@article {pmid41045876,
year = {2025},
author = {Gebert, J and Böhnke-Brandt, S and Zander, F and Indenbirken, D and Bergmann, L and Krohn, I and Perner, M},
title = {Linking microbial community composition, microbial biomass and extracellular polymeric substances to organic matter lability gradients in sediments of the tidal Elbe River.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180614},
doi = {10.1016/j.scitotenv.2025.180614},
pmid = {41045876},
issn = {1879-1026},
mesh = {*Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; Germany ; Biomass ; *Extracellular Polymeric Substance Matrix ; *Microbiota ; Archaea ; Bacteria ; *Environmental Monitoring ; },
abstract = {The port of Hamburg represents a transition zone between upstream, shallow regions of high net primary production and downstream deep and more turbulent waters in the tidal Elbe River in northwestern Germany. Correspondingly, strong gradients of degradable organic matter (OM) on a distance of a few river kilometers had been identified. This study links microbial community composition using 16S metagenomic amplicons and extracellular polymeric substances (EPS) composition to the observed gradients of sediment OM lability. It was hypothesized that lability gradients caused by higher concentrations of biogenic, autochthonous OM upstream and greater share of already stabilized OM downstream reflect in gradients of microbial community composition, diversity and EPS characteristics. Indeed, available OM was found to act as key driver regulating syntrophic microbial community composition and associated metabolic features, with location-specific overriding the effect of seasonal variations. Upstream sites with high available OM featuring lower bacterial but increased archaeal diversity and elevated methane and carbon dioxide fluxes, whereas lower OM lability downstream fostered a more diverse bacterial but decreased archaeal diversity. The ratio between microbial taxon richness and biomass correlated inversely with OM transformation rates. These patterns also reflected in increased EPS concentration produced in response to metabolic needs (i.e. polysaccharides and proteins), whereas structural components such as lipids, which can be more resistant under the prevailing anoxic conditions, remained more evenly distributed along the transect. Although bacterial relative abundances exceeded archaeal abundances (<1 %) by far, archaeal functional significance remained pivotal for the final release of carbon as methane and carbon dioxide under the mostly reducing conditions in the deposited sediment.},
}

*Geologic Sediments/microbiology/chemistry
*Rivers/microbiology/chemistry
Germany
Biomass
*Extracellular Polymeric Substance Matrix
*Microbiota
Archaea
Bacteria
*Environmental Monitoring

@article {pmid41412727,
year = {2026},
author = {Osswald, A and Wortmann, E and Wylensek, D and Kuhls, S and Coleman, OI and Peuker, K and Strigli, A and Ducarmon, QR and Larralde, M and Liang, W and Treichel, NS and Schumacher, F and Volet, C and Matysik, S and Kleigrewe, K and Gigl, M and Rohn, S and Guo, CJ and Kleuser, B and Liebisch, G and Schnieke, A and Ridlon, JM and Bernier-Latmani, R and Zeller, G and Zeissig, S and Haller, D and Flisikowski, K and Clavel, T and Ocvirk, S},
title = {Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer.},
journal = {Gut},
volume = {75},
number = {8},
pages = {1505-1519},
doi = {10.1136/gutjnl-2024-332243},
pmid = {41412727},
issn = {1468-3288},
mesh = {Animals ; *Diet, Western/adverse effects ; Humans ; *Colorectal Neoplasms/microbiology/metabolism/etiology ; Mice ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/physiology ; Deoxycholic Acid/metabolism ; Swine ; Disease Models, Animal ; Female ; Feces/microbiology ; Cell Proliferation ; Colon/microbiology ; Mice, Inbred C57BL ; Germ-Free Life ; Eubacteriales ; },
abstract = {BACKGROUND: Western diet and associated production of secondary bile acids (BAs) have been linked to the development of sporadic colorectal cancer (CRC). Despite observational studies showing that secondary BAs produced by 7α-dehydroxylating (7αDH+) gut bacteria are increased in CRC, a causal proof of their tumour-promoting effects is lacking.

OBJECTIVE: Investigate the causal role of BAs produced by 7αDH+ gut bacteria in CRC.

DESIGN: We performed feeding studies in a porcine model of CRC combined with multi-omics analyses and gnotobiotic mouse models colonised with 7αDH+ bacteria or a genetically modified strain to demonstrate causality.

RESULTS: Western diet exacerbated the CRC phenotype in APC [1311/+] pigs. This was accompanied by increased levels of the secondary BA deoxycholic acid (DCA) and higher colonic epithelial cell proliferation. The latter was counteracted by the BA-scavenging drug colestyramine. Metagenomic analysis across multiple human cohorts revealed higher occurrence of bai (BA inducible) operons from Clostridium scindens and close relatives in faeces of patients with CRC. Addition of these specific 7αDH+ bacteria (C. scindens/Extibacter muris) to defined communities of gut bacteria led to DCA production and increased colon tumour burden in mouse models of chemically or genetically induced CRC. A mutant strain of Faecalicatena contorta lacking 7αDH caused fewer colonic tumours in azoxymethane/dextran sodium sulfate treated mice and triggered less epithelial cell proliferation in human colon organoids compared with wild-type F. contorta.

CONCLUSION: This work provides functional evidence for the causal role of secondary BAs produced by gut bacteria through 7αDH in CRC under adverse dietary conditions, opening avenues for future preventive strategies.},
}

Animals
*Diet, Western/adverse effects
Humans
*Colorectal Neoplasms/microbiology/metabolism/etiology
Mice
*Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome/physiology
Deoxycholic Acid/metabolism
Swine
Disease Models, Animal
Female
Feces/microbiology
Cell Proliferation
Colon/microbiology
Mice, Inbred C57BL
Germ-Free Life
Eubacteriales

@article {pmid42106412,
year = {2026},
author = {Guo, L and Holyoak, GR and DeSilva, U},
title = {Insights from healthy mares reveal that mammalian uteri harbor a diverse virome.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42106412},
issn = {2045-2322},
mesh = {Animals ; Female ; Horses/virology ; *Uterus/virology/microbiology ; *Virome/genetics ; Phylogeny ; Microbiota ; Genome, Viral ; Bacteriophages/genetics ; },
abstract = {The Earth's estimated 10[31] virions, primarily phages, significantly impact microbial ecosystems. Despite their abundance, viromes remain relatively understudied-particularly in domestic animals. While recent studies have described a dynamic commensal microbiome in mammalian uteri, no research has yet characterized the commensal virome in a mammalian uterus. In this study, we report for the first time the presence of a sparse, but diverse native virome in the equine uterus. The resulting virome database consists of 513 non-redundant viral genomes (> 2 kb). Taxonomic annotations revealed the prevalence of taxadominated by the genera Gammaretrovirus, Mamastrovirus, Sapovirus and Rosenblumvirus. Notably, 75% of the assembled genomes represented novel species. Phylogenetic analysis revealed distinct clades suggesting unexplored viral diversity within the uterine environment. Furthermore, bacterial hosts for equine uterine phages were predicted, aligning with previous studies' findings. Most notably, the study identified antibiotic resistance genes within the virome, hinting at potential gene transfer mechanisms between bacteria and viruses. This study establishes the first uterine virome of any mammal, shedding light on a previously unexplored domain. The findings highlight the potential for phage therapy in reproductive infectious diseases and the importance of understanding the maternal gestational environment. Moreover, the study emphasizes the need for further research to expand the uterine virome databases and deepen our understanding of uterine microbiome and its implications for animal and human health.},
}

Animals
Female
Horses/virology
*Uterus/virology/microbiology
*Virome/genetics
Phylogeny
Microbiota
Genome, Viral
Bacteriophages/genetics

@article {pmid42108251,
year = {2026},
author = {Yin, M and Chen, X and Lu, R and Dong, Y and Luo, W and Tang, Z and Zeng, M and Xu, Y and Qing, Y and Xi, C and Feng, X and Guo, H and Mo, S and Luo, J},
title = {Diversity of fecal viromes and zoonotic risk assessment in captive wild felids using viral metagenomics.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42108251},
issn = {2045-2322},
support = {(Grant No. HX2023115P).//This research was supported by the grant for "Metagenomic Analysis of Viruses Carried by Amur Tigers and Leopards" (Grant No. HX2023115P)./ ; },
mesh = {Animals ; *Feces/virology ; *Metagenomics/methods ; *Virome/genetics ; *Felidae/virology ; Risk Assessment ; Animals, Wild/virology ; *Zoonoses/virology ; Phylogeny ; DNA Viruses/genetics ; *Viruses/genetics/classification ; },
abstract = {Emerging viral diseases-particularly zoonotic pathogens-affect the health and conservation of endangered felids, including Panthera tigris altaica (Amur tiger) and Panthera pardus (leopard). To address this challenge, we employed a viromics approach to investigate the diversity of the fecal virome in wild felids and assess its zoonotic potential. Using in-depth metagenomic sequencing and analysis of fecal samples from captive wild felids housed in a wildlife institution, this study characterized the enteric virome and evaluated associated risks. A total of 18 viral families and 48 viral genera were identified. The DNA virus community exhibited stability in abundance and composition, dominated by the phyla Heunggongvirae and Bamfordvirae. Within Heunggongvirae, the class Caudoviricetes was the core component, with its abundance aligning with the intestinal bacterial community, suggesting a potential role of these bacteriophages in regulating microbial ecology. Additionally, sequences of the family Poxviridae, homologous to Variola virus (VARV), were detected. In contrast, the RNA virus community displayed higher diversity and variability, with the order Ortervirales as the predominant group. Sequences highly homologous to feline leukemia virus (FeLV) were repeatedly identified, suggesting potential latent infections. The detection of sequences related to rare environmental viruses, such as Casadabanvirus, highlights the potential risk of cross-species virus transmission under captive conditions. Stability analysis revealed that dominant DNA virus groups exhibited low abundance variability across samples. In contrast, unclassified RNA viral taxa showed higher abundance variability. KEGG functional annotation mapped DNA viral contigs primarily to microbial metabolic modules. Conversely, RNA assemblies extensively mapped to eukaryotic pathways (e.g., arachidonic acid and energy metabolism); due to the total nucleic acid extraction methodology, these mappings primarily reflect co-extracted host transcriptomic background rather than viral-encoded functions, providing an indirect snapshot of the concurrent enteric microenvironment. These baseline data delineate the virome structure in captive environments and provide practical targets for zoological biosecurity and proactive veterinary surveillance.},
}

Animals
*Feces/virology
*Metagenomics/methods
*Virome/genetics
*Felidae/virology
Risk Assessment
Animals, Wild/virology
*Zoonoses/virology
Phylogeny
DNA Viruses/genetics
*Viruses/genetics/classification

@article {pmid42108276,
year = {2026},
author = {Saha, PK and Sar, P and Sarkar, S and Mukherjee, D and Kazy, SK},
title = {Deep subsurface rock-hosted chemolithotrophic bacterial communities exhibited differential CO2 assimilation and bioconversion potential under varying oxygen level.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42108276},
issn = {2045-2322},
support = {MoES/P.O.(Seismo)/1(383)/2020 dated February 10, 2022//Ministry of Earth Sciences (MoES), Government of India/ ; },
mesh = {*Carbon Dioxide/metabolism ; *Bacteria/metabolism/genetics/classification ; *Oxygen/metabolism ; *Chemoautotrophic Growth ; Metagenomics ; Metabolomics ; *Microbiota ; },
abstract = {Deep continental subsurface hosts diverse microbial ecosystems that are primarily driven by chemolithoautotrophy. In this study, we investigated deep continental igneous rock-hosted bacterial populations enriched under microoxic (ME) and anoxic (AE) conditions. Metataxonomic, metagenomics and metabolomics approaches, along with physiological analyses, were performed to elucidate community composition, CO2 utilization and possible bioconversion potential of subsurface rock enrichment cultures under chemolithoautotrophic conditions. Following prolonged incubation, ME enrichments resulted in higher microbial growth with greater species diversity than the AE cultures. Ralstonia and unclassified Comamonadaceae were predominant in both the enrichment conditions. On the other hand, Cellulomonas, Phenylobacterium, Deinococcus, Desulfurispora, etc. were relatively abundant in ME, and Solimonas, Curvibacter, Caulobacter, Novosphingobium, Anaeromyxobacter, unclassified Clostridia, etc. were abundant in AE communities. CO2/H2 utilization and organic acids production were greater in ME enrichments. Shotgun metagenomics and predictive metabolic profiling revealed CBB cycle as the predominant carbon fixation pathway in ME, whereas WL pathway was prominent in AE. Genes for hydrogen, sulfur, and nitrogen metabolisms were observed in both the enrichment cultures. HRLC-MS based untargeted metabolomics indicated the presence of valuable metabolites (organic acids, osmolytes, lipids/amides) in rock cultures, reflecting the potential of deep subsurface microorganisms for CO2 utilization and possible bioconversion to valuable biomolecules.},
}

*Carbon Dioxide/metabolism
*Bacteria/metabolism/genetics/classification
*Oxygen/metabolism
*Chemoautotrophic Growth
Metagenomics
Metabolomics
*Microbiota

@article {pmid42148573,
year = {2026},
author = {Raad, R and Mann, A and Pal, A and Parra, A and Strawn, L and Hamilton, A and Critzer, F and den Bakker, HC},
title = {Metagenomic profiling of bacterial (16S) and fungal (ITS) communities on d'Anjou pears during long-term controlled-atmosphere storage.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0411725},
pmid = {42148573},
issn = {2165-0497},
support = {AM22SCBPCA1133//Center for Produce Safety/ ; },
mesh = {*Pyrus/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Fungi/genetics/classification/isolation & purification ; *Food Storage/methods ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Fruit/microbiology ; Metagenomics ; Food Preservation/methods ; Food Microbiology ; },
abstract = {D'Anjou pears are routinely stored for up to nine months under controlled-atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears' natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends, and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability, or whether bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas (19.2% relative abundance [RA]) and Acinetobacter (3.31% RA). Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium (23.3% RA), Penicillium (9.28% RA), Botrytis (0.33% RA), and Mucor (0.14% RA) present at different storage stages.IMPORTANCEThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and possibly improve food safety throughout the supply chain.},
}

*Pyrus/microbiology
*Bacteria/genetics/classification/isolation & purification
*Fungi/genetics/classification/isolation & purification
*Food Storage/methods
RNA, Ribosomal, 16S/genetics
Microbiota/genetics
Fruit/microbiology
Metagenomics
Food Preservation/methods
Food Microbiology

@article {pmid42148581,
year = {2026},
author = {Wang, K and Zhang, D and Shen, K and Qiu, Y and Deng, B and Zhou, J and Qiu, S},
title = {Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0377525},
pmid = {42148581},
issn = {2165-0497},
support = {//Guizhou Province 2020 Science and Technology Support Plan Project/ ; },
mesh = {Fermentation ; Multiomics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Alcoholic Beverages/microbiology/analysis ; *Flavoring Agents/metabolism/analysis ; Metagenomics ; China ; Microbiota ; Metagenome ; Metabolomics ; *Archaea/genetics/classification/metabolism/isolation & purification ; },
abstract = {Daqu is an essential fermentation starter that drives the formation of the characteristic flavor of Maotai-flavor liquor, yet the ecological and metabolic mechanisms underlying its regional differentiation and maturation remain poorly resolved. Here, we performed genome-resolved metagenomic and untargeted metabolomic analyses on 48 new and aged Daqu samples collected from four major Maotai-flavor liquor-producing regions in Guizhou Province, China. We reconstructed 163 high-quality metagenome-assembled genomes (MAGs) spanning 16 bacterial and 3 archaeal phyla and identified 2,642 metabolites across ionization modes. Distinct regional microbial signatures were observed, with Jinsha Daqu showing the greatest genomic diversity and unique MAGs, whereas Maotai Daqu exhibited the highest community similarity with other regions. Aged Daqu significantly increased microbial richness and functional capacity, enriching thermophilic and spore-forming taxa (e.g., Bacillus, Lentibacillus, Kroppenstedtia) and enhancing carbohydrate-active enzymes (GH13, GH43, and GH3), amino acid degradation, lipid metabolism, and secondary metabolic pathways. Metabolomic profiling revealed elevated amino acid derivatives, fatty acids, esters, and phenolic compounds in aged Daqu, indicating intensified biochemical activity. Multi-omics integration linked dominant microorganisms-including Bacillus thuringiensis, Actinomycetaceae bacterium, and Methylocaldum szegediense to pyrazine biosynthesis, amino acid catabolism, and lipid oxidation, forming coordinated microbial-metabolite modules that underlie region-specific flavor precursor formation. These findings establish a mechanistic model in which microbial terroir, aging-driven succession, and metabolic specialization jointly shape the maturation and flavor potential of Maotai-flavor liquor.IMPORTANCEThis study provides the first genome-resolved, multi-omics framework for understanding how geographic origin and storage aging co-regulate the ecological assembly, functional specialization, and metabolic transformation of Maotai-flavor liquor. By linking specific MAGs, functional pathways, and key flavor precursors, our results offer mechanistic insights into microbial terroir and provide a scientific foundation for microbiome-guided optimization of Maotai-flavor liquor quality.},
}

Fermentation
Multiomics
*Bacteria/classification/genetics/metabolism/isolation & purification
*Alcoholic Beverages/microbiology/analysis
*Flavoring Agents/metabolism/analysis
Metagenomics
China
Microbiota
Metagenome
Metabolomics
*Archaea/genetics/classification/metabolism/isolation & purification

@article {pmid42148582,
year = {2026},
author = {Yu, L and Li, H and Yu, H and Zhou, Y and Wang, X and Luo, L},
title = {Inoculation of Bacillus velezensis SD24 enhancing the accumulation of tea catechin secondary metabolites.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0346925},
pmid = {42148582},
issn = {2165-0497},
support = {2023AH051003//Scientific Research Project of Universities in Anhui Province/ ; SKLTOF20210113//Open Fund of State Key Laboratory of Tea Plant Biology and Utilization/ ; },
mesh = {*Bacillus/metabolism/genetics/physiology ; *Catechin/metabolism/biosynthesis ; *Camellia sinensis/microbiology/metabolism ; Rhizosphere ; Secondary Metabolism ; Plant Leaves/metabolism/microbiology/chemistry ; Soil Microbiology ; Microbiota ; },
abstract = {Tea (Camellia sinensis) is a globally significant economic crop, and its desirable quality and health benefits are largely credited to catechin derivatives. Plant growth-promoting rhizobacteria (PGPR), such as Bacillus velezensis, are well-known for enhancing the environmental fitness and disease resistance of plants. However, the regulation of their impact on tea catechin biosynthesis remains unclear. While previous studies have focused on PGPR-facilitated growth promotion in crops like tomatoes and rice, the physiological mechanisms by which microbes regulate secondary metabolism in tea-especially under co-inoculation conditions-remain largely underexplored. This study examined the effects of B. velezensis SD24, isolated from tea rhizosphere soil, on catechin derivative accumulation of tea leaves by altering gene expression and the rhizosphere microbiome. Strain SD24 exhibited broad-spectrum antimicrobial activity against various pathogens due to behaving antimicrobial gene clusters. Tea plants inoculated with SD24 showed significantly increased levels of catechin derivatives in their leaves. This was likely achieved by upregulation of leucoanthocyanidin reductase and anthocyanidin reductase within the phenylpropanoid pathway. Additionally, chlorophyll content was increased. Transcriptomic analysis revealed a notable enrichment in biosynthesis of secondary natural products among the tea genes activated by SD24 inoculation. Metagenomic analysis further demonstrated that SD24 inoculation led to a restructuring of the tea rhizosphere microbiome. Notably, co-inoculation with Piriformospora indica, a beneficial endophytic fungus, suppressed SD24-induced gene expression and catechin accumulation, underscoring its antagonism toward SD24. These findings suggest that B. velezensis SD24 enhances tea quality, probably by transcriptionally activating the synthesis of catechin derivatives, a process associated with the restructuring of the rhizosphere microbiome.IMPORTANCEThe mechanisms through which plant growth-promoting rhizobacteria (PGPR) influence secondary metabolism in perennial crops remain poorly understood. This study demonstrates that Bacillus velezensis SD24, a tea rhizosphere isolate, significantly enhances the accumulation of health-beneficial catechin derivatives in tea leaves. This quality improvement is associated with transcriptionally upregulating key biosynthetic genes (LAR and ANR) and concurrently restructuring the rhizosphere microbiome. Furthermore, we reveal a critical antagonistic interaction, where the beneficial fungus Piriformospora indica suppresses these SD24-induced effects. Our findings provide crucial insights into how specific PGPR strains may directly enhance tea quality by affecting host plant metabolism and the root microbiome, highlighting the complex and tailored microbial interactions that could be harnessed for sustainable agriculture.},
}

*Bacillus/metabolism/genetics/physiology
*Catechin/metabolism/biosynthesis
*Camellia sinensis/microbiology/metabolism
Rhizosphere
Secondary Metabolism
Plant Leaves/metabolism/microbiology/chemistry
Soil Microbiology
Microbiota

@article {pmid42187250,
year = {2026},
author = {Liu, X and Kwok, L-Y and Zhang, W},
title = {Integrated gut microbiota and metabolome signatures revealed by deep metagenomic sequencing in post-stroke cognitive impairment with type 2 diabetes.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0024426},
pmid = {42187250},
issn = {2165-0497},
support = {2024ZY0168//Central Guiding Local Science and Technology Development Fund Project/ ; NMGIRT2411//Program of Innovative Research Team in Universities of Inner Mongolia Autonomous Region/ ; 2025QN03001//Natural Science Foundation of Inner Mongolia Autonomous Region of China/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/microbiology/metabolism ; *Metabolome ; *Gastrointestinal Microbiome ; *Cognitive Dysfunction/microbiology/metabolism/etiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Stroke/complications/microbiology/metabolism ; Male ; Fungi/classification/genetics/isolation & purification/metabolism ; Female ; Aged ; Feces/microbiology ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Metabolomics ; },
abstract = {UNLABELLED: Post-stroke cognitive impairment (PSCI) is significantly exacerbated in individuals with type 2 diabetes mellitus (T2DM), yet the underlying gut microbial and metabolic mechanisms remain unclear. In this study, baseline fecal samples from 28 diabetic PSCI (PSCI-DM) patients and 29 matched non-PSCI non-diabetic controls were subjected to deep metagenomic sequencing and untargeted metabolomics. Although alpha diversity was preserved, subtle but meaningful shifts were observed in bacterial and fungal composition. The PSCI-DM group exhibited depletion of beneficial butyrate-producing taxa, including Lachnospira spp. and Butyribacter intestini, and enrichment of Butyricimonas virosa. Five fungal species, including Torulaspora globosa and Pichia kudriavzevii, were significantly reduced. Metabolomic profiling identified 45 differentially abundant metabolites, with decreases in neuroprotective compounds, such as 9-oxononanoic acid, C16-ceramide, and nootkatone, and increases in metformin and bile acid derivatives. Abundances of microbial functional pathways linked to energy metabolism were elevated, while those involved in cofactor and neurotransmitter precursor synthesis were reduced. Significant correlations were found between specific microbes and metabolites, suggesting coordinated dysregulation across kingdoms. However, only a limited subset of microbial features remained independently associated with cognitive performance. Specifically, metabolites Nb-palmitoyltryptamine and pipecolic acid, and fungal species Pichia kudriavzevii showed significant correlations with Montreal cognitive assessment (MoCA) scores for cognitive impairment. These findings reveal a tripartite gut ecosystem signature in PSCI-DM and provide a mechanistic foundation for microbiota-targeted therapeutic strategies.

IMPORTANCE: In the context of type 2 diabetes, post-stroke cognitive impairment represents a clinically prevalent yet mechanistically underexplored condition with limited therapeutic options. This study combined metagenomic sequencing with non-targeted metabolomics to reveal the coordinated dysregulation of bacteria, fungi, and host-related metabolites in the gut of type 2 diabetes mellitus with post-stroke cognitive impairment (PSCI-DM) patients. The research indicates that cognitive impairment is not solely related to the overall decline in microbial diversity, but also involves the targeted reduction of neuroprotective butyrate-producing bacteria, the absence of specific gut fungi, and the corresponding reduction in neural activity and lipid metabolites. These findings collectively establish the gut microbiota-metabolite characteristics of PSCI-DM patients, providing a theoretical basis for targeted probiotic intervention measures to prevent or alleviate cognitive decline in diabetic patients after stroke.},
}

Humans
*Diabetes Mellitus, Type 2/complications/microbiology/metabolism
*Metabolome
*Gastrointestinal Microbiome
*Cognitive Dysfunction/microbiology/metabolism/etiology
Bacteria/classification/genetics/isolation & purification/metabolism
*Stroke/complications/microbiology/metabolism
Male
Fungi/classification/genetics/isolation & purification/metabolism
Female
Aged
Feces/microbiology
Metagenomics
High-Throughput Nucleotide Sequencing
Metabolomics

@article {pmid42206864,
year = {2026},
author = {Zhao, R and Biddle, JF},
title = {Community structure and methylation of microbes in an artificially forced sediment core.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0353325},
pmid = {42206864},
issn = {2165-0497},
support = {//W. M. Keck Foundation/ ; },
mesh = {*Geologic Sediments/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Archaea/genetics/classification/isolation & purification/metabolism ; *DNA Methylation ; Metagenome ; *Microbiota/genetics ; Epigenesis, Genetic ; Phylogeny ; },
abstract = {Epigenetic modifications, such as DNA methylation, may be used in prokaryotes for the adaptation of microbes to external environmental changes. In this study, we examined the microbial community structure, recovered the genomes of the dominant microbes, and tracked methylation in several dominant microbes in a 23-cm artificial sediment core formed in a settling tank that mimics the sediment formation process. Our results indicated that the prokaryotic communities only showed minor variations with depth and were dominated by bacteria (especially taxa of Deltaproteobacteria, Gammaproteobacteria, and Bacteroidota), while archaea (dominated by Bathyarchaeia) accounted for <5% of the total communities throughout the core. We detected methylation by analyzing metagenome sequencing data of methyl-specific enzyme-digested and undigested DNA. We recovered 72 high- or medium-quality metagenome-assembled genomes for the dominant taxa, for 7 of which we detected distinct downcore methylation patterns. This work highlights the diverse processes of epigenetic modification in response to the sediment burial process, which may have a long-term impact on the overall community fitness in the evolving energy-limited conditions in marine sediments.IMPORTANCEThis work reports changes in the epigenetic profiles of microbes buried in a sediment column formed under a controlled, artificially created environment. This approach removes confounding variables of bioturbation and changes in sediment flux. We also use an approach that is accessible for low amounts of DNA to determine methylation status.},
}

*Geologic Sediments/microbiology
*Bacteria/genetics/classification/isolation & purification/metabolism
*Archaea/genetics/classification/isolation & purification/metabolism
*DNA Methylation
Metagenome
*Microbiota/genetics
Epigenesis, Genetic
Phylogeny

@article {pmid42214368,
year = {2026},
author = {Karmarkar, B and Dhotre, D},
title = {Harnessing gut microbiome enzymes: Segatella copri and Stenotrophomonas maltophilia prolyl peptidases degrade gliadin peptides and improve epithelial barrier function in a celiac disease model.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0321425},
pmid = {42214368},
issn = {2165-0497},
mesh = {*Gliadin/metabolism ; *Celiac Disease/microbiology/metabolism ; Humans ; *Stenotrophomonas maltophilia/enzymology/genetics ; Caco-2 Cells ; *Gastrointestinal Microbiome ; *Prolyl Oligopeptidases/metabolism/genetics ; Intestinal Barrier Function ; Peptides/metabolism ; *Bacterial Proteins/metabolism/genetics ; },
abstract = {UNLABELLED: Celiac disease (CeD) is an autoimmune enteropathy triggered by gluten-derived peptides that resist gastrointestinal digestion, notably the proline-rich 33-mer and 11-mer gliadin epitopes. Here, we describe a rational, metagenome-based strategy to identify gut microbiome-derived prolyl peptidases capable of degrading these immunogenic peptides. Integrating metagenomic mining with structure-based in silico screening, we identified two novel enzymes PSP692 from Segatella copri and PSP464 from Stenotrophomonas maltophilia. Recombinant expression, purification, and characterization confirmed their activity under physiologically relevant conditions: PSP692 efficiently degrades the 33-mer at pH 6, while PSP464 targets the 11-mer at pH 4. Functional assays using CaCo-2 cell line, both in bi- and tri-dimensional assays, demonstrated that degradation of gliadin peptides by PSP692 and PSP464 significantly restored the expression of tight junction proteins (ZO-1 and occludin), reduced IL-6 secretion, and improved barrier integrity. These findings establish a foundational strategy for the discovery of microbiome-derived glutenases and provide both a compelling case and a methodology for data-driven discovery of functional enzymes that degrade immunogenic gliadin peptides, with translational potential as adjunct therapies in CeD and gluten-related disorders.

IMPORTANCE: Celiac disease affects 1.4% of the global population, and, as of date, a gluten-free diet (GFD) is the only therapy available. Adherence to GFD is difficult, and inadvertent exposure to gluten still occurs. To address this, various approaches are utilized to develop adjuvant therapies. These include recombinant enzymes that, to date, have been discovered by serendipity. We have outlined and validated a method to identify enzymes with potential from metagenomic data, which will also be validated experimentally.},
}

*Gliadin/metabolism
*Celiac Disease/microbiology/metabolism
Humans
*Stenotrophomonas maltophilia/enzymology/genetics
Caco-2 Cells
*Gastrointestinal Microbiome
*Prolyl Oligopeptidases/metabolism/genetics
Intestinal Barrier Function
Peptides/metabolism
*Bacterial Proteins/metabolism/genetics

@article {pmid42214386,
year = {2026},
author = {Sun, H and Dulencin, A and Kirn, TJ and Vo, J and Liachko, I and Rao, D and Manzano-Santana, J and Patel, E and Looi, C and Horton, DB and Barrett, E and Weidner, M and Bachmann, G and Panettieri, RA and Connor, BA and Rogova, M and Nagy-Szakal, D and Couto-Rodriguez, M and Kotwal, S and Wu, Q and Simon, J and Blaser, MJ and Dominguez Bello, MG},
title = {Autologous fecal microbiota transplantation restores the infant gut microbiome and metabolome after antibiotics: a case report.},
journal = {mBio},
volume = {17},
number = {7},
pages = {e0071126},
doi = {10.1128/mbio.00711-26},
pmid = {42214386},
issn = {2150-7511},
mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/adverse effects/administration & dosage ; Infant ; *Metabolome/drug effects ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/drug effects ; Feces/microbiology/chemistry ; Female ; Male ; Longitudinal Studies ; Amoxicillin/therapeutic use/adverse effects ; Metagenomics ; },
abstract = {UNLABELLED: Antibiotic exposure during infancy disrupts gut microbiome assembly during a critical developmental window. Strategies to restore these ecosystems remain limited. In the REPAIR trial (NCT06609980), eight infants were followed longitudinally; two received amoxicillin for otitis media, and one subsequently underwent autologous fecal microbiota transplantation (aFMT) using stool collected prior to antibiotic exposure. Shotgun metagenomics, Hi-C-assisted resistome profiling, and untargeted metabolomics were performed on samples collected before and after antibiotics. Amoxicillin treatment was associated with displacement of community structure, enrichment of antibiotic resistance genes (ARGs), and altered fecal metabolites, including short-chain fatty acids, bile acids, acylcarnitines, bilirubin derivatives, tricarboxylic acid (TCA) cycle metabolites, and amino acids. In the non-restored infant, microbiota composition and ARG profiles remained persistently altered during follow-up, accompanied by sustained metabolic divergence. In contrast, the aFMT-treated infant demonstrated convergence toward pre-antibiotic community structure, directional restructuring of ARG carriers -including reduction of β-lactam and tetracycline resistance genes- and metabolite profiles trending toward the pre-antibiotic baseline across analytical platforms. Although limited to a case-based comparison, these findings provide integrated ecological and functional evidence that aFMT may promote recovery following antibiotic perturbation during early-life microbiome development and support the rationale for larger controlled clinical trials.

