Me and my microbiome

I first suspected I might be inhabited by traitors when I read a research paper linking gut bacteria to obesity. I was a newspaper reporter in St. Louis in 2006 when local researchers in Jeffrey Gordon’s lab at Washington University found that the mix of bacteria in the gut can help determine whether a mouse is lean or obese. I’ve been writing about the microbiome — the microbes that inhabit the body — ever since.

As an obese person, I’ve always suspected that I have fat microbes. But it’s also possible that my bacteria are lean and my genetics, diet and lack of exercise are holding them back from revealing my inner skinny person.

Until last year, I could only speculate about the bacteria that might affect my health. You would have had to be part of a scientific study to get your microbiome analyzed, and not always with personalized results. Then last February, two microbiome sequencing services launched through the crowdsourcing website Indiegogo. Finally, I had a chance to find out how my microbes stack up against everyone else’s.

I ordered sampling kits from American Gut — a research project at the University of Colorado Boulder — and from San Francisco startup company µBiome (pronounced “you-biome”).

Both services give clients personal information about their own microbiomes while collecting data for further research (although µBiome users can elect not to share their data).

My preliminary results from µBiome cover bacteria from my mouth — specifically my inner right cheek — and my gut (based on a fecal sample). The company expects to release full results in February so that its first batch of customers can see how they compare microbially with other µBiome clients and with people in other research studies, says company spokesman Nigel Tunnacliffe.

For now, my results are what a person who opts out of participating in research will get. It’s a list, and not all that revealing. I can see the top five residents of each body site, and an interactive online display allows me to drill deeper, sometimes showing a species but more often stopping at the genus or family level. It has been both fascinating and frustrating to read the Latin names of my bacteria but not know what they do or why they’re there. It’s a bit like looking at a stranger’s yearbook; you can put names with faces but have no idea what the people are like or why you should care.

A few things did jump out at me. My mouth is full of Haemophilus, for instance, a group that includes known respiratory pathogens. So when I went to the doctor for a recurring case of bronchitis, I brought my microbe profile with me and asked if he thought those bacteria could be causing the lung infection and sinus infections I routinely struggle with. He said he didn’t know enough about the microbiome to make a judgment. Haemophilus could be a normal mouth resident, and anyway the antibiotics he prescribed to knock out the bronchitis would probably kill them too.

Another mystery: I have cyanobacteria in my guts. Yes, a photosynthetic organism in a place where, as they say, the sun doesn’t shine. David Relman, a microbiologist at Stanford University, assures me that I’m not alone in harboring cyanobacteria, but he doesn’t know if the organisms are just passing through or actually live in the intestines.

Nor am I the only person whose guts house Oscillospira, bacteria previously found only in herbivorous animals, says Daniel McDonald, a CU Boulder graduate student who donates time to the American Gut project. When I asked him if my mix of microbes is normal, he said, “We don’t know what normal is.” I also can’t tell based on my preliminary results whether my microbes tend toward fat or lean.

At press time I didn’t yet have results from American Gut, which is processing samples in batches, but when they arrive I will have a microbial profile of myself suitable for framing. It will show the most abundant bacterial residents of my gut and my skin (sampled by swabbing my forehead). I’ll see how my microbes compare with others of my age and gender, or with a similar diet and body mass index. I’ll also get to compare myself with others in the American Gut project and around the world.

For now, I’m left wondering what my microbiome means. I’ll have more insight once I can access data from both services, and running another test now that I’ve finished my antibiotics could show whether the Haemophilus in my mouth are gone and how the drugs affected my gut microbes. But ultimately, my questions and others’ about what microbes mean to weight and health can be answered only if more people are willing to be research subjects and build the databases. We need more swabs for science.

Personal microbiome testing

Service	American Gut	μBiome
Cost	$99 for one body site, $180 for two; $2,500 for complete microbiome sequence including viruses and fungi; $15,000 gene activity analysis showing microbial functions	$89 for one body site; $159 for two body sites; $399 for five body sites
Body sites tested	Gut, mouth, skin, pet’s gut	Gut, nose, mouth, genitals, skin
Data you provide	One week of detailed food logs	Two days of detailed food logs
Results	Certificate listing your top microbes and how you compare with others. An upcoming online tool will allow you to see more microbes in your sample.	Interactive online tool showing bacteria present, with links to limited information about them. Upcoming tool will compare your results to others’.
Citizen science	Yes, but participation is limited to contributing data and tracking your own microbes. Other research groups may also use American Gut data in their studies. Identifying information is removed.	Yes, customers can participate in surveys to see how particular health conditions, diets or lifestyles affect microbes. uBiome and other researchers may also use the data in anonymous form.