}

Animals
*Gastrointestinal Microbiome
Tibet
*Diet/veterinary
Sheep/microbiology
Ecosystem
Herbivory

@article {pmid40523587,
year = {2025},
author = {Valadez-Cano, C and Reyes-Prieto, A and Johnston, L and Huang, Y and Morris, H and Zamlynny, L and Comeau, AM and Beach, DG and Jamieson, RC and Lawrence, J},
title = {The co-existence of Microcoleus strains with gene variations in the anatoxin-a biosynthesis cluster can explain the different toxin profiles observed in freshwater benthic mats.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {},
number = {},
pages = {108461},
doi = {10.1016/j.toxicon.2025.108461},
pmid = {40523587},
issn = {1879-3150},
abstract = {Distinct anatoxin profiles can occur in Microcoleus-dominated benthic mats. Metagenomic data from a dihydrohomoanatoxin-a-producing mat revealed two co-occurring Microcoleus strains with variations in the anatoxin biosynthesis gene cluster. One cluster contained an anaK (F420-dependent oxidoreductase) similar to homologs from dihydroanatoxin-a-producing strains. The second contained the long anaG (polyketide-synthase) previously associated with homoanatoxin-a. Neither strain alone explained the observed toxin profile, suggesting that strain interaction contributes to the production of dihydrohomoanatoxin-a within benthic mats.},
}

@article {pmid40523415,
year = {2025},
author = {Xu, Y and Ontita, NC and Zeng, W and Huang, J and Jiang, L and Huang, X and Li, Q and Hu, P},
title = {High-efficiency nitrogen removal by cold-tolerant bacteria consortium at low temperatures.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132816},
doi = {10.1016/j.biortech.2025.132816},
pmid = {40523415},
issn = {1873-2976},
abstract = {A cold-tolerant bacteria consortium (M2) was developed to enhance nitrogen removal efficiency in wastewater treatment processes operating at low temperatures (below 15 ℃). Bacteria consortium M2 demonstrated high removal efficiencies for nitrogen (NH4[+]-N, 97.34 %; NO3[-]-N, 97.13 %; NO2[-]-N, 59.92 %). Dominated by genera including Comamonas, Pseudomonas, and Acinetobacter, M2 produced substantial extracellular polymeric substances (EPS) and unsaturated fatty acids, which mitigated cold-induced stress. Metagenomic analysis revealed the presence of cold-shock responsive genes, including unsaturated fatty acid synthase, and cpsA, which contribute to its resilience under low-temperature conditions. Moreover, M2 enhanced both nitrogen assimilation and nitrate reduction under cold stress. These findings highlight the potential of M2 as an effective and practical strategy for improving nitrogen removal in wastewater treatment facilities during winter, thereby addressing a critical operational limitation in cold-climate regions.},
}

@article {pmid40523412,
year = {2025},
author = {Li, D and Zhou, A and Mei, J and Liu, Z and Duan, H and Luo, J and He, Z and Liu, W and Ni, BJ and Yue, X},
title = {Synergy among multiple electron donors in electro-fermentation chain elongation: Accelerated directional electron transfer and enhanced microbial functions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132817},
doi = {10.1016/j.biortech.2025.132817},
pmid = {40523412},
issn = {1873-2976},
abstract = {Electro-fermentation assisted chain elongation (EF_CE) effectively converts organic waste into medium-chain fatty acids (MCFAs), yet the regulatory mechanisms involving multiple electron donors (EDs) require elucidation. This study systematically explored the synergistic effects of ethanol and lactate as EDs on MCFA biosynthesis in EF_CE systems. The cross-niche microbial associations shaped by multiple EDs coupled with inoculation with caproate-synthesizing bacteria led to a 2.9-3.9-fold increase in caproate synthesis. Metagenomic analysis revealed that multiple EDs decreased the relative abundances of genes encoding Mut in the acrylate pathway, while increasing the relative abundances of genes encoding ascB in the Wood-Ljungdahl pathway, and ADH, kor and cdhA in ethanol and lactate oxidation pathways. These findings highlight the dual role of ED synergy in directing MCFAs production and reshaping microbial networks, offering insights for improving organic waste/wastewater recycling.},
}

@article {pmid40523310,
year = {2025},
author = {Johnson, LA and Smith, DDN and Subasinghe, R and Raap, M and Richter, R and Huyben, D and Lau, C and Brown, L and Chu, J and Khomenko, O and Manning, A and Johnson, S and Hamoutene, D},
title = {Influence of aquaculture and genomic surveillance techniques on antimicrobial resistance gene profiles and microbiota detected in marine and freshwater sediments.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2024-0206},
pmid = {40523310},
issn = {1480-3275},
abstract = {Surveillance methods for antimicrobial resistance genes (ARGs) are needed to assess potential risk of antimicrobial resistance (AMR), especially in complex environmental samples with limited data on ARG distribution. This study employed target-enrichment metagenomics (bait-capture) and a Resistomap qPCR assay to assess the resistome in marine and freshwater sediments associated with active Canadian finfish aquaculture operations. Differences in resistome profiles were considered with distance to the net-pens, concentrations of three aquaculture-associated chemical residues, and microbial communities as detected with 16S rRNA gene amplicon sequencing. With bait-capture, a total of 194 ARGs and 41 replicon types were detected across the sediment samples. Differences due to aquaculture proximity were noted in the composition of the resistome, which was dominated by tetracycline resistance genes. With qPCR, 37 out of 51 ARGs targets were detected, and proximity to net-pens or region did not show changes in resistome composition. Co-occurrence networks revealed significant correlations among genera and the resistome detected with bait-capture, highlighting a potential influence of aquaculture on ARGs in the environment. This study demonstrates the utility of bait-capture and qPCR assays in detection of ARGs in both freshwater and marine sediments from aquaculture sites that will assist further ARG surveillance.},
}

@article {pmid40523202,
year = {2025},
author = {Dal Bó, B and Guo, Y and Mayr, MJ and Pereira, OS and Levin, LA and Orphan, VJ and Goffredi, SK},
title = {Methane-powered sea spiders: Diverse, epibiotic methanotrophs serve as a source of nutrition for deep-sea methane seep Sericosura.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {26},
pages = {e2501422122},
doi = {10.1073/pnas.2501422122},
pmid = {40523202},
issn = {1091-6490},
support = {OCE-2048481//NSF (NSF)/ ; OCE-2048720//NSF (NSF)/ ; OCE-2048666//NSF (NSF)/ ; },
mesh = {Animals ; *Methane/metabolism ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; Male ; *Spiders/microbiology/physiology ; Bacteria/metabolism/genetics ; Female ; Methanol/metabolism ; Pacific Ocean ; },
abstract = {Methane seeps harbor uncharacterized animal-microbe symbioses with unique nutritional strategies. Three undescribed sea spider species (family Ammotheidae; genus Sericosura) endemic to methane seeps were found along the eastern Pacific margin, from California to Alaska, hosting diverse methane- and methanol-oxidizing bacteria on their exoskeleton. δ[13]C tissue isotope values of in situ specimens corroborated methane assimilation (-45‰, on average). Live animal incubations with [13]C-labeled methane and methanol, followed by nanoscale secondary ion mass spectrometry, confirmed that carbon derived from both compounds was actively incorporated into the tissues within five days. Methano- and methylotrophs of the bacterial families Methylomonadaceae, Methylophagaceae and Methylophilaceae were abundant, based on environmental metagenomics and 16S rRNA sequencing, and fluorescence and electron microscopy confirmed dense epibiont aggregations on the sea spider exoskeleton. Egg sacs carried by the males hosted identical microbes suggesting vertical transmission. We propose that these sea spiders farm and feed on methanotrophic and methylotrophic bacteria, expanding the realm of animals known to harness C1 compounds as a carbon source. These findings advance our understanding of the biology of an understudied animal lineage, unlocking some of the unique nutritional links between the microbial and faunal food webs in the oceans.},
}

