Monday, February 19, 2018

How Does the Gut Flora Influence Our Health?

It is now widely appreciated that humans did not evolve as a
single species, but rather that humans and the microbiomes
associated with us have co-evolved as a "super-organism,"
and that our evolution as a species and the evolution of our
associated microbiomes have always been interwined.
-William Parker, Duke University

When we are born, our body is sterile, meaning our skin, lungs, and intestines don't contain any bacteria at all. When we pass through our mother's birth canal, we are exposed to outside world. Over time our body gets colonized by a diverse and distinct brew of bacterial species determined by genetics and by bacteria surrounding us.

The gut is literally at the center of our body and plays a central role in our health, just as our "gut feeling" plays a central role in our instinct. In this article, we will look at gut flora and its links to our health.

Gut Flora

There are estimated 100 trillion microbes that make our GI tract their playground, which is more than 10 times of our human cells. It is believed that imbalances in gut flora are a big part of our autoimmune problems, causing both autoimmunity and making our symptoms and antibodies worse if we already have a diagnosed autoimmune disease.[2-4]

The Gut/Immune Connection

Non-self antigen is a substance, like a bad bacteria, yeast, parasite, or virus, that is recognized as foreign and, hopefully, only these should be attacked by our immune system.

Approximately 70% of the immune system lives in our gut. Everyday we bring the outside world—in the form of food—into our body through the mouth. So our front line of defense is located in our gut. There are two important roles of our immune system's front line of defense:
  • Recognizing what is foreign, followed by
  • Sounding an alarm by telling other cells in the immune system to react if foreigners are found
Let's say that there was salmonella in something we ate for dinner last night. If things are working correctly, our dendritic cells (or antigen presenting cellsAPC) recognize the salmonella as foreign and sound an alarm to the T cells and B cells (i.e. lymphocytes), which then attack the bacteria and clear it out of our system. While the dendritic cells respond immediately, it takes a bit of time, anywhere from hours to days, for the lymphocytes to mobilize to either make more killer cells or to make antibodies to attack foreigner.

When this process goes smoothly, there are signals and messages sent between the dendritic cells and T cells that keep the immune system balance. T regulator cells (Tregs) eventually help turn the alarm off when the immune system's job is done.[17]

But if the Tregs are not working correctly, the killer cells and/or antibody-producing cells can get stuck in overdrive and become confused about what is foreign and what is not. This confusion can then cause autoimmune diseases.[2-4]  In addition, these immune cells can release many inflammatory molecules, traveling around the body and causing inflammation in our joints, hands, blood vessels, and brain.

Healthy Gut Flora Can Make Our Immune System Happy

Because so much of our immune system is in our gut, it's critical to keep our gastrointestinal system healthy and in balance. It appears that gut flora play a huge role in early infancy in helping our immune cells develop properly and in the right balance. Good bacteria (for example, Lactobacillus acidophilus, bifidobacteria, etc.) that live in our intestines have the most important influence on the function of the T cells that are located there. They can provide the following potential benefits:
  • Help the immune system learn the difference between self (including good bacteria) and non-self
    • Develop tolerance to good bacteria[2]
  • Help accelerate our immune system's response to a foreigner
  • Help regulate the balance between Th1 and Th2 responses
  • Help the T regulator cells work better
  • Stimulate the production of immunoglobulin A
    • Immunoglobulin A is a protective antibody that's one of the main defenses in our gut
  • Make short-chain fatty acids, which feed and strength all the cells that line our digestive tract, keeping them healthy[3]
  • Help form our intestinal lining (the protective barrier)
    • Interact with our immune cells to directly protect us from harmful infections and maintain the function of that barrier so that unwanted foreign proteins and infectious agents cant't seep into the bloodstream.
    • If this barrier is comprised, we can develop what is called leaky gut syndrome, a condition that can lead to autoimmune diseases.
  • Help begin the process of metabolizing toxins, which means changing their form to make them less harmful.
  • Make enzymes that improve digestion
  • Help the body process vitamins such as B12 and K.[12] So they can be better utilized and absorbed by the body.


Having enough friendly flora in our gut reduces the incidence of allergies and autoimmune diseases, and restoring and balancing these flora in the gut can treat and reverse these conditions. When the amount of healthy bacteria in our gut is too low, a condition called dysbiosis occurs.

