I recommend that people with digestive health issues reduce, NOT increase, hard to digest fermentable carbohydrates to control symptoms of IBS, acid reflux and other digestive health issues related to dysbiosis (general imbalance of gut microbes) and SIBO (small intestinal bacterial overgrowth).
This approach is outlined in my two books, Fast Tract Digestion IBS and Fast Tract Digestion Heartburn. People who implement my recommendations typically consume low to moderate levels of overall carbohydrates (under 100 grams / day) though the Fast Tract Diet is flexible for those who can tolerate higher overall carb levels – such as athletes or people who are able to process more carbs without metabolic complications and consequences. Another approach I write about in Heartburn Cured is a low carb diet. The premise is similar but less specific in that overall carbs, including fermentable carbs, are limited.
I was puzzled by a recent blog article by Jeff Leach called “Sorry low carbers, your microbiome is just not that into you”. I have a lot of respect for Jeff’s efforts to generate some data correlating changes in gut microbe populations with diet as well as his expertise in paleolithic diets. And we both seem to agree on a most important premise: Health improvements can be made by altering our gut microbiome through dietary means.
My concern centers on the main point of this particular article: people need to consume more fermentable carbohydrates such as resistant starch, fiber and oligosaccharides or they will suffer a variety of health consequences. Increasing the amount of dietary fermentable carbs shouldn’t be a problem (and may even have some health benefits) for people who do not suffer from digestive issues. However, it’s the worst advice possible for people who do. The idea that people on low carb diets are at risk for these negative health consequences is one that we need to look at very closely and any conclusions or recommendations for dietary modification should be backed by scientific evidence.
Since I am unaware of any negative health outcomes linked to reducing fermentable carbs in the diet, I wanted to understand the evidence for Jeff’s claims. According to his article, consuming too few dietary fermentable carbs reduces fermentation by gut microbes and results in a shift to a less acidic environment in the large intestine. Jeff suggests that this pH shift favors the growth of less healthy, gram-negative endotoxin-producing gut bacteria such as Bacteroides, Enterobacter, and other pathogens, but reduces the growth of butyrate-producing (gram positive, endotoxin-negative) bacteria that presumably are “more healthy” for our gut. Further, these changes can create a “classic case of microbial dysbiosis”. In this scenario, the gut microbiome of low carb dieters can lead to inflammation and leaky gut from microbially produced endotoxin (lipopolysaccharide, LPS), metabolic disease, obesity and heart disease. If these claims were true, reducing carbs might be dangerous!
When I examined these claims, I found they were not supported by the data presented or referenced in the article. The scatter plot presented showing the (lack of) correlation between fat consumption and BMI from a 7 day self-reported data set has nothing to do with gut microbes or consumption of fermentable carbs. If anything, the data simply supports that fat doesn’t make you fat. Jeff included several references to published journal articles to support his view on how critical it is to feed gut microbes to prevent these problems. I took a look at these articles to see what the evidence was:
Citation 1. This is a report of lab studies looking at the growth of some gut microbes in culture (growing poop in the laboratory) adding one type of fiber and some sugar alcohols. I am afraid I don’t see the relevance to health outcomes in people. One the other hand we know that fiber and sugar alcohols can cause huge digestive problems for many people., Also, refer to my article The Dark Side of Fiber.
Citation 2. This paper reports that fiber increases some types of gut bacteria but did not link the results to any actual health outcome. The authors discuss the hope that fiber protects against chronic diseases such as colon cancer but the only study I am aware of that showed any protective effect of fiber for colon cancer is the EPIC study conducted in Europe. One the other hand, several other studies and a pooled analysis of 13 prospective cohort studies have concluded that fiber does not protect against colon cancer.,,,
Citation 3. This paper reviewed gut microbes in the context of energy harvest, but again made no connection with health outcomes. The authors discuss the connection between bacterial lipopolysaccharide (endotoxin), a toxin associated with the cell wall of certain types of gram-negative bacteria and chronic inflammation (see Jarisch-Herxheimer reaction). However, fermentable carbs may actually increase the overall load of endotoxin-positive bacteria. The reason is that a significant number of gut bacteria (Bifidobacteria represent one of over 1000 species) are gram negative endotoxin-positive species which also feed on fermentable carbs. These organisms would be reduced on a carb limited diet.
