Deciphering diversity indices for a better understanding of microbial communities

Bo Ra Kim, Jiwon Shin, Robin B. Guevarra, Jun Hyung Lee, Doo Wan Kim, Kuk Hwan Seol, Ju Hoon Lee, Hyeun Bum Kim, Richard E. Isaacson

Research output: Contribution to journalArticlepeer-review

364 Scopus citations


The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

Original languageEnglish (US)
Pages (from-to)2089-2093
Number of pages5
JournalJournal of Microbiology and Biotechnology
Issue number12
StatePublished - Dec 2017

Bibliographical note

Funding Information:
The present study was supported by the Rural Development Administration (Project No. PJ012279), the Individual Basic Science & Engineering Research Program (No. NRF-2015R1D1A1A01061268) through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, and a research fund (14162MFDS972) from the Ministry of Food and Drug Safety, Republic of Korea.

Funding Information:
The present study was supported by the Rural Development

Publisher Copyright:
© 2017 by The Korean Society for Microbiology and Biotechnology.


  • Diversity index
  • Microbial diversity
  • Microbial ecology
  • Microbiota


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