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1,065 results for “Gut microbiota”
Thallium(I) exposure perturbs the gut microbiota and metabolic profile as well as the regional immune function of C57BL/6 J mice
<p><span>Intestinal microbes</span><span> regulate the development of diseases induced by environmental exposure. Thallium (Tl) is a highly toxic heavy metal</span><span>, </span><span>and its toxicity is rarely discussed in relation to gut microbes. Herein, we showed that Tl(I) exposure (10 ppm for two weeks) affected the alpha diversity of bacteria in </span><span>the ileum, colon, and </span><span>feces, but had little effect on the beta diversity of bacteria through 16S rRNA sequencing. LEfSe analysis revealed that Tl(I) exposure changed the abundance of intestinal microbiota along the digestive tract. Cecum metabolomic detection and analysis showed that Tl(I) exposure altered the abundance and composition of metabolites. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that Tl(I) exposure impaired amino acid, lipid, purine metabolism, and G protein-coupled receptor signalling pathways. A consistency test revealed a strong correlation, and a Pearson's correlation analysis showed an extensive interaction, between microorganisms and metabolites. Analysis of the intestinal immunity revealed that Tl(I) exposure suppressed the immune responses, which also had regional differences. These results identify the perturbation of the intestinal microenvironment by Tl exposure and provide a new explanation for Tl toxicity.</span></p>
Phylogenies related to: Codiversification of gut microbiota with humans
<p><span>The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, signals of codiversification were evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes, and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.</span></p>
Functional and metabolic alteration of gut microbiota in children with new-onset type 1 diabetes
<p>Worldwide T1D incidence has been steadily increasing annually over the past 30 years. The etiology of T1D is multifactorial, consisting of genetic susceptibility and environmental factors, including gut microbiota alterations. The comprehensive profiling of functional and metabolic dysbiosis of gut microbiota in T1D is lacking. To decipher the T1D-associated functional features of gut dysbiosis, we performed integrative metagenomic and metabolomic analyses in pediatric patients with new-onset T1D.</p>
Temporal patterns of gut microbiota in lemurs (Eulemur rubriventer) living in intact and disturbed habitats.
<p>This data set includes the R scripts (combined into one R markdown document) and input files needed to create the main text figures and major analyses for the paper "Grieneisen L, Hays A, Cook E, Blekhman R, and Tecot S. 2024. Temporal patterns of gut microbiota in lemurs (<em>Eulemur rubriventer</em>) living in intact and disturbed habitats. American Journal of Primatology." </p>
Figure 1 in Effect of Moringa olifera leaves on growth and gut microbiota of Nile tilapia (Oreochromis niloticus)
Figure 1. Growth performance parameters.
Infection of mice by the enteroaggregative E. coli strain 042 and two mutant derivatives overexpressing virulence factors: impact on disease markers, gut microbiota and concentration of SCFAs in feces
<p>This dataset contains raw sequencing data from the microbiota analysis conducted in the enteroaggregative E. coli strain 042 study. The data includes FASTQ files generated from Illumina sequencing, along with metadata describing the sample collection and processing methods.</p>
Data from "Exploring Gut Microbiota Profile Induced by Antipsychotics in Schizophrenic Patients: Insights from an Eastern European Pilot Study", Nita (Ilie) et al. 2025
<p>Dataset containing raw demultiplexed FASTQ files of the sequenced samples, generated by the Illumina MiSeq platform. </p> <p>MiSeq_demultiplexed-V3_V4-HC_SCZ.zip - MiSeq raw sequences of the V3-V4 region 16S rRNA gene from subject fecal material. This ZIP file contains the FASTQ files of the paired-end reads (R1: forward reads; R2: reverse reads) produced for each sample using the MiSeq platform.</p> <p>metadata-HC_SCZ.csv - The list of sequenced samples and associated metadata.</p>
Drivers of change and stability in the gut microbiota of an omnivorous avian migrant exposed to artificial food supplementation
<p>Human activities shape resources available to wild animals, impacting diet and likely altering their microbiota and overall health. We examined drivers shaping microbiota profiles of common cranes (Grus grus) in agricultural habitats by comparing gut microbiota and crane movement patterns (GPS-tracking) over three periods of their migratory cycle, and by analyzing the effect of artificially-supplemented food provided as part of a crane-agriculture management program. We sampled fecal droppings in Russia (non-supplemented, pre-migration) and in Israel in late fall (non-supplemented, post-migration) and winter (supplemented and non-supplemented, wintering). As supplemented food is typically homogenous, we predicted lower microbiota diversity and different composition in birds relying on supplementary feeding. We did not observe changes in microbial diversity with food supplementation, as diversity differed only