In the Earth Microbiome Project, an extensive global team has collected more than 27,000 samples from numerous, diverse environments around the globe. They analyzed the unique collections of microbes -- the microbiomes -- living in each sample to generate the first reference database of bacteria colonizing the planet.
The Earth Microbiome Project was founded in 2010 by Rob Knight, PhD, professor at UC San Diego School of Medicine and director of the Center for Microbiome Innovation at UC San Diego; Jack Gilbert, PhD, professor and faculty director of The Microbiome Center at University of Chicago and group leader in Microbial Ecology at Argonne National Laboratory; Rick Stevens, PhD, associate laboratory director at Argonne National Laboratory and professor and senior fellow at University of Chicago; and Janet Jansson, PhD, chief scientist for biology and laboratory fellow at Pacific Northwest National Laboratory. Knight, Gilbert and Jansson are also co-senior authors of the Nature paper and Stevens is a co-author.
The goal of the Earth Microbiome Project is to sample as many of the Earth's microbial communities as possible in order to advance scientific understanding of microbes and their relationships with their environments, including plants, animals and humans. This task requires the help of scientists from all over the globe. So far, the project has spanned seven continents and 43 countries, from the Arctic to the Antarctic, and more than 500 researchers have contributed to the sample and data collection. Project members are using this information as part of approximately 100 studies, half of which have been published in peer-reviewed journals.
Project members analyze bacterial diversity among various environments, geographies and chemistries by sequencing the 16S rRNA gene, a genetic marker specific for bacteria and their relatives, archaea. The 16S rRNA sequences serve as "barcodes" to identify different types of bacteria, allowing researchers to track them across samples from around the world. Earth Microbiome Project researchers also used a new method to remove sequencing errors in the data, allowing them to get a more accurate picture of the number of unique sequences in the microbiomes.
Within this first release of data, the Earth Microbiome Project team identified around 300,000 unique microbial 16S rRNA sequences, almost 90 percent of which don't have exact matches in pre-existing databases. Pre-existing 16S rRNA sequences are limited because they were not designed to allow researchers to add data in a way that's useful for the future.
Luke R. Thompson et al. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature, 2017; DOI: 10.1038/nature24621
Posted by Dr. Tim Sandle