Comparing 16S rDNA amplicon sequencing and hybridization capture for pea aphid microbiota diversity analysis

BMC Research Notes
Marie CariouSylvain Charlat

Abstract

Targeted sequencing of 16S rDNA amplicons is routinely used for microbial community profiling but this method suffers several limitations such as bias affinity of universal primers and short read size. Gene capture by hybridization represents a promising alternative. Here we used a metagenomic extract from the pea aphid Acyrthosiphon pisum to compare the performances of two widely used PCR primer pairs with DNA capture, based on solution hybrid selection. All methods produced an exhaustive description of the 8 bacterial taxa known to be present in this sample. In addition, the methods yielded similar quantitative results, with the number of reads strongly correlating with quantitative PCR controls. Both methods can thus be considered as qualitatively and quantitatively robust on such a sample with low microbial complexity.

References

Aug 2, 2006·Proceedings of the National Academy of Sciences of the United States of America·Mitchell L SoginGerhard J Herndl
Aug 19, 2007·Bioinformatics·Cécile MilitonPierre Peyret
Sep 5, 2009·Annual Review of Entomology·Kerry M OliverNancy A Moran
Oct 11, 2012·Bioinformatics·Nicolas ParisotEric Peyretaillade
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Jan 23, 2016·Methods in Molecular Biology·Céline RibièrePierre Peyret
Feb 11, 2018·Applied and Environmental Microbiology·Jolinda PollockMick Watson

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Citations

Mar 11, 2020·Frontiers in Genetics·Tobias AndermannAlexandre Antonelli

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Methods Mentioned

BETA
PCR
amplicon sequencing
in vitro transcription
chip

Software Mentioned

KASpOD
PhylArray
LightCycler 480
LightCycler

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