IMPORTANCE: Antibiotic exposure in early life disrupts the developing gut microbiome during a critical window of host-microbe interaction. However, the extent to which these disturbances resolve naturally, or can be actively reversed, remains unclear. In this study, we use longitudinal sampling in infants to examine microbiome recovery following antibiotics, with and without autologous fecal microbiota transplantation (aFMT). We show that antibiotic exposure leads to coordinated disruptions in microbial composition, antibiotic resistance genes, and metabolic profiles. While partial recovery spontaneously occurs over time, faster and more extensive restoration toward the pre-antibiotic state is observed following aFMT. These findings provide insight into the ecological dynamics of microbiome reassembly in early life and highlight the potential of using controlled perturbations to understand microbiome resilience.

CLINICAL TRIALS: This study is registered with ClinicalTrials.gov as NCT06609980.},
}

Humans
*Anti-Bacterial Agents/therapeutic use/adverse effects/administration & dosage
Infant
*Metabolome/drug effects
*Fecal Microbiota Transplantation
*Gastrointestinal Microbiome/drug effects
Feces/microbiology/chemistry
Female
Male
Longitudinal Studies
Amoxicillin/therapeutic use/adverse effects
Metagenomics

@article {pmid42214685,
year = {2026},
author = {Jiang, TA and Prioult, G and Quann, E},
title = {Microbial Biotransformation of Polyphenols and Bioactive Substrates: Implications for Metabolite-Guided Synbiotics.},
journal = {The Journal of nutrition},
volume = {156},
number = {7},
pages = {101621},
doi = {10.1016/j.tjnut.2026.101621},
pmid = {42214685},
issn = {1541-6100},
mesh = {*Polyphenols/metabolism/pharmacokinetics ; Humans ; *Synbiotics ; Biotransformation ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism ; },
abstract = {BACKGROUND: Dietary bioactive compounds-including polyphenols, alkaloids, lignans, and amino acid-derived substrates-exert well-established effects on human health but are constrained by poor bioavailability. Only 5%-10% of ingested polyphenols are absorbed in the proximal gastrointestinal tract, while the remainder undergoes biotransformation by colonic microbiota into a diverse repertoire of bioactive metabolites. Accumulating evidence indicates that these microbially derived metabolites, rather than their parent compounds, are the primary mediators of systemic benefits due to superior bioavailability, metabolic stability, anti-inflammatory and antioxidant activity, and greater specificity in modulating host metabolic and signaling pathways.

OBJECTIVES: This review aimed to synthesize recent advances in the microbial biotransformation of dietary polyphenols, amino acids, glucosinolates, and related substrates, and to evaluate how these pathways influence metabolic, cardiometabolic, neurocognitive, and immune outcomes, as well as the potential of targeted synbiotic strategies to enhance metabolite production.

METHODS: We conducted a narrative synthesis of recent literature examining microbial conversion pathways of dietary bioactives and their associated physiological effects, with a specific focus on interindividual variability in metabolite production and emerging evidence on synbiotic interventions combining probiotics with selected bioactive precursors.

RESULTS: Production of microbial metabolites varied markedly among individuals due to differences in gut microbiota composition, giving rise to distinct metabolic phenotypes (metabotypes) that influenced clinical and nutritional responsiveness. Evidence showed that microbially derived metabolites were key mediators of systemic benefits. Studies evaluating targeted synbiotics demonstrated the capacity to convert non-producers into producers, reduce interindividual variability in metabolite output, and improve clinically relevant outcomes in metabolic dysfunction, inflammation-driven disorders, and aging.

CONCLUSIONS: Metabolite-guided synbiotics represent a promising paradigm for precision nutrition by enhancing the consistency and efficacy of bioactive compound metabolism. Integration of metagenomics, metabolomics, and computational modeling will enable individualized prediction of metabolite-production capacity and accelerate the translation of microbiota-targeted interventions into practice.},
}

*Polyphenols/metabolism/pharmacokinetics
Humans
*Synbiotics
Biotransformation
*Gastrointestinal Microbiome/physiology
*Bacteria/metabolism

@article {pmid42218921,
year = {2026},
author = {Guo, F and Fu, W and Topalović, O and Zhang, Q and Li, K and Li, H and Qing, X},
title = {Genomic insights into nematode microbiomes reveal novel endosymbionts Rickettsiella.},
journal = {Molecular phylogenetics and evolution},
volume = {223},
number = {},
pages = {108650},
doi = {10.1016/j.ympev.2026.108650},
pmid = {42218921},
issn = {1095-9513},
mesh = {Animals ; *Symbiosis/genetics ; Phylogeny ; *Nematoda/microbiology/genetics ; *Microbiota/genetics ; Gene Transfer, Horizontal ; *Coxiellaceae/genetics/classification ; Wolbachia/genetics/classification ; Genome, Bacterial ; Sequence Analysis, DNA ; Metagenome ; Genomics ; Evolution, Molecular ; *Bacteroidetes/genetics/classification ; },
abstract = {BACKGROUND: Bacterial endosymbionts are key drivers of invertebrate ecology and evolution. While the diversity and functional role of the nematode microbiome remain poorly explored.

METHODOLOGY: We reconstructed and characterized 108 metagenome-assembled genomes from 10 published and 15 newly sequenced nematode genomes.

PRINCIPAL FINDINGS: We report the first evidence of Rickettsiella in nematodes and discovered novel endosymbionts Cardinium and Wolbachia in plant-parasitic nematodes. The nematode microbiome is enriched with genes for carbohydrate metabolism and the biosynthesis of essential amino acids and vitamins, indicating a potential primary role in host nutrition. Notably, mobile genetic elements like prophages and insertion sequences (IS) are widespread and carry passenger genes involved in vitamin biosynthesis, suggesting horizontal gene transfer facilitates metabolic adaptation. Genomic reduction in the nematode Rickettsiella lineage, reveals extensive gene loss, particularly in amino acid biosynthesis. Crucially, we find no evidence of purifying selection on its residual nutritional pathways, and thus cannot clearly support a mutualistic role for this association.

CONCLUSION: Our findings expand the known host range of major endosymbiont groups and reveal a spectrum of symbiotic relationships in nematodes, from putative mutualism driven by nutritional supplementation to associations with neutral or parasitic traits, shaped by pervasive horizontal gene transfer and reductive genome evolution.},
}

Animals
*Symbiosis/genetics
Phylogeny
*Nematoda/microbiology/genetics
*Microbiota/genetics
Gene Transfer, Horizontal
*Coxiellaceae/genetics/classification
Wolbachia/genetics/classification
Genome, Bacterial
Sequence Analysis, DNA
Metagenome
Genomics
Evolution, Molecular
*Bacteroidetes/genetics/classification

@article {pmid42233654,
year = {2026},
author = {Wang, W and Li, Y and Liang, Y and Wang, J and Zhang, Z and Zhang, Y and Xiao, C and Hao, H},
title = {Age-driven shifts of the camel gut microbiome and resistome in extensively reared dromedary camels.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0318325},
pmid = {42233654},
issn = {2165-0497},
support = {2024AB034//Science and Technology Bureau of Xinjiang Production and Construction Corps/ ; CZ004311//Science Fund for Distinguished Young Scholars of Xinjiang Autonomous Region/ ; 202358//Science and Technology Department of Xinjiang Uyghur Autonomous Region/ ; },
mesh = {Animals ; *Camelus/microbiology/growth & development ; *Bacteria/genetics/classification/isolation & purification/drug effects ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; Age Factors ; Feces/microbiology ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; },
abstract = {UNLABELLED: Camels are uniquely adapted to arid environments and are commonly raised in extensive grazing systems. The composition of their gut microbiome and antimicrobial resistance genes (ARGs) is expected to change with host development, but age-related patterns have not been well described. In this study, we analyzed fecal samples from juvenile (approximately 6 months old) and adult (6 years) dromedary camels kept under the same grazing management, with no recorded therapeutic antibiotic treatments during the study period. Shotgun metagenomic sequencing was used to profile bacterial communities, ARGs, and mobile genetic elements (MGEs). Juvenile camels showed lower alpha diversity and greater inter-individual variation than adults, and their gut communities were dominated by facultative anaerobes such as Escherichia and Streptococcus. Adult camels carried more stable, fiber-adapted communities enriched in Bacteroidaceae and Prevotellaceae. In parallel with these microbiome changes, the resistome also differed by age. Juveniles carried a wider range of ARGs, with higher contributions from multidrug efflux pumps and vancomycin resistance genes. Adults had a smaller and more concentrated set of ARGs, mainly β-lactamase and tetracycline resistance genes, together with lower ARG richness and diversity. MGEs also showed distinct age-related patterns: transposase genes were more common in juveniles, whereas insertion sequence-associated genes were more abundant in adults, suggesting age-specific routes of potential ARG mobility. Overall, these data indicate that maturation of the camel gut microbiome is accompanied by a reduction and focusing of the resistome and by a shift in the dominant types of MGEs. This study provides an age-stratified reference for ARG reservoirs and MGE-associated ARG mobility in camels studied under conditions with no recorded therapeutic antibiotic treatments and may be useful for future work on antimicrobial resistance in extensively managed livestock.

IMPORTANCE: Antimicrobial resistance is often studied in animals heavily exposed to antibiotics, leaving a gap in our understanding of its natural development. Camels, rarely treated with antibiotics, offer a unique model. By comparing juvenile and adult gut microbiomes, we found that early-life communities are diverse, unstable, and rich in mobile resistance genes, while adult communities are more stable and carry fewer mobile elements. These findings establish a natural baseline for how resistance genes emerge and settle without drug pressure, providing critical insights for One Health strategies aimed at limiting the spread of resistance in livestock and wildlife.},
}

Animals
*Camelus/microbiology/growth & development
*Bacteria/genetics/classification/isolation & purification/drug effects
*Gastrointestinal Microbiome/genetics
Anti-Bacterial Agents/pharmacology
Age Factors
Feces/microbiology
*Drug Resistance, Bacterial/genetics
Metagenomics

@article {pmid42262077,
year = {2026},
author = {Ran, S and Fu, S and Dai, T and Wei, H and Peng, J and Zhou, Y},
title = {Multi-omics profiling of gut-serum axis dynamics in gestational sows with different reproductive performance.},
journal = {Microbiology spectrum},
volume = {14},
number = {7},
pages = {e0113225},
pmid = {42262077},
issn = {2165-0497},
mesh = {Animals ; Female ; Swine/blood/microbiology ; Pregnancy ; Multiomics ; *Reproduction/physiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Feces/microbiology ; Litter Size ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Metabolomics ; Metagenomics ; *Serum/chemistry ; },
abstract = {UNLABELLED: Sustainable swine production hinges on optimizing sow reproductive efficiency, yet mechanisms driving healthy litter size and weak piglet rates remain unclear. This study categorized sows into high (group H) and low (group L) healthy litter size groups based on median performance. Multi-omics analyses (16S rRNA sequencing, metagenomics, and serum metabolomics) revealed distinct fecal microbiota and metabolic profiles between groups. The results showed significant differences in microbiota composition between groups L and H. Group H exhibited a marked increase in Bacteroidetes abundance (particularly Prevotella sp. CAG1092), concurrent with reduced Firmicutes populations. Metabolomic analysis identified 197 differentially abundant metabolites, with 85 metabolites significantly enriched in group H. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the differentially abundant metabolites were mainly involved in amino acid synthesis and metabolism, and multiple amino acid metabolic pathways were associated with polyamine synthesis. The correlation results showed a significant correlation (P < 0.05) between these metabolites and litter size as well as litter weight. For instance, Prevotellaceae NK3B31 abundance positively correlated with L-alanine, urea, and securinine, while Prevotella sp. CAG1092 exhibited direct associations with reproductive performance. These findings suggest that gut microbiota dysbiosis may disrupt amino acid homeostasis and polyamine regulation, potentially serving as mechanistic links to reproductive efficiency. Reproductive performance dynamically shapes gut microbiota and systemic metabolism in gestating sows, with litter size influencing fecal metabolite diversity and microbial structure. This integrative analysis establishes a framework for improving both sow productivity and economic viability in pig farming.

IMPORTANCE: Optimizing sow reproductive efficiency is vital for sustainable swine production. This study identifies gut microbiota dysbiosis and metabolic imbalances as key drivers of litter size variability. Sows with lower productivity displayed marked reductions in Bacteroidetes (notably Prevotella spp.) and disrupted amino acid/polyamine metabolism, directly linking microbial shifts to poorer litter outcomes. Integrated multi-omics approaches revealed strong correlations between specific taxa (Prevotella sp. CAG1092), metabolites (L-alanine and urea), and reproductive metrics, underscoring the gut-reproductive axis. These findings elucidate mechanistic connections between microbial ecosystems and host physiology, providing a foundation for targeted strategies like microbiota modulation or dietary interventions to enhance metabolic homeostasis and farrowing success. By bridging microbial ecology with livestock productivity, this work advances practical solutions to improve both animal health and agricultural profitability within precision farming frameworks.},
}

Animals
Female
Swine/blood/microbiology
Pregnancy
Multiomics
*Reproduction/physiology
*Bacteria/classification/genetics/isolation & purification/metabolism
Feces/microbiology
Litter Size
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Metabolomics
Metagenomics
*Serum/chemistry

@article {pmid42276012,
year = {2026},
author = {Budzinski, L and Beenken, AE and Sempert, T and Kang, GU and Abbas, A and Lietz, L and Maier, R and Mashreghi, MF and Chang, HD and Alexander, T},
title = {IgG4-related disease has a specific intestinal microbiota signature.},
journal = {EBioMedicine},
volume = {129},
number = {},
pages = {106326},
pmid = {42276012},
issn = {2352-3964},
mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; RNA, Ribosomal, 16S/genetics ; Male ; *Immunoglobulin G4-Related Disease/microbiology/diagnosis/etiology ; Middle Aged ; Flow Cytometry ; Aged ; Immunoglobulin G ; Adult ; Cross-Sectional Studies ; Feces/microbiology ; Metagenomics/methods ; },
abstract = {BACKGROUND: While the intestinal microbiome has been implicated in Immunoglobulin-4 related disease (IgG4-RD), it remains poorly characterised. Therefore, we performed a comprehensive microbiome characterisation to identify disease-specific alterations.

METHODS: In this cross-sectional study, cryopreserved stool samples from 28 patients with IgG4-RD were characterised by 16S rRNA gene sequencing and by multiparameter microbiota flow-cytometry to determine their taxonomic composition and phenotype at the single cell level. These data were evaluated in comparison with 24 healthy controls (HC) and assessed for their potential to classify IgG4-RD using random forest classification, with an independent validation cohort (12 IgG4-RD, 12 HC).

FINDINGS: Patients with IgG4-RD exhibited reduced taxonomic diversity and disease-specific alterations in the microbiome compared to HC, characterised by significantly elevated levels of several species within the Bacillota phylum. These taxonomic alterations classified patients and HC with an AUROC of 0.87 (95% CI: 0.77-0.97) but showed reduced performance in the validation cohort (AUROC 0.58, 95% CI: 0.29-0.87). Flow cytometry revealed distinct phenotypic microbiota alterations, robustly distinguishing patients with IgG4-RD from HC in both the training (AUROC 0.9, 95% CI: 0.81-0.99) and validation cohort (AUROC 0.78, 95% CI: 0.59-0.97). The IgG4-RD microbiota were predominantly DNA-low and showed no enhanced endogenous IgG4 coating, neither natively nor after in vitro incubation with autologous serum.

INTERPRETATION: Our study revealed specific alterations in the intestinal microbiota on taxonomic and phenotypic level in IgG4-RD, which potentially reflect different mechanisms of adaptations of the gut microbiota to immune disturbances specific to IgG4-RD. We provide proof-of-concept that this "microbiota fingerprint" may be suitable to identify IgG4-RD in a machine-learning approach and may provide important insights into the complexity of intestinal microbiota alterations in IgG4-RD.

FUNDING: This work was supported by grants from Rolf M. Schwiete Foundation, DFG (German Research Foundation), Innovative Medicines Initiative 2 Joint Undertaking (3 TR), and EFRE-Project.},
}

Humans
*Gastrointestinal Microbiome
Female
RNA, Ribosomal, 16S/genetics
Male
*Immunoglobulin G4-Related Disease/microbiology/diagnosis/etiology
Middle Aged
Flow Cytometry
Aged
Immunoglobulin G
Adult
Cross-Sectional Studies
Feces/microbiology
Metagenomics/methods

@article {pmid42331262,
year = {2026},
author = {He, G and Guo, X and Lu, W and Zou, Y and Zheng, J and Han, X and Hong, Y and Wei, R},
title = {Molecular features of external Auditory Canal cholesteatoma by microbial metagenomic sequencing.},
journal = {Genomics},
volume = {118},
number = {4},
pages = {111282},
doi = {10.1016/j.ygeno.2026.111282},
pmid = {42331262},
issn = {1089-8646},
mesh = {Humans ; *Cholesteatoma/microbiology ; *Ear Canal/microbiology/pathology ; Metagenomics ; *Microbiota ; *Metagenome ; Actinobacteria/genetics/isolation & purification ; Bacillota/genetics/isolation & purification ; Proteobacteria/genetics/isolation & purification ; },
abstract = {OBJECTIVE: External auditory canal cholesteatoma (EACC), a rare destructive benign lesion, causes significant hearing loss, recurrent infections, and impaired quality of life. We characterized its microbial profiles to explore associations with disease progression.

METHODS: Cholesteatoma tissues from surgically treated EACC patients (2021-2022) underwent metagenomic sequencing (Illumina MiSeq). Taxonomic composition, functional genes, and antimicrobial resistance (AMR) profiles were systematically analyzed.

RESULTS: We identified 4377 core genes revealing abundance correlations. Dominant taxa included Firmicutes (42.1%), Proteobacteria (28.6%), and Actinobacteria (19.3%), with enriched Staphylococcus (32.4%) and Corynebacterium (21.7%). Hierarchical clustering and PCA/NMDS confirmed significant taxonomic divergence. AMR profiling detected multidrug-resistant genotypes (e.g., blaTEM, mecA).

CONCLUSION: This study defines EACC's microbial complexity and its pathogenic role, advocating microbiome-targeted strategies to mitigate infections.},
}

Humans
*Cholesteatoma/microbiology
*Ear Canal/microbiology/pathology
Metagenomics
*Microbiota
*Metagenome
Actinobacteria/genetics/isolation & purification
Bacillota/genetics/isolation & purification
Proteobacteria/genetics/isolation & purification

@article {pmid42341885,
year = {2026},
author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and Giosuè, A and Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L},
title = {Ultra-processed food intake and its associations with atherogenic dyslipidemia, glycemic control, and gut microbiome features in adults with type 1 diabetes from Southern Italy.},
journal = {Diabetes research and clinical practice},
volume = {238},
number = {},
pages = {113373},
doi = {10.1016/j.diabres.2026.113373},
pmid = {42341885},
issn = {1872-8227},
mesh = {Humans ; Female ; Male ; *Diabetes Mellitus, Type 1/blood/microbiology/complications/epidemiology ; Adult ; *Glycemic Control ; *Gastrointestinal Microbiome/physiology ; *Dyslipidemias/epidemiology/blood/etiology ; Food, Processed ; Middle Aged ; Italy/epidemiology ; *Atherosclerosis/epidemiology ; *Blood Glucose/metabolism ; Glycated Hemoglobin/metabolism ; *Fast Foods/adverse effects ; Continuous Glucose Monitoring ; },
abstract = {AIMS: To examine the associations between ultra-processed food (UPF) intake, glycemic control, cardiovascular risk factors, and gut microbiome in adults with type 1 diabetes (T1D).

METHODS: In 253 adults with T1D, diet was assessed using the EPIC food-frequency questionnaire, and UPFs classified according to NOVA. Evaluations included lipid profile, HbA1c, and continuous glucose monitoring metrics. In a subgroup (n = 103), gut microbiota composition/function was analyzed using shotgun metagenomic sequencing and beta-diversity assessed by PERMANOVA. Associations were examined using multivariable regression models adjusted for age and Mediterranean diet adherence.

RESULTS: Mean UPF intake was 15.5 % of total food intake. Higher UPF intake was independently associated with higher triglycerides (β per 20 g/1000 kcal = 3.62 mg/dL; 95 %CI 1.16-6.08) and lower HDL-cholesterol (β =  - 0.98 mg/dL; 95 %CI - 1.72 to - 0.24). Sugar/artificially sweetened beverages were positively associated with triglycerides and animal-based UPFs inversely associated with HDL cholesterol. In participants on multiple daily injections or open-loop systems, ready-to-eat mixed dishes were positively associated with HbA1c. Microbiome beta-diversity significantly differed according to UPF intake. Triglycerides positively associated with microbial pathways (ketogluconate, tetrapyrrole, and acetate metabolism).

CONCLUSION: Higher UPF intake was associated with atherogenic dyslipidemia, poorer glycemic control in selected groups, and gut microbiome alterations in adults with T1D. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.},
}

Humans
Female
Male
*Diabetes Mellitus, Type 1/blood/microbiology/complications/epidemiology
Adult
*Glycemic Control
*Gastrointestinal Microbiome/physiology
*Dyslipidemias/epidemiology/blood/etiology
Food, Processed
Middle Aged
Italy/epidemiology
*Atherosclerosis/epidemiology
*Blood Glucose/metabolism
Glycated Hemoglobin/metabolism
*Fast Foods/adverse effects
Continuous Glucose Monitoring

@article {pmid42387381,
year = {2026},
author = {Andersson, O and Fagerström, A and Dannenberg, K and Kekki, J and Rode, J and Rangel, I and Lindqvist, CM and Stenmark, B},
title = {Comparison of library preparation protocols and bioinformatic pipelines in high-throughput 16S rRNA gene sequencing.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42387381},
issn = {1471-2180},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Computational Biology/methods ; *Gene Library ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; DNA, Bacterial/genetics ; Microbiota/genetics ; },
abstract = {BACKGROUND: 16S rRNA gene sequencing is widely used for bacterial community profiling in both clinical and research contexts. The expanding availability of library preparation protocols and bioinformatic pipelines increases analytical flexibility but may also introduce method-dependent biases that affect inferred microbial composition and relative abundance estimates. The relative impact of library preparation protocol, amplicon region, and bioinformatic pipeline on species-level taxonomic inference and compositional agreement remains insufficiently characterised. We therefore compared the Illumina 16S Metagenomic Sequencing Library Preparation protocol (V3-V4) and the Zymo Quick-16S Plus NGS Library Prep Kit (V1-V2 and V3-V4) in combination with two bioinformatic pipelines, nf-core/ampliseq and TRANA. Performance was assessed using defined microbial community standards and human faecal and colonic biopsy samples.

RESULTS: Pipeline choice was the dominant driver of variation in inferred community composition, exceeding the effects of amplicon regions and library preparation protocols. Genus-level profiles were broadly concordant across methods. Species-level resolution and agreement with expected community composition differed systematically between pipelines, with TRANA demonstrating lower Bray-Curtis dissimilarities to expected compositions than nf-core/ampliseq. Amplicon region had a secondary, pipeline-dependent effect, while protocol differences were minor. In clinical samples, inter-individual biological variation exceeded technical variation.

CONCLUSIONS: Bioinformatic processing substantially influenced species-level inference in short-read 16S sequencing, highlighting the importance of pipeline selection for microbiome study design and cross-study comparability.},
}

*RNA, Ribosomal, 16S/genetics
*Computational Biology/methods
*Gene Library
Humans
*High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Sequence Analysis, DNA/methods
Metagenomics/methods
DNA, Bacterial/genetics
Microbiota/genetics

@article {pmid42387604,
year = {2026},
author = {Hu, Y and Chen, JS and Zhou, MY and Huang, H and Zhou, YF and Zhou, HY and Lv, ZY},
title = {Dynamic alterations and potential roles of gut microbiota and metabolites in Angiostrongylus cantonensis-infected mice and rats.},
journal = {Infectious diseases of poverty},
volume = {15},
number = {1},
pages = {},
pmid = {42387604},
issn = {2049-9957},
support = {NPRC-2019-194-30//National Parasitic Resources Center of China/ ; 22qntd4804//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; 2021YFC2300800//National Key Research and Development Program of China/ ; 82072303//National Natural Science Foundation of China/ ; YSPTZX202133//Specific Research Fund of the Innovation Platform for Academicians of Hainan Province/ ; ZDYF2020120//Key Research and Development Program of Hainan Province/ ; ZDKJ202003//Major Science and Technology Program of Hainan Province/ ; 2020TTM007//Open Foundation of Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University/ ; },
mesh = {Animals ; Female ; *Angiostrongylus cantonensis/physiology ; Rats, Sprague-Dawley ; *Strongylida Infections/parasitology/microbiology/metabolism ; Rats ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred BALB C ; RNA, Ribosomal, 16S/genetics/analysis ; Biomarkers ; Feces ; },
abstract = {BACKGROUND: Angiostrongyliasis, a food-borne parasitic disease caused by Angiostrongylus cantonensis, is characterized by eosinophilic meningitis or meningoencephalitis, leading to serious central nervous system damage. Current diagnostic methods lack specificity or sensitivity, and the pathogenesis is complex and incompletely understood. This study aimed to comprehensively characterize the dynamic alterations in the gut microbiota and host metabolism in both suitable (rats) and non-suitable (mice) hosts following A. cantonensis infection and to identify potential metabolic biomarkers for early diagnosis.

METHODS: Female BALB/c mice and Sprague Dawley rats (n = 10/group) were infected with 30 or 100 third-stage larvae, respectively. Serum, urine, feces, and brain samples were collected longitudinally. Gut microbiota was analyzed via 16S rRNA gene sequencing and metagenomics. Host metabolism was profiled using untargeted and targeted metabolomics via ultraperformance liquid chromatography-quadrupoles/time of flight-mass spectrometry. Statistical analyses included Wilcoxon rank sum test, linear discriminant effect size analysis, Spearman correlation analysis, orthogonal partial least squares-discriminatory analysis, and receiver operating characteristic curve analysis.

RESULTS: Infection induced significant, host-specific gut microbiota dysbiosis. In infected hosts, Firmicutes decreased (P < 0.05) while Bacteroidetes increased (P < 0.05). A main difference in gut flora structure between infected hosts was observed in Prevotellaceae, which increased significantly in mice (P < 0.05) but decreased in rats (P < 0.05). Metagenomics revealed enhanced carbohydrate metabolism and fatty acid biosynthesis in gut microbes of infected mice, whereas up-regulated amino acid and vitamin metabolism were also observed in infected rats. Infection caused pronounced disruptions in host lipid and bile acid (BA) metabolism, changes in various BA types were closely related to alterations in specific bacterial genera (P < 0.05). Several metabolites, including phosphatidylcholine (16:0/18:1), 2-phenyl acetic acid, 2-octenoylglycine, lysophosphatidylcholine (18:2), O-glucuronide, and 2-carboxylic acid, were identified as potential early diagnostic biomarkers in the mouse model.

CONCLUSIONS: A. cantonensis infection causes profound host-specific dysregulation of the gut microbiome and metabolome, with severe disturbances in Firmicutes, Bacteroidetes, lipid and BA metabolism being central features. These alterations highlight the critical role of the host-gut microbiota-metabolite axis in pathogenesis and offer novel insights for developing diagnostic and therapeutic strategies.},
}

Animals
Female
*Angiostrongylus cantonensis/physiology
Rats, Sprague-Dawley
*Strongylida Infections/parasitology/microbiology/metabolism
Rats
*Gastrointestinal Microbiome
Mice
Mice, Inbred BALB C
RNA, Ribosomal, 16S/genetics/analysis
Biomarkers
Feces

@article {pmid42389510,
year = {2026},
author = {Al Shareef, ZM and Al-Shahrabi, RM and Sharif-Askari, FS and Yener, B and Bhamidimarri, PM and Bouzid, A and Talaat, IM and Bendardaf, R and Hamoudi, RA and Mote, S and Mall, R and Castiglione, F},
title = {Microbial dysbiosis and inferred functional profiling reveals the potential role of Methylobacterium in prostate cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1760700},
pmid = {42389510},
issn = {2235-2988},
mesh = {Humans ; Male ; *Methylobacterium/genetics/classification/isolation & purification/physiology ; *Prostatic Neoplasms/microbiology/pathology ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; Retrospective Studies ; Microbiota/genetics ; Prostate/microbiology/pathology ; },
abstract = {BACKGROUND AND OBJECTIVE: Prostate cancer (PCa) is a leading malignancy in men, with a multifactorial aetiology involving genetic, hormonal, and microbial factors. Although emerging evidence implicates tumour-associated microbial communities in cancer biology, microbial signatures in PCa, particularly in Arab populations, remain underexplored. This study aimed to characterize the prostate tissue microbiota in an Arab cohort and explore associations with clinical features.

METHODS: In this retrospective study, 40 formalin-fixed paraffin-embedded (FFPE) prostate tissue samples (23 PCa and 17 benign prostatic hyperplasia [BPH]) were analysed using 16S rRNA gene sequencing. Microbial diversity, taxonomic composition, and predicted functional potential inferred from 16S data were assessed using DADA2 (v1.30.0), phyllode (v1.46.0), and PICRUSt2 (v2.5.2), with taxonomic classification based on the SILVA database (release 138). Beta diversity differences were tested using PERMANOVA (999 permutations), and differential abundance analyses were corrected using false discovery rate (FDR).

KEY FINDINGS AND LIMITATIONS: PCa tissues demonstrated higher alpha diversity than BPH samples, with greater heterogeneity in beta diversity. Among the identified genera, Methylobacterium was enriched in PCa samples and remained directionally consistent after multivariable adjustment. Exploratory analyses suggested higher abundance in advanced and deceased cases; however, survival findings were limited by sample size. Functional inference indicated enrichment of predicted pathways for carbohydrate and nitrogen metabolism.

