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Research Article

Temporal and spatial variation of the human microbiota during pregnancy

Daniel B. DiGiulio, Benjamin J. Callahan, Paul J. McMurdie, Elizabeth K. Costello, Deirdre J. Lyell, Anna Robaczewska, Christine L. Sun, Daniela S. A. Goltsman, Ronald J. Wong, Gary Shaw, David K. Stevenson, View ORCID ProfileSusan P. Holmes, and David A. Relman
  1. aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
  2. bDepartment of Medicine, Stanford University School of Medicine, Stanford, CA 94305;
  3. cVeterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304;
  4. dDepartment of Statistics, Stanford University, Stanford, CA 94305;
  5. eDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305;
  6. fDepartment of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94305;
  7. gDepartment of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305

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PNAS September 1, 2015 112 (35) 11060-11065; first published August 17, 2015; https://doi.org/10.1073/pnas.1502875112
Daniel B. DiGiulio
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
bDepartment of Medicine, Stanford University School of Medicine, Stanford, CA 94305;
cVeterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304;
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Benjamin J. Callahan
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
dDepartment of Statistics, Stanford University, Stanford, CA 94305;
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Paul J. McMurdie
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
dDepartment of Statistics, Stanford University, Stanford, CA 94305;
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Elizabeth K. Costello
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
eDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305;
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Deirdre J. Lyell
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
fDepartment of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA 94305;
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Anna Robaczewska
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
bDepartment of Medicine, Stanford University School of Medicine, Stanford, CA 94305;
cVeterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304;
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Christine L. Sun
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
eDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305;
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Daniela S. A. Goltsman
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
eDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305;
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Ronald J. Wong
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
gDepartment of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
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Gary Shaw
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
gDepartment of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
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David K. Stevenson
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
gDepartment of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305
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Susan P. Holmes
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
dDepartment of Statistics, Stanford University, Stanford, CA 94305;
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  • ORCID record for Susan P. Holmes
David A. Relman
aMarch of Dimes Prematurity Research Center, Stanford University School of Medicine, Stanford, CA 94305;
bDepartment of Medicine, Stanford University School of Medicine, Stanford, CA 94305;
cVeterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304;
eDepartment of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305;
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  • For correspondence: relman@stanford.edu
  1. Edited by Jeffrey I. Gordon, Washington University School of Medicine in St. Louis, St. Louis, MO, and approved July 17, 2015 (received for review February 11, 2015)

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Significance

The human indigenous microbial communities (microbiota) play critical roles in health and may be especially important for mother and fetus during pregnancy. Using a case-control cohort of 40 women, we characterized weekly variation in the vaginal, gut, and oral microbiota during and after pregnancy. Microbiota membership remained relatively stable at each body site during pregnancy. An altered vaginal microbial community was associated with preterm birth; this finding was corroborated by an analysis of samples from an additional cohort of nine women. We also discovered an abrupt change in the vaginal microbiota at delivery that persisted in some cases for at least 1 y. Our findings suggest that pregnancy outcomes might be predicted by features of the microbiota early in gestation.

Abstract

Despite the critical role of the human microbiota in health, our understanding of microbiota compositional dynamics during and after pregnancy is incomplete. We conducted a case-control study of 49 pregnant women, 15 of whom delivered preterm. From 40 of these women, we analyzed bacterial taxonomic composition of 3,767 specimens collected prospectively and weekly during gestation and monthly after delivery from the vagina, distal gut, saliva, and tooth/gum. Linear mixed-effects modeling, medoid-based clustering, and Markov chain modeling were used to analyze community temporal trends, community structure, and vaginal community state transitions. Microbiota community taxonomic composition and diversity remained remarkably stable at all four body sites during pregnancy (P > 0.05 for trends over time). Prevalence of a Lactobacillus-poor vaginal community state type (CST 4) was inversely correlated with gestational age at delivery (P = 0.0039). Risk for preterm birth was more pronounced for subjects with CST 4 accompanied by elevated Gardnerella or Ureaplasma abundances. This finding was validated with a set of 246 vaginal specimens from nine women (four of whom delivered preterm). Most women experienced a postdelivery disturbance in the vaginal community characterized by a decrease in Lactobacillus species and an increase in diverse anaerobes such as Peptoniphilus, Prevotella, and Anaerococcus species. This disturbance was unrelated to gestational age at delivery and persisted for up to 1 y. These findings have important implications for predicting premature labor, a major global health problem, and for understanding the potential impact of a persistent, altered postpartum microbiota on maternal health, including outcomes of pregnancies following short interpregnancy intervals.

  • 16S rRNA gene
  • pregnancy
  • preterm birth
  • microbiome
  • premature labor

Footnotes

  • ↵1D.B.D. and B.J.C. contributed equally to this work.

  • ↵2To whom correspondence should be addressed. Email: relman{at}stanford.edu.
  • Author contributions: D.B.D., D.J.L., G.S., D.K.S., S.P.H., and D.A.R. designed research; D.B.D., A.R., and R.J.W. performed research; B.J.C., P.J.M., and S.P.H. contributed new reagents/analytic tools; D.B.D., B.J.C., P.J.M., E.K.C., C.L.S., D.S.A.G., S.P.H., and D.A.R. analyzed data; and D.B.D., B.J.C., P.J.M., E.K.C., C.L.S., D.S.A.G., S.P.H., and D.A.R. wrote the paper.

  • The authors declare no conflict of interest.

  • This article is a PNAS Direct Submission.

  • Data deposition: Raw sequence data have been deposited at the Sequence Read Archive (SRP no. 288562).

  • This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1502875112/-/DCSupplemental.

Freely available online through the PNAS open access option.

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Microbiota during pregnancy
Daniel B. DiGiulio, Benjamin J. Callahan, Paul J. McMurdie, Elizabeth K. Costello, Deirdre J. Lyell, Anna Robaczewska, Christine L. Sun, Daniela S. A. Goltsman, Ronald J. Wong, Gary Shaw, David K. Stevenson, Susan P. Holmes, David A. Relman
Proceedings of the National Academy of Sciences Sep 2015, 112 (35) 11060-11065; DOI: 10.1073/pnas.1502875112

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Microbiota during pregnancy
Daniel B. DiGiulio, Benjamin J. Callahan, Paul J. McMurdie, Elizabeth K. Costello, Deirdre J. Lyell, Anna Robaczewska, Christine L. Sun, Daniela S. A. Goltsman, Ronald J. Wong, Gary Shaw, David K. Stevenson, Susan P. Holmes, David A. Relman
Proceedings of the National Academy of Sciences Sep 2015, 112 (35) 11060-11065; DOI: 10.1073/pnas.1502875112
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Proceedings of the National Academy of Sciences: 112 (35)
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