Browse
Submit Data
Databases
API
Help

Dataset Information

477 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mouse gut metaproteome - MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota

ABSTRACT: The mouse stool samples were collected from different diets fed mice and bacterial cells were harvest for metaproteomic analysis for understanding the role ofdiet on gut microbiota.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mouse Gut Metagenome

SUBMITTER: Xu Zhang

LAB HEAD: Daniel Figeys

PROVIDER: PXD003527 | Pride | 2016-07-05

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Xu_20151106_HFDmice_D0_HFD1.raw	Raw
	Xu_20151106_HFDmice_D0_HFD2.raw	Raw
	Xu_20151106_HFDmice_D0_HFD3.raw	Raw
	Xu_20151106_HFDmice_D0_HFD4.raw	Raw
	Xu_20151106_HFDmice_D0_NCD1.raw	Raw

Items per page:

1 - 5 of 33

Publications

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota.

Zhang Xu X Ning Zhibin Z Mayne Janice J Moore Jasmine I JI Li Jennifer J Butcher James J Deeke Shelley Ann SA Chen Rui R Chiang Cheng-Kang CK Wen Ming M Mack David D Stintzi Alain A Figeys Daniel D

Microbiome 20160624 1

<h4>Background</h4>The gut microbiota has been shown to be closely associated with human health and disease. While next-generation sequencing can be readily used to profile the microbiota taxonomy and metabolic potential, metaproteomics is better suited for deciphering microbial biological activities. However, the application of gut metaproteomics has largely been limited due to the low efficiency of protein identification. Thus, a high-performance and easy-to-implement gut metaproteomic approac ...[more]

PMID: 27343061

Similar Datasets

Human MLI metaproteome - MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota

Project description:Human mucosal-luminal interface (MLI) samples were collected from 8 different children and bacterial cells were harvest for metaproteomic analysis for understanding the MLI microbiota functions.

2016-07-05 | PXD003528 | Pride

Deep gut metaproteomics - A deep metaproteomics approach for the study of human microbiomes

Project description:Stool samples were collected from 4 children and subjected to deep gut metaproteomics analysis for in-depth understanding the functional compositions of human gut mcirobiome.

2017-08-10 | PXD005619 | Pride

Evaluating in vitro culture medium of mouse gut microbiome

Project description:The mice stool samples were collected for culturing with different medium for understanding the role of different medium component on the microbiome.

2018-06-15 | PXD006808 | Pride

Effects of SAHA on human gut microbiome

Project description:The human stool samples were collected and processed for in vitro culturing under anaerobic condition using rapidAIM assay with or without SAHA, an lysine deacetylase inhibitor, for evaluating the effects of SAHA on human gut microbiome. Metaproteomics were used to analyze the microbiome composition and functions.

2022-03-01 | PXD016388 | Pride

Evaluating the protein extraction methods for gut metaproteomics

Project description:Human stool samples were collected, microbial cells were harvested and subjected to protein extraction using different protocols for metaproteomics analyses. The protein extraction methods differ from the usage of different lysis buffer (SDS, urea and commercially available B-Per reagent), bead beating, ultrasonication and heating. The impacts of different protein extraction methods on metaproteomics results were evaluated with multiple criteria including protein yields, peptide identifications, taxonomic compositions and functional compositions.

2017-07-17 | PXD005969 | Pride

Effects of 5 drugs on the human gut microbiome.

Project description:We processed a human stool sample and cultured the processed microbiome in vitro under anaerobic condition for 48 hours using the rapidAIM assay. The microbiome was treated with either azathioprine, ciprofolxacin, diclofenac, nicatidine, paracetamol or control DMSO. Each drug was used at three different concentrations. We compared these results to those acquired using MS1-only data.

