CTMR research in women’s reproductive health

The vaginal microbiome is an intricate and dynamic ecosystem that constantly undergoes fluctuations during a woman’s entire life. Our research aims to describe the vaginal microbiome and it’s relation to health, fertility and pregnancy. A healthy vaginal microbiome is dominated by Lactobacillus ssp. which produce lactic acid, hydrogen peroxide and various antimicrobial compounds. Bacterial vaginosis, or the loss of Lactobacillus ssp. and increase in the concentration of anaerobic microbes, is a common disorder of the vaginal microbiota among women of reproductive age and associated with adverse gynecologic and obstetric outcomes, such as sexually transmitted infections, pelvic inflammatory disease, and preterm birth. Based on the cohorts described below we are starting to understand more about the importance of the microbiota in the vagina, gut and mouth for women’s health. 

Research questions

  • Does the microbiome acquisition start in utero?
  • What composition of the microbiome is normal in healthy women? 
  • What is the effect of hormonal contraceptives on the microbiome? What are the dynamics of the vaginal microbiome during the menstrual cycle?
  • Is there a profile that is associated with pregnancy complications (e.g. pre-term birth, depression, pregnancy loss)? Can we identify patients at risk for pre-term birth or pregnancy loss?
  • Is the microbial composition (vaginal/intestinal and oral) during pregnancy associated with current depressive symptoms or with postpartum depression?
  • What is the role of the microbiome in endometriosis and fertility?
  • Does the vaginal microbiota play a role in HPV infection and the development of cervical cancer?
  • How do commonly prescribed drugs, diet and other factors affect the microbiome composition and function, and how does this affect female health?
Photo: Liza Simonsson


PlaMi – Placental Microbiome study: does microbiome acquisition start in utero?

The PlaMi study addressed a subject of much current debate in the scientific community relating to whether the placenta hosts microbiota. Positive reports on this have appeared in the public domain (Chen et al. 2017; Aagaard et al. 2014); however, these findings are also contested and believed to be due to contamination during the sampling and sequencing procedures. The observation of a placental microbiome contributes to the interesting question of when the acquisition of microbiota begins, and, as has been proposed, is an infant’s microbiota more similar to the mother’s oral microbiota than her vaginal or faecal microbiota? The PlaMi study therefore collected samples from healthy 50 women with a planned C-section and 25 with a normal vaginal delivery. Samples were taken from 3 locations of the placenta, amniotic fluid, umbilical cord blood, vernix, vagina, saliva and faces at delivery. Our study published in the American Journal of Obstetrics and Gynecology 2020 concluded that the placenta does not harbor a microbiome in healthy pregnancies at term.


SweMaMi – Swedish Maternal Microbiome project


The SweMaMi study was designed to assess the association between the maternal microbiota during pregnancy and post-partum and the risk of maternal and neonatal adverse events. The study will recruited more than 5000 pregnant women in Sweden. The research questions regarding the microbiota overlap with those from the BASIC study, but in the SweMaMi project there is a larger study population recruited from all over Sweden. Participating women were asked to complete three comprehensive online questionnaires on general health, prior medical and reproductive history, drug use, lifestyle, diet and mental health. Participants provided microbiota samples from the vagina, oral cavity and gut (faecal) at gestational week 17–19 and 28–30, and at 6–10 weeks after the expected delivery date. A faecal sample from the new-born was also collected. We have collected more than 40 000 samples from SweMaMi mothers and children. Currently, microbiome analysis is ongoing. The primary goal is to investigate associations between the microbiota profiles and preterm birth (PTB) and other pregnancy complications.

BASIC: associations between microbiota and preterm birth (and depression)


The BASIC study began in 2010 in Uppsala, and more than 6000 pregnancies have so far been included. Microbiota samples have been collected since 2016 at two time points during the course of pregnancy, during the delivery and once during the postpartum period; gestational week 17–19 and 30-32 and at 6–10 weeks after the delivery date. The research questions overlap with the SweMaMi study, but the overall aim of the BASIC regards perinatal depression and its potential biological correlates. Mothers were therefore also asked to provide blood samples for analysis of i.e. markers of inflammation

VaMiGyn –Vaginal Microbiota in Gynaecological health

The VaMiGyn study aims to define the vaginal microbiota in women, in order to provide cross-sectional data to define the normal vaginal microbiome that will be used as a baseline for other studies. This study takes advantage of the national cervical cell screening program in Sweden. All women between 23 and 60 years who were called for screening received an information letter about the study and were asked to fill in a questionnaire and give a vaginal swab at screening. A total of 2000 women undergoing HPV screening in Uppsala were recruited, with vaginal microbiota samples collected from all participants, and a faecal and oral sample from a subset of 500. Variation of the microbiota that is associated with HPV infection, HPV subtypes, HPV vaccination, as well as antibiotic usage, is investigated and women with pre-states of cervical cancer are sampled consecutively.  The VaMiGyn study was completed in 2020. Currently, analysis of the vaginal microbiome data is ongoing.

