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Review
. 2025 Jul 24;14(15):2606.
doi: 10.3390/foods14152606.

Application of Microbial Fermentation in Caffeine Degradation and Flavor Modulation of Coffee Beans

Lu-Xia Ran  1   2   3 , Xiang-Ying Wei  1   2   3 , Er-Fang Ren  1 , Jian-Feng Qin  1 , Usman Rasheed  1   2   3 , Gan-Lin Chen  1   2   3
Affiliations
Review

Application of Microbial Fermentation in Caffeine Degradation and Flavor Modulation of Coffee Beans

Lu-Xia Ran et al. Foods. .

Abstract

Coffee is one of the most widely consumed beverages worldwide, primarily due to the stimulating effects attributed to its caffeine content. However, excessive intake of caffeine results in negative effects, including palpitations, anxiety, and insomnia. Therefore, low-caffeine coffee has captivated growing consumer interest, highlighting its significant market potential. Traditional decaffeination methods often lead to non-selective extraction, resulting in a loss of desirable flavor compounds, thereby compromising coffee quality. In recent years, microbial fermentation has emerged as a promising, targeted, and safe approach for reducing caffeine content during processing. Additionally, mixed-culture fermentation further enhances coffee flavor and overcomes the drawbacks of monoculture fermentation, such as low efficiency and limited flavor profiles. Nonetheless, several challenges are yet to be resolved, including microbial tolerance to caffeine and related alkaloids, the safety of fermentation products, and elucidation of the underlying mechanisms behind microbial synergy in co-cultures. This review outlines the variety of microorganisms with the potential to degrade caffeine and the biochemical processes involved in this process. It explores how microbes tolerate caffeine, the safety of metabolites produced during fermentation, and the synergistic effects of mixed microbial cultures on the modulation of coffee flavor compounds, including esters and carbonyls. Future directions are discussed, including the screening of alkaloid-tolerant strains, constructing microbial consortia for simultaneous caffeine degradation for flavor enhancement, and developing high-quality low-caffeine coffee.

Keywords: decaffeination; flavor enhancement; low-caffeine coffee; microbial fermentation; mixed-culture.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Caffeine metabolism and degradation pathways. (a) Caffeine metabolites. (b) Proposed caffeine N-demethylation pathway in Pseudomonas putida CBB5 [47]. (c) Proposed caffeine C-8 oxidation pathway in Pseudomonas sp. CBB1 [48]. NdmA =  N1-demethylase specific for N1-methyl group of caffeine; NdmD =  reductase; NdmB =  N3-demethylase specific for N3-methyl group of theobromine; NdmCDE  =  protein complex containing N7-demethylase specific for N7-demethylation of 7-methylxanthine; Cdh =  trimeric caffeine dehydrogenase; TmuM =  trimethyluric acid monooxygenase; TumH  =  putative TM-HIU hydrolase; TmuD  =  putative TM-OHCU decarboxylase. This figure is adapted from the references [49].
Figure 2
Figure 2
Types and pathways of yeast metabolism.
Figure 3
Figure 3
Types of fermentation of coffee beans. (a) Open fermentation. (b) Submerged fermentation (c) Carbonic maceration. (d) Induced fermentation.
Figure 4
Figure 4
Effect of caffeine degradation and mixed fermentation on coffee quality.
See this image and copyright information in PMC

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