Following Coffee Production from Cherries to Cup: Microbiological and Metabolomic Analysis of Wet Processing of Coffea arabica

Abstract

A cup of coffee is the final product of a complex chain of operations. Wet postharvest processing of coffee is one of these operations, which involves a fermentation that inevitably has to be performed on-farm. During wet coffee processing, the interplay between microbial activities and endogenous bean metabolism results in a specific flavor precursor profile of the green coffee beans. Yet, how specific microbial communities and the changing chemical compositions of the beans determine the flavor of a cup of coffee remains underappreciated. Through a multiphasic approach, the establishment of the microbial communities, as well as their prevalence during wet processing ofCoffea arabica, was followed at an experimental farm in Ecuador. Also, the metabolites produced by the microorganisms and those of the coffee bean metabolism were monitored to determine their influence on the green coffee bean metabolite profile over time. The results indicated that lactic acid bacteria were prevalent well before the onset of fermentation and that the fermentation duration entailed shifts in their communities. The fermentation duration also affected the compositions of the beans, so that longer-fermented coffee had more notes that are preferred by consumers. As a consequence, researchers and coffee growers should be aware that the flavor of a cup of coffee is determined before as well as during on-farm processing and that under the right conditions, longer fermentation times can be favorable, although the opposite is often believed.IMPORTANCECoffee needs to undergo a long chain of events to transform from coffee cherries to a beverage. The coffee postharvest processing is one of the key phases that convert the freshly harvested cherries into green coffee beans before roasting and brewing. Among multiple existing processing methods, the wet processing has been usually applied for Arabica coffee and produces decent quality of both green coffee beans and the cup of coffee. In the present case study, wet processing was followed by a multiphasic approach through both microbiological and metabolomic analyses. The impacts of each processing step, especially the fermentation duration, were studied in detail. Distinct changes in microbial ecosystems, processing waters, coffee beans, and sensory quality of the brews were found. Thus, through fine-tuning of the parameters in each step, the microbial diversity and endogenous bean metabolism can be altered during coffee postharvest processing and hence provide potential to improve coffee quality.

Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil

“…Soil microbiota plays an important role in nutrient cycling by making available the required mineral nutrition available for the root system 15 . On the other hand, the microbiota in fruits play an important role during coffee fermentation by degrading the mucilage and impacting the beverage flavor 16 . That the microbial interactions are neither known nor controlled during the fermentation process 17 .…”

Application of a High-Throughput Amplicon Sequencing Method to Chart the Bacterial Communities that Are Associated with European Fermented Meats from Different Origins

“…Processing of the V4 amplicons was similar to the method described in Zhang et al [ 37 ], whereby amplicon sequence variants (ASVs) were determined using the DADA2 package (version 1.10.1) [ 38 ] and the SILVA database (version 138) [ 39 ]. For the amplicons generated with primer set Tuf387/765, taxonomy was assigned using the custom database containing 2556 tuf gene sequences as described above.…”

“…The raw data were deconvoluted by TOF-DS software (Markes). Afterward, peaks were identified based on the NIST library (National Institute of Standard and Technology, Gaitherburg, MD, USA) and the use of commercially available standards [ 37 , 41 ]. For each identified compound, the peak area was normalized to the peak area of the internal standard.…”

Amplicon-Based High-Throughput Sequencing Method Capable of Species-Level Identification of Coagulase-Negative Staphylococci in Diverse Communities

“…Processing of the MiSeq sequence data was similar to the method described by Zhang et al [37], whereby amplicon sequence variants (ASVs) were ascertained using the DADA2 package (version 1.10.1) within the open-source software environment R [38]. Taxonomy was assigned using a custom tuf gene database containing the above-mentioned 2566 tuf gene sequences of Staphylococcus species from the ENA/EBI database.…”