Recent studies don’t support the idea that fermentable dietary fibers specifically promote the growth of gram positive (entoxin-negative) bacteria over gram negative (endotoxin-positive) bacteria. The De Filippo study showed that children from Burkina Faso in Africa who consume a high fiber diet, harbored higher relative amounts of Prevotella (gram-negative, endotoxin-positive) bacteria while age-matched Italian children whose diet includes less fiber, harbored more Fimicutes (gram-positive endotoxin-negative type of bacterial types). So following the logic above suggesting that endotoxin causes inflammation and leaky gut, children in Burkina Faso who eat more fiber would be expected to have a higher risk for endotoxin-related health problems.
Another study led by microbiologist Frederic D. Bushman linked diets high in protein and animal fat with a predominant gut population of Bacteroides (gram-negative endotoxin-positive) type bacteria and diets higher in carbohydrates with a predominant gut population of Prevotella (also gram-negative endotoxin-positive) type bacteria. The point here is that both types of diet resulted in a predominance of bacteria that make endotoxin – suggested by the Leach article as “leading to inflammation and leaky, metabolic disease, obesity and heart disease.”
Jeff Gordon’s team found that obese individuals possessed more Firmicutes (gram positive, endotoxin-negative) type bacteria and less Bacteriodetes (gram negative, endotoxin-positive) type bacteria, while lean individuals had less Firmicutes and more Bacteroidetes. Does this mean lean people are more at risk for endoxin-mediated inflammatory disease?
In reality, it doesn’t really matter. There is no report I am aware documenting the Herxheimer reaction from diet-mediated changes in gut microbe populations. Bacteroidetes, Prevotella and Firmicutes type bacteria are normal inhabitants of our digestive tract. Bacterial species belonging to each of these groups have unique metabolic capabilities that cause their relative numbers to rise or fall based on the types of nutrients available to them.
Citation 4. This was a study in mice showing some fiber species caused less weight gain than fat This result is not surprising since fat has more calories and doesn’t need microbes in the mix for breakdown and energy recovery. But what does mean in terms of low carb diets and the microbiome?
Citation 5. This report talks about changes in energy harvest when calories loads are altered in obese vs. lean people. No surprise that as calories are increased you get more bacteria and more energy harvest. That is the main purpose of having a microbiome.
Citation 6. This paper talks about an in-vitro study (culturing gut bacteria in the lab) which showed that resistant starch induced a shift in the bacterial populations and more butyrate production concluding resistant starch may promote bowel health. There is no direct evidence in humans I am aware of, that more butyrate (relative to basal levels generated on a low carb diet with plenty of green leafy vegetables) improves bowel health (I am open to it if it exists).
Citation 7. This paper suggests that prebiotics (indigestible oligosaccharides) should be added to a diet of fruits and vegetables. The paper states “Prebiotics specifically stimulate the growth of endogenous microbial population groups such as bifidobacteria and lactobacilli which are perceived as being beneficial to human health”. But given that we harbor over 1000 different species of bacteria all working together, what is the actual evidence that increasing only these two organisms will optimize human health?
Citation 8. This paper promotes probiotics (such as bifidobacteria and lactobacilli) and prebiotics as “functional foods that fortify the lactate producing microflora of the human gut”. Where are the studies showing that current probiotics (save limited improvement in some studies of diarrhea) and prebiotics (more relevant to this discussion) are linked to positive health outcomes?
Citation 9. This review article suggests that diet appears to play a role in shaping the microbiota and promoting obesity-associated dysbiosis but that more work is needed to figure out the role of prebiotics and probiotics to promote healthy gut flora. Where is the data?
Clearly, our bodies have evolved an amazing partnership with over 100 trillion microorgnisms to recover vitamins and nutrients from mostly vegetative (and some animal) matter that we can’t digest. We receive an estimated 30% boost in energy thanks to our gut microbes, a benefit that has served us well allowing us to survive in times of limited food. But in modern times, with access to all types of foods 24/7, what is the healthiest diet that will optimize our gut microbiome and best protect us from disease? I don’t pretend to know the answer to this question, but one thing is for sure. The answer will be different for different people.
The real question is “how do shifts in the microbiome impact health?” We are just beginning to understand the effects of diet, lifestyle and illness, as well as medicines used to treat infections, on the gut microbiome. So far, we know that humans have certain enterotypes (the major groupings of gut bacteria) that often don’t change in response to short term dietary alterations. On the other hand the relative abundance of individual bacterial species is responsive to changes in diet in a manner that often differs for individuals. It may be tempting to speculate about what these shifts mean, but before recommending sweeping dietary changes (i.e., people on low carb diets have unhealthy microbiomes and need to alter their diet, add prebiotics, fiber, etc.), we should generate the studies to provide the evidence – in terms of health outcomes, particularly for people suffering with GERD, IBS and other SIBO and dysbiosis-mediated conditions.
