Your Gut Microbiome – Miraculous and Mysterious – Part 1

What is the Microbiome?


Research on the microbiome of the human gut is still quite new. It was not until the 1990s that we even recognized that we human beings harbour a very large and active population of a wide variety of types of tiny organisms on and within our bodies. By far the largest microbe population in human beings is in the gut. It is now becoming clear that our gut microbiome is much more than just random tiny inhabitants living in our intestines and feeding off food particles as they pass by. In fact the gut microbiome is an integral part of a healthy body, not only providing us with energy and nutrients that we would otherwise not be able to access, but also affecting many other body systems and playing a part in preventing us from developing chronic diseases. We in return provide a protected, warm, nutrient-rich environment in which these microscopic species thrive.

Remarkably, human beings are the habitat for many different microbiomes. Each of these microbiomes is a community of microbes, miniscule one-celled creatures. Our microbe population is predominantly bacteria but also includes fungi (yeasts), viruses, archaea, protozoa and eukaryotes. It is estimated that we have over 600 different species of microorganisms in our lungs and more than 1000 species on our skin. The microbiome of our gut contains between 500 and 1000 species. The stomach and small intestine have very few resident organisms, mostly due to their acidity, but also because the muscles that surround these organs contract in waves that help to move food along the digestive system thereby causing difficulties for microorganisms attempting to set up a stable community. Consequently, most of our gut microbiome resides in the colon. (1)

The total microbiome of each human being consists of somewhere between 40 trillion and 120 trillion single-celled creatures and is unique to each person. This number of cells is slightly larger than the total number of human cells in the body with a ratio of 1.3 to 1 (2,3). Previous estimates of ten times more microbe cells than human cells in the human body have been abandoned as continuing research discovers more information. Still, we are more microbe than human, making us a veritable walking ecosystem. Our bowel movements are a testament to this with 30% to 55% of their solid contents being microbes, both living and dead (4,5). The total microbiome of one human being can weigh up to 5 pounds (6).

It might seem surprising that viruses are a part of our microbiome but this is not unusual in nature. All life forms have been found to carry viruses. Most of these viruses are stable members of the human microbiome and provide benefits such as preventing infections by killing disease-causing microbes and protecting the mucosal lining of the intestine from harmful microorganisms. Sometimes however these viruses can become involved in dysbiosis, alterations in the microbiome that can have a negative impact on human health (7,8,9).

Within the human microbiome are a staggering number of genes, vastly outnumbering our human genes and prompting its nickname, the Second Genome. Latest estimates of the number of genes in our microbiome are 46 million (10) while the number of human genes is thought to be around 46,000 (11). This means that the genes in our microbiome outnumber our own genes by a factor of one thousand to one.

The potential effects that this very large mass of extra genetic material may be exerting on us is immense. We know that it is a source of genetic diversity that influences digestion and metabolism; it is an essential component of immunity; it modulates drug interactions and modifies disease (12,13). One example of the influence of our microbiome genome was discovered in a study from 2010 which found that a large part of the Japanese population are benefiting from an enzyme produced by their gut bacteria that allows them to break down carbohydrates from red algae seaweeds such as nori. Nori is the most important nutritional seaweed and is traditionally used uncooked in the preparation of sushi. Normally humans cannot breakdown the fiber present in this seaweed. So how do these Japanese people do it? It appears that bacteria in the ocean contain the genes necessary to produce this particular enzyme. Some of these bacteria remain on the uncooked seaweed when it reaches the plate. In the trip through the colon of sushi eaters these bacteria transfer the genes that code for this particular enzyme into the gut bacteria of people who commonly consume this seaweed (14).

The gut microbiome itself is also known as our “second brain” because within it is a multifaceted nervous system called the enteric nervous system. Our “first brain”, the brain found within our skull, connects to our “second brain” through the vagus nerve (as part of the gut-brain axis). The vagus nerve is the longest nerve in the human body whose many branches connect the brain to major organs and the long length of our intestines, communicating via molecules such as hormones, neurotransmitters and short-chain fatty acids. The food we eat is our most direct contact with the outside world and it is theorized that evolution developed this intricate message system to protect us from the myriad of risks we encounter in the world outside of our bodies. A huge number of messages journey along this nerve with most of them travelling from the gut to the brain, informing the brain about the status of the digestive system. But messages are sent in the other direction too. For instance, emotional stress, depression, anxiety and neuropsychiatric disorders can cause changes in the function and composition of the gut microbiome. Surprisingly the enteric nervous system is a separate entity unto itself. A digestive tract completely severed from the body can still secrete all the chemicals it needs to function and can continue to digest food. (15)

