Chapter 4 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 species8! 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 microbiome9

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.


  1. See Frank et al. (2007) or click for the open access download

  2. See the detailed estimates here: Kraal et al. (2014)