Includes bibliographical references.Progression of the HIV disease is characterised by a massive depletion of CD4+ T cells and it has been shown that patients living with a more advanced HIV infection have a higher risk of developing diarrhoea due to the disruption of the gastrointestinal microbiota caused by either the HIV-infection or the use of antibiotics and drugs such as highly active antiretroviral therapy (HAART). An imbalance in the microbial composition, attributable to a disturbed mucosal barrier, as well as increased permeability and inflammation caused by HIV, can influence the metabolic (carbohydrate fermentation) and protective functions provided by the microbiota. The effect of HIV on the intestinal microbiota has not been widely examined and those studies that have focused on HIV and the gastrointestinal tract, have investigated it mainly from a virological perspective. Consequently, the aim of the study was to ascertain whether the diversity and/or abundance of the endogenous intestinal microbiota of South African HIV-positive patients was disrupted on account of HIV within the gastrointestinal tract. An additional aim was to determine whether the administration of HAART affected the microbiota during a 6 month longitudinal study. The diversity of the intestinal microbial composition was characterised with respect to the total bacteria, Bifidobacterium and Lactobacillus species using PCR-DGGE. qPCR was used to determine the abundance of total bacteria, Bifidobacterium, Lactobacillus, Escherichia coli, the Bacteroides/Prevotella, Clostridium coccoides and Clostridium leptum groups. ... In addition, three potential intestinal pathogens (Clostridium difficile, Campylobacter jejuni and Salmonella enterica) were monitored by qPCR during this period, to determine their prevalence in the HIV-positive patients
