Rapidly processed stool swabs approximate stool microbiota profiles

Nicholas A. Bokulich, Juan Maldonado, Dae Wook Kang, Rosa Krajmalnik-Brown, James G Caporaso

Research output: Contribution to journalArticle

Abstract

Studies of the intestinal microbiome commonly utilize stool samples to measure the microbial composition in the distal gut. However, collection of stool can be difficult from some subjects under certain experimental conditions. Sampling of fecal material using sterile swabs can streamline sample collection, handling, and processing. In this study, we validate the use of swabs of fecal matter to approximate measurements of microbiota in stool using 16S rRNA gene Illumina amplicon sequencing and evaluate the effects of shipping time at ambient temperatures on accuracy. The results indicate that swab samples reliably replicate the stool microbiota bacterial composition, alpha diversity, and beta diversity when swabs are processed quickly (≤2 days) but that sample quality quickly degrades after this period and is accompanied by increased abundances of Enterobacteriaceae. Fresh swabs appear to be a viable alternative to stool sampling when standard collection methods are challenging, but extended exposure to ambient temperatures prior to processing threatens sample integrity.

Original languageEnglish (US)
Article numbere00208-19
JournalmSphere
Volume4
Issue number2
DOIs
StatePublished - Mar 1 2019

Keywords

  • 16S rRNA genes
  • Gut microbiome
  • Sample collection

ASJC Scopus subject areas

  • Microbiology
  • Molecular Biology

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  • Cite this

    Bokulich, N. A., Maldonado, J., Kang, D. W., Krajmalnik-Brown, R., & Caporaso, J. G. (2019). Rapidly processed stool swabs approximate stool microbiota profiles. mSphere, 4(2), [e00208-19]. https://doi.org/10.1128/mSphere.00208-19