The microorganisms living in and on our bodies outnumber our own cells 10 to 1. Most are benign. Some are even beneficial. But nearly every one of us also carries pathogens that could cause disease.
Understanding these incredibly complex environments – in our guts, on our skin, in our lungs – is key to understanding how we will keep ourselves healthy, extend our lives, and fight disease. But, with eight million people on Earth living in vastly different climates, eating a wide variety of diets, and carrying different genetics, teasing out the relationships among a tangled web of factors is a real challenge for researchers.
A team of scientists is working to make that task a little easier.
Samantha Graham is a fifth-year PhD candidate in computational biology at the University of Minnesota. She and Richard Abdill, the lead author on the paper, recently published the Human Microbiome Compendium and the corresponding paper “Integration of 168,000 samples reveals global patterns of the human gut microbiome” in the journal Cell. The project makes nearly 200,000 human microbiome samples from hundreds of studies around the world searchable by geography and type of organisms found.
Although these samples were already publicly available, they had been collected and processed by researchers in different ways. “The problem is that you can't really compare those samples directly,” Graham explains. “We wanted to see if we could kind of leverage all of those samples, but get rid of the artifacts of processing them differently.”
With that data set in hand, it was clear to Graham and her team that world regions have unique microbiome signatures. Those could be affected by host genetics, diet, medicine, and more.
It was also clear that the vast majority of samples come from the western, industrialized world. And that has serious implications for our understanding of health as well.
In the world of microbiome research, you don’t always know what you don’t know. “When people are doing RNA sequencing of human patients, you know all of the genes that are going to be present,” Graham explains. “Whereas in the microbiome, there are just microbes that we don't even know that they're present. And so if you don't sample those places, then there's just no way of knowing what's there.”
In other words, if we’re not looking at the whole human forest, we’re missing a whole lot of potentially important trees.
The next step for the project, Graham says, is to expand beyond the gut microbiome to others, such as skin and lungs, and to add more metadata to the data set, as well. That will likely take years more work and, of course, a team of scientists like Graham.
“Sometimes when you’re doing research, you feel like you’re on an island. But I think science is best done in a team” Graham says. “The paper we just put out involved so much work from so many people. Without any of those people we wouldn’t have gotten it done.
“So reach out to others. Don’t be afraid to ask for help, even though I think everybody hates doing that. But you need help. And it will make you as a scientist and your science better.” — Tricia Cornell