Lynn Bry, MD, PhD
The human microbiome is the compendium of organisms that live on us and in us. We like to say that the human body contains one times ten to the fourteenth cells. Fewer than 10 percent of these cells actually belong to you; the other 90 percent of cells represent bacteria and other organisms that are living in your gut, in your mouth, and on your skin. They in total comprise the human microbiome.
The organisms in the microbiome are quite diverse. You literally have many hundreds of species that are living on you at any particular time. They include organisms we’ve heard of, such as escherichia coli, but they also include a number of anaerobes. These are organisms that don’t grow well in the presence of oxygen. We also have some yeast. We have potentially viruses or bacteriophages that are also constituents of the microbiome.
In terms of where the organisms are, most of them are in your gut, so that would be your oral cavity through your intestines. That is the location of about 99 percent or more of the organisms. The rest of them are living on your skin, in your genitourinary tract, and on other bodily surfaces.
The microbiome actually impacts us in many ways. We are born sterile at birth and thereafter are rapidly colonized. Microbes provide important nutrients for us. For instance, every baby who is seen at Brigham and Women’s Hospital receives a shot of Vitamin K soon after birth. This is a vitamin that is required for appropriate clotting of the blood. It turns out that microbes in our gut produce this vitamin and when you’re not colonized with microbes you can’t produce the vitamin. That is just one example of micronutrients that microbes are producing that are helpful to us.
Microbiota also produce a variety of B vitamins, help in digestion and are essential to mature the immune system. It turns out if you don’t have bacteria living on you or in you for some period of time, you’re actually immunocompromised because your immune system has not been matured by these organisms that come to colonize you.
Exposure to antibiotics is actually the most common thing early in life that can adversely impact the microbiota. We’re working with a number of groups to study how antibiotic exposure and other things early in life can alter the microbiota and potentially make people susceptible to diseases either in childhood or later in life. Some of these diseases include food allergies, asthma, and inflammatory bowel disease. Altering the microbiota soon after birth or potentially at other points in life can have an adverse effect or make you more susceptible to certain types of diseases.
Many things alter the microbiota. It turns out your diet is probably the most important one. If you’re having pizza for breakfast one day and then you’re having cereal and oats the next day, those changes in diet will actually alter the composition of microbes within your gut.
The changes can actually be quite rapid. Studies that we have done have shown that within three days of substantively changing your diet, particularly the carbohydrate, protein and fat components, you will rapidly shift your microbiota. It’s near immediate or within a couple days that you can cause major shifts.
Outside of your human genome, your microbiome is probably the thing that influences your health and development of disease the most. So for us it’s very important to continue our evaluations of what the role of the microbiota with respect to health and disease.
Some of the areas where we have particular focus include clinical trials with groups at Boston Children’s Hospital, namely Talal Chatila’s group, to look at the role of the microbiota in the development of food allergies. We’re studying a number of children for a couple of years, those who have food allergy or those who are at risk for developing food allergy, to understand immunologically what’s going on as well as how their microbiota is developing.
We’re also studying the role of the microbiota and its interactions with infectious agents to understand how the microbiota are helping you fight off particular pathogens or to find microbiota that protect you from infections due to clostridium difficile or multi-drug resistant pathogens.
In clostridium difficile colitis we know that the microbiota is absolutely essential to the development of the disease and also to its eradication. Nationwide this organism causes many deaths annually and many hundreds of millions of dollars in healthcare costs among people who get the disease, need extended hospitalizations, and have adverse outcomes. Being able to prevent it and being able to treat it as rapidly as possible is beneficial not only to patients but to the healthcare system as well.
We’re also looking for biomarkers that are predictive of the risk of getting clostridium difficile colitis. If you have certain medical conditions and you have to go on antibiotics and you may be at risk for getting the infection can we predict if you have lost these beneficial microbes and may need supplementation sooner rather than later.
Also, if you get the infection and you’re treated say with antibiotics, which are the usual first line treatment, can we predict if those antibiotics have been effective at eradicating the pathogen but not eradicating all of the beneficial microbes. If they haven’t, we’ll let you proceed, if it looks like they have disrupted the beneficial microbes, then we would be able to come in with a therapeutic microbiota to make sure you have the organisms needed to suppress or prevent the infection from reoccurring.
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