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The Care and Feeding of Your Microbiome

If you read the history of alternative medicine in the US, you’ll be as intrigued as I was by its preoccupation with your gastrointestinal system and feces. Diet, digestion, absorption, elimination, and possessing a wondrous “inner hygiene” were recurring themes originating in the late 19th century, when Kellogg’s cereals were the mainstay health food at Michigan’s Battle Creek Sanitarium, best eaten in conjunction with your daily enema.

Because these topics were favored by alternative physicians such as chiropractors, naturopaths, and colon therapists, they were deliberately ignored or regarded with actual hostility by conventionally trained physicians. I well remember the chief of medicine calling me into his office when he learned I was opening an integrative center and snarling something like, “So now you’re going to be one of those colon-cleaning candida quacks,” his alliteration not as poetic as my own.

Even though I’d been an internist for 20 years before opening WholeHealth Chicago, I readily acknowledged I’d never come across such diagnoses as intestinal dysbiosis (intestinal bacterial imbalance), leaky gut syndrome (intestinal hyperpermeability), food sensitivities as opposed to food allergies, or chronic diseases caused by apparently harmless parasites like blastocystis and candida.

Nor did I know that chiropractors and naturopaths had for years routinely ordered tests measuring the efficiency of the digestive system from a lab I’d also never heard of, called Great Smokies Diagnostic.

As I speedily filled in what I considered a serious gap in my education, I kept wondering why these topics were simply never mentioned in medical school or residency. Conversations about this with gastroenterologist friends were really disappointing. Their ignorance seemed both willful and deliberate, as if it would be embarrassing to have some shared expertise in a field a chiropractor also knew. They’re still my friends, but, sadly, they’re still clueless. Young physicians just out of training stare at you blankly if you say “leaky gut” or “dysbiosis,” though by now just about everyone in conventional medicine finally agrees that taking probiotics after antibiotics probably can’t hurt.

Based on the numbers, you are 10% human, 90% bacteria
Maybe if all of them perused the New York Times Magazine last Sunday, they’d have an attitude change. Some of My Best Friends Are Germs by Michael Pollan (author of The Omnivore’s Dilemma and other titles) is an elegant article on our internal microbiome, that intestinal array of the several hundred microbial species whose population is currently pegged at about 100 trillion and, weighing in at about two pounds, exceeds the total number of cells in your very own body by a factor of ten.

Read the Pollan piece (virtually predicted by chiropractors and naturopaths throughout the 20th century) to better grasp these ideas:

  • The bacteria in our gut start growing inside our intestines when we’re born, the mix of bacteria pretty much determined by what we eat (breast or bottle makes a difference) and who we live with, pets included.
  • Good bacteria are related to diet. Having them improves digestion and absorption of food and enhances our immune systems. Good bacteria are also involved in our ability to manufacture vitamins, enzymes, and neurotransmitters (brain chemicals) like feel-good serotonin.
  • Bad bacteria are also diet-related, a product of junk foods, processed foods, and foods treated with chemicals and antibiotics. They rarely cause actual infection, but rather inflame and damage the delicate intestinal lining. This constant low-level damage leads to the intestine becoming excessively permeable to digested food molecules (leaky gut), which then predisposes us to food sensitivities, weight gain, diabetes, a variety of autoimmune diseases including inflammatory bowel disease (Crohn’s, ulcerative colitis), and chronic hives and other chronic skin conditions like psoriasis.
  • You didn’t misread the weight-gain part. Many chronically overweight people carry a load of intestinal bacteria that actually cause excessive amounts of food to be absorbed into the body. When the intestines of underweight mice were inoculated with the bacteria of obese mice, the underweight mice became obese and developed early diabetes.
  • The damage from bad bacteria and the subsequent intestinal hyperpermeability can trigger a steady state of body-wide chronic inflammation. One result is your arteries become inflamed, making them susceptible to premature buildup of cholesterol plaques. We can counter some of this with a daily anti-inflammatory like aspirin or turmeric, but keep reading for a list of changes you can make to avoid the damaging bacteria in the first place.
  • When you take a single course of antibiotics, the imbalance of bacteria that occurs quickly restores itself to baseline status, meaning you get your old microbiome back. Full recovery is more difficult, however, after taking multiple courses of antibiotics. Unfortunately some people have been on dozens of antibiotics throughout their lives and we don’t really know the long-term health effects of this.
  • In rare cases, a truly villainous intestinal bacteria can kill you. The antibiotic-resistant C. difficile, which can emerge in hospital patients post-antibiotic, is responsible for 14,000 US deaths annually.
  • You’ll likely be reading more about people undergoing fecal transplants to normalize their microbiome. This procedure is being done by some gastroenterologists as a treatment for drug-resistant ulcerative colitis and Crohn’s (personally, I’d take the transplant first over the immune-suppressing drugs). Currently, the going rate is about $10,000, which strikes me as routine medical greed. I know several patients who simply managed it at home. Like everything else in the world, instructions for a DIY fecal transplant are on YouTube.

