Your Microbiome: The Community Inside You

06/06/2017 11:06 am ET Updated Jun 21, 2017

We hear a lot about gut health and so-called “good” bacteria these days, but what do those things really mean? In just about every instance, people are referring to the microbes that inhabit your gastrointestinal tract, an entire community of microscopic organisms referred to as the microbiome. We all have one, and believe it or not, these microbes have co-evolved along with us so that we enjoy a symbiotic relationship with the bacteria, fungi, protozoa, and viruses living in (and also on) our bodies.

Not only is the microbiome an entire ecosystem living within your digestive system (about 95% of the microbes in and on your body are located there) — it’s actually the biggest part of you. For many years, scientists believed that 90% of the cells in our bodies were not human cells but microbes; they would often say that microbes outnumber human cells by an astounding rate of ten to one! However, an August 2016 study by Sender, Fuchs, and Milo adjusted that figure a little. We’re still majority microbes, but the number is about 40 trillion microbes to about 30 trillion human cells. And even though the gut microbiome is constantly in flux and always changing, for reasons we’ll get into in a minute, the number of our human cells almost always remains lower than the number of microbes we harbor.

The microbiome is certainly a hot topic as of late. Dozens upon dozens of articles in lifestyle magazines and on nutrition websites offer superficial discussions on the microbiome, including what the average person should know about it to live a healthier life. And the more highbrow channels have been discussing it in detail as well; there are roughly a dozen TED and TEDx talks on the human microbiome and microbes that inhabit the gastrointestinal tract. Plus, in May of 2016, the US announced the National Microbiome Initiative, which provided priority funding to scientists and researchers so that they could further study this important world of microbiota living within our bodies. Clearly, it’s not a topic that’s going to quiet down anytime soon.

Still, the human microbiome is not at all a new discovery. Although the term “microbiome” was coined quite recently — in 2001, by the late scientist Joshua Lederberg — humans have actually known about the existence of the microbiome, or the fact that humans harbor microbes in and on their bodies, since the 1600s. That’s when Dutch scientist Antonie van Leeuwenhoek first observed the microorganisms that he had scraped from his teeth using a primitive homemade microscope. Widely considered to be the father of modern microbiology, much of van Leeuwenhoek’s work, especially in the field of microorganisms, remains relevant even today.

What is a new discovery, though, is how much these microbes affect our everyday lives. We’re also just coming to a full understanding that not only are these microbes actually “good” rather than harmful, but that our own health is greatly dependent on their health! These microbes aren’t germs, in the common sense of the word — these are microbes that are essential for our wellbeing. For many people, it really may not seem like a big deal: how can these tiny microorganisms have such a big impact on you and your life? Still, a great deal of recent scientific study has revealed that in fact, the microbiome can have a tremendous effect on many aspects of your life. Believe it or not, your gut microbiome plays an enormous role in your overall health as well as your overall happiness: everything from body shape to body function to brain function to emotional health and more.

How Scientists Are Learning More

Until quite recently, not a lot was known about the inner workings of the human microbiome. However, that all changed, thanks to the innovation known as the SHIME model in the early 1990s. An acronym for Simulator of Human Intestinal Microbial Ecosystem, the SHIME is a modular gut model that mimics how the entire human gastrointestinal tract works. It has components that represent and simulate conditions in the stomach, the small intestine, the ascending colon, the transverse colon, and the descending colon. In a lab environment, the SHIME can be “fed,” much like a person would feed him or herself, and then tested at every section of the imitation digestive tract. This allows researchers to see how the microbiome of the tract is affected in real time. It’s truly a remarkable tool that allows researchers to determine how the microbes in the gut affect and regulate major systems in the human body: things like mood, appetite, health, immunity, and much more.

Currently, there are just two SHIME models in the US; one is at the US Department of Agriculture (or the USDA), and the other is at Rutgers University in New Brunswick, New Jersey. However, the most referenced SHIME model and study is from Ghent University in Belgium. In this well respected research, which was published in 2015 as a chapter in the book The Impact of Food Bioactives on Health, scientists Van de Wiele, Van den Abbeele, Ossier, Possemiers, and Marzorati outline the history of SHIME model, including different points in its development and the notable features that make it unique and better than previously used models of the human gut. They also discuss various protocols for future SHIME experiments, including the modifications that can be made at different stages. Ultimately, the goal for this and all microbiome research is to pinpoint this hidden ecosystem’s role in keeping humans healthier.

