@article {pmid42001834,
year = {2026},
author = {Ma, Z and Gao, L and Hou, W and Wu, J and Wen, X and Zhang, Y and Dong, N and Dou, X and Shan, A},
title = {(-)-Epigallocatechin-3-gallate alleviates diarrhea in piglets by suppressing the NMU-NMUR1-ILC2 axis and modulating microbiota-associated energy metabolism.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {155},
number = {},
pages = {158119},
doi = {10.1016/j.phymed.2026.158119},
pmid = {42001834},
issn = {1618-095X},
abstract = {BACKGROUND: Bacterial diarrhea is considered a global health crisis, accounting for approximately 20 % of deaths related to colorectal cancer. (-)-Epigallocatechin 3-gallate (EGCG), one of the most abundant plant-derived polyphenols in the human diet, has shown promise in managing gastrointestinal disorders. But, the systemic evidence for EGCG in alleviating the progression of diarrhea and the mechanisms involved remain unclear.

OBJECTIVES: This study aims to determine whether EGCG confers diarrhea resistance in piglets under Escherichia coli (E. coli) and what the fundamental mechanisms involved are.

METHODS: Weaned piglets were used to create a E. coli-induced intestinal disorder-diarrhea susceptibility model. Piglets were supplemented with EGCG to identify diarrhea rate and activity of enteric nervous system (ENS). The interaction between the neuromedin U receptor 1 (NMUR1) and typeⅡinnate lymphoid cells (ILC2) was analyzed using RNA sequencing (RNA-seq) and fluorescence colocalization techniques. Metagenomic and metabolomic analyses were further performed to assess the involvement of NMUR1 and the underlying mechanisms of beneficial microbes enriched by EGCG. The effects of beneficial microbes in treating intestinal morphology were investigated through histopathology, Scanning electron microscopy (SEM) and ELISA analysis methods.

RESULTS: EGCG reduced diarrhea rate in piglets by inhibiting the NMU-NMUR1-ILC2 pathway, ameliorating gut microbiota structure, and stimulating intestinal barrier. Apparently, the enteric nerve-microbial axis is linked with EGCG conferring diarrhea resistance in piglets. Mechanistically, EGCG suppressed the NMU-NMUR1-ILC2 axis to reduce the secretion of inflammatory cytokines (TNF-α, IL-6, and IL-8), while concurrently increasing the abundance of beneficial gut microbes and altering signature microbial community functions (energy metabolism pathways); accordingly, EGCG maintained the energy supply balance in gut epithelial cells and promoted the activity of goblet cell and Paneth cell by activating the AMP-activated protein kinase (AMPK)-sirtuin 1 (Sirt1) signaling pathway.

CONCLUSION: EGCG confers diarrhea resistance in E. coli piglets by maintaining intestinal mucosal barrier via the enteric nerve-microbial axis; thus, this study provides a potential prevention strategy for young mammals at risk of diarrhea.},
}

@article {pmid42002156,
year = {2026},
author = {Jeon, J and Nguyen, HT and Yeo, G and Lee, C and Cho, SK and Oh, S},
title = {Integrating metagenomics and explainable artificial intelligence for modeling of food waste treatment using full-scale anaerobic digestion.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134649},
doi = {10.1016/j.biortech.2026.134649},
pmid = {42002156},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD), a biochemical process that can convert food waste (FW) into methane, offers great promise as a sustainable form of energy production. While several attempts have been made to optimize AD systems using various mathematical models, more precise modeling approaches that fully consider the complexity of the AD process are required, leading to the adoption of artificial intelligence (AI) as a suitable alternative to numerical modeling. In line with this, the present study tested 11 AI-based models on their prediction of the methane yield for a full-scale AD process using FW as a feedstock. The models incorporated operational parameters, environmental conditions, and microbial information to improve their predictive performance, and the most precise model was a one-dimensional convolutional neural network (1D-CNN) with optimized hyperparameters. Explainable AI (XAI) was then used to determine the most important input features contributing to the predictions of the optimal AI model, thus allowing for detailed model interpretation. Methanothrix was identified as a key predictor of methane yield, and metagenomic analysis provided independent genome-level evidence broadly consistent with the XAI results. Overall, this study proposes a novel approach to the interpretation and optimization of AD performance, rather than focusing only on enhancing the predictive performance of a discrete model.},
}

@article {pmid42002784,
year = {2026},
author = {Liu, T and Fan, S and Li, J and Wang, T and Zhang, J and Wang, C},
title = {Curcumin modulates hepatic pyroptosis-autophagy crosstalk induced by aflatoxin B1 via rumen microbiota-blood-liver axis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02396-8},
pmid = {42002784},
issn = {2049-2618},
support = {2023YFD1301005//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Aflatoxins, fungal secondary metabolites from Aspergillus species, primarily causes liver and gastrointestinal damage in ruminant. Curcumin, a plant polyphenol, has been shown to possess both anti-inflammatory and antioxidant properties, in addition to regulatory effects on gut microbiota. However, research on curcumin's impact against AFB1 toxicity in ruminants is limited. This study aims to elucidate whether AFB1 induces hepatic pyroptosis and autophagy in ruminants via the rumen microbiota-blood-liver axis and the regulatory role of curcumin. The experimental design involves the administration of AFB1 and curcumin to sheep, followed by a comprehensive observation of alterations in rumen microbiota, barrier function, and the occurrence of hepatic pyroptosis and autophagy, with the aim of elucidating the mechanism of curcumin in ameliorating AFB1-induced liver injury in sheep.

RESULTS: In the experimental setup, 800 mg/kg dry matter (DM) curcumin was administered as a dietary supplement to alleviate the adverse effects of AFB1 (500 μg/kg DM) on the rumen and liver of sheep. AFB1 suppressed NH3-N and VFAs production, whereas curcumin improved VFA generation and fermentation efficiency. Curcumin mitigated AFB1-induced rumen barrier impairment by upregulating tight junction proteins (ZO-1, Occludin, Claudin-1) and reducing LPS levels, which was consistent with metagenomic data showing amelioration of microbiota dysbiosis and reduced lysis of Gram-negative bacteria. At hepatic level, curcumin downregulated the principal mediators of the TLR4-NF-κB-NLRP3 signaling pathway (TLR4, p65, and NLRP3), attenuating pyroptosis and reducing serum AST, ALT, and LDH concentrations, while reversing inflammatory infiltration and hepatic cord disruption. Furthermore, curcumin restored autophagic flux by increasing the LC3-II/LC3-I ratio and decreasing p62 accumulation, counteracting AFB1-induced autophagy inhibition.

CONCLUSIONS: Curcumin counteracts AFB1-induced rumen-liver axis dysfunction. It works by stabilizing the microbiota, maintaining barrier integrity, and dually regulating pyroptosis and autophagy. Video Abstract.},
}

@article {pmid42002835,
year = {2026},
author = {Morineau, N and Tessoulin, B and Guimard, T and Papin, M and Roquilly, A and Le Gouill, S and Montassier, E},
title = {Longitudinal gut microbiome dynamics are associated with clinical outcome and toxicity during ibrutinib therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2659397},
doi = {10.1080/19490976.2026.2659397},
pmid = {42002835},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Piperidines/adverse effects/therapeutic use ; *Adenine/analogs & derivatives/adverse effects/therapeutic use ; Male ; Female ; Middle Aged ; Aged ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification/metabolism/drug effects ; Feces/microbiology ; Treatment Outcome ; *Antineoplastic Agents/adverse effects/therapeutic use ; Adult ; },
abstract = {Accumulating evidence indicates that the gut microbiome influences therapeutic efficacy and toxicity across cancer treatments; however, its longitudinal dynamics during targeted therapies remain poorly characterized. Here, we performed whole-genome shotgun metagenomic sequencing of 291 longitudinal stool samples collected over one year from 30 patients with hematologic malignancies treated with ibrutinib. Overall gut microbial diversity remained stable at the population level but exhibited markedly divergent temporal trajectories according to clinical outcome, with progressive recovery in responders and blunted or delayed restoration in non-responders. Longitudinal modeling revealed distinct species- and pathway-level microbial dynamics between patients with treatment response or nonresponse, including enrichment of saccharolytic, short-chain fatty acid-associated taxa and metabolic pathways in responders, and expansion of bile acid-modifying, proteolytic, and inflammation-associated microbial features in non-responders. Functional profiling further demonstrated opposing temporal trends in pathways related to carbohydrate fermentation, amino-acid metabolism, and secondary bile acid synthesis. In addition, both baseline microbiome composition and longitudinal remodeling were associated with the development of ibrutinib-associated diarrhea. Together, these findings reveal coordinated, outcome-specific remodeling of the gut microbiome during ibrutinib therapy and highlight longitudinal microbiome trajectories, rather than static baseline features, as potential biomarkers of treatment response and toxicity, as well as targets for microbiome-directed interventions. In conclusion, our findings highlight a potential role of gut microbiome dynamics in modulating response to BTK inhibition and support the need for larger, prospective studies to validate these observations.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Piperidines/adverse effects/therapeutic use
*Adenine/analogs & derivatives/adverse effects/therapeutic use
Male
Female
Middle Aged
Aged
Longitudinal Studies
*Bacteria/classification/genetics/isolation & purification/metabolism/drug effects
Feces/microbiology
Treatment Outcome
*Antineoplastic Agents/adverse effects/therapeutic use
Adult

@article {pmid42003340,
year = {2026},
author = {Tong, Y and Marcelino, VR and Turnbull, R and Verbruggen, H},
title = {ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70143},
doi = {10.1111/1755-0998.70143},
pmid = {42003340},
issn = {1755-0998},
support = {2023.06155//Fundação para a Ciência e a Tecnologia/ ; DE220100965//Australian Research Council/ ; RYC2023-042907-I//Ministerio de Ciencia e Innovación/ ; //The University of Melbourne's Research Computing Services/ ; },
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Genome, Plastid ; *Eukaryota/genetics/classification ; *Software ; Phylogeny ; Metagenome ; },
abstract = {Genome-resolved metagenomics has contributed greatly to discovering prokaryotic genomes. When applied to microscopic eukaryotes (protists), challenges such as the high number of introns and repeat regions found in nuclear genomes have hampered the mining and discovery of novel protistan lineages. Organellar genomes are simpler, smaller, have higher abundance than their nuclear counterparts and contain valuable phylogenetic information, but are yet to be widely used to identify new protist lineages from metagenomes. Here we present "ChloroScan", a new bioinformatics pipeline to extract eukaryotic plastid genomes from metagenomes. It incorporates a deep learning contig classifier to identify putative plastid contigs and an automated binning module to recover bins with guidance from a curated marker gene database. Additionally, ChloroScan summarizes the results in different user-friendly formats, including annotated coding sequences and proteins for each bin. We show that ChloroScan recovers more high-quality plastid bins than MetaBAT2 for simulated metagenomes. The practical utility of ChloroScan is illustrated by recovering 16 medium to high-quality metagenome assembled genomes (MAGs) from four protist-size-fraction metagenomes, with several bins showing high taxonomic novelty. The ChloroScan code (v0.1.7) is available at https://github.com/Andyargueasae/chloroscan/tree/release_v0.1.7 under Apache-2.0 licence.},
}

*Metagenomics/methods
*Computational Biology/methods
*Genome, Plastid
*Eukaryota/genetics/classification
*Software
Phylogeny
Metagenome

@article {pmid42003642,
year = {2026},
author = {Krausfeldt, LE and Subramanian, P and Doan, D and McCauley, K and Dolan, M and Hurt, DE},
title = {DiscoVir: an automated, web-based pipeline for viral metagenomics.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0008526},
doi = {10.1128/mra.00085-26},
pmid = {42003642},
issn = {2576-098X},
abstract = {DiscoVir is an automated pipeline for viral metagenomics available in National Institute of Allergy and Infectious Diseases (NIAID)'s free web application for microbiome analysis, Nephele. DiscoVir makes viral discovery, taxonomic and functional annotation, host predictions, and diversity analyses of the virome easily accessible to researchers at all levels of expertise.},
}

@article {pmid42003644,
year = {2026},
author = {Iizuka, R and Moriya, T and Oshima, T and Uemura, S and Yohda, M},
title = {Amplicon sequence collection of putative polyethylene terephthalate hydrolases from two different composts in Japan.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0017326},
doi = {10.1128/mra.00173-26},
pmid = {42003644},
issn = {2576-098X},
abstract = {We report a collection of amplicon sequences of putative polyethylene terephthalate (PET) hydrolases from two different composts in Japan. Employing previously designed degenerate primers, we identified 31 and 22 sequences from industrial and agricultural composts, respectively, confirming the presence of highly homologous PET hydrolase genes across different compost environments.},
}

@article {pmid42003651,
year = {2026},
author = {Kocakahya, İ and Şahin, G and Büyükkahraman, E and Arıkan, M},
title = {Metagenome-assembled genomes from urban pigeon feces in Istanbul, Türkiye.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0140525},
doi = {10.1128/mra.01405-25},
pmid = {42003651},
issn = {2576-098X},
abstract = {We report herein about 101 metagenome-assembled genomes (MAGs) obtained from pigeon fecal samples collected in 2025 from the Beyazıt, Kadıköy, and Beşiktaş squares of Istanbul. The MAGs were predominantly composed of members of the phyla Firmicutes, Actinobacteria, and Proteobacteria, with a lower representation of Campylobacterota and Patescibacteriota.},
}

@article {pmid42004019,
year = {2026},
author = {Yuan, G and Zhu, X and Zhang, L and Wang, X and Wang, Y and Guo, D and Zhang, T and Wang, G and Wang, N},
title = {Shading affects the nitrogen cycling process and plant nitrogen uptake by altering the rhizosphere microbial community.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1780344},
pmid = {42004019},
issn = {1664-462X},
abstract = {Plants adapt to environmental changes by affecting the rhizosphere environment and microbial pathways. Shading affects nitrogen absorption and accumulation in plants by directly or indirectly altering the light intensity. However, the effects this has on the rhizosphere micro-environment and especially the microbial community are not fully understood. Utilizing non-targeted metabolomics and metagenomics, we investigated the changes in the microbial community structure in the cigar tobacco rhizosphere and the nitrogen cycling process and its relationship with nitrogen absorption by the plants under artificial shading conditions. Shading significantly increased the rhizosphere soil organic carbon, hydrolyzable nitrogen, ammonium nitrogen, nitrate nitrogen, and nitrogen contents in tobacco plants. Metabolomics revealed that shading significantly affected the arginine biosynthesis pathway in the rhizosphere soil, with the expression levels of L-oxornithine, citrulline and L-arginine significantly increasing. Metagenomics analysis indicated that shading significantly altered the rhizosphere microbial community structure and the nitrogen cycling process. The abundances of organic nitrogen-decomposition (gdh A, ansB) and nitrification genes (amoA_B, amoB_B, amoC_B, hao) significantly increased. Flavobacterium and Stenotrophomonas may play important roles in the nitrogen cycle in the rhizosphere. Correlation analysis indicated that Flavobacterium and Stenotrophomonas were significantly positively correlated with L-glutamic acid, L-ornithine and L-arginine (p < 0.05). These results reveal the biological mechanism by which shading affects nitrogen absorption in crops via changes in the rhizosphere microbial community and the nitrogen cycling process, providing a scientific foundation for guiding nutrient management strategies in shaded cultivation.},
}

@article {pmid42004152,
year = {2026},
author = {You, G and Wang, S and Hua, Y and Su, J and Yang, Y and Shi, B and Cen, S},
title = {A four-year misdiagnosis of spinal Burkholderia pseudomallei infection: A case report and literature review.},
journal = {IDCases},
volume = {44},
number = {},
pages = {e02558},
pmid = {42004152},
issn = {2214-2509},
abstract = {Melioidosis, traditionally an endemic disease, is increasingly reported in non-endemic regions. Its causative pathogen, Burkholderia pseudomallei, exhibits distinct characteristics from common pathogens but is prone to misdiagnosis due to clinical overlap with other infections. Despite advances in diagnostics, metagenomic next-generation sequencing (mNGS) has not been featured in case reports. We present a case of melioidosis, misdiagnosed for four years, where mNGS proved pivotal for definitive diagnosis. Based on our findings and literature review, we advocate for mNGS in melioidosis diagnosis. Furthermore, we identify subtle distinctions between melioidosis and tuberculosis amidst their similarities and propose integrating these features into a differential diagnostic framework.},
}

@article {pmid42004164,
year = {2026},
author = {Chong, KL and Liew, KJ and Salleh, FM and Chong, CS},
title = {Metagenomic insights into mangrove lignocellulolytic bacteria and functional analysis of a glucose-tolerant GH 1 β-glucosidase.},
journal = {3 Biotech},
volume = {16},
number = {5},
pages = {163},
pmid = {42004164},
issn = {2190-572X},
abstract = {UNLABELLED: Mangrove ecosystems contain abundant lignocellulosic biomass and mangrove microorganisms that are capable of degrading plant polymers. In this study, a shotgun metagenomic approach was employed to explore the bacterial communities from Tanjung Piai National Park, Malaysia and their genes involved in lignocellulosic biomass degradation. A total of 148 of carbohydrate active enzymes (CAZy) genes spanning GH, CE, and AA families were identified with lignocellulolytic abilities. These enzymes included 20 cellulases, 46 hemicellulases, and 82 lignin-modifying enzymes. Approximately 89.19% of these genes were found from underexplored bacterial lineages. A set of lignocellulolytic genes derived from diverse bacterial taxa highlighted the synergistic action of mangrove bacteria in lignocellulose degradation. To validate the functionality of these genetic resources, one of the genes (BGL3_GH1) encoding a β-glucosidase was selected for expression and characterisation. The recombinant enzyme showed optimal activity at 60 ℃ and pH 7, retained up to 75% activity at 10% (w/v) NaCl. The enzyme exhibited a 1.6 to 2.1-fold in enzyme activity with glucose concentration up to 2 M. In a two-step saccharification assay using sugarcane bagasse, supplementation with recombinant BGL3_GH1 enhanced the saccharification yield (0.0674 g g[- 1] biomass) compared with treatments using commercial cellulase or recombinant BGL3_GH1 alone. These findings reveal the functional diversity of lignocellulose-degrading genes in mangrove bacteria and identify recombinant BGL3_GH1 as a potential enzyme candidate for biomass conversion application.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04788-x.},
}

@article {pmid42004407,
year = {2026},
author = {Chu, D and Liu, N and Liu, Q and Li, X and Yang, H and Zhu, N and Liu, Z and Wang, R and Yuan, S and Fu, H},
title = {Diet-Driven Divergence in Gut Microbiota Variation Between Two Sympatric Gerbil Species.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73367},
pmid = {42004407},
issn = {2045-7758},
abstract = {Gut microbiota provide various benefits to their mammalian hosts; however, knowledge regarding interspecific differences in gut microecology remains limited. This study employed 16S rRNA sequencing combined with metagenomic functional prediction (potential functions or functional potential) to conduct a comparative analysis of the gut microbial composition and functional adaptability of two sympatrically distributed gerbil species with distinct diets: the herbivorous Rhombomys opimus (RO) and the omnivorous Meriones meridianus (MM). The results revealed that the omnivorous MM exhibited a level of gut microbial alpha diversity comparable to that of the herbivorous RO, whereas RO showed significant enrichment of norank_f__Muribaculaceae, a taxon associated with fiber degradation, and demonstrated higher abundance of genes related to complex fiber degradation. Notably, bacterial genera significantly enriched in the gut of MM, such as Lachnospiraceae_NK4A136_group and Desulfovibrio, may play important roles in maintaining gut health and enhancing chitin degradation efficiency. Furthermore, the abundance of genes related to monosaccharide and chitin degradation was significantly higher in MM than in RO. Functional network analysis indicated that the cellulose degradation gene networks in both gerbil species were predominantly synergistic, but the synergistic effect was stronger in RO than in MM (ratios of positive to negative correlation edges: 2.44: 1.59). Further analysis revealed that the monosaccharide and chitin degradation gene networks in MM both exhibited synergistic interaction patterns (ratios of positive to negative correlation edges: 1.69 and 2.95, respectively), whereas these two networks in RO were primarily antagonistic (ratios of positive to negative correlation edges: 0.831 and 0.73, respectively). This suggests that the gut microbiota of RO are more conducive to digesting complex plant fibers, while those of MM are better adapted for digesting starch and chitin. This differentiation in gut microbiota optimizes the utilization of different food resources by the two species, thereby promoting their sympatric coexistence. This study enhances our understanding of the adaptive mechanisms of gut microecology in rodents with different diets and provides an important foundation for further research on the microbial ecology of wild rodents and the mechanisms underlying sympatric species coexistence.},
}

@article {pmid42004633,
year = {2026},
author = {Monjardino, P and Azevedo, AR and Mendonça, D and Pozsgai, G and Borges, PAV and Frias, J and Toubarro, D},
title = {Metagenomic survey of fungal communities in compost from dairy plant wastewater sludge and garden trimmings.},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e174893},
pmid = {42004633},
issn = {1314-2828},
abstract = {BACKGROUND: Composting converts organic residues into stable organic matter and nutrients under aerobic conditions, improving soil properties and microbiome balance, while mitigating environmental impacts. Although microbiomes of various compost types have been studied, information is still fragmented and often not tailored to specific raw material combinations. In particular, little is known about the fungal communities involved in composting dairy plant wastewater sludge mixed with garden trimmings. This data paper contributes to filling that gap by providing a comprehensive taxonomic inventory.

