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How bacteria in the vagina change during pregnancy

The views expressed are those of the author and are not necessarily those of Scientific American.


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One thing that becomes more clear with each piece of research is that the human body is a hive of mostly harmless bacteria that live in any crevice they can reach while affecting their human host as little as possible. In some cases these bacteria can be very beneficial – preventing more dangerous bacteria from taking up residence in places like the stomach and throat. In some cases they can occasionally go rogue, get into places they shouldn’t be, and cause havoc.

Despite the relatively safe and prosperous homes that the human body provides, living on it does have it’s downsides. As the body changes, grows and falls ill the bacteria are subject to seismological shifts in their living quarters. And for bacteria that live around the female reproductive areas, pregnancy represents a pretty major shift indeed.

A labelled diagram of the female reproductive system, just so there's no confusion over which parts are being discussed. Vectorized in Inkscape by User:Mysid from a CDC image in the public domain.

Just to clarify, bacteria do not actually live in the womb (if they get inside there that can go very badly wrong) but they do set up camp along the vagina and basically any areas of the reproductive system (and indeed the body) that can be reached safely from the outside. As well as protecting against fungal and other pathogenic infections simply by colonising the available space, the vaginal bacteria also actively help to decrease the pH inside the vagina, making it harder for other infections to set up. Killing off these bacteria (as anyone who has ever taken antibiotics to deal with cystitis will be aware) can lead to the fungal infection thrush, as without the bacteria in place the fungus can take over.

In order to explore how the vaginal bacteria might change during pregnancy, researchers took 68 samples from 24 healthy pregnant women (between 18-40 confirmed weeks) and compared them to 310 samples from 60 non-pregnant controls. They isolated DNA from the vagina, sequenced it, and then organised it into different bacterial taxonomic groups. All the control women were non-menstruating at the time, and around half of them were taking hormonal contraceptives. Full details can be found in reference 1.

Overall, pregnant women showed much less diversity in bacterial species and fewer colonies present, particularly in areas up near the uterus which were very sparse indeed. In both pregnant and non-pregnant women, colonies varied throughout the vaginal area, and the dominant species were Lactobacillus spp. Some particular bacterial species were found to be more prevalent in pregnancy, although the overall diversity was reduced. This snapshot of the vaginal bacteria flora as a changing landscape; affected by internal pH and decimated by oncoming pregnancy, is a fascinating one, showing a wonderful interaction between humanity and the bacteria that live inside them.

Image from wikimedia commons, no credit supplied.

But pregnancy doesn’t just involve changes in bacteria, it also comes with a baby! The womb where the foetus grows is a comfortable and sterile environment, and suddenly in a short space of time it is required to be forcibly pushed down a narrow bacteria-laden tube into a cold unforgiving world. In a fascinating (although rather underpowered) study of infants born by either by vaginal birth or C-section, researchers (reference 2) did indeed find a difference in the bacterial communities. Babies born through vaginal delivery had typical vaginal species such as LactobacillusPrevotella, or Sneathia on their skin, throat and gut while babies born through Cesarean had picked up species of skin bacteria (StaphylococcusCorynebacterium, and Propionibacterium). Furthermore while in adults there are different bacterial species in different places (skin, gut, vagina, etc.) in the newborns it was the same bacterial species everywhere. Given that they’d only just entered the world from a sterile environment this isn’t surprising, but it does raise interesting questions about how the different species find their way into the infant and start to flourish in their own little niches.

Speaking as one of the many, many C-section babies out there I can’t say my method of birth had a huge impact on overall health, or indeed my relationship with bacteria! But what is clear is that bacteria are with us throughout our life, changing to match our bodies, and growing and fluctuating as we go through different stages of health.

Ref 1:Kjersti Aagaard, Kevin Riehle, Jun Ma, Nicola Segata4, Toni-Ann Mistretta, Cristian Coarfa, Sabeen Raza, Sean Rosenbaum, Ignatia Van den Veyver, Aleksandar Milosavljevic, Dirk Gevers, Curtis Huttenhower, Joseph Petrosino, James Versalovic (2012). A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy PloS one, 7 (6) DOI: 10.1016/j.ajog.2010.10.087

Ref 2: Maria G. Dominguez-Bello, & et al. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns Proceedings of the National Academy of Sciences, 107 (26) DOI: 10.1073/pnas.1002601107

S.E. Gould About the Author: A biochemist with a love of microbiology, the Lab Rat enjoys exploring, reading about and writing about bacteria. Having finally managed to tear herself away from university, she now works for a small company in Cambridge where she turns data into manageable words and awesome graphs. Follow on Twitter @labratting.

The views expressed are those of the author and are not necessarily those of Scientific American.





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  1. 1. connorGGbamford 10:45 am 06/16/2012

    Right so we know that the microbiome changes when you become pregnant but do we really know why and how this impacts mother/child? Also the link for the first paper, meant to be a PLoS one paper in fact links to the American Journal of Obstetrics and Gynaecology :-/

    Link to this
  2. 2. Symbiartic.km 7:22 pm 06/16/2012

    So interesting that you cite differences in bacterial colonization on vaginally birthed babies vs. those delivered by c-section. We were just contemplating the ramifications because of the swarm of articles recently in SciAm, SciAm Mind and the NYTimes on our microbiomes. How important is this initial colonization vs. your lifetime exposure from your environment? More research (or coverage of research), please. Fascinating!

    Link to this
  3. 3. Papaspud 9:35 pm 06/16/2012

    Sometimes makes you wonder, who are the real ” top of the food chain” on our planet. Sometimes it seems like bacteria are the real rulers. All of the very interesting articles that have come out lately about the microbiome really get the ole brain a twisting.

    Link to this
  4. 4. Defectivebrayne 5:32 am 06/17/2012

    I was a bit disapointed by the conference abstract in the AMJO reference, which concealed most of the data in a very low res image.
    None theless, this is a fascinating subject, as Lactobacilli growth are believed to be affected by oestrogen levels (as this triggers the release of glycogen for lactobacilli to feed on), due to their role in protecting the vagina against bad bacterial infection. One could speculate (and this is wild speculation) that the increase in lactobacilli is the cause of the low diversity of other species, and furthermore that it is implemented a protective measure against the various infections to which a human is vulnerable after pregnancy.

    Link to this
  5. 5. S.E. Gould in reply to S.E. Gould 7:24 am 06/18/2012

    Thanks for the comments!
    @Defectivebrayne: A link between hormones and bacterial growth would be fascinating, as it would provide a way for the body to kind of ‘farm’ internal bacteria to suit the circumstances rather than just being passively taken over by outside bacterial forces.
    @Papaspud: there has been some fascinating stuff recently about the human microbiome project. I’ll probably be covering more of it in the near future. As far as the food chain goes, remember the chain is connected at both ends – everything is used/eaten by everything else, there is no top!
    @Symbiartic: The recent human microbiome stuff has been fascinating to read. I will definitely be covering more of it.
    @Connor: Hmm, the paper citations and links were just taken from researchblogging.org, not sure where it went wrong. Googling the title should get you there, and it’s definitely an interesting paper.

    Link to this
  6. 6. Defectivebrayne 11:36 am 06/18/2012

    @Labrat – The link has some speculation behind it going back to the 80′s at least, when it was found that Lactobacilli can feed on human glycogen, which is produced in the vaginal walls during normal oestrus. But there are no studies that conclusively prove this relationship, although there are plenty that link oestrogen production to having lactobacilli as the dominant species of bacteria. Hopefully the vast improvements in identifying bacteria will change this.

    Link to this

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