Latest American Gut Results

Apparently the American Gut Project (also now available in England!) must have gotten a burst of energy recently.  Several people have told me that they just got results back they've been waiting nearly a year for. I also just got some results from a sample I sent them in July.

I'd like to show you all my most recent report and compare it with one from almost a year ago.


First, I'd like to say that you have to take this all with a grain of salt, because what you are about to see is simply a snapshot of what my gut looked like the morning I procured the sample, and my interpretations. Also, as we well know, fecal microbiota is not the whole story...there's also microbes that live in the mucous layer and may not be accurately reflected in a fecal sample. That said, I think that you can infer quite a bit from an American Gut Project microbe analysis.

And, as I showed in the Comparison Blog Post, some of this could be completely misleading because of the test methods or sampling errors. I wrote lots more about my first AmGut test last year on FTA as well.

I wish that I had a complete 'before' report from when I was eating a VLC type diet and not enjoying such good health as I am now, I think it would look much different, but the American Gut Project was not available back then.

These two reports represent different eating styles.  The most recent report was after about two months of a fairly high carb intake, probably 200-400g/day, from starchy carb sources like rice, potatoes, squash, plantains, gluten-free grains, seeds, and yams. I was also eating large platefuls of leafy greens and especially fresh dandelion leaves and roots, kale, chard, spinach, onions, and garlic. My goal during this time was to eat about 50g/day of total fiber with none of it coming from supplements. This way of eating was a distinct diversion from my normal way of eating, which is more represented in the potato starch supplemented diet.

Last year's report (bottom) is more the way I normally eat.  I really find myself feeling less hungry and perfectly fine eating one or two starches a day...maybe a baked potato at lunch and some rice with dinner.  My pantry is full of all kinds of cool grains, though, and I eat them often (teff, oats, quinoa, etc..). I try to get a salad or some fruit every day, which is a bit more difficult for me in Winter when I must rely on "iffy" supermarket produce. Summertime I am a fresh veggie eating machine as my garden pumps out homegrown vegetables and berries hang from every bush all around my house.  I use potato starch, inulin powder, glucomannan, dried plantains, alone or in combination, most days, to increase my fiber intake. I'm not religious about it, and rarely if ever have taken 4TBS of potato starch since I did that first test over a year ago. Usually it is more like 1-2TBS/day of potato starch and a spoonful of some other fiber. I usually try to prepare my starches so they are 'cooked and cooled' to maximize RS3.  Again, not religious about it.  I just try to get in the habit of being mindful of fiber. I think I get 20-50g of fiber most days and 100-200g of "carbs" but I don't count carefully.

Protein and fat-wise, both diets were similar.  I eat meat...lots of fish that I catch myself, moose that I harvest, eggs from my chickens, and also some store bought, conventional chicken and beef. I have never bought grass-fed meat in a store intentionally.  I think the idea of grass-fed over grain-fed is great, and if you do that, wonderful. I use Kerrygold butter sparingly, some olive oil or coconut oil in cooking. If you haven't guessed, I don't fret over macro ratios!

I have had no antibiotics in at least 10 years.  My health is great and weight is stable.  I'm not overweight or underweight.  Just right, I think.

 Here are two American Gut reports.  The top one was from a sample collected in July 2014 and the bottom from a sample collected in June 2013. In the bar charts, my sample is on the far left, and compared to other groups of people who have submitted samples, some 16,000 I believe.

Here's what jumps out at me on the reports above...

The Bifidobacteria, a general marker for health, was highest on my potato starch supplemented diet (11.3%), and well above average on the whole-food diet (4.8%).  Most people have less than 1%.

The Firmicute:Bacteroidete ratio is completely swapped between the diets. Many studies reported that a micriobiome with a greater percentage of Bacteroidetes is more likely to be associated with obesity and inflammation, in this respect, the "Potato Starch Supplemented Diet" would be considered "inflammatory" and "obese-causing."  I'm not worried, though.  This correlation has since been disproven numerous times and may only be true when no other factors, such as increased Bifidobacteria, are considered, as this paper explores:

Both the scientific literature and the popular press have heralded the association of obesity and the relative abundance of Bacteroidetes vs. Firmicutes as a robust finding. However, several recent reports question the strength of this association. Two large studies found no association between obesity and the Bacteroidetes: Firmicutes ratio. Furthermore, several publications actually report a higher ratio of Bacteroidetes to Firmicutes among obese individuals, in direct contradiction with the original findings.