NEW INFORMATION: We provide a fungus-focused dataset from 18 compost samples generated from a 1:1 (w/w) mix of garden trimmings and dairy plant wastewater sludge, collected at three process stages (thermophilic start/end; mid-cooling and maturation) under two turning regimes. Shotgun metagenomes were taxonomically annotated against NCBI taxonomy (accessed 19 Feb 2025). Only Fungi were detected within Eukarya, spanning nine phyla; Ascomycota (60.8%), Mucoromycota (17.76%), Basidiomycota (8.50%) and Chytridiomycota (7.21%) comprised 94.27% of the taxonomic features. We report 417 genera (13 >1% relative abundance each); top: Aspergillus (17.93%), Rhizopus (8.61%), Chaetomium (4.83%), Aureobasidium (3.09%), Madurella (2.85%), Paramicrosporidium (2.71%), Rhizophagus (1.88%), Rasamsonia (1.81%), Hyaloraphidium (1.39%), Thermochaetoides (1.31%), Talaromyces (1.19%), Trichoderma (1.15%), Podospora (1.06%) comprised 49.81% of the taxonomic feature abundance. Overall 663 taxa were identified (578 species, 416 genera, 230 families, 106 orders, 48 classes and 9 phyla). The dataset (DwCA; 663 occurrences) is intended to serve as a reference for compost mycobiomes and will be available via GBIF (DOI 10.15468/nmpzwr).},
}

@article {pmid42004896,
year = {2026},
author = {Pourghasem, M and Tabatabaii, SA and Modarresi, SZ and Jafari Nodoushan, A and Fadavi, N and Soflaee, M and Hosseini Vajari, A and Khazaii, F and Shahhosseini, B and Fakhimi Derakhshan, K and Sadat Mansouri, S},
title = {Fungal Infections in Pediatric Patients With Hematologic Malignancies and Stem Cell Transplantation: Impact on the Upper and Lower Respiratory Systems.},
journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2026},
number = {},
pages = {8766717},
pmid = {42004896},
issn = {1712-9532},
abstract = {Invasive fungal infections (IFIs) are a leading cause of morbidity and mortality in children with hematological malignancies as well as those undergoing hematopoietic stem cell transplantation (HSCT). Extreme immunological dysregulation secondary to severe neutropenia, T-cell lymphopenia, graft-versus-host disease (GVHD), intensive chemotherapy regimens, and conditioning therapy for HSCT, as well as primary immunodeficiencies (PIDs), render these patients highly susceptible to both opportunistic and pathogenic fungal infections. Despite advances in antifungal drugs and diagnostic tools, it is very difficult in these children to provide timely diagnosis and optimal management of IFIs because of the nonspecific clinical manifestations, the invasiveness of present diagnostic modalities in pediatric patients, and biomarker kinetics differences in various pediatric age groups, along with a lack of incorporation of immunological-pharmacological maturity-associated variability in the existing scoring systems borrowed from adults. This narrative review provides a comprehensive and contemporary assessment of the epidemiology, host-related risk factors, clinical presentations, diagnostic criteria, and management practices for IFIs in children with hematological malignancies and following HSCT. It also highlights the role of EORTC/MSGERC criteria in defining IFIs as probable, proven, and possible infections and explores the sensitivity and specificity of noninvasive methods such as the galactomannan index, polymerase chain reaction (PCR), ß-D-glucan assay, high-resolution CT scans (HRCTs), and the latest approaches including next-generation sequencing (NGS) and metagenomics. This review points out significant gaps in pediatric research studies and supports efforts to optimize healthcare use with risk-prediction models rather than just relying on current algorithms.},
}

@article {pmid42005541,
year = {2026},
author = {Naitchede, LHS and Ihearahu, OC and Saha, K and Igwe, DO and Yan, J and Osano, AA and Ray, S and Ude, G},
title = {Microbial community characterization in semi-hydroponic systems of Starbor kale (Brassica oleracea L.) grown under normal gravity and simulated microgravity.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100592},
pmid = {42005541},
issn = {2666-5174},
abstract = {Kale is a member of the Brassicaceae family and contains a range of beneficial compounds. Given the global context of climate change, various vegetable production systems using advanced technologies, such as hydroponics, are being explored to alleviate food insecurity. Herein, we characterized the comprehensive microbial community associated with Starbor kale cultivation systems under normal gravity and simulated microgravity in coco coir, representing an innovative approach compared to previous studies. The kale seedlings were planted in growth vessels set into custom 2D clinostats and placed in a CONVIRON growth chamber for 43 days. The microbial DNA from coco-coir and root samples of grown kale was extracted and subjected to shotgun metagenomic sequencing. Comparisons between components revealed a higher abundance of bacteria in the soilless, while the kale roots were dominated by Eukaryota and archaea. The phyla Pseudomonadota and Actinomycetota were highly prevalent across all samples, with relatively high abundance in the coco coir samples from horizontal clinostats (HCR) under simulated gravity and from rotating vertical clinostats (VCR). The HCR group was associated with the highest number of biomarkers (28). Both CAZymes, glycoside hydrolases and carbohydrate esterases, exhibited higher relative abundances in the coco coir samples under normal gravity, whereas carbohydrate-binding modules were more abundant in HCR and VCR. The root samples showed much higher abundances of polysaccharide lyases (ranging from 0.00088 to 0.00097) and carbohydrate esterases (ranging from 0.030 to 0.033). The top four prevalent antibiotic resistance genes were adeF, vanY, vanT, and qacG. The findings of this investigation are crucial for the cultivation of kale and leafy green agriculture in hydroponic systems.},
}

@article {pmid42005844,
year = {2026},
author = {Ibañez-Lligoña, M and Colomer-Castell, S and Campos, C and González-Camuesco, Á and Llauradó, A and Garcia-Larroy, J and Sánchez-Tejerina, D and Rando-Segura, A and Andrés, C and Esperalba, J and Nadal, P and Ferrer, R and Cortese, MF and Tabernero, D and Gregori, J and Riveiro-Barciela, M and Ruiz-Cobo, JC and Ruiz, A and Del Barco, E and Buti, M and Goya, M and Antón, A and Cano, A and Juntas-Morales, R and Quer, J},
title = {Unveiling pathogens and contaminants: refining metagenomics for clinical diagnostics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1786985},
pmid = {42005844},
issn = {1664-302X},
abstract = {INTRODUCTION: Shotgun metagenomic sequencing (mNGS), an untargeted approach that sequences all nucleic acids in a sample, has emerged as a powerful tool for pathogen detection and genome characterization. However, its implementation in clinical diagnostics remains limited due to technical challenges such as contamination and reduces sensitivity, especially in low-biomass samples.

METHODS: We applied mNGS to 144 clinical samples representing chronic infections, acute infections, and respiratory co-infections. To address contamination, we established a framework integrating negative controls, lab-specific contaminant watchlists, and computational filtering. Viral detection performance and genome recovery were assessed across sample types and viral loads.

RESULTS: Viral load was shown to be the primary determinant of sensitivity, with reliable recovery achieved only at higher titers. Our framework substantially improved contamination management, reducing false-positive signals and enhancing viral genome recovery. mNGS enabled the detection of clinically relevant co-infections and refined viral classification beyond targeted diagnostics, while also revealing the substantial risk of spurious detections in the absence of contamination-aware workflows.

DISCUSSION: These findings define practical sensitivity thresholds for clinical mNGS and underscore the need for contamination-aware workflows, particularly for low-biomass samples, while providing an open-source contaminants watchlist that enhances reliability and utility of clinical metagenomics.},
}

@article {pmid42005864,
year = {2025},
author = {Steindler, L and Durán Canché, MA and Ilan, M and Bar-Shalom, R and Lopez, JV 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 marine sponge Diacarnus erythraeanus Kelly-Borges & Vacelet, 1995, and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {466},
doi = {10.12688/wellcomeopenres.24763.2},
pmid = {42005864},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Diacarnus erythraeanus (sponge; Porifera; Demospongiae; Poecilosclerida; Podospongiidae). The genome sequence has a total length of 140.86 megabases. Most of the assembly (98.57%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.34 kilobases in length. Sixty-four binned genomes were generated from the metagenome assembly, of which 46 were classified as high-quality metagenome assembled genomes (MAGs). The microbial signature is typical of HMA sponges, including the Pseudomonadota, Chloroflexota and Acidobacteriota as dominant phyla and several candidate phyla (Poribacteria, Binatota, Latescibacterota) as well as the archaeal clade Nitrosopumilaceae in lower abundance.},
}

@article {pmid42005923,
year = {2026},
author = {Lafon, T and Weingart, M and Vaidie, J and Calfee, CS and Jacob, ST and Freund, Y and Shapiro, NI and Barraud, O and Monneret, G and van der Poll, T and Fromage, Y and François, B},
title = {Challenges in early detection and prognostication of sepsis: new approaches from the emergency department and intensive care unit.},
journal = {EClinicalMedicine},
volume = {94},
number = {},
pages = {103864},
pmid = {42005923},
issn = {2589-5370},
abstract = {In this narrative review, we aimed to provide a comprehensive overview of emerging diagnostic strategies and precision medicine approaches in sepsis, while explicitly acknowledging the heterogeneity of clinical contexts. In the Emergency Department (ED), timely recognition of infection and sepsis represents one of the most frequent and challenging tasks, which may delay management directly increasing morbidity and mortality. Even if very popular and widely used, traditional scores and routine biomarkers remain of limited interest to confirm diagnosis and predict deterioration. Nevertheless, emerging point-of-care tools hold promise such as "real-time microbiology", bedside immune profiling, and echocardiography for on-time hemodynamic phenotyping. More advanced strategies, such as omics technologies and transcriptomic signatures, offer deeper biological precision, while machine learning and artificial intelligence can integrate high-dimensional ED data to anticipate deterioration and capture the dynamic evolution of sepsis subphenotypes. Many of these tools are already feasible at the bedside and only await integration into routine ED workflows. Embedding them within dedicated sepsis pathways and multidisciplinary teams could optimize global patient care and accelerate the transition toward precision medicine in acute sepsis. Sustainable improvements in sepsis outcomes will most likely not come from isolated devices but from their integration into coordinated and sepsis-specific pathways.},
}

@article {pmid42006114,
year = {2025},
author = {Dorobantu, S and Grigorescu, A and Fratea, A and Mirauta, B and Neghina, A and Bica, G and Neacsu, A and Dumitrescu, F and Streata, I and Netea, M and Riza, AL},
title = {Strength of Omics in Uncovering Sepsis Mechanisms-A Perspective.},
journal = {Current health sciences journal},
volume = {51},
number = {4},
pages = {425-436},
pmid = {42006114},
issn = {2067-0656},
abstract = {BACKGROUND: Sepsis is a significant life-threatening condition due to a dysregulated response to infection. Large datasets yield unprecedented views and transformative insights into processes through various computational frameworks. Our aim was to highlight significant contributions from genomics, transcriptomics, proteomics in the field of sepsis, as modeled from human data. We are showcasing key findings in each omics that have improved the understanding of sepsis pathophysiology, while presenting a perspective from the group's own contribution to the field.

DISCUSSION AND CONCLUSIONS: Each of the presented omics has advanced our mechanistic understanding on sepsis pathogenicity, biomarker identification for diagnosis, prognosis, and molecular stratification purposes. Multi-omics sepsis research shows strong input from genomics, transcriptomics, proteomics. These have revealed mechanistic links and produce robust endotypes but faces challenges on the path to clinical integration. Integrative sepsis studies combine large-scale omics, paired sampling, and computational multi-omics frameworks to link molecular layers to phenotype. Addressing gaps in standardization, and age/ethnicity representation could yield actionable biomarkers, stratified therapies and improved outcomes.},
}

@article {pmid42006125,
year = {2026},
author = {Azuma, N and Wada, N and Aoki, R and Sampei, M and Mawatari, T and Saito, Y},
title = {Administration of bifidobacteria and dietary fiber improves cognitive function by increasing short-chain fatty acid-producing bacteria and reducing inflammation.},
journal = {Bioscience of microbiota, food and health},
volume = {45},
number = {2},
pages = {139-148},
pmid = {42006125},
issn = {2186-6953},
abstract = {Bifidobacterium animalis subsp. lactis GCL2505 (GCL2505), commercially known as the "BifiX" strain in Japan, reaches the intestine alive, proliferates after a single intake, and is associated with several positive health effects. A randomized, double-blind, placebo-controlled, parallel-group clinical trial of this probiotic strain in combination with inulin (a prebiotic) reported an improvement of cognitive function in the elderly. In the present study, a follow-up analysis was performed to elucidate the underlying mechanism, using a multi-omics approach that integrated a high-throughput assay of blood inflammatory markers and metagenomic analysis of the fecal bacterial composition. After probiotic and prebiotic administration, short-chain fatty acid producers such as Faecalibacterium and Bifidobacterium were increased in the gut. Moreover, in the subgroup with greater improvement in cognitive function scores, the levels of inflammatory markers were decreased. Subgroup analysis revealed that the improvement of cognitive function was associated with a reduction of inflammation and an increase of Faecalibacterium. These results suggest that GCL2505 and inulin can improve cognitive function by alleviating inflammation via an increase of short-chain fatty acid-producing bacteria, which appears to elevate levels of short-chain fatty acids, particularly acetate and butyrate, in the gut. The present results contribute to a deeper comprehension of the gut-brain axis and propose new avenues for potential therapeutic intervention in cognitive disorders.},
}

@article {pmid42006869,
year = {2026},
author = {Li, Y and Zhu, H and Zhan, Z and Li, G and Zhou, Q and Zheng, C and Huang, F},
title = {Clinical features and prognostic factors of Chlamydia psittaci pneumonia: a retrospective study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1804156},
pmid = {42006869},
issn = {2296-858X},
abstract = {BACKGROUND: Chlamydia psittaci pneumonia (CPP) is frequently misdiagnosed and can progress to severe illness. A deeper understanding of its clinical and imaging features is crucial for early detection and effective treatment.

METHODS: This retrospective study analyzed 74 patients diagnosed with CPP via metagenomic (mNGS) and targeted next-generation sequencing (tNGS) between January 2022 and September 2025. Patients were categorized into severe (n = 21) and non-severe (n = 53) groups based on established criteria for severe community-acquired pneumonia. Data on demographics, clinical manifestations, laboratory findings, and imaging characteristics were collected and compared.

RESULTS: The cohort had a median age of 60 years, with a male predominance (62.2%). A history of poultry/bird exposure was reported by 87.8% of participants. Common symptoms included fever (94.6%), cough (63.5%), and fatigue (29.7%), with no significant differences between groups. Hospitalization was significantly longer in the severe group (12.95 ± 6.08 days) than in the non-severe group (8.13 ± 3.30 days) (p < 0.001). Chest CT revealed consolidation and ground-glass opacities in all patients. Pleural effusion was significantly more common in the severe group (76.2% vs. 45.3%, p = 0.016), as was bilateral lung involvement (52.4% vs. 22.6%, p = 0.013). Multivariate analysis identified elevated D-dimer (OR = 2.737, p = 0.007) and reduced lymphocyte percentage (L%) (OR = 0.813, p = 0.026) as independent predictors of severe disease. ROC curve analysis showed an AUC of 0.765 for D-dimer and 0.739 for L% reduction. Following tetracycline or quinolone therapy, 94.6% of patients recovered, with an overall mortality rate of 5.4%.

CONCLUSION: Severe CPP is associated with prolonged hospitalization, bilateral pulmonary infiltrates, and pleural effusion. D-dimer and lymphocyte percentage are valuable prognostic indicators for disease severity. Early targeted antibiotic therapy is effective, but timely respiratory support is critical for severe cases.},
}

@article {pmid42006894,
year = {2026},
author = {Cui, T and Huang, M},
title = {Case Report: A case of refractory tuberculous peritonitis mimicking and complicating suspected encapsulating peritoneal sclerosis in a long-term peritoneal dialysis patient.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1777805},
pmid = {42006894},
issn = {2296-858X},
abstract = {BACKGROUND: Tuberculous peritonitis (TBP) is a rare but severe complication in peritoneal dialysis (PD) patients, often presenting with non-specific symptoms. Its diagnosis is particularly challenging in patients with pre-existing or co-existing peritoneal pathology, such as changes suggestive of encapsulating peritoneal sclerosis (EPS).

CASE PRESENTATION: A 59-year-old male on PD for 14 years with no prior history of peritonitis presented with recurrent abdominal pain, fever, and cloudy effluent, following a recent episode of Staphylococcus caprae peritonitis. Initial contrast-enhanced computed tomography (CT) revealed diffuse peritoneal thickening, omental "caking," and localized ascites, raising strong suspicion for EPS. However, the patient's condition relapsed despite broad-spectrum antibiotic therapy. Metagenomic next-generation sequencing (mNGS) of peritoneal fluid definitively identified Mycobacterium tuberculosis complex. The diagnosis was thus revised to TBP manifesting with secondary peritoneal inflammatory changes mimicking EPS. Management involved laparoscopic PD catheter removal, transition to hemodialysis, and initiation of a renal-adjusted anti-tuberculous regimen (levofloxacin and linezolid), leading to gradual clinical and biochemical improvement.

CONCLUSION: This case highlights that TBP can clinically and radiologically mimic EPS in long-term PD patients, leading to diagnostic delay. High clinical suspicion and the utilization of advanced molecular diagnostics like mNGS are crucial for accurate diagnosis. Catheter removal combined with appropriate anti-tuberculous therapy forms the cornerstone of management in such complex scenarios.},
}

@article {pmid42007374,
year = {2026},
author = {Jeong, UJ and Ali, M and Park, YJ and You, JS and Yoon, SS},
title = {A responder-informed gut microbial consortium enhances anti-PD-1 efficacy in a mouse cancer model.},
journal = {Microbiome research reports},
volume = {5},
number = {1},
pages = {2},
pmid = {42007374},
issn = {2771-5965},
abstract = {Aim: Immune checkpoint inhibitors (ICIs), particularly anti-programmed cell death protein 1 (PD-1) therapy, have improved cancer treatment outcomes, yet durable benefit is achieved in only a subset of patients. Growing evidence implicates the gut microbiome as a modulator of ICI responsiveness, but defined and experimentally validated microbial strategies remain limited. This study aimed to identify responder-associated gut microbes and to evaluate a defined bacterial consortium for enhancing PD-1 blockade efficacy. Methods: Publicly available shotgun metagenomic datasets from anti-PD-1-treated cancer patients were re-analyzed to compare gut microbiome profiles between responders and non-responders. Bacterial taxa reproducibly enriched in responders were selected based on consistency across analytical criteria and cultivability and assembled into a four-strain consortium (UJ-04). The immune-adjuvant potential of UJ-04, alone or combined with anti-PD-1 therapy, was evaluated in a B16-F10 melanoma mouse model, with tumor growth and immune responses assessed by flow cytometry. Results: Metagenomic re-analysis identified four commensal bacterial taxa consistently enriched in responder patients, forming the defined UJ-04 consortium. While UJ-04 alone showed minimal antitumor activity, combination treatment with anti-PD-1 significantly enhanced tumor growth inhibition compared with anti-PD-1 monotherapy. This effect was accompanied by increased intratumoral CD8[+] T cells and natural killer cells, with concordant immune trends in peripheral compartments. Conclusion: A responder-informed, defined microbial consortium functionally translates clinical microbiome associations into in vivo validation and enhances PD-1 blockade efficacy by modulating host antitumor immunity. These findings support defined bacterial consortia as microbiome-based immunomodulatory adjuncts for immunotherapy.},
}

@article {pmid42007699,
year = {2026},
author = {Carroll, AC and Hinz, A and Hicks, AMA and Khov, E and Van Bakel, T and Doukhanine, E and Fralick, M and Nott, C and Kassen, R and Thampi, N and Hug, LA and MacFadden, D and Wong, A},
title = {Targeted metatranscriptomic detection of viruses from floors for simultaneous evaluation of respiratory disease burden and viral variant identification.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0008626},
doi = {10.1128/msphere.00086-26},
pmid = {42007699},
issn = {2379-5042},
abstract = {UNLABELLED: Built environment surveillance is a proven approach for tracking disease burden of some viruses within hospitals and long-term care facilities. However, studies in clinical settings are lacking for simultaneously surveying targets in a built environment using targeted metatranscriptomics. We swabbed six discrete floor locations within an acute care center's emergency department (ED) in Ottawa, Canada, and sequenced cDNA using a 132 viral taxa panel, identifying viral burden across sampling locations and time. The determined SARS-CoV-2 variant profile across time was matched to provincial variant prevalence. The correlation between metatranscriptomic read abundances and reported cases of influenza A, SARS-CoV-2, and RSV was assessed. We quantified these via qPCR and assessed the correlation of Cq versus metatranscriptomic reads for these viruses. We sequenced a median of 1,302,882 reads per sample from 38 floor swabs collected during peak respiratory viral season (November 2022-February 2023). Diversity of viral communities varied significantly across locations in the ED. SARS-CoV-2 variant abundance shifts matched the changing infection landscape concurrently reported in Ontario. Relationships between targeted metatranscriptomic read ratios and clinical burden were not statistically significant, although we found modest correspondence between qPCR signal and read depth for RSV and SARS-CoV-2. This approach characterized the viral communities and the within-species diversity within an ED. Correlating sequencing-derived data with disease burden for three key respiratory viruses was inconsistent, with the exception of significant correlation between metatranscriptomic reads and Cq data for SARS-CoV-2. We were able to recover the distribution of clinically reported SARS-CoV-2 variants from the floor swab data.

IMPORTANCE: Environmental surveillance is useful for estimating the disease burden for certain viruses. qPCR is commonly used for surveillance of wastewater and built environments, including during the COVID-19 pandemic, but single, multiplexed reaction targets are limited. Targeted metagenomic or metatranscriptomic approaches can accurately quantify microbial populations of interest in an environment, reduce off-target sequencing, and evaluate a broader number of targets than qPCR assays. Here, we assessed the capacity of a targeted viral metatranscriptomic panel to correlate viral abundance in the hospital built environment with key pathogens of interest, including influenza A, RSV, and SARS-CoV-2. Our results suggest that targeted metatranscriptomics may identify viral communities in healthcare facilities, including strain-level detection capability. However, this approach must be validated for its effectiveness in viral surveillance that accurately reflects disease burden. This work contributes to a growing toolkit for pathogen surveillance, a critical endeavor to safeguard against outbreaks of known and emerging pathogens.},
}

@article {pmid42001152,
year = {2026},
author = {Leroy, M and Cyriaque, V and Rattei, T and Laurion, I and Comte, J},
title = {Microbiome and plasmidome shifts drive carbon, nitrogen, and greenhouse gas dynamics within transitioning permafrost.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00892-w},
pmid = {42001152},
issn = {2524-6372},
support = {2021-PR-284297//Fonds de recherche du Québec - Nature et technologie/ ; RGPIN-2020-06876//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; RGPIN-2020-06874//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; 2021-PR-284297//Fonds de recherche du Québec - Nature et technologies/ ; },
abstract = {Thermokarst lakes contribute to greenhouse gas emissions but often experience constraints on available nitrogen. However, the interactions between carbon and nitrogen cycles in these systems, especially along the terrestrial-aquatic continuum, remain poorly understood. The increased soil-water connectivity in those systems affects organic matter processing, nutrient availability, and microbial transport. In Nunavik (Quebec, Canada), we sampled along a transect from a palsa (permafrost remnant) through an emerging thermokarst lake to peatland soils and mature lake. Using hybrid metagenome co-assemblies with gene-, plasmid-, and genome-centric approaches, we explored key biogeochemical cycles and the role of plasmids in microbial adaptation along the transect. Gene annotation, metagenome-assembled genome (MAG) reconstruction, and network analysis revealed a shift from potential for anaerobic ammonium oxidation (anammox) in palsa and emerging lake to potential for nitrification in mature lake. Potential for methanogenesis transitions from hydrogenotrophic in the palsa to methylotrophic in lakes, likely driven by a bacterial consortium degrading aromatic, peat-derived compounds. Sediments may support methane production via both hydrogenotrophic and acetoclastic potential for methanogenesis, partially fueled by the action of polysaccharide lyases. Anaerobic methane oxidation (AOM) potential seems important in both peat and the mature lake; and can be coupled with nitrification and sulfate-reducing partners through extracellular electron transfer, with cytochromes playing a central role. Notably, plasmidome shifts preceded metagenomic changes, especially in genes related to carbon and methane cycling, suggesting a role for plasmids in microbial adaptation to permafrost thaw. These findings highlight the complex microbial and plasmid dynamics that drive carbon, nitrogen, and greenhouse gas cycles in permafrost ecosystems.},
}

@article {pmid42002296,
year = {2026},
author = {Yang, X and Zhang, L and Zhou, S and Wang, Z and Lv, Q and Zhao, M and Wang, C},
title = {Mechanisms Underlying Bioactive Compounds Decline in Medicinal Blaps rhynchopetera During Artificial Rearing.},
journal = {Environmental microbiology},
volume = {28},
number = {4},
pages = {e70304},
doi = {10.1111/1462-2920.70304},
pmid = {42002296},
issn = {1462-2920},
support = {2022YFC2602500//National Key Research and Development Program of China/ ; JiaoWaiSiYa[2020]619//Lancang-Mekong Cooperation Special Fund Projects/ ; SAJC202402//Chinese Academy of Sciences/ ; 2025YKZY002//Yunnan Characteristic Plant Extraction Laboratory/ ; 202449CE340005//Yunnan Provincial Science and Technology Department/ ; 202305AH340007//Yunnan Provincial Science and Technology Department/ ; },
mesh = {Animals ; *Coleoptera/microbiology/metabolism/growth & development ; *Gastrointestinal Microbiome ; Bacteria/metabolism/genetics/classification/isolation & purification ; Metabolome ; Biological Products/metabolism ; },
abstract = {Artificial rearing is essential for sustainable utilization of medicinal insects, yet its impact on bioactive compound production remains poorly understood. Here we provide preliminary evidence that rearing of the medicinal beetle Blaps rhynchopetera reshapes its gut microbiota and metabolome, beyond mere environmental effects. Metabolomic analysis revealed 727 significantly altered metabolites, with 436 compounds, many linked to analgesic and anti-inflammatory activities, markedly reduced under rearing. Network pharmacology analysis suggested that this metabolic remodelling alters the overall regulatory landscape, with reduced network complexity compared to wild counterparts. Metagenomic profiling uncovered a decline in Pseudomonadota, a phylum positively correlated with multiple bioactive metabolites. Preliminary reintroduction of four Pseudomonadota strains suggested their potential involvement in terpenoid backbone biosynthesis, a key pathway for natural product synthesis. These findings reveal an intrinsic trade-off between rearing-driven microbial homogenization and preservation of medicinal potency, highlighting the need for microbiome-informed rearing strategies.},
}

Animals
*Coleoptera/microbiology/metabolism/growth & development
*Gastrointestinal Microbiome
Bacteria/metabolism/genetics/classification/isolation & purification
Metabolome
Biological Products/metabolism

