Metaproteome Analysis and Molecular Genetics of Rat Intestinal Microbiota Reveals Section and Localization Resolved Species Distribution and Enzymatic Functionalities

The digestion of food ingredients depends on the action
of the gut microbiota and has a significant influence on the health,
especially in the case of metabolic diseases, of the host organism.
Despite the relevance of the structure and functionalities in the
microbiota for the metabolism of the host, the spatial resolution
of microbial consortia and the functionalities in the different gut
sections of the rat are mostly unknown. Since there are suitable rat
models for human metabolic diseases, the microbiota of the rat is
of special interest. Samples along the intestinal tract of rats were
investigated using metaproteomics and 16S rRNA gene pyrosequencing.
The procedures for harvesting bacteria from the mucus and the content
of the gut sections and feces were optimized leading to 2802 nonredundant
bacterial protein groups in total that were assigned to spectra measured
by liquid chromatography–tandem mass spectrometry. The majority
of 16S rRNA genes and protein groups belonged to members of Firmicutes, Bacteroidetes and Proteobacteria. The functionalities in the enzyme repertoire were compared between
the mucus and the content of the large intestine sections and the
feces samples. This spatial resolution allowed pinpointing changes
in the community to specific metabolic capacities like carbohydrate
transport and energy conservation. The results showed that the mere
analysis of feces samples reflects the functions of the gut microbiota
only to a minor extent and sheds light on the metabolic interchange
between the microbiota and the host organism.