FDA has developed, and continues to develop, reference databases for use by food safety officials, the food industry, and scientific researchers, to help ensure the safety and proper labeling of the food supply. FDA also maintains long-term food monitoring programs which are designed to gather both nutrient and safety information about the foods consumed in the United States. 

The reference databases contain genomic and other descriptive information that can be used as a resource for identifying single and multicellular organisms. Some of the databases contain information about bacterial pathogens, harmful fungi, parasites, viruses, or pests – which are undesirable to have in or around food due to their ability to cause illness, to be a vector for transmitting foodborne pathogens, or to be considered filth. Proper identification of these undesirable organisms is an essential capability in foodborne illness investigations and can help food producers and processors determine the appropriate controls required to mitigate against them throughout the food production process.

Some of the databases contain information about live microbials which may be used as ingredients in foods, including cultured foods, and dietary supplements. Still other databases contain information that allows species of plants and seafood that may appear in food or dietary supplements to be verified. Verification of ingredients is important for those who manage ingredient supplies, allowing them to ensure they are sourcing the desired ingredients/foods, that appropriate preventive controls for the ingredients/foods are in place, and that a product’s labeling complies with applicable laws and regulations. It also allows public health officials to confirm the identity of these ingredients/foods during foodborne illness outbreak investigations.

FDA’s long-term monitoring programs include the Total Diet Study, which provides information about the levels of both nutrients and contaminants that U.S. consumers are exposed to through the food supply, and the Pesticide Residue Monitoring Program, which helps FDA ensure that foods treated with pesticides are safe to eat.

Below is a list of FDA reference databases and monitoring programs, including links to the respective database or monitoring program data, and additional information about these individual efforts.

Cyclospora Database 
Database of genomic sequences from Cyclospora cayetanensis and other apicomplexan parasites from food, environmental, and clinical samples applicable for molecular epidemiology during foodborne illness outbreak investigations. 

Foodborne Viruses Database 
Database of genomic sequences from a wide range of foodborne viruses (e.g., norovirus, hepatitis A, sapovirus, etc.) isolated from food, environmental, and clinical samples. The sequences serve as references for phylogenetic analyses and epidemiologic studies linked to foodborne illnesses. 

Fungi Genome Database 
Database of whole genome sequence of fungi (molds) found in foods. The sequence information can be used for strain identification, characterization, and accurately cataloging mycotoxins (fungal toxins) from food.

GenomeTrakr Database/NCBI Pathogen Detection Portal
Database of genomic sequences and supporting metadata from foodborne pathogens isolated from food, environmental, and clinical samples. The information in the database is used regularly in foodborne illness investigations and other food safety applications. Examples of how public health officials, industry members, and researchers use this information can be found at FDA’s Whole Genome Sequencing (WGS) Program. 

Insect Database
Database of mitochondrial genomes (mitogenomes) from insect species that can potentially contaminate food products. The genomic information and corresponding metadata can be used for screening and the rapid detection of insects in foods. 

Live Microbial Ingredients Survey Database
Database of genomic sequences from non-harmful live microorganisms intentionally added to foods, including cultured foods, and dietary supplements. The sequence information can be used for strain verification and characterization. 

Pesticide Residue Monitoring Reports and Data 
Reports and data generated from the testing FDA does as part of its Pesticide Residue Monitoring Program, to help ensure that any pesticide residue remaining on food is within the safety tolerances set by the U.S. Environmental Protection Agency and that no unapproved pesticides are present. 

Plant Genome Database 
Database of genomic sequences from morphologically identified plants. The sequences are predominantly of plants considered to be foods or dietary supplements. The database also includes closely related plant species, as well as plants that are known toxin producers, contaminants, or adulterants.

Reference Standard Sequence Library (RSSL) for Seafood Identification
A searchable library of DNA reference sequences for many species of seafood. The DNA sequences can be used in conjunction with The Seafood List to assist with the proper labeling and HACCP assessment of seafood products intended for the U.S. market. 

The Seafood List 
The Seafood List is FDA's guide to determine acceptable market names for seafood sold in interstate commerce and includes a searchable database that contains the type (vertebrate, invertebrate, or crustacean), acceptable market name, common name, and scientific name for each seafood species.

Total Diet Study
FDA’s Total Diet Study (TDS) monitors levels of nutrients (for example, calcium and iron) and contaminants (for example, arsenic and lead) in foods eaten in the United States. Using these data, FDA estimates the average amount of nutrients and contaminants the entire U.S. population and subpopulations eat each day. The TDS complements FDA’s other food safety and nutrition programs.