Is starch a necessary component for a healthy gut microbota?


                  Sweet Potatoes

For the past 2 1/2 years I have been deeply entrenched in the specific carb diet. I owe my avoidance of being hospitalized to the diet (as I had been prior to starting the diet). It gave me a whole new perspective on food. I realized that virtually everything I had been doing most my life had been destructive to my health and gave me reflection on the development of my disease. It gave me self-empowerment, to know that I could heal myself and I do not have to suffer my whole life with this disease and likely have surgery one day. I began to look at food not for pleasure but as a means to put me in remission.

For those of you who are not familiar with the Specific Carb Diet, it is basically a diet designed to be therapeutic for ulcerative colitis, crohns disease, GERD, diverticulitis, and IBS. The SCD diet was based off of the therapeutic effects that elementary diets have on digestive diseases and this is well documented in the literature. Elementary diets are liquid that consist of only predigested sugars and fats. It is based on the chemical structure of foods, allowing only those that are in a readily absorbed state by the small intestine. It does this by the elimination of any polysaccharides (potatoes, wheat, grains etc) and disaccharides (lactose, table sugar, maple syrup etc) and allows only foods that contain monosaccharide which are readily absorbed through the intestinal wall. Examples of foods allowed are most all proteins, fats, most fruits, nuts, seeds and most vegetables with the exception of starchy ones. The premise of how this diet works, is that by removing complex carbs it starves the harmful bacteria in our intestines and restoring the gut bacteria balance.

Why is it important to restore the gut bacteria balance?

Certain types of gut bacteria has also been shown to have immune-regulatory properties and be protective of the gut. It does this by acting as the host first line of defense by making a physical and immunological barrier from the gut epithelium and the outside environment. A balanced healthy microbiota will use all the resources in the gut such as space and nutrients needed by a harmful opportunist pathogen to survive. Certain individual types of bacteria may exhibit certain benefits, for example lactobacilli can lower the PH in the intestines that prevents the colonization of pathogens. Gut bacteria also uses, through fermentation dietary fiber (FOS, inulin, resistant starch etc) to make beneficial compounds in the gut like short chain fatty acids like butyrate producing bacteria. Butyrate acts as a fuel for the colon cells (colonocytes) and are both therapeutic and preventative of colorectal cancer and ulcerative colitis (1).

My personal experience with the Specific Carb Diet.

 When I started the Specific Carb Diet (SCD) I was mesmerized that it worked as well as it did. Over time the positive results I initially experienced began to fade, in spite of my complete avoidance of any so called “illegals”. Most of the specific carb dieters would tell me, I was likely getting some illegal food in my diet somewhere regardless of how many times I would reevaluated the foods I was eating. As a result I would stiffen up the reins a little more by eating out less, or sometimes not all to avoid any unintentional exposure to potential things I wasn’t supposed to eat. This type of dogmatic thinking towards any approach (in my case this diet) can slow down forward progress. I fell into this trap of doing the same thing over and over and expecting different results. I figured if it worked for me before it should continue to work.

One day I was listening to a Chris Kresser Podcast and he had a guest speaker named Jeff Leach, a gut microbiome researcher and founder of the human food project. The Human food project is a project set up to further understand the effects that gut microorganisms have on the health by taking stool samples from all different types of diets and populations. So far they have 7000 people involved, which is the largest microbiome project in history. Anyone can join, and get results about the bacterial make up of your own stool and how you compare with other populations and diets and you can view that here. Anyways during the conversation the specific carb diet, or the gaps diet (essentially the same thing) came up in conversations. Kresser didn’t seem to think it was a good idea to follow such a strict approach over the long term. This is mostly just a clinical observation Kresser is stating but still important I believe.

Chris Kresser

But what I started to see is that people who stayed on that kind of protocol for a long period of time, they would improve and feel better, and then after a while they’d start to feel worse and worse and worse.  And I began to suspect that part of the reason that they were feeling worse is that the thing that they did, which was therapeutic initially, i.e. starving their gut bacteria because they had a lot of bad bacteria, then actually became harmful over time because they weren’t only starving their bad bacteria, they were also starving their good bacteria.  That’s when I started to advocate for GAPS being looked at as a more temporary therapeutic approach, and in fairness, even the creator of it, Natasha, has talked about it that way for the most part.

Jeff Leach didn’t seem to like the idea of a diet that attempts to starve bacteria in the gut microbiome ether. He thinks that it may damage the diversity of the bacteria of the gut microbiota.

