A large-scale metagenomic study for enzyme profiles using the focused identification of the NGS-based definitive enzyme research (FINDER) strategy

Jae Yoon Sung, Yong Jik Lee, Yong Joon Cho, Myeong Na Shin, Sang Jae Lee, Han Seung Lee, Hong Koh, Jin Woo Bae, Jae Ho Shin, Hyun Jung Kim, Dong Woo Lee

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)


Excavating the molecular details of many diverse enzymes from metagenomes remains challenging in agriculture, food, health, and environmental fields. We present a versatile method that accelerates metabolic enzyme discovery for highly selective gene capture in metagenomes using next-generation sequencing. Culture-independent enzyme mining of environmental DNA is based on a set of short identifying degenerate sequences specific for a wide range of enzyme superfamilies, followed by multiplexed DNA barcode sequencing. A strategy of ‘focused identification of next-generation sequencing-based definitive enzyme research’ enabled us to generate targeted enzyme datasets from metagenomes, resulting in minimal hands-on obtention of high-throughput biological diversity and potential function profiles, without being time-consuming. This method also provided a targeted inventory of predicted proteins and molecular features of metabolic activities from several metagenomic samples. We suggest that the efficiency and sensitivity of this method will accelerate the decryption of microbial diversity and the signature of proteins and their metabolism from environmental samples.

Original languageEnglish
Pages (from-to)4360-4374
Number of pages15
JournalBiotechnology and Bioengineering
Issue number11
Publication statusPublished - 2021 Nov

Bibliographical note

Funding Information:
We greatly appreciate Gwan‐Hyeong Lee for designing a set of superfamily‐specific primers and Kihwan Kim for illustrating phylum analysis. This study was supported by National Research Foundation of Korea (NRF) grants (2018M3A9H3025030 to Dong‐Woo Lee and Hyun Jung Kim, and 2016R1D1A1B04934489 to Han‐Seung Lee) funded by the Ministry of Science and ICT, a Strategic Initiative for Microbiomes in Agriculture and Food grant (916006‐2 and 918012‐4 to Dong‐Woo Lee) funded by the Ministry of Agriculture, Food and Rural Affairs, Brain Korea 21(BK21) program (Jae‐Yoon Sung was fellowship awardee by BK21 program).

Publisher Copyright:
© 2021 Wiley Periodicals LLC

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Bioengineering
  • Applied Microbiology and Biotechnology


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