Behavioral Ecology Blog

I’m liveblogging a paper that should have been read a long time ago…. An Ecological and Evolutionary Perspective on human-microbe mutualisms and disease from the October 18 issue of Nature. 1st, the abstract:

The microbial communities of humans are characteristic and complex mixtures of microorganisms that have co-evolved with their human hosts. The species that make up these communities vary between hosts as a result of restricted migration of microorganisms between hosts and strong ecological interactions within hosts, as well as host variability in terms of diet, genotype and colonization history. The shared evolutionary fate of humans and their symbiotic bacteria has selected for mutualistic interactions that are essential for human health, and ecological or genetic changes that uncouple this shared fate can result in disease. In this way, looking to ecological and evolutionary principles might provide new strategies for restoring and maintaining human health.

Now I like the idea behind this paper.. It is clear that the now widespread use of molecular typing of bacterial communities has revolutionized the way we look at bacterial diversity and community structure.

My basic criticism of this paper- and the field in general is that it seems to have lost site of the big picture- especially as it relates to bacterial species and speciation.. I have blogged in the past about bacterial species concepts (here, here, and here) and have recently been thinking on the importance of function… It’s this… so what if we have 3,000 strains or phylotypes if all of them are doing the same thing (have the same function). This is especially true when we already know that evolutionary history is reticulated and generally difficult given the mixture of clonal and sexual reproduction, lateral and horizontal gene transfer (and this means that genetic differences may not accurately reflect evolutionary history). It’s this… one of the main ways we know 2 bugs (insects) are different is because the do different things.. If in an insect- it looked and acted the same (and had VERY small genetic distance)- it would be a long time before we could convince people that these things were different in a biologically meaningful way.

Are all these divisions biologically relevant (or is this another “lumpers vs. splitters” debate a la vertebrate systematics??

Anyway, they say something interesting in the intro by noting that when comparing the bacterial occupants of the human microbiome to other terrestrial vertebrates- similarities exist (i.e. there are related lineages, but different species). They interpret this as evidence for host-microbe coevolution, and maybe their right.  To this I’d add the possability that when looking within lineages- organisms share ecological “affinity”. Bacteria of lineage X are able to inhabit the nasty conditions of the vaginal epithelium, and therefore are present in vaginas..

Question: Does common ancestry of bacteria, or of hosts best explain the patterns we observe across terrestrial vertebrtates??  (I’d be interested to see what Jon Eisen/Genomicron has to say about this)

Anyways, from there the describe mutualism, and give a few examples of micribe-human mutualism.  This section is nice, but I skipped (skimmed briefly) it.

Now sorry about the bad image (and I have nothing to say about the Oak and Palm Tree), but is there a reason why we would exect a priori that the relationship between genetic distance and lineages should go from linear to exponential as we get to the species level?  I can’t think of any, and I bet that this is good evidence that most molecular bacteriologists are “splitters”. 

 Think so?

—Some stuff on adaptive landscapes, and commonalities between pathogenic and nonpathogenic bacteria–

Paths Forward:  An excellant section and way to end the paper. I agree strongly with their assertion that the most imperative task ahead is a full characterization of various microbiomes. For this, theey propose learning about individual variation, variation over time, and correlation between community structure and behavior (diet, sexual activity, hygieic status, disease, etc). This would be an excellent 1st stup huh..