Variations in the microbiome due to storage preservatives are not large enough to obscure variations due to factors such as host population, host species, body site, and captivity

Abigail E. Asangba, Mariah E. Donohue, Alicia Lamb, Patricia C. Wright, Ali Halajian, Steven R. Leigh, Rebecca M. Stumpf

Research output: Contribution to journalArticle

Abstract

The study of the primate microbiome is critical in understanding the role of the microbial community in the host organism. To be able to isolate the main factors responsible for the differences observed in microbiomes within and between individuals, confounding factors due to technical variations need to be removed. To determine whether alterations due to preservatives outweigh differences due to factors such as host population, host species, body site, and habitat, we tested three methods (no preservative, 96% ethanol, and RNAlater) for preserving wild chimpanzee (fecal), wild lemur (fecal), wild vervet monkey (rectal, oral, nasal, otic, vaginal, and penile), and captive vervet monkey (rectal) samples. All samples were stored below − 20°C (short term) at the end of the field day and then at − 80°C until DNA extraction. Using 16S rRNA gene sequencing, we show a significant preservative effect on microbiota composition and diversity. Samples stored in ethanol and RNAlater appear to be less different compared with samples not stored in any preservative (none). Our differential analysis revealed significantly higher amounts of Enterococcaceae and Family XI in no preservative samples, Prevotellaceae and Spirochaetaceae in ethanol and RNAlater preserved samples, Oligosphaeraceae in ethanol-preserved samples, and Defluviitaleaceae in RNAlater preserved samples. While these preservative effects on the microbiome are not large enough to remove or outweigh the differences arising from biological factors (e.g., host species, body site, and habitat differences) they may promote misleading interpretations if they have large enough effect sizes compared to the biological factors (e.g., host population).

Original languageEnglish (US)
Article numbere23045
JournalAmerican journal of primatology
Volume81
Issue number10-11
DOIs
StatePublished - Oct 1 2019

Fingerprint

preservative
captivity
preservatives
ethanol
sampling
Cercopithecus aethiops
Enterococcaceae
Spirochaetaceae
habitat
primate
Lemur
microbiome
microbial community
habitats
Pan troglodytes
microbial communities
DNA
ears
mouth
Primates

Keywords

  • microbiome alterations
  • storage preservative
  • technical variation

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Animal Science and Zoology

Cite this

Variations in the microbiome due to storage preservatives are not large enough to obscure variations due to factors such as host population, host species, body site, and captivity. / Asangba, Abigail E.; Donohue, Mariah E.; Lamb, Alicia; Wright, Patricia C.; Halajian, Ali; Leigh, Steven R.; Stumpf, Rebecca M.

In: American journal of primatology, Vol. 81, No. 10-11, e23045, 01.10.2019.

Research output: Contribution to journalArticle

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