@article {pmid42002357,
year = {2026},
author = {Li, Z and Li, Z and Chu, L and Hu, S and Xue, C and Lin, H and Luo, Y and Zhang, Y and Zhang, J and Wang, Z},
title = {A novel Curcuma wenyujin-derived fructan modulates gut microbiota and metabolic pathways to ameliorate DSS-induced colitis.},
journal = {Carbohydrate polymers},
volume = {382},
number = {},
pages = {125292},
doi = {10.1016/j.carbpol.2026.125292},
pmid = {42002357},
issn = {1879-1344},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Curcuma/chemistry ; Dextran Sulfate/toxicity ; *Fructans/pharmacology/chemistry/isolation & purification/therapeutic use ; Mice, Inbred C57BL ; Male ; Metabolic Networks and Pathways/drug effects ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism ; *Colitis/chemically induced/drug therapy ; Disease Models, Animal ; },
abstract = {Ulcerative colitis (UC) involves epithelial barrier breakdown, dysregulated mucosal immunity, and dysbiosis of the gut microbiota (GM). Given the biotherapeutic potential of dietary fructans, this study aimed to isolate a neutral fructan (CWP-W-1) from Curcuma wenyujin and to characterize its chemical structure and anti-colitis effects. CWP-W-1 was purified by DEAE-Sepharose and gel-filtration chromatography. Its structure was established using HPGPC, monosaccharide profiling, FT-IR, GC-MS, and NMR. In a DSS-induced UC mouse model, CWP-W-1 treatment alleviated disease severity and weight loss, decreased the disease activity index and rectal bleeding, prevented colon shortening, and restored histological architecture, with increased goblet cells and mucin staining. Metagenomic sequencing showed that CWP-W-1 mitigated DSS-associated dysbiosis, recovering α-diversity and shifting β-diversity toward healthy controls, with decreases in Proteobacteria and enrichment of beneficial taxa. Metabolite analyses indicated that CWP-W-1 increased short-chain fatty acids (SCFAs) and remodeled the tryptophan metabolic pathway, shifting the pro-inflammatory kynurenine bias toward indole-derived aryl hydrocarbon receptor (AhR) ligands, consistent with epithelial barrier support and immune homeostasis. Collectively, these results demonstrated that CWP-W-1 was a structurally defined fructan with significant therapeutic potential for UC through coordinated modulation of barrier function, mucosal immunity, and the gut microbiota.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Curcuma/chemistry
Dextran Sulfate/toxicity
*Fructans/pharmacology/chemistry/isolation & purification/therapeutic use
Mice, Inbred C57BL
Male
Metabolic Networks and Pathways/drug effects
*Colitis, Ulcerative/drug therapy/chemically induced/metabolism
*Colitis/chemically induced/drug therapy
Disease Models, Animal

@article {pmid41803433,
year = {2026},
author = {Jalal, RS and Alshehrei, FM},
title = {Rhizospheric glycosyltransferase repertoires as a resource for enabling sustainable bioprocessing and green biocatalyst discovery.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41803433},
issn = {2045-2322},
support = {UJ-25-DR-1837//University of Jeddah/ ; },
abstract = {UNLABELLED: The rhizospheric microbiomes associated with wild plant species Moringa oleifera and Abutilon fruticosum, endemic to the arid northwestern Mecca region of Saudi Arabia, represent untapped reservoirs of genetic capability with significant implications for agriculture, biotechnology, medicine, and environmental sustainability. Leveraging high-throughput metagenomic sequencing and advanced bioinformatics, this study systematically cataloged carbohydrate-active enzymes (CAZymes), with a particular focus on glycosyltransferase (GT) families, within these root-associated microbial consortia. The analysis revealed pronounced compositional divergence between rhizospheric and bulk soil microbiomes, underscoring the influence of plant species and edaphic factors in shaping niche-specific microbial assemblages and functional repertoires. The two rhizospheric microbiomes were consistently enriched in all six CAZy classes, with lineage-specific CAZymes of GT families (GT2 and GT84 in M. oleifera and GT31, GT39, and GT66 in A. fruticosum). These lineage-specific CAZymes catalyze the synthesis of structurally diverse polysaccharides, including cellulose, chitin, β-glucans, mannans, and chondroitin, thereby positioning the rhizospheric microbiomes of Moringa oleifera and Abutilon fruticosum as promising reservoirs of biocatalysts for possible future applications in industrial applications, biomedical engineering, and environmentally sustainable technologies. The evolutionary history of these enzymes in hot, oligohydric soils suggests adaptation to thermal and water-limited conditions, which may render them particularly suitable for deployment in industrial and biotechnological bioreactors. These CAZymes are predicted to be positioned as pivotal assets for sustainable bioeconomy initiatives and possible therapeutic glycoengineering.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42974-2.},
}

@article {pmid41998767,
year = {2026},
author = {Rungrojn, A and Chaisiri, K and Thaipadungpanit, J and Batty, EM and Blacksell, SD},
title = {Bacterial communities in Thai ticks: revealing geographical and methodological gaps in surveillance-a 25-year scoping review.},
journal = {Tropical medicine and health},
volume = {54},
number = {1},
pages = {},
pmid = {41998767},
issn = {1348-8945},
support = {JCPET02//Royal Society of Tropical Medicine and Hygiene/ ; 220211/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Ticks serve as key vectors for a diverse range of bacterial pathogens that affect humans and animals worldwide. In Thailand, a comprehensive understanding of tick-associated bacterial diversity remains limited. This scoping review synthesises published data on tick-borne bacteria across Thailand from 2001 to 2025, focusing on bacterial diversity, host-vector associations, geographic distribution, and molecular detection methods. Literature searches in NCBI, Embase, and Web of Science identified 402 studies (272 after duplicate removal), of which 39 met the inclusion criteria. Ticks were collected from animals, humans, and the environment across four zoogeographical regions. Rhipicephalus, Haemaphysalis, Dermacentor, and Amblyomma were the most commonly studied genera. Eighteen bacterial genera, including both pathogens and endosymbionts, were identified, with Coxiella-like endosymbionts, Rickettsia, Anaplasma, and Ehrlichia being the predominant genera. Rhipicephalus ticks exhibited the highest bacterial diversity, while Rickettsia spp. were the most frequently detected pathogens. Conventional PCR remained the principal diagnostic method, with limited application of quantitative and metagenomic sequencing approaches. Geographic analysis revealed that most studies were concentrated in the Northern Peninsular and Central Peninsular regions, while the Continental section of the Indo-Chinese Mainland and Korat Plateau zones were under-represented, which may limit the accuracy of regional risk assessments, as surveillance gaps can underestimate both the diversity and prevalence of pathogenic organisms in these areas. This review emphasises the intricate nature of tick-host-pathogen interactions and highlights the importance of implementing standardised genomic surveillance nationwide within a One Health framework. The findings reveal key gaps in current surveillance efforts and advocate for incorporating genomic tick monitoring into Thailand's national One Health strategies to improve zoonotic disease preparedness.},
}

@article {pmid41998806,
year = {2026},
author = {Tang, R and Wang, J and Zhang, Z and Li, Y and Lan, Y and Fan, Z},
title = {Temporal Shifts in Gut Microbiota and Host Immunity During Chronic Diarrhea in an Infant Rhesus Macaque: A Longitudinal Case Study Based on Multi-Omics.},
journal = {Journal of medical primatology},
volume = {55},
number = {3},
pages = {e70074},
doi = {10.1111/jmp.70074},
pmid = {41998806},
issn = {1600-0684},
support = {2023NSFSC1935//Sichuan Province Science and Technology Support Program/ ; 32370450//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Macaca mulatta/immunology ; *Gastrointestinal Microbiome ; *Diarrhea/veterinary/microbiology/immunology ; *Monkey Diseases/immunology/microbiology ; Longitudinal Studies ; Transcriptome ; Male ; Anti-Bacterial Agents/therapeutic use ; Female ; Chronic Disease ; Multiomics ; },
abstract = {Diarrhea remains a major health challenge in captive rhesus macaques (RMs; Macaca mulatta), particularly among infants, yet the dynamic interplay between gut microbiota and host immune responses during disease progression remains poorly understood. Here, we conducted a longitudinal multi-omics study on a captive infant RM, analyzing 25 fecal metagenomes and 18 blood transcriptomes across diarrheal, antibiotic treatment, and recovery phases. Our results demonstrated that disease state was the primary driver of gut microbiota variation. The diarrheal phase was characterized by a significant reduction in microbial α-diversity and marked expansion of multidrug-resistant Enterobacteriaceae, including Escherichia, Shigella, and Salmonella, accompanied by severe depletion of probiotic genera such as Lactobacillus and Bifidobacterium. Correspondingly, antibiotic resistance genes targeting fluoroquinolones and cephalosporins accumulated substantially during diarrhea, explaining the limited efficacy of empirical antibiotic therapy. Blood transcriptome analysis revealed heightened innate immune activation, evidenced by upregulation of interferon-related genes, alongside suppression of adaptive immune pathways including interleukin-5 signaling. Integrated correlation analysis uncovered synchronized host-microbiome interactions, with inflammatory gene expression positively associated with opportunistic pathogens and negatively correlated with beneficial commensals. Clinical recovery coincided with re-establishment of probiotic populations, reduction in resistance gene burden, and normalization of immune function. These findings demonstrate that infant macaque diarrhea profoundly disrupts both gut microbial ecology and systemic immunity, supporting management strategies that prioritize targeted antimicrobial intervention and microbiome restoration over prolonged empirical antibiotic use in captive primates.},
}

Animals
*Macaca mulatta/immunology
*Gastrointestinal Microbiome
*Diarrhea/veterinary/microbiology/immunology
*Monkey Diseases/immunology/microbiology
Longitudinal Studies
Transcriptome
Male
Anti-Bacterial Agents/therapeutic use
Female
Chronic Disease
Multiomics

@article {pmid41999333,
year = {2026},
author = {Tang, X and Lu, SY and Huang, JH and Cheng, ZW and Ke, YC and Ai, CF and Liu, C and Liao, HP and Zhou, SG},
title = {Phage-Encoded Metabolic Bypass Drives Herbicide Resistance in Soil Microbiomes.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c02641},
pmid = {41999333},
issn = {1520-5851},
abstract = {Phages reshape microbial community functions through auxiliary metabolic genes (AMGs) and are increasingly recognized as active drivers of microbial adaptation. Although herbicides such as glufosinate significantly inhibit soil microbes, these communities exhibit striking resilience; however, the role of phages in facilitating this rapid adaptation remains poorly understood. Here, we dissect the temporal dynamics (days 0, 15, 30, and 60) of phage-host interactions under two contrasting stressors: the microbially toxic glufosinate and the nontoxic dicamba. We find that glufosinate transiently suppresses microbial diversity, followed by a robust recovery on day 60. This successional shift coincides with an elevated proportion of putative temperate phages (74.1%) and a strategic attenuation of bacterial antiviral systems, signaling a transition from antagonistic predation to mutualistic lysogeny. Metagenomic analyses across 23 regions in China corroborate that this temperate phage recruitment is a generalized response to field-relevant glufosinate exposure. Selection for temperate phage infections arises from asymmetric fitness costs (burdening virulent phage-susceptible hosts) and prophage integration of AMGs like gdhA. Specifically, coevolution assays reveal that glufosinate selectively penalizes virulent phage-sensitive hosts, favoring the recruitment of temperate phage infections. Furthermore, in vitro validation confirms that phage-encoded gdhA provides a compensatory metabolic bypass for ammonia detoxification, directly mitigating herbicide toxicity. Collectively, these findings delineate a phage-mediated mechanism for herbicide resistance evolution in soil microbiomes, emphasizing the need for a microbiome-informed agrochemical design to manage long-term ecological resilience.},
}

@article {pmid42000179,
year = {2026},
author = {Iakovides, IC and Vasileiadis, S and Christou, A and Karaolia, P and Mina, T and Rocha, J and Duan, Y and Beretsou, VG and Gallois, N and Changey, F and Michael, C and Coelho, LP and Manaia, CM and Merlin, C and Fatta-Kassinos, D},
title = {Storage and soil depth, in addition to wastewater treatment, govern microbiota, and mobile genetic element and antibiotic resistance markers during reclaimed water irrigation.},
journal = {Water research},
volume = {300},
number = {},
pages = {125889},
doi = {10.1016/j.watres.2026.125889},
pmid = {42000179},
issn = {1879-2448},
abstract = {Reclaimed water (RW) offers a sustainable solution for agricultural irrigation and freshwater conservation, but its microbial and chemical composition, shaped by treatment and storage processes, requires careful consideration for environmental and public health impacts. This study compared two RW types (conventional activated sludge with sand filtration and chlorination - CAS + SFC-RW - and membrane bioreactor - MBR-RW) with a tube well (TW) water control. The goal was to assess how storage influences the microbial composition, key antibiotic resistance and mobilome genes, and RW the impact on irrigated lysimeter soils during lettuce cultivation. Total bacteria were profiled using 16S rRNA gene sequencing and ddPCR, while antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were quantified by ddPCR and analysed by metagenomics. Initial RW samples had 1-1.5 orders of magnitude more 16S rRNA copies compared with the control, with significantly different bacterial and ARG/MGE profiles. Actinomycetota dominated CAS + SFC-RW, Bacteroidota the MBR-RW, and Pseudomonadota the TW water. Class 1 integrons and Tn916/Tn1545 were more abundant in CAS + SFC-RW compared with the MBR-RW. Storage reduced these differences toward convergence with the TW water profile, with putative pathogenic taxa, however, being more recalcitrant to change. RW irrigation altered soil bacterial composition, with MBR-RW having a greater impact as declared by the enhanced presence of Bacteroidota in the receiving soils. The RW influence was inversely related with vertical distance of the irrigation point, while the lettuce crop presence showed minimal/no impact. These results highlight the need for careful management of RW treatment and storage to ensure safe, resilient agricultural practices.},
}

@article {pmid42000463,
year = {2026},
author = {Devika, NT and Jayaraman, K and Nadimuthu, S and Nathamuni, SP and Sreya, PS and Jangam, AK and Katneni, VK},
title = {Gut microbial restructuring in white spot syndrome virus-infected Penaeus vannamei: Insights from long-read metagenomics.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {59},
number = {},
pages = {101834},
doi = {10.1016/j.cbd.2026.101834},
pmid = {42000463},
issn = {1878-0407},
abstract = {Microbial community restructuring following White Spot Syndrome Virus (WSSV) infection is a critical determinant in modulating the disease progression in Penaeus vannamei. In this study, full-length 16S rRNA sequencing (V1-V9) was employed to delineate the microbial shifts in healthy and WSSV-infected shrimp. The analysis revealed a pronounced reduction in Firmicutes in the WSSV-infected shrimp, a dysbiosis signature reported in WSSV-associated amplicon studies. With the advantage of full-length sequencing, this study achieved species-level resolution, identifying Vibrio alginolyticus (a known pathogen) alongside putative beneficial taxa such as Ruegeria conchae, R. arenilitoris, Demequina litorisediminis, and D.globuliformis, which were not captured in earlier amplicon-based studies. Diversity analysis demonstrated that, rather than loss of species, substantial restructuring in the form of abundance was observed between healthy and WSSV-infected shrimp, while the overall evenness of the community remained stable. Concurrently, WSSV-infection has triggered an increased abundance of core opportunistic pathogens, namely, Photobacterium damselae and V. alginolyticus, which clustered distinctly from putative beneficial taxa such as Ruegeria and Demequina species, reflecting a clear microbial imbalance. Collectively, these findings demonstrated that mortality in WSSV-infected shrimp is associated with dysbiosis characterized by a depletion of beneficial taxa and concomitant abundance of opportunistic pathogens. These insights provide a basis for developing targeted probiotic or therapeutic strategies to mitigate pathogen overgrowth.},
}

@article {pmid42000510,
year = {2026},
author = {Yu, Z and Song, S and Deng, W and Zhou, X and Wang, Y and Zhou, S},
title = {Metagenomics insights into humification improvement and antimicrobial resistance reduction during hyperthermophilic coupled with electric field composting process.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142094},
doi = {10.1016/j.jhazmat.2026.142094},
pmid = {42000510},
issn = {1873-3336},
abstract = {Compared to conventional thermophilic composting, hyperthermophilic composting elevates fermentation temperature and electric field composting facilitates oxygen transfer, with both strategies promoting humification and reshaping the microbial community structure. This study coupled hyperthermophilic composting with electric field composting (HEC) to further enhance livestock manure humification while suppressing antimicrobial resistance. A composting strategy consisting of 12-day hyperthermophilic pretreatment and 28-day electric field composting was implemented. Integrating analyses of the humification process, metagenomics, metabolic pathways, and key microbiota linked to humification and antimicrobial resistance, this study indicated that HEC strategy triggered an initial hyperthermophilic surge and sustained thermophilic, with potential enhancement of aerobic metabolic activity under the applied electric field, thereby driving microbial succession from Proteobacteria to Firmicutes and Actinobacteria. The favorable conditions and microbiota shift enhanced metabolic activity, accelerated transformation of organic substrates, and increased aromatic precursor accumulation, resulting in a 2.5-fold increase in humic acid carbon compared with conventional thermophilic composting. Meanwhile, HEC reduced antibiotic resistance genes (ARGs) abundance and diversity by suppressing resistance-associated microbiota, particularly Proteobacteria and Bacteroidetes, which predominantly harbor antibiotic efflux genes (e.g., adeF). The attenuation of ARGs abundance and diversity reached 66.1% and 74.2%, respectively, compared with 43.3% and 48.8% in conventional thermophilic composting after 40d fermentation, and meanwhile, dominant humus-forming microbiota were relatively less associated with ARGs. This study elucidated the mechanisms underlying enhanced humification and ARG mitigation during the HEC process, thereby offering an effective strategy for resource recovery from livestock manure.},
}

@article {pmid42000517,
year = {2026},
author = {Han, W and Liu, Y and Liang, X and Liu, J and Jiang, Q and Zhang, C and Zhang, Y},
title = {A Trojan Horse in the soil: Tetracycline hijacks plant organellar ribosomes to stunt growth and unbalance the rhizosphere microecology.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {141792},
doi = {10.1016/j.jhazmat.2026.141792},
pmid = {42000517},
issn = {1873-3336},
abstract = {Tetracycline, a widely used antibiotic, accumulates in agricultural soils and poses significant risks to crop development and soil health. This study elucidates novel mechanisms of TC phytotoxicity by demonstrating its specific binding to the structurally conserved A-site of ribosomal small subunit RNA (SSU rRNA) in plant mitochondria and chloroplasts-organelles of prokaryotic origin. Through integrated physiological, transcriptomic, and structural analyses, we show that TC disrupts ribosomal function, induces oxidative stress, and impairs photosynthesis and antioxidant defense in soybean, and unbalances the SSU/LSU (ribosomal large subunit RNA) rRNA ratio. We further developed a comprehensive Ecological Risk Index (ERI) framework that integrates soil physicochemical properties, enzyme activities, microbial metabolism, and community structure to evaluate soil microecological shifts under TC stress. Metagenomic analysis uncovered functional adaptations in microbial nitrogen/phosphorus cycling and emphasized the role of multidrug resistance genes-rather than tetracycline-specific resistance-via mobile genetic elements, including those from ssDNA viruses. Our findings provide unprecedented insights into the evolutionary conservation of ribosomal targets of antibiotics and establish a holistic framework for assessing the ecological impact of antibiotic residues in agroecosystems.},
}

@article {pmid42000556,
year = {2026},
author = {Snipen, L and Stoeck, T and Angell, IL and Philip, M and Pettersen, R and Majaneva, S and Ray, JL and Stokkan, M and Keeley, N and Rudi, K},
title = {Predicting sediment ecological state from metagenomes shows equal performance for taxonomic and functional features.},
journal = {Marine environmental research},
volume = {218},
number = {},
pages = {108055},
doi = {10.1016/j.marenvres.2026.108055},
pmid = {42000556},
issn = {1879-0291},
abstract = {The use of environmental microbial DNA to monitor the ecological state in seafloor sediments has many advantages and efforts are being made to find reliable biomarkers from DNA-based taxonomic profiles. However, the taxonomic composition of microbial communities can vary over time and space, while their functional characteristics typically remain consistent. Furthermore, functionality may better capture the breadth of biological complexity. Therefore, we here tested whether functional attributes of microbial communities serve as more reliable indicators of environmental quality than their taxonomic composition. To test this, we analyzed a set of Metagenome-Assembled-Genomes (MAGs) from 41 different coastal locations in Norway and Iceland, characterized by environmental impact gradients resulting from salmon aquaculture. Functional and taxonomic features extracted from these MAGs were then used to predict the ecological state of the corresponding sample sites using several supervised machine learning models and stratified feature selection. Our findings indicate that both taxonomic and functional features demonstrated comparable effectiveness in predicting environmental quality. This outcome has direct relevance for eDNA-based regulatory compliance monitoring. However, the functional insights derived from the most significant functional features identified by machine learning models remain essential for deepening our understanding of the ecological processes underpinning practical biomonitoring tools.},
}

@article {pmid42000565,
year = {2026},
author = {Wan, X and Zhan, J and Chen, Z and Wu, B},
title = {Ventilation-driven microbial and antimicrobial resistance divergence in intensive poultry houses and the associated public health risks.},
journal = {Research in veterinary science},
volume = {206},
number = {},
pages = {106196},
doi = {10.1016/j.rvsc.2026.106196},
pmid = {42000565},
issn = {1532-2661},
abstract = {Ventilation strategies in intensive poultry production systems play a critical role in shaping airborne microbial communities and the dissemination of antibiotic resistance, with potential implications for environmental and public health. In this study, bioaerosols from closed (mechanically ventilated) and open (naturally ventilated) chicken houses were systematically characterized using high-throughput metagenomic sequencing to compare microbial community composition and antibiotic resistance gene (ARG) profiles under contrasting ventilation regimes. Open chicken houses exhibited significantly higher microbial diversity (P < 0.05), reflecting increased environmental microbial inputs, while the relative abundance of the potentially antibiotic-resistant pathogen Staphylococcus aureus was also elevated. In contrast, closed chicken houses facilitated the accumulation of a core microbial community, including potential pathogens such as Helicobacter pullorum and Clostridium perfringens. Closed chicken houses showed a greater enrichment of macrolide resistance genes. In addition, the overall abundance of ARGs, expressed as ARG copies per 16S rRNA gene, was significantly higher in closed houses than in open houses (P < 0.05). Although total ARG abundance was lower in open chicken houses, the proportion of contigs harboring both ARGs and mobile genetic elements (MGEs) was significantly higher (P < 0.05), indicating increased potential for horizontal gene transfer. These findings reveal differences in microbial diversity and associated health risks between different poultry production systems and underscore the importance of optimizing ventilation strategies to control pathogen transmission and the spread of antibiotic resistance.},
}

@article {pmid42000726,
year = {2026},
author = {Zhou, X and Zhou, D and Pu, Y and Kim, H and Sun, Z and Qi, W and Jin, J and Zhang, W and Xia, M and Wang, C and Hong, S and Nguyen, LH and Jiao, N and Zheng, Y and Liu, T},
title = {Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71981-0},
pmid = {42000726},
issn = {2041-1723},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly linked to gut microbial dysbiosis, but most studies have focused on bacteria, neglecting viruses and fungi, and their interactions. Here we show that MASLD is characterized by coordinated disruption of bacterial, viral and fungal communities and by a disturbed phage-bacteria-metabolite axis associated with disease-related bile acid changes. Integrating shotgun metagenomics, fungal ITS2 sequencing, fecal metabolomics and clinical profiling in 210 patients with MASLD and 210 age- and gender-matched healthy controls, we find reduced microbial diversity and extensive remodeling of cross-kingdom ecological networks in MASLD. Ruminococcus gnavus emerges as an enriched central hub, while Faecalibacterium prausnitzii and its associated bacteriophages are depleted. Phage-host analyses further reveal reduced lytic activity against R. gnavus and loss of sulfur amino acid metabolism-related auxiliary metabolic genes, which may impair F. prausnitzii fitness. Diminished phage control may facilitate R. gnavus expansion, alongside increased fecal isodeoxycholic acid, a secondary bile acid implicated in hepatic steatosis. A diagnostic classifier integrating bacterial and viral features with clinical parameters distinguish MASLD from controls in our cohort and maintain predictive performance in two external datasets. Together, these findings uncover a disrupted phage-bacteria-metabolite axis in MASLD and provide a multi-kingdom framework for non-invasive biomarker discovery and microbiome-targeted therapies.},
}

@article {pmid42001033,
year = {2026},
author = {Galgano, S},
title = {Genomica: linear mixed model based, multiple hypothesis testing corrected, ortholog functional enrichment analysis.},
journal = {BMC bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12859-026-06450-y},
pmid = {42001033},
issn = {1471-2105},
abstract = {BACKGROUND: The analysis of ortholog genes derived from metagenomic experiments provides an invaluable opportunity to assess the functional role of microbial communities towards, for example, antimicrobial resistance or biochemical pathways under different experimental conditions. Nevertheless, the integration of the statistical analysis of these complex data sets and the enrichment of the derived significantly differential abundant orthologs is not currently facilitated by existing software. Genomica is an R package that, with minimal input from the user, allows to perform a double-step analysis of functional orthologs from the KEGG Orthology. The pipeline is carried out via combining false discovery rate corrected linear mixed models to functional enrichment analysis through integrating established R pipelines (i.e., lme4 and MicrobiomeProfiler).

