My American Gut Results

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.

myamericangut

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.

antibiotics

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:

Image Credit: Free the Animal

Image Credit: Free the Animal

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!

  • Gilles Arbour

    Thanks for sharing Laura,

    What surprises me is your Oxalobacter numbers! This type of bacteria is known to be sensitive to many antibiotics including those normally given for Lyme disease. But congratulations anyway since it is quite problematic to be without this beneficial bacteria.

    • Laura

      I did stop my antibiotics treatment about a year ago, so it’s unclear what impact that had in the long run. But yes, it’s good to know that my results seem to be good on the whole!

      • Gilles Arbour

        Interesting and puzzling! Either the antibiotics did not kill all your Oxalobacter (but why not?) or even better you were actually able to re-inoculate this bacteria into your gut. If so, how did you do that? Do you eat wild fermented foods? Do you take some special probiotics? Do you eat lots of raw veggies? Some companies are spending millions of dollars trying to figure out how to re-implement this bacteria. Hey maybe you found out! :-)

  • Tim Huntley

    Thanks for sharing your results Laura. I had been debating getting a test kit, but based on what you learned, I believe it would be worthwhile.

    FYI, I started using RS about a week ago – so far, so good.

    …TIm

  • http://none jesse

    Hi Laura,
    Thanks for posting this article. I was following “tatertots” experiment and I’m wondering where you got the dose of 1tbsp. I went back and reread some of what he wrote, since most of us are basically leveraging his experience:

    “I would start out with 1-2TBS a day mixed in something cold. Then add 1 TBS per week, until you are eating about 4TBS a day. This will give you roughly 30g RS. The studies say 50-60g/day is overkill and less than 10g/day not enough. There is no dangerous amount. Your body will digest what it can and the rest will pass through harmlessly”

    It’s implied that 1tbsp is ~7.5g of RS. It may behoove you to get at least into that 2Tbsp range for your experiment? Of course if you have unlimited cash then that’s another story, do 1tbsp, test, 2tbsp, retest, cross yourself back over to 1tbsp, retest, share all the results :) :)

    take care,
    jesse

    • Laura

      I’m starting out with 1 TBS mainly because I don’t want to assault my gut with RS and cause digestive distress. I may make it up to 4 TBS per day by the end of the month but I don’t want to make any tolerance assumptions!

      • http://none jesse

        Sounds good. The other thing I hope people start reporting when they open up and share their gut biome results is whether they were born vaginally or with a cesarian section. Some people may not want to share that, but it seems to be a real factor.

    • stacy

      What do u mix the rs into? Can it be mixed into soups and hot foods?

      • jesse

        Hi Stacy,

        It mixes well with pretty much everything… I even took it with straight water many times. I also mixed it with bone broth and turkey drippings to make an awesome gravy this past thanksgiving. When you mix it with water you will find that it settles out after a couple of minutes so you’ll want to drink it in something with a lid that you can shake, or else in something you can stir rapidly to re-assimilate the RS powder.
        best.

        edit: when i made the gravy the temp was probably high enough that the RS was destroyed, FYI.

        • stacy

          How does heat destroy rs? Isn’t starch, starch regardless of heat?

          I can’t fathom downing this in water….. Seems like it would be tolerable in sauces and such

          Also,should people with Sibo avoid this? Would it feed bad flora?

          What brand is best?

          • jesse

            Starch isn’t starch… or else we wouldn’t all be talking about a particular subset of starch called Resistant Starch :) In this case the heat breaks down the RS into regular old starch. Look at a potato for example, raw it has some significant RS and when you cook it then it is just starch. It’s a good trick if you think about it, cooking making the starch more readily digested.

            The RS is resistant in part, I believe, by it’s ability to resist digestion in the stomach and small intestine. In which case I don’t think it’s available to the bad flora in a SIBO case. But I’m not well versed in this stuff, hopefully you can google that fairly easily. Best brand is an opinion, I’m sure. I only know of one brand so that’s the one I got. However if you can’t fathom including a flavorless powder in water you may want to pursue the more traditional food routes such as raw plantains, cold potatoes, etc…

  • http://kristinerudolph.com Kristine

    Great analysis, Laura!

    I am dying with impatience to get my results back and this only makes me more interested in them. Looking forward to your re-test and n=1 experimentation.

  • Kelly

    Really interesting….would you translate mine? lol!

