scholarly journals FINE GRAINED LONGITUDINAL ANALYSIS OF COCOA BEAN FERMENTATION PROVIDES INSIGHTS INTO THE DYNAMICS OF MICROBIAL POPULATIONS

2019 ◽  
Author(s):  
M. E. Pacheco-Montealegre ◽  
L. L. Dávila-Mora ◽  
L. M. Botero-Rute ◽  
A. Reyes ◽  
A. Caro-Quintero
Keyword(s):  
Molecular Markers ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Population Analysis ◽  
Starter Cultures ◽  
Cocoa Bean ◽  
Microbial Fermentation ◽  
Single Strain ◽  
Ecological Zones ◽  
Cocoa Bean Fermentation

ABSTRACTCocoa bean fermentation is an important microbial driven process where metabolites that affect chocolate quality and aroma are produced. Although considerable research has been devoted to the yeast and bacteria species involved in this process, less attention has been paid to the role of populations and strains, which hinders its selection, monitoring and use. Here we present a study that evaluates the microbial diversity associated to the tools and bean mass during spontaneous cocoa fermentation and in two distinct agro-ecological zones in Colombia. Using high-throughput sequencing of molecular markers for bacteria and yeast, we established the dynamics at the species-level (OTUs) and strains-level (oligotypes). Our results show that cocoa bean fermentation is catalyzed by a composite of strains within each OTU and not by one single strain. Eventhough we found only a few bacterial OTUs, one Enterobacter, three of Lactic Acid Bacteria and two of Acetic Acid Bacteria, these could be further split into 6, 23 and 19 oligotypes, respectively. Only two fungal OTUs were found. Comparison between fermentations suggest that local protocols generated a specific footprint in the dynamics of the microbial communities and that tools are reservoirs of some of those groups. The population analysis shows that the oligotypes that become most dominant are the same in the two locations, coupling co-abundance and dominance analysis we suggest that a combination of Enterobacter and Acetobacter oligotypes seem more optimal for the starter cultures. In conclusion, the results presented here show that exploring the fine level dynamics of microbial fermentation is necessary to understand the patterns of the dominance of specific populations and can be used as a valuable approach to select and monitor specific bacteria for the design of starter cultures in the food industry.IMPORTANCEIn Colombia, the lack of tools to validate and standardize fermentation protocols are one of the principal reasons why Colombian cocoa beans are not recognized as “fine-flavor” and widely marketed. Because of the large influence of the microbial fermentation in cocoa quality, the present study explores the microbial dynamics using high-throughput sequencing of molecular markers in two of the most important producer regions in Colombia. The results show that the identification of dominant and transitive strains can be used to select, design and monitor starter cultures and/or the effect of adjustments in the fermentation protocols.

scholarly journals High-throughput identification of the microbial biodiversity of cocoa bean fermentation by MALDI-TOF MS

2016 ◽  
Vol 63 (5) ◽  
pp. 347-355 ◽  
Author(s):  
S. Miescher Schwenninger ◽  
S. Freimüller Leischtfeld ◽  
C. Gantenbein-Demarchi
Keyword(s):  
High Throughput ◽  
Cocoa Bean ◽  
Microbial Biodiversity ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Cocoa Bean Fermentation ◽  
Tof Ms

scholarly journals Microbial molecular markers and epidemiological surveillance in the era of high throughput sequencing: an update from the IMMEM-10 conference

2014 ◽  
Vol 165 (2) ◽  
pp. 140-153 ◽  
Author(s):  
Sylvain Brisse ◽  
Carina Brehony ◽  
Teresa Conceição ◽  
Meritxell Cubero ◽  
Corinna Glasner ◽  
...  
Keyword(s):  
Molecular Markers ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Epidemiological Surveillance

scholarly journals Composition and Origin of the Fermentation Microbiota of Mahewu, a Zimbabwean Fermented Cereal Beverage

2019 ◽  
Vol 85 (11) ◽  
Author(s):  
Felicitas Pswarayi ◽  
Michael G. Gänzle
Keyword(s):  
16S Rrna ◽  
Quantitative Pcr ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Starter Cultures ◽  
Rrna Gene ◽  
Culture Methods ◽  
Content Type ◽  
Cell Counts

