Dataset Information

Metaproteomic analysis of the infant fecal microbiome

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Other Sequences

TISSUE(S): Colon

DISEASE(S): Disease Free

SUBMITTER: Daniel Chelsky

LAB HEAD: Daniel Chelsky

PROVIDER: PXD006033 | Pride | 2019-03-29

REPOSITORIES: Pride

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Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome.

Cortes Laetitia L Wopereis Harm H Tartiere Aude A Piquenot Julie J Gouw Joost W JW Tims Sebastian S Knol Jan J Chelsky Daniel D

International journal of molecular sciences 20190321 6

A metaproteomic analysis was conducted on the fecal microbiome of eight infants to characterize global protein and pathway expression. Although mass spectrometry-based proteomics is now a routine tool, analysis of the microbiome presents specific technical challenges, including the complexity and dynamic range of member taxa, the need for well-annotated metagenomic databases, and high inter-protein sequence redundancy and similarity. In this study, an approach was developed for assessment of bio ...[more]

PMID: 30901843

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