Microdiversity of the vaginal microbiome is associated with preterm birth.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
17 08 2023
17 08 2023
Historique:
received:
01
03
2023
accepted:
07
08
2023
medline:
21
8
2023
pubmed:
18
8
2023
entrez:
17
8
2023
Statut:
epublish
Résumé
Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield insights into these associations. Here, we analyze metagenomic data from 705 vaginal samples collected during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative. We find that the vaginal microbiome of pregnancies that ended preterm exhibited unique genetic profiles. It was more genetically diverse at the species level, a result which we validate in an additional cohort, and harbored a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find that Gardnerella species drove this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence that Gardnerella spp. underwent more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our population genetics analyses reveal associations between the vaginal microbiome and PTB and suggest that evolutionary processes acting on vaginal microbes may play a role in adverse pregnancy outcomes such as PTB.
Identifiants
pubmed: 37591872
doi: 10.1038/s41467-023-40719-7
pii: 10.1038/s41467-023-40719-7
pmc: PMC10435516
doi:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4997Subventions
Organisme : NICHD NIH HHS
ID : R01 HD106017
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2023. Springer Nature Limited.
Références
PeerJ. 2019 Jul 26;7:e7359
pubmed: 31388474
Genetics. 1997 Oct;147(2):879-906
pubmed: 9335621
Genome Res. 2022 Mar;32(3):558-568
pubmed: 34987055
Sci Rep. 2017 Nov 23;7(1):16145
pubmed: 29170495
Bioinformatics. 2011 Apr 15;27(8):1164-5
pubmed: 21335321
Nature. 2019 Apr;568(7750):43-48
pubmed: 30918406
Am J Obstet Gynecol. 2003 Oct;189(4):1150-4
pubmed: 14586369
J Infect Dis. 2014 Aug 1;210(3):338-43
pubmed: 24511102
Front Microbiol. 2020 Apr 08;11:476
pubmed: 32322240
Cell Host Microbe. 2020 Dec 9;28(6):838-852.e6
pubmed: 33113351
Science. 2020 Dec 4;370(6521):
pubmed: 33273073
Reprod Sci. 2014 Jan;21(1):32-40
pubmed: 23715799
Front Public Health. 2020 Jul 24;8:326
pubmed: 32793540
Genome Res. 2018 Oct;28(10):1467-1480
pubmed: 30232199
Nat Med. 2019 Jun;25(6):1012-1021
pubmed: 31142849
J Immunol. 2009 May 1;182(9):5488-97
pubmed: 19380797
Front Microbiol. 2018 May 14;9:843
pubmed: 29867790
Int J Gynaecol Obstet. 2020 Jul;150(1):31-33
pubmed: 32524596
Med. 2021 Sep 10;2(9):1027-1049
pubmed: 34617072
Viruses. 2017 Jun 08;9(6):
pubmed: 28594392
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Nucleic Acids Res. 2020 Jan 8;48(D1):D517-D525
pubmed: 31665441
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Eur J Obstet Gynecol Reprod Biol. 2009 Jul;145(1):57-64
pubmed: 19457604
ISME J. 2017 Dec;11(12):2864-2868
pubmed: 28742071
Nat Commun. 2017 Jun 09;8:15608
pubmed: 28598419
Sci Rep. 2019 Oct 1;9(1):14095
pubmed: 31575935
Nat Microbiol. 2021 Aug;6(8):1021-1030
pubmed: 34267358
Cell Host Microbe. 2019 May 8;25(5):656-667.e8
pubmed: 31028005
Best Pract Res Clin Obstet Gynaecol. 2018 Oct;52:103-113
pubmed: 29753695
Genome Biol Evol. 2019 Oct 1;11(10):2887-2894
pubmed: 31539038
Proc Natl Acad Sci U S A. 2021 Mar 23;118(12):
