Last week, I got my results from American Gut back and let’s just say I was pretty shocked at the results.
Below, you can see the graph and table I received, demonstrating how vastly different my gut microbes are compared to most people that participated in the study.
I was taken aback by how much red made up my frequency bar (around 90%)… was this something to be concerned about? What could have made my gut bacteria shift to be predominately Firmicutes, and is that a good or bad thing? I was somewhat pacified by seeing how Michael Pollan’s gut bacteria was slightly more Firmicutes dominant than the average population, but nowhere near as much as mine was. It seemed like it was time to do some digging into the literature to determine if there was anything to be learned from this data.
One thing that was somewhat concerning to me was that I’ve recently been on a pretty serious antibiotic treatment for chronic Lyme disease. Last year, I spent about six months taking 5 different antibiotics twice a day. That’s some pretty serious antimicrobial action. I didn’t have any significant gastrointestinal symptoms from this hardcore regimen, but that’s not to say they weren’t having an impact on my gut flora. Could this have been enough to majorly shift my gut bacteria to the pattern I saw in my results?
I felt like I needed to get some more background information on what was, and wasn’t, a “normal” gut microbiome. I started my reading by checking out a guest post on Free The Animal regarding a man who goes by “Tatertot Tim” who describes his own American Gut results. He’s a habitual resistant starch consumer and someone who follows a primal or “Perfect Health Diet” type of eating pattern, so we know he eats pretty healthily. He also adds 4 tablespoons of resistant starch (RS) in the form of unmodified potato starch on a daily basis. You can see his results below:
That’s a significantly different result than mine! If you’re interested in reading about Tim’s self-study of his own bacterial breakdown, you can check it out on Free the Animal. I think he has some interesting insight into his results, especially since he’s diligent about including RS in his daily diet, and we know that this is a major food source for beneficial gut bacteria.
Jeff Leach also wrote an interesting post on the Human Food Project blog. Jeff is one of the major directors of the American Gut project and has written some great posts about the research they’ve been doing around the world. In his post entitled “Sorry low carbers, your microbiome is just not that into you”, Jeff discusses how the ingestion of fermentable substrates, in particular fiber, makes a big difference in the health of the gut bacteria. A reduction in this fermentation can cause an increase in pathogenic Proteobacteria, and a reduction in the production of butyrate, which has beneficial effects including the suppression of inflammation and resistance to metabolic and physical stress. Thus a reduction in fermentation in the gut is an undesirable outcome that may occur more frequently in diets very low in carbohydrate.
At first, I saw this as a positive, as Firmicutes are typically fiber-degrading bacteria, and I had a high level of them. Surely this must protect me against gut-related disorders such as leaky gut or inflammatory bowel disease?
However, other research struck me as this being a potential issue. For example, some research suggests that Bacteroidetes may be protective against obesity. Not that I’m obese, but I’m certainly not as “lean” as I’ve been in the past, and I’m curious as to whether or not my gut bacteria is playing a role in that at all. In mice, those with a high Firmicutes to Bacteroidetes ratio were shown to have a higher amount of body fat, which is postulated to be from Firmicutes’ increased capacity for absorbing energy from food. But these studies were done in animals… so what can I really learn from them?
According to Jeff, not much. In some personal email correspondence, he told me that “the Firmicutes to Bacteroidetes ratio is meaningless”, and that “people are working off old data that suggest higher levels of Firmicutes is associated with obesity. Not the case.” That’s reassuring! Not that I’m concerned about obesity necessarily, but I’m hoping that my ~15 pounds of weight gain during grad school can be solely attributed to stress and inadequate physical activity (which would make sense).
So what can I really glean from my results? It’s hard to make any significant conclusions, especially from one sample, but here are some interesting tidbits I came across while researching the strains in my sample:
- About 50% of my sample consisted of Lachnospiraceae and Ruminococcaceae, which have been associated with the maintenance of gut health. This is because they are active plant degraders, and produce the butyrate necessary for the health of the lining of the colon. So this means my gut might be especially proficient at turning plant fibers into short chain fatty acids that can be used for energy. Sounds like a positive!
- I had an average level of Proteobacteria, which are typically pathogenic and undesirable components of the gut. Jeff told me that these are more likely to “bloom” after antibiotics treatment. Notice Michael Pollan has a low level of those bacteria? And Tim from the Free the Animal post had nearly none? I’m wondering if this has something to do with the amount of RS that Tim consumes. I’m glad my Proteobacteria aren’t higher than the average, but that doesn’t mean I don’t think they could be lower.