Jeff Leach

I know the GAPS diet.  I don’t know the lady who wrote it, and so it’s kind of out of my pay grade to talk about it too much, but from an ecosystem restoration standpoint, it makes absolutely no sense whatsoever to starve your gut microbiome at any level.

Based on the quote above one would think that the specific carb diet/GAPS has no therapeutic use which clearly isn’t true. Jeff goes on to say that it may help in the beginning but he also doesn’t advise it in the long term.

Jeff Leach

But you know, as you said, who knows?  It seems to have some early benefits, but long term it clearly doesn’t make any sense, and I would argue that it probably doesn’t make any sense initially either.  But who knows?

I had already been toying with the idea of adding back starches to my diet, particularly sweet potatoes and this podcast is the first real source that offered a partial answer as to why this approach may have worked at first for me but then stopped. I didn’t stop here and take the opinion of these two knowledge individuals at face value, so I decided to take matters into my own hands and get a firsthand view of what was going on in terms of bacteria growth in my large intestine.

My microflora after 2 1/2 years on the Specific Carb Diet.

To do this I started researching tests that could measure the growth of different bacteria in my large intestine and the test I came up with was from metametrixs and it’s called a comprehensive stool analysis. This is a very in depth stool test that examines the amount of beneficial bacteria present in the large intestine as well as many other important information. The test I used was called the GI effects 2200 and most any functional medicine doctor will be familiar with this test. This test allowed me to really see what was going on inside my colon.

Notice the low clostridium reading

Notice the low clostridium reading

At first glance you will notice that the predominant bacteria in my colon is all over the place, some are high, some are low and they need to fall close to the middle. They call phenomenon intestinal dysbiosis, this is a condition when the intestinal microorganisms are out of balance with each other, and meaning some bacteria has overgrown and other types of bacteria is low on growth. Some opportunist pathogen may reside in the normal flora and not cause any damage to the host, but if for some reason this pathogen overgrows it can cause harm (overstimulation of the immune system). Normally your immune system and other bacteria keep commensal bacteria in check and they will have a symbiotic relationship, but when one particular species becomes overpopulated from an insult (lowered immune system, antibiotics, and insufficient dietary fiber) it can inhibit the colonization of other beneficial bacteria. On the other hand if some of these beneficial bacteria become too low, it can allow for the growth of other less desirable types of pathogenic bacteria. The human large intestine is a very balanced and complex microbiota and a delicate balance must be maintained for health, if something upsets this balance it may make the host more susceptible to a host of different diseases such as those that have an inflammatory component to them, these include neurological, digestive and metabolic .

You would expect to see a dysbiotic state such as mine after taking a round of antibiotics, but I hadn’t been on antibiotics for years prior to taking the stool test. The test results were not the way they should look in an individual with healthy gut microflora. As you see in my stool test (above) my clostridium read out was very low and my prevotella and fusobacteria was very high. This would indicate to me that the Specific Carb Diet was not doing much of a good job in balancing my gut microflora. This begs the question if the restriction of complex carbohydrates and resistant starch in my diet may have caused the insult to my microbiota diversity. So I did a bit or researching to really try to interpret the results of this stool test by breaking it apart. I have to be honest though, it was a very helpful individual by the name of Michael Briggs from the facebook group named fecal microbiota transplant that helped to open my eyes to the importance of bacteria I had low growth on, particularly clostridium (circled in the picture). This informative individual sent me this study after reviewing my stool test results.


“Clostridia, a dominant class of commensal microbe, can induce colonic regulatory T (T-reg) cells, which have a central role in the suppression of inflammatory and allergic responses (2).”

“Treg deficiency usually results from loss of the type of gut bacteria that stimulate Treg production in the lining of the intestines, i.e. species of Clostridium” (3).

Clostridium just so happens to be a very important bacteria in the colon because it converts soluble fiber (resistant starch) into these beneficial short chain fatty acids such as butyrate, as I mentioned earlier. This means that according to my stool test, I know I’m low in at least one of the beneficial t-regulatory cells producing bacteria, e.g. clostridium.

What are T-Regulatory Cells?

