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

Abstract

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.

Presence of an ultra-small microbiome in fermented cabbages

“…Although these bacteria were smaller than the general pore size of the sterilizing filter, which is 0.2 µm, and may not be harmful immediately, there is a concern that there may be potential risks when the fermented cabbages are further processed into sauces, juices, etc. Furthermore, based on a previous study ( Lee et al, 2022b ), it was suspected that USM may be in a VBNC state. Although USM was not starving due to the abundant nutrients in the fermented cabbages, it is possible that the dominance of lactic acid bacteria due to fermentation could have led to stress and difficulty in growth, resulting in conversion to ultra-small microorganisms in a VBNC state.…”

The Rising Role of Omics and Meta-Omics in Table Olive Research

“…In this review, we presented an in-depth analysis of metagenomic, metabolomic, proteomic, and transcriptomic studies concerning table olive research to date. To the best of our knowledge, there are no metaproteomic or metatranscriptomic studies on table olives, even though these approaches have already been used in other fermented foods such as kimchi, soybeans, and fermented fish [125][126][127][128][129]. Future multi-omics research on table olives can shed additional light on the connection between the microbial community composition and functionality [38,130,131].…”

The Weissella and Periweissella genera: up-to-date taxonomy, ecology, safety, biotechnological, and probiotic potential

“…The increasingly popular and worldwide consumed kimchi , a salted fermented cabbage-based Korean food (Lee et al, 2022 ), is a well-known source of W. cibaria, W. confusa, W. koreensis, W. hellenica, W. paramesenteroides, W. soli , and P. fabaria (Lee et al, 2015a ; Kim et al, 2017 ; Yoon et al, 2023 , Table 3 ). Moreover, Weissella and Periweissella spp.…”