Bacteria and other microbes were once thought of as dangerous little bugs that caused infection; however, now we know that only a small number of them are actually pathogenic. Most microbiota present on or in the human body are symbiotic species that actually help us maintain, and even boost, our health. We talked to the experts to get the lowdown on your microbiome.

The human microbiome encompasses all of the commensal microorganisms that inhabit your body. According to Dr. Kathy McCoy, scientific director of the International Microbiome Centre and professor in the Department of Physiology and Pharmacology at the University of Calgary, “Any part of the body that is exposed to the outside environment is going to have a microbial community that lives on it. That includes, of course, your digestive tract because, if you think about it, it’s actually an extension of the outside of the body, basically a tube that runs from your mouth to your anus.” The human microbiome also includes other mucosal and surface environments, such as the skin, eyes, mouth, nose, lungs and urinary genital system.

The microbiome has a profound impact on the internal body. Our gut microbial communities help us digest food, regulate our immune system, influence our metabolism and protect against other bacteria that cause disease. Generally, the greater the species richness and diversity of a person’s microbiome, the healthier it is. “We want to be nice to our microbiota and take advantage of this mutualism,” says Dr. Anita Kozyrskyj, principal investigator of the Synergy in Microbiota Research program (SyMBIOTA) and professor in the Department of Pediatrics at the University of Alberta. “What’s good for them is good for you.”

Mostly microbes

As Walt Whitman so eloquently put it, “I am large, I contain multitudes.” He was right: The human body hosts trillions of individual bacteria, fungi, viruses and other microscopic organisms. These microbes account for at least half of the total number of cells in the human body. Genetically speaking, the body encodes some 20 thousand human genes, while the microbiome encodes more than two million! “You might say that we are half-human and half-microbial, and that’s not a bad thing. We have co-evolved with our microbes and found a way to live together in synergy. Together we are a superorganism,” explains Dr. McCoy.

Humans are not born with a fully formed gut microbiome, but rather the microbial community develops over the first year of an infant’s life, undergoing substantial changes as the body learns to recognize bacterial friends and foes. The baby is initially colonized by oxygen tolerant (aerobic) microbiota, such as Proteobacteria (some of which can be pathogenic in adults), as well as more familiar species of Lactobacilli. Over time the concentrations of these types of microorganisms diminish and species of oxygen intolerant (anaerobic) bacteria—such as Bifidobacteria, Bacteroides and Firmicutes—take their place and become the typical constituents of the human microbiome. According to Dr. Kozyrskyj, “At about one year of age, your microbial community more or less resembles what it will be for the rest of your life. Some changes continue over the next couple of years, but by about three years of age, the major changes have been implemented in terms of your signature microbiome, resulting in what we might call a unique fingerprint of microbiota that is yours to keep for the rest of your life.”

Growing pains

The dynamic and evolving process of microbial colonization begins at birth, and the first exposure generally comes from the mother’s vaginal canal and gastrointestinal tract. Babies born by natural birth get a microbial boost from their mothers’ bodies that is not reflected in newborns delivered by Caesarian section; in particular, there is a substantial reduction in the group of microbes called Bacteroides. Breast milk is another important source of microbial goodness, such as Bifidobacteria, for developing infants. But that’s not all. Breast milk also contains oligosaccharides— a type of carbohydrate— that the baby’s body doesn’t use; rather, it is solely a source of nutrients for the developing community of microbiota. These initial microbial exposures set the stage for an infant’s development.

“As the infant’s gut microbiota develops, so too does its immune system. The microbiome creates signals and educates the immune system so it does not overreact to friendly bacteria or foods that are good for the baby,” explains Dr. Kozyrskyj. While brain development begins in utero, there is likewise a connection between the microbiome and the ongoing development of a baby’s brain. Dr. Kozyrskyj states, “Bacteria such as Bacteroides are really important at one year of age in terms of brain development, due to the production of a group of sophisticated metabolites called sphingolipids, which are absorbed by the body and are connected to neural development.”

External factors

Because the microbiome inhabits areas of the body that are exposed to the outside world, there is a plethora of environmental determinants that can impact it both positively and negatively. Changes in the western lifestyle over the last 60 years have had a profound effect on the human microbiome; for example, increased antibiotic use and consumption of processed foods, urbanization and a separation from natural environments. “We’ve decreased the diversity and richness of our microbiome and modified its composition,” says Dr. McCoy.

An individual’s microbiome remains relatively stable throughout life; however, diversity tends to decrease as we age. Changes to your environment, stress, lack of sleep, medication and even infections and inflammation can all result in a decrease in microbial diversity. A course of antibiotics, major dietary changes and even vigorous cleansing of the skin can also have a significant impact on the microbial community and temporarily alter it. In most cases, the microbiome can bounce back and the original composition of microbiota will return when the original conditions resume, but some microbes can be permanently lost.

