SPADA Book - April 11, 2017

Technical Assessment: Metagenomics Approaches

Environmental Samples

Bacteria

Community DNA

Amplicon (16S rRNA gene PCR)

Metagenomics

Whole genome (species)

Targeted (species)

7

FOR OFFICIAL USE ONLY

Technical Assessment: Sequencing Comparison

Targeted Methods (amplicon or enrichment)

Shotgun Metagenomics

Cost

• Cheaper

• Expensive

Bioinformatics • Signature selection and PCR design • Analysis

• Database construction • Database screening

Bias

• All methods biased in some way • Based on target selected • Need to minimize PCR or hybridization bias

• Minimally biased

Focus

• Operational Suitability

• DHS S&T (research)

8

4