HIV Exposure in Childhood to Reduced Adaptability of Oral Microbiome

Once regarded solely as potential threats to health, bacteria are now recognized as essential partners in human well-being. While the gut microbiome—the vast community of microorganisms living in the digestive tract—has been the focus of intense scientific interest, the mouth, the second most diverse microbial environment in the body, has received comparatively little attention (1^✔ ✔Trusted Source
HIV infection and exposure is associated with increased cariogenic taxa, reduced taxonomic turnover, and homogenized spatial differentiation for the supragingival microbiome

Go to source). Researchers from Penn Dental Medicine, led by Modupe O. Coker, are working to change that. A collaborative study, recently published in Microbiome, explores how early immune challenges, such as HIV exposure and infection, influence the oral microbiome in children and, in turn, affect systemic health.

“Mouth microbes are central to health—they are the first to encounter food, supporting digestion and nutrient absorption,” says Coker, assistant dean of clinical and translational research and co-senior author of the study. “But bacteria in the mouth don’t stay in the mouth—they interact with the rest of the body, influencing systemic health, and systemic health influences them in return.”

The study involved children in Nigeria divided into three groups:

• Children living with HIV and receiving highly active antiretroviral therapy (HAART)
• Children perinatally exposed to HIV but uninfected
• Children with no HIV exposure or infection

Supragingival plaque samples (above the gum line) were collected at three time points to assess microbial diversity, distribution, and changes over time.

“This population is near and dear to us,” says Coker. “Studying them gives us a unique lens into how early-life immune system challenges shape oral health and broader developmental outcomes, such as growth and cognitive function.”

Surprising Findings on Microbial Stability

The researchers examined “taxonomic turnover”—a measure of how much a microbial community changes over time. In the gut, stability is considered healthy; in the mouth, however, the opposite appears to be true.

“All children face constant changes in their oral environment—food, hormones, mixed dentition—so adaptability is important,” explains first author Allison E. Mann, assistant professor of biological anthropology at the University of Wyoming. “We found that children unexposed to HIV had more fluctuation over time, indicating adaptability. Children exposed to HIV—whether infected or not—had lower turnover, suggesting impaired flexibility.”

Lower turnover was also linked to higher levels of cavity-causing bacteria, potentially increasing the risk of dental caries in HIV-affected populations.

Disrupted Microbial Geography

The team also mapped the spatial distribution of oral microbes. Normally, distinct bacterial communities live in the front (anterior) and back (posterior) regions of the mouth. Among HIV-exposed and infected children, these differences were diminished, resulting in more homogeneous communities.

“This suggests the virus and possibly the treatment may be affecting salivary glands differently across the mouth,” says Vincent P. Richards, co-senior author and associate professor of biological sciences at Clemson University. Reduced salivary flow and increased acidity in HIV-positive children could be key factors in this shift.

A Two-Way Street Between Oral and Systemic Health

The findings highlight the cyclical relationship between oral and systemic health. Early-life disruptions to the immune system—such as HIV exposure—can alter the oral microbiome, which in turn can affect systemic health outcomes.

“We’re only beginning to understand how these interactions work,” Coker says. “This research opens the door to new prevention and treatment strategies that take both oral and systemic health into account.”

The study underscores the importance of oral health in public health strategies for children facing early immune challenges. By better understanding the oral microbiome’s adaptability—or lack thereof—scientists may one day be able to intervene early, improving both oral and overall health outcomes.

Reference:

1. HIV infection and exposure is associated with increased cariogenic taxa, reduced taxonomic turnover, and homogenized spatial differentiation for the supragingival microbiome - (https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02123-9)

Source-Medindia