ArticleScientific reports2019
First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 114 citations in OpenAlex.
- Integrated microbial-metabolomic analysis reveals how fermentation contributes to the unique flavor of African Arabica coffee.Food chemistry. Molecular sciences · 2026Article
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- Unlocking New Bioactive Peptides from Coffee Pulp: A Metagenomics and AI-Driven Discovery Paradigm.Foods (Basel, Switzerland) · 2025Article
- Soil and cherry bacterial communities predict flavor on coffee farms.Scientific reports · 2025Article
- Coffee Biotransformation in Volcanic Process: A Chemical and Sensory Analysis.Foods (Basel, Switzerland) · 2025Article
- Unveiling the Microbial Signatures of Arabica Coffee Cherries: Insights into Ripeness Specific Diversity, Functional Traits, and Implications for Quality and Safety.Foods (Basel, Switzerland) · 2025Article
- Application of ATR-FTIR for Green Arabica Bean Shelf-Life Determination in Accelerated Storage.Foods (Basel, Switzerland) · 2024Article
- Comparison of Metabarcoding and Microscopy Methodologies to Analyze Diatom Communities in Five Estuaries Along the Southern Coast of the Korean Peninsula.Microbial ecology · 2024Article
- Effects of cherries Sanitization methods and fermentation times on quality parameters of coffee beans.Heliyon · 2024Article
- Exploring Microbial Influence on Flavor Development during Coffee Processing in Humid Subtropical Climate through Metagenetic-Metabolomics Analysis.Foods (Basel, Switzerland) · 2024Article
- Metataxonomic Identification of Microorganisms during the Coffee Fermentation Process in Colombian Farms (Cesar Department).Foods (Basel, Switzerland) · 2024Article
- Evaluation of Arabica Coffee Fermentation Using Machine Learning.Foods (Basel, Switzerland) · 2024Article
- Microbial Diversity of Anaerobic-Fermented Coffee and Potential for Inhibiting Ochratoxin-ProducedFoods (Basel, Switzerland) · 2023Article
- Efficiency ofFoods (Basel, Switzerland) · 2023Article
- Understanding the Effects of Self-Induced Anaerobic Fermentation on Coffee Beans Quality: Microbiological, Metabolic, and Sensory Studies.Foods (Basel, Switzerland) · 2022Article
- Lipid Oxidation Changes of Arabica Green Coffee Beans during Accelerated Storage with Different Packaging Types.Foods (Basel, Switzerland) · 2022Article
- Does Coffee Have Terroir and How Should It Be Assessed?Foods (Basel, Switzerland) · 2022Review
- Fungi associated with the potato taste defect in coffee beans from Rwanda.Botanical studies · 2022Article
- Dissecting industrial fermentations of fine flavour cocoa through metagenomic analysis.Scientific reports · 2021Article
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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