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 language | English (US) |
---|---|
Article number | 11798 |
Journal | Scientific reports |
Volume | 14 |
Issue number | 1 |
DOIs | |
State | Published - 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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In: Scientific reports, Vol. 14, No. 1, 11798, 12.2024.
Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - Host factors are associated with vaginal microbiome structure in pregnancy in the ECHO Cohort Consortium
AU - McKee, Kimberly
AU - Bassis, Christine M.
AU - Golob, Jonathan
AU - Palazzolo, Beatrice
AU - Sen, Ananda
AU - Comstock, Sarah S.
AU - Rosas-Salazar, Christian
AU - Stanford, Joseph B.
AU - O’Connor, Thomas
AU - Gern, James E.
AU - Paneth, Nigel
AU - Dunlop, Anne L.
AU - Smith, P. Brian
AU - Newby, L. Kristin
AU - Adair, Linda
AU - Jacobson, Lisa P.
AU - Catellier, Diane
AU - McGrath, Monica
AU - Douglas, Christian
AU - Duggal, Priya
AU - Knapp, Emily
AU - Kress, Amii
AU - Blackwell, Courtney K.
AU - Mansolf, Maxwell A.
AU - Lai, Jin Shei
AU - Ho, Emily
AU - Cella, David
AU - Gershon, Richard
AU - Macy, Michelle L.
AU - Das, Suman R.
AU - Freedman, Jane E.
AU - Mallal, Simon A.
AU - McLean, John A.
AU - Shah, Ravi V.
AU - Shilts, Meghan H.
AU - Alshawabkeh, Akram N.
AU - Cordero, Jose F.
AU - Meeker, John
AU - Trasande, Leonardo
AU - Camargo, Carlos A.
AU - Hasegawa, Kohei
AU - Zhu, Zhaozhong
AU - Sullivan, Ashley F.
AU - Dabelea, Dana
AU - Perng, Wei
AU - Bekelman, Traci A.
AU - Wilkening, Greta
AU - Magzamen, Sheryl
AU - Moore, Brianna F.
AU - Starling, Anne P.
AU - Rinehart, Deborah J.
AU - Mitchell, Daphne Koinis
AU - D’Sa, Viren
AU - Deoni, Sean C.L.
AU - Mueller, Hans Georg
AU - Duarte, Cristiane S.
AU - Monk, Catherine
AU - Canino, Glorisa
AU - Posner, Jonathan
AU - Murray, Tenneill
AU - Lugo-Candelas, Claudia
AU - Dunlop, Anne L.
AU - Brennan, Patricia A.
AU - Hockett, Christine
AU - Elliott, Amy
AU - Ferrara, Assiamira
AU - Croen, Lisa A.
AU - Hedderson, Monique M.
AU - Ainsworth, John
AU - Bacharier, Leonard B.
AU - Bendixsen, Casper G.
AU - Gern, James E.
AU - Gold, Diane R.
AU - Hartert, Tina V.
AU - Jackson, Daniel J.
AU - Johnson, Christine C.
AU - Joseph, Christine L.M.
AU - Kattan, Meyer
AU - Hershey, Gurjit K.Khurana
AU - Lemanske, Robert F.
AU - Lynch, Susan V.
AU - Miller, Rachel L.
AU - O’Connor, George T.
AU - Ober, Carole
AU - Ownby, Dennis
AU - Rivera-Spoljaric, Katherine
AU - Ryan, Patrick H.
AU - Seroogy, Christine M.
AU - Singh, Anne Marie
AU - Wood, Robert A.
AU - Zoratti, Edward M.
AU - Habre, Rima
AU - Farzan, Shohreh
AU - Gilliland, Frank D.
AU - Hertz-Picciotto, Irva
AU - Bennett, Deborah H.
AU - Schweitzer, Julie B.
AU - Schmidt, Rebecca J.
AU - LaSalle, Janine M.
AU - Hipwell, Alison E.
AU - Keenan, Kate E.
AU - Karr, Catherine J.
AU - Bush, Nicole R.
AU - LeWinn, Kaja Z.
AU - Sathyanarayana, Sheela
AU - Zhao, Qi
AU - Tylavsky, Frances
AU - Carroll, Kecia N.
AU - Loftus, Christine T.
AU - Leve, Leslie D.
AU - Ganiban, Jody M.
AU - Neiderhiser, Jenae M.
AU - Weiss, Scott T.
AU - Litonjua, Augusto A.
AU - McEvoy, Cindy T.
AU - Spindel, Eliot R.
AU - Tepper, Robert S.
AU - Newschaffer, Craig J.
AU - Lyall, Kristen
AU - Volk, Heather E.
AU - Landa, Rebecca
AU - Ozonoff, Sally
AU - Piven, Joseph
AU - Hazlett, Heather
AU - Pandey, Juhi
AU - Schultz, Robert
AU - Dager, Steven
AU - Botteron, Kelly
AU - Messinger, Daniel
AU - Stone, Wendy
AU - Ames, Jennifer
AU - O’Connor, Thomas G.
AU - Miller, Richard K.
AU - Oken, Emily
AU - Hacker, Michele R.
AU - James-Todd, Tamarra
AU - O’Shea, T. Michael
AU - Fry, Rebecca C.
AU - Frazier, Jean A.
AU - Singh, Rachana
AU - Rollins, Caitlin
AU - Montgomery, Angela
AU - Vaidya, Ruben
AU - Joseph, Robert M.
AU - Washburn, Lisa K.
AU - Gogcu, Semsa
AU - Bear, Kelly
AU - Rollins, Julie V.
AU - Hooper, Stephen R.
