Life in our digestive track

Gut flora & the intestinal microbiome

What is gut flora?

Gut flora, also known as intestinal microbiota, is the complicated ecosystem of microscopic organisms within the animal digestive track. Because of their complicated makeup (the aggregated genome of all the bacteria in our lower intestine alone is many times larger than the entire human genome), it is difficult to generalize about their effects, roles, and functions. Microbiota are essential to healthy human digestion, while we provide them with nutrients and energy, creating a symbiotic relationship between the bacteria and ourselves.

[Image: 4 different Yakult flavors in Singapore. Yakult is a popular probiotic meant to stimulate the presence of Lactobacillus in the human colon.]

Case study: E. Coli

E. Coli are one of the most prevalent strains of intestinal bacteria. Most warm-blooded animals are colonized by harmless strains of E. Coli within days, if not hours, of birth. It is extraordinarily adaptive, able to survive in environments with radically different temperatures, pH levels, and O2 levels, capable of both aerobic and anaerobic respiration.

The often-studied lac operon was first discovered in E. Coli, and serves as the primary mechanism for lactose fermentation in the bacteria - since E. Coli can take up and digest excess lactose, it can alleviate the effects of lactose intolerance in humans. In the vast majority of cases, E. Coli is either harmless or beneficial to us, driving out pathogenic bacteria through competition or synthesizing vitamin K. However, particular strains can cause severe food poisoning or even death. Food contaminated with E. Coli is generally recalled.

Why does it matter?

Effects on human biology

  • Neurology

    • 95% of Serotonin in the human body is produced in the colon. Serotonin is a crucial neurotransmitter involved in everything from

    • Waking cortisol levels are lower in experimental subjects taking β-Galacto-Oligosaccharide, a probiotic. High levels of

  • Disease

    • Lactobacillus johnsonii is correlated with a longer lifespan and lower disease penetration in mice predisposed to lymphoma.

    • Microbiota can prevent infection of the gut by pathogenic bacteria through competitive inhibition. (ex: Clostridium Dificille infection, an antibiotic-resistant bacteria which can lead to severe bloating and even death, typically follows intensive antibiotic treatment which decreases the amount and variety of normal gut bacteria).

  • Firmicutes are positively correlated with obesity. However, knowing that intestinal bacteria concentrations are affected by diet, it could be that high-fat diets lead to Firmucutes colonization. It is also possible that a genetic predisposition to obesity also leads to high levels of the bacteria.

[Image: Lactobacillus Johnsonii]

Nature or nurture?

  • There is evidence of differences in gut flora in people with diabetes I, II, and certain genetic cancers. However, the difference in gut flora in people with diabetes might be a result of the dietary restrictions recommended for people with diabetes.

    • Gut flora distributions are, in part, genetically coded. This leads to two possibilities:

      • A particular gene leads to a predisposition to diabetes II, which in turn causes the host to restrict their diet, changing gut bacteria concentrations.

      • A particular gene leads to a difference in gut bacteria, which in turn might cause the host to crave sugary foods (i.e a “sweet tooth”), leading to diabetes II.

  • There is a current debate involving sterility while in the womb - though traditional medical knowledge indicates that the fetal intestine is completely sterile, and colonization follows exposure to the external environment, current research might indicate that this is not the case, and colonization begins in the womb.

  • B. Wadsworthia shows a significant uptick following a diet heavy in animal products, and is also positively correlated to obesity. This suggests that nurture, not nature, determines our gut flora.


Schmidt, K., Cowen, P. J., Harmer, C. J., Tzortzis, G., Errington, S., & Burnet, P. W. (2014). Prebiotic intake reduces the waking cortisol response and alters emotional bias in healthy volunteers. Psychopharmacology, 232(10), 1793-1801.

Intestinal bacteria modify lymphoma incidence and latency by affecting systemic inflammatory state, oxidative stress, and leukocyte genotoxicity

Westbrook A.M., Wei B., Loy A., Chang C., Braun J., Borneman J., Schiestl R.H., (...), Reliene R. (2013) Cancer Research, 73 (14) , pp. 4222-4232.

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Cross, K. (n.d.). Lactobacillus johnsonii (smooth mutant) [Photograph]

Todar, K. Pathogenic E. coli. Online Textbook of Bacteriology. University of Wisconsin–Madison Department of Bacteriology. Retrieved 2007-11-30

Dezzawong. (2009, October 31). SG Yakult 4 Flavours. [Photograph]