@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

@article {pmid42014993,
year = {2026},
author = {Dong, X and Yi, J and Wang, Y and Zhou, A and Zhang, J and Shi, L and Wang, C},
title = {Multi-omics integration analyses reveal microbiome and metabolome features in pregnant sow diarrhea induced by porcine epidemic diarrhea virus.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42014993},
issn = {1471-2180},
mesh = {Animals ; Female ; Pregnancy ; Swine ; *Coronavirus Infections/veterinary/microbiology/virology ; Multiomics ; *Diarrhea/microbiology/veterinary/virology/metabolism ; *Swine Diseases/microbiology/virology/metabolism ; *Porcine epidemic diarrhea virus ; *Metabolome ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Gastrointestinal Microbiome ; Metagenomics ; },
abstract = {Gut microbial dysbiosis and its derived-metabolites changes have been evidenced to participant in diarrhea piglets; little is known underlying the crosstalk between gut microbiota and metabolites in pregnant sow diarrhea induced with PEDV. In this study, we performed fecal metagenomic and metabolomic profiling in diarrheic pregnant sows infected with PEDV to evaluate the functional characteristics of gut microbiota and metabolites. Microbiome analysis revealed the alterations in composition and diversity of gut microbiota in diarrheic pregnant sows compared with non-diarrheic. The relative abundances of the genera Prevotella, Treponema and Bacteroides were significantly lower and the abundant of Lactobacillus and Ruminococcus were increased in diarrheic pregnant sows. In addition, we found that the increase of Ruminococcus_sp_CAG563, Mycoplasma_sp_CAG472, Prevotella_sp_CAG520, Candidatus_Melainabacteria_bacterium and Eubacterium_coprostanoligenes was the important characteristics in diarrheic pregnant sows. In addition, metabolomic analysis showed a distinct metabolic profile in diarrheic pregnant sows infected with PEDV and the differential metabolites were associated with secondary bile acid biosynthesis, protein digestion and absorption, amino acid biosynthesis. Moreover, our multi-omics data integration analysis indicated that the significant dominant bacteria in diarrheic pregnant sows were positively correlated with 5-aminovaleric acid, pantothenate, 8,4-oxyneolignan-4-xyloside and xanthine, while the predominant coexistence of Treponema, Bacteroides, and Fibrobacter promoted the production of dodecanedioic acid, sesamol and sebacic acid in non-diarrheic pregnant sows infected with PEDV. Taken together, our findings revealed the dynamic changes in the microbiota and metabolites of diarrheic pregnant sows during PEDV infection, identifying microbiota‑derived metabolites associated with host resistance, providing novel insight into the host–gut microbiota interaction.},
}

Animals
Female
Pregnancy
Swine
*Coronavirus Infections/veterinary/microbiology/virology
Multiomics
*Diarrhea/microbiology/veterinary/virology/metabolism
*Swine Diseases/microbiology/virology/metabolism
*Porcine epidemic diarrhea virus
*Metabolome
Feces/microbiology
Bacteria/classification/genetics/isolation & purification/metabolism
*Gastrointestinal Microbiome
Metagenomics

@article {pmid42045813,
year = {2026},
author = {Lindstrøm, JC and Gjerdrum, HSV and Brynildsrud, OB and Tannæs, TM and Kristoffersen, AB and Ricanek, P and Leegaard, TM and Bjørnholt, JV and Jørgensen, SB and Tunsjø, HS and Olbjørn, C and Detlie, TE and Jahnsen, J and Kristensen, VA and Høivik, ML and Hov, JR and Moen, AE and , },
title = {Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42045813},
issn = {1471-2180},
mesh = {Humans ; Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology/drug therapy ; Female ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Gastrointestinal Microbiome/drug effects/genetics ; Mesalamine/therapeutic use ; Male ; Adrenal Cortex Hormones/therapeutic use ; Adult ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; Middle Aged ; Crohn Disease/microbiology/drug therapy ; Colitis, Ulcerative/microbiology/drug therapy ; *Drug Resistance, Bacterial/genetics ; },
abstract = {INTRODUCTION: The members of the human gut microbiota contain a large diversity of genes, including antimicrobial resistance genes (ARGs) known as the gut resistome. The resistome is susceptible to alterations when compositional changes occur in the fecal and gut microbiome. Medical treatment may affect members of the gut microbiota. This study hypothesizes that medication used by patients with inflammatory bowel disease (IBD) leads to an increased prevalence and diversity of ARGs in the gut and a corresponding change in the taxonomic composition of the fecal microbiome. METHODS: Fecal samples from 16 Crohn’s Disease (CD) and 16 Ulcerative Colitis (UC) patients, and 13 symptomatic controls (patients experiencing gastrointestinal symptoms, but with no endoscopic or histologic signs of IBD at inclusion, and no evidence of IBD during follow-up, were classified as symptomatic non-IBD controls) were subjected to metagenomic sequencing. The samples were collected before initiation of IBD medication, and after one year of treatment. Patients were treated with 5- Amino Salicylic Acid, Biological treatment, and Corticosteroids, or a combination of the three. Resistance Gene Identifier Comprehensive Antibiotic Resistance Database (RGI CARD) and regression modelling were used to analyze the abundance and diversity changes in the ARGs and the taxonomy. RESULTS: We found significant associations with medicine use and abundance changes for eight resistance genes (Antibiotic Resistance Ontology (ARO) terms), four AMR gene families and 14 AMR drug classes. The use of 5-ASA was associated with abundance changes for the efflux pump efpA. This medication was also associated with significant changes in the “pyrazinamide resistant rpsA” gene family and with six drug classes (cephamycin, diaminopyrimidine, mupirocin, penem, pyrazinamide and rifamycin). Biological treatment was associated with changes in abundance of five drug classes (Zoliflodacin, lincosamide, macrolide, streptogramin and tetracycline). Corticosteroids were associated with changes in the ARO terms sul2, OXA beta-lactamase AMR gene family, and three drug classes (carbapenem, glycylcycline, and triclosan). CONCLUSIONS: All IBD medication groups were found to be associated with significant abundance changes within the fecal resistome between inclusion and follow-up time points, where corticosteroid treatment resulted in less resistance in the microbiota compared to in the persons not treated with corticosteroids (either 5-Aminosalicylic Acid or Biological treatments).},
}

Humans
Feces/microbiology
*Inflammatory Bowel Diseases/microbiology/drug therapy
Female
*Bacteria/genetics/drug effects/classification/isolation & purification
*Gastrointestinal Microbiome/drug effects/genetics
Mesalamine/therapeutic use
Male
Adrenal Cortex Hormones/therapeutic use
Adult
Anti-Bacterial Agents/pharmacology
Metagenomics
Middle Aged
Crohn Disease/microbiology/drug therapy
Colitis, Ulcerative/microbiology/drug therapy
*Drug Resistance, Bacterial/genetics

@article {pmid42080548,
year = {2026},
author = {Zhang, X and Zhong, A and Liu, Y and Zou, J and Gu, M and Zhu, X and Xu, H and Yin, S},
title = {Chronic intermittent hypoxia exacerbates hepatic steatosis in a microbiota-dependent manner in lean mice.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0016326},
pmid = {42080548},
issn = {2379-5077},
support = {2021ZD0201900//Ministry of Science and Technology of the People's Republic of China/ ; 82071030//National Natural Science Foundation of China/ ; 82071029//National Natural Science Foundation of China/ ; 18DZ2260200//Science and Technology Commission of Shanghai Municipality/ ; },
mesh = {Animals ; *Hypoxia/complications/metabolism/microbiology ; Mice ; Male ; *Fatty Liver/metabolism/microbiology/etiology ; *Gastrointestinal Microbiome ; Humans ; Liver/metabolism/pathology ; Mice, Inbred C57BL ; Disease Models, Animal ; Sleep Apnea, Obstructive/complications/metabolism ; Metabolomics ; },
abstract = {Chronic intermittent hypoxia (CIH), a hallmark pathological feature of obstructive sleep apnea (OSA), is extensively linked to hepatic steatosis in high-fat-diet-induced mice. However, the association between CIH and hepatic steatosis in lean mice, as well as the potential involvement of gut microbiota-related mechanisms, remains poorly understood. Four hundred participants in the Shanghai Sleep Health Study were included to assess the association between apnea-hypopnea index (AHI) and hepatic steatosis index (HSI). To characterize CIH-associated phenotypes and explore microbiota-related alterations in lean mice, liver histology, inflammatory cytokine profiling, metagenomic sequencing with antibiotic intervention, plasma untargeted metabolomics, and liver transcriptomics were performed. As a result, AHI was positively associated with HSI in non-obese participants. In lean mice, 16-week CIH alone induced hepatic steatosis and inflammation, accompanied by significant alterations in gut microbiota composition. Antibiotic treatment attenuated hepatic steatosis and inflammation in 16-week CIH-exposed mice. Metagenomic analysis revealed CIH-associated depletion of Bacteroides uniformis, which was reversed by antibiotic treatment. Plasma metabolomic profiling identified deoxycholic acid as a metabolite exhibiting opposite, phenotype-aligned alterations between CIH and CIH plus antibiotic groups and showing the strongest correlation with Bacteroides uniformis abundance. In parallel, liver transcriptomics revealed coordinated alterations in bile acid-related metabolic pathways and PPAR signaling consistent with CIH-induced and antibiotic-sensitive metabolic remodeling. Together, these findings indicate that prolonged CIH exposure induces hepatic lipid accumulation in lean mice and is associated with coordinated, antibiotic-sensitive alterations in gut microbiota composition, bile acid metabolism, and hepatic transcriptional programs, suggesting a potential involvement of gut microbiota-bile acid-liver interactions in CIH-associated hepatic steatosis.IMPORTANCEObstructive sleep apnea (OSA) is increasingly recognized as a contributor to metabolic dysfunction, yet its role in hepatic steatosis independent of obesity remains incompletely understood. This study shows that chronic intermittent hypoxia (CIH), a defining pathological feature of OSA, is sufficient to induce hepatic steatosis and inflammation in lean mice, independent of dietary manipulation. These findings broaden current understanding of OSA-associated liver disease beyond the context of obesity and metabolic syndrome. By integrating metagenomic sequencing, plasma metabolomics, and liver transcriptomics, this work highlights coordinated alterations in gut microbial composition, bile acid profiles, and hepatic lipid-related transcriptional programs associated with CIH exposure. Depletion of Bacteroides uniformis and elevation of deoxycholic acid were linked to CIH-induced hepatic phenotypes and were sensitive to antibiotic intervention, supporting a contributory role of gut microbiota-bile acid interactions in this process. Together, these findings underscore the potential importance of gut microbiota-host metabolic crosstalk in OSA-associated hepatic steatosis and suggest that microbiota- or bile acid-targeted strategies may warrant further investigation as adjunctive approaches for risk stratification and therapeutic intervention in OSA-related liver disease.},
}

Animals
*Hypoxia/complications/metabolism/microbiology
Mice
Male
*Fatty Liver/metabolism/microbiology/etiology
*Gastrointestinal Microbiome
Humans
Liver/metabolism/pathology
Mice, Inbred C57BL
Disease Models, Animal
Sleep Apnea, Obstructive/complications/metabolism
Metabolomics

@article {pmid42148776,
year = {2026},
author = {Guo, J and Xiang, Z-w and Hu, F-f and Zhang, S-x and Han, W-j and Ding, X and Wang, X and Ye, M-l and Chen, J-h and Rao, T and Wu, L-l and Lian, G-h and Zhang, W and Huang, Y and Chen, Y},
title = {Turicibacter sanguinis is a candidate gut microbial pathobiont that promotes metabolic dysfunction-associated steatohepatitis.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0029226},
pmid = {42148776},
issn = {2379-5077},
support = {82373960, 81974513//National Natural Science Foundation of China/ ; 2025ZZTS0793//Fundamental Research Funds for Central Universities of the Central South University/ ; 2023JJ30891, 2025JJ50675, 2026JJ50342//Natural Science Foundation of Hunan Province/ ; },
mesh = {Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; Bile Acids and Salts/metabolism ; Male ; *Fatty Liver/metabolism/microbiology ; Liver/metabolism/pathology ; Receptors, Cytoplasmic and Nuclear/metabolism ; Disease Models, Animal ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Receptor, Farnesoid X-Activated ; RNA, Ribosomal, 16S/genetics ; Signal Transduction ; Cholesterol 7-alpha-Hydroxylase/metabolism ; },
abstract = {UNLABELLED: Emerging evidence points to the gut microbiota's involvement in metabolic dysfunction-associated steatohepatitis (MASH), yet the specific causative microbes remain largely unidentified. This study aimed to identify and functionally characterize candidate microbial pathobionts to MASH progression. Differentially abundant microbes were identified by 16S rRNA sequencing in a choline-deficient, L-amino acid-defined, high-fat diet MASH model, validated in other animal MASH models and in public clinical metagenomic data sets, then screened for consistently altered gut taxa. A candidate underwent functional validation via directed oral administration in mice. Mechanisms were explored through bile acid profiling by UHPLC-MS/MS and FXR signaling analysis by qPCR and immunohistochemistry. Additionally, fecal samples from MASH patients before and after treatment were analyzed to correlate microbial abundance with treatment response. Turicibacter sanguinis was consistently enriched in all MASH models and public data sets, with abundance correlating positively with liver injury markers. Its increased abundance exacerbated steatosis, inflammation, and fibrosis in healthy and diseased mice. Mechanistically, Turicibacter sanguinis altered bile acid composition, thereby increasing conjugated and decreasing unconjugated species, and inhibited hepatic FXR signaling, accompanied by suppressed SHP and elevated CYP7A1 and SREBP1c expression, which is consistent with enhanced bile acid synthesis and lipid accumulation. Futhermore, after pharmacotherapy, reduced Turicibater sanguinis levels correlated positively with alanine aminotransferase (ALT) and aspartate aminotransferase (AST) improvements. In conclusion, Turicibacter sanguinis is a clinically relevant microbial pathogen that exacerbated MASH by inducing bile acid dysregulation and suppressing FXR signaling, highlighting its potential as a candidate biomarker for disease monitoring and motivating future evaluation of targeted microbiome interventions.

