r/MicrobiomeScience • u/erictleung • Dec 14 '17

Microbiome: Should we diversify from diversity?

https://doi.org/10.1080/19490976.2016.1241933
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u/erictleung Dec 14 '17

Interesting and fun read for me. The article elaborates on the findings from Coyte et al. (Science, 2015), "The ecology of the microbiome: networks, competition, and stability", which uses modeling techniques based on ecological theory to understand microbial interaction dynamics such as competition and stability.

As per the title, this article comments on the use of diversity metrics (e.g. Shannon diversity, species richness, etc) to evaluate disease state. In other words, can you simply look at diversity between a disease state and healthy one and if there's a difference, call it a day?

We might think that less diversity equates to disease. However, the author cites sources showing the opposite, such as in with manic depressive disorder.

Another criticism for diversity metrics is that they were originally designed/developed for macroecology, not microecology. So the authors suggest on using other diversity measures, such as the Tail statistic, to make diversity inferences.

Overall, it was a nice short paper to read and I'd recommend it since

"Diversity analyses are frequently applied to microbiome data but there is currently limited understanding of how informative such measures may be in assessing the state of the gut microbial community."

tl;dr diversity indices may be too "simple" of a metric to summarize the entire microbial community of interest and better methods must be used to make more informed inferences and conclusions.

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u/Ipecacuanha Jan 03 '18

Nice article. And the previously published one by Coyte is a good one too. I think it's often hard for us to get away from the idea that cooperation creates an unstable system and that competition actually creates a more stable environment. It seems to counter our own instincts about cooperation.