Eating “Bugs” is a Good Idea

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“Dear Pharmacist,

You’re sort of obsessed with gut health because you frequently suggest probiotics to people seeking better health. I don’t take probiotics but I do appreciate your perspective. Not one of 14 doctors over six years has ever suggested probiotics. What’s the big deal?”

–R.M., Ocala, Florida

Answer: Hmm, maybe you would not have needed 14 doctors if any one of them had warned you of the adverse health consequences of microflora deficiency? Think allergies, irritable bowel, depression, hypothyroidism, cancer and autoimmune disorders galore. The ramifications for poor probiotic status cause disease from head to toe.

A new approach to modern health care, known as medical ecology, seeks to change the way we think about bacteria. There are more than 100 trillion microbes that live inside you, that’s more than the number of actual cells that form you into a human being. You are merely the sum of the bacteria inside you, so it’s critical that the good organisms outnumber the bad ones, or else disease sets in. People who enjoy good health, do so because of their strong immune system which powers up at birth, with an assortment of healthy bacteria obtained from mother’s milk. The bacteria in a mother’s milk, for example, contains up to 600 species of organisms that prepare her baby’s digestive tract and lay the foundation for her immune system not only for childhood but well into adulthood.

Research is showing that countless species serve a good purpose in an interesting article written by Carl Zimmer entitled “How Microbes Defend and Define Us.” (New York Times. 12 June 2012). As adults, collectively-speaking, our intestinal microflora bugs weigh about 2 or 3 pounds, about as much as a brick. If you want to enjoy good health, your goal should be to make sure that of those 100 trillion bugs, most of them are good ones! While there are always going to be pathogenic organisms, it’s fair to say many members of our internal ecosystem are getting a bad rap for no reason.

Love your skin? You can thank your bacteria for that. Likewise, if you have sensitive skin, or a skin disorder such as psoriasis or eczema, you can blame your bacteria for that as well. Special skin cells  produce an important moisture layer that protects our delicate skin from toxins, keeping it supple, healthy, and also prevents it from cracking. Just as the bacteria on your skin are essential to a healthy hide, researchers are discovering even more positive effects produced by our invisible inhabitants. While researchers debate the evidence, you might continue scratching yourself to death! Why not try probiotics? They’re a very safe, inexpensive and fundamental way to promote a healthy immune response and ensure beautiful skin. Results are immediate, usually within days to just a few weeks, especially if the diet is cleaned appropriately. For more on eczema, please refer to my new ebook called “Eczema, Itchin’ for a Cure.”

Do you enjoy eating food without the discomfort of heartburn and bleeding ulcers? Thank your gut bugs because they are keeping the invaders (like H. pylori) at bay. Never get sick? Let’s hear it for the bugs! Do your best to nourish the health-promoting microorganisms because if you don’t, the bad guys are opportunistic, and they will take over the terrain, thus changing the ratio of those 100 trillion microbes. By occupying various niches in the intricate landscape of our bodies, our resident microbes protect us from foreign bacteria, fungi, and viruses. Many well-designed studies prove this.

To improve the ratio of good to bad microbes I recommend taking probiotic supplements, sold by some physicians and at health food stores. Everyone associates probiotic supplements with gastrointestinal health and relief of constipation but probiotics are great for skin health, weight, staying healthy as we head into cough and cold season (hint hint), lifting depression and believe it or not, thyroid health. Yes, that healthy bacterial garden in your gut activates approximately 30 percent of your thyroid hormone, which in turn boosts energy and burns fat.

