Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

15N labeling of mouse microbiota

ABSTRACT: This study investigated the in vivo dynamics of the microbiome using metaproteomics coupled with protein-SIP in mice.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Gut Metagenome

SUBMITTER: Xu Zhang

LAB HEAD: Daniel Figeys

PROVIDER: PXD017451 | Pride | 2021-08-26

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Mouse_184sample_2.6M.GeneSet.pep.fasta	Fasta
	Xu_20140829_15Nplight_D0_Ref1.raw	Raw
	Xu_20140829_15Nplight_D0_Ref2.raw	Raw
	Xu_20140829_15Nplight_D0_Ref3.raw	Raw
	Xu_20140829_15Nplight_D0_Ref4.raw	Raw

Items per page:

1 - 5 of 52

Publications

Studying the Temporal Dynamics of the Gut Microbiota Using Metabolic Stable Isotope Labeling and Metaproteomics.

Smyth Patrick P Zhang Xu X Ning Zhibin Z Mayne Janice J Moore Jasmine Isabelle JI Walker Krystal K Lavallée-Adam Mathieu M Figeys Daniel D

Analytical chemistry 20201130 24

The gut microbiome and its metabolic processes are dynamic systems. Surprisingly, our understanding of gut microbiome dynamics is limited. Here, we report a metaproteomic workflow that involves protein stable isotope probing (protein-SIP) and identification/quantification of partially labeled peptides. We also developed a package, which we call MetaProfiler, that corrects for false identifications and performs phylogenetic and time series analysis for the study of microbiome dynamics. From the s ...[more]

PMID: 33253538

Similar Datasets

Study of human gut microbiota from healthy adults

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

Evaluation of different protein extraction protocols to study human gut microbiota.

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

Metaproteomic analysis of gut microbiota from 30 samples of cystic fibrosis infants

Project description:The link between human gut microbiota (a complex group of microorganisms including not only bacteria but also fungi, viruses, etc.,) and the physiological state is nowadays unquestionable. Metaproteomic 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. Cystic fibrosis is a genetic disease in which the microbiota of the respiratory tract determines the patient's survival and differences in composition of gut microbiota of cystic fibrosis patients respect to healthy infants have been reported. In order to characterize this host-microbiota inter-relation, we carried out the metaproteomic study of 30 stool samples from infants with cystic fibrosis.

2022-10-11 | PXD029284 | Pride

Active thrombin is produced by intestinal epithelium to control mucosal biofilm

Project description:Healthy human and mouse colon epithelium is a major source of active thrombin, released in lumen. Using germ-free animals, we demonstrated that mucosal thrombin was directly regulated by the presence of commensal microbiota. Specific inhibition of lumenal thrombin activity caused macro-, microscopic damage and transcriptomic alterations of genes involved in host-microbiota interactions. Further, lumenal thrombin inhibition impaired the spatial segregation of microbiota biofilms, allowing bacteria to invade the mucus layer and to translocate across the epithelium. Thrombin proteolyzed the biofilm matrix of reconstituted mucosa-associated human microbiota. We demonstrated a previously unknown physiological role for epithelial thrombin that constrains biofilms at mucosal surfaces. We report that lung, bladder and skin epithelia also expressed thrombin, suggesting that this role may be applicable to other host-microbiome surfaces. Our discovery points route to new therapies targeting biofilms, important for a broad range of disorders, in the gut, and beyond.

2019-06-24 | PXD014315 | Pride

Lysine acetylation in human fecal microbiome

Project description:This study characterized the lysine acetylome in human gut microbiome samples. Briefly, the microbial peptides obtained from human mcirobiome cells were used for lysine acetylated peptide enrichment using anti-acetyl-lysine (Kac) antibody cocktail; the enriched Kac peptides were then identified and quantified using mass spectrometry.

2020-07-08 | PXD015482 | Pride

Quantitative proteomic comparison between wild type Col and sec-5 mutant using 15N metabolic labeling

Project description:SECRET AGENT (SEC) is an O-GlcNAc transferase involved in O-GlcNAcylation of many proteins. However, sec-5 null allele mutant phenotype is very subtle. To examine if there are proteins that show altered expression in the sec-5 mutant compared to wild-type Col, we designed MS experiments to identify these candidates on a global scale using 15N metabolic labeling.