2022-07-29 | PXD024845 | Pride

Relating human gut metagenome and metaproteome

Project description:Gut microbiome research is rapidly moving towards the functional characterization of the microbiota by means of shotgun meta-omics. Here, we selected a cohort of healthy subjects from an indigenous and monitored Sardinian population to analyze their gut microbiota using both shotgun metagenomics and shotgun metaproteomics. We found a considerable divergence between genetic potential and functional activity of the human healthy gut microbiota, in spite of a quite comparable taxonomic structure revealed by the two approaches. Investigation of inter-individual variability of taxonomic features revealed Bacteroides and Akkermansia as remarkably conserved and variable in abundance within the population, respectively. Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the functional activity with the higher expression rate and the lower inter-individual variability in the study cohort, highlighting the key importance of the biosynthesis of this microbial by-product for the gut homeostasis. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several gut microbiota members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis and short-chain fatty acid production). In conclusion, our results provide useful indications regarding the main functions actively exerted by the gut microbiota members of a healthy human cohort, and support metaproteomics as a valuable approach to investigate the functional role of the gut microbiota in health and disease.

2017-07-19 | PXD005780 | Pride

Spectral entropy as a measure of the metaproteome complexity

Project description:The diversity and complexity of the microbiome's genomic landscape are not always mirrored in its proteomic profile. Despite the anticipated proteomic diversity, observed complexities of microbiome sample are often lower than expected. Two main factors contribute to this discrepancy: limitations in mass spectrometry's detection sensitivity and bioinformatics challenges in metaproteomics identification. This study introduces a novel approach to evaluating sample complexity directly at the full mass spectrum (MS1) level rather than relying on peptide identifications. When analyzing under identical mass spectrometry conditions, microbiome samples displayed significantly higher complexity, as evidenced by the spectral entropy and peptide candidate entropy, compared to single-species samples. The research provides solid evidence for the complexity of microbiome in proteomics indicating the optimization potential of the bioinformatics workflow.

2024-05-27 | PXD050781 | Pride

Differential Lysis Approach Enables Selective Extraction of Taxon-Specific Proteins for Gut Metaproteomics

Project description:A differential lysis approach was developed with different strength of lysis buffers (urea and/or sodium dodecyl sulfate) and applied on human stool samples to separate different microbial species to increase the depth of metaproteomic measurements. We showed that the lysates dominating by proteins from Gram-positive (G+) or negative bacteria (G-) can be achieved by differential lysis

2023-03-27 | PXD016787 | Pride

Williams-Beuren syndrome shapes the gut microbiota metaproteome.

Project description:Williams-Beuren syndrome (WBS) is a rare genetic neurodevelopmental disorder with multi-systemic manifestations. The evidence that most subjects with WBS face gastrointestinal (GI) comorbidities, have prompted us to carry out a metaproteomic investigation of their gut microbiota (GM) profile compared to age-matched healthy subjects (CTRLs). Metaproteomic analysis was carried out on fecal samples collected from 41 individuals with WBS, and compared with samples from 45 CTRLs. Stool were extracted for high yield in bacterial protein group (PG) content, trypsin-digested and analysed by nanoLiquid Chromatography-Mass Spectrometry. Label free quantification, taxonomic assignment by the lowest common ancestor (LCA) algorithm and functional annotations by COG and KEGG databases were performed. Data were statistically interpreted by multivariate and univariate analyses. A WBS GM functional dissimilarity respect to CTRLs, regardless age distribution, was reported. The alterations in function of WBSs GM was primarily based on bacterial pathways linked to carbohydrate transport and metabolism and energy production. Influence of diet, obesity, and GI symptoms was assessed, highlighting changes in GM biochemical patterns, according to WBS subsets' stratification. The LCA-derived ecology unveiled WBS-related functionally active bacterial signatures: Bacteroidetes related to over-expressed PGs, and Firmicutes, specifically the specie Faecalibacterium prausnitzii, linked to under-expressed PGs, suggesting a depletion of beneficial bacteria. These new evidences on WBS gut dysbiosis may offer novel targets for tailored interventions.

| S-EPMC10624682 | biostudies-literature

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