Assessing the impact of storage time on the stability of stool microbiota richness, diversity, and composition

Elizabeth A Holzhausen; Maria Nikodemova; Courtney L Deblois; Jodi H Barnet; Paul E Peppard; Garret Suen; Kristen M Malecki

doi:10.1186/s13099-021-00470-0

Assessing the impact of storage time on the stability of stool microbiota richness, diversity, and composition

Gut Pathog. 2021 Dec 20;13(1):75. doi: 10.1186/s13099-021-00470-0.

Authors

Elizabeth A Holzhausen^#¹, Maria Nikodemova^#², Courtney L Deblois^{3

4}, Jodi H Barnet², Paul E Peppard², Garret Suen³, Kristen M Malecki⁵

Affiliations

¹ Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, USA. holzhausen@wisc.edu.
² Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, USA.
³ Department of Bacteriology, University of Wisconsin-Madison, Madison, USA.
⁴ Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, USA.
⁵ Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, USA. kmalecki@wisc.edu.

^# Contributed equally.

Abstract

Background: New technologies like next-generation sequencing have led to a proliferation of studies investigating the role of the gut microbiome in human health, particularly population-based studies that rely upon participant self-collection of samples. However, the impact of methodological differences in sample shipping, storage, and processing are not well-characterized for these types of studies, especially when transit times may exceed 24 h. The aim of this study was to experimentally assess microbiota stability in stool samples stored at 4 °C for durations of 6, 24, 48, 72, and 96 h with no additives to better understand effects of variable shipping times in population-based studies. These data were compared to a baseline sample that was immediately stored at - 80 °C after stool production.

Results: Compared to the baseline sample, we found that the alpha-diversity metrics Shannon's and Inverse Simpson's had excellent intra-class correlations (ICC) for all storage durations. Chao1 richness had good to excellent ICC. We found that the relative abundances of bacteria in the phyla Verrucomicrobia, Actinobacteria, and Proteobacteria had excellent ICC with baseline for all storage durations, while Firmicutes and Bacteroidetes ranged from moderate to good. We interpreted the ICCs as follows: poor: ICC < 0.50, moderate: 0.50 < ICC < 0.75, good: 0.75 < ICC < 0.90, and excellent: ICC > 0.90. Using the Bray-Curtis dissimilarity index, we found that the greatest change in community composition occurred between 0 and 24 h of storage, while community composition remained relatively stable for subsequent storage durations. Samples showed strong clustering by individual, indicating that inter-individual variability was greater than the variability associated with storage time.

Conclusions: The results of this analysis suggest that several measures of alpha diversity, relative abundance, and overall community composition are robust to storage at 4 °C for up to 96 h. We found that the overall community richness was influenced by storage duration in addition to the relative abundances of sequences within the Firmicutes and Bacteroidetes phyla. Finally, we demonstrate that inter-individual variability in microbiota composition was greater than the variability due to changing storage durations.