The effect of antibiotic treatment on the intestinal metabolome
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE25687 | GEO | 2011/02/08
SECONDARY ACCESSION(S): PRJNA135837
REPOSITORIES: GEO
Similar Datasets
Project description:The importance of the mammalian intestinal microbiota to human health has been intensely studied over the past few years. It is now clear that the interactions between human hosts and their associated microbial communities need to be characterized in molecular detail if we are to truly understand human physiology. Additionally, the study of such host-microbe interactions is likely to provide us with new strategies to manipulate such complex systems to maintain or restore homeostasis in order to prevent or cure pathological states. We describe the use of high-throughput metabolomics to shed light on the interactions between the intestinal microbiota and the host. We show that treatment with the antibiotic streptomycin disrupts intestinal homeostasis and has a profound impact on the intestinal metabolome, affecting the levels of over 87% of all metabolites detected. Many metabolic pathways that are critical for host physiology were affected, including bile acid, eicosanoid and steroid hormone synthesis. Interestingly, many of these pathways are also affected by intestinal pathogens. Dissecting the effect of both beneficial and pathogenic bacteria on some of these pathways will be instrumental in understanding the interplay between the host, the resident microbiota and incoming pathogens and may aid in the design of new therapeutic strategies that target these interactions. Age-matched female C57BL/6 mice were used. Fresh feces were collected and stored at -80 oC. Mice were then treated with 20 mg of streptomycin through oral gavage and fresh feces were collected 24 hours after treatment and stored at -80 oC until used. To extract metabolites from feces, acetonitrile was added to samples (approximately 10-25 μL of acetonitrile per 1 mg of tissue), which were then homogenized. The samples were then cleared by centrifugation and the supernatant was collected and dried at room temperature using a centrifuge equipped with a vacuum pump. All extracts were kept at -80 oC until used. For metabolic profiling, the dried extracts from mouse feces were suspended in a 2:3 mixture of water and acetonitrile (10 μL per 1 mg of tissue), vortexed and cleared by centrifugation. Supernatants were collected and used as described below. Extracts were diluted 1:5 with 60% acetonitrile containing either 0.2% formic acid (for positive ion mode) or 0.5% ammonium hydroxide (for negative ion mode) and spiked with predefined amounts of the "ES tuning mix" solution as the internal standard for mass calibration. The solutions were then infused, using a syringe pump (KDS Scientific, Holliston, USA) at a flow rate of 2.5 µL per minute, into a 12-T Apex-Qe hybrid quadrupole-FT-ICR mass spectrometer (Bruker Daltonics, Billerica, USA) equipped with an Apollo II electrospray ionization source, a quadrupole mass filter and a hexapole collision cell. Data were recorded in positive and negative ion modes with broadband detection and an FT acquisition size of 1024 kilobytes per second, within a range of m/z 150 to 1100. Under these settings, a mass resolution of ca. 100,000 (full width at half maximum, FWHM) at m/z 400 and a mass accuracy within 2 ppm or less for all detected components, following internal mass calibration, were observed. Other experimental parameters were: capillary electrospray voltage of 3600-3750 V, spray shield voltage of 3300-3450 V, source ion accumulation time of 0.1 s and collision cell ion accumulation time of 0.2 s. To increase detection sensitivity, survey scan mass spectra in positive and negative ion modes were acquired from the accumulation of 200 scans per spectrum, and duplicate acquisitions per sample were carried out to ensure data reproducibility. Raw mass spectrometry data were processed as described elsewhere (Han et al. 2008. Metabolomics. 4:128-140). To identify differences in metabolite composition between untreated and treated samples, we first filtered our list of masses for metabolites that were present on one set of samples (untreated or treated) but not the other. Additionally, we averaged the mass intensities of metabolites in each group and calculated the ratios between averaged intensities of metabolites from untreated and treated samples. To assign possible metabolite identities to the masses present in only one of the sample groups or showing at least a 2-fold change in intensities between the sample groups, the monoisotopic neutral masses of interest were queried against MassTrix (http://masstrix.org), a free-access software designed to incorporate masses into metabolic pathways. Masses were searched against the Mus musculus database within a mass error of 3 ppm. Data were analyzed by unpaired t tests with 95% confidence intervals.
2011-02-08 | E-GEOD-25687 | biostudies-arrayexpress
Project description:The microbial cell surface is a critical site of microbe-host interactions that often control infection outcomes. Defining the set of host proteins present at this interface has been challenging. Here, we used a surface biotinylation approach coupled to quantitative mass spectrometry to identify and quantify both bacterial and host proteins present on the surface of diarrheal fluid-derived V. cholerae in an infant rabbit model of cholera. Our data showed that V. cholerae surfaces were coated with numerous host proteins, whose abundance were driven by the presence of cholera toxin, including the C type lectin SP-D. Mice lacking SP-D had enhanced V. cholerae intestinal colonization. Additional host proteins (AnxA1, LPO and ZAG) capable of binding V. cholerae were also found to recognize distinct taxa of the murine intestinal microbiota, suggesting that these host factors may play roles in intestinal homeostasis in addition to host defense. Proteomic analysis of microbial surfaces is valuable for identifying host interactions that regulate infection and homeostasis with both pathogens and endogenous microbiota alike.