AU - Taylor, Genevieve
AU - Jackson, Wesley
AU - Thompson, Amanda
AU - Daniels, Julie
AU - Hernandez, Michelle
AU - Lu, Kun
AU - Msall, Michael
AU - Lenski, Madeleine
AU - Obeid, Rawad
AU - Pastyrnak, Steven L.
AU - Jensen, Elizabeth
AU - Sakai, Christina
AU - Santos, Hudson
AU - Kerver, Jean M.
AU - Paneth, Nigel
AU - Barone, Charles J.
AU - Elliott, Michael R.
AU - Ruden, Douglas M.
AU - Fussman, Chris
AU - Herbstman, Julie B.
AU - Margolis, Amy
AU - Schantz, Susan L.
AU - Geiger, Sarah Dee
AU - Aguiar, Andrea
AU - Tabb, Karen
AU - Strakovsky, Rita
AU - Woodruff, Tracey
AU - Morello-Frosch, Rachel
AU - Padula, Amy
AU - Stanford, Joseph B.
AU - Porucznik, Christina A.
AU - Giardino, Angelo P.
AU - Wright, Rosalind J.
AU - Wright, Robert O.
AU - Collett, Brent
AU - Baumann-Blackmore, Nicole
AU - Gangnon, Ronald
AU - Jackson, Daniel J.
AU - McKennan, Chris G.
AU - Wilson, Jo
AU - Altman, Matt
AU - Aschner, Judy L.
AU - Stroustrup, Annemarie
AU - Merhar, Stephanie L.
AU - Moore, Paul E.
AU - Pryhuber, Gloria S.
AU - Hudak, Mark
AU - Lyndaker, Ann Marie Reynolds
AU - Lampland, Andrea L.
AU - Rochelson, Burton
AU - Jan, Sophia
AU - Blitz, Matthew J.
AU - Katzow, Michelle W.
AU - Brown, Zenobia
AU - Chiuzan, Codruta
AU - Rafael, Timothy
AU - Lewis, Dawnette
AU - Meirowitz, Natalie
AU - Poindexter, Brenda
AU - Gebretsadik, Tebeb
AU - Osmundson, Sarah
AU - Straughen, Jennifer K.
AU - Eapen, Amy
AU - Cassidy-Bushrow, Andrea
AU - Wegienka, Ganesa
AU - Sitarik, Alex
AU - Woodcroft, Kim
AU - Urquhart, Audrey
AU - Levin, Albert
AU - Johnson-Hooper, Tisa
AU - Davidson, Brent
AU - Ma, Tengfei
AU - Barrett, Emily S.
AU - Blaser, Martin J.
AU - Dominguez-Bello, Maria Gloria
AU - Horton, Daniel B.
AU - Jimenez, Manuel
AU - Rosen, Todd
AU - Palomares, Kristy
AU - Avalos, Lyndsay A.
AU - Zhu, Yeyi
AU - Hunt, Kelly J.
AU - Newman, Roger B.
AU - Bloom, Michael S.
AU - Alkis, Mallory H.
AU - Roberts, James R.
AU - Mumford, Sunni L.
AU - Burris, Heather H.
AU - DeMauro, Sara B.
AU - Yee, Lynn M.
AU - Hamvas, Aaron
AU - Olidipo, Antonia F.
AU - Haddad, Andrew S.
AU - Eiland, Lisa R.
AU - Spillane, Nicole T.
AU - Suri, Kirin N.
AU - Fisher, Stephanie A.
AU - Goldstein, Jeffrey A.
AU - Mithal, Leena B.
AU - DeRegnier, Raye Ann O.
AU - Maitre, Nathalie L.
AU - Nguyen, Ruby H.N.
AU - JaKa, Meghan M.
AU - Sidebottom, Abbey C.
AU - Paidas, Michael J.
AU - Potter, Jo Nell E.
AU - Ruby, Natale
AU - Duthely, Lunthita
AU - Jayakumar, Arumugam
AU - Young, Karen
AU - Maldonado, Isabel
AU - Miller, Meghan
AU - Slaughter, Jonathan L.
AU - Keim, Sarah A.
AU - Lynch, Courtney D.
AU - Venkatesh, Kartik K.
AU - Whitworth, Kristina W.
AU - Symanski, Elaine
AU - Northrup, Thomas F.
AU - Mendez-Figueroa, Hector
AU - Mosquera, Ricardo A.
AU - Karagas, Margaret R.
AU - Madan, Juliette C.
AU - MacKenzie, Debra M.
AU - Lewis, Johnnye L.
AU - Rennie, Brandon J.
AU - Leventhal, Bennett L.
AU - Kim, Young Shin
AU - Bishop, Somer
AU - Nozadi, Sara S.
AU - Luo, Li
AU - Lester, Barry M.
AU - Marsit, Carmen J.
AU - Everson, Todd
AU - Loncar, Cynthia M.
AU - McGowan, Elisabeth C.
AU - Sheinkopf, Stephen J.
AU - Carter, Brian S.
AU - Check, Jennifer
AU - Helderman, Jennifer B.
AU - Neal, Charles R.
AU - Smith, Lynne M.
N1 - Publisher Copyright: © The Author(s) 2024.
PY - 2024/12
Y1 - 2024/12
N2 - 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.
AB - 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.
KW - 16S rRNA gene amplicon sequence data
KW - ECHO cohort
KW - Host factors
KW - Meta-analysis
KW - Pregnancy
KW - Vaginal microbiota structure
UR - http://www.scopus.com/inward/record.url?scp=85194130720&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85194130720&partnerID=8YFLogxK
U2 - 10.1038/s41598-024-62537-7
DO - 10.1038/s41598-024-62537-7
M3 - Article
C2 - 38782975
AN - SCOPUS:85194130720
SN - 2045-2322
VL - 14
JO - Scientific reports
JF - Scientific reports
IS - 1
M1 - 11798
ER -