@article {pmid41600629,
year = {2026},
author = {Wang, D and Sun, J and Zhang, Y and Yuan, L and Xu, X and Xue, Y and Sun, H},
title = {Integrated 13C-DNA Stable Isotope Probing and Metagenomics Approaches to Identify Bisphenol A Assimilating Microorganisms and Metabolic Pathways in Biofilms.},
journal = {Toxics},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/toxics14010080},
pmid = {41600629},
issn = {2305-6304},
support = {52100082//National Natural Science Foundation of China/ ; KYCX25_3358//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; SJCX25_1722//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; BK20240983//Natural Science Foundation of Jiangsu Province/ ; ZMF23020040//Changzhou University Research Start-up Fund Project/ ; },
abstract = {Bisphenol A (BPA) is a persistent environmental contaminant requiring effective removal strategies. Biofilms offer advantages over conventional activated sludge for refractory compound degradation, yet the specific microorganisms and mechanisms driving BPA removal in biofilms remain poorly understood. This study employed an integrated approach, combining [13]C-DNA stable isotope probing (SIP) and metagenomics to identify BPA-assimilating microorganisms and elucidate their metabolic pathways in biofilms. Two moving bed biofilm reactors (MBBRs) were operated at contrasting BPA concentrations (500 μg/L and 10 mg/L) to enrich distinct microbial communities. Using DNA-SIP, we revealed differences in assimilating bacteria across diverse concentrations of BPA-enriched biofilms. Simultaneously, we reconstructed the genomes of these assimilating bacteria, dissecting the functional genes essential to the degradation process and identifying significant gene variations among different assimilating bacteria. By integrating these gene functions, we constructed the BPA metabolic pathway, which surprisingly comprised genes from various assimilating bacteria. This research significantly advances our understanding of BPA-assimilating bacteria within biofilms and provides valuable insights for refining biofilm technologies aimed at BPA removal from wastewater.},
}

@article {pmid41599943,
year = {2026},
author = {Rocha, HR and Ribeiro, P and Rodrigues, PM and Gomes, AM and Pintado, M and Coelho, MC},
title = {Bioinformatic Insights into the Carotenoids' Role in Gut Microbiota Dynamics.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020330},
pmid = {41599943},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Carotenoids/pharmacology/chemistry ; *Computational Biology ; Humans ; Fermentation ; Lycopene/pharmacology ; Lutein/pharmacology ; Bacteria/drug effects/genetics/classification ; beta Carotene/pharmacology ; },
abstract = {Background/Objectives: Carotenoids are bioactive pigments with well-established antioxidant and immunomodulatory properties, yet their impact on gut microbiota remains poorly understood from a chemical standpoint. This study explores how carotenoid structure and gastrointestinal stability shape microbial responses combining in vitro fermentation with bioinformatic analyses. Methods: Individual carotenoids (beta (β)-carotene, lutein, lycopene) and combined carotenoids, as well as algal-derived extracts were subjected to 48 h in vitro fermentation, and microbial composition and activity were assessed through sequencing and computational analysis. Results: β-carotene and lycopene promoted acid-tolerant taxa such as Escherichia-Shigella, whereas lutein, due to its higher polarity, supported more transient fluctuations. Mixtures and algal carotenoids exhibited synergistic effects, sustaining beneficial genera including Bifidobacterium and Bacteroides and promoting structured ecological trajectories. Conclusions: These findings provide a chemistry-driven perspective on how carotenoids act as modulators of microbial ecosystems, with direct implications for the formulation of carotenoid-enriched functional foods and dietary interventions.},
}

*Gastrointestinal Microbiome/drug effects
*Carotenoids/pharmacology/chemistry
*Computational Biology
Humans
Fermentation
Lycopene/pharmacology
Lutein/pharmacology
Bacteria/drug effects/genetics/classification
beta Carotene/pharmacology

@article {pmid41599039,
year = {2026},
author = {Wang, Z and Chen, G and Yang, M and Wang, S and Fang, J and Shi, C and Gu, Y and Ning, Z},
title = {Host-Filtered Blood Nucleic Acids for Pathogen Detection: Shared Background, Sparse Signal, and Methodological Limits.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010055},
pmid = {41599039},
issn = {2076-0817},
support = {2024-PWXZ-04//New Quality Clinical Specialty Program of High-end Medical Disciplinary Construction in Shanghai Pudong New Area/ ; 2024ZDXK0019//Shanghai Municipal Health Commission, Key Discipline of Shanghai Health System, Cardiology/ ; PW2025D-01//The Scientific Research Program of Shanghai Pudong New Area Health Commission (the Joint Research and Development Program)/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Tuberculosis/microbiology/diagnosis/blood ; Microbiota/genetics ; *Cell-Free Nucleic Acids/blood/genetics ; *Coronary Artery Disease/microbiology/diagnosis/blood ; Mycobacterium tuberculosis/genetics/isolation & purification ; Male ; Female ; Cohort Studies ; },
abstract = {Plasma cell-free RNA (cfRNA) metagenomics is increasingly explored for blood-based pathogen detection, but the structure of the shared background "blood microbiome", the reproducibility of reported signals, and the practical limits of this approach remain unclear. We performed a critical re-analysis and benchmarking ("stress test") of host-filtered blood RNA sequencing data from two cohorts: a bacteriologically confirmed tuberculosis (TB) cohort (n = 51) previously used only to derive host cfRNA signatures, and a coronary artery disease (CAD) cohort (n = 16) previously reported to show a CAD-shifted "blood microbiome" enriched for periodontal taxa. Both datasets were processed with a unified pipeline combining stringent human read removal and taxonomic profiling using the latest versions of specialized tools Kraken2 and MetaPhlAn4. Across both cohorts, only a minority of non-host reads were classifiable; under strict host filtering, classified non-host reads comprised 7.3% (5.0-12.0%) in CAD and 21.8% (5.4-31.5%) in TB, still representing only a small fraction of total cfRNA. Classified non-host communities were dominated by recurrent, low-abundance taxa from skin, oral, and environmental lineages, forming a largely shared, low-complexity background in both TB and CAD. Background-derived bacterial signatures showed only modest separation between disease and control groups, with wide intra-group variability. Mycobacterium tuberculosis-assigned reads were detectable in many TB-positive samples but accounted for ≤0.001% of total cfRNA and occurred at similar orders of magnitude in a subset of TB-negative samples, precluding robust discrimination. Phylogeny-aware visualization confirmed that visually "enriched" taxa in TB-positive plasma arose mainly from background-associated clades rather than a distinct pathogen-specific cluster. Collectively, these findings provide a quantitative benchmark of the background-dominated regime and practical limits of plasma cfRNA metagenomics for pathogen detection, highlighting that practical performance is constrained more by a shared, low-complexity background and sparse pathogen-derived fragments than by large disease-specific shifts, underscoring the need for transparent host filtering, explicit background modeling, and integration with targeted or orthogonal assays.},
}

Humans
*Metagenomics/methods
*Tuberculosis/microbiology/diagnosis/blood
Microbiota/genetics
*Cell-Free Nucleic Acids/blood/genetics
*Coronary Artery Disease/microbiology/diagnosis/blood
Mycobacterium tuberculosis/genetics/isolation & purification
Male
Female
Cohort Studies

@article {pmid41598945,
year = {2026},
author = {Hirata, K and Suzuki, T and Yura, K and Asahi, T and Kataoka, K},
title = {Gut Microbiome Differences Across Mixed-Sex and Female-Only Social Rearing Regimes in Female Field Crickets Teleogryllus occipitalis (Orthoptera: Gryllidae).},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010091},
pmid = {41598945},
issn = {2075-4450},
support = {24KJ2101//Japan Society for the Promotion of Science/ ; JPJ009237//Cabinet Office/ ; },
abstract = {The insect gut microbiome contributes to various host physiological processes and behaviors, such as digestion, nutrient absorption, immunity, mate choice, and fecundity. The social environment can shape gut microbial communities. Mixed-sex vs. female-only rearing is an important social context because it differs in exposure to the opposite sex and mating opportunities, which may in turn affect female physiology that may influence their gut microbiome. Despite the growing recognition of these social-microbial interactions, most studies have relied on 16S rRNA amplicon sequencing or qPCR, which provide only coarse taxonomic resolution and limited functional insight. In this study, we used whole-genome shotgun metagenomics to examine changes in microbial diversity and functional gene composition in the female field cricket Teleogryllus occipitalis (Serville) (Orthoptera: Gryllidae) reared under two social conditions: mixed-sex rearing and female-only rearing. Species richness and diversity analyses revealed that community composition separated between females from mixed-sex and female-only rearing. Functional profiling indicated higher relative abundances of genes annotated to nutrient processing and inter-bacterial competition in females from mixed-sex rearing, whereas females from female-only rearing showed relative enrichment of genes annotated to stress resistance and nitrogen fixation. These findings provide a genome-resolved foundation for testing how social rearing conditions covary with gut microbiome composition and functional potential in female crickets.},
}

@article {pmid41598908,
year = {2026},
author = {González-Peña, R and Hidalgo-Martínez, DO and Laredo-Tiscareño, SV and Huerta, H and de Luna-Santillana, EJ and Adame-Gallegos, JR and Rodríguez-Alarcón, CA and Rubio-Tabares, E and García-Rejón, JE and Muñoz-Ramírez, ZY and Tangudu, C and Garza-Hernández, JA},
title = {Characterization of the Bacteriome of Culicoides reevesi from Chihuahua, Northern Mexico: Symbiotic and Pathogenic Associations.},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010052},
pmid = {41598908},
issn = {2075-4450},
support = {419- 395 24-23//Secretaría de Ciencia, Humanidades, Tecnología e Innovación (SECIHTI)/ ; SIP20250075//Secretaría de Investigación y Posgrado from Instituto Politécnico Nacional/ ; },
abstract = {Culicoides biting midges are vectors of veterinary and zoonotic pathogens, yet the bacteriome of several species remains unexplored. Culicoides reevesi, a poorly studied species in northern Mexico, represents an opportunity to investigate microbial associations that may influence vector biology. Adults of C. reevesi were analyzed using 16S rRNA amplicon sequencing, followed by functional prediction with PICRUSt2. Heatmaps and pathway summaries were generated to highlight dominant taxa and functions. The bacteriome was dominated by Pseudomonadota, followed by Actinomycetota, Bacillota, and Bacteroidota. Symbiotic taxa such as Asaia and Cardinium were identified alongside potentially pathogenic bacteria, including Escherichia coli, Mycobacterium avium, Vibrio parahaemolyticus, and Enterococcus faecalis. Functional predictions indicated metabolic versatility, with abundant pathways related to aerobic respiration, the TCA cycle, amino acid biosynthesis, and quorum sensing. Despite all samples being collected from the same site and date, apparent differences in bacterial composition were observed across pools, suggesting microhabitat or host-related variability. This study provides the first taxonomic and functional baseline of the C. reevesi bacteriome. The detection of both symbiotic and pathogenic bacteria highlights the dual ecological role of the microbiome in host fitness and pathogen transmission potential. In conclusion, we suggest that these microbial associations influence vector physiology and competence, providing a basis for future microbiome-based control strategies. These findings emphasize the importance of integrating microbiome analyses into entomological surveillance and vector control strategies in endemic regions.},
}

@article {pmid41598312,
year = {2026},
author = {Thant, EP and Klaysubun, C and Suwannasin, S and Dechathai, T and Singkhamanan, K and Yaikhan, T and Chaichana, N and Pomwised, R and Wonglapsuwan, M and Chusri, S and Surachat, K},
title = {Global Comparative Genomics of Stenotrophomonas maltophilia Reveals Cryptic Species Diversity, Resistome Variation, and Population Structure.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/life16010158},
pmid = {41598312},
issn = {2075-1729},
abstract = {Background:Stenotrophomonas maltophilia is an increasingly important multidrug-resistant opportunistic pathogen frequently isolated from clinical, environmental, and plant-associated niches. Despite its medical relevance, the global population structure, species-complex boundaries, and genomic determinants of antimicrobial resistance (AMR) and ecological adaptation remain poorly resolved, partly due to inconsistent annotations and fragmented genomic datasets. Methods: Approximately 2400 genome assemblies annotated as Stenotrophomonas maltophilia were available in the NCBI Assembly database at the time of query. After pre-download filtering to exclude metagenome-assembled genomes and atypical lineages, 1750 isolate genomes were retrieved and subjected to stringent quality control (completeness ≥ 90%, contamination ≤ 5%, ≤500 contigs, N50 ≥ 10 kb, and ≤1% ambiguous bases), yielding a final curated dataset of 1518 high-quality genomes used for downstream analyses. Genomes were assessed using CheckM, annotated with Prokka, and compared using average nucleotide identity (ANI), pan-genome analysis, core-genome phylogenomics, and functional annotation. AMR genes, mobile genetic elements (MGEs), and metadata (source, host, and geographic origin) were integrated to assess lineage-specific genomic features and ecological distributions. Results: ANI-based clustering resolved the S. maltophilia complex into multiple distinct genomospecies and revealed extensive misidentification of publicly deposited genomes. The pan-genome was highly open, reflecting strong genomic plasticity driven by accessory gene acquisition. Core-genome phylogeny resolved well-supported clades associated with clinical, environmental, and plant-related niches. Resistome profiling showed widespread intrinsic MDR determinants, with certain lineages enriched for efflux pumps, β-lactamases, and trimethoprim-sulfamethoxazole resistance markers. MGE analysis identified lineage-specific integrative conjugative elements, prophages, and transposases that correlated with source and geographic distribution. Conclusions: This large-scale analysis provides the most comprehensive genomic overview of the S. maltophilia complex to date. Our findings clarify species boundaries, highlight substantial taxonomic misannotation in public databases, and reveal lineage-specific AMR and mobilome patterns linked to ecological and clinical origins. The curated dataset and evolutionary insights generated here establish a foundation for global genomic surveillance, epidemiological tracking, and future studies on the evolution of antimicrobial resistance in S. maltophilia.},
}

@article {pmid41598263,
year = {2026},
author = {Liu, Y and Zhao, M and Zhong, S and Wu, G and Yang, F and Zhou, J},
title = {Review on Mining Robust Lactic Acid Bacteria for Next-Generation Silage Inoculants via Multi-Omics.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/life16010108},
pmid = {41598263},
issn = {2075-1729},
support = {2023J06019//Fujian Provincial Outstanding Youth Fund Projects/ ; KFB25053A and KFB25010A//Science and Technology Innovation Specia Fund Project of Fujian Agriculture and Forestry University/ ; },
abstract = {Lactic acid bacteria (LAB), as the core microorganisms in silage fermentation, play a crucial role in improving silage quality and ensuring feed safety, making the screening, identification, and functional characterization of LAB strains a significant research focus. Researchers initially isolate and purify LAB from various samples, followed by identification through a combination of morphological, physiological, biochemical, and molecular biological methods. Systematic screening has been conducted to identify LAB strains tolerant to extreme environments (e.g., low temperature, high temperature, high salinity) and those possessing functional traits such as antimicrobial activity, antioxidant capacity, production of feruloyl esterase and bacteriocins, as well as cellulose degradation, yielding a series of notable findings. Furthermore, modern technologies, including microbiomics, metabolomics, metagenomics, and transcriptomics, have been employed to analyze the structure and functional potential of microbial communities, as well as metabolic dynamics during the ensiling process. The addition of superior LAB inoculants not only facilitates rapid acidification to reduce nutrient loss, inhibit harmful microorganisms, and improve fermentation quality and palatability but also demonstrates potential functions such as degrading mycotoxins, adsorbing heavy metals, and reducing methane emissions. However, its application efficacy is directly constrained by factors such as strain-crop specific interactions, high dependence on raw material conditions, limited functionality of bacterial strains, and relatively high application costs. In summary, the integration of multi-omics technologies with traditional methods, along with in-depth exploration of novel resources like phyllosphere endophytic LAB, will provide new directions for developing efficient and targeted LAB inoculants for silage.},
}

@article {pmid41597762,
year = {2026},
author = {Xiong, Y and Dai, Z and He, F and Liu, R and Wang, J and Zhan, Z and Jia, H and Chen, S and Cai, L},
title = {Effect of Hantavirus Infection on the Rodent Lung Microbiome: Specific Regulatory Roles of Host Species and Virus Types.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010244},
pmid = {41597762},
issn = {2076-2607},
support = {2024JJ9472//The natural science foundation of Hunan provincial/ ; },
abstract = {The lung-targeting characteristic of Hantavirus infection and the unclear mechanism underlying its interaction with the lung microbiome hampers the development of effective prevention and control strategies. In this study, lung tissues from Apodemus agrarius and Rattus norvegicus were collected at Hantavirus surveillance sites in Hunan Province. Metagenomic sequencing was subsequently applied to compare microbiome diversity, community structure, and function between infected and uninfected groups. Then the linear discriminant analysis effect size (LEfSe) was employed to identify key biomarkers. The results indicated that after infection with Hantaan virus (HTNV), Apodemus agrarius exhibited significantly increased evenness but markedly decreased richness of lung microbial communities, as reflected by consistent reductions in the number of observed species, Abundance-based Coverage Estimator (ACE) index, and Chao1 index. In contrast, Rattus norvegicus infected with Seoul virus (SEOV) showed no significant difference in microbial richness compared with uninfected controls, and even a slight increase was observed. These findings suggest that host species and virus type may play an important role in shaping microbial community responses. Furthermore, β-diversity analysis showed that the community structure was clearly separated by the host rodent species, as well as by their virus infection status. LEfSe analysis identified taxa with discriminatory power associated with infection status. Streptococcus agalactiae and Streptococcus were associated with SEOV-infected Rattus norvegicus, while Chlamydia and Chlamydia abortus were relatively enriched in uninfected Apodemus agrarius. This exploratory study reveals preliminary association between specific host-Hantavirus pairings (HTNV-Apodemus agrarius and SEOV-Rattus norvegicus) and the rodent lung microbiome, offering potential insights for future research into viral pathogenesis.},
}

@article {pmid41597751,
year = {2026},
author = {Liu, PY and Tang, HJ and Lee, SS and Liao, CH and Huang, CH and Kuo, HY and Sheng, WH and Taiwan Metagenomic Sequencing Microbiology Study Group, },
title = {Comparative Analysis of Microbial Detection in Traditional Culture Versus Metagenomic Next-Generation Sequencing in Patients with Periprosthetic Joint Infection: A Prospective Observational Study.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010233},
pmid = {41597751},
issn = {2076-2607},
support = {M09A7321 and MOHW113-TDU-B-211-114006//the Ministry of Health and Welfare of Taiwan/ ; NSTC 113-2321-B-002-016//the National Science and Technology Council of Taiwan/ ; },
abstract = {Identifying pathogens causing periprosthetic joint infection (PJI) is a challenge for clinicians. We aimed to evaluate the application of metagenomic next-generation sequencing (mNGS) to identify pathogens in PJI. A prospective analysis was conducted of patients diagnosed PJI between 2022 and 2024 at twelve hospitals in Taiwan. Both conventional bacterial culture (CMT) and mNGS of joint fluid and debrided tissue were performed. Demographic characteristics, laboratory results and clinical outcomes were collected. The diagnostic performance of these two methods was analyzed. A total of 42 patients with a mean age of 67.9 years were enrolled in analysis. The knee was the most common joint involved (69.1%). A high proportion of patients (78.6%) received prior antibiotics within the two weeks at sample collection. mNGS identified pathogens in 28 out of 42 patients (66.7%), whereas CMT yielded positive results in 12 out of 42 patients (28.6%) (McNemar's test, p = 0.01). Staphylococcus species was the most common genus detected (n = 11), followed by Cutibacterium (n = 4). Other detected genera included Escherichia, Mycobacterium, Enterobacter, Klebsiella (n = 2 each), Acinetobacter, and Corynebacterium (n = 1 each). Our results support the idea that mNGS could serve as a valuable diagnostic tool for PJI in addition to traditional culture methods.},
}

@article {pmid41597740,
year = {2026},
author = {Lowell, JL and Brown, L},
title = {Metals and Microbes: Microbial Community Diversity and Antibiotic Resistance in the Animas River Watershed, Colorado, USA.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010222},
pmid = {41597740},
issn = {2076-2607},
support = {RL5GM118990//NIH Building Infrastructure Leading to Diversity (BUILD) Initiative (U54)/ ; },
abstract = {Antimicrobial resistant (AMR) infections are a persistent public health issue causing excess death and economic impacts globally. Because AMR in clinical settings is often acquired from nonpathogenic bacteria that surround us, environmental surveillance must be better characterized. It has been well established that metals can co-select for bacterial AMR. Furthermore, recent studies have shown that compromised microbial community diversity may lead to community invasion by antibiotic resistance genes (ARGs). Widespread legacy mining has led to acid mine drainage and metal contamination of waterways and sediments throughout the western United States, potentially compromising microbial community diversity while simultaneously selecting for AMR bacteria. Our study objectives were to survey metal contaminated sediments from the Bonita Peak Mining District (BPMD) in southwestern Colorado, USA, compared to sites downstream in Durango, CO for bacterial and ARG diversity. Sediment bacteria were characterized using 16S rRNA Ilumina and metagenomic sequencing. We found that overall, bacterial diversity was lower in metal-contaminated, acidic sites (p = 0.04). Metagenomic sequencing revealed 31 different ARGs, with those encoding for efflux pumps (mex and spe gene families) substantially more prevalent in the BPMD sites, elucidating a specific AMR marker fingerprint from the high metal concentration sediments. Raising awareness and providing antimicrobial tracking techniques to resource limited communities could help provide information needed for better antibiotic use recommendations and environmental monitoring.},
}

@article {pmid41597738,
year = {2026},
author = {Xi, D and Zhu, F and Zhang, Z and Zhou, S and Zhang, J},
title = {Forest Type Shapes Soil Microbial Carbon Metabolism: A Metagenomic Study of Subtropical Forests on Lushan Mountain.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010220},
pmid = {41597738},
issn = {2076-2607},
support = {20232BAB205020//Jiangxi Provincial Natural Science Foundation/ ; 22-315-6-18//the Science and Technology Program of Shenyang/ ; JJXC2023010//Jiujiang City's "Xuncheng Talent" Program/ ; 20242BCC32138//Jiangxi Provincial Key Laboratory of Carbon Neutrality and Ecosystem Carbon Sinks/ ; },
abstract = {Forest type strongly influences soil microbial community composition and associated carbon cycling, yet its influence on microbial functional traits remains poorly understood. In this study, metagenomics sequencing was used to investigate soil microbial communities and carbon metabolism genes across three forest types: deciduous broadleaf (DBF), mixed coniferous-broadleaf (CBMF), and coniferous forest (CF) at two soil depths (0-20 cm and 20-40 cm) on Lushan Mountain in subtropical China. The results showed that CF exhibited higher bacterial diversity and a distinct microbial composition, with an increase in Actinomycetota and Bacteroidota and a decrease in Acidobacteriota and Pseudomonadota. The Calvin cycle was the dominant carbon fixation pathway in all forests, while the relative abundance of secondary pathways (i.e., the 3-hydroxypropionate bi-cycle and reductive citrate cycle) varied significantly with forest type. Key carbon fixation genes (sucD, pckA) were more abundant in CF and CBMF, with higher levels of rpiA/B and ackA in DBF. Functional profiling further indicated that CF soils, especially in the surface layer, were enriched in glycoside hydrolases (GHs) and carbohydrate esterases (CEs), while CBMF showed a greater potential for starch and lignin degradation. Multivariate statistical analyses identified soil available phosphorus (AP) and pH as primary factors shaping microbial community variation, with AP emerging as being the dominant regulator of carbon-related functional gene abundance. Overall, the prevalence of these distinct genetic potentials across forest types underscores how vegetation composition may shape microbial functional traits, thereby influencing the stability and dynamics of the soil carbon pool in forest ecosystem.},
}

@article {pmid41597735,
year = {2026},
author = {Moser, K and Ballif, A and Pillonel, T and Concu, M and Montenegro-Borbolla, E and Nickel, B and Stampfli, C and Ruf, MT and Audry, M and Kapel, N and Gerber, S and Jacot, D and Bertelli, C and Galpérine, T},
title = {Fecal Microbiota Transplantation Donor Screening: Is Dientamoeba fragilis a Valid Criterion for Donor Exclusion? A Longitudinal Study of a Swiss Cohort.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010217},
pmid = {41597735},
issn = {2076-2607},
support = {//internal funding at the Lausanne University Hospital (CHUV)/ ; grant number 51NF40 180575//he salaries of K.M. and E.M.-B. were supported as a part of NCCR Microbiomes, a National Centre of Competence in Research, funded by the Swiss National Science Foundation/ ; },
abstract = {Dientamoeba fragilis is a protozoan of the human digestive tract, yet its transmission and pathogenic role remain poorly understood. This study aimed to evaluate its impact on the efficacy and safety of fecal microbiota transplantation (FMT) in treating recurrent Clostridioides difficile infection (rCDI). This longitudinal cohort study analyzed stool samples from FMT donors and recipients pre-treatment and at 2 and 8 weeks post-FMT. All samples were retrospectively tested using real-time PCR. Shotgun metagenomics was also performed on selected donor-recipient pairs to explore transmission. CDI cure rates, gastrointestinal adverse events (AEs), and serious adverse events (SAEs) were assessed prospectively. A total of 53 FMT were analyzed (179 samples), with 23 (43%) derived from D. fragilis-positive donor stool (4 of 10 donors, 40%). Four of 52 recipients (18.2%), initially negative and who received treatment from positive donors, tested positive post-FMT. Shotgun metagenomics could not definitely confirm transmission due to the lack of a good reference genome. No significant differences in efficacy, AE, or SAE were observed between FMT from D. fragilis-positive versus -negative donors, even in immunocompromised patients. No SAEs were attributed to FMT. D. fragilis may be transmitted via FMT without evidence of short-term clinical impact. Consequently, RT-PCR detection should be interpreted cautiously in the context of donor exclusion decisions.},
}

