title: Detailed analysis of the microbial population in Malaysian spontaneous cocoa pulp fermentations reveals a core and variable microbiota.
abstract: The fermentation of cocoa pulp is one of the few remaining large-scale spontaneous microbial processes in today's food industry. The microbiota involved in cocoa pulp fermentations is complex and variable, which leads to inconsistent production efficiency and cocoa quality. Despite intensive research in the field, a detailed and comprehensive analysis of the microbiota is still lacking, especially for the expanding Asian production region. Here, we report a large-scale, comprehensive analysis of four spontaneous Malaysian cocoa pulp fermentations across two time points in the harvest season and two fermentation methods. Our results show that the cocoa microbiota consists of a "core" and a "variable" part. The bacterial populations show a remarkable consistency, with only two dominant species, Lactobacillus fermentum and Acetobacter pasteurianus. The fungal diversity is much larger, with four dominant species occurring in all fermentations ("core" yeasts), and a large number of yeasts that only occur in lower numbers and specific fermentations ("variable" yeasts). Despite this diversity, a clear pattern emerges, with early dominance of apiculate yeasts and late dominance of Saccharomyces cerevisiae. Our results provide new insights into the microbial diversity in Malaysian cocoa pulp fermentations and pave the way for the selection of starter cultures to increase efficiency and consistency.
authors.affiliation: Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium ; Laboratory for Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.
authors.forename: Esther
authors.initials: E
authors.lastname: Meersman
authors.affiliation: Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium ; Laboratory for Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.
authors.forename: Jan
authors.initials: J
authors.lastname: Steensels
authors.affiliation: Barry Callebaut AG, Zurich, Switzerland.
authors.forename: Melissa
authors.initials: M
authors.lastname: Mathawan
authors.affiliation: Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium ; Laboratory for Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.
authors.forename: Pieter-Jan
authors.initials: PJ
authors.lastname: Wittocx
authors.affiliation: Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium ; Laboratory for Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.
authors.forename: Veerle
authors.initials: V
authors.lastname: Saels
authors.affiliation: Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium ; Laboratory for Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.
authors.forename: Nore
authors.initials: N
authors.lastname: Struyf
authors.affiliation: Barry Callebaut AG, Zurich, Switzerland.
authors.forename: Herwig
authors.initials: H
authors.lastname: Bernaert
authors.affiliation: Barry Callebaut AG, Zurich, Switzerland.
authors.forename: Gino
authors.initials: G
authors.lastname: Vrancken
authors.affiliation: Laboratory for Genetics and Genomics, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Leuven, Belgium ; Laboratory for Systems Biology, Vlaams Instituut voor Biotechnologie (VIB), Leuven, Belgium.
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Verstrepen
mesh_terms: D000091:Acetobacter / Q000302:isolation & purification*; D002099:Cacao / Q000382:microbiology*; D005285:Fermentation; D052197:Limosilactobacillus fermentum / Q000302:isolation & purification*; D008296:Malaysia; D064307:Microbiota