Safety and toxicity assessment of Lactobacillus salivarius AP-32 with Probiotic potential in vivo and in vitro.

The study evaluated elderberry extract (EBE), containing 22.45% polyphenols and 10.60% total dietary fiber, on human gut ecosystems using two Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) models inoculated with feces from donors with Type-B and Type-P enterotypes. EBE supplementation induced donor-specific changes, increasing acetic and propionic acids and total polyphenol content. It reshaped the gut microbiome by lowering the Firmicutes-Bacteroidetes ratio and boosting beneficial species such as Akkermansia muciniphila , Bifidobacterium longum , and Bacteroides dorei , while reducing harmful bacteria. Genes linked to amino acid metabolism, vitamin B6 biosynthesis, plant secondary metabolite production, and glutathione metabolism increased, with effects lasting after washout. Functional changes correlated with specific species associated with propanoate metabolism, amino acid metabolism, and plant metabolite biosynthesis. These results demonstrate that daily intake of 600 mg EBE for two weeks modulates the gut ecosystem through both individual-dependent and independent pathways, supporting personalized nutrition approaches. • Elderberry extract altered gut microbiome in vitro in a donor-specific way • Elderberry extract supplementation enriched potentially beneficial taxa • Elderberry extract enhanced acetate, propionate and polyphenol levels in gut • Elderberry extract enhanced functional gut metagenomes

Exploring Origanum dictamnus as a functional food ingredient: Phytochemical characterization and gut motility modulation.

Degradation of konjac glucomannan-modified alginate hydrogels by human gut microbiota from healthy, obese, and Inflammatory Bowel Disease (IBD) populations: Implications for customized probiotic delivery

High-amylose starch (HAS) is gaining attention in biotechnology for its thermal stability, structural resilience and health benefits. Its dense crystalline structure hinders hydrolysis by human gut enzymes, making it a promising source of type 2 resistant starch for hydro-thermal and enzymatic upgrading. 4-α-Glucanotransferases (4αGTs) of glycoside hydrolase family 77 catalyse disproportionation of α-1,4-glucan chains in HAS, enhancing functionality and nutritional properties. Here, a 4αGT, ParGT from the hyperthermophilic archaeon Pyrobaculum arsenaticum, identified in a metagenomic dataset from Pisciarelli hot spring (85°C, pH5.5; Naples, Italy), showed highest activity at 100°C and pH5.5, and specific activity of maltotriose disproportionation at 75°C of 1170U/mg. ParGT effectively modified HAS granules under controlled heating (annealing) at 75°C, altering crystallinity, surface order and chain length. Comparative analysis of native, heat-treated and ParGT-modified HAS granules from wheat, potato, maize, and barley revealed distinct effects of botanical source, enzymatic modification, and heating. Notably, ParGT increased the resistant starch (RS) contents in wheat and potato HASs subjected to in vitro digestion. Interfacial kinetics correlated the increased resistance to decreased density of glucoamylase attack sites. Overall, ParGT showed strong potential in enzyme- and hydro-thermal modifications developing starch-based ingredients for health and food applications.

Fungal dysbiosis is increasingly recognized as a critical factor in gut-related diseases, yet natural antifungal agents remain scarce. Lycopene is known to influence gut health, but its effects on fungi also remain unclear. This study investigated the impact of lycopene on the gut microbiota, particularly gut fungi. In vivo, lycopene significantly promoted the growth of beneficial species such as Lactobacillus johnsonii and altered microbial vitamin B6 metabolism. Metabolomics analysis further confirmed that lycopene enhanced vitamin B6 metabolism. In vitro fermentation using human gut microbiota confirmed similar effects. Then, inhibition of bacteria and fungi, along with the antagonism of vitamin B6, confirmed significant changes in the abundance of L. johnsonii and Trichocladium, mediated through vitamin B6 metabolism. Further monoculture experiments with Trichocladium demonstrated that vitamin B6, rather than lycopene itself, significantly reduced the abundance of Trichocladium. Structural equation modeling revealed lycopene's potential in modulating fungi within the gut ecosystem.

Large-scale metaproteomics of human gut microbiota reveals microbial functions in metabolic diseases and aging.

