Scientists decode full genome of probiotic bacterium from Japanese pickled Chinese yam

Researchers have published the complete genome sequence of Lacticaseibacillus paracasei TOKAI 83 m, a lactic acid bacterium isolated from pickled Chinese yam in Japan. The data note, released in BMC Genomic Data on 3 October 2026, fills a gap left by earlier work that had characterized the strain’s functional properties but never its full genetic blueprint.

The strain, abbreviated TK83m, first drew attention in the team’s previous research because of its ability to bind heavy metals through proteins on its cell surface. That study also indicated probiotic potential. According to the authors, the absence of a complete genome had limited efforts to analyze how the bacterium secretes proteins such as GAPDH and to assess its safety for wider use.

The newly reported genome is compact but complete. It consists of a single chromosome of 3,073,721 base pairs accompanied by five plasmids measuring 60,926, 47,796, 11,058, 8,024, and 5,087 base pairs, for a total length of 3,206,612 base pairs. The overall GC content is 46.1 percent.

Annotation of the sequence identified 3,116 protein-coding sequences, 15 rRNA genes, and 59 tRNA genes.

Safety analyses formed a central aim of the work. The authors report that these analyses supported the absence of resistance and virulence genes in the strain, a finding relevant to any future evaluation of its suitability for food or probiotic applications.

The researchers, including Tomoyuki Hibi, Takahiro Kawanabe, Yuki Nakashima, Shin Yasuda, Masashi Hirano and Hideki Kinoshita, describe the genome as a valuable resource for future studies of protein secretion mechanisms and other functional analyses of the strain.

For TK83m, the sequence now makes it possible to investigate the genetic basis of the heavy metal biosorption observed at the cell surface, although the data note itself reports the sequence and its annotation rather than new functional experiments.

As a Data Note published open access, the article is citable and carries a permanent DOI, with the publisher noting that an early version is shared to provide faster access to peer-reviewed, accepted research. The complete sequence of L. paracasei TK83m now stands as a documented resource for laboratories studying lactic acid bacteria from fermented foods and their surface protein systems.

Subject of Research: Complete genome sequence of the probiotic lactic acid bacterium Lacticaseibacillus paracasei TOKAI 83 m

Article Title: Whole-genome sequence of Lacticaseibacillus paracasei TOKAI 83 m, isolated from pickled Chinese yam in Japan

Article References: Hibi, T., Kawanabe, T., Nakashima, Y., Yasuda, S., Hirano, M., & Kinoshita, H. (2026). Whole-genome sequence of Lacticaseibacillus paracasei TOKAI 83 m, isolated from pickled Chinese yam in Japan. BMC Genomic Data. https://doi.org/10.1186/s12863-026-01485-9

Image Credits: AI Generated

DOI: 10.1186/s12863-026-01485-9

Keywords: Lacticaseibacillus paracasei, genome sequencing, probiotics, lactic acid bacteria, pickled Chinese yam, heavy metal biosorption, plasmids, CRISPR, food microbiology, BMC Genomic Data, Japan, GAPDH