The fecal microbiota of HIV infected on Antiretroviral Therapy and HIV uninfected individuals. Fecal Microbiome of HIV-infected individuals from Mexico

Fecal samples were obtained from participants who gave informed consent. 10 individuals were HIV-uninfected and 33 were HIV-infected individuals on long-term combination antiretroviral therapy (over 2 years, with undetectable plasma HIV-1 viral loads). 18 subjects were on an Efavirenz/Tenofovir Disoproxil Fumarate/Emtricitabine (EFV/TDF/FTC)-based therapy (HIV+ EFV) and 15 were taking ritonavir-boosted protease inhibitor-based therapy (HIV+ PI). DNA was extracted using the QIAamp DNA stool minikit from QIAGEN. 16S V3-V4 libraries were prepared as instructed in the 16S Metagenomic Sequencing Library Preparation. The library was denatured with 0.2N NaOH, combined with PhiX internal control (25%) and loaded on a MiSeq reagent kit V3 (2x300 cycles; Illumina). Primary analyses were performed on the MiSeq instrument. Paired end reads were joined using join_paired_ends.py of QIIME using the fastq_join method of QIIME (Quantitative Insights into Microbial Ecology.