IMPORTANCE: Metabolic dysfunction-associated steatohepatitis (MASH) is a growing global health problem with limited treatment options. Although the gut microbiome has been implicated in MASH, the specific bacterial strains that directly drive disease progression remain largely unknown. This study identified Turicibacter sanguinis as a candidate gut microbial pathobiont that promotes MASH, demonstrating its significant enrichment in both animal models and patient samples. By disrupting hepatic metabolic signaling, this bacterium promotes bile acid synthesis and exacerbates liver fat accumulation, inflammation, and fibrosis. Following effective treatment, its abundance decreased significantly in patients. These findings indicate that Turicibacter sanguinis holds promise as a potential target for developing novel microbiome-based diagnostic and therapeutic approaches for MASH.},
}

Animals
Mice
Humans
*Gastrointestinal Microbiome
Bile Acids and Salts/metabolism
Male
*Fatty Liver/metabolism/microbiology
Liver/metabolism/pathology
Receptors, Cytoplasmic and Nuclear/metabolism
Disease Models, Animal
Diet, High-Fat/adverse effects
Mice, Inbred C57BL
Receptor, Farnesoid X-Activated
RNA, Ribosomal, 16S/genetics
Signal Transduction
Cholesterol 7-alpha-Hydroxylase/metabolism

@article {pmid42171373,
year = {2026},
author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE},
title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0030526},
pmid = {42171373},
issn = {2379-5077},
support = {K08AI159619//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/genetics/immunology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Female ; *Bacterial Toxins/genetics ; *Metagenome ; *Bacteria/genetics/classification ; *Microbiota/genetics ; Machine Learning ; Computational Biology/methods ; },
abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.},
}

Humans
*Dysbiosis/microbiology/genetics/immunology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Female
*Bacterial Toxins/genetics
*Metagenome
*Bacteria/genetics/classification
*Microbiota/genetics
Machine Learning
Computational Biology/methods

@article {pmid42212786,
year = {2026},
author = {Zielińska, K and Pantiukh, K and Łabaj, PP and Kosciolek, T and Org, E},
title = {A large-scale comparative metagenomic analysis of short-read sequencing platforms indicates high taxonomic concordance and functional analysis challenge.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0171425},
pmid = {42212786},
issn = {2379-5077},
support = {PUT 1371, PRG1414//Estonian Research Competency Council/ ; 2020/38/E/NZ2/00598//Narodowe Centrum Nauki/ ; MEiN/2023/DIR/3796//Ministerstwo Edukacji i Nauki/ ; PLG/2023/016234,PLG/2024/017180//Infrastruktura PL-Grid/ ; TT17//Estonian Center of Genomics/Roadmap II, funded by the Estonian Research Council/ ; Installation Grant 3573//European Molecular Biology Organization/ ; },
mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; Sequence Analysis, DNA/methods ; },
abstract = {UNLABELLED: Driven by the increasing scale of microbiome studies and the rise of large, continuously expanding population cohorts, the volume of sequencing data is growing rapidly. As such, ensuring the comparability of data generated across different sequencing platforms has become a pressing concern in efforts to uncover robust links between the microbiome and human health. In this study, we conducted a comprehensive comparison of taxonomic and functional profiles from 1,351 matched human gut microbiome sample pairs, sequenced using both the MGISEQ-2000 (MGI) and NovaSeq 6000 (Illumina NovaSeq) platforms. Taxonomic profiles showed high concordance within and between platforms: 96.44% ± 5.96% of species were shared between MGI-MGI pairs, and 92.07% ± 5.20% were shared between MGI and NovaSeq pairs. The proportion of platform-specific species was low, at 3.42% for MGI-MGI comparisons and 5.89% for MGI-NovaSeq comparisons. No significant differences in Shannon diversity were observed for either within-platform or between-platform comparisons. However, functional profiles revealed notable discrepancies between platforms, which were attributed to differences in pre-sequencing protocols.

IMPORTANCE: Our findings demonstrate robust taxonomic comparability between MGI and NovaSeq platforms, while revealing systematic functional differences that should be carefully considered in cross-platform metagenomic studies.},
}

Humans
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification
*Gastrointestinal Microbiome/genetics
*Metagenome
Sequence Analysis, DNA/methods

@article {pmid42212790,
year = {2026},
author = {Zielińska, K and Pantiukh, K and Org, E and Łabaj, PP and Kosciolek, T},
title = {Moving from a taxonomic to a functional perspective in global microbiome analysis requires optimizing multiplexing ratios.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0014426},
pmid = {42212790},
issn = {2379-5077},
support = {PUT 1371, PRG1414//Estonian Research Council/ ; Installation Grant 3573//European Molecular Biology Organization/ ; 2025/56/C/NZ2/00481//NCN Sonatina/ ; 2020/38/E/NZ2/00598//NCN Sonata BIS/ ; MEiN/2023/DIR/3796//Minister of Science and Higher Education/ ; },
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics/classification ; Humans ; },
abstract = {Next-generation sequencing has revolutionized microbiome research, yet the transition from taxonomic to functional profiling remains a major technical challenge. While marker gene sequencing provides a widely accessible ecological view, it often lacks the resolution for actionable insights. This perspective argues that shifting to whole metagenomic sequencing is essential for mapping functional potential, such as antimicrobial resistance, and metabolic pathways. However, we identify a critical bottleneck: excessive multiplexing. High multiplexing ratios reduce the number of unique molecules per sample, leading to high duplication rates and the stochastic dropout of low-abundance genes. We demonstrate that functional profiles are far more sensitive to these library complexity issues than taxonomic ones. We recommend prioritizing total sequencing depth and reducing multiplexing to ensure sufficient unique coverage. Additionally, adopting long-read or hybrid architectures is vital for providing the genomic context necessary for strain-level resolution. These optimizations are prerequisites for robust global microbiome synthesis and translational science.},
}

*Microbiota/genetics
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
*Bacteria/genetics/classification
Humans

@article {pmid42227741,
year = {2026},
author = {Duan, J and Marques, AD and Hogenauer, M and Hwang, Y and Zhang, Y and Timperman, A and Higgins, S and Wilson, NG and Fitts, EA and Lim, HK and Bittinger, K and Moustafa, AM and Collman, RG and Bushman, FD},
title = {Optimizing methods for virome analysis based on studies of a synthetic viral community.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0018826},
pmid = {42227741},
issn = {2379-5077},
support = {U54AG089323/NH/NIH HHS/United States ; P30AI045008/NH/NIH HHS/United States ; U19AI174998/NH/NIH HHS/United States ; },
mesh = {Humans ; *Virome/genetics ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; Feces/virology ; DNA, Viral/genetics ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Saliva/virology ; Bacteriophages/genetics ; },
abstract = {Studies of whole viral populations-the "virome"-are yielding exciting new insights into biological systems, but methods are still being optimized. Here, we describe generation and use of a synthetic viral community and its use to evaluate technical challenges arising in virome analysis. We spiked the mock community into different human sample types, then passed the samples through different virus enrichment protocols and analyzed by Illumina sequencing. Compared with direct metagenomic sequencing, VLP enrichment protocols greatly increased viral read yields from stool and saliva. Four methods for DNA amplification were compared, with three showing over-amplification of small circular ssDNA viruses, most notably GenomiPhi. Studies of viral particle stability in the presence of nuclease showed that most viral genomes were stable when protected in viral particles, but phage MS2 RNA was unexpectedly labile under some of the conditions tested. Comparison of Illumina 1,000-cycle sequencing versus 300-cycle sequencing showed that longer reads supported generation of longer viral genome assemblies. We tested bacteriophage T4 DNA modified with glucosyl-hydroxymethylcytosine (ghmC) and hydroxymethylcytosine (hmC) and found that both were readily detected, though the recovery of ghmC-modified DNA was reduced compared with T4 genomes with unmodified cytosine. These studies together with published data help provide guidance for virome researchers optimizing analytical protocols.IMPORTANCEA challenge in characterizing the human virome in health and disease is identifying optimal methods for enriching the viral content of samples. Due to the tremendous abundance and diversity of viruses, capturing as broad of a range of viruses as possible for analysis is difficult and potentially complicated by unrecognized biases. This report presents the use of a synthetic viral community for methods optimization in virome studies and illustrates the feasibility and challenges of current virus enrichment strategies for high-throughput virome analysis of different human sample types.},
}

Humans
*Virome/genetics
Genome, Viral
High-Throughput Nucleotide Sequencing/methods
Feces/virology
DNA, Viral/genetics
*Metagenomics/methods
Sequence Analysis, DNA/methods
Saliva/virology
Bacteriophages/genetics

@article {pmid42233644,
year = {2026},
author = {Dubin, CA and Zhao, C and Pollard, KS and Oskotsky, T and Golob, JL and Sirota, M},
title = {Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia.},
journal = {mSystems},
volume = {11},
number = {6},
pages = {e0149825},
pmid = {42233644},
issn = {2379-5077},
support = {//March of Dimes Prematurity Research Center at UCSF/ ; },
mesh = {Female ; Humans ; *Microbiota/genetics ; *Vagina/microbiology ; *Lactobacillus crispatus/genetics ; *Uterine Cervical Dysplasia/microbiology ; Databases, Genetic ; Metagenomics/methods ; Genome, Bacterial ; },
abstract = {The vaginal microbiome plays a central role in reproductive health. Vaginal microbiome dysbiosis is associated with many adverse reproductive health outcomes, but most studies have focused on associations at the species level. The potential contribution of intraspecies microbial variation, especially gene content differences across bacterial strains, remains underexplored in reproductive health contexts. The Metagenomic Intra-Species Diversity Analysis (MIDAS) framework enables such analyses, but depends on comprehensive reference databases. We constructed a MIDAS-compatible pangenome database from over 18,000 genomes in the Vaginal Microbiome Genome Collection (VMGC). Compared to the Genome Taxonomy Database (GTDB)-derived reference, the VMGC-derived database expanded the pangenomes of prevalent vaginal species, better capturing vaginal-specific intraspecies diversity. Applying this database to vaginal samples from a cervical dysplasia cohort, we identified 13 Lactobacillus crispatus accessory genes significantly associated with cervical dysplasia, including a HicAB toxin-antitoxin system, three transcriptional regulators, and three phage-derived genes. These findings highlight the utility of body site-specific reference resources and shotgun metagenomic sequencing for uncovering intraspecies microbial variation relevant to reproductive health.IMPORTANCEThe vaginal microbiome plays a critical role in reproductive health, and different bacteria from the same species can carry different genes that influence how the strains interact with the host and other microbes. These strain-level differences are often overlooked when microbiomes are analyzed only at the species level. Existing genomic reference databases are heavily biased toward gut and environmental bacteria, leaving the genetic diversity of vaginal microbes understudied. We built a specialized reference database from over 18,000 vaginal bacterial genomes that better reflects this diversity. We then applied this resource to quantify gene-level variation in vaginal samples from a cervical dysplasia cohort. Focusing on Lactobacillus crispatus, a prevalent and often beneficial vaginal species, we identified 13 genes that were more common in women with cervical dysplasia than in controls. This work demonstrates that body site-specific genomic resources are essential for uncovering strain-level bacterial differences relevant to reproductive health.},
}

Female
Humans
*Microbiota/genetics
*Vagina/microbiology
*Lactobacillus crispatus/genetics
*Uterine Cervical Dysplasia/microbiology
Databases, Genetic
Metagenomics/methods
Genome, Bacterial

@article {pmid42348560,
year = {2026},
author = {Mani, K and Palanisamy, V and Shrestha, B and Vice, Z and Paudyal, S and Chitlapilly Dass, S},
title = {Insights into spatial dynamics of the microbiome and resistome across the conventional and organic dairy farms.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0352336},
pmid = {42348560},
issn = {1932-6203},
mesh = {Animals ; *Dairying/methods ; *Microbiota/genetics ; Cattle ; Milk/microbiology ; Farms ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Metagenomics ; Organic Agriculture ; },
abstract = {Antimicrobial resistance (AMR) poses a serious global threat to human and animal health. While AMR has been reported in various environments, its distribution across different ecological compartments within dairy farms remains poorly characterized. In this study, we used large-scale shotgun metagenomic sequencing to characterize the microbiome and resistome across multiple sampling sites within one organic and one conventional dairy farm, including teats, liners, water troughs, feed area, milking parlour mats, bedding sand, and milk. Our results indicate that microbial community composition and resistance gene profiles were largely comparable between the two study farms, with sample type (ecological niche) exerting a stronger influence on community structure than farm management type. Pseudomonadota, Bacillota, and Actinomycetota were the dominant phyla, while Aerococcus, Glutamicibacter, and Pseudomonas were the most prevalent genera. Glycopeptide resistance genes were the most abundant ARG class, followed by lincosamide and tetracycline resistance genes. Milk samples exhibited a distinct microbiome and resistome composition compared to environmental samples. Strong correlations between microbiome structure, resistome profiles, virulence factors, and metal resistance genes were observed across farm niches, highlighting the interconnected nature of microbial communities and resistance elements across dairy farm environments. These findings provide foundational data for targeted surveillance and management strategies to mitigate antimicrobial resistance in dairy production systems.},
}

Animals
*Dairying/methods
*Microbiota/genetics
Cattle
Milk/microbiology
Farms
*Bacteria/genetics/drug effects/classification
*Drug Resistance, Bacterial/genetics
Metagenome
Metagenomics
Organic Agriculture

@article {pmid42350342,
year = {2026},
author = {Lyu, R and Zhou, P and Li, Z and He, Q and Fu, X and Wen, W and Zhang, C and Zhang, T},
title = {[HLA-B27 alters gut microbial composition and promotes susceptibility to intestinal inflammation].},
journal = {Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology},
volume = {42},
number = {6},
pages = {499-510},
pmid = {42350342},
issn = {1007-8738},
mesh = {Animals ; *HLA-B27 Antigen/genetics/metabolism ; *Gastrointestinal Microbiome ; *Colitis/microbiology/chemically induced/genetics/metabolism ; Mice, Transgenic ; Humans ; Mice ; *Inflammation ; Female ; Dextran Sulfate ; },
abstract = {Objective This study aimed to investigate the impact of human leukocyte antigen B27 (HLA-B27)/β2m gene expression on the gut microbiota and metabolites, and to elucidate its role in the pathogenesis of spinal arthritis (SpA)-associated intestinal inflammation. Methods Transgenic mice expressing HLA-B27/β2m without spontaneous inflammation were employed. Integrated multi-omics analyses, including metagenomics and metabolomics, were conducted to profile microbial and metabolic changes at prenatal, early colonization, and stable colonization stages. Inflammatory susceptibility was further assessed using a dextran sulfate sodium (DSS)-induced colitis model. Results Expression of HLA-B27/β2m significantly altered the gut microbiota structure, promoting the expansion of Gram-negative bacteria and inhibiting Gram-positive populations. Metabolomic profiling revealed enhanced arachidonic acid metabolism, elevated levels of pro-inflammatory metabolites such as prostaglandins, and a reduction in anti-inflammatory flavonoids. These findings collectively indicated a pro-inflammatory intestinal microenvironment, which was corroborated by exacerbated colitis upon DSS challenge in animal models. Conclusion The HLA-B27/β2m gene modulates gut microbial composition and metabolic balance, predisposing the intestine to inflammatory responses. These results provide novel mechanistic insights into the "gut-joint axis" in SpA pathogenesis.},
}

Animals
*HLA-B27 Antigen/genetics/metabolism
*Gastrointestinal Microbiome
*Colitis/microbiology/chemically induced/genetics/metabolism
Mice, Transgenic
Humans
Mice
*Inflammation
Female
Dextran Sulfate

@article {pmid40830751,
year = {2025},
author = {Ahmad, AA and Fletcher, K and Hesford, N and Glendinning, L},
title = {Metagenomics reveals fibre fermentation and AMR pathways in red grouse (Lagopus scotica) microbiota.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {520},
pmid = {40830751},
issn = {1471-2180},
support = {BBS/E/RL/230001A/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Fundraising from the private sector//The Game and Wildlife Conservation Trust/ ; Chancellor's Fellowship//University of Edinburgh/ ; },
mesh = {Animals ; *Galliformes/microbiology ; *Metagenomics/methods ; *Dietary Fiber/metabolism ; Fermentation ; Cecum/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Scotland ; Metagenome ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: The avian caecal microbiota plays a vital role in host nutrition, enabling non-digestible, fibrous material to be converted into compounds that can be absorbed and used as an energy source by the host. The diet of adult red grouse (Lagopus scotica) is dominated by heather (Calluna vulgaris), which is particularly high in fibre. It is therefore likely that the caecal microbiota plays a key role in enabling grouse to thrive on this diet. In this study, we present the first characterisation of the caecal microbiota of red grouse using modern sequencing methods. RESULTS: We performed metagenomic sequencing on caecal content samples from fifteen red grouse from three upland estates in Scotland. From this data, we constructed and characterised twelve high-quality, species-level metagenome assembled genomes (MAGs). Eleven of these MAGs could not be assigned a taxonomic label at species level, indicating that they may be novel species. MAGs belonged to diverse taxa (5 phyla) and several encoded genes and pathways for the digestion of fibres, including cellulose, hemi-cellulose, xylooligosaccharides and pectin. Several MAGs also contained antimicrobial resistance genes, predominantly related to vancomycin resistance. CONCLUSIONS: This study is the first to reconstruct commensal microbial genomes from red grouse. The caeca contain diverse, often novel, microbial taxa capable of fermenting various fibres, potentially aiding in the digestion of the red grouse’s high-fibre diet. Further research is necessary to explore how these bacteria support red grouse nutrition and health.},
}

