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.

The quality of different coffee varieties varies, and the corresponding bioactive value of coffee processing byproducts is often overlooked. For that, we employed HPLC, GC-MS, and electronic sensory analyses to evaluate the key bioactive components, antioxidant potential, and flavor traits of green coffee bean and coffee processing byproducts of seven coffee varieties. The results showed that green coffee beans (Oe+Ie) and exocarp (Ep) possessed strong antioxidant activity and high total phenolic content (TPC), caffeine and trigonelline content. Among the varieties, DR390 contained higher levels of total phenols, caffeine, and trigonelline, whereas DR402 was rich in caffeine and chlorogenic acid. In addition, RY3 exhibited higher TPC, total flavonoid content (TFC), caffeine, and chlorogenic acid. The parchment (Pc) layer was rich in soluble sugars (1.83–5.43%), while the silverskin (Sk) contained relatively high levels of chlorogenic acid (3.58–4.69 mg/g). Flavor analysis identified eleven classes of volatile compounds in green coffee bean (Oe+Ie) and byproducts (Ep, Pc, Sk), with esters, ketones, alcohols, and aldehydes being the most prevalent. Seven key aroma compounds, including methyl salicylate, phenethyl alcohol, nonanal, and benzaldehyde, were identified across the various structural tissues of coffee fruit. Distinct flavor profiles were observed among the coffee fruit parts: green coffee bean (Oe+Ie) was nutty; the Ep showed fruity and cocoa-like aromas; the Pc and Sk exhibited papery and nutty aromas, respectively. Varieties DR397, DR402, and RY3 exhibited pronounced aroma profiles. Comprehensive analysis showed that DR402 and RY3 had higher overall scores for bioactive and flavor components than other varieties in their groups. In summary, green coffee bean (Oe+Ie) exhibited strong antioxidant activity and high levels of bioactive compounds. Coffee byproducts, such as the Ep, hold potential for extracting natural antioxidants and bioactive compounds to develop specialty products or for other high-value utilization.

Large-fruited hawthorn (Malus doumeri (Bois) Chev.) is valued for its health-promoting properties, largely attributed to its rich flavonoid content. However, little is known about the specific composition of flavonoids and the molecular mechanisms regulating their biosynthesis. The present study employed non-targeted metabolomic and transcriptomic approaches to investigate two M. doumeri germplasms (G8 and G9) that exhibited significantly different total flavonoid contents. The results indicated that the major and differential metabolites primarily include flavonoids and isoflavonoids. Differentially expressed genes were significantly enriched in phenylpropanoid and flavone and flavonol biosynthesis pathways. Integrated analysis identified several structural genes and transcription factors, including HCT (LOC114821133, LOC103403337, LOC103454980), WRKY (LOC103427630), and bHLH (LOC103422512), that were significantly upregulated in the high-flavonoid genotype (G9). qRT-PCR validation confirmed the RNA-Seq expression patterns, suggesting the potential involvement of these genes in the biosynthesis of phenylpropanoid-related metabolites, such as [6]-gingerol. Applied experiments further demonstrated that freeze-drying preserved high metabolite contents and antioxidant activity. Collectively, these findings provide insights into the compositional characteristics of the major flavonoids in M. doumeri and the biosynthesis of phenylpropanoid-derived metabolites. This study provides data support for future mechanistic validation and evaluation of processing technology applicability.