Animals
*Methane/metabolism
RNA, Ribosomal, 16S/genetics
Symbiosis
Male
*Spiders/microbiology/physiology
Bacteria/metabolism/genetics
Female
Methanol/metabolism
Pacific Ocean

@article {pmid40522529,
year = {2025},
author = {Singh, S and Kumar, M and Sarma, DK and Kumawat, M and Verma, V and Kriti, M and Tiwari, R},
title = {Advancing AMR Surveillance: Confluence of One Health and Big Data Integration : Converging One Health and Big Data for AMR.},
journal = {EcoHealth},
volume = {},
number = {},
pages = {},
pmid = {40522529},
issn = {1612-9210},
abstract = {Antibiotic resistance poses a critical global health threat, demanding robust surveillance systems to monitor its prevalence, patterns, and trends. The One Health approach has emerged as a comprehensive framework, emphasizing the interconnectedness of human health, animal health, and the environment in addressing this complex issue. This article explores the potential of One Health-based antibiotic resistance surveillance, integrating big data analytics and interdisciplinary collaboration. Challenges and opportunities in harmonizing surveillance efforts across sectors are discussed, underscoring the importance of data sharing and standardization. Advanced technologies like genomics and metagenomics are examined for understanding the genetic basis of antibiotic resistance and tracking its spread. The article also highlights the potential of real-time monitoring and early warning systems to inform evidence-based policies and antimicrobial stewardship programs. By analyzing the state-of-the-art in antibiotic resistance surveillance, this article sheds light on the transformative potential of One Health approaches, leveraging big data and interdisciplinary collaboration to combat antibiotic resistance effectively. The urgency of adopting a united global effort to safeguard the efficacy of antibiotics for future generations is emphasized.},
}

@article {pmid40521483,
year = {2025},
author = {Wang, Y and Yang, J and Hu, X and Wang, Y and Qin, S and Fan, J and He, M},
title = {Metagenomic Analysis and Core Flooding Reveals the Indigenous Bacterial Community Information and MEOR Potential of the Main Water-Drive Low-Permeability Reservoir in the Ordos Basin.},
journal = {ACS omega},
volume = {10},
number = {22},
pages = {23272-23280},
pmid = {40521483},
issn = {2470-1343},
abstract = {Oil recovery decreased with prolonged waterflood development in the main reservoirs in the Ordos Basin, and the extraction of the remaining oil was gradually difficult. To exploit oil-producing potential through microbial enhanced oil recovery (MEOR), bacterial communities of 26 samples from Yan 9, 10 layers, and 15 samples from Chang 6 layers were analyzed based on high-throughput sequencing. 1578 and 3581 amplicon sequence variants were obtained from Jurassic and Triassic samples, and α diversity analysis showed that dominant bacterial genera existed distinctly in both study areas. The distribution of the Jurassic bacteria community differed from that of the Triassic, revealed by a principal coordinate analysis. Pseudomonas (15.74%) and Sulfurospirillum (9.94%) were identified as the dominant bacteria in the Jurassic study areas, as well as Pseudomonas (33.54%) and Acinetobacter (11.41%) were the main bacteria in the Triassic reservoirs. Co-occurrence network analysis indicated that the Jurassic and Triassic study areas had both complex and unstable bacterial consortiums, which were closely connected with Proteobacteria and Firmicutes, respectively. The different development strategies and reservoir properties led to the discrepancy in indigenous bacteria distribution between the Jurassic and Triassic study areas. However, some bacteria that have been reported to have oil-displacing ability, such as Pseudomonas, Halomonas, Acinetobacter, Marinobacterium, and Marinobacter, were found in both regions, suggesting that these bacteria had extensive adaptability. Among them, the utilization of functional bacteria of Proteobacteria and Firmicutes might be conducive to enhancing oil recovery stably. Based on this, Pseudomonas aeruginosa PA2 was isolated from study areas and enhanced oil recovery by 17.85 and 11.89% during Jurassic and Triassic core flooding tests, respectively.},
}

@article {pmid40520796,
year = {2025},
author = {Chen, M and Wu, H and Xie, L and Wu, M and Lan, P},
title = {Successful management of severe pulmonary form of leptospirosis with VV-ECMO, prone ventilation, and bronchoalveolar lavage: two case reports.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1598589},
pmid = {40520796},
issn = {2296-858X},
abstract = {BACKGROUND: Leptospirosis is a globally prevalent zoonotic acute infectious disease that can rapidly progress to severe pulmonary form of leptospirosis (SPFL), leading to multiple organ failure with a high mortality rate. It is estimated that approximately 58,900 deaths occur annually due to leptospirosis, with critically ill patients admitted to intensive care units facing extremely high fatality rates. Therefore, timely and effective treatment strategies are crucial.

CASE PRESENTATION: Two patients developed fever after farm work exposure, followed by progressive dyspnea and hemoptysis, leading to hospitalization. They rapidly developed acute respiratory distress syndrome (ARDS) and diffuse alveolar hemorrhage (DAH) with severe thrombocytopenia, accompanied by a continuous decline in the ratio of the partial pressure of arterial oxygen to the fraction of inspired oxygen (PaO₂/FiO₂ [P/F]). Despite endotracheal intubation and mechanical ventilation, hypoxemia persisted. Venovenous extracorporeal membrane oxygenation (VV-ECMO) was initiated to provide oxygenation support, heparin anticoagulation was not used in the early stage. Meanwhile, prone ventilation and bronchoscopy alveolar lavage were performed to promote the clearance of pulmonary hemorrhage, along with anti-infection treatment. The diagnosis of leptospirosis was confirmed through Metagenomic Next-Generation Sequencing (mNGS). Both patients ultimately recovered, were successfully weaned from life support, discharged in stable condition, and returned to normal life.

CONCLUSION: Early VV-ECMO support, combined with prone ventilation and bronchoalveolar lavage, can improve the prognosis of patients with SPFL. mNGS testing aids in the definitive diagnosis of leptospirosis and provides a reliable basis for antibiotic selection.},
}

@article {pmid40520638,
year = {2025},
author = {Zakaria, D and Sandri, C and Modesto, M and Spiezio, C and Scarafile, D and Cedras, A and Borruso, L and Manghi, P and Trevisi, P and Segata, N and Mattarelli, P and Arita, M},
title = {Disentangling the gut microbiota of Aldabra giant tortoises of different ages and environments.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19566},
pmid = {40520638},
issn = {2167-8359},
mesh = {Animals ; *Turtles/microbiology ; *Gastrointestinal Microbiome/genetics ; Italy ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Age Factors ; Seychelles ; Environment ; Bacteria/genetics/classification ; },
abstract = {BACKGROUND: The gut microbiota plays a pivotal role in regulating the physiological functions of its host, including immunity, metabolism, and digestion. The impact of environment and age on microbiota can be assessed by observing long-lived animals across different age groups and environments. The Aldabra giant tortoise (Aldabrachelys gigantea) is an ideal species for this study due to its exceptionally long lifespan of over 100 years.

