New research helps determine what is healthy and unhealthy in the vaginal microbiome

Editor’s note: This blog about the vaginal microbiome is a good primer for this coming Monday’s Microbiome Podcast with Jacques Ravel, where we will discuss the vaginal microbiome and women’s health at length.  There will also be a special announcement during this podcast, so anyone interested should be sure to download it Monday, June 1.

The typical ‘healthy’ vaginal microbiome is dominated by a Lactobacillus.  However many women, especially those of African descent, are not dominated by this genus, and instead have a high diversity of bacteria in their vaginal tract.  This low lactobacilli, high diversity phenotype has been associated with many disease states, such as bacterial vaginosis (BV), preterm birth, and higher rates of sexually transmitted disease (STD) transmission.  (We have written about some of these diseases before, and encourage any interested reader to click the ‘vaginal microbiome’ below this story to learn more.)  Vaginal microbiome research is still in its early days though, and it is not clear why vaginal microbiome not dominated by Lactobacillus should lead to these diseases, and if this phenotype, if asymptomatic, should even be considered unhealthy.  New research though, out of Harvard University, shows that this phenotype does lead to inflammation, and that these inflammatory response can affect reproductive health and STD transmission.  They published their study in the journal Immunity last week.

The scientists studied the vaginal microbiomes of a cohort of 146 HIV negative, asymptomatic, black, South African women.  They discovered that 63% of them were not dominated by Lactobacillus, an extremely high percentage, especially compared to their counterparts in developed countries (38% of black women and 10% of white women).  Nearly half of those women were dominated by Gardneralla vaginalis, which is most commonly associated with BV, and a large percentage of the other half were diagnosed with BV after investigation.  This is especially interesting because, as stated before, all of the women in the cohort claimed to be asymptomatic, but as we are learning, many women are unaware that there is anything wrong.  Overall, the women were able to be grouped into 4 specific phenotypes, those dominated by Lactobacillus iners, those dominated by other Lactobacillus crispatus, those dominated by Gardnerella vaginalis, and those with a high diversity including Gardnerella vaginalis, Fusobacterium gonidiaformans, Prevotella bivia, and Atopobium vaginae (note the lack of Lacotbacillus in this high diversity group). 

The scientists discovered that there were no associations between each vaginal microbiome group and the rate of STDs, contraceptive use, or sexual behavior.  This is important in showing that, at least on first pass, these bacterial communities were not the result of these exogenous factors (nor did they cause them, for that matter).  They also discovered that there was only a loose association between inflammatory cells in the vaginas of these women, and whether or not they had an STD.  The loose association was only observed in women with Chlamydia, and the women with the highest levels of inflammation had no apparent STDs.

The fact that STDs were not strongly associated with inflammation led the researchers to hypothesize that the vaginal microbiome community, rather than STDs, were responsible for vaginal inflammation.  Indeed, when they compared the amount of inflammatory cells in each vagina with the different microbiome groups described earlier, they found a strong association between inflammation and the highly diverse microbiome group.   Moreover, when they tracked individual women over time, those women whose vaginal microbiomes shifted to the high diversity group also increased inflammatory responses.  The researchers then took this work a step further, and identified specific bacteria that were associated with the inflammatory response:  Prevotella amnii, Mobiluncus mulieris, Sneathia amnii, and Sneathia sanguinegens.

Finally, the researchers measured genes for specific receptors in the vagina that are known to trigger an immune response.  They discovered that those women with the high diversity vaginal microbiomes upregulated genes for these receptors, which are known to be activated by bacteria.  Making matters worse, specific immune cells that are triggered by these receptors, which are thought to be critically important to HIV transmission, were found in higher abundances in women in the high diversity vaginal microbiome group.

This paper did a really great job showing that a vaginal microbiome that lacks Lactobacillus is indeed an unhealthy state, because it creates a highly inflammatory vaginal microbiome which likely causes or contributes to many other ailments, beyond just the higher rates of HIV transmission that was demonstrated.  Unfortunately, at the moment, there are no easy ways for women to check which vaginal microbiome they have, but that should be changing soon, and we recommend that all of our readers tune into the Microbiome Podcast this coming Monday to hear a big announcement in this area. 

