In vitro human gut microbiota
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ABSTRACT:
PROVIDER: PRJNA844548 | ENA |
REPOSITORIES: ENA
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Project description:The link between the gut microbiota of a human being (a complex group of microorganism including not only bacteria but also fungi, viruses, etc.,) that form an ecosystem in his gastrointestinal tract and his physiological state is nowadays unquestionable. Metaproteomics has emerged as a useful technique to characterize this microbial community, not just taxonomically, but also focusing on specific biological processes carried out by gut microbiota that may have an effect in the host health or pathological state. In order to characterize this host-microbiota inter-relation, we carried out the metaproteomic study of 6 stool samples from 6 healthy adults. A total of 37 080 peptide sequences and 10 686 protein groups were identified in this study. Regarding taxonomic information, we found a total of 247 taxa among 105 were species. Interesting contributions of microbiota metabolism to human host physiology has also been described.
2021-07-06 | PXD020786 | Pride
Project description:ObjectiveContrary to the long-standing prerequisite of inducing selective (i.e. bifidogenic) effects, recent findings suggest that prebiotic interventions lead to ecosystem-wide microbiota shifts. Yet, a comprehensive characterization of this process is still lacking. Here, we apply 16S rDNA microbiota profiling and matching (GC-MS) metabolomics to assess the consequences of inulin fermentation both on the composition of the colon bacterial ecosystem and fecal metabolites profiles.DesignFecal samples collected during a double blind, randomized, cross-over intervention study (NCT02548247) set up to assess the effect of inulin consumption on stool frequency in healthy adults with mild constipation were analyzed. Fecal microbiota composition and metabolite profiles were linked to the study’s clinical outcome as well as to quality-of-life measurements recorded.ResultsWhile fecal metabolite profiles were not significantly altered by inulin consumption, our analyses did detect a modest effect on global microbiota composition. At the same time, specific inulin-induced changes in relative abundances of Anaerostipes, Bilophila, and Bifidobacterium were identified. The observed decrease in Bilophila abundances following inulin consumption was associated with both softer stools and a favorable change in constipation-specific quality of life measures.ConclusionsEcosystem-wide analysis of the effect of a dietary intervention with prebiotic inulin-type fructans on the colon microbiota revealed that this effect is specifically associated to three genera, one of which (Bilophila) representing a promising novel target for mechanistic research.
| EGAS00001002173 | EGA
Project description:A comparison of the in vitro effects of 2-fucosyllactose and lactose on the composition and activity of gut microbiota from infants and toddlers
| PRJNA701368 | ENA
Project description:Interactions between the gut microbial ecosystem and host lipid homeostasis are highly relevant to host physiology and metabolic diseases. We present a comprehensive multi-omics view of the effect of intestinal microbial colonization on hepatic lipid metabolism, integrating transcriptomic, proteomic, phosphoproteomic, and lipidomic analyses of liver and plasma samples from germfree and specific pathogen-free mice. Microbes induced monounsaturated fatty acid generation by stearoyl-CoA desaturase 1 and polyunsaturated fatty acid elongation by fatty acid elongase 5, leading to significant alterations in glycerophospholipid acyl-chain profiles. Germfree mice contained more abundant saturated and poly-unsaturated lipids, whereas colonized mice primarily contained mono-unsaturated lipids. A composite classification score calculated from the observed alterations in fatty acid profiles in germfree mice clearly differentiated antibiotic-treated mice from untreated controls with high sensitivity. Mechanistic investigations revealed that acetate originating from gut microbial degradation of dietary fiber serves as precursor for hepatic synthesis of C16 and C18 fatty acids and their related glycerophospholipid species that are also released into the circulation.