@article {pmid41597726,
year = {2026},
author = {Lee, HJ and Park, SH and Han, SY and Lee, JH and Kim, DU and Seo, HI},
title = {Differences in the Biliary Microbiome Between Biliary Tract Cancer and Benign Biliary Disease.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010208},
pmid = {41597726},
issn = {2076-2607},
support = {202100350001//Biomedical Research Institute, Pusan National University Hospital/ ; },
abstract = {Bile contains many bacteria that can contribute to various diseases. Therefore, identifying bile microbiome differences between benign and malignant conditions is essential. In this study, bile samples were collected aseptically from 141 patients with biliary tract cancer (BTC) or benign biliary diseases (BBDs) who underwent endoscopic retrograde cholangiopancreatography or biliary tract surgery. Quality control PCR was performed to amplify the V3-V4 region of the bacterial 16S rRNA gene. Metagenomic sequencing of bile was successfully performed in 35 of 56 samples collected from patients with BTC and 24 of 85 samples from patients with BBD. The mean alpha diversity values comprised 2.788 ± 2.833 and 2.319 ± 1.355 in the BBD and BTC groups, respectively (p = 0.399). The bacterial species (4.7%) were shared between groups, whereas 12.3% and 83% were indicated to patients with BTC and BBD, respectively. Bacteroides coprocola, Prevotella copri, and Bacteroides plebeius were more frequently identified in the bile of patients with BTC, whereas Bacteroides vulgatus and Bacteroides uniformis were more abundant in the bile of patients with BBD. Distinct patterns of microorganism abundance between the two groups of patients suggest association of bile microbiome with disease status, so its diagnostic potential should be validated in further studies.},
}

@article {pmid41597714,
year = {2026},
author = {Isgandarov, I and Abilda, Z and Kanat, R and Daurov, D and Sapakhova, Z and Daurova, A and Zhambakin, K and Volkov, D and Begaly, A and Shamekova, M},
title = {Long-Read Metagenomics Profiling for Identification of Key Microorganisms Affected by Heavy Metals at Technogenic Zones.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010196},
pmid = {41597714},
issn = {2076-2607},
support = {BR24992837//Ministry of Agriculture of the Republic of Kazakhstan/ ; },
abstract = {Heavy metal pollution poses a serious threat to soil ecosystems worldwide, as long-term exposure can alter microbial community functioning and reduce overall ecosystem resilience. This study investigated the impact of heavy metal contamination in technogenic industrial areas of the East Kazakhstan Region on soil microbial communities. Soil samples were collected for chemical and metagenomic analyses. Concentrations of Zn, Pb, Cu, and Cd were quantified by flame atomic absorption spectrometry (FAAS). Using long-read whole-metagenome nanopore sequencing, we conducted strain-level profiling of soils with different levels of metal contamination. This approach provided high-resolution taxonomic data, enabling detailed characterization of microbial community structure. Heavy metal exposure did not significantly reduce microbial diversity or richness but influences the quality of community composition. Metal-resistant taxa dominated contaminated soils. Overall, the results highlight the value of long-read sequencing for resolving strain-level responses to environmental contamination.},
}

@article {pmid41597701,
year = {2026},
author = {Mollova, D and Baev, V and Borisova, T and Rusinova, M and Iliev, I},
title = {A Metagenomic Comparison of the Colostrum Microbiome in Bulgarian Mothers by Delivery Mode: A Pilot Study.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010184},
pmid = {41597701},
issn = {2076-2607},
support = {KP-06-M81/6//Bulgarian Science Fund/ ; },
abstract = {Colostrum harbors a highly diverse microbial community, predominantly composed of genera such as Staphylococcus, Streptococcus, Lactobacillus, Bifidobacterium, and Enterococcus. The composition and diversity of this microbiota are influenced by maternal factors-including age, body mass index, lactation activity, stress levels, and gestational diabetes-as well as external factors such as mode of delivery, antibiotic exposure, diet, and geographic location. This microbial community plays a critical role in maternal and neonatal health by contributing to early gut colonization, supporting digestion, promoting immune system development, and protecting against pathogenic microorganisms through mechanisms such as antimicrobial peptide production by lactic acid bacteria. The primary aim of this study was to evaluate the impact of mode of delivery on colostrum microbiota by comparing mothers who delivered vaginally with those who underwent cesarean section. Colostrum samples from 15 mothers were subjected to DNA extraction, high-throughput sequencing, and bioinformatic analyses to characterize microbial composition and predicted functional profiles. Although substantial inter-individual variability was observed, no statistically significant differences were detected in overall microbial diversity or community structure between the two delivery groups. However, distinct bacterial taxa and functional characteristics were identified that were specific to each mode of delivery, suggesting subtle delivery-related influences on colostrum microbiota composition.},
}

@article {pmid41597665,
year = {2026},
author = {Khachatryan, A and Vardanyan, A and Zhang, R and Zhang, Y and Shi, X and Willscher, S and Nguyen, NHA and Vardanyan, N},
title = {Metagenome Insights into Armenian Acid Mine Drainage: A Novel Thermoacidophilic Iron-Oxidizing Bacterium with Perspectives for Copper Bioleaching.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010146},
pmid = {41597665},
issn = {2076-2607},
support = {22rl-031//Higher Education Science Committee of Armenia/ ; 23-YSIP-012//Higher Education Science Committee of Armenia/ ; },
abstract = {The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities' structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously "Proteobacteria") (68-72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes.},
}

@article {pmid41597664,
year = {2026},
author = {Liepa, E and Ustinova, M and Gudra, D and Roga, A and Kalnina, I and Dejus, B and Dejus, S and Strods, M and Tomsone, LE and Kibilds, J and Bartkevics, V and Berzins, A and Dumpis, U and Juhna, T and Fridmanis, D},
title = {Urban Wastewater Metagenomics Reveals the Antibiotic Resistance Gene Distribution Across Latvian Municipalities.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010145},
pmid = {41597664},
issn = {2076-2607},
support = {VPP-COVID-2020/1-0008//Latvian Council of Science/ ; No.5.2.1.1.i.0/2/24/I/CFLA/001//CFLA/ ; },
abstract = {Antimicrobial resistance (AMR) poses a global health threat, with urban wastewater systems serving as key reservoirs for resistance dissemination. This study aimed to investigate the relationships among urban environments, bacterial communities, and AMR patterns, and evaluate the specific municipal-scale drivers of resistance gene distribution. Shotgun metagenomic analysis was conducted on 45 wastewater samples collected from 15 municipalities across Latvia to determine the composition of the resistome and its correlation with local factors. The analysis identified 417 distinct antibiotic resistance genes (ARGs) belonging to 108 families, with geographic location serving as the primary driver of ARG distribution, which explained 65.87% of community variation (p = 0.001). Local industrial factors demonstrated significant effects, with food industry wastewater significantly influencing both bacterial taxonomy and ARG profiles (p < 0.05). While the presence of a regional hospital did not shape the overall municipal resistome, hospital-associated wastewater showed 19 overlapping ARGs, including clinically critical carbapenemases. Municipal wastewater systems function as geographically structured reservoirs of AMR that are shaped by localized industrial and healthcare outputs. These findings support wastewater-based AMR surveillance as a valuable tool for tracking specific resistance sources.},
}

@article {pmid41597613,
year = {2026},
author = {Jarrín-V, P and Carrión-Olmedo, JC and Loján, P and Reyes-Barriga, D and Lara, M and Oña, A and Quiroz-Moreno, C and Castillejo, P and Tenea, GN and Díaz, M and Monfort-Lanzas, P and Molina, CA},
title = {Predicted Bacterial Metabolic Landscapes of the Sumaco Volcano: A Picrust2 Analysis of 16S rRNA Data from Amazonian Ecuador.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010094},
pmid = {41597613},
issn = {2076-2607},
support = {NA//National Institute of Biological Resources (NIBR) and the Korea International Cooperation Agency (KOICA) of the Republic of Korea/ ; },
abstract = {The Sumaco volcano in Ecuador, which has a distinct geological origin from the Andes and is located in the Amazon basin, offers an opportunity to study untouched microbiomes. We explored comparative patterns of abundance from predicted functional profiling in soil samples collected along the elevation and sulfur gradients on its slopes. Using 16S rRNA gene metabarcoding, we inferred metagenome functional profiles, contrasting sample groups by altitude or soil sulfur concentration. We inferred that high-altitude communities may have higher predicted abundance for anaerobic metabolism (crotonate fermentation), coenzyme B12 synthesis, and degradation of diverse carbon sources (sugars and octane). High-sulfur soils were associated with an inferred enrichment of pathways for degrading complex organic compounds and nitrogen metabolism, reflecting adaptation to unique geochemical conditions. In contrast, low-sulfur soils are consistent with a higher predicted abundance of glycerol degradation. Within the limitation imposed by the potential weak associations of the applied predicted functional profiling to actual gene content, we propose that the inferred metabolic changes represent different ecological strategies for resource acquisition, energy generation, and stress tolerance, and they are optimized for varying conditions in this unique volcanic ecosystem. Our findings highlight how environmental gradients shape soil microbiome functional diversity and offer insights into microbial adaptation in Sumaco's exceptional geochemistry within the Amazon. Further efforts linking functional predictions back to specific taxa will offer a complete ecological perspective of the microbiome exploration in the Sumaco volcano.},
}

@article {pmid41597576,
year = {2025},
author = {Wang, L and Zhao, Y},
title = {The Response of Substrate Microbial Communities to the Addition of Mineral Nutrients During the Growth Period of Straw Mushroom Volvariella volvacea.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010056},
pmid = {41597576},
issn = {2076-2607},
support = {No. 2024YFD1200204//National Key R&D Program of China/ ; No. 21N51900500//Shanghai Committee of Science and Technology/ ; 2020-02-08-00-12-F01479//Shanghai Agricultural Commission Program/ ; KFKT2023-03//the Shanghai Key Laboratory of Agricultural Genetics and Breeding/ ; },
abstract = {Volvariella volvacea were grown on an abandoned cotton-based substrate, which was divided into two conditions: a group with added nutrients (N3P3) and a control group (CK). Using metagenomic sequencing technology, the study investigated the effect of nutrient addition during the growth process of V. volvacea on the microbial community and metabolic pathways of the substrate. The study found that the main bacteria in the N3P3 group were Proteus and Microsporidium, while in the CK group, Bacillus marinosus and Microsporidium globosa were more common. At all stages of V. volvacea growth, Proteobacteria and Firmicutes dominated. Metabolic function analysis showed that the N3P3 group significantly increased amino acid metabolism, nitrogen metabolism, genetic information processing, and cellular processes, while reducing the contents of pathogenic and saprophytic symbiotic fungi. Nitrogen metabolism, phosphorus metabolism, and carbon metabolism were closely related to the growth of V. volvacea, and nutrient addition significantly improved microbial community diversity and metabolic levels, which can be used as a substrate optimization formula. This is of great significance for the development of sustainable agriculture.},
}

@article {pmid41597535,
year = {2025},
author = {Wang, Y and Liu, S and Zheng, Z and Ma, J and Xiang, Y and Wu, L and Ding, C and Shi, Y},
title = {Deciphering the Structure and Genetic Basis of Adaptive Mechanism of Soil Microbial Communities in a Manganese Electrolysis Plant.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010015},
pmid = {41597535},
issn = {2076-2607},
support = {QKHJCZK [2021] 224//Science and Technology Program of Guizhou Province/ ; QKHCG [2023] ZD008//Guizhou Provincial Science and Technology Projects/ ; No. [2023] 026//Guizhou Key Laboratory of Green Metallurgy and Process Strengthening/ ; No. [2023] 70//Science and Technology Major Project of Tongren/ ; },
abstract = {The development of China's manganese (Mn) industries has caused severe water and soil pollution, threatening ecological and human health. Microbes are usually regarded as an important indicator of environmental pollution assessment. However, the current understanding of microbial community characteristics and their formation mechanisms in Mn production areas remains limited. In order to address this, soil properties and microbial structural characteristics across different functional zones in a typical Mn electrolysis plant in China's "Manganese Triangle" were investigated via metagenomic sequencing. Results showed soil Mn levels significantly exceeded background values, indicating high environmental risk. Acidobacteria and Proteobacteria were dominant phyla. Microbial abundance was lowest in the adjacent natural reservoir, whereas diversity was highest in the sewage treatment plant. Correlation analyses identified Mn, nitrate nitrogen, ammonium nitrogen, pH, and moisture as key environmental drivers, with Mn being the primary one. Metagenomic analysis revealed abundant Mn resistance genes, enabling microbial survival under high Mn stress. This study demonstrated that excessive Mn exposure enriched Mn-resistant genes, thereby shaping unique microbial communities dominated by Mn-resistant bacteria. These findings clarified the structural characteristics and adaptive mechanisms of soil microbial communities in Mn-contaminated areas, providing a theoretical basis for ecological risk management and bioremediation.},
}

@article {pmid41597231,
year = {2026},
author = {Feng, Y and Geng, Y and Liu, S and Huang, X and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y},
title = {Overwinter Syndrome in Grass Carp (Ctenopharyngodon idellus) Links Enteric Viral Proliferation to Mucosal Disruption via Multiomics Investigation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/cells15020157},
pmid = {41597231},
issn = {2073-4409},
support = {2024YFD2401102//National Key R&D ProgramNational Key R&D Program/ ; 2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; },
mesh = {Animals ; *Carps/virology/microbiology ; *Fish Diseases/virology/microbiology/genetics ; *Intestinal Mucosa/virology/pathology/microbiology ; Gastrointestinal Microbiome ; Metagenomics ; Transcriptome ; Multiomics ; },
abstract = {Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the 'low-temperature-pathogen' model and shifts focus to mucosal barrier dysfunction and host-microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host-microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.},
}

Animals
*Carps/virology/microbiology
*Fish Diseases/virology/microbiology/genetics
*Intestinal Mucosa/virology/pathology/microbiology
Gastrointestinal Microbiome
Metagenomics
Transcriptome
Multiomics

@article {pmid41597216,
year = {2026},
author = {Mamun, MAA and Rakib, A and Mandal, M and Li, W and Miller, DD and Chen, H and Nagarkatti, M and Nagarkatti, P and Singh, UP},
title = {VERU-111 Promotes an Anti-Tumor Response Through Restoration of Gut Microbial Homeostasis and Associated Metabolic Dysregulation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/cells15020141},
pmid = {41597216},
issn = {2073-4409},
support = {AI140405//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; *Homeostasis/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; Azoxymethane ; Dextran Sulfate ; *Antineoplastic Agents/pharmacology ; Male ; Humans ; },
abstract = {The rising global burden of colorectal cancer (CRC) has now positioned it as the third most common cancer worldwide. Chemotherapy regimens are known to disrupt the composition of the gut microbiota and lead to long-term health consequences for cancer patients. However, the alteration of gut microbiota by specific chemotherapeutic agents has been insufficiently explored until now. The purpose of this study was to assess changes in the gut microbiota following treatment with VERU-111 as a chemotherapy agent for the treatment of CRC. We thus performed a metagenomic study using 16S rRNA gene amplicon sequencing of fecal samples from different experimental groups in the azoxymethane (AOM) and dextran sodium sulfate (DSS)-induced murine model of CRC. To predict the functional potential of microbial communities, we used the resulting 16S rRNA gene sequencing data to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We found that the administration of VERU-111 led to a restructured microbial community that was characterized by increased alpha and beta diversity. Compared to the mice treated with DSS alone, VERU-111 treatment significantly increased the relative abundance of several bacterial species, including Verrucomicrobiota species, Muribaculum intestinale, Alistipes finegoldii, Turicibacter, and the well-known gut-protective bacterial species Akkermansia muciniphila. The relative abundance of Ruminococcus, which is negatively correlated with immune checkpoint blockade therapy, was diminished following VERU-111 administration. Overall, this metagenomic study suggests that the microbial shift after administration of VERU-111 is associated with suppression of several metabolic and cancer-related pathways that might, at least in part, facilitate the suppression of CRC. These favorable shifts in gut microbiota suggest a novel therapeutic dimension of using VERU-111 to treat CRC and emphasize the need for further mechanistic exploration.},
}

*Gastrointestinal Microbiome/drug effects
Animals
Mice
*Homeostasis/drug effects
*Colorectal Neoplasms/drug therapy/microbiology/metabolism/pathology
RNA, Ribosomal, 16S/genetics
Mice, Inbred C57BL
Azoxymethane
Dextran Sulfate
*Antineoplastic Agents/pharmacology
Male
Humans

@article {pmid41596861,
year = {2026},
author = {Iturritxa, E and Mesanza, N and Torija, MJ},
title = {Wild Yeasts as Reservoirs of Bacterial Diversity: Biotechnological Insights from 16S rRNA Metabarcoding.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/foods15020262},
pmid = {41596861},
issn = {2304-8158},
abstract = {Recently acquired evidence indicates that bacteria can utilise yeasts as survival niches. This study investigated the presence of hidden, intracellular bacteria (endobacteria) within wild yeasts collected from natural ecosystems and evaluated whether biotechnological processes influenced these bacterial communities. We examined the microbiotas of 28 axenic cultures of wild yeasts; these were selected due to their potential brewing and biocontrol uses and were isolated from habitats associated with Quercus and Vitis. We also analysed the microbiotas present after these strains were used to ferment beer wort. Bacterial communities were characterised using 16S rRNA gene amplicon metagenomics. The results indicate that yeast strains and their endobacterial partners have coevolved, and their compositions are shaped by the environmental conditions. Substantial bacterial diversity was detected across strains in both axenic cultures and post-fermentation samples. The ecological origin of the yeast (oak- or grape-associated) did not significantly affect the endobacterial community structure. Across all samples, the dominant phyla were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, with Proteobacteria representing over 90% of sequences. Most bacterial genera were shared between axenic and fermentation conditions. However, Escherichia and Comamonas predominated in axenic cultures, while Parvibaculum dominated after fermentation. These findings suggest that yeasts constitute stable microhabitats for bacterial communities, and their relative abundances can shift during fermentation processes.},
}

@article {pmid41596857,
year = {2026},
author = {Tsouggou, N and Korozi, E and Pemaj, V and Drosinos, EH and Kapolos, J and Papadelli, M and Skandamis, PN and Papadimitriou, K},
title = {Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/foods15020259},
pmid = {41596857},
issn = {2304-8158},
abstract = {The cheese microbiome is a complex ecosystem strongly influenced by both technological practices and the processing environment. Moving beyond traditional cultured-based methods, the integration of shotgun metagenomics into cheese microbiology has enabled in-depth resolution of microbial communities at the species and strain levels. The aim of the present study was to review recent applications of shotgun metagenomics in cheese research, underscoring its role in tracking microbial dynamics during production and in discovering genes of technological importance. In addition, the review highlights how shotgun metagenomics enables the identification of key metabolic pathways, including amino acid catabolism, lipid metabolism, and citrate degradation, among others, which are central to flavor formation and ripening. Results of the discussed literature demonstrate how microbial composition, functional traits, and overall quality of cheese are determined by factors such as raw materials, the cheesemaking environment, and artisanal practices. Moreover, it highlights the analytical potentials of shotgun metagenomics, including metagenome-assembled genomes (MAGs) reconstruction, characterization of various genes contributing to flavor-related biosynthetic pathways, bacteriocin production, antimicrobial resistance, and virulence, as well as the identification of phages and CRISPR-Cas systems. These insights obtained are crucial for ensuring product's authenticity, enabling traceability, and improving the assessment of safety and quality. Despite shotgun metagenomics' advantages, there are still analytical restrictions concerning data handling and interpretation, which need to be addressed by importing standardization steps and moving towards integrating multi-omics approaches. Such strategies will lead to more accurate and reproducible results across studies and improved resolution of active ecosystems. Ultimately, shotgun metagenomics has shifted the field from descriptive surveys to a more detailed understanding of the underlying mechanisms shaping the overall quality and safety of cheese, thus bringing innovation in modern dairy microbiology.},
}

@article {pmid41596659,
year = {2026},
author = {Sánchez-Recillas, E and Almanza-Aguilera, E and Bars-Cortina, D and Zamora-Ros, R and Godínez-Santillán, RI and Sánchez-Tusié, AA and Vergara-Castañeda, HA},
title = {Effect of Garambullo (Myrtillocactus geometrizans) Consumption on the Intestinal Microbiota Profile in an Early-Phase Rat Model of Colon Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27021014},
pmid = {41596659},
issn = {1422-0067},
support = {1560335//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; FME202404//Autonomous University of Queretaro - FONFIVE/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colonic Neoplasms/microbiology/chemically induced/pathology/drug therapy ; Male ; Rats ; Rats, Sprague-Dawley ; Disease Models, Animal ; Azoxymethane ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Dextran Sulfate ; *Plant Extracts/pharmacology ; Bacteria/genetics/classification ; },
abstract = {Bioactive compounds in food contribute to reducing the risk of developing colon cancer by modulating the gut microbiota. We have recently demonstrated that garambullo (Myrtillocactus geometrizans), an endemic fruit of Mexico rich in bioactive compounds, attenuates aberrant crypt foci in an animal model. However, its potential to modulate the gut microbiota is unknown. The main objective of this study was to evaluate whether its consumption modulates colon carcinogenesis by altering the microbiota in an in vivo model induced by azoxymethane and dextran sulfate sodium (AOM/DSS). Fecal samples were collected from twelve male Sprague-Dawley rats and analyzed for microbiota composition after 0, 8, and 16 weeks of treatment with saline (control), AOM/DSS, garambullo (G), or residue of garambullo (RG) with AOM/DSS (G+AOM/DSS and RG+AOM/DSS, respectively). Characterization of the microbiome was based on the conserved region of the 16S rRNA V3-V4 gene, and analyzed by the ZymoBIOMICS' Targeted Metagenomics Sequencing (Zymo Research) service. In an animal model induced with AOM/DSS for 8 weeks, consumption of G and its residue increased the bacterial genera Shuttleworthiia, Subdoligranulum, Lactobacillus, Faecalibacterium, and Alloprevotella (p < 0.05). Consumption of G and its residue allowed the proliferation of bacteria that produce short-chain fatty acids and are associated with protective mechanisms of the colon.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Colonic Neoplasms/microbiology/chemically induced/pathology/drug therapy
Male
Rats
Rats, Sprague-Dawley
Disease Models, Animal
Azoxymethane
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Dextran Sulfate
*Plant Extracts/pharmacology
Bacteria/genetics/classification

@article {pmid41596633,
year = {2026},
author = {Tamayo-Ordóñez, YJ and Rosas-García, NM and Bello-López, JM and Tamayo-Ordóñez, MC and Tamayo-Ordóñez, FA and Calzada-Mendoza, CC and Ayil-Gutiérrez, BA},
title = {A Possible Recently Identified Evolutionary Strategy Using Membrane-Bound Vesicle Transfer of Genetic Material to Induce Bacterial Resistance, Virulence and Pathogenicity in Klebsiella oxytoca.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020988},
pmid = {41596633},
issn = {1422-0067},
mesh = {Gene Transfer, Horizontal ; *Klebsiella oxytoca/genetics/pathogenicity ; Virulence/genetics ; Phylogeny ; Evolution, Molecular ; Virulence Factors/genetics ; Genome, Bacterial ; Klebsiella Infections/microbiology ; *Drug Resistance, Bacterial/genetics ; Humans ; COVID-19 ; },
abstract = {Klebsiella oxytoca has emerged as an important opportunistic pathogen in nosocomial infections, particularly during the COVID-19 pandemic, due to its capacity to acquire and disseminate resistance and virulence genes through horizontal gene transfer (HGT). This study presents a genome-based comparative analysis of K. oxytoca within the genus Klebsiella, aimed at exploring the evolutionary plausibility of outer membrane vesicle (OMV) associated processes in bacterial adaptation. Using publicly available reference genomes, we analyzed pangenome structure, phylogenetic relationships, and the distribution of mobile genetic elements, resistance determinants, virulence factors, and genes related to OMV biogenesis. Our results reveal a conserved set of envelope associated and stress responsive genes involved in vesiculogenic pathways, together with an extensive mobilome and resistome characteristic of the genus. Although these genomic features are consistent with conditions that may favor OMV production, they do not constitute direct evidence of functional OMV mediated horizontal gene transfer. Instead, our findings support a hypothesis generating evolutionary framework in which OMVs may act as a complementary mechanism to established gene transfer routes, including conjugation, integrative mobile elements, and bacteriophages. Overall, this study provides a genomic framework for future experimental and metagenomic investigations into the role of OMV-associated processes in antimicrobial resistance dissemination and should be interpreted as a recently identified evolutionary strategy inferred from genomic data, rather than a novel or experimentally validated mechanism.},
}

Gene Transfer, Horizontal
*Klebsiella oxytoca/genetics/pathogenicity
Virulence/genetics
Phylogeny
Evolution, Molecular
Virulence Factors/genetics
Genome, Bacterial
Klebsiella Infections/microbiology
*Drug Resistance, Bacterial/genetics
Humans
COVID-19

