Wednesday, March 25, 2015

The Human Microbiome: Cleaning it Up (Part 2)

In last month’s post I discussed the Human Microbiome. To recap, simply defined, the human microbiome is the total inclusion of every microorganism living in, on, and perhaps even around the human body. We cannot achieve or maintain health unless we respect and care for these “friendly critters” that live on our skin, nose and sinuses, mouth, esophagus, intestines, and genitals.

We learned that a newborn who is not born vaginally and not breastfed likely would not fully receive the host of beneficial bacteria that are passed from the birth mother through natural delivery and nursing. We also learned that our microbiome houses an ecosystem with thousands of species harmoniously living tissues of the human body. It is estimated that the combined microorganisms and microbial cells that live inside or on the body outnumber human cells by about ten to one!

Our gut microbiome weighs as much as our brains
about three poundsand many might say that it’s just as important. Our gut microbiome certainly not only interacts with but also can actually control our brains. It, combined with the gut itself, is deservedly called “the second brain”. People really do have gut instincts. Out of the approximately 100 trillion microbial cells in the human body, the human gut alone contains 40,000 bacterial species and that our microbiota (all the microbes of a particular site, in this case the human body) influences our health. For example, we discussed last month that 85% of our Serotonin and Dopamine transmitters are made in the large intestines, and that disruptions in the gut’s health have a huge impact on mental health.

The gut microbiome also influences tissue building and hormone regulation, obviously through nutritional absorption, but also by influencing how we metabolize the food we eat. Our gut’s health and bacterial composition affect nutrient and mineral absorption
especially zinc, calcium and magnesium. (Very much like prebiotics, which we’ll discuss later in this article). The gut microbiome also manufactures enzymes, amino acids, and short chain fatty acids; it influences how herbs, vitamins and medicine work in our bodies to help metabolize drugs, hormones and other molecules.
Last month we discussed how food, medications, pesticides, GMO and Bt toxin containing foods, stress and numerous other factors have a major negative impact on out gut microbiome. Let’s look at how we begin to reverse the damage.

Where to Start
Elimination Diet
Considering that we’ve all had multiple exposures to the offenders mentioned above and in Part I of this series, how do we heal and restore our gut health? One of the first steps an Integrative Physician, Functional Medicine Physician or Naturopathic Physician will ask you to take is to perform an elimination diet. This requires the elimination of foods that are known to be problematic and allergenic. Some of these foods may include gluten, dairy, eggs, soy, corn, sugar and nuts. Once these foods have been eliminated for a period of time, reintroduce each food, one at a time. When you do, do it in a big way. Enjoy that first serving of the food you’ve been just “DYING” to reintroduce, eat a nice, large serving and see how your body reacts. If you have sensitivity to it, you may notice brain fog, overnight weight gain, abdominal bloating, gas, abdominal pain, joint pain, skin irritation, sinus/allergy-type symptoms and/or more. 

When you eat foods to which you are sensitive, your gut will not heal. Once the sensitive foods are eliminated, however, and you are eating cleaner foods (i.e. not sprayed with herbicides and laden with Bt toxin), the healing can begin. There are many references available on the web to help you do an elimination diet. They range from a four-food elimination diet to much more comprehensive diets. Choose one that you can stick with.

Optimize Your Stomach Acid and Enzymes
Insufficient stomach acid contributes to deterioration in the microbiome. Stomach acid is your first line of defense against invading germs that you consume from your fingers, foods, toothpicks, etc. every day. If you are on a drug to reduce your stomach acid for long periods of time, this will change the microbiome downstream in your small and large intestines.

So take a little acid with your meals. Lemon in your tea or water. Vinegar in water. Betaine HCl in capsules. Swedish Bitters. All will achieve the same effect. They will raise the acid in your stomach enough to protect you against dangerous germs and help you better digest your food.

Some people may need enzymes to better breakdown food. These do not break down bacteria, but they enhance digestion and reduce the chances of food sensitivities, which in turn increase inflammation in the gut. Your stool should look like a uniformly brown banana that sinks in the toilet. Anything else suggests the need to chew your food better and or take enzymes. (Oh, and stomach acid promotes the release of enzymes!)

Prebiotics are nutrients that support and increase the growth of beneficial bacteria already residing in the small bowel and colon. Prebiotics include fructo-oligosaccharides/FRUC-to-ol-i-go-SAC-cha-rides/ (aka FOS), which are dietary soluble (dissolves in water) carbohydrate fibers from plant-based foods. FOS form a gel when in water, and include oligofructose (a dietary fiber), and inulin (a natural storage carbohydrate). FOS are in more than 36,000 species of plants, including chicory, onion, bananas, garlic, asparagus, tomatoes, cane sugar, leeks, jicama, and Jerusalem artichokes. They are the stored carbohydrates—the plant’s energy reserves.

