Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multi-omic biogeography of the gastrointestinal microbiota of a pre-weaned lamb

ABSTRACT: Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to study the pre-weaned lamb proteome and metaproteome in ten different gastrointestinal tracts: rumen, reticulum, omasum, abomasum, duodenum, jejunum, ileum, cecum, colon, and rectum.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Microbiota Ovis Aries

TISSUE(S): Reticulum, Jejunum, Duodenum, Omasum, Cecum, Rectum, Rumen, Colon, Ileum, Abomasum

SUBMITTER: Antonio Palomba

LAB HEAD: Sergio Uzzau

PROVIDER: PXD008192 | Pride | 2017-12-14

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	01_Rumen_luminal.raw	Raw
	01_Rumen_luminal_DB-Host.msf	Msf
	01_Rumen_luminal_DB1.msf	Msf
	01_Rumen_luminal_DB2.msf	Msf
	01_Rumen_mucosal.raw	Raw

Items per page:

1 - 5 of 87

Publications

Multi-Omic Biogeography of the Gastrointestinal Microbiota of a Pre-Weaned Lamb.

Palomba Antonio A Tanca Alessandro A Fraumene Cristina C Abbondio Marcello M Fancello Francesco F Atzori Alberto Stanislao AS Uzzau Sergio S

Proteomes 20171218 4

The digestive functions of the pre-weaned lamb gastrointestinal tracts (GITs) have been the subject of much research in recent years, but the microbial and host functions underlying these complex processes remain largely unknown. Here, we undertook a proof-of-principle metaproteogenomic investigation on luminal and mucosal samples collected from 10 GITs of a 30-day-old pre-weaned lamb. We demonstrate that the analysis of the diverse ecological niches along the GITs can reveal microbiota composit ...[more]

PMID: 29258228

Similar Datasets

Label-free and targeted mass tandem (TMT-labelled) global proteomic analyses on mucus from the stomach, small and large intestine of a domestic and laboratory dogs

Project description:Gastrointestinal (GI) mucus is continuously secreted and lines the entire length of the GI tract. Essential for health, it keeps the noxious luminal content away from the epithelium and propels forward the digesta. The aim of our study was to characterize the composition and structures of mucus throughout the various GI segments in dog. Mucus from the stomach, small intestine (duodenum, jejunum, ileum), and large intestine (cecum, proximal and distal colon) was collected from 5 dogs. pH and water content of GI mucus and digesta were analyzed. Composition of all GI-tract segments from a domestic and a laboratory dog was determined by label-free global proteomics. A colonic-focussed composition analysis with TMT-labelled proteomics was used on jenunal and proximal and distal colonic mucus samples from 3 laboratory and 1 domestic dog. Finally, the composition of jejunal and colonic mucus samples of 3 laboratory and 1 domestic dog was evaluated with lipidomics and metabolomics. Structural properties were investigated using cryoSEM and rheology. The proteome was similar across the different GI segments. The highest abundant secreted gel-forming mucin in the gastric mucus was mucin 5AC, whether mucin 2 had highest abundance in the intestinal mucus. Lipid and metabolite abundance was generally higher in the jejunal mucus than the colonic mucus. In conclusion, the mucus is a highly viscous and hydrated material. The proteins, lipids and metabolites were similar throughout the GI tract, although abundances depended on location. These data provide an important baseline for future studies on human and canine intestinal diseases and the dog model in drug absorption.

2022-03-07 | PXD029356 | Pride

Engineered fibre enables targeted activation of butyrate-producing microbiota in the distal gut

Project description:Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have engineered an acetylated galactoglucomannan (AcGGM) fibre from spruce trees to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. The accuracy of AcGGM was tested in an applied pig feeding trial, which resolved 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially expressed AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. We additionally observed a “butterfly effect”, whereby numerous metabolic changes and interdependent cross-feeding pathways were detected in neighboring non-mannolytic populations that produce short-chain fatty acids. Our findings show that intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with the possibility to create greater modulatory effects at large.

2020-09-28 | PXD015757 | Pride

The effect of microbial colonization on the host proteome varies by gastrointestinal location

Project description:Endogenous intestinal microbiota have wide-ranging and largely uncharacterized effects on host physiology. Here, we used reverse-phase liquid chromatography-coupled tandem mass spectrometry to define the mouse intestinal proteome in the stomach, jejunum, ileum, cecum, and proximal colon under three colonization states: germ-free, monocolonized with Bacteroides thetaiotaomicron, and conventionally raised. Our analysis revealed distinct proteomic abundance profiles along the gastrointestinal tract. Unsupervised clustering showed that host protein abundance primarily depended on gastrointestinal location rather than colonization state and specific proteins and functions that defined these locations were identified by random forest classifications. K-means clustering of protein abundance across locations revealed substantial differences in host protein production between conventionally raised mice relative to germ-free and monocolonized mice. Finally, comparison to fecal proteomic datasets suggested that the identities of stool proteins are not biased to any region of the gastrointestinal tract, but are substantially impacted by the microbiota in the distal colon.

2015-11-25 | PXD002838 | Pride

Transcription profiling of human samples from intervention study with two doses of iron (as ferrous gluconate via intestinal perfusion) to study the effect on genome wide gene expression in the small intestine

Project description:Human intervention study with two doses of iron (as ferrous gluconate via intestinal perfusion) to study the effect on genome-wide gene expression in the small intestine, in order to obtain detailed information about intestinal transcriptomics in vivo.

