Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes

Nat Commun. 2020 Sep 18;11(1):4708. doi: 10.1038/s41467-020-18543-0.

Abstract

While the field of microbiology has adapted to the study of complex microbiomes via modern meta-omics techniques, we have not updated our basic knowledge regarding the quantitative levels of DNA, RNA and protein molecules within a microbial cell, which ultimately control cellular function. Here we report the temporal measurements of absolute RNA and protein levels per gene within a mixed bacterial-archaeal consortium. Our analysis of this data reveals an absolute protein-to-RNA ratio of 102-104 for bacterial populations and 103-105 for an archaeon, which is more comparable to Eukaryotic representatives' humans and yeast. Furthermore, we use the linearity between the metaproteome and metatranscriptome over time to identify core functional guilds, hence using a fundamental biological feature (i.e., RNA/protein levels) to highlight phenotypical complementarity. Our findings show that upgrading multi-omic toolkits with traditional absolute measurements unlocks the scaling of core biological questions to dynamic and complex microbiomes, creating a deeper insight into inter-organismal relationships that drive the greater community function.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaea / genetics
  • Archaea / metabolism
  • Bacteria / genetics
  • Bacteria / metabolism
  • DNA
  • Gene Expression Profiling
  • Genome, Microbial
  • Humans
  • Metabolomics
  • Microbiota / genetics*
  • Microbiota / physiology*
  • Phenotype
  • Proteins / genetics*
  • Proteins / metabolism*
  • Proteome
  • Proteomics
  • RNA / genetics*
  • RNA / metabolism*
  • Transcriptome
  • Yeasts

Substances

  • Proteins
  • Proteome
  • RNA
  • DNA