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Cited by 131Reproductive tract infections researchMetabolomics and Mass Spectrometry StudiesGut microbiota and health

A multi-platform metabolomics approach identifies highly specific biomarkers of bacterial diversity in the vagina of pregnant and non-pregnant women

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McMillan, Amy, Rulisa, Stephen, Sumarah, Mark, Macklaim, Jean M., Renaud, Justin, Bisanz, Jordan E., Gloor, Gregory B., Reid, Gregor·2015·Scientific Reports
DOI 10.1038/srep14174PMC PMC4585667
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Abstract

Bacterial vaginosis (BV) increases transmission of HIV, enhances the risk of preterm labour and is associated with malodour. Clinical diagnosis often relies on microscopy, which may not reflect the microbiota composition accurately. We use an untargeted metabolomics approach, whereby we normalize the weight of samples prior to analysis, to obtained precise measurements of metabolites in vaginal fluid. We identify biomarkers for BV with high sensitivity and specificity (AUC = 0.99) in a cohort of 131 pregnant and non-pregnant Rwandan women and demonstrate that the vaginal metabolome is strongly associated with bacterial diversity. Metabolites associated with high diversity and clinical BV include 2-hydroxyisovalerate and γ-hydroxybutyrate (GHB), but not succinate, which is produced by both Lactobacillus crispatus and BV-associated anaerobes in vitro. Biomarkers associated with high diversity and clinical BV are independent of pregnancy status and were validated in a blinded replication cohort from Tanzania (n = 45), where we predicted clinical BV with 91% accuracy. Correlations between the metabolome and microbiota identified Gardnerella vaginalis as a putative producer of GHB and we demonstrate production by this species in vitro. This work illustrates how changes in community structure alter the chemical composition of the vagina and identifies highly specific biomarkers for a common condition.

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  • A dysbiotic state enriched with facultative anaerobic Gram-negative bacteria, such as Gardnerella vaginalis and E. coli, characterizes BV, and is strongly associated with increased UTI susceptibility and recurrence.

    “A dysbiotic state enriched with facultative anaerobic Gram-negative bacteria, such as Gardnerella vaginalis and E. coli , characterizes BV, and is strongly associated with increased UTI susceptibility and recurrence [9, 12].”

    From Vaginal microbiota and urinary tract infections in women: the protective role of vaginal lactobacilli in counteracting urinary tract infections occurrence and recurrence (2026) · cites this paper as [12]

    The paper’s opening discussion describes BV as associated with displacement of lactobacilli by mixed anaerobes, including Gardnerella. It does not describe E. coli as characteristic of BV or establish an association with UTI susceptibility or recurrence; the Methods section says women with current urinary tract infections were excluded. (LLM, conf=0.88)

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Research works printed but not linked: 51

