Ranjan Sinha

December 23, 2019

What Type of Microbiome Do You Have? Spoiler Alert: We Probably Can’t Tell

The start-stop world of microbiota classification.

As we’ve observed before, your mouth probably contains as many different bacterial species as there are animal species in the National Zoo in Washington, D.C. (about 300).
But your oral cavity is a mere minnow in bacterial diversity compared to your gut, where somewhere between 500 and 1,000 different types of bacteria hang out.

Now, with such variety and, dare I say it, imprecision (500 to 1,000 seems like a wide range to me), you really can’t blame scientists for trying to introduce some structure and classification into the microbiome.
It’s what we humans do, after all.

We classify things to help us stay organized.
Safeway and Home Depot both sell stuff, but it’s different stuff, so we call one a supermarket and the other a home improvement store, and we know where to go when we want to buy dinner, and where to go when we want to paint the kitchen.

In fact, as experts at UCSD point out, our prehistoric ancestors stayed alive to some extent because their rudimentary classification systems enabled them to know which plants and animals were safe, and which weren’t.
Of course, scientists love a good taxonomy, a systematic structure of groups and categories, and the king of taxonomies has to be Swedish scientist Carl von Linnaeus’s “Systema Naturae” published in 1735, which labels, groups and classifies every living thing.

We have him to thank for being able to identify ourselves as Homo sapiens (from the genus “Homo”, and the species “sapiens”), for instance.
So back to the microbiome, and it would clearly be helpful if there was some broad overarching way to categorize our overall gut microbiomes.
Indeed, for a while in 2011 it looked as though this might indeed be possible.
A study led by Peer Bork from the European Molecular Biology Laboratory in Germany suggested the existence of three very specific overall bacterial profiles which he called “enterotypes”.

Bork et al proposed that these might operate something rather like blood types, not dictated by age, gender, bodyweight or nationality/race.

Type 1, he said, was typical of those who eat a typical Western diet with plenty of protein and animal fats, and was dominated by high levels of Bacteroides.

Type 2 had few Bacteroides but plenty of Prevotella, which would be true of someone consuming more carbohydrates, especially fiber.

Type 3, meanwhile, was notable for high levels of Ruminococcus, a genus that sits in the Firmicutes division.

This all seemed convenient. Tidy even.
But then more science happened.

And along came a much more ambitious 2012 study, with 663 participants as opposed to 2011’s rather modest 22.
It showed that the boundaries between the enterotypes were fuzzier than the earlier work had suggested.
The new research also added the genus Methanobrevibacter to Type 3.
Sadly, to some extent, once the walls had started to crumble, they then came tumbling down.

Don’t you just hate it when that happens?

In fact, an even bigger study in 2012 (with 1,200 participants) concluded that the idea of enterotypes really didn’t stack up at all and that our microbial communities actually exist on a continuum, albeit one with a preponderance of Bacteroides or Prevotella at the ends (where most people’s microbiota sit).

Since then?
Will the jury is out, to be honest.
Some say the whole enterotypes thing doesn’t hold water, but then others (like the authors of a 2014 Korean paper) suggest that those in their study definitely fell into one of two groups.
Hmm. More work needed probably.

But there’s no denying the value of a robust taxonomy which, as Wikipedia thoughtfully reminds us, is not to be confused with taxidermy.
But come on though, has a Wikipedian seriously ever *tried* to stuff a bacterium?

Have a great week!

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