Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach

In
vitro culture based approaches are time- and cost-effective
solutions for rapidly evaluating the effects of drugs or natural compounds
against microbiomes. The nutritional composition of the culture medium
is an important determinant for effectively maintaining the gut microbiome
in vitro. This study combines orthogonal experimental design and a
metaproteomics approach to obtaining functional insights into the
effects of different medium components on the microbiome. Our results
show that the metaproteomic profile respond differently to medium
components, including inorganic salts, bile salts, mucin, and short-chain
fatty acids. Multifactor analysis of variance further revealed significant
main and interaction effects of inorganic salts, bile salts, and mucin
on the different functional groups of gut microbial proteins. While
a broad regulating effect was observed on basic metabolic pathways,
different medium components also showed significant modulations on
cell wall, membrane, and envelope biogenesis and cell motility related
functions. In particular, flagellar assembly related proteins were
significantly responsive to the presence of mucin. This study provides
information on the functional influences of medium components on the
in vitro growth of microbiome communities and gives insight on the
key components that must be considered when selecting and optimizing
media for culturing ex vivo microbiotas.