ABSTRACTMahewu is a fermented cereal beverage produced in Zimbabwe. This study determined the composition and origin of mahewu microbiota. The microbiota of mahewu samples consisted of 3 to 7 dominant strains of lactobacilli and two strains of yeasts.Enterobacteriaceaewere not detected.Candida glabratawas present in high cell counts from samples collected in summer but not from samples collected in winter. Millet malt is the only raw ingredient used in the production of mahewu and is a likely source of fermentation microbiota; therefore, malt microbiota was also analyzed by culture-dependent and high-throughput 16S rRNA gene sequencing methodologies. Millet malt contained 8 to 19 strains ofEnterobacteriaceae, lactobacilli, bacilli, and very few yeasts. Strain-specific quantitative PCR assays were established on the basis of the genome sequences ofLactobacillus fermentumFUA3588 and FUA3589 andLactobacillus plantarumFUA3590 to obtain a direct assessment of the identity of strains from malt and mahewu.L. fermentumFUA3588 and FUA3589 were detected in millet malt, demonstrating that millet malt is a main source of mahewu microbiota. Strains which were detected in summer were not detected in samples produced at the same site in winter. Model mahewu fermentations conducted with a 5-strain inoculum consisting of lactobacilli,Klebsiella pneumoniae,andCronobacter sakazakiidemonstrated that lactobacilli outcompeteEnterobacteriaceae, which sharply decreased in the first 24 h. In conclusion, mahewu microbiota is mainly derived from millet malt microbiota, but minor components of malt microbiota rapidly outcompeteEnterobacteriaceaeandBacillusspecies during fermentation.IMPORTANCEThis study provides insight into the composition and origin of the microbiota of mahewu and the composition of millet malt microbiota. Fermentation microbiota are often hypothesized to be derived from the environment, but the evidence remains inconclusive. Our findings confirm that millet malt is the major source of mahewu microbiota. By complementing culture methods with high-throughput sequencing of 16S rRNA amplicons and strain-specific quantitative PCR, this study provides evidence about the source of mahewu microbiota, which can inform the development of starter cultures for mahewu production. The study also documents the fate ofEnterobacteriaceaeduring the fermentation of mahewu. There are concerns regarding the safety of traditionally prepared mahewu, and this requires in-depth knowledge of the fermentation process. Therefore, this study elucidated millet malt microbiota and identified cultures that are able to control the high numbers ofEnterobacteriaceaethat are initially present in mahewu fermentations.

scholarly journals Rapid isolation and characterization of microsatellites in the critically endangered Mountain Bongo (Tragelaphus eurycerus isaaci)

2019 ◽  
Author(s):  
Fraser John Combe ◽  
Evelyn Taylor cox ◽  
Graeme fox ◽  
Tommy Sandri ◽  
Bradley Cain ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Population Analysis ◽  
Illumina Miseq ◽  
Model Organisms ◽  
Conservation Genomics ◽  
Adaptive Genetic Variation ◽  
Genetics Research ◽  
Isolation And Characterization ◽  
Neutral Markers

High-throughput sequencing tools promise to revolutionize many aspects of genetics research, e.g. by allowing the identification of functional adaptive genetic variation. However, the expense and expertise required to apply these tools to basic conservation questions is a challenge for applications outside academia, resulting in a so-called “conservation genomics gap” (Shafer et al. 2015). The conservation genetics paradigm is that basic information about inbreeding and gene flow are often critical to inform conservation management of small populations (Ouborg et al. 2010). This information is often needed quickly and ideally should be accessible to workers without special expertise in genomics (DeSalle & Amato 2004). While the inferential power of high-throughput sequencing to interrogate the genome is profound, the cost for population analysis is higher (though decreasing) than for traditional neutral markers. Thus, the use of neutral markers is still relevant in conservation applications. However, this assumes that neutral markers have been discovered and characterized for a given species of conservation concern, which is often untrue for non-model organisms. Here, we use a fast, cost-efficient, high-throughput sequencing method (Illumina MiSeq) to rapidly identify and characterize microsatellites in the mountain bongo (Tragelaphus eurycerus isaaci, hereafter bongo), which has a clear and timely conservation imperative but lacks any described neutral markers.

