Fig. 4.

Taxonomic distribution of proteins that are expressed by gut bacteria at the family level. The taxonomy bar-chart was built with Unipept and is based on the peptides that we identified with the Mascot-Server. In the upper row, the number of totally identified peptides with the Mascot-Server are shown for each individual. The second row shows the id (#) of the individuals within groups, which are shown in the third row. The 6-weeks longitudinal samples, label as “_T” (for time), are incorporated right to the same initial sample. Note: we are aware that the classification based on family level allows a gross interpretation of the active members and their functions. Unfortunately, the peptide information commonly obtained by metaproteomics does not allow a deeper taxonomic characterization. Analyzing the phylogeny of all peptides (after quality check) already enabled the affiliation down to family level of only approximately 50% of the peptides in each sample; the others could be either assigned to levels of phyla or order.