METHODS: Using 16S rRNA gene amplicon analysis, we analyzed 52 fecal samples from giant tortoises in Seychelles (Curieuse and Mahé islands) and in a zoological park in Italy, from very young individuals to those of >100 years old. We performed Alpha and Beta diversity analysis, relative abundance analysis, and complex upset plot analysis, comparing the results of tortoises from different environments and age groups.

RESULTS: The diversity and overall composition of the gut microbiota of tortoises were impacted mainly by geolocation rather than their age. The greater diversity of microbiota in wild tortoises was attributed to their food variance such as wild leaves and branches, compared to captive or domesticated conditions. Beta diversity analysis also revealed the contribution of both environment and age to the variation between samples, with environments accounting for a larger proportion of this contribution. Certain bacterial families, such as Spirochaetota and Fibrobacterota, were more prevalent in environments with higher fiber intake, reflecting dietary differences. Additionally, a range of host-independent environmental bacteria was found to be specific to individuals in Curieuse and not in other geolocations. On the other hand, there were no bacterial taxa specific to centenarians, whose microbial complexity was reduced compared to adult or elderly tortoises.

CONCLUSIONS: Our records showed that environment is the primary influence in the overall composition and diversity of the gut microbiota of Aldabra giant tortoises. As giant tortoises are amongst the longest-lived vertebrate animals, these findings can be utilized to monitor their health according to their ages, and enhance their conservation efforts.},
}

Animals
*Turtles/microbiology
*Gastrointestinal Microbiome/genetics
Italy
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Age Factors
Seychelles
Environment
Bacteria/genetics/classification

@article {pmid40520380,
year = {2025},
author = {Muzami, EM and Kitundu, G and Muriithi, OM and Kavoo, AM and Gichuru, VG and Mbinda, WM},
title = {Metagenomic insights to bacterial communities, functional traits, and soil health in banana smallholder agroecosystems of Kenya.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1582271},
pmid = {40520380},
issn = {1664-302X},
abstract = {Microbes inhabiting the banana rhizosphere are varied and mediate essential functions that enhance plant growth and increase crop productivity. Their abundance in soil habitats is a potential indicator of soil health and quality. Despite the well-known benefits of rhizosphere microorganisms in banana cultivation, their genomic and functional diversity remains largely unexplored within smallholder agroecosystems. In this study, we characterized the community composition and functional potential of bacteria in banana rhizospheric soils from Gituamba, Mangu and Ngenda constituencies in Kiambu County, Kenya. Using Illumina Novaseq sequencing, we analyzed 16S rRNA gene amplicons and shotgun metagenomic profiles to explore these microbial communities. Variations of soil physicochemical parameters across the study sites were assessed. The parameters varied across the sites, with soils in Gituamba and Ngenda depicting better soil fertility characteristics than Mangu. Amplicon sequencing profiles revealed higher bacterial diversity in Gituamba compared to Mangu, while the single sample from Ngenda exhibited moderate diversity. The dominant phyla across the study sites were Proteobacteria, Actinobacteria, and Cyanobacteria. Functional profiling of 16S rRNA gene amplicons showed a higher enrichment in Gituamba compared to Mangu. Overall, the functional profiling indicated that predicted metabolic pathways across the study sites were linked to genes encoded by the members of the most abundant bacterial phyla in the soil environments, majorly contributing to beneficial roles for soil health and crop yield. This study offers methods to reveal the banana rhizosphere as a rich reservoir for potential microbes of agricultural and biotechnological significance, which can promote sustainable agriculture.},
}

@article {pmid40520307,
year = {2025},
author = {Ye, S and Peng, S and Wang, X and Fan, J and Zhu, C and Huang, L and Huang, Y and Cheng, K and Ni, T and Qian, Y and Wu, X and Xu, Y},
title = {Microbial community structure and resistome dynamics on elevator buttons in response to surface disinfection practices.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1593114},
pmid = {40520307},
issn = {2296-2565},
mesh = {*Disinfection/methods ; *Disinfectants/pharmacology ; Humans ; COVID-19/prevention & control ; China ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; *Microbiota/drug effects ; SARS-CoV-2 ; },
abstract = {BACKGROUND: Disinfectants have been extensively used in public environments since the COVID-19 outbreak to help control the spread of the virus. This study aims to investigate whether disinfectant use influences the structure of bacterial communities and contributes to bacterial resistance to disinfectants and antibiotics.

METHODS: Using molecular biology techniques-including metagenomic sequencing and quantitative PCR (qPCR)-we analyzed the bacterial communities on elevator button surfaces from two tertiary hospitals, one infectious disease hospital, two quarantine hotels (designated for COVID-19 control), and five general hotels in Nanjing, Jiangsu Province, during the COVID-19 pandemic. We focused on detecting disinfectant resistance genes (DRGs), antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs).

RESULTS: Significant differences were observed in the bacterial community structures on elevator button surfaces across the four types of environments. Quarantine hotels, which implemented the most frequent disinfection protocols, exhibited distinct bacterial profiles at the phylum, genus, and species levels. Both α-diversity (within-sample diversity) and β-diversity (between-sample diversity) were lower and more distinct in quarantine hotels compared to the other environments. The abundance of DRGs, ARGs, and MGEs was also significantly higher on elevator button surfaces in quarantine hotels. Notably, antibiotic-resistant bacteria (ARBs), including Escherichia coli, Acinetobacter baumannii, and Pseudomonas aeruginosa, were detected in all four settings.

CONCLUSION: The structure of bacterial communities on elevator button surfaces varies across different environments, likely influenced by the frequency of disinfectant use. Increased resistance gene abundance in quarantine hotels suggests that disinfection practices may contribute to the selection and spread of resistant bacteria. Enhanced monitoring of disinfection effectiveness and refinement of protocols in high-risk environments such as hospitals and hotels are essential to limit the spread of resistant pathogens.},
}

*Disinfection/methods
*Disinfectants/pharmacology
Humans
COVID-19/prevention & control
China
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/drug effects
*Microbiota/drug effects
SARS-CoV-2

@article {pmid40379209,
year = {2025},
author = {Xie, D and Liu, Y and Cong, W and Qi, G and Mu, C},
title = {Pathogen Diagnostic Value of Nanopore Sequencing in Postoperative Central Nervous System Infections.},
journal = {World neurosurgery},
volume = {199},
number = {},
pages = {124090},
doi = {10.1016/j.wneu.2025.124090},
pmid = {40379209},
issn = {1878-8769},
abstract = {OBJECTIVE: To evaluate the diagnostic performance of nanopore sequencing in postoperative central nervous system infections (PCNSIs).

