Comparison of storage conditions for human vaginal microbiome studies

Guoyun Bai, Pawel Gajer, Melissa Nandy, Bing Ma, Hongqiu Yang, Joyce Sakamoto, May H. Blanchard, Jacques Ravel, Rebecca M. Brotman

Research output: Contribution to journalArticlepeer-review

56 Scopus citations


Background: The effect of storage conditions on the microbiome and metabolite composition of human biological samples has not been thoroughly investigated as a potential source of bias. We evaluated the effect of two common storage conditions used in clinical trials on the bacterial and metabolite composition of the vaginal microbiota using pyrosequencing of barcoded 16S rRNA gene sequencing and 1H-NMR analyses. Methodology/Principal Findings: Eight women were enrolled and four mid-vaginal swabs were collected by a physician from each woman. The samples were either processed immediately, stored at -80°C for 4 weeks or at -20°C for 1 week followed by transfer to -80°C for another 4 weeks prior to analysis. Statistical methods, including Kolmogorovo-Smirnov and Wilcoxon tests, were performed to evaluate the differences in vaginal bacterial community composition and metabolites between samples stored under different conditions. The results showed that there were no significant differences between samples processed immediately after collection or stored for varying durations. 1H-NMR analysis of the small molecule metabolites in vaginal secretions indicated that high levels of lactic acid were associated with Lactobacillus-dominated communities. Relative abundance of lactic acid did not appear to correlate with relative abundance of individual Lactobacillus sp. in this limited sample, although lower levels of lactic acid were observed when L. gasseri was dominant, indicating differences in metabolic output of seemingly similar communities. Conclusions/Significance: These findings benefit large-scale, field-based microbiome and metabolomic studies of the vaginal microbiota.

Original languageEnglish (US)
Article numbere36934
JournalPloS one
Issue number5
StatePublished - May 24 2012

All Science Journal Classification (ASJC) codes

  • General Biochemistry, Genetics and Molecular Biology
  • General Agricultural and Biological Sciences
  • General


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