Uncovering the female body’s secret protection against HIV

CAPE TOWN, South Africa — From where Linda-Gail Bekker sits as director of the Desmond Tutu HIV Centre in Cape Town, science has been losing ground against HIV for years, especially when it comes to young women. After all, in some parts of the country, girls who are 15 today have an 80 percent chance of acquiring HIV in their lifetimes.

“We’re really in the trenches here,” she said. “We have to bring all the technology, tools—you know, innovations—we can find to start turning that war around.”

READ MORE: How vaginal bacteria could be stoking HIV cases and blocking prevention

So when researchers announced at the International AIDS Conference in Durban, South Africa, last month that they’d linked a single strain of vaginal bacteria to higher HIV rates, it seemed like they had started to make inroads against the virus in a unique way: by identifying weaknesses in the communities of bacteria that occupy the vagina—weaknesses that could open the door for HIV. But additional research out of the conference complicates that finding and highlights how far there is to go.

The good news is that, as researchers uncover the complexity of those communities, they are also finding ways to strengthen them, crafting new tools that not only could make women less susceptible to HIV but also improve their health overall. And it highlights the vagina as a powerful HIV prevention tool in itself, said Alison Roxby, a researcher at the University of Washington who studies how the injectable contraceptive Depo-Provera impacts HIV acquisition.

“What people often don’t appreciate about the vagina is that, although many women have high risk for HIV, many of those women don’t get HIV,” said Roxby. “We have a pretty impressive protective barrier [in the vagina], so understanding how infection occurs and how it does not occur are two sides of the same coin. Both of those help prevent HIV.”

A Riskier Microbiome

Like every other surface of the human body, the vagina is colonized by millions of bacteria—some beneficial, others not so much. This is what researchers mean when they talk about the vaginal microbiome. Just like in the gut, the vagina plays host to a variety of bacteria that can either improve health or worsen it.

But first, the basics.

Lactobacillus is one of the only vaginal bacteria that produce lactic acid. When conditions are right—when Lactobacillus is the dominant bacteria in the microbiome and when the microbiome’s pH is below 3.8—it produces a kind of lactic acid that’s more than inhospitable to what Richard Cone, a professor of biophysics at Johns Hopkins University, calls “sperm and germs.” That acid can also slip into the cells of foreign viruses and bacteria and kill them. That includes common sexually transmitted infections and, yes, HIV. It’s the vaginal microbiome’s secret protector.

Bacterial vaginosis

Bacterial vaginosis. Photo credit: Lorna Rabe, Magee-Womens Research Institute

“Only humans have Lactobacillus in their vaginas,” said Cone, who has studied the microbiome for 20 years. “Humans haves the unique ability to protect against germs.”

The problem is that not every woman has a Lactobacillus-dominated microbiome. There are dozens of bacterial families that can occupy the vagina, and none are as good for HIV protection as Lactobacillus, at least as far as researchers know to date. Women without a Lactobacillus dominated microbiome are often said to have a bacterial imbalance called bacterial vaginosis (BV). For decades, researchers have known that HIV rates are higher in women with BV than women with Lactobacillus-dominant microbiomes. And for years, research has suggested that Lactobacillus is more common in white and Asian women’s microbiomes than in the microbiomes of Black and Latina women—women with far higher rates of HIV.

This may be part of the reason HIV rates are so much higher in African women, said Scott McClelland, professor of medicine, epidemiology and global health and associate director for the Center for AIDS Research International Core at the University of Washington. But up until now, it wasn’t clear if it was just generalized BV—that is, wide diversity in the vaginal microbiome—a lack of Lactobacillus in the microbiome, or some combination of the two that increases HIV risk.

“We had a more focused hypothesis,” said McClelland. “We wondered if it might be individual bacterial species or communities [or groups of specific vaginal bacteria] that were particularly strongly associated with HIV.”

Capturing the Culprits

To start with, McClelland and others began to differentiate the types of BV women can have.

Sure, some women with clinical signs of BV—lack of Lactobacillus and high inflammation, for instance—may have symptoms we associate with BV: an unpleasant, fishy smell, or excess, watery discharge. But it can also mean the presence of a variety of bacteria that cause no symptoms: Gardnerella is the most common example, but there’s also Bacterial Vaginosis Associated Bacteria 1 and 2 (BVAB1 and BVAB2), first identified in a 2005 New England Journal of Medicine article by McClelland’s colleague, David Fredricks, a professor of medicine at University of Washington’s Division of Allergy and Infectious Disease and head of a lab on the vaginal microbiome.

It could mean the presence of L. iners, which, despite being in the Lactobacillus family, has been found in women without BV but also in women with it. There are even some bacteria, like Atopobium, which is typically implicated in BV, that produce lactic acid themselves.

