Synthesize references and evidence on the use of host- and diet-derived reads as natural constant references

[mikemc]

Theoretical points

• Relevant theory for how might be used for differential absolute abundance analysis in appendix Differential absolute abundance
• Can be thought of as a natural spike-in, or a reference taxon with assumed fixed abundance.
• Can be used for proportion- or ratio-based AA inference.
• Current studies seem to use in proportion mode - use the ratio (bacterial reads) / (host + diet reads) to infer bacterial biomass; if AA of individual microbes is needed, multiply this biomass estimate by MGS proportions.
• Use in ratio-mode is more robust to bias under the MWC model for the purposes of inferring fold changes across samples; however, it may be important not to aggregate reads from different taxa (e.g. host and different plants) for this method to remain robust to bias; see appendix section Multiple reference taxa.

Key empirical refs

Human or mouse gut

• zmora2018pers
• chng2020meta
• diener2021nonr

Plants

• Arabidopsis studies by Karasov, Regalado, and Weigel et al: regalado2019comb, karasov2020ther

Other

• wallace2021thed Drosophila DNA virus metagenomics

Other notes and links

Twitter discussions

• Sean Gibbons and Jotham Suez
• Fabian Staubach on using this method w/ Drosophila