Identification of commensals and molecular components mediating trypsin degradation in the large intestine

Faecal samples were collected from germ free mice colonized with the non-trypsin-degrading 34-mix in addition to the wild type or 00502 knockout strain of P. clara. Composition of the microbiota was analysed by 16S rRNA gene sequencing. In a separate and preliminary experiment, faecal samples were collected from GF mice gavaged with faeces from a Crohn's disease patient together with the wild type or 00502 knockout strain of P. clara, and the composition of the microbiota was analysed by 16S rRNA gene sequencing. Germ free mice were colonized with the donor C microbiota (caecal contents from mouse No.5 orally gavaged with Donor C faeces) and concomitantly treated with ampicillin, metronidazole, tylosin or vehicle control. Faecal samples were collected on different dates and the microbiota composition was analysed by 16S rRNA gene sequencing to correlate the abundance of individual strains with faecal trypsin levels.