2021-07-08 | GSE179529 | GEO
Project description:The microbial cell surface is a critical site of microbe-host interactions that often control infection outcomes. Defining the set of host proteins present at this interface has been challenging. Here, we used a surface biotinylation approach coupled to quantitative mass spectrometry to identify and quantify both bacterial and host proteins present on the surface of diarrheal fluid-derived V. cholerae in an infant rabbit model of cholera. Our data showed that V. cholerae surfaces were coated with numerous host proteins, whose abundance were driven by the presence of cholera toxin, including the C type lectin SP-D. Mice lacking SP-D had enhanced V. cholerae intestinal colonization. Additional host proteins (AnxA1, LPO and ZAG) capable of binding V. cholerae were also found to recognize distinct taxa of the murine intestinal microbiota, suggesting that these host factors may play roles in intestinal homeostasis in addition to host defense. Proteomic analysis of microbial surfaces is valuable for identifying host interactions that regulate infection and homeostasis with both pathogens and endogenous microbiota alike.
2021-07-08 | GSE179528 | GEO
Project description:Background & Aims: The complex interactions between diet and the microbiota that influence mucosal inflammation and inflammatory bowel disease are poorly understood. Experimental colitis models provide the opportunity to control and systematically perturb diet and the microbiota in parallel to quantify the contributions between multiple dietary ingredients and the microbiota on host physiology and colitis. Methods: To examine the interplay of diet and the gut microbiota on host health and colitis, we fed over 40 different diets with varied macronutrient sources and concentrations to specific pathogen free or germ free mice either in the context of healthy, unchallenged animals or dextran sodium sulfate colitis model. Results: Diet influenced physiology in both health and colitis across all models, with the concentration of protein and psyllium fiber having the most profound effects. Increasing dietary protein elevated gut microbial density and worsened DSS colitis severity. Depleting gut microbial density by using germ-free animals or antibiotics negated the effect of a high protein diet. Psyllium fiber influenced host physiology and attenuated colitis severity through microbiota-dependent and microbiota-independent mechanisms. Combinatorial perturbations to dietary protein and psyllium fiber in parallel explain most variation in gut microbial density, intestinal permeability, and DSS colitis severity, and changes in one ingredient can be offset by changes in the other. Conclusions: Our results demonstrate the importance of examining complex mixtures of nutrients to understand the role of diet in intestinal inflammation. Keywords: IBD; Diet; Microbiota; Mouse Models; Systems Biology
2017-10-30 | GSE104461 | GEO
Project description:The microbial cell surface is a critical site of microbe-host interactions that often control infection outcomes. Defining the set of host proteins present at this interface has been challenging. Here, we used a surface biotinylation approach coupled to quantitative mass spectrometry to identify and quantify both bacterial and host proteins present on the surface of diarrheal fluid-derived V. cholerae in an infant rabbit model of cholera. Our data showed that V. cholerae surfaces were coated with numerous host proteins, whose abundance were driven by the presence of cholera toxin, including the C type lectin SP-D. Mice lacking SP-D had enhanced V. cholerae intestinal colonization. Additional host proteins (AnxA1, LPO and ZAG) capable of binding V. cholerae were also found to recognize distinct taxa of the murine intestinal microbiota, suggesting that these host factors may play roles in intestinal homeostasis in addition to host defense. Proteomic analysis of microbial surfaces is valuable for identifying host interactions that regulate infection and homeostasis with both pathogens and endogenous microbiota alike.
2021-10-02 | PXD027076 | Pride
Project description:Studying host-microbiota interactions is fundamental to understand mechanisms involved in intestinal inflammation and inflammatory bowel diseases. In this work, we studied these interactions in mice mono-associated with 4 bacteria and 2 yeasts, all representative of intestinal microbiota and/or associated with IBD pathogenesis: Bacteroides thetaiotaomicron, adhesive-invasive Escherichia coli (AIEC), Ruminococcus gnavus, Roseburia intestinalis, Saccharomyces boulardii and Candida albicans. Transcriptomics analyses showed that B. thetaiotaomicron had the highest immunological effect, being able to almost recapitulate the effects of a whole microbiota, and particularly induced Treg pathways. Furthermore, this analysis also pointed out the effects of E. coli AIEC LF82 on IDO activation and of S. boulardii on angiogenesis, as well as major effects of R. gnavus on metabolism. This work therefore reveals information on the role of each micro-organism and proposes several tracks to follow to better understand IBD pathogenesis and identify therapeutic targets 6 mono-associations + 2 controls (germ-free and conventionalized mice), with 5 to 7 mice per group.
