DATE: January 30, 2018
TIME: 9:00AM PST, 12:00PM EST

Infectious disease surveillance and monitoring is critical in settings where disease outbreaks and antibiotic resistance can dramatically impact human health.  Rapid and accurate detection of human pathogens between closely related strains and across phylogenetic kingdoms is paramount to mitigate disease outbreaks and to diagnose affected individuals.  Here, we use demonstrate cross-kingdom species detection by simultaneously sequencing DNA from 8 bacteria and 2 fungi in the ZymoBIOMICS control.  We test this on long-read (PacBio, oxford nanopore), short read (Illumina), and linked, long-read (10x Genomics) platforms.  We also show that these standard aliquots can be used for benchmarking a variety of tools and also characterize their epigenetic changes (base modifications).  These standards are now being used internationally as part of a large-scale effort and improving metagenomics use in the clinic, or “precision metagenomics.” 

Learning Objectives:

• Describe the impact of a sickness on the proportion of natural flora.

• List tools implemented for microbiome and metagenome data analysis and species detection, such as BLAST, MetaPhlAn, and CLARK

• Describe the utility of metagenome standards and benchmarking measures

• List the most prevalent bacteria of the skin, gastrointestinal (GI) tract, oral cavity, and urogenital tract