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Untangling the microbiome — with statistics

Untangling the microbiome — with statistics

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I first became aware that my body was covered with bacteria in a high school microbiology class. Almost everything from my skin to my intestines, I learned, is inhabited by microbes that keep me healthy. These bacteria digest nutrients or even protect me from other pathogens. Ever since I took that class, I’ve been captivated by the idea that not all microbes are out to get us.

There is a careful balance, however, between so-called “good” and “bad” bacteria when it comes to those that live in and on humans. Certain “bad” species may be linked to disease when they outnumber the “good” guys. But when you factor in that every person has their own collection of different bacteria, these links become more fragile.

This is something that I’ve thought a lot about when reading new microbiome studies done in humans: How do we know that “bad” bacteria are directly related to a disease and it’s not just a coincidence? What can we do when scientists come to different conclusions?

I recently had the chance to think more about these questions during a conversation with Stanford statistician Susan Holmes, PhD, at the American Association for the Advancement of Science annual meeting last month. Holmes has connected things like premature birth and differences in lifestyle to variation in the human microbiome. She’s also a big proponent of sharing data and repeating studies to make sure that her findings are real.

As she explained in our chat, shared by Stanford News:

The biggest source of variability in the microbiome is the person-to-person variability. It’s a problem if you’re looking for causality. That’s a red flag word for us — causality — meaning something about the bacterial community causes some disease. You actually don’t know whether it’s the bacteria or whether the bacteria are a sign of something that happened before. It’s very much individualized, so everybody’s history matters.

But one of my favorite things she said about causality in the microbiome was this:

It’s like this horrible tangled ball and a thread that you’re trying to pull out. It’s a mess, and you pull out one thread at a time, but everything is really tied together.

Parsing out which bacteria in the microbiome cause something is not an easy task. Everything is connected to the immune system, genetics and other microbes. Holmes said that if scientists are open about the decisions they made when conducting their studies, it could help explain the differences.

Erin I. Garcia de Jesus is a graduate student in the Science Communication Master’s Program at UC Santa Cruz. She loves writing about microbes, health, animals, the world we live in and surprising discoveries. 

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