MiMens – Microbiome dynamics during the menstrual cycle

The MiMens study, in collaboration with Prof Henriette Svarre Nielsen, aims to describe the vaginal microbiota in relation to the menstrual cycle in healthy women, to provide baseline data on changes in microbiota during the cycle. Three groups of each 50 healthy female volunteers have been recruited, and selected based on a regular menstrual cycle, and no use of hormonal contraception, oral contraceptive or the levonorgestrel intrauterine system. The participants have completed three visits over 6 weeks. During the study, the women have collected daily vaginal swabs, with salivary, urinary, faecal and blood samples given at study visits. Endometrial samples were also collected at some visits. The participants have undergone a gynaecological investigation and kept a diary of intercourse, bleeding etc., and completed a questionnaire on general health, prior medical and reproductive history, lifestyle, diet and mental health.

ACHVAM - Vaginal microbiota culture system

Most studies on microbiome (genomes of the microbiota) are conducted on intestinal microbiota. Studies on genital microbiome systems have still not been as properly characterized as the gut microbiota. A growing body of evidences suggests that the microbiome in genital tracts play important roles in modulating our health, however, there is no system that allows us to culture genital microbiota in vitro, which limited further mechanism studies on genital microbiota. The aim of this project is to build up a platform to culture vaginal microbiota from both Lactobacillus dominated and non-dominated individuals. Different culture media and conditions are developed for genital microbiota growth in order to define the best medium for bacteria in the genital tract, suitable for maintaining the balance of existing bacteria through time. Selected Lactobacillus strains will be characterized using both phenotypic and whole genome in silico screening pipelines.

MiRPL: Microbiota and recurrent pregnancy loss

The MiRPL study, in collaboration with Prof Henriette Svarre Nielsen in Copenhagen, investigates the microbiota profile of women with unexplained recurrent pregnancy loss. The hypothesis is that a specific composition of microbiota is present in women with immune-mediated recurrent pregnancy loss, reflecting an unbalanced immune system. MiRPL was designed to study the microbiota of the gut, mouth, vagina and endometrium in relation to pregnancy outcome and long-term prognosis, with samples taken at various time-points including prior to pregnancy, early pregnancy (gestational age 6–8 weeks), pregnancy loss or second trimester gestational age 12–14 weeks.

MiEndo: Microbiota in Endometriosis

The MiEndo study, in collaboration with Prof Henriette Svarre Nielsen, aims to compare and describe the microbiota composition in the gut, mouth, vagina, peritoneum (at operation) and in the endometriosis plaques and endometrium of women with endometriosis in relation to grade of disease, pain, quality of life and success of operation.

The study will recruit 100 women at Rikshospitalet, Copenhagen with moderate to severe disease and 20 patients with intestinal resection due to intestinal disease. Sample collection will be complete during 2022.

SweBioFertil: The role of the microbiome for fertility

In the collaboration between CTMR and Prof. Rodriguez-Wallberg, a clinical specialist of reproductive medicine and fertility at Karolinska University Hospital, the SweBioFertil cohort has been set up that is currently recruiting 1000 fertile and infertile women for longitudinal vaginal and gut microbiome sampling during their attempts to get pregnant. Associations of the microbiome to achieved pregnancy, miscarriage or live birth will be studied using the high-throughput sequencing infrastructure at CTMR. Additional mechanistic insights will be obtained by studying how vaginal immune- and metabolite profiles associate to fertility/infertility and IVF success in these cohorts. These data will be used to establish a prognostic set of biomarkers for predicting the success of fertility treatment based on mathematical modelling and machine learning approaches.