METHODS: A total of 34 patients with suspected PCNSIs after craniocerebral surgery were included from the Aviation General Hospital between June 2022 and October 2023. Cerebrospinal fluid samples were collected immediately. Clinical information was gathered for all patients, and tests including blood routine examination, biochemical analysis, microbial culture, metagenomic next-generation sequencing (mNGS), and nanopore sequencing were performed. Relevant data were compiled.

RESULTS: Among 34 patients suspected of PCNSIs, nanopore sequencing identified specific pathogenic sequences in 27 (79.41% positivity), surpassing both mNGS (73.53%) and microbial culture (55.88%). Compared to microbial culture and mNGS, nanopore sequencing demonstrated superior sensitivity (79.41%) and diagnostic performance, thereby minimizing the missed diagnosis rate of microbial culture (36.67% vs. 11.76%). Nanopore sequencing combined with microbial culture shows significant consistency with the final clinical diagnosis (K = 0.717, P < 0.05). In contrast, the consistency of using microbial culture alone with the final clinical diagnosis is lower (K = 0.289, P < 0.05), suggesting that microbial culture may have limitations in certain situations.

CONCLUSIONS: Compared to microbial culture and mNGS, nanopore sequencing has a higher pathogen detection rate and a lower missed diagnosis rate. In clinical practice, using nanopore sequencing as a supplement to microbial culture can aid in the diagnosis of PCNSIs.},
}

@article {pmid40520149,
year = {2025},
author = {Maldonado, M and Pita, L and Hentschel, U and Erpenbeck, D and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge Crambe crambe (Schmidt, 1862) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {275},
pmid = {40520149},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Crambe crambe (Porifera; Demospongiae; Poecilosclerida; Crambeidae). The host genome sequence is 143.20 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.53 kilobases in length. Several symbiotic prokaryotic genomes were assembled as MAGs, including two relevant sponge symbionts, the Candidatus Beroebacter blanensis/ AqS2 clade (Tethybacterales, Gammaproteobacteria) of LMA sponges, and the widely distributed archaeal Nitrosopumilus sp. clade.},
}

@article {pmid40519722,
year = {2025},
author = {Kong, Y and Zhang, T and Ye, X and Wu, J},
title = {Alterations of gut microbiota and metabolites in children with Crohn's disease and their correlation with disease activity.},
journal = {Translational pediatrics},
volume = {14},
number = {5},
pages = {960-971},
pmid = {40519722},
issn = {2224-4344},
abstract = {BACKGROUND: The disruption of the gut microbiota is a prominent feature seen in children with Crohn's disease (CD), impacting metabolic processes. These factors collectively contribute significantly to the onset and progression of CD. The aim of this study was to assess the variations in gut microbiota and metabolites in children with newly diagnosed CD and those in remission, and to investigate their potential correlation with clinical indexes.

METHODS: This was a retrospective study. From June 2018 and March 2024, 57 children with CD admitted to Beijing Children's Hospital were included, and 22 healthy children during the same period were selected as the control group. Their peripheral blood and fecal samples were obtained, and clinical data were collected. Analysis of the fecal microbiota and serum metabolites was conducted using metagenomic sequencing and non-targeted mass spectrometry, respectively, to compare the alteration in children with CD and healthy controls (HCs), and their correlation with clinical indexes.

RESULTS: Analysis of fecal metagenomic sequencing data revealed that the alpha diversity was significantly lower in the newly diagnosed CD group compared to the HC group, whereas it was ameliorated in the CD remission group. The beta diversity showed that the microbial structures of the three groups were obviously separated. Firmicutes was identified as the primary altered bacteria in the microbiota. Specifically, the abundance of Ruminococcus, Faecalimonas, Blautia, and Faecalibacterium were correlated with clinical indexes such as pediatric Crohn's disease activity index (PCDAI). Metabolomic analysis highlighted differences in lipid metabolism, bile acid (BA) metabolism, amino acid metabolism and energy homeostasis between the CD remission and newly diagnosed CD groups. Notably, the levels of citric acid were correlated with clinical indexes such as PCDAI, which was also potential indicator for identifying clinical activity of pediatric CD patients [area under the curve (AUC) =0.77, specificity =0.64, sensitivity =0.83].

CONCLUSIONS: The microbial diversity of children with newly diagnosed CD decreased, but then ameliorated in the remission stage. Some short-chain fatty acids (SCFAs)-producing bacteria, lipid metabolites, and energy homeostasis products were associated with clinical indexes. In particular, citric acid demonstrated specific effectiveness in identify clinical activity of pediatric CD patients, which was a potential biomarker. Further exploring the mechanism of energy homeostasis in CD is beneficial to find new therapeutic targets.},
}

@article {pmid40519668,
year = {2025},
author = {Miller, SJ and Zhang, F and Taylor, SL and Shoubridge, AP and Flynn, E and Vasil, E and Woodman, RJ and Papanicolas, LE and Rogers, GB},
title = {Oropharyngeal detection of specific gut-derived Enterobacterales is associated with increased respiratory infection risk in older adults.},
journal = {Frontiers in aging},
volume = {6},
number = {},
pages = {1566034},
pmid = {40519668},
issn = {2673-6217},
abstract = {Respiratory tract infections (RTI) are a major contributor to morbidity and mortality in later life. RTI risk factors in older populations, including declining general health, altered airway physiology, and increased pharmaceutical exposures, also contribute to changes in the oropharyngeal (OP) microbiota. We sought to investigate whether such changes predict future incidence of RTI. OP microbiota characteristics were measured in 190 residents of long-term aged care. Fifty-four participants (28.4%) experienced one or more study-defined RTIs during the 12-month follow-up period, of which 28 (14.7%) occurred within 90 days of sample collection. OP microbiota composition was significantly associated with days to RTI event (F = 1.74, R[2] = 1.02%, p = 0.04). Detection of Enterobacterales species (Enterobacter cloacae, Escherichia coli, Klebsiella oxytoca, Klebsiella pneumoniae, Klebsiella variicola, and Proteus mirabilis) were independently associated with RTI risk after covariate adjustment (subdistribution HR: 4.84; 95% CI: 1.65-14.19; p = 0.002). Strain-level analysis performed on metagenomes from contemporaneous OP and stool samples identified co-carriage of indistinguishable Enterobacterales strains in those with Enterobacterales-positive OP samples, suggesting intra-participant strain acquisition. We report OP carriage of Enterobacterales species to be a marker of future RTI risk in long-term aged care residents, reflecting the independent influence of common ageing-associated risk exposures.},
}

