More than a century after the Industrial Revolution, advances in DNA sequencing technologies have caused similarly dramatic shifts in scientific research, and one aspect is studying the planet’s biodiversity. One critical term that needs standardization is “metadata,” defined simply as “data about other data.” In Nature Biotechnology, an international team led by DOE JGI researchers has developed standards for the minimum metadata to be supplied with single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) submitted to public databases. Read more on the DOE JGI website.
JGI Researchers Release 1000+ Microbial Reference Genomes
Department of Energy Joint Genome Institute (DOE JGI) and Biosciences Environmental Genomics and Systems Biology (EGSB) division researchers have released 1,003 reference genomes for diverse bacteria and archea isolated from environments ranging from sea water and soil, to plants, and to cow rumen and termite guts. The release is the largest to date from JGI’s Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, which seeks to fill in unexplored branches of the tree of microbial life. JGI’s Supratim Mukherjee and Rekha Seshadri were co-first authors on the paper published in Nature Biotechnology; senior author Nikos Kyrpides and co-authors Natalia Ivanova, Axel Visel, Tanja Woyke, and Yasuo Yoshikuni have secondary affiliations with EGSB. The genomes are publicly available through the Integrated Microbial Genomes with Microbiomes (IMG/M) system. Read more on the JGI website.
Seeking Structure With Metagenome Sequences
In collaboration with DOE Joint Genome Institute (JGI) researchers, the team led by David Baker of the University of Washington reports that structural models have been generated for 12 percent of the protein families that previously had no structural information available. Read more at JGI News.
DOE JGI Team Unveils Earth’s Viral Diversity
“We have increased the number of viral sequences by 50x, and 99 percent of the virus families identified are not closely related to any previously sequenced virus. This provides an enormous amount of new data that would be studied in more detail in the years to come. We have more than doubled the number of microbial phyla that serve as hosts to viruses, and have created the first global viral distribution map. The amount of analysis and discoveries that we anticipate will follow this dataset cannot be overstated.”
Although the number of viruses is estimated to be at least two orders of magnitude more than the microbial cells on the planet, there are currently less than 2,200 sequenced DNA virus genomes, compared to the approximately 50,000 bacterial genomes, in sequence databases. In a study published online August 17, 2016 in Nature, DOE JGI researchers utilized the largest collection of assembled metagenomic datasets from around the world to uncover over 125,000 partial and complete viral genomes, the majority of them infecting microbes. This single effort increases the number of known viral genes by a factor of 16, and provides researchers with a unique resource of viral sequence information. Read more on the DOE JGI website.
DOE JGI Team Calls for National Microbiome Data Center
“The time is ripe to embark on the greatest endeavor to understand Earth’s microbiome. At the dawn of the third decade of microbial genomics, and well into the information age, the establishment of a national microbiome data center can pave the way to understanding the Earth’s microbiome.”
In a paper published in Trends in Microbiology, researchers from the DOE Joint Genome Institute call for the formation of a National Microbiome Data Center to efficiently manage the datasets accumulated globally. The timely publication complements the White House’s launch of a National Microbiome Initiative focused on comparing microbial communities across ecosystems to identify the “organizing principles” that shape all microbiomes. Read more on the DOE JGI website.
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