Because FOS are soluble in water (and are therefore not broken down by the upper gastrointestinal tract stomach acid and digestive enzymes during digestion), they are able to reach the colon virtually intact, where they undergo bacterial fermentation. All inulin-type prebiotics stimulate the growth of Bifidobacteria/BI-fi-do-bac-TER-i-a/ and Lactobacillus /LAC-to-ba-CIL-lus/ species, our friendly bacteria.

Another type of soluble fiber that acts as a prebiotic is called galacto-oligosaccharide, or GOS. GOS are derived from lactose and have some similarities to human milk oligosaccharides. Human milk oligosaccharides from a healthy mother’s breast milk have been shown to help lower the incidence of infectious and allergic diseases. They feed the newly established gut flora introduced during the birthing process. This unique growth then continues throughout life—but only if the individual continues to consume a prebiotic- and probiotic-rich diet. Oligosaccharides prevent infants from getting infections, and are important in stimulating the development of the new infant’s immune system.

Studies have shown that adding dietary GOS/FOS to baby formula produced changes in the stool similar to breast-fed infants. One of the ways oligosaccharides decrease the incidence of infection is by inhibiting the attachment or adhesion of pathogens to the gut surface. They also interact directly with immune cells. GOS and FOS help immune-supporting bacteria to proliferate in the colon of bottle-fed infants, children and adults.

Pectin is another natural prebiotic carbohydrate. It slows the absorption of products your body can’t use by binding to them in your digestive tract. Pectin is a soluble fiber found in pears, apples, guavas, quince, plums, gooseberries, oranges, and other citrus fruits. It binds to and eliminates waste products such as cholesterol, harmful bacteria and even toxins.

New research has shown prebiotics help to combat cancer, bone loss, and even lower cholesterol levels. As you can see, prebiotics have a broad array of health benefits.

Prebiotics have been successfully used in preventing traveler’s diarrhea, and can reduce symptoms of constipation by improving bowel movement regularity through normal gut function and by making the stool softer.

Prebiotics promote iron absorption and also promote the absorption of nutrients like calcium and magnesium, which help combat bone loss. Prebiotics also produce beneficial short-chain fatty acids such as acetate, butyrate, and propionate. Additionally, prebiotics increase insulin sensitivity by modulating gene expression in a positive way. Because they are a water-soluble fiber, prebiotics help control appetite and reduce weight.

In a study of healthy elderly, prebiotics increased cholesterol excretion in as little as four weeks. The study showed that four times the amount of cholesterol was eliminated during the prebiotic period vs. the period before taking the prebiotics. This shows how powerfully prebiotics can be in helping to excrete cholesterol.

Most prebiotics are soluble fiber, but there is a roll for non-soluble fiber too. Psyllium ferments in the large bowel and breaks down into butyric acid, which is the colon cell’s favorite food. Psyllium makes stools more normal. If you have diarrhea it will firm up you stools. If you have constipation, it will soften them.

Prebiotics complement the action of probiotics. The Food and Agriculture Organization of the United Nations (FAO) defines probiotics as "live microorganisms, which, when administered in adequate amounts, confer a health benefit on the host." Beneficial microorganisms are what make up the normal flora of a healthy gut. A gut that is not healthy and is diseased lacks many (if not most) of the beneficial microorganisms found in a healthy gut. Probiotics either serve as essential members of the intestinal microbiota or they work in a more transient fashion, affecting the microbiome as they pass through.

Like prebiotics, probiotics influence our immune system. Interestingly, most probiotic strains reduce lactose intolerance. Other probiotics help regulate our immune system and secrete “repair factories” to stimulate the production of immunoglobulins for the gut. This influence on both our innate (i.e. natural, inborn) and acquired immunity impacts the way our bodies respond to vaccines, allergies, infectious diseases, cancer cells, and inflammatory and autoimmune diseases. Probiotics produce a variety of antimicrobial substances. Probiotics also promote normal colonic blood flow and help regulate bowel motility, and play an important role in the detoxification and the breakdown of cancer-causing enzymes.