@article {pmid40519351,
year = {2025},
author = {Plazola, CE and Rehman, A and Morel, M and Vu, C and Castro, JG and Ayoade, F},
title = {Aspergillus fumigatus endocarditis in an immunocompetent host aided by metagenomic next-generation sequencing assay: case report and literature review.},
journal = {Le infezioni in medicina},
volume = {33},
number = {2},
pages = {226-232},
pmid = {40519351},
issn = {2532-8689},
abstract = {Aspergillus fumigatus endocarditis is a rare but severe infection associated with high mortality, typically affecting immunocompromised individuals. Diagnosing fungal endocarditis can be challenging due to the often negative blood cultures and nonspecific symptoms. We present a case of Aspergillus fumigatus infective endocarditis in a 59-year-old immunocompetent man with no typical risk factors, diagnosed with the assistance of metagenomic microbial plasma cell-free DNA next-generation sequencing assay (Karius test). The patient presented with ocular symptoms and was found to have a heart murmur and a hypodense liver lesion, leading to suspicion of infective endocarditis. Blood cultures failed to reveal a pathogen, but elevated fungal biomarkers and the Karius test supported Aspergillus fumigatus as the causal agent. The patient received antifungal therapy with voriconazole and liposomal amphotericin B followed by surgical intervention for mitral valve replacement. The case exemplifies the difficulty in diagnosing Aspergillus endocarditis, as blood cultures are often negative and histological confirmation may be delayed. Molecular diagnostics, such as metagenomic microbial plasma cell-free DNA next-generation sequencing assay, significantly enhance pathogen detection in culture-negative cases. However, although treatment with antifungal therapy and surgery can improve outcomes, the high mortality associated with Aspergillus endocarditis remains a critical concern, highlighting the need for further research and advancements in both diagnostic and therapeutic approaches.},
}

@article {pmid40518950,
year = {2025},
author = {Chen, C and Xu, Y and Ouyang, J and Xiong, X and Łabaj, PP and Chmielarczyk, A and Różańska, A and Zhang, H and Liu, K and Shi, T and Wu, J},
title = {VirulentHunter: deep learning-based virulence factor predictor illuminates pathogenicity in diverse microbial contexts.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
doi = {10.1093/bib/bbaf271},
pmid = {40518950},
issn = {1477-4054},
support = {32370720//National Natural Science Foundation of China/ ; 2023YFC2706503//National Key Research and Development Program of China/ ; },
mesh = {*Deep Learning ; *Virulence Factors/genetics/metabolism ; Humans ; *Mycobacterium tuberculosis/pathogenicity/genetics ; *Computational Biology/methods ; *Software ; Bacterial Proteins/genetics ; *Mycobacterium avium/pathogenicity/genetics ; },
abstract = {Virulence factors (VFs) are critical determinants of bacterial pathogenicity, but current homology-based identification methods often miss novel or divergent VFs, and many machine learning approaches neglect functional classification. Here, we present VirulentHunter, a novel deep learning framework that enable simultaneous VF identification and classification directly from protein sequences by leveraging the crucial step of fine-tuning pretrained protein language model. We curate a comprehensive VF database by integrating diverse public resources and expanding VF category annotations. Our benchmarking results demonstrate that VirulentHunter outperforms existing methods, particularly in identifying VFs lacking detectable homologs. Additionally, strain-level analysis using VirulentHunter highlights distinct pathogenicity profiles between Mycobacterium tuberculosis and Mycobacterium avium, revealing enrichment in VFs related to adherence, effector delivery systems, and immune modulation in M. tuberculosis, compared to biofilm formation and motility in M. avium. Furthermore, metagenomic profiling of gut microbiota from inflammatory bowel disease patient reveals a depletion of VFs associated with immune homeostasis. These results underscore the versatility of VirulentHunter as a powerful tool for VF analysis across diverse applications. To facilitate broader accessibility, we provide a freely accessible web service for VF prediction (http://www.unimd.org/VirulentHunter), accommodating protein sequences, genomes, and metagenomic data.},
}

*Deep Learning
*Virulence Factors/genetics/metabolism
Humans
*Mycobacterium tuberculosis/pathogenicity/genetics
*Computational Biology/methods
*Software
Bacterial Proteins/genetics
*Mycobacterium avium/pathogenicity/genetics

@article {pmid40518036,
year = {2025},
author = {Salgado, O and Martínez, O and Rivas, Y and Loyola, F},
title = {Highly Specific Virus-Host Linkages in Mesothermophilic and Circumneutral Hot Springs Microbial Communities.},
journal = {Research in microbiology},
volume = {},
number = {},
pages = {104300},
doi = {10.1016/j.resmic.2025.104300},
pmid = {40518036},
issn = {1769-7123},
abstract = {Microbial communities in hot springs are distributed globally and have been extensively characterized regarding their diversity and composition. However, most studies have focused on cellular microbes, with relatively few addressing viruses, and even fewer examining virus-host ecology. Furthermore, research on viral communities and virus-host interactions has predominantly targeted extremely thermophilic environments, leaving mesothermophilic (40-80°C) and circumneutral (pH 6-8) hot spring less explored. Here, we describe virus-host linkages using 37 metagenomic datasets obtained from 14 mesothermophilic and circumneutral hot springs. A parallel analysis of hot spring habitats-sediment, microbial mat, and water-employing diversity metrics, network analyses, and machine learning for virus-host pair identification revealed that viral communities appear to be more endemic than their hosts. Additionally, certain host taxa were identified as differentially abundant across habitats, some corresponding to specific hubs in the network analyses. Most viruses were linked to hosts within the same metagenome, with only a small fraction classified as cosmopolitan. Furthermore, nearly all virus-host pairs were exclusive to a single habitat type-sediment, microbial mat, or water. These findings suggests that virus-host linkages in mesothermophilic and circumneutral hot springs are highly specific, reflecting ecological adaptation within habitat niches.},
}

@article {pmid40517714,
year = {2025},
author = {Huang, H and Xiao, K and Shen, T and Chu, D and Xie, Z and Bi, Y and Ning, K and Yan, Y},
title = {The impact of enclosure management on the conservation and restoration of microbial community in a typical urban lake.},
journal = {The Science of the total environment},
volume = {989},
number = {},
pages = {179827},
doi = {10.1016/j.scitotenv.2025.179827},
pmid = {40517714},
issn = {1879-1026},
abstract = {Urban lake freshwater ecosystems, as vital lifelines intricately connected to human well-being, hosted microbes vital for biosynthetic and global biochemical cycles. Despite their ecological importance, current research has yet to fully elucidate how urban lake restoration efforts influence microbial diversity, community structure, and functional dynamics, leaving a significant gap in our understanding of the ecological outcomes of such interventions. Donghu Lake's ongoing restoration project employs enclosure management as a conservation strategy. To evaluate the impact of enclosure management on protecting and restoring microbial communities, we analyzed 72 metagenomic samples from the restoration waterbody. It was found that enclosure management profoundly reshaped microbial communities, making them more stable and similar to natural conditions, and boosting their biosynthetic gene encoding potential. Furthermore, research revealed antibiotic resistance genes (ARGs) tended to be preferentially hosted by specific microbes, identifying Gammaproteobacteria as a critical target for managing ARGs proliferation. These findings provide not only a fresh perspective for the understanding, but also a robust foundation for the management of urban lake freshwater ecosystems. Our findings highlight that enclosure management promotes microbial community stability and functional resilience, which are critical for restoring ecosystem services in urban lakes. This study provides actionable insights for designing targeted conservation strategies to enhance the sustainability of freshwater ecosystems under anthropogenic pressure.},
}