From our skin to our cheeks and teeth, the diversity in bacterial species found in our bodies is incredible. One place with an especially diverse bacterial ecosystem is our gut, which is estimated to contain anywhere from 500 to 1000 different species of bacteria, collectively called “gut flora” (References 1,2,3).  It’s hard to imagine isn’t it, especially because you’ve probably only heard of a handful of organisms among them the most famous Lactobacillus acidophilus, it’s sometimes on the label of yogurt, which by the way is NOT your best method of getting probiotics. I’ll explain that shortly. You may have also heard of Bifidobacterium, another good gut bug. And Lactobacillus GG (Culturelle), is very good at preventing antibiotic-induced diarrhea. There is a friendly yeast organism which some people like to supplement with too, called Saccharomyces Boulardii, it was first isolated from the fruit of mangosteen and lychee. This yeast helpful to overcome overgrowth of bad yeast like Candida and is particularly useful in children with gastroenteritis, people with recurrent Clostridium difficile infection (often induced by antibiotics like Vancomycin and Metronidazole), and also other Clostridia species that affect the brain, sometimes seen in kids with autism.  S. Boulardii supplements are sold nationwide, and can be taken with any brand of probiotic (because it is a yeast). You can ask your doctor about this over-the-counter supplement but S. Boulardii and probiotics should be fine for everyone.

I’m picky about probiotics. We all have a unique “flora fingerprint.”  No two are the same among humans. You can change your flora easily, with every meal. For example, eat a cinnamon bun and you’ve easily demolished millions of happy, healthy bacteria. All prescribed or over-the-counter medications reduce your probiotic bacterial stash so I’m disappointed to hear that not one of your 14 practitioners suggested a probiotic to restore gut flora. You must put back what medication stole or you’ll pay with your health. With probiotic supplementation, results are immediate, usually within days to weeks. Oh, and yogurt, is probably the worst way to take in probiotics since the organisms are likely dead by the time you eat it, and the dairy provides a strong casein and lactose hit. Many people are unknowingly allergic to casein and this adds another layer of problems to someone with a serious health condition. I’m just saying that for many people with chronic illness, dairy-derived probiotics are probably not the best choice.

Are you getting the message? Take probiotics, and eat foods that don’t upset the delicate balance or add to your food sensitivity burden. What you eat upsets balance, so consider eliminating artificial dyes, sweeteners and chemicals, as well as soda, white refined sugar, anything from a box that could sit in your cabinet for a year and still be eaten (!), anything food that is “fast” or refined/processed, inferior oils and fungus-promoting foods (sugar, vinegar, candy and mushrooms) Oh, and I’d prefer your diet be gluten and dairy free. Going grain-free is even better, and imperative, if only for a few months to reduce auto-immune related cytokines for those of you suffering with auto-immune disorders. The closest diet to what I’m suggesting here, and one that will help you achieve optimal health is The Phase One Diet, and another known as The Paleo Diet. Either will suit you and you’ll be impressed with the way you look within a month.

As I have often explained to my friends and family, each person has their own unique “flora fingerprint.”   This is a remarkable finding, because it speaks to the fact that each person’s body is different and should be treated as such.  It’s like your fingerprint, no two are the same among humans; same with your flora fingerprint. While some species of bacteria from a family called Bacteriodes, have found to be present in nearly every healthy adult, there are many  other species that exist in all sorts of combinations (1,2). The relative concentrations of the different strains will vary dramatically in an individual from birth, to weaning, to adolescence and adulthood. When you ingest micro-organisms from a probiotic supplement and it contains a strain that your body does not recognize your immune system perceives it as a germ and launches a low-level attack on it (think auto-immune), but the reaction could take months for you to notice, or hours. There is just no way to tell. What you want to do is avoid supplements that have a bunch of strains because the odds are that some will be foreign to you. Additionally, woman’s gut flora is altered dramatically when she becomes pregnant. So there’s a lot happening in a pregnant belly, and it directly affects the health of her fetus.

With increasing insight into this field, scientists are realizing we have a long way to go before we fully understand the complex nature of gut flora.  No doubt about that. I am still stunned when I hear health care practitioners argue about the fact that probiotics do anything for us. I was recently in a cancer lecture, and one of the world’s leading cancer experts said that probiotics were never anything he recommended in his practice! Really, because that just made me want to throw my high-heel shoes at him! If there’s one thing that boosts immune function, it’s a healthy gut flora. In my opinion, this is the simplest, cheapest and fastest way for a person to protect their health!

