Ranked species by the number of upregulated putative virulence factors in the metatranscriptome. Putative virulence factors were identified by alignment of the protein sequences from the different genomes against the Virulence Factors Database (VFDB) as described in the Methods section. Numbers in the graph refer to the absolute number of hits for the different species for the putative virulence factors identified. The numbers correspond to the total hits to different strains corresponding to the species in our database and they could be redundant. In red are members of the red complex. In orange are members of the orange complex. (A) Comparison of baseline to progressing. (B) Comparison of baseline non-progressing to baseline progressing.