2018-07-20 | PXD010412 | Pride
Project description:The link between the gut microbiota and the human physiological state has been demonstrated in recent years. High gut microbiota diversity has been linked to many beneficial functions necessary or human health, while dysbiosis has been correlated to different pathological states. In this context, the study of the gut microbiota results of high relevance been necessary the development of different techniques capable of characterizing this complex ecosystem. Metaproteomics has been proved useful in the characterization of complex protein samples becoming a suitable tool for the study of these microbial communities. However, due to the complexity of these samples, protein extraction protocols may affect metaproteomics results. In this context, we evaluated stool sample processing (SSP) and microbial cell disruption, assessing the impact of different protocol modifications in the number of peptides and proteins identified. We compared different stool processing conditions and microbial cell disruption methods in terms of protein and peptide identifications and taxonomic profiles.
2021-07-06 | PXD025659 | Pride
Project description:The adult human gut microbial community is typically dominated by two bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from E. rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the former possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole genome transcriptional profiling of both organisms in their distal gut (cecal) habitat as well as host responses, high resolution proteomic analysis of cecal contents, and biochemical assays of carbohydrate metabolism. B. thetaiotaomicron adapts to E. rectale by upregulating expression of a variety of polysaccharide utilization loci (PULs) encoding numerous glycoside hydrolase gene families, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is utilized by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of major gut bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability. The interactions between E. rectale and B. thetaiotaomicron were characterized by performing whole genome transcriptional profiling of each species after colonization of gnotobiotic mice with each organism alone, or in combination. E. rectale was also profiled during in vitro growth.
2010-05-22 | E-GEOD-14737 | biostudies-arrayexpress
Project description:The capacity of a microbial synbiotic to rescue the in vitro metabolic activity of the gut microbiome following perturbation with alcohol or antibiotics
| PRJNA689370 | ENA
Project description:The effect of oral microbiota on the intestinal microbiota has garnered growing attention as a mechanism linking periodontal diseases to systemic diseases. However, the salivary microbiota is diverse and comprises numerous bacteria with a largely similar composition in healthy individuals and periodontitis patients. Thus, the systemic effects of small differences in the oral microbiota are unclear. In this study, we explored how health-associated and periodontitis-associated salivary microbiota differently colonized the intestine and their subsequent systemic effects by analyzing the hepatic gene expression and serum metabolomic profiles. The salivary microbiota was collected from a healthy individual and a periodontitis patient and gavaged into C57BL/6NJcl[GF] mice. Samples were collected five weeks after administration. Gut microbial communities were analyzed by 16S ribosomal RNA gene sequencing. Hepatic gene expression profiles were analyzed using a DNA microarray and quantitative polymerase chain reaction. Serum metabolites were analyzed by capillary electrophoresis time-of-flight mass spectrometry. The gut microbial composition at the genus level was significantly different between periodontitis-associated microbiota-administered (PAO) and health-associated oral microbiota-administered (HAO) mice. The hepatic gene expression profile demonstrated a distinct pattern between the two groups, with higher expression of Neat1, Mt1, Mt2, and Spindlin1, which are involved in lipid and glucose metabolism. Disease-associated metabolites such as 2-hydroxyisobutyric acid and hydroxybenzoic acid were elevated in PAO mice. These metabolites were significantly correlated with Bifidobacterium, Atomobium, Campylobacter, and Haemophilus, which are characteristic taxa in PAO mice. Conversely, health-associated oral microbiota were associated with higher levels of beneficial serum metabolites in HAO mice. The multi-omics approach used in this study revealed that periodontitis-associated oral microbiota is associated with the induction of disease phenotype when they colonized the gut of germ-free mice.
2022-08-17 | GSE198570 | GEO
Project description:Three human gut microbiome samples from different individuals were cultured in an optimized culture medium with or without the presence of different sugars (10 mM glucose, 20 mM fructose, 10 mM glucose + 20 mM fructose, or 10 mM kestose). Samples were cultured in technical triplicates, and were taken at 0 hr, 1hr, 5 hr, 12 hr and 24 hr of culturing for optical density and metaproteomic analyses. Cultured microbiota cells were subjected to metaproteomics analysis using LC-MS/MS and a TMT approach.
2024-06-16 | PXD037925 | Pride