Microbiome Monitoring: Keeping Track of the Microbes in the Body

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The microbiome is the community of microbes that exist in the body, and it is possible to monitor this microbiome and even keep track of the types of microbes that are present. Two subjects in a study monitored their microbiomes for one year and recorded microbiome dynamics associated with lifestyle events. A report on the results of their study was recently published in Genome Biology.

Both subjects in the study were also authors on the paper. One subject was Eric Alm, who is a biology professor at MIT, and the other subject was Laurence David, who was Alm’s graduate student. For one year, the two participants in the study collected daily stool samples and the bacterial composition in the stool was analyzed. One of the subjects also collected saliva, so that a comparison could be made between the bacteria from the gut and the bacteria from the mouth. DNA analysis was used to determine the composition of the microbiome based on known DNA sequences of various types of bacteria. The subjects also kept track of their daily lifestyles including diet, exercise, sleep habits and mood. In addition, they used an iPhone app to record and store the data during each day.

The data that was collected on the bacteria was massive and could be considered as an example of a “big data” project. The researchers created a plotting method to simply the results for interpretation. Plots that used colors were created showing daily fluctuations in the bacteria numbers. It was recognized that the different types of bacteria could be grouped and the plots were able to display fluctuations in these groups.

Dietary changes were shown to produce daily changes in the microbiome. Certain types of foods were found to alter relative bacterial levels. For example, the bacteria Eubacterium rectale, Roseburia and Bifidobacteria and were increased when more fiber was eaten. Faecalibacterium prausnitzii and other bacteria that are known to help with prevention of inflammatory bowel disease were shown to have an increased level after eating a citrus type of food.

Each of the subjects had a major lifestyle event that affected their mibcrobiome composition dramatically. One subject had food poisoning due to Salmonella and the other subject had an experience with severe diarrhea when traveling to Thailand. In the subject that suffered with Salmonella, the percent of Salmonella in the microbiome from the cut jumped to 30 percent. In addition, the bacteria that are known to be good for health were reduced to very low levels during the infection with Salmonella. The beneficial bacteria then rose to approximately 40 percent in the microbiome after the infection and these bacteria were comprised of new strains.

An interest of the scientists that carried out the study is to learn why the microbiome returns to a state of normalcy, meaning average numbers of bacteria, after some kind of disturbance. Another interest is to learn how the immune system reacts to variations in the gut microbiome, specifically in respect to the activation of cytokines and hormones. These will likely be topics of future research studies.

Monitoring one’s microbiome daily can be seen as a major step up in the Quantified Self movement. Monitoring how many calories one eats during the day or how many steps one takes are relatively simple and the data can be interpreted easily. Keeping track of microbes in the body, however, is a much more complicated matter and it requires a lot more than a simple calculator. People who are fascinated with keeping track of things in their body should add their microbiome to the list.

By Margaret Lutze

Genome Biology
National Geographic
MIT News