CONCLUSIONS: This exploratory study identified Methylobacterium as a candidate microbial signature associated with PCa in an Arab cohort. Given the modest sample size and the inferential nature of functional predictions, these findings require validation in larger prospective studies using direct metagenomic and metabolomic approaches.},
}

Humans
Male
*Methylobacterium/genetics/classification/isolation & purification/physiology
*Prostatic Neoplasms/microbiology/pathology
RNA, Ribosomal, 16S/genetics
*Dysbiosis/microbiology
Retrospective Studies
Microbiota/genetics
Prostate/microbiology/pathology

@article {pmid42390270,
year = {2026},
author = {Varona, NS and Schellenberg, L and Barnes, W and Scholten, Y and Haas, AF and Silveira, C},
title = {Bacteriophage replication strategies are associated with organic matter energy content on coral reefs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0039526},
doi = {10.1128/msystems.00395-26},
pmid = {42390270},
issn = {2379-5077},
abstract = {Bacteriophages, viruses that infect bacteria, play a crucial role in carbon cycling within marine environments. In coral reefs, dissolved organic matter (DOM) released by benthic primary producers such as algae fuels heterotrophic microbial growth, which can be detrimental to corals. This microbialization process has been associated with the abundance and replication strategies of bacteriophages, but the direct relationship between reef DOM composition and bacteriophage communities remains unclear. Here, we combine metabolomics, metagenomes, and viromes to demonstrate that phage communities have significant relationships with DOM composition on the reefs of Curaçao, Southern Caribbean. While total viral abundances did not significantly correlate with overall dissolved organic carbon (DOC) concentration on these reefs, co-occurrence networks identified thousands of statistically significant associations between free or cell-associated viruses and organic compounds. Cell-associated phages had significantly more positive associations with compounds that had a reduced nominal oxidative state of carbon (NOSC). Furthermore, temperate phages were more frequently correlated with metabolites exhibiting higher Gibbs energy than putatively lytic phages. Six of the ten viruses with the highest number of positive associations with metabolites were temperate (i.e., encoded an integrase or were identified as a prophage), despite this network consisting of approximately 90% lytic viruses. These temperate viruses were predicted to infect members of the genus Sphingobium. Together, these findings reveal a connection between phage replication strategies and DOM energy availability, with potential implications for coral reef biogeochemistry.IMPORTANCECoral reefs are highly dynamic ecosystems where microbial communities and organic matter cycles are intricately linked. This study provides new insights into how bacteriophages interact with dissolved organic matter (DOM) composition, revealing that cell-associated bacteriophages, particularly temperate phages, are associated with more energy-rich organic compounds. These findings suggest that DOM could affect the lysis-lysogeny decision of temperate phages or that lysogeny may play an underappreciated role in shaping the reef carbon cycle. Energy-rich organic compounds have generally been associated with increased algal abundances and coral decline. By demonstrating significant connections between viral infection strategies and the energy content of DOM, our results highlight the potential for phages to influence coral reef biogeochemistry and health.},
}

@article {pmid42390679,
year = {2026},
author = {Shao, Z and Zheng, F and Sun, J and Wei, H and Sun, Y and Wang, F},
title = {Response of soil microbiomes to nano-zero-valent iron and biochar in Cr(VI)-contaminated soil remediation.},
journal = {Ecotoxicology (London, England)},
volume = {35},
number = {6},
pages = {},
pmid = {42390679},
issn = {1573-3017},
support = {2021CXGC011206//Major Scientific and Technological Innovation Project of Shandong Province/ ; },
mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; *Iron/chemistry ; *Microbiota/drug effects ; *Chromium ; *Charcoal/chemistry ; *Environmental Restoration and Remediation/methods ; Bacteria/drug effects ; *Metal Nanoparticles ; },
abstract = {Both biochar and nano-zero-valent iron (nZVI) are increasingly used to remediate soils polluted with heavy metals, such as the toxic Cr(VI). However, how soil microbiomes respond to biochar and nZVI applied in Cr(VI)-contaminated soil has not yet been clarified. The current study compared the effects of bare nZVI (B-nZVI) and starch-stabilized nZVI (S-nZVI) at 100 and 1000 mg/kg on soil enzyme activity and microbial communities in Cr(VI)-contaminated soil growing mung bean amended with or without 1% biochar. High-throughput metagenomic sequencing was conducted to determine the evenness (Simpson index), diversity (Shannon index), and richness (Chao-1 index) of soil bacteria, fungi, archaea, and viruses. Soil catalase activity was inhibited by S-nZVI but stimulated by biochar. Soil phosphatase activity was stimulated by both types of nZVI, but not influenced by biochar. The combination of 1000 mg/kg nZVI and biochar decreased bacterial and fungal evenness and diversity, but did not significantly alter their richness. Archaeal communities remained relatively stable across most treatments. The evenness and diversity of viral communities increased significantly at 1000 mg/kg S-nZVI, whereas the richness decreased conversely. PCoA showed that soil microbial community structure was significantly changed by 1000 mg/kg S-nZVI, which diminished Actinobacteria but enriched Cellvibrio. Furthermore, 1000 mg/kg S-nZVI increased the abundances of some genes involved in antioxidant enzymes and the metabolism of Fe and Cr, and decreased the abundance of C-cycling genes significantly. Overall, S-nZVI caused significant perturbations in soil microbial activity and community structure, but these adverse effects were alleviated by the incorporation of biochar.},
}

*Soil Microbiology
*Soil Pollutants/toxicity
*Iron/chemistry
*Microbiota/drug effects
*Chromium
*Charcoal/chemistry
*Environmental Restoration and Remediation/methods
Bacteria/drug effects
*Metal Nanoparticles

@article {pmid42392820,
year = {2026},
author = {Li, H and Deng, XF and Chen, H and Wang, P and Xu, HY},
title = {[Metabolomics and metagenomics reveal mechanism of Xinglou Chengqi Decoction in preventing cerebral ischemia-reperfusion injury].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {51},
number = {9},
pages = {2652-2664},
doi = {10.19540/j.cnki.cjcmm.20260107.707},
pmid = {42392820},
issn = {1001-5302},
mesh = {Animals ; *Drugs, Chinese Herbal/administration & dosage ; *Reperfusion Injury/metabolism/prevention & control/drug therapy/genetics ; Rats ; Male ; Metabolomics ; Metagenomics ; Rats, Sprague-Dawley ; *Brain Ischemia/metabolism/drug therapy/genetics ; Humans ; Oxidative Stress/drug effects ; Blood-Brain Barrier/drug effects/metabolism ; Brain/metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; },
abstract = {This study uses a rat model of middle cerebral artery occlusion and reperfusion(MCAO/R) to investigate the mechanism by which Xinglou Chengqi Decoction treats cerebral ischemia-reperfusion injury, employing metabolomics and metagenomics approaches. A rat model of MCAO/R was established to evaluate the neurological function and modified neurological severity scores. Then, the brain tissue pathology, inflammatory mediators, oxidative stress, blood-brain barrier integrity, cerebral edema, and intestinal barrier function were examined to assess the pharmacological effects of Xinglou Chengqi Decoction. Metabolomics analysis of the brain tissue and metagenomics analysis of the intestinal contents were conducted to investigate the metabolism and gut microbiota regulatory mechanisms of Xinglou Chengqi Decoction. The results suggested that Xingluo Chengqi Decoction improved the neural function, reduced the severity of cerebral infarction, attenuated oxidative stress and inflammatory factor levels, boosted blood-brain barrier factor levels, minimized cerebral edema, and strengthened intestinal mucosal barrier protection, thus treating cerebral ischemia-reperfusion injury in rats. Metabolomic analysis of the brain tissue revealed that Xinglou Chengqi Decoction primarily treated ischemic stroke through 14 potential metabolic pathways, including phenylalanine, tyrosine, and tryptophan biosynthesis, valine, leucine, and isoleucine biosynthesis, and phenylalanine metabolism. Metagenomic analysis revealed that administration of Xinglou Chengqi Decoction increased the relative abundance of Firmicutes, Clostridia and Bacilli, Clostridiales and Lactobacillales, and Lachnospiraceae and Oscillospiraceae. In addition, it influenced the biosynthesis of aminoacyl-tRNA, valine, leucine, and isoleucine, along with peptidoglycan synthesis, thereby enhancing the regulatory function of the gut microbiota. Simultaneously, Xinglou Chengqi Decoction exerts therapeutic effects through the gut-brain crosstalk mediated by substances such as amino acids and fatty acids, which act within the biosynthetic and metabolic pathways.},
}

Animals
*Drugs, Chinese Herbal/administration & dosage
*Reperfusion Injury/metabolism/prevention & control/drug therapy/genetics
Rats
Male
Metabolomics
Metagenomics
Rats, Sprague-Dawley
*Brain Ischemia/metabolism/drug therapy/genetics
Humans
Oxidative Stress/drug effects
Blood-Brain Barrier/drug effects/metabolism
Brain/metabolism/drug effects
Gastrointestinal Microbiome/drug effects
Disease Models, Animal

@article {pmid42394335,
year = {2026},
author = {Sun, X and Ding, M and Li, Y and Mu, D and Wu, J and Yu, X and Zhu, M and Sun, G and Xiang, X},
title = {[Effects and Mechanisms of a multi-strain probiotic on the gut microbiota of healthy mice].},
journal = {Wei sheng yan jiu = Journal of hygiene research},
volume = {55},
number = {3},
pages = {491-498},
doi = {10.19813/j.cnki.weishengyanjiu.2026.03.019},
pmid = {42394335},
issn = {1000-8020},
mesh = {Animals ; *Probiotics/pharmacology/administration & dosage ; Male ; Mice ; Mice, Inbred C57BL ; Lactobacillus acidophilus/physiology ; Tryptophan/metabolism ; Indoles/metabolism ; Bifidobacterium animalis/physiology ; Lacticaseibacillus rhamnosus/physiology ; Feces/microbiology ; *Microbiota ; },
abstract = {OBJECTIVE: Systematic evaluation of the regulatory effects of compound probiotics containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 and their ratios on gut microbiota composition and the tryptophan-indole metabolic pathway.

METHODS: 30 male C57BL/6 mice were randomly divided into three groups of ten mice each: Control group, Mix-A group(Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101 and Lactobacillus rhamnosus JL1, in a 1∶1∶1 ratio) and Mix-B group(same bacterial strains, in a 10∶1∶1 ratio). The composite probiotic group received daily oral administration of 0.2 mL probiotic suspension at a total concentration of 1.5 × 10~(10) CFU/mL. The control group received daily oral administration of an equal volume of PBS solution. The experimental intervention lasted for 3 weeks. At the end of the experiment, colon tissues were collected from mice to measure superoxide dismutase(SOD)and catalase(CAT)levels. Fecal samples were collected from mice at mid-and end-experiment time points for metagenomic sequencing and targeted metabolomics analysis.

RESULTS: There were no significant differences in body weight or organ indices among the three groups of mice. CAT levels were significantly higher in the Mix-B group compared to the control group(P<0.05). Metabolomic analysis revealed significantly elevated levels of indole-3-acetic acid(IAA), indole-3-lactic acid(ILA), and indole-3-carbaldehyde(IAld) in fecal samples from the Mix-B group(P <0.05). By day 22, β-diversity analysis revealed distinct microbial community structures across all 3 groups. The Mix-B group exhibited decreased Richness indices and increased dominance of specific bacterial taxa. LEfSe analysis indicated enrichment in Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Bifidobacterium animalis in Mix-A; while Mix-B group showed enrichment in Akkermansia muciniphila, Bacteroides acidifaciens, Clostridium cocleatum, and Anaerotruncus colihominis. Correlation analysis revealed significant positive correlations between Bacteroides thetaiotaomicron, Bacteroides acidifaciens, and Akkermansia muciniphila with indole metabolites including IAA, ILA, and IAld.

CONCLUSION: The compound probiotic combination containing Lactobacillus acidophilus LA-G80, Bifidobacterium animalis subsp. lactis BL-G101, and Lacticaseibacillus rhamnosus JL1 can safely modulate gut microbiota composition and enhance tryptophan-indole metabolism, which may provide a potential strategy for maintaining gut health.},
}

Animals
*Probiotics/pharmacology/administration & dosage
Male
Mice
Mice, Inbred C57BL
Lactobacillus acidophilus/physiology
Tryptophan/metabolism
Indoles/metabolism
Bifidobacterium animalis/physiology
Lacticaseibacillus rhamnosus/physiology
Feces/microbiology
*Microbiota

@article {pmid42394341,
year = {2026},
author = {Stenger, PL and Majorel, C and Valette, L and Ihage, W and Jardin-Camps, M and Jourand, P and Anton-Leberre, V},
title = {Spatial structuring dominates over seasonality in tropical coastal microbiomes: Insights from New Caledonia's Indo-Pacific lagoon.},
journal = {Journal of environmental quality},
volume = {55},
number = {4},
pages = {e70215},
doi = {10.1002/jeq2.70215},
pmid = {42394341},
issn = {1537-2537},
support = {//CRESICA (Consortium for Research, Higher Education, and Innovation in New Caledonia)/ ; //MITI-CNRS (Mission pour les initiatives transverses et interdisciplinaires)/ ; },
mesh = {New Caledonia ; Seasons ; *Seawater/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/analysis ; Bacteria/classification ; Tropical Climate ; *Environmental Monitoring ; Archaea ; Ecosystem ; },
abstract = {Tropical coastal ecosystems harbor diverse microbes essential for biogeochemical cycling and serve as sentinels of environmental change. However, microbial community profiles remain largely undocumented across the Southwest Pacific. We investigated bacterial communities in coastal and lagoonal waters surrounding Nouméa, New Caledonia, an area under increasing urban pressure. Our objective was to determine whether spatial heterogeneity or seasonal variation primarily structures these communities and how anthropogenic activities shape microbial diversity. Forty-two seawater samples were collected from seven sites spanning anthropized bays, mangrove estuaries, and offshore lagoon waters during hot and cold seasons. We found that spatial gradients explained significantly more variation in community structure (R[2] = 0.25) than seasonal changes (R[2] = 0.04), revealing distinct microbial signatures along the land-to-sea continuum. Coastal and mangrove sites harbored more copiotrophic taxa and elevated levels of predicted pathogen-associated functional pathways, though these predictions are based on 16S rRNA data, and require validation with metagenomic or functional assays. Seasonal shifts mainly involved Cyanobacteria (Synechococcus↑, Prochlorococcus↓ in warm season) and archaeal Marine Group II, reflecting temperature-mediated niche partitioning. This study establishes the first spatial and seasonal microbial inventory for New Caledonian coastal ecosystems, suggesting associations between anthropogenic influence and microbial community health. Spatial dominance highlights the potential value of local management, while temperature sensitivity of key taxa underscores the importance of integrating microbial monitoring into coastal conservation and One Health frameworks.},
}

New Caledonia
Seasons
*Seawater/microbiology
*Microbiota
RNA, Ribosomal, 16S/analysis
Bacteria/classification
Tropical Climate
*Environmental Monitoring
Archaea
Ecosystem

@article {pmid42397430,
year = {2026},
author = {Liu, Y and Jiang, W and Wang, J and Cheng, S and Cheng, C and Zhang, C and Zhang, J and Liu, C and Zhao, J and Wang, H},
title = {A special multifiber dietary mixture ameliorates Crohn's-like colitis in an IL-10[-]/[-] mouse model by promoting treg differentiation through the ETS1/RUNX1/Foxp3 axis.},
journal = {European journal of nutrition},
volume = {65},
number = {5},
pages = {},
pmid = {42397430},
issn = {1436-6215},
mesh = {Animals ; Proto-Oncogene Protein c-ets-1/metabolism/genetics ; *T-Lymphocytes, Regulatory/metabolism ; Mice ; *Crohn Disease/diet therapy/metabolism ; *Colitis/diet therapy ; Forkhead Transcription Factors/metabolism/genetics ; *Interleukin-10/genetics/metabolism/deficiency ; Disease Models, Animal ; Cell Differentiation/drug effects ; Core Binding Factor Alpha 2 Subunit/metabolism/genetics ; Mice, Knockout ; Mice, Inbred C57BL ; Gastrointestinal Microbiome ; Male ; },
abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory disorder characterized by immune dysregulation. Regulatory T cells (Tregs) play a pivotal role in maintaining mucosal tolerance, and their dysfunction directly contributes to CD pathogenesis.

METHODS: We used interleukin-10[-]/[-] mice to evaluate the therapeutic effects of a special multifiber mixture (MF) on colitis. T cell phenotypes, transcriptional profiles, gut microbiota composition, and N[6]-methyl adenosine (m6A) ribonucleic acid (RNA) methylation were analyzed using flow cytometry, RNA sequencing, metagenomics, and methylated RNA immunoprecipitation-quantitative polymerase chain reaction.

RESULTS: MF significantly reduced intestinal inflammation, restored epithelial barrier function, and promoted Treg differentiation while suppressing Th1/Th17 polarization. Integrated transcriptomic and proteomic analyses identified ETS1 as a negative regulator of Treg differentiation, modulated by gut microbiota-derived S-adenosylmethionine (SAM) through methyltransferase-like protein 3-mediated m6A methylation. MF feeding reduced SAM levels and m6A enrichment on ETS1 messenger RNA, leading to decreased ETS1 expression. Silencing of ETS1 enhanced Foxp3 expression and expanded the Treg population. RUNX1 was identified as a functional interactor of ETS1, with reciprocal expression patterns validated in both mouse models and colonic tissues from patients with CD.

CONCLUSION: MF alleviates colitis by reshaping the gut microbiota and suppressing SAM-dependent m6A methylation, resulting in ETS1 downregulation and the restoration of Treg homeostasis through the ETS1/RUNX1/Foxp3 axis. These findings reveal a mechanistic link between microbiota, epigenetics, and immunity, highlighting MF feeding as a promising nutritional intervention for CD treatment.},
}

Animals
Proto-Oncogene Protein c-ets-1/metabolism/genetics
*T-Lymphocytes, Regulatory/metabolism
Mice
*Crohn Disease/diet therapy/metabolism
*Colitis/diet therapy
Forkhead Transcription Factors/metabolism/genetics
*Interleukin-10/genetics/metabolism/deficiency
Disease Models, Animal
Cell Differentiation/drug effects
Core Binding Factor Alpha 2 Subunit/metabolism/genetics
Mice, Knockout
Mice, Inbred C57BL
Gastrointestinal Microbiome
Male

@article {pmid42397950,
year = {2026},
author = {Karthik, Y and Nanjareddy, K and Arthikala, MK},
title = {Deciphering soybean-microbiome interactions: from rhizosphere dynamics to sustainable yield enhancement.},
journal = {Plant signaling & behavior},
volume = {21},
number = {1},
pages = {2693436},
pmid = {42397950},
issn = {1559-2324},
mesh = {*Glycine max/microbiology/growth & development/metabolism ; *Rhizosphere ; *Microbiota/physiology ; Soil Microbiology ; Plant Roots/microbiology ; },
abstract = {The soybean plant (Glycine max L.) is an important crop for valuable food source because of its high levels of protein and oil, thus contributing greatly to a sustainable system for producing food through biological nitrogen fixation. Recent research supports the theory that the soybean-associated microbiome located in the rhizosphere is a crucial regulatory mechanism governing plant growth, nutrient acquisition, and stress tolerance. Additionally, advances in metagenomics, metatranscriptomics, metabolomics, and root exudate profiling via LC‒MS have shown that soybean roots alter the microbial communities found in their rhizosphere by utilizing dynamic chemical signaling and targeted microbial recruitment, thereby enhancing the ecological interpretation of the processes that drive microbiome assembly. Microbial consortia (AMF & PGPR) assess cycling through nutrients, phytohormones, suppressing diseases, as well as having a legacy effects on the productivity of agroecosystems. Factors such as plant genotype, physical and chemical soil properties, and environmental conditions greatly affect the assembly and functioning of the soybean microbiome, thus this is difficult to transfer this information to field applications. Unlike previous reviews focused primarily on biological nitrogen fixation, this review integrates recent advances in multi-omics technologies, species-level microbiome characterization, root exudate chemistry, microbiome-assisted breeding, and translational microbiome engineering approaches to provide a systems-level perspective of soybean-microbiome interactions. while also identifying significant knowledge gaps and future areas of research within this aspect of agriculture.},
}

*Glycine max/microbiology/growth & development/metabolism
*Rhizosphere
*Microbiota/physiology
Soil Microbiology
Plant Roots/microbiology

@article {pmid41313537,
year = {2026},
author = {Vishwakarma, RK and Gautam, P and Sahu, M and Nath, G and Yadav, BS},
title = {Gut Microbiome in Obesity: A Narrative Review of Mechanisms, Interventions, and Future Directions.},
journal = {Probiotics and antimicrobial proteins},
volume = {18},
number = {4},
pages = {5223-5245},
pmid = {41313537},
issn = {1867-1314},
mesh = {Humans ; *Obesity/microbiology/metabolism/therapy ; *Gastrointestinal Microbiome ; Probiotics/administration & dosage ; Animals ; Prebiotics/administration & dosage ; Dysbiosis/microbiology ; Fatty Acids, Volatile/metabolism ; },
abstract = {Obesity has reached pandemic levels worldwide and is increasingly recognized as a multifactorial condition beyond excess caloric intake and sedentary lifestyle. Accumulating evidence emphasizes that the gut microbiota (GM), primarily composed of Firmicutes and Bacteroidetes, plays a crucial role in regulating energy balance, immune response, and host metabolism. Gut dysbiosis, characterized by reduced microbial diversity and altered phylum-level composition and shifts toward commonly observed higher Firmicutes-to-Bacteroidetes ratios (although this finding is inconsistent across studies), contributes to enhanced energy harvest, systemic inflammation, and metabolic dysfunction. Key mechanisms involve GM production of short-chain fatty acids (SCFAs) and modulation of hormonal signals, including leptin, ghrelin, insulin, GLP-1, and PYY, alongside interactions via the gut-brain axis. These pathways link microbial composition to appetite regulation, fat storage, and energy balance. Emerging microbiome-targeted therapies, such as probiotics, prebiotics, dietary modulation (e.g., fiber-rich diets), fecal microbiota transplantation, and bacteriophage therapy, show promise in restoring GM balance, promoting weight loss, and improving metabolic health, though results vary and require further validation. Despite advances in metagenomics and metabolomics, gaps persist in establishing causality and long-term efficacy. The integration of GM data with host genetics, diet, and environmental factors through systems biology has the potential to facilitate personalized management of obesity. This review synthesizes the GM's role in obesity pathogenesis and hormonal regulation, highlighting therapeutic potential and research directions for microbiota-based prevention and treatment.},
}

Humans
*Obesity/microbiology/metabolism/therapy
*Gastrointestinal Microbiome
Probiotics/administration & dosage
Animals
Prebiotics/administration & dosage
Dysbiosis/microbiology
Fatty Acids, Volatile/metabolism

@article {pmid42091967,
year = {2026},
author = {Vinayagam, S and Bhowmick, IP and Rajendran, D and Arumugam, DK and Sekar, K and Renu, K and Kaur, H and Sattu, K},
title = {Genetic diversity and gut microbiome of Anopheles mosquitoes in Tamil Nadu by using COI DNA barcoding and 16S rRNA metagenomics.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42091967},
issn = {2045-2322},
support = {NER/85/2022-ECD-I//ICMR- Adhoc/ ; },
mesh = {Animals ; *Anopheles/genetics/microbiology/classification ; *RNA, Ribosomal, 16S/genetics ; *Genetic Variation ; *Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; *Gastrointestinal Microbiome/genetics ; *Electron Transport Complex IV/genetics ; Phylogeny ; India ; Bacteria/genetics/classification ; },
abstract = {Anopheles mosquitoes transmit infections to humans. Identifying the right mosquito species is crucial for vector control evaluation. This study uses COI gene DNA barcoding and 16S rRNA metagenomics to show the genetic diversity and gut microbial profile of undiscovered mosquito species. Three genera were found, including eight morphologically different Anopheles mosquitoes, and six mosquito species were molecularly validated, including An. moghulensis. The analysis of genetic diversity indicated that there is a state of balanced natural selection present. The species An. maculatus s.s. and An. stephensi exhibited nearly identical mutations, while An. moghulensis demonstrated evidence of purifying selection within the studied population. The gut microbiomes of An. moghulensis (149,377 reads), An. maculatus (51,016 reads), and An. dravidicus (33,126 reads) mosquitoes were also revealed. Afipia felis and Prevotella copri were the leading bacterial species, followed by other phyla including Proteobacteriota, Spirochaetes, and Firmicuteota. In An. moghulensis, alpha diversity assessments of Chao I incidence were dominating, whereas Shannon index was plentiful in An. maculatus s.s. mosquitoes. The mosquito's distinct bacterial species and shared microbial community are shown in the Venn diagram. These results suggest that the discovered bacterial taxa might be exploited to create vector control techniques for vector-borne illnesses.},
}

Animals
*Anopheles/genetics/microbiology/classification
*RNA, Ribosomal, 16S/genetics
*Genetic Variation
*Metagenomics/methods
*DNA Barcoding, Taxonomic/methods
*Gastrointestinal Microbiome/genetics
*Electron Transport Complex IV/genetics
Phylogeny
India
Bacteria/genetics/classification

@article {pmid42092044,
year = {2026},
author = {Loukas, A and Kalaentzis, K and Venetsianou, NK and Damianou, C and Paragkamian, S and Lagani, V and Jensen, LJ and Pafilis, E},
title = {CCMRI: a classification and curated database of climate change-related microbiome studies.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42092044},
issn = {2045-2322},
support = {2772//Hellenic Foundation for Research and Innovation/ ; },
mesh = {*Microbiota/genetics ; *Climate Change ; Metagenomics/methods ; Biocuration ; Metagenome ; *Databases, Factual ; Data Curation ; },
abstract = {Climate Change (CC) is reshaping all ecosystem processes and structures. Microbial data provide valuable insights into how microbial processes contribute to CC and how CC, in turn, alters microbial communities. However, the growing volume of environmental genomics data makes identifying CC-related records challenging. The Climate Change Metagenomic Record Index (CCMRI) has been developed to harvest metagenomic/microbiome records pertaining to CC and to provide researchers with a curated database of CC-related microbiome studies (https://ccmri.hcmr.gr). To guide interpretation, the database's 169 metagenomic studies have been labelled according to their relation to CC as CC-caused, CC-causing, and CC-mitigating. They have also been annotated with the CC phenomena they explore, like methane production, temperature rise, permafrost thawing, greenhouse gas emission, methanotrophy, and ocean acidification. To ease navigation, they have also been classified according to their biome as aquatic, terrestrial, host-associated, and engineered. The CCMRI database was initially constructed through manual curation of all aquatic and terrestrial studies in the MGnify resource. It was then expanded with the help of the CCMRI curation-assistant system. This leveraged Large Language Models to scan the remaining MGnify studies, filtered them for relevance, and proposed candidates for inclusion. With a recall greater than 90%, the system achieved high accuracy in identifying CC-related studies. The final decisions on CC-relatedness and categorization were performed by a human curator. This approach combines the efficiency of automation with human oversight and greatly reduces the curation effort, ensuring sustainability and scalability.},
}

*Microbiota/genetics
*Climate Change
Metagenomics/methods
Biocuration
Metagenome
*Databases, Factual
Data Curation

@article {pmid42121077,
year = {2026},
author = {Song, C and Li, Y and Deng, Y and He, D and Fan, X},
title = {Gut microbiota profiles associated with temporal lobe epilepsy and psychiatric comorbidities: a family-matched case-control 16S rRNA study.},
journal = {BMC neurology},
volume = {26},
number = {1},
pages = {},
pmid = {42121077},
issn = {1471-2377},
mesh = {Humans ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; *Epilepsy, Temporal Lobe/microbiology/epidemiology ; *RNA, Ribosomal, 16S/genetics ; Adult ; Case-Control Studies ; Comorbidity ; Middle Aged ; Feces/microbiology ; *Mental Disorders/microbiology/epidemiology ; },
abstract = {We investigated alterations in the intestinal microbiota of patients with temporal lobe epilepsy (TLE) and their associations with drug resistance and psychiatric comorbidities. Thirty TLE patients and 30 family-matched healthy controls sharing the same household diet were recruited, and fecal samples were analyzed by high-throughput 16S rDNA sequencing on the Illumina MiSeq [Formula: see text] bp platform. Differential abundance was assessed using Metastats and LEfSe with Benjamini-Hochberg false-discovery-rate correction, and independently validated using ANCOM-BC to account for the compositional nature of microbiome data. Community α- and β-diversity indices showed no significant differences between groups; however, ANCOM-BC identified species-level signatures in drug-resistant epilepsy, including significant depletion of Bacteroides plebeius and Coprococcus comes. Among psychiatric subgroups, Ruminococcus was significantly reduced in patients with comorbid depression, while Bilophila was enriched in those with comorbid anxiety and depression. Bacteroides stercoris distinguished the anxiety-plus-depression subgroup from the depression-only subgroup with robust support from both ANCOM and ANCOM-BC. Given the modest overall sample size ([Formula: see text] per arm) and small psychiatric and drug-resistance subgroups, these findings should be regarded as exploratory and hypothesis-generating associations rather than definitive biomarkers. They identify candidate microbial taxa warranting validation in larger, longitudinal cohorts combined with metagenomic and metabolomic approaches.},
}

Humans
Female
Male
*Gastrointestinal Microbiome/genetics
*Epilepsy, Temporal Lobe/microbiology/epidemiology
*RNA, Ribosomal, 16S/genetics
Adult
Case-Control Studies
Comorbidity
Middle Aged
Feces/microbiology
*Mental Disorders/microbiology/epidemiology

@article {pmid42121284,
year = {2026},
author = {Burkhart Colorado, AS and Nusbacher, NM and O'Connor, J and Marden, T and Higgins, J and Neff, CP and Fiorillo, S and Campbell, TB and Borok, M and Boyd, K and Sterrett, J and Palmer, BE and Lozupone, C},
title = {The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42121284},
issn = {2049-2618},
support = {R01 DK108366/DK/NIDDK NIH HHS/United States ; T15LM009451//U.S. National Library of Medicine/ ; R01 DK108366/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; Zimbabwe ; *HIV Infections/immunology/microbiology/drug therapy ; Female ; Male ; Adult ; Rural Population ; *Gastrointestinal Microbiome ; *Diet ; Urban Population ; Middle Aged ; Inflammation ; },
abstract = {BACKGROUND: People living with HIV (PLWH) suffer from chronic inflammation even with effective antiretroviral therapy (ART). A high-fat, low-fiber western-type diet has been linked with inflammation, in part through gut microbiome changes. In sub-Saharan Africa (SSA), a region with high HIV burden, urbanization has been linked with a shift from traditional agrarian towards westernized diets, and with changes in food security. To explore the relationship between diet, inflammation, and the gut microbiome in PLWH, we enrolled 1) ART Naïve PLWH who provided samples before and after 24 weeks of ART, 2) PLWH on ART at both timepoints and 3) HIV-seronegative controls. Individuals were evenly recruited from rural and urban Zimbabwe. Using a food frequency survey designed to measure intake of agrarian versus western-type food items in Zimbabwe, we determined how diet differs with urbanization, HIV-infection and treatment, and is related to inflammation and the gut microbiome.

RESULTS: Individuals residing in a rural area of Zimbabwe less frequently consumed high-fat, low-fiber western type food items and had lower consumption of diverse food items overall, except for sadza, a subsistence staple, processed from home-grown grains. Consumption of a more western-type diet correlated with lower CD4 + T cell percentage in untreated and treated PLWH and increased T cell exhaustion in PLWH on ART. PLWH on ART at time of enrollment also consumed diverse food items at a lower frequency and more often were underweight. Low food consumption correlated with muted improvements in T cell exhaustion after 24 weeks of ART. Individuals residing in the rural area had more Prevotella-rich/Bacteroides-poor microbiomes, but this was not significantly mediated by diet. Carbohydrate substrate degradation capabilities in the microbiome, based on predictions made using metagenomic polysaccharide utilization loci, correlated with dietary intake patterns.

CONCLUSIONS: Taken together, this work supports that consumption of more high-fat/low-fiber type food items has the potential to exacerbate HIV pathogenesis in a sub-Saharan setting where HIV burden is high and reinforces the importance of nutritional support for promoting immunologic response to ART in PLWH in SSA. Video Abstract.},
}

Humans
Zimbabwe
*HIV Infections/immunology/microbiology/drug therapy
Female
Male
Adult
Rural Population
*Gastrointestinal Microbiome
*Diet
Urban Population
Middle Aged
Inflammation

@article {pmid42129938,
year = {2026},
author = {Zhao, L and Wu, L and Yin, S and Gao, W and Xiang, X and Xie, Y and Guo, Y and Wang, Z},
title = {Multi-omics reveals effects of several rumen bacteria on reproductive performance of sheep.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42129938},
issn = {2049-2618},
support = {2025SNJF019//Three Agriculture Nine Party Science and Technology Cooperation Project/ ; 32573211//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Rumen/microbiology ; Sheep/microbiology/physiology ; Female ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Reproduction/physiology ; Multiomics ; Pregnancy ; Metagenomics/methods ; Metabolomics ; Litter Size ; *Gastrointestinal Microbiome ; Lactation ; },
abstract = {BACKGROUND: Mounting evidence indicates that the rumen microbiota plays a crucial role in the reproductive health of sheep. However, the potential beneficial effects of rumen microbiota on lambing performance in sheep across different stages of the reproductive cycle and the precise mechanisms underlying these effects remain unclear. We aimed to elucidate the rumen microbial regulatory network underlying differences in reproductive performance in sheep by integrating multi-stage metagenomics and metabolomics.