Probiotics consist of lactic acid-producing bacteria, non-lactic acid-producing bacteria, and non-pathogenic yeast. Lactobacillus species are lactic acid-producing probiotics, meaning they primarily produce lactic acid as a fermentation end product. Lactobacilli produce enzymes that digest and metabolize proteins and carbohydrates. They synthesize B vitamins, and vitamin K. They also break down bile salts and normalize (i.e. reduce) pro-inflammatory responses.

Most Lactobacillus probiotics are transient (i.e. short-lived) and a large number of people do not have these intestinal bacteria. There are more than 100 species, but less than 20 types are commonly used as probiotics. L gasseri, L. crispatus and L. johnsonii are a normal part of our microbiota. L. acidophilus, on the other hand, is transient and needs to be replenished on a consistent base in order to really benefit our gut. Being a vegetarian or having a plant-based diet will keep them highly colonized in the gut. Lactobacilli have antimicrobial activities against many pathogens, including H. pylori, Candida, Salmonella, Staphylococcus aureus (the culprit that causes staph infections), e.Coli, and Pseudomonas (causes blood infections and pneumonia), to name a few.

Bifidobacterium are composed of over 30 species and are strictly anaerobic (they live without oxygen). They make up 95% of the bacteria in healthy breast-fed infants. A single course of antibiotics in a child less than two years old damages this critical portion of the child’s microbiome. It may take weeks for the microbiome to recover… if it recovers at all. Bifidobacterium make B vitamins, ferment indigestible carbohydrates such as insoluble fiber, and metabolize lactose (the sugar in milk), all of which are critically important and beneficial for an infant’s development. Bifidobacterium also make up the majority of the large bowel germs in healthy adults, but their numbers may decline with age. Again, the use of antibiotics and toxins can devastate these populations. Many Bifidobacterium protect against acute diarrhea by reducing its frequency and duration, especially when caused by antibiotics. Many Bifido- species lower cholesterol, reduce DNA damage, help leaky gut syndrome, and relieve constipation and Irritable Bowel Disease.

Saccharomyces Boulardii
These are non-colonizing yeast. S. boulardii or Sacro B is a “good” yeast that has been shown to prevent and treat Clostridia difficile when caused by antibiotics. Many diarrhea-causing disorders have been treated with S. boulardii and had good outcomes. It has been used to treat AIDS-related diarrhea, Crohn’s disease, ulcerative colitis, e.Coli, Rotavirus, and cholera. S. boulardii excretes a substance that prevents bacteria toxins from binding to the intestinal wall. This yeast also has anti-Candida and anti-parasitic effects.

Replacing Our Good Bacteria
Dosing for probiotics is calculated in colony-forming units (CFU), which indicate the number of viable microorganisms able to form a colony on an agar plate. This is generally expressed in a specified amount of the product. Recommended doses vary depending on the strain or product.

What‘s the best time to take them? Anytime is OK, with food is better. (If you’re taking an antibiotic see below.)

What kind do I take? Take a variety of probiotics. Lactobacilli predominate in the small bowel and Bifido bacteria predominate in the large bowel. Healthy guts need both. Mix it up.

However, if you have an illness, get specific recommendations since some probiotics are especially formulated for specific problems and can be lifesaving.

How many do I take? Former recommendations by many integrative medicine doctors recommended around 5-8 billion CFU daily for healthy people. Generally recommendations are going up because GMO foods are killing off our healthy bugs so quickly. Many integrative doctors now recommend 25 billion CFU for healthy people. Those will illnesses will require much more. If you experience bloating or gas, take a lower dose and work up a higher level over time.

Food Probiotics
  • Yogurt: Homemade, live-culture yogurts are loaded with probiotics, but most commercial yogurts are high in sugar and have very low numbers of probiotics because of their being overly processed. Less than 1 billion per serving.
  • Goat’s milk and cheese: are particularly high in probiotics like Bifidobacterium bifudus and L. acidophilus.
  • Kefir: Similar to yogurt, it is a fermented dairy product, but combines goat’s milk and fermented kefir grains. Kefir is high in Lactobacilli and Bifidobacteria. 
  • Many fermented vegetables including cauliflower, cucumbers, tomatoes, beets and many others are now available for purchase in farmers markets and grocery stores. These are an excellent food source of probiotics. 
  • Sauerkraut: Made from fermented cabbage (and sometimes other vegetables); sauerkraut is rich in healthy, live cultures.
  • Kimchi: Made from fermented cabbage, Kimchi is a spicy and sour Asian form of pickled sauerkraut. It is typically served in Korea, but is available at Costco!
  • Miso soup: Made from fermented rye, beans, rice or barley. This probiotic-rich soup is full of Lactobacilli and Bifido bacterium.
  • Tempeh: Tempeh is fermented soybeans, probiotic-rich, and a great substitute for meat. Look for organic soybeans, though, as many are GMO.
  • Kombucha tea: Kombucha is a delicious probiotic drink that contains a high amount of healthy bacteria.
More Reasons to Support Probiotic Supplementation: Antibiotic-Associated Diarrhea (AAD)
Evidence in 63 clinical trials from over 11,000 participants showed that using probiotics decreased the risk of AAD by 42% compared to those not taking a probiotic during antibiotic therapy. AAD is diagnosed in approximately 30% of all patients on antibiotics. Probably many more have a major insult to their microbiome but remain asymptomatic.