Animals
*Galliformes/microbiology
*Metagenomics/methods
*Dietary Fiber/metabolism
Fermentation
Cecum/microbiology
*Bacteria/genetics/classification/isolation & purification/metabolism
Scotland
Metagenome
Phylogeny
*Gastrointestinal Microbiome/genetics
Sequence Analysis, DNA

@article {pmid41239203,
year = {2025},
author = {Wen, S and Sun, J and Zeng, W and Xiang, H and Zhao, M and Xiang, D},
title = {Effects of different arbuscular mycorrhizal fungi on tobacco seedling growth and their rhizosphere microecological mechanisms.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1578},
pmid = {41239203},
issn = {1471-2229},
mesh = {*Mycorrhizae/physiology ; *Rhizosphere ; *Nicotiana/growth & development/microbiology ; *Seedlings/growth & development/microbiology ; Soil Microbiology ; Plant Roots/microbiology/growth & development ; Microbiota ; },
abstract = {BACKGROUND: Numerous studies have demonstrated significant variations in the plant growth-promoting effects among different species of arbuscular mycorrhizal fungi (AMF). However, the underlying mechanisms remain incompletely understood, particularly regarding how distinct AMF species regulate the rhizosphere microbiome. RESULTS: Five AMF species (Funneliformis mosseae, Diversispora versiformis, Clariodeoglous etunicatum, Rhizophagus intraradices, and Acaulospora delicate) were inoculated to investigate their effects on tobacco seedling growth and rhizosphere microecological regulation. The results showed that all AMF inoculations significantly increased shoot and root biomass, N/P/K uptake, morphological traits (height, stem diameter, leaf area), chlorophyll content (SPAD), and root architecture (length, surface area, volume, diameter) of tobacco seedlings. Among them, the treatment inoculated with R. intraradices showed the most outstanding growth-promoting effect in all growth indicators. Metagenomic analysis indicated that AMF inoculation significantly altered the diversity and community structure of rhizosphere substrate microorganisms. Among them, R. intraradices inoculation yielded the highest microbial diversity, with an associated network exhibiting enhanced complexity. KEGG functional annotation revealed metabolic pathways (IAA biosynthesis, iron-siderophore transport regulation, exopolysaccharide production, and nutrient cycling) consistently associated with tobacco growth promotion in all AMF inoculations. However, species-specific mechanisms were observed: F. mosseae promotes tobacco seedling growth by enhancing IAA synthesis through the recruitment of beneficial microorganisms such as Nostoc, Flavisolibacter, Frateuria, and Sphingomonas. D. versiformis enhanced carbon fixation via the hydroxypropionate-hydroxybutyrate cycle, driven by the proliferation of Glaciecola, Pedococcus, Phycicoccus, and Hephaestia. C. etunicatum facilitated phosphorus/iron accumulation through organic phosphorus mineralization, phosphate transport, and iron acquisition accompanied by the recruitment of, Hartmannibacter, Lysobacter, Moheibacter, and Pseudolabrys. R. intraradices improved nitrogen assimilation through augmented nitrogen transport and assimilatory nitrate reduction (ANRA), correlated with the recruitment of Azospirillum, Sphingobium, Mesorhizobium, Paracoccus, and Parafilimonas. A. delicate stimulated plant growth via polyphosphate degradation and exopolysaccharide biosynthesis, associated with the enrichment of Segetibacter, Ferruginibacter, Hyphomicrobium and Pseudomonas. Notably, this study revealed that functional divergence in rhizosphere microbiomes associated with the five tested fungal species was primarily reflected in the abundance rather than the composition of functional genes. CONCLUSION: In summary, AMF inoculation significantly enhanced tobacco seedling biomass and agronomic traits by improving mineral nutrient assimilation efficiency and restructuring the rhizosphere microbial community. Different AMF species exhibited distinct microecological regulation patterns. This study elucidated the growth-promoting mechanisms of AMF from a microbial interaction perspective, providing a theoretical basis for establishing a sustainable tobacco cultivation system.},
}

*Mycorrhizae/physiology
*Rhizosphere
*Nicotiana/growth & development/microbiology
*Seedlings/growth & development/microbiology
Soil Microbiology
Plant Roots/microbiology/growth & development
Microbiota

@article {pmid41345617,
year = {2025},
author = {Franco-Duarte, R and Saati-Santamaría, Z and Choowong, P and Dharmarathne, G and Menéndez, E and Soares, P and Rito, T and Cheung, W and Spahr, A and Eberhard, J and Jayasinghe, TN},
title = {Oral-associated bacteria in the gut microbiome of individuals with type 2 diabetes: a secondary analysis of metagenomic data.},
journal = {BMC oral health},
volume = {25},
number = {1},
pages = {1915},
pmid = {41345617},
issn = {1472-6831},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; *Mouth/microbiology ; Secondary Data Analysis ; *Microbiota ; },
abstract = {With an astounding global prevalence, both diabetes mellitus and gum disease pose significant health concerns. Gum disease has been identified as a risk factor for diabetes mellitus, and its treatment has shown improvements in markers of glucose management. We hypothesised that bacteria commonly associated with the oral microbiome could be disproportionately present in the gut of individuals with type 2 diabetes mellitus (T2DM) compared to healthy controls, suggesting a possible association between oral-associated bacteria and metabolic dysregulation. This hypothesis is supported by known interactions between the oral microbiome and systemic health, particularly the role of inflammation in both conditions. Therefore, we aimed to conduct a secondary analysis of whole-genomic sequencing data of studies published over the last twenty years (2004–2024) related to the gut microbiome of patients with T2DM to identify oral-associated bacteria in their gut compared to healthy individuals. We searched for studies related to the gut microbiome, whole metagenomics, and T2DM in Ovid Medline, EMBASE, and Web of Science databases. Studies that included whole metagenomic data from adult populations of all genders with T2DM were selected, resulting in the reanalysis of metagenomic sequencing data from a total of 9 studies (n = 1,224 metagenomes) for bacterial species data. From the 41,689 gut microbial species identified across the selected studies, 497 were classified as of oral-associated bacteria, corresponding with entries in the Human Oral Microbiome Database (HOMD). These oral bacteria comprised 1.19% of the gut microbiome. Notably, twenty oral-associated bacterial species were statistically significant in their presence among patients with diabetes compared to healthy individuals, irrespective of their abundance. Key oral pathogens included Corynebacterium striatum, Staphylococcus capitis, Kingella kingae, Corynebacterium propinquum, Prevotella sp. oral taxon 820, Prevotella scopos, Selenomonas artemidis, Bordetella pertussis, Selenomonas sp. oral taxon 137, and Staphylococcus hominis. Specifically, periodontal pathogens such as, Porphyromonas gingivalis, Tannerella forsythia, and Capnocytophaga sp. oral taxon 332 were found to be significantly higher in patients with T2DM. These bacteria are associated with conditions like endocarditis, bacteremia, and inflammatory responses, which are prevalent in both diabetes and periodontitis. Although causal relationships cannot be directly established, our findings suggest that bacteria typically originating from the oral cavity may be more prevalent in the gut microbiome of patients with T2DM, supporting the potential role of oral-gut microbial interactions in metabolic dysregulation.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology
*Gastrointestinal Microbiome
Metagenomics
*Mouth/microbiology
Secondary Data Analysis
*Microbiota

@article {pmid41390654,
year = {2025},
author = {Manzoor, H and Jabeen, I and Saeed, MT and Kayani, MUR and Huang, L},
title = {Metagenomic analyses reveal E. coli-derived siderophores as potential signatures for breast cancer.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {84},
pmid = {41390654},
issn = {1479-5876},
mesh = {*Breast Neoplasms/microbiology/genetics/metabolism ; Humans ; *Siderophores/metabolism ; Female ; *Escherichia coli/metabolism/genetics ; *Metagenomics/methods ; Multivariate Analysis ; Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: Breast cancer remains a leading cause of cancer-related mortality in women. Recent evidence implicates the gut microbiome and metabolites in breast cancer pathogenesis. This study explores associations between gut microbial species, their predicted metabolites, and breast cancer to uncover potential mechanistic insights. METHODS: Comprehensive metagenomic analyses were conducted on the gut microbiome of pre- and postmenopausal breast cancer patients, where microbial species were profiled through AMPHORA2 and metabolites were predicted through antiSMASH. Multivariate association analysis was used to identify significant associations between specific microbial species, predicted metabolites, and breast cancer status. A custom ensemble machine learning classifier was developed to classify pre- and postmenopausal breast cancer cases and controls based on microbial and predicted metabolite features. Additionally, a synthetic microbiome dataset was generated through MIDASim to validate the reproducibility of the ML results. Using our results, we explored the underlying dynamics of identified taxa and metabolite in breast cancer through literature and statistical support. RESULTS: Our analysis identified 471 microbial species and predicted 40 key metabolites in the metagenomic data. Multivariate analysis identified significant positive associations (p-value < 0.05) of E. coli, siderophore, and thiopeptide with breast cancer. The custom ensemble model achieved accuracy and AUC as high as 78% and 90%, respectively, in classifying pre- and postmenopausal cases and controls. The high-ranking features i.e., E. coli, siderophore, and thiopeptide were consistent with the results of the multivariate association analysis, thereby substantiating their biological significance. Using these findings, we propose a mechanistic model in which E. coli secretes siderophores under iron-limited conditions in breast cancer patients, for iron sequestration from the host, which can potentially promote angiogenesis and tumor progression. CONCLUSION: Our findings suggest that microbial iron acquisition mechanisms may play a critical role in breast cancer pathophysiology. Functional validation of these mechanisms is needed to assess therapeutic potential. This study highlights gut microbiota and their metabolites as promising targets for breast cancer research and intervention.},
}

*Breast Neoplasms/microbiology/genetics/metabolism
Humans
*Siderophores/metabolism
Female
*Escherichia coli/metabolism/genetics
*Metagenomics/methods
Multivariate Analysis
Gastrointestinal Microbiome/genetics

@article {pmid41390863,
year = {2025},
author = {Tran, L and Deckers, TB and Ho, J and Lansing, L and Cunningham, M and Morfin, N and Pepinelli, M and De la Mora, A and Conflitti, IM and Gregoris, A and Wu, L and Trepanier-Leroux, D and Muntz, L and Newman, T and Vishwakarma, S and Bixby, M and Jabbari, H and Guzman-Novoa, E and Hoover, SE and Currie, RW and Pernal, SF and Giovenazzo, P and Foster, LJ and Zayed, A and Ortega Polo, R and Guarna, MM},
title = {Neonicotinoid-induced signature dysbiosis identified via metagenomic sequencing of the honey bee gut microbiome.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1211},
pmid = {41390863},
issn = {2045-2322},
support = {Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; },
mesh = {Animals ; Bees/microbiology/drug effects ; *Neonicotinoids/toxicity/adverse effects ; *Gastrointestinal Microbiome/drug effects/genetics ; Metagenomics/methods ; *Dysbiosis/chemically induced/microbiology ; *Insecticides/toxicity ; Guanidines/toxicity ; Thiamethoxam ; Metagenome ; Thiazoles/toxicity ; },
abstract = {The Western honey bee (Apis mellifera) plays an essential role in agriculture around the world. In Canada, honey bees contribute up to $7 billion in economic value annually by pollinating crops and producing honey. However, since 2006–2007 North American beekeepers have lost more than a quarter of their colonies each winter. In recent years, the losses have been up to 50% in some regions. The causes of losses are complex, including the interacting effects of nutrition, pathogens, and pesticides. Although the bee gut microbiome plays a crucial role in colony health and disease, studies on the effects of agricultural pesticides on the bee microbial community are sparse. We report the use of shotgun metagenomic sequencing to investigate bee gut microbiota changes, or dysbiosis, in response to two neonicotinoid insecticides, clothianidin and thiamethoxam. Common dysbiosis signatures included an increase in Bifidobacterium spp. after chronic sublethal exposure and an increase in Apibacter adventoris after short-term acute exposure. Other dysbiosis signatures were unique to each compound, such as an increase in Snodgrassella alvi for clothianidin and a decrease in Lactobacillus spp. for thiamethoxam. These findings enhance our understanding of how the honey bee gut microbiome responds to stressors and highlight identifiable microbial profile signatures which underscores the potential utility of gut microbiome profiling as a bee health diagnostic tool. Access to timely and accurate bee health diagnosis will inform regulatory actions to decrease and mitigate exposure to stressors and will facilitate managing and improving bee health.},
}

Animals
Bees/microbiology/drug effects
*Neonicotinoids/toxicity/adverse effects
*Gastrointestinal Microbiome/drug effects/genetics
Metagenomics/methods
*Dysbiosis/chemically induced/microbiology
*Insecticides/toxicity
Guanidines/toxicity
Thiamethoxam
Metagenome
Thiazoles/toxicity

@article {pmid41469598,
year = {2025},
author = {Mbabazi, M and Kateete, DP and Nakazzi, F and Wandera, JN and Mutesi, N and Ocan, M and Biraro, IA and Abaasa, A and Johnson, WE and Wee, B and Muwonge, A},
title = {The impact of tuberculosis and its treatment on the lung and gut microbiota: a global systematic review, meta-analysis, and amplicon-based metagenomic meta-analysis.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {219},
pmid = {41469598},
issn = {1471-2334},
mesh = {Humans ; *Lung/microbiology ; *Gastrointestinal Microbiome/drug effects ; Metagenomics ; *Tuberculosis/drug therapy/microbiology ; *Antitubercular Agents/therapeutic use ; *Microbiota/drug effects ; Metagenome ; },
abstract = {BACKGROUND: Tuberculosis (TB) remains the leading cause of bacterial disease-related mortality worldwide. While Koch’s single-agent model has long guided TB diagnostics and treatment, metagenomic studies reveal a resident lung microbiome disrupted by TB and its orally administered therapy, with downstream effects on the gut microbiome. Understanding these disruptions may uncover diagnostic and prognostic indicators. We systematically reviewed 38 studies involving 3394 individuals with TB and healthy controls across four continents to assess the impact of TB and its treatment on lung and gut microbiome diversity, structure, and composition. A meta-analysis of 29 studies and a patient-level amplicon metagenomic meta-analysis (AMMA) of 1617 individuals (1.3 billion reads) were conducted following PRISMA guidelines [PROSPERO: CRD42022329763]. RESULTS: No global consensus exists on TB's impact on lung microbial diversity. Pooled estimates suggest a reduction of ~0.14 in lung diversity and 0.41 in gut diversity. Patient-level analyses showed no overall significant difference in lung diversity (Shannon index), though reductions were evident in China but not South Africa. Conversely, gut diversity tended to be higher in TB cases. Disease status explained only 0.8–9% of variation in lung microbiota and 1.8–9% in gut communities. Composition-wise, TB was associated with depletion of anaerobic core lung genera (e.g. Prevotella, Neisseria, Veillonella, Haemophilus, Fusobacterium, Pseudomonas, Streptococcus, Porphyromonas, Treponema) and gut genera (e.g. Prevotella, Ruminococcus, Faecalibacterium, Clostridium, Roseburia, Rothia, Eubacterium, Escherichia). Treatment further reduced diversity at both sites, with additional loss of core taxa. CONCLUSION: TB is generally linked to reduced lung microbial diversity but increased gut diversity, with effects varying by country, suggesting context-specific rather than universal microbial signatures. Treatment consistently decreases diversity in both lung and gut. Although findings here primarily reflect the upper respiratory tract, they highlight potentially exploitable microbial dynamics. Future studies should integrate additional diversity metrics and broader metadata to refine these insights for advancing their clinical utility. CLINICAL TRIAL: Not applicable.},
}

Humans
*Lung/microbiology
*Gastrointestinal Microbiome/drug effects
Metagenomics
*Tuberculosis/drug therapy/microbiology
*Antitubercular Agents/therapeutic use
*Microbiota/drug effects
Metagenome

