Fig. 1
From: Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome
sProtein discovery and validation workflow in a multi-species model: SIHUMIx strains were grown as single cultures for genomic DNA isolation followed by long read sequencing and proteomics measurement. The de novo assembled, complete genomes were used as a basis to create a minimally redundant multispecies-iPtgxDB containing novel sProtein candidates. The SIHUMIx community was cultivated in chemostatic bioreactors and sampled for subsequent proteomics and metatranscriptomics measurement. sProteins of single cultures and the community cultured SIHUMIx strains were enriched and measured by LC-MS/MS. Searching MS/MS spectra against the multi-species iPtgxDB allowed to identify novel sProteins which were further screened for metatranscriptomics expression evidence of the respective genes and validated with synthetic peptides