Under maintenance

One way to maintain microbial diversity in the gut is through diet; this is where pre- and probiotics come in. Prebiotics are substances, such as fibre, which provide sustenance for the microbiota that live in the gut. Probiotics, on the other hand, are microbes that are thought to be beneficial for health, such as Lactobacillus and Bifidobacterium—naturally occurring species that reside in the gut but may also be obtained by eating fermented foods. Making healthy food choices, such as whole foods, antioxidant-rich fruits and vegetables and incorporating live bacterial cultures found in fermented foods or probiotic supplements, can help produce an environment that encourages the growth of helpful bacteria. Likewise, avoiding excess sugar, artificial sweeteners and processed foods is another way to support gut health.

It’s not all about food—proximity to nature and spending time in green spaces also benefits microbial diversity in both developing children and adults. For example, in a recent study, Dr. Kozyrskyj and her team found that living close to natural green spaces benefits the bacterial diversity of formula-fed infants living in urban areas. “It’s exciting because it is an intervention for 100-percent formula-fed infants (who are at greater risk for health consequences) that could result in a gut microbiota that is more similar to breastfed infants,” says Dr. Kozyrskyj. What’s more, this effect was especially pronounced in those homes that had a pet dog. It has been known for some time that living with a pet is associated with a reduced risk of allergic disease but it’s now also understood that dogs, specifically, help increase human microbial diversity. And it’s not just microbes; dogs sometimes bring in trace elements and minerals, some of which are used as food by our microbiomes.

Balancing act

There is a strong suggestion that loss of microbial diversity is linked to various chronic diseases, from cancer to autoimmune and allergic diseases, as well as metabolic and neurological disorders. The state of imbalance in a person’s microbiome is called dysbiosis. It is often characterized as a change or reduction in the diversity of one’s microbial community that allows for the proliferation of opportunistic bacteria that can become pathogenic in certain conditions.

Clostridium difficile (C. diff) is one such opportunistic pathogen that basically takes over the gut microbial environment. It produces toxins and attacks the colon; in some cases, it can even be fatal. It has traditionally been treated with antibiotics; however, many individuals now harbour antibiotic-resistant C. diff. Fortunately, microbiome research has made advancements in treatment and found a solution. Fecal microbial transplantation (FMT) produces dramatic results and has revolutionized the treatment of C. diff. A transplant from a healthy donor effectively cures the infection by replacing the dysbiotic microbiome with a healthy, diverse one. Dr. McCoy characterizes FMT as “the poster child of successful microbial therapy,” adding that more precise microbial therapies are currently in development and testing stages.

While diet is one way to potentially alter our microbiomes for the better, there are other novel applications of microbial therapy being explored for IBS, IBD, diabetes, Parkinson’s, MS and cancer. “One of the most exciting things about the microbiome is that it is a modifiable factor,” explains Dr. McCoy. “It’s not set in our genes— which we cannot change—but we may be able to manipulate the microbiome to promote health and treat disease.”

Gut feeling

Dr. McCoy likens the microbiome to a “forgotten organ,” explaining that “it has always been there, but it was ignored or thought to be unimportant in the past because it’s not technically in our bodies. But if you think of it as an organ, you can also think about what the organ needs to be healthy.” The microbiome works as a kind of interface between the external environment and the body, taking in information and relaying it to the immune system and other sites. “At the centre of the body is the gut microbiome and it has this amazing influence on areas that are very distal from it. Either by modulating immune cells or producing molecules and metabolites that impact various sites in the body,” says Dr. McCoy. The gut microbiome uses the food we eat to produce small molecules that are circulated and absorbed throughout the body. You may have heard of the gut-brain axis that allows for cross-communication between the gut and the brain… but it’s not the only one. Research is now focusing on how the gut microbiota and its products also communicate with the lungs, skin and vagina, for example. While live microbial communities are separated from the internal body through mucosal membranes, their products, these small molecules, are able to pass through and are critical to cross-communication between the gut microbiome and other organs in the body.

EXPERT APPROVED TIPS to nurture your microbiome

• Eat a variety of green vegetables and get a healthy dose of fibre.
• Add fermented foods to your diet to supplement the live bacterial cultures in your body.
• Spend more time in nature and let your kids play in the dirt.
• Consider adopting a pooch to add to your family’s microbiota.
• Only take antibiotics when they are absolutely necessary.
• If possible, when pregnant, avoid an unnecessary Caesarian section.
• If you can, breastfeed your baby, even for a short period of time.