by Alex Del Duca, Naturopathic Graduate

The Microbiome

Each healthy person is currently host to millions of helpful bacteria that live inside the human gut. An adult has 387 known species of bacteria living in their gut experts estimate this number is as high 35000 species[1,2]. This community of bacteria is vital for a healthy human body and are known collectively as the microbiome. This living dynamic community is affected by many factors in life from the foods we eat and many other variables from the outside world. Most notably, antibiotics are known to disrupt our gut bacteria and result in chaotic shifts of this delicate community.

How can antibiotics affect the gut?

Antibiotics are a class medication that are used to either prevent infection that may occur or help clear an active infection in the body. They act by destroying the bacterial cells and helps the body’s immune system overcome an infection. These medications however are not able to distinguish good bacteria from bad[1]. Recall the nearly 400 types of gut flora that live inside us, very often antibiotics can wipe out strains causing an imbalance.

The more common side effects of oral antibiotics are gastrointestinal in nature. When taking antibiotics certain good bacteria can be destroyed in the process of attempting to kill an undesirable infection. The favorable outcome of infection elimination comes at a cost of this imbalance known as dysbiosis. The most common side effects of dysbiosis are gas, bloating, diarrhea and distention.  If a short cycle of antibiotics are taken for a few days, typically these symptoms are mild and short lived, if present at all. Longer courses and stronger antibiotics may result in complete elimination of certain good strains. Research shows that after taking 4 days of antibiotics such as meropenem, gentamicin and vancomycin patients failed to repopulate at least 9 independent strains after 180 days[3]. The more dangerous and less common side effects of dysbiosis include an overcolinization of certain strains such as C. difficile.[3]


Broad key roles our flora play are:

  • Aiding in digestion and absorption[3]
  • Managing immune regulation and helping to keep unfavorable bacteria at bay, such as C.Difficile[3]
  • Creating a rich supply of B-Vitamins for energy generation and sleep management[3]
  • Managing gut inflammation[3]

Foundational naturopathic approaches to ensure a healthy microbiome 

Many therapeutic strategies have been developed to maintain a healthy flora. Knowing the details of what antibiotic and any health concerns prior is critical to ensure complete restoration. When looking into proper and complete healing, two major considerations must be taken into concern. First, knowing what strains may be depleted is important, antibiotics target certain types of bacteria and kill only specific strains. Taking probiotics or foods that are poor in the needed bacteria is an ineffective approach to healing. Second, ensuring care is considered for the intestinal wall and mucus membranes within. If the intestinal wall sustains damage over the course of antibiotic use then systemic effects may be seen. This concern is called intestinal permeability, also known as leaky gut. When the walls of intestines begin to loosen the GI tract loses the ability to be selective in what it lets into the body for absorption. Deleterious effects can follow including autoimmunity, food sensitivities and joint inflammation[9].

Broad approaches for overall flora health before, during and after antibiotics:

  1. Eat whole foods that are free of processing. According to a recent study, a single organic apple contains 100 million bacteria. The catch is the entire apple must be eaten core, seeds and all[10].
  2. Regular intake of soluble fiber such as beans, peas, yams and potatoes are all used as food for a healthy gut flora. Those on low carb diets ought to consider temporarily taking these foods in order to restore flora effectively. When consuming soluable fiber to help with feeding gut flora they are sometimes called prebiotics.
  3. Any amount of alcohol can cause dysbiosis even without antibiotics[11]. Ingestion of beer, wine or spirits affects every part of the digestive system from mouth to colon. When studying human trails dealcoholized wine showed mostly benefits and works as a prebiotic to support some good strains.
  4. Elimination of all artificial sweeteners appears to be supported by research when considering your gut health[12]. Studies reveal those who regularly ingested sweeteners had a decrease in bifidobacterium, lactobacillus, and bacteroides. 
  5. l-Glutamine, an amino acid, works well by helping support against leaky gut. While aiding in mucous production and patching intestinal junctions glutamine is an important part of therapy[13].
  6. Fermented foods are a source of living probiotics and deliver broad and undefined amount of good basteria, they work well by providing wise variety of strains in small amounts of food [4]. Fermented foods such as kimchi, sauerkraut and yogurt are all whole food sources to consider.
  7. Chew food with intention and patience. Eating habits are formed in early life with more concern around taste then chewing form. Digestion starts in the mouth with most of the processing starting with teeth. When proper chewing is present the digestive system is aided and works less. To put more perspective on the topic of chewing, the average human has 82,125 meals in their lifetime. These habits can impact a person’s well being and GI tract for the better.
Chew that food!

References Available Upon Request. Email info@activesolutionshealth.ca

Alex Del Duca completed his undergrad in Criminology Ontario then attended CCNM for his training as a Naturopathic Doctor. While at CCNM Alex focused on Adjunctive Cancer Care as a special interest and completed the Cancer focus shift while in his last year. He has attended many global health brigades in Nicaragua, Thailand, Arizona and Mexico. While assisting in many fundraising ventures and organizational support for NWB, he continues to be passionate and excited for the organization’s future.

Alex plans to continue outreach and global efforts to bring sustainable free Naturopathic Healthcare to places in need. He is expected to be practicing as a licensed ND on Vancouver Island by November 2019. His focuses will include Cancer Care and Regenerative Medicine. 


Gut Bacteria and Antibiotics – Friends or Foes?