  1. Ravel J. et al. Vaginal microbiome of reproductive-age women. Proc. Natl. Acad. Sci. USA 108, Suppl 1, 4680– 4687 (2011). 20534435 PMC3063603
  2. Hummelen R. et al. Deep sequencing of the vaginal microbiota of women with HIV. PLoS One 5, e12078 (2010). 20711427 PMC2920804
  3. Koumans E. H. et al. The prevalence of bacterial vaginosis in the United States, 2001-2004; associations with symptoms, sexual behaviors, and reproductive health. Sex. Transm. Dis. 34, 864– 869 (2007). 17621244
  4. Klebanoff M. A. et al. Vulvovaginal symptoms in women with bacterial vaginosis. Obstet. Gynecol. 104, 267– 272 (2004). 15291998
  5. Sobel J. D., Karpas Z. & Lorber A. Diagnosing vaginal infections through measurement of biogenic amines by ion mobility spectrometry. Eur. J. Obstet. Gynecol. Reprod. Biol. 163, 81– 84 (2012). 22520996
  6. Wolrath H., Forsum U., Larsson P. G. & Boren H. Analysis of bacterial vaginosis-related amines in vaginal fluid by gas chromatography and mass spectrometry. J. Clin. Microbiol. 39, 4026– 4031 (2001). 11682525 PMC88482
  7. Wolrath H., Stahlbom B., Hallen A. & Forsum U. Trimethylamine and trimethylamine oxide levels in normal women and women with bacterial vaginosis reflect a local metabolism in vaginal secretion as compared to urine. APMIS 113, 513– 516 (2005). 16086821
  8. Sha B. E. et al. Female genital-tract HIV load correlates inversely with Lactobacillus species but positively with bacterial vaginosis and Mycoplasma hominis. J. Infect. Dis. 191, 25– 32 (2005). 15592999
  9. Das T. R., Jahan S., Begum S. R. & Akhtar M. F. Association between bacterial vaginosis and preterm delivery. Mymensingh Med. J. 20, 115– 120 (2011). 21240174
  10. Nugent R. P., Krohn M. A. & Hillier S. L. Reliability of diagnosing bacterial vaginosis is improved by a standardized method of gram stain interpretation. J. Clin. Microbiol. 29, 297– 301 (1991). 1706728 PMC269757
  11. Amsel R. et al. Nonspecific vaginitis. Diagnostic criteria and microbial and epidemiologic associations. Am. J. Med. 74, 14– 22 (1983). 6600371
  12. Chaijareenont K., Sirimai K., Boriboonhirunsarn D. & Kiriwat O. Accuracy of Nugent’s score and each Amsel’s criteria in the diagnosis of bacterial vaginosis. J. Med. Assoc. Thai. 87, 1270– 1274 (2004). 15825698
  13. Sha B. E. et al. Utility of Amsel criteria, Nugent score, and quantitative PCR for Gardnerella vaginalis, Mycoplasma hominis, and Lactobacillus spp. for diagnosis of bacterial vaginosis in human immunodeficiency virus-infected women. J. Clin. Microbiol. 43, 4607– 4612 (2005). 16145114 PMC1234056
  14. Schwebke J. R., Hillier S. L., Sobel J. D., McGregor J. A. & Sweet R. L. Validity of the vaginal gram stain for the diagnosis of bacterial vaginosis. Obstet. Gynecol. 88, 573– 576 (1996). 8841221
  15. Mayers J. R. et al. Elevation of circulating branched-chain amino acids is an early event in human pancreatic adenocarcinoma development. Nat. Med. 20, 1193– 1198 (2014). 25261994 PMC4191991
  16. Sreekumar A. et al. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 457, 910– 914 (2009). 19212411 PMC2724746
  17. Wikoff W. R. et al. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc. Natl. Acad. Sci. USA 106, 3698– 3703 (2009). 19234110 PMC2656143
  18. Shannon C. E. The mathematical theory of communication. 1963. MD Comput. 14, 306– 317 (1997). 9230594
  19. Zhou X. et al. The vaginal bacterial communities of Japanese women resemble those of women in other racial groups. FEMS Immunol. Med. Microbiol. 58, 169– 181 (2010). 19912342 PMC2868947
  20. Ison C. A., Easmon C. S., Dawson S. G., Southerton G. & Harris J. W. Non-volatile fatty acids in the diagnosis of non-specific vaginitis. J. Clin. Pathol. 36, 1367– 1370 (1983). 6606653 PMC498570
  21. Piot P., Van Dyck E., Godts P. & Vanderheyden J. The vaginal microbial flora in non-specific vaginitis. Eur. J. Clin. Microbiol. 1, 301– 306 (1982). 6985215
  22. Al-Mushrif S., Eley A. & Jones B. M. Inhibition of chemotaxis by organic acids from anaerobes may prevent a purulent response in bacterial vaginosis. J. Med. Microbiol. 49, 1023– 1030 (2000). 11073156
  23. Kaneuchi C., Seki M. & Komagata K. Production of succinic acid from citric acid and related acids by Lactobacillus strains. Appl. Environ. Microbiol. 54, 3053– 3056 (1988). 16347795 PMC204426
  24. Bisanz J. E. et al. Microbiota at Multiple Body Sites during Pregnancy in a Rural Tanzanian Population and Effects of Moringa-Supplemented Probiotic Yogurt. Appl. Environ. Microbiol. 81, 4965– 4975 (2015). 25979893 PMC4495201
  25. Friedman J. & Alm E. J. Inferring correlation networks from genomic survey data. PLoS Comput. Biol. 8, e1002687 (2012). 23028285 PMC3447976
