File:My Oral Microbiome (7869089732).png

I sent my saliva to China,

to the largest sequencing lab in the world,

and they did a whole genome sequence of me,

and most of me is not human.

Here are the bacteria living in my mouth, a pre-launch test from the first commercial service to offer a whole genome sequence of the whole lot:

Genus — Mapped reads Prevotella — 2,573,674 Neisseria — 2,327,172 Haemophilus — 2,222,674 Streptococcus — 1,556,743 Rothia — 1,232,209 Veillonella — 945,180 Fusobacterium — 560,693 Campylobacter — 234,182 Atopobium — 231,213 Aggregatibacter — 202,541 Capnocytophaga — 116,289 Leptotrichia — 85,449 Bacteroides — 67,333 Clostridium — 41,490 Porphyromonas — 36,489 Paracoccus — 36,061 Actinobacillus — 26,650 Malassezia — 26,553 Selenomonas — 23,646 Pseudomonas — 14,293 N.gonorrhoeae — 10,950 Burkholderia — 10,630 Ruminococcus — 10,403 Staphylococcus — 9,584 Mannheimia — 8,730 Pasteurella — 8,134 Riemerella — 6,762 Megasphaera — 6,576 Streptomyces — 5,041 Laribacter — 4,230 Acinetobacter — 2,752 Other bacterium — 174,580

I saw a few things in there that struck me as quite peculiar... things that one might expect, ummm, elsewhere on the body... and so I shared the results with some microbiome experts who have a keen interest in this. Here’s what U.C. Davis Professor <a href="http://phylogenomics.wordpress.com" rel="noreferrer nofollow">Jonathan Eisen</a> had to say:

“The first thing I usually do for samples is look at % by phylum. See pie chart for yours below.

The #s for each microbial group (i.e., Staphylococcus, Neisseria, etc.) do not seem out of the ordinary too much. Though I note - some studies have found high levels of Haemophilus in oral samples, and others seem to have not found them. Not sure why at this point but looking into it. The high levels of Neisseria (the genus that N. Gonorrhoaeae is in) is a common one, so nothing to worry about there. Prior studies have sometimes found high #s of Corynebacteia. These are not there on your list.

Also - the Malassezia is interesting. It is a fungus genus. Commonly found on the skin of various mammals including humans. Some types are found to be infectious, but I think most are just hanging out doing nothing. I have never seen it in mouth-microbe data, but if it was there, it would probably be missed by most studies since they focused on bacteria.”

Eisen also pointed me to the studies below. The microbiome was one of the major topics of interest at <a href="https://www.flickr.com/photos/jurvetson/7718640428/#comment72157630919738660">scifoo</a> this year, where they claimed “20% of what’s in your blood is from the bacteria in your gut.” (I found earlier <a href="http://www.pnas.org/content/106/10/3698.long" rel="noreferrer nofollow">studies</a> supporting 10%).

Looking at the bigger picture, <a href="http://ronbarak.tumblr.com/post/28845227100/only-you-11-things-that-make-each-of-us-a-one-off-by" rel="noreferrer nofollow">New Scientist</a> summarized some of the recent findings:

“One aspect of your uniqueness isn’t, strictly speaking, part of you at all. It comes from the 100 trillion bacteria that live both on and in you. They outnumber the body’s cells 10 to 1 and in genetic terms they are even more dominant… You’re 0.7% human

A recent study found that a unique bacterial fingerprint is transferred from our fingers to the things we touch, such as a computer keyboard or mouse, and will hang around for up to two weeks [think of the forensic applications! ]

Bacteria also contribute to uniqueness by modifying our metabolism. All humans share a basic biochemistry, but layered on top of this is a microbial biochemistry that is much more diverse. The metabolites that microbes produce affect a range of things, including cholesterol and steroid metabolism.

What this ultimately means is that without our non-human component, we wouldn’t be ourselves at all.”

And in rat studies, you can turn obesity on and off with a flush and refresh of new gut bacteria. (<a href="http://www.newscientist.com/article/mg21428625.100-gutmicrobe-swap-changes-eating-habits.html" rel="noreferrer nofollow">summary</a>, <a href="http://www.sciencedaily.com/releases/2012/08/120815174902.htm" rel="noreferrer nofollow">more</a>).