Department of Medicine, New York University School of Medicine, New York, Ny 10016, USA
To identify microbial targets for treatment of HIV enteropathy, we contrasted microbiota composition between HIV-1-infected patients and HIV-negative controls in the esophagus, stomach, and duodenum as well as the mouth using a universal 16S rRNA gene survey and correlated the findings with HIV serostatus and peripheral blood T-cell counts. HIV infection was associated with an enrichment of Proteobacteria and depletion of Firmicutes in the proximal gut. In particular, environmental species Burkholderia fungorum and Bradyrhizobium pachyrhizi colonized the duodenum of HIV patients who had abnormal blood CD4+ T-cell counts but were absent in HIV-negative controls or HIV patients whose CD4 counts were normal. The two species coexisted and exhibited a decreasing trend proximally towards the stomach and esophagus and were virtually absent in the mouth. Their abundance was inversely correlated with CD4 counts but not viral load. The colonization of the duodenum by environmental bacteria reflects loss of colonization resistance in HIV infection. Their correlation with CD4 counts suggests that compromised immunity could be responsible for the observed invasion by exogenous microbes. These findings warrants further studies to elucidate their etiological role and evaluate efficacy of antibiotic therapies.