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PubMed2026

Integrated functional genomics and safety assessment of plant-growth-promoting Caryophanales from post-maize-cultivation soils.

This study aimed to evaluate six environmental bacterial strains isolated from post-maize cultivation soils as candidates for agricultural biopreparation development, using an integrated functional genomic and safety assessment framework. Building on experimental validation of plant-growth-promoting activities, the analysis included: plant-growth-promoting traits (PGPT-Pred) using PLABase; carbohydrate-active enzymes (CAZymes) relevant for lignocellulosic crop residue degradation (dbCAN3); secondary metabolite profiles (antiSMASH); and screening for virulence factors and antibiotic resistance genes (ABRicate, BTyper3).All analyzed strains possess 1,449-1,617 predicted PGPT-encoding genes (24.1-35.9% of total genes), which are strongly shaped by taxonomic relatedness, as confirmed by congruence testing against ANI-based genomic divergence. Paenibacillus amylolyticus 5mez and Priestia megaterium 7psych showed distinct functional profiles compared to Bacillus spp., while Bacillus subtilis sensu lato strains were most similar to each other. Genomic predictions suggest involvement in nutrient acquisition (N, P, K, Fe) and stress mitigation. Secondary metabolite analysis revealed high biosynthetic potential, with non-Bacillus species harbouring a large proportion of unknown gene clusters, indicating underexplored metabolite diversity. CAZyme profiling identified P. amylolyticus 5mez as the most enzyme-rich strain, while B. cereus s.s. zielonkawy showed ligninolytic potential despite low overall CAZyme abundance. The safety assessment identified B. cereus s.s. zielonkawy as toxigenic and unsuitable for use. Of the remaining strains, P. amylolyticus 5mez and Pr. megaterium 7psych demonstrated the most favourable safety profiles, exhibiting no detectable virulence factors or antibiotic resistance genes, justifying their priority use in agricultural biopreparations, pending phenotypic validation. Given the high-dimensional, low-sample-size nature of multi-trait datasets in applied microbial genomics, tailored statistical approaches, including noise-reduction-validated PCA and distance-based congruence testing, were applied; their rationale and limitations are discussed.

Soil Microbiology↗

PubMed2026

Supplementation with effective microorganisms in earthen ponds affects common carp growth and abundance of specific bacterial families.

BACKGROUND: Effective microorganisms are increasingly explored in aquaculture to improve fish health and growth without leaving harmful residues. However, their efficacy in real-world pond environments remains poorly understood. Here, we conducted a 103-day field experiment to assess the effects of supplementation with two effective commercial microorganism products on the microbial communities and growth performance of common carp (Cyprinus carpio). BACKGROUND: Effective microorganisms were added to the feed and directly to the pond water. Microbial diversity was analysed via 16 S rRNA and whole-genome shotgun sequencing across three environments: water (three time points), sediment (two time points), and fish intestine (one time point) from 25 experimental ponds. Bioinformatics processing was performed using the QIIME2 and MG-TK pipelines with taxonomic classification based on the SILVA database. The results showed that although supplemented bacterial families did not establish significantly in pond environments, fish exposed to specific effective microorganism treatments showed improved growth metrics. CONCLUSIONS: These findings suggest that effective microorganisms can increase carp growth in aquaculture without significantly altering the resident microbial communities, suggesting a promising residue-free alternative to traditional additives in aquaculture.

Animals↗

PubMed2025

Consumption of traditional Sardinian fermented milk promotes changes in the rat gut microbiota composition and functions.