@article {pmid41596486,
year = {2026},
author = {Sá, L and Machado, E and Ginani, V and Timbó, R and Romiti, R and Kurizky, P and Gomes, C},
title = {Species-Level Comparative Metagenomic Analysis of the Bacterial Abundance of the Gut Microbiome in Psoriasis, Hidradenitis Suppurativa, and Pemphigus Foliaceous Patients Using Shotgun Next-Generation Sequencing.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020838},
pmid = {41596486},
issn = {1422-0067},
support = {00193-00000279/2023-70//Fundação de Apoio à Pesquisa do Distrito Federal (FAP-DF)/ ; 445040/2023-8//National Council for Scientific and Technological Development/ ; 21/2023//Departamento de Ciência e Tecnologia, da Secretaria de Ciência, Tecnologia, Inovação e Com-plexo da Saúde, do Ministério da Saúde (Decit/SECTICS/MS)/ ; },
mesh = {Humans ; *Psoriasis/microbiology ; *Pemphigus/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Middle Aged ; Adult ; *Hidradenitis Suppurativa/microbiology ; Feces/microbiology ; *Bacteria/genetics/classification ; Aged ; },
abstract = {Recent studies have revealed a specific relationship between gut bacteria and inflammatory skin profiles. We aimed to perform a species-level comparative metagenomic analysis of the gut microbiome in patients with psoriasis, hidradenitis suppurativa (HS), and pemphigus foliaceus (PF). We included omnivorous nonsmokers and nondrinkers with psoriasis (n = 24), HS (n = 10), and PF (n = 11), as well as healthy controls (n = 10). We collected faecal samples from all patients for classic parasitological analysis. Gut microbiome analysis was conducted using shotgun next-generation sequencing. We used the Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2 bioinformatics tools to evaluate concordance and differential abundance between patients. Thirteen patients (23.64%) were diagnosed with active intestinal parasitosis. The presence of intestinal parasitosis was significantly related to immunosuppression (p = 0.009). The most abundant microorganism species found in the faeces of the patients evaluated was Escherichia coli. Psoriasis patients presented a greater abundance of bacteria from the Veillonellaceae family, whereas PF patients presented a greater abundance of Firmicutes bacteria. Patients with PF showed increased E. coli virulence and antibiotic resistance functional markers. Immunosuppression significantly influenced the presence of intestinal parasitosis as well as increased the virulence of functional markers in patients with PF receiving systemic corticosteroid therapy.},
}

Humans
*Psoriasis/microbiology
*Pemphigus/microbiology
Female
Male
*Gastrointestinal Microbiome/genetics
High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Middle Aged
Adult
*Hidradenitis Suppurativa/microbiology
Feces/microbiology
*Bacteria/genetics/classification
Aged

@article {pmid41596119,
year = {2026},
author = {Patanè, GT and Moreira, RJ and Almeida-Santos, M and Putaggio, S and Barreca, D and Oliveira, PF and Alves, MG},
title = {Anthocyanins and Metabolic Disease: A New Frontier in Precision Nutrition.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/antiox15010061},
pmid = {41596119},
issn = {2076-3921},
support = {2024.03012.BD//Fundação para a Ciência e Tecnologia/ ; UIDB/50006/2020//Laboratório Associado para a Química Verde/ ; CEECINST/00026/2018//Fundação para a Ciência e Tecnologia/ ; CDL-CTTRI-267-SGRH/2022//Fundação para a Ciência e Tecnologia/ ; UIDB/04501/2020-DOI 10.54499/UIDB/04501/2020 and UIDP/04501/2020-DOI 10.54499/UIDP/04501/2020//iBiMED/ ; },
abstract = {Metabolic syndrome (MetS) represents a global health challenge mainly driven by chronic low-grade inflammation and persistent oxidative stress (OS). Current therapeutic and nutritional strategies often fail to resolve these interconnected core pathologies due to the multifactorial nature of MetS. Anthocyanins (ACNs), a class of potent dietary flavonoids, offer significant promise due to their established pleiotropic effects, including robust antioxidant activity through modulation of the Nrf2/ARE pathway, anti-inflammatory effects via NF-κB suppression, and overall support for glucose and lipid homeostasis. However, the therapeutic efficacy of ACNs is characterized by interindividual variability, which is intrinsically linked to their low systemic bioavailability. This heterogeneity in the response is due to the complex interplay between genetic polymorphisms affecting absorption, distribution, metabolism, and excretion (ADME), as well as the specific biotransformation capacity of the gut microbiome. This review proposes that achieving the full clinical potential of ACNs requires moving beyond conventional nutritional advice. We propose that precision nutrition, which integrates multi-omics data (e.g., genomics, metagenomics, and metabolomics), can determine the individual phenotype, predict functional metabolic response, and tailor safer and effective ACN-rich interventions. This integrated, multifactorial approach is essential for optimizing the antioxidant and metabolic benefits of ACNs for the prevention and management of MetS and its associated pathologies.},
}

@article {pmid41595535,
year = {2026},
author = {Ma, Y and Wang, L and Hu, H and Shieh, AR and Li, E and He, D and He, L and Liu, Z and Paing, TM and Chen, X and Cao, Y},
title = {Composition and Function of Gut Microbiome: From Basic Omics to Precision Medicine.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010116},
pmid = {41595535},
issn = {2073-4425},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; Animals ; Genomics/methods ; Probiotics ; },
abstract = {The gut microbiome is defined as the collective assembly of microbial communities inhabiting the gut, along with their genes and metabolic products. The gut microbiome systematically regulates host metabolism, immunity, and neuroendocrine homeostasis via interspecies interaction networks and inter-organ axes. Given the importance of the gut microbiome to the host, this review integrates the composition, function, and genetic basis of the gut microbiome with host genomics to provide a systematic overview of recent advances in microbiome-host interactions. This encompasses a complete technological pipeline spanning from in vitro to in vivo models to translational medicine. This technological pipeline spans from single-bacterium CRISPR editing, organoid-microbiome co-culture, and sterile/humanized animal models to multi-omics integrated algorithms, machine learning causal inference, and individualized probiotic design. It aims to transform microbiome associations into precision intervention strategies that can be targeted and predicted for clinical application through interdisciplinary research, thereby providing the cornerstone of a new generation of precision treatment strategies for cancer, metabolic, and neurodegenerative diseases.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Precision Medicine/methods
Animals
Genomics/methods
Probiotics

@article {pmid41595438,
year = {2025},
author = {Vougiouklaki, D and Letsiou, S and Ladias, K and Tsakni, A and Mavrokefalidou, I and Siateli, Z and Halvatsiotis, P and Houhoula, D},
title = {Lactobacillus-Dominated Cervical Microbiota Revealed by Long-Read 16S rRNA Sequencing: A Greek Pilot Study.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010018},
pmid = {41595438},
issn = {2073-4425},
mesh = {Female ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Pilot Projects ; *Cervix Uteri/microbiology ; Greece ; *Lactobacillus/genetics/isolation & purification/classification ; Adult ; Middle Aged ; Vagina/microbiology ; },
abstract = {Background/Objectives: The vaginal microbiota constitutes a highly dynamic microbial ecosystem shaped by the distinct mucosal, hormonal, and immunological environment of the female genital tract. Accumulating evidence suggests that shifts in cervical microbial composition and function may influence host-microbe interactions and contribute to gynecological disease risk. Within this framework, the present study aimed to perform an in-depth genomic characterization of the cervical microbiota in a well-defined cohort of Greek women. The primary objective was to explore the functional microbial landscape by identifying dominant bacterial taxa, taxon-specific signatures, and potential microbial pathways implicated in cervical epithelial homeostasis, immune modulation, and disease susceptibility. Methods: Microbial genomic DNA was isolated from 60 cervical samples using the Magcore Bacterial Automated Kit and analyzed through full-length 16S rRNA gene sequencing using the Nanopore MinION™ platform, allowing high-resolution taxonomic assignment and enhanced functional inference. In parallel, cervical samples were screened for 14 HPV genotypes using a real-time PCR-based assay. Results: The cervical microbial communities were dominated by Lactobacillus iners, Lactobacillus crispatus, and Aerococcus christensenii, collectively representing over 75% of total microbial abundance and suggesting a functionally protective microbiota profile. A diverse set of low-abundance taxa-including Stenotrophomonas maltophilia, Stenotrophomonas pavanii, Acinetobacter septicus, Rhizobium spp. (Rhizobium rhizogenes, Rhizobium tropici, Rhizobium jaguaris), Prevotella amnii, Prevotella disiens, Brevibacterium casei, Fannyhessea vaginae, and Gemelliphila asaccharolytica-was also detected, potentially reflecting niche-specific metabolic functions or environmental microbial inputs. No HPV genotypes were detected in any of the cervical samples. Conclusions: This genomic profiling study underscores the functional dominance of Lactobacillus spp. within the cervical microbiota and highlights the contribution of low-abundance taxa that may participate in metabolic cross-feeding, immune signaling, or epithelial barrier modulation. Future large-scale, multi-omics studies integrating metagenomics and host transcriptomic data are warranted to validate microbial functional signatures as biomarkers or therapeutic targets for cervical health optimization.},
}

Female
Humans
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Pilot Projects
*Cervix Uteri/microbiology
Greece
*Lactobacillus/genetics/isolation & purification/classification
Adult
Middle Aged
Vagina/microbiology

@article {pmid41595429,
year = {2025},
author = {Wu, H and Li, J and Long, J and Liao, H and Zhan, K and Chen, H and Lei, F},
title = {Enhancing Ecological Functions in Chinese Yellow Earth: Metagenomic Evidence of Microbial and Nitrogen Cycle Reassembly by Organic Amendments.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010009},
pmid = {41595429},
issn = {2073-4425},
support = {Grants 2022YFD1901500 and 2022YFD1901505//the National Key R&D Program of China/ ; Grant U2420626//the National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil Microbiology ; Soil/chemistry ; *Nitrogen Cycle/genetics ; Metagenomics/methods ; Nitrogen/metabolism ; China ; Zea mays/growth & development ; Fertilizers ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics/classification ; Charcoal ; },
abstract = {BACKGROUND: Chinese Yellow Earth is a key subtropical agricultural resource in southwestern China; however, its productivity is limited by acidity and poor nutrient retention. This study examined how reduced nitrogen plus organic amendments affect its soil microbial structure and maize yield.

METHODS: A field experiment with four treatments evaluated reduced nitrogen fertilization amended with rice husk plus rapeseed cake (RS) or RS with biochar (BC). Soil properties (pH, nitrogen, organic matter) and maize yield were analyzed. Metagenomic analysis (NR database) characterized microbial communities, and correlation analysis with Mantel tests identified key relationships.

RESULTS: Combined organic amendments under reduced N significantly increased soil pH, nitrogen components, and organic matter, increasing maize yield by 4.41-8.97%. Metagenomics revealed enriched beneficial genera including Sphingomonas and Bradyrhizobium. Yield positively correlated with nitrate nitrogen and a beneficial microbial cluster containing Lysobacter and Reyranella, whereas Steroidobacter negatively correlated with key fertility indicators. Mantel tests revealed nitrate nitrogen as the primary correlate of functional gene community succession.

CONCLUSIONS: This study reveals that reduced nitrogen with organic amendments promotes soil improvement and microbial modulation, demonstrating potential as a sustainable practice to maintain crop productivity in Chinese Yellow Earth. The observed trend toward yield improvement underscores its promise and warrants further validation through additional trials. Overall, the findings highlight the beneficial effects of these amendments on soil health and their role in supporting sustainable subtropical agriculture under reduced nitrogen input.},
}

*Soil Microbiology
Soil/chemistry
*Nitrogen Cycle/genetics
Metagenomics/methods
Nitrogen/metabolism
China
Zea mays/growth & development
Fertilizers
*Microbiota/genetics
Metagenome
Bacteria/genetics/classification
Charcoal

@article {pmid41594879,
year = {2026},
author = {Han, H and Yang, Y and Zhu, X and Wangdwei, M and Yang, L},
title = {Age-Specific Composition and Predicted Function of Gut Microbiota in Plateau Pikas (Ochotona curzoniae).},
journal = {Biology},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/biology15020144},
pmid = {41594879},
issn = {2079-7737},
support = {202401ZR0101//Natural Science Foundation of the Xizang Autonomous Region/ ; 2021-GSP-B015//High-level Personnel Training Program of Xizang University/ ; },
abstract = {Gut microbes play a crucial role in regulating physiological processes such as host energy metabolism, nutrient absorption, and environmental adaptation. The predicted functions of gut microbes can be influenced by many factors, both extrinsic and intrinsic to the hosts. The plateau pika is a key species in the alpine ecosystem of the Qinghai-Tibet Plateau. Previous research on the plateau pika primarily examined how extrinsic factors affected its gut microbiota. However, studies on intrinsic factors are scarce. Here, we used live-trapping to capture plateau pikas and collect cecum contents. Using metagenomic sequencing of cecum content samples, we characterized and compared the gut microbial composition and predicted function of plateau pika in adult (n = 9) and juvenile (n = 9) populations. The results indicated that Bacillota and Bacteroidete were the major bacterial phyla. The core gut microbial genera were the same, but the relative abundance of Oscillospira in juveniles was significantly lower than that in adults. The changes in the proportion of cellulose-degradation-related bacterial communities in juveniles suggest that they tend to choose low-fiber diets. In this study, we found no significant differences in the gut microbial composition and diversity, KEGG level 1 metabolic pathways, or CAZy class level between adult and juvenile plateau pikas. In total, the composition and predicted functions of cecal microorganisms in juvenile and adult male plateau pikas were not different. Regarding KEGG level 2 metabolic pathways, the juvenile group had a higher relative abundance of metabolic pathways for cofactors and vitamins, terpenoids, and polyketides, whereas the adult group had a higher relative abundance of energy metabolism. However, the resulting differences remain unclear. Therefore, future research should validate the above findings on a broader spatio-temporal scale and conduct cross-species comparisons to construct a microbial ecological framework for the health management of plateau wild animals.},
}

@article {pmid41594852,
year = {2026},
author = {Zhao, Q and Li, B and Ma, J and Wei, J and Qin, W},
title = {The Gut Microbiome of the Goitered Gazelle Enables Plasticity by Responding to Environmental Factors in the Qaidam Basin.},
journal = {Biology},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/biology15020118},
pmid = {41594852},
issn = {2079-7737},
support = {32160316//National Natural Science Foundation of China/ ; },
abstract = {The Qaidam Basin on the Qinghai-Tibet Plateau is an extreme arid environment, posing severe survival challenges. The goitered gazelle (Gazella subgutturosa) is a keystone species in this fragile ecosystem, yet the ecological role of its gut microbiota and its associations with environmental drivers remain poorly understood. We collected fecal samples from gazelles across seven regions of the basin. Metagenomic sequencing was employed to characterize the gut microbiome. Statistical analyses (Mantel tests, multiple regression on matrices, co-occurrence networks) were used to link microbial composition and function with key environmental factors. The gut microbiota was dominated by fiber-degrading phyla (Firmicutes, Bacteroidota) and enriched in metabolic pathways, aligning with a high-fiber diet. Regarding environmental drivers of gut microbial composition variations, isothermality and soil organic carbon were significant predictors, likely via vegetation and environmental inoculation. Regarding environmental drivers of gut microbial function variations, winter solar radiation was uniquely associated with metabolic function without altering microbial composition, suggesting a functional plasticity-the capacity to shift metabolic profiles independently of taxonomic turnover-in response to environmental variation. The gut microbiota of the goitered gazelle exhibits a stable core composition alongside environmentally responsive functional modules. This suggests the microbiome may serve as a significant mediator of host resilience, highlighting adaptation as a dynamic interplay between host, microbiome, and environment. These insights are crucial for microbiome-assisted conservation.},
}

@article {pmid41594560,
year = {2025},
author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB},
title = {Gut Microbial Composition and Short-Chain Fatty Acid Metabolism in Cognitively Unimpaired Adults Stratified by Amyloid-β Status.},
journal = {Biomolecules},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/biom16010018},
pmid = {41594560},
issn = {2218-273X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; Female ; Male ; *Amyloid beta-Peptides/metabolism ; Aged ; Feces/microbiology/chemistry ; Middle Aged ; Alzheimer Disease/metabolism ; Cognition ; },
abstract = {Short-chain fatty acids (SCFAs) produced by gut microbial fermentation influence host metabolism and neuroinflammatory processes implicated in Alzheimer's disease (AD). However, the relationship between fecal SCFAs, microbial taxa, and cerebral amyloid-β (Aβ) burden in cognitively unimpaired individuals remains unclear. Fecal SCFAs were quantified using GC-MS, and microbial species were profiled by shotgun metagenomics in 87 participants. Associations between SCFAs, demographics, APOE ε4 status, and Aβ burden were tested using nonparametric statistics and multivariable regression. Microbial-SCFA links were evaluated using Spearman correlations and multivariate ordinations, with mediation analysis exploring potential indirect pathways. Acetate was the predominant SCFA and demonstrated the most robust microbial associations. Higher acetate concentrations were positively associated with Bacteroides ovatus and Faecalibacterium prausnitzii, whereas lower acetate levels were linked to species such as Bifidobacterium animalis and Lachnoclostridium scindens. Stratified analyses indicated that individuals with elevated Aβ burden exhibited more pronounced species-SCFA relationships, including a notable association between Bacteroides thetaiotaomicron and butyrate. Multivariate ordination further identified a significant overall coupling between SCFA profiles and microbial community structure. Mediation analysis suggested that an Oscillospiraceae species may represent a potential intermediary linking valerate concentrations with Aβ status. SCFA concentrations were not strongly influenced by demographic or genetic factors, but specific species demonstrated robust associations with acetate levels. Distinct SCFA-microbial interaction patterns in Aβ High individuals suggest subtle early gut microbial alterations linked to amyloid burden. These findings highlight the potential role of SCFA-related microbial pathways in preclinical AD.},
}

Humans
*Gastrointestinal Microbiome
*Fatty Acids, Volatile/metabolism
Female
Male
*Amyloid beta-Peptides/metabolism
Aged
Feces/microbiology/chemistry
Middle Aged
Alzheimer Disease/metabolism
Cognition

@article {pmid41594301,
year = {2026},
author = {Camatti, J and Bonasoni, MP and Santunione, AL and Cecchi, R and Radheshi, E and Carretto, E},
title = {Postmortem Microbiology in Forensic Diagnostics: Interpretation of Infectious Causes of Death and Emerging Applications.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/diagnostics16020325},
pmid = {41594301},
issn = {2075-4418},
abstract = {Background/Objectives: Postmortem microbiology has traditionally been regarded with caution in forensic practice due to concerns related to contamination, bacterial translocation, and postmortem microbial overgrowth. As a result, microbiological findings obtained after death have often been considered unreliable or of limited diagnostic value. However, growing evidence indicates that, when appropriately interpreted and integrated with autopsy findings, histopathology, and circumstantial information, postmortem microbiology can provide crucial support for cause-of-death determination. This narrative review critically examines the current role of postmortem microbiology in forensic diagnostics, with a focus on its diagnostic applications, interpretative challenges, and future perspectives. Methods/Results: The transition from conventional culture-based techniques to molecular approaches-including polymerase chain reaction, microbiome analysis, and metagenomic methods-is discussed, highlighting both their potential advantages and inherent limitations within the forensic setting. Particular attention is devoted to key interpretative issues such as postmortem interval, sampling strategies, contamination, and bacterial translocation. In addition to cause-of-death attribution, emerging applications-including postmortem interval estimation, trace evidence analysis, and artificial intelligence-based models-are reviewed. Although these approaches show promising research potential, their routine forensic applicability remains limited by methodological heterogeneity, lack of standardization, and interpretative complexity. Conclusions: In conclusion, postmortem microbiology represents a valuable diagnostic tool when applied within a multidisciplinary forensic framework. Its effective use requires cautious interpretation and integration with pathological and contextual evidence, avoiding standalone or automated conclusions. Future progress will depend on standardized methodologies, multidisciplinary collaboration, and a clear distinction between experimental research and routine forensic practice.},
}

@article {pmid41594136,
year = {2026},
author = {Kitano, T and Matsunaga, N and Akiyama, T and Azuma, T and Fujii, N and Tsukada, A and Hibino, H and Kuroda, M and Ohmagari, N},
title = {Environmental Dissemination of Antimicrobial Resistance: A Resistome-Based Comparison of Hospital and Community Wastewater Sources.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/antibiotics15010099},
pmid = {41594136},
issn = {2079-6382},
support = {JP22fk0108131//Japan Agency for Medical Research and Development/ ; JP25fk0108666//Japan Agency for Medical Research and Development/ ; },
abstract = {Background/Objectives: Comparative analysis of antimicrobial resistomes in hospital and community wastewater can provide valuable insights into the diversity and distribution of antimicrobial resistance genes (ARGs), contributing to the advancement of the One Health approach. This study aimed to characterize and compare the resistome profiles of wastewater sources from a hospital and community. Methods: Longitudinal metagenomic analysis was conducted on wastewater samples collected from the National Center for Global Health and Medicine (hospital) and a shopping mall (community) in Tokyo, Japan, between December 2019 and September 2023. ARG abundance was quantified using reads per kilobase per million mapped reads (RPKM) values, and comparative analyses were performed to identify the significantly enriched ARGs in the two sources. Results: A total of 46 monthly wastewater samples from the hospital yielded 825 unique ARGs, with a mean RPKM of 2.5 across all detected genes. In contrast, 333 ARGs were identified in the three shopping mall wastewater samples, with a mean RPKM of 2.1. Among the ARGs significantly enriched in the hospital samples, 23, including genes conferring resistance to aminoglycosides (nine groups) and β-lactam antibiotics (eight groups), exhibited significantly high RPKM values. No ARGs were found to be significantly enriched in the community wastewater samples. Conclusions: This study highlights the higher diversity and abundance of ARGs, particularly those conferring resistance to aminoglycosides and β-lactam antibiotics including carbapenems, in hospital wastewater than in community wastewater. These findings underscore the importance of continuous resistome monitoring of hospital wastewater as part of the integrated One Health surveillance strategy.},
}

@article {pmid41594088,
year = {2026},
author = {Soto-López, JD and Velásquez-González, O and Barrios-Izás, MA and Belhassen-García, M and Muñoz-Bellido, JL and Fernández-Soto, P and Muro, A},
title = {Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/antibiotics15010051},
pmid = {41594088},
issn = {2079-6382},
abstract = {BACKGROUND/OBJECTIVES: The mammalian microbiota constitutes a reservoir of antimicrobial resistance genes (ARGs), which can be shaped by environmental and anthropogenic factors. Although bat-associated bacteria have been reported to harbor diverse ARGs globally, the ecological and evolutionary determinants driving this diversity remain unclear.

METHODS: To characterize ARG diversity in wildlife exposed to contrasting levels of human influence, we analyzed homologs of resistance mechanisms from the Comprehensive Antibiotic Resistance Database in shotgun metagenomes of bat guano. Samples were collected from a colony exposed to continuous anthropogenic activity in Spain (Salamanca) and from a wild, non-impacted bat community in China (Guangdong). Metagenomic analyses revealed marked differences in taxonomic and resistome composition between sites.

RESULTS: Salamanca samples contained numerous hospital-associated genera (e.g., Mycobacterium, Staphylococcus, Corynebacterium), while Guangdong was dominated by Lactococcus, Aeromonas, and Stenotrophomonas. β-lactamases and MurA transferase homologs were the most abundant ARGs in both datasets, yet Salamanca exhibited higher richness and functional diversity (median Shannon index = 1.5; Simpson = 0.8) than Guangdong (Shannon = 1.1; Simpson = 0.66). Salamanca also showed enrichment of clinically relevant ARGs, including qacG, emrR, bacA, and acrB, conferring resistance to antibiotics critical for human medicine. In contrast, Guangdong exhibited a more restricted resistome dominated by β-lactamase and MurA homologs. Beta diversity analysis confirmed significant compositional differences between resistomes (PERMANOVA, R[2] = 0.019, F = 1.33, p = 0.001), indicating ecological rather than stochastic structuring.

CONCLUSIONS: These findings suggest that anthropogenic exposure enhances the diversity and evenness of resistance mechanisms within bat-associated microbiomes, potentially increasing their role as reservoirs of antimicrobial resistance.},
}

@article {pmid41594081,
year = {2026},
author = {Mohamed, FA and Al-Bulushi, M and Melegh, S and Timmer, B and Meszéna, R and Freytag, C and Laczkó, L and Miló, L and Urbán, P and Bőkényné-Tóth, R and Gyenesei, A and Kardos, G and Nyul, A and Urbán, E and Pál, T and Sonnevend, Á},
title = {Emergence of OXA-48-like Carbapenemase-Producing Escherichia coli in Baranya County, Hungary.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/antibiotics15010044},
pmid = {41594081},
issn = {2079-6382},
support = {300852//University of Pécs Medical School, Hungary/ ; },
abstract = {Background: Carbapenem-resistant Escherichia coli (CREC) producing OXA-48-like carbapenemase was first detected in Hungary in 2022. The aim of the present study was to characterize such strains isolated in 2022-2025 in Baranya County, Hungary. Methods: Antibiotic susceptibility and the whole-genome sequence (WGS) of E. coli isolates, identified as OXA-48-like carbapenemase producers using the CARBA-5 NG test, were established. The transferability of blaOXA-48-like plasmids was tested by conjugation. Results: Of the 6722 non-repeat E. coli isolates, 6 produced an OXA-48-like carbapenemase. They exhibited variable resistance to ertapenem and were susceptible to imipenem and meropenem. WGS revealed that all OXA-48-like producer E. coli belonged to high-risk clones: two clonally related OXA-181-producer E. coli ST405 were isolated in Hospital A, three OXA-244-producing E. coli ST38 (two identical via cgMLST from Hospital B), and an OXA-48-producing E. coli ST69. The blaOXA-48 and blaOXA-244 genes were chromosomally located, while blaOXA-181 was on a non-conjugative IncFIB-IncFIC plasmid. So far, the blaOXA-181-bearing plasmid of this incompatibility type has only been described in Ghana, but all blaOXA-48-like gene-carrying transposons in this study have already been identified in Europe and other continents. The E. coli ST38 isolates, showing close association based on core genome SNP distances to European and Qatari strains, belonged to Cluster A and harbored blaCTX-M-27. All but the E. coli ST69 isolate had cephalosporinase gene(s). Conclusions: This study describes small-scale intra-hospital transfers of OXA-48-like carbapenemase-producer E. coli. Interestingly, E. coli ST405 of Hungary carried blaOXA-181 on an IncFIB-IncFIC plasmid, which has only been reported from Africa so far.},
}

@article {pmid41594066,
year = {2025},
author = {Domingues, CPF and Rebelo, JS and Dionisio, F and Nogueira, T},
title = {Clinical and Environmental Plasmids: Antibiotic Resistance, Virulence, Mobility, and ESKAPEE Pathogens.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/antibiotics15010029},
pmid = {41594066},
issn = {2079-6382},
support = {UI/BD/153078/2022//Fundação para a Ciência e Tecnologia/ ; SFRH/BD/04631/2021//Fundação para a Ciência e Tecnologia/ ; UIDP/00329/2025//Fundação para a Ciência e Tecnologia/ ; },
abstract = {BACKGROUND/OBJECTIVES: Plasmids are autonomous DNA molecules that can replicate independently and transfer horizontally between bacterial cells. They play a key role in disseminating adaptive traits, such as antimicrobial resistance and virulence. Our study investigates the fundamental differences between plasmid populations originating from clinical/isolates and environmental/metagenomes.

