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Third, compliance with the action plan was assessed by the local guideline implementation teams' self-rating of progress; sites may therefore have rated their progress higher than the actual progress.
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Comparing baseline metabolic activities of non-progressing vs. progressing sites might give us a better understanding of the initial stages of disease and the role that the microbial community plays at this early stage of pathogenesis.
GO enrichment analysis comparing healthy sites from healthy individuals and baselines in progressing sites and non-progressing sites.
Additionally, we compared the metagenome of baseline from progressing sites and non-progressing sites with samples from healthy sites of periodontally healthy individuals from a previous study [ 1].
Other members of the community, usually not considered pathogens, showed a large number of putative virulence factors being upregulated during periodontitis progression and at baseline of progressing sites.
In spite of the commonalities in upregulated genes when comparing baselines of progressing to non-progressing sites and progression, there were also specific signatures of the two comparisons.
Interestingly, members of the red complex showed enrichment in response to antibiotics (beta-lactamase activity) during progression and even at baseline of progressing sites.
By comparing gene expression profiles before and after the manifestation of clinical disease, Yost et al. [ 2] were able to define functional signatures that distinguished the early metabolic activities occurring at progressing sites from those at non-progressing sites.
Differences in gene expression of the red complex between baseline samples from progressing vs. non-progressing showed similar enrichment of activities than when studying progressing sites.
When we compared progressing sites to their baseline, and baselines from progressing and non-progressing sites, the differences were larger.
When we compared the relative activities of viruses at baseline and progression, we observed high activity of phages and herpesvirus in the progressing sites in relation with the baseline samples (Additional file 2: Figure S14).
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