 Faecalibacterium doubled with real food only.  I love Faecalibacterium! This genus has only one species..."prausnitzii." We can call this line item F. prausnitzii, then, [plus, it's fun to say: "Fee-cali-bacteri-um prows'-nitzy."]. Why do I like it?  Easy.  It's a real workhorse, and we all seem to have it.

Faecalibacterium prausnitzii is the most abundant bacterium in the human intestinal microbiota of healthy adults, representing more than 5% of the total bacterial population. Over the past five years, an increasing number of studies have clearly described the importance of this highly metabolically active commensal bacterium as a component of the healthy human microbiota. Changes in the abundance of F. prausnitzii have been linked to dysbiosis in several human disorders. 

 Is it problematic that my F. prausnitzii was cut in half when supplementing with potato starch?  Probably not. It seems that the trade off was maybe more Bifidobacteria!

Family Lachnospiraceae doubled with real food only. This family contains 19 different genera of gut bugs. This family of microbes is undoubtedly a sign of health, and the home of the Clostridia Clusters that Mr. Heisenbug loves. They are protective of C. diff infections. If you are missing these...look out!  The fact they were cut in half does not bother me one bit, as even at 50%, I have more Lachno than the other groups of dieters!  Had they disappeared, I'd be singing a different tune!

Order EC94 20,000x enriched on real food only!  What the hell is this?  Turns out, even weirder than you could imagine. 

...EC94 accounts for 99% of sponge-derived sequences but is absent from seawater. This enigmatic OTU is only known thus far as a coral-associated clone and has only 90% similarity to the next most closely related sequences which are from sponges and thus may be true symbionts of marine invertebrates and whose unknown function is intriguing.

It looks like I haven't developed "Hamster Gutz" as some have speculated...I am turning into Sponge Bob Square Pants!

Tim Steele?

 
What the...? 

Let's look closer. This seems to be legit, reading up on EC94, it is a very unique microbe and not likely to be an error. But how did I get it in me?  Well, I do spend quite a bit of time deep-sea fishing.  I have been known to eat raw fish pulled fresh from the ocean.  I have never drank from an aquarium, but I have gulped seawater while snorkeling in the coral of Hawaii.

Is it worrisome?  Not to me.  At .04%, this means that I have maybe a tiny colony the size of a pinhead somewhere in my large intestine. The 20,000 times enrichment probably means I am the first person to show this microbe. Who knows?  Maybe it gives me super-powers like Sponge Bob.

Let's take a closer look at the bar chart:

Lack of Proteobacteria.  You'd never guess, but Proteobacteria is the second largest group of bacteria. This phylum contains 1534 species or 32.3% of all known bacteria. This is also where most known pathogens reside.  One poor person I know had an AmGut report that contained almost 40% of total Proteobacteria...and she was a very ill person.  Seeing almost no Proteobacteria makes me very happy.

Diversity. As almost every American Gut profile shows similar numbers of the "Big Two" (Bacteroidetes amd Firmicutes), I like to look much closer at what is living in the smaller section of the charts.  I think this is where we see how much diversity we have.  A recent study came out describing the gut flora as a "King" and his "court."  It excites me to see some signs of diversity in these reports, but I think it only shows that you harbor a nice court for the king, and not much can really be speculated about this from my point of view.  Maybe some day this area under the magnifying glass will expose some true gut protectors.

