@article {pmid41843710,
year = {2026},
author = {Qian, C and Jeunen, GJ and Han, W and Chan, TY and Jiang, Y and Fu, W and Seymour, M},
title = {Developing and Evaluating Aquatic Passive Sampling of Environmental DNA for Microbial Community Profiling.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70121},
pmid = {41843710},
issn = {1755-0998},
support = {MCEF21003//Marine Conservation Enhancement Fund/ ; },
mesh = {*DNA, Environmental/isolation & purification/genetics ; Biodiversity ; *Specimen Handling/methods ; Bacteria/genetics/classification ; *Microbiota ; *Metagenomics/methods ; Phylogeny ; },
abstract = {Environmental DNA (eDNA) metabarcoding has transformed biodiversity monitoring across taxa from bacteria to mammals, yet sample collection remains a major bottleneck. Passive sampling via adsorption and entrapment has emerged as a promising alternative to overcome the limitations of conventional active filtration. However, the performance of passive sampling for microbial biodiversity monitoring remains unknown. Here, we developed passive sampling-based microbial community profiling by testing five submersion times and three common eDNA extraction methods in mesocosms, and comprehensively evaluated it by comparing results with active filtration in estuarine and coastal environments. We found that passive sampling for 24 h with enzymatic extraction yielded significantly more eDNA and higher biodiversity than shorter durations and mechanical extractions. Passive sampling consistently outperformed active filtration at every field site, with average increases of >100% in eDNA yields and >50% in taxonomic and phylogenetic diversities. Additionally, active filtration and passive sampling yielded significantly different prokaryotic and microeukaryotic community compositions, driven primarily by turnover rather than nestedness (on average 4-fold larger), implying that passive sampling is better suited for spatiotemporal detection than active filtration. Passive sampling showed greater sensitivity in identifying key environmental factors (3 vs. 2) and potential environmental bioindicators (40 vs. 20) compared with active filtration. Overall, this study establishes an efficient and practical passive sampling method for microbial biodiversity monitoring and environmental assessment in aquatic environments.},
}

*DNA, Environmental/isolation & purification/genetics
Biodiversity
*Specimen Handling/methods
Bacteria/genetics/classification
*Microbiota
*Metagenomics/methods
Phylogeny

@article {pmid41843957,
year = {2026},
author = {Zhu, L and Huang, C and Tian, Y and Zuo, W and Shan, G},
title = {Targeted enhancement of ammonia assimilation and microbial community metabolic synergy in chicken manure aerobic composting mediated by tricarboxylic acid cycle modulators.},
journal = {Waste management (New York, N.Y.)},
volume = {216},
number = {},
pages = {115471},
doi = {10.1016/j.wasman.2026.115471},
pmid = {41843957},
issn = {1879-2456},
abstract = {Reducing nitrogen loss during composting is essential. To investigate the effects of directly modulating the tricarboxylic acid (TCA) cycle on microbial ammonia assimilation during composting, this study employed paired stable isotope labeling combined with metagenomic analysis to assess the role of the TCA cycle regulator citric acid (CA) in enhancing ammonia assimilation efficiency and regulating carbon-nitrogen metabolism within the microbial community. CA markedly reduced NH3 emissions (0.5-2265 ppm) and increased organic nitrogen retention (4.2%-17.7%), primarily through improved ammonia assimilation efficiency (0.06-0.22 mg N·kg[-1]·d[-1]) rather than weakened mineralization. Mechanistically, CA upregulated IDH1 (5.4%-18.5%) and increased IDH enzyme activity (0.35-0.66 IU/g), combined with NH3 uptake, balancing oxoglutarate and ammonium supply. Moreover, CA strengthened the glutamine synthetase-glutamate synthase (GS-GOGAT) pathway (3.4%-23.4%) and enzyme activity (0.08-0.74 IU/g), particularly in the initial and thermophilic phases. In addition, CA induced an upregulation (14.8%-28.4%) of genes encoding succinyl-CoA synthetase, providing sufficient energy to support the ammonia assimilation process. Furthermore, CA enhanced microbial diversity and metabolic cooperation while reducing competition, thereby promoting NH3 assimilation and glutamate synthesis. Inorganic and amino acid metabolism emerged as critical cooperative processes within core microbial populations.},
}

@article {pmid41844593,
year = {2026},
author = {Ni, N and Ding, Q and Zhang, T and Liu, C and Guo, X and Zhu, C and Wang, Q and Zhu, D and Wang, N and Luo, Y},
title = {Fragmented Microplastics Synergize with Biological Treatment To Potentiate Antibiotic Resistance Dissemination during Sewage Treatment.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c18221},
pmid = {41844593},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) are important reservoirs for antibiotic resistance genes (ARGs) and microplastics (MPs), and serve as hotspots for antibiotic resistance spread. However, actual survey data on their combined pollution along the entire sewage treatment chain remain scarce. This study integrated metagenomic sequencing and high-throughput qPCR to analyze the correlation between ARGs and MPs. The results revealed that clinically relevant and rank I high-risk intracellular antibiotic resistance genes (iARGs) were significantly enriched in the plastisphere throughout the sewage treatment process, particularly on fragmented MPs. FEAST source-tracking analysis revealed that MP-bound iARGs and extracellular ARGs in the biologically treated sewage contributed to 13-43 and 25-39% of the corresponding iARGs and eARGs detected in the effluent, respectively. Fragmented MPs also colocalized ARGs, virulence factors, and mobile genetic elements, potentially facilitating plasmid-mediated gene transfer. Acinetobacter, the primary ARG host and detected across 75 WWTPs with high ARG load, may serve as an antibiotic resistance indicator. This study highlights MP-driven ARG dissemination in WWTPs and informs resistance control strategies.},
}

@article {pmid41844673,
year = {2026},
author = {Singh, NK and Garg, P and Kumari, S and Banda, L and Patel, AM and Sindhuja, RH and Bhandari, Y and Khan, NA and Tandon, S and Jain, R and Rajesh, T and Qureshi, A and Vodapalli, A and Singha, B and Esari, D and Annan, MO and Nagabandi, T and Panda, A and Kapley, A and Nandicoori, VK and Mishra, RK and Sowpati, DT and Siva, AB and Tallapaka, KB},
title = {Metagenomic profiling of antimicrobial resistance in wastewater from metropolitan cities of India.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70702-x},
pmid = {41844673},
issn = {2041-1723},
support = {2021 HTH 018//Rockefeller Foundation/ ; },
abstract = {Wastewater-based surveillance has emerged as a powerful tool for monitoring microbial diversity, antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). In this study, wastewater samples collected from March 2022 to March 2024 from 19 locations in four metropolitan cities of India were profiled using shotgun metagenomics. Taxonomic abundance and beta diversity analyses revealed significant differences in microbial community compositions, with city-specific clustering; suggesting distinct local environmental influences. However, such distinct clusters were not evident with the ARGs. A high proportion of potentially novel metagenome-assembled genomes (MAGs) (53-70%) were identified on reconstructing the microbial genomes from the metagenomic data. ARGs conferring resistance to antibiotics such as tetracyclines and beta-lactams showed higher association with MGEs in contrast to macrolide resistance genes. Microbial co-occurrence network analysis revealed a city-specific structure and higher contribution of ARGs from specific communities of microbes. These findings underscore the complex interplay between microbial diversity, ARG dissemination, and MGEs in wastewater environments, emphasizing the need for continued surveillance, for designing appropriate mitigation strategies towards curbing the spread of antimicrobial resistance.},
}

@article {pmid41845022,
year = {2026},
author = {Selvatici, S and Jin, C and Zazula, G and Hall, E and Hewitson, S and Moots, HM and Sharif, B and Ersmark, E and Parducci, L and Dalén, L and Díez-Del-Molino, D and Oteo-García, G},
title = {Genomic identification and complete mitochondrial recovery of a Late Holocene porcupine (Erethizon dorsatum) mummy from Yukon permafrost.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41845022},
issn = {2045-2322},
mesh = {*Porcupines/genetics ; Animals ; *Genome, Mitochondrial ; Permafrost ; *Mummies ; Canada ; Fossils ; DNA, Mitochondrial/genetics ; Phylogeny ; Genomics/methods ; *Mitochondria/genetics ; },
abstract = {We identified a 3000-year-old specimen from the Traditional Territory of the Tr'ondëk Hwëch'in in central Yukon Territory, Canada as the first known mummified remains of an ancient North American porcupine (Erethizon dorsatum), known as "Ts'ey" in the Hän language, using genetic analysis and metagenomic validation. Our analysis of the sample yielded the first-ever complete ancient mitochondrial genome for (E. dorsatum) and only the second full mitogenome for the species. Its Holocene age is considerably younger than the Pleistocene megafauna typically recovered in the Yukon permafrost, demonstrating the potential for these deposits to preserve specimens from interglacial periods. Crucially, this finding confirms the presence of porcupines in the region 3000 years ago, in line with the hypothesis that this species only dispersed into Yukon and Alaska following the establishment of boreal forests after the Last Glacial Period.},
}

*Porcupines/genetics
Animals
*Genome, Mitochondrial
Permafrost
*Mummies
Canada
Fossils
DNA, Mitochondrial/genetics
Phylogeny
Genomics/methods
*Mitochondria/genetics

@article {pmid41845390,
year = {2026},
author = {Sung, H and Hyun, DW and Whon, TW and Kim, PS and Kim, HS and Lee, JY and Lee, SY and Choi, JW and Yoo, JH and Jung, MJ and Yun, JH and Lee, JY and Tak, EJ and Jeong, YS and Kim, SW and Baeg, M and Eun, YG and Lee, YC and Bae, JW},
title = {Unraveling the diagnostic and prognostic signatures of oral microbiota in head and neck cancer.},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-026-02573-z},
pmid = {41845390},
issn = {1741-7007},
support = {RS-2020-NR049315//National Research Foundation of Korea/ ; 22213MFDS537//Ministry of Food and Drug Safety/ ; },
abstract = {BACKGROUND: Head and neck cancer, predominantly squamous cell carcinoma, has emerged as a significant global health concern. Growing evidence has established a strong association between dysbiosis of the oral microbiota and both oral and systemic diseases. However, the association between the oral microbiota and head and neck cancer has not yet been fully described. This study aimed to investigate the distinct profiles of the oral microbiota in patients with head and neck cancer and their potential as diagnostic and prognostic biomarkers for head and neck cancer.

RESULTS: Comparative analyses revealed that compared to controls, the oral microbiota of patients with head and neck squamous cell carcinoma (HNSCC) exhibited an increased abundance of anaerobic, biofilm-forming bacteria, and potential pathogens. A machine learning model successfully differentiated HNSCC patients from controls with an area under the curve of 0.902. Key features of this model, such as Peptostreptococcus and Capnocytophaga, were found to be candidate biomarkers for HNSCC, with certain taxa, such as Abiotrophia, serving as prognostic indicators. Although pronounced differences in oral microbiota among HNSCC patients primarily resulted from inter-individual variations, distinct community types were identified, with the type dominated by Proteobacteria being associated with the lowest probability of survival.

CONCLUSIONS: Our findings indicate that the oral microbiota may predict HNSCC and may act as a therapeutic target to improve the prognosis of HNSCC. This investigation underscores the crucial role of oral microbial dysbiosis in the etiopathogenesis and clinical prognosis of HNSCC, making a case for further integrative metagenomic and clinical research.},
}

@article {pmid41845399,
year = {2026},
author = {Luo, J and Guo, W and Zou, S and Tan, Y and Liu, J and Song, S and Yang, H and Liang, K},
title = {Case report: thoracic syphilitic gumma masquerading as a malignant tumor in a patient with AIDS.},
journal = {AIDS research and therapy},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12981-026-00868-3},
pmid = {41845399},
issn = {1742-6405},
support = {2020-PT320-004//The Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; },
abstract = {Syphilis, a systemic infection caused by Treponema pallidum, can present with atypical and severe manifestations in people living with the human immunodeficiency virus (HIV), posing significant diagnostic challenges. We report the case of a patient with acquired immunodeficiency syndrome (AIDS) who presented with a chest wall mass. Imaging findings were initially suggestive of a malignancy. However, subsequent evaluation, guided by positive serum syphilis antibodies despite non-specific inflammatory changes on histology and a negative metagenomic next-generation sequencing (mNGS) result, led to the diagnosis of a syphilitic gumma, which was confirmed by immunohistochemical staining. The lesion entirely resolved following penicillin therapy. This case highlights a critical clinical insight: syphilis must be considered in the differential diagnosis of mass lesions in immunocompromised hosts, and immunohistochemical staining is imperative for definitive diagnosis.},
}

@article {pmid41845494,
year = {2026},
author = {Huang, Q and Du, D and Guo, J and Liu, J and Sun, P},
title = {Heat stress suppresses lactation through potential rumen-mammary communication mediated by extracellular vesicles: integrated analysis of microbiome, metabolome, and miRNA profiles.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02363-3},
pmid = {41845494},
issn = {2049-2618},
support = {2022YFD1301101//National Key Research and Development Program of China/ ; CARS-37//Earmarked Fund for China Agriculture Research System/ ; Y2025YC52//Central Public-interest Scientific Institution Basal Research Fund/ ; ASTIP-IAS07//Agricultural Science and Technology Innovation Program/ ; },
abstract = {BACKGROUND: Heat stress (HS) imposes significant physiological and economic challenges to dairy production, yet the integrative mechanisms linking rumen microbial dysbiosis, host metabolic disruption, and lactation suppression remain not yet fully understood. Emerging evidence suggests that extracellular vesicles (EVs) and their cargo, particularly microRNAs (miRNAs), may participate in systemic inter-organ communication under stress. This study aimed to elucidate how HS suppresses lactation through potential rumen-mammary communication mediated by EVs, using a comprehensive multi-omics approach.

RESULTS: Dairy cows exposed to HS exhibited elevated rectal temperatures and respiratory rates, accompanied by significant reductions in the yield of milk, milk fat and protein. Rumen fermentation was markedly impaired, with decreased pH, butyrate, and valerate proportions, and systemic inflammation was evidenced by increased pro-inflammatory cytokines and barrier dysfunction. Metagenomic profiling revealed that HS reshaped the rumen microbiome, significantly reducing the relative abundances of Prevotella, Bifidobacterium, and Lactobacillus species while enriching methanogenic and low-efficiency fermentative taxa. Functionally, HS enhanced microbial methane metabolism and suppressed carbohydrate degradation pathways, reducing the host's energy supply for milk synthesis. Metabolomic analyses supported this shift, with distinct metabolites significantly correlated with lactation performance. Notably, extracellular vesicle (EV)-derived miRNAs from both plasma and milk showed significant expression changes under HS conditions, predominantly targeting signaling pathways related to stress and immune responses, hormone regulation, and mammary gland development and function.

CONCLUSIONS: This study demonstrates that HS suppresses lactation through multi-level alterations in the rumen microbiome, metabolic homeostasis, and EV-derived miRNA signaling, collectively supporting the existence of a potential rumen-mammary communication axis. These findings offer novel insights into the pathogenesis of HS responses.},
}

@article {pmid41845521,
year = {2026},
author = {Hoepfner, C and Moreno-Perlin, T and Pérez-Llano, Y and Cardona, K and Rivera, DS and Minter, D and Guzmán, D and Batista-García, RA},
title = {Microbial diversity, metabolic specialization, and genomic novelty across polyextreme saline lakes of the Central Dry Andes.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00868-w},
pmid = {41845521},
issn = {2524-6372},
support = {ATE240004//Agencia Nacional de Investigación y Desarrollo/ ; ATE240004//Agencia Nacional de Investigación y Desarrollo/ ; ATE240004//Agencia Nacional de Investigación y Desarrollo/ ; ATE240004//Agencia Nacional de Investigación y Desarrollo/ ; PT09CB001//Swedish International Development Cooperation Agency/ ; PT09CB001//Swedish International Development Cooperation Agency/ ; Grant 31-001//Darwin Initiative/ ; Grant 31-001//Darwin Initiative/ ; Grant 31-001//Darwin Initiative/ ; Grant 31-001//Darwin Initiative/ ; Postdoctoral fellowship grant//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; },
abstract = {The high-altitude saline lakes of the Central Dry Andes are polyextreme environments characterized by hypersalinity, high alkalinity, fluctuating redox conditions, and elevated levels of trace metals (e.g., Li, As, Mn, Mg). These conditions challenge microbial life yet select for highly specialized and functionally versatile communities. Through metagenomic analyses across four lakes (Colorada, Hedionda, Mama Khumu, and Loromayu), we identified taxonomic assemblages dominated by halophilic and halotolerant bacteria (e.g., Halomonas, Marinobacter, Rhodohalobacter), phototrophic cyanobacteria and algae (Dunaliella, Chlorella), archaeal Halobacteria (Halorubrum, Natrinema, Haloterrigena), and halotolerant fungi (Aspergillus, Penicillium). Notably, Laguna Mama Khumu exhibited the highest microbial and functional diversity, reflecting its heterogeneous salinity and richer chemical gradients, whereas the most extreme lakes (Colorada and Loromayu) harbored narrower specialized communities. Across all sites, oxidative phosphorylation dominated as the primary metabolic strategy. Additional pathways such as photosynthesis, sulfur and methane cycling were especially prominent at Mama Khumu. Patterns of carbohydrate-active enzyme (CAZyme) also diverged: Loromayu harbored abundant glycoside hydrolases, indicating strong polysaccharide degradation potential, while Mama Khumu displayed a boarder and more functionally redundant CAZyme repertoire. High-quality metagenome-assembled genomes (MAGs) uncovered novel lineages (< 95% ANI to known species) encoding key traits including energy metabolism (ATP synthase, anoxygenic photosynthesis), sulfur oxidation, arsenic resistance, and heavy-metal efflux systems. These features highlight the genomic innovation fostered by polyextreme conditions. Overall, our findings showed that within a shared scaffold of aerobic respiration and halophilic resilience, local geochemistry drives divergent taxonomic and metabolic adaptations. The Bolivian Andean saline lakes thus emerge as natural laboratories for studying microbial adaptation under multiple stressors and offer promising sources for biotechnological discovery.},
}

@article {pmid41845557,
year = {2026},
author = {Dormiente, A and Mancabelli, L and Ventura, M and Longhi, G and Mergoni, G and Manfredi, M},
title = {Metagenomic Evaluation of Oral Microbiota in Patients Affected by Oral Lichen Planus: A Pilot Study.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70296},
pmid = {41845557},
issn = {1601-0825},
support = {//Bando di Ateneo per la Ricerca 2023- Azione B/ ; },
abstract = {OBJECTIVE: To characterize the oral bacterial and fungal microbiota of symptomatic oral lichen planus patients undergoing topical corticosteroid therapy and to explore microbial patterns potentially associated with subsequent oral candidiasis.

METHODS: Twelve patients with clinically and histologically confirmed OLP were enrolled. Unstimulated saliva and tongue dorsum swabs were collected at baseline and weekly for three weeks during betamethasone therapy. Bacterial communities were profiled using shallow shotgun metagenomics analyzed with METAnnotatorX2, and fungal communities through ITS sequencing and QIIME 2 workflows. Beta-diversity analyses assessed the effects of time, clinical variables, and later candidiasis development. Associations between bacterial taxa and Candida abundance were evaluated using Spearman correlations.

RESULTS: Oral candidiasis developed in three patients (25%). Microbiota composition showed marked inter-individual variability but high intra-subject stability, with no consistent shifts linked to corticosteroid therapy. Commensal taxa such as Streptococcus, Rothia, and Actinomyces were negatively associated with candidiasis and Candida abundance, whereas anaerobic species including Porphyromonas gingivalis, Prevotella multiformis, and Lachnoanaerobaculum gingivalis displayed positive correlations with fungal proliferation.

CONCLUSIONS: Despite overall stability of the oral microbiota during therapy, specific bacterial signatures were associated with subsequent Candida overgrowth. These findings suggest that cross-kingdom interactions may influence susceptibility to corticosteroid-associated candidiasis and warrant validation in larger cohorts.},
}

@article {pmid41845564,
year = {2026},
author = {Zhang, Y and Wang, DD},
title = {Gut microbiome in type 2 diabetes: insights from metagenomics, multi-omics, and diet-microbe interactions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2644682},
doi = {10.1080/19490976.2026.2644682},
pmid = {41845564},
issn = {1949-0984},
mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome ; Metagenomics ; Animals ; *Diet ; Metabolomics ; Bacteria/classification/genetics/metabolism/isolation & purification ; Proteomics ; Multiomics ; },
abstract = {Type 2 diabetes (T2D) is a heterogeneous metabolic disorder in which environmental exposures interact with host biology to drive insulin resistance and progressive β-cell dysfunction. This review synthesizes recent advances showing how the gut microbiome mediates these processes across multiple levels of resolution. First, large-scale shotgun metagenomic studies consistently identify a reproducible T2D-associated signature characterized by depletion of short-chain fatty acid-producing taxa and enrichment of opportunistic, pro-inflammatory microorganisms, while highlighting the importance of controlling for major confounders such as adiposity and glucose-lowering medications. Second, functional profiling and metabolomics link microbial community shifts to coordinated pathway changes-including reduced short-chain fatty acid and secondary bile acid production and increased endotoxin- and branched-chain amino acid-related metabolism-that influence gut barrier integrity, inflammatory tone, insulin sensitivity, and pancreatic β-cell function. Third, we discuss how integrative multi-omics (metagenomics, metatranscriptomics, proteomics, and metabolomics) can connect microbial genetic potential to in vivo activity and circulating metabolites, while introducing key challenges such as temporal variability, anatomical heterogeneity, and "dark matter" in gene and metabolite annotation. Fourth, strain-resolved analyses reveal that many disease-associated functions are carried by specific lineages within species, refining microbial targets and helping explain inconsistent species-level associations. Fifth, we summarize how diet shapes microbial ecology and function-supporting microbiome-informed precision nutrition-and highlight emerging evidence beyond bacteria, including viral and fungal community components. Finally, we outline translational opportunities and evidence gaps, emphasizing the need for diverse longitudinal cohorts, mechanistic validation, and well-controlled interventional trials to evaluate microbiome-directed strategies for T2D prevention and treatment.},
}

*Diabetes Mellitus, Type 2/microbiology/metabolism
Humans
*Gastrointestinal Microbiome
Metagenomics
Animals
*Diet
Metabolomics
Bacteria/classification/genetics/metabolism/isolation & purification
Proteomics
Multiomics

@article {pmid41846023,
year = {2026},
author = {Segovia-Cruz, JA and Zárate-Romero, A and Herrera-Hernández, MM and Loza-Tavera, H and Vargas-Suárez, M and Aceves, MA and Paz-Gonzalez, AD and Rivera, G and Montiel, NM and Schnabel-Peraza, D and Sánchez-Reyes, A},
title = {Characterization and application of two novel environmental DyP-type peroxidases as sustainable biocatalysts for textile dye treatment.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {151457},
doi = {10.1016/j.ijbiomac.2026.151457},
pmid = {41846023},
issn = {1879-0003},
abstract = {The environmental impact of synthetic textile dyes highlights the urgent need for sustainable wastewater treatment solutions. Here, we report the cloning, heterologous expression, purification, and characterization of two novel bacterial dye-decolorizing peroxidases (DyPs), named PbDyP and MbDyP, selected from the metagenome of the BP8 polyurethane-enriched microbial consortium, isolated from a landfill. Both enzymes showed an acidic pH optimum (4.0-4.5) and a moderate temperature preference (~40 °C), but they differed in stability and sensitivity to hydrogen peroxide. Spectroscopic analyses confirmed their heme-binding nature, while dynamic light scattering revealed different oligomerization states. Both enzymes achieved efficient biotransformation (>80%) of representative anthraquinone, azo, phthalocyanine, sulfur, and triphenylmethane dyes, with particularly high activity toward anthraquinone Reactive Blue 19. Following enzymatic treatment, FT-IR spectroscopy revealed structural changes in diagnostic functional groups of several dyes, such as Vat Red 10, Disperse Orange 30, Direct Black 22, and Reactive Blue 19, while UPLC-MS analysis identified a lower-mass (sulfonatooxy)ethyl-sulfonyl anilinoderivative (m/z 318.31), indicating biotransformation of the parent compound. We also conducted in vitro transformation assays for bisphenols, benzenedithiols, and substituted phenols to thoroughly assess the oxidative capabilities of the DyP-type peroxidases. Toxicity tests using Artemia salina demonstrated that, although enzymatic treatment reduced toxicity in the supernatants, the precipitated fractions remained harmful, underscoring the need for integrated remediation strategies. Overall, these findings position PbDyP and MbDyP as promising candidates for eco-friendly dye degradation, providing a foundation for their potential application in industrial wastewater treatment.},
}

@article {pmid41846078,
year = {2026},
author = {Li, Q and Yuan, J and Sun, Y and Wang, Y and Li, Y and Ni, A and Zong, Y and Yang, H and Li, X and Huang, X and Ma, H and Chen, J},
title = {Multi-omics analysis revealed that oxidative phosphorylation contributed to the heterosis for feed efficiency in laying chickens.},
journal = {Poultry science},
volume = {105},
number = {6},
pages = {106658},
doi = {10.1016/j.psj.2026.106658},
pmid = {41846078},
issn = {1525-3171},
abstract = {Improving feed efficiency has been the top priority in animal husbandry. Host genetics and gut microbiota synergistically regulate feed efficiency in laying chicken. However, the role of gut microbiota in heterosis for feed efficiency was rarely investigated. Herein, we used multi-omics data to elucidate the regulatory mechanisms of heterosis for feed efficiency in White Leghorn, Beijing-You chicken, and their reciprocal crosses. We observed divergent heterosis for residual feed intake (RFI) between two crossbreds during the laying period from 43 to 46 weeks of age. Metagenomic analysis showed the significant difference in richness and function of cecal microbiota among crossbreds and purebreds (P < 0.05), and the differential functional pathways were mainly related to metabolism. Most microorganisms (>90 %) were non-additive in crossbreds. Weighted gene co-expression network analysis and LDA effect size analysis revealed seven non-additive RFI-associated microorganisms, such as Leyella, Paraprevotella, and Zongyangia. We also identified 544 RFI-associted metabolites, which were mainly overrepresented in glycerophospholipid metabolism and oxidative phosphorylation. Integrative analysis further revealed the interactions among non-additive microorganisms, genes, and metabolites. Specifically, the non-additive expression of Zongyangia was positively correlated with UQCR10 and Ubiquinone-1 levels within the oxidative phosphorylation pathway. These factors were negatively correlated with RFI, contributing to the RFI heterosis. Our study highlighted that key microorganisms, genes, and metabolites involved in oxidative phosphorylation interact to regulate negative heterosis for RFI in laying hens. The findings established a theoretical and practical foundation for further exploring the molecular mechanisms that drive heterosis for feed efficiency.},
}

@article {pmid41846103,
year = {2026},
author = {Trzos, K and Hutsch, T and Koval, A and Śmierciak, D and Machaj, G and Molano, LG and Rehner, J and Rahman, MM and Förster, MO and Bednarek, M and Yilmaz, B and Pilarczyk-Zurek, M and Surma, S and Koziel, J and Krawczyk, M and Keller, A and Becker, SL and Ylla, G and Jura, J and Kotlinowski, J},
title = {Probiotic Lactobacillus rhamnosus mitigates PBC-like features in Mcpip1-deficient mice via modulation of gut-liver crosstalk.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {1872},
number = {5},
pages = {168216},
doi = {10.1016/j.bbadis.2026.168216},
pmid = {41846103},
issn = {1879-260X},
abstract = {BACKGROUND: Primary biliary cholangitis (PBC) is a chronic autoimmune liver disease characterized by progressive biliary destruction and cholestasis. Current therapies, including ursodeoxycholic acid (UDCA), exhibit limited efficacy in advanced disease. In this study, we investigate the therapeutic potential of microbial intervention using Lactobacillus rhamnosus (Lbr) in the Mcpip1[fl/fl]Alb[Cre] knockout mouse model of PBC, which we described previously. Knockout mice develop human PBC-like features such as bile acid dysregulation, autoantibodies, cholangiocyte hyperplasia and fibrosis.

