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Why do we care about our gut bacteria?

It turns out that despite that our gut bacteria (our “microbiome”) is only about 1-2kg of weight in our colons, our gut bacteria has at least as many genes as we (the “hosts”) do! It turns out that our microbiome has a major influence on our immune system, our metabolism, and our health!

Increasingly, there have been multiple studies linking diseases with a reduced microbiome diversity (“dysbiosis”), including Type 2 diabetes.  The association has been strong.  For example, a 2010 study titled “Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults” concluded that “type 2 diabetes in humans is associated with compositional changes in intestinal microbiota. “

Of course, that association alone does not show causality, or even possibility for therapy, but there has been recent evidence that even the blood glucose lowering effects of metformin may actually work by altering gut bacteria.

“Transplantation of the gut microbiota from patients before and after treatment to bacteria-free mice showed that the metformin-modified microbiota may at least partially explain the good effects of metformin on blood glucose control”, says Fredrik Bäckhed.

Also, experiments that induce dysbiosis demonstrate that the condition can lead to fatty-liver disease, a precursor to diabetes, establishing a relationship much stronger than association.

Changing the gut bacteria through diet

Choosing right nutrition has shown to be an effective therapy for dysbiosis.  A study titled “Diet rapidly and reproducibly alters the human gut microbiome” demonstrates that changes in diet can alter microbiome effectively within days.

The authors explain this ability to rapidly alter microbiome is likely related to evolution:

Our findings that the human gut microbiome can rapidly switch between herbivorous and carnivorous functional profiles may reflect past selective pressures during human evolution. Consumption of animal foods by our ancestors was likely volatile, depending on season and stochastic foraging success, with readily available plant foods offering a fallback source of calories and nutrients

What affects the microbiome positively?

• Prebiotics (fiber).  Non-processed plant-based foods contain prebiotics and have a positive effect on the composition and the activity of the microbiome. Prebiotics cannot be digested by the body and are fermented in the large intestines by the microbiome into short-chain fatty acids, which have been shown to improve glucose tolerance, the lipid profile, and obesity.  A 2017 study showed that inulin (a prebiotic) prevented metabolic syndrome.
• Probiotics.  Probiotics are good bacteria that are either the same as or very similar to the bacteria that are already in your body.  Foods with probiotics include some yogurts, cheeses, kefir, sauerkraut, and kimchi.  There remains some debate as to whether probiotic supplementation positively affects the microbiome in healthy individuals, summarized well in a recent Gizmodo article.

In a series of experiments involving mice and healthy human volunteers, the Israeli researchers found that probiotics only sometimes do what they’re advertised to do: change the makeup of our gut’s bacterial environment, known as the microbiome.

Still there are studies demonstrating some promise of using probiotic supplementation to treat diabetic individuals.  Per a review in Science Daily:

The present meta-analysis suggests that consuming probiotics may improve glucose metabolism by a modest degree, with a potentially greater effect when the duration of intervention is ≥8 weeks, or multiple species of probiotics are consumed.

Negative factors include:

• High Fat.  High fat (HF) diets reduce Bifidobacterium and has been associated with metabolic disease, according to a 2014 paper citing numerous studies.

The relationship between HF feeding and the development of a low-grade inflammatory tone and metabolic disease have been attributed to reduced numbers of Bifidobacterium and a higher plasma endotoxin (Gram-negative bacteria-derived lipopolysacchaide) concentration..

• Excessive meat.  Meat-based diets cause some gut bacteria to produce TMA (trimethylamin), which your liver turns into TMAO (trimethylamin N-oxide).  While a causal relationship has not yet been established, there is a compelling association between Type II diabetes and TMAO.

…this study has supported a meaningful association between plasma concentrations of TMAO and incidence of type 2 diabetes mellitus in a Chinese population. Establishing a causal correlation requires more, multi-centre studies among other ethnical populations.

• Antibiotics.  Antibiotic exposure comes not just from prescriptions but also from our farm animals and our crops.  A very readable article in The Atlantic cited a study regarding prescription use..

The study, recently published in mBio, found that just one weeklong course of antibiotics changed participants’ gut microbiomes, with the effects sometimes lasting as long as a year. After all, antibiotics don’t discriminate—as they attack the bad bacteria, the good ones are vulnerable too.

Further, a Danish population study revealed an association (not causal) between Type 2 diabetes and antibiotic use.

In this nationwide register-based study, we find an increased OR for risk of type 2 diabetes with increasing exposure to antibiotics.

Fasting and the Microbiome

Fasting is actually one powerful way to positively affect the microbiome. During fasting, the diversity of microbiome increases.

• Fasting reduces size of intestines. This creates a “housing crisis” where the total number of bacteria decreases.
• Fasting also creates an “energy crisis” and the good bacteria wins, correcting the diversity.

There is also some additional research on intermittent or “every other day fasting” (EODF) that was described in Cell Metabolism, which describes how intermittent fasting prompts the gut bacteria increase the development of beige-fat (the type that burns white fat!).

These findings provide a new gut-microbiota-driven mechanism for activating adipose tissue browning and treating metabolic diseases.

Of course, more research is required here, but I am not waiting for the research to effect changes for myself!

Refeeding and Beyond

After fasting, there must be a good “refeeding” period to feed the microbiome the right nutrition, as the size of the intestines and the energy supplies returns to normal.

The recommended refeeding at the fasting clinic Buchinger-Wilhelmi consists of:

• Fresh vegetables, fruits, whole-gain products and nuts, preferably organic
• Fewer animal products; less meat
• As little processed food as possible
• As little refined carbohydrates as possible (white flour, sugar)

In addition, regular and intermittent fasting is recommended on top of dietary changes.

Note here that ketogenic (high fat / medium protein) is NOT recommended here because of its effects of high fat and animal protein on the microbiome.