Showing posts from April, 2013

Thinking about sampling scales in host-associated microbiota

A recent publication by RT Jones, L.G. Sanchez, and N Feirer: "A cross-taxon analysis of insect-associated bacterial diversity" started me thinking about how we sample insects.  You can see the article here at PLoSONE: In this publication, the authors perform a large collection of diverse insects and then subsequently a 16S rRNA gene amplicon analysis.  They use the V1-V2 region and 454 pyrosequencing.  They use whole insects as the source of material for the DNA extractions and perform a set of bioinformatics processing steps downstream in an attempt to reduce artifacts that may lead to inflation of diversity estimates in their samples.   From their published methods, this seems to be the order in which reads were processed: 1.    Reads are truncated (to compare across the same 16S positions) and removed “low quality reads” using QIIME’s default settings – I am not sure if ampli