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The Importance of Microbiomes, Probiotics and Prebiotics

By: Elizabeth H. Trattner, A.P., D.O.M.

To first understand probiotics, readers need to understand the concept of the human microbiome. The microbiome is a microbial community of cells that outnumber regular human cells 10 to 1. There are approximately 100 trillion bacteria in the microbiome.  This community or commensal is believed to play a key role in health, disease, immunity and genetics especially in the skin, digestive system including the oral cavity, vagina and the respiratory system.  It has been found that microbes contribute more than 360 times more genes for survival than human genes, contribute to many processes in the body including digestion and immunity. ( The microbiome changes depending on state of health, disease, stress, environment, medication and other factors. We are born with a set number of bacteria and these factors can kill off the good bacteria and cause disease. This is why probiotics are helpful to health.  Probiotics are live bacteria which that help the health in the intestine and microbiome.

The microbiome is a functional anaerobic ecosystem that has an estimated 500-1000 bacteria and other cells part if our immune system.  The microbiome colonizes at birth with the introduction of bacteria via the vaginal canal and breastfeeding and skin contact with the mother. Human milk contains bifidobacteria and lactobacilli. It also contains prebiotics in the form of oligosaccharides. Oligosaccharides pass through the large intestines where they ferment with bacteria in the colon and promote growth of probiotics, or the good bacteria in the digestive system or “gut”. Other sources of prebiotics are soluble fiber which is a source of food for the microbiome... (Siri Chand Khalsa, module discussion, supplements)

In some countries, fermented food has been a part of traditional diet for thousands of years.  These foods support the heath of the microbiome and production of probiotics. (Siri Chand Khalsa, module discussion, supplements)

Probiotics supplements help surrogate and propagate a healthy biome from human flora (gut, saliva, feces, intestines and the environment. They are grown in a sterile medium and tested for permeability, mucosa attachment. In the digestive system they ferment when undigested fibers (prebiotics) which make healthy metabolites. Probiotics have an important role in protecting our health.  Modern diets have become more sterile and have eliminated contaminates, however this has depleted good bacteria.

When choosing a probiotic consider the following:

  • The specific strain
  • The dose
  • Is it for a condition or for general maintenance?
  • Will they be consumed via supplements, foods like yogurt with specific strains, or in fermented food?
  • Ensure probiotic cultures are live and preferably in a refrigerated environment.
  • If consuming yogurt make sure cultures are added after pasteurization.
  • Some strains must be enteric coated to survive stomach acid. These are lactococcus, leuconostac, L. Bulgaris. Strains such as streptococcus, lactobacillus and bifbacterium are strong enough to survive stomach acid.

Fermented foods were some of man’s first probiotic supplements.  These foods have been used in traditional cultures around the world. Some of these foods are kimchee, sauerkraut, miso, pickled vegetables, kefir, lassi, yogurt and antipasto. These foods generally are used for health maintenance. For years this is how people supplemented their diets and are still and are still effective choices today for helping introduce healthy bacteria into the body.

Although there is some debate over this topic probiotics should be taken at least 2 hours to right before a meal when stomach acid is slightly lower. When taking antibiotics, the greatest benefit is taking probiotics within 72 hours of antibiotics therapy to avoid antibiotic associated diarrhea (AAD).  It is okay to take probiotics concurrently with antibiotics but some sources suggest taking these two hours apart from each other. Take the probiotics as soon as you begin therapy and then continue until antibiotic is finished plus a few days up until a few weeks after the end of treatment to avoid AAD. (U of Wisconsin)

Maintenance doses of probiotics for children should be 5 billion CFUs daily and 10 billion CFUs of mixed strains of probiotics. For Crohn’s disease and IBS ,100 billion CFUs is recommended. (U of Wisconsin) Make sure to check for brands that are effective or the World Gastroenterology Paper ( (iHelp)

Probiotics can be taken from 2 weeks to 2 months to recolonize bowel bacteria. For other diseases such as IBS or Crohn’s disease people may need to take longer or on a daily basis. (U of Wisconsin)
Probiotics are proven to be safe but there are some reports that some people may feel gassy when beginning probiotic therapy. Contraindications for using probiotics are patients with severe acute pancreatitis. Also caution should be taken with compromised immune systems during cancer treatments or with short gut syndrome Readers who have candida need to be aware that many probiotic preparations contain dextrin, which is sugar and can exacerbate yeast propagating. (U of Wisconsin).

Probiotics have had a tremendous amount of research being publish.  There has become a huge awareness how beneficial bacteria has a positive effect on health and various medical conditions.