What the Microbiome Affects

Within our bodies, our microbiome affects just about all of our physical and emotional capabilities. Again, it may seem surprising that microorganisms can play such a major role, but they do. For example, the microbiome gives us the ability to effectively digest what we eat. We’re not born with the ability to digest most foods, but through the development of our own personal microbiome, we acquire the microbes necessary to digest foods like dairy products and certain plant fibers.

There’s also a well-established connection between a person’s microbiome and whether or not they’re going to be obese, according to an often cited 2006 study by Turnbaugh, Ley, Mahowald, Magrini, Mardis, and Gordon. In fact, according to scientists like the University of California San Diego’s Rob Knight, one of the leading researchers studying the microbiome today, scientists can tell with 90% accuracy whether a person is lean or obese just by looking at their gut microbes.

The gut microbiome can also have an impact on how predisposed a person is to things like allergies and asthma. Additionally, an unhealthy microbiome can lower a person’s immune system and make them more prone to sickness and disease, especially autoimmune diseases. More recent studies point to the role of the gut microbiome in regulating cholesterol, detoxifying any ingested poisons, and even how effective certain medications are in helping your body suppress uncomfortable symptoms and fight illness.

The Role of Diet

Nutritionists, dieticians, and food enthusiasts everywhere have quoted the wise words of food writer Michael Pollan since they were first published as the opening sentences of his 2009 book In Defense of Food: “Eat food. Not too much. Mostly plants.” As it turns out, this is also sound advice for keeping your own personal microbiome happy and healthy, as the types of microbes in your gut will follow the types of foods you eat. According to a 2015 study by Conlon and Bird, a healthy biome can be cultivated by eating a diet rich in complex carbohydrates, lean proteins, and healthy fats such as nuts and avocados. Additionally, limiting your intake of refined sugars can promote a healthy microbiome, as can regularly eating pre-biotic foods like vegetables, whole grains, and legumes as well as fermented, probiotic foods like sauerkraut and yogurt, which actually have their own beneficial biome.

Also, as mentioned above, the types of microbes that you harbor in your gastrointestinal tract can also have an impact on your body shape and weight. A 2010 study by De Filippo, Cavalieri, et al demonstrated that obesity is largely a result of our microbiome and not as much of a result of what we eat. It may be true that our diet shapes our microbiome, but our microbiome shapes how our bodies are able to use the food we eat to keep us healthy.

The Microbiome and the Brain

In recent years, scientists have shown that there’s a link between a person’s microbiome and their mood, including how likely they are to suffer from emotional disorders such as serious depression. A 2011 study by Kinross, Darzi, and Nicholson published in Genome Medicine noted that “the absence of gastrointestinal microbes in mice results in reduced production of brain-derived neurotrophic factor in the cortex and hippocampus, and an exaggerated hypothalamic-pituitary-adrenal axis response to stress.” In other words, fewer beneficial microbes have negative implications on mental health. It also suggested a link between microbes and autism, noting that the presence of a one specific microbe is higher in patients on the autism spectrum. While more research is clearly needed to establish more definitive links, these preliminary findings are fascinating, as the idea that gut microbes can affect mental health may lead to new and more innovative forms of treatment for individuals who suffer from certain cognitive conditions.

The Hygiene Hypothesis

What’s damaging our individual microbiomes? One possible explanation is known as the hygiene hypothesis — essentially, our lives are too clean, too sanitized, and too hygienic to allow these good microbes to grow in sufficient enough numbers to keep us as healthy as we should be. Think of our current standards of cleanliness: we’re taught to wash our hands very regularly with soap, most of us shower or bathe at least once a day, and when we don’t feel quite clean enough (which is often) we douse our hands and everything else in anti-bacterial sanitizer. Plus, we’re more removed from where our food comes from than we’ve ever been before, which means we’re more removed from plants and dirt and the beneficial microbes to which we’re exposed during planting and harvesting. All of this cleanliness affects our microbiome, and not in a good way.

