title: A flexible and economical barcoding approach for highly multiplexed amplicon sequencing of diverse target genes.
abstract: High throughput sequencing of phylogenetic and functional gene amplicons provides tremendous insight into the structure and functional potential of complex microbial communities. Here, we introduce a highly adaptable and economical PCR approach to barcoding and pooling libraries of numerous target genes. In this approach, we replace gene- and sequencing platform-specific fusion primers with general, interchangeable barcoding primers, enabling nearly limitless customized barcode-primer combinations. Compared to barcoding with long fusion primers, our multiple-target gene approach is more economical because it overall requires lower number of primers and is based on short primers with generally lower synthesis and purification costs. To highlight our approach, we pooled over 900 different small-subunit rRNA and functional gene amplicon libraries obtained from various environmental or host-associated microbial community samples into a single, paired-end Illumina MiSeq run. Although the amplicon regions ranged in size from approximately 290 to 720 bp, we found no significant systematic sequencing bias related to amplicon length or gene target. Our results indicate that this flexible multiplexing approach produces large, diverse, and high quality sets of amplicon sequence data for modern studies in microbial ecology.
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna Vienna, Austria.
authors.forename: Craig W
authors.initials: CW
authors.lastname: Herbold
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna Vienna, Austria.
authors.forename: Claus
authors.initials: C
authors.lastname: Pelikan
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna Vienna, Austria.
authors.forename: Orest
authors.initials: O
authors.lastname: Kuzyk
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna Vienna, Austria.
authors.forename: Bela
authors.initials: B
authors.lastname: Hausmann
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna Vienna, Austria.
authors.forename: Roey
authors.initials: R
authors.lastname: Angel
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna Vienna, Austria.
authors.forename: David
authors.initials: D
authors.lastname: Berry
authors.affiliation: Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research Network Chemistry Meets Microbiology, University of Vienna Vienna, Austria.
authors.forename: Alexander
authors.initials: A
authors.lastname: Loy
keywords: 16S rRNA; MiSeq; amoA; dsrA; dsrB; functional gene; nifH; nxrB