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Department of Energy’s Joint Genome Institute, National Center for Biotechnology Information, Lawrence Berkeley National Laboratory, Clinical and Laboratory Standards Institute

Version 2.3 of the Integrated Microbial Genomes data management system is now available from the Department of Energy’s Joint Genome Institute. The content of IMG 2.3, upgraded with new microbial genomes from the Version 23 release of the National Center for Biotechnology Information Reference Sequence collection, now includes fungi, protists, and plant genomes to enhance the breadth of comparative analysis. A new addition of particular interest to DOE is Pichia stipitis CBS 6054, a fungus with the exceptional capability to ferment xylose, five-carbon wood sugar, and yield high levels of ethanol.
The new version of IMG contains a total of 2,878 genomes, consisting of 729 bacterial, 46 archaeal, 40 eukaryotic, and 1,661 bacterial phage genomes, and 402 plasmids that did not come from a specific microbial genome sequencing project. Among these genomes, 2,609 are finished and 269 are draft genomes. IMG 2.3 contains 236 microbial genomes sequenced at DOE JGI, consisting of 157 finished and 79 draft genomes.
IMG 2.3 extensions include an expanded controlled vocabulary of IMG terms, representing over 2,300 curated product names, and a growing collection of IMG pathways that form the foundation for composite IMG networks. IMG terms, pathways, and networks are used for improving the functional characterization of genes in ongoing studies related to carbohydrate utilization, cofactor biosynthesis, and methanogenesis.
IMG 2.3 also provides enhanced support through "MyIMG Annotations," which enables users to associate related genes of interest with their curated annotations, including product name, and enzyme number. Other user interface extensions include reorganization of the organism and gene details pages and additional genome, gene, and function search capabilities.
IMG is accessible to the public here and is a collaborative effort between DOE JGI and the Lawrence Berkeley National Laboratory Biological Data Management and Technology Center. It is updated on a quarterly basis with new public and DOE JGI genomes. The next update is scheduled for December.

Clinical and Laboratory Standards Institute has published a new document, “Interpretive Criteria for Microorganism Identification by DNA Target Sequencing; Proposed Guideline (MM18-P),” which provides current information for microbial classification by gene sequencing, with particular emphasis on interpretation and reporting results. The document establishes guidelines for the systematic approach to classify bacteria and fungi by broad-range DNA sequencing.
The guideline specifies recommendations for clinical laboratories that employ amplification and Sanger-based (dideoxy-termination) sequencing of broad-range DNA targets for the identification of bacteria, mycobacteria, and fungi from cultured clinical isolates. Partial and full gene sequencing with 16S rRNA gene for identification of bacteria and mycobacteria, and Internal Transcribed Spacer regions ITS1 and ITS2 regions for identification of fungi, are addressed with inclusion of alternative DNA targets when appropriate.
For additional information, visit CLSI’s website.

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