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Genomic Analyses and Management of Agricultural and Industrial Microbial Genetic Resources

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.

More Info:
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.
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Kurtzman, Cletus
Labeda, David
O'Donnell, Kerry
Peterson, Stephen
Ward, Todd
Published Journal Articles USDA ARS (NP 108):
On the reclassification of species assigned to Candida and other anamorphic ascomycetous yeast genera based on phylogenetic circumscription
Daniel HM, Lachance MA, Kurtzman CP.
Antonie Van Leeuwenhoek. 2014 Jul;106(1):67-84.
Aspergillus pragensis sp. nov. discovered during molecular reidentification of clinical isolates belonging to Aspergillus section Candidi
Hubka V, Lyskova P, Frisvad JC, Peterson SW, Skorepova M, Kolarik M.
Med Mycol. 2014 Jun 20. [Epub ahead of print]
Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees
Busarakam K, Bull AT, Girard G, Labeda DP, van Wezel GP, Goodfellow M.
Antonie Van Leeuwenhoek. 2014 May;105(5):849-61.
Clinical, morphological, and molecular characterization of Penicillium canis, sp. nov., isolated from a dog with osteomyelitis
Langlois DK, Sutton DA, Swenson CL, Bailey CJ, Wiederhold NP, Nelson NC, Thompson EH, Wickes BL, French S, Fu J, Vilar-Saavedra P, Peterson SW.
J Clin Microbiol. 2014 Apr 30. [Epub ahead of print]
Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov
Labeda DP, Doroghazi JR, Ju KS, Metcalf WW.
Int J Syst Evol Microbiol. 2014 Mar;64(3):894-900.
Non-Journal Publications:
Fusarium euwallaceae, a novel species cultivated by a Euwallacea ambrosia beetle that threatens avocado production in Israel and California - (Abstract Only)
Evolutionary history of Ascomyceteous Yeasts - (Abstract Only)
How does the phylogenetic species concept correlate with biological characteristics of the pathogenic species in Aspergillus section Fumigati? - (Abstract Only)
A preliminary assessment of the true morels (Morchella) in Newfoundland and Labrador - (Other)
O'Donnell, K. 2014. A preliminary assessment of the true morels (Morchella) in Newfoundland and Labrador. Omphalina. V(2):3-6.
Mel-36 – preliminary description of a new morel species - (Other)
Voitk, A., Burzynski, M., O'Donnell, K., Voitk, M., Marceau, A. 2014. Mel-36 – preliminary description of a new morel species. Omphalina. V(2):7-10.
Morel species Mel-19 – preliminary report - (Other)
Beug, M., O'Donnell, K. 2014. Morel species Mel-19 – preliminary report. Omphalina. V(2):14-15.
Fusarium and other opportunistic hyaline fungi - (Book / Chapter)
The underappreciated role of phosphonates in nature - (Peer Reviewed Journal)
The ARS Culture Collection and Developments in Biotechnology - (Abstract Only)
Overview of the ARS Culture Collection - (Abstract Only)
Ward, T.J. 2013. Overview of the ARS Culture Collection. Meeting Abstract.
Culture Collections and Public Health Research - (Abstract Only)
Ward, T.J. 2013. Culture Collections and Public Health Research. Meeting Abstract.
Data management and database structure at the ARS Culture Collection - (Abstract Only)
Labeda, D.P. 2013. Data management and database structure at the ARS Culture Collection. Meeting Abstract.
The impact of culture collections on molecular identification, taxonomy, and solving real problems - (Abstract Only)
Geiser, D.M., Kang, S., Ward, T.J., O'Donnell, K., Robert, V., Crous, P.W. 2013. The impact of culture collections on molecular identification, taxonomy, and solving real problems. Meeting Abstract.