Shotgun seq. gut microbiome Sample536
Gut microbiome profiles of 327 individuals with HIV, 202 of whom on antiretroviral treatment, and 260 control participants from three diverse cohorts (Uganda, Botswana and the US) were analyzed through whole-metagenome sequencing of faecal samples. Following phenol:chloroform:isoamyl alcohol extraction, including a homogenization step, DNA and RNA fractions were separated with the AllPrep DNA/RNA Mini Kit (Qiagen). Libraries were prepared with the Nextera XT DNA Library Preparation kit (Illumina) and sequenced on the Illumina HiSeq 2500 platform, with a per-sample target of ten million paired end reads of 101 base pairs. TrimGalore! (v. 0.4.4) and KneadData (v. 0.7.2) were used to remove adaptor- and human sequences, respectively.