This cutting-edge research has shown that even between individuals of the same age, the gut flora make-up can differ quite dramatically! In other words, out of the 1000’s of possible species of bacteria, any individual may have any number or complex combination of them at once in their gut (1,2).  This news has exciting implications for our individual well-being and might offer solutions to a number of health problems (3).

As a proponent of gut health education, I was thrilled to read about a large study called the Human Microbiome Project.  Published and conducted by Dr. Julie Seger, a senior investigator at the National Human Genome Research Institute, the Human Microbiome Project tracked the bacteria species present in 242 healthy individuals over two years.  With this data, these scientists were able to create a more accurate picture of our ever-changing microbiomes. The microbiomes contain a vast amount of genetic material, which scientists can then decode as another piece of the puzzle (2,4).  It has been shown that a patient’s unique gut flora combination can even change the way they metabolize drugs, making this a very important area of research (5). If physicians were able to choose drugs on the basis of your probiotic flora fingerprint, there would be fewer adverse reactions and better outcomes. Ah, but that’s me dreaming…

Each new piece of information we learn provides us with clues for the treatment of numerous health conditions (2).  So what can you do to nurture your gut flora? I used to suggest talking to your physician about your own, individual “flora fingerprint” but then I learned from a dozen or more readers who emailed me that their physician had no knowledge of us having a “fingerprint” nor did they think too much of probiotics. This whole concept of a “flora fingerprint” will come as news to many physicians for a few more years, so just politely nod when they tell you there’s no such thing, or maybe hand them a copy of my Drug Muggers book, opened to chapter 17.   Sorry, you’re kind of on your own here, or you can speak to a naturopath, chiropractor, dietician, nurse, massage therapist or nutritionist – they usually know about the importance of probiotic supplements and gut health.

Take a high-quality probiotic supplement tailored to your specific bacterial needs.  Because every person produces their own unique fingerprint of “good” bacteria, called probiotics, it is essential that you choose a probiotic supplement. Think of your GI tract as having a beautiful garden. Pick products containing bacterial strains which nurture the growth of your own beautiful garden.  Some probiotics available in health food stores provide many strains, but taking strains that are not native to YOUR gut could cause your body to launch an attack on these new intruders. Remember, your body has an army of immune cells, sitting there waiting for germs to appear. When you take in strains of bacteria that you don’t normally make, your immune cells see that as a germ, a virtual invader that has entered seeking to destroy you and off you go, a little autoimmune problem that you’d never trace to your probiotic supplement.

My philosophy is that, with probiotics, the more, the messier.  One of my favorites supplements is Dr. Ohhira’s probiotic because it contains only those strains most common to the human microbiome. In other words, it has the strains that most of us have inside us so the body doesn’t perceive the organisms as invaders. I consider this to be among the safest formulas on the market, and use it myself. It goes back to nurturing your flora fingerprint and also this product never freeze-dries their strains, they are live and viable when you get them. The 12 strains in this product go a long way in reducing inflammatory cytokines, as well as support digestive health. It’s sold at health food stores nationwide.

Another option, for extremely sensitive people or those with multiple chemical sensitivities, I often recommend Klaire Labs “Ther-Biotic Detox Support” because it contains 3 strains only. Great for super sensitive folks, but it’s physician only so you have to go to your doctor and ask them to order it. You will have to keep this one in the refrigerator. I was unable to acquire us a coupon for this brand.

You  may have to experiment and there are other good brands, but to help those of you getting started I thought I would outline a few possible combinations. Some of these are sold OTC, and others are physician-formulated (ie Xymogen) so ask your doctor to order for you.

