Genomic Comparisons of Lactobacillus crispatus and Lactobacillus iners Reveal Potential Ecological Drivers of Community Composition in the Vagina.
Lactobacillus crispatus and Lactobacillus iners are common inhabitants of the healthy human vagina. These two species are closely related and are thought to perform similar ecological functions in the vaginal environment. Temporal data on the vaginal microbiome have shown that nontransient instances of cooccurrence are uncommon, while transitions from an L. iners-dominated community to one dominated by L. crispatus, and vice versa, occur often. This suggests that there is substantial overlap in the fundamental niches of these species. Given this apparent niche overlap, it is unclear how they have been maintained as common inhabitants of the human vagina. In this study, we characterized and compared the genomes of L. iners and L. crispatus to gain insight into possible mechanisms driving the maintenance of this species diversity. Our results highlight differences in the genomes of these two species that may facilitate the partitioning of their shared niche space. Many of the identified differences may impact the protective benefits provided to the host by these two species.



The microbial communities that inhabit the human vagina play a critical role in the maintenance of vaginal health through the production of lactic acid and lowering the environmental pH. This precludes the growth of nonindigenous organisms and protects against infectious disease. The two most common types of vaginal communities are dominated by either Lactobacillus iners or Lactobacillus crispatus, while some communities alternate between the two over time. We combined ecological theory with state-of-the-art genome analyses to characterize how these two species might partition their shared niche space in the vagina. We show that the genomes of L. iners and L. crispatus differ in many respects, several of which may drive differences in their competitive abilities in the vagina. Our results provide insight into factors that drive the complicated temporal dynamics of the vaginal microbiome and demonstrate how closely related microbial species partition shared fundamental niche space.
Institute for Bioinformatics and Evolutionary Studies and Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.
Michael T
MT
France
Institute for Bioinformatics and Evolutionary Studies and Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA.
Helena
H
Mendes-Soares
Institute for Bioinformatics and Evolutionary Studies and Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA lforney@uidaho.edu.
Larry J
0000-0003-2448-1219
LJ
Forney
D044822:Biodiversity; D019143:Evolution, Molecular; D005260:Female; D016680:Genome, Bacterial; D023281:Genomics; D006801:Humans; D007778:Lactobacillus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D000070003:Lactobacillus crispatus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D010802:Phylogeny; D014621:Vagina / Q000382:microbiology*
Genome Res. 2006 Feb;16(2):149-56
16365377
J Infect Dis. 2015 Sep 1;212(5):793-802
25676470
J Infect Dis. 2014 Oct 1;210(7):1019-28
24737800
Arch Gynecol Obstet. 2006 Jan;273(4):195-202
16208476
Science. 2008 May 23;320(5879):1081-5
18497299
Appl Environ Microbiol. 1999 Apr;65(4):1506-15
10103244
J Clin Microbiol. 2001 Nov;39(11):4026-31
11682525
Nucleic Acids Res. 1998 Jan 15;26(2):544-8
9421513
Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):2873-8
8610134
Nat Rev Microbiol. 2011 Nov 08;10(1):13-26
22064560
MBio. 2013 Aug 06;4(4):null
23919998
Crit Rev Microbiol. 2002;28(4):281-370
12546196
BMC Infect Dis. 2007 Nov 07;7:128
17986357
J Androl. 2005 Jul-Aug;26(4):459-69
15955884
Mol Microbiol. 1995 Feb;15(3):415-20
7540246
Reprod Sci. 2015 Nov;22(11):1393-8
25878210
Mol Biol Evol. 2012 Jun;29(6):1695-701
22319168
Genome Res. 2003 Sep;13(9):2178-89
12952885
Acta Med Scand. 1966 Nov;180(5):639-50
5923385
Bioinformatics. 2008 Mar 1;24(5):715-6
18227120
MBio. 2015 Mar 24;6(2):null
25805726
Biochim Biophys Acta. 1980 Jul 15;630(4):545-58
7397238
Curr Opin Genet Dev. 2005 Dec;15(6):589-94
16185861
J Clin Microbiol. 2007 Mar;45(3):1016-8
17202272
Sci Transl Med. 2012 May 2;4(132):132ra52
22553250
J Clin Microbiol. 2007 Sep;45(9):3145
17652481
Bioinformatics. 2007 Mar 15;23(6):673-9
17237039
J Bacteriol. 2010 Jul;192(13):3547-8
20435723
J Clin Endocrinol Metab. 1980 Oct;51(4):765-70
6252225
Mol Biosyst. 2015 Jun;11(6):1717-25
25959140
Nat Protoc. 2013 Apr;8(4):652-65
23471110
J Infect Dis. 2014 Jun 15;209(12):1989-99
24403560
Int J Infect Dis. 2015 Apr;33:32-6
25546169
Sci Rep. 2014 May 30;4:5136
24875844
J Bacteriol. 2014 Apr;196(7):1458-70
24488312
Nucleic Acids Res. 1999 Dec 1;27(23):4636-41
10556321
Interdiscip Perspect Infect Dis. 2008;2008:181253
19277101
Trends Ecol Evol. 2000 Aug;15(8):321-326
10884696
Immunol Rev. 2005 Aug;206:306-35
16048557
Bioinformatics. 2014 May 1;30(9):1312-3
24451623
Science. 1974 Jul 5;185(4145):27-39
17779277
J Mol Biol. 2016 Feb 22;428(4):726-31
26585406
Am J Obstet Gynecol. 2011 Feb;204(2):120.e1-5
20832044
J Clin Microbiol. 2002 Aug;40(8):2746-9
12149323
Cell Host Microbe. 2012 Apr 19;11(4):387-96
22520466
Hum Reprod. 2004 Apr;19(4):889-92
14990542
J Clin Microbiol. 2010 May;48(5):1812-9
20305015
Genome Biol Evol. 2011;3:195-208
21266540
Infect Immun. 2012 Dec;80(12):4061-70
23045475
Trends Microbiol. 1998 Jul;6(7):263-8
9717214
BMC Infect Dis. 2011 Jul 19;11:200
21771337
BMC Genomics. 2014 Dec 05;15:1070
25480015
Menopause. 2015 Jul;22(7):702-9
25535963
Vet Pathol. 2014 Mar;51(2):328-40
24318976
Proc Natl Acad Sci U S A. 2011 Mar 15;108 Suppl 1:4680-7
20534435
Reprod Sci. 2013 Jul;20(7):791-6
23202727
Microbiol Rev. 1993 Jun;57(2):434-50
8336674
N Engl J Med. 2005 Nov 3;353(18):1899-911
16267321
MBio. 2012 May 02;3(2):null
22448042
J Clin Microbiol. 1999 Mar;37(3):729-33
9986841
Bioinformatics. 2007 Nov 1;23(21):2947-8
17846036
J Bacteriol. 2011 Mar;193(5):1034-41
21169489
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Clin Infect Dis. 1997 Sep;25 Suppl 2:S123-6
9310650