METHODS: We compare three distinct plasmid genome datasets-the NCBI Reference Sequence Database (RefSeq), the Integrated Microbial Genomes & Microbiomes system (IMG/PR) from bacterial isolates (I) and microbiomes (M)-to assess how plasmid origin shapes their characteristics, including mobility types, antimicrobial resistance genes (ARGs), virulence genes (VGs) and host taxonomy.

RESULTS: We show that plasmids originating from bacterial isolates, more enriched in clinical samples, are fundamentally distinct from recovered from metagenomic data. Plasmids from isolates are larger, enriched in conjugative plasmids and display a higher frequency of ARGs and VGs than the ones assembled from metagenomes. Furthermore, ARGs are more frequently associated with highly mobile plasmids, particularly pCONJ.

CONCLUSIONS: These findings highlight the importance of plasmid origins in studies of plasmid epidemiology, functional potential and mobility.},
}

@article {pmid41593761,
year = {2026},
author = {Tigabu, A and Leung, PHM},
title = {Broad-spectrum antibiotic treatment reshapes the gut microbiome, resistome, and colonization potential of opportunistic pathogens: a metagenomics study.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00795-8},
pmid = {41593761},
issn = {1757-4749},
abstract = {BACKGROUND: The gut microbiota (GM) harbors diverse antibiotic resistance genes (ARGs), which are primarily disseminated through horizontal gene transfer (HGT), contributing to the emergence and spread of multidrug-resistant (MDR) pathogens. Broad-spectrum antibiotics are commonly used to treat a wide range of bacterial infections; however, they also exert collateral effects on non-target microbes. A comprehensive understanding of the impact of broad-spectrum antibiotic treatment on GM composition and the resistome is essential for the effective management of dysbiosis-related complications.

METHODS: Twenty-one fecal samples were collected from randomly selected study participants. Metagenomic sequencing was performed using the Illumina NovaSeq 6000 platform. FastQC v0.12.1, Trimmomatic v0.39, and Bowtie2 were used for quality control, removal of low-quality reads and adapter sequences, and host DNA removal, respectively. Metagenome assembly, gene prediction, and taxonomic annotation were conducted using MEGAHIT v1.2.9, MetaGeneMark-2, and the NCBI non-redundant protein database (nr), respectively. Resistome profiling was performed using the Comprehensive Antibiotic Resistance Database (CARD) v3.3.4. Functional annotation of protein-coding genes was carried out against the KEGG v112.0, eggNOG v5.0, and CAZy databases.

RESULTS: An enrichment of the phylum Bacillota and a depletion of Bacteroidota were observed in fecal samples from antibiotic-treated patients. Specifically, the genus Enterococcus and Streptococcus were the most prominent genera in antibiotic-treated patients, whereas Prevotella, Bacteroides, and Faecalibacterium were more abundant in healthy controls. Notably, the opportunistic pathogen E. faecium was elevated in antibiotic-treated patients. In longitudinal patients receiving augmentin treatment, the genera Escherichia and Enterococcus predominated, with E. coli and E. faecium showing increased prevalence compared with baseline in the first and second longitudinal patients, respectively. Antimicrobial resistance genes associated with antibiotic target alteration and protection were strongly linked to Bacillota, whereas efflux pump-mediated resistance mechanisms were positively associated with Bacteroidota and Pseudomonadota. The genes tetM, tet45, vanHM, vanYM, and vanRM were enriched in antibiotic-treated patients, whereas tetQ, tetW, cfxA6, adeF, vanTG, vanYB, and vanWI were more abundant in controls. Furthermore, PmrF, vanM, and CfxA were identified as principal biomarker genes in the first, second, and third augmentin-treated longitudinal patients, respectively.

CONCLUSIONS: Dysbiosis of the gut microbiota and alterations in the resistome were detected in antibiotic-treated patients. Notably, the opportunistic pathogens E. faecium and E. coli were enriched in antibiotic-treated individuals, suggesting that broad-spectrum antibiotic therapy may facilitate their proliferation and colonization, thereby contributing to dysbiosis-related complications. These findings warrant validation in larger cohorts to better elucidate the dynamics of antibiotic-induced dysbiosis and the dissemination of resistance genes.},
}

@article {pmid41593747,
year = {2026},
author = {Lin, L and Zheng, X and Tao, Y and Zhu, W and Guan, LL and Mao, S},
title = {Genome-resolved metagenomics uncovers diversity and functional landscapes of the gastrointestinal epithelium-associated microbiome in cattle.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-026-03960-z},
pmid = {41593747},
issn = {1474-760X},
support = {U2202203//NSFC-Regional Innovation and Development Joint Fund/ ; 3236114378//NSFC-International (Regional) Cooperation Research and Exchange Programme/ ; },
abstract = {BACKGROUND: The ruminant gastrointestinal epithelium harbors a diverse and functionally critical remains poorly characterized microbial community due to persistent host-derived DNA contamination in metagenomic studies.

RESULTS: We develop Dilute-MetaSeq (dilution-based metagenomic sequencing), a novel, metagenomic workflow integrating gradient dilution with multiple displacement amplification. Dilute-MetaSeq reduces host DNA interference by 52.4-fold and achieves > 90% microbial sequencing efficiency to assess gastrointestinal epithelium-associated microbiome. This enables the construction of the microbial genome atlas of gastrointestinal epithelium (MGA-GE). This comprehensive resource, comprising 1,907 nonredundant prokaryotic and 5,603 viral genomes, reveals extraordinary microbial diversity and novelty, with 41.4% of prokaryotic and 99.9% of viral genomes representing taxonomically unclassified lineages. Spatial profiling identifies the rumen and reticulum as a biodiversity hotspot dominated by epithelium-adapted Butyrivibrio and methylotrophic Methanomassiliicoccales, while functional annotation uncovers 1,200 biosynthetic gene clusters (primarily RiPPs and NRPSs) and 1,212 viral auxiliary metabolic genes linked to host metabolism modulation. Pangenome analysis of 987 strains, including a novel Butyrivibrio clade with reduced genome sizes, elevated GC content, and butyrate synthesis from amino acid-derived substrates (e.g., glutarate, lysine), highlights metabolic adaptations to the nutrient-scarce epithelial niche compared to digesta-associated microbes.

CONCLUSIONS: Collectively, the MGA-GE provides transformative insights into host-microbe-virus interactions and establishes a foundation for developing microbiome-based intervention strategies to enhance ruminant health, agricultural productivity, and bioactive discovery.},
}

@article {pmid41593721,
year = {2026},
author = {Xi, J and Tao, H and Zhang, Z and Lian, B and Sun, W and Zhang, Y and Bu, S and Yang, X and Qian, X},
title = {Captive breeding of specialty animals represents an overlooked yet critical reservoir for spreading antibiotic resistance genes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag009},
pmid = {41593721},
issn = {1751-7370},
abstract = {Driven by wildlife conservation and economic demands, captive breeding has expanded globally, intensifying wildlife-human interactions. In specialty animal breeding, particularly for species with short domestication histories and underdeveloped breeding protocols, clinically important antibiotics are commonly misused, posing potential ecological and health risks that remain largely unexplored. We collected fecal samples from three groups of musk deer (Moschus berezovskii): those exposed to clinically important antibiotics, those not exposed for six months, and wild musk deer, and analyzed their microbiomes and resistomes using metagenomic and culture-based methods. We found that captivity significantly expanded and reshaped the fecal resistome of musk deer. The antibiotic-exposed musk deer harbored a significantly higher diversity and abundance of antibiotic resistance genes (ARGs) compared to those non-exposed to antibiotics and wild deer. We observed a higher abundance of clinically important ARGs within Enterobacteriaceae in fecal samples of captive musk deer. This observation was further supported by the antibiotic susceptibility profiles of 124 Escherichia coli strains isolated from antibiotic-exposed musk deer. Seven identical mobile genetic element-associated ARGs were detected in distinct bacterial hosts across fecal samples from musk deer and farm workers, indicating potential conjugative transfer between the two groups. Our results suggest that captive breeding of specialty animals is an overlooked but significant reservoir for disseminating clinically important ARGs, and underscore the transmission risk at the animal-human interface.},
}

@article {pmid41593479,
year = {2026},
author = {Cheng, Z and Ye, Y and Gou, L and Chen, X and Zhang, L and Cao, W and Zhang, Q and Yin, H and Gao, F},
title = {Comprehensive analysis of microorganisms in severe septic patients in the intensive care unit by mNGS and microbial culture.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04730-4},
pmid = {41593479},
issn = {1471-2180},
support = {21624318//Fundamental Research Funds for the Central Universities/ ; A2024458//the Guangdong Medical Research Foundation/ ; 2021TQ0126//the China Postdoctoral Science Foundation/ ; 2021ZT09Y552//the Program for Guangdong Introducing Innovative and Entrepreneurial Teams/ ; },
abstract = {BACKGROUND: Severe sepsis is a life-threatening condition involving dysregulated systemic inflammatory responses and acute organ dysfunctions. Timely and accurate pathogen identification is critical for the effective treatment of severe septic patients in the intensive care unit (ICU). Although metagenomic next-generation sequencing (mNGS) enables the sensitive and unbiased detection of pathogens, its clinical implications in identification of causative pathogens, the association with the outcomes and the development of treatment regimens in such patients remain underexplored.

METHODS: 184 clinical samples were collected from 81 severe septic patients and subjected to mNGS analysis. Blood and bronchoalveolar lavage fluid (BAL) samples were collected from the majority of patients, while sputum, cerebrospinal fluid (CSF), pleural effusion (PE), ascites, urine, hydropericardium (HPC) and blister effusion (BE) samples were also collected from select patients. Microorganisms were detected by DNA and RNA mNGS and the top 5 microorganisms detected by mNGS in each sample were used for analysis. Microbes were isolated from most patients and the isolates were tested for drug susceptibility.

RESULTS: mNGS identified 183 top 5 microorganisms, with bacteria (92.3%), viruses (3.3%) and fungi (2.7%) as the major detected microbes. Among them, 40, 98 and 45 were pathogenic (21.9%), opportunistic (53.6%) and non-pathogenic (24.6%), respectively. Significantly more pathogenic microbes were detected in the sputum (83.3%) and the bronchoalveolar lavage fluid (BAL; 75.0%) than the blood (36.1%) by RNA mNGS (87.4%) than DNA mNGS (58.2%). Patients having the top-1 pathogenic microorganism detected by DNA mNGS or 4-5 pathogenic microorganisms detected by RNA mNGS had a poor association with clinical outcomes. Moreover, detection of R. pickettii, C. difficile and S. enterica were significantly associated with high mortality. The majority of patients (89.5%) were positive for microbial cultures. Each of these patients had at least one drug-resistant organism and nearly half (45.1%) were infected with two or more drug-resistant strains.

CONCLUSIONS: Detection of predominant pathogenic microorganisms or particular bacteria in the sputum or BAL samples by mNGS are associated with poor clinical outcomes among severe septic patients in ICU in this cohort. The high prevalence of multidrug-resistant bacteria among these patients underscores the importance of integration of mNGS with antimicrobial susceptibility assessment in the clinical practice to develop the most effective treatment regimens.},
}

@article {pmid41593440,
year = {2026},
author = {Lv, J and Liu, R and Sun, Z and Zhang, J and Zhang, Y and Zhao, X and Liu, J and Zhou, X and Zhang, M and Liu, Q and Gao, F},
title = {Gut Microbiota as Neuroimmune Modulators in Myasthenia Gravis: Mechanistic Insights from the Gut-Brain Axis to Therapeutic Innovations.},
journal = {The American journal of Chinese medicine},
volume = {},
number = {},
pages = {1-21},
doi = {10.1142/S0192415X26500023},
pmid = {41593440},
issn = {1793-6853},
abstract = {Myasthenia gravis (MG) is a chronic autoimmune disorder characterized by an immune-mediated attack on neuromuscular junction acetylcholine receptors (AChRs), and its pathogenesis is closely linked to immune dysregulation. Emerging evidence has highlighted the pivotal role of the gut microbiota in the pathophysiology of MG through immunomodulation, microbial metabolite signaling, and gut-brain axis interactions. This review combines 16S rRNA sequencing, metagenomic, and metabolomic data to reveal distinct gut microbial signatures in patients with MG. These signatures include reduced α-diversity, depletion of beneficial taxa like Bacteroides and Bifidobacterium, enrichment of pathobionts such as Escherichia and Enterococcus, and diminished levels of the short-chain fatty acids (SCFA), which were inversely correlated with disease severity. Experimental models have demonstrated that fecal microbiota transplantation (FMT) and probiotic supplementation with strains like Bifidobacterium ameliorate symptoms by restoring Th17/Treg equilibrium, suppressing the expression of pro-inflammatory cytokines including IL-6 and TNF-α, and enhancing intestinal barrier integrity. Mechanistically, gut dysbiosis exacerbates autoimmunity via NF-αB pathway activation, disrupts tryptophan metabolism and impairs gut-brain signaling. While existing studies have established microbiota-MG associations, further causal validation, personalized therapeutic strategies, and multi-omics integration remain critical priorities. Microbiota-targeted interventions, including precision FMT and metabolite delivery, hold translational potential, but their validation via large-scale randomized controlled trials and interdisciplinary approaches like AI-driven microbiota profiling is essential if they are to advance precision medicine for MG management.},
}

@article {pmid41593438,
year = {2026},
author = {Wang, X and Tian, D and Han, B and Zhao, K and Hao, W and Du, K and Li, X and Duan, Z},
title = {Exploring the impact of rumen microbiome on ovine flavor-related compounds and comparing flavor profiles between Tibetan sheep and Small-tail Han sheep.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04755-9},
pmid = {41593438},
issn = {1471-2180},
support = {2024YFF0728800//National Key Research and Development Program of China/ ; 2024-ZJ-949//the Natural Science Foundation of Qinghai Province/ ; XDA26040305//the Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {The characteristic 'mutton flavor', primarily attributed to branched-chain fatty acids (BCFAs), is influenced by various factors including rumen microbes. This study aims to elucidate the disparities in meat flavor compounds and their underlying regulatory mechanisms mediated by rumen microbes between two important sheep breeds on the Qinghai-Tibetan Plateau. We used LC-MS/MS to analyze BCFAs and rumen short-chain fatty acids (SCFAs), along with metagenomic sequencing to characterize the rumen microbiome. Compared to Tibetan sheep, Small Tail Han sheep exhibited significantly higher concentrations of BCFAs, including 4-ethyloctanoic acid (EOA) and 4-methyloctanoic acid (MOA), as well as SCFAs such as pentanoate, glutarate, and propionate. In contrast, acetate levels were inversely correlated with these fatty acids. Metagenomics revealed a predominance of Bacteroidota (formerly Bacteroidetes) and Bacillota (formerly Firmicutes) in sheep. Furthermore, random forest and LEfSe analyses identified seven bacterial biomarkers, including Lactobacillus, Ligilactobacillus, Blautia, Anaerovibrio, Selenomonas, Phocaeicola, Sodaliphilus. Functional analysis indicated differences in carbohydrate degradation capabilities of two breeds. Likewise, strong positive correlations of propionate with MOA, and glutarate with EOA were observed, respectively. The findings are expected to provide critical insights into the potential for modulating meat flavor through nutritional strategies targeting rumen microbes.},
}

@article {pmid41593363,
year = {2026},
author = {Sorensen, PO and Karaoz, U and Beller, HR and Bill, M and Bouskill, NJ and Banfied, JF and Chu, RK and Hoyt, DW and Eder, E and Eloe-Fadrosh, E and Sharrar, A and Tfaily, MM and Toyoda, J and Tolic, N and Wang, S and Wong, AR and Williams, KH and Zhong, Y and Brodie, EL},
title = {Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41593363},
issn = {2058-5276},
support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DBI-1315705//National Science Foundation (NSF)/ ; },
abstract = {Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.},
}

@article {pmid41593326,
year = {2026},
author = {Kotay, SM and Parikh, HI and Gweon, HS and Barry, K and Stoesser, N and Sarah Walker, A and Crook, DW and Vegesana, K and Mathers, AJ},
title = {Biofilm removal in hospital sink drains drives unintended surges in antibiotic resistance.},
journal = {npj antimicrobials and resistance},
volume = {4},
number = {1},
pages = {5},
pmid = {41593326},
issn = {2731-8745},
support = {BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; BAA 200-2017-96194//Center for Surveillance, Epidemiology, and Laboratory Services/ ; HPRU-2012-10041//National Institute for Health and Care Research/ ; HPRU-2012-10041//National Institute for Health and Care Research/ ; HPRU-2012-10041//National Institute for Health and Care Research/ ; },
abstract = {The prevalence and proliferation of antimicrobial-resistant bacteria is considered one of the critical issues of our time. Wastewater is a habitat for complex microbial communities where bacteria share antimicrobial-resistance genes through horizontal gene transfer. Hospital wastewater plumbing systems are an ideal reservoir for environmental and pathogenic bacteria to interface and exchange antimicrobial-resistance genes. Replacement of contaminated plumbing may be the most intuitive and widely deployed response to the detection and colonization of highly-resistant potentially pathogenic bacteria in hospital sink drains. In this study, we analyzed sink-drain biofilms from six intensive-care patient rooms using shotgun metagenomic sequencing and microbial culture. We show an evident shift in biofilm community structure toward increased abundance of Enterobacteriaceae following plumbing replacement. Higher resistome load and abundance of clinically relevant resistance and typically encountered mobile genes in the newly replaced plumbing was also observed. Taken together, these finding suggest that exchanging contaminated plumbing for new plumbing may actually have the unexpected consequence of increased abundance of Enterobacterales and antimicrobial-resistance genes in the sink drains. Disruption of preexisting complex environmental biofilms may result in an unintended microbial population shifts and a potential subsequent increase in the amount of antimicrobial-resistant Enterobacterales which are targeted for elimination.},
}

@article {pmid41593136,
year = {2026},
author = {Menke, S and Fackelmann, G and Vucetich, LM and Vucetich, JA and Forbey, JS and Sommer, S},
title = {Forage quality shapes physiological and gut microbial responses in moose (Alces alces) of Isle Royale National Park.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {3724},
pmid = {41593136},
issn = {2045-2322},
}

@article {pmid41592952,
year = {2026},
author = {Iacucci, M and Zammarchi, I and Pugliano, CL and Santacroce, G and Capobianco, I and Majumder, S and Ruffa, A and Naranjo, V and Grisan, E and Nardone, OM and Ghosh, S},
title = {Shaping the future of postoperative recurrence in Crohn's disease: personalised approaches with AI-enabled imaging and multi-omics.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337171},
pmid = {41592952},
issn = {1468-3288},
abstract = {Postoperative recurrence (POR) is a major challenge in the long-term management of Crohn's disease (CD), affecting up to 70% of patients within the first year after surgical resection. The multifactorial pathogenesis of POR complicates prevention, while evolving surgical techniques and different anastomotic configurations further hinder accurate prediction and monitoring.Current surveillance strategies, including standard ileocolonoscopy and faecal calprotectin, remain limited by suboptimal accuracy, the absence of validated scoring systems and the lack of standardised monitoring intervals. Recent advances in high-resolution endoscopic imaging, such as confocal laser endomicroscopy and endocytoscopy, enable real-time, in vivo microstructural assessment of the anastomosis, offering opportunities for earlier and more precise detection of recurrence. In parallel, developments in intestinal ultrasound and cross-sectional imaging are reshaping non-invasive monitoring by providing transmural evaluation. Beyond imaging, multiomics approaches, spanning genomics, transcriptomics, proteomics, metabolomics and metagenomics, are uncovering novel biological pathways linked to POR, providing new mechanistic insights.Artificial intelligence (AI) has the potential to integrate clinical, endoscopic, imaging and omics data into predictive multimodal models for POR, supporting individualised risk stratification, early detection and personalised treatment strategies. While promising, these innovations require prospective validation, methodological standardisation and integration into clinical workflows before translation into routine practice.This review summarises the current understanding of POR, highlights emerging diagnostic and monitoring technologies and explores how AI-enabled endoscopy and multi-omics approaches may transform future management, paving the way towards precision medicine for POR in CD.},
}

@article {pmid41592677,
year = {2026},
author = {Si, M and Xiong, X and Yun, C and Chen, Y and Niu, H and Qu, Y and Liu, M and Wang, Y and Huang, L and Long, X and Wang, W and Yang, R and Liu, R and Pang, Y and Zhen, X and Li, R and Tian, T and Qi, X and Qiao, J},
title = {Microplastics and nanoplastics in follicular fluid are associated with diminished ovarian reserve: clinical and molecular insights.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.01.074},
pmid = {41592677},
issn = {2090-1224},
abstract = {INTRODUCTION: Ovarian aging is a significant concern, yet the influencing factors remain unclear. Environmental factors are crucial determinants of diminished ovarian reserve (DOR). Microplastics and nanoplastics (MNPs) are widespread in the environment and pose health risks. The effect of MNPs on ovarian function remains uncertain.

OBJECTIVES: The study aims to investigate whether exposure to MNPs negatively affects ovarian function. In particular, the research focuses on elucidating the association between MNPs-especially polyamide 66-and DOR, and validating Parabacteroides goldsteinii (P. goldsteinii) as a potential intervention.

METHODS: We conducted a case-control study analyzing MNPs in follicular fluid from 110 DOR patients and 110 age-matched controls. A mouse MNPs-exposure model assessed ovarian function and intestinal barrier integrity. Gut microbiota alterations were analyzed by metagenomic sequencing of fecal samples from MNPs-exposed mice. P. goldsteinii was identified and selected for microbial intervention, administered via oral gavage. The human granulosa cell line (KGN) was treated with MNPs for 48 h, followed by transcriptomic sequencing to examine PI3K/AKT/mTOR pathway alterations.

RESULTS: Human follicular fluid contained multiple MNPs, with polyamide 66 (PA66) levels significantly linked to DOR. Polystyrene (PS) and polyvinyl chloride (PVC) concentrations were also higher in the DOR group. MNPs induced DOR-like phenotypes in mice, causing hormonal imbalances, disrupted estrous cycles, and increased atretic follicles, alongside intestinal barrier damage and gut microbiota dysbiosis. Notably, the abundance of P. goldsteinii and its key metabolite 7-keto-lithocholic acid was significantly reduced following MNPs exposure. Supplementation with P. goldsteinii effectively reversed MNPs-induced DOR-like phenotypes, restored hormonal homeostasis, normalized estrous cyclicity, reduced follicular atresia, and elevated 7-keto-LCA levels. Mechanistically, MNPs triggered the PI3K/AKT/mTOR pathway, impairing granulosa cell function and ovarian reserve.

CONCLUSION: These findings elucidate how exposure to MNPs may harm female ovarian function and provide potential new strategies for ameliorating reproductive disorders through the environment‒gut‒ovarian axis.},
}

@article {pmid41592665,
year = {2026},
author = {Yu, X and Lei, Z and Xu, L and Chen, S and Zeng, G and Wang, N and Lai, X and Liu, J},
title = {Disseminated Mycobacterium Abscessus Lymphadenopathy in An Anti-Interferon-γ Autoantibody Syndrome patient Treated with Anti-NTM Therapy Combined with Hemoadsorption: A Case Report.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108438},
doi = {10.1016/j.ijid.2026.108438},
pmid = {41592665},
issn = {1878-3511},
abstract = {BACKGROUND: Anti-interferon-γ autoantibody syndrome (AIGAs) is a primary immunodeficiency disorder characterized by neutralizing autoantibodies blocking IFN-γ signaling, predisposing patients to severe opportunistic infections. No definitive treatment protocol exists, and conventional therapies carry infection risks. Hemoadsorption (HA) is effective for autoimmune diseases but has not been specifically investigated for AIGAs.

CASE PRESENTATION: A 65-year-old Chinese female was admitted with 10-month painless disseminated lymphadenopathy. 18F-FDG PET/CT showed multiple hypermetabolic lymph nodes, and ultrasound-guided biopsy revealed necrotizing granulomatous inflammation. Metagenomic next-generation sequencing (mNGS) identified Mycobacterium abscessus, and ELISA confirmed high AIGA levels (88.05% at 1:3200 dilution). She received anti-nontuberculous mycobacteria (NTM) therapy (clarithromycin, minocycline, contezolid) combined with one HA session using a cytokine adsorption column. Post-treatment, AIGA levels normalized to 0% at 24 weeks and remained stable. 72-week follow-up showed resolved lymphadenopathy and reduced lymph node size/metabolic activity on PET/CT.

