Q: What is the “human microbiome?”

PVH: The human microbiome is the collection of bacteria that live in and on our bodies. It also includes some viruses and fungi, but overwhelmingly, the bacteria predominate in importance. There are as many as ten thousand bacterial species in the human microbiome, and they play a crucial role in our immune function, digestion, metabolism, and other key health-related functions.

Q: Where on the body do these bacteria reside?”

PVH: They reside mainly in our large intestine or colon, although some can be found on our skin and respiratory passages. There are very few bacteria in the stomach and small intestine because the acid levels in the stomach are so high that most bacteria are destroyed before leaving the stomach.

When I refer to our microbiome, I’m referring to our colonic microbiome, which is the main focus of scientific research.

Q: Why has the human microbiome recently taken on greater importance?

PVH: Our microbiome is a complex network of microorganisms that have a far greater effect on health than previous imagined. The composition of our personal microbiome affects both our physical and mental health.

We’re learning, for example, that the use of antibiotics can seriously disturb this network. Antibiotics have saved countless lives but, in so doing, they may kill beneficial bacteria along with disease-causing bacteria. Recent research suggests that the loss of beneficial bacteria and subsequent overpopulation by unhealthy types is related to the dramatic increase in certain illnesses: Crohn’s disease, asthma, allergies, celiac disease, Type 1 diabetes, and obesity.

Even if we never take antibiotics for an illness, antibiotics are routinely given to farm animals to prevent infections and improve their growth. We can absorb minute doses of those antibiotics when we eat or drink those animal products. Science is now trying to answer the questions: what is the cumulative effect of our exposure to antibiotics and environmental toxins, and what can we do about it?

Q: Has science found any answers?

PVH: We’re in the early stages of this new science, but already we’ve learned a great deal. In 2007, the National Institute of Health initiated the “Human Microbiome Project,” a 5-year effort to map the human microbiome. The project involved 242 healthy people. Researchers periodically sampled bacteria from various sites on and in their bodies, and the initial results were published in 2012.

They learned that the bacteria residing in the colon have a much greater effect on our health than we realized. We now know that there’s a direct connection between our microbiome health and numerous physical diseases and behavioral health disorders.

Q: Can you give an example of how the colonic bacteria affect our physical health?

PVH: Yes. There is one particularly dramatic example involving people who, while hospitalized, received multiple courses of antibiotics for certain illnesses but then became ill with a disease known as clostridia difficile, which is usually acquired in hospitals. The antibiotics used to treat their other illnesses caused an overgrowth of harmful clostridia difficile bacteria in the colon.

Clostridia difficile bacteria are normally held in check by good colonic bacteria. But when these good bacteria are destroyed by antibiotics, clostridia difficile can erupt, causing severe diarrhea and deadly inflammation in the colon. Each year clostridia difficile causes tens of thousands of deaths in the world, and hundreds of thousands of illnesses among hospital patients.

It’s undisputed that most clostridia difficile infections occur primarily as a result of antibiotic treatment, and the incidence of such infections in the United States has risen sharply in the past twenty years.

Q: Are there any remedies for clostridia difficile?

PVH: Clostridia difficile doesn’t respond well to antibiotics. However, one rather unorthodox treatment has proved very effective and is rapidly becoming the treatment of choice. The procedure is referred to as a “fecal transplant.”

Physicians take healthy fecal bacteria from the colon of a healthy person and infuse it into the colon of the ill person by means of a colonoscope. Repopulating the colon with stronger healthy bacterial strains eradicates the clostridia difficile bacterial strain, and there are no side effects. The cure rates are approaching 100% with a single infusion of healthy bacteria.

After the publication of the first studies showing the beneficial results of fecal transplants for clostridia difficile, there was such a high demand for fecal transplants by people with this disease that a fecal transplant bank, with hundreds of rigorously screened samples, was established in the United States. To simplify delivery, researchers recently have developed special time-release capsules that don’t open until they reach the colon. These capsules are made using a lab-grown set of bacteria.

Q: Have fecal transplants been used successfully in any other areas?

PVH: Yes, rather surprisingly, in the treatment of obesity. For people whose obesity could not be reduced in any other way, fecal transplants, combined with a good healthy diet to support the transplanted bacteria, have enabled some people to bring their weight within normal ranges.

In the field of colon health, we’re learning that there are what’s known as “lean bacteria” and “fat bacteria.” Those names refer to the effects of these bacterial strains on body weight. If people have large populations of lean bacteria in the colon they tend to be lean, and if they have large populations of fat bacteria, they tend to be fat. Fecal transplants have been very effective in increasing the level of lean bacteria in the colon and may become an increasingly important way of dealing with our “obesity epidemic.”

Interestingly, there are two recent scientific studies which confirm that there are good bacteria in our digestive system that help prevent overeating, and these good bacteria can be destroyed by antibiotics. An August, 2014 study showed that when antibiotics eradicated bacteria commonly found in the digestive system of mice, the mice rapidly became obese even though they ate the same amount of food as before. The study concluded that the eradicated bacteria had helped the mice maintain their normal weight by metabolizing calories efficiently.

In a later 2014 study, scientists identified a little known bacterial family that is common in people with low body weight. Mice treated with microbes from this bacterial family gained less weight than untreated mice, a result which suggests that increased amounts of this microbe may help prevent or reduce obesity in humans.

Q: I understand that scientific research has also found a connection between psychiatric disorders and disturbances in the colonic microbiome?