So the hunt was on. And at the International AIDS Conference last month, researchers unveiled their first results. First, the Center for the AIDS Programme of Research in South Africa made a splash with a special symposium, chaired by National Institutes of Allergy and Infectious Disease Director Anthony Fauci and U.S. Ambassador Deborah Birx, that revealed preliminary data that linked the presence of the vaginal bacteria Prevotella bivia (P. bivia) to a 13-fold increase in women’s risk of HIV acquisition.

But that wasn’t the only new research on the microbiome presented at the International AIDS Conference. Without much fanfare and as part of a poster session mostly about HIV prevention drugs, McClelland also presented data on the microbiome—data that didn’t jibe with the CAPRISA findings.

McClelland and his team, who first submitted grants to try to research the microbiome’s link to HIV acquisition nine years ago, did find that specific bacteria were associated with significantly higher risk of HIV acquisition, and that that acquisition rate was significant. But P. bivia wasn’t among his culprits.

They studied P. bivia, but found it had a “modest association with HIV acquisition” in McClelland’s sample of 449 women. But in the end, “we did not find a significant association between Prevotella quantity and HIV.”

Here’s what McClelland did find: Not one but a group of bacteria emerged as powerfully associated with increased HIV acquisition, including Eggerthella species type 1, Gemella asaccharolytica, Leptotrichia/Sneathia, Megasphaera, and Mycoplasma hominis.

“These five that emerged were statistically significantly associated with HIV acquisition in a concentration-dependent fashion,” he said. “This was one of the really big findings.”

Another finding, which McClelland found intriguing but cautioned against putting too much weight behind, was that different amounts of those bacteria, relative to the other bacteria present in the microbiome, were associated with different odds of HIV acquisition. It only took the smallest amount of Megasphaera to increase odds of HIV acquisition by more than three times, for instance. But for Mycoplasma hominis to have a similar impact, it needed to be present in the highest concentrations McClelland’s team calculated. Eggerthella species 1 increased women’s risk of HIV the most when it was present in moderate amounts.

That leads to a natural next question, which is that, if all five of these culprit bacteria are present in a single woman’s microbiome in the right concentrations, could that mean a much higher rate of HIV?

“Great question,” he said, “and one that we are currently exploring.”

For that, said McClelland, we need more research and more money dedicated to the microbiome. The deep molecular sequencing McClelland’s team used doesn’t come cheap.

Dr. Salim Abdool Karim, CAPRISA’s director who presented the P. bivia findings at IAC, agreed, calling McClelland’s research “exactly the kind of study that we need a lot more of.”

“I think we will find a range of bacteria associated with HIV acquisition,” Karim said. “These associations will all need to be repeatedly tested to see if they hold up in multiple settings.”

Until that replication and study can be done, McClelland discouraged women from trying to alter their microbiomes on their own.

“This is an exciting area but still a research field that is not yet ready for full transition to prevention or treatment recommendations,” McClelland said. “Without stronger data (e.g., from a randomized trial), it would be premature to tell women to try to manipulate the vaginal microbiota as a way to reduce HIV or STI risk.”

Getting Answers

But that doesn’t mean that researchers aren’t trying to find those answers. Indeed, researchers around the world are testing ways to remove detrimental bacteria, introduce Lactobacillus—and specifically one strain, L. crispatus—and otherwise armor the microbiome that is there now.

Douglas Kwon is head of a research team studying immune responses to HIV at the Harvard Medical School. “The question now is, can we leverage the vaginal microbiome to reduce HIV risk for women in sub-Saharan Africa?” he said.

Since BV is a disorder in which Lactobacillus is lacking, the first step seems to be determining if you can really kill off an already existing microbiome. This leads back to McClelland again. In separate research, McClelland is testing whether periodically and regularly treating BV, whether a woman has symptoms or not, really can reduce women’s rates of sexually transmitted infections. The trick with BV, he said, is that once you have it, it’s hard to get rid of it. Even after treatment, it often comes back.

The microbiome, it seems, wants to stay the way it is.

So McClelland and his team are testing whether periodic BV treatment with antibiotics can reduce rates of gonorrhea and Chlamydia.

He can’t specifically study whether BV treatment reduces HIV transmission, though. Most HIV trials now offer HIV prevention agents like condoms and HIV prevention pills as backup for participants. It would be unethical to do otherwise, he said. But with gonorrhea and Chlamydia, there is no such biomedical prevention, so he’s planning a Phase III clinical trial on so-called periodic presumptive treatment for BV. A subanalysis of an earlier BV treatment study he was a part of, published in June, found that periodic BV treatment reduced infection from three STIs by about 45 percent.

