Oral Paper

         Phylogenomics

Eukaryotic metagenomic identification: “off label” bioinformatics for mixed botanical samples

Presenting Author
Liz Hunter
Description
Even as the cost of genomic sequencing decreases dramatically, and the technology for longer and more accurate data improves, reliable metagenomic identification of unknown plants remains challenging. Identification of mixed samples is highly relevant for food safety questions that arise at the U.S. Food and Drug Administration for a variety of consumer products, including botanical dietary supplements. These products continue to rise in popularity, with more and more Americans purchasing and consuming them each year. They are typically ground, processed, or otherwise devoid of morphological characters, making visual methods of identification difficult. Historically, both the methods and the analysis pipelines have focused on barcodes, organellar genomes, or targeted assays for specific groups, all of which pose their own limitations. Here, we attempt to optimize and adapt some of the numerous popular workflows available for prokaryotic metagenomics to mixed botanical samples. Some of these modifications include expanded database representation for Viridiplantae using NCBI WGS, tiered identification, and enhanced filtering metrics to reduce background noise. We are also incorporating recent innovations in the field of metagenomics such as DNA sketching algorithms for taxonomic classification. Additionally, we are exploring the application of long read data to improve both the reference databases available, and the methodology used to make identifications. We hope this research will inform future studies on the best ways to leverage existing tools for prokaryotic metagenomics “off label” for mixed botanical samples.