METHODS: Six-week-old Mcpip1[fl/fl] (wild-type) and Mcpip1[fl/fl]Alb[Cre] (knockout) mice were treated with Lactobacillus rhamnosus supplementation, UDCA (15 mg/kg/day), UDCA + Lbr, and UDCA + OCA (obeticholic acid, 10 mg/kg/day) for six weeks. Treatment response was characterized by liver and gut pathology, serum biomarkers, transcriptomic profiles, and microbiome composition.

RESULTS: Treatment of Mcpip1[fl/fl]Alb[Cre] animals with Lbr decreased serum bile acids and reduced pathological cholangiocyte dysplasia in the liver, decreased leukocyte infiltration and fibrosis. RNAseq of liver tissue revealed enrichment of humoral immune responses and T cell activation pathways in knockouts, all of which were significantly attenuated by Lbr monotherapy. Gut pathology marked by increased intraepithelial lymphocyte infiltration and mucosal hypertrophy, was also normalized upon Lbr administration. Finally, probiotic treatment modulated the microbiome by increasing the Firmicutes/Bacteroidetes ratio and enriching butyrate-producing Lachnospiraceae. Administration of UDCA and UDCA+OCA had less pronounced effects: only decreased serum bile acids was detected in both groups.

CONCLUSIONS: Probiotic intervention with Lbr represents a feasible strategy to attenuate fibrotic progression in a mouse model of autoimmune cholestatic disease by modulation of the gut-microbiome-immune crosstalk.},
}

@article {pmid41846126,
year = {2026},
author = {Wang, X and Zhao, L and Teng, Y and Hu, W and Xu, Y and Ma, J and Song, J and Ren, W and Zhang, J and Zhu, H and Wang, X and Wang, Y and Luo, Y and Kuramae, EE},
title = {Decoding the adaptive strategies of versatile diazotrophs to multi-metal(loid) stress in mercury-mining impacted farmland soils.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141760},
doi = {10.1016/j.jhazmat.2026.141760},
pmid = {41846126},
issn = {1873-3336},
abstract = {Diazotrophs are crucial for Earth's nitrogen cycle via biological nitrogen fixation, while also modulating other elemental cycles and exhibiting bioremediation potential. However, their responses to co-occurring heavy metal(loid) (HM) contaminants in polluted soils remain poorly understood. Using combined nifH (encoding nitrogenase) amplicon and metagenomic sequencing, we characterized the taxonomic structure and metabolic potential of diazotrophic community across multi-HM contamination gradients in mercury-mining impacted farmlands (paddy vs. upland). Results identified selenium (upland soils: 0-3.08 mg kg[-1]) and arsenic (paddy soils: 5.38-17.1 mg kg[-1]) as the primary HMs shaping diazotrophic diversity, whereas mercury (0.067-99.6 mg kg[-1]) showed a significant but weak correlation. Selenium and mercury correlated positively with diversity in upland soils (arsenic negatively), whereas all three HMs correlated negatively in paddy soils. Diazotrophic indicator taxa varied by HM type, yet certain taxa tolerated all three HMs simultaneously-notably Chromatiaceae/Pseudomonadaceae in upland soils and Xanthobacteraceae in paddy soils. Moreover, diazotrophs in upland soils exhibited synergistic associations with functional guilds involved in HM resistance and element cycling (e.g., carbon fixation and hydrogen metabolism), contrasting with the negative correlations in paddy soils. Metagenomic binning indicated that dominant diazotrophs were primarily aerobic heterotrophs with versatile metabolic potentials, including multi-HM resistance (e.g., arsenic/mercury reduction, efflux, and antioxidation) and energy acquisition via trace gas (CO, H2), manganese, and sulfide oxidation. These findings provide novel insights into diazotrophic adaptive strategies under multi-HM stress, advancing our understanding of their ecological and environmental functions.},
}

@article {pmid41846977,
year = {2026},
author = {Sharaf, H and Bobay, LM},
title = {MetaStrainer : Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.02.709061},
pmid = {41846977},
issn = {2692-8205},
abstract = {SUMMARY: Metagenomics provides broad insights from microbial communities, but more biological relevant phenotypes are attributed to subtle changes at the strain-level rather than species. Despite development of several tools using different algorithms, resolving individual strains from short-read pair-end sequencing data remains challenging. We developed MetaStrainer , a tool capable of reconstructing strain genotypes from metagenomic data. Compared with existing approaches, MetaStrainer substantially increases genotype accuracy, correctly identifies the number of strains, and accurately estimates their relative abundances. Accuracy of reconstructed genotypes is robust to choice of mapping reference.

MetaStrainer is implemented in Python 3. Source code and instructions are available on GitHub at https://www.github.com/lbobay/MetaStrainer and on Zenodo: https://doi.org/10.5281/zenodo.17872331.

CONTACT: ljbobay@ncsu.edu.

SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.},
}

@article {pmid41847008,
year = {2026},
author = {Yancey, CE and Brumfield, KD and Ettwiller, L and Colwell, RR},
title = {Microbial Community multi-omic analysis of marsh sediment post crustacean shell compost enrichment: pathogen emergence and community response.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.06.710096},
pmid = {41847008},
issn = {2692-8205},
abstract = {Changes in nutrient availability can rapidly alter microbial processes in natural environments, with implications in biogeochemical cycling and pathogen emergence. Short-term, functional responses of microbial communities to nutrient amendment in coastal communities remain poorly understood, particularly in temperate environments. A 48-hour microcosm pulse experiment was completed in which paired metagenomic and metatranscriptomic sequencing were employed to examine how the decomposition of chitin rich substrates, namely crab and lobster shell compost, alters salt marsh microbiome structure and function. Within 48 hours of amendment, pronounced shifts in community metabolism were observed, including increased chitin degradation and utilization, stress-response, and sporulation. These responses coincided with marked decreases in genes associated with key biogeochemical processes, including carbon fixation, sulfur oxidation and reduction, and other metabolic pathways. Shell compost addition also enriched putative pathogens and virulence-associated genes, accompanied by modest transcriptional activation, notably aerolysin A (aerA) , which encodes the pore-forming exotoxin aerolysin. These results demonstrate temperate salt marsh sediment microbiomes can undergo shifts in community composition and function that is associated with chitin-rich nutrient perturbation. The sensitivity of temperate coastal systems to organic matter input and the potential for ecological and public-health relevant outcomes are underscored, notably given that chitin is among the most abundant and readily available bionutrients in aquatic ecosystems globally.},
}

@article {pmid41847199,
year = {2026},
author = {Ha, S and Kim, N and Song, CH},
title = {Age- and sex-dependent alterations of jejunal microbiota in Fischer 344 rats fed with a high-fructose, high-fat diet: depletion of Lactobacillus intestinalis in small bowel contents.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1779112},
pmid = {41847199},
issn = {1664-302X},
abstract = {INTRODUCTION: Our previous research demonstrated that a high-fat diet (HFD) induced jejunal inflammation and hepatic steatosis, suggesting that small bowel microbiota contribute to these pathologies. This study investigated age- and sex-specific alterations in jejunal microbiota following a high-fructose, high-fat diet (HFHFD) in F344 rats.

METHODS: Six-week-old and two-year-old rats of both sexes were fed an HFHFD for 8 weeks, after which jejunal contents were collected for metagenomic analysis. Taxonomic profiling and linear discriminant analysis were performed, and Spearman's rank correlation analysis was used to evaluate associations with jejunal inflammation and hepatic steatosis. Beta-diversity analysis was conducted to assess group separation. In vitro, HIEC-6 human intestinal epithelial cells were used to test the protective effect of Lactobacillus intestinalis under palmitic acid-induced lipotoxic stress.

RESULTS: HFHFD reduced the Firmicutes/Bacteroidetes ratio in young females and in aged rats of both sexes. Notably, Lactobacillus intestinalis-which supports barrier function-decreased in young males and aged females. In contrast, Akkermansia muciniphila increased across all HFHFD groups, particularly in young females and aged rats. Bacteroides vulgatus increased in aged HFHFD-fed rats of both sexes, while Bacteroides caccae was elevated in females across both age groups. Furthermore, the Lactobacillus reuteri group decreased only in young HFHFD rats. L. intestinalis and L. reuteri groups negatively correlated with jejunal inflammation and hepatic steatosis, whereas B. caccae and A. muciniphila showed positive correlations with both pathogenic phenotypes. Beta-diversity revealed a pronounced diet- and sex-dependent separation in young rats, which was attenuated in aged groups. In HIEC-6 cells, L. intestinalis significantly restored viability under palmitic acid-induced lipotoxic stress, though its conditioned medium did not.

DISCUSSION: Collectively, HFHFD induces age- and sex-dependent dysbiosis in the jejunum, and L. intestinalis may serve as a potential probiotic for metabolic dysfunction-associated steatotic liver disease.},
}

@article {pmid41847396,
year = {2026},
author = {Yan, J and Yang, H and Zhang, W and Li, Y and Yu, X and Xiong, Z and Shi, C and Hu, Y},
title = {A Case Report of Tuberculous Peritonitis with Negative GeneXpert and Positive Metagenomic Sequencing Results.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {560202},
pmid = {41847396},
issn = {1178-6973},
abstract = {A 65-year-old male patient undergoing peritoneal dialysis was diagnosed with Mycobacterium tuberculosis-related peritonitis. Initial diagnostic tests, including acid-fast smear of ascites, GeneXpert test, and Mycobacterium tuberculosis culture, yielded negative results. However, metagenomic capture sequencing (metaCAP) and metagenomic next-generation sequencing (mNGS) identified the presence of Mycobacterium tuberculosis. The patient was subsequently treated with standard anti-tuberculosis therapy, leading to clinical improvement. This case highlights the utility of advanced molecular diagnostics in identifying atypical pathogens in peritoneal dialysis-related infections.},
}

@article {pmid41847603,
year = {2026},
author = {Zhang, Y and Zhang, Y and Zhang, K and Wang, L and Huang, D and Zhen, F and Wang, R and An, C},
title = {Parameter-Specific Effects of Low-Intensity Transcranial Focused Ultrasound Stimulation on Depression-Like Behaviors in a CUMS Mouse Model.},
journal = {Neuropsychiatric disease and treatment},
volume = {22},
number = {},
pages = {586583},
pmid = {41847603},
issn = {1176-6328},
abstract = {PURPOSE: Depression is a multifactorial disorder involving neurotransmitter dysregulation, gut microbiota imbalance, and metabolic disturbances. Low-intensity transcranial focused ultrasound stimulation (LIFUS) holds promise for treating depression. However, the effects of different LIFUS parameter settings on depression-like behaviors, and their potential associations with gut microbiota and fecal metabolite changes, remain largely unexplored. This study aims to investigate the parameter-specific effects of LIFUS on depression-like behaviors in a chronic unpredictable mild stress (CUMS) mouse model, and to explore potential associations with changes in gut microbiota and fecal metabolites.

METHODS: To establish a depression model, C57BL/6 mice were subjected to CUMS, while a separate cohort was kept as a control (CON) group. The CUMS-exposed mice were then randomly divided into four groups: CUMSpo, LIFUS1, LIFUS2 and SHAM. Depressive-like behaviors were evaluated using the sucrose preference test (SPT) and forced swim test (FST). The levels of neurotransmitters and Fecal concentrations of metabolites were quantified using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Gut microbiota composition was analyzed by metagenomic sequencing, and α-diversity was assessed using the ACE, Chao1, and Shannon indices. Histopathology was assessed via HE staining.

RESULTS: LIFUS at 1.5 kHz PRF, but not 300 Hz, significantly attenuated CUMS-induced depressive-like behaviors, evidenced by increased sucrose preference and reduced immobility time, without affecting locomotor activity. This behavioral effect was accompanied by a significant increase in cortical glutamate. LIFUS2 protocol was associated with a significant increase in tryptamine, alongside a concurrent trend towards restoring the abundance of Clostridia and enhancing gut microbiota α-diversity. HE staining confirmed protocol safety.

CONCLUSION: The antidepressant-like effects of LIFUS appear to be associated with multi-systemic alterations, including changes in cortical glutamate, modulation of the gut microbiota, and specific changes in tryptophan metabolism.},
}

@article {pmid41848047,
year = {2026},
author = {Xue, R and Zhang, Y and Li, H and Li, J and Ke, W and Hu, S and Li, C and Chan, FKS and Cui, L},
title = {Persistent antimicrobial resistance during soil remediation driven by residual heavy metal co-selection.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag058},
pmid = {41848047},
issn = {1751-7370},
abstract = {Remediation of heavy metal-contaminated soil is a global priority, particularly as reclaimed land increasingly intersects with urban development and human exposure. However, the ecological consequences of soil remediation, especially its impact on antimicrobial resistance (AMR) as a global health threat, have remained poorly understood. Here, we combined single-cell Raman-D2O probing with genome-resolved metagenomics to monitor the dynamics of phenotypic and genotypic resistance to metals and antibiotics during a 120-day remediation of soils with three contamination levels from a lead-zinc smelting site. Although chemical remediation substantially reduced bioavailable metals (by 42-65%), AMR was not diminished. Instead, both phenotypic activity and gene abundance of metal- and antibiotic-resistant microorganisms increased, resulting in a 2-to 3-fold increase in AMR-associated health risks. Among 76 metagenome assembled genomes (MAGs) from phenotypic resistance communities, all Cd resistance-associated MAGs harbored multidrug resistance genes, half of which were colocalized with metal resistance determinants, and their prevalence continued to rise with remediation. These findings reveal that although remediation alleviates acute metal toxicity, residual low-concentration bioavailable metals sustain evolutionary selection for resistance, highlighting a disconnect between chemical recovery and biological safety. Moreover, the improved soil nutrient and physiochemical properties of remediated soils further promoted the proliferation of antibiotic-resistant bacteria. This study offers new ecological insights into the unintended consequences of anthropogenic interventions, underscoring the need to integrate biological safety into soil health and safety assessments.},
}

@article {pmid41848058,
year = {2026},
author = {Calusinska, M and Herold, M and Klimek, D and Bertucci, M and Lemaigre, S and Cambier, S and Zorzan, S and Leclercq, C and Dolfing, J and Westerholm, M and Müller, B and Nasirzadeh, L and Schnürer, A and Wilmes, P and Delfosse, P and Goux, X},
title = {Phylum-wide propionate degradation and its potential connection to poly-gamma-glutamate biosynthesis in Candidatus Cloacimonadota phylum.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag055},
pmid = {41848058},
issn = {1751-7370},
abstract = {The candidate phylum Cloacimonadota is frequently detected in anoxic environments such as anaerobic digestion (AD) reactors, hydrothermal vents, and deep-sea sediments, yet its metabolism remains poorly understood. Metagenomic evidence suggests capacities for amino acid fermentation, carbohydrate degradation, as well as a potential role in syntrophic propionate oxidation (SPO), a key bottleneck in AD. However, a complete methylmalonyl-CoA (mmc) pathway, central to SPO, has not been previously identified in Cloacimonadota genomes. Here, we report results from an acidified lab-scale anaerobic baffled reactor fed with sugar beet pulp, where an increase in the relative abundance of Cloacimonadota correlated with recovery of methanogenesis, resulting in increased methane content in the produced biogas. Metagenomic and metatranscriptomic analyses enabled metabolic reconstruction of the dominant Cloacimonadota OTU. Furthermore, using a curated database of 204 genome-resolved Cloacimonadota species, we characterised the phylum-level metabolic potential. Comparative genomics revealed alternative proteins, including 2-oxoglutarate:ferredoxin oxidoreductase and aspartate aminotransferase, likely to substitute for missing enzymes in the classical mmc pathway. These proteins were widely distributed and highly conserved across the analysed Cloacimonadota genomes, suggesting that this variant of the SPO pathway could represent a phylum-specific trait. Moreover, we hypothesise that these alternative pathway steps may link propionate metabolism to protein degradation and poly-γ-glutamate biosynthesis. Network analysis identified the methanogenic archaeon Methanothrix as a potential syntrophic partner, an interaction further supported by propionate-fed enrichment cultures showing co-occurrence of Cloacimonadota and Methanothrix species. Our study sheds light on the Cloacimonadota metabolism, advancing our understanding of their ecological roles and potential for biotechnological applications.},
}

@article {pmid41848770,
year = {2026},
author = {Prabhu, A and Rinke, C},
title = {ICTV Virus Taxonomy Profile: Apasviridae 2026.},
journal = {The Journal of general virology},
volume = {107},
number = {3},
pages = {},
doi = {10.1099/jgv.0.002230},
pmid = {41848770},
issn = {1465-2099},
mesh = {Genome, Viral ; *DNA Viruses/classification/genetics/isolation & purification/ultrastructure ; Phylogeny ; Virion/ultrastructure/genetics ; DNA, Viral/genetics ; *Archaeal Viruses/classification/genetics/isolation & purification/ultrastructure ; Metagenomics ; *Archaea/virology ; },
abstract = {The family Apasviridae includes dsDNA viruses associated with the marine archaeal lineage Poseidoniales. Members of this family have been identified using metagenomic analyses of brackish estuarine samples and are related to other 'magroviruses' infecting Poseidoniales archaea. The family belongs to the order Magrovirales and includes the genus Agnivirus and the species Agnivirus brisbanense. Viruses in the family possess a linear dsDNA genome of about 108 kbp and encode modules for DNA replication and virion morphogenesis, such as those relating to the formation of an icosahedral capsid and a helical tail, characteristic of members of the class Caudoviricetes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Apasviridae, which is available at ictv.global/report/apasviridae.},
}

Genome, Viral
*DNA Viruses/classification/genetics/isolation & purification/ultrastructure
Phylogeny
Virion/ultrastructure/genetics
DNA, Viral/genetics
*Archaeal Viruses/classification/genetics/isolation & purification/ultrastructure
Metagenomics
*Archaea/virology

@article {pmid41849038,
year = {2026},
author = {Biçer, Y and Sönmez, G and Turkal, G and Telli, AE and Akkurt, MY and Uçar, G},
title = {Potential use of whey in kefir production: evaluation of fermentation kinetics and microbiota.},
journal = {Food science of animal resources},
volume = {46},
number = {1},
pages = {},
pmid = {41849038},
issn = {2636-0780},
abstract = {This study was carried out on the effect of different amounts of whey on the kefir production process and the bacterial microbiota of the beverages. Fermentation was carried out by mixing commercial kefir grains with cow, sheep, and goat milk with their whey at concentrations of 0% (control group), 25%, 50%, and 75%. The bacterial microbiota in the produced beverages and the relative abundances of seven microorganisms (Lactobacillus kefiranofaciens, Lactobacillus kefiri, Lactobacillus delbrueckii, Lactococcus lactis, Streptococcus thermophilus, Leuconostoc mesenteroides, and acetic acid bacteria) were determined using metagenomic analysis targeting the V3-V4 region of 16 S rRNA gene, and quantitative polymerase chain reaction (qPCR), respectively. Lactococcus lactis and Leuconostoc mesenteroides were detected in higher abundance in whey-containing goat samples. While Lactobacillus was dominant in the cow milk samples containing 0%, 25%, and 50% whey, Enterococcus was dominant in the samples containing 75% whey. In sheep milk samples, Lactobacillus was dominant in samples with 75% and 50% whey, Lactococcus was dominant in samples with 25% whey, and Enterococcus was dominant in samples with no (0%) whey. Lactobacillus was dominant in all goat milk samples. In conclusion, high levels of lactic acid bacteria were shown to preserve their viability in the experimentally produced beverages with the addition of whey at different concentrations, and the whey could be used to produce kefir.},
}

@article {pmid41849467,
year = {2026},
author = {Ferreira, LDS and Silva, JFBR and Vilhena, MPSP and Alegria, OC and Ramos, RTJ and Sousa, MPA},
title = {Bacterial diversity of lowland soils under cocoa cultivation in Amazon.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {86},
number = {},
pages = {e295836},
doi = {10.1590/1519-6984.295836},
pmid = {41849467},
issn = {1678-4375},
mesh = {*Cacao/growth & development ; *Soil Microbiology ; Brazil ; *Biodiversity ; *Bacteria/classification/genetics ; },
abstract = {This study investigated bacterial diversity in soils from six cacao-producing islands in Mocajuba, Pará, Brazil. Using next generation sequencing shotgun metagenomic DNA, we characterized the microbial composition and ecological structure of floodplain soils cultivated with Theobroma cacao. Taxonomic classification revealed a rich bacterial community encompassing 21 phyla, 54 classes, 121 orders, 240 families, 604 genera, and 2,289 species. The dominant phyla, Actinomycetota and Pseudomonadota, are known for their ecological roles in organic matter decomposition, antibiotic production, nitrogen cycling, and plant growth promotion. Alpha diversity metrics varied among samples, with P3 showing the highest species richness and P5 exhibiting the highest Shannon, Simpson, and evenness indices, suggesting a more balanced community. Beta diversity analysis based on Bray-Curtis dissimilarity under Total Sum Scaling (TSS) normalization revealed ecological gradients ranging from 0.228 to 0.527. Spatial ordination and hierarchical clustering indicated gradual shifts in community composition, supporting the concept of a compositional continuum shaped by environmental gradients. Functionally, Burkholderia lata was dominant in P1, reflecting its role in potassium solubilization, while Streptomyces species-detected in five of the six samples-contribute to biogeochemical cycling and pathogen suppression. Bradyrhizobium and Paraburkholderia, identified in P3, P5, and P6, are associated with nitrogen fixation and plant hormone regulation. These findings reveal the ecological complexity and functional potential of cacao soil microbiomes, providing insights for sustainable management of Amazonian floodplain agroecosystems.},
}

*Cacao/growth & development
*Soil Microbiology
Brazil
*Biodiversity
*Bacteria/classification/genetics