BACKGROUND: Fermented milk products are part of the staple diet for many Mediterranean populations. Most of these traditional foods are enriched with lactobacilli and other lactic acid bacteria, as well as with metabolites resulting from lactose fermentation. Currently, there is very little scientific knowledge on how dietary supplementation with fermented milk affects the composition of the gut microbiota and its metabolic activities. RESULTS: We integrated 16 S rRNA gene-based taxonomic profiling with metaproteomics-based functional analysis to investigate gut microbiota changes in rats exposed to an 8-week dietary supplementation with casu axedu, a traditional fermented milk produced within rural communities in Sardinia (Italy). Several microbial taxa showed a significantly increased abundance at the end of the dietary treatment, including Phascolarctobacterium, Prevotella, Blautia glucerasea, and Lactococcus lactis, while Bacteroides dorei and Helicobacter rodentium were decreased compared to the control rats. Metaproteomic analysis highlighted a striking reshaping of the Prevotella proteome in agreement with its blooming in casu axedu-fed animals, suggesting an increase of the glycolytic activity through the Embden-Meyerhof-Parnas pathway over the Entner-Doudoroff pathway. Moreover, an increased production of enzymes involved in succinate biosynthesis was observed, which in turn significantly boosted the abundance of Phascolarctobacterium and its production of propionate. Fermented milk consumption also promoted microbial synthesis of branched chain essential amino acids L-valine and L-leucine. Finally, metaproteomic data indicated a reduction of bacterial virulence factors and host inflammatory markers, suggesting that the consumption of casu axedu can have beneficial effects on the gut mucosa health. CONCLUSIONS: Our integrated multi-omics approach reveals that dietary supplementation with the traditional Sardinian fermented milk, casu axedu, induces significant shifts in the rat gut microbiota composition and function, characterized by the enrichment of beneficial taxa and metabolic pathways associated with improved gut health and reduced inflammation.

Animals↗

PubMed2026

Integrated analysis of gut microbiota, serum metabolomics, and proteomics reveals novel associations with clinical symptoms in patients with cerebral infarction.

BACKGROUND: Cerebral infarction (CI) is a major cause of adult disability and mortality worldwide. Mounting evidence supports the critical role of the gut-brain axis in cerebrovascular disease progression. This study aimed to characterize the alterations in gut microbiota, serum metabolome, and serum proteome in patients with CI, and to identify multi-omics signatures associated with clinical symptoms. METHODS: A total of 20 CI patients and 20 healthy controls (HC) were enrolled. Fecal microbiota was profiled using 16 S rRNA gene high-throughput sequencing. Serum metabolomics and proteomics were analyzed using ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and data-independent acquisition (DIA) proteomics, respectively. Spearman correlation and multi-omics integration were applied to explore the associations among microbiota, metabolites, proteins, and clinical indicators. RESULTS: CI patients displayed significant gut microbiota dysbiosis, with a markedly lower gut microbiota health index (GMHI) and higher microbiota disorder index (MDI) compared with HC (P < 0.001). The genera g_norank_o_RF39 and Oxalobacter were significantly enriched in CI patients, whereas Clostridium_sensu_stricto_1 and Agathobacter were enriched in HC. Metabolomic analysis identified 445 differential metabolites, mainly involved in glycerophospholipid metabolism, phenylalanine metabolism, and caffeine metabolism. Proteomic analysis revealed 140 differentially expressed proteins linked to inflammatory responses, calcium signaling, and NF-κB signaling. Multi-omics integration showed that signature gut microbiota was strongly correlated (P < 0.005) with key serum metabolites and proteins implicated in CI pathogenesis. CONCLUSIONS: This integrated multi-omics study revealed distinct gut microbiota, serum metabolomic, and proteomic alterations in CI patients. The microbiota-metabolite-protein regulatory axes provide novel insights into the gut-brain axis in CI and may serve as potential diagnostic biomarkers or therapeutic targets.

Humans↗

PubMed2026

Comparison of clinical efficacy and gut microbiota characteristics in children with ASD treated with fecal microbiota transplantation and ketogenic diet.