Mediterraneibacter gnavus is a human symbiotic gut bacterium whose abundance often increases in patients with various diseases, such as active inflammatory bowel disease (IBD). However, the genetic factors governing its gut colonization and pathogenicity remain elusive due to the lack of genetic modification systems. In this study, we developed several genetic tools for M. gnavus, including a shuttle vector, an inducible promoter, fluorescent reporters, and systems for gene disruption and deletion. Using these genetic tools, we constructed mutants for six of the eight sortase-encoding genes in M. gnavus ATCC 29149 and identified those involved in the surface presentation of capsular polysaccharide (CPS) and superantigen-like proteins. We also identified a CPS biosynthetic gene cluster adjacent to the sortase gene and demonstrated that CPS production is crucial for competitive colonization in germ-free mouse intestines. Notably, CPS production was inversely correlated with inflammatory activity, and CPS cluster-positive strains were more prevalent in healthy individuals than in Crohn's disease patients. These findings suggest that CPS contributes to the modulation of inflammation and pathogenesis. This study highlights the potential of precise gene-modification systems to uncover genetic determinants of intestinal colonization and pathogenesis in gut bacteria.

Human gut microbiota is associated with obesity. Gut microbiota-derived extracellular vesicles (EVs), lipid coated nanoparticles secreted by bacteria, have been suggested as a communication mechanism between gut microbiota and the host. This study characterized the effect of Roux-en-Y gastric bypass (RYGB) on gut microbiota and gut microbiota-derived EVs in patients with obesity. Fecal samples were collected from 30 recruited patients at baseline and 6 months after surgery. EVs were isolated from fecal samples, and their origin and protein content were analyzed. The number of unique proteins was increased in gut microbiota-derived EVs after the surgery as compared to baseline. A significant difference in both microbiota composition (p = 0.001; PERMANOVA) and microbiota-derived EVs (p = 0.001; PERMANOVA) was observed in response to surgery. Based on 16S rRNA gene sequencing data, a random forest classifier accurately classified both gut microbiota (AUC = 0.93) and EVs (AUC = 0.80) to baseline and after surgery groups. This study found that gastric bypass surgery altered both the composition and characteristics of gut microbiota and gut microbiota-derived EVs in patients with obesity. Thus, gut microbiota-derived EVs may play a role in obesity and influence the health effects of bariatric surgery beyond the gut. Trial Registration: ClinicalTrials.gov identifier: NCT00950003.

Phages dominate the human gut virome and are known for their ability to prey on bacteria and shape microbiota. However, their response to diet has only been elucidated using small-scale studies. By integrating a massive meta-analysis of 6932 diet-associated metagenomes with a time-resolved mouse model of a high-fat diet and polysaccharide intake, the impact of diet on the gut virome and phage-bacterial interactions was systematically characterized. Diet types, particularly high-fat and polysaccharide-rich diets, exert the strongest shaping force on the gut virome, enhancing the crosstalk between phages and bacteria. High-fat diets promote changes in phage abundance across a broad taxonomic range, from 34.21% to 50.00%, drive phages of diet-associated bacteria toward a lytic lifestyle, and remarkably enrich auxiliary metabolic genes related to amino acid metabolism. Conversely, fucoidan reversed HFD-induced dysbiosis and enhanced phage-mediated horizontal gene transfer by 8.5-fold relative to the baseline. crAssphages and Parabacteroides phages may be important contributors, broadly supporting horizontal gene transfer and auxiliary metabolism or strengthening phage-host interactions in polysaccharide interventions, including fucoidan supplementation. These findings provide a comprehensive landscape of diet-driven cross-kingdom interactions and phage-mediated gene exchange in the gut, offering new insights into potential strategies for precise nutritional interventions targeting the intestinal microbiota.

The human gut microbiome is important for host health, yet over 60% of gut species remain uncultured and inaccessible to experimental manipulation. Here, we analyze 11,115 human gut metagenomes from 39 countries, 13 noncommunicable diseases, and healthy individuals to understand the clinical relevance of the uncultured microbiome worldwide. We identify 317 species linked to distinct clinical states, noting an overrepresentation of uncultured bacteria in healthy subjects. The genus CAG-170 emerged as the strongest health-associated lineage across multiple diseases and geographies, standing as the most central taxon based on ecological networks of healthy populations. We find that CAG-170 is temporally stable, with its abundance and subspecies diversity negatively correlated with gut imbalance over time. Functional predictions show CAG-170 species have greater vitamin B12 biosynthesis capacity and cross-feeding potential, providing important biological insights into this elusive genus. Our findings shed light on the underexplored role of uncultured gut species in health and disease.

Gut DNA virome enterotype dictates inflammation heterogeneity through tuning the phage-bacteria-sphingosine-intestine axis in Crohn's disease.