You can create and nurture a diverse and healthy microbiome by:

  • Avoiding antibiotics unless absolutely necessary, and then taking them for the shortest period possible. Eating antibiotic-free foods is a good choice too. Some 80% of all antibiotics used in the US are given to livestock, mainly to help them put on weight (some fruit trees are also sprayed with antibiotics). If you think about that for a second—the connection between taking antibiotics and gaining weight—you’ll have an “aha” moment. Big agribusiness gives antibiotics to livestock not to prevent or cure infection, but rather to deliberately change the animals’ intestinal bacteria to the species associated with obesity. Now go one step further: If you’re eating this antibiotic-laced meat, your intestinal bacteria will change and be identical to that of the fatted calf.
  • Increasing the fiber in your diet.  Recognize there are many kinds and your microbiome enjoys a varied menu.
  • Relaxing the sanitary regime in your home. Let your kids play in the dirt and don’t wipe everything down with hand sanitizers and antibacterial wipes (my mother would faint at this suggestion). However, washing hands with soap and water after using the toilet and before meals are non-negotiable.
  • Cutting back on or eliminating processed, low-fiber foods.
  • Adding more fermented foods to your meals: yogurt, kimchi, sauerkraut, and other pickled veggies. Beware—living foods don’t sit in jars on grocery store shelves. But they’re easy to make yourself.
  • Eating more complex carbs (fruit, veggies, whole grains, legumes) and cooking them lightly to preserve the fiber content.

I must close with an anecdote about deliberate physician ignorance.

Medical practices all over the country are routinely audited by insurance companies ever on the lookout for their version of fraud. Several years ago, we were included with other practices in an “audit sweep” by a major carrier, literally hunting down physicians who had diagnosed their patients with intestinal dysbiosis (unhealthy bacterial balance), leaky gut syndrome, and food sensitivities. One by one, our practices were called to insurance headquarters to explain what we were doing and why we shouldn’t be cited for fraud. Since physicians in the employ of insurance companies are definitely not the best and the brightest (you’ll never see an insurance medical director listed in Chicago’s Top Doctors), each practice carefully explained all about dysbiosis, leaky gut, and so forth to his obviously anti-intellectual ennui.

Finally he sneered, “You should return all the money you’ve charged us for these tests. Our consultant gastroenterologist says this is all nonsense. Don’t you dare order any of these tests again or you’ll be in serious trouble.”

So, if you’re one of our patients and we suggest that your problem merits getting tested for some aspect of leaky gut and we explain that these tests will be self-pay, out-of-pocket, well, now you know why.

Be well,
David Edelberg, MD


Leave a Comment

  1. Steve says:

    No mention of probiotic supplementation? Or did I miss it?

  2. Steve says:

    Never mind. I just read Pollan’s article. Not exactly a ringing endorsement for probiotic use.

  3. Bill Siebrandt says:

    I found this article informative reaffirming what I already know through much research in the past.
    A positive note many physicians I have met who are just beginning practice or still in medical school are better informed,health conscious and influenced by alternate holistic approaches to medicine.Great!!

  4. stephanie says:

    I would like to hear more about the prebiotic. It does not seem to be spoken of much. Michael Pollan’s article really pointed toward more prebiotic usage.

  5. Mery Krause says:

    I’m taking this to my health/weight club this morning and reading it since our topic this month is how much our gut affects our over all health, much like our oral hygiene. So, thank you Dr. E for this well written article on this very subject. The gals will love it, even though it contains some words that conjur up some negative images….haha.

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Just print this out, tape it on your refrigerator door, and stay calm.


• Runny nose
• Sneezing
• Red, swollen eyes
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• Tickly throat
• No fever

• Runny nose
• Sneezing
• Sore throat
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