in samples from non-supplemented wintering sites. However, both food supplementation and season affected bacterial community composition and led to increased abundance of specific genera (mostly Firmicutes). Cranes from the non-supplemented groups spent most of their time in agricultural fields, likely feeding on residual grain when available, while food-supplemented cranes spent most of their time at the feeding station. Thus, non-supplemented and food-supplemented diets likely diverge only in winter, when crop rotation and depletion of anthropogenic resources may lead to a more variable diet in non-supplemented sites. Our results support the role of diet in structuring bacterial communities and show that they undergo both seasonal and human-induced shifts. Movement analyses provide important clues regarding host diet and behavior towards understanding how human-induced changes shape the gut microbiota in wild animals.</p>
Does ivermectin treatment for endemic hookworm infection alter the gut microbiota of endangered Australian sea lion pups?
<p>The gut microbiota is essential for the development and maintenance of the hosts' immune system. Disturbances to the gut microbiota in early life stages can result in long-lasting impacts on host health. This study aimed to determine if topical ivermectin treatment for endemic hookworm (Uncinaria sanguinis) infection in endangered Australian sea lion (Neophoca cinerea) pups resulted in gut microbial changes. The gut microbiota was characterised for untreated (control) (n = 23) and treated (n = 23) Australian sea lion pups sampled during the 2019 and 2020/21 breeding seasons at Seal Bay, Kangaroo Island. Samples were collected pre- and post-treatment on up to four occasions over a four-to-five-month period. The gut microbiota of untreated (control) and treated pups in both seasons were dominated by five bacterial phyla, Fusobacteria, Firmicutes, Proteobacteria, Actinobacteria, and Bacteroides. A significant difference in alpha diversity between treatment groups was seen in pups sampled during the 2020/21 breeding season (p = 0.008), with higher richness and diversity in treated pups. Modeling the impact of individual pup identification (ID), capture, pup weight (kg), standard length (cm), age, and sex on beta diversity revealed that pup ID accounted for most of the variation (35% in 2019 and 42% in 2020/21), with pup ID, capture, and age being the only significant contributors to microbial variation (p < 0.05). There were no statistically significant differences in the composition of the microbiota between treatment groups in both the 2019 and 2020/21 breeding seasons, indicating that topical ivermectin treatment did not alter the composition of the gut microbiota. To our knowledge, this is the first study to characterise the gut microbiota of free-ranging Australian pinniped pups, compare the composition across multiple time points, and consider the impact of parasitic treatment on the overall diversity and microbial composition of the gut microbiota. Importantly, the lack of compositional changes in the gut microbiota with topical ivermectin treatment supports the utility of topical ivermectin as a safe and minimally invasive management strategy to enhance pup survival in this endangered species. </p>
Dataset supporting the paper "Effect of prebiotic fermentation products from primary human gut microbiota on an in vitro intestinal model"
<p>Short chain fatty acids (SCFA) originate from the bacterial fermentation of dietary fibre in the gastrointestinal tract. They are hypothesised to play a key role in microbiota–gut–brain crosstalk and the effect of individual SCFAs or mixtures thereof has been broadly studied. However, studies using fermentation products to evaluate the effect of microbiota-targeted interventions, such as prebiotics, probiotics, or diet, are sparse, particularly in humans. In addition, the complexity of these physiological processes translates as a challenge for their simulation<em> in vitro</em>. In this work, fermentation products of prebiotic-enriched media by bacteria present in primary human faecal samples were tested using an epithelium model based on a Caco-2/HT29-MTX co-culture. The prebiotics raftilose and fructo-oligosaccharides (FOS) were tested and the experimental conditions (contact time and minimal dilution) optimised to avoid cytotoxicity. None of the conditions tested compromised the intestinal epithelium integrity as verified by the TEER and the expression of the tight junction-specific protein – occludin. In addition, none of the fermentation products caused an inflammatory response as determinedby the expression of inflammatory genes by qRT-PCR. The products of fermentation of media enriched with FOS showed a moderate protective effect against the formation of reactive oxygen species. This work provides an important basis for the development of <em>in vitro</em> models using a simple approach to evaluate host-gut microbiota interactions, using co-cultures of intestinal cell lines and products of <em>in vitro</em> fermentations by primary human gut microbiota. </p>
Supplementary materials. Publication "Three-way relationships between gut microbiota, helminth assemblages and bacterial infections in wild rodent populations" by Bouilloud et al.
