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Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi

Presently, pertinent information on the ultra-small microbiome (USM) in fermented vegetables is still lacking. This study analyzed the metatranscriptome and metataxonome for the USM of kimchi. Tangential flow filtration was used to obtain a USM with a size of 0.2 μm or less from kimchi. The microbia...

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Autores principales: Lee, Hae-Won, Yoon, So-Ra, Dang, Yun-Mi, Yun, Ji-Hyun, Jeong, Hoibin, Kim, Kil-Nam, Bae, Jin-Woo, Ha, Ji-Hyoung
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9581167/
https://www.ncbi.nlm.nih.gov/pubmed/36274711
http://dx.doi.org/10.3389/fmicb.2022.1026513
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author Lee, Hae-Won
Yoon, So-Ra
Dang, Yun-Mi
Yun, Ji-Hyun
Jeong, Hoibin
Kim, Kil-Nam
Bae, Jin-Woo
Ha, Ji-Hyoung
author_facet Lee, Hae-Won
Yoon, So-Ra
Dang, Yun-Mi
Yun, Ji-Hyun
Jeong, Hoibin
Kim, Kil-Nam
Bae, Jin-Woo
Ha, Ji-Hyoung
author_sort Lee, Hae-Won
collection PubMed
description Presently, pertinent information on the ultra-small microbiome (USM) in fermented vegetables is still lacking. This study analyzed the metatranscriptome and metataxonome for the USM of kimchi. Tangential flow filtration was used to obtain a USM with a size of 0.2 μm or less from kimchi. The microbial diversity in the USM was compared with that of the normal microbiome (NM). Alpha diversity was higher in the USM than in NM, and the diversity of bacterial members of the NM was higher than that of the USM. At the phylum level, both USM and NM were dominated by Firmicutes. At the genus level, the USM and NM were dominated by Lactobacillus, Leuconostoc, and Weissella, belonging to lactic acid bacteria. However, as alpha diversity is higher in the USM than in the NM, the genus Akkermansia, belonging to the phylum Verrucomicrobia, was detected only in the USM. Compared to the NM, the USM showed a relatively higher ratio of transcripts related to “protein metabolism,” and the USM was suspected to be involved with the viable-but-nonculturable (VBNC) state. When comparing the sub-transcripts related to the “cell wall and capsule” of USM and NM, USM showed a proportion of transcripts suspected of being VBNC. In addition, the RNA virome was also identified, and both the USM and NM were confirmed to be dominated by pepper mild mottle virus (PMMoV). Additionally, the correlation between metataxonome and metatranscriptome identified USM and NM was estimated, however, only limited correlations between metataxonome and metatranscriptome were estimated. This study provided insights into the relationship between the potential metabolic activities of the USM of kimchi and the NM.
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spelling pubmed-95811672022-10-20 Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi Lee, Hae-Won Yoon, So-Ra Dang, Yun-Mi Yun, Ji-Hyun Jeong, Hoibin Kim, Kil-Nam Bae, Jin-Woo Ha, Ji-Hyoung Front Microbiol Microbiology Presently, pertinent information on the ultra-small microbiome (USM) in fermented vegetables is still lacking. This study analyzed the metatranscriptome and metataxonome for the USM of kimchi. Tangential flow filtration was used to obtain a USM with a size of 0.2 μm or less from kimchi. The microbial diversity in the USM was compared with that of the normal microbiome (NM). Alpha diversity was higher in the USM than in NM, and the diversity of bacterial members of the NM was higher than that of the USM. At the phylum level, both USM and NM were dominated by Firmicutes. At the genus level, the USM and NM were dominated by Lactobacillus, Leuconostoc, and Weissella, belonging to lactic acid bacteria. However, as alpha diversity is higher in the USM than in the NM, the genus Akkermansia, belonging to the phylum Verrucomicrobia, was detected only in the USM. Compared to the NM, the USM showed a relatively higher ratio of transcripts related to “protein metabolism,” and the USM was suspected to be involved with the viable-but-nonculturable (VBNC) state. When comparing the sub-transcripts related to the “cell wall and capsule” of USM and NM, USM showed a proportion of transcripts suspected of being VBNC. In addition, the RNA virome was also identified, and both the USM and NM were confirmed to be dominated by pepper mild mottle virus (PMMoV). Additionally, the correlation between metataxonome and metatranscriptome identified USM and NM was estimated, however, only limited correlations between metataxonome and metatranscriptome were estimated. This study provided insights into the relationship between the potential metabolic activities of the USM of kimchi and the NM. Frontiers Media S.A. 2022-10-05 /pmc/articles/PMC9581167/ /pubmed/36274711 http://dx.doi.org/10.3389/fmicb.2022.1026513 Text en Copyright © 2022 Lee, Yoon, Dang, Yun, Jeong, Kim, Bae and Ha. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Lee, Hae-Won
Yoon, So-Ra
Dang, Yun-Mi
Yun, Ji-Hyun
Jeong, Hoibin
Kim, Kil-Nam
Bae, Jin-Woo
Ha, Ji-Hyoung
Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi
title Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi
title_full Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi
title_fullStr Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi
title_full_unstemmed Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi
title_short Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi
title_sort metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the korean fermented vegetable, kimchi
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9581167/
https://www.ncbi.nlm.nih.gov/pubmed/36274711
http://dx.doi.org/10.3389/fmicb.2022.1026513
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