There are five types of dysbiosis and we can have more than one kind of it at the same time:[1]
  1. Insufficient good bacteria
    • This is the mildest form.
  2. Small intestinal bacterial overgrowth (SIB)
    • Occurs in the upper part of the small intestine when bacteria from the colon grow in the wrong place.
  3. Immunosuppressive dysbiosis
    • Toxins from harmful bacteria, yeast, or a parasite lower our levels of good bacteria and give off toxins that weaken or break down the gut lining and cause leaky gut syndrome.
    • People often get this form of dysbiosis when they have an overgrowth of yeast in the body
  4. Inflammatory dysbiosis
    • When the body has an exaggerated response to our body's imbalance of good bacteria.
    • Physical symptoms of this type of dysbiosis include muscle and joint pain in addition to digestive symptoms such as gas and bloating.
  5. Parasites
    • Can infect the digestive tract and put stress on the population of good bacteria.
    • Parasites often cause diarrhea, cramping, and bloating.
    • However, read [14] for a different perspective—the potential benefits of parasites.
Researchers at the University of Arizona College of Medicine recently reviewed the literature on this topic and found good evidence that dysbiosis plays a role in rheumatoid arthritis and, in animal studies, multiple sclerosis.[1]


Scientists don't call the microbiome "the forgotten organ" for nothing. Recent research advances have seen a tremendous improvement in our understanding of the scale, diversity, and importance of the gut flora. For example, a simple birthing choice (i.e., natural birth vs caesarean section) could make a difference:[15]
Each individual's community of gut microbes is unique and profoundly sensitive to environmental conditions, beginning at birth. Indeed, the mode of delivery during the birthing process has been shown to affect an infant's microbial profile. Communities of vaginal microbes change during pregnancy in preparation for birth, delivering beneficial microbes to the newborn.
At the time of delivery, the vagina is dominated by a pair of bacterial species, Lactobacillus and Prevotella. In contrast, infants delivered by caesarean section typically show microbial communities associated with the skin, including Staphylococcus, Corynebacterium, and Propionibacterium.
While the full implications of these distinctions are still murky, evidence suggests they may affect an infant's subsequent development and health, particularly in terms of susceptibility to pathogens.
Finally, if you have been diagnosed with any autoimmune disease, you may have dysbiosis and/or leaky gut syndrome. In that case, grab a copy of Dr. Blum's book[1] and learn how to heal your gut.


  1. Healing Your Gut (Chapter 8 of The Immune System Recovery Plan)
  2. Denise Kelly, Shaun Conway, and Rustam Aminov. Commensal gut bacteria: mechanisums of immune modulation. Trends Immunol 2005 Jun; 26(6)
  3. Laurence Macia et al. Microbial influences on epithelial integrity and immune function as a basis for inflammatory diseases. Immunol Rev 2012 Jan; 245(1): 164-76.
  4. Hsin-Jung Wu and Eric Wu. The role of gut microbiota in immune homeostasis and autoimmunity. Gut Microbes 2012 Jan-Feb; 3(1):1-11.
    • Figure 1. Commensal bacteria induce CD4+T cell differentiation.
    • Figure 2. An autoimmune arthritis model that demonstrates the link between gut microbiota and an extraintestinal disease
  5. S. Grenham et al. Brain-gut-microbe communication in health and disease. Front Physiol 2011;2:94.
  6. How Your Gut Flora Influences Your Health - Mercola
  7. How Many Microbes Are Hiding Among Us?
  8. Exploring The Invisible Universe That Lives On Us — And In Us
  9. Are Probiotics the New Prozac? (Dr. Mercola)
  10. Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology. 2013 Jun;144(7):1394-401
    • Four-week intake of an fermented milk product with probiotic (FMPP) by healthy women affected activity of brain regions that control central processing of emotion and sensation.
  11. Navel gazing: healthy gut bacteria can help you stress less
  12. Vitamins’ Old, Old Edge
  13. The Belly Buttons Will be Revealed, Slowly
  14. Can Parasites Heal the Gut? (Travel and Health)
  15. Complex World of Gut Microbes Fine-Tune Body Weight (Science Daily)
  16. Alcoholism linked to lack of intestinal bacteria
    • 26 out of the 60 alcoholics suffered from leaky gut syndrome and generally had a low amount of intestinal bacteria -- specially their levels of Faecalibacterium prausnitzii, which is known for its anti-inflammatory properties, were detected as unusually low. 
    • The leaky gut syndrome is linked to inflammation of the gut and diseases like Crohn disease.
  17. Schmidt A, Oberle N, Krammer PH. Molecular mechanisms of tregmediated T cell suppression.Frontiers in Immunology. 2012;3:p. 51. 
    • Treg exhibit multiple immunosuppressive mechanisms including: 
      • The secretion of cytokines such as transforming growth factor beta (TGFβ) and interleukin-10 (IL-10) 
      • The killing of CTL
      • The inhibition of immune cells through a cell contact mechanism

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