9 Microbes to Watch
Your gut as seen by consumer-priced sequencing technology contains many more unique microbial species than you can possibly track, at least hundreds in most people and potentially over 1000. I’ve seen 1083 different ones in my own results. And that’s just using the comparatively crude 16S technology. More comprehensive estimates based on other technology find as many as 36,000 different species1! With that much variety, how do we find the ones that matter?
Fortunately, only about 14 strains of 10 species account for 80% of a typical gut microbiome2
In this chapter, we’ll just consider the most common microbes and the overall consensus on what they do. Later, in the chapter on experiments, we’ll show more about how you can manipulate them.
What you’re really wondering is how does your sample compare to others? Do you have an unusual abundance (or lack) of a particular taxa? Is there something that might indicate a greater or lesser similarity between your sample and certain other types of people? That is a very difficult question which we’ll address over and over in this book, but for now let’s just look at overall abundances of some key microbes.
9.1 Phylum
This section is under construction
The gut microbiome of most westerners is dominated by Firmicutes and Bacteroidetes, which together make up 80% or more of the total sample. Most people also have smaller amounts of Actinobacteria, Proteobacteria and Verrucomicrobia. This overall composition is so common in healthy people that it’s tempting to assume their dominance is “natural” or “normal”, but like much else with the microbiome, the situation is different outside the western world, a clue that it’s difficult to summarize a single individual’s microbiome as “good” or “bad.” It all depends.
9.2 Genus
This section is under construction
You’re likely to hear most about the genus level because it’s the most detail that cheap sequencing technologies can get right – most of the time.
Bifidobacterium is a key component of virtually all popular probiotic supplements, partly because it is so easy to manufacture, but also due to its proven association with sleep and other aspects of health. A six month picture of my levels shows some dramatic ups and downs (See Figure @ref(fig:summarPlotBifido)).
9.3 Species
This section is under construction
When you hear the term “species”, you probably think of a specific kind of creature, like a dog or a cat. More generally, among the kinds of plants and animals we encounter in the visible world, the term “species” refers broadly to organisms that can mate with one another to produce offspring of the same kind. Cats and dogs are different species because they can’t mate with each other.
But bacteria don’t mate: they reproduce by dividing themselves in half. So how do we define a species? In fact, even terms like “parent” or “child” aren’t quite appropriate if each new cell is an identical copy of the old one. For very broad categories, like phylum or even genus, the similarities among like cells is high enough that we feel comfortable grouping them together with a common name, but at what point do we reach the lowest, most specific level.
The answer is tricky for another reason, called horizontal gene transfer, a process by which sometimes (in fact, quite often), a microbe will absorb genes from nearby organisms, altering its genome and its corresponding functions, sometimes significantly. Once that happens, the resulting new microbe can itself divide indefinitely, producing more and more copies of itself with the new gene. Although the new microbes still mostly resemble their original ancestor, if the new gene makes a protein that affects your body somehow, it might as well be an entirely different species.
See (Frank et al. 2007) or click for the open access download↩︎
See the detailed estimates here: (Kraal et al. 2014)↩︎