Plants are a rich and renewable source of compounds used in medicines, food ingredients, and cosmetics. Since growing an entire plant just to extract a few specific compounds is rather inefficient, scientists are turning to plant cell cultures as a more sustainable alternative. Cultured plant cells can act as ideal ‘biofactories’ that multiply quickly indoors and are unaffected by weather or seasons. Unfortunately, this strategy faces a long-standing problem: although plant cells contain thousands of genes capable of making diverse chemicals, only a small fraction of them are active under standard culture conditions.
One possible strategy to unlock these hidden metabolic pathways comes from the concept of microbial co-cultures, a method where different organisms are grown together so their interactions trigger the production of compounds that are previously unattainable when grown alone. Although this technique has transformed natural product discovery and synthesis in bacteria and fungi, it remains challenging in plant cells. Most bacteria either inhibit plant cell growth or kill plant cultures outright. As a result, very few safe microbial partners that can stimulate plant metabolism are known. Could endophytic bacteria, which naturally live inside plants without causing harm, be the solution?
In a recent study published in Volume 19, Issue 1 of the journal Microbial Biotechnology on January 8, 2026, a research team led by Professor Toshiki Furuya from the Department of Applied Biological Science, Tokyo University of Science (TUS), Japan, investigated this possibility using endophytic bacteria previously isolated from Japanese mustard spinach (komatsuna) and Japanese radish (daikon). The researchers tested whether these bacteria could coexist with plant cell cultures and activate new metabolic pathways. Other members of the team included Mr. Yui Aikawa (completed Master’s program in 2022), Ms. Ayano Yabuuchi (completed Master’s program in 2024), and Mr. Hiroki Kaneko (completed Master’s program in 2022), as well as Assistant Professor Takafumi Hashimoto, all from TUS at the time of the research.
“Through the analysis of komatsuna, we came up with the idea that endophytic bacteria that originally live symbiotically within plants might be able to coexist favorably with plant-cultured cells,” shares Prof. Furuya as the core idea behind the study.
The researchers focused first on tobacco BY-2 cells, a widely used model plant cell line. They introduced an endophytic bacterium called Delftia sp. BR1R-2 into the culture and compared its effects with those of common bacteria. As expected, pathogenic bacteria and even the most commonly found Escherichia coli quickly suppressed plant cell growth and caused cell death. In contrast, BR1R-2 grew alongside the plant cells without harming them.
Interestingly, chemical analysis confirmed major metabolic changes. Using high-performance liquid chromatography, the team detected increased levels of acetophenone derivatives—small molecules known for antimicrobial and pesticidal activities. At the same time, another compound ( N -caffeoylputrescine), normally abundant in tobacco cells, decreased, indicating that metabolic resources had been redirected. Extracts from the co-cultured cells also inhibited the growth of a plant pathogen, demonstrating that the newly produced molecules were biologically active.
The team conducted gene expression analyses to look further into the changes caused by co-culturing. They found that microbial growth switched on various defense-related pathways controlled by plant hormones involved in immune responses. The researchers also proved that physical contact between plant cells and bacteria was required to trigger these effects. Importantly, similar results were obtained with another endophyte from radish ( Pseudomonas sp. RS1P-1) and in Arabidopsis cultured cells. This suggests the effect is not limited to one species. “Although our study used model plants for proof-of-concept, extending the method to other plant species could enable exploitation of previously inaccessible plant metabolic pathways,” highlights Prof. Furuya.
Overall, the findings of this work point to a new way to safely stimulate plant cell metabolism using bacteria that naturally coexist with plants. “Plant immunity–activating endophytic bacteria exhibit great potential for use in altering the metabolic profile of cultured plant cells for the production of valuable phytochemicals,” notes Prof. Furuya. Thus, this promising approach may help expand the range of plant-derived compounds available through cell-based production, opening new avenues for the synthesis of more affordable pharmaceuticals, cosmetics, food additives, and functional materials.
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Reference
DOI: 10.1111/1751-7915.70297
About The Tokyo University of Science
Tokyo University of Science (TUS) is a well-known and respected university, and the largest science-specialized private research university in Japan, with four campuses in central Tokyo and its suburbs and in Hokkaido. Established in 1881, the university has continually contributed to Japan's development in science through inculcating the love for science in researchers, technicians, and educators.
With a mission of “Creating science and technology for the harmonious development of nature, human beings, and society," TUS has undertaken a wide range of research from basic to applied science. TUS has embraced a multidisciplinary approach to research and undertaken intensive study in some of today's most vital fields. TUS is a meritocracy where the best in science is recognized and nurtured. It is the only private university in Japan that has produced a Nobel Prize winner and the only private university in Asia to produce Nobel Prize winners within the natural sciences field.
Website: https://www.tus.ac.jp/en/mediarelations/
About Professor Toshiki Furuya from Tokyo University of Science (TUS)
Dr. Toshiki Furuya is a Professor at the Faculty of Science and Technology of the Department of Applied Biological Science at Tokyo University of Science (TUS), Japan. He completed his graduation and post-graduation from Waseda University in Tokyo, Japan. His areas of research include applied biochemistry, microbial metabolism, enzyme catalysis, bioproduction, and bioremediation. He has published more than 40 articles in reputed journals. He has won many awards, including the 24 th Excellent Paper Award by the Society of Biotechnology in 2016.
Funding information
This work was supported by the Japan Society for the Promotion of Science (Grant Number: 20K05812), Nagase Science Technology Foundation, and Noda Institute for Scientific Research.
Microbial Biotechnology
Experimental study
Cells
Plant Immunity–Activating Endophytic Bacteria Induce Dynamic Metabolic Changes in Cultured Plant Cells Without Inhibiting Their Growth
8-Jan-2026
The authors declare no conflicts of interest.