OBJECTIVE: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by impairments in social communication and interaction, along with restricted, repetitive patterns of behavior. It is often accompanied by gastrointestinal dysfunction and gut microbiota dysbiosis. Fecal Microbiota Transplantation (FMT) and the Ketogenic Diet (KD) are interventions targeting the gut microbiota for ASD. METHODS: 30 participants were diagnosed with ASD according to DSM-5 and ADOS-2. ASD core symptoms were evaluated with CARS and ABC. Gut microbiota composition was analyzed by shotgun metagenomic sequencing. RESULTS: Both groups demonstrated significant improvements in core symptoms. In the FMT group, the mean CARS score significantly decreased from 34.87 to 33.53 (p < 0.01); in the KD group, it declined from 35.13 to 33 (p < 0.01). The mean ABC score reduced from 79.93 to 69.33 (p = 0.064) in the FMT group and from 63.07 to 42.73 (p < 0.01) in the KD group. Following the intervention, no statistically significant changes were observed in α-diversity or β-diversity within either group. LEfSe analysis revealed distinct post-intervention microbial signatures: FMT significantly enriched butyrate-producing taxa (Wujia chipingensis, Eubacterium sp. MSJ-33, and Butyrivibrio crossotus), while KD elevated Blautia massiliensis and decreased propionate metabolism -associated taxa (Veillonella sp. S12025-13 and Veillonella nakazawae). KEGG enrichment analysis revealed that KD enriched propionate metabolism (Fold enrichment = 3.747, q = 0.010) and aromatic compound degradation (Fold enrichment = 3.591, q = 0.010). CONCLUSIONS: Both interventions significantly improved clinical symptoms among children with ASD, potentially through distinct patterns of gut microbiota modulation. CLINICAL TRIALS NUMBER: NCT06348433 (03/21/2024).

Child↗

PubMed2025

Immune-mediated indirect interaction between gut microbiota and bacterial pathogens.

BACKGROUND: In many animals, survival during infection depends on the ability to coordinate interactions between the host immune system and gut microbiota. These tripartite interactions, in turn, potentially shape pathogen virulence evolution. A key regulator of the immune system and, hence, bipartite interactions in insects is the immune deficiency (Imd) pathway, which modulates gut microbiota and pathogens by synthesizing antimicrobial peptides (AMPs) through the NF-κB transcription factor Relish. However, whether Imd-dependent AMPs mediate indirect interactions between gut microbiota and pathogens in a tripartite context remains unclear. Using RNAi-mediated knockdown of Tenebrio molitor Relish (TmRelish), we hypothesized that Imd-dependent AMPs influence indirect interaction between Providencia burhodogranariea_B (P. b_B) infection and the gut microbiota. RESULTS: TmRelish knockdown altered bipartite interactions by disrupting gut microbiota load and composition, increasing pathogen load, and ultimately leading to higher host mortality during infection. However, we did not find support for our tripartite hypothesis that Imd-dependent AMPs mediate indirect interactions between the gut microbiota and P. b_B infection, suggesting the involvement of alternative regulatory pathways or Imd-independent mechanisms. Nevertheless, our investigations of tripartite interactions showed a positive effect of P. b_B infection on gut microbiota load, which in turn stimulated the expression of a subset of AMPs. However, this upregulation of AMPs did not result in reduced P. b_B load. Notably, the gut microbiota did not affect pathogen load but promoted host survival during P. b_B infection, indicating a role in increasing host tolerance rather than resistance. CONCLUSIONS: These findings suggest that while Imd-dependent AMPs may not mediate tripartite interactions in our system, microbiota-host interactions, such as microbiota-mediated immune priming and changes in microbiota load, can shape infection outcomes. These effects on infection outcomes almost certainly exert important selective pressures on the evolution of bacterial virulence.

Animals↗

PubMed2024

The causal effect of gut microbiota on hepatic encephalopathy: a mendelian randomization analysis.

BACKGROUND: There is growing evidence for a relationship between gut microbiota and hepatic encephalopathy (HE). However, the causal nature of the relationship between gut microbiota and HE has not been thoroughly investigated. METHOD: This study utilized the large-scale genome-wide association studies (GWAS) summary statistics to evaluate the causal association between gut microbiota and HE risk. Specifically, two-sample Mendelian randomization (MR) approach was used to identify the causal microbial taxa for HE. The inverse variance weighted (IVW) method was used as the primary MR analysis. Sensitive analyses were performed to validate the robustness of the results. RESULTS: The IVW method revealed that the genus Bifidobacterium (OR = 0.363, 95% CI: 0.139-0.943, P = 0.037), the family Bifidobacteriaceae (OR = 0.359, 95% CI: 0.133-0.950, P = 0.039), and the order Bifidobacteriales (OR = 0.359, 95% CI: 0.133-0.950, P = 0.039) were negatively associated with HE. However, no causal relationship was observed among them after the Bonferroni correction test. Neither heterogeneity nor horizontal pleiotropy was found in the sensitivity analysis. CONCLUSION: Our MR study demonstrated a potential causal association between Bifidobacterium, Bifidobacteriaceae, and Bifidobacteriales and HE. This finding may provide new therapeutic targets for patients at risk of HE in the future.