@article {pmid40517504,
year = {2025},
author = {Tang, X and Liu, Y and Yang, W and Wu, Y and Yong, T and Liu, W and Lv, F and Hussain, K and Wang, Y and Gao, X and Zhang, Y},
title = {Macroplastics in soybean cultivation: Neutral on plant growth but disruptive to nitrogen-fixing microbiome.},
journal = {Ecotoxicology and environmental safety},
volume = {301},
number = {},
pages = {118499},
doi = {10.1016/j.ecoenv.2025.118499},
pmid = {40517504},
issn = {1090-2414},
abstract = {Macroplastics are an emerging yet underexplored pollutant in agricultural soils, with the potential to disrupt nitrogen (N) cycling through physical interference and microbial community shifts. While extensive studies have focused on microplastics, the effects of larger plastic debris (>2 cm) on soil-plant systems in legume cropping systems remain poorly understood. We conducted a 71-d mesocosm study utilizing [15]N isotopic tracing and metagenomic sequencing to demonstrate how macroplastics influence soybean growth and soil-soybean continuum N cycling. Soybean growth was not affected under macroplastics exposure (up to 200 kg ha[-][1]). However, macroplastics increased soil NO3[-] and NH4[+] concentrations, and elevated urease and ammonia monooxygenase activities, suggesting enhanced N availability. Paradoxically, macroplastics significantly disrupted the N-fixing microbial community, reducing the abundance of key bacteria such as Azorhizobium and Bradyrhizobium. Nitrogen fixation pathways (in log10-transformed TPM+1) were markedly suppressed in soils treated with 200 kg ha[-1] macroplastics compared to untreated soils (p < 0.001). Our findings highlight the potential risks of macroplastics posing to N cycling and microbial health in agricultural soils. This study addresses a critical knowledge gap by shifting the focus from micro- to macroplastic impacts on biogeochemical cycling.},
}

@article {pmid40517474,
year = {2025},
author = {Yu, X and Li, J and Zhou, Y and Chen, Y and Zou, L and Luo, C and Shen, C and Liu, F and Xu, J and Tang, X},
title = {Identification of the microorganisms for methane-dependent arsenate reduction in wetland using DNA-stable isotope probing and metagenomics.},
journal = {Water research},
volume = {284},
number = {},
pages = {123934},
doi = {10.1016/j.watres.2025.123934},
pmid = {40517474},
issn = {1879-2448},
abstract = {The methane-dependent arsenate reduction (M-AsR) process is recently demonstrated to enhance the release of mobile and toxic arsenite [As(III)], with critical implications for ecosystem safety in wetland ecosystem. However, the key functional microorganisms and the underlying metabolic mechanisms of M-AsR in wetland remain unclear. In this study, [13]C-labeled methane (CH4) was used as the sole carbon source to track the active microorganisms responsible for M-AsR. DNA-stable isotope probing (DNA-SIP) combined with amplicon and metagenomic sequencing was further employed to identify the microorganisms involved in M-AsR. The results showed that arsenate [As(V)] reduction occurred exclusively in the treatment amended with both CH4 and As(V). After a 50-day incubation, significant shifts in the relative abundance of functional genes (pmoA, ANME-2d mcrA and arrA) were observed in the heavy DNA fractions from the treatment amended with [13]CH4 and As(V), indicating the incorporation of [13]C into M-AsR microorganisms. Furthermore, the Methanobacterium, Methylobacter and arsenate-reducing bacteria (Chryseobacterium and Hydrogenophaga) were the predominant genera in [13]CH4-As heavy fractions and identified as the potential microorganisms responsible for M-AsR in wetland. Metagenomic analysis further confirmed that most of these microorganisms contained genes for CH4 oxidation and As(V) reduction. This multi-omics approach provides mechanistic insights into microbial mediated As(V) reduction in methane-rich wetland area.},
}

@article {pmid40517085,
year = {2025},
author = {Schoenle, A and Francis, O and Archibald, JM and Burki, F and de Vries, J and Dumack, K and Eme, L and Florent, I and Hehenberger, E and Hoffmeyer, TT and Irisarri, I and Lara, E and Leger, MM and Lukeš, J and Massana, R and Mathur, V and Nitsche, F and Strassert, JFH and Worden, AZ and Yurchenko, V and Del Campo, J and Waldvogel, AM},
title = {Protist genomics: key to understanding eukaryotic evolution.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2025.05.004},
pmid = {40517085},
issn = {0168-9525},
abstract = {All eukaryotes other than animals, plants, and fungi are protists. Protists are highly diverse and found in nearly all environments, with key roles in planetary health and biogeochemical cycles. They represent the majority of eukaryotic diversity, making them essential for understanding eukaryotic evolution. However, these mainly unicellular, microscopic organisms are understudied and the generation of protist genomes lags far behind most multicellular lineages. Current genomic methods, which are primarily designed for animals and plants, are poorly suited for protists. Advancing protist genome research requires reevaluating plant- and animal-centric genomic standards. Future efforts must leverage emerging technologies and bioinformatics tools, ultimately enhancing our understanding of eukaryotic molecular and cell biology, ecology, and evolution.},
}

@article {pmid40516682,
year = {2025},
author = {Sadah Al Azzawi, DH and Jalali, A and Rezaei, M},
title = {Metagenomic Insights into Bacterial Communities and Antibiotic Resistance Genes in Landfill-Impacted Waters.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126663},
doi = {10.1016/j.envpol.2025.126663},
pmid = {40516682},
issn = {1873-6424},
abstract = {Municipal landfills are significant sources of environmental and microbial pollution, impacting groundwater and surface water quality. This study investigated the microbial community composition and antibiotic resistance genes (ARGs) in water downstream of landfills of Gilan, Mazandaran, and Golestan provinces, Iran. Water samples were collected from seven sites, and shotgun metagenomic sequencing was used to analyze microbial diversity and ARGs. Heavy metals and BTEX (benzene, toluene, ethylbenzene, and xylene) compounds were measured using inductively coupled plasma (ICP), and gas chromatography-mass spectrometry (GC-MS) methods, respectively. Pseudomonadaceae and Enterobacteriaceae were the most abundant bacterial families, with efflux pump ARGs being the most prevalent. Concentrations of arsenic and cadmium exceeded WHO and US-EPA standards at all sites. Significant positive correlations were observed between Pseudomonadaceae abundance and lead concentration (r =0.998, p = 0.031, CI [0.966, 0.999]), and between Enterobacteriaceae abundance and chromium concentration (r =0.999, p = 0.0078, CI [0.993, 1.000]). A significant negative correlation was found between the abundance of the two-component system (TCS) gene class and BTEX concentration (r = -0.457, p = 0.014, CI [-0.72, -0.09]). Additionally, aluminum concentration negatively correlated with antibiotic inactivation (r =0.999, p = 0.018, CI [-1.000, -0.997]) and antibiotic target protection classes (r = -0.997, p = 0.048, CI [-0.999, -0.990]). These findings indicate that landfill sites significantly influence bacterial communities, promoting resistance to heavy metals and pollutants. The abundance of ARGs near landfills suggests microbial adaptation to pollution, highlighting the need for improved waste management to mitigate the spread of antibiotic resistance.},
}

