Imbalances of the Gut Flora in the GI Tract…or Dysbiosis

Dysbiosis is a fancy word for any imbalance of your gut microflora. When your microflora is disturbed in any way (too few good or too many bad), you are vulnerable to a host of GI disturbances. Dysbiosis can also be used to describe other, non-bacterial growth in the gut, such as organisms like yeast, parasites or worms. Dysbiosis can result from anything that alters the gut flora. This is most commonly caused by the use of antibiotics, GI infections (traveling overseas), GI surgery, the use of acid-suppressing medications, chronic mal-digestion, chronic constipation, chronic mental/emotional stress, the standard American diet (SAD) or food allergies (that can result from gluten sensitivity or Celiac disease).

Symptoms of Dysbiosis

  • Recurrent GI infections
  • Chronic diarrhea
  • Inflammatory bowel disease like symptoms including: cramps, diarrhea, urgency and mucus/blood in stool
  • Chronic constipation
  • Decreased cognitive function or brain fog
  • Gas/bloating and abdominal discomfort
  • Fatigue/low energy
  • Depression or anxiety
  • Chronic sinus congestion
  • Itching in the vagina, anus, or in other mucosal membranes
  • Bad breath (halitosis)

Types of Dysbiosis

  • Bacterial dysbiosis: bacterial dysbiosis results when too few of the beneficial organisms (lactobacillus or bifidobacteria) are present, or too many potential pathogens are present. Common organisms like clostridium, salmonella, shigella and campylobacter are just some of the types of bacteria that can cause dysbiotic symptoms.
  • Small bowel bacterial overgrowth: SBBO is a specific form of dysbiosis that occurs when bacteria normally found in the large intestine travel up to the small intestine, where they overgrow and add to the relatively small number of bacteria already present there., This abnormal overgrowth of bacteria can result in poor absorption of nutrients (vitamin B1w, vitamin D, iron, lipids) from our digested food and the breakdown of certain carbohydrates before the body is ready, causing GI symptoms such as upper GI gas and bloating after a meal. SBBO is prevalent in those with fibromyalgia, chronic fatigue syndrome and irritable bowel syndrome (IBS). SBBO is primarily caused by a reduction in bowel transit time with numerous potential precursors:

o   Anatomic and motor disorders that cause stasis of gut contents (surgical loops, diverticula, strictures, adhesions, tumors, fistulas, scleroderma, intestinal pseudo-obstruction, diabetic enteropathy, resection of the ileocecal valve).

o   Prior intestinal surgery

o   Jejunal diverticulosis

o   Crohn’s Disease

o   Aging

o   Achlorhydria

o   Vagotomy

o   Abnormal communication between colon and small bowel

o   Hypochlorhydria

o   PPIs (like Prilosec)

o   Stasis-low motility

o   Malnutrition

o   Collagen vascular disease

o   Immune deficiency


  • Candidiasis: Specific overgrowth of the yeast candida albicans and similar species is a special kind of dysbiosis. These organisms, which are part of the normal flora of the gut, mouth and vaginal mucus membranes can become opportunistic pathogens during overgrowth. This is usually the consequence of chronic antibiotic use, oral contraceptive use, IBS (irritable bowel syndrome), high consumption of sugars/white flour/pastries, alcohol use, or immune system suppression (caused by stress, infection, aging or other imbalances). Symptoms include:

o   Mental fog

o   Joint pain/muscle weakness

o   Fatigue

o   Skin irritations/rashes

o   Recurrent vaginal infections

  • Parasites: Parasitic infections represent a specific form of dysbiosis and are, unfortunately, more common than we would like to think. Parasites can be microscopic organisms (amoebas) or very large organisms (worms). Detecting and treating parasites is vital. Treatment might include pharmaceutical anti-parasitics, potent natural anti-parasitic supplements, high potency comprehensive probiotic supplements, and nutrients to support liver and immune health. Symptoms can include:


o   Diarrhea

o   Abdominal pain

o   Flatulence

o   Anorexia

o   Weight loss

o   Fevers/chills

o   Blood or mucus in stool

o   Fatigue

o   Urticaria (hives)

o   Reactive arthritis

o   Chronic fatigue

o   Asthma

o   constipation

Common parasites seen in the U.S. population are:

  • blastocystis hominis: a protozoan transmitted via fecal-oral route or from contaminated food or water.
  • Cryptosporidium spp: coccidian parasite transmitted person to person, zoonotic, nosocomial and raw foods and raw meat can harbor the organism.
  • Entamoeba histolytica: belongs to the ameba family of protozoa and is most common in the tropics, but we can pick it up off of unwashed fruits and vegetables.
  • Giardia lamblia: transmission occurs via fecal oral or from food and water contaminated with cysts.
  • Ascaris lumbricoides: a worm that hatches in the stomach, penetrates the intestinal wall and migrates through the liver to the lungs.
  • Enterobius vermicularis (pinworm): the most prevalent parasitic infection in the world.

Other parasites include: Dientamoeba, endolimax nana, entamoeba coli, entamoeba dispar, and strongyloides stercoralis.

Treating Dysbiosis

The Functional Medicine approach to treating dysbiosis follows the “4 Rs”.

1.       Remove: This is usually accomplished by removing the unknown problems through restriction of toxic, pro-inflammatory or potentially allergic foods and detoxification and removal of harmful organisms. It is important to allow the gut to calm down and rest and this can usually be accomplished by going on a 28 day elimination diet and detoxification protocol.

The second step is to test for which potentially harmful organisms are living in the gut so treatment can be tailored to specifically eradicate those, without harming the good bacteria that are so necessary for GI function. This can be accomplished with a breath test (H. pylori), blood tests (inflammatory markers and nutrient levels), and a CDSA (Complete Digestive Stool Analysis). Specific diagnosis leads to specific treatment.

2.       Replace: The main goals for this step are:

a.        Reduce inflammation caused by the dysbiosis. Immune system inflammation can create gut permeability (called leaky gut), which may lead to further instability of the gut.

b.      Provide specific nutrients to improve the function of the GI cells. The needs of the cells along the GI tract are unique and can be met with dietary changes and specific nutrients supplied via supplementation (enzymes, bile, acid).

c.       Improving liver and immune function. These are the systems that support the GI tract the most. By providing specific nutrients to support liver and immune function, healing can be maintained for ongoing health.

3.       Re-inoculate: Since each person’s microbiota is different and contains hundreds of different organisms, it is virtually impossible to re-seed the digestive tract simply by adding back the appropriate blend of each organism. However, many things can be done to ensure the GI environment promotes the growth of beneficial bacteria and discourages the growth of harmful organisms. Here are four keys to establishing and maintaining a healthy microbiota:

a.       Avoid disrupting events as much as possible

i.      Antibiotics

ii.      Stress

iii.      Radiation of the GI tract

iv.      Air travel

v.      GI infections

b.      Improve immune system function

c.       Reduce growth conditions that lead to dysbiosis

i.      Reduce simple carbohydrates and sugars in diet

ii.      Increase intake of inulin and probiotics

d.      Control mucosal environment with healthy organisms while commensal organisms are getting back on their feet by take probiotics and eating fermented foods.

4.       Repair: All forms of dysbiosis cause damage to the intestinal mucus membranes. The lining of the GI tract becomes vulnerable to other attacks as well as permeability to food allergens or toxins.

*It must be remembered that once an individual has candida overgrowth, reoccurrence is quite common. Individuals will need to maintain a consistent and vigilant lifestyle management program to prevent repeated incidence of candidiasis.

**These treatments may require weeks or months depending of the extent of the infection and the initial reaction to the protocol.

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