Fecal bacterial microbiome diversity in chronic HIV-infected patients in China

Abstract

The purpose of this study was to identify fecal bacterial microbiome changes in patients with chronic human immunodeficiency virus (HIV) infection in China. Bacterial 16S rRNA genes were amplified, sequenced (454 pyrosequencing), and clustered into operational taxonomic units using the QIIME software. Relative abundance at the phylum and genus levels were calculated. Alpha diversity was determined by Chao 1 and observed-species indices, and beta diversity was determined by double principal component analysis using the estimated phylogeny-based unweighted Unifrac distance matrices. Fecal samples of the patients with chronic HIV-infection tended to be enriched with bacteria of the phyla Firmicutes (47.20%±0.43 relative abundance) and Proteobacteria (37.21%±0.36) compared with those of the non-HIV infected controls (17.95%±0.06 and 3.81%±0.02, respectively). Members of the genus Bilophila were exclusively detected in samples of the non-HIV infected controls. Bacteroides and arabacteroides were more abundant in the chronic HIV-infected patients. Our study indicated that chronic HIV-infected patients in China have a fecal bacterial microbiome composition that is largely different from that found in non-HIV infected controls, and further study is needed to evaluate whether microbiome changes play a role in disease complications in the distal gut, including opportunistic infections.Emerging Microbes & Infections (2016) 5, e31; doi:10.1038/emi.2016.25; published online 6 April 2016Chinese patients with chronic HIV exhibit clear differences in their gut microbe populations compared with healthy controls. Infections and illness, along with the drugs used to treat them, can change the natural microbial ecosystem in the gut, which varies not just from person to person but also between ethnic groups. To investigate gut microbe diversity in the Chinese population, Hong-zhou Lu at Fudan University, Shanghai, together with Ben Li at Shanghai TargetDrug Ltd and co-workers, conducted a small-scale genetic sequencing study of microbial diversity in the feces of 13 patients with HIV and four healthy controls. The HIV-infected individuals exhibited significant differences compared with the controls, including reduced microbial diversity and higher levels of certain bacteria. Further investigations could clarify the role of this diversity in disease complications, and enhance understanding of differences between ethnic groups.

Keywords

• antiretroviral treatment
• feces
• HIV
• microbiome
• 16S rRNA