RESULTS: No significant difference was observed in the ruminal microbial α-diversity between sheep with high and low litter size. However, significant stage-specific segregation was observed in their community structures. We identified a cohort of key species strongly associated with litter size. These included Asaia bogorensis, Methanolobus zinderi, Erwinia gerundensis, Marinobacter sp. BSs20148, and Lactobacillus amylolyticus enriched during pregnancy; Rhizobium gallicum, Aeromonas caviae, Pseudolysobacter antarcticus, Mucilaginibacter rubeus, Thermococcus paralvinellae, and Janthinobacterium svalbardensis enriched during lactation; Pseudomonas mandelii, Gordonia sp. HY186, Arachidicoccus sp. BS20, Mesotoga prima, Acidovorax ebreus, Donacia cinerea, and Salmonella enterica enriched during estrus. Host plasma metabolomics analysis further revealed an enrichment of a set of core metabolites in the blood of high-fertility sheep, including Inositol, 2-Linoleoylglycerol, lysophosphatidylcholines and neuromodulatory substances such as tyramine and sphingosine-1-phosphate. We constructed stage-specific "rumen microbe-rumen metabolite-plasma metabolite" regulatory axes. These results suggest the influence of the rumen microbiome on plasma metabolic profiles and subsequent fertility outcomes in sheep.

CONCLUSION: We elucidate the dynamic mechanism by which the rumen microbiota in high-fertility sheep is associated with superior reproductive performance through stage-adaptive community succession and functional remodeling, which in turn may modulate the host's neuroendocrine and lipid metabolic profiles. These findings provide a new perspective for understanding the regulation of fertility in ruminants and lay a theoretical foundation for improving reproductive efficiency through nutritional strategies targeting the rumen microbiota. Video Abstract.},
}

Animals
*Rumen/microbiology
Sheep/microbiology/physiology
Female
*Bacteria/classification/genetics/isolation & purification/metabolism
*Reproduction/physiology
Multiomics
Pregnancy
Metagenomics/methods
Metabolomics
Litter Size
*Gastrointestinal Microbiome
Lactation

@article {pmid42300757,
year = {2026},
author = {Li, B and Li, S and Pei, Y and Sun, X and Ding, C and Yu, J and Zhou, M and Han, J and Yang, H and Wan, Y},
title = {Tibetan kefir grain-fermented milk attenuates DSS-induced colitis through coordinated regulation of intestinal barrier function, inflammation, and gut microbiota.},
journal = {Food & function},
volume = {17},
number = {13},
pages = {6062-6079},
doi = {10.1039/d6fo01565d},
pmid = {42300757},
issn = {2042-650X},
mesh = {Animals ; *Kefir/microbiology/analysis ; *Colitis/chemically induced ; Dextran Sulfate/adverse effects ; Intestinal Barrier Function ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; Fermentation ; Tibet ; Mice, Inbred C57BL ; Inflammation ; RAW 264.7 Cells ; Bacteria/classification/genetics/isolation & purification ; Milk ; Cultured Milk Products ; },
abstract = {This study evaluated the prophylactic efficacy of Tibetan kefir grain-fermented milk (Kefir-milk) in a dextran sulfate sodium (DSS)-induced colitis model and examined host- and fermentation-related changes associated with the intervention. Kefir-milk pretreatment attenuated disease activity, reduced colon shortening, and alleviated histopathological injury. These changes were accompanied by improved intestinal barrier-related readouts, including higher expression of ZO-1, Occludin, and MUC2, together with lower colonic MPO, TNF-α, IL-1β, and IL-6 levels. 16S rRNA profiling showed improved α-diversity, partial restoration of overall community structure, enrichment of Muribaculaceae and other genera commonly linked to intestinal homeostasis, and suppression of Escherichia-Shigella. Shotgun metagenomics indicated that the final Kefir-milk matrix was dominated by Lactobacillus-related taxa, while untargeted UPLC-HRMS/MS metabolomics revealed broad fermentation-associated remodeling of the milk metabolome, including altered relative abundances of features annotated as hippuric acid, p-cresyl sulfate, leucic acid, and phenyllactic acid. In LPS-challenged RAW264.7 macrophages, sterile filtered water-soluble extracts from Kefir-milk modulated polarization-associated marker expression and reduced pro-inflammatory cytokine responses at both transcript and protein levels. Collectively, these findings indicate that Kefir-milk attenuated DSS-induced colitis under the present experimental conditions and was associated with concurrent changes in barrier-related markers, gut microbiota, and the milk metabolome.},
}

Animals
*Kefir/microbiology/analysis
*Colitis/chemically induced
Dextran Sulfate/adverse effects
Intestinal Barrier Function
Mice
*Gastrointestinal Microbiome/drug effects
Male
Fermentation
Tibet
Mice, Inbred C57BL
Inflammation
RAW 264.7 Cells
Bacteria/classification/genetics/isolation & purification
Milk
Cultured Milk Products

@article {pmid42316995,
year = {2026},
author = {Gu, Y and Li, L and Zhang, H and Ye, T and Zhu, Q and Zhao, X and Xie, K and Ge, R and Han, J and Qin, Y},
title = {Dietary purple sweet potato anthocyanin extracts attenuate intestinal barrier decline in naturally aged mice via the microbiota-autophagy-stem cell axis.},
journal = {Food & function},
volume = {17},
number = {13},
pages = {6227-6245},
doi = {10.1039/d6fo00039h},
pmid = {42316995},
issn = {2042-650X},
mesh = {Animals ; *Anthocyanins/pharmacology ; *Ipomoea batatas/chemistry ; Mice ; *Aging/drug effects ; *Stem Cells/drug effects/metabolism ; *Plant Extracts/pharmacology ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects ; Intestinal Barrier Function/drug effects ; Male ; Intestinal Mucosa/drug effects/metabolism ; Dietary Supplements ; },
abstract = {Age-related deterioration of the intestinal epithelial barrier exacerbates systemic metabolic and functional decline, highlighting the gut as a key target for dietary interventions in healthy aging. Here, using naturally aged mice and intestinal organoids, we demonstrate that supplementation with purple sweet potato anthocyanins (PSPAs) alleviates systemic aging phenotypes, including impaired motor coordination, hepatic lipid dysregulation, insulin resistance, and cellular senescence, while concurrently restoring intestinal barrier integrity. PSPAs enhanced tight junction protein expression and epithelial architecture, independently of inflammation resolution, and promoted the proliferative and differentiation capacity of intestinal stem cells (ISCs). Metagenomic profiling revealed that PSPAs remodeled aging-associated gut microbiota composition and functions. Fecal microbiota transplantation established the causal contribution of microbiota remodeling to ISC rejuvenation, while luminal content-organoid assays confirmed the role of microbial metabolites. Integrative metabolomics identified metabolic changes linked to autophagy-related processes, including altered SCFA profiles, while transcriptomic analysis highlighted PI3K-AKT signaling as a major pathway associated with microbial and metabolic remodeling. Collectively, this multi-omics study establishes a mechanistic framework in which PSPAs alleviate aging-associated barrier decline through a "microbiota-autophagy-stem cell" axis, providing important insights into polyphenol-based strategies for gut-centered healthy aging.},
}

Animals
*Anthocyanins/pharmacology
*Ipomoea batatas/chemistry
Mice
*Aging/drug effects
*Stem Cells/drug effects/metabolism
*Plant Extracts/pharmacology
Mice, Inbred C57BL
*Gastrointestinal Microbiome/drug effects
Intestinal Barrier Function/drug effects
Male
Intestinal Mucosa/drug effects/metabolism
Dietary Supplements

@article {pmid42384916,
year = {2026},
author = {Kok, CR and Mulakken, NJ and Thissen, JB and Martí, JM and Lee, R and Trainer, JB and Goncalves, AR and Ranganathan, H and Avila-Herrera, A and Jaing, CJ and Be, NA},
title = {Meta2DB: curated shotgun metagenomic feature sets and metadata for health state prediction.},
journal = {Bioinformatics (Oxford, England)},
volume = {42},
number = {7},
pages = {},
doi = {10.1093/bioinformatics/btag422},
pmid = {42384916},
issn = {1367-4811},
support = {//Lawrence Livermore National Laboratory/ ; },
mesh = {*Metadata ; *Metagenomics/methods ; Humans ; *Databases, Genetic ; *Metagenome ; *Microbiota/genetics ; Biocuration ; Software ; },
abstract = {SUMMARY: Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13 897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on 4 January 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health.

AVAILABILITY: Data is available at https://gdo-meta2db.llnl.gov/ and https://zenodo.org/records/17315984.},
}

*Metadata
*Metagenomics/methods
Humans
*Databases, Genetic
*Metagenome
*Microbiota/genetics
Biocuration
Software

@article {pmid42386249,
year = {2026},
author = {Arenas-Montes, J and Garcia-Fernandez, H and Alcala-Diaz, JF and Boughanem, H and Allais, A and Gutierrez-Mariscal, FM and Arenas-de Larriva, AP and Ojeda-Rodriguez, A and Malagon, MM and Priego-Capote, F and Delgado-Lista, J and Perez-Martinez, P and Camargo, A and Lopez-Miranda, J},
title = {High postprandial endotoxemia is associated with recurrence of cardiovascular events in patients with coronary heart disease: from the CORDIOPREV randomized clinical trial.},
journal = {The American journal of clinical nutrition},
volume = {124},
number = {1},
pages = {101323},
doi = {10.1016/j.ajcnut.2026.101323},
pmid = {42386249},
issn = {1938-3207},
mesh = {Humans ; *Endotoxemia/complications/blood ; Male ; Female ; *Postprandial Period ; *Coronary Disease/complications/blood ; Middle Aged ; Lipopolysaccharides/blood ; Diet, Fat-Restricted ; Recurrence ; Diet, Mediterranean ; Aged ; Gastrointestinal Microbiome ; *Cardiovascular Diseases/etiology ; },
abstract = {BACKGROUND: The translocation into the systemic circulation of proinflammatory bacterial components such as lipopolysaccharide (LPS) has been linked to cardiovascular disease (CVD).

OBJECTIVES: We aimed to evaluate the association between baseline postprandial endotoxemia and the risk of suffering major adverse cardiovascular events (MACE) in patients with coronary heart disease (CHD), as well as the influence of consuming a low-fat (LF) diet or the Mediterranean (MED) diet on the associated risk.

METHODS: Our research was conducted within the framework of the CORDIOPREV Study, a clinical trial which involved 1002 patients with CHD randomly assigned to consume an LF diet or the MED diet for 7 y. A mixed meal was administered at the beginning of the study and after 3 y of follow-up. LPS plasma concentrations were measured by Limulus Amebocyte Lysate (LAL) colorimetric assay and gut microbiota was analyzed using 16S metagenomics.

RESULTS: Baseline postprandial increase in LPS plasma concentrations were associated with recurrence of MACE after a follow-up of 7 y, using Cox regression analysis [hazard ratio (HR):1.42 (1.01, 2.00)]. Patients with moderate LPS postprandial increase and consuming LF diet had higher risk of suffering MACE compared with the MED diet [HR: 1.45 (1.01, 2.09)]. Both diets reduced LPS plasma concentrations and formed a gut microbiota profile associated with a postprandial LPS decrease.

CONCLUSIONS: Our results suggest that the magnitude of postprandial endotoxemia is associated with suffering new MACE in patients with CHD, with the MED diet exercising a higher preventive role than an LF diet. Our results especially are relevant to clinical practice, supporting the measurement of postprandial endotoxemia as a tool for personalized medicine in secondary prevention. This study was registered at clinicaltrials.gov as NCT00924937.},
}

Humans
*Endotoxemia/complications/blood
Male
Female
*Postprandial Period
*Coronary Disease/complications/blood
Middle Aged
Lipopolysaccharides/blood
Diet, Fat-Restricted
Recurrence
Diet, Mediterranean
Aged
Gastrointestinal Microbiome
*Cardiovascular Diseases/etiology

@article {pmid42153646,
year = {2026},
author = {Revel-Muroz, AZ and Sonets, IV and Chistyakov, AS and Vasiluev, PA and Surovoy, YA and Ivanova, VA and Kozlovskaya, LI and Khokhlova, OE and Fursov, MV and Fursova, NK and Ulianov, SV and Tyakht, AV},
title = {Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.},
journal = {mSphere},
volume = {11},
number = {6},
pages = {e0013926},
pmid = {42153646},
issn = {2379-5042},
support = {075-15-2025-475//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Humans ; *COVID-19/microbiology ; *Metagenome ; *Lung/microbiology ; *Gastrointestinal Microbiome/genetics ; SARS-CoV-2 ; *Bacteria/genetics/classification/isolation & purification/drug effects ; Metagenomics/methods ; Plasmids/genetics ; Feces/microbiology ; Male ; Klebsiella pneumoniae/genetics ; Female ; Middle Aged ; Aged ; Candida/genetics/drug effects/isolation & purification ; Pandemics ; },
abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, particularly in intensive care units, where vulnerable patients are frequently exposed to multidrug-resistant microorganisms. The human gut microbiome serves as a key reservoir for AMR genes, which can disseminate to other body sites, including the lungs, especially during severe illness. We applied Hi-C metagenomics to stool samples from 11 critically ill COVID-19 patients and analyzed microbial isolates from their lungs to investigate intra-host transmission of AMR genes. Plasmid-resolved microbial interaction networks revealed AMR gene sharing across 13 bacterial genera, primarily from Firmicutes and Proteobacteria, with evidence of plasmid-mediated transfer across phylum boundaries and between gut and lung compartments. Notably, we identified genetically identical Klebsiella pneumoniae strains colonizing both the gut and lungs of a single patient, as well as shared plasmids carrying qnrS-1 and blaCTX-M-231 resistance genes between gut Escherichia coli and lung K. pneumoniae. In addition to bacterial pathogens, Candida yeast species isolated from both niches harbored resistance genes to multiple antifungal classes, including azoles. These findings underscore the dynamic, cross-compartmental nature of AMR dissemination within the human body and highlight the importance of integrative surveillance strategies to control resistance in clinical settings.IMPORTANCEWhile COVID-19 itself caused severe illness, many deaths were ultimately due to secondary microbial infections-often worsened by antibiotic resistance. Plasmids, which shuttle resistance genes between bacterial species, are key players in their spread, yet their roles in transmission, especially across body sites such as the gut and lungs, are to be elucidated. The use of Hi-C metagenomics allowed us to map bacterium-plasmid links in the guts of severe COVID-19 patients and reconstruct high-quality genomes of opportunistic fungi. Comparing these with lung-derived isolate genomes, we gained insight into possible intra-host dissemination routes of resistance genes. Preparing for future pandemics will require not only rapid pathogen detection but also tools to monitor microbiome health and resistance dynamics, and understanding how treatments and microbial imbalances shape infection risks.},
}

Humans
*COVID-19/microbiology
*Metagenome
*Lung/microbiology
*Gastrointestinal Microbiome/genetics
SARS-CoV-2
*Bacteria/genetics/classification/isolation & purification/drug effects
Metagenomics/methods
Plasmids/genetics
Feces/microbiology
Male
Klebsiella pneumoniae/genetics
Female
Middle Aged
Aged
Candida/genetics/drug effects/isolation & purification
Pandemics

@article {pmid42381379,
year = {2026},
author = {Vaaben, TH and Lützhøft, DO and Hedin, KA and Ahonen, L and Vazquez-Uribe, R and Sommer, MOA},
title = {Multi-omics analysis of saccharomyces boulardii supplementation reveals coordinated microbiome, metabolic, and immune signaling changes accompanying tumor suppression.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2690687},
doi = {10.1080/19490976.2026.2690687},
pmid = {42381379},
issn = {1949-0984},
mesh = {Animals ; *Probiotics/administration & dosage ; Multiomics ; *Saccharomyces boulardii/physiology ; Receptors, Aryl Hydrocarbon/metabolism/agonists ; Signal Transduction ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/immunology/microbiology/metabolism/therapy ; Mice ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {The gut microbiome shapes cancer progression and treatment responses, yet scalable microbiome-targeted interventions remain limited. We screened commercial probiotics for activation of the host aryl hydrocarbon receptor (AhR) and identified the yeast Saccharomyces boulardii as a consistent AhR activator. In an immunocompetent syngeneic colorectal cancer model, daily oral gavage of S. boulardii slowed growth of established subcutaneous tumors without detectable tumor colonization. Integrated profiling of the gut microbiome, circulating metabolites, cytokines, and tumor transcriptomes revealed a coordinated systemic response. S. boulardii increased microbial diversity and functionally rebalanced the gut microbiota, enriching taxa with lower genome-encoded biosynthetic autonomy. These changes were accompanied by elevated plasma levels of several indole metabolites, including the AhR agonists 5-hydroxyindole-3-acetic acid (5-HIAA) and indole-3-propionic acid (IPA). Targeted LC-MS/MS showed that S. boulardii can produce 5-HIAA under culture conditions, whereas IPA was not detected, suggesting that increased plasma levels of these metabolites may arise through a combination of probiotic activity and broader microbiome-associated processes. Circulating IL-17A and CTLA-4 were reduced, and tumors exhibited downregulation of programs linked to invasion, inflammation, and KRAS signaling. Multi-omics integration showed strong covariation across microbial, metabolic, immune signaling, and tumor compartments, highlighting coordinated cross-compartment responses during S. boulardii-associated tumor suppression.},
}

Animals
*Probiotics/administration & dosage
Multiomics
*Saccharomyces boulardii/physiology
Receptors, Aryl Hydrocarbon/metabolism/agonists
Signal Transduction
*Gastrointestinal Microbiome
*Colorectal Neoplasms/immunology/microbiology/metabolism/therapy
Mice
Bacteria/classification/genetics/isolation & purification

@article {pmid42385223,
year = {2026},
author = {Haque, ME and Rahman, MS and Sultana, M and Begum, A},
title = {Seasonal Restructuring of Microbial Communities and Resistomes in the Shitalakshya River, Bangladesh Revealed by Shotgun Metagenomics.},
journal = {MicrobiologyOpen},
volume = {15},
number = {4},
pages = {e70359},
pmid = {42385223},
issn = {2045-8827},
mesh = {*Rivers/microbiology/chemistry ; *Metagenomics ; Seasons ; Bangladesh ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Microbiota/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Water Quality ; Shotgun Sequencing ; },
abstract = {Urban rivers supplying drinking water face mounting pollution and AMR threats. We combined shotgun metagenomics with physicochemical analysis to investigate microbial community and resistome dynamics in Bangladesh's Shitalakshya River, a drinking water source under increasing pollution pressure, during early and peak dry seasons. Peak dry season water quality deteriorated markedly, characterized by hypoxia and elevated nutrient and organic carbon levels, which drove pronounced restructuring of the river microbiome. A distinct shift occurred from Myroides dominance toward a more diverse assemblage enriched in pollution-tolerant and opportunistic genera, notably Comamonas, Brevundimonas, Tissierella, and Aeromonas. Metagenomic profiling revealed a diverse resistome encompassing antibiotic, metal, and biocide resistance genes. Although overall antibiotic resistance gene abundance declined slightly, metal resistance genes increased more than twofold, with strong enrichment of mercury resistance determinants such as merA. Concurrent increases in multidrug efflux pump genes suggested potential co-selection driven by metal and chemical stressors. These findings indicate that dry-season pollutant concentration reshapes both microbial communities and resistance profiles through non-antibiotic selective pressures. Despite limited sampling, this study provides a baseline metagenomic snapshot of antimicrobial resistance dynamics in a climate-stressed urban river system, offering vital insights for pollution abatement and the safeguarding of drinking water safety.},
}

*Rivers/microbiology/chemistry
*Metagenomics
Seasons
Bangladesh
*Bacteria/genetics/classification/drug effects/isolation & purification
*Microbiota/genetics
*Drug Resistance, Bacterial/genetics
Metagenome
Water Quality
Shotgun Sequencing

@article {pmid41738567,
year = {2026},
author = {Ma, M and Liu, B and Zhou, J and Zhang, J and Zhang, Y and Li, W and Liu, X and Xu, D},
title = {Viral Community Profiling of RNA Viruses in Lesion Tissues From Hyriopsis cumingii With Epidemic Disease via Metatranscriptomics and VirID-Based RdRP Mining.},
journal = {Journal of fish diseases},
volume = {49},
number = {8},
pages = {e70143},
doi = {10.1111/jfd.70143},
pmid = {41738567},
issn = {1365-2761},
support = {2024SKLBC-KF02//National Key Laboratory of Aquatic Animal Disease Control and Healthy Aquaculture, 2024 Open Research Projects/ ; },
mesh = {Animals ; *RNA Viruses/genetics/classification/isolation & purification/physiology ; Phylogeny ; *Unionidae/virology ; RNA-Dependent RNA Polymerase/genetics ; Metagenomics ; Transcriptome ; Epidemics/veterinary ; *Virome ; Hepatopancreas/virology ; },
abstract = {To identify enriched pathogens and characterise the viral community associated with epidemic disease outbreaks in the freshwater mussel Hyriopsis cumingii, we performed metatranscriptomic sequencing combined with VirID-driven RNA-dependent RNA polymerase (RdRP) mining and phylogenetic analysis using hepatopancreas and intestinal samples from six severely infected individuals. Clinical observations were consistent with hallmark features of epidemic outbreaks. The sequencing yielded 86.2 Gb of raw data, of which 97.1% passed quality control, resulting in 77.7 Gb of high-quality clean data. Taxonomic annotation identified 182 viral species, predominantly unclassified viruses (45% Transcripts Per Million, TPM), followed by members of the phyla Lenarviricota (28%) and Uroviricota (17%). Phylogenetic analysis of RdRP sequences revealed 13 viral supergroups, with the Picorna-Calici supergroup showing the highest abundance (26.2% of annotated viruses) and reaching a prevalence of 39.3% in sample HcAV3. Notably, 89.6% of the identified viral RdRPs exhibited less than 70% amino acid identity to known viral sequences, highlighting the presence of extensive "viral dark matter" in this host species. This study establishes the first viral profile associated with epidemic disease in H. cumingii, providing a baseline for further etiological research on this high-mortality aquaculture disease.},
}

Animals
*RNA Viruses/genetics/classification/isolation & purification/physiology
Phylogeny
*Unionidae/virology
RNA-Dependent RNA Polymerase/genetics
Metagenomics
Transcriptome
Epidemics/veterinary
*Virome
Hepatopancreas/virology

@article {pmid42071059,
year = {2026},
author = {Gajjar, K and Panchal, D and Chaudhary, M and Raval, I and Chaudhary, D and Patel, CK and Bagatharia, S and Joshi, C and Patel, A and Dharajiya, D},
title = {Multi-omics characterization of microbial and metabolite profiles of Jeevamrit and Ghanjeevamrit cow-based bioformulations used in sustainable agriculture.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42071059},
issn = {2045-2322},
support = {GSBTM/JD(R&D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; },
mesh = {Multiomics ; Animals ; Metabolomics/methods ; *Agriculture/methods ; Cattle ; Metagenomics/methods ; Gas Chromatography-Mass Spectrometry ; *Metabolome ; Chromatography, Liquid ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/metabolism ; *Microbiota ; Soil Microbiology ; },
abstract = {Jeevamrit (JV) and Ghanjeevamrit (GH) are traditional cow-based bioformulations used in natural farming practices, and this study provides a comprehensive characterization of their microbial profiles via 16 S rRNA amplicon metagenomics and metabolite profiles via GC-MS and LC-MS analysis, with two different groups of samples: experimental preparation (EP) and farmer preparation (FP). JV and GH harbored diverse and functionally rich microbial communities, including Lactiplantibacillus, Arcobacter, Comamonas, Planifilum, Pseudomonas, Gp6, etc., associated with nutrient cycling, microbial activity, and plant growth promotion. Untargeted metabolomics revealed ~ 222 (GC-MS) and ~ 1049 (LC-MS) metabolites in Jeevamrit and ~ 96 (GC-MS) and ~ 1208 (LC-MS) metabolites in Ghanjeevamrit. These metabolites were primarily classified as organoheterocyclic compounds, organic acids, lipids, benzenoids, and organic oxygen/nitrogen compounds, and are functionally associated with nutrient solubilization, microbial metabolism, regulation of plant growth, and enhancement of stress tolerance. Multi-omics analysis revealed a clear separation of EP and FP groups with high inter-omics correlations (Jeevamrit up to r = 0.92; Ghanjeevamrit up to r = 0.91). Jeevamrit exhibited dense connectivity with predominance of positive microbial-metabolite associations, while Ghanjeevamrit displayed fewer and more balanced positive and negative correlations. Overall, the study demonstrates that Jeevamrit and Ghanjeevamrit are microbially diverse and metabolically rich bioformulations, reinforcing their roles in enhancing soil health and plant growth. Future works on strain-level diversity, functional pathways analysis, and field trials across different crops and soil types are needed for the standardization and optimization of natural farming inputs.},
}

Multiomics
Animals
Metabolomics/methods
*Agriculture/methods
Cattle
Metagenomics/methods
Gas Chromatography-Mass Spectrometry
*Metabolome
Chromatography, Liquid
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/metabolism
*Microbiota
Soil Microbiology

@article {pmid42103925,
year = {2026},
author = {Anil, and Ramesh, KB and Gouda, MNR and Subramanian, S},
title = {Microbial zonation and functional roles in the gut of white grub (Maladera insanabilis) larvae.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42103925},
issn = {2045-2322},
mesh = {Animals ; Larva/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Gastrointestinal Microbiome ; Metagenomics ; Phylogeny ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Tract/microbiology ; },
abstract = {Maladera insanabilis, a widespread and destructive agricultural pest in India, thrives in nitrogen-deficient subsoil environments due to its dependency on gut bacteria. In particular, the hindgut is an anaerobic fermentation chamber, supporting microbial-driven nitrogen transformations essential for larval development. Despite its ecological significance, detailed studies exploring gut bacterial diversity and functional role in M. insanabilis are lacking. This study integrates metagenomics, culture-based techniques, enzymatic assays, and gene expression analyses to characterize the nitrogen-cycling potential of gut microbiota along the different gut compartments. The culture-based analysis isolated 16 aerobic and 8 anaerobic bacterial strains, predominantly from Bacillota and Pseudomonadota. High-throughput 16 S rRNA Illumina sequencing revealed 134 shared amplicon sequence variants (ASVs), with distinct bacterial assemblages, Burkholderia and Pseudomonas in the foregut, Paenibacillus in the midgut, and anaerobic genera such as Bacteroides and Desulfovibrio dominating the hindgut. Functional annotation using the KEGG database indicated that anaerobic gut bacteria are actively involved in nitrification, denitrification, and nitrogen fixation. The Enzyme assays confirmed high nitrate and nitrite reductase activity, with Burkholderia contaminans and Bacillus cepacia showing the highest activities. Michaelis-Menten kinetics and Lineweaver-Burk analysis (R[2] = 0.9871) showed a higher capacity (Vmax) for nitrate and nitrite reduction; a small Km indicates a high affinity for nitrate and nitrite. Gene expression studies viz., hzo, nifH, amx, nirS, and nirK revealed a significantly high expression level in the hindgut, especially under vermicompost treatment. This study provides the first comprehensive insight into nitrogen-cycling gut bacteria in M. insanabilis, highlighting their role in host nutrition and nitrogen transformation. These findings lay a foundation for future microbiome-targeted pest control strategies aimed at disrupting nutrient acquisition in soil-dwelling grubs.},
}

Animals
Larva/microbiology
*Bacteria/genetics/classification/metabolism/isolation & purification
*Gastrointestinal Microbiome
Metagenomics
Phylogeny
Nitrogen/metabolism
RNA, Ribosomal, 16S/genetics
Gastrointestinal Tract/microbiology

@article {pmid42371206,
year = {2026},
author = {He, Y and He, G and Zhang, Q and Song, Y and Zhong, Z and Guo, Z and Xiong, J and He, T},
title = {Efficiency of nitrogen and phosphorus cycling in paddy soils is directly driven by functional gene-microbe co-occurrence networks and indirectly controlled by soil physicochemical properties.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42371206},
issn = {1573-0972},
support = {42367039//National Natural Science Foundation of China/ ; 42267038//National Natural Science Foundation of China/ ; 2022YFD1901505//the National Key Research and Development Program of China/ ; },
mesh = {*Phosphorus/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen/metabolism ; Oryza/growth & development ; *Nitrogen Cycle ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenome ; China ; Microbiota/genetics ; },
abstract = {Rice productivity in karst regions is often constrained by low nitrogen (N) and phosphorus (P) use efficiency, yet the attributes associated with reduced nutrient cycling function in medium- and low-yield paddy fields remain unclear. We selected five representative paddy soil profiles in Qianxi City, Guizhou Province, comprising one high-yield field, one medium-yield field and three low-yield fields characterised by sandy soil, water deficit or waterlogging. These profiles contained 23 diagnostic horizons, yielding 23 composite soil samples for analyses of soil physicochemical properties, enzyme activities, metagenome-derived functional gene abundance and microbial community composition. Integrative analyses, including redundancy analysis, co-occurrence networks, random forest modelling and structural equation modelling (SEM), were used to evaluate attributes associated with nitrogen and phosphorus cycling functional potential. Across paddy field types, N- and P-cycling functional genes showed distinct abundance patterns. In the waterlogged low-yield field, the abundance value of nifH reached 525.33 reads, 5.3-fold higher than that in the high-yield field. Genes associated with organic P mineralisation and regulation, including phoD, phoU and ppnK, ranged from 608 to 2,480 reads across field types. Microbial taxonomic profiles associated with N- and P-cycling functions also differed among paddy fields. Available phosphorus showed the strongest association with P-cycling functional profiles (Mantel r = 0.72). SEM showed that gene-related variables were positively associated with integrated N and P cycling functional potential (path coefficient = 0.567, P < 0.01), whereas soil microbial variables were negatively associated with this potential (- 0.619, P < 0.01). These results identify attributes associated with nutrient cycling constraints in karst paddy fields and provide a basis for targeted nutrient management.},
}

*Phosphorus/metabolism
*Soil Microbiology
*Soil/chemistry
*Nitrogen/metabolism
Oryza/growth & development
*Nitrogen Cycle
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenome
China
Microbiota/genetics

@article {pmid42374590,
year = {2026},
author = {Fürnwein, L and Tichy, J and Waldherr, M and Lehner, E and Ortbauer, M and Vassallo, Y and Sipek, B and Sterflinger, K and Piñar, G and Graf, AB},
title = {Uncovering transcriptional processes in microbial communities adapted to differing saline conditions in salt-weathered historic buildings.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42374590},
issn = {2049-2618},
support = {Heritage_2020-005_RESTOROMIC//Österreichischen Akademie der Wissenschaften/ ; },
mesh = {Austria ; *Microbiota/genetics ; Metagenome ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Sodium Chloride ; Transcriptome ; Salinity ; Adaptation, Physiological ; },
abstract = {BACKGROUND: Microbial colonization of architectural surfaces in historic buildings can cause not only aesthetic damage but also biodeterioration. One example is the colonizing microbiome on salt-weathered architectural surfaces. Halotolerant and halophilic communities on such surfaces produce colored pigments that visually alter cultural heritage sites and could potentially degrade organic binders used for mural paintings. Although the microorganisms involved in these deterioration processes have already been described, detailed information about the molecular processes that allow these communities to succeed, survive, and thrive under such extreme conditions is still lacking.