RESULTS: Only two data frames are needed as input to run Genomica, which contain data and metadata, respectively. The fast pipeline integrated within the function Genomica allows to analyze 4000 orthologs in circa 3 min. The outputs are collected in a single directory, containing publication-ready results from the linear mixed model and from the enrichment analysis. The Benjamini & Hochberg correction is applied to the results from the linear mixed model, therefore only P adjusted significant comparisons are further included in the enrichment analysis.

CONCLUSIONS: Genomica is a simple-to-use R package to analyze complex datasets, integrating a well-founded statistical analysis, accounting for the calculation of the type I error under repeated testing, with the enrichment analysis of the significantly differential abundant orthologs across experimental conditions, all with minimal input from the user.},
}

@article {pmid41803939,
year = {2026},
author = {Fauszt, P and Mikolas, M and David, P and Szoke, Z and Gashi, N and Szilagyi-Tolnai, E and Szilágyi, E and Szarvas, MM and Fazekas, ME and Kun-Nemes, A and Stagel, A and Gal, F and Czegledi, L and Biro, S and Stundl, L and Remenyik, J and Paholcsek, M},
title = {Longitudinal source-sink dynamics of fecal litter and farm indoor environmental resistomes in broiler chicken and Cherry Valley ducks.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41803939},
issn = {2524-4671},
abstract = {BACKGROUND: Antimicrobial resistance is a major One Health threat, and intensive poultry systems function as amplifiers. Although broilers and ducks are reared under similarly controlled conditions, their microecologies diverge. Integrated, longitudinal source-sink analyses quantifying overlap and directional flux between host-associated and environmental resistomes remain scarce. A two-year (2022–2024), longitudinal, commercial-scale comparison was undertaken across 15 stocking cycles under harmonized husbandry in Ross 308 broiler and Cherry Valley duck. Parallel shotgun metagenomics profiled fecal litter and farm indoor environments across standardized production, with daily monitoring in one complete cycle per system; in total, 96 pooled samples were sequenced to quantify cross-compartment overlaps.

RESULTS: Antibiotic resistance gene (ARG) reservoir dominance proved to be system-specific, duck systems were environment-centric, whereas broiler systems were fecal litter-centric. Although overall ARG diversity was similar between systems (broiler 2,542; duck 2,494 types), ducks exhibited greater compartmental divergence, with ~ 2.6-fold more environment-unique ARGs than paired fecal litter and 1.15-fold higher environmental richness than broilers. Compartment coupling also differed: broilers showed tighter host-environment overlap, while ducks were more partitioned. A shared environmental ARG pool (57.5%) indicated substantial cross-system exchange potential. Temporally, shared ARGs accumulated across the grow-out and peaked pre-depopulation. The distribution of significant ARG carrier species revealed asymmetric host-environment coupling: overlap across compartments was 66.67% in broilers versus 45.45% in ducks, notably. The impact of antimicrobial use was nuanced: short, targeted courses were associated with lower aaAMR burden overall Collectively, the recurrent detection of clinically consequential carriers (P. aeruginosa, E. coli, A. baumannii, S. aureus, K. pneumoniae, S. maltophilia, toxigenic Clostridium spp.) underscored One Health risks of zoonotic spillover and food-chain contamination.

CONCLUSION: Reservoir behavior in intensive poultry systems should be treated as system-specific, and matrix-targeted, with biofilm and humidity management prioritized in duck operations, and litter/manure control emphasized in broilers. The finisher-depopulation window emerges as a critical intervention point, warranting intensified mitigation clean-out. Finally, mitigation should extend beyond individual farms to transport crates, vehicles, shared equipment, and supply chains.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00544-x.},
}

@article {pmid41827064,
year = {2026},
author = {Yu, S and Yue, X and Yang, Q and Xu, P and Yuan, H and Tang, W and Luan, Y and Wang, Q},
title = {Omics integration reveals how the gut microbiota of Warmblood horses responds to equestrian show jumping-a short-duration, high-intensity technical exercise stress.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41827064},
issn = {2524-4671},
abstract = {BACKGROUND: Intestinal microbial homeostasis and metabolic balance play a crucial role in maintaining normal physiological function in horses. Exogenous stress involving abrupt turns and jumps during show jumping significantly impacts intestinal microbial homeostasis and metabolic balance in these animals.

RESULTS: By comparing rectal (faecal) samples from 10 Warmblood horses collected before and immediately after a show jumping competition on the same day, we observed substantial alterations in intestinal microbial homeostasis and metabolic balance post-exercise. Microbial evenness significantly increased following the competition, accompanied by enrichment of specific taxa such as Bacteroides, Ruminococcus, Prevotella, and Fibrobacter. Metabolite analysis revealed a marked decrease in antioxidant-related compounds, including orsellinic acid, 2,3-dimethyl-2-cyclohexen-1-one, and (1 R,6 R)-1,4,5,5a,6,9-hexahydrophenazine-1,6-dicarboxylate. Conversely, glucosan and thiamine pyrophosphate levels increased. Post-competition, membrane lipid metabolism pathways were significantly downregulated, while antioxidant responses and energy metabolism pathways were upregulated. Spearman correlation analysis indicated positive associations between Fibrobacter, Ruminococcus, and Prevotella with energy metabolism-related metabolites, whereas Lysinibacillus correlated positively with metabolites involved in antioxidant activity and intestinal mucosal protection.

CONCLUSION: Collectively, our findings demonstrate that show jumping induces shifts in intestinal microbial homeostasis and metabolic balance in Warmblood horses. These adaptations appear conducive to preserving epithelial integrity and enhancing energy provision to meet the demands of high-intensity exercise. This study provides novel insights into the impact of acute high-intensity exercise on equine gut microbial dynamics and metabolism, offering a theoretical basis for probiotic-based interventions to support intestinal health in sport horses.},
}

@article {pmid41992382,
year = {2026},
author = {Cuteri, V and Preziuso, S and Li, Y and Laus, F},
title = {Fecal virome at the human-animal interface: a one health perspective on an uncharted frontier.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00569-2},
pmid = {41992382},
issn = {2524-4671},
}

@article {pmid41992389,
year = {2026},
author = {Gu, S and Jiang, C and Zhang, P and Luo, S and Gong, Y and Feng, W and Xiong, J and Zhang, J and Chen, K and Ning, K and Miao, W},
title = {Unraveling the colonization process of microeukaryotic communities on artificial micro-ecological islands.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00897-5},
pmid = {41992389},
issn = {2524-6372},
support = {2022FY100400//the Science & Technology Fundamental Resources Investigation Program/ ; 2022xjkk0204//the Third Xinjiang Scientific Expedition Program/ ; U22A20454//the National Natural Science Foundation of China/ ; SNJNP2022008//the Background Resources Survey in Shennongjia National Park/ ; SNJGKL2022008//the Open Project Fund of Hubei Provincial Key Laboratory for Conservation Biology of Shennongjia Snub-nosed Monkeys/ ; },
abstract = {BACKGROUND: Micro-ecological islands provide unique habitats for microbes and play a crucial role in the functioning of aquatic ecosystems. Microbes settle on these micro-ecological islands, forming distinct microbial communities. Previous studies have provided some understanding of the colonization processes and regulatory mechanisms of protozoa in microbial communities. However, these islands are also subject to colonization by a variety of microbes beyond protozoa, and comprehensive cross-kingdom studies and their potential mechanisms remain largely unexplored.

RESULTS: Using polyurethane foam units (PFU) to simulate micro-ecological islands, we studied the colonization dynamics of microbes in two distinct aquatic ecosystems, the Yangtze River and East Lake. Over 10-day colonization survey was conducted, we applied eDNA-PFU technology combined with metagenomic sequencing to comprehensively identify species present in the microbial communities, including bacteria, fungi, flagellates, protozoa, and metazoa. We found that microeukaryotes, rather than prokaryotes, were the primary colonizers in these two aquatic ecosystems. Our study reveals a colonization process of microeukaryotes in PFUs, profoundly influenced by their motility modes. Additionally, we propose a hypothetical food web framework within micro-ecological islands that maintains community stability, representing the most fundamental biological interactions.

CONCLUSIONS: Overall, this study enriches our understanding of micro-ecological islands and provides deeper insights into the colonization processes and regulatory mechanisms of microbial communities. It highlights the practical significance of micro-ecological islands in biological resource management, environmental protection, and biodiversity conservation.},
}

@article {pmid41993122,
year = {2026},
author = {Saez-Torillo, SN and Danielsson, R and Nguyen, TQ and Lima, J and Cleveland, MA and Roehe, R and Martínez-Álvaro, M},
title = {Predicting beef diet nutritional composition and intake from rumen metagenomic profiles.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {297-309},
pmid = {41993122},
issn = {2405-6383},
abstract = {Knowledge of diet composition and intake levels in beef cattle is valuable for post hoc feed traceability and for more accurate modelling of the diet impact on methane emissions and performance traits. However, a direct measure of this information can be costly and labour-intensive and is not always feasible. In this study, rumen metagenomic data combined with machine learning algorithms were used to predict diet type, nutritional composition, and intake levels. An external validation to assess the generalizability of the models was also performed. Rumen samples were collected from 142 animals belonging to two breeds, Luing (n = 70) and Charolais crossbred (n = 72), with 425.6 ± 43.5 d old and 461.9 ± 70.2 kg body weight. The animals participated in a 56-d feeding trial and were assigned to diets differing in forage-to-concentrate ratio, with 72 animals receiving a concentrate-based diet and 70 receiving a forage-based diet. Liquid ruminal contents were collected immediately postmortem and subsequently subjected to metagenomic sequencing. Based on these sequences, the relative abundance of microbial genes (MGs), microbial genera (MTs), and phyla were determined. The log-ratio between the abundances of Verrucomicrobia and Chlorobi discriminated diet type with an average classification accuracy of 0.86 ± 0.05, while using the log-ratio transformed abundances of 4769 MTs and MGs as predictors reached 0.90 ± 0.05. All this microbiome information was used in a random forest model to predict continuous values for nutritional diet components starch, crude protein, neutral and acid detergent fibre, and metabolizable and gross energy with external validation prediction accuracy values between 0.77 and 0.83. Microbiome features important for prediction of diet components such as fibre and starch included Mitsuokella, Selenomonas, and MGs involved in flagellar assembly and aminoacyl-tRNA biosynthesis. Microbiome data were more informative for predicting the feed composition than the amount of feed consumed, which reached a prediction accuracy of 0.27 ± 0.12 for dry matter intake (DMI). However, microbiome data can still be used as a screening tool to classify DMI into low, medium, or high with a classification accuracy of 0.74. Incorporating dietary information into linear phenotypic and genetic models to predict methane production (MP) and DMI reduced root mean square error (RMSE) by 26.9% and 9.6%, respectively, in the phenotypic model. In the genetic model, only MP showed a reduction in RMSE, with a 31% improvement. These findings highlight rumen microbiome data as a valuable tool for the post hoc prediction of feed composition in beef cattle.},
}

@article {pmid41993390,
year = {2026},
author = {Hutchinson, NT and Ye, N and Jennings, M and Fang, C and Qi, N and Li, J},
title = {Engineered Lactate Catabolizing Probiotics Reveal Timescale Dependent Microbiome-Host Metabolic Coupling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.07.716956},
pmid = {41993390},
issn = {2692-8205},
abstract = {The exchange of lactate, a metabolic substrate and regulator, between the gut lumen and systemic circulation for use in host and microbial processes is well documented, but tools capable of uncovering whether this process influences host metabolic status across acute and chronic contexts are lacking. In our prior work, we engineered probiotic Bacillus subtilis PY79 to produce lactate oxidase (LOX) intracellularly, allowing it to rapidly convert intestinal lactate to pyruvate. Following oral administration, LOX reduced systemic lactate concentrations at rest and under challenge conditions, providing a platform for investigating lactate's influence on host metabolism and microbiota. In the present work, we demonstrate that acute LOX administration effectively rewired microbiota function and host energy balance, as revealed by 16S sequencing and indirect calorimetry. In silico microbial community modeling via MICOM and metagenomic inference via PICRUSt2 suggested that acute shunting of lactate to pyruvate induced microbiota remodeling towards anabolic processes, reflected by increased flux of pyruvate, acetate, and formate, alongside moderate to large increases (Cohen's d = 0.60-1.00) in pathways for fructan degradation, B-vitamin biosynthesis, and lipid synthesis. These anabolic shifts temporally aligned with transient increases in host energy expenditure (β = 1.08, p<0.05) via glucose oxidation (β = 0.01, p<0.05), hinting at functional coupling between microbial biosynthesis and host energy balance via lactate exchange. Of note, acute LOX administration also improved thermoregulation and survival following LPS-induced sepsis, demonstrating functional relevance of these metabolic effects during acute inflammatory challenge. To assess chronic effects, we administered LOX for 6 weeks during diet-induced obesity. LOX treatment persistently reduced blood lactate. However, this chronic lactate reduction did not curtail the progression of diet-induced obesity or induce sustained modulation of host energy expenditure. This disconnect between acute and chronic findings suggests that gut-centric lactate conversion affects energy balance through microbiome and/or host-dependent mechanisms, but cannot override homeostatic forces in the long term to produce clinical benefit during chronic disease. Our results validate LOX probiotics as a tool for acute metabolic augmentation, and highlight a clear homeostatic limit to gut-centric therapies. This platform may enable targeted design of probiotic interventions matched to therapeutic timescale and inform synbiotic formulations that overcome homeostatic compensation.},
}

@article {pmid41993414,
year = {2026},
author = {Liu, S and Mehta, P},
title = {Ecology of metagenomes: incorporating genotype-to-phenotype maps into ecological models.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.07.717079},
pmid = {41993414},
issn = {2692-8205},
abstract = {UNLABELLED: A major theoretical problem in community ecology is to understand how genes, organisms, and environments combine to shape the structure and diversity of ecological communities. However, most classic ecological models work entirely with phenotypic parameters, neglecting the central role played by genes. This limitation is particularly acute in microbial ecology, where the widespread use of sequencing technologies allows researchers to directly measure the genomic and metagenomic properties of communities. Here, we bridge this gap by incorporating genotype-to-phenotype maps into classical ecological models, including the generalized Lotka-Volterra model (GLV) and consumer resource models (CRMs). We focus on the case where genotype-to-phenotype maps are linear, which provides a tractable yet powerful framework for analyzing complex traits. Even in this simple setting, the resulting ecological dynamics give rise to novel gene-level ecological dynamics that can be recast entirely in terms of genes, allowing us to develop an ecology of metagenomes. We find that ecological interactions between genes lead to pervasive "metagenomic hitchhiking" - low-fitness genes can survive in the ecosystem because they are integrated into genomes of high-fitness species. We also show that phylogenetic relationships between species mold the ability of closely related strains to stably coexist in complex communities. This highlights how lineage structure and competitive interactions jointly shape community composition. Our framework provides a principled foundation for interpreting metagenomic data through the lens of ecological theory.

AUTHOR SUMMARY: Recent advances in sequencing technologies have transformed our ability to characterize microbial communities at the genomic level. However, most classic ecological models work entirely with phenotypic parameters, neglecting the central role played by genes. Here, we address this gap by extending classical ecological models to explicitly include genotype-to-phenotype maps. We focus on complex traits where the genotype-to-phenotype map is approximately linear. We show that the resulting ecological dynamics that can be recast entirely in terms of genes, allowing us to develop an ecology of metagenomes. Our framework provides a novel perspective for interpreting metagenomic data through the lens of ecological theory.},
}

@article {pmid41993507,
year = {2026},
author = {Coleman, I and Ma, J and Qian, G and Jiang, Y and Brown Kav, A and Korem, T},
title = {End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.06.712906},
pmid = {41993507},
issn = {2692-8205},
abstract = {The generation of Metagenome Assembled Genomes (MAGs) has become a standard and basic step in the analysis of metagenomic data. This multi-step process, which includes assembly, binning, refinement, and quality control, has many alternative approaches, algorithms, and parameters. Determining the ideal approach for a given ecosystem and study, or highlighting algorithmic gaps in need of additional research and development, requires rigorous benchmarking. We present MAG-E (MAG pipeline E valuator), a generalizable and expandable framework for end-to-end evaluation of entire MAG pipelines: from assembly, through binning, to quality control and filtering. MAG-E relies on simulations that are built to match an ecosystem of interest and provide a ground truth for accurate evaluation. To demonstrate the capabilities of MAG-E, we benchmark two assemblers, six binning algorithms, three binning modes, and three quality control and refinement methods in the context of the human gut microbiome. Our findings offer multiple insights into optimal MAG generation in this context. We find that metaSPAdes consistently outperforms MEGAHIT in terms of recall (completeness), and that COMEBin overall outperforms alternative binning algorithms, but has lower precision than SemiBin2. While multi-sample binning results in higher precision, as previously shown, single-sample binning has higher recall and leads to better overall performance with modern binners. Binning refinement, which combines bins from multiple different algorithms, leads to reduced performance. We further show that CheckM2 systematically overestimates completeness and underestimates contamination, and that this is partially ameliorated when using GUNC. Finally, we analyze performance at the contig level, and demonstrate that binning algorithms systematically underperform for prophages and fail to bin contigs that are shared between genomes. Overall, MAG-E offers deep insights into successes and gaps in this important analytic process.},
}

@article {pmid41993555,
year = {2026},
author = {Herzog, HM and Fang, C and Lam, L and Jin, K and Zamarioli, A and Dinh, E and Gupta, CL and Sharma, A and Moody, T and Pierce, JL and Hohl, MS and Takimoto, SW and Lyalina, S and Wentworth, KL and Yu, K and Lu, VF and Mamikunian, I and Hunt, NK and Lynch, S and Pollard, KS and Hernandez, CJ and Perrien, DS and Hsiao, EC},
title = {Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1 [R206H] -driven heterotopic ossification.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716562},
pmid = {41993555},
issn = {2692-8205},
abstract = {UNLABELLED: Inflammatory diseases cause significant morbidity and mortality, but their pathobiology is often difficult to dissect due to complex genetic-environmental interactions. Genetic forms of heterotopic ossification, such as fibrodysplasia ossificans progressiva (FOP), reduce genetic variability, allowing careful dissection of non-genetic drivers of inflammation. While >95% of FOP patients harbor the ACVR1 [R206H] mutation, patients exhibit significant variability in disease progression, suggesting a role of environmental drivers. Here, we identify the gut microbiome as a regulator of inflammation-driven HO in FOP. Metagenomic profiling of cohabitating FOP/unaffected sibling pairs revealed a pathogenic gut microbiome profile in FOP patients (Bray-Curtis, p < 0.05). In Pdgfrα-Cre/Acvr1 [R206H] (FOP) mice, gut microbiome ablation by antibiotics reduced spontaneous HO formation (47.4% reduction, p < 0.05) and reduced plasma IL-1 pathway activity. IL-1β blockade in FOP mice suppressed trauma-induced HO formation. These findings identify a gut microbiome-IL-1-HO axis with modifiable targets for developing treatments for HO and related inflammatory conditions.

ONE SENTENCE SUMMARY: Antibiotic disruption of the gut microbiome reduces HO in FOP mice via an IL-1 mediated pathway.},
}

@article {pmid41993727,
year = {2026},
author = {Sun, Y and Qiu, JW and Chen, C and Martín-Durán, JM 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 tubeworm, Lamellibrachia columna Southward, 1991 (Sabellida: Siboglinidae).},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {127},
pmid = {41993727},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Lamellibrachia columna (tubeworm; Annelida; Polychaeta; Sabellida; Siboglinidae). The genome sequence has a total length of 879.73 megabases. Most of the assembly (99.96%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.78 kilobases. Gene annotation of this assembly by Ensembl identified 21 983 protein-coding genes.},
}

@article {pmid41993799,
year = {2026},
author = {Yue, XL and Wu, YH and Zheng, DQ and Sun, C and Xu, L and Cui, L and Xu, XW},
title = {[13]C-labeled single-cell Raman sorting reveals sulfur-driven dark carbon fixation in coastal sediments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag073},
pmid = {41993799},
issn = {2730-6151},
abstract = {Chemoautotrophs drive carbon fixation in coastal sediments, but most of them remain uncultured with poorly characterized in situ activities. In this study, a cultivation-independent single-cell approach combining Raman spectroscopy with [13]C-stable isotope probing was developed to enable direct identification of active chemoautotrophs in coastal sediments using function-specific spectral biomarkers, targeted metagenomic sequencing and pure culture verification. [13]C-induced shifts in cytochrome c (749, 1129, 1312, 1589 cm[-1]) and phenylalanine (1002 cm[-1]) Raman bands were systematically evaluated and applied as functional biomarkers through investigations of both representative chemoautotrophic strains and environmental samples. The combined analysis of targeted sorting of active chemoautotrophic cells and metagenomic sequencing revealed dominant species and a complete Calvin-Benson-Bassham (CBB) cycle pathway in sulfur-oxidizing guilds. Remarkably, a novel sulfur-oxidizing chemoautotroph, Guyparkeria sp. TX1, which showed ≥99% gene sequence similarity to contigs recovered from sorted-cell metagenomes, was isolated from enrichment cultures. Its significant carbon fixation capacity provided experimental validation for the effectiveness of Raman-based in situ functional screening. This study establishes Raman-based functional biomarkers applicable to chemoautotrophic carbon fixation, enabling in situ mapping of microbial carbon fluxes. By integrating single-cell phenotypic activity with genomic potential, this work advances the mechanistic understanding of sulfur-driven dark carbon fixation, which sustains coastal blue carbon ecosystems as a keystone process.},
}

@article {pmid41993915,
year = {2026},
author = {Hoedt, EC and Burns, GL and Hedley, KE and Waller, S and Sanchez, TC and Chisolm, O and MacCallum, H and Richardson, S and Suthers, B and Pepper, E and Keely, S and Talley, NJ},
title = {Shared functional microbiome signatures in Parkinson's disease and constipation predominate irritable bowel syndrome despite taxonomic divergence.},
journal = {Brain, behavior, & immunity - health},
volume = {53},
number = {},
pages = {101218},
pmid = {41993915},
issn = {2666-3546},
abstract = {BACKGROUND: Gastrointestinal dysfunction, including constipation, is a common non-motor feature of Parkinson's disease (PD) and often precedes motor symptoms. The gut microbiome interacts with the host through neural, hormonal, and immune pathways, yet whether constipation represents a cause or consequence of PD remains unclear. Therefore, we aimed to interrogate the associations between microbiome and immune alterations in relation to constipation to provide novel insight into microbiome-gut-brain axis mechanisms in PD.

METHODS: We analysed peripheral blood mononuclear cells (PBMCs) for circulating gut-homing T cell populations and used shotgun metagenomics to profile the stool microbiome composition and functional capacity in PD patients (n = 18), healthy controls (n = 21), and individuals with constipation-predominant irritable bowel syndrome (IBS-C; n = 8). Associations between immune markers and microbial taxa were assessed, and functional pathway differences were evaluated.

RESULTS: Circulating gut-homing T cell frequencies did not differ significantly between PD and controls, but constipated PD patients showed a trend toward increased circulating gut-homing T cells. Microbiome beta-diversity analyses revealed distinct taxonomic shifts in PD and IBS-C, while functional capacity was largely conserved. Of the differential functional pathways tryptophan biosynthesis, polyamine production, and vitamin B metabolism, processes critical for neurotransmitter synthesis, epithelial integrity, and neuroimmune regulation were reduced in PD compared to IBS-C.

