Host factors are associated with vaginal microbiome structure in pregnancy in the ECHO Cohort Consortium

Kimberly McKee*, Christine M. Bassis, Jonathan Golob, Beatrice Palazzolo, Ananda Sen, Sarah S. Comstock, Christian Rosas-Salazar, Joseph B. Stanford, Thomas O’Connor, James E. Gern, Nigel Paneth, Anne L. Dunlop, P. Brian Smith, L. Kristin Newby, Linda Adair, Lisa P. Jacobson, Diane Catellier, Monica McGrath, Christian Douglas, Priya DuggalEmily Knapp, Amii Kress, Courtney K. Blackwell, Maxwell A. Mansolf, Jin Shei Lai, Emily Ho, David Cella, Richard Gershon, Michelle L. Macy, Suman R. Das, Jane E. Freedman, Simon A. Mallal, John A. McLean, Ravi V. Shah, Meghan H. Shilts, Akram N. Alshawabkeh, Jose F. Cordero, John Meeker, Leonardo Trasande, Carlos A. Camargo, Kohei Hasegawa, Zhaozhong Zhu, Ashley F. Sullivan, Dana Dabelea, Wei Perng, Traci A. Bekelman, Greta Wilkening, Sheryl Magzamen, Brianna F. Moore, Anne P. Starling, Deborah J. Rinehart, Daphne Koinis Mitchell, Viren D’Sa, Sean C.L. Deoni, Hans Georg Mueller, Cristiane S. Duarte, Catherine Monk, Glorisa Canino, Jonathan Posner, Tenneill Murray, Claudia Lugo-Candelas, Anne L. Dunlop, Patricia A. Brennan, Christine Hockett, Amy Elliott, Assiamira Ferrara, Lisa A. Croen, Monique M. Hedderson, John Ainsworth, Leonard B. Bacharier, Casper G. Bendixsen, James E. Gern, Diane R. Gold, Tina V. Hartert, Daniel J. Jackson, Christine C. Johnson, Christine L.M. Joseph, Meyer Kattan, Gurjit K.Khurana Hershey, Robert F. Lemanske, Susan V. Lynch, Rachel L. Miller, George T. O’Connor, Carole Ober, Dennis Ownby, Katherine Rivera-Spoljaric, Patrick H. Ryan, Christine M. Seroogy, Anne Marie Singh, Robert A. Wood, Edward M. Zoratti, Rima Habre, Shohreh Farzan, Frank D. Gilliland, Irva Hertz-Picciotto, Deborah H. Bennett, Julie B. Schweitzer, Rebecca J. Schmidt, Janine M. LaSalle, Alison E. Hipwell, Kate E. Keenan, Catherine J. Karr, Nicole R. Bush, Kaja Z. LeWinn, Sheela Sathyanarayana, Qi Zhao, Frances Tylavsky, Kecia N. Carroll, Christine T. Loftus, Leslie D. Leve, Jody M. Ganiban, Jenae M. Neiderhiser, Scott T. Weiss, Augusto A. Litonjua, Cindy T. McEvoy, Eliot R. Spindel, Robert S. Tepper, Craig J. Newschaffer, Kristen Lyall, Heather E. Volk, Rebecca Landa, Sally Ozonoff, Joseph Piven, Heather Hazlett, Juhi Pandey, Robert Schultz, Steven Dager, Kelly Botteron, Daniel Messinger, Wendy Stone, Jennifer Ames, Thomas G. O’Connor, Richard K. Miller, Emily Oken, Michele R. Hacker, Tamarra James-Todd, T. Michael O’Shea, Rebecca C. Fry, Jean A. Frazier, Rachana Singh, Caitlin Rollins, Angela Montgomery, Ruben Vaidya, Robert M. Joseph, Lisa K. Washburn, Semsa Gogcu, Kelly Bear, Julie V. Rollins, Stephen R. Hooper, Genevieve Taylor, Wesley Jackson, Amanda Thompson, Julie Daniels, Michelle Hernandez, Kun Lu, Michael Msall, Madeleine Lenski, Rawad Obeid, Steven L. Pastyrnak, Elizabeth Jensen, Christina Sakai, Hudson Santos, Jean M. Kerver, Nigel Paneth, Charles J. Barone, Michael R. Elliott, Douglas M. Ruden, Chris Fussman, Julie B. Herbstman, Amy Margolis, Susan L. Schantz, Sarah Dee Geiger, Andrea Aguiar, Karen Tabb, Rita Strakovsky, Tracey Woodruff, Rachel Morello-Frosch, Amy Padula, Joseph B. Stanford, Christina A. Porucznik, Angelo P. Giardino, Rosalind J. Wright, Robert O. Wright, Brent Collett, Nicole Baumann-Blackmore, Ronald Gangnon, Daniel J. Jackson, Chris G. McKennan, Jo Wilson, Matt Altman, Judy L. Aschner, Annemarie Stroustrup, Stephanie L. Merhar, Paul E. Moore, Gloria S. Pryhuber, Mark Hudak, Ann Marie Reynolds Lyndaker, Andrea L. Lampland, Burton Rochelson, Sophia Jan, Matthew J. Blitz, Michelle W. Katzow, Zenobia Brown, Codruta Chiuzan, Timothy Rafael, Dawnette Lewis, Natalie Meirowitz, Brenda Poindexter, Tebeb Gebretsadik, Sarah Osmundson, Jennifer K. Straughen, Amy Eapen, Andrea Cassidy-Bushrow, Ganesa Wegienka, Alex Sitarik, Kim Woodcroft, Audrey Urquhart, Albert Levin, Tisa Johnson-Hooper, Brent Davidson, Tengfei Ma, Emily S. Barrett, Martin J. Blaser, Maria Gloria Dominguez-Bello, Daniel B. Horton, Manuel Jimenez, Todd Rosen, Kristy Palomares, Lyndsay A. Avalos, Yeyi Zhu, Kelly J. Hunt, Roger B. Newman, Michael S. Bloom, Mallory H. Alkis, James R. Roberts, Sunni L. Mumford, Heather H. Burris, Sara B. DeMauro, Lynn M. Yee, Aaron Hamvas, Antonia F. Olidipo, Andrew S. Haddad, Lisa R. Eiland, Nicole T. Spillane, Kirin N. Suri, Stephanie A. Fisher, Jeffrey A. Goldstein, Leena B. Mithal, Raye Ann O. DeRegnier, Nathalie L. Maitre, Ruby H.N. Nguyen, Meghan M. JaKa, Abbey C. Sidebottom, Michael J. Paidas, Jo Nell E. Potter, Natale Ruby, Lunthita Duthely, Arumugam Jayakumar, Karen Young, Isabel Maldonado, Meghan Miller, Jonathan L. Slaughter, Sarah A. Keim, Courtney D. Lynch, Kartik K. Venkatesh, Kristina W. Whitworth, Elaine Symanski, Thomas F. Northrup, Hector Mendez-Figueroa, Ricardo A. Mosquera, Margaret R. Karagas, Juliette C. Madan, Debra M. MacKenzie, Johnnye L. Lewis, Brandon J. Rennie, Bennett L. Leventhal, Young Shin Kim, Somer Bishop, Sara S. Nozadi, Li Luo, Barry M. Lester, Carmen J. Marsit, Todd Everson, Cynthia M. Loncar, Elisabeth C. McGowan, Stephen J. Sheinkopf, Brian S. Carter, Jennifer Check, Jennifer B. Helderman, Charles R. Neal, Lynne M. Smith