CONCLUSION: This is the first report of single-session HA for AIGAs complicated by disseminated Mycobacterium abscessus infection. HA effectively reduced AIGA levels, controlled infection, and avoided global immunosuppression, providing a promising adjunctive therapy for AIGAs patients with severe disseminated infections.},
}

@article {pmid41592660,
year = {2026},
author = {Anburajan, P and Lee, SH and Maulana, DD and Park, HD},
title = {Functional genes and microbial interactions governing methanogenesis via direct interspecies electron transfer: Functions and emerging concepts.},
journal = {Bioresource technology},
volume = {445},
number = {},
pages = {134086},
doi = {10.1016/j.biortech.2026.134086},
pmid = {41592660},
issn = {1873-2976},
abstract = {Direct interspecies electron transfer (DIET) has emerged as an electron-exchange mechanism that enhances methane production in anaerobic digestion (AD) systems. Although the concept of direct electron exchange in syntrophic microbial communities was proposed in the early 2010 s, experimental validation and systematic recognition of methanogenesis via DIET have advanced primarily in the past decade. Significant progress has been made in identifying DIET-active microbial consortia; however, the functional genes and metabolic pathways governing these processes remain unclear. Recent advances in multi-omics approaches, including metagenomics, metatranscriptomics, and proteomics, have provided deeper insights into microbial community organization and gene-level functions underlying electron transfer in AD systems. This review synthesizes current knowledge on functional genes directly mediating DIET (e.g., pilA, omcS), as well as genes that indirectly support DIET, including hydrogenases, extracellular polymeric substance (EPS)-related genes, and methanogenesis-associated enzymes. Understanding of these functional genes is essential for optimizing AD processes and advancing bioenergy production.},
}

@article {pmid41592403,
year = {2026},
author = {Zhang, B and Wang, M and Zheng, J and Yu, C and Wei, C and Ren, J and Sun, S and Wang, G and Wang, J and Lu, Y and Lin, L and Zhang, C},
title = {Strain-specific impacts of Pichia kudriavzevii on metabolite profiles and microbial community dynamics in Chinese Baijiu fermentation: Integrated metabolomics and metagenomics analysis.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111660},
doi = {10.1016/j.ijfoodmicro.2026.111660},
pmid = {41592403},
issn = {1879-3460},
abstract = {Pichia kudriavzevii is a dominant yeast species in Chinese baijiu fermentation, yet its intraspecific diversity remains underexplored. This study used metabolomics and metagenomics analysis to investigate the impact of four distinct P. kudriavzevii strains (PK12, PK25, PK97, and PK360) on the metabolite profiles and microbial community structure in a controlled baijiu solid-state fermentation. Metabolomics analysis identified 49 key volatile compounds and 2792 non-volatile metabolites. Strain PK97 exhibited exceptional capacity for butanoic acid metabolism, inducing a 55.27-fold increase in butanoic acid and a 30.54-fold enhancement in ethyl butanoate production. Strain PK25 specialized in acetoin biosynthesis, while PK360 maximized 2-phenylethanol production. Metagenomic analysis uncovered that strains PK12, PK25, and PK360 promoted Lactobacillus acetotolerans population, increasing its relative abundance to 67.39%, 58.57%, and 71.79%, respectively. In contrast, strain PK97 orchestrated a dramatic ecological shift, elevating Enterobacter mori abundance from 0.56% to 17.60%, transforming the community from Lactobacillus-dominated to Enterobacteriaceae-enriched. Integration of metabolomic and metagenomic data revealed that strain PK97's promotion of Enterobacter mori correlated with significant upregulation of key enzymes including α-amylase (EC 3.2.1.1), enoyl-CoA hydratase (EC 4.2.1.17), and succinyl-CoA synthetase (EC 6.2.1.5), creating a metabolic environment favoring enhanced starch hydrolysis, altered TCA cycle flux, and butanoic acid accumulation. Strain PK25 specifically upregulated acetyl-CoA hydrolase (EC 3.1.2.1), facilitating acetic acid and acetoin formation. Strain PK360 enhanced glucose pyrophosphorylase (EC 2.7.7.9) and asparagine synthetase (EC 6.3.1.1) activities, accelerating galactose metabolism and amino acid transformations. These findings illustrate the impact of P. kudriavzevii intraspecific diversity on reshaping microbial ecology and flavor chemistry in Chinese baijiu, offering novel insights for targeted fermentation control and quality enhancement strategies in baijiu production.},
}

@article {pmid41592401,
year = {2026},
author = {Sandes, S and Figueiredo, N and Pires, S and Assis, D and Pedroso, S and Paiva, MJ and Neumann, E and Alvarenga, VO and Contreras-Castillo, CJ and Sant'Ana, AS},
title = {Lactic acid spraying on split carcasses reshapes microbial succession and reduces the occurrence of blown pack spoilage in vacuum-packaged beef stored at different temperatures over extended shelf life.},
journal = {International journal of food microbiology},
volume = {450},
number = {},
pages = {111659},
doi = {10.1016/j.ijfoodmicro.2026.111659},
pmid = {41592401},
issn = {1879-3460},
abstract = {Beef is a highly perishable product due to its high moisture content, neutral pH, and rich nutrient profile, which favor microbial growth and spoilage. While vacuum packaging extends shelf life by limiting aerobic bacteria, it may promote the proliferation of anaerobic and facultative anaerobic spoilage organisms, leading to blown pack spoilage. This study investigated the effects of lactic acid spraying on split carcasses categorized by two pH levels (high or ideal) on microbial succession and volatile organic compound (VOC) production in vacuum-packaged sirloins, stored at 0 °C, 4 °C, and 7 °C for up to 120 days. Using culture-based methods, 16S rRNA gene sequencing, and VOC profiling, it has been found that lactic acid treatment significantly reduced initial bacterial loads, especially in high-pH split carcasses (P < 0,05), and modulated microbial communities over time. Treated samples exhibited a lower incidence of blown pack spoilage (BPS) under specific storage time-temperature conditions. Nevertheless, bacterial changes under specific time-temperature storage conditions were characterized by a microbiota dominated by Lactococcus, Lactobacillus, Leuconostoc, Enterococcus, Carnobacterium, Hafnia-Obesumbacterium, and Serratia, regardless type of treatment. Overall microbial diversity was not significantly affected; however, the composition of dominant bacterial genera and VOC profiles differed between treated and non-treated groups, suggesting that specific bacterial taxa and compounds may serve as indicators of spoilage progression in vacuum-packed meat under defined storage conditions.},
}

@article {pmid41591867,
year = {2026},
author = {Petraro, S and Tarracchini, C and Mancabelli, L and Lugli, GA and Turroni, F and Ventura, M and Milani, C},
title = {Microbial BioRemediation Database: A Comprehensive Database of Genes Involved in Microbial Bioremediation Processes.},
journal = {MicrobiologyOpen},
volume = {15},
number = {1},
pages = {e70215},
doi = {10.1002/mbo3.70215},
pmid = {41591867},
issn = {2045-8827},
support = {//European Union, NextGeneration EU, PNRR-M4C2- I1.1, PRIN 2022 - Project Code 20229LEB99 - CUP Code D53D23014150006/ ; T5-AN-11//Piano di Sviluppo e Coesione of the Italian Ministry of Health 2014-2020/ ; },
mesh = {*Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; *Databases, Genetic ; Microbiota/genetics ; Environmental Pollutants/metabolism ; Metagenome ; Metagenomics ; },
abstract = {Environmental pollution from a wide range of compounds poses serious ecological and health risks. While bioremediation offers a promising solution, its application is limited by fragmented genomic resources and unsatisfactory understanding of microbial biodegradation pathways. Here, we developed the Microbial BioRemediation (MBR) database, freely accessible at https://probiogenomics.unipr.it/cmu, a comprehensive and manually curated repository comprising over 643,351 bacterial protein sequences associated with the degradation of 564 pollutant compounds across 25 chemical classes. Optimized for both genomic and metagenomic analyses, the Microbial BioRemediation database enables high-resolution functional and taxonomic profiling of microbial communities and individual bacterial strains. Validation using public genome and metagenome datasets from contaminated environments confirmed the database ability to detect both conserved and environment-specific biodegradation functions. Its application to host-associated microbiomes further confirmed the suitability of MBR for assessing how environmental exposures shape microbial catabolic potential across ecological contexts. The MBR database thus serves as a strategic tool for the early-stage identification and prioritization of microbial candidates for bioremediation. By enabling the in silico selection of key microbial taxa and enzymatic functions, it supports a rational pipeline that progresses toward targeted in vitro validation and experimental characterization. This integrative approach facilitates development of next-generation, tailored strategies for the remediation of complex polluted ecosystems.},
}

*Biodegradation, Environmental
*Bacteria/genetics/metabolism/classification
*Databases, Genetic
Microbiota/genetics
Environmental Pollutants/metabolism
Metagenome
Metagenomics

@article {pmid41591576,
year = {2026},
author = {Robayo, MIG and Armijo, JHC and Rosa, LH and Passarini, MRZ},
title = {Metagenomic analysis of the fungal community present in unimpacted and oil-impacted soil, South Shetland Islands, maritime Antarctica.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {62},
pmid = {41591576},
issn = {1573-0972},
support = {440218/2023-3//CNPq PROANTAR/ ; PRPPG Nº 118/2024//Institutional Program to Support Research Groups/ ; CNPq 18/2024//National Council for Scientific and Technological Development/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Fungi/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Mycobiome/genetics ; Soil/chemistry ; Islands ; Phylogeny ; Biodiversity ; Nitrogen/analysis ; },
abstract = {We assessed the fungal diversity and functional profile of two soils collected in contrasting environments: one unimpacted soil, Hennequin Point, King George Island, and the other impacted by whale oil, Whalers Bay, Deception Island, Maritime Antarctica, using metagenomic approaches. Taxonomic assignment revealed a predominance of Ascomycota in both soils. A total of 20 and 23 fungal genera were identified at King George and Deception islands, respectively. The rare genera Thermothielavioides, Pyricularia, Fulvia, and Coccidioides were detected in the Antarctic environment. The highest fungal diversity was observed in the soil of Deception Island. Canonical analysis of King George Island soil displayed higher values of total organic carbon, sulfur, and lead, which may have favored the presence of the genera Puccinia, Lachancea, and Akanthomyces. The soil of Deception Island presented correlations with higher levels of nitrogen, chromium, and iron, with a predominance of genera such as Aspergillus, Trichoderma, and Malassezia. Functional analysis revealed distinct adaptive strategies among the soils. Domains related to translation, gene regulation, and metabolic efficiency were observed for fungi in Hennequin Point soil, King George Island, suggesting resource optimization in a cold, moss-covered environment. In Deception Island soil, fungal redox metabolism, iron acquisition, and the degradation of nitrogen compounds were highlighted, reflecting adaptation to an anthropogenic soil rich in metal oxides. Both soils exhibited functional fungal networks involved in hydrolytic enzymatic pathways that may act in the decomposition of organic compounds. New sequencing must be performed due to the insufficient depth of the data. Our results indicated that the soil from Hennequin Point and Whalers Bay exhibited distinct fungal communities, which can be influenced by environmental and ecological factors such as moss, oil, and heavy metals encountered in pristine and oil-impacted soils resulting from anthropogenic activities over the years.},
}

Antarctic Regions
*Soil Microbiology
*Fungi/genetics/classification/isolation & purification
*Metagenomics/methods
*Mycobiome/genetics
Soil/chemistry
Islands
Phylogeny
Biodiversity
Nitrogen/analysis

@article {pmid41591393,
year = {2026},
author = {Walden, N and Kiefer, C and Koch, MA},
title = {Unravelling complex hybrid and polyploid evolutionary relationships using phylogenetic placement of homologous gene copies from target enrichment data.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syag007},
pmid = {41591393},
issn = {1076-836X},
abstract = {Phylogenomic datasets comprising hundreds of genes have become the standard for plant systematics and phylogenetics. However, large-scale phylogenomic studies often exclude polyploids and hybrids due to the challenges in assessing the origin of duplicated loci and incorporating them into tree reconstruction methods. Using a newly generated target enrichment dataset of 1081 genes from 452 samples from the Brassicaceae tribe Arabideae, including many hybrid and high ploidy taxa, we developed a novel approach to disentangle the evolutionary history of this phylogenetically and taxonomically challenging clade. Our approach extends beyond commonly used gene tree-species tree reconciliation techniques by using phylogenetic placement, a method adopted from metagenomics, of gene copies into a diploid tree. We show how it allows for the simultaneous assessment of the origins of ancient and recent hybrids and autopolyploids, and the detection of nested polyploidization events. Additionally, we demonstrate how synonymous substitution rates provide further evidence for the mode of polyploidization, specifically to distinguish between allo- and autopolyploidization, and to identify hybridization events involving a ghost lineage. Our approach can serve as an exploratory tool for large and complex phylogenomic datasets and can aid in identifying polyploid and hybrid clades for further analysis with specialized methods.},
}

@article {pmid41590723,
year = {2026},
author = {Atak, E and Tavčar Verdev, P and Petek, M and Coll, A and Bosch, D and Dolinar, M and Komarysta, V and Glavaš, N and Rotter, A},
title = {Identification and Cultivation of Biotechnologically Relevant Microalgal and Cyanobacterial Species Isolated from Sečovlje Salt Pans, Slovenia.},
journal = {Marine drugs},
volume = {24},
number = {1},
pages = {},
doi = {10.3390/md24010026},
pmid = {41590723},
issn = {1660-3397},
support = {L4-4564//The Slovenian Research and Innovation Agency/ ; Euro-MED 0200514//Interreg Euro-MED Program/ ; },
mesh = {*Cyanobacteria/isolation & purification/genetics/metabolism ; *Microalgae/isolation & purification/genetics ; Salinity ; Slovenia ; Metagenomics/methods ; Biodiversity ; Biotechnology/methods ; Ecosystem ; },
abstract = {Studies of complex natural environments often focus on either biodiversity or on isolating organisms with specific properties. In this study, we sought to widen this perspective and achieve both. In particular, hypersaline ecosystems, such as the Sečovlje salt pans (Slovenia), are particularly promising sources of novel bioactive compounds, as their microorganisms have evolved adaptations to desiccation and high light intensity stress. We applied shotgun metagenomics to assess microbial biodiversity under low- and high-salinity conditions, complemented by isolation and cultivation of photosynthetic microorganisms. Metagenomic analyses revealed major shifts in community composition with increasing salinity: halophilic Archaea became dominant, while bacterial abundance decreased. Eukaryotic assemblages also changed, with greater representation of salt-tolerant genera such as Dunaliella sp. Numerous additional microorganisms with biotechnological potential were identified. Samples from both petola and brine led to the isolation and cultivation of Dunaliella sp., Tetradesmus obliquus, Tetraselmis sp. and cyanobacteria Phormidium sp./Sodalinema stali, Leptolyngbya sp., and Capilliphycus guerandensis. The newly established cultures are the first collection from this hypersaline environment and provide a foundation for future biodiscovery, production optimization, and sustainable bioprocess development. The methods developed in this study constitute a Toolbox Solution that can be easily replicated in other habitats.},
}

*Cyanobacteria/isolation & purification/genetics/metabolism
*Microalgae/isolation & purification/genetics
Salinity
Slovenia
Metagenomics/methods
Biodiversity
Biotechnology/methods
Ecosystem

@article {pmid41590413,
year = {2025},
author = {Ansari, RA and Egamberdievich, KE and Raximovna, MT and Sa'dinovna, YD and Enverovna, BL and Abbasovich, AS and Muqumovich, AD and Kurbonovich, TM},
title = {Phytomycobiomes and Ecosystem Services: Mechanisms, Evidence and Routes to Application.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {1},
pages = {},
doi = {10.3390/jof12010001},
pmid = {41590413},
issn = {2309-608X},
abstract = {Phytomycobiomes refer to the fungal consortia that inhabit plant tissues and the rhizosphere. Their documented functions include nutrient mobilization, carbon retention, stress mitigation and pathogen suppression, although measurable effects often depend on plant and soil conditions. In this review, we examine the current evidence for their ecological relevance and assess the molecular approaches most commonly used to characterize them. Arbuscular Mycorrhizal (AM) fungi, endophytes and saprotrophic taxa indicate measurable gains in nutrient acquisition, disease resistance and soil aggregation, although long-term consistency is rarely evaluated. Each function appears to have an explicit mechanistic attribution, with direct links between fungal groups, enzymatic pathways and measurable ecosystem outcomes. Several sequencing-based techniques are available, yet none offer complete accuracy. Internal Transcribed Spacer (ITS) amplicon surveys provide rapid taxonomic coverage but suffer from primer bias; shotgun metagenomics offers functional insight but at significant financial cost; and quantitative polymerase chain reaction (qPCR) assays remain useful for targeted quantification, whereas long-read technologies show promise but still lack widespread adoption. The field faces a number of unresolved constraints, including limited knowledge of host range, inconsistent performance under fluctuating environmental conditions and the absence of a standardized bioinformatic pipeline. Despite these limitations, we regard phytomycobiomes as viable candidates for replacing or reducing synthetic inputs, provided their application is guided by context-specific evidence rather than broad generalization.},
}

@article {pmid41589901,
year = {2026},
author = {Engl, T and Jakubova, L and Skrob, Z and Campeggi, S and Skala, R and Folkmanova, M and Pajer, P and Chmel, M and Cajthaml, T and Strejcek, M and Suman, J and Uhlik, O},
title = {Catabolism of acetosyringone and co-metabolic transformation of 2,4,6-trichlorophenol by a novel FAD-dependent monooxygenase.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0124225},
doi = {10.1128/msystems.01242-25},
pmid = {41589901},
issn = {2379-5077},
abstract = {Acetosyringone (AS), a prototypical syringyl-type monomer of lignin, functions as a model compound for the study of microbial catabolism of S-lignin-derived aromatics. In this study, we present the discovery of a novel metabolic pathway for AS catabolism, initiated by a previously uncharacterized FAD-dependent oxidoreductase, designated AsdA. In contrast to the sole previously documented AS funneling route, which entails side chain modification and conversion to syringic acid, AsdA catalyzes direct hydroxylation of the aromatic core. This represents a mechanistically distinct entry into central metabolism. The identification of this enzyme was achieved through metagenomic and functional analyses of a bacterial consortium enriched on AS as the sole carbon source. The consortium, predominantly comprising Pseudomonas rhizophila, exhibited co-metabolic transformation of the chlorinated pollutants 2,4,6-trichlorophenol (2,4,6-TCP) and 2,6-dichlorophenol. Subsequent functional assays substantiated the hypothesis that AsdA facilitates the transformation of both AS and 2,4,6-TCP. Induction assays employing a biosensor strain derived from the bacterial isolate Pseudomonas rhizophila AS1 confirmed AS-specific upregulation of the asd gene cluster. A survey of publicly available metagenomes has revealed that asdA is narrowly distributed but enriched in rhizosphere environments, pointing to its ecological significance. In summary, the present study unveils a hitherto unrecognized route for AS transformation and identifies an enzyme that exhibits dual functions in lignin-derived aromatic catabolism and environmental pollutant transformation. While the mechanisms underlying TCP degradation are well-established, the specific enzyme responsible for the conversion to 2,6-dichloro-p-hydroquinone had remained elusive-a knowledge gap that has now been addressed by AsdA.IMPORTANCEThe microbial conversion of lignin monomers is central to the global carbon cycle, yet pathways for syringyl-derived aromatics remain poorly resolved. Here, we identify AsdA, an enzyme initiating a previously unrecognized route for acetosyringone catabolism, providing new insight into how this abundant plant-derived compound is integrated into microbial metabolism. Beyond expanding the mechanistic diversity of lignin degradation, AsdA also catalyzes a key step in the transformation of the chlorinated pollutant 2,4,6-trichlorophenol, linking natural and anthropogenic compounds within a shared metabolic framework. The restricted yet rhizosphere-enriched distribution of asdA underscores its specialized role in plant-microbe interactions. By integrating enzyme function, microbial community context, and metagenomic distribution, we demonstrate how a single catalytic activity connects metabolic pathways and ecosystem processes, illustrating a multi-scale systems biology perspective on aromatic compound turnover.},
}

@article {pmid41589896,
year = {2026},
author = {Conrad, RE and Tsementzi, D and Meziti, A and Hatt, JK and Montoya, J and Konstantinidis, KT},
title = {Metagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0258925},
doi = {10.1128/aem.02589-25},
pmid = {41589896},
issn = {1098-5336},
abstract = {Genomic and metagenomic explorations of the oceans have identified well-structured microbial assemblages showing endemic genomic adaptations with increasing depth. However, deep water column surveys have been limited, especially of the Gulf of Mexico (GoM) basin, despite its importance for human activities. To fill this gap, we report on 19 deeply sequenced (~5 Gbp/sample) shotgun metagenomes collected along a vertical gradient, from the surface to about 2,000 m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station. However, a community-level pangenome style gene content analysis revealed ~54% of predicted gene sequences to be station-specific within our GoM samples. Of the 154 medium-to-high-quality MAGs recovered, 145 represent novel species compared with the NCBI genomes and Tara Oceans MAGs databases. Two of these MAGs were relatively abundant at both surface and deep samples, revealing remarkable versatility across the water column. A few MAGs of freshwater origin (~6% of total detected) were relatively abundant at 600 m deep and 270 miles from the coast at one station, revealing that the effects of freshwater input in the GoM can sometimes be far-reaching and long-lasting. Notably, 1,447/16,068 of the total COGs detected were positively (Pearson's r ≥ 0.5) or negatively (Pearson's r ≤ -0.5) correlated with depth, including beta-lactamases, dehydrogenases, and CoA-associated oxidoreductases. Taken together, our results reveal substantial novel genome and gene diversity across the GoM's water column, and testable hypotheses for some of the diversity patterns observed.IMPORTANCETo what extent microbial communities are similar between different ocean basins at similar depths, and what the impact of freshwater input by major rivers may be on these communities, remain poorly understood issues with potentially important implications for modeling and managing marine biodiversity. In this study, we performed metagenomic sequencing and recovered 154 medium-to-high-quality metagenome-assembled genomes (MAGs) from three stations in the Gulf of Mexico (GoM) and from various depths up to about 2,000 m. Comparison to MAGs recovered from other ocean basins highlighted the unique diversity harbored by the GoM, which could be driven by more substantial input from the Mississippi River and by human activities, including offshore oil drilling. The data and results provided by this study should be useful for future comparative analysis of marine biodiversity and contribute to its more complete characterization.},
}

@article {pmid41589836,
year = {2026},
author = {Darlenski, R and Manuelyan, K and Dimova, I and Menzel, P and Schwarzer, R and Fluhr, JW and Bogdanov, I},
title = {Skin surface microbiome dynamics in the extremes: Learnings from Antarctica distinct community.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.70324},
pmid = {41589836},
issn = {1468-3083},
support = {80-25-69/3.8.2021//Bulgarian National Program for Polar Research 2017-2021/ ; },
}

@article {pmid41589125,
year = {2026},
author = {Panyako, PM and Ogada, S and Kuria, SN and Musina, J and Lichoti, JK and Ommeh, SC},
title = {Metagenomic Profiling of Fecal and Cecal Microbiota and Their Antimicrobial Resistance Genes in Indigenous Backyard Poultry.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {7306065},
pmid = {41589125},
issn = {1687-918X},
abstract = {Indigenous backyard poultry is the predominant type of poultry in developing countries. Rural smallholder farmers in these regions usually adopt the free-range (backyard) production system, which exposes the poultry to diverse environments and a broad spectrum of microorganisms that influence their diet and gut microbiota. In this cross-sectional purposive study, we evaluated the microbial community profiles of indigenous backyard poultry and their antimicrobial resistance genes (ARGs) using both cecal samples, which provide a more accurate representation of the core gut microbiota, and fecal samples, which allow for noninvasive monitoring and pathogen screening. We analyzed 32 pooled fecal and cecal samples using shotgun metagenomics, followed by functional and antimicrobial resistance (AMR) analyses to identify genes and metabolic pathways associated with poultry gut health and production. We report the presence of many commensal microorganisms in indigenous backyard poultry, with the most abundant being Bacteroidetes, Firmicutes, and Proteobacteria. The most dominant genera in the feces were Bacteroides, Methanobrevibacter, and Phocaeicola, while Bacteroides, Methanobrevibacter, and Chlamydia dominated in the ceca. No marked differences in microbial diversity were observed between the fecal and cecal samples. KEGG and COG database analyses revealed significantly enriched pathways associated with metabolism, cellular processes, and information storage and processing. Genes that confer resistance to tetracycline were the most abundant, raising concerns about the risks associated with inappropriate and excessive use of this antibiotic in poultry treatment. These findings deepen our understanding of the poultry gut microbiome, particularly regarding indigenous backyard poultry. Furthermore, the information about ARGs is a valuable indicator of antimicrobial use by rural smallholder farmers who have adopted the free-range production system in Kenya and other developing countries. These insights are crucial for farmers and the national livestock sector to monitor AMR in poultry, thereby enabling improved poultry management practices and informed policy decisions.},
}

@article {pmid41589071,
year = {2026},
author = {Caserta, MT and Mariani, TJ and Walsh, EE and Gill, SR and Gill, AL and Corbett, A and Harrington, D and Chu, C and Qiu, X},
title = {Nasal Biomarkers of Acute Illness Severity and Predictors of Recurrent Wheeze in Respiratory Syncytial Virus (RSV) Infected Infants.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag049},
pmid = {41589071},
issn = {1537-6613},
abstract = {BACKGROUND: Respiratory syncytial virus (RSV) is a leading cause of hospitalization in infants and those with RSV disease appear more likely to develop recurrent wheeze. We examined nasal airway gene expression and microbiome composition during acute primary RSV infection to test associations with illness severity and identify infants with recurrent wheeze.