CONCLUSION: Our findings highlight unique microbial and immune signatures in PD, partially overlapping with IBS-C, and underscore the importance of microbial metabolic pathways in gut-brain axis disorders. Collectively our findings suggest a contribution to dopaminergic dysfunction, neuroinflammation, and impaired gut motility. Future longitudinal studies are needed to clarify causal relationships and inform targeted interventions for PD-related gastrointestinal dysfunction.},
}

@article {pmid41993958,
year = {2026},
author = {Meng, H and Zhao, S and Jin, H and Zhang, H and Li, Q and Zhang, L and Hu, J and Kong, F and Du, X and Li, Q and Ajwad Rahim, M and Xu, L and Xue, Y},
title = {Unveiling the Role of Rumen Microbiome in Modulating Intramuscular Fat Deposition of Pingliang Red Cattle.},
journal = {Food science & nutrition},
volume = {14},
number = {4},
pages = {e71681},
pmid = {41993958},
issn = {2048-7177},
abstract = {Pingliang Red cattle is renowned for its tender meat and symmetrical intramuscular fat (IMF) deposition. Rumen microbiota are crucial for energy metabolism and nutrient acquisition in cattle, significantly influencing IMF deposition. Therefore, this study aimed to explore how rumen microbiota impact IMF deposition in Pingliang Red cattle. 34 castrated Pingliang Red cattle were subjected to the same management for 2 months, followed by centralized and unified slaughtering. Based on the measured IMF content in the longissimus dorsi, 18 cattle were selected and divided into a high-intramuscular-fat group (HIMF, n = 9) and a low-intramuscular-fat group (LIMF, n = 9). Rumen fluid was subsequently collected for metagenomic sequencing. Results showed significant differences in taxonomic abundance at both the genus and species levels, the relative abundance of carbohydrate-active enzyme (CAZy) families, and functional profiles (p < 0.05). Specific rumen microbes, such as Limosilactobacillus panis (AUC = 0.765) and Fibrobacter succinogenes (AUC = 0.753), served as potential biomarkers for HIMF deposition in Pingliang Red cattle. With the exception of Bacillus, Fibrobacter succinogenes, Limosilactobacillus panis, Prevotella intermedia, and Streptomyces exhibited positive correlations with IMF content. Functional analysis based on KEGG orthology (KO) indicated that specific enzymes promote IMF deposition by regulating the metabolism of short-chain fatty acids (SCFAs), long-chain fatty acids (LCFAs), and lipopolysaccharides, as well as insulin signaling. These findings provide a theoretical reference for regulating rumen microbial communities to improve IMF deposition.},
}

@article {pmid41994130,
year = {2026},
author = {Khan, D and Espinoza, JL and Tientcheu, PE and Otchere, ID and Mohammed, NI and Worwui, A and Nicol, MP and Kwambana-Adams, B and Antonio, M and Dupont, CL},
title = {Shotgun metagenomic profiling of bacterial microbiomes, metagenome-assembled genomes and antimicrobial resistance in respiratory and blood samples from Gambian children with pneumonia.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8724320/v1},
pmid = {41994130},
issn = {2693-5015},
abstract = {Pneumonia is a leading cause of morbidity and mortality in children, with bacterial pathogens being important etiologic agents. Most microbiome studies in pneumonia use technologies with limited taxonomical resolution and few include lung aspirate or blood samples. In this study, we assessed the microbial communities of the nasopharynx, nasopharynx/oropharynx, induced sputum, lung aspirate and blood, and recovered metagenome-assembled genomes from the same sites using shotgun metagenomics sequencing of samples from children with severe and very severe pneumonia in The Gambia. Our data show that Proteobacteria and Firmicutes were the most common phyla across the body sites, and this was largely driven by S. pneumoniae, H. influenzae/aegyptius and M. catarrhalis. Furthermore, we observed species overlap of blood and respiratory samples with average Jaccard similarity index values ranging from 34% to 58%. We recovered 60 medium and 35 high-quality MAGs in these niches including 11 S. pneumoniae , 10 H. influenzae strains and a limosilactobacillus with less than 95% Average Nucleotide Identity to any known species in GTDB-TK. We also showed that the resistomes in our MAGs were highly species specific with more than 70% of the detected AMR genes found exclusively in a single species.},
}

@article {pmid41994193,
year = {2026},
author = {Jiang, T and Yan, F and Liu, B and Li, Q and Wang, K and Ru, X and Hao, Y and Guan, Y and Wang, Y},
title = {Intraventricular hemorrhage, suspected EBV reactivation, and TBA-positive epilepsy after deep cervical lymphovenous anastomosis in Alzheimer's disease: a case report.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1791011},
pmid = {41994193},
issn = {1663-4365},
abstract = {Lymphovenous anastomosis (LVA) is emerging as a potential surgical intervention to ameliorate cervical lymphatic outflow and enhance glymphatic clearance in Alzheimer's disease (AD). However, the spectrum of neurological sequelae associated with this procedure remains poorly characterized. We report the case of a 67-years-old male with amyloid PET-confirmed AD who underwent bilateral deep cervical LVA. Twenty-three days postoperatively, he presented with high-grade fever and altered consciousness. Head CT revealed acute hemorrhage in the posterior horn of the left lateral ventricle (∼2 mL). Cerebrospinal fluid (CSF) analysis demonstrated lymphocytic pleocytosis and significantly elevated protein levels; the fluid was uniformly bloody, confirming intraventricular hemorrhage. Plasma metagenomic next-generation sequencing (mNGS) identified Epstein-Barr virus (EBV), with serology supporting reactivation. Following antiviral and empirical antibiotic therapy, the patient's condition stabilized, and the hemorrhage resolved. Four months postoperatively, he developed new-onset generalized seizures. Despite negative results from a conventional autoimmune encephalitis antibody panel in both serum and CSF, a tissue-based assay (TBA) proved positive in both samples. Seizures were successfully controlled with levetiracetam. This case suggests a potential association between invasive lymphatic procedures and a hemorrhage-infection-immune cascade in highly vulnerable AD patients with preexisting metabolic and neurodegenerative risk factors.},
}

@article {pmid41994268,
year = {2026},
author = {Zhang, F and Chen, J and Yuan, Y and Chen, J and Jiang, W and Xiang, W and Wang, N and Wu, Z and Fan, S and Zhang, K and Ma, Y and Liu, T and Zhang, J and Yu, Q and Zhang, J},
title = {The enhancing therapeutic effect of neonatal jaundice by bifidobacterium through regulating inflammation and gut microbiota in combination with phototherapy-a randomized controlled trial.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1761245},
pmid = {41994268},
issn = {1664-302X},
abstract = {BACKGROUND: Hyperbilirubinemia is among the most common conditions in neonates, and phototherapy is currently the most widely used treatment. However, it can induce side effects such as skin rashes, diarrhea, and gut microbiota dysbiosis, particularly affecting Bifidobacterium levels. This study aimed to investigate whether the supplementation of Bifidobacterium can alleviate dysbiosis and improve clinical outcomes in jaundiced neonates.

METHODS: A total of 79 jaundiced neonates were enrolled and divided into four groups: Phototherapy Control, M-16V, Bb-12, and the combined M-16V+Bb-12 group. Probiotics were administered until 30 days post-discharge, and neurodevelopment was assessed at 1.5-2 years using the Griffith Development Scales. Fecal samples collected before, during, and after treatment were analyzed using metagenomic sequencing and non-targeted metabolomics.

RESULTS: Probiotic supplementation significantly increased daily defecation frequency, accelerated the reduction rate of transcutaneous bilirubin, and shortened hospital stays. Griffith scores indicated that Bb-12 supplementation improved scores in personal-social and performance domains. Metagenomic analysis revealed significant differences in beta diversity between the control and probiotic groups; specifically, M-16V and combined supplementation increased the abundance of Bifidobacterium breve. Pathway enrichment analysis showed up-regulation of pyrimidine-containing compound metabolic processes, intramolecular transferase activity, and DNA conformation change. Metabolomics further demonstrated that combined supplementation elevated levels of 5-methyltetrahydrofolate (linked to DNA synthesis), benzoic acid and indoleacetic acid (linked to growth and development), and the anti-inflammatory metabolite indole-3-lactic acid.

DISCUSSION: For neonates receiving phototherapy, the addition of M-16 V + Bb-12 probiotics can improve the diversity of microflora, reduce the fixed value of harmful bacteria in the intestine, and enhance the excretion of bilirubin from the intestine, to improve the inflammatory damage and microbiota disorder caused by phototherapy, and achieve the effect of clinically improving jaundice, reducing bilirubin, shortening the length of hospitalization, and promoting neurodevelopment. It provides a safer and more effective treatment for neonatal jaundice.},
}

@article {pmid41994275,
year = {2026},
author = {Yu, T and Yu, Y and Zhao, J and Li, H and Lu, H and Li, Y and Peng, Y and Wang, S and Wei, W and Cheng, X},
title = {Qifuyin improves physiological frailty by regulating the intestinal flora in 3xTg-AD mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1753643},
pmid = {41994275},
issn = {1664-302X},
abstract = {OBJECTIVE: Alzheimer's disease (AD) is often accompanied by motor dysfunction, impaired limb strength, and gut microbiota disturbances. This study aimed to evaluate the effects of Qifuyin (QFY), a traditional Chinese medicine formula, on motor deficits, limb strength, aging, and gut microbiota composition in 3xTg-AD mice, a widely used model of AD.

METHODS: Male and female 3xTg-AD mice were administered QFY at low, medium, or high doses. Motor function was assessed using grip strength and rotarod tests. Aging was evaluated through aging scores. Gut microbiota composition was analyzed at the phylum, family, genus, and species levels. Functional profiling of microbiota was performed using KEGG, eggNOG, and carbohydrate-active enzyme (CAZyme) databases. Pearson correlation analyses were conducted to explore relationships between microbiota composition and motor performance.

RESULTS: QFY treatment significantly improved both absolute and normalized grip strength in male and female 3xTg-AD mice. Similarly, motor coordination, as assessed by latency to fall on the rotarod, was significantly enhanced in the groups of QFY. Aging scores were significantly reduced after the treatment of QFY. Microbiome analysis revealed that QFY treatment restored species diversity and improved the overall composition of gut microbiota, with significant increases in Muribaculaceae and decreases in Alcaligenaceae, Rhodanobacteraceae, and Spirochaetaceae. Principal component analysis (PCA) indicated that the gut microbiota composition of the QFY group resembled that of the control (Con) group. Functional analyses showed that treatment of QFY restored microbial pathways related to metabolism and genetic information processing, with significant correlations between microbial alterations and improved motor outcomes. Additionally, QFY modulated the abundance of key carbohydrate-active enzymes, including GH43 and GH35, which were positively correlated with grip strength and rotarod performance.

CONCLUSION: Qifuyin improves motor function, reduces aging-related deficits, and restores gut microbiota homeostasis in 3xTg-AD mice. These findings suggest that QFY may offer therapeutic potential for addressing frailty and motor dysfunction in AD, in association with alterations in gut microbiota composition and predicted microbial functions.},
}

@article {pmid41994276,
year = {2026},
author = {Xian, J and Li, Y and Feng, Z and Jin, Y and Cai, T and Cao, M and Cao, Y},
title = {High-fat diet-driven gut microbial sphingolipid metabolic reprogramming is associated with stress susceptibility in CUMS rats.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1802003},
pmid = {41994276},
issn = {1664-302X},
abstract = {The escalating comorbidity between depression and metabolic syndromes induced by a high-fat diet (HFD) poses a substantial social and economic burden on society. However, the precise molecular mechanisms by which a HFD qualitatively alters the basal pathophysiology of chronic unpredictable mild stress (CUMS) remain unclear. In this study, the differential roles of microbial and metabolic pathways in the onset and exacerbation of depression were investigated using CUMS rat models fed a normal diet (ND-CUMS) or HFD (HFD-CUMS). Our findings indicated that HFD intervention showed a trend toward aggravating depressive behaviors and resulted in significantly more severe neuronal injury in the hippocampus relative to the ND-CUMS group. Notably, integrated multi-omics (metagenome and metabolome) analysis revealed a crucial pathway divergence: basal CUMS depression was strongly associated with the dysregulation of glycerophospholipid metabolism, linked to microbiota such as Bacteroides thetaiotaomicron and Terrisporobacter glycolicus, while HFD triggered a predominant disruption of the sphingolipid metabolism pathway. Exploratory mediation analysis suggested that a sphingolipid-related signature that may statistically connect HFD-associated microbial shifts with neural injury and behavioral readouts. Therefore, our findings reveal a distinct mechanistic shift underpinning metabolic-comorbid depression. HFD does not merely exacerbate stress-induced depression but fundamentally transitions the underlying pathology from glycerophospholipid to sphingolipid signaling, highlighting the potential of targeting specific lipid metabolic reprogramming as a promising therapeutic strategy for combating metabolic-comorbid depression.},
}

@article {pmid41994278,
year = {2026},
author = {Dang, M and Tang, Y and Chen, J and Xie, W and Zhong, Y and Yu, B and Zhang, E and Wang, Z},
title = {Rhizospheric soil microbial community structure and metabolic characteristics of wild Cymbidium mastersii at different altitudes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1720137},
pmid = {41994278},
issn = {1664-302X},
abstract = {INTRODUCTION: Cymbidium mastersii, a perennial orchid of high ornamental value, faces severe survival challenges due to extremely low natural seed germination rates (<15%), habitat degradation, and illegal harvesting. It is listed as a Category II Nationally Protected Plant Species in China.

METHODS: We examined the rhizosphere microbial communities and metabolomes of C. mastersii across elevation gradients. We investigated the rhizospheric soil microbial community composition and metabolic characteristics of C. mastersii across different elevations.

RESULTS: The dominant bacterial phylum was Pseudomonadota, with relative abundances of 38.22% (CmL, low elevation), 36.91% (CmM, mid-elevation), and 62.54% (CmH, high elevation). While the dominant bacterial genera varied significantly with elevation, taxonomic richness exhibited a consistent decline with increasing altitude (p < 0.05, linear regression), indicating altitudinal filtering of microbial diversity. LC-MS/MS metabolomic profiling identified 1,516 metabolites, predominantly enriched in lipid and lipid-like molecules, carbohydrates and derivatives, and aromatic compounds. Functional contribution analysis revealed Bradyrhizobium as the most influential taxon (10% variance explained), displaying a nonlinear elevational response. Correlation analysis of differential metabolites confirmed significant species-metabolite correlations (P < 0.05, R > 0.7). Our findings underscore the critical role of trophic interactions in shaping rhizosphere community assembly in alpine plants, thereby contributing to the broader understanding of microbial biogeography along elevational gradients.

DISCUSSION: This study not only confirms that the altitudinal gradient serves as a key environmental filter shaping the rhizosphere microecology of C. mastersii, but more importantly, by integrating metagenomic and metabolomic approaches, we systematically reveal for the first time that altitude differentially selects for microbial taxa with specific functions, ultimately driving the restructuring of the rhizosphere metabolic environment. Moving beyond mere community description, our work aims to elucidate the underlying pathways responsible for these shifts and their potential functional implications for host plant adaptation.},
}

@article {pmid41994292,
year = {2026},
author = {Sun, M and Lei, Z and Li, B and Gao, SH and Fan, L},
title = {Virus-encoded metabolism may support environmental stress adaptation of microbial hosts in an estuarine hypoxic zone.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1785655},
pmid = {41994292},
issn = {1664-302X},
abstract = {Hypoxic zones in estuaries threaten the ecological balance and the productivity in coastal areas. However, it is poorly understood how viruses regulate metabolic processes of their microbial hosts to adapt to the hypoxic environment, and consequently impact the biogeochemical cycles in hypoxic zones. In this study, the diversity and functional potentials of the bacterial, archaeal and viral communities of a hypoxic zone at the Pearl River Estuary was characterized along with local environmental factors, with a particular focus on viral auxiliary metabolic genes (AMGs). The viral community derived from the virion fraction and the cellular fraction of the seawater were distinctly different, with the cellular fraction generating fewer unique viruses, but more types of AMGs. Overall, more AMGs were identified in samples with higher dissolved oxygen levels. Globally conserved AMGs were infrequently observed in the current samples, suggesting a certain level of adaptation of AMGs to the local environment. There were strong correlations in abundances among cyanobacteria, cyanophages, and photosynthesis AMGs, suggesting potential viral participation in estuarine primary production. Many AMGs involved in nutrient limitation endurance were found, potentially assisting their host with phosphorus, iron and B family vitamin shortages. Although putative hosts were predicted for the viruses, the functionality of their AMGs appears to be a better predictor of their distribution than the hosts they infect. Our study provides a functional insight into the viral community in poorly researched estuarine hypoxic zones, and sheds light on the potential interactions of viruses with their microbial hosts for co-adaptation to this unique environment.},
}

@article {pmid41994309,
year = {2026},
author = {Sarkar, P and Sarkar, S and Unnisa, M and Singh, AP and Inavolu, P and Rughwani, H and Jakkampudi, A and Jaggaiahgari, S and Reddy, DN and Talukdar, R},
title = {The Jejunal Microbiota in Patients With Chronic Pancreatitis: Results From a Pilot Study.},
journal = {Gastro hep advances},
volume = {5},
number = {5},
pages = {100907},
pmid = {41994309},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Chronic pancreatitis (CP) is associated with several systemic metabolic abnormalities including diabetes. While the colonic microbiota and its association with diabetes in CP have been reported, the specific composition of the small intestinal microbiota and its function in CP remains poorly understood. In this pilot study, we primarily aimed to characterize the jejunal microbiota in patients with CP and explore potential associations with diabetes.

METHODS: Jejunal aspirates were collected in a RNAlater-containing sterile container from 29 patients with CP and 10 controls. The samples were then snap lysed followed by metagenomic DNA extraction. Next-generation sequencing was performed for the variable region 3-4 of the 16SrDNA in Illumina MiSeq. After quality control, microbial profiling and functional analysis were conducted using standard bioinformatics pipelines. We also evaluated tight junction integrity in jejunal biopsy samples using immunofluorescence. Furthermore, we assessed for plasma and stool metabolites.

RESULTS: Patients with CP exhibited higher abundances of Prevotella vespertina, Prevotella oris, and Prevotella salivae, while controls demonstrated higher abundances of Prevotella scopos, Veillonella, Rothia, and Lachnospiraceae. Immunofluorescence showed decreased expression of the tight junction protein occludin in the jejunal mucosa of CP diabetic (CPD) patients compared to endoscopic controls (EC) (p.corr. CPD-EC = 0.012). No differences were seen between CP nondiabetic and endoscopic controls, and between the CP subgroups (CPND-EC = 0.29 and CPD-CPND = 1 respectively). Overall, there were significant plasma metabolomic abnormalities in patients with CP and a trend toward reduction of butyrate in the stool samples of the CP patients with diabetes.

CONCLUSION: Our observations suggest alterations in the jejunal microbiota and mucosal barrier function in CP. These were associated with lower fecal butyrate. This may contribute to the pathogenesis of associated metabolic complications in CP. Further large-scale longitudinal and mechanistic studies are needed to validate our findings.},
}

@article {pmid41994369,
year = {2026},
author = {Bao, Q and Zhang, X and Guo, J},
title = {Enterovirus D68 and mycobacterial coinfection: case report.},
journal = {Therapeutic advances in infectious disease},
volume = {13},
number = {},
pages = {20499361261432918},
pmid = {41994369},
issn = {2049-9361},
abstract = {The threat of viral epidemics to long-standing diseases, such as mycobacterial infection, is constantly evolving. Enterovirus D68 (EV-D68) is an emerging cause of respiratory infection and has raised great interest since its first outbreak in 2014. Very few studies have been done to describe the clinical aspects of the coinfection of EV-D68 and mycobacteria, so this study was conducted to help round out the understanding of this coinfection pattern. We observed three adult cases of EV-D68 and mycobacteria, who were admitted to the first affiliated hospital of Zhejiang University in August/September 2024. Only one case had a definite past history of immunodeficient disease and received long-term corticosteroid treatment, and the other two were previously healthy. The diagnoses of EV-D68 and mycobacterial infection were all simultaneously confirmed through the metagenomic Next-Generation Sequencing in bronchoalveolar lavage fluid specimens. All three patients were presented with severe respiratory symptoms, such as fever, cough, dyspnea and tachypnea, without any manifestations of central nervous system involvement. The radiological findings in chest CT scans varied from patchy opacity to massive consolidation. The individualized anti-mycobacterium treatment showed little therapeutic effect, while the improvement of symptoms and pulmonary lesions in chest CT was observed after starting or intensifying the administration of corticosteroid. All patients had a marked clinical improvement when discharged from hospital, and it took about 6-9 months for the lung lesions of mycobacterial infections to nearly resolve. These cases illustrate the potential for EV-D68 coinfection to exacerbate pulmonary inflammation in patients with mycobacterial disease, highlighting the need for vigilance regarding possible viral coinfections in settings with a high tuberculosis burden, such as China.},
}

@article {pmid41994453,
year = {2026},
author = {Zhang, W and Zhang, K and Liao, Y and Yang, Z and Xia, Z and Ke, X and Zhang, D and Chen, J and Wu, H and Hong, Y and Wang, H and Liu, Z and Suo, L and Zhang, Y and Zhang, C},
title = {Characterization of the aqueous humor microbiome in Posner-Schlossman syndrome: an exploratory metagenomic sequencing study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1780981},
pmid = {41994453},
issn = {2296-858X},
abstract = {OBJECTIVE: This study aims to characterize the aqueous humor (AH) microbiome in Posner-Schlossman syndrome (PSS) patients and evaluate its potential as a diagnostic and therapeutic target.

METHODS: Metagenomic next-generation sequencing (mNGS) was performed on 59 AH samples from patients diagnosed with PSS (n = 28) and myopia patients who underwent intraocular lens (ICL) implantation (n = 31). Taxonomic profiling and diversity analyses were conducted to characterize the microbial communities. Interactions among microbial community members were evaluated using correlation analyses.

RESULTS: Key findings revealed that intraocular microbiomes existed in both normal and diseased eyes; however, PSS patients exhibited lower microbial diversity (Shannon index, p = 0.066; Simpson index, p = 0.065) and distinct community structures (PERMANOVA, p = 0.05). Disease-specific microbial signatures were identified: Paeniglutamicibacter was uniquely enriched in the PSS group, whereas Escherichia coli dominated in the ICL group. Moreover, ecological network analysis demonstrated contrasting interaction patterns. The microbiomes in the PSS group formed stable, tightly connected networks with balanced positive/negative correlations, whereas those in the ICL group exhibited antagonistic relationships, suggesting competitive exclusion. These results challenge the traditional view of ocular sterility and reveal dynamic microbiome shifts associated with PSS pathogenesis. The enrichment of Paeniglutamicibacter in PSS may represent an associated microbial signature that could potentially reflect compensatory responses to chronic inflammation, although experimental validation is needed to confirm this hypothesis.

CONCLUSION: Our study provides preliminary evidence supporting the concept of intraocular microbiome dysbiosis in PSS, which requires validation in future studies. These findings suggest that potential microbial biomarkers warrant further investigation for their diagnostic and therapeutic implications.},
}

@article {pmid41994458,
year = {2026},
author = {Jiang, L and Ye, T and Cai, H and He, F},
title = {Case Report: A rare case of Pneumocystis jirovecii infection with left hydropneumothorax following immunotherapy for stage IVB clear cell renal cell carcinoma.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1784855},
pmid = {41994458},
issn = {2296-858X},
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is an opportunistic infection that predominantly affects immunocompromised individuals, most commonly HIV-infected patients with significantly reduced CD4+lymphocyte counts, and is associated with high clinical mortality. Currently, there are few reports of pneumothorax secondary to PJP, and most cases occur in HIV-infected populations. However, PJP complicated by hydropneumothorax in cancer patients receiving immunotherapy is exceedingly rare, with limited reports in the literature. To our knowledge, this article reports a rare clinical case of Pneumocystis jirovecii infection complicated by left-sided hydropneumothorax in a patient with stage IVB clear cell renal cell carcinoma after immunotherapy, aiming to provide valuable insights for the early diagnosis and management of PJP and its complications in cancer patients undergoing immunotherapy.

CASE: A 57-year-old male patient had previously undergone surgical treatment for left renal clear cell carcinoma, and developed recurrent metastases to the descending colon, liver, and upper pole of the left kidney after surgery, with a clinical stage of T4NxM1 stage IVB. After receiving targeted combination immunotherapy with sequential PD-1 inhibitors (toripalimab) plus anti-angiogenic agents (sunitinib, axitinib)-a regimen that enhances anti-tumor immunity but may disrupt pulmonary immune homeostasis-the patient gradually developed progressive dyspnea, chest tightness, hypoxemia, and anuria. Multiple auxiliary examinations were performed clinically, including chest X-ray, bronchoalveolar lavage, and metagenomic sequencing of pathogenic microorganisms. Based on the above examination results, the final diagnosis was Pneumocystis jirovecii pneumonia complicated by left-sided hydropneumothorax.

