Many people are familiar with the idea of probiotics, that the gut has healthy bacteria important for digestion, and these bacteria can be replenished by taking probiotics.  What many people do not understand is that the gut microbiome is made up of much more than just one type of probiotic, and that some bacteria that we consider to be harmful is living in the gut all of the time.  All of the bacteria in our gut play a role in helping us to digest foods, assimilate nutrients, and feel like our best selves, even the more “harmful” bacteria such as E.coli.  Yes, we have the dreaded E.coli in our guts even now, but the type that is found in the gut is a physiological strain and is actually considered good! The typically titled, “beneficial bacteria” that we know as “probiotics” prevent the more harmful bacteria from growing out of balance.  Our gut is an ecosystem, everything has a job, and they all keep each other in balance. 

Our gut microbiome begins forming at birth! Many of the probiotics that are found in the gut, are also found in the mouth, and the vagina.  As we pass through the birth canal we are exposed to the beneficial flora of our mother.  Probiotics are also found in our mothers breast milk.  The healthier the microbiome of our mother, the stronger ours becomes from the beginning. 

 Unfortunately, when we take medicines such as antibiotics, it destroys our good bacteria. Once this happens, there isn’t enough good bacteria to keep the “bad” bacteria in check, beginning the process of bacterial overgrowth and gut dysbiosis.  So what exactly are all of the bacteria of our gut, and what do they do? Here is some information on a few of them, but there are hundreds of different microbes found in the human gut.  

Essential Flora (aka Good Bacteria): 

Bifidobacteria: Promotes digestion and helps to stave off harmful bacteria. 

Lactobacteria: Helps with digestion, primarily glucose digestion.  Helps to digest and absorb nutrients, and helps to stave off harmful bacteria. 

E.coli: Physiologic E.coli are found in our gut even as a baby.  It is the main bacteria responsible for digesting lactose, and it also helps to produce vitamins such as K2, and many B vitamins.  On top of that, physiologic E.coli also helps to control pathogenic E.Coli that makes its way into our digestive tract through food and drink.  

Opportunistic Flora (aka Bad Bacteria): 

There are over 500 known various species of microbes that can be found in the human gut, and many of them are individual to each person.  Generally, when we think bad bacteria we think of these offenders. 

Bacteroids: There are about 22 different sub-members of this family, and it is found in the human gut.  When the gut is in a healthy state, they do not cause any problems, but when the gut is out of balance they grow out of control.  These bacteria love to eat sugars and starches, which is also what many people love to eat.  When they grow out of control they can cause severe inflammation of the gut, and are often found in abscesses of the gut.  

Clostridia: This is a family of bacteria, the most common one is known as the bacteria that causes tetanus.  The clostridia bacteria produce neurotoxins.  In a healthy gut this is not a problem, because the bacteria is controlled by the healthy flora, and a healthy gut wall will not allow toxins to pass through it.  However, when we have a leaky gut, the neurotoxins produced by this bacteria can get into our blood, pass the blood brain barrier, and cause neurological problems. Clostridia are also highly resistant to antibiotics.    

Candida Albicans: This is a type of opportunistic yeast.  When the gut is healthy, candida is under control.  However, in an unhealthy guy it flourishes as it feeds on sugars and starchy foods, and it is also antibiotic resistant.  Candida is responsible for extreme painful bloating, diarrhea, constipation, skin rashes, chronic vaginitis, chronic fatigue, and the list goes on.  

Transitional Flora: 

This represents all of the microbes that we swallow with food and drink.  In a healthy gut microbiome these bacteria pass through us without any problems.  Our body integrates the microbes it can use, and anything that is not essential or toxic is eliminated.  However, when our gut microbiome is not healthy, some of these microbes can flourish and cause disease.  


The gut microbiome is very diverse and complex.  It is pretty magical to know that within your body there are all these helpful little bacteria helping you to digest your food and absorb your nutrients. These bacteria also help to keep your immune system strong..  It is important to understand the signs and symptoms of gut dysbiosis and its causes.  In our current environment most people have been exposed to antibiotics, pesticides, harsh cleaning agents, all which can harm the beneficial flora of your gut, and disrupt the delicate balance of your gut microbiome.  I recommend nearly all patients to get on a good symbiotic supplement.  Symbiotic supplements have both probiotics, and prebiotics in them.  Prebiotics are the food that the probiotics eat.  A symbiotic supplement reintroduces beneficial bacteria into your gut, giving them something to live on so that they can thrive.  


Dr. Danielle Reghi is a licensed Acupuncturist, and holds a Masters in traditional Chinese medicine from Oregon College of Oriental Medicine, and a Doctorate of Acupuncture and Traditional Chinese Medicine from Pacific College of Health and Science. Her doctorate was focused on integrative health.  She is the owner of Zen Space Wellness, and Cupping Studio where she currently practices. She is originally from Hawaii, and currently lives in Portland Oregon with her husband, two dogs, one cat, and studio baby. Feel free to follow Danielle on Instagram at: @holisticallydriven , @zenspacepdx , or @cuppingstudio . Her business webpages are:, and


Campbell- McBride, N. (2010). GAPS: Gut and Psychology Syndrome. Medinform. 

Gates, D., Schatz, L. (2011). The Body Ecology Diet. Hay House, INC.