METHODS: Previously healthy infants with confirmed RSV infection were enrolled (Dec 2019 to Dec 2023). Clinical, demographic data, 2 anterior nasal swabs and a nasal wash were collected for metagenome and transcriptome sequencing. Disease severity was measured by the improved Global Respiratory Severity Score (iGRSS). Participants were followed for approximately 1 year after enrollment to identify recurrent wheeze. Multivariate regression models were developed to identify correlates and predictors of disease severity and recurrent wheeze, respectively.

RESULTS: 100 (90 hospitalized) infants were enrolled (mean age 3.2±2.3 months; 61% male). 405 genes (false discovery rate 0.10) were significantly and consistently associated with illness severity (iGRSS), implicating Innate Immune and Interleukin Signaling pathways. An abundance of Dolosigranulum in the nares was inversely associated with iGRSS while the abundance of Haemophilus was directly associated with iGRSS. Predictive models using nasal gene expression during acute infection had the power to classify recurrent wheeze (in-sample AUC=0.992; cross-validated AUC=0.882) while metagenomic features did not improve predictive performance.

CONCLUSIONS: We prospectively followed infants with primary RSV infection and identified associations between nasal gene expression, microbiome composition/function and acute disease severity and recurrent wheeze. Host transcriptional profiles during infection were predictive of recurrent wheeze within the following year.},
}

@article {pmid41588512,
year = {2026},
author = {Yu, S and Wu, Q and Ma, Y and Bano, S and Zhang, X},
title = {Keystone bacterial taxa drive denitrification and N2O emission via adaptive genomic and metabolic strategies in contrasting agricultural soils.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00855-1},
pmid = {41588512},
issn = {2524-6372},
support = {42577128 and 31971526//National Natural Science Foundation of China/ ; (2017YFD0200102)//Key R&D project of the Ministry of Science and Technology/ ; },
abstract = {BACKGROUND: Soil denitrification mediated by microbial communities is a major source of nitrous oxide (N2O), a potent greenhouse gas. However, the regulatory roles of keystone taxa in this process remain poorly understood, particularly under distinct edaphic conditions. Black soil (BS) and fluvo-aquic soil (FS), two representative agricultural soils in China, exhibit contrasting N2O emission potentials, offering an ideal model for exploring microbial mechanisms driving soil-specific denitrification dynamics.

RESULTS: We integrated microbial co-occurrence networks, metagenomics, and functional phenotyping to identify and characterize keystone bacterial taxa involved in denitrification across the two soil types. Structural equation modeling (SEM) and correlation analyses revealed strong associations between keystone taxa and denitrification rates and N2O emission patterns. Ensifer ASV205 was identified as a conserved keystone taxon in both soils and exhibited strain-level niche specialization. Comparative genomic analysis revealed that variations in denitrification gene composition and carbon-nitrogen metabolic pathways enabled Ensifer strains to act either as N2O producers or reducers, depending on environmental conditions.

CONCLUSIONS: Our findings demonstrate that soil-specific denitrification processes and N2O emissions are governed by keystone taxa through adaptive genomic and metabolic strategies shaped by environmental filtering. This study provides new insights into the microbial mechanisms regulating N2O emissions and lays the groundwork for developing microbiome-informed strategies to mitigate greenhouse gas emissions in agricultural soils.},
}

@article {pmid41588461,
year = {2026},
author = {Zheng, H and Payne, L and He, W and Mestre, MR and Yang, L and Dechesne, A and Pinilla-Redondo, R and Nesme, J and Sørensen, SJ},
title = {Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02297-2},
pmid = {41588461},
issn = {2049-2618},
abstract = {BACKGROUND: Bacterial antiphage defense systems play essential roles in microbial ecology, yet their dynamics within urban wastewater systems (UWS) remain poorly characterized.

RESULTS: In this study, we performed comprehensive metagenomic and plasmidome analyses on 78 wastewater samples collected during two seasons and four sampling points across UWS from three European countries. We observed a significant reduction in the abundance, diversity, and mobility potential of defense systems during biological treatment. However, these reductions were not directly correlated with changes in microbial abundance. Defense systems were significantly enriched on plasmids, particularly conjugative plasmids, where their gene density was approximately twice as high as on chromosomes and remained relatively stable across compartments. In contrast to chromosomal defense systems, plasmid-borne systems exhibited more frequent co-localization with a wide range of mobile genetic elements (MGEs)-associated genes, thereby facilitating multilayered dissemination networks. Furthermore, we detected a strong correlation between phage abundance and host defense system profiles, indicating ongoing phage-host co-evolutionary dynamics in these environments.

CONCLUSIONS: In summary, our results demonstrate that UWS reduce the abundance and diversity of bacterial defense system genes. However, plasmid-associated defense systems can persist through shared mobile genetic reservoirs. These findings underscore the critical role of plasmids in bacterial immunity and provide new insights into defense system dynamics within urban wastewater environments.},
}

@article {pmid41588320,
year = {2026},
author = {Guo, W and Yu, J and Wang, W and Wang, J and Ni, M and Zhou, M and Chen, X},
title = {Multi-kingdom fecal microbiome and virus-host interactions associated with growth performance of indigenous beef calves in Guizhou.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04631-y},
pmid = {41588320},
issn = {1471-2180},
support = {32402705//the National Natural Science Foundation of China/ ; },
}

@article {pmid41588163,
year = {2026},
author = {Young, V and Dohai, B and Halder, H and Fernandez-Macgregor, J and van Heusden, NS and Hitch, TCA and Weller, B and Hyden, P and Saha, D and Pieren, DKJ and Rittchen, S and Lambourne, L and Maseko, SB and Lin, CW and Tun, YM and Bibus, J and Pletschacher, L and Boujeant, M and Choteau, SA and Bergogne, L and Perrin, J and Ober, F and Schwehn, P and Rothballer, ST and Altmann, M and Altmann, S and Strobel, A and Rothballer, M and Tofaute, M and Kotlarz, D and Heinig, M and Clavel, T and Calderwood, MA and Vidal, M and Twizere, JC and Vincentelli, R and Krappmann, D and Boes, M and Falter, C and Rattei, T and Brun, C and Zanzoni, A and Falter-Braun, P},
title = {Effector-host interactome map links type III secretion systems in healthy gut microbiomes to immune modulation.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41588163},
issn = {2058-5276},
support = {01EA1803//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 101003633//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 210592381//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 403224013//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 11819559//Österreichische Forschungsförderungsgesellschaft (Austrian Research Promotion Agency)/ ; ANR-16-CONV-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-17-HDIM-000//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-16-CONV-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; },
abstract = {Pseudomonadota (formerly Proteobacteria) are prevalent in the commensal human gut microbiota, but also include many pathogens that rely on secretion systems to support pathogenicity by injecting proteins into host cells. Here we show that 80% of Pseudomonadota from healthy gut microbiomes also have intact type III secretion systems (T3SS). Candidate effectors predicted by machine learning display sequence and structural features that are distinct from those of pathogen effectors. Towards a systems-level functional understanding, we experimentally constructed a protein-protein meta-interactome map between human proteins and commensal effectors. Network analyses uncovered that effector-targeted neighbourhoods are enriched for genetic variation linked to microbiome-associated conditions, including autoimmune and metabolic diseases. Metagenomic analysis revealed effector enrichment in Crohn's disease but depletion in ulcerative colitis. Functionally, commensal effectors can translocate into human cells and modulate NF-κB signalling and cytokine secretion in vitro. Our findings indicate that T3SS contribute to microorganism-host cohabitation and that effector-host protein interactions may represent an underappreciated route by which commensal gut microbiota influences health.},
}

@article {pmid41588069,
year = {2026},
author = {Muñoz-Hisado, V and Bartolomé, M and Osácar, MC and Giménez, R and Cazenave, G and Garcia-Lopez, E and Moreno, A and Cid, C},
title = {Microbial communities and biomineralization potential within mountain permafrost of the Devaux ice cave in the Central Pyrenees.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37305-4},
pmid = {41588069},
issn = {2045-2322},
support = {HORIZON-MSCA-2022-PF-01 (01107943)//European Union/ ; PTA2022-021737-I//the Spanish Ministry of Science and Innovation/State Agency of Research MCIN/ ; },
abstract = {Ice caves constitute one of the last cryospheric environments studied in the meridional regions. They are undergoing a pronounced ice reduction, and are an important example of ecosystems that have not yet been thoroughly explored from a microbiological point of view. The Devaux cave, in the Central Pyrenees, still hosts perennial ice. To test whether this ice contained microbial communities, prokaryotic and eukaryotic microorganisms were searched by sequencing their 16S and 18S rRNA genes. From the taxonomic information, the potential functional pathways of these communities were predicted using bioinformatic techniques. In addition, the genome of the microorganisms housed in the perennial ice samples was investigated, and through metagenomic studies their metabolic capacity was elucidated. The cryogenic mineralization of the Devaux cave leads to the production of various Ca and Mg carbonates: calcite, aragonite, vaterite, Mg-rich calcite, and nesquehonite, whose formation may have been favored by the microorganisms in the cave. Among the genes encoding enzymes that enable reactions involved in biomineralization, those belonging to the nitrate and sulfate reduction dissimilatory pathways as well as ureases, ammonia lyases, and carbonic anhydrases were identified. This research takes a further step in the investigation of biomineralization, using the Devaux cave as a model.},
}

@article {pmid41587946,
year = {2026},
author = {Quraishi, MN and Moakes, CA and Yalchin, M and Blackwell, C and Segal, J and Ives, NJ and Magill, L and Manzoor, SE and Gerasimidis, K and McMullan, C and Mathers, J and Horniblow, R and Loi, S and Kaur, M and Loman, NJ and Sharma, N and Hawkey, P and McCune, V and Quick, J and Nicholls, S and McMurray, C and Nichols, B and Svolos, V and Raguideau, S and Kerbiriou, C and Oo, YH and Beggs, AD and Crees, N and Hansen, R and Hart, AL and Gaya, DR and Quince, C and Iqbal, TH},
title = {Mechanistic insights into FMT for the treatment of ulcerative colitis: analysis of the STOP-Colitis trial.},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjag006},
pmid = {41587946},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: Faecal microbiota transplantation (FMT) is a promising therapy for ulcerative colitis, but variable responses and unclear mechanisms limit its efficacy. We aimed to compare nasogastric versus colonic FMT delivery and define the microbial and immunological changes associated with clinical response.

METHODS: In this prospective, open-label, randomised pilot trial (STOP-Colitis), 30 adults with active ulcerative colitis were randomised to receive multi-dose FMT via nasogastric tube or colonoscopy with subsequent enemas. Key endpoints were clinical outcomes at week 8 and longitudinal multi-omic analyses of stool and biopsies to define changes in microbial composition (16S rRNA and shotgun metagenomics), short-chain fatty acids, mucosal T-cells, and host gene expression.

RESULTS: Colonic FMT was superior to nasogastric delivery, with a higher clinical response rate at week 8 (75% [9/12] vs 25% [2/8]; RR 2·94, 95% CI 0·84-10·30-per protocol analysis). Response was underpinned by successful microbial engraftment, leading to significantly increased faecal microbial diversity and enrichment of SCFA-producing taxa, including Oscillospiraceae and Christensenellaceae. This correlated with reduced faecal calprotectin. Responders showed a significant increase in mucosal regulatory T cells (P = 0·01), with a concurrent decrease in Th17 (P = 0·03) and CD8 + T cells. This anti-inflammatory shift was confirmed by mucosal transcriptomics, which revealed upregulation of metabolic pathways and downregulation of proinflammatory defence pathways in responders. (Trial registration: ISRCTN13636129).

CONCLUSION: Colonic FMT is a more effective delivery route than nasogastric administration. Clinical response is driven by the engraftment of immunomodulatory bacteria that restore a healthy host-microbe dialogue, providing rationale for developing targeted microbial therapeutics.},
}

@article {pmid41587907,
year = {2026},
author = {Ma, H and Dai, Y and Xu, C and Geng, H and Li, R and Wang, S and Yang, M},
title = {Identification of Three Novel Umami Peptides from Metagenomics of Traditional Fermented Fish, Suanyu, and Receptor Binding Mechanism via the Graph Neural Network-Based Model and Molecular Dynamics Simulation.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14362},
pmid = {41587907},
issn = {1520-5118},
abstract = {Fermented fish products are vital sources of umami peptides. In this study, a hierarchical graph attention network-based model was developed to identify candidate umami peptides. Via an integrated approach combining metagenomics, molecular docking, attention weight analysis, molecular dynamics simulations, and experimental validation, three novel umami peptides (GYSSYK, LYSDSK, and TRTKASY) were identified from the Suanyu system, a traditional fermented fish product. It was revealed that T1R1 and T1R3 could form stable complexes with these peptides involving critical residues: GLU301, ARG277, LYS328, SER384, ASP147, GLN278, and HIS71. In sensory evaluation, candidate peptides showed high umami properties with umami threshold values of 0.28 (±0.14) mg/mL. Overall, this study presents a hierarchical graph attention network-based screening methodology for the rapid screening and in-depth study of umami peptides.},
}

@article {pmid41587649,
year = {2026},
author = {Shi, J and Li, LK and Lin, LH and Li, DK and Lu, J and Saleh, SM and Zhang, TY and He, H and Dong, ZY and Xiao, Q and Xu, B and Zeng, C},
title = {Magnetic properties driving nitrogen removal improvement in magnetite-enhanced activated sludge: Mechanistic insights and process validation.},
journal = {Environmental research},
volume = {294},
number = {},
pages = {123870},
doi = {10.1016/j.envres.2026.123870},
pmid = {41587649},
issn = {1096-0953},
abstract = {The magnetite-enhanced activated sludge (MEAS) process offers a promising in situ strategy for upgrading wastewater treatment plants (WWTPs) to meet increasing treatment demands and stricter discharge regulations. Unlike conventional materials, magnetite possesses intrinsic magnetic properties, yet their influence on biological treatment efficiency and microbial ecology remains underexplored. This study systematically evaluated three types of magnetite particles with varying properties, focusing on their roles in denitrification, sludge settling, and microbial responses. Batch experiments under low carbon-to-nitrogen conditions (C/N = 4.4) demonstrated that magnetite with high saturation magnetization (65.9 emu/g) achieved 79.3 ± 10.2 % nitrate removal, 3.3 times higher than the control. It reduced the sludge volume index (SVI) from 84.7 to 28.4 mL/g by promoting compact floc formation through extracellular polymeric substance (EPS) protein conformational changes and enhanced microbe-particle interactions. It also increased bio-capacitance of the sludge and achieved a 77.0 % increase in electron transport system activity (ETSA). Surface analysis confirmed that magnetite served as a passive electron mediator rather than actively participating in redox cycling. Metagenomic sequencing further demonstrated the selective enrichment of denitrifying and magnetotactic bacteria and enrichment of key nitrogen metabolism genes (narG, nirK, narK, narH). Validation in an anaerobic-anoxic-aerobic (AAO) reactor treating real municipal wastewater achieved NH4[+]-N and total nitrogen removal efficiencies of 98.7 % and 73.6 %, respectively, meeting stringent discharge limits. These results identify saturation magnetization as a critical parameter for selecting or engineering magnetite materials and provide mechanistic insights and engineering guidance for deploying MEAS as an efficient, retrofit-friendly technology for WWTP upgrading.},
}

@article {pmid41587576,
year = {2026},
author = {Mburu, D and Kumar, S and Wang, Y and Namagerdi, AA and Bai, K and Ali, B and Minalla, A and Gonzales, KO and Abdelhalim, KA},
title = {The oxalobiome: unraveling the role of gut microbiota in oxalate metabolism and its implications for kidney health and disease management.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {584},
number = {},
pages = {120852},
doi = {10.1016/j.cca.2026.120852},
pmid = {41587576},
issn = {1873-3492},
abstract = {The oxalobiome, comprising microbial communities involved in oxalate metabolism, plays a critical role in maintaining oxalate homeostasis and preventing associated health issues, particularly calcium oxalate nephrolithiasis. Key organisms, notably Oxalobacter formigenes, are essential for degrading oxalate, yet their abundance is influenced by factors such as diet, genetics, and antibiotic use. Recent advances in research have elucidated the complex interactions between the gut microbiome and oxalate metabolism, highlighting the potential for therapeutic interventions. Innovative strategies, including RNA interference therapies (e.g., lumasiran, nedosiran), engineered probiotics, and gene-editing technologies, show promise in managing conditions like primary hyperoxaluria. However, challenges remain, including limitations in oxalate measurement techniques and variability in microbial populations. Multi-omics approaches and metagenomic analyses have enhanced our understanding of the oxalobiome, revealing novel microbial taxa and metabolic pathways involved in oxalate degradation. Despite the potential of emerging therapies, clinical translation is still in its infancy, necessitating further research to establish efficacy and safety. Future studies should focus on mechanistic insights, standardized methodologies, and targeted microbiome-based therapies to optimize management strategies for hyperoxaluria and related systemic diseases. A comprehensive understanding of the oxalobiome is essential for developing precision medicine approaches that effectively address oxalate dysregulation and improve patient outcomes.},
}

@article {pmid41587575,
year = {2026},
author = {Kongor, B and Chatterjee, R},
title = {Salivary biomarkers in early oral cancer diagnostics.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {120853},
doi = {10.1016/j.cca.2026.120853},
pmid = {41587575},
issn = {1873-3492},
abstract = {Saliva is an easily accessible bio-fluid which consists of various diagnostic components that can reflect any tumor-related changes, offering a promising non-invasive approach for more accurate and early detection of oral cancer. The primary aim of this review is to provide an integrative evaluation of salivary biomarkers for oral cancer by combining qualitative synthesis with a semi-quantitative analysis of various diagnostic parameters. The work highlights biomarker trends by understanding their diagnostic potential across molecular categories through the visual representation of these quantitative data in bar graphs and heatmaps. Comprehensive literature evaluation was performed by using search engines like Pubmed, Science Direct, Google Scholar etc. on the topic of using salivary biomarkers as an oral cancer detection tool. Relevant data on study design, demographic information, sample type, analytical method, biomarker significance etc. were qualitatively summarized. Quantitative parameters including sensitivity, specificity, accuracy and p-values were either extracted or calculated from selected studies and visualized through bar graphs and heatmaps to facilitate comparative interpretation of diagnostic performance. Multiple salivary biomarkers were identified across genomic, transcriptomic, proteomic, metabolomic, and metagenomic levels, each showing significant involvement in molecular alterations and metabolic pathway dysregulation linked to oral malignancies. This review offers a novel semi-quantitative approach that bridges comprehensive literature summarization with diagnostic data interpretation. By integrating quantitative indices into bar graphs and heatmaps, it enables rapid visual comparison of salivary biomarker performance by revealing high-performing candidates of early oral cancer detection. Thus, saliva-based diagnostics hold great potential as a non-invasive, cost-effective reliable alternative to the conventional oral cancer detection methods.},
}

@article {pmid41587207,
year = {2026},
author = {Krzynowek, A and Snoeks, J and Faust, K},
title = {PlasticEnz: An integrated database and screening tool combining homology and machine learning to identify plastic-degrading enzymes in meta-omics datasets.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013892},
doi = {10.1371/journal.pcbi.1013892},
pmid = {41587207},
issn = {1553-7358},
abstract = {PlasticEnz is a new open-source tool for detecting plastic-degrading enzymes (plastizymes) in metagenomic data by combining sequence homology-based search with machine learning techniques. It integrates custom Hidden Markov Models, DIAMOND alignments, and polymer-specific classifiers trained on ProtBERT embeddings to identify candidate depolymerases from user-provided contigs, genomes, or protein sequences. PlasticEnz supports 11 plastic polymers with ML classifiers for PET and PHB, achieving F1 > 0.7 on an independent test set. Applied to plastic-exposed microcosms and field metagenomes, the tool recovered known PETases and PHBases, distinguished plastic-contaminated from pristine environments, and clustered predictions with validated reference enzymes. PlasticEnz is fast, scalable, and user-friendly, providing a robust framework for exploring microbial plastic degradation potential in complex communities.},
}

@article {pmid41586525,
year = {2026},
author = {Díaz-González, F and Rojas-Villalobos, C and Issotta, F and Reyes-Impellizzeri, S and Hedrich, S and Johnson, DB and Temporetti, P and Quatrini, R},
title = {Trait-based meta-analysis of microbial guilds in the iron redox cycle.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0148825},
doi = {10.1128/msystems.01488-25},
pmid = {41586525},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial iron (Fe) redox cycling underpins key biogeochemical processes, yet the functional diversity, ecological roles, and trait architectures of iron-transforming microbes remain poorly synthesized across global environments. Here, we present a systematic review and trait-based meta-analysis of 387 microbial taxa spanning 314 studies and 76 years of research, integrating phenotypic, genomic, and environmental data to define ecologically coherent microbial iron redox cycle guilds. Rather than relying on taxonomy, our framework delineates first-order functional guilds-Fe(III) reducers, Fe(II) oxidizers, and dual-capacity Fe oxidizers/reducers-and resolves second-order guilds based on trait syndromes, such as acidophily, redox flexibility, or metabolic breadth. Trait profiling revealed that iron-cycling capacities frequently transcend phylogenetic boundaries, with multiple guilds converging in chemically stratified hotspots like hot springs, hydrothermal vents, and acid mine drainages. Dual-capacity Fe oxidizers/reducers (e.g., Acidithiobacillus ferrooxidans and Metallosphaera sedula) emerged as overlooked mediators of "cryptic" iron cycling, possessing genomic repertoires capable of toggling between oxidative and reductive modes in response to redox oscillations. Hierarchical clustering and kernel density analyses of ecophysiological traits highlighted niche partitioning along key environmental filters, including pH, iron availability, salinity, and temperature. Collectively, this work introduces the Guild Exploitation Pattern as a conceptual lens for understanding iron microbiome assembly, providing a data-driven foundation for predicting microbial contributions to iron cycling under changing environmental conditions.

IMPORTANCE: Iron redox reactions shape nutrient turnover, contaminant mobility, and primary productivity, yet the microbes driving these processes are often studied in isolation. By integrating decades of data into a trait-based guild framework, we reveal the ecophysiological diversity and niche differentiation of microbial iron redox cycling taxa across environments. Our synthesis exposes major gaps, such as limited trait data for >80% of dual-capacity Fe oxidizing/reducing species and highlights the need for functional trait surveys to complement metagenomics and cultivation efforts. The guild framework presented here advances predictive microbial ecology by linking metabolic traits with environmental gradients, offering a robust foundation for incorporating iron cycling into ecosystem models and biogeochemical forecasts.},
}

@article {pmid41586524,
year = {2026},
author = {Bloemen, B and Delvoye, M and Hoffman, S and Marchal, K and Vanneste, K and Fraiture, M-A and Roosens, NHC and De Keersmaecker, SCJ},
title = {Recovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0128225},
doi = {10.1128/msystems.01282-25},
pmid = {41586524},
issn = {2379-5077},
abstract = {UNLABELLED: Mobile genetic elements (MGEs) are major drivers of horizontal gene transfer, including the spread of antimicrobial resistance (AMR) genes. However, determining the microbial host of an MGE in complex microbiomes remains challenging. Here, we spike a niche-aspecific Bacillus velezensis strain carrying a plasmid and linear phage-plasmid into a batch bioreactor simulating the human gut, and use it as a spike-in control to assess the performance of Hi-C sequencing and Oxford Nanopore Technologies (ONT)-enabled DNA methylation detection to identify MGE-host pairs. To improve recovery of low-abundance genomes, we used a novel ONT adaptive sampling (AS) strategy that depletes de novo assembled, sample-specific high-abundance contigs, rather than relying on reference genomes. This approach led to an approximately twofold enrichment of low-abundance replicons, including the spike-in strain. Methylation-based host assignment failed for the B. velezensis MGEs, likely due to the absence of DNA methylation. In contrast, Hi-C successfully linked the phage-plasmid to its host, but not the plasmid, likely due to non-intact cells, and only after removing artefactual signals through bioinformatic processing. For a native Escherichia coli strain, Hi-C and methylation data linked it to two plasmids. Selective isolation and whole-genome sequencing of both the native E. coli and spike-in B. velezensis then confirmed the metagenomic observations. Our results highlight that Hi-C and methylation data can provide powerful insights into MGE-host associations, but their interpretation requires careful computational analysis and biological validation. Moreover, our AS strategy offers a cost-efficient method to boost coverage of low-abundance genomes, improving metagenomic investigation of MGEs in complex microbiomes.