RESULTS: A combined metagenome and metatranscriptome approach were employed to investigate three sampling sites located in two Austrian historic buildings displaying different environmental and saline compositions. The chapel of St. Virgil (Vienna) is a subsurface, climate-controlled environment. In contrast, the Charterhouse Mauerbach (Lower Austria) is exposed to natural fluctuations in temperature and humidity. DNA and total RNA were extracted from each sampling site simultaneously and sequenced. Two methods for gene assembly were compared and functionally evaluated. Results showed a minor bias in both methods, with improved results when they were combined. Comparison between DNA and RNA showed interesting variations in the taxonomic composition between the DNA- and RNA-based dataset, distinguishing the dormant from the active microbiome. The annotated halotolerance mechanisms in the metatranscriptomes indicated genome and proteome adaptations, showing high GC content, proteome acidification, with elevated aspartate and glutamate levels, and low isoelectric point profiles. Furthermore, the communities used both "salt-in" and "salt-out" osmoregulatory mechanisms. Pigment production was confirmed in all sampling points, revealing diverse pathways for carotenoid biosynthesis. Various protective mechanisms against oxidative stress were detected, such as those against reactive oxygen species (ROS), but also detoxification, protein folding, protein and DNA repair, and RNA chaperones. Key metabolic pathways revealed diverse pathways related to carbon, nitrogen, and sulfur cycling, linked to varying oxygen concentrations within biofilms. The results also highlighted the need for an in-depth analysis of the capabilities of the involved microorganisms.

CONCLUSIONS: The study shows highly specialized and cooperative adaptations, using both "salt-in" and "salt-out" strategies, diverse phototrophic and redox metabolisms that tightly couple C-N-S cycling.},
}

Austria
*Microbiota/genetics
Metagenome
*Bacteria/genetics/classification/isolation & purification/metabolism
Sodium Chloride
Transcriptome
Salinity
Adaptation, Physiological

@article {pmid42376319,
year = {2026},
author = {Gu, Z and Tan, Q and Mao, D and Zhang, Y and Wang, Y and He, D and Chen, S},
title = {Metagenomic analysis of human feces reveals gut microbiome role in colorectal cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1828012},
pmid = {42376319},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Feces/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Multiomics ; High-Throughput Nucleotide Sequencing ; Adult ; Metagenome ; },
abstract = {BACKGROUND: This study aimed to identify the microbiota and specific genes that are closely associated with colorectal cancer (CRC) through metagenomic sequencing and integrative multi-omics analysis.

METHODS: Fecal samples were collected from 11 healthy volunteers and 20 patients with CRC. Genomic DNA was extracted for metagenomic analysis and high-throughput sequencing. Compositional differences and correlations of the gut microbiome were compared based on species and functional diversity.

RESULTS: The overall species composition included 1,980 species, with 1,707 species identified in the CRC group and 1,525 in the healthy control group. Alpha diversity was significantly lower in the CRC group than in the healthy control group (p = 0.014). Beta diversity analysis revealed significant differences between the two groups (stress = 0.1308, p = 0.021). Based on LEfSe analysis, Shigella, Porphyromonas, Proteus, Bacteroides, Alistipes, Fusobacterium, and Escherichia were more abundant in patients with CRC, whereas Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella were significantly more abundant in the healthy control group (p < 0.05).

CONCLUSION: A multidimensional microbial diagnostic model, incorporating Shigella, Porphyromonas, Proteus, Bacteroides, Fusobacterium, Escherichia, Eubacterium, Clostridium, Dialister, Faecalibacterium, Blautia, Coprococcus, Dorea, Subdoligranulum, Megamonas, Roseburia, and Prevotella, suggests the potential to enhance early CRC screening performance. Furthermore, LptA, tnaA, envC, and argB may represent promising candidates for novel therapeutic targets, warranting further investigation.},
}

Humans
*Colorectal Neoplasms/microbiology
*Feces/microbiology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Female
Male
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Aged
Multiomics
High-Throughput Nucleotide Sequencing
Adult
Metagenome

@article {pmid42377624,
year = {2026},
author = {Mwazembe, KJ and Chauhan, A and Pathak, A and Chukwujindu, C},
title = {Isolation and characterization of microalgal growth-enhancing bacteria from a wastewater treatment facility.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42377624},
issn = {1573-0972},
mesh = {*Wastewater/microbiology ; *Microalgae/growth & development/microbiology ; Phylogeny ; *Bacteria/isolation & purification/classification/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Biomass ; Microbial Consortia ; Coculture Techniques ; Biofuels ; DNA, Bacterial/genetics ; Metagenomics ; Water Purification ; },
abstract = {Microalgae-bacteria interactions represent a promising approach for improving microalgal growth and biomass productivity, with potential applications in biofuel production, wastewater remediation, and the synthesis of value-added bioproducts. In this study, enriched microalgae consortia from the Tallahassee Wastewater Treatment Facility were first characterized using shotgun metagenomic sequencing to assess their taxonomic composition and functional potential. The consortia were dominated by Chlorella species and associated with diverse bacterial communities. Subsequently, bacterial strains were isolated and characterized to evaluate their potential as natural growth enhancers for microalgae. Eight bacterial isolates, Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., Agrobacterium tumefaciens, Citrobacter freundii, Cellulosimicrobium sp., Stenotrophomonas pavanii, and Mycobacterium sp. SMC-4 were identified through 16 S rRNA sequencing and phylogenetic analysis. The influence of these isolates on microalgae was assessed using a membrane-separated coculture system that enabled metabolite exchange without direct cell-to-cell contact. Microalgal growth, monitored through optical density (OD) at 680 nm over 18 days, showed significant enhancement across all bacterial treatments compared to the reference (microalgae without bacteria). The most pronounced effects were observed with Mesorhizobium sp., Enterococcus avium, Stenotrophomonas sp., and Agrobacterium tumefaciens, which exhibited the highest growth responses. These findings suggest that wastewater-derived bacteria can substantially enhance microalgal growth performance, likely through metabolite-mediated interactions. This study expands the repository of algal-supportive bacterial taxa and highlights the potential of targeted microalgae-bacteria consortia for scalable and sustainable bioprocessing.},
}

*Wastewater/microbiology
*Microalgae/growth & development/microbiology
Phylogeny
*Bacteria/isolation & purification/classification/genetics/metabolism
RNA, Ribosomal, 16S/genetics
Biomass
Microbial Consortia
Coculture Techniques
Biofuels
DNA, Bacterial/genetics
Metagenomics
Water Purification

@article {pmid42378712,
year = {2026},
author = {Mamie, C and Cabalzar-Wondberg, D and Turina, M and Wawrzyniak, M and Misselwitz, B and Zamboni, N and Gottier, C and Lang, S and Rogler, G and Avivar-Valderas, A and de la Rosa, O and Candela, N and Tang, J and Morsy, Y and Scharl, M},
title = {Multiomics analysis dissects the molecular foundation of perianal fistulas associated with Crohn's disease and of cryptoglandular origin.},
journal = {Journal of Crohn's & colitis},
volume = {20},
number = {6},
pages = {},
pmid = {42378712},
issn = {1876-4479},
support = {//Takeda Pharmaceutical Company Ltd/ ; },
mesh = {Humans ; *Crohn Disease/complications/genetics/microbiology ; *Rectal Fistula/genetics/microbiology/etiology/pathology/metabolism ; Multiomics ; Female ; Male ; Adult ; Epithelial-Mesenchymal Transition/genetics ; Transcriptome ; Middle Aged ; Intestinal Mucosa/pathology/metabolism ; Gastrointestinal Microbiome/genetics ; Gene Expression Profiling ; Metabolomics ; },
abstract = {BACKGROUND AND OBJECTIVE: Perianal fistulas, either of cryptoglandular origin (CgF) or associated with Crohn's disease (CDF), have limited treatment options and pose a tremendous burden for affected patients. We recently showed that the epithelial-mesenchymal transition (EMT) contributes to CDF pathogenesis, but detailed mechanisms need further evaluation. Here, we performed multiomics analysis to gain further molecular insights into fistula pathogenesis.

DESIGN: Rectal biopsies, swabs, fistula curettage, and serum samples were derived from patients with either CDF (n = 23) or CgF (n = 17) and analyzed by bulk RNA sequencing, metagenomics, untargeted metabolomics, or multiplex-ELISA, where appropriate.

RESULTS: Transcriptomics revealed striking differences in gene expression between rectal mucosa and fistula tract samples. However, the transcriptomes of CDF and CgF were comparable, and genes involved in EMT, inflammation and tumor necrosis factor signaling were prominent in both fistula types. A set of 18 genes was found to be differentially expressed in CDF and CgF and might allow discrimination. The overall microbiome composition within fistula tracts did not differ between CDF and CgF patients, but there was a significant difference in rectal microbiome compositions. On a species level, we detected an enrichment of disease-specific, pathogenic species in the fistula tracts. Of note, Bacteroides ssp., Fusobacterium animalis, and Staphylococcus aureus prevailed within CDF.

CONCLUSION: Our data demonstrate only minor differences in the transcriptome and the microbiome between CDF and CgF, but clear differences when compared to rectal mucosa biopsies. Thus, our data suggest that the molecular makeup underlying the pathophysiology of fistulas might be comparable between CDF and CgF.},
}

Humans
*Crohn Disease/complications/genetics/microbiology
*Rectal Fistula/genetics/microbiology/etiology/pathology/metabolism
Multiomics
Female
Male
Adult
Epithelial-Mesenchymal Transition/genetics
Transcriptome
Middle Aged
Intestinal Mucosa/pathology/metabolism
Gastrointestinal Microbiome/genetics
Gene Expression Profiling
Metabolomics

@article {pmid42104260,
year = {2026},
author = {Nguyen, TT and Steen, IH and Bøe, MH and Otterlei, M and Stokke, R},
title = {Arctic deep-sea hydrothermal microbiomes as a natural niche for novel antimicrobial peptides.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42104260},
issn = {1471-2180},
mesh = {*Hydrothermal Vents/microbiology ; *Antimicrobial Peptides/pharmacology/genetics/chemistry ; Arctic Regions ; *Microbiota ; Biofilms ; *Bacteria/genetics/classification/drug effects ; *Seawater/microbiology ; Archaea/genetics/classification/metabolism ; Metagenomics ; *Antimicrobial Cationic Peptides/pharmacology ; Microbial Sensitivity Tests ; },
abstract = {BACKGROUND: The escalating threat of antimicrobial resistance (AMR) has created an urgent need for new antimicrobial agents. Antimicrobial peptides (AMPs) are promising alternatives to conventional antibiotics due to their broad-spectrum activity and reduced risk of resistance development. While most AMP discovery efforts have focused on terrestrial microbes, extreme environments remain largely untapped. Deep-sea hydrothermal vent biofilms, such as those from the Arctic Mid-Ocean Ridges (AMOR), are unique ecosystems characterized by high pressure, temperature gradients, and chemical extremes. These conditions select for microorganisms with specialized adaptations, including the production of bioactive compounds that confer survival advantages. Such peptides may exhibit enhanced stability and novel mechanisms of action, making hydrothermal biofilms an exceptional resource for next-generation antimicrobials.

RESULTS: Using metagenomic and metatranscriptomic datasets from nine recently published AMOR biofilms, we predicted 961 AMP sequences with Macrel, of which 873 were unique and showed no identity to entries in the Antimicrobial Peptide Database (APD). AMPs were distributed across 51 microbial phyla, including underrepresented archaeal groups such as Asgardarchaeota, Nanoarchaeota, and Micrarchaeota. Transcriptomic profiling detected AMP expression in 25 phyla, including low-abundance candidate taxa, highlighting active AMP production. In silico minimum inhibitory concentration (MIC) prediction using APEX 1.1 suggested that 16.7% of AMPs may inhibit at least one clinically relevant pathogen, with Acinetobacter baumannii emerging as the most susceptible. Four peptides were synthesized for experimental validation; AMP OLKFNNDA_52_10 exhibited moderate in vitro activity against Staphylococcus aureus and weak activity against Escherichia coli, while showing low cytotoxicity toward human HEK293 cells. Other tested peptides displayed weak or no activity, underscoring discrepancies between computational predictions and biological outcomes.

CONCLUSIONS: Our study reveals extensive taxonomic and structural diversity of AMPs in Arctic hydrothermal vent biofilms and identifies novel candidates withbioactive potential. These findings emphasize the importance of integrating metagenomics, transcriptomics, machine learning, and experimental validation to uncover bioactive compounds from underexplored microbial ecosystems. Overall, AMOR biofilms represent a rich and untapped source of AMPs, offering new opportunities for antimicrobial drug discovery in the fight against AMR.},
}

*Hydrothermal Vents/microbiology
*Antimicrobial Peptides/pharmacology/genetics/chemistry
Arctic Regions
*Microbiota
Biofilms
*Bacteria/genetics/classification/drug effects
*Seawater/microbiology
Archaea/genetics/classification/metabolism
Metagenomics
*Antimicrobial Cationic Peptides/pharmacology
Microbial Sensitivity Tests

@article {pmid42115187,
year = {2026},
author = {Zhang, J and Chen, F and Xu, X and Zhang, L and Zhang, L and Qin, B and Li, K and Liu, Q and Hou, H and Li, Y and Liu, C and Li, Y and Shi, J and Teng, T and Wang, C and Zhou, X},
title = {Gut microbiota dysbiosis drives depression-like behavior in adolescent rats via lysine-regulated mTOR autophagy pathway.},
journal = {Translational psychiatry},
volume = {16},
number = {1},
pages = {},
pmid = {42115187},
issn = {2158-3188},
mesh = {Animals ; *Autophagy/physiology ; Rats ; *TOR Serine-Threonine Kinases/metabolism ; *Major Depressive Disorder/microbiology/metabolism ; Male ; *Dysbiosis/metabolism/complications ; *Gastrointestinal Microbiome/physiology ; *Lysine/metabolism/blood ; Rats, Sprague-Dawley ; Fecal Microbiota Transplantation ; Disease Models, Animal ; Prefrontal Cortex/metabolism ; Behavior, Animal ; Humans ; Adolescent ; Sirolimus/pharmacology ; Depression ; },
abstract = {The prevalence of major depressive disorder (MDD) is increasing globally, particularly among adolescents. Although gut-brain axis dysfunction has been implicated in adolescent depression, the mechanisms by which gut microbiota dysbiosis drives depressive behaviors and potential antidepressant targets remain unclear. In this study, fecal microbiota transplantation (FMT) was performed from either healthy controls (HCs) or adolescents with MDD into antibiotic-treated adolescent rats. FMT from MDD adolescents induced depressive-like behaviors in recipient rats. Metagenomic sequencing revealed that FMT from MDD adolescents led to alterations in gut microbiota in recipient rats. While qPCR, Western blotting, immunofluorescence, and transmission electron microscopy (TEM) confirmed that these rats exhibited prefrontal cortex (PFC) autophagy hyperactivation, evidenced by a reduction in SQSTM1/p62 levels, an elevation in the LC3-II/LC3-I ratio, upregulated Beclin1, and increased numbers of autolysosomes. Similar autophagy-related transcriptional changes were observed in peripheral blood from MDD adolescents. Furthermore, ELISA showed reduced plasma lysine levels in MDD adolescents and decreased lysine concentrations in the PFC of FMT-MDD rats. The antidepressant effect of lysine and its interaction with autophagy were explored in a chronic unpredictable mild stress (CUMS) rat model with or without rapamycin (the autophagy activator, RAPA). Lysine supplementation alleviated depressive-like behaviors and suppressed PFC autophagy hyperactivation, while these effects were abolished by RAPA co-treatment. These findings reveal lysine deficiency as a metabolic bridge between gut microbiota imbalance and neuronal autophagy dysregulation, suggesting a gut microbiota-lysine-autophagy axis as an innovative mechanism and therapeutic focus for adolescent depression.},
}

Animals
*Autophagy/physiology
Rats
*TOR Serine-Threonine Kinases/metabolism
*Major Depressive Disorder/microbiology/metabolism
Male
*Dysbiosis/metabolism/complications
*Gastrointestinal Microbiome/physiology
*Lysine/metabolism/blood
Rats, Sprague-Dawley
Fecal Microbiota Transplantation
Disease Models, Animal
Prefrontal Cortex/metabolism
Behavior, Animal
Humans
Adolescent
Sirolimus/pharmacology
Depression

@article {pmid42127418,
year = {2026},
author = {Parizadeh, M and Laforest-Lapointe, I and Serrano-Vázquez, A and Morán-Silva, P and Rojas-Velázquez, L and Torres, J and Ximénez-García, C and Arrieta, MC},
title = {Impact of maternal, infant, and household factors on early-life gut microbiome development in a rural setting.},
journal = {The ISME journal},
volume = {20},
number = {1},
pages = {},
pmid = {42127418},
issn = {1751-7370},
support = {IN219624//Dirección General de Asuntos del Personal Académico (DGAPA)/Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (PAPIIT)/ ; IN217821//Dirección General de Asuntos del Personal Académico (DGAPA)/Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica (PAPIIT)/ ; //Universidad Nacional Autónoma de Mexico/ ; //Calgary Foundation/ ; //Office of the Associate Dean Research of the University of Calgary's Cumming School of Medicine/ ; //Alberta Children's Hospital Research Institute/ ; //internal University of Calgary start-up funds/ ; //Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Female ; Humans ; Infant ; Infant, Newborn ; Bacteria/classification/genetics/isolation & purification ; Eukaryota/classification/genetics/isolation & purification ; *Family Characteristics ; Feces/microbiology ; Longitudinal Studies ; Metagenomics ; Mexico ; RNA, Ribosomal, 18S/genetics ; Rural Population ; Sequence Analysis, DNA ; *Gastrointestinal Microbiome ; },
abstract = {Early-life gut microbiome development is influenced by host, microbial, environmental, and social factors. Rural infants typically exhibit greater microbial diversity than their urban counterparts, yet microbiome maturation patterns in less industrialized settings remain underexplored. Additionally, though microbial eukaryotes are integral to gut ecology, most studies to date have focused predominantly on bacterial communities. Using shallow shotgun metagenomics and 18S ribosomal RNA gene sequencing, we characterized bacterial and eukaryotic gut microbiomes in an intensively sampled longitudinal cohort of 10 infants from a rural community in Morelos, Mexico, each followed monthly from the first to the 18th month, providing a detailed view of early-life microbiome development in a low-resource setting. Although both bacterial and eukaryotic alpha diversity increased over time, they showed distinct colonization trajectories. Age, delivery mode, and environmental exposures, such as animal contact and household factors, influenced bacterial and eukaryotic community compositions, and bacterial metabolic composition. Inter-kingdom microbial networks varied with age, with a reduction in taxonomic diversity after the first year of life. Age and birth mode also influenced changes in the overall community structure and connectivity of microbial co-occurrence patterns, but did not impact the associations among specific microbial taxa. Functional profiling revealed that bacterial metabolic potential diversified with age, whereas the mode of birth had a minimal impact on functional variation. These findings highlight the dynamic nature of bacterial and eukaryotic microbiota in early life and underscore the need to explore how rural environmental exposures shape microbial maturation, with potential implications for immune development and long-term health.},
}

Female
Humans
Infant
Infant, Newborn
Bacteria/classification/genetics/isolation & purification
Eukaryota/classification/genetics/isolation & purification
*Family Characteristics
Feces/microbiology
Longitudinal Studies
Metagenomics
Mexico
RNA, Ribosomal, 18S/genetics
Rural Population
Sequence Analysis, DNA
*Gastrointestinal Microbiome

@article {pmid42246191,
year = {2026},
author = {Das, D and Dixit, R and Pandey, M},
title = {The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Carcinogenesis.},
journal = {Journal of gastroenterology and hepatology},
volume = {41},
number = {7},
pages = {2062-2072},
doi = {10.1111/jgh.70462},
pmid = {42246191},
issn = {1440-1746},
mesh = {Humans ; *Gallbladder Neoplasms/etiology/metabolism/microbiology ; Multiomics ; *Metabolomics ; *Carcinogenesis/metabolism/genetics ; Dysbiosis/complications ; *Microbiota ; Animals ; Proteomics ; Helicobacter ; Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome ; },
abstract = {BACKGROUND: Gallbladder cancer (GBC) is a highly aggressive malignancy with a dismal prognosis, frequently diagnosed at advanced stages. While cholelithiasis is a primary risk factor, the role of the biliary microbiome and its metabolic products in driving carcinogenesis is increasingly recognized. This review synthesizes multi-omics data to elucidate the interplay between microbial dysbiosis and metabolomic shifts in GBC.

METHODS: A systematic literature search was conducted on PubMed (up to January 2026) focusing on biliary bacteria, the gut-bile axis, and multi-omics markers. A narrative synthesis integrated findings from metagenomic, metaproteomic, and metabolomic studies involving human cohorts and experimental models.

RESULTS: GBC is characterized by profound biliary dysbiosis, specifically the enrichment of Enterobacteriaceae, Streptococcus, and Helicobacter species. This taxonomic shift triggers a pro-carcinogenic metabolomic flux, where microbial 7α-dehydroxylation converts primary bile acids into secondary bile acids, such as deoxycholic acid (DCA), which induce DNA damage and promote tumor growth. Metaproteomic signatures identify bacterial proteins (e.g., QDR3, ompA) that facilitate biofilm formation and oxidative stress evasion. Furthermore, emerging paradigms like cross-species horizontal gene transfer (HGT) suggest that microbial genetic material can directly modulate host oncogenic pathways.

CONCLUSION: The GBC multi-omics landscape reveals a complex gut-bile axis where microbial and chemical factors converge. These integrated signatures offer potential as noninvasive biomarkers for early diagnosis and precision therapy.},
}

Humans
*Gallbladder Neoplasms/etiology/metabolism/microbiology
Multiomics
*Metabolomics
*Carcinogenesis/metabolism/genetics
Dysbiosis/complications
*Microbiota
Animals
Proteomics
Helicobacter
Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome

@article {pmid42362550,
year = {2026},
author = {Falshaw, N and Ducarmon, QR and King, A and Grundler, F and Mesnage, R},
title = {Remodelling of the gut virome after long-term fasting.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42362550},
issn = {2055-5008},
mesh = {*Fasting ; *Virome ; *Gastrointestinal Microbiome ; Bacteriophages/genetics/classification/isolation & purification ; Humans ; Metagenomics/methods ; Bacteria/virology/classification ; Feces/virology/microbiology ; Bacteroides/virology ; Faecalibacterium/virology ; },
abstract = {Long-term fasting is a promising strategy to restore metabolic health. Emerging evidence suggests that the gut microbiome may mediate some of fasting benefits, but the role of its viral component remains poorly understood. Using shotgun metagenomic data from a single-arm, monocentric fasting intervention, this study profiled the gut virome (n = 89 individuals, n = 241 samples) before and after 9.8 days of fasting (~ 250 kcal/day) as well as one and three months afterwards. Fasting induced a transient loss of viral diversity and a shift toward increased representation of virulent phages. External dataset validation identified 49 phages showing reproducible directional changes during fasting. Many were linked to bacterial hosts, showing concordant shifts, including depletion of Faecalibacterium-associated phages and enrichment of Bacteroides-associated phages. Cross-domain network analyses revealed denser viral-bacterial networks at the end of fast, with enriched connections to butyrate producers, suggesting phages may participate in the fasting-induced restructuring of microbial networks involving health-associated taxa. Collectively, these findings indicate that fasting remodels the gut virome cross-domain associations through reproducible, functionally relevant phage-host interactions, with reorganisation persisting for up to three months and occurring in parallel with improvements in cardiometabolic markers.},
}

*Fasting
*Virome
*Gastrointestinal Microbiome
Bacteriophages/genetics/classification/isolation & purification
Humans
Metagenomics/methods
Bacteria/virology/classification
Feces/virology/microbiology
Bacteroides/virology
Faecalibacterium/virology

@article {pmid42362787,
year = {2026},
author = {Sinha, B and Khandeparker, L},
title = {Seasonal variation in plastic-associated biofilm microbial assemblages: a microcosm approach.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {7},
pages = {},
pmid = {42362787},
issn = {1573-2959},
mesh = {*Plastics/analysis ; Seasons ; *Biofilms ; *Environmental Monitoring ; *Microbiota ; Estuaries ; Bacteria/classification ; },
abstract = {Plastic pollution in natural ecosystems creates novel niches, known as the "Plastisphere", that host heterogeneous microbial communities shaped by substrate type and environmental conditions. This study explored the effects of seasonal variation on the plastisphere evolution on different plastic substrates, oxo-degradable carrier bags (Oxo), oxo-degradable garbage bags (Oxo-G), normal plastics (N), and snack packets (Sn) for 30 days in a microcosm experiment using ambient water from the monsoon-influenced Zuari estuary. The results indicated that the early-stage (day 5) plastisphere was dominated by fast-growing r-strategists, such as Alpha- and Gamma-proteobacteria as well as Campylobacterota-related lineages, whereas mature biofilms (day 30) showed increased abundance of secondary colonisers, including Planctomycetota, Actinomycetota, and Bacteroidota. The oxo-degradable plastics emerged as preferred substrates, likely due to their prooxidant-mediated abiotic degradation and the novel nature of the conditioning film. Salinity, in conjunction with nutrient concentrations, emerged as a major driver of microbial abundance in the plastisphere. Though the putative pathogens, such as Vibrio spp. and total coliforms, were present at very low abundance in the aged plastisphere during the SW-Mon and PostM seasons, their persistence indicates their resilience even under nutrient-limited conditions. Although a closed microcosm system probably introduced bottle effects, influencing temporal changes in nutrient levels and microbial abundance, the study provides baseline insights into substrate- and season-driven patterns of plastisphere development. Overall, these findings underscore the dynamic interplay among various factors, including plastic types and seasonal environmental shifts, in shaping plastisphere maturation. This has potential implications for public health and ecosystem functioning in the natural marine environment. Employing functional metagenomics analysis in future in situ studies of plastisphere communities can provide further insights and is a way forward for predicting associated ecological risks.},
}

*Plastics/analysis
Seasons
*Biofilms
*Environmental Monitoring
*Microbiota
Estuaries
Bacteria/classification

@article {pmid42366019,
year = {2026},
author = {Wang, D and Wang, F and Sun, S and Huang, L and Sun, K and Li, Z and Feng, J},
title = {Microbe-Metabolite Interactions in Cave Soils Synergistically Regulate the Environmental Persistence of Pseudogymnoascus destructans.},
journal = {Environmental microbiology},
volume = {28},
number = {7},
pages = {e70367},
doi = {10.1111/1462-2920.70367},
pmid = {42366019},
issn = {1462-2920},
support = {32430066//National Natural Science Foundation of China/ ; 32300425//National Natural Science Foundation of China/ ; },
mesh = {*Soil Microbiology ; *Caves/microbiology ; *Ascomycota/isolation & purification/genetics/physiology ; Seasons ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Soil/chemistry ; China ; Microbiota ; Nitrogen Cycle ; },
abstract = {Pseudogymnoascus destructans (Pd), the causative agent of bat white-nose syndrome, persists in cave soils and acts as a chronic source of infection, yet the environmental processes governing this reservoir remain unclear. We performed seasonal sampling of bat cave soils in Northeast China and combined metagenomic, untargeted metabolomic and physicochemical analyses to identify drivers of Pd loads. Pd abundance tracked strong seasonal gradients in temperature, soil water content, electrical conductivity and nitrogen availability. The microbial community structure exhibited pronounced seasonal variation, primarily associated with pH, and was governed predominantly by stochastic ecological processes. Nitrogen-cycling genes showed a switch from nitrogen fixation and nitrification in summer to denitrification and nitrate reduction in winter. Antibiotic resistance genes and mobile genetic elements covaried with core bacterial taxa, while antifungal metabolites such as tetracycline, glycitin and chrysin were positively associated with putatively antagonistic genera (e.g., Rhodanobacter, Pseudomonas, Streptomyces, and Bacillus), indicating a microbe-metabolite defence network. Structural equation modelling revealed a temperature-driven cascade linking nutrient cycling, microbial communities, metabolite profiles and Pd loads. Our results show that seasonal dynamics of Pd in cave soils emerge from interactions between climate-regulated soil processes and microbe-metabolite feedbacks, with implications for environmental control of pathogenic fungi.},
}

*Soil Microbiology
*Caves/microbiology
*Ascomycota/isolation & purification/genetics/physiology
Seasons
*Bacteria/metabolism/genetics/classification/isolation & purification
Soil/chemistry
China
Microbiota
Nitrogen Cycle

@article {pmid42366665,
year = {2026},
author = {Kuzbekov, SR},
title = {[Microbiota and microbiome of the lacrimal drainage system].},
journal = {Vestnik oftalmologii},
volume = {142},
number = {3},
pages = {91-100},
doi = {10.17116/oftalma202614203191},
pmid = {42366665},
issn = {0042-465X},
mesh = {Humans ; *Microbiota ; *Lacrimal Apparatus/microbiology/physiopathology/pathology ; *Dacryocystitis/microbiology/diagnosis/physiopathology ; *Lacrimal Duct Obstruction/diagnosis ; Anti-Bacterial Agents/pharmacology ; },
abstract = {This review analyzes current concepts of the role of the microbiota and microbiome in the physiology and pathology of the human lacrimal drainage system (LDS). The terms are clearly differentiated: microbiota is the collection of living microorganisms, whereas microbiome also includes their genetic material and habitat. The article describes anatomical features of the LDS and involutional changes in adults (atrophy of the lacrimal puncta, canalicular fibrosis, and nasolacrimal duct stenosis), which predispose to tear stagnation and inflammation. The review includes a comparative analysis of the microbiological spectrum in healthy individuals and patients with dacryocystitis and canaliculitis. The composition of the flora was found to differ substantially depending on age (predominance of S. pneumoniae in children versus Staphylococcus spp. in adults) and geographical region. Metagenomic sequencing data (16S rRNA) demonstrate significantly greater microbial diversity compared with conventional culture methods, revealing a broad spectrum of aerobes, anaerobes, and fungi. The work pays particular attention to regional resistance patterns, including the high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in several Asian countries. Based on the literature data this study proposes and algorithm for empirical antibacterial therapy, taking into account the likely pathogens, as well as the indications for surgical correction, and emphasizes the prospects for creating a national map of the LDS microbiome in the Russian Federation to optimize treatment strategies for dacryocystitis and dacryostenosis.},
}

Humans
*Microbiota
*Lacrimal Apparatus/microbiology/physiopathology/pathology
*Dacryocystitis/microbiology/diagnosis/physiopathology
*Lacrimal Duct Obstruction/diagnosis
Anti-Bacterial Agents/pharmacology

@article {pmid42367778,
year = {2026},
author = {Fan, R and Zang, Q and Xu, Y and Gao, L and Zhou, J and Zang, Y},
title = {Metagenomic characterization of gut microbiota in rheumatoid arthritis-associated interstitial lung disease: taxonomic shifts and clinical correlations.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1868704},
pmid = {42367778},
issn = {1664-3224},
mesh = {Humans ; *Arthritis, Rheumatoid/complications/microbiology ; *Lung Diseases, Interstitial/microbiology/etiology ; Female ; *Metagenomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Middle Aged ; Feces/microbiology ; Aged ; *Bacteria/classification/genetics ; Dysbiosis/microbiology ; *Metagenome ; },
abstract = {BACKGROUND: Rheumatoid arthritis-associated interstitial lung disease (RA-ILD) is a severe extra-articular manifestation with limited diagnostic biomarkers. While gut microbiota dysbiosis contributes to rheumatoid arthritis (RA) pathogenesis, its specific role in RA-ILD remains poorly characterized.