Dietary fiber (DF) has a profound influence on human health mainly by modulating the gut microbiota. This review provides an overview of DF derived from cereals, legumes, fruits, vegetables, fungi, and seaweeds, specifically addressing the relationship between microbial utilization and source-specific structural characteristics (such as linking patterns, conformation, solubility, and fermentability). Due to these structural properties, different DFs display selective microbial responses that favor fermentation and the production of short-chain fatty acids (SCFAs). These microbial responses and fermentation-derived metabolites associated with DF intake may contribute to reduced risk of obesity, diabetes, inflammatory bowel disease, and other chronic disorders. This review does not address the trial heterogeneity, dose response, safety, and conflicting evidence, and much of the available evidence is largely observational and heterogeneous. Future studies should focus on dose–response trials of defined DF structures with standardized microbiome and metabolomic endpoints, including validation in human interventions. This review summarizes the DF source and structure, selective changes in the microbiota across various study types, including in vitro, animal models, and human studies, and how these relate to overall health.

Metagenomics enables detailed profiling of genes encoding antimicrobial resistance. However, most studies focus exclusively on antibiotic resistance genes (ARGs), excluding those associated with non-antibiotic antimicrobials (metals, biocides), and often rely on methods with low-sensitivity and low-specificity. Furthermore, they rarely examine populations exposed to minimal anthropogenic pollution. We analyzed fecal resistomes of 95 Wayampi individuals, an Indigenous community in remote French Guiana, using a targeted metagenomic capture platform covering 8667 genes, including ARGs, metal resistance genes (MRGs) and biocide resistance genes (BRGs) (PMID: 29335005). Resistome profiles were compared with those of Europeans to assess population-level differences. ARG richness was similar between groups (259 in Wayampi vs. 264 in Europeans, 159 shared), but MRGs + BRGs gene richness was significantly higher in Wayampi (11,930 vs. 7419). Most genes appeared in a minority of individuals (mean 5% for ARGs, 2% for MRGs + BRGs), but several ARGs for tetracyclines [tet(32), tet(40), tet(O), tet(Q), tet(W), tet(X), tetAB(P)], aminoglycosides (ant6'-I, aph3-III), macrolides (ermB, ermF, mefA), and sulfonamides (sul2) were present in all individuals. Tetracycline resistance genes predominated overall, while beta-lactam resistance genes were more common in Wayampi, and genes conferring resistance to aminoglycosides, amphenicols, and folate inhibitors were more frequent in Europeans. Among MRGs, copper and arsenic resistance genes prevailed in both groups, followed by those for zinc, iron, cobalt, and nickel. Up to 76% of Wayampiis carried acquired MRGs for copper (pcoABCDRS and tcrB), silver (silACFPRS), arsenic (ars), and mercury (mer) detoxification. Shannon diversity indices were similar for ARGs, MRGs, and BRGs, but composition and evenness differed significantly. UMAP and ADONIS analyses distinguished cohorts based on ARG profiles (p < 0.001), but not on MRGs or BRGs. Correlation analysis revealed conserved gene-sharing networks and introgression of acquired ARGs and MRGs within both gut microbiomes. The diverse and balanced Wayampi resistome reflects a less perturbed microbiome compared to industrialized populations, and reveals a background of "core" and "shell" acquired ARGs and MRGs, consistent with the "robust-yet-fragile" architecture of scale-free networks. The patchy yet resilient gene distribution suggests varying levels of conserved gene sharing highways among populations, likely shaped by long-term microbial-human evolution, and supports a broader view on acquired antimicrobial resistance. Video Abstract.

P2-like viruses (P2Vs), temperate phages of the Peduoviridae family, possess a lysogenic lifestyle that renders traditional isolation unsuitable, hindering our understanding of their diversity and ecological roles. Utilizing profile-hidden Markov models to analyze public databases, this study achieved four major advances: (1) Identified 5945 P2V genomes and built the P2V Genome Dataset (P2VGD), expanding known genomes 48-fold; (2) Phylogenetic classification into 13 superclades and 4671 genus-level clusters, a 106-fold diversity increase; (3) Identification of 757 auxiliary metabolic genes with biome-specific metatranscriptomic activities: human gut P2Vs encode antibiotic efflux and cell-wall remodeling enzymes, while oligotrophic marine P2Vs express glycan-scavenging enzymes; (4) Uncovering their widespread distribution across diverse biomes, dominated by host-associated environments but extending to under-sampled natural ecosystems. These findings greatly expand the genomic and functional understanding of P2Vs, highlighting their biological strategies in host adaptation, virus-host co-evolution, and microbiome dynamics.