Sacro B, Lactobacilli and Bifido should all be added to one’s supplement regimen when taking antibiotics that are known to increase the risk of causing Clostridia difficile., which can be life threatening.

No one knows exactly what the best regimen is to prevent AAD. A reasonable approach with any antibiotic is to take extra probiotics while on the antibiotic to reduce the damage to the microbiome. Take them 2-3 hours away from taking the antibiotics. Clearly, the antibiotics will kill the healthy probiotics if taken at the same time. Optimally, take antibiotics twice a day at breakfast and supper. Then take probiotics at lunch. Once the antibiotics are finished, double whatever you take on a regular basis for at least 2-4 weeks before returning to a lower maintenance dose. Adding Sacro B helps to decrease the risk of Candida overgrowth while on antibiotics.

Studies have shown the benefits of probiotics on the duration, frequency, shedding, immune response, and increased production of rotavirus antibodies with the treatment of probiotics.

Travelers’ Diarrhea (TD)
This infectious diarrhea is caused by a bacteria, viruses, or parasites. Many studies show a 15% reduction in risk of TD among probiotic users. Both S. boulardii and a mixture of L. acidophilus, L.casei and B. bifidum were found to be beneficial. Start probiotics 5 days before travel to lower the risk of TD. 

Irritable Bowel Syndrome
Irritable bowel syndrome (IBS) is associated with symptoms of diarrhea (IBS-D), constipation (IBS-C), and/or alternating between the two. B. infantis significantly improved symptoms in all IBS patients.

Ulcerative Colitis
VSL #3 is both a prescription and an over the counter probiotic. It was the first probiotic used to treat and cure ulcerative colitis. The original studies used nearly 4 trillion CFU daily for six months. Don’t try this with probiotics from your local health food store. It contains several Bifidobacterium, Lactobacillus, and a healthy Streptococcus. Lower doses have been effective in IBS.

Pouchitis is a post-surgical complication of ulcerative colitis. VSL#3 is effective in the prevention of onset and relapse of pouchitis after antibiotic therapy

Crohn’s Disease
Dr. Walter Crinnion, a naturopathic physician, recommends using probiotics, prebiotics and fiber for the best outcome. In a 10-subject study, probiotics containing 75 billion CFU of specific Lactobacilli and Bifidobacteria and psyllium, a non-soluble fiber were taken every day for thirteen months. 70% (7/10) had remission. Psyllium helps to heal the gut.

If You’ve Heard It Once…
The standard American diet is deficient in the right probiotics. Not only is it lacking in probiotics but it is also anti-probiotic and destructive to the good bacteria in our body. Not only does a poor diet influence our microbial makeup, but antibiotics, immunosuppressants, and gastric acid inhibitors do, too. We know this! So, what do we do about it?
  • As mentioned above, perform an elimination diet and stop eating inflammatory foods. 
  • Always choose organic food over nonorganic food or, at the very least, choose organic for the produce that ranks as the most toxic, as reported by
  • What we put on our bodies (i.e. lotions, shampoo, makeup, fragrances, and soap), and not just what we eat, influences the microbial environment in our body. Can you see why much of the bacteria in our gut/body are transient? 
  • Taking care of our microbial environment is important. When it is compromised it is also important to rebuild it, or at least maintain it as we age. Eating a pre- and probiotic-rich diet and supplementing with probiotics on a regular basis is imperative for good health. Because we live in a toxic world that is constantly challenging our healthy microbiota, taking steps to counteract their effects is only reasonable.
Content created by Elizabeth R. Vaughan, MD, and Tina Arey, BSN, RN

1 comment:

Silvio Fontana said...

Oral supplementation of Probiotics do little to colonize the colon as they are only transient and do little to help those with severely compromised GIT.