PVH: Yes. In fact, we’ve known for over fifty years that a small percentage of the people who get streptococcal throat infection or “strep throat” will later develop obsessive/compulsive disorder as a result of that bacterial infection.

But it now seems that there may a connection between certain bacterial strains in the colon and other abnormal mental health states including depression, anxiety disorders, and even autism.

Obviously, psychological factors often contribute to these illnesses, but we understand now that there can also be biological factors involving the colonic microbiome. Attacking the illness at the biological level with fecal transplants, probiotics, and special diets may soon become a more standard, and less intrusive additional treatment for difficult behavioral health issues.

Q: Looking to the future, how can we use what we’re learning about the human microbiome to lead healthier lives?

PVH: The simplest thing is to eat freshly made yogurt or kefir on a daily basis. I also believe that it may soon be possible to restore the health of a depleted microbiome simply by swallowing a probiotic, a capsule with billions of bacterial cells.

Already it’s become routine for physicians who prescribe an antibiotic for an illness – a urinary tract infection or bronchitis, for example ¬¬– to recommend that the person also eat fresh yogurt or kefir, or take a high potency capsuled probiotic to help replenish their intestinal flora during and after treatment.

Q: How do the bacteria in yogurt or kefir survive the stomach acids and reach the large intestine?

PVH: Many bacteria are killed in the stomach by the high acid levels, but some do make it through to the colon. If you’re eating a normal amount of fresh yogurt or kefir on a daily basis, you’re constantly feeding your colonic microbiome with healthy bacteria which, in time, will prove very beneficial to your health. But this practice needs to be combined with a healthy diet.

However, if you eat a diet high in sugar, that diet will cause your microbiome population to shift in the direction of bacteria that thrive on simple sugars. And these are the same bacteria that we often find in people with obesity problems or Type 2 diabetes. Fortunately, more and more people are beginning to understand that eating a fast food hamburger or a milk shake that doesn’t have any milk in it – is not healthy.

Interestingly, Paramhansa Yogananda emphasized the importance of good colon health, including eating certain foods and avoiding others. Looking at what he wrote through the lens of colon health, his recommended diet seems balanced and designed to promote overall good health, including a healthy microbiome. It’s important to note that his recommended daily diet included yogurt, which in that era was called “clabbered milk.” [See Sidebar below]

Q: Summing up, what would you say is the main outcome of the human microbiome project?

PVH: One of the main outcomes is that we now see ourselves in a symbiotic relationship with trillions of bacteria that reside mostly in our colon and are having a huge impact on our overall health. We’re beginning to learn how to have the best possible bacteria for our physical and mental well-being.

Remember we’re dealing with many, many different strains of bacteria, all living very happily in our colon. We can draw a parallel to communities: we want to make sure that the healthiest bacteria have the biggest representation in our colonic community, and the unhealthy bacteria (who are not good citizens) to be crowded out.

Paramhansa Yogananda’s Recommendations

For colon health:

  • Keep the colon clean.
  • Do not let poisons accumulate in your system
  • You cannot afford to have constipation
  • Avoid white flour.
  • Colonic poisoning comes from eating white bread
  • Eliminate the bad habit of overeating
  • Eliminate the bad habit of wrong eating.
  • Fast at least once a month to give your body a thorough house cleaning.

For overall good health:

Your daily food intake should be chosen from the following list of foods which contain all the elements needed for the proper maintenance of the body:

  • A carrot, including part of the green top
  • A lemon
  • An orange
  • An apple
  • Grapefruit
  • Small piece of banana
  • A glass of almond milk or any nut milk (grind two tablespoons of nuts thoroughly and mix with water)
  • Chopped green-leafed vegetables daily
  • One handful of unsulphured figs, dates and raisins
  • A glass of milk
  • One baked or half-boiled steam vegetable with its juice
  • One tbsp. clabbered milk (milk which has been allowed to stand in a warm place, preferably in an earthen vessel, for a day or longer, until it has soured or curdled)

Omit those foods that do not agree with you. You may increase of decrease the quantities given above, in accordance with your individual needs. It is, of course, obvious that the person doing strenuous muscular work requires more food than the sedentary worker. If you work hard during the day, you may add:

  • Whole wheat bread, fresh cheese, and a glass of milk
  • One or two boiled eggs, or one quart of milk a day, or six tablespoons of almonds with water
From East-West Magazine, May-June, 1929, and Praecepta Lessons, Vol.1 (1934) Praeceptum #3. Peter Van Houten lives at Ananda Village and is the founder and Medical Director of Sierra Family Medical Clinic near Ananda Village. He frequently writes and lectures on the brain and other “yoga and science” topics.


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    It should be emphasized that at the time Paramhansa Yogananda wrote these recommendation for the “1 glass of milk,” he most likely was talking about raw milk. At another part of his teachings he said a person could live exclusively on milk. There are many benefits associated with raw milk, and it was even used as a very successful healing treatment at Mayo Clinic in the early 1900’s; the patients lived exclusively on raw milk for many weeks. Another variation of that curative diet consisted of raw milk and some fruit. So, it was a very yogic cure!
    Likewise the clabber may have been made from raw milk, so it is not actually synonymous with yogurt. The clabber would have been vastly better for your gut health due to a much broader spectrum of healthy microbes in the raw milk.
    If a person doesn’t have access to raw milk than a high quality yogurt or kefir can be very helpful

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