CONCLUSION: Although PJP complicated by hydropneumothorax after immunotherapy is rare, it should be considered as a possible etiology when cancer patients develop progressive dyspnea with difficulty maintaining oxygen saturation after receiving immune checkpoint inhibitor-based therapy, particularly in the context of immune checkpoint inhibitor use. While biomarkers for predicting immunotherapy efficacy and irAEs are well-studied, the identification of specific biomarkers for predicting opportunistic infections like PJP in this context remains an area of active research.},
}

@article {pmid41994961,
year = {2026},
author = {Sun, QG and Zang, D and Xin, Y and Cui, J and Han, X and Chen, J},
title = {Multi-omics Analysis Reveals the Correlation of Gut Microbiota and Metabolites With Thalidomide Treatment for Chemotherapy-Induced Nausea and Vomiting in Small Cell Lung Cancer.},
journal = {Biotechnology journal},
volume = {21},
number = {4},
pages = {e70228},
doi = {10.1002/biot.70228},
pmid = {41994961},
issn = {1860-7314},
support = {82203056//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Small Cell Lung Carcinoma/drug therapy ; *Lung Neoplasms/drug therapy ; Male ; Female ; Middle Aged ; *Thalidomide/therapeutic use/adverse effects/pharmacology ; *Vomiting/chemically induced/drug therapy ; *Nausea/chemically induced/drug therapy ; Aged ; *Antineoplastic Agents/adverse effects/therapeutic use ; Metabolomics/methods ; Metabolome/drug effects ; Feces/microbiology ; Multiomics ; },
abstract = {Small cell lung cancer (SCLC) is a highly aggressive malignancy, and chemotherapy frequently causes nausea and vomiting, which can impair treatment tolerance. Because thalidomide (THD) has shown potential clinical benefit in alleviating nausea and anorexia, we investigated whether its effects might be associated with changes in gut microbial composition and metabolite profiles. Fecal samples were collected from patients with SCLC and categorized into THD-treated and control groups. Metagenomic sequencing and nontargeted metabolomic profiling were performed to characterize microbial composition and metabolic signatures. THD treatment was also associated with higher microbial alpha diversity and increased abundance of genera such as Eubacterium and Prevotella. Metabolomic analysis identified several differential metabolites, including hydrogenated MDI, becocalcidiol, β-octylglucoside, and azelaic acid. Collectively, these findings suggest that the gut microbiota-metabolite axis may be associated with the potential effects of THD on CINV and anorexia in patients with SCLC. The identified microbial taxa and metabolites may serve as candidate biomarkers or potential therapeutic targets, although further validation in larger studies is necessary.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
*Small Cell Lung Carcinoma/drug therapy
*Lung Neoplasms/drug therapy
Male
Female
Middle Aged
*Thalidomide/therapeutic use/adverse effects/pharmacology
*Vomiting/chemically induced/drug therapy
*Nausea/chemically induced/drug therapy
Aged
*Antineoplastic Agents/adverse effects/therapeutic use
Metabolomics/methods
Metabolome/drug effects
Feces/microbiology
Multiomics

@article {pmid41995327,
year = {2026},
author = {Chen, Y and Tang, X and Lu, S and Guo, L and Wang, L and Min, L and Niu, T and Zhou, Y},
title = {The diagnostic and prognostic utility of blood metagenomic next-generation sequencing for invasive pulmonary aspergillosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0338425},
doi = {10.1128/spectrum.03384-25},
pmid = {41995327},
issn = {2165-0497},
abstract = {UNLABELLED: Differentiating invasive pulmonary aspergillosis (IPA) from colonization in patients with Aspergillus-positive blood metagenomic next-generation sequencing (mNGS) remains a clinical challenge. This study aims to evaluate the diagnostic and prognostic value of blood mNGS-derived fungal load (reads per million [RPM]) and two key serological biomarkers (galactomannan [GM] and 1,3-β-D-glucan [BDG]) in distinguishing these two entities. This retrospective study enrolled 95 patients with Aspergillus detected by blood mNGS, stratified into infection (n = 60) and colonization (n = 35) groups using modified EORTC/MSGERC criteria. We analyzed clinical characteristics, co-infection spectra, and serological biomarkers (GM and BDG). Diagnostic performance was evaluated via receiver operating characteristic (ROC) analysis, and prognostic factors for 28-day mortality were identified using least absolute shrinkage and selection operator-Cox regression. Distinct co-infection patterns were observed between groups: the infection group was dominated by polymicrobial co-infections, including clinically significant pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, Mucor spp., and Human cytomegalovirus; in contrast, the colonization group primarily featured single viral co-infections. While mNGS effectively detected Aspergillus, RPM alone showed limited ability to discriminate infection from colonization, with area under the curves (AUCs) ranging from 0.406 to 0.657 across patient groups. The optimal RPM cutoff varied substantially by immune status, being highest in immunocompetent patients (RPM cutoff: 1.77). Diagnostic performance significantly improved when RPM was integrated with GM (AUC up to 0.900 at a cutoff of 0.36 optical density index) or BDG (AUC up to 0.881 pg/mL), particularly in immunocompetent individuals. RPM also correlated with albumin, hemoglobin, platelet counts, and lymphocyte counts (all P < 0.05). Multivariate analysis identified reversed halo sign (hazard ratio [HR] = 2.143), decreased ratio of partial pressure of arterial oxygen to fraction of inspired oxygen (PaO2/FiO2; HR = 1.361), and elevated lactate dehydrogenase (HR = 1.055) as independent predictors of 28-day mortality. Blood mNGS demonstrates high sensitivity for detecting Aspergillus but requires integration with serological biomarkers to differentiate IPA from colonization. The RPM can offer prognostic utility. A multimodal strategy is crucial for early diagnosis and improving outcomes in high-risk patients.

IMPORTANCE: First large-scale validation of blood mNGS for invasive pulmonary aspergillosis diagnosis-this study represents the first sizable cohort systematically evaluating blood metagenomic next-generation sequencing (mNGS) for distinguishing invasive pulmonary aspergillosis from colonization, addressing a critical gap in non-invasive diagnostic approaches for critically ill patients. Comprehensive Aspergillus co-infection profiling-we identified distinct co-infection patterns, with the infection group showing significantly higher rates of polymicrobial infections, providing crucial insights into co-infection dynamics in Aspergillosis. Optimized diagnostic integration strategy-our findings demonstrate that while mNGS-derived reads per million alone show limited diagnostic value, their integration with serological biomarkers significantly improves performance, establishing a clinically relevant multimodal diagnostic framework. Robust prognostic stratification model-through least absolute shrinkage and selection operator-Cox regression, we established a validated prognostic model identifying reversed halo sign, decreased PaO2/FiO2, and elevated lactate dehydrogenase as independent predictors of 28-day mortality, providing clinically actionable tools for risk stratification.},
}

@article {pmid41995478,
year = {2026},
author = {Conley, TE and Duncan, A and Modasia, A and Ford, AC and Pritchard, DM and Hildebrand, F and Warren, FJ and Spiller, R and Probert, CS},
title = {The Emerging Short Chain Fatty Acid Enriched Metabotype in Irritable Bowel Syndrome and Its Potential Clinical Relevance.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70677},
pmid = {41995478},
issn = {1365-2036},
abstract = {BACKGROUND: Metabolomic analysis in irritable bowel syndrome (IBS) has identified metabotypes enriched in faecal short-chain fatty acids (SCFAs), but it remains unclear whether this reflects rapid colonic transit or if these metabolites actively contribute to pathophysiology.

AIMS: We aimed to determine whether an SCFA metabotype could be identified within a cohort of patients with moderate-severe IBS-D and assess whether this metabotype associated with greater clinical severity, alterations in gut transit time and specific microbiome features.

METHODS: This was a post hoc cross-sectional exploratory analysis of baseline data from the multicentre, randomised, placebo-controlled trial of ondansetron in IBS-D (TRITON: ISRCTN17508514). Faecal volatile organic compounds were profiled by GC-MS. The microbiome was characterised by whole-genome shotgun metagenomic sequencing. Unsupervised hierarchical clustering was used to identify an SCFA-enriched metabotype and non-negative matrix factorisation (NMF) enabled the derivation of complementary metabosignatures by assessing continuous gradients in metabolite composition.

RESULTS: A SCFA-enriched metabotype was identified in 20/63 participants (31.7%). This metabotype was associated with more severe abdominal pain, urgency, increased stool frequency and faster whole-gut transit. NMF identified three metabosignatures: S3 was typified by a high proportion of SCFAs and captured the SCFA-enriched metabotype, while S1 and S2 corresponded to the non-SCFA ("Other") metabotype. SCFA relative abundance positively correlated with symptom severity and inversely correlated with transit time. The Other metabotype and S1/S2 signatures were enriched in taxa linked to slower transit, whereas S3 showed no overlapping taxa with the SCFA metabotype.

CONCLUSION: A faecal metabotype enriched in SCFAs associated with an IBS-D phenotype characterised by pain, urgency, rapid transit and higher stool frequency.},
}

@article {pmid41995796,
year = {2026},
author = {Vial, M and Costil, K and Agogué, J and Eustache, S and Heighton, S and Gissat, L and Gueuné, H and Caplat, C},
title = {Spatial and temporal variability of biofouling communities during early development in three French harbors of the English Channel.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {5},
pages = {},
pmid = {41995796},
issn = {1573-2959},
mesh = {*Biofouling/statistics & numerical data ; *Biofilms/growth & development ; *Environmental Monitoring ; France ; Aquatic Organisms/physiology ; Chlorophyll A/analysis ; Seawater/microbiology ; },
abstract = {Biofouling, the colonization of submerged surfaces by marine organisms, causes major economic losses in maritime activities. Although non-biocidal surface coatings are promoted as environmentally friendly antifouling solutions, the respective roles of surface properties and environmental conditions in shaping biofouling stages remain unclear. We hypothesized that coating surface properties primarily control early biofilm formation, whereas local environmental conditions govern subsequent macrofouling development. To test this hypothesis, we studied biofouling on two non-biocidal coatings - an anticorrosion epoxy and a fluoropolymer foul-release coating (FRC) - immersed under static conditions in three French harbors along the English Channel during the spring bloom. Early biofilm formation was assessed after 2 weeks in April, May, and June 2023 using chlorophyll a and the carbohydrate/protein ratio of extracellular polymeric substances (EPS). Macrofouling development over 3 months was evaluated through biomass, surface coverage rate, taxonomic composition, and microorganism abundances. Metagenomic analyses complemented the visual observations in Cherbourg during April and May 2023. The FRC showed a higher EPS carbohydrate/protein ratio, indicating greater resistance to initial microbial colonization, but exhibited significantly lower macrofouling intensity than the epoxy. This decoupling supports the hypothesis that surface properties and settlement processes operate at different spatial and temporal scales. Spatial variability in biofouling patterns may largely be associated with differences in nutrient availability and anthropogenic pressure. These findings demonstrate that early biofilm metrics alone cannot predict long-term fouling and highlight that antifouling performance depends on both material properties and environmental context. Integrating surface physicochemistry with site-specific ecological drivers can improve both coating design and antifouling evaluation strategies.},
}

*Biofouling/statistics & numerical data
*Biofilms/growth & development
*Environmental Monitoring
France
Aquatic Organisms/physiology
Chlorophyll A/analysis
Seawater/microbiology

@article {pmid41996042,
year = {2026},
author = {Myoung, K and Kim, S and Choi, EJ and Kim, HJ and Baek, HS and Park, WS and Hwang, JS},
title = {Integrated analysis of age-related microbiome and metabolites reveals youth-associated metabolites in young Korean women's skin.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41996042},
issn = {1618-1905},
abstract = {Alterations in the composition and functional potential of the skin microbiome are closely associated with aging. Nevertheless, integrative analyses that concurrently examine microbial composition, functional gene profiles, and skin surface metabolomics remain limited, particularly among Asian populations. In this study, we performed a comprehensive multi-omics analysis integrating skin microbiome and surface metabolomic data from Korean women to explore metabolites associated with youthful skin state. Twenty-three healthy female participants in their 20s and 60s were recruited. Skin physiological parameters were assessed, and microbiome and metabolite samples were collected from the cheek area. Unsupervised clustering of microbiome functional profiles revealed three microbial community patterns that were not strictly aligned with chronological age. Based on these patterns, samples were grouped into three functional groups. The cluster enriched in participants in their 20s showed higher relative abundance of Cutibacterium and enrichment of microbial pathways related to carbohydrate and energy metabolism. Metabolomic profiling showed that phenyllactic acid (PLA) and hydroxyphenyllactic acid were more abundant in participants in their 20s and in the functionally young cluster. These metabolite patterns were accompanied by higher abundance of genes associated with phenylalanine metabolism. In vitro experiments further showed that PLA increased procollagen production and reduced the secretion of collagen-degrading enzymes in human dermal fibroblasts under inflammatory conditions. Together, these findings suggest links between microbiome functional profiles, phenylalanine-related metabolites, and skin physiology. This study provides an integrated view of microbiome-metabolite relationships in Korean skin and identifies PLA as a candidate metabolite associated with youthful skin environments.},
}

@article {pmid41996045,
year = {2026},
author = {Mohanty, A and Pavan-Kumar, A and Chaudhari, A and Kumari, K and Kumar, P and Maurye, P},
title = {Comparative performance of traditional and commercial DNA extraction methods for fish gut microbiota analysis.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41996045},
issn = {1573-4978},
support = {FBT-PB1-01//Indian Council of Agricultural Research/ ; },
}

@article {pmid41996243,
year = {2026},
author = {Lin, D and Ma, QX and Ye, YQ and Wanek, W and Gregory, AS and Jones, DL and Graham, DW and Zhu, D and Penuelas, J and Zhu, YG},
title = {Nutrient balance regulates soil microbial health under long-term fertilization.},
journal = {Cell reports},
volume = {45},
number = {4},
pages = {117274},
doi = {10.1016/j.celrep.2026.117274},
pmid = {41996243},
issn = {2211-1247},
abstract = {Fertilizer application in intensive agriculture critically influences microbial communities. It is still unclear how long-term input of different nutrients shapes microbial eco-evolutionary strategies and ecological functions. Through 180-year-old field fertilization experiment, alongside microbial culturing, pot experiments, and comprehensive metagenomic data analysis, we show that exclusive fertilization with inorganic chemicals causes carbon-nitrogen imbalances that increase microbial resource competition and antibiotic resistance gene (ARG) levels. Viruses further amplify this expansion through "piggyback the winner" strategy. The imbalanced use of nitrogen in chemical fertilizers disrupt ecological niche connections, leading to an increase in virulent viruses and reducing microbial nutrient cycling capacity. In contrast, more balanced nutrient supplies from organic fertilization reduced microbial competition and promoted microbial growth. However, responsible antibiotic use in livestock is essential to maximizing these benefits. Our research provides insights into enhancing agricultural sustainability through the management of soil nutrient conditions.},
}

@article {pmid41996362,
year = {2026},
author = {Buni, D and Kovács, ÁB and Wehmann, E and Grózner, D and Bányai, K and Nagy, EZ and Bradbury, J and Bottinelli, M and Stefani, E and Catania, S and Lysnyansky, I and Kovács, L and Gyuranecz, M and Kreizinger, Z},
title = {Identification and detection of genetic markers associated with antimicrobial susceptibility and evaluation of efflux pump mechanisms in Mycoplasma iowae.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0347345},
doi = {10.1371/journal.pone.0347345},
pmid = {41996362},
issn = {1932-6203},
mesh = {Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; *Mycoplasma/genetics/drug effects/metabolism ; Genetic Markers ; *Drug Resistance, Bacterial/genetics ; *Bacterial Proteins/genetics/metabolism ; Promoter Regions, Genetic ; },
abstract = {Mycoplasma iowae is an economically significant pathogen that causes reduced hatchability, late embryo mortality and leg deformities, chondrodystrophy and skeletal lesions in poults. While prevention is essential in the control of infection, the appropriate administration of antibiotics may reduce economic losses during outbreaks. As a first step in the exploration of antimicrobial resistance mechanisms in M. iowae, target modification and efflux pump activity were examined in the present study. Point mutations were analyzed in previously described antibiotic binding sites in the whole genome sequences of 99 M. iowae strains. Mismatch amplification mutation assays (MAMAs) were designed and validated for the differentiation of mutations corresponding to elevated minimum inhibitory concentration (MIC) values for fluoroquinolones. Broth microdilution assays were performed to evaluate the effect of efflux pump inhibitors. In the presence of orthovanadate (OV), MIC values were significantly lower than in the absence of OV for spiramycin, tilmicosin, tylosin and oxytetracycline, which may indicate the presence of an active efflux system in M. iowae. Putative promoter regions of efflux-related genes were predicted and characterized. Genetic mutations, previously described in other bacteria, were described to be associated with elevated fluoroquinolone, macrolide and lincomycin MICs in M. iowae, although certain resistant phenotypes remained unexplained, promoting future examinations for deeper insights. The developed MAMAs may support rapid identification of M. iowae strains with elevated MIC values for fluoroquinolones. The better understanding of the efflux pump mechanisms enables the development of alternative methods for the support of therapy against this pathogen.},
}

Microbial Sensitivity Tests
*Anti-Bacterial Agents/pharmacology
*Mycoplasma/genetics/drug effects/metabolism
Genetic Markers
*Drug Resistance, Bacterial/genetics
*Bacterial Proteins/genetics/metabolism
Promoter Regions, Genetic

@article {pmid41996550,
year = {2026},
author = {Bechtner, J and Hosek, J and Schwab, C},
title = {Fecal Material of Captive Wild Animals as Source of CAZymes With Application Potential.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {27},
number = {8},
pages = {e70315},
doi = {10.1002/cbic.70315},
pmid = {41996550},
issn = {1439-7633},
support = {grant NNF22OC0079746//Novo Nordisk Fonden/ ; grant AU FF-F-2020-7//Aarhus Universitets Forskningsfond/ ; },
mesh = {Animals ; *Feces/microbiology ; *Animals, Wild/microbiology ; *Glycoside Hydrolases/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Gastrointestinal systems of mammals and birds host taxonomically complex and functionally diverse microbial communities. Microbial activities contribute to community functioning and interaction with the host but can also be exploited as a source of novel enzymes or other industrially relevant microbial traits. With the overall goal to identify new resources for carbohydrate-active enzymes (CAZymes), we bioprospected fecal microbial communities of the little-explored source of captive wild animals. Using dbcan3, we identified a CAZyome dominated by glycosyl hydrolases (GHs) specialized in degrading oligo- and polysaccharides with much lower diversity and abundance of glycosyl transferases, carboxyl esterases, polysaccharide lyases, and redox enzymes with auxiliary activity. CAZyome profiles differed between animals depending on gut physiology and diet. Crude cell extracts conferred hydrolytic activity against compositionally and structurally diverse polysaccharides and nitrophenyl-sugar analogs. We identified five candidate GH68 and GH70 enzymes with the potential to produce oligo- and polysaccharides from sucrose, highlighting that fecal metagenomes are a source of rare CAZymes with industrial relevance. Taken together, we exemplify the functional potential captive wild animal fecal microbiota and suggest such a gene pool as a largely untapped resource for the discovery of novel biotechnological applications.},
}

Animals
*Feces/microbiology
*Animals, Wild/microbiology
*Glycoside Hydrolases/metabolism
Gastrointestinal Microbiome

@article {pmid41996772,
year = {2026},
author = {Haydar, MS and Alzate Zuluaga, MY and Astolfi, S and Del Buono, D and Cesco, S and Pii, Y},
title = {Nanoparticle-rhizosphere crosstalk: Insights into transformation, microbial interaction, plant uptake and translocation.},
journal = {Chemosphere},
volume = {403},
number = {},
pages = {144936},
doi = {10.1016/j.chemosphere.2026.144936},
pmid = {41996772},
issn = {1879-1298},
abstract = {For soil-applied engineered nanomaterials, the rhizosphere is the critical frontline zone where they encounter crop roots, microbes, and soil, determining their agronomic potential and environmental risks. Within this dynamic interface, nanoparticles (NPs), depending on their surface chemistry, particle size, properties, and composition, undergo physicochemical and biological transformations that govern their stability, dissolution, mobility, availability, and ecotoxicological outcomes. This review synthesizes current mechanistic evidence linking root exudation patterns, microbial activity, and soil physico-chemical conditions to NPs aggregation, dissolution, redox conversions, and eco-/bio-corona formation. Microbial extracellular polymeric substances, low-molecular-weight metabolites, siderophores, and biofilms further reshape particle speciation, modulating ion release, immobilization, nutrient availability, and potential toxicity to soil biota and crops. Once inside roots, nanoparticles follow multiple uptake routes, including apoplastic diffusion, endocytosis, plasmodesmata-mediated transport, and vascular translocation, while undergoing in-planta transformations into ionic or ligand-bound forms with distinct physiological and agronomical consequences. These processes are strongly context-dependent, shaped by plant species, development stage, NPs concentration, and soil-climate conditions, and mediated by a tripartite molecular dialogue among NPs, microbes, and plant signalling pathways that regulate root system architecture, rhizosphere microbial recruitment, and nutrient acquisition efficiency. Advances in high-resolution and multi-omics tools-such as synchrotron-based spectroscopy, single-particle ICP-MS, NanoSIMS, stable-isotopic tracers, and metagenomics are offering new insights into these interactions under realistic agricultural scenarios. We propose an integrated agroecological framework linking rhizospheric NPs transformations to plant uptake and responses, emphasizing the need for standardized exposure metrics, realistic concentrations, and long-term field trials for safe and sustainable nanotechnology use in agriculture.},
}

@article {pmid41996801,
year = {2026},
author = {Chen, Y and Sun, Y and Yang, Y and Hu, S and Cui, K and Zhu, C and Fu, XZ and Li, CX and Jiang, P and Huang, Q},
title = {Differential distribution characteristics of heavy metal resistance genes and driving mechanisms of heavy metal speciation in river-lake system sediments.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142080},
doi = {10.1016/j.jhazmat.2026.142080},
pmid = {41996801},
issn = {1873-3336},
abstract = {River-lake systems are critical zones for heavy metal biogeochemical cycling, yet the mechanisms linking heavy metal pollution to heavy metal resistance genes (MRGs) across hydrological gradients remain elusive. This study selected the Chaohu Lake Basin as a representative river-lake system to investigate the distribution characteristics of MRGs and their driving mechanisms on heavy metal speciation. Based on metagenomic sequencing and ICP-MS analysis of 78 sediment samples collected in wet and dry seasons, we found that the resistome was dominated by multi-metal, Cu, and As resistance genes, with the arsenic resistance gene pstA identified as a consistent network hub. MRGs diversity and network complexity exhibited significant seasonal depletion and spatial heterogeneity along the river-lake gradient. Heavy metals were predominantly fractionated into the stable residual phase; however, the river-lake gradient significantly influenced the spatial distribution of bioavailable fractions. Crucially, Structural Equation Modeling (SEM) revealed a seasonal shift in the regulatory mechanisms controlling heavy metal speciation. In the wet season, the river-lake system operated under a "biologically mediated" mode, where MRGs directly facilitated the mobilization of the reducible fraction. In the dry season, it shifted to a "physicochemically driven" mode, governed primarily by basic physicochemical factors. These findings highlighted that seasonal dynamics and the river-lake gradient jointly coordinated heavy metal fate through a complex interplay of biotic and abiotic factors, providing molecular-level insights for pollution management in continuous aquatic systems.},
}

@article {pmid41996860,
year = {2026},
author = {Ji, Z and Fu, Z and Miao, L and Hang, D and Gu, A},
title = {Relationship between pesticide exposure, gut microbiota, and hypertension.},
journal = {Environment international},
volume = {211},
number = {},
pages = {110250},
doi = {10.1016/j.envint.2026.110250},
pmid = {41996860},
issn = {1873-6750},
abstract = {BACKGROUND: Both pesticide exposure and gut dysbiosis have been independently linked to an elevated risk of hypertension. However, the extent of interaction between these two factors remains poorly characterized in human populations.

METHODS: In a population-based study involving 218 adults from Jiangsu Province, China, we quantified pesticides in serum using LC-MS/MS and analyzed the gut microbiome via metagenomic sequencing. An environmental risk score (ERS) was created to represent pesticide exposure. We also used Mendelian randomization (MR) to identify causal gut microbial genera, multivariable regression for associations, and mediation analysis for potential pathways. Machine learning models were applied to differentiate hypertensive from non-hypertensive individuals based on a combined set of features.

RESULTS: Fourteen pesticides, notably bentazone and perfluorohexanesulfonate, were significantly associated with increased hypertension risk, and the ERS based on these pesticides further corroborated this association. Additionally, the overall microbiota composition was significantly associated with both pesticide exposure and hypertension status. Observational and MR analyses consistently identified branches of Clostridium as potentially contributors to hypertension risk. An interaction was observed between pesticide exposure and specific bacterial taxa. Specifically, high ERS combined with high Catenibacterium (both defined using a median split) abundance increased hypertension risk nearly fourfold. A neural network model achieved the best differentiation performance (AUC = 0.897) for hypertension.