    I have a high level of Firmicutes also (looks to be about 82% of my gut). When I did my sample, I was on a VLC diet. I’ve since been eating a pretty liberal amount of carbs. Maybe I’ll do a second sample in January with you (was going to have my husband do a sample, but he’s dragging his feet).

    Seriously, if you have a recommended resource that I can access to better translate mine – please send my way!

    Thanks for sharing!

    • Laura

      Honestly I just used PubMed to find research, which there’s little of at the moment.

  • Jess

    Great post! My results showed firmicute numbers similar to yours, though I haven’t taken any antibiotics for years, and I also have an enriched amount of Oxalobacter. I have no idea what it all means, but I’m looking forward to seeing the results of your RC experiment.
    Here’s my chart, for comparison: http://imgur.com/a/mxwUI

    • Laura

      I actually think your results look “better” than mine since you have very little Proteobacteria, which tend to be pathogens. What’s your diet like?

      • Jess

        My diet varies, but I usually try to keep it vaguely primal-ish: basically, high-quality meat, eggs, and dairy, plenty of vegetables (often cruciferous, just because I enjoy them), and some grains, all topped off with ice cream and chocolate. During the reporting period, I had been eating about 30% protein, 25% carbs, and 45% fat, including some probiotics like yogurt, raw milk, and sauerkraut (in fact, one of my “rare taxa” may possibly have come from kimchi).

  • Brad

    Laura, I take it you are not eating much of any grains or seed/grain oils? Are you pretty much on a Paleo diet? What are your macro ratios like generally? Just curious so we can understand your results with/without RS supplementing relative to your diet. thanks. -Brad-

  • ‘tatertot’ Tim

    Laura – Good job getting this out there! Can’t wait to see your results. I wish I’d have had a ‘before’.

    Here are some things to keep in mind with RS. The primary gut bugs that actually eat (ferment) the RS are the ruminococcaceae. Notice that our levels are almost exactly the same. These are one of the very stable gut bugs that are resilient to antibiotics because they come in both gram positive and gram negative flavors. Not sure which your abx were targeting, but it looks like they left plenty to go crazy on some RS.

    read more: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669169/

    When the ruminococcaceae start chowing down on their favorite meal (RS), they will produce secondary compounds that more bacteria will feed on, and finally end up with some stuff that favors bifidobacterial growth–nothing is straightforward here!

    The end result is a colon flooded with SCFA, predominately butyrate, which does amazing things, least of which is to strengthen your immune system.

    Here is a paper I stumbled across that shows how resilient our gut bugs really are and how it takes a long time to return to normal after hardcore abx. Something to read while you wait for your experiment to progress.

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3577372/

    I guess my takeaway for you is that you have plenty of RS eaters–feed them! And, all is not lost no matter how bad the antibiotics messed you up.

    • Laura

      Great, thanks for your insight Tim! I think I did pretty well on the abx treatment all things considered. I chalk it up to a good diet. Most people that go through that level of treatment have some level of GI symptoms, and I didn’t have any, so it could be worse. Dealing with my Lyme disease was the priority though! Hopefully one day they’ll figure out a treatment that doesn’t require an arsenal of antibiotics.

      Do you think taking probiotics along with the RS will make a difference in how fast the levels change? I’m envious of your Actinobacter levels and am just hoping mine will be visible on the chart by the time I’m done experimenting!

      Thanks for commenting!

      • Tim (tatertot)

        I definitely think that RS and probiotics are the magical equation!

        In 2003, I took cipro for 6 months when I was in Afghanistan and Iraq, it totally fried my guts. Gained 40 pounds, developed sleep apnea, irregular heartbeat and was in fullfledged metsyn within 2 years. I stayed that way until 2010 or so when I discovered paleo. I wish I had figured out the RS/probiotic angle way back.

        Shoot me an email if you want some good pdfs and other info on RS and stuff.

  • http://www.organicfitness.com Eirik

    Found the post from the facebook site of The Human Food Project. Thanks for sharing the results!

  • Kris

    Interesting. I wonder what the results would look like for someone following the Weston A Price Foundation’s recommendations. I don’t think Sally Fallon had hers done.

  • Pingback: The Roundup

  • Gwhiz

    Hi Laura. You might need to take a bit more than I tablespoon of potato starch – most of the research seems to indicate that at least 20gms of resistant starch (RS) is needed per day. Raw potato starch is maybe 65-80% RS, so three tablespoons a day should guarantee you get at least 20gms RS.

