The human microbiome has been the topic of thousands of research studies in the past two decades. Rapid developments in laboratory techniques and bioinformatics have brought down the cost of DNA sequencing while enabling the high-throughput analysis of thousands of samples. These developments have made it possible for researchers to study the microbial species present in a sample without having to first grow them in the laboratory.
These studies have created a wealth of knowledge on the microbes present in our gut and other body sites, and the functions they fulfill in our health. Gut microbes help us digest our food, make vitamins and other molecules that we need, support our immune systems, and help prevent infection with pathogens (microbes that can make us sick).
Fibers and starches in our diet cannot be broken down by our own enzymes, and we need to rely on our microbes to break these down. They turn these fibers into small molecules that we then can absorb. One of these molecules is butyrate, which serves as fuel for our intestinal cells, but is also taken up in our blood and is believed to have beneficial effects in other parts of our body. This influence of the gut on other organs might even reach as far as our brain, the so-called gut brain axis. Our gut is intricately connected to our brain by many nerves that end in the gut, and expressions such as “a gut feeling” and “sick to my stomach” are familiar to us. Eating lots of fiber therefore feeds our microbiome and helps the gut microbiome help its host - our body - in return.
Research has given valuable insight into the composition and function of the gut microbiome of healthy people. We’ve also learned that the gut microbiome composition in people with diseases such as diabetes, irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD) is different from that of healthy people.
Whether we are healthy or sick, we all have our own unique microbial rainforest inside of us. What determines the composition of our gut microbiome is partially determined by our own genes, and partially by our diet, lifestyle, and health. In healthy persons who eat a regular diet, the composition of the gut microbiome does not change a lot from day to day or even from month to month. But the gut microbiome can change if we make a big change in our diet (e.g. eating more fiber, becoming vegan), or if we go on an international trip, take antibiotics or other drugs, or become sick.
The uniqueness of our microbiome can have unexpected consequences. Each species in our gut has its own unique set of genes and properties. Depending on the microbial species we harbour in our gut, individual persons vary in their ability to break down fiber, or to generate butyrate and neurotransmitters such as serotonin. For example, people whose gut microbiome does not contain Oxalobacter formigenes, a bacterium that can break down oxalate in our food, have an increased risk for kidney stones. Other microbes have been found to synthesize vitamin B and K, so our dietary needs might vary depending on which microbes live in our gut.
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The composition of our gut microbiome can also determine if certain drugs work or not. An immunotherapy drug called anti-PD1, which is used to treat melanoma, has been shown to work better in some people than in others. This difference appears to be associated with the composition of a patient’s gut microbiome. Digoxin, a heart disease drug, can be inactivated by certain Eggerthella strains, making it less effective in patients who harbour such strains in their gut. The widely used painkiller acetaminophen (Tylenol) can be extremely toxic for certain individuals, depending on the species present in their gastrointestinal system.
As more and more diseases and individual drug responses are linked to the composition of our gut microbiome, stool sample analysis at the doctor’s office is likely to play an increasing role in human healthcare. Such tests will greatly help clinicians to follow their patients’ health, and to better predict which treatment or drug would work best for an individual patient.
Citizen scientists can help us extend our knowledge of human microbiomes worldwide. Human microbiomes are very different in every apart of the world, and microbiome analysis has until recently mainly focused on European and North American subjects. With the aid of citizen science we can extend our knowledge of a much more global population, and thus better help understand specific problems that affect non-Western communities in greater proportion, such as malnutrition and diarrhea.
uBiome, Inc. is a member of the World Economic Forum's 2018 class of Technology Pioneers. Explore this year's full cohort of Technology Pioneers here.