Bacterial Infections and the Microbiome, The Holistic Look from a Naturopathic Doctor

The microbiome is an important part of you.  It helps with detoxification, stimulating your immune system to protect you from bacteria, virus and even cancer.  The bacteria in your gut is key to making Vitamin K to protect your bones and to make sure dopamine gets made thus influencing your mood.  As long as your immune system is primed and your bacteria is in balance, you are less likely to suffer from mood disorders, arthritis, obesity and cancer.

Once our bacteria is out of balance, it can lead to opportunistic infections.  Things that can affect the healthy bacteria in the belly include antibiotics, food intolerances and stress.  Antibiotics will take the diversity of health bacteria down to 1-3 strains and newer studies are showing that it can take 9 months or more to return to a normal diversity of 9 or more species in the gut flora which is why we often look for alternatives in naturopathy.  Probiotics are incredibly important to protect the gut flora during antibiotics.  Food intolerances can also impact the normal bacteria by causing an inflammatory response within the gut lining and can be tested for properly with a naturopathic doctor.  Stress may be the worst attacker on the gut lining function.  It dries out the lining so the immune system can not be produced thus bad bacteria can’t be identified and removed. Digestive enzymes also can not be properly made which protect the belly by digesting foreign invaders or materials.

When bad bacteria has an opportunity, it will take over and dominate causing a multitude of functional problems such as limiting nutrient absorption and immune development in the gut.  Then it can spread to other parts of the body and create symptoms.  Bacteria such as streptococcus (includes multiple strains) are commonly known for strep throat but when it is hiding in the gut, it can cause reoccurrence and many families wonder why they have a constant struggle with strep throat.  Treating a surface infection doesn’t also manage the infection that is seeded from the belly.   Streptococcus infections in the belly can cause anxiety and belly pain as well.  Unfortunately, there is not a lot of research to connect these functional medicine ideas of gastrointestinal infections except by naturopathic doctors who are in tune with infectious disease and take time to observe the commonalities between patients.  The true test is when you treat the infection seeded in the belly and symptoms resolve or improve. This is holistic medicine.

Other problematic gastrointestinal bacterial and parasitic infections we commonly see in our naturopathic clinic are klebsiella, yersinia, enterococcus, pseudomonas, giardia, entamoeba hystolytica, blastocystitis hominis, citrobacter, clostridium difficile and toxoplasmosis. You need an integrative treatment plan to address most infections since there is almost always more than one.  Many bacterial infections are also antibiotic resistant so you really do need a naturopathic doctor who can use integrative medicine to use the tools that will work once and for all.  Natural medicine has a way or building up the body at the same time as addressing the infection.  Klebsiella is known for causing urinary tract infections but it doesn’t often show up in the urinary tests.  After treating klebsiella  in the gut, we can eliminate the chronic urinary tract infections.

The key to health and protection of our microbiome is diversity.   When our normal flora is not flourishing and we have symptoms which can range from headaches to belly pain, diarrhea, chronic infections or loss of energy, we may need to rule our bacterial infections so we can get our normal flora working for us again.  Consider our San Diego bacteria cleanse program.

We specialize in this kind of thing and see it frequently in our office so it’s not a new idea for us. Getting the right care for your body is important and tailored for your specific body in mind. At Journey of Health we are dedicated to finding the right naturopathic solutions for each patient. We proudly serve the San Diego area, providing some of the best service in naturopathic medicine. If you wish to further your own journey of health with naturopathic solutions and alternative medicines, give us a call at (619) 772-1164.


  1. Really nice and interesting article. Great information provided throughout the article. Thanks!

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