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Can We Have Too Many Gut Bacteria—Even the Good Ones?

Digestion | April 27, 2018 | Author: Naturopath

bacteria, bowel, Digestion

Can We Have Too Many Gut Bacteria—Even the Good Ones?

Friendly bacteria reside in the gastrointestinal tract and promote good digestive health by maintaining bowel regularity, supporting our immune system and even synthesising certain nutrients. Recent research has uncovered the importance of our gut microbiome—a diverse community of healthy microbes that populate our digestive system.

Supplementing with probiotics is all the rage and while there is validity in using specific strains of probiotics in certain conditions, not all strains have been evaluated in terms of efficacy and safety.

So the question stands…could certain probiotic strains be doing more harm than good? In this article we will look at some disadvantages of taking probiotics and suggest other methods to support a healthy microbiome such as healthy diet and lifestyle.

Healthy species of bacteria

We have trillions of bacteria that inhabit our whole body including our digestive tract. They are densely populated in our colon, with very small amounts in our stomach and small intestines. They co-inhabit with other microbes such as parasites, fungi and viruses.

99% of the bacteria in our colon come from about 30 to 40 species. Most bacteria belong to the genera Bacteriodes, Clostridium, Faecalibacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus and Bifidobacterium. To a lesser extent Escherichia and Lactobacillus are present.

Gas and bloating

Gas and bloatingFriendly bacteria feed on prebiotics in your digestive tract, which are indigestible carbohydrates that come from your diet. When the bacteria feed on the sugars, they excrete gases such as methane and carbon dioxide.

For this reason, having too many probiotics in your intestines, or experiencing a sudden increase in good bacteria, may cause gas and bloating.

In fact, gas and bloating are two of the most common side effects people report when they first start taking probiotic supplements. This side effect is usually mild and may go away as your body adjusts. If not, you may need to lower your dose or trial a different formulation.


Small intestinal overgrowth or SIBO for short is when bacteria cross the line into overpopulation in the small intestine. They should primarily reside in the large intestine; if they decide to get adventurous and start exploring other places, you’re in for trouble! Medical treatment usually involves antibiotics, but certain herbal antimicrobials have been shown to be just as effective. Supplementing with probiotics and prebiotics in people with SIBO is controversial—best to check with a health practitioner first.
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In rare instances, having excess good bacteria in your intestines may cause bacteraemia, which is when the bacteria overgrow, leave the intestines and enter the bloodstream. Children, the elderly and people with a compromised immune system, such as those with HIV or people taking immune-suppressing drugs, are primarily at risk. The May 2013 issue of the Journal of Clinical Gastroenterology published a case report of probiotic use causing bacteraemia in a teenage boy. He took probiotics to boost good bacteria in his intestines to treat ulcerative colitis and experienced bacteraemia after a week. He was also taking corticosteroids, which are steroid hormones that suppress the immune system.

For the average person the risk of this occurring is extremely rare. It is estimated that only one in one million people will develop an infection after supplementing with Lactobacilli bacteria.

How to naturally modify our microbiome without probiotic supplements


DietDiet has emerged as one of the most relevant factors in influencing the gut microbiome. Significant alterations in the gut microbiota have been associated with dietary changes, primarily consumption of dietary fibre from fruits, vegetables and other plants.

A diet that is varied and complex is associated with a more diversified microbiome.

In contrast a diet high in processed foods, saturated fats, animal proteins and sugar and low in fibre is associated with poor levels of healthy bacteria.


Prebiotics are a type of indigestible plant fibre which feed friendly live bacteria in the gut. Foods that are naturally high in prebiotics include oats, bananas, chicory root, artichokes, apples and leeks. Prebiotics can be supplemented and include beneficial fibres such as inulin, slippery elm, oat bran and psyllium husks.

Probiotic foods

Probiotic foods, also referred to as fermented foods, naturally contain good bacteria and yeasts which benefit our gut.

To avoid any side-effects, start off with small amounts and gradually increase

Probiotic foodsExamples of probiotic foods include natural yoghurt or kefir, kimchi, sauerkraut, tempeh, miso and kombucha.

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Unfortunately, fermented foods don’t suit everyone—especially people who are sensitive to amines and experience side-effects such as itchy skin or headaches.


The gastrointestinal tract and the gut microbiota, is sensitive to stress and stress mediators. Enteric bacteria respond to the release of stress-related neurochemical mediators by the host which can influence the response to a bacterial infection. Recent theory suggests that bacteria act as delivery vehicles for neuroactive compounds, and therefore can affect host physiology by providing neurochemicals.

If stress is affecting your digestion here are some ways to reduce its effects:

  • Try meditation, yoga or tai chi
  • Go for a walk outdoors in nature
  • Reduce screen time
  • Get a good night’s sleep
  • Eat in a relaxed manner—don’t gobble down your food
  • Try taking magnesium or calming herbs such as passionflower
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In conclusion

Even though there’s overwhelming evidence to support the use of probiotics in certain conditions there are potential side-effects. The most common side-effect is bloating and gas but in very rare cases probiotic supplementation can lead to infection. Natural ways to enhance our microbiome include reducing stress, eating plant fibres and probiotic foods.  Australia’s best online discount chemist


Guarner FMalagelada JR. Gut flora in health and disease. Lancet. 2003 Feb 8;361(9356):512-9

Fisher CK, Mehta P. Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression. PLoS One. 2014; 9(7): e102451

Sherid M, et al. Liver abscess and bacteremia caused by lactobacillus: role of probiotics? Case report and review of the literature. BMC Gastroenterol. 2016; 16: 138

Sanders ME, et al. Safety assessment of probiotics for human use. Gut Microbes. 2010 May-Jun; 1(3): 164–185

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