Wednesday, June 15

Gut flora

One of the key aspects of being healthy is maintaining a proper gut flora. Lately, this has been stressed out by many people, including Chris Kesser, Art Ayers, among others. Gut microbiome is a new area of research which will influence all areas of health, specially chronic diseases caused by inflammation. 

Fiber has been promoted for a long time as necessary and healthy. We are supposed to eat fiber because it feeds our gut bacteria and produces short chain fatty acids (SCFA) which serve as fuel to colonocytes (butyrate) and controls cell metabolism and renewal, as well as expression and synthesis of some important biomolecules (mucin, for instance). Current guidelines dictate that fiber's daily intake should be around 25-30g, the more, the better. This, from my perspective, is completely unnatural and its only purpose serves to "justify" whole grain/cereal consumption. 

Fiber is one of the great exclusions when adopting a ketogenic diet. Fiber rich foods tend to be high in starch (cereals/grains/legumes) or sugar (some fruits). Vegetables are viewed as fine by most standards, and overall tend to be just water plus fiber. So when someone restricts his carbohydrate intake to trace amounts, it is not strange that they experiment constipation. This can be potentiated by possible dehydration (not drinking enough water/electrolyte imbalance). In a nutshell, from the fiber-hypothesis, a ketogenic diet is harmful to gut flora and consequently, to health. 

Duncan et al. (1) found that when obese subjects switched to a low carbohydrate diet (24g/day) butyrate production (estimated from fecal samples) fell linearly with carbohydrate intake. Changes in bacterial species included a reduction in Roseburia intestinalis and Eubacterium rectale, both which produce butyrate from glucose from soluble sugars in vitro. Brinkworth et al (2) found that fecal butyrate excretion was 30-60% lower in subjects eating a high fat-low carbohydrate diet compared to a high carbohydrate diet. The level of Bifidobacteria also decreased. 

The results of these studies show a clear trend: carbohydrate intake and levels of butyrate correlate directly. Ergo, it is assumed that a healthy diet must have a good amount of starch/glucose and non-digestible polysaccharides to produce butyrate and promote colon health. 

In my opinion, the interpretation is backwards. Considering the effects of butyrate on colon health, increasing the number of gut bacteria capable of fermenting carbohydrates and producing butyrate is an evolutionary adaptation to a lack of dietary butyrate.

Eating a high fat diet with more butyrate (specially from butter and full fat dairy) decreases the need for species which produce butyrate. Most butyrate (approximately 85%) is absorbed in the gut, so fecal samples may not be a good indicator of overall butyrate levels in the colon. At least not the butyrate that matters. It must be kept in mind that the content of other SCFA (such as propionate and acetate) is also important. 

Gut flora is extremely succeptible to diet. It also controls almost every physiological process in our bodies. It is not rare that a decrease in the supply of essential nutrients (in this case butyrate) changes bacterial population in the gut, trying to maintain homeostasis and proper functioning. After all, it is a symbiotic phenomenon, we need them and they need us. A clear example is fasting induced adipose factor (FIAF) (3). Gut microbiota is needed to digest dietary polysaccharides. Studies with germ-free mice have shown that gut bacteria promotes absorption of monosaccharides from the gut lumen, increasing de novo hepatic lipogenesis, and promotes adiposity via supression of FIAF (4). Germ-free mice are protected from diet-induced obesity partially because of increased levels of FIAF (5). Backhed et al. made an elegant scheme of the process:

Conventionalization of adult germ-free mice with normal microbiota from conventional raised animals has a dramatic impact on metabolism and nutrient partioning, increasing bodyfat by 60% and causing insulin resistance in only 14 days. This despite reduced food intake. 

This results can be interpreted as a mechanism by which gut microbiota promote food storage during ample food intake, associated with an increase in polysaccharide supply. This depends on the amount of bacteria capable of fermenting glucose, which in turn depends on the composition of the diet*.

In conclusion, a proper ketogenic diet should not compromise gut flora. The increase in the need for non digestible carbohydrates may only be relevant when a diet is nutrient deficient. Avoiding most inflammatory foods can help reducing both the number of pathogenic bacteria and the fat storage properties associated with some glucose fermenting bacteria. 

* The importance of diet in determining the effect of gut flora in nutrient partioning has been shown recently.

ResearchBlogging.orgDuncan SH, Belenguer A, Holtrop G, Johnstone AM, Flint HJ, & Lobley GE (2007). Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Applied and environmental microbiology, 73 (4), 1073-8 PMID: 17189447


  1. Lucas

    I have personal experience with apparent effects of gut bacteria on health. The experiment involved varying the total food energy content while keeping protein and carbohydrate contributions constant (more or less) and varying fibre content. As well I have used enzymes, chelating agents (Klaire Labs) and lactulose in an attempt to reduce bacterial mass. My experiments were somewhat surprising (mostly positive). I have not seen any discussion of gut bacteria effects on lean healthy individuals which might be shed some light on my own speculations. Are you aware of any sources? The subject is somewhat indelicate so lack of general discussion is not surprising.

  2. Hi Morris,

    I think gut dysbiosis is not only related to obese subjects. You can be perfectly "healthy" (by common standars) and lean and yet suffer from altered gut flora. What exactly did your experiment involved and what where the effects noticed?

  3. Hi Lucas
    15 weeks after beginning LC diet, I began weekly fasts (33hrs) and after 6 more weeks noticed (surprise) that my nocturia disappeared or nearly so. I gradually increased the daily energy intake from 2500cal to 3300cal, 19 weeks after start of fasting (weeks are numbered from start of fasting). At that point I stopped fasting for the next 5 weeks and then gradually reduced calories to 2200 per day by week 31. I again began fasting on week 25 but at 10 day intervals after doing a 4 day fast on week 24. The improvement in nocturia diminished when fasting was stopped and later became intermittent. My findings: Bacteria gut volume and BM volume correlate cyclically with no. of days after fast ie grow with time until next fast. Also BM volume gradually increased with increasing cal intake. Weight gain between fasts was ~ 3-4 lbs, very little if any visceral. Over the last 32 weeks my weight has fluctuated between 149-154 lbs but the 7 day moving average only varied +/- 1 to 2 lb. Stool morphology also correlates as above but with noise from day to day. Absence of nocturia correlates best but (with variations) with stool morphology. During the trials glucose was between 80-120gm/day, mostly ~100gm, protein was steady (80-100gm), so change in energy was almost entirely due to fats. No correlation noted with glucose of protein. Fibre varied between 9 and 18 gm/day with no correlation noted. Enzymes & chelating agent from Klaire Labs produced no observable effect. Currently the nocturia improvement fluctuates. During the test , several variables were changed simultaneously eg resumed eating yogurt as a test (Week 26) and amount of wine consumed (low/high 2/10glasses per week). Previously casein and/or lactose resulted in joint aches if combined with stress ie fairly vigorous exercise. I will go back to starting conditions to repeat the experiment. My suspicion is that stool morphology/bacteria species is the key but as I can find no references in literature or blogs which may throw some light on my experience, I am loath to go into indelicate details and my speculations. Your post however peeked my interest. Some of my observations do not agree with common wisdom. My gut bacteria seem to be able to oxidize fats (larger BM’s) and are not very sensitive to fibre in the tested range. Also surpringly need for sleep (7 to 8-1/2) correlates with energy intake but subjective feeling of energy did not seem to change. My body temperature increases slightly with cal intake (97.2-97.4 deg F).

  4. Chronic diseases can be prevented with a healthy diet.

  5. Anonymous

    You're an idiot. Dietary butyrate is absorbed before it reaches the colon.