@article {pmid41849523,
year = {2026},
author = {Mardiyaningsih, A and Astuti, P and Widodo, W and Purwanto, P},
title = {Metagenomic analysis of Gatot, a cassava-based fermented food from Yogyakarta Indonesia: a potential source of Lactobacillaceae probiotic.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {86},
number = {},
pages = {e298140},
doi = {10.1590/1519-6984.298140},
pmid = {41849523},
issn = {1678-4375},
mesh = {*Manihot/microbiology ; Indonesia ; *Fermented Foods/microbiology ; RNA, Ribosomal, 16S/genetics ; *Lactobacillaceae/genetics/classification/isolation & purification ; *Probiotics ; DNA, Bacterial/genetics ; Metagenomics ; Food Microbiology ; Fermentation ; },
abstract = {Gatot, a traditional Indonesian fermented food product made from cassava (Manihot utilissima), is valued for its potential health benefits and contribution towards local food security. As fermentation induces a rich microbial environment that could enhance nutritional properties and produce bioactive compounds, understanding the bacterial communities involved is fundamental for optimizing their health-promoting potential. However, the bacterial diversity of Gatot across different regions remains underexplored. This study aims to detect and identify the bacterial communities in Gatot samples, as well as to measure the differences in their abundance in Gatot from three different regions in Yogyakarta. Gatot samples were collected from Bantul, Gunungkidul, and Kulon Progo regions. Genomic DNA was extracted from the samples, and DNA concentration was measured using NanoDrop and Qubit. Libraries were then prepared with Oxford Nanopore Technology kits. For bacterial identification, the V1-V9 regions of the 16S ribosomal RNA gene were amplified using 27F and 1492R primers under specific polymerase chain reaction conditions. Sequencing was performed on a GridION platform using MinKNOW (version v24.02.16) and Dorado (version v7.3.11) for high-accuracy basecalling. Quality filtering and visualization of FASTQ files were performed using NanoPlot and NanoFilt, while taxonomic classification was referenced against the NCBI 16S RefSeq database. Data analysis was completed in Pavian and RStudio. The dominant bacterial family across all samples was the Lactobacillaceae family. However, each region exhibited unique microbial signatures at the genus level: Bantul samples were dominated by Weissella, Gunungkidul by Leuconostoc, and Kulon Progo by Lactiplantibacillus. Specific species were also predominant in each location, with Weissella confusa in Bantul, Liquorilactobacillus hordei in Gunungkidul, and Lactiplantibacillus plantarum in Kulon Progo. These regional variations highlight how location-specific bacterial communities influence the fermentation profile of Gatot, potentially affecting flavor, texture, and nutritional value. This study provides the first comprehensive metagenomic analysis of Gatot's bacterial communities across different regions, offering new insights into the influence of geographical environment on microbial composition in fermented cassava products. The findings support the potential for controlled fermentation processes tailored to local microbial ecosystems, to enhance Gatot's functionality as a health-promoting food and source of probiotic.},
}

*Manihot/microbiology
Indonesia
*Fermented Foods/microbiology
RNA, Ribosomal, 16S/genetics
*Lactobacillaceae/genetics/classification/isolation & purification
*Probiotics
DNA, Bacterial/genetics
Metagenomics
Food Microbiology
Fermentation

@article {pmid41850876,
year = {2026},
author = {Regmi, H and Dritsoulas, A and Kamali, S and Stelinski, LL and Diepenbrock, LM and Duncan, L},
title = {Edge effects, tree cover and soil properties linked to the distribution of Diaprepes abbreviatus in a Florida citrus orchard.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70723},
pmid = {41850876},
issn = {1526-4998},
support = {CRDF22-013//Citrus Research and Development Foundation, Inc./ ; },
abstract = {BACKGROUND: Diaprepes root weevil (DRW, Diaprepes abbreviatus) is a major economic pest of citrus trees in Florida and the Caribbean Basin. To identify potential drivers of local patterns of weevil abundance and tree condition, we measured relationships between DRW and edaphic properties in a Florida orchard in which half the trees were initially protected from herbivores by individual protective covers (IPCs) of fabric mesh. Weevils were monitored for 2 years in 94 plots arranged in a grid pattern. Soil samples were processed for physicochemical properties, and DNA from soil organisms was subjected to metabarcoding for ITS2 rDNA, 16S rDNA, and COI mtDNA.

RESULTS: Weevils aggregated each summer along plot boundaries adjacent to a natural area of alternate hosts, consistent with an edge-biased distribution reflecting seasonal weevil migration. Fourteen months after the covers were removed, 93% of 484 prokaryote species (dominated by Bacilli, Actinobacteria, Alphaproteobacteria, and Cyanobacteria) that were most closely associated with IPC use were less abundant beneath the trees that were formerly covered than under previously uncovered trees. Soil moisture, Paenibacillus spp. diversity, and IPCs were associated with DRW patterns and tree condition including mortality.

CONCLUSIONS: Early season, edge-biased distribution of DRW should be exploited for monitoring and management efficacy. The relationship here between tree mortality and microbiome species deficits associated with IPCs supports the need for research to resolve the role of tree covers in potential trophic cascades that affect plant health. © 2026 Society of Chemical Industry.},
}

@article {pmid41663943,
year = {2026},
author = {Li, M and Yang, R and Bai, Q and Yang, Z and Huang, T and Qiao, Y and Yang, B and Chen, J and Lin, W},
title = {Manipulating root-associated microbiomes to boost drought resistance in dryland winter wheat with Streptomyces pactum Act12.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41663943},
issn = {1471-2180},
support = {32401443//National Natural Science Foundation of China/ ; 2025CYJSTX02-16//the earmarked fund for Modern Agro-industry Technology Research System of Shanxi Province/ ; },
abstract = {BACKGROUND: Drought critically compromises agricultural productivity and threatens sustainable wheat production. Streptomyces pactum Act12 confers benefits to plant growth under drought stress, but its possible effects on root-associated microbiomes remain understudied. Here, shotgun metagenome sequencing and culture-dependent approaches were integrated to investigate the responses of rhizosphere and rhizoplane microbiomes in dryland winter wheat to exogenous S. pactum Act12 and their potential linkage to plant drought resistance.

RESULTS: Seed biopriming with S. pactum Act12 increased plant aboveground dry weight at flowering (by 63.2%) and maturation (by 41.9%) stages, leading to improved grain yield (by 8.7%). Microbial inoculation reduced malondialdehyde contents in wheat leaves and roots at the flowering stage alongside compartment-specific alterations in soil microbiomes. Metagenomic analysis revealed inoculation-induced enrichment of distinct taxa in rhizosphere soils (flowering: Fibrobacterota, Altererythrobacter; maturation: Mucoromycota, Rhodospirillum) and rhizoplane soils (flowering: Pseudomonadota, Serratia; maturation: Candidatus_Pacebacteria, Variovorax). Functional profiling showed up-regulation of key pathways related to oxidative phosphorylation in inoculated rhizosphere soils at the flowering stage. In rhizoplane soils, ABC transporters and pyrimidine metabolism were up-regulated across stages upon inoculation. Two key strains isolated from rhizoplane soils, designated Glycomyces lechevalierae A4 and Microbacterium algeriense B3, demonstrated the ability to enhance drought resistance in wheat seedlings.

CONCLUSIONS: Inoculation of S. pactum Act12 heightens drought resistance in dryland winter wheat through compartment-specific phylogenetic restructuring and functional reprogramming of root-associated microbiomes.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04812-3.},
}

@article {pmid41839668,
year = {2026},
author = {Nadeem, SA and Ali, I and Hussain, H and Ullah, I and Ali, W and Alzahrani, KJ and Ali, H and Khan, ZI and Abass, KS and Rahman, RU},
title = {Metagenomic analysis of bacterial and viral communities of Aedes aegypti and Aedes albopictus.},
journal = {Journal, genetic engineering & biotechnology},
volume = {24},
number = {1},
pages = {100643},
pmid = {41839668},
issn = {2090-5920},
abstract = {BACKGROUND: The complicated relationship between the Aedes mosquito microbiome, arbovirus transmission and essential physiological processes, is extremely important. Microbial community plays a vital role in shaping vector biology, impacting critical aspects such as parasite replication within the vector, vector longevity, and ultimately, vector competence. Understanding the composition and function of the Aedes microbiome is therefore crucial for developing novel strategies to control arboviral diseases. Therefore, we aimed to identify prevalent bacterial and viral communities in Aedes mosquitoes from Pakistan.

METHODS: Ae. aegypti and Ae. albopictus were collected and from three different regions of Khyber Pakhtoonkhwa, Punjab and federal capital Islamabad. We isolated DNA and sequenced two pools of each species and conducted metagenomic analysis, identifying a variety of bacteria and viruses.

RESULTS: We found diverse bacterial and viral communities in both studied species. In Ae. aegypti, the most abundant bacterial species was Klebsiella pneumoniae followed by Acinetobacter baylyi. Ae. albopictus presented Pseudomonas putida as the most abundant bacterial species followed by Brevundimonas diminuta. Similarly in Ae. aegypti, we found that Escherichia phage HK639 was the most abundant viral species while in Ae. albopictus, it was Lactobacillus phage 2. It is important to mention that the prevalent viruses in both Aedes species belong to the Siphoviridae genus.},
}

@article {pmid41840004,
year = {2026},
author = {Das, R and Tamang, B},
title = {Metagenomic insights reveal β-glucosidase-producing lactic acid bacteria from Miyamikhri with taxiphyllin degradation potential.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-43021-w},
pmid = {41840004},
issn = {2045-2322},
}

@article {pmid41840154,
year = {2026},
author = {Garza-González, DA and Quezada-Euán, JJG and Medina-Medina, LA and Solís-Sánchez, T and O'Connor-Sánchez, A},
title = {Comparative analysis of the gut microbiota of the sympatric stingless bee species Melipona beecheii and Melipona yucatanica.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {},
pmid = {41840154},
issn = {1678-4405},
support = {INFR2016 01-269833//Consejo Nacional de Ciencia y Tecnología/ ; CAR-21861//Universidad Autónoma de Yucatán/ ; },
}

@article {pmid41840625,
year = {2026},
author = {Zhang, Y and Zhang, Q and Luo, Y and Li, X and Zhao, R and Xu, Y and Zhang, S and Bai, X and Chen, H and Li, H and Hong, Y and Xie, Z},
title = {Bifidobacterium breve inhibits colorectal cancer via extracellular vesicles containing formate acetyltransferase.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04275-8},
pmid = {41840625},
issn = {1477-3155},
support = {82574649//National Natural Science Foundation of China/ ; JCYJ20250604175304006//Shenzhen Municipal Science and Technology Innovation Council/ ; 2023B03J1382//Guangzhou Science and Technology Program/ ; 2022ZD004//Nansha Science and Technology Program/ ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is the second leading cause of cancer-related mortality worldwide. The gut microbiota exerts unique therapeutic advantages against CRC, and the probiotic Bifidobacterium breve (B. breve) has been extensively documented to suppress CRC initiation in murine models. Although the role of B. breve in CRC has been established, whether its extracellular vesicles (EVs), as key mediators of bacteria-host crosstalk, exert a functional impact remains undefined. Here, we aim to explore the therapeutic potential of B. breve-derived EVs (B.breEVs) and their active cargo, formate acetyltransferase (pflB), in CRC.

RESULTS: Integrative analysis of the curated database of human gut metagenomes cohort (GMrepo) database and an MC38 subcutaneous tumor model revealed a significant reduction of B. breve abundance in faecal samples from CRC patients and tumor-bearing mice. Administration of live B. breve or its cell-free supernatant markedly inhibited tumor growth, whereas pasteurized bacteria or GW4869-mediated EVs blockade abolished this effect, indicating that EVs are the critical effector entities. Isolated B.breEVs selectively accumulated within tumor tissue, directly triggered apoptosis of colorectal cancer cells, and elevated the proportion of IFN-γ⁺ CD8⁺ cytotoxic T lymphocytes (CTLs) in tumor while concurrently ameliorating gut microbial structure and function. Mass-spectrometric profiling identified the pflB as an important active protein within B.breEVs. Recombinant pflB selectively inhibited MC38 cell viability in vitro and significantly reduced CRC burden in vivo. RNA sequencing of tumor issue demonstrated that pflB up-regulated granzyme B, perforin1 and CTL/NK-associated transcripts, and activated the intrinsic apoptotic pathway. Immuno-combination studies further revealed that pflB plus anti-PD1 therapy markedly increased the infiltration of CD8⁺ CTL and NK cells, and enhanced their cytotoxicity compared to either monotherapy.

CONCLUSIONS: B. breve secretes pflB-loaded EVs that reshape the intestinal micro-ecology, activate CD8⁺ CTL/NK anti-tumor immunity, directly induce mitochondrial apoptosis in malignant cells, and enhance the effects of immune checkpoint blockers to overcome drug resistance, offering a precision "probiotic-EVs-active protein" triadic intervention strategy for CRC.},
}

@article {pmid41840712,
year = {2026},
author = {Xu, L and Liu, C and Chen, S and Mao, A and Zi, X and Li, J and Ge, X and Liu, Q and Wang, S and Li, X and Wu, Q and Wan, J and Zhang, Z and Xu, H and Li, J and Lin, Q and Cao, Z},
title = {Characterization of age-related changes in the gut microbiome and metabolome of Kunming dogs and their associations with police performance.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02388-8},
pmid = {41840712},
issn = {2049-2618},
support = {2023YNPKLANF004//Open Foundation of the Yunnan Provincial Key Laboratory of Animal Nutrition and Feed Science/ ; YNWR-QNBJ-2018-137//Young Talent of Yunnan Xingdian Support Project for High Level Talents/ ; 202305AC160040//Yunnan Provincial Middle-Young Academic and Technical Leader Candidate/ ; },
abstract = {BACKGROUND: Gut microbiota plays a pivotal role in regulating the host's central nervous system (CNS) activity and behavior. However, its influence on the police performance of Kunming dogs and the underlying mechanisms remain largely unexplored. This study was the first to apply multi-omics technologies to investigate the dynamic variations in gut microbiota and their metabolic profiles across different ages of Kunming dogs. Furthermore, we systematically examined the associations between these microbial alterations and police performance metrics, providing a theoretical foundation for enhancing the working capabilities of Kunming dogs through targeted modulation of intestinal microecology.

RESULTS: The study showed that puppies, young dogs and adult dogs had significantly better police performance than elderly dogs, with young dogs exhibiting the highest scores. Analysis of 16S rRNA sequencing demonstrated that gut microbial diversity and stability were highest during the young dog stage, gradually declining with age. Metagenomic analysis revealed that the abundance of Lactobacillus acidophilus, Lactobacillus johnsonii, Limosilactobacillus reuteri, Ligilactobacillus animalis and Muribaculum gordoncarteri were strongly correlated with police performance. The results of metagenome-assembled genomes (MAGs) indicated that the above species have functional genes involved in GABAergic and glutamatergic synapse pathways. Furthermore, metabolomic analysis showed that differential metabolites were enriched in the neuroactive ligand-receptor interaction pathway, in which GABA (γ-aminobutyric acid), histamine and tyramine metabolites were positively correlated with the above species and police performance.

CONCLUSION: The species L. acidophilus, L. johnsonii, L. reuteri, L. animalis, and M. gordoncarteri, which were enriched in the gut of puppies and young Kunming dogs, may potentially influence the nervous system through the production of neurotransmitters and neuromodulators, suggesting a possible association with police performance. Video Abstract.},
}

@article {pmid41840715,
year = {2026},
author = {Liang, R and Liu, X and Chen, Q and Zhang, M and Xu, Y and Shi, H and Wang, S and Jing, W},
title = {Daikenchuto ameliorates dextran sulfate sodium-induced acute and chronic ulcerative colitis by regulating gut microbiota-derived indoles to activate AhR signaling.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {},
pmid = {41840715},
issn = {1749-8546},
support = {82174059//National Natural Science Foundation of China/ ; 2022SF-123//Natural Science Foundation of Shaanxi Province/ ; 2023-ZQNY-004//Outstanding Young and Middle-Aged Scientific and Technological Talents of Shaanxi Administration of Traditional Chinese Medicine/ ; 2022-SLRH-YQ-001//Shaanxi Administration of Traditional Chinese Medicine/ ; JCYJ20250604184258076//Science and Technology Planning Project of Shenzen Municipality, China/ ; },
abstract = {BACKGROUND: Ulcerative colitis (UC), a chronic-relapsing inflammatory disease with rising prevalence worldwide, is primarily driven by intestinal epithelial barrier dysfunction resulting from gut microbial dysbiosis and metabolic disturbances. Daikenchuto (DKT), a traditional Chinese medicine formulation, is commonly used for digestive disorders. Although DKT has demonstrated therapeutic potential for gut inflammation by modulating gut microbiota, its therapeutic effects on chronic ulcerative colitis (CUC) and the related mechanisms remain elusive.

METHODS: The main components of DKT were tentatively identified using ultra-performance liquid chromatography-quadrupole-time of flight-mass spectrometry (UPLC-Q-TOF-MS), and the therapeutic effects of DKT were evaluated in the mouse models of acute colitis (AC) and CUC induced using dextran sulfate sodium. The models were validated based on alterations in the disease activity index (DAI), colonic inflammatory status, and intestinal barrier integrity. The impact of DKT on the dysbiosis of gut microbiota was evaluated using the 16S rRNA gene and metagenomic sequencing. Targeted metabolomics was conducted to quantify shifts in short-chain fatty acids and tryptophan (Trp) metabolites. To further elucidate the underlying mechanisms of DKT, key pathways were analyzed using Western blotting, immunohistochemistry, and real-time quantitative polymerase chain reaction.

RESULTS: The principal constituents of DKT were tentatively identified. DKT administration significantly alleviated the symptoms of AC and CUC, reduced inflammation, and maintained intestinal barrier function. Furthermore, DKT modulated the structure and abundance of gut microbiota. Metagenomic sequencing analysis demonstrated that DKT significantly enriched the relative abundance of Ligilactobacillus murinus, Lactobacillus taiwanensis, and Lactobacillus johnsonii. Moreover, Trp metabolism and Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathways might be the therapeutic mechanisms of DKT. Targeted metabolomics confirmed that Trp/indole was the major pathway during the therapeutic process of DKT on CUC. Further mechanistic studies demonstrated that activation of the aryl hydrocarbon receptor (AhR) signaling enhanced proliferation in the colonic crypts by stimulating IL-22 secretion and promoting STAT3 phosphorylation.

CONCLUSIONS: DKT alleviated AC and CUC in mouse models by modulating gut microbiota, restoring Trp metabolism, and activating the AhR/IL-22/STAT3 signaling pathway. These findings provide a basis for the clinical application of DKT in UC patients.},
}

@article {pmid41840729,
year = {2026},
author = {Mori, H and Fujisawa, T and Higashi, K and Tanizawa, Y and Nakagawa, Z and Nishide, H and Fujiyoshi, M and Nakamura, Y and Uchiyama, I and Matsui, M and Yamada, T},
title = {Microbiome Datahub: an open-access platform integrating environmental metadata, taxonomy, and functional annotation for comprehensive metagenome-assembled genome datasets.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02385-x},
pmid = {41840729},
issn = {2049-2618},
support = {JPMJND2206//Japan Science and Technology Agency/ ; },
abstract = {BACKGROUND: Metagenome-assembled genomes (MAGs) provide crucial insights into the genomic diversity of uncultured microbes. However, MAG datasets deposited in public repositories such as INSDC are often difficult to reuse due to heterogeneous quality, inconsistent taxonomic and functional annotations, and insufficiently curated environmental metadata. While secondary MAG databases such as MGnify, IMG/M, and SPIRE provide standardized resources, they reconstruct MAGs de novo from public metagenomic reads and therefore do not represent the original MAGs reported in publications.

RESULTS: To address this gap, we developed Microbiome Datahub, an open-access platform that systematically aggregates and re-annotates original MAGs from INSDC. We collected 214,427 MAGs, predicted genes by DFAST, performed quality assessment with CheckM, standardized taxonomic assignments with GTDB-Tk, inferred 27 phenotypic traits using Bac2Feature, assigned proteins to MBGD ortholog clusters and KEGG Orthology IDs using PZLAST, and annotated environmental metadata with the Metagenome and Microbes Environmental Ontology. Across these MAGs, the average completeness was 80.5% and contamination 1.8%; notably, the most frequent values were >95% completeness and <1% contamination, indicating that the majority of MAGs are of high quality. Comparative analyses showed that Microbiome Datahub provides phylogenetically and environmentally diverse MAGs: while the majority originated from vertebrate gut environments, a substantial number were also recovered from other habitats such as groundwater, including nearly 10,000 MAGs from the Patescibacteria. Inference of 27 phenotypic traits, including optimum growth temperature, further revealed ecological differentiation across phyla. Protein clustering revealed 56 million identity 40% clusters, with the majority unique compared with MGnify and GlobDB, and ~19% of proteins unassigned to MBGD ortholog clusters, underscoring their novelty.

CONCLUSIONS: Microbiome Datahub integrates MAG genome sequences, gene and protein predictions, quality metrics, environmental and taxonomic annotations, ortholog cluster assignments, and phenotype predictions, all accessible via a web interface, API, and bulk downloads. By combining original MAGs with curated metadata and functional annotations, Microbiome Datahub constitutes a comprehensive and reusable resource that will accelerate microbiome and microbial genomics research. Video Abstract.},
}

@article {pmid41841243,
year = {2026},
author = {Sbampato, V and Khan, AA and Tsoupras, A and De Marco, G and Ceroni, D},
title = {From Culture to Sequencing: Evolving Strategies for the Diagnosis of Pediatric Spondylodiscitis.},
journal = {Orthopaedic surgery},
volume = {},
number = {},
pages = {},
doi = {10.1111/os.70283},
pmid = {41841243},
issn = {1757-7861},
abstract = {Pediatric spondylodiscitis is a rare but clinically significant infection affecting the intervertebral disc and adjacent vertebral bodies. Diagnostic delays are common due to its nonspecific presentation and the limited sensitivity of conventional microbiological methods. Early and accurate pathogen identification is essential to guide antimicrobial therapy, minimize unnecessary invasive procedures, and prevent long-term sequelae. Traditional diagnostic tools-including laboratory tests, imaging, blood cultures, biopsy, and histopathological evaluation-remain fundamental but are often insufficient, as they may yield nonspecific results or culture-negative cases, particularly after prior antibiotic exposure or infection with fastidious organisms. In recent years, molecular approaches, ranging from polymerase chain reaction assays to metagenomic next-generation sequencing, have markedly improved diagnostic accuracy. These techniques allow rapid and comprehensive pathogen detection, including atypical or previously uncultivable organisms, thereby overcoming many limitations of conventional methods. This narrative review synthesizes current evidence on pediatric spondylodiscitis, outlining its epidemiology, clinical features, and the evolving spectrum of diagnostic strategies-from conventional methods to advanced molecular and sequencing-based technologies-while discussing future directions in this challenging field.},
}

@article {pmid41841491,
year = {2026},
author = {Vidal, E and Phanthanourak, AL and Gharib, A and Webel, H and Assis, J and Ayala-Ruano, S and Cunha, AF and Santos, A},
title = {ABaCo: addressing heterogeneity challenges in metagenomic data integration with adversarial generative models.},
journal = {Nucleic acids research},
volume = {54},
number = {5},
pages = {},
doi = {10.1093/nar/gkag227},
pmid = {41841491},
issn = {1362-4962},
support = {NNF20CC0035580//Novo Nordisk Foundation/ ; Pasteur Network, Sep/2023//Calmette & Yersin PhD Grant/ ; NNF20CC0035580//Novo Nordisk Foundation/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Software ; Microbiota/genetics ; Metagenome ; Algorithms ; },
abstract = {The rapid advancement of high-throughput metagenomics has produced extensive and heterogeneous datasets with significant implications for environmental and human health. Integrating these datasets is crucial for understanding the functional roles of microbiomes and the interactions within microbial communities. However, this integration remains challenging due to technical heterogeneity and the inherent complexity of these biological systems. To address these challenges, we introduce ABaCo, a generative model that combines a variational autoencoder with an adversarial discriminator specifically designed to handle the unique characteristics of metagenomic data. Our results demonstrate that ABaCo effectively integrates metagenomic data from multiple studies, corrects technical heterogeneity, outperforms existing methods, and preserves taxonomic-level biological signals. We have developed ABaCo as an open-source, fully documented Python library to facilitate, support and enhance metagenomics research in the scientific community.},
}

*Metagenomics/methods
Humans
*Software
Microbiota/genetics
Metagenome
Algorithms

@article {pmid41841524,
year = {2026},
author = {Akresi, JE and Do, TVT and Cui, Z and Shanmugam, NRS and Moraïs, S and Mizrahi, I and Bayer, EA and Auchtung, JM and Yin, Y},
title = {Limousia bacteria encode mucinolysome for mucin utilization in animal gut microbiomes.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2645267},
doi = {10.1080/19490976.2026.2645267},
pmid = {41841524},
issn = {1949-0984},
mesh = {*Mucins/metabolism ; Animals ; *Gastrointestinal Microbiome ; Humans ; Feces/microbiology ; Metagenome ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; },
abstract = {Mucins create a physical barrier that protects human and animal tissues from microbial pathogens. Here, we provide evidence that mucin degradation can be mediated by unique mucinolysomes, defined as extracellular cellulosome-like multi-enzyme complexes specializing in mucin degradation. We predicted the presence of mucinolysomes across 63 metagenome-assembled genomes (MAGs) and two isolated genomes of three anaerobic species of Limousia, including seven MAGs from human gut microbiome samples from six countries. We validated that mucins can support the growth of the Limousia strain ET540 as its sole carbon source, triggering the upregulation of most mucinolysome-related genes in ET540. We modeled the mucinolysome assembly by predicting cohesin‒dockerin interactions among most of the mucinolysome proteins using AlphaFold3. We performed metagenomic read mapping of 2897 fecal samples from various human cohorts and wild/domesticated animals against Limousia MAGs. We found that Limousia has a greater abundance and prevalence in farm animals than in humans. This study characterizes and adds the Limousia bacteria as unique member to the list of human and animal gut mucin glycan-degrading bacteria. Overall, we discovered that this novel gut bacteria genus (Limousia) uses a previously unrecognized molecular mechanism for highly organized mucin glycan degradation, shedding new light on microbe‒host interactions in the gastrointestinal tracts of diverse animal hosts, including humans.},
}

*Mucins/metabolism
Animals
*Gastrointestinal Microbiome
Humans
Feces/microbiology
Metagenome
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenomics

@article {pmid41841608,
year = {2026},
author = {Farsi, DN and Cotillard, A and Wilson, B and So, D and Gibson, PS and Slater, R and Probert, C and Morris, S and Scott, SM and Quinquis, L and Pichaud, M and Shetty, S and Tap, J and Le Nevé, B and Rossi, M and Whelan, K},
title = {Gut Microbiome Composition and Function, Diet and Clinical Factors in Relation to Fermentable Carbohydrate-Induced Bloating: A Double-Blind, Randomized, Crossover Trial.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000003997},
pmid = {41841608},
issn = {1572-0241},
abstract = {BACKGROUND: Specific foods are associated with abdominal bloating, which can significantly impact quality of life.

