HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral MicrobiomeOriginal paper
Karen Pendergrass is a microbiome researcher specializing in microbiome-targeted interventions (MBTIs). She systematically analyzes scientific literature to identify microbial patterns, develop hypotheses, and validate interventions. As the founder of the Microbiome Signatures Database, she bridges microbiome research with clinical practice. In 2012, based on her own investigative research, she became the first documented case of FMT for Celiac Disease, four years before the first published case study.
Read MoreWhat was studied?
This study asked how HIV infection on antiretroviral therapy (ART) reshapes the intestinal and oral microbiome across multiple sites. Researchers profiled the microbiome using 16S rRNA gene sequencing. Samples came from five locations: colon brush, colon wash, terminal ileum (TI) brush, TI wash, and saliva. Brush samples captured mucosa-adherent bacteria and wash samples captured the mucosal-luminal interface. Microbiome function was predicted with the PICRUSt and BugBase tools. Diversity was assessed with weighted and unweighted UniFrac distances, Faith's phylogenetic diversity, and the Shannon index.
Who was studied?
The cohort was 17 adults undergoing colonoscopy or sigmoidoscopy at the University of Miami in the United States. Five were HIV-positive and on ART, and 12 were HIV-negative controls. A total of 79 specimens were collected across the five sampling sites. Mean age was 51 years in the HIV group and 55 in controls, a non-significant difference. All HIV-positive patients were male, while controls were 8 female and 4 male. Hispanics were overrepresented, and most subjects were obese. Patients with IBD, colon cancer, or recent antibiotics were excluded.
What were the most important findings?
Beta diversity of all intestinal samples from HIV-positive patients differed significantly from controls (p equals 0.012). Intestinal Shannon diversity was higher in the HIV group (p equals 0.002). HIV-positive intestinal samples had greater abundance of biofilm-forming bacteria (p equals 0.009), potentially pathogenic bacteria (p equals 0.005), and Gram-negative bacteria (p equals 0.006). Predicted pathways for translation and nucleotide metabolism rose in HIV-positive patients, while lipid and carbohydrate metabolism favored controls. Differences were site-specific. Colon wash (p equals 0.013), colon brush trend, and TI wash (p equals 0.02) separated groups, but TI brush and saliva did not.
What are the greatest implications of this study?
The findings suggest HIV on ART alters the gut microbiome in a location-specific way while leaving the oral microbiome largely intact. This supports targeting specific gut regions to address dysbiosis. Using brush and wash samples separated strongly adherent mucosal bacteria from loosely associated communities, a more stable readout than stool alone. The small sample (5 HIV-positive, 12 controls), sex imbalance, and high obesity rate limit generalization. The study did not link microbiome shifts to immune measures such as CD4 T cell counts, so causation cannot be inferred.