USDA Notice of Intent to Sole Source the Analysis of Fecal Samples from Feral Pigs Using DNA Barcoding Methodology

The United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), National Wildlife Research Center (NWRC) located in Fort Collins, CO intends to issue a sole source purchase order to Jonah Ventures, LLC located in Boulder, CO for feral pig diet reconstruction analysis using DNA barcoding methodology on fecal samples.

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, the 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.

Previous NWCR diet reconstruction studies have been conducted using the DNA barcoding methodology being employed at Jonah Ventures, and there is no other company that does the assay in this particular way. The NWRC requires the data from prior studies to be comparable to the current studies by using the same methodology. This vendor is the only one that houses a database specific to wildlife and plants that will identify target species in the diet of invasive species (pigs). Furthermore, the assay that they use is unique to Jonas Ventures, and the application to wildlife is unique.

A one-time purchase order of $24,800.00 (310 samples @ $80.00/sample) is anticipated with Jonah Ventures (DUNS 078884021). The pricing is considered fair and reasonable based on comparison to other genetic testing prices of other organic samples.

This is not a request for quote, and no formal solicitation will be issued. This notice is for informational purposes only. However, all interested parties may contact the Contract Specialist listed below. Anyone interested in responding to this requirement must be able to provide compelling evidence that they can provide an equivalent analysis service in a timely manner and at a reasonable cost. Responses must be submitted electronically, via email, to michael.j.chiodi@usda.gov. The deadline for the submittal of responses is 1:00 pm eastern time, August 27, 2019.

.