First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing

Abstract

In Colombia, coffee growers use a traditional method of fermentation to remove the cherry pulp surrounding the beans. This process has a great influence on sensory quality and prestige of Colombian coffee in international markets, but has never been studied. Here we use an Illumina-based amplicon sequencing to investigate bacterial and fungal communities associated with spontaneous coffee-bean fermentation in Colombia. Microbial-derived metabolites were further analysed by high–performance liquid chromatography and gas chromatography–mass spectrometry. Highly diverse bacterial groups, comprising 160 genera belonging to 10 phyla, were found. Lactic acid bacteria (LAB), mainly represented by the genera Leuconostoc and Lactobacillus , showed relative prevalence over 60% at all sampling times. The structure of the fungal community was more homogeneous, with Pichia nakasei dominating throughout the fermentation process. Lactic acid and acetaldehyde were the major end-metabolites produced by LAB and Pichia , respectively. In addition, 20 volatile compounds were produced, comprising alcohols, organic acids, aldehydes, esters, terpenes, phenols, and hydrocarbons. Interestingly, 56 microbial genera, associated with native soil, seawater, plants, insects, and human contact, were detected for the first time in coffee fermentation. These microbial groups harbour a remarkable phenotypic diversity and may impart flavours that yield clues to the terroir of Colombian coffees.

Microorganisms in coffee fermentation: A bibliometric and systematic literature network analysis related to agriculture and beverage quality (1965-2019)

“…This cluster has only one document, therefore the authors belonging to the cluster participate in it. The study carried out by these authors makes an important contribution to the field of study by being the first description of the microbial diversity (fungi and bacteria) using cultureindependent methods in Colombian coffee beans (De Oliveira Junqueira et al, 2019).…”

“…Although studies have been carried out on microorganisms in the coffee fermentation process related to agriculture and food (beverage quality), and there is considerable progress in the field of study, it is necessary to continue researching in different parts of the world, since the presence of microorganisms and the behavior of the fermentation process is specific to each place and geographic niche; culminating in the reason why each region has distinctive flavored coffees (De Oliveira Junqueira et al, 2019). It is also important to continue conducting research related to using culture-independent methods to break-down the barriers that arise when interpreting results obtained by culture-dependent methods, as well as studies on selection and inoculation of starter cultures according to specific regional conditions.…”

Presence and persistence of Pseudomonas sp. during Caspian Sea-style spontaneous milk fermentation highlights the importance of safety and regulatory concerns for traditional and ethnic foods

“…Samples of pasteurized milk, fermentation times, and storage stability were withdrawn to perform total genomic DNA extraction and metagenetic analysis. The extraction protocol was performed according Junqueira et al (2019), with slightly modifications. The cell pellets, obtained after centrifugation of each sample at 12,000 ×g for 1 min, were resuspended in 500 µL Tris-EDTA (pH 8.0), vortexed with 10 µL of lysozyme solution at 20 mg/mL (Sigma Aldrich, San Louis, MO, USA), and incubated at 30 °C for 60 min.…”

Effect of Co-Inoculation with Pichia fermentans and Pediococcus acidilactici on Metabolite Produced During Fermentation and Volatile Composition of Coffee Beans

“…These positive interactions have been shown to promote desired sensory attributes in wine, sourdough, and yogurt. However, information about these mechanisms in coffee fermentation is scarce [40].…”

“…These positive interactions have been shown to promote desired sensory attributes in wine, sourdough, and yogurt. However, information about these mechanisms in coffee fermentation is scarce [40]. Other minor volatile compounds that increased during the fermentation processes were 1decanol, ethyl-acetaldehyde, and hexyl acetate (Figure 2).…”