pubmed: 33723043
Nat Commun. 2023 Aug 17;14(1):4997
pubmed: 37591872
Clin Microbiol Infect. 2014 Jul;20(7):629-35
pubmed: 24118384
Microb Genom. 2020 Oct;6(10):
pubmed: 33001022
Gigascience. 2021 Feb 16;10(2):
pubmed: 33590861
PLoS Comput Biol. 2022 Mar 8;18(3):e1009947
pubmed: 35259160
BMC Bioinformatics. 2020 Jun 22;21(1):257
pubmed: 32571209
Nucleic Acids Res. 2021 Jul 2;49(W1):W293-W296
pubmed: 33885785
PLoS Biol. 2019 Jan 23;17(1):e3000102
pubmed: 30673701
Mol Ecol. 2021 Oct;30(20):5094-5104
pubmed: 34387003
Nat Biotechnol. 2021 Feb;39(2):165-168
pubmed: 32868914
Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4680-7
pubmed: 20534435
NPJ Biofilms Microbiomes. 2020 Nov 12;6(1):50
pubmed: 33184260
Science. 2015 Sep 4;349(6252):1101-1106
pubmed: 26229116
Genome Res. 2017 May;27(5):824-834
pubmed: 28298430
BJOG. 2021 May;128(6):976-982
pubmed: 32970908
BJOG. 2019 Feb;126(3):349-358
pubmed: 29791775
Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):9966-9971
pubmed: 28847941
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Infect Immun. 2019 Nov 18;87(12):
pubmed: 31527125
Front Cell Infect Microbiol. 2020 Jun 23;10:293
pubmed: 32656099
BMJ Case Rep. 2014 Oct 01;2014:
pubmed: 25274558
Nat Rev Microbiol. 2008 Jun;6(6):431-40
pubmed: 18461076
BMC Med. 2018 Jan 24;16(1):9
pubmed: 29361936
mSystems. 2020 Jan 14;5(1):
pubmed: 31937678
Genome Res. 2015 Jul;25(7):1043-55
pubmed: 25977477
Proc Natl Acad Sci U S A. 2021 May 4;118(18):
pubmed: 33906949
Cell Metab. 2020 Oct 6;32(4):575-590.e7
pubmed: 32916104
Obstet Gynecol. 2010 Jan;115(1):134-140
pubmed: 20027045
Nat Biotechnol. 2021 Jun;39(6):727-736
pubmed: 33462508
Nucleic Acids Res. 2000 Jan 1;28(1):33-6
pubmed: 10592175
PLoS Biol. 2007 Sep;5(9):e225
pubmed: 17713986
Nat Microbiol. 2023 Feb;8(2):246-259
pubmed: 36635575
Trends Genet. 2020 Jan;36(1):53-67
pubmed: 31780057
Am J Obstet Gynecol. 2017 Sep;217(3):356.e1-356.e18
pubmed: 28549981
Proc Natl Acad Sci U S A. 2011 Jan 18;108(3):1128-33
pubmed: 21191099
PLoS Genet. 2008 Dec;4(12):e1000304
pubmed: 19081788
PLoS Genet. 2019 Jun 13;15(6):e1008107
pubmed: 31194736
BMC Bioinformatics. 2010 Mar 08;11:119
pubmed: 20211023
Clin Infect Dis. 2000 Jan;30(1):237
pubmed: 10619781
Open Forum Infect Dis. 2017 Feb 08;4(1):ofx020
pubmed: 28480290
Front Cell Infect Microbiol. 2021 May 13;11:622474
pubmed: 34094994
Bioinformatics. 2019 Nov 15;:
pubmed: 31730192
Microbiome. 2021 Feb 17;9(1):49
pubmed: 33597026
Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7527-32
pubmed: 20368420
Pediatr Res. 2021 May;89(6):1549-1556
pubmed: 32726798
Int J Syst Evol Microbiol. 2019 Mar;69(3):679-687
pubmed: 30648938
Lancet. 2008 Jan 5;371(9606):75-84
pubmed: 18177778
Sci Rep. 2021 Nov 23;11(1):22794
pubmed: 34815499
Proc Natl Acad Sci U S A. 2015 Sep 1;112(35):11060-5
pubmed: 26283357
Science. 2020 Nov 6;370(6517):683-687
pubmed: 33154134
Pathogens. 2021 Jun 09;10(6):
pubmed: 34207831
Microbiome. 2018 Jun 28;6(1):117
pubmed: 29954448
Nucleic Acids Res. 2019 Jan 8;47(D1):D309-D314
pubmed: 30418610
BMC Infect Dis. 2004 Feb 13;4:5
pubmed: 15018635
Nature. 2013 Jan 3;493(7430):45-50
pubmed: 23222524
Mol Biol Evol. 2020 Feb 1;37(2):593-598
pubmed: 31633780
Front Endocrinol (Lausanne). 2014 Jul 07;5:106
pubmed: 25071722