Gut Check

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By Jessica Metcalf, PhD

What exactly is the human microbiome? It’s the collection of microbial genes in and on the human body. Microbes account for about 3 lbs of our body weight on average, and microbial genes account for over 99% of the genes in our bodies. Are these microbes and their genes important? Absolutely!

The majority of our microbes are found in the gut, and these microbes (mostly bacteria) help us train our immune system, metabolize food, synthesize vitamins, and more -- the list goes on. Recent advances in DNA sequencing technology and software development have allowed us to uncover new ways in which microbes are important to our health, including associations with depression, asthma, allergies, and obesity.

So what else have we figured out?

Have you ever heard of a fecal transplant or poop pills?
A fecal transplant, when the stool from one person is put it into another person, is incredibly effective for curing patients with Clostridium difficile infections, which causes 14,000 deaths in the U.S. each year and often cannot be cured with antibiotics. Check out this visualization of the response of C. diff patients’ microbiome to a fecal transplant.

Ever wonder how we get our microbes?
We get our first really big dose of microbes as we travel through the birth canal. Here we visualize an infant’s gut microbiome development. What about babies born via C-section? They get an initial dose of skin microbes instead. Does this have health effects, and can birth canal microbes be introduced after C-section? We are studying these questions now with collaborator Dr. Maria Gloria Dominguez-Bello at NYU.

Are people living in Westernized cultures (e.g. the U.S) missing microbes?
In the U.S., most people practice intensive hygiene regiments, spend the majority of their time indoors, and have had a lot of exposure to antibiotics. As a result, our gut microbiomes have lost diversity. Our collaborator Dr. Martin Blaser writes about our missing microbes in his new book.


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I am at the Australian Centre for Ancient DNA working on Viking latrine samples collected in York, England.

If we’ve lost microbes, what microbes did our ancestors have? In a series of papers later this year, we will share what we have learned from studying Viking poop (see photo) and poop from modern populations of humans that live more traditional hunter-gatherer lifestyles.

What about other vertebrates? Do my pets have microbiomes too?
Yes, they sure do! The gut microbiome is important for all animals, not just humans. And if you have a dog at home, you share microbes with him/her (along with your other family members). In addition, as part of a project funded by the John Templeton Foundation, we are studying the co-divergence of gut microbes across the vertebrate tree of life to understand how microbes may be important for the evolution of traits such as diet specializations (e.g. eating ants) and flight. Stay tuned for results soon!

Interested? You should be. Microbes affect almost every aspect of our lives, but we still have lots to learn. Here are some ways you can contribute to the effort.

Learn. Learn more about your microbes in our massive, open online course (MOOC) entitled “Gut Check: exploring your microbiome”, which is aimed at a level understandable by the public. Our free “Poop MOOC” runs from Oct 6th – Nov 14th, and you can still join us! Weeks 4, 5, and 6 are packed with highlights of fascinating research!

Watch our cool trailer and sign up here!

Participate. What’s in your gut? Find out through the largest open-source, crowd-funded science project in the world, The American Gut Project. Claim a perk for $99 and we will send you a sampling kit, which will allow us to sequence your microbes!

Support. Help us keep the buzz going about the human microbiome! RootHouse Studios is helping us communicate our science to the public by producing a documentary film-series.

Help them raise money for this film-series through Kickstarter.


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