6:2 polyfluoroalkyl phosphate diester (6:2 diPAP) is a prevalent environmental contaminant to which humans are regularly exposed. Environmental microbes can biotransform 6:2 diPAP, and the human gut microbiome can biotransform its congener, 8:2 monoPAP. While the human gut microbiome is highly variable between individuals, potential variability in PAP biotransformation has yet to be assessed. We address this gap using six cohorts (A-F) to examine in vitro biotransformation of 6:2 diPAP by the human gut microbiome. Biotransformation pathways of 6:2 diPAP and their connections to the composition of microbial taxa were assessed using gas chromatography mass spectrometry (GC-MS), liquid chromatography tandem mass spectrometry (LC-MS/MS) and 16S rRNA amplicon sequencing. All cohorts biotransformed 6:2 diPAP but differed in their downstream perfluoroalkyl acid (PFAA) profiles, suggesting diverse biotransformation pathways. Microbial community analysis showed similar alpha diversity across cohorts, while the degree of difference between cohorts varied. The analysis confirmed the initial composition of each cohort's microbial community had a bearing on products stemming from 6:2 diPAP transformation, likely driven by low-abundance microbial taxa. These findings underscore the complexity of microbe-mediated polyfluoroalkyl substance (PFAS) transformation and highlight the need for mechanistic studies that identify the genetic controls governing PFAS transformations in the gut microbiome.

Microbiota metabolite lithocholic acid in cancer: Mechanisms and therapeutic potential.

The gut microbiome is essential for neurodevelopment via bidirectional gut-brain axis signaling, yet environmental chemicals can potentially disrupt this communication by altering community structure and xenobiotic metabolism. In this study, we investigated whether the fungicide azoxystrobin, a known metabolic disruptor, modulates microbiome composition and function to influence neurobehavior. We utilized a simplified human gut microbiota model (SIHUMIx) and a vertebrate host model (larval zebrafish) to elucidate microbiome-mediated mechanisms of xenobiotic neurotoxicity. SIHUMIx was exposed to azoxystrobin for 7 days at 10% of the acceptable daily intake, followed by recovery. Integrated metaproteomic and metabolomic analyses revealed functional reprogramming of the microbiota, characterized by upregulation of vitamin and cofactor biosynthesis, nutrient acquisition, and detoxification pathways, and decreased carbohydrate fermentation and amino acid turnover, consistent with reduced short-chain fatty acid levels. Microbiome-depleted and SIHUMIx-inoculated larvae were exposed to azoxystrobin at 4 days post fertilization and neurobehavioral outcomes were assessed after 24 h using the Visual and Acoustic Motor Response assay. Azoxystrobin exposure disrupted non-associative habituation learning independent of microbiome status but induced dark phase-hyperactivity only in colonized larvae, indicating a microbiome-dependent phenotype. Targeted metabolomics revealed lower serotonin levels in microbiome-depleted larvae relative to colonized controls, and that azoxystrobin exposure reduced serotonin in colonized larvae toward depleted levels. These results suggest that microbiota-dependent serotonergic signaling may modulate host responses to azoxystrobin. This integrated ex vivo-in vivo approach supports the concept that the microbiome is a key determinant of neurotoxic responses and underscores the importance of incorporating microbiome-mediated effects into chemical risk assessment frameworks.

Alterations of epithelial barrier integrity and immune response play a key role in the pathogenesis of allergic diseases and represent promising targets for nutritional interventions. Selected postbiotics and plant-derived compounds have been proposed as potential modulators of epithelial barrier and immune function. We investigated the effects of a novel food supplement combining heat-inactivated Lacticaseibacillus rhamnosus GG, butyrate, Quercetin, and Perilla frutescens extracts on epithelial barrier function and innate immunity in an experimental model of the human epithelial gut barrier. Exposure to the food supplement resulted in epithelial barrier integrity enhancement, consisting of increased transepithelial electrical resistance, tight-junction protein expression, mucus production, and enterocyte differentiation. Moreover, the formulation markedly stimulated the expression of the innate immunity peptides β-defensin-2 and cathelecidin LL-37. The novel food supplement induces a beneficial modulation of the epithelial gut barrier and immune response. These findings support its potential use as a functional food strategy to restore mucosal homeostasis and to promote immune tolerance in allergic diseases.

Uncovering the relationship between the human ocular surface microbiome and gut microbiome.