@article {pmid40516493,
year = {2025},
author = {Semwal, P and Shivhare, R and Majhi, B and Mishra, SK and Misra, S and Misra, A and Srivastava, S and Chauhan, PS},
title = {Endophytic bacterial's phenylalanine and trans-cinnamic acid as exogenous precursors involved in the modulating colchicine biosynthesis pathway in Gloriosa superba.},
journal = {Plant physiology and biochemistry : PPB},
volume = {227},
number = {},
pages = {110151},
doi = {10.1016/j.plaphy.2025.110151},
pmid = {40516493},
issn = {1873-2690},
abstract = {Unlocking the hidden power of endophytes reveals a novel pathway for boosting colchicine biosynthesis in Gloriosa superba. Metabolite analysis of endophyte culture filtrates identifies essential precursors i.e., phenyl ethyl alcohol, phenylalanine, trans-cinnamic acid, and benzoic acid participating in colchicine biosynthesis. Bacilli-treated Gloriosa superba plants demonstrated a remarkable increase in plant growth and colchicine content over untreated plants. Moreover, enhanced nutrient uptake (Fe, Zn, Cu, Mn) further induced the enzymatic activities critical for colchicine biosynthesis genes such as PAL, NMT, CYP450, and OMT. The metagenomic analysis associated with Bacilli-treated G. superba plants further revealed a shift in Bacillus species, and the functional pathway confirmed the upregulation of precursors in colchicine biosynthesis. Our study highlights the significant role of endophytic Bacilli on plant growth, enhanced nutrient uptake, and shifts in the endophytic microbiome to induce colchicine biosynthesis in G. Superba. It offers a detailed understanding of the endophyte's potential for deciphering its role in enhancing growth and active metabolite composition. It provides valuable insights for sustainable agriculture and unlocking new possibilities for pharmaceutical applications.},
}

@article {pmid40516400,
year = {2025},
author = {Ju, X and Sun, H and Ruan, C and Wang, H and Shi, B and Alvarez, PJJ and Yu, P},
title = {Prophage induction and quorum sensing enhance biofilm stability and resistance under ammonia-oxidizing bacteria-mediated oxidative stress.},
journal = {Water research},
volume = {284},
number = {},
pages = {124010},
doi = {10.1016/j.watres.2025.124010},
pmid = {40516400},
issn = {1879-2448},
abstract = {Ammonia-oxidizing bacteria (AOB) and prophage-carrying bacteria are prevalent in water treatment and reuse systems, yet their interactions and implications for biofilm formation and microbial risks remain insufficiently understood. Here, we demonstrate that oxidative stress arising from the metabolism of the AOB Nitrosomonas europaea induces prophage activation in lysogenized Escherichia coli (λ+). This activation triggers cellular lysis, leading to the release of intracellular components (e.g., protein and DNA) and upregulated quorum sensing (QS) followed by biosynthesis and excretion of extracellular polymeric substance (EPS). Integrated transcriptomic and proteomic analysis revealed that the presence of N. europaea significantly upregulated QS- and EPS-related genes by 2.14-2.93 and 2.81-3.11 folds in E. coli (λ+), respectively. Surviving E. coli (λ+) exhibited enhanced prophage-bacterium symbiosis and activated toxin-antitoxin systems, enhancing their resilience to environmental stress. These microbial adaptations markedly increased EPS production, fostering biofilm development and conferring enhanced biofilm resilience to disinfectants and bacterial antibiotic tolerance. Furthermore, metagenomic analysis at the microbial community wide level demonstrated that ammonia addition-driven AOB enrichment stimulated multi-species biofilm formation, promoted bacterium-phage interactions, and increased bacterial antibiotic resistance. Overall, our findings reveal that oxidative stress driven by AOB accelerates biofilm development, an overlooked phenomenon with potential to exacerbate microbial risks.},
}

@article {pmid40516324,
year = {2025},
author = {Xu, R and Li, T and Wang, Z and Wang, H and Sun, M and Xie, J and Tong, L and Peng, W and Wang, Y},
title = {Association among lean mass, gut microbiome alterations and bone mineral density in high-altitude.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {51},
number = {},
pages = {18-27},
doi = {10.1016/j.clnu.2025.05.018},
pmid = {40516324},
issn = {1532-1983},
abstract = {BACKGROUND: Body composition, particularly lean body mass, plays a pivotal role in skeletal health and has been increasingly linked to the gut microbiota (GM). However, evidence from vulnerable high-altitude populations remains scarce.

OBJECTIVE: This study aimed to evaluate the association between body composition and bone mineral density (BMD) at high altitudes and explore the potential role of GM.

METHODS: A total of 820 Tibetan participants were recruited. BMD at the lumbar spine (L1-L4) and total hip was measured using dual-energy X-ray absorptiometry (DXA). Multivariate linear regression was applied to evaluate the associations between body composition indices and BMD. Participants were stratified into low lean mass index (LLMI) and high lean mass index (HLMI) subgroups using restricted cubic splines (RCS) and body mass index. Stool samples from a subset of participants (n = 383) were analyzed to determine the relative abundances of KEGG Orthology groups.

RESULTS: LMI was positively associated with hip BMD at high altitude [β (95 % CI) = 0.005 (0.003,0.007), P < 0.05], whereas no significant association was observed with spine BMD. This correlation varied significantly by altitude (Pinter< 0.05). A similar positive relationship was observed between microbial diversity (Shannon index) and hip_BMD [hip: β (95 % CI) = 0.605 (0.165, 1.044), P < 0.05]. Compared to the HLMI group, LLMI participants exhibited greater microbial diversity (P < 0.05), higher Faecalibacteriums abundance, and lower levels of Prevotella copri (P< 0.05). Functional metagenomic analysis identified differential enrichment of microbial pathways, including riboflavin metabolism, terpenoid backbone biosynthesis, alanine, aspartate, and glutamate metabolism (P < 0.05).

CONCLUSION: These findings highlight the correlation between LMI and hip BMD among high-altitude Tibetan adults, offering a potential mechanism for the interplay between GM profiles and bone health in high-altitude populations.},
}

@article {pmid40516282,
year = {2025},
author = {Victor, MP and Radisic, V and Grevskott, DH and Marathe, NP},
title = {Hospital effluent in a low-resistance setting is responsible for dissemination of novel antibiotic resistance genes into the marine environment.},
journal = {Ecotoxicology and environmental safety},
volume = {301},
number = {},
pages = {118390},
doi = {10.1016/j.ecoenv.2025.118390},
pmid = {40516282},
issn = {1090-2414},
abstract = {Norway has low prevalence of resistance in the clinics, the contribution of hospital effluent to the spread of antimicrobial resistance (AMR) in the environment is largely unknown. The aim of our study was to determine the role of hospital sewage in dissemination of AMR by defining resistome of hospital effluent, and influent and treated-effluent from the receiving sewage treatment plant (STP) using culture-based methods and metagenomics. Around 94 % E. coli strains (n = 66) were multidrug-resistant (MDR), while 92.3 % of the Klebsiella spp. strains (n = 55) showed MDR phenotype, with some strains carrying carbapenemases, such as NDM-5 (n = 3) and KPC-3 (n = 3). Identical clones of Klebsiella michiganensis were detected in hospital effluent, influent and STP treated effluent. From approximately 238 Gigabases of sequence data, we assembled 1205 antibiotic resistance genes (ARGs) using fARGene method, of which 349 genes represented novel ARGs (< 90 % amino acid identity against known ARGs). Both known and novel ARGs (n = 54) were shared between hospital effluent and the treated effluent of the receiving STP. We assembled 523 metagenome assembled genomes (MAGs) with several representing novel taxa, of which 138 (26 %) MAGs carried 429 ARGs with > 83 % representing putative novel ARGs. Potential pathogens accounted for 60 % of the detected ARGs. Around 15.4 % MAGs were shared between hospital effluent and STP treated effluent. We demonstrate that hospital effluent in Norway has a high diversity of both known and novel ARGs. We show that hospital effluent contributes to the dissemination of not only clinically relevant pathogens but also known and novel ARGs into the receiving marine environment in Norway.},
}