Controlled studies of different diets and populations including people with digestive health issues, will certainly help. Given the variety of foods our body can use for growth and energy, it’s not a simple task to determine which type of diet is healthiest. My gut says a varied diet containing animal protein and fat along with plenty of less starchy vegetables, seeds and nuts with some seasonal fruits will likely win in the end, but I’m just speculating.
 Dear KL, Elia M, Hunter JO. Do interventions which reduce colonic bacterial fermentation improve symptoms of irritable bowel syndrome? Dig Dis Sci. 2005 Apr;50(4):758-66.
 Hyams JS. Sorbitol intolerance: an unappreciated cause of functional gastrointestinal complaints. Gastroenterology. 1983 Jan;84(1):30-3.
 Shen Q, Zhao L, Tuohy KM. High-level dietary fibre up-regulates colonic fermentation and relative abundance of saccharolytic bacteria within the human faecal microbiota in vitro. Eur J Nutr. 2012 Sep;51(6):693-705.
 Bingham SA, Day NE, Luben R, Ferrari P, et.al. Dietary fibre in food and protection against colorectal cancer in the European Prospective Investigation into Cancer and Nutrition (EPIC): an observational study. Lancet. 2003 May 3;361(9368):1496-501
 Fuchs CS, Giovannucci EL, Colditz GA, Hunter DJ, Stampfer MJ, Rosner B, Speizer FE, Willett WC. Dietary fiber and the risk of colorectal cancer and adenoma in women. N Engl J Med. 1999 Jan 21;340(3):169-76.
 Park Y, Hunter DJ, Spiegelman D, Bergkvist L, et.al. Dietary fiber intake and risk of colorectal cancer: a pooled analysis of prospective cohort studies. AMA. 2005 Dec 14;294(22):2849-57.
 Uchida K, Kono S, Yin G, Toyomura K, et.al. Dietary fiber, source foods and colorectal cancer risk: the Fukuoka Colorectal Cancer Study. Scand J Gastroenterol. 2010 Oct;45(10):1223-31.
 Giovannucci E, Rimm EB, Stampfer MJ, Colditz GA, Ascherio A, Willett WC. Intake of fat, meat, and fiber in relation to risk of colon cancer in men. Cancer Res. 1994 May 1;54(9):2390-7.
 Krajmalnik-Brown R, Ilhan ZE, Kang DW, DiBaise JK. Effects of gut microbes on nutrient absorption and energy regulation. Nutr Clin Pract. 2012 Apr;27(2):201-14.
 De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A. 2010;107:14691–6.
 Wu GD, Chen J, Hoffmann C, Bittinger K, et.al. Linking long-term dietary patterns with gut microbial enterotypes. Science. 2011 Oct 7;334(6052):105-8.
 Ley RE, Turnbaugh PJ, Klein S, Gordon JI.Microbial ecology: human gut microbes associated with obesity. Nature. 2006 Dec 21;444(7122):1022-3.
 Arora T, Loo RL, Anastasovska J, Gibson GR, et.al. Differential effects of two fermentable carbohydrates on central appetite regulation and body composition. PLoS One. 2012;7(8):e43263.
 Reiner Jumpertz, Duc Son Le, Peter J Turnbaugh, Cathy Trinidad, et.al. Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am J Clin Nutr 2011;94:58–65.
 Lesmes U, Beards EJ, Gibson GR, Tuohy KM, Shimoni E. Effects of resistant starch type III polymorphs on human colon microbiota and short chain fatty acids in human gut models. J Agric Food Chem. 2008 Jul 9;56(13):5415-21.
 Blaut M. Relationship of prebiotics and food to intestinal microflora. Eur J Nutr. 2002 Nov;41 Suppl 1:I11-6
 Saulnier DM, Kolida S, Gibson GR. Microbiology of the human intestinal tract and approaches for its dietary modulation. Curr Pharm Des. 2009;15(13):1403-14.
 Shen J, Obin MS, Zhao L. The gut microbiota, obesity and insulin resistance. Mol Aspects Med. 2013 Feb;34(1):39-58.