Mendelian Randomization Analysis↗

PubMed2026

A three-metabolite microbiota-associated signature for early risk stratification of gestational diabetes mellitus.

BACKGROUND: Gestational diabetes mellitus (GDM) is associated with adverse pregnancy outcomes and long-term metabolic and cardiovascular risk. However, oral glucose tolerance testing at 24-28 gestational weeks limits early risk stratification. Gut microbiota-associated metabolites may reflect early metabolic abnormalities, including those relevant to cardiometabolic health, but robust early-pregnancy biomarkers remain limited. METHODS: We conducted a multicenter nested case-control and prospective study involving 2,693 pregnant women. Untargeted metabolomics and metagenomics were integrated to identify GDM-associated metabolites and gut microbial alterations. Three consistently dysregulated metabolites, 3-hydroxydecanoic acid, γ-Glu-Leu, and propionic acid, were quantified by targeted LC-MS/MS. Candidate algorithms were compared using repeated 10-fold cross-validation, and a final generalized linear model was externally and prospectively validated. RESULTS: Women who later developed GDM showed an adverse early-pregnancy metabolic profile, including higher BMI, triglycerides, and platelet count. Untargeted metabolomics identified 14 persistently altered metabolites enriched in energy, oxidative stress, and amino acid metabolism pathways. Metagenomics revealed taxonomic restructuring and coordinated microbiota-metabolite associations. The three-metabolite model achieved AUCs of 0.838 (95% CI, 0.791-0.885) in training, 0.840 (95% CI, 0.769-0.911) in internal validation, 0.955 (95% CI, 0.925-0.985) and 0.917 (95% CI, 0.875-0.958) in two external cohorts, and 0.969 (95% CI, 0.937-1.000) in the prospective cohort. CONCLUSION: Early microbiota-associated metabolic dysregulation is detectable before routine GDM diagnosis. This compact three-metabolite panel may support early GDM risk stratification and provides metabolic evidence relevant to broader cardiometabolic risk assessment in pregnancy.

Humans↗

PubMed2026

Gut microbiota-driven indole-3-propionic acid and kynurenine production is associated with improved metabolic adaptation in periparturient dairy cows.

BACKGROUND: Gastrointestinal microbes convert tryptophan into various bioactive metabolites that influence host energy metabolism; however, these mechanisms are not well understood in periparturient dairy cows, which experience marked metabolic challenges during this period. RESULTS: In this study, we used periparturient dairy cows with rumen and ileal cannulas as in vivo models. Blood, rumen fluid, ileal digesta, and fecal samples were collected at four time points during the periparturient period. By combining metagenome-assembled genomes (MAGs) and targeted metabolite quantification, we characterized microbial tryptophan metabolism and associated metabolite profiles during the periparturient period. The results showed that postpartum cows exhibited significantly increased serum concentrations of triglyceride (TG), aspartate aminotransferase (AST), β-hydroxybutyrate (BHBA), and total bilirubin (T-Bil) compared with prepartum cows, together with decreased levels of several tryptophan metabolites, including indole-3-propionic acid (IPA) and kynurenine (KYN), indicating that tryptophan deficiency might aggravate metabolic disturbances. Metagenomic analysis identified 578 high-quality MAGs, of which 461 contained genes involved in microbial tryptophan metabolic pathways. Among these, the ruminal taxon CAG-791 harbors acdA and contributes to IPA production, whereas the hindgut taxon Treponema_D harbors kynB and promotes KYN formation. Decreases in both taxa were consistent with the reduced levels of these metabolites observed above. In a follow-up in vivo trial with tryptophan supplementation, the abundance of CAG-791 and Treponema_D increased, along with tryptophan-derived metabolites (IPA and KYN), which further partially mitigated metabolic disturbances. CONCLUSIONS: These findings characterize spatial and temporal changes in tryptophan metabolites and gut microbial features in periparturient dairy cows, and provide integrated evidence that alterations in tryptophan metabolism are associated with postpartum metabolic adaptation, thereby supporting the potential of tryptophan-targeted nutritional strategies to improve metabolic health in dairy cows.