@article {pmid40516202,
year = {2025},
author = {Botero, J and Basler, N and Cnockaert, M and Peeters, C and Schreiber, M and Marz, M and de Graaf, DC and Matthijnssens, J and Vandamme, P},
title = {Identification and functional genomic analyses of Bartonella isolates from honey bees, and reassessment of the taxonomy of the genus Bartonella.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {4},
pages = {126625},
doi = {10.1016/j.syapm.2025.126625},
pmid = {40516202},
issn = {1618-0984},
abstract = {We used matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and whole-genome sequence analyses to identify 90 Bartonella isolates from honey bee gut samples in Belgium. While the identification of 62 isolates as Bartonella apihabitans and three as Bartonella choladocola was straightforward, the identification of 25 Bartonella apis-like isolates was challenging. A taxonomic and functional analysis of four B. apis-like genomes and of publicly available B. apis genomes demonstrated that neither OrthoANIu and digital DNA-DNA hybridization analyses, nor functional annotation supported a clear separation of B. apis and B. apis-like genomes. Different phylogenomic analyses showed that B. apis and B. apis-like strains formed a monophyletic clade with an inconsistent internal structure. We therefore considered the remaining 25 isolates identified as B. apis. We subsequently re-addressed an earlier phylogenetic and functional divergence between three major clades of Bartonella species which differed not only in phylogenomic position and ecology, but also in genome size and genomic percentage G + C content, and in many metabolic capabilities. We propose to reclassify the single species of the Bartonella tamiae clade into the novel genus Attibartonella gen. nov., with Attibartonella tamiae comb. nov. as the type species. Similarly, we propose to reclassify species of the honey bee-associated Bartonella clade into the novel genus Ditibartonella gen. nov., with Ditibartonella apis comb. nov. as the type species. The phylogenomic analyses of publicly available genome and metagenome sequences revealed additional Ditibartonella species in honey bee samples, highlighted an evolutionary adaptation of Ditibartonella bacteria to bee hosts and suggested shared transmission routes.},
}

@article {pmid40515809,
year = {2025},
author = {Zhang, Z and Yang, Z and Lin, S and Jiang, S and Zhou, X and Li, J and Lu, W and Zhang, J},
title = {Probiotic-induced enrichment of Adlercreutzia equolifaciens increases gut microbiome wellness index and maps to lower host blood glucose levels.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2520407},
doi = {10.1080/19490976.2025.2520407},
pmid = {40515809},
issn = {1949-0984},
mesh = {Humans ; *Probiotics/administration & dosage/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Blood Glucose/analysis/metabolism ; Adult ; Middle Aged ; Metagenomics ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; },
abstract = {The gut microbiome is essential for maintaining host health, influencing gut function and metabolic regulation. While probiotics are widely used to manage gut health, evidence of their specific effects in healthy individuals remains limited. Most studies focus on diseased populations, with little attention to early interventions in individuals without major diseases. In this study, we investigated the effects of probiotics on gut health in participants free from significant health conditions. Fifty-four participants were randomly assigned to receive either a placebo or composite probiotics for 60 d. Shotgun metagenomics revealed that individuals with lower baseline Gut Microbiome Wellness Index 2 (GMWI) exhibited more decisive responses to probiotic intervention, characterized by an increased abundance of beneficial commensal bacteria, including Adlercreutzia equolifaciens. Probiotic intake significantly improved the function of the gut microbiome, reducing antibiotic resistance genes and virulence factors while enhancing carbohydrate-active enzymes. Notably, A. equolifaciens promoted the production of palmitoyl serinol, a metabolite associated with improved GMWI and preventive benefits in blood glucose. In a population-based experiment, these findings were validated in a follow-up single-strain probiotic intervention with Lacticaseibacillus casei Zhang. Our study highlights the potential of probiotics as an early intervention strategy for maintaining gut health in individuals without significant health conditions.},
}

Humans
*Probiotics/administration & dosage/pharmacology
*Gastrointestinal Microbiome/drug effects
Male
Female
*Blood Glucose/analysis/metabolism
Adult
Middle Aged
Metagenomics
Feces/microbiology
Bacteria/classification/genetics/isolation & purification
Young Adult

@article {pmid40514168,
year = {2025},
author = {Ebrahimi, F and Maleki, H and Ebrahimi, M and Beiki, AH},
title = {A novel approach to finding the compositional differences and biomarkers in gut microbiota in type 2 diabetic patients via meta-analysis, data-mining, and multivariate analysis.},
journal = {Endocrinologia, diabetes y nutricion},
volume = {72},
number = {6},
pages = {501561},
doi = {10.1016/j.endien.2025.501561},
pmid = {40514168},
issn = {2530-0180},
mesh = {*Diabetes Mellitus, Type 2/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Data Mining ; Biomarkers/analysis ; Multivariate Analysis ; Male ; Middle Aged ; Female ; },
abstract = {Type 2 diabetes mellitus (T2DM)-one of the fastest globally spreading diseases-is a chronic metabolic disorder characterized by elevated blood glucose levels. It has been suggested that the composition of gut microbiota plays key roles in the prevalence of T2DM. In this study, a novel approach of large-scale data mining and multivariate analysis of the gut microbiome of T2DM patients and healthy controls was conducted to find the key compositional differences in their microbiota and potential biomarkers of the disease.

METHODS: First, suitable datasets were identified (9 in total with 946 samples), analyzed, and their operational taxonomic units (OTUs) were computed by identical parameters to increase accuracy. The following OTUs were merged and compared based on their health status, and compositional differences detected. For biomarker identification, the OTUs were subjected to 9 different attribute weighting models. Additionally, OTUs were independently analyzed by multivariate algorithms (LEfSe test) to verify the realized biomarkers.

RESULTS: Overall, 23 genera and 4 phyla were identified as possible biomarkers. At genus level, the decrease of Bacteroides, Methanobrevibacter, Paraprevotella, and [Eubacterium] hallii group in T2DM and the increase of Prevotella, Megamonas, Megasphaera, Ligilactobacillus, and Lachnoclostridium were selected as biomarkers; and at phylum level, the increase of Synergistota and the decrease of Euryarchaeota, Desulfobacterota (Thermodesulfobacteriota), and Ptescibacteria.

CONCLUSION: This is the first study ever conducted to find the microbial compositional differences and biomarkers in T2DM using data mining models applied on a widespread metagenome dataset and verified by multivariate analysis.},
}

*Diabetes Mellitus, Type 2/microbiology
Humans
*Gastrointestinal Microbiome
*Data Mining
Biomarkers/analysis
Multivariate Analysis
Male
Middle Aged
Female