Functional diversity of microbial communities associated with fermentation processes in coffee (Coffea arabica L.)




Mucilage fermentation conducted to degrade and remove coffee mucilage, is an important stage to also define coffee quality, but each microorganism’s contribution to the final quality is not yet known. Therefore, tools are needed to easily identify this relationship in order to be used to enhance coffee quality. The present manuscript describes the behavior of the microbial communities present in fermentations conducted under various conditions, which produced differences in the sensory quality of the coffee as assessed by the community-level catabolic profile approach. The coffee samples came
from six different fermentation processes that produced coffee in two quality classifications according to the Specialty Coffee Association (SCA) protocol: very good and excellent. Functional diversity of the microbial communities and substrate consumption were compared through analysis of variance. The multidimensional scaling analysis was used to identify the similarities or differences between treatments. The indices of functional diversity revealed significant
differences and direct proportionality with the quality rating. Diversity index (H) was between 2.09 and 2.71 and Evenness was between 1.75 and 2.21. The consumption of groups of substrates was different between fermentations, especially in carbohydrates and carboxylic acids, and the greatest consumption of these was found in the excellent-quality coffee. The different fermentative processes evaluated by this technique showed a high metabolic activity related to the great diversity of substrates given to the microbial communities and microorganisms involved, causing reactions that had influence on the final quality of the product.

Key words: Catabolic profiles; Coffee quality; Diversity indices.


ANSARI, J. M. et al. Strain-level diversity of commercial probiotic isolates of Bacillus, Lactobacillus, and Saccharomyces species illustrated by molecular identification and phenotypic profiling. PLoS ONE, 14(3):e0213841, 2019.

CAVALLO, N. et al. Microbial cell-free extracts affect the biochemical characteristics and sensorial quality of sourdough bread. Food Chemistry, 237(15):159-168, 2017.

DE BRUYN, F. et al. Exploring the impacts of postharvest processing on the microbiota and metabolite profiles during green coffee bean production. Applied and Environmental Microbiology, 83(1):1-16, 2017.

DI CAGNO, R. et al. Taxonomic structure of the yeasts and lactic acid bacteria microbiota of pineapple (Ananas comosus L. Merr.) and use of autochthonous starters for minimally processing. Food Microbiology, 27(3):381-389, 2010.

ELHALIS, H.; COX, J.; ZHAO, J. Ecological diversity, evolution and metabolism of microbial communities in the wet fermentation of Australian coffee beans. International Journal of Food Microbiology, 321:108544, 2020.

EVANGELISTA, S. R. et al. Microbiological diversity associated with the spontaneous wet method of coffee fermentation. International Journal of Food Microbiology 210:102-112, 2015.

HAILE, M.; KANG, W. H. The role of microbes in coffee fermentation and their impact on coffee quality. Journal of Food Quality, 2019:e4836709, 2019.

JOËT, T. et al. Influence of environmental factors, wet processing and their interactions on the biochemical composition of green Arabica coffee beans. Food Chemistry, 118(3):693-701, 2010.

JUNQUEIRA, A. C. O. et al. First description of bacterial and fungal communities in Colombian coffee beans fermentation analysed using Illumina-based amplicon sequencing. Nature Scientific Reports, 9:e8794, 2019.

MINERVINI, F. et al. Added ingredients affect the microbiota and biochemical characteristics of durum wheat type-I sourdough. Food Microbiology, 60:112-123, 2016.

NEU, A. et al. Fermentative utilization of coffee mucilage using Bacillus coagulans and investigation of down-stream processing of fermentation broth for optically pure L (+) - lactic acid production. Bioresource Technology, 211:398-405, 2016.

PEÑUELA-MARTÍNEZ, A. E.; ZAPATA-ZAPATA, A. D.; DURANGO-RESTREPO, D. L. Performance of of different fermentation methods and the effect on coffee quality (Coffea arabica L.). Coffee Science, 13(4):465-476, 2018.

PEREIRA, G. V. M. et al. Exploring the impacts of postharvest processing on the aroma formation of coffee beans - A review. Food Chemistry, 272:441-452, 2019.

PINZARI, F. et al. Phenotype MicroArray™ system in the study of fungal functional diversity and catabolic versatility. Research in Microbiology, 167(9-10):710-722, 2016.

SAMOGGIA, A.; RIEDEL, B. Coffee consumption and purchasing behavior review: Insights for further research. Appetite, 129:70-81, 2018.

SPECIALTY COFFEE ASSOCIATION OF AMERICA- SCAA. SCAA protocols - Cupping specialty coffee. 2015. Available in: <> Access in: October, 21, 2019.

SEPÚLVEDA, W. S. et al. Consumers preference for the origin and quality attributes associated with production of specialty coffees: Results from a cross-cultural study. Food Research International, 89(Part 2):997-1003, 2016.

SILVA, C. F. et al. Succession of bacterial and fungal communities during natural coffee (Coffea arabica) fermentation. Food Microbiology, 25(8):951-957, 2008.

SIRAGUSA, S. et al. Taxonomic structure and monitoring of the dominant population of lactic acid bacteria during wheat flour sourdough type I propagation using Lactobacillus sanfranciscensis starters. Applied and Environmental Microbiology, 75(4):1099-1109, 2009.

SRIVASTAVA, N. et al. Analyzing functional microbial diversity: An overview of techniques. In: DAS, S.; DASH, H. R. Microbial diversity in the genomic era. Academic Press, p. 79-102, 2019.

TILAHUN, B. et al. Biolog identification of fermenting yeasts from fermented teff (Eragrostis teff (Zucc.)) Dough. Asian Journal of Biology, 5(4):1-7, 2018.

WEBER, K. P.; LEGGE, R. L. Community level physiological profiling. In: CUMMINS S. P. Bioremediation, methods and protocols. New York: Humana Press, Springer Science, p. 263-281. 2010.

WORKU, M. et al. Effect of altitude on biochemical composition and quality of green arabica coffee beans can be affected by shade and postharvest processing method. Food Research International, 105:278-285, 2018.

ZAK, J. et al. Functional diversity of microbial communities: A quantitative approach. Soil Biology and Biochemistry, 26(9):1101-1108, 1994.




How to Cite

PEÑUELA MARTÍNEZ, A. E.; ROMERO-TABAREZ, M.; ZAPATA-ZAPATA, A. D. Functional diversity of microbial communities associated with fermentation processes in coffee (Coffea arabica L.). Coffee Science - ISSN 1984-3909, [S. l.], v. 16, p. e161825, 2021. DOI: 10.25186/.v16i.1825. Disponível em: Acesso em: 24 jun. 2022.