The vaginal microbiome changes during and after pregnancy

The vaginal microbiome is critically important to a healthy pregnancy, and studies have shown that vaginal dysbiosis during pregnancy can lead to infection and preterm birth.  In order to help understand what the microbiome looks like throughout and just after pregnancy, researchers from England performed longitudinal studies on 42 pregnant women.  They published their results last week in Nature Scientific Reports.

The scientists sequenced the microbiomes of the 42 women throughout their pregnancies, and then for the 6 weeks afterwards for some of the women.  They discovered, in agreement with other literature on the subject, that the vaginal microbiome becomes dominated by Lactobacilli species during pregnancy.  The Lactobacilli are thought to prevent pathogens from colonizing the vagina because they produce lactic acid which decreases the overall pH of the vagina, and they secrete antibacterial toxins.  These Lactobacilli are also important as they are normally the first to colonize the new infants' guts after they pass through the birth canal. 

The researchers also learned that the microbiome shifts away from Lactobacilli and towards a more diverse microbiome in the period immediately following birth.  The new bacteria that colonize are often associated with vaginosis, and these can lead to inflammation and infection of the birth canal in some women.  The scientists suspect this shift occurs because there is a sudden drop in estrogen production upon removal of the placenta.  The increase in circulating estrogen is thought to be important for Lactobacilli colonization, so it makes sense that the rapid decrease in estrogen decreases Lactobacilli abundance.

Finally, this study showed that there were geographic and ethnic variations to the pregnant microbiome.  While each microbiome was associated with a healthy pregnancy, there were important differences, especially on the species level.  For example, Asian and Caucasian women’s pregnant microbiomes were dominated by Lactobacillus gasseri, while this species was absent in black women’s pregnant microbiomes.

This paper helps show the normal progression of the microbiome during and after pregnancy.  With the mounting evidence that the microbiome is often a contributing factor to preterm birth and some post-partum diseases, papers like this one are important to some day discovering the mechanistic basis for our microbiome's association with these issues. 

Strange, parasitic microbiome bacteria may responsible for inflammatory diseases

Electron micrograph of a type of Actinomyces, the genus of the natural host of TM7, discussed in the paper.

There are many bugs in the microbiome that cannot be cultivated, and thus are incredibly difficult to study using normal culturing techniques.  We only know about these bugs through DNA sequencing, and it often difficult to draw any substantial conclusions from this information.  One such group of bugs that is highly abundant in the microbiome is the bacterial phylum TM7.  TM7 has been associated with numerous inflammatory diseases, like vaginosis, inflammatory bowel diseases and periodontitis, and DNA analysis shows that this bug has the ability to create many toxins.  Studying this bug could lead to breakthroughs in microbiome diseases, but until now it was unculturable.  Recently though, a team of scientists from around the United States were able to cultivate these bacteria and in doing so learned what makes this bacteria so unique, and possibly so pathogenic.  The results were published in PNAS.

The team aimed their investigation at the oral microbiome, because TM7 is abundant in the mouth and highly associated with periodontitis.  They took samples of spit and realized that TM7 only could grow when another bacteria, Actinomyces odontolyticus, was present.  When they cultured these bacteria together in a saliva-like media they realized that the TM7 was physically attached to the surface of A. odontolyticus.  Through further experimentation they learned that TM7 could never grow on its own, and needed A. odontolyticus to replicate.  Furthermore, TM7 is parasitic, and kills A. odontolyticus when they are starved.

The researchers then investigated the pathogenicity of TM7.  They learned that TM7 can evade detection by the immune system for itself and A. odontolyticus.  They also discovered that the particular strain of TM7 they were studying was antibiotic resistant.  Furthermore, sequencing of the TM7 showed the strain had amongst the smallest genomes ever discovered, and relies on the A. odontolyticus for production of many essential molecules, like amino acids.  However, TM7’s small genome is very dense in the production of virulent molecules and toxins, perhaps necessary for its parasitic nature, which could also affect its human host.

This study raises many interesting points about pathogens in the microbiome.  DNA sequencing is a great start to defining the microbiome, but often times culture, or in this case co-culture is necessary to drill down into the true virulence of bacteria.  For instance, prior to this study A. odontolyticus was considered to be associated with many inflammatory diseases, but these researchers showed that it is likely TM7, not A. odontolyticus that is the true culprit.  Alas, the complexity of the microbiome often times reveals many more questions than answers.