The understanding of the human microbiome continues to grow rapidly. Innumerable projects have been launched worldwide to understand the role that the microbiome plays and its impact on human health. However, information on the role of the microbiome on HIV infection, prevention, and treatment is still limited.
Sara Gianella Weibel, MD, on behalf of Infectious Disease Advisor, talks with Nichole Klatt, PhD, associate professor in the department of pharmaceutics at University of Washington in Seattle about the importance of the human microbiome on HIV, including the next steps in research and its relevance in clinical practice.
Infectious Disease Advisor: Dr Klatt, can you tell us about the human microbiome and why is it so important for human health in general?
Nichole Klatt, PhD: The human body harbors 10 to 100 trillion symbiotic microbial cells, with more than twice as many bacterial cells than human cells. Bacteria altogether can constitute several pounds of our body weight. These bacteria are important constituents of the human microbiome and they are an important and very active part of all mucosal tissues and body fluids (oral, gut, genital, skin, airways). In fact, the microbiome is integral in many functions and likely plays a crucial role for the immunologic, hormonal, and metabolic homeostasis of the host.
Infectious Disease Advisor: What factors affect the human microbiome? For example, do we know if there are differences by geographic location, diet, sex or sexual orientation, or other factors?
Dr Klatt: There are certainly geographic differences in microbiome composition and diversity. Recent studies have also demonstrated divergences in the microbiome structure between healthy individuals from different race and ethnicity.1 The microbiome is distinct to each body site, such as lung, oral, gut, penile, and vaginal microbiomes. There are also differences within each anatomic site, such as different parts of the gastrointestinal tract or within the female reproductive tract.2There are also possibly differences related to sexual practices and lifestyle.3
A caveat of microbiome studies, however, is that the use of extremely varied material and methods has led to inconsistent findings, and future larger microbiome studies will need to control for all the behavioral and social factors.
Infectious Disease Advisor: Can we characterize people’s microbiome, and what can this tell us about their health?
Dr Klatt: Different methods can be used to characterize the human microbiome at various mucosal sites, most frequently by sequencing 16s rRNA bacterial genes. In this regard, the American Gut Microbiome Project (which is led by Dr Rob Knight, UCSD) is the world’s largest crowd-funded science project in existence. This initiative is collecting and sequencing stool samples from the entire population and enables participants to learn about their own body’s microbes while also contributing to the greater scientific knowledge. The goal is to learn how the human microbiome is associated with various aspects of our health — from associations with diet to the amount of alcohol consumed to whether or not someone has autism or any other disease. Because all de-identified data are made freely available, researchers from all over the world can access the data to ask questions about the microbiome and its association with a variety of health and lifestyle factors.
Additional advances in our understanding of the microbiome will hopefully provide exciting prospects for exploiting and manipulating the microbiome to improve our health.
Infectious Disease Advisor: Regarding HIV, does the virus itself interact with the human microbiome in either direction?
Dr Klatt: HIV infection is associated with alterations in the gut microbiome, which occur early in the course of infection and are not fully restored with antiretroviral therapy. Mucosal HIV replication and consequent depletion of CD4+ T cells in the gut is associated with epithelial barrier damage (leaky gut) and increased translocation of bacterial products from the gut into systemic blood circulation (microbial translocation). In turn, microbial translocation is associated with systemic immune activation and predicts disease progression and mortality in both untreated and treated HIV-infected individuals.4,5 However, the interactions between HIV, antiretroviral therapy, human sexual behavior, and the gut microbiome are complex and sorting out these interactions will be important to design future interventions. Also, the effect of HIV on the microbiome in other mucosal sites (eg, genital tract, oral) is not as well studied.
Infectious Disease Advisor: You recently published a paper in Science demonstrating that tenofovir efficacy in women depends on the composition of the vaginal microbiome.6 Can you tell us a little more about this study?
Dr Klatt: In our paper, we used stored samples from 688 women enrolled in the CAPRISA 004 clinical trial to investigate whether the composition of the vaginal microbiome modulates the microbicide efficacy of tenofovir gel used as pre-exposure prophylaxis (PrEP) to prevent HIV infection. In this study, cervicovaginal lavages from women who were assigned to either the tenofovir or the placebo-gel arm were analyzed by protein mass spectrometry and 16s ribosomal RNA sequencing. Our data suggest that women with non-Lactobacillus-dominant vaginal flora have decreased efficacy of tenofovir-based mucosal preventions. On the other hand, bacterial communities rich in Lactobacillus may improve efficacy of topical microbicide gels. Importantly, we found that the mechanism underlying this altered efficacy is likely that dysbiotic bacteria such as Gardnerella vaginalis can directly metabolize tenofovir, likely leading to ineffective levels of tenofovir gel in women with these bacteria. Vaginal microbiota screening could be a useful tool to enhance efficacy of HIV prevention in women.
