Tracking the Daily Microbiome

human microbiome by Hank Osuna
Human Microbiome by Hank Osuna

Humans are essentially 90% bacteria. These bacteria pepper our skin and hang out in our digestive tracts, helping to break down complex carbohydrates and keeping bad bugs in check.
We know how the human microbiome (our collection of bacteria) gets seeded during the birth process, and we know how bacterial populations change in the aftermath of a biological apocalyse, such as their human host taking a course of antibiotics. Yet we know very little about how the microbiome changes on a day-to-day basis.
Now, a team of scientists at Massachussetts Institute of Technology (MIT) have changed that by recruiting two individuals to provide samples of their poop and saliva every day for a YEAR to track their gut and oral microbiome signatures, and correlate them with lifestyle and activities.
Overall, microbe communities remained remarkably stable for months at a time. The three big variables – sleep, exercise and mood – failed to make much of an impact on microbe populations. Yet small dietary and lifestyle changes prompted rapid (next day) changes. Increasing fibre intake boosted populations of fibre-sensitive Bifidobacteria, Roseburia and Eubacteria. Bifidobacteria levels were similarly enhanced after eating live yoghurt cultures. Eating citrus fruits led to a jump in levels of Clostridiales bacteria, while dental flossing decreased saliva levels of the dental pathogen, Streptococcus mutans.
bacterial bodies bryan christie scientific american june 2012
Bacterial Bodies by Bryan Christie
The biggest changes in microbiome signatures happened in the wake of relatively rare life events. Travelling from a developed to a developing country caused numbers of Bacteriodes microbes to swell (as the host ate new foods) and increased Proteobacteria populations (as the host experienced bouts of diarrhea). These bacteria settled back down to normal levels when their host returned home. On the flip side, a bout of Salmonella food poisoning permanently wiped out a subset of native Firmicutes bacteria, which eventually got replaced by other similar species.
It appears, then, that our microbes generally go about their business in a happy, unpeturbed state. Yet inadvertently introducing them to a new experience can either result in a benevolent (often temporary) change, or a tremendously negative wipe-out event.

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