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Using pooled vaginal microbiota data from pregnancy cohorts (N = 683 participants) in the Environmental influences on Child Health Outcomes (ECHO) Program, we analyzed 16S rRNA gene amplicon sequences to identify clinical and demographic host factors that associate with vaginal microbiota structure in pregnancy both within and across diverse cohorts. Using PERMANOVA models, we assessed factors associated with vaginal community structure in pregnancy, examined whether host factors were conserved across populations, and tested the independent and combined effects of host factors on vaginal community state types (CSTs) using multinomial logistic regression models. Demographic and social factors explained a larger amount of variation in the vaginal microbiome in pregnancy than clinical factors. After adjustment, lower education, rather than self-identified race, remained a robust predictor of L. iners dominant (CST III) and diverse (CST IV) (OR = 8.44, 95% CI = 4.06–17.6 and OR = 4.18, 95% CI = 1.88–9.26, respectively). In random forest models, we identified specific taxonomic features of host factors, particularly urogenital pathogens associated with pregnancy complications (Aerococcus christensenii and Gardnerella spp.) among other facultative anaerobes and key markers of community instability (L. iners). Sociodemographic factors were robustly associated with vaginal microbiota structure in pregnancy and should be considered as sources of variation in human microbiome studies.

Original languageEnglish (US)
Article number11798
JournalScientific reports
Volume14
Issue number1
DOIs
StatePublished - Dec 2024

Keywords

  • 16S rRNA gene amplicon sequence data
  • ECHO cohort
  • Host factors
  • Meta-analysis
  • Pregnancy
  • Vaginal microbiota structure

ASJC Scopus subject areas

  • General

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