The Microbiome: Our Symbiotic Partner in Health | VitaMedica
The Microbiome

The Microbiome: Our Symbiotic Partner in Health

By David H. Rahm, M.D.


 Q: It seems like each week a new study or article comes out talking about the importance of the microbiome. What exactly is the microbiome and why are we hearing so much about this topic lately?


Your observation is correct. The microbiome (defined as the collection of microbes that inhabits the human body) is the subject of intense study and discussion these days. This is because we now recognize the significance of the various microbial communities that reside on and in our bodies and how these microbes can have far reaching effects on our health.


To help you better appreciate this vast and diverse ecological system, below I’ve answered some commonly asked questions, starting with a definition of the microbiome.


What is the Human Microbiome?

In biology, a biome is a self-contained ecosystem, where all the organisms can interact with each other and the environment in which they live. For example, a rain forest is a biome, but it is made of smaller biomes, such as a tree which is a biome for insects, and a single insect is a biome for bacteria. Accordingly, these smaller biomes are typically called microbiomes. A microbiome is a small (micro) version of this larger phenomenon – a miniature world within a larger world.


While there are hundreds of thousands of microbial species living in very different types of environments on Earth, the human microbiome is comprised of just those found in and on the average human body.


It’s amazing when you consider that the human body contains trillions of cells that are not human but microbial. Like human cells, these microbes have genes which instruct cell activity. This massive microbial community that inhabits the body and their collection of genes is called the human microbiome.


When you consider that a person inherits about 20 thousand human genes and their microbiome includes around 8 million genes, you can see why the microbiome is often referred to as the second genome. Based on these large microbial numbers, you might argue that we are more microbe than man.


The combination of human genes and microbial genes and the way they interact leads some experts to regard us more as “superorganisms” rather than simply human.


How Big is the Human Microbiome?

Whether you count the number of organisms or examine its diversity, the human microbiome is large! The microbiome is teaming with trillions of bacteria. In fact, the 100 trillion bacterial cells outnumber human cells by a factor of ten.


Although these microbes are invisible to the eye, their numbers add up. In fact, the average human microbiome weighs an estimated 2.5 pounds or about 1-2 percent of an adult’s body mass. In volume, the microbiome would fill about 3 pints.


What are the Resident Microbes?

While the human microbiome is comprised primarily of bacteria, it also includes numerous and diverse single-celled organisms called archaea plus fungi and even viruses. Like a fingerprint, the collection of microbes is unique to each individual. We know quite a bit about the bacteria that reside in the gut but far less is known about the activity of these other organisms.


Where Do the Microbes Reside?

Wherever the human body is exposed to the outside world is where microbial communities reside. The skin, nostrils, mouth, intestines, colon and urogenital tract are several areas of the body these microorganisms set up residence.


Is the Microbiome Diverse?

The microbes are a highly diverse group, with some 300 to 1,000 species belonging to different families that are adapted to live in and on the human body.


Just like different plants favor certain areas of a garden, distinct communities of microbes thrive in different regions of the body.   For example, the microbes that flourish on the skin are quite different than those that live in the deep folds of your intestines. But, the microorganisms of various body sites are similar in everyone. So, your skin microbes are likely to be more similar to another person’s skin microbes but very different than the microbes which inhabit your colon.


Like communities in your neighborhood, microbial communities differ in size and density. Some communities are sparse while others are quite dense. The gut contains the largest, densest, and most diverse microbial community in the human body. The reason is due to surface area as microbes coat and fill-in the interior spaces of the intestines and colon. If you were to flatten out the intestines, the area would cover the size of a tennis court!


Despite all of this diversity, scientists have discovered that gut bacteria can be classified into just three gut types or enterotypes regardless of age, gender, body weight and nationality. The greatest impact on the gut type is the kind of diet that is followed, with differences showing up in vegetarian and predominantly meat-eating populations.


Why is Diversity So Important?

An advantage of having a diverse microbiome is similar to having a diverse financial portfolio – it buffers you from losses in bad times. From a biological standpoint, a diverse ecosystem is generally more resilient.   And, people with large and diverse bacterial populations in their digestive tracts tend to be less prone to obesity, immune problems and other health issues than people with diminished microbial diversity.


Unfortunately, our microbiome is becoming increasingly less diverse. Known as the “disappearing microbiota hypothesis” scientists speculate that modern health practices such as bottle-feeding and Caesarean section delivery, plus lowered exposure to “germs” early in life coupled with the overuse of antibiotics and the Western diet are contributing factors to reduced microbial diversity


[See: Antibiotics & Probiotics: What You Need to Know]


What is the Human Microbiome Project?

