Gut Bacteria

Gut Bacteria

Our entire microbiome and the gut flora itself have been found to produce profound effects on the body, though generally we pay most attention to the effects of bacteria. (1)(8) Bacteria can cause common gastrointestinal symptoms like diarrhea, gas, and bloating, but they can also work on a much bigger, holistic scale. Gut bacteria can alter the foods we crave, impact the moods we feel, and even play a role in the development or prevention of certain diseases, such as stomach cancer and asthma. (19)(24)

Good vs. Bad Gut Bacteria

For some bacteria, the mechanisms responsible for their effects on preventing disease and inducing other beneficial health effects are known—these are commonly referred to as “good bacteria”. Conversely, bacteria that have known mechanisms by which they can cause disease or bodily dysfunction are often commonly referred to as “bad bacteria”.

Good Bacteria

“Good” bacteria are often those you’d find on the back of a probiotics label. For many of these bacteria, their microbial metabolism involves the production of lactic acid from the breakdown of glucose; this lactic acid can be used in fermentation processes, helping to preserve food by preventing the growth of pathogenic “bad” bacteria and their byproducts. (14)

Lactobacillus & Lactococcus

These bacterial genera, as well as several others, have been shown to produce serotonin in the gut. (5) Serotonin is known as the “mood” neurotransmitter as it contributes to the feeling of general well-being and happiness, as well as to our sleep cycles and digestive system efficiency. Lactobacillus also has anti-cancer and anti-inflammatory effects on the body and is associated with reduced symptoms of irritable bowel disease. (20)

Bad Bacteria

“Bad” bacteria are those that are pathogenic, meaning they cause disease. These are the type of bacteria for which an antibiotic may be prescribed to eradicate, particularly if an individual is exhibiting associated symptoms.

H. pylori

This pathogen infects about 50% of the global population and is associated with gastritis, ulcers in the gastrointestinal tract, and mucosal-associated lymphoid tissue cancers. (24)(20)

C. difficile & C. botulinum

C. difficile is commonly found in hospitals and can cause a serious gut infection known as pseudomembranous colitis. This inflammatory condition can cause diarrhea, severe dehydration, and fever. (9)

C. botulinum has spores that can cause fatigue, dehydration, constipation, and weakness if ingested, particularly in infants. A common food source of this is honey, though it can also be found in soil and improperly canned goods. (4)

S. aureus

This pathogen is a major cause of food poisoning, as well as diarrhea directly following antibiotic use. A common food source of S. aureus is dairy products. (17)

E. coli

This pathogen is the leading cause of urinary tract infections. Increased levels of E. coli are also associated with meningitis, irritable bowel disease, and gastroenteritis. (20)


How to Care for Your Gut

As our gut microbiota includes more than just “good” and “bad” bacteria, housing approximately 300 to 500 bacterial species with more than two million genes, creating harmony amongst these diverse species is essential to optimal health. (8)

This is achieved by ensuring there are adequate ratios and quantities of certain species in the gut to maintain this ecosystem’s natural balance. However, sometimes our gut flora may lose this harmony as a result of taking a course of antibiotics, during or following an illness, after intense treatment such as chemotherapy, or due to diet and lifestyle factors. Probiotics, prebiotics, and lifestyle changes can all help to steer our gut bacteria back in the right direction.


Probiotics are defined as “live microorganisms which when administered in adequate amounts confer a health benefit to the host.” (10) Many of the health benefits of taking probiotics are well-established and include the prevention or reduced duration of common viral infections, allergies, and lactose intolerance symptoms, a reduction of cancer-promoting enzymes, the normalization of stool passing, and a decrease in gastrointestinal effects.

Sources of probiotics include supplements and certain fermented foods and drinks such as:

  • Kombucha (fermented tea) (6)
  • Amasi and kefir (fermented milk) (18)(6)
  • Miso (fermented soybean paste) (6)
  • Kimchi (fermented vegetables) (6)
  • Tempeh (fermented boiled and dehulled soybean) (6)
  • Fermented cereals including porridge and gruel (18)
  • Cheese, cultured buttermilk, yogurt, and other fermented dairy products (18)


A prebiotic can be defined as “a selectively fermented ingredient that allows specific changes, both in the composition and/or activity in the gastrointestinal microflora, that confers benefits upon host well-being and health.” (23) Essentially, a prebiotic is food for the “good” bacteria. 

In addition to increasing “good” bacteria and consequently decreasing “bad” bacteria, intake of prebiotics offer other health benefits including:

  • Increased calcium absorption (2)
  • Improved immune system defense (2)
  • Decreased gut permeability, which may help heal a “leaky gut” (2)
  • Decreased risk of allergic reactions (2)
  • Production of good metabolites, which helps to prevent invasion of “bad” bacteria and other pathogens (2)(12)

Regarding the gut microbiota, diet can influence its diversity, composition, and quantities of the populated species. (13) In general, eating a variety of foods containing colourful vegetables and fruits is recommended, though there are specific additions and restrictions to one’s diet for targeting optimal gut health.

In addition to adding prebiotic and probiotic foods and drinks into our diet, getting a good dose of fiber on a daily basis and being mindful of fat and sugar intake can help ensure a more robust gut flora.

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