1. Dr. Ohhira’s Probiotic and Sacharomyces Boulardii (by Nutricology or Jarrow for example)
2. Klaire’s Ther-Biotic Detox Support and Sacharomyces Boulardii
3. Florastor and Xymogen’s ProbioMax

One more thing, this idea of dosage is silly. I know that supplements measure their bacterial strains in terms of CFUs or colony forming units, but this is irrelevant as far as I’m concerned. You can take 10 billion CFUs per day, but if they’re not live, viable strains that are common to your gut flora, it’s useless, and perhaps harmful. So don’t worry so much about CFUs, that’s just a designation that scientists use to compare quantities, it has nothing to do with quality. Taking a supplement that supports your “flora fingerprint” is important for both total health– your gut flora will thank you (6).

Any medication, prescribed or over-the-counter has the ability to destroy your probiotic status. Yes, you heard that right, all medicines are drug muggers of your probiotics. If you take any medication on a daily basis, you should be restoring gut flora. You must put back what medication stole or your body pays the price. On a related note, antibiotics do not discriminate between the “good” bacteria and the “bad,” so be sure to use them sparingly.  A great thing to do is take your antibiotic in the morning, and a probiotic in the evening. There is debate about whether or not to start the probiotic while you’re on the antibiotic, and I do think you should. No sense in waiting until the end of the antibiotic course, by then you will have annihilated most of your 100 trillion organisms! So do as I suggest, take them simultaneously, just separate the antibiotic from the probiotic by at least 4 hours. This ensures that your population of “good” bacteria won’t be completely destroyed while you recover from the infection.  Remember, nurturing your own “flora fingerprint” is absolutely essential for healthy digestive and immune systems, so embrace your gut flora and help keep it going strong! (6, 7)

Yeah, seriously love your gut bugs, they keep you healthy. They are stored in your appendix, so if you’ve had that organ removed, you need to be absolutely vigilant about taking high quality probiotics on a daily basis.  Generally speaking, if you begin probiotic supplementation, you may experience mild stomach discomfort, cramps and even a little bit of diarrhea, this is normal and harmless and comes with repopulating the territory. Your body has to get rid of harmful pathogens, yeast (like Candida) all while implanting cultures of healthy new organisms, the sort that make you healthy, improve mood, support blood sugar and help you lose weight. It’s worth a few days of minor discomfort for the long haul. Probiotics can be taken without regard to meals. And if you are taking a supplement of S. Boulardii (such as Florastor or one made by Xymogen or Jarrow brands), it’s okay to take those without regard to meals as well.

In this article I have only scratched the surface of gut ecology, and new developments in this area of research are happening every day.  The take home points would be that we have a unique flora fingerprint, we should NOT take probiotic supplements indiscriminately, and dump in strains that we have never seen before… and we should avoid refined sugars, processed foods, alcohol and other ‘irritants’ which affect our Microbiome status. For more information about your “flora fingerprint,” be sure to check out my Facebook page where I often post about this, and also read good books on the subject.  There are two other books that I think are fabulous as they pertain to GI health. The first one is “Boost Your Health with Bacteria” by Fred Pescatore, MD, and Karolyn A. Gazella. The other book is “Natural Alternatives to Nexium, Maalox, Tagamet and Prilosec” by Martie Whittekin, CCN. These books are devoted to improve GI flora and contain a lot of useful information.

CLICK HERE to get your copy of my book Drug Muggers: Which Medications Are Robbing Your Body of Essential Nutrients–and Natural Ways to Restore Them


1.  Zimmer, Carl.  “How Microbes Defend and Define Us.” New York Times. 12 June 2012.

2.  Zimmer, Carl.  “Tending the Body’s Microbial Garden.” New York Times.  18 Jun 2012.

3.  Sears, CL. “A dynamic partnership: Celebrating our gut flora.”  Anaerobe 11 (5): 247–251. 2005.

4.  Image: “Invisible Residents.” Published 18 Jun 2012.

5.  Wikoff, William et. al. “Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites.” PNAS. 20 Feb 2009.

6.  Cohen, Suzy.  “Dear Pharmacist: Flora fingerprint protects.” Newsday. 2 April 2011.

7.  Harmon, Katherine. “Bugs Inside: What Happens When the Microbes That Keep Us Healthy Disappear?” Scientific American. 16 Dec 2009.