OBJECTIVE: To identify responders to fiber-induced bloating and the mechanisms underpinning clinical and microbial responses.

DESIGN: Double-blind, placebo-controlled, randomized, 2-period, 2-challenge crossover trial in 41 individuals with functional bloating. Participants were randomized to 8 g/d of fructan or α-galacto-oligosaccharides (α-GOS) for 7 days with a 21-day washout. Clinical, nutritional, microbial (shotgun sequencing, metatranscriptomics) and fermentation (short-chain fatty acids, volatile organic compounds, breath hydrogen) profiles were characterized prior to each challenge to identify factors predicting response, and after the challenge to elucidate mechanisms underpinning food-induced bloating.

RESULTS: Thirty-nine participants completed both challenges (39 fructan, 40 α-GOS). Overall, seven (7/39, 17.9%) participants were fructan responders and eight (8/40, 20%) were α-GOS responders (experienced fiber-related symptom induction). Clinical metrics indicative of bloating distinguished responders and non-responders to both challenges, including greater abdominal girth (fructan, p = 0.009; α-GOS, p = 0.030). α-GOS responders had higher breath hydrogen (H2) pre-challenge than α-GOS non-responders (p = 0.011). Trends were identified within metagenomic and metatranscriptomic gut microbial analyses, with higher carbohydrate active enzyme (CAZyme) diversity in fructan responders (pre-challenge, adjusted p-value (padj) = 0.024; post-challenge, padj = 0.042), and greater increase in gene expression for gamma-aminobutyric acid (GABA) degradation in α-GOS responders (padj = 0.041).

CONCLUSION: A higher burden of GI symptoms predicts clinical response to fermentable fibers in functional bloating, while for α-GOS, higher repeated fasting breath H2 is also a predictor. Gut microbiome function and fermentation is associated with functional bloating; however, further investigations are required to draw firm conclusions for the microbial influence in this interplay.ClinicalTrials.gov (Identifier: NCT04802798).},
}

@article {pmid41841712,
year = {2026},
author = {Oganesyan, EG and Zhuk, AS and Venchakova, VV and Dolgo-Saburova, YV and Zhorzh, ON and Zhang, FM and Vasilyeva, NV and Taraskina, AE},
title = {Microbiome associated with recurrent vulvovaginal candidiasis: key characteristics and potential therapeutic targets.},
journal = {Biomeditsinskaia khimiia},
volume = {72},
number = {1},
pages = {62-74},
doi = {10.18097/PBMCR1644},
pmid = {41841712},
issn = {2310-6972},
mesh = {Humans ; Female ; *Candidiasis, Vulvovaginal/microbiology/drug therapy ; *Microbiota ; Adult ; Case-Control Studies ; *Vagina/microbiology ; Recurrence ; Lactobacillus/genetics/isolation & purification ; Prevotella ; },
abstract = {Recurrent vulvovaginal candidiasis (RVVC) is one of the most complex forms of urogenital infection in terms of its clinical burden, impact on quality of life, and difficulty in preventing relapses. The aim of this study was to comprehensively characterize the taxonomic composition and functional potential of the vaginal microbiome associated with RVVC. This case-control study included patients with RVVC and conditionally healthy women. Vaginal samples were analyzed using shotgun metagenomic sequencing, followed by taxonomic and functional annotation of the microbiome using data quality control, taxonomic classification (Kraken2, MetaPhlAn4), and functional annotation (HUMAnN 3.9). At the community structure level, the RVVC microbiome exhibited pronounced interindividual variability and did not represent a uniform microbiota configuration. The taxonomic profile of the microbiome in RVVC was characterized by an increased relative abundance of Lactobacillus iners and anaerobic taxa (Prevotella bivia, Dialister microaerophilus), forming a compact "core" of intergroup differences. Functional analysis revealed a limited but reproducible set of metabolic pathways associated with RVVC; these included pathways of purine metabolism, central carbohydrate metabolism, and biosynthesis of cofactors and cell wall components. RVVC is associated not only with changes in the taxonomic composition of the microbiota but also with a stable reconfiguration of its functional potential. The identified shifts in metabolic pathway patterns reflect a transition of the vaginal microbial community to an alternative functional state, thus highlighting the need to develop new therapeutic strategies alternative to traditional antifungal-based approaches.},
}

Humans
Female
*Candidiasis, Vulvovaginal/microbiology/drug therapy
*Microbiota
Adult
Case-Control Studies
*Vagina/microbiology
Recurrence
Lactobacillus/genetics/isolation & purification
Prevotella

@article {pmid41841737,
year = {2026},
author = {Cruz, MC and Ruhal, R and Lavin, J and Bridwell, S and Maghboli Balasjin, N and Raasch, B and Melton, R and Mayer, BK and Marshall, CW and Hristova, K},
title = {Acinetobacter spp. with lower susceptibility to quaternary ammonium compounds enriched in microbial communities of frequently used sinks.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0196825},
doi = {10.1128/aem.01968-25},
pmid = {41841737},
issn = {1098-5336},
abstract = {Sanitary environments that undergo frequent cleaning and disinfection may harbor microbial communities with potential health risks. While biofilms in healthcare settings are well studied, comparatively less is known about sink-drain microbiomes in public and educational buildings, where hundreds of people may interact with shared sink fixtures. This study characterized the spatial and temporal heterogeneity of sink-drain biofilm microbiomes in academic buildings. We sampled 16 sinks from two buildings (four floors each, with sinks closest and furthest to the bathroom entrance), which are cleaned daily with quaternary ammonium compound (QAC) disinfectants, during periods of low and high student traffic (during and after academic breaks, respectively) across winter, spring, and summer. We observed significant spatial and temporal variations in microbial assemblages. Individual sinks accounted for 43% (PERMANOVA, P < 0.0001) of the variation in microbial communities. Microbiomes in each building were dominated by two genera, which together accounted for 30% of the community composition: Acinetobacter and Enhydrobacter (also classified as Moraxella) in the newer building, and Sphingomonas and Mycobacterium in the older building. Acinetobacter abundance varied seasonally and showed higher relative abundance during periods of high traffic. Metagenomic analysis of selected sinks revealed a high prevalence of qac genes and metagenome-assembled genomes (MAGs) harboring antimicrobial resistance genes (ARGs), including A. parvus. Notably, 34%-53% of qac genes were co-localized on contigs associated with mobile genetic elements. These findings suggest that disinfected sink drains serve as persistent reservoirs of diverse microorganisms and potentially mobile resistance elements.IMPORTANCESink drains are recognized as environmental reservoirs for multidrug-resistant bacteria and have been linked to healthcare-associated outbreaks. In public and educational buildings, these microbiomes are shaped by frequent human activity, making them potential sources of exposure and contributors to the environmental dissemination of antibiotic resistance genes. Quaternary ammonium compound (QAC) disinfectants are widely used on surfaces; however, they can select for resistant taxa and co-select for antibiotic resistance. In this study, despite routine cleaning of sink surfaces with QACs, public restroom sink drains remain colonized by resilient biofilms, posing a potential risk to multiple users. Additionally, factors such as human traffic and seasonal variation may influence drain usage and microbial community composition. Elucidating how seasonal dynamics and human activity shape sink-drain biofilms is essential for understanding their role in the environmental transmission of antimicrobial resistance and informing mitigation strategies in nonclinical settings.},
}

@article {pmid41841761,
year = {2026},
author = {Ward, B and Bindels, LB and Balligand, J-L and Bearzatto, B and Bommer, G and Cani, PD and De Greef, J and Dewulf, JP and Gatto, L and Haufroid, V and Jodogne, S and Kabamba, B and Pyr Dit Ruys, S and Vertommen, D and Yombi, JC and Belkhir, L and Elens, L},
title = {Association of nasopharyngeal Dolosigranulum pigrum and Corynebacterium species with post-acute sequelae of SARS-CoV-2 in a longitudinal cohort.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0231325},
doi = {10.1128/spectrum.02313-25},
pmid = {41841761},
issn = {2165-0497},
abstract = {This longitudinal study investigated the differential composition of the nasopharyngeal microbiome in patients presenting different COVID-19 infectious phenotypes and its evolution during convalescence, with a focus on post-acute sequelae of SARS-CoV-2 (PASC) and its potential microbiome-related mechanisms. Microbiota composition was assessed for a cohort of healthy participants (n = 25), influenza patients (n = 24), and patients with moderate (n = 50) and severe (n = 57) COVID-19. Samples were collected at two time points: during the acute infection phase and at approximately 3-month follow-up. From collected nasopharyngeal swab samples, metagenomics using shotgun sequencing was performed and the microbiota composition was analyzed. Alpha and beta diversity analyses revealed no significant differences in overall community diversity between patient groups across visits. However, differential abundance testing identified specific species, such as Dolosigranulum pigrum and various Corynebacterium species, whose profiles correlated with PASC development. Furthermore, the analysis of microbial co-associations identifies commensal species, including D. pigrum and Corynebacterium species, which are less abundant in patients who develop PASC, consistent with a potential protective role suggested by experimental studies but not proven by our observational data. Antibiotic use was associated with lower levels of key protective taxa, which may increase susceptibility to PASC in case of superinfection. These findings highlight the potential importance of the nasopharyngeal microbiome in acute COVID-19 disease outcomes and suggest that preserving or restoring a balanced respiratory microbiome could mitigate the risk of COVID-19 persistent symptoms and PASC development. Our results may set the stage for future clinical interventions involving probiotics or microbial-derived metabolites to promote respiratory health post-COVID-19.IMPORTANCEThis study highlights the importance of bacteria naturally found in the upper respiratory tract, particularly the nasopharynx (the nasopharyngeal microbiome), in shaping how severely COVID-19 affects patients and whether they experience persistent symptoms, also called long-COVID or post-acute sequelae of SARS-CoV-2 (PASC). By examining microbiome samples from healthy people, influenza patients, and individuals with COVID-19 during acute and convalescent phases, we found that certain commensal bacteria, namely, Dolosigranulum pigrum and Corynebacterium species, were less abundant in individuals who developed long-COVID and more abundant in those who fully recovered. We also observed that antibiotic treatment was associated with lower abundances of these commensal taxa, in turn coinciding with a higher frequency of PASC. These findings suggest that the composition of the nasopharyngeal microbiome is associated with recovery trajectories after COVID-19 and motivate future research into treatments aimed toward the microbiome to improve respiratory health following infection.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT05557539.},
}

@article {pmid41842581,
year = {2026},
author = {Wang, X and Chen, J and Xia, J and Ma, T and Yang, W and Shan, T and He, W and Zhang, G and Xia, Z and Wang, W and Liu, Z and Zheng, Y and Nong, K and Niu, P and Chen, T},
title = {Brain-Targeted RVG-Liposomal Melatonin Ameliorates Manganese Neurotoxicity by Enhancing Neurogenesis and Modulating Systemic Amino Acid Profiles.},
journal = {Journal of pineal research},
volume = {78},
number = {2},
pages = {e70137},
doi = {10.1111/jpi.70137},
pmid = {41842581},
issn = {1600-079X},
support = {82173489//National Natural Science Foundation of China/ ; 7232234//Beijing Natural Science Foundation/ ; },
mesh = {Animals ; *Melatonin/pharmacology/administration & dosage ; Mice ; *Manganese/toxicity ; Liposomes ; *Brain/metabolism/drug effects ; *Neurogenesis/drug effects ; *Glycoproteins/pharmacology ; *Amino Acids/metabolism ; Male ; Mice, Inbred C57BL ; *Neurotoxicity Syndromes/drug therapy/metabolism ; *Neuroprotective Agents/pharmacology ; Gastrointestinal Microbiome/drug effects ; Peptide Fragments ; Viral Proteins ; },
abstract = {Chronic manganese (Mn) exposure induces severe neurotoxicity, characterized by impaired neurogenesis and disrupted metabolic homeostasis. Although melatonin (MT) possesses established neuroprotective properties, its clinical utility is hindered by poor bioavailability and limited brain delivery. Here, we developed a brain-targeted, rabies virus glycoprotein (RVG)-modified liposomal delivery system encapsulating melatonin (MT@RVG-Lip) to enhance therapeutic efficacy. Multi-omics analyses including brain and intestinal transcriptomics, serum metabolomics, and gut metagenomics were conducted to elucidate the underlying mechanisms. MT@RVG-Lip significantly improved motor deficits and enhanced neurogenesis while reducing neuroinflammation in Mn-exposed mice. Compared with regular MT and CaNa2-EDTA, MT@RVG-Lip more effectively alleviated Mn-disrupted gene expression in neurogenesis regions, particularly genes involved in amino acid metabolism. Additionally, MT@RVG-Lip demonstrated a regulatory effect on serum amino acid profiles and intestinal transporter gene expression. Gut microbiota analysis further revealed that MT@RVG-Lip partially reversed Mn-associated dysbiosis and promoted the improvement of key amino acid-related microbiota-mediated metabolic pathways. The RVG-modified liposomal formulation conferred sustained release and improved brain-targeting capability, prolonging MT bioavailability and enhancing therapeutic outcomes. These findings provide a new mechanistic framework for MT-based interventions in neurodegenerative diseases and highlight the therapeutic potential of multifunctional delivery strategies.},
}

Animals
*Melatonin/pharmacology/administration & dosage
Mice
*Manganese/toxicity
Liposomes
*Brain/metabolism/drug effects
*Neurogenesis/drug effects
*Glycoproteins/pharmacology
*Amino Acids/metabolism
Male
Mice, Inbred C57BL
*Neurotoxicity Syndromes/drug therapy/metabolism
*Neuroprotective Agents/pharmacology
Gastrointestinal Microbiome/drug effects
Peptide Fragments
Viral Proteins

@article {pmid41842880,
year = {2026},
author = {González-Mercado, VJ and Jean Lim, S and Kumar Singh, P and Sales-Martinez, S and Fernandez-Cajavilca, M and Marrero, LM and Pedro, E and D'Eramo Melkus, G},
title = {Dietary Quality and Microbiome Profiles among Rectal Cancer Patients: A Cross-Sectional Pilot Study.},
journal = {Puerto Rico health sciences journal},
volume = {45},
number = {1},
pages = {3-10},
pmid = {41842880},
issn = {2373-6011},
mesh = {Humans ; *Rectal Neoplasms/therapy/microbiology ; Male ; Female ; Middle Aged ; Pilot Projects ; *Gastrointestinal Microbiome ; *Diet ; Cross-Sectional Studies ; Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Metagenomics ; Neoadjuvant Therapy ; },
abstract = {OBJECTIVE: Examining whether gut microbial taxa abundances and predicted functional pathways correlate with dietary quality scores at the end of neoadjuvant chemoradiotherapy (nCRT) for rectal cancer (RC); identifying differentially abundant bacterial species from the pantothenate and acetyl-coenzyme A biosynthesis pathways that differ among dietary quality groups in a subset of participants.

METHODS: RC patients (n = 30) provided stool samples for 16S rRNA gene sequencing. To validate pathway predictions from the 16S rRNA gene data, stool samples from a subset of 17 participants underwent shallow shotgun metagenomics sequencing (SMS). Dietary quality was calculated using the Prime Diet Quality Score (PDQS; 24-hour recall). 16S rRNA gene data were analyzed using QIIME2, and SMS data were analyzed using HUMAnN2.

RESULTS: At the genus level, Parvimonas, Caproiciproducens, and uncultured Eggerthellaceae abundances positively correlated (Spearman's rho = 0.36 to 0.50) with PDQS scores, whereas abundances of Prevotella, Rothia, Peptostreptococcus, Paeniclostridium, Enterococcus, and Howardella correlated negatively (Spearman's rho = -0.43 to 0.36). Predicted pathways, including those related to B-vitamin biosynthesis and enzyme cofactor biosynthesis (e.g., B5/pantothenate [phosphopantothenate biosynthesis I]), were correlated with higher PDQS scores. Mean abundances of species predicted to encode the vitamin B5-CoA pathway were greater in the high- diet-quality group.

CONCLUSION: Findings suggest important associations between the taxa abundances of gut bacteria and the abundances of predicted B-vitamin biosynthesis pathways and dietary quality at the end of nCRT. Three bacterial species encoding vitamin B5-CoA biosynthesis pathways were prominent in high-dietaryquality participants.},
}

Humans
*Rectal Neoplasms/therapy/microbiology
Male
Female
Middle Aged
Pilot Projects
*Gastrointestinal Microbiome
*Diet
Cross-Sectional Studies
Aged
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Metagenomics
Neoadjuvant Therapy

@article {pmid41843187,
year = {2026},
author = {Chu, T and Wang, Q and Hu, C and Yu, J and Chen, L and Yu, Y and Wang, Y},
title = {Microalga-virus-virophage coculture reveals co-infection of multi-virophages with a giant virus.},
journal = {Archives of virology},
volume = {171},
number = {4},
pages = {},
pmid = {41843187},
issn = {1432-8798},
support = {31570112//National Natural Science Foundation of China/ ; },
mesh = {*Chlorella/virology ; Coculture Techniques ; *Microalgae/virology ; *Giant Viruses/physiology/genetics ; *Virophages/genetics/physiology ; Coinfection ; Virus Replication ; },
abstract = {Virophages parasitize the replication of co-infecting giant viruses within eukaryotic cells, forming tripartite cell-virus-virophage (CVv) systems. Tripartite interactions are well-documented in protozoa, yet comparable systems in algae remain largely unexplored at the experimental level. Here, we report an experimentally validated CVv system involving the green, single-celled microalga Chlorella sp. DSL01, Dishui Lake large algal virus 1 (DSLLAV1), and multiple Dishui Lake virophages (DSLVs). Inoculation of Chlorella sp. DSL01 at low MOI established laboratory co-cultures in which time-series PCR detected DSLLAV1 early but not after Day 10, whereas all tested virophages persisted. Metagenomic profiling of the terminal supernatant (end-point sample) indicated a virophage-dominated assemblage with DSLV3 most represented. Droplet digital PCR at discrete time points (Days 5, 10, and 15) then provided absolute counts for DSLLAV1 and DSLV1/3/7, corroborating an early DSLLAV1 peak followed by collapse and/or a delayed rise of multiple virophages coincident with host growth recovery. Nested PCR on the algal pellet detected virophages DSLV1/3/7 but not DSLLAV1. Together, these results demonstrate that Chlorella sp. DSL01 supports co-infection by DSLLAV1 and multiple virophages, establishing an experimentally validated algal CVv system and revealing multi-virophage participation in freshwater algal virus-virophage-host dynamics.},
}

*Chlorella/virology
Coculture Techniques
*Microalgae/virology
*Giant Viruses/physiology/genetics
*Virophages/genetics/physiology
Coinfection
Virus Replication

@article {pmid41843252,
year = {2026},
author = {Xia, HL and Liang, PY and Yuan, WG and Cao, XD and Sun, Y and Jiang, JZ and Yuan, LH},
title = {PhaGCN_Cluster: A Scalable and Robust Framework for Automated Classification and Discovery of Viral Dark Matter from Metagenomes.},
journal = {Interdisciplinary sciences, computational life sciences},
volume = {},
number = {},
pages = {},
pmid = {41843252},
issn = {1867-1462},
support = {No. 2022KCXTD017//Innovation Team Project of Guangdong Universities/ ; No. 324CXTD435//Natural Science Foundation of Hainan Province/ ; No. 2023TD44//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; },
abstract = {Viruses are the most abundant biological entities on Earth, playing essential roles in shaping microbial communities, driving evolution, and maintaining ecosystem functions. Metagenomic sequencing has unveiled a vast landscape of uncharacterized viral "dark matter", comprising highly divergent sequences that elude traditional taxonomic approaches. Here, we develop PhaGCN_Cluster, a next-generation viral classification tool built upon a graph convolutional neural network (GCN) framework. By integrating protein-level sequence similarity and contig-level genomic features, PhaGCN_Cluster establishes a scalable knowledge graph-based analytical system. The optimized algorithm yields significant gains in computational efficiency, supporting accurate taxonomic assignment of up to 300,000 contigs per run. Compared with existing methods, PhaGCN_Cluster demonstrates superior classification accuracy and F1-scores, particularly under conditions of low sequence similarity, and exhibits strong robustness in detecting evolutionarily distant viruses. Notably, PhaGCN_Cluster incorporates an updated logic for assigning "_like" taxa, which enhances its capacity to accommodate novel viral groups while preserving high precision-though at the cost of a slight reduction in recall. By generating high-fidelity network graphs, PhaGCN_Cluster uncovers previously unrecognized clades and bridges evolutionary gaps between reference viruses and novel sequences, thereby providing critical insights into viral diversity and evolution. PhaGCN_Cluster represents an interpretable, efficient, and scalable solution for automated virus classification. The source code of PhaGCN_Cluster is available via https://github.com/xiahaolong/PhaGCN_Cluster .},
}

@article {pmid41756930,
year = {2026},
author = {Yuan, L and Qin, Y and West-Roberts, J and Anantharaman, K and Wang, H and Zou, Y and Duan, Y and Camargo, AP and Koonin, EV and Chen, L},
title = {A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41756930},
issn = {2692-8205},
abstract = {Closely related prophages are frequently found in phylogenetically distant bacteria in the human gut, despite limited evidence of productive phage infections across broad host ranges. Thus, it remains unclear how the wide distribution of prophages could emerge. Here, we identify a potential mechanism of prophage dissemination. We describe two deeply diverged groups of conjugative megaplasmids (>300 kilobases) in the human gut microbiome, which we term Hodors. Hodors encode conserved replication, partitioning, and type IV secretion systems, together with a complex surface-associated gene module. A subset of Hodors harbor complete, intact prophage genomes, and closely related prophages are detected across phylogenetically distant Bacillota lineages, including both Bacilli and Clostridia. Further analysis indicates that Hodor-associated prophages can exist as extracellular particles and demonstrate their transcriptional activity. Our findings support a model in which conjugative megaplasmids act as composite mobile platforms that disseminate prophage genomes across bacterial lineages, providing a mechanistic explanation for the widespread occurrence of closely related prophages in phylogenetically distant gut bacteria and effectively decoupling lysogenic host range from infective host range.},
}

