Exploring how gut bacteria alter the flavor of Black Ivory coffee beans

Coffee beans that pass through the digestive tracts of animals get their unique flavors from the activity of gut microbes, report researchers from the Institute of Science Tokyo. The guts of Asian elephants that produce Black Ivory coffee (BIC) were rich in pectin-digesting bacteria. Heat-driven degradation of pectin during roasting makes coffee bitter. Bacterial activity that reduces the pectin content of BIC could be the source of its smoother, chocolaty, and less bitter flavor.

With hundreds of millions of cups consumed every day, coffee is one of the most popular beverages in the world. Many organic molecules combine to give coffee its flavor, and nearly every coffee drinker likes a different flavor profile that is “just theirs.” The food industry has developed many ways of processing coffee beans to alter the ratios of these molecules and create the unique flavors consumers can enjoy.

One particularly interesting process involves passing coffee beans through the digestive tracts of animals. An emerging example is Black Ivory coffee (BIC). BIC is made in only one elephant sanctuary in Thailand. Asian elephants are fed Arabica coffee cherries, and beans collected from their dung are processed for human consumption. BIC is prized for its smooth, chocolaty flavor, and it is less bitter than regular coffee.

A research team led by Associate Professor Takuji Yamada and Research Fellow Nodoka Chiba from the School of Life Science and Technology, the Institute of Science Tokyo (Science Tokyo), Japan, have tried to identify the biochemical processes that give BIC its unique flavor. Their work, published in Volume 15 of the journal Scientific Reports on November 18, 2025, helps uncover some of the secrets behind BIC.

“Our previous study revealed that Gluconobacter was the dominant genus in the gut of civet cats, and it may produce volatile compounds from the coffee beans, suggesting that microbial metabolism contributes to the coffee aroma,” says Yamada. He adds, “These findings raised the question of whether the gut microbiome of elephants similarly influences the flavor of BIC.”

The team analyzed fresh dung from elephants producing BIC, as well as from control elephants living in the same elephant sanctuary. The only difference in their diets is that BIC-producing elephants received an additional snack of bananas, rice bran, and whole coffee cherries. Any differences in the content and composition of fecal microbes would be due to this snack.

Yamada’s team found that BIC-producing elephants’ dung was unusually rich in pectin-digesting enzymes. 16S ribosomal RNA analysis showed that these elephants also had a more diverse gut microbiome, with an abundance of Acinetobacter and other pectin-digesting species. “Interestingly, Acinetobacter has also been detected on the surface of coffee beans. This suggests that ingestion of coffee beans may lead to the colonization of specific microbes in the gut of elephants,” remarks Yamada.

Pectin in coffee beans is partially broken down by the heat of roasting and seems to form bitter-tasting compounds such as 2-furfuryl furan. Previous studies showed that BIC had much lower levels of 2-furfuryl furan than regular coffee beans. These earlier findings appear to be explained by the discovery of pectin-digesting bacteria in the gut of BIC-producing elephants. Since pectin is partially digested as the beans pass through the elephants’ guts, there is less available to form 2-furfuryl furan when the beans are roasted.

“Our findings may highlight a potential molecular mechanism by which the gut microbiota of BIC elephants contributes to the flavor of BIC,” says Yamada as he describes these exciting findings. “Further experimental validation is required to test this hypothesis, such as a biochemical analysis of coffee bean components before and after passage through the elephant’s digestive tract,” he adds, pointing to avenues for future research into this technique for processing coffee.

Nevertheless, this study provides a foundation for further exploration of animal-microbiome interactions in food fermentation and flavor development. Continued research into specific microbial metabolic mechanisms may support the development of diverse and distinctive flavor profiles in the future!

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About Institute of Science Tokyo (Science Tokyo)
Institute of Science Tokyo (Science Tokyo) was established on October 1, 2024, following the merger between Tokyo Medical and Dental University (TMDU) and Tokyo Institute of Technology (Tokyo Tech), with the mission of “Advancing science and human wellbeing to create value for and with society.”