Infectious Disease Advisor: Do you think that the gut microbiome could have a similar effect on oral antiretroviral therapies?
Dr Klatt: That is a good question and we currently don’t know. Further studies are ongoing to investigate the role of the gut microbiome composition in pharmacokinetics of oral antiretroviral drugs.
It is important to note that one recent study among African women with a high prevalence of bacterial vaginosis found similar efficacy of daily oral PrEP for HIV prevention among women with abnormal vs healthy vaginal microbiota as defined by Nugent score,7 suggesting that the vaginal microbiome is not negatively affecting oral PrEP. However, this needs to be further studied, considering that bacterial vaginosis testing does not accurately measure vaginal microbial dysbiosis, and this should be more carefully evaluated using 16S rRNA sequencing of the microbiome of these women.
Infectious Disease Advisor: Are there any other research questions related to the microbiome and HIV that should be considered?
Dr Klatt: For the future, we need to understand the potential role of other (less well studied) microbiomes, including both non-enteric microbial communities (different body sites) as well as other domains of life beyond bacteria. For example, fungal and viral microbiomes are critical to study. We do know that there is an expansion of the enteric virome during HIV infection, but the exact meaning of this finding is not known.8 For example, certain viruses such as bacteriophage are critical for bacterial regulation, but further studies to understand their exact function and interactions are needed. The fungal microbiome is even less well known. It is clear that fungal species are important in health and there is evidence of increased fungal products in the bloodstream of HIV-infected people, which also correlate with end-organ complications.9,10However, measurements of these are still underway and critical to better understand the exact interplay of bacteria, viruses, and fungi within the human microbiome at each mucosal site.
The role of non-enteric microbiome is important, too. For example, one recent study found that uncircumcised men who became infected by HIV during the study period had higher levels of penile anaerobes compared with uncircumcised men who remained HIV negative. The authors also reported that having higher levels of penile anaerobes was associated with higher production of certain cytokines that can recruit HIV target cells to the foreskin, suggesting that anaerobes may modify HIV risk by triggering inflammation. These anaerobes can also be shared through heterosexual contacts. Modifying the penile microbiome could potentially reduce HIV acquisition in both men and women.11
Even more important than its composition is to understand the exact function of the microbiome. Many questions remain open and we (and other groups) are working hard to understand. For example what do bacteria, fungal, or viral species regulate and how? What bacterial products do bacteria make and how are those relevant for the human host? How do they regulate immunity and epithelial barrier function? How do different bacteria affect drug disposition? Currently, many of these questions do not have clear answers, and many studies are underway and still needed to better understand these questions.
Infectious Disease Advisor: Is there anything we can do (or not do) to maintain a healthy microbiome? Can we correct the microbiome in HIV-infected people using some medications or transplant the “good germs?”
Dr Klatt: The microbiome is very difficult to manipulate. Antibiotics can briefly alter the microbiome, typically with negative consequences for the immune system, and can lead to complications such as Clostridium difficile infection. Once the microbiome is dysbiotic (perturbation of the microbiome, for example in the setting of HIV infection), it is very difficult to revert. Probiotics have demonstrated some encouraging results; however, there is a great variability in different probiotics and how beneficial they are. To date, the best clinical data has come from use of VisbiomeÒ, currently used in an AIDS Clinical Trial Group trial (ClinicalTrials.gov identifier: NCT02706717) to decrease inflammation in HIV-infected individuals. Over-the-counter products such as CulturelleÒ may also have benefits, however, these have not been proven clinically and it is likely that daily dosing is needed to be effective. Alternatives include fecal transplants, but these are quite invasive and have only shown some efficacy in the case of single organism diseases such as C difficile or vancomycin-resistant enterococci infections. The results of fecal transplant in the setting of HIV infection have been variable and are probably not the best approach currently. Early initiation of antiretroviral therapy can partially prevent mucosal damage, although there is evidence that this happens very early during the course of infection.12
We critically need better approaches to enhance the microbiome to improve health in patients with HIV.