Great support for your question, dear Catherine. Such is, indeed the case. Epigenetics, and microbiota have come to highly enrich our understanding of life and evolution. The road, though, was not easy (as we know it from L. Margulis' own experience). The bibliography about this is increasingly rich and large.

Dear Catherine,

I will not get into an argument I do not know, but I am very interested.  I also have recently started to get interested in something close to the topics that you propose (although without arriving at cicardian rhythms that I follow for other reasons).

So I can only suggest a nice article by Grace Yim about "microbial metabolites constitute a large collection of cell-signaling molecules that regulate gene expression in microbial populations and possibly the interactions of these populations with the surrounding organisms" (attached). Finally, there is the long history on 'Helicobacter pylori' (I enclose a recent review).

I apologize for my small contribution with arguments that you probably already know, but I'll watch carefully what you will discuss and / or you will report.

Best wishes, Maurizio

This weekend I will try to read some of Lynn Margulis' articles.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460424/

Article Antibiotics as signaling molecules