The Microbe Alliance: Resisting Long-Term Change
For the class we discussed the resilience of soil microbes to change based on the rainfall study done by Banfield et al (2009). Our discussion reminded me of a talk I'd recently seen by Lawrence David from Duke University on the human gut microbiome. His talk was on his recent Genome Biology paper: Host lifestyle affects human microbiota on daily timescales. The paper follows two subjects (rumor has it these subjects were Lawrence and his PhD professor, Eric Alm) for a little less than a year. The subjects collected a ton of metadata along with their samples including diet. The study found that overall the subjects gut microbiota were stable and relatively unchanging. Despite the plethora of metadata they were only able to correlate a few different factors to the presence or absence of certain OTU's.
However, the authors were able to observe two large changes in the microbial gut communities of the subjects. Subject A traveled to Southeast Asia and as his diet drastically changed so did his gut microbiota. However, upon return from Southeast Asia, his gut community returned to the original community after two weeks. Subject B had food poisoning resulting in a drastic change to his gut microbiota. Subject B's gut microbiota never fully went back to the original community - however only 1.3% of reads post-infection were from new taxa and most of the community was closely related to the original community which the authors concluded was the result of a conservation of function over the conservation of specific species.
Sampling every day especially when dealing with the human gut, is a huge enterprise (hence the n of 2). However, Lawrence David et al were able to observe changes to the microbial gut communities of the subjects and the return of these communities to a stable state only because of the frequency of sampling that they did. In the Banfield et al study on grassland soil, they sampled only four times a year for two years. They did see the microbial communities change at two time points, but these changes had disappeared by the next time point indicating microbial resilience.
Although these two studies involve different environments (human gut vs. soil), they both bring up a good question: How often should we sample microbial communities to observe changes to community composition (temporary or permanent)? Across days? Across years? Across decades?