2015-08-22 | E-GEOD-63299 | biostudies-arrayexpress
Project description:Humans and their microbiota have coevolved a mutually beneficial relationship, with the human host providing a hospitable environment for the microbes, and the microbiota providing many benefits including nutritional benefits and protection from pathogen infection1. Maintaining this relationship requires careful immune balance to contain commensals within the lumen while limiting inflammatory anti-commensal responses1,2. A number of groups describe T cell antigen-specific recognition of intestinal microbes3,4. While the local environment shapes effector cell differentiation3–5 it is unclear how microbiota-specific T cells are educated in the thymus. Here we identify that early life intestinal colonization leads to trafficking of microbial antigens from the intestine to the thymus by intestinal dendritic cells (DCs) which then expand microbiota-specific T cells. Once in the periphery, microbiota-specific T cells have pathogenic potential, or can protect against related pathogens. In this way, the developing microbiota shapes and expands the thymic and peripheral T cell repertoire, allowing for enhanced recognition of intestinal microbes and pathogens.
2021-04-01 | GSE171279 | GEO
Project description:Protection against pathogens is a major function of the gut microbiota. Although bacterial natural products have emerged as crucial components of host-microbiota interactions, their exact role in microbiota-mediated protection is largely unexplored. We addressed this knowledge gap with the nematodeCaenorhabditis elegansand its microbiota isolatePseudomonas fluorescensMYb115 that is known to protect againstBacillus thuringiensis (Bt) infection. We find that MYb115-mediated protection depends on sphingolipids that are derived from an iterative type I polyketide synthase (PKS), thereby describing a noncanonical pathway of bacterial sphingolipid production. We provide evidence that MYb115-derived sphingolipids affectC. eleganstolerance to Bt infection by altering host sphingolipid metabolism. This work establishes sphingolipids as structural outputs of bacterial PKS and highlights the role of microbiota-derived sphingolipids in host protection against pathogens.
2023-10-14 | GSE245296 | GEO
Project description:Commensal bacteria influence host physiology, including immune responses, without invading host tissues. We show that proteins from segmented filamentous bacteria (SFB), which are immunomodulatory commensal microbes, are transferred into intestinal epithelial cells by adhesion-directed endocytosis that is distinct from the clathrin-dependent endocytosis of invasive pathogens. SFB transfer microbial cell wall-associated proteins, including an antigen that stimulates mucosal Th17 cell differentiation, into the cytosol of epithelial cells. Removal of CDC42 activity in vivo led to disruption of endocytosis induced by SFB, decreased epithelial antigen acquisition with consequent loss of immune modulation by SFB-specific CD4 T cells and mucosal Th17 cells. Our findings indicate direct communication between a resident gut microbe and the host and show that intestinal epithelial cells acquire antigens from commensal bacteria for generation of T-cell responses to the resident microbiota.
2019-01-10 | GSE124848 | GEO
Project description:Neural control of visceral organ function is essential for homeostasis and health. Intestinal peristalsis is critical for digestive physiology and host defence and is often dysregulated in gastrointestinal (GI) disorders. Luminal factors, such as diet and microbiota regulate neurogenic programs of gut motility, but the underlying molecular mechanisms remain unclear. Here we show that the transcription factor Aryl hydrocarbon Receptor (AhR) functions as a biosensor in intestinal neural circuits linking their functional output to the microbial environment of the gut lumen. Using nuclear RNA sequencing of mouse enteric neurons representing distinct intestinal segments and microbiota states, we demonstrate that the intrinsic neural networks of the colon exhibit unique transcriptional profiles controlled by the combined effects of host genetic programmes and microbial colonisation. Microbiota-induced expression of AhR in neurons of the distal gastrointestinal tract enables them to respond to the luminal environment and induce expression of neuron-specific effector mechanisms. Neuron-specific deletion of Ahr or constitutive overexpression of its negative feedback regulator CYP1A1, results in reduced peristaltic activity of the colon, similar to that observed in microbiota-depleted mice. Finally, expression of Ahr in enteric neurons of antibiotic-treated mice partially restores intestinal motility. Taken together, our experiments identify AhR signalling in enteric neurons as a regulatory node that integrates the luminal environment with the physiological output of intestinal neural circuits towards gut homeostasis and health. The enteric nervous system (ENS) encompasses the intrinsic neural networks of the gastrointestinal (GI) tract, which regulate most aspects of intestinal physiology, including peristalsis. In addition to host-specific genetic programmes, microbiota and diet have emerged as critical regulators of gut tissue physiology and changes in the microbial composition of the lumen often accompany GI disorders. We found that gut environmental sensor Aryl hydrocarbon receptor (AhR) is induced in colonic neurons in response to microbiota colonisation and regulates intestinal peristalsis in an AhR ligand-dependent manner. In this experiment, we used RNA sequencing to identify genes regulated in mouse colonic neurons by AhR activation.
2019-11-13 | GSE140292 | GEO