Chapter 9 - Microbial Community Composition and Predicted Functional Attributes of Antarctic Lithobionts Using Targeted Next-Generation Sequencing and Bioinformatics Tools

Publication date: 2018Source: Methods in Microbiology, Volume 45Author(s): Hyunmin Koo, Joseph A. Hakim, Casey D. Morrow, Dale T. Andersen, Asim K. BejAbstractThis chapter focuses on the rationale and implementation of a suite of software in the data management, processing, and statistical analysis used towards establishing reliable microbial community compositions, predictive functions, and other useful downstream bioinformatics analyses, using NGS data generated by the Illumina Miseq targeted metagenomics approach. This chapter also emphasizes the importance of using multiple taxonomic databases and software to obtain a comprehensive microbial community composition and associated functional profiles. We have used previously unpublished 16S rRNA amplicon-based next-generation sequencing (NGS) dataset of lithobiont communities (rock-dwelling microorganisms) of the Untersee Oasis, Antarctica, as an example of microbial communities in an atypical environment. The bioinformatics workflow includes “Module A”, which describes obtaining the NGS files from purified lithobiont metacommunity DNA; “Module B” elaborates the steps involved in processing and assessing the sequence quality, and subsequent sequence alignment against publicly available microbial taxonomic databases (i.e. Greengenes and SILVA), to designate identities to a list of operational taxonomic units representing the microbial communities. Lastly, “Module C” presents the microbial community compositions at...
Source: Methods in Microbiology - Category: Microbiology Source Type: research