Your skin is the outermost part of your body, but did you know that it is closely tied to some of your innermost parts? There’s a whole community of tiny living things in your gut microbiome that play an important role in your health.
Did you know there is a community of microscopic living things that have made your body their home? Don’t worry, though — for the most part, the bacteria, fungi, viruses and archaea (a group of ancient single-celled organisms) that live in and on your body are your friends.
Each community is known as a microbiome, and scientists have conducted a ton of research into the gut microbiome over the past two decades. It turns out that the gut microbiome is connected to nearly every aspect of human health, linked to everything from inflammatory bowel disease to anxiety and depression and even to the function of your immune system.
Researchers noticed this connection by comparing the gut microbiomes of patients with a disease to those of people who didn’t have that condition. They found that certain species would be present in different amounts, either over- or underrepresented, or sometimes just completely missing. As research technologies become more advanced (See “Sequence of Events,” below), the ability of researchers to pinpoint the exact species playing a role in causing the condition is improving.
What Our Microbes Can Teach Us
Alongside determining which species are responsible for different diseases and responses, researchers are now figuring out what those microbes are doing and how their functions impact us. To do this, they’re looking at what the microbes produce as they go about their lives: products known as metabolites.
“We house this large community of microbes in our gut, and they are all rapidly digesting any carbohydrates or proteins they find in their environment and producing thousands of different compounds,” explains Alena Pribyl, PhD, senior scientist and research officer at Microba, an Australia-based company that is doing groundbreaking research into the microbiome and how it can affect health. Some of these microbial compounds are absorbed through the cells lining our gut and into our circulation system, which distributes them throughout the body. They can then influence everything from the immune system to the skin. Dr. Pribyl says these metabolites are likely the link between the microbiome and disease. While researchers have already figured out some of the ways certain microbial metabolites help adjust the immune system, many more effects are waiting to be discovered.
In skin diseases, such as atopic dermatitis (eczema), both the skin and gut microbiomes are likely involved. (Yes, there’s a skin microbiome , too!) Specific metabolites produced by skin microbes that reduce inflammation are at lower levels in people with atopic dermatitis. Additionally, studies have observed that infants lacking the right types of gut bacteria lose some function of their immune systems and may be at greater risk of developing this disease. More research is needed, but the hope is that someday research will lead to therapies containing just the species, or even just the metabolites, that your body needs.
Eating for Microbiome Health
For now, what can we do to have a happy gut microbiome and healthy us? The answer is surprisingly simple. “The best thing you can do is to have a healthy diet with lots of diverse sources of fiber,” Dr. Pribyl says. “There are strong links with a healthy gut microbiome and eating a variety of plant-based foods such as nuts, seeds, fruits, vegetables and grains like quinoa, oats and barley.”
Research in mice has shown that your diet influences the function of the microbiome, which in turn, through metabolites, influences the function of your immune system. In 2021, a study led by researchers at the National Cancer Institute and MD Anderson Cancer Center found that melanoma patients on immunotherapy who ate the most fiber, at least 20 grams a day, survived longer without any signs of worsening disease compared to those with insufficient daily fiber intake. And in 2022, a large cohort study from King’s College London found that a healthy microbiome, achieved through a healthy diet, led to the best responses to immunotherapies.
While it might seem like this is something you’ve heard throughout your life, Dr. Pribyl says, “Research on the gut microbiome is now helping us understand the why behind the importance of having a healthy diet.”
“Sequence” of Events
OK, bear with us for a little genomics lesson here. Once scientists have a microbiome sample, they need to have the tools to analyze it. Scientists used to identify bacteria and sort them into groups of related species — a genus — based on characteristics that they could see under a microscope, such as their shape. But two unrelated species may look very similar, and this method relies on being able to grow bacteria in the laboratory, which not all bacteria like to do.
A more accurate way to identify an organism and draw its family tree is by looking at its DNA, in a process called sequencing. For the last 20 years or so, most microbiome studies have used a type of DNA sequencing known as 16S rRNA sequencing. The name of this method refers to the 16S ribosomal gene that all bacteria and archaea have. Closely related bacteria will share the same variations within that gene, and thus scientists can accurately group species into their genus, though they can’t accurately identify individual species when they look at just one gene.
However, in 2004, scientists published a method to sequence all of the DNA in a sample, not just a single gene. This allowed them to identify species of bacteria in a sample, and sometimes even subspecies, or strains. “This is called metagenomics, referring to the fact that you’re sequencing all of the genomes of the organisms that are in a sample,” Dr. Pribyl explains.
When it was first invented, this sequencing was so expensive, almost no one could do it. But gene sequencing prices have dropped to less than 1 percent of what they were two decades ago, making the process accessible for labs around the world. In addition to species identification, researchers can use this method to figure out which genes are present in the bacteria. This may help researchers figure out what the microbiome is actually doing.
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