Gastrointestinal microbiome↗

PubMed2026

A culturomics approach reveals cross-feeding capacity of intestinal pig bacteria upon release of inositol from phytate.

BACKGROUND: Phytate is the primary phosphorus storage molecule of plants and plays a major role in animal nutrition. To enhance phosphate availability and absorption in livestock, and to reduce eutrophication by liquid manure, bacterial phytases are often added to animal feed. The dephosphorylated form of phytate, the polyol myo-inositol (myo-Ins) with multiple functions in eukaryotes, is metabolized by approximately 30% of all bacterial species. RESULTS: Here, we employed a culturomics approach to identify possible metabolic interactions between phytase-producing and myo-Ins degrading bacteria in intestinal samples from pigs. Selective cultivation revealed an unexpectedly high abundance of myo-Ins degrading bacteria, suggesting substantial phytate dephosphorylation in the pig gut. Phytase activity assays performed on gut isolates showed a high degree of variability, suggesting the presence of a diverse set of phytases yet to be characterized. Furthermore, using supernatants of phytase-positive gut strains cultivated in the presence of phytate, we observed cross-feeding of myo-Ins from phytase producers to phytase-negative strains, including the pathogen Salmonella enterica serovar Typhimurium. CONCLUSIONS: The data demonstrate that a wide range of commensal bacteria can potentially benefit from phytase activity by utilizing myo-Ins, released through phytate hydrolysis, as a growth substrate. Video Abstract.

Animals↗

PubMed2026

Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium.

BACKGROUND: Foodborne pathogens, including Salmonella enterica serovar Typhimurium (S. Typhimurium), pose a significant threat to both human health and livestock productivity. The pandemic S. Typhimurium ST34 clone acquired a genomic island (SGI-4) conferring high copper resistance, an adaptation relevant in the context of the widespread use of copper sulphate at therapeutic levels in pig farming. We investigated how high dietary copper influences the piglet gut microbiota and Salmonella-microbiota interactions that may explain the global spread of S. Typhimurium ST34. RESULTS: An on-farm study combined with faecal shotgun metagenomics revealed that several potential Salmonella competitor species, including Bifidobacterium, Escherichia, and Lactobacillus, were less abundant in piglets on high-copper diets. Anaerobic and aerobic culturing alongside whole genome sequencing of 131 species and copper sulphate susceptibility testing identified copper resistance gene acquisition in selected microbes, particularly within Escherichia. Niche competition assays demonstrated that copper resistance is critical for inter-species competition under high-copper conditions, with Salmonella's Type VI Secretion System providing a distinct advantage over Escherichia in the copper-modified niche. CONCLUSIONS: Our findings suggest that copper supplementation alters the piglet gut environment, impacting competitive dynamics between pathogenic and commensal bacteria, likely to influence the zoonotic transmission of pathogens. Video Abstract.

Animals↗

PubMed2026

Mikania micrantha invasion restructures rhizosphere nitrogen cycling through enzyme activation, microbial recruitment, and allelopathic regulation.

BACKGROUND: Plant invasions profoundly influence terrestrial ecosystems by reshaping nutrient cycling processes. However, the mechanisms through which invasive plants such as Mikania micrantha modulate soil nitrogen (N) cycling and microbial communities remain insufficiently explored. Moreover, comparative studies with indigenous congener are scarce, limiting insights into whether such effects reflect species-specific strategies or genus-wide traits. This study investigates how M. micrantha modulates nitrogen metabolic pathways and rhizosphere microecology using combined metagenomic and metabolomic analyses. RESULTS: Integrated analyses revealed that M. micrantha established a distinctive "high total nitrogen-low mineral nitrogen" profile in the rhizosphere soil. Metagenomic profiling showed consistent enrichment of key ammonium assimilation enzymes, including glutamine synthetase and glutamate dehydrogenase, promoting enhanced incorporation of NH₄⁺ into organic nitrogen pools. In contrast, genes encoding nitrate reductase and nitrate transporters were significantly lower in relative abundance, limiting nitrate assimilation. Mikania micrantha also selectively enriched nitrogen-fixing microbes (notably rhizobia genera) and plant growth-promoting rhizobacteria (PGPR), thereby enhancing biological nitrogen fixation capacity. Metabolomic analysis further identified several allelopathic compounds in invaded soils at higher relative abundance, particularly epicatechin, which exhibited inhibitory effects on nitrifying bacteria. Compared with the congener Mikania cordata, which exerted weaker impacts on soil nitrogen cycling and microbial assembly, M. micrantha deployed a more comprehensive strategy integrating biochemical, microbial, and metabolic regulation. CONCLUSIONS: These findings demonstrate that under greenhouse-controlled conditions, M. micrantha reconfigures rhizosphere nitrogen cycling through a multi-dimensional strategy that couples biochemical regulation, microbial recruitment, and metabolite-mediated interference, thereby suggesting a potential mechanism that may contribute to its ecological advantage in natural settings. Video Abstract.

