Interesting new paper in PLOS One: PLOS ONE: Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities
Full citation: Kittelmann S, Seedorf H, Walters WA, Clemente JC, Knight R, et al. (2013) Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities. PLoS ONE 8(2): e47879. doi:10.1371/journal.pone.0047879
Basically, the paper describes the development and use of a PCR strategy to simultaneously characterize eukaryotic, bacterial and archaeal microbes from samples.
Primers used are summarized in Table 2
The strategy they employ attempt to correct for differences in amplification differences between the different amplicons which should therefore allow better normalization of relative abundance estimates. See results in Figure 2.
Definitely worth a look.
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Jonathan Eisen's Lab 