"The diverse spectrum of glycans, which is present in the human colon, is derived from the diet (resistant starch, arabinoxylans, inulin) or the host (mucins). To construct a microbial network unit for these specific glycans, one needs to consider the concept of a king and his court. First, there is the specific primary degrader or keystone species for this glycan (‘king’). For many of the diverse spectrum of glycans that are present in the colon, such keystone species have been proposed. As an example, resistant starch requires the presence of Ruminococcus bromii, arabinoxylans are specifically degraded by Bifidobacterium longum and Akkermansia muciniphila seems a crucial species for the initial breakdown of mucins. To produce an industrial product, i.e. an effective microbial network unit, one also needs to provide the primary degrader (‘king’) with its cross-feeding microbes (‘court’)."

SAD Report:

For comparison, here is a recent American Gut report of a person who has taken many antibiotics, is on PPIs for GERD, and eats a fairly typical SAD diet.

It has lots of Akkermansia, which seems to be a key species. Most people have a little bit of Akkermansia, but it seems to readily explode when the gut is not right. It's a mucin-degrader.  Seems to me that maybe it likes to eat gut tissue that is not healthy. This study on colorectal cancer shows elevated levels of Akkermansia:

In this study we used stool profiling to identify intestinal bacteria and metabolites that are differentially represented in humans with colorectal cancer (CRC) compared to healthy controls to identify how microbial functions may influence CRC development. ... There were no significant differences in the overall microbial community structure associated with the disease state, but several bacterial genera, particularly butyrate-producing species, were under-represented in the CRC samples, while a mucin-degrading species, Akkermansia muciniphila, was about 4-fold higher in CRC . Proportionately higher amounts of butyrate were seen in stool of healthy individuals while relative concentrations of acetate were higher in stools of CRC patients.

Not sure if you caught that...healthy guts are filled with butyrate producers.  Unhealthy guts are filled with mucin degraders.  Butyrate producers come along for the fiber!  Akkermansia shows up when the gut is unhealthy.  Maybe it's trying to help us.  I wouldn't call it a "bad" microbe, but I wouldn't want to see much of it on my report.

Nothing special to see!  Aside from the Akkermansia, this antibiotic ravaged, PPI riddled gut has basically nothing much to see.  It contains the Bacteroidetes and Firmicutes that everyone has, no Bifidobacteria, no Proteobacteria (maybe a good thing?), and hardly anything in the small area at the bottom.  This is a gut that has produced autoimmune skin disorders, a liver tumour, a teratoma, and many years of diarrhea, heartburn, indigestion, and upset tummy. This gut prevents its owner from enjoying most foods, so she eats the things that don't hurt. Unfortunately, this means no fiber, few veggies, little fat, and lots and lots of refined carbs.

F. Prausnitzii.  Remember mine were 10 and 20% on the two diets?  The SAD diet clocked F. prausnitzii in at 3%.

Family Lachnospiraceae.  Mine were 7 and 15%.  The SAD diet netted 5% of this important family.

Final Thoughts

I think all I would like to leave you with is, "EAT LOTS OF FIBER." If you've clicked around here, you know I'm not talking about Metamucil or FiberOne Cereal. 

I like the way my American Gut report looks when I was eating real foods, but to be truthful, it was a handful eating like that. It was way more servings of carbs that I normally eat and it was quite a chore to find (and eat) so many high fiber veggies. If I could eat like that all the time, I would.  I do many days per week eating tons of fiber and don't supplement with powders every day.

Do I take this as "Potato Starch Kills our Guts!" No. I think a typical, healthy, diet supplemented with potato starch, inulin powders, or other supplemental fiber types is perfectly fine and very healthy. 

I'd like to see everyone eating like the Hinds Cave Paleo Indians who consumed 135g/day of fiber.  But unless you are eating what they ate...good luck!  Variety is the key, I believe.  And consistency. 

For people with truly messed up guts...SIBO, GERD, all that.  From what I hear, supplemental starches are not working too great, and therefore you probably want to stick with cooked and cooled starches and other fibers easier on your weakened digestive systems. Animal Pharm is looking into this and Dr. Grace AKA the Gut Goddess, has some great ideas for you over there if you fall into this category.

If anyone would like to see the full taxa reports for these three AmGut reports, they can be viewed here in Excel:
High Fiber   Potato Starch Added    SAD Eater

I hope this was easy to understand.  It got a little bit longer than I intended.

Later,
Tim