I delivered the bad news to my husband on Christmas morning, “Oh no! You have the bad gut microbes!” Back in June, we sent stool samples to the American Gut project, and we happened to receive our results just in time for the holidays. My proclamation stemmed from my knowledge of several high profile scientific papers, which found that a higher ratio of a specific group of bacteria correlates with obesity (1-3). Kevin’s gut is dominated by these same bacteria. Upon further reading, however, I discovered another more comprehensive study of lean and obese people that found no signature pattern of gut microbes (4). I realized that although it is incredibly interesting to learn which microbes live inside of us, this science is still too young to jump to any definitive conclusions. Determining which bacteria inhabit our bodies is the first step in understanding how these organisms influence our health, and participating in studies such as American Gut will help to collect information such that in the future we may be able to make health recommendations based on our microbial populations.
Gut microbes? By now you may have heard that bacteria living on your body outnumber your own cells 10 to 1. These bacteria both eat and excrete as part of their daily routine, so it is not difficult to imagine that these single-celled organisms affect our bodies’ physiology. Currently, the microbes on our skin, in our mouths, genitalia, and guts are being characterized in hopes to better understand how they influence our health (for example, the Human Microbiome Project). Most of these scientific studies focus on identifying which bacteria live on us. With this information in hand, researchers can further analyze these microbes to determine their metabolic potential. After cataloging who lives on us, the next questions involve categorizing what these bacteria are capable of metabolizing -- what molecules are they releasing, and how do these compounds affect our health? But logically, we must first begin to understand “who” before we can most effectively answer “what” they are doing.
In my quest to figure out who lives on me, I joined the American Gut project. This study is interested in determining how your diet influences your microbial population. Therefore before you send in your sample, you are instructed to keep a food journal for at least a week, which details everything you consume. On the day you ship your sample, you fill out a detailed questionnaire including your daily percentage of calories from carbohydrates, protein, and fat as well as how many different species of plants you eat in any given week. Several months later, you receive a poster in the mail that summarizes your results.
Here are some of the highlights of my gut microbes:
Humans are colonized by four main groups of bacteria - predominately Bacteriodetes and Firmicutes, with smaller populations of Actinobacteria and Proteobacteria. These groups are referred to as phyla. If you remember from biology, all living organisms can be organized according to how closely they are related. As you move down the scale of kingdom, phylum, class, order, family, genus, and species, the more genetically similar two living beings are. For example, plants and animals are in different kingdoms, whereas humans share the same family with chimps, gorillas, and orangutans. The plot above shows that my gut microbiota is dominated by the phylum Bacteriodetes. In contrast, my husband contains mostly Firmicutes, which was surprising to me because we live together and eat basically the same food. I also convinced my grandmother to participate in the study. Interestingly, her gut is colonized with predominately Bacteriodetes, like me, which suggests that genetics may play a role in shaping our gut ecology.
My most abundant microbe (71.5%!) is a subgroup of Bacteriodetes, the genus Bacteriodes. This result is consistent with the finding by Wu et al. that consumption of saturated fat and animal protein increases these microbes (5). I do not eat mammals, but I do consume plenty of dairy products, which are full of these nutrients. This same study also showed that the genus Prevotella (phylum Bacteriodetes) is associated with diets rich in plant material and fiber, which unfortunately were not present in my stool despite the fact that I eat a lot of vegetables. Bacteriodes, however, can also break down plant starches. This example shows that although it is helpful to know which microbes live on me, it would be even more useful to know what metabolic functions my microbes possess and furthermore what my Bacteriodes are actually eating and excreting inside of my gut.
Switching gears to some of my bacteria in different groups, my gut contains Faecalibacterium (phylum Firmicutes), whose presence is inversely correlated with gut inflammation, which is good (6). I also have an enriched population of Sutterella, which belong to the order Burkholderiales (phlyum Proteobacteria). These bacteria may be enhanced on a diet that is high in cruciferous vegetables (broccoli, cauliflower, cabbage, etc) (7), which I do eat a lot of. If specific vegetables enrich bacterial populations in our guts, how stable is our gut ecology? Does it change after every meal? Or only after a dramatic shift in dietary habits?
Diet influences our bacterial populations because what we put in our mouth ultimately selects for the type of bacteria that will thrive in our guts. Nutrients that are not absorbed by our bodies provide fuel for our gut microbes. Can we change our microbial landscape by changing our diet? I’ll go into more detail on this topic next time, so stay tuned.
References:
1. Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, et al. Obesity alters gut microbial ecology. 2005. Proceedings of the National Academy of Sciences, 102: 11070–11075.
2. Ley RE, Turnbaugh PJ, Klein S, Gordon JI, et al. Microbial ecology: human gut microbes associated with obesity. 2006. Nature 444: 1022–1023.
3. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. A core gut microbiome in obese and lean twins. 2009. Nature 457: 480–484.
4. Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS. A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. 2014 PLoS One 9:e84689
5. Wu, G. D. et al. Linking long-term dietary patterns with gut microbial enterotypes. 2011
Science 334: 105–108
6. Willing, B. P. et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. 2010. Gastroenterology 139: 1844–1854
7. Li, Fei; Hullar, Meredith A. J.; Schwarz, Yvonne; Lampe, Johanna W. Human Gut Bacterial Communities Are Altered by Addition of Cruciferous Vegetables to a Controlled Fruit- and Vegetable-Free Diet. 2009. Journal of Nutrition 139: 1685-1691
