Do Gut Microbes Impact Human Health?

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Biologists have long known that the bacteria, protozoa, fungi, yeast, and other microbes that inhabit the guts of all animals can play a key role in their ability to survive. For example, termites cannot digest cellulose and so depend on gut microbes to break wood down into a form they can utilize. And the gut microbes of ruminant animals like cattle, deer, and elephants are largely dependent on the actions of the microbes in their rumens to break down cellulose and other material into short chain fatty acids that they can then use as an energy source. Indeed, it has long been known that feeding even monogastric animals like chickens and pigs low levels of antibiotics can actually make them grow faster and get fatter. A recent study found a correlation between childhood obesity and the use of antibiotics early in life. In mice, research has shown that a high-fat diet increases gut permeability and increased gut absorption of endotoxins that promote weight gain, inflammation, obesity, and diabetes (1). More recently, Dr. Patrice Cani and her associates found that mice fed a high-fat diet had 100X less of a specific gut bacteria (A. mucinphilia) that stimulates the production of mucous and reduces gut permeability to microbial toxins that appear to promote weight gain, inflammation, insulin resistance, and eventually diabetes in mice. By feeding these obese mice live A. mucinphilia and a "prebiotic" (fiber) Dr. Cani was able to show a marked increase in A. mucinphilia that led to a reduction in body fat and reduction in inflammation and insulin resistance (2).

The microbes that inhabit the human gut can also at least partially break down dietary fiber, especially soluble fibers like gums and pectins, into short chain fatty acids from which we can derive some energy. However, unlike ruminant mammals, the energy derived from otherwise indigestible fibers is too small to be of much import. Of course, gut microbes can also produce some nutrients like vitamin K2, although this is rarely of critical import in meeting our needs. As a result, medical research has not paid much attention to the plausible role that our gut microbes may be playing in promoting health and preventing disease. However, this is changing in the 21st century as growing evidence suggests our gut microbes are likely playing a far more important role in keeping us healthy than most health professionals thought 15 years ago. And there is growing evidence that what we eat not only nourishes us directly but also serves as food for our gut microbes. Different microbes thrive on different components of food. While some microbes produce substances that appear to keep us healthier, other microbes in our gut can make us sick. In addition, drugs (particularly antibiotics) can drastically alter our gut microbes and other microbes that inhabit other parts of our bodies.

Changing Gut Microbiome with Probiotics

Probiotics contain living microbes that can alter the gut’s microbiota. However, probiotics do not usually permanently modify the microbiota. Some strains of probiotics have been demonstrated in scientific studies to temporarily change the microbiota, but once oral intake of these microbes is discontinued, any changes to the gut's microbiota will usually be reversed. The only way to sustain a significant change in the gut's microbiota is to change the diet. Probiotics may be of some value in treating diarrhea caused by the use of antibiotics, but in most cases the evidence of their efficacy for treating a "sick" microbiota is not all that convincing. One huge problem is the colonization of the microbiome with Clostridium difficile. About 1/2 million cases of C. difficile infections occur in the USA each year and result in about 14,000 deaths annually. So far, probiotics and currently available antibiotics have proven to be pretty ineffective. Why do probiotics often have little impact on the microbiota? Probiotics are not like seeds that implant and grow into a new microbiota. Rather, probiotics are more like "tourists" who do little to alter the native “culture." What one eats helps determine which microbes will thrive and which microbes will get eliminated because they do not have enough to "eat" to sustain themselves (3).

A typical Western diet high in fat, salt and meat and low in fiber increases Bacteroids bacteria that seem to be associated with more disease. By contrast, a diet composed largely of fiber-rich plant foods can create a healthier gut microbiome high in Prevetolla bacteria (4).

Bottom Line: Although more research is needed, there's encouraging evidence that a diet with more fiber-rich plant foods and less fatty animal products, salt, and refined carbohydrates perhaps sometimes in combination with probiotics or fecal transplants may help alter the gut microbiota and treat diarrhea, especially following treatment with certain antibiotics. And it may alter the microbiota in ways that can at least reduce irritable bowel syndrome. There is growing evidence that altering the gut microbiota reduces the dangers of C. difficile infections and perhaps the risk of other diseases as well.

By James J. Kenney, PhD, FACN


  1. Cani P, et al. Diabetes 2008;57:147-81
  2. Everard, A.; Belzer, C.; Geurts, L.; Ouwerkerk, J. P.; Druart, C.; Bindels, L. B.; Guiot, Y.; Derrien, M.; Muccioli, G. G.; Delzenne, N. M.; de Vos, W. M.; Cani, P. D. (2013). "Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity". Proceedings of the National Academy of Sciences 110 (22): 9066–9071
  3. Mary Ellen Sanders. How Do We Know When Something Called “Probiotic”Is Really a Probiotic? A Guideline for Consumers and Health Care Professionals. Functional Food Reviews 2009:1;3–12
  4. Wu GD, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011;334:105-8
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