Rhizosphere↗

PubMed2026

Rumen microbiota-associated stress alleviation by creatine pyruvate in newly received cattle: a multi-omics study.

BACKGROUND: Stress experienced by newly received cattle is a significant challenge in the beef industry, frequently resulting in weakened immune responses and impaired growth. The rumen microbiota is essential to host health, and its imbalance can exacerbate stress. This study investigates the mechanisms by which creatine pyruvate (CrPyr) mitigates stress in newly received cattle through multi-omics approaches, including metagenomics, metabolomics, in vitro and in vivo experiments, and rumen microbiota transplantation (RMT) in mice. RESULTS: Our results revealed that CrPyr significantly reduces stress-related hormones (cortisol and adrenocorticotropic hormone) and inflammatory markers (IL-6, IL-1β, and TNF-α), and enhanced antioxidant capacity (SOD: 57.38 versus 46.93 U/mL, P < 0.05; GSH-Px: 305.87 versus 217.07 U/mL, P < 0.05; T-AOC: 9.62 versus 7.66 U/mL, P < 0.05). Metagenomic analysis demonstrated that CrPyr increased Prevotella abundance, a key rumen bacterium involved in volatile fatty acid (VFA) production, and enriches metabolic pathways associated with energy metabolism (ATP synthesis, and pyruvate metabolism) and antioxidant defense (glutathione metabolism, FC = 1.08, P < 0.05). In vitro and in vivo experiments, as well as RMT studies in mice, further validate these findings, demonstrating that CrPyr promote VFA synthesis and increased ATP production through the electron transport phosphorylation pathway. CONCLUSIONS: CrPyr modulates the abundance of ruminal Prevotella in transport-stressed cattle to enhance glutathione and VFA metabolism and to accelerate ATP and nucleotide synthesis, thereby alleviating stress in newly received cattle. This multimodal approach established CrPyr as an effective nutritional intervention that improves rumen function and increases livestock productivity. Video Abstract.

Animals↗

PubMed2026

Trimethylamine-producing microbe Bacillus megaterium KCTC 3007 promotes antitumor immunity in endometrial cancer via type I interferon response pathways.

BACKGROUND: Endometrial cancer (ECa) is one of the most common gynecologic malignancies, with limited therapeutic responses in metastatic or recurrent cases. The bacterial microbiota has emerged as a key modulator of carcinogenesis and antitumor immunity. However, the role of endometrial microbiota in ECa pathogenesis and prognosis remains poorly understood. METHODS: We performed comprehensive multi-omics analysis integrating metatranscriptomics, transcriptomics, and targeted metabolomics from 60 ECa and 18 benign patients. RNA sequencing enabled simultaneous profiling of active tissue-resident microbiota and host gene expression. Serum metabolomics was conducted on all patients. Identified microbial-metabolite associations were validated through in vitro co-culture experiments using peripheral blood mononuclear cells (PBMCs), cancer cell lines, RNA sequencing, and live cell imaging. RESULTS: ECa patients exhibited significantly altered microbial diversity and composition compared to benign controls. Through integrated multi-omics analysis, we identified Bacillus megaterium (BM) KCTC 3007 as a beneficial microbe associated with prolonged recurrence-free survival. In an exploratory analysis of ECa subtypes, Cupriavidus taiwanensis and Marinomonas primoryensis showed potential links to poor prognosis, although these observations warrant caution due to the limited size of certain subgroups. Tissue BM abundance positively correlated with serum trimethylamine N-oxide (TMAO) levels, particularly in postmenopausal women. In vitro experiments demonstrated that BM KCTC 3007 enhanced antitumor immunity by promoting interleukin and type I interferon expression, expanding CD8 + T cell populations, and increasing immune cell-tumor cell interactions. RNA sequencing revealed activation of interferon alpha response and immune cell proliferation pathways, with IFNAR1 identified as a key upstream regulator. TMAO treatment recapitulated these immune-activating effects, enhancing CD8 + T cell responses and preferentially inducing pyroptotic cancer cell death. CONCLUSIONS: We provide the first evidence that tissue-resident BM KCTC 3007 promotes antitumor immunity in ECa through TMAO production and subsequent type I interferon-mediated immune activation. This integrated multi-omics approach establishes a complete microbe-metabolite-host mechanistic pathway and highlights the therapeutic potential of TMAO-producing probiotic strains for ECa treatment. Video Abstract.