@article {pmid41833574,
year = {2026},
author = {Saibu, S and Obayori, OS and Diagboya, PN and Oso, SO and Shedrack, AE and Agbomeji, RO and Eletu, MO and Ajibike, OR and Ishola, FM and Adimabua, RN and Oyetibo, GO},
title = {Spatial variation in bacterial community structure and pollution response in river sediment.},
journal = {Journal of contaminant hydrology},
volume = {279},
number = {},
pages = {104923},
doi = {10.1016/j.jconhyd.2026.104923},
pmid = {41833574},
issn = {1873-6009},
abstract = {Rivers are unique ecosystems where pollution frequently occurs, altering the biogeochemical characteristics of both water bodies and sediments. However, little is known about the effects of human activities on the lower course of River Ogun. This study assessed the association between anthropogenic activities and sediment bacterial communities at the time of sampling by comparing sediment physicochemical properties and the bacterial community structures of samples. Samples were taken from four distinct sites along the lower course of the river. Bacterial community structure of these sites was investigated using the 16S rRNA gene PacBio sequencing. Total polycyclic aromatic hydrocarbons (PAHs) were lowest at Location B (6.95 mg/kg) and highest at Location A (15.6 mg/kg). The dominant bacterial phyla in the sediments were Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota. A notable abundance of Thauera was observed across all the locations, particularly at Location A, and Psychrobacter known for plastic degradation was detected exclusively at this site. Among all the sites, Location A exhibited the lowest bacterial diversity, as indicated by both species' richness and evenness, where the Thauera selenatis group and Psychrobacter maritimus were dominant. Location B exhibited the highest bacterial diversity, Location C and D displayed intermediate diversity, sharing a 40% similarity index. Environmental variables that significantly explained beta diversity patterns included pH, anthracene and fluoranthene. This study provides insights into bacterial metagenomes of a freshwater inundated with plastics, heavy metals and consortium of persistent organic compounds. The findings highlight the value of integrating metagenomic and physicochemical analyses to identify correlations that help explain the key drivers shaping ecosystem dynamics.},
}

@article {pmid41833938,
year = {2026},
author = {Li, D and Qu, ZS and Wang, C and Peng, ZH and Zhou, X and Cai, L},
title = {The Anna Karenina principle in the assembly of plant microbiome under pathogen stress.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00964-2},
pmid = {41833938},
issn = {2055-5008},
support = {U24A20343//National Natural Science Foundation of China/ ; 32300009//National Natural Science Foundation of China/ ; 32330002//National Natural Science Foundation of China/ ; XDB0810000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; },
abstract = {The Anna Karenina Principle (AKP) posits that healthy microbiomes converge toward similar compositional states, whereas dysbiotic microbiomes diverge into distinct and system-specific configurations. Despite its broad recognition in microbiome research, systematic evidence remains scarce as to whether pathogen stress drives plant microbiome assembly in accordance with AKP. To address this knowledge gap, we examined 1,410 samples from multiple compartments (bulk soil, rhizosphere soil, roots, stems, and seeds) across a continental-scale, comparing healthy and Fusarium stalk rot-infected maize using 16S rRNA gene sequencing, complemented with metagenomic sequencing of 93 selected rhizosphere and stem samples. By integrating variations of bacterial community diversity, beta dispersion, average variation degree, and a modified stochasticity ratio, we demonstrated that pathogen-induced microbiome shifts conform to AKP predictions. Notably, AKP-conforming stochastic assembly enriched oligotrophic taxa, resulting in microbial communities with higher GC content, smaller average genome size, and reduced 16S rRNA operon copy numbers. Moreover, the selective enrichment of specific functional traits (including peptidoglycan biosynthesis and degradation, chromatin structure and dynamics, and lipid transport and metabolism) was closely associated with AKP. Our findings support AKP as a useful framework for understanding plant microbiome assembly under pathogen pressure and provide new insights into plant-microbiome-pathogen interactions.},
}

@article {pmid41834217,
year = {2026},
author = {Yuan, X and Gong, H and Zhang, L and Liu, Y and Zhou, M and Liu, Y and Tang, J and Pan, S and Xu, X and Wang, Y and Zhang, X and Zhang, T and Song, J},
title = {T2DM-Induced Gut Dysbiosis Exacerbates Periodontitis Through Intestinal Barrier Disruption and Redox Imbalance.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70116},
pmid = {41834217},
issn = {1600-051X},
support = {U22A20314//National Natural Science Foundation of China/ ; 82170968//National Natural Science Foundation of China/ ; 82301082//National Natural Science Foundation of China/ ; 2022YFC2504200//National Key Research and Development Program of China/ ; 2025MD774176//China Postdoctoral Science Foundation/ ; YXQN202401//Chongqing Youth Talent Support Program/ ; },
abstract = {AIM: To investigate the potential role and underlying mechanisms of gut microbiota in type 2 diabetes mellitus (T2DM)-exacerbated periodontitis.

MATERIALS AND METHODS: A T2DM-associated periodontitis model was established in C57BL/6 mice and analysed using multi-omics sequencing (16S rRNA, metagenomics and metabolomics). Faecal microbiota transplantation (FMT) from T2DM donors was carried out in recipient mice to investigate the impact of gut dysbiosis on periodontitis. FMT from healthy donors, supplementation of intestinal barrier protectant or the metabolite oleic acid (OA) was administered to mice with T2DM-associated gut dysbiosis to examine their ameliorative effects on periodontal damage.

RESULTS: T2DM-associated gut dysbiosis, independent of hyperglycaemia, triggered intestinal barrier disruption, which disturbed systemic redox-related metabolisms and elevated oral oxidative stress, thereby aggravating periodontitis. Restoring gut microbiota via FMT from a healthy donor or protecting the intestinal barrier ameliorated periodontitis. Exogenous supplementary metabolite OA rescued periodontal damage by activating the SIRT1/FoxO1 pathway and enhancing antioxidant enzymes in mice with T2DM-associated gut dysbiosis.

CONCLUSIONS: T2DM-induced gut dysbiosis exacerbates periodontitis through intestinal barrier disruption and redox imbalance. These findings provide new adjunctive therapeutic perspectives including microbiota restoration, intestinal barrier protection and antioxidant supplementation for managing patients with T2DM-induced periodontitis.},
}

@article {pmid41834639,
year = {2026},
author = {Soliman, MS and Abbas, AM and Algebaly, HF and El-Kholy, AA and Soliman, NS},
title = {Metagenomics profiling of the lower respiratory tract microbiome and relevant respiratory pathogens in pediatric intensive care unit patients: a pilot exploratory study in Egypt.},
journal = {Acute and critical care},
volume = {41},
number = {1},
pages = {136-147},
doi = {10.4266/acc.003816},
pmid = {41834639},
issn = {2586-6060},
abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are a leading cause of mortality in children. These infections disrupt the equilibrium of lower respiratory tract (LRT) microbiota, allowing respiratory pathogens to dominate. The conventional culture method has limitations in describing complex microbiomes and may fail in the detection of respiratory pathogens. In the present study, we sought to use the advanced technology of 16S metagenomics next-generation sequencing (16SmNGS) to characterize the LRT microbiome among children with LRTIs and to identify the underlying respiratory pathogens that commonly evade detection by traditional culture.

METHODS: Twenty LRT specimens from hospitalized children with LRTIs were analyzed using 16SmNGS, as well as standard microbiological culture.

RESULTS: The 16SmNGS taxonomical analysis revealed the highest relative abundances for Streptococcus (27.7%) and Escherichia (13.3%) genera, which belong to the phyla of Firmicutes (45.4%) and Proteobacteria (45.3%), respectively. Streptococcus pneumoniae (45%), Escherichia coli (45%), Pseudomonas aeruginosa (15%), Staphylococcus aureus (10%), Acinetobacter baumannii (5%), and Haemophilus influenzae (5%) were the primary respiratory pathogens. Conventional culture failed to detect growth in 100%, 77.7%, and 55.5% of 16SmNGS-positive specimens for H. influenza, S. pneumoniae, and E. coli, respectively.

CONCLUSIONS: The 16SmNGS technique revealed a predominance of Streptococcus and Escherichia genera belonging to the phyla of Firmicutes and Proteobacteria in pediatric LRTIs. In this exploratory study, 16SmNGS was able to enhance the identification of significant respiratory pathogens, particularly those difficult to isolate in culture. However, to rule out contamination by flora, it is advisable not to interpret metagenomics results independently from culture, clinical, and radiological data. In addition, further clinical correlations are desired to reach appropriate clinical decisions.},
}

@article {pmid41834860,
year = {2026},
author = {Du, Y and Chen, L and Zhang, X and Zeng, J and Hu, C},
title = {Based on untargeted metabolomics and metagenomics: a study on the mechanism of Miao ethnomedicine Zingiber mioga (Thunb.) Rosc. in treating slow transit constipation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1751739},
pmid = {41834860},
issn = {1664-302X},
abstract = {INTRODUCTION: Slow transit constipation (STC) is a prevalent gastrointestinal disorder characterized by impaired intestinal motility, metabolic dysregulation, and gut microbial dysbiosis. Zingiber mioga (Thunb.) Rosc. (RH), a traditional medicinal-edible plant, is empirically used to alleviate gastrointestinal dysfunction, but its therapeutic mechanisms in STC remain unclear. Herein, we investigated the laxative efficacy and mechanism of RH in a rat STC model via integrated untargeted metabolomic and metagenomic analyses, providing experimental evidence for its clinical use.

METHODS: A rat STC model was established by intragastric loperamide hydrochloride (5 mg/kg) for 35 consecutive days. Thirty-six SD rats were randomly divided into six groups (n = 6): normal control, STC model, mosapride-positive control (2 mg/kg), and low- (1350 mg/kg), medium- (2700 mg/kg), high-dose (3400 mg/kg) RH groups, with concurrent drug intervention. Serum concentrations of SP, MTL, and GAS (key gastrointestinal motility regulators) were quantified. Colonic pathological damage was histopathologically evaluated, and intestinal propulsive rate was measured. Untargeted serum metabolomics and fecalmetagenomics identified differential metabolites and gut microbiota alterations.

RESULTS: Compared with the STC model, RH significantly reduced serum SP (intestinal motility inhibitor) and increased MTL/GAS (motility promoters). It also dose-dependently ameliorated colonic lesions and improved intestinal propulsive rate. Serum metabolomics identified 15 differential metabolites, mainly enriched in nitrogen metabolism, neuroactive ligand-receptor interaction, and amino acid metabolism. Fecal metagenomics showed RH restored the Eubacteriales/Lachnospirales ratio (a STC dysbiosis marker) and increased beneficial genera (e.g., Ruminococcus sp., Eubacterium sp.).

DISCUSSION AND CONCLUSION: Our findings show RH effectively ameliorates colonic injury and gastrointestinal motility in STC rats, associated with regulating gastrointestinal hormone secretion. Its benefits are likely mediated by improving dysregulated amino acid/nitrogen metabolism and modulating gut microbiota composition. This study provides mechanistic evidence for RH as a natural functional agent for STC management, laying a foundation for exploring its active components and clinical translation.},
}

@article {pmid41834868,
year = {2026},
author = {Niu, M and Pan, J and Guo, Y and Zhang, F and Guan, H and Yang, X and Li, H and Xiong, H and Zhang, Y and Chen, Y},
title = {Neonatal jaundice and the infant gut microbiome: an integrated shotgun metagenomics and bidirectional Mendelian randomization study in Xinjiang.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1761712},
pmid = {41834868},
issn = {1664-302X},
abstract = {BACKGROUND: Neonatal jaundice is a common condition, yet inter-individual variation in its onset and severity cannot be fully explained by traditional clinical risk factors. Emerging evidence suggests that the infant gut microbiome may modulate bilirubin metabolism, but its compositional and functional signatures in jaundiced neonates remain incompletely defined. This study aimed to characterize the taxonomic and functional features of the gut microbiome in neonatal pathologic jaundice and to explore potential causal links using Mendelian randomization (MR).

METHODS: We conducted a case-control study of term infants with pathologic jaundice and matched healthy controls. Stool samples were subjected to shotgun metagenomic sequencing to assess microbial diversity, taxonomic composition, functional gene repertoires, and carbohydrate-active enzyme families, and publicly available genome-wide association study summary statistics were used to perform bidirectional MR between microbiome-related traits and neonatal jaundice.

RESULTS: Alpha diversity indices did not differ significantly between groups, whereas beta diversity based on Bray-Curtis dissimilarity showed clear separation of jaundiced and control infants, indicating a restructured microbial community rather than a simple loss of richness. Jaundiced neonates exhibited increased relative abundance of Gram-negative taxa, including Escherichia coli, and reduced levels of putatively beneficial genera such as Bifidobacterium and Lactobacillus. Functionally, pathways involved in bile acid synthesis and metabolism, carbohydrate and energy metabolism, and cofactor and vitamin biosynthesis were enriched in the jaundiced group, accompanied by marked shifts in carbohydrate-active enzyme profiles. Forward MR suggested that several microbial metabolic pathways exert genetically predicted effects on jaundice risk, whereas reverse MR provided little evidence that genetic liability to jaundice substantially alters microbiome traits.

CONCLUSIONS: Neonatal pathologic jaundice is associated with distinctive compositional and functional alterations in the gut microbiome. Genetic evidence from MR supports a potential causal contribution of specific microbial pathways to jaundice risk, highlighting candidate targets for microbiome-based prevention or adjunctive therapy in early life.},
}

@article {pmid41834872,
year = {2026},
author = {Han, Z and Wang, H and Liu, X and Tian, Z and Gong, Q and Zhang, X and Li, X and Du, R and Hu, X and Xu, C},
title = {Cross-species transmission alert: a novel canine-raccoon dog coronavirus infecting an Amur Tiger in China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1764349},
pmid = {41834872},
issn = {1664-302X},
abstract = {Canine coronavirus (CCoV) is an important enteric alphacoronavirus primarily affecting canids. Here, we detected canine coronavirus RNA in a captive 9-year-old Amur tiger (Panthera tigris altaica) in China. The complete viral genome was obtained using metagenomic next-generation sequencing. Phylogenetic and recombination analyses were then performed to investigate its evolutionary relationship with canine and feline coronaviruses. The identified CCoV strain clustered within established canine coronavirus lineages and showed sequence evidence of recombination involving coronavirus strains previously reported in other carnivore species. Although the detection of viral RNA alone does not establish a causal relationship between CCoV infection and disease outcome, this study provides molecular evidence that Amur tigers are susceptible to canine coronavirus infection. These findings expand the known host range of CCoV and contribute to understanding the evolution and cross-species transmission potential of coronaviruses among carnivores.},
}

@article {pmid41834952,
year = {2026},
author = {Tu, Y and Niu, C and Huang, Z},
title = {[Analysis of the Characteristics of the Oral Virome in Metabolic Dysfunction-Associated Fatty Liver Disease].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {1},
pages = {65-72},
pmid = {41834952},
issn = {1672-173X},
mesh = {Humans ; *Virome ; *Saliva/virology ; Male ; Female ; Middle Aged ; Adult ; *Fatty Liver/virology ; *Mouth/virology ; *Dental Plaque/virology ; },
abstract = {OBJECTIVE: To investigate the characteristics of salivary and supragingival plaque viromes in patients with metabolic dysfunction-associated fatty liver disease (MAFLD), and provide new insights for noninvasive oral screening and ecological intervention for MAFLD.

METHODS: This study included 21 MAFLD patients and 20 healthy controls. Saliva and supragingival plaque samples were collected, and metagenomic sequencing was used to analyze the characteristics of the oral virome.

RESULTS: The α-diversity and β-diversity of the salivary virome did not differ significantly between MAFLD patients and healthy individuals (P > 0.05). However, compared with healthy individuals, the α-diversity (Shannon index) and β-diversity (Bray-Curtis distance) of the supragingival plaque virome showed significant differences (P = 0.0303, P = 0.001). For species with a relative abundance greater than 0.1%, 14 viral species in saliva and 5 in supragingival plaque differed significantly in relative abundance between the two groups (P < 0.05), with multiple Streptococcus phages enriched in the saliva of MAFLD patients. LEfSe and random forest analyses identified potential biomarkers in saliva and supragingival plaque. Receiver operating characteristic (ROC) curve analysis showed strong diagnostic performance for these biomarkers in both saliva (area under the curve [AUC] = 0.9548, 95% CI: 0.8898-1.0000) and supragingival plaque (AUC = 0.8952, 95% CI: 0.7774-1.0000). Spearman correlation analysis revealed associations between viral species in saliva or supragingival plaque and various disease indicators (P < 0.05). Compared with healthy individuals, MAFLD patients showed higher node counts, significant relationship numbers, and average node degrees in the co-occurrence networks of salivary and supragingival plaque viromes.

CONCLUSION: Differences in the species composition and structure of the oral virome between MAFLD patients and healthy individuals suggest that oral viral species could serve as potential biomarkers for diagnosing MAFLD.},
}

Humans
*Virome
*Saliva/virology
Male
Female
Middle Aged
Adult
*Fatty Liver/virology
*Mouth/virology
*Dental Plaque/virology

@article {pmid41835009,
year = {2026},
author = {Kariithi, HM and Volkening, JD and Mueni, SN and Helmy, MA and Afonso, CL and Chaudhari, PP and Decanini, EL},
title = {Co-detection and genomic characterization of avian rotavirus A, avian orthoreovirus, and chicken megrivirus-C using nontargeted metagenomic surveillance in Indian broiler chickens.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1690222},
pmid = {41835009},
issn = {2235-2988},
mesh = {Animals ; *Chickens/virology ; *Poultry Diseases/virology/epidemiology ; *Orthoreovirus, Avian/genetics/isolation & purification/classification ; Genome, Viral ; *Rotavirus/genetics/isolation & purification/classification ; Metagenomics ; *Reoviridae Infections/veterinary/virology/epidemiology ; Phylogeny ; India/epidemiology ; *Rotavirus Infections/veterinary/virology/epidemiology ; Coinfection/virology/veterinary ; Genotype ; High-Throughput Nucleotide Sequencing ; Genomics ; *Orthoreovirus/genetics/isolation & purification/classification ; },
abstract = {Nontargeted metagenomic surveillance of the poultry enteric virome reveals underrecognized threats to poultry health and productivity in intensive production systems. In South Asia, avian rotavirus A (AvRV-A) and avian orthoreovirus (ARV) are frequently detected in broilers by conventional diagnostics, whereas chicken megrivirus genotype C (ChMeV-C) is often identified through metagenomic surveillance. Often present in both clinical disease and coinfections, these viruses may impair gut function, immune responses, and growth performance, yet their genomic diversity and evolutionary dynamics in poultry remain poorly characterized. Here, we report complete genomes of AvRV-A, ARV, and ChMeV-C strains co-detected via nontargeted metagenomic next-generation sequencing (ntNGS) in a pooled cloacal sample comprising 150 commercial broiler chickens (19 and 33 days old) collected from three commercial farms in Kamrup Rural District, Assam, Northeast India. Despite routine vaccination, all three flocks experienced > 10% mortality, poor weight gain, and postmortem lesions including pale kidneys and hepatomegaly. Phylogenetic analyses revealed segmental clustering in ARV and AvRV-A consistent with reassortment-driven divergence, though not supported by detectable recombination, while ChMeV-C clustered within a distinct C1 sublineage, suggesting intercontinental lineage connectivity and highlighting the need to expand regional genomic baseline data. We also identified nonsynonymous single nucleotide polymorphisms in several key viral proteins, including RNA-dependent RNA polymerases (VP1 of AvRV-A, λB of ARV, and 3D of ChMeV-C), capsid proteins (VP2 and VP7 of AvRV-A, λA and σB of ARV, and VP0 and VP1 of ChMeV-C), and replication-associated nonstructural proteins. These findings expand the genomic baseline for poultry enteric viruses in South Asia, reveal novel polymorphic signatures, and underscore the value of ntNGS-based metagenomic surveillance in virus detection, diversity monitoring, and informing vaccine and biosecurity strategies.},
}

Animals
*Chickens/virology
*Poultry Diseases/virology/epidemiology
*Orthoreovirus, Avian/genetics/isolation & purification/classification
Genome, Viral
*Rotavirus/genetics/isolation & purification/classification
Metagenomics
*Reoviridae Infections/veterinary/virology/epidemiology
Phylogeny
India/epidemiology
*Rotavirus Infections/veterinary/virology/epidemiology
Coinfection/virology/veterinary
Genotype
High-Throughput Nucleotide Sequencing
Genomics
*Orthoreovirus/genetics/isolation & purification/classification

@article {pmid41835092,
year = {2026},
author = {Pérez, T and Vacelet, J and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the carnivorous sponge, Lycopodina hypogea (Vacelet & Boury-Esnault, 1996) (Poecilosclerida: Cladorhizidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {130},
pmid = {41835092},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Lycopodina hypogea (carnivorous sponge; Porifera; Demospongiae; Poecilosclerida; Cladorhizidae). The genome sequence has a total length of 235.10 megabases. Most of the assembly (98.85%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 31.1 kilobases. Gene annotation of this assembly by Ensembl identified 16 317 protein-coding genes. From the metagenome data we recovered 39 bins, of which 27 were high-quality MAGs, including four fully circularised genomes. The MAGs included archaea and bacteria involved in nitrification and sulfate-reduction as well as known sponge symbionts affiliated with Gammaproteobacteria (Candidatus Spongiihabitans, Porisulfidus) and Acidimicrobiales (Candidatus Poriferisodalaceae), among others.},
}

@article {pmid41836173,
year = {2026},
author = {Fuques, E and Massey, AL and Qureshi, F and Campos-Silva, JV and Ferreira da Silva, DJ and Peres, CA and Levi, T and Vega Thurber, RL},
title = {Large-scale metagenomic surveillance study expands the known diversity of RNA viruses in mosquito populations from the Amazon Basin.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20880},
doi = {10.7717/peerj.20880},
pmid = {41836173},
issn = {2167-8359},
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification ; *Metagenomics ; *Culicidae/virology ; Brazil ; Phylogeny ; Female ; *Mosquito Vectors/virology ; Virome ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; },
abstract = {The Amazon Basin is one of the most biologically diverse regions on Earth, yet its viral diversity remains poorly characterized. Mosquitoes are important vectors and reservoirs of RNA viruses, but little is known about the composition and structure of their viromes in remote areas of the Amazon. In this study, we performed a large-scale metagenomics survey of RNA viruses associated with mosquito populations collected from the Jurua River region in the Western Amazon Basin of Brazil. We analyzed 211 pooled samples of adult female mosquitoes collected across thirty-seven sites, representing one of the most comprehensive mosquito virome studies conducted in this region to date. Utilizing high-throughput sequencing and de novo assembly, we identified over 500 viral sequences from 18 families, including 21 complete or nearly complete genomes. Our analysis revealed 18 putative novel viral species spanning diverse families and strains of nine previously described viruses. Phylogenetic analyses also revealed undocumented diversity within several virus families, including Iflaviridae, Mesoniviridae, Phasmaviridae, Phenuiviridae, Togaviridae, and Totiviridae, encompassing both novel species and previously known viruses detected for the first time in this region. Our findings highlight the immense, yet largely unexplored, diversity of RNA viruses circulating in mosquito populations in this ecologically rich but understudied region and provide critical insights into the evolutionary dynamics of mosquito-associated viruses. By leveraging high-throughput sequencing to uncover novel viral strains, this research demonstrates the value of metagenomic approaches in expanding the known diversity, distribution, and evolutionary relationships of RNA viruses, contributing to a broader understanding of virus-mosquito interactions and genome evolution.},
}

Animals
*RNA Viruses/genetics/classification/isolation & purification
*Metagenomics
*Culicidae/virology
Brazil
Phylogeny
Female
*Mosquito Vectors/virology
Virome
Genome, Viral
High-Throughput Nucleotide Sequencing

@article {pmid41836379,
year = {2026},
author = {Wang, P and Pang, J and Xu, H and Wang, M and Lai, W and Hui, D and Cai, Q and Li, X and Zhu, J},
title = {Hemophagocytic lymphohistiocytosis directly triggered by peginterferon alfa-2b in a patient with chronic hepatitis B.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1760610},
doi = {10.3389/fimmu.2026.1760610},
pmid = {41836379},
issn = {1664-3224},
mesh = {Humans ; Male ; Adult ; *Lymphohistiocytosis, Hemophagocytic/chemically induced/diagnosis/drug therapy/etiology ; Recombinant Proteins/adverse effects/therapeutic use ; *Polyethylene Glycols/adverse effects/therapeutic use ; *Hepatitis B, Chronic/drug therapy ; *Interferon alpha-2/adverse effects ; *Antiviral Agents/adverse effects/therapeutic use ; *Interferon-alpha/adverse effects ; },
abstract = {This case report describes a 42-year-old male with chronic hepatitis B (CHB) who developed hemophagocytic lymphohistiocytosis (HLH) following treatment with peginterferon alfa-2b (PegIFN-α-2b). The patient tolerated the initial injections well. After the 16th injection in February 2025, laboratory tests revealed cytopenia, prompting discontinuation of PegIFN-α-2b. The onset of a high-grade fever approximately three weeks after drug cessation coincided with the timeframe for the drug's clearance, suggesting a continued immunostimulatory effect. HLH was diagnosed based on hyperferritinemia (>50,000 ng/mL), elevated soluble interleukin-2 receptor (sCD25), and hemophagocytosis on bone marrow biopsy. He responded well to etoposide and dexamethasone. However, his course was complicated by sequential opportunistic infections: severe anemia due to parvovirus B19 (confirmed by plasma metagenomic next-generation sequencing, mNGS) and subsequent herpes simplex virus (HSV) encephalitis (diagnosed via CSF mNGS). Both complications were managed successfully with intravenous immunoglobulin and acyclovir, respectively. This case highlights PegIFN-α-2b as a rare direct trigger of HLH in CHB and underscores the critical risk of opportunistic infections during immunosuppressive therapy, demonstrating the pivotal role of mNGS in diagnosing elusive infections in immunocompromised hosts.},
}

Humans
Male
Adult
*Lymphohistiocytosis, Hemophagocytic/chemically induced/diagnosis/drug therapy/etiology
Recombinant Proteins/adverse effects/therapeutic use
*Polyethylene Glycols/adverse effects/therapeutic use
*Hepatitis B, Chronic/drug therapy
*Interferon alpha-2/adverse effects
*Antiviral Agents/adverse effects/therapeutic use
*Interferon-alpha/adverse effects

@article {pmid41836788,
year = {2026},
author = {Cha, JH and Jeong, SA and Ye, BS and Lee, I and Jung, BY},
title = {Shotgun metagenomic analysis of the tongue-coating microbiome reveals oral microbes and their functions in older adults with dementia.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2643036},
doi = {10.1080/20002297.2026.2643036},
pmid = {41836788},
issn = {2000-2297},
abstract = {INTRODUCTION: Dementia poses a growing burden in the aging population, prompting the search for noninvasive biomarkers for early detection.

