Microbial niches in raw ingredients determine microbial community assembly during kimchi fermentation

Hye Seon Song, Tae Woong Whon, Juseok Kim, Se Hee Lee, Joon Yong Kim, Yeon Bee Kim, Hak Jong Choi, Jin Kyu Rhee, Seong Woon Roh

Research output: Contribution to journalArticlepeer-review

72 Scopus citations


Fermented foods constitute hubs of microbial consortia differentially affecting nutritional and organoleptic properties, quality, and safety. Here we show the origin source of fermentative microbes and fermentation dynamics of kimchi. We partitioned microbiota by raw ingredient (kimchi cabbage, garlic, ginger, and red pepper) to render kimchi fermented by each source-originated microbe pool and applied multi-omics (metataxonomics and metabolomics), bacterial viability, and physiochemical analyses to longitudinally collected samples. Only kimchi cabbage- and garlic-derived microbial inoculums yielded successful kimchi fermentations. The dominant fermentative microbial taxa and subsequent metabolic outputs differed by raw ingredient type: the genus Leuconostoc, Weissella, and Lactobacillus for all non-sterilized ingredients, garlic, and kimchi cabbage, respectively. Gnotobiotic kimchi inoculated by mono-, di-, and tri- isolated fermentative microbe combinations further revealed W. koreensis-mediated reversible microbial metabolic outputs. The results suggest that the raw ingredient microbial habitat niches selectively affect microbial community assembly patterns and processes during kimchi fermentation.

Original languageEnglish
Article number126481
JournalFood Chemistry
StatePublished - 15 Jul 2020

Bibliographical note

Publisher Copyright:
© 2020 Elsevier Ltd


  • Kimchi
  • Lactic acid bacteria
  • Metabolomics
  • Metataxonomics
  • Microbial community assembly


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