In an excellent post about the vaginal microbiome (the microbes that in the vagina), Dr. Rad asks:
I wonder if the idea of a ‘core microbiome’ came from Lourens Baas Becking’s oft-quoted idea in microbial ecology that ‘Everything is everywhere, but, the environment selects’? Ie putatively similar environments would lead to putatively similar microbiomes. Seems like the alternative to ‘core microbiome’ then would be the neutral theory of biodiversity. That is, if the core microbiome is hypothesized to arise from niche theory. Like I said, I ain’t no microbial ecologist.
I think there are two things going on here. When people began to look at the human microbiome, we had very small sample sizes–if you could generate ~200 sequences per sample, that was a lot–and we had very primitive ways of classifying sequences. So we were only looking at the very common stuff, and we were calling a lot of diverse organisms the same thing. So that led to a belief that there might be a core microbiome.
But the other key thing is the role of the large genomics centers in the Human Microbiome Project (note: until about a year ago, I was deeply involved in the Human Microbiome Project).
That project was developed and led by people who were genomicists, not microbial ecologists (or any other kind of ecologist; note: many moons ago, I was a marine ecologist). One concept that bacterial genomicists use in the notion of a ‘core genome’: the set of genes that are found in all members of a given bacterial species* (for instance, the best estimate for E. coli is around 1,200 out of 5,000). This is often thought of as the set of genes that ‘define’ that organism. By analogy, the core microbiome is the set of species that ‘define’ a body site.
This isn’t supposition on my part: I’ve actually heard this said multiple times.
But, as Dr. Rad notes, that concept seems to have fallen by the wayside–it appears that there are, at the very least, multiple potential core microbiomes. I’ve argued that, in healthy people, for a given body site, there might not even be definable microbiome types, although I haven’t seen the most recent data (Aside: I think with more people examined, we’ll see that, at least among the healthy, it’s a blur. A lot of the claims that microbiomes are distinct seem to fall apart once you get enough samples). It does remain to be seen if, at the functional level (what genes do), whether there is any conservation at any one body site.
To get back to Dr. Rad’s question, I’m fairly certain that the few people involved early on who were familiar with Stephen Hubbell’s The Unified Neutral Theory of Biodiversity and Biogeography did not think there would be a core microbiome. One of the early problems with a lot of the human microbiome work–and which was driven by NIH–is that it was viewed primarily as a medical genomics problem and not a community ecology one**. That’s changed, but the core microbiome concept is a legacy of that way of thinking.
*Given that many genomes or the genes called from them have errors, it’s a little trickier than this, but you get the general idea.
**I’m fairly convinced that it was originally viewed as just another
Scary Movie human genome project. However, human genomes do have a finite boundary and are very conserved (compared to a gut ecosystem). And unlike the human genome project, there is a huge ecological component to the analysis.