National collaborators

International collaborators


Selected publications

Gudnadottir, U., Du, J., Hugerth, L. W., Engstrand, L., Schuppe-Koistinen, I., Wiberg Itzel, E., Fransson, E., & Brusselaers, N. (2023). Pre-pregnancy complications - associated factors and wellbeing in early pregnancy: a Swedish cohort study. BMC Pregnancy and Childbirth, 23(1), 153. https://doi.org/10.1186/s12884-023-05479-8

The vaginal microbiome and the risk of preterm birth: a systematic review and network meta-analysis
Gudnadottir U, Debelius JW, Du J, Hugerth LW, Danielsson H, Schuppe-Koistinen I, Fransson E, Brusselaers N. Sci Rep. 2022 May 13;12(1):7926. doi: 10.1038/s41598-022-12007-9. PMID: 35562576; PMCID: PMC9106729.

The healthy female microbiome across body sites: effect of hormonal contraceptives and the menstrual cycle.
Krog MC, Hugerth LW, Fransson E, Bashir Z, Nyboe Andersen A, Edfeldt G, Engstrand L, Schuppe-Koistinen I, Nielsen HS. Hum Reprod. 2022 Jun 30;37(7):1525-1543. doi: 10.1093/humrep/deac094. PMID: 35553675.

The right bug in the right place: opportunities for bacterial vaginosis treatment.
Wu S, Hugerth LW, Schuppe-Koistinen I, Du J. NPJ Biofilms Microbiomes. 2022 May 2;8(1):34. doi: 10.1038/s41522-022-00295-y. PMID: 35501321; PMCID: PMC9061781.

The microbiome in reproductive health: protocol for a systems biology approach using a prospective, observational study design.
Krog MC, Madsen ME, Bliddal S, Bashir Z, Vexø LE, Hartwell D, Hugerth LW, Fransson E, Hamsten M, Boulund F, Wannerberger K, Engstrand L, Schuppe-Koistinen I, Nielsen HS. Hum Reprod Open. 2022 Mar 23;2022(2):hoac015. doi: 10.1093/hropen/hoac015. PMID: 35441092; PMCID: PMC9014536.

A MicroRNA Gene Panel Predicts the Vaginal Microbiota Composition
Cheng L, Kaźmierczak D, Norenhag J, Hamsten M, Fransson E, Schuppe-Koistinen I, Olovsson M, Engstrand L, Hydbring P, Du J.. mSystems. 2021 May 4;6(3):e00175-21. doi: 10.1128/mSystems.00175-21. PMID: 33947805; PMCID: PMC8269211.

Dysbiosis of the Human Oral Microbiome During the Menstrual Cycle and Vulnerability to the External Exposures of Smoking and Dietary Sugar.
Bostanci N, Krog MC, Hugerth LW, Bashir Z, Fransson E, Boulund F, Belibasakis GN, Wannerberger K, Engstrand L, Nielsen HS, Schuppe-Koistinen I. Front Cell Infect Microbiol. 2021 Mar 19;11:625229. doi: 10.3389/fcimb.2021.625229. PMID: 33816334; PMCID:

Vaginal microbiota and human papillomavirus infection among young Swedish women
Cheng L, Norenhag J, Hu YOO, Brusselaers N, Fransson E, Ährlund-Richter A, Guðnadóttir U, Angelidou P, Zha Y, Hamsten M, Schuppe-Koistinen I, Olovsson M, Engstrand L, Du J. NPJ Biofilms Microbiomes. 2020 Oct 12;6(1):39. doi: 10.1038/s41522-020-00146-8. PMID: 33046723; PMCID: PMC7552401.

No evidence for a placental microbiome in human pregnancies at term
Sterpu I, Fransson E, Hugerth LW, Du J, Pereira M, Cheng L, Radu SA, Calderón-Pérez L, Zha Y, Angelidou P, Pennhag A, Boulund F, Scheynius A, Engstrand L, Wiberg-Itzel E, Schuppe-Koistinen I. Am J Obstet Gynecol. 2021
Mar;224(3):296.e1-296.e23. doi: 10.1016/j.ajog.2020.08.103. Epub 2020 Aug 29. PMID: 32871131.

The reproductive microbiome - clinical practice recommendations for fertility specialists
García-Velasco JA, Budding D, Campe H, Malfertheiner SF, Hamamah S, Santjohanser C, Schuppe-Koistinen I, Nielsen HS, Vieira-Silva S, Laven J. Reprod Biomed Online. 2020 Sep;41(3):443-453. doi:10.1016/j.rbmo.2020.06.014. Epub 2020 Jun 27. PMID: 32753361.