CONCLUSIONS: Exposure to specific pesticides, particularly bentazone, is associated with increased hypertension risk. This relationship is influenced by interactions with gut bacteria and partially mediated through alterations in the gut microbiota. These findings highlight the role of environmental chemicals and the gut microbiome in the development of hypertension.},
}

@article {pmid41997101,
year = {2026},
author = {Liu, W and Yang, Y and Bian, J and Li, X and Lu, Z},
title = {Niche adaptation of marine heterotrophic nitrification-aerobic denitrification bacterium in mariculture wastewater treatment: Synergistic mechanism of nitrogen removal and sulfamethoxazole biotransformation.},
journal = {Water research},
volume = {300},
number = {},
pages = {125914},
doi = {10.1016/j.watres.2026.125914},
pmid = {41997101},
issn = {1879-2448},
abstract = {Efficient removal of nitrogen from mariculture wastewater (MW) by marine heterotrophic nitrification-aerobic denitrification (MHNAD) bacteria is an innovative approach to overcoming salt inhibition. However, their performance and survival strategies under long-term antibiotics exposure in real wastewater conditions remain elusive, limiting practical implementation. Here, a bench-scale biofloc-biological aerated filter (BF-BAF) system treating real MW was operated for 100 days. Under long-term exposure to sulfamethoxazole (SMX) (1.3 ± 0.4 mg/L), the stabilized nitrogen removal system achieved removal efficiencies of 97.2 ± 2.5 % and 91.6 ± 4.1 % for NH4[+]-N and SMX, respectively. MHNAD bacteria, dominated by Marinobacter and Celeribacter, were enriched (2.3-67.7 %) and identified as habitat-specific genera, while the growth of Nitrosomonas (0.02-0.04 %)-the sole ammonia-oxidizing bacteria (AOB) detected-was severely inhibited. Metagenomic analysis revealed upregulation of nitrogen assimilation (glnA and nasA) and denitrification genes (nirK and norC), driving niche differentiation. A novel MHNAD strain, Marinobacter sp. LAN01, was isolated from the settleable bioflocs. Multi-omics analysis indicated that LAN01 adapts to SMX stress by reallocating intracellular resources via NH4[+]-N assimilation (glnA-driven) and facilitates SMX degradation via N-acetylation, S-N bond cleavage, and hydrolysis. Nucleotide metabolism was downregulated to suppress DNA synthesis, thereby reducing the accumulation and transfer of sulfonamide resistance genes (sul1 and sul2). Overall, this works revealed the mechanism of synergistic nitrogen removal and antibiotic degradation, and highlighted the long-term application potential of BFT, paving the way for sustainable MW treatment.},
}

@article {pmid41997104,
year = {2026},
author = {Zhang, X and Weng, S and Zhen, Z and Tang, Z and Huang, X},
title = {Phage predation mitigates the spread of antibiotic resistance in anaerobic digestion under shortened solid retention times.},
journal = {Water research},
volume = {300},
number = {},
pages = {125921},
doi = {10.1016/j.watres.2026.125921},
pmid = {41997104},
issn = {1879-2448},
abstract = {Optimizing anaerobic digestion (AD) via shortening solid retention time (SRT) enhances methane recovery, yet the mechanistic impact of SRT reduction on antimicrobial resistance (AMR) dissemination remains underexplored. Herein, we employed metagenomics to investigate how reduced SRTs (from 60 to 5 days) regulated the dynamics of antibiotic resistance genes (ARGs) mediated by pathogenic hosts, plasmids, and phages in mesophilic and thermophilic AD systems. Shortened SRTs elevated ARG abundance by 5.9-388% under mesophilic conditions, driven by the SRT-elicited niche expansion of antibiotic-resistant bacteria (ARB) and the persistent dominance of ESKAPE pathogen Enterobacter hormaechei, the latter intrinsically harbored and transmitted high-risk ARGs (aadA, sul1, and qacEdelta1) via multi-resistant plasmids. Notably, plasmid-mediated and cross-phylum transmission substantially enhanced ARG mobility. Contrastingly, thermophilic conditions eliminated ARGs by 17.0-57.1% under shortened SRTs, driven by thermophilic ARB niche differentiation. Crucially, both homology search and phage-host prediction indicated the lack of ARGs matching between phages and hosts under reduced SRTs, denoting a negligible contribution of transduction to horizontal ARG transfer. The dominance of lytic phages (85.3%), intensified lytic phage-host interactions, and heightened abundance of lytic phages lysing ARB collectively imposed potent phage top-down control over ARG hosts, with the lytic phage predation on ARB being validated by laboratory assays. We also identified 9 high-risk digestate ARG biomarkers (ANT(6)-Ia, aadA, ermA, mel, qacEdelta1, sul1, tet44, tetM, tetQ) by integrating criteria of prevalence, gene mobility, clinical relevance, and host pathogenicity to inform monitoring. Overall, this study underlined the significance of phage predation in mitigating ARG propagation under shortened SRTs, informing the development of novel AMR control strategies in AD practices.},
}

@article {pmid41997155,
year = {2026},
author = {Yang, W and Lee, YJ and Silva, RMB and DeLiberto, A and Yancey, CE and McCallum, D and Buss, JA and Moncion, R and Ong, JL and Mabuchi, M and Hough, DM and Weigele, PR and Ettwiller, LM},
title = {The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.},
journal = {Molecular cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molcel.2026.03.027},
pmid = {41997155},
issn = {1097-4164},
abstract = {Mining phages for new enzymatic activities continues to be important for the development of new tools for biotechnology. In this study, we used MetaGPA-a method linking genotype to phenotype in metagenomic data-to identify deoxycytidine deaminases, a protein family highly associated with cytosine modifications in metaviromes. Unexpectedly, a subset of these deaminases exhibited a preference for 5-methylcytosine (5mC) over cytosine (C) in both mononucleotide and single-stranded DNA substrates. In a methylome-sequencing workflow, deamination of 5mC by these enzymes enabled direct conversion of methylated cytosine while completely eliminating any background deamination of unmodified cytosine. This direct conversion allows for precise identification of methylated sites at single-base resolution with unmatched sensitivity enabling broad applications for the simultaneous sequencing of genome and methylome.},
}

@article {pmid41997245,
year = {2026},
author = {Wang, X and Wang, X and Ai, S and Wu, F and Xi, J and Li, J and Liu, Z},
title = {Harnessing native microbes: Intermittent aeration for bioremediation of phenolic compounds contaminated freshwater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134641},
doi = {10.1016/j.biortech.2026.134641},
pmid = {41997245},
issn = {1873-2976},
abstract = {Phenolic pollutants pose persistent risks to freshwater ecosystems due to their toxicity, structural diversity, and resistance to biodegradation. This study investigated microbial community dynamics, gene-level adaptation, and biostimulation strategies for phenolic removal using native microbial community. Metagenome analyses revealed marked taxonomic shifts under phenolic stress, with engineered systems favoring modular cooperative degradation, whereas the natural community relied on dominance of stress-resistant taxa and inter-phylum horizontal gene transfer (HGT). Functional profiling identified 28 candidate KEGG Orthologs (KOs), including oxidative, ring-cleaving, and energy-support genes, enriched across core degraders such as Pseudomonas, Sphingobium, and Bordetella. Biostimulation assays demonstrated oxygen availability as the primary limiting factor: intermittent aeration (IA) enhanced phenolic degradation by 29%, while IA combined with activated carbon (IA + AC) achieved up to 75% improvement, especially for complex compounds like bisphenol A (BPA) and nitrophenol. Predictive modeling based on KO abundance and stimulation methods (R[2] = 0.75-0.88) successfully predicted degradation performance across 50 natural samples. While IA + AC provided the most consistent improvement, 15 communities achieved comparable efficiencies under IA alone, highlighting context-dependent biodegradation capacities linked to HGT and metabolic pathway diversity. These findings establish a scalable predictive framework and emphasize the importance of tailoring biostimulation strategies to native microbial capacities, offering a practical route for in situ bioremediation of phenol-contaminated freshwater systems.},
}

@article {pmid41998153,
year = {2026},
author = {Li, S and Zhu, D and Saha, K and Kundu, BB and Sonkusale, S and Britton, RA and Ajo-Franklin, CM},
title = {Synthetic microbial co-cultures for modular bioelectronic sensing in diverse environments.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41998153},
issn = {1546-1696},
support = {W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; R01 AI173318/AI/NIAID NIH HHS/United States ; R01 AI173318/AI/NIAID NIH HHS/United States ; },
abstract = {Whole-cell bioelectronic sensors are particularly well-suited for environmental and health monitoring as they can be integrated into compact electronic devices for field deployment over extended periods. However, current engineering strategies lack modularity, are limited to a few microbial chassis and depend on specialized instruments for signal detection. We present the electroactive co-culture sensing system (e[-]COSENS), a plug-and-play system for whole-cell bioelectronic sensor development. Here a 'sender' bacterium produces electron mediators in response to analytes and a 'receiver' bacterium utilizes the electron mediators to generate electrical signals via extracellular electron transfer. Modularly swapping the sender bacterium and its associated genetic sensing elements achieved bioelectronic sensing of metals, small molecules and peptides in distinct environments, such as urban waterways, milk, saliva and microbial communities. We designed a centimeter-sized bioelectronic device for portable signal readout using a household digital multimeter. The e[-]COSENS system simplifies the whole-cell bioelectronic sensor design and expands the potential of bioelectronic sensor applications.},
}

@article {pmid41998361,
year = {2026},
author = {Thiyagarasaiyar, K and Paul, D and Kerttula, J and Keski-Karhu, M and Soosaar, K and Mander, Ü and Hallin, S and Machacova, K and Pumpanen, J and Siljanen, HMP},
title = {Genetic Potential for N2O Metabolism in Tree Tissues: Insights From Nitrogen Cycling Gene Prevalence and nosZ Diversity Across Tree Species.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02773-8},
pmid = {41998361},
issn = {1432-184X},
}

@article {pmid41998362,
year = {2026},
author = {Parida, D and Dhali, SL and Bala, K and Nogueira, R},
title = {Early microbial colonization study of daily-use plastics exposed to river water.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41998362},
issn = {1573-0972},
}

@article {pmid41792614,
year = {2026},
author = {Zhou, J and Gu, T and Zhou, J and Zeng, X and Liu, Y and Chen, F and Hu, Y and Li, S},
title = {Clostridium zhoujianii sp. nov., a novel gram-negative species isolated from bat feces and its genetic characteristics.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41792614},
issn = {1471-2180},
support = {Qiankehe Platform Talent-ZDSYS [2023] 004//Key Laboratory of Microbiol and Infectious Disease prevention &Control in Guizhou Province/ ; Guo Jikong Zong Ren Han [2024] 122//Project for Public Health Talent Cultivation of China/ ; Qiankehe [2025] 024//The local science foundation of Guizhou Province guided by the Central Committee of China/ ; },
abstract = {UNLABELLED: A strictly anaerobic, rod-shaped bacterial strain, designated LP20ᵀ, was isolated from the intestinal contents of bats collected in Qiandongnan, China. Phylogenetic analysis of the 16 S rRNA gene revealed that strain LP20ᵀ shared its highest similarity with Clostridium paraputrificum ATCC 25780ᵀ (98.10%), a value below the accepted threshold for species delineation. Whole-genome sequencing further supported its taxonomic novelty, with ANI, dDDH, and AAI values to the closest relatives all falling well below species-level cutoffs. Strain LP20ᵀ exhibited unusual Gram-stain-negative morphology, grew optimally at 30–37℃ and pH 7.0–8.0, and possessed distinctive fatty acid and polar lipid profiles, including the presence of an unidentified aminophospholipid. Phenotypic assays revealed several metabolic and enzymatic traits that differentiated LP20ᵀ from its closest phylogenetic neighbors. 16 S rRNA amplicon sequencing and metagenomic screening confirmed the presence of this species in multiple bat hosts, suggesting a wider distribution within bat gut microbiomes. Functional genomic analysis indicated enrichment of genes involved in carbohydrate metabolism and a limited antibiotic resistance profile. Based on polyphasic evidence, strain LP20ᵀ represents a novel species within the genus Clostridium, for which the name Clostridium zhoujianii sp. nov. is proposed. The type strain is LP20ᵀ (= JCM 37970ᵀ = GDMCC 1.5627ᵀ).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04884-1.},
}

@article {pmid41796297,
year = {2026},
author = {Shi, K and He, Q and Wang, S and Guo, J},
title = {An adaptive weight self-distillation deep learning framework for phenotype prediction from longitudinal gut microbiome data.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41796297},
issn = {1471-2180},
support = {62562022//National Natural Science Foundation of China/ ; Guike ZY22096025//Special Funds for Guiding Local Scientific and Technological Development by the Central Government/ ; 2025JJA170175//Guangxi Natural Science Foundation/ ; Z-C20241570//Guangxi Health Commission Self-Funded Research Project/ ; },
abstract = {BACKGROUND: The gut microbiota plays a vital role in maintaining human health. In recent years, extensive researches has focused on phenotype prediction in relation to various diseases, with the gut microbiota as a key predictor. Nevertheless, most existing studies rely on single-time-point analyses, which are insufficient to capture the dynamic patterns of host states and temporal variations inherent in longitudinal data.

RESULTS: In this study, we propose a deep learning framework, AWSD-CNN-LSTM, designed to classify host phenotypes using longitudinal metagenomic data. Unlike conventional approaches that treat each time point as an independent sample, our method models the sequential samples of each individual as a whole, integrating convolutional neural network (CNN) and long short-term memory network (LSTM) to effectively capture temporal dependencies in longitudinal microbiome sequencing data. In addition, the model incorporates an adaptive point-wise self-distillation mechanism to more accurately characterize host-specific patterns. Compared with state-of-the-art methods, AWSD-CNN-LSTM demonstrates superior performance on the PROTECT, DIABIMMUNE, and Infants datasets, achieving area under the receiver operating characteristic curve (AUC) values of 0.896, 0.813, and 0.894, respectively.

CONCLUSIONS: For the task of disease phenotype classification based on temporal data, we propose a novel framework that effectively captures the characteristics of time-series data and achieves high accuracy across multiple datasets. Our approach holds promise as a potential new tool for microbial knowledge discovery.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04922-y.},
}

@article {pmid41987827,
year = {2026},
author = {Bornbusch, SL and Thacher, PR and Francisque, M and DeCandia, AL and Bortner, R and Garelle, D and Kendrick, EL and Maslanka, MT and Muletz-Wolz, CR},
title = {How "pro" are probiotics for wildlife species? Novel data, lack of evidence, and future directions.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag036},
pmid = {41987827},
issn = {2730-6151},
abstract = {Treatments that aim to purposefully manipulate host-associated microbiomes are now prevalent in human and animal medicine. Probiotics that contain live bacteria are purported to improve microbiome function and host health. Although research is advancing, commercial probiotic development has outpaced empirical study of probiotic efficacy. Probiotics are widely used in ex-situ wildlife care despite a lack of empirical study or support. We interrogate the relevance of commercial probiotics in ex-situ wildlife by (a) sequencing the composition of commercial probiotics used to treat wildlife, (b) comparing the probiotic sequences to data on the microbiomes of >900 animal species, and (c) characterizing the effects of a commercial probiotic on probiotic colonization, prevalence of a potential enteric pathogen (Clostridium perfringens), and metagenomic function in endangered black-footed ferrets (Mustela nigripes). We found mislabeling and potential contaminants in probiotics marketed for a range of species. The probiotic bacteria were rare or absent in published animal microbiomes. In black-footed ferrets, probiotic treatment induced minimal probiotic colonization, negligible functional change, and limited influence on the potential enteric pathogen. Given our findings, which reiterate concerns about the efficacy of commercial probiotics across human and animal sectors, greater effort must be put towards identifying species-specific probiotic candidates and studying alternative microbial therapies for wildlife under human care.},
}

@article {pmid41987902,
year = {2026},
author = {De, R and Kanungo, S and Mukhopadhyay, AK and Dutta, S},
title = {Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the identification of prospective prognostic markers and probiotics to protect from diarrhea: a brief report.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1729497},
pmid = {41987902},
issn = {2235-2988},
mesh = {*Diarrhea/microbiology/prevention & control ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Cross-Sectional Studies ; *Probiotics/therapeutic use ; Feces/microbiology ; Pilot Projects ; Female ; Prognosis ; Male ; High-Throughput Nucleotide Sequencing ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Prospective Studies ; Biomarkers/analysis ; DNA, Bacterial/genetics ; },
abstract = {INTRODUCTION: Diarrhea is a leading contributor of mortality globally. To mitigate its disease burden, improved prognosis and alternative therapeutic approaches must be deployed. A cross-sectional gut microbiome analysis of 23 non-diarrheal and 5 diarrheal fecal samples was conducted with the aim of meeting the WHO's GAPPD (Global Action Plan for Pneumonia and Diarrhea) goals.

HYPOTHESIS: Next-generation sequencing is a potent tool being increasingly used for epidemiological surveillance. It can help in the comparison of the structural diversity of the gut microbiome between diarrheal and non-diarrheal samples, thereby aiding in the identification of prospective prognostic and therapeutic candidates.

AIM: The pilot study was designed to identify prospective taxa that were comparatively enriched in non-diarrheal samples and to predict gut microbial community interactions.

METHODOLOGY: 16S rRNA amplicon sequencing and subsequent analysis were undertaken for taxonomic profiling and abundance interpretation of OTUs.

RESULTS: Significant differences between the two groups with respect to structural composition was revealed. Firmicutes was the most abundant phylum in the majority of the samples. The B/F ratio was consistently <1 in all diarrheal samples. A significant difference in the mean B/F ratio of the two groups was found. Proteobacteria was significantly more abundant in the diarrheal group. On the other hand, Prevotellaceae was the most abundant family in non-diarrheal samples and was suppressed significantly in diarrheal samples. Streptococcaceae was the most abundant family in 60% of diarrheal samples; where Streptococcaceae was suppressed, Bacteroideaceae and Nocardiaceae were the most abundant. In non-diarrheal samples, where Streptococcaceae was almost completely suppressed, Bifidobacteriaceae was the most abundant and significantly suppressed other families. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in the non-diarrheal group. Prevotella copri was the most abundant species in 70% of non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples, while they were absent in diarrheal samples.

CONCLUSION: The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. To our knowledge, this is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome, distinctly addressing the gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics to protect the endemic population from diarrhea and help in achieving Sustainable Development Goals 2 and 3.},
}

*Diarrhea/microbiology/prevention & control
*Gastrointestinal Microbiome/genetics
Humans
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
Cross-Sectional Studies
*Probiotics/therapeutic use
Feces/microbiology
Pilot Projects
Female
Prognosis
Male
High-Throughput Nucleotide Sequencing
Adult
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Prospective Studies
Biomarkers/analysis
DNA, Bacterial/genetics

@article {pmid41988145,
year = {2026},
author = {Liu, L and Wang, L and Zhang, P and Gan, M and Liujiang, R and Cheng, G and Ge, M},
title = {Neonatal herpes simplex virus encephalitis: a single-center retrospective study of 14 cases.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1740937},
pmid = {41988145},
issn = {2296-2360},
abstract = {BACKGROUND: This single-center retrospective study aims to analyze the clinical characteristics, treatment strategies, and outcome at discharge of neonatal-onset herpes simplex virus encephalitis (NHSE).

METHODS: We conducted a single-center retrospective case review of infants diagnosed with NHSE at the Children's Hospital of Fudan University between February 1, 2016, and February 1, 2024. Clinical data, including demographics, clinical symptoms, laboratory findings, neuroimaging results, treatment regimens, and outcomes at discharge, were collected and analyzed.

RESULTS: A total of 14 infants with NHSE (7 males, 7 females) were identified at our center, with a median age at diagnosis of 26 days (range: 7-51 days). Initial symptoms predominantly included fever and seizures, with neurological involvement (e.g., seizures, lethargy, irritability or altered mental states) in 13 cases. Physical examinations, such as bulging anterior fontanel, were noted. Herpes simplex virus (HSV)-DNA was detected in 13 cases (6 HSV-1, 7 HSV-2) through cerebrospinal fluid (CSF) polymerase chain reaction (PCR) or metagenomic testing. Among these, 9 cases were identified via CSF-PCR, with 7 testing positive on the initial examination and 2 on repeated testing. Notably, 6 cases were diagnosed using metagenomic next-generation sequencing (mNGS), all of which yielded positive results on the first test. Ten out of the 12 children often exhibited temporal lobe spikes on video electroencephalograms (VEEGs). Early magnetic resonance imaging (MRI) revealed cytotoxic edema, progressing to multicystic encephalomalacia. All received acyclovir antiviral treatment. Seven discontinued treatments, one was referred for ocular lesions, and six improved and were discharged.

CONCLUSIONS: In this single-center cohort, NHSE often presents with nonspecific fever and seizures, with late onset and absent indicative rashes, complicating early diagnosis. For newborns suspected of having NHSE, early CSF HSV-DNA testing and prompt antiviral treatment are essential to improve outcomes. Metagenomic sequencing is especially valuable for accurate, rapid diagnosis when conventional methods fail.},
}

@article {pmid41989131,
year = {2026},
author = {Schön, ME and Schvarcz, CR and Malkewitz, SV and Hinner, FC and Koslová, A and Mersdorf, U and Schimm, F and Rickert, S and Pozhydaieva, N and McBeain, K and Hackl, T and Schneider, AC and Barenhoff, K and Höfer, K and Edwards, KF and Steward, GF and Fischer, MG},
title = {Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag093},
pmid = {41989131},
issn = {1751-7370},
abstract = {Giant DNA viruses are ubiquitous among unicellular eukaryotes and occur in marine, freshwater, and terrestrial environments. Despite intense metagenomic data mining, their strain-level diversity remains largely unexplored. Here we introduce a model system comprising four isolates of a giant virus called ChlorV, which infects marine microalgae of the class Chlorarachniophyceae (Rhizaria) from station ALOHA, Hawai'i. The ChlorV genomes are 469 kbp to 493 kbp long and encode approximately 400 proteins, at least 106 of which are present in purified virions. Although the four viral genomes are highly syntenic, they differ by several insertions and deletions that often encode methyltransferases. We found that some of these methyltransferase genes correlated with specific DNA methylation patterns in the same ChlorV strain. Our study describes the first giant viruses infecting the eukaryotic supergroup Rhizaria and demonstrates how viral strain-level variation in gene content and epigenetic features may affect eco-evolutionary processes in marine microalgae.},
}

@article {pmid41989380,
year = {2026},
author = {Hontelez, S and Guthrie, M and Stobernack, T and van Baarlen, P and Rousseau, C and Boks, MP and Pereira, RR and Boekhorst, J and Kleerebezem, M},
title = {Microbiome signatures correlate with diet-mediated ADHD symptom reduction.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2659400},
doi = {10.1080/19490976.2026.2659400},
pmid = {41989380},
issn = {1949-0984},
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology ; Child ; Male ; *Gastrointestinal Microbiome ; Female ; Feces/microbiology ; *Diet ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Attention-deficit hyperactivity disorder (ADHD) is one of the most common childhood neuropsychiatric conditions. Both (epi)genetic and environmental factors are suggested to contribute to the etiology of ADHD. In the last decade, nutrition has received considerable attention as a potential environmental factor triggering ADHD behavior, particularly applying a few-foods diet (FFD) has been shown to elicit considerable behavioral improvements. These studies are observational rather than investigating underlying molecular mechanisms. The present study included 79 children (boys aged 8-10) with ADHD following a progressive, i.e., increasingly restrictive, FFD diet for 5 weeks. Minimally invasive samples (feces, urine, blood, and buccal swabs) were collected before and after the intervention to obtain a multi-omics perspective of the dietary responses in the participating children. For 63% of the participating children, a more than 40% behavior score improvement was observed, with an average improvement of 73%. The strength of diet-induced changes in ADHD symptoms among children was significantly associated with the gut microbiome composition, particularly when analyzing species-stratified abundance profiles of previously characterized gut-brain modules in the fecal metagenomic data. While integrative multi-omics analysis did not identify composite signatures linked to symptom changes, the strongest multi-omics signal confirmed compliance with the dietary intervention. Our findings implicate a role of the gut microbiome and its metabolic capacity to communicate with the central nervous system in children with food-associated ADHD.},
}

Humans
*Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology
Child
Male
*Gastrointestinal Microbiome
Female
Feces/microbiology
*Diet
Bacteria/classification/genetics/isolation & purification

