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Team Gearing Up For Gut Microbiome Crowdsourcing Project

NEW YORK (GenomeWeb News) – A group of scientists based at several institutions in the US and beyond are getting set to kick off a crowdsourcing study called the "American Gut Project," aimed at assessing gut microbial communities in 10,000 or more individuals in the US in relation to their diet and lifestyle.

"The big question is, 'Is diet driving differences in the gut microbiome?'" project organizer Jeff Leach told GenomeWeb Daily News. "There are indications that it does, but the sample sizes are small."

"We don't expect to be able to address some questions, but because of the size of the sample and because of the broad patterns we expect to see in diet and lifestyle, we think some stuff will fall out," added Leach, who has a background in archeology and a long-standing interest in diet and nutrition from an evolutionary perspective.

Also involved in leading the effort are members of the Earth Microbiome Project, including University of Colorado at Boulder bioinformatics researcher Rob Knight and Argonne National Laboratory's Jack Gilbert.

The University of Colorado's institutional review board will oversee the effort and has granted approval for the team to test up to 20,000 people for the gut microbiome project.

The study will focus on bringing in large numbers of individuals to look at how gut microbiome patterns vary with factors such as diet, age, and lifestyle.

To that end, researchers plan to collect extensive meta-data from participants, who will be asked to fill out an online questionnaire with questions on everything from their height, weight, and sex to their travel history and antibiotic use. They will also be asked to provide detailed information on their food intake over one week.

In particular, Leach said that this dietary meta-data is "critical to the project."

He noted that people with potentially related intestinal or metabolic conditions will be given the option of self-identifying, as will those following a specific diet plan, such as vegans or adherents of paleo diets.

Participants in the project must be at least three months old and reside within the US, Leach noted. Those who sign up will be asked to donate $99 through a crowd-sourcing site called indiegogo.com. They will then be provided with a home sample collection kit. Once their samples are assessed, participants will be provided with a taxonomic profile of their gut microbiome.

In addition to making the project accessible to the public, the crowdsourcing format is expected to make it possible to collect a large number of samples very quickly.

The site is expected to launch within the next few weeks. Once it does go live, it will only be open for enrollment for 21 days, Leach said. And researchers are aiming to complete their initial analyses of the samples by next spring.

The $99 donation is expected to offset but not completely cover the cost of the study, which will rely on 16S ribosomal RNA sequencing as a means of surveying the microbial members of each gut community.

"By crowd-sourcing 10,000 people to do this, we will build up a database which can be incredibly informative and useful in categorizing and cataloguing future studies," Argonne's Gilbert told GWDN.

A subset of the samples may also be subjected to more detailed analyses, including metagenomic sequencing, which provides a look at the complete collection of microbial genes present in a given sample.

The team anticipates being able to assemble some microbial genomes from the metagenomic data, Gilbert noted. In addition, they plan to take a crack at using single-cell genomics to help categorize the microbes present in each diet class, for instance.

Though most study participants will only be sampled once, researchers are already considering the possibility of inviting a few hundred participants to have their gut microbiomes sampled multiple times over the course of a year or two for follow-up phases of the study.

"From our perspective … longitudinal surveys are one of the keys to understanding the development of community structures in microbial assemblages," Gilbert said. "We need this kind of cross-sectional and longitudinal survey to really determine what the impact is of diet on the bacterial communities."

There is also the potential for creating an online forum to disseminate data from that type of ongoing analyses of some of the anonymous study participants.

For his part, Leach envisions assembling a "League of Extraordinary Microbiomes" who would fill out weekly food and lifestyle logs so that this information could be presented on a web site alongside their gut microbial data. By observing gut microbe communities in this group as they go through different life events or dietary changes, Leach explained, the public may gain an improved understanding of the microbiome and its relationship to diet, nutrition, and human health.

The American gut study is related to a larger movement that Leach founded called the Human Food Project — an effort focused on placing modern disease within a broader evolutionary perspective "through the lens of the microbiome."

Over the past few years, he noted, there has been an "explosion" in microbiome research. But missing from the equation so far, from his perspective, was a firm understanding of the healthy microbiome in humans from populations that have retained a more traditional lifestyle.

Consequently, he is hopeful that the gut microbiome, diet, lifestyle, and other data collected from American participants will be complementary to that generated through a future longitudinal microbiome study in Namibia, which will include some participants whose diet is still somewhat representative of a hunter-gatherers lifestyle. That effort — which will likely look not only at microbes in the gut, but also those in individuals' mouth, on their skin, and in their environments — is slated to kick off next year and is being done in collaboration with researchers at the University of Puerto Rico.

For more information on the American Gut Project or to sign up for alerts about when the citizen science project will go live, go to the Human Food Project website.

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