And there is real-world impact on HIV, even if he can’t prove that BV treatment specifically reduces HIV rates. The presence of other STIs increases inflammation in the genital tract, and can make a woman more susceptible to HIV all on its own.

Kwon’s lab, meanwhile, is coming at the question of microbiome change from, well, the other direction.

“It seems that most of the women in the African cohort we’ve looked at don’t have classic L. crispatus that’s described in white women in developed countries,” said Kwon. “Why is that? Where are those other bacterial taxa coming from?”

Maybe, his team has hypothesized, it comes from the other microbiome: the gut. The same kind of sequencing that allowed McClelland’s team to identify the bacteria in the microbiome associated with increased HIV acquisition can not just identify the species, but also track specific species from one part of the body to another. Kwon’s team wants to find out if some of the bacteria in the vaginal microbiome comes from the gut microbiome.

“If so, that could mean that changing the gut microbiome could also impact the vaginal microbiome,” Kwon said. If they can prove that bacteria migrate from one microbiome to the other, he said, they may be able to treat BV not with antibiotics but with probiotics.

Leveraging Lactobacillus

Another way to introduce lower-pH and lactic acid-producing Lactobacillus to women’s microbiomes is being looked at in Kwon’s lab and at the Silicon Valley biotech company Osel, Inc., separately: Infusions of Lactobacillus.

Kwon’s lab is in preclinical stages, meaning its product hasn’t been tested in humans yet. But Osel has already tested the safety of a powdered form of L. crispatus, applied directly to the microbiome via what’s essentially a tampon applicator. In the study, funded by the NIH, 61 percent of the 18 women saw L. crispatus take hold by day 28. The hope, said Osel’s Director of Research Laurel Lagenaur, is that it will replace the vaginal microbiome lost during antibiotic treatment and that it may even improve health by reducing common genital tract problems like urinary tract infections.

But that’s just one way to add Lactobacillus. Laura Ensign, assistant professor at the Center for Nanomedicine at the Wilmer Eye Institute at Johns Hopkins University, wants to try another way: Taking another cue from gut microbiome research, she wants to see if you can do not just an infusion of Lactobacillus, but a full-blown microbiome transplant.

“If you put Lactobacillus in the vagina of a woman who has BV, it’s just going to die,” said Ensign. “But if you transplant its whole environment, including its main food source, then I think it has a shot to overtake the resident BV bacteria that are left behind after antibiotic treatment.”

That food isn’t what we think of in nutritional science as prebiotics—things like flax seed meal that sustain health bacteria in the digestive tract. No, the food for vaginal bacteria already exist in the vagina. It’s in the cervicovaginal mucous, the mucous membrane that lines the vagina.

“Mucous is definitely underappreciated,” she said. “The proteins in the mucous form a net that protects the vagina. It serves a lot of different functions. It traps a lot of different matter,” including the food Lactobacillus lives on.

Ensign is in the process of designing a trial to see if such a thing is possible.

Weaponized Lactobacillus

Finally, researchers at Osel and Harvard, working separately, are engineering forms of Lactobacillus that secrete antibodies that bind to and neutralize HIV. Osel’s form is a tablet delivered vaginally, right to the spot where women are exposed to HIV most. Harvard’s is still in early development.

“People with HIV will eventually make neutralizing antibodies against HIV, but by that time, the damage has been done—the virus has already taken over,” said Osel’s Lagenaur. “But if you start with the neutralizing antibody, if you can passively deliver it… It’s just like if you’ve been bitten by a rabid dog. Doctors will give you passive anti-rabies antibodies. We’re using Lactobacillus to passively deliver antibodies.”

The Stability of the Microbiome

Still, for any of these interventions to work, all the researchers who spoke to PBS NewsHour agreed that they will have to know a lot more about the vaginal microbiome, the bacteria that live there, and how they interact with things like sperm, sex hormones and contraceptive hormones before they have solutions.

We may find that the vaginal microbiome is not that easy to displace, Kwon said. Because of this, his lab is not just working on an engineered form of Lactobacillus, but is looking beyond that to see if there are other bacteria more common in the microbiomes of African women that could also be protective. After all, he said, the microbiomes of African women evolved to be what they are for some reason. It could be that a more diverse vaginal microbiome confers advantages in certain situations. But now, in the era of HIV, they leave women at a distinct disadvantage.

He’s already begun research into the microbiomes of African women, looking for a native and protective bacteria. Lactobacillus might be the only bacteria that can protect women from HIV. But what if it’s not?

“We have to think about the fact that these bacterial communities might be relatively stable and hard to manipulate,” he said. “So leveraging the community that’s there naturally and most predictably and to use that to try to decrease HIV acquisition is another approach that’s worth looking into.”