  26. Fernandes A. D., Macklaim J. M., Linn T. G., Reid G. & Gloor G. B. ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq. PLoS One 8, e67019 (2013). 23843979 PMC3699591
  27. Sohling B. & Gottschalk G. Molecular analysis of the anaerobic succinate degradation pathway in Clostridium kluyveri. J. Bacteriol. 178, 871– 880 (1996). 8550525 PMC177737
  28. Scherf U., Sohling B., Gottschalk G., Linder D. & Buckel W. Succinate-ethanol fermentation in Clostridium kluyveri: purification and characterisation of 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA delta 3-delta 2-isomerase. Arch. Microbiol. 161, 239– 245 (1994). 8161284
  29. Macklaim J. M. et al. Comparative meta-RNA-seq of the vaginal microbiota and differential expression by Lactobacillus iners in health and dysbiosis. Microbiome 1, 12-2618– 1-12 (2013). 24450540 PMC3971606
  30. Srinivasan S. et al. Metabolic signatures of bacterial vaginosis. MBio 6, 10.1128/mBio.00204-15 (2015). PMC4453549 25873373 · DOI
  31. Liebich H. M. & Forst C. Hydroxycarboxylic and oxocarboxylic acids in urine: products from branched-chain amino acid degradation and from ketogenesis. J. Chromatogr. 309, 225– 242 (1984). 6434570
  32. Kawai S. et al. Purification and characterization of a malic enzyme from the ruminal bacterium Streptococcus bovis ATCC 15352 and cloning and sequencing of its gene. Appl. Environ. Microbiol. 62, 2692– 2700 (1996). 8702261 PMC168054
  33. Pine L., Malcolm G. B., Brooks J. B. & Daneshvar M. I. Physiological studies on the growth and utilization of sugars by Listeria species. Can. J. Microbiol. 35, 245– 254 (1989). 2501014
  34. Novak L. & Loubiere P. The metabolic network of Lactococcus lactis: distribution of (14)C-labeled substrates between catabolic and anabolic pathways. J. Bacteriol. 182, 1136– 1143 (2000). 10648541 PMC94391
  35. Yeoman C. J. et al. A multi-omic systems-based approach reveals metabolic markers of bacterial vaginosis and insight into the disease. PLoS One 8, e56111 (2013). 23405259 PMC3566083
  36. Fettweis J. M. et al. Differences in vaginal microbiome in African American women versus women of European ancestry. Microbiology 160, 2272– 2282 (2014). 25073854 PMC4178329
  37. McMillan A. et al. A multi-platform metabolomics approach identifies novel biomarkers associated with bacterial diversity in the human vagina. arXiv:1504.02816v1 [q-bio.BM] (2015). PMC4585667 26387596 · arXiv
  38. Kohlmeier K. A., Vardar B. & Christensen M. H. gamma-Hydroxybutyric acid induces actions via the GABAB receptor in arousal and motor control-related nuclei: Implications for therapeutic actions in behavioral state disorders. Neuroscience 248, 261– 277 (2013). 23791974
  39. Absalom N. et al. alpha4betadelta GABA(A) receptors are high-affinity targets for gamma-hydroxybutyric acid (GHB). Proc. Natl. Acad. Sci. USA 109, 13404– 13409 (2012). 22753476 PMC3421209
  40. Connelly W. M., Errington A. C. & Crunelli V. gamma-Hydroxybutyric acid (GHB) is not an agonist of extrasynaptic GABAA receptors. PLoS One 8, e79062 (2013). 24244421 PMC3823990
  41. Aagaard K. et al. A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy. PLoS One 7, e36466 (2012). 22719832 PMC3374618
  42. MacIntyre D. A. et al. The vaginal microbiome during pregnancy and the postpartum period in a European population. Sci. Rep. 5, 8988 (2015). 25758319 PMC4355684
  43. Laghi L. et al. Rifaximin modulates the vaginal microbiome and metabolome in women affected by bacterial vaginosis. Antimicrob. Agents Chemother. 58, 3411– 3420 (2014). 24709255 PMC4068465
  44. Gajer P. et al. Temporal dynamics of the human vaginal microbiota. Sci. Transl. Med. 4, 132ra52 (2012). PMC3722878 22553250
  45. Gloor G. B. et al. Microbiome profiling by illumina sequencing of combinatorial sequence-tagged PCR products. PLoS One 5, e15406 (2010). 21048977 PMC2964327
  46. Styczynski M. P. et al. Systematic identification of conserved metabolites in GC/MS data for metabolomics and biomarker discovery. Anal. Chem. 79, 966– 973 (2007). 17263323
  47. Kessner D., Chambers M., Burke R., Agus D. & Mallick P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24, 2534– 2536 (2008). 18606607 PMC2732273
  48. Pluskal T., Castillo S., Villar-Briones A. & Oresic M. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 11, 395-2105– 11-395 (2010). 20650010 PMC2918584
  49. Smith C. A. et al. METLIN: a metabolite mass spectral database. Ther. Drug Monit. 27, 747– 751 (2005). 16404815
  50. Wishart D. S. et al. HMDB 3.0—The Human Metabolome Database in 2013. Nucleic Acids Res. 41, D801– 7 (2013). 23161693 PMC3531200
  51. Youden W. J. Index for rating diagnostic tests. Cancer 3, 32– 35 (1950). 15405679