<p><strong>Supplementary information</strong></p> <p><strong>Supplementary Figure S1</strong>. Maps showing the sampling area (left) and localities (right) in France. Forests are indicated in green and water in blue. The four sampling localities are represented with a colored polygon. The arrow indicates the North.</p> <p> </p> <p><strong>Supplementary Figure S2</strong>. Composition of the gut bacteriota. The relative abundance of six phyla representing 99% of the total composition is represented. Individuals are grouped by sampling localities, which are ordered from North to South. (A) Bar graph shows individual variation in phyla composition (phylum=color). (B) Box and whisker plots represent median and interquartile values for each phylum. Black dots correspond to mean values, and colored dots correspond to individuals.</p> <p> </p> <p><strong>Supplementary Figure S3</strong>. Variations of alpha diversity with individual factors, for the gut bacteriota (family level), pathogenic bacteria and gastro-intestinal helminths of bank voles. Alpha diversity is estimated using the specific richness (A, B and C) and the Shannon index (D, E and F). In graphs C and F, the blue line corresponds to the linear regression line.</p> <p> </p> <p><strong>Supplementary Figure S4</strong>. Relationships between the composition of the gut bacteriota, pathogenic bacteria and gastro-intestinal helminth communities: The db-RDA triplot shows the structure of the gut bacteriota at the phylum level and the correlations with the intra-host parasite communities. The arrows correspond to the significant explanatory variables. Each point corresponds to an individual, and the colors correspond to the different sampling localities.</p> <p> </p> <p><strong>Supplementary Table S1. </strong>Variation of the Firmicutes/Bacteroidetes ratio with localities and individual factors.</p> <p> </p> <p><strong>Supplementary Table S2. </strong>Alpha diversity metrics and statistics for the gut bacteriota, pathogenic bacteria and helminth communities of bank voles.</p> <p> </p> <p><strong>Supplementary Table S3. </strong>Beta diversity metrics and statistics for the gut bacteriota, pathogenic bacteria and helminth communities of bank voles</p>
Data for "Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota"
<p>MD simulation data of OxlT. Trajectory data and NAMD input files are included. The first 500 ns trajectory that starts from the occluded conformation with a transition to the outward-open conformation is in the OxlT-occ directory. The 200 ns trajectories that start from the outward-open conformation with different protonation states of K355 are in the OxlT-out directory. </p>
Gut microbiota inter-species interactions shape the response of Clostridioides difficile to clinically relevant antibiotics
<p>In the human gut, the growth of <em>Clostridioides difficile </em>is impacted by a complex web of inter-species interactions with members of human gut microbiota. We investigate the contribution of inter-species interactions on the antibiotic response of <em>C. difficile </em>to clinically relevant antibiotics using bottom-up assembly of human gut communities. We discover two classes of microbial interactions that alter <em>C. </em>difficile’s antibiotic susceptibility: infrequent increases in tolerance at high antibiotic concentrations and frequent growth enhancements at low antibiotic concentrations. Based on genome-wide transcriptional profiling data, we demonstrate that metal sequestration due to hydrogen sulfide production by the prevalent gut species <em>Desulfovibrio piger </em>increases metronidazole tolerance of <em>C. difficile</em>. Competition with species that display higher sensitivity to the antibiotic than <em>C. difficile </em>leads to enhanced growth of <em>C. difficile </em>at low antibiotic concentrations. A dynamic computational model identifies the ecological design principles driving this effect. Our results provide a deeper understanding of ecological and molecular principles shaping <em>C. difficile</em>’s response to antibiotics, which could inform therapeutic interventions.</p>
Disruption of fish gut microbiota composition and holobiont's metabolome during a simulated Microcystis aeruginosa (Cyanobacteria) bloom
<p>This archive contains the R code, QIIME2 script and datasets used to perform the analyses and figures in the manuscript.</p>