Human beings and our gut microbiomes developed together over millions of years of evolution into a complex symbiotic relationship that is beneficial for both the human host and the microbial partners. In truth, our gut microorganisms are not just helpful for us but have become an indispensable part of a healthy body. They can break down foods that are difficult for us to digest such as fiber and resistant starch, providing energy to both themselves and the human host. But digestion is just the tip of the iceberg of valuable activities accomplished by the microbiome. The fermentation produced by the activity of the gut microbes reduces the pH of the gut, creating an inhospitable environment for disease-causing microorganisms. Gut microbes also produce short-chain fatty acids such as butyrate, propionate and acetate that are essential for gut health. Butyrate is the preferred energy source for the cells that line the human colon, promoting a healthy barrier between the intestinal contents and the vulnerable inner body components such as the bloodstream and organs. Short-chain fatty acids also have anti-inflammatory effects and are able to regulate metabolic disorders such as insulin resistance and high cholesterol; modulate the immune system; and influence gut hormones. (16) The gut microbiome can even alter the expression of human genes and influence the central nervous system causing changes in behaviour, cognition, learning and memory (15).

No matter how we come into this world we will receive a community of microbes to start us on the path of life. We leave the womb almost germ-free but, as we enter the outside world, we come into contact with the vast variety of microbiota that live on the Earth. In the weeks leading up to the birth of a baby, the mother’s body prepares for the event by increasing the population of helpful bacteria in her microbiome. For example, lactic-acid-digesting bacteria, needed by the newborn to digest breast milk, increase in number in the vagina of the mother during this time (17). During a normal birth in a hospital, babies collect the microorganisms from their mother’s birth canal, although some microbes are also picked up from the surrounding hospital environment and the attending personnel. A caesarian birth results in the child receiving a less healthy microbiome that comes from the skin of both the mother and the health professionals attending the birth and from the hospital environment. In some hospitals this situation is improved by swabbing the baby from head to toe with fecal or vaginal secretions from the mother to create a healthier microbiome for the baby. A home birth from a healthy mother likely provides the best start to a baby’s microbiome as the child will obtain its mother’s microbes as well as other microorganisms present in the people and the home in which the child will live and grow. (17)

Once out in the world, we increase the diversity of our microbiomes through breastfeeding, the best source of healthy microbes for a newborn, and also from our environment, our family and friends and even our pets (1). In addition, lifestyle factors have a major influence on the make-up of our microbiome. A healthy microbiome is highly diverse, stable and resistant to changes caused by elements such as stress, infections, antibiotics and immunosuppression. (18)


Still to come…
In the following parts of this article on the gut microbiome we’ll look more deeply into the activities of our microbiome and how our diet and lifestyle can support or discourage this complex system.



1 Kubes, P., McCoy, K. Lecture from the Western Canadian Microbiome Centre. Cumming School of Medicine, University of Calgary. The Human Biome. 2017


3 Sender, R., Fuchs, S., Milo, R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol. 2016 Aug; 14(8): e1002533.

4 Stephen, A.M., Cummings, J.H. The microbial contribution to human faecal mass. J Med Microbiol. 1980 Feb;13(1):45-56.



7 Abeles, S.r., Pride, D.T. Molecular Bases and Role of Viruses in the Human Microbiome.
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8 Roossinck, M.J. Changes in Population Dynamics in Mutualistic Viruses versus Pathogenic Viruses. Viruses. 2011; 3(1): 12-19.

9 Villareal, L.P. The source of self: genetic parasites and the origin of adaptive immunity. Ann NY Acad Sci 2009; 1178-194-232.

10 Tierney, B.T., Yang, Z., Luber, J.M. The Landscape of Genetic Content in the Gut and Oral Human Microbiome. Cell Host and Microbe. August 14, 2019; 26(2): P283-295.e8.

11 Saey, T.H. September 17, 2018. A recount of human genes ups the number to at least 46,831. Science News.

12 Grice, E.A., Segre, J.A. The Human Microbiome: Our Second Genome. Annu Rev Genomics Hum Genet. 2012; 13: 151–170.

13 Boulangé, C.L., Neves, A.L., Chilloux, J., Nicholson, J.K., Dumas, M.-E. Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Medicine. 2016;8:42.

14 Hehemann, J.-H., Correc, G., Barbeyron, T., Helbert, W., Dzjzek, M. Michel, G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature. 2010;464:908-912.

15 Lima-Ojeda, J.M., Rupprecht, R., Baghai, T.C. I Am I and My Bacterial Circumstances: Linking Gut Microbiome, Neurodevelopment, and Depression. Front. Psychiatry. 22 August 2017;

16 Oliphant, K., Allen-Vercoe, E. Macronutrient metabolism by the human gut microbiome: major fermentation byproducts and their impact on host health. Microbiome Journal. 2019; 7:91.

17 Blaser, M.J. The Human Microbiome Before Birth. Cell Host and Microbiome. November 9, 2016;20(5): 558-560.

18 Sidhu, M., Van der Poorten, D. The gut microbiome. Aust Fam Phys 2017; 46(4):206-211.

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My name is Debra Harley (BScPhm) and I welcome you to my retirement project, this website. Over the course of a life many lessons are learned, altering deeply-rooted ideas and creating new passions.

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