Thursday, June 25, 2015

Which species do I track?

At the Microbiome breakout during last week’s Quantified Self Conference, several people were interested in the list of organisms I track.

Here’s the list, along with my own results for the past seven samples: 

Bifidobacteria Longum0.00%NA0.19%0.96%0.21%0.05%0.00%species
Faecalibacterium prausnitzii9.96%6.23%0.58%9.54%13.64%10.64%16.56%species

Why this particular list? I’ll be honest: no particularly strong reasons. Most of these are derived from various conversations with the super-knowledgable Grace Liu, now based at The Gut Institute.  I strongly encourage you to follow her there, and on twitter @gut_goddess for better information.

Note: after speaking more with experts at uBiome and elsewhere, I’ve concluded that it’s okay to trust the species information for many of the organisms, including the ones above. Although 16S rRNA is not very reliable at detecting anything below the genus level in general, there are some organisms where the genus is the relevant species. Sure, I suppose it’s theoretically possible that another species may exist as part of that genus, but in reality none has been found in humans.

Also note: even the word “species” doesn’t mean the same thing for bacteria that it means when speaking of lifeforms like humans that reproduce sexually. After all, bacteria reproduce by simply dividing in half. There is no concept of of a “species divide” like that one that prevents a dog, for example, from reproducing with a cat. There is plenty of gene transfer and gene mixing that occurs among bacteria, but that often (perhaps usually) crosses the lines of what we might think of as unique species.

The bottom line: don’t get too hung up on a particular species. If something is biologically active, it may not matter whether you’re tracking at the genus level or the species level. Well, maybe it matters, but for most purposes you won’t get any closer by knowing the species name. In some ways, knowing that something is a member of a particular species can give you a false sense of confidence, when in reality science knows far less about the activities of these organisms than we would all hope.

Do you have any specific organisms that you like to track?