Many of the discoveries of the human microbiome – learning that each individual harbors far more bacterial strains than previously believed or finding the presence of disease-promoting bacteria that don’t make people ill – have been revealed through the Human Microbiome Project (HMP).


This 8-year, $194 million study funded by the National Institutes of Health, has involved over 200 scientists in 80 institutions. The HMP is focused on studying the microbes residing in five body areas, including skin, mouth, nose, colon, and vagina.


The first phase, which started in 2007, was tasked with identifying and characterizing the microorganisms which are found in healthy humans. Nearly 300 healthy individuals participated in the project. Initial findings from the Human Microbiome Project were published in the June 2012 issue of the journal Nature.


Now that a baseline of what is a “normal” microbiome has been established, scientists are shifting their focus to better understand how changes in the microbiome are associated with disease.


What is the American Gut Project?

The Human Microbiome Project and other microbiome projects worldwide have laid an important foundation for understanding the collections of microbes that inhabit all of our bodies. Until recently, opportunities for the public to get involved in such research have been limited.


The American Gut Project, initiated in 2012, gives everyone an opportunity to participate and to compare the microbes in their gut to those in the gastrointestinal tract of thousands of other people in the U.S. and around the world. The American Gut Project is also built on open-source, open-access principles.   To date, scientists have sequenced microbiota samples from more than 3,000 American adults and children. To see what they have learned so far, click here.


You (or your pet!) can participate in the American Gut Project by providing a donation (the price varies depending on how many sites you survey). You’ll need to track your diet for 7 days and wait another 6 to 9 months to get your results. Yvette La-Garde, VitaMedica’s Director of Education, participated in the American Gut Project. To see her results, click here.


A new company called uBiome lets you see the species of bacteria in your microbiome and how it compares to others in the study. You can order a kit to sample your microbiome for around $100 and obtain the results in about six weeks.


What is the Role of the Microbiome?

Given its range of metabolic activities, the human microbiome is likened to a body organ. But, unlike say a heart or liver, the importance and function of the microbiome is just beginning to be appreciated.


It has long been known that bacteria are involved in certain body processes such as digesting food and producing vitamins, but the microbiome appears have a much broader impact on our health than was previously realized.


Importantly, the community of microbes in an individual may influence their susceptibility to certain infectious diseases, as well as contribute to disorders such as obesity and diabetes. Changes in the microbiome may also contribute to the development of some chronic illnesses of the gastrointestinal system such as Crohn’s disease and irritable bowel syndrome. Some collections of microbes can determine how one responds to a particular drug treatment. The microbiome of the mother may even affect the health of her children.


[See: New Discoveries about the Microbiome]


What are the Key Functions of the Gut Microbiome?

Given their predominant location in our digestive tract, it should come as no surprise that the gut microbiome plays a key role in digestion. The beneficial bacteria help us to extract nutrients from the food we consume as they feed off complex carbohydrates that we can’t digest. The resulting end products help feed the cells that line the intestinal wall and assist the body in absorbing minerals like calcium, magnesium and iron. The microbes in our gut also manufacture some vitamins including vitamin K, B12 and biotin.


With over 70% of the body’s immune cells located in the digestive tract, the microbiome plays a crucial role in immunity. Our beneficial bacteria protect us from pathogens, viruses and bad bacteria, making our digestive tract inhospitable to these invaders.


Perhaps less well-known is that gut bacteria produce hundreds of neurochemicals that help regulate learning, memory and mood. For example, 50% of the body’s dopamine and 95% of the body’s serotonin (the body’s feel good neurotransmitter) is produced by the microbiome. Remarkably, in animal and human studies, supplementing with “good bacteria” lifted depression and reduced anxiety. Studies have also provided further evidence that early exposure to normal gut bacteria is important for brain development and behavior.


How Does the Microbiome Evolve?

Prior to birth, a newborn’s digestive tract does not harbor any bacteria. These beneficial microorganisms are acquired from the mother through the birth canal. Notably, babies born via Cesarean section acquire more of the bacteria found on the parent’s skin and lurking in the hospital. A bacterial species that is prevalent in newborns is named L. johnsonni, a helper that prepares the infant’s gastrointestinal tract to digest breast milk.


Breast milk contains over 600 species of bacteria as well as sugars that cannot be digested by the infant. These large sugar molecules or oligosaccharides nourish a beneficial bacterium called B. infantis which is crucial to the development of the infant’s digestive tract and helps keep the infant healthy by crowding out “bad” bacteria. Not surprisingly, the gut of bottle-fed babies is not optimally colonized given that these formulations contain neither prebiotics (the food) nor probiotics (beneficial bacteria).


