Thoughts on Fluidity and Inter-connectivity of Microbial Community Dynamics
This post is in response to: Shade, Ashley, Hannes Peter, Steven D. Allison, Didier L. Baho, Mercè Berga, Helmut Bürgmann, David H. Huber et al. "Fundamentals of microbial community resistance and resilience." Frontiers in microbiology 3 (2012).
Three ideas stood out to me: that their can be multiple stable states, the treatment of microbial communities as networks and the description of communities as systems of genes and their functions.
Multiple Stable States
I think that the idea that microbial communities might have multiple stable states that they can shift between is really interesting. This essentially lends weight to the notion that there is no one healthy microbiome. Instead there are dozens upon dozens of microbial communities that are "healthy". Also, microbial communities are composed of lots of different microorganisms living in concert. If the cellist suddenly dies (or leaves town), an orchestra will usually find another cellist, have someone already in the orchestra stand in or shift the music they play to not include cellos. The orchestra is no less stable, just slightly different.
Microbial communities as networks
People have been using network analysis to investigate complex traits and molecular pathways for a while now. I think that the using microbial co-occurrence to do network analysis on microbial communities is brilliant. Network analysis could potentially allow you to find/see functional groups of organisms (N fixers, etc) and might even allow you to discover common microbial "teams" (different microbes often found together). It'd be interesting to overlay functional information and metadata into the network analysis and see what falls out.
Communities as Systems of Genes and their Functions
We've talked a lot in this class about the dilemma of "who's there" vs. "what are they doing". A lot of the reason that I think we are interested in "who's there" is to try to either a) narrow in on the "who" to investigate that "what" or b) to use the "who" to estimate the "what". Genomics and high throughput sequencing techniques (amplicon gene sequencing, metagenomics, metatranscriptomics, metametabolomics, etc) allow us to more easily answer both the "who" and the "what". Although such techniques are data heavy (and thus, could cause us to drown in unanalyzed data), I think that these techniques will definitely be influential if not transformative for the whole of microbial ecology.