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The Microbiome: Our Bacteria and Us


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Our GI tract is home to trillions of live bacteria. All those bacteria, including their DNA, are called our microbiome. We host various strains and even families of strains; for instance, the family called Lactobacilli includes acidophilus, rhamnosus, casei, etc.—different strains. They all live together, mostly in the large intestine, though some do live in the small intestine as well. They are believed to outnumber our own human cells by about 3 to 1! We get these bacteria, initially, from our travels down the birth canal. Then they continue to be ingested via our food supply, especially if it includes fermented foods such as sauerkraut, kombucha, kim chi, and yogurt. It is a known fact that they need to come in on a regular basis since they don’t just colonize and live happily ever after. We need to provide our GI tract with them on a regular basis. What do these friendly bacteria do for us? Why do we need them? Only in the last several decades have we begun to answer those questions.

One of the primary jobs our bacteria accomplish for us is to assist with our digestive processes. They produce enzymes to digest various carbohydrates that our human system cannot process. They also make a variety of vitamins for us, including vitamin K, biotin, B1, and B2.

Another important gift of our bacteria is the protection of the intestinal surface, helping to prevent “leaky gut.” They are also protective in that they inhibit colonization by pathogenic microbes of all sorts, including the unwanted yeast called Candida albicans.

Our bacteria also support our immune system. From mice studies, it is known that early on, the bacteria actually mature the infant immune system. They continue to influence our immunity throughout our lifetime. They play a central role in balancing our immune system – not too little of it and not too much (autoimmunity). Particular bacteria control inflammatory processes.

If we have a predominance of good bacteria, our immune system will hum along nicely under their influence. If we have too many “bad” bacteria, our immune system can be stimulated toward high inflammation. Numerous studies connect an imbalanced microbiome (too many bad vs. too few good bacteria) to inflammatory conditions such as rheumatoid arthritis, atopic dermatitis, psoriasis, diabetes, obesity, and even fibromyalgia. Diet plays a role in maintaining balance, but antibiotics can severely alter it, allowing opportunistic microbes to take up residence.

We all know that antibiotics can be life-saving. Sometimes they are necessary. They are effective because of their ability to kill bacteria. In the process of killing an infection, however, they disrupt our microbiome. It is, after all, made of bacteria. This often allows opportunistic (problematic) strains and yeast to grow in the GI tract. Adding a probiotic supplement (billions of good bacteria) can help prevent this situation. You can add in a probiotic supplement during your antibiotic use – taking it as far away in time from the antibiotic as you can get. Some will get killed, of course, but some may survive to prevent complete destruction of your microbiome. Once the course of antibiotics is finished, it may be useful to double up on your probiotic to restore balance as quickly as you can.

The newest and perhaps most exciting data coming out of the microbiome research is about how it can communicate with the brain and affect conditions such as depression and anxiety. If it is not all in your head, it may be all in your gut! The bacteria send messages to the brain, and the brain sends messages back. Particular strains of bacteria are being researched to learn whether they influence brain function – and to figure out how they do it. This area of research is so new, it doesn’t yet have a formal name. Some call it psychobiotics. The research is fascinating. For example, Bravo et al.[1] treated healthy mice with a probiotic formulation containing Lactobacillus rhamnosus or a placebo and then subjected all animals to a battery of anxiety- and depression-related behavioral tests. Results showed that chronic treatment with Lactobacillus rhamnosus reduced anxiety-and depression-related behavior.

A recent study by Tillisch et al. (2013) provided the first direct demonstration that ingestion of probiotic bacteria can modulate brain activity in humans. Healthy women drank a fermented milk product with probiotic bacteria, a non-fermented milk product, or nothing; fMRI revealed robust alterations in the brain activity of those participants who consumed the probiotic bacteria relative to the comparison groups.[2] So make sauerkraut, eat yogurt, or take a probiotic supplement. It will do your gut good!


[1] Bravo J A, Forsythe P. Chew MV, et al. (2011). Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proceedings of the National Academy of Sciences, USA, 108, 16050–16055.
[2] Tillisch K, Labus J, Kilpatrick L, et al. (2013). Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology, 144, 1394–1401.

Ramona Richard, MS, NC

Ramona Richard, MS, NC

Ramona Richard graduated with honors from the University of California with a Bachelor’s Degree in psychology and graduated summa cum laude with a Master’s Degree in Health and Nutrition Education. She also holds a Standard Designated Teaching Credential from the State of California, is a California state-certified Nutrition Consultant and a member of the National Association of Nutrition Professionals.

Ramona has participated in nutrition education in both public and private venues, including high school and college presentations, radio and public speaking for the past 20 years. She is the owner of Radiance, a nutrition consulting company, the Director of Education for Sanesco International, and a medical technical writer.

Disclaimer: The information provided is only intended to be general educational information to the public. It does not constitute medical advice. If you have specific questions about any medical matter or if you are suffering from any medical condition, you should consult your doctor or other professional healthcare provider.

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