METHODS: We performed shotgun metagenomic sequencing on fecal samples from 41 participants: 10 RA-ILD patients, 20 RA patients without ILD (RA-non-ILD), and 11 healthy controls (HCs). We assessed alpha and beta diversity, differential abundance (Wilcoxon rank-sum tests with FDR correction), Spearman correlations with clinical parameters, microbial co-occurrence networks, and random forest classification.

RESULTS: Alpha and beta diversity did not differ significantly among groups. After FDR correction, no genus differed significantly between RA-ILD and RA-non-ILD. Exploratory analysis (uncorrected P < 0.05) revealed enrichment of Escherichia/Shigella in RA-ILD (11.72% vs. 2.66%, P = 0.003) and depletion of Roseburia (1.05% vs. 3.77%, P = 0.005) and Ruminococcus (5.98% vs. 7.85%, P = 0.032), while Faecalibacterium showed a trend toward depletion without reaching nominal significance (4.45% vs. 4.66%, P = 0.409). Correlation analysis revealed a dichotomous pattern: pro-inflammatory genera correlated positively with disease activity, while butyrate-producing genera correlated negatively. Co-occurrence network analysis showed RA patients had a more complex network than HC and RA-ILD. Random forest classification identified Bifidobacterium, unclassified_ Oscillospiraceae, and unclassified_Lachnospiraceae as top discriminators between HC and RA, and unclassified_ Bacteroidaceae, Parabacteroides, and Blautia for RA-ILD vs RA.

CONCLUSIONS: RA-ILD is associated with specific gut microbial alterations-notably Escherichia/Shigella enrichment and depletion of Roseburia and Ruminococcus-despite preserved overall diversity. These changes correlate with systemic inflammation and suggest a role for the gut microbiota in RA-ILD pathogenesis via the gut-lung axis. The identified taxa warrant validation as candidate biomarkers in larger cohorts.},
}

Humans
*Arthritis, Rheumatoid/complications/microbiology
*Lung Diseases, Interstitial/microbiology/etiology
Female
*Metagenomics/methods
Male
*Gastrointestinal Microbiome/genetics
Middle Aged
Feces/microbiology
Aged
*Bacteria/classification/genetics
Dysbiosis/microbiology
*Metagenome

@article {pmid42367784,
year = {2026},
author = {Zheng, X and Li, D and Yao, X and Luo, X and Gao, C and Yan, X},
title = {The gut microbiota-immune-brain axis in post-traumatic stress disorder: mechanistic integration and translational prospects.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1859206},
pmid = {42367784},
issn = {1664-3224},
mesh = {Humans ; *Stress Disorders, Post-Traumatic/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/immunology ; Animals ; *Brain/immunology/metabolism ; Translational Research, Biomedical ; Intestinal Barrier Function ; Neuroimmunomodulation ; },
abstract = {Post-traumatic stress disorder (PTSD) is a complex mental disorder triggered by severe traumatic events. Its pathophysiology involves not only abnormalities in fear memory circuits and neuroendocrine imbalances but also immune dysregulation and alterations in gut homeostasis. In recent years, the gut microbiota, as a crucial regulatory factor connecting the periphery and the central nervous system, has garnered widespread attention for its potential role in the development and progression of PTSD, offering a new integrative perspective for understanding this disorder. This article focuses on the "gut microbiota-immune-brain axis" framework, reviewing evidence related to changes in the composition and function of the gut microbiota in PTSD. It summarizes how these changes may influence neuroplasticity abnormalities and PTSD-related behavioral phenotypes through mechanisms involving microbial metabolite production, modulation of intestinal barrier integrity, immuno-inflammatory responses, regulation of neuroendocrine homeostasis, and blood-brain barrier dysfunction. However, these mechanistic pathways remain incompletely validated in human studies. Existing research suggests that this axis holds significant value in explaining the multisystem pathological features of PTSD. Nevertheless, challenges persist, including ambiguous causal relationships in microbiota-host interactions, limited direct clinical evidence, and insufficient translational research. Current evidence primarily stems from observational studies, preclinical models, and preliminary intervention studies. The explanatory power varies across these evidence levels: population studies primarily establish correlations, animal models facilitate mechanistic validation, metagenomic and metabolic analyses yield functional insights, while clinical intervention data remain exploratory. This article aims to elucidate the key molecular and systemic mechanisms underlying this axis in PTSD and to evaluate the potential translational value and practical limitations of microbial intervention and immune modulation strategies.},
}

Humans
*Stress Disorders, Post-Traumatic/immunology/microbiology/metabolism
*Gastrointestinal Microbiome/immunology
Animals
*Brain/immunology/metabolism
Translational Research, Biomedical
Intestinal Barrier Function
Neuroimmunomodulation

@article {pmid42371112,
year = {2026},
author = {Tang, A and Cao, Q and Wang, M and Li, W and Xu, H and Wang, Y and Niu, H and Wang, H and Ma, G and Jia, K and Feng, X and He, C and He, J and Alballa, MM and Liao, X and Tian, T and Qin, B and Yang, N and Wei, J and Sun, J and Wang, Y and Cheng, Y and Wu, Q and Yang, J and Wang, Q and Wang, X and Liu, X},
title = {The effectiveness of a plant-based milk with fermented brown rice on constipation symptoms via gut microbiota modulation: a double-blind randomized controlled trial.},
journal = {European journal of nutrition},
volume = {65},
number = {5},
pages = {},
pmid = {42371112},
issn = {1436-6215},
support = {DW080038K0000004//Xi'an Jiaotong University/ ; 82011530197//National Natural Science Foundation of China/ ; 202405212//Feihe Research Grant/ ; },
mesh = {Humans ; *Constipation/microbiology/diet therapy ; *Oryza ; Double-Blind Method ; Female ; *Plant-based Milk ; Adult ; *Gastrointestinal Microbiome/physiology ; Animals ; Middle Aged ; Fermentation ; Fermented Foods ; },
abstract = {PURPOSE: To evaluate the effects of a plant-based milk with fermented brown rice on constipation symptoms in patients with functional constipation and to identify post-intervention gut microbial alterations that may underlie potential mechanisms.

METHODS: This is a randomized controlled trial among 100 participants with functional constipation. Participants were randomly assigned to the intervention group (plant-based milk with fermented brown rice, 2 bottles/day, 500 ml in total), or the control group (an isocaloric plant protein milk, equivalent dose) for 3 weeks. The primary outcome is complete spontaneous bowel movement (CSBM) rate, while secondary outcomes include score of individual symptoms assessment of constipation, bowel movement frequency (BMF), and gut microbial changes (metagenomics).

RESULTS: A total of 99 participants completed the intervention. CSBM and BMF increased, and GSRS scores decreased over time in both groups, with no significant between-group differences. The plant-based milk with fermented brown rice relieved constipation symptoms more than the control group did, with significant between-group differences in straining, bloating and abdominal pain (all P < 0.05). The intervention group showed increases in 8 species, including three beneficial species in the genus Blautia, associated with relief of abdominal pain after the intervention. Meanwhile, machine learning models identified gut microbiota features predicting intervention responders.

CONCLUSION: Our study did not find between-group difference in CSBM, while the plant-based milk with fermented brown rice showed greater effectiveness in relieving constipation symptoms and optimizing gut microbiota. Functional species benefiting intestinal health in response to the intervention were also identified.

CLINICAL TRIAL REGISTRY: This study has been registered in the Chinese Clinical Trial Registry (https://www.chictr.org.cn/, ChiCTR2400088688).},
}

Humans
*Constipation/microbiology/diet therapy
*Oryza
Double-Blind Method
Female
*Plant-based Milk
Adult
*Gastrointestinal Microbiome/physiology
Animals
Middle Aged
Fermentation
Fermented Foods

@article {pmid42098871,
year = {2026},
author = {Biswas, P and Ahmed, S and Mondal, S and Oladokun, S and Gundogdu, O and Mallick, AI},
title = {Recombinant LAB vector-based multicomponent vaccine against Campylobacter jejuni potentially promoting a healthier microbial balance in the poultry gut.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42098871},
issn = {2049-2618},
support = {P409/2023-24//BactiVac, University of Birmingham, UK/ ; IC-12047(12)/2/2024-BP-IUCA//Indo-UK (DBT-BBSRC)/ ; BB/Y007115/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *Campylobacter jejuni/immunology/genetics ; *Campylobacter Infections/prevention & control/veterinary/immunology/microbiology ; Chickens/microbiology/immunology ; *Bacterial Vaccines/immunology/administration & dosage/genetics ; *Poultry Diseases/prevention & control/microbiology/immunology ; Protein Subunit Vaccines ; Adhesins, Bacterial/immunology/genetics ; Lactococcus lactis/genetics ; Bacterial Proteins/immunology/genetics ; *Gastrointestinal Microbiome ; Vaccines, Synthetic/immunology/administration & dosage ; Bacterial Adhesion ; Bacterial Outer Membrane Proteins ; Carrier Proteins ; },
abstract = {BACKGROUND: Diarrheal diseases remain the second leading cause of preventable death globally, particularly among children under the age of 5 in developing countries, accounting for an estimated 2-3 million deaths annually. Among bacterial pathogens causing diarrheal illness, Campylobacter jejuni (C. jejuni) remains a major contributor, particularly in low- and middle-income countries (LMICs). As a common gut pathogen, C. jejuni expresses several secretory or surface-expressed colonization proteins (SECPs), namely haemolysin co-regulated protein (Hcp), valine glycine repeats G (VgrG), Campylobacter adhesion to fibronectin (CadF), fibronectin-like protein A (FlpA), and jejuni lipoprotein A (JlpA). Most of these proteins play pivotal roles in bacterial self-survival, host-cell adhesion, and invasion of avian and non-avian hosts. To minimize C. jejuni adhesion and subsequent colonization in the avian gut, we explored the potential of a multicomponent mucosal vaccine composed of CadF, Hcp, and JlpA protein of C. jejuni.

RESULTS: For this purpose, we bioengineered a food-grade Lactic Acid-producing Bacterium, Lactococcus lactis (L. lactis), to express three key immunogenic subunits of C. jejuni, CadF, Hcp, and JlpA. Utilizing this live vector-based multicomponent mucosal vaccine platform, we investigated the immunoprotective potential of these antigens in chickens. Since the particular strain of L. lactis is non-colonizing, we used chitosan, a natural mucoadhesive, biodegradable polymer, to microencapsulate the engineered bacteria and increase their gut retention time for optimal interaction with local immune cells. Our in vivo immunization study demonstrated that oral administration of this multicomponent vaccine formulation elicited a strong local antibody response (sIgA) (p < 0.0001) and upregulated key pro-inflammatory cytokines, leading to robust mucosal immune protection (~ 1.54 log10 reduction) against the cecal colonization of C. jejuni. Beyond targeting C. jejuni, we hypothesized that the vaccine may influence the overall gut microbiota, potentially promoting a healthier microbial balance in the poultry gut. To this end, gut metagenomic analysis of vaccinated birds revealed a marked reduction in the phylum Campylobacterota (~ 2-fold), accompanied by increased abundance of the phyla Bacteroidota, as part of a beneficial microbial community.

CONCLUSIONS: Together, this study underscores the potential of a live vector-based, multicomponent mucosal vaccine as a promising, cost-effective strategy to reduce the cecal load of C. jejuni, potentially limiting the risk of foodborne transmission in poultry production systems.},
}

Animals
*Campylobacter jejuni/immunology/genetics
*Campylobacter Infections/prevention & control/veterinary/immunology/microbiology
Chickens/microbiology/immunology
*Bacterial Vaccines/immunology/administration & dosage/genetics
*Poultry Diseases/prevention & control/microbiology/immunology
Protein Subunit Vaccines
Adhesins, Bacterial/immunology/genetics
Lactococcus lactis/genetics
Bacterial Proteins/immunology/genetics
*Gastrointestinal Microbiome
Vaccines, Synthetic/immunology/administration & dosage
Bacterial Adhesion
Bacterial Outer Membrane Proteins
Carrier Proteins

@article {pmid42264245,
year = {2026},
author = {Zhao, Y and Zhang, Y and Tang, S and Peng, T and Bagadi, AH and Jia, X and Wei, Z and Han, J and Li, L and Liu, X and Kong, W and Song, S and Wei, C and Wang, J},
title = {Structural elucidation and gut barrier-protective effects of a glucomannan polysaccharide fraction from Lanzhou lily bulbs.},
journal = {International journal of biological macromolecules},
volume = {371},
number = {},
pages = {152899},
doi = {10.1016/j.ijbiomac.2026.152899},
pmid = {42264245},
issn = {1879-0003},
mesh = {Animals ; *Lilium/chemistry ; Mice ; *Mannans/chemistry/pharmacology ; Intestinal Barrier Function/drug effects ; *Polysaccharides/chemistry/pharmacology ; Dextran Sulfate ; Gastrointestinal Microbiome/drug effects ; *Plant Roots/chemistry ; Colitis/chemically induced/drug therapy ; },
abstract = {Food-derived dietary polysaccharides have attracted increasing attention as functional ingredients for ulcerative colitis (UC) management. In this study, a homogeneous polysaccharide, designated LDP, was isolated from the bulbs of Lilium davidii var. willmottiae (Lanzhou lily). Structural analyses showed that LDP had a weight-average molecular weight (MW) of 5.082 × 10[3] g/mol and was mainly composed of alternating →4)-α-D-Manp-(1 → and →4)-β-D-Glcp-(1 → residues with minor branching. Conformational analysis and molecular dynamics (MD) simulations indicated that LDP adopted an extended semi-flexible coil conformation in aqueous solution. In dextran sulfate sodium (DSS)-induced colitis mice, LDP markedly alleviated disease symptoms, as evidenced by improved survival, reduced body weight loss, a lower disease activity index and attenuated histopathological injury. Mechanistically, LDP enhanced intestinal barrier integrity, significantly increased acetic acid levels and partially restored short-chain fatty acid (SCFA)-associated beneficial taxa, including Lactobacillaceae, Bifidobacterium, Allobaculum and members of Erysipelotrichaceae/Erysipelotrichia. Integrated metagenomic, proteomic, Western blot and immunological analyses further indicated that LDP attenuated intestinal inflammation by suppressing the TAB1/MAP2K4-centered MAPK signaling pathway, as evidenced by reduced TAB1 and MAP2K4 expression and decreased p38 phosphorylation, and by restoring the Th17/Treg balance in mesenteric lymph nodes (MLNs). These findings suggested that LDP alleviated DSS-induced colitis through coordinated regulation of gut microbiota, microbial metabolism, MAPK inflammatory signaling and mucosal immunity.},
}

Animals
*Lilium/chemistry
Mice
*Mannans/chemistry/pharmacology
Intestinal Barrier Function/drug effects
*Polysaccharides/chemistry/pharmacology
Dextran Sulfate
Gastrointestinal Microbiome/drug effects
*Plant Roots/chemistry
Colitis/chemically induced/drug therapy

@article {pmid42320776,
year = {2026},
author = {Cho, MS and Lee, IS and Kim, J and Park, JW and Kim, J and Ko, SJ},
title = {Multi-herb formulations modulating gut microbiota: A systematic review and data-driven analysis.},
journal = {Journal of ethnopharmacology},
volume = {370},
number = {},
pages = {122082},
doi = {10.1016/j.jep.2026.122082},
pmid = {42320776},
issn = {1872-7573},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Plant Preparations/pharmacology ; Data Analytics ; },
abstract = {Multi-herb formulations, characterized by their complex synergistic compositions, are widely used in traditional medicine to modulate the gut microbiota. However, identifying reproducible herb-microbiota associations across disparate clinical settings remains a significant methodological challenge.

AIM OF THE STUDY: This study aims to systematically synthesize human clinical evidence to map the modulation patterns of multi-herb formulations on the gut microbiota and to identify the herbal components associated with reported directional microbial shifts.

MATERIALS AND METHODS: We conducted a systematic review and data-driven analysis of 29 clinical trials involving 954 participants in multi-herb formulation groups. To integrate findings from heterogeneous clinical settings, we employed a binarization strategy focused on statistically significant directional shifts (+1 for increase, -1 for decrease). An extreme gradient boosting (XGBoost) learning framework combined with SHapley Additive exPlanations (SHAP) was used to deconstruct these formulations and explore the predictive importance of individual constituents. To ensure the highest level of scientific integrity and prevent data leakage, the model's generalizability was rigorously validated using Leave-One-Study-Out (LOSO) cross-validation at the independent study level.

RESULTS: The LOSO validation yielded a mean accuracy of 0.84 and a macro F1-score of 0.42, indicating limited but informative cross-study pattern recognition despite the inherent heterogeneity of clinical data. Our analysis identified recurrent directional associations: formulas containing Scutellaria baicalensis Georgi were associated with reported reductions in genus-level taxa such as Escherichia-Shigella within neuropsychiatric disease contexts. Formulas containing Zingiber officinale Roscoe were associated with reported increases and decreases in selected genus-level taxa across heterogeneous disease contexts.

CONCLUSIONS: This study provides a comprehensive, evidence-based map of how multi-herb formulations modulate the human gut microbiota. By prioritizing rigorous validation and accounting for the complexity of synergistic preparations, we have identified hypothesis-generating patterns that transcend individual study variations. These findings provide a realistic foundation for future high-resolution metagenomic research and the development of standardized ethnopharmacological therapies.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Plant Preparations/pharmacology
Data Analytics

@article {pmid42359485,
year = {2026},
author = {Addy, HPK and Amedorme, D and Osei-Poku, P and Kwarteng, A},
title = {Predicted Functional Potentials of Bacterial Communities in Fermented Maize Products From Ghana, Nigeria, and Benin via 16S rRNA Amplicon Sequencing and PICRUSt2.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70272},
pmid = {42359485},
issn = {2045-8827},
mesh = {RNA, Ribosomal, 16S/genetics ; *Zea mays/microbiology ; *Fermented Foods/microbiology ; Ghana ; Nigeria ; Benin ; *Microbiota/genetics ; Fermentation ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Sequence Analysis, DNA ; Phylogeny ; Lactobacillus/genetics/metabolism ; DNA, Bacterial/genetics ; },
abstract = {Fermented maize products are integral to the diets of many African communities. Despite their cultural significance and health benefits, little is known about the metabolic potential of their microbial populations. This study utilized 16S rRNA amplicon sequencing data from the NCBI to characterize the functional capabilities of microbiomes in six maize-based fermented foods. Quality assessment and taxonomic classification were performed using QIIME2 with the SILVA 138 database, while functional predictions were generated with PICRUSt2 and analyzed in R. Taxonomic profiling revealed that Firmicutes dominated all samples, reaching peak abundance in Mawe (94.9%) and S37_Fermented_Maize (91.4%). Proteobacteria were elevated in S19_Fermented_maize (up to 36.5%) and S38_Dehulled_Maize (16.0%). At the genus level, Lactobacillus was most abundant in S5_Mawe (82.2%) and S6_Mawe (79.6%), while Acetobacter peaked in S19_Fermented_maize (32.7%). Regarding functional predictions, Lactobacillus appeared to drive key KEGG Orthologs and pathways, specifically ABC transporters, transcriptional regulation, and DNA replication mechanisms. In contrast, Weissella and Streptococcus contributed notably to peptide/nickel transport, L-lactate dehydrogenase (EC 1.1.1.27), and nucleotide biosynthesis. Acetobacter was prominent in Ogi, showing a connection with site-specific methylation (EC 2.1.1.72) and phospholipid synthesis (PHOSLIPSYN-PWY). Notably, commercial Mawe samples exhibited higher predicted activities related to transposase activity (K07496), energy metabolism, and peptidoglycan maturation (PWY0-1586). These findings demonstrate that while traditional fermentation processes maintain a consistent set of metabolic functions predominantly driven by Lactobacillus, distinct variations exist depending on product type and production approach. These predicted functions provide a baseline for further experimental validation of the metabolic contributions of microbial communities in fermented maize products.},
}

RNA, Ribosomal, 16S/genetics
*Zea mays/microbiology
*Fermented Foods/microbiology
Ghana
Nigeria
Benin
*Microbiota/genetics
Fermentation
*Bacteria/classification/genetics/metabolism/isolation & purification
Sequence Analysis, DNA
Phylogeny
Lactobacillus/genetics/metabolism
DNA, Bacterial/genetics

@article {pmid42359789,
year = {2026},
author = {Lakey, BD and Wozniak, KJ and Britton, RA and Tabor, JJ},
title = {Mucin-derived sugars act as metabolic brakes controlling growth initiation in Akkermansia muciniphila.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2691334},
pmid = {42359789},
issn = {1949-0984},
mesh = {*Mucins/metabolism/chemistry ; Animals ; Humans ; *Akkermansia/growth & development/metabolism ; Mice ; Gastrointestinal Microbiome ; Polysaccharides/metabolism ; *Dietary Sugars/metabolism ; Colon/microbiology ; Citric Acid Cycle ; *Verrucomicrobia/growth & development/metabolism ; },
abstract = {Akkermansia muciniphila is a key member of the gut microbiota and plays important roles in host metabolism and health. In the colon, A. muciniphila extracts nutrients from oligosaccharide-rich mucin glycans that comprise the mucosa. However, this environment is complex and shaped by dietary inputs, microbiome metabolism, and mucin glycan composition varying across hosts, gastrointestinal regions, and physiological states. How strains of A. muciniphila integrate these nutrient signals into growth initiation and niche colonization remains unclear. Here, we compare physiological responses of a human- and mouse-derived strain of A. muciniphila, finding that dietary sugars differentially affect these isolates, suggesting host-associated tuning of metabolic capacity. In contrast, several mucin-derived sugars impose a conserved, concentration-dependent delay in growth initiation, implicating the lag phase as a critical metabolic checkpoint for growth. Genetic suppressor analysis identified sugar kinases and a component of the tricarboxylic acid cycle as genetically encoded control points linking glycan sugar exposure to the energy balance required for growth. These findings demonstrate that mucin-derived sugars function as both nutrients and metabolic stressors, regulating growth initiation. We propose that A. muciniphila employs metabolic "brakes" to coordinate growth with mucin composition, putatively linking host glycan landscapes to microbial physiology and ecological fitness within the mucus layer.},
}

*Mucins/metabolism/chemistry
Animals
Humans
*Akkermansia/growth & development/metabolism
Mice
Gastrointestinal Microbiome
Polysaccharides/metabolism
*Dietary Sugars/metabolism
Colon/microbiology
Citric Acid Cycle
*Verrucomicrobia/growth & development/metabolism

@article {pmid42360122,
year = {2026},
author = {Banerjee, P and Al-Bayer, S and Calaor, J and Weber, S and Graham, NR and Andersen, JC and Economo, EP and Kennedy, S and Krehenwinkel, H and Gillespie, RG and Roderick, GK and Rogers, HS and Puliafico, KP},
title = {Comparison of Environmental DNA and Bulk DNA Metabarcoding for Assessing Terrestrial Arthropod Diversity Across Three Habitat Types on Guam.},
journal = {Molecular ecology resources},
volume = {26},
number = {5},
pages = {e70172},
pmid = {42360122},
issn = {1755-0998},
support = {RC21-1034//Strategic Environmental Research and Development Program/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; *Arthropods/genetics/classification ; *Biodiversity ; *Ecosystem ; Electron Transport Complex IV/genetics ; *Metagenomics/methods ; },
abstract = {DNA-based methods offer a rapid and cost-effective way for detecting species occurrence and monitoring biodiversity; among them, bulk DNA metabarcoding is well-established, and recently developed environmental DNA (eDNA)-based methods offer a non-lethal alternative. With a goal to develop suitable methods for assessing insect biodiversity for understudied island ecosystems where DNA reference libraries are incomplete, we compared established bulk DNA metabarcoding methods with eDNA across three replicated terrestrial ecosystem types (degraded forest, limestone forest, and grassland) on the island of Guam. Using two mitochondrial COI primer pairs, we performed bulk DNA metabarcoding of standard entomological collection methods (Malaise traps, pan traps, and vegetation beating), and compared the assessment of biodiversity with that from different eDNA sources (flowers, leaves, tree trunks, and spider webs). In our samples, eDNA and bulk DNA metabarcoding both detected a large proportion of overall taxa (OTUs, 86.6% and 60.3%, respectively). Although bulk DNA metabarcoding detected significantly more taxa, eDNA proved to be a reasonable non-lethal alternative. As expected, because of limitations in existing reference databases for understudied systems, species-level identification was achieved for only a few OTUs. Overall, the sampling approach was the dominant driver of arthropod diversity, explaining ~17% of the observed variation, while habitat type accounted for ~4%. Thus, each sampling approach captured some unique diversity and contributed to the complementary effect of maximizing detection. For rapid biodiversity surveys of terrestrial arthropods, we recommend integrating metabarcoding approaches, and in sensitive ecosystems where specimen capture is undesirable, eDNA offers a powerful non-lethal alternative to monitor diversity and community change.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*DNA, Environmental/genetics
*Arthropods/genetics/classification
*Biodiversity
*Ecosystem
Electron Transport Complex IV/genetics
*Metagenomics/methods

@article {pmid42353070,
year = {2026},
author = {Dang, X and Hanson, BA and Lopez, M and Miller, J and Koralnik, IJ},
title = {Cross-Compartment Virome Profiling in Human Immunodeficiency Virus Infection and Substance Use Disorder Reveals Brain-CSF-Periphery Discordance and Hepatitis B Virus in Central Nervous System.},
journal = {International journal of molecular sciences},
volume = {27},
number = {12},
pages = {},
pmid = {42353070},
issn = {1422-0067},
mesh = {Humans ; *Brain/virology ; *HIV Infections/virology/cerebrospinal fluid/complications ; *Substance-Related Disorders/virology/cerebrospinal fluid/complications ; *Virome ; *Hepatitis B virus/genetics/isolation & purification ; Female ; *Central Nervous System/virology ; Male ; *Hepatitis B/virology/cerebrospinal fluid ; Viral Load ; Adult ; },
abstract = {The diversity and abundance of the brain virome is an active field of investigation. However, how the brain virome relates to the presence of viruses outside of the nervous system remains unclear. The rationale for this study is that analyses across multiple biologically linked compartments within the same individuals provide an important opportunity to evaluate virome discordance and viral burden. To characterize viral prevalence and burden across anatomical compartments, we applied the targeted viral enrichment method ViroFind to matched postmortem brain (n = 66), cerebrospinal fluid (CSF; n = 24), and peripheral samples (spleen, peripheral blood mononuclear cells, and lymph nodes; n = 66) from individuals with and without human immunodeficiency virus (HIV) infection and substance use disorder (SUD) in the National NeuroAIDS Tissue Consortium. We detected nucleic acids from 27 viruses representing 12 taxa. Several viruses, including adenovirus, torque teno virus, Epstein-Barr virus, human herpesvirus 6 and 7, cytomegalovirus, parvovirus, and JC polyomavirus, showed significant inter-compartment differences in prevalence or burden. CSF exhibited lower overall viral diversity than brain or peripheral samples, whereas peripheral samples showed the highest viral burden. CNS viral detection was more likely when the same virus was also detected in the periphery. We also detected HBV and HCV in CNS samples despite them not being classically regarded as neurotropic. Broader virome profiling showed greater peripheral viral burden and diversity in HIV-positive than HIV-negative individuals, whereas SUD was not associated with overall viral burden differences. These findings highlight important cross-compartment differences in viral detection, including occurrence of occult HBV infection within the CNS, and support the value of CNS-periphery comparisons in virome studies. These findings can contribute to improved diagnosis and management of viral infections.},
}

Humans
*Brain/virology
*HIV Infections/virology/cerebrospinal fluid/complications
*Substance-Related Disorders/virology/cerebrospinal fluid/complications
*Virome
*Hepatitis B virus/genetics/isolation & purification
Female
*Central Nervous System/virology
Male
*Hepatitis B/virology/cerebrospinal fluid
Viral Load
Adult

@article {pmid42358948,
year = {2026},
author = {Fu, J and Shan, J and Xu, H and Zhu, Z and Yang, P and Wang, Q and Han, J and Cao, G},
title = {Altered GABA and secondary bile acids in Guillain-Barré syndrome: association with gut dysbiosis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1849216},
pmid = {42358948},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/microbiology/metabolism ; *Guillain-Barre Syndrome/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Female ; *Bile Acids and Salts/metabolism/blood ; Male ; *gamma-Aminobutyric Acid/metabolism/blood ; Adult ; Middle Aged ; Metabolomics/methods ; Metabolome ; Metagenomics ; Feces/microbiology ; Aged ; },
abstract = {OBJECTIVE: Guillain-Barré syndrome (GBS) is a rare, immune-mediated inflammatory disease of the complex peripheral nervous system that often follows acute infections, and may also be associated with long-term 'silent infections'. Long-term "silent infections" can alter the gut microbiota, which in turn may contribute to immune-mediated inflammatory diseases. Emerging evidence suggests that gut dysbiosis and altered serum metabolites are associated with GBS, but the causative link between GBS and gut microbiota remains unclear. Therefore, this study aimed to evaluate the association between gut microbiota structure and serum metabolic profile in GBS.

METHODS: Untargeted metabolomics profiling of serum and metagenomics sequencing of stool samples were performed to capture the global metabolic and microbial differences between GBS subjects and healthy controls. Multivariate statistical analyses, including PLS-DA, were applied to identify distinct clustering patterns and differential abundances of metabolites and gut microbiota. Pearson's correlation analysis was used to estimate the correlations between abundance of gut microbiota and serum metabolic profile. Seven different media were used to isolate the potential pathogens from GBS stool samples.

RESULTS: The metabolome data revealed that gamma-aminobutyric acid (GABA) metabolism and secondary cholic acid metabolism were perturbed in GBS. Specifically, GABA was increased significantly (approximately 14.3-fold), while multiple secondary cholic acids (methyl deoxycholate, glycodeoxycholic acid, glycolithocholic acid, taurolithocholic acid, and coprocholic acid) were decreased significantly in GBS subjects. Regarding the gut microbiota identified via metagenomic sequencing of stool samples, Ligilactobacillus salivarius, Enterocloster bolteae, and the opportunistic pathogenic Klebsiella pneumonia were notably more abundant in GBS subjects, while Bacteroides sp., Roseburia hominis and Paraprevotella xylaniphila were decreased significantly. In addition, pathogens such as K. pneumoniae were also isolated from GBS subjects. Further analysis of the metagenomic data revealed enrichment of prokaryotic genes involved in the GABA biosynthesis pathway, while genes associated with secondary cholic acid metabolism pathways were decreased in gut microbiome in GBS subjects. On this basis, correlation analysis revealed that changes in GABA were associated with altered levels of gut microbes including Enterococcus species, Ligilactobacillus salivarius and Enterocloster bolteae, whereas changes in secondary cholic acids were positively correlated with altered levels of Bacteroides species and Roseburia species.

