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United States Department of Agriculture

Agricultural Research Service

Research Project: Genomic Analyses and Management of Agricultural and Industrial Microbial Genetic Resources and Associated Information

Location: Bacterial Foodborne Pathogens & Mycology Research Unit

Project Number: 3620-22410-016-00
Project Type: Appropriated

Start Date: Apr 24, 2013
End Date: Apr 23, 2018

Objective:
The major goals of this project are to enhance the quality, diversity, and utility of the ARS Culture Collection holdings, including the strains held in the ARS Patent Culture Collection, and to conduct and support microbiological research that advances agricultural production, food safety, public health, and economic development. The project is designed to simplify and improve public access to well-characterized microbial strains, expand accessions associated with ARS priority research in food safety and animal health, and enhance the information content associated with accessions through comparative genomic and targeted multilocus sequence analyses of diversity and evolutionary relationships. This project is also designed to leverage the expertise and information developed from two current NP108 - Food Safety projects within the Bacterial Foodborne Pathogens and Mycology Research Unit. The genetic, phenotypic, and taxonomic information generated from the proposed research will be combined with data generated through the NP108 projects in web-accessible strain databases that enhance the utility of the collection and facilitate strain selection by the end-users. Objective 1: Safeguard (including backing-up) priority microbial genetic resources and associated information from the ARS Culture Collection in state-of-the-art genebanks. Objective 2: Identify gaps in the ARS Culture Collection's coverage of microbial genetic resources of national importance and programmatic interest to ARS, and acquire the latter. Objective 3: Conduct comparative genomic, phylogenetic, and taxonomic analyses of strains in the ARS Culture Collection, especially for actinobacteria. Objective 4: Improve ARS Culture Collection's database management to enhance inventory control, enable researchers to identify desired strains, and facilitate fulfillment of customer requests for germplasm. Enable researchers to conduct gene searches from microbial sequence databases to determine taxonomic identification and phylogenetic position of unknown samples and strains.

Approach:
More than 95,000 accessions of microbial genetic resources, including food-borne pathogenic bacteria, actinobacteria, yeasts, plant pathogenic fungi, grain storage molds, and other microbes of biomedical and biotechnological importance and associated information will be maintained in a secure centralized limited-access facility. Strain records including inventory data will be updated and maintained in an updated and improved Culture Collection Database System that also manages strain requests received from the collection website, facilitates, permanently storing the details of germplasm distributions. Germplasm held only as frozen preparations under liquid nitrogen vapor phase will be shipped to National Center for Genetic Resources Preservation (NCGRP), for backup storage as a safeguard against catastrophic loss and the backup collection of lyophilized preparations currently stored at another remote ARS facility will be consolidated there during this project cycle. Strains resulting from ARS research efforts or required to fulfill current or planned research will be acquired from collaborators or other collections after consultation with team members, collaborators, the Office of National Programs and the U.S. Culture Collection Network. The genomics of actinobacterial germplasm within the collection (specifically in the genus Streptomyces) will be evaluated through determination and evaluation of gene content in draft genome sequences of strains of significance to agriculture or biotechnology. Gene sequence data already accumulated for fungal strains within the ARS Culture Collection through associated research efforts under ARS NP108 (Food Safety, Animal and Plant Products) will be organized and made accessible in a web-based sequence database to be interconnected with the Culture Collection Strain Database System and novel species discovered in the course of this process will be fully characterized.

Last Modified: 9/10/2014
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