IMPORTANCE: Mobile genetic elements are important contributors to horizontal gene transfer, including of antimicrobial resistance genes. Understanding which microbes carry these mobile elements is vital to assess the spread of resistance. Here, we use a nanopore adaptive sampling approach to increase detection of low-abundance bacteria and mobile elements and use DNA methylation detection and Hi-C sequencing to determine mobile element hosts. By introducing a known bacterium and isolating a native strain, we could evaluate the performance of these methods, indicating that although powerful, they require careful experimental design, interpretation, and validation. However, when combined, these approaches enable a comprehensive investigation of mobile elements and gene transfer dynamics in complex environments.},
}

@article {pmid41586495,
year = {2026},
author = {Carroll, AC and Mortimer, L and Ghosh, H and Reuter, S and Grundmann, H and Brinda, K and Hanage, WP and Li, A and Paterson, A and Purssell, A and Rooney, AM and Yee, NR and Coburn, B and Able-Thomas, S and Antonio, M and McGeer, A and MacFadden, DR},
title = {Prediction of genetic relatedness of Escherichia coli using neighbor typing: a tool for rapid outbreak detection.},
journal = {Antimicrobial agents and chemotherapy},
volume = {},
number = {},
pages = {e0107125},
doi = {10.1128/aac.01071-25},
pmid = {41586495},
issn = {1098-6596},
abstract = {Identifying the genetic relatedness of resistant bacterial pathogens in healthcare settings can help identify undetected transmission events and outbreaks. However, current methods are time- and resource-intensive. We evaluated a rapid neighbor typing method paired with long-read sequencing for assessment of genetic relatedness. Utilizing a data set of primary clinical samples and published isolate data from two outbreaks of Escherichia coli, we applied genomic neighbor typing of long-read sequence data to rapidly estimate genetic relatedness. We assessed the correlation between neighbor typing predicted genetic distance and pairwise genetic distance from short-read draft whole genomes for all sample pairs. Predicted genetic trees using neighbor typing were compared to reference genetic trees generated using mash distances and maximum-likelihood (ML) methods to assess the extent of agreement, along with metrics of cluster similarity (cluster comparability and Baker's gamma index [BGI]) and tree topology similarity (generalized Robinson-Foulds [GRF] metric). For all three data sets, we found strong correlations between the reference methods and predicted genetic distances (Spearman's rho = 0.75-0.95, P < 0.001), which improved when using a lineage score-informed approach (Spearman's rho = 0.93-0.94, P < 0.001). Predicted genetic trees and clusters from neighbor typing were comparable to those generated using either mashtree or an ML method, with a range of cluster comparability of 85.8-99.5%, BGIs of 0.8-0.95, and GRF values of 0.34-0.8. Pairing the neighbor typing method with long-read sequencing can enable accurate predictions of the relatedness of E. coli samples and isolates, and could potentially be used as a rapid outbreak surveillance tool.},
}

@article {pmid41586370,
year = {2025},
author = {Zeng, B and Peng, X and Xiao, P and Nie, K and Zhang, G and Xia, L},
title = {Salt sensitivity potentiates high-salt diet-induced intestinal barrier disruption and gut microbiome dysbiosis in rats.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1718782},
pmid = {41586370},
issn = {1664-302X},
abstract = {INTRODUCTION: The high-salt diet is a prevalent eating habit associated with health risks. This study investigated the impact of high salt on intestinal barrier disruption and gut microbiome dysbiosis using Wistar and Dahl salt-sensitive rat models.

METHODS: Rats were fed a normal diet or a high-salt diet for eight weeks. Body weight and plasma inflammatory cytokines were monitored in the study. Colon tissue damage was assessed via histopathological examination, and metagenomic sequencing was utilized to analyze alterations in microbial composition, functional pathways, and biodiversity.

RESULTS: The results indicated that high salt significantly elevated pro-inflammatory cytokine levels and induced structural damage in the colon. Metagenomic analysis revealed that high salt concentrations resulted in approximately a 15% difference in microbial species composition. And led to a decrease in Alpha diversity, along with an increase in the Firmicutes/Bacteroidetes ratio. Taxon-specific alterations included reduced abundance of Lactobacillus and Clostridium, and increased abundance of Enterobacter and Bifidobacterium. Correlation analyses further revealed a positive correlation between Bifidobacterium abundance and tumor necrosis factor-α level in Dahl salt-sensitive rats.

DISCUSSION: This study illuminates the gut microbiota's role in salt-sensitivity and provides a foundational basis for developing microbiota-targeted interventions for at-risk individuals.},
}

@article {pmid41586357,
year = {2025},
author = {Wuyunsiqin, and Bai, T and Yang, D and Hashentuya, and Namila, and Jin, C and Tana, and Zhao, P and Wang, M and Menggenduxi, },
title = {Mongolian medicine Wulanwendusu-11 alleviates myocardial ischemia-reperfusion injury by modulating the intestinal microbiota and associated metabolic pathways.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1693472},
pmid = {41586357},
issn = {1664-302X},
abstract = {OBJECTIVE: Wulanwendusu-11 (WLWDS-11) is a commonly used Mongolian medicine for treating cardiovascular diseases. However, its regulating effect on intestinal flora-host metabolism in relieving chronic myocardial ischemia-reperfusion injury (MIRI) is still unclear. Therefore, this study aims to systematically explore the cardioprotective mechanism of WLWDS-11 from the perspective of metabolic interaction between intestinal microbiota and host.

METHODS: C57BL/6J mice were randomized into six experimental groups: MIRI model, sham surgery, and treatment groups for compound Danshen dripping pills (CDDP) plus three dosages of WLWDS-11 (denoted WLWDS-11-L, WLWDS-11-M, and WLWDS-11-H). General physiological indicators of mice in each group were observed, body weight, myocardial structure and pathological features were assessed by electrocardiogram, plasma cardiac enzyme levels. The cardiac function of mice was obtained by echocardiography. Immunohistochemical staining was used to detect the pathological changes in the heart. Immunofluorescence assay was used to detect the degree of apoptosis. Metabolomics and metagenomics were used to analyze treatment effects on intestinal microbiota and metabolites. Integrated analysis of the enriched oxidative phosphorylation and necrosis and apoptosis pathways. qRT-PCR and western blot were used to detect the expression of COX4I1, NDUFB8, SDHA, TFAM, RIPK1, RIPK3, MLKL and TNF-α.

RESULTS: WLWDS-11 (especially in high dose) can significantly improve the cardiac function, reduce the area of myocardial infarction and weaken apoptosis and fibrosis in MIRI mice. Metabolomic profiling revealed extensive metabolic alterations, pathway analysis implicated arginine/proline and unsaturated fatty acid metabolism, and hierarchical clustering identified specific correlations between differential flora (e.g., Kosakonia, Helicobacter spp.) and key metabolites. Integrated multi-omics analysis demonstrated that MIRI induces gut microbiota dysbiosis and systemic metabolic disturbances, characterized by the accumulation of oxidized lipids/lysophospholipids and disruption of critical metabolic pathways. The intervention of WLWDS-11 effectively reshaped the intestinal microbial community and made the metabolic spectrum return to normal. More importantly, correlation and network analysis confirmed the correlation between specific intestinal bacteria (such as Prevost, Kosakonia and Helicobacter) and host metabolites, and formed a flora-metabolite axis regulated by WLWDS-11. KEGG pathway analysis further confirmed the effects of the treatment on key pathways, including necrotizing apoptosis and oxidative phosphorylation. From the point of view of mechanism, WLWDS-11 reversed the mitochondrial dysfunction induced by MIRI by up-regulating the expressions of COX4I1, NDUFB8, SDHA and TFAM. By inhibiting the RIPK 1/RIPK 3/MLKL pathway and TNF-α, necrotizing apoptosis and inflammatory response are inhibited. These results suggest that WLWDS-11 may protect MIRI's heart by regulating the metabolic pathway of flora.

CONCLUSION: WLWDS-11 positively reshaped the gut microbial environment by suppressing pathogenic bacteria and promoting beneficial strains, thereby fostering eubiosis, attenuating cardiac pathology, and ultimately conferring cardio protection. These findings identify WLWDS-11 as a potential candidate drug and provide a molecular mechanistic basis for the clinical treatment of MIRI.},
}

@article {pmid41586308,
year = {2025},
author = {Wang, X and Ye, L and Liu, Y and Li, H and Shi, H and Zheng, L},
title = {Metagenomic analysis reveals severity-dependent microbial succession and correlation with host inflammatory response in oral and maxillofacial space infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1695928},
pmid = {41586308},
issn = {2235-2988},
mesh = {Humans ; Cross-Sectional Studies ; *Metagenomics ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Microbiota/genetics ; Aged ; Severity of Illness Index ; *Bacteria/classification/genetics/isolation & purification ; Adult ; *Inflammation/microbiology ; *Abscess/microbiology ; },
abstract = {BACKGROUND: Oral and maxillofacial space infections (OMSI) vary widely in clinical severity, yet the relationships between microbial community patterns in the abscess niche and host inflammatory responses remain incompletely characterized.

METHODS: We conducted a retrospective, cross-sectional, severity-stratified study of 197 patients diagnosed with OMSI between January 2020 and November 2023. Patients were stratified into mild (n=90), moderate (n=41), and severe (n=66) groups based on established clinical criteria. We performed mNGS on abscess pus samples to characterize the microbial community composition and assessed associations between these features and systemic inflammatory markers.

RESULTS: Although α-diversity did not differ significantly among severity groups, β-diversity analysis revealed distinct microbial communities. Pairwise analyses indicated a threshold-like community shift, characterized by a significant divergence between mild and severe infections, while the moderate group exhibited an intermediate composition that overlapped with both. Severe infections were characterized by an enrichment of Prevotella. Furthermore, analysis of predominant taxa (>30% abundance) revealed considerable microbial heterogeneity, challenging a simple monoinfection model. Notably, a machine learning-identified microbial profile comprising Streptococcus, Corynebacterium, and Pseudomonas was significantly correlated with elevated systemic inflammatory markers.

CONCLUSION: This study characterizes associations between abscess-site microbial communities and host inflammatory profiles across OMSI severity strata. Given the cross-sectional design and the lack of an external validation cohort, the present findings should be interpreted as exploratory and non-causal. Future multicenter prospective studies including independent validation cohorts are warranted to test reproducibility and to evaluate whether any candidate features possess generalizable predictive value.},
}

Humans
Cross-Sectional Studies
*Metagenomics
Male
Female
Retrospective Studies
Middle Aged
*Microbiota/genetics
Aged
Severity of Illness Index
*Bacteria/classification/genetics/isolation & purification
Adult
*Inflammation/microbiology
*Abscess/microbiology

@article {pmid41585896,
year = {2025},
author = {Jiang, H and Hu, XW and Deng, X and Huang, XJ and Chen, YL and Yang, YF and Du, Y and Ji, S and Tang, DQ},
title = {Liuwei Dihuang pills ameliorate renal injury in experimental type 2 diabetes mellitus rat by regulating host-gut microbiota interaction.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1715600},
pmid = {41585896},
issn = {1663-9812},
abstract = {BACKGROUND: Liuwei Dihuang pills (LW) are widely used as the traditional tonic prescription for the treatment of diabetes and diabetic kidney disease (DKD). This study aimed to investigate the potential mechanism underlying LW-mediated prevention and treatment of DKD from the perspective of host-gut microbiome co-metabolism.

METHODS: A rat model of DKD was established using high-fat diet and streptozotocin. Levels of type IV collagen (Col IV), fibronectin (FN), laminin (Lam), transforming growth factor-β (TGF-β), SMAD family member 7 (SMAD7), and SMAD3 in the kidneys were determined by real time-polymerase chain reaction and Western blot. Fecal metabolites were profiled using ultra-high-performance liquid chromatography-tandem mass spectrometry. Metagenomic sequencing of the feces was performed using high-throughput sequencing.

RESULTS: When combined with metformin (MET)-based therapy, LW significantly improved serum creatinine and blood urea nitrogen levels, kidney index, 24-h urine volume, urine protein content and excretion rate, and urinary creatinine and cystatin C levels. It also attenuated morphological changes. Correspondingly, LW intervention reduced the renal expression of TGF-β, SMAD3, Col IV, LAM, FN, interleukin (IL)-6, and IL-1β, while increasing SMAD7 expression. Additionally, it normalized metabolic pathway abnormalities in galactose, butyric acid, fructose, mannose, amino sugar, and nucleotide sugar metabolism. Moreover, LW regulated bacterial imbalances, notably in specific species such as Allobaculum unclassified, Escherichia coli, Pseudoflavonifractor capillosus, Desulfovibrio porci, Oscillibacter sp. CU971, Parablautia muri, Phocaeicola dorei, Phocaeicola faecalis, Phocaeicola vulgatus, and Raoultella unclassified.

CONCLUSION: The combination of LW and MET ameliorated renal impairment in DKD rats by regulating the TGF-β/SMAD signaling pathway, metabolic disturbances in endogenous metabolites, and gut microbiota dysbiosis.},
}

@article {pmid41585813,
year = {2025},
author = {Rong, F and Mingying, Z and Ying, B and Yiyun, H and Ying, Q and Zheng, X and Xiaolei, C},
title = {Pulmonary mucormycosis with bacterial coinfection in an adolescent with poorly controlled type 1 diabetes: a case report.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1724850},
pmid = {41585813},
issn = {1664-2392},
mesh = {Humans ; Female ; *Mucormycosis/complications/microbiology/drug therapy ; Child ; *Diabetes Mellitus, Type 1/complications/microbiology ; *Coinfection/microbiology/complications ; *Lung Diseases, Fungal/complications/microbiology/drug therapy ; Rhizopus/isolation & purification ; *Bacterial Infections/complications/microbiology ; },
abstract = {BACKGROUND: Pulmonary Mucormycosis (PM), a severe fungal infection affecting mainly immunocompromised individuals, is often caused by fungi like Rhizopus and Mucor. This report details a 12-year-old diabetic girl with pulmonary mucormycosis from an unusual Rhizopus species. Successful treatment involved stabilizing her blood glucose and managing multiple co-infections. This case provides important insights into diagnosing and treating rare fungal infections in diabetic children.

CASE SUMMARY: A 12-year-old girl with a two-year history of type 1 diabetes, inconsistently monitored, was hospitalized. She had a persistent cough for over ten days and a six-day high fever. Previous treatments with dexamethasone and antibiotics were ineffective. She showed symptoms of a productive cough, right-sided pleuritic chest pain, and a fever of 40°C. Examination revealed reduced breath sounds and moist rales in the right lung. Tests confirmed a severe infection, and imaging showed inflammatory consolidation, multiple cavitations, and pleural effusion in the right lung.

DIAGNOSIS: Metagenomic next-generation sequencing (mNGS) analyzes all nucleic acids from a patient's bronchoalveolar lavage fluid to identify various pathogens without traditional cultures. The analysis identified Rhizopus species and Streptococcus pneumoniae, confirming pulmonary mucormycosis with a bacterial infection. Additionally, the glycated hemoglobin (HbA1c) level was 14.3%, indicating poorly controlled diabetes.

TREATMENT: A comprehensive treatment regimen was employed. The bacterial co-infection was addressed with intravenous administration of meropenem and linezolid, while nebulized amphotericin B was utilized to treat the pulmonary mucormycosis. To mitigate the underlying risk factor, intensive glycemic control was achieved through the use of an insulin pump. Furthermore, bronchoscopy was conducted to clear respiratory secretions.

OUTCOME: After 11 days in the hospital, the patient stabilized and was discharged. At a follow-up 1.5 months later, infection markers and blood glucose levels were normal.

CONCLUSION: This case highlights the high risk of severe infections like pulmonary mucormycosis in adolescents with poorly managed type 1 diabetes. Metagenomic sequencing was crucial for quickly identifying co-infections. Successful treatment required a comprehensive approach, including targeted antimicrobial therapy, strict glycemic control, and bronchoscopic support, leading to a positive outcome.},
}

Humans
Female
*Mucormycosis/complications/microbiology/drug therapy
Child
*Diabetes Mellitus, Type 1/complications/microbiology
*Coinfection/microbiology/complications
*Lung Diseases, Fungal/complications/microbiology/drug therapy
Rhizopus/isolation & purification
*Bacterial Infections/complications/microbiology

@article {pmid41585543,
year = {2026},
author = {Li, T and Wang, Q and Lin, Y and Li, Y and Luo, Z and Zhang, W and Sun, N and Dong, H and Zhang, W and Meng, Y},
title = {Mycobacterium avium complex causing transverse pericardial sinus infection: A case report.},
journal = {IDCases},
volume = {43},
number = {},
pages = {e02479},
pmid = {41585543},
issn = {2214-2509},
abstract = {Nontuberculous mycobacteria (NTM) are increasingly recognized as significant opportunistic pathogens in humans, yet they remain rarely implicated in cardiac conditions. Here, we report a rare case of Mycobacterium avium complex (MAC) infection in the transverse pericardial sinus, an unusual site previously undocumented for NTM infection. The patient, a 68-year-old male with prior cardiac surgery, presented with recurrent fever lasting for over 10 days. Positron emission tomography/computed tomography demonstrated a hypermetabolic mass-like lesion within the transverse pericardial sinus, radiologically suggestive of an infectious process. Empirical broad-spectrum antimicrobial therapy failed to achieve clinical response. Following surgical intervention to remove lesion tissue from the transverse pericardial sinus, histopathological analysis revealed granulomatous inflammation and acid-fast bacilli, indicating NTM infection. Metagenomic next-generation sequencing (mNGS) identified MAC in the tissue sample. After starting antimycobacterial therapy, the patient's body temperature gradually returned to normal, and no recurrence was noted during a 7-month follow-up via serial surveillance imaging. This case suggests that, in patients with a history of cardiac surgery who present with unexplained pericardial or mediastinal lesions and non-diagnostic routine cultures and examinations, atypical pathogens such as NTM may warrant consideration within a broad differential diagnosis. It also illustrates the potential value of surgical intervention and mNGS in diagnosing and managing such rare infections.},
}

@article {pmid41585514,
year = {2025},
author = {Wei, C and Chen, Z},
title = {Comprehensive genome analysis uncovers the diversity of jumbo phages in the pig gut microbiome.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1697229},
pmid = {41585514},
issn = {2297-1769},
abstract = {Gut microbiome research has historically focused on bacterial communities. In contrast, the roles of viruses, especially jumbo phages, remain poorly understood. Jumbo phages are of major interest because their large genomes encode unique functions that can influence host metabolism and ecosystem dynamics. This study bridges this gap by identifying 1,545 jumbo phage genomes from 450 pig gut metagenomes. Using CRISPR spacer analysis, we predicted archaeal or bacterial hosts and reconstructed competitive phage networks within this ecosystem. Phylogenetic divergence combined with orthologous protein comparisons supported establishing 14 novel jumbo phage families. Functionally, 10 of these novel families encode auxiliary metabolic genes (AMGs) that enhance host metabolism alongside anti-defense systems including DNA methyltransferases, HNH endonucleases, and glycosyltransferases. Ecological interactions were further elucidated through co-abundance networks (n = 857 pairs) and CRISPR spacer matching (n = 425 pairs), revealing relationships between novel jumbo phages and other jumbo phages. Collectively, this work expands genomic resources for pig gut viromes and delivers new insights into jumbo phages' functional capabilities, host associations, and global prevalence.},
}

@article {pmid41585407,
year = {2025},
author = {Marcatti, R and Franco, LAM and Rocha, EC and Nardi, MS and Summa, JL and da Silva, ETBC and da Rosa, AR and de Oliveira, DC and Graciolli, G and Sabino, EC},
title = {Metagenomics enables the first detection of Trypanosoma sp. in Streblidae (Diptera: Hippoboscoidea) parasitizing bats in São Paulo, Brazil.},
journal = {Frontiers in systems biology},
volume = {5},
number = {},
pages = {1721019},
pmid = {41585407},
issn = {2674-0702},
abstract = {INTRODUCTION: Bats play important ecological roles but can also harbor a wide diversity of pathogens, including trypanosomatids. Knowledge about the circulation of Trypanosoma spp. in bat ectoparasites remains limited, particularly in peri-urban environments.

METHODS: In this study, we used shotgun metagenomic sequencing to investigate the presence of Trypanosoma spp. in streblid flies parasitizing Carollia perspicillata bats collected in a peri-urban fragment of the Atlantic Forest in São Paulo, Brazil. A small, preliminary set of pooled samples was analyzed, followed by phylogenetic reconstruction.

RESULTS: Trypanosoma sequences were detected in flies from the family Streblidae. Phylogenetic analysis showed that these sequences cluster within the Neobat 4 clade, which has previously been reported in Carollia spp. bats. This represents the first detection of Trypanosoma sp. in streblid flies parasitizing bats in São Paulo.

DISCUSSION: Although the vector competence of streblid flies for Trypanosoma transmission is still unknown, their close ecological association with bats suggests that they may serve as a non-invasive tool for pathogen surveillance when direct bat sampling is limited. This study expands the known geographic distribution of the Neobat 4 clade and contributes to understanding parasite circulation among bats and their ectoparasites.},
}

@article {pmid41585377,
year = {2026},
author = {Tollenaar, SL and Khorasaniha, R and Jovel, J and Ba, I and Voisin, A and Miller, R and Olof, H and Mahmood, R and Marrie, RA and Strachan, E and Soares, LP and Cheng, C and Janveaux, J and Zaidi, D and Bernstein, CN and Bonner, C and Bar-Or, A and Waubant, E and Yeh, EA and Graham, M and Arnold, DL and O'Mahony, J and Banwell, BL and Zhu, F and Mirza, AI and Karimi-Abdolrezaee, S and Tsai, S and Tremlett, H and McGregor, K and Willing, BP and Armstrong, H},
title = {Reduced fibre-fermenting capacity of gut microbes in multiple sclerosis may result in prebiotic dietary fibre β-fructan promoting inflammation and CNS damage.},
journal = {eGastroenterology},
volume = {4},
number = {1},
pages = {e100296},
pmid = {41585377},
issn = {2976-7296},
abstract = {BACKGROUND: Some people with multiple sclerosis display changes in their gut microbiota with separate evidence suggesting that symptoms may worsen following a high-fibre diet. We hypothesised that in people with multiple sclerosis whose gut microbiota are less able to efficiently ferment dietary fibres, unfermented β-fructans induce inflammation.

METHODS: Diet data (n=48 individuals with multiple sclerosis, n=78 unaffected controls) and stool microbiome data (n=31 individuals with multiple sclerosis, n=61 unaffected controls) were previously collected from participants. Daily fibre subtype intakes were calculated and compared with faecal shotgun metagenomic sequencing in paediatric onset multiple sclerosis and unaffected persons. Response to unfermented β-fructans was examined in a germ-free experimental autoimmune encephalomyelitis (EAE) mouse model (unable to ferment fibres). Mice were fed β-fructans or control fibre diet beginning at symptom onset (day 14). EAE scores and weights were recorded daily. Intestinal and central nervous system tissues were collected at two endpoints to examine inflammatory responses and demyelinating lesions.

RESULTS: Individuals with paediatric onset multiple sclerosis consumed less β-fructans (2.4 g/day±0.3 SD; p<0.05) than unaffected participants (3.6 g/day±0.4), which coincided with differences in the gut microbiota including lower fibre fermenting enzymes. Mice exposed to unfermented β-fructans sustained worsened EAE symptoms (day 20-28; p<0.05), immune activation in the gut and immune activation plus demyelinating lesions in the spinal cord compared with mice on control diet.

CONCLUSIONS: The gut microbiota of individuals with paediatric-onset multiple sclerosis showed reduced fibre fermenting properties, and our animal findings suggest that unfermented β-fructans can worsen demyelination and promote gut-brain axis immune activation. Lower β-fructan consumption was observed among participants with paediatric-onset multiple sclerosis. Future longitudinal studies are warranted to confirm the findings uncovered in this manuscript.},
}

@article {pmid41585260,
year = {2025},
author = {Gao, Y and Wang, X and Cheng, Y and Ye, S and Dong, X and Zhu, C},
title = {Case Report: NGS-guided rapid diagnosis of tuberculous otitis media-a rare case of dual-site Mycobacterium tuberculosis infection.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1734666},
pmid = {41585260},
issn = {2296-858X},
abstract = {BACKGROUND: Tuberculous otitis media (TOM) is an exceptionally rare form of extrapulmonary tuberculosis that was usually diagnosed only after long-standing ear discharge or profound hearing loss. This case reported a young man in whom deafness was the sentinel event leading to the discovery of pulmonary tuberculosis and molecular confirmation of concurrent TOM.

CASE PRESENTATION: A 23-year-old male presented with bilateral, progressive hearing loss that had been labeled "chronic suppurative otitis media" by local clinics. Persistent constitutional symptoms prompted chest imaging that revealed bilateral cavitary infiltrates. Broncho-alveolar lavage metagenomic next-generation sequencing identified Mycobacterium tuberculosis complex (MTBC). After transfer to our tuberculosis center, targeted NGS of serous middle-ear fluid detected MTBC; the isolate carried an rpsL K43R mutation conferring streptomycin resistance, identical to the pulmonary strain. Standard four-drug anti-tuberculosis therapy was initiated; within 4 weeks, cough and fever resolved, inflammatory markers normalized, and the pulmonary cavity showed reduction in size compared to baseline.

CONCLUSION: This case highlights that unexplained hearing loss may serve as an early indicator of disseminated tuberculosis. High-throughput sequencing of aural discharge enables rapid diagnosis of TOM, facilitates resistance-guided treatment, and helps trace the pathways of pathogen transmission.},
}

@article {pmid41584315,
year = {2026},
author = {Ibrahim, O and Aboushaala, R and Ahmed, N and Savoia, A and Ward, SO and Patel, SN and Lopez, G and Sansom, SE and Williams, B and Singh, K and Al-Harthi, L and Aboushaala, K},
title = {The diagnostic value of metagenomic next-generation sequencing versus traditional microbiological testing in native pyogenic spinal infections: A systematic review and meta-analysis.},
journal = {North American Spine Society journal},
volume = {25},
number = {},
pages = {100840},
pmid = {41584315},
issn = {2666-5484},
abstract = {BACKGROUND: Native pyogenic spinal infections (PSIs), including spondylodiscitis and vertebral osteomyelitis, are challenging to diagnose due to low culture sensitivity and delayed results. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool, but its comparative clinical utility remains uncertain. The purpose of this study is to systematically compare the diagnostic performance and clinical impact of mNGS versus conventional microbial culture in detecting pathogens responsible for native PSIs.

METHODS: The current systematic review and meta-analysis was conducted in accordance with Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A comprehensive literature search was performed across 6 major databases. Eligible studies directly compared mNGS with standard culture for native PSIs and reported diagnostic performance metrics. Data were extracted and analyzed using a random-effects model to produce pooled estimates. Study quality was assessed using the Newcastle-Ottawa Scale. Primary outcomes included pooled sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Secondary outcomes assessed diagnostic yield, time to diagnosis, treatment modification, and false-positive or contamination events.