CONCLUSION: GABA metabolism and secondary cholic acid metabolism were significantly disturbed in GBS subjects, potentially resulting from the dysbiosis of the gut microbiota. K. pneumonia and other no gut microbes were significantly enriched and isolated in GBS and may contribute to the inflammatory response in this immune-mediated inflammatory disease. These findings also suggest that GABA may be a promising biomarker for the diagnosis of GBS and that modulation of gut microbiota might impact the clinical course of GBS.},
}

Humans
*Dysbiosis/microbiology/metabolism
*Guillain-Barre Syndrome/microbiology/metabolism/blood
*Gastrointestinal Microbiome
Female
*Bile Acids and Salts/metabolism/blood
Male
*gamma-Aminobutyric Acid/metabolism/blood
Adult
Middle Aged
Metabolomics/methods
Metabolome
Metagenomics
Feces/microbiology
Aged

@article {pmid42096004,
year = {2026},
author = {Huang, YJ and Shen, ZQ and Hu, DP and Huang, YY and Chen, GY and Lin, Y and Hu, BM and Yuan, XX and Deng, GP and Li, X},
title = {Multi-Omics Analysis Reveals Inflammatory Activation and Maternal-Fetal Interface Remodeling in Spontaneous Abortion.},
journal = {Current medical science},
volume = {46},
number = {3},
pages = {791-801},
pmid = {42096004},
issn = {2523-899X},
mesh = {Humans ; Female ; Pregnancy ; Multiomics ; Adult ; *Abortion, Spontaneous/metabolism/microbiology/pathology/genetics ; *Decidua/metabolism/pathology ; *Inflammation/metabolism/pathology/genetics ; Gastrointestinal Microbiome/genetics ; Metabolomics ; Dysbiosis ; Cytokines/metabolism ; NF-kappa B/metabolism ; Signal Transduction ; *Maternal-Fetal Exchange ; },
abstract = {BACKGROUND: Spontaneous abortion (SA) is a common adverse outcome of early pregnancy, yet its underlying pathophysiological mechanisms remain incompletely understood. Accumulating evidence suggests that dysregulated inflammatory responses at the maternal-fetal interface play a critical role in pregnancy loss. However, the potential associations between alterations in gut microbiota, metabolic disturbances, and localized decidual inflammation in patients with SA have not been systematically characterized.

METHODS: Women with SA (n = 30) and those with normal early pregnancy (NP, n = 28) were enrolled in this study. Proinflammatory cytokines were quantified in decidual tissue homogenates, and histopathological and molecular analyses were performed to evaluate inflammatory activation at the maternal-fetal interface. The gut microbiota composition was profiled using shotgun metagenomic sequencing, while metabolic alterations in the feces were assessed by untargeted metabolomics. Integrated multi-omics analyses were conducted to explore associations among gut microbial dysbiosis, metabolic perturbations, decidual inflammatory signaling, and molecular alterations.

RESULTS: Compared with those from the NP group, the decidual tissues from the SA group exhibited significantly elevated levels of IL-1β and TNF-α (1.49-fold and 1.51-fold, both P < 0.0001), accompanied by pronounced histopathological abnormalities. Enhanced activation of the NF-κB signaling pathway was observed at the maternal-fetal interface in SA patients. Metagenomic analyses revealed distinct differences in the gut microbiota composition and community structure between the two groups, with differentially abundant bacterial taxa identified (LDA score > 2.0). Consistent with these findings, fecal metabolomic profiling clearly revealed differences between SA and NP patients, with differentially abundant metabolites (VIP > 1.0, adjusted P < 0.05) predominantly enriched in lipid metabolism, amino acid metabolism, and immune-related pathways. In addition, the expression of leucine-rich repeat-containing G protein-coupled receptor 6 was significantly upregulated (P < 0.0001) in the decidual tissue of SA patients.

CONCLUSIONS: These findings indicate that SA is associated with localized inflammatory activation at the maternal-fetal interface, dysregulation of decidual molecular activity, gut microbiota dysbiosis, and metabolic perturbations. Integrated multi-omics analyses suggest potential interactions among these factors that may be linked to decidual dysfunction during early pregnancy, providing new insights into the complex pathophysiology of SA.},
}

Humans
Female
Pregnancy
Multiomics
Adult
*Abortion, Spontaneous/metabolism/microbiology/pathology/genetics
*Decidua/metabolism/pathology
*Inflammation/metabolism/pathology/genetics
Gastrointestinal Microbiome/genetics
Metabolomics
Dysbiosis
Cytokines/metabolism
NF-kappa B/metabolism
Signal Transduction
*Maternal-Fetal Exchange

@article {pmid42350492,
year = {2026},
author = {Dini, H and Chenghang, S and Tong, X and Yixin, L and Tianchun, P and Shunfu, H and Yanqiang, Y and Yibo, H},
title = {Integrated analyses of metagenomics, metabolomics and culture-based assays reveal functional roles of gut microbiota in Felidae.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01066-9},
pmid = {42350492},
issn = {2055-5008},
support = {32370552//National Natural Science Foundation of China/ ; 32325010//National Natural Science Foundation of China/ ; 2023YFF1304800//National Key Program of Research and Development of Ministry of Science and Technology/ ; },
abstract = {The functional roles of gut microbiota in carnivores remain poorly understood. Here, we integrated metagenomics, metabolomics, proteomics and culture-based functional assays to characterize metabolic potential of gut microbiota across 14 captive Felidae species. Comparative metagenomics analysis revealed that the Felidae gut microbiome is distinct from that of non-Felidae and reflects carnivorous dietary patterns. Genus-level core microbiota were dominated by Clostridium, Collinsella and Bacteroides, with functional enrichment in carbohydrate and amino acid metabolism. Of 219 reconstructed metagenome-assembled genomes (MAGs), 27 were identified as core MAGs containing proteases- and lipases- encoding genes, with ATP-dependent Clp proteases predominating and enriched KEGG orthologs mainly associated with amino acid metabolism. Fecal metabolomics identified 1316 metabolites shared among Felidae species, with KEGG analysis showing they were involved in amino acid and lipid metabolism and significantly enriched in protein digestion and absorption pathway. The amino acid- and lipid-related metabolites were correlated with the relative abundance of core MAGs. Culture-based assays revealed proteolytic and lipolytic activities across isolates, supported by proteomics evidence of predominant ATP-dependent proteases. In vitro fermentation with representative isolates generated fatty-acid-dominated metabolites consistent with fecal metabolomic profiles. Together, our findings demonstrate that Felidae gut microbiota play a critical role in amino acid metabolism for carnivory.},
}

@article {pmid42350494,
year = {2026},
author = {Beiko, RG and Tolman, J and Barawi, SS and Fares, M and Murthy, SSN and Knox, T and Mackie, CM and Grundke, I and Jeffery, NW and Stanley, RRE and Sieben, V and LaRoche, J},
title = {Automated eDNA and eRNA profiling for biodiversity monitoring in marine and freshwater ecosystems.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-58421-1},
pmid = {42350494},
issn = {2045-2322},
abstract = {Biodiversity monitoring is essential to measure the impacts of pollution, invasive species, and the longer-term effects of climate change. Automated samplers enable temporally flexible, remote collection of environmental DNA (eDNA), improving access to time-sensitive events. The Dartmouth Ocean Technologies (DOT) Preserving eDNA Sampler has proven effective in multi-month marine deployments, but further validation is needed across a broader range of habitats and water chemistries, and to establish its suitability for collection and assessment of environmental RNA (eRNA). In this study, we collected samples near the surface (1-1.5 m depth) of a brackish pond, a freshwater lake, and two marine harbours. We identified patterns of species turnover consistent with transitions among aquatic environments, including invasive species such as smallmouth bass and chain pickerel in the freshwater lake. Automated deployment in Halifax Harbour following a significant rainfall event detected nearly ten times as many probable fecal-associated bacteria by proportion at this site relative to Lunenburg Harbour. Preserved eRNA allowed the identification of taxa below the eDNA limit of detection. Our pilot study demonstrates the feasibility of using the DOT sampler for longer-term biomonitoring in a diverse range of aquatic habitats, yielding ecological insights that would not be attainable through manual sampling alone.},
}

@article {pmid42352268,
year = {2026},
author = {Tita, GV and Fogas, CR and Slavescu, KC and Tantau, VM and Medan, SA and Serban, DE},
title = {Persistent Gut Microbiota Dysbiosis in Pediatric Crohn's Disease: A Next-Generation Sequencing Pilot Study.},
journal = {Biomolecules},
volume = {16},
number = {6},
pages = {},
pmid = {42352268},
issn = {2218-273X},
mesh = {Humans ; *Crohn Disease/microbiology ; *Dysbiosis/microbiology/genetics ; Pilot Projects ; Female ; Male ; Child ; *Gastrointestinal Microbiome/genetics ; *High-Throughput Nucleotide Sequencing ; Prospective Studies ; Adolescent ; Metagenomics ; Eubacteriales ; },
abstract = {Background: Crohn's disease (CD) is characterized by gut microbiota alterations including reduced microbial diversity, loss of commensal species, and increased abundance of opportunistic taxa. Methods: This prospective study was conducted between 2022 and 2024 at the Emergency Clinical Hospital for Children, Cluj-Napoca. Children with CD and healthy controls were evaluated. The gut microbiota was analyzed using shotgun metagenomics. Bioinformatic processing assessed alpha and beta diversity, core microbiome composition, and differential taxa. Results: Ten patients with CD and eight healthy children were included; five patients were re-evaluated after a median interval of 14 weeks. The Shannon index was significantly lower in CD patients compared with controls (p = 0.037). Beta diversity analysis suggested partial separation between CD at diagnosis and controls (p = 0.041). An inverse correlation was observed between the Shannon index and the clinical score (p = 0.028). Ruminococcus gnavus was among the taxa contributing to group separation. At follow-up, all patients were in clinical remission, while 80% had achieved biological remission and mucosal healing. They showed persistently reduced alpha diversity and distinct microbial communities compared with controls (p = 0.028 and p = 0.005, respectively). Conclusions: Pediatric CD was correlated with dysbiosis that persisted despite remission. Reduced alpha diversity was associated with greater disease severity at diagnosis.},
}

Humans
*Crohn Disease/microbiology
*Dysbiosis/microbiology/genetics
Pilot Projects
Female
Male
Child
*Gastrointestinal Microbiome/genetics
*High-Throughput Nucleotide Sequencing
Prospective Studies
Adolescent
Metagenomics
Eubacteriales

@article {pmid42352384,
year = {2026},
author = {Brown, JL and Mahadevan, P and Middlebrooks, M},
title = {Bacterial Community Composition and Functional Potential of the Kleptoplastic Sea Slug Elysia papillosa.},
journal = {Biomolecules},
volume = {16},
number = {6},
pages = {},
pmid = {42352384},
issn = {2218-273X},
support = {OURI//University of Tampa/ ; },
mesh = {Animals ; *Gastropoda/microbiology ; *Microbiota ; *Bacteria/genetics/classification ; Phylogeny ; },
abstract = {Certain sacoglossan sea slugs, often known as "solar-powered sea slugs", are a group of marine gastropods that have the unique ability to photosynthesize by stealing functional chloroplasts from algae. The sacoglossan Elysia papillosa can maintain functional chloroplasts for up to two weeks after feeding. The microbiome of these slugs may play a crucial role in their metabolism, immunity, development, but more importantly their photosynthesis. Shotgun metagenomic sequencing was conducted on four samples of E. papillosa in order to characterize their microbiome. Sequences were classified and relative abundance was quantified with Centrifuger and functional data was examined using SqueezeMeta. Bacteria were analyzed by taxonomic groups and hypothesized function to the sea slug was determined with literature analysis. All samples were dominated by phyla Actinomycetota, Bacillota, Patescibacteriota, and Pseudomonadota. The presence of the phyla Bacteroidota and Bacillota was notable in all samples, which contain species known to produce enzymes that break down polysaccharides. It is possible that these bacteria could assist in degradation of the polysaccharide xylan found in the cell walls of Penicillus, the algal food source of E. papillosa. One species that was found in all samples was Cutibacterium acnes which has been shown to be an important component of the gut microbiota in other marine invertebrates and may provide the host with vitamin B12 and other beneficial nutrients. Many of these bacteria may be opportunistic rather than commensal. As a result, more research is required to describe the interactions between the slug and its microbiome, but this preliminary report provides a valuable starting point for identifying the microbiome make-up to further understanding of these relationships.},
}

Animals
*Gastropoda/microbiology
*Microbiota
*Bacteria/genetics/classification
Phylogeny

@article {pmid42353029,
year = {2026},
author = {Xu, HJ and Liu, QL and Zhang, YF and Cuan, SN and Jia, Z and Qiao, D},
title = {Metagenomic Insights into Gut Microbiota Alterations Following Dendrobium huoshanense Water Extract Intervention in Streptozotocin-Induced Type 1 Diabetic Rats.},
journal = {International journal of molecular sciences},
volume = {27},
number = {12},
pages = {},
pmid = {42353029},
issn = {1422-0067},
support = {no//the platform of the Traditional Chinese Medicine Institute of Anhui Dabie Mountain/ ; },
mesh = {Animals ; *Dendrobium/chemistry ; Rats ; *Plant Extracts/pharmacology/chemistry ; *Diabetes Mellitus, Experimental/drug therapy/microbiology ; *Diabetes Mellitus, Type 1/drug therapy/microbiology/chemically induced ; *Gastrointestinal Microbiome/drug effects ; Male ; Metagenomics/methods ; *Hypoglycemic Agents/pharmacology ; Rats, Sprague-Dawley ; Streptozocin ; Water/chemistry ; Metagenome ; },
abstract = {Dendrobium huoshanense water extract (DHWE) exhibits hypoglycemic effects in streptozotocin-induced type 1 diabetic (STZ-T1D) rats. However, its regulatory impact on the gut microbiota of T1D rats remains largely unclear. In this study, metagenomic sequencing was employed to characterize alterations in the gut microbiota of STZ-T1D rats following DHWE intervention, aiming to explore associations between DHWE-mediated gut microbial changes and T1D-related phenotypes. The results showed that 1300 mg/kg·BW/day DHWE did not significantly affect gut microbial α-diversity (p > 0.05), but drove the β-diversity structure toward that of normal rats. Meanwhile, DHWE significantly reduced the Bacteroidota/Bacillota ratio (p < 0.05), Megamonas (p < 0.01), Megamonas funiformis (p < 0.01), and notably increased the relative abundances of Adlercreutzia (p < 0.01), Adlercreutzia equolifaciens (p < 0.01) in STZ-T1D rats. Furthermore, functional annotation revealed that DHWE enriched multiple metabolic pathways, including streptomycin biosynthesis, ansamycins biosynthesis, galactose metabolism, ether lipid metabolism, and caprolactam degradation. Collectively, these findings demonstrate that DHWE reshapes gut microbiota composition and function in STZ-T1D rats, offering new clues regarding how gut microbial changes may contribute to the modulatory effects of Dendrobium huoshanense in T1D conditions.},
}

Animals
*Dendrobium/chemistry
Rats
*Plant Extracts/pharmacology/chemistry
*Diabetes Mellitus, Experimental/drug therapy/microbiology
*Diabetes Mellitus, Type 1/drug therapy/microbiology/chemically induced
*Gastrointestinal Microbiome/drug effects
Male
Metagenomics/methods
*Hypoglycemic Agents/pharmacology
Rats, Sprague-Dawley
Streptozocin
Water/chemistry
Metagenome

@article {pmid41787302,
year = {2026},
author = {Li, Y and Liu, L and Long, M and Guan, D and Deng, W},
title = {Habitat-driven variation in gut microbiome composition and function of the pygmy grasshopper (Tetrix japonica) across diverse ecosystems in China.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41787302},
issn = {1471-2164},
support = {2023GXNSFDA026037//Natural Science Foundation of Guangxi Province,China/ ; 32360124//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Ecosystem ; China ; *Grasshoppers/microbiology/physiology ; *Gastrointestinal Microbiome ; Metagenomics ; Bacteria/classification/genetics ; Metagenome ; Biodiversity ; Phylogeny ; },
abstract = {BACKGROUND: The gut microbiome plays an important role in insect adaptation, yet how habitat variation shapes microbial communities in pygmy grasshoppers remains unclear. We investigated this question using Tetrix japonica, which inhabits diverse ecosystems across China and provides an ideal model to study microbiome-environment interactions. Shotgun metagenomic sequencing was performed on gut samples from six populations representing coniferous forest, broadleaf forests in Shandong and Shaanxi, grassland, shrubland, and laboratory-reared populations. RESULTS: Microbial diversity and community composition varied significantly among habitats, with field populations exhibiting higher diversity than laboratory-reared ones. Despite environmental differences, a core microbiome comprising 1,162 shared species was consistently detected, suggesting stable symbiotic relationships. Habitat-specific microbial signatures were most evident between forest and grassland populations, with lignocellulose-degrading taxa enriched in forest habitats. Moreover, geographic separation between Shandong and Shaanxi broadleaf forests led to distinct microbial profiles despite similar vegetation. Functional analysis revealed differential enrichment of genes related to plant polymer degradation, nitrogen cycling, and secondary metabolite biosynthesis across habitats. CONCLUSION: These findings demonstrate that both habitat conditions and geography influence gut microbiome assembly in T. japonica, with microbiome plasticity facilitating adaptation. The reduced diversity observed in laboratory populations highlights the importance of natural habitats for maintaining functional microbiome integrity.},
}

Animals
*Ecosystem
China
*Grasshoppers/microbiology/physiology
*Gastrointestinal Microbiome
Metagenomics
Bacteria/classification/genetics
Metagenome
Biodiversity
Phylogeny

@article {pmid41796197,
year = {2026},
author = {Sujeeth, NK and Dharani Bommi, KB and Manojkumar, S and Angayarkanni, J and Gnanadesigan, M},
title = {Microbiome signatures of mangroves and salt marsh halophyte rhizosphere soil sediments: a metagenomic approach.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41796197},
issn = {2045-2322},
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Microbiota/genetics ; *Wetlands ; *Salt-Tolerant Plants/microbiology ; *Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Phylogeny ; Metagenome ; India ; Avicennia/microbiology ; *Geologic Sediments/microbiology ; Archaea/genetics/classification ; },
abstract = {In this research, the rhizosphere soil microbiome diversity of mangrove trees such as Avicennia marina, Ceriops tagal & Rhizophora apiculata and salt marsh halophytes Suaeda maritima, Suaeda monoica and Sesuvium portulacastrum from Karankadu mangroves of Tamil Nadu, India was investigated. The collected sample was profiled by 16S rRNA Illumina NovaSeq 6000 platform sequencing of V3–V4 amplicon region by metagenomic approach to investigate the bacterial communities related with the different mangrove species. Root-associated microbes of the mangrove trees play important roles in protecting and maintaining mangrove ecosystems. Bacteria were the most abundant domain followed by Archaea and Eukaryota; Proteobacteria, Actinobacteria, Firmicutes, Fibrobacterota, Chlorobiota, and Bacteroidota were found to be predominant phyla present in all samples; Unculturable environmental microbes were also detected, particularly abundant in S. maritima and S. monoica samples. Staphylococcus aureus, Vibrio parahaemolyticus, Klebsiella pneumoniae, Salmonella enterica, Streptomyces griseocarneus were the most abundant species observed in this study. The variations in bacterial community structure across these ecosystems may be influenced by the distinct environmental conditions of each sampled mangrove habitat. For the first time, our findings highlight the richness of microbial diversity in the Karankadu mangroves, providing essential baseline data and revealing differences between mangrove trees and halophytes. This study offers valuable insights for further investigation into the mechanisms governing rhizosphere microbiome interactions with their host environment.},
}

*Rhizosphere
*Metagenomics/methods
*Microbiota/genetics
*Wetlands
*Salt-Tolerant Plants/microbiology
*Soil Microbiology
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Phylogeny
Metagenome
India
Avicennia/microbiology
*Geologic Sediments/microbiology
Archaea/genetics/classification

@article {pmid41826827,
year = {2026},
author = {Duduk, B and Galic, I and Stanojević, N and Stankovic, N and Rekanović, E},
title = {Microbial diversity of plant pathogens and insect endosymbionts in Reptalus artemisiae.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41826827},
issn = {1471-2180},
support = {451-03-136/2025-03/200214//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-136/2025-03/200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; },
mesh = {Animals ; *Symbiosis ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; *Hemiptera/microbiology ; *Plant Diseases/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Biodiversity ; },
abstract = {BACKGROUND: Phloem-sap-feeding planthopper Reptalus artemisiae is an emerging vector of rubbery taproot disease (RTD) and syndrome basses richesses (SBR) in sugar beet, diseases associated with 'Candidatus Phytoplasma solani' and 'Candidatus Arsenophonus phytopathogenicus', respectively. Despite studies on related cixiids, the microbiome of R. artemisiae remains uncharacterized. Using a PCR-free metagenomic long-read shotgun sequencing approach, this study investigates the bacterial diversity associated with R. artemisiae, and provides genomic insight into two plant pathogens 'Ca. P. solani' and 'Ca. A. phytopathogenicus'. RESULTS: Taxonomic assignment revealed six prokaryotic taxa in R. artemisiae: two plant pathogens ('Ca. P. solani' and 'Ca. A. phytopathogenicus') and four insect endosymbionts – three primary endosymbionts ('Candidatus Vidania', 'Candidatus Purcelliella', and 'Candidatus Karelsulcia') and a secondary endosymbiont (Wolbachia). Community profiles showed a consistent presence of all four endosymbionts across five evaluated R. artemisiae individuals. Phylogenetic analyses of 16S rRNA gene sequences of primary endosymbionts confirmed strong congruence with the cytochrome oxidase subunit I phylogeny of the insect host, indicative of long coevolution and vertical transmission. In contrast, plant pathogen presence in R. artemisiae varied, with 'Ca. P. solani' and 'Ca. A. phytopathogenicus' each detected in three individuals. Genome assembly yielded a complete 774 kb circular chromosome for 'Ca. P. solani' with streamlined metabolism featuring limited biosynthetic pathways, but a full arsenal of genes related to host–pathogen interactions and pathogenicity typical for this biotrophs. The draft genome of 'Ca. A. phytopathogenicus' comprising 18 scaffolds totalling 3.11 Mb and two plasmids shows a self-sufficient metabolism with several missing metabolic modules and presence of genomic islands, virulence factors, and a dynamic mobilome indicating a bacterium in transition that is reorganizing its genetic material, possibly in response to host interactions. CONCLUSION: These findings represent the first in-depth characterization of R. artemisiae microbiome, highlighting a stable endosymbiont consortium and variable pathogen presence that emphasize ecological complexity in vector-pathogen-endosymbiont interactions. The assembled genomes enhance the understanding of microbial ecology, pathogen adaptation and transmission, offering resources for comparative genomics and potential applications in disease management strategies.},
}

Animals
*Symbiosis
*Bacteria/classification/genetics/isolation & purification
Phylogeny
*Hemiptera/microbiology
*Plant Diseases/microbiology
Metagenomics
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA
Biodiversity

@article {pmid41866421,
year = {2026},
author = {Mathur, S and Prasad, M and Kumar, S and Chaurasia, A and Ranjan, R},
title = {A metagenomic survey of the rhizosphere bacterial community of P. longum from the herbal garden, Dayalbagh Educational Institute (D.E.I), Agra, India.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41866421},
issn = {1573-0972},
mesh = {*Rhizosphere ; India ; *Soil Microbiology ; *Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; *Piper/microbiology ; Phylogeny ; Soil/chemistry ; Plants, Medicinal/microbiology ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Proteobacteria/genetics ; },
abstract = {The rhizosphere of medicinal plants harbors complex microbial communities that plays a key role in nutrient cycling, plant growth, and environmental adaptation. Piper longum L., an important medicinal plant, remains poorly explored with respect to its rhizospheric microbiome. In this study, rhizospheric soil samples of P. longum were collected at the spike stage from the Herbal Garden of Dayalbagh Educational Institute, Agra, India, and analyzed using metagenomic approach. Soil physicochemical analysis revealed a neutral to slightly alkaline pH with moderate nutrient availability, indicating favorable conditions for microbial activity. High-throughput Illumina sequencing generated ~ 19.94 million paired-end reads (~ 5.92 Gb), which were assembled into 97,432 scaffolds (52.26 Mb total length), and 45,876 protein-coding genes were predicted. Taxonomic profiling revealed dominance of Proteobacteria (42%), followed by Actinobacteria (13.9%), Thaumarchaeota (13.16%), Chloroflexi (8.21%), and Acidobacteria (7.28%). At the genus level, Nitrososphaera was the most abundant (23.58%), with Candidatus Nitrososphaera gargensis as the predominant species (11.21%), indicating an active microbial community of ammonia-oxidizing archaea involved in nitrogen fixation. Functional annotation using COG, KEGG, Pfam, GO, and FIGfams databases revealed enrichment of genes associated with amino acid transport and metabolism, carbohydrate metabolism, energy production, and environmental adaptation. Overall, this study provides the first metagenomic baseline of the P. longum rhizosphere microbiome and highlights its potential role in nutrient cycling and sustainable cultivation.},
}

*Rhizosphere
India
*Soil Microbiology
*Metagenomics
*Bacteria/classification/genetics/isolation & purification
*Piper/microbiology
Phylogeny
Soil/chemistry
Plants, Medicinal/microbiology
High-Throughput Nucleotide Sequencing
Microbiota/genetics
Metagenome
RNA, Ribosomal, 16S/genetics
Proteobacteria/genetics

@article {pmid41882608,
year = {2026},
author = {Chen, M and Wu, Z and Du, Y and Jiang, J and Feng, J},
title = {Construction of caries risk assessment scale and oral microecology analysis of adolescents with fixed orthodontic treatment.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {},
pmid = {41882608},
issn = {1472-6831},
mesh = {Humans ; Adolescent ; *Dental Caries/microbiology/etiology ; Risk Assessment/methods ; Female ; Male ; *Orthodontic Appliances, Fixed/adverse effects ; *Microbiota ; Dental Plaque/microbiology ; },
abstract = {OBJECTIVE: This study aimed to develop and initially validate a caries risk assessment scale for adolescents undergoing fixed orthodontic treatment, and to exploratorily analyze the potential association between oral microbiota and caries risk levels. METHODS: Clinical examinations and questionnaires were conducted on 210 adolescent orthodontic patients before orthodontic treatment and at 1st, 3rd, and 6th month, and the caries risk assessment scale was constructed according to the correlation statistics. Six patients in low-risk group and middle-risk group were randomly selected. Dental plaque samples were collected before orthodontic treatment and 1st month, respectively. Bioinformatics analyses were performed to explore differences in microbial community composition and function. RESULTS: The caries risk assessment scale involves 7 factors, such as simplified debris index (DI-S), brushing time, and frequency of sugar intake. Differences in scale scores before and during orthodontic treatment at the 1st, 3rd, and 6th months correlated with the presence of caries at the corresponding orthodontic stages (P < 0.001). Differences in scores at 1st month correlated with the presence or absence of caries at 3rd and 6th month (P < 0.05). The differences in scores at 3rd month correlated with the caries status at 6th month (P < 0.001). The caries risk related Glycan biosynthesis and metabolism pathways were positively correlated with Prevotella_jejuni, Prevotella_scopos and Candidatus_Nanosynbacter_sp._HMT-352 (P < 0.01). The Carbohydrate Metabolism pathways were positively correlated with Prevotella_melaninogenica, Prevotella_jejuni, Prevotella_scopos and Candidatus_Nanosynbacter_sp._HMT-352 (P < 0.01). CONCLUSIONS: A practical caries risk assessment scale for orthodontic adolescents was established and shows promise for cross-sectional risk stratificationthroughout the orthodontic treatment cycle. Its longitudinal predictive efficacy requires further validation with appropriate statistical models. The microbial findings, particularly the involvement of Candidatus_Nanosynbacter_sp._HMT-352 in relevant metabolic pathways, are preliminary and hypothesis-generating. These results are constrained by the study's limited sample size and the lack of a high-risk comparator group, necessitating confirmation in larger, more comprehensive future studies.},
}

Humans
Adolescent
*Dental Caries/microbiology/etiology
Risk Assessment/methods
Female
Male
*Orthodontic Appliances, Fixed/adverse effects
*Microbiota
Dental Plaque/microbiology

@article {pmid41902972,
year = {2026},
author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Sierra, JL and Pagaza-Straffon, EC and Hurtado-Ramírez, JM and Quispe-Ricalde, MA and Castelán-Sánchez, HG and Dávila-Ramos, S},
title = {Unveiling a Microbial Treasure Trove: Phylogenetic Diversity and Bioremediation Potential in a High-Altitude Andean Saline System.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41902972},
issn = {1432-184X},
support = {227-2015-FONDECYT//Fondo Nacional de Desarrollo Científico, Tecnológico y de Innovación Tecnológica/ ; Contract No. 23 2018 UNSAAC//UNSAAC/ ; grant No. 103.5/15/10446//Programa de Mejoramiento del Profesorado, Universidad Autónoma del Estado de Morelos, Secretaría de Educación Pública/ ; },
mesh = {*Phylogeny ; *Archaea/genetics/classification/metabolism/isolation & purification ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Altitude ; Biodegradation, Environmental ; Peru ; Soil Microbiology ; Metagenome ; *Microbiota ; Biodiversity ; Metagenomics ; },
abstract = {The reconstruction of metagenome-assembled genomes (MAGs) has improved our knowledge of how microbiomes perform biological and chemical processes in diverse ecosystems, including extreme environments. However, in Latin America, these ecosystems have received insufficient attention. In this study, we used shotgun metagenomics to reconstruct MAGs in Acos a high-altitude intermediate saline system in Cusco, Peru. Most of the MAGs detected were classified only at the phylum level, indicating significant phylogenetic novelty. Of particular note is the presence of two poorly characterized archaeal MAGs from the genus Methanonatronarchaeum, belonging to the phylum Halobacteriota. All reconstructed MAGs displayed a broad spectrum of metabolic pathways associated with the nitrogen and sulfur cycles, indicating metabolic versatility that allows them to cope with the harsh conditions of the saline environment. Both bacterial and archaeal MAGs are enriched in various metabolic processes related to the metabolism of amino acid and nitrogenous compounds; this could indicate a mechanism for adapting to osmotic stress. Among the genes detected, those involved in the degradation of the common herbicide atrazine were identified; this provides information on potential microbial mediation processes for the bioremediation of contaminated soils. Furthermore, and equally important, these habitats harbor a great diversity of viruses, many of which have unknown in current databases. Taxonomic classification revealed bacteriophages belonging to the class Caudoviricetes, specifically the families Myoviridae, Siphoviridae, and Podoviridae. Overall, our work provides high-quality MAGs that expand current knowledge of the diversity, function, and ecological dynamics of Bacteria, Archaea, and viruses in high-altitude intermediate saline environments.},
}

*Phylogeny
*Archaea/genetics/classification/metabolism/isolation & purification
*Bacteria/genetics/classification/metabolism/isolation & purification
Altitude
Biodegradation, Environmental
Peru
Soil Microbiology
Metagenome
*Microbiota
Biodiversity
Metagenomics

