When we take a swab and perform 16S sequencing we assume that this gives us a picture of who is present in a bacterial community. But actually what we’re measuring is what DNA is present on that surface. This technique doesn’t tell us who is alive, who is dead, who is viable, who is non-viable, who actually lives and is metabolically active in that community, and who was just randomly deposited there.
A number of approaches are aimed at better understanding a community. These include PMA, flow cytometry, DNA degradation clocks, metatranscriptomics and others.
Parag Vaishampayan from JPL and myself are organizing a workshop May 13-14 at UC Davis to discuss this topic and the various techniques and approaches people are using to address this issue. The workshop will be small, to keep it discussion oriented and by invitation only. If you’re interested in attending, or have a recommendation of someone to include, please drop me a line (email@example.com).
Also looking for discussion topics if there’s anything you think would be good to cover as such a workshop. We’ll be sure to tweet and blog about the discussion as much as possible!