Question:
Where to find an inventory of all microbial genomes?
Answer:
Researchers in US and Germany have started to compile an inventory of all microbial genomes, called the “Genomic Encyclopedia of Bacteria and Archea”.
Scientists from the United States and Germany have published a study that serves as the start of a comprehensive genomic encyclopedia of all microbes on Earth. The Genomic Encyclopedia of Bacteria and Archaea (GEBA) aims to represent all major branches of microorganisms. To date, the project has compiled nearly 1000 bacterial and archaeal genomes. One estimate suggests there are 150 million species of prokaryotes left to sequence, so the genomes collected thus far have barely scratched the surface of microbial diversity. Most were chosen for sequencing on the basis of their physiology, such as for their roles in disease or their economic impact (e.g., an ability to produce biofuels), and have left vast gaps in the prokaryotic tree of life.
In fact, currently available genomes represent a highly biased perspective, according to the study's authors. Jonathan Eisen, a professor at the University of California Davis Genome Center and lead author compared this selective sequencing to making a map of the world and only mapping three cities.
The authors decided to take a phylogenetic approach and sequence representatives from across the major branches of the prokaryotic tree. Phylogenetics is the study of evolutionary relatedness, where organisms are grouped in trees based on their genetic relationship. The team sampled 56 genomes to maximize phylogenetic coverage. What they found was surprising. In the bacterial species H. ochraceum, the team discovered a homologue of actin, which was previously thought only to exist in eukaryotes as a cytoskeletal structural protein. This new find reinforces the potential of novel discoveries given a wider genomic sampling of the tree of life, according to the authors. The team included researchers at the US Department of Energy Joint Genome Institute, UC Davis Genome Center, the German Collection of Microorganisms and Cell Cultures, the Lawrence Livermore National Laboratory, and the University of Virginia.
The study, “A phylogeny-driven genomic encyclopaedia of bacteria and archaea,” was published in the Dec. 24 issue of Nature.
Question:
Which are the suggestions of the ASM (American Society for Microbiology) about the genome sequencing?
Answer:
ASM calls for standardized, open annotation of sequencing efforts
The American Academy of Microbiology, a division of the American Society for Microbiology, issued a comprehensive report this month on the state of large-scale genome sequencing projects, including suggestions for future collaborative efforts. The American Academy of Microbiology, the leadership group of the American Society for Microbiology (ASM), issued a report on large-scale genome sequencing this month, stemming from their September 2008 meeting in Washington, D.C. The comprehensive report includes a summary of the colloquium, the potential implications of large-scale sequencing projects, and recommendations for future research. The report, “Large-scale sequencing: the future of genomic sciences?” represents opinions derived from colloquium participants from across the U.S. and Canada. In the report, the group emphasizes the importance of coordinated and systematic quality control among sequencing centers; the types of data that should accompany sequencing efforts (i.e., phenotypic and ecological information for phylogenetic context); consistency, organization, and maintenance of annotation data; and specific cultivation procedures (criteria for selecting organisms to sequence, culture development, cell isolation methods, etc.).
The report also lays out specific experimental design and data collection methodologies to encourage consistency among genome projects. As new technologies and information become available, the definition of what comprises a genome¯the sequence, transcriptome, proteome, and eventually other features¯will change over time, participants said. Participants also predict that the development of a standardized, open annotation model would encourage new collaborations and “instill a feeling of collective ownership of the process of the data” among research institutions. “Better interfaces are needed between the existing genome centers and scientists and between large-scale protein structure institutions and genome sequencing groups,” the report reads. “Institutional and agency pipelines make it difficult to collaborate across agency lines.” The American Academy of Microbiology also recommends that genomes be re-annotated over time to keep up with advancements in techniques. The community could then curate and update data so that new information, such as refined functions, would be readily available to all. Keywords: large-scale sequencing ASM annotation community.
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