Probiotics – The Gut Flora

In an ecosystem, we have many organisms living in harmony where they mutually benefit from each other. Just like an ecosystem, our human bodies are a home to many bacteria that help us maintain our digestive tract. For decades we are starting to learn that there are good bacteria versus bad bacteria that lives within our digestive tract. The good bacteria are what we call the gut flora, microbiota, microbiome, and other names. These bacteria mostly live in the large intestine and they digest the food that could not be processed, aka indigestible food, by the body into nutrients. These indigestible foods are called fiber that is found in fruits and vegetables. Fiber is digested by the gut flora into butyrate and propionate, which is absorbed by the cells in the large intestine as nutrients. Many of you might be thinking how exactly could bacteria be considered a flora or a fauna since they are single cell organisms that are neither plants nor animals.

In many ways, the flora of the gut is a metaphor for bacteria that helps nourishes the body. Just like plants that allow the ecosystem to thrive, the bacteria ensure that the bad bacteria does not populate in the area. The body temperature and moisture is such a perfect environment for many infectious critters that many of them are trying to occupy the area. The good bacteria, however, occupies the area in a large enough group to prevent the bad bacteria from thriving.

Unfortunately, the use of antibiotics is non-selective in what they kill and the gut flora gets eradicated with the pathogens. This is an opportunity for pathogens to grow in the vacant areas of the gut to cause problems. In many cases, the pathogens that occupy the area lead to a decrease in intestinal movement leading to poor digestion. Luckily these microbiome can re-flourish through the use of probiotics. According to the Joint FAO/WHO Expert Consultation, “probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host.” Probiotics do not perfectly repopulate the gut with the same strains of bacteria, but is still able to return some of the flora back enough to prevent pathogens and intestinal problems.

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Disclaimer: The next 3 paragraphs will confuse you if you do not have a background in science especially in immunology.

If we could imagine how plants provide energy at the bottom of the food chain, we can think of bacteria, aka microbiome, that help provide nutrients to the body. Plants also provide a home and a camouflaging terrain to many animals; the microbiome also provides protection to the body by regulating the immune system. Reviewing the histology briefly of the digestive system, the Peyer’s patches are found in the ileum portion of the small intestine. Because nutrients get absorbed in the small intestine, the body needs a defense system that detects pathogens and foreign substances before pathogens can affect the body systemically. The Peyer’s patches, in a sense, screen and destroy foreign particles when needed in the digestive tract. The microbiome plays an important component in maintaining immune tolerance. What is immune tolerance?

Our immune system is very intelligent at detecting foreign particles such as a protein from a virus or a structure from a bacterium. The immune cells must be good at distinguishing foreign particles from self. The immune cells that I am specifically referring to are called T-cells. Whenever T-cells attack its own body, these are called self-reacting T-cells and they would usually lead to an autoimmune condition. Immune tolerance is the reason why T-cells do not attack our own body. The body is able to have an immune tolerance through regulatory T-cells. The regulatory T-cells suppress self-reacting T-cells.

The microbiome that lives in the intestine influences the opportunity for immune challenges allowing them to influence the function of regulatory T-cells. Studies have shown that the lack of microbiome leads to an increase in unnecessary inflammatory processes. The gut bacteria are then very crucial to maintaining the immune system.

For more information on this topic, like this post and I will post more information on probiotics.


Jafarnejad S, Shab-Bidar S, Speakman JR, Parastui K, Daneshi-Maskooni M, Djafarian K. Probiotics Reduce the Risk of Antibiotic-Associated Diarrhea in Adults (18-64 Years) but Not the Elderly (>65 Years): A Meta-Analysis.Nutr Clin Pract. 2016 Apr 29. pii: 0884533616639399. [Epub ahead of print] Review. PubMed PMID: 27130655.

 Ford AC, Quigley EM, Lacy BE, Lembo AJ, Saito YA, Schiller LR, Soffer EE, Spiegel BM, Moayyedi P. Efficacy of prebiotics, probiotics, and synbiotics in irritable bowel syndrome and chronic idiopathic constipation: systematic review and meta-analysis. Am J Gastroenterol. 2014 Oct;109(10):1547-61; quiz 1546, 1562. doi: 10.1038/ajg.2014.202. Epub 2014 Jul 29. Review. PubMed PMID: 25070051.





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