[daemonk]

Are you guys depleting host or enriching microbial? Are you analyzing the data as a composition via log contrasts? Are you using available pipelines (kraken, metaphlan, etc) or something custom? Any plans on doing a functional pathway analysis (ie. humann pipeline) on top of the microbial analysis?

[david_l_lin]

Great questions! We implement a host-depletion step in both the wet lab, to increase sequencing depth of the microbiome, and dry lab. You may be concerned about potential bias introduced, and we've done some extensive research with our depletion and sequencing methods to reduce the cost of the test while also maintaining integrity of the microbiome profiles.

Regarding pipelines: we use a custom pipeline that is similar in principle to available pipelines you mentioned (part of our secret sauce). We are actively working on functional analysis, as we hope to eventually develop targeted therapeutics that exploit microbial pathways to prevent disease.

[daemonk]

Thanks for the response. I think protocol-bias is something that will be hard to control for. The collection kit, extraction method, library prep method can influence the results significantly from my experience. For example, we've seen significant differences in results between tagmentation-based lib prep vs ligation-based.