@article {pmid41904207,
year = {2026},
author = {Yan, Y and Zhen, W and Hongxia, S and Zhenhong, S and Xianghui, M and Na, W and Li, S and Defeng, W},
title = {Impact of Lactobacillus johnsonii on glycemic control and lipid metabolism in type 2 diabetes with circadian disruption.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41904207},
issn = {2045-2322},
support = {(BJK2024152)//Funded by Science and Technology Project of Hebei Education Department/ ; (20241988)//Hebei Province Medical Science Research Project Plan for 2024/ ; (No. [2020] No.23).//Project Fund of Clinical Medicine Excellent Talents funded by Hebei Provincial Department of Finance/ ; },
mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism/blood ; Humans ; Animals ; Male ; *Lipid Metabolism ; *Glycemic Control ; Blood Glucose/metabolism ; Female ; *Lactobacillus johnsonii/physiology ; *Circadian Rhythm ; Mice ; Middle Aged ; Gastrointestinal Microbiome ; Feces/microbiology ; *Probiotics/administration & dosage ; },
abstract = {Although most patients with type 2 diabetes mellitus (T2DM) and circadian rhythm disruption have poor blood glucose control, a fraction of patients with T2DM and circadian rhythm disruption who still have good blood glucose control. Previous studies have shown that individuals with circadian rhythm disruption are more prone to developing T2DM, and the occurrence of T2DM is associated with the gut microbiota. However, the role of gut microbiota in patients with T2DM and circadian rhythm disruption remains unclear. Stool samples were collected from 6 patients with poorly controlled type 2 diabetes mellitus (T2DM) and circadian rhythm disruption, as well as from 6 patients with well-controlled T2DM and circadian rhythm disruption. Metagenomic sequencing was performed on the stool samples. Compared to the well-controlled group, the abundance of Lactobacillus johnsonii(L. johnsonii) was significantly decreased in the poorly controlled group. To investigate the effects of L. johnsonii supplementation on glucose and lipid metabolism, diabetic mice with circadian rhythm disruption were administered L. johnsonii and their metabolic indicators were measured. Metagenomic sequencing of the gut microbiota revealed a higher microbial diversity in the well blood glucose controlled type 2 diabetes combined with disrupted circadian rhythm group (W-T2D-RD). Additionally, a significant decrease in the abundance of L. johnsonii was observed in patients with poor blood glucose controlled type 2 diabetes combined with disrupted circadian rhythm group (P-T2D-RD) when compared to those with W-T2D-RD. Following supplementation of L. johnsonii to the mice in the type 2 diabetes mellitus rhythm disruption Lactobacillus johnsonii group (T2DM-RD-L), the fasting blood glucose levels and postprandial blood glucose levels were significantly reduced. Additionally, total cholesterol and low-density lipoprotein levels decreased, high-density lipoprotein levels increased in the T2DM-RD-L group. Lactobacillus johnsonii has a positive impact on both glucose and lipid metabolism in patients with type 2 diabetes mellitus and circadian rhythm disruption.},
}

*Diabetes Mellitus, Type 2/microbiology/metabolism/blood
Humans
Animals
Male
*Lipid Metabolism
*Glycemic Control
Blood Glucose/metabolism
Female
*Lactobacillus johnsonii/physiology
*Circadian Rhythm
Mice
Middle Aged
Gastrointestinal Microbiome
Feces/microbiology
*Probiotics/administration & dosage

@article {pmid41905975,
year = {2026},
author = {Barbe, V and de Toro-Martín, J and Garneau, V and Couture, P and Roy, D and Couillard, C and Marette, A and Vohl, MC},
title = {Functional gut microbiome signatures underlying interindividual variability in metabolic responses to red raspberry consumption.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41905975},
issn = {2045-2322},
mesh = {Humans ; *Rubus ; *Gastrointestinal Microbiome ; Metagenomics ; Feces/microbiology ; C-Reactive Protein/metabolism ; Metagenome ; Triglycerides/blood ; },
abstract = {Red raspberries have been shown to exert beneficial effects on immunometabolic health in numerous studies; however, these effects are subject to interindividual variability. Building on a previous transcriptomic-based clustering analysis from an 8-week randomized controlled trial in which 24 individuals consumed 280 g of red raspberries daily, we investigated whether functional metagenomic profiling may enhance our understanding of the observed interindividual variability in metabolic responses. Participants were classified as responders (n = 13) or non-responders (n = 11) based on prior clustering approaches, which identified significant reductions in plasma levels of C-reactive protein (CRP), triglycerides, and total cholesterol in responders. Microbial DNA extracted from fecal samples collected before and after the intervention was sequenced, and carbohydrate-active enzyme (CAZyme) counts were generated using a bioinformatics pipeline. Differential analysis revealed distinct functional metagenomic profiles between responders and non-responders. Multiple linear regressions identified potential associations between baseline CAZyme levels and changes in CRP, with contrasting trends observed between responders and non-responders. CBM8 and CBM49 were among the highlighted CAZymes. GH5 and several GH5 subfamilies were also identified as candidate CAZymes associated with interindividual variability observed in metabolic responses. These findings support the integration of microbiome-derived functional data alongside other omics to improve precision nutrition strategies.},
}

Humans
*Rubus
*Gastrointestinal Microbiome
Metagenomics
Feces/microbiology
C-Reactive Protein/metabolism
Metagenome
Triglycerides/blood

@article {pmid41910822,
year = {2026},
author = {Kumar, V and Nautiyal, CS},
title = {From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41910822},
issn = {1573-0972},
mesh = {*Endophytes/genetics/physiology/classification ; *Symbiosis ; *Agroecology ; Genomics ; *Plants/microbiology ; Multiomics ; Agriculture ; Ecosystem ; Microbiota ; Metagenomics ; Bacteria/genetics/classification ; },
abstract = {Plants, together with their resident endophytes, constitute a functional holobiont whose integrated traits enable plant growth, stress resilience, disease resistance, and ecosystem remediation. This review discusses advances across ten converging domains that are reshaping research and applications of endophytes, including the following: genomics and metagenomics that identify core genes for colonization, nitrogen fixation, hormone modulation, and stress adaptation; functional genomics and systems biology deciphering host-microbe signaling networks; synthetic biology and CRISPR-based tools for the rational improvement of beneficial traits; microbiome engineering aimed at designing and stabilizing endophytic consortia; multi-omics integration connecting genomic, transcriptomic, proteomic, and metabolomic layers during colonization and under stress; environmental and climatic factors shaping endosphere diversity; bioinformatic platforms predicting biosynthetic gene clusters, secretomes, and metabolic potential; and agricultural and environmental applications in biocontrol and bioremediation. Remaining challenges are the uncultured majority of endophytes, context-dependent transitions between mutualism and pathogenicity, limited field validation, and evolving biosafety frameworks. Thus, the forward framework developed here emphasizes the importance of standard strain benchmarking, causal multi-omics workflows, synthetic community design, and multisite agronomic trials. For their part, endophytes form a scalable, climate-resilient platform for the dual purposes of sustainable agriculture and environmental restoration. In the process, endophytes are emerging as a tractable and scalable foundation for climate-resilient biotechnology, wherein molecular innovation connects with field-level sustainability.},
}

*Endophytes/genetics/physiology/classification
*Symbiosis
*Agroecology
Genomics
*Plants/microbiology
Multiomics
Agriculture
Ecosystem
Microbiota
Metagenomics
Bacteria/genetics/classification

@article {pmid41915167,
year = {2026},
author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E},
title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {41915167},
issn = {1432-184X},
mesh = {*Microbiota ; Large Language Models ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Microbiome studies reveal the taxonomic and functional composition of microbial communities inhabiting many diverse environments. Comprehensive microbiome repositories, such as MGnify, organize data into studies, each consisting of multiple sequencing runs or assemblies and accompanying metadata. This structure enables integrative, large-scale, cross-study analyses, leading to broader insights across ecosystems, hosts, and experimental contexts. Despite extensive microbiome research, methods for defining similarity between studies and validating those similarity metrics, remain insufficiently established, especially for large-scale analyses. To address this, we evaluate whether taxonomic and functional similarities from MGnify can serve as reliable indicators of study relatedness between study pairs, testing multiple metrics against conceptual relatedness (e.g., shared environments, goals, or methods). To scale validation, we introduce a framework that applies a Large Language Model (LLM) to study descriptions, categorizing study pairs by relatedness. Our results show that functional similarity correlates more strongly with LLM-inferred study relatedness than taxonomic similarity, highlighting both the promise and limitations of current metrics. Via the above, we demonstrate the value of combining microbial profiles with LLM-driven semantic reasoning to navigate the expanding landscape of metagenomic research.},
}

*Microbiota
Large Language Models
*Bacteria/classification/genetics/isolation & purification

@article {pmid41917812,
year = {2026},
author = {Shi, K and Zhang, H and Ji, L and Li, W and Zhang, Q and Liu, N and Liu, J and Guo, S and Huang, S and Chen, Y and Zhang, X and Wang, W and Lei, W and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ma, X and Yang, H and Zhang, W},
title = {Systemic remodeling of the multi-organ virome following Echinococcus infection in mice.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41917812},
issn = {1471-2180},
support = {No. 2023YFD1801300//the National Key Research and Development Programs of China/ ; No. 82341106//the National Natural Science Foundation of China/ ; No. 202208170046//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents-Leading Talents/ ; },
mesh = {Animals ; *Virome/genetics ; Mice ; Liver/virology/parasitology ; Phylogeny ; *Echinococcosis/virology/parasitology ; Lung/virology/parasitology ; Metagenomics ; *Echinococcus/virology ; *Viruses/classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; Female ; },
abstract = {The interaction between parasitic infection and the host virome represents a frontier issue in microbial ecology, yet how Echinococcus infection affects the multi-organ virome and whether these alterations hold diagnostic or interventional potential remains poorly understood. In this study, we performed viral metagenomic sequencing on gut, liver, and lung samples from both infected and uninfected mice, integrating community structure clustering, diversity indices, and differential analyses, including STAMP and LEfSe. Our results reveal that Echinococcus infection induced significant tissue-specific virome remodeling. Compared to healthy controls, gut virome diversity increased, characterized by marked expansion of the class Caudoviricetes, particularly the family Siphoviridae (LDA > 4), alongside Picornaviridae enrichment (LDA > 4). In contrast, virome diversity decreased in both the liver and lung, with significant enrichment of Reoviridae (LDA > 4) in the liver and Retroviridae (LDA > 4) in the lung, respectively. Conversely, Picobirnaviridae (LDA > 4) was significantly reduced in the infected liver and lung. Based on phylogenetic analysis, Echinococcus infection significantly altered the murine gut viral community, with eukaryotic viruses (e.g., norovirus, picobirnavirus, and picornavirus) detected exclusively in infected animals, while bacteriophage populations remained stable across groups. Phage host prediction further revealed that phages enriched in infected samples targeted opportunistic pathogens (Clostridium septicum, Trueperella pyogenes), whereas control phages predominantly targeted commensals (Bacteroides thetaiotaomicron). Together, these findings demonstrate that Echinococcus infection drives both eukaryotic virus enrichment and a shift in phage predation toward pathogens, suggesting that infection-induced immune modulation creates a permissive environment for viral replication and associated bacterial dysbiosis.},
}

Animals
*Virome/genetics
Mice
Liver/virology/parasitology
Phylogeny
*Echinococcosis/virology/parasitology
Lung/virology/parasitology
Metagenomics
*Echinococcus/virology
*Viruses/classification/genetics/isolation & purification
Gastrointestinal Microbiome
Female

@article {pmid41942856,
year = {2026},
author = {Liu, SW and Wang, XX and Xian, LY and Zou, DW and Huang, YF and He, XL and He, F and Wang, XT},
title = {Metagenomic analysis of intestinal microbiota characteristic differences between patients with ankylosing spondylitis and healthy individuals.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41942856},
issn = {1471-2180},
support = {2023JH2/101700219//Liaoning Province Science and Technology Plan Joint Project (Applied Basic Research Project)/ ; },
mesh = {Humans ; *Spondylitis, Ankylosing/microbiology ; Male ; Adult ; Female ; *Gastrointestinal Microbiome/genetics ; *Metagenomics ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Biodiversity ; },
abstract = {BACKGROUND: To explore the differences in intestinal microbiota between patients with ankylosing spondylitis (AS) and healthy individuals (HC) in terms of genetic, species composition, and functional levels, and to reveal the role of intestinal microorganisms in the pathogenesis of AS. METHODS: This study selected 17 AS patients (AS group) and 17 healthy subjects (HC group) from the Affiliated Hospital of Liaoning University of Traditional Chinese Medicine between August to October 2024. Basic clinical data, as well as the Bath Ankylosing Spondylitis Disease Activity Index (BASDAI), Visual Analogue Scale (VAS) score, of the AS group, were collected. Fresh fecal samples were also collected for metagenomic sequencing. Differences in microbiota were analyzed using methods including Alpha diversity analysis, species abundance analysis, Principal Coordinates Analysis (PCoA), Non-metric Multidimensional Scaling (NMDS), DESeq2 analysis, Linear Discriminant Analysis Effect Size (LEfSe), and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation. RESULTS: The number of unique genes in the AS group (566,526) was higher than that in the HC group (406,609). At the species level, there were no significant differences in Alpha diversity or the overall microbial structure (revealed by PCoA and NMDS) between the two groups (p > 0.05). However, significant differences in abundance were observed at the family, genus, and species levels. DESeq2 identified a total of 43 differential species, among which 22 species had increased abundance and 21 species had decreased abundance in the AS group. LEfSe analysis showed that the HC group had 16 dominant bacterial species, while the AS group had only Neoporus faecalis as the dominant species. There were differences in KEGG Level 3 functional pathways between the two groups, but no statistically significant difference was found in the overall functional structure (p = 0.698). Functional enrichment analysis revealed that AS-specific genes were primarily enriched in neurodegenerative disease pathways, protein processing in the endoplasmic reticulum, and autophagy-related pathways, with substantial contributions from genera including Bacteroides, Streptococcus, Eubacterium, and Faecalibacterium. However, neither individual differential species nor their functional pathways showed significant correlations with clinical disease activity scores (BASDAI and VAS)。. CONCLUSION: The studies indicated that although there was no significant difference in the overall diversity of intestinal microbiota between AS patients and healthy individuals, there were obvious distinctions in genetic composition, specific bacterial species, and functional pathways, suggesting that intestinal microorganisms may be involved in the pathogenesis of AS.},
}

Humans
*Spondylitis, Ankylosing/microbiology
Male
Adult
Female
*Gastrointestinal Microbiome/genetics
*Metagenomics
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Biodiversity

@article {pmid41961352,
year = {2026},
author = {Cao, XY and Tian, JJ and Zhang, W and Chen, CL and Ma, H},
title = {Puerarin Alleviates Depression via Integrated Regulation of TLR4/MyD88/NF-κB Signaling and Gut Microbiota-Metabolic Axis.},
journal = {Neurochemical research},
volume = {51},
number = {2},
pages = {},
pmid = {41961352},
issn = {1573-6903},
mesh = {Animals ; *Toll-Like Receptor 4/metabolism ; Male ; *Depression/drug therapy/metabolism ; *Isoflavones/therapeutic use/pharmacology ; Signal Transduction/drug effects ; *Myeloid Differentiation Factor 88/metabolism ; *Gastrointestinal Microbiome/drug effects/physiology ; *NF-kappa B/metabolism ; Rats ; Rats, Sprague-Dawley ; *Antidepressive Agents/therapeutic use/pharmacology ; Hippocampus/metabolism/drug effects ; },
abstract = {Depression is a highly prevalent mental disorder in which dysfunction of the gut microbiota is implicated as a significant factor in its pathogenesis. Puerarin has been suggested to alleviate depression via the microbe-gut-brain axis (MGBA), although the precise mechanisms remain elusive. This study aimed to elucidate the association between the antidepressant effects of puerarin and its role in regulating intestinal flora imbalance and inhibiting subsequent activation of the LPS/TLR4 inflammatory pathway from metabolomics and metagenomics perspectives. A rat model of depression was established using a 6-week chronic unpredictable mild stress (CUMS) protocol. Depressive-like behaviors were assessed through the sucrose preference test (SPT), forced swim test (FST), and open field test (OFT). Inflammatory cytokines (TNF-α, IL-1β, IL-6), LPS, corticosterone, and 5-HT were measured via ELISA. Hippocampal and colonic protein expression of TLR4, MyD88, IκBα, and NF-κB was analyzed by western blot. Colon tissue integrity was evaluated using H&E staining, PAS staining, and transmission electron microscopy. Immunofluorescence was employed to detect Iba-1+ microglia, TLR4+ cells, and ZO-1 expression. Fecal metabolomics and metagenomics were conducted to identify differential metabolites and microbial composition, followed by KEGG and KO enrichment analyses to predict relevant pathways. Spearman correlation analysis was used to explore relationships among gut microbiota, metabolites, and behavioral indices. Puerarin markedly ameliorated depression-like behaviors in CUMS rats. Concurrently, puerarin inhibited the LPS/TLR4 signaling pathway and its downstream pro-inflammatory mediators in both the hippocampus and colon, resulting in a significant reduction in inflammatory responses across these regions, as well as in the serum. Metagenomic sequencing revealed that puerarin suppressed inflammation-associated bacteria, enhanced the abundance of Firmicutes, and induced alterations in the microbial community structure and composition. Metabolomic analysis demonstrated that puerarin could counteract dysregulated fecal metabolism, identifying 17 metabolites as potential key mediators in restoring metabolic homeostasis in CUMS rats. These biomarkers were implicated in several metabolic pathways, including Aminoacyl-tRNA biosynthesis, Pyrimidine metabolism, Alanine, Aspartate, and Glutamate metabolism. Puerarin may exert its antidepressant effects by modulating the gut microbial structure and metabolite profiles, thereby alleviating inflammatory stress in the colon, bloodstream, and hippocampus, potentially through inhibition of the LPS/TLR4 signaling pathway.},
}

Animals
*Toll-Like Receptor 4/metabolism
Male
*Depression/drug therapy/metabolism
*Isoflavones/therapeutic use/pharmacology
Signal Transduction/drug effects
*Myeloid Differentiation Factor 88/metabolism
*Gastrointestinal Microbiome/drug effects/physiology
*NF-kappa B/metabolism
Rats
Rats, Sprague-Dawley
*Antidepressive Agents/therapeutic use/pharmacology
Hippocampus/metabolism/drug effects

@article {pmid41973308,
year = {2026},
author = {Aydin, F and Çek, Ş},
title = {Mineral-microbiota interactions in aquaculture: implications for fish gut health and nutrition.},
journal = {Veterinary research communications},
volume = {50},
number = {4},
pages = {},
pmid = {41973308},
issn = {1573-7446},
mesh = {Animals ; *Aquaculture ; *Fishes/microbiology/physiology ; Dietary Supplements/analysis ; Animal Feed/analysis ; *Gastrointestinal Microbiome/drug effects/physiology ; *Minerals/metabolism/administration & dosage ; Diet/veterinary ; Animal Nutritional Physiological Phenomena ; Gastrointestinal Tract/microbiology ; },
abstract = {Dietary minerals and gut microbiota engage in a dynamic, bidirectional relationship that shapes the health, immune competence, and productive performance of farmed fish and shrimp. This review explores the bidirectional interactions between mineral supplementation and microbial communities within the gastrointestinal tract of farmed fish and examines the effects of individual and combined mineral supplementation including iron, zinc, magnesium, selenium, manganese, and copper in inorganic, organic, and nanoparticle forms on the intestinal microbiota and histomorphology of farmed aquatic species. Minerals serve essential physiological roles while simultaneously modulating microbial diversity, composition, and metabolic activity; conversely, the gut microbiota influences mineral bioavailability and absorption through enzymatic transformations and competitive uptake. Studies conducted on yellow catfish, largemouth bass, golden pompano, grouper, Nile tilapia, Chinese tongue sole, Pacific white shrimp, channel catfish, zebrafish, and Oriental river prawn were comprehensively examined. Findings indicate that organic and nanoparticle mineral forms generally exhibit higher bioavailability and more favorable effects on intestinal health compared to conventional inorganic sources, with partial substitution strategies (e.g., ~ 50% organic mineral replacement) yielding optimal outcomes in combined formulations. Optimized mineral supplementation was further associated with enrichment of beneficial microbiota, enhanced mucosal barrier integrity through goblet cell proliferation, and reinforcement of innate immune responses, collectively supporting nutrient assimilation, growth performance, and disease resistance. However, the reviewed studies share critical limitations: species diversity was narrow, experimental durations were short (8–80 days), no trial encompassed a full reproductive cycle, and the mechanisms underlying mineral–microbiota crosstalk remain incompletely understood. Synergistic or antagonistic interactions among Zn, Cu, Mn, Fe, and Se are inadequately characterized, and dose optimization specific to species, age, and physiological status has not been achieved. Future research should incorporate long-term and multigenerational designs, metagenomic and metabolomic analyses, comparative multi-mineral trials, and the integration of microbiome-based diagnostics to tailor mineral interventions, alongside validation under commercial aquaculture conditions and ecotoxicological assessment of nanoparticles in aquatic environments.},
}

Animals
*Aquaculture
*Fishes/microbiology/physiology
Dietary Supplements/analysis
Animal Feed/analysis
*Gastrointestinal Microbiome/drug effects/physiology
*Minerals/metabolism/administration & dosage
Diet/veterinary
Animal Nutritional Physiological Phenomena
Gastrointestinal Tract/microbiology

@article {pmid41975427,
year = {2026},
author = {Zhang, Z and Bai, J and Liu, Y and Wang, J and Lv, Z and Tang, L and Wang, R and Gao, L and Liu, C and Lu, S and Fu, X and Ni, J and Wan, P},
title = {Effects of synthetic breast milk on the gut metagenome and whole blood transcriptome in lambs.},
journal = {BMC veterinary research},
volume = {22},
number = {1},
pages = {},
pmid = {41975427},
issn = {1746-6148},
support = {NYHXGG.2023AA206-3//Agricultural GG Project of Xinjiang Production and Construction Corps/ ; 2025AB5012//Tacheng Talents Project/ ; 2025AA01504//Project of Major Science and Technology Project of the Corps/ ; 2022TSYCCX0124//Young Science and Technology Top Talent Program of Tianshan Talent Training Program in Xinjiang Province/ ; XJARS-09-26//Xinjiang Agriculture Research System/ ; CARS-39-07//China Agriculture Research System/ ; },
mesh = {Animals ; *Transcriptome ; Sheep/blood/microbiology ; Female ; *Gastrointestinal Microbiome ; *Metagenome ; Feces/microbiology ; *Milk ; *Milk Substitutes ; Animal Feed/analysis ; },
abstract = {Early postnatal nutrition is crucial for the growth and development of lambs, and artificial milk formulas are widely used as alternatives to breast milk in intensive sheep production. However, the molecular and microbial mechanisms underlying the differences between breast milk and formula feeding remain unclear. This study aimed to compare the fecal metagenomic and whole blood transcriptomic profiles of lambs fed breast milk (BF group) and commercial formula (FF group) from 4 to 45 days of age, to provide a theoretical basis for optimizing formula compositions. A total of 6 lambs were randomly divided into two groups (n = 3 per group), with body weight and body dimensions measured at 45 days of age, followed by fecal metagenomic sequencing and whole blood transcriptomic sequencing. The results showed that BF lambs had significantly higher body weight, body length, heart girth, and chest width than FF lambs. Metagenomic analysis revealed that at the phylum level, Bacteroidetes was enriched in FF lambs, whereas Firmicutes predominated in BF lambs. Differential abundance was also observed at the genus level (higher Desulfovibrio in FF lambs) and the pathway level, with BF lambs enriched in quorum sensing and FF lambs showing higher abundances of pathways related to ubiquinone and other terpenoid-quinone biosynthesis. Moreover, transcriptomic analysis identified 3290 differentially expressed genes (DEGs) between the two groups, with DEGs mainly enriched in metabolic pathways, mTOR signaling pathway, osteoclast differentiation, B cell receptor signaling pathway and MAPK signaling pathway. Collectively, compared with FF, BF enhanced lamb growth, optimized gut microbiome structure and modulated blood transcriptomic profiles related to metabolism, signaling and immunity. These findings highlight the key microbial taxa and functional pathways modulated by breastfeeding, providing valuable insights for the development of more effective milk formula alternatives.},
}

Animals
*Transcriptome
Sheep/blood/microbiology
Female
*Gastrointestinal Microbiome
*Metagenome
Feces/microbiology
*Milk
*Milk Substitutes
Animal Feed/analysis

@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},
mesh = {*Rivers/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; *Plastics/chemistry ; *Bacteria/classification/genetics/isolation & purification/growth & development ; Biofilms/growth & development ; Phylogeny ; Water Microbiology ; Biodiversity ; DNA, Bacterial/genetics ; Polyethylene ; Polyethylene Terephthalates ; Microbiota ; },
abstract = {In rivers, microorganisms colonize plastic surfaces, initiating processes that can lead to their microbial decomposition. Our study investigates the bacterial community composition and diversity on the surfaces of plastics used daily, such as polyethylene terephthalate (PET) and low-density polyethylene (LDPE), which were exposed to river water from the Aller and Fusche rivers. Glass was used for comparison purposes. 16s rRNA sequencing revealed that the type of surface and the native microbial community in the river water, including the water quality, significantly influenced biofilm community assembly. River water samples, especially from the Fusche site, supported the highest microbial richness, while plastic exhibited moderate diversity, and glass beads hosted the lowest richness and diversity. Proteobacteria and Bacteroidetes dominated across all samples, with notable enrichment of functionally relevant families such as Rhodobacteraceae and Comamonadaceae. Ecologically relevant genera such as Flavobacterium, Hydrogenophaga, Rhodoferax, Sediminibacterium, and Rhodobacter dominated across samples. Alpha diversity reflected the richness of taxa within each sample, while beta diversity revealed distinct clustering based on both plastic type and site, indicating the influence of ecological pressure and niche partitioning. These findings highlight the capacity of plastic surfaces to harbour diverse and specialised bacterial assemblages, with implications for biogeochemical cycling, pollutant interactions, and potential microbial degradation pathways. This work contributes to deciphering the ecological roles of biofilms in freshwater plastisphere micro-environments and underscores the importance of material-specific microbial dynamics in assessing environmental risks.},
}

*Rivers/microbiology/chemistry
RNA, Ribosomal, 16S/genetics
*Plastics/chemistry
*Bacteria/classification/genetics/isolation & purification/growth & development
Biofilms/growth & development
Phylogeny
Water Microbiology
Biodiversity
DNA, Bacterial/genetics
Polyethylene
Polyethylene Terephthalates
Microbiota

@article {pmid42010622,
year = {2026},
author = {Goldstein, C and Lavy, I and Sun, T and Ennis, D and Shreffler, WG and Yuan, Q and Virkud, YV and Martin, VM and Yassour, M},
title = {Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42010622},
issn = {1756-994X},
support = {1685-3680//Gerber Foundation/ ; 230465//Demarest Lloyd Jr Foundation/ ; 229711//the Food Allergy Science Initiative/ ; K23AI151555//National Institute of Allergy and Infectious Diseases of the US/ ; K23AI130408//Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity/ ; },
mesh = {Humans ; Infant ; *Proctocolitis/microbiology/etiology ; *Food Hypersensitivity/microbiology ; Female ; Male ; *Gastrointestinal Microbiome ; Feces/microbiology ; Metagenomics/methods ; *Dietary Proteins/adverse effects ; Metagenome ; },
abstract = {BACKGROUND: The complex relationship between the gut microbiome and immune system development during infancy is considered a key factor in the rising rates of pediatric allergic diseases. Food protein-induced allergic proctocolitis (AP), the earliest identified form of non-IgE-mediated food allergy in infants, occurs at the mucosal surface where dietary proteins, intestinal microbes, and immune cells directly interact, and increases the risk for life threatening IgE-mediated food allergy, making it an important model for understanding early food allergic disease development. The question of how specific microbial compositions and functional pathways contribute to AP development and progression remains poorly understood. METHODS: We performed metagenomic sequencing on 740 longitudinal stool samples from 163 infants (84 with AP, 79 without AP) enrolled in the prospective GMAP cohort. Taxonomic profiling, functional pathway analysis, strain-level characterization, and machine learning-based classification were applied to identify microbial differences across disease stages. RESULTS: Here we show that infants with AP exhibit different microbial compositions, characterized by enrichment of Escherichia coli and Bifidobacterium bifidum during early life, including pre-symptomatic stages, while species like Bifidobacterium breve and Klebsiella species are more abundant in infants without AP. These findings suggest the presence of microbial signatures that may be detectable before clinical symptoms emerge, and demonstrate that strain-level differences within E. coli populations may represent AP-associated lineages with distinct gene content profiles that were not previously recognized. For example, biofilm formation and cell adhesion genes in E. coli were particularly enriched in AP-associated clades. Short chain fatty acid (SCFA) and other functional pathways were also associated with AP, including reduced SCFA production during the symptomatic phase, and then a potentially compensatory increased production following AP resolution. CONCLUSIONS: Our results provide the first comprehensive strain-level characterization of the gut microbiome in AP, and functional implications, and generate new hypotheses to be tested regarding candidate microbial features associated with AP for future biomarker discovery and/or intervention targets. This work advances our understanding of how specific microbial taxa and functional pathways may contribute to non-IgE-mediated food allergies and opens new avenues for microbiome-targeted therapeutic approaches as well as novel prevention targets for IgE-mediated food allergies.},
}

Humans
Infant
*Proctocolitis/microbiology/etiology
*Food Hypersensitivity/microbiology
Female
Male
*Gastrointestinal Microbiome
Feces/microbiology
Metagenomics/methods
*Dietary Proteins/adverse effects
Metagenome

@article {pmid42012708,
year = {2026},
author = {Kværner, AS and Birkeland, E and Avershina, E and Botteri, E and Bucher-Johannessen, C and Knudsen, MD and Hjartåker, A and Page, CM and Hov, JR and Song, M and Randel, KR and Hoff, G and Rounge, TB and Berstad, P},
title = {Alcohol consumption and colorectal carcinogenesis: an exploration of the gut microbial pathway as a potential mediator.},
journal = {European journal of nutrition},
volume = {65},
number = {4},
pages = {},
pmid = {42012708},
issn = {1436-6215},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology ; *Alcohol Drinking/adverse effects ; *Gastrointestinal Microbiome ; Male ; Middle Aged ; Female ; Aged ; Risk Factors ; *Carcinogenesis ; Feces/microbiology ; },
abstract = {BACKGROUND: Alcohol consumption is one of the major risk factors of colorectal cancer (CRC), yet the mechanisms underlying this relationship, particularly the role of gut microbes, are not fully understood. OBJECTIVE: To study associations of alcohol intake with the gut microbiome and colorectal lesions among CRC screening participants. Of particular interest was the potential role of gut microbes in mediating the association between alcohol intake and colorectal lesions. METHODS: Screening participants with a positive faecal immunochemical test at ages 55–77 were eligible for the CRCbiome study. Alcohol intake was assessed using a validated, semi-quantitative food frequency questionnaire and linked with shotgun metagenome based gut microbial profiles to study associations with screen-detected colorectal lesions. The potential role of alcohol-associated gut microbes in mediating the association between alcohol intake and colorectal lesions was examined using causal mediation analysis. RESULTS: Of 1468 participants with dietary data, 414 were diagnosed with advanced lesions. Alcohol intake was positively associated with advanced lesions in a dose-dependent manner (ptrend = 0.008), with odds ratio of 1.09 (95% confidence interval, 1.00, 1.19) per 10 g/day increase. Compared to non-consumers, those consuming alcohol were characterized by a distinct microbial profile, manifested as modest, but consistent, shifts in α- and β-diversity, and differentially abundant bacteria. A causal mediation analysis showed that 12% of the association between alcohol intake and advanced lesions was mediated by alcohol-associated gut bacteria. CONCLUSION: Alcohol consumption was associated with a distinct microbial profile, which partly explained the association between alcohol intake and advanced colorectal lesions. Trial registration: The BCSN is registered at clinicaltrials.gov (National clinical trial (NCT) no. 01538550).},
}

Humans
*Colorectal Neoplasms/microbiology/epidemiology
*Alcohol Drinking/adverse effects
*Gastrointestinal Microbiome
Male
Middle Aged
Female
Aged
Risk Factors
*Carcinogenesis
Feces/microbiology