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High-Throughput rRNA Gene Sequencing Reveals High and Complex Bacterial Diversity Associated with Brazilian Coffee Bean Fermentation

Dão Pedro de Carvalho Netosmall orcid_display_4pp, Gilberto Vinícius de Melo Pereirasmall orcid_display_4pp, Júlio César de Carvalhosmall orcid_display_4pp, Vanete Thomaz Soccolsmall orcid_display_4pp and Carlos Ricardo Soccol*small orcid_display_4pp


Bioprocess Engineering and Biotechnology Department, Federal University of Paraná Curitiba, PR 81531-980, Brazil




Article history:
Received: July 27, 2017
Accepted: December 6, 2017




Key words:
lactic acid bacteria, coffee fermentation, bacterial dynamics, Fructobacillus sp.




Summary:
Coffee bean fermentation is a spontaneous, on-farm process involving the action of different microbial groups, including bacteria and fungi. In this study, high-throughput sequencing approach was employed to study the diversity and dynamics of bacteria associated with Brazilian coffee bean fermentation. The total DNA from fermenting coffee samples was extracted at different time points, and the 16S rRNA gene with segments around the V4 variable region was sequenced by Illumina high-throughput platform. Using this approach, the presence of over eighty bacterial genera was determined, many of which have been detected for the first time during coffee bean fermentation, including Fructobacillus, Pseudonocardia, Pedobacter, Sphingomonas and Hymenobacter. The presence of Fructobacillus suggests an influence of these bacteria on fructose metabolism during coffee fermentation. Temporal analysis showed a strong dominance of lactic acid bacteria with over 97 % of read sequences at the end of fermentation, mainly represented by the Leuconostoc and Lactococcus. Metabolism of lactic acid bacteria was associated with the high formation of lactic acid during fermentation, as determined by HPLC analysis. The results reported in this study confirm the underestimation of bacterial diversity associated with coffee fermentation. New microbial groups reported in this study may be explored as functional starter cultures for on-farm coffee processing.




*Corresponding author:  tel3  +554133613191
                                           fax2  +554133613695
                                            email3  soccol@ufpr.br




Paper was presented at the 7th International Forum on Industrial Bioprocessing - IFIBiop 2017, May 21-24, 2017, Wuxi, PR China

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