MATERIALS AND METHODS: We performed shotgun metagenomic sequencing of tongue-coating samples from older adults with dementia (n = 30) and cognitively healthy controls (n = 28) to identify oral microbiome signatures.

RESULTS: The analysis revealed distinct microbial compositions associated with dementia, including an enrichment of Veillonella parvula in dementia patients, whereas Lautropia dentalis was more abundant in healthy controls. We also identified functional alterations in the microbiome in the dementia group, including increased abundance of the histidine degradation and biotin biosynthesis pathways, whereas ubiquinol biosynthesis was more abundant in the healthy control group. The abundance of several microbial taxa and metabolic pathways were correlated with scores on the Korean Mini-Mental State Examination 2nd edition (K-MMSE), a clinical assessment of dementia severity. Prevotella pleuritidis, Actinomyces sp., Leptotrichia buccalis, and Leptotrichia sp. were positively correlated, whereas Oribacterium parvum was negatively associated with K-MMSE scores. Among the metabolic pathways, glutamine/glutamate biosynthesis was positively correlated with cognitive performance.

CONCLUSIONS: These results suggest that specific oral taxa and their metabolic functions are associated with cognitive status and may reflect underlying neurodegenerative processes.},
}

@article {pmid41836789,
year = {2026},
author = {Manzoor, M and Pussinen, PJ and Saarela, RK and Pitkälä, K and Hiltunen, K and Mäntylä, P},
title = {Denture-associated oral microbiome in dentate and edentulous older adults living in long-term care facilities.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2641915},
doi = {10.1080/20002297.2026.2641915},
pmid = {41836789},
issn = {2000-2297},
abstract = {BACKGROUND: The denture-associated oral microbiome (DAOM) may act as reservoirs of pathogenic microorganisms with potential health effects.

OBJECTIVES: To characterize the compositional and functional activity of the DAOM in dentate and edentulous older adults residing in long-term care facilities (LTCFs).

METHODS: Participants (51 dentate and 56 edentulous) aged ≥64 years were recruited from the Finnish Oral Health Studies in Older Adults. Clinical oral examinations were performed, and biofilm samples for shotgun metagenomics were collected from the acrylic surface of removable dentures. Diversity indices, taxonomic composition, and functional pathways were assessed to characterize DAOM.

RESULTS: Alpha diversity was similar, whereas beta diversity showed modest differences between groups. Dentate participants had a higher abundance of Streptococcus mutans, Veillonella parvula, and Parascardovia denticolens, whereas edentulous participants were enriched with Haemophilus parainfluenzae and Propionibacterium acidifaciens. Edentulous participants had reduced microbial network stability and interconnectedness but highly active microbial metabolic functions, particularly those associated with Streptococcus pneumoniae.

CONCLUSION: Although tooth loss does not markedly alter the overall microbial diversity of DAOM, it is associated with distinct taxonomic and functional shifts. Edentulous individuals have less stable and less interconnected microbial networks alongside heightened metabolic activity, reflecting notable changes in the DAOM of older adults living in LTCFs.},
}

@article {pmid41837347,
year = {2026},
author = {Arnold, MJ and Bergner, LM and Malik, H and Ten Doeschate, M and Davison, NJ and Brownlow, A and Mollentze, N and Babayan, SA and Streicker, DG},
title = {Drivers of Viral Diversity and Sharing in Marine Mammals.},
journal = {Molecular ecology},
volume = {35},
number = {6},
pages = {e70294},
doi = {10.1111/mec.70294},
pmid = {41837347},
issn = {1365-294X},
support = {217221/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; 218518/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; BB/V003798/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DEB 2011069/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; PLP-2020-362//Leverhulme Trust/ ; NE/X01424X/1//Natural Environment Research Council/ ; INV-003079/GATES/Gates Foundation/United States ; INV-030025/GATES/Gates Foundation/United States ; MC_UU_00034/3/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Animals ; *Viruses/genetics/classification ; Scotland ; *Aquatic Organisms/virology ; *Cetacea/virology ; *Mammals/virology ; },
abstract = {Knowledge of viral infection in marine mammals, a group severely threatened by human activity, is largely limited to the pathology and epidemiology of few endemic viruses. The recent emergence in marine mammals of high-consequence viruses, such as H5N1 avian influenza and rabies, underscores the importance of understanding the ecology of viral transmission in these species. Metatranscriptomic approaches now enable relatively unbiased characterisation of full viral communities that can reveal ecological and evolutionary drivers of infection. We sequenced RNA from 15 marine mammal species (42 pools, 237 tissues, 128 animals) sampled in Scotland through the Scottish Marine Animal Strandings Scheme. Viral sequences were detected in 41 of 42 pools, representing more than 120 distinct viral taxonomic units (vOTUs). Virus host network analysis showed that viral communities were partly structured by host taxonomy, with clear differences between seals and cetaceans. However, vOTUs were frequently shared between species, mirroring reported ecological interactions, including cross-order sharing between seals and cetaceans. Generalised linear models showed no effect of host taxonomy on viral richness. Instead, age was the strongest predictor: juvenile pools contained roughly twice as many viral taxa as adults and more than neonates, indicating that changing population demography may impact viral transmission in marine mammals. These results provide a basis for understanding how anthropogenic stressors may exacerbate viral transmission in marine mammals and demonstrate the increasing practicality of using genomics to understand ecological and evolutionary drivers of virus infection in natural populations.},
}

Animals
*Viruses/genetics/classification
Scotland
*Aquatic Organisms/virology
*Cetacea/virology
*Mammals/virology

@article {pmid41837390,
year = {2026},
author = {Abagnale, V and Palacin-Lizarbe, C and Paul, D and Kerttula, J and Ronkainen, J and Siljanen, HMP},
title = {Activity and Abundance of Nitrous Oxide Reducing Bacteria in Platismatia glauca: An Epiphytic Lichen in the Boreal Spruce Forest.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70279},
doi = {10.1111/1462-2920.70279},
pmid = {41837390},
issn = {1462-2920},
support = {342362//Academy of Finland/ ; 346516//Academy of Finland/ ; 361980//Academy of Finland/ ; 337550//Academy of Finland/ ; 357905//Academy of Finland/ ; 359343//Academy of Finland/ ; 202400252//Maj ja Tor Nesslingin Säätio/ ; 20231200//OLVI-Säätiö/ ; },
mesh = {*Picea/microbiology ; *Lichens/microbiology ; *Nitrous Oxide/metabolism ; Finland ; Oxidoreductases/genetics/metabolism ; Taiga ; *Bacteria/metabolism/genetics/isolation & purification/classification ; Forests ; Oxidation-Reduction ; Oxygen/metabolism ; },
abstract = {The nitrous oxide (N2O) dynamics in boreal forests are better known at the ecosystem scale, with greater uncertainty associated with specific ecosystem compartments. We investigated the N2O dynamics of the lichen Platismatia glauca in boreal forests near Kuopio, North Savo, Finland. At the study sites, P. glauca is the most abundant lichen colonising Norway spruce (Picea abies). Despite their abundance, the contribution of epiphytic lichens like P. glauca to N2O dynamics in boreal forests has received little attention. By incubating P. glauca, we assessed the effects of moisture, temperature, and oxygen availability on its N2O dynamics. We observed net N2O consumption potential, particularly at +5°C at aerobic condition. Quantitative real-time PCR analysis targeting the N2O reductase gene fragment (nosZ) revealed that it was present and active in both in situ and incubated lichens. nosZ transcription was higher at +5°C. Clade I nosZ was dominant, with most sequences affiliated with the order Rhizobiales. We confirmed the presence of nosZ gene with targeted metagenomics sequencing. Our results demonstrate that P. glauca acts as a net consumer of N2O, with potential ranging between 0.1 and 0.4 ng N2O-N g DW[-1] h[-1] under aerobic conditions.},
}

*Picea/microbiology
*Lichens/microbiology
*Nitrous Oxide/metabolism
Finland
Oxidoreductases/genetics/metabolism
Taiga
*Bacteria/metabolism/genetics/isolation & purification/classification
Forests
Oxidation-Reduction
Oxygen/metabolism

@article {pmid41837422,
year = {2026},
author = {Mwasya, SK and Okanda, D and Odoyo, S and Katama, EN and Lewa, C and Lambisia, AW and Githinji, G and Agoti, CN},
title = {Eight coding-complete genomes of human metapneumovirus recovered by virus metagenomics in coastal Kenya, 2021-2024.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0006526},
doi = {10.1128/mra.00065-26},
pmid = {41837422},
issn = {2576-098X},
abstract = {Few human metapneumovirus coding-complete genomes are available from Africa despite significance in optimizing local molecular diagnostics and global phylogeographic analysis. We report eight genomes recovered following nanopore metagenomic sequencing of samples collected in coastal Kenya (2021-2024). These fell into sub-lineages A2b/A2.2.1 (n = 3), A2c-wt/A2.2.2 (n = 4), and B1 (n = 1).},
}

@article {pmid41837616,
year = {2026},
author = {Fleres, G and Kline, EG and Squires, KM and Tate, T and Creager, HM and Shields, RK and Van Tyne, D},
title = {Within-patient evolution of Pseudomonas aeruginosa populations during antimicrobial treatment.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0065625},
doi = {10.1128/msphere.00656-25},
pmid = {41837616},
issn = {2379-5042},
abstract = {UNLABELLED: Multidrug-resistant (MDR) Pseudomonas aeruginosa infections pose a major challenge to effective treatment. Understanding genomic adaptations during antimicrobial therapy in patients infected with this pathogen is crucial for preventing therapeutic failure. Here, we investigated the population diversity and evolution of P. aeruginosa collected longitudinally from six patients who evolved multidrug-resistant infections. Serial clinical P. aeruginosa single-colony isolates (n = 63) and culture-enriched metagenomic population samples (n = 39) were collected and subjected to whole-genome sequencing. The resulting data were used to characterize and compare the species composition, multi-locus sequence types (STs), and resistance-associated mutations present within each sample type. Single-colony isolate sequencing showed that each patient was infected with a single P. aeruginosa strain that accumulated mutations and became increasingly more antibiotic-resistant over time. Mutations in genes associated with β-lactam resistance, including ampC, ftsI, and mexR, arose over time and corresponded with changes in antimicrobial susceptibility in single-colony isolates. Species profiling of culture-enriched metagenomic populations revealed that all samples contained P. aeruginosa, but also additional gram-negative pathogens. Metagenomic analysis of culture-enriched populations identified resistance-associated mutations at low frequency, many of which were not identified in single-colony isolates from the same sample. In some cases, resistance-associated mutations initially detected at low frequency rose to fixation after antimicrobial treatment. Overall, this study shows that population-based metagenomic sequencing effectively captures the within-patient genomic diversity of P. aeruginosa during antimicrobial therapy and could aid the detection and interpretation of resistance-associated mutations in this pathogen.

IMPORTANCE: Pseudomonas aeruginosa infections are notoriously difficult to treat and are associated with high rates of morbidity and mortality. While the genetic basis of resistance in P. aeruginosa is well documented in vitro, less is known about how resistance evolves within patients during antibiotic therapy. Standard approaches based on analysis of clonal isolates may miss within-patient diversity, potentially overlooking low-frequency mutations that contribute to treatment failure. In this study, we compared single-colony isolate whole-genome sequencing with culture-enriched metagenomic sequencing to monitor the evolution of P. aeruginosa populations in patients receiving antibiotic therapy. The culture-enriched metagenomic approach enabled the detection of emerging resistance mutations, such as low-frequency variants in ampC and ftsI, before these variants rose to fixation. It also revealed genetically resistant subpopulations missed by isolate sequencing alone. Overall, our findings highlight the value of population-based metagenomic sequencing in capturing bacterial adaptation during infection and underscore its potential to improve resistance surveillance and guide personalized antimicrobial therapy.},
}

@article {pmid41837716,
year = {2026},
author = {Pantiukh, K and Krigul, KL and Aasmets, O and Org, E},
title = {Metagenome-assembled genomes from a population-based cohort uncover novel gut species and within-species diversity, revealing prevalent disease associations.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0011426},
doi = {10.1128/msystems.00114-26},
pmid = {41837716},
issn = {2379-5077},
abstract = {UNLABELLED: Metagenomic profiling has advanced the understanding of microbe-host interactions. However, widely used read-based approaches are limited by incomplete reference databases and the inability to resolve strain-level variation. Here, we present a scalable, genome-resolved framework that integrates population-specific metagenome-assembled genomes (MAGs) to discover novel species, within-species diversity, and disease associations. From 1,878 deeply sequenced samples in the Estonian Microbiome Cohort (EstMB-deep), we reconstructed 84,762 MAGs representing 2,257 species, including 353 (15.6%) previously uncharacterized species reaching up to 30% relative abundances in some individuals. We integrated these MAGs with the Unified Human Gastrointestinal Genome collection to create an expanded reference (GUTrep), enabling profiling of 2,509 EstMB individuals and testing associations with 33 prevalent diseases. Of the 25 diseases with significant associations, 8 involved newly identified species, underscoring the value of population-specific MAGs. To quantify within-species diversity, we developed the genome unit number (GUN), a novel MAG-based metric that informed within-species analyses. Based on normalized GUN, we prioritized Odoribacter splanchnicus, a prevalent species with the lowest within-species heterogeneity, yielding sufficient power for a within-species association study. We identified two dominant genome units, GU-N1 and GU-N2, with distinct gene repertoires and divergent disease associations. Notably, GU-N1 was negatively associated with gastritis, duodenitis, and hypertensive heart disease, associations undetected at the species level. Our study expands the human gut reference landscape, demonstrates the importance of population-specific MAGs for uncovering novel microbial diversity, and reveals new disease associations at the within-species level obscured at higher taxonomic levels, highlighting the need for genome-resolved approaches in microbiome research.

IMPORTANCE: Microbiome studies increasingly recognize that species-level profiles can mask critical within-species differences relevant to health and disease. However, our work shows that within-species diversity varies drastically across gut microbes, with some species exhibiting almost as many distinct within-species clusters as recovered genomes, making association studies at the within-species level essentially intractable. To address this, we introduce the genome unit number (GUN), a scalable metric for quantifying within-species structure. Using GUN, we demonstrate that only species with limited within-species diversity, such as Odoribacter splanchnicus, currently allow for robust within-species association testing. These findings emphasize the need to systematically evaluate species structure across the gut microbiome and call for the development of new computational and statistical approaches to enable meaningful within-species analyses in highly diverse species.},
}

@article {pmid41838353,
year = {2026},
author = {Xu, Q and Wang, M and Wang, H and Wu, Z and Li, X and Sun, J and Yang, Z and He, N and Sun, Y and Zhang, H and Zhong, Y and Xiao, L and Li, S and Zou, Y},
title = {Lactobacillus gasseri TF08-1 Alleviates DSS-Induced Acute Colitis by Protecting Intestinal Epithelial Barrier.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41838353},
issn = {1867-1314},
support = {2025YFA1310200//Ministry of Science and Technology of the People's Republic of China/ ; U25A2015//National Natural Science Foundation of China/ ; JCYJ20241202124801003//Shenzhen Municipal Government of China/ ; },
}

@article {pmid41838746,
year = {2026},
author = {Adachi, K and Chikaraishi, Y and Nomura, S and Goto-Inoue, N and Zaima, N and Kuriya, Y and Araki, M and Morioka, K and Yanagimoto, T and Nakaya, M and Yamamoto, J},
title = {New insights into the feeding behaviour of the Japanese squid Todarodes pacificus paralarvae, and a combined analysis of metagenome and amino acid isotope ratios.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0340579},
doi = {10.1371/journal.pone.0340579},
pmid = {41838746},
issn = {1932-6203},
mesh = {Animals ; *Decapodiformes/physiology/microbiology/genetics ; *Feeding Behavior/physiology ; *Metagenome ; *Amino Acids/metabolism/analysis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The Japanese flying squid Todarodes pacificus (Ommastrephidae) is a commercially and ecologically important species; however, there remains much room for investigation in its early life phase, especially its diet in wild environments. After excising the digestive gland (cecum sac) of wild paralarvae of T. pacificus using Laser Microdissection (LMD), the dietary species were estimated via metagenomic analysis. The 16S rRNA analysis predominantly detected Burkholderiales and Xanthomonadales, regardless of mantle length (ML) of T. pacificus and capture area. COI (Cytochrome c oxidase subunit I) analysis detected in various organisms including Discosea, Arthropoda, Nemertea, Porifera, golden algae, and fungi (Ascomycota and Basidiomycota), which were found irregularly. About half of the paralarval cecum sacs were found empty during the histological analysis. We also estimated the trophic position (TP) of wild paralarvae in the same sea region via stable isotope analysis of amino acids. The TP estimated was 3.0 for all larval groups regardless of ML, suggesting that the trophic tendency of paralarvae is carnivorous, likely feeding on herbivorous organisms. Taken together, our results suggest that the paralarvae feed mostly on various kinds of living herbivorous organisms and partly on detritus.},
}

Animals
*Decapodiformes/physiology/microbiology/genetics
*Feeding Behavior/physiology
*Metagenome
*Amino Acids/metabolism/analysis
RNA, Ribosomal, 16S/genetics

@article {pmid41838875,
year = {2026},
author = {Chen, Q and Zhang, B and Peng, C and Huang, J and Liu, Z and Shen, X and Jiang, C},
title = {Kun-peng enables scalable and accurate pan-domain metagenomic classification.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
doi = {10.1093/bib/bbag119},
pmid = {41838875},
issn = {1477-4054},
support = {82341109//National Natural Science Foundation of China/ ; 82173645//National Natural Science Foundation of China/ ; },
mesh = {*Metagenomics/methods ; *Metagenome ; Humans ; Databases, Genetic ; *Software ; Computational Biology/methods ; Algorithms ; },
abstract = {Comprehensive pan-domain metagenomic classification is increasingly constrained by the memory and runtime costs of building and querying the rapidly expanding reference genome space. We introduce Kun-peng, a taxonomic classifier powered by an intelligent block-partitioned database structure and optimized search strategies, enabling ultra-scalable, memory-efficient pan-domain profiling. Using the Critical Assessment of Metagenome Interpretation II benchmark, Kun-peng substantially reduces the memory usage of database-building and querying by up to 24-fold, and accelerates sample classification by up to 4.73-fold compared with Kraken2. Kun-peng achieves competitive accuracy with fewer false positives than Kraken2, Centrifuger, and even KrakenUniq, while maintaining consistently high sensitivity across diverse datasets. In a real-world evaluation of 586 metagenomic samples spanning air, water, soil, and human-associated environments, we performed classification using a 4.3 TB pan-domain database comprising 204,477 genomes, which was built by Kun-peng with only 4.1 GB peak memory. Kun-peng processed each sample in 0.2-11.2 min with 4.0-35.4 GB peak memory, corresponding to a 54-473-fold reduction in memory usage relative to Kraken2. Compared with Sylph, Kun-peng achieved up to a 46-fold speedup while requiring 21-fold less memory. Kun-peng classified 69.8%-94.3% of reads, improving coverage by 20%-60% over the standard Kraken2 database with 62,026 genomes. This improvement reflects expanded reference coverage, although a small fraction of false positives is inherent to k-mer-based methods. Overall, Kun-peng effectively eliminates the long-standing memory bottleneck in pan-domain database building and classification, enabling rapid and scalable pan-domain taxonomic analysis of complex environmental, ecological, and exposomic sequencing datasets.},
}

*Metagenomics/methods
*Metagenome
Humans
Databases, Genetic
*Software
Computational Biology/methods
Algorithms

@article {pmid41839407,
year = {2026},
author = {Chen, S and Zhao, A and Zhang, W and Liu, Q and Li, D},
title = {Metabolic reprogramming disrupts the resistome-mobilome nexus and enhances bio-sanitization in synthetic microbial community-mediated composting.},
journal = {Bioresource technology},
volume = {449},
number = {},
pages = {134433},
doi = {10.1016/j.biortech.2026.134433},
pmid = {41839407},
issn = {1873-2976},
abstract = {The persistence of antibiotic resistance genes (ARGs) and pathogens during manure composting poses critical risks within the One Health framework. However, the ecological and metabolic mechanisms by which microbiome engineering disrupts the dissemination of these biohazards remain poorly understood. This study evaluated a thermophilic lignocellulose-degrading synthetic microbial community (SynCom, comprising Bacillus cereus, Achromobacter sp., Pseudomonas sp., Cladosporium sp., and Trichoderma harzianum) in mitigating these risks. KEGG analysis highlighted a pivotal metabolic reprogramming from a biofilm-dependent defense-survival model to an active motility-metabolism mode, characterized by depleted lipopolysaccharide biosynthesis and enriched flagellar assembly. This metabolic shift implies a fitness cost trade-off that physically restricts horizontal gene transfer (HGT) opportunities. Metagenomic analysis showed SynCom inoculation caused a transient ARG rebound followed by profound attenuation. While thermophilic hosts temporarily enriched specific ARGs, SynCom ultimately achieved a significant reduction in multidrug resistance genes and virulence factors by intensifying thermophilic fermentation. Mantel correlation analysis revealed the SynCom-driven rapid decrease in carbon/nitrogen ratio and enhanced humification were critical environmental drivers, restricting ARGs and alleviating co-selection pressure on metal resistance genes. Network analysis demonstrated SynCom induced a structural collapse of high-risk interactomes (reducing potential host-gene associations by 26.6%), effectively disrupting ARG and mobile genetic element connections by suppressing key recombinases (XerD, IntI1) and eliminating Pseudomonadota hub hosts. Consequently, deep bio-sanitization was achieved by synchronously eliminating high-risk pathogens (e.g., Pseudomonas aeruginosa), phytopathogens, and specific virulence factors. These findings indicate that SynCom provides a robust microbiome engineering strategy to disrupt the genetic dissemination of biohazards and ensure organic fertilizer biosafety.},
}

@article {pmid41839411,
year = {2026},
author = {Duan, Z and Kong, X and Yue, J and Han, X and Zhu, G and Yu, H},
title = {Integrated multi-barrier attenuation of antibiotic resistance genes by self-elevating ultra-high temperature composting: Phase-resolved evidence for within-process risk reduction.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134432},
doi = {10.1016/j.biortech.2026.134432},
pmid = {41839411},
issn = {1873-2976},
abstract = {The dissemination of antibiotic resistance genes (ARGs) from livestock manure poses risks to environmental and public health, while conventional composting often shows limited and inconsistent ARG attenuation. Here, we evaluated ARG and mobile genetic element (MGE) dynamics during self-elevating ultra-high temperature composting (sf-HTC) and examined phase-resolved associations among thermal conditions, microbial succession, MGE patterns, and humification indicators using metagenomics, network analysis, and structural equation modeling (SEM). Sf-HTC reduced the absolute abundance of total ARGs and MGEs by 98.86% within 28 days. High-risk ARG classes (tetracycline and sulfonamide-resistance genes) decreased by > 94.3%, outperforming traditional composting (TC). The hyperthermophilic phase coincided with the largest decreases in ARGs and with enrichment of thermophilic genera (Calditerricola and Thermophilum) and increased microbial network complexity. SEM further suggested that the thermal regime, reductions in MGEs, and increased humification were major, interrelated pathways statistically associated with ARG reduction (standardized path coefficients: 0.97, -1.41, and 0.78, respectively). Sf-HTC also promoted humic acid accumulation (up to 58.9 g/kg) and more aromatic dissolved organic matter, which was consistent with enhanced immobilization potential for residual ARGs. Overall, our results support a phase-resolved "thermal-biological-chemical" multi-barrier conceptual model for ARG attenuation during sf-HTC and highlight its potential for reducing resistome burdens in agricultural organic wastes.},
}

@article {pmid41830297,
year = {2026},
author = {Chen, W and Zhang, L and Zhang, W},
title = {Integrated multi-omics elucidates the microbial-metabolite interplay governing antioxidant capacity in mung bean sour liquid.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70579},
pmid = {41830297},
issn = {1097-0010},
support = {262102111058//Department of Science and Technology of Henan Province, P.R. China/ ; },
abstract = {BACKGROUND: Mung bean sour liquid (MBSL) is a traditional fermented food, yet the microbial-metabolic basis of its antioxidant capacity is unclear. This study employed integrated metagenomics and metabolomics to elucidate the dynamic formation of antioxidant biomarkers during fermentation.

RESULTS: The mid-fermentation stage (6-12 h) was critical for antioxidant development, marked by peak accumulation of key biomarkers such as phenyllactic acid, epigallocatechin and catechin. Antioxidant activity [2,2-diphenyl-1-picrylhydrazyl/2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)] (DPPH/ABTS) significantly increased during this period, reaching 77.4% and 74.5% by 24 h. These changes were directly correlated with specific Lactobacillus spp. (e.g. Lactobacillus curvatus and Lactobacillus mudanjiangensis). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed stage-specific metabolic reprogramming, from early activation of amino acid/lipid metabolism to late-phase downregulation of central carbon metabolism. Correlation networks further linked these Lactobacilli to key carbohydrate-active enzymes (CAZy), such as glycoside hydrolases.

CONCLUSION: This study decipheedr the microbial-driven metabolomic remodeling that governs antioxidant capacity in MBSL, demonstrating a clear temporal alignment between key metabolite accumulation and functional enhancement. This work decodes the scientific basis of its traditional value and establishes a robust foundation for its targeted optimization and development as a health-promoting functional beverage. © 2026 Society of Chemical Industry.},
}

@article {pmid41830759,
year = {2026},
author = {Nasir, MM and Qayyum, H and Shuhui, S and Ali, A and Kayani, MUR},
title = {MetaBolt: A computationally efficient pipeline for the rapid recovery of metagenome-assembled genomes.},
journal = {Computational biology and chemistry},
volume = {123},
number = {},
pages = {109006},
doi = {10.1016/j.compbiolchem.2026.109006},
pmid = {41830759},
issn = {1476-928X},
abstract = {Metagenome-resolved metagenomics refers to the recovery of metagenome-assembled genomes from the metagenomic datasets. It is a multi-step and laborious process that requires substantial computational resources and technical expertise. Though various semi-automated pipelines have been developed to automate the recovery process, high computational requirements remain a major bottleneck. Since de novo assembly is the key step that consumes higher computational time and resources, optimizing this step can address the underlying challenges. Hence, to address these limitations, we introduce MetaBolt, an automated Nextflow-based pipeline designed for the rapid recovery of metagenome-assembled genomes from short-read metagenomic datasets. Based on an empirically optimized set of k-mers for MEGAHIT-based assembly, this pipeline offers a unique solution. When tested on both real and simulated metagenomic datasets, it consistently exhibited efficient performance within reduced computational time. From gut metagenomes, MetaBolt recovered MAGs at a 2.3 and 3.8-times faster rate than nf-core/mag and MetaWRAP, respectively, while recovering ∼5% more high-quality MAGs compared to the other two pipelines. Whereas, in the case of real metagenome samples, it reduced the computational times to 2-4%, particularly for low-biomass samples. By integrating optimized assembly parameters with automated workflow management, MetaBolt lowers computational barriers to genome-resolved metagenomics without compromising output quality. MetaBolt is available on the web at https://github.com/muneebdev7/metabolt.},
}

@article {pmid41830810,
year = {2026},
author = {Martins, IB and Silva, JM and Almeida, JR},
title = {A systematic review and benchmarking of modern metagenomic tools for taxonomic classification.},
journal = {Computers in biology and medicine},
volume = {206},
number = {},
pages = {111600},
doi = {10.1016/j.compbiomed.2026.111600},
pmid = {41830810},
issn = {1879-0534},
abstract = {Advancements in metagenomics have been driven by the continuous development of bioinformatic tools, particularly taxonomic classification software, which are central to the accurate characterization of microbial communities. However, establishing direct comparisons between these tools remains challenging due to variations in evaluation metrics, reference databases, and input data types. In this study, we present a systematic review of recently developed metagenomic taxonomic classification tools. Of the 31 identified tools, nine satisfied all functional and methodological criteria for the benchmark analysis. We evaluated their accuracy and computational performance using a standardized dataset derived from the NCBI RefSeq database. Our analysis revealed that most of these tools are domain-specific, each excelling in particular areas. Tools like TAMA, CAMITAX and PhyloFlash achieved higher accuracy for prokaryotic organisms, while ViWrap and PhaBOX achieved higher accuracy for viral classifications. SqueezeMeta achieved high F1 scores across most domains, though its assembly-based architecture limits effectiveness on highly diverse samples. MegaPath-Nano was least affected by increased mutation rates. The execution time varied widely among the tools, with domain-specific and machine learning-based tools generally being faster, while tools like BASTA had longer runtimes and lower accuracy. This review synthesizes performance results for current tools, providing an overview of their strengths and computational methodologies.},
}

@article {pmid41831184,
year = {2026},
author = {Rangamaran, VR and Sushmitha, TJ and Tamilmani, KK and Murugesan, H and Venkataraman, P and Arunachalam, R and Pramanik, R and Dharne, M and Gopal, D},
title = {Integrated omics analyses reveal insights into microbial dark matter associated with deep-sea water in Central Indian Ocean.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {},
pmid = {41831184},
issn = {1573-0972},
support = {DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; DOM//Ministry of Earth Sciences/ ; },
}

@article {pmid41831290,
year = {2026},
author = {Tang, Z and Li, Y and Zhang, L and Xi, B and Tan, W and Yuan, Y},
title = {Space-for-time substitution reveals mechanisms driving heavy metal induced dynamics of antibiotic resistance genes of varying risk levels in landfill leachate.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141740},
doi = {10.1016/j.jhazmat.2026.141740},
pmid = {41831290},
issn = {1873-3336},
abstract = {Landfills are recognized as persistent reservoirs of antibiotic resistance genes (ARGs); however, the temporal dynamics of their risk profiles after closure remain poorly understood. Because long-term monitoring of ARG risks in landfill leachate is challenging, a "space-for-time" substitution was employed to characterize ARGs, metal resistance genes (MRGs), mobile genetic elements (MGEs), and microbial hosts in landfill leachate at three stages: unclosed landfills (UL), landfills closed for 1-5 years (CF), and landfills closed for more than 6 years (CS). Metagenomic analyses identified 518 ARG subtypes across 22 classes. ARG abundance peaked in the CF stage (1.28 copies/cell), significantly higher than in UL (0.292 copies/cell) and CS (0.597 copies/cell) stages (p < 0.05). Elevated concentrations of nickel, copper, and arsenic during the CF stage promoted ARG enrichment via co-selection, primarily driven by efflux pump-mediated cross-resistance and co-resistance within ARG-MRG clusters. IntI1 was strongly linked to high-risk ARGs, indicating horizontal gene transfer as a major dissemination pathway. Key bacterial hosts, including Pseudomonas spp. and Escherichia coli, harbored both ARGs and MRGs. These findings highlight the early post-closure period (1-5 years) as a critical surveillance window and support targeted monitoring of high-risk ARGs, MGEs, indicator taxa, and heavy metals to mitigate environmental dissemination of antibiotic resistance.},
}

@article {pmid41831647,
year = {2026},
author = {Tashiguano, VM and Sierra, K and Black, T and Sirmon, M and Leeds, P and Jones, J and Doster, J and Smith, C and Jia, Z and Garner, L and Cho, S and Hanna, J and Trout, K and Almasri, M and Li, H and Morey, A},
title = {A Multidisciplinary Approach for Predicting the Microbiological Spoilage of Chicken Breast Fillets due to Cold-chain Disruption.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100754},
doi = {10.1016/j.jfp.2026.100754},
pmid = {41831647},
issn = {1944-9097},
abstract = {Cold-chain disruptions during storage and distribution of raw poultry can significantly reduce product shelf-life and safety. This study evaluated the effects of short-term cyclic temperature abuse (TA) on the retail shelf-life of fresh chicken breast, using a multidisciplinary approach that combined food microbiology, machine learning (ML), metagenomics, and volatile compound (VC) analysis. Boneless, skinless chicken breast trays (n = 450) were obtained from a commercial poultry processor and transported under refrigeration (4°C) to Auburn University. In three independent trials, trays were randomly assigned to one of three treatments: (1) Control at 4°C for 24 h; (2) TA Cycle 1: alternating 30 min at 4°C and 1 h at 30°C; and (3) TA Cycle 2: alternating 30 min at 4°C and 1 h at 37°C. TA cycles lasted 7.5 h, after which all trays were stored at 4°C. Samples were analyzed on days 0, 2, 4, 6, and 8 for aerobic, facultative anaerobic, and lactic acid bacteria (LAB) counts, and for VCs using an electronic nose. Rinsates from Trial 3 were stored at -80°C for metagenomic analysis. TA Cycle 2 resulted in the highest spoilage rates, followed by TA Cycle 1. A neural network model moderately predicted bacterial growth (R[2] = 0.65-0.75 for aerobic and facultative anaerobic microorganisms; lower for LAB). Metagenomics demonstrated a shift toward Pseudomonas spp. dominance under TA conditions, while control samples retained microbial diversity. These findings underscore that even short-term TA significantly alters the microbiome and accelerates spoilage in raw poultry, emphasizing the importance of cold-chain integrity. Practical Relevance. This study shows that short, high-temperature abuse events from refrigeration failure, handling delays, or other supply chain disruptions can accelerate spoilage in raw chicken. By combining rapid spoilage-detection tools with predictive models, poultry producers and retailers may better monitor these events, helping to maintain cold-chain integrity and reduce losses.},
}

@article {pmid41831799,
year = {2026},
author = {Qi, H and Wu, R and Liao, J and Alvarez, PJJ and Yu, P},
title = {Longitudinal multi-omics reveal phase-dependent viral adaptive strategies and functional potential during formation of algal-bacterial granular sludge.},
journal = {Bioresource technology},
volume = {449},
number = {},
pages = {134410},
doi = {10.1016/j.biortech.2026.134410},
pmid = {41831799},
issn = {1873-2976},
abstract = {Virus-prokaryote interactions within microbial aggregates critically influence microbiome function and stability, yet the interactive dynamics during microbial aggregation remain largely unexplored. Here, longitudinal multi-omics revealed that prokaryotic host community diversity underwent decline and subsequent recovery during algal-bacterial granular sludge (ABGS) formation from activated sludge. Declined host diversity in the collapse phase enriched for lysogenic viruses and facilitated virus-host mutualistic symbiosis, during which the proportion of lysogenic metagenome-assembled genomes (MAGs) peaked at 84% (841,649 TPM), with auxiliary metabolic genes (AMGs) primarily involved in genetic information processing and amino acid metabolism. Moreover, low host diversity increased viral microdiversity by 1.97-fold and selected for virion structure genes that were conducive to viral fitness and replication. As host diversity recovered during the recovery phase, viruses and hosts engaged in an evolutionary arms race, with both host defense systems (DS) (Spearman's Rho = 0.68, P < 0.05) and viral anti-defense systems (ADS) (Spearman's Rho = 0.51, P < 0.05) enriched along with granule maturation. Furthermore, active lysogenic infections were accompanied by the dissemination of AMGs predominantly associated with the metabolism of cofactors, vitamins, terpenoids, and polyketides. Despite their phase-dependent functional profiles, lysogenic phages with AMGs putatively enhanced the structural and functional stability of the microbiome during ABGS formation. Overall, our study unveils a phase-dependent co-evolutionary interplay between viruses and prokaryotic hosts during ABGS formation, providing insights into virus-mediated microbial structural and functional resilience in engineered ecosystems.},
}

@article {pmid41831800,
year = {2026},
author = {Xie, J and Zhu, W and Wang, W and Min, B and Xu, J and Xie, L},
title = {Optimizing anaerobic digestion for antibiotic degradation and antimicrobial resistance mitigation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134409},
doi = {10.1016/j.biortech.2026.134409},
pmid = {41831800},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) is widely applied to treat antibiotic pharmaceutical wastewater for antimicrobial resistance mitigation and synchronous bio-energy recovery. However, process efficiency and risk control depend critically on operational strategies. Here, we systematically evaluated the roles of feedstock composition and digestive temperature in optimizing lincomycin-containing AD. Glucose-rich mesophilic digestion achieved superior lincomycin degradation and methane recovery compared to thermophilic and protein-rich systems. Transformation product analysis suggested that glucose-rich feedstock might facilitate the furan ring-opening step during lincomycin degradation, possibly owing to structural and metabolic similarities between glucose and lincomycin. The enrichment of lincomycin-degrading Clostridium and Methanobacterium in response to glucose-rich mesophilic condition, together with their potential syntrophic interaction, further supported the accelerated lincomycin degradation and methanation. Metagenome-assembled genome analysis revealed that protein-rich and thermophilic operation intensified the proliferation of host consortia harboring gene clusters with antibiotic resistance gene-mobile genetic element (ARG-MGE) co-occurrence, and induced putative horizontal transfer of ARG, resulting in the increased ARG abundance. ARG proliferation in thermophilic systems was associated with enrichment of lincomycin-resistant consortia (JAAYZQ01 sp034428935 and Tenuifilum sp018056955) after antibiotic exposure, which preferentially enriched under higher-temperature conditions. In contrast, glucose-rich digesters exhibited a reduced potential for horizontal gene transfer mediated by MGEs and natural conjugation. Overall, feedstock composition exerted a greater influence on antimicrobial resistance dissemination compared to temperature. Collectively, our findings provide an operational framework for sustainable treatment and valorization of antibiotic-containing wastewater.},
}

@article {pmid41831863,
year = {2026},
author = {Patel, SS and Shree, T and Kumar, A},
title = {Microbial consortia interactions and bioremediation of pesticides: A review on designing, mechanism and efficacy.},
journal = {Pesticide biochemistry and physiology},
volume = {219},
number = {},
pages = {106993},
doi = {10.1016/j.pestbp.2026.106993},
pmid = {41831863},
issn = {1095-9939},
mesh = {*Pesticides/metabolism ; Biodegradation, Environmental ; *Microbial Consortia ; Soil Microbiology ; *Soil Pollutants/metabolism ; },
abstract = {Ecosystems and human health are at serious risk due to the extensive application of pesticides in the agricultural system for controlling pests and diseases. The use of microbial consortia (MicroCons) has emerged as a promising solution for the remediation of pesticide-contaminated soil, offering a sustainable and eco-friendly alternative to physical and chemical methods; however, a systematic review on this aspect is still lacking. This comprehensive review provides an in-depth analysis of the current knowledge on microbial consortia-based remediation of pesticides in agricultural soil. Efficacy of single-strain vs multiple strains in MicroCons have been discussed to unravel the workload distribution between microbial strains in pesticide degradation. We also discuss the design and optimization of microbial consortia for remediation, highlighting the role of advanced tools and the mechanisms of MicroCons action. Furthermore, emerging trends and future directions in the field, including the potential of synthetic biology, machine learning (ML), and artificial intelligence (AI) are also covered. This review aims to critically expand the mechanistic understanding of how microbe-mediated remediation strategies might reduce pesticide phytotoxicity, enhance crop production in pesticide-stressed soils, and inspire future research and practices in MicroCons-based remediation to achieve the Sustainable Development Goals (SDGs).},
}

*Pesticides/metabolism
Biodegradation, Environmental
*Microbial Consortia
Soil Microbiology
*Soil Pollutants/metabolism

@article {pmid41831922,
year = {2026},
author = {Kashyap, B and Jayaraj, H and Rajpal, S and Sidiq, Z and Arora, VK},
title = {Landscape of metagenomics: fight against tuberculosis and other infectious disease in India.},
journal = {The Indian journal of tuberculosis},
volume = {73},
number = {1},
pages = {13-16},
doi = {10.1016/j.ijtb.2026.02.012},
pmid = {41831922},
issn = {0019-5707},
mesh = {Humans ; *Metagenomics/methods ; India ; *Tuberculosis/diagnosis ; High-Throughput Nucleotide Sequencing ; },
abstract = {Metagenomics is an evolving diagnostic tool worldwide for studying microorganisms which cannot be cultured in routine laboratory settings. From Sanger sequencing to Next Generation Sequencing like Illumina, and now Oxford Nanopore sequencing has been a boon in detecting difficult-to-diagnose infectious disease conditions and delivering patient-tailored treatment. In developing countries like India, these advancements in diagnostics aid in decreasing disease burden, growing antimicrobial resistance and to study new microorganism.},
}

Humans
*Metagenomics/methods
India
*Tuberculosis/diagnosis
High-Throughput Nucleotide Sequencing

@article {pmid41832076,
year = {2026},
author = {Gundra, SR and Jiang, W and Aouida, M and Wang, Q and Kazlak, AM and Elbehery, AHA and Saleh, A and Masood, M and Ghouneimy, A and Mahfouz, M},
title = {Characterization and engineering of highly efficient Cas12j genome editors.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2026.02.001},
pmid = {41832076},
issn = {1879-3096},
abstract = {The large size of widely used CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) enzymes limits their delivery for therapeutic applications. Cas12j nucleases offer a hypercompact alternative but show modest editing efficiency. To overcome this limitation, we identified eight novel Cas12j orthologs from viral metagenomes, which in their native form exhibit low editing activity in mammalian cells. We therefore engineered T5 exonuclease-Cas12j fusions, resulting in substantially enhanced genome-editing activity across multiple mammalian cell types, reaching levels comparable to established compact CRISPR-Cas editors. Intriguingly, robust cellular editing occurred in the presence of a previously unrecognized trinucleotide sequence context within the target DNA. Furthermore, we developed Cas12j-based adenine base editors by coupling catalytically inactive Cas12j orthologs with adenine deaminase, enabling efficient A-to-G base conversion in mammalian cells. This study expands the CRISPR toolbox by establishing engineering principles that convert compact Cas12j nucleases into efficient and modular genome-editing platforms well suited for delivery-constrained therapeutic applications.},
}

@article {pmid41832122,
year = {2026},
author = {Van Etten, J and Johnson, MD},
title = {The ecology of horizontal gene transfer.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2026.02.002},
pmid = {41832122},
issn = {0168-9525},
abstract = {Horizontal gene transfer (HGT) generates genetic variation in populations across all domains of life; however, most studies focus on individual transfers and functional information derived therefrom. This is useful but does not consider DNA transfer more broadly, that is, nongene transfers, donor-recipient dynamics, or trends and background levels that may help infer ecological information. Here, we review the mechanistic underpinnings of DNA transfer, literature from diverse fields that addresses HGT on a community basis and the associated methodological challenges, and propose a framework for conceptualizing the process of DNA transfer, highlighting DNA mobility as a feature of community ecology and DNA itself as a public good. These ideas coalesce to support DNA transfer as a fundamental ecological phenomenon that remains largely unmeasured.},
}

@article {pmid41832496,
year = {2026},
author = {Ali, S and Hassan, M and Essam, T and Abdelmalek, S and Al-Amry, KF},
title = {Antimicrobial resistance profiling in poultry industry: a culture-independent resistome analysis and risk factor assessment.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05334-w},
pmid = {41832496},
issn = {1746-6148},
}

@article {pmid41833387,
year = {2026},
author = {Han, Z and Wang, Y and Yang, J},
title = {Physiological and Biochemical Changes and Microbial Community Succession During the Postharvest Rot Process of Stropharia rugosoannulata.},
journal = {The Journal of general and applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.2323/jgam.2026.03.001},
pmid = {41833387},
issn = {1349-8037},
abstract = {This study systematically elucidated the microbial community succession and functional gene dynamics during the postharvest spoilage process of Stropharia rugosoannulata by integrating physiological and biochemical indicators with metagenomic analysis. The experimental results demonstrated that as storage time extended, the activities of antioxidant enzymes (superoxide dismutase, peroxidase) in S. rugosoannulata significantly declined, while the content of membrane lipid peroxidation product malondialdehyde increased, leading to compromised cell membrane integrity and creating favorable conditions for microbial colonization. Metagenomic analysis revealed that during the spoilage phase (post-harvest day 14), the relative abundance of Pseudomonadota increased to 85.7%, with Pseudomonas replacing Ewingella as the absolutely dominant microbial population. Further functional gene analysis showed that the post-harvest day 14 exhibited significant enrichment of glycosyltransferases (GT0, GT1, GT2, GT4) and carbohydrate-binding modules (CBM10, CBM16, CBM50), along with pectinase (GH78), chitinase (GH19), and polysaccharide-modifying enzymes (CE4, CE11). This indicated a metabolic shift towards cell wall synthesis and substrate recognition. In contrast, the post-harvest day 7, prior to fruiting body softening, demonstrated high expression of glycoside hydrolases (GH1, GH2, GH4, GH94) and carbohydrate esterase CE8, focusing on the degradation of cellulose and starch. These findings, for the first time from a molecular ecology perspective, clarify that the essence of postharvest spoilage in S. rugosoannulata is a quality deterioration process driven by a Pseudomonas-dominated microbial community. The study provided a basis for the development of targeted antibacterial preservation strategies.},
}

@article {pmid41829938,
year = {2026},
author = {Kroplewski, B and Przybyłowicz, KE and Sawicki, T and Przemieniecki, SW},
title = {Supplementation with Animal- and Plant-Derived Proteins Modulates the Structure and Predicted Metabolic Potential of the Gut Microbiota in Elite Football Players.},
journal = {Nutrients},
volume = {18},
number = {5},
pages = {},
doi = {10.3390/nu18050768},
pmid = {41829938},
issn = {2072-6643},
support = {MEiN/2023/DPI/2862//Minister of Science Republic of Poland/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Dietary Supplements ; Male ; Whey Proteins/administration & dosage ; Young Adult ; Adult ; Pea Proteins/administration & dosage ; *Plant Proteins/administration & dosage ; Oryza ; Resistance Training ; *Soccer ; RNA, Ribosomal, 16S/genetics ; Athletes ; *Animal Proteins, Dietary/administration & dosage ; Animals ; },
abstract = {BACKGROUND/OBJECTIVES: The primary outcome of this 8-week randomized, controlled, parallel trial was to assess longitudinal shifts in gut microbiota structure and predicted metabolic potential in 45 elite football players following protein supplementation.

METHODS: Participants combined resistance training with daily intake (30 g) of whey protein concentrate (WPC), pea protein isolate (PPI), rice protein isolate (RPI), or a plant-protein blend (MIX). For the acquisition of prokaryotic metataxonomic data, the V3-V8 region of the 16S rRNA gene was sequenced using Oxford Nanopore Technology (ONT). Functional potential was inferred through the MACADAM database and STAMP software. Strict dietary monitoring and gravimetric adherence checks were performed to isolate the intervention effect.

RESULTS: While microbial alpha-diversity indices (Chao1, Shannon, Simpson) remained stable across all groups, significant source-specific shifts in taxonomic structure and predicted metabolic activity were identified. Whey protein concentrate (WPC) was associated with an increase in Bacteroidetes abundance and greater balance within the microbial community structure, whereas pea protein isolate (PPI) and the MIX correlated with reduced fermentative bacteria and elevated taxa potentially involved in cadaverine biosynthesis. Rice protein isolate (RPI) supplementation was associated with a higher predicted representation of taxa involved in succinate-to-butyrate fermentation pathways. These functional markers and differential responses of selected bacterial groups to particular protein types were observed.

