Measuring the absolute abundance of the microbiome by adding yeast containing 16S rRNA gene from a hyperthermophile

Ju Yeong Kim, Myung hee Yi, Myungjun Kim, Seogwon Lee, Hye Su Moon, Dongeun Yong, Tai Soon Yong

Research output: Contribution to journalArticlepeer-review

1 Citation (Scopus)


High-throughput sequencing (HTS) of 16S rRNA gene amplicons provides compositional information regarding the microbial community, but not the absolute abundance of the bacteria. We aimed to develop a standardized method for quantifying the absolute abundance of bacteria in microbiome studies. To demonstrate the utility of our approach, we quantified the number of bacteria from the compositional data of the fecal and cecal microbiomes. The 16S rRNA gene of a hyperthermophile, Thermus aquaticus, was cloned into Pichia pastoris (yeast) genome, and an equivalent amount of the yeast was added to the stool and cecal samples of mice before DNA extraction. 16S rRNA gene library construction and HTS were performed after DNA extraction. The absolute abundances of bacteria were calculated using T. aquaticus reads. The average relative abundances of T. aquaticus in the five stool and five cecal samples were 0.95% and 0.33%, respectively, indicating that the number of bacteria in a cecum sample is 2.9 times higher than that in a stool sample. The method proposed for quantifying the absolute abundance of the bacterial population in this study is expected to overcome the limitation of showing only compositional data in most microbiome studies.

Original languageEnglish
Article numbere1220
Issue number4
Publication statusPublished - 2021 Aug

Bibliographical note

Funding Information:
This study was supported by a grant from the National Research Foundation of Korea (NRF) funded by the Korean Government (MEST; numbers NRF‐2019R1A2B5B01069843 and 2020R1I1A2074562).

Publisher Copyright:
© 2021 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

All Science Journal Classification (ASJC) codes

  • Microbiology


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