Key Points of the Research 
・We conducted a detailed comparative analysis of the whole genomes of the Bacillus subtilis strains
　used to make the traditional Japanese food “Natto” and a strain isolated from “Bekang,” a similar
　fermented food produced in Mizoram, India. 
・The results revealed that the Bekang strain is a “distant relative” of the Japanese Natto bacteria when
　viewed on the “family tree” (evolutionary lineage). 
・However, surprisingly, the set of “tools” (functional genes) used to ferment soybeans was found to
　be nearly identical to that of the Japanese Natto bacteria. 
・This is a significant discovery suggesting that even bacteria evolving in completely different
　locations have acquired and maintained similar gene sets to adapt to the same “soybean fermentation”
environment. 

Researchers 
・Principal Investigator: Yukio Nagano (Professor, Faculty of Agriculture, Saga University) 
・Co-Investigator: Kiyohiko Seki (Lecturer, Faculty of Agriculture, Saga University) 

Overview of Research Results 
A research group led by Professor Yukio Nagano and Lecturer Kiyohiko Seki of the Faculty of Agriculture at Saga University conducted a large-scale comparative genomic analysis of Bacillus subtilis var. natto, the bacteria essential for making “Natto” (a staple of the Japanese dining table), and its closely related bacteria. 

The study focused on a single bacterial strain isolated from “Bekang,” a traditional fermented soybean food produced in Northeast India and Western Myanmar. Like Japanese Natto, Bekang is known for its distinctive stickiness and stringiness. 

When the research group analyzed the DNA of this Bekang-derived strain, they found that on the “basic family tree” (core genome), it is a distinct lineage clearly separated from the Japanese Natto bacteria group. Its closest evolutionary “neighbor” was found to be the bacteria from “Kinema,” a fermented food from Nepal. 

However, when investigating the composition of “genes for adapting to the environment” (accessory genome) possessed by each bacterium, a contradictory fact emerged: this Bekang strain is functionally most similar to the Japanese Natto bacteria group. 

In other words, although the Bekang strain has a different “birth (lineage),” its “professional skills (gene set)” for fermenting soybeans are nearly identical to those of Japanese Natto bacteria. This suggests that bacteria may have evolved by acquiring or maintaining necessary gene sets to survive in the specific environment of “soybean fermentation.” 

This study unravels a part of the complex history of how microorganisms evolved to create fermented foods useful to humans. At the same time, it is an intriguing case scientifically demonstrating that diverse Asian food cultures are connected even at the invisible genetic level of microorganisms. While Natto is often thought of as unique to Japan, “brother-like” foods created by bacteria with “identical tools” at the genetic level actually exist in distant parts of Asia. 

Publication Information 
・Journal: Scientific Reports (Nature Portfolio) 
・Title: Conserved accessory genes link a phylogenetically distinct Bacillus subtilis strain from
　　　 Indian bekang to the Japanese natto clade 
・Publication Date: December 17, 2025, at 7:00 PM
・URL : https://doi.org/10.1038/s41598-025-29683-y

Future Outlook 
The “bacterial genome analysis pipeline” developed in this study is applicable not only to Natto bacteria but also to various bacteria used in food manufacturing. For instance, it is expected to be useful as a technology for accurately diagnosing and managing bacterial properties at the genetic level, such as selecting strains to create more delicious fermented foods and quality control in factories. 

Additionally, our research group is widely recruiting companies and research institutions interested in collaborative research utilizing this genomic analysis technology for food development and quality control. 

Researchmap Links 
・Yukio Nagano: https://researchmap.jp/read0211401 
・Kiyohiko Seki: https://researchmap.jp/read0092215 

Contact Information 
　Yukio Nagano, Professor  Faculty of Agriculture, Saga University 
　　E-mail: nagano@cc.saga-u.ac.jp 

Photo of Bekang 1 (provided by Dr. Santhosha Dasarapu, Vishnu Institute of Pharmaceutical Education & Research).

Photo of Bekang 2 (provided by Dr. Santhosha Dasarapu, Vishnu Institute of Pharmaceutical Education & Research).