Female↗

PubMed2026

Characterization of the gut phageome and functional genes carried by phages in laying hens with fatty liver hemorrhagic syndrome.

BACKGROUND: The gut microbiota is closely associated with the development of fatty liver hemorrhagic syndrome (FLHS); however, the function of its viral component, particularly bacteriophages, remains poorly understood. This study compared clinical parameters and the cecal phageome between 30-week-old (W30) and 50-week-old (W50) laying hens to characterize gut phages in the context of this metabolic disorder. RESULTS: Clinical analysis revealed that the W50 group exhibited typical FLHS, accompanied by elevated serum liver function and lipid markers (P < 0.05). Functional prediction of the gut microbiota suggested a reduced lipid-metabolic capacity in W50 compared to the W30 group. A total of 20,274 phage genomes were identified from the two groups. These phages were primarily classified into 67 viral families, including Salasmaviridae, Herelleviridae, Suoliviridae, Peduoviridae, Crevaviridae, and Casjensviridae. The families Druskaviridae, Felixviridae, and Stanwilliamsviridae were uniquely detected in the W50 group. The phage community structure differed significantly between groups, with both phage diversity and richness markedly lower in W50 (P < 0.05). LEfSe analysis revealed that phage taxa such as Stegnyidae, Herpelidae, and Chasovidae were significantly enriched in the W50 group, whereas Crewdviridae, Salasmaviridae, and Castroviridae were predominantly enriched in the W30 group. Functional annotation showed that these phages encode numerous metabolism-related genes and carry antimicrobial resistance genes (ARGs) as well as virulence factor genes. Notably, the diversity of ARGs carried by W50 phages was significantly higher (P < 0.05), and ARG-rank analysis indicated a greater potential risk to human health. CONCLUSIONS: This study provides the first characterization of the gut phageome associated with FLHS in laying hens and confirms that gut phages constitute an important reservoir of ARGs. These findings offer a new perspective for understanding the pathogenesis of this disease and its associated public health risks. Video Abstract.

Animals↗

PubMed2026

Capsaicin ameliorates glycemic levels via gut microbiota-derived 5-aminolevulinic acid in mice.

BACKGROUND: Capsaicin, a natural alkaloid in chili peppers, regulates glycemic levels; however, its mechanisms and therapeutic potential remain unclear. This study aimed to elucidate the role of gut microbiota and their metabolites in mediating capsaicin's glycemic regulatory effects. We conducted experiments in specific pathogen-free (SPF) and germ-free (GF) mice, transient receptor potential vanilloid 1 (TRPV1) receptor ablation studies, and fecal microbiota transplantation (FMT) to demonstrate the involvement of gut microbiota in capsaicin-mediated glycemic control. Metagenomics and metabolomics analyses were employed to identify key microbial strains and metabolic pathways. Keystone strains and metabolites were supplemented in GF mice without capsaicin intervention to validate their effects on glycemic regulation. In vitro co-culture experiments were performed to investigate the mutualistic relationships among keystone strains under capsaicin treatment. RESULTS: Gut microbiota constitute an important component of capsaicin-mediated glycemic regulation, acting in concert with but not solely dependent on TRPV1 signaling. Gut microbiota altered by capsaicin promote the production of 5-aminolevulinic acid (5-ALA), which contributes to heme synthesis and enhances glycemic control. Supplementation with Akkermansia muciniphila, Ligilactobacillus murinus, or 5-ALA in GF mice recapitulates the glycemic benefits of capsaicin. Furthermore, capsaicin enriches Akkermansia muciniphila, which in turn supports the growth of Ligilactobacillus murinus. CONCLUSION: Capsaicin-induced changes in the gut microbiota promote 5-ALA synthesis, leading to improved glycemic control. These findings suggest that dietary or probiotic interventions targeting gut microbiota, particularly Akkermansia muciniphila and 5-ALA, may offer promising strategies for managing glycemic disorders, including type 2 diabetes (T2D). Video Abstract.

