Has anyone ever used 16S rDNA pyrosequencing to identify gut microbiota populations? We have a PyroMark Q96 and I would like to adapt the sequencing protocol to assess gut microbiota in faecal samples.
Cummings, P. J., Ahmed, R., Durocher, J. A., Jessen, A., Vardi, T., Obom, K. M. Pyrosequencing for Microbial Identification and Characterization. J. Vis. Exp. (78), e50405, doi:10.3791/50405 (2013).
However, pyrosequencing is relatively old, and most of the amplicon sequencing now a days are illumina based.
Initially parallel sequencing for microbial population studies was generally by pyrosequencing on the Life sciences 454 instrument. The company was acquired by Roche who discontinued the instrument 2013. I am not sure if your instrument has some of the same limitiations, (e.g. homopolymer issues) but a great deal of work was done to get good metagenomic data from the 454 instrument. I think you can access archived versions of the Mothur pipeline with good error correction techniques. https://mothur.org/wiki/454_sop/
Thank you, Dr. Frank R Burns, Dr. Abhijeet Singh for the informative answers.
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