Community structures and genomic features of undesirable white colony-forming yeasts on fermented vegetables

Joon Yong Kim; Juseok Kim; In-Tae Cha; Min Young Jung; Hye Seon Song; Yeon Bee Kim; Changsu Lee; Seung-Yeon Kang; Jin-Woo Bae; Yoon-E Choi; Tae-Woon Kim; Seong Woon Roh

doi:10.1007/s12275-019-8487-y

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Community structures and genomic features of undesirable white colony-forming yeasts on fermented vegetables: Joon Yong Kim ¹, Juseok Kim ^2,3, In-Tae Cha ², Min Young Jung ², Hye Seon Song ², Yeon Bee Kim ², Changsu Lee ², Seung-Yeon Kang ², Jin-Woo Bae ¹, Yoon-E Choi ³, Tae-Woon Kim ², Seong Woon Roh ²; Journal of Microbiology 2019;57(1):30-37.
DOI: https://doi.org/10.1007/s12275-019-8487-y
Published online: October 25, 2018

¹Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea, ²Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea, ³Division of Environmental Science & Ecological Engineering, Korea University, Seoul 02841, Republic of Korea¹Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea, ²Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju 61755, Republic of Korea, ³Division of Environmental Science & Ecological Engineering, Korea University, Seoul 02841, Republic of Korea

Corresponding author: Tae-Woon Kim , Tel: +82-62-610-1778,
Seong Woon Roh , Tel: +82-62-610-1778,

Received: 4 September 2018 • Revised: 27 September 2018 • Accepted: 28 September 2018

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Abstract

White colony-forming yeasts (WCFYs) often appear in fermented foods, depending on the storage method. Despite the ongoing research on fermented foods, the community and genome features of WCFYs have not been well studied. In this study, the community structures of WCFYs on fermented vegetables (kimchi) prepared with various raw materials were investigated using deep sequencing. Only eight operational taxonomic units (OTUs) were detected, indicating that the community structure of WCFYs on kimchi is very simple. The five most abundant OTUs represented Pichia kluyveri, Yarrowia lipolytica, Candida sake, Hanseniaspora uvarum, and Kazachstania servazzii. Using a culture-dependent
method
, 41 strains representing the five major OTUs were isolated from the surface of the food samples. Whole genomes of the five major yeast strains were sequenced and annotated. The total genome length for the strains ranged from 8.97 Mbp to 21.32 Mbp. This is the first study to report genome sequences of the two yeasts Pichia kluyveri and Candida sake. Genome analysis indicated that each yeast strain had core metabolic pathways such as oxidative phosphorylation; purine metabolism; glycolysis/gluconeogenesis; aminoacyl- tRNA biosynthesis; citrate cycle; but strain specific pathways were also found. In addition, no toxin or antimicrobial resistance genes were identified. Our study provides genome information for five WCFY strains that may highlight their potential beneficial or harmful metabolic effects in fermented vegetables.

Keywords: white colony-forming yeast;fermented vegetable;kimchi;community structure;genomic feature

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Community structures and genomic features of undesirable white colony-forming yeasts on fermented vegetables

J. Microbiol. 2019;57(1):30-37. Published online October 25, 2018

DOI: https://doi.org/10.1007/s12275-019-8487-y

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