Yujin Kim, Hojun Sung, Yeon Bee Kim, Hye Seon Song, Mi-Ja Jung, Jisu Lee, Min Ji Lee, Se Hee Lee, Seong Woon Roh, Jin-Woo Bae, Tae Woong Whon
{"title":"无菌发酵对无菌蔬菜全基因表达的影响","authors":"Yujin Kim, Hojun Sung, Yeon Bee Kim, Hye Seon Song, Mi-Ja Jung, Jisu Lee, Min Ji Lee, Se Hee Lee, Seong Woon Roh, Jin-Woo Bae, Tae Woong Whon","doi":"10.1111/ppl.14502","DOIUrl":null,"url":null,"abstract":"<p><p>Existing research has underscored the vital interplay between host organisms and their associated microbiomes, which affects health and function. In both plants and animals, host factors critically shape microbial communities and influence growth, health, and immunity. Post-harvest plants, such as those used in kimchi, a traditional Korean dish, offer a unique avenue for exploring host-microbe dynamics during fermentation. Despite the emphasis on lactic acid bacteria (LAB) in fermentation studies, the roles of host factors remain unclear. This study aimed to investigate the influence of these factors on plant transcriptomes during kimchi fermentation. We individually inoculated nine LAB strains into germ-free kimchi to generate LAB-mono-associated gnotobiotic kimchi and performed RNA-sequencing analysis for the host vegetables during fermentation. The transcriptomes of post-harvest vegetables in kimchi change over time, and microbes affect the transcriptome profiles of vegetables. Differentially expressed gene analyses revealed that microbes affected the temporal expression profiles of several genes in the plant transcriptomes in unique directions depending on the introduced LAB strains. Cluster analysis with other publicly available transcriptomes of post-harvest vegetables and fruits further revealed that the plant transcriptome is more profoundly influenced by the environment harboring the host than by host phylogeny. Our results bridge the gap in understanding the bidirectional relationship between host vegetables and microbes during food fermentation, illuminating the complex interplay between vegetable transcriptomes, fermentative microbes, and the fermentation process in food production. The different transcriptomic responses elicited by specific LAB strains suggest the possibility of microbial manipulation to achieve the desired fermentation outcomes.</p>","PeriodicalId":20164,"journal":{"name":"Physiologia plantarum","volume":null,"pages":null},"PeriodicalIF":5.4000,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Effects of gnotobiotic fermentation on global gene expression of germ-free vegetables.\",\"authors\":\"Yujin Kim, Hojun Sung, Yeon Bee Kim, Hye Seon Song, Mi-Ja Jung, Jisu Lee, Min Ji Lee, Se Hee Lee, Seong Woon Roh, Jin-Woo Bae, Tae Woong Whon\",\"doi\":\"10.1111/ppl.14502\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Existing research has underscored the vital interplay between host organisms and their associated microbiomes, which affects health and function. In both plants and animals, host factors critically shape microbial communities and influence growth, health, and immunity. Post-harvest plants, such as those used in kimchi, a traditional Korean dish, offer a unique avenue for exploring host-microbe dynamics during fermentation. Despite the emphasis on lactic acid bacteria (LAB) in fermentation studies, the roles of host factors remain unclear. This study aimed to investigate the influence of these factors on plant transcriptomes during kimchi fermentation. We individually inoculated nine LAB strains into germ-free kimchi to generate LAB-mono-associated gnotobiotic kimchi and performed RNA-sequencing analysis for the host vegetables during fermentation. The transcriptomes of post-harvest vegetables in kimchi change over time, and microbes affect the transcriptome profiles of vegetables. Differentially expressed gene analyses revealed that microbes affected the temporal expression profiles of several genes in the plant transcriptomes in unique directions depending on the introduced LAB strains. Cluster analysis with other publicly available transcriptomes of post-harvest vegetables and fruits further revealed that the plant transcriptome is more profoundly influenced by the environment harboring the host than by host phylogeny. Our results bridge the gap in understanding the bidirectional relationship between host vegetables and microbes during food fermentation, illuminating the complex interplay between vegetable transcriptomes, fermentative microbes, and the fermentation process in food production. The different transcriptomic responses elicited by specific LAB strains suggest the possibility of microbial manipulation to achieve the desired fermentation outcomes.</p>\",\"PeriodicalId\":20164,\"journal\":{\"name\":\"Physiologia plantarum\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":5.4000,\"publicationDate\":\"2024-09-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Physiologia plantarum\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1111/ppl.14502\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"PLANT SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Physiologia plantarum","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1111/ppl.14502","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
Effects of gnotobiotic fermentation on global gene expression of germ-free vegetables.
Existing research has underscored the vital interplay between host organisms and their associated microbiomes, which affects health and function. In both plants and animals, host factors critically shape microbial communities and influence growth, health, and immunity. Post-harvest plants, such as those used in kimchi, a traditional Korean dish, offer a unique avenue for exploring host-microbe dynamics during fermentation. Despite the emphasis on lactic acid bacteria (LAB) in fermentation studies, the roles of host factors remain unclear. This study aimed to investigate the influence of these factors on plant transcriptomes during kimchi fermentation. We individually inoculated nine LAB strains into germ-free kimchi to generate LAB-mono-associated gnotobiotic kimchi and performed RNA-sequencing analysis for the host vegetables during fermentation. The transcriptomes of post-harvest vegetables in kimchi change over time, and microbes affect the transcriptome profiles of vegetables. Differentially expressed gene analyses revealed that microbes affected the temporal expression profiles of several genes in the plant transcriptomes in unique directions depending on the introduced LAB strains. Cluster analysis with other publicly available transcriptomes of post-harvest vegetables and fruits further revealed that the plant transcriptome is more profoundly influenced by the environment harboring the host than by host phylogeny. Our results bridge the gap in understanding the bidirectional relationship between host vegetables and microbes during food fermentation, illuminating the complex interplay between vegetable transcriptomes, fermentative microbes, and the fermentation process in food production. The different transcriptomic responses elicited by specific LAB strains suggest the possibility of microbial manipulation to achieve the desired fermentation outcomes.
期刊介绍:
Physiologia Plantarum is an international journal committed to publishing the best full-length original research papers that advance our understanding of primary mechanisms of plant development, growth and productivity as well as plant interactions with the biotic and abiotic environment. All organisational levels of experimental plant biology – from molecular and cell biology, biochemistry and biophysics to ecophysiology and global change biology – fall within the scope of the journal. The content is distributed between 5 main subject areas supervised by Subject Editors specialised in the respective domain: (1) biochemistry and metabolism, (2) ecophysiology, stress and adaptation, (3) uptake, transport and assimilation, (4) development, growth and differentiation, (5) photobiology and photosynthesis.