Other Microbiome-Disrupting Practices (and How to Reverse Them)

As mentioned above, eating a healthy diet is a pro-active way to keep your microbiome healthy. Getting enough sleep and enough activity will also go a long way in keeping your microbiome healthy. Additionally, high levels of stress can be damaging to your microbiome; lowering your stress can help tremendously.

A huge microbiome disruptor is the use of antibiotics, especially among children. While these drugs are wonderful for fighting bacterial infections, they can also effectively destroy a healthy microbiome and lead to a handful of other negative health implications. In fact, it’s been shown that children who take a course of antibiotics in the first six months of their lives are more likely to become obese.

Indeed, they can be quite damaging for individuals who have less than stellar microbiomes to begin with, as their microbiomes are much slower to recover than that of an otherwise healthy person who takes the occasional prescribed antibiotic. A person with a poor microbiome is often more likely to get sick, and the more antibiotics he or she takes, the less the microbiome is able to fully recover. In extreme cases, a poor microbiome hit with repeated cycles of antibiotics can result in an infestation of Clostridium difficile, or C. diff. colitis, a specific strain of bacteria that can cause severe diarrhea and inflammation.

While avoiding antibiotics at all costs may not be practical, as they are quite effective as fighting certain types of infections, it’s important for patients to talk to their doctors about being judicious with these drugs. And in severe cases, new treatments like Fecal and Microbiota Transplants (typically referred to as FMT and often just called fecal transplants) offer a relatively new but promising way to improve the microbiome, cut down C. diff infestations, and even cure diseases from irritable bowel syndrome and obesity to autism and clinical depression. It’s not as straightforward as it sounds, or, frankly, as gross as it sounds: FMT is moving healthy microbes from a donor into an ill recipient, typically via an enema. Scientists like neuropath Dr. Mark Davis likens the procedure to moving healthy soil to a burn site to replenish plant life in the area: it puts the healthy microbes into an otherwise barren space and encourages positive growth.

Weed, Seed, and Feed

What can you do to promote good gut health and cultivate a healthy microbiome? After all, this is a small ecosystem within your body, and you’ve got quite a lot of control over how healthy it is and, by extension, how healthy you are. Noted microbiome expert Dr. Robynne Chutkan sometimes refers to the microbiome as a” gut garden,” and this is an apt metaphor for not only what the microbiome is, but how you can impact it.

As discussed above, the types of foods you eat directly affect what kinds of microbes you have: the good kind that will keep you healthy, or the harmful kind that will leave you predisposed to illness. So, much like you would care for a plant or a tree, you’ve got to weed, seed, and feed your microbiome. First, you want to weed out the foods that negatively impact your microbiome, including sodas, artificial sugars, and processed foods. You’ll also want to eliminate excess use of antibiotics, since they kill off many of the beneficial microbes, and it’s a good idea to limit damaging lifestyle choices that diminish your overall gut health. Next, to keep your microbiome healthy, feed it with prebiotics so that it may flourish; these include bananas, onions, and raw garlic. Finally, seed your microbiome regularly with probiotics, such as yogurt, kombucha, and sauerkraut. Many organizations around the world are leading the discussion on how to help improve your microbiome. Much like a garden, you can weed, feed and seed your microbiome, to keep your gut—and overall—health in good shape.

Respect the Microbiome!

It’s more than half of who you are, so you want to ensure that you take good care of your microbiome, quite simply, by taking good care of yourself. What’s more, look for the role of the microbiome to be further fleshed out and the insistence that it be cared for increased in the future. Indeed, this could mean a whole new way that we think of wellness, sickness, and treatment for the next generation. Will microbe-based therapies replace conventional surgical and medical approaches? It’s hard to say for sure, but these treatments are currently being studied, and they clearly present advantages, as they’re a much less invasive, more of a way to treat the problem and not the symptoms.

For now, one thing is clear: you’ve got to respect your microbiome.

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