The oral microbial community (microbiota) plays a critical role in human health 
and disease. Alterations in the oral microbiota may be associated with disorders 
such as gingivitis, periodontitis, childhood caries, alveolar osteitis, oral 
candidiasis and endodontic infections. In the immunosuppressed population, the 
spectrum of potential oral disease is even broader, encompassing candidiasis, 
necrotizing gingivitis, parotid gland enlargement, Kaposi's sarcoma, oral warts 
and other diseases. Here, we used 454 pyrosequencing of bacterial 16S rRNA genes 
to examine the oral microbiome of saliva, mucosal and tooth samples from 
HIV-positive and negative children. Patient demographics and clinical 
characteristics were collected from a cross-section of patients undergoing 
routine dental care. Multiple specimens from different sampling sites in the 
mouth were collected for each patient. The goal of the study was to observe the 
potential diversity of the oral microbiota among individual patients, sample 
locations, HIV status and various dental characteristics. We found that there 
were significant differences in the microbiome among the enrolled patients, and 
between sampling locations. The analysis was complicated by uneven enrollment in 
the patient cohorts, with only five HIV-negative patients enrolled in the study 
and by the rapid improvement in the health of HIV-infected children between the 
time the study was conceived and completed. The generally good oral health of 
the HIV-negative patients limited the number of dental plaque samples that could 
be collected. We did not identify significant differences between 
well-controlled HIV-positive patients and HIV-negative controls, suggesting that 
well-controlled HIV-positive patients essentially harbor similar oral flora 
compared to patients without HIV. Nor were significant differences in the oral 
microbiota identified between different teeth or with different dental 
characteristics. Additional studies are needed to better characterize the oral 
microbiome in children and those with poorly-controlled HIV infections.