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Maintaining a Healthful Microbiome

The Feeding and Care of your Microbiome – How do we insure that the 13 trillion cells that make up the human body, live harmoniously with 130 trillion bacterial cells?  by Elizabeth George MD

Happy Multi Talented Microbiome

What is our “microbiome”?

Our microbiome is the ecosystem of bacteria that lives in mutual benefit (symbiotically) with us in our guts, mouths, noses, and on our skin. Amazingly, the 13 trillion cells that make up the human body, live harmoniously with 130 trillion bacterial cells! Our 20,000 human genes coexist with 5 million to 8 million bacterial genes (some times referred to as the “second human genome”) These bacteria, when in balance, play a key role in every organ system – digestion, our immune systems, circulation, nervous system, musculoskeletal. They protect us by stimulating our immune system, reducing inflammation and helping to digest our food as well as produce nutrients.

They can perform these beneficial roles in your health as long as you feed them the right foods.

The good news is, if you’ve been following a whole foods plant based lifestyle you actually have been nourishing your microbiome

You’re plant based eating is encouraging the helpful bacteria to take hold. Studies shows that it takes just several weeks to months of a plant based diet for your microbiome to shift to a healthy balance.  It will stay that way as long as you keep feeding it well. Along with the amazing array of vitamins, minerals, antioxidants key to our organ systems, plants provide fiber. Plant fiber is the key “food” for healthy bacteria. If you’ve always followed plant strong eating habits, this is another good reason to stick to it!

The Standard American Diet encourages a less helpful — even harmful — microbiome.

On the other hand, the Standard American Diet (SAD), low in fiber and high in the sugar, salt and fat of highly processed foods and excessive animal products, does not nourish your gut bacteria (nor you). Research is showing that the SAD encourages a more harmful group of bacteria to thrive and it also causes a decrease in the variety of bacteria.

The microbiome can produce 3000 different molecules with biologic activity.

How the gut bacteria accomplish their important roles is very complex, and research provides new information daily. For example, by looking at the gene sequences of human bacteria it has been estimated that they produce 3000 different molecules with biologic activity; these molecules act as “messengers” to the immune system, to the gut wall, to the brain and numerous other activities – some even inhibit harmful bacteria.

How does the microbiome impact our immune system and defenses? Interestingly, animals raised without microbes essentially lack a functioning immune system. Gut bacteria stimulate B lymphocytes in the gut wall to divide and become active. These “B cells” are important in fighting harmful bacteria and viruses. Another example, messenger molecules and butyrate, a bacterial nutrient product from fiber, strengthen our gut wall – one of our body’s first lines of defense from toxins and infections.

What’s leaky gut? The butyrate that bacteria make from the fiber in our diet (in all those wonderful fruits, veggies, legumes, whole grains) is an important source of intestinal cell energy. Without it, the gut doesn’t effectively maintain it’s “tight junctions” between cells. Inflammatory molecules, such as endotoxins, from the bacteria that predominate in the SAD, also harm the tight junction. This allows toxins from the environment, including all those unpronounceable food additives, to get in through the gut wall. This leaky, inflamed gut not only contributes to inflammation in our bodies, but also causes cramps, diarrhea and many cases of irritable bowel.

Do gut bacteria “eat” meat? Well, sort of, but not the bacteria you really want to encourage. Standard American diets are very high in meat – meat at most meals. This encourages growth of different bacteria needed to break down the amino acid Carnitine from animal protein. These bacteria break Carnitine into TMA (trimethlamine), which is absorbed and then oxidized in the liver to TMAO.  TMAO is  a very inflammatory molecule that contributes to coronary artery plaque formation. (one of the links between meat and heart disease) Our body makes Carnitine, so we don’t need to get it in our diet and trigger this whole negative process.

Is there a connection between gut bacteria and cancer?  Yes – there are many mechanisms for this. One example is that the butyrate produced when healthy gut bacteria ferments fibers, plays a role in discouraging tumor formation. Interesting note here –gut bacteria fermentation is similar to the way cabbage is turned into sauerkraut! A link has also been shown between the bacteria present in chronic gingivitis (gum infection – often associated with smoking and with the SAD) and pancreatic cancer.

What’s the association between gut bacteria and obesity? This is too complex for a simple answer – hold onto your hats. Research in the past decade indicate that the obesity problem could be the contributed to by the kind of bacteria you harbor.   Guess what – the same SAD foods that contribute to obesity are the ones that encourage disruptive bacteria. These bacteria cause inflammation that impacts how insulin functions and even decreases our leptin (the “I’m full” messanger molecule.) So the SAD is a double whammy – it’s loaded with non-nutritive calorie dense food, and the gut bacteria it supports, contribute to the metabolic disarray.   This could be why a whole food plant based diet significantly improves glucose control, including reversing pre-diabetes and, with perseverance, often reversing diabetes.

Will probiotics “fix” the problem? They might be helpful in rebalancing your bacteria, but only if you feed them the right foods. Taking probiotics is kind of like putting goldfish in a fish tank – you’ve got to feed them the right food if you want them to stay alive. But probiotics aren’t really needed to restore bacterial balance; your body will do it, if you give the bacteria a high fiber diet (and leave out the junk food, meat and dairy).

How do antibiotics affect the microbiome? Not surprisingly antibiotics can wipe out some of your healthy bacteria and allow resistant ones to thrive. Double whammy again – lose the benefit of the good bacteria, and the overgrowth of “bad” bacteria, for example C. Difficile causes inflammation and diarrhea. This is a good reason to avoid unnecessary antibiotics – they’re not needed for upper respiratory infections, not even bronchitis, all of which are caused by viruses.  Another problem with animal products is their production relies heavily on multiple antibiotics to prevent and treat infections that arise in crowded conditions.

And our microbiome contributes some important vitamins! Among the molecules a healthy microbiome produces are folate, niacin, biotin, thiamine and B12 – sort of “insurance” added to dietary intake. These are key to numerous metabolic pathways in all organ systems.

What will keep my microbiome happy?   Eat food made from plants, not made in plants!!  Keep following your whole foods plant based lifestyle.  Parents – to give your children a good start on a healthy microbiome, have a vaginal birth if at all possible, breast feed, get your children a puppy and let them play outdoors. There is even a study that shows that exercise encourages a healthy microbiome!

The above artist’s renderings of happy gut bacteria, and of the “gut brain connection” is from a JAMA (Journal of the Medical Association) article The Unraveling of the Influence of Gut Microbes on the Mind by M.J.  Friedrich JAMA, 2015:313(17)

Read more about your microbiome at this Mayo Clinic website



An Adventure is a community-based 28-day program that can kick-start you on a lifetime of healthier eating with a whole foods, plant based lifestyle.

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