The Vaginal Microbiome

An overview of large studies on the human vaginal microbiome. Please leave a comment if I missed an important paper, which is extremely likely. This is just a first draft, and this post is meant to be continuously updated.

Scientific papers, most recent first

The vaginal microbiome during pregnancy and the postpartum period in a European population – David A. MacIntyre – Scientific Reports – March 2015

  • Subjects: 42 British women with term delivery, sampled longitudinally, 3 ethnic groups
  • DNA extraction: bead-beating + QIAamp DNA Mini kit
  • Sequencing: V1-V2 region, MiSeq, 2,113,251 reads, 14088 reads/sample (rarefied to 1916?)

The composition and stability of the vaginal microbiota of normal pregnant women is different from that of non-pregnant women – Roberto Romero – Microbiome – February 2014

  • Subjects: 32 non-pregnant women, 22 pregnant women who delivered on time
  • DNA extraction: Bead-beating, ZR Fecal DNA extraction kit (ZYMO Research)
  • Sequencing: V1-V2 region, 454 FLX Titanium, 2,946,507 reads, 2878 reads/sample

Diversity of the Vaginal Microbiome Correlates With Preterm Birth – Richard W. Hyman – Reproductive Sciences – January 2014

  • Subjects: 88 pregnant women (various ethnicities), 143 swabs
  • DNA extraction: QIAgen DNeasy Tissue and Blood Kit
  • Sequencing: 8F-1492R, clone library, Sanger sequencing, read from one end? not clear.
    Number of clones not clear?

Diverse Vaginal Microbiomes in Reproductive-Age Women with Vulvovaginal Candidiasis
Mu-Biao Liu – PLOS ONE – November 2013

  • Subjects: 95 women, some with BV or VVC, 226 swabs
  • DNA extraction: DNA Magnetic Sand Extract kit (BioEAsy,China)
  • Sequencing: V6 region, Illumina HiSeq 2000, 1,026,382 reads, 4,542 reads/sample

A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy – Kjersti Aagaard – PLOS ONE – June 2012

  • Subjects: 24 pregnant women, 60 non-pregnant controls, multiple timepoints/subject
  • DNA extraction: PowerSoil DNA Isolation Kit
  • Sequencing: V3-V5 region, 454 FLX Titanium, 2.5 million reads, 6837 reads/sample

$$ Temporal Dynamics of the Human Vaginal Microbiota – Pawel Gajer – Science Translational Medicine – May 2012

  • Subjects: 32 women, 937 samples
  • DNA extraction: Bead-beating with ZR Fecal DNA extraction kit (Zymo Research)
  • Sequencing: V1-V2 region, 454 Titanium, 2,522,080 reads, 2692 sequences/sample

Vaginal Microbiome and Epithelial Gene Array in Post-Menopausal Women with Moderate to Severe Dryness – Ruben Hummelen – PLOS ONE – November 2011

  • Subjects: 32 post-menopausal women, some sampled over 10 weeks
  • DNA extraction: Instagene (Bio-Rad)
  • Sequencing: V6 region, Illumina, 1,758,430, 17,410 reads/sample

Vaginal microbiome of reproductive-age women – Jacques Ravel – PNAS USA – March 2011

  • Subjects: 396 North American women representing four ethnic groups
  • DNA extraction: Bead beating combined with QIAamp DNA mini kit
  • Sequencing: V1-V2 region, 454 FLX, 897,345 good-quality reads, 2200 reads/sample

Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women – Xia Zhou – The ISME Journal – May 2007

  • Subjects: 144 women, 2 ethnicities
  • DNA extraction: not listed
  • Sequencing: T-RFLP, clone library , 6000 clones, 90 clones/sample

Microbes on the human vaginal epithelium – Richard W. Hyman – PNAS USA – April 2005

  • Subjects: 20 women
  • DNA extraction: QIAgen DNAeasy
  • Sequencing: 8F x 1492R, ~1000-2000 clones per subject

Review papers

The vaginal microbiome: rethinking health and diseases – Bing Ma – Annual Reviews in Microbiology – September 2013

Understanding vaginal microbiome complexity from an ecological perspective – Roxana J. Hickey – Translational Research – October 2012

A New Era of the Vaginal Microbiome: Advances Using Next-Generation Sequencing – Jennifer M. Fettweis – Chemistry & Biodiversity – May 2012

The vaginal microbiome in health and disease – Bryan A. White – Trends in Endocrinology & Metabolism – October 2011

The vaginal microbiome: new information about genital tract flora using molecular based techniques – RF Lamont – BJOG: An International Journal of Obstetrics & Gynaecology
– April 2011

News articles

Sweet Peach won’t make vaginas smell like fruit or taste of Diet Coke – Hannah Jane Parkinson – The Guardian – November 2014

What’s in Your Vagina? A healthy microbiome, hopefully. Moises Velasquez-Manoff – Slate – January 2013

Characterizing the “Healthy” Vagina – Jef Akst – The Scientist – May 2014


5 thoughts on “The Vaginal Microbiome

  1. I find it interesting that there is more articles re the pregnant/postpartum vaginal microbiome – but it makes sense; the ‘passing on’ of the microbial load during baby’s passage through the birth canal etc.
    I wonder what could be drawn from understanding of microbiomes to aid in the evolutionary-psychology explanations of behaviour: ie., baby takes on her first gut-full of bacteria, so aiding her survival; infinitely ‘clean’ (overuse of antibacterial cleaning agents) environments are an evolutionary step backwards because they result in a reduction of immune capabilities in the long term.
    I can understand that behaviour facilitates the creation of and maintenance of various microbiomes – but what can be said about how the microbiome affects ongoing behaviour choices? could there be a cause-effect? Specifically with vaginal microbiomes, is there a physiological basis for humans preferring serial monogamy? a subconscious requirement to maintain a steady-state/equilibrium in the vaginal ‘milieu’.
    It will take a while to read through even this selection of papers – thankyou!! – and right now I’m wishing for more free-reading hours before dawn…


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