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When examining faeces samples, scientists find evidence of health and disease



Daniel McDonald is Scientific Director of the American Good Project, University of California San Diego


Have you ever wondered what's going on in your cabin? Maybe not. But that's what we think every day of the American Gut Project, the world's largest microbiome Citizen Science project, located at the UC San Diego School of Medicine. And we do not just think about it. We develop new state-of-the-art analytical methods – in the lab and on the computer – to analyze the DNA and molecules that produce microbes in the gut. Everyone can send us their shit, and we'll tell them what's going on!

But that probably still sounds pretty weird. Why do we want to send people their waste? After all, you usually just flush it in the toilet. However, Poop's microbial ecology and molecular landscape is incredibly complex and we are just beginning to discover which microbes are critical to your health and why. Microbes are responsible for breaking down the fiber in your diet and they produce important nutrients, including butyrate, which feeds the cells in your gut. Over the past decade, we and other researchers around the world have uncovered the consequences of disrupting this microbial community on the onset of disease.

Diseases associated with gut microbiotics now include obesity and kwashiorkor (a severe form of malnutrition), liver disease, heart disease, and perhaps most surprisingly, depression and Parkinson's.

However, these studies have focused on carefully selected individuals that may exclude other types of microbes found in diverse populations of humans. And so we are actively seeking as many types of faeces samples as possible, collecting the life and health information from each participant so we can uncover unknown relationships between microbes and health and disease.

Living in your gut depends on the food you eat

In our first major release, we describe what we have learned from more than 10,000 participants. For each of these samples, we decoded the DNA of the bacteria and Archaea, another microscopic resident, in each stool sample to get an idea of ​​the microbial species present and their relative abundance. We also examined the types of genes and molecules present on a few hundred particularly interesting samples from participants that included extreme plant consumption and the use of antibiotics. After removing all personal identifiers, we then deposited the data in public so that any researcher, student, educator, doctor or patient could reuse it and build on the results.

One of the most exciting discoveries was that the greater the variety of plants in the diet, the greater the diversity of microbes in their guts. More excitingly, the microbes differed not only dramatically between those who ate little versus many plants, but also the repertoire of molecules that produce these communities. The intestinal bacteria of those eating more species of plants can break down food using alternative routes of metabolism and produce different types of molecules. This is a big deal because we did not think that eating a lot of plants has a significant effect on the gut. But the data shows differently.

Antibiotics and the microbes in your gut

We also looked at people who took antibiotics the week before the sample was sent, and compared them with stool samples from people who had not taken any antibiotics in the past year. Not surprisingly, the microbial diversity of antibiotic users has been drastically reduced. But, unexpectedly, there were more types of molecules. In this case, these molecules appear to be associated with exposure to antibiotics. We need to understand what these chemicals are and what they do to our bodies and our microbes. We are not sure why there is a leap in the diversity of chemicals when fewer types of microbes are present. This is just another of many mysteries we need to explore now.

But we found something even more unexpected and disturbing. We were able to prove agricultural antibiotics – those fed to animals such as chickens and cows – to many people who claimed that they had not taken antibiotics the year before they were sampled!

This means that antibiotics used for fattening animals reared on industrial farms could enter our bodies where they could alter or harm the microbes in our gut. That would certainly be an unintended consequence.

British versus American Club

Although most of our analysis focused on individuals in the United States, individuals in the UK were able to participate through a sister project called British Good. During our work, we found that the study of several populations was incredibly strong.

For example, we found significant differences in sample diversity from these two different Western populations: people in the UK seemed to harbor a more diverse population of microbes.

One of our findings described in our paper examined a compound that we discovered between the composition of the microbiome and individuals with depression. Samples from both sides of the Atlantic were consistent in the US and UK populations. This shows that disease microbiome relationships are valid in different populations, at least if you use the same consistent methods. (The American Good Project is part of the Earth Microbiome Project, and we use the same, expert-approved and well-tested protocols.)

Unfortunately, for most countries, we have at least one sample from every dozen countries. We have few or no examples for this project. That's why we're actively working with colleagues around the world to find out how to translate outcomes between populations in general, and to address some of the major chronic diseases that humanity faces today, such as metabolic disorders. To do this, we're launching a new initiative called The Microsetta Initiative, which includes the American estate and UK property projects.

Please support us in our quest to advance microbiome science – perhaps your poop is the key to saving lives.

  The Conversation

This article was originally published on The Conversation .


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