@article {pmid41491791,
year = {2026},
author = {Seo, J and Araneta, RP and Lee, JH and Montecillo, JA and Yoo, HJ and Lee, YY and Park, CM and Cho, A and Lee, H and Yoon, HY and Kim, MJ and Kim, JM and Lee, YH and Lee, NY and Park, NJ and Han, HS and Seo, I and Chong, GO},
title = {Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {2},
pmid = {41491791},
issn = {1471-2180},
support = {RS-2023-KH135444//Ministry of Health and Welfare/ ; },
mesh = {*Vagina/microbiology ; Female ; *Specimen Handling/methods/standards ; *Microbiota/genetics ; Humans ; DNA, Bacterial/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; DNA Contamination ; },
abstract = {BACKGROUND: Studies on understanding female health from a microbial perspective have proliferated in recent years; however, validated protocols for swab materials, storage conditions, and host DNA depletion remain limited for vaginal microbiome studies. This study investigates these critical aspects to enhance microbial profiling accuracy. RESULTS: Three swab materials were evaluated, with minimal variations in bacterial composition observed across different swab materials. The DNA yield and host DNA contamination remained comparable. Mock samples, used to assess the effects of storage conditions (without freezing, -20 °C, and -80 °C), revealed no significant impact on microbial composition. Additionally, the NEBNext® Microbiome DNA Enrichment Kit demonstrated effective performance in host DNA removal and bacterial community recovery, even with reduced reagent volumes. CONCLUSIONS: These findings underscore the importance of optimizing swab selection and host DNA depletion strategies to enhance microbiome profiling in clinical samples.},
}

*Vagina/microbiology
Female
*Specimen Handling/methods/standards
*Microbiota/genetics
Humans
DNA, Bacterial/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Metagenomics/methods
DNA Contamination

@article {pmid41498995,
year = {2026},
author = {Yan, X and Liao, X and Zhang, L and Li, L and Liu, K and Lyu, Z and Hu, A},
title = {Genome-centric metagenomes unveiling microbial functional potential in a glacier river in the Mount everest.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {1},
pages = {32},
pmid = {41498995},
issn = {1573-0972},
support = {42430404//National Natural Science Foundation of China/ ; },
mesh = {*Rivers/microbiology ; *Metagenome ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Ice Cover/microbiology ; Altitude ; *Microbiota/genetics ; Geologic Sediments/microbiology ; Metagenomics ; Phylogeny ; Ecosystem ; Nitrogen/metabolism ; Shotgun Sequencing ; },
abstract = {High-altitude rivers constitute ideal model systems for studying microbial roles in elemental cycling within complex ecosystems. Previous studies primarily addressed microbial community assembly, specific taxonomic groups, or antibiotic resistance gene risks, resulting in limited understanding of biogeochemical cycling profiles. Here, shotgun metagenomic sequencing was employed to profile the metabolic potential of planktonic and benthic microbiomes in the glacial-fed Rongbu River. We sequenced nine water and nine sediment samples along an altitudinal gradient, reconstructing 279 medium-to-high-quality metagenome-assembled genomes (MAGs), with 246 representing unclassified MAGs. Functional analyses revealed divergent niche specialization between habitats: (i) water MAGs encoded multifunctional carbohydrate-active enzymes (CAZymes), targeting labile polysaccharides while coupling nitrogen-sulfur metabolism to enhance nitrogen assimilation; and (ii) sediment MAGs specialized in complex polysaccharide degradation, exhibiting enriched denitrification and sulfide oxidation genes. Notably, a total of 13 plastic degradation genes (PDGs) were identified, which indicated altitudinal partitioning: high-elevation communities showed PBAT-degrading potential, while low-elevation MAGs harbored PVA-degrading genes. These findings indicated that altitude governed the spatial distribution of distinct biogeochemical potentials in high-altitude rivers. This study advances our understanding of elemental cycling processes in alpine river ecosystems.},
}

*Rivers/microbiology
*Metagenome
*Bacteria/genetics/classification/isolation & purification/metabolism
*Ice Cover/microbiology
Altitude
*Microbiota/genetics
Geologic Sediments/microbiology
Metagenomics
Phylogeny
Ecosystem
Nitrogen/metabolism
Shotgun Sequencing

@article {pmid41514270,
year = {2026},
author = {González-Rovira, M and Sainz-Bueno, JA and García-Díaz, L and Martínez-Pancorbo, C and Sánchez, J and Gutiérrez, G and Magoutas, K and Mesías-Pérez, A and Mellado, E and Payne, M and Sousa, C and Moreno, ML},
title = {Unveiling balanced prenatal microbial colonization in amniotic fluid through an integrated culture and sequencing approach.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {273},
pmid = {41514270},
issn = {1479-5876},
support = {PID2024-157768OB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; SUBN/2019/005//Federación de Asociaciones de Celíacos de España (FACE)/ ; US-15332/I+D+I//FEDER ANDALUCIA/ ; },
mesh = {Humans ; *Amniotic Fluid/microbiology ; Female ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/growth & development/isolation & purification ; *Sequence Analysis, DNA/methods ; Antimicrobial Peptides/metabolism ; Microbiota ; },
abstract = {BACKGROUND: The evidence of a low-biomass microbial community in the amniotic fluid (AF) is challenging the traditional concept of a sterile womb. To clarify microbial presence and host responses, a comprehensive, multi-methodological approach is required. METHODS: We designed an optimized culturing strategy that maximized microorganism recovery by implementing differential centrifugation and concentration of AF samples, followed by plating onto four distinct selective media types and incubation under both stringent aerobic (up to two weeks) and prolonged anaerobic (up to four weeks) conditions, including an initial pre-enrichment step in Brain Heart Infusion (BHI) broth for low-abundance organisms. These results were combined with PacBio 16S rRNA gene sequencing, Illumina shotgun metagenomics, and antimicrobial peptides (AMP) detection. Using this approach, we characterized microbial presence in 154 AF samples across gestational stages. Data normality was assessed with the Shapiro-Wilk test, guiding the selection of both parametric and non-parametric tests, and a p-value of < 0.05 was considered statistically significant. RESULTS: We detected culturable microorganisms in 33.1% of samples, with a higher proportion in elective caesarean Sect. (55.0%) compared to amniocentesis (29.5%), suggesting increased microbial load toward term. We applied stringent contamination controls, and repeatedly recovered viable microorganisms Bacillus, Cutibacterium, Micrococcus, and Staphylococcus, with Cutibacterium acnes and Staphylococcus epidermidis common. Both sequencing methods revealed a low-biomass, low-diversity microbial community with high inter-individual variability. Notably, striking microbial discordance in diamniotic twin pregnancies, challenged intrauterine homogeneity. Higher Human Beta Defensin (HBD) -1 levels correlated with absence of culturable bacteria or microbial DNA, while levels of HBD-1, HBD-3, and LL-37 were reduced in Staphylococcus-positive samples, suggesting a dynamic interplay between specific bacteria and host defences. CONCLUSIONS: Our findings indicate that viable bacteria and/or DNA can transiently access the prenatal environment microbial balance. We propose a novel perspective of a potential regulatory axis between microorganisms and AMP.},
}

Humans
*Amniotic Fluid/microbiology
Female
Pregnancy
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/growth & development/isolation & purification
*Sequence Analysis, DNA/methods
Antimicrobial Peptides/metabolism
Microbiota

@article {pmid41524778,
year = {2026},
author = {Sundaray, JK and Roy, D and Mohapatra, M and Mohanty, D and Das, II and Parida, CK},
title = {Metagenomic profiling of fish-associated microbiota: ecological perspectives from freshwater to marine environment-a review.},
journal = {Archives of microbiology},
volume = {208},
number = {2},
pages = {105},
pmid = {41524778},
issn = {1432-072X},
support = {Project Code: 1006449//Centre for Agricultural Bioinformatics (CABin) Project/ ; },
mesh = {Animals ; *Fishes/microbiology ; Fresh Water/microbiology ; *Metagenomics/methods ; Seawater/microbiology ; *Microbiota ; Ecosystem ; Skin Microbiome ; *Bacteria/classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; Aquaculture ; },
abstract = {Microorganisms play pivotal roles in maintaining host physiology and ecosystem balance, with fish-associated microbiomes offering unique insights due to the diverse habitats and feeding behaviours of their hosts. This review comprehensively explores the diversity, composition, and functional roles of gut and skin-associated microbial communities in fish across freshwater, brackish, and marine environments, with emphasis on recent advancements in metagenomic methodologies. Culture-independent techniques, particularly high-throughput and third-generation sequencing technologies, have revolutionized our ability to uncover microbial diversity, gene functions, and interspecies interactions. The fish gut microbiome, heavily influenced by factors such as diet, habitat, and host species, contributes significantly to nutrient metabolism, immune modulation, and physiological adaptation. Similarly, the skin microbiota provides a critical first line of defence, offering protection through competitive exclusion and antimicrobial activity. Functional metagenomics reveals microbial contributions to host metabolism, energy homeostasis, xenobiotic degradation, and environmental adaptation via the gut-brain axis and metabolic pathways. Emerging evidence highlights the bidirectional relationships between microbiota and host phenotypic plasticity. This review underscores the importance of integrative metagenomic approaches to decode complex microbial functions and their ecological relevance in aquaculture, with implications for sustainable fish health management, disease prevention, and improved productivity.},
}

Animals
*Fishes/microbiology
Fresh Water/microbiology
*Metagenomics/methods
Seawater/microbiology
*Microbiota
Ecosystem
Skin Microbiome
*Bacteria/classification/genetics/isolation & purification
Gastrointestinal Microbiome
Aquaculture

@article {pmid41530663,
year = {2026},
author = {Yu, HL and Elsheikha, HM and Liang, HR and Qin, SY and Peng, P and Liu, J and Tang, Y and Guo, L and Ni, HB and Xie, LH and Lei, CC and Su, JW and Yu, MY and Qin, Y and Jiang, J and Liu, J and Xu, Y and Zhang, XX},
title = {Blastocystis infection enhances vitamins B and K2 biosynthesis in the Tibetan antelope (Pantholops hodgsonii) gut microbiota.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {40},
pmid = {41530663},
issn = {1471-2164},
support = {2023YFF1305403//the National Key Research and Development Program of China/ ; 2022KJ169//the Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Antelopes/microbiology/parasitology/metabolism ; *Blastocystis/physiology ; Metagenome ; *Vitamin B Complex/biosynthesis ; Humans ; },
abstract = {The gut microbiota of the Tibetan antelope (Pantholops hodgsonii) plays a vital role in host nutrition, particularly by contributing to the biosynthesis of essential micronutrients such as vitamins B and K2. In this study, we integrated existing P. hodgsonii gut metagenome-assembled genomes with healthy and Blastocystis-infected gut metagenomic samples to investigate microbial strategies for vitamins B and K2 production, as well as the potential modulation of these biosynthetic pathways in the gut of P. hodgsonii. From a total of 33,925 metagenome-assembled genomes, we identified 14,549 non-redundant genomes encoding 182 KEGG orthologs linked to vitamin biosynthesis. Among these, 2,115 high-quality genomes were predicted to synthesize at least one vitamin de novo, yet only 2.9% could produce four or more vitamins. Comparative analyses across multiple host species, including humans, chickens, cats, and mice, revealed that members of the phyla Bacillota_A and Bacteroidetes consistently serve as primary contributors to microbial vitamin biosynthesis. Blastocystis infection was associated with a significant increase in the abundance and diversity of vitamin biosynthesis genes, reflecting adaptive shifts in microbial metabolism. Detailed genomic analyses of the thiamine biosynthesis pathway highlighted the core contributions of Bacillota_A, Bacteroidota, Verrucomicrobiota, and Methanobacteriota, underscoring complex taxonomic cooperation. These results provide novel insights into the functional specialization and taxonomic composition of the P. hodgsonii gut microbiota, offering novel insights into microbial adaptation and metabolic cooperation that support host nutritional homeostasis and resilience in extreme environments.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Antelopes/microbiology/parasitology/metabolism
*Blastocystis/physiology
Metagenome
*Vitamin B Complex/biosynthesis
Humans

@article {pmid41549250,
year = {2026},
author = {Ye, L and Cao, L and Du, Q and Xu, R and Han, Y and Liu, J},
title = {Fecal metagenome and plasma metabolome analyses reveal changes in gut microbiota composition and plasma metabolites in rats with abemaciclib-induced diarrhea.},
journal = {BMC gastroenterology},
volume = {26},
number = {1},
pages = {},
pmid = {41549250},
issn = {1471-230X},
support = {No:2023MW35//This work was supported by the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16) and Minhang District Health Commission of Shanghai Municipality(No:2023MW35)./ ; mwyjyx16//the Outstanding Young Medical Technical and Pharmaceutical Talents Development Program of the Healthcare System in Minhang District, Shanghai(No: mwyjyx16)/ ; },
mesh = {Animals ; Female ; *Benzimidazoles/adverse effects ; *Diarrhea/chemically induced/microbiology/blood/pathology/metabolism ; *Gastrointestinal Microbiome/drug effects/genetics ; *Feces/microbiology ; *Metabolome ; *Aminopyridines/adverse effects ; Rats ; *Metagenome ; Rats, Sprague-Dawley ; Intestinal Mucosa/pathology ; },
abstract = {Abemaciclib-induced diarrhea is a common side effect of HR+/ HER2 − breast cancer treatment. The aim of this study was to explore changes in gut microbiota composition and plasma metabolites in rats with abemaciclib-induced diarrhea. Female rats were randomly divided into abemaciclib (orally administered abemaciclib, n = 12) and control (orally administered 0.9% saline, n = 6) groups. When the rats reached grade 3 diarrhea, the jejunum, ileum, and colon tissues were collected for histological analysis to assess intestinal mucosal damage. Rat feces were obtained for metagenomic analysis to analyze changes in the gut microbial composition. Rat plasma was used for untargeted metabolomic analysis to analyze plasma metabolic alterations. Pearson’s correlation analysis was conducted to examine the association between differential gut microbiota and differential plasma metabolites, and a microbiota-metabolite-pathway network was constructed. Rats in the abemaciclib group developed noticeable diarrhea and exhibited histopathological changes in the ileal epithelium and jejunum. In the abemaciclib group, α-diversity indices (Shannon, Simpson, and Invsimpsom) were significantly lower than in the control group, with reductions of 0.5, 0.01, and 52.77, respectively. Firmicutes, Bacteroidetes, and Proteobacteria were the most abundant phyla in all groups. Compared with the control group, the abundance of Firmicutes remarkably decreased in the abemaciclib group, whereas that of Proteobacteria and Verrucomicrobia dramatically increased. Differentially abundant species in the abemaciclib group included Escherichia coli, Butyricimonas virosa, Desulfovibrionaceae bacterium, and Helicobacter ganmani. Functional analysis showed that pathways related to carbohydrate metabolism were significantly altered. Additionally, 319 metabolites were differentially expressed between the two groups, including trimethylamine N-oxide, sarsasapogenin, tyrosol, brinzolamide, and cis-3-hexenyl acetate. Multiple pathways, including mTOR signaling pathway, were significantly enriched by differential metabolites. Furthermore, close associations between differential microbiota and metabolites were observed, and numerousmicrobiota-metabolite-pathway axes were identified, such as Pseudodesulfovibrio mercurii/Desulfovibrionaceae bacterium-cis-3-hexenyl acetate-alpha-linolenic acid metabolism. Our findings revealed that abemaciclib alters the gut microbiota composition, plasma metabolite profiles, and their related metabolic pathways in SD rats, and these changes are closely associated with the occurrence of diarrhea. However, this association does not establish a causal relationship, and further in-depth mechanistic studies are required for validation.},
}