    Best of luck with the gut bacteria!

    • http://www.ancestralizeme.com/ Laura Schoenfeld, MPH

      Thanks for the input, Gwhiz! I’ll try to work up to 4 tbs per day so I don’t get too many gut side effects.

  • Heisenbug

    Hi Laura! I was really excited to see this post (h/t Tim for letting me know) — finally some more data the ancestral community can use!

    As I think you know, your firmi is high because you have very high Lachnospiraceae. Lachno is synonymous with Clostridia XIVa, which is what most studies refer to them as. So you’ll find a lot more (positive) info about them by using that term. I find they are almost always negatively correlated with disease (metabolic, ibd, autoimmune). I’ve written quite a bit about them already, and plan to continue (http://mrheisenbug.wordpress.com). Also, I’ve never seen high firmicute implicated in any negative finding, save for the shaky obesity link. But high bacteroidetes, on the other hand, has been found in a lot of disease-specific studies (type 1, metabolic disease, etc.).

    I’m really curious as to where those high Lachno’s come from! Could you give us an idea of your plant consumption? Do you consider yourself to consume a lot of fermentable fiber-rich plants on a daily basis? Anything out of the ordinary that you regularly consume?

    Boosting bifido definitely seems like a worthy goal. I’ll be really interested to see if the RS does that — it would explain a lot in terms of its effects. But I wonder if the probiotics would interfere with assessing that. After all, what we’re really after is to see how diet affects microbiome composition, right? Exogenous probiotics certainly don’t hurt, but bacterial counts tend to go right back to where they were when you started them. Prebiotics/diet are more lasting, and probably how nature intended it. Jeff Leach wrote about that here (http://humanfoodproject.com/probiotics-or-prebiotics-which-would-darwin-choose/).

    So perhaps it would make sense to have a 7 – 10 day “wash out” period where you stop the probiotics before sampling? Otherwise we won’t know if it’s the RS or the probiotics if your bifido is higher. But just a thought. Good luck and thanks for doing this.

    • http://www.ancestralizeme.com/ Laura Schoenfeld, MPH

      Thanks for sharing Heisenbug! I don’t think I eat an enormous amount of plant foods lately, though I have been better about it in the past. I tend to eat starchy plants a fair bit, as well as fermented foods including dairy.

      That’s a good idea to stop taking probiotics before sampling to make sure I don’t screw up the results. I’m hoping that by taking both pre- and probiotics that I’ll increase my chances of making an impact on my gut flora. We’ll see what happens!

      • Ross H

        I had read your column before and I had no idea you were fighting off lyme disease. It’s definitely beatable and don’t let the hype scare you. Antibiotics will definitely affect your test results. Don’t be afraid to continue eating yogurt, (but stop the probiotic pills) while preparing to do another test. The Straus organic whole milk variety is one of the only decent yogurts I know of. I’ve had way better results just drinking raw milk though.

  • Pingback: Meeting My Microbiome | Phoenix Helix

  • Cameron

    HI Laura, thanks for your comments. I came across your post and found that it is similar to mine. I eat a modified paleo diet (Terry Wahls version) and I do eat starch (mostly sweet potatoes) regularly. I haven’t taken any antibiotics for years. So, our diets are different, as well as ages, and medicinal history, yet there are similarities in our microbiomes (at least at the genus level). I’m more heavily weighted towards Firmicutes than even you, with just small amounts of Proteobacteria and Bacteroidetes. And don’t worry, I’m super fit with less than 12% body fat, so the supposed obesity connection is clearly false. I was also quite surprised at what I thought would be a much more balanced microbiome. But, I have confidence in my diet and health regiment, so I’m taking it all as very positive. Good luck!

  • bigmyc

    Wow. All that data and I found no mention of yeast colonies (candida albicans). Perhaps I just scanned past that part or perhaps yeast is completely non-present in your pro-biotic biome although, that is unlikely from what I’ve read in numerous sources. On second thought, was this just a measure of bacterium in your gut? That might explain the omission of any discussion of yeast….Your input?

    • Kelly

      Bigmyc – the American Gut project doesn’t measure yeasts or parasites. They told me that they only get as detailed as the genus level of bacteria. I had hoped that maybe the data would be more detailed also, but it was still fascinating to find out the other data about my gut.