The gut microbiota in chronic obstructive pulmonary disease varies by CT-verified emphysema status
<p><strong><span>Background and aim</span> </strong></p> <p><span>The association of the gut microbiota to </span><span>chronic obstructive pulmonary disease (COPD)</span><span> phenotypes is underexplored. We aimed to compare</span><span> stool samples from COPD patients and healthy controls and relate findings to common COPD phenotypes. </span></p> <p><strong><span>Methods</span></strong></p> <p><span>Single-centre case-control study with 62 current and former smoking COPD patients and 49 controls. DNA was extracted from stool samples, and the V3V4-region of the bacterial 16S-rRNA gene was sequenced. Emphysema was defined based on thoracic computed tomography (CT thorax) low attenuating areas ≥/<10% at threshold -950 and -910 Hounsfield units respectively. Microbial data were analysed with QIIME 2 and R.</span></p> <p><strong><span>Results</span></strong></p> <p><span>The genus Veillonella was decreased and a genus belonging to class Clostridia was increased in COPD compared to healthy controls. Beta diversity measure Bray Curtis differed in emphysema compared to controls, and 27 genera were differentially abundant in emphysema vs. controls. Nine of these genera belonged to the family Lachnospiraceae. Lung function, blood counts and COPD assessment test scores were correlated with the relative abundance of several genera. Some of the genera showing the strongest correlation to lung function belonged to the family Lachnospiraceae. </span></p> <p><strong><span>Conclusion</span></strong></p> <p><span>We found small but statistically significant differences in the gut microbiota of COPD versus controls. Larger differences were seen in the gut microbiota according to CT-verified emphysema status. Correlations between the gut microbiota and lung function, blood cell counts, and CAT score were found. </span></p>
Immune stimulation induced changes to the native gut microbiota of bumble bees
<p>Understanding factors influencing the maintenance and membership of beneficial host-associated microbial communities is central to understanding ecological, evolutionary, and health consequences of these communities for their hosts. Host immunity is often implicated as a potential regulator of these microbiota. However, conversely, immunity may play a disruptive role, with immune responses to infection causing collateral damage. Such effects may be more prominent from innate immune responses, with more rapid-acting and relatively non-specific components. We investigated how upregulation of antibacterial immunity in the bumble bee <em>Bombus</em> <em>impatiens</em> affects the core gut microbiota, testing the hypothesis of immunity-induced perturbation of the beneficial microbiota structure. Freshly emerged adult bees received a native microbiota inoculation before being subjected to non-pathogenic immune stimulation treatments. We quantified the microbial community using 16S rRNA amplicon sequencing and targeted qPCR. We find colonization of the core member <em>Gilliamella</em> is altered by immune stimulation treatment. Additionally, a positive association in communities between <em>Gilliamella</em> and another core bacteria, <em>Snodgrassella</em> <em>alvi</em>, is perturbed. These changes are indicative of immune-response-induced dysbiosis. As such, the potential for collateral perturbation of beneficial microbial communities upon a host's innate immune response may contribute to immune costs, shaping the evolutionary optimization of immune investment.</p>
Understanding the Role of Gut Microbiota in Hyperphagia in Prader-Willi Syndrome
ClinicalTrials.gov study NCT05541003. IPD Sharing: NO. Countries: 1. Publications: 7.
Effects of Probiotics on Gut Microbiota, Endocannabinoid and Immune Activation and Symptoms of Fatigue in Dancers
ClinicalTrials.gov study NCT05567653. IPD Sharing: NO. Countries: 1. Publications: 46.
Effects of S. Boulardii and Amoxicillin/Clavulanate on Gut Microbiota
ClinicalTrials.gov study NCT01473368. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Metagenomic & Metabolomic Study: Bifidobacterium Probiotic Effects on Gut Microbiota & SCFA in Preterm NICU Infants
ClinicalTrials.gov study NCT07213414. IPD Sharing: NO. Countries: 1. Publications: 1.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
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