Animals
Female
*Benzimidazoles/adverse effects
*Diarrhea/chemically induced/microbiology/blood/pathology/metabolism
*Gastrointestinal Microbiome/drug effects/genetics
*Feces/microbiology
*Metabolome
*Aminopyridines/adverse effects
Rats
*Metagenome
Rats, Sprague-Dawley
Intestinal Mucosa/pathology

@article {pmid41588320,
year = {2026},
author = {Guo, W and Yu, J and Wang, W and Wang, J and Ni, M and Zhou, M and Chen, X},
title = {Multi-kingdom fecal microbiome and virus-host interactions associated with growth performance of indigenous beef calves in Guizhou.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41588320},
issn = {1471-2180},
support = {32402705//the National Natural Science Foundation of China/ ; },
mesh = {Animals ; Cattle/growth & development/microbiology ; *Feces/microbiology/virology ; *Bacteria/classification/genetics/isolation & purification ; Fatty Acids, Volatile/analysis/metabolism ; *Gastrointestinal Microbiome ; Archaea/classification/genetics/isolation & purification ; *Host Microbial Interactions ; *Viruses/classification/genetics/isolation & purification ; Rumen/microbiology ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: The associations between the gut microbiome and growth performance in calves have been investigated; however, most existing studies have primarily focused on rumen microbiomes. Whether fecal microbiomes in terms of composition and function are altered among calves with different growth rates remains unclear. Therefore, the objective of this study was to investigate how fecal microbiomes influence calf growth rates. A total of 16 beef calves under the same management were recruited and classified into two groups based on their growth rates (average daily gain: ADG; 4-month-old, n = 8 per group x 2 growth rate groups). At 4 months of age, fecal samples were collected from the rectum for the quantification of volatile fatty acids (VFAs) and characterization of microbial communities via metagenomic sequencing. RESULTS: The VFA profiles did not differ between the two groups. Calves with higher growth rates exhibited lower bacterial and archaeal Shannon diversity, and the overall microbial community structure showed a clear separation between the two groups. Moreover, fecal bacterial and archaeal species associated with improved growth performance were identified, characterized by the enrichment of Alistipes shahii, Alistipes onderdonkii, Bifidobacterium thermophilum, Akkermansia glycaniphila, and Methanobrevibacter sp. AbM4 in calves with higher growth rates. In addition, the metabolic pathways involved in lipid and amino acid metabolism and CAZyme genes linked to carbohydrate degradation were enriched in the calves with better growth performance. The viral community composition and diversity differed between the two groups, with lower diversity observed in calves exhibiting higher growth rates. Additionally, viruses predicted to infect bacterial hosts such as Prevotella and Succinivibrio, which are involved in carbohydrate degradation, were positively associated with ADG. Interestingly, a virus associated with Methanobrevibacter sp017652345 exhibited a positive correlation with ADG. The relationships between fecal microbes and host phenotypic traits were divergent between the two groups. CONCLUSIONS: These findings suggest that fecal microbiomes are associated with calf growth rates through potential multi-kingdom interactions, particularly those between viruses and their prokaryotic hosts, indicating possible avenues to improve animal performance via microbiome modulation.},
}

Animals
Cattle/growth & development/microbiology
*Feces/microbiology/virology
*Bacteria/classification/genetics/isolation & purification
Fatty Acids, Volatile/analysis/metabolism
*Gastrointestinal Microbiome
Archaea/classification/genetics/isolation & purification
*Host Microbial Interactions
*Viruses/classification/genetics/isolation & purification
Rumen/microbiology
Metagenomics
Metagenome

@article {pmid41593136,
year = {2026},
author = {Menke, S and Fackelmann, G and Vucetich, LM and Vucetich, JA and Forbey, JS and Sommer, S},
title = {Forage quality shapes physiological and gut microbial responses in moose (Alces alces) of Isle Royale National Park.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {3724},
pmid = {41593136},
issn = {2045-2322},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Deer/microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Diet ; Seasons ; Bacteria/genetics/classification ; *Animal Feed/analysis ; },
abstract = {Plant secondary compounds (PSCs) impose physiological and nutritional constraints on herbivores, yet many species continue to rely on PSC-rich forage during critical periods of the year. Moose (Alces alces) on Isle Royale National Park depend heavily on balsam fir (Abies balsamea) during winter, exposing them to a chemically defended and nutritionally limited diet. To investigate how this foraging strategy shapes both physiological responses and gut microbial communities, we integrated fecal diet composition, urinary markers of detoxification and nutritional status, 16S rRNA gene sequencing, and shotgun metagenomic profiling from free ranging moose of two separated populations from the western and eastern region of the island. Balsam fir consumption varied strongly by region and was positively associated with glucuronic acid to creatinine (GA:C) and urea nitrogen to creatinine (UN:C) ratios, indicating increased detoxification activity and reduced nutritional condition. Microbial alpha diversity declined with higher fir intake in nutritionally limited individuals, while beta diversity differed by region, balsam fir consumption, and UN:C. Several bacterial genera responded to PSC exposure, including increases in the butyrate-producing genus Roseburia and shifts in network prominence of Phascolarctobacterium. Metagenomic data revealed pathways involved in the degradation of aromatic and terpenoid PSCs, although pathway abundances did not differ significantly with balsam fir consumption after multiple testing correction. These results show that winter foraging on balsam fir produces coordinated dietary, physiological, and microbial patterns, with both host and gut microbial detoxification capacities interacting to accommodate the chemical and nutritional challenges of a PSC-rich winter diet.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Deer/microbiology/physiology
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Diet
Seasons
Bacteria/genetics/classification
*Animal Feed/analysis

@article {pmid41604101,
year = {2026},
author = {Nihel, AB and Rania, AD and Hamadou, OH and Ghiles, G and Imen, B and Fatma, A and Ali, A and Basma, M and Hayet, S and Radhouan, G and Leila, AK and Mokdad-Gargouri, R},
title = {Nanopore sequencing of the Tunisian gut microbiome: effect of the DNA extraction methods.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {47},
pmid = {41604101},
issn = {1678-4405},
support = {952583//H2020 European Research Council/ ; },
mesh = {Humans ; *Nanopore Sequencing/methods ; *DNA, Bacterial/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {High-throughput sequencing technologies have revolutionized the field of microbiome research, offering unprecedented insights into microbial diversity, community structure, and evolution. In this study, we compared three DNA extraction methods including; enzymatic lysis (ELM), commercial kit (CKM) and Phenol/Chloroform (PCAI) for their efficacy in microbiome taxonomy using Nanopore Sequencing. Metagenomic analysis of DNA extracted from stool samples were analyzed to determine the variability in microbial compositions. Our results revealed significant differences in DNA yield, microbial diversity, and community structure among the extraction methods tested. Globally, Phocaeicola_vulgatus, Ruminococcus_bicirculans, Faecalibacterium_prausnitzii, Prevotella copri, and Bacteroides ovatus are the most abundant identified species in all the samples. Further, the results showed that Ruminococcus_bicirculans is the most abundant specie identified in ELM, whereas the richness of Bacteroides_fragilis is higher in PCAI than ELM and CKM-processed samples. Our findings underscore the importance of methods selection in microbiome research and provide insights into optimizing DNA extraction protocols for nanopore sequencing.},
}

Humans
*Nanopore Sequencing/methods
*DNA, Bacterial/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Metagenomics/methods
High-Throughput Nucleotide Sequencing

@article {pmid41606550,
year = {2026},
author = {Zhang, X and Xu, J and Chen, M and Wu, Y and Chen, D and Xu, X and He, X},
title = {Aspergillus fumigatus in mechanically ventilated pneumonia- independent mortality risk and synergistic microbiome signatures from a multicenter mNGS cohort.},
journal = {BMC pulmonary medicine},
volume = {26},
number = {1},
pages = {},
pmid = {41606550},
issn = {1471-2466},
support = {2022GYX28//Lishui Public Welfare Technology Application Research Program Project/ ; },
mesh = {Humans ; Male ; Female ; Retrospective Studies ; *Aspergillus fumigatus/isolation & purification ; *Respiration, Artificial/adverse effects ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Aged ; Risk Factors ; China/epidemiology ; *Microbiota ; *Pneumonia/microbiology/mortality ; High-Throughput Nucleotide Sequencing ; Metagenomics ; },
abstract = {AIM OF THE STUDY: Invasive aspergillosis is a life-threatening complication in mechanically ventilated patients with pneumonia, predominantly caused by Aspergillus fumigatus. However, its independent mortality risk and early-warning strategies in critically ill populations remain unclear. METHODS: In this multicenter retrospective cohort study, we enrolled 1567 mechanically ventilated patients with severe pneumonia who underwent bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) across 12 tertiary hospitals in China (January 2019–March 2023). Propensity score matching (1:1) balanced confounders, and Cox regression quantified the independent mortality risk of A. fumigatus infection. RESULTS: The A. fumigatus detection rate was 10.27% (161/1567). Post-matching, 28-day mortality was significantly higher in A. fumigatus-positive versus negative cohorts (66% vs 47%, p = 0.001). Multivariable analysis confirmed A. fumigatus as an independent mortality risk factor (HR = 1.79, 95%CI 1.49–2.17, p < 0.001), with significant associations to underlying renal disease (19% vs 12%, p = 0.005), connective tissue disease (7% vs 4%, p = 0.026), and multi-organ dysfunction (ep < 0.05). Microbial community analysis revealed co-colonization synergies with Enterococcus faecium, Enterococcus faecalis, Candida albicans, HSV-1, and EBV. CONCLUSIONS: A. fumigatus infection independently increases 28-day mortality risk in mechanically ventilated patients. Early intensified screening and intervention are warranted for individuals with ≥ 3 organ dysfunctions, underlying renal/connective tissue diseases, or respiratory co-colonization by synergistic microbes.},
}

Humans
Male
Female
Retrospective Studies
*Aspergillus fumigatus/isolation & purification
*Respiration, Artificial/adverse effects
Bronchoalveolar Lavage Fluid/microbiology
Middle Aged
Aged
Risk Factors
China/epidemiology
*Microbiota
*Pneumonia/microbiology/mortality
High-Throughput Nucleotide Sequencing
Metagenomics

@article {pmid41612181,
year = {2026},
author = {Zhang, J and Deng, J and He, B and Wang, H and Lin, D and Li, J and Zhong, Q and Chen, Y and Liao, S and Wang, J and Wang, Y and Su, M and Guo, X},
title = {The study on the identification of cross-boundary microbiome enterotypes between high-altitude and coastal populations and their predictive value.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41612181},
issn = {1471-2180},
support = {2024B03J0562//the Science and Technology Program of Guangzhou/ ; },
mesh = {Humans ; *Altitude ; China/epidemiology ; *Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/microbiology/epidemiology ; *Adenoma/microbiology ; Male ; Female ; Archaea/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; Metagenomics/methods ; },
abstract = {OBJECTIVE: To investigate the differences in gut microbiome composition among multi-center populations from coastal and high-altitude regions of China and their association with colorectal adenoma (CRA). METHODS AND ANALYSIS: Metagenomic sequencing was performed on stool samples collected from 295 participants. Diversity, principal component, and linear discriminant analyses were conducted to assess microbial composition and functional differences related to geography and disease status. RESULTS: In high-altitude populations, bacterial enterotypes were predominantly Prevotella, fungal enterotypes Saccharomyces, and archaeal enterotypes Methanobrevibacter, differing from those in coastal populations. Combining bacterial, fungal, and archaeal features improved classification accuracy between high-altitude and coastal populations (AUC = 0.84) and between high-altitude and coastal adenoma patients (AUC = 0.85). Specific enterotypes were observed to correlate significantly with metabolic pathways in high-altitude populations. CONCLUSION: Significant differences in gut microbiome enterotypes exist across geographic populations, with specific enterotypes in high-altitude populations potentially associated with a lower prevalence of CRA. These findings provide new insights into the gut microbiome–geography relationship and support microbiome-based diagnostic and therapeutic strategies.},
}

Humans
*Altitude
China/epidemiology
*Bacteria/classification/genetics/isolation & purification
Feces/microbiology
*Gastrointestinal Microbiome/genetics
*Colorectal Neoplasms/microbiology/epidemiology
*Adenoma/microbiology
Male
Female
Archaea/classification/genetics/isolation & purification
Fungi/classification/genetics/isolation & purification
Metagenomics/methods

@article {pmid41618136,
year = {2026},
author = {Liu, J and Elsheikha, HM and Lei, CC and Qin, SY and Liu, Y and Ni, HB and Qin, Y and Yu, HL and Su, JW and Chen, BN and Jiang, J and Sun, HT and Zhang, XX},
title = {Genome-resolved analysis of bile acid-metabolizing microbiota in Tibetan antelope (Pantholops hodgsonii).},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41618136},
issn = {1471-2180},
support = {2025ZD01900110//National Science and Technology Major Project for Prevention and Control of Emerging and Re-emerging Infectious Diseases/ ; 2022KJ169//Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Antelopes/microbiology ; *Gastrointestinal Microbiome/genetics ; Tibet ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Phylogeny ; Metagenome ; Amidohydrolases/genetics ; Genome, Bacterial ; },
abstract = {BACKGROUND: The Tibetan antelope (Pantholops hodgsonii), an iconic species endemic to the Qinghai-Tibet Plateau, thrives at altitudes of 4,500–5,000 m under conditions of extreme hypoxia, cold, and limited nutrition. As a critical mediator of host physiology, the gut microbiome may play a key role in supporting these adaptations. RESULTS: This study presents the first genome-centric investigation of bile acid (BA) metabolism in the gut microbiome of the Tibetan antelope, unveiling unique microbial pathways that potentially facilitate survival in harsh environments. Comparative analysis of metagenome-assembled genomes revealed that the antelope’s BA-metabolizing microbiota is taxonomically distinct from that of other Caprinae species and humans, with only two of the top ten BA-producing genera shared across groups. Importantly, individuals infected with Blastocystis exhibited marked differences in BA-related KEGG ortholog (KO) profiles compared to uninfected counterparts. Our findings highlight that the proportion of bile salt hydrolase (K01442) genes in the gut microbiota of Tibetan antelopes is higher than that in other Caprinae species and humans. Among them, the genus Alistipes carries the highest proportion of K01442 in the Tibetan antelope’s gut microbiota. Additionally, infection-associated KO gene shifts were observed, suggesting a microbial contribution to the Tibetan antelope’s remarkable physiological resilience. CONCLUSIONS: In Tibetan antelopes, Alistipes was the dominant genus associated with bile acid synthesis. While bile acid synthesis KO distributions were broadly similar across species, K01442 higher proportion than other in Tibetan antelope gut microbiomes. Furthermore, Blastocystis infection altered three key bile acid synthesis KOs and induced distinct shifts in gut microbiome composition.},
}

Animals
*Bile Acids and Salts/metabolism
*Antelopes/microbiology
*Gastrointestinal Microbiome/genetics
Tibet
*Bacteria/classification/genetics/metabolism/isolation & purification
Phylogeny
Metagenome
Amidohydrolases/genetics
Genome, Bacterial