Psychoneuroimmunology in the context of perinatal depression - Tools for improved clinical practice
Fransson E.
Brain, Behavior, & Immunity - Health (2021)

Metabolic Profiling Indicates Diversity in the Metabolic Physiologies Associated With Maternal Postpartum Depressive Symptoms
Bränn E, Malavaki C, Fransson E, Ioannidi M-K, Henriksson HE, Papadopoulos FC, Chrousos GP, Klapa MI and Skalkidou A
Frontiers in Psychiatry (2021)

A microRNA gene panel predicts the vaginal microbiota composition.
Cheng LQ, Kazmierczak D, Norenhag J, Hamsten M, Fransson E, Schuppe-Koistinen I, Olovsson M, Engstrand L, Hydbring P*, Du J*
mSystems (2021)

Human papilloma virus (HPV) prevalence upon HPV vaccination in Swedish youth--a review based on our findings 2008-2018, and perspectives on cancer prevention.
Du J, Ährlund-Richter A, Näsman A, Dalianis T ​​​
Archives of Gynecology and Obstetrics (2021)

Human Papillomavirus Vaccines: An Updated Review.
Cheng LQ, Wang Y, Du J.
Vaccines (2020)

Dysbiosis of the Human Oral Microbiome During the Menstrual Cycle and Vulnerability to the External Exposures of Smoking and Dietary Sugar
Bostanci N, Krog MC, Hugerth LW, Bashir Z, Fransson E, Boulund F, Belibasakis GN, Wannerberger K, Engstrand L, Nielsen HS and Schuppe-Koistinen I
Frontiers in Cellular and Infection Microbiology (2021)

Assessment of In Vitro and In Silico Protocols for Sequence-Based Characterization of the Human Vaginal Microbiome
Luisa W. Hugerth, Marcela Pereira, Yinghua Zha, Maike Seifert, Vilde Kaldhusdal, Fredrik Boulund, Maria C. Krog, Zahra Bashir, Marica Hamsten, Emma Fransson, Henriette Svarre-Nielsen, Ina Schuppe-Koistinen, Lars Engstrand
mSphere (2020)

Vaginal microbiota and human papillomavirus infection among young Swedish women
Liqin Cheng, Johanna Norenhag, Yue O. O. Hu, Nele Brusselaers, Emma Fransson, Andreas Ährlund-Richter, Unnur Guðnadóttir, Pia Angelidou, Yinghua Zha, Marica Hamsten, Ina Schuppe-Koistinen, Matts Olovsson, Lars Engstrand & Juan Du
npj Biofilms and Microbiomes (2020)

No evidence for a placental microbiome in human pregnancies at term.
Sterpu I, Fransson E, Hugerth LW, Du J, Pereira M, CHENG L,Radu SA, Calderón-Pérez L, Zha Y, Angelidou P, Pennhag A, Boulund F, Scheyniusa, Engstrand L, Wiberg-Itzel E, Schuppe-Koistinen I
American Journal of Obstetrics and Gynecology (2020)

The reproductive microbiome - clinical practice recommendations for fertility specialists. 
García-Velasco JA, Budding D, Campe H, et al. 
Reprod Biomed Online. 2020;41(3):443-453. 

The vaginal microbiota, human papillomavirus and cervical dysplasia: a systematic review and network meta-analysis.
Norenhag J, Du J, Olovsson M, Verstraelen H, Engstrand L, Brusselaers N
BJOG 2019 Jun;():

Vaginal dysbiosis and the risk of human papillomavirus and cervical cancer: systematic review and meta-analysis.
Brusselaers N, Shrestha S, van de Wijgert J, Verstraelen H
Am. J. Obstet. Gynecol. 2019 Jul;221(1):9-18.e8

Inflammatory markers in women with postpartum depressive symptoms.
Bränn E, Fransson E, White RA, Papadopoulos FC, Edvinsson Å, Kamali-Moghaddam M, et al
J. Neurosci. Res. 2018 Sep;():.

Changes in Cervical Human Papillomavirus (HPV) Prevalence at a Youth Clinic in Stockholm, Sweden, a Decade After the Introduction of the HPV Vaccine.
Ährlund-Richter A, Cheng L, Hu YOO, Svensson M, Pennhag AAL, Ursu RG, et al
Front Cell Infect Microbiol 2019 ;9():59

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Du Juan

Principal Researcher
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Gabriella Edfeldt

Postdoctoral Researcher
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Emma Fransson

Affiliated to Research

Nicole Wagner

Postdoctoral Researcher
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Yafei Xing

Laura Poole