scholarly journals Diversity of Yeasts Involved in Cocoa Fermentation of Six Major Cocoa-Producing Regions in Ivory Coast

2017 ◽  
Vol 13 (30) ◽  
pp. 496 ◽  
Author(s):  
Odilon Koff ◽  
Lamine Samagaci ◽  
Bernadette Goualie ◽  
Sebastien Niamke
Keyword(s):  
Ivory Coast ◽  
Growth Dynamics ◽  
Rflp Analysis ◽  
Starter Cultures ◽  
Raw Material ◽  
Intraspecific Diversity ◽  
Cocoa Bean ◽  
Pichia Kudriavzevii ◽  
Cocoa Bean Fermentation ◽  
Cocoa Fermentation

Cocoa beans (Theobroma cacao L.) are the raw material for chocolate production. Fermentation of cocoa pulp is crucial for developing chocolate flavor precursors. This fermentation is led by a succession of complex microbial communities where yeasts play key roles during the first stages of the process. In this study, we identified and analyzed the growth dynamics of yeasts involved in cocoa bean fermentation of six major cocoaproducing regions in Ivory Coast. A total of 743 yeasts were isolated, and were identified by sequencing of D1/D2 regions of 26S rDNA gene. These isolates included 11 species with a predominance of Pichia kudriavzevii (44,81 %), Pichia kluyveri (20,99 %) and Saccharomyces cerevisiae (18,97 %) respectively. In addition, the length polymorphism of the genetic marker ITS1-5.8S-ITS2 and PCR-RFLP analysis revealed an intraspecific diversity within the three-main species involved in cocoa fermentation of six major local regions in Ivory Coast. This intraspecific diversity could be exploited for selecting appropriate starter cultures.

scholarly journals Indigenous Yeast, Lactic Acid Bacteria, and Acetic Acid Bacteria from Cocoa Bean Fermentation in Indonesia Can Inhibit Fungal-Growth-Producing Mycotoxins

Fermentation ◽  
2021 ◽  
Vol 7 (3) ◽  
pp. 192
Author(s):  
Endang Sutriswati Rahayu ◽  
Rokhmat Triyadi ◽  
Rosyida N. B. Khusna ◽  
Titiek Farianti Djaafar ◽  
Tyas Utami ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Ochratoxin A ◽  
Lactobacillus Plantarum ◽  
Acetic Acid Bacteria ◽  
Starter Cultures ◽  
Cocoa Bean ◽  
Cocoa Bean Fermentation ◽  
Candida Famata

Cocoa bean fermentation is an important process in the manufacturing of cocoa products. It involves microbes, such as lactic acid bacteria, yeast, and acetic acid bacteria. The presence of mold in cocoa bean fermentation is undesired, as it reduces the quality and may produce mycotoxins, which can cause poisoning and death. Aspergillus niger is a fungus that produces ochratoxin A, which is often found in dried agricultural products such as seeds and cereals. In this study, we applied indigenous Candida famata HY-37, Lactobacillus plantarum HL-15, and Acetobacter spp. HA-37 as starter cultures for cocoa bean fermentation. We found that the use of L. plantarum HL-15 individually or in combination Candida famata HY-37, Lactobacillus plantarum HL-15, and Acetobacter spp. HA-37 as a starter for cocoa bean fermentation can inhibit the growth of A. niger YAC-9 and the synthesis of ochratoxin A during fermentation and drying. With biological methods that use indigenous Lactobacillus plantarum HL-15 individually or in combination with Candida famata HY-37 and Acetobacter spp. HA-37, we successfully inhibited contamination by ochratoxin-A-producing fungi. Thus, the three indigenous microbes should be used in cocoa bean fermentation to inhibit the growth of fungi that produce mycotoxins and thus improve the quality.

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