@article {pmid41629500,
year = {2026},
author = {Levhar, N and Hadar, R and Braun, T and Shacham, H and Algavi, Y and Naamneh, R and Efroni, G and Agranovich, B and Abramovich, I and Talan Asher, A and Picard, O and Yavzori, M and Lahat, A and Yablecovitch, D and Kopylov, U and Denson, L and Borenstein, E and Eliakim, R and Ben-Horin, S and Amir, A and Haberman, Y},
title = {Fecal metabolic signals are associated with changes in microbiota and systemic metabolic pathways in Crohn's disease.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {6991},
pmid = {41629500},
issn = {2045-2322},
support = {758313//ERC/ ; 785/22//Israel Science Foundation/ ; 4361//Israel Science, Culture, and Sport/ ; 1165359//LITWIN IBD PIONEERS AWARDS/ ; 41/11//I-CORE program/ ; },
mesh = {Humans ; *Crohn Disease/microbiology/metabolism ; *Feces/microbiology/chemistry ; *Metabolic Networks and Pathways ; Female ; Male ; Biomarkers ; Adult ; Metabolomics/methods ; *Gastrointestinal Microbiome ; *Microbiota ; Metabolome ; Dysbiosis/microbiology/metabolism ; Metagenomics ; },
abstract = {Metabolites play a crucial role in the interactions between the host and its microbiome, influencing disease pathogenesis. To explore metabolic signals linked to Crohn’s Disease (CD), we analyzed paired fecal and serum metabolomics, combined with microbial characterization. Metabolites were identified using liquid chromatography-mass spectrometry, and microbial data were obtained through V4-16 S sequencing and shotgun metagenomics. 202 serum and 294 fecal samples from 80 CD patients and 43 healthy controls were included. Longitudinal analysis highlighted individual variations in metabolic signals and microbial composition. 6602 significant correlations were identified between fecal metabolites and microbes, implying their involvement in microbial-driven disease pathways. Notably, five CD-enriched fecal carbohydrates positively correlated with oral bacteria (e.g., Veillonella parvula, Veillonella dispar, Streptococcus). Additionally, arachidonic acid and three of its derivatives were associated with R. gnavus and Fusobacteria, often implicated in CD pathogenesis. Active CD, defined clinically or by elevated biomarkers (CRP, fecal-calprotectin), exhibited heterogeneous metabolic signatures, with consistent associations between fecal metabolites and established microbial-based indices (CD-related dysbiosis index and alpha diversity). This suggests that specific fecal metabolites potentially sustain microbial imbalances and that targeting metabolic and microbial shifts may offer novel strategies to promote healthier states in CD.},
}

Humans
*Crohn Disease/microbiology/metabolism
*Feces/microbiology/chemistry
*Metabolic Networks and Pathways
Female
Male
Biomarkers
Adult
Metabolomics/methods
*Gastrointestinal Microbiome
*Microbiota
Metabolome
Dysbiosis/microbiology/metabolism
Metagenomics

@article {pmid41629813,
year = {2026},
author = {Astudillo-Guerrero, C and Garrido, Á and Masferrer, D and Sepúlveda, C and Olavarría, L and Del Campo, R and Bravo-Sagua, R and Cubero, FJ and Salech, F and Thumala-Dockendorff, D and Urrutia, PJ and Quera, R and Bunout, D and Espinoza, R and Jorquera, G},
title = {Randomized, double-blind, placebo-controlled trial of fecal microbiota transplantation from young physically active donors to promote resilient aging: clinical trial protocol (ARMOR study).},
journal = {BMC geriatrics},
volume = {26},
number = {1},
pages = {},
pmid = {41629813},
issn = {1471-2318},
mesh = {Humans ; Double-Blind Method ; *Fecal Microbiota Transplantation/methods ; Aged ; *Aging/physiology ; Male ; Female ; Aged, 80 and over ; *Sarcopenia/therapy ; Randomized Controlled Trials as Topic ; Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; },
abstract = {BACKGROUND: Sarcopenia, characterized by the progressive loss of skeletal muscle mass and strength in older adults, is a key determinant of frailty and functional decline. Affecting up to 15% of individuals aged 65–80 years and more than 50% of those over 80, sarcopenia not only compromises physical autonomy but also increases the risk of metabolic dysfunction and cognitive decline. Emerging evidence suggests that age-related gut microbiota dysbiosis contributes to these impairments by reducing microbial diversity and altering host metabolic signaling, leading to chronic inflammation and mitochondrial dysfunction. The present study aims to evaluate the safety, tolerability, and preliminary efficacy of oral fecal microbiota transplantation derived from young, physically active donors administered to older adults, focusing on outcomes related to functional autonomy, muscle performance, metabolism and cognition. METHODS: This is a double-blind, randomized, placebo-controlled clinical trial involving community-dwelling adults aged 65–84 years. Participants will be randomized 1:1 to receive either FMT capsules or placebo following a short course of oral rifaximin (or placebo). Assessments will be performed at baseline and at 4, 8, and 20 weeks post-intervention. The primary outcomes are safety and tolerability, as well as changes in the Global Index of Functional Autonomy (GDLAM battery) and muscle strength. Secondary outcomes include gait speed, body composition (DXA), metabolic biomarkers, gut microbiota composition (shotgun metagenomics), cognitive performance, and psychological well-being. EXPECTED IMPACT: By restoring microbial diversity and function, FMT from young, active donors may enhance muscle quality, cognitive resilience, and metabolic health in older adults. This study introduces a novel, non-invasive therapeutic approach based on lyophilized and encapsulated microbiota, offering a feasible and scalable strategy to promote healthy aging. TRIAL REGISTRATION: ClinicalTrials.gov NCT06649981. Date of registration October 21, 2024.},
}

Humans
Double-Blind Method
*Fecal Microbiota Transplantation/methods
Aged
*Aging/physiology
Male
Female
Aged, 80 and over
*Sarcopenia/therapy
Randomized Controlled Trials as Topic
Gastrointestinal Microbiome/physiology
*Exercise/physiology

@article {pmid41629888,
year = {2026},
author = {Luo, M and Xiao, X and Wu, Y},
title = {Impact of phototherapy on gut microbiota composition and function in neonates with hyperbilirubinemia: a metagenomic analysis.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {},
pmid = {41629888},
issn = {1471-2431},
support = {No. YTWS20210102//Science and Technology Funding Program of Yantian District Bureau of Science and Technology/ ; },
mesh = {Humans ; *Phototherapy ; *Hyperbilirubinemia, Neonatal/therapy/microbiology ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Longitudinal Studies ; Metagenomics ; Male ; Feces/microbiology ; Female ; },
abstract = {BACKGROUND: Phototherapy serves as the primary treatment for neonatal hyperbilirubinemia (NH). This research aims to investigate the impact of phototherapy on the gut microbiota of NH, and to provide reliable theoretical evidence for the clinical application of phototherapy in such cases. METHODS: In this self-controlled longitudinal study, 26 newborns diagnosed with NH were enrolled. Fecal samples were collected before (pre-treatment) and 48 h after (post-treatment) initiating phototherapy. The gut microbiota was profiled using high-throughput 16 S ribosomal RNA (rRNA) gene sequencing. Gut microbiota composition and diversity were analyzed using standard bioinformatics pipelines. Data were processed with standard bioinformatics tools for taxonomic annotation, diversity analysis, and functional prediction based on the COG, KEGG, and MetaCyc databases. Statistical significance was assessed using the Wilcoxon signed-rank test (P < 0.05). RESULTS: While no significant differences were observed at the species level, analysis at the genus level revealed significant alterations in the gut microbiota. The genera Clostridium and Megamonas were identified as significantly increased post-phototherapy. Linear discriminant analysis effect size (LEfSe) analysis further confirmed distinct microbial signatures between the two groups: pre-treatment samples were enriched with families such as Porphyromonadaceae, Lachnospiraceae, Alcaligenaceae, Ruminococcaceae, Moraxellaceae, and the order Pseudomonadales. In contrast, post-treatment samples were predominantly characterized by the class Erysipelotrichi and its associated taxa (Erysipelotrichales and Erysipelotrichaceae). α-diversity indices (Sobs, Chao, Shannon, Simpson) showed no significant differences between the two groups, whereas β-diversity analysis indicated significant microbial community separation (P < 0.05). Predicted functional profiles (based on 16 S rRNA gene data using PICRUSt2) suggested predominant roles in metabolism, genetic information processing, and biosynthesis. However, no significant differences were observed between the pre- and post-treatment groups. CONCLUSIONS: Phototherapy significantly modulated the gut microbial composition of neonates with NH, notably increasing the abundance of Clostridium and Megamonas, and shifting the community towards Erysipelotrichi, while overall microbial functional capacity remained stable. These findings highlight the dynamic yet resilient nature of the neonatal gut microbiota under phototherapy and provide a foundation for microbiome-informed management strategies in neonatal hyperbilirubinemia.},
}

Humans
*Phototherapy
*Hyperbilirubinemia, Neonatal/therapy/microbiology
Infant, Newborn
*Gastrointestinal Microbiome/genetics
Longitudinal Studies
Metagenomics
Male
Feces/microbiology
Female

@article {pmid41634410,
year = {2026},
author = {Chen, YJ and Ho, HJ and Tseng, CH and Chen, YF and Shieh, JJ and Wu, CY},
title = {Akkermansia Muciniphila Ameliorates Imiquimod-Induced Skin Thickening, Colitis, and Gut Microbiota Alterations: A Metagenome Association Study.},
journal = {Inflammation},
volume = {49},
number = {1},
pages = {78},
pmid = {41634410},
issn = {1573-2576},
support = {NSTC 108-2314-B-075A-008//National Science Technology Council/ ; 110-2314-B-075A-008//National Science Technology Council, Taiwan/ ; TCVGH- 1136801B//Taichung Veterans General Hospital/ ; },
mesh = {Animals ; *Colitis/chemically induced/microbiology/prevention & control ; Mice ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects/physiology ; *Imiquimod/toxicity ; *Metagenome ; *Skin/pathology/drug effects ; Akkermansia ; Male ; *Verrucomicrobia ; Feces/microbiology ; },
abstract = {A decreased abundance of fecal Akkermansia muciniphila (Akk) has been observed in patients with psoriasis and psoriatic arthritis. The potential beneficial effects of Akk in managing psoriasis have been proposed, yet results remain inconsistent and mechanisms unclear. Using imiquimod (IMQ)-treated C57BL/6 mice, we conducted a metagenomic association study of pasteurized Akk (pAkk) in the IMQ mice through whole-genome shotgun sequencing. We also performed a dextran sodium sulfate (DSS)-induced colitis experiment and an intestinal permeability test. The association among pAkk supplements, skin thickness, inflammatory profiles, fecal microbiota alterations, functional genetic predictions, intestinal epithelium inflammation, and barrier integrity was investigated. The study demonstrated that pAkk supplementation ameliorated IMQ-induced skin thickening, weight loss, spleen weight gain, serum IL-17A, TNF-α levels, and DSS-induced colitis. pAkk supplementation was linked to greater fecal microbial diversity and alterations in fecal microbiota composition, with increased prevalence of Muribaculaceae, Bifidobacterium pseudolongum, Desulfovirionaceae, Erysipelotrichaceae, and Alistipes ihumi, which have been implicated in the Gamma-Aminobutyric Acid (GABA) shunt, cholinergic synapse, cell cycle, and Mitogen-Activated Protein Kinase (MAPK) pathways. In conclusion, pAkk may mitigate IMQ-induced skin thickening and DSS-induced colitis, associated with reduced levels of TNF-α and IL-17A. pAkk supplementation alters fecal microbiota and metabolic pathways in IMQ-treated mice.},
}

Animals
*Colitis/chemically induced/microbiology/prevention & control
Mice
Mice, Inbred C57BL
*Gastrointestinal Microbiome/drug effects/physiology
*Imiquimod/toxicity
*Metagenome
*Skin/pathology/drug effects
Akkermansia
Male
*Verrucomicrobia
Feces/microbiology

@article {pmid41634542,
year = {2026},
author = {Sun, M and Wei, J and Wang, M and Xu, H and Ma, W and Wang, Y},
title = {Research on the process of synergistic degradation of corn straw by probiotics-enzymes based on microbiome and metabolomics.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41634542},
issn = {1471-2180},
support = {CARS-39-27//National Wool Sheep Industry Technology System/ ; jytms20231736//Liaoning Provincial Department of Education General Project/ ; 2024010768-JH3/107, 2024012131-JH4/4800//Liaoning Provincial Natural Science Foundation Project/ ; S202410160014//College Student Innovation Project/ ; },
mesh = {*Zea mays/microbiology/metabolism/chemistry ; Fermentation ; *Probiotics/metabolism ; Metabolomics ; *Microbiota ; Laccase/metabolism ; *Enzymes/metabolism ; Lactobacillus/metabolism ; Peroxidases/metabolism ; Bacillus subtilis/metabolism ; Cellulose/metabolism ; Bacteria/metabolism/classification/genetics ; Cellulase/metabolism ; },
abstract = {BACKGROUND: Probiotics enzyme co-fermentation significantly improves the use efficiency and nutritional value of crop straw, although the underlying synergies are not clear. METHODS: The experiment used corn straw as the raw material. It was treated with a 0.2% composite enzyme preparation containing cellulase, xylanase, lignin peroxidase, manganese peroxidase, and laccase. A composite microbial inoculant was also added at a total inoculum level of 1 × 10[8] CFU/g, using a ratio of Lactobacillus, yeast, and Bacillus subtilis of 3:2:1. After thorough mixing, the solution was sprayed evenly onto the straw surface. Fermentation proceeded under room temperature conditions. Multipoint random sampling was carried out on days 7, 14, 21, and 28. By integrating metagenomic, metabolomic, and conventional analytical approaches, this study systematically investigated microbial community structure, dynamic metabolic pathways, and fermentation quality during the process. RESULTS: The application of a probiotics-enzyme composite led to a clear improvement in fermentation quality. It also reduced the cellulose content of corn stover compared to the untreated control. The results showed that major microbial taxa, such as Proteobacteria and Firmicutes, are influenced by environmental factors like pH and lactic acid. These microbes significantly degraded fibre components (p < 0.05) by secreting extracellular enzymes and organic acids. This process encouraged the accumulation of raw proteins and dipeptides. Key metabolic pathways, such as pyrimidine metabolism and the TCA cycle, were significantly enhanced. This led to the synthesis of valuable metabolites, including mevalonate and biopterin, which have increased antioxidant and metabolic properties. CONCLUSION: The research results demonstrate that the “microbiota structure—metabolic function—fermentation quality” relationship constitutes a complex and mutually influential system, providing important theoretical support for targeted microbial community regulation and optimization of fermentation processes in straw.},
}

*Zea mays/microbiology/metabolism/chemistry
Fermentation
*Probiotics/metabolism
Metabolomics
*Microbiota
Laccase/metabolism
*Enzymes/metabolism
Lactobacillus/metabolism
Peroxidases/metabolism
Bacillus subtilis/metabolism
Cellulose/metabolism
Bacteria/metabolism/classification/genetics
Cellulase/metabolism