T-Regulatory cells (AKA T-regs) provide a brake on the specific immune response; they impede on the activity of T-lymphocytes and B-lymphocytes. Many autoimmune conditions are associated with a deficiency of T-regulatory cell, in fact some sources go as far to say all autoimmunity begins in the gut. They call this theory the old friends, or hygiene hypothesis, this theory states that the rise in autoimmune condition are more prevalent today than ever because we live in such a sterile environment and this has cause a deviation in the gut microbiota. Most of human history was spent outside exposed to dirt, bacteria, pathogens and helminth so our immune systems are programmed to be able to fight off and live in harmony with these infections and bacteria. With the relatively clean living environment, diet and the addition of antibiotics, it has caused humans to have a less diverse microbiome and this leads to less of the “old Friend” that act as inducers of immune regulation. The theory attempts to explain why autoimmune diseases are higher in numbers in high-income developed countries than they are in third world, more indigenous countries (4) (5).

What are the issues with the specific carb diet on the long term?

It is probable that my low clostridium growth on my stool test was a result of me following a diet (SCD/GAPS) that restricted the type of fiber certain types of bacteria prefer to ferment (6). I believe this is a valid assumption, I came across a mouse feeding study that shown a decrease in microbiota diversity in the intestines of mice that were put on an elementary diet (what the SCD/GAPS diet is modeled after) compared to a normal (7). The specific carb diet lacks most sources of resistant starch because starch is not allowed on it. Resistant starch has been shown to benefit the microbiota in many different ways by providing a substrate for carb feeding bacteria to live on. There are lots of papers and studies on the benefits of resistant starch and free the animal has done a lot of work on this.

The GAPS and SCD diet removes starches and often this can lead to an over reliance on sugars in the place of starches as a source of carbohydrates. Some of the main sources of carbs on the SCD/GAPS diet will be often be high sugar (fructose) fruits and veggies in the replacement of complex carbs, this can perpetuate small intestinal bacterial overgrowth. The fructose can feed these microbes in places where you don’t want them (the small intestine) but deprive the microbes in the small intestine where they are supposed to be in higher numbers. In addition to this many individuals with digestive issues have fructose malabsorption (8).

The nature of removing starch from the diet makes it very difficult to get enough carbs in the diet, often leading to going low carb at times. I fell into this trap because most places wouldn’t have the SCD legal carb (winter squash, carrots, and fresh fruit) sources readily available whenever I was away from home. Very low carb diets can be therapeutic for people who are overweight, have metabolic syndrome, neurodevelopmental disorders or epilepsy but this is usually not the case with individuals seeking out the SCD diet or the GAPS diet who tend to be underweight and undernourished (9).

My N=1 experience with adding back starch to my diet

After years of strictly adhering to the specific carb diet I was a bit concerned as to what would happen when I ate a sweet potato. Even after all the research I put into the potential benefits I could gain from adding resistant starches and complex carbs to my diet and the fact that the diet had begun to stop working I was still second guessing it. After I finally worked up the courage to eat the potato I felt nothing, no gurgling, gas or discomfort whatsoever. It’s almost like I was expecting something bad to happen but it never did, in fact just the opposite happened. It actually helped my digestion, energy and helped me regain some of the weight I had lost during the flare.

 Should I try the specific Carb Diet?

It depends, the fact remains that the diet did help in the beginning and I directly observed that in myself by tracking my serum inflammation markers. It is also hard to ignore all the millions who have been helped on the diet as well as the UMass Medical School study and the Rush University Medical Center study. Many individual factors come into play and making a one size fits all approach is never a good thing when talking about complex human beings. For a select few it seems that as they begin the Specific Carb diet they become completely healed of all their intestinal problems, some are even lucky enough to be able to go back to a less restricted diet after a few years of following the diet, but these individuals seem to be the exception not the rule. Most individuals have to follow the SCD/GAPS diet for a very long time and in the diets defense, it was never really designed to be a life long diet. It is also worth mentioning that it seems pretty clear that the diet will work for you in the beginning according to the studies, this may have value when trying to bring yourself out of a flare.

Many different pathogens can be a perpetuator of intestinal distress. Different pathogens can benefit from different sources, for example, some pathogens can utilize fructose whereas some types of eukaryotic type pathogen have been shown to be able to utilize ketones. Many pathogens can also feed on resistant starch as well, this could be a possible explanation of the successes many have on the SCD/GAPS diet. I think the diet is very valuable tool especially in the beginning and in no way am I trying to discredit the diet. Things are rarely black and white when dealing with unique biochemical, and genetic individual differences.

The American gut project opened my eyes to the fact that we may need many different types of fiber (not just those allowed on SCD) to feed a wide diversity of healthy microorganisms living in our gut for long term health. My recommendation would be to anyone who is following the SCD and not getting better, consider adding some safe starches back in and see how you feel. In my next post I will explain to you how I replaced those missing bacterial species through fecal microbiota transplantation.


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