PXD006033

PXD006033 is an original dataset announced via ProteomeXchange.

Title	Metaproteomic analysis of the infant fecal microbiome
Description	A metaproteomics analysis was conducted on the infant fecal microbiome to characterize global protein expression in 8 samples obtained from infants with a range of early-life experiences. Samples included breast-, formula- or mixed-fed, mode of delivery, and antibiotic treatment and one set of monozygotic twins. Although label-free mass spectrometry-based proteomics is routinely used for the identification and quantification of thousands of proteins in complex samples, the metaproteomic analysis of the gut microbiome presents particular technical challenges. Among them: the extreme complexity and dynamic range of member taxa/species, the need for matched, well-annotated metagenomics databases, and the high inter-protein sequence redundancy/similarity between related members. In this study, a metaproteomic approach was developed for assessment of the biological phenotype and functioning, as a complement to 16S rRNA sequencing analysis to identify constituent taxa. A sample preparation method was developed for recovery and lysis of bacterial cells, followed by trypsin digestion, and pre-fractionation using Strong Cation Exchange chromatography. Samples were then subjected to high performance LC-MS/MS. Data was searched against the Human Microbiome Project database, and a homology-based meta-clustering strategy was used to combine peptides from multiple species into representative proteins. Bacterial taxonomies were also identified, based on species-specific protein sequences, and protein metaclusters were assigned to pathways and functional groups. The results obtained demonstrate the applicability of this approach for performing qualitative comparisons of human fecal microbiome composition, physiology and metabolism, and also provided a more detailed assessment of microbial composition in comparison to 16S rRNA.
HostingRepository	PRIDE
AnnounceDate	2019-03-29
AnnouncementXML	Submission_2019-03-29_11:56:32.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD006033
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Daniel Chelsky
SpeciesList	scientific name: other sequences; NCBI TaxID: 28384;
ModificationList	Oxidation
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-03-06 05:35:18	ID requested
⏵ 1	2019-03-29 11:56:33	announced

Cortes L, Wopereis H, Tartiere A, Piquenot J, Gouw JW, Tims S, Knol J, Chelsky D, Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome. Int J Mol Sci, 20(6):(2019) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: Human, Fecal, Microbiome, Proteomics

Daniel Chelsky
contact affiliation	Caprion Biosciences Inc.
contact email	dchelsky@caprion.com
lab head
Daniel Chelsky
contact affiliation	Caprion Biosciences
contact email	dchelsky@caprion.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD006033
     1. Label: PRIDE project
     2. Name: Metaproteomic analysis of the infant fecal microbiome