The 100K Pathogen Genome Project was launched in July 2012 by Bart Weimer (UC Davis) as an academic, public, and private partnership. It aims to sequence the genomes of 100,000 infectious microorganisms to create a database of bacterial genome sequences for use in public health, outbreak detection, and bacterial pathogen detection. This will speed up the diagnosis of

foodborne illness Foodborne illness (also foodborne disease and food poisoning) is any illness resulting from the spoilage of contaminated food by pathogenic bacteria, viruses, or parasites that contaminate food, as well as prions (the agents of mad cow disease) ...

es and shorten infectious disease outbreaks. The 100K Pathogen Genome Project is a public-private collaborative project to sequence the genomes of 100,000 infectious microorganisms. The 100K Genome Project will provide a roadmap for developing tests to identify pathogens and trace their origins more quickly. Partners announced in the launch of the project were

UC Davis The University of California, Davis (UC Davis, UCD, or Davis) is a public land-grant research university near Davis, California. Named a Public Ivy, it is the northernmost of the ten campuses of the University of California system. The institut ...

Agilent Technologies Agilent Technologies, Inc. is an American life sciences company that provides instruments, software, services, and consumables for the entire laboratory workflow. Its global headquarters is located in Santa Clara, California. Agilent was establi ...

, and the US

Food and Drug Administration The United States Food and Drug Administration (FDA or US FDA) is a List of United States federal agencies, federal agency of the United States Department of Health and Human Services, Department of Health and Human Services. The FDA is respon ...

, with the US

Centers for Disease Control and Prevention The Centers for Disease Control and Prevention (CDC) is the national public health agency of the United States. It is a United States federal agency, under the Department of Health and Human Services, and is headquartered in Atlanta, Georgi ...

and the

US Department of Agriculture The United States Department of Agriculture (USDA) is the United States federal executive departments, federal executive department responsible for developing and executing federal laws related to farming, forestry, rural economic development, ...

noted as collaborators. As the project has proceeded, the partnership has evolved to include or replace these founding partners. The 100K Pathogen Genome Project was selected by the IBM/Mars Food Safety Consortium for metagenomic sequences. The 100K Pathogen Genome Project is conducting high-throughput

next-generation sequencing Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation s ...

(NGS) to investigate the genomes of targeted

microorganism A microorganism, or microbe,, ''mikros'', "small") and ''organism'' from the el, ὀργανισμός, ''organismós'', "organism"). It is usually written as a single word but is sometimes hyphenated (''micro-organism''), especially in olde ...

s, with

whole genome sequencing Whole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a s ...

to be carried out on a small number of microorganisms for use as a

reference genome A reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by scientists as a representative example of the set of genes in one idealized individual organism of a species. As they are assemble ...

. Most bacterial strains will be sequenced and assembled as draft genomes; however, the project has also produced closed genomes for a variety of enteric pathogens in the 100K bioproject. This strategy enables worldwide collaboration to identify sets of genetic biomarkers associated with important pathogen traits. This five-year microbial pathogen project will result in a free, public database containing the sequence information for each pathogen's genome. The completed gene sequences will be stored in the

National Institutes of Health The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late ...

(

NIH The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late ...

)'s

National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...

(

NCBI The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...

)'s public database. Using the database, scientists will be able to develop new methods of controlling disease-causing bacteria in the food chain.

References

External links

100K Pathogen Genome Project

GOLD:Genomes OnLine Database

Genome Project Database

SUPERFAMILY

The sea urchin genome database

NRCPB
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