Shotgun Sequencing of Termite and Anaerobic Digester Metagenomes

DNA samples described in previous 16S rRNA community profiling studies were used in the present study for shotgun sequencing. These comprised four termite samples; MC05, MC06, MC07, and IN01 (Abdul Rahman et al., 2015 (link)) and six anaerobic digester samples taken from 3 reactors (AD1-3) at two time points (day 96 and 362; Vanwonterghem et al., 2014 (link)). A publicly available sheep rumen metagenome (BioProject acc. PRJNA214227) was also included in the study together with two reference genomes; F. succinogenes S85 (BioProject acc. PRJNA41169) and C. alkaliphilus ACht1 (BioProject acc. PRJNA195589). Shotgun libraries were prepared using the Nextera XT Sample Preparation Kit (or TruSeq DNA Sample Preparation Kits v2 for AD1-3 day 96) (Illumina, San Diego, CA, USA) and library DNA concentrations were measured using the QuantIT kit (Molecular probes, Carsbad, CA, USA) and equimolar-pooled for sequencing. Between a quarter and a third of an Illumina HiSeq 2000 flowcell of paired-end sequences (2 × 100 bp with an average fragment size of 320) were obtained for each library.