Ultramicrobacteria in various fermented cabbages

Abstract

Little is known about the ultramicrobial communities of foods. Several bacteria, including pathogenic species, can form ultramicrobial communities when exposed to harsh conditions, making their detection via conventional culture techniques difficult. This study aimed to explore ultramicrobial communities within the microbial communities of fermented cabbage products, such as kimchi, sauerkraut, and suancai, which are produced through specific manufacturing methods based on the laws and culture of respective regions. We used single-molecule real-time sequencing with tangential flow filtration for fermented cabbages after pre-filtration and transmission electron microscopy to confirm the identity of ultramicrobacteria (UMB).To the best of our knowledge, this is the first study to identify the differences between ultramicrobial communities and microbial communities of fermented cabbages. Although the size of the ultramicrobial communities was smaller than that of the latter, their diversity was not lower. In addition, some UMB underwent cell shrinkage due to unfavorable environments, while others maintained their small size regardless. Major pathogens were not detected in the ultramicrobial communities of fermented cabbages. Nevertheless, several suspicious strains were detected. Our method can be used to screen food materials for the presence of UMB undetectable via conventional methods. Ultramicrobial and microbial communities were efficiently separated using tangential flow filtration and analyzed via single-molecule real-time sequencing. The ultramicrobial communities of fermented vegetables were different from conventional microbial communities. This study provides new insights into the ecology of UMB in foods.

Presence of an ultra-small microbiome in fermented cabbages

“…S1 . The fermented cabbage samples were stored in chilled conditions at approximately 4 °C until filtration ( Lee et al, 2022a ).…”

“…A vacuum pump (2546C-10; Welch Materials Inc., Shanghai, China) was used to aid the filtration process by reducing the pressure during the pre-filtration step. Before pre-filtration, the polypropylene capsule filter and tubing were sterilized with a solution of sodium hypochlorite 0.1% (v/v) ( Lee et al, 2022a ).…”

“…Based on their results, we used a cassette filter based on PVDF (Durapore 0.22 µm) for TFF to separate the USM < 0.2 µm and the NM > 0.2 µm. The USM and NM isolated via TFF were stored in a refrigerator at 4 °C until DNA extraction ( Lee et al, 2022a ).…”

“…USM cannot be detected using the currently available culture-dependent methods and can therefore pass through sterilization filters with a pore size of ≤ 0.2 µm ( Nakai, 2020 ). Therefore, USM remains a potential threat to food hygiene ( Lee et al, 2022a ).…”

“…In Asia, the type of cabbage preferred differs from that in Europe and is processed and consumed under the name “kimchi” in Korea and “suancai” in China. In El Salvador, cabbage is processed and consumed as “curtido” ( Lee et al, 2022a ).…”