2006-05-01 | E-MEXP-325 | biostudies-arrayexpress

Comparative analysis of chicken Intestinal Intraepithelial lymphocytes (IEL) following Eimeria acervulina (EA), E. maxima (EM), or E. tenella (ET) infection

Project description:Relative expression levels of mRNAs in chicken IEL experimentally infected with EA, EM, or ET were measured at 1 to 6 days post-infection (dpi) following primary and secondary infections. One week-old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of EA, EM, or ET. One week later, the infected chickens were challenged with an identical inoculum of the homologous parasite. Intestinal samples were collected daily from 5 birds in a treatment group at from 1 to 6 dpi following primary and secondary infections. Cecum, duodenum, and jejunum were collected from the birds challenged with E. acervulina, E. maxima, and E. tenella, respectively. Uninfected control samples and one of the 3 infection group samples were labeled with different fluorescent dyes and hybridized simultaneously on the same slide using a reference design with a dye swap protocol. Thirty seven-condition experiment, Non-infected control vs. Primary or secondary EA, EM, or ET infected IEL at 1 to 6. Biological replicates: 2 replicates with dye-switching from each infection groups. Two replicates per array.

2011-08-14 | E-GEOD-31213 | biostudies-arrayexpress

Label-free and targeted mass tandem (TMT-labelled) global proteomic analyses on mucus from the stomach, small and large intestine of pigLabel-free and targeted mass tandem (TMT-labelled) global proteomic analyses on mucus from the stomach, small and large intestine of pig

Project description:The gastrointestinal mucus is a hydrogel that lines the luminal side of the gastrointestinal epithelium, offering barrier protection from pathogens and lubrication of the intraluminal contents. These barrier properties likewise affect nutrients and drugs that need to penetrate the mucus to reach the epithelium prior to absorption. In order to assess the potential impact of the mucus on drug absorption, we need information about the nature of the gastrointestinal mucus. Today, most of the relevant available literature is mainly derived from rodent studies. In this work, we used a larger animal species; the pig model to characterize the mucus throughout the length of the gastrointestinal tract. This is the first report of the physiological properties (physical appearance, pH and water content), composition and structural profiling of the porcine gastrointestinal mucus. Gastrointestinal mucus was collected from the stomach, small intestine (duodenum, jejunum, ileum) and large intestine (cecum, proximal and distal colon) from slaughtered pigs. The composition of the mucus was characterized both with labelfree and TMT proteomics, with lipidomics and metabolomics. The structural profiling was determined with rheological measurements and cryo-Scanning Electron Microscopy. These findings allow for direct comparisons between the characteristics of mucus from various segments and can be further utilized to improve our understanding of the role of the mucus on region dependent drug absorption. Additionally, the present work is expected to contribute to the assessment of the porcine model as a preclinical species in the drug development process.

2022-03-07 | PXD029371 | Pride

Transcription profiling of human duodenal mucosa from healthy volunteers perfused with 0.055 M glutamine (10 ml/min) in saline at 10 cm distally from the pylorus for 4 h or continuous injection of 0.055 M glucose in saline

Project description:Intestinal perfusion of a 40-cm segment of the small intestine in 8 healthy volunteers. 2 test days, overnight fast. Gastroduodenoscopy for tissue sampling and positioning of perfusion catheter. Continuous injection of 0.055 M glutamine (10 ml/min) in saline at 10 cm distally from the pylorus for 4 h or continuous injection of 0.055 M glucose in saline. After the injection a second gastroduodenoscopy takes place for tissue sampling. In total we have 4 samples per individual (placebo-before; placebo-after; glutamine-before; and glutamine-after injection.

2007-12-06 | E-MEXP-941 | biostudies-arrayexpress

Lysine acetylation of microbiome

Project description:This project study and comprehensively characterize the lysine acetyltion in the human gut microbiome using antibody-based enrichment strategry and Orbitrap mass spectrometer. The technique has also been applied to study the microbiome in pediatric Crohn's disease and control subjects in order to understand the functional alterations of microbiome in IBD.

2020-07-08 | PXD013427 | Pride

Peptidomics of enteroendocrine cells and characterisation of potential effects of a novel preprogastrin derived-peptide on glucose tolerance in lean mice

Project description:To analyse the peptidomics of mouse enteroendocrine cells (EECs) and human gastrointestinal (GI) tissue and identify novel gut derived peptides. High resolution nano-flow liquid chromatography mass spectrometry (LCMS) was performed on (i) flow-cytometry purified NeuroD1 positive cells from mouse and homogenised human intestinal biopsies, (ii) supernatants from primary murine intestinal cultures, (iii) intestinal homogenates from mice fed high fat diet. Candidate bioactive peptides were selected on the basis of species conservation, high expression/biosynthesis in EECs and evidence of regulated secretion in vitro. Candidate novel gut-derived peptides were chronically administered to mice to assess effects on food intake and glucose tolerance.

2021-03-29 | PXD024050 | Pride

Transcriptome along the murine developing gut

Project description:Hox genes are required for the development of the intestinal caecum, a major organ of species eating plants. We have analysed the transcriptional regulation of Hoxd genes in caecal buds and show that they are controlled by a series of enhancers located in a gene desert telomeric to the HoxD cluster. The start site of two neighboring and opposite long non-coding RNAs, Hotdog and Twin of Hotdog, specifically transcribed in the caecum, contacts the expressed Hoxd genes in the framework of a topological domain, a large domain of interactions, which ensures a robust transcription of these genes during caecum budding. We show that hedgehogs have kept this regulatory potential despite the absence of caecum, suggesting that these enhancers are used in other developmental situations. In this context, we discuss some striking similarities between the caecum and the limb buds, suggesting the implementation of a common budding tool-kit. Transcriptional activity at the HoxD locus in the murine developing gut at E13, Differential gene expression analysis along the murine developing gut

2013-10-23 | E-GEOD-44366 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data