‘Who is doing what in our gastrointestinal system’ is a challenging question. Although 16S rDNA sequencing can identify community members (‘who’) and metagenomics can resolve the functional diversity (‘what’), assigning a distinct gene function or metabolic pathway to an individual bacterium is difficult.
The current project aims to identify and locate taxonomic groups involved in (i) plasmid encoded antibiotic resistance gene transfer and (ii) digestion of xylan dietary fiber in microbial ecosystems from human gastrointestinal origin with the novel epicPCR approach. The Emulsion, Paired Isolation and Concatenation PCR (epicPCR) method will be adapted to link taxonomic markers (16S rRNA gene) with plasmid encoded lactamase genes or chromosomally located endoxylanase genes in the Mucosal Simulator of the Human Intestinal Microbial Ecosystem (M-SHIME). This approach will be combined with several experimental setups to test the impact of antibiotics,
plasmid conjugation inhibitors and pre-/probiotics on the community composition and location.
These findings will lead to a better insight into the understudied field of antibiotic resistance spreading and xylan dietary fiber digestion in the human gastrointestinal tract. In a final experiment, the feasibility of an integrated reverse transcriptase step in the epicPCR protocol will be evaluated. This would enable linking transcriptional data with specific taxonomic groups, which
will be valuable for further fundamental research.