Animals↗

PubMed2026

Precisely designed keystone metabolites boost shrimp disease resistance by recruiting symbionts via the lipoxin A4-AP-1 pathway.

BACKGROUND: Gut metabolites and symbionts are indispensable for host health, yet the precise identification of keystone metabolites and construction of synthetic microbial communities (SynComs) to enhance disease resistance remains limited. RESULTS: Using Litopenaeus vannamei as a model, we identified pyruvic acid and DL-glutamine (1:2) as keystone metabolites by borrowing the microbial ecology principles of bio-indicators and driver taxa. Dietary supplementation with these metabolites sufficiently protected shrimp from white feces syndrome (WFS). Multi-omics analyses demonstrated that keystone metabolites exerted positive effects by enriching beneficial Ruegeria lacuscaerulensis, Bacillus subtilis and Nioella nitratireducens, strengthening the gut network stability, and enhancing shrimp immunity, which collectively potentiated WFS resistance. The recruited three strains were consumers and producers of the two keystone metabolites, and discriminative strains between healthy and diseased shrimp across global datasets. A SynCom constructed from the three strains (4:3:2) replicated the efficacy of keystone metabolites. Both keystone metabolites and SynCom elevated shrimp gut and hepatopancreas lipoxin A4 (LXA4) levels, which suppressed the pro-inflammatory transcription factor AP-1, as validated by in vivo inhibition assay. CONCLUSIONS: Our findings demonstrate that precisely designed keystone metabolites enhance shrimp disease resistance through the recruitment of key symbionts-LXA4-AP-1 axis. The rationally designed keystone metabolites and SynCom are compelling biocontrol solutions in improving host disease resistance. Video Abstract.

Animals↗

PubMed2026

Convergent evolution of intestinal lineages in the phylum Methanobacteriota.

BACKGROUND: Representatives of the phylum Methanobacteriota occur in various anoxic environments, but only members of the genera Methanosphaera and Methanobrevibacter exclusively colonize the digestive tract of animals. Recent phylogenomic analyses revealed that the genus Methanobrevibacter, which harbors the majority of the intestinal species, is severely underclassified and represents a family-level taxon, "Methanobrevibacteraceae", that evolved entirely in the digestive tract of animals. RESULTS: Comparative genome analysis of 158 species of Methanobacteriota, including uncultured representatives in the Genome Taxonomy Database (GTDB), demonstrated that the intestinal lineages are clearly separated from the remaining members of the phylum. They differ from the non-intestinal lineages in genome size, GC content, coding density, an increased number of pseudogenes and adhesin-like proteins, and show numerous adaptations to the copiotrophic gut environment. A decreased biosynthetic potential led to a dependence on other community members and limits the dispersal of intestinal species into other habitats, which is reflected in coevolutionary patterns with their major host groups among arthropods, ungulates, and primates. Certain lineages even engaged in symbiotic associations with intestinal protists, presumably benefiting from the H2 produced by the hydrogenosomes of their anaerobic hosts. CONCLUSIONS: Our results reveal that the transition of free-living Methanobacteriota to a host-associated lifestyle involves the same genomic changes that were previously recognized in gut bacteria and bacterial endosymbionts of protists, reflecting resemblances between the two prokaryotic domains that are caused by evolutionary convergence in similar environments.

Animals↗