- Blautia, which was comparatively abundant in my sample, is another interesting genus which metabolizes hydrogen and carbon dioxide (H2/CO2) to acetate, and ferments fibers and carbohydrates such as cellobiose, fructose, galactose, glucose, lactose, maltose, mannose, and more. Acetate is another fuel for the cells of the gut lining, so I’d see this as a potential positive.
- Sutterella is a Proteobacteria, and probably one of the major components of this phylum in my gut. Oddly enough, these bacteria are found to be higher in children with autism. Obviously I don’t have autism so I’m not that concerned about this link specifically, but it’s worth acknowledging that I have a relatively high load of this undesirable bacteria.
- Betaproteobacteria can also be pathogenic, including the rare genus Burkholderia, which was present in my sample. What does this mean? Who knows. I did work on a horse farm in Australia for 3 months, so I suppose it’s possible I picked that bacteria up while working there. I’d like to hope it’s not something that is causing any significant issues for me. I’m not thrilled that this class is the most “enriched” of my sample though.
- My Oxalobacter genus was enriched as well, and these bacteria have been associated with a reduced risk of kidney stones. I count this as a positive.
- Holdemania is not a pathogen, and that’s about all I could find out about this newly discovered bacteria.
- My Ruminococcus bacteria were not only proportionally numerous in my sample, but also well-enriched. Some Ruminococcus types are excellent resistant starch degraders, and can also degrade cellulose which is abundant in plant fiber. However, some Ruminococcus types are mucin degraders, which can increase the risk for IBD since mucin is protective of the gut lining. I can’t tell which of these bacteria are more dominant in my sample, so I can’t really make any guesses about whether this is good or not. Might just be a wash.
- Supposedly, resistant starch is effective at reducing Firmicutes and increasing Actinobacteria and Bacteroidetes. This would explain Tim’s high proportion of those two phylum, and perhaps it could be a strategy for me to increase those two types of bacteria in my gut. The question is, though, do I really want to increase those bacterial types? And what would be the benefit? If I could reduce the number of Proteobacteria in my gut, I think that could be an improvement. And who knows, perhaps a higher level of Bacteroidetes could assist with weight management? It’s hard to tell what might happen, if anything!
So in light of the research I did, I’ve decided to run a little experiment. I’m going to try consuming at least 1 tablespoon of unmodified potato starch (resistant starch) on a daily basis, along with probiotic powder from Designs for Health. This probiotic contains Bifidobacterium, which is a Actinobacteria and may provide a range of beneficial health effects, including “the regulation of intestinal microbial homeostasis, the inhibition of pathogens and harmful bacteria that colonize and/or infect the gut mucosa, the modulation of local and systemic immune responses, the repression of procarcinogenic enzymatic activities within the microbiota, the production of vitamins, and the bioconversion of a number of dietary compounds into bioactive molecules.” The probiotic also contains Lactobacillus, which is a Firmicutes and may “allow for the proliferation of sensitive yet beneficial microbes that are important parts of the fecal flora, and in doing so can help in replacing useful bacteria in the intestinal tract after heavy antibiotic usage.” Sounds like that could be useful in my case!
I’m really curious to see if this protocol has any significant effects on my gut bacteria. My ideal outcome based on my cursory research is that my Proteobacteria (yellow-orange) levels would decrease, my Bacteroidetes (orange) would increase, and my Actinobacteria (yellow) would be at a measurable level, since right now it appears that I have very little in comparison to the other classes. I’m torn about whether having a high proportion of Firmicutes is really an issue. I’d like to think its from my high consumption of plant foods, but who knows. I’m not concerned if those stay the same, though.
I’ll be doing the resistant starch + probiotic protocol for the next month, and then I’ll retest using the same type of kit I had my original test done with. While this won’t really allow me to make any major conclusions about the health benefits of this protocol, I will be able to see if this method is able to significantly shift my gut bacteria to what I perceive to be a healthier balance. Of course, it’s difficult to know if there will be any real benefit to doing this experiment, but I’m under the impression that it at least won’t be harmful. (I’m not the only one who is trying this out!)
I’ll run the test again near the end of January, and then when I get my results back, I’ll share them with you all! Should be an interesting experiment!