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Authors
McMillan, A., Rulisa, S., Sumarah, M., Macklaim, J. M., Renaud, J., Bisanz, J. E., Gloor, G. B., & Reid, G.
Affiliations
  • Western University (CA)
  • University of Rwanda (RW)
  • Agriculture and Agri-Food Canada (CA)
Corresponding author
Reid, Gregor
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2015-09-21
Volume
5
Issue
1
Pages
14174-14174
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/srep14174
PMC
PMC4585667
OpenAlex
W1921359935
Cited by
131
References
3
Citations by year
2026: 8 · 2025: 8 · 2024: 4 · 2023: 14 · 2022: 12 · 2021: 17 · 2020: 16 · 2019: 10 · 2018: 20 · 2017: 12 · 2016: 8 · 2015: 2
FWCI
11.79
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • Federal Open Science Repository of Canada / Le Dépôt fédéral de science ouverte du Canada (submittedVersion, cc-by)
  • Scholarship@Western (Western University) (submittedVersion)
  • arXiv (Cornell University)
Funders
Canadian Institutes of Health Research
Topics
  • Life Sciences › Immunology and Microbiology › Microbiology › Reproductive tract infections research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Keywords
bacterial vaginosis, biomarkers, bacterial diversity, Gardnerella vaginalis, gamma-hydroxybutyric acid, succinic acid, Lactobacillus crispatus, pregnancy, vaginal microbiota, untargeted metabolomics, diagnostic biomarkers
MeSH terms
Adult, Female, Gardnerella vaginalis, Humans, Lactobacillus, Middle Aged, Pregnancy, Rwanda, Sodium Oxybate, Vagina, Valerates, Biomarkers, Vaginosis, Bacterial, Biodiversity, Metabolomics, Young Adult, Microbiota

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