By Kanika Khanna
In this journey called life, we are not alone. We are inhabited by around 39 trillion microbial cells that account for ~57% of all cells in our body, making us half human and half microbes. This consortium of microbial species (including bacteria, fungi, viruses, and archaea) is referred to as the ‘human microbiome’ and the gut is home to more microbes than any other body part. Microbes present in the gut (and hence our poop) contribute to our health in a variety of ways including metabolism and immunity.
Humans are exposed to their first set of microbes right as they find their way through their mother’s birth canal, which seeds the infant with microbes. As we grow, we develop a so called ‘microbial fingerprint,’ with our microbiome being shaped by our lifestyle, diet, and environmental factors.
“If you’re a fruit fly, at least, your microbes determine who you want to have sex with. [In humans], they help us digest our food. They help educate our immune system. They help us resist disease, and they may even be affecting our behavior,” says Rob Knight during his 2014 TED talk. Knight, a Professor of Pediatrics and Computer Science & Engineering at University of California, San Diego is the founding Director of the Center for Microbiome Innovation, which provides a platform for researchers with different expertise including biological and physical sciences, clinical medicine, and computer science to come together to accelerate microbiome research. The past decade has seen significant research efforts focused on the role of the gut microbiome. The gut microbiome has been linked to an array of health conditions including, but not limited to diabetes, obesity, depression, and autism.
Launched in 2008, the Human Microbiome Project was the first large-scale multi-institutional collaboration including University of Maryland, Berkeley lab, Joint Genome Institute, and University of Colorado Boulder. The government-funded interdisciplinary study characterized the microbial communities from 300 healthy volunteers from different sites on their bodies. Since it is extremely difficult to distinguish different microbial species from one another under a microscope just by looking at them, scientists extracted DNA sequences of microbes. Using computational techniques, they could then map these DNA sequences to the microbial species they belong to. However, the study was limited by sample size and demographics and it was difficult to build correlations and trends with respect to microbiome and health with such a finite dataset.
In 2010, the Earth Microbiome Project (EMP) was born out of a curiosity to sample microbial communities across the globe using crowdsourced sample collection from researchers all across the globe. The notion was to create a database of microbes in order to characterize ecosystems by composition of microbes and their interactions. This study witnessed participation of researchers from 43 countries and 200,000 samples. These samples ranged from Gulf of Mexico, the analysis of which helped in identification of microbes that had genes for degrading oil, to those from Alaskan glaciers, which may help track the extent of global warming by monitoring changes within microbial communities in glaciers over time.
The drive to better understand the human microbiome across a wide range of age groups and geographical locations and its relation to health and disease led Knight and Jeff Leach to found the American Gut Project (AGP) in November 2012 as a part of EMP. The AGP is now the largest open-source, crowd funded microbiome citizen science project in the world with over 15,000 samples from all over the world. The project allows participants to learn about their own microbes and in return, they contribute to a greater scientific effort to understand the relationship between microbiome and health. They recently published their first study this year on May 15 in mSystems. “With AGP, we’ve been fortunate to raise over $2 million, [and collect] thousands of stool samples and hundreds of mouth and skin samples from people living in 40+ countries around the world. It’s truly amazing how enthusiastic people are to help science,” says Embriette Hyde, former Project Manager in Knight’s lab and co-author of the study.
The procedure to become a citizen scientist is pretty simple. For $99, you can purchase a kit and send your stool/skin/mouth sample. You will then be mailed a report about the composition of your microbiome and de-identified data is deposited into a public domain for research by other scientists. Participants are also asked about their dietary habits in the form of a comprehensive picture-based food frequency questionnaire. This has led to some critical findings such as people who eat more than 30 types of plants in a week have a more diverse gut microbial community and reduced prevalence of antibiotic resistance genes as compared to people who eat less than 10 types of plants in a week.
As of May 15, there were 17,667 participants in the AGP. It is a living data set with participants being added on a daily basis. Currently, most of the participants are from USA, UK or Australia. Daniel McDonald, current AGP manager and first author of the study hopes to improve global participation by launching the Microsetta Initiative which aims to expand the effort of collection of microbial samples from rest of the world’s population. In addition, participants donating their samples on a timely basis have potential to reveal novel insights into the possible connections between the microbiome and disease. “Many studies are showing that longitudinal data collections provide more useful information in terms of disease detection,” says Hyde.
To accomplish these goals, these microbiome researchers need the help of many citizen scientists, or as McDonald puts it, “we want your poop!”
Kanika Khanna is Ph.D. student in the Division of Biological Sciences at University of California, San Diego. Enthusiastic about tiny microbes, she is currently visualizing bacterial cellular processes at high resolution using new modalities in the field of cryo-electron microscopy.