@article {pmid41654923,
year = {2026},
author = {Dong, R and Lu, Y and Zheng, J and Zhuang, Y and Ma, Y and Cao, L and Li, Y and Kane, Y and Zhang, C and Li, YY},
title = {First-year dynamics of the plasma virome and cytokine profile in infants born to mothers with syphilis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41654923},
issn = {1479-5876},
support = {202403AC100011//Key research and development program of Yunnan Province/ ; RLXZ20230001//The "Xingdian Talents" Support Project of Yunnan Province/ ; YWLCYXZX2023300076//The Project of AIDS Bureau of Yunnan Province, the Yunnan Province Clinical Center for Skin Immune Diseases/ ; 2024XKTDYS01//The First-Class Discipline Team of Kunming Medical University/ ; 82203934//The National Natural Science Foundation of China/ ; },
mesh = {Humans ; Female ; *Cytokines/blood ; Pregnancy ; *Virome ; Infant, Newborn ; Infant ; *Syphilis/blood/virology ; Adult ; Infectious Disease Transmission, Vertical ; *Mothers ; Phylogeny ; Longitudinal Studies ; },
abstract = {BACKGROUND: The early-life development of the human plasma virome and its immunological implications remain poorly understood. We aimed to explore the dynamic interplay between viral colonization and immune maturation in infancy. METHODS: We conducted a retrospective longitudinal study of the plasma virome and cytokine profile in a cohort of 77 pregnant women with syphilis and their 89 infants. Plasma samples were collected from mothers at delivery and infants at multiple time points (the first day, and at 3, 6, 9 and 12 months of age). Virome composition was characterized via metagenomic sequencing, and 27 cytokine concentrations were quantified using multiplex immunoassays. The impacts of delivery mode, feeding patterns, and anti-syphilitic treatment on the development of plasma virome were investigated. Mother-infant vertical transmission of anelloviruses was validated by phylogenetic analysis with MEGA (v1.2.9). RESULTS: The infant plasma virome was composed mainly of host-associated viruses (42.5%, primarily Anelloviridae) and phages (45.5%). Phages dominated the neonatal plasma virome at birth, but declined accompanied with a rapid expansion of host-derived viruses (96.1% at 12 months) during the first year of life. Human-host viruses were rarely detected in neonates at birth, with their richness and abundance increaing notably after 3 months of life. Shared human-host viruses with mothers were observed at the neonates at birth and increased in virus number and abundance in the first year of life. Mother-to-infant perinatal vertical transmission of anelloviruses were validated by transmission cluster analysis using all identified anelloviruses ORF1 lineages at delivery. Delivery mode, environment exposure, and feeding pattern had no significant effect on virome diversity. Compared with their mothers, the neonates exhibited higher plasma levels of eotaxin, FGF basic, GM-CSF, MCP-1, MIP-1α, MIP-1β, VEGF, IFN-γ, IL-5, IL-9, IL-10, IL-17 A, and TNF-α at birth. During months 3 to 6, infant IL-6 levels declined, while IL-13 and IP-10 levels gradually increased. From month 3, Anelloviridae abundance positively correlated with IL-6, IL-9, IL-10, IP-10, MCP-1, MIP-1α, MIP-1β, and TNF-α in infants, and with MCP-1 and MIP-1α in maternal plasma. CONCLUSION: Our findings reveal dynamic developmental trajectories of the virome and immune system and suggest that early virome exposures may influence immune development, providing a basis for future maternal-child health interventions.},
}

Humans
Female
*Cytokines/blood
Pregnancy
*Virome
Infant, Newborn
Infant
*Syphilis/blood/virology
Adult
Infectious Disease Transmission, Vertical
*Mothers
Phylogeny
Longitudinal Studies

@article {pmid41661326,
year = {2026},
author = {Umemura, A and Sasaki, A and Sasaki, D and Iizuka, A and Chiba, M and Aihara, K and Ubukata, N and Kumagai, H and Tanahashi, Y and Iwasaki, T and Ando, T and Nitta, H},
title = {Impact of laparoscopic sleeve gastrectomy on gut and oral microbiota diversity, weight loss, and the metabolic outcomes.},
journal = {Surgery today},
volume = {56},
number = {7},
pages = {1351-1359},
pmid = {41661326},
issn = {1436-2813},
mesh = {Humans ; *Weight Loss ; *Gastrectomy/methods ; Female ; *Laparoscopy/methods ; Male ; Treatment Outcome ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; *Obesity, Morbid/surgery/microbiology/metabolism ; *Bariatric Surgery/methods ; *Mouth/microbiology ; },
abstract = {PURPOSE: Metabolic and bariatric surgery (MBS) alters the gut microbiota (GM). Changes in oral microbiota (OM) after MBS have not yet been thoroughly investigated. In this study, we evaluated the changes in GM and OM before and after laparoscopic sleeve gastrectomy (LSG) in patients with severe obesity and investigated the relationship between improvements in GM/OM, weight loss, and the metabolic effects. METHODS: Thirty-seven severely obese patients who underwent LSG were enrolled in this study. We retrieved samples from the feces and oral mucosa from baseline to 1-year after LSG. These samples were subjected to a 16 S rRNA metagenomic analysis using a next-generation sequencer. We evaluated the significant changes in GM/OM and compared the results with clinical outcomes. RESULTS: Regarding OM diversity, g_Actinomyces (p = 0.003), o_Rothia (p = 0.020), and g_Streptococcus (p = 0.004) increased. With regard to GM, g_Slackia (p = 0.039), g_Bacillus (p = 0.030), g_Roseburia (p = 0.027), and g_Faecalibacterium (P = 0.003) increased, the proportion of p_ Firmicutes increased, and p_Bacteroidetes decreased in both groups. Changes in g_Akkermansia did not contribute to GM/OM diversity. The weight loss and remission rates of type 2 diabetes were higher in patients with increased normal oral flora and a recovery of g_Faecalibacterium in GM. CONCLUSIONS: We clarified that the LSG reconstructs GM/OM as weight loss and the metabolic effects are enhanced.},
}

Humans
*Weight Loss
*Gastrectomy/methods
Female
*Laparoscopy/methods
Male
Treatment Outcome
*Gastrointestinal Microbiome
Adult
Middle Aged
*Obesity, Morbid/surgery/microbiology/metabolism
*Bariatric Surgery/methods
*Mouth/microbiology

@article {pmid41663924,
year = {2026},
author = {Li, B and Shi, X and Yao, X and Yan, Y and Wu, K and Zhang, C and Ren, Y},
title = {Association of the residual feed intake (RFI) with the rumen microbiota composition and metabolism in Dorper-Hu crossbred lambs.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41663924},
issn = {1471-2180},
support = {2020BQ53//The Science and Technology Innovation Program of Shanxi Agricultural University/ ; SXBYKY2021037//Shanxi Province Outstanding Doctor Award Fund/ ; J202011313//"1331 Project" Key Disciplines of Animal Sciences, Shanxi Province/ ; Modern Agro-industry Technology Research System in Shanxi Province//Modern Agro-industry Technology Research System in Shanxi Province/ ; },
mesh = {Animals ; *Rumen/microbiology/metabolism ; *Animal Feed/analysis ; Sheep/microbiology/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Gastrointestinal Microbiome ; Metabolomics ; *Eating ; Metabolome ; Metagenomics ; Digestion ; },
abstract = {BACKGROUND: Improving feed efficiency in livestock is crucial for sustainable animal production. Residual feed intake (RFI) is a superior metric that accurately assesses feed efficiency. Animals with a low RFI (LRFI) usually consume less feed than animals with a high RFI (HRFI). Ruminal microbiota plays an important role in feed digestion in sheep. It is essential to elucidate the associations between rumen microbial composition, metabolic profiles, and growth performance of lambs with differing RFI by metagenomic sequencing and metabolomic profiling. RESULTS: Although no significant differences were observed in growth performance, LRFI lambs exhibited significantly lower dry matter intake (P < 0.05) and improved feed efficiency. Integrative metagenomic and metabolomics analysis revealed that the LRFI group showed enrichment of bacteria (Prevotella, Roseburia, and Pseudoscardovia) (P < 0.05) and metabolites (N-Acetylneuraminic acid 9-phosphate, N-Succinyl-L-glutamate, 5-hydroxyindolepyruvate, pelargonidin, sinapic acid, and spermidine) associated with efficient nitrogen metabolism, enhanced microbial protein synthesis, and antioxidant activity. By contrast, the HRFI group was characterized by increased abundance of microorganisms (Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) (P < 0.05), coupled with elevated levels of metabolites (histidinal, tetrahydrocorticosterone, and sakuranetin). Correlation networks identified positive correlations among Prevotella, unclassified f_Prevotellaceae, several amino acid intermediates and specific flavonoids, and the host traits of reduced DMI and RFI. Conversely, the genera Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina were positively correlated with the increased DMI and RFI. CONCLUSIONS: Efficient (low-RFI) animals exhibited a Prevotella-driven microbiome and a distinct metabolome characterized by enrichment of several amino acid intermediates and specific flavonoids, while a more diverse but methanogen-related microbial community (such as Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) is present in inefficient (HRFI) sheep. The identified microbial and metabolic profiles provide potential biomarkers for breeding feed-efficient animals and developing targeted nutritional interventions to improve ruminant production sustainability.},
}

Animals
*Rumen/microbiology/metabolism
*Animal Feed/analysis
Sheep/microbiology/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
*Gastrointestinal Microbiome
Metabolomics
*Eating
Metabolome
Metagenomics
Digestion

@article {pmid41663943,
year = {2026},
author = {Li, M and Yang, R and Bai, Q and Yang, Z and Huang, T and Qiao, Y and Yang, B and Chen, J and Lin, W},
title = {Manipulating root-associated microbiomes to boost drought resistance in dryland winter wheat with Streptomyces pactum Act12.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41663943},
issn = {1471-2180},
support = {32401443//National Natural Science Foundation of China/ ; 2025CYJSTX02-16//the earmarked fund for Modern Agro-industry Technology Research System of Shanxi Province/ ; },
mesh = {*Triticum/microbiology/growth & development/physiology ; Drought Resistance ; *Plant Roots/microbiology ; Soil Microbiology ; Rhizosphere ; *Microbiota ; *Streptomyces/physiology ; Droughts ; Bacteria/classification/genetics/isolation & purification ; Metagenomics ; },
abstract = {BACKGROUND: Drought critically compromises agricultural productivity and threatens sustainable wheat production. Streptomyces pactum Act12 confers benefits to plant growth under drought stress, but its possible effects on root-associated microbiomes remain understudied. Here, shotgun metagenome sequencing and culture-dependent approaches were integrated to investigate the responses of rhizosphere and rhizoplane microbiomes in dryland winter wheat to exogenous S. pactum Act12 and their potential linkage to plant drought resistance. RESULTS: Seed biopriming with S. pactum Act12 increased plant aboveground dry weight at flowering (by 63.2%) and maturation (by 41.9%) stages, leading to improved grain yield (by 8.7%). Microbial inoculation reduced malondialdehyde contents in wheat leaves and roots at the flowering stage alongside compartment-specific alterations in soil microbiomes. Metagenomic analysis revealed inoculation-induced enrichment of distinct taxa in rhizosphere soils (flowering: Fibrobacterota, Altererythrobacter; maturation: Mucoromycota, Rhodospirillum) and rhizoplane soils (flowering: Pseudomonadota, Serratia; maturation: Candidatus_Pacebacteria, Variovorax). Functional profiling showed up-regulation of key pathways related to oxidative phosphorylation in inoculated rhizosphere soils at the flowering stage. In rhizoplane soils, ABC transporters and pyrimidine metabolism were up-regulated across stages upon inoculation. Two key strains isolated from rhizoplane soils, designated Glycomyces lechevalierae A4 and Microbacterium algeriense B3, demonstrated the ability to enhance drought resistance in wheat seedlings. CONCLUSIONS: Inoculation of S. pactum Act12 heightens drought resistance in dryland winter wheat through compartment-specific phylogenetic restructuring and functional reprogramming of root-associated microbiomes.},
}

*Triticum/microbiology/growth & development/physiology
Drought Resistance
*Plant Roots/microbiology
Soil Microbiology
Rhizosphere
*Microbiota
*Streptomyces/physiology
Droughts
Bacteria/classification/genetics/isolation & purification
Metagenomics

@article {pmid41691172,
year = {2026},
author = {Motta, H and Perin, APA and Rosin, GF and Reuwsaat, JCV and Mocelin, I and Lopes, FC and Mayer, FQ and de Medeiros, VP and Brum, IS and Baethgen, LF and Gregianini, TS and Staats, CC and Vainstein, MH and Kmetzsch, L},
title = {SARS-CoV-2 Infection disrupts lower respiratory tract microbiome function and interactions.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41691172},
issn = {1471-2180},
support = {405934/2022-0//Instituto Nacional de Ciência e Tecnologia (INCT FUNVIR)/ ; 408717/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 22/2551-0000396-6//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS)/ ; },
mesh = {Humans ; *Microbiota/genetics ; *COVID-19/microbiology ; SARS-CoV-2 ; *Bacteria/classification/genetics/isolation & purification ; Nasopharynx/microbiology ; *Respiratory System/microbiology ; Female ; Retrospective Studies ; Brazil ; Male ; Middle Aged ; *Respiratory Tract Infections/microbiology ; Adult ; Metagenomics ; },
abstract = {BACKGROUND: The respiratory microbiome plays a critical role in host defense mechanisms and influences disease outcomes. However, the impact of SARS-CoV-2 infection on microbial community composition, function, and resistance potential across different respiratory tract compartments remains incompletely understood. To address this, we analyzed 127 retrospective respiratory samples from SARS-CoV-2-positive and negative patients from Southern Brazil. The dataset included nasopharyngeal swabs from the upper respiratory tract (URT) and samples from the lower respiratory tract (LRT) of patients with Severe Acute Respiratory Infection (SARI). Microbial taxonomic profiles, diversity, co-occurrence networks, functional pathways, and antibiotic resistance genes (ARGs) were assessed through shotgun metagenomic sequencing. RESULTS: SARS-CoV-2 infection did not affect diversity in the URT, but was associated with altered bacterial beta diversity in the LRT. The LRT microbial composition was markedly altered in SARS-CoV-2-positive cases, with reduced abundance of pathogens such as Stenotrophomonas and Pseudomonas and an increased prevalence of Prevotella and Alloprevotella. Co-occurrence network analysis uncovered a loss of complexity in SARS-CoV-2-positive URT samples and the emergence of novel interactions associated with infection in the LRT. Functional profiling demonstrated that SARS-CoV-2-positive LRT samples were enriched in metabolic pathways, whereas SARS-CoV-2-negative LRT samples were enriched in virulence pathways. Resistome profiling indicated minimal differences in ARG diversity and mechanism distribution, although SARS-CoV-2-negative LRT samples exhibited higher ARG abundance. CONCLUSION: SARS-CoV-2 infection reshapes the composition, interactions, and functional potential of the LRT microbiome, while the URT remains relatively stable. These findings underscore the compartment-specific impact of SARS-CoV-2 infection on the respiratory microbiome.},
}

Humans
*Microbiota/genetics
*COVID-19/microbiology
SARS-CoV-2
*Bacteria/classification/genetics/isolation & purification
Nasopharynx/microbiology
*Respiratory System/microbiology
Female
Retrospective Studies
Brazil
Male
Middle Aged
*Respiratory Tract Infections/microbiology
Adult
Metagenomics

@article {pmid41697296,
year = {2026},
author = {Chengcheng, L and Yanduo, Z and Zhebin, W and Jianzhang, L and Yangtao, Z and Jun, L and Yu, L and Felemban, HR and Alyahyawy, OY and Alhomodi, AF and Hadadi, F and Shaibah, A and Bingzhi, L and Xianwei, W},
title = {Metagenomic analysis of fecal microbial communities in dairy goats from different farms.},
journal = {Protoplasma},
volume = {263},
number = {3},
pages = {1031-1045},
pmid = {41697296},
issn = {1615-6102},
mesh = {Animals ; *Goats/microbiology ; *Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Dairying ; *Farms ; *Microbiota/genetics ; Female ; },
abstract = {This study aims to investigate the differences in the microbial community structure of goat manure under various breeding environments, providing scientific evidence and theoretical support for healthy breeding practices. Gut microbiota is a key determinant of feed conversion, disease resistance and overall productivity in ruminants. The gut microbiome is an integral part of the digestive system. Its composition and functional traits markedly influence digestive efficiency, immune development, gut homeostasis and reproductive performance. Using four goat dairy farms in the Yangling, Shaanxi Province as study subjects, fecal samples were collected and analyzed using 16S rRNA sequencing technology, combined with α-diversity indices and β-diversity analysis. The results revealed significant differences in the microbial community structure of goat feces across different farms, with each farm exhibiting unique microbial communities. Each farm harboured distinct microbial signatures and functional profiles, providing microbiota-based targets for precision management of Guanzhong dairy goats.},
}

Animals
*Goats/microbiology
*Feces/microbiology
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Dairying
*Farms
*Microbiota/genetics
Female

