Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes.

ABSTRACT: The genome of a microorganism encodes its potential functions that can be implemented through expressed proteins. It remains elusive how a protein's selective expression depends on its metabolic essentiality to microbial growth or its ability to claim resources as ecological niches. To reveal a protein's metabolic or ecological role, we developed a computational pipeline, which pairs metagenomics and metaproteomics data to quantify each protein's gene-level and protein-level functional redundancy simultaneously. We first illustrated the idea behind the pipeline using simulated data of a consumer-resource model. We then validated it using real data from human and mouse gut microbiome samples. In particular, we analyzed ABC-type transporters and ribosomal proteins, confirming that the metabo

SUBMITTER: Wang T 

PROVIDER: S-EPMC11131966 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature