Gut Microbes: or, Why You Ought to Invite Your Trillions of Brand New Best Friends to Dinner

I recently gave a couple of demonstrations at the Canterbury Farmers Market and the Warner Area Farmers Market. The theme was great recipes that feature complex carbohydrates to feed your gut flora.

“Huh?” you may be asking. Read the article below for the lowdown on our microbe friends and why it’s important to feed them. And then look for my next post featuring the recipes I cooked up. Believe me, nobody was choking that rich-in-complex-carbohydrates-food down. Au contraire – people loved it. And I KNOW their microbial body-mates did, too.

Why you need to invite your trillions of microbe friends to dinner, and feed them what they like to eat:

Our bodies contain trillions of micro-organisms – they outnumber human cells by 10 to 1. There are upwards of 100 trillion bacterial cells alone (that doesn’t count things like fungi and other micro-organisms) on our skin and inside of us.

We used to think of these organisms as harmful germs, but it has become clear in recent years that though some them do make us sick, most of them are essential for human health.

In 2008 the National Institutes of Health started the Human Microbiome Project, a 5 year, 115 million dollar project to partner with researchers to map the human micro-biome. Scientists are looking at 5 sites – oral, skin, vaginal, gut and nasal-lung – and identifying the microbes living there and how they affect human health.

The greatest diversity of micro-flora is in the gut. Most are bacteria, but there are a few other things like fungi and yeasts as well. It’s thought that there are at least 1000 different microbial species that inhabit the human gut, and each of us has at least 160 of them.

One of the most important things these microbes do for us is to ferment the carbohydrates that our stomachs and small intestines lack the enzymes to digest. When these carbohydrates reach our large intestine the micro-flora living there can produce the enzymes that will break them down and ferment them.

These bacteria have a symbiotic relationship with us – they take what they need to survive from the complex carbohydrates that reach them (think fiber), and donate to us by-products that they don’t need, primarily short chain fatty acids. These provide we human hosts a huge amount of nutrition and energy that we can’t make for ourselves.

The microbes also help to synthesize important vitamins, like B vitamins and vitamin K, and can break down harmful toxins that have entered our bodies, fighting not only things we’ve ingested that might make us sick immediately, but also things that might give us cancer. They can also influence the production of neurotransmitters and so are involved in brain function; they may even be involved in mental illnesses.

Another essential task they perform is training our immune systems; this happens in a variety of ways. For example, some bacteria train the gut mucosa to produce antibodies that kill harmful pathogens while leaving the good microflora alone. Others encourage T-cells that produce antibodies to turn on. One kind of T cell, the T Helper 17 cells, are suspected of becoming overactive and causing autoimmune diseases like MS and Rheumatoid Arthritis as well as some forms of cancer, and it is now believed that specific gut bacteria may control these overactive cells.

Gut flora also seem to be involved in the production of hormones that tell the body to store fat. It is known that obese people have very different kinds of gut flora than leaner people, and as obese people lose weight, their gut flora changes to look more like that of thinner people. Just how these gut flora contribute to obesity isn’t completely understood, but it may be that they are capable of extracting more calories from foods than other kinds of bacteria.

If you eat lots of complex carbohydrates, like vegetables, your gut will be dominated by bacteria in the family Prevotella; most people in developing countries have gut bacteria in this category. If you eat lots of meat and fat, your gut will be dominated by the family Bacteriodes; most people in Western countries have this kind of gut bacteria. Even vegetarians and vegans, if they eat enough fat and processed foods, can have this kind of gut “enterotype.” Such a diet may be related to inflammatory bowel disease and other inflammatory disorders.

It is very likely, according to early research, that “metabolic syndrome,” the combination of obesity, diabetes type 2, and high blood pressure that plagues more and more people every year, is linked to the kind of bacteria we have in our guts. It has been shown experimentally that changing diet will change gut bacteria, leading to an increase in the number of species that inhabit us, and knocking back populations of some kinds of microbes that might contribute to obesity.

The research so far seems to indicate that most of us could improve our health by eating lots more complex carbohydrates, primarily foods that come from plants and that have not been heavily processed. This gives your gut flora lots of undigested carbohydrates to ferment and feed on, providing the human host with many health benefits. So in order to grow good gut microbes and reap all the health and psychological benefits of a vibrant personal gut biome, many of us need to change our diets.

Here are a few pointers on how to do this:

  • Try to eat a lot more plants than you do animal products. Look for recipes that use a little meat to a lot of vegetables, like stews and stir fries.
  • Shop the edges of the grocery store, where the whole foods are located, and skip as much as possible the aisles that contain processed foods. Just because something is labeled “gluten-free,” “organic,” or “low-fat” does not mean it’s good for you.
  • Try to eat as many different plants as you can. Try for 30 different plants a week. I know this sounds like a lot, but remember that adding some chopped up parsley to a sauce counts as 1 plant. If we sneak lots of little things like this into our diets, we can get to 30 quickly.
  • Try to eat more of the actual plant. For example, don’t just eat the florets on broccoli – eat the stem, too. In many cases, the greatest nutrition in a plant is in its skin. Potatoes are a good example of this. Skins are high in complex carbohydrates, and are great for your gut microbes. They will slow down how fast you metabolize the starches and sugars in the rest of the potato. Remember, though, that skins from conventional produce can be loaded with pesticides – potatoes are notorious for this. So, if you aren’t eating organic produce, it may be best to toss the skin. At the very least, wash thoroughly (though this may not remove all contaminants).
  • Learn more about which vegetables and fruits contain the most nutrition (and the least) and try to pack your diet with the best ones. I recommend Jo Robinson’s book Eating on the Wild Side – she has done a tremendous amount of research on plant nutrition and also includes great advice about which varieties to grow or seek out at farmers markets, as well as storing and cooking foods to retain their nutrients.
  • Some foods have “probiotic” qualities – that is, they already contain bacteria that are good for our guts. Some examples are kimchee, sauerkraut, yogurt and kefir, though there are many more. Eat them – they’re good for you. And try making your own. I recommend Sandor Katz’s book Wild Fermentation to learn how.
  • Be aware that, unfortunately, some complex carbohydrates can cause gastric problems in some people. Such problems can be life-threatening, as in celiac disease, where an allergy to the gluten in wheat and some other grains can so degrade the lining of the digestive tract that microbes leak into the blood stream and make the individual extremely ill. For most of us though, such gastric problems amount to uncomfortable bloating, excess gas and, sometimes, constipation or diarrhea – the by-products of happy microbes madly fermenting the food you eat. If you already have such symptoms, or you begin to experience them after you begin eating more complex carbohydrates, talk to your doctor about trying a FODMAP elimination diet. FODMAP stands for Fermentable Oligo-, Di-, and Mono-saccharides And Polyols. I recommend the book IBS: Free at Last! by Patsy Catsos for an in-depth description of the diet.
  • Go do some research on the research. Here are some websites to start with: – a link for the NIH Human Microbiome Project.
  • – home of the American Gut Project.
  • Avoid antibiotics when you can do so safely, because they can destroy many of your beneficial gut flora. Avoid conventionally raised meat, because many of these animals are fed antibiotics, and this practice may contribute to the development of antibiotic-resistant microbes.


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