Data from: Assessment of a 16S rRNA amplicon Illumina sequencing procedure for studying the microbiome of a symbiont-rich aphid genus

The bacterial communities inhabiting arthropods are generally dominated by
a few endosymbionts that play an important role in the ecology of their
hosts. Rather than comparing bacterial species richness across samples,
ecological studies on arthropod endosymbionts often seek to identify the
main bacterial strains associated with each specimen studied. The
filtering out of contaminants from the results and the accurate taxonomic
assignment of sequences are therefore crucial in arthropod microbiome
studies. We aimed here to validate an Illumina 16S rRNA gene sequencing
protocol and analytical pipeline for investigating endosymbiotic bacteria
associated with aphids. Using replicate DNA samples from 12 species
(Aphididae: Lachninae, Cinara) and several controls, we removed individual
sequences not meeting a minimum threshold number of reads in each sample
and carried out taxonomic assignment for the remaining sequences. With
this approach, we show that: i) contaminants accounted for a negligible
proportion of the bacteria identified in our samples; ii) the taxonomic
composition of our samples and the relative abundance of reads assigned to
a taxon were very similar across PCR and DNA replicates for each aphid
sample; in particular, bacterial DNA concentration had no impact on the
results. Furthermore, by analysing the distribution of unique sequences
across samples rather than aggregating them into operational taxonomic
units (OTUs), we gained insight into the specificity of endosymbionts for
their hosts. Our results confirm that Serratia symbiotica is often present
in Cinara species, in addition to the primary symbiont, Buchnera
aphidicola. Furthermore, our findings reveal new symbiotic associations
with Erwinia and Sodalis-related bacteria. We conclude with suggestions
for generating and analysing 16S rRNA gene sequences for arthropod
endosymbiont studies.