The following conditions (iHelp) have demonstrated benefits from probiotic therapy:

  • Prevention of atopic dermatitis in children (iHelp)
  • Gastroenteritis in children (iHelp)
  • Preterm birth children with lower or abnormal or reduced probiotic colonization.
  • Antibiotic associated diarrhea
  • Acute diarrhea in both adults and children
  • IBS, Crohn’s, pouchitis, and inflammatory bowel disease
  • Women’s vaginal health
  • Men’s genital health (Price, PLOS one paper 2010)
  • Food Allergies
  • Vancomyacin resistant C. diificile
  • Increased immunomodulation
  • Anti-tumoral and anti-mutagenic effects
  • During gestation to keep digestive issues at bay (Deshponde, 2008). They also keep vagina healthy so during birth the baby is introduced to healthy bacteria.
  • The elderly, to reduce infectious disease and those who are in care centers and hospitals. Probiotics also help regularity as well which is an issue with the elderly.
  • Emerging research with anxiety and inflammatory bowel disorders (Graff 2009)
  • Osteoporosis and Vit D absorption (Jones)

How to take probiotics:

  • For general health 3-10 billion CFUs of mixed strains.
  • For children 5 billion CFUs of mixed strains
  • For Antibiotic associated diarrhea including C. difficile 10 billion CFU beginning immediately after starting antibiotic therapy of a combination of L.rhamnosus, L.acidophilous and saccoramycesceine.
  • Acute diarrhea, enterococcus faecium 1 billion CFUs  three times a day.
  • IBS use bifidbacterium animalis dn 1730100
  • Mild ulcerative colitis, combination of VSL#3 a proprietary mixed of probiotics
  • Urogenital infections especially Bacterial Vaginosis LRhamosis GR-1, LReuteriRC14
  • Make sure to keep live cultures in the refrigerator or a cool dark place. To ensure products contain what specific strains and potency check  


Prebioitcs are important ingredients found both in foods and supplements. They promote the growth and activity of good bacteria in our gastrointestinal tract (U of Wisconsin). They are essentially food for our microbiome. (SC) Prebioitcs are usually carbohydrates (fiber) that are not digested when they reach the large intestine Examples of these are FOS(Fructoogliosaccarides), inulin, and oligosaccharides. They are also found in tubers including Jerusalem artichokes, burdock root, chicory, leeks, honey garlic, asparagus and garlic and onions as well.  FOS are important because they not only have a prebiotic effect but also improve mineral absorption, decrease serum cholesterol triglycerides and lipids. (Sabeter-Molina, 2009) Generally Americans consume about 1-4 g of inulin type food. Doses can be as high as 4-10 grams for the treatment of constipation. FOS also benefits functions in the gastrointestinal tract such as stool productions, absorption of calcium and minerals, increases our immunity and resistance for infections, decreases transit time and increases bifidobacteria in the colon. Aside from ingesting foods that contain soluble and insoluble fibers preparations can be bought either separately or with probiotics called synbioitcs. Prebiotics are also found in breast milk. Prebiotics can be well tolerated.  If patients have IBS or other bowel disorders the patient should consult a highly knowledgeable practitioner as many prebiotics may aggravate their condition. Many prebiotics are included in a group of foods called FODMAPS (an acronym to describe specific foods that have been found to aggravate IBS and other GI disorders. (SC)

About the Author: Elizabeth H. Trattner, A.P., D.O.M. is a Florida and National Board Certified Doctor of Oriental Medicine and Acupuncture and holds a certificate from the Annemarie Colbin Natural Gourmet Cookery School in New York City.  Elizabeth specializes in women’s health, weight management, allergies, autoimmune diseases and environmental illnesses.  For the past  fifteen years she has been advancing the concepts of Integrative Medicine, combining her expertise in acupuncture and oriental medicine with nutritional counseling and women’s health. By drawing on the principles of Traditional Chinese Medicine, 17 years of training under Andrew Weil, MD and other natural modalities, she helps patients improve and take control of their health and optimal weight. In the spring of 2008, she was invited to attend and participate in a prestigious medical rotation at the University of Arizona’s Center of Integrative Medicine founded by Dr. Weil. She is the only acupuncture physician in the country with this designation.  

Elizabeth is a contributing author for several publications and websites on Alternative Medicine including: Cosmetic Dermatology: Principles and Practice by Dr. Leslie Baumann; On the Cutting Edge, published by the American Diabetic Association, "Diabetes and Traditional Chinese Medicine: Managing a Modern Epidemic with Ancient Medicine"; Ask Dr. Weil at; and  Elizabeth has also been featured in hundreds of national publications and online magazines as a medical source for health, wellness and green beauty, including Newsweek, Huffington Post, Nylon, Hello Flo, Health Magazine, Natural Health Magazine, Elle Magazine, Stylecaster, and Organic Spa Magazine among others. Her personal journey overcoming several near-death experiences and health obstacles has been featured in national magazines and spotlighted on the Oprah Winfrey Show alongside her friend and mentor Dr. Andrew Weil. She has appeared on numerous television programs as a wellness expert.

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