RESULTS: A total of 1,227 patients from 12 studies were included, encompassing those with suspected or confirmed native PSIs. Pooled sensitivity and specificity of mNGS were 89.7% (95% CI: 85.6-93.1%) and 86.2% (95% CI: 80.5-91.0%), respectively. mNGS demonstrated a significantly higher diagnostic yield (69-90%) compared to culture (27.2-44.7%) and enabled faster diagnosis (range, 17.7-48 hours). mNGS informed antimicrobial selection in up to 70.3% of cases and detected a broader pathogen spectrum. The incidence of false positives was low (range, 1-5) but non-negligible, emphasizing the need for careful interpretation.

CONCLUSIONS: mNGS outperforms conventional culture in sensitivity, speed, and breadth of pathogen detection in native PSIs and supports more tailored antimicrobial therapy. However, careful interpretation is necessary due to potential false positives. These findings support the integration of mNGS into clinical workflows, particularly in complex or culture-negative infections.},
}

@article {pmid41582887,
year = {2026},
author = {Zhang, C and Atashgahi, S and Bosma, TNP and Smidt, H},
title = {Organohalide respiration by a Desulforhopalus-dominated community.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag007},
pmid = {41582887},
issn = {1751-7370},
abstract = {Marine sediments harbour diverse organohalide-respiring bacteria (OHRB), but their functional roles and metabolic interactions remains poorly understood. To investigate these interactions, we obtained and characterized a debrominating consortium from Aarhus Bay marine sediments. The consortium transformed 2,6-dibromophenol (2,6-DBP) to phenol under sulfate-reducing conditions, with bacterial growth demonstrating respiratory energy conservation. Metagenomic analysis and binning revealed five new species-level populations (>85% complete, <3% contaminated) dominated by Desulforhopalus (bin.5). Critically, bin.5 encodes a thiolytic tetrachloro-p-hydroquinone (TPh-) reductive dehalogenase (RDase), previously characterized only in aerobic bacteria, representing evidence of this enzyme functioning in a strictly anaerobic sulfate-reducing bacterium. Two additional populations (Desulfoplanes bin.3 and Marinifilaceae bin.4) encoded two and one putative respiratory corrinoid-dependent RDase, respectively. Transcription of all four RDase genes was rapidly induced upon 2,6-DBP addition, indicating multi-population response. Acetylene inhibited debromination post-transcriptionally without affecting RDase gene transcription, or sulfate metabolism, confirming RDase-mediated catalysis. Genome analysis indicated bin.5 encodes a near-complete vitamin B12 biosynthesis pathway (lacking only cbiJ, which can be bypassed through alternative reductases), consistent with debromination activity independent of exogenous B12 addition. Comparative genomics identified Marinifilum and Ancylomarina as candidate OHRB taxa, substantially expanding known phylogenetic diversity of marine organohalide respirers. This work reveals previously unrecognized biochemical versatility in anaerobic dehalogenation and demonstrates metabolic self-sufficiency enabling organohalide respiration in oligotrophic marine sediments.},
}

@article {pmid41582618,
year = {2026},
author = {Wu, X and Lim, KJ and Ma, Y and Gu, J and Jiang, Y and Zhu, L and Chen, Y and Sun, J},
title = {The Effects of Soy Protein-Rich Meals on Muscle Health of Older Adults Are Linked to Gut Microbiome Modifications.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {1},
pages = {e70212},
pmid = {41582618},
issn = {2190-6009},
mesh = {Humans ; Male ; Female ; Aged ; *Gastrointestinal Microbiome/drug effects ; *Soybean Proteins/administration & dosage/pharmacology ; Aged, 80 and over ; *Muscle, Skeletal/physiology ; *Meals ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; *Sarcopenia/diet therapy ; },
abstract = {BACKGROUND: Sarcopenia is characterized by accelerated muscle mass and function loss in older adults. The role of nutritional interventions in sarcopenia is uncertain. This study investigates whether a soy protein-rich diet can enhance muscle health in older adults via gut microbiota changes.

METHODS: A 12-week randomized controlled trial was conducted with 84 older adults from a long-term care facility. Participants in the intervention group consumed three daily meals containing 10 g of soy protein (totalling 30 g/day), while the control group maintained their usual diets. Faecal samples from 53 participants were collected at Weeks 0, 6 and 12. We assessed changes in muscle function, gut microbiota composition and faecal short-chain fatty acids (SCFA).

RESULTS: The intervention group showed preserved calf circumference, while the control group experienced a decrease (W12-W0: Intervention, 0.56 ± 0.22 cm; Control, -0.91 ± 0.26 cm, p(interaction) < 0.001). Metagenomic analysis revealed significant alterations in gut microbiota among intervention participants who showed improvement in muscle performance parameters. The intervention increased SCFA-producing bacteria (Roseburia faecis, Intervention: 0.42 ± 0.21%, Control: -0.06 ± 0.16, p(interaction) < 0.05; Agathobaculum butyriciproducens, Intervention: 0.02 ± 0.007%, p(time) < 0.01, Control: -0.04 ± 0.01) and decreased species associated with poorer muscle outcomes (Alistipes putredinis, Intervention: -0.88 ± 0.40%, Control: 0.62 ± 0.63, p(interaction) < 0.05; Eubacterium_sp_CAG_38, Intervention: -0.64 ± 0.28%, Control: 0.10 ± 0.22, p(interaction) < 0.05). Functional pathway analysis showed enrichment of anaerobic amino acid degradation pathways and vitamin biosynthesis, with depletion of inflammatory pathways, particularly lipopolysaccharide biosynthesis. Microbiome phenotype prediction revealed a decrease in aerobic bacteria abundance in the intervention group (W12-W0, Intervention: -0.004 ± 0.002; Control: 0.001 ± 0.001, p(interaction) < 0.05). Interaction (group × time) for SCFA was not statistically significant; within-group increases at Week 6 were observed in only the intervention group (butyric acid, Intervention: 0.74 ± 0.34 mg/g, p(time) < 0.05, Control: 0.12 ± 0.43 mg/g; isobutyric acid, Intervention: 0.14 ± 0.08 mg/g, p(time) < 0.05, Control: 0.08 ± 0.10 mg/g; isovaleric acid, Intervention: 0.27 ± 0.14 mg/g, p(time) < 0.05; Control: 0.16 ± 0.20 mg/g), with partial reversal by Week 12. These changes, positively correlated with improved muscle function parameters, suggest intervention benefits on gut health and muscle function.

CONCLUSION: A soy protein-rich intervention improved muscle health in older adults through beneficial gut microbiota. These findings support the gut-muscle axis hypothesis and suggest dietary soy protein may alleviate sarcopenia by promoting a healthier gut microbiome.},
}

Humans
Male
Female
Aged
*Gastrointestinal Microbiome/drug effects
*Soybean Proteins/administration & dosage/pharmacology
Aged, 80 and over
*Muscle, Skeletal/physiology
*Meals
Feces/microbiology
Fatty Acids, Volatile/metabolism
*Sarcopenia/diet therapy

@article {pmid41582602,
year = {2026},
author = {Hernani, R and Albert, E and Hernani-Morales, C and Zúñiga, S and Benzaquén, A and González-Castillo, L and Colomer, E and Morell, J and Català-Senent, JF and Piñana, JL and Giménez, E and Pérez, A and Hernández-Boluda, JC and Arroyo, I and Rivada, M and Barber, T and Alemany, T and Santacatalina, E and Rentero-Garrido, P and Terol, MJ and Díaz, R and Navarro, D and Solano, C},
title = {Microbiome-Based Modeling of CAR-T Therapy Response in Lymphoma: Insights From Shotgun Metagenomics Sequencing.},
journal = {European journal of haematology},
volume = {},
number = {},
pages = {},
doi = {10.1111/ejh.70121},
pmid = {41582602},
issn = {1600-0609},
support = {//Fundación FERO and the Fundación para la Promoción de Acciones Solidarias/ ; //European Union through the Operational Program of the European Regional Development Fund/ ; CA23/00007//bioinformatics technician/ ; //2023 Strategic Action in Health/ ; //Instituto de Salud Carlos III/ ; //European Union/ ; },
abstract = {The interplay between the commensal microbiota and the mammalian immune system may influence the outcomes of T cell-driven cancer immunotherapies. However, clinical studies supporting microbiota-based interventions in chimeric antigen receptor T-cell (CAR-T) therapy remain scarce. This study included 30 adult patients with B-cell lymphoma treated with axicabtagene ciloleucel (axi-cel) or 4-1BB investigational product. Shotgun metagenomics sequencing (SMS) of fecal samples, collected before lymphodepletion and 1 month post infusion, enabled species-level resolution. We also trained 25 microbiome-based machine-learning (ML) models for response prediction. Neither prior "high-risk" antibiotics exposure nor alpha diversity influenced toxicity, response, or survival. However, dysbiosis was observed between 11 healthy controls and patients, particularly in those treated with axi-cel. SMS identified species associated with clinical outcomes. Increased abundance of Alistipes senegalensis and Alistipes onderdonkii correlated with lower neurotoxicity and improved survival, respectively. Bifidobacterium longum was associated with reduced cytokine release syndrome, whereas Bifidobacterium adolescentis, Bifidobacterium bifidum, and Bifidobacterium breve correlated with poorer survival. ML models demonstrated strong predictive performance, with some identifying non-responders using only six species selected by the Boruta method (Bacteroides xylanisolvens, Bifidobacterium bifidum, Bifidobacterium breve, Eubacteriaceae bacterium Marseille-Q4139, Negativibacillus massiliensis, and Sellimonas intestinalis). These findings deepen current knowledge and support prospective microbiota-based strategies in CAR-T therapy.},
}

@article {pmid41582543,
year = {2026},
author = {Tang, ZH and Lin, ZN and Li, JX and Liu, FC and Cao, J and Chen, SF and Huang, KY and Li, HF and Hu, DS and Huang, JF and Gu, DF and Lu, XF},
title = {Plasma Metabolites Mediate the Associations of Gut Microbial Diversity with Ambulatory Blood Pressure and Its Variability.},
journal = {Biomedical and environmental sciences : BES},
volume = {39},
number = {1},
pages = {26-35},
doi = {10.3967/bes2025.089},
pmid = {41582543},
issn = {2214-0190},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Blood Pressure ; *Hypertension/microbiology ; Prospective Studies ; Aged ; Blood Pressure Monitoring, Ambulatory ; China ; Adult ; },
abstract = {OBJECTIVE: Evidence suggests that depleted gut microbial α-diversity is associated with hypertension; however, whether metabolic markers affect this relationship remains unknown. We aimed to determine the potential metabolites mediating the associations of α-diversity with blood pressure (BP) and BP variability (BPV).

METHODS: Metagenomics and plasma targeted metabolomics were conducted on 523 Chinese participants from the MetaSalt study. The 24-hour, daytime, and nighttime BP and BPV were calculated based on ambulatory BP measurements. Linear mixed models were used to characterize the relationships between α-diversity (Shannon and Chao1 index) and BP indices. Mediation analyses were performed to assess the contribution of metabolites to the observed associations. The influence of key metabolites on hypertension was further evaluated in a prospective cohort of 2,169 participants.

RESULTS: Gut microbial richness (Chao1) was negatively associated with 24-hour systolic BP, daytime systolic BP, daytime diastolic BP, 24-hour systolic BPV, and nighttime systolic BPV (P < 0.05). Moreover, 26 metabolites were strongly associated with richness (Bonferroni P < 0.05). Among them, four key metabolites (imidazole propionate, 2-hydroxy-3-methylbutyric acid, homovanillic acid, and hydrocinnamic acid) mediated the associations between richness and BP indices (proportions of mediating effects: 14.1%-67.4%). These key metabolites were also associated with hypertension in the prospective cohort. For example, each 1-standard deviation unit increase in hydrocinnamic acid significantly reduced the risk of prevalent (OR [95% CI] = 0.90 [0.82, 0.99]; P = 0.03) and incident hypertension (HR [95% CI] = 0.83 [0.71, 0.96]; P = 0.01).

CONCLUSION: Our results suggest that gut microbial richness correlates with lower BP and BPV, and that certain metabolites mediate these associations. These findings provide novel insights into the pathogenesis and prevention of hypertension.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
Middle Aged
*Blood Pressure
*Hypertension/microbiology
Prospective Studies
Aged
Blood Pressure Monitoring, Ambulatory
China
Adult

@article {pmid41582242,
year = {2026},
author = {Chethan, D and Kavya, BS and Arati, and Chandana, R and Gowtham, HP and Ashika, S and Chanchala, S and Nagaraju, N and Reddy, CNL and Kunjeti, SG and Ningaraju, TM},
title = {Endophyte profiling of tomato leaf curl virus (ToLCV) resistant and susceptible tomato genotypes: Insights into microbial diversity and growth promotion.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37677-7},
pmid = {41582242},
issn = {2045-2322},
abstract = {Tomato (Solanum lycopersicum L.) is one of the most widely cultivated vegetable crops globally. Still, its productivity is significantly constrained by tomato leaf curl virus (ToLCV), a devastating begomovirus transmitted by whiteflies. This study examined the diversity and plant growth-promoting potential of culturable endophytes associated with tomato cultivars differing in resistance to tomato leaf curl virus (ToLCV). A total of 59 fungal and bacterial endophytes were isolated. Resistant cultivars (Nandi, Sankranthi, and Vybhav) harboured more diverse and compositionally distinct communities than the susceptible cultivar Arka Vikas, as indicated by Shannon, Simpson, and Chao-1 indices and multivariate analyses. Several isolates, particularly from the genera Xylaria, Fusarium, Arcopilus, Epicoccum, Bacillus, Pseudomonas, Stutzerimonas, and Paenibacillus, displayed strong nutrient-solubilizing traits in vitro, highlighting their potential as plant growth-promoting candidates. Eleven promising isolates were further evaluated on the susceptible cultivar Arka Vikas. At 30 days after sowing, Epicoccum nigrum and Bacillus subtilis significantly increased seedling height, biomass, and leaf number relative to the control. Overall, the study reveals that resistant cultivars are associated with greater culturable endophyte diversity and identifies several isolates with strong potential for promoting plant growth. Future research should assess the antiviral potential of these endophytes under ToLCV challenge and employ metagenomic studies to elucidate their functional roles in enhancing plant health.},
}

@article {pmid41582156,
year = {2026},
author = {Shi, LD and Ercoli, MF and Kim, J and de Araujo Junior, AT and Estera-Molina, K and Soni, S and Weitz, TS and Shigenaga, AM and Dukovski, I and Sachdeva, R and Turumtay, H and Louie, KB and Bowen, BP and Kosina, SM and Scheller, HV and Pett-Ridge, J and Segrè, D and Northen, TR and Ronald, PC and Banfield, JF},
title = {Reduced methane emissions in transgenic rice genotypes are associated with altered rhizosphere microbial hydrogen cycling.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68640-9},
pmid = {41582156},
issn = {2041-1723},
support = {INV-037174/GATES/Gates Foundation/United States ; },
abstract = {Rice paddies significantly contribute to atmospheric methane (CH4). Here, we show that two independent rice genotypes overexpressing genes for PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY) reduce cumulative CH4 emissions by 38% (PSY1) and 58% (PSY2) over 70 days of growth compared with controls. Genome-resolved metatranscriptomic data from PSY rhizosphere soils reveal lower ratios of gene activities for (mostly hydrogenotrophic) CH4 production versus consumption, decreased activity of H2-producing genes, and increased activity of bacterial H2 oxidation pathways. Metabolic modeling using metagenomic and metabolomic data predicts elevated H2 oxidation and suppressed H2 production in the PSY rhizosphere. Assembled genomes of rhizosphere H2-oxidizing bacteria are enriched in genes utilizing gluconeogenic acids compared with H2-producing counterparts, and their activities are likely stimulated by elevated levels of gluconeogenic acids, primarily amino acids, in PSY root exudates. Overall, our study indicates that decreased CH4 emissions are due to a lower amount of H2 available for hydrogenotrophic methanogenesis and provides a powerful strategy to mitigate CH4 emissions from increasingly widespread rice cultivation.},
}

@article {pmid41581932,
year = {2026},
author = {Selvaraj, C and Desai, D and Santos-Villalobos, SL and Jayaprakashvel, M and Muthezhilan, R and Singh, SK},
title = {Marine-derived antimicrobial peptides (AMPs): Blue biotechnological assets for sustainable healthcare and circular bioeconomy.},
journal = {Advances in protein chemistry and structural biology},
volume = {149},
number = {},
pages = {171-201},
doi = {10.1016/bs.apcsb.2025.08.002},
pmid = {41581932},
issn = {1876-1631},
mesh = {*Biotechnology/economics ; *Antimicrobial Peptides/chemistry/pharmacology ; *Aquatic Organisms/chemistry ; Humans ; Animals ; Delivery of Health Care/economics ; *Anti-Bacterial Agents/pharmacology/chemistry ; },
abstract = {The global antimicrobial resistance (AMR) crisis drives the demand for novel therapeutics, positioning marine-derived antimicrobial peptides (AMPs) as sustainable alternatives with unique structural and functional advantages. These cationic, amphipathic molecules, from the source of diverse marine organisms, such as invertebrates, extremophiles, and cyanobacteria, exhibit broad-spectrum activity against drug-resistant pathogens through mechanisms like membrane disruption and immunomodulation. Their low resistance propensity and multifunctional bioactivity (eg., antioxidant, antimicrobial, anticancer) underscore therapeutic potential beyond the conventional antibiotics. Advances in genomic and metagenomic tools, machine learning, and synthetic biology are revolutionizing AMP discovery, enabling targeted mining of marine biodiversity and peptide optimization for enhanced stability and specificity. Biotechnological innovations support scalable production through heterologous expression and marine biomass valorization, which aligns with the principles of the circular economy. Marine-sourced AMPs demonstrate transformative applications across various healthcare, aquaculture, food safety, and environmental remediation, that majorly reduce the dependence on synthetic chemicals. Their integration into blue bioeconomy frameworks is promoting sustainable bio-prospects, marine ecosystem conservation, and progress towards the United Nations Sustainable Development Goals. This review narrates the collective research and also addresses the critical challenges, including production scalability and regulatory frameworks, to outline a clear pathway for the marine sourced AMP commercialization. By bridging the antimicrobial innovation with circular biotechnology, marine-sourced AMPs are exemplifying the ocean's role as a reservoir of sustainable solutions for global health and bioeconomic resilience.},
}

*Biotechnology/economics
*Antimicrobial Peptides/chemistry/pharmacology
*Aquatic Organisms/chemistry
Humans
Animals
Delivery of Health Care/economics
*Anti-Bacterial Agents/pharmacology/chemistry

@article {pmid41581489,
year = {2026},
author = {Liu, Z and Zhao, F and Li, Q and Shang, Q and Fang, D and Li, X and Li, H and He, Q and Zhang, D and Cheng, J and Zhu, Y and Li, Z and Silva, AS and Chen, J},
title = {Multi-omics chemical and biochemical profiling reveals ellagic acid enhances insulin sensitivity via gut microbiota-tryptophan-indole signaling mechanism.},
journal = {Food chemistry},
volume = {505},
number = {},
pages = {147984},
doi = {10.1016/j.foodchem.2026.147984},
pmid = {41581489},
issn = {1873-7072},
abstract = {Ellagic acid (EA) is a dietary polyphenol with limited systemic bioavailability, resulting in substantial intestinal exposure. However, the biochemical mechanisms by which EA modulates gut microbiota and metabolism remain unclear. Here, EA improved glucose tolerance and enhanced insulin sensitivity, with histology confirming reduced lipid accumulation and restored tissue architecture in liver, skeletal muscle, brown adipose tissue, and mesenteric fat. Consistently, metagenomic analysis showed that EA enriched Akkermansia muciniphila, Muribaculum intestinale, and Duncaniella dubosii, while reducing Lachnoclostridium phocaeense. These microbial shifts were accompanied by elevated levels of tryptophan-derived metabolites-indole-3-propionic acid, indole, and indole-3-acrylic acid-known to enhance insulin sensitivity. Lipidomics revealed EA decreased triacylglycerols and ceramides, along with restored phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine levels. Transcriptomics revealed EA suppressed hepatic lipogenesis, inhibited MAPK signaling in skeletal muscle, activated thermogenic and oxidative phosphorylation in adipose tissues. Our findings highlight EA, a food-derived polyphenol, might alleviate insulin resistance through a gut microbiota-indole metabolite-multi-tissue axis.},
}

@article {pmid41581464,
year = {2026},
author = {Trinh, HP and Lee, SH and Park, HD},
title = {Nitrogen loading fluctuations impact microbial community assembly and functional redundancy in anammox reactors.},
journal = {Water research},
volume = {293},
number = {},
pages = {125434},
doi = {10.1016/j.watres.2026.125434},
pmid = {41581464},
issn = {1879-2448},
abstract = {Nitrogen loading rate (NLR) fluctuations are common in full-scale anammox systems and can compromise process stability, yet the ecological mechanisms underlying system resilience under disturbed conditions remain insufficiently understood. This study investigated how different intensities of NLR disturbances influence microbial community assembly processes and functional redundancy, and how these ecological responses shape nitrogen removal performance. Two anammox sequencing batch reactors were operated for 180 days under either stable (R1) or fluctuating (R2) NLR conditions. Moderate NLR fluctuations (1.4-fold, Phase A) enhanced nitrogen removal efficiency (up to 99.7%) and increased the relative abundance of anammox bacteria to 26.4%, whereas severe fluctuations (2.0-fold, Phase B) caused deterioration in nitrogen removal efficiency (to 72.2%) and a decline in anammox bacteria abundance (7.1%). Metagenome-assembled genome analysis revealed pathway-level reorganization of nitrogen metabolism under fluctuating conditions, with increases in anammox-associated genes (hzsABC and hdh/hao-like) and the DNRA gene (nrfAH) during Phase A, followed by partial declines in Phase B. Neutral community modeling showed that stochastic processes dominated microbial assembly under moderate fluctuations (R[2] = 0.77), promoting coexistence and community adaptability, while deterministic selection prevailed under severe fluctuations (R[2] = 0.56). Functional redundancy exhibited a similar non-linear response, increasing under moderate disturbance (0.73) and declining sharply under severe disturbance (0.48), indicating reduced buffering capacity. These findings provide quantitative insight into the mechanistic link between loading disturbances and ecosystem resilience, offering a foundation for developing operational strategies that enhance the robustness of anammox-based nitrogen removal systems.},
}

@article {pmid41581442,
year = {2026},
author = {Chen, Y and Huang, S and Zhang, S and Wang, H and Song, X and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Yang, H and Shan, T and Wang, X and Zhang, W},
title = {Viral metagenomics reveals the RNA viral composition of herbivorous wildlife on the Qinghai-Tibet Plateau.},
journal = {Virology},
volume = {617},
number = {},
pages = {110814},
doi = {10.1016/j.virol.2026.110814},
pmid = {41581442},
issn = {1096-0341},
abstract = {RNA viruses, a widely distributed group of pathogens in nature, possess exceptionally high genetic diversity and rapid evolutionary potential. High-altitude ecosystems, represented by the Qinghai-Tibet Plateau, with their unique environmental conditions, may harbor distinct viral communities. However, there remains a lack of systematic understanding regarding the composition and distribution of RNA viruses in wildlife under such extreme environments. In this study, a total of 741 fecal samples were collected from three regions on the Qinghai-Tibet Plateau, and viral metagenomics technology was used to reveal the composition and diversity of RNA viruses in the fecal samples of six species of herbivorous wild animals on the plateau. We identified a substantial abundance of RNA viruses, classified into 18 distinct viral families. Furthermore, the structure of the viral communities varied among different host species. Through assembly, 28 viral sequences belonging to the families Astroviridae, Picornaviridae, Picobirnaviridae, Tobaniviridae, and Caliciviridae were identified. Phylogenetic analysis revealed that the newly identified viral strains share close relationships with viruses found in humans, marmots, and other mammals. The results indicate that wildlife in this region are reservoirs of unidentified RNA viruses, some of which may pose potential threats to public health and the animal husbandry. These findings provide crucial scientific evidence and data support for future virus surveillance, ecological risk assessment, and the prevention and control of emerging infectious diseases at their source.},
}

@article {pmid41581397,
year = {2026},
author = {Fan, Y and Wang, Y and Liu, D and Yao, Y and Liu, J and Zhao, J and Dong, L and Wang, C and Liu, W},
title = {Exposure evidence and transmission characteristics of biological aerosols in a high-rise building.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141221},
doi = {10.1016/j.jhazmat.2026.141221},
pmid = {41581397},
issn = {1873-3336},
abstract = {Indoor bioaerosols originating from residential drainage systems have the potential to migrate into living spaces, possibly posing a respiratory concern. By coupling the technology of metagenomic shotgun sequencing with fluorescein tracers, the residents living on the same drainage riser of a 17-story residence and their associated sewage wells were studied to analyse the microbial spectrum of indoor bioaerosols and the spatiotemporal distribution characteristics of their lateral and longitudinal propagation. The air samples collected from these apartments and the sewage samples collected from corresponding sewage wells revealed that the relative abundances of P. aeruginosa and A. baumannii of the bacterial community in the air reached 30% and 10 % respectively. Moreover, the fecal indicator bacterium S. enterica could be detected, confirming the presence of the "fecal-water-air"" chain. Tracer experiments further revealed that a breach in water seals allowed aerosols of less than 0.5 µm cross-floor to diffuse over three layers within 19 min through the stack effect, with upwards deposition 2.5-3.1 times greater than downwards deposition. Even though the water seals remained intact, a single toilet flush could horizontally spread 0.3 µm biological aerosols into adjacent rooms within 6 min. In summary, the contribution of the drainage system to indoor bioaerosols was confirmed for the first time in both genetic sequencing and aerosol transport dimensions, providing a reference basis for the biosafety design of high-rise residential buildings.},
}