CONCLUSIONS: The data indicate complex interactions between supplement type, exposure duration, and microbiome response, underscoring the necessity for individualized dietary recommendations and supplementation strategies to optimize gut health and training adaptation in professional football players.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Dietary Supplements
Male
Whey Proteins/administration & dosage
Young Adult
Adult
Pea Proteins/administration & dosage
*Plant Proteins/administration & dosage
Oryza
Resistance Training
*Soccer
RNA, Ribosomal, 16S/genetics
Athletes
*Animal Proteins, Dietary/administration & dosage
Animals

@article {pmid41829143,
year = {2026},
author = {Song, D and Song, L and Luo, Y and Chen, J and Zhang, C and Yang, L},
title = {Innovative Systems Biology in Baijiu Fermentation: Unveiling Omics Landscapes and Microbial Synergy.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/foods15050871},
pmid = {41829143},
issn = {2304-8158},
support = {NSFC 32460269//National Natural Science Foundation of China/ ; QianKeHeJiChu- ZD[2025]018//Guizhou Provincial Basic Research Program (Natural Science)/ ; MTXYTD202501//The Science and Technology Innovation Team of Maotai Institute/ ; mygccrc[2022]011//Research Foundation for Scientific Scholars of Moutai Institute/ ; mygccrc [2022]013//Research Foundation for Scientific Scholars of Moutai Institute/ ; mygccrc [2022]026//Research Foundation for Scientific Scholars of Moutai Institute/ ; XYNJ20240104//Moutai Institute & Guangdong Li'er'an Chemical Group Co., Ltd./ ; },
abstract = {The production of Chinese Baijiu relies on the synergistic metabolism of multi-species microbial communities in an open environment. Its intricate microbial succession and flavor formation mechanisms have long been considered complex systems that are difficult to fully deconstruct. Traditional culture-dependent techniques inherently fail to comprehensively capture the actual functional roles and dynamic regulation of "viable but non-culturable" (VBNC) microorganisms within this complex system. In recent years, the rapid advancement of multi-omics technologies has offered a novel perspective for elucidating the underlying fermentation mechanisms of Baijiu. This paper systematically reviews the recent progress in the application of metagenomics, metatranscriptomics, metaproteomics, and metabolomics in Baijiu research. Specific focus is placed on the unique contributions of these tools to resolving microbial community structural diversity, mining key functional genes and enzymes, uncovering microbial stress response mechanisms under environmental fluctuations, identifying phages and spoilage microorganisms, and tracing the metabolic pathways of flavor substances. Furthermore, the pivotal role of multi-omics integration strategies in constructing "microbe-metabolite" regulatory networks is highlighted. Finally, current challenges regarding standardization and data integration are discussed, with an outlook on leveraging omics big data to promote digital monitoring and intelligent brewing in the Baijiu industry.},
}

@article {pmid41828944,
year = {2026},
author = {Xu, S and Zhang, B and Liang, W and Jia, M and Guo, X and Su, B and Wang, R and Pan, Y and Lin, Y and Li, X and Hu, D and Yan, D},
title = {Comparative Analysis of Gut Microbiota and Metabolome of Captive Male Malayan Pangolins with Normal and Abnormal Reproduction.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {5},
pages = {},
doi = {10.3390/ani16050735},
pmid = {41828944},
issn = {2076-2615},
support = {1(2024GXNSFBA010369);2(Forestry Science No. 202301);3(JA-23-03-01); 5(2024RT05)//1Guangxi Natural Science Foundation;2Basic Research Project of Guangxi Forestry Research Institute; 3Key Laboratory Project of Guangxi Characteristic Economic Forest Cultivation and Utilization;4Guangxi's first batch of Young Talents Support Program (Natu/ ; },
abstract = {Ex-situ conservation and captive breeding are important measures for protecting endangered species. However, captive conditions inhibit reproduction in some wild animals, especially males. Under captive conditions, which differentially expressed microbiota and metabolites significantly influence or are key to reproductive performance? This study aimed to investigate the effects of differentially expressed microbiota and metabolites on reproductive performance, including male Malayan pangolins with normal reproductive behavior (NR, with natural mating behavior) and those with abnormal reproductive behavior (AR, without natural mating behavior). Five male Malayan pangolins with normal reproductive behavior and eight with abnormal reproductive behavior were divided into NR and AR groups. Fresh fecal samples were collected for metagenomic and metabolomic analysis. The results showed that Bacillota, Pseudomonadota, Bacteroidota, Actinomycetota, and Fusobacteriota were the dominant phyla. Escherichia, Lactobacillus, Lactococcus, Limosilactobacillus, and Ligilactobacillus were the dominant genera. The abundance of Absiella, Butyribacter, and Candidatus Scatovivens in the gut of the NR group was significantly higher than in the AR group (p < 0.05), while the abundance of Clostridium, Mycoplasmopsis, and Facklamia in the gut of the AR group was significantly higher than in the NR group. A total of 94 differentially expressed metabolites were identified, with Argininosuccinic acid and Cortol significantly upregulated in the AR group, and gamma-Aminobutyric acid and gamma-Glutamylglutamic acid significantly downregulated. These microbiota and metabolites can be screened as potential key biomarkers that might influence the reproductive performance of male pangolins. These findings provide important insights into the husbandry and management of captive pangolins and other endangered wild animals.},
}

@article {pmid41828642,
year = {2026},
author = {Sadurski, J and Ostrowska, M and Staniszewski, A and Waśko, A},
title = {Genomic Plasticity and Functional Reweighting Facilitate Microbial Adaptation During the Ripening of Artisanal Goat Cheese.},
journal = {International journal of molecular sciences},
volume = {27},
number = {5},
pages = {},
doi = {10.3390/ijms27052426},
pmid = {41828642},
issn = {1422-0067},
mesh = {*Cheese/microbiology ; Animals ; Goats ; *Genome, Bacterial ; *Adaptation, Physiological/genetics ; Metagenomics/methods ; Metagenome ; Food Microbiology ; Phylogeny ; },
abstract = {This study presents a genome-resolved shotgun metagenomic analysis of artisanal raw-milk goat cheese from the Masurian region of Poland, addressing the limited understanding of strain-level diversification and functional restructuring during traditional cheese ripening. While microbial succession in cheese has been widely described, comprehensive genome-resolved analyses integrating strain-level genomic heterogeneity, pathway reweighting, and mobile genetic elements in artisanal goat cheese remain scarce. By combining taxonomic profiling with metagenome-assembled genome (MAG) reconstruction and pathway-level functional analysis, we characterised microbial succession and genome plasticity across ripening stages. Genome reconstruction yielded 37 MAGs during early ripening and 141 MAGs in mature cheese, revealing increased genome recoverability and pronounced strain-level heterogeneity within dominant taxa, including Lactiplantibacillus plantarum, Lacticaseibacillus paracasei, and Lactococcus lactis. Alpha diversity increased in mature samples, consistent with progressive community restructuring. Functional profiling demonstrated coordinated metabolic reweighting, particularly within carbohydrate metabolism, while amino acid and lipid metabolism remained proportionally stable. Genome-resolved analyses further identified tetracycline- and sulfonamide-associated resistance determinants and diverse bacteriophages targeting lactic acid bacteria, highlighting the role of mobile genetic elements in horizontal gene transfer and microevolutionary adaptation during ripening.},
}

*Cheese/microbiology
Animals
Goats
*Genome, Bacterial
*Adaptation, Physiological/genetics
Metagenomics/methods
Metagenome
Food Microbiology
Phylogeny

@article {pmid41828538,
year = {2026},
author = {Chen, J and Xu, Y and Liu, Z},
title = {Enzymatic Synergy-Driven Biotransformation Generates a Postbiotic-Rich Functional Matrix That Reprograms Gut Microbiota Metabolic Pathways Under Stress Conditions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {5},
pages = {},
doi = {10.3390/ijms27052313},
pmid = {41828538},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome ; Animals ; Biotransformation ; Mice ; *Stress, Physiological ; Fermentation ; *Metabolic Networks and Pathways ; Lactiplantibacillus plantarum/metabolism ; Metabolomics/methods ; Male ; },
abstract = {The physiological efficacy of plant-based matrices is often limited because bioactive compounds are sequestered within complex lignocellulosic architectures, restricting their release and downstream activity. Fermentation-driven enzymatic biotransformation can overcome these structural barriers; however, the mechanisms by which fermentation-derived, non-viable functional ingredients (postbiotics) confer benefits remain incompletely defined. Here, we examined whether a postbiotic-rich, co-fermented plant matrix enhances host resilience under metabolic stress and whether such effects are accompanied by a remodeling of gut microbial functional capacity. A functional plant matrix was produced by solid-state co-fermentation using two Lactobacillus plantarum strains selected for complementary lignocellulolytic profiles. Untargeted metabolomics and deep shotgun metagenomic sequencing were integrated with a hydrocortisone-induced murine metabolic stress model to quantify substrate remodeling, host neuroendocrine/behavioral outcomes, and microbiome functional reprogramming. Co-fermentation markedly remodeled the phytochemical landscape, increasing extractable flavonoids and generating distinct metabolite clusters. In vivo, administration of the postbiotic-rich matrix partially normalized stress-responsive neuroendocrine markers (ACTH, TRH, and testosterone) and improved behavioral outcomes in open-field and forced swim assays. These systemic changes were paralleled by a coordinated shift in microbial functional potential, including the enrichment of carbohydrate-active enzyme (CAZyme) families involved in complex polysaccharide utilization (e.g., AA9, GH129, CE14) and attenuation of phosphotransferase system modules and cytochrome P450-related functions. Enzymatic synergy-driven biotransformation yields a postbiotic-rich functional matrix that is associated with a selective remodeling of gut microbiome metabolic potential under stress and concomitant improvement in host physiological resilience. This study underscores microbial functional remodeling as a critical mechanistic interface linking fermentation-modified substrates to host physiological recovery, providing a molecular framework for the development of targeted postbiotic interventions.},
}

*Gastrointestinal Microbiome
Animals
Biotransformation
Mice
*Stress, Physiological
Fermentation
*Metabolic Networks and Pathways
Lactiplantibacillus plantarum/metabolism
Metabolomics/methods
Male

@article {pmid41827905,
year = {2026},
author = {Braile, A and Bani, A and Hosseininasab, SF and Regno, ND and Orabona, N and Bove, A and Braile, M},
title = {Profiling Osteoporosis via Integrated Multi-Omics Technologies.},
journal = {Cells},
volume = {15},
number = {5},
pages = {},
doi = {10.3390/cells15050472},
pmid = {41827905},
issn = {2073-4409},
mesh = {Humans ; *Osteoporosis/genetics/metabolism ; *Metabolomics/methods ; Proteomics/methods ; *Genomics/methods ; Biomarkers/metabolism ; Epigenomics ; Multiomics ; },
abstract = {BACKGROUND: Osteoporosis is a complex disorder involving bone loss and muscle degeneration. Multi-omics technologies provide novel insights into its molecular mechanisms and may support biomarker discovery, patient stratification, and therapeutic development.

OBJECTIVE: This scoping review aimed to synthesize current evidence on the application of multi-omics approaches in osteoporosis, focusing on molecular insights, methodological diversity, and translational potential.

METHODS: A literature search of PubMed, Embase, and Scopus retrieved 433 records using the keywords "osteoporosis," "osteosarcopenia," and "omics." After removing duplicates and screening titles, abstracts, and full texts, 30 studies met the inclusion criteria. Data on study populations, biological samples, multi-omics techniques, and integration methods were extracted.

RESULTS: Studies employed transcriptomics, proteomics, metabolomics, lipidomics, epigenomics, and metagenomics, often combined in multi-omics analyses with computational modeling. Key pathways included osteoclast differentiation, immune regulation, ferroptosis, and microbiome-metabolite interactions. Multi-omics integration enabled the identification of molecular subtypes, candidate biomarkers, and potential therapeutic targets. Limitations included small or single-center cohorts, heterogeneous designs, and limited validation, restricting generalizability and clinical translation.

CONCLUSIONS: Multi-omics approaches offer a powerful framework to uncover the molecular mechanisms underlying bone and muscle degeneration and to guide precision diagnostics and interventions. Future studies should prioritize large, multicenter, longitudinal designs integrating multi-omics data with clinical and functional validation to facilitate clinical application.},
}

Humans
*Osteoporosis/genetics/metabolism
*Metabolomics/methods
Proteomics/methods
*Genomics/methods
Biomarkers/metabolism
Epigenomics
Multiomics

@article {pmid41827072,
year = {2026},
author = {Takkar, B and Maddheshiya, A and Adhikary, P and Reddy, VA and Majumder, PP and Mukherjee, S and Das, T and , },
title = {Gut microbiome changes in people with diabetic retinopathy in India. DRMS-India report # 1: operational protocol and trends from first 100 participants.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00821-9},
pmid = {41827072},
issn = {1757-4749},
abstract = {BACKGROUND: Diabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus (DM), and the leading cause of vision impairment and blindness. India is among the top three countries in DM prevalence, and both DM and DR are projected to rise sharply in the future. There is no accepted strategy for the prevention of DR other than DM control. Recent studies suggest that DM is associated with alterations in a core group of gut microbiota, and progression to DR may be influenced by changes within this core group, highlighting a potential link between DR and gut microbiome. We studied these changes in a protocol-driven large case-control study, the Diabetic Retinopathy Microbiome Study-India (DRMS-India: CTRI/2024/02/062511), analysed the results of the first 100 individuals, and evaluated variations in gut microbiome in DR.

METHODS: The DRMS is designed to recruit 462 people aged ≥ 30 years into three cohorts: healthy controls (HCs), DM, and DR, at 17 independent sites in India. Shotgun metagenomic sequencing of first-pass morning fecal samples is performed at a centralized laboratory and correlated with disease status, lifestyle, dietary, and systemic factors.

RESULTS: The first 100 participants included 26 HC, 33 DM, and 41 DR. The trends showed the DR group had 1, 6, and 10 unique core phyla, genera, and species, respectively. Alpha diversity was highest in the DR group; Beta diversity plots showed separate clusters of HCs and DR, with DM overlapping both. Firmicutes (highest in DR), Proteobacteria (highest in DM), Bacteroidetes, and Actinobacteria (highest in HC) were common phyla. Segatella was the most common genus, and Segatella copri was the most common species across all groups to date. Most microbial gene families were annotated to Molecular Functions (MF), and the pathways attributed to carbohydrate, amino acid, lipid, and nucleotide metabolism, indicating distinct functional adaptations in their gut microbiome.

CONCLUSION: Trends from the first 100 individuals indicate that the gut microbiome of Indians with DR exhibits discriminatory features in microbial diversity and abundance, as well as in gene families and pathways that impact host gut metabolism. Data trends from DRMS-India indicate a region-specific non-invasive biomarker that may guide preventive therapy for DR.},
}

@article {pmid41827056,
year = {2026},
author = {Chen, X and Xu, X and Lin, Y and Shi, X and Wang, D and Zhang, T},
title = {Pilea: profiling bacterial growth dynamics from metagenomes with sketching.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02374-0},
pmid = {41827056},
issn = {2049-2618},
support = {T21-705/20-N//University Grants Committee/ ; },
abstract = {BACKGROUND: Quantifying bacteria's growth rates is essential for understanding their ecological roles and for building predictive models in environmental and clinical settings. Peak-to-trough ratios (PTRs) derived from shotgun metagenomes offer a culture-independent proxy for in situ growth rates of bacterial species, yet their reliable computation remains challenging.

RESULTS: We introduce Pilea (https://github.com/xinehc/pilea), an alignment-free, sketching-based method that incorporates statistical models for robust PTR estimation. Pilea achieves speed improvements over existing methods while also enhancing accuracy, as demonstrated on both simulated and real datasets.

CONCLUSIONS: By scaling efficiently to comprehensive reference collections such as the Genome Taxonomy Database (GTDB), Pilea enables large-scale analyses of bacterial growth dynamics across biomes, unlocking new insights for ecological research. Video Abstract.},
}

@article {pmid41826937,
year = {2026},
author = {Ma, X and Zhang, R and Zuo, L and Liang, X and Geng, J and Xia, Y},
title = {When cough leads to infarction: systemic arterial embolism as a sentinel complication of insidious pulmonary mucormycosis in an immunocompetent patient.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04230-1},
pmid = {41826937},
issn = {1471-2466},
support = {2024YFC2309202//National Key Research and Development Program of China/ ; 202402AA310055//Yunnan Provincial Department of Science and Technology Major Science and Technology Special Program/ ; },
}

@article {pmid41826874,
year = {2026},
author = {Wang, H and Fu, Y and Xu, H and Song, X and Huang, S and Chen, Y and Xu, J and Li, W and Zhang, J and Wu, P and Shen, Q and Yang, S and Wang, X and Liu, Y and Ji, L and Li, Y and Yang, H and Tang, J and Zhou, C and Zhang, W},
title = {Viromic profiling of amniotic fluid reveals distinct viral communities associated with maternal health status.},
journal = {BMC pregnancy and childbirth},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12884-026-08933-5},
pmid = {41826874},
issn = {1471-2393},
support = {No. 2023YFD1801300//National Key Research and Development Programs of China/ ; no. 82341106//National Natural Science Foundation of China/ ; JSYGY-1-2023-03(03)//Hospital Management Innovation Research Project of Jiangsu Provincial Hospital Association/ ; Nos. SH2023058, SH2022092 and SH2024091//Social Development Projects in Zhenjiang/ ; },
}

@article {pmid41826873,
year = {2026},
author = {Wang, X and Tian, W and Tian, X and Qin, X and Ma, Y and Yang, T and Cao, S and Wu, L and Feng, H and Ma, B},
title = {Metagenomic analysis of wolfberry branch substrates under tomato cultivation without additional nitrogen fertilization.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08573-z},
pmid = {41826873},
issn = {1471-2229},
support = {32160706//National Natural Science Foundation of China/ ; 2023GKLRLX09//Science and Technology Innovation Leading Talent Program of Ningxia Hui Autonomous Region/ ; },
}

@article {pmid41826827,
year = {2026},
author = {Duduk, B and Galic, I and Stanojević, N and Stankovic, N and Rekanović, E},
title = {Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04915-x},
pmid = {41826827},
issn = {1471-2180},
support = {451-03-136/2025-03/200214//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-136/2025-03/200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; },
}

@article {pmid41825740,
year = {2026},
author = {Alvarado, DA and Holthaus, TA and Martell, S and Southey, NL and Atallah, M and Sarma, R and Revilla, D and Brown, M and Mehta, T and Khan, NA and Holscher, HD},
title = {Effects of Soluble Corn Fiber Consumption on Executive Functions and Gut Microbiota in Middle to Older Age Adults: A Randomized Controlled Crossover Trial.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101473},
doi = {10.1016/j.tjnut.2026.101473},
pmid = {41825740},
issn = {1541-6100},
abstract = {BACKGROUND: Dietary fiber may support cognition through gastrointestinal-microbiota mechanisms, but clinical evidence is limited.

OBJECTIVES: We aimed to determine whether soluble corn fiber (SCF) improved cognition and altered fecal microbiota and fermentation end products in adults.

METHODS: In a randomized, double-blind, crossover trial, 42 healthy adults (45-75y) consumed SCF (18g/d) or a maltodextrin placebo control (CON: 22g/d) for 4 weeks, separated by a washout. Cognitive outcomes included executive function with event-related potentials, relational memory, neuropsychological performance, and mood. Secondary outcomes included fecal microbiota, metabolomics, and gastrointestinal tolerance. Tertiary analyses related microbial and metabolite changes to cognitive improvements using correlation, mediation, and moderation models, and explored SCF fermentation pathways with 16S-predicted functional profiling, shotgun metagenomics and in vitro culturing.

RESULTS: SCF improved reaction times (RT) during congruent (β = -9.8 ms, 95% CI: [-18.4, -1.2], FDR P = 0.01) and incongruent (β = -14.2 ms, 95% CI: [-22.8, -5.6], FDR P = 0.003) flanker trials and increased Parabacteroides (∼4-fold, β = 1.44 log, 95% CI [1.01, 1.88], FDR P < 0.001). At the SCF endpoint, congruent RT tended to be inversely associated with fecal acetate (ρ = -0.33) and propionate (ρ = -0.36), while Parabacteroides was marginally positively associated with acetate (ρ = 0.34) (all FDR P < 0.1). Moderation analyses indicated that SCF-RT relation varied by Parabacteroides magnitude change. At endpoint, SCF increased predicted functional potential of carbohydrate-related KOs and pathways (FDR P < 0.05). In vitro culturing confirmed P. distasonis ferments SCF.

CONCLUSION: SCF consumption improved attentional inhibition, altered the gut microbiota, and selectively enriched Parabacteroides. Although mediation analyses did not support a direct microbiota-to-cognition pathway, moderation analyses suggested that SCF-related cognitive effects may depend in part on Parabacteroides abundance. Collectively, these findings suggest that certain cognitive benefits of SCF consumption may be partly underpinned by the gut microbiota.

CLINICAL TRIAL REGISTRY: NCT05066425 (https://clinicaltrials.gov/study/NCT05066425).},
}

@article {pmid41615376,
year = {2026},
author = {Eichler, H and Butta, NV and Riddell, A and Augustsson, C and Kjalke, M and Jensen, K and Paramo-Florencio, A and Astermark, J and Chowdary, P and Jiménez-Yuste, V},
title = {Investigation of the Suitability of the ROTEM Assay to Measure Coagulation Potential in Blood From Patients on Concizumab Prophylaxis.},
journal = {Haemophilia : the official journal of the World Federation of Hemophilia},
volume = {32},
number = {2},
pages = {490-498},
pmid = {41615376},
issn = {1365-2516},
support = {//Novo Nordisk A/S/ ; },
mesh = {Humans ; *Thrombelastography/methods ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Blood Coagulation/drug effects ; *Hemophilia A/drug therapy/blood ; Blood Coagulation Tests/methods ; Male ; Adult ; },
abstract = {BACKGROUND: Rotational thromboelastometry (ROTEM) aims to measure the coagulation potential in whole blood. Concizumab, an anti-tissue factor pathway inhibitor (TFPI) antibody for prophylaxis in haemophilia, enhances tissue factor (TF)-initiated coagulation by preventing inhibition of activated factor X (FXa), thus increasing thrombin generation.

OBJECTIVES: To evaluate a modified ROTEM assay for monitoring patients on concizumab prophylaxis.

METHODS: The TF reagent (r_exTEM) was diluted 50,000-fold to make the ROTEM assay sensitive to haemophilia and to concizumab. The effect of concizumab was evaluated in the modified ROTEM in haemophilia A (HA)-like blood (normal blood with added anti-FVIII antibody). ROTEM analysis was performed in blood from patients participating in the explorer7/8 trials during 24 weeks of concizumab prophylaxis. Rotrol N plasma was used as quality control.

RESULTS: In vitro experiments showed concizumab concentration-dependent reduction in clot time (CT) and increase in clot development (α-angle) in HA-like blood. At three of four clinical sites, CT and clot development were stable, variance of the control plasma was ≤12.4% and TF content of the diluted reagent (r_exTEM) was consistent. At these three sites, the correlation between CT versus concizumab exposure, free TFPI and thrombin generation assay parameters was weak (-0.508 to +0.359). Prothrombin time positively correlated with CT (0.523) and negatively correlated with α-angle (-0.659).

CONCLUSION: Due to the poor correlation between ROTEM parameters, concizumab exposure, free TFPI and thrombin generation parameters and the lack of consistent and reliable performance of the modified ROTEM assay, it cannot be recommended for general monitoring of patients on concizumab prophylaxis.},
}

Humans
*Thrombelastography/methods
*Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology
*Blood Coagulation/drug effects
*Hemophilia A/drug therapy/blood
Blood Coagulation Tests/methods
Male
Adult

@article {pmid41825563,
year = {2026},
author = {An, M and Yu, J and Lin, X and Lu, Y and Li, X and He, J and Zhao, G},
title = {Multi-stage synthetic microbial consortia outperform single-stage augmentation by remodeling metabolism and mediating function-stability trade-off in anaerobic digestion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134417},
doi = {10.1016/j.biortech.2026.134417},
pmid = {41825563},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) of food waste often suffers from low methane yield and volatile fatty acids (VFAs) accumulation, primarily due to inefficiencies or imbalances within the native microbial community. To address these metabolic and ecological limitations, we constructed two synthetic microbial communities (SynComs) using a function-driven strategy: a methanogen-only consortium (SynCom-J) and a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members (SynCom-YSJ). Both SynComs were introduced into semi-continuous reactors that already harbored a metabolically complete native microbiome, serving as bioaugmentation agents. When fed daily with partially hydrolyzed feedstock containing residual macromolecular organics and short-chain VFAs, SynCom-YSJ consistently outperformed SynCom-J during the entire hydraulic retention time. Compared to the non-bioaugmented control under identical operating conditions, SynCom-YSJ increased methane yield by 22% (vs. 8% for SynCom-J) and nearly eliminated the start-up lag phase, while both consortia reduced propionate accumulation by 1.6-fold. Successful colonization of the SynComs reshaped the AD microenvironment-characterized by elevated acetate, reduced propionate, and a moderate, non-inhibitory increase in total ammonia nitrogen-thereby imposing deterministic selection on the resident community. Metagenomic analysis revealed that SynCom-YSJ triggered broader metabolic reprogramming, upregulating genes involved in hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis. Notably, a trade-off between microbial network stability and process performance emerged: SynCom-J promoted a more robust network, whereas SynCom-YSJ formed a more complex and high-efficiency network that prioritized methane yield. This study demonstrates that coordinated multi-stage bioaugmentation optimizes methanogenesis through targeted metabolic remodeling and provides an ecology-informed design principle for engineering SynComs that balance system performance with stability. These findings highlight the potential of multi-stage bioaugmentation to enhance both functional robustness and system resilience in food waste AD.},
}