2022-02-04 | PXD030575 | Pride

15N Stable-isotope-labeling in Arabidopsis (SILIA) quantitative MS analysis of the AtACINUS interactome

Project description:AtACINUS protein is involved in regulation of alternative transcription and splicing(AS). Identifying interaction partners and protein complex compositions for AtACINUS can produce valuable information on the mechanisms by which they regulate transcription and AS, as well as post-translational modifications on AtACINUS. A homozygous 35S::AtACINUS-GFP/acinus-2 plant was selected for similar protein expression level to the endogenous AtACINUS protein of wild-type plants using a native α-AtACINUS antibody. We isolated putative AtACINUS interaction partners from young Arabidopsis seedlings using the native α-AtACINUS antibody. Plants expressing TAP-GFP under 35S promoter were used as controls.

2020-12-02 | PXD020700 | Pride

Sequence database choice significantly affects taxonomic and functional metaproteomic results in gut microbiota studies

Project description:Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics (the study of the whole protein complement of a microbial community) can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Here we present a systematic investigation of variables concerning database construction and annotation, and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. Taxonomic and functional results were revealed to be strongly database-dependent, especially when dealing with mouse samples. As a striking example, in mouse the Firmicutes/Bacteroidetes ratio varied up to 10-fold depending on the database used. Finally, we provide recommendations regarding metagenomic sequence processing aimed at maximizing gut metaproteome characterization, and contribute to identify an optimized pipeline for metaproteomic data analysis.

2016-10-10 | PXD004039 | Pride

Dual roles of HSP70 chaperone HSPA1 in quality control of nascent and newly synthesized proteins

Project description:Exposure to heat stress triggers a well-defined acute response marked by HSF1-dependent transcriptional upregulation of heat shock proteins. Cells allowed to recover acquire thermotolerance, but this adaptation is poorly understood. By quantitative proteomics, we discovered selective upregulation of HSP70-family chaperone HSPA1 and its co-factors, HSPH1 and DNAJB1, in MCF7 breast cancer cells acquiring thermotolerance. HSPA1 was found to have dual function during heat stress response: (i) during acute stress, it promotes the recruitment of the 26S proteasome to translating ribosomes, thus poising cells for rapid protein degradation and resumption of protein synthesis upon recovery; (ii) during thermotolerance, HSPA1 together with HSPH1 maintains ubiquitylated nascent/newly synthesized proteins in a soluble state required for their efficient proteasomal clearance. Consistently, deletion of HSPH1 impedes thermotolerance and esophageal tumor growth in mice, thus providing a potential explanation for the poor prognosis of digestive tract cancers with low HSPH1, and nominating HSPH1 as a cancer drug target. We propose dual roles of HSPA1 either alone or in complex with HSPH1 and DNAJB1 in promoting quality control of nascent/newly synthesized proteins and cellular thermotolerance.

2021-05-02 | PXD025123 | Pride

Discovery of human breast cancer cell MCF7 heat induced proteins by LC-MS/MS

Project description:Co-translational degradation via the ubiquitin-proteasome system mediates quality control of 15 – 25% of nascent proteins, a proportion that is known to increase dramatically under proteotoxic stress conditions. Whereas the ubiquitylation machinery involved has been characterized, mechanisms coordinating the proteasomal destruction of ribosome-attached nascent proteins remain poorly defined. In pursuit of such mechanisms, we discovered dual cooperation of the HSP70 family member HSPA1 with the 26S proteasome: First, in response to proteotoxic stress, HSPA1 promotes proteasome recruitment to translating 80S ribosomes in a manner independent of nascent chain ubiquitylation. Secondly, HSPA1, in association with its cognate nucleotide exchange factor HSPH1, maintains co-translationally ubiquitylated proteins in a soluble state required for efficient proteasomal degradation.

2021-09-09 | PXD020140 | Pride

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