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mikemc / differential-abundance-theory

A manuscript exploring the effects of taxonomic bias on microbiome differential-abundance analysis.
https://mikemc.github.io/differential-abundance-theory
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Synthesize spike-in approach of Zemb et al 2020 #6

Closed mikemc closed 2 years ago

mikemc commented 3 years ago

Zemb O, Achard CS, Hamelin J, De Almeida M, Gabinaud B, Cauquil L, Verschuren LMG, Godon J. 2020. Absolute quantitation of microbes using 16S rRNA gene metabarcoding: A rapid normalization of relative abundances by quantitative PCR targeting a 16S rRNA gene spike‐in standard. Microbiologyopen 9:1–21. doi:10.1002/mbo3.977 https://onlinelibrary.wiley.com/doi/abs/10.1002/mbo3.977

At least two interesting things to consider in this study

  1. they apply the synthetic DNA standard prior to DNA extraction
  2. They use qPCR of the synthetic standard and use this info somehow

The earlier experiment of Tkacz et al (2018) is also relevant

mikemc commented 3 years ago

rao2021mult compare cell and DNA spike-ins (both pre-extraction) in p7 of their SI methods. They interpret their results as suggesting that cell spikes are better as a catch for DNA extraction failures.