@article {pmid41699578,
year = {2026},
author = {Wu, H and Li, N and Yang, S and Qiu, J and Zhang, M and Wang, L and Gao, R and Wu, L and Yu, Q and Cheng, X},
title = {Prevotella denticola promotes caries by inducing oral microbial dysbiosis.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {},
pmid = {41699578},
issn = {1472-6831},
support = {82170937//the National Nature Science Foundation of China/ ; 81800955//the National Nature Science Foundation of China/ ; (No. 2025GH-YBXM-033)//External Cooperation Areas of the Key Research and Development (R&D) Program of Shaanxi Province/ ; LCB202408//the Special Project of the National Clinical Research Center for Oral Diseases/ ; },
mesh = {Humans ; *Dental Caries/microbiology ; *Dysbiosis/microbiology ; Biofilms/growth & development ; *Dental Plaque/microbiology ; Adult ; *Prevotella ; Microbiota ; Female ; Male ; Metagenomics ; },
abstract = {BACKGROUND: While the role of oral microbial dysbiosis in cariogenicity is widely appreciated, it remains unclear whether some resident microorganisms are active contributors in this process. Recently, increasing evidence showed that Prevotella spp. are associated with caries whereas the identified roles at species level remain undefined. This study aimed to analyze the effects of Prevotella denticola on microbial ecosystems and pathogenic mechanisms associated with caries. METHODS: Here, we applied metagenomics to supragingival microbiota (dental plaque) samples from 62 adults to identify disease-relevant species. P. denticola was highly enriched in caries-affected individuals (P < 0.001). The dynamic biofilm formation, spatial arrangement, and cariogenic activity of oral biofilms with or without P. denticola were examined via multiscale/computational imaging and virulence assays. RESULTS: P. denticola, exerting a previously unidentified mechanism in supragingival biofilms, promoted oral biofilm cariogenicity through altering the microbial ecosystem and biofilm structure. In vivo studies demonstrated that P. denticola induced the formation of a more cariogenic biofilm on supragingival tooth surfaces. CONCLUSIONS: Collectively, P. denticola has an ecological impact on the mixed oral microbiota and disrupts microbial equilibrium. These findings indicated that P. denticola infection plays a critical role in caries occurrence.},
}

Humans
*Dental Caries/microbiology
*Dysbiosis/microbiology
Biofilms/growth & development
*Dental Plaque/microbiology
Adult
*Prevotella
Microbiota
Female
Male
Metagenomics

@article {pmid41699596,
year = {2026},
author = {Hu, S and Chen, T and Liu, X and Wu, Z and Wang, X},
title = {Effects of aerobic exercise on inflammation and gut microbiota in obese mice: a metagenomic and metabolomic analysis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41699596},
issn = {1479-5876},
support = {2025AFB925//Natural Science Foundation of Hubei Province/ ; XZ202501ZR0140//Key project of Natural Science Foundation of Tibet Autonomous Region/ ; SNSBJKJJHXM2024023//Shannan Science and Technology Plan Project/ ; Yz2024179//National Resource Center for the First-Year Experience and Students in Transition, University of South Carolina/ ; JY2024066//the University-level teaching and research project of Yangtze University/ ; (25Y117)//Philosophical and Social Science Research Project of the Education Department of Hubei Province/ ; 2025csz005//Key Project of Social Sciences Fund of Yangtze University/ ; },
mesh = {Animals ; *Physical Conditioning, Animal ; Male ; *Inflammation/microbiology/pathology/blood ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/genetics ; *Metabolomics ; Mice, Obese ; Insulin Resistance ; *Metagenomics ; Diet, High-Fat ; *Obesity/microbiology ; Body Weight ; Cytokines/metabolism ; Mice ; Lipids/blood ; },
abstract = {BACKGROUND: Aerobic exercise can ameliorate insulin resistance (IR). However, the mechanism by which aerobic exercise regulates the gut microbiome to ameliorate IR and obesity remains unexplored. METHODS: Obese models were established by feeding C57BL/6 male mice a high-fat diet. A total of 26 mice were randomly divided into control group (group A, N = 8) and high-fat diet group (HFD group, N = 18). Successfully modeled mice were further assigned to model group (group B, N = 8) and exercise group (group C, N = 8). Group C underwent a 6-week treadmill exercise program (12 m/min, 60 min per day, 5 days per week). After intervention, colon tissue morphology was observed through hematoxylin-eosin staining, serum lipids and inflammatory indicators levels were detected by ELISA. The changes in the intestinal microbiota of the mice were also examined using metagenomic sequencing and UPLC-MS non-targeted metabolomics. RESULTS: Compared with the group A, the body weight, TC, TG, LDL-C, blood glucose, insulin, and IR in the group B significantly increased (P < 0.01), while the levels of pro-inflammatory cytokines TXNIP, TNF-α, NLRP3, IL-1β, and IL-18 significantly increased (P < 0.05 or P < 0.01). Compared with the group B, aerobic exercise reduced the body weight, TC, blood glucose, insulin, IR, TXNIP, TNF-α and other indicators in obese mice (P < 0.05 or P < 0.01). Moreover, aerobic exercise can regulate the imbalance of the intestinal flora in obese mice and ameliorate the disorder of metabolites. The metabolic pathways including arachidonic acid metabolism and histidine metabolism showed the most significant differences after the intervention of aerobic exercise. CONCLUSIONS: In conclusion, aerobic exercise can ameliorate glucose and lipid metabolism, IR, inflammatory response, and regulate the intestinal microecology and metabolic disorders in obese mice. The mechanism may be closely related to enhancing the diversity of intestinal flora, regulating the metabolism of arachidonic acid and histidine.},
}

Animals
*Physical Conditioning, Animal
Male
*Inflammation/microbiology/pathology/blood
Mice, Inbred C57BL
*Gastrointestinal Microbiome/genetics
*Metabolomics
Mice, Obese
Insulin Resistance
*Metagenomics
Diet, High-Fat
*Obesity/microbiology
Body Weight
Cytokines/metabolism
Mice
Lipids/blood

@article {pmid41706260,
year = {2026},
author = {Matsumoto, M and Shiotani, A and Osawa, M and Handa, O and Matsumoto, H and Umegaki, E and Yonezawa, H and Osaki, T},
title = {Metagenomic analysis of the intragastric and oral microbiome associated with gastric carcinogenesis after Helicobacter pylori eradication.},
journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association},
volume = {29},
number = {2},
pages = {338-346},
pmid = {41706260},
issn = {1436-3305},
support = {Research Project Grant//Kawasaki Medical School/ ; },
mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology ; *Helicobacter pylori/isolation & purification ; *Helicobacter Infections/drug therapy/microbiology/complications ; Female ; Male ; *Microbiota/genetics ; Middle Aged ; Metagenomics/methods ; Aged ; Case-Control Studies ; Saliva/microbiology ; Carcinogenesis ; Gastric Mucosa/microbiology ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Few reports have investigated bacterial microbiome in relation to gastric cancer after eradication of Helicobacter pylori (H. pylori). We aimed to conduct a genetic analysis of the gastric and oral microbiome, to identify its association with development of gastric cancer after H. pylori eradication. METHODS: The patients with prior endoscopic submucosal dissection (ESD) history after eradication (cancer patients) and control patients after eradication who underwent upper gastrointestinal endoscopy at Kawasaki Medical School Hospital from May 2021 to March 2023 were enrolled. Saliva and gastric mucus samples were collected and profiled by 16S rRNA gene amplicon sequencing. RESULTS: The subjects consisted of 24 cancer patients and 27 controls. The abundance of the genus Rothia in gastric mucus of the cancer patients was significantly higher compared to the controls. Conversely, the genus Parvimonas was significantly less abundant in the cancer patients. These differences in salivary samples between the two groups were not observed. The abundance of the genus Parvimonas in the gastric mucous was associated with the gastric atrophy, but genus Rothia was not. CONCLUSIONS: Genus Rothia may have some influence on carcinogenesis following H. pylori eradication.},
}

Humans
*Stomach Neoplasms/microbiology/pathology
*Helicobacter pylori/isolation & purification
*Helicobacter Infections/drug therapy/microbiology/complications
Female
Male
*Microbiota/genetics
Middle Aged
Metagenomics/methods
Aged
Case-Control Studies
Saliva/microbiology
Carcinogenesis
Gastric Mucosa/microbiology
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid41709052,
year = {2026},
author = {Idris, H and Hairi, HH and Ahmad, A and Danish-Daniel, M and Zin, NM and Sanderson, RA and Raja Yahya, MFZ and Majhool, AA and Hassan, MY and Azman, MAZ},
title = {Revealing actinobacterial diversity inhabiting Malaysian Beach Ridges Interspersed with Swales (BRIS) soil : insights from culture-dependent and metagenomic approaches.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {29},
number = {3},
pages = {301-313},
pmid = {41709052},
issn = {1618-1905},
mesh = {*Actinobacteria/classification/genetics/isolation & purification ; *Soil Microbiology ; Malaysia ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics/chemistry ; *Biodiversity ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {The discovery of novel antibiotics remains a pressing global challenge as many known microorganisms continue to yield compounds already present in existing drugs. To overcome this limitation, bioprospecting in underexplored and extreme environments using both culture-dependent and culture-independent strategies has become essential. In this study, we investigated the microbial diversity of Beach Ridges Interspersed with Swales (BRIS) soil from Setiu, Terengganu, Malaysia—an environment characterized by poor nutrient retention, low water-holding capacity, and acidic conditions with lack information available on their microbial community composition. Therefore, this study was conducted with the main objectives to investigate actinomycetes community composition in BRIS soil using metagenomics and culture-dependent approaches. To address these objectives, a dual approach was employed: (i) culture-dependent isolation of actinomycetes using selective media, followed by morphological and 16S rRNA gene-based phylogenetic analysis, and (ii) culture-independent high-throughput sequencing of the 16S rRNA gene (Illumina MiSeq) to characterize the broader microbial community. Results from the selective isolation yielded 180 actinomycete isolates grouped into 69 colour-based categories, with 15 representatives identified by 16S rRNA sequencing as belonging predominantly to Streptomyces, alongside the rare genus Dermacoccus. In contrast, metagenomic analysis revealed a far richer microbial landscape comprising 4719 OTUs, 32 bacterial phyla, and 380 genera, including a high proportion of uncultured taxa. Notably, actinobacterial diversity was dominated by Acidothermus, whereas Streptomyces predominated in culture-dependent isolation, highlighting the complementary nature of both approaches. These findings confirm that BRIS soil harbours unique microbial communities shaped by its physicochemical conditions, with potential as a reservoir for rare actinomycetes and novel bioactive compounds. The study provides the first combined culture-dependent and metagenomic insight into BRIS soil microbiota and underscores its promise for future pharmaceutical and biotechnological exploration.},
}

*Actinobacteria/classification/genetics/isolation & purification
*Soil Microbiology
Malaysia
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics/chemistry
*Biodiversity
Sequence Analysis, DNA
DNA, Ribosomal/genetics/chemistry

@article {pmid41711914,
year = {2026},
author = {Demin, K and Onasenko, K and Beletskaya, A and Tsoy, A and Boyko, M and Kulikov, M and Kulikova, D and Prazdnova, E},
title = {Studying organosulfonate metabolism in southern Russia chernozem soil microbial community: ubiquity of the desulfonation pathways and possible mixotrophy in common soil heterotrophs.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {201},
pmid = {41711914},
issn = {1432-072X},
support = {SP-12-23-04//Priority 2030/ ; },
mesh = {*Soil Microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Russia ; *Microbiota ; Alkanesulfonates/metabolism ; Taurine/metabolism ; Metagenomics ; Sulfites/metabolism ; Phylogeny ; Soil/chemistry ; Oxidation-Reduction ; },
abstract = {Microbial metabolism of organosulfonates (OS) have been researched for at least three decades. However, the studies conducted so far were heavily focused on marine ecosystems, while in terrestrial ecosystems microbial desulfonation pathways are poorly characterized. Here we describe culturable microbial community of chernozem soil from the perspective of OS-based metabolism. Using the metagenomic and culture-dependent approaches, we compare microbial isolates grown on OS to the isolates enriched using common media for soil bacteria and show that there is no substantial difference in terms of taxonomy and OS metabolism genes representation. Alkanesulfonates and taurine are the primary OS compounds metabolized by soil bacteria through ssuDE and tauD enzymatic systems, while other OS desulfonation pathways are rare or absent. Actinobacterial and alphaproteobacterial representatives were the dominant part of OS-utilization community. We show in vitro taurine desulfonation and subsequent re-utilization of produced sulfite by soil actinobacterial isolates of Streptomyces anulatus and Arthrobacter siccitolerans. We hypothesize that microbial desulfonation coupled to sulfite oxidation may be a strategy to generate energy from both organic and inorganic molecules oxidation in heterotrophs (that is, mixotrophy). Finally, it is that OS-metabolism represents a ubiquitous metabolic capability rather than a niche trait, interlinking key biogeochemical cycles, particularly sulfur, nitrogen, and carbon.},
}

*Soil Microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Russia
*Microbiota
Alkanesulfonates/metabolism
Taurine/metabolism
Metagenomics
Sulfites/metabolism
Phylogeny
Soil/chemistry
Oxidation-Reduction

@article {pmid41714980,
year = {2026},
author = {Ceylani, T and Teker, HT and Önlü, H and Ünver, T and Allahverdi, H and Şahin, E and Atalan, E},
title = {Multi-omics insights into gut microbiota-metabolite interactions under probiotic intervention in a developmental cafeteria diet model.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {41714980},
issn = {1471-2164},
support = {FOA-2024-3587//Inönü University Scientific Research Projects Coordination Unit (BAP)/ ; },
mesh = {Animals ; *Probiotics/pharmacology ; Male ; Multiomics ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Diet ; Rats, Wistar ; Fatty Acids, Volatile/metabolism ; Metagenomics ; Metabolomics ; Indoles/metabolism ; },
abstract = {BACKGROUND: The developmental phase is a pivotal biological period for the maturation of the gut microbiota and the establishment of lifelong metabolic health. During these period, dietary patterns that induce dysbiosis, such as the high-fat, low-fiber “cafeteria diet,” disrupt the production of key metabolites in the gut-metabolite axis, including short chain fatty acids (SCFAs) and indole-3-propionic acid (IPA). This study employs a multi-omics approach to examine the impact of cafeteria diet exposure during the developmental period (days 21–56) in 21-day-old male Wistar rats on microbiota composition, SCFA, and IPA levels, and to assess the extent to which concurrent probiotic administration can mitigate these disruptions. RESULTS: The cafeteria diet led to a marked reduction in alpha diversity indices (Shannon p = 0.021; Simpson p = 0.034) and altered the Firmicutes/Bacteroidetes ratio (p = 0.015). Beta diversity analysis indicated a distinct separation between groups (PERMANOVA p = 0.002). Metabolite analysis revealed significant reductions in acetic acid (p = 0.004), isobutyric acid (p = 0.094), butyric acid (p = 0.0014), valeric acid (p = 0.0001), heptanoic acid (p = 0.0125), and IPA (p = 0.002), whereas probiotic administration largely restored these levels. At the species level, cafeteria diet markedly increased Segatella copri, while probiotic intervention partially restored beneficial taxa such as Faecalibacterium prausnitzii and butyrate-producing genera (Anaerostipes hadrus, Intestinimonas butyriciproducens, Blautia wexlerae, and Flintibacter sp. KGMB00164), as evidenced primarily by shotgun metagenomics. Correlation analysis further revealed strong positive associations between butyrate and F. prausnitzii (ρ = 0.65, p = 0.003) and between IPA and B. longum (ρ = 0.68, p = 0.002). Collectively, these results highlight the protective role of probiotic intervention against diet-induced dysbiosis by reinforcing microbiota metabolite interactions. CONCLUSIONS: By integrating metagenomic and metabolomic analyses, this multi-omics study demonstrates that exposure to a high-fat cafeteria diet during the developmental period disrupts microbiota composition and metabolite production, whereas concurrent probiotic administration largely prevent these effects, serving a protective role in the gut-metabolite axis. The study underscores the potential of early-life probiotic intervention, supports SCFA and IPA production, as a critical strategy to optimize microbiota-metabolite interactions and promote long-term gut and systemic health.},
}