Comparison of fecal collection methods for microbiota studies in Bangladesh

Emily Vogtmann, Jun Chen, Muhammad G. Kibriya, Yu Chen, Tariqul Islam, Mahbubul Eunes, Alauddin Ahmed, Jabun Naher, Anisur Rahman, Amnon Amir, Jianxin Shi, Christian C. Abnet, Heidi Nelson, Rob Knight, Nicholas Chia, Habibul Ahsan, Rashmi Sinhaa

Research output: Contribution to journalArticlepeer-review


To our knowledge, fecal microbiota collection methods have not been evaluated in low- and middle-income countries. Therefore, we evaluated five different fecal sample collection methods for technical reproducibility, stability, and accuracy within the Health Effects of Arsenic Longitudinal Study (HEALS) in Bangladesh. Fifty participants from the HEALS provided fecal samples in the clinic which were aliquoted into no solution, 95% ethanol, RNAlater, postdevelopment fecal occult blood test (FOBT) cards, and fecal immunochemical test (FIT) tubes. Half of the aliquots were frozen immediately at -80°C (day 0) and the remaining samples were left at ambient temperature for 96 h and then frozen (day 4). Intraclass correlation coefficients (ICC) were calculated for the relative abundances of the top three phyla, for two alpha diversity measures, and for four beta diversity measures. The duplicate samples had relatively high ICCs for technical reproducibility at day 0 and day 4 (range, 0.79 to 0.99). The FOBT card and samples preserved in RNAlater and 95% ethanol had the highest ICCs for stability over 4 days. The FIT tube had lower stability measures overall. In comparison to the "gold standard" method using immediately frozen fecal samples with no solution, the ICCs for many of the microbial metrics were low, but the rank order appeared to be preserved as seen by the Spearman correlation. The FOBT cards, 95% ethanol, and RNAlater were effective fecal preservatives. These fecal collection methods are optimal for future cohort studies, particularly in low- and middle-income countries.

Original languageEnglish (US)
Article numbere00361-17
JournalApplied and Environmental Microbiology
Issue number10
StatePublished - May 1 2017


  • Feces
  • Low/middle-income countries
  • Microbiota
  • Sampling methods
  • Stability

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Food Science
  • Biotechnology
  • Ecology


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