What is the microbiome?

The word microbiome  describes the trillions of viruses, fungi, and bacteria that live on or within the human body in various habitats such as the skin, mouth, colon and vagina.  Each site has characteristics, including pH, water and oxygen content, temperature, and chemical metabolites, that favor certain bacteria over others.  Our normal flora can cause disease particularly if they are introduced into a different environment, such as from aspiration, surgery  or trauma.  Among these conditions represent the most common cases seen by an infectious diseases physician, such as pneumonia, surgical site infection, diverticular abscess, dental abscess, and urinary tract infections.  However, most of the times, our microbiome is either harmless, a state known as commensalism (+ for bacteria, 0 for host)  or even beneficial and important to human health, a relationship known as mutualism (+ for both).

What is the gut microbiome?  How do gut bacteria affect the digestive tract?

As a child grows, the gut microbiome expands to include numerous microbial species, the top being Firmicutes and Bacteroides (both accounting for 3/4 of gut flora), Bifidobacteria and E. coli.  Near adolescence, a child’s microbiome reaches a peak of diversity before it reduces to what is seen in a normal, healthy adult (Heiman M, Greenway F, 2016).  Greater gut diversity has been associated with health and wellness, and less diversity is associated with disease states. Diet is the principle driver of microbiome diversity (discussed below). 

The bacteria housed in the gut can fulfill several benefits in the human host.  Certain bacteria, such as Bacteroides activate the gut immunity, causing the intestinal mucosa to express a gut antibody (secretory IgA).  Other bacteria, such as Bifidobacteria and Lactobacillus, provide competitive inhibition, keeping harmful bacteria from adhering to the intestinal wall and potentially causing an infection.  These bacteria reduce the risk of microbial or toxin translocation, or “leaky gut syndrome” (I will refer to it as microbial translocation).  In microbial translocation, bacteria and/or toxins (e.g. lipopolysaccharide from E. coli) gain entry into deeper tissues or even the portal bloodstream (which drains into the liver) through weaknesses in the intestinal cell barrier.  Microbial translocation may contribute to disease manifestations, such as liver abscess, local processes like diverticulitis and appendicitis, irritable bowel syndrome (IBS) and even endocarditis (There is a certain pathogen Streptococcus bovis that is associated with colon cancer). Some chronic diseases increase the risk of microbial translocation, including Crohn’s disease, celiac disease, lupus, cirrhosis, HIV, and diabetes.

What are some of the other effects of the gut microbiome?

The gut microbiome helps control how the body responds to an infection by communicating with the immune system, and those communications keep the immune system from attacking beneficial bacteria. As Vitamin A strengthens the immune system, the gut bacteria control the amount of active Vitamin A in the system to keep the immune system from becoming overactive. In 2018, researchers at Brown University found that inflammatory bowel disease was caused by disrupted communications between the gut microbiome and the immune system.

What is gut dysbiosis or bacterial overgrowth? How can you improve your gut microbiome?
Gut dysbiosis, or bacterial overgrowth, represents an imbalance between beneficial and harmful bacteria, where selection pressures favor the growth of more harmful bacteria and less microbial diversity.  The multiple causes include behavior (alcohol, hygiene, etc), certain medications, some chronic disease, antibiotics, and significant stress.

Behavior.  Diet has a strong effect on microbiome.  In the infant, breast milk provides an advantage for the growth of Bifidobacterium, which is not as prevalent in infants fed formula.  In adults, an intake of higher fruit and vegetable fiber, even if done for a short period of time, results in greater diversity of gut bacteria.  A western diet, high in animal protein, sugar and starch and low in fibers leads to a predominance of Bacteroides. 

Medications.  The main medications involved that can lead to dysbiosis includes antibiotics, proton pump inhibitors, steroids and chemotherapy.  Antibiotics can selectively wipe out certain bacteria or have a more generalized action, depending on the spectrum of the effect.  The more broad-spectrum an antibiotic, the greater the risk for significant gut dysbiosis.  Antibiotics such as fluoroquinolones, clindamycin and cephalosporins are among the greatest risk factors for Clostridium difficile (C. diff), known for toxin-associated diarrhea and more severe colitis.  The resulting infection causes symptoms like abdominal pain, watery diarrhea, nausea, and fever.  Proton pump inhibitors, and to a lesser extent H2 blockers (zantac, pepcid, etc) reduce the acid that is produced by the parietal cells of the stomach.  Acid is an important defense to bacterial populations ingested in food or drink.  This type of medication has been associated with an increased risk of C. diff, traveler’s disease, and gut dysbiosis or bacterial overgrowth.  Prednisone and other anti-inflammatory modulate the immune system.  There is also an impairment of glucose synthesis, referred to as a diabetogenic effect.  This can lead to an increase in populations of yeast and other microbes.  Some chemotherapies affect white blood cell lines temporarily, the greatest immune being the gut, and can be a source of gut translocation and fever. 

Disease conditions.  Gut dysbiosis has co-associated with a variety of conditions including irritable bowel syndrome, diabetes, inflammatory bowel disease, obesity, Type 2 diabetes, rheumatoid arthritis, psoriasis and atopic eczema.  Whether a particular microbiome signature is found in a specific disease state (e.g. cancer) is the subject of research efforts.

A healthy diet ensures a healthy microbiome.

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