@article {pmid41989870,
year = {2026},
author = {Zhu, YC and Deng, Y and Zeng, JQ},
title = {Effects of concurrent Helicobacter pylori infection and small intestinal bacterial overgrowth on the gut microbiota and metabolic profiles: A multi-omics study.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02894},
pmid = {41989870},
issn = {1588-2640},
abstract = {This study investigated the synergistic effects of Helicobacter pylori (Hp) infection and small intestinal bacterial overgrowth (SIBO) on the gut microbiota structure and metabolic profiles and elucidate the underlying pathophysiological mechanisms. Forty-two patients with gastrointestinal symptoms were recruited and assigned to group A (Hp+ SIBO+), B (Hp+ SIBO-), C (Hp- SIBO+), or D (Hp- SIBO-) based on their Hp infection and SIBO status. Fecal samples were collected for metagenomic sequencing and untargeted metabolomic analysis. The associations between microbiota and metabolites were evaluated using alpha/beta diversity analysis, differential species screening, metabolite identification, and Procrustes/Spearman correlation analysis. Neither Hp infection nor SIBO significantly altered the alpha or beta diversity of the gut microbiota (both P > 0.05). However, specific shifts in microbial abundance were observed. Specifically, the abundance of short-chain fatty acid-producing bacteria such as Megamonas was significantly decreased in the SIBO+ groups. Metabolomic analysis revealed significant enrichment of inflammatory metabolites (e.g., prostaglandin derivatives) in group A, disordered bile acid conjugates (e.g., chenodeoxycholylisoleucine) and nucleotide metabolism in SIBO+ groups, and abnormal lipid/carbohydrate metabolism pathways in Hp+ groups. Multi-omics integration analysis indicated a strong coupling between the microbial structure and metabolic profiles (Procrustes analysis, P < 0.05). In group A, the abundance of Faecalibacterium and Hominenteromicrobium was negatively correlated with bile acid levels, suggesting impaired bile acid transformation. Hp infection and SIBO might synergistically exacerbate gut ecological and metabolic disorders by reshaping specific microbiota and metabolic networks (enhanced inflammatory response, disrupted bile acid circulation). Their co-occurrence produces additive effects, which could explain the aggravated clinical symptoms. This study provides a theoretical basis for interventions targeting microbiota-metabolite interactions, such as probiotics and bile acid modulators.},
}

@article {pmid41990029,
year = {2026},
author = {Sun, Y and Zhang, M and Wang, X and Huang, X and Yu, Y and Pan, H and Li, H and Shi, L and Yang, W and Zhang, C and Ding, B and Liu, X and Li, J and Qian, C and Cheng, B and Zhang, C and Ran, J and Li, M},
title = {Gut Microbiota of Gray Snub-Nosed Monkeys: Adaptation to Seasonal Variations Through Energy Compensation and Thermogenesis.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70092},
pmid = {41990029},
issn = {1749-4877},
support = {32330015//National Natural Science Foundation of China/ ; 32070404//National Natural Science Foundation of China/ ; QLKH [2023] 11//Guizhou Forestry Administration Scientific Research Project/ ; QLKH [2025] 11//Guizhou Forestry Administration Scientific Research Project/ ; //Investigation of Nationally Protected Wildlife Species in Tongren Region/ ; GZKPC-2025-01//Guizhou Province/ ; QCZH [2023]82//Protection and Restoration of Forests and Grasslands in 2024 from the Central Finance/ ; [2023]188//Guizhou Science and Technology Support Plan Project/ ; QKHFQ [2023]009//Construction of Capacity for Ecosystem Optimization and Innovation in Key Ecological Zones of Guizhou Province/ ; YWZ[2024]005//Construction of Capacity for Ecosystem Optimization and Innovation in Key Ecological Zones of Guizhou Province/ ; QKHPT[2021]5625//Guizhou Outstanding Young Scientist Program/ ; QJJ[2024]337//Natural Science Research Projects of the Education Department of Guizhou Province/ ; [2022]031//Guizhou Provincial Department of Education/ ; 2024BS011//Doctoral Program of the Science Research Foundation of Guizhou Education University/ ; 2024BS006//Doctoral Program of the Science Research Foundation of Guizhou Education University/ ; },
abstract = {As an extremely endangered species, the gray snub-nosed monkey (Rhinopithecus brelichi) relies on its gut microbiota for adaptation to environmental changes, particularly in coping with fluctuations in energy and nutrient availability. In this study, we employed metagenomic, metatranscriptomic, and widely targeted metabolomic analyses to characterize the gut microbiota of gray snub-nosed monkeys. Based on metagenome-assembled genomes (MAGs), we recovered 1229 non-redundant MAGs. Among them, a total of 103 MAGs exhibited significant seasonal variation, primarily belonging to the phyla Bacillota_A, Bacteroidota, and Bacillota_I. During winter, metagenomic results indicated that the gut microbiota exhibited an enhanced capacity to produce energy substrates such as amino acids, short-chain fatty acids, pyruvate, and acetyl-CoA, with increased conversion of these substrates. Metatranscriptomic analysis further confirmed that key carbon cycle-related genes and metabolic pathways were significantly upregulated in winter. Additionally, metabolite analysis indicated significantly lower levels of amino acids in winter fecal samples, suggesting that gray snub-nosed monkeys efficiently absorb and utilize metabolites, with the gut microbiota likely contributing to energy compensation. Notably, the gut microbiota may also synergistically support the host's non-shivering thermogenesis, helping maintain physiological functions in extreme cold conditions. This study elucidates the cooperative role of the gut microbiota in helping gray snub-nosed monkeys adapt to seasonal environmental fluctuations, providing new insights into how gut microbiota optimize winter energy utilization-an understanding with important implications for the conservation of endangered wildlife.},
}

@article {pmid41990134,
year = {2026},
author = {Chen, X and Wang, Y and Feng, J and Chen, H and Yao, B and Li, F and Yang, Q and Qu, J},
title = {Hypobaric hypoxia affects gut microbiota of rats through affected community assembly, reduced network resilience, and metabolic reprogramming.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag039},
pmid = {41990134},
issn = {1574-6941},
abstract = {In host-microbe interactions, host diet and environmental stress are key driving factors shaping the gut microbiota. Although previous studies have shown that hypoxia affects the structure and function of the gut microbiota in rodents, most have relied on 16S rRNA gene sequencing and lacked analysis of community assembly mechanisms, co-occurrence networks, and functional pathways. Here, we used metagenomic next-generation sequencing (mNGS) to examine the gut microbiota of rats exposed to hypobaric hypoxia (WH, simulated 6000 m altitude) compared to WL group (2100 m altitude). Hypoxia significantly altered β-diversity of gut microbiota, but did not affect its α-diversity. Community assembly was primarily governed by stochastic processes, with hypoxia stress reducing their impact. Microbial co-occurrence networks were dominated by positive correlations, although network resilience and stability declined under hypoxia. Helicobacter and Eubacterium were identified as high-abundance differentiating genera, and Akkermansia muciniphila was significantly enriched in WH group. Functional analysis revealed alterations in pathways related to protein synthesis and carbohydrate metabolism, suggesting that hypoxia may affect nutrient utilization by the host. Overall, these findings provide a comprehensive view of how hypoxic stress reshapes the gut microbiota of rats, offering new insights into microbial dynamics under environmental stress.},
}

@article {pmid41990403,
year = {2026},
author = {Zhao, J and Li, T and Huang, H and Servellita, V and Sotomayor-Gonzalez, A and Yakovleva, O and Wang, X and Ragupathy, V and Biswas, S and Barilko, P and Sun, E and Huynh, S and Hunsicker, M and DeQuach, J and Morales, JD and Highbarger, H and Dewar, RL and Porth, C and Denny, TN and McGivern, DR and Chiu, CY and Hewlett, I},
title = {Development and genomic characterization of a diverse HIV-1 variant reference panel for nucleic acid-based testing.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {184},
number = {},
pages = {105941},
doi = {10.1016/j.jcv.2026.105941},
pmid = {41990403},
issn = {1873-5967},
abstract = {BACKGROUND: The high worldwide genetic diversity of HIV poses significant challenges for its detection and diagnosis by nucleic acid testing (NAT). Well-characterized reference panels are important for evaluating the analytical performance of HIV tests.

OBJECTIVE: To develop a reference panel for HIV NAT that reflects the genetic diversity of circulating strains.

STUDY DESIGN: HIV was cultured from blood specimens collected from blood donor and clinical sites in Cameroon. Metagenomic next-generation sequencing in combination with spiked primer enrichment along with Sanger sequencing were used to sequence 101 cultured HIV-1 samples representing 59 strains. To establish an HIV-1 variant reference panel, a diverse subset of cultured viruses was analyzed in multiple laboratories with different assays to determine consensus viral loads.

RESULTS: Near full-length HIV-1 genomes, with an average of 9589 base pairs (bp), were recovered from 37 (62.7%) of the 59 strains. The whole genome sequences of 28 strains exhibited more than 95% similarity to our previously reported genomes obtained by Sanger sequencing. An HIV variant reference panel for NAT comprising 18 diverse HIV-1 strains was developed. The panel included four subtypes, four circulating recombinant forms, and eight unique recombinant forms. Strains were prepared at low (n = 18, 2.53 log10 copies/mL), medium (n = 18, 3.61 log10 copies/mL), and high viral loads (n = 15, 4.66 log10 copies/mL), yielding 51 panel members in total.

CONCLUSION: This diverse HIV reference panel can be used to evaluate the performance of HIV NAT and is available upon request to developers and manufacturers of HIV tests.},
}

@article {pmid41990622,
year = {2026},
author = {Liu, L and Wang, C and Qi, WK and Zhang, SJ and Li, YY and Peng, Y},
title = {Mechanisms of aerobic simultaneous nitrogen removal under low COD/N conditions: Diffusion-reaction coupling and particle size effects via self-recirculating microgranular system.},
journal = {Water research},
volume = {300},
number = {},
pages = {125937},
doi = {10.1016/j.watres.2026.125937},
pmid = {41990622},
issn = {1879-2448},
abstract = {Nitrogen removal from ammonium-rich, carbon-limited wastewater remains constrained in continuous-flow microgranular sludge systems. In this study, a three-stage up-flow self-recirculating microgranular sludge reactor was developed to investigate nitrogen removal mechanisms under low chemical oxygen demand to nitrogen ratios (COD/N < 2.5) and high influent total nitrogen (TN > 400 mg/L). During long-term operation, the system achieved stable removal efficiencies of ammonium (98%), TN (94%), and COD (95%). Under ammonium stress, particle size decreased to a mean diameter of 249.2 μm, forming stable, non-flocculent microaggregates. Microgranules < 0.2 mm exhibited pronounced simultaneous partial nitrification-denitrification (SPND) and simultaneous nitrification-denitrification (SND) activities under aerobic conditions. Simultaneous nitrogen removal (SNR) activity peaked at 0.52 g TN/(g VSS·d) at a DO of 2 mg/L. In contrast, microgranules > 0.2 mm primarily followed SND-dominated pathways. Their SNR activity increased with DO and reached a maximum of 0.46 g TN/(g VSS·d). Microbial community and metagenomic analyses revealed a redox-stratified functional structural organization. Rubrivivax (11.5%) dominated the surface layer, likely linking organic matter degradation with nitrogen oxide reduction. Hyphomicrobium (11.9%) was enriched in intermediate layers and was associated with SND. In the core, the co-enrichment of Hyphomicrobium (7.2%) and Methylotenera (6.1%) supported the coupling of SND and SPND processes. These findings provide a basis for improving nitrogen removal from ammonium-rich, carbon-limited wastewater.},
}

@article {pmid41990624,
year = {2026},
author = {Wang, G and Yang, F and Xu, S and Lin, D and Yang, R and Yan, P and Chen, Y and Fang, F and Guo, J},
title = {Microbial niches and metabolism drive spatial heterogeneity of hydroxyapatite precipitation in aerobic granular sludge.},
journal = {Water research},
volume = {300},
number = {},
pages = {125923},
doi = {10.1016/j.watres.2026.125923},
pmid = {41990624},
issn = {1879-2448},
abstract = {Biologically induced phosphate precipitation (BIPP) in aerobic granular sludge (AGS) provides a promising approach to address phosphorus removal instability and granule structural fragility in practical applications. However, the roles of microbial communities, ecological niches, and metabolic activities in driving phosphate precipitation and shaping its spatial distribution within AGS remain underexplored. This study systematically investigates AGS physicochemical properties, reactor performance, phosphorus speciation, precipitation composition and distribution, microbial community structure, and metabolic activity using sodium propionate (RP) and sodium acetate (RA) as sole carbon sources. The findings reveal for the first time the mechanisms by which microbial communities, ecological niches, and metabolic functions regulate phosphate precipitation and determine its spatial heterogeneity. BIPP contributes 22.6% and 60.1% of total phosphorus removal in RP and RA, respectively, thereby enhancing phosphorus removal efficiency and granule structural stability. Multi-scale analyses-including Standards, Measurements and Testing, Raman spectroscopy, X-ray diffraction, scanning electron microscopy-energy dispersive X-ray spectroscopy, and micro-computed tomography-reveal that hydroxyapatite (HAP) predominantly accumulates in the outer region of RP granules but in the inner region of RA granules. Periodic water quality variations, fluorescence in situ hybridization, granule-stratified sequencing, and metagenomic analyses indicate that the spatial heterogeneity of HAP is driven by the ecological niche separation and metabolic activities of polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). In RP granules, PAO‑driven anaerobic phosphate release creates a high‑phosphate microenvironment, which promotes HAP formation in the granule outer region. In RA, GAO‑mediated endogenous denitrification increases local pH, thereby inducing HAP precipitation in the granule interior. Overall, this study elucidates the mechanisms underlying the spatial heterogeneity of phosphate precipitation in AGS from the perspectives of microbial community structure, ecological niches, and metabolic pathways. These findings provide guidance for optimizing AGS systems to achieve efficient phosphorus removal and stable operation.},
}

@article {pmid41990657,
year = {2026},
author = {Ye, YQ and Lin, D and Shen, LQ and Wu, D and Li, Y and Wang, YF and Zhu, D},
title = {Viral communities as mirrors and vectors: Tracing antibiotic resistome distribution and dissemination across diverse habitats in Macao.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142056},
doi = {10.1016/j.jhazmat.2026.142056},
pmid = {41990657},
issn = {1873-3336},
abstract = {Virus-mediated transmission of antibiotic resistance genes (ARGs) is increasingly recognized as a significant threat to global human health. However, the role of viral communities in ARGs dissemination across highly urbanized coastal regions containing with diverse habitats remains poorly understood. Here, we conducted shotgun metagenomic analyses on 49 samples collected from four habitats (urban sewage, soil, sediment, and coastal water) in Macao China, to characterize their viral communities and resistome profiles. We identified 23,579 viral operational taxonomic units (vOTUs) and 965 ARGs subtypes across these habitats. Viral community composition and total ARGs profiles exhibited system-scale spatial concordance, with a distance-decay trend, together with a positive association between viral ARGs and total ARGs abundance. Approximately 62.80% of ARGs subtypes were shared among habitats, suggesting a high degree of compositional overlap in resistome profiles among habitats. Urban sewage and coastal waters showed enriched viral abundance and ARGs diversity, with high-risk ARGs in sewage being 10.3- and 24.7-fold greater than in soils and sediments. High-risk ARGs (e.g., macB, udg) showed co-occurrence with virulence factor genes (VFGs) on viral contigs, and prophages were identified within Pseudomonadota and Bacteroidota, the dominant groups for phages and ARGs. The co-occurrence of ARGs and auxiliary metabolic genes (AMGs) within these hosts suggests that phages may facilitate the propagation of ARGs while enhancing host adaptability, thereby promoting their enrichment. By integrating multi-habitat analyses in human-impacted coastal regions, this study highlights the potential role of viruses in ARGs dissemination and informs resistome surveillance.},
}

@article {pmid41991090,
year = {2026},
author = {Lee, JS and Jeon, YJ and Kim, TH and Khan, W and Yun, YM},
title = {Multiscale destabilization of anaerobic digestion by chloramphenicol: Divergence between methanogen detectability and methane recovery.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134635},
doi = {10.1016/j.biortech.2026.134635},
pmid = {41991090},
issn = {1873-2976},
abstract = {Antibiotic residues in livestock waste streams can affect anaerobic digestion (AD), yet their functional impact on microbial viability and metabolic pathways remains unclear. This study evaluated concentration-dependent effects of chloramphenicol (CAP) by integrating process kinetics, cellular integrity, dissolved-phase responses, and functional gene profiles. Methane yield was maintained at ≤ 50 mg/L CAP but declined sharply at higher concentrations, reaching near-complete inhibition at 1,000 mg/L. Estimated inhibition thresholds were derived as IC30 = 285 mg/L, IC60 = 535 mg/L, and IC90 = 852 mg/L from the fitted concentration-response relationship. Severe inhibition coincided with residual organic acid accumulation, pH decline, and enrichment of propionate and butyrate fractions with undetectable acetate. Flow cytometry revealed a marked CAP-dependent decline in intact biomass, with live-cell (P2) counts decreasing from 4.8 × 10[6] cells/mL in the control to 1.0 × 10[5] cells/mL at 1,000 mg/L, accompanied by increased forward- (FSC-A) and side-scatter (SSC-A) area indicative of structural stress. Fluorescence excitation-emission matrix (FEEM) analysis showed concentration-dependent enrichment of soluble microbial products (SMPs) fluorescence, and inoculum-only incubation confirmed biomass-associated solubilization under CAP exposure. Although methanogens remained numerically detectable (76.0% vs. 81.1%), key genes related to cofactor synthesis and electron transfer (comD, frhB, fwdA/fwdC, mcr) declined substantially at 1,000 mg/L. These convergent signals were consistent with multiscale destabilization. Given that microbial activity was not directly measured, the observed discrepancy between methanogen detectability and methane recovery should be interpreted as indicative of a potential functional imbalance rather than definitive evidence of functional decoupling.},
}

@article {pmid41991504,
year = {2026},
author = {Elhani, I and Bredon, M and Enea, D and Desmons, A and Arrive, L and Bazille, C and Lefevre, A and Aouba, A and Bigot, A and de Moreuil, C and Alonso, I and Blasco, H and Creusot, L and Dupuy, C and Emond, P and Krasniqi, P and Lamaziere, A and Oeuvray, C and Rainteau, D and Svrcek, M and Rolhion, N and Sokol, H and Georgin-Lavialle, S},
title = {Functional changes in the gut microbiota are associated with the intestinal phenotype in A20 haploinsufficiency.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {37},
number = {4},
pages = {e70343},
doi = {10.1111/pai.70343},
pmid = {41991504},
issn = {1399-3038},
support = {//snfmi-remi/ ; //fai2r/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Haploinsufficiency ; Female ; Male ; *Tumor Necrosis Factor alpha-Induced Protein 3/genetics ; Child ; Phenotype ; Feces/microbiology ; Adolescent ; *Inflammatory Bowel Diseases/genetics ; Child, Preschool ; Bile Acids and Salts/metabolism ; },
abstract = {BACKGROUND: A20 haploinsufficiency (HA20) is an autoinflammatory disease driven by pathogenic variants in TNFAIP3, which plays a crucial role in regulating immune responses. The clinical manifestations of HA20 resemble those of inflammatory bowel disease (IBD), with prominent gastrointestinal (GI) involvement. Given the well-established association between gut microbiota alterations and IBD, this study aimed to describe the GI involvement of HA20 patients and to investigate their fecal microbiota using shotgun sequencing and metabolomics.

METHODS: This study included 16 HA20 patients and 22 healthy age and sex-matched controls. GI clinical phenotype, liver imaging, and liver and GI tissue histology were assessed. Shotgun metagenomic sequencing was performed on fecal DNA. Fecal metabolomic profiling of bile acids, short-chain fatty acids (SCFAs), and tryptophan metabolites was performed.

RESULTS: Liver imaging revealed chronic liver disease in 3/5 patients, showing as liver dysmorphia and portal hypertension. Histological analysis showed lymphoplasmocytic infiltrate of the GI tract and the liver. The fecal microbiota of HA20 patients was characterized by marked alterations, including a reduction in microbial diversity and an increase in the pro-inflammatory bacterium Ruminococcus gnavus. Microbial bile acid deconjugation and desulfation were impaired. Additionally, tryptophan metabolism was altered, with a shift towards the kynurenine pathway.

CONCLUSION: Our results show that HA20 is associated with gut microbiota alterations and significant disruptions in metabolic pathways, particularly involving bile acids. These alterations could contribute to the chronic inflammation observed in HA20. These findings highlight the role of the gut-liver axis and of mucosal barrier dysfunction in HA20.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Haploinsufficiency
Female
Male
*Tumor Necrosis Factor alpha-Induced Protein 3/genetics
Child
Phenotype
Feces/microbiology
Adolescent
*Inflammatory Bowel Diseases/genetics
Child, Preschool
Bile Acids and Salts/metabolism

@article {pmid41991911,
year = {2026},
author = {Liu, Y and Huang, P and Zhang, C and Dong, Q and Wang, X and Tian, F and Zhao, J and Sun, Z and Chen, L and Chen, W and Zhai, Q},
title = {A microbiome catalog of Chinese traditional artisanal cheeses provides insights into functional and microbial diversity.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71929-4},
pmid = {41991911},
issn = {2041-1723},
support = {32425044//China National Funds for Distinguished Young Scientists/ ; 2022YFD2100703//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; },
abstract = {Cheese has been consumed globally over millennia and serves as a natural reservoir of diverse microorganisms. Chinese traditional cheeses rely on natural fermentation and have unique physiochemical and microbial characteristics compared to European cheeses. However, there is a major knowledge gap in the understanding of Chinese cheese microbiome. Here, we present a curated Cheese microbiome catalog (cCMC) consisting of 3327 high-quality metagenome-assembled genomes, recovered from metagenomic sequencing of 235 Chinese cheese samples covering all traditional artisanal cheese-producing regions in China, together with 198 publicly available non-Chinese cheese metagenomic datasets. This catalog represents 395 nonredundant species spanning 50 families, including 85 putative novel species. We identified six lactic acid bacteria species enriched in Chinese cheeses, and confirmed that the unique presence of Acetobacteraceae contributes to improving the nutritional quality of Chinese cheese. A total of 8851 biosynthetic gene clusters were detected from cCMC, with over 57% classified as novel. We demonstrated that SNP-level variations among different Lactobacillus helveticus strains are associated with differences in β-galactosidase thermostability. Using the cCMC database, we developed a synthetic microbial community as the starter culture for Qula, a yak milk-based Chinese cheese produced by the Tibetans. Overall, the cCMC provides a comprehensive resource of cheese to enable future attempts on large-scale industrial production of naturally fermented cheeses with distinctive ethnic features.},
}

@article {pmid41965542,
year = {2026},
author = {Priya, S and Sridhar, SB and Shareef, J and Wadhwa, T and Balusamy, B and Meenakshi, DU and Sundram, S and Malviya, R},
title = {Epidemiology, diagnosis and emerging therapies for Lyme disease of the Northern Hemisphere.},
journal = {International journal of emergency medicine},
volume = {19},
number = {1},
pages = {},
pmid = {41965542},
issn = {1865-1372},
abstract = {BACKGROUND: Lyme disease is the most widespread tick-borne infection in the Northern Hemisphere and is challenging to diagnose and treat due to its changing clinical presentation, antigenic variation, tissue tropism, and the expanding distribution of vectors. This review includes ecology, pathogenesis, diagnostics, treatment, post-treatment, prevention, and novel translational approaches.

METHODS: A literature review was conducted to include literature published between January 2000 and March 2026 in PubMed/MEDLINE, Scopus, and Web of Science, with landmark studies used where applicable. Original research, clinical trials, systematic reviews, and major public health reports were prioritised.

RESULTS: Two-tier serology is the most common diagnostic technique, but it has limited sensitivity in early infection and does not distinguish between active and past infection. Culture and PCR are only useful in a few instances. The use of new technologies such as multiomics biomarkers, metagenomics, T-cell assays, and AI-enhanced diagnostics is promising but has not yet been tested in a prospective multicentre study. Most of the early and disseminated disease can be treated with standard antibiotics, whereas the long-term therapy of PTLD is not justified and can cause more adverse effects. These preventive and curative advancements involve VLA15 vaccination, anti-tick and reservoir-specific approaches, microbiome-engineered vectors, and anti-persister/ biofilm.

CONCLUSION: Lyme disease requires combined prevention, improved diagnostics, enhanced biomarker research, and well-designed PTLD trials. The short-term benefits will be based on the optimisation of existing diagnostics and vector control, and the long-term benefits will be based on rigorous validation of vaccines, biomarkers, and specific therapies.},
}