Shotgun metaproteomics of the human distal gut microbiota
The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes.
- Research Organization:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- Earth Sciences Division
- DOE Contract Number:
- DE-AC02-05CH11231
- OSTI ID:
- 943452
- Report Number(s):
- LBNL-1134E; TRN: US200902%%204
- Journal Information:
- International Society for Microbial Ecology Journal, Journal Name: International Society for Microbial Ecology Journal
- Country of Publication:
- United States
- Language:
- English
Similar Records
Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life
Development of an Enhanced Metaproteomic Approach for Deepening the Microbiome Characterization of the Human Infant Gut