DNA Diet Reconstruction

USDA APHIS intends to contract for DNA Diet Reconstruction services on a sole source basis with Jonah Ventures. Any vendors capable of meeting this requirement are encouraged to send a capability statement to the contracting officer prior to 12:01 PM CST on 09/09/2016. Statement of Work Background A recently-developed method to determine the diet of animals is deoxyribose nucleic acid (DNA) barcoding. When animals consume organisms, not all of the prey DNA is digested before defecation. As such, DNA can be isolated from feces and then used to reconstruct the animal's diet (Valentini et al. 2009, Kowalczyk et al. 2011). With this technique, total DNA is extracted from the sample, DNA is amplified using primers that capture all possible plant and animal taxa, and the polymerase chain reaction (PCR) amplified DNA is sequenced. A reference database is then used to match resulting sequences to given taxa with the relative abundance of sequences from individual taxa in each fecal sample used as an index of the amount of each plant and animal consumed by the target species. An important key to the process is to identify the best primers to use as there is a balance between species specificity, universality, and sequence length. For herbivores, many studies have used the intron of the gene that codes for chloroplast tRNA for leucine (trnL), which is relatively short (40-140 bp), has been sequenced for many species, and has relatively high species specificity. To reconstruct the animals in the diet, a portion of the cytochrome oxidase subunit 1 (COI) is used. Scope The contractor will conduct DNA barcoding on 550 fecal samples from feral swine, rodents, lizards, and birds. Metabarcoding along with proprietary bioinformatics pipelines will be used to determine the diet of these animals. Tasks Contractor will extract total DNA from the 550 frozen fecal samples. DNA will be amplified using primers that capture all possible plant and animal taxa, and the polymerase chain reaction (PCR) amplified DNA will then be sequenced. A reference database of diet species, assembled or acquired by the vendor for use in analyses, will be used to match resulting sequences to given plant and animal taxa with the relative abundance of sequences from individual plant and animal taxa in each fecal sample used as an index of the amount of each taxa consumed by the animal. Delivery Contractor will deliver sequencing results in a spreadsheet along with any assessments of sequencing quality and performance statistics. All samples will be submitted and dollars spent by March, 2017. Government-furnished property N/A Security There are no security requirements associated with this contract. Place of performance Performance will be at the contractor's facility. Period of performance Government shall deliver samples via overnight shipping after contract award. Vendor will submit results to the government no later than 45 days after receiving samples. Statement on sole source provider There is currently no other vendor in the United States that offers this service commercially.