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J Microbiol Methods. 2013 Nov;95(2):149-55. doi: 10.1016/j.mimet.2013.08.007. Epub 2013 Aug 19.

Minimization of chloroplast contamination in 16S rRNA gene pyrosequencing of insect herbivore bacterial communities.

Author information

1
Department of Bacteriology, 6145 Microbial Sciences Building, 1550 Linden Dr, University of Wisconsin-Madison, Madison, WI 53706, United States. Electronic address: hanshew@wisc.edu.

Abstract

Chloroplast sequence contamination in 16S ribosomal RNA gene (16S) analyses can be particularly problematic when sampling microbial communities in plants and folivorous arthropods. We previously encountered high levels of plastid contamination in herbivorous insect samples when we used the predominant 454 pyrosequencing 16S methodologies described in the literature. 799F, a primer previously found to exclude chloroplast sequences, was modified to enhance its efficacy, and we describe, in detail, our methodology throughout amplicon pyrosequencing. Thirteen versions of 799F were assessed for the exclusion of chloroplast sequences from our samples. We found that a shift in the mismatch between 799F and chloroplast 16S resulted in significant reduction of chloroplast reads. Our results also indicate that amplifying sequences from environmental samples in a two-step PCR process, with the addition of the multiplex identifiers and 454 adapters in a second round of PCR, further improved primer specificity. Primers that included 3' phosphorothioate bonds, which were designed to block primer degradation, did not amplify consistently across samples. The different forward primers do not appear to bias the bacterial communities detected. We provide a methodological framework for reducing chloroplast reads in high-throughput sequencing data sets that can be applied to a number of environmental samples and sequencing techniques.

KEYWORDS:

16S rRNA Gene; 454 Pyrosequencing; Chloroplast; Insect; Symbiosis

PMID:
23968645
PMCID:
PMC4133986
DOI:
10.1016/j.mimet.2013.08.007
[Indexed for MEDLINE]
Free PMC Article

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