B. infantis which belongs to a group of bacteria called Bifidobacterium makes up the largest group of bacteria in the intestines of babies. But as we age, the percentage of this group in our intestinal tract decreases.


During the first year of life, an infant’s immune system develops and this early education on who’s friend or foe has implications later in life. Disruption of the intestinal tract at an early age can have far reaching effects later in life. Many researchers have advised that children who take high levels of antibiotics are at greater risk of developing allergies and asthma later on. A recent study in mice showed that when given antibiotics early in life, the gut microbes normalize but the effects on metabolism are permanent leading to a greater chance of becoming obese later in life.


By age 3, the bacteria that reside in our gut resembles that of the adult community or locality in which we live.   Although the composition of bacterial species may be subject to transient changes, the unique composition of an individual’s microbiota remains remarkably constant over time. Importantly, our microbiome is likely to be similar to that of a sibling or someone we live with demonstrating the role that genetics and environment play in shaping our microbiome.


Watch this visual representation from the Human Microbiome Project to see how the microbial community changes in a newborn to age 3 where it resembles that of the adult’s gut community.


What Causes Microbial Imbalance?

While our mix of bacterial species stays remarkably the same over time, environmental conditions including stress, drugs, gastrointestinal surgery, infections and toxic agents, can alter our microbial balance.


The most common cause of dysbiosis, or the imbalance of bacteria in the microbiome, is antibiotics.   Indeed, some bacteria like Clostridium difficile are adapted for invading and establishing themselves in disrupted ecosystems. The widespread use of antibiotics in the West may explain why we have a lower diversity of microbes than rural populations living in other parts of the world.


Once C. difficile dominates it can be difficult to resolve. Bacteriotherapy with fecal transplants, uses a small amount of fecal matter from a healthy individual and transplants it to a sick patient to restore the gut microbiome. This new therapy has a greater than 90% success rate in treating this type of bacterial infection.


What About Diet and the Microbiome?

Throughout time, the genes we inherited from our ancestors have co-evolved with the bacterial genes that are present throughout our digestive tract. And, while the genes we inherit are relatively fixed, it increasingly appears that it may be possible to reshape the genes governed by our resident microbes.


The reason? Microbes evolve so quickly (their average life expectancy is about 20 minutes), that their genetic composition can change rapidly – in as little as 24 hours. This allows the bacterium to adapt quickly to changes in the environment. This tremendous flexibility allows us to respond to threats and opportunities that we did not evolve in our own genome.


This evolutionary advantage helped us thrive when food was scarce. Due to their short lifespan, bacteria could respond quickly to dietary changes and this helped us survive. Today, the problem is that the Western diet, featuring highly-processed, high glycemic load, calorie-dense foods, feeds our stomach but starves the important residents in our digestive tract. In particular, a lack of fiber is testing how quickly our microbiota can adapt to these dietary changes.


Studies done in animals and in humans have demonstrated that the microbiome can be greatly influenced by what is eaten. These studies have shown that a typical Western diet that is high in fat and simple carbohydrates, and low in fiber encourages a type of “obese” bacterial family to populate our GI tract. Conversely, a diet high in plant-based foods and fiber encourages a type of “slim” bacterial family to develop in our digestive tract.


In studies, when animals were switched from a low-fat, plant-rich diet to a high-fat, high-sugar diet, the microbiota was changed after only one day on the junk food. Like their human counterparts, mice fed a Western diet became obese.


How do I Restore My Microbiome?

Whether you’ve been on a course of antibiotics or have been splurging on junk food, the good news is that within a matter of weeks, you can begin to restore your microbiome by eating a healthy diet.


A healthy diet features complex carbohydrates (vegetables and fruit) plus some lean meat and mainly unsaturated fats. But, if you want to ensure a robust microbiome, be sure to eat plenty of foods that contain prebiotics. These non-digestible fibers nourish the beneficial bacteria and can be found in a number of vegetables, fruits, grains and roots. Good sources of prebiotics include artichoke, asparagus, bananas, berries, carrots, garlic, jicama, leeks, legumes, onion, radishes and tomatoes.


David H. Rahm, M.D. is the founder and medical director of The Wellness Center, a medical clinic located in Long Beach, CA. Dr. Rahm is also president and medical director of VitaMedica. Dr. Rahm is one of a select group of conventional medical doctors who have education and expertise in functional medicine and nutritional science. Over the past 20 years, Dr. Rahm has published articles in the plastic surgery literature and educated physicians about the importance of good peri-operative nutrition.