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The Human Microbiota

By: Dr. Emeka Enwere

Human civilization has been punctuated, every so often, with close, personal, and often deadly interactions with microscopic organisms. These microbes – call them pathogens, or infectious agents, or just germs – are responsible for such moderately-notable events as the Black Death, the 1918 flu, smallpox, and, more recently, the Ebola epidemic. Over the past 150 years, we’ve spent trillions of dollars, and uncountable laboratory research-hours, finding new and better drugs and vaccines with which to control these microbes. It’s safe to say that the idea that “microbes are bad” is universally imprinted upon the human consciousness.

But are they really all that bad?

It turns out that the answer, in many ways, is no.

Most microbes are actually harmless, and many are beneficial. If you were to count all the cells in the (healthy) body, inside and out, you would find that there are as many microbial cells as there are human cells. Most of those microbes are bacteria which live in the lining of the gut. Normal gut bacteria serve a very important protective role – they prevent the growth of harmful bacteria, by competing with them for food and space. Removing normal bacteria from the gut leaves it vulnerable to infection by harmful bacteria that would normally never have a chance to survive.

This is the case, for example, when someone is infected with Clostridium difficile. C. difficile, or often just C. diff, is a bacterium that causes life-threatening gastroenteritis, with symptoms including pain, severe diarrhea, inflammation of the colon, and kidney failure. Paradoxically, most people contract this infection while in hospital, usually right after a course of antibiotic treatment. The Latin “difficile” in the name gives an idea of how difficult the infection is to cure. With normal treatment – which, ironically, involves giving the patient more antibiotics – C. difficile infection has a very high recurrence rate, leaving the patient playing a game of whack-a-mole with one antibiotic after another. Antibiotics are not very selective in choosing which bacteria to kill; normal intestinal bacteria die along with the harmful ones, and it only takes a few surviving C. difficile bacteria to restart the entire disease. Consequently, one of the most effective ways to permanently cure a C. difficile infection is to transplant normal bacteria back into the gut. These transplanted bacteria do what antibiotics cannot – they kill the C. difficile bacteria, and keep them from growing back.

The microbes that live with us more-or-less permanently make up the human microbiota. There are about 40 trillion of these microbes, from a thousand different families, and they are found in almost every part of the body, including the brain. Their benefits start, quite literally, at birth. The infant’s gut is colonized with healthy microbes during birth, where they help to teach the immune system the difference between good and bad bacteria. This process is helped by a protein in milk, called lactoferrin, which stimulates the immune cells in the gut that need to be educated. These cells then “learn” the features of normal gut bacteria, and learn not to react to these bacteria. This training process goes awry in pre-term infants, where, without both breast milk and a dose of healthy gut bacteria, the immune system will attack the gut itself. The condition is called necrotizing enterocolitis, and is a major cause of mortality in pre-term infants. Supplementing these infants with both bacteria and lactoferrin prevents both the enterocolitis and infection by harmful microbes1,2.

The gut microbiota has another important education role, which is to teach the immune system about allergens. This happens in a narrow window of time, usually within the first three years of life, in which the immune system can be trained to see dander, pollen, and other allergens as “food” and generally ignore them. A healthy, well-developed gut microbiota is necessary for this “tolerance training”, as is, of course, plenty of exposure to those allergens. In a large Canadian study on the role of gut microbiota on childhood development, the investigators found that a poorly-developed microbiota in children as young as three months old predicted the development of asthma later in life3.

The benefits of a healthy gut microbiota are numerous, but still poorly understood; it is only of late that advances in genetic technology have allowed detailed research into this area. So far, the evidence is clear that the influence of gut microbiota extends to every system in the body. There is evidence connecting the gut to metabolic disorders, cardiovascular disease, psychiatric conditions, gastrointestinal disorders, airway infections and even cancer. The gut microbiota could be described as the “second genome” – conditions like obesity can be transmitted through these bacteria from mother to child4, and even between individuals5. It’s safe to say that to lead a healthy life, you should care for your bacteria. They’ll care for you, too.

Here are a few hints on ways to keep your microbiota healthy:

  • Maintain a high-fiber diet: Bacteria in the gut turn fiber into short-chain fatty acids (SCFAs), which have numerous health benefits. They create an acidic environment in the colon that kills harmful bacteria. They also fuel the growth and maintenance of intestinal cells, suppress inflammation. They are also the active agents involved in training the immune system on the difference between healthy and harmful products. Foods that are high in fiber include legumes (beans and peas), sprouts, and whole-grains.
  • Take probiotics: The right probiotic can help restore, support and advance your gut microbiota, protecting against infections and chronic inflammation.
  • Relax: Stress disrupts the balance of bacteria in the gut, producing negative effects on other systems of the body6.


1.        Manzoni, P., Rinaldi, M., Cattani, S., Pugni, L., Romeo, M. G., Messner, H., Stolfi, I., Decembrino, L., Laforgia, N., Vagnarelli, F., et al. (2009). Bovine lactoferrin supplementation for prevention of late-onset sepsis in very low-birth-weight neonates: a randomized trial. JAMA 302: 1421–8.

2.        Meyer, M. P. and Alexander, T. (2017). Reduction in necrotizing enterocolitis and improved outcomes in preterm infants following routine supplementation with Lactobacillus GG in combination with bovine lactoferrin. Journal of Neonatal-Perinatal Medicine 10: 249–255.

3.        Arrieta, M.-C., Stiemsma, L. T., Dimitriu, P. A., Thorson, L., Russell, S., Yurist-Doutsch, S., Kuzeljevic, B., Gold, M. J., Britton, H. M., Lefebvre, D. L., et al. (2015). Early infancy microbial and metabolic alterations affect risk of childhood asthma. Science Translational Medicine 7: 307ra152-307ra152.

4.        Tun, H. M., Bridgman, S. L., Chari, R., Field, C. J., Guttman, D. S., Becker, A. B., Mandhane, P. J., Turvey, S. E., Subbarao, P., Sears, M. R., et al. (2018). Roles of Birth Mode and Infant Gut Microbiota in Intergenerational Transmission of Overweight and Obesity From Mother to Offspring. JAMA Pediatrics 172: 368.

5.        Fei, N. and Zhao, L. (2013). An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. ISME Journal 7: 880–884.

6.        Gur, T. L., Worly, B. L. and Bailey, M. T. (2015). Stress and the Commensal Microbiota: Importance in Parturition and Infant Neurodevelopment. Frontiers in Psychiatry 6: 5.


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